This is a review of manuscript CiSESI-2018-02-0016 submitted to Computing in Science & Engineering: "CoRR — The Cloud of Reproducible Records" (Congo, Traoré, Hill and Wheeler, 2018). OVERVIEW While a number of tools have been developed over recent years for run-time capture of computational provenance artefacts and metadata (referred to in the manuscript as "Computation Version Control" or CVC), such as Sumatra, CDE, Reprozip, recipy and noWorkflow, these tools generally lack an easy way to review and share provenance records through a web-based graphical interface, such as is provided by Github, Gitlab, Bitbucket, etc. for software version control systems such as Git or Mercurial. In some cases, no graphical interface is available at all. In others, the graphical interface runs only locally, and is not accessible over the web. Where web-based tools do exist (example) they are (i) difficult to deploy and (ii) specific to a given provenance capture tool: there is essentially no interoperability between such tools. This manuscript reports on CoRR, a collaborative web platform that aims to solve the limitations outlined above by being easy to deploy (using a modern cloud architecture approach) and by providing a common graphical interface for different provenance capture tools. The manuscript outlines the case for CoRR, briefly reviews Sumatra, CDE and Reprozip, presents the CoRR architecture and interface, then presents a case study of using CoRR together with the three provenance capture tools previously reviewed. CoRR clearly fills an important gap in the landscape of tools for reproducible computational research, and has the potential to expand the usage of run-time provenance capture in scientific computation, just as Github has done for usage of version control systems. The manuscript is a very good fit for the Reproducible Research track of CiSE (Barba _et al._, 2017). As such, the manuscript should be ACCEPTED AFTER MINOR REVISIONS. SUGGESTIONS FOR IMPROVING THE MANUSCRIPT. Terminology While almost everyone agrees on the need to distinguish "repeatable", "reproducible" and "replicable", there is considerable disagreement over what each term refers to (Plesser, 2018). While your use of terms seem to be largely consistent with one of the more widely used conventions, to minimize confusion it would be desirable to cite a source for your definitions (e.g. Fabien _et al._, 2018, although there are many others). The term "computational provenance" seems to be well established for what is called "CVC" in the manuscript. Rather than coining a new term, I suggest reusing the existing one. This will better integrate the article into the wider literature on this topic, and make it easier to find through search engines. Structure Overall, I think the manuscript is well structured. However, I think there is a lack of balance between the sections: - The section "The main elements views in CoRR" seems unecessarily detailed, describing toolbox actions with a level of detail appropriate for a user manual, but not for a CiSE article. - The manuscript has almost no information on the REST API. While it would not be appropriate to give detailed documentation, some examples of the REST endpoints and the document format(s) used would be helpful. - The machine learning examples used in the case study are described in considerable detail, but this information is then hardly used in the rest of the manuscript; I think this session could be considerably shortened. - The "Results" section is very minimal; I would expect at least to see some screenshots of how the different records are represented in CoRR. In addition, the "Reproducibility Effort" is not well explained; the phrase "is the tool representation directly reproducible after a download from CoRR" does not give me a clear idea of what steps are involved. Inaccuracies and missing references - _"Sumatra (created in 2009), CDE (created in 2010) and ReproZip (created in 2013) are some of the most used CVC tools."_ What is the source for the assertion that these are among the most used tools? Do you have any numbers for this? - There is a web-accessible API and web UI for Sumatra, "sumatra-server", separate from Sumatra's internal, local web-browser UI. This does support dissemination of records and multiple users. However, it is not widely used and is not interoperable with other provenance capture tools. - It is not true that _"Sumatra makes copies of the output files only if placed in a folder named Data."_ Sumatra does not make copies by default (only if the "archive" option is used), rather it stores the file system path or URL together with a hash of the file contents. It is also not necessary to use a specific folder name, this is fully configurable ("Data" is just the default). Language/style There are frequent minor grammatical errors and some typos (e.g. "ReroZip", "CORRR"). I recommend that all co-authors carefully re-read the manuscript to correct these. Style issues: - Please spell out "OS" in the introduction. From the context, it becomes clear that it means "operating system", but the abbreviation is also often use for "open source". - The sentence _"The uncovering of recent frauds, irreproducibility facts and concerns from major journals publications, have enforced new requirements in scientific results corroborations"_ is hard to understand. What are _"irreproducibility facts and concerns"_? What are _"major journals"_? Who is doing the enforcing? - _"We refer to these software and services as CVC tools"_. The antecedent of this sentence is three sentences earlier, which makes it hard to understand what is being referred to. - It is not usual in a scientific context to explicitly use titles, as in "Dr Rosebrock". I think it would be more appropriate to use the name of the book and the author's surname the first time the book is cited, and then use just the surname ("Rosebrock") subsequently. Discussion of existing literature In the context of interoperability, which is one of the main benefits of CoRR, the authors should discuss previous efforts to enable interoperability of representations of computational provenance, such as the ProvONE data model, which builds on the W3C PROV standard. Would it be possible to support PROV-compatible representations (i.e. some form of RDF) through the CoRR API? DISCLAIMER For the sake of transparency, it should be noted that I am the principal developer of Sumatra, one of the software tools reviewed in the manuscript and used in the case study. REFERENCES Lorena A. Barba & George K. Thiruvathukal (2017). Reproducible Research for Computing in Science & Engineering. _Computing in Science & Engineering_ 19:85–87. http://doi.org/10.1109/mcse.2017.3971172 Plesser, H. E. (2018). Reproducibility vs. replicability: A brief history of a confused terminology. _Frontiers in Neuroinformatics_ 11:76. https://doi.org/10.3389/fninf.2017.00076 Fabien C. Y. Benureau, Nicolas P. Rougier (2018). Re-run Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions. _Frontiers in Neuroinformatics_ 11:69. https://doi.org/10.3389/fninf.2017.00069

Review authored by Marielle Cavrois, Nadia Roan, and Ibraheem AliGladstone Institute of Virology and ImmunologyUniversity of California San FranciscoThis is a journal club review of Systems analysis by mass cytometry identifies susceptibility of latent HIV-infected T cells to targeting of p38 and mTOR pathways. Fong et al. 2018. bioRxiv doi: https://doi.org/10.1101/371922  Fong and colleagues present a very interesting study investigating signaling pathways and biomarkers that are dysregulated in cells exposed to HIV-1. Using a combination of mass cytometry and pharmacological approaches, the authors find that HIV-1 exposed cells are sensitized to cell death caused by T cell activation through disruption of the p38 and mTOR signaling pathways, and then demonstrate that ex vivo treatment of cells from ART-suppressed HIV-infected individuals with drugs targeting these pathways can decrease the proportion of latently-infected cells. This study is of importance as finding ways to therapeutically eliminate latently-infected cells is needed. Major Comments: Use of CyTOF to study the intracellular signaling pathways elicited during HIV infection is a valuable approach to identify novel ways to target HIV-infected cells therapeutically. Targeting intrinsic cell death pathways in latently-infected cells is an exciting approach to try to eliminate the persistent reservoir. However, since the majority of the experiments conducted were in vitro, and many in vitro models of HIV latency exist, the paper would benefit from a more thorough explanation and justification of this particular model of HIV latency. For example, Figure 1A could have more clearly delineated the experimental timeline of infection and stimulation (e.g., illustrating the fact that two rounds of stimulation were used: one to render cells permissive to infection, the second to reactivate latent cells). This would have been more helpful than images depicting the barcoding and cytof methodology, which could be described in the methods section. Furthermore, it should be acknowledged that the HIV-exposed cells consist of 3 cell populations: those that are productively infected, those that are latently infected, and those that are exposed but remain uninfected (broadly termed “bystander cells”, which can include both cells that fused to virus as well as those that did not). It is important to note that when the authors restimulate the HIV-exposed population of cells, they are restimulating a mixed population of these 3 populations, which can interconvert (e.g., p24- can become p24+). (As a side note, the cells should be called p55Gag – vs. +, since intracellular Gag is not p24). This, along with the fact that p24- cells may be predominantly bystander cells and not latently-infected cells, makes it difficult to assess how specific the identified signaling pathways are for latent cells. Also, the authors should clarify why they used different sets of subpopulations in different sections of the paper: sometimes, analysis was performed on the bulk population of HIV-exposed cells, other times on gated populations of p24+ vs. p24- cells.One valuable tool that exists in the field are the so-called dual-reporter viruses, that distinguish between latently- vs. productively-infected cells, \cite{Battivelli2018,Calvanese2013}. The in vitro part of the study could be markedly strengthened by validating the main results through use of such a system, or another system where a pure population of latently-infected cells can be obtained. One of the main readouts the authors used for sensitization to cell death in HIV exposed cells was Cleaved Caspase 3 (CC3). It would have benefitted the reader to have seen the gating strategy leading up to the population of cells that did or did not express CC3. In particular, it is important to know whether cells were gated from the live population as assessed by a viability dye, since dead/dying cells tend to be non-specifically sticky to antibodies.  Additional markers of cell death would have also been valuable in the FACS and CyTOF analyses. DREVI appears to be a powerful tool to infer associations and identify signaling pathways in play, but as many are not familiar with the nature of this analysis tool, a more thorough explanation of how it works, how it should be interpreted, and how it reveals insights that couldn’t be deciphered from the original datasets, would be helpful. Additional Comments:Regarding Figure 1B, were the productively-infected population pre-gated on the CD4- cells? (since HIV downmodulates CD4 upon productive infection)  Regarding Fie. S1E, are all the position Gag+ cells also expressing TAT?  On a minor note, the text Page 5 line 8 should be edited to read Figure 1B There appears to be overlap between the populations labeled as Uninfected (UI), Exposed-Uninfected (EU), and Latent Infected (LI) (Fig. S2, Fig. 2D-F). As indicated above, the LI contains many bystander cells, a fact that should be taken into consideration during the analysis. What is the advantage of analyzing the data in the way presented in Fig. 2E-F over the methods shown in Fig. 2C? Could the authors give their thoughts as to why p-S6 is only upregulated in only a subset of actively infected cells? In Figure 3E it would have been helpful to have known how many donors were used for each of the conditions in these experiments. In Figure 5 the authors should comment on the dosage of ganetespib and INK128 used and whether these concentrations are those that can be achieved in vivo, and the extent to which these doses were cytotoxic. Cell viability info would have been particularly helpful for Fig. 5 G-H since it appears that the treatment preferentially kills latently infected cells. It is important for the reader to know what is the extent of cell death observed after the 3 days of treatment with ganetespib, INK128, or a combination of the two. The authors could also comment on whether pre-treatment with ganetespib and INK128 might affect the ability of cells to be effectively stimulated by PMA/ionomycin as done in TILDA, since these treatments may target similar pathways? On a minor note there is no panel J in Figure 5 (see text page 14). 

Yusuf patut dijadikan model dalam pengembangan sumber daya manusia masa kini. Menjadi model dalam arti dapat diteladani, ditiru. Yusuf adalah sosok yang beriman, berilmu dan berakhlak mulia. Kompetensinya dapat diandalkan dalam memberi kontribusi positif bagi kehidupan yang ada di sekitarnya. Kualitas unggul yang dimilikinya berbeda dengan saudara-saudaranya dalam berbagai aspek. Yusuf diakui bahwa ia dipenuhi Roh Tuhan, cerdas dan berperilaku seperti Yesus Kristus. Menurut Alkitab, “Tetapi TUHAN menyertai Yusuf, sehingga ia menjadi seorang yang selalu berhasil dalam pekerjaannya; maka tinggallah ia di rumah tuannya, orang Mesir itu.  Setelah dilihat oleh tuannya, bahwa Yusuf disertai TUHAN dan bahwa TUHAN membuat berhasil segala sesuatu yang dikerjakannya, maka Yusuf mendapat kasih tuannya, dan ia boleh melayani dia; kepada Yusuf diberikannya kuasa atas rumahnya dan segala miliknya  diserahkannya pada kekuasaan Yusuf. Sejak ia memberikan kuasa dalam rumahnya dan atas segala miliknya kepada Yusuf, TUHAN memberkati rumah orang Mesir itu karena Yusuf, sehingga berkat TUHAN ada atas segala miliknya, baik yang di rumah maupun yang di ladang. Segala miliknya diserahkannya pada kekuasaan Yusuf, dan dengan bantuan Yusuf ia tidak usah lagi mengatur apa-apapun selain dari makanannya sendiri. Adapun Yusuf itu manis sikapnya dan elok parasnya.” (Kejadian 39:2-6)             Perlu dijelaskan bahwa konteks ayat-ayat tersebut adalah Yusuf seorang budak belian yang bekerja di rumah Potifar, tuannya. Ia dinyatakan berhasil dan menjadi kepercayaan bagi tuannya. Yusuf menampilkan performa kerja dengan kecerdasan yang utuh berimbang, berintegritas, bertaqwa dan sanggup mengalahkan godaan. Ketika Yusuf difitnah dan dipenjarakan, Yusuf pun mampu mempertahankan kualitas personal dan kinerjanya mendapat pujian dari kepala penjara. Iman dan karakternya tidak luntur meski dia mengalami penderitaan sejak ia dijual oleh saudara-saudaranya, dipekerjakan sebagai budak hingga ia dijebloskan ke dalam tahanan. Alkitab mencatat bahwa di penjara, Yusuf menolong mengartikan mimpi rekannya. Bahkan pada saat Yusuf dipromosikan oleh Firaun menjadi pejabat di Mesir mutu karakternya tidak merosot.   Alkitab mempertegas, “Sementara itu Yusuf telah menjadi mangkubumi di negeri itu; dialah yang menjual gandum kepada seluruh rakyat negeri itu. Jadi ketika saudara-saudara Yusuf datang, kepadanyalah mereka menghadap dan sujud dengan mukanya sampai ke tanah.” (Kejadian 42:6) “Ketika Yusuf telah pulang, mereka membawa persembahan yang ada pada mereka itu kepada Yusuf di dalam rumah, lalu sujud kepadanya sampai ke tanah.”(Kejadian 43:26) “Ketika Yehuda dan saudara-saudaranya sampai ke dalam rumah Yusuf, Yusuf masih ada di situ, sujudlah mereka sampai ke tanah di depannya.”(Kejadian 44:14).  Bagian ini memberi konfirmasi bahwa mimpi Yusuf telah menjadi kenyataan. Meski pun mimpi tersebut pada awalnya tidak mendapat dukungan dari pihak keluarganya, namun kini Yusuf tidak berubah. Kepada saudara-saudaranya, Yusuf berkata: “Tetapi sekarang, janganlah bersusah hati dan janganlah menyesali diri, karena kamu menjual aku ke sini, sebab untuk memelihara kehidupanlah Allah menyuruh aku mendahului kamu.  Karena telah dua tahun ada kelaparan dalam negeri ini dan selama lima tahun lagi orang tidak akan membajak atau menuai. Maka Allah telah menyuruh aku mendahului kamu untuk menjamin kelanjutan keturunanmu di bumi ini dan untuk memelihara hidupmu, sehingga sebagian besar dari padamu tertolong.  Jadi bukanlah kamu yang menyuruh aku ke sini, tetapi Allah; Dialah yang telah menempatkan aku sebagai bapa bagi Firaun dan tuan atas seluruh istananya dan sebagai kuasa atas seluruh tanah Mesir.”(Kejadian 45:5-8)   Yusuf menambahkan pula, “Memang kamu telah mereka-rekakan yang jahat terhadap aku, tetapi Allah telah mereka-rekakannya untuk kebaikan, dengan maksud melakukan seperti yang terjadi sekarang ini, yakni memelihara hidup suatu bangsa yang besar.”(Kejadian 50:20) Keluhuran karakter Yusuf tidak luntur oleh situasi di luar dirinya – meski ia dijual oleh saudara-saudara, dijadikan budak, difitnah lalu dipenjara – hingga ia menjadi orang yang terhormat dan berkuasa – karakter Yusuf konsisten, berakhlak mulia, berilmu, beriman tangguh dan terus memberi kontribusi positif bagi kemanusiaan.(*)\citep*{marbun2017}

Firman Tuhan dalam Perayaan Natal 2017 dikutip dari Kitab Kolose 3:15, "Hendaklah damai sejahtera Kristus memerintah dalam hatimu, karena untuk itulah kamu telah dipanggil menjadi satu tubuh. Dan bersyukurlah." Alkitab versi Bahasa Indonesia Sehari-hari, "Hendaklah keputusan-keputusanmu ditentukan oleh kedamaian yang diberikan oleh Kristus di dalam hatimu. Sebab Allah memanggil kalian untuk menjadi anggota satu tubuh, supaya kalian hidup dalam kedamaian dari Kristus itu. Hendaklah kalian berterima kasih."Kata Yunani 'damai sejahtera' "eirene" dari kata dasar "eiro" yang berarti "satu", utuh, tidak kurang. Kata eirene dalam bahasa Ibrani 'shalom' yang artinya "lengkap, sejahtera, damai, aman, sehat, makmur, tenang, bersahabat - hubungan manusia dengan Tuhan. oleh sebab itu maksud ayat tersebut tidak dapat dilepaskan dari ayat 3:1-4, "Karena itu, kalau kamu dibangkitkan bersama dengan Kristus, carilah perkara yang di atas, di mana Kristus ada, duduk di sebelah kanan Allah. Pikirkanlah perkara yang di atas, bukan yang di bumi. Sebab kamu telah mati dan hidupmu tersembunyi bersama dengan Kristus di dalam Allah. Apabila Kristus, yang adalah hidup kita, menyatakan diri kelak, kamupun akan menyatakan diri bersama dengan Dia dalam kemuliaan."Berdasarkan itu, dipahami bahwa damai sejahtera adalah salah satu faedah keselamatan yang diterima oleh orang-orang yang berdamai dengan Allah. Paulus dalam Filipi 4:7 menulis, "Maka sejahtera dari Allah yang tidak mungkin dapat dimengerti manusia, akan menjaga hati dan pikiranmu yang sudah bersatu dengan Kristus Yesus."(BIS) Dengan demikian, jika kita berseru kepada Allah dari hati yang tinggal di dalam Kristus dan Firman-Nya (Yohanes 15:7), maka damai sejahtera Allah akan membanjiri jiwa kita. Damai sejahtera ini adalah kesentosaan batin yang dibawa oleh Roh Kudus (Roma 8:15-16). Perasaan sejahtera itu meliputi keyakinan yang teguh bahwa Yesus dekat. Damai sejahtera itu memberi rasa yakin yang mendalam bahwa kasih Allah sedang dan terus-menerus bekerja di dalam kehidupan kita demi kebaikan.(Roma 8:28) Kata "memerintah" dalam bahasa Yunani "brabeuo" satu istilah atletik yang masa kini disebut "wasit, hakim pertandingan, juri". Pemegang otoritas "memutuskan" sesuai dengan aturan main. Hati manusia sebagai pusat kendali moral, memerlukan damai sejahtera sebagai juri pengendali. Bila hati dipimpin oleh juri yang bernama amarah, benci, dendam, maka buahnya dapat diprediksi. Sebaliknya, bila hati dipimpin oleh juri yang benar bernama damai sejahtera maka jiwa terasa utuh. Hidup terasa baik-baik saja, sebab damai sejahtera bertakhta di dalam pusat kehidupan.Oleh sebab itu, setiap orang harus menjawab pertanyaan ini secara jujur, "Siapa yang sedang memerintah di dalam hatiku?" Apakah semangat damai -- "sudah, sedang, terus menerus" atau "belum" -- memerintah dalam hatimu? Waspadalah karena hati bisa diduduki oleh 'spirit' politik identitas, eksklusivisme, fanatisme dan kaki tangannya. Hati itu juga dapat dirajai oleh 'spirit positif' berupa rasa sayang, persaudaraan, rasa hormat. Hati manusia sepanjang zaman menjadi arena pergulatan berbagai ideologi. Generasi manusia dibesarkan dengan ideologi yang disemaikan dalam dadanya. Buah perilaku tergantung pada 'raja yang memperhamba hati'. Bila damai sejahtera memimpin hati, maka perbedaan menjadi ramah keharmonisan.\citep*{marbun2018}

Disentangling unspecific and specific transgenerational immune priming components in host-parasite interactionsFrida Ben-Ami, Christian Orlic, Roland R. Regoes doi: https://doi.org/10.1101/429498bioRxiv, 9/27/2018Overview and take-home messages:In this study, the authors tackle the topic of transgenerational immune priming in invertebrates. The authors designed a large experiment taking advantage of clonal Daphnia to test whether infecting parental generations with different parasite strains improves the offspring's resistance to that parasite overall and if yes, if they resist that specific strain more effectively than other strains. This experiment essentially tests the specificity of immune priming at a very fine "strain" scale. The results did not support parental infection strain differentially affecting offspring resistance to different strains, suggesting that immune priming is not specific to the strain level in this system. However, a mathematical model the authors developed for that study fits the data exceptionally well, which means this model could potentially be used in a predictive manner for this or similar systems. Additionally, the unexpected result that one strain actually facilitates specific infection in the offspring is surprising and opens the door to additional inquiry and future experimentation. Overall this study is very interesting and well-presented, but there are a few concerns that could be addressed and improved in the next version of the manuscript.

Book Review:Creativity and Critique in Online Learning: Exploring and Examining Innovations in Online Pedagogy Edited by Jacqueline Baxter, George Callaghan, and Jean McAvoy. Switzerland: Springer International Publishing, 2018 (xxiii + 278 pages, ISBN 978-3-319-78297-3, € 109,99) Saortua MarbunSekolah Tinggi Ilmu Ekonomi Triatma Mulya Bali Indonesia  saortuam@gmail.com | http://orcid.org/0000-0003-1521-7694  

For many years, it has been speculated that consciousness and cognition could be the based on quantum information  \cite{sep-qt-consciousness} which opposes the view that quantum coherence, the primary basis of quantum computing \cite{nielsen_chuang_2010}, cannot survive in complex biological systems \cite{Koch_2006,Tegmark_2000}. However, recent findings in photosynthesis \cite{Engel_2007,Collini_2010} have challenged this view suggesting that only long-range quantum coherence between molecules can account for its efficiency in light-harvesting. Here, we investigated if long-range quantum coherence may also play a decisive role in brain function. We found surprisingly that the cardiac pressure pulse evoked zero-quantum coherence (iZQC) \cite{Warren_1998} which were by a magnitude higher than theoretically expected. From this finding, we concluded that underlying physiological process is - cautiously speaking - of an unknown macroscopic non-classical kind. The process reveals it importance by it temporal appearance; during consciousness it is highly synchronized with the cardiac pulse, while during sleep, no or only sporadic iZQC could be detected. This findings suggest that this non-classical phenomenon is most likely a necessity for consciousness. 

Careful and thoughtful experimental design is crucial to the success of any SIP experiment. This chapter discusses the essential aspects of designing a SIP experiment, focusing primarily on DNA- and RNA-SIP. The design aspects discussed here begin with considerations for carrying out the incubation, such as, the effect of choosing different stable isotopes and target biomolecules, how enriched should a labelled substrate be, what concentration to use and how long the incubation should take. Then tips and pitfalls in the technical execution of SIP are listed, including how much nucleic acids should be loaded, how many fractions to collect and what centrifuge rotor to use. Lastly, a brief overview of the current methods for analysing SIP data is presented, focusing on high-throughput amplicon sequencing, together with a discussion on how the choice of analysis method might affect the experimental design.

Among the top challenges of reproducible computational science are: (1) creation, curation, usage and publication of research software; (2) acceptance, adoption and standardization of open-science practices; (3) misalignment with academic incentive structures and institutional processes for career progression. I will address here mainly the first two, proposing a praxis of reproducible computational science.

BOOK REVIEWStrangers and Friends at the Welcome Table: Contemporary Christianities in the American South, By  James Hudnut-Beumler, Chapel Hill, NC., University of North Carolina Press., 2018., ISBN. 978-1-4696-4037-2., i-x., 1-289 pp., Hardcover $27.47.   Hudnut-Beumler presents this fascinating chronicle of Christianity for more than the past 75 years, as an overall image of the dominant religion in some of the Southern states of America. The author narrates experiences, believes and faithful practices of Christians in both rural and urban communities. The book is thus a critical analysis of different religious communities, especially their intrinsic difficulties in smoothing down differences connecting to religion, myths, and peculiarity of culture among Christians. This book, therefore, presents the author’s notion that to understand Christianity in the twenty-first century; one has to engage diverse perceptions of Christian practices.The writer narrated his life experiences since childhood when the family traveled from Michigan, to visit relatives in South Webster, Ohio. The author recounts the differences in accent practices, for instance, the high number of small churches along a small main street. The author also recalls unique religious and cultural traditions such as attending church services on Sunday and Wednesday nights, when different church bells rang at different times. Writer, therefore, creates a distinctive impression of the American South, as a place retaining a broad historical sense, concerning differences in race, kinship, faith, myths, and geographical settings. The author tries to find out the intensity of this cultural distinctiveness, and its homogeneity with the contemporary American culture, since the observable differences might be either functionless or essential in the current evolving society.According to the writer, there is extreme segregation of faith among Christians in the South, whom he refers to as a “religion of the lost cause” that glamorize the civil war. The writer narrates how the white, Protestants and other conservative Christian communities still dominate the South. This narration on religion is fascinating due to the included range of stories concerning practices by different Christian groups, for instance, the rattlesnakes and holiness. The author also narrates how the Catholic Church tries to reconnect with communities by cleaning up the aftermath of calamities, for example, the 2015 mass shooting at Charleston's Emanuel A.M.E. Church, where the faithful try to enhance reconciliation by teaching Christian values of morality and forgiveness. The author also presents the church clean-up exercise, after hurricane Katrina, and Mississippi floods. The author depicts the rapid emergence of other megachurches, different parenting behaviors, where there appear to be more home-schooling systems for children on a matter that are common in contemporary society such as theories concern with the creation and gay Christians. Writer, therefore, presents the rapid social diversity and unpredictable changes such as revolution from the Spanish language used in church services to a more robust Christian home-schooling system that seems to rival the public education system.The writer also presents a different picture form the customarily perceived notion indicating that all southern Christians are Christian whites and are conservative especially on political matters since the analysis involves the ideologies, practices, and outlook among current Southern Christians. According to Writer, Christianity is America’s dominant faith. However, a predominant difference grapples the South, regarding practices meant to provide meaning, purpose, and identity. The region has many megachurches than other American areas, for instance, this south region has five times the number of churches in the Northeastern region. All these churches are fully utilized and house multi-denominational practitioners who are highly involved with their congregations.Different churches exist within the same setting, for instance, “the church of God, Church of Christ, Southern Baptist Convention, the church of God in Christ and National Baptist Convention” all consist of over forty percent of the Southern population, who are highly involved members. Other than the Baptist churches, others include the Methodist, Pentecostal, Presbyterian, Holiness, Episcopal and other non-denominational churches common along back streets and roads heading out of town. Contrary, in America, only 16% Catholics and 19% evangelical Lutherans reach such a high level of involvement in Christianity. The writer indicates that religion is not a private practice but a more public practice, noticeable through the manifestation of the number of praying families or individuals in public places such as restaurants and the large billboards along highways publicizing all sort of religious practices. Some of America's Southern cosmopolitan cities with the most significant percentage of practicing Christians include Dallas 78%, Atlanta 76%, Boston 57%, Seattle 52%, and San Francisco at 48%. This statistics, therefore, depicts that the South seems more religious and portrays a stronger Christian base.Conversely, Writer presents a different perspective depicting lack of commonness of Christian practices in the south. The author shows the diversity of views, levels of dissent, procedures concern with practicing faith, loving others, interpreting sin, and fellowshipping. These Christians may, therefore, join in the hymn of "I want to eat at the welcome table" but when these "Strangers and Friends" join at the "Welcome Table," there is either friendship or unfamiliarity among them depending on lifestyle, practices, and beliefs.Christians in the South maintain a firm worship grip of ancestors and institutions of the past. Human imaginations still intimately connect to military services and sacrifices during the civil war that ended over 150 years ago. Christians in the contemporary South therefore always link current situations and meaning of conflicts to effects of past occurrences such as the legacy of slavery and consider such phenomena honorable.The author dramatically captures religion in the southern political arena, where legislatures, leaderboards and a large number of citizens consider the south as predominantly religious. However, the writer shows the different Christian practices in the contemporary South, the origin, and contradictions within the cultural and religious setting. Although the modern South remains highly religious, distinct and dominated by Christians, there is a steady change of status, to the diversification of meaning and interpretation of the expression "Christianity."

Nitrogen fixation and assimilation processes are vital to the functioning of any ecosystem. Nevertheless, studying these processes using ¹⁵N-based stable isotope probing was so far limited because of technical challenges related to the relative rarity of nitrogen in nucleic acids and proteins compared to carbon, and because of its absence in lipids. However, the recent adoption of high-throughput sequencing and statistical modelling methods to SIP studies increased the sensitivity of the method and enabled overcoming some of the challenges. This chapter describes in detail how to perform DNA- and RNA-SIP using ¹⁵N.

We will discuss today how quantum effects emerge in degenerate gases and how they are connected to problems that come traditionally from condensed-matter physics.

In todays lecture we will study spontaneous emission its connection with absorption and how we can control it certain situations.

OverviewIn this experiment we will try to prove that the gamma rays created from the annihilation of positrons with electrons resulting from the decay of Na22 into Ne22 conserve both energy and momentum.Questions1) Explain what the SCA does for you in this experiment.        In this experiment the single channel analyser will determine if the pulse coming from the amplifier is in the specified range  necessary to have come from an electron-positron annihilation event. This is necessary as the decay products of our sample also include a higher energy gamma ray that is produced when the an excited electron on the Ne22  product falls back to its rest energy.2) Explain how the NaI detector works.        The NaI detector works by advantage of the photo-electric effect. When a photon goes into the crystal an electron is often ejected in the same direction as the motion of the photon. This electron then heads toward our photo-multiplier tube which uses successive dynodes held at a potential relative to each other to further eject electrons. The end result should be a cascade of electrons large enough that we can take a reading of voltage from the capacitor at the end of photo-multiplier tube. 3) Explain why the coincidence detector is so important.        The coincidence detector is important to maintain that any two pulse coming from detector A and B are coming from the same event and not from two random events occurring at the same time.4) Explain how you will count your pulses        For this experiment we were able to count pulses by two methods. First, by a slightly more difficult method, we were able to count gamma rays collected at either detector with a labview program set to count a pulse when the single channel analyser (SCA) detected a pulse within a specified amplitude. Square wave pulses generated by both SCA's were then sent to the coincidence detector in our NIM bin where counts were only made when two pulses were within \(50nm\) of each other. I consider this slightly more difficult than the next method used as it was necessary to use a stop watch and the counter switch to make sure that counts were only made in the 60 second time frame that we specified for the collection of coincidence data. The start button on the labview program as well needed to be pushed when data collection began, which of course required another person and some caution in the timing of all the necessary buttons. In the second method we were able to collect all necessary data through labview with the addition of a coincidence detector and program courtesy of Dr. Professor Chair Extraordinaire Ayars. With this addition we were able to collect single counts from both detectors and coincidences all with a specified time interval and without the need of coordination by multiple people thereby reducing random error.Set-upThis block diagram was taken directly from Positron-Electron lab handout.

We have seen that we can understand matter with increasing complexity from the simple two-level system up to molecules. We further studied, how they can be control by classical electromagnetic fields to a very high accuracy. In the last lecture we also studied how we can understand the electromagnetic field as an ensemble of quantum mechanical photon modes. So in today’s lecture we will focus on the interaction between atoms and light, which is in a particularly clean set-up, namely cavity quantum electrodynamics. The fundamental ingredients are sketched in Fig. [305911].

We will study the existance of vibrational and rotational levels in molecules. It allows us investigate the transitions of molecules and introduce the Franck-Condon principle. Finally, we will study how such intruiging molecules are used for the study of the permanent electric dipole moment of the electron.

In this lecture we will discuss a systematic approach to build up molecules from more complex atoms.

In the last lecture we have seen that we can typically treat complex atomic systems within the central field approximation. &&=& {2} ^2_{_i} + V_ (r_i) \right)}_{_0} + \left( {r_{ij}} - S(r_i) \right)}_{_1} So we we can can treat atoms through the shell structure known from the atom, but the screening lifts the l degeneracy. For a single outer electron, we have even seen how this screening can be described by the quantum defect. We would now like to go beyond this simple picture and discuss the following questions: - How should the residual term $_1$ be taken into account? - How do we properly take into account the Pauli principle ? - How can we treat the fine-splitting ? ON THE RESIDUAL COUPLING If we ignore the residual coupling, we obtain a spherically symmetric problem, which implies that the angular momentum $_i$ of each electron is conserved. This conservation will be broken by $_{1}$. However, these forces are internal, which implies that the total angular momentum $ = \sum_i _i$ is conserved. So we should label the states in the complex Hamiltonian by $$. The total angular momentum will then set the symmetry of the spatial wavefunction. As already discussed in some detail for the He atom, this has wide-reaching consquence on the spin degree of freedom through exchange interaction. THE PAULI PRINCIPLE AND SPIN - According to the Pauli principle, each single-particle state can be occupied only by one electron. After distributing all electrons over different single-particle eigenstates (“orbitals”), the resulting state needs to be fully antisymmetrized (Slater determinant). - There is a simplification for atoms with many electrons: The angular momenta and spins of a complete subshell with n,  l,  {m−l, ⋯, ml} add to zero and can be ignored in the further considerations (“shell structure”). Note that this is often broken in molecular binding! - Alkali atoms are the simplest atoms with shell structure: All but one _valence_ electron add to L = 0, S = 0. The ground state thus has L = 0, S = 1/2. - For more complex atoms, the valence electrons couple to a total orbital angular momentum L with a given symmetry according to particle exchange. Let us have a look at two examples for light atoms, starting with : - 1s² → L = 0, S = 0. The corresponding term is ¹S - 1s2s → L = 0, {S = 0, S = 1}. The corresponding terms are ¹S and ³S. . The electronic configuration of is: _{L=0,\,S=0} 3p^2 Per valence electron we have l = 1 and s = 1/2. So we get L = 0, 1, 2 and S = 0, 1. Here S = 1 means symmetry and S = 0 antisymmetry with respect to particle exchange. In principle we can form the following terms: ^1S,\,^3S,\,^1P,\,^3P,\,^1D,\,^3D Which of these terms can be fully antisymmetrized? Here, only the terms ¹S, ³P and ¹D fulfill Pauli’s principle. In general the exchange interaction (seen in the discussion of He), will then lower the energy of the states with high spins. Optional: Symmetry of the L states We can construct the following L-states for them: &= ^{l_1},^{m_{l_1}};^{l_2},^{m_{l_2}}} &= {} ( ^{m_{l_1}},^{m_{l_2}}} - ) &= {}(^{m_{l_1}},^{m_{l_2}}} - + ) The states and are symmetric and the state is antisymmetric with respect to particle exchange.

After our discussion of extremely simple atoms like hydrogen and helium, we will now discuss the most important properties of more complex atoms. We will see, how we can categorize them and discuss some of the general properties

We will finish our discussion of the Helium atom. Most importantly, we will dive into the strong separation between singlet and triplet states.

We will discuss the creation of entangled photons and how they can be used for the test of Bell's inequalities.

In this lecture we will use the hydrogen atom to study static perturbations in form of external magnetic fields and relativistic effects, leading to the fine structure splitting.

We will continue with some properties of the hydrogen atom. First compare it to the harmonic oscillator, then look into dipole transitions and end with the coupling to static magnetic fields.

In this lecture we will discuss the main properties of the hydrogen atom.