Simple dilution of semen is the oldest method to process semen for artificial insemination with either fresh or cooled. This was developed prior to the optimization centrifugation techniques for semen through a combination of trial and error and research. Simple dilution and is a faster method to process semen, is easy to use and works in many circumstances. For on farm semen use a 1:1 (v/v) semen to extender ratio is used. A variety of other techniques have been developed, such as cushion centrifugation, density gradient centrifugation and sperm filtration. Cushion centrifugation is used to concentrate the sperm and allows higher centrifugation speeds than centrifugation alone. This allows for improved recovery rates of sperm. Density gradient centrifugation has been used to select for morphologically normal sperm but suffers from low recovery rates. Processing sperm with this technique can result in improved motility and improved DNA integrity of sperm. Sperm filtration is another method to concentrate sperm without the use of centrifugation; however, this technique has lower recovery rates compared to cushion centrifugation. This review will discuss these techniques in the application of processing equine semen for either fresh or cooled-shipped use.

Introduction: A closed inguinal castration technique was compared with field castrations based on the post-operative (p.o.) inflammatory marker Serum Amyloid A (SAA). Third day p.o. SAA, which has been related to trauma, has been reported after field castrations in four different studies in literature between 500 mg/l and 700 mg/l. These values were compared with SAA values measured on day three after routine castration using a closed inguinal approach applied under general anaesthesia under strict aseptic conditions. Materials and Methods: 51 Male horses were presented for routine castration. Serum was collected pre-operatively and on day 3 post operatively. Castration was performed using a closed inguinal approach in dorsal recumbence under general anaesthesia. The vaginal process was retrieved by blunt dissection over an inguinal skin incision. The closed proximal vaginal process was crushed by a Sand emasculator and ligated at this site. Vaginal Process with content was cut off 10 mm distal to the ligated site. Skin incisions were closed intra cutaneously. Antibiotics or anti-inflammatory drugs were not applied. Results: 48 horses tested negative (SAA< 3mg/l) pre-operatively. Two ponies and one standardbred showed pre-operative 5mg/l, 7mg/l and 75mg/l respectively. Mean SAA value of all 51 horses, three days post operatively, measured 94mg/l. 27 Horses showed no elevation in SAA (<3mg/l). Only 8 horses showed SAA values >100mg/l, of which 4 horses > 500mg/l, (514mg/l, 747mg/l, 1110 mg/l and 1160 mg/l) possibly related to additional trauma. Excluding these 4 cases results in a mean SAA value of 27mg/l. Conclusion: Castrations, using a closed inguinal approach, in which proper surgical standards can be maintained, proved to be far less traumatic than field castrations.

In this paper, global h-stability of nonlinear positive Cohen-Grossberg neural network (PCGNN) system with time-varying delays is studied by means of a direct analysis method. By selecting the appropriate h function and determining its differential expression, global h-stability is converted into two types of known stability, that is Lagrangian exponential stability and global exponential stability. For the sake of improving the accuracy of the stability results, we spare no effort to optimize the fitting effect of the system state trajectory by changing the differential expression of the h function. In addition, two examples are given to verify the feasibility and effectiveness of this method in PCGNN.

Structural biology: the Transformational Eraby

A document by Tim van Timmeren. Click on the document to view its contents.

Background: As indicated by longitudinal observation, autism has difficulty controlling emotions to a certain extent in early childhood, and most children’s emotional and behavioral problems are further aggravated with the growth of age. This study aimed at exploring the correlation between white matter and white matter fiber bundle connectivity characteristics and their emotional regulation ability in children with autism using machine learning methods, which can lay an empirical basis for early clinical intervention of autism. Methods: 55 high risk of autism spectrum disorder (HR-ASD) children and 52 typical development (TD) children were selected to complete the skull 3D-T1 structure and diffusion tensor imaging (DTI). The emotional regulation ability of the two groups was compared using the still-face paradigm (SFP). The classification and regression models of white matter characteristics and white matter fiber bundle connections of emotion regulation ability in the HR-ASD group were built based on the machine learning method. Results: The volume of the right amygdala (R2=0.245) and the volume of the right hippocampus (R2=0.197) affected constructive emotion regulation strategies. FA (R2=0.34) and MD (R2=0.37) had the predictive effect on self-stimulating behavio. White matter fiber bundle connection predicted constructive regulation strategies (positive edging R2=0.333, negative edging R2=0.334) and mother-seeking behaviors (positive edging R2=0.667, negative edging R2=0.363). Conclusion: The emotional regulation ability of HR-ASD children is significantly correlated with the connections of multiple white matter fiber bundles, which is a potential neuro-biomarker of emotional regulation ability.

Changes on the muscle quality of Wuchang bream exposed to different ammonia nitrogen (AN) models during transportation were investigated. Upon AN stressing, fish gill apparently injured, resulting in the increases of ROS content, apoptosis rate, and adjacent gap of muscle cells, and the blurring of muscle fibers. These bio-physiologic changes depended on AN exposure model, e.g., concentration and time. Among different models, the fish exposed to high concentration AN (50 mg/ L) showed the highest drip loss and lowest shear force under short time (3 h) and long time (24 h), respectively. Lightness of the fish exposed to low concentration AN for long time was the highest, and the lowest yellowness for the one exposed to fluctuate concentration AN for long time. The mechanism on changes of muscle quality by AN exposure was mainly related to the upregulation of MAPK/p53, NF-κB and PI3K/AKT signaling pathways to modulate apoptosis.

A Case of Varicella due to Primary Varicella Zoster Virus Infection Followed by Cytomegalovirus Reactivation on the Background of an Immunocompromised Condition Hizuru Tomita, MD1, Yoshimasa Nobeyama, MD1, Miya Morishima, MD1, Akihiko Asahina, MD11. Department of Dermatology, The Jikei University School of Medicine, Tokyo, JapanCorresponding author:Yoshimasa Nobeyama, MDDepartment of Dermatology, The Jikei University School of Medicine,3-25-8, Minato-ku, Tokyo, 105-8461, JapanE-mail: nobederm@jikei.ac.jpThe authors have no conflict of interest to declare.The authors have no financial support in the case report.977 words, 3 figures.Key words: varicella zoster virus infection, varicella, Cytomegalovirus activation, systemic lupus erythematosus, immunocompromised condition.

NUT carcinoma (NC) is an exceedingly rare and poorly differentiated carcinoma characterised by BDR4:NUTM1 gene translocation. It typically affects young adults, and due to its dismal clinical course, standardized therapeutic recommendations are lacking. In this study, we present a successful multimodal treatment approach for a 13-year-old boy diagnosed with primary chest NC harboring a novel NUTM1 rearrangement, achieving complete continuous remission 21 months after diagnosis.

Standard management of pediatric Non-Hodgkin’s Lymphoma (NHL) patients have included an initial assessment of the disease at presentation to establish it’s extent. This “staging” process has historically assigned patients using traditional classifications which were established decades ago when, like other pediatric malignancies, the more extensive involvement of the cancer for a patient directly correlated with the patient’s long term survival[[1]](#ref-0001). Advances in radiologic technology have evolved in the way the disease extent was evaluated, moving from conventional radiographs, to computerized tomography (CT) to magnetic resonance imaging (MRI) to most recently positron emission tomography (PET)[[2]](#ref-0002). Despite the development and use of PET scans for decades for various cancer diagnoses, the role of PET scans for NHL remains unclear[[3]](#ref-0003). Indeed, its value for many conditions is its ability to assess the response to initial therapy and establish the patient’s risk stratification guiding the remaining treatment plan[[4]](#ref-0004). Such efforts have not occurred in clinical trials of NHL and thus we are left to examine case series and try to discern its value for this disease.

Introduction: Breast cancer is a leading cause of cancer-related deaths in females[1], and circular RNAs (circRNAs) have emerged as a novel class of noncoding RNAs that play regulatory roles in angiogenesis and cancer progression. The study of the expression patterns and functional roles of circRNAs in breast cancer has become an area of growing interest. The aim of this study was to investigate the relationship between hsa-circ-00001724 gene expression and breast cancer. method: Circular RNAs were extracted from tissue samples and cDNAs were synthesized, followed by RT-PCR of the glyceraldehyde-3-phosphate dehydrogenase gene as an internal control to ensure the quality of the synthesized cDNA samples. Negative controls were used in RT-PCR and qRT-PCR to exclude contamination with genomic DNA and PCR materials, and a positive control test was also performed. The most appropriate primer sequences were selected using OligoAnalyzer software and the NCBI website, and real-time PCR using SYBR Green was used to examine expression changes. The CT number was determined from the data obtained, and the resulting graphs were examined in terms of dimer formation. The Ct values of normal and tumor samples of the CIRC gene were also subjected to a parametric Kolmogorov-Smirnov test. Results: Real-time PCR reaction results revealed that the hsa-circ-00001724 gene had lower expression in cancer tumor samples than in non-tumor samples. Conclusion: Based on these results, it is hypothesized that hsa-circ-00001724 may serve as a potential biomarker for breast cancer diagnosis and prognosis, and may also be a potential target for therapeutic purposes.

Biopharmaceuticals, including therapeutic antibodies, are rapidly growing products in the pharmaceutical market. Mammalian cells, such as Chinese hamster ovary (CHO) cells, are widely used as production hosts because recombinant antibodies require complex three-dimensional structures modified with sugar chains. Recombinant protein production using mammalian cells is generally performed in conjunction with cell growth. In this study, we developed a technology that controls cell growth and recombinant protein production to induce recombinant protein production with arbitrary timing. Expression of green fluorescent protein (GFP) gene and a single-chain antibody fused with the Fc-region of the human IgG1 (scFv-Fc) gene can be induced and mediated by the estrogen receptor-based artificial transcription factor Gal4-ERT2-VP16 and corresponding inducer drugs. We generated CHO cells using an artificial gene expression system. The addition of various concentrations of inducer drugs to the culture medium allowed control of proliferation and transgene expression of the engineered CHO cells. Use of 4-hydroxytamoxifen, an antagonist of estrogen, as an inducing agent yielded high gene expression at a concentration more than 10-fold lower than that of β-estradiol. When scFv-Fc was continuously produced under inducing conditions, stable production was possible for more than 2 weeks while maintaining high specific productivity (57 pg cell-1 day-1). This artificial gene expression control system that utilizes the estrogen response of estrogen receptors can be an effective method for inducible production of biopharmaceuticals.

Commercial off-the-shelf (COTS) components have been widely used in the aerospace at home and abroad, but there is no systematic theory of quantitative evaluation of the risk. Therefore, based on Shannon’s information entropy, the risk information entropy is proposed to describe the risk uncertainty of COTS components in space application. And a theoretical framework of COTS components space application is established, which includes calculation and decrease of the entropy. According to whether the failure mode and failure frequency ratio are known, different risk information entropy models are established for components. Based on this, a system risk information entropy model is established, and a continuous optimization method for the risk information entropy model is proposed. In addition, it introduces how to achieve system entropy reduction from several aspects, such as selection guidance, application certification, reliability reinforcement, and status detection.

A document by Miguel Vicente. Click on the document to view its contents.

Poncet’s disease: an Uncommon Presentation of a Common Disease in Sudan

IntroductionAmniotic fluid embolism (AFE) is an acute and unpredictable pregnancy complication, with a vital distress for the mother and fetus, occurring most often during labor or in immediate postpartum. In addition, it occurs in 2-8 per 100,000 pregnancies. Recently, it has been proposed that amniotic fluid embolism is a complement-related allergic syndrome of pregnancy that produces vasospasm, edema, and early-onset disseminated intravascular coagulation (DIC). It is one of the leading causes of unexpected obstetrical death. The mortality of AFE is very high, varying from 20 to 60% . Early recognition and prompt resuscitation are critical factors for the treatment of AFE. Here we report a case of amniotic fluid embolism successfully treated by multidisciplinary treatment.

Glycomics is an up-and-coming field for the life sciences, proposed as a new concept after genomics and proteomics, with a focus on the structure and function of glycans. The purpose of this review is to provide a brief overview of research progress in the vital areas of glycomics, such as functional glycan structure, glycosylation and disease, and to suggest possible new insights for the next field of glycomics. Glycomics is an up-and-coming field for the life sciences, proposed as a new concept after genomics and proteomics, with a focus on the structure and function of glycans. The purpose of this review is to provide a brief overview of research progress in the vital areas of glycomics, such as functional glycan structure, glycosylation and disease, and to suggest possible new insights for the next field of glycomics.

Contaminants derived from consumables, reagents, and sample handling often negatively affect LC-MS data acquisition. In proteomics experiments, they can markedly reduce identification performance, reproducibility, and quantitative robustness. Here, we introduce a data analysis workflow combining MS1 feature extraction in Skyline with HowDirty, an R-markdown-based tool, that automatically generates an interactive report on the molecular contaminant level in LC-MS data sets. To facilitate the interpretation of the results, the HTML report is self-contained and self-explanatory, including plots that can be easily interpreted. The R package HowDirty is available from https://github.com/DavidGZ1/HowDirty. To demonstrate a showcase scenario for the application of HowDirty, we assessed the impact of ultrafiltration units from different providers on sample purity after filter-assisted sample preparation (FASP) digestion. This allowed us to select the filter units with the lowest contamination risk. Notably, the filter units with the lowest contaminant levels showed higher reproducibility regarding the number of peptides and proteins identified. Overall, HowDirty enables the efficient evaluation of sample quality covering a wide range of common contaminant groups that typically impair LC-MS analyses, facilitating taking corrective or preventive actions to minimize instrument downtime.

A document by Haleema Qayyum Abbasi. Click on the document to view its contents.

The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) causes a global pandemic named COVID-19. That virus causes a range of human respiratory tract infections; that severity varies from relatively mild to severe respiratory injury syndrome. It has indicated that some individuals might offer susceptibility to SARS‐CoV‐2 infection due to genetic factors. ACE2, TMPRSS2, TYK2, SLC6A20, and IFNAR2 human genes are involved in the pathogenesis of coronavirus in various populations and geographic territories; Therefore, examining the genetic variants of these genes can determine their association with the severity of the COVID-19 disease. In this study, the Whole-Exome Sequencing (WES) technique was used to identify variants of the mentioned human genes concerning the presence or absence of SARS‐CoV‐2 infection in the cohort of 100 individuals from Iran; that may modulate viral infectivity and make some individuals more vulnerable than others. Next, the frequency of variants found in the Iranian population was compared with those belonging to reference individuals from the 1000 Genomes Project, genomAD, and ExAC. In addition, due to the extraordinary importance of the protein’s three-dimensional structure in maintaining the optimal function of the protein, also protein modeling was performed for the essential found variants. The ACE2 gene showed a high level of polymorphism. While TMPRSS2 is less polymorphic. The variants rs759499720/ACE2، rs776459296/ACE2، rs386818798/TMPRSS2، rs771922681/TYK2، rs753470142/TYK2، c.675G>T/TYK2، rs147760034/SLC6A20، rs139008024/SLC6A20, and rs759744926/IFNAR2 showed a significant association with SARS-CoV-2 infection and COVID-19. These variants have previously been detected in studies.

Sigmodontines (Rodentia: Cricetidae), the largest living radiation of Neotropical rodents (90 genera, 489 species), show about 10% having specializations related to a semiaquatic habitat. In addition, this mode of life is unequally distributed among the several clades which compose the subfamily, concentrated in the Ichthyomyini and in a few large-bodied Oryzomyini. The observed taxonomical and geographical pattern is here discussed in a biogeographical historical context. As working hypothesis is advanced that the risk of predation (exerted by animalivorous fresh-water vertebrates) shaped and limited since the late Miocene the semiaquatic performance of the subfamily. Moreover, by exploring the fossil record can also be argued that during the Pleistocene is registered an important number of amphibious sigmodontines extinctions. Therefore, the scarcity of living semiaquatic sigmodontine rodents can be attributed to a combination of an undervalued habitat (mostly by risk of predation) plus a recent pauperization (by a sum of biological extinctions) of the members of that guild. A shallow comparison of the sigmodontine case against murids suggests that continental waterbodies resulted partially refractory to muroid colonizations.

Rampant environmental change and forest destruction push elephants, both Asian and African, to explore human spaces to fulfil their dietary and ecological requirements. Many ‘novel’ elephant behaviour in sharing spaces come to the limelight. Elephant calf burial is reported in African literature but remains absent from the Asian context. We concretely report calf burials by Asian elephants in the eastern Himalayan floodplains of the north Bengal landscape. The study area consists of fragmented forests, tea gardens, agricultural lands, and defence establishments, among others. Tea gardens form the majority of elephant corridors, and we explain the burial strategy of elephants in the trenches of tea gardens. We present four case reports of calf burials by elephants. We aimed to understand the perimortem strategy and postmortem behaviour of Asian elephants. The major findings reflect that the carcasses were carried through trunks and legs for a distance before burying in a ‘legs-upright-position’. We further investigated the underlying reason for calf deaths through postmortem examinations. Direct human intervention was not recorded in any of the four deaths. Through opportunistic observation, digital photography and fieldnotes, and postmortem examination report, we suggest that the carcasses were buried in an abnormal recumbent style irrespective of the reason for calf deaths. Through long-term observation, we further report that the elephants in this region clearly avoid the paths where carcasses were buried, attributing to “bad milestones” and “bad omens”. We discuss and connect the literature of two distinct elephant species and also compared thanatological studies of other sentient nonhuman species. Keywords: Thanatology, animal behaviour, Asian elephant, calf burial, eastern Himalayas, tea gardens

Although the role of multiple cues in mate choice have been widely studied, the consequences thereof for receivers remain poorly understood, especially when there is a mismatch between cues. We address this using the spider mite Tetranychus urticae, in which virgin females are highly valuable mates compared to mated females, given first male sperm precedence. We tested how the presence of females of different mating status, and of cues they left in the substrate affected mating behaviour as well as male costs. Male mating attempts were solely affected by substrate cues, being more frequent on patches with cues of virgins, while female acceptance and number of mating events were independently affected by both female identity and substrate cues, being higher when cues stemmed from virgins. Once copulation started, its duration depended mainly on the mating status of the female being fertilized, with the overall amount of time spent mating being higher in matings with virgins than in those with mated females. Male survival costs mirrored their investment in mating, with patches with a mismatch between cues showing intermediate survival costs. The substrate cues left by females are thus instrumental for males to find their mates, but they can also lead to males paying a high survival cost while not reaping the benefit of mating effectively, which suggest they are less reliable but more efficient than cues on females. The benefit of using redundant cues will then hinge upon the frequency of mismatch between cues, which itself should vary with the dynamics of populations.

The control performance of model predictive control (MPC) strongly depends on the accuracy of the model description. To better capture and predict the dynamic behaviors of the controlled plant, a non-parametric model which is regressed by the Gaussian Process (GP) is proposed in this paper to evaluate the unknown deviation between the nominal model and the physical system. Firstly, an efficient MPC formulation that integrates a nominal model with GP model which evaluates the unmodeled dynamics is designed for safe and robust maneuver planning. Secondly, the geometric hard constraints for collision avoidance between ego cars and obstacles are softened by using a relaxed barrier function for optimization efficiency. A configuration space convexification algorithm is designed for convexifying the corridor constraints in path pre-selection and re-planned for obstacle avoidance. The control performance of the learning-based MPC is demonstrated and compared with the standard MPC strategy under two typical scenarios. Numerical simulation as well as experiment results indicate that the proposed method could keep the safety, stability, and maneuverability of the ego vehicle during obstacle avoidance.