A document by Pronab Pal. Click on the document to view its contents.

A document by Garett Maag. Click on the document to view its contents.

Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge disparity of genomic features. However, existing genome architecture studies are taxon biased, and thus a wider picture should be obtained by expanding the taxonomic scope. Moreover, the extent to which genomic architecture determines the typology of loci recovered in reduced representation sequencing techniques with digestion enzymes is largely unexplored. Here, we observed that whereas plants mostly increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. We found positive correlations between the percentage of loci obtained with in-silico digestion using 2b-enzymes mapping in introns, exons and intergenic categories and the percentage of these regions in the genome. However, exonic regions showed a significant enrichment regardless of the enzyme used. Moreover, the percentage of loci retained after secondary reductions varied with selective-adaptors and genome GC content. In summary, we show that genome architecture has an impact on the markers obtained in reduced representation sequencing that should be considered in conservation genomics for correct wildlife management.

Globally, the diversity of arthropods and the plants upon which they rely are under increasing pressure due to a combination of biotic and abiotic anthropogenic stressors. Unfortunately, conventional survey methods used to monitor ecosystems are often challenging to conduct at large scales. Pan traps are a commonly used pollinator survey method and environmental DNA (eDNA) metabarcoding of pan-trap water may offer a high-throughput alternative to aid in the detection of both arthropods and the plant resources they rely on. Here, we examined if eDNA metabarcoding can be used to identify arthropod and plant species from pan-trap water, and invesitigated the effect of different DNA extraction methods. We then compared plant species identified by metabarcoding with observation-based floral surveys and also assessed the contribution of airborne plant DNA (plant DNA not carried by arthropods) using marble traps to reduce putative false positives in the pan trap dataset. Arthropod eDNA was only detected in 17% of pan trap samples and there was minimal overlap between the eDNA results and morphological identifications. In contrast, for plants, we detected 64 taxa, of which 53 were unique to the eDNA dataset, and no differences were identified between the two extraction kits. We were able to significantly reduce the contribution of airborne plant DNA to the final dataset using marble traps. This study demonstrates that eDNA metabarcoding of pan-trap water can detect plant resources used by arthropods and highlights the potential for eDNA metabarcoding to be applied to investigations of plant-animal interactions.

Background: A new one SARS-CoV-2 Variant of Concern (VoC), Omicron, was born in a world weary of COVID-19, which anger and frustration with the pandemic was widespread, with wide-ranging negative impacts on health, social and economic well-being. The Omicron variant, which main types was BA5.2and BF.7 in China, in December 2022 to January 2023 leaded to off-target of the S and N genes, and the kits used were not adequately and independently evaluated when these agents are studied and developed. To ensure the accuracy of coronavirus test results, performance verification of commercial Real-Time quantitative PCR (RT-qPCR) was required. Objective: We performed a clinical evaluation for two Real Time SARS-CoV-2 assay, and to verify them based on different detection reagents and different clinical specimens. Methods: We performed clinical evaluations of two existing Chinese SARS-CoV-2 RT-qPCR kits COVID-19 nucleic acid detection kits (e-Diagnostic Biomedical, Wuhan, China) and 2019-nCoV nucleic acid diagnostic kits (Fosun Biotechnology, Shanghai, China) using BSD ( Bondson) (Guangzhou Bondson Biotechnology Co. Ltd.;batch number 2022101), quality controls provided by the inspection center and a large number of clinically confirmed specimens. Overall, through the BDS performance verification reference product kit, It was best used to verify the performance of the reagent through a large number of clinical specimens for further verification. Results: The coincidence rate for Fosun and e-Diagnostic kits were individually 95% and 100%. Verified that the detection limit for Fosun and e-Diagnostic kits was 300copies/mL. All were below the detection limit for Fosun reagent was 300copies/mL. e-Diagnostic was 500copies/mL. Fosun had the largest CV for ORF1ab and N gene at the the detection limit concentration(4.80%,3.49%), while e-Diagnostic had the smaller (0.93%,1.10%). Negative results were tested in cross-reactivity. During the verification of clinical samples, sequencing analyses had shown that Fosun single gene miss rate was relatively high, especially ORF1ab, followed by N gene miss rate. we survey that all N genes were detected in clinical specimens, ,ORFab dropout (i.e., a negative/low result) occurred in (10.8%) of 225 Omicron variant. Conclusions: Our results endorse the use of these two commercial kits for the diagnosis of SARS-CoV-2 in China, as their clinical performance has been fully validated by a large number of clinically confirmed cases.

In time-of-use tariff period partition, clustering algorithms are commonly used. However, as load demands become more diverse in this big data era, large amount of non-linear data makes conventional clustering algorithms methods no longer be applicable in this field alone. Facing high-time-resolution daily load data with strong non-linearity, we propose a new method to partition periods. It consists of an improved fuzzy c-means clustering algorithm and a correction method for abnormal periods. Firstly, we propose modified fuzzy membership functions to improve the initialization of clustering for operation efficiency. Secondly, the method for calculating the fuzzy parameters based on the loss function is given. Thirdly, the initial period partition is obtained by the improved clustering. Next, the recognition model and fuzzy subsethood-based correction model for abnormal periods are structed, then the corrected period partition is confirmed. Finally, the effectiveness of the proposed methods is verified by two daily load data with a time resolution of 5 minutes.

With the widespread use of electric vehicles, the rapid development of power electronics and smart grids making more and more nonlinear devices connected to the grid, the power quality problem is becoming more and more prominent, and active power filters (APFs) are widely used to reduce the harmonic voltage and current in the grid. In this paper, the optimal configuration and dimensions of APFs for distribution networks based on the improved Beluga whale optimization (IBWO) are proposed. The IBWO algorithm proposed in this paper is characterized by fast convergence and high accuracy. The objective of the method proposed in this paper is to reduce the number of APFs used and the investment cost, while making the total voltage harmonic distortion rate (VTHD) and the individual VTHD of the grid meet the requirements. Finally, this paper verifies the effectiveness and feasibility of the proposed method by an example in an IEEE-18 bus test system, and the results show that the proposed method is effective in optimizing the location and capacity of multiple APFs.

In the context of the energy crisis, the development of low-carbon integrated energy systems has become a prominent research area. This article addresses the challenges posed by high energy consumption and emissions in integrated energy systems by proposing a multi-stage planning method for low-carbon integrated energy that considers load time transfer characteristics. The first step involves examining the time transfer characteristics of demand response and analyzing the economic benefits of integrated energy systems participating in the electricity-carbon market. Subsequently, a multi-stage green low-carbon planning model for the integrated energy system is constructed. To validate the effectiveness of the proposed model, actual calculation results are obtained. These results demonstrate that demand response, specifically in data centers, can significantly reduce the operational costs of integrated energy systems. Furthermore, the multi-stage low-carbon planning approach is shown to be more reasonable and economically beneficial compared to single-stage planning. Overall, this research article provides insights into the development of low-carbon integrated energy systems within the context of the energy crisis. By considering load time transfer characteristics and employing a multi-stage planning method, the article highlights the potential for reducing costs and improving the overall efficiency of integrated energy systems.

Australia Day, celebrated on January 26, is rooted in Australia’s colonial history and causes pain for many of Australia’s First Peoples. This study was the first to investigate predictors of Australians’ attitudes towards the date, whilst exploring whether intervention may improve attitudes towards a date-change. An Australian community sample ( N=559) were recruited through social media for an anonymous survey. Participants indicated their support for date-change, and responded to a variety of demographic (e.g., Age) and sociodemographic (e.g., Racism) questions, then being randomly allocated to an intervention statement, indicating their final attitudes post-intervention. Findings suggest sociodemographic factors were more important predictors than demographics, with Racism ( β =.50***), Traditionalism ( β =.18**), Patriotism ( β =.13*) and Age ( β =.10*) significantly predicting participants’ date-change resistance. Racism demonstrated the most predictive strength, underscoring the importance of a date-change, with those open to change often identifying any alternative date should not offend First Peoples. In addition, intervention produced significant improvement in participants’ date-change attitudes, among those able to become more open to a date-change; however, differences were not present between intervention conditions. This illuminates the factors predicting Australians’ attitudes towards Australia Day, whilst demonstrating a potential path towards date-change through intervention.If you wish to learn more about this study, please contact the primary author at morea005@mymail.unisa.edu.au or find the published article in Analyses of Social Issues and Public Policy.

A document by FATİH ÇİFTÇİ. Click on the document to view its contents.

Even parasites have parasites. By definition, a hyperparasite is an organism capable of parasitizing another parasite. Hyperparasitism caused by fungi is a common phenomenon in nature, but it has been poorly studied. This life history strategy evolved several times in the fungal tree of life, and is crucial in the maintenance of ecosystems as well as in the mediation of parasite–host interactions. Although the interest for hyperparasitic fungi is growing in the context of biological control, hyperparasitism is not ecologically and evolutionarily understood. This chapter summarizes the most relevant aspects of the terminology, diversity, and ecology of hyperparasitic fungi on both fungal and non-fungal hosts. We also discuss the problems related to molecular research on hyperparasitic fungi. As they represent a hidden source of diversity, it is necessary to increase sampling efforts and to undertake further morphological, molecular, and ecological studies to understand these fungi and their potential biotechnological and pharmaceutical uses. 

Leaf micromorphological characters of the genus Adiantum L. were studied using standard protocols of light microscopy (LM). The study was aimed at investigation of morpho-anatomical variation in three species of genus Adiantum viz A. capillus veneris, A. venustum and A. incisum sampled along the altitude as an ecological variable. Stomatal density, number and type of subsidiary cells, stomatal complex type and stomatal index were studied through light microscopy (LM). Results revealed that leaf length decreased with increase in altitude. Stomatal type varied from anisocytic to diacytic in A. capillus veneris as well as in A. venustum whereas it was restricted to anomocytic in Adiantum incisum. Unweighted paired group method using arithmetic averages (UPGMA) was used to examine the similarities among the species . A. capillus veneris was found to be the most adapted species showing epistomatic, hypostomatic and amphistomatic leaf types. Hypostomatic and amphistomatic leaf type were found in A. vensutum whereas A. incisum was found to be restricted only to hypostomatic leaves. Cluster analysis using UPGMA explained that A.capillus veneris usually thrives in areas of lower altitude, while the occurrence of A.venustum as well as A. Incisum in higher altitudes reveals a narrow range of adaptations for latter. Moreover, absence of stomata on abaxial surface in both A.venustum as well as A.incisum indicates the relationship of these two species with ambient ecological conditions on higher altitude. Variations in stomatal types within and among the species confirm that stomatal density and complex type are key factors for species delimitation. Research Highlights

Purpose: This study examines which vaccination organization system performed best in the COVID-19 pandemic to improve future vaccination organization. Study design: The vaccination organization of every federal state is categorized as decentralized or centralized and analysed based on their daily vaccination rates and the vaccination time series of the federal state with the highest vaccination rate is analysed by using the Event Study Methodology [ESM]. Findings: In Germany’s federal state with the highest vaccination rate (i.e., Saarland), the change from a system of availability-based offerings to a pre-registration with preferences and automatic appointment allocation system was a significant performance factor. Originality: A quasi-experimental study with a different vaccination organization is setup and the Event Study Methodology [ESM] is applied to the vaccination context. Research limitations: This study is limited on the vaccination organization of high-developped countries with a comprehensive health system such as Germany. Practical implications: A pre-registration and automatic appointment allocation system is recommended as best practice to policy makers and pandemic managers for their vaccination organization given the first half-year experience in the COVID-19 pandemic. Social implications: A cumulative additional vaccination rate of 8.44 per 100 inhabitants and an 14% overperformance is found. The implementation of this system for whole Germany would have resulted in 4% higher protection, estimated 26’596 less infections, US$ 7 million less hospitalization costs, and earlier relaxation of lockdown of two months.

Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here we took advantage of a hybrid to simplify genome assembly and present high quality chromosome level assemblies for both species. These assemblies show high levels completeness with BUSCOs of 94.5% for A. artemisiifolia and 96.1% for A. trifida and LTR Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half the genome is comprised of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida, and this is similar to other species in the Heliantheae alliance . Single copies of herbicide resistance associated genes PPX2L, HPPD, and ALS where found, while 2 copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. The evolution of genome structure has differed among these two Ambrosia species. The genome of A. trifida has undergone greater rearrangement, possibly the result of cataclysmic reorganization through chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae alliance the clearest feature of its genome. When compared other Heliantheae alliance species, this allowed us to reconstruct the common ancestor’s karyotype – a key step for further development of our understanding of the evolution and diversification of this economically and allergenically important group.

We isolated and identified 261 aerobic bacterial strains and 121 fungal strains from the lesions of 140 Thoroughbred racehorses with infectious dermatitis. Drug susceptibility testing was performed for the bacteria isolated. Each specimen was then classified into three categories based on the type of microorganism isolated: i) Group C, coagulase-positive staphylococci (CPS); ii) Group F, pathogenic fungi; and iii) Group N, other resident microorganisms not classified in other groups. Skin rash morphology and the course of treatment were examined for correlations with group classification. The results showed no relationship between skin rash morphology and group classification. As for the course of treatment, most cases required topical application of antibiotics selected based on drug sensitivity testing of the affected area to achieve resolution of symptoms. These included multiple cases from Group F in which pathogenic fungi such as Trichophyton spp. were isolated. Infectious dermatitis in racehorses is currently treated simply by differentiating between bacterial and fungal infections through experience-based visual inspection and palpation alone, and by providing pharmacotherapies such as antibiotics or antifungal agents. However, the present findings suggest that treatment based upon practitioner experience and skin rash morphology alone may be ineffective. Regardless of the morphology, the affected area should be thoroughly cleansed first with an antiseptic that is effective against both bacteria and fungi. If improvement is still not seen, medications should be introduced based on microbial identification and drug susceptibility testing.

A document by SLL & LLS. Click on the document to view its contents.

Sarcomas represent less than 1% of all malignant tumors. Undifferentiated Embryonal Sarcoma (UES) of the liver is the third most common pediatric liver cancer. The main differential diagnoses are mesenchymal hamartoma, hepatoblastoma, and biliary embryonal rhabdomyosarcoma. Definitive diagnosis is confirmed by histopathology and immunohistochemical. 4-year-old male patient with fever, abdominal pain and palpable hepatomegaly was found. Magnetic Resonance Imaging (MRI) with an unifocal cystic hepatic mass, with compression and displacement of vascular structures, but without invasion; hamartoma was suspected. The management was a right hepatectomy. Immunohistochemistry studies were positive for UES. Adjuvant chemotherapy was started with a good response.

Gestational diabetes mellitus, pre-eclampsia and future cardiovascular disease: need to consider both BMI and gestational weight gain to investigate the linkLionel Carbillon1, 3, Amélie Benbara1, Emmanuel Cosson2, 31Department of Obstetrics and Gynecology, Paris-Seine Saint Denis University Hospitals, Assistance Publique – Hopitaux de Paris, Paris 13 University, France2 Department of Endocrinology, Diabetology, Nutrition, Paris-Seine Saint Denis University Hospitals, Assistance Publique – Hôpitaux de Paris, France3Sorbonne North Paris University

Introduction Methods guidance and appraisal tools for systematic reviews require specification of the question and eligibility criteria for the review (‘PICO for the review’). Less emphasis has been given to specifying the question and criteria for each synthesis (‘PICO for each synthesis’), yet decisions about which studies to include in each synthesis can critically influence the utility and findings of a review. This paper describes the rationale and methods for developing the InSynQ (Intervention Synthesis Questions) tool for planning and reporting synthesis questions in reviews of interventions. The aim is to provide transparency about the basis of the tool and contribute to evidence on methods for developing guidance for research conduct and reporting. Methods Informed by EQUATOR Network methods, we (1) established a project group; (2) examined reporting of the ‘PICO for each synthesis’ in published reviews; (3) reviewed existing reporting guidance and the Cochrane Handbook for Systematic Reviews of Interventions; (4) drafted items with elaboration, explanation and examples; (5) conducted consultation meetings, an evaluation survey and pilot test; (6) incorporated feedback. Results Existing reporting guidelines do not distinguish the review and synthesis PICO, with limited coverage of the elements needed to specify the PICO for each synthesis. Using the PRISMA 2020 format, the draft tool contained 10 items with essential and additional reporting elements, explanation and examples. Revisions arising from feedback (>30 people), included adding an eleventh item on consumer and stakeholder involvement, a figure explaining PICO for each synthesis, and integrating examples into elements/explanations. All respondents to the evaluation survey (12 people) said the tool would help them plan or appraise synthesis questions. InSynQ is available at https://InSynQ.info. Conclusion Transparent reporting of the development process contributes to the evidence-base for methods to develop guidance. It may improve uptake of InSynQ, in turn enhancing the clarity of syntheses.

This research presents a novel numerical method for estimating solutions to higher-order differential equations with initial value problems (IVPs). By directly integrating a system of third and fourth-order differential equations using a 2-point implicit algorithm built with collocation and interpolation, significant improvements in efficiency are achieved. The proposed hybrid method, incorporating the first and second derivatives of the discrete algorithm, enhances accuracy and convergence rates. Convergence analysis confirms the zero-stability and consistency of the method, and numerical experiments demonstrate its superiority over existing methods for solving third and fourth-order equation systems. This work contributes a valuable numerical approach for efficient and accurate estimation of higher-order differential equations with IVPs.

Background: This study aims to preliminarily explore the impact of delayed influenza virus nucleic acid conversion (more than five days) to negative on treatment and length of hospital stay in children with severe influenza. Methods: This was a single-center retrospective study. General information, influenza virus nucleic acid test (per 3-5 days) results after receiving antiviral medication, antiviral drug usage, comorbid infections, invasive mechanical ventilation, and discharge prognosis of children with severe influenza were collected. Results: A total of 39 patients were included in the study. The patients were divided into four groups based on the time when the patient’s viral nucleic acid turned to negative after receiving antiviral medication: 3-5 days (35.8%, 14/39), 6-10 days (38.4%, 15/39), >10 days (12.8%, 5/39), and maintaining as positive when discharge (12.8%, 5/39). More than half of pediatric patients with severe influenza exhibited delayed nucleic acid conversion (more than 5 days) after antiviral medication. The >10 days group had a longer time from onset to PICU admission, PICU stay, and antiviral drug use duration, as well as a higher proportion of CBP use (P < 0.05, respectively). Within the first 3 days of PICU admission, the proportion of patients with persistently reduced lymphocytes was lower in the 3-5 days group (28.6% (4/14)) than other two groups (P > 0.05). Conclusions: Delayed nucleic acid conversion was associated with longer PICU length of stay. Persistent fever, co-infections, and impaired cellular immune function may contribute to the delay.

Iron deficiency is a common challenge faced by cyanobacteria in oceanic environments and the acclimation to iron deficiency is crucial for their survival. In response to iron deficiency, many cyanobacterial species induce the production of a pigment-protein complex called IsiA. IsiA proteins associate with photosystem I (PSI) and can function as light-harvesting antennas or dissipate excess energy. They may also serve as Chl storage during iron limitation and aid in the recovery of the photosynthetic apparatus. In this study we examined the functional role of IsiA in cells of Synechocystis sp. PCC 6803 grown under iron-limitation conditions by measuring the cellular IsiA content and its capability to transfer energy to PSI. We specifically test the effect of the oligomeric state of PSI by comparing wild-type (WT) Synechocystis sp. PCC 6803 to mutants lacking specific subunits of PSI, namely PsaL/PsaI (Δ psaL mutant) and PsaF/PsaJ (ΔFIJL mutant). Time-resolved fluorescence spectroscopy revealed that IsiA formed functional PSI 3-IsiA 18 supercomplexes, wherein IsiA effectively transfers energy to PSI on a timescale of 10 ps at room temperature, confirming the primary role of IsiA as an accessory light-harvesting antenna to PSI. However, a significant fraction (40%) remained unconnected to PSI in the form of IsiA aggregates, supporting the notion of a dual functional role of IsiA. The absence of PsaL and PsaF subunits led to reduced accumulation of IsiA under iron deficiency with PSI monomers only binding 3-4 IsiA complexes on average. Taken together, the results show that IsiA is capable of transferring energy to trimeric and to monomeric PSI but to varying degrees and that the acclimatory production of IsiA under iron stress is controlled by its ability to perform its light-harvesting function.

D-amino acids are the D stereoisomers of common L-amino acids found in proteins. In the past two decades, the occurrence of D-amino acids in plants has been reported and circumstantial evidence for a role in several processes has been provided, including the interaction with soil microorganisms or an interference with cellular signalling. However, examples are relatively scarce and D-amino acids can also be detrimental, some of them inhibiting growth and development. Thus, the persistence of a D-amino acid metabolism in plants is rather surprising and evolutive origins of D-amino acid metabolism is presently unclear. Systemic analysis of sequences associated with enzymes of D-amino acid metabolism shows that they are not simply inherited from cyanobacterial metabolism. In effect, the history of enzymes of plant D-amino acid metabolism likely involves several steps, cellular compartments, gene transfers and losses. Regardless of evolutive steps, enzymes of D-amino acid metabolism like D-amino acid transferases or racemases have been kept by higher plants and not simply eliminated, hence it is likely that they fulfil important metabolic roles, which can be illustrated with serine, tryptophan, and folate metabolism. We suggest that D-amino acid metabolism was perhaps crucial to support metabolic functions required during land plants evolution.

The number of SARS-CoV-2 recombinants identified during the pandemic has increased since the era of Omicron variants, but XBB.1.5 (or Omicron 23A) is the first lineage comprised of hybrid genomes to predominate at the country and global scales. Very interestingly, the XBB.1.5 recombinant, like the Marseille-4B subvariant (B.1.160/20A.EU2) and the pandemic variant B.1.1.7 (20I/Alpha) previously, has its ORF8 gene inactivated by a stop codon. XBB.1.5 was generated through two successive main events: a recombination between SARS-CoV-2 of lineages BA.2.10.1.1 (BJ.1) and BA.2 75.3.1.1.1 (BM.1.1.1) that generated the XBB (22F) lineage; then ORF8 gene inactivation by a stop codon. We further identified that a stop codon was present at 89 (74%) codons of the ORF8 gene in ≥1 of 15,222,404 genomes available in GISAID, and at 15 codons (12%) in ≥1,000 genomes. Thus, it is very likely that stop codons in ORF8 gene contributed on at least 3 occasions and independently during the SARS-CoV-2 pandemic to the evolutionary success of a lineage that became transiently predominant, most recently XBB.1.5. Such association of gene loss with evolutionary success, which suits the recently described Mistigri rule, is an important biological phenomenon very unknown in virology while largely described in cellular organisms.