bluuebunny/crossref_metadata_2025_split huggingface dataset:
The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes
Authors: Abalde Samuel , Tellgren-Roth Christian , Heintz Julia , Vinnere Pettersson Olga , Jondelius Ulf 
Published: September 2023

Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group’s main clades and whose origin has been dated more than 400 million years ago.Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades.Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system.Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
A novel bispecific antibody dual-targeting approach for enhanced neutralization against fast-evolving SARS-CoV-2 variants
Authors: Kim Ji Woong , Kim Hyun Jung , Heo Kyun , Lee Yoonwoo , Jang Hui Jeong , Lee Ho-Young , Park Jun Won , Cho Yea Bin , Lee Ji Hyun , Shin Ha Gyeong , Yang Ha Rim , Choi Hye Lim , Shim Hyun Bo , Lee Sukmook 
Published: September 2023

IntroductionThe emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has caused unprecedented health and socioeconomic crises, necessitating the immediate development of highly effective neutralizing antibodies. Despite recent advancements in anti-SARS-CoV-2 receptor-binding domain (RBD)-specific monoclonal antibodies (mAbs) derived from convalescent patient samples, their efficacy against emerging variants has been limited. In this study, we present a novel dual-targeting strategy using bispecific antibodies (bsAbs) that specifically recognize both the SARS-CoV-2 RBD and fusion peptide (FP), crucial domains for viral attachment to the host cell membrane and fusion in SARS-CoV-2 infection. MethodsUsing phage display technology, we rapidly isolated FP-specific mAbs from an established human recombinant antibody library, identifying K107.1 with a nanomolar affinity for SARS-CoV-2 FP. Furthermore, we generated K203.A, a new bsAb built in immunoglobulin G4-(single-chain variable fragment)2 forms and demonstrating a high manufacturing yield and nanomolar affinity to both the RBD and FP, by fusing K102.1, our previously reported RBD-specific mAb, with K107.1. ResultsOur comprehensive in vitro functional analyses revealed that the K203.A bsAb significantly outperformed the parental RBD-specific mAb in terms of neutralization efficacy against SARS-CoV-2 variants. Furthermore, intravenous monotherapy with K203.A demonstrated potent in vivo neutralizing activity without significant in vivo toxicity in a mouse model infected with a SARS-CoV-2 variant. ConclusionThese findings present a novel bsAb dual-targeting strategy, directed at SARS-CoV-2 RBD and FP, as an effective approach for rapid development and management against continuously evolving SARS-CoV-2 variants.
Composition of planktonic foraminifera test-bound organic material and implications for carbon cycle reconstructions
Authors: Paoloni Tommaso , Hoogakker Babette , Navarro Rodriguez Alba , Pereira Ryan , McClymont Erin L. , Jovane Luigi , Magill Clayton 
Published: September 2023

IntroductionForaminiferal shells are extensively used to reconstruct the marine environment in the geological past. The foraminifera test-bound organic material (FBOM), sheltered by the test from potential diagenetic alteration and contamination, has great feasibility to improve our understanding of carbon and nitrogen cycling. The FBOM δ13C has been proposed as a proxy for reconstructing past environmental conditions. However, to fully exploit the proxy potential of FBOM, its molecular composition and the influence of the latter on the FBOM δ13C need to be assessed.MethodHere we use a novel combination of gas chromatography-mass spectrometry, flame ionization detection (GC-MS/FID) and liquid chromatography organic carbon and nitrogen detection (LC-OCD/ OND) analyses to study the FBOM chemical composition.ResultsOur results indicate that polysaccharides and proteins dominate FBOM, as proposed by earlier studies, with no evidence of detectable lipids (alkyl lipids, trimethylsilyl ethers of fatty alcohols, trimethylsilyl esters of fatty acids and steranes derivatives were targeted).DiscussionPrevious studies suggested that FBOM δ13C may be used to reconstruct past atmospheric CO2 concentrations. However, our results indicate that the use of FBOM δ13C to reconstruct CO2 carries an approximate uncertainty of ±21 ppm for past atmospheric CO2 abundance. We suggest that FBOM δ13C can be used as a novel proxy to reconstruct particulate organic material (POM) δ13C. This is also supported by the recently confirmed minor fractionation between POM and FBOM δ13C.
Male infertility risk and gut microbiota: a Mendelian randomization study
Authors: Fu Zhi-da , Wang Yao , Yan Hong-li 
Published: September 2023

BackgroundIn recent decades, the decline of male sperm quality has become a worldwide phenomenon, with sperm quality of critical importance for the ability to conceive naturally. Recent studies suggest that male fertility function is closely linked to the gut microbiota, however, the cause-and-effect association between the gut microbiota and male infertility risk is currently unclear.MethodsWe performed one two-sample Mendelian randomization (MR) study, which uses summary data on human gut microbiota from the MiBioGen consortium as factors of exposure. FinnGen Consortium R8 data was used to obtain GWAS data for male infertility. To evaluate cause-and-effect associations linking gut microbiota and male infertility risk with multiple Mendelian randomization methods, we included inverse variance weighted (IVW), MR-Egger, and Maximum Likelihood (ML) Ratio. The heterogeneity of instrumental variables was evaluated through Cochran's Q, Rucker's Q, and leave-one-out analysis methods.ResultsWe found a positive association between Allisonella, Anaerotruncus, Barnesiella, Intestinibacter, and Lactococcus with male infertility risk according to the MR analysis results. Bacteroides Romboutsia, Ruminococcaceae (NK4A2140group), and Ruminococcaceae (UCG011) play a protective function in male infertility pathogenesis.ConclusionIt was found that gut microbiota and infertility are causally related in this study. In subsequent studies, there is a need to build a larger and more comprehensive GWAS database on male infertility, which will reveal the underlying mechanisms for gut microbiota and male infertility. There is a need for randomized controlled trials for validating the protective effect of the associated gut microbiota against male infertility risk, and for exploring the associated mechanisms.
Circulating vitamin levels mediate the causal relationship between gut microbiota and cholecystitis: a two-step bidirectional Mendelian randomization study
Authors: Miao Changhong , Xiao Lu , Xu Xinyi , Huang Shuoxuan , Liu Jiajin , Chen Kuang 
Published: September 2023

BackgroundThe relationship between gut microbiota and the occurrence of cholecystitis remains unclear. Existing research lacks a clear understanding of how circulating vitamin levels modulate this relationship. Therefore, our study aims to investigate whether circulating vitamin levels mediate the causal relationship between gut microbiota and cholecystitis using a two-step bidirectional Mendelian randomization approach.MethodsIn this study, we initially employed Linkage Disequilibrium Score Regression (LDSC) analysis to assess the genetic correlation of five circulating vitamin level genome-wide association study (GWAS) summary datasets, thereby avoiding potential sample overlap. Subsequently, we conducted a two-step analysis to investigate the causal effects between gut microbiota and cholecystitis. In the second step, we explored the causal relationship between circulating vitamin levels and cholecystitis and identified the mediating role of vitamin D. The primary method used for causal analysis was the inverse variance-weighted approach. We performed additional sensitivity analyses to ensure result robustness, including the cML-MA method and reverse Mendelian randomization (MR) analysis.ResultsAn increment of one standard deviation in RuminococcaceaeUCG003 was associated with a 25% increased risk of cholecystitis (OR = 1.25, 95%CI = 1.01–1.54, p = 0.04), along with a 3% decrease in 25-hydroxyvitamin D levels (OR = 0.97, 95%CI = 0.944–0.998, p = 0.04). However, following the rigorous Bonferroni correction, every one standard deviation decrease in circulating vitamin D levels was associated with a 33% increased risk of cholecystitis (OR = 0.67, 95%CI = 0.49–0.90, p = 0.008, Padjust = 0.04). Thus, the potential link between gut microbiota and cholecystitis risk might be mediated by circulating vitamin D levels (proportion mediated = 5.5%). Sensitivity analyses provided no evidence of pleiotropy.ConclusionOur study results suggest that an elevated abundance of specific gut microbiota is associated with an increased susceptibility to cholecystitis, with the causal relationship being mediated by circulating vitamin D levels. Further large-scale randomized controlled trials are necessary to validate the causal effects of gut microbiota on cholecystitis risk. This study provides novel insights into cholecystitis prevention through the regulation of gut microbiota.
Case report: Early onset de novo FSGS in a child after kidney transplantation—a successful treatment
Authors: Carvajal Abreu Karla , Loos Sebastian , Fischer Lutz , Pape Lars , Wiech Thorsten , Kemper Markus J. , Tönshoff Burkhard , Oh Jun , Schild Raphael 
Published: September 2023

BackgroundEarly onset de novo focal segmental glomerular sclerosis (FSGS) in the kidney allograft in patients without FSGS in the native kidney is a rare disorder in children. It usually occurs mostly beyond the first year after kidney transplantation and often leads to graft loss. Standardized treatment protocols have not yet been established.Case descriptionWe describe a boy with early onset de novo FSGS in the transplanted kidney and non-selective glomerular proteinuria (maximum albumin-to-creatinine ratio of 3.8 g/g; normal range, ≤0.03 g/g creatinine). Manifestation occurred at 30 days posttransplant and was accompanied by a significant graft dysfunction (eGFR 61 ml/min per 1.73 m2). Treatment with 25 sessions of plasmapheresis over 14 weeks and three consecutive days of methylprednisolone pulse therapy (10 mg/kg per day) followed by oral prednisolone as rejection prophylaxis (3.73 mg/m2 per day) led to sustained remission of proteinuria (albumin-to-creatinine ratio of 0.028 g/g) and normalization of graft function (eGFR 92 ml/min per 1.73 m2) after 14 weeks. The follow-up period was 36 months.ConclusionsThis case underlines the efficacy of immunosuppressive and antibody eliminating therapy in early onset de novo FSGS after kidney transplantation.
Year-round growth potential and moisture stress tolerance of buckwheat (Fagopyrum esculentum L.) under fragile hill ecosystems of the Eastern Himalayas (India)
Authors: Rangappa Krishnappa , Rajkhowa Dipjyoti , Layek Jayanta , Das Anup , Saikia Uday Sankar , Mahanta Kaberi , Sarma Anjan Kumar , Moirangthem Prabha , Mishra Vinay Kumar , Deshmukh Nishant Anandrao , Rajbonshi Namrata , Kandpal Basant K. 
Published: September 2023

IntroductionUnder a changing climate, the fragile ecosystems of the Eastern Himalayas (EH) are persistently challenged by prolonged dry spells and erratic rainfall. Identification of suitable high-yielding crops with higher moisture stress tolerance and adaptability is paramount for the region. Although the region received a good amount of rainfall in the rainy season, the winter months, viz., November to March, rarely received any rain. Even within the rainy season, there are several intermittent drought spells that hinder crop productivity.MethodsThe present study has used field and microcosm experiments to assess the year-round cultivation potential and extent of moisture stress tolerance in the lesser-known buckwheat crop of the region.Results and discussionSowing of buckwheat from mid-September to mid-December produced better grain yield, the highest being when sowing in October (9.83 q ha−1) and the crop was found suitable to grow all through the year for higher green biomass (12.6–38.4 q ha−1). The moisture stress tolerance of buckwheat was significantly enhanced by increased total root length and root surface area by 12.4 and 34.7%, respectively. Increased photo-protective carotenoids, chlorophyll b, and favorable stomatal attributes with substantial epicuticular wax have significantly improved the moisture stress tolerance of Buckwheat. In addition, leaf proline was found 25.4% higher and total soluble protein, reducing sugar, and cell membrane stability were found 29.2, 38.1, and 36.5% lower compared to the control, respectively. A significantly lower rate of water loss (25.6%) with its stomatal and non-stomatal adaptations and versatile pollen structural traits under moisture stress over control, make the buckwheat crop potentially more stress tolerant and economical crop for EH of India.
The Global Burden of Vascular Intestinal Disorders in 204 Countries and Territories From 1990 to 2019: Global Burden of Diseases Study
Authors: Jiang Tianxiang , Cai Zhaolun , Mu Mingchun , Zhao Zhou , Shen Chaoyong , Zhang Bo 
Published: September 2023

Objectives: Assess the prevalence, mortality, and disability-adjusted life years (DALYs) of vascular intestinal disorders (VID) from 1990 to 2019.Methods: This study conducted a secondary data analysis utilizing the Global Burden of Diseases Study 2019. The prevalence, mortality and DALYs of VID were analyzed by sex, age and socio-demographic index (SDI), respectively. Analyses were performed by using R software.Results: Globally, the number of prevalent VID cases increased from 100,158 (95% uncertainty interval: 89,428–114,013) in 1,990–175,740 (157,941–198,969) in 2019. However, the age-standardized rates (ASR) of VID prevalence declined from 2.47 (95% uncertainty interval: 2.24–2.76) per 100,000 population to 2.21 (1.98–2.48) per 100,000 population between 1990 and 2019. Furthermore, the ASR of mortality also decreased from 1990 to 2019. Between 1990 and 2019, the regions with high and high-middle level exhibited the highest diseases burden.Conclusion: Globally, the diseases burden associated with VID demonstrated a decline from 1990 to 2019. However, concerted efforts are still required to enhance measures to combat VID within countries categorized as high and high-middle SDI.
Seasonal Dynamics and Physiological Age of Ixodid Ticks Collected from Dogs
Authors: Petrović Aleksandra , Stanić Ksenija , Popović Aleksandra , Ivanović Ivana , Supić Dejan , Marinković Dušan , Bursić Vojislava 
Published: September 2023

In order to reproduce and complete life cycles, ticks have to feed on different hosts, thus participating as vectors and reservoirs in the maintenance and circulation of different pathogens. Since dogs can serve as suitable hosts for numerous tick species, the aims of this study were to determine tick species and their seasonal occurrence on pet dogs and to compare the accuracy of three indices frequently used to calculate engorged female physiological age. Ticks were collected from dogs brought to veterinary clinics. Three indices were analyzed: scutal index, alloscutal/scutal index ratio, and physiological age index. Four tick species were identified: Ixodes ricinus, Dermacentor marginatus, D. reticulatus, and Rhipicephalus sanguineus group, and the last was the most abundant. The highest number of collected ticks was in April, but two species were continuously active throughout the year. The statistical analyses distinguished the physiological age index as more precise because of lower variability. Dog owners usually ignore regular dog anti-tick treatments throughout the year, as they are not aware that ticks could be active during the winter months. Tick surveillance is unquestionably important in order to monitor and prevent the distribution of these vectors and also the diseases they transmit.
Analysis of the High Temperature Plastic Deformation Characteristics of 18CrNi4A Steel and Establishment of a Modified Johnson–Cook Constitutive Model
Authors: Wang Zhen , Jiang Chuang , Wei Bingyang , Wang Yongqiang 
Published: September 2023

To investigate the plastic deformation behavior of 18CrNi4A steel at high temperatures, an isothermal hot compression test was conducted on a Thermecmastor-Z series test machine at deformation temperatures from 1273 K to 1423 K and strain rates ranging from 0.01 s−1 to 10 s−1. The effects of these two factors on the flow stress were analyzed. Based on the true stress–strain experimental curves, the original Johnson–Cook constitutive model was applied to determine the flow stress data under different deformation conditions. The prediction results of the model were compared with the experimental data. The main reason for the large deviation observed between them was that the coupling relationship between the deformation temperature and the strain rate was not considered, so the original Johnson–Cook model was modified. The correlation coefficient and average absolute relative error of the original Johnson–Cook model were 0.962 and 16.36%. The prediction accuracy of the modified Johnson–Cook model was improved to 0.991 and 5.58%, respectively. The results show that the modified Johnson–Cook model exhibits higher prediction precision, which is beneficial for the broader application of 18CrNi4A steel in the industry.
Genetic Structure of Juvenile Stages of Phocanema bulbosum (Nematoda, Chromadorea: Anisakidae) Parasitizing Commercial Fish, Atlantic Cod Gadus morhua, and American Plaice Hippoglossoides platessoides in the Barents Sea
Authors: Gordeev Ilya I. , Bakay Yuri I. , Kalashnikova Marina Yu. , Logvinenko Andrey D. , Emelianova Olga R. , Sokolov Sergey G. 
Published: September 2023

Atlantic cod Gadus morhua and American plaice Hippoglossoides platessoides are two of the most commercially valuable species in the Barents Sea (FAO Area 27). They are considered as an important but neglected source of zoonotic risk associated with nematodes from the genus Phocanema. The abundance of Phocanema spp. in a fish host individual in the Barents Sea may be quite high, which is convenient for studying the genetic structure of its populations. A total of 69 third-stage juveniles of Phocanema spp. were isolated from the liver, the mesentery, and the musculature of G. morhua and H. platessoides and genotyped by the mtDNA Cox2 gene. Almost all these juveniles (68) were molecularly identified as P. bulbosum. The mtDNA Cox2 gene was also used to reveal the haplotype diversity and the genetic structure of P. bulbosum. A comparison of the specimens examined in this study with each other and with the haplotypes previously identified by us in the White Sea showed that there were no significant differences between the groups from different hosts and from different catch areas.
Weight Loss Promotion in Individuals with Obesity through Gut Microbiota Alterations with a Multiphase Modified Ketogenic Diet
Authors: Wang Hongchao , Lv Xinchen , Zhao Sijia , Yuan Weiwei , Zhou Qunyan , Sadiq Faizan Ahmed , Zhao Jianxin , Lu Wenwei , Wu Wenjun 
Published: September 2023

The occurrence of obesity and related metabolic disorders is rising, necessitating effective long-term weight management strategies. With growing interest in the potential role of gut microbes due to their association with responses to different weight loss diets, understanding the mechanisms underlying the interactions between diet, gut microbiota, and weight loss remains a challenge. This study aimed to investigate the potential impact of a multiphase dietary protocol, incorporating an improved ketogenic diet (MDP-i-KD), on weight loss and the gut microbiota. Using metagenomic sequencing, we comprehensively analyzed the taxonomic and functional composition of the gut microbiota in 13 participants before and after a 12-week MDP-i-KD intervention. The results revealed a significant reduction in BMI (9.2% weight loss) among obese participants following the MDP-i-KD intervention. Machine learning analysis identified seven key microbial species highly correlated with MDP-i-KD, with Parabacteroides distasonis exhibiting the highest response. Additionally, the co-occurrence network of the gut microbiota in post-weight-loss participants demonstrated a healthier state. Notably, metabolic pathways related to nucleotide biosynthesis, aromatic amino acid synthesis, and starch degradation were enriched in pre-intervention participants and positively correlated with BMI. Furthermore, species associated with obesity, such as Blautia obeum and Ruminococcus torques, played pivotal roles in regulating these metabolic activities. In conclusion, the MDP-i-KD intervention may assist in weight management by modulating the composition and metabolic functions of the gut microbiota. Parabacteroides distasonis, Blautia obeum, and Ruminococcus torques could be key targets for gut microbiota-based obesity interventions.