bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studying protein–protein interaction through side-chain modeling method OPUS-Mut
Authors: Xu Gang , Wang Yilin , Wang Qinghua , Ma Jianpeng 
Published: August 2022

Abstract
Protein side chains are vitally important to many biological processes such as protein–protein interaction. In this study, we evaluate the performance of our previous released side-chain modeling method OPUS-Mut, together with some other methods, on three oligomer datasets, CASP14 (11), CAMEO-Homo (65) and CAMEO-Hetero (21). The results show that OPUS-Mut outperforms other methods measured by all residues or by the interfacial residues. We also demonstrate our method on evaluating protein–protein docking pose on a dataset Oligomer-Dock (75) created using the top 10 predictions from ZDOCK 3.0.2. Our scoring function correctly identifies the native pose as the top-1 in 45 out of 75 targets. Different from traditional scoring functions, our method is based on the overall side-chain packing favorableness in accordance with the local packing environment. It emphasizes the significance of side chains and provides a new and effective scoring term for studying protein–protein interaction.
Detection of Circulating Tumor Cells in Cerebrospinal Fluid of Patients with Suspected Breast Cancer Leptomeningeal Metastases: A Prospective Study
Authors: Darlix Amélie , Cayrefourcq Laure , Pouderoux Stéphane , Menjot de Champfleur Nicolas , Bievelez Alexis , Jacot William , Leaha Cristina , Thezenas Simon , Alix-Panabières Catherine 
Published: August 2022

Abstract

Background
The diagnosis of breast cancer (BC)-related leptomeningeal metastases (LM) relies on the detection of tumor cells in cerebrospinal fluid (CSF) using conventional cytology (gold standard). However, the sensitivity of this technique is low. Our goal was to evaluate whether circulating tumor cell (CTC) detection in CSF using the CellSearch® system could be used for LM diagnosis.

Methods
This prospective, monocentric study included adult patients with suspected BC-related LM. The clinical sensitivity and specificity of CTC detection in CSF for LM diagnosis were calculated relative to conventional CSF cytology.

Results
Forty-nine eligible patients were included and 40 were evaluable (CTC detection technical failure: n = 8, eligibility criteria failure: n = 1). Cytology was positive in 18/40 patients. CTCs were detected in these 18 patients (median: 5824 CTC, range: 93 to 45052) and in 5/22 patients with negative cytology (median: 2 CTC, range: 1 to 44). The detection of ≥1 CSF CTC was associated with a clinical sensitivity of 100% (95% CI, 82.4–100) and a specificity of 77.3% (95% CI, 64.3–90.3) for LM diagnosis. HER2+ CTCs were detected in the CSF of 40.6% of patients with HER2− BC (median: 500 CTC, range: 13 to 28 320).

Conclusions
The clinical sensitivity of CTC detection in CSF with the CellSearch® system for LM diagnosis is higher than that of CSF cytology. CTC detection in patients with negative cytology, however, must be further investigated. The finding of HER2+ CTCs in patients with HER2− BC suggests that the HER2 status of LM should be evaluated to increase the treatment opportunities for these patients.
A roadmap for the functional annotation of protein families: a community perspective
Authors: de Crécy-lagard Valérie , Amorin de Hegedus Rocio , Arighi Cecilia , Babor Jill , Bateman Alex , Blaby Ian , Blaby-Haas Crysten , Bridge Alan J , Burley Stephen K , Cleveland Stacey , Colwell Lucy J , Conesa Ana , Dallago Christian , Danchin Antoine , de Waard Anita , Deutschbauer Adam , Dias Raquel , Ding Yousong , Fang Gang , Friedberg Iddo , Gerlt John , Goldford Joshua , Gorelik Mark , Gyori Benjamin M , Henry Christopher , Hutinet Geoffrey , Jaroch Marshall , Karp Peter D , Kondratova Liudmyla , Lu Zhiyong , Marchler-Bauer Aron , Martin Maria-Jesus , McWhite Claire , Moghe Gaurav D , Monaghan Paul , Morgat Anne , Mungall Christopher J , Natale Darren A , Nelson William C , O’Donoghue Seán , Orengo Christine , O’Toole Katherine H , Radivojac Predrag , Reed Colbie , Roberts Richard J , Rodionov Dmitri , Rodionova Irina A , Rudolf Jeffrey D , Saleh Lana , Sheynkman Gloria , Thibaud-Nissen Francoise , Thomas Paul D , Uetz Peter , Vallenet David , Carter Erica Watson , Weigele Peter R , Wood Valerie , Wood-Charlson Elisha M , Xu Jin 
Published: August 2022

AbstractOver the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.
Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana
Authors: Mo Changjuan , Wu Zhengdan , Shang Xiaohong , Shi Pingli , Wei Minghua , Wang Haiyan , Xiao Liang , Cao Sheng , Lu Liuying , Zeng Wendan , Yan Huabing , Kong Qiusheng 
Published: August 2022

Abstract
Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.
Linkage mapping reveals loci that underlie differences in Caenorhabditis elegans growth
Authors: Nyaanga Joy , Andersen Erik C 
Published: August 2022

Abstract
Growth rate and body size are complex traits that contribute to the fitness of organisms. The identification of loci that underlie differences in these traits provides insights into the genetic contributions to development. Leveraging Caenorhabditis elegans as a tractable metazoan model for quantitative genetics, we can identify genomic regions that underlie differences in growth. We measured postembryonic growth of the laboratory-adapted wild-type strain (N2) and a wild strain from Hawaii (CB4856) and found differences in body size. Using linkage mapping, we identified three distinct quantitative trait loci (QTL) on chromosomes IV, V, and X that are associated with variation in body growth. We further examined these growth-associated quantitative trait loci using chromosome substitution strains and near-isogenic lines and validated the chromosome X quantitative trait loci. In addition, we generated a list of candidate genes for the chromosome X quantitative trait loci. These genes could potentially contribute to differences in animal growth and should be evaluated in subsequent studies. Our work reveals the genetic architecture underlying animal growth variation and highlights the genetic complexity of growth in Caenorhabditis elegans natural populations.
A Chromosome-Scale Genome Assembly of aHelicoverpa zeaStrain Resistant toBacillus thuringiensisCry1Ac Insecticidal Protein
Authors: Stahlke Amanda R , Chang Jennifer , Tembrock Luke R , Sim Sheina B , Chudalayandi Sivanandan , Geib Scott M , Scheffler Brian E , Perera Omaththage P , Gilligan Todd M , Childers Anna K , Hackett Kevin J , Coates Brad S 
Published: August 2022

AbstractHelicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.
Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids
Authors: Santer Mario , Kupczok Anne , Dagan Tal , Uecker Hildegard 
Published: August 2022

Abstract
Theoretical population genetics has been mostly developed for sexually reproducing diploid and for monoploid (haploid) organisms, focusing on eukaryotes. The evolution of bacteria and archaea is often studied by models for the allele dynamics in monoploid populations. However, many prokaryotic organisms harbor multicopy replicons—chromosomes and plasmids—and theory for the allele dynamics in populations of polyploid prokaryotes remains lacking. Here, we present a population genetics model for replicons with multiple copies in the cell. Using this model, we characterize the fixation process of a dominant beneficial mutation at 2 levels: the phenotype and the genotype. Our results show that depending on the mode of replication and segregation, the fixation of the mutant phenotype may precede genotypic fixation by many generations; we term this time interval the heterozygosity window. We furthermore derive concise analytical expressions for the occurrence and length of the heterozygosity window, showing that it emerges if the copy number is high and selection strong. Within the heterozygosity window, the population is phenotypically adapted, while both alleles persist in the population. Replicon ploidy thus allows for the maintenance of genetic variation following phenotypic adaptation and consequently for reversibility in adaptation to fluctuating environmental conditions.
The Mental Health Benefit of Friend Networks in Older Korean Americans: The Conditioning Effect of Family Type
Authors: Jang Yuri , Park Nan Sook , Park Juyoung , Chiriboga David A , Haley William E , Kim Miyong T 
Published: August 2022

Abstract

Objectives
We identified types of family relationships of older Korean Americans and examined how the mental health benefit of friend networks might be conditioned by family type.

Methods
Data were from 2,070 participants in the Study of Older Korean Americans, a multistate survey of Korean immigrants aged 60 and older (Mage = 73.3, standard deviation [SD] = 8.01). To identify family types, latent profile analysis (LPA) was performed with marital status, living arrangement, family network, positive and negative interactions with family members, and family mistreatment. Linear regression models examined how mental distress was associated with friend networks and family types, as well as their interactions.

Results
LPA identified 5 family types: close-knit, intimate but distant, detached, connected but dysfunctional, and dysfunctional. Greater distress was associated with smaller friend networks and belonging to the detached, connected but dysfunctional, and dysfunctional family types in comparison to the close-knit type. The interaction model showed that people in the connected but dysfunctional and dysfunctional groups had a stronger association between friend networks and mental distress than the counterparts in the close-knit group.

Discussion
We not only confirmed the health-promoting role of friend networks and the value of a close-knit family but also found that the benefit of friend networks was pronounced when quality of the family relationship was impaired. Our findings called renewed attention to older immigrants’ social convoys of family and friends, suggesting that the enhancement of friend networks could be particularly advantageous for older immigrants with dysfunctional family relationships.
Fishing tactics and the effect of resource depletion and interference during the exploitation of local patches of flatfish
Authors: Rijnsdorp A D , Aarts G , Hintzen N T , van Rijssel J C , Winter A M , Poos J J 
Published: August 2022

Abstract
The fine-scale exploitation pattern of fishers and the interactions among fishing vessels determine their impact on exploited populations, habitats, and ecosystems. This study used a unique combination of high resolution data of fishing tracks (positions recorded at 1 and 6 min intervals) and catch rates of sole (Solea solea) and plaice (Pleuronectes platessa) per tow, to study how pulse trawl (PUL) and tickler chain beam trawl (TBT) fishers exploit patches of concealed flatfish. PUL and TBT fishers had similar tactics. Effort was concentrated in the core of the patch. PUL fishers trawled in a systematic manner with successive tows segments placed parallel to each other at a median distance of ∼200 m. In 45% of the cores, simultaneous trawling by multiple PUL vessels occurred. A total of 40% of the cores were revisited in the following week, of which 50% were re-exploited. Catch rate in the core was ∼50% higher than the background catch rate and decreased over time due to resource depletion and interference related to the response of flatfish to the fishing activities. Interference contributed up to 67% to the decline in catch rate and was larger in TBT than in PUL.
Randomized clinical trial of nitazoxanide or sofosbuvir/daclatasvir for the prevention of SARS-CoV-2 infection
Authors: Sokhela Simiso , Bosch Bronwyn , Hill Andrew , Simmons Bryony , Woods Joana , Johnstone Hilary , Akpomiemie Godspower , Ellis Leah , Owen Andrew , Casas Carmen Perez , Venter Willem Daniel Francois 
Published: August 2022

Abstract

Background
The COVER trial evaluated whether nitazoxanide or sofosbuvir/daclatasvir could lower the risk of SARS-CoV-2 infection. Nitazoxanide was selected given its favourable pharmacokinetics and in vitro antiviral effects against SARS-CoV-2. Sofosbuvir/daclatasvir had shown favourable results in early clinical trials.

Methods
In this clinical trial in Johannesburg, South Africa, healthcare workers and others at high risk of infection were randomized to 24 weeks of either nitazoxanide or sofosbuvir/daclatasvir as prevention, or standard prevention advice only. Participants were evaluated every 4 weeks for COVID-19 symptoms and had antibody and PCR testing. The primary endpoint was positive SARS-CoV-2 PCR and/or serology ≥7 days after randomization, regardless of symptoms. A Poisson regression model was used to estimate the incidence rate ratios of confirmed SARS-CoV-2 between each experimental arm and control.

Results
Between December 2020 and January 2022, 828 participants were enrolled. COVID-19 infections were confirmed in 100 participants on nitazoxanide (2234 per 1000 person-years; 95% CI 1837–2718), 87 on sofosbuvir/daclatasvir (2125 per 1000 person-years; 95% CI 1722–2622) and 111 in the control arm (1849 per 1000 person-years; 95% CI 1535–2227). There were no significant differences in the primary endpoint between the treatment arms, and the results met the criteria for futility. In the safety analysis, the frequency of grade 3 or 4 adverse events was low and similar across arms.

Conclusions
In this randomized trial, nitazoxanide and sofosbuvir/daclatasvir had no significant preventative effect on infection with SARS-CoV-2 among healthcare workers and others at high risk of infection.
Relationship between rumen microbial differences and traits among Hu sheep, Tan sheep, and Dorper sheep
Authors: Cheng Jiangbo , Zhang Xiaoxue , Xu Dan , Zhang Deyin , Zhang Yukun , Song Qizhi , Li Xiaolong , Zhao Yuan , Zhao Liming , Li Wenxin , Wang Jianghui , Zhou Bubo , Lin Changchun , Yang Xiaobin , Zhai Rui , Cui Panpan , Zeng Xiwen , Huang Yongliang , Ma Zongwu , Liu Jia , Wang Weimin 
Published: August 2022

Abstract
Rumen microbes play an important role in the growth and development of ruminants. Differences in variety will affect the rumen community structure. The three excellent sheep breeds were selected for this study (Hu sheep, Tan sheep, and Dorper sheep) have different uses and origins. The sheep were raised on the same diet to 180 d of age in a consistent environment. 16S rDNA V3 to V4 region sequencing was used to assess the rumen microbes of 180 individuals (60 per breed). There were differences in microbial diversity among different sheep breeds (P &lt; 0.05). Principal coordinate analysis showed that the three varieties were separated, but also partially overlapped. Linear discriminant analysis effect size identified a total of 19 biomarkers in three breeds. Of these biomarkers, five in Hu sheep were significantly negatively correlated with average feed conversion rate (P &lt; 0.05). Six biomarkers were identified in the rumen of Dorper sheep, among which Ruminococcus was significantly positively correlated with body weight at 80 d (P &lt; 0.05). In Tan sheep, Rikenellaceae_RC9_gut_group was significantly positively correlated with meat fat, and significantly positively correlated with volatile fatty acids (VFAs), such as butyric acid and isobutyric acid (P &lt; 0.05). The Rikenellaceae_RC9_gut_group may regulate Tan mutton fat deposition by affecting the concentration of VFAs. Functional prediction revealed enrichment differences of functional pathways among different sheep breeds were small. All were enriched in functions, such as fermentation and chemoheterotrophy. The results show that there are differences in the rumen microorganisms of the different sheep breeds, and that the microorganisms influence the host.
Keeping up with the miRNAs: current paradigms of the biogenesis pathway
Authors: Mencia Regina , Gonzalo Lucía , Tossolini Ileana , Manavella Pablo A 
Published: August 2022

AbstractFor many years we have studied the processes involved in producing miRNAs in plants and the numerous differences from their metazoan counterpart. A well-defined catalytic process, mostly carried out by the RNase III enzyme DICER-LIKE1 (DCL1), it was identified early after the discovery of RNAi and was followed by the isolation of a plethora of miRNA biogenesis cofactors. The production of miRNAs, which later are loaded in ARGONAUTE (AGO) proteins to perform their RNA silencing functions both within the cell and non-cell autonomously, appears to be a highly regulated and dynamic process. Many regulatory events during miRNA biogenesis require the action of specific proteins. However, in recent years, many post-transcriptional modifications, structural features, and coupling with other cellular processing emerged as critical elements controlling the production of miRNA and, thus, a plant’s physiology. This review discusses new evidence that has changed the way we understand how miRNAs are produced in plants. We also provide an updated view of the miRNA biogenesis pathways, focusing on the gaps in our knowledge and the most compelling questions that remain open.
Diagnostic Efficiency of Serum-Based Infrared Spectroscopy in Detecting Breast Cancer: A Meta-Analysis
Authors: Pabico Louise Julie , Jaron Jennica Naiomi , Mosqueda Marc Erickson , Wu Jorge Jaesen , Tiongco Raphael Enrique , Albano Pia Marie 
Published: August 2022

Abstract

Background
The advancement of Fourier transform infrared (FTIR) spectroscopy as a potential diagnostic tool in the clinical setting has been studied over the years, particularly its application in cancer diagnostics.

Objective
To summarize previous research on FTIR spectroscopy in detecting breast cancer using serum specimens.

Methods
Related literature was searched and screened from various databases. Relevant data were then extracted, tabulated, and analyzed using Meta-DiSc 1.4 software.

Results
Sensitivity and specificity rates were 90% to 100% and 80% to 95%, respectively. The area under the receiver operating characteristic curve was at 0.9729, indicating that serum analysis via FTIR spectroscopy can accurately discriminate between healthy individuals and patients with breast cancer.

Conclusion
Overall, FTIR spectroscopy for breast cancer diagnosis using serum specimens shows promising results. However, further studies are still needed to validate these claims.
A Meta-Analysis on the Association of Colibactin-Producing pks+ Escherichia coli with the Development of Colorectal Cancer
Authors: Gaab Marcianne Elaine , Lozano Prim Olivette , Ibañez Danica , Manese Korina Diane , Riego Fatima May , Tiongco Raphael Enrique , Albano Pia Marie 
Published: August 2022

Abstract

Objective
Previous studies on the association between pks+Escherichia coli and colorectal cancer (CRC) demonstrated conflicting results. Hence, we performed a meta-analysis to obtain more precise estimates.

Methods
Related literature was obtained from PubMed, ScienceDirect, Google Scholar, and Cochrane Library. Data were then extracted, summarized, and subjected to analysis using Review Manager 5.4 by computing for the pooled odds ratios at the 95% confidence interval.

Results
Overall analysis showed that individuals carrying pks+E coli had a greater risk of developing CRC. Subgroup analysis further showed that individuals from Western countries carrying pks+E coli and individuals with pks+E coli in their tissue samples had increased risk of developing CRC.

Conclusion
Results of this meta-analysis suggest that individuals with pks+E coli have a greater risk of developing CRC. However, more studies are needed to confirm our claims.