bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accessing the topological Mott insulator in cold atom quantum simulators with realistic Rydberg dressing
Authors: Cardarelli Lorenzo , Julià-Farré Sergi , Lewenstein Maciej , Dauphin Alexandre , Müller Markus 
Published: February 2023

Abstract
The interplay between many-body interactions and the kinetic energy gives rise to rich phase diagrams hosting, among others, interaction-induced topological phases. These phases are characterized by both a local order parameter and a global topological invariant, and can exhibit exotic ground states such as self-trapped polarons and interaction-induced edge states. In this work, we investigate a realistic scenario for the quantum simulation of such systems using cold Rydberg-dressed atoms in optical lattices. We consider spinless fermions on a checkerboard lattice, interacting via the tunable-range effective potential induced by the Rydberg dressing. We perform a detailed analysis of the phase diagram at half- and incommensurate fillings, in the mean-field approximation. We furthermore study the stability of the phases with respect to temperature within the mean-field approximation and with respect to quantum fluctuations using the density matrix renormalization group method. Finally, we propose an implementation protocol, and in particular identify attainable regimes of experimental parameters in which the topological properties of the model become accessible. Our work thereby opens a realistic pathway to the outstanding experimental observation of this predicted phase in state-of-the-art cold atom quantum simulators.
MSGCL: inferring miRNA–disease associations based on multi-view self-supervised graph structure contrastive learning
Authors: Ruan Xinru , Jiang Changzhi , Lin Peixuan , Lin Yuan , Liu Juan , Huang Shaohui , Liu Xiangrong 
Published: February 2023

AbstractPotential miRNA–disease associations (MDA) play an important role in the discovery of complex human disease etiology. Therefore, MDA prediction is an attractive research topic in the field of biomedical machine learning. Recently, several models have been proposed for this task, but their performance limited by over-reliance on relevant network information with noisy graph structure connections. However, the application of self-supervised graph structure learning to MDA tasks remains unexplored. Our study is the first to use multi-view self-supervised contrastive learning (MSGCL) for MDA prediction. Specifically, we generated a learner view without association labels of miRNAs and diseases as input, and utilized the known association network to generate an anchor view that provides guiding signals for the learner view. The graph structure was optimized by designing a contrastive loss to maximize the consistency between the anchor and learner views. Our model is similar to a pre-trained model that continuously optimizes upstream tasks for high-quality association graph topology, thereby enhancing the latent representation of association predictions. The experimental results show that our proposed method outperforms state-of-the-art methods by 2.79$\%$ and 3.20$\%$ in area under the receiver operating characteristic curve (AUC) and area under the precision/recall curve (AUPR), respectively.
Persistent Tor-algebra for protein–protein interaction analysis
Authors: Liu Xiang , Feng Huitao , Lü Zhi , Xia Kelin 
Published: February 2023

AbstractProtein–protein interactions (PPIs) play crucial roles in almost all biological processes from cell-signaling and membrane transport to metabolism and immune systems. Efficient characterization of PPIs at the molecular level is key to the fundamental understanding of PPI mechanisms. Even with the gigantic amount of PPI models from graphs, networks, geometry and topology, it remains as a great challenge to design functional models that efficiently characterize the complicated multiphysical information within PPIs. Here we propose persistent Tor-algebra (PTA) model for a unified algebraic representation of the multiphysical interactions. Mathematically, our PTA is inherently algebraic data analysis. In our PTA model, protein structures and interactions are described as a series of face rings and Tor modules, from which PTA model is developed. The multiphysical information within/between biomolecules are implicitly characterized by PTA and further represented as PTA barcodes. To test our PTA models, we consider PTA-based ensemble learning for PPI binding affinity prediction. The two most commonly used datasets, i.e. SKEMPI and AB-Bind, are employed. It has been found that our model outperforms all the existing models as far as we know. Mathematically, our PTA model provides a highly efficient way for the characterization of molecular structures and interactions.
MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations
Authors: Liu Hui , Jin Ye , Ding Hanjing 
Published: February 2023

AbstractThe preprocessed initial files that feed the molecular dynamics (MD) simulation packages dramatically influence the outcome of the simulations. However, the popular MD simulation packages depend, to a great extent, on the user’s experience in the preparation of MD simulation systems. In this work, we present an easy-to-use tool called MDBuilder, a PyMOL plugin that assists researchers in building the starting structures for multiple popular MD simulation packages. MDBuilder is not only designed to assist MD beginners to overcome the steep learning curve by providing a menu-oriented, point-and-click user graphic interface (GUI), but also to provide an alternative way to prepare the input files for some highly scalable CHARMM force field-based MD simulation packages. The platform-independent GUI is implemented as a PyMOL plugin using the Python language, and it has been tested on Windows and Linux platforms. The source code and documentation of MDBuilder can be downloaded freely from https://github.com/HuiLiuCode/MDBuilder under the GNU General Public License.
polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies
Authors: Chang Jennifer , Stahlke Amanda R , Chudalayandi Sivanandan , Rosen Benjamin D , Childers Anna K , Severin Andrew J 
Published: February 2023

AbstractLong-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.
Why and how do consumers use dietary supplements? A systematic review and thematic analysis
Authors: Wang Yun , Neilson Leighann C , Ji Shaobo 
Published: February 2023

SummaryUsing the input-process-output (IPO) model as an organizing framework, this paper provides an overview of the literature on multiple dimensions of dietary supplement (DS) consumption. Based on a systematic review of 174 studies from different disciplines over two decades, we pinpointed the key topics that have been examined in this growing body of literature and identified the major themes within DS consumption. Moreover, we integrated the major themes in inputs, processes, and outputs to develop a comprehensive understanding of individuals’ DS consumption behaviors, motivations, and social mechanisms underlying such behaviors. This research has implications for health consumption and promotion research. We identified DS consumption as a social–cultural process in which individuals practice lifelong self-learning and socialization activities through which lay health knowledge may be developed. Accordingly, their DS use motives may be related to health improvement or not (e.g. identity expressions), which are formed during interactions with various stakeholders in the health marketplace. When confronting the contemporary health promotion culture and self-care paradigm, it is important for researchers to deepen our knowledge of consumers’ motives for DS consumption and the underlying social mechanisms to aid consumers’ health consumption decisions and guide the multiple stakeholders in the health marketplace.
Rare genetic variants underlie outlying levels of DNA methylation and gene-expression
Authors: Chundru V Kartik , Marioni Riccardo E , Prendergast James G D , Lin Tian , Beveridge Allan J , Martin Nicholas G , Montgomery Grant W , Hume David A , Deary Ian J , Visscher Peter M , Wray Naomi R , McRae Allan F 
Published: February 2023

Abstract
Testing the effect of rare variants on phenotypic variation is difficult due to the need for extremely large cohorts to identify associated variants given expected effect sizes. An alternative approach is to investigate the effect of rare genetic variants on DNA methylation (DNAm) as effect sizes are expected to be larger for molecular traits compared with complex traits. Here, we investigate DNAm in healthy ageing populations—the Lothian Birth Cohorts of 1921 and 1936—and identify both transient and stable outlying DNAm levels across the genome. We find an enrichment of rare genetic single nucleotide polymorphisms (SNPs) within 1 kb of DNAm sites in individuals with stable outlying DNAm, implying genetic control of this extreme variation. Using a family-based cohort, the Brisbane Systems Genetics Study, we observed increased sharing of DNAm outliers among more closely related individuals, consistent with these outliers being driven by rare genetic variation. We demonstrated that outlying DNAm levels have a functional consequence on gene expression levels, with extreme levels of DNAm being associated with gene expression levels toward the tails of the population distribution. This study demonstrates the role of rare SNPs in the phenotypic variation of DNAm and the effect of extreme levels of DNAm on gene expression.
Safety Analysis of Preoperative Anti-TNF-α Therapy in Pediatric IBD After Intestinal Resection: A Systematic Review and Meta-analysis
Authors: Bajzát Dorina , Kéri Adrienn F , Imrei Marcell , Kói Tamás , Párniczky Andrea , Hegyi Péter , Kovács Kinga , Váncsa Szilárd , Müller Katalin Eszter 
Published: February 2023

Abstract

Background
Biological agents have transformed the management of inflammatory bowel disease (IBD). However, intestinal resection is still unavoidable in complicated IBD. It is still under debate whether antitumor necrosis factor (TNF)-α is related to higher postoperative complications in children with IBD. Therefore, we aimed to analyze data on preoperative anti-TNF-α and postoperative complications in pediatric IBD.

Methods
We conducted a systematic literature search in 4 databases for studies that compared the incidence of postoperative complications between children with IBD who received anti-TNF-α treatment within 12 weeks prior to intestinal resection and who did not receive anti-TNF-α before the operation. To analyze this question, pooled odds ratios (ORs) were calculated with 95% confidence intervals (CIs). Odds ratios higher than 1 mean higher complication rate among children treated with preoperative anti-TNF-α, whereas an OR lower than 1 means lower complication rate. The I² value was calculated to measure the strength of the between-study heterogeneity, where a smaller percentage means the lower heterogeneity.

Results
We found 8 eligible articles with 526 pediatric patients with IBD. The primary outcome was the overall complication. The pooled OR of overall complications was 1.38 (95% CI, 0.10-18.76; P = .65; I2 = 34%) in contrast, the OR of infectious and noninfectious complications were 0.59 (95% CI, 0.21-1.69; P = .16; I2 = 0%) and 0.48 (95% CI, 0.18-1.25; p = .09; I2 = 0%), although both showed a nonsignificant result.

Conclusion
There is no significant association between preoperative anti-TNF-α therapy and postoperative complications in children with IBD after intestinal resection. However, the evidence is low due to the low number of studies investigating this question.
Legal Mobilisations, Trade Unions and Radical Social Change: A Case Study of the IWGB
Authors: Adams Zoe 
Published: February 2023

Abstract
In recent years, a number of new style trade unions have emerged which are said to exhibit a more ‘radical’ orientation to social change than more ‘traditional’ trade unions. This has raised questions as to the significance of the willingness of these new style trade unions to mobilise the law in pursuit of that change, and in particular, to engage in so-called ‘strategic litigation’. Through a case study of some of the legal mobilisations of one of the more well-known new style trade unions in the UK, the Independent Workers of Great Britain union (IWGB), drawing on insights from the literature on legal mobilisation, and supplementing this with insights from the Marxist theory of the legal form, this paper will highlight the distinctiveness of these new style trade unions and explain the basis of their radical potential, before showing how that potential is limited, or negated, by the particular way in which they engage with law in practice. The paper will conclude with some observation as to what a more radical orientation to the law might look like for social organisations and trade unions in practice.
Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya, Gasteracanthinae)
Authors: Agnarsson Ingi , Starrett James , Babbitz Zachary , Bond Jason E , Gregorič Matjaž , Christian Raberahona Onjaherizo , Williams Steven , Kuntner Matjaž 
Published: February 2023

AbstractSpiders are notoriously solitary and cannibalistic, with instances of colonial or social lifestyles in only about 50-60, or ~0.1% of 50,000 described species. Population analyses indicate that most colonies consist of multiple cohorts formed by close relatives. Territorial social spiders facultatively form colonies by interlinking individual webs, but further cooperation is infrequent, and only among juveniles or (rarely) females. In spiders therefore, aggregations of males outside of the male-male competition context has been unknown. Here, we report on a discovery of a kite spider from Madagascar that exhibits unique colonies. We found colonies of the newly described araneid Isoxya manangonan. sp. formed by up to 41 interconnected, single-cohort adult female webs with up to 38 adult males aggregating on a central, single, nonsticky line. With males resting tightly together, we found no evidence for male-male aggression. Genetic analyses from RAD sequencing suggest that most colonies consist of unrelated individuals. Furthermore, genetic variability of males was somewhat less than that of females. Single cohort colonies made up purely of adults, and peaceful male aggregations, have not previously been observed in spiders. Although direct behavioral observations are preliminary, we speculate based on the available evidence that these colonies may represent a novel and first case of lekking in spiders.
Effects of five carbohydrate sources on cat diet digestibility, postprandial glucose, insulin response, and gut microbiomes
Authors: Zhang Shu , Ren Yang , Huang Yuqin , Wang Yingchun , Dang Han , Shan Tizhong 
Published: February 2023

AbstractCat obesity has become a serious problem that affects cats’ lives and welfare. Knowing how to control obesity in pet cats and its mechanism is urgently needed. Here, by feeding 30 cats different diets for 28 d, we explored the effects of 5 cat foods with potato, sweet potato, cassava, rice, and wheat as the main carbohydrate sources on the glycolipid metabolism of pet cats. The results showed that dietary carbohydrate sources did not affect the normal growth performance and stool scores of cats. Notably, we found that the starch gelatinization degree of sweet potato and cassava cat food were higher than those of other groups, while the rice diets had the highest digestibility, but the difference was not significant (P &gt; 0.05). Furthermore, cats fed cassava diets had lower postprandial glucose responses. The mean glucose value, maximum glucose value, AUC0–360 min, AUC≤30 min, and AUC≥30 min in the cassava group were lower than those in other dietary groups (P &gt; 0.05). In addition, we found that the carbohydrate source had a minimal effect on serum biochemical immune indices, but the blood lipid indices, such as TG, TC, HDL, and LDL of cats fed the cassava diet were maintained at a low level compared with other groups (P &gt; 0.05). In addition, diets with different carbohydrate sources affect the gut microbial composition, and sweet potato and cassava diets tend to increase the diversity of gut microbiota with a higher Shannon index and Simpson index. The abundance of Fusobacterium, Veillonella, and Actinobacillus was significantly higher in sweet potato diet-fed cats (P &lt; 0.05), while the abundance of Delftia, Shinella, Rothia, and Hydrogenophage was highest in cassava diet-fed cats (P &lt; 0.05). Collectively, this study revealed that cassava and sweet potato diets have a better effect on feeding value, controlling blood glucose and blood lipids, and improving the intestinal flora of pet cats, which is worth developing dietary formulations to alleviate pet obesity.
Insecticide Resistance Status ofAedes albopictus(Diptera:Culicidae) Populations from Cuba
Authors: Piedra Luis Augusto , Rodriguez Maria Magdalena , Lopez Isabel , Ruiz Armando , Martinez Liss Claudia , Garcia Israel , Rey Jorge , Bisset Juan Andres 
Published: February 2023

AbstractAedes albopictus (Skuse, 1894) is one of the major vectors for arboviruses such as dengue, Zika, and chikungunya. Originally from Southeast Asia, this species has spread to Africa, Europe, and the Americas, including Cuba. This spread has been favored by its great adaptability to variable temperatures and to the resistance of its eggs to desiccation. Chemical control of mosquitoes is an essential alternative to stop arbovirus transmission, but insecticide resistance status of the Cuban Ae. albopictus populations is unknown. For this study, Ae. albopictus larvae and adults were collected from two municipalities in Havana, Cuba in 2019. Adult bioassays for deltamethrin, cypermethrin, lambda-cyhalothrin, chlorpyrifos, propoxur, and bendiocarb susceptibility were conducted according to CDC methodology. Larval bioassays for temephos susceptibility were performed following WHO protocols. Resistance profiles for α and β-esterases, glutathione S-transferase (GST), and multifunction oxidases (MFO) pathways were constructed and analyzed. Resistance to temephos and deltamethrin was detected in Mulgoba and Plaza field populations, but resistance to lambda-cyhalothrin was only found in the Plaza colony. Plaza colony exhibited a higher expression level to all four metabolic enzymes and α-esterases and GTS were over-expressed in Mulgoba. The development of insecticide resistance in Cuban Ae. albopictus populations makes it imperative that we develop integrated control strategies to minimize the development of resistance and provide effective vector control that prevents the onset of arbovirus epidemics.
Human papillomavirus–associated cancer incidence by disaggregated Asian American, Native Hawaiian, and other Pacific Islander ethnicity
Authors: Shing Jaimie Z , Corbin Jereme , Kreimer Aimée R , Carvajal Loretto J , Taparra Kekoa , Shiels Meredith S , Vo Jacqueline B 
Published: February 2023

AbstractBackgroundAsian Americans and Native Hawaiians and other Pacific Islanders have suboptimal human papillomavirus (HPV) vaccination and cancer screening rates. Asian Americans and NHPIs are often aggregated, masking disparities characterized by varying colonization and immigration patterns and cultural and religious beliefs between populations and ethnicities. We examined the incidence of HPV-associated cancers across disaggregated Asian American and NHPI ethnicities.MethodsUsing the Surveillance, Epidemiology, and End Results Detailed Asian/Pacific Islander database, we calculated 1990 to 2014 sex-specific, age-standardized HPV-associated cancer incidence of cervical carcinoma, oropharyngeal squamous cell carcinoma (SCC), vulvar SCC, vaginal SCC, anal SCC, and penile SCC by ethnicity: Asian Indian and Pakistani, Chinese, Filipino, Japanese, Kampuchean, Korean, Laotian, Native Hawaiian, other Pacific Islander, and Vietnamese. Trends by calendar period (1990 to 1996, 1997 to 2002, 2003 to 2008, 2009 to 2014) were estimated using Joinpoint regression.ResultsThe most common HPV-associated cancer was cervical carcinoma in women and oropharyngeal SCC in men. During 1990 to 2014, cervical carcinoma incidence per 100 000 ranged from 4.5 (Asian Indian and Pakistani) to 20.7 (Laotian). Cervical carcinoma incidence only statistically significantly declined for Asian Indian and Pakistani, Filipino, Korean, Laotian, and Vietnamese women (range = 19.9% to 44.1% decline per period). Among men, oropharyngeal SCC incidence per 100 000 ranged from 1.1 (Chinese) to 5.1 (Native Hawaiian). Oropharyngeal SCC incidence only statistically significantly increased (31.0% increase per period) for Japanese men. Heterogeneity across ethnicities were observed for other cancer sites.ConclusionsHPV-associated cancer incidence varied widely between Asian Americans and NHPIs and by ethnicity, underscoring the need for improved data capture of ethnic groups in research and more tailored interventions to better address health disparities between Asian American and NHPI populations.
A rare case of survival after traumatic blunt ventricular rupture
Authors: Yang Ryan , Van Gent Michael , Clements Thomas , Cotton Bryan , Wandling Michael 
Published: February 2023

AbstractA male in his 40s presented to the trauma center via air ambulance after colliding with a cement wall at highway speeds. Cross-sectional imaging revealed a right ventricular pseudoaneurysm, confirmed by echocardiography. He was taken emergently to the operating room where he was found to have a pericardial laceration, hemopericardium and a right ventricular rupture, which was primarily repaired. Postoperatively, the patient was transferred to intensive care and after 34 days in the hospital was ultimately discharged home.