bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term outcomes of large artery thromboangiitis obliterans and comparison with small artery thromboangiitis obliterans
Authors: Lee Sang Ah , Jeong Min-Jae , Ko Gi-Young , Hwang Hee Sang , Gwon Dong Il , Choi Eol , Kwon Tae-Won , Cho Yong-Pil 
Published: January 2022

Abstract
Although the distribution of arterial involvement is still the subject of controversy for defining the diagnostic criteria for thromboangiitis obliterans (TAO), several reports have described TAO involving the more proximal arterial segment. This study aimed to investigate the clinical characteristics and outcomes of large artery TAO in comparison with those of small artery TAO.
Between January 2007 and July 2019, 83 consecutive symptomatic patients with a diagnosis of lower extremity TAO were stratified according to the most proximal arterial involvement, with the cutoff level of the adductor canal as a reference (large artery TAO versus small artery TAO), and analyzed retrospectively. The study outcomes included any amputations and major amputations.
The large artery TAO group consisted of 30 patients (36.1%), and the small artery TAO group consisted of 53 patients (63.9%). In terms of clinical symptoms and signs, the proportion of major tissue loss (Rutherford class 6) was significantly higher among patients with large artery TAO than among those with small artery TAO (13.3% versus 0%, P = .02). Any amputation rate was similar between the large and small artery TAO groups during the median follow-up period of 148 months (range, 0–376 months) (43.3% versus 28.3%, P = .16). However, the major amputation rate was significantly higher among patients with large artery TAO (13.3% versus 0%, P = .02). On Kaplan–Meier survival analysis of the cumulative event-free rates, although there was a similar 10-year amputation-free survival rate (P = .24) between the 2 groups, the large artery TAO group had a significantly lower 10-year major amputation-free survival rate (P < .01) than the small artery TAO group.
Large artery TAO is a limb-threatening condition and had a worse prognosis than small artery TAO.
Compensatory swallowing methods in a patient with dysphagia due to lateral medullary syndrome—vacuum and prolonged swallowing
Authors: Kunieda Kenjiro , Sugiyama Junya , Nomoto Akiko , Ohno Tomohisa , Shigematsu Takashi , Fujishima Ichiro 
Published: January 2022

Abstract

Introduction:
The nature of pharyngeal swallowing function during the course of recovery of dysphagia due to lateral medullary syndrome (LMS) is unclear. Vacuum swallowing is a compensatory swallowing method that improves the pharyngeal passage of a bolus by creating negative pressure during swallowing in the esophagus in patients with dysphagia due to LMS. We present a case involving a patient with dysphagia due to LMS who involuntarily acquired a swallowing method with prolonged and increased pharyngeal contraction and vacuum swallowing.

Patient concerns:
We report a unique case involving a 52-year-old patient with dysphagia due to LMS. His dysphagia was severe but improved gradually with swallowing rehabilitation. The patient involuntarily acquired a swallowing method with prolonged and increased pharyngeal contraction and vacuum swallowing.

Diagnosis:
The patient presented with dysphagia due to left LMS. A videofluoroscopic examination of swallowing revealed pharyngeal residue.

Interventions:
Forty-five days after the onset of the dysphagia, the swallowing pressure along the pharynx and esophagus was measured using high-resolution manometry.

Outcomes:
Vacuum swallowing was observed in six out of 19 swallows (32.5%). The velopharyngeal contractile integral (CI) and mesohypopharyngeal CI values increased during swallowing, reflecting prolonged and increased pharyngeal contraction. We named this swallowing method “prolonged swallowing.”

Conclusion:
The findings in this case indicate that vacuum and prolonged swallowing may be compensatory swallowing methods observed in individuals recovering from dysphagia due to LMS. Further research is needed to clarify the relationship between these swallowing methods and the pathophysiology, prognosis, and treatment of dysphagia in patients with LMS.
Using a Virtual Platform for Conducting Grandfamily Research
Authors: Song MinKyoung , Bessette Hannah C. , Hayman Laura L. , Lyons Karen S. , Winters-Stone Kerri M. , Roberts Davis Mary C. , Musil Carol M. 
Published: January 2022

Background
Because of the COVID-19 pandemic, our research team quickly pivoted from planned face-to-face interaction with participants to virtual interactions. During this transition, we discovered invaluable new practices for conducting research remotely, including collecting physiological data.

Objective
Our objective was to describe the methodological challenges we encountered when conducting this research virtually with grandparent–grandchild dyads and describe the strategies we developed to overcome those challenges. Of primary focus were procedures for finger-stick blood sample collection. Of secondary focus were procedures for conducting virtual-based research with older adults and across multiple generations.

Methods
During an observational study utilizing a virtual platform with 11 grandparent–grandchild dyads (mean age: 64.2 ± 5.0 years for grandparents and 9.3 ± 1.9 years for grandchildren), we documented lessons learned (based on the discussion within our team and feedback we have received from participants) that could be applicable for other, similar research endeavors.

Results
We found several challenges in collecting blood samples, including staff were unfamiliar with providing online instruction and participants needed to develop familiarity with the blood sample collection process (without having in-person assistance), and we had to develop methods for delivering blood sample collection kits to participants safely. We also found that it took longer than expected to run procedures—a challenge that might be encountered when conducting any type of dyadic research utilizing a virtual platform—particularly involving older adults and across multiple generations. In addition, it was challenging to keep child participants engaged in the virtual interactions. We document how we employed targeted strategies to overcome those obstacles. Recommendations for strategies from our team include to provide comprehensive and clear instruction/materials on blood sampling procedure, offer generous support throughout the blood collection process, be prepared to divide study visits into more than one session as needed, proactively anticipate potential roadblocks, and carefully consider the participants’ developmental stages and attention span.

Discussion
The insights we gained will help inform future research with grandparent–grandchild dyads in remote or rural populations utilizing virtual platforms.
Brief Report: Insomnia and Risk of Myocardial Infarction Among People With HIV
Authors: Luu Brandon R. , Nance Robin M. , Delaney Joseph A. C. , Ruderman Stephanie A. , Heckbert Susan R. , Budoff Matthew J. , Mathews William C. , Moore Richard D. , Feinstein Matthew J. , Burkholder Greer A. , Mugavero Michael J. , Eron Joseph J. , Saag Michael S. , Kitahata Mari M. , Crane Heidi M. , Whitney Bridget M. 
Published: January 2022

Background:
Insomnia is common among people with HIV (PWH) and may be associated with increased risk of myocardial infarction (MI). This study examines the association between insomnia and MI by MI type among PWH.

Setting:
Longitudinal cohort study of PWH at 5 Centers for AIDS Research Network of Integrated Clinical Systems sites.

Methods:
Clinical data and patient-reported measures and outcomes from PWH in care between 2005 and 2018 were used in this study. Insomnia, measured at baseline, was defined as having difficulty falling or staying asleep with bothersome symptoms. The Centers for AIDS Research Network of Integrated Clinical Systems centrally adjudicates MIs using expert reviewers, with distinction between type 1 MI (T1MI) and type 2 MI (T2MI). Associations between insomnia and first incident MI by MI type were measured using separate Cox proportional hazard models adjusted for age, sex, race/ethnicity, traditional cardiovascular disease risk factors (hypertension, dyslipidemia, poor kidney function, diabetes, and smoking), HIV markers (antiretroviral therapy, viral suppression, and CD4 cell count), and stimulant use (cocaine/crack and methamphetamine).

Results:
Among 12,448 PWH, 48% reported insomnia. Over a median of 4.4 years of follow-up, 158 T1MIs and 109 T2MIs were identified; approximately half of T2MIs were attributed to sepsis or stimulant use. After adjustment for potential confounders, we found no association between insomnia and T1MI (hazard ratio = 1.05, 95% confidence interval: 0.76 to 1.45) and a 65% increased risk of T2MI among PWH reporting insomnia compared with PWH without insomnia (hazard ratio = 1.65, 95% confidence interval: 1.11 to 2.45).

Conclusions:
PWH reporting insomnia are at an increased risk of T2MI, but not T1MI, compared with PWH without insomnia, highlighting the importance of distinguishing MI types among PWH.
A Case of Cystic Intrahepatic Cholangiocarcinoma Mimicking a Cyst
Authors: Chen Chun-Meng , Wang Jianqiang , Cao Chun-Xiao , Chen Min , Huang Bin 
Published: January 2022

Abstract
Intrahepatic cholangiocarcinoma (ICC) classically presents as irregular soft tissue lesions. Very rarely, ICC may manifest as a predominantly cystic mass. Here, we describe a 59-year-old man who was referred to the hospital due to abdominal pain. The presentation was highly suggestive of a hepatic cyst based on MRI. 18F-FDG PET/CT could not exclude a malignant hepatic tumor due to the high metabolism in the margin. Subsequently, the patient underwent a left hemihepatectomy. Histopathology revealed malignant ICC.
The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies
Authors: Strauss Eli D. , Curley James P. , Shizuka Daizaburo , Hobson Elizabeth A. 
Published: January 2022

A century ago, foundational work by Thorleif Schjelderup-Ebbe described a ‘pecking order’ in chicken societies, where individuals could be ordered according to their ability to exert their influence over their group-mates. Now known as dominance hierarchies, these structures have been shown to influence a plethora of individual characteristics and outcomes, situating dominance research as a pillar of the study of modern social ecology and evolution. Here, we first review some of the major questions that have been answered about dominance hierarchies in the last 100 years. Next, we introduce the contributions to this theme issue and summarize how they provide ongoing insight in the epistemology, physiology and neurobiology, hierarchical structure, and dynamics of dominance. These contributions employ the full range of research approaches available to modern biologists. Cross-cutting themes emerging from these contributions include a focus on cognitive underpinnings of dominance, the application of network-analytical approaches, and the utility of experimental rank manipulations for revealing causal relationships. Reflection on the last 100 years of dominance research reveals how Schjelderup-Ebbe's early ideas and the subsequent research helped drive a shift from an essentialist view of species characteristics to the modern recognition of rich inter-individual variation in social, behavioural and physiological phenotypes.
This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.
The build-up of dominance hierarchies in eusocial insects
Authors: Shimoji Hiroyuki , Dobata Shigeto 
Published: January 2022

Reproductive division of labour is a hallmark of eusocial insects. However, its stability can often be hampered by the potential for reproduction by otherwise sterile nest-mates. Dominance hierarchy has a crucial role in some species in regulating which individuals reproduce. Compared with those in vertebrates, the dominance hierarchies in eusocial insects tend to involve many more individuals, and should require additional selective forces unique to them. Here, we provide an overview of a series of studies on dominance hierarchies in eusocial insects. Although reported from diverse eusocial taxa, dominance hierarchies have been extensively studied in paper wasps and ponerine ants. Starting from molecular physiological attributes of individuals, we describe how the emergence of dominance hierarchies can be understood as a kind of self-organizing process through individual memory and local behavioural interactions. The resulting global structures can be captured by using network analyses. Lastly, we argue the adaptive significance of dominance hierarchies from the standpoint of sterile subordinates. Kin selection, underpinned by relatedness between nest-mates, is key to the subordinates' acceptance of their positions in the hierarchies.This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.
Dominance in a socially dynamic setting: hierarchical structure and conflict dynamics in ravens' foraging groups
Authors: Boucherie Palmyre H. , Gallego-Abenza Mario , Massen Jorg J. M. , Bugnyar Thomas 
Published: January 2022

Dominance hierarchies typically emerge in systems where group members regularly encounter and compete for resources. In birds, the ‘open’ and dynamic structure of foraging groups may prevent the emergence of structured hierarchies, although this assumption have hardly been tested. We report on agonistic data for ravensCorvus corax, collected over two 18-month periods for 183 marked individuals of a wild (fluid) population and 51 birds from six captive (stable) groups. We show that the dominance structure (steep and transitive) in wild foraging groups is strikingly similar to that found in captivity. In the wild, we found that higher ranks are mainly occupied by males, older and more aggressive individuals that also tend to receive fewer aggressions. Exploring the mechanisms sustaining the wild dominance structure, we confirmed that males are more aggressive than females and, with age, tend to receive fewer aggressions than females. Males that are about to leave the foraging groups for some months are less aggressive than newcomers or locals, while newcomers are specifically targeted by aggressions in their first year (as juveniles). Taken together, our results indicate that the socially dynamic conditions ravens face during foraging do not hinder, but provide opportunities for, using (advanced) social cognition.This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.
Emergence of size-structured dominance hierarchies through size-dependent feedback
Authors: Hamilton Ian M. , Benincasa Macie D. 
Published: January 2022

Size-based dominance hierarchies influence fitness, group size and population dynamics and link dominance structure to evolutionary and ecological outcomes. While larger individuals often gain dominance, social status may influence growth and size in return, resulting in feedbacks among status, growth and size. Here, we present two models evaluating how these feedbacks influence the emergence of size structure in a dominance hierarchy. In the first, size influences competition for food and investment in suppressing growth of groupmates. Stable size differences emerged when suppression was greatest for similarly sized individuals and size had little effect on competition for food. The model predicted size divergence when size strongly affected competition for food. In the second model, we used a dynamic game to solve for optimal investment in growth suppression as a function of size structure. Investment in growth suppression was favoured only when dominants and subordinates were similar in size, generating size ratios different than those expected by chance. Variation in the feedbacks among growth, size and status can explain variation in emergent size structure of dominance hierarchies and its consequences for conflict within groups.
This article is part of the theme issue ‘The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies’.
GFAP: ultra-fast and accurate gene functional annotation software for plants
Authors: Xu Dong , Jin Kangming , Jiang Heling , Gong Desheng , Yang Jinbao , Yu Wenjuan , Yang Yingxue , Li Jihong , Pan Weihua 
Published: January 2022

AbstractSequence alignment is the basis of gene functional annotation for unknow sequences. Selecting closely related species as the reference species should be an effective way to improve the accuracy of gene annotation for plants, compared with only based on one or some model plants. Therefore, limited species number in previous software or website is disadvantageous for plant gene annotation.Here, we collected the protein sequences of 236 plant species with known genomic information from 63 families. After that, these sequences were annotated by pfam, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases to construct our databases. Furthermore, we developed the software, Gene Annotation Software for Plants (GFAP), to perform gene annotation using our databases. GFAP, an open-source software running on Windows and MacOS systems, is an efficient and network independent tool. GFAP can search the protein domain, GO and KEGG information for 43000 genes within 4 minutes. In addition, GFAP can also perform the sequence alignment, statistical analysis and drawing. The website of https://gitee.com/simon198912167815/gfap-database provides the software, databases, testing data and video tutorials for users.GFAP contained large amount of plant-species information. We believe that it will become a powerful tool in gene annotation using closely related species for phytologists.
Cytocapsular tubes and networks function as physical superdefence freeway systems conducting conventional cancer drug pan-resistant tumor metastasis
Authors: Yi Tingfang , Wagner Gerhard 
Published: January 2022

AbstractCancer drug pan-resistant tumor metastasis (cdp-rtm) is a major source of cancer lethality. Cytocapsular tubes (CCTs) and their networks are physical membrane-enclosed freeway systems for cancer cell dissemination across tissues and organs in vivo. Whether cytocapsular tube superlarge biomembranes function as superdenfence and conduct cdp-rtm is unknown. It is also unknown whether conventional cancer drug development methods, including cancer cell line derived xenograft (CDX) and patient cancer cell derived xenograft (PDX), generate cytocapsular tubes (CCTs). It is also unclear whether xenografts can be created that contain CCTs for efficient cancer drug development. Here, we investigated CCT functions related to cancer drug resistance, CCTs in CDX and PDX and CCT xenograft (CCTX). Using clinical cancer tissues, we discovered that CCTs potently shielded against multiple chemotherapy treatments with diverse conventional cancer drugs. Next, our quantitative analyses show that CCT biomembrane drug barriers significantly increase cancer drug resistance by 6.6-folds to14-folds. We found that conventional CDX and PDX animal models do not generate CCTs in these xenografts. By mimicking in vivo cancer cell environments for cancer patient cancer cell culturing, we have successfully isolated CH-5high/CH-6high subpopulations of patient breast cancer cells and pancreas cancer cells that are propertied with cytocapsular tube generation capacities and engender large quantities of CCTs in mouse xenografts. Biochemical and immunohistochemistry analyses demonstrated that CCTs in these xenografts are similar to those in clinical cancer tissues. In summary, our research has identified that CCTs and networks function as physical superdefence freeway systems conducting conventional cancer drug pan-resistant tumor metastasis, and developed a CCTX platform for highly efficient cancer drug development, which pave avenues for more efficient development of effective and precise cancer drugs for tumor cure at both personal and broad-spectrum levels.
Maternal smoking during pregnancy and type 1 diabetes in the offspring: A nationwide register-based study with family-based designs
Authors: Wei Yuxia , Andersson Tomas , Edstorp Jessica , Löfvenborg Josefin E. , Talbäck Mats , Feychting Maria , Carlsson Sofia 
Published: January 2022

AbstractObjectivesMaternal smoking during pregnancy is associated with a reduced risk of type 1 diabetes (T1D) in the offspring. We investigated whether this association is consistent with a causal interpretation by accounting for familial (shared genetic and environmental) factors using family-based, quasi-experimental designs.DesignA nationwide, prospective cohort study and a nested case-control study (quasi-experiment) comparing children with T1D to their age-matched siblings (or cousins).SettingSwedish national registers.ParticipantsWe included 2,995,321 children born in Sweden between 1983 and 2014.ExposureInformation on maternal smoking during pregnancy was retrieved from the Swedish Medical Birth Register.Main outcome measuresChildren were followed for a diagnosis of T1D until 2020 through the National Patient, Diabetes and Prescribed Drug Registers.ResultsA total of 18,617 children developed T1D, with a median age at diagnosis of 9.4 years. The sibling and cousin comparison design included 14,284 and 7,988 of these children, respectively. Maternal smoking during pregnancy was associated with a 22% lower risk of offspring T1D in the full cohort (hazard ratio: 0.78, 95% confidence interval [CI]: 0.75 to 0.82) in the multivariable-adjusted model. The corresponding odds ratio was 0.78 (95% CI: 0.69 to 0.88) in the sibling and 0.72 (95% CI: 0.66 to 0.79) in the cousin comparison analysis.ConclusionsThis nationwide, family-based study provides support for a protective effect of maternal smoking on offspring T1D. Mechanistic studies are needed to elucidate the underlying pathways behind this link.
Direct Comparison of SARS-CoV-2 Nasal RT-PCR and Rapid Antigen Test (BinaxNOW™) at a Community Testing Site During an Omicron Surge
Authors: Schrom John , Marquez Carina , Pilarowski Genay , Wang Grace , Mitchell Anthea , Puccinelli Robert , Black Doug , Rojas Susana , Ribeiro Salustiano , Martinez Jacqueline , Jones Diane , Nakamura Robert , Jain Vivek , Petersen Maya , DeRisi Joe , Havlir Diane 
Published: January 2022

AbstractIn 731 persons seeking COVID-19 testing at a walk-up San Francisco community site in January 2022, simultaneous nasal rapid antigen testing (BinaxNOW™) and RT-PCR testing was performed. There were 296 (40.5%) positive tests by RT-PCR; 98.5% of a random sample (N=67) were the omicron variant. Sensitivity of a single antigen test was 95.2% (95% CI 92-98%); 82.1% (95% CI 77-87%) and 65.2% (95% CI 60-71%) for Ct threshold of < 30, < 35 and no threshold, respectively. We also compared BinaxNOW™ to RT-PCR from oral cheek swabs to nasal swabs (N=75); oral cheek specimen was significantly less sensitive than nasal swab. A single BinaxNOW™ oral cheek rapid antigen test failed to detect 91% (20 of 22) of specimens that were BinaxNOW™ positive from the standard nasal sampling. In a separate direct comparison of BinaxNOW™ between specimens collected from nasal or throat (tonsillar) swab (N=115), sensitivity was 97.7% for nasal and 48.8% for throat swabs that were PCR-positive on nasal swab with a Ct threshold < 30. Among persons with either a nasal or throat RT-PCR positive swab with Ct<30, BinaxNOW™ sensitivity was 85.7% for nasal and 89.8% for nasal plus throat swabs. BinaxNOW continues to be a very useful diagnostic during the omicron surge; oral (throat or cheek swab) should not replace nasal swabs due to significantly reduced sensitivity compared to nasal. As currently recommended, repeat testing should be done for high-risk persons with an initial negative antigen test result.