bluuebunny/crossref_metadata_2025_split huggingface dataset:
BERT6mA: prediction of DNA N6-methyladenine site using deep learning-based approaches
Authors: Tsukiyama Sho , Hasan Md Mehedi , Deng Hong-Wen , Kurata Hiroyuki 
Published: February 2022

AbstractN6-methyladenine (6mA) is associated with important roles in DNA replication, DNA repair, transcription, regulation of gene expression. Several experimental methods were used to identify DNA modifications. However, these experimental methods are costly and time-consuming. To detect the 6mA and complement these shortcomings of experimental methods, we proposed a novel, deep leaning approach called BERT6mA. To compare the BERT6mA with other deep learning approaches, we used the benchmark datasets including 11 species. The BERT6mA presented the highest AUCs in eight species in independent tests. Furthermore, BERT6mA showed higher and comparable performance with the state-of-the-art models while the BERT6mA showed poor performances in a few species with a small sample size. To overcome this issue, pretraining and fine-tuning between two species were applied to the BERT6mA. The pretrained and fine-tuned models on specific species presented higher performances than other models even for the species with a small sample size. In addition to the prediction, we analyzed the attention weights generated by BERT6mA to reveal how the BERT6mA model extracts critical features responsible for the 6mA prediction. To facilitate biological sciences, the BERT6mA online web server and its source codes are freely accessible at https://github.com/kuratahiroyuki/BERT6mA.git, respectively.
Moving forwards, sideways and up in the air: observations on the locomotion of semiterrestrial tadpoles (Cycloramphidae)
Authors: Sabbag Ariadne Fares , Dos Santos Dias Pedro Henrique , Brasileiro Cinthia A , Haddad Célio F B , Wassersug Richard J 
Published: February 2022

Abstract
Semiterrestrial tadpoles live on wet rock surfaces and have evolved independently in at least seven anuran families. They have a flat venter, laterally compressed keratinized jaws and elongated, largely finless tails. When threatened, they can jump. Here, we describe the kinematics of locomotion for semiterrestrial tadpoles of the genera Cycloramphus and Thoropa (Cycloramphidae). Forward locomotion can be accomplished solely by the upper jaw cyclically engaging and disengaging from the substrate. Undulating tail movements, in contrast, cause the tadpoles to move laterally, like sidewinding snakes, rather than forwards. Jumping is an explosive escape behaviour with an unpredictable trajectory. Jumping requires rapid elevation of the head and extension of the torso and tail. This is made possible by epaxial musculature that extends onto the cranium and movement of the tail in the sagittal plane. Tadpoles near metamorphosis extend their hindlimbs symmetrically when jumping, even when the limbs are too small to provide thrust. The rapid rostral elevation of the snout, extension of the trunk and symmetrical extension of the hindlimbs is a kinematic pattern shared with post-metamorphic frogs when they jump. This suggests that semiterrestrial tadpoles use essentially the same neural programme as that used by frogs to jump.
Distributed Cox proportional hazards regression using summary-level information
Authors: Li Dongdong , Lu Wenbin , Shu Di , Toh Sengwee , Wang Rui 
Published: February 2022

SummaryIndividual-level data sharing across multiple sites can be infeasible due to privacy and logistical concerns. This article proposes a general distributed methodology to fit Cox proportional hazards models without sharing individual-level data in multi-site studies. We make inferences on the log hazard ratios based on an approximated partial likelihood score function that uses only summary-level statistics. This approach can be applied to both stratified and unstratified models, accommodate both discrete and continuous exposure variables, and permit the adjustment of multiple covariates. In particular, the fitting of stratified Cox models can be carried out with only one file transfer of summary-level information. We derive the asymptotic properties of the proposed estimators and compare the proposed estimators with the maximum partial likelihood estimators using pooled individual-level data and meta-analysis methods through simulation studies. We apply the proposed method to a real-world data set to examine the effect of sleeve gastrectomy versus Roux-en-Y gastric bypass on the time to first postoperative readmission.
Shame and Pride among Social Workers in Israel: A Concept Map
Authors: Savaya Rivka 
Published: February 2022

Abstract
The research on shame and pride among social workers is in its infancy. Given the potential consequences of these emotions on social workers and social work practice, this study had two main aims: (i) to identify practice situations in which social workers in Israel felt shame and pride and (ii) to classify and map these situations into conceptual domains. A concept mapping approach was used to achieve these aims. Eighty social workers recruited via social networks and snowballing participated in the statement generation of experiences of shame and pride in their daily practice. The sample was diverse in terms of seniority, role (managerial/frontline), populations served and agencies. The process yielded ten clusters, six of them representing sources of shame and four sources of pride. Based on the statements comprising the clusters, it can be argued that the ability of social workers to advance change can serve as an organising concept for comparing shame and pride. Not being able to promote desired change induces shame, while promoting such change fosters pride. These outcomes can be explained by self-discrepancy theory. The article discusses the implications of the study's results for theory, practice and research.
Structural and functional brain alterations in patients with myasthenia gravis
Authors: Klaus Benita , Müller Patrick , van Wickeren Nora , Dordevic Milos , Schmicker Marlen , Zdunczyk Yael , Brigadski Tanja , Leßmann Volkmar , Vielhaber Stefan , Schreiber Stefanie , Müller Notger G. 
Published: February 2022

Abstract
Myasthenia gravis is an autoimmune disease affecting neuromuscular transmission and causing skeletal muscle weakness. Additionally, systemic inflammation, cognitive deficits and autonomic dysfunction have been described. However, little is known about myasthenia gravis-related reorganization of the brain. In this study, we thus investigated the structural and functional brain changes in myasthenia gravis patients. Eleven myasthenia gravis patients (age: 70.64 ± 9.27; 11 males) were compared to age-, sex- and education-matched healthy controls (age: 70.18 ± 8.98; 11 males). Most of the patients (n = 10, 0.91%) received cholinesterase inhibitors. Structural brain changes were determined by applying voxel-based morphometry using high-resolution T1-weighted sequences. Functional brain changes were assessed with a neuropsychological test battery (including attention, memory and executive functions), a spatial orientation task and brain-derived neurotrophic factor blood levels. Myasthenia gravis patients showed significant grey matter volume reductions in the cingulate gyrus, in the inferior parietal lobe and in the fusiform gyrus. Furthermore, myasthenia gravis patients showed significantly lower performance in executive functions, working memory (Spatial Span, P = 0.034, d = 1.466), verbal episodic memory (P = 0.003, d = 1.468) and somatosensory-related spatial orientation (Triangle Completion Test, P = 0.003, d = 1.200). Additionally, serum brain-derived neurotrophic factor levels were significantly higher in myasthenia gravis patients (P = 0.001, d = 2.040). Our results indicate that myasthenia gravis is associated with structural and functional brain alterations. Especially the grey matter volume changes in the cingulate gyrus and the inferior parietal lobe could be associated with cognitive deficits in memory and executive functions. Furthermore, deficits in somatosensory-related spatial orientation could be associated with the lower volumes in the inferior parietal lobe. Future research is needed to replicate these findings independently in a larger sample and to investigate the underlying mechanisms in more detail.
An amyloid beta vaccine that safely drives immunity to a key pathological species in Alzheimer’s disease: pyroglutamate amyloid beta
Authors: Vukicevic M. , Fiorini E. , Siegert S. , Carpintero R. , Rincon-Restrepo M. , Lopez-Deber P. , Piot N. , Ayer M. , Rentero I. , Babolin C. , Bravo-Veyrat S. , Giriens V. , Morici C. , Beuzelin M. , Gesbert A. , Rivot S. , Depretti S. , Donati P. , Streffer J. , Pfeifer A. , Kosco-Vilbois M. H. 
Published: February 2022

Abstract
Pyroglutamate amyloid beta3–42 (pGlu-Abeta3–42), a highly amyloidogenic and neurotoxic form of Abeta, is N-terminally truncated to form a pyroglutamate and has recently been proposed as a key target for immunotherapy. Optimized ACI-24, a vaccine in development for the treatment and prevention of Alzheimer’s disease, focuses the antibody response on the first 15 N-terminal amino acids of Abeta (Abeta1–15). Importantly, clinical data with an initial version of ACI-24 incorporating Abeta1–15, established the vaccine’s safety and tolerability with evidence of immunogenicity. To explore optimized ACI-24’s capacity to generate antibodies to pGlu-Abeta3–42, pre-clinical studies were carried out. Vaccinating mice and non-human primates demonstrated that optimized ACI-24 was well-tolerated and induced an antibody response against Abeta1–42 as expected, as well as high titres of IgG reactive with pyroGlu-Abeta. Epitope mapping of the polyclonal response confirmed these findings revealing broad coverage of epitopes particularly for Abeta peptides mimicking where cleavage occurs to form pGlu-Abeta3–42. These data are in striking contrast to results obtained with other clinically tested Abeta targeting vaccines which generated restricted and limited antibody diversity. Taken together, our findings demonstrate that optimized ACI-24 vaccination represents a breakthrough to provide a safe immune response with a broader Abeta sequence recognition compared to previously tested vaccines, creating binders to pathogenic forms of Abeta important in pathogenesis including pGlu-Abeta3–42.
ALK-Fusion Transcripts Can Be Detected in Extracellular Vesicles (EVs) from Nonsmall Cell Lung Cancer Cell Lines and Patient Plasma: Toward EV-Based Noninvasive Testing
Authors: Sánchez-Herrero Estela , Campos-Silva Carmen , Cáceres-Martell Yaiza , Robado de Lope Lucía , Sanz-Moreno Sandra , Serna-Blasco Roberto , Rodríguez-Festa Alejandro , Ares Trotta Dunixe , Martín-Acosta Paloma , Patiño Cristina , Coronado María José , Beneitez Alexandra , Jara Ricardo , Lago-Baameiro Nerea , Camino Tamara , Cruz-Bermúdez Alberto , Pardo María , González-Rumayor Víctor , Valés-Gómez Mar , Provencio Mariano , Romero Atocha 
Published: February 2022

Abstract

Background
ALK rearrangements are present in 5% of nonsmall cell lung cancer (NSCLC) tumors and identify patients who can benefit from ALK inhibitors. ALK fusions testing using liquid biopsies, although challenging, can expand the therapeutic options for ALK-positive NSCLC patients considerably. RNA inside extracellular vesicles (EVs) is protected from RNases and other environmental factors, constituting a promising source for noninvasive fusion transcript detection.

Methods
EVs from H3122 and H2228 cell lines, harboring EML4-ALK variant 1 (E13; A20) and variant 3 (E6a/b; A20), respectively, were successfully isolated by sequential centrifugation of cell culture supernatants. EVs were also isolated from plasma samples of 16 ALK-positive NSCLC patients collected before treatment initiation.

Results
Purified EVs from cell cultures were characterized by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and flow cytometry. Western blot and confocal microscopy confirmed the expression of EV-specific markers as well as the expression of EML4-ALK-fusion proteins in EV fractions from H3122 and H2228 cell lines. In addition, RNA from EV fractions derived from cell culture was analyzed by digital PCR (dPCR) and ALK-fusion transcripts were clearly detected. Similarly, plasma-derived EVs were characterized by NTA, flow cytometry, and the ExoView platform, the last showing that EV-specific markers captured EV populations containing ALK-fusion protein. Finally, ALK fusions were identified in 50% (8/16) of plasma EV-enriched fractions by dPCR, confirming the presence of fusion transcripts in EV fractions.

Conclusions
ALK-fusion transcripts can be detected in EV-enriched fractions. These results set the stage for the development of EV-based noninvasive ALK testing.
An Examination of the Context-Linked Influences on the Achievement Outcomes of African American Male High School Seniors
Authors: Clayton M Annette , Teasley Martell L 
Published: February 2022

Abstract
Although students must successfully navigate transition years in school in pursuit of sustained academic success, not enough is known about the context-linked experiences of African American male adolescents as they seek to traverse their senior year, one of the most important pivotal points in time for all students. This study examined the relationship between perceptions of support from significant others, exposure to contextual risks, and two achievement outcomes in a representative sample of 139 African American male high school seniors. At this critical juncture in their education career, teacher support was predictive of higher grade point average (GPA), and a specific type of family support was associated with lower GPA. Qualitative analysis revealed similarities and differences in types of support reported to have had an impact on the participants’ success in school. Results from the study confirm one hypothesis that exposure to contextual risks predicts poorer achievement outcomes. Findings affirm the need for tailored interventions that target and strengthen the systems of support within the social environment of academically at-risk African American male students.
The Smoot-Hawley Trade War
Authors: Mitchener Kris James , O'Rourke Kevin Hjortshøj , Wandschneider Kirsten 
Published: February 2022

AbstractWe document the outbreak of a trade war after the United States adopted the Smoot-Hawley tariff in June 1930. U.S. trade partners initially protested, with many eventually choosing to retaliate with tariffs. Using a new quarterly dataset on bilateral trade for ninety-nine countries, we show that U.S. exports to retaliators fell by 28%–32%. Using a second new dataset on U.S. exports at the product level, we find that the most important U.S. exports to retaliating markets were particularly affected, suggesting a possible mechanism whereby the United States was targeted despite most-favoured-nation obligations. The retaliators’ welfare gains from trade fell by 8%–16%.
Oncological outcome of segmentectomy for early-stage non-small-cell lung cancer with invasive characteristics: a multicentre study
Authors: Kagimoto Atsushi , Tsutani Yasuhiro , Shimada Yoshihisa , Mimae Takahiro , Miyata Yoshihiro , Ito Hiroyuki , Nakayama Haruhiko , Ikeda Norihiko , Okada Morihito 
Published: February 2022

Abstract

OBJECTIVES
Segmentectomy can provide oncologically acceptable results for small-sized non-small-cell lung cancer (NSCLC). However, in cases of NSCLC with pathological invasive characteristics such as lymphatic invasion (LY), vascular invasion (V), pleural invasion (PL) and/or lymph node metastasis, the feasibility of segmentectomy is not known.

METHODS
The patients included in the study (i) underwent lobectomy or segmentectomy for NSCLC with invasive characteristics such as LY, V, PL or pathological lymph node metastasis; (ii) presented with a node-negative, solid component-predominant tumour (consolidation tumour ratio &gt;50%) on preoperative computed tomography; (iii) had a whole-tumour size of 2 cm or less; and (iv) presented between January 2010 and December 2019 to one of the 3 institutions. Cumulative incidences of recurrence (CIRs) after segmentectomy and lobectomy were compared.

RESULTS
A total of 321 patients were included. Segmentectomy and lobectomy were performed in 80 (24.9%) and 241 (75.1%) patients, respectively. There was no significant difference in CIR between segmentectomy (5-year CIR rate, 17.2%) and lobectomy patients (5-year CIR rate, 27.8%, P = 0.135). In the propensity score-matched cohort, there was no significant difference in CIR between segmentectomy (5-year CIR rate, 19.1%) and lobectomy patients (5-year CIR rate, 19.2%; P = 0.650). In the multivariable analysis using inverse probability of treatment weighting and surgical method, segmentectomy was not a significant predictor of worse CIR (P = 0.920).

CONCLUSIONS
Segmentectomy is feasible for clinically early-stage NSCLC irrespective of the presence of LY, V, PL or lymph node metastasis.
Cardiopulmonary exercise testing in patients with asymptomatic left ventricular dysfunction: lack of prognostic predictive power of ventilatory variables
Authors: Corrà Ugo , Giordano Andrea , Gambarin Fabiana Isabella , Gnemmi Marco , Marcassa Claudio , Pistono Massimo 
Published: February 2022

Abstract

Aims
The indication for cardiopulmonary exercise testing (CPET) in predictive evaluation has been extended beyond chronic heart failure (HF) patients to include asymptomatic left ventricular dysfunction (ALVD) patients, but its prognostic value is still unclear. We aimed to verify if CPET can predict outcome in ALVD and to identify which of the CPET parameters predictive in chronic HF are also effective in ALVD patients.

Methods and results
We screened ALVD (LVEF ≤ 40% without HF symptoms) and HF patients for cardiac death, and compared peak oxygen consumption (pVO2), exertional oscillatory ventilation (EOV), and ventilatory response (VE/VCO2 slope) between survivors and non-survivors. Asymptomatic left ventricular dysfunction and HF patients formed the study population (585 ALVD and 695 HF). Both groups had similar male prevalence (98% vs. 98%; P = 0.345) but ALVD patients were younger (52 ± 10 vs. 60 ± 10 years, P = 0.004). Cardiac death was observed in 142 patients (5% of ALVD, 15% of HF). Exertional oscillatory ventilation occurred in 4% of ALVD, whereas VE/VCO2 slope was significantly lower (30 ± 7 vs. 35 ± 4) and pVO2 higher (16 ± 4 vs. 14 ± 3 mL/kg/min) than in chronic HF patients. Asymptomatic left ventricular dysfunction non-survivors had a significantly greater EOV incidence (13% vs. 3%, P = 0.003), lower pVO2 (13 ± 4 vs. 16 ± 3 mL/kg/min P = 0.000) and higher VE/VCO2 slope (33 ± 7 vs. 31 ± 5, P = 0.032). No ventilatory parameter had prognostic value at multivariable analysis in ALVD patients.

Conclusions
Cardiopulmonary exercise testing can predict events in ALVD patients, but the risk stratification relies on different parameters than in HF patients. Further analysis in a multi-centre trial is required to better quantify the predictive impact of CPET risk parameters in ALVD patients.
The psychosocial impact of quarantine due to exposure to COVID-19 among healthcare workers in Israel
Authors: HaGani Neta , Eilon Yael , Zeevi Sagit , Vaknin Liat , Baruch Hagar 
Published: February 2022

Summary
Quarantine is an essential practice during pandemics but it could have negative effects. There are currently no studies on the experiences of health care workers (HCWs) in quarantine during the coronavirus disease pandemic. The aim of this study was to assess the psychosocial effects of quarantine on tertiary hospital HCWs who were exposed to coronavirus. A cross-sectional study on the psychological wellbeing, needs and resources of HCWs during quarantine was conducted using an online survey in a large tertiary hospital. In total, 148 quarantined HCWs participated in this study. Overall self-reported psychological wellbeing scores were high (5.22 ± 1.11). Physicians had higher psychological wellbeing compared to nurses (5.58 ± 1.05 and 4.83 ± 1.21, respectively). Being a nurse, separation from family during quarantine, experiencing public shaming and longer quarantine period were associated with lower psychological wellbeing and higher needs. Working from home and confidence in safety at work was associated with fewer needs during quarantine. Nurses might be a risk group for the negative influences of quarantine. The ability to remain connected to work by working from home could have a protective effect on HCWs’ psychological wellbeing. More efforts should be implemented in order to support HCWs in quarantine and after their return to work.
Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk
Authors: Li Yafang , Xiao Xiangjun , Li Jianrong , Byun Jinyoung , Cheng Chao , Bossé Yohan , McKay James , Albanes Demetrios , Lam Stephen , Tardon Adonina , Chen Chu , Bojesen Stig E , Landi Maria T , Johansson Mattias , Risch Angela , Bickeböller Heike , Wichmann H-Erich , Christiani David C , Rennert Gad , Arnold Susanne , Goodman Gary , Field John K , Davies Michael P A , Shete Sanjay S , Le Marchand Loic , Melander Olle , Brunnström Hans , Liu Geoffrey , Hung Rayjean J , Andrew Angeline S , Kiemeney Lambertus A , Shen Hongbing , Sun Ryan , Zienolddiny Shan , Grankvist Kjell , Johansson Mikael , Caporaso Neil , Teare Dawn M , Hong Yun-Chul , Lazarus Philip , Schabath Matthew B , Aldrich Melinda C , Schwartz Ann G , Gorlov Ivan , Purrington Kristen , Yang Ping , Liu Yanhong , Han Younghun , Bailey-Wilson Joan E , Pinney Susan M , Mandal Diptasri , Willey James C , Gaba Colette , Brennan Paul , Amos Christopher I ,   INTEGRAL-ILCCO lung cancer consortium
Published: February 2022

Abstract
Differences by sex in lung cancer incidence and mortality have been reported which cannot be fully explained by sex differences in smoking behavior, implying existence of genetic and molecular basis for sex disparity in lung cancer development. However, the information about sex dimorphism in lung cancer risk is quite limited despite the great success in lung cancer association studies. By adopting a stringent two-stage analysis strategy, we performed a genome-wide gene–sex interaction analysis using genotypes from a lung cancer cohort including ~ 47 000 individuals with European ancestry. Three low-frequency variants (minor allele frequency &lt; 0.05), rs17662871 [odds ratio (OR) = 0.71, P = 4.29×10−8); rs79942605 (OR = 2.17, P = 2.81×10−8) and rs208908 (OR = 0.70, P = 4.54×10−8) were identified with different risk effect of lung cancer between men and women. Further expression quantitative trait loci and functional annotation analysis suggested rs208908 affects lung cancer risk through differential regulation of Coxsackie virus and adenovirus receptor gene expression in lung tissues between men and women. Our study is one of the first studies to provide novel insights about the genetic and molecular basis for sex disparity in lung cancer development.