bluuebunny/crossref_metadata_2025_split huggingface dataset:
APOBEC3B expression is promoted by lincNMR collaborating with TGF-β–Smad pathway
Authors: Ota Kosuke , Sakai Satoshi , Ohhata Tatsuya , Suzuki Takahito , Uchida Chiharu , Niida Hiroyuki , Kitagawa Masatoshi 
Published: November 2022

Abstract
Long non-coding RNAs (lncRNAs) participate in carcinogenesis and cancer malignancies. Transforming growth factor-β (TGF-β) is involved in various cellular processes including cancer progression. We performed comprehensive RNA sequencing analyses to identify lncRNAs regulated by TGF-β and found that lincNMR (long intergenic noncoding RNA–nucleotide metabolism regulator, also identified as MAP3K9-DT) was induced by TGF-β in various cell lines. There are several variants of lincNMR (hereafter lincNMRs) in the lincNMR/MAP3K9-DT locus, and their expression was increased by TGF-β. TGF-β-mediated induction of lincNMRs was decreased by depletion of Smad2/3 in Huh7, suggesting that the TGF-β–Smad pathway is involved in lincNMRs expression. We also found that APOBEC3B but not other APOBEC family members were a target gene of lincNMRs. APOBEC3B, a cytidine deaminase, promotes C to U mutation and highly expressed in various human cancers. Although it is associated with cancer progression, regulatory mechanisms of APOBEC3B expression have not been fully elucidated. We performed RNA immunoprecipitation assays and proved that lincNMRs bound to endogenous Smad2 in Huh7 cells. The increased activity of the promoter of APOBEC3B induced by overexpression of Smad2/3 was inhibited by depletion of lincNMRs. These data suggest that lincNMRs participate in APOBEC3B expression by collaborating with TGF-β–Smad pathway. High expression of lincNMRs was positively correlated with high expression of APOBEC3B in various cancer cell lines. Overexpression of APOBEC3B as well as lincNMR was found in human cancers such as hepatic and lung cancers and was associated with their poor prognosis, suggesting that lincNMR may contribute to tumor malignancy via enhanced expression of APOBEC3B.
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens
Authors: Kaur Sandeep , Payne Michael , Luo Lijuan , Octavia Sophie , Tanaka Mark M , Sintchenko Vitali , Lan Ruiting 
Published: November 2022

Abstract
Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions. The MGT designation for isolates is stable, and the assignment is faster than the existing approaches. MGT’s utility has been demonstrated in multiple species. This paper presents a publicly accessible web service called MGTdb, which enables the assignment of MGT STs to isolates, along with their storage, retrieval and analysis. The MGTdb web service enables upload of genome data as sequence reads or alleles, which are processed and assigned MGT identifiers. Additionally, any newly sequenced isolates deposited in the National Center for Biotechnology Information’s Sequence Read Archive are also regularly retrieved (currently daily), processed, assigned MGT identifiers and made publicly available in MGTdb. Interactive visualization tools are presented to assist analysis, along with capabilities to download publicly available isolates and assignments for use with external software. MGTdb is currently available for Salmonella enterica serovars Typhimurium and Enteritidis and Vibrio cholerae. We demonstrate the usability of MGTdb through three case studies — to study the long-term national surveillance of S. Typhimurium, the local epidemiology and outbreaks of S. Typhimurium, and the global epidemiology of V. cholerae. Thus, MGTdb enables epidemiological and microbiological investigations at multiple levels of resolution for all publicly available isolates of these pathogens.
Database URL: https://mgtdb.unsw.edu.au
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data
Authors: Delorme Arnaud , Truong Dung , Youn Choonhan , Sivagnanam Subhashini , Stirm Claire , Yoshimoto Kenneth , Poldrack Russell A , Majumdar Amitava , Makeig Scott 
Published: November 2022

Abstract
To preserve scientific data created by publicly and/or philanthropically funded research projects and to make it ready for exploitation using recent and ongoing advances in advanced and large-scale computational modeling methods, publicly available data must use in common, now-evolving standards for formatting, identifying and annotating should share data. The OpenNeuro.org archive, built first as a repository for magnetic resonance imaging data based on the Brain Imaging Data Structure formatting standards, aims to house and share all types of human neuroimaging data. Here, we present NEMAR.org, a web gateway to OpenNeuro data for human neuroelectromagnetic data. NEMAR allows users to search through, visually explore and assess the quality of shared electroencephalography (EEG), magnetoencephalography and intracranial EEG data and then to directly process selected data using high-performance computing resources of the San Diego Supercomputer Center via the Neuroscience Gateway (nsgportal.org, NSG), a freely available web portal to high-performance computing serving a variety of neuroscientific analysis environments and tools. Combined, OpenNeuro, NEMAR and NSG form an efficient, integrated data, tools and compute resource for human neuroimaging data analysis and meta-analysis.
Database URL: https://nemar.org
Segmental volumetric analysis with a ventilated or perfused area: identifying the intersegmental plane
Authors: Kitazume Mai , Tane Shinya , Shimizu Nahoko , Kitamura Yoshitaka , Maniwa Yoshimasa , Nishio Wataru 
Published: November 2022

Abstract

OBJECTIVES
Two methods are available to identify the intersegmental plane during segmentectomy: the inflation-deflation method, based on the ventilation area, and injection of indocyanine green, based on the pulmonary arterial distribution. However, whether the intersegmental plane created by these 2 methods matches remains unknown. Our goal was to identify the demarcation lines based on bronchial and arterial territories using 3-dimensional computed tomography-based volumetry.

METHODS
We collected data from patients who underwent thoracoscopic segmentectomy in our hospital between April 2012 and May 2021. Three-dimensional images were reconstructed from the preoperative contrast-enhanced computed tomography data using the SYNAPSE VINCENT software program. The volume of the affected area and the distance of the tumour from the intersegmental plane were calculated based on each affected artery and bronchus. Each calculated volume was compared to each affected segment using a paired t-test.

RESULTS
Of 195 patients, 114 underwent upper lobe segmentectomy, and 81 underwent lower lobe segmentectomy. In upper lobe segmentectomy, the affected arterial segmental volume was smaller than the bronchial volume (505.0 ml vs 539.4 ml, P &lt; 0.001). In lower lobe segmentectomy, there was no significant difference between arterial and bronchial volumes (234.6 ml vs 236.9 ml, P = 0.607). The volume of the affected arterial segmental lung and the distance of the tumour from the intersegmental plane were significantly smaller than the bronchial volume in upper lobe segmentectomies.

CONCLUSIONS
As per the results, the affected segmental volume delineated by the indocyanine green method would be underestimated in upper lobe segmentectomy.
State-of-the-art management of dysplastic Barrett's esophagus
Authors: Vantanasiri Kornpong , Iyer Prasad G 
Published: November 2022

Abstract
Endoscopic eradication therapy (EET) has become a standard of care for treatment of dysplastic Barrett’s esophagus (BE) and early Barrett’s neoplasia. EET mainly consists of removal of any visible lesions via endoscopic resection and eradication of all remaining Barrett’s mucosa using endoscopic ablation. Endoscopic mucosal resection and endoscopic submucosal dissection are the two available resection techniques. After complete resection of all visible lesions, it is crucial to perform endoscopic ablation to ensure complete eradication of the remaining Barrett’s segment. Endoscopic ablation can be done either with thermal techniques, including radiofrequency ablation and argon plasma coagulation, or cryotherapy techniques. The primary end point of EET is achieving complete remission of intestinal metaplasia (CRIM) to decrease the risk of dysplastic recurrence after successful EET. After CRIM is achieved, a standardized endoscopic surveillance protocol needs to be implemented for early detection of BE recurrence.
Prestige and financial stability: motivating factors to pursue a doctor of pharmacy degree
Authors: Osmond Dane , Shcherbakova Natalia , Huston Sally 
Published: November 2022

AbstractObjectiveThis study aims to identify factors influencing students’ decision to pursue a doctorate in pharmacy (PharmD).MethodsFocus-group interviews and quantitative surveys were used in sequence to investigate pharmacy students’ motivations. A total of 36 current PharmD students from two US colleges of pharmacy participated in five focus groups. The resulting qualitative findings, along with existing literature, informed the development of a survey questionnaire, which was then administered to two cohorts of first-year pharmacy students at one of the participating colleges.Key findingsIdentified themes include prestige of a doctorate, patient interaction, career versatility, and pharmacy school’s lower intensity vis-à-vis medical school. A total of 110 first-year pharmacy students from a 4-year program (average (SD) age 23 (5); 65% female) completed the survey (98.5% response rate). The order of factors that respondents ranked as important or somewhat important for choosing pharmacy include: financial stability (n = 107 (97%)), prestige of a doctorate degree ((n = 97 (88%)), good work-life balance ((n = 96 (87%)), the opportunity to use critical thinking skills ((n = 93 (85%)), having patient interaction and communication ((n = 91 (83%)), and being in a profession or service ((n = 91 (83%)).ConclusionsUS PharmD students are mainly drawn by job and financial stability, prestige of a doctorate, and a good work-life balance.
Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture
Authors: Swanson Mark T , Henson Michael W , Handika Heru , Achmadi Anang S , Anita Syahfitri , Rowe Kevin C , Esselstyn Jacob A 
Published: November 2022

AbstractFaunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.
Radiation-driven warping of accretion discs due to X-ray bursts
Authors: Ballantyne D R 
Published: November 2022

ABSTRACT
The outpouring of radiation during an X-ray burst can affect the properties of accretion discs around neutron stars: the corona can cool and collapse, the inner regions can be bled away due to enhanced accretion, and the additional heating will lead to changes in the disc height. In this paper, we investigate whether radiation from bursts can cause the disc to distort through a warping instability. Working in the limit of isotropic viscosity and linear growth, we find that bursts are more likely to drive disc warps when they have larger luminosities and longer durations. Therefore, warps will be most probable during intermediate-duration bursts (IMDBs) and superbursts with evidence for photospheric radius expansion. Further, the development of warps depends on the disc viscosity with larger values of α increasing the likelihood of warp growth. We perform time-dependent evolution calculations of the development of warps during type I bursts and IMDBs. Depending on the initial warp prior to the burst, we find that the burst produces warps at r ≲ 50rg that rapidly grow and decay on second-long time-scales, or ones that grow more slowly and cover a large fraction of the disc. The pulsations of warp at small radii appear to have the properties needed to explain the achromatic fluctuations that have been observed during the tails of some IMDBs. The large-scale, slowly growing warps could account for the large reflection strengths and absorbing column densities inferred late in the 4U 1820-30 and 4U 1636-53 superbursts.
A common origin for the fundamental plane of quiescent and star-forming galaxies in the EAGLE simulations
Authors: de Graaff Anna , Franx Marijn , Bell Eric F , Bezanson Rachel , Schaller Matthieu , Schaye Joop , van der Wel Arjen 
Published: November 2022

ABSTRACT
We use the EAGLE cosmological simulations to perform a comprehensive and systematic analysis of the z = 0.1 fundamental plane (FP), the tight relation between galaxy size, mass, and velocity dispersion. We first measure the total mass and velocity dispersion (including both random and rotational motions) within the effective radius to show that simulated galaxies obey a total mass FP that is very close to the virial relation ($\lt 10{{\ \rm per\ cent}}$ deviation), indicating that the effects of non-homology are weak. When we instead use the stellar mass, we find a strong deviation from the virial plane, which is driven by variations in the dark matter content. The dark matter fraction is a smooth function of the size and stellar mass, and thereby sets the coefficients of the stellar mass FP without substantially increasing the scatter. Hence, both star-forming and quiescent galaxies obey the same FP, with equally low scatter ($0.02\,$dex). We employ simulations with a variable stellar initial mass function (IMF) to show that IMF variations have a modest additional effect on this FP. Moreover, when we use luminosity-weighted mock observations of the size and spatially integrated velocity dispersion, the inferred FP changes only slightly. However, the scatter increases significantly, due to the luminosity-weighting and line-of-sight projection of the velocity dispersions, and measurement uncertainties on the half-light radii. Importantly, we find significant differences between the simulated FP and observations, which likely reflects a systematic difference in the stellar mass distributions. Therefore, we suggest the stellar mass FP offers a simple test for cosmological simulations, requiring minimal post-processing of simulation data.
Incidence proportion and prognosis of leptomeningeal disease among patients with breast vs. non-breast primaries
Authors: Lamba Nayan , Cagney Daniel N , Catalano Paul J , Elhalawani Hesham , Haas-Kogan Daphne A , Wen Patrick Y , Wagle Nikhil , Lin Nancy U , Aizer Ayal A , Tanguturi Shyam 
Published: November 2022

Abstract

Background
Leptomeningeal disease (LMD) is a relatively uncommon manifestation of advanced cancer. Patients with LMD carry a poor prognosis and often decline rapidly, complicating inclusion in clinical trials. Identification of LMD subsets of greater incidence and more favorable prognosis might facilitate dedicated clinical trials in the future. We hypothesized that patients with breast cancer may represent such a population and sought to assess the relative incidence and prognosis of LMD secondary to breast vs. non-breast primaries.

Methods
We identified 2411 patients with intracranial metastases secondary to breast (N = 501) and non-breast (N = 1910) primaries at Brigham and Women’s Hospital/Dana-Farber Cancer Institute between 1996 and 2020, of whom 112 presented with and an additional 161 subsequently developed LMD. A log-rank test and Cox modeling were used to compare outcomes in patients with breast vs. non-breast primaries.

Results
Among patients with newly diagnosed intracranial disease, the incidence proportion of concurrent LMD was 11.4% vs. 2.9% among patients with breast vs. non-breast primaries (P &lt; .001). Development of LMD among initially LMD-naïve patients was also more common among patients with breast vs. non-breast primaries (HR = 1.49 [1.05–2.11], P = .03). Patients with LMD secondary to breast vs. non-breast primaries displayed lower all-cause mortality (HR 0.70 [0.52–0.93], P = .01; median survival: 5.2 vs. 2.4 months, respectively), with a greater numerical difference observed in patients with LMD at intracranial involvement (7.4 vs. 2.6 months, respectively).

Conclusions
Patients with breast cancer and LMD may represent an ideal population for clinical trials given the higher incidence and potentially more favorable prognosis seen in this population.
Dietary energy intake across the menstrual cycle: a narrative review
Authors: Rogan Michaela M , Black Katherine E 
Published: November 2022

AbstractFemales are often underrepresented in the scientific literature, but awareness of the need for female-specific research is increasing. Review articles have been published on the effects of the menstrual cycle on aspects of exercise performance and physiology, yet to date no research has reviewed the effect of menstrual cycle phase on dietary energy intake. Fluctuations in endogenous sex hormones across the menstrual cycle influence a range of physiological processes, including those involved in nutritional status. Observational research typically quantifies female athletes’ nutritional intakes at a single time point; however, this may provide inaccurate information if dietary intake fluctuates across the menstrual cycle. Similarly, this may have implications for interventional research, where dietary intake is often poorly controlled or monitored. This review aimed to synthesize the published literature on dietary energy intakes of naturally menstruating females in various phases of the menstrual cycle. The review critiques the relevant literature in light of recent publications on good practice for female research, explores the impact of the menstrual cycle on energy intake, identifies gaps within the evidence base, and informs future research. Overall, energy intake appears to be lower in the follicular phase compared with the luteal phase, with a particular decrease in the days leading up to and including ovulation. The magnitude of these fluctuations is not yet clearly quantifiable and most likely varies, both between individuals, and from cycle to cycle. This review notes the lack of high-quality research investigating the energy intakes of females across the menstrual cycle, and the very limited data available for female athletes and others who undertake large amounts of physical activity. It also highlights the need for researchers to take into consideration anovulatory cycles and the potential effects of premenstrual disorders on dietary intake.
Intravenous Cyclophosphamide Therapy for Anti-IFN-γ Autoantibody-Associated Talaromyces marneffei Infection
Authors: Zeng Wen , Tang Mengxin , Yang Meiling , Fang Gaoneng , Tang Shudan , Zhang Jianquan 
Published: November 2022

Abstract
High titers of anti-interferon-γ autoantibodies (AIGAs) are an important factor leading to persistent, relapsed, and refractory infections in HIV-negative hosts infected with Talaromyces marneffei (TM). We report 5 patients treated with pulses of high-dose intravenous cyclophosphamide (IVCY) who were followed for 2 years. Before IVCY therapy, all patients had multiple relapses, with a median (interquartile range [IQR]) of 2 (1–3) instances of relapse. The median serum AIGA titers (IQR) were 58 753 (41 203–89 605) ng/mL at diagnosis, 48 189.4 (15 537–83 375) ng/mL before IVCY therapy, and 10 721.2 (5637–13 245) ng/mL at the end of IVCY therapy (P &lt; .05). After 3 months of follow-up, the median AIGA titers (IQR) rose gradually to 21 232.6 (9896–45 626) ng/mL, and to 37 464.2 (19 872–58 321) ng/mL at 24 months (P &lt; .05). Five patients discontinued antimicrobial therapy within 3–12 months after completion of IVCY therapy, but only 1 patient had a relapse. In conclusion, pulses of short-term and high-dose IVCY can effectively reduce AIGA titers.
Children With Cerebral Palsy Show Higher Static—But Not Higher Dynamic—Motor Fatigability in Grip and Pinch Tasks Than Children With Typical Development Do
Authors: Brauers Lieke , Smeets Rob , Feys Peter , Gordon Andrew M , Janssen-Potten Yvonne , Ortibus Els , Feys Hilde , Rameckers Eugene , Klingels Katrijn 
Published: November 2022

Abstract

Objective
The purpose of this study was to investigate differences in static and dynamic motor fatigability during grip and pinch tasks between children with unilateral spastic cerebral palsy (USCP) and children with typical development (TD) and between preferred and nonpreferred hands.

Methods
Fifty-three children with USCP and 53 age-matched children with TD (mean = 11 years 1 month; SD = 3 years 8 months) participated in 30-second maximum exertion sustained and repeated grip and pinch tasks. For sustained tasks, the Static Fatigue Index and the ratio of mean force between the first and last thirds of the curve were calculated. For repeated tasks, the ratio of mean force and the ratio of numbers of peaks between the first and last thirds of the curve were calculated.

Results
Higher Static Fatigue Index scores for grip and pinch were found with USCP in both hands and between hands in both groups. Dynamic motor fatigability showed inconsistent results, with higher levels of fatigability in children with TD than in children with USCP for grip in the ratio of mean force between the first and last thirds of the curve in nonpreferred hands and in the ratio of number of peaks between the first and last thirds of the curve in preferred hands.

Conclusion
Higher motor fatigability in children with USCP than in children with TD was found for static but not dynamic grip and pinch. Underlying mechanisms may play different roles in static and dynamic motor fatigability.

Impact
These results highlight that static motor fatigability in grip and pinch tasks should be part of a comprehensive upper limb assessment and that this could be the target of individualized interventions.