bluuebunny/crossref_metadata_2025_split huggingface dataset:
EnrichrBot: Twitter bot tracking tweets about human genes
Authors: Bartal Alon , Lachmann Alexander , Clarke Daniel J B , Seiden Allison H , Jagodnik Kathleen M , Ma’ayan Avi 
Published: April 2020

Abstract

Motivation
Micro-blogging with Twitter to communicate new results, discuss ideas and share techniques is becoming central. While most Twitter users are real people, the Twitter API provides the opportunity to develop Twitter bots and to analyze global trends in tweets.

Results
EnrichrBot is a bot that tracks and tweets information about human genes implementing six principal functions: (i) tweeting information about under-studied genes including non-coding lncRNAs, (ii) replying to requests for information about genes, (iii) responding to GWASbot, another bot that tweets Manhattan plots from genome-wide association study analysis of the UK Biobank, (iv) tweeting randomly selected gene sets from the Enrichr database for analysis with Enrichr, (v) responding to mentions of human genes in tweets with additional information about these genes and (vi) tweeting a weekly report about the most trending genes on Twitter.

Availability and implementation
https://twitter.com/botenrichr; source code: https://github.com/MaayanLab/EnrichrBot.

Supplementary information
Supplementary data are available at Bioinformatics online.
Metronidazole-associated Neurologic Events: A Nested Case-control Study
Authors: Daneman Nick , Cheng Yi , Gomes Tara , Guan Jun , Mamdani Muhammad M , Saxena Farah E , Juurlink David N 
Published: April 2020

Abstract

Background
Case reports have described instances of peripheral and central nervous system toxicity during treatment with metronidazole; however, no large-scale studies have examined this association.

Methods
We conducted a population-based nested case-control study of adults aged 66 years or older living in Ontario, Canada, between 1 April 2003 and 31 March 2017. Cases were individuals who attended hospital for any of cerebellar dysfunction, encephalopathy, or peripheral neuropathy within 100 days of a prescription for either metronidazole or clindamycin. We matched each case patient with up to 10 event-free control subjects who also received metronidazole or clindamycin. We used conditional logistic regression to test the association between metronidazole exposure and neurologic events, with clindamycin as the reference exposure.

Results
We identified 1212 cases with recent use of either metronidazole or clindamycin and 12 098 controls. Neurologic adverse events were associated with an increased odds of metronidazole exposure compared to clindamycin (odds ratio [OR], 1.72 [95% confidence interval {CI}, 1.53–1.94]), which persisted after accounting for patient demographics, comorbidities, and other medication exposures (adjusted odds ratio [aOR], 1.43 [95% CI, 1.26–1.63]). We found a consistent association limited to either central (aOR, 1.46 [95% CI, 1.27–1.68]) or peripheral (aOR, 1.34 [95% CI, 1.02–1.76]) nervous system events. Among metronidazole recipients, the overall incidence of neurologic events at 100 days was approximately 0.25%.

Conclusions
Metronidazole is associated with an increased risk of adverse peripheral and central nervous system events relative to clindamycin. Clinicians and patients should be aware of these rare but potentially serious adverse events.
Neoadjuvant Phase II Trial of Chemoradiotherapy in Patients With Resectable and Borderline Resectable Pancreatic Cancer
Authors: Thanikachalam Kannan , Damarla Vijay , Seixas Trevor , Dobrosotskaya Irina , Wollner Ira , Kwon David , Winters Kenneth , Raoufi Mohammad , Li Jia , Siddiqui Farzan , Khan Gazala 
Published: April 2020

Background:
Pancreatic ductal adenocarcinoma is a largely incurable cancer. Surgical resection remains the only potential option for cure. Even in surgically resectable patients, only about 10% to 20% are long-term survivors. Emerging data suggest a role for neoadjuvant therapy to target occult micrometastatic disease.

Aim:
To report our institutional experience with a novel neoadjuvant chemoradiation (CRT) regimen in resectable and borderline resectable pancreatic cancer.

Materials and Methods:
Patients were treated with 2 cycles of induction chemotherapy with FOLFOX and then received CRT with gemcitabine and intensity-modulated radiotherapy (IMRT).

Results:
From April 2014 to June 2017, 24 patients were enrolled. Eighteen patients were borderline resectable and 6 patients were resectable. All patients received induction chemotherapy with FOLFOX. Thirteen patients underwent pancreatectomy after CRT with a resection rate of 62%. R0 resection achieved in 11 patients (84.6%) and 2 patients had R1 resection (15.4%). For patients who underwent resection, the median progression-free survival (PFS) was 31 months, 1-year PFS rate was 69.2% (95% confidence interval [CI], 0.48-0.99), and 2-year PFS rate was 51.9% (95% CI, 0.3-0.89). Median overall survival (OS) was 34.8 months (95% CI, 1.045 to infinity), 1-year OS rate was 91.7% (95% CI, 0.77-1.0), and 2-year OS rate was 75% (95% CI, 0.54-1.0). Median CA 19-9 at screening for patients who underwent surgery was 659 (range, 18 to 2154), which decreased to 146.9 (range, 18 to 462) after CRT before resection.

Conclusion:
Neoadjuvant therapy for borderline resectable and resectable pancreatic ductal adenocarcinoma with CRT facilitated R0 resection in 84% patients who underwent surgery.
A New Anatomy Finding of Levator Aponeurosis and Müller Muscle at Pretarsal Plate in Asian Males
Authors: Zhang Minchen , Wu Jun , Chen Lulu , Ren Zijian , Gao Weicheng 
Published: April 2020

Purpose:
To examine the fine anatomic structures between levator aponeurosis and Müller muscle in front of the tarsus.

Materials and Methods:
Postmortem specimens of 6 Chinese males (5 elderly men, aging from 68 to 86 years; 1 child, 10 years old) were used. A 3-μm thickness sagittal section of the central part of the upper eyelid was prepared, and the samples were examined microscopically by using hematoxylin–eosin, Masson trichrome, and anti-smooth muscle actin antibodies staining.

Results:
There are 2 new findings in this study, one is the posterior layer of the levator aponeurosis and the other is the extensions of Müller muscle. The posterior levator aponeurosis had different insertion patterns that approximately paralleled the extension line of the levator aponeurosis at the confluence of attachment site of the orbital septum on the levator superioris. Below the confluence, it took the form of a layered insertion, and then extended to the orbicularis oculi muscle and subcutaneous tissue rather than inserting directly into tarsus. The Müller muscle was a multilayered structure at the upper border of tarsus. The superior Müller muscle extended above the peripheral arcade, and the inferior Müller muscle tendon was attached to the surface of tarsus with an Umbrella-shaped fiber.

Conclusions:
The authors discovered that the levator aponeurosis had different insertion patterns of the posterior layers. The Müller muscle gave branches at the peripheral arcade: the anterior one crossed the peripheral arcade and extended to the tarsus, and the posterior one attached and extended to the tarsus.
18FDG PET/CT in Primary Cutaneous Diffuse Large B-Cell Lymphoma Leg Type
Authors: Dejust Sébastien , Morland David , Durot Eric , Grange Florent , Papathanassiou Dimitri 
Published: April 2020

Abstract
An 86-year-old woman was referred for a rare but aggressive subtype of primary cutaneous lymphoma of the right lower limb: diffuse large B-cell lymphoma leg type. Initial evaluation by whole-body 18F-FDG PET/CT showed intense hypermetabolic activity of multiple cutaneous and subcutaneous nodules of the distal third of the right leg. Follow-up evaluations by 18F-FDG PET/CT showed complete response after 4 and 8 cycles of appropriate rituximab combination with polychemotherapy. Although no specific recommendations are available, our case stresses the major role of 18F-FDG PET/CT for initial extension and treatment response evaluation in clinical practice of primary cutaneous diffuse large B-cell lymphoma leg type.
Mindfulness related changes in grey matter: A Systematic Review and Meta-analysis
Authors: Pernet Cyril R. , Belov Nikolai , Delorme Arnaud , Zammit Alison 
Published: April 2020

AbstractKnowing target regions undergoing structural changes caused by behavioural interventions is paramount in evaluating the effectiveness of such practices. Here, using a systematic review approach, we identified 25 peer-reviewed magnetic resonance imaging (MRI) studies demonstrating grey matter changes related to mindfulness meditation. An activation likelihood estimation (ALE) analysis (n=16) revealed the right anterior ventral insula as the only significant region with consistent effect across studies, whilst an additional functional connectivity analysis indicates that both left and right insulae, and the anterior cingulate gyrus with adjacent paracingulate gyri should also be considered in future studies. Statistical meta-analyses suggest medium to strong effect sizes from Cohen’s d ∼0.8 in the right insula to ∼1 using maxima across the whole brain. The systematic review revealed design issues with selection, information, attrition and confirmation biases, in addition to weak statistical power. In conclusion, our analyses show that mindfulness meditation practice does induce grey matter changes but also that improvements in methodology are needed to establish mindfulness as a therapeutic intervention.
Early-life exposure to perfluorinated alkyl substances modulates lipid metabolism in progression to celiac disease
Authors: Sinisalu Lisanna , Sen Partho , Salihović Samira , Virtanen Suvi M. , Hyöty Heikki , Ilonen Jorma , Toppari Jorma , Veijola Riitta , Orešič Matej , Knip Mikael , Hyötyläinen Tuulia 
Published: April 2020

AbstractOBJECTIVESCeliac disease (CD) is a systemic immune-mediated disorder with increased frequency in the developed countries over the last decades implicating the potential causal role of various environmental triggers in addition to gluten. Herein, we apply determination of perfluorinated alkyl substances (PFAS) and combine the results with the determination of bile acids (BAs) and molecular lipids, with the aim to elucidate the impact of prenatal exposure on risk of progression to CD in a prospective series of children prior the first exposure to gluten (at birth and at 3 months of age).METHODSWe analyzed PFAS, BAs and lipidomic profiles in 76 plasma samples at birth and at 3 months of age in the Type 1 Diabetes Prediction and Prevention (DIPP) study (n=17 progressors to CD, n=16 healthy controls, HCs).RESULTSPlasma PFAS levels showed a significant inverse association with the age of CD diagnosis in infants who later progressed to the disease. Associations between BAs and triacylglycerols (TGs) showed different patterns already at birth in CD progressors, indicative of different absorption of lipids in these infants.DISCUSSIONPFAS exposure may modulate lipid and BA metabolism, and the impact is different in the infants who develop CD later in life, in comparison to HCs. The results indicate more efficient uptake of PFAS in such infants. Higher PFAS exposure during prenatal and early life may accelerate the progression to CD in the genetically predisposed children.Study HighlightsWHAT IS KNOWNSeveral observational studies have implicated a role of early life environmental triggers other than gluten in the development of CD. This is supported by the findings showing dysregulation of lipids already prior to the first introduction of gluten.WHAT IS NEW HEREWe show that prenatal exposure to perfluorinated compounds is associated with changes in the lipid metabolism, most likely through the bile acids, and that a high exposure during prenatal and early life may accelerate the progression to CD in the genetically predisposed children.TRANSLATIONAL IMPACTExposure to environmental chemicals may impact the rate of progression to CD and should be assessed as a potential risk factor of CD in larger clinical cohort settings.
Anxiety, worry and perceived stress in the world due to the COVID-19 pandemic, March 2020. Preliminary results
Authors: Gamonal Limcaoco Rosario Sinta , Mateos Enrique Montero , Fernández Juan Matías , Roncero Carlos 
Published: April 2020

AbstractIntroductionSince the beginning of the outbreak in China, ending 2019, the Novel Coronavirus (COVID-19) has spread subsequently to the rest of the world causing an on-going pandemic. The World Health Organisation (WHO) declared COVID-19 “a public health emergency of international concern.” Taking into consideration the lockdown and quarantine situation, a research team of doctors from the Hospital of Salamanca, decided to do an evaluation of the current emotional state on the general population with a web-based survey in English and in Spanish, which was considered a useful and fast method that could help us determine how people perceived stress and worry due to the COVID-19.MethodsThe survey included a 22 items, gathering information in 3 sections: Sociodemographic data, the Perceived Stress Scale (PSS-10) by Cohen and additional queries that assessed the current worry and change of behaviours due to this pandemic.ResultsThe survey received 1091 respondents from 41 countries, from March 17 to the 1st of April, 2020. The mean age of the respondents was 43.1 (14.2) years old, and more than two thirds were women. 21.1% were health personnel. The mean of the PSS-10 score was 17.4 (6.4). Significantly higher scores were observed among women, youth, students, and among those who expressed concern and those who perceived increased susceptibility to the COVID-19. In contrast, no significant differences were observed between the health professionals and the general population. A weak correlation was observed between mean relative volume RSV of the last 28 days and the number of cases reported (rho = 0.31, p <0.001) and deaths (rho = 0.28, p <0.001).DiscussionWith these results the researchers describe an increase of affective symptoms due to the COVID-19. This pandemic is raising the anxiety levels. The findings of the study show the affective and cognitive alterations people are going through. This survey is the first attempt to measure the psychological consequences this pandemic is having, in order to be able to provide the support to confront this global issue, addressing the mental health care that will be needed.
Big fish in small tanks:Stunting in the Deccan Mahseer,Tor khudree(Sykes 1849)
Authors: Varma Vishwanath , Raghavan Rajeev , Binoy V. V. 
Published: April 2020

ABSTRACTThe diminished growth and stunting of the Deccan mahseer,Tor khudree(Sykes 1849), a mega-fish, endemic to peninsular India is recorded for the first time under high-density laboratory conditions, and its implications for conservation and aquaculture discussed.
DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform
Authors: George Sophie , Xu Yifei , Rodger Gillian , Morgan Marcus , Sanderson Nicholas D. , Hoosdally Sarah J. , Thulborn Samantha , Robinson Esther , Rathod Priti , Walker A. Sarah , Peto Timothy E. A. , Crook Derrick W. , Dingle Kate E. 
Published: April 2020

ABSTRACTMycobacterium tuberculosis(MTB) is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for Oxford Nanopore Technologies (ONT) sequencing direct from MTB positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat-inactivation (99°C/30min) and enrichment for Mycobacteria DNA was achieved using an equal volume of thermo-protection buffer (4M KCl, 0.05M HEPES buffer pH7.5, 0.1% DTT). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermo-degradation, which renders it a poor template for sequencing. Initial validation employed Mycobacteria DNA (extracted or intracellular). Next, mock clinical samples (infection-negative human sputum spiked 0-105BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat-inactivation. DNA was extracted and sequenced. Human DNA degraded faster than Mycobacteria DNA, resulting in target enrichment. Four replicate experiments each demonstrated detection at 101BCG cells/ml, with 31-59 MTB complex reads. Maximal genome coverage (>97% at 5x-depth) was achieved at 104BCG cells/ml; >91% coverage (1x depth) at 103BCG cells/ml. Final validation employed MTB positive clinical samples (n=20), revealed initial sample volumes ≥1ml typically yielded higher mean depth of MTB genome coverage, the overall range 0.55-81.02. A mean depth of 3 gave >96% one-fold TB genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% five-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of MTB genomes was facilitated by a low cost thermo-protection buffer.
Clustering of desmosomal cadherins by desmoplakin is essential for cell-cell adhesion
Authors: Wanuske Marie-Therès , Brantschen Dominique , Schinner Camilla , Stüdle Chiara , Walter Elias , Hiermaier Matthias , Vielmuth Franziska , Waschke Jens , Spindler Volker 
Published: April 2020

ABSTRACTDesmoplakin (Dp) localizes to desmosomes, linking clusters of desmosomal adhesion molecules to the intermediate filament cytoskeleton. Here, we generated Dp knockout (ko) cell lines of human keratinocytes to study the impact on desmosomal adhesion molecules and desmosome turnover using atomic force microscopy and superresolution imaging. In comparison to ko of another desmosomal component, plakoglobin (Pg), loss of Dp resulted in absence of desmosomes and drastically impaired cell cohesion. In Dp ko, the desmosomal adhesion molecules desmoglein 2 (Dsg2) and desmocollin 3 (Dsc3) were redistributed into small clusters in the cell membrane with no further increase in loss of intercellular adhesion by silencing of Dsg2. This suggests that extradesmosomal cadherins do not significantly contribute to cell cohesion but rather localization within desmosomes is required. Our data outline a crucial role of Dp for both desmosomal molecule clustering and mature desmosome formation and provide novel insights into the regulation of intercellular adhesion.
Understanding customer loyalty in the coffee shop industry (A survey in Jakarta, Indonesia)
Authors: Dhisasmito Prameswari Purnamadewi , Kumar Suresh 
Published: April 2020

PurposeThe purpose of this study is to identify the drivers of loyalty model in the coffee shop industry in Indonesia based on service quality, store atmosphere and price fairness mediated by customer satisfaction.Design/methodology/approachThe sample size used for this study was 384 customers from 16 most comfortable coffee shops in Jakarta based on Nibble's survey. Confirmatory factor analysis was employed to confirm the attributes of each factor and to assess the validity and reliability, average variance extracted and composite reliability was applied. Further hypothesis testing was performed using structural equation modeling.FindingsThe result shows that customer loyalty is affected by service quality – comprising 5 subdimensions: tangible, reliability, responsiveness, assurance and empathy – and price fairness mediated by customer satisfaction. It was found that service quality plays a significant role in the coffee shop industry in Indonesia. However, the store atmosphere was found rejected.Originality/valueThis is the first study integrating service quality, store atmosphere, price fairness and customer satisfaction to study the customer loyalty model in the coffee shop industry in Jakarta.
An analysis of the determinants of failure processes in UK SMEs
Authors: Makropoulos Alexios , Weir Charlie , Zhang Xin 
Published: April 2020

PurposeThis paper has two purposes. First, it evaluates the extent to which different failure processes are present in failed UK SMEs, by considering non-financial metrics including director characteristics, in addition to the financial ones. Second, it analyses the determinants of the transition to failure in relation to the different failure processes that have been identified.Design/methodology/approachThe study is based on a sample of failed UK SMEs. The data covers financial ratios, board characteristics, the macroeconomic environment, sectoral details and regional information. First, failure processes are identified using a combination of factor analysis and cluster analysis. Second, the determinants of firms' transition to failure for the whole sample and in the individual failure clusters are analysed using panel data analysis.FindingsFour different firm failure processes were identified. Director characteristics differ between firm failure processes. We find evidence that director characteristics including director age and board gender structure, affect the transition to failure of UK SMEs. We also find that different factors affect the different failure processes.Originality/valueThe paper is the first to analyse the reasons for failure of UK SMEs in the firm failure process context by considering non-financial metrics such as the characteristics of the firms' directors. In addition the paper also identifies a number of different determinants that affect the various failure processes. This finding is important because it suggests that policies designed to reduce the incidence of firm failure should take account of the different failure processes.
Frequency, clinical characteristics, and determinants of partial remission in type 1 diabetes: Different patterns in children and adults
Authors: Zhong Ting , Tang Rong , Xie Yuting , Liu Fang , Li Xia , Zhou Zhiguang 
Published: April 2020

AbstractBackgroundPartial remission (PR) is a special stage in type 1 diabetes (T1D). The different patterns of PR frequency, characteristics, and determinants in juvenile and adult patients are unclear, and data on Chinese are lacking.MethodsA total of 186 children and 114 adults with T1D who were regularly followed up in a cohort were included for analysis. PR was defined according to C‐peptide ≥300 pmol/L or index of insulin dose‐adjusted hemoglobin A1c ≤9, as previously recommended. C‐peptide and islet autoantibodies were determined with chemiluminescence and radioimmunoassay, respectively.ResultsThe frequency of PR in children was higher than that in adults, with the proportion being 69.9% and 58.8%, respectively (P < .05). For juvenile‐onset T1D, the frequency of PR gradually decreased as the onset age decreased, from 87.5% in 13‐ to 18‐year olds to 46.5% in under 6‐year olds. Multivariable analyses showed that onset age and male sex were positively related with the frequency of PR in children, while the related factors in adults were initial glycosylated hemoglobin A1c and C‐peptide levels. The median PR duration was similar in children (14.8 ± 1.2 months) and adults (16.4 ± 1.9 months). Older onset age was related with a longer PR duration in children, but no such associations were found in adult individuals.ConclusionsChildren and adults with T1D have different patterns on PR frequency, clinical characteristics, and determinants. For patients during this special phase, the relatively high C‐peptide level and to reduce insulin dosage accordingly should be emphasized in clinical practice.