bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of and Associations With Distress and Professional Burnout Among Otolaryngologists: Part I, Trainees
Authors: Larson David P. , Carlson Matthew L. , Lohse Christine M. , O’Brien Erin K. , Kircher Matthew L. , Gurgel Richard K. , Hunter Jacob B. , Micco Alan G. , Nogan Stephen J. , O’Connell Brendan P. , Rangarajan Sanjeet V. , Rivas Alejandro , Sweeney Alex D. , Wanna George B. , Weisskopf Peter A. , Choby Garret 
Published: September 2020

ObjectiveTo assess the prevalence of distress and burnout in otolaryngology trainees, including associations with relevant sociodemographic and professional factors, and to compare these results with those of attending otolaryngologists.Study DesignA cross‐sectional survey of trainees and attending physicians.SettingTwelve academic otolaryngology programs.MethodsDistress and burnout were measured with the Expanded Physician Well‐being Index and the 2‐item Maslach Burnout Inventory. The Patient Health Questionnaire–2 and Generalized Anxiety Disorder–2 were used to screen for depressive disorders and anxiety disorders, respectively. Associations with sociodemographic and professional characteristics were assessed.ResultsOf the 613 surveys administered to trainees and attending physicians, 340 were completed (56%). Among 154 trainees, distress was present in 49%, professional burnout in 35%, positive depressive disorder screening in 5%, and positive anxiety disorder screening in 16%. In univariable analysis, female gender, hours worked in a typical week (HW), and nights on call in a typical week (NOC) were significantly associated with distress. In multivariable analysis, female gender (odds ratio, 3.91; P =. 001) and HW (odds ratio for each 10 HW, 1.89; P =. 003) remained significantly associated with distress. Female gender, HW, and NOC were significantly associated with burnout univariably, although only HW (odds ratio for each 10 HW, 1.92; P =. 003) remained significantly associated with burnout in a multivariable setting. Attending physicians had less distress than trainees (P =. 02) and felt less callous and less emotionally hardened than trainees (P <. 001).ConclusionOtolaryngology trainees experience significant work‐place distress (49%) and burnout (35%). Gender, HW, and NOC had the strongest associations with distress and burnout.
Change and continuity in Finnish drinking in the 21st century
Authors: Tigerstedt Christoffer , Makela Pia , Karlsson Thomas , Härkönen Janne , Lintonen Tomi , Warpenius Katariina 
Published: September 2020

Aim: Alcohol consumption and policy in Finland have undergone a variety of changes in the two last decades. In several cases, trends in both consumption and policy have shifted direction when moving from the first decade of the 21st century to the second one. The aim of the overview is to summarise the trends. Data: The overview draws on results primarily from the cross-sectional Finnish Drinking Habits Survey (FDHS) in 2000, 2008 and 2016, and also from the whole series including altogether seven separate data collections carried out every eight years from 1968 to 2016 and mainly covering Finns aged 15–69 years. Response rates show a falling trend (78% in 2000, 74% in 2008 and 60% in 2016). The overview also makes use of data collected within the European School Survey Project on Alcohol and other Drugs (ESPAD) and, for the elderly, the National FinSote study carried out by the Finnish Institute for Health and Welfare (THL). Results: After an all-time high of 12.7 litres of pure alcohol per capita 15 years and over in 2007, total consumption of alcohol had decreased by 21% by the year 2019. Underage drinking has decreased ever since the millennium shift. Older people’s drinking has continued increasing or levelled out. Along with reduced total consumption, heavy episodic drinking (HED) has also decreased, but the differences between manual and white-collar workers in HED have continued to grow. Drinking alcoholic beverages with meals has also declined since 2008. Liberal and restrictive alcohol policy measures have alternated. Conclusions: Finnish drinking culture seems to change at a slow pace; several typical drinking habits have remained unchanged.
Faecal microbiota transplantation for Clostridioides difficile infection: Four years’ experience of the Netherlands Donor Feces Bank
Authors: Terveer Elisabeth M , Vendrik Karuna EW , Ooijevaar Rogier E , van Lingen Emilie , Boeije‐Koppenol Eline , van Nood Els , Goorhuis Abraham , Bauer Martijn P , van Beurden Yvette H , Dijkgraaf Marcel GW , Mulder Chris JJ , Vandenbroucke‐Grauls Christina MJE , Seegers Jos FML , van Prehn Joffrey , Verspaget Hein W , Kuijper Ed J , Keller Josbert J 
Published: September 2020

BackgroundThe Netherlands Donor Feces Bank provides standardized ready‐to‐use donor faecal suspensions for faecal microbiota transplantation treatment of patients with recurrent Clostridioides difficile infection.ObjectiveThe purpose of this study was evaluation of safety, feasibility and outcome of faecal microbiota transplantation facilitated by a national stool bank.MethodsThe methods used included: observational cohort study of donors and recipients of faecal suspensions; assessment of donor screening and patient selection performed by an expert panel of medical microbiologists, gastroenterologists and infectious disease specialists; and patient outcome evaluated at different timepoints after faecal microbiota transplantation.ResultsOf 871 volunteers who registered as a potential faeces donor, 16 (2%) became active donors. Nine donors stopped or were excluded after a mean donation period of 5.7 months. In 2016–2019, 47 (27%) of 176 requests for faecal microbiota transplantations were deemed not indicated by the expert panel. In total, 129 patients with recurrent C. difficile infection were treated with 143 faecal suspensions in 40 different hospitals. The cure rate at two months after a single infusion was 89% (107/120). Of 84 patients, long‐term follow‐up (median 42 weeks) was available and sustained cure was achieved in 61 (73%). Early C. difficile infection relapses (within two months after faecal microbiota transplantation) and late recurrences (after more than two months) occurred more frequently in patients who received non‐C. difficile antibiotics within three weeks after faecal microbiota transplantation and in moderately to severely immunocompromised patients. Of 21 patients with C. difficile infection after faecal microbiota transplantation, 14 were cured with anti‐C. difficile antibiotics and seven with a second transplantation. No faecal microbiota transplantation‐related serious adverse events were observed, but gastro‐intestinal complaints (nausea, abdominal pain or diarrhoea) persisted in 32% of the treated patients at long‐term follow‐up.ConclusionFaecal suspensions provided by a centralized stool bank, supported by a multidisciplinary expert team, resulted in effective, appropriate and safe application of faecal microbiota transplantation for recurrent C. difficile infection.Level of evidenceLevel II, prospective cohort study
Fusion partner–specific mutation profiles and KRAS mutations as adverse prognostic factors in MLL-rearranged AML
Authors: Matsuo Hidemasa , Yoshida Kenichi , Nakatani Kana , Harata Yutarou , Higashitani Moe , Ito Yuri , Kamikubo Yasuhiko , Shiozawa Yusuke , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Okada Ai , Nannya Yasuhito , Takeda June , Ueno Hiroo , Kiyokawa Nobutaka , Tomizawa Daisuke , Taga Takashi , Tawa Akio , Miyano Satoru , Meggendorfer Manja , Haferlach Claudia , Ogawa Seishi , Adachi Souichi 
Published: September 2020

Abstract
Mixed-lineage leukemia (MLL) gene rearrangements are among the most frequent chromosomal abnormalities in acute myeloid leukemia (AML). MLL fusion patterns are associated with the patient’s prognosis; however, their relationship with driver mutations is unclear. We conducted sequence analyses of 338 genes in pediatric patients with MLL-rearranged (MLL-r) AML (n = 56; JPLSG AML-05 study) alongside data from the TARGET study’s pediatric cohorts with MLL-r AML (n = 104), non–MLL-r AML (n = 581), and adult MLL-r AML (n = 81). KRAS mutations were most frequent in pediatric patients with high-risk MLL fusions (MLL-MLLLT10, MLL-MLLT4, and MLL-MLLT1). Pediatric patients with MLL-r AML (n = 160) and a KRAS mutation (KRAS-MT) had a significantly worse prognosis than those without a KRAS mutation (KRAS-WT) (5-year event-free survival [EFS]: 51.8% vs 18.3%, P &lt; .0001; 5-year overall survival [OS]: 67.3% vs 44.3%, P = .003). The adverse prognostic impact of KRAS mutations was confirmed in adult MLL-r AML. KRAS mutations were associated with adverse prognoses in pediatric patients with both high-risk (MLLT10+MLLT4+MLLT1; n = 60) and intermediate-to-low–risk (MLLT3+ELL+others; n = 100) MLL fusions. The prognosis did not differ significantly between patients with non–MLL-r AML with KRAS-WT or KRAS-MT. Multivariate analysis showed the presence of a KRAS mutation to be an independent prognostic factor for EFS (hazard ratio [HR], 2.21; 95% confidence interval [CI], 1.35-3.59; P = .002) and OS (HR, 1.85; 95% CI, 1.01-3.31; P = .045) in MLL-r AML. The mutation is a distinct adverse prognostic factor in MLL-r AML, regardless of risk subgroup, and is potentially useful for accurate treatment stratification. This trial was registered at the UMIN (University Hospital Medical Information Network) Clinical Trials Registry (UMIN-CTR; http://www.umin.ac.jp/ctr/index.htm) as #UMIN000000511.
TRIP - T cell receptor/immunoglobulin profiler
Authors: Kotouza Maria Th. , Gemenetzi Katerina , Galigalidou Chrysi , Vlachonikola Elisavet , Pechlivanis Nikolaos , Agathangelidis Andreas , Sandaltzopoulos Raphael , Mitkas Pericles A. , Stamatopoulos Kostas , Chatzidimitriou Anastasia , Psomopoulos Fotis E. ,   on behalf of the Hellenic Precision Medicine Network in Oncology
Published: September 2020

Abstract
Background
Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling, through a number of interoperable modules. These provide detailed information about antigen receptor gene rearrangements, including variable (V), diversity (D) and joining (J) gene usage, CDR3 amino acid and nucleotide composition and clonality of both T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG), and characteristics of the somatic hypermutation within the BcR IG genes. TRIP is a web application implemented in R shiny.

Results
Two sets of experiments have been performed in order to evaluate the efficiency and performance of the TRIP tool. The first used a number of synthetic datasets, ranging from 250k to 1M sequences, and established the linear response time of the tool (about 6 h for 1M sequences processed through the entire BcR IG data pipeline). The reproducibility of the tool was tested comparing the results produced by the main TRIP workflow with the results from a previous pipeline used on the Galaxy platform. As expected, no significant differences were noted between the two tools; although the preselection process seems to be stricter within the TRIP pipeline, about 0.1% more rearrangements were filtered out, with no impact on the final results.

Conclusions
TRIP is a software framework that provides analytical services on antigen receptor gene sequence data. It is accurate and contains functions for data wrangling, cleaning, analysis and visualization, enabling the user to build a pipeline tailored to their needs. TRIP is publicly available at https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler.
Proteome of larval metamorphosis induced by epinephrine in the Fujian oyster Crassostrea angulata
Authors: Di Guilan , Xiao Xiaohuo , Tong Ming Him , Chen Xinhua , Li Li , Huang Miaoqin , Zhou Long , Ke Caihuan 
Published: September 2020

Abstract
Background
The Fujian oyster Crassostrea angulata is an economically important species that has typical settlement and metamorphosis stages. The development of the oyster involves complex morphological and physiological changes, the molecular mechanisms of which are as yet unclear.

Results
In this study, changes in proteins were investigated during larval settlement and metamorphosis of Crassostrea angulata using epinephrine induction. Protein abundance and identity were characterized using label-free quantitative proteomics, tandem mass spectrometry (MS/ MS), and Mascot methods. The results showed that more than 50% (764 out of 1471) of the quantified proteins were characterized as differentially expressed. Notably, more than two-thirds of the differentially expressed proteins were down-regulated in epinephrine-induced larvae. The results showed that “metabolic process” was closely related to the development of settlement and metamorphosis; 5 × 10− 4 M epinephrine induced direct metamorphosis of larvae and was non-toxic. Calmodulin and MAPK pathways were involved in the regulation of settlement of the oyster. Expression levels of immune-related proteins increased during metamorphosis. Hepatic lectin-like proteins, cadherins, calmodulin, calreticulin, and cytoskeletal proteins were involved in metamorphosis. The nervous system may be remodeled in larval metamorphosis induced by epinephrine. Expression levels of proteins that were enriched in the epinephrine signaling pathway may reflect the developmental stage of the larvae, that may reflect whether or not larvae were directly involved in metamorphosis when the larvae were treated with epinephrine.

Conclusion
The study provides insight into proteins that function in energy metabolism, immune responses, settlement and metamorphosis, and shell formation in C. angulata. The results contribute valuable information for further research on larval settlement and metamorphosis.

Graphical abstract
Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis
Authors: Vu Nga T. T. , Zenger Kyall R. , Guppy Jarrod L. , Sellars Melony J. , Silva Catarina N. S. , Kjeldsen Shannon R. , Jerry Dean R. 
Published: September 2020

Abstract
Background
Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management.

Results
Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001–0.107; p <  0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations.

Conclusion
This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.
Molecular epidemiology and risk factors of Stenotrophomonas maltophilia infections in a Chinese teaching hospital
Authors: Duan Zhongliang , Qin Juanxiu , Liu Yao , Li Cui , Ying Chunmei 
Published: September 2020

Abstract
Background
Stenotrophomonas maltophilia (S. maltophilia) is an important opportunistic pathogen that can be isolated in hospitals. With the abuse of broad spectrum antibiotics and invasive surgical devices, the rate of S. maltophilia infection is increasing every year. This study was an epidemiological analysis of the clinical and molecular characteristics of S. maltophilia infection in a Chinese teaching hospital. The goal was to obtain a comprehensive understanding of the status of S. maltophilia infection to provide strong epidemiological data for the prevention and treatment of S. maltophilia infection.

Results
A total of 93 isolates from Renji Hospital affiliated with the Shanghai Jiaotong University School of Medicine were included, in which 62 isolates were from male patients. In addition, 81 isolates were isolated from sputum samples. A total of 86 patients had underlying diseases. All patients received antibiotics. Multilocus sequence typing (MLST) analysis indicated that 61 different sequence types (STs) were found (including 45 novel STs), and MLST did not show significantly dominant STs. Pulsed field gel electrophoresis (PFGE) results showed that 93 isolates could be divided into 73 clusters, and they also showed weak genetic linkages between isolates. The resistant rates to trimethoprim/sulfamethoxazole (TMP/SMX) and levofloxacin were 9.7 and 4.3%, respectively, and all isolates were susceptible to minocycline. Four virulence gene’s loci Stmpr1, Stmpr2, Smf-1, and Smlt3773 were positive in 79.6, 91.4, 94.6, and 52.7% of the isolates, respectively. Three biofilm genes rmlA, spgM, and rpfF were positive in 82.8, 92.5, and 64.5% of the isolates, respectively. Mean biofilm forming level of OD492 was 0.54 ± 0.49. We did not find any significant difference between different genders and different age-groups. We retrospectively analyzed data from patients in the intensive care unit (ICU) and the control group. The independent risk factors of those who were infected in the ICU included immunosuppression and the increased antibiotic usage.

Conclusions
Most of the patients had prior medical usage histories and baseline diseases. The positive rate of virulence genes was high, the drug resistance rate of S. maltophilia was low, and the biofilm formation ability was strong. The increased use of antibiotics was an independent risk factor for S. maltophilia infection, which should receive more attention. No obvious clonal transmissions were found in the same departments.
Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. chow (Orchidaceae)
Authors: Wang Yanhua , Gao Yugang , Zang Pu , Xu Yue 
Published: September 2020

Abstract
Background
Gastrodia elata Bl. f. glauca S. Chow is a medicinal plant. G. elata f. glauca is unavoidably infected by pathogens in their growth process. In previous work, we have successfully isolated and identified Penicillium oxalicum from fungal diseased tubers of G. elata f. glauca. As a widespread epidemic, this fungal disease seriously affected the yield and quality of G. elata f. glauca. We speculate that the healthy G. elata F. glauca might carry resistance genes, which can resist against fungal disease. In this study, healthy and fungal diseased mature tubers of G. elata f. glauca from Changbai Mountain area were used as experimental materials to help us find potential resistance genes against the fungal disease.

Results
A total of 7540 differentially expressed Unigenes (DEGs) were identified (FDR < 0.01, log2FC > 2). The current study screened 10 potential resistance genes. They were attached to transcription factors (TFs) in plant hormone signal transduction pathway and plant pathogen interaction pathway, including WRKY22, GH3, TIFY/JAZ, ERF1, WRKY33, TGA. In addition, four of these genes were closely related to jasmonic acid signaling pathway.

Conclusions
The immune response mechanism of fungal disease in G. elata f. glauca is a complex biological process, involving plant hormones such as ethylene, jasmonic acid, salicylic acid and disease-resistant transcription factors such as WRKY, TGA.
Mild hypercapnia improves brain tissue oxygen tension but not diffusion limitation in asphyxial cardiac arrest: an experimental study in pigs
Authors: Zhou Dawei , Li Zhimin , Zhang Shaolan , Wu Lei , Li Yiyuan , Shi Guangzhi , Zhou Jianxin 
Published: September 2020

Abstract
Background
We sought to evaluate the effect of mild hypercapnia on brain tissue oxygen tension (Pbto2) and diffusion limitation (impaired ability of oxygen extraction) in a porcine post asphyxial cardiac arrest model.

Methods
In 16 Bama pigs, asphyxial cardiac arrest was induced by endotracheal tube clamping and remained untreated for another 4 min. After return of spontaneous circulation (ROSC), animals were randomly assigned to mild hypercapnia (end-tidal carbon dioxide (EtCO2): 45 ~ 50 mmHg) and normocapnia (EtCO2: 35 ~ 40 mmHg) groups for 12 h. Intracranial pressure (ICP), Pbto2, and brain tissue temperature were invasively measured by multimodality monitors. Blood gas analysis, neuron specific enolase (NSE), and S100β were tested at baseline, ROSC 1 h, 6 h, and 12 h. Generalized mixed model with a compound symmetry covariance matrix was used to compare the time-variables of the two groups.

Results
Twelve (75%) pigs had ROSC and 11 pigs survived for the study period, with 6 pigs in mild hypercapnia group and 5 in the normocapnia group. The mean EtCO2 in the mild hypercapnia was significantly higher than normocapnia group (48 vs 38 mmHg, p <  0.001). Compared with normocapnia, mild hypercapnia group had higher Pbto2 (p <  0.001), slightly higher mean arterial pressure (p = 0.012) and ICP (p = 0.009). There were no differences in cerebral perfusion pressure (p = 0.106), gradient of partial pressure of jugular venous bulb oxygen (Pjvo2) and Pbto2 (p = 0.262), difference of partial pressure of jugular venous CO2 and arterial CO2 (p = 0.546), cardiac output (p = 0.712), NSE (p = 0.822), and S100β (p = 0.759) between the two groups.

Conclusions
Short term mild hypercapnia post-resuscitation could improve Pbto2. However, no corresponding improvements in the gradient of Pjvo2 to Pbto2 and biomarkers of neurological recovery were observed in the porcine asphyxial cardiac arrest model.