bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptic genetic structure and copy‐number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum
Authors: Dauphin Benjamin , de Freitas Pereira Maíra , Kohler Annegret , Grigoriev Igor V. , Barry Kerrie , Na Hyunsoo , Amirebrahimi Mojgan , Lipzen Anna , Martin Francis , Peter Martina , Croll Daniel 
Published: September 2021

SummaryEctomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho‐species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore‐forming structures but with a massively enlarged genome. We carried out whole‐genome sequencing to identify single‐nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy‐number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome‐wide structural variation, lineage‐specific recombination and low continent‐wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra‐specific functional variation in this major symbiosis.
Bacterial community dynamics on bats and the implications for pathogen resistance
Authors: Li Aoqiang , Li Zhongle , Dai Wentao , Parise Katy L. , Leng Haixia , Jin Longru , Liu Sen , Sun Keping , Hoyt Joseph R. , Feng Jiang 
Published: September 2021

SummaryThe bats skin microbiota plays an important role in reducing pathogen infection, including the deadly fungal pathogen Pseudogymnoascus destructans, the causative agent of white‐nose syndrome. However, the dynamic of skin bacterial communities response to environmental perturbations remains poorly described. We characterized skin bacterial community over time and space in Rhinolophus ferrumequinum, a species with high resistance to the infection with P. destructans. We collected environmental covariate data to determine what factors influenced changes in community structure. We observed significant temporal and spatial shifts in the skin bacterial community, which was mainly associated with variation in operational taxonomic units. The skin bacterial community differed by the environmental microbial reservoirs and was most influenced by host body condition, bat roosting temperature and geographic distance between sites, but was not influenced by pathogen infection. Furthermore, the skin microbiota was enriched in particular taxa with antifungal abilities, such as Enterococcus, Burkholderia, Flavobacterium, Pseudomonas, Corynebacterium and Rhodococcus. And specific strains of Pseudomonas, Corynebacterium and Rhodococcus even inhibited P. destructans growth. Our findings provide new insights in characterizing the variation in bacterial communities can inform us about the processes of driving community assembly and predict the host's ability to resist or survive pathogen infection.
Seasonal variation in emergency surgical conditions
Authors: Lee Martin Siu‐chung , So Owen Chun‐hin , Wong Kevin KF , Leung Siu‐kee 
Published: September 2021

AbstractAimSeasonality has been shown to affect incidence of emergency surgical conditions in the West. There is yet no local data to suggest the causal relationship between seasonality and emergency surgical conditions. We aim to investigate on the effects of seasonal variation on common general surgical conditions for (i) ruptured abdominal aortic aneurysm, (ii) perforated peptic ulcer disease, (iii) ischaemic bowel, and (iv) acute cholecystitis in the New Territory West Cluster (NTWC).MethodThe present study was a retrospective study of 7653 patients who underwent emergency operations from 1 July 2008 to 30 June 2018 in the NTWC. Seasonality was defined according to the Chinese lunar calendar. Seasonal variation in the aforementioned surgical conditions were studied by emergency operations performed and recorded by the cluster's Surgical Outcomes Monitoring and Improvement Programme (SOMIP) data. The primary outcome is to analyse the presence of overall seasonal variation across the four seasons for each surgical condition by the goodness of fit test. The secondary outcome is to analyse the relationship of each season (Spring, Summer, Fall, Winter) and extreme weather condition, in this study, the cold weather warning signal, on the surgical conditions by the 2 × 2 Chi‐square test.ResultsFor primary outcome, statistically significant variation exists in all general surgical conditions except ischaemic bowel across the four seasons. For secondary outcomes, statistically significant relationships exist between each season and different surgical conditions. Moreover, cold weather warning has a statistically significant relationship with emergent surgeries for perforated peptic ulcer disease and ruptured abdominal aortic aneurysm.ConclusionThere is seasonal variation in emergency surgical conditions.
The impact and restoration of colorectal services during the coronavirus disease 2019 pandemic: A view from Oxford
Authors: Yeung Trevor , Merchant Julia , Chen Patrick , Smart Corinne , Ghafoor Hamira , Woodhouse Fran , James David , Symons Nicholas , Boyce Stephen , Jones Oliver , George Bruce , Lindsey Ian 
Published: September 2021

AbstractAimThe coronavirus pandemic has significantly disrupted the way we deliver healthcare worldwide. We have been flexible and creative in order to continue providing elective colorectal cancer operations and to restart services for benign cases during the recovery period of the pandemic. In this paper, we describe the impact of coronavirus on our elective services and how we have implemented new patient pathways to allow us to continue providing patient care.Patients and MethodsData on major colorectal elective resections were prospectively collected in an Enhanced Recovery After Surgery (ERAS) database. Data on the number of proctology cases and telemed appointments were collected from the hospital theatre information management system and electronic patient record system, respectively.ResultsDuring the pandemic, there was a complete shift towards cancer cases, with benign services and proctology cases being placed on hold. Hospital length of stay was reduced. We implemented earlier hospital discharge and more intense telephone follow‐up after elective major surgery. This has not resulted in an increase in postoperative complications, nor any increase in readmission to hospital. During the recovery phase, we have introduced a higher proportion of telemed consultations, including one‐stop telemed proctology clinics, resulting in straight to tests or investigations.ConclusionWe have created a streamlined multidisciplinary pathway to reinstate our elective colorectal services as soon as possible and to minimise potential harm caused to patients whose treatment have been delayed. We anticipate many of these changes will be permanently incorporated into our clinical practice once the pandemic is over.
Liver injury during hepatectomy
Authors: Fan Sheung‐tat 
Published: September 2021

AbstractDuring hepatectomy the liver may sustain various forms of injury due to inflow occlusion, congestion, raised intraductal pressure from bile duct obstruction, choledochoscopy and electrohydraulic lithotripsy, and portal hyperperfusion related to small liver remnant. This review elaborates the possible mechanism of liver injury during hepatectomy and their prevention.
Trauma‐focused psychotherapies for post‐traumatic stress disorder: A systematic review and network meta‐analysis
Authors: Jericho Brooke , Luo Aileen , Berle David 
Published: September 2021

AbstractIntroductionMeta‐analytic reviews suggest similar outcomes across trauma‐focused psychotherapies for adults with post‐traumatic stress disorder (PTSD). However, this conclusion may be premature due to suboptimal statistical‐review methodologies. Network meta‐analysis (NMA) allows a detailed rank‐ordering of the efficacy of established psychotherapy interventions derived from indirect evidence as well as results from direct head‐to‐head comparisons.ObjectiveWe sought to determine the efficacy and attrition rates of psychotherapy interventions for PTSD by applying NMA.MethodsWe searched EMBASE, PsychINFO, PTSDPubs and PubMed for randomised controlled trials that compared psychotherapies either head‐to‐head or against controls for adults with PTSD. A frequentist NMA was used to compare direct and indirect effects to determine the efficacy and attrition rates of psychotherapy interventions.ResultsOf the 5649 papers identified, 82 trials comprising of 5838 patients were included. The network comprised 17 psychotherapies and four control conditions. Network estimates indicated superior efficacy of meta‐cognitive therapy and cognitive processing therapy over other psychotherapies (ESs between = 0.26 and 2.32). Written exposure therapy and narrative exposure therapy were associated with lower risk of drop out when considered alongside other psychotherapies. Confidence in the network meta‐analytic estimates was considered moderate for both outcomes.ConclusionsIn broad terms, therapeutic commensurability was evident. Nevertheless, with additional studies and larger sample sizes, meta‐cognitive and written exposure therapies could indeed differentiate themselves from other approaches as having favourable efficacy and acceptability respectively. These findings may inform clinical decision‐making, as well as guide future research for PTSD.
Are market mechanisms associated with alcohol and other drug treatment outcomes?
Authors: Ritter Alison , van de Ven Katinka , Vuong Thu , Chalmers Jenny , Dobbins Timothy , Livingston Michael , Berends Lynda 
Published: September 2021

AbstractBackground and AimsThe configuration of alcohol and other drug treatment service systems has been influenced by the uptake of market mechanisms for treatment funding and purchasing. This study measured the impact of market mechanisms for funding and purchasing alcohol and drug treatment services on client outcomes.DesignAn observational cross‐sectional study, employing multi‐level analysis: episodes of care data, nested within person‐level data, nested within treatment site and nested within organization.Setting and participantsOne hundred and seventy‐eight alcohol and other drug treatment service sites in Australia.MeasurementsClient outcome variables were length of stay and successful treatment completion. Predictor variables were competitive tendering, number of funding contracts, recurrent funding, the ratio of episodes to staff, type of professions, years of clinical experience, staff turnover and type of provider (government; non‐government). Analyses controlled for drug type, type of treatment received and client characteristics.FindingsThere were no significant associations between the procurement and contracting variables and length of stay [incidence rate ratios (IRRs) ranged between 1.01 and 1.07, all P > 0.05; Bayes factors (BF) < 0.03], and inconclusive results for treatment completion [odds ratios (ORs) ranged between 1.04 and 1.15, all P > 0.05, BF = 0.51–0.63]. Having an alcohol and other drug (AOD) work‐force relative to an ‘other’ work‐force (IRR = 0.79, P = 0.021) and lower case‐loads (IRR = 0.99, P = 0.047) may be associated with longer stay in treatment. Receiving services from a government compared to non‐government provider may also be associated with less treatment completion (OR = 0.34, P = 0.023, BF = 2.14).ConclusionsThere appears to be no association between client outcomes and procurement and funding contract arrangements for alcohol and drug treatment services.
Opioid use disorder and its association with self‐reported difficulties participating in social activities
Authors: Ashrafioun Lisham , Allan Nicholas P. , Stecker Tracy A. 
Published: September 2021

AbstractBackground and ObjectivesDifficulties participating in social activities are associated with increased mortality and are underemphasized in addressing the opioid epidemic. This study assessed the association of difficulties participating in social activities and opioid use disorder (OUD) and suicidal ideation and suicide attempts and difficulties participating in social activities among individuals with OUD.MethodsData on OUD, difficulties participating in social activities, suicidal ideation, suicide attempts, and other characteristics were assessed in 398,962 respondents from the 2008–2017 National Survey of Drug Use and Health. Logistic regressions examined the association of difficulties participating in social activities and OUD, and then among only respondents with OUD, difficulties participating in social activities and suicidal ideation and suicide attempts.ResultsRespondents with OUD reported higher levels of difficulties participating in social activities compared with respondents without OUD (severe difficulties: odds ratio [OR] = 4.10, 95% confidence interval [CI] = 3.40–4.93). Among those with OUD, difficulties participating in social activities were associated with suicidal ideation (severe difficulties: OR = 2.45, 95% CI = 1.77–3.38), but not attempts.Conclusion and Scientific SignificanceThe findings indicate that people with OUD experience difficulties participating in social activities and these difficulties are associated with suicidal ideation. It may be important to address difficulties participating in social activities within the context of OUD treatment, potentially as it relates to suicide prevention. This is the first study utilizing 10 years of nationally representative data to assess difficulties participating in social activities, OUD, and suicidal ideation and suicide attempts. Difficulties participating in social activities represent an under‐addressed, potentially important therapeutic target to address OUD.
Trajectories of asthma and allergy symptoms from childhood to adulthood
Authors: Forster Felix , Ege Markus Johannes , Gerlich Jessica , Weinmann Tobias , Kreißl Sylvia , Weinmayr Gudrun , Genuneit Jon , Nowak Dennis , von Mutius Erika , Vogelberg Christian , Radon Katja 
Published: September 2021

AbstractBackgroundPhenotypes of asthma and allergic diseases are mainly studied separately for children and adults. To explore the role of adolescence and young adulthood, we investigated symptom trajectories at the transition from childhood into adulthood.MethodsLatent class analysis (LCA) was conducted in a population initially recruited for the German arm of Phase II of the International Study of Asthma and Allergies in Childhood and followed‐up three times until their early 30s (N=2267). Indicators included in LCA were 12‐month prevalences of symptoms of wheeze, rhinoconjunctivitis, and eczema. Latent classes were further characterised regarding important traits such as skin prick tests. Logistic regression models were used to investigate associations with environmental determinants such as smoking and occupational exposures.ResultsSix latent classes were identified: an asymptomatic one as well as three with single and two with co‐occurring symptoms. All trajectories essentially established between baseline assessment at around 10 years and the first follow‐up at around 17 years. Probabilities for symptoms increased from childhood to adolescence, especially for wheeze‐related latent classes, while they remained constant in adulthood. Wheeze‐related latent classes were also positively associated with exposures during adolescence (e.g. active smoking).ConclusionDistinct trajectories of asthma and allergy symptoms establish from childhood through adolescence and stabilize during early adulthood. This pattern was most notable in wheeze‐related latent classes which also showed the strongest positive associations with environmental exposures in adolescence/young adulthood. Therefore, not only childhood but also adolescence is relevant for disease development and offers considerable potential for prevention and health promotion.
Perinatal outcome after selective termination in dichorionic twins discordant for congenital anomalies
Authors: Bennasar Mar , Ponce Júlia , Torres Ximena , Gómez Olga , Sabrià Joan , Gratacós Eduard , Borrell Antoni , Martínez Josep M. 
Published: September 2021

AbstractIntroductionOur objective was to evaluate the perinatal outcome of selective termination of dichorionic twin pregnancies with discordant anomalies, according to gestational age at time of procedure.Material and methodsRetrospective review of 147 dichorionic twin pregnancies referred to our Fetal Medicine Unit between 2003 and 2018 for selective termination. Gestational age at delivery, fetal loss, and overall and 28‐day post‐delivery survival rates, were evaluated according to gestational age at time of procedure. Selective termination procedure was defined as early, intermediate, and late when performed before 18 weeks, between 18 and 23 weeks, and after 23 weeks, respectively. Kruskal–Wallis and chi‐squared test were used to compare groups.ResultsOverall survival at 28 days post‐delivery, pregnancy loss, and preterm delivery before 32 weeks of gestation rates were 93.4%, 6.9%, and 15.5%, respectively. When stratified by gestational age at procedure, intermediate selective termination was associated with a lower survival rate than early and late procedures (86% vs. 96.9% and 100%, respectively; p = 0.035), and a nonsignificant trend for higher pregnancy loss (12% vs. 3.1%). Preterm delivery before 32 weeks of gestation occurred in 27% of late procedures, which was significantly higher than in early (9.5%) and intermediate (18.2%) procedures.ConclusionsSelective termination in dichorionic twin pregnancies with discordant fetal anomaly is associated with low pregnancy loss and preterm delivery rate, primarily when performed before 18 weeks. When legally possible, late procedures can be a good alternative, particularly in those cases diagnosed beyond the 18th week of gestation.
Intestinal chemosensitivity in irritable bowel syndrome associates with small intestinal TRPV channel expression
Authors: Grover Madhusudan , Berumen Antonio , Peters Stephanie , Wei Ting , Breen‐Lyles Margaret , Harmsen William S. , Busciglio Irene , Burton Duane , Vazquez Roque Maria , DeVault Kenneth R. , Camilleri Michael , Wallace Michael , Dasari Surendra , Neumann Helmut , Houghton Lesley A. 
Published: September 2021

SummaryBackgroundIrritable bowel syndrome (IBS) patients often experience meal‐associated symptoms. However, the underlying mechanisms are unclear.AimTo determine small intestinal mechanisms of lipid‐induced symptoms and rectal hypersensitivity in IBSMethodsWe recruited 26 IBS patients (12 IBS‐C, 14 IBS‐D) and 15 healthy volunteers (HV). In vivo permeability was assessed using saccharide excretion assay. Rectal sensitivity was assessed using a barostat before and after small bowel lipid infusion; symptoms were assessed throughout. Next, an extended upper endoscopy with probe‐based confocal laser endomicroscopy (pCLE) was performed with changes induced by lipids. Duodenal and jejunal mucosal biopsies were obtained for transcriptomics.ResultsFollowing lipid infusion, a higher proportion of HV than IBS patients reported no pain, no nausea, no fullness and no urgency (P < 0.05 for all). In a model adjusted for sex and anxiety, IBS‐C and IBS‐D patients had lower thresholds for first rectal sensation (P = 0.0007) and pain (P = 0.004) than HV. In vivo small intestinal permeability and mean pCLE scores were similar between IBS patients and HV. Post‐lipid, pCLE scores were higher than pre‐lipid but were not different between groups. Baseline duodenal transient receptor potential vanilloid (TRPV) 1 and 3 expression was increased in IBS‐D, and TRPV3 in IBS‐C. Duodenal TRPV1 expression correlated with abdominal pain (r = 0.51, FDR = 0.01), and inversely with first rectal sensation (r = −0.48, FDR = 0.01) and pain (r = −0.41, FDR = 0.02) thresholds.ConclusionLipid infusion elicits a greater symptom response in IBS patients than HV, which is associated with small intestinal expression of TRPV channels. TRPV‐mediated small intestinal chemosensitivity may mediate post‐meal symptoms in IBS.
Estimating body weight of pigs from posture analysis using a depth camera
Authors: Okayama Tsuyoshi , Kubota Yoshifumi , Toyoda Atsushi , Kohari Daisuke , Noguchi Go 
Published: September 2021

AbstractA noninvasive method for estimating the body weight (BW) of a pig considering its posture using a low‐cost depth camera (Kinect v2) was proposed. A total of 150 pigs were used, and 738 depth images (point clouds) were obtained for them. The pig “volume” was calculated from the pig point cloud, and it was found to have a very high correlation to BW. To evaluate the posture of a pig quantitatively, seven posture angles were calculated based on the “spine” extracted from a pig point cloud. We found the posture angles representing the height of the head position correlated with the accuracy of BW estimation using the “volume.” Based on this finding, we proposed an “adjusted volume,” which was adjusted based on the relationship between the posture angles and the estimation error. The BW of pigs was estimated using the simple regression model with the “adjusted volume,” and the MAPE and RMSPE were 4.87% and 6.13%, respectively. The accuracy of the suggested model was similar to that of the volume‐based estimation models of other studies that used only data with an appropriate pig posture for BW estimation.
Flow adhesion of whole blood to P‐selectin: a prognostic biomarker for vaso‐occlusive crisis in sickle cell disease
Authors: Hines Patrick C. , Callaghan Michael U. , Zaidi Ahmar U. , Gao Xiufeng , Liu Ke , White Jennell , Tarasev Michael 
Published: September 2021

SummaryBlood cell adhesion to P‐selectin and vascular cell adhesion molecule‐1 (VCAM‐1) contributes to the pathophysiology of vaso‐occlusion crisis (VOC) events in individuals with sickle cell disease (SCD). We evaluated the use of standardized flow adhesion biomarkers in a six‐month, 35‐subjects longitudinal study (ELIPSIS). Flow adhesion of whole blood on P‐selectin (FA‐WB‐Psel) and VCAM1 (FA‐WB‐VCAM), and of isolated white blood cells on P‐selectin (FA‐WBC‐Psel) and VCAM‐1 (FA‐WBC‐VCAM) were elevated on VOC days compared with non‐VOC days, but only FA‐WB‐Psel reached statistical significance (P = 0·015). Optimal cut‐off values were established with Cox regression models for FA‐WB‐Psel [46 cells/mm²; hazard ratio (HR): 2·3; 95% confidence interval (CI):1·4–4·0; P = 0·01] and FA‐WB‐VCAM (408 cells/mm², HR:1·8; 95% CI: 0·9–3·45; P = 0·01). A combined (FA‐WB‐Psel and FA‐WB‐VCAM) multimarker risk score was also significantly (P = 0·0006) correlated with VOC risk that was two‐fold higher for intermediate and 5·64‐fold higher for high score. The concordance (C)‐index for the multimarker score was 0·63 in the six‐month period (95% CI: 0·56–0·70), indicating a better ability to distinguish patient risk of VOC, compared to individual biomarkers FA‐WB‐VCAM (C‐index: 0·57; 95% CI: 0·49–0·65) or FA‐WB‐Psel (C‐index: 0·58; 95% CI: 0·53–0·62). The presented multimarker score can be used to risk‐stratify individuals with SCD during their steady state into low, intermediate, and high‐risk strata for self‐reported VOCs. Such risk stratification could help focus healthcare resources more efficiently to maintiain health, personalize treatment selection to each patient’s individual needs, and potentially reduce healthcare costs.