bluuebunny/crossref_metadata_2025_split huggingface dataset:
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat
Authors: Feng Kewei , Cui Licao , Wang Le , Shan Dai , Tong Wei , Deng Pingchuan , Yan Zhaogui , Wang Mengxing , Zhan Haoshuang , Wu Xiaotong , He Weiming , Zhou Xianqiang , Ji Jingjing , Zhang Guiping , Mao Long , Karafiátová Miroslava , Šimková Hana , Doležel Jaroslav , Du Xianghong , Zhao Shancen , Luo Ming‐Cheng , Han Dejun , Zhang Chi , Kang Zhensheng , Appels Rudi , Edwards David , Nie Xiaojun , Weining Song 
Published: August 2019

SummaryWheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication‐related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.
Beyond rest and quiescence (endodormancy and ecodormancy): A novel model for quantifying plant–environment interaction in bud dormancy release
Authors: Lundell Robin , Hänninen Heikki , Saarinen Timo , Åström Helena , Zhang Rui 
Published: August 2019

AbstractBud dormancy of plants has traditionally been explained either by physiological growth arresting conditions in the bud or by unfavourable environmental conditions, such as non‐growth‐promoting low air temperatures. This conceptual dichotomy has provided the framework also for developing process‐based plant phenology models. Here, we propose a novel model that in addition to covering the classical dichotomy as a special case also allows the quantification of an interaction of physiological and environmental factors. According to this plant–environment interaction suggested conceptually decades ago, rather than being unambiguous, the concept of “non‐growth‐promoting low air temperature” depends on the dormancy status of the plant. We parameterized the model with experimental results of growth onset for seven boreal plant species and found that based on the strength of the interaction, the species can be classified into three dormancy types, only one of which represents the traditional dichotomy. We also tested the model with four species in an independent experiment. Our study suggests that interaction of environmental and physiological factors may be involved in many such phenomena that have until now been considered simply as plant traits without any considerations of effects of the environmental factors.
Successful long‐term outcome after combined hematopoietic stem cell transplantation and small bowel transplantation: A case report and review of the literature
Authors: Na Sera , Saldana Blachy Davila , Peredo‐Pinto Helka , Gonzalez Corina Elena , Kroemer Alexander Helmut , Hawksworth Jason , Matsumoto Cal Satoshi , Yazigi Nada , Kaufman Stuart , Fishbein Thomas Marlon , Khan Khalid 
Published: August 2019

AbstractCombining HSCT with SOT is an unusual and challenging undertaking given the complexities of immune modulation, the need to balance comorbidities, and the cumulative potential for complications. Early life‐threatening complications include infections and related effects, graft rejection, and GVHD can be expected to be increased especially if the HSCT is indicated for high‐risk cases such as individuals with severe combined immune deficiency and SOT that includes an intestine graft. Herein, we report such a case. Our patient is unique as a long‐term survivor. We review the literature and the features of our case, especially the timing of transplants and human leukocyte antigen matching for HSCT that resulted in a successful outcome and discuss how this may be applied to others in the future.
Monitoring intra‐abdominal pressure after liver transplantation in children
Authors: Deindl Philipp , Wagner Jula , Herden Uta , Schulz‐Jürgensen Sebastian , Schild Raphael , Vettorazzi Eik , Bergers Marlies , Keck Maike , Singer Dominique , Fischer Lutz , Herrmann Jochen 
Published: August 2019

AbstractIAH after LTX can impair perfusion and threaten graft viability. This study aimed to assess the feasibility of longitudinal IAP measurements as an IAH screening method in children after LTX. A cohort of 23 children with a mean age (range) 3.1 (3 months–14 years) who underwent LTX between May 2017 and February 2018 were evaluated retrospectively. Longitudinal IAP measurements were compared to bedside Doppler US monitoring data. In total, 425 IAP measurements and 257 US examinations were performed. The mean ± SD (range) time expenditure for IAP measurement was 1.9 ± 0.4 (0.5‐3.2) minutes. The mean post‐operative IAP was 7.9 ± 3.6 (1‐25) mm Hg. IAH (IAP ≥ 10 mm Hg) was noted in 102 (24%) of 257 measurements. Agitation had a significant impact on IAP (estimate: 9.3 mm Hg, CI: 6.72‐11.97, P < .01). In patients with TAC, IAP was increased (6.7 ± 2.1 vs 8.7 ± 3.1 mm Hg, P = .02) while peak portal venous velocities decreased (38 ± 27 vs 26 ± 22 cm/s, P = .03) after patch reduction. An abdominal compartment syndrome with severely impaired vascular flow was noted in one patient. Episodes of elevated IAP were noted in a large proportion of patients, underscoring the need for IAP monitoring in pediatric liver transplant recipients. The safety and low time expenditure associated with IAP measurement could be included easily into standard nursing procedures for these patients.
Housing Allowance and Rents: Evidence from a Stepwise Subsidy Scheme*
Authors: Eerola Essi , Lyytikäinen Teemu 
Published: August 2019

AbstractIn this paper, we study the effect of housing demand subsidies on rents using discontinuities in the Finnish housing allowance system as a quasi‐experimental setting. The stepwise dependence of housing allowance on the floor area of the dwelling and on the year of construction of the building causes economically and statistically significant discontinuities in the amounts of housing allowances. However, our results show that there are no discontinuities in the rents paid by the recipients of housing allowance at these cut‐offs. Instead, differences in the amounts of housing allowance are translated roughly one‐to‐one into differences in the rent net of housing allowance.
The use of genome sequencing to investigate an outbreak of hospital‐acquired mucormycosis in transplant patients
Authors: Marek Caitlyn , Croxen Matthew A. , Dingle Tanis C. , Bharat Amrita , Schwartz Ilan S. , Wiens Rhoda , Smith Stephanie 
Published: August 2019

AbstractWe report three cases of hospital‐acquired mucormycosis in heart and lung transplant patients over a 6‐month period. Traditional epidemiological investigation tools were used to look for a common link between patients to explain the outbreak. Genome sequencing of each fungal strain was used to supplement the investigation. By disproving a close genetic link between infecting strains of mucormycosis, we were able to conclude the outbreak investigation. Genome sequencing is a novel tool that can be used in addition to traditional epidemiologic investigations to help determine linkage of patients during outbreak investigations.
Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae
Authors: Ma Mengxiao , Burd Christopher G. 
Published: August 2019

AbstractThe endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome‐to‐Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.
Cytosolic aggregates in presence of non‐translocated proteins perturb endoplasmic reticulum structure and dynamics
Authors: Mookherjee Debdatto , Majumder Priyanka , Mukherjee Rukmini , Chatterjee Debmita , Kaul Zenia , Das Subhrangshu , Sougrat Rachid , Chakrabarti Saikat , Chakrabarti Oishee 
Published: August 2019

AbstractPresence of cytosolic protein aggregates and membrane damage are two common attributes of neurodegenerative diseases. These aggregates delay degradation of non‐translocated protein precursors leading to their persistence and accumulation in the cytosol. Here, we find that cells with intracellular protein aggregates (of cytosolic prion protein or huntingtin) destabilize the endoplasmic reticulum (ER) morphology and dynamics when non‐translocated protein load is high. This affects trafficking of proteins out from the ER, relative distribution of the rough and smooth ER and three‐way junctions that are essential for the structural integrity of the membrane network. The changes in ER membranes may be due to high aggregation tendency of the ER structural proteins—reticulons, and altered distribution of those associated with the three‐way ER junctions—Lunapark. Reticulon4 is seen to be enriched in the aggregate fractions in presence of non‐translocated protein precursors. This could be mitigated by improving signal sequence efficiencies of the proteins targeted to the ER. These were observed using PrP variants and the seven‐pass transmembrane protein (CRFR1) with different signal sequences that led to diverse translocation efficiencies. This identifies a previously unappreciated consequence of cytosolic aggregates on non‐translocated precursor proteins—their persistent presence affects ER morphology and dynamics. This may be one of the ways in which cytosolic aggregates can affect endomembranes during neurodegenerative disease.
Central serous chorioretinopathy: risk factors for serous retinal detachment in fellow eyes
Authors: Shinojima Ari , Mehanna Chadi , Lavia Carlo Alessandro , Gaudric Alain , Tadayoni Ramin , Bousquet Elodie 
Published: August 2019

Background/AimsTo assess risk factors for serous retinal detachment (SRD) in the fellow eye of patients with central serous chorioretinopathy (CSC) based on clinical data and multimodal imaging findings, including baseline late-phase indocyanine green angiography (ICGA).MethodsConsecutive patients with unilateral CSC were retrospectively assessed. Inclusion criteria were the availability of late-phase ICGA and a spectral-domain optical coherence tomography (OCT) macular cube for both eyes at baseline and over 3 months. Subsequent OCT of fellow eyes was reviewed to detect the development of SRD during the follow-up. Baseline medical data and multimodal imaging findings were analysed using Kaplan-Meier survival curves (log-rank test).ResultsSixty-eight patients with unilateral CSC were included. An SRD was detected in 19% of fellow eyes during a mean follow-up of 25.8±18.7 months. Hyperfluorescent plaques on midphase ICGA, hypofluorescent foci on late-phase ICGA, retinal pigment epithelium changes on fundus autofluorescence and fluorescein angiography abnormalities were associated with the occurrence of SRD (log-rank test; p<0.001, p=0.02, p=0.002 and p=0.001, respectively).ConclusionThese results suggest that the fellow eyes with specific findings on multimodal imaging in patients with unilateral CSC should be carefully followed up for possible incidence of CSC.
Return to play after surgery for isolated unstable syndesmotic ankle injuries (West Point grade IIB and III) in 110 male professional football players: a retrospective cohort study
Authors: D'Hooghe Pieter , Grassi Alberto , Alkhelaifi Khalid , Calder James , Baltes Thomas PA , Zaffagnini Stefano , Ekstrand Jan 
Published: August 2019

ObjectivesTo evaluate time to return to play following surgical stabilisation of isolated unstable syndesmosis injuries in a cohort of professional male football players.MethodsAll professional football players undergoing surgery for isolated unstable syndesmosis injury (West Point grade ≥IIB) at a specialised Orthopaedic and Sports Medicine Hospital were followed up until return to play (minimum ≥6 months). Players with a stable syndesmosis, injuries older than 6 weeks, concomitant medial or lateral malleolar fracture or previous ankle surgery were excluded. During rehabilitation, time required to return to sports-specific rehabilitation, team training and first match play, were recorded.ResultsBetween January 2012 and December 2017, a total of 110 male professional football players were included. The mean time required to begin on field rehabilitation was 37±12 days, while the mean time to return to team training was 72±28 days. The first official match was played on average 103±28 days postoperatively. Multivariable analysis revealed that the severity of injury, the concomitant presence of talar cartilage injury and the age of the player were significantly associated (p<0.00001) with time to return to on field rehabilitation, team training and match play.ConclusionIn this cohort of professional football players, surgical stabilisation of isolated unstable syndesmosis injuries (West Point grade ≥IIB) allowed for relatively quick return to play. High grade injury (West Point grade III), concomitant cartilage injury and greater age were associated with longer return to play times.Level of evidenceLongitudinal observational cohort study (level II).
Lack of effects of evidence-based, individualised counselling on medication use in insured patients with mild hypertension in China: a randomised controlled trial
Authors: Di Mengyang , Mao Chen , Yang Zuyao , Ding Hong , Liu Qu , Liu Shuiming , Guo Hongbo , Jiang Kunhua , Tang Jinling 
Published: August 2019

ObjectiveTo evaluate whether evidence-based, individualised (EBI) counselling regarding hypertension and the treatment would affect medication use in insured patients with mild hypertension in China.MethodsWe conducted a parallel-group, randomised controlled trial in two primary care centres in Shenzhen, a metropolitan city in China. Patients with mild primary hypertension, 10-year risk of cardiovascular diseases (CVDs) lower than 20% and no history of CVDs were recruited and randomly allocated to two groups. EBI plus general counselling was provided to the intervention group and general counselling alone to the control group. EBI counselling included information on the 10-year CVD risk and treatment benefit in terms of absolute risk reduction estimated for each individual and information on average side effects and costs of antihypertensive drugs. The outcomes included use of antihypertensive drugs and adherence to the treatment at 6-month follow-up, with the former being primary outcome.ResultsTwo hundred and ten patients were recruited, with 103 and 107 allocated to the intervention and control groups, respectively. At baseline, 62.4% of the patients were taking antihypertensive drugs that were all covered by health insurance. At the end of 6-month follow-up, there was no statistically significant difference in the rate of medication use between the intervention group and the control group (65.0% vs 57.9%; OR=1.35, 95% CI: 0.77 to 2.36). The difference in adherence rate between the two groups was not statistically significant either (43.7% vs 40.2%; OR=1.15, 95% CI 0.67 to 2.00]). The results were robust in sensitivity analyses that used different cutoffs to define the two outcomes.ConclusionsThe EBI counselling by health educators other than the caring physicians had little impact on treatment choices and drug-taking behaviours in insured patients with mild primary hypertension in this study. It remains unclear whether EBI counselling would make a difference in uninsured patients, especially when conducted by the caring physicians.Trial registration numberChiCTR-TRC-14004169.
Tracking development assistance for reproductive, maternal, newborn, child and adolescent health in conflict-affected countries
Authors: Li Zhihui , Richter Linda , Lu Chunling 
Published: August 2019

BackgroundLittle is known about the patterns of development assistance (DA) for each component of reproductive, maternal, newborn, child and adolescent health (RMNCAH) in conflict-affected countries nor about the DA allocation in relation to the burden of disease.MethodsWe tracked DA to RMNCAH in general and to each of its four components: reproductive health (RH), maternal and newborn health (MNH), child health (CH) and adolescent health (AH), in 25 conflict-affected countries between 2003 and 2017. We compared DA and disability-adjusted life years (DALYs) for each component. Using keyword searching and funding allocation methods, we produced two sets of estimates: DA primarily targeting RMNCAH (lower bound) and DA both primarily and partially for RMNCAH or DA not explicitly targeting RMNCAH but benefiting it (upper bound).FindingsBetween 2003 and 2017, we identified 46 833 projects among the 25 countries that targeted RMNCAH. During the study period, DA to RMNCAH increased by seven-fold from $0.5 billion to $3.6 billion, with a slowdown since 2013. Cumulatively, RH received the largest proportion of DA to RMNCAH (50%) with 84% of its funding earmarked for HIV/AIDS, which contributed to less than 6% of the total RMNCAH-related DALYs. AH received 3% of the DA-RMNCAH but contributed 15% to the RMNCAH-related DALYs. Non-communicable diseases caused more than one-third of the DALYs among adolescents, but received only 3% of DA to AH. RMNCAH-inclusive estimates showed consistent results.ConclusionWhile there was a substantial increase in funding to RMNCAH in conflict-affected countries over the period of study, some health issues with high disease burden (eg, AH and non-communicable diseases) received a disproportionately small portion of aid for RMNCAH. We recommend that donors increase investment to RMNCAH in conflict-affected countries, particularly in areas where the burden of disease or the potential benefit of investment is likely to be high.
Comparison of different approaches to antibiotic restriction in food-producing animals: stratified results from a systematic review and meta-analysis
Authors: Tang Karen L , Caffrey Niamh P , Nóbrega Diego B , Cork Susan C , Ronksley Paul E , Barkema Herman W , Polachek Alicia J , Ganshorn Heather , Sharma Nishan , Kellner James D , Checkley Sylvia L , Ghali William A 
Published: August 2019

BackgroundWe have previously reported, in a systematic review of 181 studies, that restriction of antibiotic use in food-producing animals is associated with a reduction in antibiotic-resistant bacterial isolates. While informative, that report did not concretely specify whether different types of restriction are associated with differential effectiveness in reducing resistance. We undertook a sub-analysis of the systematic review to address this question.MethodsWe created a classification scheme of different approaches to antibiotic restriction: (1) complete restriction; (2) single antibiotic-class restriction; (3) single antibiotic restriction; (4) all non-therapeutic use restriction; (5) growth promoter and prophylaxis restriction; (6) growth promoter restriction and (7) other/undetermined. All studies in the original systematic review that were amenable to meta-analysis were included into this substudy and coded by intervention type. Meta-analyses were conducted using random effects models, stratified by intervention type.ResultsA total of 127 studies were included. The most frequently studied intervention type was complete restriction (n=51), followed by restriction of non-therapeutic (n=33) and growth promoter (n=19) indications. None examined growth promoter and prophylaxis restrictions together. Three and seven studies examined single antibiotic-class and single antibiotic restrictions, respectively; these two intervention types were not significantly associated with reductions in antibiotic resistance. Though complete restrictions were associated with a 15% reduction in antibiotic resistance, less prohibitive approaches also demonstrated reduction in antibiotic resistance of 9%–30%.ConclusionBroad interventions that restrict global antibiotic use appear to be more effective in reducing antibiotic resistance compared with restrictions that narrowly target one specific antibiotic or antibiotic class. Importantly, interventions that allow for therapeutic antibiotic use appear similarly effective compared with those that restrict all uses of antibiotics, suggesting that complete bans are not necessary. These findings directly inform the creation of specific policies to restrict antibiotic use in food-producing animals.