bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Simplified Comorbidity Index: a new tool for prediction of nonrelapse mortality in allo-HCT
Authors: Shouval Roni , Fein Joshua A. , Cho Christina , Avecilla Scott T. , Ruiz Josel , Tomas Ana Alarcon , Sanchez-Escamilla Miriam , Flores Nerea Castillo , Yáñez Lucrecia , Barker Juliet N. , Dahi Parastoo , Giralt Sergio A. , Geyer Alexander I. , Gyurkocza Boglarka , Jakubowski Ann A. , Lin Richard J. , O’Reilly Richard J. , Papadopoulos Esperanza B. , Politikos Ioannis , Ponce Doris M. , Sauter Craig S. , Scordo Michael , Shaffer Brian , Shah Gunjan L. , Sullivan James P. , Tamari Roni , van den Brink Marcel R. M. , Young James W. , Nagler Arnon , Devlin Sean , Shimoni Avichai , Perales Miguel-Angel 
Published: September 2021

Abstract
Individual comorbidities have distinct contributions to nonrelapse mortality (NRM) following allogeneic hematopoietic cell transplantation (allo-HCT). We studied the impact of comorbidities individually and in combination in a single-center cohort of 573 adult patients who underwent CD34-selected allo-HCT following myeloablative conditioning. Pulmonary disease, moderate to severe hepatic comorbidity, cardiac disease of any type, and renal dysfunction were associated with increased NRM in multivariable Cox regression models. A Simplified Comorbidity Index (SCI) composed of the 4 comorbidities predictive of NRM, as well as age &gt;60 years, stratified patients into 5 groups with a stepwise increase in NRM. NRM rates ranged from 11.4% to 49.9% by stratum, with adjusted hazard ratios of 1.84, 2.59, 3.57, and 5.38. The SCI was also applicable in an external cohort of 230 patients who underwent allo-HCT with unmanipulated grafts following intermediate-intensity conditioning. The area under the receiver operating characteristic curve (AUC) of the SCI for 1-year NRM was 70.3 and 72.0 over the development and external-validation cohorts, respectively; corresponding AUCs of the Hematopoietic Cell Transplantation–specific Comorbidity Index (HCT-CI) were 61.7 and 65.7. In summary, a small set of comorbidities, aggregated into the SCI, is highly predictive of NRM. The new index stratifies patients into distinct risk groups, was validated in an external cohort, and provides higher discrimination than does the HCT-CI.
Plasma and rhADAMTS13 reduce trauma-induced organ failure by restoring the ADAMTS13-VWF axis
Authors: Kleinveld Derek J. B. , Simons Derek D. G. , Dekimpe Charlotte , Deconinck Shannen J. , Sloos Pieter H. , Maas M. Adrie W. , Kers Jesper , Muia Joshua , Brohi Karim , Voorberg Jan , Vanhoorelbeke Karen , Hollmann Markus W. , Juffermans Nicole P. ,   on behalf of BloodNet
Published: September 2021

Abstract
Trauma-induced organ failure is characterized by endothelial dysfunction. The aim of this study was to investigate the role of von Willebrand factor (VWF) and its cleaving enzyme, ADAMTS13 (a disintegrin and metalloproteinase with thrombospondin type 1 motifs, member 13) in the occurrence of endothelial permeability and organ failure in trauma. In an observational study in a level-1 trauma center, 169 adult trauma patients with clinical signs of shock and/or severe injuries were included. Trauma was associated with low ADAMTS13 and high VWF antigen levels, thus generating an imbalance of ADAMTS13 to VWF. Patients who developed organ failure (23%) had greater ADAMTS13-to-VWF imbalances, persistently lower platelet counts, and elevated levels of high-molecular-weight VWF multimers compared with those without organ failure, suggesting microthrombi formation. To investigate the effect of replenishing low ADAMTS13 levels on endothelial permeability and organ failure using either recombinant human ADAMTS13 (rhADAMTS13) or plasma transfusion, a rat model of trauma-induced shock and transfusion was used. Rats in traumatic hemorrhagic shock were randomized to receive crystalloids, crystalloids supplemented with rhADAMTS13, or plasma transfusion. A 70-kDa fluorescein isothiocyanate–labeled dextran was injected to determine endothelial leakage. Additionally, organs were histologically assessed. Both plasma transfusion and rhADAMTS13 were associated with a reduction in pulmonary endothelial permeability and organ injury when compared with resuscitation with crystalloids, but only rhADAMTS13 resulted in significant improvement of a trauma-induced decline in ADAMTS13 levels. We conclude that rhADAMTS13 and plasma transfusion can reduce organ failure following trauma. These findings implicate the ADAMTS13-VWF axis in the pathogenesis of organ failure.
A near complete genome for goat genetic and genomic research
Authors: Li Ran , Yang Peng , Dai Xuelei , Asadollahpour Nanaei Hojjat , Fang Wenwen , Yang Zhirui , Cai Yudong , Zheng Zhuqing , Wang Xihong , Jiang Yu 
Published: September 2021

Abstract
Background
Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds.

Results
Here, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip.

Conclusions
The updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.
Cardiac evaluation in adults with dengue virus infection by serial echocardiography
Authors: Mansanguan Chayasin , Hanboonkunupakarn Borimas , Muangnoicharoen Sant , Huntrup Arun , Poolcharoen Akkapon , Mansanguan Suyanee , Piyaphanee Watcharapong , Phumratanaprapin Weerapong 
Published: September 2021

Abstract
Background
Dengue virus infection (DVI) is a major health problem in many parts of the world. Its manifestations range from asymptomatic infections to severe disease. Although cardiac involvement has been reported in DVI, its incidence has not yet been well established.

Methods
From July 2016 to January 2018, patients hospitalized at the Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Thailand, with dengue virus infection confirmed by positive NS1 or positive dengue immunoglobulin M findings, participated in the study. We characterized the incidence and change in cardiac function by serial echocardiography and levels of troponin-T and creatine kinase-myocardial band (CK-MB) on the day of admission, the day of defervescence, the first day of hypotension (if any), and at 2 week follow-up.

Results
Of the 81 patients evaluated, 6 (7.41%) exhibited elevated biomarker levels. There was no difference in clinical presentation amongst dengue fever, dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS), except for the amount of bleeding. Cardiac involvement was found in 22.2% of patients: 3 (3.70%) had left ventricular systolic dysfunction, 3 (3.70%) had transient diastolic dysfunction, 6 (7.41%) had increased levels of at least one cardiac biomarker (troponin-T or CK-MB), and 6 (7.41%) had small pericardial effusion. Myocarditis was suspected in only two patients (with DHF); thus, myocarditis was uncommon in patients with dengue virus infection. Three patients developed DSS during admission and were transferred to the intensive care unit.

Conclusion
Cardiac involvement in adults with dengue infection was common, ranging from elevated cardiac biomarker to myocarditis. Abnormalities in cardiac function had resolved spontaneously by the day of follow-up, without specific treatment. We found that DHF was a significant risk factor for cardiac involvement. Echocardiography is the investigation of choice for evaluating the haemodynamic status of patients with DVI, especially in severe dengue.
Effects of warm compress on tear film, blink pattern and Meibomian gland function in dry eyes after corneal refractive surgery
Authors: Zhou Xueyi , Shen Yang , Shang Jianmin , Zhou Xingtao 
Published: September 2021

Abstract
Background
To assess the effects of warm compress (WC) on tear film lipid layer, blink pattern and Meibomian gland function in patients with dry eye following femtosecond laser small incision lenticule extraction (SMILE) and laser-assisted subepithelial keratomileusis (LASEK).

Methods
We enrolled 37 eyes of 37 participants, each with dry eye for more than 2 years following SMILE (25 eyes) or LASEK (12 eyes). WC was performed using a spontaneously heating eye mask. Tear film break-up time (TBUT), tear film lipid layer thickness (TFLLT), blink pattern, Meibomian secretory function scores (MGS), visual acuity, spherical equivalent (SE), keratometry, central corneal thickness (CCT) and aberration were assessed before and after WC.

Results
After WC, the following mean values all increased relative to baselines: CCT, SE, minimum (Min-), maximum (Max-) and average (Ave-) TFLLT, TBUT, total MGS (TMGS), number of glands secreting any liquid (MGL), and complete blink rate (CBR) (p values ranging from < 0.001 to 0.042). Partial blink frequency (PBF) and partial blink rate (PBR) decreased (p = 0.002 in both cases). The decrease of PBF was higher in SMILE subgroup than in LASEK (p = 0.030). TBUT variation was positively correlated with that of Ave-TFLLT and TMGS (p = 0.046, 0.028, respectively). Max-TFLLT variation was correlated with that of TMGS (p = 0.020).

Conclusions
WC may temporarily increase tear film thickness and stability, decrease partial blink, and partly augment Meibomian gland function in dry eye patients after corneal refractive surgeries. Future studies are required to investigate long term clinical efficacy and safety.
Longitudinal relationships among problematic mobile phone use, bedtime procrastination, sleep quality and depressive symptoms in Chinese college students: a cross-lagged panel analysis
Authors: Cui Guanghui , Yin Yongtian , Li Shaojie , Chen Lei , Liu Xinyao , Tang Kaixuan , Li Yawen 
Published: September 2021

Abstract
Background
Cross-sectional and longitudinal studies have found that problematic mobile phone use, bedtime procrastination, sleep quality, and depressive symptoms are strongly associated. However, studies are inconsistent regarding whether problematic mobile phone use predicts depressive symptoms or vice versa, and sleep factors have been infrequently focused on in this regard. In addition, few studies have examined the longitudinal associations and directions of effects between these factors. Therefore, this study aims to explore the longitudinal relationship among problematic mobile phone use, bedtime procrastination, sleep quality, and depressive symptoms in college students.

Methods
Overall, 1181 college students completed questionnaires on problematic mobile phone use, bedtime procrastination, sleep quality, and depressive symptoms at two time points 12 months apart. A cross-lagged model was used to examine the longitudinal relationship between these factors.

Results
Cross-lagged analyses showed significant bidirectional relationships of problematic mobile phone use with bedtime procrastination and depressive symptoms. Additionally, there were also significant bidirectional relationships of sleep quality with bedtime procrastination and depressive symptoms. Problematic mobile phone use predicted subsequent sleep quality one-way, and bedtime procrastination predicted subsequent depressive symptoms one-way.

Conclusions
This study further expands our understanding of the longitudinal and bidirectional relationships among problematic mobile phone use, bedtime procrastination, sleep quality and depressive symptoms and helps school mental health educators design targeted interventions to reduce problematic mobile phone use, sleep problems, and depressive symptoms among college students.
Homelessness during COVID-19: challenges, responses, and lessons learned from homeless service providers in Tippecanoe County, Indiana
Authors: Rodriguez Natalia M. , Lahey Alexa M. , MacNeill Justin J. , Martinez Rebecca G. , Teo Nina E. , Ruiz Yumary 
Published: September 2021

Abstract
Background
The COVID-19 pandemic laid bare some of the United States’ most devastating health and social inequities faced by people experiencing homelessness. Homeless populations experience disproportionate rates of underlying health conditions, stigma and marginalization that often disenfranchise them from health and social services, and living conditions that potentiate the risk of COVID-19 transmission and adverse outcomes.

Methods
Guided by the socio-ecological model, this community-based participatory research study examined the impacts of the COVID-19 public health crisis on people experiencing homelessness in Tippecanoe County, Indiana, and the ways in which homeless service providers prepared for, experienced, and responded to the pandemic. Eighteen (18) semi-structured interviews were conducted with representatives of 15 community-based organizations, including shelters and other homeless service providers.

Results
Qualitative content analysis revealed myriad challenges at the individual and interpersonal levels faced by people experiencing homelessness as a result of the pandemic, and multilevel responses for COVID-19 impact mitigation in this community. Many of the emergency measures put in place by homeless service providers in Tippecanoe County, Indiana created opportunities for innovative solutions to longstanding challenges faced by homeless populations that are informing better service delivery moving forward, even beyond the COVID-19 pandemic.

Conclusions
Community-based organizations, including homeless shelters, are uniquely qualified to inform pandemic response and disaster risk mitigation in order to respond appropriately to the specific needs of people experiencing homelessness. The lessons learned and shared by homeless service providers on the frontline during the COVID-19 pandemic have important implications to improve future disaster response for homeless and other vulnerable populations.
Chronic cough caused by choledochoduodenal fistula: a case report
Authors: Cao Jiaofei , Hu Yue , Jin Shaojun , Chen Fei , Li Li , Huang Huaqiong 
Published: September 2021

Abstract
Background
Chronic cough is characterized by cough as the only or main symptom, with a duration of more than 8 weeks and no obvious abnormality in chest X-ray examination. Its etiology is complex, including respiratory disease, digestive system disease, circulation system disease, and psychological disease. Although a set of etiological diagnosis procedures for chronic cough have been established, it is still difficult to diagnose chronic cough and there are still some patients with misdiagnosis.

Case presentation
We present a case of a 54-year-old female patient who had chronic cough for 28 years. Physical examination had no positive signs and she denied any illness causing cough like tuberculosis, rhinitis. Recurrent clinic visits and symptomatic treatment didn’t improve the condition. Finally, gastroscopy identified the possible etiology of choledochoduodenal fistula that was proved by surgery. And after surgery, the patient's cough symptoms were significantly improved.

Conclusion
We report a rare case of chronic cough caused by choledochoduodenal fistula which demonstrates our as yet inadequate recognition of the etiology and pathogenesis. Written informed consent was obtained from the patient.
Knowledge of end-of-life wishes by physicians and family caregivers in cancer patients
Authors: Calvache Jose A , Moreno Socorro , Prue Gillian , Reid Joanne , Ahmedzai Sam H , Arango-Gutierrez Angelica , Ardila Liliana , Arroyo Lucia I , de Vries Esther 
Published: September 2021

Abstract
Objectives
To describe communication regarding cancer patient’s end-of-life (EoL) wishes by physicians and family caregivers.

Methods
An online questionnaire and telephone-based surveys were performed with physicians and family caregivers respectively in three teaching hospitals in Colombia which had been involved in the EoL care of cancer patients.

Results
For 138 deceased patients we obtained responses from physicians and family caregivers. In 32 % physicians reported they spoke to the caregiver and in 17 % with the patient regarding EoL decisions. In most cases lacking a conversation, physicians indicated the treatment option was “clearly the best for the patient” or that it was “not necessary to discuss treatment with the patient”.
Twenty-six percent of the caregivers indicated that someone from the medical team spoke with the patient about treatment, and in 67% who had a conversation, caregivers felt that the provided information was unclear or incomplete. Physicians and family caregivers were aware if the patient had any advance care directive in 6% and 26% of cases, respectively, with low absolute agreement (34%).

Conclusions
There is a lack of open conversation regarding EoL in patients with advanced cancer with their physicians and family caregivers in Colombia. Communication strategies are urgently needed.
Reproductive issues in carriers of germline pathogenic variants in the BRCA1/2 genes: an expert meeting
Authors: Buonomo Barbara , Massarotti Claudia , Dellino Miriam , Anserini Paola , Ferrari Alberta , Campanella Maria , Magnotti Mirosa , De Stefano Cristofaro , Peccatori Fedro Alessandro , Lambertini Matteo 
Published: September 2021

AbstractBackgroundHealthy individuals and patients with cancer who are carriers of germline pathogenic variants in theBRCA1/2genes face multiple reproductive challenges that require appropriate counseling and specific expertise.Main bodyOn December 5th–7th, 2019, patient advocates and physicians with expertise in the field of reproductive medicine, fertility preservation, and oncology were invited to “San Giuseppe Moscati” Hospital in Avellino (Italy) for a workshop on reproductive management of women with germline pathogenic variants in the BRCA1/2 genes. From the discussion regarding the current evidence and future prospective in the field, eight main research questions were formulated and eight recommendations were developed regarding fertility, fertility preservation, preimplantation genetic testing, and pregnancy in healthy carriers and patients with cancer.ConclusionSeveral misconceptions about the topic persist among health care providers and patients often resulting in a discontinuous and suboptimal management. With the aim to offer patient-tailored counseling about reproductive issues, both awareness of current evidences and research should be promoted.
Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data
Authors: Munday James D. , Jarvis Christopher I. , Gimma Amy , Wong Kerry L. M. , van Zandvoort Kevin ,   CMMID COVID-19 Working Group, Liu Yang , Hellewell Joel , Davies Nicholas G. , Villabona-Arenas C. Julian , Eggo Rosalind M. , Endo Akira , Bosse Nikos I. , Gibbs Hamish P. , Pearson Carl A. B. , Sun Fiona Yueqian , Jit Mark , O’Reilly Kathleen , Jafari Yalda , Atkins Katherine E. , Waterlow Naomi R. , Rosello Alicia , Chan Yung-Wai Desmond , Foss Anna M. , Quilty Billy J. , Russell Timothy W. , Flasche Stefan , Procter Simon R. , Waites William , Barnard Rosanna C. , Kucharski Adam J. , Jombart Thibaut , Medley Graham , Lowe Rachel , Krauer Fabienne , Tully Damien C. , Prem Kiesha , Lei Jiayao , Brady Oliver , Sandmann Frank G. , Meakin Sophie R. , Abbas Kaja , Knight Gwenan M. , Quaife Matthew , Koltai Mihaly , Abbott Sam , Clifford Samuel , Funk Sebastian , Edmunds W. John 
Published: September 2021

Abstract
Background
Schools were closed in England on 4 January 2021 as part of increased national restrictions to curb transmission of SARS-CoV-2. The UK government reopened schools on 8 March. Although there was evidence of lower individual-level transmission risk amongst children compared to adults, the combined effects of this with increased contact rates in school settings and the resulting impact on the overall transmission rate in the population were not clear.

Methods
We measured social contacts of > 5000 participants weekly from March 2020, including periods when schools were both open and closed, amongst other restrictions. We combined these data with estimates of the susceptibility and infectiousness of children compared with adults to estimate the impact of reopening schools on the reproduction number.

Results
Our analysis indicates that reopening all schools under the same measures as previous periods that combined lockdown with face-to-face schooling would be likely to increase the reproduction number substantially. Assuming a baseline of 0.8, we estimated a likely increase to between 1.0 and 1.5 with the reopening of all schools or to between 0.9 and 1.2 reopening primary or secondary schools alone.

Conclusion
Our results suggest that reopening schools would likely halt the fall in cases observed between January and March 2021 and would risk a return to rising infections, but these estimates relied heavily on the latest estimates or reproduction number and the validity of the susceptibility and infectiousness profiles we used at the time of reopening.