bluuebunny/crossref_metadata_2025_split huggingface dataset:
powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis
Authors: Dong Xianjun , Li Xiaoqi , Chang Tzuu-Wang , Weiss Scott T. , Qiu Weiliang 
Published: December 2020

AbstractSummaryGenome-wide association studies (GWAS) have revealed thousands of genetic loci for common diseases. One of the main challenges in the post-GWAS era is to understand the causality of the genetic variants. Expression quantitative trait locus (eQTL) analysis has been proven to be an effective way to address this question by examining the relationship between gene expression and genetic variation in a sufficiently powered cohort. However, it is often tricky to determine the sample size at which a variant with a specific allele frequency will be detected to associate with gene expression with sufficient power. This is particularly demanding with single-cell RNAseq studies. Therefore, a user-friendly tool to perform power analysis for eQTL at both bulk tissue and single-cell level will be critical. Here, we presented an R package called powerEQTL with flexible functions to calculate power, minimal sample size, or detectable minor allele frequency in both bulk tissue and single-cell eQTL analysis. A user-friendly, program-free web application is also provided, allowing customers to calculate and visualize the parameters interactively.Availability and implementationThe powerEQTL R package source code and online tutorial are freely available at CRAN:https://cran.r-project.org/web/packages/powerEQTL/. The R shiny application is publicly hosted athttps://bwhbioinfo.shinyapps.io/powerEQTL/.ContactXianjun Dong (xdong@rics.bwh.harvard.edu), Weiliang Qiu (weiliang.qiu@sanofi.com)Supplementary informationSupplementary data are available at Bioinformatics online.
On-demand food delivery: investigating the economic performances
Authors: Seghezzi Arianna , Mangiaracina Riccardo 
Published: December 2020

PurposeThis paper focusses on on-demand food delivery (ODFD), i.e. the delivery of freshly prepared meals to customers' homes, enabled by the use of online platforms. In ODFD, a key process is represented by last-mile deliveries (LMDs): they directly affect customers (the delivery price influences their purchase intention), riders (the compensation drives their willingness to perform deliveries) and platforms (deliveries are very expensive). In this context, this work aims to investigate the economic performances of ODFD LMDs.Design/methodology/approachThis study adopts a multi-method threefold process. First, it develops a model that – after the generation of customers' demand and the assignment of deliveries to available riders – identifies incomes and costs faced by an ODFD operator. Second, the model is applied to a base case in Milan (Italy). Third, sensitivity analyses are performed (on daily demand and riders' salary).FindingsThe analyses allow – besides the identification of significant values associated to ODFD profitability – to draw general insights about delivery price (e.g. free delivery is not economically sustainable), daily demand (e.g. greater demand values do not only improve positive results but also worsen negative ones) and fixed/variable wage mix (e.g. increasing the variable wage enhances the profitability for platforms).Originality/valueOn the academic side, this word enhances extant literature about ODFD, proposing a model – with multidisciplinary implications – to strategically investigate profitability conditions of LMDs. On the managerial side, it provides support for (logistics/marketing) ODFD practitioners since it allows to evaluate the potential impact of significant decisions on profitability.
Hemodialysis‐related headache: Still a challenge in 2020? Effect of conventional versus online hemodiafiltration from a study in Casablanca, Morocco
Authors: Hazim Asmaa , Adarmouch Latifa , Eloury Aida , Aasfara Jehanne , Asly Mouna , Slassi Ilham 
Published: December 2020

AbstractHemodialysis‐related headache (HRH) is a well‐known clinical event. It is considered as one of the most commonly reported neurological symptoms among hemodialysis patients. Its epidemiological, physiological, clinical, and therapeutic data remain scarce and are poorly studied. Our aim was to determine the frequency of HRH in the region of Casablanca, Morocco, to describe its clinical characteristics and to explore the hypothesis that renal replacement techniques, such as conventional versus online hemodiafiltration may have an association on clinical adverse effects like HRH. A descriptive, cross‐sectional, and multicentric study was carried out among 100 chronic hemodialysis patients for at least 6 months. HRH was defined according to criteria published by the International Classification of Headache Disorder third edition beta version (ICHD3β) [1]. Two different HD‐modalities (standard HD and OL‐HDF) have been investigated in order to explore their impact on HRH. Headache was reported by 60% of the patients including 41.6% of hemodialysis‐related headache. HRH had on average a duration of 7.4 hours, pulsatile among 38% of interviewed patients and of moderate intensity in 48% of cases. In total, 51.3% of patients undergoing conventional hemodialysis modality reported HRH compared to 12.5% undergoing online hemodiafiltration technique (OL‐HDF) (P = .008). Hemodialysis‐related headache remains a poorly studied clinical event despite its high prevalence. Its diagnosis, management, and especially its prevention remain a challenge for the neurologist and the nephrologist. Our results suggest that OL‐HDF is a promising therapeutic and preventive tool to reduce the incidence of HRH.
Evaluation of CorvisST biomechanical parameters and anterior segment optical coherence tomography for diagnosing forme fruste keratoconus
Authors: Shiga Suguru , Kojima Takashi , Nishida Tomoya , Nakamura Tomoaki , Ichikawa Kazuo 
Published: December 2020

AbstractPurposeTo investigate the utility of biomechanical property measurements using a Scheimpflug‐based tonometer (SBT) and/or anterior segment optical coherence tomography (AS‐OCT) for diagnosing forme fruste keratoconus (FFK).MethodsIn this retrospective interventional case series, 23 eyes with FFK of 23 consecutive patients and 52 eyes of 52 healthy volunteers who visited our keratoconus outpatient clinic were enrolled. Logistic regression analysis was conducted to determine the causal relationship between FFK diagnosis and each parameter.ResultsWhen only SBT was used, the corneal stiffness parameter, stiffness parameter A1 (SP‐A1) and the corneal velocity at first applanation were selected as explanatory variables, and sensitivity, specificity and area under the receiver operating characteristic curve (AUROC) were 82.9%, 86.9% and 0.938, respectively. When only AS‐OCT parameters were used, the posterior corneal asymmetric component and central corneal thickness were selected, and the sensitivity, specificity and AUROC were 82.6%, 94.2% and 0.893, respectively. When parameters from both methods were used, SP‐A1 and the posterior corneal asymmetry component derived from Fourier analysis were selected as explanatory variables, and sensitivity, specificity and AUROC were 91.30%, 90.38% and 0.947, respectively. No significant differences in AUROC were observed between diagnoses using each device and the combination of both devices (AS‐OCT versus SBT, p = 0.314; integrated parameters versus AS‐OCT, p = 0.081; integrated parameters versus SBT, p = 0.234).ConclusionOptimization of SBT and AS‐OCT parameters allowed for the diagnosis of FFK at a clinically usable level. Forme fruste keratoconus (FFK) diagnosis integrating biomechanical properties with AS‐OCT showed no superiority compared to diagnosis based on a single device.
Distribution of ocular biometry in young Chinese eyes: The Anyang University Students Eye Study
Authors: Sun Yunyun , Wei Shifei , Li Shiming , Cao Kai , Hu Jianping , Yang Xiaohui , Lin Caixia , An Wenzai , Guo Jiyuan , Li He , Fu Jing , Wang Ningli 
Published: December 2020

AbstractPurposeTo investigate the distribution of ocular biometric parameters and its association to refraction in university students in central China.MethodsOcular biometric parameters including axial length (AL), central corneal thickness (CCT), keratometry power (K), anterior chamber depth (AQD) and lens thickness (LT) were measured by an optical biometry in a cohort of university students. Corneal radius of curvature (CR), lens position (LP), lens power (PBennett), vitreous chamber depth (VCD) and AL to corneal radius ratio (AL/CR) were calculated. Cycloplegic refraction was measured using an autorefractor.ResultsA total of 7650 undergraduate students participated in this study, with a mean age of 20.0 ± 1.4 years. The following ocular biometric parameters were measured: AL (24.78 ± 1.21 mm), CCT (539.83 ± 33.03 μm), AQD (3.23 ± 0.25 mm), LT (3.47 ± 0.18 mm), CR (7.79 ± 0.27 mm), LP (4.97 ± 0.23 mm), VCD (17.55 ± 1.15 mm), PBennett (25.00 ± 1.07 dioptres) and AL/CR (3.18 ± 0.15). Male subjects were found to have longer AL, thicker CCT, flatter CR, thinner lens, deeper AQD and VCD than female ones. Myopic subjects were found to have longer AL, thinner CCT, steeper CR, thinner and posterior lens, deeper AQD and VCD, lower PBennett and larger AL/CR than emmetropes and hyperopes. Spherical equivalent (SE) showed a negative correlation with AL/CR (r = −0.914), AL (r = −0.755) and VCD (r = −0.751).ConclusionsThis study provided a range of reference values for the main ocular biometric parameters in young adults and reported their distributions based on gender and refractive status. Our study indicates that SE has a strong correlation with AL/CR ratio, AL and VCD.
Learning Part Generation and Assembly for Sketching Man‐Made Objects
Authors: Du Dong , Zhu Heming , Nie Yinyu , Han Xiaoguang , Cui Shuguang , Yu Yizhou , Liu Ligang 
Published: December 2020

AbstractModeling 3D objects on existing software usually requires a heavy amount of interactions, especially for users who lack basic knowledge of 3D geometry. Sketch‐based modeling is a solution to ease the modelling procedure and thus has been researched for decades. However, modelling a man‐made shape with complex structures remains challenging. Existing methods adopt advanced deep learning techniques to map holistic sketches to 3D shapes. They are still bottlenecked to deal with complicated topologies. In this paper, we decouple the task of sketch2shape into a part generation module and a part assembling module, where deep learning methods are leveraged for the implementation of both modules. By changing the focus from holistic shapes to individual parts, it eases the learning process of the shape generator and guarantees high‐quality outputs. With the learned automated part assembler, users only need a little manual tuning to obtain a desired layout. Extensive experiments and user studies demonstrate the usefulness of our proposed system.
Explaining the worldwide distributions of two highly mobile species: Cakile edentula and Cakile maritima
Authors: Shaw Elliot C. , Fowler Rachael , Ohadi Sara , Bayly Michael J. , Barrett Rosemary A. , Tibbits Josquin , Strand Allan , Willis Charles G. , Donohue Kathleen , Robeck Philipp , Cousens Roger D. 
Published: December 2020

AbstractAimIf we are able to determine the geographic origin of an invasion, as well as its known area of introduction, we can better appreciate the innate environmental tolerance of a species and the strength of selection for adaptation that colonizing populations have undergone. It also enables us to maximize the success of searches for effective biological control agents. We determined the number of successful colonization events that have occurred throughout the world for two Cakile species and compared the climates from which they originated, in which they established and then spread.LocationWorldwide.TaxonSea‐Rockets (Cakile spp.), Brassicaceae.MethodsWe used a high‐throughput sequencing and a genome skimming approach combined with Bayesian Inference phylogenetics to examine variation in entire chloroplast genomes and regions of nuclear ribosomal DNA within native and introduced areas. Databases were used to compare climates between native ranges and introduced regions for multiple clades within each species.ResultsAt least seven clades have invaded different regions of the world. In most cases we were able to identify their source regions and climates. The environmental bottlenecks differed in intensity: while some clades colonized into climates that were similar to climates in their native range, other clades had a very broad innate environmental tolerance such that new invasions succeeded beyond the climate range of native populations. We found clear evidence of hybridization—specifically, chloroplast capture—between two species in Australia.ConclusionsResults here show that these species are sometimes capable of colonizing in climates that are beyond the climate range of native populations. Whether successful colonization beyond native climate niches requires de novo adaptation, or whether it represents an innate broad fundamental niche requires further investigation. Cakile species provide an excellent opportunity to study replicated climate adaptation trajectories.
How Do Religion and Sexual Orientation Affect Support for U.S. Presidential Candidates? Evidence from a Survey Experiment
Authors: Beyerlein Kraig , Klocek Jason 
Published: December 2020

AbstractA growing body of research has examined how candidates’ religionorsexual orientation affect voting likelihood among the U.S. public. No systematic study, however, has focused on thecombinedeffect of these traits. We draw on the intersectionality literature to develop and test hypotheses for this neglected, but important, combination. Results from an original survey experiment conducted in late June 2019 demonstrate that all respondents, as well as the Republican subgroup, tend to disapprove of a gay, religious candidate relative to other options (i.e., gay, nonreligious; straight, religious; and straight, nonreligious). Even Democrats expressed little support except when a straight, religious candidate was the alternative. Our findings underscore the need to study how overlapping—rather than discrete—traits influence political views and behaviors. They also raise important questions about the future of U.S. identity politics. Efforts to rally Republican and Democrat voters by mixing particular types of traits may not be a very effective strategy.
Type IV secretion systems: Advances in structure, function, and activation
Authors: Costa Tiago R. D. , Harb Laith , Khara Pratick , Zeng Lanying , Hu Bo , Christie Peter J. 
Published: December 2020

AbstractBacterial type IV secretion systems (T4SSs) are a functionally diverse translocation superfamily. They consist mainly of two large subfamilies: (i) conjugation systems that mediate interbacterial DNA transfer and (ii) effector translocators that deliver effector macromolecules into prokaryotic or eukaryotic cells. A few other T4SSs export DNA or proteins to the milieu, or import exogenous DNA. The T4SSs are defined by 6 or 12 conserved “core” subunits that respectively elaborate “minimized” systems in Gram‐positive or ‐negative bacteria. However, many “expanded” T4SSs are built from “core” subunits plus numerous others that are system‐specific, which presumptively broadens functional capabilities. Recently, there has been exciting progress in defining T4SS assembly pathways and architectures using a combination of fluorescence and cryoelectron microscopy. This review will highlight advances in our knowledge of structure–function relationships for model Gram‐negative bacterial T4SSs, including “minimized” systems resembling the Agrobacterium tumefaciens VirB/VirD4 T4SS and “expanded” systems represented by the Helicobacter pylori Cag, Legionella pneumophila Dot/Icm, and F plasmid‐encoded Tra T4SSs. Detailed studies of these model systems are generating new insights, some at atomic resolution, to long‐standing questions concerning mechanisms of substrate recruitment, T4SS channel architecture, conjugative pilus assembly, and machine adaptations contributing to T4SS functional versatility.
Comparison of pediatric brain‐dead donors to donation after circulatory death donors in the United States
Authors: Ghavam Ahmeneh , Thompson Nathan E. , Lee Jane 
Published: December 2020

AbstractIn pediatrics, an increasing need for transplantable organs exists. This study aimed to describe the epidemiology of pediatric deceased donors in the United States. This retrospective observational study utilized data from the Organ Procurement and Transplantation Network (OPTN) from 2000 to 2015. Patients were stratified based on method of organ donation. Demographic variables and mechanism of death were then compared. A total of 14,481 deceased pediatric organ donors, donation after brain death (DBD) and donation after circulatory death (DCD), were included in the study, of which 8% were DCD donors. A significant difference (p<0.001) existed between the two donor groups with respect to ethnicity and mechanism of death. The annual trend of DCD and DBD donors showed an inverse relationship. During the 15‐year study period the number of DBD donors decreased from 985 to 785 per year while DCD donors increased from 15 to 146 per year. As well, overall organs transplanted per year decreased from 3,475 to 3,117 over the 15‐year study period. Significant differences exist between pediatric DBD donors and DCD donors, specifically with respect to ethnicity and mechanism of death. The number of pediatric DBD donors is decreasing while the number of pediatric DCD is slowly rising, making it increasingly important to be able to characterize these donors to better identify eligible DCD donors to optimize organ utilization.
T cell phenotype in paediatric heart transplant recipients
Authors: Mengrelis Konstantinos , Kucera Filip , Shahid Nadia , Watt Eleanor , Ross Susan , Lau Ching‐In , Adams Stuart , Gilmour Kimberly , Pils Dietmar , Crompton Tessa , Burch Michael , Davies E. Graham 
Published: December 2020

AbstractPaediatric heart transplantation recipients suffer an increased incidence of infectious, autoimmune and allergic problems. The relative roles of thymus excision and immunosuppressive treatments in contributing to these sequelae are not clear. We compared the immunological phenotypes of 25 heart transplant recipients (Tx), 10 children who underwent thymus excision during non‐transplantation cardiac surgery (TE) and 25 age range–matched controls, in two age bands: 1‐9 and 10‐16 years. Significant differences from controls were seen mainly in the younger age band with Tx showing lower CD3 and CD4 cell counts whilst TE showed lower CD8 cell counts. Naïve T cell and recent thymic emigrant proportions and counts were significantly lower than controls in both groups in the lower age band. T cell recombination excision circle (TREC) levels were lower than controls in both groups in both age bands. There were no differences in regulatory T cells, but in those undergoing thymus excision in infancy, their proportions were higher in TE than Tx, a possible direct effect of immunosuppression. T cell receptor V beta spectratyping showed fewer peaks in both groups than in controls (predominantly in the older age band). Thymus excision in infancy was associated with lower CD8 cell counts and higher proportions of Tregs in TE compared to Tx. These data are consistent with thymus excision, particularly in infancy, being the most important influence on immunological phenotype after heart transplantation.
Impact of sarcopenia in infants with liver transplantation for biliary atresia
Authors: Takeda Masahiro , Sakamoto Seisuke , Uchida Hajime , Shimizu Seiichi , Yanagi Yusuke , Fukuda Akinari , Nosaka Shunsuke , Kasahara Mureo 
Published: December 2020

AbstractWhile sarcopenia is an important predictor of LT outcomes in adults, few studies have examined the association of sarcopenia with LT outcomes in pediatric patients. We investigated the clinical influence of sarcopenia on the post‐transplant outcomes in infants with BA. To define sarcopenia in infants, the cross‐sectional area of the tPMA in 93 healthy control infants was measured by computed tomography. Sarcopenia was defined as a tPMA lower than two standard deviations below the mean of healthy control infants. Eighty‐nine infants with BA with a median age at LT of 7.6 months old were enrolled. The clinical characteristics and outcomes of LT were verified in the sarcopenia group (n = 21) and non‐sarcopenia group (n = 68). The sarcopenia group had a significantly longer operation time and greater blood loss during LT than the non‐sarcopenia group (P = .03 and 0.02). The incidence of portal vein stenosis and post‐operative bloodstream infection was also significantly higher in the sarcopenia group than in the non‐sarcopenia group (23.8% vs 4.4%, P = .02 and 28.6% vs 10.3%, P = .04, respectively). The total length of hospital stay did not differ significantly. The 1‐year patient and graft survival rates tended to be lower in the sarcopenia group than in the non‐sarcopenia group (90.5% vs 98.5%, P = .07 and 85.7% vs 97.1%, P = .05, respectively). Sarcopenia in infants with BA may be associated with the patient survival and serve as an effective marker for post‐operative outcomes of LT.
Death Attitudes in Clergy Work: Death Attitudes and Their Linkage to Work Orientation and Wellbeing among the Finnish Clergy
Authors: Tervo-Niemelä Kati 
Published: December 2020

Abstract
In this study, the focus is on death attitudes among the clergy in the Evangelical Lutheran Church of Finland and their role in clergy work. The aim is to find out whether these attitudes have any practical relevance in clergy work and to see if the death attitudes are linked to the work orientation and wellbeing among the clergy. The death attitudes are measured by the Death Attitude Profile-Revised DAP-R (N=650). The results show that death attitudes have a multifaceted role in clergy work. Negative death attitudes were linked to an outward motivational orientation in work and lower levels of work wellbeing, and positive, on the other hand, to lower levels of burnout and higher levels of work engagement. These results show the importance of the competence related to death in clergy work and these notions should be acknowledged in the education and further education of the clergy.
The Function of Speech Acts in a Vatican II Declaration: Gravissimum Educationis
Authors: van Gestel Toon , van Iersel Fred , de Groot Kees 
Published: December 2020

Abstract
This paper provides an analysis of Gravissimum Educationis, the Vatican II declaration on Christian Education. The paper focusses on speech acts as text signals for an ideal reader within the declaration’s communication framework. To date, speech acts have not been scrutinized in Vatican II constitutions, decrees, or declarations. An analysis of performative utterances in Gravissimum Educationis is presented on the basis of J.R. Searle’s taxonomy on speech acts. The major finding is that in its speech acts, Gravissimum Educationis, as a Vatican II declaration, stands out from previous ecclesiastical documents. As a new form of Church language, it is innovative and, as such, may fit in well with the panegyric literary genre.