bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thick Fibrous Septa on Liver Biopsy Specimens Predict the Development of Decompensation in Patients With Compensated Cirrhosis
Authors: Jain Dhanpat , Sreenivasan Prithvi , Inayat Irteza , Deng Yanhong , Ciarleglio Maria M , Garcia-Tsao Guadalupe 
Published: February 2021

Abstract

Objectives
In compensated cirrhosis, thick fibrous septa and small nodules on liver biopsy specimens correlate with the presence of clinically significant portal hypertension (CSPH). In turn, CSPH is the strongest predictor of cirrhosis decompensation. The aim of the study was to correlate liver biopsy specimen characteristics with the development of decompensation in patients with compensated cirrhosis.

Methods
Patients with compensated cirrhosis and a concurrent liver biopsy specimen were reviewed. Semiquantitative grading of septal thickness and nodule size was performed. Primary end point was development of clinical decompensation. In total, 168 patients (median age, 49 years; 76% men) were included in the study; the most common etiology was viral.

Results
In a median follow-up of 50 months, 43 (26%) patients developed clinical decompensation (60% ascites, 16% encephalopathy, 12% variceal hemorrhage, 7% jaundice, and 5% mixed). On univariate analysis, septal width was significantly associated with decompensation, but nodule size was not. On multivariate analysis including model for end-stage liver disease score, serum albumin, and septal width, albumin and septal width were independent predictors of decompensation.

Conclusions
Histologic cirrhosis in compensated patients can be subclassified by severity based on septal thickness, with thick septa denoting worse prognosis.
Survey of Clinical and Anatomic Pathology Laboratory Infrastructure in Mozambique
Authors: Ismail Mamudo R , Noormahomed Emília V , Lawicki Shaun , Eichbaum Quentin 
Published: February 2021

Abstract

Objectives
Pathology services are limited in most areas of sub-Saharan Africa. This study’s aim was to survey anatomic and clinical pathology services and laboratory infrastructure in Mozambique.

Methods
A survey was conducted from October-December 2018 across the four central hospitals of Mozambique to determine infrastructure and pathology services available.

Results
Most laboratory/pathology services in Mozambique are limited to the four central hospitals. Only 14 pathologists practice in the country despite a population of 29.5 million for the world’s fifth worst workforce/population ratio. Approximately 35,000 anatomic pathology specimens are evaluated annually. Standard services across chemistry, hematology, microbiology, and blood bank are available at the four central hospitals. Esoteric laboratory testing and immunohistochemistry are generally only available in Maputo.

Conclusions
While most pathology services are available in Mozambique, many are available only at the Maputo laboratory. Expansion of pathology services and infrastructure will improve provision of effective and efficient health care as access to timely and accurate clinical diagnoses increases in Mozambique.
Separating Algorithms From Questions and Causal Inference With Unmeasured Exposures: An Application to Birth Cohort Studies of Early Body Mass Index Rebound
Authors: Aris Izzuddin M , Sarvet Aaron L , Stensrud Mats J , Neugebauer Romain , Li Ling-Jun , Hivert Marie-France , Oken Emily , Young Jessica G 
Published: February 2021

Abstract
Observational studies reporting on adjusted associations between childhood body mass index (BMI; weight (kg)/height (m)2) rebound and subsequent cardiometabolic outcomes have often not paid explicit attention to causal inference, including definition of a target causal effect and assumptions for unbiased estimation of that effect. Using data from 649 children in a Boston, Massachusetts–area cohort recruited in 1999–2002, we considered effects of stochastic interventions on a chosen subset of modifiable yet unmeasured exposures expected to be associated with early (&lt;age 4 years) BMI rebound (a proxy measure) on adolescent cardiometabolic outcomes. We considered assumptions under which these effects might be identified with available data. This leads to an analysis where the proxy, rather than the exposure, acts as the exposure in the algorithm. We applied targeted maximum likelihood estimation, a doubly robust approach that naturally incorporates machine learning for nuisance parameters (e.g., propensity score). We found a protective effect of an intervention that assigns modifiable exposures according to the distribution in the observational study of persons without (vs. with) early BMI rebound for fat mass index (fat mass (kg)/ height (m)2; −1.39 units, 95% confidence interval: −1.63, −0.72) but weaker or no effects for other cardiometabolic outcomes. Our results clarify distinctions between algorithms and causal questions, encouraging explicit thinking in causal inference with complex exposures.
RNA2HLA: HLA-based quality control of RNA-seq datasets
Authors: Chelysheva Irina , Pollard Andrew J , O’Connor Daniel 
Published: February 2021

Abstract
RNA-sequencing (RNA-seq) is a widely used approach for accessing the transcriptome in biomedical research. Studies frequently include multiple samples taken from the same individual at various time points or under different conditions, correct assignment of those samples to each particular participant is evidently of great importance. Here, we propose taking advantage of typing the highly polymorphic genes from the human leukocyte antigen (HLA) complex in order to verify the correct allocation of RNA-seq samples to individuals. We introduce RNA2HLA, a novel quality control (QC) tool for performing study-wide HLA-typing for RNA-seq data and thereby identifying the samples from the common source. RNA2HLA allows precise allocation and grouping of RNA samples based on their HLA types. Strikingly, RNA2HLA revealed wrongly assigned samples from publicly available datasets and thereby demonstrated the importance of this tool for the quality control of RNA-seq studies. In addition, our tool successfully extracts HLA alleles in four-digital resolution and can be used to perform massive HLA-typing from RNA-seq based studies, which will serve multiple research purposes beyond sample QC.
Rank normalization empowers at-test for microbiome differential abundance analysis while controlling for false discoveries
Authors: Davis Matthew L , Huang Yuan , Wang Kai 
Published: February 2021

AbstractA major task in the analysis of microbiome data is to identify microbes associated with differing biological conditions. Before conducting analysis, raw data must first be adjusted so that counts from different samples are comparable. A typical approach is to estimate normalization factors by which all counts in a sample are multiplied or divided. However, the inherent variation associated with estimation of normalization factors are often not accounted for in subsequent analysis, leading to a loss of precision. Rank normalization is a nonparametric alternative to the estimation of normalization factors in which each count for a microbial feature is replaced by its intrasample rank. Although rank normalization has been successfully applied to microarray analysis in the past, it has yet to be explored for microbiome data, which is characterized by high frequencies of 0s, strongly correlated features and compositionality. We propose to use rank normalization as an alternative to the estimation of normalization factors and examine its performance when paired with a two-sample t-test. On a rigorous 3rd-party benchmarking simulation, it is shown to offer strong control over the false discovery rate, and at sample sizes greater than 50 per treatment group, to offer an improvement in performance over commonly used normalization factors paired with t-tests, Wilcoxon rank-sum tests and methodologies implemented by R packages. On two real datasets, it yielded valid and reproducible results that were strongly in agreement with the original findings and the existing literature, further demonstrating its robustness and future potential. Availability: The data underlying this article are available online along with R code and supplementary materials at https://github.com/matthewlouisdavisBioStat/Rank-Normalization-Empowers-a-T-Test.
Good alimentation can overcome the negative effects of climate change on growth in reptiles
Authors: Rueda-Zozaya Pilar , Plasman Melissa , Reynoso Víctor Hugo 
Published: February 2021

AbstractClimate change may lead to higher nest temperatures, which may increase embryo development rate but reduce hatchling size and growth. Larger body size permits better performance, making growth an important fitness trait. In ectotherms, growth is affected by temperature and food quality. To segregate the effects of incubation temperature vs. alimentation on the growth of the Mexican black spiny-tailed iguana, Ctenosaura pectinata, we incubated eggs at 29 or 32 °C, and hatchlings were kept at 30 °C and fed either high- or low-quality food for 1 year, with body size and mass being recorded every 2 weeks. Iguanas incubated at 29 °C grew faster than those incubated at 32 °C. However, food quality had a larger effect on growth than incubation temperature; iguanas fed with high-quality food reached larger body sizes. Growth models suggested that differences in growth between incubation temperatures and food types remain throughout their lives. We found that incubation temperature had long-lasting effects on an ectotherm, and higher incubation temperatures might lead to reduced growth and maturation at a later age. However, food might transcend the effect of increased incubation temperature; therefore, good alimentation might mitigate effects of climate change on growth.
Exponential distribution of velocities and power distribution of quiescent periods in the spontaneous movement patterns of three hunting spiders
Authors: Baatrup Erik , Rasmussen Anders O , Malte Hans , Toft Søren 
Published: February 2021

Abstract
Here, we investigate the spontaneous locomotor patterns in three spiders with different hunting strategies. The locomotor activity of adult wolf spiders Pardosa amentata, with a sit-and-move hunting strategy, has previously been demonstrated to follow strictly mathematical rules, with most time spent at lower velocities and exponentially decreasing time spent at increasing velocities. Likewise, they have an abundance of short quiescent (resting) periods following a power decay function towards longer quiescent periods. In the present study, we explored whether similar distributions were expressed in juveniles of P. amentata and in two other spider species with different hunting strategies: the sit-and-wait spider Xysticus cristatus and the actively searching sac spider Clubiona phragmitis. We found that all three spider species followed the same two general rules of movement. However, there were differences among the three species. On a logarithmic scale of exponential velocities and a double-logarithmic scale of the rest power decay function, the slopes of the lines for the three species differed. We propose that these differences reflect the behavioural and locomotor differences of the three hunting strategies. Furthermore, we compare our results with similar movement distributions in single cells, fruit flies, mice and even humans.
Dimension reduction for covariates in network data
Authors: Zhao Junlong , Liu Xiumin , Wang Hansheng , Leng Chenlei 
Published: February 2021

Summary
A problem of major interest in network data analysis is to explain the strength of connections using context information. To achieve this, we introduce a novel approach, called network-supervised dimension reduction, in which covariates are projected onto low-dimensional spaces to reveal the linkage pattern without assuming a model. We propose a new loss function for estimating the parameters in the resulting linear projection, based on the notion that closer proximity in the low-dimension projection corresponds to stronger connections. Interestingly, the convergence rate of our estimator is found to depend on a network effect factor, which is the smallest number that can partition a graph in a manner similar to the graph colouring problem. Our method has interesting connections to principal component analysis and linear discriminant analysis, which we exploit for clustering and community detection. The proposed approach is further illustrated by numerical experiments and analysis of a pulsar candidates dataset from astronomy.
The Importance of Considering Functional Outcome and Self-awareness in the Assessment of Care Needs: Initial Evaluation of the Brain Injury Needs Indicator
Authors: Copstick S , Ramos S D S , Griffiths T , Wallace A 
Published: February 2021

AbstractThe relationship between self-awareness (insight) and outcome following acquired brain injury (ABI) is well recognised, but evidence suggests that information regarding brain injury and its cognitive impact is not adequately conveyed to social workers, or appropriately considered when assessing support needs and a person’s capacity to make decisions about their care. The Brain Injury Needs Indicator (BINI) provides a solution, by enabling the valid assessment of the needs of those with brain injuries living in a community setting. This paper investigated associations between impaired insight, functional outcome of brain injury, and level of risk, and validated the use of the BINI as an indicator of need. A high prevalence of severe disability (73 per cent) and low insight (30 per cent) was found in a sample of thirty individuals with ABI. The composite BINI score was the measure most strongly related with a clinical assessment of risk (rs = 0.72, N = 26). Self-report methods may underestimate support needs, especially in those with low levels of insight into their difficulties. The BINI, which combines outcome post-ABI with a measure of insight, provides a more accurate estimate of risk than either measure individually. It is important to include both areas in individual needs assessments.
An Implementable Conversation Between Foucault and Chinese Virtue Ethics in the Context of Youth Social Work
Authors: He Longtao , van Heugten Kate 
Published: February 2021

AbstractRecently, virtue ethics has been increasingly considered as one of the most appropriate alternative ethical frameworks for youth social work internationally and in China. Extant literature has the tendency to emphasise cultural difference and neglect the universality of (virtue) ethics; instead, this article aims to inspire a balanced theoretical conversation on similarities between western (Foucauldian) and Chinese virtue ethics (mainly classical Confucianism and Daoism) supported by examples from case studies. Three areas are addressed: (i) similarities in the interior (personal) dimension and the exterior (relational) dimension of the self; (ii) the situational and universal features of virtue ethics, and the need for a reflective approach to balance both; and (iii) ethical cultivation of the reflective approach. These key themes add to a body of knowledge for the development of a virtue ethics framework for Chinese youth social work.
Temporal Trends of Candidemia Incidence Rates and Potential Contributions of Infection Control Initiatives Over 18 Years Within the United States Veterans Health Administration System: A Joinpoint Time-Series Analysis
Authors: Suzuki Hiroyuki , Perencevich Eli N , Diekema Daniel J , Livorsi Daniel J , Nair Rajeshwari , Kralovic Stephen M , Roselle Gary A , Goto Michihiko 
Published: February 2021

Abstract

Background
Candidemia is one of the most common causes of nosocomial bloodstream infections, but the impacts of factors affecting its incidence have not been evaluated.

Methods
We analyzed a retrospective cohort of all candidemia patients at 130 acute care hospitals in the Veterans Health Administration (VHA) system from January 2000 through December 2017. Cases were classified as hospital-onset (HO) and non-hospital-onset (NHO). We used Joinpoint regression analysis to assess temporal associations between significant changes in candidemia incidence rates and guidelines or horizontal infection control (IC) interventions.

Results
Over 18 years, 17 661 candidemia episodes were identified. Incidence rates of HO cases were increasing until the mid-2000s, followed by a sustained decline, while NHO cases showed a steady decline. The first change in HO candidemia incidence rates (August 2004 [95% confidence interval {CI}, February 2003–April 2005]) was preceded by the publication of catheter-related bloodstream infection (CRBSI) prevention guidelines and the CRBSI surveillance initiation. The second (September 2007 [95% CI, September 2006–June 2009]) had close temporal proximity to the expansion of IC resources within the VHA system. Collectively, these trend changes resulted in a 77.1% reduction in HO candidemia incidence rates since its peak in 2004.

Conclusions
A substantial and sustained systemwide reduction in candidemia incidence rates was observed after the publication of guidelines, VHA initiatives about CRBSI reporting and education on CRBSI prevention, and the systemwide expansion of IC resources.
Asymmetric Competition on a New Battleground? Middle Eastern Perspectives on Sino-US Rivalry
Authors: She Gangzheng 
Published: February 2021

Abstract
During the last few years, and especially since the outbreak of the COVID-19 pandemic, growing number of Middle East scholars and analysts have been closely observing an escalation of tensions between China and the United States and their impact beyond bilateral ties. Considering the major differences of focus and approach among these observers, this article aims to review systematically such Middle Eastern perspectives, both globally and regionally, on the emerging Sino-US rivalry. Certain Middle East analysts regard Beijing and Washington as largely “homogeneous” extra-regional powers competing in international politics, economy, and technology. Many others emphasise their “heterogeneity,” arguing that the essence of Sino-US confrontation lies in the clash of two models. Most Middle East scholars note that, in contrast to Washington’s waning influence, Beijing’s growing presence in the region during the past decade has rendered the Middle East a “new battleground” for the two great powers. Although China and the United States still have shared interests in certain regional affairs, most intellectuals focus on and collectively identify five domains across the Middle East wherein Beijing and Washington are locked in asymmetric competition. In light of both the opportunities and challenges that the emerging Sino-US rivalry engenders, Middle Eastern observers raise various policy suggestions, and debate on whether regional players should proactively take advantage of this great power competition, cautiously hedge against strategic uncertainty and risk, or constructively help reduce hostility between the United States and the People’s Republic of China.
Starvation on First or Second Day of Adulthood Reverses Larval-Stage Decision to Migrate in Beet Webworm (Lepidoptera: Pyralidae)
Authors: Cheng Yunxia , Sappington Thomas W , Luo Lizhi , Zhang Lei , Jiang Xingfu 
Published: February 2021

Abstract
A facultative commitment to adult migration in the larval stage can be modified again after adult emergence in some Lepidoptera when influenced by an appropriate environmental cue during a sensitive stage. This phenomenon is termed secondary regulation of migration. The sensitive stage in adult beet webworm, Loxostege sticticalis L. (Lepidoptera: Pyralidae), was determined experimentally by starvation of presumed migrant females reared from gregarious-phase larvae (induced by crowding at 10 larvae per 650-ml jar). When presumed migrant adults were starved for 24 h on either of the first 2 d after emergence, the preoviposition period was shortened. In contrast, preoviposition periods were not significantly shortened for migrants starved on day 3 or when starvation lasted for more than 1 d after emergence. Because the preoviposition period corresponds to the migratory period in beet webworm, the results suggest that the first 2 d of adult life in the beet webworm is the sensitive stage during which presumed migrants can be switched to residents by an appropriate environmental cue. During the sensitive stage or not, starvation did not influence lifetime fecundity, oviposition period, longevity, or hatching rate of eggs laid by the starvation-stressed moths. Starvation on the first day also increased tethered flight performance and accelerated both flight muscle and ovarian development. The results suggest that a pulse of starvation in the sensitive period may inhibit the expected migration by accelerating and compressing the cycle of migratory flight muscle development and degeneration, while accelerating ovarian development, which is normally suppressed until after migration.
Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems
Authors: Cerecetto Victoria , Smalla Kornelia , Nesme Joseph , Garaycochea Silvia , Fresia Pablo , Sørensen Søren Johannes , Babin Doreen , Leoni Carolina 
Published: February 2021

ABSTRACTConventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.