bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological mechanisms underlying aridity thresholds in global drylands
Authors: Berdugo Miguel , Vidiella Blai , Solé Ricard V. , Maestre Fernando T. 
Published: October 2021

Abstract

With ongoing climate change, the probability of crossing environmental thresholds promoting abrupt changes in ecosystem structure and functioning is higher than ever. In drylands (areas where it rains <65% of what could be potentially evaporated), recent research has shown how the crossing of three aridity thresholds [at aridity (1‐Aridity Index) values of 0.54, 0.70 and 0.80] leads to abrupt changes on ecosystem structural and functional attributes. Despite the importance of these findings and their implications to develop effective monitoring and adaptation actions to combat climate change and desertification, we lack a proper understanding of the mechanisms unleashing these abrupt shifts.

Here we review multiple mechanisms that may explain the existence of aridity thresholds observed across global drylands, and discuss the potential amplification mechanisms that may underpin hypothetical abrupt temporal shifts with climate change.

We propose that each aridity threshold is caused by different and specific mechanisms. The first threshold is mainly caused by physiological mechanisms of plant adaptation to water shortages. The second threshold is unleashed by different mechanisms involving soil processes and plant–soil interactions such as soil erosion, plant community shifts and nutrient cycling and circulation. The collapse of vegetation observed once the third aridity threshold (0.8) is crossed is caused by the mechanisms related to the survival limits of plants that may cause sudden cover and diversity losses and plant–atmospheric feedbacks that link vegetation collapse with further climate aridification.

By identifying, revising and linking relevant mechanisms to each aridity threshold observed, we provide a set of specific hypotheses and identify knowledge gaps concerning the study of threshold emergence in drylands. We were also able to establish plausible factors that are context dependent and may influence the occurrence of abrupt ecosystem changes in time. Our review may help to focus future research efforts on aridity thresholds and to develop strategies to monitor, adapt to or even revert abrupt ecosystem changes across global drylands.

A free Plain Language Summary can be found within the Supporting Information of this article.
Do Firms Time Changes in Accounting Estimates to Manage Earnings?†
Authors: Chung Philip Keunho , Geiger Marshall A. , Paik Daniel Gyung , Rabe Collin 
Published: October 2021

ABSTRACTPrior earnings management research often focuses on specific accounts or on estimations of discretionary accruals but provides only limited insight into the methods firms actually use to manage earnings. In order to begin exploration of some of the operational details regarding how earnings are managed, we investigate whether firms time their decisions to make changes in accounting estimates (CAEs) in consideration of their earnings benchmarks. Using CAE data across all accounts from 2006 to 2018, we find that 28.1% of income‐increasing CAEs are implemented in quarters where pre‐CAE earnings are below a forecasted earnings benchmark but inclusion of the CAE effectively allows the firm to meet the benchmark. We find that income‐increasing CAEs are more likely implemented when a firm's pre‐CAE earnings are further below the benchmark. We also find that firms are more likely to implement income‐decreasing CAEs under two scenarios: (i) when pre‐CAE earnings are relatively high, as a way either to smooth earnings or to “bury bad news,” and (ii) when pre‐CAE earnings are already low, as a way to take a financial “big bath” and position the firm for positive future earnings. In addition, we present evidence that firms using CAEs to achieve an earnings benchmark face financial consequences in terms of poorer immediate stock price performance and subsequent return on assets. Our conclusions hold after performing several additional analyses, including consideration of other discretionary options, addressing endogeneity concerns, and conducting falsification tests. In sum, we contribute to the earnings management literature by presenting consistent evidence that firms appear to time CAEs to meet earnings benchmarks or achieve other reporting objectives.
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes
Authors: Tribble Carrie M. , Freyman William A. , Landis Michael J. , Lim Jun Ying , Barido‐Sottani Joellë , Kopperud Bjørn Tore , Hӧhna Sebastian , May Michael R. 
Published: October 2021

AbstractStatistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing and communicating their key results.We presentRevGadgets, anRpackage for creating publication‐quality figures from the results of a large variety of phylogenetic analyses performed inRevBayes(and other phylogenetic software packages).We demonstrate how to useRevGadgetsthrough a set of vignettes that cover the most common use cases that researchers will encounter.RevGadgetsis an open‐source, extensible package that will continue to evolve in parallel withRevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses.
ontoFAST: An R package for interactive and semi‐automatic annotation of characters with biological ontologies
Authors: Tarasov Sergei , Mikó István , Yoder Matthew Jon 
Published: October 2021

Abstract

Ontologies are becoming a fundamental technology for analysing phenotypic data. The commonly used Entity–Quality (EQ) provides rich semantics for annotating phenotypes and characters using ontologies. However, EQ syntax might be time inefficient if this granularity is unnecessary for downstream analysis.

We present an R package ontoFAST that aids fast annotations of characters with biological ontologies. ontoFAST takes a biomedical ontology in OBO format and a list of characters as input, and produces a list of mappings from characters to ontology terms as output.

The annotations produced by ontoFAST can be exported in CSV format for downstream analysis. Additionally, ontoFAST provides (a) functions for constructing simple queries of characters against ontologies and (b) helper function for exporting and visualizing complex ontological hierarchies and their relationships.

ontoFAST enhances integration of ontological and phylogenetic methods and supports data interoperability between R applications. Ontology tools are underrepresented in R ecosystem and we hope that ontoFAST will stimulate their further development.
Externally attached biologgers cause compensatory body mass loss in birds
Authors: Portugal Steven J. , White Craig R. 
Published: October 2021

Abstract

Animal‐borne logging devices are now commonly used to record and monitor the movements, physiology and behaviours of free‐living animals. It is imperative that the impacts these devices have on the animals themselves are minimised.

One important consideration is the interaction between the body mass of the animal and the mass of the device.

Using captive homing pigeons, we demonstrate that birds lose the equivalent amount of body mass compared to that of the logging device attached. With our experiments, we calculated that the compensatory mass loss because of the logging device equates to a total loss of 1,140 kJ of energy to the bird, over the 25‐day period. This equates to 32% per day of their total daily energy budget.

We suggest that practitioners of biologging give due consideration to the possibility of a device‐induced decrease in body mass when making decisions regarding device size, and when considering the period of the time of the year at which devices are attached.

It appears, based on the results of the present study, that device attachment is likely to be most disruptive during periods of regulated mass change, especially when periods of mass gain precede periods in which stored energy reserves are extensively utilised.

These findings have significant consequences for anyone using biologging technology on both wild and captive volant animals. Further studies utilising captive birds are now needed to fully understand how context‐ and species‐dependent physiological responses to externally attached devices are.
Advancing research on recurrent pregnancy loss: Overcoming obstacles and opportunities for translation
Authors: Girardi Guillermina , Bremer Andrew A. 
Published: October 2021

AbstractRecurrent pregnancy loss (RPL) is one of the most complex and challenging scenarios in reproductive medicine. New theories about the mechanisms behind RPL have recently emerged, highlighting the multifactorial nature of this serious pregnancy complication. Unfortunately, these preclinical observations are rarely validated in the human scenario, where treatment remains ineffective and empirical. New technologies such as organoids, organ‐on‐a‐chip, and 3D printing can be used to characterize the molecular cross talk between the uterine environment with its unique inflammatory cells and the developing embryo. Understanding the mechanisms behind RPL and identifying mediators and effectors and validating these targets for prevention and therapy in humans will have a profound impact on women's health.
Racial Identity, Group Consciousness, and Attitudes: A Framework for Assessing Multiracial Self‐Classification
Authors: Davenport Lauren D. , Iyengar Shanto , Westwood Sean J. 
Published: October 2021

AbstractMultiracial self‐classifiers are the fastest‐growing racial population in the United States. While their rise signals a departure from norms of hypodescent, little is known about the sociopolitical meanings attached to multiracial labels. Here, we develop a theoretical framework for understanding multiracials’ sense of racial group identity, linked fate, and racial attitudes. Examining a national opinion survey that samples more than 1200 multiracial adults, we compare the identity and attitudinal profiles of the two largest multiracial groups in the United States—White‐Asians and White‐Blacks—with those of their component monoracial groups. We find that while White‐Asians and White‐Blacks often distinguish themselves from their component races, on balance, the assertion of dual racial membership signals greater solidarity and/or affect toward the minority race. These findings suggest that members of these multiracial populations are likely to align themselves relatively more with their minority background than with Whites on political issues that are racial in nature.
Progressive decline of function in renal allografts with normal 1‐year biopsies: Gene expression studies fail to identify a classifier
Authors: Park Walter D. , Kim Dean Y. , Mai Martin L. , Reddy Kunam S. , Gonwa Thomas , Ryan Margaret S. , Herrera Hernandez Loren P. , Smith Maxwell L. , Geiger Xochiquetzal J. , Turkevi‐Nagy Sandor , Cornell Lynn D. , Smith Byron H. , Kremers Walter K. , Stegall Mark D. 
Published: October 2021

AbstractHistologic findings on 1‐year biopsies such as inflammation with fibrosis and transplant glomerulopathy predict renal allograft loss by 5 years. However, almost half of the patients with graft loss have a 1‐year biopsy that is either normal or has only interstitial fibrosis. The goal of this study was to determine if there was a gene expression profile in these relatively normal 1‐year biopsies that predicted subsequent decline in renal function. Using transcriptome microarrays we measured intragraft mRNA levels in a retrospective Discovery cohort (170 patients with a normal/minimal fibrosis 1‐year biopsy, 54 with progressive decline in function/graft loss and 116 with stable function) and developed a nested 10‐fold cross‐validated gene classifier that predicted progressive decline in renal function (positive predictive value = 38 ± 34%%; negative predictive value = 73 ± 30%, c‐statistic = .59). In a prospective, multicenter Validation cohort (270 patients with Normal/Interstitial Fibrosis [IF]), the classifier had a 20% positive predictive value, 85% negative predictive value and .58 c‐statistic. Importantly, the majority of patients with graft loss in the prospective study had 1‐year biopsies scored as Normal or IF. We conclude predicting graft loss in many renal allograft recipients (i.e., those with a relatively normal 1‐year biopsy and eGFR > 40) remains difficult.
Kidney utilization and outcomes of liver transplant recipients who were listed for kidney after liver transplant after the implementation of safety net policy
Authors: Homkrailas Piyavadee , Ayoub Walid S. , Martin Paul , Bunnapradist Suphamai 
Published: October 2021

AbstractIn 2017, United Network for Organ Sharing (UNOS) established the safety net policy with set criteria for offering kidney transplantation (KT) for patients who developed end‐stage renal disease between 60 and 365 days after liver transplant (LT). We provide an update on the impact of the policy. We analyzed UNOS data of liver recipients transplanted between 1987 and 2020 who developed acute kidney injury requiring dialysis within 60 days before or after LT and subsequently listed for KT. We identified 407 patients who were listed for kidney after LT before policy and 248 patients after policy. Median waiting time to KT was shorter after policy (324 days vs. 2827 days). There was a higher proportion of candidates who were listed for subsequent KT within 1‐year after policy (94.8% vs. 63.6%). KT rate was also higher after policy (87.7 vs. 30.7 per 100 patient‐years at risk). Most importantly, we started to observe a net negative kidney utilization in end‐stage liver disease setting (i.e., summation of simultaneous liver kidney and kidney after liver transplant in the first‐year after LT has decreased from 1086 to 876 transplants in 2019). Such findings are consistent with a more efficient system and more appropriate allocation of organs.
Cemiplimab in advanced cutaneous squamous cell carcinoma
Authors: Naik Piyu Parth 
Published: October 2021

AbstractCemiplimab, a high‐affinity, highly potent human monoclonal antibody that binds to the programmed death‐1 (PD‐1)/programmed death ligand‐1 (PD‐L1) receptor, is the only drug to attain Food and Drug Administration (FDA) approval and marketing authorization from the European Commission for use in patients with metastatic and locally advanced cutaneous squamous cell carcinoma (CSCC) who are not candidates for curative surgery or curative radiation therapy as a first‐ or later‐line treatment. In pivotal phase II clinical testing, cemiplimab showed rapid and substantial antitumor efficacy and acceptable safety. This systematic review was aimed at evaluating the efficacy and safety of cemiplimab in patients with advanced CSCC. To this end, I reviewed EMBASE, MEDLINE, PubMed, and clinical trial registries/databases by using the following keywords alone or in combination: “cemiplimab,” “Libtayo,” “cutaneous squamous cell carcinoma,” “REGN2810,” and “SER439684.” Cemiplimab showed clinical efficacy and considerable safety and was associated with low rates of treatment discontinuation (7%) and death (3%). However, the current recommendation is primarily based on only phase II clinical testing due to the absence of an approved comparator agent.
Keyworker mediated enhancement of physical health in patients with first episode psychosis: A feasibility/acceptability study
Authors: Broughan John , McCombe Geoff , Lim Jayleigh , O'Keeffe Donal , Brown Katherine , Clarke Mary , Corcoran Ciarán , Hanlon David , Kelly Ned , Lyne John , McGorry Patrick , O' Brien Sinéad , O' Connor Karen , O' Mahony Karen , Scott Seamus , Wycherley Elizabeth , Cullen Walter 
Published: October 2021

AbstractAimEarly intervention for people experiencing first episode psychosis is a priority, and keyworkers are vital to such services. However, keyworkers' roles in addressing first episode psychosis patients' physical health are under researched. This study addresses this knowledge gap by evaluating a keyworker‐mediated intervention promoting physical health among first episode psychosis patients.MethodsThe study was informed by the Medical Research Council's Framework for Complex Interventions to Improve Health. First episode psychosis participants were recruited from three Irish mental health services. The intervention was evaluated in terms of its feasibility/acceptability.ResultsFeasibility outcomes were mixed (recruitment rate = 24/68 [35.3%]; retention rate = 18/24 [75%]). The baseline sample was predominantly male (M:F ratio = 13:6; Med age = 25 y; IQR = 23‐42 y). Common health issues among participants included overweightness/obesity (n = 11) and substance use (smoking/alcohol consumption [n = 19]). Participants' initial health priorities included exercising more (n = 10), improving diet (n = 6), weight loss (n = 7) and using various health/healthcare services. The intervention's acceptability was evidenced by the appreciation participants had for physical health keyworkers' support, as well as the healthy lifestyle, which the intervention promoted. Acceptability was somewhat compromised by a low‐recruitment rate, variable linkages between keyworkers and general practitioners (GPs) and COVID‐19 restrictions.ConclusionsPhysical health‐oriented keyworker interventions for first episode psychosis patients show promise and further evaluation of such initiatives is warranted. Future interventions should be mindful of participant recruitment challenges, strategies to enhance relationships between keyworkers and GPs, and if necessary, they should mitigate COVID‐19 restrictions' impacts on care.
Reasons and consequences of COVID‐19 vaccine failure in patients with chronic lymphocytic leukemia
Authors: Morawska Marta 
Published: October 2021

AbstractPeople with hematologic malignancies are at a high risk of morbidity and mortality from COVID‐19. The response to vaccination is highly limited in patients with chronic lymphocytic leukemia. Less than half of the patients develop antibody response, suggesting that they remain at risk of SARS‐CoV‐2 infection even after the vaccination. Reasons for inadequate response to COVID‐19 vaccination in chronic lymphocytic leukemia are multifactorial and attributed to disease‐related immune dysregulation and patient‐ and therapy‐related factors. The negative predictors of response to vaccination include hypogammaglobulinemia, advanced age, current active treatment, and past treatment anti‐CD20 monoclonal antibodies. Despite using booster doses and heterologous immunization to improve humoral and cellular immunity, some patients with chronic lymphocytic leukemia will fail to respond. Active treatment at the time of vaccination and a recent history of anti‐CD20 monoclonal antibodies use are the strongest predictors of the non‐response. Current data support informing patients with chronic lymphocytic leukemia and other hematologic malignancies about the risk of infection regardless of vaccination. These individuals and members of their households should continue extreme preventive actions despite relaxed local regulations. Other emerging non‐vaccine preventive strategies include passive and post‐exposure prevention with monoclonal antibodies.
Estimating soil chemical properties by diffuse reflectance spectroscopy: Promise versus reality
Authors: McBride Murray B. 
Published: October 2021

AbstractDiffuse reflectance spectroscopy in the visible and near‐infrared (VNIR) spectral range has increasingly been utilised in recent years to measure soil properties, including organic carbon and macronutrient content, cation exchange capacity, pH, and even trace metal concentration. Proponents have even suggested that conventional laboratory soil testing methods can ultimately be replaced by these less laborious and more rapid spectroscopic methods. However, to this point in time, reflectance spectroscopy has not demonstrated accuracy comparable to that of conventional physical–chemical testing methods. This review explains why correlations between VNIR spectral features and specific chemical properties within selected sets of soil samples are indirect at best and therefore cannot be trusted more universally to predict soil chemical properties in larger and less homogeneous sample sets. Because mathematical manipulation of the raw spectral data has become increasingly complex and obscure to the users, particularly when machine learning is employed, the possibility exists that the correlations found and the predictions made are based on chance relationships resulting from overfitting the spectral data to include random noise in addition to any real trends. It is concluded that, for real‐world soil testing for agronomic and environmental purposes (e.g. available nutrient and trace metal levels), spectral reflectance methods are not sufficiently reliable to replace conventional testing. Conversely, these reflectance methods show utility and convenience in measuring general trends across landscapes in levels of soil organic matter, carbonates, soluble salts and specific clay minerals.Highlights
VNIR reflectance spectroscopy is reviewed as a method to measure soil properties.
Estimating most soil chemical properties by VNIR relies on indirect or proxy correlations.
Complex regression models used in predicting soil properties may overstate accuracy.
Reflectance spectroscopy has lower reliability and extrapolability than conventional soil testing.
Osteoclast density is not increased in bone adjacent to radiolucencies (cysts) in juvenile equine medial femoral condyles
Authors: Fortin‐Trahan Rosalie , Lemirre Thibaut , Santschi Elizabeth M. , Janes Jennifer G. , Richard Hélène , Fogarty Ursula , Beauchamp Guy , Girard Christiane A. , Laverty Sheila 
Published: October 2021

SummaryBackgroundThere is a knowledge gap about how equine MFC subchondral radiolucencies (SR) arise and evolve. Osteoclasts are believed to have a role but have not been studied in situ.ObjectivesTo measure and compare osteoclast density and the percentage of chondroclasts in healthy and MFC SR specimens from juvenile Thoroughbreds.Study designCadaveric study.MethodsMedial femoral condyles (MFC) from a tissue bank of equine stifles were studied. Inclusion criteria were MFCs (≤8 months old) with a computed tomography SR lesion and histological focal failure of endochondral ossification (L group). Contralateral, lesion‐free, MFCs were a control group (CC). Osteochondral slabs were cut through the lesion (L), a healthy site immediately caudal to the lesion, (internal control; IC) and the contralateral, site‐matched controls (CC). Histological sections were immunostained with Cathepsin K for osteoclast counting. Osteoclasts in contact with the growth cartilage (chondroclasts) were also counted. The sections were segmented into regions of interest (ROI) at different depths in the subchondral bone: ROI1 (0‐1 mm), ROI2 (1‐3 mm) and ROI3 (3‐6 mm). Osteoclasts were counted and the bone area was measured in each ROI to calculate their density. Chondroclasts were counted in ROI1.ResultsSections were studied from L and IC (n = 6) and CC sites (n = 5). Osteoclast density was significantly higher in ROI1 when compared with ROI3 in all groups. Although higher osteoclast density was measured in ROI1 in the L group, no significant differences were detected when compared with control ROIs. The proportion of chondroclasts in ROI1 was lower in the L sections when compared with controls but no significant differences were detected.Main limitationsLimited sample size.ConclusionsOsteoclasts are important actors in MFC subchondral bone development, digesting both growth cartilage (chondroclasts) and bone, but the pathophysiology of early MFC SRs cannot be explained solely by an increased osteoclast presence in the subchondral bone.