bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring population histories for ancient genomes using genome-wide genealogies
Authors: Speidel Leo , Cassidy Lara , Davies Robert W. , Hellenthal Garrett , Skoglund Pontus , Myers Simon R. 
Published: February 2021

AbstractAncient genomes anchor genealogies in directly observed historical genetic variation, and contextualise ancestral lineages with archaeological insights into their geography and lifestyles. We introduce an extension of theRelatealgorithm to incorporate ancient genomes and reconstruct the joint genealogies of 14 previously published high-coverage ancients and 278 present-day individuals of the Simons Genome Diversity Project. As the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies, we additionally present a fast and scalable method,Colate,for inferring coalescence rates between low-coverage genomes without requiring phasing or imputation. Our method leverages sharing patterns of mutations dated using a genealogy to construct a likelihood, which is maximised using an expectation-maximisation algorithm. We applyColateto 430 ancient human shotgun genomes of >0.5x mean coverage. UsingRelateandColate,we characterise dynamic population structure, such as repeated partial population replacements in Ireland, and gene-flow between early farmer and European hunter-gatherer groups. We further show that the previously reported increase in the TCC/TTC mutation rate, which is strongest in West Eurasians among present-day people, was already widespread across West Eurasia in the Late Glacial Period ~10k - 15k years ago, is strongest in Neolithic and Anatolian farmers, and is remarkably well predicted by the coalescence rates between other genomes and a 10,000-year-old Anatolian individual. This suggests that the driver of this signal originated in ancestors of ancient Anatolia >14k years ago, but was already absent by the Mesolithic and may indicate a genetic link between the Near East and European hunter-gatherer groups in the Late Paleolithic.
Urban development project goals and the role of professional ignorance: ambiguous policy objectives and their consequences
Authors: Styhre Alexander , Brorström Sara 
Published: February 2021

PurposeDrawing on the literature on professional ignorance, here defined in affirmative terms as the capacity to act regardless of the incompleteness of available information in organizations and professional communities, the article reports empirical material from an urban development project wherein policy makers' instructions are vague and, in certain domains, inconsistent with market conditions.Design/methodology/approachUrban development projects regularly include uncertainty and risk taking, and policy makers' stated objectives regarding project goals may be incomplete or merely signal a political ambition. In such situations, first-line project participants need to make decisions as if uncertainties regarding policy objectives are manageable and preferably minimal. The purpose of the article is to substantiate the proposition that professional ignorance is a key mechanism in incomplete or imperfect governance systems.FindingsProject participants actively questioned policy but acted on the instructions just the same, which is indicative of how professional ignorance is supportive of governance system that relies on first-line market actors and agencies to implement also incomplete or vaguely stated policy objectives. Incomplete policies derive from challenges in political deliberation and bargaining processes, uncertainty regarding the future and shifting preferences among policy makers and constituencies more widely. In practice, incomplete policies regularly include issues for first-level actors (e.g. on the urban development project level) to handle and to reconcile in their day-to-day work.Originality/valueOn basis of an empirical study of a major urban development project, the study contributes to a growing literature that recognizes the value of professional ignorance in governance systems and in project management practice. The study invites further scholarly research that takes an affirmative of professional ignorance but without overlooking its risks and potential malfunctions.
Experimental investigation on WEDM performance analysis using grey-fuzzy integrated with TLBO algorithm for Inconel 625: comparison with GA and SA
Authors: Kumar Anshuman , Upadhyay Chandramani , Shashikant Shashikant 
Published: February 2021

Purpose
In the present study, wire electro-discharge machining (WEDM) of Inconel 625 (In-625) is performed with the machining parameter such as spark-on time, spark-off time, wire-speed, wire tension and servo voltage. The purpose of this study is to find the most favorable machining parameter setting with respect to WEDM performance such as material removal rate (MRR) and surface roughness (RA).

Design/methodology/approach
Taguchi’s L27 orthogonal array has been used to design the experiments with varying machining parameters into three-level four factors. A hybrid multi-optimization technique has been purposed with grey relation analysis and fuzzy inference system integrated with teaching learning-based optimization to achieve optimum machinability (MRR and RA in present case). The obtained result has been compared with two evolutionary optimization tools via a genetic algorithm and simulated annealing.

Findings
It has been found that proposed hybrid technique taking minimum computational time, provide better solution and avoid priority weightage calculation by decision-makers. A confirmation test has been performed at single and multi-optimal parameter settings. The decision-makers have been chosen to select any single or multi-parameter setting as per the industry’s demand.

Originality/value
The proposed optimization technique provides better machinability of In-625 using zinc-coated brass wire electrode during WEDM operation.
The multilevel analysis of students’ achievement: Evidence from Morocco
Authors: Chatri Abdellatif , Chahbi Otman , Snihji Mustapha 
Published: February 2021

AbstractThis paper, using multi‐level modelling, sought to highlight student‐level and school‐level characteristics that differentiate the academic performance in mathematics from a sample of 6080 Moroccan secondary students who participated in the 2011 Trends in International Mathematics and Science Study (TIMSS) test. The results indicated little evidence to support the Heyneman–Loxley effect, as they showed that individual and family characteristics were the strongest determinants of achievement compared to the schools’ factors. Students scored higher when they were boys, were younger, were more self‐confident, were more ambitious, and felt secure in school. They also scored higher when they came from families with a higher socioeconomic status, particularly when their parents were able to ensure the availability of learning resources, and were of a higher level of education. Finally, schools were matter for their pupil achievement mainly through the location channel, as urban pupils outperformed rural ones. However, the other school characteristics, including those related to teachers, played a negative, or at best neutral, role in pupil outcomes. These findings have important public policy implications. Redesigning education policy towards improving the school's environment and fostering inclusivity would be needed to enhance learning performance of Moroccan students.
Anti‐PD1 versus anti‐PD‐L1 immunotherapy in first‐line therapy for advanced non‐small cell lung cancer: A systematic review and meta‐analysis
Authors: Brito Angelo Borsarelli Carvalho , Camandaroba Marcos Pedro Guedes , de Lima Vladmir Cláudio Cordeiro 
Published: February 2021

AbstractBackgroundDue to the increasing number of trials with immune checkpoint inhibitors (ICIs) in the first‐line therapy of non‐small cell lung cancer (NSCLC) patients, we performed a systematic review and meta‐analyses to investigate the difference between anti PD‐1 and PD‐L1 antibodies, used alone or in combination with chemotherapy, through adjusted indirect analysis to minimize the potential bias regarding overall survival (OS), progression‐free survival (PFS), overall response rate (ORR) and grade 3–5 adverse events (AEs).MethodsA systematic review of studies reporting clinical outcomes and toxicity associated with first‐line therapy employing anti‐PD1 or anti‐PD‐L1 antibodies alone, or in combination with chemotherapy, to treat metastatic, treatment‐naïve NSCLC patients was performed. Primary outcomes were OS, PFS, ORR and grade 3–5 AEs. We used a random‐effects model to generate pooled estimates for proportions. Meta‐analyses using pooled risk ratios were performed for binary outcomes from comparative studies with the random effects model.ResultsA total of 13 eligible studies met our eligibility criteria, including 7673 patients. In the ICI‐chemotherapy combination subgroup, we observed that anti‐PD1 therapy was associated with better OS (p = 0.022) and PFS (p = 0.029) compared with anti‐PD‐L1 therapy. In the monotherapy subgroup, there was no statistical difference between the use of anti‐PD‐1 and anti‐PD‐L1 for OS and PFS. With regard to ORR and toxicity, in the ICI‐chemotherapy combination subgroup, we observed a trend of better ORR (p = 0.12) with the use of anti‐PD1 therapy and less frequent grade 3–5 AEs compared to the use of anti‐PD‐L1 therapy (p = 0.0302). In the monotherapy subgroup, there was no statistical difference between the use of anti‐PD‐1 and anti‐PD‐L1 regarding ORR and toxicity.ConclusionsOur study suggests that PD‐1 drug plus chemotherapy is superior to anti‐PD‐L1 plus chemotherapy for NSCLC; nevertheless, as monotherapy, both strategies appear to be similar.
Metabolome analysis reveals important compounds related to dwarfing effect of interstock on scion in pear
Authors: Cui Zhenhua , Zhang Huan , Galarneau Erin R.‐A. , Yang Yingjie , Li Dingli , Song Jiankun , Ma Chunhui , Zhang Shaoling , Wang Ran 
Published: February 2021

AbstractThe utilisation of interstocks or rootstocks to reduce tree size has long been used in orchards. In the present study, we characterised the dwarfing effect of “OHF51” (Pyrus communis “Old Home” × “Farmingdale”) when used as interstock compared with callery pear (Pyrus calleryana Decne.). Shorter trees, smaller canopy, smaller trunk diameter and lower height of the first branch were found in trees with “OHF51” as the interstock as compared to callery pear. Metabolome analysis showed that the interstock altered the metabolite profiles of both the scion and the rootstock. The number of identified differential metabolites in scions, interstocks and roots were 8, 39 and 12, respectively, with “OHF51” interstock as compared to the same positions with callery as the interstock. Flavonoids and phenolic acids/derivatives were most altered in concentration. The concentrations of flavonoids procyanidin B2 and procyanidin B3 were remarkably higher in both the scion shoots and the interstock because of “OHF51,” while the concentration of two monosucroses, D‐sorbitol and D‐mannitol, were drastically reduced in roots with “OHF51” interstock present. The reallocation of carbohydrates from shoot to root could be influenced by the interstock, which participates in the regulation of scion growth in the spring season. Flavonoids and phenolic acids/derivatives are understood to be key compounds involved in the reduction of scion growth.
Need‐resource indicators and nonprofit human services organization density
Authors: Sevak Kunal Y. , Baker LaKami 
Published: February 2021

AbstractThe challenges facing the US nonprofit human services organizations (NHSOs) in securing philanthropic resources and the resulting pressure for increased commercialization are well‐known in the nonprofit literature. However, there is still limited research on how such financial challenges are likely to affect their location choices, particularly in a post‐recession context. Using organizational ecology theory, we conducted a nationwide longitudinal study covering the period of the US 2008 recession to examine whether resource availability is more likely to predict the density of NHSOs than human needs. We used secondary data on a variety of socioeconomic variables from the National Center for Charitable Statistics and the US census survey in a linear multivariate regression analysis. The findings supported a majority of hypotheses, suggesting that NHSOs pursuing earned income are less (versus more) likely to be established in regions where the socioeconomic factors indicate a high (versus low) level of human needs. These findings suggest a counterintuitive trend in the establishment of NHSOs and present cautionary information on pursuing commercial activities in the human services sector.
A consequentialist ethical analysis of federal funding of elective abortions
Authors: Gleeson Emile I. , Guerrini Christi J. 
Published: February 2021

AbstractInsurance coverage of abortion varies widely across the United States and is an extensively debated issue. Medicaid coverage of abortion is particularly relevant because the majority of abortion patients are poor or low‐income and are thus often covered by Medicaid. Since the Hyde Amendment was first passed in 1976, federal Medicaid funds have been banned from covering the costs of elective abortion. Although states are allowed to use their own funds to cover abortions for their Medicaid recipients, only 17 states currently do so. Of these 17 states, only five cover abortion costs voluntarily; the others do so pursuant to court order. The medical literature includes few ethical analyses of the Hyde Amendment’s ban on Medicaid funding of elective abortions. To fill this gap, we perform an ethical analysis of federal policy to fund elective abortions using a consequentialist approach focused on consequences for pregnant women and their children.
Identifying regions of inhomogeneities in spatial processes via an M‐RA and mixture priors
Authors: Benedetti Marco H. , Berrocal Veronica J. , Narisetty Naveen N. 
Published: February 2021

AbstractSoils have been heralded as a hidden resource that can be leveraged to mitigate and address some of the major global environmental challenges. Specifically, the organic carbon stored in soils, called soil organic carbon (SOC), can, through proper soil management, help offset fuel emissions, increase food productivity, and improve water quality. As collecting data on SOC are costly and time‐consuming, not much data on SOC are available, although understanding the spatial variability in SOC is of fundamental importance for effective soil management. In this manuscript, we propose a modeling framework that can be used to gain a better understanding of the dependence structure of a spatial process by identifying regions within a spatial domain where the process displays the same spatial correlation range. To achieve this goal, we propose a generalization of the multiresolution approximation (M‐RA) modeling framework of Katzfuss originally introduced as a strategy to reduce the computational burden encountered when analyzing massive spatial datasets. To allow for the possibility that the correlation of a spatial process might be characterized by a different range in different subregions of a spatial domain, we provide the M‐RA basis functions weights with a two‐component mixture prior with one of the mixture components a shrinking prior. We call our approach the mixture M‐RA. Application of the mixture M‐RA model to both stationary and nonstationary data show that the mixture M‐RA model can handle both types of data, can correctly establish the type of spatial dependence structure in the data (e.g., stationary versus not), and can identify regions of local stationarity.
Nbs1‐mediated DNA damage repair pathway regulates haematopoietic stem cell development and embryonic haematopoiesis
Authors: Chen Yu , Sun Jie , Ju Zhenyu , Wang Zhao‐Qi , Li Tangliang 
Published: February 2021

AbstractObjectivesDNA damages pose threats to haematopoietic stem cells (HSC) maintenance and haematopoietic system homeostasis. Quiescent HSCs in adult mouse bone marrow are resistant to DNA damage, while human umbilical cord blood‐derived proliferative HSCs are prone to cell death upon ionizing radiation. Murine embryonic HSCs proliferate in foetal livers and divide symmetrically to generate HSC pool. How murine embryonic HSCs respond to DNA damages is not well‐defined.Materials and methodsMice models with DNA repair molecule Nbs1 or Nbs1/p53 specifically deleted in embryonic HSCs were generated. FACS analysis, in vitro and in vivo HSC differentiation assays, qPCR, immunofluorescence and Western blotting were used to delineate roles of Nbs1‐p53 signaling in HSCs and haematopoietic progenitors.ResultsNbs1 deficiency results in persistent DNA breaks in embryonic HSCs, compromises embryonic HSC development and finally results in mouse perinatal lethality. The persistent DNA breaks in Nbs1 deficient embryonic HSCs render cell cycle arrest, while driving a higher rate of cell death in haematopoietic progenitors. Although Nbs1 deficiency promotes Atm‐Chk2‐p53 axis activation in HSCs and their progenies, ablation of p53 in Nbs1 deficient HSCs accelerates embryonic lethality.ConclusionsOur study discloses that DNA double‐strand repair molecule Nbs1 is essential in embryonic HSC development and haematopoiesis. Persistent DNA damages result in distinct cell fate in HSCs and haematopoietic progenitors. Nbs1 null HSCs tend to be maintained through cell cycle arrest, while Nbs1 null haematopoietic progenitors commit cell death. The discrepancies are mediated possibly by different magnitude of p53 signaling.
Point‐of‐care ultrasound during the COVID‐19 pandemic: A multidisciplinary approach between intensivists and echocardiographers
Authors: Yuriditsky Eugene , Saric Muhamed , Horowitz James M. 
Published: February 2021

AbstractPurposeThe coronavirus disease‐2019 (COVID‐19) led to a large influx of critically ill patients and altered echocardiography laboratory workflow. We developed a point‐of‐care ultrasound (POCUS) first approach to patients requiring echocardiography and describe our workflow and findings.MethodsWe performed a single‐center retrospective analysis of all POCUS studies performed on critically ill patients with COVID‐19. Sonography was performed by intensivists, uploaded and archived, and rapidly reviewed by echocardiographers. We evaluated each study based on the number of views obtained. Additionally, we provide a description of the workflow during the COVID‐19 surge at a tertiary care hospital in New York City.ResultsFifty patients had POCUS studies performed by intensivists and reviewed by echocardiographers obviating the need for sonographer‐performed studies. Of the 48 cardiac POCUS studies, 17% of patients had 4 of 4 standard views available while 53% had 3 of 4 standard views. The parasternal long‐axis view was obtained on 81%, subxiphoid view on 79%, apical 4‐chamber view on 71%, and parasternal short‐axis view on 63% of patients.ConclusionsOur POCUS workflow allowed intensivists to perform cardiac sonography for rapid bedside diagnosis of pathology with immediate interpretation performed by echocardiographers. At least 3 views were obtained in the majority of cases.
Lagged and dormant season climate better predict plant vital rates than climate during the growing season
Authors: Evers Sanne M. , Knight Tiffany M. , Inouye David W. , Miller Tom E. X. , Salguero‐Gómez Roberto , Iler Amy M. , Compagnoni Aldo 
Published: February 2021

AbstractUnderstanding the effects of climate on the vital rates (e.g., survival, development, reproduction) and dynamics of natural populations is a long‐standing quest in ecology, with ever‐increasing relevance in the face of climate change. However, linking climate drivers to demographic processes requires identifying the appropriate time windows during which climate influences vital rates. Researchers often do not have access to the long‐term data required to test a large number of windows, and are thus forced to make a priori choices. In this study, we first synthesize the literature to assess current a priori choices employed in studies performed on 104 plant species that link climate drivers with demographic responses. Second, we use a sliding‐window approach to investigate which combination of climate drivers and temporal window have the best predictive ability for vital rates of four perennial plant species that each have over a decade of demographic data (Helianthella quinquenervis, Frasera speciosa, Cylindriopuntia imbricata, and Cryptantha flava). Our literature review shows that most studies consider time windows in only the year preceding the measurement of the vital rate(s) of interest, and focus on annual or growing season temporal scales. In contrast, our sliding‐window analysis shows that in only four out of 13 vital rates the selected climate drivers have time windows that align with, or are similar to, the growing season. For many vital rates, the best window lagged more than 1 year and up to 4 years before the measurement of the vital rate. Our results demonstrate that for the vital rates of these four species, climate drivers that are lagged or outside of the growing season are the norm. Our study suggests that considering climatic predictors that fall outside of the most recent growing season will improve our understanding of how climate affects population dynamics.
A latitudinal gradient of microbial β‐diversity in continental paddy soils
Authors: Xiao Xian , Zhang Na , Ni Haowei , Yang Yunfeng , Zhou Jizhong , Sun Bo , Liang Yuting 
Published: February 2021

AbstractAimThe β‐diversity of plants and animals generally decreases with increasing latitudes. Here, we tested whether this relationship also holds for soil microbes at both functional and taxonomic levels.LocationChina.Time periodBetween June and October 2013.Major taxa studiedSoil archaea, bacteria, and functional genes.MethodsWe used a spatially explicit ‘L‐shaped’ sampling strategy in 39 paddy fields in China to study the pattern of soil microbial β‐diversity (i.e., species turnover, βz) across a latitudinal gradient (19.75° N to 47.58° N), with 11 soil samples taken within a 100 m × 100 m plot from each field. Archaeal and bacterial communities were analysed by sequencing 16S ribosomal RNA gene amplicons using Illumina MiSeq; microbial functional genes involved in C/N/P/S cycling were detected by GeoChip.ResultsWe showed that the microbial β‐diversity varied considerably across taxonomic and functional groups. For both soil microbial communities and functional genes, β‐diversity decreased significantly along elevated latitudes at the continental scale. Woesearchaeota of archaeal communities, Bacteroidetes of bacterial communities, and the functional genes involved in methane production displayed the greatest decreases. Both mean temperature during the growing season of rice plants and paddy soil heterogeneity contributed to the latitudinal patterns. Further analyses indicated that temperature was more important than soil heterogeneity in driving the β‐diversity of microbial communities and functional genes.Main conclusionsThese results highlight the importance of temperature‐driven soil microbial β‐diversity and suggest the potential to predict the changes of microbial diversity with climate change.