bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deforestation risk in the Peruvian Amazon basin
Authors: Rojas Eduardo , Zutta Brian R , Velazco Yessenia K , Montoya-Zumaeta Javier G , Salvà-Catarineu Montserrat 
Published: October 2021

SummaryThe prevention of tropical forest deforestation is essential for mitigating climate change. We tested the machine learning algorithm Maxent to predict deforestation across the Peruvian Amazon. We used official annual 2001–2019 deforestation data to develop a predictive model and to test the model’s accuracy using near-real-time forest loss data for 2020. Distance from agricultural land and distance from roads were the predictor variables that contributed most to the final model, indicating that a narrower set of variables contribute nearly 80% of the information necessary for prediction at scale. The permutation importance indicating variable information not present in the other variables was also highest for distance from agricultural land and distance from roads, at 40.5% and 14.3%, respectively. The predictive model registered 73.2% of the 2020 early alerts in a high or very high risk category; less than 1% of forest cover in national protected areas were registered as very high risk, but buffer zones were far more vulnerable, with 15% of forest cover being in this category. To our knowledge, this is the first study to use 19 years of annual data for deforestation risk. The open-source machine learning method could be applied to other forest regions, at scale, to improve strategies for reducing future deforestation.
Segments: An alternative rainfall problem
Authors: ACHTEN PETER 
Published: October 2021

Abstract
Elliot Soloway’s Rainfall problem is a well-known and well-studied problem to investigate the problem-solving strategies of programmers. Kathi Fisler investigated this programming challenge from the point of view of functional programmers. She showed that this particular challenge gives rise to five different high-level solution strategies, of which three are predominant and cover over 80% of all chosen solutions. In this study, we put forward the Segments problem as an alternative challenge to investigate the problem-solving skills of functional programmers. Analysis of the student solutions, their high-level solution strategies, and corresponding archetype solutions shows that the Segments problem gives rise to seven different high-level solution strategies that can be further divided into 17 subclasses. The Segments problem is particularly suited to investigate problem-solving skills that involve list processing and higher-order functions.
Empathic communication in dignity therapy: Feasibility of measurement and descriptive findings
Authors: Bylund Carma L. , Taylor Greenberry , Mroz Emily , Wilkie Diana J. , Yao Yingwei , Emanuel Linda , Fitchett George , Handzo George , Chochinov Harvey Max , Bluck Susan 
Published: October 2021

AbstractObjectiveDignity therapy (DT) is a guided process conducted by a health professional for reviewing one's life to promote dignity through the illness process. Empathic communication has been shown to be important in clinical interactions but has yet to be examined in the DT interview session. The Empathic Communication Coding System (ECCS) is a validated, reliable coding system used in clinical interactions. The aims of this study were (1) to assess the feasibility of the ECCS in DT sessions and (2) to describe the process of empathic communication during DT sessions.MethodsWe conducted a secondary analysis of 25 transcripts of DT sessions with older cancer patients. These DT sessions were collected as part of larger randomized controlled trial. We revised the ECCS and then coded the transcripts using the new ECCS-DT. Two coders achieved inter-rater reliability (κ = 0.84) on 20% of the transcripts and then independently coded the remaining transcripts.ResultsParticipants were individuals with cancer between the ages of 55 and 75. We developed the ECCS-DT with four empathic response categories: acknowledgment, reflection, validation, and shared experience. We found that of the 235 idea units, 198 had at least one of the four empathic responses present. Of the total 25 DT sessions, 17 had at least one empathic response present in all idea units.Significance of resultsThis feasibility study is an essential first step in our larger program of research to understand how empathic communication may play a role in DT outcomes. We aim to replicate findings in a larger sample and also investigate the linkage empathic communication may have in the DT session to positive patient outcomes. These findings, in turn, may lead to further refinement of training for dignity therapists, development of research into empathy as a mediator of outcomes, and generation of new interventions.
Diversity of white Guinea yam (Dioscorea rotundataPoir.) cultivars from Benin as revealed by agro-morphological traits and SNP markers
Authors: Agre Paterne A. , Dassou Anicet G. , Loko Laura E. Y. , Idossou Roger , Dadonougbo Eric , Gbaguidi Anicet , Mondo Jean M. , Muyideen Yusuf , Adebola Patrick O. , Asiedu Robert , Dansi Alexandre A. , Asfaw Asrat 
Published: October 2021

AbstractWhite Guinea yam (Dioscorea rotundataPoir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding.
Hidden Casualties: The Links between Armed Conflict and Intimate Partner Violence in Colombia
Authors: Svallfors Signe 
Published: October 2021

AbstractThe Colombian peace process was internationally celebrated for its unprecedented focus on women's experiences of war, but the everyday violence women that may face in their homes was not acknowledged. This article explores the links between exposure to local armed conflict violence and individual women's experiences of intimate partner violence. I combine pooled nationally representative data on individual women's experiences of intimate partner violence with information about the intensity of conflict during 2004–16. Results of fixed-effects linear probability models show that conflict was generally linked to a slightly elevated risk of women experiencing emotional, physical, and sexual violence perpetrated by their partner. Among women who had experienced intimate partner violence, conflict was related to an increased probability of being partnered at interview, which could reflect women staying in abusive relationships because conflict normalizes violence or increases women's reluctance to leave those relationships.
Frontline yet at the back of the queue – improving access and adaptations to CBT for Black African and Caribbean communities
Authors: Lawton Leila , McRae Melissa , Gordon Lorraine 
Published: October 2021

AbstractThis paper focuses on the Black minority ethnic population (Black British, Black African, Black Caribbean) and uses the term BME in reference to this group. Only 6.2% of BME people access psychological intervention for common mental disorders. In provision of cognitive behavioural therapy (CBT) the diversity in global majority populations1requires culturally specific informed and responsive approaches. The Improving Access to Psychological Therapies (IAPT) programme needs to be accountable, culturally congruent and strategic, to ensure accessibility and improve outcomes for BME people. According to the Mental Health Foundation (2019), a higher percentage of Black, Asian and other minority ethnic populations (BAME) are diagnosed with common, severe and complex mental health disorders. Despite the weight of literature on this, little has changed. The NHS Implementation Plan outlines trajectories for increased access and reduced attrition within mental health services, addressing inequalities for BAME populations.Evidence-based guidance and audits for provision of culturally sensitive and adapted therapies are presented in the pioneering (IAPT) BAME Positive Practice Guide (PPG). However, there are no funding arrangements or formal integrated frameworks to support implementation. The COVID-19 global pandemic and the high-profile death of George Floyd tragically exposed and highlighted the consequences of systemic racism. Understanding of the importance of service and clinical anti-racist practice is imperative for CBT therapists. Implementation of the BAME PPG audit tool ensures review of race equity in access, engagement, adaptation and workforce within IAPT and other mental health services. This could transform lives.Key learning aims(1)To understand the barriers (individual, societal and systemic) to accessing psychological therapies such as CBT and the impact on CBT treatment outcomes specifically for black minority ethnic (BME) populations.(2)To recognise barriers to implementation of formal frameworks for equitable access to psychological therapies such as CBT for BME communities.(3)To assist services and therapists to implement evidence-based learning, on cultural adaptations, to address barriers in access, retention and completion of CBT.(4)To provide examples of services that have taken successful actions to address the issues identified in the earlier points.
Stream Transport and Substrate Controls on Nitrous Oxide Yields From Hyporheic Zone Denitrification
Authors: Winnick M. J. 
Published: October 2021

AbstractRivers and streams act as globally significant sources of nitrous oxide (N2O) to the atmosphere, in part through denitrification reactions that will increase in response to ongoing anthropogenic nitrogen loading. While many factors that contribute to the release of N2O relative to inert dinitrogen (N2) are well described, the ability to predict N2O yields from streams remains a fundamental challenge. Here, I revisit results from the second Lotic Intersite Nitrogen eXperiments (LINX II) in the context of turbulent hyporheic exchange. Denitrification efficiency, or the fraction of nitrate delivered to the streambed by stream turbulence that is chemically reduced, emerges as the single best predictor of N2O yields and underpins the first statistically significant models of inter‐site N2O yields. This mechanistic connection is supported by reactive transport modeling of hyporheic zone denitrification representing advective flowpaths, flowpath mixing, and diffusion‐dominated anoxic microzones. Simulated N2O yields are inversely correlated with denitrification efficiency; however, advective models are unable to capture low LINX II N2O yields at low denitrification efficiencies. Hyporheic zone mixing exacerbates this inability to capture observed N2O yields via the promotion of N2O release from fast, oxic flowpaths. Instead, anoxic microzones are required to account for LINX II observations through consistently low N2O yields and the consumption of upstream‐produced N2O. Together, these results provide a framework for controls on stream N2O yields and suggest that stream corridor restoration designs aimed at increasing the capacity of hyporheic zones to remediate nitrate loading, as opposed to increasing hyporheic exchange, will also reduce proportional N2O emissions.
Development of a highly controlled system for large-area, directional printing of quasi-1D nanomaterials
Authors: Christou Adamos , Liu Fengyuan , Dahiya Ravinder 
Published: October 2021

AbstractPrinting is a promising method for the large-scale, high-throughput, and low-cost fabrication of electronics. Specifically, the contact printing approach shows great potential for realizing high-performance electronics with aligned quasi-1D materials. Despite being known for more than a decade, reports on a precisely controlled system to carry out contact printing are rare and printed nanowires (NWs) suffer from issues such as location-to-location and batch-to-batch variations. To address this problem, we present here a novel design for a tailor-made contact printing system with highly accurate control of printing parameters (applied force: 0–6 N ± 0.3%, sliding velocity: 0–200 mm/s, sliding distance: 0–100 mm) to enable the uniform printing of nanowires (NWs) aligned along 93% of the large printed area (1 cm2). The system employs self-leveling platforms to achieve optimal alignment between substrates, whereas the fully automated process minimizes human-induced variation. The printing dynamics of the developed system are explored on both rigid and flexible substrates. The uniformity in printing is carefully examined by a series of scanning electron microscopy (SEM) images and by fabricating a 5 × 5 array of NW-based photodetectors. This work will pave the way for the future realization of highly uniform, large-area electronics based on printed NWs.
BRD9 inhibition promotes PUMA-dependent apoptosis and augments the effect of imatinib in gastrointestinal stromal tumors
Authors: Mu Jianfeng , Sun Xuezeng , Zhao Zhipeng , Sun Hao , Sun Pengda 
Published: October 2021

AbstractGastrointestinal stromal tumors (GISTs) are primarily characterized by activating mutations of tyrosine kinase or platelet-derived growth factor receptor alpha. Although the revolutionary therapeutic outcomes of imatinib are well known, the long-term benefits of imatinib are still unclear. The effects of BRD9, a recently identified subunit of noncanonical BAF complex (ncBAF) chromatin remodeling complexes, in GISTs are not clear. In the current study, we evaluated the functional role of BRD9 in GIST progression. Our findings demonstrated that the expression of BRD9 was upregulated in GIST tissues. The downregulation or inhibition of BRD9 could significantly reduce cellular proliferation, and facilitates apoptosis in GISTs. BRD9 inhibition could promote PUMA-dependent apoptosis in GISTs and enhance imatinib activity in vitro and in vivo. BRD9 inhibition synergizes with imatinib in GISTs by inducing PUMA upregulation. Mechanism study revealed that BRD9 inhibition promotes PUMA induction via the TUFT1/AKT/GSK-3β/p65 axis. Furthermore, imatinib also upregulates PUMA by targeting AKT/GSK-3β/p65 axis. In conclusion, our results indicated that BRD9 plays a key role in the progression of GISTs. Inhibition of BRD9 is a novel therapeutic strategy in GISTs treated alone or in combination with imatinib.
Isolation of a panel of ultra-potent human antibodies neutralizing SARS-CoV-2 and viral variants of concern
Authors: Gorchakov Andrey A. , Kulemzin Sergey V. , Guselnikov Sergey V. , Baranov Konstantin O. , Belovezhets Tatyana N. , Mechetina Ludmila V. , Volkova Olga Yu. , Najakshin Alexander M. , Chikaev Nikolai A. , Chikaev Anton N. , Solodkov Pavel P. , Larichev Victor F. , Gulyaeva Marina A. , Markhaev Alexander G. , Kononova Yulia V. , Alekseyev Alexander Yu. , Shestopalov Alexander M. , Yusubalieva Gaukhar M. , Klypa Tatiana V. , Ivanov Alexander V. , Valuev-Elliston Vladimir T. , Baklaushev Vladimir P. , Taranin Alexander V. 
Published: October 2021

AbstractIn the absence of virus-targeting small-molecule drugs approved for the treatment and prevention of COVID-19, broadening the repertoire of potent SARS-CoV-2-neutralizing antibodies represents an important area of research in response to the ongoing pandemic. Systematic analysis of such antibodies and their combinations can be particularly instrumental for identification of candidates that may prove resistant to the emerging viral escape variants. Here, we isolated a panel of 23 RBD-specific human monoclonal antibodies from the B cells of convalescent patients. A surprisingly large proportion of such antibodies displayed potent virus-neutralizing activity both in vitro and in vivo. Four of the isolated nAbs can be categorized as ultrapotent with an apparent IC100 below 16 ng/mL. We show that individual nAbs as well as dual combinations thereof retain activity against currently circulating SARS-CoV-2 variants of concern (such as B.1.1.7, B.1.351, B.1.617, and C.37), as well as against other viral variants. When used as a prophylactics or therapeutics, these nAbs could potently suppress viral replication and prevent lung pathology in SARS-CoV-2-infected hamsters. Our data contribute to the rational development of oligoclonal therapeutic nAb cocktails mitigating the risk of SARS-CoV-2 escape.
mTOR-related synaptic pathology causes autism spectrum disorder-associated functional hyperconnectivity
Authors: Pagani Marco , Barsotti Noemi , Bertero Alice , Trakoshis Stavros , Ulysse Laura , Locarno Andrea , Miseviciute Ieva , De Felice Alessia , Canella Carola , Supekar Kaustubh , Galbusera Alberto , Menon Vinod , Tonini Raffaella , Deco Gustavo , Lombardo Michael V. , Pasqualetti Massimo , Gozzi Alessandro 
Published: October 2021

AbstractPostmortem studies have revealed increased density of excitatory synapses in the brains of individuals with autism spectrum disorder (ASD), with a putative link to aberrant mTOR-dependent synaptic pruning. ASD is also characterized by atypical macroscale functional connectivity as measured with resting-state fMRI (rsfMRI). These observations raise the question of whether excess of synapses causes aberrant functional connectivity in ASD. Using rsfMRI, electrophysiology and in silico modelling in Tsc2 haploinsufficient mice, we show that mTOR-dependent increased spine density is associated with ASD -like stereotypies and cortico-striatal hyperconnectivity. These deficits are completely rescued by pharmacological inhibition of mTOR. Notably, we further demonstrate that children with idiopathic ASD exhibit analogous cortical-striatal hyperconnectivity, and document that this connectivity fingerprint is enriched for ASD-dysregulated genes interacting with mTOR or Tsc2. Finally, we show that the identified transcriptomic signature is predominantly expressed in a subset of children with autism, thereby defining a segregable autism subtype. Our findings causally link mTOR-related synaptic pathology to large-scale network aberrations, revealing a unifying multi-scale framework that mechanistically reconciles developmental synaptopathy and functional hyperconnectivity in autism.
Friction modulation in limbless, three-dimensional gaits and heterogeneous terrains
Authors: Zhang Xiaotian , Naughton Noel , Parthasarathy Tejaswin , Gazzola Mattia 
Published: October 2021

AbstractMotivated by a possible convergence of terrestrial limbless locomotion strategies ultimately determined by interfacial effects, we show how both 3D gait alterations and locomotory adaptations to heterogeneous terrains can be understood through the lens of local friction modulation. Via an effective-friction modeling approach, compounded by 3D simulations, the emergence and disappearance of a range of locomotory behaviors observed in nature is systematically explained in relation to inhabited environments. Our approach also simplifies the treatment of terrain heterogeneity, whereby even solid obstacles may be seen as high friction regions, which we confirm against experiments of snakes ‘diffracting’ while traversing rows of posts, similar to optical waves. We further this optic analogy by illustrating snake refraction, reflection and lens focusing. We use these insights to engineer surface friction patterns and demonstrate passive snake navigation in complex topographies. Overall, our study outlines a unified view that connects active and passive 3D mechanics with heterogeneous interfacial effects to explain a broad set of biological observations, and potentially inspire engineering design.
Regulation of local GTP availability controls RAC1 activity and cell invasion
Authors: Bianchi-Smiraglia Anna , Wolff David W. , Marston Daniel J. , Deng Zhiyong , Han Zhannan , Moparthy Sudha , Wombacher Rebecca M. , Mussell Ashley L. , Shen Shichen , Chen Jialin , Yun Dong-Hyun , O’Brien Cox Anderson , Furdui Cristina M. , Hurley Edward , Feltri Maria Laura , Qu Jun , Hollis Thomas , Kengne Jules Berlin Nde , Fongang Bernard , Sousa Rui J. , Kandel Mikhail E. , Kandel Eugene S. , Hahn Klaus M. , Nikiforov Mikhail A. 
Published: October 2021

AbstractPhysiological changes in GTP levels in live cells have never been considered a regulatory step of RAC1 activation because intracellular GTP concentration (determined by chromatography or mass spectrometry) was shown to be substantially higher than the in vitro RAC1 GTP dissociation constant (RAC1-GTP Kd). Here, by combining genetically encoded GTP biosensors and a RAC1 activity biosensor, we demonstrated that GTP levels fluctuating around RAC1-GTP Kd correlated with changes in RAC1 activity in live cells. Furthermore, RAC1 co-localized in protrusions of invading cells with several guanylate metabolism enzymes, including rate-limiting inosine monophosphate dehydrogenase 2 (IMPDH2), which was partially due to direct RAC1-IMPDH2 interaction. Substitution of endogenous IMPDH2 with IMPDH2 mutants incapable of binding RAC1 did not affect total intracellular GTP levels but suppressed RAC1 activity. Targeting IMPDH2 away from the plasma membrane did not alter total intracellular GTP pools but decreased GTP levels in cell protrusions, RAC1 activity, and cell invasion. These data provide a mechanism of regulation of RAC1 activity by local GTP pools in live cells.
Faecal miRNA profiles associated with age, sex, BMI, and lifestyle habits in healthy individuals
Authors: Francavilla Antonio , Gagliardi Amedeo , Piaggeschi Giulia , Tarallo Sonia , Cordero Francesca , Pensa Ruggero G. , Impeduglia Alessia , Caviglia Gian Paolo , Ribaldone Davide Giuseppe , Gallo Gaetano , Grioni Sara , Ferrero Giulio , Pardini Barbara , Naccarati Alessio 
Published: October 2021

AbstractFor their stability and detectability faecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. However, there is no evidence on how stool miRNA profiles change according to an individual’s age, sex, and body mass index (BMI) or how lifestyle habits influence the expression levels of these molecules. We explored the relationship between the stool miRNA levels and common traits (sex, age, BMI, and menopausal status) or lifestyle habits (physical activity, smoking status, coffee, and alcohol consumption) as derived by a self-reported questionnaire, using small RNA-sequencing data of samples from 335 healthy subjects. We detected 151 differentially expressed miRNAs associated with one variable and 52 associated with at least two. Differences in miR-638 levels were associated with age, sex, BMI, and smoking status. The highest number of differentially expressed miRNAs was associated with BMI (n = 92) and smoking status (n = 84), with several miRNAs shared between them. Functional enrichment analyses revealed the involvement of the miRNA target genes in pathways coherent with the analysed variables. Our findings suggest that miRNA profiles in stool may reflect common traits and lifestyle habits and should be considered in relation to disease and association studies based on faecal miRNA expression.