bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-decadal destabilization of vegetation activity on the Mongolian Plateau
Authors: Zhao Xia , Shen Haihua , Geng Xiaoqing , Fang Jingyun 
Published: January 2021

Abstract
Steppes on the Mongolian Plateau, mainly within the Republic of Mongolia and the Inner Mongolia Autonomous Region (IMAR) of China, have been subjected to widespread degradation as a result of climate change and human utilization. Field experiments and long-term observations suggest that the productivity of degraded grassland ecosystems might show greater instability, i.e. stronger interannual variation in vegetation activities, when driven by climate change. However, it remains unknown whether this hypothesized destabilization of steppe vegetation activity has occurred in the past three decades and how this destabilization has fed back to livestock production on the plateau. Herein, we define temporal instability of vegetation activity using three indicators, the start and end of the growing season as indicated by the normalized difference vegetation index (NDVI) and the mean growing-season NDVI, and examine their trends between 1983 and 2015. Our results show a significant destabilization of vegetation activity over a large proportion of the total steppe area. Compared with the IMAR, vegetation destabilization has occurred to a significantly higher extent in Mongolia. Climate warming, drying and interannual climate variability accounted for approximately 60%–80% of the vegetation destabilization. The destabilization of steppe productivity was significantly associated with the interannual variability of livestock production in Mongolia, while the interannual variability of steppe productivity and livestock production were decoupled in the IMAR. Our findings highlight the need to improve livestock production systems and conserve degraded grasslands for sustainable development in view of the destabilization of steppe productivity on the Mongolian Plateau.
Protein interactions with chemical vapor deposited graphene modified by substrate
Authors: Brightbill Eleanor L , Young Katherine T , Gezahagne Hilena F , Jin Decarle S , Hitchcock Bryce , Vogel Eric M 
Published: January 2021

Abstract
Graphene has been utilized in sensors to detect a wide range of biomolecules (e.g. glucose, DNA, antigens, enzyme activity, dopamine) using various sensing modalities (e.g. surface plasmon resonance, potentiometry, electro-impedance spectroscopy, cyclic voltammetry). However, while graphene-based biosensors have been demonstrated in many different architectures, little attention has been given to the effects of the substrate that supports the atomically thin graphene layer. In this work, we investigate protein adhesion of model small (lysozyme), medium (bovine serum albumin), and large (fibrinogen) proteins on monolayer graphene with support substrates of varying hydrophobicity and surface polarity. Ex situ adsorption is measured via ellipsometry. For Au and Si support substrates, in situ adhesion of lysozyme is measured via quartz crystal microbalance. The results indicate that not only the equilibrium attachment, but also the kinetics of interaction, can be affected by the substrate. Overall, a more hydrophobic substrate leads to a larger amount of adsorption to graphene. Moreover, the effect is only observed with monolayer graphene, where no substrate effect is observed with the addition of a second graphene layer. This work indicates that the substrate of a graphene-based biosensor is an important but currently overlooked parameter when understanding and optimizing the performance of the device. The level of non-selective protein adsorption on graphene can be independently engineered through modifying the support substrate without directly modifying the graphene itself.
Microstructure and mechanical properties of aluminum/steel bimetal using compound casting with electroless nickel plating
Authors: Bao Ziming , Wang Sheng , Han Renheng , Tang Ming , Zhao Chengzhi , Zhang Hexin 
Published: January 2021

Abstract
The surface of steel substrate was pretreated by nickel plating and Aluminum/nickel-plated steel bimetal was prepared by compound casting. After liquid aluminum was casted on the surface of the nickel-plated steel, it was placed in a heat preservation device and temperature set at 760 °C. In the compound casting process of molten aluminum and nickel-plated steel, good metallurgical bonding is formed between aluminum and steel by means of diffusion. Subsequently, the microstructure of the aluminum/nickel-plated steel bimetal was examined using Scanning Electron Microscopy (SEM) and Energy Dispersive Spectroscopy (EDS) techniques. The phase composition of the intermediate layer was analyzed by x-ray diffraction (XRD). Further, the bonding properties and fracture mechanism of the intermediate layer were analyzed by measuring the corresponding Vickers microhardness and shear strength. The results show that the intermediate layer is divided into two layers. In addition, intermetallic compounds appear in the intermediate layer; Al5Fe2, near the steel side, and Al8Fe2Si, near the aluminum side. The main phases in the intermediate layer are α-Al, α-Fe, Al5Fe2, Al5FeSi and Al8Fe2Si. The microhardness of the intermediate layer of the aluminum/steel bimetal is higher than that of both the aluminum matrix and steel matrix. It is observed that the thickness of the intermediate layer of the aluminum/nickel-plated steel bimetal increases with the increase of the holding time. When the holding time was 15 min, the intermediate layer of the aluminum/nickel-plated steel bimetal exhibits the highest shear strength, i.e. 13.4 MPa. The fracture of the aluminum/steel bimetal is a brittle fracture, and starts from the intermediate layer. The results show that nickel plating on steel substrate can obviously improve the casting properties of an aluminum/steel bimetal.
Electrospun fabrication and direct coating of bio-degradable fibrous composite on orthopedic Titanium implant: Synthesis and Characterizations
Authors: Al Aboody Mohammed Saleh 
Published: January 2021

Abstract
For orthopedic bone regeneration, an extracellular matrix (ECM) mimicking the composite’s ability has been highly expected by natural hard tissue along with their bio-activeness, bio-compatibleness, and bio-degradable properties. An electrospinning approach is one of the high potential processes to manufacture the porous material, and the method has highly recommended for the production of porous fibrous materials in the presence of various active compounds owing to its uniqueness of producing randomly oriented fibrous matrices with appropriate porosity. In this work, we report the fibrous composite coating process on the orthopedic titanium (Ti) plate during the process of electrospinning by simply fixing the Ti metal on the aluminum foil in the drum collector. This approach gives the bio-compatible Ti implant with ECM mimicking properties. The bio-activeness of that implant will be obtained through the presence of minerals (Sr2+ and Ce3+) substituted hydroxyapatite (MHAP) particles. The formation of the desired composites and their phase characteristics were carefully evaluated by Fourier Transform Infra-Red (FTIR) spectroscopy and X-ray diffraction (XRD) analysis, respectively. The formation of a fibrous network and various minerals in an appropriate manner were established by a scanning electron microscope (SEM) and energy dispersive X-ray analyzer (EDX) instruments. The important notable thing is their Vickers hardness was very lower for the Poly(3-hydroxybutyrate) (PHB) polymer containing fibrous composite. These results strongly suggest the conclusion that the synthesized fibrous composite coated material will act as a better ECM mimicking implant for orthopedic applications.
Impacts of Medicaid Expansion Before Conception on Prepregnancy Health, Pregnancy Health, and Outcomes
Authors: Margerison Claire E , Kaestner Robert , Chen Jiajia , MacCallum-Bridges Colleen 
Published: January 2021

Abstract
Preconception health care is heralded as an essential method of improving pregnancy health and outcomes. However, access to health care for low-income US women of reproductive age has been limited because of a lack of health insurance. Expansions of Medicaid program eligibility under the Affordable Care Act (as well as prior expansions in some states) have changed this circumstance and expanded health insurance coverage for low-income women. These Medicaid expansions provide an opportunity to assess whether obtaining health insurance coverage improves prepregnancy and pregnancy health and reduces prevalence of adverse pregnancy outcomes. We tested this hypothesis using vital statistics data from 2011–2017 on singleton births to female US residents aged 15–44 years. We examined associations between preconception exposure to Medicaid expansion and measures of prepregnancy health, pregnancy health, and pregnancy outcomes using a difference-in-differences empirical approach. Increased Medicaid eligibility was not associated with improvements in prepregnancy or pregnancy health measures and did not reduce the prevalence of adverse birth outcomes (e.g., prevalence of preterm birth increased by 0.1 percentage point (95% confidence interval: −0.2, 0.3)). Increasing Medicaid eligibility alone may be insufficient to improve prepregnancy or pregnancy health and birth outcomes. Preconception programming in combination with attention to other structural determinants of pregnancy health is needed.
Compression of quantification uncertainty for scRNA-seq counts
Authors: Van Buren Scott , Sarkar Hirak , Srivastava Avi , Rashid Naim U , Patro Rob , Love Michael I 
Published: January 2021

AbstractMotivationQuantification estimates of gene expression from single-cell RNA-seq (scRNA-seq) data have inherent uncertainty due to reads that map to multiple genes. Many existing scRNA-seq quantification pipelines ignore multi-mapping reads and therefore underestimate expected read counts for many genes. alevin accounts for multi-mapping reads and allows for the generation of ‘inferential replicates’, which reflect quantification uncertainty. Previous methods have shown improved performance when incorporating these replicates into statistical analyses, but storage and use of these replicates increases computation time and memory requirements.ResultsWe demonstrate that storing only the mean and variance from a set of inferential replicates (‘compression’) is sufficient to capture gene-level quantification uncertainty, while reducing disk storage to as low as 9% of original storage, and memory usage when loading data to as low as 6%. Using these values, we generate ‘pseudo-inferential’ replicates from a negative binomial distribution and propose a general procedure for incorporating these replicates into a proposed statistical testing framework. When applying this procedure to trajectory-based differential expression analyses, we show false positives are reduced by more than a third for genes with high levels of quantification uncertainty. We additionally extend the Swish method to incorporate pseudo-inferential replicates and demonstrate improvements in computation time and memory usage without any loss in performance. Lastly, we show that discarding multi-mapping reads can result in significant underestimation of counts for functionally important genes in a real dataset.Availability and implementationmakeInfReps and splitSwish are implemented in the R/Bioconductor fishpond package available at https://bioconductor.org/packages/fishpond. Analyses and simulated datasets can be found in the paper’s GitHub repo at https://github.com/skvanburen/scUncertaintyPaperCode.Supplementary informationSupplementary data are available at Bioinformatics online.
ProDerAl: reference position dependent alignment
Authors: Crysup Benjamin , Budowle Bruce , Woerner August E 
Published: January 2021

Abstract

Motivation
Current read-mapping software uses a singular specification of alignment parameters with respect to the reference. In the presence of varying reference structures (such as the repetitive regions of the human genome), alignments can be improved if those parameters are allowed vary.

Results
To that end, the C++ program ProDerAl was written to refine previously generated alignments using varying parameters for these problematic regions. Synthetic benchmarks show that this realignment can result in an order of magnitude fewer misaligned bases.

Availability and implementation
*Nix users can retrieve the source from GitHub (https://github.com/Benjamin-Crysup/proderal.git). Windows binary available at https://github.com/Benjamin-Crysup/proderal/releases/download/v1.1/proderal.zip.

Supplementary information
Supplementary data are available at Bioinformatics online.
Gender, risk assessment and coercive control: Contradictions in terms?
Authors: Barlow Charlotte , Walklate Sandra 
Published: January 2021

AbstractIn December 2015, the criminal offence of coercive control was introduced in England and Wales. Whilst, in this legislation, this concept is presumed to be gender-neutral, there is widespread agreement that coercive control is gendered. Using empirical data gathered in one police force area in the South of England, this paper offers an exploration of the feasibility of the extent to which existing risk assessment practices and understandings of risk embedded within them, can incorporate the phenomenon of coercive control. The findings highlight concerns about gender-blind, incident-led (rather than process-led) approaches to assessing risk when these approaches are set against victim/survivor concerns. These concerns highlight the inherent problems embedded in the contemporary gender-blind embrace of the concept of risk as assumed in practices of risk assessment.
Do reciprocal herkogamy and pollinators affect legitimate pollen flow in distylous species of Rubiaceae?
Authors: Furtado Marco Túlio , Matias Raphael , Pérez-Barrales Rocio , Consolaro Hélder 
Published: January 2021

AbstractThe function of the reciprocal position of anthers and stigmas of the floral morphs in distylous flowers is to promote cross-pollination between morphs (legitimate pollination). Deviations from reciprocity can negatively affect the rates of legitimate pollen deposition, but other floral traits or the pollination environment might contribute to the function of distyly. In populations of four species of Palicourea and Psychotria, we quantified reciprocity using adaptive inaccuracy and measured the stigmatic lobe length to estimate how these traits influenced legitimate pollen deposition. We described the functional groups of pollinators and compared legitimate pollen flow between morphs in populations visited by different groups. Variations in reciprocity and stigmatic lobe length correlated with the rates of legitimate pollen depositions, with more reciprocal stigmas and longer stigmatic lobes presenting proportionally more legitimate pollen. Populations most frequently visited by bees or with generalized pollination displayed asymmetries in pollen flow between morphs, but with higher legitimate pollination in the S-morph. In contrast, L- and S-flowers showed similar legitimate pollen deposition in the population predominantly visited by hummingbirds. Our results suggest that reciprocity affects the function of distyly; however, floral traits such as stigmatic lobe length and the pollination environment can also influence the rates of legitimate pollen.
Sequence of clinical and neurodegeneration events in Parkinson’s disease progression
Authors: Oxtoby Neil P , Leyland Louise-Ann , Aksman Leon M , Thomas George E C , Bunting Emma L , Wijeratne Peter A , Young Alexandra L , Zarkali Angelika , Tan Manuela M X , Bremner Fion D , Keane Pearse A , Morris Huw R , Schrag Anette E , Alexander Daniel C , Weil Rimona S 
Published: January 2021

Abstract
Dementia is one of the most debilitating aspects of Parkinson’s disease. There are no validated biomarkers that can track Parkinson’s disease progression, nor accurately identify patients who will develop dementia and when. Understanding the sequence of observable changes in Parkinson’s disease in people at elevated risk for developing dementia could provide an integrated biomarker for identifying and managing individuals who will develop Parkinson’s dementia. We aimed to estimate the sequence of clinical and neurodegeneration events, and variability in this sequence, using data-driven statistical modelling in two separate Parkinson’s cohorts, focusing on patients at elevated risk for dementia due to their age at symptom onset. We updated a novel version of an event-based model that has only recently been extended to cope naturally with clinical data, enabling its application in Parkinson’s disease for the first time. The observational cohorts included healthy control subjects and patients with Parkinson’s disease, of whom those diagnosed at age 65 or older were classified as having high risk of dementia. The model estimates that Parkinson’s progression in patients at elevated risk for dementia starts with classic prodromal features of Parkinson’s disease (olfaction, sleep), followed by early deficits in visual cognition and increased brain iron content, followed later by a less certain ordering of neurodegeneration in the substantia nigra and cortex, neuropsychological cognitive deficits, retinal thinning in dopamine layers, and further deficits in visual cognition. Importantly, we also characterize variation in the sequence. We found consistent, cross-validated results within cohorts, and agreement between cohorts on the subset of features available in both cohorts. Our sequencing results add powerful support to the increasing body of evidence suggesting that visual processing specifically is affected early in patients with Parkinson’s disease at elevated risk of dementia. This opens a route to earlier and more precise detection, as well as a more detailed understanding of the pathological mechanisms underpinning Parkinson’s dementia.
A review of potential biomarkers for assessing physical and psychological trauma in paediatric burns
Authors: Carlton Morgan , Voisey Joanne , Parker Tony J , Punyadeera Chamindie , Cuttle Leila 
Published: January 2021

Abstract
Biological markers that evaluate physical healing as well as psychological impact of a burn are essential for effective treatment of paediatric burns. The objective of this review is to summarize the evidence supporting the use of biomarkers in children with burns. An extensive review of the literature was performed using PubMed. A total of 59 biomarkers were identified relating to burn presence, specifically relating to processes involved in inflammation, wound healing, growth and metabolism. In addition, biomarkers involved in the stress response cascade following a burn trauma were also identified. Although many biomarkers have been identified that are potentially associated with burn-related physical and psychological trauma, an understanding of burn biology is still lacking in children. We propose that future research in the field of children’s burns should be conducted using broad screening methods for identifying potential biomarkers, examine the biological interactions of different biomarkers, utilize child-appropriate biological fluids such as urine or saliva, and include a range of different severity burns. Through further research, the biological response to burn injury may be fully realized and clinically relevant diagnostic tests and treatment therapies utilizing these biomarkers could be developed, for the improvement of healing outcomes in paediatric burn patients.
A Structure–Function Substrate of Memory for Spatial Configurations in Medial and Lateral Temporal Cortices
Authors: Tavakol Shahin , Li Qiongling , Royer Jessica , Vos de Wael Reinder , Larivière Sara , Lowe Alex , Paquola Casey , Jefferies Elizabeth , Hartley Tom , Bernasconi Andrea , Bernasconi Neda , Smallwood Jonathan , Bohbot Veronique , Caciagli Lorenzo , Bernhardt Boris 
Published: January 2021

Abstract
Prior research has shown a role of the medial temporal lobe, particularly the hippocampal–parahippocampal complex, in spatial cognition. Here, we developed a new paradigm, the conformational shift spatial task (CSST), which examines the ability to encode and retrieve spatial relations between unrelated items. This task is short, uses symbolic cues, incorporates two difficulty levels, and can be administered inside the scanner. A cohort of 48 healthy young adults underwent the CSST, together with a set of behavioral measures and multimodal magnetic resonance imaging (MRI). Inter-individual differences in CSST performance correlated with scores on an established spatial memory paradigm, but neither with episodic memory nor mnemonic discrimination, supporting specificity. Analyzing high-resolution structural MRI data, individuals with better spatial memory showed thicker medial and lateral temporal cortices. Functional relevance of these findings was supported by task-based functional MRI analysis in the same participants and ad hoc meta-analysis. Exploratory resting-state functional MRI analyses centered on clusters of morphological effects revealed additional modulation of intrinsic network integration, particularly between lateral and medial temporal structures. Our work presents a novel spatial memory paradigm and supports an integrated structure–function substrate in the human temporal lobe. Task paradigms are programmed in python and made open access.
Accounting for Subjectivity in Experimental Research on Human Olfaction
Authors: Mantel Marylou , Roy Jean-Michel , Bensafi Moustafa 
Published: January 2021

Abstract
Although olfaction is a modality with great interindividual perceptual disparities, its subjective dimension has been let aside in modern research, in line with the overall neglect of consciousness in experimental psychology. However, following the renewed interest for the neural bases of consciousness, some methodological leads have been proposed to include subjectivity in experimental protocols. Here, we argue that adapting such methods to the field of olfaction will allow to rigorously acquire subjective reports, and we present several ways to do so. This will improve the understanding of diversity in odor perception and its underlying neural mechanisms.