bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increase in beaver dams controls surface water and thermokarst dynamics in an Arctic tundra region, Baldwin Peninsula, northwestern Alaska
Authors: Jones Benjamin M , Tape Ken D , Clark Jason A , Nitze Ingmar , Grosse Guido , Disbrow Jeff 
Published: March 2020

Abstract
Beavers are starting to colonize low arctic tundra regions in Alaska and Canada, which has implications for surface water changes and ice-rich permafrost degradation. In this study, we assessed the spatial and temporal dynamics of beaver dam building in relation to surface water dynamics and thermokarst landforms using sub-meter resolution satellite imagery acquired between 2002 and 2019 for two tundra areas in northwestern Alaska. In a 100 km2 study area near Kotzebue, the number of dams increased markedly from 2 to 98 between 2002 and 2019. In a 430 km2 study area encompassing the entire northern Baldwin Peninsula, the number of dams increased from 94 to 409 between 2010 and 2019, indicating a regional trend. Correlating data on beaver dam numbers with surface water area mapped for 12 individual years between 2002 and 2019 for the Kotzebue study area showed a significant positive correlation (R2 = 0.61; p < .003). Beaver-influenced waterbodies accounted for two-thirds of the 8.3% increase in total surface water area in the Kotzebue study area during the 17 year period. Beavers specifically targeted thermokarst landforms in their dam building activities. Flooding of drained thermokarst lake basins accounted for 68% of beaver-influenced surface water increases, damming of lake outlets accounted for 26%, and damming of beaded streams accounted for 6%. Surface water increases resulting from beaver dam building likely exacerbated permafrost degradation in the region, but dam failure also factored into the drainage of several thermokarst lakes in the northern Baldwin Peninsula study region, which could promote local permafrost aggradation in freshly exposed lake sediments. Our findings highlight that beaver-driven ecosystem engineering must be carefully considered when accounting for changes occurring in some permafrost regions, and in particular, regional surface water dynamics in low Arctic and Boreal landscapes.
Role of additives in silica-supported polyethylenimine adsorbents for CO2 adsorption
Authors: Fang Qianxi , Huang Weiqiu , Wang Hongning 
Published: March 2020

Abstract
SiO2 aerogels were prepared by sol-gel method and methyl alkylation reaction using TEOS as silicon sources. Silica-supported polyethylenimine (PEI/SiO2) adsorbents for CO2 adsorption were prepare by grafting techniques, in which mesoporous SiO2 aerogel was loaded with PEI and organic compounds functionalized by hydroxyl or amino groups as dopants. CO2 adsorption isotherms of PEI amine-modified SiO2 aerogels were measured and the results show that the maximum CO2 adsorption capacity (1.8 mmol g−1) was obtained over a doped SA-PEI-N-Y loaded with 45% PEI and 15% N-Y (N-[3-(Trimethoxysilyl)propyl]ethylenediamine, denoted as N-Y). In addition, SA-PEI-N-Y has stronger thermal stability than SA-PEI-60% in nitrogen from room temperature to 800 °C at a heating rate of 10 °C min−1. It turns out that N-[3-(Trimethoxysilyl)propyl]ethylenediamine is the best dopant.
Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders
Authors: Bozkurt Varolgüneş Yasemin , Bereau Tristan , Rudzinski Joseph F 
Published: March 2020

Abstract
Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential features of the underlying system. Data-driven techniques provide a systematic route to constructing this landscape, without the need for extensive a priori intuition into the relevant driving forces. In particular, autoencoders are powerful tools for dimensionality reduction, as they naturally force an information bottleneck and, thereby, a low-dimensional embedding of the essential features. While variational autoencoders ensure continuity of the embedding by assuming a unimodal Gaussian prior, this is at odds with the multi-basin free-energy landscapes that typically arise from the identification of meaningful collective variables. In this work, we incorporate this physical intuition into the prior by employing a Gaussian mixture variational autoencoder (GMVAE), which encourages the separation of metastable states within the embedding. The GMVAE performs dimensionality reduction and clustering within a single unified framework, and is capable of identifying the inherent dimensionality of the input data, in terms of the number of Gaussians required to categorize the data. We illustrate our approach on two toy models, alanine dipeptide, and a challenging disordered peptide ensemble, demonstrating the enhanced clustering effect of the GMVAE prior compared to standard VAEs. The resulting embeddings appear to be promising representations for constructing Markov state models, highlighting the transferability of the dimensionality reduction from static equilibrium properties to dynamics.
Projective modules with unique maximal submodules are cyclic
Authors: Sato Masahisa 
Published: March 2020

There is a question formulated by R. Ware in 1971. That is, if a projective right

R
R

-module

P
P

has a unique maximal submodule

L
L

, then

L
L

is the largest maximal submodule of

P
P

. First we give a structure theorem for such a projective module. Next we define the notion of a minimal generator set and give an affirmative answer to this question by using this notion. In the last section, we give an example of a non-quasi-small module to discuss whether the answer to this question is affirmative or negative. The key theorem in Comm. Algebra 31 (2003), pp. 4195–4241 asserts that answer to this question is negative. But our example seems to be a counterexample of this key theorem.
A Reappraisal of Superficial Pleomorphic Liposarcoma
Authors: Berg Scott Hilliard , Massoud Cathy Meade , Jackson-Cook Colleen , Boikos Sosipatros Alexander , Smith Steven Christopher , Mochel Mark Cameron 
Published: March 2020

Abstract

Objectives
Superficial pleomorphic liposarcoma (PL) has a favorable prognosis compared to deeply seated PL. Given developments in the classification of lipomatous neoplasms, we reappraised a series of cases.

Methods
Retrospective clinicopathologic evaluation and genome-wide single-nucleotide polymorphism (SNP) microarray studies were performed for cases previously designated superficial PL.

Results
Four cases were identified (age, 48-70 years). Two were dermally confined, whereas two were superficial subcutaneous; no recurrences or metastases were reported. Tumors demonstrated pleomorphic spindled morphology with variable cellularity. Multivacuolated atypical lipoblasts were focal in 3 and abundant in 1. Dermal tumors demonstrated atypical cells within sclerotic collagen. Genome-wide SNP microarray studies revealed consistent gains and losses, including losses at the 13q14.2 locus encompassing RB1 and DLEU2 and deletion/disruption of the TP53 locus. Although subcutaneous examples showed genomic changes similar to deep PL, the dermal examples showed fewer genetic alterations, including changes reported in the spectrum of atypical spindle cell/pleomorphic lipomatous tumors (ASPLT). All lacked MDM2 amplification.

Conclusions
Careful integration of histologic and genetic features may improve classification of lipomatous neoplasms with atypia, allowing reclassification of some superficial PL as ASPLT.
The multiple roles of chemokines in the mechanisms of stent biocompatibility
Authors: Ravindran Dhanya , Karimi Galougahi Keyvan , Tan Joanne T M , Kavurma Mary M , Bursill Christina A 
Published: March 2020

Abstract
While the advent of drug-eluting stents has been clinically effective in substantially reducing the rates of major stent-related adverse events compared with bare metal stents, vascular biological problems such as neointimal hyperplasia, delayed re-endothelialization, late stent thrombosis are not eliminated and, increasingly, neoatherosclerosis is the underlying mechanism for very late stent failure. Further understanding regarding the mechanisms underlying the biological responses to stent deployment is therefore required so that new and improved therapies can be developed. This review will discuss the accumulating evidence that the chemokines, small inflammatory proteins, play a role in each key biological process of stent biocompatibility. It will address the chemokine system in its specialized roles in regulating the multiple facets of vascular biocompatibility including neointimal hyperplasia, endothelial progenitor cell (EPC) mobilization and re-endothelialization after vascular injury, platelet activation and thrombosis, as well as neoatherosclerosis. The evidence in this review suggests that chemokine-targeting strategies may be effective in controlling the pathobiological processes that lead to stent failure. Preclinical studies provide evidence that inhibition of specific chemokines and/or broad-spectrum inhibition of the CC-chemokine class prevents neointimal hyperplasia, reduces thrombosis and suppresses the development of neoatherosclerosis. In contrast, however, to these apparent deleterious effects of chemokines on stent biocompatibility, the CXC chemokine, CXCL12, is essential for the mobilization and recruitment of EPCs that make important contributions to re-endothelialization post-stent deployment. This suggests that future chemokine inhibition strategies would need to be correctly targeted so that all key stent biocompatibility areas could be addressed, without compromising important adaptive biological responses.
Integrating image caption information into biomedical document classification in support of biocuration
Authors: Jiang Xiangying , Li Pengyuan , Kadin James , Blake Judith A , Ringwald Martin , Shatkay Hagit 
Published: March 2020

Abstract

Gathering information from the scientific literature is essential for biomedical research, as much knowledge is conveyed through publications. However, the large and rapidly increasing publication rate makes it impractical for researchers to quickly identify all and only those documents related to their interest. As such, automated biomedical document classification attracts much interest. Such classification is critical in the curation of biological databases, because biocurators must scan through a vast number of articles to identify pertinent information within documents most relevant to the database. This is a slow, labor-intensive process that can benefit from effective automation.

We present a document classification scheme aiming to identify papers containing information relevant to a specific topic, among a large collection of articles, for supporting the biocuration classification task. Our framework is based on a meta-classification scheme we have introduced before; here we incorporate into it features gathered from figure captions, in addition to those obtained from titles and abstracts. We trained and tested our classifier over a large imbalanced dataset, originally curated by the Gene Expression Database (GXD). GXD collects all the gene expression information in the Mouse Genome Informatics (MGI) resource. As part of the MGI literature classification pipeline, GXD curators identify MGI-selected papers that are relevant for GXD. The dataset consists of ~60 000 documents (5469 labeled as relevant; 52 866 as irrelevant), gathered throughout 2012–2016, in which each document is represented by the text of its title, abstract and figure captions. Our classifier attains precision 0.698, recall 0.784, f-measure 0.738 and Matthews correlation coefficient 0.711, demonstrating that the proposed framework effectively addresses the high imbalance in the GXD classification task. Moreover, our classifier’s performance is significantly improved by utilizing information from image captions compared to using titles and abstracts alone; this observation clearly demonstrates that image captions provide substantial information for supporting biomedical document classification and curation.

Database URL:
Toxicity of Baits and Their Effects on Population Suppression of Anastrepha fraterculus (Diptera: Tephritidae): Implications for Field Management
Authors: Nunes Marcelo Z , Baronio Cleber A , Schutze Inana X , Bernardi Daniel , Arioli Cristiano J , Junior Ruben M , Botton Marcos 
Published: March 2020

Abstract
Anastrepha fraterculus (Wiedemann, 1830) is the main pest of fruit in southern Brazil. The use of toxic baits is one of the alternatives for its management. In this study, the toxic baits Anamed + malathion (10,000 mg/liter), Flyral 1.25% + malathion (2,000 mg/liter), and Gelsura (alpha-cypermethrin, 2,000 and 4,000 mg/liter) were highly toxic to the adults of A. fraterculus (lethal time [LT50] &lt; 7 h). In contrast, Success 0.02 CB had an LT50 of 48.4 h. In the absence of rain, all the formulations had residual effects (&gt;90% mortality) on A. fraterculus adults up to 21 d after treatment (DAT). In the presence of 5, 25, and 50 mm of rainfall, there was a significant reduction in the residual effect over time. However, with up to 50 mm of rain, Anamed + malathion and Gelsura 2,000 and 4,000 mg/liter caused between 43.0 and 79.0% of mortality. In the field, during two consecutive seasons (2015/2016 and 2016/2017), applications of Gelsura 2,000 mg/liter (four applications/season) caused population suppression of the pest throughout the apple fruiting period. However, in the 2016/2017 season, in the area using Gelsura, a higher percentage (≈12%) of apple fruits damaged by A. fraterculus females was observed when compared with the area with insecticide application (damage &lt;3%). The toxic bait Gelsura (2,000 and 4.000 mg/liter) was shown to be promising for use in the management of A. fraterculus, with results similar to those with the application of synthetic insecticides.
A Court with Many Faces: Judicial Characters and Modes of Norm Development in the European Court of Human Rights
Authors: Yildiz Ezgi 
Published: March 2020

Abstract
It is well established in the literature that international courts make law and develop norms. Yet there is no systematic analysis of how adjudication refashions a given norm’s trajectory. This article addresses this gap by combining legal analysis with social science methods. It takes a closer look at the European Court of Human Rights and provides a framework for understanding how court rulings develop norms – that is, how judicial decisions modify norms’ content or scope. The framework is composed of a typology of court characters (arbitrator, entrepreneur and delineator) and the distinct modes of norm development that each character typically generates (incremental/inconspicuous, pronounced and peripheral development). The typology is informed by interviews carried out at the Court as well as the literature on judicial review and, in particular, the debate on judicial activism and restraint. Unlike the concepts of judicial activism and restraint, these characters are not antithetical, but complementary. I show how court characters complement one another by looking at the case of the norm against torture under Article 3 of the European Convention on Human Rights. I examine 157 judgments issued between 1967 and 2006. I find that the percentage of entrepreneur rulings considerably decreased in the post-1998 period, while arbitrator rulings increased by nearly the same amount. My analysis of nearly four decades of jurisprudence not only sheds light on how the Court operates but also furthers our understanding of how it refashions codified norms.
Using a group medical visit model to promote healthy behaviour change with an underserved population
Authors: Russell Holly Ann , Sanders Mechelle , Moll Lynn , Murphy Melanie , Lanigan Angela M , Carroll Jennifer K 
Published: March 2020

AbstractBackgroundModels of care are needed to address physical activity, nutrition promotion and weight loss in primary care settings, especially with underserved populations who are disproportionately affected by chronic illness. Group medical visits (GMVs) are one approach that can help overcome some of the barriers to behaviour change in underserved populations, including the amount of time required to care for these patients due to socio-economic stressors and psychosocial complexities (1). GMVs have been shown to improve care in coronary artery disease and diabetes, but more evidence is needed in underserved settings.ObjectiveThis project sought to evaluate a GMV incorporating a physical activity component in an underserved patient population, measuring biometric and motivation outcome measures.MethodsThis project used a pre–post intervention study design through patient surveys at baseline and 12 weeks. We included validated motivational measures along with self-reported demographic information. A GMV intervention promoting physical activity and nutrition to promote weight loss was delivered by an interdisciplinary primary care team and community partners in a Federally Qualified Health Center in Rochester, NY. The intervention consisted of six, 2-hour sessions that occurred every other week at the clinic site.ResultsParticipants lost a significant amount of weight and maintained the weight loss at 6 months. In addition, there was a significant improvement in motivation measures.ConclusionThis study provides preliminary evidence that our GMV model can improve weight loss and autonomous motivation in an underserved population. This project has potential for scalability and sustainability.
Metagenomic investigation of African dust events in the Caribbean
Authors: Waters Samantha Marie , Purdue S K , Armstrong R , Detrés Y 
Published: March 2020

ABSTRACT
African dust from the Sahara and Sahel regions of Northern Africa is blown intercontinental distances and is the highest portion of atmospheric dust generated each year. During the Northern Hemisphere summer months (boreal summer), these dust events travel into the Caribbean and southern United States. While viability assays, microscopy and bacterial amplicon analyses have shown that dust-associated microbes may be diverse, the specific microbial taxa that are transported intercontinental distances with these dust events remain poorly characterized. To provide new insights into these issues, five metagenomes of Saharan dust events occurring in the Caribbean, collected in the summer months of 2002 and 2008, were analyzed. The data revealed that similar microbial composition existed between three out of the five of the distinct dust events and that fungi were a prominent feature of the metagenomes compared to other environmental samples. These results have implications for better understanding of microbial transport through the atmosphere and may implicate that the dust-associated microbial load transiting the Atlantic with Saharan dust is similar from year to year.
Metagenome analyses reveal the role of Clostridium perfringens in alfalfa silage anaerobic deterioration
Authors: Zheng Mingli , Niu Dongze , Jiang Di , Li Rongrong , Meng Lin , Xu Chuncheng 
Published: March 2020

ABSTRACT
The clostridial fermentation caused by the outgrowth of Clostridia was mainly responsible for the silage anaerobic deterioration. Our previous results showed that Clostridium perfringens dominated the clostridial community in poor-fermented alfalfa silage. This study was conducted to further examine the role of C. perfringens in silage anaerobic deterioration through fermentation products and the microbial community analyses. Direct-cut alfalfa was ensiled with C. perfringens contamination (CKC) or with the addition of Lactobacillus plantarum, sucrose and C. perfringens (LSC). Contamination with C. perfringens enhanced the clostridial fermentation in CKC silage, as indicated by high contents of butyric acid, ammonia nitrogen and Clostridia, while LSC silage was well preserved. The genera Bifidobacterium, Garciella and Clostridium dominated the bacterial community in CKC silage, while predominate genus was replaced by Lactobacillus in LSC silage. The clostridial community in CKC silage was dominated by Garciella sp. (26.9 to 58.1%) and C. tyrobutyricum (24.4 to 48.6%), while the relative abundance of C. perfringens was below 5.0%. Therefore, the effect of Clostridia contamination on ensiling fermentation was dependent on the ensilability of the silage material. Garciella sp. and C. tyrobutyricum, rather than C. perfringens, played dominant role in the clostridial fermentation in CKC silage.
Enzyme immobilization offers a robust tool to scale up the production of longer, diverse, natural glycosaminoglycan oligosaccharides
Authors: Alabbas Alhumaidi , Desai Umesh R 
Published: March 2020

AbstractAlthough structurally diverse, longer glycosaminoglycan (GAG) oligosaccharides are critical to understand human biology, few are available. The major bottleneck has been the predominant production of oligosaccharides, primarily disaccharides, upon enzymatic depolymerization of GAGs. In this work, we employ enzyme immobilization to prepare hexasaccharide and longer sequences of chondroitin sulfate in good yields with reasonable homogeneity. Immobilized chondroitinase ABC displayed good efficiency, robust operational pH range, broad thermal stability, high recycle ability and excellent distribution of products in comparison to the free enzyme. Diverse sequences could be chromatographically resolved into well-defined peaks and characterized using LC-MS. Enzyme immobilization technology could enable easier access to diverse longer GAG sequences.
The Ethics of Creating and Using Human-Animal Chimeras
Authors: Devolder Katrien , Yip Lauren J , Douglas Thomas 
Published: March 2020

Abstract
Rapid advances in gene-editing and stem-cell technology have expanded the range of possible future applications in human-animal chimera research. Most notably, recent developments may allow researchers to generate whole personalized human organs in pigs for the purpose of transplantation into human patients. Though human-animal chimera research in small animals, such as mice, is routine, human-animal chimeric techniques are now increasingly being applied to larger animals. Moreover, these chimeras include increasing amounts of human material, which is potentially present in more morally significant locations, such as the brain and the reproductive system. These developments raise important ethical questions about whether we should create such chimeras, and if so, how we should treat them. Answers to these ethical questions are needed to inform the development of policies regulating human-animal chimera research and its applications. Here, we provide a review of some of the most important or widespread ethical concerns.