bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating Exposure to Three Commonly Used, Potentially Carcinogenic Pesticides (Chlorolathonil, 2,4-D, and Glyphosate) Among Agricultural Workers in Canada
Authors: Rydz Ela , Larsen Kristian , Peters Cheryl E 
Published: October 2020

Abstract

Objectives
Certain pesticides have been associated with adverse health outcomes including cancer and reproductive harms. However, little is known about the prevalence of occupational pesticide exposure among agricultural workers in Canada. The purpose of this study was to estimate the prevalence and likelihood of occupational exposure to pesticides in Canada’s agricultural industry, using three commonly used, potentially carcinogenic pesticides [chlorothalonil, 2,4-dichlorophenoxyacetic acid (2,4-D), and glyphosate] as an example.

Methods
Estimates were calculated using the Canadian Census of Population and the Census of Agriculture. The number of workers and the proportion of farms applying ‘herbicides’ or ‘fungicides’ by farm type was estimated using survey data from the Census of Agriculture. These values were multiplied to yield the potential number of workers at risk of exposure. Likelihood of exposure (i.e. exposed, probably exposed, and possibly exposed) was then qualitatively assigned using information on crop type, primary expected tasks, crop production practices, and residue transfer data. Additional agricultural workers who are at risk of exposure but not captured by the Census of Agriculture were identified using the 2016 Census of Population.

Results
An estimated range of 37 700–55 800 workers (11–13% of agricultural workers) were exposed to glyphosate in Canada while 30 800–43 600 workers (9–11%) and 9000–14 100 (2.9–3.2%) were exposed to 2,4-D and chlorothalonil, respectively. Approximately 70–75% of workers at risk of exposure were considered probably or possibly exposed to any of the pesticides. Glyphosate exposure was most common among workers in oilseed (29% of oilseed farm workers exposed) and dry pea/bean farms (28%), along with those providing support activities for farms (31%). 2,4-D exposure was most common in corn (28%), other grain (28%), and soybean farms (27%), while chlorothalonil exposure was more likely among greenhouse, nursery, and floriculture workers (42%), workers on farms (28%, for occupations not captured by the Census of Agriculture, specifically), and those providing support activities for farms (20%). Regional variations broadly reflected differences in farm types by province.

Conclusions
This study estimated the prevalence of occupational exposure to three pesticides in Canada. Seasonal and temporary agricultural workers, which were captured by the Census of Agriculture, contributed to many additionally exposed workers. A large percent of the workers who were considered at risk of exposure were considered probably or possibly exposed, indicating a need for enhanced data collection and availability on pesticide use data in Canada. The study’s methods can be applied to estimate workers’ exposures to other pesticides within the agricultural industry.
Unveiling the immune infiltrate modulation in cancer and response to immunotherapy by MIXTURE—an enhanced deconvolution method
Authors: Fernández Elmer A , Mahmoud Yamil D , Veigas Florencia , Rocha Darío , Miranda Matías , Merlo Joaquín , Balzarini Mónica , Lujan Hugo D , Rabinovich Gabriel A , Girotti María Romina 
Published: October 2020

Abstract
The accurate quantification of tumor-infiltrating immune cells turns crucial to uncover their role in tumor immune escape, to determine patient prognosis and to predict response to immune checkpoint blockade. Current state-of-the-art methods that quantify immune cells from tumor biopsies using gene expression data apply computational deconvolution methods that present multicollinearity and estimation errors resulting in the overestimation or underestimation of the diversity of infiltrating immune cells and their quantity. To overcome such limitations, we developed MIXTURE, a new ν-support vector regression-based noise constrained recursive feature selection algorithm based on validated immune cell molecular signatures. MIXTURE provides increased robustness to cell type identification and proportion estimation, outperforms the current methods, and is available to the wider scientific community. We applied MIXTURE to transcriptomic data from tumor biopsies and found relevant novel associations between the components of the immune infiltrate and molecular subtypes, tumor driver biomarkers, tumor mutational burden, microsatellite instability, intratumor heterogeneity, cytolytic score, programmed cell death ligand 1 expression, patients’ survival and response to anti-cytotoxic T-lymphocyte-associated antigen 4 and anti-programmed cell death protein 1 immunotherapy.
Prediction of protein–carbohydrate complex binding affinity using structural features
Authors: Siva Shanmugam N R , Jino Blessy J , Veluraja K , Gromiha M Michael 
Published: October 2020

Abstract
Protein–carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein–carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein–carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein–carbohydrate complexes belonging to six categories of protein–carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149 kcal/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein–Carbohydrate Affinity Predictor, for predicting the binding affinity of protein–carbohydrate complexes. The web server is freely accessible at https://web.iitm.ac.in/bioinfo2/pcapred/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.
Comparative viromes of Culicoides and mosquitoes reveal their consistency and diversity in viral profiles
Authors: Liu Lin , Shen Qin , Li Nan , He Yuwen , Han Na , Wang Xianyue , Meng Jinxin , Peng Yousong , Pan Mei , Jin Yuting , Jiang Taijiao , Tan Wenjie , Wang Jinglin , Wu Aiping 
Published: October 2020

Abstract
The genus Culicoides includes biting midges, some of which are vectors for viruses that cause diseases in humans and animals. Knowledge of the roles of Culicoides in viral ecology is inadequate. We collected ~300 000 samples of Culicoides and mosquitoes in 15 representative regions within Yunnan, China. Using mosquitoes as reference vectors, we designed a comparative virome strategy to study the viral composition, diversity, hosts and spatiotemporal distribution of Culicoides. A map of viromes in Culicoides and mosquitoes in Yunan province, China, was constructed. At the same locations, Culicoides and mosquitoes usually share a similar viral diversity. At least 10 important pathogenic viruses were detected from Culicoides. Many novel viruses were discovered, including 21 segmented viruses of Flaviviridae, 180 viruses of Monjiviricetes and 130 viruses of Bunyavirales. The findings demonstrate that Culicoides is an important part of viral ecology and should be studied and monitored for potentially emerging viruses.
EphB3 interacts with initiator caspases and FHL-2 to activate dependence receptor cell death in oligodendrocytes after brain injury
Authors: Tsenkina Yanina , Tapanes Stephen A , Díaz Madelen M , Titus David J , Gajavelli Shyam , Bullock Ross , Atkins Coleen M , Liebl Daniel J 
Published: October 2020

Abstract
Clinical trials examining neuroprotective strategies after brain injury, including those targeting cell death mechanisms, have been underwhelming. This may be in part due to an incomplete understanding of the signalling mechanisms that induce cell death after traumatic brain injury. The recent identification of a new family of death receptors that initiate pro-cell death signals in the absence of their ligand, called dependence receptors, provides new insight into the factors that contribute to brain injury. Here, we show that blocking the dependence receptor signalling of EphB3 improves oligodendrocyte cell survival in a murine controlled cortical impact injury model, which leads to improved myelin sparing, axonal conductance and behavioural recovery. EphB3 also functions as a cysteine-aspartic protease substrate, where the recruitment of injury-dependent adaptor protein Dral/FHL-2 together with capsase-8 or -9 leads to EphB3 cleavage to initiate cell death signals in murine and human traumatic brain-injured patients, supporting a conserved mechanism of cell death. These pro-apoptotic responses can be blocked via exogenous ephrinB3 ligand administration leading to improved oligodendrocyte survival. In short, our findings identify a novel mechanism of oligodendrocyte cell death in the traumatically injured brain that may reflect an important neuroprotective strategy in patients.
Weakly Supervised Sentiment-Specific Region Discovery for VSA
Authors: Xue Luoyang , Xu Ang , Mao Qirong , Gao Lijian , Chen Jie 
Published: October 2020

Abstract
Local information has significant contributions to visual sentiment analysis (VSA). Recent studies about local region discovery need manually annotate region location. Affective local information learning and automatic discovery of sentiment-specific region are still the challenges in VSA. In this paper, we propose an end-to-end VSA method for weakly supervised sentiment-specific region discovery. Our method contains two branches: an automatic sentiment-specific region discovery branch and a sentiment analysis branch. In the sentiment-specific region discovery branch, a region proposal network with multiple convolution kernels is proposed to generate candidate affective regions. Then, we design the multiple instance learning (MIL) loss to remove redundant and noisy candidate regions. Finally, the sentiment analysis branch integrates both holistic and localized information obtained in the first branch by feature map coupling for final sentiment classification. Our method automatically discovers sentiment-specific regions by the constraint of MIL loss function without object-level labels. Quantitative and qualitative evaluations on four benchmark affective datasets demonstrate that our proposed method outperforms the state-of-the-art methods.
Which Pitfall Traps and Sampling Effort to Choose to Evaluate Cropping System Effects on Spider and Carabid Assemblages?
Authors: Gardarin Antoine , Valantin-Morison Muriel 
Published: October 2020

AbstractIn arable agroecosystems, arthropod communities often have a reduced abundance and diversity, which represents a challenge for sampling techniques needed to detect small differences among these simplified communities. We evaluated the suitability of pitfall traps for comparing the effects of cropping systems on arthropod communities. In a field experiment, we compared the effects of two pitfall trap diameters, the type of preserving fluid and the sampling effort on three metrics (activity density, taxonomic richness, and community weighted mean [CWM] of body size) for carabids and spiders. Trap size affected the observed composition of communities, with large traps yielding a higher proportion of spiders, and a higher richness and CWM body size for both taxa. The type of preserving fluid had a weaker effect. Simulations with various sampling efforts showed that only very different communities could be distinguished with less than 10 traps per field or less than 30 field replicates. Fewer traps were required to find differences between cropping systems for body size than for other metrics. Carabid activity density and body size, and spider genus richness, were the variables better distinguishing between cropping systems with the smallest sampling effort. A high sampling effort was required for comparing activity density and richness across cropping systems. Selection of the most appropriate trap design, metrics, and crops are the main factors for optimizing the trade-off between sampling effort and the ability to detect arthropod community responses to habitat management.
Artemisinin susceptibility in the malaria parasitePlasmodium falciparum: propellers, adaptor proteins and the need for cellular healing
Authors: Sutherland Colin J , Henrici Ryan C , Artavanis-Tsakonas Katerina 
Published: October 2020

ABSTRACTStudies of the susceptibility of Plasmodium falciparum to the artemisinin family of antimalarial drugs provide a complex picture of partial resistance (tolerance) associated with increased parasite survival in vitro and in vivo. We present an overview of the genetic loci that, in mutant form, can independently elicit parasite tolerance. These encode Kelch propeller domain protein PfK13, ubiquitin hydrolase UBP-1, actin filament-organising protein Coronin, also carrying a propeller domain, and the trafficking adaptor subunit AP-2μ. Detailed studies of these proteins and the functional basis of artemisinin tolerance in blood-stage parasites are enabling a new synthesis of our understanding to date. To guide further experimental work, we present two major conclusions. First, we propose a dual-component model of artemisinin tolerance in P. falciparum comprising suppression of artemisinin activation in early ring stage by reducing endocytic haemoglobin capture from host cytosol, coupled with enhancement of cellular healing mechanisms in surviving cells. Second, these two independent requirements limit the likelihood of development of complete artemisinin resistance by P. falciparum, favouring deployment of existing drugs in new schedules designed to exploit these biological limits, thus extending the useful life of current combination therapies.
MN1overexpression with varying tumor grade is a promising predictor of survival of glioma patients
Authors: Saini Masum , Jha Ajaya Nand , Tangri Rajiv , Qudratullah Md , Ali Sher 
Published: October 2020

AbstractGliomas have substantial mortality to incidence rate ratio and a dismal clinical course. Newer molecular insights, therefore, are imperative to refine glioma diagnosis, prognosis and therapy. Meningioma 1 (MN1) gene is a transcriptional co-regulator implicated in other malignancies, albeit its significance in glioma pathology remains to be explored. IGFBP5 is regulated transcriptionally by MN1 and IGF1 and is associated with higher glioma grade and shorter survival time, prompting us to ascertain their correlation in these tumors. We quantified the expression of MN1, IGFBP5 and IGF1 in 40 glioma samples and examined their interrelatedness. MN1 mRNA-protein inter-correlation and the gene’s copy number were evaluated in these tumors. Publicly available TCGA datasets were used to examine the association of MN1 expression levels with patient survival and for validating our findings. We observed MN1 overexpression correlated with low-grade (LGGs) and not high-grade gliomas and is not determined by the copy number alteration of the gene. Notably, gliomas with upregulated MN1 have better overall survival (OS) and progression-free survival (PFS). IGFBP5 expression associated inversely with MN1 expression levels in gliomas but correlated positively with IGF1 expression in only LGGs. This suggests a potential grade-specific interplay between repressive and activating roles of MN1 and IGF1, respectively, in the regulation of IGFBP5. Thus, MN1 overexpression, a promising predictor of OS and PFS in gliomas, may serve as a prognostic biomarker in clinical practice to categorize patients with survival advantage.
Endometrial function in women with polycystic ovary syndrome: a comprehensive review
Authors: Palomba Stefano , Piltonen Terhi T , Giudice Linda C 
Published: October 2020

Abstract

BACKGROUND
Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility. An endometrial component has been suggested to contribute to subfertility and poor reproductive outcomes in affected women.

OBJECTIVE AND RATIONALE
The aim of this review was to determine whether there is sufficient evidence to support that endometrial function is altered in women with PCOS, whether clinical features of PCOS affect the endometrium, and whether there are evidence-based interventions to improve endometrial dysfunction in PCOS women.

SEARCH METHODS
An extensive literature search was performed from 1970 up to July 2020 using PubMed and Web of Science without language restriction. The search included all titles and abstracts assessing a relationship between PCOS and endometrial function, the role played by clinical and biochemical/hormonal factors related to PCOS and endometrial function, and the potential interventions aimed to improve endometrial function in women with PCOS. All published papers were included if considered relevant. Studies having a specific topic/hypothesis regarding endometrial cancer/hyperplasia in women with PCOS were excluded from the analysis.

OUTCOMES
Experimental and clinical data suggest that the endometrium differs in women with PCOS when compared to healthy controls. Clinical characteristics related to the syndrome, alone and/or in combination, may contribute to dysregulation of endometrial expression of sex hormone receptors and co-receptors, increase endometrial insulin-resistance with impaired glucose transport and utilization, and result in chronic low-grade inflammation, immune dysfunction, altered uterine vascularity, abnormal endometrial gene expression and cellular abnormalities in women with PCOS. Among several interventions to improve endometrial function in women with PCOS, to date, only lifestyle modification, metformin and bariatric surgery have the highest scientific evidence for clinical benefit.

WIDER IMPLICATIONS
Endometrial dysfunction and abnormal trophoblast invasion and placentation in PCOS women can predispose to miscarriage and pregnancy complications. Thus, patients and their health care providers should advise about these risks. Although currently no intervention can be universally recommended to reverse endometrial dysfunction in PCOS women, lifestyle modifications and metformin may improve underlying endometrial dysfunction and pregnancy outcomes in obese and/or insulin resistant patients. Bariatric surgery has shown its efficacy in severely obese PCOS patients, but a careful evaluation of the benefit/risk ratio is warranted. Large scale randomized controlled clinical trials should address these possibilities.
Quantifying the increase in fishing efficiency due to the use of drifting FADs equipped with echosounders in tropical tuna purse seine fisheries
Authors: Wain Gwenaëlle , Guéry Loreleï , Kaplan David Michael , Gaertner Daniel 
Published: October 2020

Abstract
Numerous pelagic species are known to associate with floating objects (FOBs), including tropical tunas. Purse seiners use this behaviour to facilitate the capture of tropical tunas by deploying artificial drifting fish aggregating devices (dFADs). One major recent change has been the integration of echosounders in satellite-tracked GPS buoys attached to FOBs, allowing fishers to remotely estimate fishable biomass. Understanding the effects of this new technology on catch of the three main tuna species (yellowfin tuna, Thunnus albacares; bigeye tuna, Thunnus obesus; and skipjack tuna, Katsuwonus pelamis) is important to accurately correct for this change in catch-per-unit-effort (CPUE) indices used for stock assessments. We analysed catch data from the French purse seine fleet for the period 2010–2017 in the Indian Ocean to assess the impact of this fleet’s switch to echosounder buoys around 2012. Results indicate that echosounders do not increase the probability a set will be succesful, but they have a positive effect on catch per set, with catches on average increasing by ≈2−2.5 tonnes per set (≈10%) when made on the vessel's own dFADs equipped with an echosounder buoy. Increases were due to a decrease in sets below ≈25 tonnes and an increase in those greater than ≈25 tonnes, with a non-linear transition around this threshold. This increase explains the considerable investment of purse seiners in echosounder buoys, but also raises concerns about bias in stock size estimates based on CPUE if we do not correct for this fishing efficiency increase.
Donor reliance and the impact on neglected tropical disease programme delivery: reflections and solutions for change from programme management perspectives
Authors: Kollie Karsor , Siakeh Alice , Zawolo Georgina , Wickenden Anna , Theobald Sally , Rogers Emerson , Zaizay Zeela , Thomson Rachael , Dean Laura 
Published: October 2020

Abstract
Health systems within many developing countries are reliant on donor funding and non-governmental development organisations (NGDOs); this has had positive results but also presents challenges to sustainability and national ownership, with national programmes needing to respond to changing donor priorities. Simultaneously, the WHO neglected tropical disease (NTD) roadmap 2021–2030 calls for increased country ownership and domestically financed NTD programmes. Focusing on Liberia and blending primary research from the COUNTDOWN consortium and personal programmatic experience, this commentary reflects on the sustainability and financing of NTD programme delivery within the current context. We explore the successes and challenges of current models of collaboration and opportunities to improve country ownership and sustainability.