bluuebunny/crossref_metadata_2025_split huggingface dataset:
How do interventions impact malaria dynamics between neighboring countries? A case study with Botswana and Zimbabwe
Authors: Agusto Folashade , Goldberg Amy , Ortega Omayra , Ponce Joan , Zaytseva Sofya , Sindi Suzanne , Blower Sally 
Published: December 2019

AbstractMalaria is a vector-borne disease that is responsible for over 400,000 deaths per year. Although countries around the world have taken measures to decrease the incidence of malaria, many regions remain endemic. Indeed, progress towards elimination has stalled in multiple countries. While control efforts are largely focused at the national level, the movement of individuals between countries may complicate the efficacy of elimination efforts. Here, we consider the case of neighboring countries Botswana and Zimbabwe, connected by human mobility. Both have improved malaria rates in recent years with differing success. We use a two-patch Ross-MacDonald Model with Lagrangian human mobility to examine the coupled disease dynamics between these two countries. In particular, we are interested in the impact that interventions for controlling malaria applied in one country can have on the incidence of malaria in the other country. We find that dynamics and interventions in Zimbabwe can dramatically influence pathways to elimination in Botswana, largely driven by Zimbabwe’s population size and larger basic reproduction number.
The nucleus acts as a ruler tailoring cell responses to spatial constraints
Authors: Lomakin A.J. , Cattin C.J. , Cuvelier D. , Alraies Z. , Molina M. , Nader G. , Srivastava N. , Garcia-Arcos J.M. , Zhitnyak I.Y. , Bhargava A. , Driscoll M.K. , Welf E.S. , Fiolka R. , Petrie R.J. , Manel N. , Lennon-Duménil A.M. , Müller D.J. , Piel M. 
Published: December 2019

AbstractThe microscopic environment inside a metazoan organism is highly crowded. Whether individual cells can tailor their behavior to the limited space remains unclear. Here, we found that cells measure the degree of spatial confinement using their largest and stiffest organelle, the nucleus. Cell confinement below a resting nucleus size deforms the nucleus, which expands and stretches its envelope. This activates signaling to the actomyosin cortexvianuclear envelope stretch-sensitive proteins, upregulating cell contractility. We established that the tailored contractile response constitutes a nuclear ruler-based signaling pathway involved in migratory cell behaviors. Cells rely on the nuclear ruler to modulate the motive force enabling their passage through restrictive pores in complex three-dimensional (3D) environments, a process relevant to cancer cell invasion, immune responses and embryonic development.One Sentence SummaryNuclear envelope expansion above a threshold triggers a contractile cell response and thus acts as a ruler for the degree of cell deformation.
A complex IRES at the 5’-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate
Authors: Neupane Ritam , Pisareva Vera P. , Rodríguez Carlos F. , Pisarev Andrey V. , Fernández Israel S. 
Published: December 2019

AbstractRNA viruses are pervasive entities in the biosphere with significant impact in human health and economically important livestock. As strict cellular parasites, RNA viruses abuse host resources, redirecting them towards viral replication needs. Taking control of the cellular apparatus for protein production is a requirement for virus progression and diverse strategies of cellular mimicry and/or ribosome hijacking evolved to ensure this control. Especially in complex eukaryotes, translation is a sophisticated process, with multiple mechanisms acting on ribosomes and mRNAs. The initiation stage of translation is specially regulated, involving multiple steps and the engagement of numerous initiation factors some of them of high complexity. The use of structured RNA sequences, called Internal Ribosomal Entry Sites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5’-UTR of a viral RNA assembles a functional translation initiation complex via an uAUG intermediate, redirecting the cellular machinery for protein production towards viral messengers. The IRES features a novel extended, multi-domain architecture, circling the 40S head, leveraging ribosomal sites not previously described to be exploited by any IRES. The structures and accompanying functional data, illustrate the importance of 5’-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs. Given the large number of new viruses metagenomic studies have uncovered, the quantity and diversity of mechanisms for translation hijacking encrypted in viral sequences may be seriously underestimated. Exploring this diversity could reveal novel avenues in the fight against these molecular pathogens.
MB-GAN: Microbiome Simulation via Generative Adversarial Network
Authors: Rong Ruichen , Jiang Shuang , Xu Lin , Xiao Guanghua , Xie Yang , Liu Dajiang J. , Li Qiwei , Zhan Xiaowei 
Published: December 2019

AbstractSimulation is a critical component of experimental design and evaluation of analysis methods in microbiome association studies. However, statistically modeling the microbiome data is challenging since that the complex structure in the real data is difficult to be fully represented by statistical models. To address this challenge, we designed a novel simulation framework for microbiome data using a generative adversarial network (GAN), called MB-GAN, by utilizing methodology advancements from the deep learning community. MB-GAN can automatically learn from a given dataset and compute simulated datasets that are indistinguishable from it. When MB-GAN was applied to a case-control microbiome study of 396 samples, we demonstrated that the simulated data and the original data had similar first-order and second-order properties, including sparsity, diversities, and taxa-taxa correlations. These advantages are suitable for further microbiome methodology development where high fidelity microbiome data are needed.
WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition
Authors: Hu Yinlei , Li Bin , Zhang Wen , Liu Nianping , Cai Pengfei , Chen Falai , Qu Kun 
Published: December 2019

ABSTRACTThe low capture rate of expressed RNAs from single-cell sequencing technology is one of the major obstacles to downstream functional genomics analyses. Recently, a number of imputation methods have emerged for single-cell transcriptome data, however, recovering missing values in very sparse expression matrices remains a substantial challenge. Here, we propose a new algorithm, WEDGE (WEighted Decomposition of Gene Expression), to impute gene expression matrices by using a biased low-rank matrix decomposition method (bLRMD). WEDGE successfully recovered expression matrices, reproduced the cell-wise and gene-wise correlations, and improved the clustering of cells, performing impressively for applications with multiple cell type datasets with high dropout rates. Overall, this study demonstrates a potent approach for imputing sparse expression matrix data, and our WEDGE algorithm should help many researchers to more profitably explore the biological meanings embedded in their scRNA-seq datasets.
Comprehensive identification of HSP70/HSC70 Chaperone Clients in Human Cells
Authors: Ryu Seung Woo , Stewart Rose , Pectol Chase , Ender Nicolette , Wimalarathne Oshadi , Lee Ji-Hoon , Zanini Carlos P. , Harvey Antony , Huibregtse Jon , Mueller Peter , Paull Tanya T. 
Published: December 2019

AbstractThe HSP70 family of chaperones are the front-line of protection from stress-induced misfolding and aggregation of polypeptides in most organisms and are responsible for promoting the stability, folding, and degradation of clients to maintain cellular protein homeostasis. Here we demonstrate quantitative identification of HSP70 and HSC70 clients using an ubiquitin-mediated proximity tagging strategy and show that, despite their high degree of similarity, these enzymes have largely non-overlapping specificities. Both proteins show a preference for association with newly synthesized polypeptides but each responds differently to changes in the stoichiometry of proteins in obligate multi-subunit complexes. In addition, expression of an ALS-associated SOD1 mutant protein induces changes in HSP70 and HSC70 client association and aggregation toward polypeptides with predicted disorder, indicating that there are global effects from a single misfolded protein that extend to many clients within chaperone networks. Together these findings show that the ubiquitin-mediated UBAIT fusion system can efficiently isolate the complex interactome of HSP chaperone family proteins under normal and stress conditions.
Perceptual detection depends on spike count integration
Authors: Cone Jackson J. , Bade Morgan L. , Masse Nicolas Y. , Page Elizabeth A. , Freedman David J. , Maunsell John H.R. 
Published: December 2019

AbstractWhenever the retinal image changes some neurons in visual cortex increase their rate of firing, while others decrease their rate of firing. Linking specific sets of neuronal responses with perception and behavior is essential for understanding mechanisms of neural circuit computation. We trained mice to perform visual detection tasks and used optogenetic perturbations to increase or decrease neuronal spiking primary visual cortex (V1). Perceptual reports were always enhanced by increments in V1 spike counts and impaired by decrements, even when increments and decrements were delivered to the same neuronal populations. Moreover, detecting changes in cortical activity depended on spike count integration rather than instantaneous changes in spiking. Recurrent neural networks trained in the task similarly relied on increments in neuronal activity when activity was costly. This work clarifies neuronal decoding strategies employed by cerebral cortex to translate cortical spiking into percepts that can be used to guide behavior.
Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing
Authors: Price Alexander M. , Hayer Katharina E. , McIntyre Alexa B.R. , Gokhale Nandan S. , Abebe Jonathan S. , Della Fera Ashley N. , Mason Christopher E. , Horner Stacy M. , Wilson Angus C. , Depledge Daniel P. , Weitzman Matthew D. 
Published: December 2019

AbstractAdenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, we profiled m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.
Parallel siRNA screens to identify kinase and phosphatase modulators of NF-κB activity following DNA damage
Authors: Sfikas Alexandros , Banks Peter , Su Ling-I , Schlossmacher George , Perkins Neil D , Yemm Adrian I 
Published: December 2019

AbstractDNA damage, such as that experienced by people undergoing chemotherapy, can directly activate NF-κB signalling which in turn can lead to resistance to genotoxic stress. NF-κB signalling is highly regulated by phosphorylation, but the enzymes required for these processes remain largely unknown. Identifying those enzymes responsible for regulating NF-κB activity may yield attractive targets for new clinical therapies, as well as provide the basis for better understanding of signalling network crosstalk. Here we present datasets from two independent RNAi screens using a stable NF-κB reporter U2OS cell line with the aim of identifying enzymes that alter NF-κB activity in response to DNA damage following etoposide and ionising radiation treatments. Although we observed high internal validity and specificity to NF-κB modulation within the screens, there was a striking dissimilarity between the results of the two different screens. These data therefore provide a cautionary lesson regarding the use of RNAi screening but also provide new candidates for kinase and phosphatase regulation of NF-κB activity in response to genotoxic stress.
Cohesive slope failure analysis using methods combining smoothed particle hydrodynamics and response surface function
Authors: Li Liang , Chu Xuesong , Yu Guangming 
Published: December 2019

Purpose
The paper aims to construct a method to simulate the relationship between the parameters of soil properties and the area of sliding mass of the true slip surface of a landslide.

Design/methodology/approach
The smoothed particle hydrodynamics (SPH) algorithm is used to calibrate a response surface function which is adopted to quantify the area of sliding mass of the true slip surface for each failure sample in Monte Carlo simulation. The proposed method is illustrated through a homogeneous and a heterogeneous cohesive soil slope.

Findings
The comparison of the results between the proposed method and the traditional method using the slip surface with minimum factor of safety (FSmin) to quantify the failure consequence has shown that the landslide risk tends to be attributed to a variety of risk sources, and that the use of a slip surface with FSmin to quantify the consequence of a landslide underestimates the landslide risk value. The difference of the risk value between the proposed method and the traditional method increases dramatically as the uncertainty of soil properties becomes significant.

Practical implications
A geotechnical engineer could use the proposed method to perform slope failure analysis.

Originality/value
The failure consequence of a landslide can be rationally predicted using the proposed method.
Short-term and long-term quality of service
Authors: Ojasalo Jukka 
Published: December 2019

Purpose
The purpose of this study is to introduce concepts for understanding and managing short- and long-term development of customer satisfaction related to service quality.

Design/methodology/approach
This study is based on empirical qualitative research in professional business-to-business services. The data were collected from in-depth interviews of highly experienced consultants and analyzed in terms of the content of the qualitative data.

Findings
This study empirically identifies situations where the level of customer satisfaction with a single service rendered changes over time and is different in short and long term. It finds different short- and long-term quality levels both during a service process and in the post-purchase evaluation period. It finds that sometimes long-term quality can be provided only at the expense of short-term quality and vice versa.

Research limitations/implications
The concepts of short- and long-term quality provide a simple and effective conceptual tool for understanding potential short- and long-term differences in customer satisfaction as well as the reasons for it.

Practical implications
The study highlights the importance of considering quality dynamics at the level of a service rendered, both during the service process and in the post-purchase period. It helps in developing effective ways to understand and manage changes in customer satisfaction in the short and long term. It helps in developing strategies for communicating the overall value of a service to customers in “no pain, no gain” cases.

Social implications
This study provides concepts for analyzing wicked problems.

Originality/value
Dynamics of quality and satisfaction in services have received very little attention in research studies although the existence and relevance of the phenomenon was recognized long ago. This study introduces new concepts for understanding this phenomenon further by focusing on the short- and long-term effects of the service quality.
Quantitative impacts of mandatory integrated reporting
Authors: Conway Elaine 
Published: December 2019

Purpose
This paper aims to examine the impact of the 2011 mandatory introduction of integrated reporting (<IR>) on the financial performance, risk and institutional shareholding of listed companies in South Africa to assess whether there is a benefit to <IR> and which may encourage greater adoption of it globally. It contrasts the results with two other African stock exchanges (Nigeria and Egypt with no mandatory <IR>) and examines whether <IR> quality also has an impact on these and on environmental, social and governance (ESG) disclosure scores.

Design/methodology/approach
A series of multivariate ordinary least squares regressions was estimated on a range of financial, risk, institutional and ESG data from firms on the three African stock exchanges, between 2006 and 2015.

Findings
Financial performance and risk in South African firms appear to have decreased since the start of mandatory reporting, but institutional shareholding has increased. The production of higher quality reports is associated with decreased financial performance and risk, higher institutional shareholding and increased ESG scores.

Originality/value
This study is first to test the quantitative effects of <IR> and <IR> quality on a broad range of financial performance and risk measures and the level of institutional shareholding. It also adds to the literature by assessing how the quality of <IR> can impact the ESG scoring of the business. Hence, this study is of interest to firms looking to adopt <IR> for its benefits and to regulatory bodies considering the mandatory adoption of <IR> in support of achievement of national social and environmental goals.
Expression of OPN3 in lung adenocarcinoma promotes epithelial‐mesenchymal transition and tumor metastasis
Authors: Xu Chao , Wang Ruixia , Yang Yanfang , Xu Tongyi , Li Yan , Xu Jie , Jiang Zhansheng 
Published: December 2019

BackgroundLung adenocarcinoma is the most common pathological lung cancer and an important cause of cancer‐related death. Metastasis is a major underlying reason for poor prognosis of lung adenocarcinoma. Opsin3 (OPN3), a member of the guanine nucleotide‐binding protein‐coupled receptor superfamily, has been identified to affect the apoptosis of hepatoma cells by modulating the phosphorylation of Akt and Bcl2/Bax. However, the expression and role of OPN3 in lung adenocarcinoma remains unclear.MethodsOpsin3 expression in lung adenocarcinoma tissues was detected by western blot, qPCR, and immunohistochemistry. Changes in cell migration and invasion ability resulting from the change of OPN3 expression level were detected by wound healing and transwell migration assays. Changes in the markers of epithelial‐mesenchymal transformation were detected by western blot and qPCR.ResultsOpsin3 expression in lung adenocarcinoma tissues was higher than that in normal lung tissues. Patients with high expression of OPN3 had lower survival rates. Owing to overexpression of OPN3, the HCC827 cells showed enhanced invasion and migration ability in vitro. Upon decreasing the expression of OPN3, the invasion and migration ability of the A549 cells decreased.ConclusionOur study demonstrated for the first time that OPN3 gene enhanced the metastasis in lung adenocarcinoma, and its overexpression promoted epithelial‐mesenchymal transition.Key pointsA significant finding of the study was that OPN3 acted an oncogene in promoting lung adenocarcinoma metastasis. Our study complemented the research on the expression and function of OPN3 in lung adenocarcinoma.
Influence of tumor characteristics on correction differences between cone‐beam computed tomography‐guided patient setup strategies in stereotactic body radiation therapy for lung cancer
Authors: Jang Seong Soon , Park Suk Young , Cho Eun Youn , Yang Po Song , Huh Gil Ja , Yang Young Jun 
Published: December 2019

AbstractBackgroundTo evaluate the correction differences between vertebra and tumor matching as cone‐beam computed tomography (CBCT)‐guided setup strategies in lung stereotactic body radiation therapy (SBRT), and the correlations with tumor characteristics such as size, mobility, and location.MethodsThe manual registrations for 33 lung tumors treated with SBRT were retrospectively performed by matching thoracic vertebrae for vertebra matching and then by matching CBCT‐visualized tumors within the internal target volume obtained from a four‐dimensional CT dataset for tumor matching.ResultsThe mean correction difference between the two matching methods during the SBRT fractions was larger in the anterior‐posterior direction (2.7 mm) than in the superior‐inferior (2.1 mm) and left‐right (1.4 mm) directions, with differences of less than 5 mm in 90% of the total 134 CBCT fractions. The X‐axis and direct distances from the central axis to the tumor had significant correlations with the correction differences in all three directions, while the mobility‐related parameters were correlated only in the superior‐inferior direction. The absolute differences in lung‐dose parameters after applying the margins (3.4–6.5 mm) required for the setup errors from vertebra matching relative to tumor matching were mild, with values of 1.95 Gy for the mean lung dose and 3.9% for V20.ConclusionThe setup differences between vertebra and tumor matching in the CBCT‐guided setup without rotation correction were increased in tumors located long distances from the central axis. The additional safety margins of 3.4–6.5 mm were required for the setup errors from vertebra matching.Key pointsSignificant findings of the studyThe correction difference between the vertebra and tumor matching as CBCT‐guided setup strategies was the largest in the anterior‐posterior direction and significantly correlated with the X‐axis and direct distances from the central axis to the tumor.What this study addsSetup differences between vertebra and tumor matching in the CBCT‐guided setup were increased in tumors located long distances from the central axis.The additional safety margins of 3.4–6.5 mm were required for the setup errors from vertebra matching.
Knowledge of vitamin A deficiency and crop adoption: Evidence from a field experiment in Mozambique
Authors: Caeiro Rute M. , Vicente Pedro C. 
Published: December 2019

AbstractVitamin A deficiency is a widespread public health problem in Sub‐Saharan Africa. This paper analyzes the impact of an intervention fighting vitamin A deficiency through the promotion of production and consumption of orange‐fleshed sweet potato (OFSP). We conducted a randomized evaluation of OFSP‐related training to female farmers in Mozambique, who were also the primary caretakers of preschool children. The treatment consisted of group and individual‐level training where basic knowledge about nutrition was taught, and planting and cooking skills related specifically to OFSP were developed. We find considerable increases in nutrition‐related knowledge, as well as knowledge about cooking and planting OFSP, which persist after more than a year. We also observe clear evidence of adoption of OFSP for production in the short‐ and medium‐run, which spreads through social networks.