bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional profiling of Vibrio cholerae O1 following exposure to human anti- lipopolysaccharide monoclonal antibodies
Authors: Baranova Danielle E , Willsey Graham G , Levinson Kara J , Smith Carol , Wade Joseph , Mantis Nicholas J 
Published: June 2020

ABSTRACT
Following an episode of cholera, a rapidly dehydrating, watery diarrhea caused by the Gram-negative bacterium, Vibrio cholerae O1, humans mount a robust anti-lipopolysaccharide (LPS) antibody response that is associated with immunity to subsequent re-infection. In neonatal mouse and rabbit models of cholera, passively administered anti-LPS polyclonal and monoclonal (MAb) antibodies reduce V. cholerae colonization of the intestinal epithelia by inhibiting bacterial motility and promoting vibrio agglutination. Here we demonstrate that human anti-LPS IgG MAbs also arrest V. cholerae motility and induce bacterial paralysis. A subset of those MAbs also triggered V. cholerae to secrete an extracellular matrix (ECM). To identify changes in gene expression that accompany antibody exposure and that may account for motility arrest and ECM production, we subjected V. cholerae O1 El Tor to RNA-seq analysis after treatment with ZAC-3 IgG, a high affinity MAb directed against the core/lipid A region of LPS. We identified &gt; 160 genes whose expression was altered following ZAC-3 IgG treatment, although canonical outer membrane stress regulons were not among them. ompS (VCA1028), a porin associated with virulence and indirectly regulated by ToxT, and norR (VCA0182), a σ54-dependent transcription factor involved in late stages of infection, were two upregulated genes worth noting.
Population and Stand-Level Inference in Forest Inventory with Penalized Splines
Authors: Magnussen Steen , Stelzer Anne-Sophie , Kändler Gerald 
Published: June 2020

AbstractPenalized splines have potential to decrease estimates of variance in forest inventories with a design-based population-level inference, and a model-based domain-level inference by decreasing the likelihood of a model misspecification. We provide examples with second-order (B2) B-splines and radial basis (RB) functions as extensions to a linear working model (WM). Bias was not prominent, yet greater with B2 and in particular with RB than with WM, and decreased with sample size. Important reductions in the variance of a population mean were achieved with both B2 and RB, but at the domain-level only with RB. The proposed regression estimator of variance generated estimates of variance being slightly smaller than the observed variance. A consistent and larger underestimation was seen with the popular difference estimator of variance.Study Implications: Forest inventories supported by light detection and range (LiDAR) data require—in the estimation phase—a model for linking LiDAR metrics to attributes of interest. Formulating a parametric model can be a challenge and unsatisfactory if the goodness of fit varies across the range of the attribute of interest. A semiparametric model provides more flexibility and lessens the chance of a model misspecification, albeit with the potential of overfitting. A penalty directed at reducing overfitting is required. A flexible semiparametric model is potentially also better suited for applications to small areas like stands than a parametric model. We demonstrate that important reductions in variance are indeed possible, but also that they depend on the form of the nonparametric part of the chosen model and the level of inference (population versus domains). With regard to practical application, reliable estimates of forest attributes at stand-level are of special interest within the scope of forest-management planning, as silvicultural treatments are always stand-oriented, at least with small-scale forestry under Central European conditions, and stand-related volume (basal area, tree density) belongs to the set of relevant parameters for management decisions regarding harvest and regeneration measures.
Organic farming in India: a vision towards a healthy nation
Authors: Das Suryatapa , Chatterjee Annalakshmi , Pal Tapan Kumar 
Published: June 2020

Abstract
Food quality and safety are the two important factors that have gained ever-increasing attention in general consumers. Conventionally grown foods have immense adverse health effects due to the presence of higher pesticide residue, more nitrate, heavy metals, hormones, antibiotic residue, and also genetically modified organisms. Moreover, conventionally grown foods are less nutritious and contain lesser amounts of protective antioxidants. In the quest for safer food, the demand for organically grown foods has increased during the last decades due to their probable health benefits and food safety concerns. Organic food production is defined as cultivation without the application of chemical fertilizers and synthetic pesticides or genetically modified organisms, growth hormones, and antibiotics. The popularity of organically grown foods is increasing day by day owing to their nutritional and health benefits. Organic farming also protects the environment and has a greater socio-economic impact on a nation. India is a country that is bestowed with indigenous skills and potentiality for growth in organic agriculture. Although India was far behind in the adoption of organic farming due to several reasons, presently it has achieved rapid growth in organic agriculture and now becomes one of the largest organic producers in the world. Therefore, organic farming has a great impact on the health of a nation like India by ensuring sustainable development.
Neighborhood Effects on the Health of Chinese Older Adults: Beyond the Rural and Urban Dichotomy
Authors: Li Yuekang , Wang Yi , Morrow-Howell Nancy 
Published: June 2020

Abstract

Background and Objectives
The associations between physical frailty and depressive symptoms among older individuals were established in the existing literature. Taking the person–environment perspective, we argue that neighborhood environment could either buffer the stress derived from being physically vulnerable or worsen it by adding another layer of stressors in the environmental context when physical health declined. The objectives of this study were to explore to what extent the neighborhood-level characteristics moderate the relationship between physical frailty and depressive symptoms.

Research Design and Methods
Using the China Health and Retirement Longitudinal Study 2011 wave, 6,245 individuals aged 60 years and older were included for analyses. Multilevel mixed-effects models were fitted to examine the moderating effects of urbanicity and neighborhood-level socioeconomic status (SES) on the relationship between frailty and depressive symptoms among older adults, controlling for individual-level characteristics.

Results
Results showed a stronger relationship between deterioration in physical health and depressive symptoms in rural neighborhoods and neighborhoods with lower SES, after controlling for individual-level SES. Also, the moderating effects of the neighborhood-level socioeconomic factors remained after controlling for urbanicity, indicating that neighborhood SES works beyond the rural–urban contexts.

Discussion and Implications
Findings from this study demonstrate the important roles of neighborhood socioeconomic characteristics in reshaping, and the need to redefine, China’s rural–urban dichotomy. The findings also identified neighborhoods with low SES as potential targets for policy and practice to reduce the stress associated with health decline.
User innovation and network effects: the case of video games
Authors: Abrate Graziano , Menozzi Anna 
Published: June 2020

AbstractNew models of knowledge creation are emerging, where the user community is a major source of innovation development. But, how does user innovation impact on producer sales, and the other way round? In this article, the mutual benefits deriving from the user–producer interaction are analyzed in terms of network effects and on a basis of a unique panel dataset of weekly observations in the context of video games and their user-generated, free modifications. The estimates of a system of equations modeling the original good’s retail demand function and the user innovation dynamics show that user-generated complements spur the demand for the original product and smooth the consumer price sensitivity. User innovation increases with the crowd of complementors up to a certain threshold and decreases afterwards, thus following a non-monotonic pattern.
Bias factor, maximum bias and the E-value: insight and extended applications
Authors: Cusson Alexandre , Infante-Rivard Claire 
Published: June 2020

Abstract

Background
Unmeasured confounding can bias the relationship between exposure and outcome. Sensitivity analyses generate bias-adjusted measures but these are not much used; this may change with the availability of the E-value (for evidence for causality in observational studies), appealing for its ease of calculation. However, as currently proposed, the E-value has some practical limitations that may reduce its use.

Methods
We first provide some insight into the relationship between two established measures for unmeasured confounding: ‘the bias factor’ and the maximum value this bias factor can take (‘the B bias’). These measures are the statistical foundation for the E-value. We use them to develop new E-value formulas for situations when it is not currently applicable such as e.g. when, not unusually, a negative relation between unmeasured confounder and outcome and a positive one with exposure are postulated. We also provide E-values on the odds ratio scale because, currently, even when using the odds ratio as the study measure in the calculation of E-value, the result is to be interpreted as a relative risk, which is somewhat inconvenient.

Results
The additional formulas for the E-value measure make it applicable in all possible scenarios defined by the combined directions between unmeasured confounder and both the exposure and outcome. In addition, E-value measures can now be interpreted as odds ratios if the observed results are reported on the same scale.

Conclusions
The E-value is part of newer sensitivity analyses methods for unmeasured confounding. We provide insight into its structure, underscoring its advantages and limitations, and expand its applications.
Racial Disparity of Coronavirus Disease 2019 in African American Communities
Authors: Kullar Ravina , Marcelin Jasmine R , Swartz Talia H , Piggott Damani A , Macias Gil Raul , Mathew Trini A , Tan Tina 
Published: June 2020

Abstract
The coronavirus disease 2019 (COVID-19) pandemic has unveiled unsettling disparities in the outcome of the disease among African Americans. These disparities are not new but are rooted in structural inequities that must be addressed to adequately care for communities of color. We describe the historical context of these structural inequities, their impact on the progression of COVID-19 in the African American (black) community, and suggest a multifaceted approach to addressing these healthcare disparities. (Of note, terminology from survey data cited for this article varied from blacks, African Americans, or both; for consistency, we use African Americans throughout.)
Massive Release of CD9+ Microvesicles in Human Immunodeficiency Virus Infection, Regardless of Virologic Control
Authors: Poveda Eva , Tabernilla Andrés , Fitzgerald Wendy , Salgado-Barreira Ángel , Grandal Marta , Pérez Alexandre , Mariño Ana , Álvarez Hortensia , Valcarce Nieves , González-García Juan , Bernardino José Ignacio , Gutierrez Félix , Fujioka Hisashi , Crespo Manuel , Ruiz-Mateos Ezequiel , Margolis Leonid , Lederman Michael M , Freeman Michael L 
Published: June 2020

Abstract

Background
The role of extracellular vesicles (EVs) in human immunodeficiency virus (HIV) pathogenesis is unknown. We examine the cellular origin of plasma microvesicles (MVs), a type of ectocytosis-derived EV, the presence of mitochondria in MVs, and their relationship to circulating cell-free mitochondrial deoxyribonucleic acid (ccf-mtDNA) in HIV-infected patients and controls.

Methods
Five participant groups were defined: 30 antiretroviral therapy (ART)-naive; 30 ART-treated with nondetectable viremia; 30 elite controllers; 30 viremic controllers; and 30 HIV-uninfected controls. Microvesicles were quantified and characterized from plasma samples by flow cytometry. MitoTrackerDeepRed identified MVs containing mitochondria and ccf-mtDNA was quantified by real-time polymerase chain reaction.

Results
Microvesicle numbers were expanded at least 10-fold in all HIV-infected groups compared with controls. More than 79% were platelet-derived MVs. Proportions of MVs containing mitochondria (22.3% vs 41.6%) and MV mitochondrial density (706 vs 1346) were significantly lower among HIV-infected subjects than controls, lowest levels for those on ART. Microvesicle numbers correlated with ccf-mtDNA levels that were higher among HIV-infected patients.

Conclusions
A massive release of platelet-derived MVs occurs during HIV infection. Some MVs contain mitochondria, but their proportion and mitochondrial densities were lower in HIV infection than in controls. Platelet-derived MVs may be biomarkers of platelet activation, possibly reflecting pathogenesis even in absence of HIV replication.
Group Testing for Severe Acute Respiratory Syndrome– Coronavirus 2 to Enable Rapid Scale-up of Testing and Real-Time Surveillance of Incidence
Authors: Pilcher Christopher D , Westreich Daniel , Hudgens Michael G 
Published: June 2020

Abstract
High-throughput molecular testing for severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) may be enabled by group testing in which pools of specimens are screened, and individual specimens tested only after a pool tests positive. Several laboratories have recently published examples of pooling strategies applied to SARS-CoV-2 specimens, but overall guidance on efficient pooling strategies is lacking. Therefore we developed a model of the efficiency and accuracy of specimen pooling algorithms based on available data on SAR-CoV-2 viral dynamics. For a fixed number of tests, we estimate that programs using group testing could screen 2–20 times as many specimens compared with individual testing, increase the total number of true positive infections identified, and improve the positive predictive value of results. We compare outcomes that may be expected in different testing situations and provide general recommendations for group testing implementation. A free, publicly-available Web calculator is provided to help inform laboratory decisions on SARS-CoV-2 pooling algorithms.
Autosomal recessive complete STAT1 deficiency caused by compound heterozygous intronic mutations
Authors: Sakata Sonoko , Tsumura Miyuki , Matsubayashi Tadashi , Karakawa Shuhei , Kimura Shunsuke , Tamaura Moe , Okano Tsubasa , Naruto Takuya , Mizoguchi Yoko , Kagawa Reiko , Nishimura Shiho , Imai Kohsuke , Le Voyer Tom , Casanova Jean-Laurent , Bustamante Jacinta , Morio Tomohiro , Ohara Osamu , Kobayashi Masao , Okada Satoshi 
Published: June 2020

Abstract
Autosomal recessive (AR) complete signal transducer and activator of transcription 1 (STAT1) deficiency is an extremely rare primary immunodeficiency that causes life-threatening mycobacterial and viral infections. Only seven patients from five unrelated families with this disorder have been so far reported. All causal STAT1 mutations reported are exonic and homozygous. We studied a patient with susceptibility to mycobacteria and virus infections, resulting in identification of AR complete STAT1 deficiency due to compound heterozygous mutations, both located in introns: c.128+2 T&gt;G and c.542-8 A&gt;G. Both mutations were the first intronic STAT1 mutations to cause AR complete STAT1 deficiency. Targeted RNA-seq documented the impairment of STAT1 mRNA expression and contributed to the identification of the intronic mutations. The patient’s cells showed a lack of STAT1 expression and phosphorylation, and severe impairment of the cellular response to IFN-γ and IFN-α. The case reflects the importance of accurate clinical diagnosis and precise evaluation, to include intronic mutations, in the comprehensive genomic study when the patient lacks molecular pathogenesis. In conclusion, AR complete STAT1 deficiency can be caused by compound heterozygous and intronic mutations. Targeted RNA-seq-based systemic gene expression assay may help to increase diagnostic yield in inconclusive cases after comprehensive genomic study.
Democratizing EHR analyses with FIDDLE: a flexible data-driven preprocessing pipeline for structured clinical data
Authors: Tang Shengpu , Davarmanesh Parmida , Song Yanmeng , Koutra Danai , Sjoding Michael W , Wiens Jenna 
Published: June 2020

Abstract

Objective
In applying machine learning (ML) to electronic health record (EHR) data, many decisions must be made before any ML is applied; such preprocessing requires substantial effort and can be labor-intensive. As the role of ML in health care grows, there is an increasing need for systematic and reproducible preprocessing techniques for EHR data. Thus, we developed FIDDLE (Flexible Data-Driven Pipeline), an open-source framework that streamlines the preprocessing of data extracted from the EHR.

Materials and Methods
Largely data-driven, FIDDLE systematically transforms structured EHR data into feature vectors, limiting the number of decisions a user must make while incorporating good practices from the literature. To demonstrate its utility and flexibility, we conducted a proof-of-concept experiment in which we applied FIDDLE to 2 publicly available EHR data sets collected from intensive care units: MIMIC-III and the eICU Collaborative Research Database. We trained different ML models to predict 3 clinically important outcomes: in-hospital mortality, acute respiratory failure, and shock. We evaluated models using the area under the receiver operating characteristics curve (AUROC), and compared it to several baselines.

Results
Across tasks, FIDDLE extracted 2,528 to 7,403 features from MIMIC-III and eICU, respectively. On all tasks, FIDDLE-based models achieved good discriminative performance, with AUROCs of 0.757–0.886, comparable to the performance of MIMIC-Extract, a preprocessing pipeline designed specifically for MIMIC-III. Furthermore, our results showed that FIDDLE is generalizable across different prediction times, ML algorithms, and data sets, while being relatively robust to different settings of user-defined arguments.

Conclusions
FIDDLE, an open-source preprocessing pipeline, facilitates applying ML to structured EHR data. By accelerating and standardizing labor-intensive preprocessing, FIDDLE can help stimulate progress in building clinically useful ML tools for EHR data.
Growing Trends in the Efficient and Selective Extraction of Compounds in Complex Matrices Using Molecularly Imprinted Polymers and Their Relevance to Toxicological Analysis
Authors: Mulder Haley A , Halquist Matthew S 
Published: June 2020

Abstract
In the world of forensic and clinical toxicology, proper sample preparation is one of the key steps in identification and quantification of drugs of abuse. Traditional extraction methods such as solid-phase extraction and liquid−liquid extraction are often laborious and nonselective for the target analytes being measured. Molecularly imprinted polymers (MIPs) can be synthesized for sample extraction and their versatility allows the polymer to be employed in off-line, benchtop extractions or on/in-line instrument extractions, offering a faster and more selective sample preparation without the risk of interfering matrix effects. This review details the synthesis and applications of MIP materials for the extraction of drug compounds from biological matrices in publications from 1994 to today.
Forest Ownership Patterns in the Western Upper Peninsula of Michigan, USA
Authors: Zupko Robert 
Published: June 2020

AbstractAbstract In heavily forested rural areas, tax-incentivization programs are commonly employed to encourage timber production and harvesting activities. Because of growing interest in developing woody-biomass-based biofuels in the Western Upper Peninsula of Michigan, USA, we analyzed property records to determine who the regional actors are along with what role tax-incentivization programs may play. We found that a minority of entities collectively control 77 percent of the land in the region; however, family forest owners collectively own 23 percent of the land. Although tax-incentive programs are commonly used by commercial forests, the requirements of the primary program in Michigan program appear to preclude most family forests in the region. Accordingly, this study suggests that a greater understanding of reluctance of family forests to enroll in secondary programs is needed, or a lowering of forestland requirements to permit more family forests to enroll.Study ImplicationsIn heavily forested rural areas, the development of local forest resources has been suggested as a means of developing the local economy. One means of using the forest resources is through the development of woody-biomass-based biofuel or bioenergy programs. As these programs are dependent upon harvesting to supply the relevant feedstocks, tax-incentivization programs, such as Michigan’s Commercial Forest Land (CFL), may be used to encourage commercial timber production and overcome resistance to harvesting by nonindustrial private forest (NIPF) owners. These findings suggest such programs are likely to be well to fully subscribed by commercial forests. However, the implementation of these programs (ex., minimum of 40 ac. of forestland) may preclude a significant number of family forests from being able to enroll, which may be a contributing factor to low subscription rates. As a result, policymakers wishing to encourage enrollment by family forests in tax-incentivization programs should consider the practical realities of regional family ownership (i.e., average forestland acreage) in developing the programs.
Laparoscopic sigmoidectomy for sigmoid colon cancer with left-sided inferior vena cava and persistent descending mesocolon
Authors: Kawakami Masayo , Nakazato Hidetsugu , Tomiyama Takeshi , Tomori Takehiko , Miyagi Jun , Nagayoshi Seiji , Ohmine Yasushi 
Published: June 2020

Abstract
Left-sided inferior vena cava (IVC) is a rare congenital malformation, as is persistent descending mesocolon, a developmental anomaly in which the colonic mesentery does not fuse with the dorsal abdominal wall. Although these anomalies are mostly asymptomatic, they should be identified preoperatively to avoid iatrogenic injury. We report a case of sigmoid colon cancer in a patient with both anomalies. The patient was an 80-year-old man whose preoperative computed tomography (CT) scan showed that the IVC ascended vertically along the left side of the abdominal aorta, and the descending colon was at the abdominal midline. Coronal CT was particularly useful for visualizing these anomalies. With this better understanding of the malpositioned anatomy, we successfully performed laparoscopic sigmoidectomy with lymph node dissection. Careful evaluation of preoperative CT imaging based on a clear understanding of such anatomical anomalies is particularly important for performing safe laparoscopic surgery.