bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rate of BCG Immunization in HIV-Exposed Infants in a Selected Primary Health Centre in Southern Nigeria: Implications of No Vaccine Policy for HIV-Positive Infants
Authors: Ekanem A M , Oloyede I P , Ekrikpo U E , Idung A U , Edward E 
Published: May 2020

Abstract

Background
Maternal and infant HIV status influences the decision of BCG immunization of infants at birth. The objective of this study was to determine the HIV status of HIV-exposed infants (HEIs) by the first HIV DNA PCR test and the rate of BCG uptake among the HEIs who were confirmed HIV negative.

Methods
This was a retrospective descriptive cross-sectional study involving the review of results of 99 dried blood samples (DBS) for the first HIV DNA PCR test of HEIs whose mothers were diagnosed HIV positive on presentation of the infants at first immunization visit at a Primary Health Centre from January 2018 to January 2019.

Results
Of the 99 DBS examined, 86; 86.9% (95% CI 80.1–93.6) were HIV negative, 9; 9.1% (95% CI 3.3–14.8) were positive while the results of 4 (4.0%) infants were not in the register. Only 7; 7.1% (95% CI 1.9–12.2) of the 99 HEIs returned for BCG immunization at the centre. BCG immunization status of the HEIs after first PCR results was not significantly associated with sex of the infants or availability of phone number of the guardians (p = 0.70 and 0.12, respectively).

Conclusion
The majority of HEIs were HIV negative at first HIV DNA PCR test. Few of these HIV negative infants returned for BCG immunization. Hence, all HEIs should be given BCG immunization according to WHO GAVCS committee recommendation on BCG immunization for settings with poor HIV diagnostic and treatment facilities for mothers and infants.
Per- and poly-fluoroalkyl substances and bone mineral density
Authors: Colicino Elena , Pedretti Nicolo Foppa , Busgang Stefanie A. , Gennings Chris 
Published: May 2020

Background:
Per- and poly-fluoroalkyl substances (PFAS) are chemicals, detected in 95% of Americans, that induce osteotoxicity and modulate hormones, thereby influencing bone health. Previous studies found associations between individual PFAS and bone mineral density in adults but did not analyze their combined effects.

Objective:
To extend weighted quantile sum (WQS) regression to a Bayesian framework (Bayesian extension of the WQS regression [BWQS]) and determine the association between a mixture of serum PFAS and mineral density in lumbar spine, total, and neck femur in 499 adults from the 2013 to 2014 National Health and Nutrition Examination Survey (NHANES).

Methods:
We used BWQS to assess the combined association of eight PFAS, as a mixture, with bone mineral density in adults. As secondary analyses, we focused on vulnerable populations (men over 50 years and postmenopausal women). Analyses were adjusted for sociodemographic factors. Sensitivity analyses included bone mineral density associations with individual compounds and results from WQS regressions.

Results:
The mean age was 55 years old (SD = 1) with average spine, total, and neck femur mineral densities of 1.01 (SD = 0.01), 0.95 (SD = 0.01), and 0.78 (SD = 0.01) gm/cm2, respectively. PFAS mixture levels showed no evidence of association with mineral density (spine: β = −0.004; 95% credible interval [CrI] = −0.04, 0.04; total femur: β = 0.002; 95% CrI = −0.04, 0.05; femur neck: β = 0.005; 95%CrI = −0.03, 0.04) in the overall population. Results were also null in vulnerable populations. Findings were consistent across sensitivity analyses.

Conclusions:
We introduced a Bayesian extension of WQS and found no evidence of the association between PFAS mixture and bone mineral density.
Identification of distinct clinical phenotypes in mechanically ventilated patients with acute brain dysfunction using cluster analysis
Authors: Souza-Dantas Vicente Cés , Dal-Pizzol Felipe , Tomasi Cristiane D. , Spector Nelson , Soares Márcio , Bozza Fernando A. , Póvoa Pedro , Salluh Jorge I. F. 
Published: May 2020

Abstract
Acute brain dysfunction (ABD) is a frequent and severe syndrome occurring in critically ill patients and early identification of high-risk patients is paramount. In the present analysis, we propose a clinically applicable model for early phenotype identification of ABD at the bedside in mechanically ventilated patients, improving the recognition of patients with prolonged ABD.
Prospective cohort with 629 mechanically ventilated patients in two medical-surgical intensive care units at academic centers. We applied cluster analysis to identify phenotypes using clinical and biological data. We then tested the association of phenotypes and its respective clinical outcomes. We performed a validation on a new cohort of patients select on subsequent patients admitted to the participants intensive care units.
A model with 3 phenotypes best described the study population. A 4-variable model including medical admission, sepsis diagnosis, simplified acute physiologic score II and basal serum C-reactive protein (CRP) accurately classified each phenotype (area under curve 0.82; 95% CI, 0.79–0.86). Phenotype A had the shorter duration of ABD (median, 1 day), while phenotypes B and C had progressively longer duration of ABD (median, 3 and 6 days, respectively; P < .0001). There was an association between the duration of ABD and the baseline CRP levels and simplified acute physiology score II score (sensitivity and specificity of 80%). To increase the sensitivity of the model, we added CRP kinetics. By day 1, a CRP < 1.0 times the initial level was associated with a shorter duration of ABD (specificity 0.98).
A model based on widely available clinical variables could provide phenotypes associated with the duration of ABD. Phenotypes with longer duration of ABD (phenotypes B and C) are characterized by more severe inflammation and by significantly worse clinical outcomes.
Respiratory Neurophysiology in Intensive Care Unit
Authors: Swash Michael , de Carvalho Mamede 
Published: May 2020

Summary:
Patients with intensive care unit-acquired weakness have an increased risk of prolonged mechanical ventilation, which is a risk factor for prolonged stay and mortality. The most common cause of this problem is weakness of the diaphragm, which can derive from phrenic nerve injury associated with critical neuropathy, or with the complex multiorgan failure/systemic respiratory response syndrome causing muscle fiber lesion. Two conventional neurophysiological techniques are useful to investigate the respiratory muscles, phrenic nerve conduction, and needle electromyography of the accessory respiratory muscles and diaphragm. Phrenic nerve stimulation is a standard noninvasive technique; amplitude of the motor response can be reduced because of muscle fiber inexcitability or axonal loss. Electromyography of the diaphragm is an invasive method but is safe if performed as indicated. It can reveal neurogenic or myopathic motor units. Although these neurophysiological methods have limitations in the investigation of intensive care unit patients with severe respiratory involvement, normal phrenic nerve responses should exclude marked axonal loss and indicate a better prognosis.
Characterization of the Diffusion Signal of Breast Tissues using Multi-exponential Models
Authors: Rodríguez-Soto Ana E. , Andreassen Maren M. Sjaastad , Conlin Christopher C. , Park Helen H. , Ahn Grace S. , Bartsch Hauke , Kuperman Joshua , Vidić Igor , Ojeda-Fournier Haydee , Wallace Anne M. , Hahn Michael , Seibert Tyler M. , Jerome Neil Peter , Østlie Agnes , Bathen Tone Frost , Goa Pål Erik , Rakow-Penner Rebecca , Dale Anders M. 
Published: May 2020

AbstractBackgroundDiffusion-weighted magnetic resonance imaging (DW-MRI) has demonstrated potential as an exogenous contrast-free diagnostic tool for breast cancer screening. Advanced non-Gaussian models of the DW-MRI signal provide insight into the tissue microstructure. Restriction spectrum imaging (RSI) is a mathematical framework that improves tumor conspicuity by decomposing the DW-MRI signal into separate diffusion components. The number of diffusion components and corresponding apparent diffusion coefficients (ADCs) optimal for RSI are organ-specific and determined empirically. The outputs of RSI are the signal contributions of each separable diffusion component.PurposeTo understand the diffusion-weighted MRI signal of cancerous and healthy breast tissues in the context of RSI.Study TypeProspective.Populations74 women, from two sites, with pathology-proven breast cancer.Field Strength/Sequence3.0TAssessmentThe DW-MRI signal was described using a linear combination of a variable number of exponential components. The ADC for each component was estimated across all voxels from control and cancer regions of interest (ROIs), patients and sites. Once ADCs were determined, the signal contributions of each diffusion component were estimated using these fixed ADC values. Conventional ADC (mono-exponential) values were also estimated.Statistical TestsThe relative fitting residual and relative Bayesian information criterion (BIC) were assessed. The signal contributions of each diffusion component were compared using analysis of variance (ANOVA) and post-hoc tests.ResultsEstimated ADCs for the bi-exponential model were D1,2 = 2.0 × 10−5 and D2,2 = 2.2 × 10−3 mm2/s, and D1,3=0, D2,3 = 1.4 × 10−3 and D3,3=10.2 × 10−3 mm2/s for tri-exponential model, which in practice is reduced to a bi-exponential model with an offset, or a three-component model. The relative fitting residuals of conventional ADC, bi-exponential and three-component models in control ROIs were 2.1%, 1.62%, and 1.03%, and 3.3%, 1.0%, and 0.3% for cancer ROIs. BIC was smaller for the three-component model, indicating an improved fitting of breast DW-MRI data compared to the bi-exponential model.ConclusionBreast DW-MRI signal was best described using a tri-exponential model. The signal contributions of the slower component in bi- or tri-exponential models were larger in tumor lesions. These data may be used as differential features between healthy and malignant breast tissues.
Effectiveness of the strategies implemented in Sri Lanka for controlling the COVID–19 outbreak
Authors: Erandi K.K.W.H. , Mahasinghe A.C. , Perera S.S.N. , Jayasinghe S. 
Published: May 2020

AbstractIn order to bring the new coronavirus pandemic in the country under control, the government of Sri Lanka implemented a set of control strategies including social distancing, quarantine, lockdowns, travel restrictions and isolation of villages. The aim of this study is to investigate the effectiveness of the overall control process with the aid of classical compartment models and network models. Our results indicate that the prevailing control strategies are effective with at least 50% contact rate reduction or with at least 40% isolation of the contact history of infected population.
Altered substance P signaling underlies perivascular sensory nerve dysfunction in inflammatory bowel disease
Authors: Norton Charles E. , Borgmann Elizabeth A. , Hart Marcia L. , Jones Benjamin W. , Franklin Craig , Boerman Erika M 
Published: May 2020

AbstractObjectiveInflammatory Bowel Disease (IBD) is associated with cardiovascular disease risk and impaired intestinal blood flow, but the functional role of perivascular nerves that control vasomotor function of mesenteric arteries (MAs) perfusing the intestine is unknown in IBD. Because perivascular sensory nerves and their transmitters calcitonin gene-related peptide (CGRP) and substance P (SP) are important mediators of both vasodilation and inflammatory responses, our objective was to identify IBD-related deficits in perivascular sensory nerve function and vascular neurotransmitter signaling.Approach and ResultsIn MAs from an IL-10−/−mouse model, we found that IBD significantly impairs EFS-mediated sensory vasodilation and sensory inhibition of sympathetic vasoconstriction, despite decreased sympathetic nerve density and vasoconstriction. The MA content and EFS-mediated release of both CGRP and SP are slightly decreased with IBD, but IBD has different effects on each transmitter. CGRP nerve density, receptor expression, hyperpolarization and vasodilation are preserved with IBD. In contrast, SP nerve density and receptor expression are increased, and SP hyperpolarization and vasodilation are impaired with IBD. A critical finding is that blocking neurokinin 1 (SP) receptors restored EFS-mediated sensory vasodilation and enhanced CGRP-mediated vasodilation in MAs from IBD but not Control mice.ConclusionsAn aberrant role for the perivascular sensory neurotransmitter SP and its downstream signaling in MAs underlies vascular dysfunction with IBD. With IBD, SP signaling impedes CGRP-mediated sensory vasodilation, contributing to impaired blood flow. Substance P and NK1 receptors may represent an important target for treating vascular dysfunction in IBD.
Synergistic Material-Topography Combinations to Achieve Immunomodulatory Osteogenic Biomaterials
Authors: Burroughs Laurence , Amer Mahetab H. , Vassey Matthew , Koch Britta , Figueredo Grazziela P , Mukonoweshuro Blessing , Mikulskis Paulius , Vasilevich Aliaksei , Vermeulen Steven , Dryden Ian L. , Winkler David A. , Ghaemmaghami Amir M. , Rose Felicity R. A. J. , de Boer Jan , Alexander Morgan R. 
Published: May 2020

AbstractHuman mesenchymal stem cells (hMSCs) are widely represented in ongoing regenerative medicine clinical trials due to their ease of autologous implantation. In bone regeneration, crosstalk between macrophages and hMSCs is critical with macrophages playing a key role in the recruitment and differentiation of hMSCs. However, engineered biomaterials able to both direct hMSC fate and modulate macrophage phenotype have not yet been identified. A novel combinatorial chemistry-microtopography screening platform, theChemoTopoChip, is used to identify materials suitable for bone regeneration by screening with human immortalized mesenchymal stem cells (hiMSCs) and human macrophages. The osteoinduction achieved in hiMSCs cultured on the “hit” materials in basal media is comparable to that seen when cells are cultured in osteogenic media, illustrating that these materials offer a materials-induced alternative in bone-regenerative applications. These also exhibit immunomodulatory effects, concurrently polarizing macrophages towards a pro-healing phenotype. Control of cell response is achieved when both chemistry and topography are recruited to instruct the required cell phenotype, combining synergistically. The large library of materials reveals that the relative roles of microtopography and material chemistry are similar, and machine learning identifies key material and topographical features for cell-instruction.
Reducing Sanger Confirmation Testing through False Positive Prediction Algorithms
Authors: Holt James M. , Wilk Melissa , Sundlof Brett , Nakouzi Ghunwa , Bick David , Lyon Elaine 
Published: May 2020

AbstractPurposeClinical genome sequencing (cGS) followed by orthogonal confirmatory testing is standard practice. While orthogonal testing significantly improves specificity it also results in increased turn-around-time and cost of testing. The purpose of this study is to evaluate machine learning models trained to identify false positive variants in cGS data to reduce the need for orthogonal testing.MethodsWe sequenced five reference human genome samples characterized by the Genome in a Bottle Consortium (GIAB) and compared the results to an established set of variants for each genome referred to as a ‘truth-set’. We then trained machine learning models to identify variants that were labeled as false positives.ResultsAfter training, the models identified 99.5% of the false positive heterozygous single nucleotide variants (SNVs) and heterozygous insertions/deletions variants (indels) while reducing confirmatory testing of true positive SNVs to 1.67% and indels to 20.29%. Employing the algorithm in clinical practice reduced orthogonal testing using dideoxynucleotide (Sanger) sequencing by 78.22%.ConclusionOur results indicate that a low false positive call rate can be maintained while significantly reducing the need for confirmatory testing. The framework that generated our models and results is publicly available athttps://github.com/HudsonAlpha/STEVE.
Bt cotton sustainability needs integration of complementary technologies for the cotton farmers in India
Authors: Gujar GT , Mayee CD , Choudhary B , Suresh A 
Published: May 2020

AbstractBiased conclusions of long-term impact of Bt cotton published in Nature Plants March 2020 threatens to derail technological development. We therefore advocate integrating available technologies for sustainability of Bt adoption in India and prospecting for all including biotechnological developments.
Epigenetic therapy remodels the immune synaptic cytoskeleton to potentiate cancer susceptibility to γδ T cells
Authors: Weng Rueyhung R. , Lu Hsuan-Hsuan , Lin Chien-Ting , Fan Chia-Chi , Lin Rong-Shan , Huang Tai-Chung , Lin Shu-Yung , Huang Yi-Jhen , Juan Yi-Hsiu , Wu Yi-Chieh , Hung Zheng-Ci , Liu Chi , Lin Xuan-Hui , Hsieh Wan-Chen , Chiu Tzu-Yuan , Liao Jung-Chi , Chiu Yen-Ling , Chen Shih-Yu , Yu Chong-Jen , Tsai Hsing-Chen 
Published: May 2020

ABSTRACTγδ T cells are a distinct subgroup of T cells that bridge the innate and adaptive immune systems and can attack cancer or virus-infected cells in an MHC-unrestricted manner. Despite its antitumor ability in both autologous and allogeneic settings, earlier trials of adoptive γδ T cell transfer in solid tumors had limited success due to limitations in cell expansion and the lack of a strategy to modulate tumor lytic interactions between γδ T and cancer cells. Here, we show through quantitative surface proteomics and gene enrichment analyses that DNA methyltransferase inhibitors (DNMTis) upregulate multiple surface molecules related to γδ T cell activation in cancer cells. DNMTi treatment of human lung cancer potentiates tumor lysis byex vivo-expanded γδ T cells using a clinical-grade expansion protocol developed by our team to enrich for the Vδ1 subset while preserving their antitumor effector functions. Mechanistically, DNMTis enhance immune synapse formation and stabilize the synaptic cleft to facilitate γδ T-mediated tumor lysis. Through integrated analysis of RNA-seq, DNA methylation, and ATAC-seq, we demonstrate that depletion of DNMTs induces coordinated pattern alterations of immune synaptic-cytoskeletal networks at the cancer side of the immune synapse. In addition, single-cell mass cytometry reveals enrichment of polyfunctional γδ T subsets by DNMTis. Combined DNMTi and adoptive γδ T transfer in a mouse lung cancer model offers a significant survival benefit. Consistently, the DNMTi-associated cytoskeleton signature identifies a subset of lung cancer patients with improved survival. Our results demonstrate that epigenetic mechanisms are crucial for cytoskeletal remodeling in cancer to potentiate immune attack and support a combinatorial strategy of DNMTis and γδ T cell-based immunotherapy in lung cancer management.One Sentence SummaryDNA methyltransferase inhibitors potentiate the killing of lung cancer by γδ T cells through remodeling cytoskeletal-immune synaptic networks.
Detecting neural state transitions underlying event segmentation
Authors: Geerligs Linda , van Gerven Marcel , Güçlü Umut 
Published: May 2020

AbstractSegmenting perceptual experience into meaningful events is a key cognitive process that helps us make sense of what is happening around us in the moment, as well as helping us recall past events. Nevertheless, little is known about the underlying neural mechanisms of the event segmentation process. Recent work has suggested that event segmentation can be linked to regional changes in neural activity patterns. Accurate methods for identifying such activity changes are important to allow further investigation of the neural basis of event segmentation and its link to the temporal processing hierarchy of the brain. In this study, we introduce a new set of elegant and simple methods to study these mechanisms. We introduce a method for identifying the boundaries between neural states in a brain area and a complementary one for identifying the number of neural states. Furthermore, we present the results of a comprehensive set of simulations and analyses of empirical fMRI data to provide guidelines for reliable estimation of neural states and show that our proposed methods outperform the current state-of-the-art in the literature. This methodological innovation will allow researchers to make headway in investigating the neural basis of event segmentation and information processing during naturalistic stimulation.HighlightsBoundaries between meaningful events are related to neural state transitions.Neural states are temporarily stable regional brain activity patterns.We introduce novel methods for data-driven detection of neural state boundaries.These methods can identify the location and the number of neural state boundaries.Simulations and empirical data support the reliability and validity of our methods.
The influence of auditory attention on rhythmic speech entrainment
Authors: Sokoliuk Rodika , Degano Giulio , Melloni Lucia , Noppeney Uta , Cruse Damian 
Published: May 2020

ABSTRACTLanguage comprehension relies on integrating words into progressively more complex structures, like phrases and sentences. This hierarchical structure building is reflected in rhythmic neural activity across multiple timescales in E/MEG (Ding et al., 2016, 2017).How does selective attention across levels of the hierarchy influence the expression of these rhythms?We investigated these questions in an EEG study of 72 healthy human volunteers listening to streams of monosyllabic isochronous English words that were either unrelated (scrambled condition) or composed of four-word-sequences building meaningful sentences (sentential condition). Importantly, there were no physical cues between four-word-sentences but boundaries were marked by syntactic structure and thematic role assignment. Participants were divided into three attention groups: from passive listening(passive group)to attending to individual words(word group)or sentences(sentence group).Thepassiveandword groupwere naïve to the sentential structure of the stimulus material, while thesentence groupwere not.We found significant entrainment at word- and sentence rate across all three groups, with sentence entrainment linked to left middle temporal gyrus and right superior temporal gyrus. Goal-directed attention to words did not enhance word-rate-entrainment suggesting that word entrainment relies on largely automatic mechanisms. Importantly, goal-directed attention to sentences relative to words significantly increased sentence-rate-entrainment over left inferior frontal gyrus. This attentional modulation of rhythmic EEG activity at the sentential level highlights the role of attention in integrating individual words into complex linguistic structures.SIGNIFICANCE STATEMENTNeural activity is known to entrain to physical characteristics of auditory stimuli. However, entrainment also occurs with structures lacking physical cues but rather require comprehension of the stimulus’ meaning – for example, entrainment to sentences in speech even without acoustic gaps separating these higher linguistic structures.We investigated how goal-directed attention to low-level (words) and high-level (sentences) linguistic structures influences entrainment strength. Whilst sentence entrainment occurred independently of selective attention, it increased with goal-directed attention towards sentences. Conversely, no such attentional effect was found for word entrainment.While goal-directed attention towards sentences strengthens entrainment, it is no prerequisite for it to occur, suggesting that low attentional effort is required for sentence comprehension, potentially reflecting the importance of speech in humans.