bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning to identify socio-behavioural predictors of HIV positivity in East and Southern Africa
Authors: Orel Erol , Esra Rachel , Estill Janne , Marchand-Maillet Stéphane , Merzouki Aziza , Keiser Olivia 
Published: January 2020

AbstractBackgroundThere is a need for high yield HIV testing strategies to reach epidemic control. We aimed to predict the HIV status of individuals based on socio-behavioural characteristics.MethodsWe analysed over 3,200 variables from the most recent Demographic Health Survey from 10 countries in East and Southern Africa. We trained four machine-learning algorithms and selected the best based on the f1 score. Training and validation were done on 80% of the data. The model was tested on the remaining 20% and on a left-out country which was rotated around. The best algorithm was retrained on the variables which were most predictive. We studied two scenarios: one aiming to identify 95% of people living with HIV (PLHIV) and one aiming to identify individuals with 95% or higher probability of being HIV positive.FindingsOverall 55,151 males and 69,626 females were included. XGBoost performed best in predicting HIV with a mean f1 of 76·8% [95% confidence interval 76·0%-77·6%] for males and 78·8% [78·2%-79·4%] for females. Among the ten most predictive variables, nine were identical for both sexes: longitude, latitude and, altitude of place of residence, current age, age of most recent partner, total lifetime number of sexual partners, years lived in current place of residence, condom use during last intercourse and, wealth index. Model performance based on these variables decreased minimally. For the first scenario, 7 males and 5 females would need to be tested to identify one HIV positive person. For the second scenario, 4·2% of males and 6·2% of females would have been identified as high-risk population.InterpretationWe were able to identify PLHIV and those at high risk of infection who may be offered pre-exposure prophylaxis and/or voluntary medical male circumcision. These findings can inform the implementation of HIV prevention and testing strategies.FundingSwiss National Science Foundation.
A global lipid map defines a network essential for Zika virus replication
Authors: Leier Hans C. , Weinstein Jules B. , Kyle Jennifer E. , Lee Joon-Yong , Bramer Lisa M. , Stratton Kelly G. , Kempthorne Douglas , Navratil Aaron R. , Tafesse Endala G. , Hornemann Thorsten , Messer William B. , Dennis Edward A. , Metz Thomas O. , Barklis Eric , Tafesse Fikadu G. 
Published: January 2020

AbstractZika virus (ZIKV), an arbovirus of global concern, remodels intracellular membranes to form replication sites. How ZIKV dysregulates lipid networks to allow this, and consequences for disease, is poorly understood. Here, we performed comprehensive lipidomics to create a lipid network map during ZIKV infection. We found that ZIKV significantly alters host lipid composition, with the most striking changes seen within subclasses of sphingolipids. Ectopic expression of ZIKV NS4B protein resulted in similar changes, demonstrating a role for NS4B in modulating sphingolipid pathways. Disruption of sphingolipid biosynthesis in various cell types, including human neural progenitor cells, blocked ZIKV infection. Additionally, the sphingolipid ceramide redistributes to ZIKV replication sites and increasing ceramide levels by multiple pathways sensitizes cells to ZIKV infection. Thus, we identify a sphingolipid metabolic network with a critical role in ZIKV replication and show that ceramide flux is a key mediator of ZIKV infection.
Effect of irradiation on the survival and susceptibility of femaleAnopheles arabiensisto natural isolates ofPlasmodium falciparum
Authors: Guissou Edwige , Poda Serge , Hien François de Sales Domombabele , Yerbanga Serge Rakiswende , Da Dari Frédéric Yannick , Cohuet Anna , Fournet Florence , Roux Olivier , Maiga Hamidou , Diabaté Abdoulaye , Gilles Jeremie , Bouyer Jérémy , Ouédraogo Anicet G. , Rayaissé Jean-Baptiste , Lefèvre Thierry , Dabiré Kounbobr Roch 
Published: January 2020

AbstractBackgroundThe sterile insect technique (SIT) is a vector control strategy relying on the mass release of sterile males into wild vector populations. Current sex separation techniques are not fully efficient and could lead to the release of a small proportion of females. It is therefore important to evaluate the effect of irradiation on the ability of released females to transmit pathogens. This study aimed to assess the effect of irradiation on the survival and competence ofAnopheles arabiensisfemales forPlasmodium falciparum inlaboratory conditions.MethodsPupae were irradiated at 95 Gy, a sterilizing dose of gamma-rays from Caesium-137 source, and emerging adult females were challenged with one of 14 natural isolates ofP. falciparum. Seven days post-bloodmeal (dpbm), irradiated and unirradiated-control females were dissected to assess the presence of oocysts. On 14 dpbm, oocyst rupture in mosquito midguts and sporozoite dissemination in head/thoraces were also examined. Two assays were performed to gauge the effect of irradiation onAn. arabiensissurvival. First, the survivorship of irradiated and unirradiated-control mosquitoes exposed to each parasite isolate was monitored. Second, how parasite infection and irradiation interact to influence mosquito lifespan was also assessed by including a group of uninfected unirradiated mosquitoes.ResultsOverall, irradiation reduced the proportion of infected mosquitoes but this effect was inconsistent among parasite isolates. Second, there was no significant effect of irradiation on the number of developing oocysts. Third, the proportion of ruptured oocysts at 14 dpbm was higher in irradiated-than in control-unirradiated females, suggesting that irradiation might speed up parasite development. Fourth, irradiation had varying effects on female survival with either a negative effect (assay 1) or no effect (assay 2).ConclusionCombining these effects into an epidemiological model could help quantifying the net effect of irradiation on malaria transmission in this system. Together, our data indicate that irradiated femaleAn. arabiensiscould contribute to malaria transmission, and highlight the need for perfect sexing tools which would prevent the release of females as part of SIT programs.
Molecular and cellular heterogeneity of gastric cancer explained by methylation-driven key regulators
Authors: Yoo Seungyeul , Chen Quan , Wang Li , Wang Wenhui , Chakravarthy Ankur , Busuttil Rita , Boussioutas Alex , Liu Dan , She Junjun , Fenton Tim R. , Zhang Jiangwen , Fan Xiaodan , Leung Suet-Yi , Zhu Jun 
Published: January 2020

AbstractGastric cancer (GC) is a heterogeneous disease of diverse genetic, genomic, and epigenetic alterations. Tumor microenvironment (TME) also contributes to the heterogeneity of GC. To investigate GC heterogeneity, we developed an Integrative Sequential Causality Test (ISCT) to identify key regulators of GC by integrating DNA methylation, copy number variation, and transcriptomic data. Applying ISCT to three GC cohorts containing methylation, CNV and transcriptomic data, 11 common methylation-driven key regulators (ADHFE1, CDO1, CRYAB, FSTL1, GPT, PKP3, PTPRCAP, RAB25, RHOH, SFN, and SORD) were identified. Based on these 11 genes, gastric tumors were clustered into 3 clusters which were associated with known molecular subtypes, Lauren classification, tumor stage, and patient survival, suggesting significance of the methylation-driven key regulators in molecular and histological heterogeneity of GC. We further showed that chemotherapy benefit was different in the 3 GC clusters and varied depending on the tumor stage. Both immune/stromal proportions in TME and tumor cell genomic variations contributed to expression variations of the 11 methylation-driven key regulators and to the GC heterogeneity.
Tailored polymeric, photovoltaic, and near-infrared-responsive neuroprosthesis
Authors: Leccardi Marta Jole Ildelfonsa Airaghi , Chenais Naïg Aurelia Ludmilla , Ferlauto Laura , Kawecki Maciej , Geneviève Zollinger Elodie , Ghezzi Diego 
Published: January 2020

AbstractOrganic materials, such as conjugated polymers, are attractive building blocks for bioelectronic interfaces. In particular, organic semiconductors showed excellent performances in light-mediated excitation and silencing of neuronal cells and tissues. However, the main challenges of these organic photovoltaic interfaces compared to inorganic prostheses are the limited stability of conjugated polymers in the aqueous environment and the exploitation of materials only responsive in the visible spectrum. In this report, we show a new photovoltaic organic interface tailored for neuronal stimulation in the near-infrared spectrum. Also, we adjusted the organic materials by chemical modification in order to improve the stability in aqueous environment and to modulate the photoelectrical stimulation efficiency. As proof of principle, we tested this interface for retinal stimulation. Our results provide an efficient, reliable, and stable implant applicable for neural stimulation.
Xenobiotic compounds modulate cytotoxicity of Aβ amyloids and interact with neuroprotective chaperone L-PGDS
Authors: Yi Kimberly Low Jia , Phillips Margaret , Pervushin Konstantin 
Published: January 2020

AbstractA positive association of the exposure to different classes of xenobiotics such as commonly prescribed drugs and polycyclic aromatic hydrocarbons (PAH) typically those found in air pollution-related particulate matter with Alzheimer’s disease (AD) may point to direct physical interaction of those compounds with the amyloid formation and clearance processes. In this study, for the first time, we provide evidence of such interactions for three representative compounds from prescription drugs and air pollution, e.g. anticholinergic drugs Chlorpheniramine, a common antihistamine, and Trazodone, an antidepressant as well as 9,10-PQ, a common PAH anthraquinone abundantly present in diesel exhaust and associated with AD. We demonstrate that these three compounds bind to the lipophilic compound carrier and neuroprotective amyloid beta (Aβ) chaperone lipocalin-type prostaglandin D synthase (L-PGDS) with high affinity attenuating its neuroprotective chaperone function with Chlorpheniramine exhibiting markedly stronger inhibitory effects. We also show that these compounds directly interact with Aβ(1-40) increasing the fibril’s yield with altered fibril morphology and increased the cytotoxicity of the resulting fibrils. We propose that exposure to some xenobiotics in the peripheral tissues such as gut and lungs might result in the accumulation of these compounds in the brain facilitated by the carrier function of L-PGDS. This might lead to attenuation of its neuroprotective function and direct modification of Aβ amyloid morphology and cytotoxicity. This hypothesis might provide a mechanistic link between exposure to xenobiotic compounds and the increased risk of Alzheimer’s disease.Graphical Abstract
Highly Efficient Antibiofilm and Antifungal Activity of Green Propolis againstCandidaspecies in dentistry material
Authors: Bezerra Carolina Rabelo Falcão , Assunção Borges Katia Regina , Alves Rita de Nazaré Silva , Teles Amanda Mara , Pimentel Rodrigues Igor Vinicius , da Silva Marcos Antonio Custódio Neto , Nascimento Maria do Desterro Soares Brandão , Bezerra Geusa Felipa de Barros 
Published: January 2020

AbstractBackgroundThis study evaluated the influence of green propolis’ extract on the adhesion and biofilm formation ofCandidaspecies on dentistry material.MethodsPhytochemical analysis of green propolis’ extract was performed by High Performance Liquid Chromatography. Adhesion was quantified in a Neubauer chamber, counting the number of yeast cells adhered to the fragments; Biofilm formation was determined by counting the number of colony forming units (CFU). The intensity of biofilm formation adhesion was classified as negative, weak, moderate, strong and very strong. Fifteen compounds were identified in green propolis extract, mainly flavonoids.ResultsAll strains were able to adhere and form biofilm on the surface of the orthodontic materials studied. In steel and resin, the adhesion intensity of the yeast cells was weak at all incubation times, except forC. parapsilosisandC. tropicaliswhich at 12hs showed moderate intensity. Regarding biofilm formation (24 and 48 hours), it was observed in the steel thatC. albicanshad moderate intensity at 24 and 48 hours;C. parapsilosisat 24 and 48 hours had very strong intensity;C. tropicalisat 24 hours had strong intensity and at 48 hours very strong. While in the resin, all species at 24 and 48 hours had strong intensity, except forC. tropicaliswhich at 48 hours had very strong intensity. Green propolis extract showed antifungal activity and was able to inhibit both adhesion and biofilm formation at 2.5 μg/mL.ConclusionsThis study reinforces the idea that green propolis has antifungal activity and interferes with virulence factors ofCandidaspecies.
Dietary and Biological Assessment of Omega-3 Status of Collegiate Athletes: A Cross-Sectional Analysis
Authors: Ritz Peter P. , Rogers Mark B. , Zabinsky Jennifer S. , Hedrick Valisa E. , Rockwell John A. , Rimer Ernest , Kostelnik Samantha , Hulver Matthew W. , Rockwell Michelle S. 
Published: January 2020

AbstractOmega-3 fatty acids (ω-3 FA) play a number of important functions in health and human performance. While previous research has suggested that low ω-3 FA status is prevalent in the general population, little information about athletes’ ω-3 FA status is available. The purpose of this study was to assess the omega-3 fatty acid (ω-3 FA) status of collegiate athletes. Dietary ω-3 FA intake was evaluated in athletes from nine NCAA Division I institutions (n=1,528, 51% male, 19.9 ± 1.4 years of age, 29 sports represented) via food frequency questionnaire. Omega-3 Index (O3i) was assessed using a dried blood spot sample in a subset of these athletes (n=228). Only 6% (n = 93) of athletes achieved the Academy of Nutrition & Dietetics’ recommendation to consume 500 mg of the ω-3 FA’s docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) per day. Use of ω-3 FA supplements was reported by 15% (n = 229) of participants. O3i was 4.33 ± 0.81%, with zero participants meeting the O3i benchmark of 8% associated with the lowest risk of cardiovascular disease. Every additional weekly serving of fish or seafood was associated with an absolute O3i increase of 0.27%. Overall, sub-optimal ω-3 FA status was observed among a large, geographically diverse group of male and female collegiate athletes. These findings may inform interventions aimed at improving ω-3 FA status of collegiate athletes. Further research on athlete-specific ω-3 FA requirements is needed.
Effects of C-peptide replacement therapy on bone microarchitecture parameters in streptozotocin-diabetic rats
Authors: Maurotti Samantha , Russo Cristina , Musolino Vincenzo , Nucera Saverio , Gliozzi Micaela , Scicchitano Miriam , Bosco Francesca , Morittu Valeria Maria , Ragusa Monica , Mazza Elisa , Gazzaruso Carmine , Britti Domenico , Valenti Maria Teresa , Deiana Michela , Romeo Stefano , Giannini Sandro , Carbonare Luca Dalle , Mollace Vincenzo , Pujia Arturo , Montalcini Tiziana 
Published: January 2020

AbstractPathological pathways involved in the development of diabetic complications are still unclear. Several studies suggested a pathogenic role of C-peptide deficiency in vascular and neuropathic complications. However, to date, the role of C-peptide on diabetes-related bone loss has not been investigated. The objective of this study was to test the effects of a 6-week regimen of rat C-peptide infusion on bone by combining micro-CT imaging with histological testing.Twenty-three, four-month-old male Wistar rats were randomly divided into three groups: Normal control group; Sham diabetic control group; Diabetic plus C-peptide group. Diabetes was induced by injection of streptozotocin. Rat C-peptide was delivered via subcutaneously osmopumps. We assessed several trabecular microarchitectural parameters and cellular and matrix proteins in bone tissue sections.At the end of the study, both the normal control and diabetic plus C-peptide groups had a higher tibia weight than the diabetic control group (p= 0.05 andp= 0.02, respectively). C-peptide levels significantly and positively correlated with the trabecular thickness (r= 0.45, p=0.08) and negatively with structure model index (r= −0.40, p=0.09). Furthermore, it positively correlated with one of the histological assessments (i.e. PLIN1 score; p=0.02). Micro-CT evaluation showed significant inter-group differences in trabecular thickness (p=0.02), trabecular space (p= 0.05) and cross-sectional thickness (p=0.05). Diabetic plus C-peptide group showed a higher trabecular thickness (p<0.001), cross-sectional thickness (p=0.03) and a lower trabecular space (p=0.05) than the normal control group. Both the normal control and diabetic plus C-peptide groups had more Runx-2 and PLIN1 positive cells in comparison to the diabetic control group (p = 0.045 and p = 0.034).For the first time we demonstrated that the diabetic rats receiving rat C-peptide had higher quality of trabecular bone, than diabetic rats not receiving it. C-peptide could have a role in the prevention of diabetes-related bone loss.
Systematically gap-filling the genome-scale metabolic model of CHO cells
Authors: Fouladiha Hamideh , Marashi Sayed-Amir , Li Shangzhong , Li Zerong , Masson Helen O. , Vaziri Behrouz , Lewis Nathan E. 
Published: January 2020

AbstractObjectiveChinese hamster ovary (CHO) cells are the leading cell factories for producing recombinant proteins in the biopharmaceutical industry. In this regard, constraint-based metabolic models are useful platforms to perform computational analysis of cell metabolism. These models need to be regularly updated in order to include the latest biochemical data of the cells, and to increase their predictive power. Here, we provide an update toiCHO1766, the metabolic model of CHO cells.ResultsWe expanded the existing model of Chinese hamster metabolism with the help of four gap-filling approaches, leading to the addition of 773 new reactions and 335 new genes. We incorporated these into an updated genome-scale metabolic network model of CHO cells, namediCHO2101. In this updated model, the number of reactions and pathways capable of carrying flux is substantially increased.ConclusionsThe present CHO model is an important step towards more complete metabolic models of CHO cells.
Abnormal center of mass control during balance: a new biomarker of falls in people with Parkinson’s disease
Authors: McKay J. Lucas , Lang Kimberly C. , Bong Sistania M. , Hackney Madeleine. E. , Factor Stewart A. , Ting Lena H. 
Published: January 2020

AbstractAlthough Parkinson disease (PD) causes profound balance impairments, we know very little about how PD impacts the sensorimotor networks we rely on for automatically maintaining balance control. In young healthy people and animals, muscles are activated in a precise temporal and spatial organization when the center of body mass (CoM) is unexpectedly moved that is largely automatic and determined by feedback of CoM motion. Here, we show that PD alters the sensitivity of the sensorimotor feedback transformation. Importantly, sensorimotor feedback transformations for balance in PD remain temporally precise, but become spatially diffuse by recruiting additional muscle activity in antagonist muscles during balance responses. The abnormal antagonist muscle activity remains precisely time-locked to sensorimotor feedback signals encoding undesirable motion of the body in space. Further, among people with PD, the sensitivity of abnormal antagonist muscle activity to CoM motion varies directly with the number of recent falls. Our work shows that in people with PD, sensorimotor feedback transformations for balance are intact but disinhibited in antagonist muscles, likely contributing to balance deficits and falls.
Effects of pharmacological modulators of α-synuclein and tau aggregation and internalization
Authors: Dominguez-Meijide Antonio , Vasili Eftychia , König Annekatrin , Cima-Omori Maria-Sol , Leonov Andrei , Ryazanov Sergey , Zweckstetter Markus , Griesinger Christian , Outeiro Tiago F. 
Published: January 2020

AbstractParkinson’s disease (PD) and Alzheimer’s disease (AD) are common neurodegenerative disorders of the elderly and, therefore, affect a growing number of patients worldwide. Both diseases share, as a common hallmark, the accumulation of characteristic protein aggregates, known as Lewy bodies (LB) in PD, and neurofibrillary tangles in AD. LBs are primarily composed of misfolded α-synuclein (aSyn), and neurofibrillary tangles are primarily composed of tau protein. Importantly, upon pathological evaluation, most AD and PD/Lewy body dementia cases exhibit mixed pathology, with the co-occurrence of both Lewy bodies and neurofibrillary tangles, among other protein inclusions. Recent studies suggest that both aSyn and tau pathology can spread and propagate through neuronal connections. Therefore, it is important to investigate the mechanisms underlying aggregation and propagation of these proteins for the development of novel therapeutic strategies. Here, we assessed the effects of different pharmacological interventions on the aggregation and internalization of tau and aSyn. We found that anle138b and epigallocatechin gallate decrease aSyn aggregation, that fulvic acid attenuates aggregation of the repeat domain of tau, and that dynasore reduces tau internalization. Establishing the effects of small molecules with different chemical properties on the aggregation and spreading of aSyn and tau will be important for the development of future therapeutic interventions.
Between-subject prediction reveals a shared representational geometry in the rodent hippocampus
Authors: Chen Hung-Tu , Manning Jeremy R. , van der Meer Matthijs A. A. 
Published: January 2020

SummaryThe rodent hippocampus constructs statistically independent representations across environments (“global remapping”) and assigns individual neuron firing fields to locations within an environment in an apparently random fashion, processes thought to contribute to the role of the hippocampus in episodic memory. This random mapping implies that it should be challenging to predict hippocampal encoding of a given experience in one subject based on the encoding of that same experience in another subject. Contrary to this prediction, we find that by constructing a common representational space across rats in which neural activity is aligned using geometric operations (rotation, reflection, and translation; “hyperalignment”), we can predict data of “right” trials (R) on a T-maze in a target rat based on 1) the “left” trials (L) of the target rat, and 2) the relationship between L and R trials from a different source rat. These cross-subject predictions relied on ensemble activity patterns including both firing rate and field location, and outperformed a number of control mappings, such as those based on permuted data that broke the relationship between L and R activity for individual neurons, and those based solely on within-subject prediction. This work constitutes proof-of-principle for successful cross-subject prediction of ensemble activity patterns in the hippocampus, and provides new insights in understanding how different experiences are structured, enabling further work identifying what aspects of experience encoding are shared vs. unique to an individual.