bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of IL-12, IL12R polymorphisms and serum IL-12 levels with high-risk human papillomavirus susceptibility in rural women from Luohe, Henan, China
Authors: Song Jiayu , Zhang Qingwei , Wang Rong , Sun Mingzhen , Jin Shaoju 
Published: September 2019

Abstract

Background:
Interleukin 12 (IL-12) and interleukin 12 receptor (IL12R), key inflammatory cytokines in the immune system, participate in bridging the innate immunity and adaptive immunity. No previous work has reported the role of IL-12 and IL12R in high-risk human papillomavirus (hrHPV) susceptibility. The purpose of this study was to investigate the association of IL-12, IL12R polymorphisms, and serum IL-12 levels with hrHPV susceptibility in rural women from Luohe, Henan, China.

Methods:
Two hundred sixty cases with hrHPV infection and 260 healthy controls were selected. Enzyme-linked immunosorbent assays were used to detect the serum IL-12 levels, and the polymorphisms of IL12B rs3212227, IL12RB1 rs393548, and IL12RB1 rs436857 were determined using DNA sequencing.

Results:
The serum IL-12 levels were significantly lower in cases with hrHPV infection compared with those in healthy controls (P < .01).There was no significant difference in IL12 rs3212227, IL12RB1rs436857, and IL12RB1rs393548 genotype and allele frequencies between cases and controls (P > .05). Furthermore, with respect to the IL12 rs3212227 polymorphism with serum IL-12 levels, although serum IL-12 levels were lower in cases than in controls, we did not find any differences between serum IL-12 levels and genotypes in cases(P > .05).

Conclusions:
Our data demonstrates that low serum IL-12 levels may be associated with hrHPV susceptibility but are not associated with IL-12 gene polymorphisms; furthermore, IL-12 and IL12R gene polymorphisms may not contribute susceptibility to hrHPV in rural women from Luohe, Henan, China.
Arterial wall structural changes in noncirrhotic chronic hepatitis C patients
Authors: Sliem Hamdy A. , Salem Ahmed S. , Hussien Walid M. , El Sayed Hind R.A. 
Published: September 2019

Background
Hepatitis C virus (HCV) infection is a major overall health predicament. Patients with HCV infection may progress to hepatic and extrahepatic complications. There are emerging groups of data on accelerated vascular changes triggering subclinical atherosclerosis. Nevertheless, whether these changes are associated with an increased risk of morbidity and mortality is unclear.

Aim
To determine subclinical arterial wall structural changes in noncirrhotic chronic hepatitis C patients and the impact of possible cofactors.

Patients and methods
Forty-two patients with noncirrhotic chronic HCV and 42 healthy controls matched in terms of age and sex were subjected to clinical, biochemical, and imaging measures for the evaluation of arterial wall changes (aortic elasticity/stiffness and carotid intima-media thickness). Elasticity was evaluated by measuring the aortic diameter and pulse wave velocity.

Results
Nonsignificant greater mean aortic diameter was found among the cases than the control group (P = 0.67). The mean carotid intima-media thickness was quite similar in both groups (P = 0.12). The mean pulse wave velocity measures were twice those in the cases than the control group, indicating greater tendencies toward arterial stiffness among patients with HCV (P < 0.001). There was no significant relationship between any of the laboratory investigations (lipid and HCV-RNA values) and any of the vascular imaging investigations.

Conclusion
Aortic diameter and aortic stiffness are increased among chronic hepatitis C patients than healthy controls; however, there is no significant difference in carotid intima thickness.
Comparisons of Depression, Sexual Function, and Quality of Life Between Women With Gynecological Cancers and Race-Matched Healthy Controls
Authors: Bai Jinbing , Belcher Sarah M. , Meador Rebecca , Daniel Gaea , Shelton Joseph , Patel Pretesh , Dolan Mary , Arluck Jessica , Khanna Namita , Horowitz Ira , Liu Tian , Watkins Bruner Deborah 
Published: September 2019

Background
Although higher incidence and mortality of gynecological cancer (GynCa) are documented in black compared with white women, few studies have documented quality of life (QOL) or healthy control comparisons.

Objective
This study compared depression, sexual function, and QOL between patients with GynCa and race-matched healthy controls.

Methods
Patients with GynCa and healthy controls completed the Patient Health Questionnaire-9, Female Sexual Function Index, and Functional Assessment of Cancer Therapy–General measures at baseline; GynCa patients were assessed again at 6 months post–radiation therapy (RT).

Results
Analyses included 84 participants (51% white, 49% black), including 28 GynCa patients and 56 controls with similar marital status. Compared with healthy controls, patients were younger, had a higher body mass index, and had more depression (P = .01); 82% of the patients and 71% of the healthy controls met criteria for sexual dysfunction at baseline (P = .29). Patients pre-RT had greater sexual dysfunction and lower QOL (P = .001) than controls did; patients at 6-month post-RT showed improved sexual function scores compared with pre-RT, with similar results to controls. White GynCa patients reported less sexual desire (P = .02), more pain (P = .05), and lower total Female Sexual Function Index scores (P = .01) than did black GynCa patients. Both black and white GynCa patients reported lower total QOL than their race-matched controls did (P = .07 and P = .002).

Conclusions
Women with GynCa reported more depression and lower QOL than did healthy controls pre-RT. Among GynCa patients, white women had more sexual dysfunction than black women did.

Implications for Practice
The differences in sexual dysfunction between white and black women with GynCa suggest developing guidelines directing routine sexual assessment and rehabilitation in women treated for GynCa.
Point mass dynamics on spherical hypersurfaces
Authors: Dritschel David G. 
Published: September 2019

The equations of motion are derived for a system of point masses on the (hyper)surface

S

n

of a sphere embedded in

R

n
+
1

for any dimension
n
> 1. Owing to the symmetry of the surface, the equations take a particularly simple form when using the Cartesian coordinates of

R

n
+
1

. The constraint that the distance of the
j
th mass ∥

r

j

∥ from the origin remains constant (i.e. each mass remains on the surface) is automatically satisfied by the equations of motion. Moreover, the equations are a Hamiltonian system with a conserved energy as well as a host of conserved angular momenta. Several examples are illustrated in dimensions
n
= 2 (the sphere) and
n
= 3 (the glome).

This article is part of the theme issue ‘Topological and geometrical aspects of mass and vortex dynamics’.
Gels for Live Analysis of Compartmentalized Environments (GLAnCE): A Tissue Model to Probe Tumour Phenotypes at Tumour-Stroma Interfaces
Authors: D’Arcangelo Elisa , Wu Nila C. , Chen Tianhao , Shahaj Andi , Cadavid Jose L. , Huang Linwen , Ailles Laurie , McGuigan Alison P. 
Published: September 2019

AbstractThe interface between a tumour and the adjacent stroma is a site of great importance for tumour development. At this site, carcinoma cells are highly proliferative, undergo invasive phenotypic changes, and directly interact with surrounding stromal cells, such as cancer-associated fibroblasts (CAFs) which further exert pro-tumorigenic effects. Here we describe the development of GLAnCE (Gels for Live Analysis of Compartmentalized Environments), an easy-to-use hydrogel-culture platform for investigating CAF-tumour cell interaction dynamics in vitro at a tumour-stroma interface. GLAnCE enables observation of CAF-mediated enhancement of both tumour cell proliferation and invasion at the tumour-stroma interface in real time, as well as stratification between phenotypes at the interface versus in the bulk tumour tissue compartment. We found that CAF presence resulted in the establishment of an invasion-permissive, interface-specific matrix environment, that leads to carcinoma cell movement outwards from the tumour edge and tumour cell invasion. Furthermore, the spatial stratification capability of GLAnCE was leveraged to discern differences between tumour cell epithelial-to-mesenchymal (EMT) transition genes induced by paracrine signaling from CAFs versus genes induced by interface-specific, CAF-mediated microenvironment. GLAnCE combines high usability and tissue complexity, to provide a powerful in vitro platform to probe mechanisms of tumour cell movement specific to the microenvironment at the tumour-stroma interface.
ATF4 regulates neuronal death in models of Parkinson’s Disease
Authors: Demmings Matthew D. , Petroff Gillian N. , Tarnowski-Garner Heather E. , Cregan Sean P. 
Published: September 2019

AbstractParkinson’s Disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra resulting in severe motor impairments. However, the mechanisms underlying this neuronal loss remain largely unknown. Activating Transcription Factor 4 (ATF4), a key mediator of the Integrated Stress Response (ISR), is a transcription factor that during prolonged activation can induce the expression of pro-apoptotic target genes. Oxidative stress and ER stress have been implicated in PD and these factors are known to activate the ISR. In this study, we have determined, that both PD neurotoxins (MPP+ and 6-OHDA) and α-synuclein aggregation induced by pre-formed human alpha-synuclein fibrils (PFFs) cause sustained upregulation of ATF4 expression in mouse primary cortical and mesencephalic neurons. Furthermore, we demonstrate that PD neurotoxins induce the expression of the pro-apoptotic factors Chop, Trb3 and Puma in an ATF4-dependent manner. Importantly, using neurons derived from ATF4 +/+ and ATF4 -/- mice, we demonstrate that ATF4 promotes neuronal apoptosis and dopaminergic cell loss in cellular models of PD. Finally, we demonstrate that the eIF2α kinase inhibitor C16 suppresses MPP+ and 6-OHDA induced ATF4 activation and protects against PD neurotoxin induced neuronal death. Taken together these results indicate that ATF4 is a key regulator of dopaminergic cell death induced by PD neurotoxins and pathogenic α-synuclein aggregates and highlight the ISR as a potential therapeutic target in PD.
Increases in structural shortest path lengths provide information about the distal neurophysiological consequences of focal brain lesions
Authors: Griffis Joseph C. , Metcalf Nicholas V. , Corbetta Maurizio , Shulman Gordon L. 
Published: September 2019

AbstractFocal brain lesions disrupt resting-state functional connectivity, but the underlying structural mechanisms are unclear. Here, we examined the direct and indirect effects of structural disconnections on resting-state functional connectivity in a large sample of sub-acute stroke patients with heterogeneous brain lesions. We defined direct disconnections as the loss of direct structural connections between two regions, and indirect disconnections as increases in the shortest structural path length between two regions that lack direct structural connections. On average, nearly 20% of all region pairs suffered either a direct or indirect disconnection by the lesions in our sample. Importantly, both directly and indirectly disconnected region pairs showed more severe functional connectivity disruptions than region pairs with spared direct and indirect connections, respectively, although functional connectivity disruptions tended to be most severe between region pairs that sustained direct structural disconnections. Together, these results emphasize the widespread impacts of focal brain lesions on the structural connectome, and show that these impacts are reflected by disruptions of the functional connectome. Further, they indicate that in addition to direct structural disconnections, lesion-induced increases in the structural shortest path lengths between indirectly structurally connected region pairs provide information about the remote functional disruptions caused by focal brain lesions.
Cerebral perfusion and metabolism coupling during a critical time window provides rapid assessment of cardiac arrest severity and prognosis in a preclinical model
Authors: Wilson R. H. , Crouzet C. , Torabzadeh M. , Bazrafkan A. , Maki N. , Alcocer J. , Tromberg B. J. , Choi B. , Akbari Y. 
Published: September 2019

AbstractImproved quantitative understanding of the dynamic relationship among cerebral blood flow, oxygen consumption, and electrical activity is important to clinicians treating acute brain injury. Such knowledge would elucidate the neurovascular response to ischemia, helping to potentially guide treatment. Using a multimodal optical imaging platform and a clinically-relevant rat model of cardiac arrest (CA) and cardiopulmonary resuscitation (CPR), we continuously measured cerebral blood flow (CBF), brain tissue oxygenation (StO2), cerebral metabolic rate of oxygen (CMRO2), and cerebral electrical activity (electrocorticography; ECoG). Multiple phases of cerebral hemodynamic recovery, with different degrees of mismatch between CBF and CMRO2, were observed following CPR. At 1 min post-resuscitation, we observed that the ratio CBF/CMRO2 is indicative of CA duration/severity and prognostic (with 87% accuracy) of short-term neurological recovery measured by the re-initiation of ECoG activity. These measurements provide the earliest known metrics for assessment of CA severity and prognosis post-CPR. Interestingly, the accuracy of this information is lost beyond 2-3 minutes post-CPR, highlighting a critical, easily overlooked, period immediately post-CPR. These metrics do not require pre-resuscitation data, underscoring translational potential in emergency-response settings when pre-CA information is unavailable. These metrics encourage validation in human studies, potentially offering real-time feedback during CA/CPR to optimize neurological outcome.
Antigenicity and Potential Use of A Novel Brucella Multiepitope Recombinant Protein in the Diagnosis of Brucellosis
Authors: Yin Dehui , Bai Qiongqiong , Li Li , Xu Lichun , Xu Kun , Li Juan 
Published: September 2019

AbstractCurrently, brucellosis is a reemerged zoonotic infectious disease with an increased incidence in recent years. A simple, rapid and sensitive method for diagnosing brucellosis has important significance for early diagnosis and early treatment, which can help to reduce medical burden and economic loss. Previously, a multiple epitope recombinant protein was constructed based on linear B-cell epitope prediction tools. In this study, the recombinant protein was used as an antigen to study the immune response produced by immunized mice, and goat serum was used to verify its diagnostic accuracy.The production of antibodies was successfully induced in the vaccinated mice. Through analyzing the serum antibody subtypes, the primary antibody was identified as IgG. Flow cytometric analysis revealed that the percentage of CD4+, CD8+ and the CD4+/CD8+ ratios were increased by T cell subsets in mouse splenocytes, indicating that the recombinant protein induced a strong immune response in mice and that it had strong immunoreactivity. Using indirect ELISA, the recombinant protein correctly diagnosed positive and negative brucellosis samples. Compared with the whole bacterial antigen, the recombinant protein had a weaker sensitivity but a stronger specificity.In this study, animal experiments showed that the recombinant protein had good antigenicity, and indirect ELISA indicates that it can be used as an antigen to diagnose brucellosis. Therefore, the recombinant protein is a potential candidate antigen for brucellosis vaccine development and serological diagnosis.
HaploHide: A Data Hiding Framework for Privacy Enhanced Sharing of Personal Genetic Data
Authors: Harmanci Arif , Jiang Xiaoqian , Zhi Degui 
Published: September 2019

AbstractPersonal genetic data is becoming a digital commodity as millions of individuals have direct access to and control of their genetic information. This information must be protected as it can be used for reidentification and potential discrimination of individuals and relatives. While there is a great incentive to share and use genetic information, there are limited number of practical approaches for protecting it when individuals would like to make use of their genomes in clinical and recreational settings. To enable privacy-enhanced usage of genomic data by individuals, we propose a crowd-blending-based framework where portions of the individual’s haplotype is “hidden” within a large sample of other haplotypes. The hiding framework is motivated by the existence of large-scale population panels that we utilize for generation of the crowd of haplotypes in which the individual’s haplotype is hidden. We demonstrate the usage of hiding in two different scenarios: Sharing of variant alleles on genes and sharing of GWAS variant alleles. We evaluate hiding framework by testing reidentification of hidden individuals using numerous measures of individual reidentification. In these settings, we discuss how effective hiding can be accomplished when the adversary does not have access to auxiliary identifying information. Compared to the existing approaches for protecting privacy, which require substantial changes in the computational infrastructure, e.g., homomorphic encryption, hiding-based framework does not incur any changes to the infrastructure. However, the processing must be performed for every sample in the crowd and therefore data processing cost will increase as the crowd size increases.
Mechanism of gating and partial agonist action in the glycine receptor
Authors: Yu Jie , Zhu Hongtao , Lape Remigijus , Greiner Timo , Shahoei Rezvan , Wang Yuhang , Du Juan , Lü Wei , Tajkhorshid Emad , Sivilotti Lucia , Gouaux Eric 
Published: September 2019

SummaryThe glycine receptor is a pentameric, neurotransmitter-activated ion channel that transitions between closed/resting, open and desensitized states. Glycine, a full agonist, produces an open channel probability (Po) of ∼1.0 while partial agonists, such as taurine and γ-amino butyric acid (GABA) yield submaximal Po values. Despite extensive studies of pentameric Cys-loop receptors, there is little knowledge of the molecular mechanisms underpinning partial agonist action and how the receptor transitions from the closed to open and to desensitized conformations. Here we use electrophysiology and molecular dynamics (MD) simulations, together with a large ensemble of single particle cryo-EM reconstructions, to show how agonists populate agonist-bound yet closed channel states, thus explaining their lesser efficacy, yet also populate agonist-bound open and desensitized states. Measurements within the neurotransmitter binding pocket, as a function of bound agonist, provide a metric to correlate the extent of agonist-induced conformational changes to open channel probability across the Cys-loop receptor family.
Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project
Authors: Fan Guanngyi , Song Yue , Huang Xiaoyun , Yang Liandong , Zhang Suyu , Zhang Mengqi , Yang Xianwei , Chang Yue , Zhang He , Li Yongxin , Liu Shanshan , Yu Lili , Seim Inge , Feng Chenguang , Wang Wen , Wang Kun , Wang Jing , Xu Xun , Yang Huanming , Chen Nansheng , Liu Xin , He Shunping 
Published: September 2019

AbstractWith more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Here, we announce the Fish10K project, an international collaborative project or initiative? aiming to sequence 10,000 representative fish genomes under a systematic context within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, and sequencing and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 93 species chosen for technology development.
Natural representation of composite data with replicated autoencoders
Authors: Negri Matteo , Bergamini Davide , Baldassi Carlo , Zecchina Riccardo , Feinauer Christoph 
Published: September 2019

ABSTRACTGenerative processes in biology and other fields often produce data that can be regarded as resulting from a composition of basic features. Here we present an unsupervised method based on autoencoders for inferring these basic features of data. The main novelty in our approach is that the training is based on the optimization of the ‘local entropy’ rather than the standard loss, resulting in a more robust inference, and enhancing the performance on this type of data considerably. Algorithmically, this is realized by training an interacting system of replicated autoencoders. We apply this method to synthetic and protein sequence data, and show that it is able to infer a hidden representation that correlates well with the underlying generative process, without requiring any prior knowledge.AUTHOR SUMMARYExtracting compositional features from noisy data and identifying the corresponding generative models is a fundamental challenge across sciences. The composition of elementary features can have highly non-linear effects which makes them very hard to identify from experimental data.In biology, for instance, one challenge is to identify the key steps or components of molecular and cellular processes. Representative examples are the modeling of protein sequences as the composition of patterns influenced by phylogeny or the identification of gene clusters in which the presence of specific genes depends on the evolutionary history of the cell.Here we present an unsupervised machine learning technique for the analysis of compositional data which is based on entropic neural autoencoders. Our approach aims at finding deep autoencoders that are highly invariant with respect to perturbations in the inputs and in the parameters. The procedure is efficient to implement and we have validated it both on synthetic and protein sequence data, where it can be shown that the latent variables of the autoencoders are non trivially correlated with the true underlying generative processes. Our results suggests that the local entropy approach represents a general valuable tool for the extraction of compositional features in hard unsupervised learning problems.