bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nadir CD4 Is Negatively Associated With Antinuclear Antibody Detection in HCV/HIV-Coinfected Patients
Authors: Poizot-Martin Isabelle , Rosenthal Eric , Gilbert Camille , Cano Carla E. , Simon Anne , Lascoux-Combe Caroline , Alric Laurent , Gervais Anne , Neau Didier , Esterle Laure , Salmon Dominique , Sogni Philippe , Wittkop Linda ,   for the ANRS CO13 HEPAVIH Study Group
Published: December 2018

Background:
Hepatitis C virus (HCV) and HIV infections are associated with higher risk of autoimmune diseases and T-cell dysfunction.

Setting:
We evaluate prevalence and factors associated with the presence of autoimmune antinuclear (ANA), anti–smooth muscle actin (aSMA), and anti–liver kidney microsome (aLKM1) antibodies (Ab) in HCV/HIV-coinfected patients during the post–combined antiretroviral therapy era.

Methods:
A cross-sectional observational study nested in the ANRS CO13 HEPAVIH cohort (NCT number: NCT03324633). We selected patients with both ANA testing and T-cell immunophenotyping determination during the cohort follow-up and collected aLKM1 and aSMA data when available. Logistic regression models were built to determine factors associated with the presence of auto-Ab.

Results:
Two hundred twenty-three HCV/HIV-coinfected patients fulfilled selection criteria. Prevalence of ANA and aSMA was 43.5% and 23.2%, respectively, and both were detected in 13.3% of patients. Isolated aSMA were detected in 9.9% and aLKM1 in 2 patients. In multivariable analysis, only a low nadir CD4 T-cell count was significantly associated with ANA detection.

Conclusions:
ANA and aSMA detection remain frequent in HCV/HIV-coinfected patients during the post–combined antiretroviral therapy era, despite fair immune restoration. These results advocate for a close monitoring of ANA before immune checkpoint inhibitor therapy in these patients with greater caution for those with a low nadir CD4 T-cell count.
Antiretroviral Drug Concentrations in Breastmilk, Maternal HIV Viral Load, and HIV Transmission to the Infant: Results From the BAN Study
Authors: Davis Nicole L. , Corbett Amanda , Kaullen Josh , Nelson Julie A. E. , Chasela Charles S. , Sichali Dorothy , Hudgens Michael G. , Miller William C. , Jamieson Denise J. , Kourtis Athena P. ,   on behalf of the BAN Study Team
Published: December 2018

Background:
Concentration of antiretroviral (ARV) drug found in plasma, and amounts of drug excreted into breastmilk, may affect HIV viral load and potentially perinatal HIV transmission.

Methods:
In this cohort study with 2-phase sampling, we included mothers randomized to postpartum maternal ARVs or daily infant nevirapine during 28 weeks of breastfeeding in the Breastfeeding, Antiretrovirals, and Nutrition study. Among these, we included all mothers who transmitted HIV to their infants between 2 and 28 weeks and 15% of mothers who did not (n = 27 and 227, respectively). Spearman correlation coefficients (r2) were used to assess the correlation between maternal plasma and breastmilk ARV concentration. Associations between the median effective drug concentration (EC50) and detectable maternal viral load (plasma: >40 copies per milliliter, breastmilk: >56 copies per milliliter) were assessed using mixed-effects models. Cox models were used to estimate the association between maternal or infant plasma drug concentration and breastmilk HIV transmission from 2 to 28 weeks.

Results:
All ARV compounds exhibited substantial correlations between maternal plasma and breastmilk concentrations (r2: 0.85–0.98, P-value <0.0001). Having plasma drug concentration above the EC50 was associated with lower odds of having detectable HIV RNA [maternal plasma odds ratio (OR) 0.64, 95% confidence interval (CI): 0.45 to 0.91; breastmilk OR 0.22, 95% CI: 0.14 to 0.35] and a reduced rate of breastmilk HIV transmission (hazard ratio 0.40, 95% CI: 0.18 to 0.93). Having breastmilk drug concentration above the EC50 was also associated with lower odds of having detectable maternal HIV RNA (plasma OR 0.62, 95% CI: 0.45 to 0.85; breastmilk OR 0.42, 95% CI: 0.29 to 0.59).

Conclusions:
Ensuring adequate drug concentration is important for viral suppression and preventing breastmilk HIV transmission.
Update on prevention of cytomegalovirus in hematopoietic cell transplantation
Authors: Dadwal Sanjeet S. 
Published: December 2018

Purpose of review
Cytomegalovirus infection (CMVi) has been the troll of allogeneic hematopoietic cell transplantation (allo-HCT). Over the last 4 decades various approaches have been adopted to minimize the burden from CMVi. There has been major advancement in the management of CMVi in HCT within the last few years that is poised to change the approaches employed in preventing and managing CMVi. This review will summarize recent advances and potential future development in the management of CMV in HCT.

Recent finding
The major development has been the approval of letermovir for the prevention of CMVi in allo-HCT recipients. Also, with the potential availability of tests that can determine host CMV immunity a risk adapted approach to CMV prevention may become a possibility.

Summary
The landscape of CMV prevention is about to change with the approval of a new anti-CMV antiviral that is safe and effective. However, the prophylaxis may lead to late onset CMVi in the context of ongoing risk factors after stopping prophylaxis and measures to counter this shifting epidemiology will need further research; such as extending the prophylaxis in high-risk patients vs. immunotherapy with vaccination and T-cell therapy.
Performance of Anti–Topoisomerase I Antibody Testing by Multiple-Bead, Enzyme-Linked Immunosorbent Assay and Immunodiffusion in a University Setting
Authors: Homer Kate LaRiviere , Warren Jeffrey , Karayev Dmitry , Khanna Puja P. , Young Amber , Nagaraja Vivek , Metzger Allan L. , Khanna Dinesh 
Published: December 2018

Background/Objective
The criterion standard for anti–topoisomerase I antibody (anti–topo I antibody) testing in systemic sclerosis (SSc) uses immunodiffusion (ID) techniques, but enzyme-linked immunosorbent assay (ELISA) and multiple-bead technology are often used in current settings to save time and cost. Our aim was to assess the performance of the multiple-bead assay, ELISA, and ID testing methods.

Methods
We conducted a retrospective study of patients at the University of Michigan whose extractable nuclear antigen 10 autoantibody panel tested positive for the anti–topo I antibody by multiple-bead technology during a 1-year period. All samples positive by multiple-bead assay were sent to the RDL Laboratories and reflexed for ELISA, and all anti–topo I antibodies positive by ELISA were further tested by ID. Clinical data were reviewed by a rheumatologist and assessed for presence of SSc. Data were analyzed via frequency tables.

Results
Approximately 9500 extractable nuclear antigen 10 panels were ordered by physicians at the University of Michigan. Of these, 129 patients were positive for the anti–topo I antibody by multiple-bead assay, 51 were positive by multiple-bead assay and ELISA, and 21 were positive by multiple-bead assay, ELISA, and ID. We found that 26.4% of patients positive by multiple-bead assay, 47.1% positive by multiple-bead assay and ELISA, and 95.2% positive by multiple-bead assay, ELISA, and ID had SSc.

Conclusions
Multiple-bead assays have a high rate of false-positive results for the anti–topo I antibody in patients without clinical evidence of SSc. A stepwise approach of confirmation of positive multiple-bead assay results using both ELISA and ID improves the predictive value of antibody testing for the diagnosis of SSc.
A Novel Preservation Solution Containing a JNK Inhibitory Peptide Efficiently Improves Islet Yield for Porcine Islet Isolation
Authors: Noguchi Hirofumi , Miyagi-Shiohira Chika , Nakashima Yoshiki , Ebi Nana , Hamada Eri , Tamaki Yoshihito , Kuwae Kazuho , Kitamura Shinji , Kobayashi Naoya , Saitoh Issei , Watanabe Masami 
Published: December 2018

Background
For islet transplantation, pancreas preservation in University of Wisconsin (UW) solution is associated with disadvantages, such as collagenase inhibition, resulting in poor islet yield and islets with poor viability. In this study, we evaluated a novel preservation solution, the extracellular-type c-Jun N-terminal kinase (JNK) inhibitor-containing (EJ) solution.

Methods
The EJ solution has high sodium-low potassium composition with low viscosity compared to UW solution. Moreover, EJ solution contains a recently developed JNK inhibitor from our laboratory.

Results
We first compared the performance of EJ solution with that of UW solution. Islet yield before and after purification was significantly higher in the EJ group than in the UW group. Second, we compared the performance of EJ solution with that of EJ solution without the JNK inhibitor (EJ-J solution). After pancreas preservation in EJ solution, JNK activity was maintained at a relatively low level during islet isolation. Islet yield before and after purification was significantly higher in the EJ group than in the EJ-J group. After islet transplantation into streptozotocin-induced diabetic mice, blood glucose levels reached the normoglycemic range in 61.5% and 7.7% of diabetic mice in the EJ and EJ-J groups, respectively. Moreover, EJ solution exhibited reduced inhibition of collagenase digestion compared with UW solution.

Conclusions
Advantages of EJ solution over UW solution were inhibition of JNK activity and reduced collagenase inhibition. EJ solution may therefore be more suitable for islet isolation than UW solution.
Physics of pre-wetted, lubricated and impregnated surfaces: a review
Authors: Bormashenko Edward 
Published: December 2018

Wetting phenomena occurring on pre-wetted flat and rough solid surfaces are reviewed. The wetting of lubricated flat surfaces is strongly correlated with the tribological properties of a solid/lubricant pair. The phenomena taking place on micro- and nano-rough oil-impregnated surfaces have attracted the attention of the scientific community due to their numerous promising applications as omniphobic, self-healing, anti-icing and anti-bacterial interfaces. On the other hand, these phenomena are rich in their physical content. The effects observed on natural and artificial, bioinspired oil-impregnated surfaces are discussed, including electrowetting of oil-impregnated surfaces, enabling low-voltage reversible control of the droplet shape.This article is part of the theme issue ‘Bioinspired materials and surfaces for green science and technology’.
Lessons from nature for green science and technology: an overview and bioinspired superliquiphobic/philic surfaces
Authors: Bhushan Bharat 
Published: December 2018

Nature has developed materials, objects and processes that function from the macroscale to the nanoscale. The emerging field of biomimetics allows one to mimic biology or nature to develop nanomaterials, nanodevices and processes which provide desirable properties. The biologically inspired materials and structured surfaces are being explored for various commercial applications. These should have minimum human impact on the environment, leading to eco-friendly or green science and technology. There are a large number of flora and fauna including bacteria, plants, land and aquatic animals, and seashells with properties of commercial interest. The paper presents an overview of the general field of biomimetics followed by a detailed overview of mechanisms, fabrication techniques and characterization of superliquiphobic/philic surfaces and their applications.This article is part of the theme issue ‘Bioinspired materials and surfaces for green science and technology’.
Water condensation and transport on bioinspired triangular patterns with heterogeneous wettability at a low temperature
Authors: Song Dong , Bhushan Bharat 
Published: December 2018

Desert beetles and cactus plants collect water from fog in arid regions. The desert beetle uses heterogeneous wettability to transport water to its mouth. A cactus uses conical spines which provide Laplace pressure gradient to transport water to its base. In this study, bioinspired triangular patterns with various wettability and different from the surrounding regions were investigated to transport condensed water from ambient air. A low temperature of 5°C was used to decrease saturated vapour pressure to promote water condensation. Results from this study can be used to enhance the performance of water collection systems.
This article is part of the theme issue ‘Bioinspired materials and surfaces for green science and technology’.
Predicting complex genetic phenotypes using error propagation in weighted networks
Authors: El Mhamdi El Mahdi , Kucharavy Andrei , Guerraoui Rachid , Li Rong 
Published: December 2018

AbstractNetwork-biology view of biological systems is a ubiquitous abstraction that emerged in the last two decades to allow a high-level understanding of principles governing them. However, the principles according to which biological systems are organized are still unclear. Here, we investigate if biological networks could be approximated as overlapping, feed-forward networks where the nodes have non-linear activation functions. Such networks have been shown to be universal approximators and their stability has been explored in the context of artificial neural networks. Mathematical formalization of this model followed by numerical simulations based on genomic data allowed us to accurately predict the statistics of gene essentiality in yeast and hence indicate that biological networks might be better understood as a distributed system, comprising potentially unreliable components.
High-dimensional Bayesian network inference from systems genetics data using genetic node ordering
Authors: Wang Lingfei , Audenaert Pieter , Michoel Tom 
Published: December 2018

AbstractStudying the impact of genetic variation on gene regulatory networks is essential to understand the biological mechanisms by which genetic variation causes variation in phenotypes. Bayesian networks provide an elegant statistical approach for multi-trait genetic mapping and modelling causal trait relationships. However, inferring Bayesian gene networks from high-dimensional genetics and genomics data is challenging, because the number of possible networks scales super-exponentially with the number of nodes, and the computational cost of conventional Bayesian network inference methods quickly becomes prohibitive. We propose an alternative method to infer high-quality Bayesian gene networks that easily scales to thousands of genes. Our method first reconstructs a node ordering by conducting pairwise causal inference tests between genes, which then allows to infer a Bayesian network via a series of independent variable selection problems, one for each gene. We demonstrate using simulated and real systems genetics data that this results in a Bayesian network with equal, and sometimes better, likelihood than the conventional methods, while having a significantly higher over-lap with groundtruth networks and being orders of magnitude faster. Moreover our method allows for a unified false discovery rate control across genes and individual edges, and thus a rigorous and easily interpretable way for tuning the sparsity level of the inferred network. Bayesian network inference using pairwise node ordering is a highly efficient approach for reconstructing gene regulatory networks when prior information for the inclusion of edges exists or can be inferred from the available data.
Sensory coding and causal impact of mouse cortex in a visual decision
Authors: Zatka-Haas Peter , Steinmetz Nicholas A. , Carandini Matteo , Harris Kenneth D. 
Published: December 2018

AbstractCorrelates of sensory stimuli and motor actions are found in multiple cortical areas, but such correlates do not indicate whether these areas are causally relevant to task performance. We trained mice to discriminate visual contrast and report their decision by turning a wheel. Widefield calcium imaging and Neuropixels recordings in cortex revealed stimulus-related activity in visual (VIS) and frontal (MOs) areas, and widespread movement-related activity across the whole dorsal cortex. Optogenetic inactivation biased choices only when targeted at VIS and MOs, at times corresponding to peak stimulus decoding. A neurometric model based on summing and subtracting activity in VIS and MOs successfully described behavioral performance and predicted the effect of optogenetic inactivation. Thus, local sensory signals in visual and frontal cortex play a causal role in task performance, while widespread dorsal cortical signals correlating with movement reflect processes that do not play a causal role.
Low Computational-cost Cell Detection Method for Calcium Imaging Data
Authors: Ito Tsubasa , Ota Keisuke , Ueno Kanako , Oisi Yasuhiro , Matsubara Chie , Kobayashi Kenta , Ohkura Masamichi , Nakai Junichi , Murayama Masanori , Aonishi Toru 
Published: December 2018

AbstractThe rapid progress of calcium imaging has reached a point where the activity of tens of thousands of cells can be recorded simultaneously. However, the huge amount of data in such records makes it difficult to carry out cell detection manually. Consequently, because the cell detection is the first step of multicellular data analysis, there is a pressing need for automatic cell detection methods for large-scale image data. Automatic cell detection algorithms have been pioneered by a handful of research groups. Such algorithms, however, assume a conventional field of view (FOV) (i.e. 512 × 512 pixels) and need a significantly higher computational power for a wider FOV to work within a practical period of time. To overcome this issue, we propose a method called low computational-cost cell detection (LCCD), which can complete its processing even on the latest ultra-large FOV data within a practical period of time. We compared it with two previously proposed methods, constrained non-negative matrix factorization (CNMF) and Suite2P. We found that LCCD makes it possible to detect cells from a huge-amount of high-density imaging data within a shorter period of time and with an accuracy comparable to or better than those of CNMF and Suite2P.
Use of IFNγ/IL10 ratio for stratification of hydrocortisone therapy in patients with septic shock
Authors: König Rainer , Kolte Amol , Ahlers Olaf , Oswald Marcus , Röll Daniela , Dimopoulos George , Tsangaris Iraklis , Antoniadou Eleni , Bogatsch Holger , Löffler Markus , Sprung Charles L. , Singer Mervyn , Brunkhorst Frank , Oppert Michael , Gerlach Herwig , Claus Ralf A. , Coldewey Sina M. , Briegel Josef , Giamarellos-Bourboulis Evangelos J. , Keh Didier , Bauer Michael 
Published: December 2018

AbstractBackgroundLarge clinical trials testing hydrocortisone therapy in septic shock have produced conflicting results. Subgroups may however benefit depending on their individual immune response.MethodsWe performed an exploratory analysis of the CORTICUS trial database employing machine learning to a panel of 137 variables collected from 83 patients (60 survivors, 23 non-survivors) including demographic and clinical measures, organ failure scores, leukocyte counts and circulating cytokine levels. The identified biomarker was validated against data collected from patients enrolled into a cohort of the Hellenic Sepsis Study Group (HSSG) (n=162) and two data sets of two other clinical trials.Ex vivostudies were performed on this biomarker to assess a possible mechanistic role.ResultsA low serum IFNγ/IL10 ratio predicted increased survival in the hydrocortisone group whereas a high ratio predicted better survival in the placebo group. Using this ratio for a decision rule, we found significant improvement in survival in the groups of patients being in compliance with the prediction rule (discovery set: OR=3.03 [95% Cl: 1.05-8.75], P=0.031, validation set: OR=2.01 [95% CI: 1.04-3.88], P=0.026). Applying the rule to two further, smaller datasets showed the same tendency. Mechanistic studies revealed that IFNγ/IL10 was negatively associated with pathogen load in spiked human blood. Anin silicoanalysis of published IFNγ and IL10 values in bacteremic and non-bacteremic SIRS patients supported this association between the ratio and pathogen burden.ConclusionIf confirmed prospectively, the IFNγ/IL10 ratio could be used as a rapidly available theranostic for use of hydrocortisone therapy in septic shock.
The Effect of Compound Kushen Injection on Cancer Cells: Integrated Identification of Candidate Molecular Mechanisms
Authors: Cui Jian , Qu Zhipeng , Harata-Lee Yuka , Shen Hanyuan , Nwe Aung Thazin , Wang Wei , Daniel Kortschak R. , Adelson David L 
Published: December 2018

AbstractBackgroundBecause Traditional Chinese Medicine (TCM) preparations are often combinations of multiple herbs containing hundreds of compounds, they have been difficult to study. Compound Kushen Injection (CKI) is a complex mixture cancer treatment used in Chinese hospitals for over twenty years.PurposeTo demonstrate that a systematic analysis of molecular changes resulting from complex mixtures of bioactives from TCM can identify a core set of differentially expressed (DE) genes and a reproducible set of candidate pathways.Study DesignWe used a cancer cell culture model to measure the effect of CKI on cell cycle phases, apoptosis and correlate those phenotypes with CKI induced changes in gene expression.MethodsWe treated cancer cells with CKI in order to generate and analyse high-throughput transcriptome data from two cancer cell lines. We integrated these differential gene expression results with previously reported results.ResultsCKI induced cell-cycle arrest and apoptosis and altered the expression of 363 core candidate genes associated with cell cycle, apoptosis, DNA replication/repair and various cancer pathways. Of these, 7 are clinically relevant to cancer diagnosis or therapy and 14 are cell cycle regulators, and most of these 21 candidates are downregulated by CKI. Comparison of our core candidate genes to a database of plant medicinal compounds and their effects on gene expression identified one-to-one, one-to-many and many-to-many regulatory relationships between compounds in CKI and DE genes.ConclusionsBy identifying promising candidate pathways and genes associated with CKI based on our transcriptome-based analysis, we have shown this approach is useful for the systematic analysis of molecular changes resulting from complex mixtures of bioactives.