bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Method of Human Adipose-Derived Stem Cell Isolation with Resultant Increased Cell Yield
Authors: Tevlin Ruth , McArdle Adrian , Brett Elizabeth , Chung Michael T. , Paik Kevin , Seo Eun Young , Walmsley Graham G. , Duldulao Christopher R. , Atashroo David , Zielins Elizabeth , Vistnes Stephanie , Chan Charles K. F. , Wan Derrick C. , Longaker Michael T. 
Published: August 2016

Background:
The authors have developed a novel protocol for isolating adipose-derived stem cells from human lipoaspirate. In this study, they compare their new method to a previously published standard protocol.

Methods:
Human adipose-derived stem cell isolation was performed using two methods to compare cell yield, cell viability, cell proliferation, and regenerative potential. The new and conventional isolation methods differ in two key areas: the collagenase digestion buffer constituents and the use of an orbital shaker. The osteogenic and adipogenic potential of adipose-derived stem cells isolated using both protocols was assessed in vitro, and gene expression analysis was performed. To assess the ability of the isolated cells to generate bone in vivo, the authors created critical-size calvarial defects in mice, which were treated with adipose-derived stem cells loaded onto hydroxyapatite-coated poly(lactic-co-glycolic acid) scaffolds. To test the ability of the isolated cells to enhance adipogenesis, the cells were added to lipoaspirate and placed beneath the scalp of immunocompromised mice. Fat graft volume retention was subsequently assessed by serial computed tomographic volumetric scanning.

Results:
The new method resulted in a 10-fold increased yield of adipose-derived stem cells compared with the conventional method. Cells harvested using the new method demonstrated significantly increased cell viability and proliferation in vitro (p < 0.05). New method cells also demonstrated significantly enhanced osteogenic and adipogenic differentiation capacity in vitro (p < 0.05) in comparison with the conventional method cells. Both cell groups demonstrated equivalent osteogenic and adipogenic regenerative potential in mice.

Conclusions:
The authors have developed a protocol that maximizes the yield of adipose-derived stem cells derived from lipoaspirate. The new method cells have increased osteogenic and adipogenic potential in vitro and are not inferior to conventional method cells in terms of their ability to generate bone and fat in vivo.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, V.
Immune Activation by Mycobacterium t uberculosis in HIV-Infected and -Uninfected Subjects
Authors: Wyndham-Thomas Chloé , Corbière Véronique , Selis Elodie , Payen Marie-Christine , Goffard Jean-Christophe , Van Vooren Jean-Paul , Mascart Françoise , Dirix Violette 
Published: August 2016

Introduction:
This study investigates the influence of Mycobacterium tuberculosis infection on immune activation biomarkers, both in HIV-infected and -uninfected subjects.

Methods:
Forty-eight treatment-naive HIV-infected patients and 74 HIV-uninfected subjects were recruited and divided into groups according to their M. tuberculosis infection status: latent tuberculosis infection (LTBI), active tuberculosis (TB), and no evidence of M. tuberculosis infection. The expression of cellular markers CD38 and HLA-DR on circulating CD8+ T lymphocytes and the plasmatic levels of soluble markers interleukin-6, sCD14, and D-Dimer were measured and compared between groups. The HIV-infected patients with no evidence of M. tuberculosis or with LTBI who initiated antiretroviral treatment were tested again for these biomarkers once viral suppression was reached.

Results:
In both HIV-infected and -uninfected groups, patients with TB had higher levels of immune activation markers than subjects with LTBI and with no evidence of M. tuberculosis. Among the HIV-uninfected subjects, no significant difference in biomarker level was found between those presenting LTBI and those with no evidence of M. tuberculosis. The effect of LTBI on activation biomarkers in the HIV-infected groups was inconclusive because of the small number of individuals in the HIV+/LTBI group. sCD14 and D-Dimer levels were significantly higher in the TB-only group than in the HIV-only group.

Discussion:
Although TB is associated with an increase in biomarkers of immune activation, the effect of LTBI is less evident. Further investigation is warranted, and according to our results, soluble markers may offer greater sensitivity for the evaluation of M. tuberculosis–associated immune activation than cellular markers.
Nanoflow-Nanospray Mass Spectrometry Metabolomics Reveals Disruption of the Urinary Metabolite Profiles of HIV-Positive Patients on Combination Antiretroviral Therapy
Authors: Chetwynd Andrew J. , Samarawickrama Amanda , Vera Jaime H. , Bremner Stephen A. , Abdul-Sada Alaa , Gilleece Yvonne , Holt Stephen G. , Hill Elizabeth M. 
Published: August 2016

Background:The use of combination antiretroviral therapy (cART) has substantially improved the outlook for patients with HIV infection. However, lifelong exposure to cART is also associated with adverse metabolic changes and an enhanced risk of renal, hepatic, and cardiovascular dysfunction. This study investigated disruptions of the urinary metabolome of cART-exposed patients, thereby furthering our understanding of some of the side effects of pharmaceutical intervention.Methods:HIV-positive patients were recruited from an HIV clinic and divided into cART-naive and cART-exposed groups. HIV-negative patients were recruited from a sexual health clinic. All 89 subjects were white males. Targeted biochemistry analyses were performed on plasma samples. Urine samples were collected after an overnight fast and analyzed with a highly sensitive untargeted metabolomic method using nanoflow/nanospray liquid chromatography–time-of-flight mass spectrometry. Data sets were analyzed using projection modeling to detect metabolite markers of cART exposure.Results:Metabolites or parent compounds of all cART drugs were detected in urine extracts of all but one of the cART-exposed patients confirming adherence to the pharmaceutical regimen. Analysis of urine samples from patients on cART revealed significant reductions in selected bile acids, lipid, nucleoside, and androgen metabolites. However, plasma concentrations of free or conjugated testosterone remained unchanged indicating possible disruption of androgen transport or excretion in urine of patients on cART.Conclusions:Discovery-based metabolomics reveals the potential to identify novel markers of cART intervention and metabolite disruption in HIV-positive patients, which may enable investigation of the efficacy, compliance, and side effects of these pharmaceutical mixtures to be investigated.
Brief Report: Preventing HIV-1 Infection in Women Using Oral Preexposure Prophylaxis: A Meta-analysis of Current Evidence
Authors: Hanscom Brett , Janes Holly E. , Guarino Peter D. , Huang Ying , Brown Elizabeth R. , Chen Ying Qing , Hammer Scott M. , Gilbert Peter B. , Donnell Deborah J. 
Published: August 2016

Abstract:
The World Health Organization has issued an early release revision to its antiretroviral guidelines in which PrEP (pre-exposure prophylaxis in the form of daily oral, fixed dose combination tenofovir disoproxil fumarate/emtricitabine) is recommended as a prevention option to all people at substantial risk of acquiring HIV. However, lack of effectiveness in 2 major women-only PrEP trials, VOICE and FEM-PrEP, continues to be a cause for concern about achieving effectiveness for women in Southern Africa. We conducted a series of meta-analyses of oral effectiveness of tenofovir disoproxil fumarate/emtricitabine in women including all 5 randomized placebo-controlled trials that included women. An adherence-based meta-analysis model showed that with high levels of adherence (75%), oral PrEP is estimated to be effective (relative risk = 0.39, 95% confidence interval: 0.25 to 0.60). Provided that these results apply to women in Southern Africa, future prevention trial designs in that region should account for potentially reduced HIV incidence when PrEP is available.
Congenital myopathies: not only a paediatric topic
Authors: Jungbluth Heinz , Voermans Nicol C. 
Published: August 2016

Purpose of review
This article reviews adult presentations of the major congenital myopathies – central core disease, multiminicore disease, centronuclear myopathy and nemaline myopathy – with an emphasis on common genetic backgrounds, typical clinicopathological features and differential diagnosis.

Recent findings
The congenital myopathies are a genetically heterogeneous group of conditions with characteristic histopathological features. Although essentially considered paediatric conditions, some forms – in particular those due to dominant mutations in the skeletal muscle ryanodine receptor (RYR1), the dynamin 2 (DNM2), the amphiphysin 2 (BIN1) and the Kelch repeat-and BTB/POZ domain-containing protein 13 (KBTBD13) gene – may present late into adulthood. Moreover, dominant RYR1 mutations associated with the malignant hyperthermia susceptibility trait have been recently identified as a common cause of (exertional) rhabdomyolysis presenting throughout life. In addition, improved standards of care and development of new therapies will result in an increasing number of patients with early-onset presentations transitioning to the adult neuromuscular clinic. Lastly, if nemaline rods are the predominant histopathological feature, acquired treatable conditions have to be considered in the differential diagnosis.

Summary
Recently identified genotypes and phenotypes indicate a spectrum of the congenital myopathies extending into late adulthood, with important implications for clinical practice.
The Modular Adaptive Ribosome
Authors: Yadav Anupama , Radhakrishnan Aparna , Panda Anshuman , Singh Amartya , Sinha Himanshu , Bhanot Gyan 
Published: August 2016

ABSTRACTThe ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5’UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.
Systems Biomedicine of Rabies Delineates the Affected Signaling pathways
Authors: Jamalkandi Sadegh Azimzadeh , Pourbadie Hamid Gholami , Mirzaie Mehdi , Mozhgani Sayed Hamid Reza , Noorbakhsh Farsheed , Vaziri Behrouz , Gholami Alireza , Ansari-Pour Naser , Jafari Mohieddin 
Published: August 2016

AbstractThe prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein-protein interaction network (PPIN) of infected cells to elucidate biological signaling transduction pathways affected by rabies virus. To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.
FOXA1 directs H3K4 monomethylation at enhancers via recruitment of the methyltransferase MLL3
Authors: Jozwik Kamila M. , Chernukhin Igor , Serandour Aurelien A. , Nagarajan Sankari , Carroll Jason S. 
Published: August 2016

AbstractFOXA1 is a pioneer factor that is important in hormone dependent cancer cells to stabilise nuclear receptors, such as estrogen receptor (ER) to chromatin. FOXA1 binds to enhancers regions that are enriched in H3K4mono- and dimethylation (H3K4me1, H3K4me2) histone marks and evidence suggests that these marks are requisite events for FOXA1 to associate with enhancers to initate subsequent gene expression events. However, exogenous expression of FOXA1 has been shown to induce H3K4me1 and H3K4me2 signal at enhancer elements and the order of events and the functional importance of these events is not clear. We performed a FOXA1 Rapid Immunoprecipitation Mass Spectrometry of Endogenous Proteins (RIME) screen in ERα-positive MCF-7 breast cancer cells in order to identify FOXA1 interacting partners and we found histone-lysine N-methyltransferase (MLL3) as the top FOXA1 interacting protein. MLL3 is typically thought to induce H3K4me3 at promoter regions, but recent findings suggest it may contribute to H3K4me1 deposition, in line with our observation that MLL3 associates with an enhancer specific protein. We performed MLL3 ChIP-seq in breast cancer cells and unexpectedly found that MLL3 binds mostly at non-promoter regions enhancers, in contrast to the prevailing hypothesis. MLL3 was shown to occupy regions marked by FOXA1 occupancy and as expected, H3K4me1 and H3K4me2. MLL3 binding was dependent on FOXA1, indicating that FOXA1 recruits MLL3 to chromatin. Motif analysis and subsequent genomic mapping revealed a role for Grainy head like protein-2 (GRHL2) which was shown to co-occupy regions of the chromatin with MLL3. Regions occupied by all three factors, namely FOXA1, MLL3 and GRHL2, were most enriched in H3K4me1. MLL3 silencing decreased H3K4me1 at enhancer elements, but had no appreciable impact on H3K4me3 at enhancer elements. We identify a complex relationship between FOXA1, MLL3 and H3K4me1 at enhancers in breast cancer and propose a mechanism whereby the pioneer factor FOXA1 can interact with a chromatin modifier MLL3, recruiting it to chromatin to facilitate the deposition of H3K4me1 histone marks, subsequently demarcating active enhancer elements.
PubData: search engine for bioinformatics databases worldwide
Authors: Khomtchouk Bohdan B. , Vand Kasra A. , Wahlestedt Thor , Khomtchouk Kelly , Sayed Mohammed K. , Wahlestedt Claes 
Published: August 2016

AbstractWe propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the user’s search preferences.PubData is hosted as a user-friendly, cross-platform graphical user interface program developed using PyQt:http://www.pubdata.bio. The methods are implemented in Python, and are available as part of the PubData project at:https://github.com/Bohdan-Khomtchouk/PubData.
Understanding the contributions of visual stimuli to contextual fear conditioning: a proof-of-concept study using LCD screens
Authors: Murawski Nathen J. , Asok Arun 
Published: August 2016

AbstractThe precise contribution of visual information to contextual fear-learning and discrimination has remained elusive. To better understand this contribution, we coupled the context pre-exposure facilitation effect (CPFE) fear conditioning paradigm with presentations of distinct visual scenes displayed on 4 LCD screens surrounding a conditioning chamber. Adult male Long-Evans rats received non-reinforced context pre-exposure on Day 1, an immediate 1.5 mA foot shock on Day 2, and a non-reinforced context test on Day 3. Rats were pre-exposed to either digital Context (dCtx) A, dCtx B, a distinct Context C, or no context on Day 1. Context A and B were identical except for the visual image displayed on the LCD monitors. Immediate shock and retention testing occurred in dCtx A. Rats pre-exposed dCtx A showed the CPFE with significantly higher levels of freezing compared to learning controls. Rats pre-exposed to Context B failed to show the CPFE, with freezing that did not differ significantly from any group. The results suggest that 1) visual information contributes to contextual fear learning in rats and that 2) visual components of the context can be parametrically controlled via LCD screens. Our approach offers a simple modification to contextual fear conditioning whereby the visual features of a context can be precisely controlled to better understand how rodents discriminate and generalize fear across environments.
What is the link between stringent response, endoribonuclease encoding Type II Toxin-Antitoxin systems and persistence?
Authors: Ramisetty Bhaskar Chandra Mohan , Ghosh Dimpy , Chowdhury Maoumita Roy , Santhosh Ramachandran Sarojini 
Published: August 2016

AbstractPersistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is Toxin-Antitoxin systems (TAS) which are also implicated in a wide range of stress-related phenomena. In a report (Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140-1150) an interesting link between ppGpp mediated stringent response, TAS and persistence was proposed. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins. The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for Lon-dependent degradation of YefM, the antitoxin of YefM/YoeB TAS. The Δ10 strain, anEscherichia coliMG1655 derivative in which the ten TAS are deleted, is more sensitive to Ciprofloxacin and Ampicillin compared to wild-type MG1655. Furthermore, we show that the Δ10 strain has relatively lower fitness compared to the wild type and hence, we argue that the implications based on this strain are void. We conclude that there is no direct and specific link between stringent response and the regulation of TAS. The link between TAS and persistence is inconclusive due to altered fitness of Δ10 strain and hence requires thorough inspection and debate.ImportanceA model connecting stringent response, endoribonuclease encoding Type II Toxin-Antitoxin systems (TAS) and persistence is widely propagated. It states that “accumulation of ppGpp results in accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxin rendering toxins free to induce persistence”. This work presents a contradiction to and challenges the model. Experimental evidence, literature survey as well as rationale are provided to show that inorganic polyphosphate is not required for the degradation of YefM, the antitoxin in YefM/YoeB TAS. The Δ10 strain is relatively more sensitive to Ciprofloxacin and Ampicillin as well as has lowered fitness. This is likely because of the polar effects on the adjacent genes caused by the genetic manipulation of multiple TAS loci.
Non-Mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (Humulus lupulusL.)
Authors: Zhang Dong , Pitra Nicholi J. , Coles Mark C. , Buckler Edward S. , Matthews Paul D. 
Published: August 2016

AbstractGenome-wide meiotic recombination structures, sex chromosomes, and candidate genes for sex determination were discovered amongHumulusspp. by application of a novel, high-density molecular marker system: ~1.2M single nucleotide polymorphisms (SNPs) were profiled with genotyping-by-sequencing (GBS) among 4512 worldwide accessions, including 4396 cultivars and landraces and 116 wild accessions of hops. Pre-qualified GBS markers were validated by inferences on families, population structures and phylogeny. Candidate genes discovered for several traits, including sex and drought stress-resistance, demonstrate the quality and utility of GBS SNPs for genome-wide association studies (GWAS) and Fst analysis in hops. Most importantly, pseudo-testcross mappings in F1 families delineated non-random linkage of Mendelian and non-Mendelian markers: structures that are indicative of unusual meiotic events which may have driven the evolution and cultivation of hops.
NovelblaKPC-carrying species identified in the hospital environment
Authors: Phan Hang T.T. , Aiken Zoie , Akinremi Oluwafemi , Cawthorne Julie , Dodgson Andrew , Downes Angela , Ellington Matthew , George Ryan , Mathers Amy , Stoesser Nicole , Thomas Stephanie ,   on behalf of the TRACE Investigators’ Group
Published: August 2016

AbstractblaKPC, encoding one of five dominant global carbapenemase families, is increasingly identified in environmental species difficult to characterize using routine diagnostic methods, with epidemiological and clinical implications. During environmental hospital infection prevention and control investigations (Manchester, UK) we used whole genome sequencing to confirm species identification for isolates infrequently associated withblaKPCand/or difficult to classify by MALDI-ToF. Four previously undescribedblaKPC-carrying species were identified from the hospital environment, including a putative, novelEnterobacterspecies.