bluuebunny/crossref_metadata_2025_split huggingface dataset:
The influence of posterior visual pathway damage on visual information processing speed in multiple sclerosis
Authors: Gabilondo Iñigo , Rilo Oiane , Ojeda Natalia , Pena Javier , Gómez-Gastiasoro Ainara , Mendibe Bilbao Mar , Rodríguez-Antigüedad Alfredo , Cabrera Alberto , Diez Ibai , Ibarretxe-Bilbao Naroa 
Published: November 2016

Background: The injury of visual pathway and abnormalities of visual processing speed (VPS) are frequent in MS, but their association remains unexplored. Objective: To evaluate the impact of posterior visual pathway structural and functional integrity on VPS of MS patients. Methods: Cross-sectional study of 30 MS patients and 28 controls, evaluating the association of a VPS tests composite (Salthouse Perceptual Comparison test, Trail Making Test A and Symbol Digit Modalities Test) with 3T MRI visual cortex thickness, optic radiations (OR) diffusion tensor imaging indexes, and medial visual component (MVC) functional connectivity (FC) (MVC-MVC FC (iFC) and MVC-brain FC (eFC)) by linear regression, removing the effect of premorbid IQ, fatigue, and depression. Results: V2 atrophy, lower OR fractional anisotropy (FA) and MVC FC significantly influenced VPS in MS (at none or lesser extent in controls), even after removing the effect of Expanded Disability Status Scale and previous optic neuritis (V2 ( r2 = 0.210): β = +0.366, p = 0.046; OR FA ( r2 = 0.243): β = +0.378, p = 0.034; MVC iFC, for example, left cuneus ( r2 = 0.450): β = −0.613, p < 0.001; MVC eFC, for example, right precuneus-postcentral gyrus ( r2 = 0.368): β = −0.466, p = 0.002). Conclusion: Posterior visual pathway integrity, structural (V2 thickness and OR FA) and functional (MVC FC), may explain respectively up to 24% and 45% of VPS variability in MS.
Natural killer cell subpopulations are associated with MRI activity in a relapsing-remitting multiple sclerosis patient cohort from Australia
Authors: Caruana P , Lemmert K , Ribbons K , Lea R , Lechner-Scott J 
Published: November 2016

Background: The importance of the innate immune system in multiple sclerosis (MS) is increasingly recognized and the role of natural killer (NK) cells in controlling autoimmunity may be an important modulator of disease activity. Objective: To examine NK subsets in MS patients on different treatments and to evaluate the role of NK subsets as indicators for disease activity. Methods: We measured NK subset levels in blood obtained from 110 relapsing-remitting MS patients. Patients were either off treatment or on treatment with natalizumab, fingolimod, glatiramer acetate or beta-interferon. Disease activity was defined according to ‘No Evidence of Disease Activity’ (NEDA) criteria within an observation period of up to 2.4 years. The mean NK subset levels were compared among treatment groups using multivariate analysis of variance (ANOVA) and association analysis with disease activity performed using multi-factor logistic regression. Results: Our analysis revealed differences in NK cells and subsets on treatment compared to off treatment ( p < 0.0005). A high proportion of bright NK cells were significantly associated with stable magnetic resonance imaging (MRI) imaging after adjusting for treatment effects ( p < 0.05). Conclusion: The independent association of NK subsets with MRI stability needs to be confirmed in prospective studies to test their usefulness in predicting disease activity in MS patients.
The production of Norwegian tones by multilingual non-native speakers
Authors: Steien Guri Bordal , van Dommelen Wim A 
Published: November 2016

Aim and objectives/purpose/research questions: The aim of this study is to examine the extent to which multilingual second language (L2) speakers of Norwegian manage to produce lexical pitch accents (L*H¯ or H*LH¯) as expected in natural spontaneous speech. Using native speech as a reference, we analyse realizations of multilingual speakers whose respective dominant languages are Lingala, a lexical tone language, and Swahili, a non-tonal language with fixed stress, and hypothesize that this difference might be reflected in the speakers’ competence in the East Norwegian tone system. Design/methodology/approach: We examined a corpus of spontaneous speech produced by eight L2 speakers and two native speakers of East Norwegian. Acoustic analysis was performed to collect fundamental frequency (f0) contours of 60 accentual phrases per speaker. Data and analysis: For LH and HLH tonal patterns, measuring points were defined for quantitative evaluation of f0 values. Relevant aspects investigated were (a) pattern consistency, (b) f0 dynamic range and (c) rate of f0 change. Pattern consistency data were statistically evaluated using chi-square testing. The dynamic range and rate of f0 change data were explored through to linear mixed effects models. Findings/conclusions: We found no really substantial differences between the speaker groups in the parameters we examined, neither between the L2 speakers and the Norwegian natives nor between the Lingala and Swahili speakers. Originality and significance/implications: This study is a contribution to the scarcely explored area of L2 acquisition of tones. It is concerned with languages that have received little or no attention in the field: Norwegian, Lingala and Swahili. Participants are multilinguals who have extensive language learning experience. Further, the study is based on a corpus of spontaneous speech.
Shoulder Arthroplasty Outcomes in Patients With Multiple Reported Drug Allergies
Authors: Rosenthal Brett D. , Knesek Michael J. , Kahlenberg Cynthia A. , Mai Harry , Saltzman Matthew D. 
Published: November 2016

Background: The presence of multiple allergies has been correlated with worse outcomes for patients undergoing hip and knee arthroplasty, but the effect of allergies has not yet been elucidated with respect to shoulder arthroplasty. Purpose/Hypothesis: The purpose of this study is to identify any discrepancies in shoulder arthroplasty outcomes with respect to reported drug allergies. We hypothesized that patients with multiple drug allergies would have inferior outcomes. Study Design: Cohort study; Level of evidence, 3. Methods: Included in the analysis were a single surgeon’s cases between 2009 and 2014 of primary total shoulder arthroplasty with a minimum of 180 days of follow-up. Cases with fracture as the indication were excluded. Preoperative and postoperative metrics included visual analog scale (VAS) for pain, forward flexion range of motion, and Simple Shoulder Test (SST) results, and postoperative patient satisfaction scores were also collected. Chi-square and 1-way analysis of variance with Tukey post hoc analyses were performed when appropriate. Results: A total of 98 patients were included (no allergies, n = 51; single allergy, n = 21; multiple allergies, n = 26). The proportion of females was greater with increasing number of allergies (no allergies, 31%; single allergies, 47%; multiple allergies, 88%; Pearson χ2 = 22.5; P < .0001). Both preoperatively and postoperatively, no difference was found between cohorts with respect to SST score, VAS score, or forward flexion. There was also no difference in postoperative satisfaction between cohorts. No difference between cohorts was identified when comparing the pre- to postoperative change in SST scores, VAS scores, or forward flexion. Conclusion: The presence of single or multiple allergies is not correlated with worse outcomes after primary anatomic total shoulder arthroplasty.
GEN3VA: aggregation and analysis of gene expression signatures from related studies
Authors: Gundersen Gregory W. , Jagodnik Kathleen M. , Woodland Holly , Fernandez Nicholas F. , Sani Kevin , Dohlman Anders B. , Ung Peter Man-Un , Monteiro Caroline D. , Schlessinger Avner , Ma’ayan Avi 
Published: November 2016

Abstract
Background
Genome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies. Such data is deposited into data repositories such as the Gene Expression Omnibus (GEO) for potential reuse. However, these repositories currently do not provide simple interfaces to systematically analyze collections of related studies.

Results
Here we present GENE Expression and Enrichment Vector Analyzer (GEN3VA), a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO. Each tagged collection of signatures is presented in a report that consists of heatmaps of the differentially expressed genes; principal component analysis of all signatures; enrichment analysis with several gene set libraries across all signatures, which we term enrichment vector analysis; and global mapping of small molecules that are predicted to reverse or mimic each signature in the aggregate. We demonstrate how GEN3VA can be used to identify common molecular mechanisms of aging by analyzing tagged signatures from 244 studies that compared young vs. old tissues in mammalian systems. In a second case study, we collected 86 signatures from treatment of human cells with dexamethasone, a glucocorticoid receptor (GR) agonist. Our analysis confirms consensus GR target genes and predicts potential drug mimickers.

Conclusions
GEN3VA can be used to identify, aggregate, and analyze themed collections of gene expression signatures from diverse but related studies. Such integrative analyses can be used to address concerns about data reproducibility, confirm results across labs, and discover new collective knowledge by data reuse. GEN3VA is an open-source web-based system that is freely available at: http://amp.pharm.mssm.edu/gen3va.
Nutrition surveillance using a small open cohort: experience from Burkina Faso
Authors: Altmann Mathias , Fermanian Christophe , Jiao Boshen , Altare Chiara , Loada Martin , Myatt Mark 
Published: November 2016

Abstract
Background
Nutritional surveillance remains generally weak and early warning systems are needed in areas with high burden of acute under-nutrition. In order to enhance insight into nutritional surveillance, a community-based sentinel sites approach, known as the Listening Posts (LP) Project, was piloted in Burkina Faso by Action Contre la Faim (ACF). This paper presents ACF’s experience with the LP approach and investigates potential selection and observational biases.

Methods
Six primary sampling units (PSUs) were selected in each livelihood zone using the centric systematic area sampling methodology. In each PSU, 22 children aged between 6 and 24 months were selected by proximity sampling. The prevalence of GAM for each month from January 2011 to December 2013 was estimated using a Bayesian normal–normal conjugate analysis followed by PROBIT estimation. To validate the LP approach in detecting changes over time, the time trends of MUAC from LP and from five cross-sectional surveys were modelled using polynomial regression and compared by using a Wald test. The differences between prevalence estimates from the two data sources were used to assess selection and observational biases.

Results
The 95 % credible interval around GAM prevalence estimates using LP approach ranged between +6.5 %/−6.0 % on a prevalence of 36.1 % and +3.5 %/−2.9 % on a prevalence of 10.8 %. LP and cross-sectional surveys time trend models were well correlated (p = 0.6337). Although LP showed a slight but significant trend for GAM to decrease over time at a rate of −0.26 %/visit, the prevalence estimates from the two data sources showed good agreement over a 3-year period.

Conclusions
The LP methodology has proved to be valid in following trends of GAM prevalence for a period of 3 years without selection bias. However, a slight observational bias was observed, requiring a periodical reselection of the sentinel sites. This kind of surveillance project is suited to use in areas with high burden of acute under-nutrition where early warning systems are strongly needed. Advocacy is necessary to develop sustainable nutrition surveillance system and to support the use of surveillance data in guiding nutritional programs.
Effect of concomitant use of memantine on mortality and efficacy outcomes of galantamine-treated patients with Alzheimer’s disease: post-hoc analysis of a randomized placebo-controlled study
Authors: Hager Klaus , Baseman Alan S. , Nye Jeffrey S. , Brashear H. Robert , Han John , Sano Mary , Davis Bonnie , Richards Henry M. 
Published: November 2016

Abstract
Background
A large, prospective, 2-year, randomized study in patients with mild-to-moderate Alzheimer’s disease or mixed dementia demonstrated reductions in mortality and cognitive/functional decline in galantamine-treated patients. A post-hoc analysis was conducted to study the effect of (the presence or absence of) concomitant memantine use on treatment outcome.

Methods
Randomized patients (N = 2045) were divided into subgroups based on memantine use. Analyses included demographic and clinical characteristics (age, nursing home placement, Mini-Mental State Examination (MMSE) and Disability Assessment for Dementia (DAD) scores) and mortality endpoints.

Results
Overall, 496 (24.3 %) patients were memantine users and were older (mean (SD), 74.0 (8.76) vs 72.8 (8.76), p = 0.008), with lower MMSE scores (18.2 (4.16) vs 19.2 (4.02), p < 0.0001) and DAD scores (58.0 (23.49) vs 62.5 (20.52), p < 0.0001) than nonusers. Mortality rates (per 100 patient-years) in memantine nonusers (n = 1549) were lower for galantamine (1.39) vs placebo-treated patients (4.15). In memantine users, mortality rates were similar for placebo-treated (4.49) and galantamine-treated patients (5.57). In memantine nonusers at 24 months, the decline in MMSE scores (effect size (95 % CI) 0.25 (0.14; 0.36)) and DAD scores (0.17 (0.06; 0.28)) from baseline was lower in galantamine patients vs placebo patients. The absence of these benefits in memantine users could not be explained by baseline age, MMSE, or DAD scores.

Conclusion
This post-hoc analysis shows that the beneficial effects of galantamine at 2 years post treatment were not observed in patients who had been placed on background memantine. The reasons for memantine treatment and the possibility of interaction between memantine and galantamine merit further investigation.

Trial registration
ClinicalTrials.gov NCT00679627. Registered 15 May 2008.
Microvesicles secreted from equine amniotic-derived cells and their potential role in reducing inflammation in endometrial cells in an in-vitro model
Authors: Perrini Claudia , Strillacci Maria Giuseppina , Bagnato Alessandro , Esposti Paola , Marini Maria Giovanna , Corradetti Bruna , Bizzaro Davide , Idda Antonella , Ledda Sergio , Capra Emanuele , Pizzi Flavia , Lange-Consiglio Anna , Cremonesi Fausto 
Published: November 2016

Abstract
Background
It is known that a paracrine mechanism exists between mesenchymal stem cells and target cells. This process may involve microvesicles (MVs) as an integral component of cell-to-cell communication.

Methods
In this context, this study aims to understand the efficacy of MVs in in-vitro endometrial stressed cells in view of potential healing in in-vivo studies. For this purpose, the presence and type of MVs secreted by amniotic mesenchymal stem cells (AMCs) were investigated and the response of endometrial cells to MVs was studied using a dose-response curve at different concentrations and times. Moreover, the ability of MVs to counteract the in vitro stress in endometrial cells induced by lipopolysaccharide was studied by measuring the rate of apoptosis and cell proliferation, the expression of some pro-inflammatory genes such as tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin 1β (IL-1β), and metalloproteinases (MMP) 1 and 13, and the release of some pro- or anti-inflammatory cytokines.

Results
MVs secreted by the AMCs ranged in size from 100 to 200 nm. The incorporation of MVs was gradual over time and peaked at 72 h. MVs reduced the apoptosis rate, increased cell proliferation values, downregulated pro-inflammatory gene expression, and decreased the secretion of pro-inflammatory cytokines.

Conclusion
Our data suggest that some microRNAs could contribute to counteracting in-vivo inflammation of endometrial tissue.
Phenotypic correction of Fanconi anemia cells in the murine bone marrow after carrier cell mediated delivery of lentiviral vector
Authors: Chakkaramakkil Verghese Santhosh , Goloviznina Natalya A. , Kurre Peter 
Published: November 2016

AbstractFanconi anemia (FA) is an autosomal-recessive disorder associated with hematopoietic failure and it is a candidate for hematopoietic stem cell (HSC)-directed gene therapy. However, the characteristically reduced HSC numbers found in FA patients, their ineffective mobilization from the marrow, and re-oxygenation damage during ex vivo manipulation have precluded clinical success using conventional in vitro approaches. We previously demonstrated that lentiviral vector (LV) particles reversibly attach to the cell surface where they gain protection from serum complement neutralization. We reasoned that cellular delivery of LV to the bone marrow niche could avoid detrimental losses during FA HSC mobilization and in vitro modification. Here, we demonstrate that a VSV-G pseudotyped lentivector, carrying the FANCC transgene, can be transmitted from carrier to bystander cells. In cell culture and transplantation models of FA, we further demonstrate that LV carrier cells migrate along SDF-1α gradients and transfer vector particles that stably integrate and phenotypically correct the characteristic DNA alkylator sensitivity in murine and human FA-deficient target bystander cells. Altogether, we demonstrate that cellular homing mechanisms can be harnessed for the functional phenotype correction in murine FA hematopoietic cells.
MarvelD3 regulates the c-Jun N-terminal kinase pathway during eye development in Xenopus
Authors: Vacca Barbara , Sanchez-Heras Elena , Steed Emily , Balda Maria S. , Ohnuma Shin-Ichi , Sasai Noriaki , Mayor Roberto , Matter Karl 
Published: November 2016

ABSTRACT
Ocular morphogenesis requires several signalling pathways controlling the expression of transcription factors and cell-cycle regulators. However, despite a well-known mechanism, the dialogue between those signals and factors remains to be unveiled. Here, we identify a requirement for MarvelD3, a tight junction transmembrane protein, in eye morphogenesis in Xenopus. MarvelD3 depletion led to an abnormally pigmented eye or even an eye-less phenotype, which was rescued by ectopic MarvelD3 expression. Altering MarvelD3 expression led to deregulated expression of cell-cycle regulators and transcription factors required for eye development. The eye phenotype was rescued by increased c-Jun terminal Kinase activation. Thus, MarvelD3 links tight junctions and modulation of the JNK pathway to eye morphogenesis.
Alternative exon usage creates novel transcript variants of tumor suppressor SHREW-1 gene with differential tissue expression profile
Authors: Klemmt Petra A. B. , Resch Eduard , Smyrek Isabell , Engels Knut , Stelzer Ernst H. K. , Starzinski-Powitz Anna 
Published: November 2016

ABSTRACTShrew-1, also called AJAP1, is a transmembrane protein associated with E-cadherin-mediated adherence junctions and a putative tumor suppressor. Apart from its interaction with β-catenin and involvement in E-cadherin internalization, little structure or function information exists. Here we explored shrew-1 expression during postnatal differentiation of mammary gland as a model system. Immunohistological analyses with antibodies against either the extracellular or the cytoplasmic domains of shrew-1 consistently revealed the expression of full-length shrew-1 in myoepithelial cells, but only part of it in luminal cells. While shrew-1 localization remained unaltered in myoepithelial cells, nuclear localization occurred in luminal cells during lactation. Based on these observations, we identified two unknown shrew-1 transcript variants encoding N-terminally truncated proteins. The smallest shrew-1 protein lacks the extracellular domain and is most likely the only variant present in luminal cells. RNA analyses of human tissues confirmed that the novel transcript variants of shrew-1 exist in vivo and exhibit a differential tissue expression profile. We conclude that our findings are essential for the understanding and interpretation of future functional and interactome analyses of shrew-1 variants.
RNA-dependent disassembly of nuclear bodies
Authors: Musinova Yana R. , Lisitsyna Olga M. , Sorokin Dmitry V. , Arifulin Eugene A. , Smirnova Tatiana A. , Zinovkin Roman A. , Potashnikova Daria M. , Vassetzky Yegor S. , Sheval Eugene V. 
Published: November 2016

ABSTRACT
Nuclear bodies are membraneless organelles that play important roles in genome functioning. A specific type of nuclear bodies known as interphase prenucleolar bodies (iPNBs) are formed in the nucleoplasm after hypotonic stress from partially disassembled nucleoli. iPNBs are then disassembled, and the nucleoli are reformed simultaneously. Here, we show that diffusion of B23 molecules (also known as nucleophosmin, NPM1) from iPNBs, but not fusion of iPNBs with the nucleoli, contributes to the transfer of B23 from iPNBs to the nucleoli. Maturation of pre-ribosomal RNAs (rRNAs) and the subsequent outflow of mature rRNAs from iPNBs led to the disassembly of iPNBs. We found that B23 transfer was dependent on the synthesis of pre-rRNA molecules in nucleoli; these pre-rRNA molecules interacted with B23 and led to its accumulation within nucleoli. The transfer of B23 between iPNBs and nucleoli was accomplished through a nucleoplasmic pool of B23, and increased nucleoplasmic B23 content retarded disassembly, whereas B23 depletion accelerated disassembly. Our results suggest that iPNB disassembly and nucleolus assembly might be coupled through RNA-dependent exchange of nucleolar proteins, creating a highly dynamic system with long-distance correlations between spatially distinct processes.
SIRT2 regulates nuclear envelope reassembly through ANKLE2 deacetylation
Authors: Kaufmann Tanja , Kukolj Eva , Brachner Andreas , Beltzung Etienne , Bruno Melania , Kostrhon Sebastian , Opravil Susanne , Hudecz Otto , Mechtler Karl , Warren Graham , Slade Dea 
Published: November 2016

ABSTRACT
Sirtuin 2 (SIRT2) is an NAD-dependent deacetylase known to regulate microtubule dynamics and cell cycle progression. SIRT2 has also been implicated in the pathology of cancer, neurodegenerative diseases and progeria. Here, we show that SIRT2 depletion or overexpression causes nuclear envelope reassembly defects. We link this phenotype to the recently identified regulator of nuclear envelope reassembly ANKLE2. ANKLE2 acetylation at K302 and phosphorylation at S662 are dynamically regulated throughout the cell cycle by SIRT2 and are essential for normal nuclear envelope reassembly. The function of SIRT2 therefore extends beyond the regulation of microtubules to include the regulation of nuclear envelope dynamics.