bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recovery process of bilaterally injured corticoreticulospinal tracts in a patient with subarachnoid hemorrhage
Authors: Jang Sung Ho , Chang Chul Hoon , Jung Young Jin , Seo You Sung 
Published: December 2018

Abstract

Rationale:
A few studies using diffusion tensor tractography (DTT) have demonstrated recovery of injured corticoreticulospinal tract (CRT) in patients with intracerebral hemorrhage and infarct. However, no study reported on a patient who showed peri-infarct reorganization of an injured CRT following a middle cerebral artery territory infarct.

Patient concerns:
A 56-year-old right-handed male patient was diagnosed as spontaneous subarachnoid hemorrhage (SAH) and intraventricular hemorrhage (IVH) and underwent clipping for a ruptured anterior communicating artery aneurysm and right frontal extraventricular drainage for IVH at the department of neurosurgery of a university hospital. After onset, he presented with complete weakness of both legs.

Diagnoses:
The patient was diagnosed as spontaneous SAH and IVH.

Interventions:
Clinical assessment and DTT were performed at 1, 3, 6, and 20 months after onset.

Outcomes:
The weakness of both legs showed slow recovery for 10 months until 11 months after onset (medical research council: 6 months; 3/3 and 11 months; 4/4). As a result, he was able to walk independently on an even floor at 6 months and on stairs at 11 months after onset. The discontinued both CRTs on 1-month DTT were restored to the cerebral cortex on 3-month DTT, and then thickened consecutively on 6-month and 20-month DTTs.

Lessons:
The recovery process of injured CRTs concurrent with recovery of leg weakness was demonstrated in a patient with SAH using DTT. This study has important implications in terms of regaining gait function by the recovery of bilaterally injured CRTs which was facilitated by the long-term rehabilitation.
Optical coherence tomography guided successful treatment without stent implantation in a patient with non-ST-segment elevation myocardial infarction caused by plaque rapture
Authors: Zhang Fei-Fei , Dang Yi , Hao Qing-Qing , Xie Yue-Tao , Li Shu-Ren , Qi Xiao-Yong 
Published: December 2018

Abstract

Rationale:
Primary percutaneous coronary intervention (PPCI) with immediate stenting provides effective revascularization. While the risks of no-reflow, stent thrombosis, stent undersizing, and malapposition reduced the benefits in patients with high burden thrombosis. Intravascular imaging, especially optical coherence tomography (OCT), offers potential in optimization of percutaneous coronary intervention.

Patient concerns:
A 51-year-old male underwent coronary angiography (CAG) due to chest pain with minimal ST-segment depression of the electrocardiogram.

Diagnoses:
Urgent CAG revealed burden thrombus in the mid left anterior descending coronary artery (LAD) with TIMI grade I distal flow.

Interventions:
After aspiration thrombectomy, OCT was used to evaluate the target lesion of non-ST-segment elevation myocardial infarction (NSTEMI) and conservative treatment without stent implantation was selected.

Outcomes:
CAG repeated 1 month after PPCI revealed TIMI grade III blood flow in LAD and only minimal stenosis in the target lesion. OCT showed a cavity formation due to plaque rupture and MLA increased after thrombus dissolution. Follow-up was uneventful at 6 months.

Lessons:
OCT may be useful imaging modality to identify the characteristic of culprit lesion of acute myocardial infarction and subsequently guide individual treatment.
The efficacy of first-line regimens for Helicobacter pylori eradication in different continents
Authors: Zamani Mohammad , Zamani Vahid , Derakhshan Mohammad H. , Shokri-Shirvani Javad 
Published: December 2018

Abstract

Background:
Striking prevalence of Helicobacter pylori infection has been convoluted with considerable resistance to various antibiotics worldwide. Although many eradication regimens have been introduced as the first-line therapies against H pylori, lack of appropriate multiple comparison studies makes hard to implement such results to the clinical practice. This project attempts to utilize a comprehensive network meta-analysis to pool the results of clinical trial comparing various first-line eradication therapies simultaneously in different continents.

Methods:
We will include all randomized controlled trials assessing the first-line regimens for treatment of H pylori published in last 10 years. We will search the databases of PubMed, EMBASE, Scopus, Web of Science and Cochrane Central Register of Controlled Trials, International Standard Randomised Controlled Trial Number registry, World Health Organisation International Clinical Trials Registry Platform, and ClinicalTrials.gov for randomized controlled trials published since January 2009 without language limitation. The primary and secondary outcomes will be H pylori eradication rate and adverse events, respectively. Subgroup analyses will be conducted for different continents. Two reviewers will independently contribute in study selection and data extraction. For evaluating quality of studies, Cochrane Collaboration tool score will be used. We will conduct network meta-analysis for treatment comparisons using STATA software version 13.

Results:
These findings will be submitted to a peer-reviewed journal for publication.

Conclusion:
Our results will provide the guidance for clinicians in deferent regions to select the best possible therapeutic regimen for treatment of H pylori infected patients.

Registration number:
This systematic review and network meta-analysis has been registered in the PROSPERO International Prospective Register of Systematic Reviews, with registration number CRD42017077061.
The Timed Up and Go Test in Children: Does Protocol Choice Matter? A Systematic Review
Authors: Verbecque Evi , Schepens Kirsten , Theré Joke , Schepens Bénédicte , Klingels Katrijn , Hallemans Ann 
Published: December 2018

Purpose:
Results on reliability and normative data for the Timed Up and Go test (TUG) in children who are developing typically are systematically reviewed.

Summary of Key Points:
Six different TUG protocols are presented for which normative data are available for ages 3 to 18 years. TUG time is consistent within and between raters and sessions and is influenced by age. The choice of protocol, self-selected versus fastest walking speed, and use of a motivational aspect and of the outcome calculation affect TUG time as well as its consistency within and between sessions.

Conclusions:
A standard protocol for the TUG is lacking and should be developed with attention to reliability.

Recommendations for Clinical Practice:
If the TUG is to be used as a screening tool for dynamic balance control, clinicians need to apply protocols that include fastest walking speed motivation.
Enhancer features that drive formation of transcriptional condensates
Authors: Shrinivas Krishna , Sabari Benjamin R. , Coffey Eliot L. , Klein Isaac A. , Boija Ann , Zamudio Alicia V. , Schuijers Jurian , Hannett Nancy M. , Sharp Phillip A. , Young Richard A. , Chakraborty Arup K. 
Published: December 2018

SummaryEnhancers, DNA elements that regulate gene expression, contain transcription factor (TF) binding sites. TFs bind short sequence motifs that are present throughout the genome at much higher frequency than active enhancers, and so the features that define active enhancers are not well understood. We show that DNA elements with TF binding site valency, density, and binding affinity above sharply defined thresholds can recruit TFs and coactivators in condensates by the cooperative process of phase separation. We demonstrate that weak cooperative interactions between IDRs of TFs and coactivators in combination with specific TF-DNA interactions are required for forming such transcriptional condensates. IDR-IDR interactions are relatively non-specific with the same molecular interactions shared by many TFs and coactivators, and phase separation is a universal cooperative mechanism. Therefore, whether a genomic locus is an enhancer that can assemble a transcriptional condensate is determined predominantly by its cognate TFs’ binding site valency and density.
Historical abundance and distributions of Salpa thompsoni hot spots in the Southern Ocean, with projections for further ocean warming
Authors: Słomska Angelika Wanda , Panasiuk Anna , Weydmann-Zwolicka Agata , Wawrzynek-Borejko Justyna , Konik Marta , Siegel Volker 
Published: December 2018

AbstractOver the last three decades, a significant variability in Salpa thompsoni occurrence has been observed as a response to the environmental fluctuations of the Southern Ocean ecosystem, e.g. changes in sea surface temperature as well as shrinking of ice-cover extent around the cold Antarctic waters.This study presents the historical data of salps abundance from the southwest Atlantic Sector of the Southern Ocean and covers time span of 20 years. Presented dataset allowed to track previous fluctuations in Antarctic salp abundance and enabled to combine their distribution with different bottom depth, thermal and ice conditions. The subsequent goal of this work was to reveal hot spots of salps location and to predict the future range of S. thompsoni distribution with upcoming climate warming in the next 50 years.Results of our study revealed that the highest salp number was located mostly in the shallow shelf waters with ice-cover and lower temperature. In the studied area, Salpa thompsoni hot spot distributions have been located mostly around Elephant Island but also within islands around Brensfield and Gerlache Straits, as well as to the south near the cold Bellingshausen Sea. The inference of future salp distribution demonstrated that the range of S. thompsoni would presumably move southwards enlarging their habitat area by nearly 500 000 km2.
Increasing the resolution and precision of psychiatric GWAS by re-imputing summary statistics using a large, diverse reference panel
Authors: Chatzinakos Chris , Lee Donghyung , Cai Na , Vladimirov Vladimir I. , Webb Bradley T. , Riley Brien P. , Flint Jonathan , Kendler Kenneth S. , Ressler Kerry J. , Daskalakis Nikolaos P. , Bacanu Silviu-Alin 
Published: December 2018

ABSTRACTGenotype imputation across populations of mixed ancestry is critical for optimal discovery in large-scale genome-wide association studies (GWAS). Methods for direct imputation of GWAS summary statistics were previously shown to be practically as accurate as summary statistics produced after raw genotype imputation, while incurring orders of magnitude lower computational burden. Given that direct imputation needs a precise estimation of linkage-disequilibrium (LD) and that most of the methods using a small reference panel e.g., ~2,500 subject coming from the 1000 Genome Project, there is a great need for much larger and more diverse reference panels. To accurately estimate the LD needed for an exhaustive analysis of any cosmopolitan cohort, we developed DISTMIX2. DISTMIX2: i) uses a much larger and more diverse reference panel and ii) estimates weights of ethnic mixture based solely on Z-scores (when AFs are not available). We applied DISTMIX2 to GWAS summary statistics from the Psychiatric Genetic Consortium (PGC). DISTMIX2 uncovered signals in numerous new regions, with most of these findings coming from the rarer variants. Rarer variants provide much sharper location for the signals compared with common variants, as the LD for rare variants extends over a lower distance than for common ones. For example, while the original PGC post-traumatic stress disorder (PTSD) study found only 3 marginal signals for common variants, we now uncover a very strong signal for a rare variant in PKN2, a gene associated with neuronal and hippocampal development. Thus, DISTMIX2 provides a robust and fast (re)imputation approach for most Psychiatric GWAS studies.
A novel non-invasive method to detect gut barrier related changes during a gastrointestinal nematode infection
Authors: Ahmed Norus , Affinass Nicole , Heitlinger Emanuel , Kühl Anja A. , Xenophontos Natasa , Jarquin Victor Hugo , Jost Jenny , Steinfelder Svenja , Hartmann Susanne 
Published: December 2018

AbstractCurrently, methods for monitoring changes of gut barrier integrity and the associated immune response via non-invasive means are limited. Therefore, we aimed to develop a novel non-invasive technique to investigate immunological host responses representing gut barrier changes in response to infection. We identified the mucous layer on feces from mice to be mainly composed of exfoliated intestinal epithelial cells. Expression of RELM-β, a gene prominently expressed in intestinal nematode infections, was used as an indicator of intestinal cellular barrier changes to infection. RELM-β was detected as early as 6 days post-infection (dpi) in exfoliated epithelial cells. Interestingly, RELM-β expression also mirrored the quality of the immune response, with higher amounts being detectable in a secondary infection and in high dose nematode infection in laboratory mice. This technique was also applicable to captured worm-infected wild house mice. We have therefore developed a novel non-invasive method reflecting gut barrier changes associated with alterations in cellular responses to a gastrointestinal nematode infection.
Semantic Probing: Feasibility of using sequential probes to decode what is on a user’s mind
Authors: Dijkstra Karen , Farquhar Jason , Desain Peter 
Published: December 2018

ABSTRACTIn this paper, we investigate the feasibility of using multiple sequential probe words to decode their relatedness to an active semantic concept on a user’s mind from the respective electrophysiological brain responses. If feasible, this relatedness information could be used by a Brain Computer Interface to infer that semantic concept, by integrating the knowledge of the relationship between the multiple probe words and the ‘unknown’ target. Such a BCI can take advantage of the N400: an event related potential that is sensitive to semantic content of a stimulus in relation to an established semantic context. However, it is unknown whether the N400 is suited for the multiple probing paradigm we propose, as other intervening words might distract from the established context (i.e., the target word). We perform an experiment in which we present up to ten words after an initial target word, and find no attenuation of the strength of the N400 in grand average ERPs and no decrease in classification accuracy for probes occurring later in the sequences. These results lay the groundwork for the development of a BCI that infers the concept on a user’s mind through repeated probing.
Revisiting the window of opportunity for co-transcriptional splicing efficiency and fidelity
Authors: Aslanzadeh Vahid , Beggs Jean D. 
Published: December 2018

AbstractRecently, we reported that changes in transcription elongation rate affect the efficiency and fidelity of precursor mRNA (pre-mRNA) splicing, especially of ribosomal protein (RP) transcripts. Here, we analyse these results in more detail, finding that the majority of RP transcripts with non-consensus 5’ splice sites have reduced splicing efficiency with faster transcription elongation, and improved efficiency with slower elongation, as might be predicted by the “window of opportunity” model for co-transcriptional splicing. In contrast, both faster and slower elongation reduce splicing fidelity, often for the same splicing events, and both faster and slower transcription increase fidelity with a different set of splicing events. We propose that certain non-consensus 5’ splice sites in ribosomal protein transcripts confer a stronger effect of transcription elongation rate on splicing efficiency, possibly by causing a rate-limiting step that delays activation of spliceosomes. The effects of different rates of transcription elongation on splicing fidelity are more difficult to explain by a simple window of opportunity model. We discuss these new findings in the context of current models of co-transcriptional splicing and splicing fidelity.
Image-based Phenotyping and Disease Screening of Multiple Populations for resistance to Verticillium dahliae in cultivated strawberry Fragaria x ananassa
Authors: Cockerton H.M. , Li B. , Vickerstaff R. J. , Eyre C. A. , Sargent D. J. , Armitage A. D. , Marina-Montes C. , Garcia A. , Passey A. J. , Simpson D. W. , Harrison R. J. 
Published: December 2018

1.0AbstractVerticillium dahliae is a highly detrimental pathogen of soil cultivated strawberry (Fragaria x ananassa). Breeding of Verticillium wilt resistance into commercially viable strawberry cultivars can help mitigate the impact of the disease. In this study we describe novel sources of resistance identified in biparental strawberry populations, creating a wealth of data for breeders to exploit. Pathogen-informed experiments have allowed the differentiation of subclade-specific resistance responses, through studying V. dahliae subclade II-1 specific resistance in the cultivar ‘Redgauntlet’ and subclade II-2 specific resistance in ‘Fenella’ and ‘Chandler’.A large-scale low-cost phenotyping platform was developed utilising automated unmanned vehicles and near infrared imaging cameras to assess field-based disease trials. The images were used to calculate disease susceptibility for infected plants through the normalized difference vegetation index score. The automated disease scores showed a strong correlation with the manual scores.A co-dominant resistant QTL; FaRVd3D, present in both ‘Redgauntlet’ and ‘Hapil’ cultivars exhibited a major effect of 18.3 % when the two resistance alleles were combined. Another allele, FaRVd5D, identified in the ‘Emily’ cultivar was associated with an increase in Verticillium wilt susceptibility of 17.2%, though whether this allele truly represents a susceptibility factor requires further research, due to the nature of the bi-parental cross.Markers identified in bi-parental populations were validated across a set of 92 accessions to determine whether they remained closely linked to resistance genes in the wider germplasm. The resistant markers FaRVd2B from ‘Redgauntlet’ and FaRVd6D from ‘Chandler’ were associated with resistance across the wider germplasm. Furthermore, comparison of imaging versus manual phenotyping revealed the automated platform could identify three out of four disease resistance markers. As such, this automated wilt disease phenotyping platform is considered to be a good, time saving, substitute for manual assessment.
Blockade of β-adrenergic receptor signaling improves cancer vaccine efficacy through its effect on naive CD8+T-cell priming
Authors: Daher Clara , Vimeux Lene , Stoeva Ralitsa , Peranzoni Elisa , Bismuth Georges , Donnadieu Emmanuel , Bercovici Nadège , Trautmann Alain , Feuillet Vincent 
Published: December 2018

Abstractβ-adrenergic receptor (β-AR) signaling, by acting directly on tumor cells and angiogenesis, has been showed to exert pro-tumoral effects. Growing evidence also suggests that β-AR expressed by immune cells affect the associated anti-tumor immune response. However, how and where β-AR signaling impinges the anti-tumor immune response is still unclear. Using a mouse model of vaccine-based immunotherapy, we show here that propranolol, a non-selective β-blocker, strongly improved the efficacy of the vaccine by enhancing the frequency of CD8+T lymphocytes infiltrating the tumor (TILs). However, propranolol had no obvious effect on the reactivity of CD8+TILs, a result further strengthened byex-vivoexperiments showing that these cells are insensitive to AR signaling triggered by adrenaline or noradrenaline. In contrast, we show that naive CD8+T cell activation was strongly inhibited by β-AR signaling and that the beneficial effect of propranolol mainly occurred during their initial priming phase. We also demonstrate that the differential sensitivity of CD8+TILs and naive CD8+T cells is related to their activation status sinceinvitro-activated CD8+T cells behaved similarly to CD8+TILs, both exhibiting a down-regulation of the β2-AR expression. These results reveal that the initial priming phase of the anti-tumor response in the tumor-draining lymph node is a decisive part of the suppressive effect of β-AR signaling on the CD8+T-cell response against cancer. These findings provide a rationale for the strategic use of clinically available β-blockers in patients to improve cancer immunotherapies such as anti-cancer vaccination strategies.
Imbalanced Nucleocytoskeletal Connections Create Common Polarity Defects in Progeria and Physiological Aging
Authors: Chang Wakam , Wang Yuexia , Gant Luxton G.W. , Östlund Cecilia , Worman Howard J. , Gundersen Gregg G. 
Published: December 2018

AbstractStudies of the accelerated aging disorder Hutchinson-Gilford progeria syndrome (HGPS) can potentially reveal cellular defects associated with physiological aging. HGPS results from expression and abnormal nuclear envelope association of a farnesylated, truncated variant of prelamin A called progerin. We surveyed the diffusional mobilities of nuclear membrane proteins to identify proximal effects of progerin expression. The mobilities of three proteins were reduced in fibroblasts from children with HGPS compared to normal fibroblasts: SUN2, nesprin-2G, and emerin. These proteins function together in nuclear movement and centrosome orientation in fibroblasts polarizing for migration. Both processes were impaired in fibroblasts from children with HGPS and in NIH3T3 fibroblasts expressing progerin, but were restored by inhibiting protein farnesylation. Progerin affected both the coupling of the nucleus to actin cables and the oriented flow of the cables necessary for nuclear movement and centrosome orientation. Progerin overexpression increased levels of SUN1, which couples the nucleus to microtubules through nesprin-2G and dynein, and microtubule association with the nucleus. Reducing microtubule-nuclear connections through SUN1 depletion or dynein inhibition rescued the polarity defects. Nuclear movement and centrosome orientation were also defective in fibroblasts from normal individuals over 60 years old and both defects were rescued by reducing the increased level of SUN1 in these cells or inhibiting dynein. Our results identify imbalanced nuclear engagement of the cytoskeleton (microtubules, high; actin filaments, low) as the basis for intrinsic cell polarity defects in HGPS and physiological aging and suggest that rebalancing the connections can ameliorate the defects.SignificanceThe rare, premature aging syndrome HGPS arises from expression of a pathological prelamin A variant, termed progerin. Studies of progerin may identify treatments for HGPS and reveal novel cellular and molecular characteristics of normal aging. Here, we show that progerin selectively affects mobilities of three nuclear membrane proteins, SUN2, nesprin-2G and emerin that position the nucleus and establish cell polarity essential for migration. We find that both processes are defective in fibroblasts from children with HGPS and aged (> 60 years) individuals. The mechanism underlying these defects is excessive interaction of the nucleus with microtubules. Our work identifies nuclear-based defects in cell polarization as intrinsic factors in premature and physiological aging and suggests means for correcting them.