bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improvement in Hepatic Fibrosis Biomarkers Associated With Chemokine Receptor Inactivation Through Mutation or Therapeutic Blockade
Authors: Sherman Kenneth E , Abdel-Hameed Enass , Rouster Susan D , Shata Mohamed Tarek M , Blackard Jason T , Safaie Parham , Kroner Barbara , Preiss Liliana , Horn Paul S , Kottilil Shyam 
Published: September 2018

AbstractBackgroundThe C-C chemokine receptor Type 5 (CCR5) is a key receptor for human immunodeficiency virus type 1 (HIV-1) entry into T-cells and a variant allele, CCR5 delta-32, is associated with decreased viral replication and disease progression. Active HIV-1 replication is highly associated with accelerated rates of hepatic fibrosis. We postulated that CCR5 plays a role in the development of hepatic fibrosis and evaluated the longitudinal effect of natural or drug-induced CCR5 mutation and blockade on biomarkers of liver fibrosis in HIV-1 patients.MethodsTo accomplish this goal, we examined 2 distinct cohorts. First, we evaluated fibrosis markers in the Multicenter Hemophilia Cohort Studies (MHCS), which included subjects with HIV and hepatitis C virus (HCV) coinfection with the CCR5 delta-32 allele. We also evaluated an HIV-1 infected cohort that was treated with a dual CCR5/CCR2 antagonist, cenicriviroc. The enhanced liver fibrosis (ELF) index was validated against liver histology obtained from HCV/HIV and HCV patients and demonstrated strong correlation with fibrosis stage.ResultsIn both the MHCS patients and patients treated with cenicriviroc, CCR5 mutation or blockade was associated with a significant decrease in the ELF index. Among the patients with the delta-32 allele, the ELF index rate significantly decreased in sequential samples as compared to CCR5 wild-type patients (P = .043). This was not observed in control subjects treated with efavirenz nor with a lower dose of 100 mg cenicriviroc.ConclusionThese findings suggest that hepatic fibrosis in HIV-1 infected patients can be modulated by the mutation of CCR5 and/or use of CCR5/CCR2 blockade agents.Clinical Trials RegistrationNCT01338883.
The fascinating world of non-coding RNA and how it may help to unravel the mysteries of tooth movement regulation
Authors: Proff Peter , Kirschneck Christian 
Published: September 2018

Summary
The innovative study presented by Huang and co-workers in this issue of the European Journal of Orthodontics is one of the first giving insight into the mostly disregarded world of non-coding ribonucleic acids in orthodontics. In other fields of science non-coding ribonucleic acids have been shown to play a major role in the regulation of cell metabolism as well as the aetiology of diseases such as cancer, Alzheimer’s disease, and periodontitis. Their pilot study on the possible function of differentially expressed long non-coding ribonucleic acids during mechanical compression of periodontal ligament stem cells, as well as methodological approach of whole-transcriptome sequencing with bioinformatory analyses, provides ample possibilities for future basic orthodontic research, which will hopefully greatly expand our knowledge of tooth movement regulation. This field could provide new therapeutic opportunities and diagnostic and treatment aids for orthodontists as well as our patients. This commentary will discuss the implications and importance of the findings of Huang and co-workers in the context of current research in orthodontics and molecular biology.
Children’s motivation overcame parental hesitation: active school transportation in Sweden
Authors: Rutberg Stina , Lindqvist Anna-Karin 
Published: September 2018

Abstract
To meet the recommendation of 60 min of daily physical activity, children can be encouraged to walk or bike to school, which is known as active school transportation (AST). The aim of this study was to describe parents’ attitudes to AST and to explore their experience when implementing interventions to promote it. To explore parent’s experiences, we collected pre- and post-intervention data via three questionnaires, using both closed and open questioning techniques. The pre-intervention questionnaire informed development of the intervention. Open-ended questions (pre- and post-) were analyzed with qualitative content analysis. In the intervention, there were 42 children, with 63 parents answering pre-intervention questionnaires and 44 answering a post-intervention questionnaire. The analysis resulted in one main theme: children’s motivation and active travel reduces parents’ perception of problems, along with three subthemes: parental concerns and suggestions for solutions, children’s motivation guides parental choice of transport mode, and trying it changes attitudes. In conclusion, it is beneficial to use the enthusiasm and motivation of children to overcome parental hesitation with AST. In addition, it is critical to acknowledge their concerns, as they are the gatekeepers to the children’s use of AST and it is valuable to empower parents when designing relevant interventions. Interventions to increase AST could preferably target changed behavior, and parents’ confidence in their children’s ability to use active transport in a safe and effective way, vs focusing on changing parental attitudes.
Loss of CRB2 in Müller glial cells modifies a CRB1-associated retinitis pigmentosa phenotype into a Leber congenital amaurosis phenotype
Authors: Quinn Peter M , Mulder Aat A , Henrique Alves C , Desrosiers Mélissa , de Vries Sharon I , Klooster Jan , Dalkara Deniz , Koster Abraham J , Jost Carolina R , Wijnholds Jan 
Published: September 2018

Abstract
Variations in the human Crumbs homolog-1 (CRB1) gene lead to an array of retinal dystrophies including early onset of retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) in children. To investigate the physiological roles of CRB1 and CRB2 in retinal Müller glial cells (MGCs), we analysed mouse retinas lacking both proteins in MGC. The peripheral retina showed a faster progression of dystrophy than the central retina. The central retina showed retinal folds, disruptions at the outer limiting membrane, protrusion of photoreceptor nuclei into the inner and outer segment layers and ingression of photoreceptor nuclei into the photoreceptor synaptic layer. The peripheral retina showed a complete loss of the photoreceptor synapse layer, intermingling of photoreceptor nuclei within the inner nuclear layer and ectopic photoreceptor cells in the ganglion cell layer. Electroretinography showed severe attenuation of the scotopic a-wave at 1 month of age with responses below detection levels at 3 months of age. The double knockout mouse retinas mimicked a phenotype equivalent to a clinical LCA phenotype due to loss of CRB1. Localization of CRB1 and CRB2 in non-human primate (NHP) retinas was analyzed at the ultrastructural level. We found that NHP CRB1 and CRB2 proteins localized to the subapical region adjacent to adherens junctions at the outer limiting membrane in MGC and photoreceptors. Our data suggest that loss of CRB2 in MGC aggravates the CRB1-associated RP-like phenotype towards an LCA-like phenotype.
Extent of Resection and Residual Tumor Thresholds for Postoperative Total Seizure Freedom in Epileptic Adult Patients Harboring a Supratentorial Diffuse Low-Grade Glioma
Authors: Still Megan E H , Roux Alexandre , Huberfeld Gilles , Bauchet Luc , Baron Marie-Hélène , Fontaine Denys , Blonski Marie , Mandonnet Emmanuel , Guillevin Remy , Guyotat Jacques , Taillandier Luc , Capelle Laurent , Duffau Hugues , Pallud Johan 
Published: September 2018

Abstract

BACKGROUND
Epileptic seizures impair quality of life in diffuse low-grade glioma (DLGG) patients. Tumor resection significantly impacts postoperative seizure control, but the precise extent of resection (EOR) required for optimal seizure control is not clear yet.

OBJECTIVE
To identify the EOR and residual tumor volume that correlated to postoperative seizure control, defined as a total seizure freedom (Class 1A in reference to Engel classification system) with and without antiepileptic drugs in patients undergoing surgical resection of supratentorial DLGG.

METHODS
A retrospective review was conducted of all patients who underwent first-line surgical resection of supratentorial DLGG who presented with preoperative seizures without adjuvant oncological treatment. EOR and residual tumor volume were quantified from pre- and post-operative magnetic resonance imagings. Receiver operating characteristic curves were plotted to determine the EOR and residual tumor volume that corresponded to optimal postoperative seizure control.

RESULTS
Of the 346 included patients, 65.5% had controlled seizures postoperatively, with higher age at resection (adjusted OR per unit, 1.03 [95% confidence interval:1.01-1.06], P = .043) and higher percentage of resection (adjusted OR per unit, 1.02 [95% confidence interval:1.00-1.03], P < .001) found as independent predictors of postoperative seizure control. Optimal EOR was ≥91% and optimal residual tumor volume was ≤19 cc to improve postoperative seizure control.

CONCLUSION
Postoperative seizure control is more likely when EOR is ≥91% and/or when residual tumor volume is ≤19 cc in supratentorial DLGG gliomas who present with seizures. Resected peritumoral cortex should, however, be taken into account in future studies.
Longitudinal Cognitive Performance in Individuals at Ultrahigh Risk for Psychosis: A 10-year Follow-up
Authors: Allott Kelly , Wood Stephen J , Yuen Hok Pan , Yung Alison R , Nelson Barnaby , Brewer Warrick J , Spiliotacopoulos Daniela , Bruxner Annie , Simmons Magenta , Broussard Christina , Mallawaarachchi Sumudu , Pantelis Christos , McGorry Patrick D , Lin Ashleigh 
Published: September 2018

AbstractIt remains unclear whether the onset of psychosis is associated with deterioration in cognitive performance. The aim of this study was to examine the course of cognitive performance in an ultrahigh risk (UHR) cohort, and whether change in cognition is associated with transition to psychosis and change in functioning. Consecutive admissions to Personal Assessment and Crisis Evaluation (PACE) Clinic between May 1994 and July 2000 who had completed a comprehensive cognitive assessment at baseline and follow-up were eligible (N = 80). Follow-up ranged from 7.3 to 13.4 years (M = 10.4 years; SD = 1.5). In the whole sample, significant improvements were observed on the Similarities (P = .03), Information (P < .01), Digit Symbol Coding (P < .01), and Trail Making Test-B (P = .01) tasks, whereas performance on the Rey Auditory Verbal Learning Test (Trials 1–3) declined significantly (P < .01) over the follow-up period. Change in performance on cognitive measures was not significantly associated with transition status. Taking time to transition into account, those who transitioned after 1 year showed significant decline on Digit Symbol Coding, whereas those who did not transition improved on this measure (P = .01; effect size [ES] = 0.85). Small positive correlations were observed between improvements in functioning and improvements in performance on Digit Symbol Coding and Arithmetic (0.24, P = .03 and 0.28, P = .01, respectively). In summary, the onset of psychosis was not associated with deterioration in cognitive ability. However, specific findings suggest that immediate verbal learning and memory, and processing speed may be relevant domains for future risk models and early intervention research in UHR individuals.
Prostaglandin F2α-induced TGFβ-PMEPA1 pathway is a critical mediator of epithelial plasticity and ovarian carcinoma progression
Authors: Jiménez-Segovia Alba , Mota Alba , Rojo-Sebastián Alejandro , Barrocal Beatriz , Rynne-Vidal Angela , García-Bermejo María-Laura , Gómez-Bris Raquel , Hawinkels Lukas J.A.C. , Sandoval Pilar , Garcia-Escudero Ramon , López-Cabrera Manuel , Moreno-Bueno Gema , Fresno Manuel , Stamatakis Konstantinos 
Published: September 2018

ABSTRACTProstaglandin (PG) F2αhas been scarcely studied in cancer. We have identified a new role for PGF2αin ovarian cancer, stimulating the production of TGFβ and the consequent induction of PMEPA1. We show that this induction increases cell plasticity and proliferation, enhancing tumor growth through PMEPA1. Thus, PMEPA1 overexpression in ovarian carcinoma cells, significantly increased cell proliferation rates, whereas PMEPA1 silencing decreased proliferation. In addition, PMEPA1 overexpression buffered TGFβ signaling, via reduction of SMAD-dependent signaling. PMEPA1 overexpressing cells acquired an epithelial morphology, associated to higher E-cadherin expression levels while β-catenin nuclear translocation was inhibited. Interestingly, in mouse xenografts, PMEPA1 overexpressing ovarian cells had a clear survival and proliferative advantage, resulting in higher metastatic capacity, while PMEPA1 silencing had the opposite effect. Furthermore, high PMEPA1 expression in a cohort of advanced ovarian cancer patients was observed, correlating with E-cadherin expression. Most importantly, high PMEPA1 mRNA levels were associated with lower patient survival.SignificanceThis work identifies Prostaglandin F2αas an inducer, through NFAT, of TGFβ and together with this up-regulate PMEPA1, which is identified both as a drug target and as a prognostic biomarker in ovarian tumors, potentially useful in clinical practice.
Computationally designing antimicrobial peptides forAcinectobacter Baumannii
Authors: Majumder Ayan , Biswal Malay Ranjan , Prakash Meher K. 
Published: September 2018

AbstractAcinetobacter Baumannii,which is mostly contracted in hospital stays, has been developing resistance to all available antibiotics, including the last line of drugs, such as carbapenem. Because of its quick adaptation there is an immediate need to design new antibiotics, possibly antimicrobial peptides (AMPs) to which bacteria do not develop resistance easily. Our threefold goal was to curate the available activity of AMPs on the same strain ofA. Baumannii, build a neural network model for predicting their activity and use it to rationally pre-screen for lead generation from the thousands of naturally occurring AMPs. By curating and analyzing the recent activity data from 81 AMPs on ATCC 19606 strain, we develop a quantitative AMP activity prediction model. We selected three other models with comparable performance against a test set with known activities. With the goal of inspiring further studies on AMP drug candidates and their rational shortlisting, we made activity predictions for the entire database of AMPs using all the models. To handle the uncertainty of training with a small data set, highlighted peptides which had consistent results from all models.
Impact of recreational fisheries management on fish biodiversity in gravel pit lakes with contrasts to unmanaged lakes
Authors: Matern S. , Emmrich M. , Klefoth T. , Wolter C. , Wegener N. , Arlinghaus R. 
Published: September 2018

AbstractGravel pit lakes constitute novel ecosystems that can be colonized by fishes through natural or anthropogenic pathways. Many of these man-made lakes are used by recreational anglers and experience regular fish stocking. Recreationally unmanaged gravel pits may also be affected by fish introductions, e.g., through illegal fish releases, thereby contributing to the formation of site-specific communities. Our objective was to compare the fish biodiversity in gravel pit lakes with and without the recent influence of recreational fisheries management. We sampled 23 small (< 20 ha) gravel pit lakes (16 managed and 7 unmanaged) in north-western Germany and compared fish community and diversity metrics obtained using littoral electrofishing and multimesh gillnet catch per unit effort data. Given the size of the lakes we sampled we expected species poor communities and elevated fish diversity in the managed systems due to stocking. The two lake types were primarily mesotrophic and did not differ in key abiotic and biotic environmental characteristics. Both lakes types hosted similar fish abundance and biomass, but were substantially different in terms of the fish community structure and species richness. Fish were present in all lakes with at least three species. We discovered a higher α-diversity and a lower β-diversity in managed gravel pit lakes compared to unmanaged lakes. Thus, recreational fisheries management appeared to foster homogenization of fish communities, likely because fisheries managers stock these lakes with desired fish species (e.g., piscivorous fishes and large bodied cyprinids). However, we also detected anthropogenic pathways in the colonization of unmanaged gravel pit lakes, presumably from illegal releases by private people. Importantly, hardly any non-native species were detected in the gravel pits we studied, suggesting that recreational fisheries management not necessarily promotes the spread of exotic species.Significance StatementLittle is known about fish communities in artificially created gravel pit lakes. We compared those managed by recreational fishers with those lacking fisheries management in north-western Germany. We found fishes in all gravel pit lakes and demonstrated a higher α-diversity but more homogenized fish communities in managed gravel pit lakes compared to unmanaged lakes. We did not detect the establishment of relevant abundances of non-natives fishes despite intensive fisheries management.
PolyA tracks and poly-lysine repeats are the Achilles heel ofPlasmodium falciparum
Authors: Djuranovic Slavica Pavlovic , Erath Jessey , Andrews Ryan J , Bayguinov Peter O , Chung Joyce J , Chalker Douglas L , Fitzpatrick James AJ , Moss Walter N , Szczesny Pawel , Djuranovic Sergej 
Published: September 2018

AbstractPlasmodium falciparum, the causative agent of human malaria, is an apicomplexan parasite with a complex, multi-host life cycle. Sixty percent of transcripts from its extreme AT-rich (81%) genome possess coding polyadenosine (polyA) runs, distinguishing the parasite from its hosts and other sequenced organisms. Recent studies indicate that transcripts with polyA runs encoding poly-lysine are hot spots for ribosome stalling and frameshifting, eliciting mRNA surveillance pathways and attenuating protein synthesis in the majority of prokaryotic and eukaryotic organisms. Here, we show that theP. falciparumtranslational machinery is paradigm-breaking. Using bioinformatic and biochemical approaches, we demonstrate that both endogenous genes and reporter sequences containing long polyA runs are efficiently and accurately transcribed and translated inP. falciparumcells. Translation of polyA tracks in the parasite does not elicit any response from mRNA surveillance pathways usually seen in host human cells or organisms with similar AT content. The translation efficiency and accuracy of the parasite protein synthesis machinery reveals a unique role of ribosomes in the evolution and adaptation ofP. falciparumto an AU-rich transcriptome and polybasic amino sequences. Finally, we show that the ability ofP. falciparumto synthesize long poly-lysine repeats has given this parasite a unique protein exportome and an advantage in infectivity that can be suppressed by addition of exogenous poly-basic polymers.
Logarithmic molecular sampling for next-generation sequencing
Authors: Horn Caroline , Salzman Julia 
Published: September 2018

AbstractNext-generation sequencing enables measurement of chemical and biological signals at high throughput and falling cost. Conventional sequencing requires increasing sampling depth to improve signal to noise discrimination, a costly procedure that is also impossible when biological material is limiting. We introduce a new general sampling theory, Molecular Entropy encodinG (MEG), which uses biophysical principles to functionally encode molecular abundance before sampling. SeQUential DepletIon and enriCHment (SQUICH) is a specific example of MEG that, in theory and simulation, enables sampling at a logarithmic or better rate to achieve the same precision as attained with conventional sequencing. In proof-of-principle experiments, SQUICH reduces sequencing depth by a factor of 10. MEG is a general solution to a fundamental problem in molecular sampling and enables a new generation of efficient, precise molecular measurement at logarithmic or better sampling depth.
Generation of four iPSC lines from peripheral blood mononuclear cells (PBMCs) of an Attention Deficit Hyperactivity Disorder (ADHD) individual and a healthy sibling in an Australia-Caucasian family
Authors: Tong Janette , Lee Kyung Min , Liu Xiaodong , Nefzger Christian M , Vijayakumar Prasidhee , Hawi Ziarih , Pang Ken C , Parish Clare L , Polo Jose M , Bellgrove Mark A 
Published: September 2018

AbstractPeripheral blood mononuclear cells were donated by a male teenager with clinically diagnosed Attention Deficit Hyperactivity Disorder under the Diagnostic and Statistical Manual of Mental Disorders IV criteria and his unaffected male sibling. Induced pluripotent stem cells were developed using integration-free Sendai Reprogramming factors containing OCT, SOX2, KLF4, and c-MYC. All four iPSC lines displayed pluripotent cell morphology, pluripotency-associated factors at protein level, alkaline phosphatase enzymatic activity, male karyotype of 46, XY, and in vitro differentiation capacity into all the three germ layers and negative for Mycoplasma.
lncDIFF: a novel distribution-free method for differential expression analysis of long non-coding RNA
Authors: Li Qian , Yu Xiaoqing , Chaudhary Ritu , Slebos Robbert JC , Chung Christine H. , Wang Xuefeng 
Published: September 2018

ABSTRACTMotivationLong non-coding RNA expression data has been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing does not effectively accommodate low abundant genes, as commonly observed in lncRNA. We propose a novel and robust statistical method lncDIFF to detect differential expressed (DE) genes without assuming the true density on normalized counts.ResultslncDIFF adopts the generalized linear model with zero-inflated exponential quasi likelihood to estimate group effect on normalized counts, and employs the likelihood ratio test to detect differential expressed genes. The proposed method and tool is suitable for data processed with standard RNA-Seq preprocessing and normalization pipelines. Simulation results illustrate that lncDIFF detects DE genes with more power and lower false discovery rate regardless of the data pattern. The analysis on a head and neck squamous cell carcinomas study also confirms that lncDIFF has better sensitivity in identifying novel lncRNA genes with relatively large fold change and prognostic value.Availability and ImplementationlncDIFF is an R package available athttps://github.com/qianli10000/lncDIFF.Supplementary InformationSupplementary Data are available at Bioinformatics online.
A simple, robust, and low-cost method to produce the PURE cell - free system
Authors: Lavickova Barbora , Maerkl Sebastian J. 
Published: September 2018

AbstractWe demonstrate a simple, robust, and low-cost method for producing the PURE cell-free transcription-translation system. Our OnePot PURE system achieved a protein synthesis yield of 156 µg/mL at a cost of 0.09 USD/µL, leading to a 14-fold improvement in cost normalized protein synthesis yield over existing PURE systems. The OnePot method makes the PURE system easy to generate and allows it to be readily optimized and modified.