bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic Hydrocephalus Following Mumps Encephalitis: Neuropathological Correlates and Review
Authors: MacRae Cassie , Varma Hemant 
Published: December 2019

Abstract
Hydrocephalus is a rare and devastating complication of mumps encephalitis. The histopathological correlates of mumps infection in central nervous system tissues are not well-characterized. We present the case of a 54-year-old patient who suffered long-term neuropsychiatric sequelae and hydrocephalus as a consequence of a childhood mumps infection. Brain autopsy revealed significant dilation of the lateral and third ventricles. Aqueductal stenosis was not observed on premortem imaging or on gross examination. Histology revealed loss of ependymal epithelium throughout the aqueduct and ventricular system. Macrophage conglomerates were identified within the cerebral aqueduct at the level of the pons in addition to subjacent periaqueductal gliosis and scattered Rosenthal fibers. Together, these findings support primary ependymal injury as a pathophysiological mechanism in the development of chronic hydrocephalus following mumps infection. Finally, we review the existing literature and discuss potential mechanisms of disease.
An epidemiology report for primary central nervous system tumors in adolescents and young adults: a nationwide population-based study in France, 2008–2013
Authors: Ng Sam , Zouaoui Sonia , Bessaoud Faiza , Rigau Valérie , Roux Alexandre , Darlix Amélie , Bauchet Fabienne , Mathieu-Daudé Hélène , Trétarre Brigitte , Figarella-Branger Dominique , Pallud Johan , Frappaz Didier , Roujeau Thomas , Bauchet Luc 
Published: December 2019

Abstract

Background
Primary central nervous system tumors (PCNST) among adolescents and young adults (AYA, 15–39 y) have rarely been reported. We present a nationwide report of PCNST histologically confirmed in the French AYA population between 2008 and 2013.

Methods
Patients were identified through the French Brain Tumor Database (FBTDB), a national dataset that includes prospectively all histologically confirmed cases of PCNST in France. Patients aged 15 to 39 years with histologically confirmed PCNST diagnosed between 2008 and 2013 were included. For each of the 143 histological subtypes of PCNST, crude rates, sex, surgery, and age distribution were provided. To enable international comparisons, age-standardized incidence rates were adjusted to the world-standard, European, and USA populations.

Results
For 6 years, 9661 PCNST (males/females: 4701/4960) were histologically confirmed in the French AYA population. The overall crude rate was 8.15 per 100 000 person-years. Overall, age-standardized incidence rates were (per 100 000 person-years, population of reference: world/Europe/USA): 7.64/8.07/8.21, respectively. Among patients aged 15–24 years, the crude rate was 5.13 per 100 000. Among patients aged 25–39 years, the crude rate was 10.10 per 100 000. Age-standardized incidence rates were reported for each of the 143 histological subtypes. Moreover, for each histological subtype, data were detailed by sex, age, type of surgery (surgical resection or biopsy), and cryopreserved samples.

Conclusion
These data represent an exhaustive report of all histologically confirmed cases of PCNST with their frequency and distribution in the French AYA population in 2008–2013. For the first time in this age group, complete histological subtypes and rare tumor identification are detailed.
Par6 regulates cell cycle progression through enhancement of Akt/PI3K/GSK‐3β signaling pathway activation in glioma
Authors: Liu Pei , Zhu Chenchen , Luo Juanjuan , Lan Sheng , Su Dongsheng , Wang Qiongjin , Wei Zhe , Cui Wei , Xu Chuan , Yang Xiaojun 
Published: December 2019

AbstractAs the key factor of the polarity protein complex, Par6 not only regulates polarization processes, but also plays important roles in tumor metastasis and progression in many epithelium malignancy tumors. Here, we showed that Par6 is an essential component in glioma tumorigenesis. Our results indicated the aberrant expression of Par6 in malignant glioma tissues and cell lines. We found that the regulation of Par6 expression induces cell proliferation and tumor growth in vivo and in vitro. Additionally, RNA‐seq revealed the effects of Par6 were associated with cyclin D1‐regulated cell cycle progression in glioma cells. Moreover, our results demonstrated that the regulation of Par6 can enhance the activation of Akt/PI3K signaling pathway, and subsequently upregulate the expression level of GSK‐3β protein, which then regulate cyclin D1‐mediated cell cycle regulation. Furthermore, we found that TGF‐β‐induced the upregulation of Par6 expression may be involved in this process. The pathological analysis confirmed the correlation between Par6 expression and the prognosis in human glioma tissues, suggesting the regulation of Par6 expression regulates glioma tumorigenesis and progression. Thus, our findings showed that Par6 might be a potential biomarker for the diagnosis and providing a therapeutic strategy for the treatment of malignant glioma.
Post‐natal co‐development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets
Authors: Arnaud Alexis Pierre , Rome Véronique , Richard Marion , Formal Michèle , David‐Le Gall Sandrine , Boudry Gaëlle 
Published: December 2019

AbstractGut microbiota and intestinal barrier co‐develop after birth, establishing a homeostatic state whereby mucosal cells cohabit with commensal bacteria. We hypothesized that this post‐natal co‐development follows different timings depending on the intestinal site considered. Jejunal, ileal, and colonic luminal contents and mucosa were sampled in suckling piglets at post‐natal day (PND) 0, 2, 7, 14, and 28. Jejunal, ileal, and colonic luminal microbiota (evaluated by 16S DNA sequencing followed by beta‐diversity analysis) clustered at PND2 but colonic microbiota diverge afterwards (P < .05). Mucosal permeability, evaluated in Ussing chambers, increased with age in the jejunum and ileum (P < .05) but not the colon. Expression of pattern recognition receptor (PRR) exhibited different patterns (gradual or sharp increase, decrease, or no change with age, P < .05) depending on PRR and intestinal site considered. Principal component analysis of mucosa data revealed clear clustering of colonic samples, irrespective of the age and clustering of jejunal and ileal samples, with gradual changes with age. Correlation analysis highlighted three families correlating with mucosal parameters: Enterobacteriaceae in the jejunum, Peptostreptococcaceae in the ileum, and Micrococcaceae in the colon. In conclusion, small and large intestine display close microbiota composition early in life but distinct mucosal phenotype and follow very different post‐natal development.
Evaluating the Feasibility of an Emergency Department Physical Therapy Intervention for Acute Low Back Pain
Authors: Kim Howard S. , Strickland Kyle J. , Pinto Daniel , Arroyo Christina , Courtney D. Mark , McCarthy Danielle M. , Lambert Bruce L. 
Published: December 2019

Purpose:
Integration of physical therapists into the emergency department (ED) setting is a relatively new practice in the United States. It is currently unknown whether patients are able to retain the skills and knowledge delivered during a brief ED physical therapy (PT) intervention, and whether patients participate in recommended home exercises or follow-up for a return visit.

Methods:
This is a prospective feasibility study of 30 ED patients with acute low back pain who were evaluated by an ED physical therapist, given individualized instruction in 3 prescribed home exercises, and discharged home with both printed and online instructions of the 3 prescribed exercises. Enrolled patients returned 1 week after their initial ED visit for an in-person demonstrated performance evaluation of the prescribed home exercises; patients also self-reported the frequency of home exercise performance in the week after ED discharge.

Results:
Thirty patients were enrolled, and 27 patients (90.0%) returned for the in-person evaluation at a median of 7.5 days. The most frequently prescribed exercises were prone positioning to press up on elbows (70.4% of participants), transverse abdominal contraction with posterior pelvic tilt (70.4%), and supine lower trunk rotation (44.4%). Twenty of 27 patients (74.0%) were able to successfully demonstrate performance of all 3 prescribed exercises. Participants reported performing any home exercise a median of 3 times (interquartile range 2-5) in the week following their index ED visit.

Conclusions:
A brief PT intervention delivered in the ED for acute low back pain is feasible with respect to patient follow-up, demonstrated performance of prescribed home exercises, and participation in home exercise therapy.
Genetic Overlap Between Type 2 Diabetes and Depression in a Sri Lankan Population Twin Sample
Authors: Kan Carol , Jayaweera Kaushalya , Adikari Anushka , Siribaddana Sisira , Zavos Helena M.S. , Harber-Aschan Lisa , Sumathipala Athula , Hotopf Matthew , Ismail Khalida , Rijsdijk Frühling 
Published: December 2019

ABSTRACT

Objective
Results from twin studies examining the genetic overlap between type 2 diabetes and depression are currently inconclusive. This question has not been addressed in non-Western populations. We aimed to examine whether there are common genetic factors between type 2 diabetes and depression in a Sri Lankan population using genetic model-fitting analysis.

Method
The Colombo Twin and Singleton Study–Phase 2 consists of 2019 singletons, and 842 monozygotic and 578 dizygotic twin pairs. The primary outcomes were self-reported type 2 diabetes diagnosis and Beck Depression Inventory scores. Standard bivariate twin models were fitted to estimate the genetic and environmental (co)variance of type 2 diabetes and depression.

Results
In the best-fitting model, the phenotypic correlation between type 2 diabetes and depression was significant in female individuals only (r = 0.15 [0.08–0.21]). This association was primarily attributed to a significant genetic correlation between the traits (rA = 0.53 [0.19–0.98]).

Conclusions
In female individuals, but not male individuals, we found a significant genetic overlap between type 2 diabetes and depression in the context of a modest phenotypic correlation.
Challenges to achieving and maintaining viral suppression among children living with HIV
Authors: Kakkar Fatima , Lee Terry , Hawkes Michael T. , Brophy Jason , Lindy Samson , Singer Joel , Dieumegard Hinatea , Sauve Laura , Alimenti Ariane , Vaudry Wendy , Seigel Sandra , Tan Ben , Karatzios Christos , Lamarre Valerie , Read Stanley , Soudeyns Hugo , Bitnun Ari 
Published: December 2019

Objectives:
The objective of this study was to determine the time to, and durability of, viral suppression, among Canadian children living with HIV after initiation of combination antiretroviral therapy (cART).

Design:
Prospective, multicenter Canadian cohort study (Early Pediatric Initiation Canada Child Cure Cohort), using both prospective and retrospectively collected data.

Methods:
Kaplan–Meir survival estimates with Cox regression were used to determine the time to and risk factors for viral suppression, defined as two consecutive undetectable viral loads (<50 copies/ml) at least 30 days apart after initiation of cART.

Results:
A total of 228 children were enrolled between December 2014 and December 2018. The time to viral suppression was significantly shorter among children initiating cART after 5 ≤ 5 vs. years or less of age [adjusted hazard ratio (aHR) 1.57, 95% confidence interval (CI) 1.13–2.20], among those born after 2010 vs. prior (aHR 1.71, 95% CI 1.04–2.79), and among those without child protection services involvement (aHR 1.44, 95% CI 1.03–2.01). Overall, 27% of children had a viral rebound within 3 years of achieving viral suppression; the risk of viral rebound was significantly lower among children initiating cART after 5 vs. 5 years or less of age [adjusted odds ratio (aOR): 0.32, 95% CI 0.13–0.81], those whose families had not received social assistance (aOR 0.16, 95% CI 0.06–0.46), and females vs. males (aOR 0.51, 95% CI 0.26–0.99).

Conclusion:
Only 73% of the children in the Early Pediatric Initiation Canada Child Cure Cohort had maintained viral suppression 3 years after it was first achieved. Age at cART initiation, and socioeconomic factors were predictors of both time to viral suppression and risk of viral rebound in this cohort.
HIV preexposure prophylaxis with tenofovir disoproxil fumarate/emtricitabine and changes in kidney function and tubular health
Authors: Ascher Simon B. , Scherzer Rebecca , Estrella Michelle M. , Shigenaga Judy , Spaulding Kimberly A. , Glidden David V. , Mehrotra Megha L. , Defechereux Patricia , Gandhi Monica , Grant Robert M. , Shlipak Michael G. , Jotwani Vasantha 
Published: December 2019

Objective:
To evaluate the effects of HIV preexposure prophylaxis (PrEP) with tenofovir disoproxial fumurate (TDF)/emtricitabine (FTC) on kidney function and kidney tubular health.

Design:
The Iniciativa Profilaxis Pre-Exposicion open-label extension (iPrEx-OLE) study enrolled former PrEP trial participants to receive open-label TDF/FTC. This study included 123 iPrEx-OLE participants who demonstrated PrEP adherence.

Methods:
We compared estimated glomerular filtration rate calculated using serum creatinine (eGFRcr), serum cystatin C (eGFRcys), and in combination (eGFRcr-cys), and a panel of 14 urine biomarkers reflecting kidney tubular health before and 6 months after PrEP initiation.

Results:
At baseline, mean eGFRcr, eGFRcys, and eGFRcr-cys were 108.3, 107.0, and 111.1 ml/min per 1.73 m2, respectively. Six months after PrEP initiation, eGFRcr declined by −4% (95% CI: −5.7 to −2.4%), eGFRcys declined by −3.3% (95% CI: −8.3 to 1.9%), and eGFRcr-cys declined by −4.1% (95% CI: −7.5 to −0.7%). From the urine biomarker panel, α1-microglobulin and β2-microglobulin increased by 22.7% (95% CI: 11.8--34.7%) and 14.1% (95% CI: −6.1 to 38.6%), whereas chitinase-3-like 1 protein and monocyte chemoattractant protein-1 decreased by −37.7% (95% CI: −53.0 to −17.3%) and −15.6% (95% CI: −31.6 to 4.2%), respectively. Ten of the 14 urine biomarkers, including albumin, had estimated changes of less than 12% with wide confidence intervals.

Conclusion:
Six months of PrEP with TDF/FTC was associated with decreases in eGFRcr and eGFRcys. We also observed for the first time changes in flour of 14 urine biomarkers reflecting kidney tubular health. These findings demonstrate that PrEP has direct effects on eGFR and the proximal tubule.
Measuring the Position of the Mandibular Foramen in Relation to the Dentoalveolar Plane in Pierre Robin Patients: Establishing Safety of the Horizontal Osteotomy
Authors: Do Nicholas T. , Klement Kristen A. , Denny Arlen D. 
Published: December 2019

Background:Mandibular distraction with horizontal osteotomy of the ramus and vertical distraction vector has successfully treated airway obstruction in young Pierre Robin patients. Placing the osteotomy just above the dentoalveolar plane can minimize damage to the inferior alveolar nerve. This study maps the position of the mandibular foramen relative to the height of the dentoalveolar plane to demonstrate the safety of this technique in Pierre Robin neonates.Methods:Retrospective review of 3D CT scans of Pierre Robin patients was performed with inclusion criteria: ≤1 year of age, bilateral micrognathia requiring surgical intervention for airway (ie, tracheostomy versus mandibular distraction), no prior mandible surgery, and pre-operative 3D CT study. Demographic information collected included: age at CT scan, age at surgery, and genetic diagnosis. Using the 3D study of each patient's right mandible, a line at the level of the mandibular dentoalveolar plane was drawn across the lingual surface of the ramus and the distance to the mandibular foramen at a length perpendicular to the dentoalveolar plane line was then measured.Results:Fifteen patients were included in the study (at least 9 Pierre Robin). Average age at time of CT scan was 71.4 days old. The mandibular foramen was below the level of the dentoalveolar plane in all cases at an average distance of 4.7 mm. Average ramus height 46.2±13.4Conclusions:The dentoalveolar plane was consistently above the mandibular foramen in all patients. Thus, the horizontal corticotomy at a level just above the mandibular dentoalveolar plane spares the inferior alveolar nerve in neonatal Pierre Robin patients undergoing vertical vector mandibular distraction.
The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin
Authors: Maji Ajoy , Padinhateeri Ranjith , Mitra Mithun K. 
Published: December 2019

AbstractAn important question in the context of the 3D organization of chromosomes is the mechanism of formation of large loops between distant base pairs. Recent experiments suggest that the formation of loops might be mediated by Loop Extrusion Factor proteins like cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA, and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low effective diffusion constants leads to times that are unphysically large. The puzzle then is the following, how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle, and show that while at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration, they can reduce loop formation times due to a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone, and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes.
Nanopore long reads enable the first complete genome assembly of a MalaysianVibrio parahaemolyticusisolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease
Authors: Gan Han Ming , Austin Christopher M. 
Published: December 2019

AbstractBackgroundVibrio parahaemolyticusMVP1 was isolated from a Malaysian aquaculture farm affected with shrimp acute hepatopancreatic necrosis disease (AHPND). Its genome was previously sequenced on the Illumina MiSeq platform and assembledde novoproducing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood.MethodsThe genome of Vibrio parahaemolyticus MVP1 was sequenced on the Nanopore MinION device to obtain long reads that can span longer repeats and improve genome contiguity.De novogenome assembly was subsequently performed using long-read only assembler (Flye) followed by genome polishing as well as hybrid assembler (Unicycler).ResultsLong-read only assembly produced three complete circular MVP1 contigs consisting of chromosome 1, chromosome 2 and the pVa plasmid thatpirABvpbinary toxin genes. Polishing of the long read assembly with Illumina short reads was necessary to remove indel errors. The complete assembly of the pVa plasmid could not be achieved using Illumina reads due to the presence of identical repetitive elements flanking the binary toxin genes leading to multiple contigs. Whereas these regions were fully spanned by the Nanopore long reads resulting in a single contig. In addition, alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed the presence of a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of all publicly availableV. parahaemolyticusgenomes revealed the presence of a single AinS-family quorum-sensing system in this species that can be targeted for future microbial management.ConclusionsWe generated the first chromosome-scale genome assembly of a MalaysianpirABVp-bearingV. parahaemolyticusisolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features ofV. parahaemolyticusMVP1 that may be associated with host colonization and pathogenicity.
Fibroblast Protection ofBorrelia burgdorferifrom Doxycycline, Cefuroxime and Daptomycin Combination is Eliminated by Oregano or Carvacrol Essential Oil
Authors: Bai Chunxiang , Yang Hua , Cui Peng , Quan Rong , Zhang Ying 
Published: December 2019

AbstractBorrelia burgdorfericould be occasionally recovered from patients after antibiotic treatment, which indicates it may resist eradication by antibiotic and host defense mechanisms. Skin fibroblast cells have previously been shown to protect the killing ofB. burgdorferiby ceftriaxone, a powerful antibiotic commonly used to treat Lyme disease. In this study, we evaluated if fibroblast cells could also protect against the doxycycline+ cefuroxime+ daptomycin drug combination which has previously been shown to completely eradicate highly persistent biofilm-like microcolonies ofB. burgdorferi.To do so, we utilized a GFP-labeledB. burgdorferifor infection of murine fibroblast cells and assessed the effect of the drug combination on killing the bacteria in the presence or absence of the fibroblast cells. Surprisingly, we found that fibroblasts could protectB. burgdorferifrom being completely killed by the drug combination doxycycline, cefuroxime and daptomycin, which eradicatedB. burgdorfericompletely in the absence of fibroblast cells. Interestingly, addition of essential oil carvacrol or oregano at 0.1% could enhance the activity of the doxycycline+ cefuroxime+ daptomycin drug combination and led to complete eradication ofB. burgdorferieven in the presence of fibroblast cells. Further studies are needed to determine if the essential oil drug combinations could eradicate persistentB. burgdorferiinfection in vivo in animal models. Our study provides a useful and convenientex vivomodel for evaluating different drug regimens needed for developing more effective treatment of persistent Lyme disease in the future.