bluuebunny/crossref_metadata_2025 huggingface dataset:
Control of septin filament flexibility and bundling by subunit composition and nucleotide interactions
Authors: Khan Anum , Newby Jay , Gladfelter Amy S.
Published: January 2018

Septins self-assemble into heteromeric rods and filaments to act as scaffolds and modulate membrane properties. How cells tune the biophysical properties of septin filaments to control filament flexibility and length, and in turn the size, shape, and position of higher-order septin structures, is not well understood. We examined how rod composition and nucleotide availability influence physical properties of septins such as annealing, fragmentation, bundling, and bending. We found that septin complexes have symmetric termini, even when both Shs1 and Cdc11 are coexpressed. The relative proportion of Cdc11/Shs1 septin complexes controls the biophysical properties of filaments and influences the rate of annealing, fragmentation, and filament flexibility. Additionally, the presence and apparent exchange of guanine nucleotide also alters filament length and bundling. An Shs1 mutant that is predicted to alter nucleotide hydrolysis has altered filament length and dynamics in cells and impacts cell morphogenesis. These data show that modulating filament properties through rod composition and nucleotide binding can control formation of septin assemblies that have distinct physical properties and functions.
I Will Give You My Vote but Not My Money: Preferences for Public versus Private Action in Addressing Social Issues
Authors: Norwood Franklin Bailey , Tonsor Glynn , Lusk Jayson L
Published: January 2018

This study explores the extent to which individuals will support public action but, in its absence, will not commit their own voluntary efforts. An internet survey was administered to over 3,500 individuals with hypothetical scenarios in which they could donate their own money toward a cause and/or support government action. When asked to choose between public or private action, most chose a combination of the two, suggesting that public and private partnerships are the preferred vehicle for solutions to social problems. Close to 20% indicated they would vote for laws to confront an issue but not contribute their own private donations.
Microarray is an efficient tool for circRNA profiling
Authors: Li Shasha , Teng Shuaishuai , Xu Junquan , Su Guannan , Zhang Yu , Zhao Jianqing , Zhang Suwei , Wang Haiyan , Qin Wenyan , Lu Zhi John , Guo Yong , Zhu Qianyong , Wang Dong
Published: January 2018

Circular RNAs (circRNAs) are emerging as a new class of endogenous and regulatory noncoding RNAs in latest years. With the widespread application of RNA sequencing (RNA-seq) technology and bioinformatics prediction, large numbers of circRNAs have been identified. However, at present, we lack a comprehensive characterization of all these circRNAs in interested samples. In this study, we integrated 87 935 circRNAs sequences that cover most of circRNAs identified till now represented in circBase to design microarray probes targeting back-splice site of each circRNA to profile expression of those circRNAs. By comparing the circRNA detection efficiency of RNA-seq with this circRNA microarray, we revealed that microarray is more efficient than RNA-seq for circRNA profiling. Then, we found ∼80 000 circRNAs were expressed in cervical tumors and matched normal tissues, and ∼25 000 of them were differently expressed. Notably, many of these circRNAs detected by this microarray can be validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) or RNA-seq. Strikingly, as many as ∼18 000 circRNAs could be robustly detected in cell-free plasma samples, and the expression of ∼2700 of them differed after surgery for tumor removal. Our findings provided a comprehensive and genome-wide characterization of circRNAs in paired normal tissues and tumors and plasma samples from multiple individuals. In addition, we also provide a rich resource with 41 microarray data sets and 10 RNA-seq data sets and strong evidences for circRNA expression in cervical cancer. In conclusion, circRNAs could be efficiently profiled by circRNA microarray to target their reported back-splice sites in interested samples.
PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling
Authors: Na Joong Chae , Lee Jong-Chan , Rhee Je-Keun , Shin Soo-Yong
Published: January 2018

Motivation

Single-individual haplotyping (SIH) is critical in genomic association studies and genetic diseases analysis. However, most genomic analysis studies do not perform haplotype-phasing analysis due to its complexity. Several computational methods have been developed to solve the SIH problem, but these approaches have not generated sufficiently reliable haplotypes.

Results

Here, we propose a novel SIH algorithm, called PEATH (Probabilistic Evolutionary Algorithm with Toggling for Haplotyping), to achieve more accurate and reliable haplotyping. The proposed PEATH method was compared to the most recent algorithms in terms of the phased length, N50 length, switch error rate and minimum error correction. The PEATH algorithm consistently provides the best phase and N50 lengths, as long as possible, given datasets. In addition, verification of the simulation data demonstrated that the PEATH method outperforms other methods on high noisy data. Additionally, the experimental results of a real dataset confirmed that the PEATH method achieved comparable or better accuracy.

Availability and implementation

Source code of PEATH is available at https://github.com/jcna99/PEATH.

Supplementary information

Supplementary data are available at Bioinformatics online.
Potential of Human Nucleus Pulposus-Like Cells Derived From Umbilical Cord to Treat Degenerative Disc Disease
Authors: Perez-Cruet Mick , Beeravolu Naimisha , McKee Christina , Brougham Jared , Khan Irfan , Bakshi Shreeya , Chaudhry G Rasul
Published: January 2018

BACKGROUND

Degenerative disc disease (DDD) is a common spinal disorder that manifests with neck and lower back pain caused by the degeneration of intervertebral discs (IVDs). Currently, there is no treatment to cure this debilitating ailment.

OBJECTIVE

To investigate the potential of nucleus pulposus (NP)-like cells (NPCs) derived from human umbilical cord mesenchymal stem cells (MSCs) to restore degenerated IVDs using a rabbit DDD model.

METHODS

NPCs differentiated from MSCs were characterized using quantitative real-time reverse transcription polymerase chain reaction and immunocytochemical analysis. MSCs and NPCs were labeled with fluorescent dye, PKH26, and transplanted into degenerated IVDs of a rabbit model of DDD (n = 9 each). Magnetic resonance imaging of the IVDs was performed before and after IVD degeneration, and following cell transplantation. IVDs were extracted 8 wk post-transplantation and analyzed by various biochemical, immunohistological, and molecular techniques.

RESULTS

NPC derivatives of MSCs expressed known NP-specific genes, SOX9, ACAN, COL2, FOXF1, and KRT19. Transplanted cells survived, dispersed, and integrated into the degenerated IVDs. IVDs augmented with NPCs showed significant improvement in the histology, cellularity, sulfated glycosaminoglycan and water contents of the NP. In addition, expression of human genes, SOX9, ACAN, COL2, FOXF1, KRT19, PAX6, CA12, and COMP, as well as proteins, SOX9, ACAN, COL2, and FOXF1, suggest NP biosynthesis due to transplantation of NPCs. Based on these results, a molecular mechanism for NP regeneration was proposed.

CONCLUSION

The findings of this study demonstrating feasibility and efficacy of NPCs to regenerate NP should spur interest for clinical studies to treat DDD using cell therapy.
Current management of distal biceps tears
Authors: Howard Michael
Published: January 2018

Although not reported to be common, rupture of the distal biceps tendon is an injury that results in a loss of supination and flexion strength. The injury is most commonly caused by eccentric load on a flexed elbow. At the time of injury, a noticeable “pop or tear” is usually experienced and a clinical deformity is often apparent. Current treatment for this injury is often anatomic surgical reattachment of the tendon to the radial tuberosity. This article is a brief review highlighting recent literature in the past year that adds to our understanding of treatment.
Cohesive Polydensified Matrix Hyaluronic Acid for the Treatment of Etched-In Fine Facial Lines: A 6-Month, Open-Label Clinical Trial
Authors: Black Jeanette M. , Gross Todd M. , Murcia Crystal L. , Jones Derek H.
Published: January 2018

BACKGROUND

Available hyaluronic acid dermal fillers have unique biophysical properties that influence their clinical utility, longevity, and aesthetic outcomes.

OBJECTIVE

To evaluate the effectiveness and durability of a cohesive polydensified matrix hyaluronic acid dermal filler (CPM-HA) for the treatment of etched-in fine facial lines.

MATERIALS AND METHODS

Subjects with etched-in fine lines of the forehead, cutaneous lip, melolabial folds, nasolabial folds, and/or radial cheek received treatment with CPM-HA mixed with lidocaine and epinephrine, with an optional touch-up treatment at Week 2, if deemed necessary. Response to treatment (as measured by the Merz Aesthetics Scales, Lemperle Facial Wrinkle Scales, and subject self-assessment) and safety/tolerability were monitored over the course of 26 weeks.

RESULTS

Thirty-one subjects received treatment with CPM-HA to 1 or more facial areas. All 5 treatment areas showed clinically meaningful and statistically significant improvements in average clinician rating scale scores at all study visits (p < .001 vs baseline). Most subjects reported maintained improvement from baseline of 50% or more throughout the 26-week study. Injection site reactions were mild and resolved without intervention.

CONCLUSION

Cohesive polydensified matrix hyaluronic acid dermal filler treatment was well tolerated and provided consistent and durable improvement in the appearance of a diverse range of etched-in fine facial lines.
The Infectious and Noninfectious Etiology, Clinical Picture and Outcome of Neutropenia in Immunocompetent Hospitalized Children
Authors: David Odeya , Fruchtman Yariv , Sergienko Ruslan , Kapelushnik Joseph , Leibovitz Eugene
Published: January 2018

Background:

Acquired neutropenia in immunocompetent children is common, and its differential diagnosis ranges from benign causes to life-threatening diseases. We described the etiology, clinical picture and outcome of new-onset neutropenia in immunocompetent children assessed in the emergency department and hospitalized at our medical center.

Methods:

Previously healthy children admitted with neutropenia (absolute neutrophil count <1.5 × 109/L) were included. Serious bacterial infections were defined as culture-positive blood, urine, cerebrospinal fluid, articular fluid or stool infections, pneumonia, Brucellosis and Rickettsiosis.

Results:

A total of 601 patients (5 days–202 months old) were enrolled; 3 (0.5%), 48 (8%), 165 (27.5%) and 385 (64%) had absolute neutrophil counts <0.2, 0.2–0.5, 0.5–1.0 and 1.0–1.5 × 109/L, respectively. Associated leukopenia and thrombocytopenia were diagnosed in 186 (39%) and 71 (11.8%) patients. Three hundred sixteen of 601 (52.6%) and 519 of 601 (86.4%) were <2 or 36 months of age, respectively. Fever at admission was present in 27.6% patients. Serious bacterial infections were diagnosed in 106 (17.6%) patients. Brucellosis and rickettsiosis were diagnosed in 8 of 52 (15.4%) and 9 of 39 (23.1%) tests obtained. Respiratory syncytial virus was diagnosed in 17 of 33 (51.5%) nasal washes. An infectious etiology was determined in 171 (28.5%) patients. Acute leukemia was diagnosed in 6 patients. A significant correlation was found between resolution of neutropenia and patient age, infectious etiology and severity of neutropenia.

Conclusions:

(1) Severe neutropenia was rare; (2) More than half of patients were <2 months of age; (3) An infectious etiology was diagnosed in a high number of patients, and serious bacterial infections were frequent and (4) Brucella spp. and rickettsial infections were frequent etiologies associated with neutropenia in our setting.
Novel approach to characterising individuals with low back-related leg pain: cluster identification with latent class analysis and 12-month follow-up
Authors: Stynes Siobhán , Konstantinou Kika , Ogollah Reuben , Hay Elaine M. , Dunn Kate M.
Published: January 2018

Traditionally, low back-related leg pain (LBLP) is diagnosed clinically as referred leg pain or sciatica (nerve root involvement). However, within the spectrum of LBLP, we hypothesised that there may be other unrecognised patient subgroups. This study aimed to identify clusters of patients with LBLP using latent class analysis and describe their clinical course. The study population was 609 LBLP primary care consulters. Variables from clinical assessment were included in the latent class analysis. Characteristics of the statistically identified clusters were compared, and their clinical course over 1 year was described. A 5 cluster solution was optimal. Cluster 1 (n = 104) had mild leg pain severity and was considered to represent a referred leg pain group with no clinical signs, suggesting nerve root involvement (sciatica). Cluster 2 (n = 122), cluster 3 (n = 188), and cluster 4 (n = 69) had mild, moderate, and severe pain and disability, respectively, and response to clinical assessment items suggested categories of mild, moderate, and severe sciatica. Cluster 5 (n = 126) had high pain and disability, longer pain duration, and more comorbidities and was difficult to map to a clinical diagnosis. Most improvement for pain and disability was seen in the first 4 months for all clusters. At 12 months, the proportion of patients reporting recovery ranged from 27% for cluster 5 to 45% for cluster 2 (mild sciatica). This is the first study that empirically shows the variability in profile and clinical course of patients with LBLP including sciatica. More homogenous groups were identified, which could be considered in future clinical and research settings.
Factors Associated With Delayed Discharge on General Medicine Service at an Academic Medical Center
Authors: Rohatgi Nidhi , Kane Marlena , Winget Marcy , Haji-Sheikhi Farnoosh , Ahuja Neera
Published: January 2018

Lack of collaboration between care teams and patients/families has been associated with delayed discharge from the hospital. In this study, we determine whether patients' awareness of the estimated date of discharge (EDD) was associated with a decrease in delayed discharge, and determine the factors associated with a delayed discharge. A total of 221 patients admitted to the General Medicine service between July and September 2014 were included in the study. Estimated date of discharge was identified within 36 hours of admission. The bedside nurse communicated this EDD to the patient/family. Patients were interviewed to identify whether they were aware of their EDD. Bedside nurses were interviewed to identify barriers to discharge. In our study, 49.8% of the patients had a delayed discharge. Patients who were aware of their EDD were less likely to have a delayed discharge (odds ratio [OR], 0.3 [95% confidence interval (CI), 0.1–0.6], p < .001). Patients who were discharged on Saturday or Sunday (OR, 4.8 [95% CI, 1.7–14.6], p < .001) and patients who were waiting for physicians' consult (OR, 4.5 [95% CI, 1.6–14.4], p = .007) were more likely to have a delayed discharge. Early identification of the EDD and communicating it with the care team and the patient/family, mobilizing resources for safe weekend discharges, and creating efficient process for consultations might decrease delayed discharges.
Both α-1-antitrypsin Z phenotypes and low caeruloplasmin levels are over-represented in alcohol and nonalcoholic fatty liver disease cirrhotic patients undergoing liver transplant in Ireland
Authors: El-Rayah El-Gaily A. , Twomey Patrick J. , Wallace Eleanor M. , McCormick Peter A.
Published: January 2018

Objectives

Alcoholic liver disease and nonalcoholic fatty liver disease (NAFLD) are steatotic liver diseases and major causes of cirrhosis. Only a minority of patients with risk factors develop cirrhosis and genetic cofactors may be important in pathogenesis. Mutations in the Wilson’s and α-1-antitrypsin genes are not uncommon and we speculated that they may act as cofactors.

Methods

We investigated α-1-antitrypsin phenotyes and caeruloplasmin levels in patients undergoing elective liver transplantation. We compared patients with alcohol and NAFLD with nonsteatotic liver disease patients: viral hepatitis B or C, autoimmune hepatitis, primary biliary cholangitis and primary sclerosing cholangitis.

Results

Two hundred and thirty-one patients were included in the study. Pretransplant caeruloplasmin levels and α-1-antitrypsin phenotypes were available in 197 and 112 patients, respectively. α-1-Antitrypsin Z phenotypes were significantly more common in the alcohol and NAFLD group: 12/56 versus 3/56 (P<0.05). Serum caeruloplasmin (0.3±0.01 vs. 0.39±0.01 g/l, P<0.01) and serum copper levels (13.5±0.9 vs. 19.3±0.9 μmol/l, P<0.01) were significantly lower in the alcohol and NAFLD patients compared with the viral and autoimmune patients.

Conclusion

In this study, we found the α-1-antitrypsin Z phenotype was more common, and serum caeruloplasmin and copper levels were lower in patients with fatty liver diseases. We suggest that mutations in the α-1-antitrypsin and Wilson’s genes may act as cofactors in the pathogenesis of fatty liver diseases.
Effects of Interruptions on Triage Process in Emergency Department
Authors: Johnson Kimberly D. , Gillespie Gordon L. , Vance Kimberly
Published: January 2018

For 130 million people seeking emergency treatment in the United States, incomplete or inaccurate triage examination can result in delays, which could compromise patient outcomes. The purpose of this study was to identify triage interruptions and determine how interruptions affect the triage process. A significant difference was seen in triage duration between interrupted and uninterrupted interviews. Understanding the impact of interruptions on patient outcomes will allow nurses and other health care providers to develop interventions to mitigate the impact.
Renal Replacement Therapy in the Critically Ill Child*
Authors: Westrope Claire A. , Fleming Sarah , Kapetanstrataki Melpo , Parslow Roger C. , Morris Kevin P.
Published: January 2018

Objectives:

Although renal replacement therapy is widely used in critically ill children, there have been few comprehensive population-based studies of its use. This article describes renal replacement therapy use, and associated outcomes, in critically ill children across the United Kingdom in the largest cohort study of this patient group.

Design:

A retrospective observational study using prospectively collected data.

Setting:

Data from the Pediatric Intensive Care Audit Network database which collects data on all children admitted to U.K. PICUs.

Patients:

Children (< 16 yr) in PICU who received renal replacement therapy between January 1, 2005, and December 31, 2012, were identified.

Interventions:

Individual-level data including age, underlying diagnosis, modality (peritoneal dialysis and continuous extracorporeal techniques [continuous renal replacement therapy]), duration of renal replacement therapy, PICU length of stay, and survival were extracted.

Measurements and Main Results:

Three-thousand eight-hundred twenty-five of 129,809 PICU admissions (2.9%) received renal replacement therapy in 30 of 33 centers. Volumes of renal replacement therapy varied considerably from 0% to 8.6% of PICU admissions per unit, but volume was not associated with patient survival. Overall survival to PICU discharge (73.8%) was higher than previous reports. Mortality risk was related to age, with lower risk in older children compared with neonates (odds ratio, 0.6; 95% CI, 0.5–0.8) although mortality did not increase over the age of 1 year; mode of renal replacement therapy, with lower risk in peritoneal dialysis than continuous renal replacement therapy methodologies (odds ratio, 0.7; 0.5–0.9); duration of renal replacement therapy (odds ratio, 1.02/d; 95% CI, 1.01–1.04); and primary diagnosis, with the lowest survival in liver disease patients (53.9%).

Conclusions:

This study describes current renal replacement therapy use across the United Kingdom and associated outcomes. We describe a number of factors associated with outcome, including age, underlying diagnosis, and renal replacement therapy modality which will need to be factored into future trial design.
Gadolinium Accumulation in the Deep Cerebellar Nuclei and Globus Pallidus After Exposure to Linear but Not Macrocyclic Gadolinium-Based Contrast Agents in a Retrospective Pig Study With High Similarity to Clinical Conditions
Authors: Boyken Janina , Frenzel Thomas , Lohrke Jessica , Jost Gregor , Pietsch Hubertus
Published: January 2018

Objective

The aim of this retrospective study was to determine the gadolinium (Gd) concentration in different brain areas in a pig cohort that received repeated administration of Gd-based contrast agents (GBCAs) at standard doses over several years, comparable with a clinical setting.

Material and Methods

Brain tissue was collected from 13 Göttingen mini pigs that had received repeated intravenous injections of gadopentetate dimeglumine (Gd-DTPA; Magnevist) and/or gadobutrol (Gadovist). The animals have been included in several preclinical imaging studies since 2008 and received cumulative Gd doses ranging from 7 to 129 mmol per animal over an extended period. Two animals with no history of administration of GBCA were included as controls. Brain autopsies were performed not earlier than 8 and not later than 38 months after the last GBCA application. Tissues from multiple brain areas including cerebellar and cerebral deep nuclei, cerebellar and cerebral cortex, and pons were analyzed for Gd using inductively coupled plasma mass spectrometry.

Results

Of the 13 animals, 8 received up to 48 injections of gadobutrol and Gd-DTPA and 5 received up to 29 injections of gadobutrol only. In animals that had received both Gd-DTPA and gadobutrol, a median (interquartile range) Gd concentration of 1.0 nmol/g tissue (0.44-1.42) was measured in the cerebellar nuclei and 0.53 nmol/g (0.29-0.62) in the globus pallidus. The Gd concentration in these areas in gadobutrol-only animals was 50-fold lower with median concentrations of 0.02 nmol/g (0.01-0.02) for cerebellar nuclei and 0.01 nmol/g (0.01-0.01) for globus pallidus and was comparable with control animals with no GBCA history. Accordingly, in animals that received both GBCAs, the amount of residual Gd correlated with the administered dose of Gd-DTPA (P ≤ 0.002) but not with the total Gd dose, consisting of Gd-DTPA and gadobutrol. The Gd concentration in cortical tissue and in the pons was very low (≤0.07 nmol/g tissue) in all animals analyzed.

Conclusion

Multiple exposure to macrocyclic gadobutrol is not associated with Gd deposition in brain tissue of healthy pigs. A single additional administration of linear Gd-DTPA is sufficient for Gd accumulation in the nucleus dentatus and globus pallidus, underlining the importance of obtaining a complete GBCA history in clinical studies.
Posterior Compartment Surgery Provides No Differential Benefit for Defecatory Symptoms Before or After Concomitant Mesh-Augmented Apical Suspension
Authors: Arunachalam Divya , Hale Douglass S. , Heit Michael H.
Published: January 2018

Objectives

The aim of this study was to determine the value of posterior compartment surgery during concomitant mesh-augmented apical suspension by comparing obstructed defecatory symptoms after laparoscopic sacrocolpopexy (LSC) with LSC with posterior repair (LSC + PR) and laparoscopic sacrocolpoperineopexy (LSCP) procedures.

Methods

This was a retrospective cohort study of women who underwent LSC, LSC + PR, and LSCP between July 2007 and July 2016 at a tertiary referral center in Indianapolis, Ind. Our primary outcome was differential change in Colorectal-Anal Distress Inventory (CRADI-8) and Colorectal-Anal Impact Questionnaire (CRAIQ-7) scores between the groups including patient-specific symptoms of splinting, straining, incomplete emptying, and pain with defecation. Our secondary outcomes were the rates of postoperative persistent, new, and resolved obstructed defecation symptoms. Anatomic outcomes were also compared between the groups as measured by change in Pelvic Organ Prolapse Quantification System points Ap, GH, and PB.

Results

A total of 312 women were included in the study (47 LSC, 133 LSC + PR, and 132 LSCP), with a median follow-up time of 366 days. The majority of patients who underwent surgery had stage III pelvic organ prolapse (61%). Baseline demographics were similar between groups, including preoperative CRADI-8 and CRAIQ-7 scores. All surgical groups demonstrated improvement in CRADI-8 and CRAIQ-7 scores postoperatively (P < 0.001). However, despite differential change in Pelvic Organ Prolapse Quantification System points Ap, GH, and PB, there was no change in CRADI-8 and CRAIQ-7 scores or rates of persistent, new, and resolved symptoms of splinting to defecate, incomplete emptying, and pain with defecation between the groups. The only factor that seemed to be differentially improved by the addition of a posterior compartment repair was postoperative straining. There was a greater rate of de novo straining in the LSC group compared with LSCP (P = 0.01) (LSC + PR v LSCP, P = NS, for both).

Conclusions

We cannot recommend posterior compartment surgery as providing any patient-centered benefit beyond improved cosmesis because the addition of perineal body stabilization either before (LSCP) or posterior repair after (LSC + PR) concomitant mesh-augmented apical suspension did not differentially affect bowel symptoms compared with LSC alone.
Unique perceptuomotor control of stone hammers in wild monkeys
Authors: Mangalam Madhur , Pacheco Matheus Maia , Izar Patrícia , Visalberghi Elisabetta , Fragaszy Dorothy Munkenbeck
Published: January 2018

We analysed the patterns of coordination of striking movement and perceptuomotor control of stone hammers in wild bearded capuchin monkeys,
Sapajus libidinosus
as they cracked open palm nut using hammers of different mass, a habitual behaviour in our study population. We aimed to determine why these monkeys cannot produce conchoidally fractured flakes as do contemporary human knappers or as did prehistoric hominin knappers. We found that the monkeys altered their patterns of coordination of movement to accommodate changes in hammer mass. By altering their patterns of coordination, the monkeys kept the strike's amplitude and the hammer's velocity at impact constant with respect to hammer mass. In doing so, the hammer's kinetic energy at impact—which determines the propagation of a fracture/crack in a nut—varied across hammers of different mass. The monkeys did not control the hammer's kinetic energy at impact, the key parameter a perceiver-actor should control while knapping stones. These findings support the hypothesis that the perceptuomotor control of stone hammers in wild bearded capuchin monkeys is inadequate to produce conchoidally fractured flakes by knapping stones, as do humans.
Incremental distribution of strontium and zinc in great ape and fossil hominin cementum using synchrotron X-ray fluorescence mapping
Authors: Dean Christopher , Le Cabec Adeline , Spiers Kathryn , Zhang Yi , Garrevoet Jan
Published: January 2018

Cementum and the incremental markings it contains have been widely studied as a means of ageing animals and retrieving information about diet and nutrition. The distribution of trace elements in great ape and fossil hominin cementum has not been studied previously. Synchrotron X-ray fluorescence (SXRF) enables rapid scanning of large tissue areas with high resolution of elemental distributions. First, we used SXRF to map calcium, phosphorus, strontium and zinc distributions in great ape dentine and cementum. At higher resolution, we compared zinc and strontium distributions in cellular and acellular cementum in regions where clear incremental markings were expressed. We then mapped trace element distributions in fossil hominin dentine and cementum from the 1.55–1.65 million year old site of Koobi Fora, Kenya. Zinc, in particular, is a precise marker of cementum increments in great apes, and is retained in fossil hominin cementum, but does not correspond well with the more diffuse fluctuations observed in strontium distribution. Cementum is unusual among mineralized tissues in retaining so much zinc. This is known to reduce the acid solubility of hydroxyapatite and so may confer resistance to resorption by osteoclasts in the dynamic remodelling environment of the periodontal ligament and alveolar bone.
Reference values of gait using APDM movement monitoring inertial sensor system
Authors: Fang Xin , Liu Chuandao , Jiang Zhongli
Published: January 2018

Normal gait data reported show variability depending on specific equipment and techniques. Reference values of initial contact angle (ICA) and toe-off angle (TOA) are still lacking. We present a normative gait database of 292 healthy adults using the APDM Movement Monitoring inertial sensor system across a large age span of adulthood. Data were collected as participants completed a walk test for 2 min. Normalization was conducted and two factors were extracted by a factor analysis. Six reference gait variables under each factor were presented and the impacts of age, gender and BMI were evaluated by MANOVA and ANCOVA. ICA and TOA were highly correlated with speed and stride length. ICA was significantly larger in men, whereas larger TOA could be observed in women in all age groups but could not achieve significant difference. Overweight and obese adults walked at significantly lower speed, shorter stride length, reduced cadence and longer gait cycle duration. TOA was smaller in the obese group. However, the differences in ICA were not significant. Reference gait values described herein were valuable for identifying and interpreting gait phenomena using APDM®, contributing to rehabilitation of gait dysfunction.
Transcriptomic inspection revealed a possible pathway regulating the formation of the high-quality brush hair in Chinese Haimen goat (
Capra hircus
)
Authors: Ji Dejun , Yang Bo , Li Yongjun , Cai Miaoying , Zhang Wei , Cheng Guohu , Guo Haiyan
Published: January 2018

The high-quality brush hair, or Type III brush hair, is coarse hair but with a tip and little medulla, which uniquely grows in the cervical carina of Chinese Haimen goat (
Capra hircus
). To unveil the mechanism of the formation of Type III brush hair in Haimen goats, transcriptomic RNAseq technology was used for screening of differentially expressed genes (DEGs) in the skin samples of the Type III and the non-Type III hair goats, and these DEGs were analysed by KEGG pathway analysis. The results showed that a total of 295 DEGs were obtained, mainly from three main functional types: cellular component, molecular function and biological process. These DEGs were mainly enriched in three KEGG pathways, such as protein processing in endoplasmic reticulum, MAPK, and complement and coagulation cascades. These DEGs gave hints to a possible mechanism, under which heat stress possibly initiated the formation. The study provided some useful biological information, which could give a new view about the roles of certain factors in hair growth and give hints on the mechanism of the formation of the Type III brush hair in Chinese Haimen goat.
Parenting behaviour is highly heritable in male stickleback
Authors: Bell Alison M. , Trapp Rebecca , Keagy Jason
Published: January 2018

Parental care is critical for fitness, yet little is known about its genetic basis. Here, we estimate the heritability of parenting behaviour in a species famous for its diversity and its behavioural repertoire: three-spined stickleback (
Gasterosteus aculeatus
). Male three-spined stickleback are the sole providers of parental care that is necessary for offspring survival; therefore, this system offers the opportunity to study the inheritance of parental behaviour when selection is primarily acting on males. Fanning behaviour is a conspicuous parental behaviour that is readily quantified in this species. We show that the heritability of fanning behaviour is ≥0.9 and significantly different from zero within a freshwater population. Moreover, there was abundant genetic variation for fanning behaviour, indicating that it could readily evolve. These results suggest that parenting behaviour is tractable for further genetic dissection in this system.
In vitro
evaluation of the effect of C-4 substitution on methylation of 7,8-dihydroxycoumarin: metabolic profile and catalytic kinetics
Authors: Xia Yang-Liu , Dou Tong-Yi , Liu Yong , Wang Ping , Ge Guang-Bo , Yang Ling
Published: January 2018

Daphnetin (7,8-dihydroxycoumarin (7,8-DHC)) and its C-4 derivatives have multiple pharmacological activities, but the poor metabolic stability of these catechols has severely restricted their application in the clinic. Methylation plays important roles in catechol elimination, although thus far the effects of structural modifications on the metabolic selectivity and the catalytic efficacy of human catechol-
O
-methyltransferase (COMT) remain unclear. This study was aimed at exploring the structure–methylation relationship of daphnetin and its C-4 derivatives, including 4-methyl, 4-phenyl and 4-acetic acid daphnetin. It was achieved by identifying the methylated products generated and by careful characterization of the reaction kinetics. These catechols are selectively metabolized to the corresponding 8-
O
-methyl conjugates, and this regioselective methylation could be elucidated by flexible docking, in which all the 8-OH groups of these catechols are much closer than the 7-OH groups to catalytic residue LYS144 and methyl donor AdoMet. The results of the kinetic analyses revealed that the Cl
int
values of the compounds could be strongly affected by the C-4 substitutions, which could be partially explained by the electronic effects of the C-4 substituents and the coordination modes of 7,8- dihydroxycoumarins in the active site of COMT. These findings provide helpful guidance for further structural modification of 7,8-DHCs to improve metabolic stability.
Individual variation in reproductive behaviour is linked to temporal heterogeneity in predation risk
Authors: Barbosa Miguel , Deacon Amy E. , Janeiro Maria Joao , Ramnarine Indar , Morrissey Michael Blair , Magurran Anne E.
Published: January 2018

Variation in predation risk is a major driver of ecological and evolutionary change, and, in turn, of geographical variation in behaviour. While predation risk is rarely constant in natural populations, the extent to which variation in predation risk shapes individual behaviour in wild populations remains unclear. Here, we investigated individual differences in reproductive behaviour in 16 Trinidadian guppy populations and related it to the observed variation in predator biomass each population experienced. Our results show that high heterogeneity in predator biomass is linked to individual behavioural diversification. Increased within-population heterogeneity in predator biomass is also associated with behavioural polymorphism. Some individuals adjust the frequency of consensual mating behaviour in response to differences in sex ratio context, while others display constantly at elevated frequencies. This pattern is analogous to a ‘live fast, die young’ pace-of-life syndrome. Notably, both high and low mean differences in predator biomass led to a homogenization of individual frequency of consensual mating displays. Overall, our results demonstrate that individual behavioural variation is associated with heterogeneity in predator biomass, but not necessarily with changes in mean values of predator biomass. We suggest that heterogeneity in predator biomass is an informative predictor of adaptive responses to changes in biotic conditions.
Tetrapod distribution and temperature rise during the Permian–Triassic mass extinction
Authors: Bernardi Massimo , Petti Fabio Massimo , Benton Michael J.
Published: January 2018

The Permian–Triassic mass extinction (PTME) had an enormous impact on life in three ways: by substantially reducing diversity, by reshuffling the composition of ecosystems and by expelling life from the tropics following episodes of intense global warming. But was there really an ‘equatorial tetrapod gap', and how long did it last? Here, we consider both skeletal and footprint data, and find a more complex pattern: (i) tetrapods were distributed both at high and low latitudes during this time; (ii) there was a clear geographic disjunction through the PTME, with tetrapod distribution shifting 10–15° poleward; and (iii) there was a rapid expansion phase across the whole of Pangea following the PTME. These changes are consistent with a model of generalized migration of tetrapods to higher latitudinal, cooler regions, to escape from the superhot equatorial climate in the earliest Triassic, but the effect was shorter in time scale, and not as pronounced as had been proposed. In the recovery phase following the PTME, this episode of forced range expansion also appears to have promoted the emergence and radiation of entirely new groups, such as the archosaurs, including the dinosaurs.
Lactobacillus panisapium sp. nov., from honeybee Apis cerana bee bread
Authors: Wang Cong , Huang Yan , Li Li , Guo Jun , Wu Zhengyun , Deng Yu , Dai Lirong , Ma Shichun
Published: January 2018

A novel facultatively anaerobic, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative bacterium of the genus

Lactobacillus

, designated strain Bb 2-3T, was isolated from bee bread of Apis cerana collected from a hive in Kunming, China. The strain was regular rod-shaped. Optimal growth occurred at 37 °C, pH 6.5 with 5.0 g l−1 NaCl. The predominant fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 iso. Respiratory quinones were not detected. Seven glycolipids, three lipids, phosphatidylglycerol and diphosphatidylglycerol were detected. The peptidoglycan type A4α l-Lys-d-Asp was determined. Strain Bb 2-3T was closely related to

Lactobacillus bombicola

DSM 28793T,

Lactobacillus apis

LMG 26964T and

Lactobacillus helsingborgensis

DSM 26265T, with 97.8, 97.6 and 97.0 % 16S rRNA gene sequence similarity, respectively. A comparison of two housekeeping genes, rpoA and pheS, revealed that strain Bb 2-3T was well separated from the reference strains of species of the genus

Lactobacillus

. The average nucleotide identity between strain Bb 2-3T and the type strains of closely related species was lower than the 95–96 % threshold value for delineation of genomic prokaryotic species. The G+C content of the genomic DNA of strain Bb 2-3T was 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain Bb 2-3T is proposed to represent a novel species of the genus

Lactobacillus

, for which we propose the name Lactobacillus panisapium sp. nov. The type strain is Bb 2-3T (=DSM 102188T=ACCC 19955T).
First report of Lyme disease in Nepal
Authors: Pun Sher Bahadur , Agrawal Sumit , Jha Santoshananda , Bhandari Lila Nath , Chalise Bimal Sharma , Mishra Abadhesh , Shah Rajesh
Published: January 2018

Introduction. Lyme disease is a tick-borne illness caused by the spirochete Borrelia burgdorferi and is widely reported in the USA, Central Europe, South East Asia and Latin America. Until recently, no scientific report regarding Lyme disease in Nepal had been published.

Case presentation. A 32-year-old, previously healthy female visited the hospital with a history of joint pains, fatigue, neck stiffness, tingling sensation and headache. She was initially treated for typhoid fever, brucellosis and malaria, but did not show significant improvement. Doxycycline was prescribed empirically for 3 weeks for the treatment of suspected tick-borne illness. A two-tiered immunoglobulin laboratory testing confirmed Borrelia burgdorferi. She developed post-treatment Lyme disease syndrome after completion of antibiotic therapy.

Conclusion. To the best of our knowledge, this is the first report of Lyme disease in Nepal and probably the first documented case of post-treatment Lyme disease syndrome in Asia. Lyme disease might have been overlooked in Nepal and, therefore, patients having clinical signs and symptoms similar to Lyme disease should not be disregarded in differential diagnosis.
First case report of sepsis caused by Rhizobium pusense in Japan
Authors: Kuchibiro Tomokazu , Hirayama Katsuhisa , Houdai Katsuyuki , Nakamura Tatsuya , Ohnuma Kenichirou , Tomida Junko , Kawamura Yoshiaki
Published: January 2018

Introduction. Species of the genus Rhizobium are opportunistic, usually saprophytic, glucose-non-fermenting, Gram-negative bacilli found in agricultural soil. Rhizobium pusense infections are the least common Rhizobium infections and have low incidence.

Case presentation. Herein, we report the first case of sepsis with R. pusense in Japan in a 67-year-old Japanese woman with a history of hyperlipidaemia, hypertension, diabetes, hypothyroidism and osteoporosis. She had undergone cerebrovascular treatment because she was diagnosed with a subarachnoid haemorrhage. The results of postoperative blood culture showed oxidase-positive, urease-positive, non-lactose-fermenting Gram-stain-negative rods. Using the Vitek2 system, the isolate was distinctly identified as Rhizobium radiobacter. However, 16S rRNA gene sequencing showed 99.93 % similarity with the type strain of R. pusense and 99.06 % similarity with the type strain of R. radiobacter. Additional gene sequencing analysis using recA (97.2 %) and atpD (96.2 %) also showed that the isolated strain is most closely related to R. pusense. The patient was cured by treatment using intravenous meropenem (3 g/d) for 4 weeks and was discharged safely.

Conclusion. The definite source of sepsis was unknown. However, the possibility of having been infected through the catheter during the cerebrovascular operation was speculated.
Targeted epigenomic changes to the maize methylome resulting from tissue culture
Authors: Han Zhaoxue , Crisp Peter A. , Stelpflug Scott , Kaeppler Shawn M. , Li Qing , Springer Nathan M.
Published: January 2018

DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. A sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ~15Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines suggesting the existence of a targeted process for altering epigenetic state during tissue culture. The consistent changes induced by tissue culture include both gains and losses of DNA methylation and can affect CG, CHG or both contexts within a region. The majority of changes in DNA methylation exhibit stable inheritance although there is some evidence for stochastic reacquisition of the initial epigenetic state in some individuals. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus
Authors: Charrier N. Pierre , Couton Marjorie , Voordouw Maarten J. , Rais Olivier , Durand-Hermouet Axelle , Hervet Caroline , Plantard Olivier , Rispe Claude
Published: January 2018

Background

Ixodes ricinus is the most important vector of tick-borne-diseases in Europe. A better knowledge of its genome and transcriptome is important for developing control strategies. Previous transcriptomic studies of I. ricinus have focused on gene expression during the blood meal in specific tissues. To obtain a broader picture of changes in gene expression during the blood meal, our study analysed the transcriptome at the level of the whole body for both nymphal and adult ticks. I. ricinus ticks from a highly inbred colony at the University of Neuchâtel were used. We also analysed previously published RNAseq studies to compare the genetic variation between three wild strains and three lab strains, including the strain from Neuchâtel.

Results

RNA was extracted from whole tick bodies and the cDNA was sequenced, producing 162,872,698 paired-end reads. Our reference transcriptome contained 179,682 contigs, of which 31% were annotated using Trinotate. Gene expression was compared between ticks that differed with respect to stage (nymph, adult), sex (female, male), and feeding status (unfed, partially fed). We found that blood feeding in nymphs and female adult ticks increased the expression of cuticle-associated genes. Using a set of 5,422 single nucleotide polymorphisms to calculate the heterozygosity, we found that the wild tick populations of I. ricinus had much higher levels of heterozygosity than the three lab populations.

Conclusion

Using high throughput strand-oriented sequencing for whole ticks in different stages and feeding conditions, we obtained a de novo assembly that significantly increased the genomic resources available for I. ricinus. Our study illustrates the importance of analysing the transcriptome at the level of the whole body to gain additional insights into how gene expression changes over the life cycle of an organism. Our comparison of several RNAseq datasets shows the power of transcriptomic data to accurately characterize genetic polymorphism and for comparing different populations or sources of sequencing material.