bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skeletal Dysplasia Mutations Effect on Human Filamins’ Structure and Mechanosensing
Authors: Seppälä Jonne , Bernardi Rafael C. , Haataja Tatu J. K. , Hellman Maarit , Pentikäinen Olli T. , Schulten Klaus , Permi Perttu , Ylänne Jari , Pentikäinen Ulla 
Published: June 2017

AbstractCells’ ability to sense mechanical cues in their environment is crucial for fundamental cellular processes, leading defects in mechanosensing to be linked to many diseases. The actin cross-linking protein Filamin has an important role in the conversion of mechanical forces into biochemical signals. Here, we reveal how mutations in Filamin genes known to cause Larsen syndrome and Frontometaphyseal dysplasia can affect the structure and therefore function of Filamin domains 16 and 17. Employing X-ray crystallography, the structure of these domains was first solved for the human Filamin B. The interaction seen between domains 16 and 17 is broken by shear force as revealed by steered molecular dynamics simulations. The effects of skeletal dysplasia associated mutations of the structure and mechanosensing properties of Filamin were studied by combining various experimental and theoretical techniques. The results showed that Larsen syndrome associated mutations destabilize or even unfold domain 17. Interestingly, those Filamin functions that are mediated via domain 17 interactions with other proteins are not necessarily affected as strongly interacting peptide binding to mutated domain 17 induces at least partial domain folding. Mutation associated to Frontometaphyseal dysplasia, in turn, transforms 16–17 fragment from compact to an elongated form destroying the force-regulated domain pair.
Computer-aided implant design for the restoration of cranial defects
Authors: Chen Xiaojun , Xu Lu , Li Xing , Egger Jan 
Published: June 2017

AbstractPatient-specific cranial implants are important and necessary in the surgery of cranial defect restoration. However, traditional methods of manual design of cranial implants are complicated and time-consuming. Our purpose is to develop a novel software named EasyCrania to design the cranial implants conveniently and efficiently. The process can be divided into five steps, which are mirroring model, clipping surface, surface fitting, the generation of the initial implant and the generation of the final implant. The main concept of our method is to use the geometry information of the mirrored model as the base to generate the final implant. The comparative studies demonstrated that the EasyCrania can improve the efficiency of cranial implant design significantly. And, the intra- and inter-rater reliability of the software were stable, which were 87.07 ± 1.6% and 87.73 ± 1.4% respectively.
Effects of naftopidil on double-J stent-related discomfort: a multicenter, randomized, double-blinded, placebo-controlled study
Authors: Oh Jong Jin , Lee Sangchul , Cho Sung Yong , Lee Sang Wook , Cho Min Chul , Na Woong , Park Ju Hyeon , Lee Seung Bae , Ahh Soyeon , Jeong Chang Wook 
Published: June 2017

AbstractTo evaluate the effect of naftopidil 75 mg once daily for ureteral double-J (DJ) stent-related discomfort after a ureteroscopic procedure using a multicenter, randomized, double-blinded, placebo-controlled study. 100 patients with indwelled retrograde DJ ureteral stents after ureteroscopic stone removal or retrograde intrarenal surgery (RIRS) were randomized 1:1 to receive either placebo or naftopidil during the stenting period. At the time of stent removal, the Ureteral Stent Symptom Questionnaire (USSQ), the International Prostate Symptom Score and the total amount of used analgesics were reported. Of the 92 patients who completed the study, 49 patients were enrolled in the placebo group, and 43 patients in the naftopidil group. USSQ urinary symptom scores (30.90 vs. 29.23, p = 0.299) and USSQ body pain scores (22.28 vs. 19.58, respectively, p = 0.286) were lower in the naftopidil group than in the placebo group, but the difference was not significant. Multivariate analysis showed that the use of a ureteral access sheath during RIRS was the only significant predictor of postoperative DJ-related pain (OR = 2.736, p = 0.031). The use of naftopidil once daily did not significantly reduce DJ ureteral stent-related discomfort. Larger-scaled prospective studies should be conducted to evaluate the effects of naftopidil on DJ stent-related symptoms and surgeries.
Electroporation as a vaccine delivery system and a natural adjuvant to intradermal administration of plasmid DNA in macaques
Authors: Todorova Biliana , Adam Lucille , Culina Slobodan , Boisgard Raphaël , Martinon Frédéric , Cosma Antonio , Ustav Mart , Kortulewski Thierry , Le Grand Roger , Chapon Catherine 
Published: June 2017

AbstractIn vivoelectroporation (EP) is used to enhance the uptake of nucleic acids and its association with DNA vaccination greatly stimulates immune responses to vaccine antigens delivered through the skin. However, the effect of EP on cutaneous cell behavior, the dynamics of immune cell recruitment and local inflammatory factors, have not been fully described. Here, we show that intradermal DNA vaccination combined with EP extends antigen expression to the epidermis and the subcutaneous skin muscle in non-human primates.In vivofibered confocal microscopy and dynamicex vivoimaging revealed that EP promotes the mobility of Langerhans cells (LC) and their interactions with transfected cells prior to their migration from the epidermis. At the peak of vaccine expression, we detected antigen in damaged keratinocyte areas in the epidermis and we characterized recruited immune cells in the skin, the hypodermis and the subcutaneous muscle. EP alone was sufficient to induce the production of pro-inflammatory cytokines in the skin and significantly increased local concentrations of Transforming Growth Factor (TGF)-alpha and IL-12. Our results show the kinetics of inflammatory processes in response to EP of the skin, and reveal its potential as a vaccine adjuvant.
Magnetic resonance imaging of fetal persistent left superior vena cava
Authors: Dong Su-Zhen , Zhu Ming 
Published: June 2017

AbstractThis study aimed to evaluate the diagnostic accuracy of fetal magnetic resonance imaging (MRI) for persistent left superior vena cava (LSVC). Prenatal echocardiography (echo) and/or ultrasound (US) and MRI data for 49 fetuses with persistent LSVC, confirmed via postnatal diagnoses between January 2010 and October 2015, were retrospectively reviewed. All prenatal MRI was performed at 1.5 T. Imaging sequences included steady-state free-precession (SSFP), single-shot turbo spin echo (SSTSE), and other sequences. All 49 cases of fetal persistent LSVC were correctly diagnosed via MRI, but only 34 cases (69.4%) were correctly diagnosed via an initial US and/or echo before MRI. Of the 15 cases that were not correctly diagnosed via US and/or echo, 8 had congenital heart diseases (CHDs) and 7 were without CHDs; however, they were associated with extracardiac abnormalities or maternal obesity. Thirty-five cases were associated with other cardiovascular abnormalities; 8, with extracardiac abnormalities; and 6, with no associated condition. In 44 (89.8%) cases, the innominate veins were absent; the remaining cases had innominate veins. In 14.3% of patients (7 cases), the persistent LSVC drained directly into the atrium. Fetal MRI can detect persistent LSVC and play an adjunctive role along with US in the evaluation of persistent LSVC.
Using the International Classification of Functioning, Disability and Health in Assessment and Intervention of School-Aged Children With Language Impairments
Authors: Westby Carol , Washington Karla N. 
Published: June 2017

Purpose
The aim of this tutorial is to support speech-language pathologists' (SLPs') application of the International Classification of Functioning, Disability and Health (ICF) in assessment and treatment practices with children with language impairment.

Method
This tutorial reviews the framework of the ICF, describes the implications of the ICF for SLPs, distinguishes between students' capacity to perform a skill in a structured context and the actual performance of that skill in naturalistic contexts, and provides a case study of an elementary school child to demonstrate how the principles of the ICF can guide assessment and intervention.

Implications
The Scope of Practice and Preferred Practice documents for the American Speech-Language-Hearing Association identify the ICF as the framework for practice in speech-language pathology. This tutorial will facilitate clinicians' ability to identify personal and environmental factors that influence students' skill capacity and skill performance, assess students' capacity and performance, and develop impairment-based and socially based language goals linked to Common Core State Standards that build students' language capacity and their communicative performance in naturalistic contexts.
Fetomaternal and Pediatric Toxoplasmosis
Authors: Oz Helieh 
Published: June 2017

AbstractToxoplasmosis is one of the most important causes of foodborne illnesses and inflammatory complications, as well as congenital disorders. Promiscuous Toxoplasma is transmitted by contaminated food and animal produce, water, vegetations, fruits, and sexually through semen. Toxoplasma infects nucleated cells with a unique tropism for muscles and central nervous system and a mind bugging malicious effect. Pregnant women with acute or reactivated toxoplasmosis can transmit Toxoplasma via transplacental transmission to the fetus. The severity of congenital toxoplasmosis depends on the gestation period, as infection in early pregnancy causes more severe consequences. Congenital toxoplasmosis complications include miscarriage, encephalitis, neurological retardation, mental illnesses, auditory, and visual inflammatory disorders, cardiovascular abnormalities, and pains. Current therapies are inefficient for congenital and chronic toxoplasmosis or have severe side effects with life-threatening complications. There is an urgent need for effective and safe therapeutic modalities to treat complications of toxoplasmosis and effective vaccines to eliminate the infectious agent. This investigation will discuss the pathogenesis of fetomaternal, congenital, and pediatric toxoplasmosis, the currently available therapies in practice, and explore those therapeutic modalities in experimental stages for promising future trials.
Synthesis, Characterisation, Molecular Docking, Anti-microbial and Anti-diabetic Screening of Substituted 4-indolylphenyl-6-arylpyrimidine-2-imine Derivatives
Authors: Ramya Veerasamy , Vembu Santhirakasu , Ariharasivakumar Ganesan , Gopalakrishnan Manathusamy 
Published: June 2017

AbstractThe purpose of the research is to synthesise a novel series of (E)-2-(4-(1H-indol-3-yl)-6-p-substituted phenylpyrimidin-2-yl)dimethylguanidine derivatives since 3-(1H-indol-3-yl)-1-p-substituted phenylprop-2-en-1-one and evaluate their molecular docking studies, antimicrobial, and anti-diabetic activities. Among all the synthesized compounds (11a-g), compound 11a exhibits excellent CDOCKER energy (−11.36 kcal/mol). The entire compounds (11a-g) confirm very good antimicrobial activity towards the tested microorganisms. In the in vitro anti-diabetic studies, compounds (11a, 11c, and 11g) confirm higher alpha-amylase and alpha-glucosidase inhibition activity. In the in vivo anti-diabetic activities, the synthesized compounds (11a-g) (10 mg/kg, p.o.) investigated by the streptozotocin (60 mg/kg, ip) –nicotinamide (120 mg/kg, p.o.) – induced model in adult male albino Wistar rat and these derivatives show considerable fasting blood glucose level when compared to metformin hydrochloride a potent and well-known anti-diabetic drug as a reference.
Curcumin Promotes Apoptosis of Activated Hepatic Stellate Cells by Inhibiting Protein Expression of the MyD88 Pathway
Authors: He Ya-Jun , Kuchta Kenny , Deng Yan-Mei , Cameron Silke , Lin Yu , Liu Xu-You , Ye Guo-Ron , Lv Xia , Kobayashi Yuta , Shu Jian-Chang 
Published: June 2017

AbstractActivation and proliferation of hepatic stellate cells (HSC) play an important role in the progress of liver fibrosis. HSC activation occurs in response to inflammatory cytokines, cellular interactions with immune cells, and morphogenetic signals. The literature hints to a role of the adaptor protein MyD88 in fibrosis. Although curcumin has been shown to exert inhibitory effects on the proliferation of HSC in vitro, its influence on the MyD88 pathway in HSC has remained unclear. Here, we investigated whether curcumin accelerates apoptosis of HSC through the MyD88 pathway. HSC (rat HSC T6) were divided into a control group, MyD88 small interfering RNA (siRNA) group, curcumin group, and curcumin + MyD88 siRNA group. The MyD88 siRNA groups were exposed to siRNA for 48 h. The curcumin groups were cultured in the presence of curcumin for 24 h. Apoptosis was detected by flow cytometry. For Toll-like receptor (TLR) 2 and 4 as well as MyD88 and the dependent factors NF-κB, TNF-α, and IL-1β, mRNA expression was detected by reverse transcription polymerase chain reaction (RT-PCR). For MyD88, protein expression was further observed by Western Blot. Both curcumin and MyD88 siRNA inhibited the mRNA expression of MyD88 pathway-related effectors (TLR2, TLR4, NF-κB, TNF-α, IL-1β) in HSC. Furthermore, both treatments reduced the expression of MyD88 protein in HSC and promoted their apoptosis. These effects were more obvious in the curcumin + MyD88 siRNA group. This study demonstrates that curcumin promotes apoptosis of activated HSC by inhibiting the expression of cytokines related to the MyD88 pathway. It elucidates the possible mechanisms of curcumin in inducing apoptosis of HSC through the MyD88 pathway.
Temporal Patterns of Migration and Spawning of River Herring in Coastal Massachusetts
Authors: Rosset Julianne , Roy Allison H. , Gahagan Benjamin I. , Whiteley Andrew R. , Armstrong Michael P. , Sheppard John J. , Jordaan Adrian 
Published: June 2017

AbstractMigrations of springtime Alewife Alosa pseudoharengus and Blueback Herring A. aestivalis, collectively referred to as river herring, are monitored in many rivers along the Atlantic coast to estimate population sizes. While these estimates give an indication of annual differences in the number of returning adults, links to the subsequent timing and duration of spawning and freshwater juvenile productivity remain equivocal. In this study, we captured juvenile river herring at night in 20 coastal Massachusetts lakes using a purse seine and extracted otoliths to derive daily fish ages and back‐calculate spawn dates. Estimates of spawning dates were compared with fishway counts of migrating adults to assess differences in migration timing and the timing and duration of spawning. We observed a distinct delay between the beginning of the adult migration run and the start of spawning, ranging from 7 to 28 d across the 20 lakes. Spawning continued 13–48 d after adults stopped migrating into freshwater, further demonstrating a pronounced delay in spawning following migration. Across the study sites the duration of spawning (43–76 d) was longer but not related to the duration of migration (29–66 d). The extended spawning period is consistent with recent studies suggesting that Alewives are indeterminate spawners. The long duration in freshwater provides the opportunity for top‐down (i.e., predation on zooplankton) and bottom‐up (i.e., food for avian, fish, and other predators) effects, with implications for freshwater food webs and nutrient cycling. General patterns of spawn timing and duration can be incorporated into population models and used to estimate temporal changes in productivity associated with variable timing and density of spawning river herring in lakes.
Concurrently Assessing Survey Mode and Sample Size in Off-Site Angler Surveys
Authors: Barrett Boyd N. , Poorten Brett , Cooper Andrew B. , Haider Wolfgang 
Published: June 2017

Abstract
Off-site angler surveys are commonly administered via two or more survey modes in the form of a mixed-mode survey. Mixed-mode surveys allow survey administrators to attain the benefits inherent to different survey modes, reduce total survey error, and control survey cost. However, these benefits can only be simultaneously attained after undertaking sample size planning. Sample size planning is a trade-off analysis wherein a researcher concurrently assesses survey administration cost, the accuracy and precision of estimates, the magnitude and direction of biases, and variance of the test statistic to determine an optimal sample size. We used data from an off-site angler survey administered to anglers targeting White Sturgeon Acipenser transmontanus to illustrate a systematic approach to sample size planning. Our survey design included a mixed-mode design with three survey modes (e-mail, mail, and telephone) and a two-phase sampling design that had a first contact and a follow-up contact with a subsample of nonrespondents. Sample size planning was undertaken in the form of a sensitivity analysis wherein four survey design alternatives were simulated and assessed based on four criteria (i.e., bias, precision, accuracy, and cost). We also incorporated tests for nonresponse bias and survey mode effect. We found that (1) response rates were lower for e-mail surveys (22%) than for mail surveys and telephone surveys (39–44%); (2) nonresponse bias did not have a substantial effect on survey estimates from the mixed-mode design; and (3) estimates (total effort and total catch) from the mail and e-mail survey modes were significantly different, indicating a survey mode effect. The high variability of anglers’ annual catch made survey estimates highly imprecise at lower sample sizes. The level of acceptable error varies for each study. Therefore, a systematic approach to sample size planning is necessary to determine the point where acceptable error is reached while considering multiple survey design alternatives.
Received September 25, 2016; accepted April 24, 2017 Published online June 19, 2017
Population Dynamics and Reproduction of Mediterranean Green Crab Carcinus aestuarii in Parila Lagoon (Neretva Estuary, Adriatic Sea, Croatia) as Fishery Management Tools
Authors: Glamuzina Luka , Conides Alexis , Mancinelli Giorgio , Dobroslavić Tatjana , Bartulović Vlasta , Matić-Skoko Sanja , Glamuzina Branko 
Published: June 2017

Abstract
Population structure, age, growth, mortality, and reproduction patterns of the Mediterranean green crab Carcinus aestuarii were determined for the native population in Parila Lagoon (Neretva Estuary, Middle Adriatic, Croatia). The population size structure showed two distinct cohorts: (1) specimens with a carapace width of 20–34 mm and dominated by females and (2) large-sized specimens with a carapace width &gt; 34 mm with males significantly dominating and no females found above 46 mm. Males appeared to grow faster than females in the first and second year of the life cycle. Most of the natural mortality (70.4%) occurred during the first year of life. This indicates high predation pressure from fish and other crab species on small-sized (less than 25 mm) C. aestuarii cohorts. The peak of ovigerous female occurrence occurred in January 2015. A very small percentage of ovigerous females appeared in June 2015. The 50% ovigerous size for the population was estimated at a carapace width of 29.65 mm and weight of 10.39 g. The average fecundity was 61,017 eggs/female, with an average fecundity per gram of female wet weight of 4,804 eggs. The biological characteristics and population dynamics of C. aestuarii show that life history traits of this species (such as the smallest and average ovigerous female size, the mortality rate during the first year of life or the establishment of a second year, and a late-spring reproduction period) should be used to monitor potential changes in ecosystem properties of Mediterranean transitional waters and to manage potential fisheries.
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments
Authors: Uvarovskii Alexey , Dieterich Christoph 
Published: June 2017

Abstract

Motivation
Metabolic labelling of RNA is a well-established and powerful method to estimate RNA synthesis and decay rates. The pulseR R package simplifies the analysis of RNA-seq count data that emerge from corresponding pulse-chase experiments.

Results
The pulseR package provides a flexible interface and readily accommodates numerous different experimental designs. To our knowledge, it is the first publicly available software solution that models count data with the more appropriate negative-binomial model. Moreover, pulseR handles labelled and unlabelled spike-in sets in its workflow and accounts for potential labeling biases (e.g. number of uridine residues).

Availability and implementation
The pulseR package is freely available at https://github.com/dieterich-lab/pulseR under the GPLv3.0 licence.

Supplementary information
Supplementary data are available at Bioinformatics online.
Practical considerations for large-scale gut microbiome studies
Authors: Vandeputte Doris , Tito Raul Y. , Vanleeuwen Rianne , Falony Gwen , Raes Jeroen 
Published: June 2017

Abstract
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.