bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal bone pneumatization in cystic fibrosis: A correlation with genotype?
Authors: Berkhout Maaike C. , van Rooden Cornelis J. , Aalbers Ralph C. , el Bouazzaoui Lahssan H. , Fokkens Wytske J. , Rijntjes Evert , Heijerman Harry G. M. 
Published: December 2013

Objectives/HypothesisParanasal sinus pneumatization in patients with cystic fibrosis (CF) is less extensive compared to the general population and seems to be correlated to CF genotype. Interestingly, in CF patients temporal bone pneumatization (TBP) is more extensive compared to the general population, and middle ear pathology is generally uncommon in CF. It is debated whether TBP is influenced environmentally or genetically. The aim of the present study was to investigate pneumatization of the temporal bone in patients with CF and to correlate this with genotype and paranasal sinus volume.Study DesignProspective collection of data.MethodsIn 104 adult CF patients, computed tomography of the temporal bone and the paranasal sinuses was performed. TBP was graded using a validated scoring system. Patients were divided into two groups, mild and severe CF, based on their mutations in the CF transmembrane conductance regulator gene.ResultsOf the 31 patients with mild CF, 71% had extensive TBP, and of the 73 patients with severe CF, 82% had extensive pneumatization of the temporal bone. TBP did not differ significantly for CF genotype, and TBP was not correlated to paranasal sinus volume.ConclusionsWhereas paranasal sinus pneumatization in CF patients seems to be related to CF genotype among other influencing factors, this study showed no correlation between TBP and CF genotype. TBP was not correlated to paranasal sinus volume. Hypothetically, in CF, pneumatization of the temporal bone is under a different influence than paranasal sinus pneumatization.Level of Evidence4 Laryngoscope, 124:1682–1686, 2014
Small nerve fiber involvement in patients referred for fibromyalgia
Authors: Giannoccaro Maria Pia , Donadio Vincenzo , Incensi Alex , Avoni Patrizia , Liguori Rocco 
Published: December 2013

ABSTRACTIntroduction: Fibromyalgia (FM) is a chronic syndrome characterized by widespread pain often accompanied by other symptoms suggestive of neuropathic pain. We evaluated patients for small fiber neuropathy (SFN) who were referred for fibromyalgia (FM). Methods: We studied 20 consecutive subjects with primary FM. Patients underwent neurological examination, nerve conduction studies, and skin biopsies from distal leg and thigh. Results: Electrodiagnostic studies were normal in all patients. SFN was diagnosed in 6 patients by reduced epidermal nerve fiber density. These patients also showed abnormalities of both adrenergic and cholinergic fibers. Conclusions: A subset of FM subjects have SFN, which may contribute to their sensory and autonomic symptoms. Skin biopsy should be considered in the diagnostic work‐up of FM. Muscle Nerve 49: 757–759, 2014
Use of acoustics to deter bark beetles from entering tree material
Authors: Aflitto Nicholas C , Hofstetter Richard W 
Published: December 2013

AbstractBACKGROUNDAcoustic technology is a potential tool to protect wood materials and eventually live trees from colonization by bark beetles. Bark beetles such as the southern pine beetle Dendroctonus frontalis, western pine beetle D. brevicomis and pine engraver Ips pini (Coleoptera: Curculionidae) use chemical and acoustic cues to communicate and to locate potential mates and host trees. In this study, the efficacy of sound treatments on D. frontalis, D. brevicomis and I. pini entry into tree materials was tested.RESULTSAcoustic treatments significantly influenced whether beetles entered pine logs in the laboratory. Playback of artificial sounds reduced D. brevicomis entry into logs, and playback of stress call sounds reduced D. frontalis entry into logs. Sound treatments had no effect on I. pini entry into logs.CONCLUSIONThe reduction in bark beetle entry into logs using particular acoustic treatments indicates that sound could be used as a viable management tool. © 2013 Society of Chemical Industry
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data
Authors: Hu Xihao , Wong Thomas K. F. , Lu Zhi John , Chan Ting Fung , Lau Terrence Chi Kong , Yiu Siu Ming , Yip Kevin Y. 
Published: December 2013

AbstractMotivation: High-throughput sequencing has been used to probe RNA structures, by treating RNAs with reagents that preferentially cleave or mark certain nucleotides according to their local structures, followed by sequencing of the resulting fragments. The data produced contain valuable information for studying various RNA properties.Results: We developed methods for statistically modeling these structure-probing data and extracting structural features from them. We show that the extracted features can be used to predict RNA ‘zipcodes’ in yeast, regions bound by the She complex in asymmetric localization. The prediction accuracy was better than using raw RNA probing data or sequence features. We further demonstrate the use of the extracted features in identifying binding sites of RNA binding proteins from whole-transcriptome global photoactivatable-ribonucleoside-enhanced cross-linking and immunopurification (gPAR-CLIP) data.Availability: The source code of our implemented methods is available at http://yiplab.cse.cuhk.edu.hk/probrna/.Contact: kevinyip@cse.cuhk.edu.hkSupplementary information: Supplementary data are available at Bioinformatics online.
Manipulation of EAT-2 expression promotes induction of multiple beneficial regulatory and effector functions of the human innate immune system as a novel immunomodulatory strategy
Authors: Aldhamen Yasser A. , Seregin Sergey S. , Aylsworth Charles F. , Godbehere Sarah , Amalfitano Andrea 
Published: December 2013

Abstract
The signaling lymphocytic activation molecule (SLAM) receptor-associated adaptor Ewing’s sarcoma-associated transcript-2 (EAT-2) is primarily expressed in innate immune cells including dendritic cells (DCs), macrophages and NK cells. A recent human HIV vaccine study confirmed that EAT-2 expression was associated with the enhanced immunogenicity induced by the MRKAd5/HIV vaccine. We previously harnessed the capability of EAT-2 to modulate signaling mediated by SLAM receptors and demonstrated that by incorporating EAT-2 expression into vaccines, one could enhance innate and adaptive immune responses in mice, even in the face of pre-existing immunity to the vaccine vectors. Herein, we investigated the innate immune responses of human cells exposed to EAT-2-over-expressing vaccines. Our results demonstrate that EAT-2 over-expression can significantly alter the kinetics of critical pro-inflammatory cytokine and chemokine responses elaborated by human PBMCs. In addition, enhanced DC maturation and increased monocyte phagocytosis were observed in EAT-2-transduced human cells. We also found that EAT-2 over-expression improved antigen presentation by human cells. Moreover, EAT-2 over-expression increased the anti-tumor activity of human NK cells against K562 tumor cell targets. Many of these responses were extinguished with use of an EAT-2 variant carrying a mutant SH2 domain (R31Q), suggesting a critical role for the interaction between EAT-2 and SLAM receptors in mediating these responses. In conclusion, these results provide evidence that EAT-2 interacts with key components of multiple arms of the human innate immune system, and that this role highlights the potential for targeting EAT-2 functions so as to improve a number of human immunotherapeutic approaches, including vaccine development.
Single‐Center Experience With 1‐Step Low‐Profile Percutaneous Endoscopic Gastrostomy in Children
Authors: Pattamanuch Nicole , Novak Inna , Loizides Anthony , Montalvo Andrea , Thompson John , Rivas Yolanda , Pan Debra 
Published: December 2013

ABSTRACTObjectives:The 1‐step low‐profile percutaneous endoscopic gastrostomy (1‐step PEG) uses a single procedure that allows immediate use of a low‐profile device. The aim of the present study was to provide our experience with this device and to analyze complications and outcomes after the initial placement.Methods:We performed a retrospective chart review of pediatric patients with 1‐step PEG placement done by our pediatric gastroenterologists between 2006 and June 2011. Patients were studied for a minimum period of 6 months.Results:A total of 121 patients were included in our study, with 23% infants. The most common indication for 1‐step PEG placement was swallowing dysfunction in children with neurological impairment (49%). Postplacement complications included granulation tissue (52%), cellulitis (23%), leakage (21%), vomiting (17%), tissue breakdown (8%), failed placement (6%), embedded bolster (5%), perforation (0.8%), and bowel obstruction (0.8%). One‐step PEG was maintained in 46 patients (38%). In the remaining 75 patients (62%), PEGs were changed to a balloon device in 66 patients and were completely removed in 9 patients. The most common indications for change were damaged PEG (19/75) and issues with size (11/75). The time to change ranged from <1 month to >4 years (14 ± 1.3 months). Sixty‐eight percent of 1‐step PEG changes/removal was performed with an obturator under brief inhalated anesthesia.Conclusions:The 1‐step PEG has complication rates and outcomes comparable with standard PEGs.
Low Temperature-Responsive Changes in the Anther Transcriptome’s Repeat Sequences Are Indicative of Stress Sensitivity and Pollen Sterility in Rice Strains
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Authors: Ishiguro Seiya , Ogasawara Kei , Fujino Kaien , Sato Yutaka , Kishima Yuji 
Published: December 2013

Abstract
Genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine responses to low temperatures in rice (Oryza sativa). We focused particularly on the rice anther at the booting stage, because a low temperature at this stage can result in pollen abortion. The five rice strains examined in this study showed different pollen fertilities due to a low-temperature treatment during the booting stage. The microarray analyses demonstrated that the low-temperature stress caused genome-wide changes in the transcriptional activities not only of genes but also of repeat sequences in the rice anther. The degree of the temperature-responsive changes varied among the five rice strains. Interestingly, the low-temperature-sensitive strains revealed more changes in the transcriptome when compared with the tolerant strains. The expression patterns of the repeat sequences, including miniature inverted-repeat transposable elements, transposons, and retrotransposons, were correlated with the pollen fertilities of the five strains, with the highest correlation coefficient being 0.979. Even in the low-temperature-sensitive strains, the transcriptomes displayed distinct expression patterns. The elements responding to the low temperatures were evenly distributed throughout the genome, and the major cis-motifs involved in temperature-responsive changes were undetectable from the upstream sequences in the corresponding repeats. The genome-wide responses of transcription to the temperature shift may be associated with chromatin dynamics, which facilitates environmental plasticity. A genome-wide analysis using repeat sequences suggested that stress tolerance could be conferred by insensitivity to the stimuli.
Control of the toxic plantColchicum autumnalein semi‐natural grasslands: effects of cutting treatments on demography and diversity
Authors: Winter Silvia , Jung Linda S. , Eckstein R. Lutz , Otte Annette , Donath Tobias W. , Kriechbaum Monika 
Published: December 2013

SummarySemi‐natural grasslands are important habitats for the conservation of biodiversity in Europe. High population densities of toxicColchicum autumnalein these grasslands may cause problems for livestock and the marketing of hay. Consequently, farmers may either intensify grassland management to reduceC. autumnalein the fodder or abandon the land; both practices will lead to a loss of biodiversity. Previous studies suggesting early cutting to controlC. autumnaledid not consider population dynamics and the effects on plant diversity.We conducted a four‐year experiment in six regions within Austria and Germany, applying five cutting treatments in 16C. autumnalepopulations to test the effects of cutting date and frequency onC. autumnaleand co‐occurring vegetation. Demographic data were evaluated with matrix population models, life‐table response experiment (LTRE),anovaandmanova. Vegetation data were analysed with multiresponse permutation procedures (MRPP),anovaandmanova.Population growth rate was significantly reduced in plots cut in early and late May compared to plots cut in June (control).Plants cut in late April or early May showed the lowest survival probability. Significantly fewer large vegetative plants developed capsules in the following year when cut in early or late May.LTREanalysis showed that differences in the population growth rate between the control and early cut treatments were mainly the result of a reduced survival and growth and an increased retrogression to smaller stages.Multiresponse permutation procedures revealed no differences in vegetation composition between treatments except for one site in 2011. There were no differences in Shannon index, evenness or species turnover rate within any year.Synthesis and applications. The greatest reduction in vitality ofColchicum autumnalewas observed in grasslands cut in late April or early May. After three years of early cutting, no reduction in plant species diversity was observed. The second cut should be postponed to July to enable seed shed of plants. Grassland management decisions to control toxicC. autumnalemust be made in close cooperation with nature conservation authorities to consider site characteristics and requirements of endangered species.
Land‐use intensity and the effects of organic farming on biodiversity: a hierarchical meta‐analysis
Authors: Tuck Sean L. , Winqvist Camilla , Mota Flávia , Ahnström Johan , Turnbull Lindsay A. , Bengtsson Janne 
Published: December 2013

Summary

The benefits of organic farming to biodiversity in agricultural landscapes continue to be hotly debated, emphasizing the importance of precisely quantifying the effect of organic vs. conventional farming.

We conducted an updated hierarchical meta‐analysis of studies that compared biodiversity under organic and conventional farming methods, measured as species richness. We calculated effect sizes for 184 observations garnered from 94 studies, and for each study, we obtained three standardized measures reflecting land‐use intensity. We investigated the stability of effect sizes through time, publication bias due to the ‘file drawer’ problem, and consider whether the current literature is representative of global organic farming patterns.

On average, organic farming increased species richness by about 30%. This result has been robust over the last 30 years of published studies and shows no sign of diminishing.

Organic farming had a greater effect on biodiversity as the percentage of the landscape consisting of arable fields increased, that is, it is higher in intensively farmed regions. The average effect size and the response to agricultural intensification depend on taxonomic group, functional group and crop type.

There is some evidence for publication bias in the literature; however, our results are robust to its impact. Current studies are heavily biased towards northern and western Europe and North America, while other regions with large areas of organic farming remain poorly investigated.

Synthesis and applications. Our analysis affirms that organic farming has large positive effects on biodiversity compared with conventional farming, but that the effect size varies with the organism group and crop studied, and is greater in landscapes with higher land‐use intensity. Decisions about where to site organic farms to maximize biodiversity will, however, depend on the costs as well as the potential benefits. Current studies have been heavily biased towards agricultural systems in the developed world. We recommend that future studies pay greater attention to other regions, in particular, areas with tropical, subtropical and Mediterranean climates, in which very few studies have been conducted.
Have coffee producers benefited from the new domestic cherry market? Evidence using panel data from Rwanda
Authors: Murekezi Abdoul , Jin Songqing , Loveridge Scott 
Published: December 2013

AbstractThe article assesses the effects of the new domestic cherry market on coffee‐growing households in Rwanda using panel data. Findings from combined first differenced with instrumental variable specification and other estimation methods provide evidence that farmers who sell to the cherry market do not increase their expenditures compared to farmers selling to the traditional parchment market. The different time lags in terms of when farmers started selling to the new cherry market may explain the lack of statistically significant differences across the two groups. It is possible that farmers will adjust their expenditure patterns in subsequent periods after year‐over‐year market trends become more apparent to them.
Stability of paramedian inserted palatal mini‐implants at the initial healing period: a controlled clinical study
Authors: Nienkemper Manuel , Pauls Alexander , Ludwig Björn , Drescher Dieter 
Published: December 2013

AbstractObjectivesTo assess the stability development of paramedian in comparison with midpalatal inserted mini‐implants.Material and methodsThe test group consisted of 21 consecutively treated patients (13.7 ± 4.6 years). In each patient, a mini‐implant was inserted paramedian in the anterior palate. Measurement of the insertion depth (ID), the maximum insertion torque (IT), and resonance frequency analysis (RFA) was performed at T0. RFA was repeated after 2 weeks (T1), 4 weeks (T2), and 6 weeks (T3). Correlations between measuring methods were calculated. RFA values at different times were tested for statistical differences. Data were compared with a group of patients who received median mini‐implants of the same size.ResultsInitial stability was 14.06 ± 4.35 Ncm (IT) and 26.60 ± 5.28 ISQ (RFA) with an ID of 7.02 ± 1.04 mm. RFA and IT (r = 0.49, P = 0.023) showed a moderate significant correlation. Stability remained relatively constant, showing no significant differences between measurement times. Overall, RFA values decreased non‐significantly by 2.25 ± 6.85 ISQ to a level of 24.35 ± 5.39 after 6 weeks. Comparing development of stability over time, it was found that significant differences were present at T0 and T1 (T0: −9.54 ISQ, P < 0.0001; T1: −3.69, P = 0.041).ConclusionsParamedian inserted mini‐implants provided sufficient stability. Showing a lower primary stability, RFA values did not differ from the control group from week four on, as no significant decrease in stability occurred at the initial healing period.
Wide local extension and higher proliferation indices are characteristic features of symptomatic lobular neoplasias (LNs) and LNs with an early invasive component
Authors: Katsurada Yuka , Yoshida Masayuki , Maeshima Akiko Miyagi , Ikeda Katsuhide , Shibata Tatsuhiro , Kinoshita Takayuki , Matsubara Osamu , Tsuda Hitoshi 
Published: December 2013

AimsLobular neoplasias (LNs) are typically small, clinically undetectable breast lesions, but some LNs are of clinical significance. The aim of this study was to clarify the histopathological characteristics of clinically overt (symptomatic) LNs and early invasive LNs.Methods and resultsSixty‐two surgically resected LNs, including eight with early invasion (≤10 mm), were classified into the following groups: (i) symptomatic and occult; and (ii) early invasive and non‐invasive. Six histopathological factors, including the Ki67 labelling index (LI), were assessed and analysed by logistic regression models. On multivariate analysis, tumour size (P = 0.008), mitotic counts (P = 0.006) and Ki67 LI (P = 0.035) were risk factors for symptomatic features, and tumour size (P = 0.009) and Ki67 LI (P = 0.015) were risk factors for early invasive lesions. In the eight LNs with invasion, the symptomatic and occult subgroups showed differing nuclear atypia and structural patterns, but both lesions extended widely (22–96 mm).ConclusionsWide extension and higher proliferation activity were characteristic features of symptomatic LNs and LNs with early invasion.
A proliferation‐inducing ligand in atopic dermatitis and vitiligo
Authors: Ibrahim Zeinab A. , Ghaly Nahla R. , El‐Tatawy Rania A. , Khalil Shereen M. , El‐Batch Manal M. 
Published: December 2013

AbstractBackgroundA proliferation‐inducing ligand (APRIL) is a tumor necrosis factor (TNF) superfamily member ligand that stimulates B cells in vitro and in vivo. It also plays an important role in T cell activation and survival.ObjectivesThis study was conducted to evaluate serum levels of APRIL in patients with atopic dermatitis (AD) and vitiligo and their correlation with disease activity.MethodsA total of 100 subjects were included; these comprised 40 AD patients, 40 vitiligo patients, and 20 control subjects. Serum APRIL levels were measured and their relationships with the severity of AD and activity of vitiligo evaluated according to scores on the SCORAD (SCORing of Atopic Dermatitis) and VIDA (Vitiligo Disease Activity) indices, respectively.ResultsThe serum level of APRIL was significantly higher in AD patients than in the control group. Serum APRIL in patients with severe AD showed a statistically significant difference with serum APRIL in patients with either mild or moderate AD. Serum APRIL was significantly higher in vitiligo patients than in the control group. Differences in serum APRIL among patients with different VIDA scores were significant only between patients with VIDA scores of +1 and +4. Statistically significant positive correlations emerged between serum APRIL and activity of AD (r = 0.939) and vitiligo (r = 0.740).ConclusionsAPRIL may play a role in the pathogeneses of AD and vitiligo and could be used as an objective marker for the assessment of AD severity and vitiligo activity. Further studies are required to clarify the precise mechanism of APRIL in the pathogeneses of AD and vitiligo and to test the possible use of APRIL inhibitors as novel modalities of therapy.