bluuebunny/crossref_metadata_2025_split huggingface dataset:
Post‐traumatic stress disorder and its risk factors in Japanese patients living with implantable cardioverter defibrillators: A preliminary examination
Authors: Kobayashi Sayaka , Nishimura Katsuji , Suzuki Tsuyoshi , Shiga Tsuyoshi , Ishigooka Jun 
Published: September 2013

AbstractBackgroundTrauma reactions, including post‐traumatic stress disorder (PTSD), in patients with implantable cardioverter defibrillators (ICDs) have recently garnered increased attention. The aim of this preliminary study was to examine the incidence of and risk factors for PTSD and to assess its impact on psychosocial distress and health‐related quality of life (QOL) in Japanese patients with ICD.MethodsSeventy‐four outpatients with ICD (63 men, 11 women; age 59.3±13.6 years) completed a questionnaire comprising a modified PTSD Checklist Specified for a stressor that included arrhythmias and ICD shocks, the Zung Self‐Rating Depression Scale (SDS), the State‐Trait Anxiety Inventory (STAI)‐State scale, and Medical Outcomes Study 36‐item Short‐Form (SF‐36) for health‐related QOL. We compared relevant sociodemographic and medical variables of patients with and without PTSD. The mean number of days since ICD implantation was 2471±703.ResultsOf 74 patients, 28 (37.8%) had received ICDs for secondary prevention, 42 (56.8%) had experienced ICD shocks, 36 (48.6%) had experienced ≥1 appropriate ICD shock, and 12 (16.2%) had experienced electrical storms. We diagnosed 19 patients (25.8%) with PTSD. Compared with the non‐PTSD group, the PTSD group had significantly higher SDS and STAI‐S scores and significantly lower scores in all eight subscales of the SF‐36. Multiple logistic regression analysis identified experiencing ≥1 appropriate ICD shock (odds ratio [OR]: 6.0, 95% confidence interval [CI]: 1.45–24.63, and p<0.013) and anxiolytic use (OR: 15.0, 95% CI: 3.38–66.26, and p<0.001) as independent risk factors for PTSD.ConclusionsOur study shows that PTSD in patients with ICD has significant psychosocial impact with associated impairment of both physical and mental QOL and suggests that, in particular, patients who experience appropriate ICD shocks or take anxiolytics require psychiatric/psychological intervention.
Tea‐drinking habit among new university students: Associated factors
Authors: Tseng Hsiu Chen , Wang Chi‐Jane , Cheng Shu Hui , Sun Zih‐Jie , Chen Po See , Lee Chih‐Ting , Lin Shih‐Hsien , Yang Yen Kuang , Yang Yi‐Ching 
Published: September 2013

AbstractThe habit of drinking tea is highly prevalent in Asian countries. The aim of this study was to investigate the prevalence of tea drinking and to explore the correlated factors on tea drinking among young new students in the university, using a validated self‐reported questionnaire. This study was carried out with 5936 new students in a university in Taiwan. It comprised a self‐administered structured questionnaire, including items related to personal and medical history, and lifestyle habits, using the Pittsburgh Sleep Quality Index (PSQI) and the 12‐item Chinese Health Questionnaire (CHQ‐12). Anthropometric measurements and laboratory tests were also performed. In total, 2065 (36.1%) students were in the tea‐drinking group. Multiple logistic regression analysis showed the following factors were significant predictors of tea drinking: postgraduate students (p < 0.001), coffee drinking (p < 0.001), alcohol drinking (p < 0.001), minor mental morbidity (p = 0.009), poorer sleepers (p = 0.037), higher body mass index (p = 0.004), and sugar‐sweetened beverage consumption (p < 0.001). Our data showed that the tea‐drinking habit was correlated with higher body mass index, which was contrary to the findings of a previous study. In clinical practice, perhaps we could consider more tea‐drinking‐related factors when we suggest tea consumption.
Spiral resonators for on-chip laser frequency stabilization
Authors: Lee Hansuek , Suh Myoung-Gyun , Chen Tong , Li Jiang , Diddams Scott A. , Vahala Kerry J. 
Published: September 2013

AbstractFrequency references are indispensable to radio, microwave and time keeping systems, with far reaching applications in navigation, communication, remote sensing and basic science. Over the past decade, there has been an optical revolution in time keeping and microwave generation that promises to ultimately impact all of these areas. Indeed, the most precise clocks and lowest noise microwave signals are now based on a laser with short-term stability derived from a reference cavity. In spite of the tremendous progress, these systems remain essentially laboratory devices and there is interest in their miniaturization, even towards on-chip systems. Here we describe a chip-based optical reference cavity that uses spatial averaging of thermorefractive noise to enhance resonator stability. Stabilized fibre lasers exhibit relative Allan deviation of 3.9 × 10−13 at 400 μs averaging time and an effective linewidth <100 Hz by achieving over 26 dB of phase-noise reduction.
Numerical Model for Artificial Cilia
Authors: Stark Holger 
Published: September 2013

Artificial cilia attached to bounding surfaces are highly interesting for transporting and mixing fluids which is an essential task in microfluidics. The chapter introduces a numerical model for artificial cilia based on a bead‐spring chain with bending rigidity whose beads interact hydrodynamically. We explain in detail how one implements the model in its viscous fluid environment using self‐ and cross‐mobilities. In particular, we describe how one treats the bounding surface with its no‐slip boundary condition to which the cilium is attached. The characteristic sperm number compares bending to frictional forces and helps to classify the dynamic behavior of the actuated filament.
The second part of the chapter addresses the numerical modeling of a superparamagnetic filament actuated by an external magnetic field which is a very attractive realization of an artificial cilium. The chapter reviews our numerical work, where we explore how the filament can be used for pumping fluid. Our investigations demonstrate that three‐dimensional strokes have a considerably higher pumping performance than their two‐dimensional counterparts. In addition, we mimic metachronal waves in a line of beating cilia by applying actuating fields to each filament separately with a constant phase shift between nearest neighbors. We demonstrate that a specific phase shift enhances the pumping performance strongly and thereby reveal an essential property of metachronal waves in nature.
Putative antirecombinase Srs2 DNA helicase promotes noncrossover homologous recombination avoiding loss of heterozygosity
Authors: Miura Tohru , Shibata Takehiko , Kusano Kohji 
Published: September 2013

Significance
Human health is generally maintained even when important genes are mutated because the human genome is diploid, with two sets of genomic DNA. Thus, various genes are heterozygous, with one functional and one defective allele at their loci. Somatic cells often incur DNA double-strand breaks by the direct effects of DNA-damaging agents, including oxidative stress, and indirectly, such as through DNA replication-fork collapse at damaged sites. Double-strand breaks are repaired through recombination processes, including homologous recombination and nonhomologous end-joining. These processes include the risk of losing a functional allele, called loss of heterozygosity (LOH). This study revealed that a putative antirecombinase, Srs2 DNA helicase, is a key enzyme to promote LOH-less recombination repair of double-strand breaks.
Structural features of Argonaute–GW182 protein interactions
Authors: Pfaff Janina , Hennig Janosch , Herzog Franz , Aebersold Ruedi , Sattler Michael , Niessing Dierk , Meister Gunter 
Published: September 2013

Significance
MicroRNAs (miRNAs) are short RNA molecules that negatively regulate the expression of protein-coding genes in many eukaryotes. In order to do so, miRNAs interact with a member of the Argonaute (Ago) protein family and guide it to partially complementary sequences on mRNAs. Ago proteins interact with a member of the GW182 protein family, which, in turn, recruits additional factors and coordinates all downstream steps. In our study, we have characterized Ago–GW182 protein interactions using biochemical and biophysical methods. We define the interaction surfaces on GW182 and Ago proteins and provide a model for the binding mechanism and specificity.
Early evolution of the T-box transcription factor family
Authors: Sebé-Pedrós Arnau , Ariza-Cosano Ana , Weirauch Matthew T. , Leininger Sven , Yang Ally , Torruella Guifré , Adamski Marcin , Adamska Maja , Hughes Timothy R. , Gómez-Skarmeta José Luis , Ruiz-Trillo Iñaki 
Published: September 2013

SignificanceThe T-box transcription factors are key players in animal development and they were considered strictly animal-specific. We show that T-box genes have instead an important premetazoan evolutionary history, being present in several nonmetazoan unicellular taxa. Notably, we find thatCapsaspora owczarzaki, a unicellular relative of animals, has a Brachyury homolog functionally conserved with metazoans. Through experiments inXenopus, we demonstrate thatC. owczarzakiBrachyury lacks, however, the target specificity displayed by metazoan Brachyury homologs, including sponges. This suggests that the subfunctionalization of T-box classes was established at the onset of Metazoa through new interactions with cofactors, concomitantly with the diversification of the T-box family.
Protein evolution along phylogenetic histories under structurally constrained substitution models
Authors: Arenas Miguel , Dos Santos Helena G. , Posada David , Bastolla Ugo 
Published: September 2013

AbstractMotivation: Models of molecular evolution aim at describing the evolutionary processes at the molecular level. However, current models rarely incorporate information from protein structure. Conversely, structure-based models of protein evolution have not been commonly applied to simulate sequence evolution in a phylogenetic framework, and they often ignore relevant evolutionary processes such as recombination. A simulation evolutionary framework that integrates substitution models that account for protein structure stability should be able to generate more realistic in silico evolved proteins for a variety of purposes.Results: We developed a method to simulate protein evolution that combines models of protein folding stability, such that the fitness depends on the stability of the native state both with respect to unfolding and misfolding, with phylogenetic histories that can be either specified by the user or simulated with the coalescent under complex evolutionary scenarios, including recombination, demographics and migration. We have implemented this framework in a computer program called ProteinEvolver. Remarkably, comparing these models with empirical amino acid replacement models, we found that the former produce amino acid distributions closer to distributions observed in real protein families, and proteins that are predicted to be more stable. Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process.Availability: ProteinEvolver is written in C, can run in parallel and is freely available from http://code.google.com/p/proteinevolver/.Contact: marenas@cbm.uam.esSupplementary information: Supplementary data are available at Bioinformatics online.
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database
Authors: Pedersen Brent S. , Yang Ivana V. , De Subhajyoti 
Published: September 2013

Abstract
Motivation: The biological significance of genomic features is often context dependent. Annotating a particular dataset with existing external data can provide insight into function.
Results: We present CruzDB, a fast and intuitive programmatic interface to the University of California, Santa Cruz (UCSC) genome browser that facilitates integrative analyses of diverse local and remotely hosted datasets. We showcase the syntax of CruzDB using microRNA binding sites as examples, and further demonstrate its utility with three biological discoveries. First, DNA replication timing is stratified in gene regions—exons tend to replicate early and introns late during S phase. Second, several non-coding variants associated with cognitive functions map to lincRNA transcripts of relevant function, suggesting potential function of these regulatory RNAs in neuronal diseases. Third, lamina-associated genomic regions are highly enriched in olfaction-related genes, indicating a role of nuclear organization in their regulation.
Availability: CruzDB is available at https://github.com/brentp/cruzdb under the MIT open-source license.
Contact: bpederse@gmail.com or subhajyoti.de@ucdenver.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Complement protein C3 exacerbates prion disease in a mouse model of chronic wasting disease
Authors: Michel Brady , Ferguson Adam , Johnson Theodore , Bender Heather , Meyerett-Reid Crystal , Wyckoff A. Christy , Pulford Bruce , Telling Glenn C. , Zabel Mark D. 
Published: September 2013

Abstract
Accumulating evidence shows a critical role of the complement system in facilitating attachment of prions to both B cells and follicular dendritic cells and assisting in prion replication. Complement activation intensifies disease in prion-infected animals, and elimination of complement components inhibits prion accumulation, replication and pathogenesis. Chronic wasting disease (CWD) is a highly infectious prion disease of captive and free-ranging cervid populations that utilizes the complement system for efficient peripheral prion replication and most likely efficient horizontal transmission. Here we show that complete genetic or transient pharmacological depletion of C3 prolongs incubation times and significantly delays splenic accumulation in a CWD transgenic mouse model. Using a semi-quantitative prion amplification scoring system we show that C3 impacts disease progression in the early stages of disease by slowing the rate of prion accumulation and/or replication. The delayed kinetics in prion replication correlate with delayed disease kinetics in mice deficient in C3. Taken together, these data support a critical role of C3 in peripheral CWD prion pathogenesis.
The AP-1 transcription factor JunD activates the leukocyte immunoglobulin-like receptor 1 distal promoter
Authors: Davidson Chelsea L. , Cameron Lisa E. , Burshtyn Deborah N. 
Published: September 2013

Abstract
Leukocyte immunoglobulin-like receptor 1 (LILRB1) is an inhibitory receptor that binds classical and non-classical MHC-I as well as UL18, a viral MHC-I homolog. LILRB1 is encoded within the leukocyte receptor complex and is widely expressed on immune cells. Two distinct promoters used differentially by lymphoid and myeloid cells were previously identified, but little is known regarding molecular regulation of each promoter or cell-type-specific usage. Here, we have investigated the transcriptional regulation of human LILRB1 focusing on elements that drive expression in NK cells. We found that while both the distal and proximal promoter regions are active in reporter plasmids in lymphoid and myeloid cells, the proximal promoter is used minimally to transcribe LILRB1 in NK cells compared with monocytes. We defined a 120-bp core region of transcriptional activity in the distal promoter that can bind several factors in NK cell nuclear extracts. Within this region, we investigated overlapping putative AP-1 sites. An inhibitor of JNK decreased LILRB1 transcript in a LILRB1+ NK cell line. Upon examining binding of specific AP-1 factors, we found JunD associated with the LILRB1 distal promoter. Finally, depletion of JunD led to a decrease in distal promoter transcript, indicating an activating role for JunD in regulation of LILRB1 transcription. This study presents the first description of regions/factors required for activity of the LILRB1 distal promoter, the first description of a role for JunD in NK cells and suggests a potential mechanism for dynamic regulation of LILRB1 by cytokines.
A synchrotron jet from a post-asymptotic giant branch star
Authors: Pérez-Sánchez A. F. , Vlemmings W. H. T. , Tafoya D. , Chapman J. M. 
Published: September 2013

Abstract
The evolution of low- and intermediate-initial-mass stars beyond the asymptotic giant branch (AGB) remains poorly understood. High-velocity outflows launched shortly after the AGB phase are thought to be the primary shaping mechanism of bipolar and multipolar planetary nebulae. However, little is known about the launching and driving mechanism for these jets, whose momentum and energy often far exceed the energy that can be provided by radiation pressure alone. Here, we report on the direct evidence of a magnetically collimated jet shaping the bipolar morphology of the circumstellar envelope of a post-AGB star. We present radio continuum observations of the post-AGB star IRAS 15445−5449 (OH 326.5−0.4) which has water masers tracing a fast bipolar outflow. Our observations confirm the earlier observed steep negative spectral index of the spectral energy distribution (SED) above ∼3 GHz, and resolve, for the first time, the emission to originate from a radio jet, proving the existence of such jets around a post-AGB star. The SED is consistent with a synchrotron jet embedded in a sheath of thermal electrons. We find a close correspondence between the extent and direction of the synchrotron jet and the bipolar shape of the object observed at other wavelengths, suggesting that the jet is responsible for the source morphology. The jet is collimated by a magnetic field of the order of mG at almost 7000 au from the central star. We recover observations from the Australia Telescope Compact Array archive that indicate that the emission measure of the thermal component has increased by a factor of 3 between 1998 and 2005 after which it has remained constant. The short time-scale evolution of the radio emission suggests a short lifetime for the jet. The observations of a synchrotron jet from a post-AGB star with characteristics similar to those from protostars and young stellar objects, for instance, suggest that magnetic launching and collimation is a common feature of astrophysical jets.
Critical Role of Interleukin-11 in Isoflurane-mediated Protection against Ischemic Acute Kidney Injury in Mice
Authors: Ham Ahrom , Kim Mihwa , Kim Joo Yun , Brown Kevin M. , Yeh James , D’Agati Vivette D. , Lee H. Thomas 
Published: September 2013

Abstract

Background:
Isoflurane releases renal tubular transforming growth factor-β1 (TGF-β1) and protects against ischemic acute kidney injury. Recent studies suggest that TGF-β1 can induce a cytoprotective cytokine interleukin (IL)-11. In this study, the authors tested the hypothesis that isoflurane protects against ischemic acute kidney injury by direct induction of renal tubular IL-11 synthesis.

Methods:
Human kidney proximal tubule cells were treated with 1.25–2.5% isoflurane or carrier gas (room air + 5% carbon dioxide) for 0–16 h. The authors also anesthetized C57BL/6 mice with 1.2% isoflurane or with equianesthetic dose of pentobarbital for 4 h. In addition, the authors subjected IL-11 receptor (IL-11R) wild-type, IL-11R–deficient, or IL-11 neutralized mice to 30-min renal ischemia followed by reperfusion under 4 h of anesthesia with pentobarbital or isoflurane (1.2%).

Results:
Isoflurane increased IL-11 synthesis in human (approximately 300–500% increase, N = 6) and mouse (23 ± 4 [mean ± SD] fold over carrier gas group, N = 4) proximal tubule cells that were attenuated by a TGF-β1–neutralizing antibody. Mice anesthetized with isoflurane showed significantly increased kidney IL-11 messenger RNA (13.8 ± 2 fold over carrier gas group, N = 4) and protein (31 ± 9 vs. 18 ± 2 pg/mg protein or approximately 80% increase, N = 4) expression compared with pentobarbital-anesthetized mice, and this increase was also attenuated by a TGF-β1–neutralizing antibody. Furthermore, isoflurane-mediated renal protection in IL-11R wild-type mice was absent in IL-11R–deficient mice or in IL-11R wild-type mice treated with IL-11–neutralizing antibody (N = 4–6).

Conclusion:
In this study, the authors suggest that isoflurane induces renal tubular IL-11 via TGF-β1 signaling to protect against ischemic acute kidney injury.
Human Milk Oligosaccharides Protect Against Enteropathogenic Escherichia coli Attachment In Vitro and EPEC Colonization in Suckling Mice
Authors: Manthey Carolin F. , Autran Chloe A. , Eckmann Lars , Bode Lars 
Published: September 2013

ABSTRACTBreast‐feeding reduces the risk of enteric bacterial infections in newborns in part because of human milk oligosaccharides (HMOs), complex glycans that are present in human milk, but not in infant formula. Enteropathogenic Escherichia coli (EPEC) are attaching/effacing pathogens that cause serious diarrheal illness with potentially high mortality in infants. We isolated HMOs from pooled human milk and found that they significantly reduce EPEC attachment to cultured epithelial cells. In suckling mice, administration of HMOs significantly reduced colonization with EPEC compared with untreated controls. These data suggest an essential role for HMOs in the prevention of EPEC infections in human infants.
Primary Spontaneous Cerebrospinal Fluid Leaks and Idiopathic Intracranial Hypertension
Authors: Pérez Mario A. , Bialer Omer Y. , Bruce Beau B. , Newman Nancy J. , Biousse Valérie 
Published: September 2013

Introduction:
Idiopathic intracranial hypertension (IIH) is increasingly recognized as a cause of spontaneous cerebrospinal fluid (CSF) leak in the otolarnygological and neurosurgical literature. The diagnosis of IIH in patients with spontaneous CSF leaks typically is made a few weeks after surgical repair of the leak when symptoms and signs of elevated intracranial pressure (ICP) appear.

Methods:
Case reports and literature review. Two young obese women developed spontaneous CSF rhinorrhea related to an empty sella in one and a cribriform plate encephalocele in the other. Both patients underwent surgical repair of the CSF leak. A few weeks later, they developed chronic headaches and bilateral papilledema. Lumbar punctures showed elevated CSF opening pressures with normal CSF contents, with temporary improvement of headaches. A man with a 3-year history of untreated IIH developed spontaneous CSF rhinorrhea. He experienced improvement of his headaches and papilledema after a CSF shunting procedure, and the rhinorrhea resolved after endoscopic repair of the leak.

Results:
These cases and the literature review confirm a definite association between IIH and spontaneous CSF leak based on: 1) similar demographics; 2) increased ICP in some patients with spontaneous CSF leak after leak repair; 3) higher rate of leak recurrence in patients with raised ICP; 4) patients with intracranial hypertension secondary to tumors may develop CSF leak, confirming that raised ICP from other causes than IIH can cause CSF leak.

Conclusions:
CSF leak occasionally may keep IIH patients symptom-free; however, classic symptoms and signs of intracranial hypertension may develop after a CSF leak is repaired, exposing these patients to a high risk of recurrence of the leak unless an ICP-lowering intervention is performed.