bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of developmental alcohol exposure vs. intubation stress on BDNF and TrkB expression in the hippocampus and frontal cortex of neonatal rats
Authors: Boschen K.E. , Criss K.J. , Palamarchouk V. , Roth T.L. , Klintsova A.Y. 
Published: April 2015

AbstractThird trimester‐equivalent alcohol exposure causes significant deficits in hippocampal and cortical neuroplasticity, resulting in alterations to dendritic arborization, hippocampal adult neurogenesis, and performance on learning tasks. The current study investigated the impact of neonatal alcohol exposure (postnatal days 4–9, 5.25 g/kg/day) on expression of brain‐derived neurotrophic factor (BDNF) and the tropomyosin‐related kinase B (TrkB) receptor in the hippocampal and frontal cortex of infant Long–Evans rats. Levels of BDNF protein were increased in the hippocampus, but not frontal cortex, of alcohol‐exposed rats 24 h after the last dose, when compared with undisturbed (but not sham‐intubated) control animals. BDNF protein levels showed a trend toward increase in hippocampus of sham‐intubated animals as well, suggesting an effect of the intubation procedure. TrkB protein was increased in the hippocampus of alcohol‐exposed animals compared to sham‐intubated pups, indicating an alcohol‐specific effect on receptor expression. In addition, expression of bdnf total mRNA in alcohol‐exposed and sham‐intubated pups was enhanced in the hippocampus; however, there was a differential effect of alcohol and intubation stress on exon I‐ and IV‐specific mRNA transcripts. Further, plasma corticosterone was found to be increased in both alcohol‐exposed and sham‐intubated pups compared to undisturbed animals. Upregulation of BDNF could potentially represent a neuroprotective mechanism activated following alcohol exposure or stress. The results suggest that alcohol exposure and stress have both overlapping and unique effects on BDNF, and highlight the need for the stress of intubation to be taken into consideration in studies that implement this route of drug delivery.
XXXIX.—Transformations of Hypergeometric Functions of Two Variables
Authors: Erdélyi A. 
Published: April 2015

I. There are several methods for obtaining transformations of hypergeometric functions of two variables.Firstly, by transformation of the hypergeometric series. When the double series is rewritten as an infinite sum of hypergeometric functions of one variable, the known transformation theory of such functions can be applied to each term. This method is quite simple and, in a limited range, very effective for discovering transformations as well as proving them.Secondly, by transformation of the systems of partial differential equations satisfied by the hypergeometric functions. This method, though simple in theory, is rather laborious in practice and not very useful for discovering new transformations.
Local–global overlap in diversity informs mechanisms of bacterial biogeography
Authors: Livermore Joshua A , Jones Stuart E 
Published: April 2015

Abstract
Spatial variation in environmental conditions and barriers to organism movement are thought to be important factors for generating endemic species, thus enhancing global diversity. Recent microbial ecology research suggested that the entire diversity of bacteria in the global oceans could be recovered at a single site, thus inferring a lack of bacterial endemism. We argue this is not the case in the global ocean, but might be in other bacterial ecosystems with higher dispersal rates and lower global diversity, like the human gut. We quantified the degree to which local and global bacterial diversity overlap in a diverse set of ecosystems. Upon comparison of observed local–global diversity overlap with predictions from a neutral biogeography model, human-associated microbiomes (gut, skin, mouth) behaved much closer to neutral expectations whereas soil, lake and marine communities deviated strongly from the neutral expectations. This is likely a result of differences in dispersal rate among ‘patches’, global diversity of these systems, and local densities of bacterial cells. It appears that overlap of local and global bacterial diversity is surprisingly large (but likely not one-hundred percent), and most importantly this overlap appears to be predictable based upon traditional biogeographic parameters like community size, global diversity, inter-patch environmental heterogeneity and patch connectivity.
Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
Authors: Kay Gemma L. , Sergeant Martin J. , Zhou Zhemin , Chan Jacqueline Z.-M. , Millard Andrew , Quick Joshua , Szikossy Ildikó , Pap Ildikó , Spigelman Mark , Loman Nicholas J. , Achtman Mark , Donoghue Helen D. , Pallen Mark J. 
Published: April 2015

AbstractTuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at ‘peak TB’ relate to what we see today. Here we describe 14 genome sequences of M. tuberculosis, representing 12 distinct genotypes, obtained from human remains from eighteenth-century Hungary using metagenomics. All our historic genotypes belong to M. tuberculosis Lineage 4. Bayesian phylogenetic dating, based on samples with well-documented dates, places the most recent common ancestor of this lineage in the late Roman period. We find that most bodies yielded more than one M. tuberculosis genotype and we document an intimate epidemiological link between infections in two long-dead individuals. Our results suggest that metagenomic approaches usefully inform detection and characterization of historical and contemporary infections.
Information flow between interacting human brains: Identification, validation, and relationship to social expertise
Authors: Bilek Edda , Ruf Matthias , Schäfer Axel , Akdeniz Ceren , Calhoun Vince D. , Schmahl Christian , Demanuele Charmaine , Tost Heike , Kirsch Peter , Meyer-Lindenberg Andreas 
Published: April 2015

Significance
Social interaction is the likely driver of human brain evolution, critical for health, and underlies phenomena as varied as childhood development, stock market behavior, and much of what is studied in the humanities. However, appropriate experimental methods to study the underlying brain processes are still developing and technically challenging. Here, we extend previous pioneering approaches in neuroimaging [functional MRI (fMRI) hyperscanning] to provide a method for studying information flow between interacting humans in a two-person approach. A scan environment enabling synchronized data acquisition and interaction-based fMRI tasks is described. We provide a generally applicable analysis method to identify interacting brain systems. Specific social brain systems are identified as drivers of interaction in humans, and we find a link to a measure of social expertise.
Telomere dysfunction causes alveolar stem cell failure
Authors: Alder Jonathan K. , Barkauskas Christina E. , Limjunyawong Nathachit , Stanley Susan E. , Kembou Frant , Tuder Rubin M. , Hogan Brigid L. M. , Mitzner Wayne , Armanios Mary 
Published: April 2015

Significance
Idiopathic pulmonary fibrosis and emphysema are leading causes of mortality, but there are no effective therapies. Mutations in telomerase are the most common identifiable risk factor for idiopathic pulmonary fibrosis. They also predispose to severe emphysema in smokers, occurring at a frequency similar to α-1 antitrypsin deficiency. The work shown here points to alveolar stem cell senescence as a driver of these pathologies. Epithelial stem cell failure was associated with secondary inflammatory recruitment and exquisite susceptibility to injury from “second hits.” The findings suggest that efforts to reverse the stem cell failure state directly, rather than its secondary consequences, may be an effective therapy approach in telomere-mediated lung disease.
Detection of endogenous and food-derived collagen dipeptide prolylhydroxyproline (Pro-Hyp) in allergic contact dermatitis-affected mouse ear
Authors: Kusubata Masashi , Koyama Yoh-ichi , Tometsuka Chisa , Shigemura Yasutaka , Sato Kenji 
Published: April 2015

Abstract
Generation of collagen dipeptides and deposition of orally administered prolylhydroxyproline (Pro-Hyp) in local inflammatory sites were examined in mice with hapten (2,4-dinitrofluorobenzene)-induced dermatitis in the ear. Pro-Hyp content in the hapten-treated ear was significantly higher in the chronic phase of contact dermatitis than the vehicle control. In contrast, hydroxyprolylglycine contents remained at lower levels in all cases compared to Pro-Hyp. Four hours after the ingestion of [13C5,15N]Pro and [13C5,15N]Pro-Hyp, labeled-Pro-Hyp and Pro, respectively, appeared only in the ear with dermatitis. Thus, Pro-Hyp is generated and degraded as part of the rapid synthesis and degradation of collagen in the ear with dermatitis. In addition to the endogenously generated Pro-Hyp, the orally administered Pro-Hyp was deposited in the ears.
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system
Authors: Zhu Fan , Shi Lihong , Engel James Douglas , Guan Yuanfang 
Published: April 2015

Abstract
Motivation: Modeling regulatory networks using expression data observed in a differentiation process may help identify context-specific interactions. The outcome of the current algorithms highly depends on the quality and quantity of a single time-course dataset, and the performance may be compromised for datasets with a limited number of samples.
Results: In this work, we report a multi-layer graphical model that is capable of leveraging many publicly available time-course datasets, as well as a cell lineage-specific data with small sample size, to model regulatory networks specific to a differentiation process. First, a collection of network inference methods are used to predict the regulatory relationships in individual public datasets. Then, the inferred directional relationships are weighted and integrated together by evaluating against the cell lineage-specific dataset. To test the accuracy of this algorithm, we collected a time-course RNA-Seq dataset during human erythropoiesis to infer regulatory relationships specific to this differentiation process. The resulting erythroid-specific regulatory network reveals novel regulatory relationships activated in erythropoiesis, which were further validated by genome-wide TR4 binding studies using ChIP-seq. These erythropoiesis-specific regulatory relationships were not identifiable by single dataset-based methods or context-independent integrations. Analysis of the predicted targets reveals that they are all closely associated with hematopoietic lineage differentiation.
Availability and implementation: The predicted erythroid regulatory network is available at http://guanlab.ccmb.med.umich.edu/data/inferenceNetwork/.
Contact: gyuanfan@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data
Authors: Alon Shahar , Erew Muhammad , Eisenberg Eli 
Published: April 2015

Abstract
Summary: DREAM: detecting RNA editing associated with microRNAs, is a webserver for the identification of mature microRNA editing events using deep sequencing data. Raw microRNA sequencing reads can be provided as input, the reads are aligned against the genome and custom scripts process the data, search for potential editing sites and assess the statistical significance of the findings. The output is a text file with the location and the statistical description of all the putative editing sites detected.
Availability and implementation: DREAM is freely available on the web at http://www.cs.tau.ac.il/∼mirnaed/.
Contact: elieis@post.tau.ac.il
Three minimal sequences found in Ebola virus genomes and absent from human DNA
Authors: Silva Raquel M. , Pratas Diogo , Castro Luísa , Pinho Armando J. , Ferreira Paulo J. S. G. 
Published: April 2015

Abstract
Motivation: Ebola virus causes high mortality hemorrhagic fevers, with more than 25 000 cases and 10 000 deaths in the current outbreak. Only experimental therapies are available, thus, novel diagnosis tools and druggable targets are needed.
Results: Analysis of Ebola virus genomes from the current outbreak reveals the presence of short DNA sequences that appear nowhere in the human genome. We identify the shortest such sequences with lengths between 12 and 14. Only three absent sequences of length 12 exist and they consistently appear at the same location on two of the Ebola virus proteins, in all Ebola virus genomes, but nowhere in the human genome. The alignment-free method used is able to identify pathogen-specific signatures for quick and precise action against infectious agents, of which the current Ebola virus outbreak provides a compelling example.
Availability and Implementation: EAGLE is freely available for non-commercial purposes at http://bioinformatics.ua.pt/software/eagle.
Contact: raquelsilva@ua.pt; pratas@ua.pt
Supplementary Information: Supplementary data are available at Bioinformatics online.
Enterococcus faecalislipoteichoic acid suppressesAggregatibacter actinomycetemcomitanslipopolysaccharide-induced IL-8 expression in human periodontal ligament cells
Authors: Im Jintaek , Baik Jung Eun , Kim Kyoung Whun , Kang Seok-Seong , Jeon Jun Ho , Park Ok-Jin , Kim Hyun Young , Kum Kee-Yeon , Yun Cheol-Heui , Han Seung Hyun 
Published: April 2015

AbstractPeriodontitis is caused by multi-bacterial infection and Aggregatibacter actinomycetemcomitans and Enterococcus faecalis are closely associated with inflammatory periodontal diseases. Although lipopolysaccharide (LPS) of A. actinomycetemcomitans (Aa.LPS) and lipoteichoic acid of E. faecalis (Ef.LTA) are considered to be major virulence factors evoking inflammatory responses, their combinatorial effect on the induction of chemokines has not been investigated. In this study, we investigated the interaction between Aa.LPS and Ef.LTA on IL-8 expression in human periodontal ligament (PDL) cells. Aa.LPS, but not Ef.LTA, substantially induced IL-8 expression at the protein and mRNA levels. Interestingly, Ef.LTA suppressed Aa.LPS-induced IL-8 expression without affecting the binding of Aa.LPS to Toll-like receptor (TLR) 4. Ef.LTA reduced Aa.LPS-induced phosphorylation of mitogen-activated protein kinases, including ERK, JNK and p38 kinase. Furthermore, Ef.LTA inhibited the Aa.LPS-induced transcriptional activities of the activating protein 1, CCAAT/enhancer-binding protein and nuclear factor-kappa B transcription factors, all of which are known to regulate IL-8 gene expression. Ef.LTA augmented the expression of IL-1 receptor–associated kinase-M (IRAK-M), a negative regulator of TLR intracellular signaling pathways, in the presence of Aa.LPS at both the mRNA and protein levels. Small interfering RNA silencing IRAK-M reversed the attenuation of Aa.LPS-induced IL-8 expression by Ef.LTA. Collectively, these results suggest that Ef.LTA down-regulates Aa.LPS-induced IL-8 expression in human PDL cells through up-regulation of the negative regulator IRAK-M.
Lack of IL-17 signaling decreases liver fibrosis in murine schistosomiasis japonica
Authors: Zhang Yuxia , Huang Dake , Gao Wenda , Yan Jun , Zhou Wanling , Hou Xin , Liu Miao , Ren Cuiping , Wang Siying , Shen Jijia 
Published: April 2015

Abstract
Accumulating evidence has identified the profibrogenic properties of IL-17A in organ fibrosis. However, the role of IL-17A signal in liver fibrosis induced by Schistosoma japonicum infection remains unclear. In this study, we investigated liver fibrosis in wild-type (WT) and IL-17RA−/− mice upon S. japonicum infection. Hepatic IL-17A, IL-17C, IL-17E (IL-25), IL-17F, IL-17RA, IL-17RB and IL-17RC transcript levels were determined by RT-PCR. IL-17A+ cells were analyzed by flow cytometry and confocal microscopy among granuloma cells. Immunostaining of IL-17R was performed on liver sections. Collagen deposition was assessed by Van Gieson’s staining. IL-17A, IL-17C, IL-17E, IL-17F, IL-17RA and IL-17RC mRNA levels were dramatically increased in fibrotic livers. Among granuloma cells, CD3+ and CD3− lymphocytes, neutrophils and macrophages were found to express IL-17A. Compared to WT, IL-17RA−/− mice displayed attenuated granulomatous inflammation, liver fibrosis, improved liver function and high survival. Meanwhile, α-smooth muscle actin staining and the expression of fibrogenic genes (transforming growth factor β, IL-13 and collagen-I) as well as IL-17A–induced proinflammatory mediators (IL-1β, IL-6, tumor necrosis factor α, CXCL1 and CXCL2) and proteinases (MMP3 and TIMP1) involved in fibrosis were markedly reduced in IL-17RA−/− mice. In addition, Th2 cytokines IL-4 and IL-17E (IL-25) were also decreased in IL-17RA−/− mice. These results indicated that IL-17A signal contributes to the pathogenesis of liver fibrosis in murine schistosomiasis. This effect was induced possibly by activating hepatic stellate cells and stimulating the release of proinflammatory cytokines and chemokines. Furthermore, the Th2 response was also enhanced by IL-17A signals. Our data demonstrate that IL-17A may serve as a promising target for antifibrotic therapy.
Dizziness
Authors: Brody David L 
Published: April 2015

Dizziness means many different things to different people: lightheadedness, vertigo, poor balance, mental fogginess, and others concerns. Lightheadedness, meaning a feeling like the patient may pass out, is usually due to low blood pressure, often orthostatic hypotension. Vertigo, meaning a sensation of spinning or movement, can be an inner ear problem or a brain problem: Stop toxic substances; if there is nystagmus, refer to ENT for a full evaluation; perform the Dix-Hallpike maneuver to assess for benign paroxysmal positional vertigo; and refer to physical therapy for repositioning maneuvers if positive; consider vestibular rehabilitation; consider a short course of medication such as scopolamine or meclizine; consider ordering an MRI scan of the brain, as sometimes the concussion unmasks another unrelated problem. Dizziness meaning “mental fogginess” usually turns out to be attention deficit. Dizziness meaning vague and nonspecific malaise usually turns out to be fatigue, depression, or anxiety.
Blurry Vision
Authors: Brody David L 
Published: April 2015

Blurry vision after concussion can mean many different things. A loss of acuity in one eye is often due to direct injury to the eye. Intact acuity in each eye, but worse vision with both eyes open is often due to a subtle cranial nerve injury. Subtle 3rd cranial nerve or 4th cranial injuries typically cause vision to be worse looking up or down, whereas 6th nerve injuries are typically worse looking to one side. Visual attention deficit is sometimes described as blurry vision. Migraine auras often cause visual impairment. The chapter suggests modes of treatment for these situations. Paroxysmal changes in vision after concussion should be treated as presumptive migraine, or migraine equivalent even if there is no severe headache. Patients will benefit from best-corrected vision when starting aggressive cognitive rehabilitation even if preexisting visual impairments did not impair them much in everyday life before the concussion.
Special Topics in Children
Authors: Brody David L 
Published: April 2015

This chapter discusses special rules for children under 12 with concussion: (1) Take the history twice: once from the child and once from the parents or guardians. Young children can reliably report headache, nausea, balance problems, problems concentrating, and irritability. Other concerns as well as preinjury problems should be assessed from the parents or guardians. (2) Use age-appropriate language and simplified assessments of severity. (3) Carefully assess for secondary gain factors. A child may either overreport or underreport symptoms to please the parents or guardians. (4) With regard to return to school, sports, and daily life, help the parents or guardians find the “middle way”: not too protective and not too lax. (5) In complex concussion, assess for attention deficit and atypical presentations of migraine, depression, and anxiety. (6) Consider treatment with glucose.
Common Problems, Realistic Solutions
Authors: Saint Sanjay 
Published: April 2015

A hospital-wide intervention is rolled out. There are changes in the team leadership and many operational adjustments: supplies ordered, procedures redesigned, nursing assignments altered. Three major types of troublemakers are described: the active resisters, the organizational constipators, and the timeservers. Motivations range from opposition to any kind of change to a personal animus toward the project champions to a determination to do as little extra work as possible. Requests by patients and their families may be used to try to get around bladder bundle items or a member of the project team may approach nurses with a patronizing attitude. The team cheers short-term progress to encourage staff compliance, solicits concrete criticism as a path to improvement, and adjusts the implementation process to allow for special circumstances. Efforts to use the electronic medical record to game the system must be squelched.
Taking on C. Difficile
Authors: Saint Sanjay 
Published: April 2015

The adaptive approach used in the previous chapters to prevent CAUTI is applied to an initiative to prevent Clostridium difficile infection. These two initiatives differ in terms of their scope, the members of their teams, and the elements of their bundles. For preventing C. difficile, for example, the most important bundle item is antimicrobial stewardship, since the use of broad-spectrum antibiotics vastly increases a person’s risk of becoming infected. Infectious disease physicians or clinical pharmacists examine the circumstances of antimicrobial prescriptions they have filled to see whether they meet infection prevention standards; if not, the prescribing physician will receive prompt feedback. Differences aside, the basic elements of the CAUTI framework apply, from the C-suite’s decision to go ahead with the initiative to the tactics used to sell the C. difficile bundle to the hospital staff.
Smoothed particle hydrodynamics with smoothed pseudo-density
Authors: Yamamoto Satoko , Saitoh Takayuki R. , Makino Junichiro 
Published: April 2015

Abstract
In this paper, we present a new formulation of smoothed particle hydrodynamics (SPH), which, unlike the standard SPH (SSPH), is well behaved at the contact discontinuity. The SSPH scheme cannot handle discontinuities in density (e.g., the contact discontinuity and the free surface), because it requires that the density of fluid is positive and continuous everywhere. Thus there is inconsistency in the formulation of the SSPH scheme at discontinuities of the fluid density. To solve this problem, we introduce a new quantity associated with particles and the “density” of that quantity. This “density” evolves through the usual continuity equation with an additional artificial diffusion term, in order to guarantee the continuity of the “density.” We use this “density,” or pseudo-density, instead of the mass density, to formulate our SPH scheme. We call our new method SPH with smoothed pseudo-density, and we show that it is physically consistent and can handle discontinuities quite well.