bluuebunny/crossref_metadata_2025_split huggingface dataset:
Some Effects of Bone-Conducted Masking
Authors: Schoeny Zahrl G. , Goetzinger Cornelius P. , Knox Albert W. 
Published: August 2014

Twenty subjects with normal hearing and 20 subjects with sensori-neural hearing loss were examined relative to the effects of wide- and narrow-band white noise delivered by bone conduction at the forehead; differences between thresholds with interrupted- and continuous-tone presentation under the conditions of quiet, wide-band noise, narrow-band noise; the difference between threshold shifts at 1 000 and 2 000 cps when the SAL masking technique is used; and differences between SAL and conventional bone-conduction thresholds at 1 000 or 2 000 cps.
Narrow-band noise produced less shift than wide-band noise under all conditions Differences between interrupted- and continuous-tone presentation yielded better thresholds. Shifts at 1 000 cps and 2 000 cps were significantly different, with the shift at 1 000 cps being greater.
Efficacy of Speech Therapy with Educable Mentally Retarded Children
Authors: Wilson Frank B. 
Published: August 2014

A two-phase study was conducted to evaluate the articulatory abilities of 777 educable mentally retarded children between the ages of 6 to 16 years in a public school setting. In Phase I, an analysis of articulation acquisition by mental age was computed. The children were then divided into speech-deviant and normal groups, and the articulatory skills of the speech deviant group were analyzed. Substitution and omission errors tended to decrease with increasing mental age, but distortion errors increased.
Phase II was an attempt to evaluate the effect of articulation therapy on sound error reduction over a three-year period. The speech-deviant group was subdivided into three groups: Experimental, Placebo, and Control. Differences in sound error reduction among the three groups were not significant.
Imitative Altruism by Deaf Children
Authors: Schwartz Tanis , Bryan James H. 
Published: August 2014

The study was designed to investigate the influence of a behavioral model upon hearing-impaired children’s behavior and judgments. Children from a residential school for the deaf witnessed a model practice either charity or greed and preach charity, greed, or normatively neutral material.
A significant effect was obtained for the practices of the model; 30 of the 32 subjects imitated the behavior of the model to whom he had been exposed. Results are discussed regarding their implication for theories of altruistic behavior and remedial programs for the deaf.
Three Studies of Deficits in Pantomimic Expression and Pantomimic Recognition in Aphasia
Authors: Duffy Robert J. , Duffy Joseph R. 
Published: August 2014

Studies were conducted to investigate aphasic deficits in pantomimic behaviors. Three groups of subjects were used: 47 aphasics; 27 right-hemisphere-damaged; and 11 controls.
Study I replicates a previous study of pantomimic recognition deficits (Duffy, Duffy, & Pearson, 1975) and essentially duplicates the previous findings of significant deficits of pantomimic recognition in aphasic subjects that are highly correlated with their verbal deficits.
Study II examines the relationship between deficits in pantomimic recognition and expression; and the relationships between these two nonverbal behaviors mad aphasic verbal deficits. Zero order correlations, partial correlations, and multiple regression analyses are presented. The results show that aphasics exhibit significant deficits in both pantomimic expression and recognition; and, that both of these are highly correlated with aphasic verbal deficits.
Study III is an investigation of tour causal theories of aphasic deficits in pantomimic expression. Zero order correlations, partial correlations, and multiple regression analyses are presented. It is concluded that aphasic pantomimic expressive deficits are not caused by general intellectual deficit or limb apraxia; but, they are associated with a central symbolic disorder or a verbal mediation deficit.
The implications of these studies for an understanding of the nature of aphasia as a syndrome which includes both verbal and nonverbal impairments are discussed.
Procedures for Verification of Electrode Placement in EMG Studies of Orofacial and Mandibular Muscles
Authors: O'Dwyer Nicolas J. , Quinn Peter T. , Guitar Barry E. , Andrews Gavin , Neilson Peter D. 
Published: August 2014

Many muscles used in speech are small and intimately interconnected. There is a need for anatomical and physiological data which would allow identification of the particular muscle fibers being recorded in electromyographic (EMG) investigations.
EMG recordings were taken from eighteen orofacial and mandibular muscles while gestures believed to be specific to each muscle were performed. The anatomic criteria for the placement of the electrodes, the quality of the EMG spikes and interference patterns obtained, and the degree of differentiation of the temporal sequence of activity from that in neighboring muscles were used to decide on the degree of certainty that a particular muscle was being recorded. The appropriateness of each gesture as a stimulus to any muscle was determined on the basis of the level of activation occurring with the gesture relative to other muscles and its degree of variability between subjects.
Highway proximity and black carbon from cookstoves as a risk factor for higher blood pressure in rural China
Authors: Baumgartner Jill , Zhang Yuanxun , Schauer James J. , Huang Wei , Wang Yuqin , Ezzati Majid 
Published: August 2014

SignificanceAir pollution is a leading health risk factor and important contributor to regional climate change in China and other parts of Asia. China’s particulate matter (PM) air pollution dramatically exceeds health guidelines and is impacted by industrial emissions, motor vehicles, and household use of biomass and coal fuels. Black carbon (BC) from biomass and fossil fuel burning is a major climate-forcing component of PM. We found that BC exposure from biomass smoke is more strongly associated with blood pressure than total PM mass, and that coexposure to motor vehicle emissions may strengthen BC’s impact. Air pollution mitigation efforts focusing on reducing combustion pollution are likely to have major benefits for climate and human health.
The transition between the niche and neutral regimes in ecology
Authors: Fisher Charles K. , Mehta Pankaj 
Published: August 2014

Significance
In recent years, there has been a vigorous debate among ecologists over the merits of two contrasting models of biodiversity: the niche and neutral theories of ecology. Using two different theoretical models of ecological dynamics, we show that there is a transition between a selection-dominated regime (the niche phase) and a drift-dominated regime (the neutral phase). This is analogous to the phase diagram of water, which can be in the solid, liquid, or gas phase, depending on the temperature and pressure. Our results demonstrate how the niche and neutral theories both emerge from the same underlying ecological principles.
Src promotes GTPase activity of Ras via tyrosine 32 phosphorylation
Authors: Bunda Severa , Heir Pardeep , Srikumar Tharan , Cook Jonathan D. , Burrell Kelly , Kano Yoshihito , Lee Jeffrey E. , Zadeh Gelareh , Raught Brian , Ohh Michael 
Published: August 2014

Significance
Despite the well-established connection between Ras and Src, there currently is no evidence of direct interaction between these two proteins. We show here that Src binds to and phosphorylates GTP-loaded Ras on a conserved Y32 residue within the switch I region. It has been shown that Raf binds to Ras with an affinity 1,000-fold greater than that of GAP. However, it has remained unclear how GAP is able to outcompete Raf for Ras upon Raf displacement. We show here that Y32 phosphorylation inhibits Raf binding to Ras and concomitantly promotes GAP association and GTP hydrolysis, thereby ensuring unidirectionality to the Ras GTPase cycle. These findings reveal new fundamental mechanistic insight into how Src negatively regulates Ras.
The Cap1–claudin-4 regulatory pathway is important for renal chloride reabsorption and blood pressure regulation
Authors: Gong Yongfeng , Yu Miao , Yang Jing , Gonzales Ernie , Perez Ronaldo , Hou Mingli , Tripathi Piyush , Hering-Smith Kathleen S. , Hamm L. Lee , Hou Jianghui 
Published: August 2014

Significance
How the kidney handles chloride reabsorption has long been a mystery. Here, we have discovered a pathway in the kidney that utilizes channel-activating protease 1 and claudin-4 to physiologically regulate tight junction permeability to chloride. Such a pathway not only is important in renal regulation of chloride but also may play key roles in chloride transport across many other epithelia such as the lung, the salivary gland, and the skin. This discovery also attests to a concept of “druggable” tight junction. Proteases or protease-dependent mechanisms may be developed as pharmacological tools to transiently regulate tight junction permeability in the kidney, the intestine, and the blood–brain barrier.
Inhibition of Borna disease virus replication by an endogenous bornavirus-like element in the ground squirrel genome
Authors: Fujino Kan , Horie Masayuki , Honda Tomoyuki , Merriman Dana K. , Tomonaga Keizo 
Published: August 2014

Significance
Sequences derived from ancient viruses have been shown to make up a substantial part of animal genomes. Bornaviruses, a genus of nonsegmented, negative-sense RNA virus, also have left their DNA copies in the genomes of a number of vertebrate lineages. Recent studies have demonstrated that some endogenous bornavirus-like elements (EBLs) may have acquired functions in their hosts as a result of exaptation. In this study, we show that protein encoded by an EBL in the genome of the thirteen-lined ground squirrel efficiently blocks infection and replication of extant bornavirus. To our knowledge, this is the first report showing that endogenous nonretroviral RNA virus elements may function in antiviral defense, providing a potential role for RNA virus endogenization in host evolution.
A critical reanalysis of the relationship between genomics and well-being
Authors: Brown Nicholas J. L. , MacDonald Douglas A. , Samanta Manoj Pratim , Friedman Harris L. , Coyne James C. 
Published: August 2014

SignificanceThis article critically reanalyzes the work of Fredrickson et al. [Fredrickson BL, et al. (2013)Proc Natl Acad Sci USA110(33):13684–13689], which claimed to show that distinct dimensions of psychological well-being are differentially correlated with levels of expression of a selection of genes associated with distinct forms of immune response. We show that not only is Fredrickson et al.’s article conceptually deficient, but more crucially, that their statistical analyses are fatally flawed, to the point that their claimed results are in fact essentially meaningless. We believe that our findings may have implications for the reevaluation of other published genomics research based on comparable statistical analyses and that a variant of our methodology might be useful for such a reevaluation.
Transcription factor PREP1 induces EMT and metastasis by controlling the TGF-β–SMAD3 pathway in non-small cell lung adenocarcinoma
Authors: Risolino Maurizio , Mandia Nadia , Iavarone Francescopaolo , Dardaei Leila , Longobardi Elena , Fernandez Serena , Talotta Francesco , Bianchi Fabrizio , Pisati Federica , Spaggiari Lorenzo , Harter Patrick N. , Mittelbronn Michel , Schulte Dorothea , Incoronato Mariarosaria , Di Fiore Pier Paolo , Blasi Francesco , Verde Pasquale 
Published: August 2014

Significance
Epithelial–mesenchymal transition (EMT) is a transdifferentiation program implicated in tumor cell dissemination, controlled by networks of transcription complexes responsive to paracrine factors, such as TGF-β. Pre–B-cell leukemia homeobox (Pbx)-regulating protein-1 (PREP1) is a ubiquitous homeodomain transcription factor involved in early development, genomic stability, insulin sensitivity, and hematopoiesis. PREP1 is a haploinsufficient oncosuppressor in mouse tumorigenesis. By characterizing PREP1 as a novel regulator of EMT in human lung adenocarcinoma, we show that PREP1 also harbors prometastatic properties. While autosustaining its activity by stabilizing its transcriptional partner PBX1, PREP1 modulates the responsiveness of lung cancer cells to TGF-β by controlling the expression of two proinvasive transcription factors (SMAD3 and Fos-related antigen 1) implicated in metastasis mechanisms. Thus, PREP1 represents a novel, promising therapeutic target in non-small cell lung cancer.
Ultrafast tissue staining with chemical tags
Authors: Kohl Johannes , Ng Julian , Cachero Sebastian , Ciabatti Ernesto , Dolan Michael-John , Sutcliffe Ben , Tozer Adam , Ruehle Sabine , Krueger Daniel , Frechter Shahar , Branco Tiago , Tripodi Marco , Jefferis Gregory S. X. E. 
Published: August 2014

Significance
Cellular and subcellular structures in thick biological samples typically are visualized either by genetically encoded fluorescent proteins or by antibody staining against proteins of interest. However, both approaches have drawbacks. Fluorescent proteins do not survive treatments for tissue preservation well, are available in only a few colors, and often emit weak signals. Antibody stainings are slow, do not penetrate thick samples well, and often result in considerable background staining. We have overcome these limitations by using genetically encoded chemical tags that result in rapid, even staining of thick biological samples with high-signal and low-background labeling. We introduce tools for flies and mice that drastically improve the speed and specificity for labeling genetically marked cells in biological tissues.
Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization
Authors: Le Nouën Cyril , Brock Linda G. , Luongo Cindy , McCarty Thomas , Yang Lijuan , Mehedi Masfique , Wimmer Eckard , Mueller Steffen , Collins Peter L. , Buchholz Ursula J. , DiNapoli Joshua M. 
Published: August 2014

Significance
Human respiratory syncytial virus (RSV) is the most important viral agent of serious pediatric respiratory-tract disease. We designed new live attenuated RSV vaccine candidates by codon-pair deoptimization (CPD). Specifically, viral ORFs were recoded to increase the usage of underrepresented codon pairs, leaving amino acid coding unchanged. CPD viruses were temperature-sensitive and grew less efficiently in vitro than wild-type RSV. In addition, the CPD viruses exhibited a range of restriction in mice and African green monkeys that compared favorably with existing attenuated strains presently in clinical studies. This study produced examples of a new type of vaccine candidate for RSV and showed that CPD of a nonsegmented negative-strand RNA virus can rapidly generate vaccine candidates with a range of attenuation.
Ghrelin promotes hepatic lipogenesis by activation of mTOR-PPARγ signaling pathway
Authors: Li Ziru , Xu Geyang , Qin Yan , Zhang Chao , Tang Hong , Yin Yue , Xiang Xinxin , Li Yin , Zhao Jing , Mulholland Michael , Zhang Weizhen 
Published: August 2014

Significance
The peripheral effect of ghrelin on energy metabolism has been controversial. Our study demonstrates a direct peripheral effect of ghrelin to increase de novo lipogenesis in hepatocytes. Moreover, we define mammalian target of rapamycin (mTOR)-peroxisome proliferator-activated receptor-γ (PPARγ) signaling pathway as the intracellular target of ghrelin in hepatocytes. The effect of ghrelin is mediated by the direct interaction between raptor and PPARγ. Our study identifies a previously unidentified pathway to treat NFALD via targeting hepatic ghrelin receptor/mTOR/PPARγ.
Induction of broadly cross-reactive antibody responses to the influenza HA stem region following H5N1 vaccination in humans
Authors: Ellebedy Ali H. , Krammer Florian , Li Gui-Mei , Miller Matthew S. , Chiu Christopher , Wrammert Jens , Chang Cathy Y. , Davis Carl W. , McCausland Megan , Elbein Rivka , Edupuganti Srilatha , Spearman Paul , Andrews Sarah F. , Wilson Patrick C. , García-Sastre Adolfo , Mulligan Mark J. , Mehta Aneesh K. , Palese Peter , Ahmed Rafi 
Published: August 2014

Significance
Vaccination is the most effective means of attaining protection against influenza viruses. However, the constantly evolving nature of influenza viruses enables them to escape preexisting immune surveillance, and thus thwarts public health efforts to control influenza annual epidemics and occasional pandemics. One solution is to elicit antibodies directed against highly conserved epitopes, such as those within the stem region of influenza HA, the principal target of virus-neutralizing antibody responses. This study shows that annual influenza vaccines induce antibody responses that are largely directed against the highly variable HA head region. In contrast, heterologous immunization with HA derived from influenza strains that are currently not circulating in humans (e.g. H5N1) can substantially increase HA stem-specific responses.
Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition
Authors: Zadran Sohila , Arumugam Rameshkumar , Herschman Harvey , Phelps Michael E. , Levine R. D. 
Published: August 2014

Significance
Epithelial-to-mesenchymal transition (EMT) has been investigated extensively in cancer progression. Tumor cells induced to undergo an EMT acquire mesenchymal, invasive properties. We apply methods developed in chemical reaction dynamics to characterize the changing transcriptional profile during an EMT and trace the temporal unfolding of the transition on a free energy landscape. The analysis identifies three EMT stages, including passage through an intermediate, low-energy maturation state. The uphill energy requirements during the ascent past maturation correlate with an increase in ATP production. A stable cell machinery whose performance remains unperturbed underlies the EMT.
What is the Impact of Comorbid Depression on Adolescent Substance Abuse Treatment?
Authors: Hersh Jacqueline , Curry John F. , Kaminer Yifrah 
Published: August 2014

Background Substance use disorders (SUDs) are among the most common psychiatric diagnoses in adolescents. Some research suggests that comorbid depression in adolescents with SUD is associated with increased likelihood of alcohol dependence, poorer social competence, and greater risk for suicide attempts. However, little is known about how depression influences adolescent substance abuse treatment retention and outcomes. Methods This review aimed to summarize the effects of comorbid depression on treatment retention and outcomes across 13 adolescent SUD treatment studies. Results Results indicated that depression has a mixed relationship with treatment retention and outcomes, exerting a negative, positive, or nonsignificant effect depending on aspects of the study. Conclusions More research needs to be done, particularly addressing the potential mediators and moderators of the relationship between depression and SUD outcomes. Importantly, recognizing that the studies varied widely in hypotheses and research methods, the field needs to develop more standardized methods to allow for a clearer understanding of the role of comorbid depression.
Towards a piRNA prediction using multiple kernel fusion and support vector machine
Authors: Brayet Jocelyn , Zehraoui Farida , Jeanson-Leh Laurence , Israeli David , Tahi Fariza 
Published: August 2014

Abstract
Motivation: Piwi-interacting RNA (piRNA) is the most recently discovered and the least investigated class of Argonaute/Piwi protein-interacting small non-coding RNAs. The piRNAs are mostly known to be involved in protecting the genome from invasive transposable elements. But recent discoveries suggest their involvement in the pathophysiology of diseases, such as cancer. Their identification is therefore an important task, and computational methods are needed. However, the lack of conserved piRNA sequences and structural elements makes this identification challenging and difficult.
Results: In the present study, we propose a new modular and extensible machine learning method based on multiple kernels and a support vector machine (SVM) classifier for piRNA identification. Very few piRNA features are known to date. The use of a multiple kernels approach allows editing, adding or removing piRNA features that can be heterogeneous in a modular manner according to their relevance in a given species. Our algorithm is based on a combination of the previously identified features [sequence features (k-mer motifs and a uridine at the first position) and piRNAs cluster feature] and a new telomere/centromere vicinity feature. These features are heterogeneous, and the kernels allow to unify their representation. The proposed algorithm, named piRPred, gives promising results on Drosophila and Human data and outscores previously published piRNA identification algorithms.
Availability and implementation: piRPred is freely available to non-commercial users on our Web server EvryRNA http://EvryRNA.ibisc.univ-evry.fr
Contact: tahi@ibisc.univ-evry.fr
Estimating the activity of transcription factors by the effect on their target genes
Authors: Schacht Theresa , Oswald Marcus , Eils Roland , Eichmüller Stefan B. , König Rainer 
Published: August 2014

Abstract
Motivation: Understanding regulation of transcription is central for elucidating cellular regulation. Several statistical and mechanistic models have come up the last couple of years explaining gene transcription levels using information of potential transcriptional regulators as transcription factors (TFs) and information from epigenetic modifications. The activity of TFs is often inferred by their transcription levels, promoter binding and epigenetic effects. However, in principle, these methods do not take hard-to-measure influences such as post-transcriptional modifications into account.
Results: For TFs, we present a novel concept circumventing this problem. We estimate the regulatory activity of TFs using their cumulative effects on their target genes. We established our model using expression data of 59 cell lines from the National Cancer Institute. The trained model was applied to an independent expression dataset of melanoma cells yielding excellent expression predictions and elucidated regulation of melanogenesis.
Availability and implementation: Using mixed-integer linear programming, we implemented a switch-like optimization enabling a constrained but optimal selection of TFs and optimal model selection estimating their effects. The method is generic and can also be applied to further regulators of transcription.
Contact: rainer.koenig@uni-jena.de
Supplementary information: Supplementary data are available at Bioinformatics online.