bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneity of the Transmembrane Protein Conformation in Purple Membranes Identified by Infrared Nanospectroscopy
Authors: Giliberti Valeria , Badioli Michela , Nucara Alessandro , Calvani Paolo , Ritter Eglof , Puskar Ljiljana , Aziz Emad Flear , Hegemann Peter , Schade Ulrich , Ortolani Michele , Baldassarre Leonetta 
Published: September 2017

AbstractCell membranes are intrinsically heterogeneous, as the local protein and lipid distribution is critical to physiological processes. Even in template systems embedding a single protein type, like purple membranes, there can be a different local response to external stimuli or environmental factors, resulting in heterogeneous conformational changes. Despite the dramatic advances of microspectroscopy techniques, the identification of the conformation heterogeneity is still a challenging task. Tip‐enhanced infrared nanospectroscopy is here used to identify conformational changes connected to the hydration state of the transmembrane proteins contained in a 50 nm diameter cell membrane area, without the need for fluorescent labels. In dried purple membrane monolayers, areas with fully hydrated proteins are found among large numbers of molecules with randomly distributed hydration states. Infrared nanospectroscopy results are compared to the spectra obtained with diffraction‐limited infrared techniques based on the use of synchrotron radiation, in which the diffraction limit still prevents the observation of nanoscale heterogeneity.
Scalable processing and autocovariance computation of big functional data
Authors: Brisaboa Nieves R. , Cao Ricardo , Paramá José R. , Silva‐Coira Fernando 
Published: September 2017

SummaryThis paper presents 2 main contributions. The first is a compact representation of huge sets of functional data or trajectories of continuous‐time stochastic processes, which allows keeping the data always compressed even during the processing in main memory. It is oriented to facilitate the efficient computation of the sample autocovariance function without a previous decompression of the data set, by using only partial local decoding. The second contribution is a new memory‐efficient algorithm to compute the sample autocovariance function. The combination of the compact representation and the new memory‐efficient algorithm obtained in our experiments the following benefits. The compressed data occupy in the disk 75% of the space needed by the original data. The computation of the autocovariance function used up to 13 times less main memory, and run 65% faster than the classical method implemented, for example, in the R package.
Proteomic identification of synaptic caspase substrates
Authors: Victor Ken G. , Heffron Daniel S. , Sokolowski Jennifer D. , Majumdar Usnish , Leblanc Andrea , Mandell James W. 
Published: September 2017

AbstractThe dismantling and elimination of excess neurons and their connections (pruning) is essential for brain development and may be aberrantly reactivated in some neurodegenerative diseases. Growing evidence implicates caspase‐mediated apoptotic and nonapoptotic cascades in the dysfunction and death of neurons in neurodegenerative disorders such as Alzheimer's, Parkinson, and Huntington's diseases. It is the cleaved caspase substrates that are the effectors of synapse elimination. However, their identities, specific cleavage sites, and functional consequences of cleavage are largely unknown. An important gap in our knowledge is a comprehensive catalog of synapse‐specific or synapse‐enriched caspase targets. Traditional biochemical approaches have revealed only a small number of neuronal caspase targets. Instead, we utilized a gel‐based proteomics approach to enable the first global analysis of caspase‐mediated cleavage events in mammalian brain synapses, employing both an in vitro system with recombinant activated caspases and an in vivo model of ethanol‐induced neuronal apoptosis. Of the more than 70 putative cleavage substrates that were identified, 22 were previously known caspase substrates. Among the novel targets identified and validated by Western blot were the proton pump ATPase subunit ATP6V1B2 and the N‐ethylmaleimide‐sensitive fusion protein (NSF). Our work represents the first comprehensive, proteome‐wide screen for proteolytic targets of caspases in neuronal synapses. Our discoveries will have significance for both furthering basic understanding of roles of caspases in synaptic plasticity and synaptic loss in neurodegeneration, and on a more immediately practical level, may provide candidate biomarkers for measuring synapse loss in human disease states.
Differentiating households to analyze consumption patterns: a data mining study on official household budget data
Authors: Değirmenci Tuğba , Özbakır Lale 
Published: September 2017

Official data, administered by National Statistic Institutes (NSIs), play crucial role for being a major element of the governmental economic and social decision‐making process. This strategic role raises a significant necessity for statistical authorities to adopt new data tools to shift the statistical quality of the published data to a higher level. Data mining (DM) techniques and algorithms are promising tools to provide new ways to mine the crucial, complex, and voluminous official data to complement or substitute the traditional and lagged‐behind tools that NSIs have been using. This study addresses this potential utilization of DM tools on official data with a specific problem in an important survey for official statistics: Household Budget Survey. Through this study, clustering techniques are employed to characterize the household types and association rule mining technique is used to mine consumption patterns for each differentiated type. It is aimed to integrate the proposed model into data preprocessing procedure of the NSI to be able to engage in the real time analyses and to contribute exactness and timeliness of the data. WIREs Data Mining Knowl Discov 2018, 8:e1227. doi: 10.1002/widm.1227This article is categorized under:

Algorithmic Development > Association Rules
Application Areas > Government and Public Sector
Application Areas > Industry Specific Applications
Small molecule signaling, regulation, and potential applications in cellular therapeutics
Authors: McNerney Monica P. , Styczynski Mark P. 
Published: September 2017

Small molecules have many important roles across the tree of life: they regulate processes from metabolism to transcription, they enable signaling within and between species, and they serve as the biochemical building blocks for cells. They also represent valuable phenotypic endpoints that are promising for use as biomarkers of disease states. In the context of engineering cell‐based therapeutics, they hold particularly great promise for enabling finer control over the therapeutic cells and allowing them to be responsive to extracellular cues. The natural signaling and regulatory functions of small molecules can be harnessed and rewired to control cell activity and delivery of therapeutic payloads, potentially increasing efficacy while decreasing toxicity. To that end, this review considers small molecule‐mediated regulation and signaling in bacteria. We first discuss some of the most prominent applications and aspirations for responsive cell‐based therapeutics. We then describe the transport, signaling, and regulation associated with three classes of molecules that may be exploited in the engineering of therapeutic bacteria: amino acids, fatty acids, and quorum‐sensing signaling molecules. We also present examples of existing engineering efforts to generate cells that sense and respond to levels of different small molecules. Finally, we discuss future directions for how small molecule‐mediated regulation could be harnessed for therapeutic applications, as well as some critical considerations for the ultimate success of such endeavors. WIREs Syst Biol Med 2018, 10:e1405. doi: 10.1002/wsbm.1405This article is categorized under:

Biological Mechanisms > Cell Signaling
Biological Mechanisms > Metabolism
Translational, Genomic, and Systems Medicine > Therapeutic Methods
Comparison of comprehensive and abstinence‐only sexuality education in young African American adolescents
Authors: Shepherd Lindsay M. , Sly Kaye F. , Girard Jeffrey M. 
Published: September 2017

ABSTRACTThe purpose of this study was to identify predictors of sexual behavior and condom use in African American adolescents, as well as to evaluate the effectiveness of comprehensive sexuality and abstinence‐only education to reduce adolescent sexual behavior and increase condom use. Participants included 450 adolescents aged 12–14 years in the southern United States. Regression analyses showed favorable attitudes toward sexual behavior and social norms significantly predicted recent sexual behavior, and favorable attitudes toward condoms significantly predicted condom usage. Self‐efficacy was not found to be predictive of adolescents' sexual behavior or condom use. There were no significant differences in recent sexual behavior based on type of sexuality education. Adolescents who received abstinence‐only education had reduced favorable attitudes toward condom use, and were more likely to have unprotected sex than the comparison group. Findings suggest that adolescents who receive abstinence‐only education are at greater risk of engaging in unprotected sex.
Maximizing Efficiency and Reducing Robotic Surgery Costs Using the NASA Task Load Index
Authors: Walters Carrie , Webb Paula J. 
Published: September 2017

AbstractPerioperative leaders at our facility were struggling to meet efficiency targets for robotic surgery procedures while also maintaining the satisfaction of the surgical team. We developed a human resources time and motion study tool and used it in conjunction with the NASA Task Load Index to observe and analyze the required workload of personnel assigned to 25 robotic surgery procedures. The time and motion study identified opportunities to enlist the help of nonlicensed support personnel to ensure safe patient care and improve OR efficiency. Using the NASA Task Load Index demonstrated that high temporal, effort, and physical demands existed for personnel assisting with and performing robotic surgery. We believe that this process could be used to develop cost‐effective staffing models, resulting in safe and efficient care for all surgical patients.
The impacts of maternal iron deficiency and being overweight during pregnancy on neurodevelopment of the offspring
Authors: Berglund Staffan K. , Torres-Espínola Francisco J. , García-Valdés Luz , Segura Mª Teresa , Martínez-Zaldívar Cristina , Padilla Carmen , Rueda Ricardo , Pérez García Miguel , McArdle Harry J. , Campoy Cristina 
Published: October 2017

AbstractBoth maternal Fe deficiency (ID) and being overweight or obese (Ow/Ob, BMI≥25 kg/m2) may negatively affect offspring brain development. However, the two risk factors correlate and their independent effects on infant neurodevelopment are unclear. PREOBE is a prospective observational study that included 331 pregnant Spanish women, of whom 166 had pre-gestational Ow/Ob. Fe status was analysed at 34 weeks and at delivery, and babies were assessed using Bayley III scales of neurodevelopment at 18 months. In confounder-adjusted analyses, maternal ID at 34 weeks was associated with lower composite motor scores at 18 months (mean 113·3 (sd9·9)v. 117·1 (sd9·2),P=0·039). Further, the offspring of mothers with ID at delivery had lower cognitive scores (114·0 (sd9·7)v. 121·5 (sd10·9),P=0·039) and lower receptive, expressive and composite (99·5 (sd8·6)v. 107·6 (sd8·3),P=0·004) language scores. The negative associations between maternal ID at delivery and Bayley scores remained even when adjusting for maternal Ow/Ob and gestational diabetes. Similarly, maternal Ow/Ob correlated with lower gross motor scores in the offspring (12·3 (sd2·0)v. 13·0 (sd2·1),P=0·037), a correlation that remained when adjusting for maternal ID. In conclusion, maternal ID and pre-gestational Ow/Ob are both negatively associated with Bayley scores at 18 months, but independently and on different subscales. These results should be taken into account when considering Fe supplementation for pregnant women.
The natural history of risky drinking and associated harms from adolescence to young adulthood: findings from the Australian Temperament Project
Authors: Betts K. S. , Alati R. , Baker P. , Letcher P. , Hutchinson D. , Youssef G. , Olsson C. A. 
Published: September 2017

BackgroundWe aimed to describe the natural history of heavy episodic drinking (HED) and associated harms from adolescence to young adulthood in a large Australian population cohort study.MethodThe Australian Temperament Project consists of mothers and babies (4–8 months) recruited from Infant Welfare Centres and followed every 2 to 4 years until age 28 years. Analyses were based on data from 1156 young people (497 male; 659 female) surveyed repeatedly at ages 16, 18, 20, 24 and 28 years. We used dual processes latent class growth analysis to estimate trajectories of HED and associated harms, employing a piecewise approach to model the hypothesized rise and subsequent fall across adolescence and the late twenties, respectively.ResultsWe identified four sex-specific trajectories and observed little evidence of maturing-out across the twenties. In males, a normative pattern of increasing HED across the twenties with little related harm was observed (40% of the male sample). Early and late starter groups that peaked in harms at age 20 years with only minor attenuation in binging thereafter were also observed (6.1% and 35%, respectively). In females, a normative pattern of increasing, but moderate, HED with little related harm was observed (44% of the female sample). Early and late starter groups were also identified (18% and 17%, respectively); however, unlike males, the female late starter group showed a pattern of increasing HED and related harms.ConclusionsContinued patterns of risky alcohol use and related harms are apparent for both males and females across the twenties.
Variations in phonological working memory: Linking early language experiences and language learning outcomes
Authors: PIERCE LARA J. , GENESEE FRED , DELCENSERIE AUDREY , MORGAN GARY 
Published: September 2017

ABSTRACTIn order to build complex language from perceptual input, children must have access to a powerful information processing system that can analyze, store, and use regularities in the signal to which the child is exposed. In this article, we propose that one of the most important parts of this underlying machinery is the linked set of cognitive and language processing components that comprise the child's developing working memory (WM). To examine this hypothesis, we explore how variations in the timing, quality, and quantity of language input during the earliest stages of development are related to variations in WM, especially phonological WM (PWM), and in turn language learning outcomes. In order to tease apart the relationships between early language experience, WM, and language development, we review research findings from studies of groups of language learners who clearly differ with respect to these aspects of input. Specifically, we consider the development of PWM in children with delayed exposure to language, that is, children born profoundly deaf and exposed to oral language following cochlear implantation and internationally adopted children who have delayed exposed to the adoption language; children who experience impoverished language input, that is, children who experience early bouts of otitis media and signing deaf children born to nonsigning hearing parents; and children with enriched early language input, that is, simultaneous bilinguals and second language learners.
Bovine leukaemia virus DNA in fresh milk and raw beef for human consumption
Authors: OLAYA-GALÁN N. N. , CORREDOR-FIGUEROA A. P. , GUZMÁN-GARZÓN T. C. , RÍOS-HERNANDEZ K. S. , SALAS-CÁRDENAS S. P. , PATARROYO M. A. , GUTIERREZ M. F. 
Published: September 2017

SUMMARYBovine leukaemia virus (BLV) is the causative agent of enzootic bovine leucosis, which has been reported worldwide. BLV has been found recently in human tissue and it could have a significant impact on human health. A possible hypothesis regarding viral entry to humans is through the consumption of infected foodstuffs. This study was aimed at detecting the presence of BLV DNA in raw beef and fresh milk for human consumption. Nested PCR directed at the BLV gag gene (272 bp) was used as a diagnostic test. PCR products were confirmed by Sanger sequencing. Forty-nine per cent of the samples proved positive for the presence of proviral DNA. This is the first study highlighting the presence of the BLV gag gene in meat products for human consumption and confirms the presence of the viral DNA in raw milk, as in previous reports. The presence of viral DNA in food products could suggest that viral particles may also be found. Further studies are needed to confirm the presence of infected viral particles, even though the present findings could represent a first approach to BLV transmission to humans through foodstuff consumption.
Discontinuous hydration alters seed germination under stress of two populations of cactus that occur in different ecosystems in Northeast Brazil
Authors: Lima Ayslan T. , Meiado Marcos V. 
Published: September 2017

AbstractThe water uptake by the seed in arid and semi-arid ecosystems may not be continuous, but may occur in hydration and dehydration cycles (HD). In order to investigate the benefits of discontinuous hydration on seed germination of Pilosocereus catingicola subsp. salvadorensis subjected to environmental stresses, an imbibition curve was determined and times X, Y and Z selected, corresponding to 25, 50 and 75% of the first phase of imbibition, respectively. Seeds of two populations (Caatinga and Restinga) were subjected to 0, 1, 2 and 3 HD cycles, with 48 h of dehydration. Water and saline stress responses were tested at five osmotic potentials (0.0, –0.1, –0.3, –0.6 and –0.9 MPa). Discontinuous hydration provided greater tolerance to water and saline stress in the seeds from the Caatinga region. When the seeds were subjected to water stress, the reduction of the mean germination time (MGT) provided by HD cycles decreased with increasing concentration of the solution. In saline stress, the reduction of MGT was greater in the solutions with the highest concentrations. We conclude that the seeds of the same species collected from populations located in different ecosystems have different germination responses after passage through discontinuous hydration and HD cycles. This provides greater tolerance to environmental stresses but with different responses among populations.
Regulation of antilipopolysaccharide factors, ALFPm3 and ALFPm6, in Penaeus monodon
Authors: Kamsaeng Pitchayanan , Tassanakajon Anchalee , Somboonwiwat Kunlaya 
Published: September 2017

AbstractALFPm6, a member of antimicrobial peptide in the antilipopolysaccharide factor (ALF) family from Penaeus monodon, plays important roles in shrimp immunity against pathogens. However, its antimicrobial activity and underlying mechanism have not been reported. The synthetic cyclic ALFPm6#29–52 peptide (cALFPm6#29–52) corresponding to the ALFPm6 LPS-binding domain can agglutinate and exhibited bacterial killing activity toward a Gram-negative bacterium, Escherichia coli 363 and Gram-positive bacteria, Bacillus megaterium, Aerococcus viridans, and Micrococcus luteus, with MIC values of 25–50 μM. Specifically, ALFPm6 and ALFPm3, the most abundant ALF isoforms, are different in terms of gene expression patterns upon pathogen infections. Herein, the regulation of ALFPm3 and ALFPm6 gene expression was studied. The 5′-upstream and promoter sequences were identified and the putative transcription factor (TF)-binding sites were predicted. The narrow down assay indicated that the ALFPm3 promoter and partial promoter of the ALFPm6 active regions were located at nucleotide positions (−814/+302) and (−282/+85), respectively. Mutagenesis of selected TF-binding sites revealed that Rel/NF-κB (−280/−270) of ALFPm3 and C/EBPβ (−88/−78) and Sp1 (−249/−238) sites of ALFPm6 were the activator-binding sites. Knockdown of the PmMyD88 and PmRelish genes in V. harveyi-infected shrimp suggested that the ALFPm3 gene was regulated by Toll and IMD pathways, while the ALFPm6 gene was regulated by the Toll pathway.
Impact of hepatocellular carcinoma heterogeneity on computed tomography as a prognostic indicator
Authors: Kiryu Shigeru , Akai Hiroyuki , Nojima Masanori , Hasegawa Kiyoshi , Shinkawa Hiroji , Kokudo Norihiro , Yasaka Koichiro , Ohtomo Kuni 
Published: September 2017

AbstractWe assessed the relationship between the heterogeneity of HCC on preoperative non-contrast-enhanced CT and patient prognosis. The heterogeneity of CT images from 122 patients was assessed and texture feature parameters such as mean, standard deviation (SD), entropy, mean of the positive pixels (MPP), skewness, and kurtosis were obtained using filtration. The relationship between CT texture features and 5-year overall survival (OS) or disease-free survival (DFS) was assessed. Multivariate regression analysis was performed to evaluate the independence of texture feature from clinical or pathological parameters. The Kaplan-Meier curves for OS or DFS was significantly different between patient groups dichotomized by cut-off values for all CT texture parameters with filtration at at least one filter level. Multivariate regression analysis showed the independence of most CT texture parameters on clinical and pathological parameters for OS with filtration at at least one filter level and without filtration except kurtosis. SD, entropy, and MPP with coarse filter, and skewness without filtration showed a significant correlation for DFS. CT texture features of non-contrast-enhanced CT images showed a relationship with HCC prognosis. Multivariate regression analysis showed the possibility of CT texture feature increase the prognostic prediction of HCC by clinical and pathological information.
Chronic sun exposure-related fusion oncogenes EGFR-PPARGC1A in cutaneous squamous cell carcinoma
Authors: Egashira Sho , Jinnin Masatoshi , Ajino Manami , Shimozono Naoki , Okamoto Sayo , Tasaki Yukino , Hirano Ayaka , Ide Maho , Kajihara Ikko , Aoi Jun , Harada Miho , Igata Toshikatsu , Masuguchi Shinichi , Fukushima Satoshi , Ihn Hironobu 
Published: September 2017

AbstractCutaneous squamous cell carcinoma (cSCC) differs from SCC of other organs in its strong association with chronic sun exposure. However, the specific driver mutations in cSCC remain unknown. Fusion genes in established cSCC cell lines (A431 and DJM-1) were predicted by transcriptome sequence, and validated by Sanger sequence, fluorescence in situ hybridization and G-banding. By transcriptome sequencing, we identified fusion gene EGFR-PPARGC1A in A431, which were expressed in 31 of 102 cSCCs. The lesions harboring the fusion gene tended to be located in sun-exposed areas. In vivo cutaneous implantation of EGFR-PPARGC1A-expressing NIH3T3 induced tumors resembling human cSCC, indicating its potent tumorigenicity. NIH3T3 transfected with EGFR-PPARGC1A as well as A431 showed increased cell proliferation activity. With regard to underlying mechanism, EGFR-PPARGC1A protein causes constitutive tyrosine phosphorylation, and induces the phosphorylation of wild-type full-length epidermal growth factor receptor (EGFR) by dimerization. Conversely, the RNAi-mediated attenuation of EGFR or CRISPR/Cas9-mediated knockdown of the fusion gene in A431 led to a decrease in the cell number, and may have therapeutic value. Our findings advance the knowledge concerning genetic causes of cSCC and the function of EGFR, with potential implications for new diagnostic and therapeutic approaches.