bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico mutational studies of Hsp70 disclose sites with distinct functional attributes
Authors: Ozbaykal Gizem , Rana Atilgan Ali , Atilgan Canan 
Published: September 2015

ABSTRACTThe Mutation‐Minimization Method (MuMi) to study the local response of proteins to point mutations has been introduced here. The heat shock protein Hsp70 as the test system since it displays features that have been studied in great detail has been used here. It has many conserved residues, serves several different functions on each of its domains, and displays interdomain allostery. For the analysis of spatial arrangement of residues within the protein, the network properties of the wild type (WT) protein as well as its all single alanine residue mutants using MuMi has been investigated. The measures to express the amount of change from the WT structure upon mutation and compare these deviations to find potential critical sites have been proposed. The functional significance of the potential sites to the parameter that uncovers them has been mapped. It was found that sites directly involved in binding were sensitive to mutations and were characterized by large displacements. On the other hand, sites that steer large conformational changes typically had increased reachability upon alanine mutations occurring elsewhere in the protein. Finally, residues that control communication within and between domains reside on the largest number of paths connecting pairs of residues in the protein. Proteins 2015; 83:2077–2090. © 2015 Wiley Periodicals, Inc.
An amino acid code for irregular and mixed protein packing
Authors: Joo Hyun , Chavan Archana G. , Fraga Keith J. , Tsai Jerry 
Published: September 2015

ABSTRACTTo advance our understanding of protein tertiary structure, the development of the knob‐socket model is completed in an analysis of the packing in irregular coil and turn secondary structure packing as well as between mixed secondary structure. The knob‐socket model simplifies packing based on repeated patterns of two motifs: a three‐residue socket for packing within secondary (2°) structure and a four‐residue knob‐socket for tertiary (3°) packing. For coil and turn secondary structure, knob‐sockets allow identification of a correlation between amino acid composition and tertiary arrangements in space. Coil contributes almost as much as α‐helices to tertiary packing. In irregular sockets, Gly, Pro, Asp, and Ser are favored, while in irregular knobs, the preference order is Arg, Asp, Pro, Asn, Thr, Leu, and Gly. Cys, His,Met, and Trp are not favored in either. In mixed packing, the knob amino acid preferences are a function of the socket that they are packing into, whereas the amino acid composition of the sockets does not depend on the secondary structure of the knob. A unique motif of a coil knob with an XYZ β‐sheet socket may potentially function to inhibit β‐sheet extension. In addition, analysis of the preferred crossing angles for strands within a β‐sheet and mixed α‐helice/β‐sheet identifies canonical packing patterns useful in protein design. Lastly, the knob‐socket model abstracts the complexity of protein tertiary structure into an intuitive packing surface topology map. Proteins 2015; 83:2147–2161. © 2015 Wiley Periodicals, Inc.
Integration of QUARK and I‐TASSER for Ab Initio Protein Structure Prediction in CASP11
Authors: Zhang Wenxuan , Yang Jianyi , He Baoji , Walker Sara Elizabeth , Zhang Hongjiu , Govindarajoo Brandon , Virtanen Jouko , Xue Zhidong , Shen Hong‐Bin , Zhang Yang 
Published: September 2015

ABSTRACTWe tested two pipelines developed for template‐free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free‐modeling (FM) targets have the model successfully constructed by QUARK with a TM‐score above 0.4, including the first model of T0837‐D1, which has a TM‐score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high‐resolution contact map prediction derived from fragment‐based distance‐profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang‐Server pipeline, weakly scoring threading templates are re‐ordered by the structural similarity to the ab initio folding models, which are then reassembled by I‐TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I‐TASSER pipeline with a TM‐score above 0.4. The robustness of the I‐TASSER pipeline can stem from the composite fragment‐assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long‐range beta‐strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76–86. © 2015 Wiley Periodicals, Inc.
Temporal flickering of contrast agents for enhanced optical imaging
Authors: Ilovitsh Tali , Zalevsky Zeev 
Published: September 2015

The temporal flickering of contrast agents that labels a biological sample is a unique modality for cellular imaging with single molecule sensitivity. It improves the signal‐to‐noise ratio statistics associated with the noisy in vivo environment and has promising applications in single particle tracking and super‐resolution microscopy techniques. The flickering can be triggered either statistically through the mechanism of temporal fluctuations of the emitter or through external modulation. The enriching toolbox of contrast agents that are feasible for biomedical imaging for the flickering methods will be discussed, with emphasis on the emerging field of flickering gold nanoparticles and the lock‐in detection mechanism. WIREs Nanomed Nanobiotechnol 2016, 8:439–448. doi: 10.1002/wnan.1375This article is categorized under:

Diagnostic Tools > In Vitro Nanoparticle-Based Sensing
Diagnostic Tools > In Vivo Nanodiagnostics and Imaging
How experiential service‐learning affects student perceptions of education in their careers and as a wildlife management activity
Authors: Stevenson Kathryn T. , Peterson M. Nils 
Published: September 2015

ABSTRACTWildlife education has long been critiqued for leaving students entering the workforce deficient in skills such as communication, public relations, and problem solving. This challenge may emerge from both curricula and instructional techniques focused on technical expertise rather than soft skills. Researchers have suggested several instructional techniques to address this challenge but have not empirically examined their effectiveness. This study examined how an environmental‐education service‐learning project affected undergraduate wildlife science students' perceptions of education as a possible career and how important they considered education as a wildlife management activity using a pre‐posttreatment comparison between 36 wildlife students at North Carolina State University (Raleigh, NC, USA, during spring 2014) participating in an environmental‐education service‐learning project and 23 wildlife students from the same cohort who were not. In the pretest, few (10.3%) students from either group saw K–12 education as a future career, but most (98.3%) saw education as an important wildlife management activity. Most (82.0%) students also predicted they would need educator skills in their careers, but more females than males saw this as likely. The treatment was positively related to students' belief they would use teaching skills in future careers and that a career in K–12 education would be fulfilling. These results suggest that service‐learning projects may be an effective tool to boost interest in education both as a career and as a wildlife management activity among future wildlife professionals regardless of gender, but that especially high interest among females could provide guidance for training and recruitment efforts attempting to mitigate the gender gap among wildlife professionals. © 2015 The Wildlife Society.
Nervous system involvement in Farber disease
Authors: Cappellari Alberto M. , Torcoletti Marta , Triulzi Fabio , Corona Fabrizia 
Published: September 2015

AbstractA 30 months‐old boy with Farber disease developed nystagmus 12 months after hematopoietic stem cell transplantation (HSCT). At 40 months, gait ataxia was evident, and brain MRI showed increased size of pericerebellar sulci and 4th ventricle. EMG showed denervation in the tongue and upper limb muscles, consistent with motor neuron disease. HSCT improves the peripheral manifestations of Farber disease, but may not prevent the progressive neurological deterioration.
Evolving Epidemiology ofStaphylococcus aureusBacteremia
Authors: Rhee Yoona , Aroutcheva Alla , Hota Bala , Weinstein Robert A. , Popovich Kyle J. 
Published: September 2015

BACKGROUNDMethicillin-resistantStaphylococcus aureus(MRSA) infections due to USA300 have become widespread in community and healthcare settings. It is unclear whether risk factors for bloodstream infections (BSIs) differ by strain type.OBJECTIVETo examine the epidemiology ofS. aureusBSIs, including USA300 and non-USA300 MRSA strains.DESIGNRetrospective observational study with molecular analysis.SETTINGLarge urban public hospital.PATIENTSIndividuals withS. aureusBSIs from January 1, 2007 through December 31, 2013.METHODSWe used electronic surveillance data to identify cases ofS. aureusBSI. Available MRSA isolates were analyzed by pulsed-field gel electrophoresis. Poisson regression was used to evaluate changes in BSI incidence over time. Risk factor data were collected by medical chart review and logistic regression was used for multivariate analysis of risk factors.RESULTSA total of 1,015 cases ofS. aureusBSIs were identified during the study period; 36% were due to MRSA. The incidence of hospital-onset (HO) MRSA BSIs decreased while that of community-onset (CO) MRSA BSIs remained stable. The rate of CO– and HO– methicillin-susceptibleS. aureusinfections both decreased over time. More than half of HO-MRSA BSIs were due to the USA300 strain type and for 4 years, the proportion of HO-MRSA BSIs due to USA300 exceeded 60%. On multivariate analysis, current or former drug use was the only epidemiologic risk factor for CO- or HO-MRSA BSIs due to USA300 strains.CONCLUSIONSUSA300 MRSA is endemic in communities and hospitals and certain populations (eg, those who use illicit drugs) may benefit from enhanced prevention efforts in the community.Infect. Control Hosp. Epidemiol.2015;36(12):1417–1422
RELIGIOUS FREEDOM VERSUS SEXUAL EXPRESSION: A GUIDE
Authors: Alvaré Helen M. 
Published: September 2015

AbstractClaimed rights to sexual expression unlinked to the creation of children are among the strongest challenges facing the free exercise of religion in the United States today. Such rights gained importance by means of a series of Supreme Court opinions associating consensual sexual expression unlinked to children with human dignity and even personal identity. These were accompanied by legal and cultural movements, led by more privileged Americans, diminishing children's rights in favor of adults', in the context of sex, marriage, and parenting. Laws and regulations protecting and promoting sexual expression detached from children are powerfully affecting religious institutions that operate health care, educational, and social services available to all Americans; the Catholic Church is a particularly prominent supplier of all of these services. Respecting the Catholic Church, it is possible but quite difficult to maintain respect for its free exercise of religion in the current environment, potentially by highlighting its measurable contributions to the common good. It might also be useful to show the close link between Catholic teachings on sex and marriage and the entire Catholic cosmology, such that coercing Catholics to behave otherwise is tantamount to coercing them to practice a different faith.
Factors associated with nutritional decline in hospitalised medical and surgical patients admitted for 7 d or more: a prospective cohort study
Authors: Allard Johane P. , Keller Heather , Teterina Anastasia , Jeejeebhoy Khursheed N. , Laporte Manon , Duerksen Donald R. , Gramlich Leah , Payette Helene , Bernier Paule , Davidson Bridget , Lou Wendy 
Published: September 2015

AbstractThis prospective cohort study was conducted in eighteen Canadian hospitals with the aim of examining factors associated with nutritional decline in medical and surgical patients. Nutritional decline was defined based on subjective global assessment (SGA) performed at admission and discharge. Data were collected on demographics, medical information, food intake and patients’ satisfaction with nutrition care and meals during hospitalisation; 424 long-stay (≥7 d) patients were included; 38 % of them had surgery; 51 % were malnourished at admission (SGA B or C); 37 % had in-hospital changes in SGA; 19·6 % deteriorated (14·6 % from SGA A to B/C and 5 % from SGA B to C); 17·4 % improved (10·6 % from SGA B to A, 6·8 % from SGA C to B/A); and 63·0 % patients were stable (34·4 % were SGA A, 21·3 % SGA B, 7·3 % SGA C). One SGA C patient had weight loss ≥5 %, likely due to fluid loss and was designated as stable. A subset of 364 patients with admission SGA A and B was included in the multiple logistic regression models to determine factors associated with nutritional decline. After controlling for SGA at admission and the presence of a surgical procedure, lower admission BMI, cancer, two or more diagnostic categories, new in-hospital infection, reduced food intake, dissatisfaction with food quality and illness affecting food intake were factors significantly associated with nutritional decline in medical patients. For surgical patients, only male sex was associated with nutritional decline. Factors associated with nutritional decline are different in medical and surgical patients. Identifying these factors may assist nutritional care.
Urinary isoflavonoids and risk of type 2 diabetes: a prospective investigation in US women
Authors: Ding Ming , Franke Adrian A. , Rosner Bernard A. , Giovannucci Edward , van Dam Rob M. , Tworoger Shelley S. , Hu Frank B. , Sun Qi 
Published: September 2015

AbstractTo examine the association between urinary excretion of isoflavonoids and risk of type 2 diabetes (T2D), we conducted a nested case–control study among 1111 T2D pairs identified during 1995–2008 in the Nurses’ Health Study (NHS) and NHSII, who were free of diabetes, CVD and cancer at urine sample collection. Urinary excretion of daidzein and genistein, as well as their metabolites O-desmethylangolensin (O-DMA), dihydrogenistein (DHGE) and dihydrodaidzein (DHDE) was assayed using liquid chromatography MS. Self-reported T2D incident cases were confirmed using a validated questionnaire. Higher urinary excretion of daidzein and genistein was associated with a lower risk of T2D in the combined cohorts. Comparing extreme tertiles of the urinary markers, the OR of T2D were 0·71 (95 % CI 0·55, 0·93) for daidzein and 0·74 (95 % CI 0·56, 0·97) for genistein, although the test for linear trend was not significant for genistein (Ptrend=0·03 and 0·15, respectively). DMA, DHDE and DHGE were non-significantly associated with a lower T2D risk. The inverse association of daidzein with T2D risk was stronger among post-menopausal women who did not use hormone replacement therapy (Pinteraction=0·001): the OR was 0·58 (95 % CI 0·34, 0·97) comparing extreme tertiles among these women. In conclusion, urinary excretion of isoflavones was associated with a lower T2D risk in US women, especially among post-menopausal women who did not use hormone. Further research is warranted to replicate these observations among western populations with similarly low overall isoflavone intake.
The Dynamics of Race and Ethnicity in the US Coal Industry
Authors: William Trotter Joe 
Published: September 2015

AbstractBy the turn of the twenty-first century, scholars had transformed our understanding of class, race, and ethnicity in the rise and demise of the US coal industry. Under the twin impact of the modern Black Freedom Movement and the rise of the New Labor History, studies of American labor and race relations fragmented during the late twentieth century. Following the lead of pioneering labor historian Herbert Gutman, one influential body of scholarship resuscitated the early history of the United Mine Workers of America and accented the emergence of remarkable forms of labor solidarity across the color line during the industrial era. Before this scholarship could gain a firm footing in the historiography of labor and working-class history, however, social activist and labor scholar Herbert Hill forcefully argued that emerging emphases on interracial working-class cooperation downplayed the persistence of racial divisions even during the most promising episodes of labor unity. In significant ways, the Hill−Gutman debate fueled the florescence of whiteness studies and the myriad ways that both capital and labor benefitted from a racially stratified workforce. Based upon this rapidly expanding historiography of coalminers in America, this essay explores how the overlapping experiences of black and white miners established the foundation for modes of cooperation as well as conflict, but the persistence of white supremacist ideology and social practices repeatedly undermined sometimes heroic movements to bridge the chasm between black and white workers.
Retinotopic organization of extrastriate cortex in the owl monkey—dorsal and lateral areas
Authors: SERENO MARTIN I. , MCDONALD COLIN T. , ALLMAN JOHN M. 
Published: September 2015

AbstractDense retinotopy data sets were obtained by microelectrode visual receptive field mapping in dorsal and lateral visual cortex of anesthetized owl monkeys. The cortex was then physically flatmounted and stained for myelin or cytochrome oxidase. Retinotopic mapping data were digitized, interpolated to a uniform grid, analyzed using the visual field sign technique—which locally distinguishes mirror image from nonmirror image visual field representations—and correlated with the myelin or cytochrome oxidase patterns. The region between V2 (nonmirror) and MT (nonmirror) contains three areas—DLp (mirror), DLi (nonmirror), and DLa/MTc (mirror). DM (mirror) was thin anteroposteriorly, and its reduced upper field bent somewhat anteriorly away from V2. DI (nonmirror) directly adjoined V2 (nonmirror) and contained only an upper field representation that also adjoined upper field DM (mirror). Retinotopy was used to define area VPP (nonmirror), which adjoins DM anteriorly, area FSTd (mirror), which adjoins MT ventrolaterally, and TP (mirror), which adjoins MT and DLa/MTc dorsoanteriorly. There was additional retinotopic and architectonic evidence for five more subdivisions of dorsal and lateral extrastriate cortex—TA (nonmirror), MSTd (mirror), MSTv (nonmirror), FSTv (nonmirror), and PP (mirror). Our data appear quite similar to data from marmosets, though our field sign-based areal subdivisions are slightly different. The region immediately anterior to the superiorly located central lower visual field V2 varied substantially between individuals, but always contained upper fields immediately touching lower visual field V2. This region appears to vary even more between species. Though we provide a summary diagram, given within- and between-species variation, it should be regarded as a guide to parsing complex retinotopy rather than a literal representation of any individual, or as the only way to agglomerate the complex mosaic of partial upper and lower field, mirror- and nonmirror-image patches into areas.
Adaptation of the HIV Stigma Scale in Spaniards with HIV
Authors: Fuster-RuizdeApodaca Maria José , Molero Fernando , Holgado Francisco Pablo , Ubillos Silvia 
Published: September 2015

AbstractThe primary goal of this study was to adapt Berger, Ferrans, & Lahley (2001) HIV Stigma Scale in Spain, using Bunn, Solomon, Miller, & Forehand (2007) version. A second goal assessed whether the four-factor structure of the adapted scale could be explained by two higher-order dimensions, perceived external stigma and internalized stigma. A first qualitative study (N = 40 people with HIV, aged 28–59) was used to adapt the items and test content validity. A second quantitative study analyzed construct and criterion validity. In this study participants were 557 people with HIV, aged 18–76. The adapted HIV Stigma Scale for use in Spain (HSSS) showed a good internal consistency (α = .88) and good construct validity. Confirmatory Factor Analyses yielded a first-order, four-factor structure and a higher-order, bidimensional structure with the two expected factors (RMSEA = .051, 90% CI [.046, .056]; RMR = .073; GFI = .96; AGFI = .96; CFI = .98). Negative relations were found between stigma and quality of life (r = –.39; p < .01), self-efficacy to cope with stigma (r = –.50; p < .01) and the degree of HIV status disclosure (r = –.35; p < .01). Moreover, the people who had suffered AIDS-related opportunistic infections had a higher score in the Perceived External Stigma dimension than those who had not suffered them, t (493) = 3.02, p = .003, d = 0.26.
Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody
Authors: Ying Tianlei , Prabakaran Ponraj , Du Lanying , Shi Wei , Feng Yang , Wang Yanping , Wang Lingshu , Li Wei , Jiang Shibo , Dimitrov Dimiter S. , Zhou Tongqing 
Published: September 2015

AbstractThe MERS-CoV is an emerging virus, which already infected more than 1,300 humans with high (∼36%) mortality. Here, we show that m336, an exceptionally potent human anti-MERS-CoV antibody, is almost germline with only one somatic mutation in the heavy chain. The structure of Fab m336 in complex with the MERS-CoV receptor-binding domain reveals that its IGHV1-69-derived heavy chain provides more than 85% binding surface and that its epitope almost completely overlaps with the receptor-binding site. Analysis of antibodies from 69 healthy humans suggests an important role of the V(D)J recombination-generated junctional and allele-specific residues for achieving high affinity of binding at such low levels of somatic hypermutation. Our results also have important implications for development of vaccine immunogens based on the newly identified m336 epitope as well as for elucidation of mechanisms of neutralization by m336-like antibodies and their elicitation in vivo.