bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular mechanism of multispecific recognition of Calmodulin through conformational changes
Authors: Liu Fei , Chu Xiakun , Lu H. Peter , Wang Jin 
Published: May 2017

Significance
Understanding how Calmodulin (CaM) is able to recruit more than 300 binding targets is crucial for solving the multispecificity in molecular recognition. To address the molecular mechanism for CaM recognition, we studied the association process that simultaneously involves both the local conformational change of CaM and the global conformational changes of CaM-binding peptide skMLCK with molecular simulations. An energy landscape with a mixture of the atypical “induced fit,” the atypical “conformational selection,” and “simultaneously binding–folding” is uncovered for the CaM–peptide recognition process. The underlying interactions, which lead to this complicated association process, are found to fine-tune the multiple conformational changes during the recognition process, leading to high affinity and specificity. The association characteristic proposed for CaM and skMLCK can provide insights toward multispecific binding of CaM with its target.
Inducible
Fgf13
ablation enhances caveolae-mediated cardioprotection during cardiac pressure overload
Authors: Wei Eric Q. , Sinden Daniel S. , Mao Lan , Zhang Hailin , Wang Chuan , Pitt Geoffrey S. 
Published: May 2017

Significance
In response to chronic pressure overload, the heart undergoes pathological hypertrophy associated with adverse remodeling, fibrosis, and cardiac dysfunction. Caveolae, membrane invaginations that organize protective signaling pathways and provide a reservoir to buffer membrane tension, can ameliorate maladaptive hypertrophy. However, the factors that govern caveolae assembly in the heart are not fully understood. Here, we report that the fibroblast growth factor (FGF) homologous factor FGF13 is a negative regulator of caveolae density in cardiomyocytes. Adult mice lacking FGF13 in the heart have increased caveolae abundance in cardiomyocytes and are thereby protected from the pathological effects of chronic pressure overload. Our findings, identifying an unexpected role for FGF13, provide insight into the mechanisms underlying caveolae-mediated adaptation to cardiac stress.
Visual working memory buffers information retrieved from visual long-term memory
Authors: Fukuda Keisuke , Woodman Geoffrey F. 
Published: May 2017

Significance
How do we retrieve long-term memory? Here, we show that by measuring subjects’ electroencephalogram (EEG), we can directly observe the dynamic process of long-term memory retrieval. Our findings suggest that retrieved information becomes consciously available by being represented in a working-memory format that is similar to that used to represent new perceptual inputs. Furthermore, we show that our EEG measures can track the process of retrieving and combining two long-term memories acquired separately (e.g., image of a horse and a pair of wings) into one working-memory representation (e.g., a Pegasus). Thus, our results not only provide direct neural support for a long-assumed theory of memory retrieval but also demonstrate how flexible retrieval allows for creative thought.
Optimal incentives for collective intelligence
Authors: Mann Richard P. , Helbing Dirk 
Published: May 2017

Significance
Diversity of information and expertise among group members has been identified as a crucial ingredient of collective intelligence. However, many factors tend to reduce the diversity of groups, such as herding, groupthink, and conformity. We show why the individual incentives in financial and prediction markets and the scientific community reduce diversity of information and how these incentives can be changed to improve the accuracy of collective forecasting. Our results, therefore, suggest ways to improve the poor performance of collective forecasting seen in recent political events and how to change career rewards to make scientific research more successful.
A normalization model suggests that attention changes the weighting of inputs between visual areas
Authors: Ruff Douglas A. , Cohen Marlene R. 
Published: May 2017

Significance
Visual attention dramatically improves the perception of attended stimuli, but the mechanism by which this improvement occurs is unknown. Here we combine simultaneous recordings in multiple visual cortical areas, electrical microstimulation paired with multineuron recordings, and a descriptive normalization model to probe the mechanisms underlying attention. We found that the relationship between the activity in different visual areas is well described by normalization and that a mechanism that changes the weights of connections between areas can best describe our physiological observations. This study shows that normalization can explain interactions between neurons in different areas and provides a framework for using multiarea recordings and stimulation techniques to probe the neural mechanisms underlying neuronal computations.
Nasal-associated lymphoid tissues (NALTs) support the recall but not priming of influenza virus-specific cytotoxic T cells
Authors: Pizzolla Angela , Wang Zhongfang , Groom Joanna R. , Kedzierska Katherine , Brooks Andrew G. , Reading Patrick C. , Wakim Linda M. 
Published: May 2017

Significance
The upper respiratory tract (URT) is the first contact site for inhaled pathogens and intranasal vaccines, and is serviced by a network of lymphoid-tissues, including draining lymph nodes and nasal-associated lymphoid tissues (NALTs). Whether these lymphoid structures have distinct roles in facilitating T-cell immunity to inhaled antigens is unclear. We show, following antigen delivery into the URT, NALTs failed to support naïve T-cell priming; however, they supported the recall expansion of memory T cells. Although antigen delivery to the URT may not induce effective T-cell priming, it would be an effective means of boosting responses in the context of preexisting T-cell immunity. These results have significant implications for intranasal vaccines that deliver antigen to NALTs and aim to elicit protective T-cell immunity.
Brd4 modulates the innate immune response through Mnk2–eIF4E pathway-dependent translational control of IκBα
Authors: Bao Yan , Wu Xuewei , Chen Jinjing , Hu Xiangming , Zeng Fuxing , Cheng Jianjun , Jin Hong , Lin Xin , Chen Lin-Feng 
Published: May 2017

SignificanceWe generated myeloid lineage-specificBrd4conditional-knockout mice and demonstrated the critical role ofBrd4in the innate immune response in vivo.Brd4CKO mice were resistant to LPS-induced sepsis but were more susceptible to bacterial infection. Deletion ofBrd4in macrophages decreased the TLR-mediated inflammatory cytokine expression. We also uncovered a mechanism by which Brd4 regulates the NF-κB signaling via initiation of translation. In response to LPS stimulation, deletion ofBrd4in macrophages led to the sustained expression ofMknk2and the enhanced activation of eIF4E, which stimulates the translation of IκBα mRNA, resulting in decreased NF-κB–dependent inflammatory gene expression and compromised innate immune response.
Variation in the β-endorphin, oxytocin, and dopamine receptor genes is associated with different dimensions of human sociality
Authors: Pearce Eiluned , Wlodarski Rafael , Machin Anna , Dunbar Robin I. M. 
Published: May 2017

Significance
Social behavior in mammals is underpinned by a number of social neuropeptides. Most studies, however, focus on a single neuropeptide (often oxytocin), and invariably only in the context of reproductive relationships. Here, we examine the associations between the six main social neuropeptides (endorphins, oxytocin, vasopressin, dopamine, serotonin, and testosterone) and social indices in three separate social domains (disposition, dyadic/romantic relationships, and social network). We show that each neuropeptide is quite specific in its domain of influence, although endorphins and dopamine influence all three social domains. The results suggest that the social importance of endorphins may have been underestimated.
Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization
Authors: Sergeyev Ivan V. , Itin Boris , Rogawski Rivkah , Day Loren A. , McDermott Ann E. 
Published: May 2017

Significance
This work presents a technique for dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) solid-state NMR studies of complex proteins and biological assemblies. The sequential side-chain correlation approach streamlines the site-specific assignment of NMR peaks in multidimensional spectra, a critical step in determining structural information such as distances. When combined with DNP enhancement, fast MAS, and nonuniform sampling, this technique allows for faster data acquisition than previously possible. Applied to the intact Pf1 bacteriophage, sequential side-chain correlation spectra have enabled a virtually complete assignment using DNP data alone. These assignments shed insight into the chemical shift and linewidth changes associated with cryogenic temperatures. Our data point to hydration as a key variable influencing these parameters.
Novel quantum phase transition from bounded to extensive entanglement
Authors: Zhang Zhao , Ahmadain Amr , Klich Israel 
Published: May 2017

Significance
One of the main quests of many-body physics and quantum information is to understand various quantum phases and in particular the entanglement present in them. In this work we have uncovered a unique, physically transparent quantum phase transition in a spin chain where entanglement entropy itself jumps from low scaling, most typical for gapped models and short-range correlations, to a critical phase where the scaling exhibits an extraordinary amount of entanglement. This discovery pushes the boundaries of a possible range of nonlocal quantum correlations displayed by local Hamiltonians and opens a door to fundamental and practical questions about the interplay of entanglement and locality in many-body systems.
Metaphors of womanhood in the literary works of contemporary Indian writers
Authors: Ahuja Atula , Techacharoenrungrueang Suparak , Luksaneeyanawin Sudaporn 
Published: May 2017

Abstract
This study examines the notion of womanhood in the literary works of contemporary Indian authors by analyzing conceptual metaphors of womanhood. More specifically, the data collected in this study are metaphorical expressions (MEs) from nine fictional works set in India’s three main ethnically and linguistically diverse regions occupied by three linguistic groups, namely, the Indo-Aryan, the Dravidian, and the Tibeto-Burmese. The identification of MEs follows the Metaphor Identification Procedure VU University Amsterdam (MIPVU; Steen et al. 2010a). The analysis focuses on cross-cultural variation in conceptual metaphor, applying Conceptual Metaphor Theory (CMT; Lakoff & Johnson 1980) and the cognitive dimension of socio-cultural diversity proposed by Kövecses (2008). Through the analysis of conceptual metaphor, the paper provides insights into the current social context regarding the status and roles of women in India.
Salmon nasal cartilage proteoglycan enhances growth of normal human dermal fibroblast through Erk1/2 phosphorylation
Authors: Sano Masahiro , Shang Yi , Nakane Akio , Saito Tomoaki 
Published: May 2017

AbstractProteoglycan (PG) is a heavily glycosylated protein, localized to cell surface and extracellular matrix, and has various functions. Recently, it has been gradually revealed that PG interacts with various growth factors and morphogens and regulates cellular functions. Although salmon nasal cartilage PG (Salmon-PG) increases proliferation of immortalized cells, its mechanism remains unclear. In this study, we confirmed the effect of Salmon-PG on normal human dermal fibroblast (NHDF) and investigated the mechanism of PG action on NHDF. Salmon-PG dose- and time-dependently increased NHDF proliferation. Receptor tyrosine kinase array revealed that Salmon-PG increased only Erk1/2 signaling. Erk1/2 phosphorylation was significantly increased by Salmon-PG in a time-(10 min) and dose-(400 or 800 μg/mL) dependent manner. MEK inhibitor suppressed the enhancement of NHDF proliferation by Salmon-PG. The overall findings indicate that Salmon-PG plays a role as a growth factor in NHDF via Erk1/2 activation, suggesting that Salmon-PG contributes to the maintenance of skin homeostasis.
Characterization and comparison of recombinant honeybee chymotrypsin-like protease (HCLPase) expressed in Escherichia coli and insect cells
Authors: Matsuoka Takuma , Kawashima Takuji , Nakamura Tadashi , Yabe Tomio 
Published: May 2017

Abstract
We previously found a novel chymotrypsin-like protease in honeybee, designated as HCLPase. The recombinant enzyme expressed in insect cells was produced and compared to that in Escherichia coli. Both enzymes showed equivalent molecular size and specificity. However, HCLPase produced in insect cells showed higher specific activity. The C-terminal cleavage sites of HCLPase were phenylalanine, leucine, and tyrosine residues.
Enrolment, content and assessment: a review of examinable senior secondary (16–19 year olds) physical education courses: an international perspective
Authors: Whittle Rachael Jayne , Benson Amanda Clare , Telford Amanda 
Published: May 2017

ABSTRACTSenior secondary physical education courses for certification continue to attract increasing student enrolments amidst international concerns for the state and status of physical education in schools. Curricula analysis of senior secondary physical education has typically focussed on courses in local contexts. This review aims to contribute to the current discussion around physical education curricula through a document analysis of 15 senior secondary physical education courses for certification. Results from the analysis of curricula documents reveal similarities in subject aims, objectives and rationales, subject specific content and assessment. Senior secondary physical education is firmly based in both the biophysical and sociocultural fields of study and draws on a broad range of disciplines from which to study human movement. The stated rationales of the courses reviewed suggested that an understanding of the complex interrelationships between content areas underpins senior secondary physical education; however content was mostly prescribed in stand‐alone units. This review identified more similarities than differences in content and assessment practices in senior secondary physical education, a point of distinction between the courses reviewed was those that assess physical performance and those that do not. Internal assessment provided for a variety of tasks to determine student learning, however, external assessment was dominated by a written examination.
Development of two short measures for recovery and stress in sport
Authors: Nässi Anu , Ferrauti Alexander , Meyer Tim , Pfeiffer Mark , Kellmann Michael 
Published: May 2017

AbstractThe Acute Recovery and Stress Scale (ARSS) and the Short Recovery and Stress Scale were first established in German for the purposes of monitoring athletes’ current recovery‐stress states in an economical and multidimensional manner. The aim of this paper is to document the development and initial validation of the English versions of these two psychometric monitoring tools. A total of 267 English‐speaking athletes from a variety of team and individual sports participated in the study. The English versions demonstrated satisfactory internal consistency for both instruments (Cronbach α of. 74–.89). Furthermore, good model fit was found for the eight scales of the ARSS, matching the structure and results of the German counterparts. Correlations among and between the scales reciprocate the theoretical constructs of stress and recovery, supporting the construct validity of the scales. Correlation coefficients within stress and recovery ranged between rs = .29 and. 68. The correlations between stress and recovery varied between rs = −.29 and −.64. These constructs were further supported by correlations with the scores of the Recovery‐Stress Questionnaire for Athletes, thereby showing convergent validity. The findings demonstrate initial validity and reliability of the two measures and reflect the results of the German versions. However, further research is needed before applying these scales in practical settings.
EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons
Authors: Hui Xinjie , Hu Yueming , Sun Ming-An , Shu Xingsheng , Han Rongfei , Ge Qinggang , Wang Yejun 
Published: May 2017

Abstract

Motivation
In genome-wide rate comparison studies, there is a big challenge for effective identification of an appropriate number of significant features objectively, since traditional statistical comparisons without multi-testing correction can generate a large number of false positives while multi-testing correction tremendously decreases the statistic power.

Results
In this study, we proposed a new exact test based on the translation of rate comparison to two binomial distributions. With modeling and real datasets, the exact binomial test (EBT) showed an advantage in balancing the statistical precision and power, by providing an appropriate size of significant features for further studies. Both correlation analysis and bootstrapping tests demonstrated that EBT is as robust as the typical rate-comparison methods, e.g. χ2 test, Fisher’s exact test and Binomial test. Performance comparison among machine learning models with features identified by different statistical tests further demonstrated the advantage of EBT. The new test was also applied to analyze the genome-wide somatic gene mutation rate difference between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), two main lung cancer subtypes and a list of new markers were identified that could be lineage-specifically associated with carcinogenesis of LUAD and LUSC, respectively. Interestingly, three cilia genes were found selectively with high mutation rates in LUSC, possibly implying the importance of cilia dysfunction in the carcinogenesis.

Availability and implementation
An R package implementing EBT could be downloaded from the website freely: http://www.szu-bioinf.org/EBT.

Supplementary information
Supplementary data are available at Bioinformatics online.
Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests
Authors: Le Trang T , Simmons W Kyle , Misaki Masaya , Bodurka Jerzy , White Bill C , Savitz Jonathan , McKinney Brett A 
Published: May 2017

Abstract

Motivation
Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n, these differential privacy methods are susceptible to overfitting.

Methods
We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection.

Results
On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder.

Availability and implementation
Code available at http://insilico.utulsa.edu/software/privateEC.

Supplementary information
Supplementary data are available at Bioinformatics online.
Captive Ancestry Upwardly Biases Estimates of Relative Reproductive Success
Authors: Willoughby Janna R , Christie Mark R 
Published: May 2017

Abstract
Supplementation programs, which release captive-born individuals into the wild, are commonly used to demographically bolster declining populations. In order to evaluate the effectiveness of these programs, the reproductive success of captive-born individuals released into the wild is often compared to the reproductive success of wild-born individuals in the recipient population (relative reproductive success, RRS). However, if there are heritable reductions in fitness associated with captive breeding, gene flow from captive-born individuals into the wild population can reduce the fitness of the wild population. Here, we show that when captive ancestry in the wild population reduces mean population fitness, estimates of RRS are upwardly biased, meaning that the relative fitness of captive-born individuals is over-estimated. Furthermore, the magnitude of this bias increases with the length of time that a supplementation program has been releasing captive-born individuals. This phenomenon has long-term conservation impacts since management decisions regarding the design of a supplementation program and the number of individuals to release can be based, at least in part, on RRS estimates. Therefore, we urge caution in the interpretation of relative fitness measures when the captive ancestry of the wild population cannot be precisely measured.