bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary pathway analysis and unified classification of East Asian lineage of Mycobacterium tuberculosis
Authors: Shitikov Egor , Kolchenko Sergey , Mokrousov Igor , Bespyatykh Julia , Ischenko Dmitry , Ilina Elena , Govorun Vadim 
Published: August 2017

AbstractDue to its rapid spread and association with the numerous outbreaks, the global spread of East Asian lineage of Mycobacterium tuberculosis strains presents a global concern. Although there were many attempts to describe its population structure, no consensus has been reached yet. To define unbiased classification that will facilitate future studies of this lineage, we analyzed the performance and congruence of eight different genotyping schemes based on phylogenetic analysis of 1,398 strains from 32 countries using whole-genome sequencing (WGS) data. We confirm that East Asian lineage comprises two major clades, designated proto-Beijing, which harbors unusual 43-signal spoligoprofile, and Beijing, with well-known spoligoprofile (deleted signals from 1 to 34). We show that different genotyping methods give high consistency results in description of ancient Beijing strains while the classification of modern Beijing strains is significantly divergent due to star-shaped phylogeny. Using WGS data we intersect different studies and for the first time provide balanced classification with well-defined major groups and their genetic markers. Our reconstructed phylogenetic tree can also be used for further analysis of epidemiologically important clusters and their ancestors as well as white spots of unclassified strains, which are prospective areas of research.
Discovery and characterization of the feline miRNAome
Authors: Laganà Alessandro , Dirksen Wessel P. , Supsavhad Wachiraphan , Yilmaz Ayse Selen , Ozer Hatice G. , Feller James D. , Vala Kiersten A. , Croce Carlo M. , Rosol Thomas J. 
Published: August 2017

AbstractThe domestic cat is an important human companion animal that can also serve as a relevant model for ~250 genetic diseases, many metabolic and degenerative conditions, and forms of cancer that are analogous to human disorders. MicroRNAs (miRNAs) play a crucial role in many biological processes and their dysregulation has a significant impact on important cellular pathways and is linked to a variety of diseases. While many species already have a well-defined and characterized miRNAome, miRNAs have not been carefully studied in cats. As a result, there are no feline miRNAs present in the reference miRNA databases, diminishing the usefulness of medical research on spontaneous disease in cats for applicability to both feline and human disease. This study was undertaken to define and characterize the cat miRNAome in normal feline tissues. High-throughput sequencing was performed on 12 different normal cat tissues. 271 candidate feline miRNA precursors, encoding a total of 475 mature sequences, were identified, including several novel cat-specific miRNAs. Several analyses were performed to characterize the discovered miRNAs, including tissue distribution of the precursors and mature sequences, genomic distribution of miRNA genes and identification of clusters, and isomiR characterization. Many of the miRNAs were regulated in a tissue/organ-specific manner.
Self‐biased CMOS LC VCO based on trans‐conductance linearisation technique
Authors: Ji Xincun , Xia Xiaojuan , He Lin , Guo Yufeng 
Published: August 2017

Introduction: A self‐biased low‐phase noise CMOS LC VCO (employing both nMOS and pMOS switching transistors) based on the trans‐conductance linearisation of active devices is proposed. The self‐biased push–pull configuration with resistors between the LC tank and device drain, not only reduces power consumption, but also is capable of removing the RF choking inductor needed in NMOS‐only or PMOS‐only topology, which results into a compact chip area. A capacitive‐coupled feedback from the drain and LC tank improves the oscillation amplitude and reduces the tank loading. The proposed VCO is fabricated and measured with a 65 nm CMOS process. The core chip area is 0.12 mm2. The measured oscillation frequency ranges from 3.96 to 6.1 GHz, the phase noise at 1 MHz offset is from −123 to −125 dBc/Hz, with a power dissipation from 13 to 23 mW under a 1.3 V supply voltage across the frequency tuning range. The achieved figure‐of‐merit with tuning range (FoMT) from 196.5 to 199.5 dBc/Hz.
Study on the difference of chemical composition of insulator contamination on UHV‐AC and ‐DC transmission lines
Authors: Li Lee , Jiang Yunpeng , Lu Ming , Liu Zehui , Hua Kui , Li Zhe 
Published: August 2017

For the ultra high voltage (UHV)‐DC and UHV‐AC transmission lines, their contamination characteristics are different. Thus, researching the contamination polluted degree of UHV‐AC and UHV‐DC lines by geoaccumulation index and enrichment factor method is an ingenious method. This study analyses and compares the chemical composition of contamination on parallel energised UHV‐DC (800 kV) and UHV‐AC (1000 kV) overhead transmission lines. The results indicate that the major cations of insulator contamination are Ca2+, and NH4+, and the major anions of insulator contamination are SO42− and NO3− both on UHV‐DC and UHV‐AC lines. For the UHV‐DC line, the concentrations of the same cations on the insulator bottom surface are higher than that of on the top surface. However, on the UHV‐AC line, the same cation concentrations on the bottom surface close to the one on the top surface. The metallic elements of Ca2+ and Zn2+ are in seriously polluted degree. Also, the polluted degree of contamination on UHV‐DC insulator is more serious than UHV‐AC insulator. This study considers that field charging plays an important role in accumulating contamination.
Inverted-region electron transfer as a mechanism for enhancing photosynthetic solar energy conversion efficiency
Authors: Makita Hiroki , Hastings Gary 
Published: August 2017

Significance
Inverted-region electron transfer is widely suggested to be an important mechanism contributing to photosynthetic efficiency. However, this mechanism has never been demonstrated in any native photosynthetic system under physiological conditions. Here, inverted-region electron transfer is demonstrated in a native photosynthetic protein complex under physiological conditions. Furthermore, inverted-region electron transfer is shown quantitatively to be an important mechanism underlying the very high efficiency associated with solar energy conversion in photosystem I in situ.
Parallelisms and affectivity in the negotiation of optimal social proximity
Authors: Dutra Rosália 
Published: August 2017

AbstractThis paper explores the ways in which speakers exchange information about themselves, and the world around them, in order to create an optimal social space in which interaction and engagement may be successfully accomplished. Success, in turn, the paper argues, depends on speakers making communicative gestures that involve the expression of certain aspects of their inner world: their preferences, attitudes, interests, beliefs, characterizations, points of view, values, assessments, likes, dislikes, and related notions that are rooted in how they feel about the world. Drawing from multi-party conversational data, the paper argues that resonance is one of the most productive outlets for the construction of ordinary evaluative/emotive stances. In fact, it is through the social practice of resonance itself that the amorphous and subtle nature of affect and emotions takes shape. The utterances that are selected for resonance, the subsequent resonant patterns, and the frequency in which the pattern is reproduced in order to secure the intended meaning are also briefly addressed in the paper.
Stance management in oral narrative
Authors: Sakita Tomoko I. 
Published: August 2017

AbstractThis paper investigates how actively the speaker engages in taking stance at various levels in oral narrative. By usingDu Bois’ (2007)stance theory, it shows that the meta-stance markerwell, a discourse marker that performs the management of stance relations in conversational interaction (Sakita 2013a), plays a significant role in oral narrative as well.Wellmarks two central modes of stance-taking in a narrative. First,wellmanages the changes of local-spectrum stance-taking that occur among the utterances of/about characters or of the speakers who speak in their immediate, locally shared consciousness. Second,welltypically manages the narrator’s broad-spectrum stance-taking with respect to the narrative event as a coherent whole. The latter corresponds to the use ofwellthat is claimed to be unique for the context of the narrative (Norrick 2001). However, this paper shows thatwellin both local- and broad-spectrum scope functions as a meta-stance marker by managing stance relations. The paper demonstrates that stance is often embedded and effectively highlighted in resonance (Du Bois 2014), both in dialogic and monologic contexts.
Resonance as a resource for stance-taking in narratives
Authors: Nir Bracha 
Published: August 2017

AbstractThis paper traces the recurrence and manipulation of devices in monologic narrative texts produced by university students based on a semi-structured elicitation. It focuses on a detailed analysis of multiple texts produced by different speaker-writers of Hebrew, to illustrate the function of structural resonance of both clauses and combinations of clauses (Clause Packages). The analyses show that while lexical devices reflect a more distanced (less evaluative) discourse stance (Berman 2005), the use of creative resonance (Du Bois 2014) between syntactic structures can either enhance or undermine the narrator’s own explicit perspective on events. Stance is thus not only highlighted by resonance in monologic texts (Sakita this issue); in fact, stance is engaged with in a way that is very similar to what has been illustrated for dialogue (Dori-Hacohen this issue; Dutra this issue; Nir & Zima this issue). It is suggested that the power of this engagement can be fully assessed only if lexical and syntactic resonance are systematically analyzed.
On the online effects of subjectivity encoded in causal connectives
Authors: Li Fang , Mak Willem M. , Evers-Vermeul Jacqueline , Sanders Ted J. M. 
Published: August 2017

AbstractCausal relations between sentences differ in terms of subjectivity: they can be objective (based on facts) or subjective (based on reasoning). Subjective relations lead to longer reading times than objective relations. Causal connectives differ in the degree to which they encode this subjectivity. The Chinese connectiveskejian‘so’ andyin’er‘so’ specify a high and low degree of subjectivity, respectively, whereassuoyi‘so’ is underspecified for subjectivity. In an eye-tracking experiment we compare the effect of the specificity of these connectives in subjective and objective relations. In objective relations, the specificity of the connective has no effect on reading times. In subjective relations, reading times are shorter in sentences with the specified connectivekejianthan in sentences with the underspecified connectivesuoyi. These results suggest that readers prefer to interpret a relation as objective. Computing subjective relations requires extra processing time, which is diminished when the connective encodes the subjectivity.
A Conceptual Model for Water Sensitive City in Surabaya
Authors: Pamungkas A , Tucunan K P , Navastara A , Idajati H , Pratomoatmojo N A 
Published: August 2017

Abstract
Frequent inundated areas, low quality of water supply, highly dependent water sources from external are some key problems in Surabaya water balance. Many aspects of urban development have stimulated those problems. To uncover the complexity of water balance in Surabaya, a conceptual model for water sensitive city is constructed to find the optimum solution. A system dynamic modeling is utilized to assist and enrich the idea of conceptual model. A secondary analysis to a wide range data directs the process in making a conceptual model. FGD involving many experts from multidiscipline are also used to finalize the conceptual model. Based on those methods, the model has four main sub models that are; flooding, land use change, water demand and water supply. The model consists of 35 key variables illustrating challenges in Surabaya urban water.
Land Prices Heading Skyward? An Analysis of Farmland Values across Tanzania
Authors: Wineman Ayala , Jayne Thomas S 
Published: August 2017

AbstractLand markets are developing rapidly in Africa, though there remains a dearth of analysis regarding the direction and correlates of land prices and their implications for public policy in the region. This paper examines trends in land values and the factors influencing these trends in Tanzania. Real land prices rose significantly between 2009 and 2013 by 5.67% per year. A hedonic analysis of land values suggests that improved incentives for farming, urbanization and rising population density, and improved tenure security are possible drivers of rising land prices. We conclude by considering the potential policy implications arising from this work.
Integrative structural and dynamical biology with PLUMED-ISDB
Authors: Bonomi Massimiliano , Camilloni Carlo 
Published: August 2017

Abstract

Summary
Accurate structural models of biological systems can be obtained by properly combining experimental data with a priori physico–chemical knowledge. Here we present PLUMED-ISDB, an open-source, freely-available module of the popular PLUMED library, which enables the simultaneous determination of structure and dynamics of conformationally heterogeneous systems by integrating experimental data with a priori information. This integration is achieved using metainference, a general Bayesian framework that accounts for both noise in the data and their ensemble-averaged nature. PLUMED-ISDB implements different types of experimental data, such as several NMR observables, FRET, SAXS and cryo-electron microscopy data, and enables modelling structure and dynamics of individual proteins, protein complexes, membrane proteins, RNA and DNA, using a variety of enhanced sampling methods and resolutions of the system.

Availability and implementation
PLUMED-ISDB is freely available at www.plumed.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Occurrence and Covariation of Binge Eating and Compensatory Behaviors Across Early to Mid-Adolescence
Authors: Davis Heather A , Ortiz Anna Marie L , Smith Gregory T 
Published: August 2017

AbstractThe purpose of this study was to examine the occurrence and covariation of four eating disorder behaviors across the elementary, middle, and high school years. In a sample of 1,906 youth measured over 5 years at nine time points, from the past year of elementary school through the second year of high school, binge eating, purging (self-induced vomiting), compensatory exercise, and fasting behavior were assessed by self-report. Over the 5-year period, rates of binge eating and purging increased but rates of compensatory exercise and fasting decreased. Girls and boys did not differ in their rates of engagement in any of the behaviors. Within time, the behaviors covaried modestly. Health-care professionals are advised to assess each behavior individually, rather than base interventions on the presence or absence of a diagnosable eating disorder. Gender should not be a basis for assessing for the presence of any of these behaviors.
Overcoming Clopidogrel Resistance: Three Promising Novel Antiplatelet Drugs Developed in China
Authors: Xie Hong-Guang , Jia Yu-Meng , Tai Ting , Ji Jin-Zi 
Published: August 2017

Abstract:
Clopidogrel is one of the most frequently prescribed drugs worldwide; however, the presence of clopidogrel resistance and high susceptibility to genetic variations and drug interactions are facilitating the development of other antiplatelet drugs. To overcome clopidogrel resistance, several promising clopidogrel analogues have been developed in China, such as vicagrel (and its deuterated analogues), PLD-301, and W1. These novel chemical analogues are all characterized by much faster and more efficient bioconversion to clopidogrel thiolactone (or 2-oxo-clopidogrel, the precursor of clopidogrel active metabolite) in the intestine than clopidogrel itself through bypassing the first-step P450-mediated oxidation of clopidogrel in the liver. Of them, metabolic conversion of vicagrel and PLD-301 to 2-oxo-clopidogrel is catalyzed by intestinal carboxylesterase 2 and alkaline phosphatase, respectively. In this review article, we summarized all evidence on highly efficient bioconversion to their shared precursor of clopidogrel active metabolite and the mechanisms underlying such a pronounced improvement. These drugs in the pipeline would be promising antiplatelet drugs that could be superior to clopidogrel in future patient care.
Time-course Study on Left Ventricular Function in a Rabbit Model of Ischemia–reperfusion Injury With Morphine Preconditioning
Authors: Zhao Baihua , Liu Chengxiao , Pu Darong , Zeng Shi , Dai Xi , Liu Minghui 
Published: August 2017

Aims:
To analyze the left ventricular longitudinal function in a rabbit model of myocardial ischemia reperfusion with morphine preconditioning through strain rate imaging and to evaluate the effect of morphine preconditioning.

Methods:
A myocardial ischemia–reperfusion model was induced by occlusion and recanalization of the coronary artery in 40 male New Zealand white rabbits, which were divided into a sham group, morphine group, and vehicle control group. Routine echocardiography data were recorded 1 day before and within 28 days after the operation. Dynamic images were also collected and analyzed off-line using Doppler tissue imaging software.

Results:
On the first day after the operation, the global and regional systolic functions of the left ventricle in the morphine and vehicle control groups were lower than those in the sham group. After ischemia reperfusion, some of the values of the above-mentioned parameters decreased over time, which was more obvious in the vehicle control group at each examined time point.

Conclusions:
The current study revealed that detection of changes in regional myocardial function after myocardial ischemia reperfusion by strain rate imaging is objective and accurate. In addition, our results indicated that morphine preconditioning significantly attenuates myocardial ischemia–reperfusion injury in rabbits.
A Proposal for Updated Standards of Photographic Documentation in Aesthetic Medicine
Authors: Prantl Lukas , Brandl Dirk , Ceballos Patricia 
Published: August 2017

Summary:
In 1998, DiBernardo et al. published a very helpful standardization of comparative (before and after) photographic documentation. These standards prevail to this day. Although most of them are useful for objective documentation of aesthetic results, there are at least 3 reasons why an update is necessary at this time: First, DiBernardo et al. focused on the prevalent standards of medical photography at that time. From a modern perspective, these standards are antiquated and not always correct. Second, silver-based analog photography has mutated into digital photography. Digitalization offers virtually unlimited potential for image manipulation using a vast array of digital Apps and tools including, but not limited to, image editing software like Photoshop. Digitalization has given rise to new questions, particularly regarding appropriate use of editing techniques to maximize or increase objectivity. Third, we suggest changes to a very small number of their medical standards in the interest of obtaining a better or more objective documentation of aesthetic results. This article is structured into 3 sections and is intended as a new proposal for photographic and medical standards for the documentation of aesthetic interventions:
1. The photographic standards.
2. The medical standards.
3. Description of editing tools which should be used to increase objectivity.
The Association of Fat and Lean Tissue With Whole Body and Spine Bone Mineral Density Is Modified by HIV Status and Sex in Children and Youth
Authors: Jacobson Denise L. , Lindsey Jane C. , Coull Brent A. , Mulligan Kathleen , Bhagwat Priya , Aldrovandi Grace M. 
Published: August 2017

Background:
HIV-infected (HIV-pos) male children/youth showed lower bone mineral density at sexual maturity than HIV-uninfected (HIV-neg) females. It is not known whether complications of HIV disease, including abnormal body fat distribution, contribute to lower bone accrual in male HIV-pos adolescents.

Methods:
In a cross-sectional study, we evaluated the relationship between body composition (fat and lean mass) and bone mass in HIV-pos and HIV-neg children/youth and determined if it is modified by HIV status and sex. We used generalized estimating equations to simultaneously model the effect of fat/lean mass on multiple bone outcomes, including total body bone mineral density and bone mineral content and spine bone mineral density. We evaluated effect modification by HIV and sex.

Results:
The analysis cohort consisted of 143 HIV-neg and 236 HIV-pos, of whom 55% were black non-Hispanic and 53% were male. Ages ranged from 7 to < 25 years. Half of the children/youth were at Tanner stage 1 and 20% at Tanner 5. Fat mass was more strongly positively correlated with bone mass in HIV-neg than HIV-pos children/youth and these relationships were more evident for total body bone than spine outcomes. Within HIV strata, fat mass and bone were more correlated in female than male children/youth. The relationship between lean mass and bone varied by sex, but not by HIV status.

Conclusions:
HIV disease diminishes the positive relationship of greater fat mass on bone mass in children/youth. Disruptions in body fat distribution, which are common in HIV disease, may have an impact on bone accretion during pubertal development.
Future Application of Multitheory Model of Health Behavior Change for Skin Cancer Prevention Behaviors
Authors: Martin Brian , Nahar Vinayak K. , Boyas Javier F. , Jacks Stephanie K. , Brodell Robert T. , Sharma Manoj 
Published: August 2017

ABSTRACT
Skin cancer is a global health issue and constitutes the most common form of cancer worldwide. Exposure to ultraviolet radiation is a primary skin cancer risk. Engaging in sun protection behavior could mitigate this risk. Several sociobehavioral theories can be used to better explain and predict health behaviors. Unfortunately, application of theories has yielded mixed results with variable predictability. Most importantly, they do not impact long-term changes in behavior. Therefore, there is still a need to develop theoretical models that better explain and predict health behaviors, in particular, sun-safe behaviors. A recently proposed health behavior theory, called the multitheory model of health behavior change, may be the answer. The multitheory model has been shown to be effective in changing attitudes toward other health behaviors such as physical activity, portion size control, and sleep deprivation. It is unique from established health behavior theories because it emphasizes long-term change over short-term behavior modification, which is more likely associated with relapse. It does this by separating factors that lead to short-term change from those that promote long-term behavior adoption. This article presents the application of the principles of multitheory model to skin cancer preventative behaviors.