bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study
Authors: Dai Jiaan , Yu Fengchao , Li Ning , Yu Weichuan 
Published: March 2018

AbstractMotivationAnalyzing tandem mass spectrometry data to recognize peptides in a sample is the fundamental task in computational proteomics. Traditional peptide identification algorithms perform well when identifying unmodified peptides. However, when peptides have post-translational modifications (PTMs), these methods cannot provide satisfactory results. Recently, Chick et al., 2015 and Yu et al., 2016 proposed the spectrum-based and tag-based open search methods, respectively, to identify peptides with PTMs. While the performance of these two methods is promising, the identification results vary greatly with respect to the quality of tandem mass spectra and the number of PTMs in peptides. This motivates us to systematically study the relationship between the performance of open search methods and quality parameters of tandem mass spectrum data, as well as the number of PTMs in peptides.ResultsThrough large-scale simulations, we obtain the performance trend when simulated tandem mass spectra are of different quality. We propose an analytical model to describe the relationship between the probability of obtaining correct identifications and the spectrum quality as well as the number of PTMs. Based on the analytical model, we can quantitatively describe the necessary condition to effectively apply open search methods.AvailabilitySource codes of the simulation are available at http://bioinformatics.ust.hk/PST.html.Contactboningli@ust.hk or eeyu@ust.hkSupplementary informationSupplementary data are available at Bioinformatics online.
Minimally invasive deep-brain imaging through a 50 μm-core multimode fibre
Authors: Vasquez-Lopez Sebastian A. , Koren Vadim , Plöschner Martin , Padamsey Zahid , Čižmár Tomáš , Emptage Nigel J. 
Published: March 2018

AbstractAchieving optical access to deep-brain structures represents an important step towards the goal of understanding the mammalian central nervous system. The complex refractive index distribution within brain tissue introduces severe aberrations to long-distance light propagation thereby prohibiting image reconstruction using currently available non-invasive techniques. In an attempt to overcome this challenge endoscopic approaches have been adopted, principally in the form of fibre bundles or GRIN-lens based endoscopes. Unfortunately, these approaches create substantial mechanical lesions of the tissue precipitating neuropathological responses that include inflammation and gliosis. Together, lesions and the associated neuropathology may compromise neural circuit performance. By replacing Fourier-based image relay with a holographic approach, we have been able to reduce the volume of tissue lesion by more than 100-fold, while preserving diffraction-limited imaging performance. Here we demonstrate high-resolution fluorescence imaging of neuronal structures, dendrites and synaptic specialisations, in deep-brain regions of living mice. These results represent a major breakthrough in the compromise between high-resolution imaging and tissue damage, heralding new possibilities for deep-brain imaging in vivo.
C. elegansavoidance ofPseudomonas: thioredoxin shapes the sensory response to bacterially produced nitric oxide
Authors: Hao Yingsong , Yang Wenxing , Ren Jing , Hall Qi , Zhang Yun , Kaplan Joshua M. 
Published: March 2018

AbstractWe show thatC. elegansavoids a bacterial pathogenPseudomonas aeruginosa(PA14) by detecting PA14-produced nitric oxide (NO). PA14 mutants deficient for NO production fail to elicit avoidance and NO donors repel worms. PA14 and NO avoidance are mediated by the ASJ chemosensory neurons, which respond to NO with intracellular calcium rises. PA14 avoidance and NO-evoked calcium responses require receptor guanylate cyclases (DAF-11 and GCY-27), and cyclic nucleotide gated ion channels (TAX-2 and -4). ASJ exhibits calcium increases at both the onset and removal of NO. These NO-evoked ON and OFF calcium transients are affected by a redox sensing protein, TRX-1/thioredoxin. TRX-1’s trans-nitrosylation activity inhibits the ON transient whereas TRX-1’s de-nitrosylation activity promotes the OFF transient. Thus,C. elegansexploits bacterially produced NO as a cue to mediate avoidance and TRX-1 functions as an NO-sensor that endows ASJ with a bi-phasic response to NO exposure.
Network-Based Biomarkers Enable Cross-Disease Biomarker Discovery
Authors: Haider Syed , Yao Cindy Q. , Sabine Vicky S. , Grzadkowski Michal , Stimper Vincent , Starmans Maud H.W. , Wang Jianxin , Nguyen Francis , Moon Nathalie C. , Lin Xihui , Drake Camilla , Crozier Cheryl A. , Brookes Cassandra L. , van de Velde Cornelis J.H. , Hasenburg Annette , Kieback Dirk G. , Markopoulos Christos J. , Dirix Luc Y. , Seynaeve Caroline , Rea Daniel W. , Kasprzyk Arek , Lambin Philippe , Lio Pietro , Bartlett John M.S. , Boutros Paul C. 
Published: March 2018

AbstractBiomarkers lie at the heart of precision medicine, biodiversity monitoring, agricultural pathogen detection, amongst others. Surprisingly, while rapid genomic profiling is becoming ubiquitous, the development of biomarkers almost always involves the application of bespoke techniques that cannot be directly applied to other datasets. There is an urgent need for a systematic methodology to create biologically-interpretable molecular models that robustly predict key phenotypes. We therefore created SIMMS: an algorithm that fragments pathways into functional modules and uses these to predict phenotypes. We applied SIMMS to multiple data-types across four diseases, and in each it reproducibly identified subtypes, made superior predictions to the best bespoke approaches, and identified known and novel signaling nodes. To demonstrate its ability on a new dataset, we measured 33 genes/nodes of the PIK3CA pathway in 1,734 FFPE breast tumours and created a four-subnetwork prediction model. This model significantly out-performed existing clinically-used molecular tests in an independent 1,742-patient validation cohort. SIMMS is generic and can work with any molecular data or biological network, and is freely available at:https://cran.r-project.org/web/packages/SIMMS.
A method for faster purification of serine proteinases fromBothrops alternatusandBothrops moojenisnake venoms
Authors: Heleno M.A.G. , Santos L.D. , Ferreira R.S. , Barraviera B 
Published: March 2018

ABSTRACTSnake venoms are important sources of substances with a variety of pharmacological activities. Among the different proteins present in these venoms, snake venom serine proteinases (SVSPs) have important effects on the hemostatic system that influence the hemodynamic properties of blood.Bothropsgenus snakes presented their venom richly composed of SVSPs thrombin-like, and the isolation of these enzymes is of great interest. In 1994, the Center for the Study of Venoms and Venomous Animals (CEVAP) - UNESP standardized the fibrin sealant derived from snake venom, replacing the bovine thrombin by gyroxin thrombin-like enzyme fromCrotalus durissus terrificus(Rattlesnake) and human plasma fibrinogen by buffaloes cryoprecipitate. Despite chromatographic techniques for the purification of gyroxin be well grounded in the literature, that income is considered low. Thus, in addition to gyroxin, other thrombin-like enzymes could be employed in the composition of the new fibrin sealant after being standardized to the purifying and chromatographic performance and widely evaluated for biological activities. Therefore, it is extremely important that in our lab is deployed, standardized and validated a method for the chromatographic purification of other thrombin-like enzymes such as found in Bothrops snake venoms. Thus a two-step chromatographic procedure was developed to routinely purify serine proteinases fromBothrops alternatusandB. moojenisnakes venoms to provide new enzymes for improving the CEVAP’s heterologous fibrin sealant.
Adjutant: an R-based tool to support topic discovery for systematic and literature reviews
Authors: Crisan Anamaria , Munzner Tamara , Gardy Jennifer L. 
Published: March 2018

AbstractSummaryAdjutant is an open-source, interactive, and R-based application to support mining PubMed for a systematic or a literature review. Given a PubMed-compatible search query, Adjutant downloads the relevant articles and allows the user to perform an unsupervised clustering analysis to identify data-driven topic clusters. Users can also sample documents using different strategies to obtain a more manageable dataset for further analysis. Adjutant makes explicit trade-offs between speed and accuracy, which are modifiable by the user, such that a complete analysis of several thousand documents can take a few minutes. All analytic datasets generated by Adjutant are saved, allowing users to easily conduct other downstream analyses that Adjutant does not explicitly support.Availability and ImplementationAdjutant is implemented in R, using Shiny, and is available athttps://github.com/amcrisan/Adjutant
Abnormal mortgage delinquencies as housing crisis early symptoms
Authors: Parnes Dror 
Published: March 2018

PurposeThe purpose of this paper is to analyze the differences between the actual mortgage prompt and late payments and their respective expected measures from 2004 to 2010 to spot early symptoms of housing crisis.Design/methodology/approachThis paper explores these discrepancies across the entire US market and along various delinquency lengths of 30, 60 and 90 days. This paper constructs a Bayesian forecasting model that relies on prior distributional properties of diverse time horizons.FindingsAbnormal mortgage delinquency rates are identified in real time and can be served as early symptoms for housing crisis.Practical implicationsThe statistical scheme proposed in this paper can function as a valuable predictive tool for lending institutions, bank audit companies, regulatory bodies and real estate professional investors who examine changes in economic settings and trends in short sale leads.Social implicationsThe abnormal mortgage delinquencies can serve as indicators of changes in economic fundamentals and early signs of a mounting housing crisis.Originality/valueThis paper presents a unique statistical technique in the context of mortgage delinquencies.
Religious aspects in psychiatry and psychotherapy
Authors: Schwarz Silke 
Published: March 2018

PurposeThe purpose of this paper is to explore the role of religion in psychiatry and psychotherapy and it introduces a context-oriented approach to religion.Design/methodology/approachThe paper opted for a selective literature review to highlight significant issues with regard to mainstream psychology.FindingsIt provides a short summary on the historical neglect and exclusion from clinical practice and shows how religion was integrated into the mainstream of psychotherapy and psychiatry. A quantitative and universalistic approach to religion is dominant. The widespread approach to religious coping by Pargament is presented as well as related findings with regard to religion and mental health.Research limitations/implicationsThe paper includes implications for the development of a context-oriented inclusion of religion and encourages for associated empirical research.Originality/valueWith a critical inclusion of contexts, professionals may stay alerted to the issue that health and disorders are not ontological facts but contain moral codes of a current society. It takes the social context and unequal power relations as the starting point for a partisan cooperation with the affected persons.
The marginalization of religion in end of life care: signs of microaggression?
Authors: Pentaris Panagiotis 
Published: March 2018

PurposeService users very often interpret and respond to their experiences of death, dying and bereavement through a religious or spiritual lens. However, recent trends in religion and belief have influenced how professionals respond to indicators such as faith. Since the post-war years in Britain, and due to the transfer of services from church to state, as well as the change in the religious landscape, language has largely secularized. When people start addressing religion and belief again, they lack the appropriate literacy to do so, this is termed religious literacy by Dinham (2015). The purpose of this paper is to explore how professionals in end of life (EOL) care respond to service users’ religious and spiritual indicators, through the lens of religious literacy.Design/methodology/approachThe paper draws from an ethnographic study undertaken across hospices in England, UK. In this study, healthcare professionals (HCPs) were observed for one calendar year.FindingsResults show that lack of religious literacy on the part of HCPs may lead to subtle and unintentional microaggression. Three types of indications of microinvalidation have been noted: verbal, non-verbal and environmental.Originality/valueThis paper innovates in offering a first-hand phenomenological interpretation of observations in the field. The research data capture visually the impact of lack of religious literacy, an achievement which adds to the dialogue about service user rights in EOL care.
Impact of financial inclusion on poverty alleviation through cooperative banks
Authors: Lal Tarsem 
Published: March 2018

Purpose
The purpose of this paper is to examine the impact of financial inclusion on poverty alleviation through cooperative banks.

Design/methodology/approach
In order to fulfil the objectives of the study, primary data were collected from 540 beneficiaries of cooperative banks operating in three northern states of India, i.e., J&K, Himachal Pradesh (HP) and Punjab using purposive sampling during July-December 2015. The technique of factor analysis had been used for summarisation of the total data into minimum factors. For checking the validity and reliability of the data, the second-order CFA was performed. Statistical techniques like one-way ANOVA, t-test and SEM were used for data analysis.

Findings
The study results reveal that financial inclusion through cooperative banks has a direct and significant impact on poverty alleviation. The study highlights that access to basic financial services such as savings, loans, insurance, credit, etc., through financial inclusion has generated a positive impact on the lives of the poor and help them to come out of the clutches of poverty.

Research limitations/implications
The study was conducted amidst few limitations. First, the in-depth analysis of the study is restricted to three northern states only because of limited resources and time availability. Second, the study is limited to the perception of financial inclusion beneficiaries only, which, in future, could be carried further on the perception of other stakeholders such as bank officials, business correspondents, village panchayats, etc.

Originality/value
The study makes contribution towards the financial inclusion literature relating to poverty alleviation and fulfils the research gap to some extent by assessing the impact of financial inclusion on poverty alleviation through cooperative banks. This paper can help the policymakers and other stakeholders of cooperative banks in promoting banking habits among poor rural households both at the national and international level.
Exploring the mediating role of social capital in the relationship between financial intermediation and financial inclusion in rural Uganda
Authors: Bongomin George Okello Candiya , Munene John C. , Ntayi Joseph Mpeera , Malinga Charles Akol 
Published: March 2018

Purpose
The purpose of this paper is to establish the mediating role of social capital in the relationship between financial intermediation and financial inclusion in rural Uganda.

Design/methodology/approach
The current study used cross-sectional research design and a semi-structured questionnaire was used to collect data for this study. The study applied structural equation modeling through bootstrap approach in AMOS to establish the mediating role of social capital in the relationship between financial intermediation and financial inclusion.

Findings
The results indicated that social capital significantly mediates the relationship between financial intermediation and financial inclusion in rural Uganda. Therefore, it can be deduced that social capital among the poor play an important role in promoting financial intermediation for improved financial inclusion in rural Uganda.

Research limitations/implications
Although the sample was large, it may not be generalized to other segments of the population. Data were collected from only poor households located in rural Uganda. Besides, the study was cross-sectional, thus, limiting efforts in investigating certain characteristics of the sample over time. Perhaps future studies could adopt the use of longitudinal research design.

Practical implications
Financial institutions such as banks should rely on social capital as a substitute for physical collateral in order to promote financial inclusion, especially among the poor in rural Uganda.

Originality/value
This study provides empirical evidence on phenomenon not studied in rural areas in Sub-Saharan Africa where the poor use social capital embedded in customs and norms for doing business. The results highlight the importance of social capital in mediating the relationship between financial intermediation and financial inclusion of the poor in rural Uganda.
Factors influencing farmer’s perceptions and behavior toward pesticide use in Malaysia
Authors: Ali Jamal , Yusof Norhafezah , Abd. Aziz Fadzli Shah 
Published: March 2018

Purpose
The purpose of this paper is to examine the factors believed to influence the behavior of 1,042 rice farmers in Malaysia regarding the overuse of pesticides. Frequent overuse of pesticide will have an impact on human health and the environment, which lead to greater expenditure on health care.

Design/methodology/approach
The theoretical models of compliance behavior tested include the basic deterrence model, which focuses on the enforcement of regulation as a key determinant of compliance. The models integrate economic theory with theories of social behavior to account for motivations expected, influencing individuals’ decisions on whether to follow the regulation on using pesticides.

Findings
Significance tests reported that the information regarding the danger of using pesticides, the perception toward the impact on the environment and the expected impact on health influences the compliance behavior of using pesticides.

Research limitations/implications
These findings highlight the necessity for the policy makers to design an effective program which gives more information and provide training related to the risk and the safe handling of pesticides.

Practical implications
The farmers who receive information and training related to handling of pesticides become more cautious in the use of pesticides. Countries involved in agriculture and the use of pesticides widely by their farmers need to emphasize continuous training and periodic information dissemination.

Social implications
The implication drawn is rice farmers should be encouraged to practice new methods in rice planting, especially in the integrated pest management method.

Originality/value
These research findings suggest that the overuse of pesticides in the rice farming continues to be an important problem.
Performance analysis of high-stiffness bearing composited by hydrostatic cavities and tilting pads with preload
Authors: Chen Runlin , Wang Jianlei , Yuan XiaoYang , Li Longlong , Cui Yahui 
Published: March 2018

Purpose
To meet the high stiffness requirement of bearings used in high-precision spindles, this paper aims to propose a novel kind of bearing composited by hydrostatic cavities and tilting pads with preload.

Design/methodology/approach
Cavities are cut on the oil seal surface of a hybrid bearing, in which the tilting pads are set up. The load of the bearing is carried by the hydrostatic cavities and tilting pads. The structural features of this compound bearing and the controlling variables of the main stiffness coefficient are presented. Two basic design principles are proposed on the basis of equal machining clearance (EMC) and equal installation clearance (EIC).

Findings
The theoretical analysis indicates that the stiffness of compound bearings under the EMC condition increases to infinity monotonously when the preload coefficient of the tilting pad tends to 1, while the stiffness under the EIC condition has a peak value. Therefore, a synthetic design principle is proposed by synthetically using the above-mentioned two principles. The applicable range of the three principles is discussed through an example.

Originality/value
The study about technological combination of hydrostatic cavity and tilting pad in this paper can provide suggestions for the design of a high-stiffness bearing in a precision spindle.
Online condition monitoring of misaligned meshing gears using wear debris and oil quality sensors
Authors: Kumar Paras , Hirani Harish , Agrawal Atul Kumar 
Published: March 2018

Purpose
This paper aims to investigate the effect of misalignment on wear of spur gears and on oil degradation using online sensors.

Design/methodology/approach
The misalignment effect on gears is created through a self-alignment bearing, and is measured using laser alignment system. Several online sensors such as Fe-concentration sensor, moisture sensor, oil condition sensor, oil temperature sensor and metallic particle sensor are installed in the gear test rig to monitor lubricant quality and wear debris in real time to assess gearbox failure.

Findings
Offset and angular misalignments are detected in both vertical and horizontal planes. The failure of misaligned gear is observed at both the ends and on both the surfaces of the gear teeth. Larger-size ferrous and non-ferrous particles are traced by metallic particle sensor due to gear and seal wear caused by misalignment. Scanning electron microscope (SEM) images examine chuck, spherical and flat platelet particles, and confirm the presence of fatigue (pitting) and adhesion (scuffing) wear mechanism. Energy-dispersive X-ray spectroscopy analysis of SEM particles traces carbon (C) and iron (Fe) elements due to gear failure.

Originality/value
Gear misalignment is one of the major causes of gearbox failure and the lubricant analysis is as important as wear debris analysis. A reliable online gearbox condition monitoring system is developed by integrating wear and oil analyses for misaligned spur gear pair in contact.