bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-Organizing Maps to Validate Anti-Pollution Policies
Authors: Arroyo Ángel , Cambra Carlos , Herrero Álvaro , Tricio Verónica , Corchado Emilio 
Published: October 2019

Abstract
This study presents the application of self-organizing maps to air-quality data in order to analyze episodes of high pollution in Madrid (Spain’s capital city). The goal of this work is to explore the dataset and then compare several scenarios with similar atmospheric conditions (periods of high Nitrogen dioxide concentration): some of them when no actions were taken and some when traffic restrictions were imposed. The levels of main pollutants, recorded at these stations for eleven days at four different times from 2015 to 2018, are analyzed in order to determine the effectiveness of the anti-pollution measures. The visualization of trajectories on the self-organizing map let us clearly see the evolution of pollution levels and consequently evaluate the effectiveness of the taken measures, after and during the protocol activation time.
In vitro Acquisition and Retention of Low-Pathogenic Avian Influenza H9N2 by Musca domestica (Diptera: Muscidae)
Authors: Salamatian Iman , Moshaverinia Ali , Razmyar Jamshid , Ghaemi Mehran 
Published: October 2019

AbstractAvian influenza virus (AIV) H9N2 emerged in the 1990s as an economically important disease in poultry and occasionally infects humans and other mammals. The aim of this study was to evaluate the acquisition and retention of H9N2 AIV on and within the house fly, Musca domestica (Linnaeus 1758), under laboratory conditions. In first experiment, 100 adult house flies were divided into control and treatment groups equally. Treatment group was fed with a meal containing H9N2 virus, while control group was supplied with an identical meal without virus. Fifteen minutes after exposure in each group, flies were washed twice to remove surface particles, disinfected and then homogenized for testing. The two external body surface washes and the homogenate samples were tested for H9N2 to distinguish exterior from interior viral load. Second experiment was performed likewise but five flies from each group were taken at 0, 6, 24, 48, 72, 96, and 120 h post-exposure. All samples were subjected to real-time reverse-transcription polymerase chain reaction (RRT-PCR) for detecting H9-Specific viral RNA. Results of the first experiment showed that viral RNA was detectable in both of external surface and homogenates samples. Second experiment revealed that persistence of H9N2 AIVs on external body surface and within the body of M. domestica were 24 and 96 h, respectively. Moreover, viral RNAs concentration declined during the time after exposure to AIV H9N2 either outside or within house flies. Overall, house fly was able to acquire and preserve H9N2 AIV experimentally, which may contribute the spread of virus among poultry farms.
Developing a Music-Based Selective Attention Training Program for Toddlers with Developmental Disabilities
Authors: Lantigua Katherine 
Published: October 2019

Abstract
The purpose of this article was to describe the development of a music-based selective attention training (MSAT) program to improve selective attention in toddlers with developmental disabilities. Selective attention is the ability to attend despite distractors, and it is a developmentally appropriate skill for toddlers because they have the neural connections to begin selectively attending. Music can potentially impact selective attention due to overlapping neural processing areas for both selective attention and music engagement (i.e., listening to and playing music). The MSAT program development involved several steps, including observations, reviewing literature to outline the Therapeutic Function of Music (TFM), participating in training, offering parent and teacher information sessions, designing session evaluation forms, and facilitating 19 weeks of group and individual sessions at an early intervention setting. Program development resulted in an MSAT program manual designed to improve selective attention in toddlers with developmental disabilities. The clinician found that specific auditory and visual distractors that are familiar and preferred by toddlers could be used to practice selective attention. Introducing distractors at predictable time points within the music experience gave toddlers multiple opportunities to practice ignoring the distractors and focusing on the target task. Evaluation of this MSAT program, its utility for stakeholders such as music therapists and early childhood professionals, and implications for the development of future music-based programs in early intervention are discussed.
NPInter v4.0: an integrated database of ncRNA interactions
Authors: Teng Xueyi , Chen Xiaomin , Xue Hua , Tang Yiheng , Zhang Peng , Kang Quan , Hao Yajing , Chen Runsheng , Zhao Yi , He Shunmin 
Published: October 2019

AbstractNoncoding RNAs (ncRNAs) play crucial regulatory roles in a variety of biological circuits. To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database (http://bigdata.ibp.ac.cn/npinter). Since the last version of NPInter was issued, a rapidly growing number of studies have reported novel interactions and accumulated numerous high-throughput interactome data. We have therefore updated NPInter to its fourth edition in which are integrated 600 000 new experimentally identified ncRNA interactions. ncRNA–DNA interactions derived from ChIRP-seq data and circular RNA interactions have been included in the database. Additionally, disease associations were annotated to the interacting molecules. The database website has also been redesigned with a more user-friendly interface and several additional functional modules. Overall, NPInter v4.0 now provides more comprehensive data and services for researchers working on ncRNAs and their interactions with other biomolecules.
Antimicrobial Stewardship Review of Automated Candidemia Alerts Using the Epic Stewardship Module Improves Bundle-of-Care Adherence
Authors: Pettit Natasha N , Han Zhe , Nguyen Cynthia T , Choksi Anish , Charnot-Katsikas Angella , Beavis Kathleen G , Tesic Vera , Pisano Jennifer 
Published: October 2019

Abstract

Background
Antimicrobial stewardship interventions utilizing real-time alerting through the electronic medical record enable timely implementation of the bundle of care (BOC) for patients with severe infections, such as candidemia. Automated alerting for candidemia using the Epic stewardship module has been in place since July 2015 at our medical center. We sought to assess the impact of these alerts.

Methods
All adult inpatients with candidemia between April 1, 2011, and March 31, 2012 (pre-intervention), and June 30, 2016, and July 1, 2017 (post-intervention), were evaluated for BOC adherence. We also evaluated the impact on timeliness to initiate targeted therapy, length of stay (LOS), and 30-day mortality.

Results
Eighty-four patients were included, 42 in the pre- and 42 in the post-intervention group. Adherence to BOC was significantly improved, from 48% (pre-intervention) to 83% (post-intervention; P = .001). The median time to initiation of therapy was 4.8 hours vs 3.3 hours (P = .58), the median LOS was 24 and 18 days (P = .28), and 30-day mortality was 19% and 26% (P = .60) in the pre- and post-intervention groups, respectively.

Conclusions
Antimicrobial stewardship program review of automated alerts identifying patients with candidemia resulted in significantly improved BOC adherence and was associated with a 1.5-hour reduction in time to initiation of antifungal therapy. No significant change was observed with 30-day mortality or LOS.
Evaluation of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry and ClinPro Tools as a Rapid Tool for Typing Streptococcus pyogenes
Authors: Tadros Manal , Cabrera Ana , Matukas Larissa M , Muller Matthew 
Published: October 2019

Abstract

Background
Timely strain typing of group A Streptococci (GAS) is necessary to guide outbreak recognition and investigation. We evaluated the use of (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) combined with cluster analysis software to rapidly distinguish between related and unrelated GAS isolates in real-time.

Methods
We developed and validated a typing model using 177 GAS isolates with known emm types. The typing model was created using 43 isolates, which included 8 different emm types, and then validated using 134 GAS isolates of known emm types that were not included in model generation.

Results
Twelve spectra were generated from each isolate during validation. The overall accuracy of the model was 74% at a cutoff value of 80%. The model performed well with emm types 4, 59, and 74 but showed poor accuracy for emm types 1, 3, 12, 28, and 101. To evaluate the ability of this tool to perform typing in an outbreak situation, we evaluated a virtual outbreak model using a “virtual outbreak strain; emm74” compared with a non-outbreak group or an “outgroup “ of other emm types. External validation of this model showed an accuracy of 91.4%.

Conclusions
This approach has the potential to provide meaningful information that can be used in real time to identify and manage GAS outbreaks. Choosing isolates characterized by whole genome sequencing rather than emm typing for model generation should improve the accuracy of this approach in rapidly identifying related and unrelated GAS strains.
Thirty years after water privatization—is the English model the envy of the world?
Authors: Helm Dieter 
Published: October 2019

AbstractThe paper considers whether water privatization 30 years ago has delivered the promised superior performance to nationalization, which remains the dominant model in Europe. The paper sets out the arguments at privatization, in particular in relation to efficiency, the managerial incentives, the role of private-sector balance sheets in facilitating investment, and the impacts on the cost of capital. Alternative explanations of relative performance, notably the regulation model adopted, are highlighted, and the paper concludes by outlining an alternative model of water regulation which better marries up public responsibilities and private incentives.
Longitudinal clusters of pain and stiffness in polymyalgia rheumatica: 2-year results from the PMR Cohort Study
Authors: Muller Sara , Whittle Rebecca , Hider Samantha L , Belcher John , Helliwell Toby , Morton Chris , Hughes Emily , Lawton Sarah A , Mallen Christian D 
Published: October 2019

Abstract

Objectives
To investigate potential subgroups of primary care–diagnosed patients with PMR based on self-reported pain and stiffness severity over time.

Methods
A total of 652 people with an incident PMR diagnosis were recruited from English general practices and completed a baseline postal questionnaire. They were followed up with a further six questionnaires over a 2 year period. A total of 446 people completed the 2 year follow-up. Pain and stiffness were reported on a 0–10 numerical rating scale. Latent class growth analysis was used to estimate the joint trajectories of pain and stiffness over time. A combination of statistical and clinical considerations was used to choose the number of clusters. Characteristics of the classes were described.

Results
Five clusters were identified. One cluster represented the profile of ‘classical’ PMR symptoms and one represented sustained symptoms that may not be PMR. The other three clusters displayed a partial recovery, a recovery followed by worsening and a slow, but sustained recovery. Those displaying classical PMR symptoms were in better overall health at diagnosis than the other groups.

Conclusion
PMR is a heterogeneous condition, with a number of phenotypes. The spectrum of presentation, as well as varying responses to treatment, may be related to underlying health status at diagnosis. Future research should seek to stratify patients at diagnosis to identify those likely to have a poor recovery and in need of an alternative treatment pathway. Clinicians should be aware of the different experiences of patients and monitor symptoms closely, even where there is initial improvement.
Heart Failure Self-care Associated With Brain Injury in Executive Control Regions
Authors: Choi Sarah , Roy Bhaswati , Kumar Rajesh , Fonarow Gregg C. , Woo Mary A. 
Published: October 2019

Background:
Inadequate self-care is linked to poor health outcomes in heart failure (HF). Self-care depends on decision-making abilities, but links between self-care and brain injury to executive decision-making regulatory areas (prefrontal cortices) are unclear.

Objective:
We investigated the relationships between HF self-care and status of prefrontal cortices.

Methods:
Magnetic resonance imaging–based diffusion tensor imaging was performed in 21 patients with HF (age, 53.8 ± 7.9 years; 15 men; left ventricular ejection fraction, 25.1% ± 6.1%), and self-care and executive function were measured with the Self-care of Heart Failure Index (SCHFI) and Trail Making Test B. Using diffusion tensor imaging data, mean diffusivity (MD) maps were calculated and region-of-interest analyses were performed on the left and right prefrontal brain areas. Statistical analyses consisted of partial correlations (covariates, age, and gender).

Results:
The mean ± SD SCHFI scores were 70.78 ± 11.37 for maintenance, 70 ± 17.32 for management, and 74.91 ± 15.76 for confidence. The mean ± SD Trail Making Test B score was 90.2 ± 73.3 seconds. The mean ± SD MD values (higher values indicate tissue injury) of the left and right prefrontal cortices were 1.46 ± 0.16 (×10−3 mm2/s) and 1.44 ± 0.14 (×10−3 mm2/s), respectively. Significant negative correlations emerged between prefrontal MD values and SCHFI maintenance (left/right, r = −0.64/−0.70; P < .003) and SCHFI management (r = −0.93/−0.86; P < .003). Significant positive correlations were observed between prefrontal MD values and Trail Making Test B (r = 0.71/0.74; P < .001). A nonsignificant correlation emerged between prefrontal MD values and SCHFI confidence scores.

Conclusions:
Brain tissue integrity in executive function regulatory regions is associated with HF self-care for maintenance and management. The findings indicate that protection and brain injury repair in executive control areas may improve HF self-care.
Interaction of the Motor Protein SecA and the Bacterial Protein Translocation Channel SecYEG in the Absence of ATP
Authors: Winkler Klemens , Karner Andreas , Horner Andreas , Hannesschlaeger Christof , Knyazev Denis , Siligan Christine , Zimmermann Mirjam , Kuttner Roland , Pohl Peter , Preiner Johannes 
Published: October 2019

ABSTRACTTranslocation of many secretory proteins through the bacterial plasma membrane is facilitated by a complex of the SecYEG channel with the motor protein SecA. The ATP-free complex is unstable in detergent, raising the question how SecA may perform several rounds of ATP hydrolysis without being released from the membrane embedded SecYEG. Here we show that dual recognition of (i) SecYEG and (ii) vicinal acidic lipids confers an apparent nanomolar affinity. High-speed atomic force microscopy visualizes the complexes between monomeric SecA and SecYEG as being stable for tens of seconds. These long-lasting events and complementary shorter ones both give rise to single ion channel openings of equal duration. Furthermore, luminescence resonance energy transfer reveals two conformations of the SecYEG-SecA complex that differ in the protrusion depth of SecA’s two-helix finger into SecYEG’s aqueous channel. Such movement of the finger is in line with the power stroke mechanism of protein translocation.
Parallel 1024-ch Cyclic Voltammetry on Monolithic CMOS Electrochemical Detector Array
Authors: White Kevin A. , Mulberry Geoffrey , Kim Brian N. 
Published: October 2019

AbstractLarge-scale microelectrode arrays offers enhanced spatiotemporal resolution in electrophysiology studies.. In this paper, we discuss the design and performance of an electrochemical detector array which is capable of 1024-ch parallel cyclic voltammetry (CV) as well as other electrochemical measurements. The electrochemical detector is fabricated using a custom-designed CMOS chip which integrates both the circuity and on-chip microelectrode array, to operate and record from electrochemical measurements. For parallel 1024-ch recordings, 1024 capacitor-based integrating transimpedance amplifiers (TIA) are designed and integrated. The TIA design features the bipolar capabilities for measuring both negative and positive electrochemical currents due to reduction and oxidation of molecules. The resulted dynamic range of this TIA is −700 pA – 1968 pA. CV can be used to examine the quality of electrochemical electrodes by measuring the double-layer capacitance. Double-layer capacitance forms at the electrode-electrolyte interface and is a function of the effective area of the electrode. Thus, a contaminated electrode can have smaller effective area resulting in smaller double-layer capacitance. Using the parallel CV capability of the monolithic CMOS device, the double layer capacitance of all 1024 electrodes are simultaneously measured to examine the status of the electrodes’ surface in real time. The initial measurement of the electrode array showed a mean capacitance of 466 pF. After plasma treatment to remove contamination on the electrode’s surface, the increased capacitance was 1.36nF nearly tripling the effective surface area. We have successfully developed of 1024-ch electrochemical detector array using the monolithic CMOS sensor. The CV functionality was validated by measuring the double-layer capacitance of the on-chip electrode array. This method can accelerate the characterization of a massive electrode array before analytical experiments to provide well-controlled electrochemical electrodes, which is crucial in conducting reliable electrochemical measurements.
Citizen-Centered, Auditable, and Privacy-Preserving Population Genomics
Authors: Grishin Dennis , Raisaro Jean Louis , Troncoso-Pastoriza Juan Ramón , Obbad Kamal , Quinn Kevin , Misbach Mickaël , Gollhardt Jared , Sa Joao , Fellay Jacques , Church George M. , Hubaux Jean-Pierre 
Published: October 2019

AbstractThe growing number of health-data breaches, the use of genomic databases for law enforcement purposes and the lack of transparency of personal-genomics companies are raising unprecedented privacy concerns. To enable a secure exploration of genomic datasets with controlled and transparent data access, we propose a novel approach that combines cryptographic privacy-preserving technologies, such as homomorphic encryption and secure multi-party computation, with the auditability of blockchains. This approach provides strong security guarantees against realistic threat models by empowering individual citizens to decide who can query and access their genomic data and by ensuring end-to-end data confidentiality. Our open-source implementation supports queries on the encrypted genomic data of hundreds of thousands of individuals, with minimal overhead. Our work opens a path towards multi-functional, privacy-preserving genomic-data analysis.One Sentence SummaryA citizen-centered open-source response to the privacy concerns that hinder population genomics, based on modern cryptography.
TEsorter: lineage-level classification of transposable elements using conserved protein domains
Authors: Zhang Ren-Gang , Wang Zhao-Xuan , Ou Shujun , Li Guang-Yuan 
Published: October 2019

AbstractSummaryTransposable elements (TEs) constitute an import part in eukaryotic genomes, but their classification, especially in the lineage or clade level, is still challenging. For this purpose, we propose TEsorter, which is based on conserved protein domains of TEs. It is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs). Its results can also directly reflect phylogenetic relationships and diversities of the classified LTR-RTs.AvailabilityThe code in Python is freely available at https://github.com/zhangrengang/TEsorter.
Adaptive time scales in recurrent neural networks
Authors: Quax Silvan C. , D’Asaro Michele , van Gerven Marcel A. J. 
Published: October 2019

AbstractRecurrent neural network models have become widely used in computational neuroscience to model the dynamics of neural populations as well as in machine learning applications to model data with temporal dependencies. The different variants of RNNs commonly used in these scientific fields can be derived as discrete time approximations of the instantaneous firing rate of a population of neurons. The time constants of the neuronal process are generally ignored in these approximations, while learning these time constants could possibly inform us about the time scales underlying temporal processes and enhance the expressive capacity of the network. To investigate the potential of adaptive time constants, we compare the standard Elman approximation to a more lenient one that still accounts for the time scales at which processes unfold. We show that such a model with adaptive time scales performs better on predicting temporal data, increasing the memory capacity of recurrent neural networks, and allows recovery of the time scales at which the underlying processes unfold.
Association between breastfeeding and DNA methylation over the life course: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC)
Authors: Hartwig Fernando Pires , Smith George Davey , Simpkin Andrew J , Victora Cesar Gomes , Relton Caroline L. , Caramaschi Doretta 
Published: October 2019

AbstractBackgroundBreastfeeding is associated with short and long-term health benefits. Long-term effects might be mediated by epigenetic mechanisms, yet a recent systematic review indicated that the literature on this topic is scarce. We performed the first epigenome-wide association study of infant feeding, comparing breastfed vs non-breastfed children. We measured DNA methylation in children from peripheral blood collected in childhood (age 7, N=640) and adolescence (age 15-17, N=709) within the Accessible Resource for Integrated Epigenomic Studies (ARIES) project, part of the larger Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Cord blood methylation (N=702) was used as a negative control for potential pre-natal residual confounding.ResultsTwo differentially-methylated sites presented directionally-consistent associations with breastfeeding at ages 7 and 15-17, but not at birth. Twelve differentially-methylated regions in relation to breastfeeding were identified, and for three of them there was evidence of directional concordance between ages 7 and 15-17, but not between birth and age 7.ConclusionsOur findings indicate that DNA methylation in childhood and adolescence may be predicted by breastfeeding, but further studies with sufficiently large samples for replication are required to identify robust associations.
raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML
Authors: Edler Daniel , Klein Johannes , Antonelli Alexandre , Silvestro Daniele 
Published: October 2019

AbstractRaxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front-end to set up and run phylogenetic analyses. Our program offers automated pipelines for analyses that require multiple successive calls of RAxML and built-in functions to concatenate alignment files while automatically specifying the appropriate partition settings. In addition to RAxML 8.x, raxmlGUI 2.0 also supports the new RAxML Next Generation. RaxmlGUI facilitates phylogenetic analyses by coupling an intuitive interface with the unmatched performance of RAxML.