bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity
Authors: Chiner-Oms Álvaro , González-Candelas Fernando , Comas Iñaki 
Published: February 2018

AbstractEvery year, species of theMycobacterium tuberculosiscomplex (MTBC) kill more people than any other infectious disease caused by a single agent. As a consequence of its global distribution and parallel evolution with the human host the bacteria is not genetically homogeneous. The observed genetic heterogeneity has relevance at different phenotypic levels, from gene expression to epidemiological dynamics. However, current systems biology datasets have focused on the laboratory reference strain H37Rv. By using large expression datasets testing the role of almost two hundred transcription factors, we have constructed computational models to grab the expression dynamics ofMycobacterium tuberculosisH37Rv genes. However, we have found that many of those transcription factors are deleted or likely dysfunctional across strains of the MTBC. As a result, we failed to predict expression changes in strains with a different genetic background when compared with experimental data. These results highlight the importance of designing systems biology approaches that take into account the genetic diversity of tubercle bacilli, or any other pathogen, if we want to identify universal targets for vaccines, diagnostics and treatments.
Electrical devices from top-down structured platinum diselenide films
Authors: Yim Chanyoung , Passi Vikram , Lemme Max C. , Duesberg Georg S. , Ó Coileáin Cormac , Pallecchi Emiliano , Fadil Dalal , McEvoy Niall 
Published: February 2018

AbstractPlatinum diselenide (PtSe2) is an exciting new member of the two-dimensional (2D) transition metal dichalcogenide (TMD) family. It has a semimetal to semiconductor transition when approaching monolayer thickness and has already shown significant potential for use in device applications. Notably, PtSe2 can be grown at low temperature making it potentially suitable for industrial usage. Here, we address thickness-dependent transport properties and investigate electrical contacts to PtSe2, a crucial and universal element of TMD-based electronic devices. PtSe2 films have been synthesized at various thicknesses and structured to allow contact engineering and the accurate extraction of electrical properties. Contact resistivity and sheet resistance extracted from transmission line method (TLM) measurements are compared for different contact metals and different PtSe2 film thicknesses. Furthermore, the transition from semimetal to semiconductor in PtSe2 has been indirectly verified by electrical characterization in field-effect devices. Finally, the influence of edge contacts at the metal–PtSe2 interface has been studied by nanostructuring the contact area using electron beam lithography. By increasing the edge contact length, the contact resistivity was improved by up to 70% compared to devices with conventional top contacts. The results presented here represent crucial steps toward realizing high-performance nanoelectronic devices based on group-10 TMDs.
Accumulation of persistent tungsten in bone as in situ generated polytungstate
Authors: VanderSchee Cassidy R. , Kuter David , Bolt Alicia M. , Lo Feng-Chun , Feng Renfei , Thieme Juergen , Chen-Wiegart Yu-chen Karen , Williams Garth , Mann Koren K. , Bohle D. Scott 
Published: February 2018

AbstractTungsten accumulates in bone but is neither labile nor inert once absorbed. Tungsten’s relatively high cytosolic solubility and availability are problematic given its association with childhood lymphocytic leukemia. In light of tungsten’s technological prevalence, and the increased concern of regulatory agencies, here we characterize the chemical form and localization in mice exposed to tungsten through drinking water. Using X-ray fluorescence spectroscopy, we report accumulation of tungsten in bone tissue with some sites having ~10-fold greater intensities than background levels. The long bone tissue studied includes cortical, cancellous and bone marrow. Persistence of tungsten in cortical bone tissue following removal of the source indicates that it is retained in an insoluble form. The X-ray absorption near-edge structure spectra for tungsten in these tissues indicate that it is no longer in the originally administered form, orthotungstate, but rather resembles the heteropolytungsate species, phosphotungstate.
Deep Brain Stimulation of the Subthalamic Nucleus Parameter Optimization for Vowel Acoustics and Speech Intelligibility in Parkinson's Disease
Authors: Knowles Thea , Adams Scott , Abeyesekera Anita , Mancinelli Cynthia , Gilmore Greydon , Jog Mandar 
Published: February 2018

Purpose
The settings of 3 electrical stimulation parameters were adjusted in 12 speakers with Parkinson's disease (PD) with deep brain stimulation of the subthalamic nucleus (STN-DBS) to examine their effects on vowel acoustics and speech intelligibility.

Method
Participants were tested under permutations of low, mid, and high STN-DBS frequency, voltage, and pulse width settings. At each session, participants recited a sentence. Acoustic characteristics of vowel production were extracted, and naive listeners provided estimates of speech intelligibility.

Results
Overall, lower-frequency STN-DBS stimulation (60 Hz) was found to lead to improvements in intelligibility and acoustic vowel expansion. An interaction between speaker sex and STN-DBS stimulation was found for vowel measures. The combination of low frequency, mid to high voltage, and low to mid pulse width led to optimal speech outcomes; however, these settings did not demonstrate significant speech outcome differences compared with the standard clinical STN-DBS settings, likely due to substantial individual variability.

Conclusions
Although lower-frequency STN-DBS stimulation was found to yield consistent improvements in speech outcomes, it was not found to necessarily lead to the best speech outcomes for all participants. Nevertheless, frequency may serve as a starting point to explore settings that will optimize an individual's speech outcomes following STN-DBS surgery.

Supplemental Material

https://doi.org/10.23641/asha.5899228
Communicative Function Use of Preschoolers and Mothers From Differing Racial and Socioeconomic Groups
Authors: Fannin Danai Kasambira , Barbarin Oscar A. , Crais Elizabeth R. 
Published: February 2018

Purpose
This study explores whether communicative function (CF: reasons for communicating) use differs by socioeconomic status (SES), race/ethnicity, or gender among preschoolers and their mothers.

Method

Mother–preschooler dyads (
N
= 95) from the National Center for Early Development and Learning's (2005) study of family and social environments were observed during 1 structured learning and free-play interaction. CFs were coded by trained independent raters.

Results
Children used all CFs at similar rates, but those from low SES homes produced fewer utterances and less reasoning, whereas boys used less self-maintaining and more predicting. African American mothers produced more directing and less responding than European American and Latino American mothers, and Latino American mothers produced more utterances than European American mothers. Mothers from low SES homes did more directing and less responding.

Conclusions
Mothers exhibited more sociocultural differences in CFs than children; this suggests that maternal demographic characteristics may influence CF production more than child demographics at school entry. Children from low SES homes talking less and boys producing less self-maintaining coincided with patterns previously detected in pragmatic literature. Overall, preschoolers from racial/ethnic minority and low SES homes were not less deft with CF usage, which may inform how their pragmatic skills are described.

Supplemental Material

https://doi.org/10.23641/asha.5890255
Switched‐bandwidth SAW‐based bandpass filters with flat group delay
Authors: Psychogiou D. , Gómez‐García R. 
Published: February 2018

Tunable surface‐acoustic‐wave‐(SAW)‐based bandpass filters (BPFs) with flat in‐band group delay (τg) and variable passband bandwidth (BW) are reported. They are based on N hybrid acoustic‐wave‐lumped‐element‐resonator (AWLR) modules shaped by one lumped‐element resonator and K RF‐switched SAW resonators that are arranged in a Gaussian‐type source‐to‐load impedance‐inverter network. Fractional bandwidth (FBW) tuning is achieved by reconfiguring the number of SAW resonators within the AWLR modules. Major advantages of the proposed filter concept when compared to conventional SAW BPFs are as follows: (i) they do not depend on the electromechanical coupling coefficient (kt2) of the SAW resonators – FBW>kt2 can be realised –, (ii) they do not require lossy elements or SAW resonators with different frequencies, and (iii) they can be tuned. For experimental‐validation purposes, a 433.9 MHz two‐pole/four‐transmission‐zero prototype was built and measured. It exhibited flat‐in‐band‐τg passbands with discretely‐tunable BW between 0.18 and 0.45 MHz (i.e. 2.5:1 tuning ratio).
AC‐electric‐field‐induced parthenogenesis of mouse oocyte
Authors: Huang Hong‐Yuan , Kao Wei‐Lun , Wang Yi‐Wen , Yao Da‐Jeng 
Published: February 2018

To prevent parthenogenesis effect under embryo formation from sperms and oocyte, this study demonstrates that parthenogenesis of the oocyte of an ICR mouse can be induced with an AC electric field and without sperm insemination. The mouse oocytes were trapped with a positive dielectrophoretic force at the electrodes on an ITO‐glass chip. The rates of parthenogenesis were tested under conditions of varied intensity of electric field from 33.35 kV/m to 266.8 kV/m and trapping durations 1, 3, 5 and 10 min. The results indicated that there is no significant statistical difference with varied trapping time (p > 0.1); with AC p‐DEP electric activation, there is a significant statistical difference for 133.6 kV/m and 266.8 kV/m of electric field (p = 0.0013 and 0.0001 vs. control group respectively). The rate of parthenogenesis of the control group, oocytes with no electric activation, was 10.17±0.17% (n = 205). The rates of parthenogenesis were 51.65±7.8% (n = 27) at electric field 133.6 kV/m and 79.9±4.85% (n = 35) at 266.8 kV/m. The viability of these oocytes treated with an electric field exceeded 80%; this method of electric activation is hence safe for a mouse oocyte.
ALS Mimics
Authors: Hansel Anna , Dorst Johannes , Rosenbohm Angela , Hübers Annemarie , Ludolph Albert 
Published: February 2018

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Most patients die within 2–5 years of symptom onset due to the lack of effective therapy options. A diagnostic delay is encountered quite often, since disease progression as well as site and speed of onset may vary significantly. Some diseases can mimic features of ALS, especially in early stages. It is very important to differentiate those mimics from ALS as potentially treatable conditions might be missed otherwise. ALS typically affects the upper as well as the lower motor neuron, which implies that diseases sharing at least one of these clinical features have to be considered in the differential diagnosis. The following conditions should be taken into account as a differential diagnosis for ALS with predominant affection of the lower motor neuron: Immune mediated neuropathies such as multifocal motor neuropathy (MMN) with pronounced distal paresis without striking atrophy signs and conduction blocks in electroneurography, and chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) with common signs of sensibility disturbances, areflexia and cytoalbuminologic dissociation in the cerebrospinal fluid (CSF). Sporadic inclusion body myositis (sIBM) with typical biopsy findings and clinically predominant affection of the finger flexors. Spinal and bulbar muscular atrophy (SBMA), in which androgen receptor (AR-)gene testing and clinical signs of androgen insensitivity will help to differentiate the disease from ALS. Hirayama disease shows cold paresis; a cervical MRI scan and a normal neurography will help to confirm the diagnosis. In benign fasciculation syndrome, there is no muscle paresis or atrophy, and acute denervation cannot be detected in the EMG. In spinal muscular atrophy (SMA), testing for the SMN gene will help to differentiate the condition from ALS; furthermore, SMA is a very rare disease in adults. As a differential diagnosis for ALS with both clinical affection of the upper and lower motor neuron e. g. metabolic diseases such as adrenoleukodystrophy, metachromatic leukodystrophy and Tay-Sachs disease should be taken into account. Here, laboratory tests are the most important steps for a correct diagnosis. Cervical myelopathy is also capable of affecting the upper and lower motor neuron, but can easily be differentiated by a cervical MRI scan. As a differential diagnosis of ALS with predominant affection of the upper motor neuron, we discuss hereditary spastic paraparesis (HSP) which presents with a symmetric spasticity of the legs. The MRI often shows atrophy of the spinal cord, and SPG gene testing is done to differentiate HSP from ALS.
QTc Time Correlates with Amitriptyline and Venlafaxine Serum Levels in Elderly Psychiatric Inpatients
Authors: Hefner Gudrun , Hahn Martina , Hohner Matthias , Roll Sybille , Klimke Ansgar , Hiemke Christoph 
Published: February 2018

Abstract
Introduction Many antidepressants cause QT prolongation but the classification of cardiac risk of these drugs varies markedly in different published lists. This retrospective study analyzed the correlation of QTc time with amitriptyline and venlafaxine serum level in elderly psychiatric inpatients.
Methods Elderly inpatients aged≥65 years for whom venlafaxine or amitriptyline serum level had been measured were selected retrospectively from a therapeutic drug monitoring database and screened for an electrocardiogram measurement at the time of blood withdrawal. The correlation of amitriptyline or venlafaxine serum levels with QTc time was examined by using Pearson’s correlation analysis.
Results Amitriptyline serum levels (n=11) correlated significantly with QTc time (r=0.918, p<0.001, CI 95%). Venlafaxine serum levels (n=27) also correlated significantly with QTc time (r=0.382, p<0.05, CI 95%).
Discussion Amitriptyline and venlafaxine induce QT prolongation depending on drug concentrations in blood. Its extent, however, is very low when drug serum levels are within the therapeutic range. Future pharmacokinetic studies that correlate drug serum level and QT time should classify the cardiac risk of drugs based on the grade of the regression line in relation to the therapeutic range.
Genetic manipulation of structural color in bacterial colonies
Authors: Johansen Villads Egede , Catón Laura , Hamidjaja Raditijo , Oosterink Els , Wilts Bodo D. , Rasmussen Torben Sølbeck , Sherlock Michael Mario , Ingham Colin J. , Vignolini Silvia 
Published: February 2018

Significance
We demonstrate the genetic modification of structural color in a living system by using bacteria Iridescent 1 (IR1) as a model system. IR1 colonies consist of rod-shaped bacteria that pack in a dense hexagonal arrangement through gliding and growth, thus interfering with light to give a bright, green, and glittering appearance. By generating IR1 mutants and mapping their optical properties, we show that genetic alterations can change colony organization and thus their visual appearance. The findings provide insight into the genes controlling structural color, which is important for evolutionary studies and for understanding biological formation at the nanoscale. At the same time, it is an important step toward directed engineering of photonic systems from living organisms.
Processing backward translation at intermediate L2 proficiency
Authors: Rafi Reza 
Published: February 2018

Abstract
This study opens a window into the mapping of the lexical structure of bilinguals as they reach intermediate-level L2 proficiency. A group of 32 Persian-speaking English learners participated in a translation recognition task, where they had to decide whether the sequentially presented English-Persian word pairs were translation equivalents. The Persian words in the experimental trials were not translation equivalents, but they either shared lexical or semantic features with the correct translations or shared phonological features with the preceding English words. For example, the Persian word /bɒːzuː/ in the word pair arm – /bɒːzuː/ was manipulated to create three categories of ‘no’ trials: (a) orthographically related to the translation equivalent (arm – /bɒːziː/ ‘game’), (b) semantically related to the translation equivalent (arm – /ʃɒːne/ ‘shoulder’), (c) phonologically related to the English word (arm – /ɒːrmɒːn/ ‘goal’). A significant interference effect was observed in response to the items in the first two categories, which indicates extensive utilization of both lexical and conceptual links in backward translation. However, the observed interference effect in the third category did not reach statistical significance, which calls into question the integrated activation of L1 and L2 prior to high level L2 proficiency. These results are discussed within the context of the Revised Hierarchical Model (Kroll & Stewart, 1994) and the Bilingual Interactive Activation Plus model (Dijkstra & Van Heuven, 2002).
Near-synonymy in morphological structures
Authors: O’Neill Paul 
Published: February 2018

AbstractThis article examines the concept of defectivity in the verbal system of Spanish, Portuguese and Catalan. Building on previous studies on defective verbs in Spanish and Portuguese I investigate why there are no such defective verbs in Catalan. I conclude that the structure of the verbal paradigm in Catalan non-first conjugation verbs is radically different from that of the other languages; Catalan verbs constitute paradigms which correspond to regular patterns of inflection whereas Spanish and Portuguese display non-predictable types of root allomorphy which require all non-first conjugation verbs to have a memorised form for the rhizotonic forms of the verb. Theoretically, this type of defectivity poses problems for models of inflectional morphology and suggests that the patterns of frequent verbs can become general rules for all verbs of a particular conjugation.
Are there dead persons?
Authors: Stokes Patrick 
Published: February 2018

AbstractSchechtman’s ‘Person Life View’ (PLV) offers an account of personal identity whereby persons are the unified loci of our practical and ethical judgment. PLV also recognises infants and permanent vegetative state patients as being persons. I argue that the way PLV handles these cases yields an unexpected result: the dead also remain persons, contrary to the widely-accepted ‘Termination Thesis.’ Even more surprisingly, this actually counts in PLV’s favor: in light of our social and ethical practices which treat the dead as moral patients, PLV gives a more plausible account of the status of the dead than its rival theories.
A review of biostratigraphic studies in the olistostrome deposits of Karangsambung Formation
Authors: Hendrizan Marfasran 
Published: February 2018

Abstract
Planktonic foraminifera is widely used for marine sediment biostratigraphy. Foraminiferal biostratigraphy of Karangsambung Formation is relatively rare to be investigated by previous researchers. A review of foraminiferal biostratigraphy is expected to be early work to perform a research about the ages of Tertiary rock formations in Karangsambung. The research area is formed by olistostrome process; a sedimentary slide deposit characterized by bodies of harder rock mixed and dispersed in a matrix. Biostratigraphic studies based on foraminifera and nannoplankton in Karangsambung Formation are still qualitative analysis using fossils biomarker. However, the age of this formation is still debatable based on foraminifera and nannofossil analysis. Two explanations of debatable ages in Karangsambung Formation that is possibly developed in Karangsambung area: firstly, Karangsambung Formation is characterized by normal sedimentation in some places and other regions such Kali Welaran and Clebok, Village as a product of olistostrome, and secondly, Karangsambung Formation is olistostrome deposit. However, micropaleontology sampling and analysis in matrix clays from olistostrome were ignored causing biostratigraphical results in those matrix clays occurred in normal sedimentation process and achieving the age of middle Eocene to Oligocene. We suppose previous authors picked samples in matrix of Karangsambung Formation from several river sections, which will make misinterpretation of the age of Karangsambung Formation. The age of middle to late Eocene probably is the dates of the older sediment that was reworked by sliding and sampling process and accumulated in Karangsambung Formation. The date of Karangsambung Fm is in Oligocene period based on a finding of several calcareous nannofossils. Detailed micropaleontological analysis of olistostrome deposits in Karangsambung Formation should be reevaluated for new finding of the accurate dating. Re-evaluation should start from detailed sedimentological mapping of Karangsambung Fm transects based on previous authors especially Kali Welaran, Jatibungkus transect and Clebok section followed by systematic sampling of normal sedimentation process from olistostrome products and matrix clays of olistostrome Karangsambung Formation. Finally, quantitative method of micropaleontological analysis can be applied to identify the age of Karangsambung Formation.
Interactive and coordinated visualization approaches for biological data analysis
Authors: Cruz António , Arrais Joel P , Machado Penousal 
Published: February 2018

AbstractThe field of computational biology has become largely dependent on data visualization tools to analyze the increasing quantities of data gathered through the use of new and growing technologies. Aside from the volume, which often results in large amounts of noise and complex relationships with no clear structure, the visualization of biological data sets is hindered by their heterogeneity, as data are obtained from different sources and contain a wide variety of attributes, including spatial and temporal information. This requires visualization approaches that are able to not only represent various data structures simultaneously but also provide exploratory methods that allow the identification of meaningful relationships that would not be perceptible through data analysis algorithms alone. In this article, we present a survey of visualization approaches applied to the analysis of biological data. We focus on graph-based visualizations and tools that use coordinated multiple views to represent high-dimensional multivariate data, in particular time series gene expression, protein–protein interaction networks and biological pathways. We then discuss how these methods can be used to help solve the current challenges surrounding the visualization of complex biological data sets.