bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of ligand-gated conformational changes in enzyme catalysis
Authors: Moreira Cátia , Calixto Ana Rita , Richard John P. , Kamerlin Shina Caroline Lynn 
Published: October 2019

Abstract
Structural and biochemical studies on diverse enzymes have highlighted the importance of ligand-gated conformational changes in enzyme catalysis, where the intrinsic binding energy of the common phosphoryl group of their substrates is used to drive energetically unfavorable conformational changes in catalytic loops, from inactive open to catalytically competent closed conformations. However, computational studies have historically been unable to capture the activating role of these conformational changes. Here, we discuss recent experimental and computational studies, which can remarkably pinpoint the role of ligand-gated conformational changes in enzyme catalysis, even when not modeling the loop dynamics explicitly. Finally, through our joint analyses of these data, we demonstrate how the synergy between theory and experiment is crucial for furthering our understanding of enzyme catalysis.
Adipocyte dedifferentiation in health and diseases
Authors: Song Tongxing , Kuang Shihuan 
Published: October 2019

Abstract
Adipose tissues collectively as an endocrine organ and energy storage are crucial for systemic metabolic homeostasis. The major cell type in the adipose tissue, the adipocytes or fat cells, are remarkably plastic and can increase or decrease their size and number to adapt to changes in systemic or local metabolism. Changes in adipocyte size occur through hypertrophy or atrophy, and changes in cell numbers mainly involve de novo generation of new cells or death of existing cells. Recently, dedifferentiation, whereby a mature adipocyte is reverted to an undifferentiated progenitor-like status, has been reported as a mechanism underlying adipocyte plasticity. Dedifferentiation of mature adipocytes has been observed under both physiological and pathological conditions. This review covers several aspects of adipocyte dedifferentiation, its relevance to adipose tissue function, molecular pathways that drive dedifferentiation, and the potential of therapeutic targeting adipocyte dedifferentiation in human health and metabolic diseases.
Update on Academic and Clinical Training in Cleft Palate/Craniofacial Anomalies for Speech-Language Pathology Students
Authors: Mills Brooke , Hardin-Jones Mary 
Published: October 2019

Purpose
The purpose of this study was to survey speech-language pathology master's programs regarding their academic and clinical coverage of cleft palate/craniofacial anomalies.

Method
A link to a 19-item survey was sent via e-mail to the program directors of 271 accredited graduate programs in speech-language pathology. Information was also obtained via university websites to verify survey responses.

Results
The response rate was 86% with 232 of 271 programs completing all or part of the survey. Twenty-four percent of respondents indicated their program offers a dedicated and required course in cleft palate/craniofacial anomalies, 22% offer an elective course, and 51% embed this content in other courses. Respondents reported that their students frequently (7%), sometimes (58%), or rarely (34%) receive clinical experience with this population.

Conclusion
Our findings suggest that an increasing number of academic programs are eliminating dedicated coursework in cleft palate/craniofacial anomalies and are embedding such content in other courses. A legitimate concern resulting from this consolidation of coursework is the degree to which feeding, articulation, and resonance difficulties associated with cleft palate/craniofacial anomalies are being addressed elsewhere in the curriculum.
The 3HSP catalogue of extreme and high-synchrotron peaked blazars
Authors: Chang Y.-L. , Arsioli B. , Giommi P. , Padovani P. , Brandt C. H. 
Published: October 2019

Aims. High-synchrotron peaked blazars (HSPs or HBLs) play a central role in very high-energy (VHE) γ-ray astronomy, and likely in neutrino astronomy. Currently, the largest compilation of HSP blazars, the 2WHSP sample, includes 1691 sources, but it is not complete in the radio or in the X-ray band. In order to provide a larger and more accurate set of HSP blazars that is useful for future statistical studies and to plan for VHE/TeV observations, we present the 3HSP catalogue, the largest sample of extreme and high-synchrotron peaked (EHSP; HSP) blazars and blazar candidates.
Methods. We implemented several ways to improve the size and the completeness of the 2WHSP catalogue and reduced the selection biases to be taken into consideration in population studies. By discarding the IR constraint and relaxing the radio–IR and IR–X-ray slope criteria, we were able to select more sources with νpeak close to the 1015 Hz threshold and objects where the host galaxy dominates the flux. The selection of extra sources now commences with a cross-matching between radio and X-ray surveys, applying a simple flux ratio cut. We also considered Fermi-LAT catalogues to find reasonable HSP-candidates that are detected in the γ-ray band but are not included in X-ray or radio source catalogues. The new method, and the use of newly available multi-frequency data, allowed us to add 395 sources to the sample, to remove 73 2WHSP sources that were previously flagged as uncertain and could not be confirmed as genuine HSP blazars, and to update parameters obtained by fitting the synchrotron component.
Results. The 3HSP catalogue includes 2013 sources, 88% of which with a redshift estimation, a much higher percentage than in any other list of HSP blazars. All new γ-ray detections are described in the First and Second Brazil ICRANet γ-ray blazar catalogues (1BIGB & 2BIGB) also taking into account the 4FGL list of γ-ray sources published by the Fermi Large Area Telescope (Fermi-LAT) team. Moreover, the cross-matching between the 2WHSP, 2FHL HSP, and IceCube neutrino positions suggests that HSPs are likely counterparts of neutrino events, which implies the 3HSP catalogue is also useful in that respect. The 3HSP catalogue shows improved completeness compared to its predecessors, the 1WHSP and 2WHSP catalogues, and follows the track of their increasing relevance for VHE astronomy.
Link between E–B polarization modes and gas column density from interstellar dust emission
Authors: Bracco Andrea , Ghosh Tuhin , Boulanger François , Aumont Jonathan 
Published: October 2019

Context. The analysis of the Planck polarization E and B mode power spectra of interstellar dust emission at 353 GHz recently raised new questions concerning the impact of Galactic foregrounds on the detection of the polarization of the cosmic microwave background (CMB) and on the physical properties of the interstellar medium (ISM). In the diffuse ISM at high latitude a clear E–B asymmetry is observed that has twice as much power in E modes as in B modes; there is also a positive correlation between the total power, T, and both E and B modes, which is currently interpreted in terms of the link between the structure of interstellar matter and that of the Galactic magnetic field.
Aims. In this paper we aim to extend the Planck analysis of the high latitude sky to low Galactic latitudes, investigating the correlation between the T–E–B auto- and cross-correlation power spectra with the gas column density from the diffuse ISM to molecular clouds.
Methods. We divided the sky between Galactic latitudes |b| > 5° and |b| < 60° in 552 circular patches, with an area of ~400°2, and we studied the cross-correlations between the T–E–B power spectra and the column density of each patch using the latest release of the Planck polarization data.
Results. We find that the B-to-E power ratio (DlBB/DlEE) and the TE correlation ratio (rTE) depend on column density. While the former increases going from the diffuse ISM to molecular clouds in the Gould Belt, the latter decreases. This systematic variation must be related to actual changes in ISM properties. The data show significant scatter about this mean trend. The variations of DlBB/DlEE and rTE are observed to be anticorrelated for all column densities. In the diffuse ISM, the variance of these two ratios is consistent with a stochastic non-Gaussian model in which the values of DlBB/DlEE and rTE are fixed. We finally discuss the dependences of TB and EB with column density, which are however hampered by instrumental noise.
Conclusions. For the first time, this work shows significant variations of the T–E–B power spectra of dust polarized emission across a large portion of the Galaxy. Their dependence on multipole and gas column density is key for accurate forecasts of next generation CMB experiments and for constraining present models of ISM physics (i.e., dust properties and interstellar turbulence), which are considered responsible for the observed T–E–B signals.
Lithium in red giant stars: Constraining non-standard mixing with large surveys in the Gaia era
Authors: Charbonnel C. , Lagarde N. , Jasniewicz G. , North P. L. , Shetrone M. , Krugler Hollek J. , Smith V. V. , Smiljanic R. , Palacios A. , Ottoni G. 
Published: October 2019

Context. Li is extensively known to be a good tracer of non-standard mixing processes occurring in stellar interiors.
Aims. We present the results of a new large Li survey in red giant stars and combine it with surveys from the literature to probe the impact of rotation-induced mixing and thermohaline double-diffusive instability along stellar evolution.
Methods. We determined the surface Li abundance for a sample of 829 giant stars with accurate Gaia parallaxes for a large sub-sample (810 stars) complemented with accurate HIPPARCOS parallaxes (19 stars). The spectra of our sample of northern and southern giant stars were obtained in three ground-based observatories (Observatoire de Haute-Provence, ESO-La Silla, and the Mc Donald Observatory). We determined the atmospheric parameters (Teff, log(g) and [Fe/H]), and the Li abundance. We used Gaia parallaxes and photometry to determine the luminosity of our objects and we estimated the mass and evolution status of each sample star with a maximum-likelihood technique using stellar evolution models computed with the STAREVOL code. We compared the observed Li behaviour with predictions from stellar models, including rotation and thermohaline mixing. The same approach was used for stars from selected Li surveys from the literature.
Results. Rotation-induced mixing accounts nicely for the Li behaviour in stars warmer than about 4200 K, independently of the mass domain. For stars with masses lower than 2 M⊙ thermohaline mixing leads to further Li depletion below the Teff of the RGB bump (about 4000 K), and on the early asymptotic giant branch, as observed. Depending on the definition we adopt, we find between 0.8 and 2.2% of Li-rich giants in our new sample.
Conclusions.Gaia puts a new spin on the understanding of mixing processes in stars, and our study confirms the importance of rotation-induced processes and of thermohaline mixing. However asteroseismology is required to definitively pinpoint the actual evolution status of Li-rich giants.
Using neural networks to predict the outcome of refractive surgery for myopia
Authors: Balidis Miltos , Papadopoulou Ioanna , Malandris Dimitris , Zachariadis Zachos , Sakellaris Dimitrios , Vakalis Thanos , Asteriadis Solon , Tranos Paris , Loukovitis Eleftherios , Poulos Marios , Gatzioufas Zisis , Anogeianakis George 
Published: October 2019

Introduction: Refractive Surgery (RS), has advanced immensely in the last decades, utilizing methods and techniques that fulfill stringent criteria for safety, efficacy, cost-effectiveness, and predictability of the refractive outcome. Still, a non-negligible percentage of RS require corrective retreatment. In addition, surgeons should be able to advise their patients, beforehand, as to the probability that corrective RS will be necessary. The present article addresses these issues with regard to myopia and explores the use of Neural Networks as a solution to the problem of the prediction of the RS outcome.

Methods: We used a computerized query to select patients who underwent RS with any of the available surgical techniques (PRK, LASEK, Epi-LASIK, LASIK) between January 2010 and July 2017 and we investigated 13 factors which are related to RS. The data were normalized by forcing the weights used in the forward and backward propagations to be binary; each integer was represented by a 12-bit serial code, so that following this preprocessing stage, the vector of the data values of all 13 parameters was encoded in a binary vector of 1 × (13 × 12) = 1 × 156 size. Following the preprocessing stage, eight independent Learning Vector Quantization (LVQ) networks were created in random way using the function Ivqnet of Matlab, each one of them responding to one query with (0 retreat class) or (1 correct class). The results of the eight LVQs were then averaged to permit a best estimate of the network’s performance while a voting procedure by the neural nets was used to arrive at the outcome

Results: Our algorithm was able to predict in a statistically significant way (as evidenced by Cohen’s Kappa test result of 0.7595) the need for retreatment after initial RS with good sensitivity (0.8756) and specificity (0.9286).

Conclusion: The results permit us to be optimistic about the future of using neural networks for the prediction of the outcome and, eventually, the planning of RS.
Prevalence of ‘one and done’ in adenoma detection rates: results from the New Hampshire Colonoscopy Registry
Authors: Fedewa Stacey A. , Anderson Joseph C. , Robinson Christina M. , Weiss Julie E. , Smith Robert A. , Siegel Rebecca L. , Jemal Ahmedin , Butterly Lynn F. 
Published: October 2019

Abstract
Background and study aims Adenoma detection rate (ADR), the proportion of an endoscopist’s screening colonoscopies in which at least one adenoma is found, is an established quality metric. Several publications have suggested that a technique referred to as “one and done,” where less attention is paid to additional polyp detection following discovery of one likely adenoma, may be occurring 1
2
3. To investigate whether this practice occurs and provide additional context to the significance of ADR, we examined ADR by single and multiple adenomas in the statewide New Hampshire Colonoscopy Registry (NHCR).
Patients and methods A total of 25,324 NHCR patients receiving screening colonoscopies between 2009 and 2014 by 69 endoscopists were analyzed. ADR was dichotomized into high (≥ 20 %) and low (< 20 %) based on 2006 recommended targets in place during the time of the study. ADR-plus (the average number of adenomas in colonoscopies with > 1 adenoma) was dichotomized at mean values into high (≥ 1.5) and low (< 1.5). As suggested by others, a high ADR but low ADR-plus was used to indicate the “one and done” approach.
Results Among endoscopists with an ADR ≥ 20 %, only 5 (7.2 %) had low ADR-plus values and were classified as “one and done.” Results for serrated polyp detection were similar. ADR and ADR-plus decreased monotonically with increasing years since residency (P values for trend ADR = 0.02; ADR-plus = 0.003) after adjusting for patient risk factors.
Conclusion “One and done” infrequently occurred among endoscopists with high ADR in a large statewide registry. The need to replace ADR with other polyp detection metrics (such as ADR-plus) to accurately ascertain performance quality is not supported by these findings.
Reprogramming Nonribosomal Peptide Synthesis by Surgical Mutation
Authors: Niquille David L. , Hansen Douglas A. , Hilvert Donald 
Published: October 2019

Nonribosomal peptide synthetases produce highly modified bioactive peptides, many of which are used therapeutically. As such, they have been the target of intense protein engineering to enable biosynthetic access to peptide variants with improved drug properties or altered bioactivities. In this account, we describe our ongoing efforts to reprogram nonribosomal peptide synthesis by surgical mutation. In contrast to ribosomal biosynthesis, nonribosomal peptide synthesis has proven difficult to engineer, arguably due to a lack of suitable tools. To address this limitation, we have established a high-throughput assay that provides unprecedented control over the gatekeeper adenylation domains responsible for building block selection and incorporation. Expansion of this strategy to other building blocks and domains promises to make it a powerful evolutionary platform for tailoring assembly lines for custom synthesis of peptide therapeutics.1.	Nonribosomal Peptides2.	Reprogramming A Domains for Clickable Amino Acids3	A High-Throughput A Domain Assay4	Reprogramming A Domains for β-Amino Acids5	Downstream Processing6	Conclusions and Outlook
Frequency-Following Response with Speech Stimulus: Comparison between Two Methods of Stimulation
Authors: Sanguebuche Taissane Rodrigues , Silva Luize Caroline Lima da , Peixe Bruna Pias , Silva Débora Durigon da , Garcia Michele Vargas 
Published: October 2019

Introduction Frequency-following response with speech stimulus (FFR-speech) is a subcortical potential that satisfactorily evaluates the processing of verbal information. However, there still are differences in the literature regarding its analysis and stimulation protocol.
Objective To compare two stimulation protocols for the capture of FFR-speech, to identify the percentage of occurrence of the waves among them and to compare it with the specialized literature, as well as to describe the interpeaks of its waves.
Method Considering the eligibility criteria, the sample consisted of 30 normal-hearing adults, with no complaints of speech comprehension. All of them were submitted to a basic audiological evaluation, to brainstem auditory evoked potential with click stimulus, and to FFR-speech. In the latter, 2 types of stimulation were performed, 3 series of 1,000 sweeps, and 2 series of 3,000 sweeps, for subsequent analysis of the resulting wave, in which we tried to mark the peak V followed by valleys A, C, D, E, F, and O.
Results Differences in latency and interpeaks were not found between the protocols. In general, a higher occurrence of waves in the stimulation of 2 series of 3,000 sweeps was observed, but only the A valley presented a significant difference. When the values of the waves were compared with the literature, the V and A waves showed fewer occurrences in the present study.
Conclusion The protocol of 2 series of 3,000 sweeps was better for FFR-speech in the studied equipment, considering the higher occurrence of waves, even though it is inferior to the specialized literature. Furthermore, it was possible to describe interpeak values and to observe no difference between the studied protocols
Incidence of Stent Thrombosis after Endovascular Treatment of Iliofemoral or Caval Veins in Patients with the Postthrombotic Syndrome
Authors: Sebastian Tim , Spirk David , Engelberger Rolf P. , Dopheide Jörn F. , Baumann Frederic A. , Barco Stefano , Spescha Rebecca , Leeger Claudia , Kucher Nils 
Published: October 2019

Abstract
Background Patients with postthrombotic syndrome (PTS) treated with stents are at risk of stent thrombosis (ST). The incidence of ST in the presence and absence of anticoagulation therapy (AT) is unknown. Risk factors are not well understood.
Patients and Methods From the prospective Swiss Venous Stent registry, we conducted a subgroup analysis of 136 consecutive patients with PTS. Incidence of ST was estimated from duplex ultrasound or venography, and reported for the time on and off AT. Baseline, procedural, and follow-up data were evaluated to identify factors associated with ST.
Results Median follow-up was 20 (interquartile range [IQR] 9–40) months. AT was stopped in 43 (32%) patients after 12 (IQR 6–14) months. Cumulative incidence of ST was 13.7% (95% confidence interval [CI] 7.8–19.6%) and 21.2% (95% CI 13.2–29.2%) during the first 6 and 36 months, respectively. The time-adjusted incidence rate was 11.2 (95% CI 7.7–16.2) events per 100 patient-years, 11.3 (95% CI 7.3–17.3) for the period on, and 11.2 (95% CI 5.3–23.6) for the period off AT. May–Thurner syndrome (MTS) was associated with decreased incidence of ST (hazard ratio [HR] 0.37, 95% CI 0.15–0.91), whereas age < 40 years (HR 2.26, 95% CI 1.03–4.94), stents below the common femoral vein (HR 3.03, 95% CI 1.28–7.19), and postthrombotic inflow veins (HR 2.92, 95% CI 1.36–6.25) were associated with increased incidence.
Conclusion The 6-month incidence of ST was considerably high. Beyond 6 months, consecutive annual incidence rates persisted at 4.1 and 3.4% per year thereafter. Patients with higher incidence of ST were younger, had stents below the common femoral vein, postthrombotic leg inflow veins, and less often MTS. Incidence rates for the period on and off AT must be interpreted with caution.
Clinical Trial Registration The study is registered on the National Institutes of Health Web site (ClinicalTrials.gov; identifier NCT02433054).
Acute Pulmonary Exacerbations in Cystic Fibrosis
Authors: Goss Christopher H. 
Published: October 2019

AbstractWith the improving survival of cystic fibrosis (CF) patients and the advent of highly effective cystic fibrosis transmembrane conductance regulator therapy, the clinical spectrum of this complex multisystem disease continues to evolve. One of the most important clinical events for patients with CF in the course of this disease is an acute pulmonary exacerbation. Clinical and microbial epidemiology studies of CF pulmonary exacerbations continue to provide important insight into the disease course, prognosis, and complications. This work has now led to a number of large scale clinical trials with the goal of improving the treatment paradigm for CF pulmonary exacerbation. The primary goal of this review is to provide a summary of the pathophysiology, the clinical epidemiology, microbial epidemiology, outcome and the treatment of CF pulmonary exacerbation.
On locative alternation verbs in Mandarin Chinese
Authors: Kuo Pei-Jung 
Published: October 2019

AbstractThis paper focuses on both single and compound locative alternation verbs in Mandarin Chinese. First, three particular properties of locative alternation verbs are introduced and compared cross-linguistically with examples from Japanese and English. Next, three properties are explored further and possible explanations are provided for the observed similarities and differences between the languages. Finally, the syntactic patterns of locative alternation verbs in Mandarin Chinese are investigated in the Sinica Corpus. The results show that the “oblique argument-verb-accusative argument” sentence pattern has the highest percentage of appearance. This finding echoesLin’s (2008)claim that Chinese is not only a “topic prominent” language, but also a “locative prominent” language.
Time passing is relative motion
Authors: Hsiung Hui-Ju , Chen Chao-Jan 
Published: October 2019

AbstractThis paper reexamines the conceptual metaphortime passing is motionand deals with the problem of mapping inconsistency between the “moving ego” and “moving time” models in this conceptual metaphor. We argue that time is conceptualized as a system consisting of a dynamic component and a static component, which we call time-flow and time-landscape respectively. Adopting the notion of relative motion, we propose that the “moving ego” and “moving time” viewpoints are actually due to a shift in perspective within the same frame of relative motion. We then propose a unified metaphor about time passing, namelytime passing is relative motion. In this metaphor, the ego is carried by the time-flow to move past time-landmarks over the time-landscape. We also propose that time is specifically conceptualized as a river in Chinese under this conceptual metaphor.