bluuebunny/crossref_metadata_2025_split huggingface dataset:
A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy
Authors: Bauer Daniela , Meinhold Sarah , Jakob Roman P. , Stigler Johannes , Merkel Ulrich , Maier Timm , Rief Matthias , Žoldák Gabriel 
Published: April 2018

Significance
Proteins with a similar structure can have largely different folding properties. Although some fold readily, others can only assume their native structure through the help of chaperone proteins. Partially folded intermediates play a key role in defining those folding differences. However, owing to their transient nature, they are not amenable to the structural investigation. Using a combination of single-molecule mechanics, protein engineering, and crystallography, we identified a stable native-like functional nucleus, which is a critical intermediate for spontaneous folding of the Hsp70 nucleotide-binding domain. Based on our findings, we engineered a chimera turning a homologous but folding-incompetent protein into a spontaneously folding protein that is enzymatically active. Our results have implications for the folding of actin from the same superfamily.
A selective class of inhibitors for the CLC-Ka chloride ion channel
Authors: Koster Anna K. , Wood Chase A. P. , Thomas-Tran Rhiannon , Chavan Tanmay S. , Almqvist Jonas , Choi Kee-Hyun , Du Bois J. , Maduke Merritt 
Published: April 2018

SignificanceChloride ion channels and transporters (CLCs) are critical to cardiovascular, neurological, and musculoskeletal function. Small molecules capable of selectively inhibiting CLCs would serve as valuable tools for investigating CLC function and would have potential applications for treating CLC-related disorders. The lack of such agents has impeded efforts to study this family of proteins. This work introduces a class of inhibitors with unprecedented selectivity for a single CLC homolog, CLC-Ka. Insights gained through experiments to validate a predicted ligand binding site and to evaluate structure–activity relationships rationalize inhibitor potency and CLC-Ka selectivity. Our findings provide tools for studies of CLC-Ka function and will assist subsequent efforts to advance specific molecular probes for different CLC homologs.
Spelling-gate
Authors: Richardson Kay 
Published: April 2018

AbstractBack in 2009, the Labour British Prime Minister Gordon Brown was attacked for “bad spelling” in a condolence letter written personally by him to the mother of a soldier who died in combat, and publicised by The Sun newspaper. “Spelling” here acts as a leveller of hierarchical differences in the national political culture, with ruler and subject both publicly disciplined by the same standard language ideology. Previous research on orthography as social practice has tended to focus on deliberate manipulation of fixed spellings; this article extends the approach to unconventional spellings that have come about ‘by mistake’, and also widens it, to consider aspects of orthography other than spelling, focusing on the look of the Prime Minister’s handwriting. At issue, semiotically, are meanings such as ‘the personal touch’ and ‘respect’.
Parasympathetic activity delayed after self‐paced exercise
Authors: Trojbicz Lucas Rosiello , Damasceno Mayara Vieira , Pasqua Leonardo Alves , Gáspari Arthur Fernandes , Lima‐Silva Adriano Eduardo , Bertuzzi Rômulo 
Published: April 2018

AbstractThe main purpose of this study was to compare the effect of the constant load and self‐paced exercise with similar total work on autonomic control after endurance exercise. Ten physically active men were submitted to (i) a maximal incremental exercise test, (ii) a 4‐km cycling time trial (4‐km TT), and (iii) a constant workload test with identical total external work performed at 4‐km TT. Gas exchange was measured throughout the tests, while blood lactate, heart rate, and heart rate variability (HRV) were measured during the passive recovery. Power output measured at the last lap (i.e. 3600–4000 m) of 4‐km TT (316 ± 89 W) was statistically higher than power output measured at the end of the constant workload exercise (211 ± 42 W). The 4‐km TT produced higher values of blood lactate concentration (8.8 ± 2.1 mmol L−1) than the constant workload test (7.8 ± 2.1 mmol L−1). The heart rate recovery measured at 60 s (constant workload: 37 ± 7 bpm; 4‐km TT: 30 ± 6) and 120 s (constant workload: 57 ± 9 bpm; 4‐km TT: 51 ± 9 bpm) were higher in the constant workload than in the self‐paced exercise. The HRV (i.e. RMSSD30s) was statistically higher in the constant load exercise measured at 120, 420, 450, 480, 540, and 570 s than the self‐paced exercise. These findings suggest that the autonomic control responses were dependent of the endurance exercise modalities, with parasympathetic activity being delayed after self‐paced exercise, as evidenced by post‐exercise heart rate indices.
Calibration of mass and conventional mass of weights 2 kg, 1 kg, 200 g, 50 g, 1 g and 200 mg
Authors: Becerra Luis Omar , Peña Luis Manuel , Vargas Boris Escalante , Almonte Luz Cori , Martín Quiroga Rojas Aldo , Bermúdez Coronel lvaro , Soto Jhon J Escobar , Naula Wilson , Florencio Arnaldo , Valenzuela a Lourdes , Alfaro Olman Ramos , Peña Marcela Prenda 
Published: April 2018

This report describes the results of a supplementary comparison between SIM NMIs, which was carried out to evaluate the consistency of the measurements of calibration in high accuracy mass standards using the normalized error criteria (2 kg, 1 kg, 200 g, 50 g, 1 g and 200 mg). The supplementary comparison was carried out from April 2012 to July 2013.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Comparative analysis of tissue reconstruction algorithms for 3D histology
Authors: Kartasalo Kimmo , Latonen Leena , Vihinen Jorma , Visakorpi Tapio , Nykter Matti , Ruusuvuori Pekka 
Published: April 2018

Abstract

Motivation
Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking.

Results
We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.

Availability and implementation
Code: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702.

Supplementary information
Supplementary data are available at Bioinformatics online.
BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates
Authors: Goren Emily , Liu Peng , Wang Chao , Wang Chong 
Published: April 2018

AbstractMotivationChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level.ResultsWe propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually.Availability and implementationSource code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R.Supplementary informationSupplementary data are available at Bioinformatics online.
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC
Authors: Liu Bin , Weng Fan , Huang De-Shuang , Chou Kuo-Chen 
Published: April 2018

Abstract

Motivation
DNA replication is the key of the genetic information transmission, and it is initiated from the replication origins. Identifying the replication origins is crucial for understanding the mechanism of DNA replication. Although several discriminative computational predictors were proposed to identify DNA replication origins of yeast species, they could only be used to identify very tiny parts (250 or 300 bp) of the replication origins. Besides, none of the existing predictors could successfully capture the ‘GC asymmetry bias’ of yeast species reported by experimental observations. Hence it would not be surprising why their power is so limited. To grasp the CG asymmetry feature and make the prediction able to cover the entire replication regions of yeast species, we develop a new predictor called ‘iRO-3wPseKNC’.

Results
Rigorous cross validations on the benchmark datasets from four yeast species (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis and Pichia pastoris) have indicated that the proposed predictor is really very powerful for predicting the entire DNA duplication origins.

Availability and implementation
The web-server for the iRO-3wPseKNC predictor is available at http://bioinformatics.hitsz.edu.cn/iRO-3wPseKNC/, by which users can easily get their desired results without the need to go through the mathematical details.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Effect of Antibiotic Selection Pressure on the Nasopharyngeal Macrolide Resistome: A Cluster-randomized Trial
Authors: Keenan Jeremy D , Chin Stephanie A , Amza Abdou , Kadri Boubacar , Nassirou Baido , Cevallos Vicky , Cotter Sun Y , Zhou Zhaoxia , West Sheila K , Bailey Robin L , Porco Travis C , Lietman Thomas M ,   Rapid Elimination of Trachoma (PRET) Study Group
Published: April 2018

Abstract

Background
Frequent use of antibiotics is thought to create selection pressure by clearing susceptible bacteria and allowing resistant bacteria to spread in a community. A cluster-randomized trial comparing 2 different frequencies of mass azithromycin distributions for trachoma provided a convenient experiment for determining the causal relationship between antibiotic consumption and antibiotic resistance.

Methods
Twenty-four communities were randomized to either annual or biannual mass azithromycin distributions for trachoma. Randomization was stratified on health catchment area and trachoma prevalence. Swabs were processed for the genetic macrolide resistance determinants ermB and mefA/E in a masked fashion from a random sample of 120 preschool children before treatment and another 120 children after 2 years of mass antibiotics.

Results
Macrolide resistance determinants were similar in the 12 annually and 12 biannually treated communities before treatment, with a median prevalence among preschool children of 20% (interquartile range [IQR], 10%–40%) in each group. By 24 months, macrolide resistance determinants were found more commonly in the biannually treated communities (median, 60% [IQR, 50%–80%]) than the annually treated communities (median, 40% [IQR, 20%–40%]; P &lt; .001). Adjusting for baseline, the 24-month prevalence of macrolide resistance determinants in the biannual group was 29.4% higher than that of the annual group (95% confidence interval, 10.5%–56.7%).

Conclusions
This randomized trial used direct genetic methods to confirm the causal relationship of community antibiotic consumption and antibiotic resistance. Communities randomized to less frequent use of antibiotics had a significantly lower prevalence of genetic antibiotic resistance determinants.

Clinical Trials Registration
NCT00792922.
Multiple Class I and Class II Haemophilus ducreyi Strains Cause Cutaneous Ulcers in Children on an Endemic Island
Authors: Grant Jacob C , González-Beiras Camila , Amick Kristen M , Fortney Kate R , Gangaiah Dharanesh , Humphreys Tricia L , Mitjà Oriol , Abecasis Ana , Spinola Stanley M 
Published: April 2018

Abstract

Background
Together with Treponema pallidum subspecies pertenue, Haemophilus ducreyi is a major cause of exudative cutaneous ulcers (CUs) in children. For H. ducreyi, both class I and class II strains, asymptomatic colonization, and environmental reservoirs have been found in endemic regions, but the epidemiology of this infection is unknown.

Methods
Based on published whole-genome sequences of H. ducreyi CU strains, a single-locus typing system was developed and applied to H. ducreyi–positive CU samples obtained prior to, 1 year after, and 2 years after the initiation of a mass drug administration campaign to eradicate CU on Lihir Island in Papua New Guinea. DNA from the CU samples was amplified with class I and class II dsrA-specific primers and sequenced; the samples were classified into dsrA types, which were geospatially mapped. Selection pressure analysis was performed on the dsrA sequences.

Results
Thirty-seven samples contained class I sequences, 27 contained class II sequences, and 13 contained both. There were 5 class I and 4 class II types circulating on the island; 3 types accounted for approximately 87% of the strains. The composition and geospatial distribution of the types varied little over time and there was no evidence of selection pressure.

Conclusions
Multiple strains of H. ducreyi cause CU on an endemic island and coinfections are common. In contrast to recent findings with T. pallidum pertenue, strain composition is not affected by antibiotic pressure, consistent with environmental reservoirs of H. ducreyi. Such reservoirs must be addressed to achieve eradication of H. ducreyi.
Comparing plant and animal glutamate receptors: common traits but different fates?
Authors: Wudick Michael M , Michard Erwan , Oliveira Nunes Custódio , Feijó José A 
Published: April 2018

AbstractAnimal ionotropic glutamate receptors (iGluRs) are ligand-gated channels whose evolution is intimately linked to that of the nervous system, where the agonist glutamate and co-agonists glycine/d-serine act as neurotransmitters or neuromodulators. While iGluRs are specialized in neuronal communication, plant glutamate receptor-like (GLR) homologs have evolved many plant-specific physiological functions, such as sperm signaling in moss, pollen tube growth, root meristem proliferation, innate immune, and wound responses. GLRs have been associated with Ca2+ signaling by directly channeling its extracellular influx into the cytosol. Nevertheless, very limited information on functional properties of GLRs is available, and we mostly rely on structure/function data obtained for animal iGluRs to interpret experimental results obtained for plant GLRs. Yet, a deeper characterization and better understanding of plant GLRs is progressively unveiling original and different functions when compared with their mammalian counterparts. Here, we review the function of plant GLRs comparing their predicted structure and physiological roles with those of the well-documented roles of iGluRs. We conclude that interpreting GLR function based on comparison with their animal counterparts calls for caution, especially when presuming physiological roles and the mode of action for plant GLRs, and when comparing iGluRs in neuronal tissues with those in peripheral, non-neuronal tissues.
Very high-energy gamma-ray signature of ultrahigh-energy cosmic ray acceleration in Centaurus A
Authors: Joshi Jagdish C , Miranda Luis Salvador , Razzaque Soebur , Yang Lili 
Published: April 2018

Abstract
The association of at least a dozen ultrahigh-energy cosmic ray (UHECR) events with energy ≳ 55 EeV detected by the Pierre Auger Observatory from the direction of Centaurus-A, the nearest radio galaxy, supports the scenario of UHECR acceleration in the jets of radio galaxies. In this work, we model radio to very high energy (VHE,≳ 100 GeV) γ-ray emission from Cen A, including GeV hardness detected by Fermi–LAT and TeV emission detected by the High Energy Stereoscopic System (HESS). We consider two scenarios: (i) two-zone synchrotron self-Compton (SSC) and external-Compton (EC) models, (ii) two-zone SSC, EC, and photohadronic emission from cosmic ray interactions. The GeV hardness observed by Fermi–LAT can be explained using these two scenarios, where zone 2 EC emission is very important. Hadronic emission in scenario (ii) can explain VHE data with the same spectral slope as obtained through fitting UHECRs from Cen A. The peak luminosity in cosmic ray proton at 1 TeV, to explain the VHE γ-ray data is ≈2.5 × 1046 erg s−1. The bolometric luminosity in cosmic ray protons is consistent with the luminosity required to explain the origin of 13 UHECR signal events that are correlated with Cen A.
Evidence-Based Optimization of Post-Treatment Surveillance for Skull Base Chordomas Based on Local and Distant Disease Progression
Authors: Freeman Jacob L , Kaufmann Ascher B , Everson Richard G , DeMonte Franco , Raza Shaan M 
Published: April 2018

Abstract

BACKGROUND
There are no guidelines regarding post-treatment surveillance specific to skull base chordomas.

OBJECTIVE
To determine an optimal imaging surveillance schedule to detect both local and distant metastatic skull base chordoma recurrences.

METHODS
A retrospective review of 91 patients who underwent treatment for skull base chordoma between 1993 and 2017 was conducted. Time to and location of local and distant recurrence(s) were cataloged. Existing chordoma surveillance recommendations (National Comprehensive Cancer Network [NCCN], London and South East Sarcoma Network [LSESN], European Society for Medical Oncology [ESMO], Chordoma Global Consensus Group [CGCG]) were applied to our cohort to compare the number of recurrent patients and months of undiagnosed tumor growth between surveillances. These findings were used to inform the creation of a revised imaging surveillance protocol (MD Anderson Cancer Center Chordoma Imaging Protocol [MDACC-CIP]), presented here.

RESULTS
Thirty-four patients with 79 local/systemic recurrences met inclusion criteria. Mean age at diagnosis and follow-up time were 45 yr and 79 mo, respectively. The MDACC-CIP imaging protocol significantly reduced the time to diagnosis of recurrence compared with the LSESN and CGCG/ESMO imaging protocols for surveillance of local disease with a cumulative/average of 576/16.9 (LSESN), 336/9.8 (CGCG), and 170/5.0 (MDACC-CIP) months of undetected growth, respectively. The NCCN and MDACC-CIP guidelines for distant metastatic surveillance identified a cumulative/average of 65/6.5 and 51/5.1 mo of undetected growth, respectively, and were not significantly different.

CONCLUSION
The MDACC-CIP for skull base chordoma accounts for recurrence trends unique to this disease, including a higher rate of leptomeningeal spread than sacrococcygeal primaries, resulting in improved sensitivity and prompt diagnosis.
Planets around the evolved stars 24 Boötis and γ Libra: A 30 d-period planet and a double giant-planet system in possible 7:3 MMR
Authors: Takarada Takuya , Sato Bun’ei , Omiya Masashi , Harakawa Hiroki , Nagasawa Makiko , Izumiura Hideyuki , Kambe Eiji , Takeda Yoichi , Yoshida Michitoshi , Itoh Yoichi , Ando Hiroyasu , Kokubo Eiichiro , Ida Shigeru 
Published: April 2018

Abstract
We report the detection of planets around two evolved giant stars from radial velocity measurements at Okayama Astrophysical observatory. 24 Boo (G3 IV) has a mass of $0.99\,M_{\odot }$, a radius of $10.64\,R_{\odot }$, and a metallicity of [Fe/H] = −0.77. The star hosts one planet with a minimum mass of 0.91 MJup and an orbital period of 30.35 d. The planet has one of the shortest orbital periods among those ever found around evolved stars using radial-velocity methods. The stellar radial velocities show additional periodicity with 150 d, which can probably be attributed to stellar activity. The star is one of the lowest-metallicity stars orbited by planets currently known. γ Lib (K0 III) is also a metal-poor giant with a mass of $1.47\,M_{\odot }$, a radius of $11.1\,R_{\odot }$, and [Fe/H] = −0.30. The star hosts two planets with minimum masses of 1.02 MJup and 4.58 MJup, and periods of 415 d and 964 d, respectively. The star has the second-lowest metallicity among the giant stars hosting more than two planets. Dynamical stability analysis for the γ Lib system sets the minimum orbital inclination angle to be about 70° and suggests that the planets are in 7:3 mean-motion resonance, though the current best-fitting orbits for the radial-velocity data are not totally regular.
Development and Evaluation of the Boston University Osteoarthritis Functional Pain Short Form (BU-OA-FPS)
Authors: Goode Adam P , Ni Pengshend , Jette Alan , Fitzgerald G Kelley 
Published: April 2018

AbstractBackgroundPragmatic studies have gained popularity, thus emphasizing the need for patient-reported outcomes (PRO) to be integrated into electronic health records.ObjectiveThis study describes the development of a customized short form from the Boston University Osteoarthritis Functional Assessment PRO (BU-OA-PRO) for a specific pragmatic clinical trial.MethodsA Functional Pain Short Form was created from an existing item bank of deidentified data in the BU-OA-PRO. Item response theory (IRT) methods were used to select items. Reliability was measured with the Cronbach alpha, then with IRT simulation methods. To examine validity, ceiling and floor effects, correlations between the short-form scores and scores from the BU-OA-PRO and the Western Ontario McMasters University Osteoarthritis Index (WOMAC) Pain and Difficulty subscales, and the area under the curve (AUC) were calculated. A minimum detectable change at 90% confidence (MDC90) was calculated based on a calibration sample.ResultsThe BU-OA-PRO was reduced from 126 items to 10 items to create the BU-OA Functional Pain Short Form (BU-OA-FPS). The Cronbach alpha indicated high internal consistency (0.91), and reliability distribution estimates were 0.96 (uniform) and 0.92 (normal). Low ceiling effects (4.57%) and floor effects (0%) were found. Moderate-to-high correlations between the BU-OA-PRO and BU-OA-FPS were found with WOMAC Pain (BU-OA-FPS = 0.67; BU-OA-PRO = 0.64) and Difficulty (BU-OA-FPS = 0.73; BU-OA-PRO = 0.69) subscales. The correlation between the BU-OA-PRO and BU-OA-FPS was 0.94. The AUC ranged from 0.80 to 0.88. The MDC90 was approximately 6 standardized points.ConclusionsThe BU-OA-FPS provides reliable and valid measurement of functional pain. Pragmatic studies may consider the BU-OA-FPS for use in electronic health records to capture outcomes.