bluuebunny/crossref_metadata_2025_split huggingface dataset:
2D 1T′-MoS2-WS2 van der Waals heterostructure for hydrogen evolution reaction: dispersion-corrected density functional theory calculations
Authors: Obligacion Joseph Kyle A , Putungan Darwin Barayang 
Published: July 2020

Abstract
Dispersion-corrected density functional theory calculations were implemented to investigate structural characteristics, as well as the hydrogen evolution reaction (HER) capability of 2D 1T′ phase MoS2-WS2 van der Waals heterostructures. Two van der Waals corrections were utilized in the study, namely DFT-D3 (semi-empirical-based) and vdW-DF2-B86R (ab-initio-based) corrections. Results show that the DFT-D3 correction stabilized the binding of the monolayers consistent with experimental observations, with binding energy per unit cell of -0.54 eV/cell. The Gibbs free energy of hydrogen adsorption ΔG

ads,H
, which is the lone descriptor of HER, were calculated for the two known adsorption sites in the 1T′ phase, termed S1 (sulfur site with elongated bonds, more active for HER) and S2 (sulfur site with compressed bonds, less active for HER). It is revealed that at the van der Waals region, the S1 and S2 sites, acting as a single adsorption site, become active for HER, with significantly lowered value of ΔG

ads,H
at 0.20-0.24 eV. This is linked to the synergistic interaction of the two sites in adsorbing hydrogen. In terms of electronic structure, the enhanced states in the vicinity of the Fermi level for the interacting S1 and S2 sites at the van der Waals region resulted from orbital hybridization among 3p states of the sulfur sites from the inner top and bottom surfaces. The merging of the two sites at the van der Waals region would result to HER efficiency that is expected to be higher by a factor of 2 compared to that on the top and bottom surfaces. This work has showed that 2D heterostructures could be of importance in catalysis, particularly in HER. Furthermore, it is showed that building a 2D heterostructure could be a good alternative to the application of strain in improving HER capability of 1T′ 2D materials without compromising the adsorption properties of other sites.
Unsupervised classification of single-molecule data with autoencoders and transfer learning
Authors: Vladyka Anton , Albrecht Tim 
Published: July 2020

Abstract
Datasets from single-molecule experiments often reflect a large variety of molecular behaviour. The exploration of such datasets can be challenging, especially if knowledge about the data is limited and a priori assumptions about expected data characteristics are to be avoided. Indeed, searching for pre-defined signal characteristics is sometimes useful, but it can also lead to information loss and the introduction of expectation bias. Here, we demonstrate how Transfer Learning-enhanced dimensionality reduction can be employed to identify and quantify hidden features in single-molecule charge transport data, in an unsupervised manner. Taking advantage of open-access neural networks trained on millions of seemingly unrelated image data, our results also show how Deep Learning methodologies can readily be employed, even if the amount of problem-specific, ‘own’ data is limited.
A rapid point-of-care ultrasound marker for muscle mass and muscle strength in older adults
Authors: Madden Kenneth M , Feldman Boris , Arishenkoff Shane , Meneilly Graydon S 
Published: July 2020

Abstract

Background/Objectives
Sarcopenia is defined as the gradual age-associated loss of both muscle quantity and strength in older adults, and is associated with increased mortality, falls, fractures and hospitalisations. Current sarcopenia criteria use dual-energy X-ray absorptiometry (DXA) measures of muscle mass, a test that cannot be performed at the bedside, unlike point-of-care ultrasound (PoCUS). We examined the association between ultrasonic measures of muscle thickness (MT, vastus medialis muscle thickness) and measures of muscle quantity and strength in older adults.

Methods
A total of 150 older adults (age ≥ 65; mean age 80.0 ± 0.5 years, 66 women, 84 men) were recruited sequentially from geriatric medicine clinics. Each subject had lean body mass (LBM, by bioimpedance assay), grip strength, mid-arm biceps circumference (MABC), gait speed and MT measured. All initial models were adjusted for biological sex.

Results
In our final parsimonious models, MT showed a strong significant correlation with all measures of muscle mass, including LBM (Standardised β = 0.204 ± 0.058, R2 = 0.577, P &lt; 0.001) and MABC (Standardised β = 0.141 ± 0.067, R2 = 0.417, P = 0.038). With respect to measures of muscle quality, there was a strong significant correlation with grip strength (Standardised β = 0.118 ± 0.115, R2 = 0.511, P &lt; 0.001) but not with subject performance (gait speed).

Conclusions
MT showed strong correlations with both measures of muscle mass (LBM and MABC) and with muscle strength (grip strength). Although more work needs to be done, PoCUS shows potential as a screening tool for sarcopenia in older adults.
Identification of critical factors for forming collaborative relationships between physicians and pharmacists
Authors: Turner Kyle M , Nelson Cory A , Pestka Deborah L , Sorensen Todd D 
Published: July 2020

Abstract

Purpose
The purpose of this study was to identify and describe strategies that have successfully achieved collaboration among physicians and pharmacists providing comprehensive medication management (CMM) to support development of CMM services.

Methods
A 2-phase, mixed-methods approach was employed to identify successful strategies for building pharmacist–physician relationships in primary care clinic settings. Phase I used a qualitative approach to identify strategies deemed successful in building relationships with physicians. An advisory group of pharmacists with experience building CMM practices assisted in the development of minimum criteria characterizing pharmacists as having strong collaborative relationships. Semi-structured interviews were conducted with 10 interviewees meeting established criteria. Researchers coded interview transcripts and identified the resulting strategies. Phase II employed a survey instrument to determine how frequently identified strategies are used and evaluate the relative level of perceived impact of each strategy, which was distributed to a national audience of pharmacists practicing in ambulatory care settings. Responses from pharmacists meeting prespecified criteria were included in the analysis.

Results
Thirty-three strategies were identified and grouped into 8 themes. In phase II, 104 survey respondents met defined criteria and were eligible to endorse use of identified strategies and rate their relative influence.

Conclusions
Thirty-three strategies were identified and grouped into 8 themes to aid pharmacists practicing CMM in developing stronger collaborative relationships with physician colleagues. A national sampling found many of these strategies were employed by a majority of pharmacists, who had found them to be influential in creating collaborative relationships.
Intramuscular Insertion of a Radiofrequency Microneedling Device for Facial Rejuvenation: A New Technique and Case Reports
Authors: Kornstein Andrew N 
Published: July 2020

Abstract

Skin laxity and dynamic rhytids that signify facial aging are due, in part, to atrophic changes and volume redistribution in the underlying layers of the face: the bone and soft tissue. A microneedling device that delivers bipolar radiofrequency (RF) energy directly to the reticular dermis has been shown to yield rejuvenated, tighter skin in 100% of patients. Herein, the author describes a modification to the standard dermal technique in which the skin is gently gathered with the nondominant hand, and the microneedling device is tilted to deliver RF energy to the mimetic muscles—including the frontalis, orbicularis oculi, and orbicularis oris—as well as the dermis. Muscle penetration was inferred by intraoperative bleeding and postoperative bruising, neither of which is typical of standard RF microneedling. Preliminary findings suggest that the modified procedure may yield greater aesthetic benefits than achieved with dermal application alone, including subtle lifting of the brow and oral commissure, upper-lip shortening with vermilion eversion, tightening of the lower-lid fat pads, and reduction in lateral-canthal rhytids. Although this modified technique will need to be optimized and evaluated in large, controlled studies, the initial results presented herein are encouraging.

Level of Evidence: 5
A Comparative Nesting Study of Red-tailed Hawks and Harris’ Hawks in Southern Arizona
Authors: Mader William J. 
Published: July 2020

Abstract
I studied the nesting of Red-tailed Hawks in the Sonoran Desert of Arizona in 1969-1976, emphasizing its ecology relative to the Harris' Hawk, a species that I have found to be sometimes polyandrous and have nest helpers. Red-tails averaged 2.32 eggs per clutch (59 nests) and Harris' Hawks 2.96 (50 nests). The clutch size distributions of the two species were significantly different. Nest success was 81% for Red-tails and 68% for Harris' Hawks, but may actually be slightly lower because a nest was considered successful if a chick was raised to an age of at least 28 days but not always to fledging. For Red-tails, the average number of chicks produced was 1.55 per nest attempt (42 nests) and for Harris' Hawks 1.60 (50 nests). Red-tails nested exclusively in saguaro cacti, but the more agile Harris' Hawks used not only easily accessible saguaro sites but enclosed tree sites as well. Nest site availability seemed to have no significant role in population regulation. The nesting cycle of the Red-tailed Hawk, from egg laying to fledging, was from February to June; for Harris' Hawks it was from February to early December (because of second broods). Optimum habitat and greater hunting versatility in the Harris' Hawk may allow it a less restricted breeding season in saguaro-palo verde desert than the Red-tail by providing essential food resources. These two factors, and nest helping if it is common, probably contribute to maximizing the productivity of Harris' Hawks in an arid environment with variable food resources.
Sexual Size Dimorphism and Survival of Male and Female Blackbirds (Icteridae)
Authors: Searcy William A. , Yasukawa Ken 
Published: July 2020

Abstract
In a between-species comparison of icterids, male survival decreases relative to female survival as the degree of sexual size dimorphism increases. This result is consistent with the hypothesis that male size is limited by survival selection in icterids; the degree of size dimorphism is known to correlate with the degree of polygyny in icterids, however, so the decreased relative survival of males in dimorphic species may be caused by some correlate of polygyny other than large size.
Survival estimates based on records of recovery of dead birds show positive correlations between male size and male survival and between female size and female survival, but survival estimates based on recaptures of live birds fail to show such relationships.
Timing of Shorebird Migration in Relation to Prey Depletion
Authors: Schneider David C. , Harrington Brian A. 
Published: July 2020

Abstract
The southward departure of migratory shorebirds (Charadrii) before the collapse of food supplies on the breeding grounds would seem to disprove the hypothesis that migratory timing is a trait actively maintained by selective pressures created by seasonal production of food supplies. In this study we looked at seasonal changes in the food supplies of shorebirds at a migratory stopover to see if dwindling food supplies here might explain early arrival from Arctic breeding grounds. For the three earliest migrants through Plymouth, Massachusetts we found substantial reductions of prey densities (7-90%) during migration (July-September). Reductions in prey density were not substantial before September for a later migrant. Caging experiments showed that the reductions in density of infaunal prey were due to predation. If these reductions are sufficient to cause energetic deficits among late arrivals, then competition may be an important selective agent in shaping migratory patterns.
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning
Authors: Tang Yi-Jun , Pang Yi-He , Liu Bin 
Published: July 2020

Abstract

Motivation
Related to many important biological functions, intrinsically disordered regions (IDRs) are widely distributed in proteins. Accurate prediction of IDRs is critical for the protein structure and function analysis. However, the existing computational methods construct the predictive models solely in the sequence space, failing to convert the sequence space into the ‘semantic space’ to reflect the structure characteristics of proteins. Furthermore, although the length-dependent predictors showed promising results, new fusion strategies should be explored to improve their predictive performance and the generalization.

Results
In this study, we applied the Sequence to Sequence Learning (Seq2Seq) derived from natural language processing (NLP) to map protein sequences to ‘semantic space’ to reflect the structure patterns with the help of predicted residue–residue contacts (CCMs) and other sequence-based features. Furthermore, the Attention mechanism was used to capture the global associations between all residue pairs in the proteins. Three length-dependent predictors were constructed: IDP-Seq2Seq-L for long disordered region prediction, IDP-Seq2Seq-S for short disordered region prediction and IDP-Seq2Seq-G for both long and short disordered region predictions. Finally, these three predictors were fused into one predictor called IDP-Seq2Seq to improve the discriminative power and generalization. Experimental results on four independent test datasets and the CASP test dataset showed that IDP-Seq2Seq is insensitive with the ratios of long and short disordered regions and outperforms other competing methods.

Availability and implementation
For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the powerful new predictor has been established at http://bliulab.net/IDP-Seq2Seq/. It is anticipated that IDP-Seq2Seq will become a very useful tool for identification of IDRs.

Supplementary information
Supplementary data are available at Bioinformatics online.
Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports
Authors: Bressem Keno K , Adams Lisa C , Gaudin Robert A , Tröltzsch Daniel , Hamm Bernd , Makowski Marcus R , Schüle Chan-Yong , Vahldiek Janis L , Niehues Stefan M 
Published: July 2020

Abstract

Motivation
The development of deep, bidirectional transformers such as Bidirectional Encoder Representations from Transformers (BERT) led to an outperformance of several Natural Language Processing (NLP) benchmarks. Especially in radiology, large amounts of free-text data are generated in daily clinical workflow. These report texts could be of particular use for the generation of labels in machine learning, especially for image classification. However, as report texts are mostly unstructured, advanced NLP methods are needed to enable accurate text classification. While neural networks can be used for this purpose, they must first be trained on large amounts of manually labelled data to achieve good results. In contrast, BERT models can be pre-trained on unlabelled data and then only require fine tuning on a small amount of manually labelled data to achieve even better results.

Results
Using BERT to identify the most important findings in intensive care chest radiograph reports, we achieve areas under the receiver operation characteristics curve of 0.98 for congestion, 0.97 for effusion, 0.97 for consolidation and 0.99 for pneumothorax, surpassing the accuracy of previous approaches with comparatively little annotation effort. Our approach could therefore help to improve information extraction from free-text medical reports.
Availability  and implementation
We make the source code for fine-tuning the BERT-models freely available at https://github.com/fast-raidiology/bert-for-radiology.

Supplementary information
Supplementary data are available at Bioinformatics online.
netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling
Authors: Dong Zhengyang , Alterovitz Gil 
Published: July 2020

Abstract

Motivation
Single-cell RNA sequencing allows us to study cell heterogeneity at an unprecedented cell-level resolution and identify known and new cell populations. Current cell labeling pipeline uses unsupervised clustering and assigns labels to clusters by manual inspection. However, this pipeline does not utilize available gold-standard labels because there are usually too few of them to be useful to most computational methods. This article aims to facilitate cell labeling with a semi-supervised method in an alternative pipeline, in which a few gold-standard labels are first identified and then extended to the rest of the cells computationally.

Results
We built a semi-supervised dimensionality reduction method, a network-enhanced autoencoder (netAE). Tested on three public datasets, netAE outperforms various dimensionality reduction baselines and achieves satisfactory classification accuracy even when the labeled set is very small, without disrupting the similarity structure of the original space.

Availability and implementation
The code of netAE is available on GitHub: https://github.com/LeoZDong/netAE.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prospective investigations of concentration–clinical response for immunosuppressive drugs provide the scientific basis for therapeutic drug monitoring
Authors: Shaw Leslie M , Kaplan Bruce , Brayman Kenneth L 
Published: July 2020

AbstractThe performance of prospective concentration–clinical response investigations during the early stages of the development of new therapeutic agents can provide a more rigorous basis for therapeutic drug monitoring than the traditional retrospective review of drug concentrations vs clinical outcome. Here we discuss the application of the multicenter randomized concentration-controlled clinical trial study design, and related study designs, as applied to older commonly used and monitored drugs and to two new immunosuppressant drugs, mycophenolate mofetil and tacrolimus. Such studies can provide a more rigorous basis for assessing the risk/benefit associated with a target drug concentration in the individual patient and for designing future prospective pharmacokinetic and therapeutic drug monitoring investigations.
Bone formation and resorption biological markers in cosmonauts during and after a 180-day space flight (Euromir 95)
Authors: Caillot-Augusseau Anne , Lafage-Proust Marie-Héléne , Soler Claude , Pernod Josiane , Dubois Francis , Alexandre Christian 
Published: July 2020

AbstractLong-term spaceflights induce bone loss as a result of profound modifications of bone remodeling, the modalities of which remain unknown in humans. We measured intact parathyroid hormone (PTH) and serum calcium; for bone formation, serum concentrations of bone alkaline phosphatase (BAP), intact osteocalcin (iBGP), and type 1 procollagen propeptide (PICP); for resorption, urinary concentrations (normalized by creatinine) of procollagen C-telopeptide (CTX), free and bound deoxypyridinoline (F and B D-Pyr), and Pyr in a 36-year-old cosmonaut (RTO), before (days −180, −60, and −15), during (from days 10 to 178, n = 12), and after (days +7, +15, +25, and +90) a 180-day spaceflight, in another cosmonaut (ASW) before and after the flight. Flight PTH tended to decrease by 48% and postflight PTH increased by 98%. During the flight, BAP, iBGP, and PICP decreased by 27%, 38%, and 28% respectively in CM1, and increased by 54%, 35%, and 78% after the flight. F D-Pyr and CTX increased by 54% and 78% during the flight and decreased by 29% and 40% after the flight, respectively. We showed for the first time in humans that microgravity induced an uncoupling of bone remodeling between formation and resorption that could account for bone loss.
Calibrated user-friendly reverse transcriptase-PCR assay: quantitation of epidermal growth factor receptor mRNA
Authors: Bor Mustafa Vakur , Sørensen Boe Sandahl , Rammer Paul , Nexø Ebba 
Published: July 2020

AbstractWe report a competitive reverse transcriptase-PCR (RT-PCR) assay and a calibrated user-friendly RT-PCR assay (CURT-PCR) for epidermal growth factor receptor (EGFR) mRNA. A calibrator was prepared from isolated rat liver RNA, and the amount of EGFR mRNA was determined by competitive RT-PCR. In CURT-PCR, a calibration curve was developed by plotting the ratio between the amount of PCR product originating from the calibrator and the RNA internal standard vs the amount of EGFR mRNA present in the calibrator. A fixed amount of RNA internal standard was coamplified with the EGFR mRNA present in the calibrator or in the sample, using the same primer set. The primers were chosen in regions of the EGFR mRNA that show 100% homology between human, rat, and mouse. The amount of EGFR in the unknown samples was calculated from the calibration curve based on the ratio between PCR product originating from the sample and the corresponding RNA internal standard. Competitive RT-PCR and CURT-PCR were used for rat liver samples from 21 different animals. Comparable results were obtained by the two methods. The imprecision of the CURT-PCR method was 8% (n = 20), and the imprecision of the traditional competitive RT-PCR was 16% (n = 17). We conclude that the CURT-PCR method developed is suitable for routine applications such as quantitation of EGFR expression in tumor biopsies. The imprecision is relatively low. Furthermore, the use of a calibration curve makes it possible to analyze a large number of samples in one analytical run and to accept or reject the results according to existing rules for quality assurance.
Development and validation of an automated latex-enhanced immunoassay for prealbumin
Authors: Holownia Peter , Newman David J , Thakkar Hansa , Bedzyk William D , Crane Helen , Olabiran Yemi , Davey Carol L , Price Christopher P 
Published: July 2020

AbstractThe measurement of circulating prealbumin has been shown to be clinically useful in the assessment of nutritional status, both as an initial screen and in the monitoring of nutritional recovery. We describe a fully automated, noncompetitive, homogenous, light-scattering immunoassay that has been developed for this analyte on a Dimension® (Dade) analyzer. A sheep anti-prealbumin IgG fraction was covalently coupled to 40-nm chloromethyl styrene particles and, after the addition of sample, polyethylene glycol-assisted immunoagglutination was monitored by turbidimetry. The prealbumin working assay range was 8–550 mg/L at a sample volume of 2 μL and a reaction time of 6.5 min. When data were analyzed using ANOVA, total and within-run assay imprecision values (CVs) were 1–5%, and calibration and reagent stabilities were in excess of 40 days. Mean analytical recoveries were 102% ± 4% (SD), and there was no lack of parallelism. Hemolysis, lipemia, and bilirubin did not interfere. Both plasma anticoagulated with heparin or EDTA and serum from plain or serum-separation tubes were acceptable as sample matrices. Comparison with the Beckman Array® method gave a Passing and Bablok regression of: Dimension analyzer = 1.01Beckman + 7.1 (n = 103), using a common calibrator. We conclude that the prealbumin method is appropriate for clinical use according to the analytical criteria used in this study.