bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive ergonomics of DNA-algorithms
Authors: Stepanyan I V 
Published: April 2021

Abstract
To improve the ergonomic qualities of graphical interfaces and optimize the visual perception of large data presented in text form, a method of information processing based on DNA algorithms is proposed. These algorithms were developed by the author in the study of the molecular genetic and structural properties of long nucleotide sequences. The result of processing information presented in text form is an object of discrete geometry, two-dimensional projections of which can serve for visual identification of the internal structure of information, as well as for interpretation as characteristic symbols. At the same time, the considered transformations have the property of visualizing the characteristic cluster structure of information. It is shown that genetic nucleotide sequences, as well as texts in natural language, lend themselves to visual classification, which contributes to an increase in the productivity of mental work when analyzing big data. It is shown that DNA algorithms can reduce the load on the visual analyzer during the initial examination of data presented in text form. This makes it possible to apply this method when operators interact with various information streams and text data of arbitrary nature, as well as to improve the ergonomic qualities of specialized graphical interfaces.
The research of a movement dynamics two-legged robot with spring-loaded weight
Authors: Bordyugov D V , Briskin E S , Sharonov N G 
Published: April 2021

Abstract
The movement of a two-legged robot which moves due to oscillations of a load with a given mass fixed on the robot body with the help of the springs, is considered in this research. By changing parameters, such as mass of the load, stiffness of the springs, size of the robot’s body and the initial speed of movement, the various trajectories of movement are executed. In this article mathematical model and calculation results have been presented.
About the geometrical form of the underwater robot platform with non-parallel system the anchor-rope propulsion
Authors: Briskin E S , Sharonov N G , Kalinin Y V , Samozheev I A 
Published: April 2021

Abstract
The underwater mobile transport robot, which is a platform assembled from the polygonal pontoon modules, is considered. The system are used anchor-rope movers, which ensures high stability and energy efficiency of the entire system due to interaction with the bottom surface. The aim of the study is to select the geometric shape of the module according to such criteria as specific heat losses in the movers, the length of the step and the tension of the ropes. The formulated criteria characterize the energy consumption and the level of dynamic loads in the considered dynamic system, and the achievement of their optimal values contributes to the increase of autonomy. It takes into account not only the exchange rate resistance to movement, but also the influence of the current, which, depending on the direction, can both promote the movement of the platform and counteract it.
Synthesis of algorithm for stabilization of spatial position of manipulator gripper of parallel structure
Authors: Dyashkin-Titov V V , Zhoga V V 
Published: April 2021

Abstract
Method of synthesis of kinematic algorithm of stabilization of spatial position of manipulator gripper of parallel-serial structure relative to given position is described in work. Coordinates and speeds and accelerations of generalized coordinates of manipulator are taken as control parameters. Analytical ratios of the control signals of the drive electric motors are obtained, which ensure the movement of the working body of the manipulator in the vicinity of the designated point. Numerical examples of the implementation of the obtained control laws are given.
The results of the impact theory application in modeling the gear shifting processes in automatic transmissions
Authors: Korendyasev G K , Salamandra K B , Tyves L I 
Published: April 2021

AbstractThe process of gear shifting in vehicles automatic transmissions is considered in the paper as the shock interaction of transmission elements. Two mathematical models are proposed and considered for simulation the gear shifting processes. Computer simulation of the models’ movement during acceleration of a vehicle, as well as modes of low - and high-frequency gear shift cycling (self-oscillations of the output shaft of the gearbox) is carried out. Methods for decreasing the amplitude of the gearbox output shaft oscillations caused by the impact nature of gear shifting are proposed.
Research of the process of creating a vacuum on air-permeable surfaces
Authors: Lapikov M A , Kalinin Y V , Makarov A M , Serdobintsev Y P 
Published: April 2021

Abstract
A research of the process of vacuuming on air-permeable surfaces is carried out. A mathematical model is presented for calculating the parameters of the gas filtration process through porous surfaces during their vacuumation. This model allows you to calculate the parameters of vacuum systems for gripping devices necessary for reliable capture of breathable materials.
Precise positioning of mechanisms based on dynamics
Authors: Orekhov S Y , Masyuk V M , Kuznetsov V S , Dolgolenko S P , Kislov K G 
Published: April 2021

Abstract
The purpose of this work is to study the factors that affect the positioning accuracy and find a way to determine the positioning accuracy of a mechatronic system. The paper investigates a model of a hexapod manipulator with six degrees of freedom. A mathematical model of the manipulator has been built. The study of the dependence of the positioning accuracy on the influence of external forces was carried out. It is concluded that manipulators of a parallel structure are applicable for light loads.
Development of a skid for manual contact welding with the machine movement in the working areas
Authors: Boslovyak P V , Dvoretsky V V 
Published: April 2021

Abstract
There is represented the creation of a skid for manual contact welding. It consists of a metal structure of the skid itself and a movement carriage. Strength and stiffness calculations of the metal structure of the skid and of the carriage were performed. A full-scale sample of the skid assembly result is shown.
Calculation and comparative analysis of bucket of the belt elevator
Authors: Boslovyak P V , Shagimardanov V R 
Published: April 2021

Abstract
The calculations of the bucket of a belt elevator for two working cases are presented - at the moment of scooping up the load by the bucket and at the moment of transporting the load into the vertical direction. A 3D model of the bucket was developed in the SolidWorks software package. The calculations of strength and stiffness of the bucket were performed. A comparative analysis of one size range of a bucket with different thicknesses of its walls is carried out.
The influence of 3D printing layer height on frictional properties of ABS plastic
Authors: Slavkina V E , Shitov A O , Lopatina Yu A 
Published: April 2021

Abstract
This work is devoted to the study of tribotechanical properties of 3D printed samples from ABS plastic. The results of determining the coefficient of friction and mass wear of the samples obtained by 3D-printing with different printing heights during the friction testing on machine II 5018 are presented. It is shown that in order to reduce the coefficient of friction and mass wear of the ABS plastic specimen, it is recommended to produce specimens with a higher print height. 3D printed parts with 0.3 mm layer height have shown the best results because of greater layer adhesion.
Feasibility of patient-reported outcome research in acute geriatric medicine: an approach to the ‘post-hospital syndrome’
Authors: Franke Alexander D 
Published: April 2021

Abstract

Background
A patient’s self-reported health-related quality of life (HRQoL) can be quantified by a patient-reported outcome measure (PROM). A patient’s HRQoL can provide another avenue to understand the ‘post-hospital syndrome’, a period after hospital discharge that a patient remains vulnerable to subsequent re-admission. The purpose of the study was to establish the feasibility of collecting HRQoL of older inpatients treated for acute illnesses on medical ward. Feasibility of the PROM would be qualitatively judged upon completion time, response rate and sensitivity to change in HRQoL over time.

Methods
A prospective observational cohort of consecutively admitted patients to a step-down medical ward over 1 year. The COOP/WONCA chart was the PROM. Patients were interviewed by the author face-to-face within 48 hours of admission and then 2 weeks after discharge by telephone.

Results
From the 300 patients admitted, 182 were excluded. Of the remaining 118, median age was 78 years (interquartile range, IQR, 64–86 years), and 71 (60.2%) were female. Proxies were used for 26 (22%) patients. Ninety-two (78%) completed follow-up. The participants were contacted at a median of 14 days (IQR, 13–16) after discharge. Exploratory analyses found that the COOP/WONCA had test–retest responsiveness, that is detected change in HRQoL over time.

Conclusion
The completion time of 3 minutes, high response rate (78%) and test–retest responsiveness are evidence that collecting PROs from acutely unwell elderly patients using the COOP/WONCA is feasible. PRO research could become fundamental to the understanding of the ‘post-hospital syndrome’.
Clinicopathologic Findings in Patients With Initial Diagnosis of Extranodal Marginal Zone B-Cell Lymphoma of Mucosa-Associated Lymphoid Tissue (MALT) in Colorectal Mucosa
Authors: Soma Lorinda A , Smith Stephen D , Reddy Prathima , Edlefsen Kerstin L , Wu David , Cherian Sindhu , Chen Xueyan , Zhou Yi , Reddi Deepti , Fromm Jonathan R 
Published: April 2021

Abstract

Objectives
To evaluate clinicopathologic features, management, and behavior of colorectal extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT).

Methods
Clinical data, laboratory studies, and radiographic records were reviewed (2005-2018), and fluorescence in situ hybridization studies were performed.

Results
Eleven patients were identified, six of whom were discovered as an incidental finding on endoscopy. Morphologic and immunophenotypic features were similar to MALT lymphomas at other sites except that lymphoepithelial lesions were uncommon. Three of nine patients were positive for BIRC3/MALT1 fusions, two of whom had identical B-cell clones identified in subsequent gastric biopsy specimens. Eight of 10 patients had no clinically evaluable disease after observation (±antibiotics; n = 4) or radiation/chemotherapy (n = 4).

Conclusions
Patients with incidental and localized colonic MALT lymphoma demonstrated an excellent prognosis with conservative management, although longer follow-up and data based on consistent staging and surveillance methods (including gastric evaluation) are necessary for informed management.
How I Diagnose Angioimmunoblastic T-Cell Lymphoma
Authors: Xie Yi , Jaffe Elaine S 
Published: April 2021

Abstract

Objectives
Angioimmunoblastic T-cell lymphoma (AITL) is a subtype of peripheral T-cell lymphoma derived from T-follicular helper cells. For pathologists, diagnosing AITL may be challenging due to its wide clinical and histopathologic spectrum, which can mimic a variety of reactive and neoplastic processes.

Methods
We summarize and discuss the clinicopathologic features of AITL, emphasizing diagnostic tools available to the practicing pathologist. Common diagnostic dilemmas are discussed.

Results
AITL exhibits various histologic patterns and is often associated with a prominent microenvironment that can obscure the neoplastic cells. Atypical B-cell proliferations, which can take a number of forms, are common in AITL, and clonal B-cell expansion can be seen. The atypical B cells can closely resemble Hodgkin/Reed-Sternberg cells, leading to misdiagnosis as classic Hodgkin lymphoma. Molecular studies have revealed recurrent genetic alterations, which can aid in differential diagnosis, particularly in problematic cases.

Conclusions
Given the complex diagnostic challenges in AITL, an integrated approach, incorporating clinical, morphologic, immunophenotypic, and molecular findings, is helpful to reach an accurate diagnosis.
Body Mass Index and Mortality Among Adults With Incident Myocardial Infarction
Authors: Al-Shaar Laila , Li Yanping , Rimm Eric B , Manson JoAnn E , Rosner Bernard , Hu Frank B , Stampfer Meir J , Willett Walter C 
Published: April 2021

Abstract
The relationship between body mass index (BMI; weight (kg)/height (m)2) and mortality among survivors of myocardial infarction (MI) remains controversial. We examined the relationships of BMI before and after MI and change in weight with all-cause mortality among participants in the Nurses’ Health Study (1980–2016) and Health Professionals Follow-up Study (1988–2016) cohorts. During a follow-up period of up to 36 years, we documented 4,856 participants with incident nonfatal MI, among whom 2,407 died during follow-up. For pre-MI and post-MI BMI, overweight was not associated with lower mortality. Obesity (BMI ≥30) was associated with higher risk of mortality. Compared with participants with post-MI BMI of 22.5–24.9, hazard ratios were 1.16 (95% confidence interval (CI): 1.01, 1.34) for BMI 30.0–34.9 and 1.52 (95% CI: 1.27, 1.83) for BMI ≥35.0 (P for trend &lt; 0.001). Compared with stable weight from before MI to after MI, a reduction of more than 4 BMI units was associated with increased mortality (hazard ratio = 1.53, 95%: CI: 1.28, 1.83). This increase was seen only among participants who lost weight without improving their physical activity or diet. Our findings showed no survival benefit of excess adiposity in relation to risk of mortality. Weight loss from before to after MI without lifestyle improvement may reflect reverse causation and disease severity.
Clinical impact of pharmacist-led antibiotic stewardship programs in outpatient settings in the United States: A scoping review
Authors: St. Louis James , Okere Arinze Nkemdirim 
Published: April 2021

Abstract

Purpose
To provide an overview of the impact of pharmacist interventions on antibiotic prescribing and the resultant clinical outcomes in an outpatient antibiotic stewardship program (ASP) in the United States.

Methods
Reports on studies of pharmacist-led ASP interventions implemented in US outpatient settings published from January 2000 to November 2020 and indexed in PubMed or Google Scholar were included. Additionally, studies documented at the ClinicalTrials.gov website were evaluated. Study selection was based on predetermined inclusion criteria; only randomized controlled trials, observational studies, nonrandomized controlled trials, and case-control studies conducted in outpatient settings in the United States were included. The primary outcome was the observed differences in antibiotic prescribing or clinical benefits between pharmacist-led ASP interventions and usual care.

Results
Of the 196 studies retrieved for full-text review, a cumulative total of 15 studies were included for final evaluation. Upon analysis, we observed that there was no consistent methodology in the implementation of ASPs and, in most cases, the outcome of interest varied. Nonetheless, there was a trend toward improvement in antibiotic prescribing with pharmacist interventions in ASPs compared with that under usual care (P &lt; 0.05). However, the results of these studies are not easily generalizable.

Conclusion
Our findings suggest a need for a consistent approach for the practical application of outpatient pharmacist-led ASPs. Managed care organizations could play a significant role in ensuring the successful implementation of pharmacist-led ASPs in outpatient settings.
Molecular characterization and enzyme inhibition studies of NADP+- farnesol dehydrogenase from diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae)
Authors: Zifruddin Anis-Nadyra , Mohamad-Khalid Khairunnisa-Atiqah , Suhaimi Saidi-Adha , Mohamed-Hussein Zeti-Azura , Hassan Maizom 
Published: April 2021

ABSTRACT
Juvenile hormone III (JH III) plays an important role in insect reproduction, development, and behavior. The second branch of JH III production includes oxidation of farnesol to farnesal by farnesol dehydrogenase. This study reported the identification and characterization of Plutella xylostella farnesol dehydrogenase (PxFoLDH). Our results showed that PxFoLDH belongs to the short-chain dehydrogenase/reductase superfamily, consisting of a single domain with a structurally conserved Rossman fold, an NAD(P) (H)-binding region and a structurally diverse C-terminal region. The purified enzyme displayed maximum activity at 55$\ $°C with pH 9.5 and was stable in the temperature below 70$\ ^\circ $C. PxFoLDH was determined to be a monomer with a relative molecular weight of 27 kDa and highly specific for trans, trans-farnesol, and NADP+. Among analog inhibitors tested, farnesyl acetate was the most effective inhibitor with the lowest Ki value of 0.02 µm. Our findings showed this purified enzyme may represent as NADP+-farnesol dehydrogenase.
Barricyclin D1—a dimeric ellagitannin with a macrocyclic structure—and accompanying tannins from Barringtonia racemosa
Authors: Yoshikawa Shinji , Chen Lih-Geeng , Yoshimura Morio , Amakura Yoshiaki , Hatano Tsutomu , Taniguchi Shoko 
Published: April 2021

ABSTRACT
Our examination of high molecular weight polyphenolic constituents in the leaves of Barringtonia racemosa of the family Lecythidaceae uncovered 5 previously undescribed ellagitannins. One, barringtin M1 (1), among them was a hydrolysable tannin monomer, while remaining 4, barringtins D1 (2), D2 (3), D3 (4), and barricyclin D1 (5), were all dimers. Barricyclin D1 had a first macrocyclic structure formed from casuarictin (6) and tellimagrandin I (7), and the other ellagitannins had structures related to 5. Two additional known phenolics, valoneic acid dilactone (8) and schimawalin A (9), were also isolated from the leaves. These results suggested that the leaves of B. racemosa are a natural resource rich in hydrolysable tannin oligomers.
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants
Authors: Wang Ye , Jiang Yuchao , Yao Bing , Huang Kun , Liu Yunlong , Wang Yue , Qin Xiao , Saykin Andrew J , Chen Li 
Published: April 2021

AbstractUnderstanding the functional consequence of noncoding variants is of great interest. Though genome-wide association studies or quantitative trait locus analyses have identified variants associated with traits or molecular phenotypes, most of them are located in the noncoding regions, making the identification of causal variants a particular challenge. Existing computational approaches developed for prioritizing noncoding variants produce inconsistent and even conflicting results. To address these challenges, we propose a novel statistical learning framework, which directly integrates the precomputed functional scores from representative scoring methods. It will maximize the usage of integrated methods by automatically learning the relative contribution of each method and produce an ensemble score as the final prediction. The framework consists of two modes. The first ‘context-free’ mode is trained using curated causal regulatory variants from a wide range of context and is applicable to predict regulatory variants of unknown and diverse context. The second ‘context-dependent’ mode further improves the prediction when the training and testing variants are from the same context. By evaluating the framework via both simulation and empirical studies, we demonstrate that it outperforms integrated scoring methods and the ensemble score successfully prioritizes experimentally validated regulatory variants in multiple risk loci.
Clustering single-cell RNA-seq data by rank constrained similarity learning
Authors: Mei Qinglin , Li Guojun , Su Zhengchang 
Published: April 2021

Abstract

Motivation
Recent breakthroughs of single-cell RNA sequencing (scRNA-seq) technologies offer an exciting opportunity to identify heterogeneous cell types in complex tissues. However, the unavoidable biological noise and technical artifacts in scRNA-seq data as well as the high dimensionality of expression vectors make the problem highly challenging. Consequently, although numerous tools have been developed, their accuracy remains to be improved.

Results
Here, we introduce a novel clustering algorithm and tool RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both local similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman’s rank correlations of a cell’s expression vector with those of other cells to measure its global similarity, and adaptively learns neighbor representation of a cell as its local similarity. The overall similarity of a cell to other cells is a linear combination of its global similarity and local similarity. RCSL automatically estimates the number of cell types defined in the similarity matrix, and identifies them by constructing a block-diagonal matrix, such that its distance to the similarity matrix is minimized. Each block-diagonal submatrix is a cell cluster/type, corresponding to a connected component in the cognate similarity graph. When tested on 16 benchmark scRNA-seq datasets in which the cell types are well-annotated, RCSL substantially outperformed six state-of-the-art methods in accuracy and robustness as measured by three metrics.

Availability and implementation
The RCSL algorithm is implemented in R and can be freely downloaded at https://cran.r-project.org/web/packages/RCSL/index.html.

Supplementary information
Supplementary data are available at Bioinformatics online.