bluuebunny/crossref_metadata_2025_split huggingface dataset:
ConSIG: consistent discovery of molecular signature from OMIC data
Authors: Li Fengcheng , Yin Jiayi , Lu Mingkun , Yang Qingxia , Zeng Zhenyu , Zhang Bing , Li Zhaorong , Qiu Yunqing , Dai Haibin , Chen Yuzong , Zhu Feng 
Published: June 2022

Abstract
The discovery of proper molecular signature from OMIC data is indispensable for determining biological state, physiological condition, disease etiology, and therapeutic response. However, the identified signature is reported to be highly inconsistent, and there is little overlap among the signatures identified from different biological datasets. Such inconsistency raises doubts about the reliability of reported signatures and significantly hampers its biological and clinical applications. Herein, an online tool, ConSIG, was constructed to realize consistent discovery of gene/protein signature from any uploaded transcriptomic/proteomic data. This tool is unique in a) integrating a novel strategy capable of significantly enhancing the consistency of signature discovery, b) determining the optimal signature by collective assessment, and c) confirming the biological relevance by enriching the disease/gene ontology. With the increasingly accumulated concerns about signature consistency and biological relevance, this online tool is expected to be used as an essential complement to other existing tools for OMIC-based signature discovery. ConSIG is freely accessible to all users without login requirement at https://idrblab.org/consig/
TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats
Authors: Luu Gordon T , Freitas Michael A , Lizama-Chamu Itzel , McCaughey Catherine S , Sanchez Laura M , Wang Mingxun 
Published: June 2022

AbstractMotivationAdvances in mass spectrometry have led to the development of mass spectrometers with ion mobility spectrometry capabilities and dual-source instrumentation; however, the current software ecosystem lacks interoperability with downstream data analysis using open-source software and pipelines.ResultsHere, we present TIMSCONVERT, a data conversion high-throughput workflow from timsTOF Pro/fleX mass spectrometer raw data files to mzML and imzML formats that incorporates ion mobility data while maintaining compatibility with data analysis tools. We showcase several examples using data acquired across different experiments and acquisition modalities on the timsTOF fleX MS.Availability and implementationTIMSCONVERT and its documentation can be found at https://github.com/gtluu/timsconvert and is available as a standalone command-line interface tool for Windows and Linux, NextFlow workflow and online in the Global Natural Products Social (GNPS) platform.Supplementary informationSupplementary data are available at Bioinformatics online.
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences
Authors: Li Jun , Zhang Sicheng , Zhang Dong , Chen Shi-Jie 
Published: June 2022

AbstractSummaryRNA 3D structures are critical for understanding their functions and for RNA-targeted drug design. However, experimental determination of RNA 3D structures is laborious and technically challenging, leading to the huge gap between the number of sequences and the availability of RNA structures. Therefore, the computer-aided structure prediction of RNA 3D structures from sequences becomes a highly desirable solution to this problem. Here, we present a pipeline server for RNA 3D structure prediction from sequences that integrates the Vfold2D, Vfold3D and VfoldLA programs. The Vfold2D program can incorporate the SHAPE experimental data in 2D structure prediction. The pipeline can also automatically extract 2D structural constraints from the Rfam database. Furthermore, with a significantly expanded 3D template database for various motifs, this Vfold-Pipeline server can efficiently return accurate 3D structure predictions or reliable initial 3D structures for further refinement.Availability and implementationhttp://rna.physics.missouri.edu/vfoldPipeline/index.html. The data underlying this article have been provided in the article and in its online supplementary material.Supplementary informationSupplementary data are available at Bioinformatics online.
Modelling and analysis of an 80-MW parabolic trough concentrated solar power plant in Sudan
Authors: Bashir Abdallah Adil Awad , Özbey Mustafa 
Published: June 2022

Abstract
Concentrated solar power plants can play a significant role in alleviating Sudan’s energy crisis. These plants can be established and implemented in Sudan, as their potential is considerably high due to the climate conditions in Sudan. This study investigates the design of a parabolic trough concentrated solar power plant in Sudan and analyzes its technical and economic feasibility. The simulation of the plant’s model used System Advisor Model (SAM) software. To determine the best location for the construction of the plant, data from 15 cities in Sudan were compared with each other based on their solar radiation and land properties. Wadi Halfa, a city in the northern region of Sudan, was chosen as the location due to its good topographical properties and climate conditions. The results show that the proposed plant can generate 281.145 GWh of electricity annually with a capacity factor of 40.1% and an overall efficiency of 15%. Additionally, a simple cost analysis of the plant indicates a levelized cost of electricity of 0.155 $/kWh. As the study results are consistent with the characteristics of similar plants, the proposed plant is considered technically and economically feasible under the conditions at its location.
Perinatally Human Immunodeficiency Virus–Infected Adolescents and Young Adults Demonstrate Distinct BNT162b2 Messenger RNA Coronavirus Disease 2019 Vaccine Immunogenicity
Authors: Morrocchi Elena , Pighi Chiara , Pascucci Giuseppe Rubens , Cotugno Nicola , Medri Chiara , Amodio Donato , Colagrossi Luna , Ruggiero Alessandra , Manno Emma Concetta , Casamento Tumeo Chiara , Bernardi Stefania , Smolen Kinga K , Perno Carlo Federico , Ozonoff Al , Rossi Paolo , Levy Ofer , Palma Paolo 
Published: June 2022

Abstract

Background
Immunization of vulnerable populations with distinct immunity often results in suboptimal immunogenicity, durability, and efficacy.

Methods
Safety and immunogenicity profiles of BNT162b2 messenger RNA coronavirus disease 2019 (COVID-19) vaccine, among people living with human immunodeficiency virus (HIV), were evaluated in 28 perinatally HIV-infected patients under antiretroviral therapy (ART) and 65 healthy controls (HCs) with no previous history of COVID-19. Thus, we measured severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–specific humoral and CD4+ T cell responses. Samples were collected before vaccination (baseline, day [D] 0), at the second dose (D21), and at 4 weeks (D28) and 6 months (D180) after D0. Proteomic profiles at D0 and D28 were assessed with a multiplexed proximity extension assay (Olink) on plasma samples.

Results
All HIV-infected patients mounted similar anti–SARS-CoV-2 humoral responses to those of HCs, albeit with lower titers of anti-trimeric S at D28 (P = .01). Only peripheral blood mononuclear cells of HIV-infected patients demonstrated at D28 an impaired ability to expand their specific (CD40L+) CD4+ T-cell populations. Similar humoral titers were maintained between the 2 groups at 6-months follow-up. We additionally correlated baseline protein levels to either humoral or cellular responses, identifying clusters of molecules involved in immune response regulation with inverse profiles between the 2 study groups.

Conclusions
Responses of ART-treated HIV-infected patients, compared to those of HCs, were characterized by distinct features especially within the proteomic compartment, supporting their eligibility to an additional dose, similarly to the HC schedule.
Daily Social Interactions and Momentary Loneliness: The Role of Trait Loneliness and Neuroticism
Authors: Zhaoyang Ruixue , Harrington Karra D , Scott Stacey B , Graham-Engeland Jennifer E , Sliwinski Martin J 
Published: June 2022

Abstract

Objectives
Loneliness has been linked to poor mental and physical health outcomes in later life. Little is known about how daily social interactions relate to older adults’ everyday experiences of loneliness. This study examined the dynamic associations between social interactions and the momentary feelings of loneliness in older adults’ daily lives. We further examined whether individual differences in trait loneliness and neuroticism influenced the extent to which daily social interactions were related to moment-to-moment changes in loneliness.

Method
Participants were 317 community-dwelling older adults (aged 70–90 years) who reported their social interactions and momentary feelings of loneliness 5 times daily for 14 consecutive days using smartphones.

Results
Having more frequent, more pleasant, and in-person social interactions, as well as interactions with family and friends specifically, significantly predicted lower momentary loneliness a few hours later. Higher levels of momentary loneliness, in turn, predicted less likelihood of engaging in these types of social interactions subsequently. In addition, older adults with higher (vs lower) traits of loneliness and neuroticism experienced greater decreases in momentary feelings of loneliness after having more frequent or pleasant social interactions, or interactions with family members.

Discussion
These results expand our understanding of the dynamic associations between daily social interactions and loneliness in later life and provide insights to inform future research, including the possibility of behavioral interventions that target social interactions to reduce the risk for loneliness.
Actor and Partner Effect of Loneliness on Episodic Memory and Verbal Fluency: A Dyadic Multilevel Analysis of Romantic Couples Across 28 Countries
Authors: Luchetti Martina , Ledermann Thomas , Aschwanden Damaris , Nikitin Jana , O’Súilleabháin Páraic S , Stephan Yannick , Terracciano Antonio , Sutin Angelina R 
Published: June 2022

Abstract

Objectives
There is evidence that loneliness is detrimental to cognitive health. Most studies, however, do not consider the association between loneliness and cognition in the context of close relationships, such as a spouse or romantic partner. This study examines loneliness, experienced by both the individual and their romantic partner, and cognitive performance.

Methods
Data were from 24,689 opposite-sex couples (49,378 participants) from 28 countries in the Survey of Health, Aging and Retirement in Europe. Each couple participant reported loneliness and completed memory and verbal fluency tasks. A multilevel sex-stratified analysis was used to account for the nested data structure and evaluate actor and partner effects of loneliness on cognitive performance for male and female partners.

Results
Consistent with the literature, there were small actor effects of loneliness on memory and verbal fluency for both males and females: A person’s own loneliness was associated negatively with their cognitive performance on both tasks. There were also small partner effects: A person with a partner who was lonely tended to have worse cognitive performance above and beyond their own loneliness. Actor and partners effects were similar for male and female partners, replicated in most countries, and generally held controlling for age, education, household size, and disease burden. For memory, loneliness effects were slightly stronger among older participants.

Discussion
Both the experience of loneliness and loneliness of a partner have a negative association with cognitive health.
Can we use seismic reflection data to infer the interconnectivity of fracture networks?
Authors: Rubino J Germán , Barbosa Nicolás D , Hunziker Jürg , Holliger Klaus 
Published: June 2022

Summary
While variations of seismic reflection amplitudes with incidence angle (AVA) and azimuth have been widely used to provide information on geometric characteristics of fractures, this attribute has, as of yet, not been linked to fracture interconnectivity, which tends to govern the hydraulic property of the affected formation. This is due to limitations of the forward models considered to represent the corresponding seismic responses. Based on a poroelastic upscaling procedure and a subsequent plane-wave analysis, we show for the first time that seismic reflection coefficients are highly sensitive to fracture interconnectivity. Moreover, our results suggest that crossplots of commonly used AVA coefficients can be used to delineate regions of fractured formations with higher or lower fracture interconnectivity. This sensitivity is due to changes of the stiffening effect of the fluid contained within interconnected fractures in response to wave-induced fluid-pressure diffusion, a physical process that has not been previously accounted for in seismic reflection analyses.
Single-stage off-pump repair of coarctation of the aorta and ventricular septal defects in children
Authors: Kulyabin Yuriy Y , Voitov Alexey V , Nichay Nataliya R , Soynov Ilya A , Zubritskiy Alexey V , Bogachev-Prokophiev Alexander V 
Published: June 2022

Abstract

OBJECTIVES
The appropriate approach for surgical repair of coarctation of the aorta with a ventricular septal defect (VSD) remains controversial. This study evaluated the outcomes of primary repair of VSDs with periventricular device closure without cardiopulmonary bypass through a left thoracotomy in patients without arch hypoplasia.

METHODS
We selected 21 patients aged &lt;1 year, including 7 neonates, who underwent repair of coarctation of the aorta with periventricular device closure of a VSD.

RESULTS
The median occluder size was 6 (range, 5–8) mm. The median mechanical ventilation time was 14 (range, 2–68) h, and the median duration of hospital stay was 11 (range, 7–16) days. No reoperations were required to correct VSD shunting, and the median residual shunt size was 1 (range, 1–2) mm. The median follow-up period was 13 (range, 4–31) months. No late deaths were reported, and no haemodynamically significant pressure gradient at the anastomotic site was observed. The median distal aortic arch z-score was 0.39 (range, −0.1–to 0.9). Only 1 patient had a permanent pacemaker implanted towards the end of the follow-up period.

CONCLUSIONS
Periventricular device closure can be used safely for closure of VSD in children with coarctation of the aorta without a hypoplastic aortic arch, even in neonates, to reduce the risk of prolonged cardiopulmonary bypass. This hybrid approach can be performed with a low incidence of rhythm disturbances and residual shunting. However, a meticulous assessment of the VSD anatomy is essential to avoid any unfavourable events.
Validation of the 3M™ Molecular Detection Assay 2—STEC Gene Screen (stx) for Detection of Shiga Toxin Gene (stx1 and/or stx2) in Dried Cannabis Flower and Dried Hemp Flower: AOAC Performance Tested MethodSM 071903
Authors: Rosauer Micki L , Lopez-Velasco Gabriela , Silbernagel Karen M , Horine Leo , Tudor Alexandra 
Published: June 2022

Abstract

Background
The 3M™ Molecular Detection Assay 2—STEC Gene Screen (stx) method is based on gene amplification by the use of real-time loop-mediated isothermal amplification when used with the 3M Molecular Detection System for the rapid and specific detection of Shiga toxin gene (stx1 and/or stx2) from Shiga toxin-producing Escherichia coli (STEC) in enriched products. The 3M Molecular Detection Assay 2—STEC Gene Screen (stx) was approved as AOAC Performance Tested MethodSM Certificate No. 071903.

Objective
This matrix extension study evaluated the 3M Molecular Detection Assay 2—STEC Gene Screen (stx) method for detection of STECs in dried cannabis flower [&gt;0.3% delta 9-tetrahydrocannabinol (THC)] and dried hemp flower (≤0.3% THC) at a 10 g test portion size.

Method
Testing followed procedures outlined in 3M Molecular Detection Assay 2—STEC Gene Screen (stx) product instructions and Standard Method Performance Requirement (SMPR®) for Detection of Shiga Toxin-Producing Escherichia coli in Cannabis and Cannabis Products (AOAC SMPR 2020.012). The method was evaluated at low, high, and non-inoculated levels.

Results
Results showed no statistically significant difference between the presumptive positive 3M Molecular Detection Assay 2—STEC Gene Screen (stx) results and the SMPR 2020.012 recommended cultural confirmations.

Conclusions
This study provides data that demonstrate the 3M Molecular Detection Assay 2—STEC Gene Screen (stx) is a reliable method for the rapid and specific detection of STECs in dried cannabis flower and dried hemp flower.

Highlights
The 3M Molecular Detection Assay 2—STEC Gene Screen (stx) method is suitable for the rapid and specific detection of STECs in dried cannabis flower and dried hemp flower.
Relative habitability of exoplanet systems with two giant planets
Authors: Bailey Nora A , Fabrycky Daniel C 
Published: June 2022

ABSTRACT
The architecture of a planetary system can influence the habitability of a planet via orbital effects, particularly in the areas of stability and eccentricity. Some of these effects are readily apparent, particularly when they occur on short time-scales that are easily numerically calculable. However, the appearance and evolution of life can take place on gigayear time-scales, long enough that secular effects become important. These effects are difficult to investigate, as a direct integration requires significant computational time. In this paper, we apply a semi-analytic framework in conjunction with N-body integrations and predictive techniques to determine the relative habitability for an Earth-like planet in a system with two giant companions over a multidimensional parameter space. Relative habitability quantifies the integrated habitability probability compared to a system containing only a single Earth-like planet. We find trends with mass, eccentricity, location, spacing, inclination, and alignment of the giant planets, including configurations where the system is more habitable due to the giant planets. As long as the system remains stable, a moderate eccentricity excitation of the terrestrial planet can be beneficial by increasing the outer boundary of the habitable zone through higher mean irradiance. In our simulations, the median (±1σ) habitable planet has an eccentricity of $0.11^{+0.16}_{-0.08}$, though it started circular. Low-mass, widely separated, and moderately eccentric perturbing giants can accomplish this, an ‘ultra-habitable’ configuration of companions.
Quadrupole and octupole order resonances in non-restricted hierarchical planetary systems
Authors: Lei Hanlun , Huang Xiumin 
Published: June 2022

ABSTRACT
Non-restricted hierarchical three-body configurations are common in various scales of astrophysical systems. Dynamical structures of the quadrupole-order resonance (the von Zeipel–Lidov–Kozai resonance) and the octupole-order resonance (the apsidal resonance) under the non-restricted hierarchical planetary systems are investigated in this work by taking advantage of perturbative treatments. Under the quadrupole-order Hamiltonian model, the distribution of libration and circulation regions as well as the distribution of flipping region are analytically explored in the parameter space spanned by the conserved quantities. The fundamental frequencies of system are produced and then the nominal location of octupole-order resonance is identified. From the viewpoint of perturbative theory, the quadrupole-order Hamiltonian determines the unperturbed dynamical model and the octupole-order Hamiltonian plays a role of perturbation to the quadrupole-order dynamics. The resonant Hamiltonian for octupole-order resonances is formulated by means of averaging theory, giving rise to a new constant of motion. Phase portraits are produced to analyse dynamical structures of octupole-order resonance, including resonant centres, saddle points, dynamical separatrices and islands of libration. By analysing phase portraits, it is found that there are four branches of libration centre and eight libration zones in the considered space. Applications to orbit flips show that there are five flipping regions.
Shifting the Focus to Teachers: A New Approach for Music Therapists Working in Schools
Authors: Steele Megan , McFerran Katrina Skewes , Crooke Alexander Hew Dale 
Published: June 2022

AbstractThis paper presents a new approach for music therapists in schools wishing to support the work of teachers. This music therapy approach is underpinned by theoretical resources drawn from community music therapy and a critical inclusive approach to education. Illustrative examples of the first authors’ music therapy practice as part of a teacher professional learning program, Music for Classroom Wellbeing, are offered. Two practice principles, “focus on the teacher” and “enable sharing,” are presented to provide a framework for music therapists striving to support teachers. Following these principles may allow teachers to grow their musicality, teaching, and self-care practices. This paper concludes with implications of reframing the focus of music therapy practice with teachers for other music therapists working in the current performance-driven schooling system.
Comparison of Motivational Short Interventions to Improve Smokers’ Health Behavior (The COSMOS Study): A Pragmatic Cluster-Randomized Two-Arm Trial in General Practice
Authors: Grischott Thomas , Senn Oliver , Frei Anja , Rosemann Thomas , Neuner-Jehle Stefan 
Published: June 2022

Abstract

Introduction
Helping smokers to quit is an important task of general practitioners (GPs). However, achieving tobacco abstinence is difficult, and smokers who fail may still want to improve their health in other ways. Therefore, Swiss GPs developed a multithematic coaching concept that encourages health behavior changes beyond smoking cessation alone.

Aims and Methods
To compare the effectiveness of such coaching with state-of-the-art smoking cessation counseling, we conducted a pragmatic cluster-randomized two-arm trial with 56 GPs in German-speaking Switzerland and 149 of their cigarette smoking patients. GPs were instructed in either multithematic health coaching or smoking cessation counseling. After 12 months, we compared their patients’ improvements in cigarette consumption, body weight, physical inactivity, alcohol consumption, stress, unhealthy diet, and a health behavior of their own choice, using hierarchical logistic regression models and Fisher’s exact and t tests.

Results
Over 95% of all participants achieved clinically relevant improvements in at least one health behavior, with no difference between study arms (health coaching vs. smoking cessation counseling: aOR = 1.21, 95% CI = [0.03–50.76]; and aOR = 1.78, 95% CI = [0.51–6.25] after non-responder imputation). Rates of clinically relevant improvements in the individual health behaviors did not differ between study arms either (they were most frequent in physical activity, achieved by 3 out of 4 patients), nor did the extent of the improvements.

Conclusions
Multithematic health coaching and state-of-the art smoking cessation counseling were found to be comparable interventions, both in terms of smoking cessation success and, quite unexpectedly, their effects on other health behaviors.

Implications
The findings of our study suggest that in general practice, multithematic health coaching is an effective smoking cessation intervention, and conversely, monothematic smoking cessation counseling also achieves the beneficial effects of a multithematic health behavior intervention. This opens up the possibility for GPs to support their smoking patients in improving their health behavior in additional and more flexible ways.