bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network approaches for modeling the effect of drugs and diseases
Authors: Rintala T J , Ghosh Arindam , Fortino V 
Published: June 2022

AbstractThe network approach is quickly becoming a fundamental building block of computational methods aiming at elucidating the mechanism of action (MoA) and therapeutic effect of drugs. By modeling the effect of drugs and diseases on different biological networks, it is possible to better explain the interplay between disease perturbations and drug targets as well as how drug compounds induce favorable biological responses and/or adverse effects. Omics technologies have been extensively used to generate the data needed to study the mechanisms of action of drugs and diseases. These data are often exploited to define condition-specific networks and to study whether drugs can reverse disease perturbations. In this review, we describe network data mining algorithms that are commonly used to study drug’s MoA and to improve our understanding of the basis of chronic diseases. These methods can support fundamental stages of the drug development process, including the identification of putative drug targets, the in silico screening of drug compounds and drug combinations for the treatment of diseases. We also discuss recent studies using biological and omics-driven networks to search for possible repurposed FDA-approved drug treatments for SARS-CoV-2 infections (COVID-19).
Regional associations of white matter hyperintensities and early cortical amyloid pathology
Authors: Lorenzini Luigi , Ansems Loes T , Lopes Alves Isadora , Ingala Silvia , Vállez García David , Tomassen Jori , Sudre Carole , Salvadó Gemma , Shekari Mahnaz , Operto Gregory , Brugulat-Serrat Anna , Sánchez-Benavides Gonzalo , ten Kate Mara , Tijms Betty , Wink Alle Meije , Mutsaerts Henk J M M , den Braber Anouk , Visser Pieter Jelle , van Berckel Bart N M , Gispert Juan Domingo , Barkhof Frederik , Collij Lyduine E ,   the EPAD consortium for the ALFA cohort, Beteta Annabella , Brugulat Anna , Cacciaglia Raffaele , Cañas Alba , Deulofeu Carme , Cumplido Irene , Dominguez Ruth , Emilio Maria , Fauria Karine , Fuentes Sherezade , Hernandez Laura , Huesa Gema , Huguet Jordi , Marne Paula , Menchón Tania , Polo Albina , Pradas Sandra , Rodriguez-Fernandez Blanca , Sala-Vila Aleix , Sánchez-Benavides Gonzalo , Soteras Anna , Vilanova Marc 
Published: June 2022

Abstract
White matter hyperintensities (WMHs) have a heterogeneous aetiology, associated with both vascular risk factors and amyloidosis due to Alzheimer’s disease. While spatial distribution of both amyloid and WM lesions carry important information for the underlying pathogenic mechanisms, the regional relationship between these two pathologies and their joint contribution to early cognitive deterioration remains largely unexplored.
We included 662 non-demented participants from three Amyloid Imaging to Prevent Alzheimer’s disease (AMYPAD)-affiliated cohorts: EPAD-LCS (N = 176), ALFA+ (N = 310), and EMIF-AD PreclinAD Twin60++ (N = 176). Using PET imaging, cortical amyloid burden was assessed regionally within early accumulating regions (medial orbitofrontal, precuneus, and cuneus) and globally, using the Centiloid method. Regional WMH volume was computed using Bayesian Model Selection. Global associations between WMH, amyloid, and cardiovascular risk scores (Framingham and CAIDE) were assessed using linear models. Partial least square (PLS) regression was used to identify regional associations. Models were adjusted for age, sex, and APOE-e4 status. Individual PLS scores were then related to cognitive performance in 4 domains (attention, memory, executive functioning, and language).
While no significant global association was found, the PLS model yielded two components of interest. In the first PLS component, a fronto-parietal WMH pattern was associated with medial orbitofrontal–precuneal amyloid, vascular risk, and age. Component 2 showed a posterior WMH pattern associated with precuneus-cuneus amyloid, less related to age or vascular risk. Component 1 was associated with lower performance in all cognitive domains, while component 2 only with worse memory.
In a large pre-dementia population, we observed two distinct patterns of regional associations between WMH and amyloid burden, and demonstrated their joint influence on cognitive processes. These two components could reflect the existence of vascular-dependent and -independent manifestations of WMH-amyloid regional association that might be related to distinct primary pathophysiology.
New smart home energy management systems based on inclining block-rate pricing scheme
Authors: Elazab Rasha , Saif Omar , Amin Metwally Amr M A , Daowd Mohamed 
Published: June 2022

AbstractThere are wide applications of block-rate pricing schemes in many countries. However, there are no significant studies that apply this common tariff for smart home energy management systems. In this paper, a three-time-frame energy management scheme has been proposed for photovoltaic (PV)-powered grid-connected smart homes based on the well-known mixed-integer linear programming optimization technique. This paper provides three original and novel smart home energy management algorithms that depend on the most common residential tariff specifically in developing countries. Three different management concepts have been studied for a typical Egyptian house. The concepts of shifting load, vehicle-to-home and reducing air conditioning have been tested according to a commonly applied slab tariff. The proposed scheme considers the home battery extending lifetime constraints. It also preserves comfortable lifestyle limits for home users according to Arab housing climatic conditions and culture. Moreover, the economic feasibility of integrated PV modules for the studied home has been verified according to the Egyptian tariff. The proposed energy management scheme of PV-powered home reduces the electrical power bill significantly in a wide range from 61% to only 19% of the default case bill according to the applied management technique.
Simultaneous Determination of Metabolites Related to Arginine Metabolism in Rat plasma by Hydrophilic Interaction Chromatography–Tandem Mass Spectrometry
Authors: Wang Ying , Li ZhiRong , Chen RongXiang 
Published: June 2022

AbstractArginine and its metabolites play important roles in pain and analgesia. This study aimed to develop a comprehensive quantification method for amino acids and metabolites related to arginine metabolism in rat plasma by hydrophilic interaction chromatography–tandem mass spectrometry (HILIC–MS/MS). Rat plasma was diluted to reduce the matrix effect and deproteinized with acetonitrile. The analytes were separated on a Syncronis HILIC column with a gradient elution. MS analysis was performed in positive ion mode with an electrospray ionization source using multiple reaction monitoring technology. All calibration curves for the 10 analytes showed good linear regression (R2 &gt; 0.99). The limits of detection (LODs) were in the range of 0.9–13.4 μg/L. The established method was validated for intra-day and inter-day precisions (relative standard deviation [RSDs] &lt; 6.21%) and accuracy (average recovery ranged from 87.34% to 100.35% with the RSD values less than 11.41%). This method was successfully applied to characterize dynamic alterations in the plasma of rats with neuropathic pain and thus provide service to explore the mechanism of action between metabolite changes and clinical disease.
Lung transplant and severe coronary artery disease: results from a single-centre experience
Authors: Franz Maximilian , Siemeni Thierry , Aburahma Khalil , Yablonski Pavel , Poyanmehr Reza , Avsar Murat , Bobylev Dmitry , Sommer Wiebke , Boethig Dietmar , Greer Mark , Gottlieb Jens , Tudorache Igor , Hoeper Marius M , Warnecke Gregor , Haverich Axel , Kuehn Christian , Ius Fabio , Salman Jawad 
Published: June 2022

Abstract

OBJECTIVES
The management of severe coronary artery disease at the time of a lung transplant remains a challenge. We analysed the short- and long-term outcomes of lung transplant recipients with severe coronary artery disease.

METHODS
Records of adult patients who received transplants at our institution between April 2010 and February 2021 were reviewed retrospectively. Severe coronary artery disease was defined as coronary stenosis ≥70% (main stem ≥50%) seen on the coronary angiographic scans performed before or at the time of listing. Patient characteristics, perioperative and long-term outcomes were compared between patients with and without severe coronary artery disease.

RESULTS
Among 896 patients who received lung transplants who had undergone coronary angiography before the transplant, 77 (8.5%) had severe coronary artery disease; the remaining 819 (91.5%) did not. Patients with severe coronary artery disease were older (p &lt; 0.0001), more often male (p &lt; 0.0001) and received transplants more often for pulmonary fibrosis (p = 0.0007). The median (interquartile range) follow-up was 46 (20–76) months. At the Cox multivariable analysis, severe coronary artery disease was not associated with death. Patients with pretransplant percutaneous transluminal coronary angioplasty and patients with coronary artery bypass graft surgery concomitant to a transplant had survival equivalent to that of patients without severe coronary artery disease (p = 0.513; p = 0.556).

CONCLUSIONS
Severe coronary artery disease was not associated with decreased survival after a lung transplant. Concomitant coronary artery bypass graft surgery and pretransplant percutaneous transluminal coronary angioplasty can be used for revascularization.
Coexistence of blaNDM-1, blaOXA-51, blaOXA-23, and armA in conjunction with novel mutations detected in RND efflux pump regulators in tigecycline resistant clinical isolates of Acinetobacter baumannii
Authors: Sawant Ajit Ramesh , Pagal Sudhakar , Amar Ashutosh Kumar , Panda Lipsa , devi C Sheela , Shashikala P , Kanungo Reba , Prashanth K 
Published: June 2022

Abstract
This study has investigated a total of 51 Acinetobacter baumannii isolates for the prevalence of resistant determinants in tigecycline susceptible and non-susceptible clinical isolates of A. baumannii. Antimicrobial susceptibility testing revealed 74% of isolates were tigecycline resistant. Mutations in RND-efflux pump regulatory genes and the expression of efflux pump genes were measured in tigecycline resistant isolates. There was a strong co-relation between the blaNDM-1 and armA wherein majority of the isolates that are positive for blaNDM-1 have also harbored armA. Compared with TSAB (tigecycline susceptible A. baumannii), TNAB (tigecycline non-susceptible A. baumannii) isolates show increased distribution of blaNDM-1 (P = 0.048), blaIMP-1 (P&lt; 0.0001) and blaOXA-51 (P = 0.0029) carbapenemase genes. The variants of RND-efflux pump regulatory genes due to amino-acid mutations in adeS (F12S, K84E, W61R, N268H and Q299R) and adeL (G21R and Q262R) were identified in tigecycline resistant isolates as well as ISAba1 mediated disruption of adeN were observed causing overexpression of adeIJK efflux pump. Additionally, mutations in adeRS were also associated with increased expression of adeABC efflux pump. Besides, TNAB isolates showed significantly (P&lt; 0.0001) higher ability of biofilm formation as compared to TSAB isolates. The tigecycline resistance due to mutations in contemporary A. baumannii isolates having a higher ability to form biofilm may pose therapeutic difficulties.
A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree
Authors: He Jiaoyu , Bao Shanfei , Deng Junhang , Li Qiufu , Ma Shiyu , Liu Yiran , Cui Yanru , Zhu Yuqi , Wei Xia , Ding Xianping , Ke Kehui , Chen Chaojie 
Published: June 2022

Abstract
Artocarpus nanchuanensis (Moraceae), which is naturally distributed in China, is a representative and extremely endangered tree species. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation information for A. nanchuanensis using integrated approaches, including Illumina, Nanopore sequencing platform, and Hi-C. A total of 128.71 Gb of raw Nanopore reads were generated from 20-kb libraries, and 123.38 Gb of clean reads were obtained after filtration with 160.34× coverage depth and a 17.48-kb average read length. The final assembled A. nanchuanensis genome was 769.44 Mb with a 2.09 Mb contig N50, and 99.62% (766.50 Mb) of the assembled data was assigned to 28 pseudochromosomes.
In total, 39,596 genes (95.10%, 39,596/41,636) were successfully annotated, and 129 metabolic pathways were detected. Plants disease resistance/insect resistance genes, plant–pathogen interaction metabolic pathways, and abundant biosynthesis pathways of vitamins, flavonoid, and gingerol were detected. Unigene reveals the basis of species-specific functions, and gene family in contraction and expansion generally implies strong functional differences in the evolution. Compared with other related species, a total of 512 unigenes, 309 gene families in contraction, and 559 gene families in expansion were detected in A. nanchuanensis.
This A. nanchuanensis genome information provides an important resource to expand our understanding of the unique biological processes, nutritional and medicinal benefits, and evolutionary relationship of this species. The study of gene function and metabolic pathway in A. nanchuanensis may reveal the theoretical basis of a special trait in A. nanchuanensis and promote the study and utilization of its rare medicinal value.
A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?
Authors: Bandrowski Anita 
Published: June 2022

Abstract
Research resource identifiers (RRIDs) are persistent unique identifiers for scientific resources used to conduct studies such as reagents and tools. Inclusion of these identifiers into the scientific literature has been demonstrated to improve the reproducibility of papers because resources, like antibodies, are easier to find, making methods easier to reproduce. RRIDs also dramatically reduce the use of problematic resources, such as contaminated cell lines. The addition of RRIDs into a manuscript means that authors have to look up information that they may have previously omitted or confront information about problems that may have been reported about their resources. The use of RRIDs is primarily driven by champion journals, such as GigaScience and others. Although still nascent, this practice lays important groundwork for citation types that can cover non-traditional scholarly output, such as software tools and key reagents; giving authors of various types of tools scholarly credit for their contributions.
On the Image of the Period Map for Polarized Hyperkähler Manifolds
Authors: Song Jieao 
Published: June 2022

Abstract
The moduli space for polarized hyperkähler manifolds of ${\textrm {K3}^{[m]}}$-type or ${\textrm {Kum}}_m$-type with a given polarization type is not necessarily connected, which is a phenomenon that only happens for $m$ large. The period map restricted to each connected component gives an open embedding into the period domain, and the complement of the image is a finite union of Heegner divisors. We give a simplified formula for the number of connected components, as well as a simplified criterion to enumerate the Heegner divisors in the complement. In particular, we show that the image of the period map may be different when restricted to different components of the moduli space.
Some New Results in Quantitative Diophantine Approximation
Authors: Ghosh Anish , Kumaraswamy V Vinay 
Published: June 2022

Abstract
In this article we establish two new results on quantitative Diophantine approximation for one-parameter families of diagonal ternary indefinite forms. In the first result, we consider quadratic forms taking values at prime points. In the second, we examine inhomogeneous forms of arbitrary degree taking values at integer points.
Resource Sharing in Households with Children: A Generalized Model and Empirical Evidence from the UK
Authors: Bargain Olivier , Donni Olivier , Hentati Imen 
Published: June 2022

AbstractWe suggest a generalized collective model of consumption that extends Browning, Chiappori, and Lewbel to couples with children. Economies of scale are defined using a general form of Barten scales. We identify resource sharing among household members and, originally, the contribution of each parent to the expenditure on children. We provide a tractable estimation approach based on a simple demand system for male and female clothing, that is, two exclusive goods commonly available in standard surveys. We illustrate the method on thirty years of expenditure data for the UK. We relax the independence of the sharing rule on total expenditure and actually find that women’s shares increase with living standards. This, and progress in education levels, explains most of the reduction in intra-household inequality over the period.
The complex of Fas-associated factor 1 with Hsp70 stabilizes the adherens junction integrity by suppressing RhoA activation
Authors: Song Soonhwa , Park Joon Kyu , Shin Sang Chul , Lee Jae-Jin , Hong Seung Kon , Song In-Kang , Kim Bokyung , Song Eun Joo , Lee Kong-Joo , Kim Eunice EunKyeong 
Published: June 2022

Abstract
Fas-associated factor 1 (FAF1) is a scaffolding protein that plays multiple functions, and dysregulation of FAF1 is associated with many types of diseases such as cancers. FAF1 contains multiple ubiquitin-related domains (UBA, UBL1, UBL2, UAS, and UBX), each domain interacting with a specific partner. In particular, the interaction of UBL1 with heat shock protein 70 (Hsp70) is associated with tumor formation, although the molecular understanding remains unknown. In this study, the structural analysis revealed that His160 of FAF1 is important for its interaction with Hsp70. The association of Hsp70 with FAF1 is required for the interaction with IQGAP1. FAF1 negatively regulates RhoA activation by FAF1–Hsp70 complex formation, which then interacts with IQGAP1. These steps play a key role in maintaining the stability of cell-to-cell junction. We conclude that FAF1 plays a critical role in the structure and function of adherens junction during tissue homeostasis and morphogenesis by suppressing RhoA activation, which induces the activation of Rho-associated protein kinase, phosphorylation of myosin light chain, formation of actin stress fiber, and disruption of adherens junction. In addition, depletion of FAF1 increased collective invasion in a 3D spheroid cell culture. These results provide insight into how the FAF1–Hsp70 complex acts as a novel regulator of the adherens junction integrity. The complex can be a potential therapeutic target to inhibit tumorigenesis and metastasis.
First Record ofBrachymeria podagrica(Hymenoptera: Chalcididae) in Bisha City, Asir Region, Saudi Arabia
Authors: Abd Al Galil Fahd Mohammed , Al-Keridis Lamya Ahmed , Al-Mekhlafi Fahd A , Al-Amri Abdulaziz Mohammed , Al-Khalifa Mohammed S 
Published: June 2022

AbstractChalcid Brachymeria podagrica (Fabricius), formerly known as Brachymeria fonscolombei (Dufour), is a parasitoid wasp that infests dipteran larvae of fly, Sarcophaga dux (Thomson), (Diptera: Sarcophagidae) recovered from the dead body of sheep in Bisha City, Asir region–Saudi Arabia. S. dux larvae were infested by B. podagrica. The first instar larvae and pupae of B. podagrica were found inside the larvae and pupae of S. dux. The adults of the parasitic wasp emerged from the pupae of the host. Adults and larvae of the parasitoid wasp were observed under a dissecting microscope. Identification was made by following the identification keys. It was confirmed that it was B. podagrica, which is herewith reported for the first time in Saudi Arabia.
Evaluation of antipsychotic medication adherence and its relation to negative and positive psychiatric symptoms
Authors: Khdour Maher , Salman Aroub 
Published: June 2022

Abstract

Objectives
The aim of this study was to assess antipsychotic medication adherence and its relation to Psychiatric symptoms in a sample of patients with schizophrenia in Palestine.

Methods
Patients were recruited from the governmental psychiatry clinic in Ramallah in a cross-sectional study. The self-reported Morisky–Green–Levine (MGL) scale was used to measure patients’ adherence. Psychiatric symptoms were measured using the expanded Brief Psychiatric Rating Scale (BPRS-E).

Key findings
Of the 130 participants in the study, 78 (60%) were men and mean age was 41.8 ± 9.8 years 70 (53.8%). of the sample participants were classified as low-adherent while 60 (46.2%) of patients classified as high adherent. That negative symptom scores of high adherence group are significantly lower than low adherence group (12.5 vs. 15.0, P = 0.002) and lower depression anxiety scores (18.3 vs. 22.1, P &lt; 0.001) indicated that high adherence group had lower depression, anxiety, social isolation, anxiety and suicidal ideation symptoms than low-adherence group. The multivariate regression model demonstrated that four variables remain significant and associated with nonadherence; no formal education (OR = 2.11; CI: 0.8–3.8; P = 0.04), age (OR = 2.88; CI: 1.2–4.4; P = 0.01), having comorbidity (OR = 3.2; CI: 1.9–4.3; P = 0.01) and having higher negative symptoms scores (OR = 2.5; CI: 1.2–3.9; P = 0.03); as they are positively correlated to nonadherence.

Conclusion
Medication nonadherence was significant, and it was linked to poor psychiatric outcomes and adherence scores were unaffected by medication-related variables.
Assessment of Jordanian physicians’ knowledge about venous thromboembolism risk and management among COVID-19 patients
Authors: Zaini Mohammad , Abu Farha Rana , Abutayeh Reem , Alsaud Wesam , Hammoudeh Ayman , Al-Shudifat Abdel-Ellah , Al-Kharabsheh Thamer 
Published: June 2022

Abstract

Objectives
The aim of this study was to assess Jordanian physicians’ awareness about venous thromboembolism (VTE) risk among COVID-19 patients and its treatment protocol.

Methods
This was a cross-sectional-based survey that was conducted in Jordan in 2020. During the study period, a convenience sample of physicians working in various Jordanian hospitals were invited to participate in this study. Physicians’ knowledge was evaluated and physicians gained one point for each correct answer. Then, a knowledge score out of 23 was calculated for each.

Key findings
In this study, 102 physicians were recruited. Results from this study showed that most of the physicians realize that all COVID-19 patients need VTE risk assessment (n = 69, 67.6%). Regarding VTE prophylaxis, the majority of physicians (n = 91, 89.2%) agreed that low molecular weight heparin (LMWH) is the best prophylactic option for mild-moderate COVID-19 patients with high VTE risk. Regarding severe/critically ill COVID-19 patients, 75.5% of physicians (n = 77) recognized that LMWH is the correct prophylactic option in this case, while 80.4% of them (n = 82) knew that mechanical prevention is the preferred prophylactic option for severe/critically ill COVID-19 patients with high bleeding risk. Moreover, 77.5% of physicians (n = 79) knew that LMWH is the treatment of choice for COVID-19 patients diagnosed with VTE. Finally, linear regression analysis showed that consultants had an overall higher knowledge score about VTE prevention and treatment in COVID-19 patients compared with residents (P = 0.009).

Conclusion
All physicians knew about VTE risk factors for COVID-19 patients. However, consultants showed better awareness of VTE prophylaxis and treatment compared with residents. We recommend educational workshops be conducted to enhance physicians’ knowledge and awareness about VTE thromboprophylaxis and management in COVID-19 patients.