bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moonlighting protein prediction using physico-chemical and evolutional properties via machine learning methods
Authors: Shirafkan Farshid , Gharaghani Sajjad , Rahimian Karim , Sajedi Reza , Zahiri Javad 
Published: December 2020

Abstract
Background: Moonlighting proteins (MPs) are a subclass of multifunctional proteins in which more than one independent or usually distinct function occurs in a single polypeptide chain. Identification of unknown cellular processes, understanding novel protein mechanisms, improving the prediction of protein functions, and gaining information about protein evolution are the main reasons to study MPs. They also play an important role in disease pathways and drug-target discovery. Since detecting MPs experimentally is quite a challenge, most of them were detected randomly. Therefore, introducing an appropriate computational approach seems to be rational. Results: In this study, we would like to represent a competent model for detecting moonlighting and non-moonlighting proteins by extracted features from protein sequences. Then, we will represent a scheme for detecting outlier proteins. To do so, 15 distinct feature vectors were used to study each one's effect on detecting MPs. Furthermore, 8 different classification methods were assessed to find the best performance. To detect outliers, each one of the classifications was implemented 100 times by 10 fold cross-validation on feature vectors, then proteins which miss classified 80 times or more, were grouped. This process was applied to every single feature vector and in the end, the intersection of these groups was determined as the outlier proteins. The results of 10 fold cross-validation on a dataset of 351 samples (containing 215 moonlighting and 136 non-moonlighting proteins) show that the decision tree method on all feature vectors has the highest performance among all methods in this research and also in other available methods. Besides, the study of outliers shows that 57 of 351 proteins in the dataset could be an appropriate candidate for the outlier. Among the outlier proteins, there are non-moonlighting proteins (such as P69797) that have been misclassified by 8 different classification methods with 16 different feature types. Because these moonlighting proteins have been obtained by computational methods, the results of this study could reduce the likelihood of hypothesizing that, these proteins are non-moonlighting. Conclusions: Moonlighting proteins are difficult to identify by experiments. Our method enables identification of novel moonlighting proteins using distinct feature vectors. It also indicates that a number of non-moonlight proteins are likely to be moonlight.
Room-temperature Diffusion of Metal Clusters on Graphene
Authors: Zarshenas Mohammad , Gervilla Víctor , Sangiovanni Davide , Sarakinos Kostas 
Published: December 2020

Abstract
We study the diffusion dynamics, the diffusion mechanisms, and the adsorption energetics of Ag, Au, Cu, and Pd, dimers, as well as of Ag trimers on single-layer graphene (SLG) by means of ab initio molecular dynamics (AIMD) simulations and density-functional theory (DFT) calculations. The simulations show that Ag, Cu, and Au clusters exhibit a super-diffusive pattern characterized by long jumps, which can be explained by the flat potential energy landscape (PEL) (corrugation of a few tens of meV) encountered by those clusters on SLG. Pd dimers, instead, diffuse in a pattern that is reminiscent of conventional random walk, which is consistent with a significantly rougher PEL of the order of 100 meV. Moreover, our data show that all clusters exhibit diffusion mechanisms that include both concerted translation and rotation. The overall results of the present study provide key insights for modeling the growth of metal layers and nanostructures on graphene and other van der Waals materials, which is a prerequisite for the directed growth of multifunctional metal contacts in a broad range of enabling devices.
Thymol-based Chitosan Nanogels Have Strong Antibacterial and Anti-biofilm Effects on Multidrug-resistant Pathogens
Authors: Gharaghie Tohid Piri , Biranvand Sheida , Shirin Neda Jegargoshe , Elahianfar Yalda , Ghahari Somayeh , Ghahari Sajjad 
Published: December 2020

Abstract
Introduction: The discovery of antibiotics for the treatment of bacterial infections was one of the most important advances in medical history, but unfortunately bacteria are highly adaptable, and overuse of antibiotics has made many bacteria resistant to antibiotics. In the present study, the antibacterial and antibiofilm effects of Thymol-based chitosan nanogels were investigated.Materials & Methods:After clinical screening of MDR strains from the hospital environment, the morphological characteristics of the synthesized nanoparticles were identified using SEM, DLS, XRD and FTIR and the efficiency of encapsulation, stability and drug release were evaluated. After determining the MIC concentration of nanoparticles, the expression of OmpA and PgaB biofilm genes were determined by q-Real-Time PCR and the antibacterial and cytotoxic properties of the nanoparticles were determined by well diffusion and MTT methods, respectively.Results:Three bacteria Pseudomonas, Acinetobacter and Staphylococcus were identified as MDR strains and the antibacterial and antibiofilm properties of nanoparticles with a size of 82.71 nm, encapsulation efficiency of 76.54% and stability up to 60 days at 4 °C were evaluated. The results of the biological study showed strong antibacterial properties of Thymol-based chitosan nanoparticles by reducing the expression of OmpA and PgaB biofilm genes at a significant level of P ≤ 0.05 and reducing antibiotic resistance compared to the free drug thymol and chitosan nanogels. Thymol-based chitosan nanogels at concentrations of 0.125 to 256μg/mL showed the lowest cytotoxicity against HEK-293 compared to chitosan and free Thymol nanogels.Discussion and Conclusion: The results of the study showed the very strong antibacterial properties of Thymol-based chitosan nanogels against MDR strains such as Staphylococcus, Acinetobacter and Pseudomonas as the challenging bacteria of the century. Therefore, the use of Thymol-based chitosan nanogels can be reported as a new application strategy with high potential in the pharmaceutical industry.
Analysis of Cytokines in Serum and Bronchoalveolar Lavage Fluid in Patients with Immune-Checkpoint Inhibitor Associated Pneumonitis: a Parallel Cohort Study
Authors: Kowalski Benedikt , Valaperti Alan , Steiner Urs C , Scholtze Dieter , Wieser Stephan , Vonow-Eisenring Maya , Widmer Andrea , Bezel Pascal , Kohler Malcolm , Franzen Daniel 
Published: December 2020

Abstract
BackgroundImmune-checkpoint inhibitors (ICI) present a new treatment for malignancies by boosting the immune system. This has led to a variety of immune-related adverse events, including ICI-associated pneumonitis (ICIaP). Diagnosis thereof is often challenging, and its pathogenesis has not yet been fully understood. The aim of this parallel cohort study was to investigate cytokines in serum and bronchoalveolar lavage fluid (BALF) expressed in patients with ICI-associated pneumonitis compared to healthy individuals.MethodsFrom January 2018 until June 2019, 401 adult patients with various lung diseases were prospectively enrolled in a BALF- and serum biobank, called BALOTHEK. Of these, 12 patients were diagnosed with ICIaP (Pembrolizumab, Ipilimumab, or both, and Durvalumab) and included in this parallel cohort study. Additionally, 12 healthy subjects from the biobank served as matched control group. The following 11 cytokines were simultaneously analyzed in BALF and serum of each study participant: interferon gamma, tumor necrosis factor alpha, interleukin (IL) 1b, IL-2, IL-4, IL-5, IL-6, IL-8, IL-12p70, IL-13 and IL-17A. This study was approved by the local ethic review committee (BASEC-ID 2017-02307 and 2018-01724).ResultsAbsolute number and percentage of lymphocytes in BALF of patients with ICIaP were significantly higher compared to control group. For the investigated cytokines in serum and BALF, a significant increase of IL-6 levels was shown for patients with ICIaP (p=0.044, adjusted for multiple comparisons). ConclusionCytokine profile assessed in BALF shows promising potential for facilitating diagnosis and understanding of pathophysiology of ICIaP. IL-6 may not only contribute to better understanding of pathophysiology but also herald therapeutic implications for Tocilizumab.
Mining peptides against SARS-CoV-2 entry from constructed RBMs-hACE2 isomer libraries using machine learning and molecular docking
Authors: He Xiaotong 
Published: December 2020

Abstract
Cellular entry of SARS-CoV-2 initiates from the protein-protein interactions (PPIs) between viral surface protein S and human angiotensin converting enzyme 2 (hACE2). Peptide-based drugs have the advantage of small molecule compounds to block such viral-host PPIs. Thus the viral targetregions on hACE2 have been believed as promising templates for designing specific inhibitory peptides against SARS-CoV-2 infection. However, starting from a few potential templates, in silico design and prediction between binding affinity and bioactivities in vivo are very challenging, herein a novel design strategy was implemented by mining constructed template isomer libraries using feature filters, supervised classifier and peptide protein docking.Applying these methods and the isomer libraries, 4 peptides were identified from 12 millions candidates owing to their distinct stability, interaction activity, inhibitory specificity, binding affinity, transmembrane potentials and effective conformation. These results have supplied a panel of specific anti-COVID19 leads for further drug development, supporting a new feasible antiviral strategy for targeting both intracellular and extracellular SARS-CoV-2 S proteins simultaneously. The methods have provided a useful tool for mining antiviral-peptides against viral diseases.
Role of Social Network in Decision Making for Increasing Uptake and Continuing Use of Long Acting Reversible (LARC) Methods in Pakistan
Authors: Sarfraz Mariyam , Hamid Saima , Rawstorne Patrick , Ali Moazzam , Jayasuriya Rohan 
Published: December 2020

Abstract
Background: Despite evidence from recent Demographic Health Surveys that show 98% of the adult Pakistani population have an awareness of at least one modern contraceptive method, only 25% of married couples in Pakistan used a modern method of contraception. Of the modern contraceptive methods, LARC usage has increased only, from 2.1% to 3%. This low uptake is puzzling in the context of high awareness of LARC methods and its availability through public sector facilities at subsidized costs. This study aimed to understand the social influences in initiating and continuing use of an LARC methods for contraception in a rural setting in Pakistan.Methods: In-depth interviews were conducted with 27 women who were using a LARC method for contraception. Data was managed using NVivo 12 and themes were identified using a comparative content analysis approach to analyze the transcripts.Results: Four key themes, supported by sub-themes relating to a temporal model, was identified to explain women’s experiences with initiating and continuing use of a LARC. The themes were (i) Use of trusted networks for information on LARCs; (ii) Personal motivation and family support in decision to use LARC; (iii) Choice of LARC methods and access to providers; and (iv) Social and professional support instrumental in long term use of LARC. Results highlight the significant role of immediate social network of female family members in supporting the women in initiating LARCs and maintaining their use.Conclusion: This study contributes to an in depth understanding of the decision-making process of women who adopted LARC and maintained its use. Women who proceeded to use an LARC and who persisted with its use despite the experience of side effects and social pressures, were able to do so with support from other female family members and spouse.
Delimiting cryptic species in a shark with a low dispersal capability
Authors: Fahmi Fahmi , Tibbetts Ian , Bennett Mike , Dudgeon Chris 
Published: December 2020

Abstract
BackgroundDelimiting cryptic species in elasmobranchs is a major challenge in modern taxonomy due the lack of available phenotypic features. Employing stand-alone genetics in splitting a cryptic species may prove problematic for further studies and for implementing conservation management. In this study, we examined mitochondrial DNA and genome-wide nuclear single nucleotide polymorphisms (SNPs) in the brown-banded bambooshark, Chiloscyllium punctatum to evaluate potential cryptic species and the species-population boundary in the group.ResultsOur results found four operational taxonomic units (OTUs) within C. punctatum from the Indo-Australian region. Each OTU can be interpreted differently depending on available supporting information. Similarly, we confirmed that comprehensive sampling over the species' geographic distribution was essential to determine the boundary between population and cryptic species.ConclusionWe provide suggestions about what should be considered prior to split cryptic species and the designation of new species.
Depression in patients with knee osteoarthritis: risk factors and associations with joint symptoms
Authors: Zheng Shuang , Tu Liudan , Cicuttini Flavia , Zhu Zhaohua , Han Weiyu , Antony Benny , Wluka Anita E. , Winzenberg Tania , Aitken Dawn , Blizzard Leigh , Jones Graeme , Ding Changhai 
Published: December 2020

Abstract
Background: To describe demographic and clinical factors associated with the presence and incidence of depression and explore the temporal relationship between depression and joint symptoms in patients with symptomatic knee osteoarthritis (OA). Methods: 397 participants were selected from a randomized controlled trial in people with symptomatic knee OA and vitamin D deficiency (age 63.3 ± 7.1 year, 48.6% female). Depression severity and knee joint symptoms were assessed using the patient health questionnaire (PHQ-9) and the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), respectively, at baseline and 24 months. Results: The presence and incidence of depression was 25.4% and 11.2%, respectively. At baseline, having younger age, a higher body mass index (BMI), greater scores of WOMAC pain (PR: 1.05, 95%CI:1.03, 1.07), dysfunction (PR: 1.02, 95%CI:1.01, 1.02) and stiffness (PR: 1.05, 95%CI: 1.02, 1.09), lower education level, having more than one comorbidity and having two or more painful body sites were significantly associated with a higher presence of depression. Over 24 months, being female, having a higher WOMAC pain (RR: 1.05, 95%CI: 1.02, 1.09) and dysfunction score (RR: 1.02, 95%CI: 1.01, 1.03) at baseline and having two or more painful sites were significantly associated with a higher incidence of depression. In contrast, baseline depression was not associated with changes in knee joint symptoms over 24 months. Conclusion: Knee OA risk factors and joint symptoms, along with co-existing multi-site pain are associated with the presence and development of depression. This suggests that managing common OA risk factors and joint symptoms may be important for prevention and treatment depression in patients with knee OA.Trial registration: ClinicalTrials.gov identifier: NCT01176344Anzctr.org.au identifier: ACTRN12610000495022
Comparative study on lesions of reproductive disorders of cows and female dromedary camels slaughtered at Addis Ababa, Adama and Akaki abbatoirs with bacterial isolation and characterization
Authors: Mandefro Aynalem , Ayana Tilaye Demissie , Hunderra Gemechu Chala , Gebrezihar Tadesse Gidey , Boru Bulto Giro , Desta Natnael Teshager 
Published: December 2020

Abstract
Background: Reproduction is a basic prerequisite to efficient livestock production. Reproductive performance depends upon the normal structure and function of genital organs. Methods: A cross-sectional study was conducted from November 2016 to May 2017 to identify and compare the frequency of pathological lesions in the reproductive tract and to isolate bacteria associated to uterine lesions in female dromedary camels and cows slaughtered at Akaki camel slaughter house and Addis Ababa and Adama municipal abattoirs. Abattoirs were visited once per week for 28 weeks during which three to seven animals on average were slaughtered per day. A purposive sampling technique was employed to examine reproductive tracts of all slaughtered animals (280; 140 cows and 140 camels). Following gross inspection at abattoirs, tissue samples with lesion were collected for histopathological and bacteriological investigation. Result: Various pathological lesions with different degrees of severity were observed in 48 (34.2%) and 51 (36.4%) of dromedary camels and cows, respectively. Uterine lesions were the most prevalent 21.4% lesions observed in dromedary camels followed by ovarian lesions 7.14%; while in cows, ovarian lesions were the major prevalent 16.4% lesions followed by uterine lesion 14.2%. The result showed that there were 56 bacteria isolated from cows uterine lesion with Staphylococcus species 28.5%, Streptococci species 19.6%, Coynebacterium species 8.9%, Escherichia coli 26.78%, Salmonella species 10.7% and Klebsiella species 5.35% being the prominent isolates; while in camels, there were 45 bacteria isolated with Escherichia coli 35.5%, Staphylococcus species 26.6%, Streptococcus species 13.3%, Pseudomonas species 6.6 %, Proteus species 4.4%, Salmonella species 8.8% and Klebsiella species 4.4% being the most frequently isolated. The result showed that the major isolates were similar with slightly higher in cows. Histopathologically, endometrial glands degeneration, sloughing of epithelium, peri-glandular cuffing and infiltrations of inflammatory cell were some of characteristic changes observed in uterus. Conclusions: Pathological lesions in reproductive organs in female dromedary camels and cows showed great prevalence, with similarity in bacterial isolates between the two species. The role of each reproductive lesions and bacterial isolates incriminated as causes of reproductive failures in this livestock species needs further investigation.
A systematic review assessing the under-representation of elderly adults in COVID-19 trials
Authors: Prendki Virginie , Tau Noam , Avni Tomer , Falcone Marco , Huttner Angela , Kaiser Laurent , Paul Mical , Leibovici-Weissmann Yaara , Yahav Dafna 
Published: December 2020

Abstract
BackgroundCoronavirus disease (COVID-19) has caused a pandemic threatening millions of people worldwide. Yet studies specifically assessing the geriatric population are scarce. We aimed to examine the participation of elderly patients in therapeutic or prophylactic trials on COVID-19.MethodsIn this review, randomized controlled trials (RCTs; n=12) comparing therapeutic or prophylactic interventions registered on preprint repositories and/or published since December 2019 were analyzed. We searched in PubMed, leading journals websites, and preprint repositories for RCTs and large observational studies. We aimed to describe the age of included patients, the presence of an upper age limit and of adjusted analyses on age, any exclusion criteria that could limit participation of elderly adults such as comorbidities, cognitive impairment, limitation of life expectancy; and the assessment of long-term outcomes such as the need of rehabilitation or institutionalization. Mean participant ages were reported and compared with observational studies.ResultsTwelve RCTs assessing drug therapy for COVID-19 were included. Mean age of patients included in RCTs was 56.3 years. An upper age limit was applied in three published trials (25%) and in 200/650 (31%) trials registered at clinicaltrials.gov. One trial reported a subgroup analysis in patients ≥65. Patients were excluded for liver-function abnormalities in eight trials, renal disease in six, cardiac disease or risk of torsade de pointes in five, and four for cognitive or mental criteria, which are frequent comorbidities in the oldest patients. Only three trials allowed a family member to provide consent. Patients enrolled in RCTs were on average 20 years younger than those included in large (n≥1000) observational studies. Seven studies had as their primary outcome a clinical endpoint, but none reported cognitive, functional or quality of life outcomes or need for rehabilitation or long-term care facility placement.ConclusionsElderly patients are clearly underrepresented in RCTs, although they comprise the population hardest hit by the COVID-19 pandemic. Long-term outcomes such as the need of rehabilitation or institutionalization were not reported. Future investigations should target specifically this vulnerable population.
IFI27 may predict and evaluate the severity of respiratory syncytial virus infection in preterm infants
Authors: Gao Junyan , Zhu Xueping , Wu Mingfu , Jiang Lijun , Wang Fudong , He Shan 
Published: December 2020

Abstract
Background: Preterm infants are a special population that vulnerable to respiratory syncytial virus (RSV) infection and the lower respiratory tract infections (LRTIs) caused by RSV could be severe and even life-threating. The purpose of the present study was to identify candidate genes of preterm infants who are susceptible to RSV infection and provide a new insight into the pathogenesis of RSV infection.Methods: Three datasets (GSE77087, GSE69606 and GSE41374) containing 183 blood samples of RSV infected patients and 33 blood samples of healthy controls from Gene Expression Omnibus (GEO) database were downloaded and the differentially expressed genes (DEGs) were screened out. The function and pathway enrichments were analyzed through Database for Annotation, Visualization and Integrated Discovery (DAVID) website. The protein‐protein interaction (PPI) network for DEGs was constructed through Search Tool for the Retrieval of Interacting Genes (STRING). The module analysis was performed by Cytoscape software and hub genes were identified. Clinical verification was employed to verify the expression level of top five hub genes among 72 infants including 50 RSV infected patients and 22 non-RSV-infected patients hospitalized in our center. Further, the RSV infected infants with high-expression IFI27 and those with low-expression IFI27 were compared (defined as higher or lower than the median mRNA level). Finally, the gene set enrichment analysis (GSEA) focusing on IFI27 was carried out.Results: Totally, 4028 DEGs were screened out and among which, 131 most significant DEGs were selected. Subsequently, 13 hub genes were identified, and function and pathway enrichments of hub genes mainly were: response to virus, defense response to virus, regulation of viral genome replication and regulation of viral life cycle. Furthermore, IFI27 was confirmed to be the most significantly expressed in clinical verification. Gene sets associated with calcium signaling pathway, arachidonic acid metabolism, extracellular matrix receptor interaction and so on were significantly enriched when IFI27 was highly expressed. Moreover, high-expression IFI27 was associated with more severe cases (p=0.041), more requirements of mechanical ventilation (p=0.034), more frequent hospitalization (p<0.001) and longer cumulative hospital stay (p=0.012).Conclusion: IFI27 might serve to predict RSV infection and evaluate the severity of RSV infection in preterm infants.