bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Liquid-liquid phase Separation in 3D Genome Organization
Authors: Li Tingting , Xing Jiaqing , Li Tao , Li Teng , Li Weihua 
Published: September 2020

Abstract
Many proteins have been demonstrated to participate in 3D genome organization through liquid-liquid phase separation (LLPS) such as RNPII, HP1a. However, systematic investigation of relationships between LLPS and 3D genome organization remains lacking. Here, we predicted the intrinsic disordered regions (IDRs) and modular domains of all human proteins and performed GSEA analysis according to their proportions of IDRs. Our results showed that main biological processes involved in 3D genome organization are highly enriched with IDRs, including chromatin organization, RNA splicing and histone modification, demonstrating the key role of LLPS in regulating nuclear structure. Of the 3885 IDR-rich proteins, 1427 proteins are involved in 3D genome organization. IDR regions of these proteins have strong preference of Ser, Leu, Pro, Ala, Gly, Glu and Lys, and lack of hydrophobic amino acids such as Trp, Tyr, Phe and Met, suggesting dipolar interactions rather than aromatic-involved interactions involved. Further motif enrichment analysis suggests that RNA recognition motif and zinc finger motif are the two most abundant repeatedly-occurred modular domains within IDR-containing proteins. Finally, we developed a Shiny APP named phasepro that interactively analyze and visualize a protein’s potential of LLPS, including IDRs, motifs, amino acid preferences and electric charges.
The Effect of Cognitive- Behavioral Counseling on the Sexual Compatibility of New Married Couples: A Clinical Trial Study&nbsp;
Authors: Allahyari Parvin , Kolivand Mitra , Namdari Arash , Rahmani Khaled 
Published: September 2020

Abstract
Objective: sexual desire is an integral part of an identity and character of a human being, that affect how to behave with spouse. This study aimed to study the effect of cognitive-behavioral counseling (CBT) on sexual compatibility of new married couples in Sanandaj City in 2018. Method: This was a randomized clinical trial study and participants were 80 new married couples whose information was recorded at the premarital counseling centers that were randomly divided into intervention and control groups. Intervention group received 8 weekly 120-minute sessions of group consultation with cognitive-behavioral approach. Data were collected before the intervention, after 8 weeks of counseling, and two months after the last counseling session using the National Sexual Compatibility Scale. Data were analyzed using chi-square inferential statistics and independent t-test or nonparametric Mann-Whitney test. analysis of covariance was used to control of potential confounders. Results: The mean values of sexual compatibility in two intervention and control groups before counseling were 94.20±3.30 and 93.41±6.84 respectively. These scores reached to 100.11±2.96 in the intervention group and 98.83±3.66 in the control group immediately after the intervention. Also two months after the end of counseling, this rate was 101.98±4.03 in the intervention group and 98.83±3.66 in the control group. The intra-group comparison of sexual adjustment scores before and after counseling and two months after the intervention, showed a statistically significant difference (P <0.001). The trend of changes in the control group was not significant (P >0.05). There was a significant difference between two groups in level of scores two months after the intervention (P <0.001). Conclusion: CBT was effective in improving the level of sexual compatibility between new married couples. It is recommended to use this method of counseling, along with other services provided at pre-marriage counseling centers, to continue and improve the quality of sex and vitality of couples.
Comparing Efficacy of Cerclage and Adjunctive Therapy (Cerclage &amp; Pessary) in Prevention of Preterm Birth in Pregnant Women with Cervical Insufficiency: A Randomized Clinical Trial.
Authors: Arjmandifar Mitra , Moshfeghi Maryam , Mohammadi Maryam , Eftekhari Mahya 
Published: September 2020

Abstract
Background: Cervical insufficiency is the responsible factor for 15-25% of pregnancy loss in the second trimester. Midwifery specialists sometimes prefer to use adjunctive therapy in combination with cerclage surgery for management of cervical insufficiency. The aim of this study was to evaluate the effectiveness of adjunctive pessary therapy after cerclage in improving perinatal and neonatal outcome and increasing satisfaction in women with cervical insufficiency.Methods: This concurrent randomized clinical trial was conducted at the infertility department of Royan Institute, Tehran, Iran from May 2018 to May 2020. In this trial, 170 singleton pregnant women, diagnosed with cervical insufficiency, of gestational age 14 to 26 weeks, were enrolled. Patients were randomized 1:1 to receive either cervical cerclage or pessary after cerclage. The primary outcomes were gestational age at the time of delivery and the percentage of preterm labor (<37 weeks). The secondary outcomes were the method of delivery, neonatal outcomes, maternal adverse events and maternal satisfaction of interventions.Results: Preterm birth before 37 weeks of gestation occurred in 16 women (19.3%) in the pessary group and 17 women (21%) in the control group (between-group difference, 1.11%; 95%CI 0.518−2.388%). In the survival analysis to 37 WK of gestation, the incidence of preterm birth was not significantly different between the two groups (Relative Risk (RR), 1; 95%CI, 0.161-6.202). Based on survival analysis, the incidence of vaginal bleeding and pelvic pain significantly differed between the two groups (RR, 2.68; 95%CI (1.31-5.46)) and (RR, 1.73; 95%CI (1.04-2.87), respectively. The mean score of satisfaction in the intervention group (5.73) was significantly higher than the control group (5.25), (between-group difference, 0.47; 95%CI (0.10-0.84).Conclusions: The placement of an adjunctive pessary for pregnant women with singleton pregnancy and a cervical insufficiency, did not result in a lower rate of preterm delivery before 37 weeks of gestation compared to cerclage alone. However, the complications of pregnancy after the intervention until delivery, were less in these women, while the level of satisfaction was higher. Trial registration: Iranian Registry of Clinical Trials (IRCT20180302038914N1), May 5,2018.
The Long-term Recovery of Parotid Glands and Oral QOL&nbsp;in Nasopharyngeal Cancer Treated by Intensity-modulated Radiotherapy&nbsp;
Authors: Tasaka Shun , Jingu Keiichi , Takahashi Noriyoshi , Matsushita Haruo , Umezawa Rei , Yamamoto Takaya , Ishikawa Yojiro , Takeda kazuya , Suzuki Yu , Kadoya Noriyuki 
Published: September 2020

Abstract
BackgroundXerostomia is one of the most common adverse events of radiotherapy in head and neck cancer patients. The purpose of this study was to evaluate longitudinal volume the change of parotid gland after radiotherapy for nasopharyngeal cancer and the relationship between parotid irradiation dose and xerostomia symptoms.Methods We retrospectively analyzed longitudinal changing of parotid gland volumes in 20 patients treated by intensity-modulated radiotherapy (IMRT). We assessed xerostomia 4 years or more after IMRT by measuring the degree of oral moisture and oral QOL evaluation.ResultsThe relative parotid volumes at 0-6, 7-18, 19-30, 31-42, 43-54 and 55-66 months after IMRT were67.9 ± 10.1%, 67.7 ± 13.6%, 74.3 ± 12.5%, 75.8 ± 12.4%, 78.3 ± 17.4%, and 75.3% ± 17.7%, respectively. The parotid volume had recovered significantly at 31-42 months after IMRT, especially in parotid receiving less than 40 Gy. The mean irradiated dose for bilateral parotids showed negative correlations with oral QOL score and oral moisture. ConclusionThe mean irradiated dose for the parotid should be reduce as much as possible to improve oral QOL long after IMRT.
Designing an Evidence-Based Behavior Change Strategy to Promote Antibiotic Use in Primary Healthcare in Gezira State, Sudan
Authors: Lohiniva Anna-Leena , Elwali Einas S. , Abuobaida Duha , Abdulrahim Ashwag , Bukuluki Paul , Talaat Maha 
Published: September 2020

Abstract
Background: Abuse of antibiotics is a major contributing factor to the emergence of antibiotic resistance (ABR) globally. Misuse of antibiotics is common also in Sudan. Objectives: The project aimed to develop a theory driven behavior change strategy based on local understanding of drivers of antibiotic use at primary healthcare settings in Gezira State in Sudan. Methods: The strategy was designed based on the Theoretical Domains Framework to identify behavioral barriers and the Behavior Change Wheel to select appropriate behavior change techniques The process included (1) a formative qualitative research study (2) a knowledge co-production workshop that utilized the results of the qualitative study and aimed to design a salient, legitimate and credible behavior change strategy identifying relevant behavior change techniques (BCTs) to overcome key barriers. Results: The main TDF domains that emerged from the discussions were knowledge of antibiotics and AMR, skills to answer patient demand on antibiotics, prescription habits and work exhaustion, social influences, intention to change prescription practices and environmental factors. The main TDF domains that emerged through discussions with patients were antibiotic use habits, social influences, professional role belief in capabilities and intention to change. The workshop discussions resulted in the selection of five BTCs that included education, training, modeling, enablement and persuasion. Conclusion: This study, using the TDF and BCW taxonomy, identified that antibiotic prescribing is influenced by social and contextual factors. Knowledge co- production offered real benefits in addressing these complexities to come up with a set of context appropriate behavior change interventions.
Effects of the COVID-19 pandemic and lockdown on the mental and physical health of adults with Prader-Willi Syndrome
Authors: Mosbah Helena , Coupaye Muriel , Jacques Flavien , Tauber Maithé , Clément Karine , Oppert Jean-Michel , Poitou Christine 
Published: September 2020

Abstract
Background
Prader-Willi syndrome (PWS) is a neurodevelopmental disorder with hypothalamic dysfunction leading to obesity and behavioral disabilities, including eating disorders (EDs). We evaluated the effects of COVID-19 infection and lockdown on mental and physical health in PWS. At the end of April, 85 adults with PWS completed a self-administered questionnaire, including lockdown conditions, physical activity (PA), ED, and medical and behavioral outcomes. Body weight was measured at home and self-reported.
Results
Patients (53% women, 45% disomic) were assessed, with a mean age of 28.1 ± 8.7 years and body mass index (BMI) of 37 ± 11 kg/m². Seventy percent lived in the Paris region (France) and were confined with their parents. The mean weight change was 1.0 ± 3.3 kg. We compared patients showing weight loss (n = 39, -3.3 ± 2.9 kg) to patients showing weight gain (n = 22, + 2.3 ± 1.5 kg): BMI was lower (34.6 ± 9.2 versus 40.4 ± 9.5 kg/m², p = 0.02), PA increased (26% versus 5%, p = 0.04), and EDs improved (51% versus 14%, p = 0.005). Behavioral disorders increased for 13% of the cohort. Three individuals (3.5%) were diagnosed with non-severe COVID-19.
Conclusion
Lockdown during the COVID-19 pandemic was associated with positive effects in most French adults with PWS, with weight loss probably associated with a more favourable environment during this period. We observed no severe forms of COVID-19.
Could Graph Neural Networks Learn Better Molecular Representation for Drug Discovery? A Comparison Study of Descriptor-based and Graph-based Models
Authors: Jiang Dejun , Wu Zhenxing , Hsieh Chang-Yu , Chen Guangyong , Liao Ben , Wang Zhe , Shen Chao , Cao Dongsheng , Wu Jian , Hou Tingjun 
Published: September 2020

Abstract
Graph neural networks (GNN) has been considered as an attractive modelling method for molecular property prediction, and numerous studies have shown that GNN could yield more promising results than traditional descriptor-based methods. In this study, based on 11 public datasets covering various property endpoints, the predictive capacity and computational efficiency of the prediction models developed by eight machine learning (ML) algorithms, including four descriptor-based models (SVM, XGBoost, RF and DNN) and four graph-based models (GCN, GAT, MPNN and Attentive FP), were extensively tested and compared. The results demonstrate that on average the descriptor-based models outperform the graph-based models in terms of prediction accuracy and computational efficiency. SVM generally achieves the best predictions for the regression tasks. Both RF and XGBoost can achieve reliable predictions for the classification tasks, and some of the graph-based models, such as Attentive FP and GCN, can yield outstanding performance for a fraction of larger or multi-task datasets. In terms of computational cost, XGBoost and RF are the two most efficient algorithms and only need a few seconds to train a model even for a large dataset. The model interpretations by the SHAP method can effectively explore the established domain knowledge for the descriptor-based models. Finally, we explored use of these models for virtual screening (VS) towards HIV and demonstrated that different ML algorithms offer diverse VS profiles. All in all, we believe that the off-the-shelf descriptor-based models still can be directly employed to accurately predict various chemical endpoints with excellent computability and interpretability.
Tau Conformers in FTLD-MAPT&nbsp; Undergo Liquid-liquid Phase Separation and Perturb the Nuclear Envelope
Authors: Kang Sang-Gyun , Han Zhuang Zhuang , Daude Nathalie , McNamara Emily , Wohlgemuth Serene , Safar Jiri G. , Mok Sue-Ann , Westaway David 
Published: September 2020

Abstract
Background: Germline mutations in the MAPT gene cause some forms of frontotemporal lobar degeneration (FTLD). Recent studies show that a single mutation in MAPT can promote alternative tau misfolding pathways engendering divergent tau conforms and representing clinical heterogeneity, and that under conditions of cell-free molecular crowding the repertoire of tau forms can include liquid-liquid phase separation (LLPS). Methods: Neuronal nuclear morphologies in FTLD patients and TgTauP301L transgenic mice were analyzed by immunohistochemistry of nuclear lamina. Tau conformers associated with a common behavioral variant of frontotemporal dementia were cloned by endpoint dilution; the cells were assayed for viability and biochemical markers of cell death and were also assessed by video microscopy and photobleaching to determine dynamic aspects of aggregate formation.Results: Analysis of post-mortem tissues from aged neurologically normal controls and other neurodegenerative syndromes indicated that microtubule-associated nuclear clefts were associated with chronological aging and disruptions of the nuclear envelope with FTLD-MAPT. Tau conformers present in FTLD cases and transduced into reporter cells had a high propensity to condense on the nuclear envelope and to disrupt nuclear-cytoplasmic transport. Nuclear envelope fluorescent tau signals and small fluorescent inclusions in a stable clonal line behaved as a demixed liquid state under live cell conditions; indicative of LLPS effects, these droplets exhibited spherical morphology, fusion events and recovery from photobleaching. While pathogenic mutations in some proteins can interfere with physiological functions of membrane-less organelles, a disease-causing MAPT mutation perturbed nuclear-cytoplasmic transport by gain-of-function formation of LLPS on the nuclear envelope, this acting as a molecular cue to trigger regulated cell death. Thioflavin S-positive intracellular aggregates were prevalent in tau-derived inclusions with a size bigger than 3 µm2, inferring that a threshold of critical mass in the liquid state condensation may drive liquid-solid phase transitions. Conclusions: Our findings indicate that within a spectrum of alternative conformers, tau undergoing LLPS is a notably toxic species; demixed droplets on the nuclear envelope hindering nuclear-cytoplasmic transport can serve to trigger cytotoxic pathways and may act as nurseries for the abundant fibrillar structures present at end-stage disease.
Association between past tuberculosis epidemic and COVID-19-related mortality through latent infection by natural immunity
Authors: Inoue Kazuo , Kashima Saori 
Published: September 2020

Abstract
The coronavirus disease (COVID-19) pandemic has created a remarkable and varying impact in each region, which calls for broad attention. Recently, the Bacillus Calmette-Guérin (BCG) vaccination has been regarded as a potential candidate to explain this difference. Herein, we hypothesised that past tuberculosis epidemic may act as a latent explanatory factor for the worldwide difference in COVID-19 impact. We compared two indicators of past tuberculosis epidemic, namely, incidence (90 countries for the incidence rate in 1990) and mortality (28 countries for the mortality rate in 1950) with COVID-19 mortality rate. An inverse relationship exists between both past epidemic indicators and COVID-19 mortality. The rate ratio of the cumulative COVID-19 mortality per 1 million was 1.08 (95% confidence interval [CI]: 0.98–1.18) per 1 unit decrease in the incidence rate of tuberculosis per 100,000 people. This association existed even after adjusting for potential confounders (elderly rate, diabetes prevalence, mortality rate from cardiovascular disease, and gross domestic product per capita) [adjusted rate ratio: 1.05, 95% CI: (1.03–1.08)]. After latent infection, Mycobacterium tuberculosis survives in the human body and may continue to stimulate trained immunity for lifetime. Our study has revealed one possible mechanism underlying the region-based variation in the COVID-19 impact.
Sarcoglycan A Mutation in Miniature Dachshund Dogs Causes Limb Girdle Muscular Dystrophy 2D
Authors: Mickelson James R , Minor Katie M , Guo Ling T , Friedenberg Steven G , Cullen Jonah N , Ciavarella Amanda , Hambrook Lydia E , Brenner Karen M , Helmond Sarah E , Marks Stanley L , Shelton G Diane 
Published: September 2020

Abstract
BackgroundA cohort of related miniature dachshund dogs with exercise intolerance, stiff gait, dysphagia, myoglobinuria and markedly elevated serum creatine kinase activities were identified. MethodsMuscle biopsy histopathology, immunofluorescence microscopy, and western blotting, were combined to identify the specific pathologic phenotype of the myopathy, and whole genome SNP array genotype data and whole genome sequencing were combined to determine its genetic basis.ResultsMuscle biopsies were dystrophic. Sarcoglycanopathy, a form of limb-girdle muscular dystrophy, was suspected based on immunostaining and western blotting, where α, β, and γ-sarcoglycan were all absent or reduced. Genetic mapping and whole genome sequencing identified a premature stop codon mutation in the sarcoglycan A subunit gene ( SGCA ). Affected dachshunds were confirmed on several continents. ConclusionsThis first SGCA mutation found in dogs adds to the literature of genetic bases of canine muscular dystrophies and their usefulness as comparative models of human disease.
Inclusion double light refraction the apoplast in shoots development structure the Picea obovata and P. abies (Pinaceae)
Authors: Скупченко В.Б. 
Published: September 2020

Включения апопласта с двойным светопреломлением (ВАДС) обнаружены в паренхиме коры укороченного стебля зрелой почки. Исследование этих включений в электронном микроскопе показало, что они содержат электронопрозрачные компоненты, которые погружены в осмиофильную электроноплотную среду. Двойным светопреломлением включений оболочек клеток обладает липидный компонент, в кристаллической форме составляющий их наибольшую часть.

В формирующихся побегах ВАДС появляются вначале ранней весной в зачатках хвои. Затем ВАДС накапливаются в меристеме коровой паренхимы укороченного стебля новой терминальной почки. В последующем ВАДС откладываются в паренхиме коры удлиненного стебля охвоенной части молодого побега, который при этом включается в активный продольный рост. ВАДС, появившиеся в зонах активного роста тканей, остаются в них продолжительное время. В мезофилле хвои ВАДС располагаются на оболочках клеток, в основном обращенных к полостям межклетников.

Вероятно, в начале своего появления ВАДС образуют некоторый фонд метаболитов, участвующих в поддержании активных ростовых процессов меристем, расположенных под покровами почки. В дальнейшем, они могут представлять собой место депонирования метаболитов, выводимых из обмена веществ. Значительное накопление ВАДС, имеющих липофильное окружение, может вызвать торможение транспирации хвои и газообмена клеток мезофилла. Возможно, накопление ВАДС представляет собой один из факторов старения хвои и паренхимных тканей коры побегов.
Inclusion double light refraction the apoplast (VADS) are discovered in parenchyma cortexes shortcut stem mature bud. The research of these inclusion in electronic microscope has shown that they contain the electrontransparent components, which are shipped in osmiofil electrondencity ambience. Double light refraction inclusion cell walls hutches possesses lipid component in crystalline form forming their most part.

In development shoot VADS appear the early springtime in primordium needls. Then VADS are accumulated in meristem cortexes parenchyma shortcut stem new terminal bud. In the following VADS are postponed in parenchyma cortexes stem needls part of the young shoot, which is herewith included in active longitudal growing. VADS, come up for zone of the active growing fabric, remain long-lasting time in them. In mesophyll pine-needles VADS are situated on the walls of cells, basically turned to intercellular spaces.

Probably, at the beginning initially its appearances VADS form certain fund a metabolities, participating in maintenance active growing processes meristems, located under cover of the bud. Hereinafter, they can present itself place of the deposition metabolities, taken out from metabolism. The Significant accumulation VADS, having lipophyl encirclement, can cause the braking an transpiration to pine-needles and gas exchange of the cells mesophyll. Possible, accumulation VADS presents itself one of the factor of the ageing to pine-needles and parenchym tissues of the shoot cortex.