Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication protein A (RPA) sumoylation positively influences the DNA damage checkpoint response in yeast

The DNA damage response relies on protein modifications to elicit physiological changes required for coping with genotoxic conditions. Besides canonical DNA damage checkpoint–mediated phosphorylation, DNA damage–induced sumoylation has recently been shown to promote genotoxin survival. Cross-talk between these two pathways exists in both yeast and human cells. In particular, sumoylation is required for optimal checkpoint function, but the underlying mechanisms are not well-understood. To address this question, we examined the sumoylation of the first responder to DNA lesions, the ssDNA-binding protein complex replication protein A (RPA) in budding yeast (Saccharomyces cerevisiae). We delineated the sumoylation sites of the RPA large subunit, Rfa1 on the basis of previous and new mapping data. Findings using a sumoylation-defective Rfa1 mutant suggested that Rfa1 sumoylation acts in parallel with the 9-1-1 checkpoint complex to enhance the DNA damage checkpoint response. Mechanistically, sumoylated Rfa1 fostered an interaction with a checkpoint adaptor protein, Sgs1, and contributed to checkpoint kinase activation. Our results suggest that SUMO-based modulation of a DNA damage sensor positively influences the checkpoint response.
Inhomogeneity of Free Volumes in Metallic Glasses under Tension

In this work, the deformation of Zr2Cu metallic glass (MG) under uniaxial tensile stress was investigated at the atomic level using a series of synchrotron radiation techniques combined with molecular dynamics simulation. A new approach to the quantitative detection of free volumes in MGs was designed and it was found that free volumes increase in the elastic stage, slowly expand in the yield stage, and finally reach saturation in the plastic stage. In addition, in different regions of the MG model, free volumes exhibited inhomogeneity under stress, in terms of size, density, and distribution. In particular, the expansion of free volumes in the center region was much more rapid than those in the other regions. It is interesting that the density of free volumes in the center region abnormally decreased with strain. It was revealed that the atomic-level stress between different regions may contribute to the inhomogeneity of free volumes under stress. In addition, the inhomogeneous change of free volumes during the deformation was confirmed by the evolution of local atomic shear strains in different regions. The present work provides in-depth insight into the deformation mechanisms of MGs.
HyperTools: A Python toolbox for visualizing and manipulating high-dimensional data

Data visualizations can reveal trends and patterns that are not otherwise obvious from the raw data or summary statistics. While visualizing low-dimensional data is relatively straightforward (for example, plotting the change in a variable over time as (x,y) coordinates on a graph), it is not always obvious how to visualize high-dimensional datasets in a similarly intuitive way. Here we present HypeTools, a Python toolbox for visualizing and manipulating large, high-dimensional datasets. Our primary approach is to use dimensionality reduction techniques (Pearson, 1901; Tipping & Bishop, 1999) to embed high-dimensional datasets in a lower-dimensional space, and plot the data using a simple (yet powerful) API with many options for data manipulation [e.g. hyperalignment (Haxby et al., 2011), clustering, normalizing, etc.] and plot styling. The toolbox is designed around the notion of data trajectories and point clouds. Just as the position of an object moving through space can be visualized as a 3D trajectory, HyperTools uses dimensionality reduction algorithms to create similar 2D and 3D trajectories for time series of high-dimensional observations. The trajectories may be plotted as interactive static plots or visualized as animations. These same dimensionality reduction and alignment algorithms can also reveal structure in static datasets (e.g. collections of observations or attributes). We present several examples showcasing how using our toolbox to explore data through trajectories and low-dimensional embeddings can reveal deep insights into datasets across a wide variety of domains.
Instant Outcome Evaluation of Microwave Ablation With Subtraction CT in an In Vivo Porcine Model

Objectives The aim of this study was to investigate whether the accuracy of multislice contrast-enhanced computed tomography (MS-CECT) may be improved by performing additional subtraction CT. Materials and Methods Thirty-five microwave ablations were performed under CT guidance in 12 healthy and anesthetized pigs. Preablation and postablation MS-CECT scans were obtained in arterial and venous contrast phases. These scans were reconstructed and subtracted from each other. Lesion size was measured in a region of interest drawn around the ablation area. Computed tomography measurements were compared with standardized macroscopic images of explanted liver tissue, obtained immediately after ablation. Paired correlation and Bland-Altman analyses were performed for assessing agreement between modalities and ratings. Results The correlation between lesion size measured in CT and histology was very strong for subtracted images (r = 0.91; 95% confidence interval [CI], 0.8–0.96) and strong for standard MS-CECT images (r = 0.85; 95% CI, 0.68–0.93). Interrater agreement for all measurements was excellent (intraclass correlation coefficient, 0.99; 95% CI, 0.98–0.99 for subtraction and intraclass correlation coefficient, 0.99; 95% CI, 0.98–1.00 for MS-CECT). All differences were statistically significant (P < 0.05). Conclusions Subtraction CT was superior to nonsubtracted MS-CECT in measurement of liver lesion size after microwave ablation in a porcine model, achieving a very strong correlation with pathologic measurement and a significantly lower overestimation of lesion size compared with MS-CECT.
Perinatal diagnosis and management of early-onset Marfan syndrome: case report and systematic review

Abstract Early onset Marfan syndrome is the most severe form of Marfan syndrome diagnosed during perinatal period. Early onset Marfan syndrome is associated with high mortality rates, usually within the first 2 years of life. First, we present a case of prenatally diagnosed early onset Marfan syndrome in a dichorionic diamniotic twin pregnancy, where suspicion was raised at 35 weeks of gestation. Ultrasound and fetal magnetic resonance imaging were used to assess prenatal findings in the affected fetus. She presented right diaphragmatic eventration, elongation of humerus and femur and subluxation of the crystalline lens. She died 3 months after birth. Secondly, we present a PubMed-based review of the published articles on early onset Marfan syndrome, with pre- or postnatal suspicion or diagnosis. We found 39 articles published between 1981 and 2017, arising information on 55 cases. Including ours, early onset Marfan syndrome was prenatally diagnosed in 34.54% of the cases. In these cases, the most frequent prenatal findings were cardiomegaly, dilatation of the great vessels and mitral or tricuspid regurgitation. Mortality rate during the first 15 months after birth was 73.68%. In the postnatally diagnosed cases, the most frequent findings were arachnodactyly, dilatation of the great vessels and mitral or tricuspid regurgitation. Mortality rate was 61.11%. Overall genetic confirmation was performed in 67.27% of the cases. Prenatal diagnosis of early onset Marfan syndrome is challenging but of utmost importance, since management should take place in a tertiary care center, by a multidisciplinary team. Differential diagnosis is essential in order to perform an adequate genetic counseling.
The Influence of Harsh Parenting and Parental Warmth During Childhood on Later Involvement in Prison Misconduct

Research has shown that childhood victimization is associated with later involvement in delinquency. Prevalence rates of childhood victimization also tend to be higher among prison inmates compared with the general population. However, it has rarely been examined if childhood experiences—both negative and positive—have an effect on prison misconduct. We analyzed self-report data from more than 4,800 male and female adult prisoners in Germany to examine if childhood experiences of harsh parenting and parental warmth are associated with physical inmate-on-inmate violence. We also assessed the inmates’ attitude toward violence and examined if violence approval mediates the relationship between childhood experiences and violent misconduct. The results of the structural equation models show that both harsh parenting and positive, caring parental behavior have a small, but significant effect on violent prison misconduct, which is completely mediated by the inmates’ attitude toward violence. Furthermore, the results suggest that the same model holds for both male and female inmates, indicating that childhood victimization is not a gender-responsive need. The strength of the direct association between violence approval and violent misconduct underscores the need to assess the inmates’ attitude toward violence to identify those most at risk of engaging in violence during incarceration.
Kiekie, a new Neotropical spider genus of Ctenidae (Cteninae, Araneae).

Kiekie gen. nov. is newly proposed to accommodate 11 Neotropical Ctenidae species. With the exception of one species from Colombia, they are all distributed in Central America. Two species are transferred from Ctenus: Kiekie sinuatipes (F.O. Pickard-Cambridge, 1897) comb. nov. from Costa Rica, and K. curvipes (Keyserling, 1881) comb. nov., with broader distribution from Mexico to Panama. Ctenus incolans (F.O. Pickard-Cambridge, 1900) is synonymized with Kiekie curvipes. Nine species are newly described. Kiekie garifuna sp. nov. was collected in Guatemala and Honduras. Four species were collected in Costa Rica: Kiekie sanjose sp. nov., K. verbena sp. nov., K. sarapiqui sp. nov., and K. griswoldi sp. nov. Two species were collected in Panama: Kiekie barrocolorado sp. nov. and K. panamensis sp. nov. Kiekie montanensis sp. nov. was collected in Costa Rica and Panama. Kiekie antioquia sp. nov., from Colombia, was the only species collected in South America. To support the description and further identification of the genus and its species, we provide illustrations of male and female genitalia, habitus and modified metatarsus of the male leg IV, measurements and diagnostic characters. We also provide a distributional map of the specimens herein recorded. Taxonomic changes are based in recent cladistics analysis, showing that at least two species belong to a well-supported clade, sister group of Africactenus Hyatt, 1954. We discuss the phylogenetic relationship of the group and the evolution of key morphological characters.
Stafne bone defects radiographic features in panoramic radiographs: Assessment of 91 cases

Background To evaluate 91 cases of Stafne bone defect (SBD) in panoramic radiographs (PR) to determine the prevalence of different SBD variants, considering age, gender, and side. Additionally, to assess the most frequent imaging features of SBD. Material and Methods Participant data were collected from 91 SBD cases with PR imaging. First, SBDs were classified according to their location, as anterior, posterior, or ramus variant. SBD imaging features were classified according to radiographic imaging findings, assessing margins, degree of internal radiolucency, shape, topographic relationship between the defect and mandibular border, location of the defect according to mandibular teeth, and locularity. The topographic relationship between the SBD and the mandibular canal was described for the inferior variant only. Mean sizes were also described. Results A total of 92 SBD cases were evaluated from 91 radiographs. One case presented multiple defects. Mean patient age was 60.80 years. Men were more affected than women. The most frequent SBD variant was the posterior variant, and the least frequent was the ramus variant. The most observed radiographic features were thick sclerotic bone margin in the entire contour of the defect, partially radiolucent internal content, oval shape, continuity with mandible base without discontinuity of mandible border, third molar region location, and unilocular shape. With the posterior variant only, the most common topographic relationship between the defect and the upper wall of the mandibular canal was the defect located below the upper wall and continuous with the inferior wall of the mandibular canal. Conclusions The knowledge of common SBD radiographic imaging features in PR can help dental practitioners with the differential diagnosis of SBD. Key words:Panoramic radiograph, mandible, bone cysts, salivary glands, Stafne bone defect.
Inhibitory effects of fruit berry extracts on Streptococcus mutans biofilms

Dark-colored fruit berries are a rich source of polyphenols that could provide innovative bioactive molecules as natural weapons against dental caries. High-quality extracts of cranberry, blueberry, and strawberry, and a combination of the three berry extracts (Orophenol), were used to treat 24-h-old Streptococcus mutans biofilms. The grown biofilms were treated with the berry extracts at concentrations ranging from 62.5 to 500 μg ml-1 . Treated biofilms were assessed for metabolic activity, acidogenicity, biovolumes, structural organization, and bacterial viability. The biofilms treated with the cranberry and Orophenol extracts exhibited the most significant reductions in metabolic activity, acid production, and bacterial/exopolysaccharide (EPS) biovolumes, while their structural architecture appeared less compact than the control-treated biofilms. The blueberry extract produced significant reductions in metabolic activity and acidogenicity only at the highest concentration tested, without significantly affecting bacterial/EPS biovolumes or biofilm architecture. Strawberry extracts had no significant effects on S. mutans biofilms. None of the berry extracts were bactericidal for S. mutans. The results indicate that cranberry extract was the most effective extract in disrupting S. mutans virulence properties without significantly affecting bacterial viability. This suggests a potential ecological role for cranberry phenols as non-bactericidal agents capable of modulating pathogenicity of cariogenic biofilms.
Association of Malnutrition Inflammation Score With Anthropometric Parameters, Depression, and Quality of Life in Hemodialysis Patients

Abstract Objective: Hemodialysis patients may be at risk for malnutrition due to catabolic effects caused by dialysis, loss of amino acids, inadequate nutrient intake, acidosis, and inflammation. Malnutrition may have negative effects on quality of life, mortality, and disease prognosis. This study was conducted to determine the relationship between anthropometric parameters, depression, and quality of life with Malnutrition Inflammation Score (MIS) on 55 patients aged between 18 and 65 years (36 males and 19 females) who have dialysis treatment for 3 days per week for at least 3 months due to end-stage renal disease. Methods: Patients were evaluated with MIS, Subjective Global Assessment (SGA), Beck Depression Inventory (BDI), and Satisfaction with Life Scale (SWLS). In addition, anthropometric (body weight, height, mid-upper arm circumference [MUAC]) and body composition measurements of patients were taken, body mass index (BMI) values were calculated, and biochemical parameters (albumin, C-reactive protein [CRP], and total iron binding capacity [TIBC]) were analyzed. Results: At the end of the study, 14.5% of the patients according to SGA, were classified as malnourished. There was a statistically significant positive correlation of BDI, duration of dialysis, and CRP with MIS. However, MIS had a statistically significant negative correlation with SWLS, body weight, and MUAC (p < 0.05). Conclusion: MIS is an effective screening tool for assessing malnutrition and quality of life in hemodialysis patients. However, there is a need for studies to identify cutoff points of MIS.
Scribble-Based 3D Shape Segmentation via Weakly-Supervised Learning

Shape segmentation is a fundamental problem in shape analysis. Previous research shows that prior knowledge helps to improve the segmentation accuracy and quality. However, completely labeling each 3D shape in a large training data set requires a heavy manual workload. In this paper, we propose a novel weakly-supervised algorithm for segmenting 3D shapes using deep learning. Our method jointly propagates information from scribbles to unlabeled faces and learns deep neural network parameters. Therefore, it does not rely on completely labeled training shapes and only needs a really simple and convenient scribble-based partially labeling process, instead of the extremely time-consuming and tedious fully labeling processes. Various experimental results demonstrate the proposed method's superior segmentation performance over the previous unsupervised approaches and comparable segmentation performance to the state-of-the-art fully supervised methods.
Study of DNA-Binding Activity and Antibacterial Effect of Escitalopram Oxalate, an Extensively Prescribed Antidepressant

Abstract Escitalopram oxalate (EO) is considered as one of the extensively prescribed antidepressant drug in Turkey and some other countries, therefore this research was aimed to study the interaction of the drug with DNA and study of the substance effect on bacterial growth. The absorption value of the drug solution at 238 nm was increased when DNA was added gradually to it and it showed hyperchromism effect. The value obtained for DNA binding constant (Kb) was 0.035 M −1. When we added the CuCl2 2H2O to the mixture, any breakage was not shown in double strand DNA in comparison with control DNA. In addition low concentration of EO couldn’t protect DNA (0.5273 µmole bp) against Hydroxyl free radical (0.12 µmole) although it could protect the DNA when it was at the same or higher concentrations (0.5273, 5.273 and 252.73 µmole) than the DNA concentration. In addition, MIC of the drug for E.coli and Bacillus subtilis was almost 0.185 mM and 0.55 mM respectively. The E.coli strain was killed at concentrations 45, 15, 5 mM while the Bacillus subtilis was stable against all of the concentrations.
Acute HIV Infection in Youth: Protocol for the Adolescent Trials Network 147 (ATN147) Comprehensive Adolescent Research and Engagement Studies (CARES) Study

Background Early treatment studies have shown that prompt treatment of HIV with combination antiretroviral therapy (cART) can limit the size of latent viral reservoirs, thereby providing clinical and public health benefits. Studies have demonstrated that adolescents have a greater capacity for immune reconstitution than adults. Nevertheless, adolescents who acquired HIV through sexual transmission have not been included in early treatment studies because of challenges in identification and adherence to cART. Objective This study aimed to identify and promptly treat with cART youth aged 12 to 24 years in Los Angeles and New Orleans who have acute, recent, or established HIV infection, as determined by Fiebig stages 1 to 6 determined by viral RNA polymerase chain reaction, p24 antigen presence, and HIV-1 antigen Western blot. The protocol recommends treatment on the day of diagnosis when feasible. Surveillance and dedicated behavioral strategies are used to retain them in care and optimize adherence. Through serial follow-up, HIV biomarkers and response to antiretroviral therapy (ART) are assessed. The study aims to assess viral dynamics, decay and persistence of viral reservoirs over time, and correlate these data with the duration of viral suppression. Methods A total of 72 youth (36 acutely infected and 36 treatment naïve controls) are enrolled across clinical sites using a current community-based strategy and direct referrals. Youth are prescribed ART according to the standard of care HIV-1 management guidelines and followed for a period of 2 years. Assessments are conducted at specific time points throughout these 2 years of follow-up for monitoring of adherence to ART, viral load, magnitude of HIV reservoirs, and presence of coinfections. Results The study began enrolling youth in July 2017 across study sites in Los Angeles and New Orleans. As of September 30, 2018, a total of 37 youth were enrolled, 12 with recently acquired, 16 with established HIV infection as determined by Fiebig staging, and 9 pending determination of Fiebig status. Recruitment and enrollment are ongoing. Conclusions We hypothesize that the size of the HIV reservoir and immune activation markers will be different across groups treated with cART, that is, those with acute or recent HIV infection and those with established infection. Adolescents treated early who are virally suppressed will have diminished HIV reservoirs than those with established infection. These youth may be potential candidates for a possible HIV vaccine and additional HIV remission intervention trials. Our study will inform future studies of viral remission strategies. International Registered Report Identifier (IRRID) DERR1-10.2196/10807
Neoplasms—Comparative Pathology of Growth in Animals, Plants and Man

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OXTR methylation modulates exogenous oxytocin effects on human brain activity during social interaction

Oxytocin (OT) effects on brain function and behavior are mediated by the oxytocin receptor (OXTR). The distribution of OXTR in the brain can profoundly influence social behavior. Emerging evidence suggests that DNA methylation of OXTR influences OXTR expression. Previously, we conducted a pharmaco‐functional Magnetic Resonance Imaging (fMRI) study in which healthy subjects were randomized to 24 IU intranasal OT or placebo and imaged with fMRI while playing a dyadic social interaction task known as the iterated Prisoner's Dilemma (PD) game with same‐sex partners. Here, we investigate whether DNA methylation of OXTR modulates the effect of intranasal OT on the neural response to positive and negative social interactions in the PD game. OXTR methylation did not modulate OT effects within brain regions where we previously reported OT effects in response to reciprocated (caudate nucleus) and unreciprocated cooperation (amygdala and anterior insula). However, OXTR methylation did modulate OT effects on the response to both reciprocated and unreciprocated cooperation in other brain regions such as the precuneus and visual cortex. Further restricting the analysis to OXTR rs53576 GG individuals revealed that OXTR methylation modulated OT effects on the precuneus response to reciprocated cooperation in men, the lateral septum response to reciprocated cooperation in women, and the visual cortex response to unreciprocated cooperation in men. These results suggest that OXTR methylation status may influence OT effects on mentalizing, attention and reward processing during social interactions. OXTR methylation may be important to consider if exogenous OT is used to treat social behavioral disorders in the future.