Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Pressure on Diffusion and Vacancy Formation in MgO from Nonempirical Free-Energy Integrations

The free energies of vacancy pair formation and migration in MgO were computed via molecular dynamics using free-energy integrations and a nonempirical ionic model with no adjustable parameters. The intrinsic diffusion constant for MgO was obtained at pressures from 0 to 140GPa and temperatures from 1000 to 5000K. Excellent agreement was found with the zero pressure diffusion data within experimental error. The homologous temperature model which relates diffusion to the melting curve describes well our high pressure results within our theoretical framework. {copyright} {ital 1997} {ital The American Physical Society}
Dramatic Perezhivanie as a driver of executive functions development through role-play in early childhood: Theoretical framework and experimental evidence

Role-play in early childhood is associated with development of executive functions (EFs), although study results remain inconsistent. Due to the complex nature of the role-play, the underlying mechanisms of these associations are not obvious. In this article, play is viewed in the framework of the cultural-historical approach as a special social situation that can become the social situation of development if it results in dramatic perezhivanie of a child. In this study, we compared the level of EFs and play behavior between two play contexts: play guided by an adult and one with less adult involvement. Play behavior was analyzed based on five behavioral measures suggested to be the markers of dramatic perezhivanie. Measures of EFs were taken before and after the experimental procedure. Results show that dramatic perezhivanie might be considered a driver of EFs development through role-play in early childhood. As well as this, the involvement of an adult into play was associated with different patterns of EFs dynamics before and after the intervention. Future work can investigate if the construct of dramatic perezhivanie, microsocial situation of development, and micro-crisis might explain variability of the study results on the association between the role-play and child development.
The associations of maternal and children’s gut microbiota with the development of atopic dermatitis for children aged 2 years

Background It is critical to investigate the underlying pathophysiological mechanisms in the development of atopic dermatitis. The microbiota hypothesis suggested that the development of allergic diseases may be attributed to the gut microbiota of mother-offspring pairs. The purpose of this study was to investigate the relationship among maternal-offspring gut microbiota and the subsequent development of atopic dermatitis in infants and toddlers at 2 years old. Methods A total of 36 maternal-offspring pairs were enrolled and followed up to 2 years postpartum in central China. Demographic information and stool samples were collected perinatally from pregnant mothers and again postpartum from their respective offspring at the following time intervals: time of birth, 6 months, 1 year and 2 years. Stool samples were sequenced with the 16S Illumina MiSeq platform. Logistic regression analysis was used to explore the differences in gut microbiota between the atopic dermatitis group and control group. Results Our results showed that mothers of infants and toddlers with atopic dermatitis had higher abundance of Candidatus_Stoquefichus and Pseudomonas in pregnancy and that infants and toddlers with atopic dermatitis had higher abundance of Eubacterium_xylanophilum_group at birth, Ruminococcus_gauvreauii_group at 1 year and UCG-002 at 2 years, and lower abundance of Gemella and Veillonella at 2 years. Additionally, the results demonstrated a lower abundance of Prevotella in mothers of infants and toddlers with atopic dermatitis compared to mothers of the control group, although no statistical difference was found in the subsequent analysis. Conclusion The results of this study support that gut microbiota status among mother-offspring pairs appears to be associated with the pathophysiological development of pediatric atopic dermatitis.
Impact of low skeletal muscle mass and quality on clinical outcomes in patients with head and neck cancer undergoing (chemo)radiation

The study aimed to explore the impact of low skeletal muscle mass and quality on survival outcomes and treatment tolerance in patients undergoing radical chemo-radiation therapy for head and neck cancer (HNC). This is significant given the growing interest in sarcopenia as a possible negative predictive/prognostic factor of disease progression and survival. From 2010 to 2017, 225 patients were included in the study. Pre-treatment computed tomography (CT) scans of HNC patients undergoing (chemo)radiation therapy were retrospectively reviewed. The skeletal muscle area, normalized for height to obtain the skeletal muscle index (SMI), the skeletal muscle density (SMD) and the intramuscular adipose tissue area (IMAT) were measured at the level of the L3 vertebra. Low SMD and low SMI were defined according to previously reported thresholds, while high IMAT was defined using population-specific cut-point analysis. SMI, SMD, and IMAT were also measured at the proximal thigh (PT) level and tested as continuous variables. Clinical morpho-functional parameters, baseline nutritional markers with a known or suspected impact on HNC treatment, clinical outcomes and sarcopenia were also collected. In multivariate analyses, adjusted by age, sex, stage, diabetes, body mass index (BMI), and weight loss, L3-SMI was not significantly associated with survival, while poor muscle quality was negatively associated with overall survival (OS) (HR = 1.88, 95% CI = 1.09–3.23, p = 0.022 and HR = 2.04, 95% CI = 1.27–3.27, p = 0.003, for low L3-SMD and high L3-IMAT, respectively), progression-free survival (PFS) (HR = 2.26, 95% CI = 1.39–3.66, p = 0.001 and HR = 1.97, 95% CI = 1.30–2.97, p = 0.001, for low L3-SMD and high L3-IMAT, respectively) and cancer-specific survival (CSS) (HR = 2.40, 95% CI = 1.28–4.51, p = 0.006 and HR = 1.81, 95% CI = 1.04–3.13, p = 0.034, for low L3-SMD and high L3-IMAT, respectively). Indices at the PT level, tested as continuous variables, showed that increasing PT-SMI and PT-SMD were significant protective factors for all survival outcomes (for OS: HR for one cm2/m2 increase in PT-SMI 0.96; 95% CI = 0.94–0.98; p = 0.001 and HR for one HU increase in PT-SMD 0.90; 95% CI = 0.85–0.94; p < 0.001, respectively). PT-IMAT was a significant risk factor only in the case of CSS (HR for one cm2 increase 1.02; 95% CI = 1.00–1.03; p = 0.046). In conclusion, pre-treatment low muscle quality is a strong prognostic indicator of death risk in patients affected by HNC and undergoing (chemo)radiotherapy with curative intent.
Promoting wellbeing and empowerment via Youth First: Exploring psychosocial outcomes of a school-based resilience intervention in Bihar, India

Youth worldwide are struggling with increased mental health concerns. As youth in low- and middle-income countries make up more than 20% of the world’s population, finding ways to improve their psychosocial wellbeing is crucial. CorStone’s Youth First program is a school-based psychosocial resilience program that seeks to improve the mental, physical, social, and educational wellbeing of early adolescents. The program is delivered via trained government schoolteachers who facilitate students’ learning and development in small groups using a discussion and activity-based curriculum. In August 2021, a study among 322 adolescents was conducted to investigate and compare program participants’ and non- participants’ understanding and use of inter- and intra-personal psychosocial skills. Focus group discussions were held with students in eight intervention schools and four comparable schools not receiving the intervention (control). Through the focus group discussions, students provided their opinions, thoughts, and ideas about vignettes describing challenges that youth in their communities frequently face, including early marriage and financial pressures. Analysis integrated qualitative and quantitative approaches, consisting of an iterative thematic analysis process followed by quantizing data and conducting t-tests. Youth who had received Youth First had greater awareness of problems, perspective-taking, problem-solving strategies, helping approaches, awareness of their own strengths, and visions for the future, when compared with the control group. Findings provide insights into potential outcomes for measurement in future evaluations of mental health promotion and prevention programs among youth in low- and middle-income countries.
Associations between dietary copper intake, general obesity and abdominal obesity risk: A nationwide cohort study in China

Objective Copper plays a crucial role in redox reactions. The aims of this research are to examine the effects of copper consumption on general obesity and abdominal obesity risk. Methods Overall, data of 13,282 participants were obtained from the China Health and Nutrition Survey (1997–2011). A combination of individual 24-h recall and household survey was used to assess dietary intake. Time-dependent mixed effect Cox regression model treating family as a random effect were used to assess the associations between quintiles of copper intake, general obesity and abdominal obesity risk. Obesity was defined by BMI ≥ 28 kg/m2, and abdominal obesity was defined as waist circumference ≥85 cm in men and ≥80 cm in women. Results During follow-up, 1,073 and 4,583 incident cases of general obesity and abdominal obesity occurred respectively. There were U-shaped associations of dietary copper intakes with general obesity and abdominal obesity (P for nonlinearity <0.001). In the general obesity track, compared with quintile 3 (reference category), participants in the top quintile and bottom quintile showed higher general obesity risk (HR, 2.00; 95%CI: 1.63, 2.45 for the top quintile, HR, 1.34; 95%CI: 1.08, 1.68 for the bottom quintile). In the abdominal obesity track, compared with quintile 3, the top quintile and bottom quintile were also associated with a significantly increased risk of abdominal obesity (HR, 1.68; 95%CI: 1.52, 1.87 for the top quintile, HR, 1.36; 95%CI: 1.22, 1.52 for the bottom quintile). Conclusions We demonstrated U-shaped associations between dietary copper, general and abdominal obesity risk in Chinese and emphasized the importance of maintaining appropriate copper intake level for the prevention of obesity.
The Star Formation Rate Density of the Universe at z = 0.24 and 0.4 from Hα

Knowledge of both the global star formation history of the universe and the nature of individual star-forming galaxies at different look-back times is essential to our understanding of galaxy formation and evolution. Deep redshift surveys suggest star-formation activity increases by an order of magnitude from z = 0 to ~1. As a direct test of whether substantial evolution in star-formation activity has occurred, we need to measure the star formation rate (SFR) density and the properties of the corresponding star-forming galaxy populations at different redshifts, using similar techniques. The main goal of this work is to extend the Universidad Complutense de Madrid (UCM) survey of emission-line galaxies to higher redshifts. (continues)
Overall adjustment acupuncture improves osteoporosis and exerts an endocrine-modulating effect in ovariectomized rats

Background Acupuncture is a widely practiced, convenient, and safe treatment modality within complementary and integrative medicine. Increasing studies have revealed the efficacy of acupuncture for the treatment of osteoporosis in both human and non-human subjects. The aim of the present study was to assess the improvement of osteoporosis after overall adjustment acupuncture (OA) as well as its endocrine-modulating effect in an ovariectomized rat model. Methods In total, 32 female Sprague–Dawley (SD) rats were randomly divided into the sham, model, ovariectomy+estrogen (OVX+E), and OVX+OA (OVX+A) groups with eight rats in each group. The postmenopausal osteoporosis (PMOP) rat model was induced by bilateral ovariectomy. At 12 weeks after surgery, rats in the OVX+E group received estradiol (0.2 mg/kg/i.g./qod) for 12 weeks, and rats in the OVX+A group were treated with acupuncture at Zusanli (ST36), Shenshu (BL23), and Dazhu (BL11) points (qod) for 12 weeks. At the end of the treatment, all rats were sacrificed, and the body weight, uterus index, bone mineral density (BMD), bone mineral content (BMC), bone trabeculae structural parameters, femoral biomechanical properties, femoral histomorphology, and several hormone levels were examined. Results In OVX rats, OA abrogated the body weight gain and improved osteoporosis in terms of BMD, BMC, bone trabeculae structural parameters, bone strength, and bone tissue histomorphology. Moreover, OA modulated the serum levels of estradiol, corticotropin releasing hormone (CRH), adrenocorticotropic hormone (ACTH), and corticosterone (CORT). Conclusions OA improves osteoporosis and exerts an endocrine-modulating effect in ovariectomized rats.
Convergence properties of detonation simulations

ABSTRACT We present a high-resolution convergence study of detonation initiated by a temperature gradient in a stoichiometric hydrogen–oxygen mixture using the PENCIL CODE and compare with a code that employs a fifth order weighted essentially non-oscillating (WENO) scheme. With Mach numbers reaching 10–30, a certain amount of shock viscosity is needed in the PENCIL CODE to remove or reduce numerical pressure oscillations on the grid scale at the position of the shock. Detonation is found to occur for intermediate values of the shock viscosity parameter. At fixed values of this parameter, the numerical error associated with those small wiggles in the pressure profile is found to decrease with decreasing mesh width like down to . With the WENO scheme, solutions are smooth at , but no detonation is obtained for . This is argued to be an artifact of a decoupling between pressure and reaction fronts.
Metabolic diversity in a collection of wild and cultivated Brassica rapa subspecies

Brassica rapa (B. rapa) and its subspecies contain many bioactive metabolites that are important for plant defense and human health. This study aimed at investigating the metabolite composition and variation among a large collection of B. rapa genotypes, including subspecies and their accessions. Metabolite profiling of leaves of 102 B. rapa genotypes was performed using ultra-performance liquid chromatography coupled with a photodiode array detector and quadrupole time-of-flight mass spectrometry (UPLC-PDA-QTOF-MS/MS). In total, 346 metabolites belonging to different chemical classes were tentatively identified; 36 out of them were assigned with high confidence using authentic standards and 184 were those reported in B. rapa leaves for the first time. The accumulation and variation of metabolites among genotypes were characterized and compared to their phylogenetic distance. We found 47 metabolites, mostly representing anthocyanins, flavonols, and hydroxycinnamic acid derivatives that displayed a significant correlation to the phylogenetic relatedness and determined four major phylometabolic branches; 1) Chinese cabbage, 2) yellow sarson and rapid cycling, 3) the mizuna-komatsuna-turnip-caitai; and 4) a mixed cluster. These metabolites denote the selective pressure on the metabolic network during B. rapa breeding. We present a unique study that combines metabolite profiling data with phylogenetic analysis in a large collection of B. rapa subspecies. We showed how selective breeding utilizes the biochemical potential of wild B. rapa leading to highly diverse metabolic phenotypes. Our work provides the basis for further studies on B. rapa metabolism and nutritional traits improvement.
Revised Catalog of GALEX Ultraviolet Sources. I. The All-Sky Survey: GUVcat_AIS

The Galaxy Evolution Explorer (GALEX) imaged the sky in two ultraviolet (UV) bands, far-UV (FUV, λeff ∼ 1528 Å), and near-UV (NUV, λeff ∼ 2310 Å), delivering the first comprehensive sky surveys at these wavelengths. The GALEX database contains FUV and NUV images, ∼500 million source measurements and over 100,000 low-resolution UV spectra. The UV surveys are a unique resource for statistical studies of hot stellar objects, z ≲ 2 QSOs, star-forming galaxies, nebulae and the interstellar medium, and provide a roadmap for planning future UV instrumentation and follow-up observing programs. We present science-enhanced, “clean” catalogs of GALEX UV sources, with useful tags to facilitate scientific investigations. The catalogs are an improved and expanded version of our previous catalogs of UV sources (BCScat). With respect to BCScat, we have patched 640 fields for which the pipeline had improperly coadded non-overlapping observations, and we provide a version with a larger sky coverage (about 10%) by relaxing the restriction to the central area of the GALEX field to 1. °1 diameter (GUVcat_AIS_fov055), as well as the cleaner, more restrictive version using only the 1° central portion of each field as in BCScat (GUVcat_AIS_fov050). We added new tags to facilitate selection and cleaning of statistical samples for science applications: we flag sources within the footprint of extended objects (nearby galaxies, stellar clusters) so that these regions can be excluded for estimating source density. As in our previous catalogs, in GUVcat duplicate measurements of the same source are removed, so that each astrophysical object has only one entry. Such a unique-source catalog is needed to study the density and distributions of sources, and to match UV sources with catalogs at other wavelengths. The catalog includes all observations from the All-Sky Imaging Survey (AIS), the survey with the largest area coverage, with both FUV and NUV detectors exposed: over 28,700 fields, made up of a total of 57,000 observations (“visits”). The total area covered, when overlaps are removed and gaps are accounted for, is 24,790 square degrees for GUVcat_AIS_fov055 (GUVcat_AIS_fov055) and 22,125 square degrees for (GUVcat_AIS_fov050). The total numbers of “unique” AIS sources (eliminating duplicate measurements) are 82,992,086 ( ) and 69,772,677 ( ). The typical depth of the GUVcat_AIS catalog is FUV = 19.9, NUV = 20.8 AB mag.
Improved NGS-based detection of microsatellite instability using tumor-only data

Microsatellite instability (MSI) is a molecular signature of mismatch repair deficiency (dMMR), a predictive marker of immune checkpoint inhibitor therapy response. Despite its recognized pan-cancer value, most methods only support detection of this signature in colorectal cancer. In addition to the tissue-specific differences that impact the sensitivity of MSI detection in other tissues, the performance of most methods is also affected by patient ethnicity, tumor content, and other sample-specific properties. These limitations are particularly important when only tumor samples are available and restrict the performance and adoption of MSI testing. Here we introduce MSIdetect, a novel solution for NGS-based MSI detection. MSIdetect models the impact of indel burden and tumor content on read coverage at a set of homopolymer regions that we found are minimally impacted by sample-specific factors. We validated MSIdetect in 139 Formalin-Fixed Paraffin-Embedded (FFPE) clinical samples from colorectal and endometrial cancer as well as other more challenging tumor types, such as glioma or sebaceous adenoma or carcinoma. Based on analysis of these samples, MSIdetect displays 100% specificity and 96.3% sensitivity. Limit of detection analysis supports that MSIdetect is sensitive even in samples with relatively low tumor content and limited microsatellite instability. Finally, the results obtained using MSIdetect in tumor-only data correlate well (R=0.988) with what is obtained using tumor-normal matched pairs, demonstrating that the solution addresses the challenges posed by MSI detection from tumor-only data. The accuracy of MSI detection by MSIdetect in different cancer types coupled with the flexibility afforded by NGS-based testing will support the adoption of MSI testing in the clinical setting and increase the number of patients identified that are likely to benefit from immune checkpoint inhibitor therapy.
Gut microbiota, pathogenic proteins and neurodegenerative diseases

As the world’s population ages, neurodegenerative diseases (NDs) have brought a great burden to the world. However, effective treatment measures have not been found to alleviate the occurrence and development of NDs. Abnormal accumulation of pathogenic proteins is an important cause of NDs. Therefore, effective inhibition of the accumulation of pathogenic proteins has become a priority. As the second brain of human, the gut plays an important role in regulate emotion and cognition functions. Recent studies have reported that the disturbance of gut microbiota (GM) is closely related to accumulation of pathogenic proteins in NDs. On the one hand, pathogenic proteins directly produced by GM are transmitted from the gut to the central center via vagus nerve. On the other hand, The harmful substances produced by GM enter the peripheral circulation through intestinal barrier and cause inflammation, or cross the blood–brain barrier into the central center to cause inflammation, and cytokines produced by the central center cause the production of pathogenic proteins. These pathogenic proteins can produced by the above two aspects can cause the activation of central microglia and further lead to NDs development. In addition, certain GM and metabolites have been shown to have neuroprotective effects. Therefore, modulating GM may be a potential clinical therapeutic approach for NDs. In this review, we summarized the possible mechanism of NDs caused by abnormal accumulation of pathogenic proteins mediated by GM to induce the activation of central microglia, cause central inflammation and explore the therapeutic potential of dietary therapy and fecal microbiota transplantation (FMT) in NDs.