Miracle-dz/UniFAR-FTUs huggingface dataset:
Granular layEr Simulator: Design and Multi-GPU Simulation of the Cerebellar Granular Layer

In modern computational modeling, neuroscientists need to reproduce long-lasting activity of large-scale networks, where neurons are described by highly complex mathematical models. These aspects strongly increase the computational load of the simulations, which can be efficiently performed by exploiting parallel systems to reduce the processing times. Graphics Processing Unit (GPU) devices meet this need providing on desktop High Performance Computing. In this work, authors describe a novel Granular layEr Simulator development implemented on a multi-GPU system capable of reconstructing the cerebellar granular layer in a 3D space and reproducing its neuronal activity. The reconstruction is characterized by a high level of novelty and realism considering axonal/dendritic field geometries, oriented in the 3D space, and following convergence/divergence rates provided in literature. Neurons are modeled using Hodgkin and Huxley representations. The network is validated by reproducing typical behaviors which are well-documented in the literature, such as the center-surround organization. The reconstruction of a network, whose volume is 600 × 150 × 1,200 μm3 with 432,000 granules, 972 Golgi cells, 32,399 glomeruli, and 4,051 mossy fibers, takes 235 s on an Intel i9 processor. The 10 s activity reproduction takes only 4.34 and 3.37 h exploiting a single and multi-GPU desktop system (with one or two NVIDIA RTX 2080 GPU, respectively). Moreover, the code takes only 3.52 and 2.44 h if run on one or two NVIDIA V100 GPU, respectively. The relevant speedups reached (up to ~38× in the single-GPU version, and ~55× in the multi-GPU) clearly demonstrate that the GPU technology is highly suitable for realistic large network simulations.
A Theoretical Analysis of Mixing Length for Atmospheric Models From Micro to Large Scales

A new mixing length adapted to the constraints of the hectometric-scale gray zone of turbulence for neutral and convective boundary layers is proposed. It combines a mixing length for mesoscale simulations, where the turbulence is fully subgrid and a mixing length for Large-Eddy Simulations, where the coarsest turbulent eddies are explicitly resolved. The mixing length is built for isotropic turbulence schemes, as well as schemes using the horizontal homogeneity assumption. This mixing length is tested over three boundary layer cases: a free convective case, a neutral case and a cold air outbreak case. The later combines turbulence from thermal and dynamical origins as well as presence of clouds. With this new mixing length, the turbulence scheme produces the right proportion between subgrid and resolved turbulent exchanges in Large Eddy Simulations, in the gray zone and at the mesoscale. This opens the way of using a single mixing length whatever the grid mesh of the atmospheric model, the evolution stage or the depth of the boundary layer.
The Legal Vulnerability Model for Same-Sex Parent Families: A Mixed Methods Systematic Review and Theoretical Integration

Globally, parents and children in same-sex parent families are impacted by many laws related to the parental sexual orientation. These laws vary considerably from one country to another, ranging from full legal recognition to criminalization. The psychological consequences of living in an ambiguous or hostile legal climate likely interfere with parental health, family functioning, and child development. However, a systematic evidence synthesis of the pertinent literature and its placement within a broader psychological model are currently lacking. The aims of this review were thus (1) to systematically review qualitative and quantitative evidence on the impact of sexual orientation laws on same-sex parent families in key domains and (2) to place these findings within a broader model informed by minority stress and family theories. Our review was preregistered and conducted in line with PRISMA guidelines. We searched for qualitative, quantitative, and mixed methods studies on the impact of sexual orientation laws on target outcomes (parental health, family functioning, child outcomes) via systematic database search (PubMed, Scopus, Web of Science) and forward-backward searches. Fifty-five studies published between 1999 and 2020 were eligible for inclusion and were synthesized using a data-based convergent synthesis design. Thirteen descriptive and three overarching analytical themes were identified through thematic synthesis. Linking our findings with minority stress and family theories, we propose a novel legal vulnerability model for same-sex parent families. The model posits that legal vulnerability constitutes an increased risk for parental and child health as well as family functioning through individual and shared pathways between family members. Additionally, the model introduces counteractions that families engage in on the personal, familial, and systemic level to mitigate the impact of legal vulnerability, as well as moderators on the contextual, familial, couple, and individual level that modulate this impact. Implications for research and clinical practice are discussed.
Extending the Spatio-Temporal Applicability of DISPATCH Soil Moisture Downscaling Algorithm: A Study Case Using SMAP, MODIS and Sentinel-3 Data

DISPATCH is a disaggregation algorithm of the low-resolution soil moisture (SM) estimates derived from passive microwave observations. It provides disaggregated SM data at typically 1 km resolution by using the soil evaporative efficiency (SEE) estimated from optical/thermal data collected around solar noon. DISPATCH is based on the relationship between the evapo-transpiration rate and the surface SM under non-energy-limited conditions and hence is well adapted for semi-arid regions with generally low cloud cover and sparse vegetation. The objective of this paper is to extend the spatio-temporal coverage of DISPATCH data by 1) including more densely vegetated areas and 2) assessing the usefulness of thermal data collected earlier in the morning. Especially, we evaluate the performance of the Temperature Vegetation Dryness Index (TVDI) instead of SEE in the DISPATCH algorithm over vegetated areas (called vegetation-extended DISPATCH) and we quantify the increase in coverage using Sentinel-3 (overpass at around 09:30 am) instead of MODIS (overpass at around 10:30 am and 1:30 pm for Terra and Aqua, respectively) data. In this study, DISPATCH is applied to 36 km resolution Soil Moisture Active and Passive SM data over three 50 km by 50 km areas in Spain and France to assess the effectiveness of the approach over temperate and semi-arid regions. The use of TVDI within DISPATCH increases the coverage of disaggregated images by 9 and 14% over the temperate and semi-arid sites, respectively. Moreover, including the vegetated pixels in the validation areas increases the overall correlation between satellite and in situ SM from 0.36 to 0.43 and from 0.41 to 0.79 for the temperate and semi-arid regions, respectively. The use of Sentinel-3 can increase the spatio-temporal coverage by up to 44% over the considered MODIS tile, while the overlapping disaggregated data sets derived from Sentinel-3 and MODIS land surface temperature data are strongly correlated (around 0.7). Additionally, the correlation between satellite and in situ SM is significantly better for DISPATCH (0.39–0.80) than for the Copernicus Sentinel-1-based (−0.03 to 0.69) and SMAP/S1 (0.37–0.74) product over the three studies (temperate and semi-arid) areas, with an increase in yearly valid retrievals for the vegetation-extended DISPATCH algorithm.
Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes

Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
Sonographic Characteristics of Papillary Thyroid Carcinoma With Coexistent Hashimoto’s Thyroiditis in the Preoperative Prediction of Central Lymph Node Metastasis

The purpose of this study was to evaluate the usefulness of the sonographic characteristics of papillary thyroid carcinoma (PTC) with Hashimoto’s thyroiditis (HT) for predicting central lymph node metastasis (CLNM). One hundred thirty-three patients who underwent thyroidectomy and central cervical lymph node dissection for PTC with coexistent HT were retrospectively analyzed. All PTCs with HT were preoperatively evaluated by ultrasound (US) regarding their nodular number, size, component, shape, margin, echogenicity, calcification, capsule contact with protrusion, vascularity and contrast enhanced ultrasound (CEUS) parameters. Univariate analysis demonstrated that patients with PTCs with HT and CLNM more frequently had age ≤ 45 years, size > 10 mm, a wider than tall shape, microcalcification, hypo-enhancement and peak intensity index < 1 than those without CLNM (all p<0.05). Binary logistic regression analysis demonstrated that size > 10 mm and CEUS hypo-enhancement were independent characteristics for the presence of CLNM. Our study indicated that preoperative US characteristics could offer help in predicting CLNM in PTCs with coexistent HT.
Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema

Identification of the offending organism and appropriate antimicrobial therapy are crucial for treating empyema. Diagnosis of empyema is largely obscured by the conventional bacterial cultivation and PCR process that has relatively low sensitivity, leading to limited understanding of the etiopathogenesis, microbiology, and role of antibiotics in the pleural cavity. To expand our understanding of its pathophysiology, we have carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure. Our results showed that the variation of microbiota in the pleural effusion is generally stratified, not continuous. There are two distinct microbiome clusters observed in the forty-five samples: HA-SA type and LA-SA type. The categorization is mostly driven by species composition: HA-SA type is marked by Staphylococcus aureus as the core species, with other enriched 6 bacteria and 3 fungi, forming a low diversity and highly stable microbial community; whereas the LA-SA type has a more diverse microbial community with a distinct set of bacterial species that are assumed to be the oral origin. The microbial community does not shape the dominant antibiotic resistance classes which were common in the two types, while the increase of microbial diversity was correlated with the increase in antibiotic resistance genes. The existence of well-balanced microbial symbiotic states might respond differently to pathogen colonization and drug intake. This study provides a deeper understanding of the pathobiology of pleural empyema and suggests that potential resistance genes may hinder the antimicrobial therapy of empyema.
Serum Protein N-Glycosylation Signatures of Neuroblastoma

Background Neuroblastoma is the most common extracranial childhood solid tumor which accounts for 10% of the malignancies and 15% of the cancer fatalities in children. N-glycosylation is one of the most frequent post-translation protein modification playing a vital role in numerous cancers. N-glycosylation changes in neuroblastoma patient serum have not been studied in existing reports. The comprehensive analyses of serum N-glycomics in neuroblastoma can provide useful information of potential disease biomarkers and new insights of the pathophysiology in neuroblastoma. Methods The total serum protein N-glycosylation was analyzed in 33 neuroblastoma patients and 40 age- and sex-matched non-malignant controls. N-glycans were enzymatically released, derivatized to discriminate linkage-specific sialic acid, purified by HILIC-SPE, and identified by MALDI-TOF-MS. Peak areas were acquired by the software of MALDI-MS sample acquisition, processed and analyzed by the software of Progenesis MALDI. Results Three glyco-subclasses and six individual N-glycans were significantly changed in neuroblastoma patients compared with controls. The decreased levels of high mannose N-glycans, hybrid N-glycans, and increased levels of α2,3-sialylated N-glycans, multi-branched sialylated N-glycans were observed in neuroblastoma patients. what is more, a glycan panel combining those six individual N-glycans showed a strong discrimination performance, with an AUC value of 0.8477. Conclusions This study provides new insights into N-glycosylation characteristics in neuroblastoma patient serum. The analyses of total serum protein N-glycosylation could discriminate neuroblastoma patients from non-malignant controls. The alterations of the N-glycomics may play a suggestive role for neuroblastoma diagnosis and advance our understanding of the pathophysiology in neuroblastoma.
Development and Interplay of Two Orthogonal Fault Systems in the NW Qaidam Basin, Northern Tibetan Plateau

How fold and thrust belts (FTBs) evolve over time and space in a transpressional regime remains poorly understood. Based on high-resolution 3D seismic reflection data and remote sensing images, we herein present a detailed structural analysis of the Cenozoic faults in the NW margin of the Qaidam Basin that is bounded to the north by the left-reverse Altyn Tagh fault system. Two sets of orthogonal, basement-involved faults with contrasting geometries, kinematics, and temporal development are identified. One set consists of generally E-W-striking, N-dipping, reverse faults with a component of sinistral shear. They are parallel or subparallel to the Altyn Tagh fault system, led to southward tilting of the basement, and formed a local unconformity between the middle Miocene Shangyoushashan formation and underlying strata. They developed in an out-of-sequence order, and were mostly active during 43.8–15.3 Ma but in relatively tectonic quiescence with limited weak reactivation since then. The second set is mainly composed of the NNW-striking reverse faults with dextral shear components. They are approximately perpendicular to the Altyn Tagh fault system, and intensively active since ∼15.3 Ma, much later than the initiation of the E-W-striking faults. Together with published results, we ascribe the development of these two sets of orthogonal faults as the transition from transpression to left lateral slip on the central segment of the Altyn Tagh fault system. The two fault sets interplayed with each other in two ways: 1) the older E-W-striking faults were offset by younger NNW-striking faults, and 2) the younger NNW-striking faults curved to link with the preexisting E-W-striking faults. Our findings reveal that transpressional-dominated FTBs evolve in a more complicated way than the contractional-dominated ones, and more site-based case studies are needed to reveal the underlying primary principles.
Association of Diabetic Retinopathy With Stroke: A Systematic Review and Meta-Analysis

Background: The population-based studies conducted thus far do not provide conclusive evidence of the link between diabetic retinopathy (DR) and stroke. The aim of the present systematic review was to determine whether DR is specifically associated with stroke. Methods: MEDLINE, Embase, and Web of Science were systematically searched from their inception to July 31, 2020. All cohort studies that reported associations between the presence of DR and incident stroke were included. The pooled hazard ratios (HRs), pooled risk ratios (RRs), and 95% confidence intervals (CIs) were calculated. Results: The meta-analysis included 19 cohort studies involving 81,452 diabetic patients. The pooled effect size of any DR related to stroke was 1.25 for HR (95% CI: 1.12–1.39; P < 0.0001) and 1.96 for RR (95% CI: 1.60–2.39; P < 0.0001). Subgroup analysis for the type of diabetes yielded pooled HR of 1.29 (95% CI: 1.10–1.50; P = 0.001) in patients with type 2 diabetes mellitus (T2DM). The pooled RR was 2.29 (95% CI: 1.77–2.96; P < 0.0001) in patients with T2DM. Two studies addressed the DR-related stroke among type 1 diabetes mellitus (T1DM) patients. One study found a significant association between DR and stroke (OR: 1.6; 95% CI: 1.1–2.3; P < 0.01), while the other did not identify an association between these two conditions (RR: 1.40; 95% CI: 0.62–2.18; P = 0.178). Conclusions: The presence of DR is associated with an increased risk of stroke in diabetic patients. This correlation is robust in T2DM patients but uncertain in T1DM patients. Our findings indicate that DR is an important biomarker for the prediction of stroke. To further validate the role of DR in stroke-risk stratification, additional research is required on the association between the stage of DR and stroke risk, and more studies including T1DM patients are necessary.
From Talent Identification to Novo Basquete Brasil (NBB): Multifactorial Analysis of the Career Progression in Youth Brazilian Elite Basketball

This study examined individual, task, and environmental constraints that influence the career progression of youth Brazilian elite basketball players and the probability of reaching Novo Basquete Brasil (NBB) and to determine if the association of the relative age effect (RAE) is a key factor in the career progression. The sample consisted of 4,692 male players who were registered to participate in at least one U15, U17, or U22 youth Brazilian basketball championship between 2004 and 2018. Athletes who reached a high-performance level were coded like NBB players (9.6%). The birthdates, height, body mass, playing position, geographic region, club, competition category, and team performance were retrieved from the official data archive of the Brazilian Basketball Confederation and the National Basketball League. The maturity status was estimated using the predicted age at peak height velocity. A binary logistic regression examined the influence of each characteristic on the probability of a youth Brazilian basketball player to reach the NBB. The receiver operating characteristic (ROC) curves and the associated area under the curve (AUC) were used to assess the discriminant ability of the model. The taller and younger players not selected early into national teams, without specialization by playing position, who participated in U22 national championship, migrated to the southeast region, and remained in the formation process over time have a greater chance to reach the NBB. The ROC curve demonstrated an AUC of 93%. A combination of individual, task, and environmental characteristics influences the sport career of a young Brazilian basketball player in reaching the NBB. Further, early-maturing athletes have a greater chance to reach higher performances. RAE influences lower-level categories, but not a “NBB player's” career progression. The coaches, stakeholders, and practitioners should perform a holistic evaluation of sport talent in terms of a constraint-based theoretical model with the aim of avoiding bias produced by the maturational status and RAE in the youth Brazilian elite basketball.
Compliance and Self-Reporting During the COVID-19 Pandemic: A Cross-Cultural Study of Trust and Self-Conscious Emotions in the United States, Italy, and South Korea

The coronavirus COVID-19 pandemic is an unprecedented health crisis. Many governments around the world have responded by implementing lockdown measures of various degrees of intensity. To be effective, these measures must rely on citizens’ cooperation. In the present study, we drew samples from the United States (N = 597), Italy (N = 606), and South Korea (N = 693) and examined predictors of compliance with social distancing and intentions to report the infection to both authorities and acquaintances. Data were collected between April 6th and 8th 2020. We investigated the role of cultural orientations of horizontal and vertical individualism and collectivism, self-conscious emotions of shame and guilt related to the infection and trust in the government’s action. Across all countries, vertical collectivism (VC) predicted stronger shame, whereas horizontal collectivism predicted stronger trust in the government. Only in the United States, VC was associated with stronger trust. Stronger feelings of shame predicted lower compliance and intentions to report the infection to both authorities and acquaintances. In contrast, guilt was associated with stronger intentions to report the infection to the authorities. Finally, trust was associated with stronger compliance and intentions to report the infection to the authorities. Unlike Italy and South Korea, the association between trust on compliance was not statistically significant in the United States, implications of the findings, and directions for future research are discussed.