Miracle-dz/UniFAR-FTUs huggingface dataset:
Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution

Prions are self-propagating alternative states of protein domains. They are linked to both diseases and functional protein roles in eukaryotes. Prion-forming domains in Saccharomyces cerevisiae are typically domains with high intrinsic protein disorder (i.e., that remain unfolded in the cell during at least some part of their functioning), that are converted to self-replicating amyloid forms. S. cerevisiae is a member of the fungal class Saccharomycetes, during the evolution of which a large population of prion-like domains has appeared. It is still unclear what principles might govern the molecular evolution of prion-forming domains, and intrinsically disordered domains generally. Here, it is discovered that in a set of such prion-forming domains some evolve in the fungal class Saccharomycetes in such a way as to absorb general mutation biases across millions of years, whereas others do not, indicating a spectrum of selection pressures on composition and sequence. Thus, if the bias-absorbing prion formers are conserving a prion-forming capability, then this capability is not interfered with by the absorption of bias changes over the duration of evolutionary epochs. Evidence is discovered for selective constraint against the occurrence of lysine residues (which likely disrupt prion formation) in S. cerevisiae prion-forming domains as they evolve across Saccharomycetes. These results provide a case study of the absorption of mutational trends by compositionally biased domains, and suggest methodology for assessing selection pressures on the composition of intrinsically disordered regions.
Investigating Cumulative Exposures among 3- to 4-Year-Old Children Using Wearable Ultrafine Particle Sensors and Language Environment Devices: A Pilot and Feasibility Study

Interdisciplinary approaches are needed to measure the additive or multiplicative impacts of chemical and non-chemical stressors on child development outcomes. The lack of interdisciplinary approaches to environmental health and child development has led to a gap in the development of effective intervention strategies. It is hypothesized that a broader systems approach can support more effective interventions over time. To achieve these goals, detailed study protocols are needed. Researchers in child development typically focus on psychosocial stressors. Less attention is paid to chemical and non-chemical stressors and how the interaction of these stressors may impact child development. This feasibility study aims to bridge the gap between child development and environmental epidemiology research by trialing novel methods of gathering ultrafine particle data with a wearable air sensor, while simultaneously gathering language and noise data with the Language Environment Analysis (LENA) system. Additionally, psychosocial data (e.g., parenting quality, caregiver depression, and household chaos) was gathered from parent reports. Child participants (age 3–4 years) completed cognitive tasks to assess self-regulation and receptive language skills, and provided a biospecimen analyzed for inflammatory biomarkers. Data collection was completed at two time points, roughly corresponding to fall and spring. Twenty-six participants were recruited for baseline data, and 11 participants completed a follow-up session. Preliminary results indicate that it is feasible to gather personal Particulate Matter (PM2.5), language, and noise data, cognitive assessments, and biospecimens from our sample of 3-4-year-old children. While there are obstacles to overcome when working with this age group, future studies can benefit from adapting lessons learned regarding recruitment strategies, study design, and protocol implementation.
High-Resolution U-Net: Preserving Image Details for Cultivated Land Extraction

Accurate and efficient extraction of cultivated land data is of great significance for agricultural resource monitoring and national food security. Deep-learning-based classification of remote-sensing images overcomes the two difficulties of traditional learning methods (e.g., support vector machine (SVM), K-nearest neighbors (KNN), and random forest (RF)) when extracting the cultivated land: (1) the limited performance when extracting the same land-cover type with the high intra-class spectral variation, such as cultivated land with both vegetation and non-vegetation cover, and (2) the limited generalization ability for handling a large dataset to apply the model to different locations. However, the “pooling” process in most deep convolutional networks, which attempts to enlarge the sensing field of the kernel by involving the upscale process, leads to significant detail loss in the output, including the edges, gradients, and image texture details. To solve this problem, in this study we proposed a new end-to-end extraction algorithm, a high-resolution U-Net (HRU-Net), to preserve the image details by improving the skip connection structure and the loss function of the original U-Net. The proposed HRU-Net was tested in Xinjiang Province, China to extract the cultivated land from Landsat Thematic Mapper (TM) images. The result showed that the HRU-Net achieved better performance (Acc: 92.81%; kappa: 0.81; F1-score: 0.90) than the U-Net++ (Acc: 91.74%; kappa: 0.79; F1-score: 0.89), the original U-Net (Acc: 89.83%; kappa: 0.74; F1-score: 0.86), and the Random Forest model (Acc: 76.13%; kappa: 0.48; F1-score: 0.69). The robustness of the proposed model for the intra-class spectral variation and the accuracy of the edge details were also compared, and this showed that the HRU-Net obtained more accurate edge details and had less influence from the intra-class spectral variation. The model proposed in this study can be further applied to other land cover types that have more spectral diversity and require more details of extraction.
Diagnostic Accuracy of Magnetic Resonance Images and Weight-Bearing Radiographs in Patients With Arthroscopic-Proven Medial Osteoarthritis of the Knee

Aims: The aim of this study is to analyze the diagnostic value of weight-bearing radiographs, magnetic resonance images (MRI), and the combination of both in osteoarthritic knees when using arthroscopic findings as the “gold standard” to compare with. Methods: A total of 59 patients were studied because of chronic pain in 1 of their knees. Radiographs were classified according to Kellgren-Lawrence scale. Magnetic resonance images were classified according to Vallotton, and arthroscopic findings according to Outerbridge criteria. Results: Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy were, respectively, 75.0%, 60.0%, 56.2%, 77.8%, and 66.1% for weight-bearing radiographs, and 70.8%, 88.6%, 81.0%, 81.6%, and 81.4% for MRI. Logistic regression analysis showed that a weight-bearing radiograph added to MRI offered no additional diagnostic value compared with MRI alone (P < .001). Conclusions: Magnetic resonance images presented higher specificity, positive and negative predictive values, and accuracy than weight-bearing radiographs for knee osteoarthritis. The combination of radiographs and MRI did not improve the diagnostic accuracy, compared with MRI alone.
Is There a Link between Different Types of Alcoholic Drinks and Obesity? An Analysis of 280,183 UK Biobank Participants

Understanding the associations between types of alcoholic drinks and adiposity has public health relevance, considering that adult overweight and obesity prevalence are increasing worldwide. We aimed to evaluate the association between overall alcohol consumption and types of alcohol drinks with markers of adiposity from the UK Biobank baseline data (n = 280,183, 48.3% female). Generalized linear models were used to examine the associations between alcohol consumption with body mass index (BMI) and body fat percentage. Those drinking within the public health guidelines had a lower BMI by 1.34 kg/m2 (95% CI 1.42, 1.26 kg/m2) compared to never drinkers. Association between alcohol consumption and body fat percentage were not statistically significant. Compared to those who never drink wines (red wine, champagne and fortified wine), drinkers of these alcoholic beverages had lower BMI (difference of −0.75 kg/m2, 95% CI −0.78, −0.72 kg/m2; −0.48 kg/m2, 95% CI −0.52, −0.45 kg/m2; and −0.24 kg/m2, 95% CI −0.29, −0.18 kg/m2, respectively). Beer and spirits drinkers had higher BMI compared to never drinkers of beer and spirits (difference of 0.18 kg/m2, 95% CI 0.14, 0.22 kg/m2 and 0.64 kg/m2, 95% CI 0.61, 0.68 kg/m2, respectively). Our data did not find a link between alcohol drinking and higher risk of obesity.
Identification and Detection of Bioactive Peptides in Milk and Dairy Products: Remarks about Agro-Foods

Food-based components represent major sources of functional bioactive compounds. Milk is a rich source of multiple bioactive peptides that not only help to fulfill consumers ‘nutritional requirements but also play a significant role in preventing several health disorders. Understanding the chemical composition of milk and its products is critical for producing consistent and high-quality dairy products and functional dairy ingredients. Over the last two decades, peptides have gained significant attention by scientific evidence for its beneficial health impacts besides their established nutrient value. Increasing awareness of essential milk proteins has facilitated the development of novel milk protein products that are progressively required for nutritional benefits. The need to better understand the beneficial effects of milk-protein derived peptides has, therefore, led to the development of analytical approaches for the isolation, separation and identification of bioactive peptides in complex dairy products. Continuous emphasis is on the biological function and nutritional characteristics of milk constituents using several powerful techniques, namely omics, model cell lines, gut microbiome analysis and imaging techniques. This review briefly describes the state-of-the-art approach of peptidomics and lipidomics profiling approaches for the identification and detection of milk-derived bioactive peptides while taking into account recent progress in their analysis and emphasizing the difficulty of analysis of these functional and endogenous peptides.
Parental Factors Associated with Obesity in Korean Adolescents

Parental characteristics can influence adolescent obesity. However, the influence of parental characteristics on obesity may differ depending on the adolescent’s sex. This study evaluated parental characteristics that were associated with obesity in male and female adolescents. This study involved the secondary data analysis of cross-sectional survey data that were collected from June to September 2015. The study subjects included 1621 eighth-grade students. The study variables included sex, age, body mass index, household income, parental weight, parental perceptions of the child’s body, parental lifestyle, and parental social support for healthy eating and physical activity. The association between parental factors and adolescent obesity was analyzed via logistic regression analysis for each sex. Among male students, the fathers’ and mothers’ overweight status, fathers’ underestimation and overestimation of male adolescent weight, mothers’ dietary habits, and the mothers’ physical activity level were identified as obesity-associated factors. Among female students, the mothers’ overweight status, underestimation of female adolescent weight by fathers, dietary habits, and the physical activity level of fathers were significantly associated with adolescent obesity. The mothers’ overweight status and the underestimation of weight by fathers were strongly associated with obesity in male and female adolescents. Parental involvement in obesity-intervention programs could help prevent adolescent obesity.
Los tricomas foliares en la caracterización de un grupo de especies del género Quercus, sección Lobatae (Fagaceae)

TRICHOME DISTRIBUTION ON THE ABAXIAL SURFACES OF MATURE LEAVES, ANDTRICHOME TYPES WERE EXAMINED UNDER SCANNING ELECTRON MICROSCOPE (SEM) FOR 25 QUERCUS (SECTION LOBATAE) SPECIES. TWO TRICHOME GROUPS WERE ESTABLISHED: GLANDULAR AND NONGLANDULAR. THE NON-GLANDULAR ONES ARE CLASSIFIED INTO FOUR TYPES: STIPITATE-FASCICULATE, SESSILE-FASCICULATE, MULTIRADIATE, AND STELLATE. THE STIPITATEFASCICULATE TYPE WAS MORE COMMONLY FOUND IN ALL EXAMINED SPECIES.
Baseline Predictors of Survival, Neurological Recovery, Cognitive Function, Neuropsychiatric Outcomes, and Return to Work in Patients after a Severe Traumatic Brain Injury: an Updated Review

Introduction: Severe traumatic brain injury (sTBI) is a common cause of death and disability worldwide, with long-term squeal among survivors that include cognitive deficits, psychosocial and neuropsychiatric dysfunction, failure to return to pre-injury levels of work, school and inter-personal relationships, and overall reduced quality of and satisfaction with life. Aim: The aim of this work is to review the current literature on baseline predictors of outcomes in adults post sTBI. Method: Most of available literature on baseline predictors of outcomes in adults post sTBI were reviewed and summarized in this work. Results: Currently, a sizeable number of composite predictors of mortality and overall function exists; however, these instruments tend to over-estimate poor outcomes and fail to address issues like cognition, psychosocial/ neuropsychiatric dysfunction, and return to work or school. Conclusion: This article reviews currently-identified predictors of all these outcomes.
Synthesis, crystal structure at 219 K and Hirshfeld surface analyses of 1,4,6-trimethylquinoxaline-2,3(1H,4H)-dione monohydrate

The asymmetric unit of the title compound, C11H12N2O2·H2O, contains a disordered molecule of 1,4,6-trimethyl-1,4-dihydro-quinoxaline-2,3-dione and a solvent water molecule. In the crystal, molecules are linked by O—H⋯O and C—H⋯O hydrogen bonds into layers lying parallel to (10). The Hirshfeld surface analysis is carried out.
Low level laser therapy as a modality to attenuate cytokine storm at multiple levels, enhance recovery, and reduce the use of ventilators in COVID-19

The global pandemic COVID-19 is a contagious disease and its mortality rates ranging from 1% to 5% are likely due to acute respiratory distress syndrome (ARDS), and cytokine storm. A significant proportion of patients who require intubation succumb to the disease, despite the availability of ventilators and the best treatment practices. Researchers worldwide are in search of anti-inflammatory medicines in the hope of finding a cure for COVID-19. Low-level laser therapy (LLLT) has strong, anti-inflammatory effects confirmed by meta-analyses, and it may be therapeutic to ARDS. LLLT has been used for pain management, wound healing, and other health conditions by physicians, physiotherapists, and nurses worldwide for decades. In addition, it has been used in veterinary medicine for respiratory tract disease such as pneumonia. Laser light with low-power intensity is applied to the surface of the skin to produce local and systemic effects. Based on the clinical experience, peer-reviewed studies, and solid laboratory data in experimental animal models, LLLT attenuates cytokine storm at multiple levels and reduces the major inflammatory metabolites. LLLT is a safe, effective, low-cost modality without any side-effects that may be combined with conventional treatment of ARDS. We summarize the effects of LLLT on pulmonary inflammation and we provide a protocol for augmenting medical treatment in COVID-19 patients. LLLT combined with conventional medical therapy has the potential to prevent the progression of COVID-19, minimize the length of time needed on a ventilator, enhance the healing process, and shorten recovery time.
Impacts of antimicrobial growth promoters used in broiler chicken production on the emergence of antibiotic resistance in commensal E. coli and Salmonella

ii Table of contents.iii List of tables.vi List of figures . vii List of abbreviations.viii Acknowledgements . ix Dedication . xi Chapter I. Review of the literature . 1 I.
COLD-PCR Method for Early Detection of Antiviral Drug-Resistance Mutations in Treatment-Naive Children with Chronic Hepatitis B

We investigated Nucleos(t)ide-analogue (NA)-resistance mutations (mt) in 142 treatment-naive children with Chronic Hepatitis B (CHB), using a sensitive co-amplification at lower denaturation temperature (COLD)-PCR with Sanger DNA sequencing. An NA resistance-associated mt in the hepatitis B virus (HBV) reverse transcriptase (RT) was found in 66.2% of the patients, with nonclassical mt contributing the most (64.8%). Significantly higher frequencies of Lamivudine (LMV) and Adefovir dipivoxil (ADF) resistance-associated mt were found in genotypes B and C, respectively (ORLMV/ADF: 1495.000; 95% CI: 89.800–24,889.032; p < 0.001). Single-point mt associated to LMV and ADF resistance were detected in 59.9% of the tested children with rtV207M (38.0%) and rtN238T (9.9%) being the most frequent. Multiple-point mt were found only in 8 cases (5.6%): 6 children carried double mt (rtV207M + rtL229V; rtV207M + rtI233V; rtV207I + rtV207M × 2 cases; rtV207M + rtS213T; rtN238A + rtS256G) relating to LMV or/and ADF resistance and 3 children carried triple mt (rtL180M + rtM204I + rtN238T; rtV207M + rtS213T + rtS256G) or quadruple mt (rtL180M + rtM204V + rtV207I/M) for LMV-ADF resistance and Entecavir-reduced susceptibility. Our data indicate that significantly higher frequencies of LMV and ADF-associated mutations were found in treatment-naïve children infected with HBV genotypes B and C, respectively. The developed COLD-PCR method and obtained data may contribute to the development of suitable treatments for children with CHB.
Crystal structure analysis of ethyl 6-(4-methoxyphenyl)-1-methyl-4-methylsulfanyl-3-phenyl-1H-pyrazolo[3,4-b]pyridine-5-carboxylate

In the title compound, the dihedral angle between the fused pyrazole and pyridine rings is 1.76 (7)°. The benzene and methoxy phenyl rings make dihedral angles of 44.8 (5) and 63.86 (5)°, respectively, with the pyrazolo[3,4-b] pyridine moiety. An intramolecular short S⋯O contact [3.215 (2) Å] is observed. The crystal packing features C—H⋯π interactions.
Une Approche Hybride pour Calculer l’Enveloppe Visuelle d’Objets Complexes A Hybrid Approach for Computing Visual Hulls of Complex Objects

This paper addresses the problem of computing visual hulls from image contours. We propose a new hybrid approach which overcomes the precision-complexity trade-off inherent to voxel based approaches by taking advantage of surface based approaches. To this aim, we introduce a space discretization which does not rely on a regular grid, where most cells are ineffective, but rather on an irregular grid where sample points lie on the surface of the visual hull. Such a grid is composed of tetrahedral cells obtained by applying a Delaunay triangulation on the sample points. These cells are carved afterward according to image silhouette information. The proposed approach keeps the robustness of volumetric approaches while drastically improving their precision and reducing their time and space complexities. It thus allows modeling of objects with complex geometry, and it also makes real time feasible for precise models. Applications to real time object modeling are discussed and preliminary results with synthetic and real data are presented.
Discovery and biological function identification of Agrobacterium T-complex recruiting protein.

Agrobacterium tumefaciens is a phytopathogenic bacterium that causes the crown gall tumor disease in some dicotyledonous plants by transferring a segment of DNA(T -DNA) from its Ti-plasmid to plant cells and genetically transforming the host cells.Agrobacterium transfers the T-DNA in the form of protein-single-stranded-T-DNA(called T-complex). T-complex is transferred to the host cell through the type IV secretion system(T4SS). The recognition between T-complex and T4SS is fulfilled by a T-complex recruiting protein.This paper will briefly review the discovery of the Agrobacterium T-complex recruiting protein and the progress in identifying the biological function of the Agrobacterium T-complex recruiting protein.
Applications of social norms theory to other health and social justice issues.

There is growing interest in the application of social norms theory to issues of social justice and to health problems other than alcohol abuse, along with funding of social norms interventions to address sexual assault and violence prevention by a number of Federal agencies. In light of this interest, this chapter will review the theoretical assumptions of the social norms approach, assess the relevance of the theory to other health and social justice issues, and provide examples of social norms interventions for sexual assault prevention for men, eating problems among women, second-hand effects of binge drinking, and anti-bias programming.
Developing landscape frameworks for regional conservation planning; an approach integrating fauna spatial distributions and ecological principles

Habitat loss, degradation and fragmentation are heavily implicated in the decline of biodiversity throughout the world. Numerous conservation programmes have emerged in the attempt to deal with these primary threats but they are often isolated and disparate, foregoing opportunities for integrated, cumulative approaches and benefits. This paper describes an approach that, through the integration of species' modelled distributions, and the application of landscape ecology principles, systematically considers the spatial requirements of priority forest fauna as surrogates for biodiversity across the landscape. With the aid of innovative Geographic Information System analysis tools, key habitats and corridors for priority faunal assemblages are delineated across north-east New South Wales. The mapped outputs from this study provide spatially complete, data-driven, systematically derived conservation frameworks for the region. The frameworks provide an explicit basis for regional protected area networks and a landscape context for regional conservation planning. As predicted high conservation value habitats, the mapped key habitats and corridors are also focus areas for the protection, enhancement and restoration of native vegetation. The Geographic Information System-referenced key habitats and corridors conservation frameworks have been adopted for conservation planning in north-east New South Wales, including "off-reserve" planning (e.g., government and community-based programmes at regional, catchment and local levels), and "on-reserve" planning (e.g., national park and nature reserve management planning). The approach is applicable to other regions, wherever Geographic Information System-based spatial mapping, describing habitat quality for fauna species, can be collated.
Assessment of the network of protected areas for birds in Taiwan with regard to functional and phylogenetic diversity

In Taiwan, conserved areas represent more than 20% of the current jurisdiction, which is about twice that of the proportion of protected land worldwide. In this study, we explored the spatial distribution of bird assemblages in Taiwan. By analysing functional and phylogenetic diversity relative to elevational gradient, we assessed the network of bird protected areas. Hotspots of species richness were located at the coastal areas of northern and western Taiwan, although hotspots for protected bird species were located in the mountain areas. We found that phylogenetically close birds have similar trait values, and the protected species were evenly distributed in the functional and phylogenetic trees. The assemblages in higher-elevation areas were more phylogenetically clumped than those in lower-elevation areas, indicating that, in addition to elevational gradient, phylogenetic constraint may be a crucial factor that influences bird distribution in Taiwan. However, the current bird protected areas in Taiwan may overly depend on species richness and overlook the importance of the overall phylogenetic diversity.