Miracle-dz/UniFAR-FTUs huggingface dataset:
Subgrouping School-Aged Children with Autism Spectrum Disorder Based on Co-Occurring Psychopathology

Background: Symptom heterogeneity within autism spectrum disorder (ASD) is compounded by co-occurring psychopathology. Considering that some psychiatric disorders present together more often than others, deriving subgroups of individuals with ASD based on co-occurring psychopathology could better our understanding of symptom patterns existing within this population. This study's purpose was to derive subgroups of school-aged children with ASD based on co-occurring psychopathology while controlling for age and sex and to examine correlates of subgroup membership. Method: Six latent class models were estimated with a sample from the Simons Simplex Collection (n = 2,092), using dichotomized categories (borderline/clinical versus normal range) from five of the DSM-Oriented Scales of the Child Behavior Checklist for Ages 6 to 18 as indicator variables. We evaluated the predictive value of intellectual disability and three groups of medical conditions (allergies/autoimmune disorders, gastrointestinal disorders, and neurological disorders) on subgroup membership using multinomial logistic regression. Results: Four subgroups emerged based on the combined presence/absence of psychiatric symptoms: "Low Psychopathology," "Externalizing Problems," "Internalizing Problems," and "High Psychopathology. " Gastrointestinal disorders, the strongest predictor, was associated with increased odds of belonging to the "Externalizing Problems," "Internalizing Problems," and "High Psychopathology" subgroups over the "Low Psychopathology" subgroup, whereas intellectual disability was associated with decreased odds. Neurological disorders was also associated with increased odds of belonging to the "Internalizing Problems" and "High Psychopathology" subgroups. Conclusion: Patterns of psychopathology exist within school-aged children with ASD and are correlated with intellectual disability as well as specific medical conditions, providing guidance for clinical practice and etiology-driven research.
Therapy Assistant Staffing and Patient Quality Outcomes in Skilled Nursing Facilities

Therapy staffing declined in response to Medicare payment policy that removes incentives for intensive physical and occupational therapy in skilled nursing facilities, with therapy assistant staffing more impacted than therapist staffing. However, it is unknown whether therapy assistant staffing is associated with patient outcomes. Using 2017 national data, we examined associations between therapy assistant staffing and three outcomes: patient functional improvement, community discharge, and hospital readmissions, controlling for therapy intensity and facility characteristics. Assistant staffing was not associated with functional improvement. Compared with employing no assistants, staffing 25% to 75% occupational therapy assistants and 25% to 50% physical therapist assistants were associated with more community discharges. Higher occupational therapy assistant staffing was associated with higher readmissions. Higher intensity physical therapy was associated with better quality across outcomes. Skilled nursing facilities seeking to maximize profit while maintaining quality may be successful by choosing to employ more physical therapy assistants rather than sacrificing physical therapy intensity.
Interdependence between lignocellulosic biomasses, enzymatic hydrolysis and yeast cell factories in biorefineries

Biorefineries have a pivotal role in the bioeconomy scenario for the transition from fossil‐based processes towards more sustainable ones relying on renewable resources. Lignocellulose is a prominent feedstock since its abundance and relatively low cost. Microorganisms are often protagonists of biorefineries, as they contribute both to the enzymatic degradation of lignocellulose complex polymers and to the fermentative conversion of the hydrolyzed biomasses into fine and bulk chemicals. Enzymes have therefore become crucial for the development of sustainable biorefineries, being able to provide nutrients to cells from lignocellulose. Enzymatic hydrolysis can be performed by a portfolio of natural enzymes that degrade lignocellulose, often combined into cocktails. As enzymes can be deployed in different operative settings, such as separate hydrolysis and fermentation (SHF) or simultaneous saccharification and fermentation (SSF), their characteristics need to be combined with microbial ones to maximize the process. We therefore reviewed how the optimization of lignocellulose enzymatic hydrolysis can ameliorate bioethanol production when Saccharomyces cerevisiae is used as cell factory. Expanding beyond biofuels, enzymatic cocktail optimization can also be pivotal to unlock the potential of non‐Saccharomyces yeasts, which, thanks to broader substrate utilization, inhibitor resistance and peculiar metabolism, can widen the array of feedstocks and products of biorefineries.
Scalar turbulent behavior in the roughness sublayer of an Amazonian forest

Abstract. An important current problem in micrometeorology is the characterization of turbulence in the roughness sublayer (RSL), where most of the measurements above tall forests are made. There, scalar turbulent fluctuations display significant departures from the predictions of Monin–Obukhov similarity theory (MOST). In this work, we analyze turbulence data of virtual temperature, carbon dioxide, and water vapor in the RSL above an Amazonian forest (with a canopy height of 40 m), measured at 39.4 and 81.6 m above the ground under unstable conditions. We found that dimensionless statistics related to the rate of dissipation of turbulence kinetic energy (TKE) and the scalar variance display significant departures from MOST as expected, whereas the vertical velocity variance follows MOST much more closely. Much better agreement between the dimensionless statistics with the Obukhov similarity variable, however, was found for the subset of measurements made at a low zenith angle Z, in the range 0°
Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja.

PREMISE Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population-level differentiation in floral phenotype and genetic sequence variation among recently diverged Castilleja to explore patterns of diversification under different scenarios of reproductive isolation. METHODS Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespread C. sessiliflora and the more restricted C. purpurea species complex. RESULTS We document that C. sessiliflora and the C. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation within C. sessiliflora across floral morphs and geography and less differentiation among species of the C. purpurea complex. CONCLUSIONS Patterns of genetic distance in C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In the C. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco-evolutionary paths.
Multi‐omics profiling of a CHO cell culture system unravels the effect of culture pH on cell growth, antibody titer, and product quality

A robust monoclonal antibody (mAb) bioprocess requires physiological parameters such as temperature, pH, or dissolved oxygen to be well‐controlled as even small variations in them could potentially impact the final product quality. For instance, pH substantially affects N‐glycosylation, protein aggregation, and charge variant profiles, as well as mAb productivity. However, relatively less is known about how pH jointly influences product quality and titer. In this study, we investigated the effect of pH on culture performance, product titer, and quality profiles by applying longitudinal multi‐omics profiling, including transcriptomics, proteomics, metabolomics, and glycomics, at three different culture pH set points. The subsequent systematic analysis of multi‐omics data showed that pH set points differentially regulated various intracellular pathways including intracellular vesicular trafficking, cell cycle, and apoptosis, thereby resulting in differences in specific productivity, product titer, and quality profiles. In addition, a time‐dependent variation in mAb N‐glycosylation profiles, independent of pH, was identified to be mainly due to the accumulation of mAb proteins in the endoplasmic reticulum disrupting cellular homeostasis over culture time. Overall, this multi‐omics‐based study provides an in‐depth understanding of the intracellular processes in mAb‐producing CHO cell line under varied pH conditions, and could serve as a baseline for enabling the quality optimization and control of mAb production.
Theoretical substitutions between dairy products and all-cause and cause-specific mortality. Results from the Danish diet, cancer and health cohort

Abstract A daily intake of dairy products is recommended in many countries in order to maintain optimal health throughout life. However, evidence regarding the association between intake of individual dairy products and mortality is limited. We therfore, explored associations between intake of different dairy products and all-cause and cause-specific mortality using specified theoretical substitution analyses. We analysed data from 55 775 Danish men and women aged 50–64 years between 1993 and 1997. Information about dairy product intake at baseline was collected using a validated food frequency questionnaire. Information about vital status and causes of death was obtained through national registers. Measures of associations were calculated using Cox proportional hazards regression. During a median follow-up of 19·0 years, 11 586 participants died. For all-cause mortality, we observed that the intake of low-fat milk, whole-fat milk or low-fat yogurt products in place of cheese was associated with a higher rate of death (hazard ratios between 1·03 and 1·12 per serving/d substituted). The same pattern was present for CVD mortality. For cancer mortality, whole-fat milk and low-fat yogurt products in place of cheese were also associated with a higher rate of death for men while for women, whole-fat milk in place of buttermilk was associated with a higher cancer mortality rate. The results appeared robust in several sensitivity analyses. Our results suggest that intake of low-fat milk, whole-fat milk or low-fat yogurt products in place of cheese is associated with a higher rate of all-cause and cause-specific mortality.
Complete Genome Sequence of a Bacteroides fragilis Bacteriophage, vB_BfrS_NCTC

Bacteroides fragilis is an obligate anaerobe and a common gut commensal bacterium that is also an important opportunistic pathogen. Here, we present the complete genome sequence of the circularly permuted B. fragilis bacteriophage vB_BfrS_NCTC. It comprises 47,160 bp, with 69 open reading frames. ABSTRACT Bacteroides fragilis is an obligate anaerobe and a common gut commensal bacterium that is also an important opportunistic pathogen. Here, we present the complete genome sequence of the circularly permuted B. fragilis bacteriophage vB_BfrS_NCTC. It comprises 47,160 bp, with 69 open reading frames.
Clinical presentation of inguinal hernia among adults in Uyo, Nigeria

Background: Inguinal hernia is a common pathology seen by the general surgeon in the outpatient clinic. Its spectrum of clinical features on presentation significantly varies from the asymptomatic to the complicated. Objective: To identify and audit the common clinical presentation and presence of known risk factors for inguinal hernia among adult patients with inguinal hernias presenting to an outpatient clinic. Methods: The study involved adults presenting over 1 year at a surgical clinic with a clinical diagnosis of inguinal hernia. Data on age, sex, family history, abdominal pain, constipation, chronic cough, previous hernia surgery as well as features of bladder outlet obstruction and intra-abdominal mass were recorded into a format. Analysis into a simple percentage, mean, and standard deviation was done with SPSS version 17 (SPSS Inc. Chicago, IL, USA). Results: Sixty-five patients were enrolled in the study, comprising 49 males (75.4%) and 16 females (24.6%), M:F = 3:1. The mean age was 45.6 years (SD ± 16.9). The 16–40-year age group had the highest incidence of 29 cases (44.6%) of inguinal hernia. A family history of inguinal hernia (31 cases [47.7%]) and history of previous inguinal hernia surgery (15 cases [23.1%])) was observed. Ten patients with previous surgery presented with a contralateral hernia and 5 with a recurrence. Other factors were chronic constipation 10 cases, smoking 9 cases, chronic cough 8 cases, dysuria 7 cases, enlarged prostate 6 cases, abdominal mass 4 cases, and urethral stricture 1 case. Conclusion: Inguinal hernia is common among young and middle-aged adults in our series. Many patients have features suggestive of complications at presentation. Family history and past inguinal hernia surgery were important risk factors.
Interleukin19 gene polymorphism and its serum level in acne vulgaris patients

ABSTRACT Numerous cytokines are involved in acne vulgaris pathogenesis, though few studies correlate interleukin IL-19 to acne vulgaris. So this study aimed to assess the IL-19 (rs 2243191) gene polymorphism and its serum level in acne vulgaris. This case–control study involved 90 acne vulgaris cases and 90 age- and sex-matched controls. Acne severity was assessed according to Global Acne Grading System (GAGS), and serum IL-19 was assessed by ELISA and IL-19 (rs 2243191) gene polymorphism was assessed by real time PCR. This study showed that acne cases had significantly higher IL-19 levels than controls. Also, its level was significantly higher in severe cases than moderate and mild cases. Regarding IL-19 gene polymorphism (rs 2243191), TT and CT genotypes were significantly higher in patients than in controls. The incidence of minor allele T was greater in patients than in controls. There were significant differences between IL-19 genotypes and disease severity. Serum IL-19 was significantly higher in genotypes TT and CT acne cases than in those with genotype CC. We concluded that TT genotype of IL-19 might be a hereditary risk factor for acne vulgaris development. It is associated with a high IL-19 serum level, which could be a marker of acne severity.
Genetic Influence on Nociceptive Processing in the Human Brain—A Twin Study

Abstract Nociceptive processing in the human brain is complex and involves several brain structures and varies across individuals. Determining the structures that contribute to interindividual differences in nociceptive processing is likely to improve our understanding of why some individuals feel more pain than others. Here, we found specific parts of the cerebral response to nociception that are under genetic influence by employing a classic twin-design. We found genetic influences on nociceptive processing in the midcingulate cortex and bilateral posterior insula. In addition to brain activations, we found genetic contributions to large-scale functional connectivity (FC) during nociceptive processing. We conclude that additive genetics influence specific brain regions involved in nociceptive processing. The genetic influence on FC during nociceptive processing is not limited to core nociceptive brain regions, such as the dorsal posterior insula and somatosensory areas, but also involves cognitive and affective brain circuitry. These findings improve our understanding of human pain perception and increases chances to find new treatments for clinical pain.
Photobiomodulation with polychromatic light (600–1200 nm) improves fat graft survival by increasing adipocyte viability, neovascularization, and reducing inflammation in a rat model

Unpredictability with the final volume and viability of the graft are the major concerns in fat grafting. An experimental study was conducted to increase graft retention using photobiomodulation (PBM) with polychromatic light in near‐infrared region (600–1200 nm) by utilizing its stimulatory effects on angiogenesis, neovascularization, adipocyte viability, and anti‐inflammatory properties.
Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene

Abstract Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.
Human dystrophin expressing chimeric (DEC) cell therapy ameliorates cardiac, respiratory, and skeletal muscle's function in Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a progressive and lethal disease, caused by X‐linked mutations of the dystrophin encoding gene. The lack of dystrophin leads to muscle weakness, degeneration, fibrosis, and progressive loss of skeletal, cardiac, and respiratory muscle function resulting in premature death due to the cardiac and respiratory failure. There is no cure for DMD and current therapies neither cure nor arrest disease progression. Thus, there is an urgent need to develop new approaches and safer therapies for DMD patients. We have previously reported functional improvements which correlated with increased dystrophin expression following transplantation of dystrophin expressing chimeric (DEC) cells of myoblast origin to the mdx mouse models of DMD. In this study, we demonstrated that systemic‐intraosseous transplantation of DEC human cells derived from myoblasts of normal and DMD‐affected donors, increased dystrophin expression in cardiac, respiratory, and skeletal muscles of the mdx/scid mouse model of DMD. DEC transplant correlated with preservation of ejection fraction and fractional shortening on echocardiography, improved respiratory function on plethysmography, and improved strength and function of the limb skeletal muscles. Enhanced function was associated with improved muscle histopathology, revealing reduced mdx pathology, fibrosis, decreased inflammation, and preserved muscle morphology and architecture. Our findings confirm that DECs generate a systemic protective effect in DMD‐affected target organs. Therefore, DECs represents a novel therapeutic approach with the potential to preserve or enhance multiorgan function of the skeletal, cardiac, and respiratory muscles critical for the well‐being of DMD patients.
Infrared spectroscopy and forensic entomology: Can this union work? A literature review

For more than two decades, infrared spectroscopy techniques combined with multivariate analysis have been efficiently applied in several entomological fields, such as Taxonomy and Toxicology. However, little is known about its use and applicability in Forensic entomology (FE) field, with vibrational techniques such as Near‐infrared spectroscopy (NIRS) and Medium‐infrared spectroscopy (MIRS) underutilized in forensic sciences. Thus, this work describes the potential of NIRS, MIRS, and other spectroscopic methodologies, for entomological analysis in FE, as well as discusses its future uses for criminal or civil investigations. After a thorough research on scientific journals database, a total of 33 publications were found in scientific journals, with direct or indirect application to FE, including experimental applications of NIRS and MIRS in taxonomic discrimination of species, larval age prediction, detection of toxic substances in insects from environments or crime scenes, and detection of internal or external infestations by live or dead insects in stored products. Besides, NIRS and MIRS combined with multivariate analysis were efficient, inexpensive, fast, and non‐destructive analytical tools. However, more than 51% of the spectroscopic publications are concentrated in the stored products field, and so we discuss the need for expansion and more direct application in other FE areas. We hope the number of articles continues to increase, and as NIRS and MIRS technology progress, they advance in forensic research and routine use.