Miracle-dz/UniFAR-FTUs huggingface dataset:
Decreased theory of mind skills, increased emotion dysregulation and insight levels in adolescents diagnosed with obsessive compulsive disorder

Abstract Background: An abnormal interaction between cognition and emotion may contribute to the development of obsessive-compulsive disorder (OCD). Aims: In this study, we aimed to evaluate theory of mind and emotion regulation skills in adolescents diagnosed with OCD. In addition, the results were evaluated in accordance with patients’ insight levels. Methods: This study was conducted with 50 patients, who were aged between 11 and 16 and who were newly diagnosed with OCD and 50 healthy individuals. The Turkish version of the Schedule for Affective Disorders and Schizophrenia for School Age Children – Present and Lifetime was used to diagnose OCD and other comorbidities. The Children’s Yale–Brown Obsessive Compulsive Scale, the Children’s Depression Inventory, and the State-Trait Anxiety Inventory for Children were used for clinical evaluation. The intelligence levels were assessed using the Wechsler Intelligence Scale for Children-Revised Short Form. Reading the Mind in the Eyes Test was used in patients. The Difficulties in Emotion Regulation Scale was also used to evaluate the skills of regulating emotions. Results: Patients with OCD had lower ability with regard to reading minds in the eyes and emotion regulation than the healthy individuals. Patients with OCD, who had a poor insight, had more difficulty in reading minds in the eyes and emotion regulation than those with good insight. Conclusions: This study supports the idea that OCD is related to deficits in theory of mind and emotion regulation skills. Thus, further studies are required to confirm the findings of this study.
Disparate Candida albicans Biofilm Formation in Clinical Lipid Emulsions Due to Capric Acid-Mediated Inhibition

Receipt of parenteral nutrition (PN) remains an independent risk factor for developing catheter-related bloodstream infections (CR-BSI) caused by fungi, including by the polymorphic fungus Candida albicans, which is notoriously adept at forming drug-resistant biofilm structures. Among a variety of macronutrients, PN solutions contain lipid emulsions to supply daily essential fats and are often delivered via central venous catheters (CVCs). ABSTRACT Receipt of parenteral nutrition (PN) remains an independent risk factor for developing catheter-related bloodstream infections (CR-BSI) caused by fungi, including by the polymorphic fungus Candida albicans, which is notoriously adept at forming drug-resistant biofilm structures. Among a variety of macronutrients, PN solutions contain lipid emulsions to supply daily essential fats and are often delivered via central venous catheters (CVCs). Therefore, using an in vitro biofilm model system, we sought to determine whether various clinical lipid emulsions differentially impacted biofilm growth in C. albicans. We observed that the lipid emulsions Intralipid and Omegaven both stimulated C. albicans biofilm formation during growth in minimal medium or a macronutrient PN solution. Conversely, Smoflipid inhibited C. albicans biofilm formation by approximately 50%. Follow-up studies revealed that while Smoflipid did not impair C. albicans growth, it did significantly inhibit hypha formation and hyphal elongation. Moreover, growth inhibition could be recapitulated in Intralipid when supplemented with capric acid—a fatty acid present in Smoflipid but absent in Intralipid. Capric acid was also found to dose dependently inhibit C. albicans biofilm formation in PN solutions. This is the first study to directly compare different clinical lipid emulsions for their capacity to affect C. albicans biofilm growth. Results derived from this study necessitate further research regarding different lipid emulsions and rates of fungus-associated CR-BSIs.
JAK–STAT inhibition impairs K‐RAS‐driven lung adenocarcinoma progression

Oncogenic K‐RAS has been difficult to target and currently there is no K‐RAS‐based targeted therapy available for patients suffering from K‐RAS‐driven lung adenocarcinoma (AC). Alternatively, targeting K‐RAS‐downstream effectors, K‐RAS‐cooperating signaling pathways or cancer hallmarks, such as tumor‐promoting inflammation, has been shown to be a promising therapeutic strategy. Since the JAK–STAT pathway is considered to be a central player in inflammation‐mediated tumorigenesis, we investigated here the implication of JAK–STAT signaling and the therapeutic potential of JAK1/2 inhibition in K‐RAS‐driven lung AC. Our data showed that JAK1 and JAK2 are activated in human lung AC and that increased activation of JAK–STAT signaling correlated with disease progression and K‐RAS activity in human lung AC. Accordingly, administration of the JAK1/2 selective tyrosine kinase inhibitor ruxolitinib reduced proliferation of tumor cells and effectively reduced tumor progression in immunodeficient and immunocompetent mouse models of K‐RAS‐driven lung AC. Notably, JAK1/2 inhibition led to the establishment of an antitumorigenic tumor microenvironment, characterized by decreased levels of tumor‐promoting chemokines and cytokines and reduced numbers of infiltrating myeloid derived suppressor cells, thereby impairing tumor growth. Taken together, we identified JAK1/2 inhibition as promising therapy for K‐RAS‐driven lung AC.
Malignant lymphoma in granulomatosis with polyangiitis: subtypes, clinical characteristics and prognosis

Several autoimmune and inflammatory conditions, such as rheumatoid arthritis (RA) and primary Sj€ ogrens’s syndrome (pSS), have repeatedly been linked to an increased risk of malignant lymphoma [1,2]. Certain inflammatory conditions are also associated with the development of specific lymphoma subtypes such as mucosa-associated lymphoid tissue (MALT) lymphoma in pSS and diffuse large B-cell lymphoma (DLBCL) in RA. The underlying mechanisms behind this association remain unclear. The highly increased risk of developing MALT lymphoma of the parotid gland in pSS indicates that local inflammatory processes can promote lymphoma development at the site of chronic inflammation [3]. In RA, an association between disease severity and risk of lymphoma has been shown. Granulomatosis with polyangiitis (GPA), formerly Wegener’s granulomatosis, is a systemic small vessel vasculitis associated with the presence of anti-neutrophil cytoplasmic antibodies (ANCA) and characterized by granulomatous inflammation and necrotizing vasculitis of the airways and kidneys but possibly affecting any organ system. An increased risk of lymphoma in patients with GPA has been reported in several epidemiological studies [4,5]. However, very little is known about risk factors for lymphoma development in this group, possible relation to disease severity, treatment and lymphoma subtypes or the prognosis for the lymphomas. This is the first published study on GPA and lymphoma, giving detailed information on the GPA characteristics and possible risk factors for lymphoma and also lymphoma subtypes treatment and survival.
Adherence to a Mediterranean-like Diet as a Protective Factor Against COPD: A Nested Case-Control Study

Abstract A diet rich in nutrients has been suggested to have protective effects against the development of chronic obstructive pulmonary disease (COPD). Since the traditional Mediterranean diet is high in nutrients, including antioxidants, vitamins, and minerals, it is of interest to study as a protective factor against COPD. Our aim was therefore to study its associations with development of COPD using population-based prospective data from the Västerbotten Intervention Programme (VIP) cohort. Data on diet from 370 individuals, who later visited the Department of Medicine at the University Hospital, Umeå, Sweden, with a diagnosis of COPD, were compared to 1432 controls. Adherence to a Mediterranean diet was assessed by a modified version of the Mediterranean diet score (MDS). Cases were diagnosed with COPD 11.1 years (mean) (standard deviation [SD] 4.5 years) after first stating their dietary habits in the VIP at a mean age of 55.5 years (SD 6.6 years). Higher MDS was associated with a higher level of education and not living alone. After adjustment for co-habiting and education level, individuals with an intermediate MDS and those with the highest MDS had a lower odds of developing COPD (odds ratio [OR] 0.73, 95% confidence interval [CI] 0.56–0.95; OR 0.56, 95% CI 0.37–0.86, respectively). These results remained also after adjustment for smoking intensity, i.e., numbers of cigarettes smoked per day (OR 0.73, 95% CI 0.53–0.99; OR 0.59, 95% CI 0.35–0.97), respectively). To conclude, adherence to a Mediterranean-like diet seems to be inversely associated with the development of COPD.
Healthy Planet, Healthy Youth: A Food Systems Education and Promotion Intervention to Improve Adolescent Diet Quality and Reduce Food Waste

Emerging evidence suggests a link between young people's interest in alternative food production practices and dietary quality. The primary purpose of this study was to examine the impact of a student-driven sustainable food systems education and promotion intervention on adolescent school lunch selection, consumption, and waste behaviors. Sixth grade science teachers at two middle schools (n = 268 students) implemented a standards-based curriculum on sustainable food systems, addressing the environmental impacts of food choices and food waste. The cumulating curriculum activity required the 6th grade students to share their food systems knowledge with their 7th and 8th grade counterparts (n = 426) through a cafeteria promotional campaign to discourage food waste. School-wide monthly plate waste assessments were used to evaluate changes in vegetable consumption and overall plate waste using a previously validated digital photography method. At baseline, the intervention students consumed significantly less vegetables relative to the control group (47.1% and 71.8% of vegetables selected, respectively (p = 0.006). This disparity was eliminated after the intervention with the intervention group consuming 69.4% and the control consuming 68.1% of selected vegetables (p = 0.848). At five months follow up, the intervention group wasted significantly less salad bar vegetables compared to the control group (24.2 g and 50.1 g respectively (p = 0.029). These findings suggest that food systems education can be used to promote improved dietary behaviors among adolescent youth.
“Bring Your Own Device (BYOD)” for Face to Face and Virtual Collaborative Learning in EFL in Secondary School: A mixed methods Investigation

iii ACKNOWLEDGMENT . iv DEDICATION . iv TABLES OF CONTENTS . v LIST OF TABLES . ix LIST OF FIGURES . x LIST OF ABBREVIATIONS . xi CHAPTER 1: INTRODUCTION TO THE STUDY .
Biomass losses resulting from insect and disease invasions in US forests

Significance Forests provide a wide variety of vital ecosystem services but are increasingly affected by anthropogenic disturbances. Among these, invasions by nonnative pests can adversely affect ecosystem services. Comprehensive estimates of the impacts of nonnative pest on forest biomass loss are limited, however. Using more than 92,000 field plots, we quantified pest-induced biomass loss across the conterminous United States for the first time. We show that invasive pests are causing significant shifts in carbon dynamics in US forests. In addition, >40% of the total live biomass in US forests is at risk for invasion by currently established pest species. Our findings are of potential significance in justifying the selection of future policy options and in future carbon dynamics modeling research. Worldwide, forests are increasingly affected by nonnative insects and diseases, some of which cause substantial tree mortality. Forests in the United States have been invaded by a particularly large number (>450) of tree-feeding pest species. While information exists about the ecological impacts of certain pests, region-wide assessments of the composite ecosystem impacts of all species are limited. Here we analyze 92,978 forest plots distributed across the conterminous United States to estimate biomass loss associated with elevated mortality rates caused by the 15 most damaging nonnative forest pests. We find that these species combined caused an additional (i.e., above background levels) tree mortality rate of 5.53 TgC per year. Compensation, in the form of increased growth and recruitment of nonhost species, was not detectable when measured across entire invaded ranges but does occur several decades following pest invasions. In addition, 41.1% of the total live forest biomass in the conterminous United States is at risk of future loss from these 15 pests. These results indicate that forest pest invasions, driven primarily by globalization, represent a huge risk to US forests and have significant impacts on carbon dynamics.
Subject specific hand and forearm musculoskeletal 3D geometries using high-resolution MR images

Abstract Magnetic medical imaging (MRI) is commonly used to 3D rendering of musculoskeletal structures. However, due to technical limitations of the device e.g. the coil, high-spacial resolution is available only for a small field of view. However in the case of hand and forearm investigation, and due to the long tendon and small bones, both high special and a large field of view are required. It is the aim of this study to propose the in silico enlargement of the field of view to 3D visualise all hand’s bones and tendons paths. Using MRI clinical routine sequence, we detailed a procedure of hand immobilisation by alginate and registration of up to four consecutive MRI volume acquisitions. In order to validate our method, we evaluated the accuracy of the anatomical structures segmentation (i), the robustness of the registration by a sensitivity analysis (ii) and the accuracy of the 3D reconstruction by comparison with computer tomography imaging (iii). The results demonstrated a mean error of 1 mm on the 3D external surface and of 0.94 mm on the localisation of the hand bones. We also tested different hand sizes and showed that the field of view could be increased up to 2.3 time compared to the original one.
Relationship between perception of emotional home atmosphere and fruit and vegetable consumption in European adolescents: results from the I.Family survey

Abstract Objective: Consumption of fruits and vegetables (F&V) among adolescents falls below recommendations in many Western countries. The impact of social and emotional aspects of family life on adolescent dietary behaviour may contribute to this, yet remains under-investigated. The present study examines the association between adolescents’ perceptions of emotional home atmosphere (EHA) and their F&V consumption frequency. Design: An FFQ was used to assess F&V consumption frequency. EHA was assessed by an eight-item measure with three subscales: perceived home warmth, strictness and relational tension. EHA subscales were used as binary variables: a score equal to or above the median value was considered as a higher perception, while a score below the median was considered as a lower perception of the EHA in question. Country differences in meeting the European 5-a-day recommendations were described. Further, the association between EHA and F&V consumption frequency was investigated using multiple linear regression. Setting: Regional examination centres in eight European countries. Participants: Adolescents (n 3196) aged 12–18 years. Results: The mean F&V consumption frequency was 3·27 (sd 2·84) times/d. Only 16·1 % of boys and 18 % of girls in our study sample met the recommendation of five F&V daily. After controlling for age, sex, education level of the parents and country of origin, perceived home warmth was associated with a 16 (95 % CI 9, 22) % higher F&V consumption frequency (P < 0·001). Conclusions: F&V consumption frequency was suboptimal in the survey areas. Interventions targeting perceived warmth as a component of EHA could potentially have a positive effect on adolescents’ dietary behaviour.
Metabolomics-Based Studies Assessing Exercise-Induced Alterations of the Human Metabolome: A Systematic Review

This systematic review provides a qualitative appraisal of 24 high-quality metabolomics-based studies published over the past decade exploring exercise-induced alterations of the human metabolome. Of these papers, 63% focused on acute metabolite changes following intense and prolonged exercise. The best studies utilized liquid chromatography mass spectrometry (LC-MS/MS) analytical platforms with large chemical standard libraries and strong, multivariate bioinformatics support. These studies reported large-fold changes in diverse lipid-related metabolites, with more than 100 increasing two-fold or greater within a few hours post-exercise. Metabolite shifts, even after strenuous exercise, typically return to near pre-exercise levels after one day of recovery. Few studies investigated metabolite changes following acute exercise bouts of shorter durations (< 60 min) and workload volumes. Plasma metabolite shifts in these types of studies are modest in comparison. More cross-sectional and exercise training studies are needed to improve scientific understanding of the human system’s response to varying, chronic exercise workloads. The findings derived from this review provide direction for future investigations focused on the body’s metabolome response to exercise.
Using Dependency Tree Grammar to Enhance the Reordering Model of Statistical Machine Translation Systems

We propose three novel reordering models for statistical machine translation. These reordering models use dependency tree to improve the translation quality. All reordering models are utilized as features in a log linear framework and therefore guide the decoder to make better decisions about reordering. These reordering models are tested on two English-Persian parallel corpora with different statistics and domains. The BLEU score is improved by 2.5 on the first corpus and by 1.2 on the other.
Human GNPTAB stuttering mutations engineered into mice cause vocalization deficits and astrocyte pathology in the corpus callosum

Significance Stuttering is a common neurodevelopmental disorder. However, the neurological causes of this disorder are poorly understood. The disorder is highly genetic, and recent discoveries have found several genes involved in this disorder, but how these lead to the unique clinical features of stuttering has been unknown. We have shown that mice carrying human stuttering mutations display vocalization deficits that recreate the salient features of human stuttering. In these mice, we have used several different complementary techniques to identify a specific deficit in astrocytes, a type of glial cell prominent in white matter tracts, particularly in the corpus callosum of these mice. These findings suggest astrocytes as a site of the neuropathology, leading to a deficit in interhemispheric connectivity in stuttering. Stuttering is a common neurodevelopmental disorder that has been associated with mutations in genes involved in intracellular trafficking. However, the cellular mechanisms leading to stuttering remain unknown. Engineering a mutation in N-acetylglucosamine-1-phosphate transferase subunits α and β (GNPTAB) found in humans who stutter into the mouse Gnptab gene resulted in deficits in the flow of ultrasonic vocalizations similar to speech deficits of humans who stutter. Here we show that other human stuttering mutations introduced into this mouse gene, Gnptab Ser321Gly and Ala455Ser, produce the same vocalization deficit in 8-day-old pup isolation calls and do not affect other nonvocal behaviors. Immunohistochemistry showed a marked decrease in staining of astrocytes, particularly in the corpus callosum of the Gnptab Ser321Gly homozygote mice compared to wild-type littermates, while the staining of cerebellar Purkinje cells, oligodendrocytes, microglial cells, and dopaminergic neurons was not significantly different. Diffusion tensor imaging also detected deficits in the corpus callosum of the Gnptab Ser321Gly mice. Using a range of cell type-specific Cre-drivers and a Gnptab conditional knockout line, we found that only astrocyte-specific Gnptab-deficient mice displayed a similar vocalization deficit. These data suggest that vocalization defects in mice carrying human stuttering mutations in Gnptab derive from abnormalities in astrocytes, particularly in the corpus callosum, and provide support for hypotheses that focus on deficits in interhemispheric communication in stuttering.
Phased implementation of pathogen‐reduced platelets in a health system facilitates increased manufacturing at the blood center

Pathogen reduction treatment (PRT) reduces the risk of transfusion‐transmitted infections from established and emerging organisms. Manufacturing, however, is complex. In our university health system, we phased in pathogen‐reduced platelets (PR PLTs) by patient population. We then assessed the implementation strategy and investigated factors in the supply chain that prevented us from meeting the goal of providing greater than 90% PR PLTs within 6 months.
Put a Bow on It: Knotted Antibiotics Take Center Stage

Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products produced across all domains of life. The lasso peptides, a subclass of RiPPs with a lasso-like structure, are structurally and functionally unique compared to other known peptide antibiotics in that the linear peptide is literally “tied in a knot” during its post-translational maturation. This underexplored class of peptides brings chemical diversity and unique modes of action to the antibiotic space. To date, eight different lasso peptides have been shown to target three known molecular machines: RNA polymerase, the lipid II precursor in peptidoglycan biosynthesis, and the ClpC1 subunit of the Clp protease involved in protein homeostasis. Here, we discuss the current knowledge on lasso peptide biosynthesis as well as their antibiotic activity, molecular targets, and mechanisms of action.
Identification of new hypoxia‐regulated epithelial‐mesenchymal transition marker genes labeled by H3K4 acetylation

Hypoxia‐induced epithelial‐mesenchymal transition (EMT) involves the interplay between chromatin modifiers histone deacetylase 3 (HDAC3) and WDR5. The histone mark histone 3 lysine 4 acetylation (H3K4Ac) is observed in the promoter regions of various EMT marker genes (eg, CDH1 and VIM). To further define the genome‐wide location of H3K4Ac, a chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP‐seq) analysis was performed using a head and neck squamous cell carcinoma (HNSCC) FaDu cell line under normoxia and hypoxia. H3K4Ac was found to be located mainly around the transcription start site. Coupled with analysis of gene expression by RNA sequencing and using a HDAC3 knockdown cell line, 10 new genes (BMI1, GLI1, SMO, FOXF1, SIRT2, etc) that were labeled by H3K4Ac and regulated by HDAC3 were identified. Overexpression or knockdown of GLI1/SMO increased or repressed the in vitro migration and invasion activity in OECM‐1/FaDu cells, respectively. In HNSCC patients, coexpression of GLI1 and SMO in primary tumors correlated with metastasis. Our results identify new EMT marker genes that may play a significant role in hypoxia‐induced EMT and metastasis and further provide diagnostic and prognostic implications.