Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses

Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
Primary Immunodeficiency and Cancer Predisposition Revisited: Embedding Two Closely Related Concepts Into an Integrative Conceptual Framework

Common understanding suggests that the normal function of a “healthy” immune system safe-guards and protects against the development of malignancies, whereas a genetically impaired one might increase the likelihood of their manifestation. This view is primarily based on and apparently supported by an increased incidence of such diseases in patients with specific forms of immunodeficiencies that are caused by high penetrant gene defects. As I will review and discuss herein, such constellations merely represent the tip of an iceberg. The overall situation is by far more varied and complex, especially if one takes into account the growing difficulties to define what actually constitutes an immunodeficiency and what defines a cancer predisposition. The enormous advances in genome sequencing, in bioinformatic analyses and in the functional in vitro and in vivo assessment of novel findings together with the availability of large databases provide us with a wealth of information that steadily increases the number of sequence variants that concur with clinically more or less recognizable immunological problems and their consequences. Since many of the newly identified hard-core defects are exceedingly rare, their tumor predisposing effect is difficult to ascertain. The analyses of large data sets, on the other hand, continuously supply us with low penetrant variants that, at least in statistical terms, are clearly tumor predisposing, although their specific relevance for the respective carriers still needs to be carefully assessed on an individual basis. Finally, defects and variants that affect the same gene families and pathways in both a constitutional and somatic setting underscore the fact that immunodeficiencies and cancer predisposition can be viewed as two closely related errors of development. Depending on the particular genetic and/or environmental context as well as the respective stage of development, the same changes can have either a neutral, predisposing and, in some instances, even a protective effect. To understand the interaction between the immune system, be it “normal” or “deficient” and tumor predisposition and development on a systemic level, one therefore needs to focus on the structure and dynamic functional organization of the entire immune system rather than on its isolated individual components alone.
Can Gender and Age Impact on Response Pattern of Depressive Symptoms Among College Students? A Differential Item Functioning Analysis

Background: Self-reported depressive complaints among college students might indicate different degrees of severity of depressive states. Through the framework of item response theory, we aim to describe the pattern of responses to items of the Beck Depression Inventory-II (BDI-II), in terms of endorsement probability and discrimination along the continuum of depression. Potential differential item functioning of the scale items of the BDI-II is investigated, by gender and age, to compare across sub-groups of students. Methods: The 21-item BDI-II was cross-sectionally administered to a representative sample of 12,677 Brazilian college students. Reliability was evaluated based on Cronbach's alpha coefficient. Severity (bi) and discrimination (a) parameters of each BDI-II items were calculated through the graded response model. The influence of gender and age were tested for differential item functioning (DIF) within the item response theory-based approach. Results: The BDI-II presented good reliability (α = 0.91). Women and younger students significantly presented a higher likelihood of depression (cut-off > 13) than men and older counterparts. In general, participants endorsed more easily cognitive-somatic items than affective items of the scale. “Guilty feelings,” “suicidal thoughts,” and “loss of interest in sex” were the items that most likely indicated depression severity (b ≥ 3.60). However, all BDI-II items showed moderate-to-high discrimination (a ≥ 1.32) for depressive state. While two items were flagged for DIF, “crying” and “loss of interest in sex,” respectively for gender and age, the global weight of these items on the total score was negligible. Conclusions: Although respondents' gender and age might present influence on response pattern of depressive symptoms, the measures of self-reported symptoms have not inflated severity scores. These findings provide further support to the validity of using BDI-II for assessing depression in academic contexts and highlight the value of considering gender- and age-related common symptoms of depression.
The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa

Interactions between the gut microbiome and the brain are of increasing interest to both researchers and clinicians. Evidence is mounting on the causal role of an altered gut microbiome in inflammatory diseases such as arthritis, inflammatory bowel disease, obesity and diabetes, and psychiatric diseases like anxiety and depression. Mechanisms include altered energy harvest from food, hormonal changes, increased gut permeability, inflammation, immune response, and a direct influence on the brain and behavior. Anorexia nervosa (AN) is the third most common disease in adolescence and exacts a high burden on patients and caregivers. It often becomes chronic and has the highest mortality of all psychiatric diseases. As AN is characterized by nutritional restrictions, weight loss, and severe behavioral symptoms including weight phobia, comorbid anxiety and depression, accompanied by endocrine alterations, increased inflammation, and immune response, exploring the role of the gut microbiome is crucial. Here, we present an overview of the potential mechanisms of interaction between the gut microbiome, the host and particularly the brain in AN and summarize the initial findings of microbiome research on AN. We conclude by identifying future research directions and potential therapeutic approaches, including nutritional interventions, probiotics, prebiotics and food supplements, that could become important additions to current AN therapy.
Delayed Spine Pruning of Direct Pathway Spiny Projection Neurons in a Mouse Model of Parkinson’s Disease

In animal models of Parkinson’s disease (PD), principal striatal spiny projection neurons (SPNs) lose axospinous synapses. However, there has been a disagreement about whether this loss is restricted to a specific type of SPN or not, as some studies have reported pruning in both direct pathway SPNs and indirect pathway SPNs, while others have found this pruning to be restricted to indirect pathway SPNs. One possible explanation for the discrepancy is the period between the induction of the parkinsonian state and the assessment of spine loss. To test this hypothesis, transgenic mice were subjected to unilateral 6-hydroxydopamine (6-OHDA) lesions of nigrostriatal dopaminergic neurons and then direct pathway SPNs examined in ex vivo brain slices using two photon laser scanning microscopy either one or 2 months afterwards. These studies revealed that 1 month after the lesion, there was no loss of spines in direct pathway SPNs. However, 2 months after the lesion, spine loss was significant in direct pathway SPNs. In addition to reconciling the existing literature on the impact of the parkinsonian state on axospinous synapse elimination in SPNs, our results suggest that the delayed spine loss in direct pathway SPNs is not driven by homeostatic mechanisms [as posited for indirect pathway (iSPNs)], but rather by network pathophysiology.
Phylogeographic Distribution of Human and Hare Francisella Tularensis Subsp. Holarctica Strains in the Netherlands and Its Pathology in European Brown Hares (Lepus Europaeus)

Sequence-based typing of Francisella tularensis has led to insights in the evolutionary developments of tularemia. In Europe, two major basal clades of F. tularensis subsp. holarctica exist, with a distinct geographical distribution. Basal clade B.6 is primarily found in Western Europe, while basal clade B.12 occurs predominantly in the central and eastern parts of Europe. There are indications that tularemia is geographically expanding and that strains from the two clades might differ in pathogenicity, with basal clade B.6 strains being potentially more virulent than basal clade B.12. This study provides information on genotypes detected in the Netherlands during 2011–2017. Data are presented for seven autochthonous human cases and for 29 European brown hares (Lepus europaeus) with laboratory confirmed tularemia. Associated disease patterns are described for 25 European brown hares which underwent post-mortem examination. The basal clades B.6 and B.12 are present both in humans and in European brown hares in the Netherlands, with a patchy geographical distribution. For both genotypes the main pathological findings in hares associated with tularemia were severe (sub)acute necrotizing hepatitis and splenitis as well as necrotizing lesions and hemorrhages in several other organs. Pneumonia was significantly more common in the B.6 than in the B.12 cases. In conclusion, the two major basal clades present in different parts in Europe are both present in the Netherlands. In hares found dead, both genotypes were associated with severe acute disease affecting multiple organs. Hepatitis and splenitis were common pathological findings in hares infected with either genotype, but pneumonia occurred significantly more frequently in hares infected with the B.6 genotype compared to hares infected with the B.12 genotype.
SERPINs—From Trap to Treatment

Excessive enzyme activity often has pathological consequences. This for example is the case in thrombosis and hereditary angioedema, where serine proteases of the coagulation system and kallikrein-kinin system are excessively active. Serine proteases are controlled by SERPINs (serine protease inhibitors). We here describe the basic biochemical mechanisms behind SERPIN activity and identify key determinants that influence their function. We explore the clinical phenotypes of several SERPIN deficiencies and review studies where SERPINs are being used beyond replacement therapy. Excitingly, rare human SERPIN mutations have led us and others to believe that it is possible to refine SERPINs toward desired behavior for the treatment of enzyme-driven pathology.
No Money, No Problem: Enhanced Reward Positivity in the Absence of Monetary Reward

The reward-related positivity (RewP) is an event-related potential (ERP) with a positive amplitude occurring approximately 250–350 ms post-feedback at frontocentral electroencephalogram (EEG) electrode sites. The RewP is typically elicited in monetary gambling tasks and has a relatively larger amplitude for positive vs. negative outcomes. However, the extent to which RewP amplitude is modulated by non-monetary feedback is less clear. To address this issue, EEG was used to record reward-related electrocortical activity during a simple non-monetary gambling task. We hypothesized that the RewP would be enhanced for non-monetary wins relative to losses, which was supported by the results. In our supplementary material, we provide additional analyses suggesting that this effect was not observed for the P3. In sum, RewP amplitudes were larger for positive (nonmonetary) feedback relative to negative feedback at frontocentral electrode sites—suggesting that monetary reward is not necessary to elicit the RewP.
Patients’ Comprehension of Mindfulness-Based Cognitive Behavioral Therapy in an Outpatient Clinic for Resistant Depression: A Cross-Sectional Study

The current study investigated the comprehension of mindfulness-based cognitive behavioral therapy (MBCT) by patients with resistant depression at the Psychiatry Institute of the Federal University of Rio de Janeiro, Brazil. This was the first time the model was used in the institution to treat these patients. In this study, 45 patients were invited to participate in a baseline session of MBCT that consisted in the explanation of the model and experimental exercises conducted by two experienced therapists. Twenty eight patients accepted to participate. At the end of the intervention, the patients completed a self-administered questionnaire designed by our ambulatory to assess their understanding of the method’s goals. Patients with anxiety disorder was also accessed for group comparison. More than 75% of the patients rated the intervention as comprehensible and workable. Compared to patients with depression, patients with anxiety had a better understanding of the mindfulness framework (6.5%) and the meaning of cognitive behavioral therapy (17.6%). Patients that completed the intervention described the baseline session of MBCT as comprehensive and acceptable. These results may allow possible future developments in the practice of mindfulness as a treatment applicable in many condition and settings even in the Brazilian context.
Characterization of Clinically Relevant Strains of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Occurring in Environmental Sources in a Rural Area of China by Using Whole-Genome Sequencing

Klebsiella pneumoniae is a gram-negative, opportunistic pathogen, and a common cause of healthcare-associated infections such as pneumonia, septicemia, and urinary tract infection. The purpose of this study was to survey the occurrence of and characterize K. pneumoniae in different environmental sources in a rural area of Shandong province, China. Two hundred and thirty-one samples from different environmental sources in 12 villages were screened for extended-spectrum β-lactamase-(ESBL)-producing K. pneumoniae, and 14 (6%) samples were positive. All isolates were multidrug-resistant and a few of them belonged to clinically relevant strains which are known to cause hospital outbreaks worldwide. Serotypes, virulence genes, serum survival, and phagocytosis survival were analyzed and the results showed the presence of virulence factors associated with highly virulent clones and a high degree of phagocytosis survivability, indicating the potential virulence of these isolates. These results emphasize the need for further studies designed to elucidate the role of the environment in transmission and dissemination of ESBL-producing K. pneumoniae and the potential risk posed to human and environmental health.
Military Veterans and Their PTSD Service Dogs: Associations Between Training Methods, PTSD Severity, Dog Behavior, and the Human-Animal Bond

Introduction: Psychiatric service dogs are increasingly being sought out by military veterans as a complementary intervention for posttraumatic stress disorder (PTSD). After receiving a service dog, many veterans continue training their service dog at home. Our objective was to explore the associations between training methods, PTSD severity, service dog behavior, and the veteran-service dog bond in a population of military veterans with PTSD. Methods: Post-9/11 military veterans with PTSD who had received a psychiatric service dog were recruited from a national service dog provider. A total of 111 veterans (M = 40.1 ± 8.3 years, 80% male) participated in an online survey regarding frequency of training methods, PTSD symptom severity, service dog behavior, and the human-animal bond. Service dogs were predominately Labrador Retriever purebreds or mixes of various breeds (66% male) and mostly obtained from shelters or rescues (58%). Training methods were divided into five categories: positive reinforcement (e.g., physical praise), negative punishment (e.g., ignoring the dog), positive punishment (e.g., verbal correction), dominance (e.g., alpha roll), and bond-based (e.g., co-sleeping). Data were analyzed using general linear models. Results: Veterans self-reported using all five categories of training methods at least once a month. More frequent use of positive punishment was associated with less closeness with their service dog (p = 0.02), more fear (p = 0.003), less eye contact (p < 0.0001), and less trainability (p = 0.04). More frequent use of positive reinforcement was associated with higher closeness to their service dog (p = 0.002) and perceived increased attachment behavior (p = 0.002) and playfulness (p = 0.002). More frequent use of bond-based methods was associated with higher closeness to their service dog (p = 0.02). PTSD severity was not significantly associated with reported dog behavior, temperament, or veteran-service dog closeness. Conclusion: Military veterans with PTSD service dogs reported using many training methods that were associated with different outcomes. In general, the reported use of positive reinforcement or bond-based training methods were associated with reporting more positive outcomes while the reported use of positive punishment was associated with reporting more negative outcomes. Educating service dog organizations and recipients about the impacts of training methods could be beneficial for service dog efficacy and welfare.
Revisiting the Role of Insulin-Like Growth Factor-I Receptor Stimulating Activity and the Apolipoprotein E in Alzheimer’s Disease

Background: Alterations in insulin-like growth factor I (IGF-I) signaling have been associated with dementia and Alzheimer’s disease (AD). Studies on the association between IGF-I levels and dementia risk have been inconclusive. We reported earlier that higher levels of IGF-I receptor stimulating activity are associated with a higher prevalence and incidence of dementia. Objective: In the present study, we test the robustness of the association between IGF-I receptor stimulating activity and dementia by extending the follow-up period to 16 years and investigate possible effect modification by apolipoprotein E (ApoE). Methods: At baseline, circulating IGF-I receptor stimulating activity was determined by the IGF-I kinase receptor activation (KIRA) assay in 1,014 elderly from the Rotterdam Study. Dementia was assessed from baseline (1997–1999) to follow-up in January 2015. Associations of IGF-I receptor stimulating activity and incident dementia were assessed with Cox proportional hazards models. Results: During 10,752 person-years of follow-up, 174 people developed dementia. In the extended follow-up we no longer observed a dose-response relationship between IGF-I receptor stimulating activity and risk of dementia [adjusted odds ratio 1.11; 95% confidence interval (CI) 0.97–1.28]. Interestingly, we found evidence of an interaction between ApoE-ε4 and tertiles of IGF-I receptor stimulating activity. IGF-I receptor stimulating activity in the median and top tertiles was related to increased dementia incidence in hetero- and homozygotes of the ApoE-ε4 allele, but did not show any association with dementia risk in people without the ApoE-ε4 allele (adjusted odds ratio medium vs. low IGF-I receptor stimulating activity in ApoE-ε4 carriers: 1.45; 95% CI 1.00–2.12). These findings suggest a threshold effect in ApoE-ε4 carriers. In line with the hypothesis that downregulation of IGF-I signaling is associated with increased dementia risk, ApoE-ε4 homozygotes without prevalent dementia displayed lower levels of IGF-I receptor stimulating activity than heterozygotes and non-carriers. Conclusion: The findings shed new light on the association between IGF-I signaling and the neuropathology of dementia and ask for replication in other cohorts, using measures of IGF-I receptor stimulating activity rather than total serum levels as putative markers of dementia risk.
The Name Is the Game: Nicknames as Predictors of Personality and Mating Strategy in Online Dating

Objective: We investigated the communicative function of online dating user names. Our aim was to assess if it is possible to correctly guess personality traits of a user simply by reading his/her nickname. Method: We had 69 nickname users (average age: 33.59 years, 36 female) complete questionnaires assessing their personality (Big 5 + narcissism) and mating strategy (short- vs. long-term). We then checked (using a total of 638 participants, average age: 26.83 years, 355 female), whether personality and mating strategy of the nickname users could be assessed correctly based only on the nickname. We also captured the motivation to contact the user behind a nickname and looked at linguistic features of the nicknames. Results: We found that personality and mating strategy could be inferred from a nickname. Furthermore, going by trends, women were better at intersexual personality judgments, whereas men were better in intrasexual judgements. We also found several correlates of the motivation to con-tact the person behind the nickname. Among other factors, long nicknames seemed to deter people from contacting the nickname user. Conclusions: Findings display that humans are capable of making accurate personality judgements in computer-mediated communication by means of even small cues like nicknames.