Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Sequencing of Listeria monocytogenes Reveals Major Gene Expression Changes in Response to Lactic Acid Stress Exposure but a Less Pronounced Response to Oxidative Stress

Listeria monocytogenes is a well-characterized pathogen that represents a major threat to food safety. In this study, we examine the chromosomal and plasmid transcriptomes of two different L. monocytogenes strains, 6179 [belonging to sequence type (ST) 121] and R479a (ST8), in response to 30 min exposure to oxidative (0.01% hydrogen peroxide) and acid (1% lactic acid, pH 3.4) stress. The exposure to oxidative stress resulted in 102 and 9 differentially expressed (DE) genes in the chromosomal transcriptomes of 6179 and R479a, respectively. In contrast, 2280 and 2151 DE genes were observed in the respective chromosomal transcriptomes of 6179 and R479a in response to lactic acid stress. During lactic acid stress, we observed upregulation of numerous genes known to be involved in the L. monocytogenes stress response, including multiple members of the σB regulon, many of which have not been functionally characterized. Among these genes, homologs of lmo2230 were highly upregulated in both strains. Most notably, the σB-dependent non-coding RNA Rli47 was by far the most highly expressed gene in both 6179 and R479a, accounting for an average of 28 and 38% of all mapped reads in the respective chromosomal transcriptomes. In response to oxidative stress, one DE gene was identified in the 6179 plasmid transcriptome, and no DE genes were observed in the transcriptome of the R479a plasmid. However, lactic acid exposure resulted in upregulation of the stress response gene clpL, among others, on the 6179 plasmid. In R479a, a number of uncharacterized plasmid genes were upregulated, indicating a potential role in stress response. Furthermore, an average of 65% of all mapped transcriptome reads for the R479a plasmid following acid stress were mapped to an intergenic region bearing similarity to riboswitches involved in transition metal resistance. The results of this study support the conclusion that members of the σB regulon, particularly lmo2230 and the non-coding RNA Rli47, play an integral role in the response of L. monocytogenes to acid stress. Furthermore, we report the first global transcriptome sequencing analysis of L. monocytogenes plasmid gene expression and identify a putative, plasmid-encoded riboswitch with potential involvement in response to acid exposure.
Effectiveness of Transitional Interventions in Improving Patient Outcomes and Service Use After Discharge From Psychiatric Inpatient Care: A Systematic Review and Meta-Analysis

Background: The transition from psychiatric hospital to community is often hindered by challenges that influence community adjustment and continuity of care. Transitional interventions with bridging components are provided prior to discharge and continue beyond inpatient care. They provide continuity of care and may be effective in preventing readmission. We aimed to assess the effectiveness of transitional interventions with predischarge and postdischarge components in reducing readmissions and improving health-related or social outcomes of patients discharged from psychiatric hospitals. Methods: We conducted a systematic review by searching electronic databases (MEDLINE, Embase, Cochrane Library, CINAHL, PsycINFO, and Psyndex) and included randomized, nonrandomized, and one-group study designs. A random effects meta-analysis was conducted with randomized controlled trials (RCTs) reporting data on readmission rates. Other study designs were synthesized qualitatively. Results: After screening 2,673 publications, 16 studies (10 RCTs, three quasi-experimental, and three cohort studies) were included and nine RCTs were included in the meta-analysis. The tested interventions included components from case management, psychoeducation, cognitive behavioral therapy, and peer support. All studies with significant improvements in at least one outcome provided elements of case management, most frequently in combination with cognitive behavioral therapy and psychoeducation. Readmission rates during follow-up ranged between 13% and 63% in intervention groups and 19% and 69% in control groups. Overall, we found an odds ratio of 0.76 (95% confidence interval = 0.55–1.05) for readmission due to transitional interventions. Heterogeneity was low at only 31% (p = 0.17) and the funnel plot indicated no obvious publication biases. Conclusions: We observed that transitional interventions with bridging components were no more effective in reducing readmission than treatment as usual; however, these results are based on limited evidence. Therefore, additional high-quality research is required to conclude the effectiveness of transitional interventions. Nevertheless, transitional interventions with bridging components are preferred by service users and could be an alternative to strategies regularly employed.
The Potential Role of the Early Maladaptive Schema in Behavioral Addictions Among Late Adolescents and Young Adults

Background Behavioral addiction (BA) is a recent concept in psychiatry. Few studies have investigated the relationship between BA and early maladaptive schemas (EMSs). EMS is the core of Schema Therapy (ST). According to the ST model, psychiatric disorders result from the development of EMSs in response to unmet emotional needs in childhood. Bach et al. (2018) grouped the 18 EMSs into four domains: (1) disconnection and rejection; (2) impaired autonomy and performance; (3) excessive responsibility and standards; and (4) impaired limits. This study aims to assess the possible association of the most frequent BAs with EMSs in a large group of late adolescents and young adults and to evaluate their self-perceived quality of life (QoL). Methods A battery of psychological tests assessing food addiction (FA), gambling disorder (GD), internet addiction (IA), and QoL was administered to 1,075 late adolescents and young adults (N = 637; 59.3% women). A forward-stepwise logistic regression model was run to identify which variables were associated with BAs. Results Food addiction was more frequent among women and GD among men, while IA was equally distributed. Regarding the EMSs, participants with FA or IA showed significantly higher scores on all four-schema domains, whereas those with GD exhibited higher scores on impaired autonomy and performance and impaired limits. Besides, average scores of all domains increased with the association of two or more comorbid BAs. Self-perceived QoL was lower for participants with FA and IA, but not for those with GD; the presence of comorbid BAs was associated with lower Physical Component Summary (PCS) and Mental Component Summary (MCS) scores. Finally, specific EMS domains and demographic variables were associated with each BA. Conclusion Late adolescents and young adults with FA or IA have a lower perception of their mental and physical health. The most striking result is that FA appears to be associated with the disconnection and rejection schema domain, IA with all the schema domains (except for impaired autonomy and performance), and GD with impaired autonomy and performance schema domain. In conclusion, our findings suggest that EMS should be systematically assessed during psychotherapy of patients with BAs.
Strategies to Target ISG15 and USP18 Toward Therapeutic Applications

The interferon (IFN)-stimulated gene product 15 (ISG15) represents an ubiquitin-like protein (Ubl), which in a process termed ISGylation can be covalently linked to target substrates via a cascade of E1, E2, and E3 enzymes. Furthermore, ISG15 exerts functions in its free form both, as an intracellular and as a secreted protein. In agreement with its role as a type I IFN effector, most functions of ISG15 and ISGylation are linked to the anti-pathogenic response. However, also key roles in other cellular processes such as protein translation, cytoskeleton dynamics, exosome secretion, autophagy or genome stability and cancer were described. Ubiquitin-specific protease 18 (USP18) constitutes the major ISG15 specific protease which counteracts ISG15 conjugation. Remarkably, USP18 also functions as a critical negative regulator of the IFN response irrespective of its enzymatic activity. Concordantly, lack of USP18 function causes fatal interferonopathies in humans and mice. The negative regulatory function of USP18 in IFN signaling is regulated by various protein–protein interactions and its stability is controlled via proteasomal degradation. The broad repertoire of physiological functions and regulation of ISG15 and USP18 offers a variety of potential intervention strategies which might be of therapeutic use. Due to the high mutation rates of pathogens which are often species specific and constantly give rise to a variety of immune evasion mechanisms, immune effector systems are under constant evolutionarily pressure. Therefore, it is not surprising that considerable differences in ISG15 with respect to function and sequence exist even among closely related species. Hence, it is essential to thoroughly evaluate the translational potential of results obtained in model organisms especially for therapeutic strategies. This review covers existing and conceptual assay systems to target and identify modulators of ISG15, ISGylation, USP18 function, and protein–protein interactions within this context. Strategies comprise mouse models for translational perspectives, cell-based and biochemical assays as well as chemical probes.
Gene Expression in the Salivary Gland of Rhipicephalus (Boophilus) microplus Fed on Tick-Susceptible and Tick-Resistant Hosts

The success of cattle tick fixation largely depends on the secretion of substances that alter the immune response of the host. The majority of these substances are expressed by the parasite salivary gland and secreted in tick saliva. It is known that hosts can mount immune responses against ticks and bovine European breeds, and bovine industrial crossbreeds are more susceptible to infestations than are Bos indicus cattle. To identify candidates for the development of novel control strategies for the cattle tick Rhipicephalus (Boophilus) microplus, a salivary gland transcriptome analysis of engorged females fed on susceptible or resistant hosts was performed. Using RNA-Seq, transcriptomes were de novo assembled and produced a total of 235,451 contigs with 93.3% transcriptome completeness. Differential expression analysis identified 137 sequences as differentially expressed genes (DEGs) between ticks raised on tick-susceptible or tick-resistant cattle. DEGs predicted to be secreted proteins include innexins, which are transmembrane proteins that form gap junction channels; the transporters Na+/dicarboxylate, Na+/tricarboxylate, and phosphate transporter and a putative monocarboxylate transporter; a phosphoinositol 4-phosphate adaptor protein; a cysteine-rich protein containing a trypsin inhibitor-like (TIL) domain; a putative defense protein 3 containing a reeler domain; and an F-actin-uncapping protein LRRC16A with a CARMIL_C domain; these genes were upregulated in ticks fed on tick-susceptible cattle. DEGs predicted to be non-secreted proteins included a small heat shock protein and the negative elongation factor B-like, both acting in a coordinated manner to increase HSP transcript levels in the salivary glands of the ticks fed on tick-susceptible cattle; the 26S protease regulatory subunit 6B and another chaperone with similarity to calnexin, also upregulated in ticks fed on tick-susceptible cattle; an EF-hand calcium binding protein and a serine carboxypeptidase (SCP), both involved in the blood coagulation cascade and upregulated in ticks fed on tick-susceptible cattle; and two ribosomal proteins, the 60S acidic ribosomal protein P2 and the 60S ribosomal protein L19. These results help to characterize cattle tick salivary gland gene expression in tick-susceptible and tick-resistant hosts and suggest new putative targets for the control of tick infestations, as those genes involved in the mechanism of stress response during blood feeding.
Music Perception Testing Reveals Advantages and Continued Challenges for Children Using Bilateral Cochlear Implants

A modified version of the child’s Montreal Battery of Evaluation of Amusia (cMBEA) was used to assess music perception in children using bilateral cochlear implants. Our overall aim was to promote better performance by children with CIs on the cMBEA by modifying the complement of instruments used in the test and adding pieces transposed in frequency. The 10 test trials played by piano were removed and two high and two low frequency trials added to each of five subtests (20 additional). The modified cMBEA was completed by 14 children using bilateral cochlear implants and 23 peers with normal hearing. Results were compared with performance on the original version of the cMBEA previously reported in groups of similar aged children: 2 groups with normal hearing (n = 23: Hopyan et al., 2012; n = 16: Polonenko et al., 2017), 1 group using bilateral cochlear implants (CIs) (n = 26: Polonenko et al., 2017), 1 group using bimodal (hearing aid and CI) devices (n = 8: Polonenko et al., 2017), and 1 group using unilateral CI (n = 23: Hopyan et al., 2012). Children with normal hearing had high scores on the modified version of the cMBEA and there were no significant score differences from children with normal hearing who completed the original cMBEA. Children with CIs showed no significant improvement in scores on the modified cMBEA compared to peers with CIs who completed the original version of the test. The group with bilateral CIs who completed the modified cMBEA showed a trend toward better abilities to remember music compared to children listening through a unilateral CI but effects were smaller than in previous cohorts of children with bilateral CIs and bimodal devices who completed the original cMBEA. Results confirmed that musical perception changes with the type of instrument and is better for music transposed to higher rather than lower frequencies for children with normal hearing but not for children using bilateral CIs. Overall, the modified version of the cMBEA revealed that modifications to music do not overcome the limitations of the CI to improve music perception for children.
Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential

A current trend in winemaking has highlighted the beneficial contribution of non-Saccharomyces yeasts to wine quality. Hanseniaspora uvarum is one of the more represented non-Saccharomyces species onto grape berries and plays a critical role in influencing the wine sensory profile, in terms of complexity and organoleptic richness. In this work, we analyzed a group of H. uvarum indigenous wine strains as for genetic as for technological traits, such as resistance to SO2 and β-glucosidase activity. Three strains were selected for genome sequencing, assembly and comparative genomic analyses at species and genus level. Hanseniaspora genomes appeared compact and contained a moderate number of genes, while rarefaction analyses suggested an open accessory genome, reflecting a rather incomplete representation of the Hanseniaspora gene pool in the currently available genomes. The analyses of patterns of functional annotation in the three indigenous H. uvarum strains showed distinct enrichment for several PFAM protein domains. In particular, for certain traits, such as flocculation related protein domains, the genetic prediction correlated well with relative flocculation phenotypes at lab-scale. This feature, together with the enrichment for oligo-peptide transport and lipid and amino acid metabolism domains, reveals a promising potential of these indigenous strains to be applied in fermentation processes and modulation of wine flavor and aroma. This study also contributes to increasing the catalog of publicly available genomes from H. uvarum strains isolated from natural grape samples and provides a good roadmap for unraveling the biodiversity and the biotechnological potential of these non-Saccharomyces yeasts.
ASSESSING HEALTH SYSTEM RESPONSIVENESS AFTER THE IMPLEMENTATION OF HEALTH SYSTEM REFORM: A CASE STUDY OF SANANDAJ, 2014- 2015

2 تملاس داصتقا و تيريدم هورگ ،تشادهب هدكشناد ،نارهت يكشزپ مولع هاگشناد ،ينامرد يتشادهب تامدخ تيريدم يصصخت يارتكد يوجشناد 3 لماوع تاقيقحت زكرم ،يژولويمديپا يصصخت يارتكد ،رايداتسا جدننس ،ناتسدرك يكشزپ مولع هاگشناد ،تملاس رب رثوم يعامتجا طبار هدنسيون : يدارم دابق ، :يناشن ،جدننس خ ي نابا ،نارادساپ وربور ي لته داش ي ، هاگشناد مولع كشزپ ي ،ناتسدرك هدكشناد كشزپ ي ، هورگ پا ي مد ي ژولو ي و رامآ ز ي تس ي رتكد دابق دارم ي ، نفلت 08733131366 ، :كينورتكلا تسپ moradi_gh@yahoo.com تفايرد خيرات : 10 / 04 / 94 ؛ شريذپ : 09 / 08 / 94
Metabolic Pathway Profiling in Intracellular and Extracellular Environments of Streptococcus thermophilus During pH-Controlled Batch Fermentations

Elucidating the metabolite profiles during the growth of Streptococcus thermophilus is beneficial for understanding its growth characteristics. The changes in the intracellular and extracellular concentrations of carbohydrates, nucleotides, amino sugars, nucleoside sugars, fatty acids, and amino acids, as well as their metabolites over time, were investigated by metabolomics technology. Most metabolites of nucleotides were highly accumulated in the intracellular environment after the mid-exponential phase. Increases in the intracellular unsaturated fatty acids and N-acetyl-glucosamine and N-acetyl-muramoate recycling provided potential evidence that cell envelope remodeling occurred after the mid-exponential phase. At the later fermentation stages, potentially functional metabolite produced by glycine was highly accumulated in the intracellular environment. Additionally, potential toxic metabolites produced by phenylalanine and tyrosine could not be excreted into the extracellular environment in a timely basis. The accumulation of large amounts of these metabolites might be the primary cause of the overconsumption of amino acids and influence the growth of S. thermophilus.
Where Are We With Human Lice? A Review of the Current State of Knowledge

Pediculus humanus is an obligate bloodsucking ectoparasite of human that includes two ecotypes, head louse and body louse, which differ slightly in morphology and biology, but have distinct ecologies. Phylogenetically, they are classified on six mitochondrial clades (A, B, C, D, E, and F), head louse encompasses the full genetic diversity of clades, while body louse belongs to clades A and D. Recent studies suggested that not only body louse, but also head louse can transmit disease, which warrants greater attention as a serious public health problem. The recent sequencing of body louse genome confirmed that P. humanus has the smallest genome of any hemimetabolous insect reported to date, and also revealed numerous interesting characteristics in the nuclear and mitochondrial genomes. The transcriptome analyses showed that body and head lice were almost genetically identical. Indeed, the phenotypic flexibility associated with the emergence of body lice, is probably a result of regulatory changes, perhaps epigenetic in origin, triggered by environmental signals. Current lice control strategies have proven unsuccessful. For instance, ivermectin represents a relatively new and very promising pediculicide. However, ivermectin resistance in the field has begun to be reported. Therefore, novel opportunities for pest control strategies are needed. Our objective here is to review the current state of knowledge on the biology, epidemiology, phylogeny, disease-vector and control of this fascinating and very intimate human parasite.
Tactical Variables Related to Gaining the Ball in Advanced Zones of the Soccer Pitch: Analysis of Differences Among Elite Teams and the Effect of Contextual Variables

Attacking tactical variables have been commonly studied in soccer to analyze teams’ performance. However, few studies investigated defensive tactical variables during match-play and the influence of contextual variables on them. The aims of the present study were (1) to examine the defensive behaviors of soccer teams when gaining the ball in advanced zones of the pitch and (2) to evaluate the effect of contextual variables on these defensive behaviors. A sample of 1,095 defensive pieces of play initiated in the opposing half of the pitch obtained from 10 matches of the season 2010/11 of La Liga and involving 13 teams was collected using the semiautomated tracking system Amisco Pro. Five defensive tactical variables, the outcome of defensive pieces of play, and contextual variables (i.e., match status, venue, quality of opposition, and match period) were recorded for every defensive piece initiated in the opposing half of the pitch. Results showed that there were significant differences among teams in the outcome of defensive pieces of play originating from the opposing half (χ2 = 111.87, p < 0.01, φc = 0.22), and in the outcome of offensive pieces of play following ball gains (χ2 = 49.92, p < 0.001, φc = 0.22). Cluster analysis revealed four groups describing different defensive behaviors from high-pressure to a defense close to their own goal. Match status (χ2 = 25.87, p < 0.05, φc = 0.11) and quality of opposition (χ2 = 21.19, p < 0.05, φc = 0.10) were the contextual variables that showed a significant effect on defensive pieces of play initiated in the opposite half of the pitch. Teams winning gained more balls in the zone close to their own goal, and losing teams gained more balls in advanced zones of the pitch. Moreover, the greater the quality of the opponent the lesser the chance of gaining the ball in advanced zones of the pitch. Neither venue or match period influenced the defensive pieces of play analyzed. Soccer teams could employ a similar analysis to improve their performance and prepare for opposition teams in competition.
Influence of the Tumor Microenvironment on NK Cell Function in Solid Tumors

Natural killer (NK) cells are a population of innate lymphoid cells playing a pivotal role in host immune responses against infection and tumor growth. These cells have a powerful cytotoxic activity orchestrated by an intricate network of inhibitory and activating signals. The importance of NK cells in controlling tumor growth and in mediating a robust anti-metastatic effect has been demonstrated in different experimental mouse cancer models. Consistently, high density of tumor-infiltrating NK cells has been linked with a good prognosis in multiple human solid tumors. However, there are also tumors that appear to be refractory to NK cell-mediated killing for the presence of an immunosuppressive microenvironment affecting NK cell function. Immunotherapeutic strategies aimed at restoring and increasing the cytotoxic activity of NK cells in solid tumors, including the adoptive transfer of NK and CAR-NK cells, are currently employed in preclinical and clinical studies. In this review, we outline recent advances supporting the direct role of NK cells in controlling expansion of solid tumors and their prognostic value in human cancers. We summarize the mechanisms adopted by cancer cells and the tumor microenvironment to affect NK cell function, and finally we evaluate current strategies to augment the antitumor function of NK cells for the treatment of solid tumors.