Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality of Cancer Care in Switzerland: Going Beyond Traditional Quality Indicators by Collecting Patient-Reported Experiences of Cancer Care

Background: High-quality cancer care should be effective, safe, accessible, efficient, equitable, and responsive to patients’ needs. In Switzerland, information on the safety and effectiveness of cancer care is available, but not on responsiveness. Systematic and comprehensive reports from patients on cancer care are missing and needed to complete the assessment of the quality of cancer care. Evidence: Patient-reported experiences of cancer care are key to evaluate responsiveness of care and drive quality improvement initiatives in oncology practice. Studies have found that responsive care leads to more positive experiences of care, which can lead to more effective treatments and health benefits. Policy Options and Recommendations: Our first recommendation is to develop a position statement on the importance and value of patient-reported experiences of cancer care. Our second recommendation is to systematically collect patients’ experiences of cancer care at the national level, through a dedicated national cancer-specific measurement program or through the integration of patient-reported experiences measures in cancer registries. Conclusion: The systematic collection of patient-reported experiences of cancer care provides essential information on what matters to patients in addition to traditional clinical information, including patients as partners of the overall assessment of healthcare performance.
Gene Expression Profile Analysis of Human Epidermal Keratinocytes Expressing Human Papillomavirus Type 8 E7

Background: Human papillomavirus type 8 (HPV8) has been implicated in the progress of non-melanoma skin cancers and their precursor lesions. The HPV8 E7 oncoprotein plays a key role in the tumorigenesis of HPV-associated cutaneous tumors. However, the exact role of HPV8 E7 in human epidermal carcinogenesis has not been fully elucidated. Methods: To investigate the potential carcinogenic effects of HPV8 E7 on epithelial cells, we used RNA-sequencing technology to analyze the gene expression profile of HPV8 E7-overexpressed normal human epidermal keratinocytes (NHEKs). Results: RNA-sequencing revealed 831 differentially expressed genes (DEGs) between HPV8 E7-expressing NHEKs and control cells, among which, 631 genes were significantly upregulated, and 200 were downregulated. Gene ontology annotation enrichment analysis showed that HPV8 E7 mainly affected the expression of genes associated with protein heterodimerization activity, DNA binding, nucleosomes, and nucleosome assembly. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that overexpression of HPV8 E7 affected the expression of gene clusters associated with viral carcinogenesis and transcriptional misregulation in cancer and necroptosis signaling pathways that reportedly play crucial roles in HPV infection promotion and cancer progression. We also found the DEGs, such as HKDC1 and TNFAIP3, were associated with epigenetic modifications, immune regulation, and metabolic pathways. Conclusion: Our results demonstrate that the pro-carcinogenic effect of HPV8 expression in epithelial cells may be attributed to the regulatory effect of oncogene E7 on gene expression associated with epigenetic modifications and immune and metabolic status-associated gene expression. Although our data are based on an in vitro experiment, it provides the theoretical evidence that the development of squamous cell carcinoma can be caused by HPV.
Recombination in Positive-Strand RNA Viruses

RNA recombination is a major driver of genetic shifts tightly linked to the evolution of RNA viruses. Genomic recombination contributes substantially to the emergence of new viral lineages, expansion in host tropism, adaptations to new environments, and virulence and pathogenesis. Here, we review some of the recent progress that has advanced our understanding of recombination in positive-strand RNA viruses, including recombination triggers and the mechanisms behind them. The study of RNA recombination aids in predicting the probability and outcome of viral recombination events, and in the design of viruses with reduced recombination frequency as candidates for the development of live attenuated vaccines. Surveillance of viral recombination should remain a priority in the detection of emergent viral strains, a goal that can only be accomplished by expanding our understanding of how these events are triggered and regulated.
Specificity of Nuclear Size Scaling in Frog Erythrocytes

In eukaryotes, the cell has the ability to modulate the size of the nucleus depending on the surrounding environment, to enable nuclear functions such as DNA replication and transcription. From previous analyses of nuclear size scaling in various cell types and species, it has been found that eukaryotic cells have a conserved scaling rule, in which the nuclear size correlates with both cell size and genomic content. However, there are few studies that have focused on a certain cell type and systematically analyzed the size scaling properties in individual species (intra-species) and among species (inter-species), and thus, the difference in the scaling rules among cell types and species is not well understood. In the present study, we analyzed the size scaling relationship among three parameters, nuclear size, cell size, and genomic content, in our measured datasets of terminally differentiated erythrocytes of five Anura frogs and collected datasets of different species classes from published papers. In the datasets of isolated erythrocytes from individual frogs, we found a very weak correlation between the measured nuclear and cell cross-sectional areas. Within the erythrocytes of individual species, the correlation of the nuclear area with the cell area showed a very low hypoallometric relationship, in which the relative nuclear size decreased when the cell size increased. These scaling trends in intra-species erythrocytes are not comparable to the known general correlation in other cell types. When comparing parameters across species, the nuclear areas correlated with both cell areas and genomic contents among the five frogs and the collected datasets in each species class. However, the contribution of genomic content to nuclear size determination was smaller than that of the cell area in all species classes. In particular, the estimated degree of the contribution of genomic content was greater in the amphibian class than in other classes. Together with our imaging analysis of structural components in nuclear membranes, we hypothesized that the observed specific features in nuclear size scaling are achieved by the weak interaction of the chromatin with the nuclear membrane seen in frog erythrocytes.
Shoplifting Behavior Among Patients With an Eating Disorder at a Medical Correctional Center in Japan: A Cross-Sectional Study

Purpose In Japan, the incarceration of patients with eating disorders (EDs) owing to repeated shoplifting has become a social issue. This study examined the shoplifting behavior of inmates with EDs at our medical correctional center, with the objective of delineating their characteristics, identifying an adequate treatment plan, and preventing recidivism. Methods The participants consisted of 32 incarcerated patients with EDs (22 females, 10 males) charged with shoplifting, from a medical correctional center in East Japan. A cross-sectional study was employed. Data were collected by retrieving the patients' medical records and through individual interviews conducted by psychiatrists. Results The food-specific shoplifting ED group (those who had never shoplifted anything other than food) had a core pathology of the binge-purge type of anorexia nervosa with juvenile onset (p = 0.044). Furthermore, they demonstrated an average gap of 8 years between the onset of ED and their first shoplifting episode. The non-specific shoplifting ED group (those who shoplifted food and other items) typically shoplifted before the onset of ED (p = 0.001). They experienced the onset of ED after incarceration (p = 0.004) and had comorbid disorders (p = 0.024). The food-specific group required a psychosocial approach focusing on maintaining healthy body weight and mental stability, whereas the non-specific group required multiple forms of support for substance abuse and behavioral addiction, as well as interventions to reduce impulsive behavior. Conclusion Early intervention is necessary to improve the prognosis of patients with EDs and shoplifting behavior.
A Strategic Review on Carbon Quantum Dots for Cancer-Diagnostics and Treatment

The understanding of the genesis of life-threatening cancer and its invasion calls for urgent development of novel technologies for real-time observations, early diagnosis, and treatment. Quantum dots (QDs) grabbed the spotlight in oncology owing to their excellent photostability, bright fluorescence, high biocompatibility, good electrical and chemical stability with minimum invasiveness. Recently, carbon QDs (CQDs) have become popular over toxic inorganic QDs in the area of bioimaging, biosensing, and drug delivery. Further, CQDs derived from natural sources like biomolecules and medicinal plants have drawn attention because of their one-pot, low-cost and ease of synthesis, along with remarkable tunable optical properties and biocompatibility. This review introduces the synthesis and properties of CQDs derived from natural sources, focusing on the applicability of CQD-based technologies as nano-theranostics for the diagnosis and treatment of cancer. Furthermore, the current issues and future directions for the transformation of CQDs-based nanotechnologies to clinical applications are highlighted.
Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis

Eggplant (Solanum melongena L.; 2n = 24) is one of the most important Solanaceae vegetables and is primarily cultivated in China (approximately 42% of world production) and India (approximately 39%). Thousand-grain weight (TGW) is an important trait that affects eggplant breeding cost and variety promotion. This trait is controlled by quantitative trait loci (QTLs); however, no quantitative trait loci (QTL) has been reported for TGW in eggplant so far, and its potential genetic basis remain unclear. In this study, two eggplant lines, 17C01 (P1, wild resource, small seed) and 17C02 (P2, cultivar, large seed), were crossed to develop F1, F2 (308 lines), BC1P1 (44 lines), and BC1P2 (44 lines) populations for quantitative trait association analysis. The TGWs of P1, P2 and F1 were determined as 3.00, 3.98 and 3.77 g, respectively. The PG-ADI (polygene-controlled additive-dominance-epistasis) genetic model was identified as the optimal model for TGW and the polygene heritability value in the F2 generation was as high as 80.87%. A high-quality genetic linkage bin map was constructed with resequencing analysis. The map contained 3,918 recombination bins on 12 chromosomes, and the total length was 1,384.62 cM. A major QTL (named as TGW9.1) located on chromosome 9 was identified to be strongly associated with eggplant TGW, with a phenotypic variance explanation of 20.51%. A total of 45 annotated genes were identified in the genetic region of TGW9.1. Based on the annotation of Eggplant genome V3 and orthologous genes in Arabidopsis thaliana, one candidate gene SMEL_009g329850 (SmGTS1, encoding a putative ubiquitin ligase) contains 4 SNPs and 2 Indels consecutive intron mutations in the flank of the same exon in P1. SmGTS1 displayed significantly higher expression in P1 and was selected as a potential candidate gene controlling TGW in eggplant. The present results contribute to shed light on the genetic basis of the traits exploitable in future eggplant marker-assisted selection (MAS) breeding.
Genomic Insights Into Sclerotinia Basal Stalk Rot Resistance Introgressed From Wild Helianthus praecox Into Cultivated Sunflower (Helianthus annuus L.)

Crop wild relatives of the cultivated sunflower (Helianthus annuus L.) are a valuable resource for its sustainable production. Helianthus praecox ssp. runyonii is a wild sunflower known for its resistance against diseases caused by the fungus, Sclerotinia sclerotiorum (Lib.) de Bary, which infects over 400 broadleaf hosts including many important food crops. The objective of this research was to dissect the Sclerotinia basal stalk rot (BSR) resistance introgressed from H. praecox ssp. runyonii into cultivated sunflower. An advanced backcross quantitative trait loci (AB-QTL) mapping population was developed from the cross of a H. praecox accession with cultivated sunflower lines. The AB-QTL population was evaluated for BSR resistance in the field during the summers of 2017–2018 and in the greenhouse in the spring of 2018. Highly significant genetic variations (p < 0.001) were observed for the BSR disease in the field and greenhouse with a moderately high broad-sense heritability (H2) ranging from 0.66 to 0.73. Genotyping-by-sequencing approach was used to genotype the parents and the progeny lines of the AB-QTL population. A genetic linkage map spanning 1,802.95 cM was constructed using 1,755 single nucleotide polymorphism (SNP) markers mapped on 17 sunflower chromosomes. A total of 19 BSR resistance QTL were detected on nine sunflower chromosomes, each explaining 2.21%–16.99% of the phenotypic variance for resistance in the AB-QTL population. Sixteen of the 19 QTL had alleles conferring increased BSR resistance derived from the H. praecox parent. SNP markers flanking the identified QTL will facilitate marker-assisted breeding to combat the disease in sunflower.
Learning From the Study Fleet: Maintenance of a Large-Scale Reference Fleet for Northeast U.S. Fisheries

Logbook data from commercial fisheries are a vital component in the machinery of management, including tracking the volume of catches and allocating catch spatially. At the same time, logbooks can provide a unique window into the ecological and sociological conditions in marine fisheries, where fishermen interact with marine species and environments frequently and broadly. Traditional logbooks, however, often are not sufficiently standardized (when personal logs), or lack the detail (when regulatory documents) required to adequately understand fisheries ecosystems. The Study Fleet program, operated by the Northeast Fisheries Science Center’s Cooperative Research Branch, was developed to address these shortfalls by engaging members of the fishing industry in collecting high-resolution catch, effort, and environmental data using electronic logbooks. Since its inception, the Study Fleet has expanded from a small project focused on collecting detailed catch information from the New England multispecies groundfish fishery to a program with a wider scope encompassing a variety of fisheries, gears, and environmental parameters from North Carolina to Maine U.S. Over the years, a number of lessons have been learned about recruiting and supporting industry partners, managing the data, evolving technical specifications, and the challenges associated with analyzing and applying self-reported fisheries data. Here we describe the current state of the program and provide summaries of the Study Fleet program operations and outcomes from 2007-2020, with an eye towards successes, challenges, and applicability of the approach in other regions. We suggest other reference fleet programs, as well as other developing fishery dependent data collections (e.g., electronic monitoring programs), develop detailed roadmaps for each data collection to keep participants engaged as collaborators, target specific fisheries to keep resources from being stretched too thin, and partner with data users early. Additionally, we suggest programs invest in the long-term participation of individual fishermen, carefully weigh the pros and cons of involvement in regulatory reporting, and plan data products and applications well in advance to ensure that the sampling scheme and granularity of the data meet the needs of stock assessment, ecosystem, and oceanographic scientists.
The Probiotic Lactobacillus paracasei Ameliorates Diarrhea Cause by Escherichia coli O8 via Gut Microbiota Modulation1

Introduction Koumiss is a fermented horse milk food containing abundant probiotics. Lactobacillus paracasei is a bacterial strain isolated from koumiss that helps regulate the intestinal microbiota. One of the major cause of diarrhea is an imbalance of the intestinal flora. The aim of this study was to investigate whether Lactobacillus paracasei can ameliorate E. coli-induced diarrhea and modulate the gut microbiota. Methods Mouse models of diarrhea were established via intragastric E. coli O8 administration. We then attempted to prevent or treat diarrhea in the mice via intragastric administration of a 3 × 108 CFU/mL L. paracasei cell suspension. The severity of diarrhea was evaluated based on the body weight, diarrhea rate, and index, fecal diameter, ileum injury, hematoxylin-eosin (H&E) staining, and diamine oxidase (DAO) and zonulin expression. Expression of the tight junction (TJ) proteins claudin-1, occludin, and zona occludens (ZO-)1 were detected by immunohistochemistry (IHC). Gastrointestinal mRNA expression levels of interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF)-α were detected by real-time polymerase chain reaction (RT-PCR). The microbial composition was analyzed by 16s rRNA sequencing. Results The L. paracasei demonstrated excellent therapeutic efficacy against diarrhea. It elevated the TJ protein levels and downregulated proinflammatory cytokines IL-6, IL-1β, TNF-α, and p65, myosin light chain 2 (MLC2), myosin light chain kinase (MLCK). Moreover L. paracasei increased those bacteria, which can product short-chain fatty acid (SCFA) such Alistipes, Odoribacter, Roseburia, and Oscillibacter. Conclusion L. paracasei ameliorated diarrhea by inhibiting activation of the nuclear factor kappa B (NF-κB)-MLCK pathway and increasing the abundance of gut microbiota that produce SCFA.
Some features of steady separated flow from low speed to hypersonic

Steady non-vortex shedding base flow behind a bluff body is considered. Such a flow is characterised by the flow separation at the trailing edge of the body with an emerging shear layer which reattaches on the axis with strong recompression and recirculating flow bounded by the base, the shear layer, and the axis. Steady wake flows behind a bluff body at low speeds have been studied for more than a century (for example, Kirchhoff; Riabouchinsky). Recently, research on steady bluff body wake flow at low speeds has been reviewed and reinterpreted by Roshko. Roshko has also commented on some basic aspects of steady supersonic base flow following on from Chapman and Korst analyses. In the present paper, we examine the steady base flow features both at low speeds and supersonic speeds in the light of Roshko’s model and expand on some further aspects of base flows at supersonic and hypersonic speeds, not covered by Roshko.
Trauma Disrupts Reinforcement Learning in Rats—A Novel Animal Model of Chronic Stress Exposure

Trauma, as well as chronic stress that characterizes a modern fast-paced lifestyle, contributes to numerous psychopathologies and psychological problems. Psychiatric patients with traumas, as well as healthy individuals who experienced traumas in the past, are often characterized by diminished cognitive abilities. In our protocol, we used an animal model to explore the influence of chronic trauma on cognitive abilities and behavior in the group of 20 rats (Rattus norvegicus). The experimental group was introduced to chronic (12 consecutive days) exposure to predator odor (bobcat urine). We measured the reinforcement learning of each individual before and after the exposition via the Probabilistic Selection Task (PST) and we used Social Interaction Test (SIT) to assess the behavioral changes of each individual before and after the trauma. In the experimental group, there was a significant decrease in reinforcement learning after exposure to a single trauma (Wilcoxon Test, p = 0.034) as well as after 11 days of chronic trauma (Wilcoxon-test, p = 0.01) in comparison to pre-trauma performance. The control group, which was not exposed to predator odor but underwent the same testing protocol, did not present significant deterioration in reinforcement learning. In cross-group comparisons, there was no difference between the experimental and control group in PST before odor protocol (U Mann-Whitney two-sided, p = 0.909). After exposure to chronic trauma, the experimental group deteriorated in PST performance compared to control (U Mann-Whitney Two-sided, p = 0.0005). In SIT, the experimental group spent less time in an Interaction Zone with an unfamiliar rat after trauma protocol (Wilcoxon two-sided test, p = 0.019). Major strengths of our models are: (1) protocol allows investigating reinforcement learning before and after exposition to chronic trauma, with the same group of rats, (2) translational scope, as the PST is displayed on touchscreen, similarly to human studies, (3) protocol delivers chronic trauma that impairs reward learning, but behaviorally does not induce full-blown anhedonia, thus rats performed voluntarily throughout all the procedures.
Sex-Specific Transcriptomic Signatures in Brain Regions Critical for Neuropathic Pain-Induced Depression

Neuropathic pain is a chronic debilitating condition with a high comorbidity with depression. Clinical reports and animal studies have suggested that both the medial prefrontal cortex (mPFC) and the anterior cingulate cortex (ACC) are critically implicated in regulating the affective symptoms of neuropathic pain. Neuropathic pain induces differential long-term structural, functional, and biochemical changes in both regions, which are thought to be regulated by multiple waves of gene transcription. However, the differences in the transcriptomic profiles changed by neuropathic pain between these regions are largely unknown. Furthermore, women are more susceptible to pain and depression than men. The molecular mechanisms underlying this sexual dimorphism remain to be explored. Here, we performed RNA sequencing and analyzed the transcriptomic profiles of the mPFC and ACC of female and male mice at 2 weeks after spared nerve injury (SNI), an early time point when the mice began to show mild depressive symptoms. Our results showed that the SNI-induced transcriptomic changes in female and male mice were largely distinct. Interestingly, the female mice exhibited more robust transcriptomic changes in the ACC than male, whereas the opposite pattern occurred in the mPFC. Cell type enrichment analyses revealed that the differentially expressed genes involved genes enriched in neurons, various types of glia and endothelial cells. We further performed gene set enrichment analysis (GSEA), which revealed significant de-enrichment of myelin sheath development in both female and male mPFC after SNI. In the female ACC, gene sets for synaptic organization were enriched, and gene sets for extracellular matrix were de-enriched after SNI, while such signatures were absent in male ACC. Collectively, these findings revealed region-specific and sexual dimorphism at the transcriptional levels induced by neuropathic pain, and provided novel therapeutic targets for chronic pain and its associated affective disorders.