Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and validation of a nutrition knowledge questionnaire for a Canadian population

Abstract Objective The present study aimed to develop and validate a nutrition knowledge questionnaire in a sample of French Canadians from the province of Quebec, taking into account dietary guidelines. Design A thirty-eight-item questionnaire was developed by the research team and evaluated for content validity by an expert panel, and then administered to respondents. Face validity and construct validity were measured in a pre-test. Exploratory factor analysis and covariance structure analysis were performed to verify the structure of the questionnaire and identify problematic items. Internal consistency and test–retest reliability were evaluated through a validation study. Setting Online survey. Subjects Six nutrition and psychology experts, fifteen registered dietitians (RD) and 180 lay people participated. Results Content validity evaluation resulted in the removal of two items and reformulation of one item. Following face validity, one item was reformulated. Construct validity was found to be adequate, with higher scores for RD v. non-RD (21·5 (sd 2·1) v. 15·7 (sd 3·0) out of 24, P<0·001). Exploratory factor analysis revealed that the questionnaire contained only one factor. Covariance structure analysis led to removal of sixteen items. Internal consistency for the overall questionnaire was adequate (Cronbach’s α=0·73). Assessment of test–retest reliability resulted in significant associations for the total knowledge score (r=0·59, P<0·001). Conclusions This nutrition knowledge questionnaire was found to be a suitable instrument which can be used to measure levels of nutrition knowledge in a Canadian population. It could also serve as a model for the development of similar instruments in other populations.
Impact of Silymarin enriched semen extender on bull sperm preservability

Objective: To explore the effect of silymarin on bull spermatozoa during cooling and cryopreservation. Methods: Pooled bull semen were diluted by Tris-Citrate-Fructose egg yolk diluents, purified silymarin powder (obtained from the milk thistle silybum marianum), purchased from Unipharma, Al Obour city, Egypt, was soaked in Tris-citric acid-fructose diluent for 48 h at 10 °C making a stock solution (70 mg/mL), from this stock solution we obtained concentrations of 0.18 mg/mL, 0.36 mg/mL, 0.54 mg/mL, 0.72 mg/mL, 0.90 mg/mL in addition to the control (0.00 mg/mL) reaching a final volume of 5 mL in each tube. Egg yolk was added to each tube to obtain silymarin enriched semen extender (SEE) with 20% egg yolk, cooled slowly up to 5 °C and equilibrated for 4 h. Semen was packed into 0.25 mL polyvinyl French straws (IMV, France). After equilibration periods, the straws were placed horizontally on a rack and frozen in a vapor 4 cm above liquid nitrogen for 10 min and were then dipped in liquid nitrogen. Extended semen was subjected to evaluation (motility, alive%, abnormality%, intact sperm membrane (HOST)% and conception rate) in both chilled and frozen semen. Results: [Table 1] revealed that Sperm motility of the concentrations 2, 3 and 4 after 8 d of chilling were significantly (P<0.02) higher than control. Sperm motility of the concentration 2 (45.00%±2.89%) after 9 d of chilling was higher than control and the other concentrations. Addition of SEE in concentration 1 and 2 gave post thawing sperm motility as high as the control (47.50±2.81 and 45.00±2.58, respectively) while other concentration have lower effects on motility as compared to the control. Addition of silymarin improved post thawing alive% and was significantly higher (P<0.000 1) than the control. SEE decreased significantly (P<0.000 1) the % of post thawing abnormal sperm in concentration 3 and 4 (11.83±0.65 and 16.00±0.58, respectively). SEE improved significantly (P<0.018) the % of post thawing intact spermatozoa membranes (HOST%) in concentrations 2, 4 and 5 (71.17±0.83, 71.83±0.91 and 75.00±3.42, respectively) [Table 2]. Conclusion: It could be concluded that silymarin as a natural additive to semen extenders improved preservability in both chilled and frozen bull semen.
Pathological Analysis of Stress Urinary Incontinence in Females using Artificial Neural Networks

Objectives: To mathematically investigate urethral pressure and influencing parameters of stress urinary incontinence (SUI) in women, with focus on the clinical aspects of the mathematical modeling. Method: Several patients' data are extracted from UPP and urodynamic documents and their relation and affinities are modeled using an artificial neural network (ANN) model. The studied parameter is urethral pressure as a function of two variables: the age of the patient and the position in which the pressure was measured across the urethra (normalized length). Results: The ANN-generated surface, showing the relation between the chosen parameters and the urethral pressure in the studied patients, is more efficient than the surface generated by conventional mathematical methods for clinical analysis, with multi-sample analysis being obtained. For example, in elderly people, there are many low-pressure zones throughout the urethra length, indicating that there is more incontinence in old age. Conclusion: The predictions of urethral pressure made by the trained neural network model in relation to the studied effective parameters can be used to build a medical assistance system in order to help clinicians diagnose urinary incontinence problems more efficiently.
Regulation of Human Natural Killer Cell IFN-γ Production by MicroRNA-146a via Targeting the NF-κB Signaling Pathway

Natural killer (NK) cells are one group of innate lymphocytes that are important for host defense against malignancy and viruses. MicroRNAs (miRNAs) play a critical role in regulating responses of immune cells including NK cells. Accumulating evidence suggests that miR-146a is involved in the regulation of immune responses. However, the mechanism by which miR-146a regulates NK cell function is largely unknown. In the current study, we found that miR-146a intrinsically regulated NK cell function. Forced overexpression of miR-146a decreased IFN-γ production, whereas downregulation of miR-146a by anti-miR-146a significantly enhanced IFN-γ production in the human NK-92 cell line and primary human NK cells upon stimulation with IL-12 or co-stimulation with IL-12 and IL-18. Mechanistically, miR-146a regulated IFN-γ production via NF-κB, as evidenced in NK-92 cells, by downregulation of NF-κB p65 phosphorylation when miR-146a was overexpressed but upregulation of NF-κB p65 phosphorylation when anti-miR-146a was overexpressed. miR-146a directly targeted IRAK1 and TRAF6, the upstream signaling components of the NF-κB signaling pathway. This direct targeting mechanism confirmed the above gain- and loss-of-function approaches. However, the potent IFN-γ-producing subset, CD56bright NK cells, expressed higher levels of miR-146a than the lesser IFN-γ-producing subset, CD56dim NK cells. We also observed that co-stimulation of IL-12 and IL-18 significantly increased miR-146a expression in bulk NK cells and in the CD56bright subset in a time-dependent manner, correlating with augmented IFN-γ production. These data suggest that miR-146a plays a negative role in IFN-γ production by human NK cells and this miRNA may be critical in preventing NK cells from being super activated and overproducing IFN-γ.
Apathy, fatigue and quality of life in patients with Parkinson's disease

Recommendations for revision of the original version of Unified Parkinson’s Disease Rating Scale (UPDRS) were published based on its critique. Subsequently, a Movement Disorders Society (MDS)- sponsored revision designated as the Movement Disorder Society-Unified Parkinson’s Disease Rating Scale (MDS-UPDRS) was presented. After its successful clinimetric testing, a program for translation and validation of non-English versions of the MDS-UPDRS was initiated. The aim of this study was to validate and confirm the factor structure of the Slovak translation of the MDS-UPDRS. We examined 354 patients with Parkinson’s disease in all Hoehn and Yahr stages with the Slovak version of MDS-UPDRS. The average age of our sample was 68 ± 9.5 years and average disease duration was 6.7 ± 5.1 years. Slovak data were compared using confirmatory factor analysis with the original English data. A pre-specified criterion for approving the Slovak translation as an official version of the MDS-UPDRS was a comparative fit index (CFI) ≥ 0.90 for all four parts of the Slovak MDS-UPDRS. Exploratory factor analysis was performed to explore the underlying factor structure without the constraint of a pre-specified factor structure. For all four parts of the Slovak MDS-UPDRS, the CFI, in comparison with the English-language factor structure, was 0.91 or greater. Isolated differences in the factor structure of the Slovak MDS-UPDRS were identified by exploratory factor analysis compared with the English version.
Mycophenolate Mofetil in Combination with Steroids for Treatment of C3 Glomerulopathy: A Case Series.

BACKGROUND AND OBJECTIVES C3 glomerulopathy is a form of complement-mediated GN. Immunosuppressive therapy may be beneficial in the treatment of C3 glomerulopathy. Mycophenolate mofetil is an attractive treatment option given its role in the treatment of other complement-mediated diseases and the results of the Spanish Group for the Study of Glomerular Diseases C3 Study. Here, we study the outcomes of patients with C3 glomerulopathy treated with steroids and mycophenolate mofetil. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We conducted a retrospective chart review of patients in the C3 glomerulopathy registry at Columbia University and identified patients treated with mycophenolate mofetil for at least 3 months and follow-up for at least 1 year. We studied clinical, histologic, and genetic data for the whole group and compared data for those who achieved complete or partial remission (responders) with those who did not achieve remission (nonresponders). We compared remission with mycophenolate mofetil with remission with other immunosuppressive regimens. RESULTS We identified 30 patients who met inclusion criteria. Median age was 25 years old (interquartile range, 18-36), median creatinine was 1.07 mg/dl (interquartile range, 0.79-1.69), and median proteinuria was 3200 mg/g creatinine (interquartile range, 1720-6759). The median follow-up time was 32 months (interquartile range, 21-68). Twenty (67%) patients were classified as responders. There were no significant differences in baseline characteristics between responders and nonresponders, although initial proteinuria was lower (median 2468 mg/g creatinine) in responders compared with nonresponders (median 5000 mg/g creatinine) and soluble membrane attack complex levels were higher in responders compared with nonresponders. For those tapered off mycophenolate mofetil, relapse rate was 50%. Genome-wide analysis on complement genes was done, and in 12 patients, we found 18 variants predicted to be damaging. None of these variants were previously reported to be pathogenic. Mycophenolate mofetil with steroids outperformed other immunosuppressive regimens. CONCLUSIONS Among patients who tolerated mycophenolate mofetil, combination therapy with steroids induced remission in 67% of this cohort. Heavier proteinuria at the start of therapy and lower soluble membrane attack complex levels were associated with treatment resistance.
A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology

RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples. By combining Reverse Transcription-Multiple Ligation-dependent Amplification method and next generation sequencing technology, RT-MLPSeq overcomes the limit of probe length in multiplex ligation-dependent probe amplification assay and thus could detect expression levels of transcripts without quantitative limitations. We proved that different RT-MLPSeq probes targeting on the same transcripts have highly consistent results and the starting RNA/cDNA input could be as little as 1 ng. RT-MLPSeq also presented consistent relative RNA levels of selected 13 genes with reverse transcription quantitative PCR. Finally, we demonstrated the application of the new RT-MLPSeq method by measuring the mRNA expression levels of 21 genes which can be used for accurate calculation of the breast cancer recurrence score – an index that has been widely used for managing breast cancer patients.
An Adjacent-Line-Merging Writeback Scheme for STT-RAM last-level caches

Spin-Transfer Torque RAM (STT-RAM) has a higher density than SRAM and non-volatility, and is expected to be used as the last-level cache (LLC) of a microprocessor. One technical issue is that, since the energy cost of write access requests for an STT-RAM LLC is expensive, the total energy consumption of the STT-RAM LLC may increase for some write-intensive applications. Therefore, this paper proposes an Adjacent-Line-Merging Writeback Scheme. The proposed scheme dynamically merges two adjacent lines and write them back to the STT-RAM LLC as one line. The evaluation results show that the proposed scheme can reduce the energy consumption by up to 28%, and 10.4% on average.
FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro

Myxoid liposarcomas account for more than one third of liposarcomas and about 10% of all adult soft tissue sarcomas. The tumors are characterized by specific chromosomal translocations leading to the chimeric oncogenes FUS-DDIT3 or EWS1R-DDIT3. The encoded fusion proteins act as aberrant transcription factors. Therefore, we implemented comparative expression analyses using whole-genome microarrays in tumor and fat tissue samples. We aimed at identifying differentially expressed genes which may serve as diagnostic or prognostic biomarkers or as therapeutic targets. Microarray analyses revealed overexpression of FGFR2 and other members of the FGF/FGFR family. Overexpression of FGFR2 was validated by qPCR, immunohistochemistry and western blot analysis in primary tumor samples. Treatment of the myxoid liposarcoma cell lines MLS 402 and MLS 1765 with the FGFR inhibitors PD173074, TKI258 (dovitinib) and BGJ398 as well as specific siRNAs reduced cell proliferation, induced apoptosis and delayed cell migration. Combination of FGFR inhibitors with trabectedin further increased the effect. Our study demonstrates overexpression of FGFR2 and a functional role of FGFR signaling in myxoid liposarcoma. As FGFR inhibition showed effects on proliferation and cell migration and induced apoptosis in vitro, our data indicate the potential use of FGFR inhibitors as a targeted therapy for these tumors.
Early and Concurrent Features of ADHD and Sensory Over-Responsivity Symptom Clusters

Objective: This study aimed to characterize clusters of children based on ADHD and sensory over-responsivity (SOR) symptoms, and to compare their markers. Method: Parents of 922 infants completed the Infant–Toddler Social and Emotional Assessment (ITSEA) Sensory Sensitivity, Attention, and Activity/Impulsivity scales at three time points during early childhood and the Child Behavior Checklist (CBCL) and SensOR inventory during elementary school age. Results: Four school-age clusters emerged from the CBCL ADHD and SensOR scores: (a) elevated SOR symptoms only (n = 35); (b) elevated ADHD symptoms only (n = 38); (c) elevated ADHD and SOR symptoms (ADHD + S, n = 35); and (d) low ADHD and SOR symptoms (n = 814). The SOR and ADHD + S clusters had higher early Sensitivity scores than the ADHD and Low clusters. The ADHD and ADHD + S clusters differed from the SOR and Low clusters in their early Attention and Activity/Impulsivity scores. Conclusion: SOR and ADHD symptoms occur independently and consistently over time.
Age and the economics of an emergency medical admission—what factors determine costs?

Background: The ageing of the population may be anticipated to increase demand on hospital resources. We have investigated the relationship between hospital episode costs and age profile in a single centre. Methods: All Emergency Medical admissions (33 732 episodes) to an Irish hospital over a 6-year period, categorized into three age groups, were evaluated against total hospital episode costs. Univariate and adjusted incidence rate ratios (IRRs) were calculated using zero truncated Poisson regression. Results: The total hospital episode cost increased with age (P < 0.001). The multi-variable Poisson regression model demonstrated that the most important drivers of overall costs were Acute Illness Severity—IRR 1.36 (95% CI: 1.30, 1.41), Sepsis Status −1.46 (95% CI: 1.42, 1.51) and Chronic Disabling Disease Score -1.25 (95% CI: 1.22, 1.27) and the Age Group as exemplified for those >85 years IRR 1.23 (95% CI: 1.15, 1.32). Conclusion: Total hospital episode costs are a product of clinical complexity with contributions from the Acute Illness Severity, Co-Morbidity, Chronic Disabling Disease Score and Sepsis Status. However age is also an important contributor and an increasing patient age profile will have a predictable impact on total hospital episode costs.
Fibroblast growth factor 23 modifies the pharmacological effects of angiotensin receptor blockade in experimental renal fibrosis

Background. Blockade of the renin–angiotensin–aldosterone system (RAAS) retards progression of chronic kidney disease. Yet, in many patients, the renoprotective effect is incomplete. A high circulating level of the phosphaturic hormone fibroblast growth factor 23 is associated with an impaired response to RAAS blockade–based therapy in clinical studies. Therefore, we addressed whether administration of recombinant fibroblast growth factor 23 (FGF23) interferes with the efficacy of angiotensin receptor blocker (ARB) treatment in a mouse model of renal fibrosis [unilateral ureteral obstruction (UUO)]. Methods. UUO mice were treated with losartan (100 mg/L in drinking water), recombinant FGF23 (160 ng/kg i.p. twice daily), their combination or vehicle (n = 10 per group). Seven days after the UUO procedure, kidney tissue was analyzed for markers of RAAS activity, inflammation and fibrosis using real-time PCR and immunohistochemistry. Results. In the contralateral (non-affected) kidneys of ARB-treated UUO mice, administration of FGF23 reversed the induction of renin, ACE, ACE2 and AT1 receptor mRNA expression, suggesting interference with the physiological response to RAAS blockade by FGF23. Furthermore, recombinant FGF23 infusion prevented ARB-induced klotho upregulation in contralateral kidneys. In the UUO kidneys, klotho was majorly reduced in all groups. Pro-inflammatory gene expression (MCP-1, TNF-&agr;) induced in UUO kidneys was reduced by ARB treatment; this anti-inflammatory effect was reversed by FGF23. In contrast, ARB-induced reduction of (pre-)fibrotic gene expression was not reversed by FGF23. Conclusions. Our findings show pharmacological interaction between exogenous FGF23 and losartan, thus serving as a proof of principle for crosstalk between the FGF23–klotho axis and RAAS.
Permeability Surface of Deep Middle Cerebral Artery Territory on Computed Tomographic Perfusion Predicts Hemorrhagic Transformation After Stroke

Background and Purpose— Permeability surface (PS) on computed tomographic perfusion reflects blood–brain barrier permeability and is related to hemorrhagic transformation (HT). HT of deep middle cerebral artery (MCA) territory can occur after recanalization of proximal large-vessel occlusion. We aimed to determine the relationship between HT and PS of deep MCA territory. Methods— We retrospectively reviewed 70 consecutive acute ischemic stroke patients presenting with occlusion of the distal internal carotid artery or M1 segment of the MCA. All patients underwent computed tomographic perfusion within 6 hours after symptom onset. Computed tomographic perfusion data were postprocessed to generate maps of different perfusion parameters. Risk factors were identified for increased deep MCA territory PS. Receiver operating characteristic curve analysis was performed to calculate the optimal PS threshold to predict HT of deep MCA territory. Results— Increased PS was associated with HT of deep MCA territory. After adjustments for age, sex, onset time to computed tomographic perfusion, and baseline National Institutes of Health Stroke Scale, poor collateral status (odds ratio, 7.8; 95% confidence interval, 1.67–37.14; P=0.009) and proximal MCA-M1 occlusion (odds ratio, 4.12; 95% confidence interval, 1.03–16.52; P=0.045) were independently associated with increased deep MCA territory PS. Relative PS most accurately predicted HT of deep MCA territory (area under curve, 0.94; optimal threshold, 2.89). Conclusions— Increased PS can predict HT of deep MCA territory after recanalization therapy for cerebral proximal large-vessel occlusion. Proximal MCA-M1 complete occlusion and distal internal carotid artery occlusion in conjunction with poor collaterals elevate deep MCA territory PS.
A multi-fingerprint browser for the ZINC database

To confirm the activity of an initial small molecule ‘hit compound’ from an activity screening, one needs to probe the structure–activity relationships by testing close analogs. The multi-fingerprint browser presented here (http://dcb-reymond23.unibe.ch:8080/MCSS/) enables one to rapidly identify such close analogs among commercially available compounds in the ZINC database (>13 million molecules). The browser retrieves nearest neighbors of any query molecule in multi-dimensional chemical spaces defined by four different fingerprints, each of which represents relevant structural and pharmacophoric features in a different way: sFP (substructure fingerprint), ECFP4 (extended connectivity fingerprint), MQNs (molecular quantum numbers) and SMIfp (SMILES fingerprint). Distances are calculated using the city-block distance, a similarity measure that performs as well as Tanimoto similarity but is much faster to compute. The list of up to 1000 nearest neighbors of any query molecule is retrieved by the browser and can be then clustered using the K-means clustering algorithm to produce a focused list of analogs with likely similar bioactivity to be considered for experimental evaluation.