Miracle-dz/UniFAR-FTUs huggingface dataset:
Mixed directional false discovery rate control in multiple pairwise comparisons using weighted p‐values

In many applications, researchers are interested in making q pairwise comparisons among k test groups on the basis of m outcome variables. Often, m is very large. For example, such situations arise in gene expression microarray studies involving several experimental groups. Researchers are often not only interested in identifying differentially expressed genes between a given pair of experimental groups, but are also interested in making directional inferences such as whether a gene is up‐ or downregulated in one treatment group relative to another. In such situations, in addition to the usual errors such as false positive (Type I error) and false negative (Type II error), one may commit directional error (Type III error). For example, in a dose response microarray study, a gene may be declared to be upregulated in the high dose group compared to the low dose group when it is not. In this paper, we introduce a mixed directional false discovery rate (mdFDR) controlling procedure using weighted p‐values to select positives in different directions. The weights are defined as the inverse of two times the proportion of either positive or negative discoveries. The proposed procedure has been proved mathematically to control the mdFDR at level α and to have a larger power (which is defined as the expected proportion of nontrue null hypotheses) than the GSP10 procedure proposed by Guo et al. (2010). Simulation studies and real data analysis are also conducted to show the outperformance of the proposed procedure than the GSP10 procedure.
[Study of the mechanism of thyroid hormone disrupted by pentachlorophenol in FRTL-5 cell].

OBJECTIVE To study the mechanism of thyroid hormone action disrupted mechanism by pentachlorophenol in FRTL-5 cells. METHODS In the study solvent control group (DMSO), positive control group in iodide uptake measurements (perchlorate sodium) and three pentachlorophenol groups were designed. FRTL-5 cells were treated at the doses of 0.1 microg/ml, 0.3 microg/ml and 0.5 microg/ml of pentachlorophenol for 24 hours. The proliferation of FRTL-5 cells was assayed by 3H - TdR, and the concentrations of thyroglobulin in culture were assayed by RIA. In iodide uptake measurements, and the 125I uptake of FRTL-5 cells was tested in 12 h and 24 h. RESULTS Pentachlorophenol had no effect on the proliferation of FRTL-5 cells, and the concentrations of thyroglobulin in culture were decreased at the levels of group 0.3 microg/ml and 0.5 microg/ml. The iodide uptakes of FRTL-5 cells were significantly increased at the levels of group 0.33 microg/ml and 0.5 microg/ml in 12 h. Perchlorate sodium made significant decreases of the iodide uptake of FRTL-5 cells in 12h and 24h. CONCLUSION The mechanism of the thyroid hormone action disrupted by pentachlorophenol may be associated with descreasing thyroglobulin in FRTL-5 cells.
“Turning to One’s Own World”

Purpose: Although past research has focused on the coping strategies of family caregivers, how immigrant caregivers cope with the demands of caregiving remains unknown. This study examines the strategies immigrant caregivers use to relieve the burden of care. Method: A qualitative study based on 17 immigrant women caregivers using purposive and snowball sampling was done. Semistructured interviews and testimonies were obtained and analyzed using grounded theory procedures. Findings: Turning to one’s world describes how caregivers seek relief from the burden of care. They escape virtually, go to a private place, make those they care for their own, and decide to go home. These mechanisms enable them to escape from the world of caregiving in which they find themselves. Discussion and Conclusions: Findings reveal the significance of family connections and networks for immigrants to achieve burden relief. Implications for Practice: The importance of promoting positive working environments and raising awareness about immigrant caregivers’ need for rest.
A Comparison of Three Skating Techniques and the Diagonal Stride on Heart Rate Responses and Speed in Cross-Country Skiing

The purpose of this study was to compare the heart rate responses and the speed of three different skating techniques and the diagonal stride in cross-country skiing. The subjects were ten elite male cross-country ski racers, 16 to 25 years of age. They skied a 3.04-km loop of various terrain four separate times, using a different technique for each trial. A thirty-minute recovery period was allowed between each trial. Heart rate and skiing velocities were analyzed over a flat, an uphill, and a downhill section, as well as for the total loop. No significant differences (p greater than 0.05) were found in heart rate values between the four techniques on all sections of the course, while heart rates were significantly different over the three different sections. Skiing velocities were significantly different (p less than 0.05) between the diagonal stride and all skating techniques, the diagonal stride being the slowest technique, and this, for all sections. Energy costs while skiing were estimated on the basis of individual HR/VO2 curve determined under laboratory conditions. Since no differences in HR were found between the four techniques, no differences in energy costs were found. These energy costs represented between 69 and 73% of max VO2, and between 87 and 89% of max HR for the 3.04-km loop. Thus, for the same estimated energy expenditure, greater speeds (16%) were achieved with the skating techniques than with the diagonal stride.
Effect of Maternal Body Mass Index on the Retinal Microvasculature in Pregnancy

OBJECTIVE: To estimate the effects of maternal body mass index (BMI) and pregnancy weight gain on the retinal microvasculature among pregnant women. METHODS: We studied 814 pregnant women aged 18–46 years who were recruited as part of the Growing Up in Singapore Toward Health Outcomes study, an ongoing birth cohort study from two government hospitals in Singapore since 2009. Recalled prepregnancy weight was recorded, and maternal anthropometric measurements of weight and height were performed at 26 weeks of gestation together with retinal photography. RESULTS: In multiple linear regression models, each standard deviation increase of 26-week pregnancy BMI (4.57) was associated with narrower retinal arteriolar caliber (by 1.58 micrometers, P<.001), wider venular caliber (by 1.28 micrometers, P=.02), and increased retinal venular tortuosity (P=.01). Compared with mothers with normal weight, obese mothers (prepregnancy BMI greater than 30.0) had narrower retinal arteriolar caliber (118.81 compared with 123.38 micrometers, P<.001), wider retinal venular caliber (175.81 compared with 173.01 micrometers; P<.01), and increased retinal venular tortuosity (129.92 compared with 121.49×10−6; P<.01). Pregnant women whose BMI-specific weight gain from prepregnancy to 26 weeks of gestation was above Institute of Medicine recommendations had narrower retinal arteriolar caliber (120.68 micrometers) than women with ideal (121.91 micrometers) and less than ideal weight gain (123.17), respectively (Ptrend=.05). CONCLUSION: These data indicate that greater prepregnancy BMI and pregnancy BMI are associated with adverse retinal microvascular measures, suggesting that maternal obesity has an effect on her microcirculation. LEVEL OF EVIDENCE: III
Neuromuscular Activity During Whole-Body Vibration of Different Amplitudes and Footwear Conditions: Implications for Prescription of Vibratory Stimulation

Marín, PJ, Bunker, D, Rhea, MR, and Ayllón, FN. Neuromuscular activity during whole-body vibration of different amplitudes and footwear conditions: implications for prescription of vibratory stimulation. J Strength Cond Res 23(8): 2311-2316, 2009-This study investigated the magnitude of whole-body vibration (WBV) at 30 Hz induced in surface electromyography root-mean-square (EMGrms) signals of different amplitudes and footwear conditions of unloaded isometric half squat (100o). For this purpose, 10 healthy and active males (age 28.7 ± 4.6 yr; height 180 ± 5.9 cm; and weight 90 ± 13.4 kg) volunteered to participate in this study. Subjects were exposed to the WBV treatment using a vibration platform (FreeMotion Fitness iTonic). The subjects were exposed randomly to 4 different treatments of WBV: with shoes 2 mm amplitude, without shoes 2 mm, with shoes 4 mm, and without shoes 4 mm. The EMGrms signals were recorded from the vastus lateralis and the gastrocnemius medialis muscle during the different conditions. The WBV treatments resulted in a significantly higher (p ≤ 0.05) EMGrms compared with unloaded isometric half squat (without WBV). The WBV treatment that induced the highest EMGrms signals of the vastus lateralis was during the amplitude of 4 mm without shoes (+62.7%; p < 0.01), whereas 4 mm with shoes induced the highest EMGrms signals of the gastrocnemius medialis (+142.7%; p < 0.01). These data suggest that wearing shoes does alter the neuromuscular response to WBV stimuli, and exercise professionals should consider such differences when using WBV to target neuromuscular activation of such muscle groups. In this study, the magnitude of the WBV effect was clearly higher with the amplitude 4 mm versus 2 mm for the vastus lateralis muscle and gastrocnemius medialis muscle. The vastus lateralis showed the greatest activity without shoes and at amplitude of 4 mm. The maximal activation for the gastrocnemius medialis was measured with shoes at 4 mm.
Personality characteristics of psychotic patients as possible motivating factors for participating in group psychotherapy.

BACKGROUND This study aimed to examine the relationship between some personality characteristics of patients diagnosed with psychotic disorders and the quality of their engagement in psychodynamic group psychotherapy. Given that previous research has shown that self-stigma is significantly negatively associated with the engagement of patients, the measure of self-stigma was used as a correlate of patients' motivation to participate in group psychotherapy. SUBJECTS AND METHODS A total of 48 outpatients (52.1% women; mean age 35.30 years) attending group psychodynamic psychotherapy completed The Inventory of Personality Organization, The Pathological Narcissism Inventory, The Measure of Parental Style, The Relationship Questionnaire, and The Internalized Stigma of Mental Illness scale. RESULTS The findings showed that patients with higher levels of self-stigma have unhealthy attachments styles, perceived their mothers' parental style as indifferent and achieved greater scores on narcissistic vulnerability scale. They are also are prone to primitive psychological defences, have poorly integrated identity, and achieved lower scores on reality testing dimension. CONCLUSION Taking into account the limitations of this study, these findings may contribute to improved understanding of the quality of participation and engagement of psychotic patients in group psychotherapy, and may help to develop more effective therapeutic approaches.
The recognition of distorted DNA structures by HMG-D: a footprinting and molecular modelling study.

The high mobility group (HMG) domain is a DNA binding motif found in some eukaryotic chromosomal proteins and transcription factors. This domain binds in the minor groove of DNA inducing a sharp bend and also preferentially binds to certain distorted DNA structures. Although structures of sequence-specific HMG domains with their cognate double-helical DNA binding sites have been solved, the nature of the interaction of the domain with distorted DNA remains to be established. In this study we have investigated the interaction of HMG-D, a Drosophila counterpart of the vertebrate HMG1, with a DNA oligomer containing a bulge of two adenine residues. We show by footprinting that HMG-D binds preferentially on one side of the bulged DNA. Based on these data and on the published NMR structures of the HMG domain of HMG-D and the LEF-1-DNA complex, we modelled the HMG-D - bulged DNA complex. This model predicts that two residues, Val32 and Thr33, in the loop between alpha-helices I and II are inserted deep into the "hole" in the DNA formed by the two missing bases on one strand of the DNA bulge. Mutation of these residues confirmed that both are required for the efficient binding and bending of DNA by HMG-D. We discuss both the role of this loop in the recognition of distorted DNA structures by non-sequence specific HMG domain proteins and that of the basic tail in stabilising the induced DNA bend.
Minimizing Misdiagnosis: Psychometric Criteria for Possible or Probable Memory Impairment

Background/Aims: Memory impairment can be easily misdiagnosed in older adults because obtaining some low scores is common. The objective of the present study is to present new psychometric criteria for determining ‘possible’ and ‘probable’ memory impairment. Methods: We propose criteria based on an analysis of performance from 450 healthy older adults (55–87 years old) on 3 measures from the WMS-III: Logical Memory, Word List, and Visual Reproduction. These measures yield 8 age-adjusted scores for learning, recall, and recognition. The proposed criteria for memory impairment are based on the prevalence of low scores when simultaneously examining all 8 scores and are stratified by current intelligence, estimated premorbid intelligence, and education. The criteria are subsequently validated on 100 healthy older adults and 34 patients with ‘possible’ or ‘probable’ Alzheimer’s Disease (AD). Results: Tables with cutoffs and false-positive rates are presented for clinical use. In the validation cohort there were no misclassifications in AD patients. Conclusion: This study presents steps in the development of proposed psychometric criteria that, in conjunction with clinical judgment, could minimize the misdiagnosis of memory impairment. It is important to reduce misdiagnosis in order to (a) optimize patient care, (b) provide an accurate foundation for identifying biological and neurological markers, and (c) successfully develop disease-modifying treatments. Further validation in a sample of older adults with lesser degrees of cognitive impairment is needed.
Effects of dietary supplementation of fermented Ginkgo biloba L. residues on growth performance, nutrient digestibility, serum biochemical parameters and immune function in weaned piglets.

This study evaluated the effects of fermented Ginkgo biloba L. residues (FGBLR) on growth performance, nutrient digestibility, serum biochemical parameters and immune function in weaned piglets. Pigs were allotted to five dietary treatments, including negative control (NC: antibiotic free basal diet), positive control (PC) (NC + 30 mg apramycin/kg) and FGBLR-50, 100, 150 (NC + 50, 100, 150 g FGBLR/kg). Pigs in FGBLR-100 and PC treatments showed increased final body weight, average daily gain, gain:feed and apparent total tract digestibility of dry matter, N and gross energy (P < 0.05) compared with NC, FGBLR-50 and FGBLR-150 treatments, In addition, pigs fed with FGBLR-100 diet showed higher serum total protein, albumin, alkaline phosphatase, glucose, hemoglobin, total iron, total iron binding capacity, superoxide dismutase and glutathione superoxide dismutase levels, and lower serum blood urea nitrogen, malondialdehyde, glutamic-pyruvic transaminase, glutamic-oxalacetic transaminase, triglyceride and total cholesterol levels than those fed with PC and NC diets (P < 0.05). Moreover, feeding FGBLR-100 could increase levels of immunoglobulin G (IgG), IgA and IgM, as well as lymphocyte transformation rates, ratio of CD4+ to CD8+ cells and proportions of CD2+, CD4+, B, major histocompatibility complex (MHC)-I and MHC-II cells, and can decrease proportion of CD8+ cells in blood of piglets compared with PC and NC groups (P < 0.05). These results indicate that dietary supplementation with 10% of FGBLR showed greatest beneficial effects on growth performance, nutrient digestibility, serum biochemical parameters and immune function in weaned piglets, which were superior to antibiotic supplemental diets.
Development of a CFD urethral model to study flow-generated vortices under different conditions of prostatic obstruction

A novel, non-invasive method to diagnose bladder outlet obstruction involves the recording of noise with a contact microphone pressed against the perineum (between anus and scrotum). This noise results from flow-generated vortices caused by prostatic obstruction. We developed a computational fluid dynamic (CFD) urethral model including urethral geometry to study the relation between generated noise and the degree of obstruction. This model comprised a bladder, bladder neck, prostate and urethra. Calculations were carried out at four bladder pressures, five degrees of obstruction and three obstruction shapes. For each of the sixty simulations, the velocity and pressure distributions along the urethra were calculated including wall shear stresses to localize flow transition from disturbed to normal. Negative pressures at the obstruction outlet induced recirculation of flow. The location of transition was independent of the applied bladder pressure, but it depended primarily on the degree and secondarily on the shape of the obstruction. Based on the presented results, we hypothesize that the location of the maximum amplitude of perineal noise mainly depends on the degree and shape of the prostatic obstruction. Our future aim is to test our hypothesis in male patients and to extend the presented model to 3D with a viscoelastic urethral wall to calculate the fluid–wall interaction.
Exercise training and mouse mammary tumour metastasis.

The present study was designed to address whether exercise influences the experimental metastasis of a mouse mammary tumour; a related issue was the impact of timing of exercise onset relative to tumour exposure on NK and LAK mediated cytotoxicity. After 8 weeks of forced treadmill exercise or voluntary wheel running or remaining sedentary, female BALB/c mice received an intravenous (i.v.) injection of female BALB/c mice received an intravenous (i.v.) injection of MMT line 66 tumour cells. Mice were then randomized into continuation of activity (TT, WW), cessation of activity (TS, WS), initiation of activity (ST, SW) and maintenance of sedentary condition (SS) for three weeks. Tumour control (TC) mice, who were matched to the SS mice for age, received an i.v. injection of heat-killed MMT 66 tumour cells. In total there were 8 groups including the tumour control. The average number of lung tumours did not differ by activity condition; however, the mice in the continuous treadmill group (TT) tended to have a higher tumour multiplicity (162 +/- 22) and those in the treadmill x sedentary condition (TS) tended to have lower tumour multiplicity (109 +/- 16) compared with the other groups except the SW group (95 +/- 15). The lymphokine activated killer activity in the spleen was significantly elevated in the TS (49 +/- 3%) and WS (44 +/- 3%) mice compared with the sedentary animals (30 +/- 3%) (p < 0.003 and 0.05, respectively). NK activity was lower in the mice that had stopped exercising (TS and WS) after injection of tumour compared with sedentary animals. These data suggest that although exercise training influences natural immune cytotoxic mechanisms in vitro, this may not translate into clinically significant changes in tumour burden. The dissociation between natural immunity and tumour outcome may reflect the relative resistance of the tumour line to lysis by natural killer cells. It remains to be tested if infusion of IL-2 (to induce LAK activity) in exercise trained animals results in fewer tumour metastases.
Factors Associated with Baroreflex Sensitivity: Association with Morning Blood Pressure

Baroreflex sensitivity (BRS) is a primary mechanism for acute and chronic control of blood pressure (BP). However, there are few data showing the relationship between BRS and ambulatory BP (ABP). We assessed the hypothesis that BRS specifically contributes to some specific parameters of ABP in never-treated hypertensive/normotensive subjects. We studied 128 subjects (mean age: 54.5±13 years, 60% male) consisting of 92 untreated hypertensive and 36 normotensive subjects. Radial tonometric BP and simultaneous RR interval were recorded for 10 min, and the Valsalva maneuver was performed 3 times for each subject. BRS was calculated in two ways: the spontaneous-BRS by the spectral method, and the Valsalva-BRS by the slope method, using commercial software. ABP monitoring was performed on the same day as the BRS test. Of 128 subjects, we obtained BRS from 111 subjects with the Valsalva method and 123 subjects with the spontaneous method. Univariate analyses showed that the Valsalva-BRS was negatively correlated only with morning systolic BP (r=−0.21, p=0.03). Multivariable analyses showed that the Valsalva-BRS (ms/mmHg) was independently associated with the morning systolic BP (β=−0.26, p=0.022), even after adjusting for age, sex, body mass index, presence of diabetes, duration of hypertension, clinic systolic BP and pulse rates. The spontaneous-BRS estimates were inversely correlated with clinic pulse rates in the same model. In conclusion, impaired BRS evaluated by the Valsalva method was associated with high morning BP level, independent of other confounders. Morning hypertension might be partly mediated by impaired BRS.
High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei

Despite the unique phenotypic properties and clinical importance of Penicillium marneffei, the polyketide synthase genes in its genome have never been characterized. Twenty‐three putative polyketide synthase genes and two putative polyketide synthase nonribosomal peptide‐synthase hybrid genes were identified in the P. marneffei genome, a diversity much higher than found in other pathogenic thermal dimorphic fungi, such as Histoplasma capsulatum (one polyketide synthase gene) and Coccidioides immitis (10 polyketide synthase genes). These genes were evenly distributed on the phylogenetic tree with polyketide synthase genes of Aspergillus and other fungi, indicating that the high diversity was not a result of lineage‐specific gene expansion through recent gene duplication. The melanin‐biosynthesis gene cluster had gene order and orientations identical to those in the Talaromyces stipitatus (a teleomorph of Penicillium emmonsii) genome. Phylogenetically, all six genes of the melanin‐biosynthesis gene cluster in P. marneffei were also most closely related to those in T. stipitatus, with high bootstrap supports. The polyketide synthase gene of the melanin‐biosynthesis gene cluster (alb1) in P. marneffei was knocked down, which was accompanied by loss of melanin pigment production and reduced ornamentation in conidia. The survival of mice challenged with the alb1 knockdown mutant was significantly better than those challenged with wild‐type P. marneffei (P < 0.005). The sterilizing doses of hydrogen peroxide, leading to a 50% reduction in survival of conidia, were 11 min for wild‐type P. marneffei and 6 min for the alb1 knockdown mutant of P. marneffei, implying that the melanin‐biosynthesis gene cluster contributed to virulence through decreased susceptibility to killing by hydrogen peroxide.