Miracle-dz/UniFAR-FTUs huggingface dataset:
Relation between the Supplemental Nutritional Assistance Program cycle and dietary quality in low-income African Americans in Baltimore, Maryland.

BACKGROUND There has been limited research regarding the Supplemental Nutritional Assistance Program (SNAP) and recipients' dietary quality during the days and weeks after benefit disbursement. OBJECTIVE We examined the relation between participants' stages in the SNAP cycle and their macronutrient consumption, Healthy Eating Index (HEI) scores, and fruit and vegetable intake. DESIGN In this cross-sectional study, we analyzed single 24-h dietary recalls collected from 244 African American SNAP participants recruited near 24 corner stores in Baltimore City. A multiple linear regression analysis and bootstrapping were used. RESULTS Among participants who received a SNAP benefit ≤15 d before being surveyed, energy intake adjusted for minimum energy requirements (-4.49%; 95% CI: -8.77%, -0.15%) and HEI dairy scores (-0.12; 95% CI: -0.22, -0.01) were lower for each 1-d increase in the time since SNAP distribution (TSSD). Among participants who received SNAP benefits >15 d before being surveyed, energy intake (1.35%; 95% CI: 0.01%, 2.73%), energy intake adjusted for minimum energy requirements (3.86%; 95% CI: 0.06%, 7.96%), total fat intake (1.96%; 95% CI: 0.29%, 3.8%), saturated fat intake (2.02%; 95% CI: 0.23%, 4.01%), and protein intake (2.09%; 95% CI: 0.70%, 3.62%) were higher per each 1-d increase in the TSSD. CONCLUSIONS These findings suggest that the relation between the TSSD and macronutrient intake might be U-shaped, with higher intake of calories, fat, and protein in individuals in the very early and late stages of their SNAP cycles. Foods high in these nutrients might be cheaper, more accessible, and have a longer shelf-life than healthier options, such as fruit, vegetables, and whole grains, for SNAP participants when their benefits run out. Additional efforts are needed to investigate the effect of the TSSD on dietary intake by using a longitudinal design and to improve the quality of dietary intake in African American SNAP participants.
Moment decay rates of stochastic differential equations with time-varying delay

One of the most important questions, especially in applications, is how to choose a decay function in the study of stability for a concrete equation. Motivated by the fact that the coefficients of the considered equation mainly suggest the choice of the decay function, the point of analysis in the paper is to carry out the Lyapunov function approach and to state coercivity conditions dependent on decay in the study of the pth moment stability with a general decay rate for a certain stochastic differential equation with variable time delay. Some criteria including the usual exponential decay are discussed, particularly the ones with a concave decay, special cases of which are polynomial and logarithmic decays. Some consequences and examples are given to illustrate the theory. 2010 Mathematics Subject Classification. 60H10, 60H35.
healthcare performance : Applying the Canadian health indicators framework at the provincial-territorial level Permalink

Background: Since, at the health system level, there is little research into the possible interrelationships among the various indicators of health, healthcare performance, non-medical determinants of health, and community and health system characteristics, we conducted this study to explore such interrelationships using the Canadian Health Indicators Framework. Methods: We conducted univariate correlational analyses with health and healthcare performance as outcomes using recent Canadian data and the ten Canadian provinces and three territories as units of the analyses. For health, 6 indicators were included. Sixteen healthcare performance indicators, 12 non-medical determinants of health and 16 indicators of community and health system characteristics were also included as independent variables for the analysis. A set of decision rules was applied to guide the choice of what was considered actual and preferred performance associations. Results: Health (28%) correlates more frequently with non-medical determinants than healthcare does (12%), in the preferred direction. Better health is only correlated with better healthcare performance in 13% of the cases in the preferred direction. Better health (24%) is also more frequently correlated with community and health system characteristics than healthcare is (13%), in the preferred direction. Conclusion: Canadian health performance is a function of multiple factors, the most frequent of which may be the non-medical determinants of health and the community characteristics as against healthcare performance. The contribution of healthcare to health may be limited only to relatively small groups which stand to benefit from effective healthcare, but its overall effect may be diluted in summary measures of population health. Interpreting multidimensional, multi-indicator performance data in their proper context may be more complex than hitherto believed. Published: 01 December 2005 BMC Health Services Research 2005, 5:76 doi:10.1186/1472-6963-5-76 Received: 09 May 2005 Accepted: 01 December 2005 This article is available from: http://www.biomedcentral. com/1472-6963/5/76 © 2005 Arah and Westert; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Thermal and mechanical pain sensitization in patients with osteoarthritis of the knee

ABSTRACT Objective: The aim was to assess sensitization using quantitative sensory testing in mechanical and thermal modes in individuals with and without osteoarthritis (OA) of the knee. Pain thresholds were correlated with functionality, symptoms of depression and intensity of pain. Methods: Thirty control volunteers and 30 patients with OA of the knee were assessed. Punctate pain thresholds using Von Frey filaments and thermal pain thresholds using a Thermal Sensory Analyzer were evaluated in the periarticular region of the knee and forearm. Using a digital pressure algometer, pressure pain thresholds were assessed in the periarticular region of the knee and on the root exit zone on the lumbar and sacral spine. Results: Punctate, pressure, and thermal pain thresholds differed significantly between participants with and without OA (p < 0.05). Values in those with OA were consistent with pain sensitization. Pressure pain thresholds also showed moderate and negative correlations with data on functionality, symptoms of depression and intensity of pain (−0.36 < r > −0.56), contributing up to 30% of their variability. Conclusions: Allodynia and hyperalgesia were demonstrated in the OA group, suggesting central sensitization in patients with mild to moderate severity of joint damage. Correlation between mechanical hypersensitivity and psychosocial factors seems to be small, despite of its significance.
Biochemical and Biophysical Characterization of Recombinant Yeast Proteasome Maturation Factor Ump1

Protein degradation is essential for maintaining cellular homeostasis. The proteasome is the central enzyme responsible for non-lysosomal protein degradation in eukaryotic cells. Although proteasome assembly is not yet completely understood, a number of cofactors required for proper assembly and maturation have been identified. Ump is a short-lived maturation factor required for the efficient biogenesis of the 20S proteasome. Upon the association of the two precursor complexes, Ump is encased and is rapidly degraded after the proteolytic sites in the interior of the nascent proteasome are activated. In order to further understand the mechanisms behind proteasomal maturation, we expressed and purified yeast Ump in E. coli for biophysical and structural analysis. We show that recombinant Ump is purified as a mixture of different oligomeric species and that oligomerization is mediated by intermolecular disulfide bond formation involving the only cysteine residue present in the protein. Furthermore, a combination of bioinformatic, biochemical and structural analysis revealed that Ump shows characteristics of an intrinsically disordered protein, which might become structured only upon interaction with the proteasome subunits.
The relationship between polymorphisms of XRCC5 genes with astrocytoma prognosis in the Han Chinese population

Background Gliomas are highly malignant with a poor prognosis. Studies have reported that DNA repair genes influence risk for glioma, but its relationship with prognosis is unclear. In this study, we want to explore the relationship between DNA repair genes (XRCC3, XRCC4 and XRCC5) and prognosis of astrocytoma in the Chinese Han population. Materials and Methods 160 astrocytoma cases were recruited in our study. Survival probabilities were estimated by using Kaplan–Meier analysis, and significant differences were analyzed by using the log-rank test. Cox proportional hazards models were used to analyze the associations between genotypes with astrocytoma survival. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated using multivariable models. All tests were two-sided and p < 0.05 was considered to be significant. Results The SNP (rs9288516) in XRCC5 (HR: 1.69, 95%CI: 1.04 - 2.77, p = 0.049), surgical approach (HR: 0.61, 95%CI: 0.43 - 0.88, p = 0.003) and chemotherapy (HR: 0.71, 95%CI: 0.50 - 0.99, p = 0.029) were associated with astrocytoma prognosis. Further, the “A/A” genotype of rs9288516 in XRCC5 (HR: 1.67, 95%CI: 1.02 - 2.72, p = 0.042) had significantly outcomes after adjusting for potential confounders, patients with poor tumor differentiation and the coexistence of the unfavorable genotypes. Conclusion These results suggest that polymorphisms of XRCC5 play an important role in astrocytoma prognosis in the Chinese Han population which could be used in the determination of astrocytoma prognosis in clinical researches.
Reliability and responsiveness of measures of pain in people with osteoarthritis of the knee: a psychometric evaluation

Abstract Purpose: To examine the fit between data from the Short Form McGill Pain Questionnaire (SF-MPQ-2) and the Rasch model, and to explore the reliability and internal responsiveness of measures of pain in people with knee osteoarthritis. Methods: Participants with knee osteoarthritis completed the SF-MPQ-2, Intermittent and Constant Osteoarthritis Pain questionnaire (ICOAP) and painDETECT. Participants were sent the same questionnaires 3 and 6 months later. Results: Fit to the Rasch model was not achieved for the SF-MPQ-2 Total scale. The Continuous subscale yielded adequate fit statistics after splitting item 10 on uniform DIF for gender, and removing item 9. The Intermittent subscale fit the Rasch model after rescoring items. The Neuropathic subscale had relatively good fit to the model. Test–retest reliability was satisfactory for most scales using both original and Rasch scoring ranging from fair to substantial. Effect sizes ranged from 0.13 to 1.79 indicating good internal responsiveness for most scales. Conclusions: These findings support the use of ICOAP subscales as reliable and responsive measure of pain in people with knee osteoarthritis. The MPQ-SF-2 subscales found to be acceptable alternatives. Implications for Rehabilitation The McGill Pain Questionnaire short version 2 is not a unidimensional scale in people with knee osteoarthritis, whereas three of the subscales are unidimensional. The McGill Pain Questionnaire short version 2 Affective subscale does not have good measurement properties for people with knee osteoarthritis. The McGill Pain Questionnaire short version 2 and the Intermittent and Constant Osteoarthritis Pain scales can be used to assess change over time. The painDETECT performs better as a screening measure than as an outcome measure.
Is Young Age a Limiting Factor When Training Balance? Effects of Child-Oriented Balance Training in Children and Adolescents.

PURPOSE Balance training (BT) studies in children reported conflicting results without evidence for improvements in children under the age of 8. The aim of this study therefore was to compare BT adaptations in children of different age groups to clarify whether young age prevents positive training outcomes. METHODS The effects of 5 weeks of child-oriented BT were tested in 77 (38 girls and 39 boys) participants of different age groups (6-7 y, 11-12 y, and 14-15 y) and compared with age-matched controls. Static and dynamic postural control, explosive strength, and jump height were assessed. RESULTS Across age groups, dynamic postural sway decreased (-18.7%; P = .012; [Formula: see text]) and explosive force increased (8.6%; P = .040; [Formula: see text]) in the intervention groups. Age-specific improvements were observed in dynamic postural sway, with greatest effects in the youngest group (-28.8%; P = .026; r = .61). CONCLUSION In contrast to previous research using adult-oriented balance exercises, this study demonstrated for the first time that postural control can be trained from as early as the age of 6 years in children when using child-oriented BT. Therefore, the conception of the training seems to be essential in improving balance skills in young children.
Effects of propylene glycol or elevated luteinizing hormone during follicle development on ovulation, fertilization, and early embryo development†

Abstract Seventeen nonlactating Holstein cows were superovulated in a Latin-square designed experiment to determine the effects of increased propylene glycol (PROP) and luteinizing hormone (LH) during antral follicle development on ovarian function, fertilization, and early embryo quality. PROP was orally drenched every 4 h for 7 days to induce hyperinsulinemia and associated metabolic changes. LH concentrations were altered by increasing LH (3-fold) during last 2 days of superovulation. Treatment groups were as follows: (1) control—oral drenching with water plus low-LH preparation; (2) high LH(HLH)—water plus HLH preparation; (3) PROP—drenching with PROP plus low LH; (4) PROP/HLH—PROP plus HLH. PROP increased glucose (P < 0.05) and insulin (P < 0.02) concentrations at all time points analyzed. Neither PROP nor LH affected numbers of follicles > 9 mm at time of gonadotropin-releasing hormone-induced LH surge, although percentage of these follicles that ovulated was decreased by both PROP (P = 0.002) and LH (P = 0.048). In addition, PROP tended (P = 0.056) to decrease total number of ovulations. PROP reduced (P = 0.028) fertilization rate, while LH tended (P = 0.092) to increase fertilization rate. There was no effect of either PROP or LH on any measure of embryo quality including percentage of embryos that were degenerate, quality 1, or quality 1 and 2 of total structures collected or fertilized structures. These results indicate that acute elevation in insulin during the preovulatory follicular wave can decrease percentage of large follicles that ovulate, particularly when combined with increased LH, and reduce fertilization of ovulated oocytes. Summary Sentence High circulating insulin, due to treatment with propylene glycol every 4 h during final week before ovulation, reduced risk of ovulation of large follicles, reduced fertilization of ovulated oocytes, but had no effect on later embryo development.
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation

In cullin-RING E3 ubiquitin ligases, substrate binding proteins, such as VHL-box, SOCS-box or the F-box proteins, recruit substrates for ubiquitination, accurately positioning and orienting the substrates for ubiquitin transfer. Yet, how the E3 machinery precisely positions the substrate is unknown. Here, we simulated nine substrate binding proteins: Skp2, Fbw7, β-TrCP1, Cdc4, Fbs1, TIR1, pVHL, SOCS2, and SOCS4, in the unbound form and bound to Skp1, ASK1 or Elongin C. All nine proteins have two domains: one binds to the substrate; the other to E3 ligase modules Skp1/ASK1/Elongin C. We discovered that in all cases the flexible inter-domain linker serves as a hinge, rotating the substrate binding domain, optimally and accurately positioning it for ubiquitin transfer. We observed a conserved proline in the linker of all nine proteins. In all cases, the prolines pucker substantially and the pucker is associated with the backbone rotation toward the E2/ubiquitin. We further observed that the linker flexibility could be regulated allosterically by binding events associated with either domain. We conclude that the flexible linker in the substrate binding proteins orients the substrate for the ubiquitin transfer. Our findings provide a mechanism for ubiquitination and polyubiquitination, illustrating that these processes are under conformational control.
Nephron progenitor cell death elicits a limited compensatory response associated with interstitial expansion in the neonatal kidney

ABSTRACT The final nephron number in an adult kidney is regulated by nephron progenitor cell availability and collecting duct branching in the fetal period. Fetal environmental perturbations that cause reductions in cell numbers in these two compartments result in low nephron endowment. Previous work has shown that maternal dietary factors influence nephron progenitor cell availability, with both caloric restriction and protein deprivation leading to reduced cell numbers through apoptosis. In this study, we evaluate the consequences of inducing nephron progenitor cell death on progenitor niche dynamics and on nephron endowment. Depletion of approximately 40% of nephron progenitor cells by expression of diphtheria toxin A at embryonic day 15 in the mouse results in 10-20% nephron reduction in the neonatal period. Analysis of cell numbers within the progenitor cell pool following induction of apoptosis reveals a compensatory response in which surviving progenitor cells increase their proliferation and replenish the niche. The proliferative response is temporally associated with infiltration of macrophages into the nephrogenic zone. Colony stimulating factor 1 (CSF1) has a mitogenic effect on nephron progenitor cells, providing a potential explanation for the compensatory proliferation. However, CSF1 also promotes interstitial cell proliferation, and the compensatory response is associated with interstitial expansion in recovering kidneys which can be pharmacologically inhibited by treatment with clodronate liposomes. Our findings suggest that the fetal kidney employs a macrophage-dependent compensatory regenerative mechanism to respond to acute injury caused by death of nephron progenitor cells, but that this regenerative response is associated with neonatal interstitial expansion. Editor's choice: Formation of the kidney relies on maintaining progenitor cells throughout development. The authors find that apoptotic loss of nephron progenitor cells provokes compensatory proliferation mediated by trophic factors released by phagocytes.
The Prostate, Lung, Colorectal and Ovarian Cancer (PLCO) Screening Trial Pathology Tissue Resource

Background: Pathology tissue specimens with associated epidemiologic and clinical data are valuable for cancer research. The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial undertook a large-scale effort to create a public resource of pathology tissues from PLCO participants who developed a cancer during the trial. Methods: Formalin-fixed paraffin-embedded tissue blocks were obtained from pathology laboratories on a loan basis for central processing of tissue microarrays, with additional free-standing tissue cores collected for nucleic acid extraction. Results: Pathology tissue specimens were obtained for prostate cancer (n = 1,052), lung cancer (n = 434), colorectal cancer (n = 675) and adenoma (n = 658), ovarian cancer and borderline tumors (n = 212), breast cancer (n = 870), and bladder cancer (n = 204). The process of creating this resource was complex, involving multidisciplinary teams with expertise in pathology, epidemiology, information technology, project management, and specialized laboratories. Conclusions: Creating the PLCO tissue resource required a multistep process, including obtaining medical records and contacting pathology departments where pathology materials were stored after obtaining necessary patient consent and authorization. The potential to link tissue biomarkers to prospectively collected epidemiologic information, screening and clinical data, and matched blood or buccal samples offers valuable opportunities to study etiologic heterogeneity, mechanisms of carcinogenesis, and biomarkers for early detection and prognosis. Impact: The methods and protocols developed for this effort, and the detailed description of this resource provided here, will be useful for those seeking to use PLCO pathology tissue specimens for their research and may also inform future tissue collection efforts in other settings. Cancer Epidemiol Biomarkers Prev; 25(12); 1635–42. ©2016 AACR.
Directed Interaction Between Monkey Premotor and Posterior Parietal Cortex During Motor-Goal Retrieval from Working Memory

Abstract Goal-directed behavior requires cognitive control of action, putatively by means of frontal-lobe impact on posterior brain areas. We investigated frontoparietal directed interaction (DI) in monkeys during memory-guided rule-based reaches, to test if DI supports motor-goal selection or working memory (WM) processes. We computed DI between the parietal reach region (PRR) and dorsal premotor cortex (PMd) with a Granger-causality measure of intracortical local field potentials (LFP). LFP mostly in the beta (12–32 Hz) and low-frequency (f≤10Hz) ranges contributed to DI. During movement withholding, beta-band activity in PRR had a Granger-causal effect on PMd independent of WM content. Complementary, low-frequency PMd activity had a transient Granger-causing effect on PRR specifically during WM retrieval of spatial motor goals, while no DI was associated with preliminary motor-goal selection. Our results support the idea that premotor and posterior parietal cortices interact functionally to achieve cognitive control during goal-directed behavior, in particular, that frontal-to-parietal interaction occurs during retrieval of motor-goal information from spatial WM.
KBQ - A Tool for Knowledge Base Quality Assessment Using Evolution Analysis

Knowledge bases are becoming essential components for tasks that require automation with some degrees of intelligence. It is crucial to establish automatic and timely checks to ensure highlevel quality of the knowledge base content (i.e., entities, types, and relations). In this paper, we present KBQ, a tool that automates the detection and report generation of quality issues for evolving knowledge bases. KBQ analyzes the evolution of a KB by measuring the frequency of change, the change pattern, the change impact and the causes of changes of resources and properties. Data collection and profiling tasks are performed using Loupe, an online tool for linked data profiling. We describe KBQ in action on two different use cases, and we report the benefits that it introduced. KBQ is published as open source project, and a demo is available at http: //datascience.ismb. it/shiny/KBQ/