Miracle-dz/UniFAR-FTUs huggingface dataset:
Trapping DNA Replication Origins from the Human Genome

Synthesis of chromosomal DNA is initiated from multiple origins of replication in higher eukaryotes; however, little is known about these origins’ structures. We isolated the origin-derived nascent DNAs from a human repair-deficient cell line by blocking the replication forks near the origins using two different origin-trapping methods (i.e., UV- or chemical crosslinker-treatment and cell synchronization in early S phase using DNA replication inhibitors). Single-stranded DNAs (of 0.5–3 kb) that accumulated after such treatments were labeled with bromodeoxyuridine (BrdU). BrdU-labeled DNA was immunopurified after fractionation by alkaline sucrose density gradient centrifugation and cloned by complementary-strand synthesis and PCR amplification. Competitive PCR revealed an increased abundance of DNA derived from known replication origins (c-myc and lamin B2 genes) in the nascent DNA fractions from the UV-treated or crosslinked cells. Nucleotide sequences of 85 and 208 kb were obtained from the two libraries (I and II) prepared from the UV-treated log-phase cells and early S phase arrested cells, respectively. The libraries differed from each other in their G+C composition and replication-related motif contents, suggesting that differences existed between the origin fragments isolated by the two different origin-trapping methods. The replication activities for seven out of 12 putative origin loci from the early-S phase cells were shown by competitive PCR. We mapped 117 (library I) and 172 (library II) putative origin loci to the human genome; approximately 60% and 50% of these loci were assigned to the G-band and intragenic regions, respectively. Analyses of the flanking sequences of the mapped loci suggested that the putative origin loci tended to associate with genes (including conserved sites) and DNase I hypersensitive sites; however, poor correlations were found between such loci and the CpG islands, transcription start sites, and K27-acetylated histone H3 peaks.
Serological Survey for Foot-and-Mouth Disease Virus in Wildlife in Eastern Africa and Estimation of Test Parameters of a Nonstructural Protein Enzyme-Linked Immunosorbent Assay for Buffalo

ABSTRACT In this study we estimate the seroprevalence of foot-and-mouth disease virus (FMDV) in wildlife from eastern and central Africa. Sera were sourced from between 1994 and 2002 from a rinderpest surveillance program. Our study compared a nonstructural protein enzyme-linked immunosorbent assay (Cedi test) with a virus neutralization test. The study shows that there is only a low seroprevalence of FMDV in sampled nonbuffalo species. The seroprevalence in the Cape buffalo was high for SAT2, lower for SAT1, and lowest for SAT3. As the SAT2 serotype was most prevalent, the Cedi test largely reflected the occurrence of SAT2-positive animals. The results also suggest that SAT2 became dominant around 1998, with a large increase in seroprevalence. The sensitivity and specificity of the Cedi test were estimated by comparison to the combined virus neutralization test results from all three SAT tests. A Bayesian implementation of the Hui-Walter latent class model was used to estimate the test parameters. The model permits estimation in the absence of a gold standard test. The final model, using noninformative priors and assuming conditional independence of test performance, estimated Cedi test sensitivity at 87.7% and specificity at 87.3%. These estimates are similar to those for domestic bovines; they suggest that the Cedi test is a useful tool for screening buffalo for infection with the various serotypes of FMDV.
Psoriasis of the nails associated with disability in a large number of patients: results of a recent interview with 1,728 patients.

BACKGROUND AND OBJECTIVE Occurrence rates of clinical features of nail psoriasis vary considerably in the literature. Little information is available on subjective complaints of patients affected by psoriasis of the nails. METHOD Interviews with 1,728 psoriatic patients concerning their nail changes and complaints are reviewed. RESULTS The results indicate that pitting and deformation are the most common clinical aberrations in psoriatic nails, with a positive association between the duration of skin lesions and nail psoriasis. No relation was found between age and nail psoriasis in this group. Remarkably, 51.8% of patients suffered from pain-caused by the nail changes, and a large group of patients was restricted in their daily activities, housekeeping and/or profession (58.9, 56.1, 47.9%). Treatment was disappointing: only 19.3% showed marked improvement during treatment. CONCLUSION This indicates that psoriasis of the nails is a more important individual and social-economic problem than previously assumed and that development of new treatments is needed.
Learning Confidence for Out-of-Distribution Detection in Neural Networks

Modern neural networks are very powerful predictive models, but they are often incapable of recognizing when their predictions may be wrong. Closely related to this is the task of out-of-distribution detection, where a network must determine whether or not an input is outside of the set on which it is expected to safely perform. To jointly address these issues, we propose a method of learning confidence estimates for neural networks that is simple to implement and produces intuitively interpretable outputs. We demonstrate that on the task of out-of-distribution detection, our technique surpasses recently proposed techniques which construct confidence based on the network's output distribution, without requiring any additional labels or access to out-of-distribution examples. Additionally, we address the problem of calibrating out-of-distribution detectors, where we demonstrate that misclassified in-distribution examples can be used as a proxy for out-of-distribution examples.
Electrocardiographic unrecognized myocardial infarction does not improve prediction of cardiovascular events beyond traditional risk factors. The Tromsø Study

Background Unrecognized myocardial infarction (MI) is a frequent and intriguing entity associated with a similar risk of death as recognized MI. Previous studies have not fully addressed whether the poor prognosis is explained by traditional cardiovascular risk factors. We investigated whether electrocardiographically detected unrecognized MI was independently associated with cardiovascular events and death and whether it improved prediction for future MI in a general population. Design Prospective cohort study. Methods We studied 5686 women and men without clinically recognized MI at baseline in 2007–2008. We assessed the risk of future MI, stroke and all-cause mortality in persons with unrecognized MI compared with persons with no MI during 31,051 person-years of follow-up. Results In the unadjusted analyses, unrecognized MI was associated with increased risk of future recognized MI (hazard ratio 1.84, 95% confidence interval (CI) 1.15–2.96) and all-cause mortality (hazard ratio 1.78, 95% CI 1.21–2.61), but not stroke (hazard ratio 1.09, 95% CI 0.56–2.17). The associations did not remain significant after adjustment for traditional risk factors (hazard ratio 1.25, 95% CI 0.76–2.06 and hazard ratio 1.38, 95% CI 0.93–2.05) for MI and all-cause mortality respectively. Unrecognized MI did not improve risk prediction for future recognized MI using the Framingham Risk Score (p = 0.96) or the European Systematic COronary Risk Evaluation (p = 0.65). There was no significant sex interaction regarding any of the endpoints. Conclusion Electrocardiographic unrecognized MI was not significantly associated with future risk of MI, stroke or all-cause mortality in the general population after adjustment for the traditional cardiovascular risk factors, and it did not improve prediction of future MI.
Robust stability and performance analysis for multiple model adaptive controllers

For an Estimation Based Multiple Model Switched Adaptive Control (EMMSAC) algorithm controlling a MIMO minimal LTI plant, lp, 1 ≤ p ≤ ∞ bounds on the gain from the input and output disturbances to the internal signals are obtained which are invariant to the number of models in the plant model set. For a compact uncertainty set it is shown that a realisable EMMSAC algorithm achieves robust stability for any plant within the uncertainty set.
Dose-response of women's health-related quality of life (HRQoL) and life satisfaction to physical activity.

BACKGROUND To examine the dose-response relationship between health related quality of life (HRQoL) and life satisfaction (outcomes) and duration of recreational physical activity (exposure). Further, to explore whether these relationships depend on type of physical activity (PA). METHODS 793 Australian rural-living women self-reported on duration of recreational PA; HRQoL via SF-36 Mental Component Summary (MCS) and Physical Component Summary (PCS); and a life satisfaction scale. ANOVAs and ANCOVAs investigated differences in outcomes (MCS, PCS, and life satisfaction) between tertiles of exposure to recreational PA, and types of PA (club sport, gymnasium, walking), with adjustment for potential confounders. RESULTS A significant positive dose-response relationship was found between PCS and level of PA. Furthermore, this relationship depended on type of PA, with club-sport participants recording higher PCS than non-club-sport participants in all but the highest tertile of exposure. Life satisfaction and MCS were not significantly related to level of PA. CONCLUSION Physical health was positively associated with level of recreational PA, with club sport participation contributing greater benefits at low to moderate exposures than participation in gymnasium or walking activities.
The Clinical Significance of Uric Acid and Complement Activation in the Progression of IgA Nephropathy

Background/Aims: The aim of this study is to investigate the utility of clinical [age, gender, mean arterial pressure (MAP)] and laboratory parameters [eGFR, hemoglobin (Hgb), serum levels of creatinine, uric acid, albumin, proteinuria, hematuria] and also histopathological lesions (Oxford classification parameters, crescents, intensity and pattern of staining for C3, C1Q, IgA, IgG, IgM) as progression markers in patients with IgA Nephropathy (IgAN). Methods: A total of 111 IgAN patients with a follow-up period >1 year or who reached kidney failure [GFR category G5 chronic kidney disease (CKD)] <1 year were investigated. Primary endpoint was the development of kidney failure or eGFR decline ≥50% from the baseline. Kaplan-Meier and Cox proportional hazards analyses were performed. Results: Mean follow-up period was 33±29 months. Thirty-seven (33.3%) patients progressed to kidney failure and 4 (3.6%) patients developed eGFR decline ≥50% from the baseline after a median of 23 and 65 months, respectively. In multivariate Cox regression analysis, baseline levels of Hgb (HR:0.782, 95% CI 0.559-0.973, p=0.037), serum uric acid (HR:1.293, 95% CI 1.023-1.621, p=0.046), eGFR (HR:0.966, 95% CI 0.947-0.984, p=0.004) and intensity of C3 staining (HR:1.550, 95% CI 1.198-1.976, p=0.049) predicted primary endpoint. Serum uric acid level was associated independently with T score (β=0.303, p=0.005) in patients with eGFR>30 ml/min/m2. Conclusions: Hyperuricemia and the deposition of C3 are independent risk factors for IgAN progression.
Subsidence Trends of Volturno River Coastal Plain (Northern Campania, Southern Italy) Inferred by SAR Interferometry Data

The Volturno Plain is one of the largest alluvial plains of peninsular Italy, which is one of the most susceptible plains to coastal hazards. This area is characterized by both natural and human-induced subsidence. This present study is based on the post-processing, analysis and mapping of the available Persistent Scatterer interferometry datasets. The latter were derived from the combination of both ascending and descending orbits of three different radar satellite systems during an observation period of almost two decades (June 1992–September 2010). The main output of this study is a map of vertical deformation, which provides new insights into the areal variability of the ground deformation processes (subsidence/uplift) of Volturno plain over the last few decades. The vertical displacement values obtained by the post-processing of the interferometric data show that the Volturno river plain is characterized by significant subsidence in the central axial sectors and in the river mouth area. Moderate uplift is detected in the eastern part of the plain, whereas other sectors of the study area are characterized by moderate subsidence and/or stability. On the basis of the analyzed subsoil stratigraphy, we inferred that the subsidence recorded in the Volturno plain is mainly a consequence of a natural process related to the compaction of the fluvial and palustrine deposits that form the alluvial plain. The anthropic influences (e.g., water exploitation, urbanization) are substantially considered to be an additional factor that may enhance subsidence only locally. The uplift mapped in the eastern sector of the plain is related to the tectonic activity. The study of the subsidence in the Volturno plain is a valuable tool for river flood analyses and the assessment of the coastal inundation hazards and related risk mitigation.
The VLA-COSMOS 3 GHz Large Project: The infrared- radio correlation of star-forming galaxies and AGN to z ≲ 6

We examine the behaviour of the infrared-radio correlation (IRRC) over the range 0 <z ≲ 6 using new, highly sensitive 3 GHz observations with the Karl G. Jansky Very Large Array (VLA) and infrared data from the Herschel Space Observatory in the 2 deg^2 COSMOS field. We distinguish between objects where emission is believed to arise solely from star-formation, and those where an active galactic nucleus (AGN) is thought to be present. We account for non-detections in the radio or in the infrared using a doubly-censored survival analysis. We find that the IRRC of star-forming galaxies, quantified by the infrared-to-1.4 GHz radio luminosity ratio (q_(TIR)), decreases with increasing redshift: q_(TIR)(z) = (2.88 ± 0.03)(1 + z)^(−0.19 ± 0.01). This is consistent with several previous results from the literature. Moderate-to-high radiative luminosity AGN do not follow the same q_(TIR)(z) trend as star-forming galaxies, having a lower normalisation and steeper decrease with redshift. We cannot rule out the possibility that unidentified AGN contributions only to the radio regime may be steepening the observed q_(TIR)(z) trend of the star-forming galaxy population. We demonstrate that the choice of the average radio spectral index directly affects the normalisation, as well as the derived trend with redshift of the IRRC. An increasing fractional contribution to the observed 3 GHz flux by free-free emission of star-forming galaxies may also affect the derived evolution. However, we find that the standard (M82-based) assumption of the typical radio spectral energy distribution (SED) for star-forming galaxies is inconsistent with our results. This suggests a more complex shape of the typical radio SED for star-forming galaxies, and that imperfect K corrections in the radio may govern the derived trend of decreasing q_(TIR) with increasing redshift. A more detailed understanding of the radio spectrum is therefore required for robust K corrections in the radio and to fully understand the cosmic evolution of the IRRC. Lastly, we present a redshift-dependent relation between rest-frame 1.4 GHz radio luminosity and star formation rate taking the derived redshift trend into account.
Survey on Recent Designs of Compliant Micro-/Nano-Positioning Stages

Micromanipulation is a hot topic due to its enabling role in various research fields. In order to perform a high precision operation at a small scale, compliant mechanisms have been proposed and applied for decades. In microscale manipulation, micro-/nano-positioning is the most fundamental operation because a precision positioning is the premise of subsequent operations. This paper is concentrated on reviewing the state-of-the-art research on complaint micro-/nano-positioning stage design in recent years. It involves the major processes and components for designing a compliant positioning stage, e.g., actuator selection, stroke amplifier design, connecting scheme of the multi-DOF stage and structure optimization. The review provides a reference to design a compliant micro-/nano-positioning stage for pertinent applications.
Scabies among primary schoolchildren in Egypt: sociomedical environmental study in Kafr El-Sheikh administrative area

Background/objectives Scabies is a major global public health issue that might affect people from all socioeconomic levels. The primary contributing factors in contracting scabies seem to be poverty and overcrowded living conditions. Scabies often spreads among schoolchildren quite rapidly, owing to their close contact and overcrowding within the schools. However, limited information is available about its risk factors and the socioeconomic correlates among schoolchildren in Egypt. This study aimed to assess the prevalence of scabies and its risk factors among primary schoolchildren in Kafr El-Sheikh administrative area, Egypt. Methods This cross-sectional descriptive study was performed on primary schoolchildren in urban and rural areas of Kafr El-Sheikh administrative area. A predesigned questionnaire was used for data collection from the randomly selected 2,104 children, and clinical dermatological examination was done for them. Results Out of 2,104 children studied, there were 92 cases of scabies with a prevalence of 4.4%. The prevalence of scabies infestation in male students was 3.9%, while it was 4.8% in females, with no statistical significance. The results showed significant variations in the risk of scabies infestation by factors such as residence, paternal education and occupation, maternal education, sleeping with others, having animals at home, dealing with animals outside the house, type of building for living, family history of itchy rash, and sharing clothes with others. Conclusion In our community, scabies is still an important health problem affecting schoolchildren, especially in rural areas. It is characterized by a complex web of causation, particularly poor living conditions and low level of parents’ education.
The relationships between shoulder pain, range of motion, and disability in patients with shoulder dysfunction.

BACKGROUND Shoulder dysfunction is a major cause of musculoskeletal pain in general population. A variety of shoulder disorders can cause a reduction in shoulder range of motion and subsequent disability. OBJECTIVE To investigate the relationship between the shoulder pain, range of motion, and disability in patients with shoulder dysfunction. METHODS Sixty-four patients (49 men and 15 women) with shoulder disorders with a varying diagnosis including, adhesive capsulitis, rotator cuff injury, impingement syndrome, acromio-clavicular pain, and instability, participated in this cross-sectional study. Participants were asked to report the shoulder pain intensity and level of disability on a numerical rating scale (NRS) and the shoulder pain and disability index (SPADI), respectively. In addition, the active shoulder range of motion was evaluated. RESULTS The Spearman rank correlation coefficient was used to investigate the association between the shoulder pain, range of motion, and disability. A good negative correlation found between the shoulder abduction, flexion, and rotation range of motion with the NRS score (rho =-0.710 to -0.747). A moderate negative correlation found between the extension and the NRS score (rho =-0.643). A good negative correlation found between abduction and the SPADI total score (rho =-0.714). A moderate negative correlation found between the shoulder flexion and rotation range of motion with the SPADI total score (rho =-0.547 to -0.694). A fair negative correlation found between the extension and the SPADI total score (rho =-0.495). A moderated positive correlation found between the NRS and the SPADI total score (rho = 0.667). CONCLUSIONS The flexion, abduction, and rotation ROMs were most significantly associated with severity of pain and the physical disability in patients with shoulder dysfunction. Further, longitudinal studies are required to confirm these results.
Type 2 Diabetes and Depression

Purpose The purpose of the current study was to determine the feasibility, acceptability, and preliminary effectiveness of an integrated self-management intervention that simultaneously targets diabetes and depression self-management in a primary care clinic that serves the Latino immigrant community. Methods The integrated intervention included behavioral activation and motivational interviewing techniques. It was developed with patient, family member, and provider stakeholders, and it comprised 6 individual sessions, followed by 2 monthly booster sessions. Eighteen Latino immigrants participated in an open trial of the intervention. A1C levels were examined at baseline and postintervention. Participants also completed measures of depression, diabetes self-management behaviors, patient activation, and diabetes-related self-efficacy and gave open-ended feedback about the intervention. Results Feasibility of delivering the intervention in the primary care setting and acceptability to the target population were demonstrated. Among participants completing the intervention, A1C levels decreased significantly from baseline. A significant reduction in depressive symptoms and an improvement in diabetes self-management behaviors, patient activation, and diabetes-related self-efficacy were observed. Qualitative responses from participants indicated unilateral positive responses to the intervention and endorsed its continuation in the clinic. Conclusions This pilot trial demonstrated the feasibility and acceptability of an integrated self-management intervention for diabetes and depression. In addition, preliminary data suggest that the intervention may have a positive impact on diabetes and depression-related outcomes. Further evaluation is warranted.
Multiwalled carbon-nanotubes-sheet actuators: theoretical and experimental investigations

In this paper we present experimental measurements as well as a theoretical model for the chemo-electro-mechanical behavior of multi walled (MWNT) carbon nanotubes sheet actuators. Investigations of MWNT paper as an actuator and the analysis of the experimental and theoretical characteristics are special features of the presented work. The influencing parameters of the actuation behavior such as thickness of sheet materials and electrolyte concentration have been investigated. We report the experimentally measured active displacement varying quadratically with the applied electric field and non-linearly with the electrolyte concentration. In the theoretical part, we present a macroscopic actuation model for the global displacement behavior of MWNT materials. Finally, a comparison between the theoretical and the experimental investigations has been conducted.