Miracle-dz/UniFAR-FTUs huggingface dataset:
Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.
Effectiveness of holistic neuropsychological rehabilitation for Spanish population with acquired brain injury measured using Rasch analysis.

INTRODUCTION The Rasch model is increasingly used in the field of rehabilitation because it improves the accuracy of measurements of patient status and their changes after therapy. OBJECTIVE To determine the long-term effectiveness of a holistic neuropsychological rehabilitation program for Spanish outpatients with acquired brain injury (ABI) using Rasch analysis. METHODS Eighteen patients (ten with long evolution - patients who started the program > 6 months after ABI- and eight with short evolution) and their relatives attended the program for 6 months. Patients' and relatives' answers to the European Brain Injury Questionnaire and the Frontal Systems Behavior Scale at 3 time points (pre-intervention. post-intervention and 12 month follow-up) were transformed into linear measures called logits. RESULTS The linear measures revealed significant improvements with large effects at the follow-up assessment on cognitive and executive functioning, social and emotional self-regulation, apathy and mood. At follow-up, the short evolution group achieved greater improvements in mood and cognitive functioning than the long evolution patients. CONCLUSIONS The program showed long-term effectiveness for most of the variables, and it was more effective for mood and cognitive functioning when patients were treated early. Relatives played a key role in the effectiveness of the rehabilitation program.
Good Exemplars of Natural Scene Categories Elicit Clearer Patterns than Bad Exemplars but Not Greater BOLD Activity

Within the range of images that we might categorize as a “beach”, for example, some will be more representative of that category than others. Here we first confirmed that humans could categorize “good” exemplars better than “bad” exemplars of six scene categories and then explored whether brain regions previously implicated in natural scene categorization showed a similar sensitivity to how well an image exemplifies a category. In a behavioral experiment participants were more accurate and faster at categorizing good than bad exemplars of natural scenes. In an fMRI experiment participants passively viewed blocks of good or bad exemplars from the same six categories. A multi-voxel pattern classifier trained to discriminate among category blocks showed higher decoding accuracy for good than bad exemplars in the PPA, RSC and V1. This difference in decoding accuracy cannot be explained by differences in overall BOLD signal, as average BOLD activity was either equivalent or higher for bad than good scenes in these areas. These results provide further evidence that V1, RSC and the PPA not only contain information relevant for natural scene categorization, but their activity patterns mirror the fundamentally graded nature of human categories. Analysis of the image statistics of our good and bad exemplars shows that variability in low-level features and image structure is higher among bad than good exemplars. A simulation of our neuroimaging experiment suggests that such a difference in variance could account for the observed differences in decoding accuracy. These results are consistent with both low-level models of scene categorization and models that build categories around a prototype.
Modified Weibull Distribution for Analyzing the Tensile Strength of Bamboo Fibers

There is growing evidence that the standard Weibull strength distribution is not always accurate for the description of variability in tensile strength and its dependence on the gauge size of brittle fibers. In this work, a modified Weibull model by incorporating the diameter variation of bamboo fiber is proposed to investigate the effect of fiber length and diameter on the tensile strength. Fiber strengths are obtained for lengths ranging from 20 to 60 mm and diameters ranging from 196.6 to 584.3 μm through tensile tests. It is shown that as the within-fiber diameter variation increases, the fracture strength of the bamboo fiber decreases. In addition, the accuracy of using weak-link scaling predictions based on the standard and modified Weibull distribution are assessed, which indicates that the use of the modified distribution provides better correlation with the experimental data than the standard model. The result highlights the accuracy of the modified Weibull model for characterizing the strength and predicting the size dependence of bamboo fiber.
A Multisite, Randomized Controlled Clinical Trial of Computerized Cognitive Remediation Therapy for Schizophrenia

The effectiveness of cognitive remediation therapy (CRT) for the neuropsychological deficits seen in schizophrenia is supported by meta-analysis. However, a recent methodologically rigorous trial had negative findings. In this study, 130 chronic schizophrenic patients were randomly assigned to computerized CRT, an active computerized control condition (CC) or treatment as usual (TAU). Primary outcome measures were 2 ecologically valid batteries of executive function and memory, rated under blind conditions; other executive and memory tests and a measure of overall cognitive function were also employed. Carer ratings of executive and memory failures in daily life were obtained before and after treatment. Computerized CRT was found to produce improvement on the training tasks, but this did not transfer to gains on the primary outcome measures and most other neuropsychological tests in comparison to either CC or TAU conditions. Nor did the intervention result in benefits on carer ratings of daily life cognitive failures. According to this study, computerized CRT is not effective in schizophrenia. The use of both active and passive CCs suggests that nature of the control group is not an important factor influencing results.
Symbolic Number Abilities Predict Later Approximate Number System Acuity in Preschool Children

An ongoing debate in research on numerical cognition concerns the extent to which the approximate number system and symbolic number knowledge influence each other during development. The current study aims at establishing the direction of the developmental association between these two kinds of abilities at an early age. Fifty-seven children of 3–4 years performed two assessments at 7 months interval. In each assessment, children's precision in discriminating numerosities as well as their capacity to manipulate number words and Arabic digits was measured. By comparing relationships between pairs of measures across the two time points, we were able to assess the predictive direction of the link. Our data indicate that both cardinality proficiency and symbolic number knowledge predict later accuracy in numerosity comparison whereas the reverse links are not significant. The present findings are the first to provide longitudinal evidence that the early acquisition of symbolic numbers is an important precursor in the developmental refinement of the approximate number representation system.
Structured Prediction Theory Based on Factor Graph Complexity

We present a general theoretical analysis of structured prediction with a series of new results. We give new data-dependent margin guarantees for structured prediction for a very wide family of loss functions and a general family of hypotheses, with an arbitrary factor graph decomposition. These are the tightest margin bounds known for both standard multi-class and general structured prediction problems. Our guarantees are expressed in terms of a data-dependent complexity measure, factor graph complexity, which we show can be estimated from data and bounded in terms of familiar quantities. We further extend our theory by leveraging the principle of Voted Risk Minimization (VRM) and show that learning is possible even with complex factor graphs. We present new learning bounds for this advanced setting, which we use to design two new algorithms, Voted Conditional Random Field (VCRF) and Voted Structured Boosting (StructBoost). These algorithms can make use of complex features and factor graphs and yet benefit from favorable learning guarantees. We also report the results of experiments with VCRF on several datasets to validate our theory.
Self-Regulation as a Mediator in the Relationship between Self-Efficacy, Task Value and Active Procrastination

This study investigated the relationships between self-efficacy, task value, and active procrastination; and what role does self-regulation strategies play in these relationships. A total of 426 pre-service teachers, 223 males and 203 females, studying in colleges of education in North-Western Nigeria participated in the study. A set of self-report questionnaire was used to assess the participants’ levels of procrastination, self-efficacy, task value beliefs, and self-regulation strategies. Structural equation modelling (SEM) was employed as statistical technique for data analysis of the study. The results, based on the hypothesized structural model, which overall goodness-of-fit indices indicate good model fit, revealed that self-efficacy and task value beliefs were not directly significant predictors of active procrastination. However, mediation analysis, which was conducted based on SEM or modern approach, showed that there was an evidence of indirect effect of the variables on active procrastination through self-regulation. Test of mediation by bootstrapping method established significant mediating role of self-regulation in the relationship between self-efficacy, task value and active procrastination. Theoretical and practical implications of the study, as well as recommendations for future research, have been presented.
Understanding the pathway between the transplant experience and health‐related quality of life outcomes in adolescents

Abstract: Developments in solid organ transplantation have resulted in improved survival for children with advanced kidney, liver, and heart disease; however, concerns have been raised regarding the quality of life of survivors. This study examined HRQOL in adolescent transplant recipients. We examined the influence of demographic, treatment regimen, and family factors on physical and mental health domains of HRQOL. The current single‐center investigation involved 68 solid organ transplant recipients and their parents. All families participated in a structured interview to collect information on demographics, characteristics of the adolescents’ disease and treatment regimen, family functioning, and HRQOL for parents and adolescents. Using hierarchical regression analyses, predictive models of physical functioning and mental health outcomes for adolescent transplant recipients were developed for parent‐proxy and adolescent self‐report. Perceived frequency of medication side‐effects and family conflict significantly contributed to adolescent physical functioning and mental health outcomes. Taken together, transplant consequences and family environment significantly impact physical and mental health outcomes in adolescent transplant recipients. Our findings demonstrate the need for pharmacological considerations and psychological interventions to address these areas.
Effects of a Plant Sterol or Stanol Enriched Mixed Meal on Postprandial Lipid Metabolism in Healthy Subjects

Background Evidence is increasing that plant sterols and stanols not only lower fasting serum low-density lipoprotein concentrations, but also those of triglycerides (TG). Insight into effects of these components on postprandial TG metabolism, an emerging risk factor for cardiovascular disease, is missing. Objective Our objective was to examine the 8-hour postprandial response after consuming plant sterol or stanol enriched margarine as part of a mixed meal. Methods This postprandial study was part of a randomized crossover study in which 42 subjects consumed plant sterol enriched (3 g/d plant sterols), plant stanol enriched (3 g/d plant stanols), and control margarines for 4 weeks. After each period, subjects consumed a shake enriched with 3g plant sterols (sterol period), 3g plant stanols (stanol period) or no addition (control period). Subjects received a second shake with no addition after 4 hours. Results TG and apoB48 incremental areas under the curves (iAUC) of the total (0-8h) and 1st meal response (0-4h) were comparable between the meals and in all age categories (I:18-35y, II:36-52y, III:53-69y). In subjects aged 53-69y, TG iAUC after the 2nd meal (4-8h) was higher in the stanol period as compared with the sterol (63.1±53.0 mmol/L/min; P < 0.01) and the control period (43.2±52.4 mmol/L/min; P < 0.05). ApoB48 iAUC after the 2nd meal was higher after the stanol than after the sterol period (67.1±77.0 mg/L/min; P < 0.05) and tended to be higher than after the control period (43.1±64.5 mg/L/min; P = 0.08) in subjects aged 53-69y. These increased postprandial responses may be due to reduced lipoprotein lipase activity, since postprandial apoCIII/II ratios were increased after stanol consumption compared with the control meal. Conclusion Postprandial TG and apoB48 responses are age-dependently increased after plant stanol consumption, which might be related to a changed clearance of triglyceride-rich lipoproteins. Trial Registration ClinicalTrials.gov NCT01559428
Next-Generation Sequencing of Disseminated Tumor Cells

Disseminated tumor cells (DTCs) detected in the bone marrow have been shown as an independent prognostic factor for women with breast cancer. However, the mechanisms behind the tumor cell dissemination are still unclear and more detailed knowledge is needed to fully understand why some cells remain dormant and others metastasize. Sequencing of single cells has opened for the possibility to dissect the genetic content of subclones of a primary tumor, as well as DTCs. Previous studies of genetic changes in DTCs have employed single-cell array comparative genomic hybridization which provides information about larger aberrations. To date, next-generation sequencing provides the possibility to discover new, smaller, and copy neutral genetic changes. In this study, we performed whole-genome amplification and subsequently next-generation sequencing to analyze DTCs from two breast cancer patients. We compared copy-number profiles of the DTCs and the corresponding primary tumor generated from sequencing and SNP-comparative genomic hybridization (CGH) data, respectively. While one tumor revealed mostly whole-arm gains and losses, the other had more complex alterations, as well as subclonal amplification and deletions. Whole-arm gains or losses in the primary tumor were in general also observed in the corresponding DTC. Both primary tumors showed amplification of chromosome 1q and deletion of parts of chromosome 16q, which was recaptured in the corresponding DTCs. Interestingly, clear differences were also observed, indicating that the DTC underwent further evolution at the copy-number level. This study provides a proof-of-principle for sequencing of DTCs and correlation with primary copy-number profiles. The analyses allow insight into tumor cell dissemination and show ongoing copy-number evolution in DTCs compared to the primary tumors.
University of Birmingham Analysis of the role of COP9 Signalosome (CSN) subunits in K562; the first link between CSN and autophagy

Background: The COP9/signalosome (CSN) is a highly conserved eight subunit complex that, by deneddylating cullins in cullin-based E3 ubiquitin ligases, regulates protein degradation. Although studied in model human cell lines such as HeLa, very little is known about the role of the CSN in haemopoietic cells. Results: Greater than 95% knockdown of the non-catalytic subunit CSN2 and the deneddylating subunit CSN5 of the CSN was achieved in the human myeloid progenitor cell line K562. CSN2 knockdown led to a reduction of both CSN5 protein and mRNA whilst CSN5 knockdown had little effect on CSN2. Both knockdowns inhibited CSN deneddylase function as demonstrated by accumulation of neddylated Cul1. Furthermore, both knockdowns resulted in the sequential loss of Skp2, Cdc4 and β -TrCP F-box proteins. These proteins were rescued by the proteasome inhibitor MG132, indicating the autocatalytic degradation of F-box proteins upon loss of CSN2 or CSN5. Interestingly, altered F-box protein gene expression was also observed in CSN2 and CSN5 knockdowns, suggesting a potential role of the CSN in regulating F-box protein transcription. Loss of either CSN subunit dramatically reduced cell growth but resulted in distinct patterns of cell death. CSN5 knockdown caused mitotic defects, G2/M arrest and apoptotic cell death. CSN2 knockdown resulted in non-apoptotic cell death associated with accumulation of both the autophagy marker LC3-II and autophagic vacuoles. Treatment of vector control K562 cells with the autophagy inhibitors 3-methyladenine and bafilomycin A1 recapitulated the growth kinetics, vacuolar morphology and LC3-II accumulation of CSN2 knockdown cells indicating that the cellular phenotype of CSN2 cells arises from autophagy inhibition. Finally, loss of CSN2 was associated with the formation of a CSN5 containing subcomplex. Conclusion: We conclude that CSN2 is required for CSN integrity and the stability of individual CSN subunits, and postulate that CSN2 loss results in a phenotype distinct from that of cells lacking CSN5 possibly as a consequence of altered CSN5 activity within a resultant CSN subcomplex. Our data present the first evidence for the sequential loss of F-box proteins upon CSN manipulation and are the first to identify a potential link between CSN function and autophagy.
A Multi-Band Burst-Mode Clock and Data Recovery Circuit

A multi-band burst-mode clock and data recovery (BMCDR) circuit is presented. The available data rates are 2488.32 Mbps, 1244.16 Mbps, 622.08 Mbps, and 155.52 Mbps, which are specified in a gigabit-capable passive optical network (GPON) [1]. A half-rate and lowjitter gated voltage-controlled oscillator (GVCO) and a phase-controlled frequency divider are used to achieve the multi-band reception. The proposed BMCDR circuit has been fabricated in a 0.18 μm CMOS process. Its active area is 0.41 mm2 and consumes 70 mW including I/O buffers from a 1.8 V supply. key words: multi-band, burst-mode, clock and data recovery, voltagecontrolled oscillator
Elimination Rate Constant Describing Clearance of Infused Fluid from Plasma Is Independent of Large Infusion Volumes of 0.9% Saline in Sheep

Background: The purpose of this study was to determine the influence of varying large crystalloid infusion volumes, ranging from a volume that has been safely administered to volunteers to a volume that greatly exceeds a practical volume for studies in normovolemic humans, of rapidly infused 0.9% saline on the elimination rate constant in sheep. Methods: Six sheep underwent three randomly ordered, 20 min, intravenous infusions of 0.9% saline in volumes of 25 ml/kg, 50 ml/kg and 100 ml/kg. Repeated measurements of arterial plasma dilution were analyzed using the volume kinetic approach to determine the apparent volumes of the central (V1) and peripheral (V2) body fluid spaces, the elimination rate constant (kr) describing clearance from the central fluid space and the rate constant (kt) for the diffusion of fluid between the central and the peripheral fluid spaces. The latter constant was split in to two constants, one describing flow out from the central fluid space and one describing flow into the central fluid space. Urinary output was measured in all sheep. Results: kr was comparable at each infused volume (38.3 ± 4.5, 32.2 ± 4.2, and 36.7 ± 7.0 ml/min, respectively, in the 25 ml/kg, 50 ml/kg, and 100 ml/kg protocols). However, for the largest infusion, other kinetic parameters were influenced by the magnitude of the infusion. V2 was significantly increased (P < 0.05) and the area under the dilution-time curve divided by the infused volume was 20% lower for the largest infusion (P < 0.03). Although urinary output increased as the infusion volume increased, only 59% of the administered volume had been excreted at 180 min after the 100 ml/kg infusion as compared with approximately 90% after the other two infusions (P < 0.01). Conclusions: Elimination from the central fluid space of large, rapidly infused volumes of saline solution is independent of infused volume. Larger volumes are apparently cleared from the central fluid space (V1) by expansion of a peripheral volume (V2) as renal excretion fails to increase in proportion to the volume of infused fluid.
Association between Obesity and Serum 25(OH)D Concentrations in Older Mexican Adults

Background: Vitamin D is essential for maintaining bone mineralization and calcium homeostasis, and prevents falls and fractures in older adults. Mexico is undergoing an epidemiologic and demographic transition with increasing obesity rates. The study’s aim was to determine the association of obesity with serum 25-hydroxyvitamin D [25(OH)D] concentrations in older Mexican adults. Methods: Data from 1772 Mexicans, aged ≥50 years, enrolled in a sub-sample of the 3rd wave of the Mexican Health and Aging Study, were included. Serum 25(OH)D concentrations were used to define vitamin D status, and were categorized into tertiles. Body mass index measures were used to categorize older adults into under/normal weight, overweight, and obese groups. Multinomial logistic regression models were used to assess the relationship, adjusting for potential confounders. Results: Approximately 40% and 37% of older Mexican adults were either overweight or obese, respectively. Compared to under/normal weight older Mexicans, obese adults were 1.78 times (95% Confidence Interval (CI) 1.27–2.48) and 1.94 times (95% CI 1.40–2.68) more associated with the first and second tertile concentrations of serum 25(OH)D, respectively. Overweight adults were 1.52 times (95% CI 1.12–2.06) more associated with the second tertile of serum 25(OH)D concentration than under/normal weight adults. Conclusion: Overweight/Obesity was found to be significantly associated with low concentrations of serum 25(OH) in older Mexican adults.
Differential reactivity of human mammary artery and saphenous vein to prostaglandin E2: Implication for cardiovascular grafts

Human internal mammary arteries (IMA) and saphenous veins (SV) are frequently used for coronary artery bypass graft surgery. Intra‐ and postoperatively, the bypass grafts are exposed to inflammatory conditions, under which there is a striking increase in the synthesis of prostaglandin E2 (PGE2). In this context, the physiological response of these vascular grafts to PGE2 is highly relevant. The aim of this study was thus to characterize the PGE2 receptor subtypes (EP1, EP2, EP3 or EP4) involved in modulation of the vascular tone in these two vessels.