Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous quantitative assessment of circulating cell-free mitochondrial and nuclear DNA by multiplex real-time PCR

Quantification of circulating nucleic acids in plasma and serum could be used as a non-invasive diagnostic tool for monitoring a wide variety of diseases and conditions. We describe here a rapid, simple and accurate multiplex real-time PCR method for direct synchronized analysis of circulating cell-free (ccf) mitochondrial (mtDNA) and nuclear (nDNA) DNA in plasma and serum samples. The method is based on one-step multiplex real-time PCR using a FAM-labeled MGB probe and primers to amplify the mtDNA sequence of the ATP 8 gene, and a VIC-labeled MGB probe and primers to amplify the nDNA sequence of the glycerinaldehyde-3-phosphate-dehydrogenase (GAPDH) gene, in plasma and serum samples simultaneously. The efficiencies of the multiplex assays were measured in serial dilutions. Based on the simulation of the PCR reaction kinetics, the relative quantities of ccf mtDNA were calculated using a very simple equation. Using our optimised real-time PCR conditions, close to 100% efficiency was obtained from the two assays. The two assays performed in the dilution series showed very good and reproducible correlation to each other. This optimised multiplex real-time PCR protocol can be widely used for synchronized quantification of mtDNA and nDNA in different samples, with a very high rate of efficiency.
Optimal stepwise experimental design for pairwise functional interaction studies

MOTIVATION Pairwise experimental perturbation is increasingly used to probe gene and protein function because these studies offer powerful insight into the activity and regulation of biological systems. Symmetric two-dimensional datasets, such as pairwise genetic interactions are amenable to an optimally designed measurement procedure because of the equivalence of cases and conditions where fewer experimental measurements may be required to extract the underlying structure. RESULTS We show that optimal experimental design can provide improvements in efficiency when collecting data in an iterative manner. We develop a method built on a statistical clustering model for symmetric data and the Fisher information uncertainty estimates, and we also provide simple heuristic approaches that have comparable performance. Using yeast epistatic miniarrays as an example, we show that correct assignment of the major subnetworks could be achieved with <50% of the measurements in the complete dataset. Optimization is likely to become critical as pairwise functional studies extend to more complex mammalian systems where all by all experiments are currently intractable.
“What Do You Mean by Spirituality? Please Draw Me a Picture!” Complementary Faith-Based Addiction Treatment in Switzerland From the Client's Perspective

This article reviews: (1) the relative importance of spirituality and religion in Switzerland and the United States, (2) the rationale for faith-based addiction intervention programs and the drawbacks of measurement approaches, and (3) results from a pilot study exploring the meaning of spirituality and religiosity from the consumer's perspective. Twenty-three patients entering the Swiss Südhang clinic in-patient alcohol user treatment program during the first five months in 2012 participated upon their admission in a video-taped drawing task, designed to provide their personal visualized definitions of the terms “spirituality” and “religiosity. ” Nine dimensions emerged pointing to a high complexity of the concepts.
Retrospective review of the efficacy and safety of repeated pulsed and continuous radiofrequency lesioning of the dorsal root ganglion/segmental nerve for lumbar radicular pain.

BACKGROUND Chronic lumbosacral radicular pain is a common source of radiating leg pain seen in pain management patients. These patients are frequently managed conservatively with multiple modalities including medications, physical therapy, and epidural steroid injections. Radiofrequency has been used to treat chronic radicular pain for over 30 years; however, there is a paucity of literature about the safety and efficacy of repeat radiofrequency lesioning. OBJECTIVES To determine the safety, success rate, and duration of pain relief of repeat pulsed radiofrequency (PRF) and continuous radiofrequency (CRF) lesioning of the dorsal root ganglion (DRG)/ sacral segmental nerves (SN) in patients with chronic lumbosacral radicular pain. STUDY DESIGN Retrospective chart review SETTING Outpatient multidisciplinary pain center METHODS Medical record review of patients who were treated with pulsed and continuous radiofrequency lesioning of the lumbar dorsal root ganglia and segmental nerves and who reported initial success were evaluated for recurrence of pain and repeat radiofrequency treatment. Responses to subsequent treatments were compared to initial treatments for success rates, average duration of relief, and adverse neurologic side-effects. LIMITATIONS Retrospective chart review without a control group. RESULTS Twenty-six women and 24 men were identified who received 50% pain relief or better after PRF and CRF of the lumbar DRG/ sacral SN for lumbosacral radicular pain. The mean age was 62 years (range, 25-86). The mean duration of relief for the 40 patients who had 2 treatments was 4.7 months (range 0-24; Se [standard error] 0.74). Twenty-eight patients had 3 treatments with an average duration of relief of 4.5 months (range 0-19 months; Se 0.74). Twenty patients had 4 treatments with a mean duration of relief of 4.4 months (range 0.5-18; Se 0.95) and 18 patients who had 5 or more treatments received an average duration of relief of 4.3 months (range 0.5-18; Se 1.03). The average duration of relief and success frequency remained constant after each subsequent radiofrequency treatment. Of the 50 total patients, there was only 1 reported complication, specifically, transient thigh numbness which resolved after one week. CONCLUSIONS Repeated pulsed and continuous radiofrequency ablation of the lumbar dorsal root ganglion/segmental nerve shows promise to be a safe and effective long-term palliative management for lumbosacral radicular pain in some patients.
Prevalence of Depression among Households in Three Capital Cities of Pakistan: Need to Revise the Mental Health Policy

Background Pakistan, among the other developing countries, has a higher prevalence rate of depression because of the current social adversities. There is, thus, a great need for systematic studies on prevalence of depression. The current study aims at exploring the prevalence of depression among households in three capital cities of Pakistan. Methodology and Principal Findings A sample of N = 820 was randomly selected, and a cross sectional telephone-based study was conducted for a duration of six months. It was found that there was a regional variation in prevalence rates for depression among the three cities. Lahore had the highest number of depressives (53.4%), as compared to Quetta (43.9%) and Karachi (35.7%). Middle age, female gender and secondary school level of education were significantly associated with depression among the study group. Conclusions/Significance The different rates of prevalence among the three cities could be attributed to local cultural influence, geographical locations and social adversities. There is a need for revision of existing health policy by the government.
A Hamming Embedding Kernel with Informative Bag-of-Visual Words for Video Semantic Indexing

In this article, we propose a novel Hamming embedding kernel with informative bag-of-visual words to address two main problems existing in traditional BoW approaches for video semantic indexing. First, Hamming embedding is employed to alleviate the information loss caused by SIFT quantization. The Hamming distances between keypoints in the same cell are calculated and integrated into the SVM kernel to better discriminate different image samples. Second, to highlight the concept-specific visual information, we propose to weight the visual words according to their informativeness for detecting specific concepts. We show that our proposed kernels can significantly improve the performance of concept detection.
THE CAUSES OF NATURAL SELECTION

We discuss the necessary and sufficient conditions for identifying the cause of natural selection on a phenotypic trait. We reexamine the observational methods recently proposed for measuring selection in natural populations and illustrate why the multivariate analysis of selection is insufficient for identifying the causal agents of selection. We discuss how the observational approach of multivariate selection analysis can be complemented by experimental manipulations of the phenotypic distribution and the environment to identify not only how selection is operating on the phenotypic distribution but also why it operates in the observed manner. A significant point of departure of our work from recent discussions is in regard to the role of the environment in the study of natural selection. Instead of viewing the environment as a source of unwanted variation that obscures the relationship between phenotype and fitness, we view fitness as arising from the interaction of the phenotype with the environment. The biotic and abiotic environment is the context that gives rise to the relationship between phenotype and fitness (selection). The analysis of the causes of selection is in essence a problem in ecology. The experimental study of the association between selection gradients and environmental characteristics is necessary to identify the agents of natural selection. We recommend research methods for identifying the agency of selection that depend upon a reciprocity between the observational approach of multivariate selection analysis and the manipulative approach of field experiments in evolutionary ecology.
Time analysis of frequency coded chipless RFID tag based on CPW multi-band resonators

This paper presents the time domain study of a frequency encoded chipless ultra-wideband radio frequency identification (UWB RFID) tag. A seven bit multi-resonator integrated with two modified coplanar waveguide (CPW) circular monopole antennas are used to develop chipless RFID tag. The designed monopole antennas and multi-resonator are characterized using full wave simulation program. Complete RFID system is modeled and time domain characteristics of the pulse received at the receiver's antenna is studied. The spectral signature (SS) based identification of the designed tag is done by frequency encoding of incident interrogating signals covering frequency range from 6 GHz to 8 GHz. The distinguishable features of the incident pulse encoded by four different tags are studied and compared. Moreover, the signatures of the interrogating pulses encoded by the designed tags at three different orientation is also studied. Results show that the encoded pulse exhibits different signatures compared to the incident pulse that can be easily distinguished in time domain.
Mesenchymal stem cells can be recruited to wounded tissue via hepatocyte growth factor‐loaded biomaterials

Mesenchymal stem cells (MSC) are precursor cells of mesodermal tissue and, because of their trophic phenotype, they are known to play beneficial roles in wound healing. In addition, various tissue engineering strategies are based on MSC/biomaterial constructs. As the isolation and expansion of MSCs is a long‐term process, a major goal is to develop an endogenous stem cell recruitment system that circumvents all ex vivo steps generally used for tissue engineering. Therefore collagen and silk fibroin were loaded with hepatocyte growth factor (HGF), a chemoattractant for MSCs. Collagen was mixed with HGF during polymerization, while silk fibroin and HGF were produced as fusion proteins by transgenic silkworms. To demonstrate release of active HGF, enzyme‐linked immunosorbent assay, in vitro migration assays and animal studies were performed to demonstrate MSC migration in vivo, followed by detailed examinations of the immunological effects of the biomaterials. Hepatocyte growth factor was released burst‐like, both from silk fibroin and collagen during the first 8 h and gradually for up to 168 h in vitro. Directed migration in vitro was demonstrated when MSCs were exposed to HGF. In vivo, HGF‐loaded collagen and silk fibroin were tolerated as subcutaneous implants. In addition, it was proved that endogenous MSCs were recruited from the local environment. These results show for the first time recruitment of endogenous MSCs to HGF‐loaded collagen (fast degradable) and silk fibroin scaffolds (long‐term degradable) in vitro and in vivo. This knowledge could be applied to make off‐the‐shelf, readily available constructs for use in patients with chronic wound or burns. Copyright © 2016 John Wiley & Sons, Ltd.
Secure Auditing for SSL Transactions

Although SSL is certainly the dominant security protocol in use for electronic transactions, it has no real provision for dispute resolution. Digital signatures, the traditional approach to this problem, have seen little deployment, largely due to the lack of of ubiquitous client-side PKI and the need to modify both client and server software to add signature capability. This paper describes an alternate approach without these drawbacks. We use a novel combination of passive session recording, secure hardware and playback to pro vide third-party auditing capability for SSL transactions without changes to the applications on either side.
Strength Training Reduces Injury Rate in Elite Young Soccer Players During One Season

Abstract Zouita, S, Zouita, ABM, Kebsi, W, Dupont, G, Ben Abderrahman, A, Ben Salah, FZ, and Zouhal, H. Strength training reduces injury rate in elite young soccer players during one season. J Strength Cond Res 30(5): 1295–1307, 2016—The purpose of this study was to examine the effect of strength training on physical fitness parameters and injuries occurrence in young elite soccer players. Fifty-two elite young soccer players (13–14 years) were divided on a randomized order into experimental group (EG, n = 26) and control group (CG, n = 26). For EG, 2 to 3 sessions of strength training (90 minutes) were introduced weekly in their training program for 12 weeks (4 × 3 weeks separated by 1-week recovery). Sprint tests (10-20-30 m), T-test time, and jumping tests were measured at the start (T0), at the middle (T1), and at the end of the experiment period (T2). The injury rate was recorded by the medical and fitness training staff throughout the soccer season. Compared to CG, EG performed significantly better in sprint running and T-test time at T2 (p < 0.01). Similarly, the improvement amount for jumping tests was significantly greater (p ⩽ 0.05) in EG than in CG. A total of 17 injuries were recorded over the soccer season. The rate was higher in CG (13 injuries) than in training group (4 injuries). This study showed that strength training accurately and efficiently scheduled in youth soccer players, induced performance improvement, and reduced the rate of injuries.
The Valuation of American Options on Multiple Assets

In this paper we provide valuation formulas for several types of American options on two or more assets. Our contribution is twofold. First, we characterize the optimal exercise regions and provide valuation formulas for a number of American option contracts on multiple underlying assets with convex payoff functions. Examples include options on the maximum of two assets, dual strike options, spread options, exchange options, options on the product and powers of the product, and options on the arithmetic average of two assets. Second, we derive results for American option contracts with nonconvex payoffs, such as American capped exchange options. For this option we explicitly identify the optimal exercise boundary and provide a decomposition of the price in terms of a capped exchange option with automatic exercise at the cap and an early exercise premium involving the benefits of exercising prior to reaching the cap. Besides generalizing the current literature on American option valuation our analysis has implications for the theory of investment under uncertainty. A specialization of one of our models also provides a new representation formula for an American capped option on a single underlying asset.
Location and Dynamics of the Immunodominant CD8 T Cell Response to SIVΔnef Immunization and SIVmac251 Vaginal Challenge

Live-attenuated SIV vaccines (LAVs) have been the most effective to date in preventing or partially controlling infection by wild-type SIV in non-human primate models of HIV-1 transmission to women acting by mechanisms of protection that are not well understood. To gain insights into mechanisms of protection by LAVs that could aid development of effective vaccines to prevent HIV-1 transmission to women, we used in situ tetramer staining to determine whether increased densities or changes in the local distribution of SIV-specific CD8 T cells correlated with the maturation of SIVΔnef vaccine-induced protection prior to and after intra-vaginal challenge with wild-type SIVmac251. We evaluated the immunodominant Mamu-A1*001:01/Gag (CM9) and Mamu-A1*001:01/Tat (SL8) epitope response in genital and lymphoid tissues, and found that tetramer+ cells were present at all time points examined. In the cervical vaginal tissues, most tetramer+ cells were distributed diffusely throughout the lamina propria or co-localized with other CD8 T cells within lymphoid aggregates. The distribution and densities of the tetramer+ cells at the portal of entry did not correlate with the maturation of protection or change after challenge. Given these findings, we discuss the possibility that changes in other aspects of the immune system, including the quality of the resident population of virus-specific effector CD8 T cells could contribute to maturation of protection, as well as the potential for vaccine strategies that further increase the size and quality of this effector population to prevent HIV-1 transmission.
Arabidopsis thaliana mTERF proteins: evolution and functional classification

Organellar gene expression (OGE) is crucial for plant development, photosynthesis, and respiration, but our understanding of the mechanisms that control it is still relatively poor. Thus, OGE requires various nucleus-encoded proteins that promote transcription, splicing, trimming, and editing of organellar RNAs, and regulate translation. In metazoans, proteins of the mitochondrial Transcription tERmination Factor (mTERF) family interact with the mitochondrial chromosome and regulate transcriptional initiation and termination. Sequencing of the Arabidopsis thaliana genome led to the identification of a diversified MTERF gene family but, in contrast to mammalian mTERFs, knowledge about the function of these proteins in photosynthetic organisms is scarce. In this hypothesis article, I show that tandem duplications and one block duplication contributed to the large number of MTERF genes in A. thaliana, and propose that the expansion of the family is related to the evolution of land plants. The MTERF genes—especially the duplicated genes—display a number of distinct mRNA accumulation patterns, suggesting functional diversification of mTERF proteins to increase adaptability to environmental changes. Indeed, hypothetical functions for the different mTERF proteins can be predicted using co-expression analysis and gene ontology (GO) annotations. On this basis, mTERF proteins can be sorted into five groups. Members of the “chloroplast” and “chloroplast-associated” clusters are principally involved in chloroplast gene expression, embryogenesis, and protein catabolism, while representatives of the “mitochondrial” cluster seem to participate in DNA and RNA metabolism in that organelle. Moreover, members of the “mitochondrion-associated” cluster and the “low expression” group may act in the nucleus and/or the cytosol. As proteins involved in OGE and presumably nuclear gene expression (NGE), mTERFs are ideal candidates for the coordination of the expression of organelle and nuclear genomes.
“Keep on Keeping On, Even When It’s Hard!”

The current study examined adolescent persistence as a mediator between authoritative parenting and adolescents’ school engagement, prosocial behavior, and delinquency. Participants were taken from Time 2, 3, and 4 of the Flourishing Families Project and included 325 two-parent families with a child between the ages of 11 and 14 at Time 2 (mean age = 12.34, SD = 1.06, 52% female), 96% of whom had complete data for Time 4 (2 years later). Analyses suggested that authoritative fathering at Time 2 (but not mothering) was positively associated with adolescent persistence at Time 3, and adolescent persistence was positively related to school engagement and negatively related to delinquency at Time 4. Discussion focuses on the importance of the socialization of persistence during adolescence.
Model-independent description of $B\rightarrow D \pi \ell \nu$ decays

In this contribution we present a novel, model-independent description of semileptonic $B\rightarrow D \pi \ell \nu$ decays. In addition, we discuss recent developments in the understanding of coupled-channel $D \pi$-$D \eta$-$D_s K$ S-wave scattering and, for the first time, apply them to semileptonic decays. We not only obtain model-independent predictions for kinematic distributions in $B\rightarrow D \pi \ell \nu$ decays, but also rule out the hypothesis that the gap between the inclusive $B\rightarrow X\ell\nu$ branching fraction and the sum over exclusive channels is made up predominantly by $B\rightarrow D^{(\ast)} \eta \ell \nu$ decays.
A Theory of Strategy and the Role of Leaders in it

This paper formally deﬁnes a (project or business) strategy as the ‘ minimum set of decisions (suﬃcient) to guide all other decisions ’ and derives it as the equilibrium outcome of a game where a manager can look ahead, do an overall optimization, and announce decisions at a cost. Strategy is thus like a suﬃcient statistic for an optimal plan of action – or the minimum set of actions you need to ﬁx in order to trigger a target equilibrium. It serves as an organizational tool to eﬃciently guide a whole organization towards an optimal outcome. The paper then analyzes when and how strategy creates value (including when an uninformed strategy can create value), what characteristics make a decision ‘strategic’, why diﬀerent people may consider diﬀerent decisions ‘strategic’, why important decision makers should be involved in strategy development, and why leaders with strong vision are more likely to propose a strategy and their strategies are more likely to be implemented. It also shows how understanding the structure of strategy may enable a strategist to develop the optimal strategy without doing a comprehensive optimization.