Miracle-dz/UniFAR-FTUs huggingface dataset:
Limb-girdle muscular dystrophies: Where next after six decades from the first proposal (Review)

Limb-girdle muscular dystrophies (LGMD) are a heterogeneous group of disorders, which has led to certain investigators disputing its rationality. The mutual feature of LGMD is limb-girdle affection. Magnetic resonance imaging (MRI), perioral skin biopsies, blood-based assays, reverse-protein arrays, proteomic analyses, gene chips and next generation sequencing are the leading diagnostic techniques for LGMD and gene, cell and pharmaceutical treatments are the mainstay therapies for these genetic disorders. Recently, more highlights have been shed on disease biomarkers to follow up disease progression and to monitor therapeutic responsiveness in future trials. In this study, we review LGMD from a variety of aspects, paying specific attention to newly evolving research, with the purpose of bringing this information into the clinical setting to aid the development of novel therapeutic strategies for this hereditary disease. In conclusion, substantial progress in our ability to diagnose and treat LGMD has been made in recent decades, however enhancing our understanding of the detailed pathophysiology of LGMD may enhance our ability to improve disease outcome in subsequent years.
EFFECTIVENESS OF EIGHTH ORDER RUNGE-KUTTA METHOD TO SOLVE THE MATHEMATICAL MODEL OF MALARIA DISEASE TRANSMISSION

Abstrak. Banyak permasalahan di lingkungan kehidupan kita yang dapat dibentuk ke dalam model matematika sehingga dapat dianalisis secara matematik. Salah satu permasalahan itu adalah kejadian endemi, seperti transmisi penyakit malaria. Model matematika transmisi penyakit malaria berbentuk system Persamaan Diferensial Biasa (PDB) non linier orde satu. Dalam tulisan ini akan dibahas efektivitas dan efisiensi metode Runge-Kutta orde delapan yang dibandingkan dengan metode Adams Bashforth-Moulton orde sembilan. Selain itu juga akan dicari sifat-sifat, formula, konvergenitas, dan format pemrograman MATLAB dari metode itu. Efektivitas suatu metode bergantung pada error. Sedangkan efisiensi bergantung pada waktu tempuh suatu metode untuk menyelesaikan masalah. Metode pengumpulan data yang digunakan adalah metode dokumentasi dan eksperimen. Hasil dari tulisan ini yaitu sifat dan formula metode Runge-Kutta orde delapan, pembuktian konvergensi metode tersebut secara teoritis, dan format pemrograman yang hasilnya digunakan untuk menentukan metode yang paling efektif dan efisien untuk menyelesaikan model transmisi penyakit malaria. Kata kunci : Efektivitas, Efisiensi, Metode Runge-Kutta, Transmisi malaria.
Relationships between the Brief Multidimensional Measure of Religiousness/Spirituality and health outcomes for a heterogeneous rehabilitation population.

PURPOSE To determine relationships between the Brief Multidimensional Measure of Religiousness/Spirituality (BMMRS; i.e., positive/negative spirituality, forgiveness, religious practices, positive/negative congregational support) and physical and mental health (Medical Outcomes Scale-Short Form 36; SF-36) for individuals with chronic disabilities. RESEARCH METHOD A cross-sectional analysis of 118 individuals evaluated in outpatient settings, including 61 with traumatic brain injury (TBI), 32 with cerebral vascular accidents (CVA), and 25 with spinal cord injury (SCI). RESULTS Three of 6 BMMRS factor scores (i.e., positive spiritual experience, forgiveness, negative spiritual experience) were significantly correlated with the SF-36 General Health Perception (GHP) scale, and only 1 of 6 BMMRS factor scores (i.e., negative spiritual experience) was significantly and negatively correlated with the SF-36 General Mental Health (GMH) scale. BMMRS scales did not significantly predict either physical or mental health in hierarchical multiple regressions. CONCLUSIONS Positive spiritual experiences and willingness to forgive are related to better physical health, while negative spiritual experiences are related to worse physical and mental health for individuals with chronic disabilities. Future research using the BMMRS will benefit from using a 6-factor model that evaluates positive/negative spiritual experiences, religious practices, and positive/negative congregational support. Interventions to accentuate positive spiritual beliefs (e.g., forgiveness protocols, etc.) and reduce negative spiritual beliefs for individuals with chronic disabilities are suggested.
Altered Sodium Channel Expression in Second-Order Spinal Sensory Neurons Contributes to Pain after Peripheral Nerve Injury

Peripheral nerve injury is known to upregulate the rapidly repriming Nav1.3 sodium channel within first-order spinal sensory neurons. In this study, we hypothesized that (1) after peripheral nerve injury, second-order dorsal horn neurons abnormally express Nav1.3, which (2) contributes to the responsiveness of these dorsal horn neurons and to pain-related behaviors. To test these hypotheses, adult rats underwent chronic constriction injury (CCI) of the sciatic nerve. Ten days after CCI, allodynia and hyperalgesia were evident. In situ hybridization, quantitative reverse transcription-PCR, and immunocytochemical analysis revealed upregulation of Nav1.3 in dorsal horn nociceptive neurons but not in astrocytes or microglia, and unit recordings demonstrated hyperresponsiveness of dorsal horn sensory neurons. Intrathecal antisense oligodeoxynucleotides targeting Nav1.3 decreased the expression of Nav1.3 mRNA and protein, reduced the hyperresponsiveness of dorsal horn neurons, and attenuated pain-related behaviors after CCI, all of which returned after cessation of antisense delivery. These results demonstrate for the first time that sodium channel expression is altered within higher-order spinal sensory neurons after peripheral nerve injury and suggest a link between misexpression of the Nav1.3 sodium channel and central mechanisms that contribute to neuropathic pain after peripheral nerve injury.
QUEST-RA: quantitative clinical assessment of patients with rheumatoid arthritis seen in standard rheumatology care in 15 countries

Objective: To conduct a cross-sectional review of non-selected consecutive outpatients with rheumatoid arthritis (RA) as part of standard clinical care in 15 countries for an overview of the characteristics of patients with RA. Methods: The review included current disease activity using data from clinical assessment and a patient self-report questionnaire, which was translated into each language. Data on demographic, disease and treatment-related variables were collected and analysed using descriptive statistics. Variation in disease activity on DAS28 (disease activity score on 28-joint count) within and between countries was graphically analysed. A median regression model was applied to analyse differences in disease activity between countries. Results: Between January 2005 and October 2006, the QUEST-RA (Quantitative Patient Questionnaires in Standard Monitoring of Patients with Rheumatoid Arthritis) project included 4363 patients from 48 sites in 15 countries; 78% were female, >90% Caucasian, mean age was 57 years and mean disease duration was 11.5 years. More than 80% of patients had been treated with methotrexate in all but three countries. Overall, patients had an active disease with a median DAS28 of 4.0, with a significant variation between countries (p<0.001). Among 42 sites with >50 patients included, low disease activity of DAS28 ⩽3.2 was found in the majority of patients in seven sites in five countries; in eight sites in five other countries, >50% of patients had high disease activity of DAS28 >5.1. Conclusions: This international multicentre cross-sectional database provides an overview of clinical status and treatments of patients with RA in standard clinical care in 2005–6 including countries that are infrequently involved in clinical research projects.
Program performance spectrum

Real-time and embedded applications often need to satisfy several non-functional properties such as timing. Consequently, performance validation is a crucial stage before the deployment of real-time and embedded software. Cache memories are often used to bridge the performance gap between a processor and memory subsystems. As a result, the analysis of caches plays a key role in the performance validation of real-time, embedded software. In this paper, we propose a novel approach to compute the cache performance signature of an entire program. Our technique is based on exploring the input domain through different path programs. Two paths belong to the same path program if they follow the same set of control flow edges but may vary in the iterations of loops encountered. Our experiments with several subject programs show that the different paths grouped into a path program have very similar and often exactly same cache performance. Our path program exploration can be viewed as partitioning the input domain of the program. Each partition is associated with its cache performance and a symbolic formula capturing the set of program inputs which constitutes the partition. We show that such a partitioning technique has wide spread usages in performance prediction, testing, debugging and design space exploration.
Fragile Watermarking for JPEG-2000 Images

Fragile watermarking is designed to protect content integrity of digital data, meaning to detect any change in the content as well as localize areas that have been changed. In this paper, we propose a fragile watermarking scheme which embeds dual watermarks (one is naturally fragile and the other is actually robust) in JPEG-2000 compressed images with ROI (region of interest) selection. In this scheme, the fragile watermark is embedded in ROI coefficients at the first decomposition layer, while the robust watermark embedded in ROB (region of backgrounds) coefficients at the third decomposition layer. The combinational working of them is not only capable of detecting malicious changes precisely and flexibly but also estimating the degree of alteration to discriminate intended attacks from unintended ones (e.g., such normal image processing as compression, low-pass filtering, sharpening, etc). Experiments show that our functionally fragile watermarking scheme is scalable in view of detecting attack’s intension as well as accuracy in localizing the tampered areas.
Is there still a need for albumin infusions to treat patients with liver disease?

The course of patients with cirrhosis is frequently complicated by derangement of body fluid homeostasis which results in accumulation of large amounts of extracellular fluid in the peritoneal cavity and interstitial tissue.1 Investigations performed in the 1940s proposed that the formation of ascites and oedema was related to an imbalance in Starling's equilibrium in splanchnic and systemic capillaries caused by increased hydrostatic pressure due to portal hypertension and reduced oncotic pressure because of the low serum albumin levels characteristic of cirrhosis, which would favour the passage of fluid from the intravascular compartment to the interstitial tissue.2-4 Later studies showed that patients with cirrhosis and ascites have marked circulatory dysfunction, characterised mainly by low systemic vascular resistance and arterial pressure, abnormal distribution of blood volume, with reduced central blood volume, and marked stimulation of vasoconstrictor and antinatriuretic systems (that is, the renin-angiotensin-aldosterone system and sympathetic nervous system). 5 6 In some patients this circulatory dysfunction is so intense that renal perfusion is greatly reduced leading to severe impairment of renal function, a condition known as hepatorenal syndrome.7Considering all of these factors it is not surprising that albumin infusions have been used for many years in the management of patients with cirrhosis and ascites in an attempt to reduce the formation of ascites and/or improve circulatory and renal function.8 In the current decade the use of albumin in cirrhosis has regained attention because of the demonstration that patients with large ascites can be treated safely with large volume paracentesis associated with albumin infusions.9 While some of these indications for albumin infusions are supported by the results of randomised studies, others are based on clinical experience and have not been proved in prospective investigations. Therefore, the use of albumin infusions in patients with cirrhosis is controversial. Recently, …
Utilizing multiple unreliable channels in remote stabilization of linear systems

This paper is concerned with the remote control problem where the measurements at multiple sensors are transmitted to a remote controller over separate communication channels. The channels are unreliable in that messages are randomly lost. Several conditions are obtained on the loss probabilities for achieving stochastic stability of the controlled system. The results clarify the limitations imposed by the unstable dynamics of the plant and the constraints in communication.
COX-2 inhibition prevents downregulation of key renal water and sodium transport proteins in response to bilateral ureteral obstruction.

Bilateral ureteral obstruction (BUO) is associated with marked changes in the expression of renal aquaporins (AQPs) and sodium transport proteins. To examine the role of prostaglandin in this response, we investigated whether 24-h BUO changed the expression of cyclooxygenases (COX-1 and -2) in the kidney and tested the effect of the selective COX-2 inhibitor parecoxib (5 mg.kg(-1). day(-1) via osmotic minipumps) on AQPs and sodium transport. Sham and BUO kidneys were analyzed by semiquantitative immunoblotting, and a subset of kidneys was perfusion fixed for immunocytochemistry. BUO caused a significant 14-fold induction of inner medullary COX-2 (14.40 +/- 1.8 vs. 1.0 +/- 0.4, n = 6; P < 0.0001) and a reduction in medullary tissue osmolality, whereas COX-1 did not change. Immunohistochemistry confirmed increased COX-2 labeling associated with medullary interstitial cells. COX isoforms did not change in cortex/outer medulla after 24-h BUO. In BUO kidneys, inner medullary AQP2 expression was reduced, and this decrease was prevented by parecoxib. In the inner stripe of outer medulla, the type 3 Na(+)/H(+) exchanger (NHE3) and apical Na(+)-K(+)-2Cl(-) cotransporter (BSC-1) were significantly reduced by BUO, and this decrease was significantly attenuated by parecoxib. Immunohistochemistry for AQP2, NHE3, and BSC-1 confirmed the effect of parecoxib. Parecoxib had no significant effect on the Na-K-ATPase alpha(1)-subunit, type II Na-P(i) cotransporter, or AQP3. In conclusion, acute BUO leads to marked upregulation of COX-2 in inner medulla and selective COX-2 inhibition prevents dysregulation of AQP2, BSC-1, and NHE3 in response to BUO. These data indicate that COX-2 may be an important factor contributing to the impaired renal water and sodium handling in response to BUO.
Data-Driven Objectness

We propose a data-driven approach to estimate the likelihood that an image segment corresponds to a scene object (its “objectness”) by comparing it to a large collection of example object regions. We demonstrate that when the application domain is known, for example, in our case activity of daily living (ADL), we can capture the regularity of the domain specific objects using millions of exemplar object regions. Our approach to estimating the objectness of an image region proceeds in two steps: 1) finding the exemplar regions that are the most similar to the input image segment; 2) calculating the objectness of the image segment by combining segment properties, mutual consistency across the nearest exemplar regions, and the prior probability of each exemplar region. In previous work, parametric objectness models were built from a small number of manually annotated objects regions, instead, our data-driven approach uses 5 million object regions along with their metadata information. Results on multiple data sets demonstrates our data-driven approach compared to the existing model based techniques. We also show the application of our approach in improving the performance of object discovery algorithms.
A tertiary care-primary care partnership model for medically complex and fragile children and youth with special health care needs.

OBJECTIVE To evaluate the impact of a tertiary care center special needs program that partners with families and primary care physicians to ensure seamless inpatient and outpatient care and assist in providing medical homes. DESIGN Up to 3 years of preenrollment and postenrollment data were compared for patients in the special needs program from July 1, 2002, through June 30, 2005. SETTING A tertiary care center pediatric hospital and medical school serving urban and rural patients. PARTICIPANTS A total of 227 of 230 medically complex and fragile children and youth with special needs who had a wide range of chronic disorders and were enrolled in the special needs program. INTERVENTIONS Care coordination provided by a special needs program pediatric nurse case manager with or without a special needs program physician. MAIN OUTCOME MEASURES Preenrollment and postenrollment tertiary care center resource utilization, charges, and payments. RESULTS A statistically significant decrease was found in the number of hospitalizations, number of hospital days, and tertiary care center charges and payments, and an increase was found in the use of outpatient services. Aggregate data revealed a decrease in hospital days from 7926 to 3831, an increase in clinic visits from 3150 to 5420, and a decrease in tertiary care center payments of $10.7 million. The special needs program budget for fiscal year 2005 had a deficit of $400,000. CONCLUSION This tertiary care-primary care partnership model improved health care and reduced costs with relatively modest institutional support.
Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA

A phylogenetic analysis of the Solanaceae based on chloroplast DNA variation is presented. Restriction site maps were determined for 79 species (52 genera) for 11 restriction enzymes. Sequences of two chloroplast genes, rbch and ndhF, were determined for 30 and 36 species respectively, including six genera not sampled in the restriction site survey. The results are presented as three separate analyses examining relationships at different hierarchical levels. The resulting cladograms provide the basis for a provisional new infrafamilial classification. This classification includes seven subfamilies, three of which are further subdivided into tribes, two of which are further subdivided into subtribes. This classification is compared to the contemporary classification of A. Hunziker, G. Barboza, L. Bernadello & A.A. Cocucci (in prep.).
VInTiMe : Combining High-Level Finesse with Low-Level Muscle to Verify Real-Time Systems ?

In this work we present the VInTiMe (Verifier of INtegrated TImed ModEls) suite of tools that combines high-level expressive power, unassisted property-preserving model-reduction and low-level distributed model checking power to describe and verify complex Real-Time Systems designs and their properties.
The ICSI 2007 language recognition system

In this paper, we describe the ICSI 2007 language recognition system. The system constitutes a variant of the classic PPRLM (parallel phone recognizer followed by language modeling) approach. We used a combination of frame-by-frame multilayer perceptron (MLP) phone classifiers for English, Arabic, and Mandarin and one open loop hidden Markov Model (HMM) phone recognizer (trained on English data). The maximum likelihood language modeling is substituted by support-vectormachines (SVMs) as a more powerful, discriminative classifi cation method. Rank normalization is used as a normalization method superior to mean-variance normalization. Results are presented on the NIST 2005 language recognition evaluation (LRE05) set and a test set taken from the LRE07 training corpus. The average NIST cost of the system on the LRE05 set is 0.0886.
On control and optimization of cascading phenomena in a class of dynamic networks

The primary goal of this thesis is to study transmission line reactance tweaking, as a mechanism for both post-disturbance control and pre-disturbance resilience enhancement in a transmission network, and develop an optimization framework for evaluating the efficacy of this mechanism in both scenarios. We start by developing a mixed-integer linear programming (MILP) formulation for tracking the redistribution of direct current (DC) flows and the graph-theoretic evolution of network topology over the course of cascading failures. Next, we propose a min-max setup for studying the impact of post-disturbance reactance tweaking on the resilience of the system to a worst-case N-k disturbance and devise a MILP reformulation scheme for the underlying bilevel nonconvex mixed-integer nonlinear program (MINLP) to facilitate the computation of its optimal solution. We then develop a MILP framework for computing the exact value of a tight upper bound on the efficacy of post-disturbance reactance tweaking among the set of all possible Nk disturbances for a given k and a given bus load scenario. Our numerical case study suggests that post-disturbance reactance tweaking, even on only a small number of lines, can considerably reduce the amount of load shed in some scenarios in the tested system. As for pre-disturbance resilience enhancement, we develop a MILP reformulation for approximating the bilevel MINLP that seeks to assess the efficacy of pre-disturbance reactance tweaking in reducing the number of lines that will fail over the propagation of cascading failures in the event of a worst-case-scenario N-k disturbance. We also give a MILP framework for computing an approximate upper bound on the efficacy of this mechanism among the set of all N-k contingencies for a given k. Our numerical case study suggests that pre-disturbance reactance tweaking on a few transmission lines can, in some cases, prevent the failure of multiple transmission lines over the course of cascading failures in the tested system.
Application of Personas in User Interface Design for Educational Software

In the current cautious business climate, development of large new software has become rarer as the cost pressure has increased. User interfaces (UI), the most important part of a system for end users and critical for system success, remain notoriously user-unfriendly. This makes it imperative to identify practical tools that small software projects can use to help them maximise UI design quality while minimising cost.This research looks at two similar small systems and investigates the usefulness of the concept of personas for UI design evaluation. Following the Goal-Directed Design approach, personas are defined along classes of users. The tasks of each persona are established via user-centred requirements. Each task is then performed with consideration to established usability heuristics. Overall, the question is whether the initial use of personas in the design phase might have resulted in fundamentally different UI choices.It was concluded that the approach of identifying personas and performing their tasks in evaluating the UIs of both software systems was most definitely a process that helped introduce clarity and a form of accountable reasoning into the UI evaluation process. For both systems, it could be reasoned that the UI design would have been fundamentally different in some aspects if personas were used. However, personas were less helpful when it came to diagnose and describe user frustrations that had not so much to do with UI design as such, but with general usability issues. In this case they were mainly related to discrepancies and inconsistencies in the underlying business logic or simply bad programming, pointing to deficiencies in other areas of the software development life cycle (SDLC).