Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the CDC safe water-storage intervention to improve the microbiological quality of point-of-use drinking water in rural communities in South Africa

The use of different concentrations of sodium hypochlorite solutions (placebo; 1% and 3.5% sodium hypochlorite solutions) and 2 water-storage containers (traditional plastic container and the improved CDC safe water-storage container) as interventions in 2 rural communities using different water sources (improved vs. unimproved) was evaluated over a period of 4 months. Standard methods were used to determine the presence of indicator organisms (total coliforms, faecal coliforms, Escherichia coli, faecal enterococci, Clostridium perfringens, male-specific F-RNA and somatic coliphages) in the water samples. The results indicated that the 1% and the 3.5% sodium hypochlorite solutions effectively reduced the numbers of indicator microorganisms to undetectable counts in both types of water-storage containers. However, no statistical differences were seen between the 2 types of water-storage containers in the numbers of indicator microorganisms present in the stored water with the addition of a placebo sodium hypochlorite solution. Compliance of households with the use of the sodium hypochlorite intervention ranged between 60% and 100%. A household questionnaire survey indicated an urgent need for education concerning the risk of waterborne diseases, the proper use of safe household water-storage devices and water treatment processes and improvement of hygiene and sanitation practices in these rural households.
The Six-Variable Model - Context Modelling Enabling Systematic Reuse of Control Software

A control system usually consists of some control software as well as sensors and actuators to monitor and control certain quantities in the environment. The context of the control software thus consists of the sensors and actuators it uses and the environment. When starting development of the control software, its context is often not predefined or given. There are contextual decisions the developers can make (e.g. which sensors/actuators/other systems to use). By means of these decisions, the context is defined step by step. Existing approaches (like the Four-Variable Model) call for documenting the environmental quantities (monitored, controlled, input, and output variables) that are relevant after making these contextual decisions. The environmental quantities that have originally been relevant (i.e. before deciding which sensors/actuators/other systems to use) are not documented. This results in problems when the software shall later on be reused in another, slightly different setting (e.g. with additional sensors). Then, it is hard for developers to decide which environmental quantities are still relevant for the software. In this paper, we suggest an extended version of the Four-Variable Model, the Six-Variable Model, and, based on that, a context modelling method, that combines existing approaches. The benefit of our method is that the environmental quantities that are relevant before and after decision making are documented as well as the contextual decisions themselves and the options that were selectable. In this way, later reuse of the software is facilitated.
Bitumen Rejuvenator Diffusion as Influenced by Ageing

ABSTRACT This paper describes studies to illuminate the process of mixing old and new binder during asphalt recycling, or, more precisely, mixing by diffusion. FTIR-ATR (Fourier Transform Infrared Spectroscopy by Attenuated Total Reflectance) is used to study effects of the degree of ageing on the diffusion process. Generally, diffusion rates are influenced by temperature, size and shape of the diffusing molecules and the viscosity of the media in which the diffusion takes place. Since bitumen ageing normally leads to a considerable increase in viscosity, it was decided to investigate its influence on the diffusion process. The results presented in this study imply that it is the maltene phase viscosity that governs the diffusion rate rather than the viscosity of the bitumen as a whole. As the changes in maltene viscosity due to ageing are found to be small, it is postulated that ageing does not have a significant effect on the diffusion process.
I. Dynamics, Bifurcations and Stability of Patterns in PDEs

My research interests lie in the areas of dynamical systems, bifurcation theory, nonlinear dynamics and mathematical biology. Namely, I am interested in the dynamics, bifurcations and stability of patterns and waves in partial differential equations (PDEs) and networks, and their applications to pattern formation in physics, chemistry and biology. Understanding the spontaneous formation and dynamics of spatio-temporal patterns in non-equilibrium systems is one of the major challenges in nonlinear science. What follows is a more detailed discussion of several specific problems I worked on, progress to date and plans for future. The approach that I use is to reduce (if possible) the infinite dimensional PDEs to a finite system of ordinary differential equations (ODEs) using center manifold reduction, Liapunov-Schmidt reduction, reduction of the dimension based on the symmetry of the dynamical system, spatial dynamics, orbit space reduction or reduction to the time map or Poincaré map and to analyse the low-dimesional models using appropriate mathematical tools. I also do numerical simulations with Maple, Matlab, AUTO and other mathematical software to get insights into the dynamics of PDEs and networks.
Obstructive Sleep Apnea Among Express Bus Drivers in Malaysia: Important Indicators for Screening

Objectives: Obstructive sleep apnea (OSA) has been identified as one of the significant risk factors for motor vehicle crashes (MVCs). In the interest of public safety, this study was conducted to determine the prevalence of OSA and its associated factors among express bus drivers in Malaysia. Identifying factors or conditions related with OSA is very important because they can be used as indicators to subject a person to a confirmatory diagnosis using polysomnography testing. Methods: Two hundred eighty-nine randomly selected express bus drivers from 5 express bus companies participated in the study. Information on demography, medical history, clinical symptoms, and signs of OSA were collected by a designated medical officer and the diagnosis of OSA was done based on the Apnea Hypopnoea Index (AHI) from polysomnography testing. Results: Based on AHI, 128 (44.3%) subjects were diagnosed as having OSA with 83 (28.7%), 26 (9.0%), and 26 (6.6%) classified as mild, moderate, and severe OSA, respectively. Multiple logistic regression analysis results showed that age (odds ratio [OR] = 1.05, 95% confidence interval [CI] 1.01–1.09), snoring (OR = 3.54, 95% CI 1.91–6.57), body mass index (BMI; OR = 1.17, 95% CI 1.09–1.25), hypertension (OR = 1.87, 95% CI 1.02–3.40), and neck circumference (OR = 1.31, 95% CI 1.18–1.46) were significantly associated with OSA status. Conclusions: The results supported the need for identifying the risk group for OSA among express bus drivers and the need to diagnose them early for an early intervention.
Whole-exome sequencing reveals novel mutations and epigenetic regulation in hypopharyngeal carcinoma

Hypopharyngeal cancer (HPC) frequently presents at an advanced stage, resulting in poor prognosis. Although combined surgical therapy and chemoradiotherapy have improved the survival for patients with HPC over the past 3 decades, the mortality rate in late-stage diagnosis of HPC is unsatisfactory. In this study, we performed whole-exome sequencing (WES) of 23 hypopharyngeal tumor and paired adjacent normal tissue to identify novel candidate driver genes associated with hypopharyngeal carcinoma. We identified several copy number variants (CNVs) and 15 somatic mutation genes that were associated with hypopharyngeal carcinoma. Mutations in nine new genes (PRB4, NSD1, REC8, ZNF772, ZNF69, EI24, CYFIP2, NEFH, KRTAP4-5) were also indentified. PRB4 and NSD1 expression were significantly upregulated in hypopharyngeal carcinoma, which was confirmed in an independent cohort using IHC. There was a positive relationship between PRB4 and NSD1. Downregulation of PRB4 by siRNA could inhibit cell growth, colony formation and cell invasion. Notably, we here demonstrate that NSD1 could bind to the promoter regions of PRB4 and activate promoter activity by reducing the binding of H3K27me2 and increasing the binding of H3K36me2 on PRB4 promoter. In summary, we pinpoint the predominant mutations in hypopharyngeal carcinoma by WES, highlighting the substantial genetic alterations contributing to hypopharyngeal carcinoma tumorigenesis. We also indentify a novel epigenetically regulatory between PRB4 and NSD1 that contribute to hypopharyngeal carcinoma tumorigenesis. They may become potential prognostic biomarkers and therapeutic target for hypopharyngeal carcinoma treatment.
Graph Aggregation

Graph aggregation is the process of computing a single output graph that constitutes a good compromise between several input graphs, each provided by a different source. One needs to perform graph aggregation in a wide variety of situations, e.g., when applying a voting rule (graphs as preference orders), when consolidating conflicting views regarding the relationships between arguments in a debate (graphs as abstract argumentation frameworks), or when computing a consensus between several alternative clusterings of a given dataset (graphs as equivalence relations). Other potential applications include belief merging, data integration, and social network analysis. In this short paper, we review a recently introduced formal framework for graph aggregation that is grounded in social choice theory. Our focus is on understanding which properties shared by the individual input graphs will transfer to the output graph returned by a given aggregation rule. Our main result is a powerful impossibility theorem that generalises Arrow's seminal result regarding the aggregation of preference orders to a large collection of different types of graphs. We also provide a discussion of existing and potential applications of graph aggregation.
A constrained optimization approach to multiuser detection

Interference cancellation or multiuser detection schemes are of great interest to the CDMA community because of their potential ability to treat the near-far problem and significantly reduce interference levels. A linear adaptive multiuser detection scheme based on constrained optimization is presented, constraints are constructed from knowledge of users' codes and associated timing. Both single- and multiple-constraint detectors are derived and shown to have interesting relationships to existing detectors. Simulation results, presented in the form of bit error rate curves, demonstrate the receiver's performance in an additive white Gaussian noise (AWGN) channel.
Cartilage ablation studies using mid-IR free electron laser

The ablation rate of articular cartilage and fibrocartilage (meniscus), were quantified to examine wavelength and tissue-composition dependence of ablation efficiency for selected mid-infrared wavelengths. The wavelengths tested were 2.9 um (water dominant absorption), 6.1 (protein and water absorption) and 6.45 um (protein dominant absorption) generated by the Free Electron Laser (FEL) at Vanderbilt University. The measurement of tissue mass removal using a microbalance during laser ablation was conducted to determine the ablation rates of cartilage. The technique can be accurate over methods such as profilometer and histology sectioning where tissue surface and the crater morphology may be affected by tissue processing. The ablation efficiency was found to be dependent upon the wavelength. Both articular cartilage and meniscus (fibrocartilage) ablations at 6.1 um were more efficient than those at the other wavelengths evaluated. We observed the lowest ablation efficiency of both types of cartilage with the 6.45 um wavelength, possibly due to the reduction in water absorption at this wavelength in comparison to the other wavelengths that were evaluated.
Postprandial Triglyceride Response in Men: Role of Overweight, Abdominal Fat and Nutrition

Objective: The study analyses i) the effect of overweight, waist circumference and dietary habits on postprandial (pp) triglyceride (TG) response and compares ii) pp TG response with fasting TG levels and iii) pp TG peak values with TG-AUC (area under curve) with respect to cardiometabolic risk assessment. Methods: In 100 men (44–68 years) body composition (air-displacement plethysmography), dietary habits, cardiometabolic risk and pp lipid metabolism (standardised lipid load) were assessed. A pp TG peak value of 260 mg/dl was used as a cut-off to classify TG normal- and high-responders. Results: pp TG response had positive associations with BMI (r = 0.24; p < 0.05), fat mass (r = 0.28; p < 0.01), waist circumference (r = 0.33; p < 0.01), systolic blood pressure (r = 0.21; p < 0.05), fasting (r = 0.29; p < 0.01) and pp glucose (r = 0.40; p < 0.001), fasting (r = 0.38; p < 0.001) and pp insulin levels (r = 0.46; p < 0.001), and inverse associations with HDL-C (r = –0.43; p < 0.001) and intake of dietary fibre (r = –0.31; p < 0.05). Fasting TG levels had a greater contribution to the variance in 12 of 14 cardiometabolic risk factors compared to pp TG response. TG-AUC was highly correlated to cardiometabolic risk. Conclusion: Overweight, abdominal fat and a low intake of dietary fibre were determinants of increased pp TG response. Contrary to findings in younger normal-weight men, fasting TG levels had a stronger association with cardio metabolic risk compared to pp TG response. This might be explained by differences in fat mass.
ADS-5102 (Amantadine) Extended-Release Capsules for Levodopa-Induced Dyskinesia in Parkinson Disease (EASE LID Study): A Randomized Clinical Trial

Importance Medical treatment of levodopa-induced dyskinesia (LID) in Parkinson disease (PD) is an unmet need. Objective To evaluate the efficacy and safety of ADS-5102 (amantadine) extended-release 274-mg capsules for treatment of LID in patients with PD. Design, Setting, and Participants A randomized, double-blind, placebo-controlled clinical trial was conducted between May 7, 2014, and July 22, 2015, at 44 North American sites among patients with PD treated with levodopa who experienced at least 1 hour of troublesome dyskinesia per day with at least mild functional impact. Interventions Patients were randomized to receive placebo or 274 mg of ADS-5102 administered orally at bedtime for up to 25 weeks. Main Outcomes and Measures The primary efficacy analysis was the change from baseline to week 12 in the Unified Dyskinesia Rating Scale total score for ADS-5102 vs placebo in the modified intent-to-treat population. OFF time (amount of time the PD medication is not controlling motor symptoms) was a key secondary end point. Safety analyses included all patients who received the study drug (ADS-5102 or placebo). Results A total of 189 patients were screened, and 126 were randomized; the modified intent-to-treat population included 121 patients (51 women and 70 men; mean [SD] age, 64.7 [9.1] years). At week 12, the least-squares mean (SE) change in the Unified Dyskinesia Rating Scale score was –15.9 (1.6) for ADS-5102 (n = 63) and –8.0 (1.6) for placebo (n = 58) (treatment difference, –7.9; 95% CI, –12.5 to –3.3; P < .001). OFF time decreased by a mean (SE) of 0.6 (0.3) hours for ADS-5102 and increased by 0.3 (0.3) hours for placebo (treatment difference, –0.9 hours; 95% CI, –1.6 to –0.2; P = .02). Common adverse events for ADS-5102 vs placebo included visual hallucinations (15 [23.8%] vs 1 [1.7%]), peripheral edema (15 [23.8%] vs 0), and dizziness (14 [22.2%] vs 0). Adverse events led to treatment discontinuation for 13 patients receiving ADS-5102 (20.6%) vs 4 patients receiving placebo (6.9%). Conclusions and Relevance ADS-5102, 274 mg at bedtime, may be an effective treatment for LID. An additional benefit is reduced OFF time. To our knowledge, this is the first demonstration of an oral treatment reducing both LID and OFF time in patients with PD with dyskinesia. Trial Registration clinicaltrials.gov Identifier: NCT02136914
Online System Identification and Adaptive Control for PEM Fuel Cell Maximum Efficiency Tracking

This paper addresses an adaptive control approach for a maximum efficiency tracking of a proton exchange membrane fuel cell. The adaptive control has an online identification system that estimates the fuel cell efficiency behavior parameters and an optimization module that is responsible for providing the best operating conditions. The proposed approach does not require a cell-precise model and is not sensitive to the initial operating conditions and has been successfully tested on a 500-W proton exchange membrane fuel cell. A comparative study with the airflow control strategy shows that this adaptive control can improve the fuel cell efficiency up to 10%. Since the proposed adaptive control requires little knowledge of the fuel cell model, it can be easily used for similar fuel cells.
Pilot-based Fast Estimation of Frequency Offset and Channel for OFDM

A new fast algorithm is proposed for estimating the CFO based on the pilot structure in M. Morelli et al. (1999), H.K. Song et al., (2000). The new method first identifies a coarse estimation of the CFO and then refines it by a least square (LS) method. It always gives a more accurate estimation than the multi-stage method in H.K. Song et al. (2000) and is better than the method in M. Morelli et al. (1999) at low SNR. It is only slightly worse than the maximum likelihood estimator at high SNR. Furthermore, the proposed method can be used for CFO tracking. Also, in this paper, channel estimation by using the same pilot block is considered. The best values for the non-null subcarriers are found to optimize the channel estimation and peak to average power ratio (PAPR) simultaneously. Simulations demonstrate that the proposed methods are effective
Remodeling the cell surface distribution of membrane proteins during the development of epithelial cell polarity

The development of polarized epithelial cells from unpolarized precursor cells follows induction of cell-cell contacts and requires resorting of proteins into different membrane domains. We show that in MDCK cells the distributions of two membrane proteins, Dg-1 and E- cadherin, become restricted to the basal-lateral membrane domain within 8 h of cell-cell contact. During this time, however, 60-80% of newly synthesized Dg-1 and E-cadherin is delivered directly to the forming apical membrane and then rapidly removed, while the remainder is delivered to the basal-lateral membrane and has a longer residence time. Direct delivery of greater than 95% of these proteins from the Golgi complex to the basal-lateral membrane occurs greater than 48 h later. In contrast, we show that two apical proteins are efficiently delivered and restricted to the apical cell surface within 2 h after cell-cell contact. These results provide insight into mechanisms involved in the development of epithelial cell surface polarity, and the establishment of protein sorting pathways in polarized cells.
In vitro Intestinal Degradation and Absorption of Chondroitin Sulfate, a Glycosaminoglycan Drug

Summary Chondroitin sulfate (CAS 24967-93-9, CS) is a natural polymer of a disaccharide consisting of glucuronic acid and N-acetyl glucosamine which is sulfated either in the 4 or 6 position. It is administered orally as a slow acting drug to treat osteoarthritis, though there is much debate about its effectiveness and its mode of action, given that macromolecules are not normally absorbed in the gastrointestinal (GI) tract. Initially using a spectro-photometric assay, the stability of CS was tested in the presence of both tissues and lumenal contents of stomach, small intestine, cecum and colon. There was no degradation by the contents of the stomach or small intestine or in any of the tissues. Degradation only took place in the contents of the colon and particularly the cecum. Using 14C-radiolabelled CS it was shown that the cecum contents degraded CS down to the component disac-charides. The 14C-radiolabelled CS was also used to investigate the transport of CS across the different parts of the GI tract in vitro. The CS was transported across the small intestine in low amounts in the intact form, probably by the mechanism of endocytosis. In the colon and the cecum, higher amounts of radioactivity were transported, but most of the radioactivity was in the form of the degradation products, the disacchar-ides. This study shows that small amounts of CS may cross the upper intestine intact, but in the distal GI tract the molecule is effectively degraded, presumably by the enzymes in the intestinal flora.
Convergent Interactive Inference with Leaky Joins

One of the primary challenges in graphical models is inference, or re-constructing a marginal probability from the graphical model’s factorized representation. While tractable for some graphs, the cost of inference grows exponentially with the graphical model’s complexity, necessitating approximation for more complex graphs. For interactive applications, latency is the dominant concern, making approximate inference the only feasible option. Unfortunately, approximate inference can be wasteful for interactive applications, as exact inference can still converge faster, even for moderately complex inference problems. In this paper, we propose a new family of convergent inference algorithms (CIAs) that bridge the gap between approximations and exact solutions, providing early, incrementally improving approximations that become exact after a finite period of time. We describe two specific CIAs based on a cryptographic technique called linear congruential generators, including a novel incremental join algorithm for dense relations called Leaky Joins. We conclude with experiments that demonstrate the utility of Leaky Joins for convergent inference: On both synthetic and real-world probabilistic graphical models, Leaky Joins converge to exact marginal probabilities almost as fast as state of the art exact inference algorithms, while simultaneously achieving approximations that are almost as good as state of the art approximation algorithms.
The Effect of Arm Position on Lower Extremity Kinematics during a Single Limb Drop Landing: A Preliminary Study

Anterior cruciate ligament (ACL) injuries occur most commonly during non-contact situations, such as landing from a jump. Arm position has been shown to affect the loading of the lower extremity and therefore alter the potential injury risk. This study aimed to investigate the effect of arm position on lower extremity kinematics during single limb drop landings. Eight recreational American football players performed single limb drop landings on their preferential limb in four different conditions; (1) control (arms free); (2) arms to landing limb side; (3) arms in front of body; and (4) arms away from landing limb side. Kinematics of the hip, knee and ankle were recorded in both the sagittal and frontal planes at initial ground contact and maximum. Results showed that there was a significant decrease in maximum hip flexion and a significant increase in peak dorsiflexion when landing with arms away from the landing-side limb. Since decreased hip flexion and increased ankle dorsiflexion have been proposed to increase the likelihood of ACL injury, it would appear that landing with arms away from the landing-side limb may increase the risk of ACL injury, and therefore athletes should avoid this position when landing from a jump.