Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein features identification for machine learning-based prediction of protein-protein interactions

The long awaited challenge of post-genomic era and systems biology research is computational prediction of protein-protein interactions (PPIs) that ultimately lead to protein functions prediction. The important research questions is how protein complexes with known sequence and structure be used to identify and classify protein binding sites, and how to infer knowledge from these classification such as predicting PPIs of proteins with unknown sequence and structure. Several machine learning techniques have been applied for the prediction of PPIs, but the accuracy of their prediction wholly depends on the number of features being used for training. In this paper, we have performed a survey of protein features used for the prediction of PPIs. The open research challenges and opportunities in the area have also been discussed.
Good bargains and reputable sellers - An experimental investigation of electronic feedback systems

Electronic reputation mechanisms aim at signaling the quality of traders and at hampering misbehavior. When a buyer rates a seller, the main aspect to keep into account should be the consistency between the good’s advertised characteristics and the actual good itself. On the other hand, the buyer’s satisfaction may also be related to the surplus stemming from the transaction, i.e. whether or not the purchase was a good bargain. This constitutes a possible source of distortion in the way sellers are rated. Using an experimental investigation, we find that the transaction payoff is in fact a significant factor driving the feedback. Conversely, the match (or mismatch) between the ex-ante advertised description and the item received is comparatively less important, and may be offset by the effect of the payoff. This result accounts for the occurrence on some e-marketplace contexts of sellers getting away with inflated descriptions of the goods on sale without compromising their reputation.
An acoustic investigation of vowel variation in Gitksan

The research question for this thesis is: How does vowel quality vary across Gitksan speakers, and what sociolinguistic factors may be influencing this variation? Answering this question requires both that I show what the variation is, and why it may be that way; I have approached these questions by conducting a study in two parts. First, I conducted a demographic survey and ethnographically-informed qualitative interview with nine Gitksan speakers. Second, I performed an acoustic analysis of vowel variation across these same speakers. The acoustic results lead me to conclude that the low and front vowels show the most variation between speakers. My findings allowed me to add to our understanding of individual variation across speakers and communities. Although further investigation is needed to come to a conclusion about the generalizability of these results, the overarching contribution of my work is to add phonetic detail to previous descriptions of variation between speakers within the Interior Tsimshianic dialect continuum.
Interpretation of the Gamma Interferon Test for Diagnosis of Subclinical Paratuberculosis in Cattle

ABSTRACT A group of 252 cattle without clinical signs of paratuberculosis (paraTB) in 10 herds infected with paraTB and a group of 117 cattle in 5 herds without paraTB were selected. Whole-blood samples were stimulated with bovine, avian, and johnin purified protein derivative (PPD) and examined for gamma interferon (IFN-γ) release. For diagnosis of paraTB, satisfactory estimated specificities (95 to 99%) could be obtained by johnin PPD stimulation irrespective of interpretation relative to bovine PPD or no-antigen stimulation alone, but numbers of test positives in the infected herds varied from 64 to 112 with different interpretation criteria. For a limited number of test-positive animals, no change in the test results could be observed with increasing antigen concentrations but IFN-γ responses were significantly reduced (P < 0.0001) and four out of seven reactors tested negative when stimulation was performed on day-old samples. Denmark is free of bovine tuberculosis, but cross-reactivity with paraTB could be documented for cattle more than 14 months old in paraTB-infected herds compared with those in non-paraTB-infected herds. In both paraTB-free and paraTB-infected herds, false positives were observed when the test was applied to calves less than 15 months of age. Until novel antigen formulations more specific for these diseases are available, interpretation of the IFN-γ test must be individually adjusted to fit specific needs and the context within which the test is applied and, for paraTB, the test seems most appropriate for use as a supportive tool for evaluation of disease-preventive measures in young stock.
The structuring for development and management waqf properties in Malaysia

There are several methods that can be utilized to enhance the productivity of endownment (waqf) assets.These assets can be rented out to interested parties or used for various economic activities such as agriculture and livestock farming.In cases where the above methods are deemed unsuitable, then the Nazir should try to find other alternatives to make the waqf land productive.Endownment (waqf) trustees should also explore other avenues to optimize the usage of endowment land under their care. Thus, real estate investment can be used as an alternative to develop the endowment land. Real estate/property investment on waqf assets can be implemented by constructing commercial buildings such as supermarkets, accommodation (hotels) and residential estates.The development of these lands will lead to the creation of new waqf assets. This research is undertaken to study the methods used to commercially develop a Waqf land located in Seberang Jaya, Penang carried out by the Islamic Religious Council of Pulau Pinang (IRCPP) with UDA Holding Bhd. management expertise and cooperation, the productivity of a waqf land (known as Settee Aishah) was optimised and successfully developed into a residential estate known as Settee Aishah Waqf Residential Estate.
Does Market Concentration Preclude Risk Taking in Baking

We analyse risk-taking behaviour of banks in the context of a model based on spatial competition. Banks mobilise deposits by offering deposit rates. We show that when the market concentration is low, banks invest in the gambling asset. On the other hand, for sufficiently high levels of market concentration, all banks choose the prudent asset to invest in, and some depositors may even be left out of the market. Our results suggest a discontinuous relation between market concentration and social welfare.
Simulation of muscle and adipose tissue deformation in the passive human pharynx

Quantifying the contribution of passive mechanical deformation in the human pharynx to upper airway collapse is fundamental to understanding the competing biomechanical processes that maintain airway patency. This study uses finite element analysis to examine deformation in the passive human pharynx using an intricate 3D anatomical model based on computed tomography scan images. Linear elastic properties are assigned to bone, cartilage, ligament, tendon, and membrane structures based on a survey of values reported in the literature. Velopharyngeal and oropharyngeal cross-sectional area versus airway pressure slopes are determined as functions of Young's moduli of muscle and adipose tissue. In vivo pharyngeal mechanics for small deformations near atmospheric pressure are matched by altering Young's moduli of muscle and adipose tissue. The results indicate that Young's moduli ranging from 0.33 to 14 kPa for muscle and adipose tissue matched the in vivo range of area versus pressure slopes. The developed anatomical model and determined Young's moduli range are expected to be useful as a starting point for more complex simulations of human upper airway collapse and obstructive sleep apnea therapy.
Liver X Receptor Regulates Rheumatoid Arthritis Fibroblast-like Synoviocyte Invasiveness, Matrix Metalloproteinase 2 Activation, Interleukin-6 and CXCL10

Fibroblast-like synoviocyte (FLS) invasiveness correlates with articular damage in rheumatoid arthritis (RA), yet little is known about its regulation. In this study we aimed to determine the role of the nuclear receptor liver X receptor (LXR) in FLS invasion. FLS were isolated from synovial tissues obtained from RA patients and from DA rats with pristane-induced arthritis. Invasion was tested on Matrigel-coated chambers in the presence of the LXR agonist T0901317, or control vehicle. FLS were cultured in the presence or absence of T0901317, and supernatants were used to quantify matrix metalloproteinase 1 (MMP-1), MMP-2, MMP-3, interleukin-6 (IL-6), tumor necrosis factor-α and C-X-C motif chemokine ligand 10 (CXCL10). Nuclear factor-κB (NF-κB) (p65) and Akt activation, actin cytoskeleton, cell morphology and lamellipodia formation were also determined. The LXR agonist T0901317 significantly reduced DA FLS invasion by 99% (P ≤ 0.001), and RA FLS invasion by 96% (P ≤ 0.001), compared with control. T0901317-induced suppression of invasion was associated with reduced production of activated MMP-2, IL-6 and CXCL10 by RA FLS, and with reduction of actin filament reorganization and reduced polarized formation of lamellipodia. T0901317 also prevented both IL-1β-induced and IL-6-induced FLS invasion. NF-κB (p65) and Akt activation were not significantly affected by T0901317. This is the first description of a role for LXR in the regulation of FLS invasion and in processes and pathways implicated both in invasion as well as in inflammatory responses. These findings provide a new rationale for considering LXR agonists as therapeutic agents aimed at reducing both inflammation and FLS-mediated invasion and destruction in RA.
Identifying and Responding to Depression in Adult Cancer Patients: Evaluating the Efficacy of a Pilot Communication Skills Training Program for Oncology Nurses

Depression is a common response among cancer patients to their diagnosis and treatment; however, it goes undetected by healthcare providers in about 50% of cases. Communication skills training has been suggested as means to help nurses detect and respond to patient depression. We developed and pilot tested a communication skills training workshop based around 6 strategies. The training program consisted of 2 half-day experiential workshops that included didactic teaching, exemplary video, and role play. The aim of the study was to evaluate the effectiveness of the communication skills training. Fifteen nurses were recruited from the ambulatory nursing service at (redacted). Standardized patient assessments were used to measure strategy uptake. The presence of each strategy was rated on a 4-point scale from "not attempted" to "successfully attempted. " Nurses also completed evaluations of the training program. The nurses attempted 3 of 6 strategies more commonly after training, and a trend to significance was observed in a fourth strategy. The nurses reported more confidence to deal with patient depression and had greater self-efficacy. This short training program demonstrated success in improving nurse communication skills and confidence in dealing with patient depression. A larger trial of the training is planned.
Temporal Influence Blocking: Minimizing the Effect of Misinformation in Social Networks

The diffusion of rumors is a major concern for web users. Limiting the spread of rumor on social networks has become an important task. One approach is to identify nodes to start a truth campaign such that when users are aware of the truth, they would not believe or propagate the rumor. However, existing works do not take into account the delays of information diffusion or the time point beyond which propagation of misinformation is no longer critical. In this paper, we consider a more realistic situation where information is propagated with delays and the goal is to reduce the number of rumor-infected users before a deadline. We call this the Temporal Influence Blocking (TIB) problem. We propose a two-phase solution called TIB-Solver to select k nodes to start a truth campaign such that the number of users reached by a rumor is minimized. Experiments show that the proposed TIBSolver outperforms the state-of-the-art algorithms in terms of both effectiveness and efficiency.
FruitGame: A Simulation Tool to Evaluate Supply Chain Logistics and the Effects of Information Sharing for Fresh Produce

One of the main difficulties in effective supply chain management is the presence of organizational barriers. Even within the same firm, information sharing may be difficult to attain because of “political” issues. In the paper we illustrate an in-progress extension of a simulation tool for performance evaluation of supply chains for fresh produce distribution. In such a context, item perishability is an important issue, either because of characteristics of the product itself, or because shelf life is traded off against quality. Because of demand uncertainty, when too many items are stocked, discount sales are needed to clear the shelves, and goods may even be scrapped with a corresponding loss of profit. We concentrate on a large retail chain where a possibly large number of retail stores is served by a single distribution center, acting as a transit point to optimize transportation of goods received from suppliers. Suitable models must be used both for ordering decisions at the retail store level and for allocation decisions when the distribution center does not receive enough goods to meet orders. In such a case, a simple proportional allocation is often used, because of its simplicity and “political neutrality. ” With a simple simulation exercise, we illustrate how this policy ignores retail store peculiarities in terms of demand uncertainty and responsiveness to discount sales or sensitivity to quality, resulting in a potentially suboptimal performance.
Interpretation of mixed models and marginal models with cohort attrition due to death and drop-out

Mixed models estimated by maximum likelihood and marginal models estimated by generalized estimating equations are the standard methods for the analysis of longitudinal data. However, their use is highly debated when attrition may be due to death. While some authors consider that mixed model estimates are interpretable only in an immortal cohort, we show that their subject-specific interpretation still holds in the population currently alive, but their population-averaged interpretation is valid only in the immortal cohort. We propose an approximation of the population-averaged mean among the population alive that highlights the difference with the population-averaged mean in the immortal cohort. The interpretation of ML estimates of mixed models and joint models for the marker and the time-to-death as well as unweighted and weighted GEE of marginal models is then illustrated in a simulation study and in an application regarding cognitive decline in the elderly.
ESTIMATING THE VOLATILITY OF DEPOSIT BANKS’ CREDIT STOCK WITH A SWARCH MODEL

In this study, the volatility of deposit banks’ credit stock in Turkey is investigated by using weekly data from June 2000 through June 2007. To determine the high and low volatility states, two state switching autoregressive conditional heteroscedasticity (SWARCH) models are estimated. The economic and political events that resulted in high volatility in credit stock volume are also analyzed. Results show that volatility of credit stock volume in Turkey is sensitive to domestic government bonds’ interest rate and foreign portfolio investments. The volatility of credit stock volume is also affected by political events.
The Benefits of Evaluating Tracker Performance Using Pixel-Wise Segmentations

For years, the ground truth data for evaluating object trackers consists of axis-aligned or oriented boxes. This greatly reduces the workload of labeling the datasets in the common benchmarks. Nevertheless, boxes are a very coarse approximation of an object and the approximation by a box has a large degree of ambiguity. Furthermore, tracking approaches that are not restricted to boxes cannot be evaluated within the benchmarks without adding a penalty to them. We present a simple extension to the VOT evaluation procedure that enables to include these approaches. Furthermore, we present upper bounds for trackers restricted to boxes. Moreover, we present a new measure that captures how well an approach can cope with scale changes without the need of frame-wise labels. We present a learning-based approach which helps to identify frames with heavy occlusion automatically. The framework is tested on the segmentations of the VOT2016 dataset.
Surveying a Subsea Lava Flow Using the Autonomous Benthic Explorer (abe)

This paper summarizes results from the first science deployment of the Autonomous Benthic Explorer (ABE), conducted on the Juan de Fuca Ridge (46°N, 129°W) at depths between 2200 and 2400 m. Using long baseline acoustic transponders, the ABE descended with precision to a preassigned starting point, then executed dead-reckoned tracklines. It followed the bottom at distances between 7 and 20 m using an acoustic fathometer as a reference sensor. The ABE mapped a new subsea lava flow with a magnetometer, imaged the seafloor with a stereo snapshot video system, and mapped a hydro thermal plume with conductivity and temperature sensors. The ABE completed 7 successful dives and covered over 35 km of tracklines. Detailed power records were logged, which permits extrapolation of the ABE's performance to other missions and higher capacity batteries.
Maternal sensitivity and infant attachment security in Korea: Cross-cultural validation of the Strange Situation

The present study sought to analyze infant and maternal behavior both during theStrange Situation Procedure (SSP) and a free play session in a Korean sample (N = 87) to help understand whether mother–infant attachment relationships are universal or culture-specific. Distributions of attachment classifications in the Korean sample were compared with a cross-national sample. Behavior of mothers and infants following the two separation episodes in the SSP, including mothers' proximity to their infants and infants' approach to the caregiver, was also observed, as was the association between maternal sensitivity observed during free play session and infant security. The percentage of Korean infants classified as secure versus insecure mirrored the global distribution, however, only one Korean baby was classified as avoidant. Following the separation episodes in the Strange Situation, Korean mothers were more likely than mothers in Ainsworth's Baltimore sample to approach their babies immediately and sit beside them throughout the reunion episodes, even when their babies were no longer distressed. Also, Korean babies less often approached their mothers during reunions than did infants in the Baltimore sample. Finally, the link between maternal sensitivity and infant security was significant. The findings support the idea that the basic secure base function of attachment is universal and the SSP is a valid measure of secure attachment, but cultural differences in caregiving may result in variations in how this function is manifested.
Re‐Screening serotonin receptors for genetic variants identifies population and molecular genetic complexity

We have re‐screened the genes for the 5‐HT1A, 5‐HT2A, 5‐HT2C, and 5‐HT7 serotonin receptors for genetic variants in a large African‐American and Caucasian‐American population sample. We have identified eight novel variants in these genes including four that are predicted to cause amino acid substitutions. These variants are additional candidates for association studies of behavioral disorders such as depression and schizophrenia as well as quantitative personality traits. We have also detected some, but not all, previously identified variants in these genes suggesting that many previously identified variants are unique to specific populations. The results of this study, and previous screens of serotonin receptors, demonstrate that the genes for serotonin receptors display marked population and molecular genetic complexity. These levels of complexity may have a substantial effect on genetic association studies of human behavioral variability related to these genes. We discuss the implications of these findings and propose methods to address complexity in genetic association studies. © 2003 Wiley‐Liss, Inc.
Simulation of drug release from biodegradable polymeric microspheres with bulk and surface erosions.

New models are developed to account for the kinetics of drug release from porous, biodegradable polymeric microspheres under the schemes of bulk erosion and surface erosion of the polymer matrix, respectively. Three mechanisms of drug release, namely, drug diffusion, drug dissolution, and polymer erosion jointly govern the overall release process. For bulk erosion, the model incorporates an erosion term into the dissolution and diffusion equation and is solved numerically for various boundary conditions. Dissolution and erosion are defined in the model by introducing three equations which take into account the drug concentration in the liquid phase, virtual solid phase, and effective solid phase. For surface erosion, drug concentrations in liquid and solid phases are defined and a substitution is introduced to convert the moving-boundary problem to a fixed-boundary problem. The resulting differential equations are solved simultaneously to obtain the concentration profile in the liquid and solid phases, respectively. Numerical solutions are provided to illustrate the effects of drug dissolution constant, drug diffusion coefficient, and erosion rate constant. In general, increasing erosion rate, diffusivity, dissolution, and decreasing particle radius enhance the drug release rate. Predictions from the models are also compared with experimental data to verify their validity and possible improvements are proposed.
Education and training as Successful strategies employed by women to accede to leadership positions in the public sector in kenya

The purpose of this research is to examine the successful strategies adopted by women to accede to leadership in the public sector in Kenya. The sector is the policy making and implementation nucleus of the country. Women in Kenya, though making significant entries into the public service, are still grossly underrepresented in senior management and public decision-making positions (Suda, 2002). It is pertinent that all players who contribute to the wellbeing of society are brought on board through strategies such as education that may be employed to ensure distributive inclusion. Several studies have been carried out on the factors that hinder women from acceding to the leadership and decision making levels. However few studies have investigated strategies that women may employ to accede to the pertinent positions of policy making. This study adopted exploratory research design while the population is the non elected women leaders in the public sector in Kenya. Samples were drawn using stratified random sampling across the public sector. Questionnaires were employed to collect data. The data obtained was analyzed quantitatively. A simple linear regression model was used to model the data and corresponding analysis carried out. The study principally concluded that