Miracle-dz/UniFAR-FTUs huggingface dataset:
In Silico Putative Drug Target Identification in Enterobacter Cloacae and Homology Modelling of a Candidate Drug Target

Enterobacter cloacae is a clinically significant Gram-negative, facultatively-anaerobic, rod-shaped bacterium belonging to the family of Enterobacteriaceae. It has emerged as a prevalent nosocomial pathogen due to high level resistance to disinfec- tants and antimicrobial agents. The availability of complete genome sequence of E. cloacae has paved the new way to identify the novel drug targets. In the present work comparative analysis of the metabolic pathways of the pathogen and host was performed to identify the novel drug targets involved in pathogen but absent in Homo sapiens. All enzymes involved in the metabolic pathways of E. cloacae were searched against the proteome of H. sapiens using the BLASTp program. The threshold of percentage identity was set to as 0.001, and the query coverage < 50. Using these parameters approximately 44 unique putative targets were identified. Out of those non-homologous targets, 22 coding genes for putative targets were identified as essential genes from the DEG database. Based on extensive literature search, 8 targets such as UDP-N-acetylmuramoyl-L-alanyl-D-gluta- mate synthetase, UDP-N-acetylmuramate-L-alanine ligase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2, 6-diaminopimelate ligase, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase, UDP-N-acetylmuramate-L-alanine ligase (MurC) α-isopro- pylmalate synthase, UDP-N-Acetylglucosamine Enolpyruvyl Transferase, UDP-N-acetylenolpyruvylglucosamine reductase and Aspartate beta-semialdehyde dehydrogenase were identified as potential drug targets. Among these drug targets, UDP-N-acetylmu - ramate-L-alanine ligase (MurC) was chosen as potential therapeutic drug target. The homology modeling of MurC was performed using SWISS-MODEL and HHPred servers respectively. Subsequently, all the predicted models were evaluated using the SAVES server. The stereochemical parameters of all 3D models suggest that the best model was predicted by HHPred server. In order the refine the modeled structure, energy minimization was also performed using Deep View tool. The refined 3D structure was further validated by ProSA server. In future, the 3D structure of MurC in E. cloacae might be exploited for the discovery of novel inhibitors that could potentially inhibit this nosocomial pathogen.
Effects of moderate weight loss and orlistat on insulin resistance, regional adiposity, and fatty acids in type 2 diabetes.

OBJECTIVE Moderate weight loss is recommended for overweight and obese patients with type 2 diabetes, and conjunctive use of weight loss medication has been advocated. The current study examined weight loss-dependent and -independent effects of the intestinal lipase inhibitor orlistat at 6 months of treatment, using behavioral intervention (Int) combined with randomized, double-blinded, placebo (P)-controlled treatment with orlistat (O). RESEARCH DESIGN AND METHODS Metabolic control, insulin sensitivity (IS), regional fat distribution, and fat content in liver and muscle were measured in 39 volunteers with type 2 diabetes in whom all antidiabetic medication was withdrawn 1 month preceding randomization. Weight loss was equivalent in the Int+O and Int+P groups, respectively (-10.3 +/- 1.3 vs. -8.9 +/- 1.1%), and there were identical decreases in visceral adipose tissue (VAT), fat mass (FM), thigh adiposity, and hepatic steatosis. RESULTS Weight loss resulted in substantial improvement (P < 0.001) in HbA(1c) (-1.6 +/- 0.3 vs. -1.0 +/- 0.4%; NS between groups). IS improved significantly more with orlistat (Delta2.2 +/- 0.4 vs. Delta1.2 +/- 0.4 mg. min(-1). kg(-1) fat-free mass [FFM]; P < 0.05), and plasma free fatty acid (FFA) levels were strongly correlated with IS (r = 0.56; P < 0.001). Orlistat caused greater reductions in fasting plasma FFA (Delta-154 +/- 22 vs. Delta-51 +/- 33 micro mol/l; P < 0.05), insulin-suppressed FFA (Delta-119 +/- 23 vs. Delta-87 +/- 34 micro mol/l; P < 0.05), and fasting plasma glucose (FPG; -62 +/- 9 vs. -32 +/- 8 mg/dl; P = 0.02). Changes in HbA(1c) were correlated with DeltaIS (r = -0.41; P < 0.01) but not with weight loss per se. CONCLUSIONS At equivalent weight loss, conjunctive use of orlistat resulted in greater improvement in FFA levels and IS.
A comparison of tests for Hardy-Weinberg equilibrium.

The various tests for the goodness of fit of a population to Hardy-Weinberg equilibrium are compared with respect to their power and the accuracy of their distributional approximations. The tests are similar in terms of power. However, when one or more alleles are rare (with frequencies of less than .45 to .21 for n = 10 and 200, respectively) some of the tests are not able to detect outbreeding. When all but one allele are rare (frequencies of less than .40 to .15 for n = 10 and 200, respectively) none of the tests are able to detect outbreeding. In terms of distributional assumptions, there are two situations: (i) Test of hypothesis (when a preset significance level is chosen and the null hypothesis accepted or rejected at that level); here the chi square test with conditional expectations, the Freeman-Tukey test and the Mantel-Li test, all without continuity correction, were found to be best; they were closely followed by the chi square test and conditional chi square test, both with a continuity correction of 1/4, and by the Elston-Forthofer average test. (ii) Test of significance (when the obtained level of significance is used as strength against the null hypothesis); here the chi square test and conditional chi square test, both with a continuity correction of 1/4, and the average test were found to be best.
The TrkC receptor induces apoptosis when the dependence receptor notion meets the neurotrophin paradigm

The TrkC/NT-3 receptor/ligand pair is believed to be part of the classic neurotrophic theory claiming that neuronal death occurs by default when neurotrophic factors become limited, through loss of survival signals. Here, we show that TrkC is a dependence receptor and, as such, induces caspase-dependent apoptotic death in the absence of NT-3 in immortalized cells, a proapoptotic activity inhibited by the presence of NT-3. This proapoptotic activity of TrkC relies on the caspase-mediated cleavage of the intracellular domain of TrkC, which permits the release of a proapoptotic fragment. This fragment induces apoptosis through a caspase-9-dependent mechanism. Finally, we show that the death of dorsal root ganglion (DRG) neurons provoked by NT-3 withdrawal is inhibited when TrkC-proapoptotic activity is antagonized. Thus, the death of neurons upon disappearance of NT-3 is not only due to a loss of survival signals but also to the active proapoptotic activity of the unbound TrkC dependence receptor.
Acoustic scattering from superspheroidal objects

A T-matrix technique has been used to study acoustic scattering from extended axisymmetric objects. The objects are formed using the mathematical function for a “superellipse” [i.e, (x/a) s + (z/b) s = 1, where s=2n, n=1,2,3,…], and revolving around the z-axis. For s=2, the object is a spheroid with aspect reason α=b/a. As s increases, the shape of the object approaches a cylinder of radius a and length 2b. The method allows the scattered field to be determined for all azimuth angles as a function of frequency, and allows comparisons to be made with other methods for describing the scattering of objects of this type. The results have direct applications in the interpretation of acoustic scattering from oceanic objects such as the swim bladders of some fish, and zooplankton.
Adaptive load balancing in mobile ad hoc networks

In this paper, we propose a prediction based adaptive load balancing mechanism for mobile ad hoc networks. This mechanism can cooperate with any kind of multipath source routing protocol. It distributes traffic load among multiple disjoint paths based on the measurement and prediction of network traffic. In order to predict network traffic accurately, we first analyze the traffic data collected in our mobile ad hoc network testbed and find out that ad hoc networks traffic is self-similar. Then, we propose a traffic predictor based on wavelet analysis. The simulation results show that our loading balancing approach can distribute traffic properly and lead to a decrease of traffic load imbalance of multiple paths and network congestion. As a result, it reduces the end-to-end packet delay and packet dropping probability and balances the energy consumption of the network.
A Study on User Authentication Methodology Using Numeric Password and Fingerprint Biometric Information

The prevalence of computers and the development of the Internet made us able to easily access information. As people are concerned about user information security, the interest of the user authentication method is growing. The most common computer authentication method is the use of alphanumerical usernames and passwords. The password authentication systems currently used are easy, but only if you know the password, as the user authentication is vulnerable. User authentication using fingerprints, only the user with the information that is specific to the authentication security is strong. But there are disadvantage such as the user cannot change the authentication key. In this study, we proposed authentication methodology that combines numeric-based password and biometric-based fingerprint authentication system. Use the information in the user's fingerprint, authentication keys to obtain security. Also, using numeric-based password can to easily change the password; the authentication keys were designed to provide flexibility.
Excess Morbidity and Cost of Failure to Achieve Targets for Blood Pressure Control in Europe

Aim: To estimate the burden of failing to achieve targets for blood pressure (BP) control in France, Germany, Italy, Sweden and the UK. Methods: A cost of illness model was constructed to estimate the impact of uncontrolled hypertension to each national healthcare system. Prevalence of uncontrolled hypertension was taken from published data. Relationships between achieved BP and the cardiovascular events of symptomatic acute myocardial infarction, congestive heart failure and stroke were estimated from the HOT study. Costs were taken from public sources. The acute medical costs of these events were estimated at current prevalence of uncontrolled hypertension and if BP were treated to target. Results: The model estimated that 29 million adults in the five countries (13% population) have BP levels above 160/95 mmHg, and an additional 46 million (21% population) have BP in the range 140/90-160/95 mmHg. The model estimated that healthcare system costs of 1.26 billion euros could be avoided if hypertension management did achieve BP targets. This does not consider the cost of interventions required to reduce the risk of cardiovascular disease. Conclusions: Failing to achieve BP targets contributes substantially to healthcare system costs and preventable events in the countries studies.
Job insecurity, extrinsic and intrinsic job satisfaction and affective organisational commitment of maintenance workers in a parastatal

The objective of this study was to assess the relationship between job insecurity, job satisfaction and affective organisational commitment of maintenance workers ( N = 178) in a parastatal in Gauteng. A cross-sectional design was used. Stratified random samples of maintenance workers ( N = 178) were taken. The Job Insecurity Inventory, Minnesota Job Satisfaction Questionnaire and Organisational Commitment Questionnaire were used as measuring instruments. The results revealed small but significant relationships between job insecurity and extrinsic job satisfaction and job insecurity and affective organisational commitment. Job satisfaction was found to mediate the relationship between job insecurity and affective organisational commitment.
Lenient Learning in Independent-Learner Stochastic Cooperative Games

We introduce the Lenient Multiagent Reinforcement Learning 2 (LMRL2) algorithm for independent-learner stochastic cooperative games. LMRL2 is designed to overcome a pathology called relative overgeneralization, and to do so while still performing well in games with stochastic transitions, stochastic rewards, and miscoordination. We discuss the existing literature, then compare LMRL2 against other algorithms drawn from the literature which can be used for games of this kind: traditional ("Distributed") Q-learning, Hysteretic Q-learning, WoLF-PHC, SOoN, and (for repeated games only) FMQ. The results show that LMRL2 is very effective in both of our measures (complete and correct policies), and is found in the top rank more often than any other technique. LMRL2 is also easy to tune: though it has many available parameters, almost all of them stay at default settings. Generally the algorithm is optimally tuned with a single parameter, if any. We then examine and discuss a number of side-issues and options for LMRL2.
Engineering of integrated devices on electro-optical chip: grating couplers, algorithms, and switches

The technology of modern purely electrical computers requires more electrical wiring for intra-chip and inter-chip communications as the number of cores increases. Consequently, energy consumption increases due to heat dissipation from low bandwidth electric wires. The conversion of electrical signals to optical signals has been proposed in the future electro-optical computers as a way of addressing this issue. Much work has gone into the design, fabrication, and testing of components of new optical elements that can be implemented in chips fabricated in unmodified CMOS processes. In this Ph.D. thesis advances are achieved through engineering of various integrated optical and electro-optical devices on the chip, algorithms for automatic engineering of integrated optical devices, and measurement methods that enable understanding of integrated device behavior. The highly unidirectional uniform optical grating couplers are simulated, and compared experimentally with typical uniform gratings on the same chip. Here, the method of comparison of devices in symmetrical structures is presented. An algorithm for the design of a grating that launches a beam with an arbitrary magnitude and flat phase front is described. As an extension of this, the second algorithm for the design of a grating that launches a beam (here, focusing) with an arbitrary magnitude and phase front is presented. An automatic algorithm which, from the 2D device contour file after optical proximity correction, builds up any 3D optical device further simulated in 3D-FDTD is described. The obtained device can be compared with the designed device before fabrication occurs. An electronically-controlled optical switch with free-carrier injection, which can switch digital optical signals from one waveguide into other, is described. This switch is many times smaller, faster and more energy efficient than a recent optical switch based on a traditional Mach-Zehnder interferometer. Next, three different measurement methods are presented and experimentally confirmed. The first method enables measurement of current through the heater in the complex diode topology on the chip. The second method is for measuring the desired temperature on the chip for tests of integrated devices. The third method is for automated measurement of angles of optical fibers for the coupling with the gratings. Thesis Supervisor: Peter L. Hagelstein Title: Associate Professor of Electrical Engineering
Outage capacity analysis for SIMO Nakagami-m fading channel in spectrum sharing environment

In this paper, we consider the spectrum sharing cognitive radio system, wherein single-input multiple-output fading channel is assumed. Subject to joint average interference constraint and peak interference constraint of primary user, the outage capacity of cognitive user involving joint beamforming and power control is analyzed. We derive the optimal transmission power and beamforming weights of cognitive user for outage capacity, and the expressions of outage probability for a given outage capacity under the most versatile Nakagami-m fading model are presented. When the Nakagami fading parameter m are integers, the expressions are exhibited in closed-form, which avoid complex numerical integrals. Besides, we also investigate the delay-limited capacity and the zero-outage interference constraint, which are related with zero-outage transmission. Large amount of simulations are conducted to corroborate our theoretical results.
Harnessing ISA diversity: Design of a heterogeneous-ISA chip multiprocessor

Heterogeneous multicore architectures have the potential for high performance and energy efficiency. These architectures may be composed of small power-efficient cores, large high-performance cores, and/or specialized cores that accelerate the performance of a particular class of computation. Architects have explored multiple dimensions of heterogeneity, both in terms of micro-architecture and specialization. While early work constrained the cores to share a single ISA, this work shows that allowing heterogeneous ISAs further extends the effectiveness of such architectures. This work exploits the diversity offered by three modern ISAs: Thumb, x86-64, and Alpha. This architecture has the potential to outperform the best single-ISA heterogeneous architecture by as much as 21%, with 23% energy savings and a reduction of 32% in Energy Delay Product.
MOLECULAR DYNAMICS OF ATOMIC CLUSTERS: AN OBJECT ORIENTED APPROACH

The purpose of the project was to develop a graphical user interface (GUI) to simulate and display the interactions of a small amount of atoms in a cluster, specifically with interactions defined by a pairwise Lennard-Jones potential energy. Another goal of the project was to design the coding of the program in such a way that it would reflect how the various parts of the program interacted with each other. To this end four classes were developed: an atom, a cluster, a base simulation, and a molecular dynamics Lennard-Jones simulation. The atom class contained all the information that was necessary for the simulations, such as the potential energy of the atom. The program was designed with the ability to add new types of simulations, with no need to significantly modify the GUI code. In the GUI program the ability to watch the simulation as it takes place was introduced, as well as the ability to modify how the atoms themselves appear. Results are presented for a specific system, a cluster of rare gas atoms. A histogram of the potential energy is bimodal for a small (N appprox. 30-200 atom) cluster, a quantitative measure of the two qualitatively different regions--surface and bulk.
Hypnosis and Smoking Cessation: The State of the Science

In his letter to the editor in this Journal, Dr. Yager (2009) is spot on target when he suggests that clinicians may mistakenly come to view the immediate results of hypnotic smoking cessation treatments (and by implication, other hypnotic treatments) as representative of long-term treatment success. Dr. Yager wisely calls for formal research in place of anecdotal case reports that lack the benefit of follow-up data. To his credit, Dr. Yager analyzed a colleague's outcome data and determined that after a period of 60 days, 22% of patients surveyed did not resume smoking. Evaluating clinical findings is of paramount importance insofar as hypnosis is a widely used smoking cessation method. In one survey (Sood, Ebbert, Sood, & Stevens, 2006) of 1,177 patients at an outpatient tobacco treatment specialty clinic, 27% reported they used complementary and alternative medicine techniques such as hypnosis, relaxation, acupuncture, and meditation. Respondents indicated that the treatment of greatest interest for use in the future was hypnosis. Yet the fact that a treatment is widely used provides no warrant that it has an empirical base that supports its ubiquity. We (Lynn & Green) entered the arena of smoking cessation treatment more than 25 years ago in response to the overblown claims of itinerant hypnotists who set up shop in hotels in our community and touted hypnosis as a highly effective technique that virtually locked-in success in achieving nicotine abstinence. Even at that time, a cursory review of the literature revealed that neither hypnosis, nor any other intervention, could reliably alleviate nicotine addiction. In this article, we examine smoking cessation studies from anecdotal case studies that date back to 1847, when hypnotic techniques were first used to control the use of tobacco, to increasingly sophisticated contemporary research. Early studies well illustrate Yager's point about the dangers of relying on anecdotal reports. In fact, in one of the first reviews on hypnosis and smoking cessation, Johnston and Donoghue (1971) reported success rates as high as 94% (Von Dedenroth, 1964) based largely on anecdotal or clinical case reports. Nearly a decade later, Holroyd (1980) examined 17 reports and concluded that more sessions are better than fewer sessions, that individualized treatments are superior to standardized suggestions, and that adjunctive treatment such as telephone contact
Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins

Comparative genomics has revealed many examples in which the same function is performed by unrelated or distantly related proteins in different cellular lineages. In some cases, this has been explained by the replacement of the original gene by a paralogue or non‐homologue, a phenomenon known as non‐orthologous gene displacement. Such gene displacement probably occurred early on in the history of proteins involved in DNA replication, repair, recombination and transcription (DNA informational proteins), i.e. just after the divergence of archaea, bacteria and eukarya from the last universal cellular ancestor (LUCA). This would explain why many DNA informational proteins are not orthologues between the three domains of life. However, in many cases, the origin of the displacing genes is obscure, as they do not even have detectable homologues in another domain. I suggest here that the original cellular DNA informational proteins have often been replaced by proteins of viral or plasmid origin. As viral and plasmid‐encoded proteins are usually very divergent from their cellular counterparts, this would explain the puzzling phylogenies and distribution of many DNA informational proteins between the three domains of life.
Towards a rate-based TCP protocol for the Web

TCP's sliding window flow control mechanism often leads to bursty packet traffic in the Internet. In the presence of network congestion, multiple packet losses can occur degrading the performance of TCP and the user-perceived performance of the Web. This paper presents a rate-based pacing (RBP) mechanism for TCP flow control. This mechanism can reduce the burstiness of TCP packet transmission and improve document transfer performance. Simulation is used to evaluate the performance of this mechanism. Our RBP TCP protocol is found to provide similar performance to Reno TCP in terms of throughput and packet loss for bulk data transfers, but lower packet loss and 10-20% lower latency than Reno TCP for Web-like document transfers.