Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of protein-protein binding sites by incorporating the physicochemical properties and stationary wavelet transforms into pseudo amino acid composition

With the explosive growth of protein sequences entering into protein data banks in the post-genomic era, it is highly demanded to develop automated methods for rapidly and effectively identifying the protein–protein binding sites (PPBSs) based on the sequence information alone. To address this problem, we proposed a predictor called iPPBS-PseAAC, in which each amino acid residue site of the proteins concerned was treated as a 15-tuple peptide segment generated by sliding a window along the protein chains with its center aligned with the target residue. The working peptide segment is further formulated by a general form of pseudo amino acid composition via the following procedures: (1) it is converted into a numerical series via the physicochemical properties of amino acids; (2) the numerical series is subsequently converted into a 20-D feature vector by means of the stationary wavelet transform technique. Formed by many individual “Random Forest” classifiers, the operation engine to run prediction is a two-layer ensemble classifier, with the 1st-layer voting out the best training data-set from many bootstrap systems and the 2nd-layer voting out the most relevant one from seven physicochemical properties. Cross-validation tests indicate that the new predictor is very promising, meaning that many important key features, which are deeply hidden in complicated protein sequences, can be extracted via the wavelets transform approach, quite consistent with the facts that many important biological functions of proteins can be elucidated with their low-frequency internal motions. The web server of iPPBS-PseAAC is accessible at http://www.jci-bioinfo.cn/iPPBS-PseAAC, by which users can easily acquire their desired results without the need to follow the complicated mathematical equations involved.
Clustered Treatment Assignments and Sensitivity to Unmeasured Biases in Observational Studies

Clustered treatment assignment occurs when individuals are grouped into clusters prior to treatment and whole clusters, not individuals, are assigned to treatment or control. In randomized trials, clustered assignments may be required because the treatment must be applied to all children in a classroom, or to all patients at a clinic, or to all radio listeners in the same media market. The most common cluster randomized design pairs 2S clusters into S pairs based on similar pretreatment covariates, then picks one cluster in each pair at random for treatment, the other cluster being assigned to control. Typically, group randomization increases sampling variability and so is less efficient, less powerful, than randomization at the individual level, but it may be unavoidable when it is impractical to treat just a few people within each cluster. Related issues arise in nonrandomized, observational studies of treatment effects, but in this case one must examine the sensitivity of conclusions to bias from nonrandom selection of clusters for treatment. Although clustered assignment increases sampling variability in observational studies, as it does in randomized experiments, it also tends to decrease sensitivity to unmeasured biases, and as the number of cluster pairs increases the latter effect overtakes the former, dominating it when allowance is made for nontrivial biases in treatment assignment. Intuitively, a given magnitude of departure from random assignment can do more harm if it acts on individual students than if it is restricted to act on whole classes, because the bias is unable to pick the strongest individual students for treatment, and this is especially true if a serious effort is made to pair clusters that appeared similar prior to treatment. We examine this issue using an asymptotic measure, the design sensitivity, some inequalities that exploit convexity, simulation, and an application concerned with the flooding of villages in Bangladesh.
Link scheduling and multi-path routing in wireless mesh networks. (Ordonnancement des liens et routage de multiple chemins pour les réseaux maillés sans fil)

We present algorithmic solutions for two problems related to the wireless network interference. The first one proposes to schedule the links of a given set of routes under the assumption of a heavy-traffic pattern. We assume some TDMA protocol provides a background of synchronized time slots and seek to schedule the routes' links to maximize the number of packets that get delivered to their destinations per time slot. Our approach is to construct an undirected graph G and to heuristically obtain node multicolorings for G that can be turned into efficient link schedules. In G each node represents a link to be scheduled and the edges are set up to represent every possible interference for any given set of interference assumptions. We present two multicoloring-based heuristics and study their performance through extensive simulations. One of the two heuristics is based on relaxing the notion of a node multicoloring by dynamically exploiting the availability of communication opportunities that would otherwise be wasted. We have found that, as a consequence, its performance is significantly superior to the other's. In the second proposal, we consider wireless mesh networks and the problem of routing end-to-end traffic over multiple paths for the same origin-destination pair with minimal interference. We introduce a heuristic for path determination with two distinguishing characteristics. First, it works by refining an extant set of paths, determined previously by a single- or multi-path routing algorithm. Second, it is totally local, in the sense that it can be run by each of the origins on information that is available no farther in the network than the node's immediate neighborhood. We have conducted extensive computational experiments with the new heuristic, using AODV and OLSR as well as their multi-path variants as the underlying routing method. For one TDMA setting running a path-oriented link scheduling algorithm and two different CSMA settings (802.11 protocol), we have demonstrated that the new heuristic is capable of improving the average throughput network-wide. When working from the paths generated by the multi-path routing algorithms, the heuristic is also capable to provide a more evenly distributed traffic pattern.
Improving mental state in early imprisonment.

BACKGROUND Pre-trial prisoners have high rates of mental disorder, but to date, little is known about mental state change or stability among them. AIM The aim of this study was to describe mental state change over the first 4 weeks of imprisonment. METHODS Two hundred and fifty-seven new pre-trial male prisoners consented to participate in a prospective interview study. Recruited men tended to be younger than non-recruited men, but otherwise similar. Mental state was assessed 1 and 4 weeks after reception, using the Comprehensive Psychopathological Rating Scale and two self-rating instruments [the 90-item symptom checklist (SCL-90); the Beck Depression Inventory]. RESULTS After 4 weeks, 170 of the men were still in prison. In their demographics, previous offending, imprisonment, mental health histories or mental health ratings at initial interview, they did not differ from the 87 who were bailed, transferred, sentenced or had their case discontinued. The most sensitive of the rating schedules - the SCL-90 - identified only one new case among the 170 men, but the more illness-specific ratings suggested up to a 10% emergence of new cases by then. By contrast, while two-thirds of the men remained cases according to the SCL-90, about half of the men who had initial interview illness ratings were no longer 'cases'. DISCUSSION AND IMPLICATIONS FOR PRACTICE Measured in terms of 'caseness', distress is likely to be apparent on reception into prison and relatively resistant to change compared with symptoms of mental disorder per se. One-off screening at reception could be misleading. A limitation of our study is that we could measure mental state only twice. A third measure would have clarified whether, in such circumstances, the trend towards improvement is sustained, but brevity of residence in any one prison at this stage tends to preclude this.
Automating Black-Box Property Based Testing

Black-box property based testing tools like QuickCheck allow developers to write elegant logical specifications of their programs, while still permitting unrestricted use of the same language features and libraries that simplify writing the programs themselves. This is an improvement over unit testing because a single property can replace a large collection of test cases, and over more heavy-weight white-box testing frameworks that impose restrictions on how properties and tested code are written. In most cases the developer only needs to write a function returning a boolean, something any developer is capable of without additional training. This thesis aims to further lower the threshold for using property based testing by automating some problematic areas, most notably generating test data for user defined data types. Writing procedures for random test data generation by hand is time consuming and error prone, and most fully automatic algorithms give very poor random distributions for practical cases. Several fully automatic algorithms for generating test data are presented in this thesis, along with implementations as Haskell libraries. These algorithms all fit nicely within a framework called sized functors, allowing re-usable generator definitions to be constructed automatically or by hand using a few simple combinators. Test quality is another difficulty with property based testing. When a property fails to find a counterexample there is always some uncertainty in the strength of the property as a specification. To address this problem we introduce a black-box variant of mutation testing. Usually mutation testing involves automatically introducing errors (mutations) in the source code of a tested program to see if a test suite can detect it. Using higher order functions, we mutate functions without accessing their source code. The result is a very light-weight mutation testing procedure that automatically estimates property strength for QuickCheck properties.
Implementation and evaluation of a docking‐rescoring method using molecular footprint comparisons

A docking‐rescoring method, based on per‐residue van der Waals (VDW), electrostatic (ES), or hydrogen bond (HB) energies has been developed to aid discovery of ligands that have interaction signatures with a target (footprints) similar to that of a reference. Biologically useful references could include known drugs, inhibitors, substrates, transition states, or side‐chains that mediate protein‐protein interactions. Termed footprint similarity (FPS) score, the method, as implemented in the program DOCK, was validated and characterized using: (1) pose identification, (2) crossdocking, (3) enrichment, and (4) virtual screening. Improvements in pose identification (6–12%) were obtained using footprint‐based (FPSVDW+ES) vs. standard DOCK (DCEVDW+ES) scoring as evaluated on three large datasets (680–775 systems) from the SB2010 database. Enhanced pose identification was also observed using FPS (45.4% or 70.9%) compared with DCE (17.8%) methods to rank challenging crossdocking ensembles from carbonic anhydrase. Enrichment tests, for three representative systems, revealed FPSVDW+ES scoring yields significant early fold enrichment in the top 10% of ranked databases. For EGFR, top FPS poses are nicely accommodated in the molecular envelope defined by the reference in comparison with DCE, which yields distinct molecular weight bias toward larger molecules. Results from a representative virtual screen of ca. 1 million compounds additionally illustrate how ligands with footprints similar to a known inhibitor can readily be identified from within large commercially available databases. By providing an alternative way to rank ligand poses in a simple yet directed manner we anticipate that FPS scoring will be a useful tool for docking and structure‐based design. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
CD 8 Lineage-specific Regulation of Interleukin-7 Receptor Expression by the Transcriptional Repressor Gfi 1 *

Davinna L. Ligons, Ceren Tuncer, Brett A. Linowes, Izzet Mehmet Akcay, Sema Kurtulus, Emre Deniz, Belkis Atasever Arslan, Safak Isil Cevik, Hilary R. Keller, Megan A. Luckey, Lionel Feigenbaum, Tarik Möröy , Tulin Ersahin**, Rengul Atalay**, Batu Erman, and Jung-Hyun Park From the Experimental Immunology Branch, National Cancer Institute, Bethesda, Maryland 20892, the Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Tuzla, Istanbul 34956, Turkey, the Science Applications International Corporation-Frederick, National Cancer Institute–Frederick Cancer Research and Development Center, Frederick, Maryland 21702, the Institut de Recherches cliniques de Montréal, Département de microbiologie et immunologie, Université de Montréal, Montréal (Québec) H2W 1R7, Canada, the **Department of Molecular Biology and Genetics, Bilkent University, Bilkent, Ankara 06800 Turkey, and the Sabanci University, Nanotechnology Research and Application Center, SUNUM, Istanbul 34956, Turkey
Vertical ladder climbing by the HRP-2 humanoid robot

We report the results obtained from our trials in making the HRP-2 humanoid robot climb vertical industrial-norm ladders. We integrated our multi-contact planner and multi-objective QP control as basic components. First, a set of contacts to climb the ladder is planned off-line and provided as an input for a finite state machine that sequences tasks to be realized by our multi-objective model-based QP in closed-loop control. The trials we made revealed that hardware changes are to be made on the HRP-2, and the software has to be made more robust. Yet, we confirmed that HRP-2 has power capability to climb real industrial ladders, such as those found in nuclear power plants and large scale manufacturings (e.g. airliners, shipyards and buildings).
Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase

Abstract Reverse transcriptase (RT) catalyzes the conversion of the viral RNA into an integration-competent double-stranded DNA, with a variety of enzymatic activities that include the ability to displace a non-template strand concomitantly with polymerization. Here, using high-resolution optical tweezers to follow the activity of the murine leukemia Virus RT, we show that strand-displacement polymerization is frequently interrupted. Abundant pauses are modulated by the strength of the DNA duplex ∼8 bp ahead, indicating the existence of uncharacterized RT/DNA interactions, and correspond to backtracking of the enzyme, whose recovery is also modulated by the duplex strength. Dissociation and reinitiation events, which induce long periods of inactivity and are likely the rate-limiting step in the synthesis of the genome in vivo, are modulated by the template structure and the viral nucleocapsid protein. Our results emphasize the potential regulatory role of conserved structural motifs, and may provide useful information for the development of potent and specific inhibitors.
Problem based learning at the Nelson R Mandela School of Medicine

A problem-based learning curriculum was phased in to replace our traditional lecture-based curriculum in 2001. True integration, both vertically and horizontally of the basic sciences and clinical disciplines, is reflected in each unit of learning in the first three years. The teaching programme is centrally coordinated and students work in small groups while guided by clinical and non-clinical facilitators. In the last two years, teaching and learning becomes more clinical as students rotate through the clinical disciplines. Both formative and summative assessment (including OSCE and OSPE) is used. Students have to pass each independent, clinical assessment in their final year. This paper highlights the problems and solutions of our transition to PBL. We advocate that staff and students should collaborate in the review to allow resource poor countries to find a model suitable for their unique conditions. Our programme combines the advantages of both the PBL and the traditional pedagogies.
Attitude Determination for Small Satellites with Modest Pointing Constraints

This monograph reports on the development of the attitude determination backbone of the Ionospheric Observation Nanosatellite Formation (ION-F). Three spacecraft with similarly modest pointing constraints comprise the ION-F constellation. Pointing requirements for the constellation are dictated by the formation flying mission objective and communication demands. To satisfy pointing requirements the attitude control system for each spacecraft will require attitude estimates with accuracies on the order of 1 degree. An investigation into sensor suites capable of satisfying this requirement within the additional monetary, mass, and power constraints imposed by the ION-F program was carried out. Ultimately, a gyroless magnetometer-based Kalman filter was chosen as the attitude determination backbone. A high fidelity simulation created specifically for ION-F spacecraft revealed the filter was capable of attitude errors below 1.6◦ (1σ) and rate errors below 0.006 deg sec . Further tests using actual telemetered data from the Danish Oersted satellite were performed with satisfactory results. Other sensors may be added to this backbone to increase accuracy and speed filter convergence. For example, the possibility of incorporating solar panel data into the filter was examined. It was concluded that under fairly general conditions solar panel data speeds initial filter convergence and may also be used to estimate magnetometer mounting misalignments. Although designed for the ION-F constellation, the attitude determination system described in this paper is generically applicable to many small spacecraft in inclined low-earth orbit. The 1-2 degree accuracy of which the system is capable lends itself well to small satellite applications such as formation flying and imaging or docking with other spacecraft.
No evidence of HIV and SIV sequences in two separate lots of polio vaccines used in the first U.S. polio vaccine campaign.

We obtained sealed vials of two different polio vaccine lots, expiration date 1955, which were used in the first U.S. polio vaccine campaign. These early lots were pulled from the market because they contained live infectious poliovirus which caused polio in some of the vaccines. Theoretically, these vaccines could have contained other infectious retroviruses, including HIV. No viral sequences were detected using RT-PCR analyses with primers capable of amplifying chimpanzee SIV and HIV-1-related viruses nor with primers for macaque SIV, sooty mangabey SIV, and HIV-2-related viruses. Poliovirus sequences were readily amplified by RT-PCR, suggesting that the technique used would have detected SIV or HIV sequences, if present.
BeeMo, a Monte Carlo Simulation Agent for Playing Parameterized Poker Squares

We investigated Parameterized Poker Squares to approximate an optimal game playing agent. We organized our inquiry along three dimensions: partial hand representation, search algorithms, and partial hand utility learning. For each dimension we implemented and evaluated several designs, among which we selected the best strategies to use for BeeMo, our final product. BeeMo uses a parallel flat Monte-Carlo search. The search is guided by a heuristic based on hand patterns utilities, which are learned through an iterative improvement method involving Monte-Carlo simulations and optimized greedy search.
Design and synthesis of cationic Aib‐containing antimicrobial peptides: conformational and biological studies

Development of antimicrobial peptides has attracted considerable attention in recent years due to the excessive use of antibiotics, which has led to multiresistant bacteria. Cationic amphiphilic Aib‐containing peptide models Ac‐(Aib‐Arg‐Aib‐Leu)n‐NH2, n = 1–4, and sequential cationic polypeptides (Arg‐X‐Gly)n, X = Ala, Val, Leu, were prepared and studied for their antimicrobial and hemolytic activity, as well as for their proteolytic stability. Ac‐(Aib‐Arg‐Aib‐Leu)n‐NH2, n = 2, 3 and the polypeptide (Arg‐Leu‐Gly)n exhibited significant antimicrobial activity, and they were nontoxic at their MIC values and resistant, in particular the Aib‐peptide models, to enzymatic degradation. The conformational characteristics of the peptide models were studied by circular dichroism (CD). Structure‐activity relationship studies revealed the importance of the amphipathic α‐helical conformation of the reported peptides in inducing antimicrobial effects. It is concluded that peptide models comprising cationic amino acids (Arg), helicogenic and noncoding residues (Aib) and/or hydrophobic and helix‐promoting components (Leu) may lead to the development of antimicrobial therapeutics. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
The Medical Appointment Scheduler

In order to enhance our understanding of how to best improve patient care, it was necessary to initially identify key questions that patients ask most frequently by recording actual calls made by home hemodialysis patients to a dialysis clinic over a three-month period. From an initial analysis of the recorded conversations, one of the most frequent reasons for patient calls was for scheduling concerns. Since the use of automated systems often enable a quicker response to patients' needs and alleviate time demands on the personnel that have to answer these calls, an automated scheduling system was designed and implemented to address this concern. The SCHEDULER is a mixed-initiative spoken dialogue system that allows a patient to schedule an appointment with a provider over the telephone. The system was implemented using SPEECHBUILDER, a utility developed by the Spoken Language System group at M.I. T. that helps automatically configure human language technology servers to create a new conversational system. We describe the system architecture, general considerations in the design, and a preliminary evaluation of the system.
Lingual Luring by Mangrove Saltmarsh Snakes (Nerodia Clarkii Compressicauda)

Abstract Very few cases of predatory luring by squamate reptiles involve body parts other than the tail. Here, I report the use of the tongue by Mangrove Saltmarsh Snakes (Nerodia clarkii compressicauda) to lure prey, a behavior thus far adequately described for only one other snake species. Fishes are the only verified component of the diet of these snakes and are effectively attracted by the luring behavior. Lingual luring by these snakes is particularly unique in that the tongue is curled upon itself distally such that a conspicuous loop is formed at its terminus. The rapid oscillations typical of chemosensory tongue flicks are absent, though the terminal loop does exhibit some vertical and horizontal movement. The duration of luring tongue flicks is significantly greater than the duration of chemosensory tongue flicks.