Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved Walker A Ser Residues in the Catalytic Sites of P-glycoprotein Are Critical for Catalysis and Involved Primarily at the Transition State Step*

P-glycoprotein mutants S430A/T and S1073A/T, affecting conserved Walker A Ser residues, were characterized to elucidate molecular roles of the Ser and functioning of the two P-glycoprotein catalytic sites. Results showed the Ser-OH is critical for MgATPase activity and formation of the normal transition state, although not for initial MgATP binding. Mutation to Ala in either catalytic site abolished MgATPase and transition state formation in both sites, whereas Thr mutants had similar MgATPase to wild-type. Trapping of 1 mol of MgADP/mol of P-glycoprotein by vanadate, shown here with pure protein, yielded full inhibition of ATPase. Thus, congruent with previous work, both sites must be intact and must interact for catalysis. Equivalent mutations (Ala or Thr) in the two catalytic sites had identical effects on a wide range of activities, emphasizing that the two catalytic sites function symmetrically. The role of the Ser-OH is to coordinate Mg2+ in MgATP, but only at the stage of the transition state are its effects tangible. Initial substrate binding is apparently to an “open” catalytic site conformation, where the Ser-OH is dispensable. This changes to a “closed” conformation required to attain the transition state, in which the Ser-OH is a critical ligand. Formation of the latter conformation requires both sites; both sites may provide direct ligands to the transition state.
Recurrent excitation in neocortical circuits

The majority of synapses in the mammalian cortex originate from cortical neurons. Indeed, the largest input to cortical cells comes from neighboring excitatory cells. However, most models of cortical development and processing do not reflect the anatomy and physiology of feedback excitation and are restricted to serial feedforward excitation. This report describes how populations of neurons in cat visual cortex can use excitatory feedback, characterized as an effective "network conductance", to amplify their feedforward input signals and demonstrates how neuronal discharge can be kept proportional to stimulus strength despite strong, recurrent connections that threaten to cause runaway excitation. These principles are incorporated into models of cortical direction and orientation selectivity that emphasize the basic design principles of cortical architectures.
Verb Classes and Alternations in Bangla, German, English, and Korean

In this report, we investigate the relationship between the semantic and syntactic properties of verbs. Our work is based on the English Verb Classes and Alternations of (Levin, 1993). We explore how these classes are manifested in other languages, in particular, in Bangla, German, and Korean. Our report includes a survey and classification of several hundred verbs from these languages into the cross-linguistic equivalents of Levin''s classes. We also explore ways in which our findings may be used to enhance WordNet in two ways: making the English syntactic information of WordNet more fine-grained, and making WordNet multilingual.
ReBA: a tool for generating binary adapters for evolving java libraries

Although in theory the APIs of software libraries and frameworks should be stable, they change in practice. This forces clients of the library API to change as well, making software maintenance expensive. Changing a client might not even be an option if its source code is missing or certain policies forbid its change. By giving a library both the old and the new API, clients can be shielded from API changes and can run with the new version of the library. This demo presents our tool, ReBA, that automatically generates compatibility layers between new library APIs and old clients. In the first stage, ReBA generates another version of the library, called adapted-library, that supports both the old and the new APIs. In the second stage, ReBA shrinks the adapted-library into a minimal, client-specific compatibility layer containing only classes truly required by the client. Evaluation on controlled experiments and case studies using Eclipse core libraries shows that our approach effectively adapts clients to new library versions, and is efficient.
The transplanted hairline: leg room for improvement.

BACKGROUND The large caliber of head hair in hair transplantation imparts a coarse hairline, whereas natural hairlines are typically softer. In hirsute individuals, transplantation of leg hair to the hairline may result in a superior aesthetic appearance. OBSERVATION A total of 1025 leg hair follicles in 1 patient were grafted to an area 0.5 to 1.0 cm in front of and 0.5 to 1.0 cm internal to the vanguard hair of the original hairline and temporal recesses; the other patient received approximately 1000 leg hairs and 600 head hairs to advance and soften his hairline and to create a custom widow's peak. Transplantation resulted in a fully grown and soft-looking hairline after 9 months in the first patient, with growth of 75% to 80% of the transplanted leg hair. The mean length of the transplanted leg hair was longer than the length of the original leg hair, with less curliness but similar hair width. Transplanted leg hair width was significantly finer compared with existing head hair width. After 4 years, results were sustained, minimizing concerns that subsequent hair loss might result from leg hair cycle variations. In the second patient, similar results were observed at 3 years. CONCLUSION The use of leg hair in transplantation provides additional options in patients with hairlines that need to be refined.
A Novel Window-Based Corner Detection Algorithm for Gray-Scale Images

In computer vision, the corners of an object play an important role in shape representation and analysis. In this paper, we describe a new approach to corner detection in a digital image based on the assumption that corners are image points with high information content, and hence corners in an image exist in the regions having considerably high intensity variations. Consequently, a complex corner response function (CRF) is computed only within the regions with considerable high intensity variation instead of entire image reducing the computational cost of the whole procedure. Experiments are conducted with the help of a few images showed the efficiency of the technique, both in terms of execution time and false positive corners.
Input data reduction for the prediction of financial time series

The prediction of financial time series using artificial neural networks has been the subject of many publications, even if the predictability of financial series remains a subject of scientific debate in the financial literature. Facing this difficulty, analysts often consider a large number of exogenous indicators, which makes the fitting of neural networks extremely difficult. In this paper, we analyse how to aggregate a large number of indicators into a smaller number using (possibly nonlinear) projection methods. Nonlinear projection methods are shown to be equivalent to linear principal component analysis when the prediction tool used on the new variables is linear. The methodology developed in this paper is validated on data from the BEL20 (Belgian top-20) market index.
Global Transcriptome Analysis of the Cold Shock Response of Shewanellaoneidensis MR-1 and Mutational Analysis of Its ClassicalCold ShockProteins

ABSTRACT This study presents a global transcriptional analysis of the cold shock response of Shewanella oneidensis MR-1 after a temperature downshift from 30°C to 8 or 15°C based on time series microarray experiments. More than 700 genes were found to be significantly affected (P ≤ 0.05) upon cold shock challenge, especially at 8°C. The temporal gene expression patterns of the classical cold shock genes varied, and only some of them, most notably so1648 and so2787, were differentially regulated in response to a temperature downshift. The global response of S. oneidensis to cold shock was also characterized by the up-regulation of genes encoding membrane proteins, DNA metabolism and translation apparatus components, metabolic proteins, regulatory proteins, and hypothetical proteins. Most of the metabolic proteins affected are involved in catalytic processes that generate NADH or NADPH. Mutational analyses confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also indicated that So1648 may function only at very low temperatures.
Improving web database search incorporating users query information

The growing importance and need of data processing for information extraction is vital for Web databases. Due to the sheer size and volume of databases, retrieval of relevant information as needed by users has become a cumbersome process. Information seekers are faced by information overloading - too many result sets are returned for their queries. Moreover, too few or no results are returned if a specific query is asked. This paper proposes a ranking algorithm that gives higher preference to a user's current search and also utilizes profile information in order to obtain the relevant results for a user's query.
Transmembrane Topology Pattern and Detection of Transmembrane Protein Functions

Transmembrane (TM) proteins (TMPs) have important roles in the biological organisms [1, 2]. With the rapid increasing of the number of TMPs, a lot of efforts are made in attempt to classify TMP functions by sequence analysis, and in fact, some databases aimed for it have been constructed (e.g., Pfam [3]). Which characteristics of TMP could provide us important clues to its function? We suppose that the TMP topology information that is readily available in the sequence data is a good prospect for this purpose. In this study, we assume that a TMP function is defined by its TM topology: the number of transmembrane segments (tms), loop length and N-terminus location. In order to detect TMP functions, we especially focus on its loop length [4, 5] and simplify TM topology by classifying the loop length into two categories (i.e., “short” and “long”) and express it as the topology pattern. Then we examine how TMP functions correspond to topology patterns.
Biocompatibility of precious metals for medical applications

Abstract: This chapter will firstly look at the terminology that defines ‘biocompatibility’. It will then look at how, where, why and in what forms precious metals are used in the human body, and will look at reports in the literature that show acceptable and unacceptable biological reactions to precious metals in the body. The effect of alloying and the microstructure of precious metals (alloy preparation) on biocompatibility will also be discussed. Finally, the future of precious metals for medical applications will be debated.
CuteForce – Deep Deterministic HPSG Parsing

We present a deterministic HPSG parser capable of processing text incrementally with very fast parsing times. Our system demonstrates an efficient data-driven approach that achieves a high level of precision. Through a series of experiments in different configurations, we evaluate our system and compare it to current state-of-the-art within the field, and show that high quality deterministic parsing is realistic even for a 'deep' unification-based precision grammar.
Elimination Techniques of Redundant Data Transfers Among GPUs and CPU on Recursive Stream-Based Applications

Applying the stream-based computing approach, the general purpose computing on graphics processing units has become to be considered as a breakthrough to overcome the performance bottleneck as seen in the recent CPU architecture. However, the program potentially includes the data transfer overhead if it has recursive I/Os. During the recursive operation in the GPU-based program, the output streams are copied to the input ones and this overhead degrades the performance. This paper proposes the best method to eliminate the transfer overheads and shows design and implementation of the method based on CUDA and OpenCL. The experimental evaluation using realistic applications shows the method eliminates the transfer overhead and the method exploits the potential performance of GPU.
Computing Crime: Information Technology, Police Effectiveness and the Organization of Policing

How does information technology (IT) affect the organization of police work? How does it in turn affect police crime-fighting effectiveness? To answer these questions, we construct a new panel data set of police departments covering 1987-2003. We find that while IT adoption had substantial effects on a wide range of police organizational practices, it had, by itself, a negligible impact on crime-fighting effectiveness. These results are robust to various methods for controlling for agency-level characteristics and the endogeneity of IT use. We then suggest and test two explanations for this puzzle. First, we demonstrate that use of a particular technology, computerized record-keeping, increased recorded crime rates. Second, we provide evidence that IT investments only had a substantial impact on crime clearance rates and crime rates when undertaken as part of a broad set of complementary organizational practices such as those in the Compstat program.
Exercise training leads to a reduction of elevated myostatin levels in patients with chronic heart failure

Background: In chronic heart failure (CHF), cardiac cachexia is often associated with the terminal stage of this disease. In animal studies it has been demonstrated that myostatin, a key regulator of skeletal muscle mass, is elevated in advanced stages of this syndrome. Design: The aim of the present study was to investigate the expression of myostatin in patients with late stage CHF (NYHA IIIb) in comparison to healthy subjects. Furthermore the effects of physical exercise on myostatin were analyzed. Methods: Twenty-four patients were either randomized to a sedentary control group (CHF-S) or exercise training (CHF-E). At baseline and after 12 weeks mRNA and myostatin protein in the peripheral skeletal muscle as well as myostatin serum concentration were measured. Furthermore 12 age-matched healthy men were compared to all patients at baseline (HC). Results: CHF patients showed a two-fold increase of myostatin mRNA (p = 0.05) and a 1.7-fold (p = 0.01) augmentation of protein content in skeletal muscle compared to healthy subjects. In late-stage CHF, exercise training led to a 36% reduction of the mRNA and a 23% decrease of the myostatin protein compared to baseline. The serum concentration of myostatin revealed no significant alteration between the groups. Conclusion: In the skeletal muscle, myostatin increases significantly in the course of CHF. The observed effects of a significant reduction of myostatin in skeletal muscle after 12 weeks of exercise training demonstrate the reversibility of molecular changes that might be able to halt the devastating process of muscle wasting in chronic heart failure.
Formation of Monoterpenes in Antirrhinum majus and Clarkia breweri Flowers Involves Heterodimeric Geranyl Diphosphate Synthases

The precursor of all monoterpenes is the C10 acyclic intermediate geranyl diphosphate (GPP), which is formed from the C5 compounds isopentenyl diphosphate and dimethylallyl diphosphate by GPP synthase (GPPS). We have discovered that Antirrhinum majus (snapdragon) and Clarkia breweri, two species whose floral scent is rich in monoterpenes, both possess a heterodimeric GPPS like that previously reported from Mentha piperita (peppermint). The A. majus and C. breweri cDNAs encode proteins with 53% and 45% amino acid sequence identity, respectively, to the M. piperita GPPS small subunit (GPPS.SSU). Expression of these cDNAs in Escherichia coli yielded no detectable prenyltransferase activity. However, when each of these cDNAs was coexpressed with the M. piperita GPPS large subunit (GPPS.LSU), which shares functional motifs and a high level of amino acid sequence identity with geranylgeranyl diphosphate synthases (GGPPS), active GPPS was obtained. Using a homology-based cloning strategy, a GPPS.LSU cDNA also was isolated from A. majus. Its coexpression in E. coli with A. majus GPPS.SSU yielded a functional heterodimer that catalyzed the synthesis of GPP as a main product. The expression in E. coli of A. majus GPPS.LSU by itself yielded active GGPPS, indicating that in contrast with M. piperita GPPS.LSU, A. majus GPPS.LSU is a functional GGPPS on its own. Analyses of tissue-specific, developmental, and rhythmic changes in the mRNA and protein levels of GPPS.SSU in A. majus flowers revealed that these levels correlate closely with monoterpene emission, whereas GPPS.LSU mRNA levels did not, indicating that the levels of GPPS.SSU, but not GPPS.LSU, might play a key role in regulating the formation of GPPS and, thus, monoterpene biosynthesis.
K-nearest-neighbor conditional entropy approach for the assessment of the short-term complexity of cardiovascular control

Complexity analysis of short-term cardiovascular control is traditionally performed using entropy-based approaches including corrective terms or strategies to cope with the loss of reliability of conditional distributions with pattern length. This study proposes a new approach aiming at the estimation of conditional entropy (CE) from short data segments (about 250 samples) based on the k-nearest-neighbor technique. The main advantages are: (i) the control of the loss of reliability of the conditional distributions with the pattern length without introducing a priori information; (ii) the assessment of complexity indexes without fixing the pattern length to an arbitrary low value. The approach, referred to as k-nearest-neighbor conditional entropy (KNNCE), was contrasted with corrected approximate entropy (CApEn), sample entropy (SampEn) and corrected CE (CCE), being the most frequently exploited approaches for entropy-based complexity analysis of short cardiovascular series. Complexity indexes were evaluated during the selective pharmacological blockade of the vagal and/or sympathetic branches of the autonomic nervous system. We found that KNNCE was more powerful than CCE in detecting the decrease of complexity of heart period variability imposed by double autonomic blockade. In addition, KNNCE provides indexes indistinguishable from those derived from CApEn and SampEn. Since this result was obtained without using strategies to correct the CE estimate and without fixing the embedding dimension to an arbitrary low value, KNNCE is potentially more valuable than CCE, CApEn and SampEn when the number of past samples most useful to reduce the uncertainty of future behaviors is high and/or variable among conditions and/or groups.
THE HARAPPAN QUESTION

One of the major problems of interpretation of earl y Indian history has been the inconsistencies between the Harappan (Indu s Valley) civilisation and the Rigvedic literature. Problems arise from th e fact that the Harappan Civilisation was at its peak around second millenni um BC (Allchin and Allchin, 1989 page 131). The period of creation of the Rigveda has also been put around 4000 to 2000 BC, though the writing down of the text has been dated to a much later period around 2000 BC or later. The Rigvedic literature and its subsequent developments have als o been in the Indian subcontinent. There has therefore been a strong tem ptation to connect the Harappans to the Vedic Civilisation. However, there are several problems with this association, most graphically portrayed i n the ‘horse problem’ (Thapar, 2003). Horses are integral to most Rigvedi c ritualistic customs while they are absent in the Harappan sites. There are several other problems also. We re-visit this controversy in the light of some recent developments and suggest that the Harappans belonge d to the ancient Homo sapiens who separated from the humans migratin g from Africa as early as sixty thousand years ago and travelled alo ng the coast of the Arabian Sea (Wells, 2003). This group lost touch wi th the group that migrated to the Mediterranean and evolved independe ntly of them. We suggest that it was this group that set up the Hara ppan civilisation. We suggest that the group that went to the Mediterrane an eventually moved east at the end of the Ice ages and passing through northern Iraq, Iran and Afghanistan entered India (the Indo – Iranians) whe re they met the earlier migrants who had come along the seas. They met at t he Harappan sites sometime around two and a half thousand years BC. W e base this suggestion on new data on the genetic make up of ab original Indian tribes (Thangaraj et al., 2002) and other studies of human migration, dating of separation of languages (Gray and Atkinson, 2003) a nd broad based studies of prehistoric human evolution (Mithen, 200 3) as well as other evidence about the appearance of horses in Asia, et c. We propose that the Vedas were composed by the Indo Iranian but they in cluded upon the learning of the Harappans and this mix of knowledge is also visible in the Vedic literature, especially in the astronomical in formation in the literature.
Attention Deficit Hyperactivity Disorder - A Review, Dental Implications and Treatment Recommendations for Dental Professionals

Attention deficit hyperactivity disorder (ADHD) is a highly prevalent neurodevelopmental disorder in childhood. It is characterized by definite behavioral patterns of inattention, impulsivity and hyperactivity, which might lead to performance problems in the social, educational, or work environments. This article reviews the current evidence about the diagnosis and treatment of children and adolescents with ADHD based on the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition. Along with the discussion of etiology, classification, diagnosis and treatment approaches based on a survey of web tools primarily the MEDLINE database, the article also aims at reviewing the dental implications and recommendations for dental practitioners regarding management of children with ADHD
IceWind Inter-comparison of Icing Production Loss Models

General information Publication status: Published Organisations: Department of Wind Energy, Meteorology, Wind Energy Systems, Department of Electrical Engineering, Center for Electric Power and Energy, Energy Analytics and Markets, Kjeller Vindteknikk AS, VTT Technical Research Centre of Finland, WeatherTech Scandinavia AB, Vestas Wind Systems AS Contributors: Davis, N. , Hahmann, A. N. , Clausen, N. , Pinson, P., Zagar, M. , Byrkjedal, Ø. , Karlsson, T. , Wallenius, T. , Turkia, V. , Söderberg, S. , Baltscheffsky, M. Publication date: 2014 Media of output: PowerPoint
WoLFram- A Word Level Framework for Formal Verification

Due to high computational costs of formal verification on pure Boolean level, proof techniques on the word level, like Satisfiability Modulo Theories (SMT), were proposed. Verification methods originally based on Boolean satisfiability (SAT) can directly benefit from this progress. In this work we present the word level framework WoLFram that enables the development of applications for formal verification of systems independent of the underlying proof technique. The framework is partitioned into an application layer, a core engine and a back-end layer. A wide range of applications is implemented, e.g.~equivalence and property checking including algorithms for coverage/property analysis, debugging and robustness checking. The back-end supports Boolean as well as word level techniques, like SMT and Constraint Solving (CSP). This makes WoLFram a stable backbone for the development and quick evaluation of emerging verification techniques.