Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Pockets: Inventory, Shape, and Comparison

The shape of the protein surface dictates what interactions are possible with other macromolecules, but defining discrete pockets or possible interaction sites remains difficult. First, there is the problem of defining the extent of the pocket. Second, one has to characterize the shape of each pocket. Third, one needs to make quantitative comparisons between pockets on different proteins. An elegant solution to these problems is to sort all surface and solvent points by travel depth and then collect a hierarchical tree of pockets. The connectivity of the tree is determined via the deepest saddle points between each pair of neighboring pockets. The resulting pocket surfaces tessellate the entire protein surface, producing a complete inventory of pockets. This method of identifying pockets also allows one to easily compute important shape metrics, including the problematic pocket volume, surface area, and mouth size. Pockets are also annotated with their lining residue lists and polarity and with other residue-based properties. Using this tree and the various shape metrics pockets can be merged, grouped, or filtered for further analysis. Since this method includes the entire surface, it guarantees that any pocket of interest will be found among the output pockets, unlike all previous methods of pocket identification. The resulting hierarchy of pockets is easy to visualize and aids users in higher level analysis. Comparison of pockets is done by using the shape metrics, avoiding the complex shape alignment problem. Example applications show that the method facilitates pocket comparison along mutational or time-dependent series. Pockets from families of proteins can be examined using multiple pocket tree alignments to see how ligand binding sites or how other pockets have changed with evolution. Our method is called CLIPPERS for complete liberal inventory of protein pockets elucidating and reporting on shape.
Double (antidrome) conduction in the central nervous system

In a paper presented to the Society last year, I drew attention to some striking instances of “long conduction” through the bulbospinal cord, and among others to the following singular one. If after transection over the bulbospinal axis the funiculus gracilis be excited, e. g. , at the calamus scriptorius, the excitation evokes movement (contraction, relaxation) in the idiolateral hind limb. If instead of f.gracilis the funiculus cuneatus be excited the movement (contraction, relaxation) is in the idiolateral forelimb.
An examination of sport fandom in Australia: Socialization, team identification, and fan behavior

To examine sport fandom in Australia, a convenience sample of 163 university students (62% males, 38% females, M = 21.3) attending a large, multi-sector institution located in a western suburb of Melbourne voluntarily completed a 25-item questionnaire survey which included the Sport Fandom Questionnaire (Wann, 2002) and the Sport Spectator Identification Scale (Wann and Branscombe, 1993). Descriptive and inferential statistics revealed that males chose ‘friends’ as their most influential sport fan socialization agent while females ranked friends, parents and school about the same. Male socialization agents were very important for both sexes with ‘father’ chosen most influential. Males scored higher on every measure of sport fandom behavior including attending sports events, watching sports on television, listening to sports on the radio, engaging in a sports conversation with others, and accessing sport information via the Internet. Australian Football League teams were chosen ‘favorite team’ by 81 percent of the total sample; selection was unrelated to the respondent’s sex. Compared with similar data obtained from US, Norwegian and Greek university student samples, these Australian students were judged greater sport consumers and more heavily identified with the sport fan role and a favorite team.
Quantum mechanics writ large

Some two centuries before the quantum revolution, Newton (1) suggested that corpuscles of light generate waves in an aethereal medium like skipping stones generate waves in water, with their motion then being affected by these aether waves. Times have changed. Light corpuscles are now known as photons, and the majority of physicists have dispensed with the notion of aether. Nevertheless, certain features of Newton's metaphor live on in one particular version of quantum mechanics. According to pilot wave theory, first proposed by de Broglie (2) and later developed by Bohm (3) with Einstein's encouragement, microscopic elements such as photons and electrons consist of both particle and wave, the former being guided by the latter. Although this physical picture has not been widely accepted, it has had some notable proponents, including Bell (4). Its principal appeal is that it restores realism and determinism to quantum mechanics, its weakness that the physical nature of the guiding wave field remains unclear. At the time that pilot wave theory was developed and then overtaken by the Copenhagen interpretation as the standard view of quantum mechanics, there was no macroscopic pilot wave analog to draw upon. Now there is.
Biofouling control using microparticles carrying a biocide

This study presents a new technological approach to minimize the use of antimicrobial (AMB) agents and their deleterious effects, based on the principle of drug-delivery systems whereby the AMB chemicals are transported on microparticles. The efficacy of microparticles carrying the quaternary ammonium compound (QAC), benzyldimethyldodecyl ammonium chloride (BDMDAC), was assessed against Pseudomonas fluorescens in both the planktonic and the biofilm state. The microparticles were prepared using a layer-by-layer (LBL) self-assembly technique. Oppositely charged molecules of polyethyleneimine (PEI), sodium polystyrene sulfonate (PSS), and BDMDAC were assembled on polystyrene (PS) cores. BDMDAC-coated particles were observed by CryoSEM and their composition analyzed by X-ray microanalysis. Zeta potential measurements indicated that changes in surface charge were compatible with a BDMDAC/particle interaction. This biocidal carrier structure had significant stability, verified by the release of only 15% of the BDMDAC when immersed in water for 18 months. Biocidal carrier activity was evaluated by determining the survival ratio of P. fluorescens planktonic and biofilm cells after different exposure periods to BDMDAC-coated particles. Tests with biofilm cells were also performed with the free QAC. An efficient AMB effect (minimum bactericidal concentration) against suspended cells was found for a concentration of 9.2 mg l−1 of BDMDAC on coated particles after incubation for 30 min and 6.5 mg l−1 of BDMDAC on coated particles after 60 min. Exposure of biofilms to PS-PEI/PSS/BDMDAC (0.87 mg l−1) resulted in a decrease in viability of 60.5% and 66.5% of the total biofilm population for 30 and 60 min exposure times, respectively. Exposure for 60 min to 6.33 mg l−1 and 11.75 mg l−1 of BDMDAC in PS-PEI/PSS/BDMDAC particles promoted inactivation of 80.6% and 87.2% of the total population, respectively. The AMB effects obtained with the application of free BDMDAC were statistically similar to those promoted by the application of BDMDAC coated particles. The overall results indicate that this novel AMB strategy has potential for the control of microbial growth of planktonic cells and biofouling. Moreover, the technique allows the reuse of AMB molecules and consequently reduces the environmental risks associated with excessive use of AMB agents, thereby providing real benefits to public health.
Could testosterone have a therapeutic role in prostate cancer?

PURPOSE To discuss the role of membrane androgen receptors and to investigate the potential role of testosterone-albumin conjugate in the prostate cancer (PCa) treatment. MATERIALS AND METHODS We identified studies published from 1990 onwards by searching the MEDLINE database of the National Library of Medicine. Initial search terms were "androgen receptors, cytoplasmic androgen receptor, and membrane androgen receptor" combined with "testosterone, testosterone-albumin conjugate, and prostate cancer treatment". RESULTS The androgen receptor plays a critical role in both development and progression of PCa. The latter is associated with changes in the androgen receptor axis and more precisely, with its conversion from a paracrine dependent signaling pathway for proliferation and survival of prostatic cells to an independent autocrine process. This malignant conversion is due to functional changes in which the androgen receptor activates not only normal genomic, but also novel non-genomic signaling pathways, which are not present in normal prostatic epithelial cells. Thus, treatments for neoadjuvant, adjuvant, and recurrent disease, all center on the regulation and manipulation of the androgen pathway. Recent discoveries however offer strong evidence of a direct apoptotic action induced by activation of the membrane androgen receptor by testosterone-albumin conjugates. CONCLUSION Investigation of the molecular pathways of apoptosis through activation of the membrane androgen receptors in the androgen-independent PCa cell is important on the one hand because future manipulation of this mechanism can help with understanding and interpreting unknown to date characteristics of PCa and on the other hand, can contribute to the establishment of activators of membrane androgen receptors. In addition, study of the testosterone-albumin complex can constitute the basis for future treatments for PCa.
The Efficacy of Telehealth-Delivered Speech and Language Intervention for Primary School-Age Children: A Systematic Review

The purpose of this article is to determine if telehealth-delivered speech-language pathology interventions are as effective as traditional in-person delivery for primary school-age children with speech and/or language difficulties. A systematic review was conducted (in accordance with PRISMA guidelines) using five databases, two journals and reference lists. Titles and abstracts were screened for inclusion, with relevant studies reviewed in full-text. Initial searches identified 132 articles. Following exclusion of non-relevant studies, seven articles remained for inclusion. Results revealed both telehealth and in-person participants made significant and similar improvements when treatment effects were measured through five of the six outcome measures. Findings showed there is limited but promising evidence to support telehealth for delivering speech-language pathology intervention services to school-age children. Whilst this is encouraging, particularly for rural children where in-person services are limited, more rigorous study designs are required to support the efficacy of telehealth for this population.
OF ERP SYSTEM IMPLEMENTATION – A CASE STUDY OF PROJECT-DRIVEN ENTERPRISE

Enterprise resource planning (ERP) systems are an application software implemented in a great number of manufacturing companies worldwide. The implementation of an ERP system is performed to integrate business processes, allocate company’s resources efficiently and provide important data for decision support. Implementing an ERP system is expensive and time-consuming. A lot of research activities are focused on key success factors of ERP implementations. But what does a successful implementation of an ERP system mean? If an ERP project is completed according to the schedule, the budget was not exceeded and the scope was realized, does this mean that the implementation was successful? The implementation of an ERP system is a long-term undertaking, and not only a short-term project that is finished just after the system installation. Especially for a project driven enterprise that realizes engineer-to-order production, the evaluation should encompass a long period of time. In this article a methodology of ERP system implementation dedicated for project driven enterprises is presented. The methodology is based on a set of assumptions and limitations that enable to indicate if the strategic goal of the ERP implementation is reached. The evaluation of ERP projects is based on the calculation of different productivity ratios of the enterprise in several periods. An illustrative example is given.
Grasping the meaning of leisure: developing a self-report measurement tool.

A self-report measurement tool for the assessment of what people feel when involved in leisure activities is described. The new instrument is composed of nine scales: Perceived freedom, Intrinsic motivation, Goal-orientation, Relation to work, Active-passive participation, Optimal incongruity, Social interaction, Perceived competence , and Discretionary time availability . In a sample of 335 subjects the scales showed high internal consistency, and confirmatory factor analysis supported the hypothesized internal structure. Multidimensional scaling techniques revealed three higher-order underlying dimensions: effort level, social interaction, and purpose. Future directions for developing the instrument are discussed, as well as implications for the conceptualization of leisure.
Quarkonium Production at the Tevatron through Soft Colour Interactions

The direct charmonium and bottomonium production rate observed at highpl in pp collisions at the Tevatron is factors of ten larger than predictions based on conventional perturbative &CD. We show that this excess can be accounted for by our model for soft colour interactions, previously introduced . to describe in a novel way the large rapidity gap events observed at HERA. (Submitted to Physical Review Letters) Typeset using REVTjjX *Work supported in part by the Swedish Natural Science Research Council and the U.S. Department of Energy, contract DE-AC03-76SF00515.
Development of Categorical Representations for "Above" and "Below" Spatial Relations in 3- to 7-Month-Old Infants.

A series of experiments examined the abilities of infants to form categorical representations for the spatial relations above and below. Experiment 1 provided evidence that 3- to 4-month-olds can form categorical representations for above and below when a diamond shape was presented above or below a horizontal bar. Experiments 2 and 3 showed that 3- and 4-month-olds did not form categorical representations for above and below when a number of discriminably different shapes (e.g., a diamond, a triangle, a dot) appeared above or below the bar. These more abstract categorical representations for above and below were formed by 6-to 7-month-olds (Experiment 4). The findings suggest an experientially or maturationally based trend, from concrete to abstract, in the categorical representation of common spatial relations.
Recovery from severe mental illness: an intrapersonal and functional outcome definition

To promote research and improved clinical practice, three criteria are proposed to define recovery from severe mental illness: hope, self-responsibility and 'getting on with life' beyond illness. Each of these criteria can be measured at the intrapsychic-subjective, interpersonal-behavioral,and environmental levels.The criteria were identified through cumulative experiences of a decade of clinical services research at the New Hampshire-Dartmouth Psychiatric Research Center, contributions from consumers and family advocates, and focus groups. Measures of each criterion are proposed through the use of extant assessment instruments such as the Beck Hopelessness Scale, Locus of Control Questionnaire, instrumental and social role functioning scales,and subjective ratings of quality of life. Collateral sources of information are required to assure that the measures of the criteria for recovery are reliable, accurate and valid. The criteria selected to define recovery have already instigated the use of a broad array of tools to assess the course and outcome of schizophrenia in research and clinical practice. Concentrating on the importance of self-responsibility as a criterion should have the spin-off benefit of encouraging psychiatrists to more actively involve their clients in a collaborative enterprise for pharmacotherapy, including education in disease management and shared decision-making. To promote recovery using the three component definition will require rehabilitation practitioners to provide services that should facilitate clients managing and directing their own lives with greater autonomy. Services that enable clients to develop the social and independent living skills needed for community reintegration will engender hope, self-responsibility, and the development of a functional person who has recovered from a disabling mental disorder. Operationalizing recovery should accelerate hypothesis-testing research on this construct, including determining the attributes of treatment and rehabilitation services that are associated with optimal states of recovery.
L2 stability for quantized linear systems with saturations

Abstract This paper deals with ultimate bounded stability analysis and stabilization conditions for systems involving input saturation and quantized control law, which corresponds to the state quantization case. The state feedback control design problem is then addressed. Theoretical results to ensure the ultimate boundedness and the L 2 stability of the closed-loop system are presented both in local as well as global contexts. The saturation and quantized nonlinearities are tackled through the use of some modified sector conditions. The proposed conditions are then cast in convex optimization problems aiming at maximizing the region of attraction of the closed-loop system and minimizing the set in which the closed-loop trajectories are ultimately bounded, maximizing the bound of admissible L 2 disturbances or maximizing the L 2 -gain from the disturbance to the regulated output.
Training and experience as predictors of job satisfaction and work motivation when using computers: a correlational study

Abstract This paper examines the extent to which the previous work experience and method of training to use computer systems augment the predictability of the motivation and satisfaction of computer users. A sample of 154 computer users are studied, utilizing a version of the Job Diagnostic Survey questionnaire (Hackman and Oldham 1975). The job characteristics model upon which the questionnaire is based contends that the internal work motivation and general job satisfaction of job holders can be predicted from core job characteristics (task identity, task significance, skill variety, autonomy, and feedback from the job itself)- Results show that type of training and previous experience add little more to the job-holder's job satisfaction and internal work motivation than is predicted by the job characteristics model. The implications of the results for the management and staffing of computer-based systems are noted. Limitations of the data are recognized.
A deep ROSAT survey - XII. The X-ray spectra of faint ROSAT sources

Optical spectroscopy has enabled us to identify the optical counterparts to over 200 faint X-ray sources to a flux limit of S(0.5 2keV ) = 4 × 10 15 ergs 1 cm 2 on 5 deep ROSAT fields. Here we present a spectral analysis of all the X-ray sources to investigate claims that the average source spectra harden at faint X-ray flux. From a hardness ratio analysis we confirm that the average spectra from 0.5 − 2keV harden from an equivalent photon index of = 2 . 2 at S(0.5 2keV ) = 1 ×10 13 ergs 1 cm 2 to ≃ 1.7 below 1 ×10 14 ergs 1 cm 2 . These spectral changes are due to the emergence of an unidentified source population rather than the class of X-ray QSOs already identified. The 128 QSOs detected so far show no evidence for spectral hardening over this energy range and retain a mean photon index of = 2 . 2. Recent work suggests that many of the remaining unidentified sources are X-ray luminous galaxies. Taking a subset identified as the most likely galaxy candidates we find that these show significantly harder spectra than QSOs. The emission line galaxies in particular show spectra more consistent with the residual X-ray background, with = 1 . 51 ±0.1 from 0.1 − 2keV. Individually the galaxies appear to be a mixture of absorbed and unabsorbed X-ray sources. Combined with recent cross-correlation results and work on the source number count distribution, these results suggest that we may be uncovering the missing hard component of the cosmic X-ray background.
Transition-Based Dependency Parsing Exploiting Supertags

Lexical information, including surface word form and part-of-speech (POS) information, plays a crucial role when predicting ambiguous dependency relationships in dependency parsing. However, for resolving dependency ambiguities, surface word information may be too sparse, while POS information may be too coarse. Supertags, which are lexical templates that represent rich syntactic information, have been shown to provide effective features at an intermediate level on the coarse-to-fine scale. In this work, we present a supertag design framework that allows us to instantiate various supertag sets based on the dependency structures. Using this framework, we instantiate various supertag sets and utilize them as features in transition-based dependency parsing systems. Performing experiments on the Penn Treebank and Universal Dependencies data sets, we show that our supertags are effective for transition-based parsers in multilingual parsing as well as English parsing. The comparison of the results of the different supertag sets shows that it is crucial to incorporate the head directionality, head labels, and dependent possession information in supertags to improve the parser performance.
Animating the Dance Archives

Dance notation systems such as Labanotation provide a means to record the scores that are necessary for dance reconstruction and archival recording. To make Labanotation scores more accessible to dancers, choreographers and researchers the LabanDancer system has been developed to translate Labanotation scores recorded in the LabanWriter editor into 3-d human figure animations. The challenges involved in developing this translator are discussed.