Miracle-dz/UniFAR-FTUs huggingface dataset:
Overall Performance of Functional Site Comparison Cutoffs Number of Matches Dali Z Score PINTS E Value Dali PINTS Both Only Dali Only

hydrolases (Wilson et al., 2004). Fold similarities thus Assigning function to structures is an important asoften require additional investigation of key residues pect of structural genomics projects, since they frebefore functions can be inferred (Babbitt, 2003). quently provide structures for uncharacterized proTo assign functions more explicitly, several methods teins. Similarities uncovered by structure alignment have been developed to look for similarities between can suggest a similar function, even in the absence functional sites, regardless of whether or not there is a of sequence similarity. For proteins adopting novel similarity in overall fold (e.g., Artymiuk et al., 1994a; folds or those with many functions, this strategy can Kleywegt, 1999; Russell, 1998; Wallace et al., 1997), and fail, but functional clues can still come from compariwe have recently presented a statistical model for such son of local functional sites involving a few key researches (Stark et al., 2003). Application of these methsidues. Here we assess the general applicability of ods has uncovered many interesting examples (e.g., functional site comparison through the study of 157 Lorentzen et al., 2003; Sanishvili et al., 2003), though proteins solved by structural genomics initiatives. For there is still no general picture of their applicability based 17, the method bolsters confidence in predictions made on an analysis of a large test set. based on overall fold similarity. For another 12 with There are an increasing number of protein structures new folds, it suggests functions, including a putative of unknown function: between 2001 and 2003, the numphosphotyrosine binding site in the Archaeal protein ber of structural genomics protein structures has risen Mth1187 and an active site for a ribose isomerase. from only 3 to 228, and in the first four months of this The approach is applied weekly to all new structures, year, already 164 structures became available (Berman et providing a resource for those interested in using al., 2000). This makes automated approaches to assign structure to infer function. function on a large scale highly relevant in structural biol-
Spectroscopic and Imaging Study of Combined W and Mo$X$-pinches at 1 MA$Z$-pinch Generators

Experiments with X-pinches made with both Mo and W wires have been performed on 1-MA pulsed power generators at Cornell University and University of Nevada, Reno. X-ray images and spectra have been studied and compared for three different configurations of X-pinch loads with Mo and W wires. For all X-pinches, the image size decreases with decreasing wavelength and photoconducting diode (PCD) signals show multiple bursts except for one variant of the mixed Mo and W configurations. Time-gated, as well as time-integrated, images indicate the presence of radiation from energetic electrons. Previous experience with application of L-shell Mo modeling to various Z- and X-pinch experiments helped to determine plasma parameters in the X-pinches studied here, and permitted identification of M-shell W spectral features useful for plasma parameter estimation
Monte Carlo Sensitivity Analysis of Unknown Parameters in Hazardous Materials Transportation Risk Assessment

The US Department of Transportation was interested in the risks associated with transporting Hydrazine in tanks with and without relief devices. Hydrazine is both highly toxic and flammable, as well as corrosive. Consequently, there was a conflict as to whether a relief device should be used or not. Data were not available on the impact of relief devices on release probabilities or the impact of Hydrazine on the likelihood of fires and explosions. In this paper, a Monte Carlo sensitivity analysis of the unknown parameters was used to assess the risks associated with highway transport of Hydrazine. To help determine whether or not relief devices should be used, fault trees and event trees were used to model the sequences of events that could lead to adverse consequences during transport of Hydrazine. The event probabilities in the event trees were derived as functions of the parameters whose effects were not known. The impacts of these parameters on the risk of toxic exposures, fires, and explosions were analyzed through a Monte Carlo sensitivity analysis and analyzed statistically through an analysis of variance. The analysis allowed the determination of which of the unknown parameters had a significant impact on the risks. It also provided the necessary support to a critical transportation decision even though the values of several key parameters were not known.
Balanced Dual Composite Right/Left-Handed Microstrip Line With Modified Complementary Split-Ring Resonators

This letter presents a dual composite right/left-handed microstrip line loaded with modified complementary split-ring resonators. In this particular case, the well-known resonant particle employed has been capacitively loaded in order to obtain a balanced frequency response. The inclusion of this capacitive element has two main effects. On the one hand, the right-and left-handed bands are interchanged; on the other hand, the possibility to control the position of the right-handed band, while maintaining the left-handed one unaltered. Consequently, it is relatively simple to design balanced transmission lines with improved bandwidth and reconfigurable properties. In addition, the equivalent circuit that describes the electromagnetic behavior of the structure has been obtained. Finally, a prototype has been fabricated and measured to confirm experimentally the validity of the proposed design.
Signaling of Apoptosis through TLRs Critically Involves Toll/IL-1 Receptor Domain-Containing Adapter Inducing IFN-β, but Not MyD88, in Bacteria-Infected Murine Macrophages1

TLRs are important sensors of the innate immune system that serve to identify conserved microbial components to mount a protective immune response. They furthermore control the survival of the challenged cell by governing the induction of pro- and antiapoptotic signaling pathways. Pathogenic Yersinia spp. uncouple the balance of life and death signals in infected macrophages, which compels the macrophage to undergo apoptosis. The initiation of apoptosis by Yersinia infection specifically involves TLR4 signaling, although Yersinia can activate TLR2 and TLR4. In this study we characterized the roles of downstream TLR adapter proteins in the induction of TLR-responsive apoptosis. Experiments using murine macrophages defective for MyD88 or Toll/IL-1R domain-containing adapter inducing IFN-β (TRIF) revealed that deficiency of TRIF, but not of MyD88, provides protection against Yersinia-mediated cell death. Similarly, apoptosis provoked by treatment of macrophages with the TLR4 agonist LPS in the presence of a proteasome inhibitor was inhibited in TRIF-defective, but not in MyD88-negative, cells. The transfection of macrophages with TRIF furthermore potently promoted macrophage apoptosis, a process that involved activation of a Fas-associated death domain- and caspase-8-dependent apoptotic pathway. These data indicate a crucial function of TRIF as proapoptotic signal transducer in bacteria-infected murine macrophages, an activity that is not prominent for MyD88. The ability to elicit TRIF-dependent apoptosis was not restricted to TLR4 activation, but was also demonstrated for TLR3 agonists. Together, these results argue for a specific proapoptotic activity of TRIF as part of the host innate immune response to bacterial or viral infection.
Development and Evaluation of pH-Responsive Cyclodextrin-Based in situ Gel of Paliperidone for Intranasal Delivery

Paliperidone (PLPD) is approved for treatment and management of schizophrenia. The current study demonstrates the potential of in situ gel of PLPD for nasal delivery. The permeation of drug through sheep nasal mucosa was analyzed since the nose-to-brain pathway has been indicated for delivering drugs to the brain. The carbopol 934 (CP)- and hydroxypropyl methyl cellulose K4M (HPMC)-based in situ gels containing 0.2% CP and 0.4% w/v HPMC were optimized using experimental design software. The use of hydroxypropyl-β-cyclodextrin (HP-β-CD) in nasal permeation of drug was investigated. Transmucosal permeation of PLPD was examined using sheep nasal mucosa. The in situ gels of PLPD exhibited satisfactory mucoadhesion and showed sustained drug release. The mucocilliary toxicity and histopathological examination confirmed that the nasal mucosa architecture remains unaffected after treatment with PLPD in situ gel. The formulation containing HP-β-CD complex of PLPD exhibited higher rate of drug permeation through sheep nasal mucosa revealing the role of HP-β-CD as nasal absorption enhancer. Thus, CP- and HPMC-based pH-triggered in situ gel containing HP-β-CD-drug inclusion complex demonstrates a novel nasal delivery of PLPD.
Molecular analysis of highly enriched populations of T-cell-depleted monocytes

CD4+ T lymphocytes and monocytes/macrophages are important components of the immune system. Blood monocytes are usually targeted for studies of the human macrophage lineage cells because of their accessibility through blood sampling. Most separation techniques currently available to obtain human monocytes either require large volumes of blood or do not yield a monocyte fraction sufficiently depleted of other cell types. We have developed a simple strategy to isolate a highly enriched population of monocytes from small volumes (< 6 ml) of peripheral blood by using an anti-CD14 monoclonal antibody and magnetic microspheres. Yields of monocytes ranged from 75 to 80% of CD14+ cells in peripheral blood. CD4+ T cells were subsequently selected from the monocyte-depleted peripheral blood by using an anti-CD4 monoclonal antibody and immunomagnetic beads. The effectiveness of immunomagnetic selection to yield a monocyte population highly depleted of T cells was analyzed by using a sensitive molecular strategy based on PCR amplification and detection of T-cell receptor (TCR) gene rearrangements. The relative frequency of rearranged TCRs within the monocyte population was compared with the frequency of rearranged TCRs within the CD4+ T-cell fraction from the same individual. Molecular analysis indicated that a viable monocyte population which contains fewer than 2% residual T lymphocytes can be consistently selected from small aliquots of blood.
MODIFICATION OF DIE CAST HYPOETECTIC AL-SI ALLOY WITH DIFFERENT SOURCES OF NICKEL AND ITS EFFECT ON MECHANICAL PROPERTIES

The mechanical properties of Al-Si alloys are strongly influenced by the size, shape and distribution of Si phase present in the microstructure. In order to improve the mechanical properties these alloys subjected to modification. Normal additions like those that Na, P, Ti B, Sr etc used for this purpose but in present investigation, two sources of Ni like 5wt% NiCl2.6H2O and 5wt % NiCl2 added which can alter the microstructure and mechanical properties similarly as the addition of Na, P, Ti, B, Sr etc. The hardness value remains almost same but tensile strength and % elongation improves very well after the additions of 5wt% NiCl2.6H2O and 5 wt% NiCl2.
Exploring why some terminally ill people die in hospital when home was their preferred choice

Objective This small study was designed to gain a better understanding of issues that led to hospital admission of palliative care clients who had a preference for home death, but died in hospital. Design A mixed method approach was chosen for the study using descriptive analysis of routinely collected client demographic and clinical data, and conventional content analysis of case note entries. Setting The study was undertaken in two community based palliative care services located in rural South Australia. Subjects.The case notes of fourteen deceased adults registered with the Northern Yorke Peninsula and Port Pirie Palliative Care Services, with a recorded preferred site of death (PSD) of home and who died in hospital were studied. Main outcome measure Understanding of issues that may have led to hospital admission of palliative care clients who had a preference for home death but who died in hospital. Results The findings reported here focus only on the qualitative aspect of the study. Issues that may lead to hospital. admission include unstable symptoms, deteriorating condition, client/caregiver decision making, lack of services over twenty four hours and the caregiver’s ability to manage client care. Conclusion Services can now consider these findings and develop local strategies to improve support for clients with apreference to die at home, and in particular, those that focus on improving caregiver training and information.
Feasibility and reproducibility of neurochemical profile quantification in the human hippocampus at 3 T

Hippocampal dysfunction is known to be associated with several neurological and neuropsychiatric disorders such as Alzheimer's disease, epilepsy, schizophrenia and depression; therefore, there has been significant clinical interest in studying hippocampal neurochemistry. However, the hippocampus is a challenging region to study using 1H MRS, hence the use of MRS for clinical research in this region has been limited. Our goal was therefore to investigate the feasibility of obtaining high‐quality hippocampal spectra that allow reliable quantification of a neurochemical profile and to establish inter‐session reproducibility of hippocampal MRS, including reproducibility of voxel placement, spectral quality and neurochemical concentrations. Ten healthy volunteers were scanned in two consecutive sessions using a standard clinical 3 T MR scanner. Neurochemical profiles were obtained with a short‐echo (TE = 28 ms) semi‐LASER localization sequence from a relatively small (~4 mL) voxel that covered about 62% of the hippocampal volume as calculated from segmentation of T1‐weighted images. Voxel composition was highly reproducible between sessions, with test–retest coefficients of variation (CVs) of 3.5% and 7.5% for gray and white matter volume fraction, respectively. Excellent signal‐to‐noise ratio (~54 based on the N‐acetylaspartate (NAA) methyl peak in non‐apodized spectra) and linewidths (~9 Hz for water) were achieved reproducibly in all subjects. The spectral quality allowed quantification of NAA, total choline, total creatine, myo‐inositol and glutamate with high scan–rescan reproducibility (CV ≤ 6%) and quantification precision (Cramér–Rao lower bound, CRLB < 9%). Four other metabolites, including glutathione and glucose, were quantified with scan–rescan CV below 20%. Therefore, the highly optimized, short‐echo semi‐LASER sequence together with FASTMAP shimming substantially improved the reproducibility and number of quantifiable metabolites relative to prior reports. In addition, the between‐session variation in metabolite concentrations, as well as CRLB, was lower than the between‐subject variation of the concentrations for most metabolites, indicating that the method has the sensitivity to detect inter‐individual differences in the healthy brain. Copyright © 2015 John Wiley & Sons, Ltd.
Information Flows at OS Level Unmask Sophisticated Android Malware

The detection of new Android malware is far from being a relaxing job. Indeed, each day new Android malware appear in the market and it remains difficult to quickly identify them. Unfortunately users still pay the lack of real efficient tools able to detect zero day malware that have no known signature. The difficulty is that most of the existing approaches rely on static analysis coupled with the ability of malware to hide their malicious code. Thus, we believe that it should be easier to study what malware do instead of what they contain. In this article, we propose to unmask Android malware hidden among benign applications using the observed information flows at the OS level. For achieving such a goal, we introduce a simple characterization of all the accountable information flows of a standard benign application. With such a model for benign apps, we lead some experiments evidencing that malware present some deviations from the expected normal behavior. Experiments show that our model recognizes most of the 3206 tested benign applications and spots most of the tested sophisticated malware (ransomware, rootkits, bootkit).
The relationship between pre-fitting expectations and willingness to use hearing aids

Hearing-aid use in the elderly population is problematic since not all people who would benefit from hearing aids actually obtain one. In this study, the relationship between pre-fitting expectations and willingness to use hearing aids is addressed. One hundred adult hearing aid candidates (mean age 68.6 years) were randomly recruited from eight different private ENT practices. The subjects completed a questionnaire comprising a number of different aspects of expectation and some additional variables potentially influencing willingness to use hearing aids. Based on the outcome of the questionnaire a linear regression model predicting motivation to use hearing aids was calculated and evaluated. Among the 11 parameters evaluated three contributed significantly to the model of willingness. The three predictor variables were expectations towards improvement of quality of life, stigmatization, and self-rated hearing ability. They accounted for about 55% of the variability in the data for willingness. Examination of a sub-sample three months after the survey had taken place revealed a distinct relationship between willingness and the decision to obtain or decline hearing aids. In conclusion, the results strongly encourage supporting positive expectations in order to motivate individuals with hearing impairment to use hearing systems.
Front-Back Confusion Resolution in 3D Sound Localization with HRTF Databases

Sound localization plays an important role in everyday life of a human for as long as people have lived on the Earth. It helps us to understand and separate sounds coming from different sound sources and to catch necessary information from the acoustical world. Several cues for localizing a position of a sound source, such as ITD, HRTF, recorded by dummy head microphones, are investigated in this paper. We used signals which were considered to be basic signals of an imaginary round-shaped room. Our goal of the research was to localize random signals produced from different positions using the information about basic signals. One of the main issues during sound localization was the problem of front-back confusion, which was successfully resolved by using reference signals. In this paper we propose sound localization algorithm with front-back confusion resolution.
Technical Memorandum Number 820 Cooperative Strategies for Manufacturing Planning with Negotiable Third-Party Capacity by Xiaoqiang Cai

We consider a model where a group of manufacturers outsource finishing operations to a single third-party. Depending on the demand for her capacity, the third-party announces daily booking costs that may take on one of two prices regular or peak price. Each manufacturer books chunks of production capacity (called manufacturing windows) so as to optimize his booking and tardiness costs subject to window availability at the third party. For days that capacity is booked the manufacturer has the option to purchase overtime at a higher hourly rate. Upon booking her capacity to the manufacturers, the third-party computes the monetary benefit that could be achieved if all manufacturers cooperated to obtain an overall optimal solution. Then, using cooperative game theory she devises a savings sharing scheme so that, in monetary terms, every manufacturer is better off with the coordinated schedule than what each could get for himself by cooperating with a subset of manufacturers. For her work, the third party withholds a portion ρ of the booking revenue paid by the manufacturers for days that were utilized in the original schedule but released after coordination. Subsequently, the third-party has the option to resell her capacity for those days. Through this model we come up with insights that indicate that cooperation amongst manufacturers reduces costs by about 20%. ∗This research was initiated while the second author visited The Chinese University of Hong Kong, and was supported in part by the Research Grants Council of HK under Earmarked Grants No. CUHK 4166/01E and CUHK 4170/03E. †Department of Systems Engineering and Engineering Management, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, xqcai@se.cuhk. edu.hk ‡Weatherhead School of Management, Department of Operations, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, OH 44106-7235, gxv5@case.edu
An exploratory review of pre-qualification interprofessional education evaluations

Abstract There are diverse perceptions about the primary purpose of evaluation. In interprofessional education (IPE), there has been a perceived focus on evaluating against the outcome of improved collaborative practice and quality of care. This paper presents an exploration of the nature and purpose of evaluation methods commonly utilized in the IPE literature with its focus on outcomes-based evaluation and particularly the Kirkpatrick framework. It categorises recent evaluations of pre-qualification (pre-certification) IPE interventions. Of the 90 studies included, most evaluated soon after the educational intervention, only five specifically referred to an evaluation framework and the most frequently used tool was the RIPLS. There was a noteworthy reliance on students’ self-rated perceptions of their attitudes towards collaborative practice collected through surveys, focus groups and interviews. There appears to be a need to reconsider the type of evaluation required. In conclusion, this paper offers recommendations for evaluation practice that is moving towards realist approaches; describes the longer term effects of interventions on attitudes and behaviour; develops and validates data collection tools including direct observation of practice and more comprehensively engages with all stakeholders to ensure that evaluation activities are not only focused on improving IPE but also on enhancing our understanding of interprofessional practice.