Miracle-dz/UniFAR-FTUs huggingface dataset:
On 'globbicity' of low-resolution protein structures.

Using Harker's [Harker (1953). Acta Cryst. 6, 731-736] idea of spherically averaged polyatomic groups or 'globs' as the units of structure suitable for analyzing low-resolution diffraction data from protein crystals, 'globbic' scattering factors have been calculated for main-chain peptide units and amino-acid side-chain groups to 3 A resolution via Debye's [Debye (1915). Ann. Phys. (Leipzig), 46, 809-823] scattering formula. It is shown that the scattering factors are insensitive to intra-globbic conformational variation and can be approximated fairly well by a single-Gaussian formula, i.e. fg(s) = Zg exp(-1.7Zgs2), where s = (sin theta)/lambda and Zg is the total electron count for the atoms of the glob. Phase errors due to the globbic approximation and their effect on electron-density maps at 3.5 A resolution have been assessed via calculations for the crambin structure; this analysis indicates that the globbic scattering factors will be useful in efforts to develop procedures for direct-methods phasing of diffraction data to approximately 3.5 A resolution from protein crystals.
The Temperament of Members of Learning Communities

Learning networks are designed to build the capacity of the organization to promote and support ongoing school improvement, not to bring about a quick fix, to complete specific tasks, or to prescribe solutions to specific problems. But change is a process of breaking out of old paradigms to do things differently and to do different things.
Aging, Chronic Illness and Self-Concept: A Study of Women with Osteoporosis

ABSTRACT The coalescence of aging and chronic illness may alter the relationships between the meanings of aging and chronic illness and the self-concept. Using Rosenberg's conceptualization of self-concept (1979), a qualitative study was designed and data collected from twenty-eight women with osteoporosis. Three types of self-concepts emerged from the data: the confident self, the contradictory self and the disparaged self. A description of these types is presented highlighting the reciprocal relationship among meanings of aging and chronic illness and self-concept and including discussion of the strategies used to enhance, protect and maintain self-concept despite changes brought on by aging and chronic illness.
Immediate early gene expression in response to cerebral ischemia. Friend or foe?

BACKGROUND Cerebral ischemia is a potent modulator of gene expression. Immediate early genes undergo rapid induction after both global and focal cerebral ischemia. Many immediate early genes code for transcription factors. Additional genes, including those encoding for neurotrophic factors and neurotransmitter systems, are induced in a delayed fashion after cerebral ischemia. The functional significance of early and late gene regulation after cerebral ischemia requires further investigation. These changes may be beneficial (friend) or detrimental (foe). Many of the genes are likely neuroprotective and important for recovery, but others may be involved in ischemic cell death mediated by apoptosis. SUMMARY OF REVIEW We review evidence that supports the hypothesis that cell death after cerebral ischemia occurs through the dual pathways of ischemic necrosis and apoptosis. CONCLUSIONS Gene regulation, including immediate early genes, is required for programmed neuronal death after trophic factor deprivation and is predicted to be involved in apoptosis triggered by cerebral ischemia. Novel therapies following cerebral ischemia may be directed at genes mediating either recovery or apoptosis.
British language diversity surveys (1977–87): A critical examination

Abstract. The last ten years of surveys of users of languages in addition to English in Britain are examined here through a review of the work of three bodies, which have operated mainly in London schools: The Inner London Education Authority Language Census, The Survey of Linguistic Diversity in London Schools, and The Linguistic Minorities Project. Various flaws and problems in the methodology of these surveys are discussed. Methodological problems in the nature of language diversity surveys as social surveys, as linguistic research, and as ideological activities, are summarised. The conclusion is made that under‐reporting has occurred in all cases. Some suggestions for future practice are indicated.
Development and Validation of the Child Improvement Locus of Control (CILC) Scales

Two studies were conducted to develop and validate the Child Improvement Locus of Control (CILC) scales. In Study 1, 145 parents of autistic children completed a questionnaire tapping beliefs about their children's improvement. Oblique factor analysis yielded five scales assessing parents' beliefs in (1) Chance, (2) Divine Influence, (3) Parent, i4) Professional, and (5) Child as factors influencing child improvement. Alphas for the five scales were generally acceptable, with only the Chance scale (α = .58) failing to demonstrate adequate internal consistency. Correlations with the Multidimensional Health Locus of Control Scales suggested good construct validity. In Study 2, 175 parents of physically ill children were given the CILC items. Factor analysis perfectly replicated the five factors in Study 1. Alphas ranged from . 69 to . 80. The following relationships, offering further evidence of construct validity, were observed: (1) Parental beliefs in Child influence increased with child age; (2) belief in .
NoC monitoring: impact on the design flow

Networks-on-chip (NoCs) are a scalable interconnects solution to large scale multiprocessor systems on chip and are rapidly becoming reality. As the ratio of embedded cores per I/O pin increases, the run-time observability becomes a bottleneck. Run-time NoC monitoring can alleviate this problem. As NoCs are the result of sophisticated synthesis design flows, monitoring must be taken into account during this process. We present several scalable alternatives for NoC monitoring. The alternatives vary from using physically separated interconnects for user data and monitoring data, to a completely shared single interconnect. For each alternative we evaluate area cost, required design flow modifications, non-intrusiveness and reusability of monitoring resources for application communication traffic. An interesting trade-off is presented showing that what is area efficient requires efforts in modifying the NoC design flow and in achieving non-intrusiveness. All the experiments are done in the context of the /Ethereal NoC and design flow
A Comparison of High-Level Design Tools for SoC-FPGA on Disparity Map Calculation Example

Modern SoC-FPGA that consists of FPGA with embedded ARM cores is being popularized as an embedded vision system platform. However, the design approach of SoC-FPGA applications still follows traditional hardware-software separate workflow, which becomes the barrier of rapid product design and iteration on SoC-FPGA. High-Level Synthesis (HLS) and OpenCL-based system-level design approaches provide programmers the possibility to design SoC-FGPA at system-level with an unified development environment for both hardware and software. To evaluate the feasibility of high-level design approach especially for embedded vision applications, Vivado HLS and Altera SDK for OpenCL, representative and most popular commercial tools in market, are selected as evaluation design tools, disparity map calculation as targeting application. In this paper, hardware accelerators of disparity map calculation are designed with both tools and implemented on Zedboard and SoCKit development board, respectively. Comparisons between design tools are made in aspects of supporting directives, accelerator design process, and generated hardware performance. The results show that both tools can generate efficient hardware for disparity map calculation application with much less developing time. Moreover, we can also state that, more directives (e.g., interface type, array reshape, resource type specification) are supported, but more hardware knowledge is required, in Vivado HLS. In contrast, Altera SDK for OpenCL is relatively easier for software programmers who is new to hardware, but with the price of more resources usage on FPGA for similar hardware accelerator generation.
Efficient Construction of Multiple Geometrical Alignments for the Comparison of Protein Binding Sites

We proceed from a method for protein structure comparison in which information about the geometry and physico-chemical properties of such structures are represented in the form of labeled point clouds, that is, a set of labeled points in three-dimensional Euclidean space. Two point clouds are then compared by computing an optimal spatial superposition. This approach has recently been introduced in the literature and was shown to produce very good similarity scores. It does not, however, establish an alignment in the sense of a one-to-one correspondence between the basic units of two or more protein structures. From a biological point of view, alignments of this kind are of great interest, as they offer important information about evolution, heredity, and the mutual correspondence between molecular constituents. In this paper, we therefore developed a method for computing pairwise or multiple alignments of protein structures on the basis of labeled point cloud superpositions.
Political Science, Biometric Theory, and Twin Studies: A Methodological Introduction

As political scientists begin to incorporate biological influences as explanatory factors in political behavior, the need to present a methodological road map for utilizing biometric genetic theory and twin data is apparent. The classical twin design (CTD) remains the most popular design for initial examinations of the source of variance among social and political behaviors, and a vast majority of advanced variance components models as well as some molecular analyses are extensions of the CTD. Thus, it is appropriate to begin a series of works with the CTD and its most common variants. The CTD has strong roots in biometrical genetic theory and provides estimates of the correlations between observed traits of monozygotic and dizygotic twins in terms of underlying genetic and environmental influences. The majority of these analyses utilize SEMs of observed covariances for both twin types to assess the relative importance of these “latent” factors.
A Boron-Boron Triple Bond

A complex with a boron-boron triple bond expands the range of genuine triple bonds known to chemists. Although carbon readily forms double and even triple bonds, such bonds are much rarer between the heavier elements of the same group or between atoms of other main groups of the periodic system. Chemists have succeeded in creating some such molecules, such as double-bonded silicon compounds, although they are usually highly reactive. On page 1420 of this issue, Braunschweig et al. (1) report the synthesis of one such highly unusual chemical compound, which has a boron-boron triple bond.
ERA: A Framework for Economic Resource Allocation for the Cloud

Cloud computing has reached significant maturity from a systems perspective, but currently deployed solutions rely on rather basic economics mechanisms that yield suboptimal allocation of the costly hardware resources. In this paper we present Economic Resource Allocation (ERA), a complete framework for scheduling and pricing cloud resources, aimed at increasing the efficiency of cloud resources usage by allocating resources according to economic principles. The ERA architecture carefully abstracts the underlying cloud infrastructure, enabling the development of scheduling and pricing algorithms independently of the concrete lower-level cloud infrastructure and independently of its concerns. Specifically, ERA is designed as a flexible layer that can sit on top of any cloud system and interfaces with both the cloud resource manager and with the users who reserve resources to run their jobs. The jobs are scheduled based on prices that are dynamically calculated according to the predicted demand. Additionally, ERA provides a key internal API to pluggable algorithmic modules that include scheduling, pricing and demand prediction. We provide a proof-of-concept software and demonstrate the effectiveness of the architecture by testing ERA over both public and private cloud systems -- Azure Batch of Microsoft and Hadoop/YARN. A broader intent of our work is to foster collaborations between economics and system communities. To that end, we have developed a simulation platform via which economics and system experts can test their algorithmic implementations.
Position paper:system design issues for broadband content delivery services

Broadband access network technologies such as ADSL and FTTH (Fiber To The Home) are becoming increasingly popular in Japan. In line with this trend, new broadband content delivery services using streaming technology and CDN technology are starting to appear. However, there are various issues that need to be addressed in order to provide high- quality services. This position aims to encourage discussion of the system design issues involved in the establishment of broadband content and broadband communication services. We also address the real deployment of broadband content delivery system and services.
Regional Ischemic Ventricular Dysfunction in Myocardium Supplied by a Narrowed Coronary Artery with Increasing Halothane Concentration in the Dog

The effects of increasing inspired halothane concentration (0.5, 1.0, 1.5, 2.0 per cent) upon left ventricular myocardium supplied by a critically narrowed coronary artery and a normal coronary artery were studied in 11 open-chested dogs. Regional ventricular function was measured by continuous recording of ventricular segment length using pairs of implanted miniature ultrasonic length detectors in the left anterior descending coronary artery (LAD) and left circumflex coronary artery (LC) territories before and during critical stenosis of the LAD by a micrometer-controlled snare. Critical narrowing was documented by ischemic regional ventricular function (i.e., post-systolic shortening; systolic lengthening) limited to the LAD territory when FIo2 = 0 for 90 seconds. Hemodynamic variables (aortic, left atrial and left ventricular pressure, and heart rate) were measured, ECG lead II was recorded, and the first derivative of left ventricular pressure (LV dP/dt) and coronary perfusion pressure derived for each halothane concentration before and during LAD narrowing. Increasing halothane was associated with equivalent progressive depression of global ventricular function before and during LAD constriction. Prior to LAD constriction, no ischemic changes in regional function occurred. Regional ventricular function was normal during 0.5 percent halothane in the presence of LAD constriction. With increasing halothane during LAD constriction, ischemic regional ventricular function was observed in the LAD territory in eight of eleven hearts, whereas regional ventricular function remained normal in the LC territory. The epicardial ECG was recorded in three dogs and was insensitive as an indicator of ischemia, becoming abnormal only after severe ischemic changes were established. In these studies, in which heart rate remained constant, arterial blood pressure and LV dP/dt decreased, and left ventricular end-diastolic pressure increased, decrease in blood flow and oxygen delivery due to a lower perfusion pressure distal to the coronary artery narrowing appears to be primarily responsible for the observations. The authors hypothesize that clinically unapparent episodes of regional myocardial ischemia distal to narrowed coronary arteries may be an important cause of perioperative myocardial infarction.
Role of 4-1BB ligand in costimulation of T lymphocyte growth and its upregulation on M12 B lymphomas by cAMP

K46J B lymphomas express a T cell costimulatory activity that is not inhibited by CTLA-4Ig, anti-B7-1, anti-B7-2, anti-intercellular adhesion molecule 1 or antibodies to heat stable antigen. In this paper we report that this costimulatory activity is mediated at least in part by 4-1BB ligand, a member of the tumor necrosis factor (TNF) gene family that binds to 4-1BB, a T cell activation antigen with homology to the TNF/nerve growth factor receptor family. A fusion protein between 4-1BB and alkaline phosphatase (4-1BB-AP) blocks T cell activation by K46J lymphomas in both an antigen-specific system and with polyclonally (anti-CD3) activated T cells. 4-1BB-AP also blocks antigen presentation by normal spleen cells. When the antigen- presenting cells express B7 molecules as well as 4-1BB ligand, we find that B7 molecules and 4-1BB-AP both contribute to T cell activation. These data suggest that 4-1BB ligand plays an important role in costimulation of IL-2 production and proliferation by T cells. The B lymphoma M12 expresses low levels of 4-1BB-L but can be induced to express higher levels by treatment of the B cells with cAMP, which also induces B7-1 and B7-2 in these cells. Thus cAMP appears to coordinately induce several costimulatory molecules on B cells.
Evaluation of pantoprazole formulations in different dissolution apparatus using biorelevant medium

Abstract Purpose: The study was developed to compare the in vitro dissolution profile of pantoprazole (CAS 102625-70-7) formulations in both The United State Pharmacopeia (USP) apparatus 2 and by applying biorelevant medium. Moreover, an in vitro – in vivo relationship was proposed considering in vivo data from previously published study Methods: In vitro dissolution profile were evaluated in biorelevant medium in USP apparatus 2 and 3 and the dissolution curves were either compared by the similarity factor (f2) or a model-independent approach. The fraction of drug dissolved in vitro in apparatus 2 was compared with the fraction of drug absorbed in vivo, which was obtained from a retro-spective in vivo study. An in vitro – in vivo relationship analysis was then applied to elucidate the overall absorption characteristics of formulations Results: The dissolution profiles of formulations demonstrated similar disposition in biorelevant medium in both USP apparatus 2 and 3. The dissolution profiles were described by f2 model in apparatus 2 and Weibull's function in apparatus 3. The vitro–in vivo relationship analysis showed that the formulation exhibited permeability rate-limiting absorption. Conclusion: Biorelevant medium in both USP apparatus 2 and 3 may be used as a tool to predict in vivo disposition of formulations of pantoprazole. Furthermore, it can be argued that biowaiver can be granted for enteric coated formulations of pantoprazole on the basis of in vitro dissolution profile.
Non-specialism and shifting academic identities: a sign of the times?

This paper focuses upon the largely under-recognised, under-researched world of non-specialist teaching in Higher Education (HE). Three categories of non-specialist teaching were devised from findings from a qualitative study aimed at exploring the reality of non-specialist teaching at two UK HE institutions. The implicit expectation of teaching as a non-specialist was perceived by staff as a consequence of broader, sector-wide changes in the role of the contemporary academic. Whilst clearly recognised as an implicit expectation of the lecturer role, non-specialist teaching was found to be a cause for tension in how lecturers perceived themselves as HE professionals and their academic identity. The need to recognise implications of non-specialist teaching in terms of support structures was a key conclusion and paramount in order to enable staff to manage tensions and conflicts arising from their increasingly fragmented and multifaceted work.
Hyperglycemia or high hemoglobin A1C: Which one is more associated with morbidity and mortality after coronary artery bypass graft surgery?

PROPOSE Our aim was to determine which criterion- hyperglycemia or high levels of glycosylated hemoglobin (HbA1C) is more associated with increased mortality and morbidity after coronary artery bypass graft (CABG). METHODS Two hundred and sixteen patients who underwent elective CABG were enrolled in this prospective study. In order to compare postoperative outcomes regarding HbA1c and fasting blood sugar (FBS) levels, the patients were divided into two groups based on plasma HbA1c levels >7% or ≤7% and FBS >126 mg/dl or ≤126 mg/dl. RESULTS Of 216 studied patients, 165 and 51 cases had levels of HbA1C ≤7% and HbA1c >7% respectively. Furthermore, 129 and 87 patients had levels of FBS of ≤126 mg/dl and FBS of >126 mg/dl respectively. Multivariate analyses revealed that patients with high HbA1C levels experienced significantly higher rates of postoperative re-intubation [P = 0.001, OR (95% CI) = 8.15 (2.88-23.09)], wound infection [P = 0.001, OR (95% CI) = 8.15 (2.88-23.09)] and bleeding [P = 0.027, OR (95% CI) = 2.18 (1.10-4.35)]. In addition, hyperglycemic patients had a higher frequency of arrhythmias [P = 0.001, OR (95% CI) = 3.07 (1.69-5.59)], atelectasis [P = 0.029, OR (95% CI) = 1.88 (1.07-3.30)] and wound infection [P = 0.001, OR (95% CI) = 8.75 (2.45-31.25)]. CONCLUSION Higher levels of both HbA1C and FBS contribute to the increased risk of morbidity but not mortality rates in post-CABG surgery patients; yet further studies are required to distinguish "a better predictor" of postoperative adverse events.
Noncompartmental kinetic analysis of DCE‐MRI data from malignant tumors: Application to glioblastoma treated with bevacizumab

Dynamic contrast enhanced MRI contrast agent kinetics in malignant tumors are typically complex, requiring multicompartment tumor models for adequate description. For consistent comparisons among tumors or among successive studies of the same tumor, we propose to estimate the total contrast agent–accessible volume fraction of tumor, including blood plasma, vpe, and an average transfer rate constant across all tumor compartments, Ktrans.av, by fitting a three‐compartment tumor model and then calculating the area under the tumor impulse‐response function (= vpe) and the ratio area under the tumor impulse response function over mean residence time in tumor (= Ktrans.av). If the duration of dynamic contrast enhanced MRI was too short to extrapolate the tumor impulse‐response function to infinity with any confidence, then conditional parameters v pe* and Ktrans.av* should be calculated from the available incomplete impulse response function. Median decreases of 33% were found for both v pe* and Ktrans.av* in glioblastoma patients (n = 16) 24 hours after the administration of bevacizumab (P < 0.001). Median total contrast‐enhancing tumor volume was reduced by 18% (P < 0.0001). The combined changes of tumor volume, v pe* , and Ktrans.av* suggest a reduction of true vpe, possibly accompanied by a reduction of true Ktrans.av. The proposed method provides estimates of a scale and a shape parameter to describe contrast agent kinetics of varying complexity in a uniform way. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Stabilization of luciferase from Renilla reniformis using random mutations

We expressed luciferase (RLuc) from Renilla reniformis in Escherichia coli. RLuc was purified using a Ni-NTA column and subsequently characterized. It was unstable in acidic solutions and at 30°C. To increase the stability of RLuc, the Rluc gene was randomly mutated using error-prone polymerase chain reaction. E. coli harboring the mutated gene was screened by detecting luminescence on a plate containing the substrate coelenterazine at 34°C. Three mutants, i.e. N264SS287P, N178D and F116LI137V, were obtained. The solubilities and specific activities of these mutants were higher than those of the wild type. Furthermore, the N264SS287P mutant maintained stability at a temperature approximately 5°C higher than that of the wild type, while denaturation of the F116LI137V mutant started at a temperature that was 5°C lower than the wild type, and ended at a temperature that was 7°C higher. We examined the obtained mutations using thermal shift assays and a computer program Coot in this study.