Miracle-dz/UniFAR-FTUs huggingface dataset:
EBP, a Program for Protein Identification Using Multiple Tandem Mass Spectrometry Datasets*S

MS/MS combined with database search methods can identify the proteins present in complex mixtures. High throughput methods that infer probable peptide sequences from enzymatically digested protein samples create a challenge in how best to aggregate the evidence for candidate proteins. Typically the results of multiple technical and/or biological replicate experiments must be combined to maximize sensitivity. We present a statistical method for estimating probabilities of protein expression that integrates peptide sequence identifications from multiple search algorithms and replicate experimental runs. The method was applied to create a repository of 797 non-homologous zebrafish (Danio rerio) proteins, at an empirically validated false identification rate under 1%, as a resource for the development of targeted quantitative proteomics assays. We have implemented this statistical method as an analytic module that can be integrated with an existing suite of open-source proteomics software.
Housing Prices in Tucson, Arizona

The hedonic approach is used to analyze selling prices for housing units in greater Tucson, Arizona, during 1998. Using over 6,400 Multiple Listing Service transactions, ordinary least-squares regression is used to estimate implicit prices for the amount of living space, age of the unit, and other housing attributes in this rapidly growing southwestern city. Price premiums are estimated for nine different real estate districts, which realtors believe are different housing submarkets. Regression estimates are also given for the difference between original list price and selling price, thereby indicating how sellers and buyers differentially evaluated housing attributes. Nearly 3,700 transactions (from an overlapping data set) were geocoded, and these cases are examined in somewhat more detail. Spatial heterogeneity in selling prices is addressed but spatial dependency is not. The statistics of the hedonic price functions compare favorably with those for other U.S. cities.
NB-FEB: An Easy-to-Use and Scalable Universal Synchronization Primitive for Parallel Programming

This paper addresses the problem of universal synchronization primitives that can support scalable thread synchronization for large-scale many-core architectures. The universal synchronization primitives that have been deployed widely in conventional architectures, are the compare-and-swap (CAS) and load-linked/store-conditional (LL/SC) primitives. However, such synchronization primitives are expected to reach their scalability limits in the evolution to many-core architectures with thousands of cores. We introduce a non-blocking full/empty bit primitive, or NB-FEB for short, as a promising synchronization primitive for parallel programming on may-core architectures. We show that the NB-FEB primitive is universal, scalable, feasible and convenient to use. NB-FEB, together with registers, can solve the consensus problem for an arbitrary number of processes (universality). NB-FEB is combinable, namely its memory requests to the same memory location can be combined into only one memory request, which consequently mitigates performance degradation due to synchronization "hot spots" (scalability). Since NB-FEB is a variant of the original full/empty bit that always returns a value instead of waiting for a conditional flag, it is as feasible as the original full/empty bit, which has been implemented in many computer systems (feasibility). The original full/empty bit is well-known as a special-purpose primitive for fast producer-consumer synchronization and has been used extensively in the specific domain of applications. In this paper, we show that NB-FEB can be deployed easily as a general-purpose primitive. Using NB-FEB, we construct a non-blocking software transactional memory system called NBFEB-STM, which can be used to handle concurrent threads conveniently. NBFEB-STM is space efficient: the space complexity of each object updated by N concurrent threads/transactions is Θ(N), the optimal.
The Stress and Vascular Catastrophes in Newborn Rats: Mechanisms Preceding and Accompanying the Brain Hemorrhages

In this study, we analyzed the time-depended scenario of stress response cascade preceding and accompanying brain hemorrhages in newborn rats using an interdisciplinary approach based on: a morphological analysis of brain tissues, coherent-domain optical technologies for visualization of the cerebral blood flow, monitoring of the cerebral oxygenation and the deformability of red blood cells (RBCs). Using a model of stress-induced brain hemorrhages (sound stress, 120 dB, 370 Hz), we studied changes in neonatal brain 2, 4, 6, 8 h after stress (the pre-hemorrhage, latent period) and 24 h after stress (the post-hemorrhage period). We found that latent period of brain hemorrhages is accompanied by gradual pathological changes in systemic, metabolic, and cellular levels of stress. The incidence of brain hemorrhages is characterized by a progression of these changes and the irreversible cell death in the brain areas involved in higher mental functions. These processes are realized via a time-depended reduction of cerebral venous blood flow and oxygenation that was accompanied by an increase in RBCs deformability. The significant depletion of the molecular layer of the prefrontal cortex and the pyramidal neurons, which are crucial for associative learning and attention, is developed as a consequence of homeostasis imbalance. Thus, stress-induced processes preceding and accompanying brain hemorrhages in neonatal period contribute to serious injuries of the brain blood circulation, cerebral metabolic activity and structural elements of cognitive function. These results are an informative platform for further studies of mechanisms underlying stress-induced brain hemorrhages during the first days of life that will improve the future generation's health.
NAVIDOMASS: Structural-based Approaches Towards Handling Historical Documents

In the context of the NAVIDOMASS project, the problematic of this paper concerns the clustering of historical document images. We propose a structural-based framework to handle the ancient ornamental letters data-sets. The contribution, firstly, consists of examining the structural (i.e. graph) representation of the ornamental letters, secondly, the graph matching problem is applied to the resulted graph-based representations. In addition, a comparison between the structural (graphs) and statistical (generic Fourier descriptor) techniques is drawn.
RHETORICAL ETHNICITY OF PERMANENT SOJOURNERS: THE CASE OF ISRAELI IMMIGRANTS IN THE CHICAGO AREA

Immigrants who perceive their stay in the host country as a temporary stay are known as sojourners. In this article I examine the sojourn experience and ethnic attachment of Israeli immigrants in Chicago. I portray the sojourn experience as a dynamic process, in which the orientation towards the place of residence, and the experience of being a stranger can be changed over time. This process is analysed by giving close attention to sojourners who remain in the host country without any concrete plans or without a definite date of returning to the homeland. Those of them who maintain their general wish to return to the homeland are labelled in this study as `permanent sojourners', and their orientation towards their place of residence represents a compromise between the `sojourner' and the `settler' types of orientation. The findings reveal that Israeli `permanent sojourners' express a unique form of ethnicity, which I term `rhetorical ethnicity'. The manifestation and meaning of this form of ethnicity are discussed in the light of new forms of ethnicity in the United States. The findings and conclusions of this article are based on a field study of two discrete status groups of Israeli immigrants in the Chicago area.
More than a mirage: A large‐scale assessment centre with more dimension variance than exercise variance

Assessment centres (ACs) are widely recognized to be among the best tools for assessing and developing management talent (Assessment Centres and Global Talent Management, 2011, Gower: London). Yet, the current consensus about the construct validity of ACs is that exercises rather than dimensions explain the majority of variance in ratings. Because much of the data on which these conclusions are based are now old, it is worthwhile to periodically re-examine this issue to see whether well-implemented designs produce better measurements of dimensions. We present results from 1,205 executive-level leaders from Fortune 500 firms across Europe and North America, who participated in developmental ACs that use modern design principles where assessors were formally examined to ensure they had a common frame or reference. Our results showed that while dimensions and exercises mutually determined ratings, more variation was owing to dimensions. Practitioner Points Modern assessment centre designs can yield dimension scores that reflect dimensions more than exercises; The psychometric characteristics of operational ACs should be regularly monitored as the characteristics of any single AC may differ widely from meta-analytic averages.
The McDonaldization Thesis:

The issue addressed here is whether the spread of rationalization, or what I have termed `McDonaldization', is inexorable. That issue is examined spatially and temporally. Spatially, what we are witnessing is the increasingly global dissemination of rationalization, much of it emanating from the United States. The temporal growth is discussed from the point of view of the expansion of McDonaldization to birth and before and death and beyond; rationalization is coming to contain the entire life course (and more). Evidence of expansion does not, of course, necessarily mean that growth is inevitable. There are some hopeful social developments and there are some things that individuals can do, but it is difficult at this point to envision anything powerful enough to stem the tide in the direction of rationalization.
Modernizing wide-area grid communications for distributed energy resource applications using MQTT publish-subscribe protocol

This paper introduces the MQTT publish-subscribe protocol as a suitable transport mechanism to support next generation Distributed Energy Resource (DER) applications. DER applications such as Automated Demand Response (ADR) systems will be integral to the stability of a future grid with increasing non-synchronous penetration. These systems require secure, extensible and low latency communications in order to operate. There are currently no such suitable protocols, thus MQTT is suggested as a suitable transport mechanism. The authors' testbed ADR heating platform is introduced as a suitable platform for further work in this area.
A Web Services Approach to Model Management in DSS

Model management is an important research topic in the Decision Support Systems. Current research focuses on methods and theories to improve shareability, and effective utilization of decision models in an organization. This paper presents a Web services approach to the representation and design of model base in organizational model management. Ontology is used for the model base design, and “decision ontology” is proposed for model management. XML is used for the exchangeable representation of decision ontology. The proposed methods and theories are used in the construction of a DSS for R&D project selection at the National Natural Science Foundation of China (NSFC). The proposed approach makes use of the Web services technologies, it allows the sharing and reuse of decision models in the Internet environment.
Using Multilevel, Multisource Needs Assessment Data for Planning Community Interventions

African Americans and Latinos share higher rates of cardiovascular disease (CVD) and diabetes compared with Whites. These diseases have common risk factors that are amenable to primary and secondary prevention. The goal of the Chicago REACH 2010–Lawndale Health Promotion Project is to eliminate disparities related to CVD and diabetes experienced by African Americans and Latinos in two contiguous Chicago neighborhoods using a community-based prevention approach. This article shares findings from the Phase 1 participatory planning process and discusses the implications these findings and lessons learned may have for programs aiming to reduce health disparities in multiethnic communities. The triangulation of data sources from the planning phase enriched interpretation and led to more creative and feasible suggestions for programmatic interventions across the four levels of the ecological framework. Multisource data yielded useful information for program planning and a better understanding of the cultural differences and similarities between African Americans and Latinos.
A quantitative description of stimulation-induced changes in transmitter release at the frog neuromuscular junction

Endplate potentials were recorded from frog sartorius neuromuscular junctions under conditions of greatly reduced quantal contents to develop a quantitative description of stimulation-induced changes in transmitter release. Four general models relating potentiation, augmentation, and the first and second components of facilitation to transmitter release were developed. These models were then tested by incorporating equations for the kinetic properties of the four components of increased transmitter release and examining the ability of the resulting sets of equations to predict stimulation-induced changes in transmitter release. Three of the models were essentially consistent with the observation that augmentation had a multiplicative type relationship to facilitation. These models could also predict the effect of frequency and duration of stimulation on endplate potential (EPP) amplitude during and after prolonged (40 s) trains including the response to step changes in stimulation rate. These models extend by about two orders of magnitude the duration of stimulation-induced changes in transmitter release that can be accounted for, and show that the combined kinetic properties of potentiation, augmentation, and the two components of facilitation are generally sufficient to account for these changes.
Involvement of the stringent response in degradation of glutamine phosphoribosylpyrophosphate amidotransferase in Bacillus subtilis

Glutamine phosphoribosylpyrophosphate amidotransferase, the first enzyme of purine biosynthesis, has previously been shown to be rapidly inactivated and degraded in Bacillus subtilis cells at the end of growth. The loss of enzyme activity appears to involve the oxidation of an iron-sulfur cluster in the enzyme. The degradation of the inactive enzyme involves some elements of the stringent response because it is inhibited in relA and relC mutants. Intracellular pools of guanosine tetra- and pentaphosphate were measured by an improved extraction procedure in cells that had been manipulated in various ways to induce or inhibit amidotransferase degradation. The results are consistent with the hypothesis that one or both of these nucleotides stimulates the synthesis of a protein involved in degradation. An elevated level of these nucleotides was not required for the continued degradation of amidotransferase once it had begun.
Modeling of Evolution to Secure Application System: from Requirements Model to Software Architecture

This paper describes an approach to modeling the evolution of an application system to a secure application system in terms of the software requirements model and software architecture model. The requirements for security services are captured separately from application requirements, and the security services are encapsulated in connectors in the software architecture, separately from the components providing functional services. In this paper, the evolution of requirements and software architecture models to their corresponding security models is described in the center of security requirement conditions. A security requirement condition is maintained consistently from the security requirements model to secure software architecture. In the requirements model and software architecture for a secure system, a security service is fulfilled if a security requirement condition holds. An electronic commerce system is considered to demonstrate the approach.
A meeting of minds: interdisciplinary research in the health sciences in Canada

Brought together by the newly formed Canadian Academy of Health Sciences (CAHS), recognized national leaders in the 6 health sciences disciplines consider the environment for conducting interdisciplinary health research (IDHR) in Canada. Based on first-hand knowledge and thoughtful reflection, the authors argue that although much progress has been made in support of IDHR in Canada, the practical experience of researchers does not always bear this out. This article examines government, industry and academia to identify the cultural and structural characteristics that demand, promote or prevent IDHR in each sector. At its heart is the question, How can universities best support and enhance IDHR, not only for the benefit of science, but also to meet the growing needs of industry and government for intellectual capital? Focusing on the predominant health sciences disciplines, the authors define IDHR as a team of researchers, solidly grounded in their respective disciplines, who come together around an important and challenging health issue, the research question for which is determined by a shared understanding in an interactive and iterative process. In addition, they suggest that IDHR is directly linked to translational research, which is the application of basic science to clinical practice and the generation of scientific questions through clinical observation. This analysis of academic, industry and government sectors is not intended to offer rigorous data on the current state of IDHR in Canada. Rather, the goal is to stimulate research-policy dialogue by suggesting a number of immediate measures that can help promote IDHR in Canada. Recommended measures to support IDHR are aimed at better resourcing and recognition (by universities and granting agencies), along with novel approaches to training, such as government-and industry-based studentships. In addition, we recommend that professional organizations reconsider their policies on publication and governance. Although intended to maintain professional scopes of practice, these policies also serve to entrench disciplinary boundaries in research. We conclude by suggesting a number of research questions for a more rigorous assessment of the climate for IDHR in Canada. We call for an inventory and comparative analysis of academic centres, institutes and consortiums in Canada that strive to facilitate IDHR; an examination of the impact of professional organizations on health research, and on IDHR in particular; and a systematic review of research training opportunities that promote IDHR, with a view to identifying and replicating proven models.
A new multidisciplinary approach to integrating best evidence into musculoskeletal practice.

RATIONALE The effective integration of research evidence into everyday clinical practice continues to be an important challenge. AIMS The group aimed to answer locally relevant clinical question and produce recommendations for practice based on the best available evidence. METHODS Through a new initiative, a multidisciplinary group with a specific interest in musculoskeletal disease has been established in order to help address this problem. The group consists of clinical and academic professionals including physiotherapists, occupational therapists, nurses, clinical researchers and information technology librarians representing the health economy. RESULTS Results from the group's activities are shared locally through presentations and clinical algorithms and nationally through conference presentations and the National Electronic Library for Health. CONCLUSION As well as clinical recommendations, other benefits of the group have been improved networking, enhanced continual professional development and identifying areas in need of further research.
Robust and efficient point registration based on clusters and Generalized Radial Basis Functions (C-GRBF)

Radial Basis Functions (RBF) are effective in modeling regularization stabilizers, and have been successfully utilized in several point-based registration algorithms. Unfortunately the solutions usually require the inversion of a matrix or solving a linear system, whose computational cost grows rapidly with the increase of the input data size. In this paper, we present a fast and robust approximation remedy for this issue. Our model formulates the registration objective function under the Generalized Radial Basis Function (GRBF) framework w.r. t the cluster centers of one point set. With fewer variables, an computationally efficient registration is achieved, which updates the non-rigid transformation and the correspondence matrix simultaneously. Since the cluster centers often capture the global structure of the point sets very well, enhanced registration robustness is also resulted due to the less likelihood of trapping into local minima. This is especially beneficial in the context of large or/and unevenly distributed data sets. By means of experiments on real and synthetic data, we demonstrate the improvements made over several state-of-the-art solutions.
The Tradeoff Between Speed and Optimality in Hierarchical Search

Abstraction works by replacing a state space, SS, by another, "abstract" space that is easier to search, SS′. There are two well-known strategies for employing the "abstract" solutions found in SS′ to guide search in the original space. The first uses the lengths of the abstract solutions as a heuristic for an A* search of SS. This always produces optimal solutions. The second strategy uses the steps in the abstract solutions as subgoals for the search in SS. This strategy does not guarantee optimality, but it does tend to find a solution quickly. In this paper, we study the tradeoffs between the loss of optimality and the gain of speed in moving from the one strategy to the other. To perform the study, we introduce two continuous parameters whose extreme values represent these two strategies. Because the parameters are continuous we end up with a whole family of strategies that lie between these two. Using these parameters, we give extensive empirical results of the effects of perturbing the parameters on searches in eight different benchmarks. This allows us to track a continuous trade-off between optimality and speed throughout the space of hierarchic searches.ion works by replacing a state space, SS, by another, "abstract" space that is easier to search, SS′. There are two well-known strategies for employing the "abstract" solutions found in SS′ to guide search in the original space. The first uses the lengths of the abstract solutions as a heuristic for an A* search of SS. This always produces optimal solutions. The second strategy uses the steps in the abstract solutions as subgoals for the search in SS. This strategy does not guarantee optimality, but it does tend to find a solution quickly. In this paper, we study the tradeoffs between the loss of optimality and the gain of speed in moving from the one strategy to the other. To perform the study, we introduce two continuous parameters whose extreme values represent these two strategies. Because the parameters are continuous we end up with a whole family of strategies that lie between these two. Using these parameters, we give extensive empirical results of the effects of perturbing the parameters on searches in eight different benchmarks. This allows us to track a continuous trade-off between optimality and speed throughout the space of hierarchic searches. The Tradeoff Between Speed and Optimality in Hierarchical Search R.C. Holte1, M.B. Perez1, R.M. Zimmer2, A.J. MacDonald3