Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining evolutionary information and neural networks to predict protein secondary structure

Using evolutionary information contained in multiple sequence alignments as input to neural networks, secondary structure can be predicted at significantly increased accuracy. Here, we extend our previous three‐level system of neural networks by using additional input information derived from multiple alignments. Using a position‐specific conservation weight as part of the input increases performance. Using the number of insertions and deletions reduces the tendency for overprediction and increases overall accuracy. Addition of the global amino acid content yields a further improvement, mainly in predicting structural class. The final network system has a sustained overall accuracy of 71.6% in a multiple cross‐validation test on 126 unique protein chains. A test on a new set of 124 recently solved protein structures that have no significant sequence similarity to the learning set confirms the high level of accuracy. The average cross‐validated accuracy for all 250 sequence‐unique chains is above 72%. Using various data sets, the method is compared to alternative prediction methods, some of which also use multiple alignments: the performance advantage of the network system is at least 6 percentage points in three‐state accuracy. In addition, the network estimates secondary structure content from multiple sequence alignments about as well as circular dichroism spectroscopy on a single protein and classifies 75% of the 250 proteins correctly into one of four protein structural classes. Of particular practical importance is the definition of a position‐specific reliability index. For 40% of all residues the method has a sustained three‐state accuracy of 88%, as high as the overall average for homology modelling. A further strength of the method is greatly increased accuracy in predicting the placement of secondary structure segments. © 1994 Wiley‐Liss, Inc.
Removal of EEG Noise and Artifact Using Blind Source Separation

Summary: A study was performed to investigate and compare the relative performance of blind signal separation (BSS) algorithms at separating common types of contamination from EEG. The study develops a novel framework for investigating and comparing the relative performance of BSS algorithms that incorporates a realistic EEG simulation with a known mixture of known signals and an objective performance metric. The key finding is that although BSS is an effective and powerful tool for separating and removing contamination from EEG, the quality of the separation is highly dependant on the type of contamination, the degree of contamination, and the choice of BSS algorithm. BSS appears to be most effective at separating muscle and blink contamination and less effective at saccadic and tracking contamination. For all types of contamination, principal components analysis is a strong performer when the contamination is greater in amplitude than the brain signal whereas other algorithms such as second-order blind inference and Infomax are generally better for specific types of contamination of lower amplitude.
S-RVM: a secure design for a high-performance java virtual machine

Reference protection mechanisms, which control the propagation of references, are commonly used to isolate and to provide protection for components that execute within a shared runtime. These mechanisms often incur an overhead for maintaining the isolation or introduce inefficiencies in the communication between the components. This paper proposes a novel approach for component isolation that avoids runtime overheads by controlling references at compile time. We use the proposed approach to build S-RVM, a Java Virtual Machine based on JikesRVM, which enhances JikesRVM's security by isolating the VM from the application. Our experiments show that on the average S-RVM incurs no performance overhead when executing optimised code.
Application of 31P MR Spectroscopy to the Brain Tumors

Objective To evaluate the clinical feasibility and obtain useful parameters of 31P magnetic resonance spectroscopy (MRS) study for making the differential diagnosis of brain tumors. Materials and Methods Twenty-eight patients with brain tumorous lesions (22 cases of brain tumor and 6 cases of abscess) and 11 normal volunteers were included. The patients were classified into the astrocytoma group, lymphoma group, metastasis group and the abscess group. We obtained the intracellular pH and the metabolite ratios of phosphomonoesters/phosophodiesters (PME/PDE), PME/inorganic phosphate (Pi), PDE/Pi, PME/adenosine triphosphate (ATP), PDE/ATP, PME/phosphocreatine (PCr), PDE/PCr, PCr/ATP, PCr/Pi, and ATP/Pi, and evaluated the statistical significances. Results The brain tumors had a tendency of alkalization (pH = 7.28 ± 0.27, p = 0.090), especially the pH of the lymphoma was significantly increased (pH = 7.45 ± 0.32, p = 0.013). The brain tumor group showed increased PME/PDE ratio compared with that in the normal control group (p = 0.012). The ratios of PME/PDE, PDE/Pi, PME/PCr and PDE/PCr showed statistically significant differences between each brain lesion groups (p < 0.05). The astrocytoma showed an increased PME/PDE and PME/PCr ratio. The ratios of PDE/Pi, PME/PCr, and PDE/PCr in lymphoma group were lower than those in the control group and astrocytoma group. The metastasis group showed an increased PME/PDE ratio, compared with that in the normal control group. Conclusion We have obtained the clinically applicable 31P MRS, and the pH, PME/PDE, PDE/Pi, PME/PCr, and PDE/PCr ratios are helpful for differentiating among the different types of brain tumors.
Dynamic Semantics and the Geometry of Meaning

1 As prominently demonstrated in theoretical physics, the formal language of mathematics may be very useful for describing aspects of reality. That does not mean that the mathematical instruments are intended to capture a precise picture of reality. Instead, processes of abstraction and idealization are omnipresent generating an apparently very close fit between preexisting, pleasant mathematical structures and an idealized/abstracted picture of reality, which is studied in science. In a target article published in Theoretical Linguistics, Stokhof and van Lambalgen [42] analyzed the role of idealizations and abstractions as part of “the construction of modern linguistics. ” In the present short note we develop some ideas which were presented earlier as a comment on this article [10]. The main tenet of the target article was that (most) parts of modern linguistics are based on the idea of idealization rather than the idea of abstraction, which the authors consider as more useful. Even when the authors address the ‘Generative tradition’, in most parts of their analysis they do not exclude other developments in semantics and pragmatics:
The Advanced Encryption Standard-Cipher-based Message Authentication Code-Pseudo-Random Function-128 (AES-CMAC-PRF-128) Algorithm for the Internet Key Exchange Protocol (IKE)

Some implementations of IP Security (IPsec) may want to use a pseudo- random function (PRF) based on the Advanced Encryption Standard (AES). This memo describes such an algorithm, called AES-CMAC-PRF-128. It supports fixed and variable key sizes. [STANDARDS-TRACK]
IMPROVE THE PERFORMANCE OF EPOXY RESIN AND POLY (VINYL BUTYRAL) AS AN ALUMINUM METAL ADHESION

The present work is mainly concerned with study the performance of epoxy resin which blended with poly (vinyl butyral) in order to be used as adhesive for aluminum metal. A different weight ratios of poly (vinyl butyral) was blended with epoxy resin (1090 wt %) and these blends were cured at different conditions; time (10-60) minutes and temperature (100-200 C o ), different mechanical properties (shear stress, elongation and peeling stress) were carried out on the prepared samples. Box – Wilson design method was adopted to find useful relationships between the three variables [(weight ratios and curing conditions (time & temperature)] with mechanical properties shear stress, elongation and peeling stress , it was found that the best adhesive properties of the prepared sample (i.e. best mechanical properties) obtained with the weight ratio of (40) wt% epoxy resin and (60) wt% poly (vinyl butyral) while the best curing condition obtained at a temperature of 160 C o for (30) min.
MICROMANIPULATION OF MICROTOOLS MADE OF SU-8 BY INTEGRATED OPTICAL TWEEZERS

We propose a novel cell manipulation method of Integrated Optical Tweezers (IOT) with microtools made of negative photoresist, SU-8 (MicroChem). This microtool is made by photolithography and hence it has complex shape. IOT is a novel optical tweezers integrating Time-Shared Scanning (TSS) [1] for high speed manipulation of a few objects and Generalized Phase Contrast (GPC) [2] for trapping a lot of objects. Here we propose IOT as the combined manipulation method and demonstrate manipulation of SU-8 microtools. This proposed noncontact manipulation method worked well as we expected.
Alterations of Dendritic Cells in Sepsis: Featured Role in Immunoparalysis

Sepsis, the leading cause of mortality in intensive care unit, is characterized by hyperinflammatory response in the early stage and followed by a period of immunosuppression. This immune disorder is believed to be the potent factor that is tightly associated with high mortality in sepsis. Dendritic cells (DCs) serve as professional antigen-presenting cells that play a vital role in immune response by activating T lymphocytes. During the progression of sepsis, DCs have been reported to take part in the aberrant immune response and be necessary for survival. Therefore, a better understanding of the DCs pathology will be undoubtedly beneficial for resolving the problems occurring in sepsis. This review discusses effects of sepsis on DCs number and function, including surface molecules expression, cytokines secretion, and T cell activation, and the underlying mechanism as well as some potential therapeutic strategies.
Flexible Management of Shared Groupware Objects

Synchronous groupware brings together users, which are geographically distributed, but connected via a network. In this paper we describe an object manager, which simplifies synchronous groupware development. It offers a variety of services for controlling an application's shared data, including flexible object distribution, flexible object coupling, latecomer support and configurable concurrency control. After a brief description of the development platform and the object manager basic concepts we focus on its configurable services, e.g. consistency maintenance and object coupling. A description of the runtime architecture and directions for future work conclude the paper.
The Relationship between Professional Development and Student Learning: Exploring the Link through Design Research Figure 1. Design Approach to Professional Development. Professional Development Design 1. Increase Comfort with Unit 2. Increase Comfort with Technology 3. Increase Content Knowledge St

The national dialogue on science education includes two themes. The first is the call for standards based reforms in education expressed both by the American Association for the The second is the call for greater accountability for student learning on a multitude of levels, as exemplified in the " No Child Left Behind Act " (U.S. Department of Education, 2002). One response to such demands is to increase teacher professional development in the hope of enabling the teacher to teach that deemed necessary, while holding the teachers accountable when they fail to do so. Despite the fact that the national spotlight is focused on teacher instruction and student learning, little research has been done linking teacher learning in professional development directly to student learning Highly Interactive Computing in Education (hi-ce) we developed a design approach to professional development that affords us the opportunity to address the key question of teacher learning from professional development and its link to evidence of student learning. Our method illustrates the interdependence between the study and implementation of professional development and its impact in the classroom. In this paper we use variations of our design approach for professional development as a template to examine professional development and the resulting learning, examining its usefulness both as an evaluative as well as a diagnostic tool in professional development design. We evaluate professional development through analyzing the workshop enactments and post-workshop interviews with teachers to identify the content and strategies used and the expressed impact on the teacher learning. Next we apply our design approach to professional development to two different classroom investigations. Through these case analyses we demonstrate both the diagnostic and evaluative nature of our design cycle for professional development. Our investigation examines teachers' " knowing that, " as measured through teachers' expressed learning from professional development, and " knowing how, " as witnessed in classroom observations. As Ryle (1949) has suggested, " knowing that " and " knowing how " are not only different, but distinct ways of knowing. Teachers' " knowing how " manifests itself in action which we observe and we measure the professional development's success or failure by investigating resulting student achievement. However, investigating the " knowing how " aspect of teacher learning is time consuming and labor intensive. By analyzing the workshops and teachers reported learning from the workshops " know that " , we create a sketch of the professional …
Chinese Web Scale Linguistic Datasets and Toolkit

The web provides a huge collection of web pages for researchers to study natural languages. However, processing web scale texts is not an easy task and needs many computational and linguistic resources. In this paper, we introduce two Chinese parts-of-speech tagged web-scale datasets and describe tools that make them easy to use for NLP applications. The first is a Chinese segmented and POS-tagged dataset, in which the materials are selected from the ClueWeb09 dataset. The second is a Chinese POS n-gram corpus extracted from the POS-tagged dataset. Tools to access the POS-tagged dataset and the POS n-gram corpus are presented. The two datasets will be released to the public along with their tools.
How device properties influence energy-delay metrics and the energy-efficiency of parallel computations

Semiconductor device engineers are hard-pressed to relate observed device-level properties of potential CMOS replacements to computation performance. We address this challenge by developing a model linking device properties to algorithm parallelism, total computational work, and degree of voltage and frequency scaling. We then use the model to provide insight into how device properties influence execution time, average power dissipation, and overall energy usage of parallel algorithms executing in the presence of hardware concurrency. The model facilitates studying tradeoffs: It lets researchers formulate joint energy-delay metrics that account for device properties. We support our analysis with data from a dozen large digital circuit designs, and we validate the models we present using performance and power measurements of a parallel algorithm executing on a state-of-the-art low-power multicore processor.
Simultaneous Finite Automata: An Efficient Data-Parallel Model for Regular Expression Matching

Automata play important roles in wide area of computing and the growth of multicores calls for their efficient parallel implementation. Though it is known in theory that we can perform the computation of a finite automaton in parallel by simulating transitions, its implementation has a large overhead due to the simulation. In this paper we propose a new automaton called simultaneous finite automaton (SFA) for efficient parallel computation of an automaton. The key idea is to extend an automaton so that it involves the simulation of transitions. Since an SFA itself has a good property of parallelism, we can develop easily a parallel implementation without overheads. We have implemented a regular expression matcher based on SFA, and it has achieved over 10-times speedups on an environment with dual hexa-core CPUs in a typical case.
Intra-articular methotrexate in knee synovitis.

OBJECTIVE To test whether methotrexate prolongs the effect of intra-articular corticosteroid in suppressing knee synovitis. METHODS Thirty-eight patients with chronic knee synovitis were randomly allocated to receive intra-articular triamcinolone hexacetonide with or without methotrexate. Variables were knee pain and swelling, assessor and patient global assessment, morning stiffness, ESR and CRP. The primary endpoint was the duration of improvement. RESULTS After treatment, both groups of patients demonstrated a significant improvement in all variables. However, there was no significant difference between the two groups in the degree or duration of the response. No side-effects were encountered with methotrexate apart from a slight elevation of transaminase levels in some patients. CONCLUSIONS In the context of this study, the addition of methotrexate to triamcinolone did not add significantly to the clinical response to intra-articular corticosteroid in chronic knee synovitis. However, further controlled studies using different designs are probably warranted.
Limits on Turbulent H I Fluctuations toward PSR B0329+54 on Scales between 0.0025 and 12.5 AU

We have measured the H I absorption toward pulsar B0329+54 using the Green Bank Telescope during 18 epochs between 2002 June 30 and 2003 October 10. Three observing epochs consisted of a continuous period of 20 hr each, while 15 epochs were 1-2 hr each. We calculate the structure function of H I absorption variations toward the pulsar on timescales of 10 minutes to 16 months, which using the proper motion of 95 km s-1 and the parallactic distance of 1.03 kpc measured toward B0329+54 (Brisken et al.), corresponds to angular scales of 0.37 μas to 23.8 mas and samples structures between 0.0025 and 12.5 AU, assuming H I gas halfway to the pulsar and ignoring scintillation effects. We find no evidence for any turbulent H I absorption fluctuations toward B0329+54, with the following upper limits on Δτ for various absorption features: 0.026 at -31, -21, -18, and +4 km s-1; 0.12 at -11 km s-1; and 0.055 at -1 km s-1.
Basal or stress-induced cortisol and asthma development: the TRAILS study

We examined the association between: 1) cortisol levels and asthma or asthma development; 2) cortisol levels upon stress and asthma. In addition, we performed a post hoc meta-analysis on results from the literature. Cortisol, cortisol upon stress, asthma (doctor diagnosis of asthma and/or symptoms and/or treatment in the past 12 months) and asthma development (asthma at a specific survey while not having asthma at the previous survey(s)) were assessed in the TRAILS study (n=2230, mean age at survey 1 11 years, survey 2 14 years and survey 3 16 years). Logistic regression models were used to study associations between: 1) cortisol (cortisol awakening response, area under the curve (AUC) with respect to the ground (AUCg) or with respect to the increase (AUCi), and evening cortisol) and asthma or asthma development; 2) cortisol upon stress (AUCg or AUCi) and asthma. The meta-analyses included nine case–control articles on basal cortisol in asthma. No significant association was found between: 1) cortisol and asthma (age 11 years) or asthma development (age 14 or 16 years); 2) cortisol upon stress and asthma (age 16 years). The meta-analysis found lower morning and evening cortisol levels in asthmatics compared to non-asthmatics; however, the summary estimates were not significant. We found no evidence supporting a role for cortisol in asthma and asthma development.
Concurrent checking and unidirectional errors in multiple-valued circuits

The concept of unateness for multiple-valued logic circuits and its usefulness for concurrent checking through the use of unidirectional error-detecting codes are examined. Three such codes are adapted for multivalued logic, and the set of operators which provide an internally unate circuit is described. For each code, modifications are provided to incorporate testing for primary input faults. Some area overhead evaluations are performed using benchmarks implemented on binary and quaternary programmable logic arrays. <<ETX>>
Fundamental Latency Trade-off in Architecting DRAM Caches: Outperforming Impractical SRAM-Tags with a Simple and Practical Design

This paper analyzes the design trade-offs in architecting large-scale DRAM caches. Prior research, including the recent work from Loh and Hill, have organized DRAM caches similar to conventional caches. In this paper, we contend that some of the basic design decisions typically made for conventional caches (such as serialization of tag and data access, large associativity, and update of replacement state) are detrimental to the performance of DRAM caches, as they exacerbate the already high hit latency. We show that higher performance can be obtained by optimizing the DRAM cache architecture first for latency, and then for hit rate. We propose a latency-optimized cache architecture, called Alloy Cache, that eliminates the delay due to tag serialization by streaming tag and data together in a single burst. We also propose a simple and highly effective Memory Access Predictor that incurs a storage overhead of 96 bytes per core and a latency of 1 cycle. It helps service cache misses faster without the need to wait for a cache miss detection in the common case. Our evaluations show that our latency-optimized cache design significantly outperforms both the recent proposal from Loh and Hill, as well as an impractical SRAM Tag-Store design that incurs an unacceptable overhead of several tens of megabytes. On average, the proposal from Loh and Hill provides 8.7% performance improvement, the "idealized" SRAM Tag design provides 24%, and our simple latency-optimized design provides 35%.
Using the Saint George's Respiratory Questionnaire to evaluate quality of life in patients with chronic obstructive pulmonary disease: validating a new version for use in Brazil.

OBJECTIVE The objective of this study was to evaluate the applicability of a modified version of the Saint George's Respiratory Questionnaire. The version evaluated elicits "agree" and "do not agree", rather than "yes" and "no", responses. The intention is to facilitate the comprehension of double-negative questions and to promote better recollection of symptoms by patients by shortening their symptom histories from 12 months to 3 months. METHODS A total of 30 clinically stable patients with chronic obstructive pulmonary disease were evaluated. The Saint George's Respiratory Questionnaire and the modified version of the same were administered 15 days apart. RESULTS All of the patients presented health-related alterations in their quality of life. Comparing mean scores between the two questionnaires, the greatest difference was seen in the Symptoms domain. No significant differences were found in any of the remaining domains or in the total scores. In a subsequent analysis, significant correlations between the two questionnaires were found in all domains: Symptoms (r = 0.71; p < 0.001); Activity (r = 0.75; p < 0.001); Impact (r = 0.73; p < 0.001) and Total (r = 0.86; p < 0.001). CONCLUSION The modified version of the Saint George's Respiratory Questionnaire is as effective as the original in gauging quality of life. However, various symptoms recollection time frames should be investigated in order to determine which would be the best time frame to employ in the analysis.