Miracle-dz/UniFAR-FTUs huggingface dataset:
VAMP2 Marks Quiescent Satellite Cells and Myotubes, but not Activated Myoblasts

We examined the expression and intracellular localization of vesicle-associated membrane protein 2 (VAMP2) during the differentiation of skeletal muscle cells by immunofluorescence microscopy. In isolated single myofibers, VAMP2 was expressed in quiescent satellite cells, downregulated in proliferating myoblastic cells, and re-expressed with differentiation. In the myoblastic cell line C2C12, VAMP2 was expressed at a low level in the proliferating stage, and then increased after differentiation into myotubes. Based on these results, we propose that VAMP2 can be used as a molecular marker for both quiescent satellite cells and myotubes, but not for proliferating myoblasts. We also found the partial colocalization of VAMP2 with transferrin- or Rab11-labeled vesicles in myotubes, suggesting a role of VAMP2 in the trafficking of recycling endosomes.
Optimizing long-term treatment of rheumatoid arthritis with systematic documentation

About 1% of the population suffers from rheumatoid arthritis. They not only experience pain, but during the course of the disease their mobility is reduced due to a deterioration of their joints. To retard this destructive process an assortment of drugs are available today, however, for optimal results both medication and dosage have to be tailored for each individual patient. RCQM is a clinical information system that moderates this process: within the confines of the examination routine, physicians gather more than 100 clinical and functional parameters (time needed <; 10 minutes). The amassed data are morphed into more useable information by applying scoring algorithms (e.g. Disease Activity Score (DAS), Health Assessment Questionnaire (HAQ)), which is subsequently interpreted as a function of time. The resulting DAS trends and patterns are ultimately used for treatment optimization and as a measure for the quality of patient outcome. Graphical data acquisition and information visualization support the entire interaction between doctor and patient. Both are equally informed of the course of the disease and, in practice, treatment decisions are made jointly. The task of documentation becomes an integral part of the dialog with the patient. This yields an increased level of decision quality, higher compliance, and verifiable patient empowerment.
Using affinity perturbations to detect web traffic anomalies

—The initial training phase of machine learning algorithms is usually computationally expensive as it involves the processing of huge matrices. Evolving datasets are challenging from this point of view because changing behavior requires updating the training. We propose a method for updating the training proﬁle efﬁciently and a sliding window algorithm for online processing of the data in smaller fractions. This assumes the data is modeled by a kernel method that includes spectral decomposition. We demonstrate the algorithm with a web server request log where an actual intrusion attack is known to happen. Updating the kernel dynamically using a sliding window technique, prevents the problem of single initial training and can process evolving datasets more efﬁciently.
Role of shear-stress-induced VEGF expression in endothelial cell survival

Vascular endothelial growth factor (VEGF) plays a crucial role in developmental and pathological angiogenesis. Expression of VEGF in quiescent adult tissue suggests a potential role in the maintenance of mature blood vessels. We demonstrate, using a Vegf–lacZ reporter mouse model, that VEGF is expressed by arterial but not by venous or capillary endothelial cells (ECs) in vivo. Using an in vitro model, we show that arterial shear stress of human umbilical vein ECs (HUVECs) decreases apoptosis and increases VEGF expression, which is mediated by the induction of Krüppel-like factor 2 (KLF2). Additionally, shear stress stimulates the expression of VEGF receptor 2 (VEGFR2) and is associated with its activation. Knockdown of VEGF in shear stressed HUVECs blocks the protective effect of shear stress, resulting in EC apoptosis equivalent to that in control ECs cultured under static conditions. Similarly, treatment of ECs subjected to arterial shear stress with the VEGF receptor tyrosine kinase inhibitor SU1498, or VEGFR2 neutralizing antiserum, led to increased apoptosis, demonstrating that the mechanoprotection from increased shear is mediated by VEGFR2. Taken together, these studies suggest that arterial flow induces VEGF–VEGFR2 autocrine–juxtacrine signaling, which is a previously unidentified mechanism for vascular EC survival in adult arterial blood vessels.
Cloning, Expression, and Characterization of a Thermophilic Endoglucanase, AcCel12B from Acidothermus cellulolyticus 11B

The gene ABK52392 from the thermophilic bacterium Acidothermus cellulolyticus 11B was predicted to be endoglucanase and classified into glycoside hydrolase family 12. ABK52392 encodes a protein containing a catalytic domain and a carbohydrate binding module. ABK52392 was cloned and functionally expressed in Escherichia coli. After purification by Ni-NTA agarose affinity chromatography and Q-Sepharose® Fast Flow chromatography, the properties of the recombinant protein (AcCel12B) were characterized. AcCel12B exhibited optimal activity at pH 4.5 and 75 °C. The half-lives of AcCel12B at 60 and 70 °C were about 90 and 2 h, respectively, under acidic conditions. The specific hydrolytic activities of AcCel12B at 70 °C and pH 4.5 for sodium carboxymethylcellulose (CMC) and regenerated amorphous cellulose (RAC) were 118.3 and 104.0 U·mg−1, respectively. The Km and Vmax of AcCel12B for CMC were 25.47 mg·mL−1 and 131.75 U·mg−1, respectively. The time course of hydrolysis for RAC was investigated by measuring reducing ends in the soluble and insoluble phases. The total hydrolysis rate rapidly decreased after the early stage of incubation and the generation of insoluble reducing ends decreased earlier than that of soluble reducing ends. High thermostability of the cellulase indicates its potential commercial significance and it could be exploited for industrial application in the future.
SPECIFICITY OF THE ANTIBODIES PRODUCED BY SINGLE CELLS FOLLOWING IMMUNIZATION WITH ANTIGENS BEARING TWO TYPES OF ANTIGENIC DETERMINANTS

A combination of double immunofluorescent technique and radioautographic localization of radioactive antigens was used to investigate the question whether single antibody-producing cells can make antibodies of more than one specificity after immunization with antigens bearing more than one determinant. When guinea pig γ2-globulins, containing the F(ab')2 and Fc determinants, were used to immunize rabbits, a small percentage of cells (3.7%) were stained with both the anti-F(ab')2 and anti-Fc reagents. These results were shown to be due to the lack of absolute specificity of the detecting antigen and antibody reagents which can be obtained for use in this system. However, when immunological systems such as hapten-protein conjugates were used, and where completely specific antigen and antibody reagents could be prepared, the results were unequivocal. The individual lymph node cells from rabbits or guinea pigs immunized with hapten-protein conjugates produced antibodies against the hapten or antibodies against the antigenic determinants of the carrier molecule, never antibodies against both specificities.
From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways

ABSTRACT Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD, coaD, and ribF), are discussed in detail.
A KNOWLEDGE-LEAN STRUCTURAL ENGINEERING DESIGN EXPERT SYSTEM Andrs

In this paper we present the GENCAD expert system which helps solve problems involving the structural design of tall buildings, pecifically focusing on the ways that the buildings resist lateral movements. One of the features of this type of design problem is that there doesn’t seem to be a lot of knowledge that can be made explicit about solving problems in the domain in order to program an expert system with it. Whether this lack of explicit knowledge is due to the complexity of the designs involved; to the implicit, intuitive, nature of the knowledge used by human experts; or to other factors, it still hinders the construction of a robust knowledgebased expert system. Our methodology has therefore been to make GENCAD a knowledge-lean expert system. This has been achieved by performing a careful task analysis of the problem-solving task and domain, and by implementing the required subtasks as much as possible using artificial intelligence methods that require little or no explicitly-coded domainand task-specific knowledge. We present here our analysis and our implementation of GENCAD.
A Hindi speech recognizer for an agricultural video search application

Voice user interfaces for ICTD applications have immense potential in their ability to reach to a large illiterate or semi-literate population in these regions where text-based interfaces are of little use. However, building speech systems for a new language is a highly resource intensive task. There have been attempts in the past to develop techniques to circumvent the need for large amounts of data and technical expertise required to build such systems. In this paper we present the development and evaluation of an application specific speech recognizer for Hindi. We use the Salaam method [4] to bootstrap a high quality speech engine in English to develop a mobile speech based agricultural video search for farmers in India. With very little training data for a 79 word vocabulary we are able to achieve >90% accuracies for test and field deployments. We report some observations from field that we believe are critical to the effective development and usability of a speech application in ICTD.
Combining TMS and tACS for Closed-Loop Phase-Dependent Modulation of Corticospinal Excitability: A Feasibility Study

Background: The corticospinal excitability indexed by motor evoked potentials (MEPs) following transcranial magnetic stimulation (TMS) of the sensorimotor cortex is characterized by large variability. The instantaneous phase of cortical oscillations at the time of the stimulation has been suggested as a possible source of this variability. To explore this hypothesis, a specific phase needs to be targeted by TMS pulses with high temporal precision. Objective: The aim of this feasibility study was to introduce a methodology capable of exploring the effects of phase-dependent stimulation by the concurrent application of alternating current stimulation (tACS) and TMS. Method: We applied online calibration and closed-loop TMS to target four specific phases (0°, 90°, 180° and 270°) of simultaneous 20 Hz tACS over the primary motor cortex (M1) of seven healthy subjects. Result: The integrated stimulation system was capable of hitting the target phase with high precision (SD ± 2.05 ms, i.e., ± 14.45°) inducing phase-dependent MEP modulation with a phase lag (CI95% = −40.37° to −99.61°) which was stable across subjects (p = 0.001). Conclusion: The combination of different neuromodulation techniques facilitates highly specific brain state-dependent stimulation, and may constitute a valuable tool for exploring the physiological and therapeutic effect of phase-dependent stimulation, e.g., in the context of neurorehabilitation.
Databases and Natural Language Interfaces

A Natural Language Interface for Databases allows users of multimedia kiosks to formulate natural language questions. User questions are first translated into a logic language and subsequently into Structured Query Language (SQL), which is processed by a database management system to return the answer. This paper focuses on the translation stage. Special attention is devoted to the conceptual model, a relational database that organizes all the data supporting the translation process. The translation algorithm is presented and commented examples are used to better understand its functioning.
Bias in the Estimation of Non-Linear Transformations of the Conditional Variance of Returns

Many applications in finance use a non-linear transformation of the variance of returns. While the sample variance is an unbiased and consistent estimator of the population variance of returns, non-linear transformations of the sample variance will be consistent but biased. For estimates of non-linear transformations of the unconditional variance, this will rarely be a problem in practice, since sample sizes employed in finance are typically large. However, estimators of the conditional variance typically use sample sizes that are effectively much smaller, particularly those that apply an exponential weighting to returns such as GARCH or EMWA. Consequently, the bias is likely to be more important in estimating non-linear transformations of the conditional variance. In this paper, we derive a simple analytical approximation for the unconditional bias in estimators of non-linear transformations of the conditional variance, under the assumption that returns are conditionally normally distributed, and that the true conditional variance is generated by an arbitrary stochastic volatility model. As an illustration, we estimate the bias inherent in the RiskMetrics approach to the calculation of value at risk.
Comparison and evaluation of knowledge modeling techniques towards the definition of a global approach: MNEMO (Methodology for kNowledgE acquisition and MOdelling)

It is commonly believed that the success of a company lies in the management of its knowledge, which is strategic resource for innovation and continuity. However, the most valuable knowledge is also tacit. It is difficult to be preserved, to be made reusable and to be enhanced, because it lies in people's minds and it is hard to express and share. Knowledge engineering techniques have been adapted and used for knowledge management, especially, for the acquisition and modelling of this kind of knowledge. In this paper, we present MNEMO (Methodology for kNowledgE acquisition and MOdelling), a mixed methodological approach, which combines the strengths of two of the mentioned techniques, CommonKADS and MASK (Method of Analysis and Structuring Knowledge), both analyzed and evaluated through real applications in specific domains. The goal is to dispose of a global method, which aims to be more complete and flexible for knowledge management purposes, with particular attention to modelling activity.
Beyond Binary Program Transformation

We describe a number of program transformation and analysis tools developed at SRI to tackle bloatware from three angles: slicing binaries to exclude unnecessary components, transformation of different copies of the same binary to create diversity and reduce the potential impact of an attack, and verification-based super-optimization to prune unreachable code and harden vulnerable code. At the core of these approaches is code transformation: we must add, remove, or change a binary without altering its desired behavior (but potentially removing some of its undesired behavior). The challenge is to ensure that these transformations are correct. We argue that a formal model of intermediate code representation (e.g., LLVM or JVM bytecode) is the right level of abstraction to address this challenge.
Lower prosthesis-specific 10-year revision rate with crosslinked than with non-crosslinked polyethylene in primary total knee arthroplasty

Background and purpose — While highly crosslinked polyethylene has shown reduced in vivo wear and lower rates of revision for total hip arthroplasty, there have been few long-term studies on its use in total knee arthroplasty (TKA). We compared the rate of revision of non-crosslinked polyethylene to that of crosslinked polyethylene in patients who underwent TKA for osteoarthritis. Patients and methods — We examined data from the Australian Orthopaedic Association National Joint Replacement Registry on 302,214 primary TKA procedures with non-crosslinked polyethylene and 83,890 procedures with crosslinked polyethylene, all of which were performed for osteoarthritis. The survivorship of the different polyethylenes was estimated using the Kaplan-Meier method and was compared using proportional hazard models. Results — The 10-year cumulative revision rate for non-crosslinked polyethylene was 5.8% (95% CI: 5.7–6.0) and for crosslinked polyethylene it was 3.5% (95% CI: 3.2–3.8) (> 6.5-year HR = 2.2 (1.5–3.1); p < 0.001). There was no effect of surgical volume or method of prosthesis fixation on outcome. There were 4 different TKA designs that had a minimum of 2,500 procedures in at least 1 of the polyethylene groups and a follow-up of ≥ 5 years. 2 of these, the NexGen and the Natural Knee II, had a lower rate of revision for crosslinked polyethylene. The Scorpio NRG/Series 7000 and the Triathlon Knee did not show a lower rate of revision for crosslinked polyethylene. Interpretation — There is a lower rate of revision for crosslinked polyethylene in TKA, and this appears to be prosthesis-specific and when it occurs is most evident in patients < 65 years of age. The difference in revision rates was mainly due to revisions because of lysis and loosening.
Using cross-species comparisons and a neurobiological framework to understand early social deprivation effects on behavioral development

Abstract Building upon the transactional model of brain development, we explore the impact of early maternal deprivation on neural development and plasticity in three neural systems: hyperactivity/impulsivity, executive function, and hypothalamic–pituitary–adrenal axis functioning across rodent, nonhuman primate, and human studies. Recognizing the complexity of early maternal–infant interactions, we limit our cross-species comparisons to data from rodent models of artificial rearing, nonhuman primate studies of peer rearing, and the relations between these two experimental approaches and human studies of children exposed to the early severe psychosocial deprivation associated with institutional care. In addition to discussing the strengths and limitations of these paradigms, we present the current state of research on the neurobiological impact of early maternal deprivation and the evidence of sensitive periods, noting methodological challenges. Integrating data across preclinical animal models and human studies, we speculate about the underlying biological mechanisms; the differential impact of deprivation due to temporal factors including onset, offset, and duration of the exposure; and the possibility and consequences of reopening of sensitive periods during adolescence.
President's Commission on Critical Infrastructure Protection and Presidential Decision Directive 63

Historical perspective on threats and challenges: the President's Commission on Critical Infrastructure Protection (PCCIP) and Presidential Decision Directive (PDD) 63. In recognition of threats to our national infrastructures, President Clinton signed the Executive Order 13010 on July 15, 1996, establishing the PCCIP. The Commission was chartered to conduct a comprehensive review and recommend a national policy for protecting critical infrastructures and assuring their continued operation. The Commission's landmark report—Critical Foundations: Protecting America's Infrastructures—is discussed along with the case and strategy for action in terms of infrastructure interdependencies. An overview of the subsequent PDD 63 is covered, along with research and development needs. Keywords: critical infrastructure protection; President's Commission; Executive Order 13010; Presidential Decision Directive 63; interdependencies; partnership; R&D
The Relevance of the Microphysical and Radiative Properties of Cirrus Clouds to Climate and Climatic Feedback

Abstract This paper examines the effects of the relationship between cirrus cloud ice water content and cloud temperature on climate change. A simple mechanistic climate model is used to study the feedback between ice water content and temperature. The central question studied in this paper concerns the extent to which both the radiative and microphysical properties of cirrus cloud influence such a feedback. To address this question, a parameterization of the albedo and emissivity of clouds is introduced. Observations that relate the ice water content to cloud temperature are incorporated in the parameterization to introduce a temperature dependence to both albedo and emittance. The cloud properties relevant to the cloud feedback are expressed as functions of particles size re, asymmetry parameter g and cloud temperature and analyses of aircraft measurements, lidar and ground based radiometer data are used to select re and g. It was shown that scattering calculations assuming spherical particles with a di.
The Relative Importance of Strength and Weight in Processing New Information in the College Football Betting Market

Griffin and Tversky (1992) suggest that individuals, when formulating posterior probabilities based on the available evidence, tend to overreact to a new piece of evidence's strength while underreacting to the relative importance of its weight. We test this prediction using the college football betting market, a market that is commonly employed in tests for efficiency and rationality. Using average points in excess of the spread and streak against the spread as measures for strength and weight, respectively, we find that bettors overreact to strength and underreact to weight. These results are consistent with the predictions of Griffin and Tversky, as well as with the findings of Sorescu and Subrahmanyam (2006) and Barberis, Shleifer, and Vishny (1998) in financial market settings. Our work also provides insight into how behavioral biases might affect price-formation processes in other markets.
Asset Price Fluctuations in Japan: What Role for Monetary Policy?

This paper examines the nature of fundamental disturbances that have accounted for fluctuations in Japanese nominal and real land prices during the post-war period. A distinction is made between macroeconomic supply and demand shocks, as well as land-market specific shocks, in the context of a dynamic structural VAR model. The results indicate that shocks to aggregate demand-a category encompassing most monetary policy shifts-explain only a small part of the movement in land prices around the longer-term rising trend. Aggregate supply shocks are an important explanatory factor. Much of the variance in land prices also is attributable to factors originating in the land market itself, potentially including speculative bubbles.