gebhart/patrepeval huggingface dataset:
Transcription termination at intrinsic terminators: the role of the RNA hairpin. (1995)

Intrinsic termination of transcription in Escherichia coli involves the formation of an RNA hairpin in the nascent RNA. This hairpin plays a central role in the release of the transcript and polymerase at intrinsic termination sites on the DNA template. We have created variants of the lambda tR2 terminator hairpin and examined the relationship between the structure and stability of this hairpin and the template positions and efficiencies of termination. The results were used to test the simple nucleic acid destabilization model of Yager and von Hippel and showed that this model must be modified to provide a distinct role for the rU-rich sequence in the nascent RNA, since a perfect palindromic sequence that is sufficiently long to form an RNA hairpin that could destabilize the entire putative 12-bp RNA-DNA hybrid does not trigger termination at the expected positions. Rather, our results show that both a stable terminator hairpin and the run of 6-8 rU residues that immediately follows are required for effective intrinsic termination and that termination occurs at specific and invariant template positions relative to these two components. Possible structural or kinetic modifications of the simple model are proposed in the light of these findings and of recent results implicating "inchworming" and possible conformational heterogeneity of transcription complexes in intrinsic termination. Thus, these findings argue that the structure and dimensions of the hairpin are important determinants of the termination-elongation decision and suggest that a complete mechanism is likely to involve specific interactions of the polymerase, the RNA terminator hairpin, and, perhaps, the dT-rich template sequence that codes for the run of rU residues at the 3' end of the nascent transcript.
Pathogenesis of Asthma (2008)

While asthma is considered an inflammatory disorder of the conducting airways, it is becoming increasingly apparent that the disease is heterogeneous with respect to immunopathology, clinical phenotypes, response to therapies, and natural history. Once considered purely an allergic disorder dominated by Th2-type lymphocytes, IgE, mast cells, eosinophils, macrophages, and cytokines, the disease also involves local epithelial, mesenchymal, vascular and neurologic events that are involved in directing the Th2 phenotype to the lung and through aberrant injury-repair mechanisms to remodeling of the airway wall. Structural cells provide the necessary "soil" upon which the "seeds" of the inflammatory response are able to take root and maintain a chronic phenotype and upon which are superimposed acute and subacute episodes usually driven by environmental factors such as exposure to allergens, microorganisms, pollutants or caused by inadequate antiinflammatory treatment. Greater consideration of additional immunologic and inflammatory pathways are revealing new ways of intervening in the prevention and treatment of the disease. Thus increased focus on environmental factors beyond allergic exposure (such as virus infection, air pollution, and diet) are identifying targets in structural as well as immune and inflammatory cells at which to direct new interventions.
In Vivo Testing of Renilla Luciferase Substrate Analogs in an Orthotopic Murine Model of Human Glioblastoma (2006)

In vivo bioluminescent imaging using cells expressing Renilla luciferase is becoming increasingly common. Hindrances to the more widespread use of Renilla luciferase are the high autoluminescence of its natural substrate, coelenterazine, in plasma, the relatively high absorbance by tissue of the light emitted by the enzyme-substrate reaction; rapid clearance of the substrate; and significant cost. These factors, save for the cost, which has its own limiting effect on use, can combine to reduce the sensitivity of in vivo assays utilizing this reporter system, and methods of increasing light output or decreasing autoluminescence could be of great benefit. A number of analogs of coelenterazine are being investigated may accomplish one or both of these goals. In this study that we report on the testing of two new substrate analogs, EnduRen and ViViren, manufactured by Promega Corporation, in an orthotopic murine model of human glioblastoma expressing Renilla luciferase. We have tested these analogs in this cell line both in vitro and in vivo, and find that the substrate viviren results in significantly greater light output than the natural substrate or the other analog EnduRen. This new substrate could be valuable for studies where greater sensitivity is important.
Comparison of Thermodynamic Properties of Simulated Liquid Silica and Water (1997)

We conduct extensive molecular dynamics computer simulations of a rigid-ion model of liquid silica [L.V. Woodcock et al., J. Chem. Phys. 65, 1565 (1976)], evaluating thermodynamic and transport properties over a wide range of pressure and temperature. We find numerous similarities with behavior found in simulations of supercooled water, including a line of density maxima that passes through a maximum temperature as a function of pressure, and the emergence as temperature decreases of maxima in isotherms of the isothermal compressibility as a function of density.
Improved muscle-derived expression of human coagulation factor IX from a skeletal actin/CMV hybrid enhancer/promoter (2000)

Abstract Hemophilia B is caused by the absence of functional coagulation factor IX (F.IX) and represents an important model for treatment of genetic diseases by gene therapy. Recent studies have shown that intramuscular injection of an adeno-associated viral (AAV) vector into mice and hemophilia B dogs results in vector dose–dependent, long-term expression of biologically active F.IX at therapeutic levels. In this study, we demonstrate that levels of expression of approximately 300 ng/mL (6% of normal human F.IX levels) can be reached by intramuscular injection of mice using a 2- to 4-fold lower vector dose (1 × 1011 vector genomes/mouse, injected into 4 intramuscular sites) than previously described. This was accomplished through the use of an improved expression cassette that uses the cytomegalovirus (CMV) immediate early enhancer/promoter in combination with a 1.2-kilobase portion of human skeletal actin promoter. These results correlated with enhanced levels of F.IX transcript and secreted F.IX protein in transduced murine C2C12 myotubes. Systemic F.IX expression from constructs containing the CMV enhancer/promoter alone was 120 to 200 ng/mL in mice injected with 1 × 1011vector genomes. Muscle-specific promoters performed poorly for F.IX transgene expression in vitro and in vivo. However, the incorporation of a sequence from the -skeletal actin promoter containing at least 1 muscle-specific enhancer and 1 enhancer-like element further improved muscle-derived expression of F.IX from a CMV enhancer/promoter-driven expression cassette over previously published results. These findings will allow the design of a clinical protocol for therapeutic levels of F.IX expression with lower vector doses, thus enhancing efficacy and safety of the protocol.
The VTrace tool: building a system tracer for Windows NT and Windows 2000 (2000)

This article describes the techniques used to construct VTrace, a system tracer for Windows NT and Windows 2000. VTrace collects data about processes, threads, messages, disk operations, network operations, and devices. The technique uses a DLL loaded into the address space of every process to intercept Win32 system calls; establishes hook functions for Windows NT kernel system calls; modifies the context switch code in memory to log context switches; and uses device filters to log accesses to devices.
ChemInform Abstract: Modification of C‐Terminal Peptides to Form Peptide Enamides: Synthesis of Chondriamides A and C. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Auditory filter shapes in forward masking as a function of level (1982)

Thresholds were measured for 1-kHz, 5-ms sinusoidal signals following noise maskers with a spectral notch of variable width centered at 1 kHz. In one set of conditions threshold was measured as a function of notch width for three fixed noise levels: 30, 40, and 50 dB SPL/Hz. In order to compensate for the decay of masking, each signal threshold was transformed to the level of a flat-spectrum noise which would give the same masking effect. In a second set of conditions the noise level required for threshold was measured as a function of notch width for three fixed signal levels, separated by 5 dB. The auditory filters derived from the data were essentially the same for the two sets of conditions, and did not vary significantly with masker or signal level. The filters had a mean 3-dB bandwidth of 90 Hz.
Online Server and Workload Management for Joint Optimization of Electricity Cost and Carbon Footprint Across Data Centers (2014)

Internet data centers, typically distributed across the world in order to provide timely and reliable Internet service, have been increasingly pressurized to reduce their carbon footprint and electricity cost. Particularly, data centers will soon be required to abide by carbon capping polices which impose carbon footprint limits to encourage brown energy conservation. We propose an online algorithm, called OnlineCC, for minimizing the operational cost while satisfying the carbon footprint reduction target of a set of geo-distributed data centers. OnlineCC makes use of Lyapunov optimization technique while operating without long-term future information, making it attractive in the presence of uncertainties associated with data center information e.g., input workload. We prove that OnlineCC achieves a near optimal operational cost (electricity cost) compared to the optimal algorithm with future information, while bounding the potential violation of carbon footprint target, depending on the Lyapunov control parameter, namely V. We also give a heuristic for finding V which significantly shortens the search space to adjust its value. Finally, we perform a trace-based simulation study and a small scale experiment to complement the analysis. The results show that OnlineCC reduces cost by more than 18% compared to a prediction-based online solution while resulting in equal or smaller carbon footprint.
Visual tracking with online Multiple Instance Learning (2009)

In this paper, we address the problem of learning an adaptive appearance model for object tracking. In particular, a class of tracking techniques called “tracking by detection” have been shown to give promising results at real-time speeds. These methods train a discriminative classifier in an online manner to separate the object from the background. This classifier bootstraps itself by using the current tracker state to extract positive and negative examples from the current frame. Slight inaccuracies in the tracker can therefore lead to incorrectly labeled training examples, which degrades the classifier and can cause further drift. In this paper we show that using Multiple Instance Learning (MIL) instead of traditional supervised learning avoids these problems, and can therefore lead to a more robust tracker with fewer parameter tweaks. We present a novel online MIL algorithm for object tracking that achieves superior results with real-time performance.
Monoclonal antibodies against the muscle-specific N-terminus of dystrophin: characterization of dystrophin in a muscular dystrophy patient with a frameshift deletion of exons 3-7. (1993)

The first three exons of the human muscle dystrophin gene were expressed as a beta-galactosidase fusion protein. This protein was then used to prepare two monoclonal antibodies (mAbs) which react with native dystrophin on frozen muscle sections and with denatured dystrophin on western blots but which do not cross-react with the dystrophin-related protein, utrophin. Both mAbs recognized dystrophin in muscular dystrophy (MD) patients with deletions of exon 3, and further mapping with 11 overlapping synthetic peptides showed that they both recognize an epitope encoded by the muscle-specific exon 1. Neither mAb recognizes the brain dystrophin isoform, confirming the prediction from mRNA data that this has a different N-terminus. One Becker MD patient with a frameshift deletion of exons 3-7 is shown to produce dystrophin which reacts with the N-terminal mAbs, as well as with mAbs which bind on the C-terminal side of the deletion. The data suggest that transcription begins at the normal muscle dystrophin promoter and that the normal reading frame is restored after the deletion. A number of mechanisms have been proposed for restoration of the reading frame after deletion of exons 3-7, but those which predict dystrophin with an abnormal N-terminus do not appear to be major mechanisms in this patient.
Hip fractures: A review of predictors affecting Functional Independence Measure, ambulation and rehabilitation length of stay during inpatient rehabilitation in Singapore General Hospital (2015)

Introduction: Osteoporotic hip fractures receiving surgery are common and early rehabilitation is needed in the acute hospital setting. In Singapore, many receive rehabilitation after hip surgery in a tertiary hospital, and various clinical variables may be predictors of functional outcomes. Methods: We retrospectively reviewed 68 patients who went through inpatient rehabilitation in Singapore General Hospital. The primary outcomes of this study were to identify predictors which affect Functional Independence Measure (FIM) efficiency and motor FIM gain at discharge. The secondary outcomes include predictors affecting ambulation distance at discharge and rehabilitation length of stay (RLOS). Results: Age, dementia and days from fracture to surgery are important predictors of FIM efficiency; age and FIM efficiency are important predictors of ambulation distance; and type of fracture is an important predictor of RLOS. Patients of age &lt;75 (OR 2.419, p=0.002), absence of dementia (OR 2.570, p=0.045) and those who received surgery &lt;3 days from fracture onset (OR 2.529, p=0.036) achieved greater FIM efficiency. Younger patients of age &lt;75 (OR 23.177, p=0.030) and those with FIM efficiency of more than 7 points per week (OR 38.963, p=0.05) achieved greater ambulation distance at discharge. Type of hip fracture is an important predictor for RLOS, with neck of femur fracture patients having shorter RLOS (OR 7.186, p=0.005). Conclusion: Age, dementia, days from fracture to surgery and type of hip fractures are important predictors of early functional outcomes in inpatient rehabilitation setting.
Lysosomal cysteine proteases (cathepsins): promising drug targets (2003)

Papain-like lysosomal cysteine proteases are processive and digestive enzymes expressed in organisms from bacteria to humans. Their ubiquity alone makes them potential drug targets, with the assumption that appropriate specificities may be achieved. These enzymes have rather short active-site clefts, comprising three well defined substrate-binding subsites (S2, S1 and S1') and additionally have comparatively broad binding areas (S4, S3, S2', S3'). This geometry distinguishes them from other protease classes, such as serine and aspartic proteases, with six and eight substrate-binding sites, respectively. Exopeptidases (cathepsins B, C, H and X), in contrast to endopeptidases (such as cathepsins L, S, V and F), possess structural features that facilitate binding of N- and C-terminal groups of substrates in the active-site cleft. Other than a clear preference for free chain termini in the case of exopeptidases, the substrate-binding sites exhibit no strict specificities. Instead, their subsite preferences arise more from specific exclusions of substrate type. This presents a challenge for the design of inhibitors to target a specific cathepsin: only the cumulative effect of an assembly of inhibitor fragments can produce the desired result. The small number of papain-like lysosomal cysteine proteases (11 human enzymes are known) and the small number of substrate-binding sites calls for a innovative and empirical approach.
Phenomena of liquid drop impact on solid and liquid surfaces (1993)

The fluid dynamic phenomena of liquid drop impact are described and reviewed. These phenomena include bouncing, spreading and splashing on solid surfaces, and bouncing, coalescence and splashing on liquid surfaces. Further, cavitation and the entrainment of gas into an impacted liquid may be observed. In order to distinguish properly between the results of different experiments different impact scenarios are discussed. The specific conditions under which the above phenomena did occur in experiments are analyzed and the characteristics of drop impact phenomena are described in detail.
II. Synthesis of indigogenic substrates for esterases (1958)

Abstract Oxidative conversion of indoxyl or a substituted indoxyl into the corresponding indigoid dye is a chromogenic reaction suitable for application in cytochemical staining methods for the localization of cellular enzymes. The synthesis is described of a series of substituted indoxyl acetates for comparative testing as model chromogenic substrates for esterases, and for study of the potentialities of the general chromogenic principle.
Rotary Engine Geometry (1977)

Most of the mathematics implicit in the famous rotary combustion engine of Felix Wankel predates the engine by a few centuries. We will survey in this note the classical roots of rotary engine geometry; non-mathematical background material can be found in [2]. We begin with several definitions that lead to an elegant result, known as the Bernoulli-Goldbach-Euler double generation theorem, that nicely relates the triangular rotor to its housing (bore).
Analysis of multi-factor influence on measurement of water content in crude oil and its prediction model (2008)

The measurement of water content in crude oil based on method of dielectric coefficient is affected by multi-factor, including temperature, salinity content, flow states of oil/water mixture and output characteristic of measuring-sensor, is regarded as a multi-input and single-output nonlinear system with time-variance, strong uncertainty and randomicity. In this paper, a measuring system based on multi-sensor is designed for experiment of oil/water two-phase flow, the influence relationship and complexity of multi-factor in the parameter detection of oil/water mixture is developed by numerical simulation combined with theoretical computation. Moreover, a multi-sensor data fusion method based on artificial neural network is presented to establish a prediction model for water content in crude oil, the simulation result shows this method is effective to deal with the influence of nonlinear characteristic of measuring-sensor, temperature and salinity on measurement of water content in crude oil, evidently improving the measuring accuracy of water content.
The Prevalence and Clinical Features of Internal Disc Disruption in Patients With Chronic Low Back Pain (1995)

A diagnosis of internal disc disruption can be made in a significant proportion of patients with chronic low back pain, but no conventional clinical test can discriminate patients with internal disc disruption from patients with other conditions.
Retinoid‐enhanced gap junctional communication is achieved by increased levels of connexin 43 mRNA and protein (1990)

Natural and synthetic retinoids are potent inhibitors of experimental carcinogenesis in animals and cause reversion of premalignant lesions in humans. In the model C3H 10T1/2 cell system, retinoids enhance postconfluent growth control, reversibly inhibit carcinogen-induced transformation, and enhance gap junctional intercellular communication. These effects are highly correlated. 10T1/2 cells were found to express low levels of connexin 43, a gap junctional protein first found in the heart. After treatment of confluent 10T1/2 cells with the synthetic retinoid tetrahydrotetramethylnapthalenylpropenylbenzoic acid (TTNPB), levels of connexin 43 mRNA and protein increased within 6 h of treatment, while elevation of junctional communication was detected within 12-18 h. The maximally effective concentration of TTNPB (10(-8) M) caused an approximate 10-fold elevation of connexin 43 gene transcripts after 72 h. Indirect immunofluorescence microscopy using a polyclonal antibody to the synthetic C-terminal region of connexin 43 demonstrated that TTNPB induced many fluorescent plaques in regions of cell-cell contact. These results provide a molecular basis for the retinoid-enhanced junctional communication in 10T1/2 cells. It is proposed that one action of retinoids is to modulate the intercellular transfer of signal molecules. These could mediate many of the physiological actions of retinoids on growth control and carcinogenesis.
Chondrocyte-matrix attachment complexes mediate survival and differentiation (1998)

Integrin mediated cell-extracellular matrix interactions are required for survival and differentiation of many cell types. In this review, the cell-matrix attachment complex (CMAX) is described for chondrocytes. The evidence that integrin-mediated signal transduction is necessary for normal chondrocyte differentiation and survival in various culture conditions and in vivo are reviewed. The possible signal transduction pathways stimulated by the extracellular matrix components are discussed with a review of current data from chondrocyte experiments. In addition, the influence of parathyroid hormone and transforming growth factor beta on chondrocyte survival has been included as they may function in concert with integrin mediated signal transduction. Finally, specific changes in gene expression preceding apoptosis are discussed. The current understanding of how integrin-mediated signals prevent apoptosis and implications of anchorage-dependent survival for development and differentiation of the chondrocyte phenotype are discussed.
Genetic and vascular modifiers of age-sensitive cognitive skills: Effects of COMT, BDNF, ApoE, and hypertension. (2009)

Several single nucleotide polymorphisms have been linked to neural and cognitive variation in healthy adults. We examined contribution of three polymorphisms frequently associated with individual differences in cognition (Catechol-O-Methyl-Transferase Val158Met, Brain-Derived-Neurotrophic-Factor Val66Met, and Apolipoprotein E epsilon4) and a vascular risk factor (hypertension) in a sample of 189 volunteers (age 18-82). Genotypes were determined from buccal culture samples, and cognitive performance was assessed in 4 age-sensitive domains?fluid intelligence, executive function (inhibition), associative memory, and processing speed. We found that younger age and COMT Met/Met genotype, associated with low COMT activity and higher prefrontal dopamine content, were independently linked to better performance in most of the tested domains. Homozygotes for Val allele of BDNF polymorphism exhibited better associative memory and faster speed of processing than the Met allele carriers, with greater effect for women and persons with hypertension. Carriers of ApoE epsilon4 allele evidenced steeper age-related increase in costs of Stroop color interference, but showed no negative effects on memory. The findings indicate that age-related cognitive performance is differentially affected by distinct genetic factors and their interactions with vascular health status.
LINC transmitter (1991)

An LINC transmitter exploiting modern DSP techniques is described, together with a method for significantly reducing the bandwidth of the processing required. Practical results are presented which show the linearity of the transmitter to compare favourably with established linearising techniques such as Cartesian feedback.