gebhart/patrepeval huggingface dataset:
Rationalization of the Difference in Lifetime of Two Covalent Sialosyl−Enzyme Intermediates of <i>Trypanosoma rangeli</i> Sialidase (2008)

The difference in lifetime with respect to hydrolysis of two covalent syalosyl-enzyme intermediates of two difluorinated sialic acid analogues ( 1 and 2) bound to Trypanosoma rangeli sialidase is rationalized based on quantum mechanical calculations. The two intermediates differ only in a single functional group, acetamide in the sialidase- 1 complex and hydroxyl in the sialidase- 2 complex. It is shown that the acetamide group, which is also present in the natural substrate, increases the pKa of a catalytic base (Asp60) through electrostatic repulsion with the carbonyl oxygen on the ligand. This oxygen is absent in 2, resulting in a less basic Asp60 residue and, hence, a longer lifetime of the silaidase- 2 complex. Presumably, the lifetime of a sialidase inhibitor complex could be increased further by substituents that stabilize the negative charge on (and lowers the pKa value of) Asp60 in T. rangeli sialidase.
CDK5RAP2 Is a Pericentriolar Protein That Functions in Centrosomal Attachment of the γ-Tubulin Ring Complex (2007)

Microtubule nucleation and organization by the centrosome require gamma-tubulin, a protein that exists in a macromolecular complex called the gamma-tubulin ring complex (gammaTuRC). We report characterization of CDK5RAP2, a novel centrosomal protein whose mutations have been linked to autosomal recessive primary microcephaly. In somatic cells, CDK5RAP2 localizes throughout the pericentriolar material in all stages of the cell cycle. When overexpressed, CDK5RAP2 assembled a subset of centrosomal proteins including gamma-tubulin onto the centrosomes or under the microtubule-disrupting conditions into microtubule-nucleating clusters in the cytoplasm. CDK5RAP2 associates with the gammaTuRC via a short conserved sequence present in several related proteins found in a range of organisms from fungi to mammals. The binding of CDK5RAP2 is required for gammaTuRC attachment to the centrosome but not for gammaTuRC assembly. Perturbing CDK5RAP2 function delocalized gamma-tubulin from the centrosomes and inhibited centrosomal microtubule nucleation, thus leading to disorganization of interphase microtubule arrays and formation of anastral mitotic spindles. Together, CDK5RAP2 is a pericentriolar structural component that functions in gammaTuRC attachment and therefore in the microtubule organizing function of the centrosome. Our findings suggest that centrosome malfunction due to the CDK5RAP2 mutations may underlie autosomal recessive primary microcephaly.
Differentiating Cortical Areas Related to Pain Perception From Stimulus Identification: Temporal Analysis of fMRI Activity (1999)

In a recent functional magnetic resonance imaging study (fMRI), we reported the cortical areas activated in a thermal painful task and compared the extent of overlap between this cortical network and those activated during a vibrotactile task and a motor task. In the present study we examine the temporal properties of the cortical activations for all three tasks and use linear systems identification techniques to functionally differentiate the cortical regions identified in the painful thermal task. Cortical activity was examined in the contralateral middle third of the brain of 10 right-handed subjects, using echo-planar imaging and a surface coil. In another eight subjects the temporal properties of the thermal task were examined psychophysically. The fMRI impulse response function was estimated from the cortical activations in the vibrotactile and motor tasks and shown to correspond to earlier reports. Given the fMRI impulse response function and the time courses for the thermal stimulus and the associated pain ratings, predictor functions were generated. The correlation between these predictor functions and cortical activations in the painful thermal task indicated a gradual transition of information processing anteroposteriorly in the parietal cortex. Within this region, activity in the anterior areas more closely reflected thermal stimulus parameters, whereas activity more posteriorly was better related to the temporal properties of pain perception. Insular cortex at the level of the anterior commissure was the region best related to the thermal stimulus, and Brodmann's area 5/7 was the region best related to the pain perception. The functional implications of these observations are discussed.
Dual constellation diversity-enhanced modulation for network-coded bidirectional relaying in an asymmetric channel (2009)

In this paper, we consider a modulation scheme for a network-coded bi-directional relaying (CBR) scheme in which two different signals from mutually communicating nodes are network-coded in the relay node. It employs dual constellations as a useful means of dealing with its performance degradation in the CBR over asymmetric channel (i.e., the different signal-to-noise ratio in each link), which provide not only a diversity gain from the symbol repetition but also a coding gain from the constellation rearrangement to protect the network-coded symbols. We study the channel utilization and bit error rate performance of the different CBR schemes to show that the proposed diversity-enhanced CBR system always outperforms other existing systems as long as traffic load is properly balanced along the bi-directional links.
An Intramolecular Photocyclization to from the Azepino [3,4,5-cd] Indole System (1988)

Abstract Azepino [3,4,5-cd] indoles 5a and 5b are formed in good yield via the intramolecular photocyclization of N-chloracetyl-3-aminomethylinodles.
The electronic numerical integrator and computer (ENIAC) (1946)

This paper was first published in Mathematical Tables and Other Aids to Computation just after the ENIAC was announced in 1946. It was the major source of technical information about the machine for the scientific world of the time. Even today it ranks as one of the classic descriptions of the ENIAC. This paper is reprinted by the kind permission of the American Mathematical Society and the National Academy of Sciences.
Hedgehog Signaling Alters Adipocyte Maturation of Human Mesenchymal Stem Cells (2008)

Human stem cells are powerful tools by which to investigate molecular mechanisms of cell growth and differentiation under normal and pathological conditions. Hedgehog signaling, the dysregulation of which causes several pathologies, such as congenital defects and cancer, is involved in several cell differentiation processes and interferes with adipocyte differentiation of rodent cells. The present study was aimed at investigating the effect of Hedgehog pathway modulation on adipocyte phenotype using different sources of human mesenchymal cells, such as bone marrow stromal cells and human multipotent adipose-derived stem cells. We bring evidence that Hedgehog signaling decreases during human adipocyte differentiation. Inhibition of this pathway is not sufficient to trigger adipogenesis, but activation of Hedgehog pathway alters adipocyte morphology as well as insulin sensitivity. Analysis of glycerol-3-phosphate dehydrogenase activity and expression of adipocyte marker genes indicate that activation of Hedgehog signaling by purmorphamine impairs adipogenesis. In sharp contrast to reports in rodent cells, the maturation process, but not the early steps of human mesenchymal stem cell differentiation, is affected by Hedgehog activation. Hedgehog interferes with adipocyte differentiation by targeting CCAAT enhancer-binding protein alpha and peroxisome proliferator-activated receptor (PPAR) gamma2 expression, whereas PPARgamma1 level remains unaffected. Although Hedgehog pathway stimulation does not modify the total number of adipocytes, adipogenesis appears dramatically impaired, with reduced lipid accumulation, a decrease in adipocyte-specific markers, and acquisition of an insulin-resistant phenotype. This study indicates that a decrease in Hedgehog signaling is necessary but not sufficient to trigger adipocyte differentiation and unveils a striking difference in the adipocyte differentiation process between rodent and human mesenchymal stem cells.
Risk of Hemorrhagic Stroke With Aspirin Use (2005)

When considering whether aspirin is appropriate, the absolute therapeutic cardiovascular benefits of aspirin must be balanced with the possible risks associated with its use, with the most serious being hemorrhagic stroke.
Relationships of the Area under the Curve/MIC Ratio to Different Integral Endpoints of the Antimicrobial Effect: Gemifloxacin Pharmacodynamics in an In Vitro Dynamic Model (2001)

Most integral endpoints of the antimicrobial effect are determined over an arbitrarily chosen time period, such as the dosing interval (tau), regardless of the actual effect duration. Unlike the tau-related endpoints, the intensity of the antimicrobial effect (I(E)) does consider its duration-from time zero to the time when bacterial counts on the regrowth curve achieve the same maximal numbers as in the absence of the antimicrobial. To examine the possible impact of this fundamental difference on the relationships of the antimicrobial effect to the ratio of the area under the concentration-time curve (AUC) to the MIC, a clinical isolate of Staphylococcus aureus was exposed to simulated gemifloxacin pharmacokinetics over a 40-fold range of AUC/MIC ratios, from 11 to 466 h. In each run, I(E) and four tau-related endpoints, including the area under the time-kill curve (AUBC), the area above the curve (AAC), the area between the control growth and time-kill curves (ABBC), and the ABBC related to the area under the control growth curve (AUGC), were calculated for tau = 24 h. Unlike the I(E), which displayed pseudolinear relationships with the AUC/MIC ratio; each tau-related endpoint showed a distinct saturation at potentially therapeutic AUC/MIC ratios (116 to 466 h) when the antimicrobial effect persisted longer than tau. This saturation results from the underestimation of the true effect and may be eliminated if ABBC, AAC, and AUBC (but not AUGC) are modified and determined in the same manner as the I(E) to consider the actual effect duration. These data suggest a marginal value of the tau-related endpoints as indices of the total antimicrobial effect. Since all of them respond to AUC/MIC ratio changes less than the I(E), the latter is preferable in comparative pharmacodynamic studies.
New liquid-chromatographic method for measuring polyethylene glycol in urine. (1986)

The various Mr fractions of polyethylene glycol (PEG) in human urine are quantified by "high-pressure" liquid chromatography. A simple preparation step involving lyophilization and chloroform extraction of the sample is required. Aliquots (10 microL) are chromatographed isocratically in equivolume mixtures of methanol and water on a column of styrene divinylbenzene and the refractive index of the effluent is measured. The results vary linearly with the concentrations of standards up to at least 10 g/L, and the six major fractions are clearly identifiable in injected samples containing 2 g or more of total PEG per liter. As little as 4 g/L can be precisely quantified, but for assessing the individual fractions, we recommend a minimum sample concentration of 7 g/L. Analytical recovery of PEG added to urine controls was 90%. Urines collected during 6 h from 11 human subjects after each had ingested 5.6 g of PEG showed no interference from endogenous compounds. We find this method to be a simple, labor-saving means of quantifying urinary PEG in the clinical laboratory.
Realizing quantum controlled phase flip through cavity QED (2004)

We propose a scheme to realize quantum controlled phase flip (CPF) between two rare-earth ions embedded in the respective microsphere cavity via interacting with a single-photon pulse in sequence. The numerical simulations illuminate that the CPF gate between ions is robust and scalable with extremely high fidelity and low error rate. Our scheme is more applicable than other schemes presented before based on current laboratory cavity-QED technology, and it is possible to be used as an applied unit gate in future quantum computation and quantum communication.
A developmental analysis of oligodendroglial integrins in primary cells: changes in αv-associated β subunits during differentiation (1994)

We have examined the expression of integrins on primary oligodendroglial cells during the differentiation of the proliferative oligodendrocyte precursor (O-2A progenitor) cell to the postmitotic oligodendrocyte. Cells of the oligodendrocyte lineage expressed a limited repertoire of integrins: alpha 6 beta 1 and alpha v integrins including alpha v beta 1, alpha v beta 3 and alpha v beta 5, as well as a potentially novel integrin alpha v beta 80 kDa. Integrin expression was developmentally regulated; during differentiation alpha v beta 1 was reduced and alpha v beta 5 upregulated. These results suggest that laminin and vitronectin are important extracellular matrix ligands for oligodendrocytes, and provide a rational explanation for previous observations that RGD peptides inhibit the expression of myelin-specific genes. They also suggest a simple model by which switching of integrin beta subunits might regulate differentiation. As chimeric beta 1 integrins with a beta 5 cytoplasmic domain support proliferation less well than normal beta 1 integrins (Pasqualini and Hemler (1994), J. Cell Biol. 125, 447-460) the switch from alpha v beta 1 to alpha v beta 5 might play a key instructive role in the cessation of proliferation and subsequent differentiation.
The Relations Between Family Environment and Violence Exposure Among Youth: Findings From the National Survey of Adolescents (2005)

A national household probability sample of 4,023 adolescents (ages 12 to 17) completed telephone interviews assessing demographics, adverse family environment, and violence exposure. Logistic regressions examined relations among family environment and each violence exposure type, controlling for demographics and other violence exposures. Relationships between family environment and violence exposure varied, depending on type of violence reported, most notably between intrafamilial versus extrafamilial violence. After controlling for family environment, exposure to one violence type significantly increased the likelihood of other violence exposures. Family substance use and not always living with a natural parent were significantly associated with all three types of violence exposure. Findings indicate that clinical assessments should include a thorough evaluation of family environment and violence exposure and also highlight the need for treatment to focus on the adolescent and broader family unit. Future research is needed to further examine these complex interrelationships and their associations with adolescent outcomes.
Characterization of Substance P‐Like Immunoreactivity and Tachykinin‐Encoding mRNAs in Rat Medullary Thyroid Carcinoma Cell Lines (1992)

Rat thyroid tissue and three rat medullary thyroid carcinoma cell lines, 6-23, WE4/2, and CA77, have been examined for substance P (SP) and SP-like peptide expression. Analysis by combined HPLC and radioimmunoassay revealed the presence of SP in thyroid and 6-23 cell extracts. The presence of SP-encoding mRNAs was also detected in 6-23 cells by solution hybridization-nuclease protection analysis. SP-encoding mRNA expression was increased (fourfold) by maintaining the 6-23 cells in low serum (2%) for 4 or 10 days. The 6-23 cells also expressed other SP-like immunoreactive species, which were chromatographically and immunologically distinct from established tachykinin peptides. WE4/2 cells did not contain SP but did display SP-like immunoreactivity (SPLI), which migrated like the unidentified SPLI in 6-23 cells. CA77 cells did not contain SP or SP-encoding mRNA but did contain SPLI that migrated identically to the unidentified SPLI in the other cell lines. This novel SPLI was detected with an antiserum directed against the SP carboxyl terminus and to a lesser extent with an antiserum directed against the neurokinin A carboxyl terminus, but it showed minimal cross-reactivity using an antiserum directed against the midportion of SP. Treatment with 50 mM KCl resulted in secretion of this SPLI from CA77 cells. Gel filtration analysis demonstrated that this novel SPLI had an apparent molecular weight of approximately 1,000. These results are discussed in terms of cell lines that express tachykinin peptides and in terms of the molecular nature of the new SPLI detected in CA77 cells.
Scalable and Efficient Video Coding Using 3-D Modeling (2006)

In this paper, we present a three-dimensional (3D) model-based video coding scheme for streaming static scene video in a compact way but also enabling time and spatial scalability according to network or terminal capability and providing 3D functionalities. The proposed format is based on encoding the sequence of reconstructed models using second-generation wavelets, and efficiently multiplexing the resulting geometric, topological, texture, and camera motion binary representations. The wavelets decomposition can be adaptive in order to fit to images and scene contents. To ensure time scalability, this representation is based on a common connectivity for all 3D models, which also allows straightforward morphing between successive models ensuring visual continuity at no additional cost. The method proves to be better than previous methods for video encoding of static scenes, even better than state-of-the-art video coders such as H264 (also known as MPEG AVC). Another application of our approach are smoothing camera path for suppression of jitter from hand-held acquisition and the fast transmission and real-time visualization of virtual environments obtained by video capture, for virtual or augmented reality and interactive walk-through in photo-realistic 3D environments around the original camera path
Likelihood Ratios for a Sleep Apnea Clinical Prediction Rule (1994)

Nocturnal polysomnography, the standard diagnostic test for sleep apnea, is an expensive and limited resource. In order to help identify the urgency of need for treatment, we determined which clinical features were most useful for establishing an accurate estimate of the probability that a patient had sleep apnea. Of 263 physician-referred patients, 200 were eligible for the study and 180 (90%) completed it. All patients had their histories recorded with a standard questionnaire, and underwent anthropomorphic measurements and nocturnal polysomnography. Sleep apnea was defined as more than 10 episodes of apnea or hypopnea per hour of sleep. Multiple linear and logistic regression models predictive of sleep apnea were compared with physicians' subjective impressions and previously reported models. Likelihood ratios were calculated for several levels of a sleep apnea clinical score produced by one of the linear models. Predictors of sleep apnea in the final model (R2 = 0.34) included neck circumference, hypertension, habitual snoring, and bed partner reports of nocturnal gasping/choking respirations. This model was superior to physician impression, slightly inferior to more detailed linear and logistic models, and comparable to previously reported models. A sleep apnea clinical score of less than 5 had a likelihood ratio of 0.25 (95% CI: 0.15 to 0.42) and a corresponding posttest probability of 17%, while a score of greater than 15 had a likelihood ratio of 5.17 (95% CI: 2.54 to 10.51) and posttest probability of 81%. These likelihood ratios can simply and accurately determined the probability of whether a patient has sleep apnea.
Rough set theory: a data mining tool for semiconductor manufacturing (2001)

The growing volume of information poses interesting challenges and calls for tools that discover properties of data. Data mining has emerged as a discipline that contributes tools for data analysis, discovery of new knowledge, and autonomous decisionmaking. In this paper, the basic concepts of rough set theory and other aspects of data mining are introduced. The rough set theory offers a viable approach for extraction of decision rules from data sets. The extracted rules can be used for making predictions in the semiconductor industry and other applications. This contrasts other approaches such as regression analysis and neural networks where a single model is built. One of the goals of data mining is to extract meaningful knowledge. The power, generality, accuracy, and longevity of decision rules can be increased by the application of concepts from systems engineering and evolutionary computation introduced in this paper. A new rule-structuring algorithm is proposed. The concepts presented in the paper are illustrated with examples.
Suppression of the Inflammatory Immune Response Prevents the Development of Chronic Biofilm Infection Due to Methicillin-Resistant Staphylococcus aureus (2011)

Staphylococcus aureus is a common cause of prosthetic implant infections, which can become chronic due to the ability of S. aureus to grow as a biofilm. Little is known about adaptive immune responses to these infections in vivo. We hypothesized that S. aureus elicits inflammatory Th1/Th17 responses, associated with biofilm formation, instead of protective Th2/Treg responses. We used an adapted mouse model of biofilm-mediated prosthetic implant infection to determine chronic infection rates, Treg cell frequencies, and local cytokine levels in Th1-biased C57BL/6 and Th2-biased BALB/c mice. All C57BL/6 mice developed chronic S. aureus implant infection at all time points tested. However, over 75% of BALB/c mice spontaneously cleared the infection without adjunctive therapy and demonstrated higher levels of Th2 cytokines and anti-inflammatory Treg cells. When chronic infection rates in mice deficient in the Th2 cytokine interleukin-4 (IL-4) via STAT6 mutation in a BALB/c background were assessed, the mice were unable to clear the S. aureus implant infection. Additionally, BALB/c mice depleted of Treg cells via an anti-CD25 monoclonal antibody (MAb) were also unable to clear the infection. In contrast, the C57BL/6 mice that were susceptible to infection were able to eliminate S. aureus biofilm populations on infected intramedullary pins once the Th1 and Th17 responses were diminished by MAb treatment with anti-IL-12 p40. Together, these results indicate that Th2/Treg responses are mechanisms of protection against chronic S. aureus implant infection, as opposed to Th1/Th17 responses, which may play a role in the development of chronic infection.
GSM SIMs as web servers (2000)

GSM SIMs are operator-trusted security servers in GSM, performing computations on behalf of a GSM subscriber. This paper outlines a prototype that integrates the GSM security infrastructure into the Internet: The idea is to extend a GSM SIM to a security server for a GSM subscriber in the Internet. Such a WebSIM, like any other server in the Internet, speaks TCP/IP and is transparently accessible from Internet hosts via HTTP. Specific services offered by SIMs, e.g. authentication, can be accessed from the Internet using CGI scripts.
Optimization of a continuous-time maximum power point tracking algorithm in the presence of noise (2010)

This paper introduces an analysis of the effect of noise on a continuous-time maximum power point tracking (MPPT) algorithm for photovoltaic systems, leading to an optimization of the system parameters. The results of this are then compared to discrete-time algorithms. This analysis provides a better understanding of how noise affects the performance of MPPT algorithms and how well those effects can be mitigated.