gebhart/patrepeval huggingface dataset:
Multimodal speaker detection using error feedback dynamic Bayesian networks (2002)

Design and development of novel human-computer interfaces poses a challenging problem: actions and intentions of users have to be inferred from sequences of noisy and ambiguous multi-sensory data such as video and sound. Temporal fusion of multiple sensors has been efficiently formulated using dynamic Bayesian networks (DBNs) which allows the power of statistical inference and learning to be combined with contextual knowledge of the problem. Unfortunately simple learning methods can cause such appealing models to fail when the data exhibits complex behavior. We formulate a learning framework for DBNs based on error-feedback and statistical boosting theory. We apply this framework to the problem of audio/visual speaker detection in an interactive kiosk environment using "off-the-shelf" visual and audio sensors (face, skin, texture, mouth motion, and silence detectors). Detection results obtained in this setup demonstrate superiority of our learning framework over that of the classical ML learning in DBNs.
Anti-cocaine vaccines: antibody protection against relapse (2003)

The past decade has seen the development of several vaccines against illicit-drugs. These include vaccines for producing antibodies against cocaine, heroin, methamphetamine and nicotine. The present focus is on anti-cocaine vaccines, as more research has been conducted with these vaccines than other vaccines targeted against a drug of abuse. Attention needs to be given to the structure of the hapten being conjugated, the characteristics of the carrier protein for conjugation with the hapten and the immunisation regimen for antibody production. These issues have an impact on the level of and variability in the anti-cocaine antibodies actively induced and, consequently, on the pharmacokinetic and pharmacodynamic properties of the vaccine. These issues also have an impact on the preclinical and clinical success of the vaccine in protecting against drug use and relapse. If an anti-cocaine vaccine is to be clinically useful, it must induce a sufficient level of antibody in the blood to prevent easy surmountability of protection by continued cocaine use and should be compatible with other treatment medications that may be simultaneously administered.
Exploration of sequence space for protein engineering (2001)

The process of protein engineering is currently evolving towards a heuristic understanding of the sequence-function relationship. Improved DNA sequencing capacity, efficient protein function characterization and improved quality of data points in conjunction with well-established statistical tools from other industries are changing the protein engineering field. Algorithms capturing the heuristic sequence-function relationships will have a drastic impact on the field of protein engineering. In this review, several alternative approaches to quantitatively assess sequence space are discussed and the relatively few examples of wet-lab validation of statistical sequence-function characterization/correlation are described.
Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry for Detection of Antibiotic Resistance Mechanisms: from Research to Routine Diagnosis (2013)

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied as an identification procedure in clinical microbiology and has been widely used in routine laboratory practice because of its economical and diagnostic benefits. The range of applications of MALDI-TOF MS has been growing constantly, from rapid species identification to labor-intensive proteomic studies of bacterial physiology. The purpose of this review is to summarize the contribution of the studies already performed with MALDI-TOF MS concerning antibiotic resistance and to analyze future perspectives in this field. We believe that current research should continue in four main directions, including the detection of antibiotic modifications by degrading enzymes, the detection of resistance mechanism determinants through proteomic studies of multiresistant bacteria, and the analysis of modifications of target sites, such as ribosomal methylation. The quantification of antibiotics is suggested as a new approach to study influx and efflux in bacterial cells. The results of the presented studies demonstrate that MALDI-TOF MS is a relevant tool for the detection of antibiotic resistance and opens new avenues for both clinical and experimental microbiology.
Pathway and regulation of erythritol formation in Leuconostoc oenos (1993)

It was recently observed that Leuconostoc oenos GM, a wine lactic acid bacterium, produced erythritol anaerobically from glucose but not from fructose or ribose and that this production was almost absent in the presence of O2. In this study, the pathway of formation of erythritol from glucose in L. oenos was shown to involve the isomerization of glucose 6-phosphate to fructose 6-phosphate by a phosphoglucose isomerase, the cleavage of fructose 6-phosphate by a phosphoketolase, the reduction of erythrose 4-phosphate by an erythritol 4-phosphate dehydrogenase and, finally, the hydrolysis of erythritol 4-phosphate to erythritol by a phosphatase. Fructose 6-phosphate phosphoketolase was copurified with xylulose 5-phosphate phosphoketolase, and the activity of the latter was competitively inhibited by fructose 6-phosphate, with a Ki of 26 mM, corresponding to the Km of fructose 6-phosphate phosphoketolase (22 mM). These results suggest that the two phosphoketolase activities are borne by a single enzyme. Extracts of L. oenos were also found to contain NAD(P)H oxidase, which must be largely responsible for the reoxidation of NADPH and NADH in cells incubated in the presence of O2. In cells incubated with glucose, the concentrations of glucose 6-phosphate and of fructose 6-phosphate were higher in the absence of O2 than in its presence, explaining the stimulation by anaerobiosis of erythritol production. The increase in the hexose 6-phosphate concentration is presumably the result of a functional inhibition of glucose 6-phosphate dehydrogenase because of a reduction in the availability of NADP.
Targeting HER‐2/neu for active‐specific immunotherapy in a mouse model of spontaneous breast cancer (1999)

The identification of tumor-associated antigens has led to increased interest in vaccination strategies to treat and/or prevent cancer. This study examined the feasibility of active-specific immunotherapy against the breast-tumor antigen HER-2/neu using a HER-2/neu transgenic (rNeu-TG) mouse model. rNeu-TG mice develop spontaneous breast tumors after pregnancy, indicating that they fail to mount an effective immune response against rNeu. Allogeneic fibroblasts expressing HER-2/neu were used as a cell-based vaccine. Vaccination induced a rNeu-specific anti-tumor immune response that prevented tumor formation of transplanted breast-tumor cells, and also protected mice from spontaneous tumor formation. Both T-cell-mediated and humoral immune responses were detectable in vaccinated mice. Vaccination also protected tumor-bearing mice from a challenge with cell suspensions isolated from spontaneous tumors, indicating that rNeu-TG mice are not tolerant to rNeu, even after spontaneous tumor formation. However, established spontaneous tumors themselves were never affected. This observation correlated with T-cell infiltrations in the injected but not in the established spontaneous tumor. Thus, allogeneic fibroblasts are efficient vaccine vectors to prime a specific immune response against an over-expressed tumor antigen. Moreover, our results suggest striking differences in the immunological requirements for the rejection of an established vs. a transplanted tumor. Int. J. Cancer 83:393–400, 1999. © 1999 Wiley-Liss, Inc.
Genetically Modified Mice Models for Alzheimers Disease (2006)

Transgenic mice models for Alzheimer's disease (AD) are essential to the understanding of disease pathophysiology, develop robust behavioral models and predict outcomes from pharmacological interventions. In the last 10 years, numerous mice models have been developed particularly focusing on the amyloid precursor protein-processing pathway and Tau pathology since brain amyloid deposits and Tau tangles are some of the primary neuropathological consequences of AD. Current views on the amyloid hypothesis and mice models relating to the role of soluble Abeta oligomers and intracellular Abeta in AD pathophysiology will be reviewed. Several novel transgenic mice models that have recently been developed and their potential impact on understanding disease pathogenesis will also be summarized.
Characterization of the CD200 Receptor Family in Mice and Humans and Their Interactions with CD200 (2003)

CD200 (OX2) is a broadly distributed cell surface glycoprotein that interacts with a structurally related receptor (CD200R) expressed on rodent myeloid cells and is involved in regulation of macrophage function. We report the first characterization of human CD200R (hCD200R) and define its binding characteristics to hCD200. We also report the identification of a closely related gene to hCD200R, designated hCD200RLa, and four mouse CD200R-related genes (termed mCD200RLa-d). CD200, CD200R, and CD200R-related genes were closely linked in humans and mice, suggesting that these genes arose by gene duplication. The distributions of the receptor genes were determined by quantitative RT-PCR, and protein expression was confirmed by a set of novel mAbs. The distribution of mouse and human CD200R was similar, with strongest labeling of macrophages and neutrophils, but also other leukocytes, including monocytes, mast cells, and T lymphocytes. Two mCD200 receptor-like family members, designated mCD200RLa and mCD200RLb, were shown to pair with the activatory adaptor protein, DAP12, suggesting that these receptors would transmit strong activating signals in contrast to the apparent inhibitory signal delivered by triggering the CD200R. Despite substantial sequence homology with mCD200R, mCD200RLa and mCD200RLb did not bind mCD200, and presently have unknown ligands. The CD200 receptor gene family resembles the signal regulatory proteins and killer Ig-related receptors in having receptor family members with potential activatory and inhibitory functions that may play important roles in immune regulation and balance. Because manipulation of the CD200-CD200R interaction affects the outcome of rodent disease models, targeting of this pathway may have therapeutic utility.
Molecular Sieving by theBacillus megateriumCell Wall and Protoplast (1971)

Passive permeabilities of the cell wall and protoplast of Bacillus megaterium strain KM were characterized by use of 50 hydrophilic probing molecules (tritiated water, sugars, dextrans, glycols, and polyglycols) which varied widely in size. Weight per cent uptake values (R(w)) were measured at diffusional equilibrium under conditions that negated the influences of adsorption or active transport. Plots of R(w) for intact cells as a function of number-average molecular weight ( M(n)) or Einstein-Stokes hydrodynamic radius ( r(ES)) of the solutes showed three phases: a protoplast uptake phase with a polydisperse exclusion threshold of M(n) = 0.6 x 10(3) to 1.1 x 10(3), r(ES) = 0.6 to 1.1 nm; a cell wall uptake phase with a polydisperse exclusion threshold of M(n) = 0.7 x 10(5) to 1.2 x 10(5), r(ES) congruent with 8.3 nm; and a total exclusion phase. Isolated cell walls showed only the latter two phases. However, it became evident that the cell wall selectively passed only the smallest molecules in a heterodisperse polymer sample. When the molecular-weight distributions of polyglycol samples ( M(n) = 1,000, 1,450, and 3,350) were determined by analytical gel chromatography before and after uptake by intact cells or isolated cell walls, a quasi-monodisperse exclusion threshold was obtained corresponding to M(n) = 1,200, r(ES) = 1.1 nm. The permeability of isolated protoplasts was assessed by the relative ability of solutes to effect osmotic stabilization. An indefinite exclusion threshold, evident even with monodisperse sugars, was attributed to lengthwise orientation of the penetrating rod-shaped molecules. Altogether, the best estimate of the limiting equivalent porosity of the protoplast was 0.4 to 0.6 nm in radius and of the cell wall, 1.1 nm.
Tunable Colors in Opals and Inverse Opal Photonic Crystals (2010)

Abstract Colloidal photonic crystals and materials derived from colloidal crystals can exhibit distinct structural colors that result from incomplete photonic band gaps. Through rational materials design, the colors of such photonic crystals can be tuned reversibly by external physical and chemical stimuli. Such stimuli include solvent and dye infiltration, applied electric or magnetic fields, mechanical deformation, light irradiation, temperature changes, changes in pH, and specific molecular interactions. Reversible color changes result from alterations in lattice spacings, filling fractions, and refractive index of system components. This review article highlights the different systems and mechanisms for achieving tunable color based on opaline materials with close‐packed or non‐close‐packed structural elements and inverse opal photonic crystals. Inorganic and polymeric systems, such as hydrogels, metallopolymers, and elastomers are discussed.
Toroidal Microphones (1969)

“Toroidal” microphones are defined as microphones having toroid-shaped directional characteristics, i.e., they have minimum sensitivity along the rotational axis of the toroid and maximum sensitivity in the plane perpendicular to that axis. Several practical designs of toroidal microphones based on second-order gradient receivers are proposed and analyzed as to directional characteristics and frequency response. Experimental microphones are presented, some of which use a Helmholtz resonator tuned to the lower end of the frequency range to compensate the ω2 dependence of the second-order gradient receivers and to improve the over-all signal-to-noise ratio of the microphones. Measurements show that the microphone sensitivity in a plane through the rotational axis obeys approximately the expected cosine-squared law. In the direction of the rotational axis, the sensitivity at midfrequencies was found to be typically 20 dB lower than the sensitivity in the plane normal to that axis. The equalized frequency response in this plane is within ±3 dB from 0.3 to 2.5 kHz. Sensitivities are about −80 dBV/μbar. Using existing low-noise pre-amplifiers, this corresponds to a signal-to-noise ratio of about 35 dB for speech at conversational levels.
Phenotypic modulation in sub-populations of human articular chondrocytes in vitro (1990)

Human articular cartilage has been separated into surface (approx. 15% of tissue depth) and deep zones (remaining tissue) and the constituent chondrocytes released by enzymic digestion. Subsequent culture either as a low density monolayer or as a suspension over agarose revealed distinct morphological and synthetic behaviour in the two populations. Whilst in monolayer these morphological differences disappeared with time in culture, over agarose they remained. Surface zone cells formed two types of cell cluster; one that was highly cellular with little extracellular matrix, and the other less frequent, which formed copious amounts of fibrillar matrix. Both types of cluster were surrounded by a layer of flattened chondrocytes. In contrast, deep cells formed a single cluster type that lacked a surrounding cell layer, but formed large amounts of sparse cartilage-like matrix and comprised morphologically typical chondrocytes. In monolayer, both populations gradually ceased to synthesise cartilage matrix components with the exception of link protein. In suspension, whilst the chondrogenic phenotype per se was preserved, there was, nevertheless, a loss in qualitative synthetic heterogeneity, which exists between surface and deep cells, that was not accompanied by changes in the differential rate of 35S incorporation into proteoglycan. Under these conditions, surface cells that normally do not synthesise keratan sulphate initiated de novo synthesis of this glycosaminoglycan. Consequently, it appears that the observed modulation in synthetic ability of the cell sub-populations is independent of the cluster morphology, which, once established, remains constant throughout the culture period.
Soft tissue fixation to bone (1986)

This experiment was designed to compare the immediate fixation strengths of various methods of soft tissue fixation techniques. The fixation techniques tested were the barbed staple, stone staple, suture techniques, screw with spiked plastic washer, and the screw with spiked soft tissue plate. Cadaveric soft tissue specimens were classified into three distinct morphologic types: capsular, tendinous, and extensor mechanism tissue. Each specimen was fixed to bone by one of the fixation techniques. The specimens were loaded in a cyclical fashion until fixation failure occurred. One hundred thirty-seven trials were performed. The screws with the spiked plastic washer and soft tissue plate proved superior overall for all three tissue types. The stone staple was the poorest technique tested. Therefore, if cyclic loading or tension is anticipated at the fixation site, the fixation technique of choice would be the screw with spiked plastic washer or soft tissue fixation plate.
Antigen-Specific Inhibition of Effector T Cell Function in Humans after Injection of Immature Dendritic Cells (2001)

Immunostimulatory properties of dendritic cells (DCs) are linked to their maturation state. Injection of mature DCs rapidly enhances antigen-specific CD4+ and CD8+ T cell immunity in humans. Here we describe the immune response to a single injection of immature DCs pulsed with influenza matrix peptide (MP) and keyhole limpet hemocyanin (KLH) in two healthy subjects. In contrast to prior findings using mature DCs, injection of immature DCs in both subjects led to the specific inhibition of MP-specific CD8+ T cell effector function in freshly isolated T cells and the appearance of MP-specific interleukin 10-producing cells. When pre- and postimmunization T cells were boosted in culture, there were greater numbers of MP-specific major histocompatibility complex tetramer-binding cells after immunization, but these had reduced interferon production and lacked killer activity. These data demonstrate the feasibility of antigen-specific inhibition of effector T cell function in vivo in humans and urge caution with the use of immature DCs when trying to enhance tumor or microbial immunity.
Laser-Doppler Flowmetry in Neurosurgery (1993)

Laser-Doppler flowmetry (LDF) provides a reliable measurement of local cerebral blood flow (lCBF) as demonstrated by multiple validation studies. This article evaluates the clinical applications of LDF in neurosurgery. With the availability of modified probes, it is possible to carry out LDF monitoring of neurosurgical patients in the intensive care unit. Currently, there are multiple systemic and intracranial parameters that are interactive and separately monitored. A multi-channeled digital data acquisition system allows these data to be compiled in a single computer environment for the interpretation of lCBF changes. Guidelines are suggested for the clinical use of LDF monitoring, and the technical features of monitoring including the interpretation of data are summarized.
Characterization and regulation of the NADP-linked 7 alpha-hydroxysteroid dehydrogenase gene from Clostridium sordellii (1994)

A bile acid-inducible NADP-linked 7 alpha-hydroxysteroid dehydrogenase (7 alpha-HSDH) from Clostridium sordellii ATCC 9714 was purified 310-fold by ion-exchange, gel filtration, and dye-ligand affinity chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the purified enzyme showed one predominant peptide band (30,000 Da). The N-terminal sequence was determined, and the corresponding oligonucleotides were synthesized and used to screen EcoRI and HindIII genomic digests of C. sordellii. Two separate fragments (4,500 bp, EcoRI; 3,200 bp, HindIII) were subsequently cloned by ligation to pUC19 and transformation into Escherichia coli DH5 alpha-MCR. The EcoRI fragment was shown to contain a truncated 7 alpha-HSDH gene, while the HindIII fragment contained the entire coding region. E. coli clones containing the HindIII insert expressed high levels of an NADP-linked 7 alpha-HSDH. Nucleotide sequence analyses suggest that the 7 alpha-HSDH is encoded by a monocistronic transcriptional unit, with DNA sequence elements resembling rho-independent terminators located in both the upstream and downstream flanking regions. The transcriptional start site was located by primer extension analysis. Northern (RNA) blot analysis indicated that induction is mediated at the transcriptional level in response to the presence of bile acid in the growth medium. In addition, growth-phase-dependent expression is observed in uninduced cultures. Analysis of the predicted protein sequence indicates that the enzyme can be classified in the short-chain dehydrogenase group.
The reaction of mono- and di-functional alkylating agents with nucleic acids (1961)

1961 6. Preliminary figures for androstenol excretion in urine are given. In the age group 18-45 years they ranged from 19 to 2630 ,ug./24 hr. in men and from 66 to 1010 ,ug./24 hr. in women. This work was carried out partly during
The Role of Growth Hormone in Modulation of the Immune Responsea (1990)

Growth hormone was originally discovered because of its ability to promote linear growth in rodents and humans. It is now known that this molecule also augments a number of activities of leukocytes, such as antibody synthesis, cytolytic activity of T lymphocytes, natural killer cell activity, differentiation of neutrophils, production of tumor necrosis factor-alpha (TNF-alpha), and the synthesis of a thymic hormone known as thymulin. We have shown that growth hormone mimics one action of interferon-gamma (IFN-gamma) by augmenting the production of superoxide anion by macrophages and neutrophils. Growth hormone also is synthesized by leukocytes, which creates the possibility that it may act locally as a cytokine in lymphoid tissue. These findings show that a hormone that was originally isolated from the pituitary gland is involved in regulating host defense responses of leukocytes.
Src-family Tyrosine Kinases in Activation of ERK-1 and p85/p110-phosphatidylinositol 3-Kinase by G/CCKBReceptors (1999)

We have analyzed in Chinese hamster ovary cells the upstream mediators by which the G protein-coupled receptor, gastrin/CCKB, activates the extracellular-regulated kinases (ERKs) and p85/p110-phosphatidylinositol 3-kinase (PI 3-kinase) pathways. Overexpression of an inhibitory mutant of Shc completely blocked gastrin-stimulated Shc.Grb2 complex formation but partially inhibited ERK-1 activation by this peptide. Expression of Csk, which inactivates Src-family kinases, totally inhibited gastrin-induced Src-like activity detected in anti-Src and anti-Shc precipitates but diminished by 50% Shc phosphorylation and ERK-1 activation. We observed a rapid tyrosine phosphorylation of insulin receptor substrate-1 (IRS-1) and an increase in Src-like kinase activity in anti-IRS-1 immunoprecipitates from gastrin-stimulated cells, suggesting that IRS-1 may be a direct substrate of Src. This hypothesis was supported by the inhibition of gastrin-induced Src. IRS-1 complex formation and IRS-1 phosphorylation in Csk-transfected cells. In addition, the increase in PI 3-kinase activity measured in anti-p85 or anti-IRS-1 precipitates following gastrin stimulation was abolished by Csk. Our results demonstrate the existence of two mechanisms in gastrin-mediated ERKs activation. One requires Shc phosphorylation by Src-family kinases, and the other one is independent of these two proteins. They also indicate that tyrosine phosphorylation of IRS-1 by Src-family kinases could lead to the recruitment and the activation of the p85/p110-PI 3-kinase in response to gastrin.