gebhart/patrepeval huggingface dataset:
Facial Action Unit Recognition using Temporal Templates and Particle Filtering with Factorized Likelihoods (2005)

Automatic recognition of human facial expressions is a challenging problem with many applications in human-computer interaction. Most of the existing facial expression analyzers succeed only in recognizing a few basic emotions, such as anger or happiness. In contrast, the system we wish to demonstrate recognizes a large range of facial behavior by recognizing facial action units (AUs, i.e. atomic facial signals). Our system performs AU recognition using temporal templates as input data and a combined kNN-rulebase two-stage classifier. Besides demonstrating the facial action recognizer, we will demonstrate a new point-tracking algorithm based on particle filtering with factorized likelihoods that we use for the registration of the input data.
VectorBase: a data resource for invertebrate vector genomics (2008)

VectorBase (http://www.vectorbase.org) is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. Since our last report VectorBase has initiated a community annotation system, a microarray and gene expression repository and controlled vocabularies for anatomy and insecticide resistance. We have continued to develop both the software infrastructure and tools for interrogating the stored data.
Activated Carbon Adsorption (2005)

High surface area, a microporous structure, and a high degree of surface reactivity make activated carbons versatile adsorbents, particularly effective in the adsorption of organic and inorganic pollutants from aqueous solutions. Activated Carbon Adsorption introduces the parameters and mechanisms involved in the activated carbon adsorption
Adenine Nucleotide Analogues Locked in a Northern Methanocarba Conformation:  Enhanced Stability and Potency as P2Y1 Receptor Agonists (2002)

Preference for the Northern (N) ring conformation of the ribose moiety of nucleotide 5'-triphosphate agonists at P2Y(1), P2Y(2), P2Y(4), and P2Y(11) receptors, but not P2Y(6) receptors, was established using a ring-constrained methanocarba (a 3.1.0-bicyclohexane) ring as a ribose substitute (Kim et al. J. Med. Chem. 2002, 45, 208-218.). We have now combined the ring-constrained (N)-methanocarba modification of adenine nucleotides with other functionalities known to enhance potency at P2 receptors. The potency of the newly synthesized analogues was determined in the stimulation of phospholipase C through activation of turkey erythrocyte P2Y(1) or human P2Y(1) and P2Y(2) receptors stably expressed in astrocytoma cells. An (N)-methanocarba-2-methylthio-ADP analogue displayed an EC(50) at the hP2Y(1) receptor of 0.40 nM and was 55-fold more potent than the corresponding triphosphate and 16-fold more potent than the riboside 5'-diphosphate. 2-Cl-(N)-methanocarba-ATP and its N(6)-Me analogue were also highly selective, full agonists at P2Y(1) receptors. The (N)-methanocarba-2-methylthio and 2-chloromonophosphate analogues were full agonists exhibiting micromolar potency at P2Y(1) receptors, while the corresponding ribosides were inactive. Although beta,gamma-methylene-ATP was inactive at P2Y receptors, beta,gamma-methylene-(N)-methanocarba-ATP was a potent hP2Y(1) receptor agonist with an EC(50) of 160 nM and was selective versus hP2Y(2) and hP2Y(4) receptors. The rates of hydrolysis of Northern (N) and Southern (S) methanocarba analogues of AMP by rat 5'-ectonucleotidase were negligible. The rates of hydrolysis of the corresponding triphosphates by recombinant rat NTPDase1 and 2 were studied. Both isomers were hydrolyzed by NTPDase 1 at about half the rate of ATP hydrolysis. The (N) isomer was hardly hydrolyzed by NTPDase 2, while the (S) isomer was hydrolyzed at one-third of the rate of ATP hydrolysis. This suggests that new, more stable and selective nucleotide agonists may be designed on the basis of the (N)-conformation, which greatly enhanced potency at P2Y(1) receptors.
Metabolism of dibutylphthalate and phthalate by Micrococcus sp. strain 12B (1982)

Micrococcus sp. strain 12B was isolated by enriching for growth with dibutylphthalate as the sole carbon and energy source. A pathway for the metabolism of dibutylphthalate and phthalate by micrococcus sp. strain 12B is proposed: dibutylphthalate leads to monobutylphthalate leads to phthalate leads to 3,4-dihydro-3,4-dihydroxyphthalate leads to 3,4-dihydroxyphthalate leads to protocatechuate (3,4-dihdroxybenzoate). Protocatechuate is metabolized both by the meta-cleavage pathway through 4-carboxy-2-hydroxymuconic semialdehyde and 4-carboxy-2-hydroxymuconate to pyruvate and oxaloacetate and by the ortho-cleavage pathway to beta-ketoadipate. Dibutylphthalate- and phthalate-grown cells readily oxidized dibutylphthalate, phthalate, 3,4-dihydroxyphthalate, and protocatechuate. Extracts of cells grown with dibutylphthalate or phthalate contained the 3,4-dihydroxyphthalate decarboxylase and the enzymes of the protocatechuater 4,5-meta-cleavage pathway. Extracts of dibutylphthalate-grown cells also contained the protocatechuate ortho-cleavage pathway enzymes. The dibutylphthalate-hydrolyzing esterase and 3,4-dihydroxyphthalate decarboxylase were constitutively synthesized; phthalate-3,4-dioxygenase (and possibly the "dihydrodiol" dehydrogenase) was inducible by phthalate or a metabolite occurring before protocatechuate in the pathway; two protocatechuate oxygenases and subsequent enzymes were inducible by protocatechuate or a subsequent metabolic product. During growth at 37 degrees C, strain 12B gave clones at high frequency that had lost the ability to grow with phthalate esters. One of these nonrevertible mutants, strain 12B-Cl, lacked all of the enzymes required for the metabolism of dibutylphthalate through the protocatechuate meta-cleavage pathway. Enzymes for the metabolism of protocatechuate by the ortho-cleavage pathway were present in this strain grown with p-hydroxybenzoate or protocatechuate.
New Challenges in Biomaterials (1994)

Significant opportunities and challenges exist in the creation and characterization of biomaterials. Materials have been designed for contact with blood, as replacements for soft and hard tissues, as adhesives, and as dental materials. Current methods of synthesis and characterization of these materials are outlined. Approaches for controlling the interface between tissue and biomaterials and ways in which the engineered materials may contribute to medicine are considered.
Modulation of Neutrophil Apoptosis and the Resolution of Inflammation through β2 Integrins (2013)

Precise control of the neutrophil death program provides a balance between their defense functions and safe clearance, whereas impaired regulation of neutrophil death is thought to contribute to a wide range of inflammatory pathologies. Apoptosis is essential for neutrophil functional shutdown, removal of emigrated neutrophils, and timely resolution of inflammation. Neutrophils receive survival and pro-apoptosis cues from the inflammatory microenvironment and integrate these signals through surface receptors and common downstream mechanisms. Among these receptors are the leukocyte-specific membrane receptors β2 integrins that are best known for regulating adhesion and phagocytosis. Accumulating evidence indicate that outside-in signaling through the β2 integrin Mac-1 can generate contrasting cues in neutrophils, leading to promotion of their survival or apoptosis. Binding of Mac-1 to its ligands ICAM-1, fibrinogen, or the azurophilic granule enzyme myeloperoxidase suppresses apoptosis, whereas Mac-1-mediated phagocytosis of bacteria evokes apoptotic cell death. Mac-1 signaling is also target for the anti-inflammatory, pro-resolving mediators, including lipoxin A4, aspirin-triggered lipoxin A4, and resolvin E1. This review focuses on molecular mechanisms underlying Mac-1 regulation of neutrophil apoptosis and highlights recent advances how hierarchy of survival and pro-apoptosis signals can be harnessed to facilitate neutrophil apoptosis and the resolution of inflammation.
Nitrite Catalyzes Reductive Nitrosylation of the Water-Soluble Ferri-Heme Model FeIII(TPPS) to FeII(TPPS)(NO) (2002)

Quantitative investigation of the reaction of the ferri-heme model compound Fe(III)(TPPS)(H(2)O)(2) (1) to give Fe(II)(TPPS)(NO) (2) (TPPS = tetra(4-sulfonato-phenyl)porphinato) in buffered aqueous solution demonstrates a slow pH-independent reductive nitrosylation pathway in the pH range 4-6. The rate of this reaction is subject to modest general base catalysis. In the course of this study, a surprising catalytic pathway whereby nitrite ion (NO(2)(-)) strongly catalyzes the reduction of 1 to 2 under reductive nitrosylation conditions was demonstrated.
The Brown Protein of Drosophila melanogaster is Similar to the White Protein and to Components of Active Transport Complexes (1988)

The brown gene of Drosophila melanogaster is required for deposition of pteridine pigments in the compound eye and other tissues. We isolated a ca. 150-kilobase region including brown by microdissection and chromosome walking using cosmids. Among the cDNAs identified by hybridization to the cosmids, one class hybridized to a genomic region that is interrupted in two brown mutants, bw and In(2LR)CK, and to 2.8- and 3.0-kilobase poly(A)+ RNAs which are altered in the mutants. Nucleotide sequencing of these cDNAs revealed that the two transcripts differ as a consequence of alternative poly(A) addition and that both encode the same predicted protein of 675 amino acids. Searches of available databases for amino acid sequence similarities detected a striking overall similarity of this predicted protein to that of the D. melanogaster white gene. The N-terminal portion aligned with the HisP family of membrane-associated ATP-binding proteins, most of which are subunits of active transport complexes in bacteria, and to two regions of the multidrug resistance P-glycoprotein. The C-terminal portion showed a structural similarity to integral membrane components of the same complexes. Taken together with earlier biochemical evidence that brown and white gene products are necessary for uptake of a pteridine precursor and genetic evidence that brown and white proteins interact, our results are consistent with suggestions that these proteins are subunits of a pteridine precursor permease.
Rotavirus Replication: Plus-Sense Templates for Double-Stranded RNA Synthesis Are Made in Viroplasms (2004)

Rotavirus plus-strand RNAs not only direct protein synthesis but also serve as templates for the synthesis of the segmented double-stranded RNA (dsRNA) genome. In this study, we identified short-interfering RNAs (siRNAs) for viral genes 5, 8, and 9 that suppressed the expression of NSP1, a nonessential protein; NSP2, a component of viral replication factories (viroplasms); and VP7, an outer capsid protein, respectively. The loss of NSP2 expression inhibited viroplasm formation, genome replication, virion assembly, and synthesis of the other viral proteins. In contrast, the loss of VP7 expression had no effect on genome replication; instead, it inhibited only outer-capsid morphogenesis. Similarly, neither genome replication nor any other event of the viral life cycle was affected by the loss of NSP1. The data indicate that plus-strand RNAs templating dsRNA synthesis within viroplasms are not susceptible to siRNA-induced RNase degradation. In contrast, plus-strand RNAs templating protein synthesis in the cytosol are susceptible to degradation and thus are not the likely source of plus-strand RNAs for dsRNA synthesis in viroplasms. Indeed, immunofluorescence analysis of bromouridine (BrU)-labeled RNA made in infected cells provided evidence that plus-strand RNAs are synthesized within viroplasms. Furthermore, transfection of BrU-labeled viral plus-strand RNA into infected cells suggested that plus-strand RNAs introduced into the cytosol do not localize to viroplasms. From these results, we propose that plus-strand RNAs synthesized within viroplasms are the primary source of templates for genome replication and that trafficking pathways do not exist within the cytosol that transport plus-strand RNAs to viroplasms. The lack of such pathways confounds the development of reverse genetics systems for rotavirus.
The Effect of Recombinant Human Hyaluronidase on Dexamethasone Penetration into the Posterior Segment of the Eye After Sub-Tenon's Injection (2006)

Sub-Tenon's coinjection of rHuPH20 with DM resulted in a general increase in DM levels in ocular tissues and the serum, with significant increase in the choroid and the retina, 3 h after administration.
Flavodoxin:Quinone Reductase (FqrB): a Redox Partner of Pyruvate:Ferredoxin Oxidoreductase That Reversibly Couples Pyruvate Oxidation to NADPH Production in Helicobacter pylori and Campylobacter jejuni (2007)

Pyruvate-dependent reduction of NADP has been demonstrated in cell extracts of the human gastric pathogen Helicobacter pylori. However, NADP is not a substrate of purified pyruvate:ferredoxin oxidoreductase (PFOR), suggesting that other redox active enzymes mediate this reaction. Here we show that fqrB (HP1164), which is essential and highly conserved among the epsilonproteobacteria, exhibits NADPH oxidoreductase activity. FqrB was purified by nickel interaction chromatography following overexpression in Escherichia coli. The protein contained flavin adenine dinucleotide and exhibited NADPH quinone reductase activity with menadione or benzoquinone and weak activity with cytochrome c, molecular oxygen, and 5,5'-dithio-bis-2-nitrobenzoic acid (DTNB). FqrB exhibited a ping-pong catalytic mechanism, a k(cat) of 122 s(-1), and an apparent K(m) of 14 muM for menadione and 26 muM for NADPH. FqrB also reduced flavodoxin (FldA), the electron carrier of PFOR. In coupled enzyme assays with purified PFOR and FldA, FqrB reduced NADP in a pyruvate- and reduced coenzyme A (CoA)-dependent manner. Moreover, in the presence of NADPH, CO(2), and acetyl-CoA, the PFOR:FldA:FqrB complex generated pyruvate via CO(2) fixation. PFOR was the rate-limiting enzyme in the complex, and nitazoxanide, a specific inhibitor of PFOR of H. pylori and Campylobacter jejuni, also inhibited NADP reduction in cell-free lysates. These capnophilic (CO(2)-requiring) organisms contain gaps in pathways of central metabolism that would benefit substantially from pyruvate formation via CO(2) fixation. Thus, FqrB provides a novel function in pyruvate metabolism and, together with production of superoxide anions via quinone reduction under high oxygen tensions, contributes to the unique microaerobic lifestyle that defines the epsilonproteobacterial group.
T cell recognition of carbohydrates on type II collagen. (1994)

A critical event in an immune response is the T cell recognition of peptides bound to major histocompatibility complex (MHC) molecules on the surface of an antigen presenting cell (APC). Although the majority of eukaryotic proteins are glycosylated, it has not yet been shown that T cell recognition of such proteins involves recognition of the bound carbohydrates. Type II collagen (CII), the major protein constituent of joint cartilage, is posttranslationally modified by hydroxylation and glycosylation of lysines. In this report we show that posttranslational modifications of the immunodominant peptide CII(256-270) generate a structural determinant that is distinct from the determinant represented by the corresponding synthetic peptide. Elimination of carbohydrates, present on CII, by two different biochemical methods revealed that the carbohydrates, O-linked to the hydroxylysines within the CII(256-270) determinant, were crucial for the reactivity towards the posttranslationally modified peptide. Furthermore, a T cell hybridoma specific for the glycosylated determinant was stimulated by tryptic CII-peptides presented by fixed APCs, thus showing that the carbohydrates are involved in the trimolecular complex T cell receptor/peptide/MHC. Finally, the importance of the bound carbohydrates for the arthritogenicity of CII was investigated by comparing the development of arthritis after immunization with carbohydrate-depleted and glycosylated CII, respectively. Incidence, time of onset, and severity of the disease were significantly affected by the elimination of carbohydrates, whereas no significant difference in anti-CII antibody titers was seen.
[Cadherins in malignancies of the female genital tract]. (2005)

Cadherins are a superfamily of adhesion molecules that mediate Ca++ -dependent cell-cell adhesion necessary for normal morphogenesis and maintenance of tissue integrity. A classical cadherin molecule, such as E-cadherin, is a glycoprotein made up of three parts: an extracellular portion composed of five identical domains, a transmembrane portion composed of a single domain and a cytoplasmic portion composed of two domains. The cytoplasmic portion is anchored by means of cytoplasmic catenins to the cytoskeleton. The three amino acids sequence, histidine, alanine and valine (HAV motif) located at the most external domain of the extracellular portion, plays a key role in homophilic recognition between two cadherin molecules and cell-cell adhesion. Loss of cell-cell adhesion may be a prerequisite for malignant transformation and the invasive behavior of malignant tumors. Research of cadherin in malignancies has attracted much attention since cadherins may be proven to be reliable markers of biological behavior and prognosis The studies on cadherin in malignancies of the female genital tract have shown the following results: 1) in malignant transformation of the ovarian surface epithelium (OSE) and in epithelial ovarian carcinoma confined to the ovary (Stage I) there is a switch from N-cadherin expression to E-cadherin expression; 2) In advanced-stage epithelial ovarian carcinoma (Stages II-IV) the results are at odds: some investigators have shown a loss of E-cadherin expression most often because of hypermethylation of the promoter region of the gene, while others have demonstrated an increase in E-cadherin expression; 3) In endometrial carcinoma, E-cadherin expression is decreasing and P-cadherin expression is increasing with worsening of histologic type and differentiation, increased penetration into the myometrium, spread beyond the uterus and involvement of pelvic lymph nodes; 4) In squamous cell carcinoma of the uterine cervix E-cadherin expression is decreasing with tumor progression and in adenocarcinoma of the uterine cervix P-cadherin expression is increasing with tumor progression. It is hoped that the development of drugs that amend cell-cell adhesion will improve the prognosis of patients in whom tumor progression is associated with decrease or loss of cadherin expression.
Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase (1993)

The structure of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA2Gln and ATP refined at 2.5-A resolution reveals structural details of the catalytic center and allows description of the specific roles of individual amino acid residues in substrate binding and catalysis. The reactive moieties of the ATP and tRNA substrates are positioned within hydrogen-bonding distance of each other. Model-building has been used to position the glutamine substrate in an adjacent cavity with its reactive carboxylate adjacent to the alpha-phosphate of ATP; the interactions of the carboxyamide side chain suggest a structural rationale for the way in which the enzyme discriminates against glutamate. The binding site for a manganese ion has also been identified bridging the beta- and gamma-phosphates of the ATP. The well-known HIGH and KMSKS sequence motifs interact directly with each other as well as with the ATP, providing a structural rationale for their simultaneous conservation in all class I synthetases. The KMSKS loop adopts a well-ordered and catalytically productive conformation as a consequence of interactions made with the proximal beta-barrel domain. While there are no protein side chains near the reaction site that might function in acid-base catalysis, the side chains of two residues, His43 and Lys270, are positioned to assist in stabilizing the expected pentacovalent intermediate at the alpha-phosphate. Transfer of glutamine to the 3'-terminal tRNA ribose may well proceed by intramolecular catalysis involving proton abstraction by a phosphate oxygen atom of glutaminyl adenylate. Catalytic competence of the crystalline enzyme is directly shown by its ability to hydrolyze ATP and release pyrophosphate when crystals of the ternary complex are soaked in mother liquor containing glutamine.
Postlicensure evaluation of the effectiveness of seven valent pneumococcal conjugate vaccine (2001)

The introduction and routine use of pneumococcal conjugate vaccine in our population have been associated with a substantial reduction in invasive disease incidence in children <5 years of age.
Prospective of human butyrylcholinesterase as a detoxifying antidote and potential regulator of controlled‐release drugs (2000)

Butyrylcholinesterase from human plasma (HuBChE) is a potential drug candidate that can be employed in several therapeutic fields. This is attributed to the unique structure of the enzyme that allows selective accommodation of a variety of substrates and inhibitors, some of which are excluded from the catalytic gorge of acetylcholinesterase. Enhancement of endogenous levels of HuBChE can protect against the toxicity of organophosphate pesticides and nerve agents, reduce risks of complications due to cocaine abuse, reverse muscle relaxant-induced apnea following surgery anesthesia, and alleviate symptoms caused by local anesthetics. It can be used either prophylactically or as a treatment drug. Treatment with HuBChE offers replacement therapy of traditional pharmacological antidotes that suffer from several disadvantages. In addition, endogenous HuBChE is capable of biotransformation of ester- or carbamate-bond containing prodrugs to active therapeutic molecules, and has the potential of improvement of bioavailability and safety of numerous drugs with sales records. In certain cases HuBChE may be administered before, with, or after the prodrug. HuBChE is absorbed in high yield from muscles and its circulatory stability is sufficient to provide significant therapeutic levels for several days, even after a single dose load. Based on limited studies with partially purified HuBChE, the enzyme seems to lack significant physiological incompatibilities in humans that may prevent its use as a drug. Clinical trials aimed at providing pharmacokinetic data and evaluation of safety issues of acute and chronic administration of purified HuBChE are expected to advance the concept of using the enzyme as a multipurpose drug. Drug Dev. Res. 50:298–308, 2000. © 2000 Wiley-Liss, Inc.