gebhart/patrepeval huggingface dataset:
MEKK1 activates both IκB kinase α and IκB kinase β (1998)

A critical step in the signal-induced activation of the transcription factor NF-kappaB is the site-specific phosphorylation of its inhibitor, IkappaB, that targets the latter for degradation by the ubiquitin-proteasome pathway. We have previously shown that mitogen-activated protein kinase/ERK kinase kinase 1 (MEKK1) can induce both this site-specific phosphorylation of IkappaB alpha at Ser-32 and Ser-36 in vivo and the activity of a high molecular weight IkappaB kinase complex in vitro. Subsequently, others have identified two proteins, IkappaB kinase alpha (IKK-alpha) and IkappaB kinase beta (IKK-beta), that are present in a tumor necrosis factor alpha-inducible, high molecular weight IkappaB kinase complex. These kinases are believed to directly phosphorylate IkappaB based on the examination of the kinase activities of IKK immunoprecipitates, but more rigorous proof of this has yet to be demonstrated. We show herein that recombinant IKK-alpha and IKK-beta can, in fact, directly phosphorylate IkappaB alpha at Ser-32 and Ser-36, as well as homologous residues in IkappaB beta in vitro, and thus are bona fide IkappaB kinases. We also show that MEKK1 can induce the activation of both IKK-alpha and IKK-beta in vivo. Finally, we show that IKK-alpha is present in the MEKK1-inducible, high molecular weight IkappaB kinase complex and treatment of this complex with MEKK1 induces phosphorylation of IKK-alpha in vitro. We conclude that IKK-alpha and IKK-beta can mediate the NF-kappaB-inducing activity of MEKK1.
Mechanism of Cisplatin Ototoxicity: Antioxidant System (1995)

The dose and duration limiting toxic effects of cisplatin are ototoxicity and nephrotoxicity. While several studies have attempted to shed some light on the causes of nephrotoxicity, the reasons for ototoxicity induced by cisplatin are poorly understood. Therefore, this investigation was undertaken to delineate the potential mechanisms underlying cisplatin ototoxicity. The role of glutathione (GSH), oxidized glutathione (GSSG) and malondialdehyde levels, and antioxidant enzyme activities [superoxide dismutase, catalase, GSH peroxidase, and GSH reductase] were examined in cochlear toxicity following an acute dose of cisplatin. Male Wistar rats were treated with various doses of cisplatin. Pretreatment auditory brain stem evoked responses (ABR) were performed and then post-treatment ABRs and endocochlear potentials were also performed after three days. Acute cochlear toxicity (ototoxicity) was evidenced as elevated hearing thresholds and prolonged wave I latencies in response to various stimuli (clicks and tone bursts at 2, 8, 16 and 32 kHz) on ABRs. The endocochlear potentials were reduced (50% control) in cisplatin-treated rats as compared to control animals. The rats were sacrificed and cochleae isolated. The GSH, GSSG and malondialdehyde levels, and antioxidant enzyme activities were determined. Cisplatin ototoxicity correlated with a decrease in cochlear GSH [0.45 +/- 0.012 nmol/mg] after cisplatin administration compared to 0.95-012 nmol/mg in control cochleae (P < 0.05). Superoxide dismutase, catalase activities and malondialdehyde levels were significantly increased in the cochleae of cisplatin injected rats. Cochlear GSH-peroxidase and GSH reductase activity significantly decreased after cisplatin administration.(ABSTRACT TRUNCATED AT 250 WORDS)
Max-Margin Markov Networks (2003)

3) networks incorporate both kernels, which efficiently deal with highdimensional features, and the ability to capture correlations in structured data.We present an efficient algorithm for learning M 3 networks based on a compact quadratic program formulation. We provide a new theoretical bound for general-ization in structured domains. Experiments on the task of handwritten character recognition, demonstrate very significant gains over previous approaches. 1 Introduction In supervised classification, our goal is to classify instances into some set of discrete cat-egories. Recently, support vector machines (SVMs) have demonstrated impressive successes on a broad range of tasks, including document classification, character recognition,image recognition, and many more. SVMs owe a great part of their success to their ability to use kernels, allowing the classifier to exploit a very high-dimensional (possibly eveninfinite-dimensional) feature space. In addition to their empirical success, SVMs are also appealing due to the existence of strong generalization guarantees, derived from the margin-maximizing properties of the learning algorithm.
Technical aspects of islet preparation and transplantation (2003)

Abstract The introduction of insulin therapy for the management of diabetes mellitus is arguably the greatest milestone in the history of modern medicine. β-cell replacement therapy is the only treatment that reestablishes and maintains long-term physiological normoglycemia. Until recently, successful clinical outcomes of pancreas transplantation for patients with long-standing diabetes were much superior to that of islet transplantation. Significant advances in islet isolation and purification technology, the development of more specific and less diabetogenic immunosuppressants and the prophylactic administration of antiviral agents have rekindled a worldwide interest in islet transplantation. This chapter will review the rationale of islet transplantation and the development of islet isolation and purification. The challenges facing clinical islet transplantation in the twenty-first century will also be introduced.
Double Determinant Immuno‐Polymerase Chain Reaction: A Sensitive Method for Detecting Circulating Antigens in Human Sera (1995)

A sensitive method for the detection of antigens in sera, termed double determinant immunopolymerase chain reaction (double determinant immuno-PCR) was developed, using two monoclonal antibodies (MoAbs), in which the antigens are sandwiched, and a specific DNA molecule is used as a marker. Instead of the antigen itself, the first MoAb to bind the circulating antigens was immobilized. After the biotinylated second MoAb was bound to the antigen, free streptavidin was used to attach a biotinylated DNA to the biotinylated second MoAb. The biotinylated DNA complexed with antigen-antibody-streptavidin was amplified by PCR, and the PCR products were analyzed by Southern blot hybridization after agarose gel electrophoresis. Compared with the conventional enzyme linked immunosorbent assay (ELISA) using soluble intercellular adhesion molecule-1 (sICAM-1) in the supernatant of cultured Panc-1 cells as an antigen, our double determinant immuno-PCR was 10(3) times more sensitive in terms of the detection limit. Not only in culture medium, but also in sera from gastric cancer patients of high sICAM-1 titer, an approximately 10(3)-fold enhancement in detection sensitivity was obtained compared with ELISA. In addition, this system can detect the antigen in sera at a level below the detection limit of traditional ELISA methods with high sensitivity. Thus, double determinant immuno-PCR has the significant advantage that it can be readily applied to any antigen-antibody system for which two MoAbs are available.
Visible‐Light‐Promoted Stereoselective Alkylation by Combining Heterogeneous Photocatalysis with Organocatalysis (2012)

Dream team: Heterogeneous inorganic semiconductors and chiral organocatalysts team up for the stereoselective photocatalytic formation of carbon–carbon bonds. However, the connection between the organic and inorganic catalysts should not be too tight: Covalent immobilization inactivates the system.
Membrane-mirror-based autostereoscopic display for tele-operation and teleprescence applications (2000)

An autostereoscopic display for telepresence and tele- operation applications has been developed at the University of Strathclyde in Glasgow, Scotland. The research is a collaborative effort between the Imaging Group and the Transparent Telepresence Research Group, both based at Strathclyde. A key component of the display is the directional screen; a 1.2-m diameter Stretchable Membrane Mirror is currently used. This patented technology enables large diameter, small f No., mirrors to be produced at a fraction of the cost of conventional optics. Another key element of the present system is an anthropomorphic and anthropometric stereo camera sensor platform. Thus, in addition to mirror development, research areas include sensor platform design focused on sight, hearing, research areas include sensor platform design focused on sight, hearing, and smell, telecommunications, display systems for all visual, aural and other senses, tele-operation, and augmented reality. The sensor platform is located at the remote site and transmits live video to the home location. Applications for this technology are as diverse as they are numerous, ranging from bomb disposal and other hazardous environment applications to tele-conferencing, sales, education and entertainment.
Crossflow filtration of baker's yeast with periodical stopping of permeation flow and bubbling (1995)

The periodical stopping of permeation flow was applied to increase the permeation flux in crossflow filtration of commercially available baker's yeast cell suspension. The permeation flux after 3 h filtration in the crossflow filtration increased to 8 x 10(-5) m(3) /m(2) s (290 L/m(2) h) from 2 x 10(-5) m(3)/m(2) s (72 L/m(2) h) by applying the periodical stopping of permeation. Introduction of air bubbles during the stopping period of permeation further increased the flux.(c) John Wiley & Sons, Inc.
Labeling of Mesenchymal Stem Cells by Bioconjugated Quantum Dots (2007)

Long-term labeling of stem cells during self-replication and differentiation benefits investigations of development and tissue regeneration. We report the labeling of human mesenchymal stem cells (hMSCs) with RGD-conjugated quantum dots (QDs) during self-replication, and multilineage differentiations into osteogenic, chondrogenic, and adipogenic cells. QD-labeled hMSCs remained viable as unlabeled hMSCs from the same subpopulation. These findings suggest the use of bioconjugated QDs as an effective probe for long-term labeling of stem cells.
Regulation of RasGRP via a Phorbol Ester-Responsive C1 Domain (1998)

As part of a cDNA library screen for clones that induce transformation of NIH 3T3 fibroblasts, we have isolated a cDNA encoding the murine homolog of the guanine nucleotide exchange factor RasGRP. A point mutation predicted to prevent interaction with Ras abolished the ability of murine RasGRP (mRasGRP) to transform fibroblasts and to activate mitogen-activated protein kinases (MAP kinases). MAP kinase activation via mRasGRP was enhanced by coexpression of H-, K-, and N-Ras and was partially suppressed by coexpression of dominant negative forms of H- and K-Ras. The C terminus of mRasGRP contains a pair of EF hands and a C1 domain which is very similar to the phorbol ester- and diacylglycerol-binding C1 domains of protein kinase Cs. The EF hands could be deleted without affecting the ability of mRasGRP to transform NIH 3T3 cells. In contrast, deletion of the C1 domain or an adjacent cluster of basic amino acids eliminated the transforming activity of mRasGRP. Transformation and MAP kinase activation via mRasGRP were restored if the deleted C1 domain was replaced either by a membrane-localizing prenylation signal or by a diacylglycerol- and phorbol ester-binding C1 domain of protein kinase C. The transforming activity of mRasGRP could be regulated by phorbol ester when serum concentrations were low, and this effect of phorbol ester was dependent on the C1 domain of mRasGRP. The C1 domain could also confer phorbol myristate acetate-regulated transforming activity on a prenylation-defective mutant of K-Ras. The C1 domain mediated the translocation of mRasGRP to cell membranes in response to either phorbol ester or serum stimulation. These results suggest that the primary mechanism of activation of mRasGRP in fibroblasts is through its recruitment to diacylglycerol-enriched membranes. mRasGRP is expressed in lymphoid tissues and the brain, as well as in some lymphoid cell lines. In these cells, RasGRP has the potential to serve as a direct link between receptors which stimulate diacylglycerol-generating phospholipase Cs and the activation of Ras.
Biological Control of Physical Properties of Tendon Adhesions (1968)

From the Department of Surgery, University of North Carolina School, of Medicine, Chapel Hill, North Carolina 27514
Biosynthesis of medium-chain fatty acids by mammary epithelial cells from virgin rats (1983)

Epithelial cells were isolated from the undifferentiated mammary glands of mature virgin female rats, and their lipogenic characteristics were studied. These cells synthesized predominantly medium-chain fatty acids, albeit at a low rate. In contrast, whole tissue from mammary glands of virgin rats synthesized predominantly long-chain fatty acids at a relatively higher rate, indicating that the lipogenic activity is dominated by the adipocyte component of the gland. Enzyme assays revealed that thioesterase II, the enzyme which regulates production of medium-chain fatty acids by the fatty acid synthetase, was present at a high activity in the undifferentiated mammary epithelial cells of virgin rats. Immunohistochemical studies confirmed this observation and showed that the regulatory enzyme was present exclusively in the epithelial cells lining the alveolar and ductal elements of the undifferentiated gland. This study demonstrates that the potential to elaborate tissue-specific medium-chain fatty acids is already expressed in the undifferentiated tissue of virgin rats and is not acquired as a result of the differentiation associated with the lactogenic phase of development. In this species mammary epithelial cells apparently synthesize predominantly medium-chain fatty acids at all stages of development, and only the overall rate of synthesis is increased on induction of the fatty acid synthetase during lactogenesis.
A Knowledge Based System for Assisting in Differential Diagnosis of Chemically Dependent/Mentally Ill Patients (1991)

Summary This paper discusses the use of Knowledge Base 2.1, a computer program that administers a response dependent, structured interview to evaluate the presence of psychiatric disorders within the chemical dependency treatment setting. The writer reviews the problems commonly encountered when conducting clinical interviews, psychometric examinations and differentially diagnosing psychiatric disorders within this special population. Knowledge Base 2.1 utilizes combined computer techniques of rule driven logic, pattern matching, and an original algorithm that accomplishes a “real time retandardization” of the complete database. With each administration, standardization is implemented in an effort to adequately consider the effects of chemical dependency on psychological test performance and normative information regarding symptoms. Knowledge Base 2.1 also functions as a research tool inasmuch as all patient responses to this structured interview are permanently stored in computer files for ongoing analysis.
SREBP-2 regulates gut peptide secretion through intestinal bitter taste receptor signaling in mice (2008)

Bitter taste-sensing G protein-coupled receptors (type 2 taste receptors [T2Rs]) are expressed in taste receptor cells of the tongue, where they play an important role in limiting ingestion of bitter-tasting, potentially toxic compounds. T2Rs are also expressed in gut-derived enteroendocrine cells, where they have also been hypothesized to play a role in limiting toxin absorption. In this study, we have shown that T2R gene expression in both cultured mouse enteroendocrine cells and mouse intestine is regulated by the cholesterol-sensitive SREBP-2. In addition, T2R stimulation of cholecystokinin (CCK) secretion was enhanced directly by SREBP-2 in cultured cells and in mice fed chow supplemented with lovastatin and ezetimibe (L/E) to decrease dietary sterol absorption and increase nuclear activity of SREBP-2. Low-cholesterol diets are naturally composed of high amounts of plant matter that is likely to contain dietary toxins, and CCK is known to improve dietary absorption of fats, slow gastric emptying, and decrease food intake. Thus, these studies suggest that SREBP-2 activation of bitter signaling receptors in the intestine may sensitize the gut to a low-fat diet and to potential accompanying food-borne toxins that make it past the initial aversive response in the mouth.
An update on regional brain volume differences associated with mood disorders (2005)

Purpose of review Structural brain changes are apparent in some magnetic resonance imaging studies of patients with mood disorders, but results are inconsistent. The focus of this review is to examine whether there are demographic or clinical characteristics of people with mood disorders that are associated with regional brain volume changes. A systematic search of the literature in English, from January 2004 to July 2005, was performed on MEDLINE. References cited in all reports were searched iteratively to identify missing studies. Recent findings Recent studies have focused on factors that might help to reconcile the divergent reports of regional brain volume changes in major depressive disorder and bipolar disorder. Small hippocampal volumes are apparent in patients with recurrent major depressive disorder, but not generally reported early in the course of adult onset depression. Small hippocampal volumes may be apparent in patients with childhood onset illness. Small hippocampal volumes are infrequently reported in bipolar disorder, but studies to date have not accounted for illness history or treatment status. Changes in amygdala volumes are inconsistently reported in patients with major depressive disorder or bipolar disorder. There are relatively fewer reports of other brain regions, including the areas of the frontal cortex and striatum. An extensive preclinical literature suggests that various psychotropic medications may have neurotrophic and neuroprotective effects, making documentation of treatment history essential. Summary Patients’ age, sex, age at onset of disease, course of illness and treatment status may affect the detection of regional brain volume changes in people with mood disorders.
A Single Domain of the Estrogen Receptor Confers Deoxyribonucleic Acid Binding and Transcriptional Activation of the Rat Prolactin Gene (1988)

Binding of ligand to the estrogen receptor, a member of the steroid receptor gene family, rapidly increases PRL gene transcription. A 15 base pair core sequence 5'TTGTCACTATGTCCT-3' greater than 1.5 kilobase upstream from the rat PRL gene transcription start site is necessary for receptor binding, demonstrates interaction with the receptor DNA binding domain, and confers estrogen regulation. Transient cotransfection of expression plasmids encoding mutant estrogen receptors with a luciferase reporter plasmid under regulation of the rat PRL estrogen regulatory element were used to investigate the minimal information necessary and sufficient for activation of gene transcription. These analyses confirmed the absolute requirement for the receptor DNA binding domain in positive regulation of transcription, and revealed that removal of amino-terminal domains reduced, but did not abolish transcriptional effects. In contrast, truncation of the receptor immediately carboxy-terminal to the DNA binding domain resulted in constitutive activation of the receptor. The observations that removal of the steroid binding domain results in a constitutively active transcriptional factor, and that the amino-terminal domains are not required for transcriptional effect provides evidence that for two members of the steroid receptor gene family (the glucocorticoid and estrogen receptors), a relatively short DNA binding domain is sufficient for transcriptional activation. These results are likely to be prototypic for other members of this family of transcriptional factors.
Three dimensional tracking of fluorescent microparticles using a photon-limited double-helix response system (2008)

We demonstrate three-dimensional tracking of fluorescent microparticles, with a computational optical system whose point spread function (PSF) has been engineered to have two twisting lobes along the optical axis, generating a three-dimensional (3D) double-helix (DH) PSF. An information theoretical comparison in photon limited systems shows that the DH-PSF delivers higher Fisher information for 3D localization than the standard PSF. Hence, DH-PSF systems provide better position estimation accuracy. Experiments demonstrate average position estimation accuracies under 14nm and 37nm in the transverse and axial dimensions respectively. The system determines the 3D position of multiple particles with a single image and tracks them over time while providing their velocities.
In Situ Assembled Mass-Transport Controlling Micromembranes and Their Application in Implanted Amperometric Glucose Sensors (2000)

Micromembranes were assembled by sequentially chemisorbing polyanions and polycations on miniature (5 x 10(-4) cm2) enzyme electrodes. The sequential chemisorption process allowed the simultaneous tailoring of their sensitivity, dynamic range, drift, and selectivity. When assembled on tips of 250-microm-diameter gold wires coated with redox polymer-"wired" glucose oxidase, they allowed tailoring of the glucose electrodes for > 2 nA/mM sensitivity; 0-30 mM dynamic range; drift of < or =5% per 24 h at 37 degrees C at 15 mM glucose concentration; and < or =5% current increment by the combination of 0.1 mM ascorbate, 0.2 mM acetaminophen, and 0.5 mM urate. The membranes also retained transition metal ions that bound to and damaged the redox polymer "wiring" the enzyme. The electrodes were tested in the jugular veins and in the intrascapular subcutaneous region of anaesthetized and heparinized nondiabetic Sprague-Dawley rats, in which rapid changes of glycemia were forced by intravenous injections of glucose and insulin. After one-point in vivo calibration of the electrodes, all of the 152 data points were clinically accurate when it was assumed that after insulin injection the glycemia in the subcutaneous fluid lags by 9 min behind that of blood withdrawn from the insulin-injected vein.
NadA, a Novel Vaccine Candidate of Neisseria meningitidis (2002)

Neisseria meningitidis is a human pathogen, which, in spite of antibiotic therapy, is still a major cause of mortality due to sepsis and meningitis. Here we describe NadA, a novel surface antigen of N. meningitidis that is present in 52 out of 53 strains of hypervirulent lineages electrophoretic types (ET) ET37, ET5, and cluster A4. The gene is absent in the hypervirulent lineage III, in N. gonorrhoeae and in the commensal species N. lactamica and N. cinerea. The guanine/cytosine content, lower than the chromosome, suggests acquisition by horizontal gene transfer and subsequent limited evolution to generate three well-conserved alleles. NadA has a predicted molecular structure strikingly similar to a novel class of adhesins (YadA and UspA2), forms high molecular weight oligomers, and binds to epithelial cells in vitro supporting the hypothesis that NadA is important for host cell interaction. NadA induces strong bactericidal antibodies and is protective in the infant rat model suggesting that this protein may represent a novel antigen for a vaccine able to control meningococcal disease caused by three hypervirulent lineages.