gebhart/patrepeval huggingface dataset:
Rapid Chemoenzymatic Synthesis of Monodisperse Hyaluronan Oligosaccharides with Immobilized Enzyme Reactors (2003)

We describe the chemoenzymatic synthesis of a variety of monodisperse hyaluronan (beta 4-glucuronic acid-beta 3-N-acetylglucosamine (HA)) oligosaccharides. Potential medical applications for HA oligosaccharides (approximately 10-20 sugars in length) include killing cancerous tumors and enhancing wound vascularization. Previously, the lack of defined oligosaccharides has limited the exploration of these sugars as components of new therapeutics. The Pasteurella multocida HA synthase, pmHAS, a polymerizing enzyme that normally elongates HA chains rapidly (approximately 1-100 sugars/s), was converted by mutagenesis into two single-action glycosyltransferases (glucuronic acid transferase and N-acetylglucosamine transferase). The two resulting enzymes were purified and immobilized individually onto solid supports. The two types of enzyme reactors were used in an alternating fashion to produce extremely pure sugar polymers of a single length (up to HA20) in a controlled, stepwise fashion without purification of the intermediates. These molecules are the longest, non-block, monodisperse synthetic oligosaccharides hitherto reported. This technology platform is also amenable to the synthesis of medicant-tagged or radioactive oligosaccharides for biomedical testing. Furthermore, these experiments with immobilized mutant enzymes prove both that pmHAS-catalyzed polymerization is non-processive and that a monomer of enzyme is the functional catalytic unit.
A trench transistor cross-point DRAM cell (1985)

A 1T DRAM cell with both the transistor and the capacitor fabricated on the sidewalls of a deep trench is described. Trench Transistor Cell (TTC) fabrication and characterization are discussed.
The role of BAFF in immune function and implications for autoimmunity (2005)

BAFF [B-cell activating factor belonging to the tumor necrosis factor (TNF) family] is a ligand that is required for peripheral B-cell survival and homeostasis. In addition to mediating B-cell survival, BAFF also regulates expression of certain B-cell-surface proteins, such as CD21/35. BAFF deficiency results in a reduced number of peripheral B cells and a diminished ability to mount robust humoral immune responses. Overexpression of BAFF has been linked to murine and human autoimmunity, and recent data provide clues as to how excess BAFF may allow the emergence of autoreactive B cells. In vivo animal testing with BAFF inhibitors has generated exciting data that support the pathway as a target for modulating B cells. The role of BAFF in B-cell biology, T-cell biology, and autoimmunity is discussed, as well as current efforts to develop BAFF inhibitors for clinical testing in autoimmune disorders.
Carboxylesterases expressed in human colon tumor tissue and their role in CPT-11 hydrolysis. (2003)

We conclude that CES2 is the most abundant carboxylesterase in colon tumors that is responsible for CPT-11 hydrolysis. This pilot study reinforces the hypothesis that there is a large interindividual variation in expression of carboxylesterases that may contribute to variation in therapeutic outcome and/or toxicity of CPT-11 therapy for colon cancer.
Detection and characterization of weak affinity antibody antigen recognition with biomolecular interaction analysis (1997)

In biological systems, weak-affinity interactions (association constant, Ka, of less than approximately 10(4) M-1) between biomolecules are common and essential to the integrity of such units. However, studies of weak biological interactions are difficult due to the scarcity of analytical methods available for the bioscientist. In this communication, we report on the use of biosensors based on surface plasmon resonance to detect and characterize weak affinity antibody-antigen interactions. Monoclonal antibodies towards carbohydrate antigens were immobilized on sensor surfaces and were used to detect weak binding of the carbohydrate tetraglucose of dissociation constant, Kd, in the millimolar range. Sensorgrams were received in the form of square pulses where the kinetic rate constants were difficult to assess due to the rapid association and dissociation of the antigen to/from the immobilized antibody.
Single-Chain Antibody-Mediated Intracellular Retention of ErbB-2 Impairs Neu Differentiation Factor and Epidermal Growth Factor Signaling (1995)

ErbB-2 becomes rapidly phosphorylated and activated following treatment of many cell lines with epidermal growth factor (EGF) or Neu differentiation factor (NDF). However, these factors do not directly bind ErbB-2, and its activation is likely to be mediated via transmodulation by other members of the type I/EGF receptor (EGFR)-related family of receptor tyrosine kinases. The precise role of ErbB-2 in the transduction of the signals elicited by EGF and NDF is unclear. We have used a novel approach to study the role of ErbB-2 in signaling through this family of receptors. An ErbB-2-specific single-chain antibody, designed to prevent transit through the endoplasmic reticulum and cell surface localization of ErbB-2, has been expressed in T47D mammary carcinoma cells, which express all four known members of the EGFR family. We show that cell surface expression of ErbB-2 was selectively suppressed in these cells and that the activation of the mitogen-activated protein kinase pathway and p70/p85S6K, induction of c-fos expression, and stimulation of growth by NDF were dramatically impaired. Activation of mitogen-activated protein kinase and p70/p85S6K and induction of c-fos expression by EGF were also significantly reduced. We conclude that in T47D cells, ErbB-2 is a major NDF signal transducer and a potentiator of the EGF signal. Thus, our observations demonstrate that ErbB-2 plays a central role in the type I/EGFR-related family of receptors and that receptor transmodulation represents a crucial step in growth factor signaling.
A novel passive protected SONET bidirectional self-healing ring architecture (1992)

Among SONET ring alternatives, the four-fiber bidirectional self-healing ring architecture (BSHR/4) has the highest available capacity and can work with today's systems with minimum change. A cost-effective implementation for a BSHR/4 which uses a totally passive ring as the protection ring of the BSHR/4 is presented. The ring uses a SONET ring to carry working traffic and a passive ring to carry protection traffic in case of network component failures. The passive ring, which is composed of optical switches and optical amplifiers, is essentially an optical add-drop protection ring. The optical signal add-drop is controlled by SONET add-drop multiplexers using existing SONET self-healing protocols. A SONET control scheme for this implementation is also discussed. The proposed BSHR/4 not only has a significant cost advantage over conventional implementations, but also can easily evolve from any two-fiber ring, with a minimum capital investment and offering twice the capacity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nucleobase transporters (2000)

Purines and pyrimidines play a key role in nucleic acid and nucleotide metabolism of all cells. In addition, they can be used as nitrogen sources in plants and many microorganisms. Transport of nucleobases across biological membranes is mediated by specific transmembrane transport proteins. Nucleobase transporters have been identified genetically and/or physiologically in bacteria, fungi, protozoa, algae, plants and mammals. A limited number of bacterial and fungal transporter genes have been cloned and analysed in great detail at the molecular level. Very recently, nucleobase transporters have been identified in plants. In other systems, with less accessible genetics, such as vertebrates and protozoa, no nucleobase transporter genes have been identified, and the transporters have been characterized and classified by physiological and biochemical approaches instead. In this review, it is shown that nucleobase transporters and similar sequences of unknown function present in databases constitute three basic families, which will be designated NAT, PRT and PUP. The first includes members from archea, eubacteria, fungi, plants and metazoa, the second is restricted to prokaryotes and fungi, and the last one is only found in plants. Interestingly, mammalian ascorbate transporters are homologous to NAT sequences. The function of different nucleobase transporters is also described, as is how their expression is regulated and what is currently known about their structure-function relationships. Common features emerging from these studies are expected to prove critical in understanding what governs nucleobase transporter specificity and in selecting proper model microbial systems for cloning and studying plant, protozoan and mammalian nucleobase transporters of agricultural, pharmacological and medical importance.
Tinnitus and vertigo in healthy senior citizens without a history of noise exposure. (1987)

The prevalence of tinnitus and dizziness in healthy elderly adults has been uncertain. This study investigated 267 people between the ages of 57 and 91 1/2 years. The subjects had no history of noise exposure, systemic diseases associated with tinnitus or disequilibrium, and had normal otoscopic examination results. Twenty-four percent reported tinnitus. Five percent experienced dizziness. Additional studies will help clarify the prevalence of these symptoms in the elderly "normal" population.
Mutations of the p53 gene in B-cell lymphoblastic acute leukemia: a report on 60 cases. (1992)

Exons 5 to 8 of the p53 gene were examined for mutations in 60 patients with B-cell acute lymphoblastic leukemia (ALL), including 50 cases of precursor-B-cell ALL, nine cases of Burkitt (L3) ALL and one case of atypical ALL with surface immunoglobulins and t(8:14) translocation but L2 morphology. Karyotype was available in all patients. DNA was analyzed by polymerase chain reaction, single strand conformation polymorphism analysis, and nucleotide sequencing. Three patients showed point mutations in exons 7 or 8, including two of the nine patients with Burkitt ALL and one of the 50 patients with precursor-B-cell ALL. These findings suggest that p53 gene mutations are rare in precursor-B-cell ALL but may be more frequent in Burkitt ALL. In the three patients with p53 mutations, however, the relevance of those mutations to the development or progression of leukemia remained uncertain.
The American-European Consensus Conference On Ards. Definitions, Mechanisms, Relevant Outcomes, And Clinical Trial Coordination (1994)

The acute respiratory distress syndrome (ARDS), a process of nonhydrostatic pulmonary edema and hypoxemia associated with a variety of etiologies, carries a high morbidity, mortality (10 to 90%), and financial cost. The reported annual incidence in the United States is 150,000 cases, but this figure has been challenged, and it may be different in Europe. Part of the reason for these uncertainties are the heterogeneity of diseases underlying ARDS and the lack of uniform definitions for ARDS. Thus, those who wish to know the true incidence and outcome of this clinical syndrome are stymied. The American-European Consensus Committee on ARDS was formed to focus on these issues and on the pathophysiologic mechanisms of the process. It was felt that international coordination between North America and Europe in clinical studies of ARDS was becoming increasingly important in order to address the recent plethora of potential therapeutic agents for the prevention and treatment of ARDS.
Supramolecular Assemblies of Amphiphilic Homopolymers (2009)

Amphiphilic molecules self-assemble in solvents because of the differential solvation of the hydrophilic and lipophilic functionalities. Small-molecule surfactants have long been known to form micelles in water that can solubilize lipophilic guest molecules in their water-excluded interior. Polymeric surfactants based on block copolymers are also known to form several types of aggregates in water owing either to the mutual incompatibility of the blocks or better solvation of one of the blocks by the solvent. Incorporating amphiphilicity at smaller length scales in polymers would provide an avenue to capture the interesting properties of macromolecules and fine tune their supramolecular assemblies. To address this issue, we designed and synthesized amphiphilic homopolymers containing hydrophilic and lipophilic functionalities in the monomer. Such a polymer can be imagined to be a string of small-molecule surfactants tethered together such that the hydrophilic and lipophilic functionalities are located on opposite faces, rendering the assemblies facially amphiphilic. This feature article describes the self-assembly of our amphiphilic homopolymers in polar and apolar solvents. These homopolymers not only form micelles in water but also form inverse micelles in organic solvents. Subtle changes to the molecular structure have been demonstrated to yield vesicles in water and inverted micelles in organic solvents. The characterization of these assemblies and their applications in separations, catalysis, and sensing are described here.
Utilization of major fucosylated and sialylated human milk oligosaccharides by isolated human gut microbes (2013)

Human milk oligosaccharides (HMOS) are not digested in the proximal intestine. In distal intestine, HMOS collectively modify the microbiota, but the response of individual bacteria to individual components of the HMOS is not well defined. Here, each of 25 major isolates of the human intestinal microbiota was fed individual major fucosylated and sialylated HMOS in anaerobic culture. This allowed for an assessment of the influence of specific HMOS on the growth and metabolic products of individual microbiota bacteria. Most Bifidobacteria spp. and Bacteroides spp. grew, induced α-L-fucosidase activity, and produced abundant lactate or short-chain fatty acids (SCFAs) when fed 2'-fucosyllactose (2'-FL), 3-FL, and lactodifucotetraose (LDFT). Lactobacillus delbrueckii ATCC7830, Enterococcus faecalis ATCC19433, and Streptococcus thermophilus ATCC19258 exhibited slight growth, pH reduction, and lactate production when supplemented with 2'-FL or 3-FL, but not LDFT. Supplementation with 3'-sialyllactose (3'-SL) and 6'-SL promoted moderate growth of Bifidobacterium longum JCM7007, 7009, 7010, 7011, 1272, 11347, ATCC15708, Bacteroides vulgatus ATCC8482, and B. thetaiotaomicron ATCC29148; accordingly, these bacteria exhibited greater neuraminidase activity and produced copious lactate, SCFA, or both. Lactobacillus delbrueckii ATCC7830 also consumed 6'-SL. In contrast, Clostridium spp., L. rhamnosus ATCC53103, E. faecalis ATCC29200, Staphylococcus spp., Enterobacter spp., and Escherichia coli K12 did not consume milk oligosaccharides nor produce appreciable acidic fermentation products. Specific Bifidobacteria and Bacteroides differentially digest specific individual HMOS, with the major fucosylated milk oligosaccharides most strongly stimulating key species of mutualist symbionts. This suggests strategies for treating dysbiosis of the microbiota and associated inflammatory disorders.
Aberrant Signaling Pathways in Glioma (2011)

Glioblastoma multiforme (GBM), a WHO grade IV malignant glioma, is the most common and lethal primary brain tumor in adults; few treatments are available. Median survival rates range from 12-15 months. The biological characteristics of this tumor are exemplified by prominent proliferation, active invasiveness, and rich angiogenesis. This is mainly due to highly deregulated signaling pathways in the tumor. Studies of these signaling pathways have greatly increased our understanding of the biology and clinical behavior of GBM. An integrated view of signal transduction will provide a more useful approach in designing novel therapies for this devastating disease. In this review, we summarize the current understanding of GBM signaling pathways with a focus on potential molecular targets for anti-signaling molecular therapies.
Porous biodegradable polymeric scaffolds prepared by thermally induced phase separation (1999)

Poly(L-lactic acid) and its copolymers with D-lactic and glycolic acid were used to fabricate various porous biodegradable scaffolds suitable for tissue engineering and drug delivery based on a thermally induced phase separation (TIPS) technique. A variety of parameters involved in TIPS process, such as types of polymers, polymer concentration, solvent/nonsolvent ratio, and quenching temperature, were examined in detail to produce a wide array of micro- and macroporous structures. A mixture of dioxane and water was used for a binary composition of solvent and nonsolvent, respectively. In particular, the coarsening effect of pore enlargement affected by controlling the quenching temperature was used for the generation of a macroporous open cellular structure with pore diameters above 100 microm. The use of amorphous polymers with a slow cooling rate resulted in a macroporous open cellular structure, whereas that of semicrystalline polymers with a fast cooling rate generated a microporous closed cellular structure. The fabricated porous devices loaded with recombinant human growth hormone (rhGH) were tested for the controlled delivery of rhGH, as a potential additional means to cell delivery.
Ellagic acid effects on the carcinogenicity, DNA-binding and metabolism of 7,12-dimethylbenz(a)anthracene (DMBA). (1992)

Naturally-occurring components of the human food supply have recently received attention as possible agents for cancer chemoprevention. The plant phenol ellagic acid has been reported to be an effective inhibitor of carcinogen metabolism and certain chemically-induced tumors. Therefore, we evaluated the efficacy of ellagic acid in inhibiting DMBA metabolism, DNA-binding and the initiation of DMBA-induced carcinogenesis in rat mammary tissue. Mammary epithelial cell aggregates were isolated from rats fed control and ellagic acid (0.4 and 0.8%) containing diets. When incubated with DMBA, aggregates from ellagic acid-fed rats exhibited a significant but modest inhibition of DMBA metabolism and DNA-binding. An inhibition of DMBA-DNA binding and DMBA metabolism in secondary cultures of mammary epithelial cells also was detected only when ellagic acid was added at 150 molar excess compared to DMBA. The feeding of ellagic acid (0.8%) to rats for 28 days prior to the administration of DMBA resulted in a 21% reduction in mammary tumor incidence at 21 weeks which was, however, not statistically significant. Together, these results indicate that, in contrast to its effects with other carcinogens in other tissues, ellagic acid is not a potent inhibitor of DMBA metabolism, DNA-binding and carcinogenicity with rat mammary tissue.
Experience with the Vacuum Assisted Closure Negative Pressure Technique in the Treatment of Non-healing Diabetic and Dysvascular Wounds (2002)

The purpose of this study is to report our experience with the Vacuum Assisted Closure (VAC) negative pressure technique in patients with non-healing wounds of the foot, ankle, and lower limb. We retrospectively reviewed 17 patients with non-healing wounds of the lower extremity who underwent treatment using the Vacuum Assisted Closure (VAC) device. Thirteen of 17 (76%) had diabetes mellitus, nine of whom were insulin-dependent, and 10 of whom had associated peripheral neuropathy. Eight of 17 (47%) had severe peripheral vascular disease. All had failed previous management with serial wound debridements and dressing changes; 15 of 17 (88%) had previously completed at least one course of oral antibiotics. Thirteen of 17 (76%) had previously undergone operative irrigation and debridement of the wounds; six of 17 (35%) had previously undergone revascularization procedures of the involved extremity. Five of 17 (29%) had wounds necessitating an amputation procedure prior to the present treatment; seven of 17 (41%) had failed treatment with local growth factors prior to the present treatment. Average length of treatment with the VAC device was 8.2 weeks. Fourteen of 17 (82%) wounds successfully healed; four underwent split-thickness skin grafting for wound closure; four were briefly treated with local growth factors; six were treated with only dressing changes following VAC treatment. Three of 17 (18%) wounds failed VAC treatment; all three patients had diabetes and had wounds located in the midfoot or forefoot; two of three had severe peripheral vascular disease. Our results indicate that the Vacuum Assisted Closure negative pressure technique is emerging as an acceptable option for wound care of the lower extremity. Not all patients are candidates for such treatment; those patients with severe peripheral vascular disease or smaller forefoot wounds may be best treated by other modalities. Larger wounds seem to be better suited for skin grafting or two-stage primary closure.
Actividad inmunomoduladora del extracto de metanol de la cabeza floral de Sphaeranthus indicus Linn (2004)

El extracto de metanol y sus fracciones de eter de petroleo, cloroformo y metanol sobrante de las cabezas florales de Sphaeranthus indicus Linn demostraron su eficacia al aumentar la actividad fagocitica, el titulo de anticuerpos de la hemaglutinacion y la hipersensibilidad de tipo retardado, mientras que solo la fraccion de metanol restante resulto activa en la normalizacion de los niveles de leucocitos totales en el caso de la mielosupresion inducida por ciclofosfamida en ratones. Por tanto, el presente estudio revela que el farmaco augura buenos resultados como agente inmunomodulador, al actuar como estimulante de la inmunidad celular y humoral y de la funcion fagocitica.
Phosphoribosyl anthranilate isomerase from Thermotoga maritima is an extremely stable and active homodimer (1996)

The metabolism of hyperthermophilic microorganisms can function properly at temperatures close to 100 degrees C. It follows that they are equipped with both thermostable enzymes and mechanisms that handle labile metabolites. We wanted to understand how stable and active phosphoribosyl anthranilate isomerase (tPRAI) from the hyperthermophile Thermotoga maritima is at its optimum growth temperature of 80 degrees C, and how its thermolabile substrate, N-(5'-phosphoribosyl)-anthranilate (PRA), is protected from rapid decomposition. To this end, the trpF gene of T. maritima was expressed heterologously in Escherichia coli and tPRAI was purified. In contrast to most PRAIs from mesophiles, which are monomers with the eightfold beta alpha (or TIM) barrel fold, tPRAI is a homodimer. It is strongly resistant toward inactivation by temperatures up to 95 degrees C, by acidification to pH 3.2, and by proteases in the presence and absence of detergents. tPRAI is about 35-fold more active at its physiologic temperature than is the enzyme from E. coli (ePRAI) at 37 degrees C. This high catalytic efficiency of tPRAI is likely to complete successfully with the rapid spontaneous hydrolysis of PRA at 80 degrees C. Thus, with respect to both stability and function, tPRAI appears well adapted to the extreme habitat of T. maritima. Single crystals of tPRAI have been obtained that are suitable for X-ray analysis at high resolution.