gebhart/patrepeval huggingface dataset:
Photochemical Immobilization of Anthraquinone Conjugated Oligonucleotides and PCR Amplicons on Solid Surfaces (2000)

Ligand immobilization on solid surfaces is an essential step in fields such as diagnostics, bio sensor manufacturing, and new material sciences in general. In this paper a photochemical approach based on anthraquinone as the chromophore is presented. Photochemical procedures offer special advantages as they are able to generate highly reactive species in an orientation specific manner. As presented here, anthraquinone (AQ) mediated covalent DNA immobilization appears to be superior to currently known procedures. A synthetic procedure providing AQ-phosphoramidites is presented. These reagents facilitate AQ conjugation during routine DNA synthesis, thus enabling the AQ-oligonucleotides to be immobilized in a very convenient and efficient manner. AQ-conjugated PCR primers can be used directly in PCR. When the PCR is performed in solution, the amplicons can be immobilized after the PCR. Moreover, when the primers are immobilized prior to the PCR, a solid-phase PCR can be performed and the amplicons are thus produced directly on the solid support.
The hypoalgesic effect of tramadol in relation to CYP2D6* (1996)

Tramadol inhibits norepinephrine reuptake, stimulates serotonin release, and acts with mu-opioid receptors by way of its metabolite (+)-M1. Formation of M1 seems to depend on the genetic polymorphic CYP2D6. The analgesic effect of 2 mg/kg tramadol was evaluated in 15 extensive and 12 poor metabolizers of sparteine in two parallel, randomized, double-blind, placebo-controlled crossover studies that used experimental pain models. In extensive metabolizers, tramadol increased pressure pain detection (p = 0.03) and tolerance (p = 0.06) thresholds, as well as thresholds for eliciting nociceptive reflexes, after single (p = 0.0002) and repeated (p = 0.06) stimulation of the sural nerve. Peak pain and pain area in the cold pressor test were reduced (p = 0.0006 and 0.0009). In poor metabolizers, only thresholds to pressure pain tolerance (p = 0.02) and nociceptive reflexes after single stimulation (p = 0.04) were increased and the reflex threshold was less increased in poor metabolizers than in extensive metabolizers (p = 0.02). The serum concentration of (+)-M1 2 to 10 hours after tramadol ranged from 10 to 100 ng/L in extensive metabolizers, whereas in poor metabolizers serum concentrations of (+)-M1 were below or around the detection limit of 3 ng/ml. It is concluded that formation of (+)-M1 by way of CYP2D6 is important for the effect of tramadol on experimental pain.
Optimization of the single-strand conformation polymorphism (SSCP) technique for detection of point mutations (1993)

The efficiency of detection of single base substitutions by single-stranded conformation polymorphism (SSCP) analysis was tested on 86 randomly distributed point mutations in a 193-bp-long DNA fragment of the mouse beta-globin gene. Multiple parameters were varied, including electrophoresis temperature, buffer concentration, gel concentration, acrylamide-to-bis-acrylamide ratio, and/or addition of different compounds to the gel matrix. Gels with a higher concentration of acrylamide and lower crosslinking gave optimal separation, and all 86 mutations can be clearly distinguished from the wild type on a 5% or 7.5% (2.6% C) acrylamide gel at 4 degrees C. Most of the mutations are also resolvable from wild type on gels with 5% urea or formamide, or 10% dimethylsulfoxide or sucrose. The relative position of the purine and pyrimidine-rich single strands were followed by an asymmetric PCR-SSCP technique. We found that most of the informativity comes from the purine rich strand, which appears to be much more sensitive to changes in the gel. The position or type of mutation showed no correlation with its ability to be detected. However, the neighboring base sequence around the mutation appears to have an effect on mobility. For example, A-->G substitutions in GC-rich regions significantly increase the mobility shift of the purine-rich strand, while most G-->A changes decrease it. We conclude that SSCP is a very efficient method for the detection of point mutations, if the parameters that effect the separation are optimized for a particular DNA fragment.
Transcriptional Activity of Potent Glucocorticoids: Relevance of Glucocorticoid Receptor Isoforms and Drug Metabolites (2003)

As compared to standard glucocorticoids (GC), prednicarbate (PC) is favorable in the treatment of eczema due to its high benefit/risk ratio. The remarkable anti-inflammatory effects of PC are in strong contrast to its reported low glucocorticoid receptor (GR) binding affinity. In transfected COS-7 cells we related the transcriptional potencies of PC, its metabolites and conventional GC to their receptor binding properties. Moreover, the expression pattern of the human GR isoform hGRα and its mutual dominant negative inhibitor hGRβ in skin cells have been investigated as well as the influence of hGRβ on receptor binding and transactivation. hGRα mRNA and protein was largely overexpressed in skin cells. hGRβ showed no influence on hGRα binding and transactivation. Concentration response curves indicated the greater transactivation potency of betamethasone 17-valerate followed by dexamethasone and prednisolone 17-ethylcarbonate. Native PC appeared almost as potent as dexamethasone. With both a strong correlation was observed between transactivation and GR binding.
Src-mediated Tyrosine Phosphorylation of Dynamin Is Required for β2-Adrenergic Receptor Internalization and Mitogen-activated Protein Kinase Signaling (1999)

Some forms of G protein-coupled receptor signaling, such as activation of mitogen-activated protein kinase cascade as well as resensitization of receptors after hormone-induced desensitization, require receptor internalization via dynamin-dependent clathrin-coated pit mechanisms. Here we demonstrate that activation of beta2-adrenergic receptors (beta2-ARs) leads to c-Src-mediated tyrosine phosphorylation of dynamin, which is required for receptor internalization. Two tyrosine residues, Tyr231 and Tyr597, are identified as the major phosphorylation sites. Mutation of these residues to phenylalanine dramatically decreases the c-Src-mediated phosphorylation of dynamin following beta2-AR stimulation. Moreover, expression of Y231F/Y597F dynamin inhibits beta2-AR internalization and the isoproterenol-stimulated mitogen-activated protein kinase activation. Thus, agonist-induced, c-Src-mediated tyrosine phosphorylation of dynamin is essential for its function in clathrin mediated G protein-coupled receptor endocytosis.
Estrogens and Progression of Diabetic Kidney Damage (2011)

It is generally accepted that estrogens affect and modulate the development and progression of chronic kidney diseases (CKD) not related to diabetes. Clinical studies have indeed demonstrated that the severity and rate of progression of renal damage tends to be greater among men, compared with women. Experimental studies also support the notion that female sex is protective and male sex permissive, for the development of CKD in non-diabetics, through the opposing actions of estrogens and testosterone. However, when we consider diabetes-induced kidney damage, in the setting of either type 1 or type 2 diabetes, the contribution of gender to the progression of renal disease is somewhat uncertain. Previous studies on the effects of estrogens in the pathogenesis of progressive kidney damage have primarily focused on mesangial cells. More recently, data on the effects of estrogens on podocytes, the cell type whose role may include initiation of progressive diabetic renal disease, became available. The aim of this review will be to summarize the main clinical and experimental data on the effects of estrogens on the progression of diabetes-induced kidney injury. In particular, we will highlight the possible biological effects of estrogens on podocytes, especially considering those critical for the pathogenesis of diabetic kidney damage.
Reaching out to physicians. (1998)

One of the nation's largest physician practice management companies is rolling out to virtual private network to collect, analyze and disseminate outcomes data to physicians via the Internet.
DNA Markers from Different Linkage Regions of Watermelon Genome Useful in Differentiating among Closely Related Watermelon Genotypes (2007)

A genetic linkage map was previously constructed for watermelon using a wide testcross population [{Plant Accession Griffin 14113; Citrullus lanatus var. citroides (L.H. Baiely) Mansf.} × the watermelon cultivar New Hampshire Midget; NHM {( Citrullus lanatus (Thunb.) Matsum. &amp; Nakai var. lanatus )} × United States Plant Introduction (PI) 386015 { Citrullus colocynthis (L.) Schrad.}]. One-hundred forty-six markers [randomly amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), amplified fragment length polymorphism (AFLP), and sequence-related amplified polymorphism (SRAP) markers] unique to NHM and representing different linkage groups on the map were tested for polymorphism among 24 watermelon cultivars limited in genetic diversity. Five (9.4%) of 53 RAPD, six (40.0%) of 15 ISSR, 30 (81.0%) of 37 AFLP, and 33 (80.5%) of 41 SRAP markers tested produced polymorphism among the 24 cultivars. The polymorphic markers used in this study are scattered throughout the watermelon genome. However, a large number (19 of the 30) of AFLP markers clustered on one linkage group on the map. The SRAP markers proved to be most effective in producing polymorphism and in representing different linkage regions of watermelon genome. The polymorphic markers represent all 10 large linkage groups and five of the nine small linkage groups (altogether 15 of 19 linkage groups) of the genetic linkage map constructed so far for watermelon. These polymorphic markers can be useful in DNA fingerprinting of cultivars, in testing seed purity of breeding lines, and in identifying triploid (seedless) hybrid watermelons derived from crosses between closely related tetraploid and diploid lines.
A Drop-In Concept for Deep Borehole Canister Emplacement (2011)

Disposal of high-level nuclear waste in deep boreholes drilled into crystalline bedrock (i.e., “granite”) is an interesting repository alternative of long standing. Work at MIT over the past two decades, and more recently in collaboration with the Sandia National Laboratory, has examined a broad spectrum of design aspects associated with this approach. For emplacement, past reports suggest using steel cables to lower each canister into the borehole. This process would require many years to complete and precise control to safely lower the canisters thousands of meters. The current study evaluated a simple, rapid, “passive” procedure for emplacement of canisters in a deep borehole: free-fall release into a water-flooded borehole. The project involves both analytic modeling and 1/5th scale experiments on a laboratory mockup. Experiments showed good agreement and validated the model. Depending on the inputs used for the mass and dimensions of the full scale canister and the viscosity of water, the model predicted terminal velocities of 2.4-2.6 m/s (4.5-5.8 mph). Further experiments showed that this could be reduced by 50% by making the surface hydraulically rough. Based on these predictions and a structural analysis, there seems to be little risk of damage when a canister reaches the bottom of the borehole or impacts the stack of previously loaded canisters. For reference, dropping the canister in air from a height of only 0.3 m (1 ft) would result in an impact velocity of 2.44 m/s. Cost estimates for the conventional drill string based method were developed, and the drop-in method was concluded to reduce emplacement costs and time by a minimum of 70%, down to $700,000 per borehole. It is concluded that a simple drop-in procedure deserves serious consideration for adoption as a standard procedure for borehole loading.
Index organizations for object-oriented database systems (1995)

We present an indexing technique providing support for queries involving complex, nested objects and inheritance hierarchies. This technique is compared with two techniques obtained from more traditional organizations. The three techniques are evaluated using an analytical cost model. The discussion is cast in the framework of object-oriented databases. However, results are applicable to data management systems characterized by features such as complex objects and inheritance hierarchies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fertility Studies with Antisperm Antibodies (1994)

Serum obtained from an infertile subject possessed antibodies that interacted with a human sperm glycoprotein with an estimated M(r) of 17,550 and pI of 5.65 containing 17.7% neutral hexoses and designated as the BS-17 component. Polyclonal antibodies raised against the BS-17 antigen blocked the capacity of human sperm to fertilize zona-free hamster ova in vitro; however, the antibodies did not influence the binding of human sperm to zone-free ova or alter the motility of human sperm. The antibodies inhibited the capacity of mouse sperm to fertilize ova upon in vivo insemination. The BS-17 antigen was detected in human, rat, mouse, rabbit, and hamster sperm by an immunocytochemical method, using polyclonal anti-BS-17 antibodies. Intense staining occurred over the surface of the acrosomal region of all mammalian sperm. The results suggest that the production of anti-BS-17 antibodies contribute to infertility by preventing the capacitation of sperm and/or by blocking the ability of capacitated sperm to fertilize the egg.
Is α-T catenin (VR22) an Alzheimer’s disease risk gene? (2007)

This is the first study to report evidence of an association between a potentially functional, non-synonymous SNP in VR22 and the risk for Alzheimer's disease. As the underlying effects are probably small, and are only seen in families with multiple affected members, the population-wide significance of this finding remains to be determined.
GENTAMICIN FOR THE PRACTICING UROLOGIST: REVIEW OF EFFICACY, SINGLE DAILY DOSING AND “SWITCH” THERAPY (2000)

Gentamicin remains a valuable drug in urology. Once daily dosing and switch therapy offer the potential to increase effectiveness and convenience while decreasing toxicity and costs.
Preprocessor Selection for Machine Learning Pipelines (2018)

Much of the work in metalearning has focused on classifier selection, combined more recently with hyperparameter optimization, with little concern for data preprocessing. Yet, it is generally well accepted that machine learning applications require not only model building, but also data preprocessing. In other words, practical solutions consist of pipelines of machine learning operators rather than single algorithms. Interestingly, our experiments suggest that, on average, data preprocessing hinders accuracy, while the best performing pipelines do actually make use of preprocessors. Here, we conduct an extensive empirical study over a wide range of learning algorithms and preprocessors, and use metalearning to determine when one should make use of preprocessors in ML pipeline design.
Texture splats for 3D scalar and vector field visualization (1993)

Volume visualization is becoming an important tool for understanding large 3D data sets. A popular technique for volume rendering is known as splatting. With new hardware architectures offering substantial improvements in the performance of rendering texture mapped objects, we present textured splats. An ideal reconstruction function for 3D signals is developed which can be used as a texture map for a splat. Extensions to the basic splatting technique are then developed to additionally represent vector fields. >
Conquering the CNN Over-Parameterization Dilemma: A Volterra Filtering Approach for Action Recognition (2020)

The importance of inference in Machine Learning (ML) has led to an explosive number of different proposals in ML, and particularly in Deep Learning. In an attempt to reduce the complexity of Convolutional Neural Networks, we propose a Volterra filter-inspired Network architecture. This architecture introduces controlled non-linearities in the form of interactions between the delayed input samples of data. We propose a cascaded implementation of Volterra Filtering so as to significantly reduce the number of parameters required to carry out the same classification task as that of a conventional Neural Network. We demonstrate an efficient parallel implementation of this Volterra Neural Network (VNN), along with its remarkable performance while retaining a relatively simpler and potentially more tractable structure. Furthermore, we show a rather sophisticated adaptation of this network to nonlinearly fuse the RGB (spatial) information and the Optical Flow (temporal) information of a video sequence for action recognition. The proposed approach is evaluated on UCF-101 and HMDB-51 datasets for action recognition, and is shown to outperform state of the art CNN approaches.
Engineered Root Bacteria Release Plant-Available Phosphate from Phytate (2019)

Microorganisms that release plant-available phosphate from natural soil phosphate stores may serve as biological alternatives to costly and environmentally damaging phosphate fertilizers. To explore this possibility, we engineered a collection of root bacteria to release plant-available orthophosphate from phytate, an abundant phosphate source in many soils. We identified 82 phylogenetically diverse phytase genes, refactored their sequences for optimal expression in <i>Proteobacteria</i>, and then synthesized and engineered them into the genomes of three root-colonizing bacteria. Liquid culture assays revealed 41 engineered strains with high levels of phytate hydrolysis. Among these, we identified 12 strains across three bacterial hosts that confer a growth advantage on the model plant <i>Arabidopsis thaliana</i> when phytate is the sole phosphate source. These data demonstrate that DNA synthesis approaches can be used to generate plant-associated strains with novel phosphate-solubilizing capabilities.<b>IMPORTANCE</b> Phosphate fertilizers are essential for high-yield agriculture yet are costly and environmentally damaging. Microbes that release soluble phosphate from naturally occurring sources in the soil are appealing, as they may reduce the need for such fertilizers. In this study, we used synthetic biology approaches to create a collection of engineered root-associated microbes with the ability to release phosphate from phytate. We demonstrate that these strains improve plant growth under phosphorus-limited conditions. This represents a first step in the development of phosphate-mining bacteria for future use in crop systems.
Safety issues in telesurgery - summary (1995)

Telemedicine involves the application of high technology to medicine with a particular focus on the exploitation of modern communication technologies. Although the great interest in the field is relatively recent, a much earlier example can be traced to the psychiatrist Cecil Wittson in 1959, with his work in of telediagnosis, where he conducted consultations via interactive television. More recently the United States and the European Community have formed initiatives to provide funding for the conception and implementation of specific telemedicine systems: for linking urban specialists to rural generalists who lack training in speciality areas such as paediatric radiology; medical war operations; and to provide humanitarian assistance and disaster relief. The dependability of such systems is of critical interest to clinicians, manufacturers, and more importantly patients. The focus of this paper concerns the issues of safety in systems used in telesurgery.
Human Immunodeficiency Virus Type 1 Envelope gp120 Induces a Stop Signal and Virological Synapse Formation in Noninfected CD4+T Cells (2008)

Human immunodeficiency virus type 1 (HIV-1)-infected T cells form a virological synapse with noninfected CD4(+) T cells in order to efficiently transfer HIV-1 virions from cell to cell. The virological synapse is a specialized cellular junction that is similar in some respects to the immunological synapse involved in T-cell activation and effector functions mediated by the T-cell antigen receptor. The immunological synapse stops T-cell migration to allow a sustained interaction between T-cells and antigen-presenting cells. Here, we have asked whether HIV-1 envelope gp120 presented on a surface to mimic an HIV-1-infected cell also delivers a stop signal and if this is sufficient to induce a virological synapse. We demonstrate that HIV-1 gp120-presenting surfaces arrested the migration of primary activated CD4 T cells that occurs spontaneously in the presence of ICAM-1 and induced the formation of a virological synapse, which was characterized by segregated supramolecular structures with a central cluster of envelope surrounded by a ring of ICAM-1. The virological synapse was formed transiently, with the initiation of migration within 30 min. Thus, HIV-1 gp120-presenting surfaces induce a transient stop signal and supramolecular segregation in noninfected CD4(+) T cells.
Phenelfamycins, a novel complex of elfamycin-type antibiotics. I. Discovery, taxonomy and fermentation. (1988)

Phenelfamycins A, B, C, E, F and unphenelfamycin have been discovered in the fermentation broth of two soil isolates, designated AB 999F-80 and AB 1047T-33. These isolates were identified as strains of Streptomyces violaceoniger. The antibiotics were selected for their activity against anaerobic bacteria.
Evidence of Aluminum Loading in Infants Receiving Intravenous Therapy (1985)

To investigate the possibility that premature infants may be vulnerable to aluminum toxicity acquired through intravenous feeding, we prospectively studied plasma and urinary aluminum concentrations in 18 premature infants receiving intravenous therapy and in 8 term infants receiving no intravenous therapy. We also measured bone aluminum concentrations in autopsy specimens from 23 infants, including 6 who had received at least three weeks of intravenous therapy. Premature infants who received intravenous therapy had high plasma and urinary aluminum concentrations, as compared with normal controls: plasma aluminum, 36.78 +/- 45.30 vs. 5.17 +/- 3.1 micrograms per liter (mean +/- S.D., P less than 0.0001); urinary aluminum:creatinine ratio, 5.4 +/- 4.6 vs. 0.64 +/- 0.75 (P less than 0.01). The bone aluminum concentration was 10 times higher in infants who had received at least three weeks of intravenous therapy than in those who had received limited intravenous therapy: 20.16 +/- 13.4 vs. 1.98 +/- 1.44 mg per kilogram of dry weight (P less than 0.0001). Creatinine clearances corrected for weight did not reach expected adult values until 34 weeks of gestation. Many commonly used intravenous solutions are found to be highly contaminated with aluminum. We conclude that infants receiving intravenous therapy have aluminum loading, which is reflected in increased urinary excretion and elevated concentrations in plasma and bone. Such infants may be at high risk for aluminum intoxication secondary to increased parenteral exposure and poor renal clearance.
Synthesis of some 4‐acetyl‐3,5‐dioxo‐2,3,4,5‐tetrahydro[1]benzoxepine or benzothiepine and 6‐acetyl‐5,7‐dioxo‐6,7,8,9‐tetrahydro‐5H‐benzocycloheptene derivatives (1985)

Abstract The title compounds were prepared from benzoxepino‐, benzothiepino‐ or benzocycloheptaisoxazolones which in turn were synthetized from simple materials.