gebhart/patrepeval huggingface dataset:
AT-hook motifs identified in a wide variety of DNA-binding proteins (1998)

The AT-hook is a small DNA-binding protein motif which was first described in the high mobility group non-histone chromosomal protein HMG-I(Y). Since its discovery, this motif has been observed in other DNA-binding proteins from a wide range of organisms. Using pattern searches and position-dependent matrices, we have extracted the AT-hook motifs present in a non-redundant protein sequence database. We have classified these motifs into three types according to their sequence similarity and have found that they are prevalent in many eukaryotic nuclear proteins in single or multiple copies. Furthermore, AT-hook motifs are frequently associated with known functional domains seen in chromatin proteins and in DNA-binding proteins (e.g. histone folds, homeodomains and zinc fingers). In general, it appears that the AT-hook motif is an auxiliary protein motif cooperating with other DNA-binding activities and facilitating changes in the structure of the DNA either as a polypeptide on its own [e.g. HMG-I(Y)] or as part of a multidomain protein [e.g. Swi2p in Saccharomyces cerevisiae or HRX (ALL-1) in Homo sapiens]. It is most interesting that this motif seems to be quite specific to known or predicted chromosomal/DNA-binding proteins, suggesting that it may act as a versatile minor groove tether.
A supervised machine learning algorithm for arrhythmia analysis (2002)

A new machine learning algorithm for the diagnosis of cardiac arrhythmia from standard 12 lead ECG recordings is presented. The algorithm is called VF15 for Voting Feature Intervals. VF15 is a supervised and inductive learning algorithm for inducing classification knowledge from examples. The input to VF15 is a training set of records. Each record contains clinical measurements, from ECG signals and some other information such as sex, age, and weight, along with the decision of an expert cardiologist. The knowledge representation is based on a recent technique called Feature Intervals, where a concept is represented by the projections of the training cases on each feature separately. Classification in VF15 is based on a majority voting among the class predictions made by each feature separately. The comparison of the VF15 algorithm indicates that it outperforms other standard algorithms such as Naive Bayesian and Nearest Neighbor classifiers.
On the circular polarization operation of annular-ring microstrip antennas (1999)

Circular polarization (CP) operation of an annular-ring microstrip antenna with a pair of inserted slits at its fundamental TM/sub 11/ mode is proposed and experimentally investigated. Two examples of the proposed antenna fed using a microstrip line at the inner and outer patch boundaries are studied. Results show that the proposed antenna can have good CP performance and, moreover, the required antenna size at a fixed CP operation can be much less than that of a conventional circularly polarized circular microstrip antenna operated at the TM/sub 11/ mode. Details of the proposed antenna for CP operation are described and experimental results of the CP performance are presented and discussed.
Induction of Anergy by Antibody Blockade of TCR in Myelin Oligodendrocyte Glycoprotein-Specific Cells (2008)

Previous studies have found that a 95% reduction in TCR expression does not adversely affect response to foreign Ags, indicating that T cells have an excess of TCR for Ag recognition. Because self-reactive T cells may have low affinity for peptide:MHC, we investigated whether myelin-reactive T cells require these excess TCR for optimal response. To test this concept, mAb were used to effectively reduce the TCR of Valpha3.2 and Vbeta11 TCR transgenic mice (referred to as 2D2). After masking the TCR with either continuous or prepulsed anti-Valpha3.2 Ab, 2D2 cells were immediately stimulated with myelin oligodendrocyte glycoprotein (MOG)(35-55). These cells have a dramatic Ab dose-dependent reduction in proliferation, with a small reduction in TCR expression leading to a 50% reduction in proliferation in vitro. Additionally, 2D2 cells, treated with anti-Valpha3.2 Ab and peptide for 7 days, were re-stimulated with MOG and continue to have a dose-dependent reduction in proliferation. TCR quantitation identified the same amount of TCR on the Ab/peptide treatment compared with the peptide-only control. These results point out that the combination of reduced TCR and peptide challenge leads to a phenotypic change resulting in T cell anergy. Importantly, adoptive transfer of these anergic T cells upon autoimmune disease induction had a marked reduction in disease severity compared with untreated MOG-specific CD4(+) T cells, which had significant autoimmune disease manifested by optic neuritis and death. Thus, reduction of TCR expression may provide a potential therapy for self-reactive T cells involved in autoimmune diseases through the induction of anergy.
Regulation of Osteoclast Differentiation (2006)

The osteoclast (OCL) is derived from the cells in monocyte-macrophage lineage. The earliest identifiable OCL precursor is the granulocyte-macrophage colony-forming unit (CFU-GM), which gives rise to granulocytes, monocytes, and OCL. CFU-GM-derived cells then differentiate to committed OCL precursors, which are post-mitotic cells, and fuse to form multinucleated OCL. A variety of factors both positively and negatively regulate OCL formation and activity. These include growth factors, such as macrophage colony-simulating factor, which simulates the proliferation and prevents apoptosis of early OCL precursors, and RANK ligand (RANKL), which is the primary mediator of OCL formation. Most factors that induce OCL differentiation, such as PTHrP, IL-11, and prostaglandins, do so by inducing expression of RANKL on the surface of immature osteoblasts. Osteoprotegerin is a decoy receptor that blocks RANKL activity. In addition, OCL produce autocrine-paracrine factors that regulate OCL formation, such as IL-6, which is produced at high levels by OCL in Paget's disease and increases OCL formation. We screened human and murine OCL cDNA libraries to identify autocrine-paracrine factors that regulate OCL activity. We identified annexin-II, MIP-1alpha, ADAM8, eosinophil chemotactic factor, and OCL inhibitor factors 1 and 2 as factors involved in OCL formation. Most recently, we have identified the receptor for ADAM8, alpha9beta1 integrin, which appears to be critical for normal OCL activity. OCL differentiation is controlled by exogenous hormones and cytokines as well as autocrine-paracrine factors that positively or negatively regulate OCL proliferation and differentiation.
Ambulatory Blood Pressure Monitoring: Technique and Application in the Study of Cardiac Dysfunction and Congestive Heart Failure (2001)

Ambulatory blood pressure monitoring has become a widely used method of blood pressure and heart rate evaluation in the free-living subject. Recently, ambulatory monitoring has become covered by Medicare for the evaluation of "white-coat" hypertension. Although the technique provides only intermittent readings throughout the 24-hour period, average blood pressures obtained in this way correlate well with a variety of hypertensive disease processes and are also a better prognostic marker for future cardiovascular events than office blood pressure. Ambulatory blood pressure averages also correlate well with indices of diastolic dysfunction. In patients with congestive cardiac failure and systolic dysfunction, ambulatory monitoring suggests an impaired circadian blood pressure profile with high nocturnal blood pressure. Further research is needed on the relationship between ambulatory blood pressure and cardiac dysfunction, as well as the impact of observed circadian blood pressure changes on outcome. (c)2001 CHF, Inc.
A Subclass of bHLH Proteins Required for Cardiac Morphogenesis (1995)

Skeletal muscle development is controlled by a family of muscle-specific basic helix-loop-helix (bHLH) transcription factors. Two bHLH genes, dHAND and eHAND, have now been isolated that are expressed in the bilateral heart primordia and subsequently throughout the primitive tubular heart and its derivatives during chick and mouse embryogenesis. Incubation of stage 8 chick embryos with dHAND and eHAND antisense oligonucleotides revealed that either oligonucleotide alone had no effect on embryonic development, whereas together they arrested development at the looping heart tube stage. Thus, dHAND and eHAND may play redundant roles in the regulation of the morphogenetic events of vertebrate heart development.
Advanced endoscopic imaging: 3-d laparoscopic endoscopy. (1994)

Video imaging technology has significantly enhanced the performance of minimally invasive surgical procedures. However, a major limiting factor for the endoscopic surgeon is to work in a 3-dimensional field while viewing a two-dimensional video image. Advances in electronic video imaging have resulted in satisfactory image quality yet the lack of depth perception with standard 2-dimensional video system results in the surgeon having to rely on indirect evidence to assess the third dimension. To gauge depth, one may have to rely on touching the tissues with endoscopic instruments or estimate the relative movement of the instruments in relation to the intra-abdominal organs. These maneuvers result in a reduction in the speed of surgery and may cause unnecessary tissue trauma. Recently a number of manufacturers have developed three-dimensional (3-D) video systems which significantly improve visualization and enhance the ability of the surgeon to perform delicate endoscopic dissection and suturing. These 3-D video systems may also improve the education of surgeons-in-training as they would have a better understanding of 3-dimensional anatomy during laparoscopic surgery.
When are Surface Plasmon Polaritons Excited in the Kretschmann-Raether Configuration? (2015)

It is widely believed that the reflection minimum in a Kretschmann-Raether experiment results from direct coupling into surface plasmon polariton modes. Our experimental results provide a surprising discrepancy between the leakage radiation patterns of surface plasmon polaritons (SPPs) launched on a layered gold/germanium film compared to the K-R minimum, clearly challenging this belief. We provide definitive evidence that the reflectance dip in K-R experiments does not correlate with excitation of an SPP mode, but rather corresponds to a particular type of perfectly absorbing (PA) mode. Results from rigorous electrodynamics simulations show that the PA mode can only exist under external driving, whereas the SPP can exist in regions free from direct interaction with the driving field. These simulations show that it is possible to indirectly excite propagating SPPs guided by the reflectance minimum in a K-R experiment, but demonstrate the efficiency can be lower by more than a factor of 3. We find that optimal coupling into the SPP can be guided by the square magnitude of the Fresnel transmission amplitude.
A Copper Cofactor for the Ethylene Receptor ETR1 from Arabidopsis (1999)

The ETR1 receptor from Arabidopsis binds the gaseous hormone ethylene. A copper ion associated with the ethylene-binding domain is required for high-affinity ethylene-binding activity. A missense mutation in the domain that renders the plant insensitive to ethylene eliminates both ethylene binding and the interaction of copper with the receptor. A sequence from the genome of the cyanobacterium Synechocystis sp. strain 6803 that shows homology to the ethylene-binding domain of ETR1 encodes a functional ethylene-binding protein. On the basis of sequence conservation between the Arabidopsis and the cyanobacterial ethylene-binding domains and on in vitro mutagenesis of ETR1, a structural model for this copper-based ethylene sensor domain is presented.
Binding of Paxillin to the α9 Integrin Cytoplasmic Domain Inhibits Cell Spreading (2001)

alpha(9)beta(1) integrin is a member of the beta(1) integrin family, plays an important role in extravasation of neutrophils at sites of acute inflammation, and is required for the normal development of the lymphatic system. The alpha(9) and alpha(4) integrin subunits are most closely related and form a subfamily of integrin alpha subunits. Previously, we have reported that the alpha(4) cytoplasmic domain directly and tightly binds paxillin, an intracellular signaling adaptor molecule. This interaction accounts for some of the unusual functional responses to alpha(4) integrin-mediated cell adhesion, including stimulation of cell migration and inhibition of cell spreading and focal adhesion formation. In the current studies, we have examined the interaction between the alpha(9) cytoplasmic domain and paxillin. Here we report that the alpha(9) cytoplasmic domain binds paxillin directly and tightly and that the alpha(9)-paxillin association inhibits cell spreading. We have identified amino acid residues in the alpha(9) cytoplasmic domain, Trp(999) and Trp(1001), that are critical for paxillin binding, and alanine substitution of either Trp(999) or Trp(1001) blocks paxillin binding. Furthermore, these mutations also reverse the effect of the alpha(9) cytoplasmic domain on cell spreading. Thus, the alpha(9) and alpha(4) integrin subunits form a paxillin-binding subfamily of integrin alpha subunits, and direct binding of paxillin to the alpha(9) cytoplasmic domain mediates some of the biological activities of the alpha(9)beta(1) integrin.
Investigation of rock salt layer creep and its effects on casing collapse (2020)

Casing collapse is one of the costly incidents in the oil industry. In the oil fields of southwest Iran, most casing collapses have occurred in Gachsaran formation, and the halite rock salt layer in this formation may be the main cause for these incidents because of its peculiar creep behavior. In this research, triaxial creep experiments have been conducted on Gachsaran salt samples under various temperatures and differential stresses. The main purpose was to determine the creep characteristics of Gachsaran rock salt, and to examine the role of creep in several casing collapses that occurred in this formation. Results indicated that the halite rock salt of Gachsaran formation basically obeys the power law; however, its creep parameters are quite different from other halite rocks elsewhere. The time-dependent creep of Gachsaran rock salt exhibits strong sensitivity to temperature change; however, its sensitivity to variation of differential stress is rather low. The numerical simulation of the rock salt creep in a real oil well demonstrated the importance of creep and reservoir conditions on the safety factor of the tubing related to casing collapse.
Absolute pKaDeterminations for Substituted Phenols (2002)

The CBS-QB3 method was used to calculate the gas-phase free energy difference between 20 phenols and their respective anions, and the CPCM continuum solvation method was applied to calculate the free energy differences of solvation for the phenols and their anions. The CPCM solvation calculations were performed on both gas-phase and solvent-phase optimized structures. Absolute pK(a) calculations with solvated phase optimized structures for the CPCM calculations yielded standard deviations and root-mean-square errors of less than 0.4 pK(a) unit. This study is the most accurate absolute determination of the pK(a) values of phenols, and is among the most accurate of any such calculations for any group of compounds. The ability to make accurate predictions of pK(a) values using a coherent, well-defined approach, without external approximations or fitting to experimental data, is of general importance to the chemical community. The solvated phase optimized structures of the anions are absolutely critical to obtain this level of accuracy, and yield a more realistic charge separation between the negatively charged oxygen and the ring system of the phenoxide anions.
Synapse Loss May Be a Minor Contributor to Decreased Regional Cerebral Blood Flow in Alzheimer Disease (2003)

In this study we tested the hypothesis that synapse loss contributes to decreased regional cerebral blood flow (rCBF) in Alzheimer disease (AD). We compared antemortem rCBF and postmortem analysis of synaptophysin, as a measure of synapse loss, in 13 cases of AD. rCBF studies were performed using inhaled xenon gas (Xe-133), which yields quantitative results. Synapse loss was evaluated in postmortem brain samples using an enzyme-linked immunosorbant assay (ELISA) that measures synaptophysin, with results expressed as picomoles synaptophysin/10 mg brain. Synaptophysin was expressed either as concentration (QS method) or as the ratio of the concentration to the combined results in frontal, temporal and parietal lobe (RS method). There was no correlation between synapse loss and rCBF using the QS method and only borderline significance between right SPECT and right temporal synaptophysin using the RS method. The results of this study suggest that synapse loss may be a minor contributor to the decreased rCBF observed in AD.
Elevation of gastric pH with ranitidine does not affect the release characteristics of sustained release ibuprofen tablets (1988)

The effect of elevating gastric pH on the release characteristics of a single unit sustained release (SR) ibuprofen tablet (MOTRIN-SR, Upjohn) was evaluated in 12 young, healthy men. Using a randomized crossover-type design, each subject received three treatments--ibuprofen SR 800 mg, ranitidine 300 mg followed by ibuprofen SR 800 mg, and conventional ibuprofen tablets (2 x 400 mg). Gastric pH, which was monitored radiotelemetrically, was maintained above pH 6 for at least 4 h after pretreatment with ranitidine. In absence of ranitidine, the pH remained mostly below pH 3. Serum levels of ibuprofen were measured for 24 h and urine was collected for 48 h after each treatment. Similarity of the serum levels after the two treatments with ibuprofen SR 800 mg indicated that the release of ibuprofen was unaffected by elevation in gastric pH. Comparison of profiles with the immediate release dosage form indicated that dose dumping did not occur in any subject.
Administration of substances to laboratory animals: routes of administration and factors to consider. (2011)

Administration of substances to laboratory animals requires careful consideration and planning to optimize delivery of the agent to the animal while minimizing potential adverse experiences from the procedure. For all species, many different routes are available for administration of substances. The research team and IACUC members should be aware of reasons for selecting specific routes and of training and competency necessary for personnel to use these routes effectively. Once a route is selected, issues such as volume of administration, site of delivery, pH of the substance, and other factors must be considered to refine the technique. Inadequate training or inattention to detail during this aspect of a study may result in unintentional adverse effects on experimental animals and confounded results.
Invitation to Organic Chemistry (1998)

Carbon compounds - bonding and structure alkanes alkyl halides alcohols ehters alkees alkynes conjugated dienes aromatics carbon radicals determination of structure - spectroscopy amines carbonyl compounds carboxylic adics derivatives of carboxylic acids proteins optica activity synthetic polymers introduction to biological chemistry.
Kinetics of cellular proliferation after arterial injury. I. Smooth muscle growth in the absence of endothelium. (1983)

Intimal smooth muscle (SMC) proliferation was examined in the rat left carotid in regions lacking endothelium for prolonged periods of time. Arteries of animals injected with tritiated thymidine and Evans blue were examined at intervals between 0 and 12 weeks. The endothelial layer was regenerated from the ends of the denuded segment but failed to cover the central third of the artery by 12 weeks. Autoradiography on samples from this central region (stained blue) and the endothelialized ends (white) showed that SMC proliferation reached a maximum at 48 hours in the media (46%) and at 96 hours in the intima (73%). Subsequently, the thymidine index declined to baseline (0.06%) by 4 weeks throughout the media and by 8 weeks in the intima covered by endothelium. SMC proliferation persisted at a high level (3.8%) at the surface of the intima lacking endothelium even at 12 weeks. Despite continued proliferation of luminal SMC, total arterial SMC number was the same at 2 and 12 weeks. These results support the concept that intimal SMC proliferation after arterial injury is an acute event related to the initial injury process. Persistent proliferation of luminal SMC does not result in an increase in intimal cell number.
Characterization of the human immunoglobulin kappa gene 3' enhancer: functional importance of three motifs that demonstrate B-cell-specific in vivo footprints. (1992)

Using a combination of in vivo footprinting and site-directed mutagenesis, we have functionally characterized an enhancer located 12 kb downstream of the human immunoglobulin kappa constant-region gene. The core enhancer region is highly homologous to the murine 3' kappa enhancer. However, in addition to two regulatory elements homologous to the functional motifs of the murine enhancer, we find a third positive regulatory element in the human enhancer. This element is associated with an 11/12-bp direct repeat (DR) that is well conserved in the murine locus but was not recognized as functionally important in the murine enhancer. Mutation of any of the three motifs of the human enhancer decreases its activity to 3 to 20% of the wild-type level, indicating cooperative interaction between these elements. The DR motif does not resemble any known enhancer element and does not appear to function as a transcriptional activator on its own when present in multiple copies. Interestingly, nuclear extracts from both B- and T-cell lines contain factors binding to DR in vitro, but in vivo footprinting shows no evidence of protein-DNA binding in the T-cell line. This finding suggests that an additional regulatory mechanism, such as the effect of chromatin configuration on accessibility, may be involved in the B-cell-restricted activity of the human 3' kappa enhancer.
Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation (1996)

We developed a multiplex, solid-phase minisequencing method to detect multiple single-nucleotide polymorphisms in an undivided sample. The amplified DNA templates are first captured on a manifold. Then, with multiple minisequencing primers of various sizes, single-nucleotide extension reactions are carried out simultaneously with fluorescently labeled dideoxynucleotides. The size of the extended product, determined by using a DNA sequencing instrument, defines the site of the polymorphisms, and the incorporated nucleotide gives the identity of the nucleotide at each site. HLA-DQA1 typing was used as a model system to evaluate the method. The DR2 subgroup of the HLA-DRB1 gene was typed along with the DQA1 gene to demonstrate the feasibility of the method in analyzing multiple genes at multiple sites simultaneously. The method is generally applicable for screening any single-nucleotide polymorphisms or point mutations, and its manifold format allows practical handling of large numbers of samples.