gebhart/patrepeval huggingface dataset:
Myocardial Aging and Senescence: Where Have the Stem Cells Gone? (2004)

Heart failure remains a leading cause of hospital admissions and mortality in the elderly, and current interventional approaches often fail to treat the underlying cause of pathogenesis. Preservation of structure and function in the aging myocardium is most likely to be successful via ongoing cellular repair and replacement, as well as survival of existing cardiomyocytes that generate contractile force. Research has led to a paradigm shift driven by application of stem cells to generate cardiovascular cell lineages. Early controversial findings of pluripotent precursors adopting cardiac phenotypes are now widely accepted, and current debate centers upon the efficiency of progenitor cell incorporation into the myocardium. Much work remains to be done in determining the relevant progenitor cell population and optimizing conditions for efficient differentiation and integration. Significant implications exist for treatment of pathologically damaged or aging myocardium since future interventional approaches will capitalize upon the use of cardiac stem cells as therapeutic reagents.
Development of a method for predicting the performance and wear of PDC (polycrystalline diamond compact) drill bits (1987)

A method is developed for predicting cutter forces, temperatures, and wear on PDC bits as well as integrated bit performance parameters such as weight-on-bit, drilling torque, and bit imbalance. A computer code called PDCWEAR has been developed to make this method available as a tool for general bit design and analysis. The method uses single-cutter data to provide a measure of rock drillability and employs theoretical considerations to account for interaction among closely spaced cutters on the bit. Experimental data are presented to establish the effects of cutter size and wearflat area on the forces that develop during rock cutting. Waterjet assistance is shown to significantly reduce cutting forces, thereby potentially extending bit life and reducing weight-on-bit and torque requirements in hard rock. The effects of several other design and operating parameters on bit life and drilling performance are also investigated.
Querying time series data based on similarity (2000)

We study similarity queries for time series data where similarity is defined, in a fairly general way, in terms of a distance function and a set of affine transformations on the Fourier series representation of a sequence. We identify a safe set of transformations supporting a wide variety of comparisons and show that this set is rich enough to formulate operations such as moving average and time scaling. We also show that queries expressed using safe transformations can efficiently be computed without prior knowledge of the transformations. We present a query processing algorithm that uses the underlying multidimensional index built over the data set to efficiently answer similarity queries. Our experiments show that the performance of this algorithm is competitive to that of processing ordinary (exact match) queries using the index, and much faster than sequential scanning. We propose a generalization of this algorithm for simultaneously handling multiple transformations at a time, and give experimental results on the performance of the generalized algorithm.
cDNA Cloning and Characterization of eck, an Epithelial Cell Receptor Protein-Tyrosine Kinase in the eph/elk Family of Protein Kinases (1990)

A human epithelial (HeLa) cDNA library was screened with degenerate oligonucleotides designed to hybridize to highly conserved regions of protein-tyrosine kinases. One cDNA from this screen was shown to contain a putative protein-tyrosine kinase catalytic domain and subsequently used to isolate another cDNA from a human keratinocyte library that encompasses the entire coding region of a 976-amino-acid polypeptide. The predicted protein has an external domain of 534 amino acids with a presumptive N-terminal signal peptide, a transmembrane domain, and a cytoplasmic domain of 418 amino acids that includes a canonical protein-tyrosine kinase catalytic domain. Molecular phylogeny indicates that this protein kinase is closely related to eph and elk and that this receptor family is more closely related to the non-receptor protein-tyrosine kinase families than to other receptor protein-tyrosine kinases. Antibodies raised against a TrpE fusion protein immunoprecipitated a 130-kDa protein that became phosphorylated on tyrosine in immune complex kinase assays, indicating that this protein is a bona fide protein-tyrosine kinase. Analysis of RNA from 13 adult rat organs showed that the eck gene is expressed most highly in tissues that contain a high proportion of epithelial cells, e.g., skin, intestine, lung, and ovary. Several cell lines of epithelial origin were found to express the eck protein kinase at the protein and RNA levels. Immunohistochemical analysis of several rat organs also showed staining in epithelial cells. These observations prompted us to name this protein kinase eck, for epithelial cell kinase.
Statins Induce the Accumulation of Regulatory T Cells in Atherosclerotic Plaque (2012)

CD4⁺CD25⁺ regulatory T cells (Tregs) mediate immune suppression and prevent autoimmune disorders. Recently, Tregs were found to present in atherosclerotic lesions and play an important role in the progression of atherosclerosis. Statins have immunomodulatory properties, and the effect of statins on atherosclerosis depends in part on their immunomodulatory mechanisms. We sought to determine whether statins exhibit an effect on Tregs in atherosclerotic plaques and in peripheral circulation of patients with acute coronary syndrome (ACS). In an in vivo experiment, we induced atherosclerotic plaques in apolipoprotein E-deficient (ApoE⁻/⁻) mice. The mice were randomly divided into two groups for 6-wk treatment: simvastatin (50 mg/kg/d) or vehicle (control). Simvastatin significantly increased the number of Tregs and the expression of Treg marker Foxp3 (Forkhead/winged helix transcription factor), transforming growth factor (TGF)-β and interleukin (IL)-10 in atherosclerotic plaques. Moreover, simvastatin played an important role in modulating the balance between antiinflammatory (Tregs and Th2 cells) and proinflammatory (Th17 and Th1 cells) subsets of T cells. In an in vitro experiment, peripheral blood mononuclear cells (PBMCs) were isolated from patients with ACS and incubated with simvastatin. After an incubation for 96 h, simvastatin significantly enhanced the frequency and functional suppressive properties of Tregs. Therefore, statin treatment may influence Tregs in atherosclerotic lesions. Furthermore, statins improved the quantity and suppressive function of Tregs in ACS patients.
IL-7 stimulates CSF-induced proliferation of murine bone marrow macrophages and Mac-1+ myeloid progenitors in vitro. (1994)

The role of IL-7 as an important stimulator of the growth of B and T cell precursors, as well as mature T cells, is well established. In contrast, the role of IL-7 in myelopoiesis has not been characterized thoroughly, and thus, IL-7 has been regarded as a lymphoid lineage-restricted cytokine. However, we have recently reported that IL-7 enhanced CSF-induced myeloid proliferation of primitive murine hematopoietic (Lin-Sca-1+) progenitors, whereas IL-7 did not affect significantly the proliferation of a population of more mature (Lin-) progenitors. The present study was initiated to investigate further whether IL-7 might affect CSF-induced proliferation of subpopulations of committed myeloid progenitors as well as mature bone marrow macrophages. IL-7 enhanced macrophage colony-stimulating factor (CSF-1)-induced colony formation of single bone marrow macrophages 90%, whereas IL-7 alone had no effect. Furthermore, IL-7, in a concentration-dependent manner, increased the proliferation of mononuclear cells expressing the Mac-1 Ag (Mac-1+ mononuclear cells (MNC); CD11b) up to fivefold in response to CSF-1, granulocyte macrophage-CSF (GM-CSF), or IL-3. In contrast, no effect of IL-7 was observed on Mac-1- MNC. The synergistic effect of IL-7 on Mac-1+ MNC was caused by an increase in macrophage colonies (CFU-M) and mixed granulocyte-macrophage colonies (CFU-GM), whereas the total number of granulocyte colonies (CFU-G) was not affected. This suggests that IL-7 can provide proliferative signals to Mac-1+ progenitors with a macrophage potential, but not to progenitors committed to pure granulocyte differentiation.
Study on the Chemical Constituent from the Seed of Litchi chinensis Sonn. (2004)

Seed of Litchi chinensis Sonn. is a traditional Chinese medicine, having curative effects on gastric disease, diabetes,and relieving pain.[1] Two new compounds 4-O-p-coumaroylquinic acid butyl ester (1) and 3-O-p-coumaroylquinic acid butyl ester (2), along with five known compounds: 5-O-p-coumaroylquinic acid butyl ester (3),[2] 3-O-p-coumaroylquinic acid methyl ester (4),[3] n-butyl-1-β-D-fructopyranoside (5),[4] D-1-O-methylmyo-inositol (6)[5] and 1H-imidazole-2,3-dihydro-2-oxo-4-carboxylic acid methyl ester (7)[5] were isolated and purified from the ethanol extracts of the seed of L.chinensis Sonn. Their structures, shown in Figure 1, were elucidated by ESI-MS, 1H NMR and 13C NMR, including 2DNMR spectroscopy.……
Cross-geography scientific data transferring trends and behavior (2018)

Wide area data transfers play an important role in many science applications but rely on expensive infrastructure that often delivers disappointing performance in practice. In response, we present a systematic examination of a large set of data transfer log data to characterize transfer characteristics, including the nature of the datasets transferred, achieved throughput, user behavior, and resource usage. This analysis yields new insights that can help design better data transfer tools, optimize networking and edge resources used for transfers, and improve the performance and experience for end users. Our analysis shows that (i) most of the datasets as well as individual files transferred are very small; (ii) data corruption is not negligible for large data transfers; and (iii) the data transfer nodes utilization is low. Insights gained from our analysis suggest directions for further analysis.
Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. (1989)

In a significant fraction of the Escherichia coli cytosolic proteins, the N-terminal methionine residue incorporated during the translation initiation step is excised. The N-terminal methionine excision is catalyzed by methionyl-aminopeptidase (MAP). Previous studies have suggested that the action of this enzyme could depend mainly on the nature of the second amino acid residue in the polypeptide chain. In this study, to achieve a systematic analysis of the specificity of MAP action, each of the 20 amino acids was introduced at the penultimate position of methionyl-tRNA synthetase of E. coli and the extent of in vivo methionine excision was measured. To facilitate variant protein purification and N-terminal sequence determination, an expression shuttle vector based on protein fusion with beta-galactosidase was used. From our results, methionine excision catalyzed by MAP is shown to obey the following rule: the catalytic efficiency of MAP, and therefore the extent of cleavage, decreases in parallel with the increasing of the maximal side-chain length of the amino acid in the penultimate position. This molecular model accounts for the rate of N-terminal methionine excision in E. coli, as deduced from the analysis of 100 protein N-terminal sequences.
A randomized, controlled study to assess the efficacy and safety of lotilaner (Credelio™) in controlling ticks in client-owned dogs in Europe (2017)

Under European field conditions, lotilaner flavoured chewable tablets administered monthly, were > 98% effective in eliminating live ticks from the first post-treatment assessment (Day 7) through Day 56 and maintained 100% of dogs tick-free on Days 70 and 84. Lotilaner was safe, providing superior tick control to FSM administered according to the same schedule.
Involvement of Hematopoietic Progenitor Kinase 1 in T Cell Receptor Signaling (2001)

Hematopoietic progenitor kinase 1 (HPK1), a mammalian Ste20-related serine/threonine protein kinase, is a hematopoietic-specific upstream activator of the c-Jun N-terminal kinase. Here, we provide evidence to demonstrate the involvement of HPK1 in T cell receptor (TCR) signaling. HPK1 was activated and tyrosine-phosphorylated with similar kinetics following TCR/CD3 or pervanadate stimulation. Co-expression of protein-tyrosine kinases, Lck and Zap70, with HPK1 led to HPK1 activation and tyrosine phosphorylation in transfected mammalian cells. Upon TCR/CD3 stimulation, HPK1 formed inducible complexes with the adapters Nck and Crk with different kinetics, whereas it constitutively interacted with the adapters Grb2 and CrkL in Jurkat T cells. Interestingly, HPK1 also inducibly associated with linker for activation of T cells (LAT) through its proline-rich motif and translocated into glycolipid-enriched microdomains (also called lipid rafts) following TCR/CD3 stimulation, suggesting a critical role for LAT in the regulation of HPK1. Together, these results identify HPK1 as a new component of TCR signaling. T cell-specific signaling molecules Lck, Zap70, and LAT play roles in the regulation of HPK1 during TCR signaling. Differential complex formation between HPK1 and adapters highlights the possible involvement of HPK1 in multiple signaling pathways in T cells.
Tractional retinal detachment following intravitreal bevacizumab (Avastin) in patients with severe proliferative diabetic retinopathy (2007)

TRD may occur or progress shortly following administration of intravitreal bevacizumab in patients with severe PDR.
Synthesis and Evaluation of Indenopyrazoles as Cyclin-Dependent Kinase Inhibitors. 3. Structure Activity Relationships at C3 (2002)

The identification of indeno[1,2-c]pyrazol-4-ones as inhibitors of cyclin-dependent kinases (CDKs) has led to the discovery of a series of novel and potent compounds. Herein, we report the effects of substitutions at C3 of the indeno[1,2-c]pyrazol-4-one core with alkyls, heterocycles, and substituted phenyls. Substitutions at the para position of the phenyl ring at C3 were generally well-tolerated; however, larger groups were generally inactive. For alkyls directly attached to C3, longer chain substituents were not tolerated; however, shorter alkyl groups and cyclic alkyls were acceptable. In general, the heterocycles at C3 gave the most potent analogues. One such heterocycle, 24j, was examined in detail and was determined to have a biological profile consistent with CDK inhibition. An X-ray crystal structure of one of the alkyl compounds, 13q, complexed with CDK2 was determined and showed the inhibitor residing in the adenosine 5'-triphosphate pocket of the enzyme.
Multistage hybrid active appearance model matching: segmentation of left and right ventricles in cardiac MR images (2001)

A fully automated approach to segmentation of the left and right cardiac ventricles from magnetic resonance (MR) images is reported. A novel multistage hybrid appearance model methodology is presented in which a hybrid active shape model/active appearance model (AAM) stage helps avoid local minima of the matching function. This yields an overall more favorable matching result. An automated initialization method is introduced making the approach fully automated. Our method was trained in a set of 102 MR images and tested in a separate set of 60 images. In all testing cases, the matching resulted in a visually plausible and accurate mapping of the model to the image data. Average signed border positioning errors did not exceed 0.3 mm in any of the three determined contours-left-ventricular (LV) epicardium, LV and right-ventricular (RV) endocardium. The area measurements derived from the three contours correlated well with the independent standard (r = 0.96, 0.96, 0.90), with slopes and intercepts of the regression lines close to one and zero, respectively. Testing the reproducibility of the method demonstrated an unbiased performance with small range of error as assessed via Bland-Altman statistic. In direct border positioning error comparison, the multistage method significantly outperformed the conventional AAM (p < 0.001). The developed method promises to facilitate fully automated quantitative analysis of LV and RV morphology and function in clinical setting.
Fundamentals of Spun Yarn Technology (2003)

Existing textbooks covering the subject of yarn manufacture largely concentrate on describing the workings of machines. Fundamentals of Spun Yarn Technology presents complete coverage of yarn manufacture and technology and current research findings on the structure and properties of spun yarns. Written by a well-known and respected authority on tex
Depletion of tumor‐induced Treg prior to reconstitution rescues enhanced priming of tumor‐specific, therapeutic effector T cells in lymphopenic hosts (2009)

We reported previously that vaccination of reconstituted, lymphopenic mice resulted in a higher frequency of tumor-specific effector T cells with therapeutic activity than vaccination of normal mice. Here, we show that lymphopenic mice reconstituted with spleen cells from tumor-bearing mice (TBM), a situation that resembles the clinical condition, failed to generate tumor-specific T cells with therapeutic efficacy. However, depletion of CD25(+) Treg from the spleen cells of TBM restored tumor-specific priming and therapeutic efficacy. Adding back TBM CD25(+) Treg to CD25(-) naïve and TBM donor T cells prior to reconstitution confirmed their suppressive role. CD25(+) Treg from TBM prevented priming of tumor-specific T cells since subsequent depletion of CD4(+) T cells did not restore therapeutic efficacy. This effect may not be antigen-specific as three histologically distinct tumors generated CD25(+) Treg that could suppress the T-cell immune response to a melanoma vaccine. Importantly, since ex vivo depletion of CD25(+) Treg from TBM spleen cells prior to reconstitution and vaccination fully restored the generation of therapeutic effector T cells, even in animals with established tumor burden, we have initiated a translational clinical trial of this strategy in patients with metastatic melanoma.
Coated Microneedles for Drug Delivery to the Eye (2007)

This study demonstrated for the first time that coated microneedles can deliver drugs into the eye via intrascleral and intracorneal routes. This minimally invasive approach may avoid the complications associated with intraocular injection and systemic administration.
Homologous recombination between rrn operons rearranges the chromosome in host-specialized species of Salmonella (1998)

Partial digestion with I-CeuI, which digests bacterial DNA at the gene coding for the large subunit rRNA, established the rrn genomic skeleton (the distance in kb between rRNA operons) in 56 strains of Salmonella, from Salmonella Reference B (SARB) set. All had seven I-CeuI sites, indicating seven rrn operons. The order of I-CeuI fragments was ABCDEFG in S. typhimurium LT2 and in 31 other species, mostly host-generalists; in S. typhi, S. paratyphi C, S. gallinarum, and S. pullorum (host-specialized species), these fragments are rearranged, due to homologous recombination between the rrn operons. Rearrangements, such as inversions and translocations not involving the rrn operons, are rare. I-CeuI fragments of some species are larger than the norm, suggesting the insertion of unique blocks of DNA by lateral transfer from other species.
Collaborative Beamfocusing Radio (COBRA) (2013)

A Ziva team has recently demonstrated a novel technique called Collaborative Beamfocusing Radios (COBRA) which enables an ad-hoc collection of distributed commercial off-the-shelf software defined radios to coherently align and beamform to a remote radio. COBRA promises to operate even in high multipath and non-line-of-sight environments as well as mobile applications without resorting to computationally expensive closed loop techniques that are currently unable to operate with significant movement. COBRA exploits two key technologies to achieve coherent beamforming. The first is Time Reversal (TR) which compensates for multipath and automatically discovers the optimal spatio-temporal matched filter to enable peak signal gains (up to 20 dB) and diffraction-limited focusing at the intended receiver in NLOS and severe multipath environments. The second is time-aligned buffering which enables TR to synchronize distributed transmitters into a collaborative array. This time alignment algorithm avoids causality violations through the use of reciprocal buffering. Preserving spatio-temporal reciprocity through the TR capture and retransmission process achieves coherent alignment across multiple radios at ~GHz carriers using only standard quartz-oscillators. COBRA has been demonstrated in the lab, aligning two off-the-shelf software defined radios over-the-air to an accuracy of better than 2 degrees of carrier alignment at 450 MHz. The COBRA algorithms are lightweight, with computation in 5 ms on a smartphone class microprocessor. COBRA also has low start-up latency, achieving high accuracy from a cold-start in 30 ms. The COBRA technique opens up a large number of new capabilities in communications, and electronic warfare including selective spatial jamming, geolocation and anti-geolocation.
Engineering and analysis of protease fine specificity via site-directed mutagenesis (2013)

I would first like to thank my advisor, Brent Iverson, for the opportunity to work in his lab, for his guidance, and for his constant encouragement during my time here at the University of Texas.Thank you for truly caring about all of the students in your lab, in your classes, and at the University of Texas, and thank you for teaching us all, by your example, the importance of work-life balance.Thank you to all of the members of my lab past and present for help with lab equipment, bouncing ideas back and forth, making it to the intramural soccer finals with me at least four times (but never actually winning), putting the tape around my lab goggles to fix them even though they were never broken, and for making my time at UT enjoyable.Thank you to Garen, Chelsea, Stevan, Little Mike, and Medium Mike for making me feel so welcome in the lab when I first got to UT. Thank you to Amy for putting up with my music, to Maria for helping me retrieve my HPLC data when I was hundreds of miles from the machine, to Cameron for always keeping the lab interesting, thank you to Brian for inspiring me with your kindness, and thank you to Liz for always celebrating the most obscure holidays
Low voltage low power sub-threshold operational amplifier in 180nm CMOS (2017)

A two-stage operational amplifier for biomedical applications is presented in this paper. In the Op-Amp design, all transistors have been operated in sub-threshold region for low voltage low power application. The proposed Op-Amp has been designed based on TSMC foundry 180nm process and simulated in Cadence analog design environment. The proposed circuit generates a 40dB gain, 114 KHz UGBW, 72 deg phase margin & total power consumption is just 112nW with 0.8V battery.
Solventless Attachment of Long-Chain Molecules to Poly(ethylene-alt-maleic anhydride) Copolymer Surfaces (1998)

Surface functionalization of poly(ethylene-alt-maleic anhydride) copolymer films with trifluoroethylamine and amine terminated polyethers (Jeffamines) to form amide linkages has been shown to proceed to high levels of conversion.