gebhart/patrepeval huggingface dataset:
Coagulation and inflammatory markers in Alzheimer's and vascular dementia (2004)

Alzheimer's disease is classified as a degenerative dementia while vascular dementia is known to be associated with atherothrombosis and classical vascular risk factors. However, over the last decade, there is increasing evidence of the role of haemostatic factors and inflammatory mechanisms in the pathogenesis of Alzheimer's disease. Serum markers of hypercoagulability and markers of inflammation could lead to thrombosis, accelerated atherogenesis and resulting dementia of both Alzheimer's and vascular dementia. In this case control study, we studied these serum markers of coagulation and inflammation in patients suffering from dementia.
Implementation of a Drilling Microchip for Downhole Data Acquisition (2017)

Abstract First and secondgeneration drilling microchipsare compared side by side on design architecture, system components, sensors, output signal, build materials etc. Temperature microchips were field tested in an on-shore well. From the 20 deployed microchips, 6 passed through the bit nozzles and survived the drilling process without causing any downtime to the operation. The data recorded by different microchips showed excellent consistency over the downhole part of the trip, from inside of the drill pipe up the annulus to the surface. This is the first time that a drilling microchip was successfully deployed while drilling, and a complete set of data recorded throughout the entire trip from drill pipe, to the annulus, all the way to the flow line and shale shaker. The consistent results from the microchip provide valuable information for a wide range of drilling activities.
Emerging Drug Candidates of Dipeptidyl Peptidase IV (DPP IV) Inhibitor Class for the Treatment of Type 2 Diabetes (2009)

Dipeptidyl peptidase IV (DPP IV) is a key regulator of insulin-stimulating hormones, glucagon-like peptide (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), thus it is a promising target for the treatment of Type 2 Diabetes mellitus (T2DM). Inhibition of plasma DPP IV enzyme leads to enhanced endogenous GLP-1 and GIP activity, which ultimately results in the potentiation of insulin secretion by pancreatic beta-cells and subsequent lowering of blood glucose levels, HbA[1(c)], glucagon secretion and liver glucose production. Various classes of structurally different DPP IV inhibitors are currently being explored and few of them such as Sitagliptin and Vildagliptin were successfully launched. These drugs have been approved as a once-daily oral monotherapy or as a combination therapy with current anti-diabetic agents like pioglitazone, glibenclamide, metformin etc. for the treatment of T2DM. Several other novel DPP IV inhibitors are in pipeline. The present review summarizes the latest preclinical and clinical trial data of different DPP IV inhibitors with a special emphasis on their DPP8/9 fold selectivity and therapeutic advantages over GLP-1 based approach.
P38 MAP kinase mediates transforming growth factor-β2 transcription in human keloid fibroblasts (2006)

Keloids are abnormal fibrous growths of the dermis that develop only in response to wounding and represent a form of benign skin tumor. Previous studies have shown increased protein levels of TGF-beta in keloid tissue, suggesting a strong association with keloid formation leading us to examine mechanisms for why it is more highly expressed in keloids. Here, we use serum stimulation as an in vitro model to mimic a component of the wound microenvironment and examine differential gene expression in keloid human fibroblasts (KFs) vs. normal human fibroblasts (NFs). Transcription of TGF-beta2 was rapid and peaked between 1 and 6 h after serum stimulation in KFs vs. NFs. We confirmed increased TGF-beta activity in the conditioned medium from KFs, but not NFs. Inhibition of second messenger signaling pathways demonstrated that only the p38 MAPK inhibitor SB-203580 could block upregulation of TGF-beta2 following serum stimulation in KFs. Immunoblotting demonstrated that p38 MAPK was phosphorylated within 15 min and was maintained at a high level in KFs but not in NFs. The transcription factors activating transcription factor-2 and Elk-1 are activated by p38 MAPK, and also showed rapid and prolonged phosphorylation kinetics in KFs but not in NFs. In conclusion, increased TGF-beta2 transcription in response to serum stimulation in KFs appears to be mediated by the p38 MAPK pathway. This suggests the mechanism of keloid pathogenesis may be due in part to an inherent difference in how the fibroblasts respond to wounding.
Amino Acids and Peptides; 67.1Easy Preparation and Use of Benzyloxycarbonyl Derivatives of Amino Acid Chlorides and α-Hydroxycarboxylic Acid Chlorides (1988)

N-Benzyloxycarbonyl amino acid chlorides and α-benzyloxycarbonyloxy carboxylic acid chlorides are readily available by treating the corresponding carboxylic acids with 1-chloro-N,N,2-trimethyl-1-propen-1-amine. They can be immediately reacted with O-, N- and C-nucleophiles to afford peptides, ketones and esters.
Enhanced efficacy and safety of nanoparticle albumin-bound nab-docetaxel versus taxotere. (2006)

5438 Background: Docetaxel (Taxotere) is currently formulated in the surfactant Tween 80. Removal of surfactants from taxane formulations e.g., in the case of nanoparticle albumin-bound paclitaxel (Abraxane) resulted in significantly higher response rates and greater safety (Gradishar, JCO, 2005, 23:7794). Tween 80 strongly inhibited the binding of taxanes to albumin, possibly inhibiting albumin based drug transport via the gp60 endothelial receptor (Desai, EORTC-NCI-AACR, 2004) and consequent reduction of albumin-binding to tumor secreted SPARC. Herein, we compared the efficacy, toxicity, and pharmacokinetics (PK) of nab-docetaxel vs Taxotere. Methods: Nanoparticle nab-docetaxel was prepared using nab technology and characterized. Nab-docetaxel and Taxotere were tested in vivo against HCT-116 human colon carcinoma xenograft in nude mice (n=10/group) at equitoxic doses of 22 mg/kg of nab-docetaxel and 15 mg/kg of Taxotere, on a q4dx3 schedule. Single dose toxicity (TOX) of nab-docetaxel was compared to Taxotere in rats at 25, 50, 75, 100, and 125 mg/kg (N=3 per group). Multiple dose TOX of nab-docetaxel was compared to Taxotere in rats at 5, 10, 15, 30, and 50 mg/kg on a q4dx3 schedule (N=3 per group). PK of nab-docetaxel and Taxotere were evaluated in rats at 10, 20, and 30 mg/kg (N=3 per group). Results: In vivo, both nab-docetaxel and Taxotere were effective against HCT-116. However, at equitoxic dose, as measured by weight loss, nab-docetaxel exhibited significantly higher antitumor activity versus Taxotere (p
Robust time-optimal control - Frequency domain approach (1994)

The design of nonrobust and robust time-optimal controllers for linear systems in the frequency domain is presented. The bang-bang profile is represented as the superposition of time-delayed step inputs or the output of a time-delay filter subject to a step input. A parameter optimization problem is formulated to minimize the final time of the maneuver with the constraint that the time-delay filter cancels all of the poles of the system. The issue of robustness to errors in the model is addressed by placing multiple zeros of the time-delay filter at the estimated locations of the poles of the system. The design technique is illustrated on representative models of large space structures, for rest-to-rest, time-optimal, and robust time-optimal maneuvers. Spin-up maneuvers are shown to be special cases of the general formulation. IME-OPTIMAL control of flexible spacecraft is a topic of current interest.1 Many computational approaches and analyses have been presented in the recent literature to deal with the effects of flexibility. Most of these works deal with planar (singleaxis) rest-to-rest maneuvers under two categories: near-minimumtime control and exact-minimum-time control. The first category of methods is based on smooth approximations to minimum-time control for an equivalent rigid body. This class of methods has been shown to be well suited when applied moments or torques are produced by either throttlable thrusters or reaction wheels.2'3 Higher modes of the system are not excited due to the smoothness of the control profile. The second category of methods deals with on-off thrusters directly. Rajan4 formulates the problem including
Impaired apoptosis in mitogen-stimulated lymphocytes of patients with multiple sclerosis (1999)

We investigated the sensitivity to cell death of peripheral blood mononuclear cells (PBMCs) from patients with multiple sclerosis (MS). PBMCs from MS patients, following PHA stimulation, were less sensitive to cell death than those from healthy donors (mean +/- s.e.m., 22.5 +/- 1.9 in MS patients vs 36.5 +/- 2.8 in healthy controls; p = 0.0003). However, when Fas-agonist antibody was added, the increase in respect to apoptosis induced by mitogen alone was even higher in MS patients than in controls. In addition, PHA-activated PBMCs from MS patients showed higher surface expression of Fas than controls, while Bcl-2 expression was decreased. This finding raised the question of whether an impaired generation of apoptotic signals may be contributing to the immune component of MS.
Long-Range and Local Structure in the Layered Oxide Li1.2Co0.4Mn0.4O2 (2011)

The layered oxides being considered as intercalation compounds for lithium batteries display significant differences between the long-range crystal structure and local arrangements around individual atoms. These differences are important, because the local atomic environments affect Li-ion transport and, hence, the oxide’s rate capability, by determining activation barrier energies, by blocking or opening Li-diffusion pathways, etc. Traditional diffraction methods provide key information on the average crystal structure. However, no single experimental technique can unequivocally determine the average long-range crystal structure and the distribution of local environments over crystallographic distances while retaining atomic-scale resolution. Therefore, in this study, we have employed a combination of diffraction, microscopy, and spectroscopy techniques to investigate the long-range (∼1 μm) and local structure (≤1 nm) of Li1.2Co0.4Mn0.4O2, which is a model compound for layered oxides being considered for transportation applications. We find that Li1.2Co0.4Mn0.4O2 contains mostly Mn4+ in Li2MnO3-like atomic environments and Co3+ in LiCoO2-like atomic environments, which are intimately mixed over length scales of ≥2−3 nm, resulting in a Li1.2Co0.4Mn0.4O2 crystallite composition that appears homogeneous over the long-range. In addition, we observed a quasi-random distribution of locally monoclinic structures, topotaxially integrated within a rhombohedral-NaFeO2 framework. Based on these observations, we propose a dendritic microstructure model for Li1.2Co0.4Mn0.4O2 consisting of well integrated LiCoO2- and Li2MnO3-like structures.
Two Hypothetical Proteins of Human Aortic Adventitia, with Ig Kappa, Collagenous, and Aromatic-Rich Motifs (1996)

Two of five clones, selected from an expression library of aortic adventitia, encode unique hypothetical proteins sharing sequences of Ig kappa, gly/pro rich (collagenous) motifs, and aromatic motifs that occur in several proteins of the extracellular matrix. Both proteins have a similar domain structure with at least 8 regions: (1) Ig kappa (84-120 residues in length); (2) ser/thr-rich motif (44-63); (3) a second Ig kappa motif (9-12); (4) either a possible calcium-binding motif or a gly/pro rich sequence (35-43); (5) an aromatic rich sequence (6-7); (6) another gly/pro rich sequence (62-72); (7) a third Ig kappa sequence (26-28); and (8) a C-terminal 68-70 residue sequence with another aromatic motif.
Macroscopic Three-Dimensional Arrays of Fe Nanoparticles Supported in Aligned Carbon Nanotubes (2001)

A novel route to regularly arrange Fe nanoparticles in three-dimensions over large areas, just like a crystalline cubic lattice of atoms, is reported. The cylindrical Fe particles, acting as the catalyst for carbon nanotube formation by conventional chemical vapor deposition method, are located in the nanotube cavities. The inner nanotube cavities protect and support the Fe particles, which are periodically spaced in the aligned nanotubes. The interparticle spacings can be well-controlled simply by adjusting the feeding interval of ferrocene during the nanotube growth process. Carbon nanotubes, which can carry foreign particles because of capillarity, show potential use in manipulating nanoparticles that otherwise have a strong tendency to aggregate and merge.
Endothelial Nitric Oxide Synthase Deficiency Produces Accelerated Nephropathy in Diabetic Mice (2006)

Functionally significant polymorphisms in endothelial nitric oxide synthase (eNOS) and reduced vascular eNOS activity have been associated with increased human diabetic nephropathy (DN), but the pathogenic role of eNOS deficiency in the development of DN has not yet been confirmed. This study characterizes the severity of DN in eNOS(-/-) mice that were backcrossed to C57BLKS/J db/db mice. Although the severity of hyperglycemia was similar to C57BLKS/J db/db mice, by 26 wk, eNOS(-/-) C57BLKS/J db/db mice exhibited dramatic albuminuria, arteriolar hyalinosis, increased glomerular basement membrane thickness, mesangial expansion, mesangiolysis, and focal segmental and early nodular glomerulosclerosis. Even more remarkable, eNOS(-/-) C57BLKS db/db exhibited decreases in GFR to levels <50% of that in eNOS(+/+) C57BLKS db/db, as confirmed by increased serum creatinine. In summary, eNOS(-/-) db/db mice provide the most robust model of type II DN that has been described to date and support a role for deficient eNOS-derived NO production in the pathogenesis of DN.
Expression and regulation of WNT8A and WNT8B mRNAs in human tumor cell lines: Up-regulation of WNT8B mRNA by β-estradiol in MCF-7 cells, and down-regulation of WNT8A and WNT8B mRNAs by retinoic acid in NT2 cells (2002)

Xenopus wnt-8 (Xwnt-8) is one of the most potent Wnts to activate the WNT - beta-catenin - TCF signaling pathway. We have previously cloned and characterized WNT8A and WNT8B, two human homologues of Xwnt-8. Here, we investigated expression and regulation of WNT8A and WNT8B mRNAs in human tumor cell lines by using cDNA-PCR. WNT8A mRNA was undetectable in 7 pancreatic cancer cell lines, but WNT8B mRNA was detected in pancreatic cancer cell lines PSN-1, BxPC-3, MIA PaCa-2. Both WNT8A and WNT8B mRNAs were undetectable in 7 brain tumor cell lines. Although WNT8A mRNA was undetectable in 3 breast cancer cell lines, WNT8B mRNA was detected in the breast cancer cell line MCF-7. WNT8B mRNA, but not WNT8A mRNA, was significantly up-regulated by beta-estradiol in MCF-7 cells. WNT8A mRNA was detected in embryonal tumor cell lines NEC-14, NCC-IT, and NT2, while WNT8B mRNA was detected in embryonal tumor cell lines NEC-8, NEC-14, and NT2. Because NT2 cells differentiate into neuronal cells after all-trans retinoic-acid treatment, effects of all-trans retinoic acid on mRNA expression of WNT8A and WNT8B were next investigated. WNT8A and WNT8B mRNAs were down-regulated together in NT2 cells after all-trans retinoic-acid treatment. WNT8A and WNT8B might play key roles in embryonal tumors and embryonic stem cells through synergistic activation of the beta-catenin - TCF signaling pathway.
Coseismic surface deformation from air photos: The Kickapoo step over in the 1992 Landers rupture (2006)

Coseismic deformation of the ground can be measured from aerial views taken before and after an earthquake. We chose the area of the Kickapoo‐Landers step over along the 1992 Landers earthquake zone, using air photos (scale 1:40,000) scanned at 0.4 m resolution. Two photos acquired after the earthquake are used to assess the accuracy and to evaluate various sources of noise. Optical distortions, film deformation, scanning errors, or errors in viewing parameters can yield metric bias at wavelength larger than 1 km. Offset field at shorter wavelength is more reliable and mainly affected by temporal decorrelation of the images induced by changes in radiometry with time. Temporal decorrelation and resulting uncertainty on offsets are estimated locally from the correlation degree between the images. Relative surface displacements are measured independently every about 15 m and with uncertainty typically below 10 cm (RMS). The offset field reveals most of the surface ruptures mapped in the field. The fault slip is accurate to about 7 cm (RMS) and measured independently every 200 m from stacked profiles. Slip distribution compares well with field measurements at the kilometric scale but reveals local discrepancies suggesting that deformation is generally, although not systematically, localized on the major fault zone located in the field. This type of data can provide useful insight into the fault zone's mechanical properties. Our measurements indicate that elastic coseismic strain near the fault zone can be as large as 0.5 × 10 −3 , while anelastic yielding was attained for strain in excess of about 1–2 × 10 −3 .
Compression with side information using turbo codes (2003)

We show that turbo codes can come close to the Slepian-Wolf bound in lossless distributed source coding. In the asymmetric scenario considered, X and Y are statistically dependent signals and X is encoded with no knowledge of Y. However, Y is known as side information at the decoder. We use a system based on turbo codes to send X at a rate close to H(X|Y). We apply our system to binary sequences and simulations show performance close to the information-theoretic limit. For distributed source coding of Gaussian sequences, our results show significant improvement over previous work. The scheme also performs well for joint source-channel coding.
Development of kNN QSAR Models for 3-Arylisoquinoline Antitumor Agents (2011)

Variable selection k nearest neighbor QSAR modeling approach was applied to a data set of 80 3-arylisoquinolines exhibiting cytotoxicity against human lung tumor cell line (A-549). All compounds were characterized with molecular topology descriptors calculated with the MolconnZ program. Seven compounds were randomly selected from the original dataset and used as an external validation set. The remaining subset of 73 compounds was divided into multiple training (56 to 61 compounds) and test (17 to 12 compounds) sets using a chemical diversity sampling method developed in this group. Highly predictive models characterized by the leave-one out cross-validated <TEX>$R^2$</TEX> (<TEX>$q^2$</TEX>) values greater than 0.8 for the training sets and <TEX>$R^2$</TEX> values greater than 0.7 for the test sets have been obtained. The robustness of models was confirmed by the Y-randomization test: all models built using training sets with randomly shuffled activities were characterized by low <TEX>$q^2{\leq}0.26$</TEX> and <TEX>$R^2{\leq}0.22$</TEX> for training and test sets, respectively. Twelve best models (with the highest values of both <TEX>$q^2$</TEX> and <TEX>$R^2$</TEX>) predicted the activities of the external validation set of seven compounds with <TEX>$R^2$</TEX> ranging from 0.71 to 0.93.
Parenteral iron formulations differentially affect MCP-1, HO-1, and NGAL gene expression and renal responses to injury (2010)

Despite their prooxidant effects, ferric iron compounds are routinely administered to patients with renal disease to correct Fe deficiency. This study assessed relative degrees to which three clinically employed Fe formulations [Fe sucrose (FeS); Fe gluconate (FeG); ferumoxytol (FMX)] impact renal redox- sensitive signaling, cytotoxicity, and responses to superimposed stress [endotoxin; glycerol-induced acute renal failure (ARF)]. Cultured human proximal tubule (HK-2) cells, isolated proximal tubule segments (PTS), or mice were exposed to variable, but equal, amounts of FeS, FeG, or FMX. Oxidant-stimulated signaling was assessed by heme oxygenase-1 (HO-1) or monocyte chemoattractant protein (MCP)-1 mRNA induction. Cell injury was gauged by MTT assay (HK-2 cells), %LDH release (PTS), or renal cortical neutrophil gelatinase-associated lipoprotein (NGAL) protein/mRNA levels. Endotoxin sensitivity and ARF severity were assessed by TNF-alpha and blood urea nitrogen concentrations, respectively. FeS and FeG induced lethal cell injury (in HK-2 cells, PTS), increased HO-1 and MCP-1 mRNAs (HK-2 cells; in vivo), and markedly raised plasma ( approximately 10 times), and renal cortical ( approximately 3 times) NGAL protein levels. Both renal and extrarenal (e.g., hepatic) NGAL production likely contributed to these results, based on assessments of tissue and HK-2 cell NGAL mRNA. FeS pretreatment exacerbated endotoxemia. However, it conferred marked protection against the glycerol model of ARF (halving azotemia). FMX appeared to be "bioneutral," as it exerted none of the above noted FeS/FeG effects. We conclude that 1) parenteral iron formulations that stimulate redox signaling can evoke cyto/nephrotoxicity; 2) secondary adaptive responses to this injury (e.g., HO-1/NGAL induction) can initiate a renal tubular cytoresistant state; this suggests a potential new clinical application for intravenous Fe therapy; and 3) FMX is bioneutral regarding these responses. The clinical implication(s) of the latter, vis a vis the treatment of Fe deficiency in renal disease patients, remains to be defined.
Expression of Resistance to Barley Stripe Mosaic Virus in Barley and Oat Protoplasts (1990)

Mesophyll protoplasts from both susceptible and resistant hosts were inoculated with RNA purified from barley stripe mosaic virus (BSMV) strains CV52 and CV42 using the polyethylene glycol (PEG) method. Protoplasts derived from the susceptible Hordeum vulgare L. cv. Black Hulless were susceptible to both BSMV strains, as indicated by fluorescein isothiocyanate staining and ELISA. More than 80% of protoplasts derived from an oat cultivar resistant to CV52, but not to CV42, were readily infected by either CV52 or CV42. Protoplasts from 10 barley lines resistant to CV42 remained resistant to CV42, although a limited number of protoplasts were infected. Functional resistance in the cultured barley protoplasts, but not in those from oat plants, suggests that resistance in these barley lines may be the result of restriction of replication, whereas resistance in oat plants is more likely due to restriction of cell-to-cell movement.
A comparison of selected mRNA and protein abundances in human liver (1997)

In order to obtain an estimate of the overall level of correlation between mRNA and protein abundances for a well-characterized pharmaceutically relevant biological system, we have analyzed human liver by quantitative two-dimensional electrophoresis (for protein abundances) and by Transcript Image methodology (for mRNA abundances). Incyte's LifeSeq database was searched for expressed sequence tag (EST) sequences corresponding to a series of 23 proteins identified on 2-D maps in the Large Scale Biology (LSB) Molecular Anatomy database, resulting in estimated abundances for 19 messages (4 were undetected) among 7926 liver clones sequenced. A correlation coefficient of 0.48 was obtained between the mRNA and protein abundances determined by the two approaches, suggesting that post-transcriptional regulation of gene expression is a frequent phenomenon in higher organisms. A comparison with published data (Kawamoto, S., et al., Gene 1996, 174, 151-158) on the abundances of liver mRNAs for plasma proteins (secreted by the liver) suggests that higher abundance messages are strongly enriched in secreted sequences. Our data confirms this: of the 50 most abundant liver mRNAs, 29 coded for secreted proteins, while none of the 50 most abundant proteins appeared to be secreted products (although four plasma and red blood cell proteins were present in this group as contaminants from tissue blood).