gebhart/patrepeval huggingface dataset:
Inflammation and nitric oxide production in skeletal muscle of type 2 diabetic patients (2004)

An inflammatory process may be involved in nitric oxide production in skeletal muscle of type 2 diabetic patients. Nitric oxide generation in skeletal muscle was assessed in 14 non-complicated type 2 diabetic patients and in 12 healthy subjects. In samples of quadriceps femoris muscle, endothelial nitric oxide synthase (eNOS), inducible nitric oxide synthase (iNOS), nitrite, nitrate and nitrotyrosine were determined. The macrophage-specific antigen CD163, the T-cell membrane factor CD154 and tumour necrosis factor-alpha (TNF-alpha) were also assayed. In six patients, ultrastructural analysis of muscle was performed. Nitrites and nitrates were increased in patients as compared to controls (22.7+/-4.5 and 32.7+/-7.0 vs 16.0+/-2.9 and 22.8+/-4.0 micromol/mg protein; P<0.001, Mann-Whitney U test). Endothelial NOS was similar in diabetic and control subjects (36.4+/-13.8 vs 36.3+/-6.8 ng/mg protein), contrasting with the significant increase of iNOS recorded in patients (34.3+/-13.0 vs 8.5+/-2.8 ng/mg protein, P<0.00002). Nitrotyrosine levels were higher in the patient than in the control group (42.1+/-24.4 vs 10.3+/-2.5 ng/mg protein, P<0.00002), as were CD163 (10-fold) and TNF-alpha (fourfold) levels. Furthermore, CD154 levels were detectable only in the patient samples (10.2+/-5.3 ng/mg protein). By multiple-regression analysis, changes in glycated haemoglobin values could predict 96% variation in nitrotyrosine. Macrophages were present in all muscle samples analysed by electromicroscopy. The increased levels of CD163, CD154 and TNF-alpha indicate that an inflammatory process occurs in skeletal muscle of type 2 diabetic patients. This may contribute to iNOS induction, muscle damage and insulin resistance.
Nucleotide sequence of cloned cDNA coding for pumpkin 11‐S globulin β subunit (1988)

cDNA coding for preproglobulin beta, a precursor protein of 11-S globulin beta subunit, was cloned and the nucleotide sequence has been determined. The sequence covers the whole coding region (1440 base pairs) with 5' and 3' noncoding region (30 and 214 base pairs, respectively). The deduced amino acid sequence of preproglobulin beta consists of a 21-amino-acid N-terminal signal peptide, preceding the acidic gamma polypeptide region (275 amino acids) and the subsequent basic delta region (184 amino acids). The site for post-translational cleavage of the precursor polypeptide to make the gamma and delta chains is estimated to be located between the asparagine-glycine residues. The N-terminal amino acid of the gamma chain of mature 11-S globulin beta subunit was reported to be blocked by 5-oxoproline (pyroglutamic acid) [Ohmiya et al. (1980) Plant Cell Physiol. 21, 157-167]. It was shown that the blocked N-terminal amino acid is coded as a glutamine residue. The derived amino acid sequence was also compared with those of precursor proteins of other 11-S globulins such as soybean glycinin, cotton beta globulin, pea legumin and rape 11-S globulin by dot matrix analysis.
Proteoglycan-mediated Inhibition of Aβ Proteolysis (1995)

Senile plaques of Alzheimer's disease brain contain, in addition to beta amyloid peptide (A beta), multiple proteoglycans. Systemic amyloidotic deposits also routinely contain proteoglycan, suggesting that these glycoconjugates are generally involved in amyloid plaque formation and/or persistence. We demonstrate that heparan sulfate proteoglycan (HSPG) and chondroitin sulfate proteoglycan (CSPG) inhibit the proteolytic degradation of fibrillar, but not non-fibrillar, A beta at physiological pH. In accordance with the proteolysis studies, high affinity binding of proteoglycans to fibrillar A beta(1-40) and A beta(1-42) is observed from pH 4 to 9, whereas appreciable binding of HSPG or CSPG to non-fibrillar peptide is only seen at pH < 6. This differing pH dependence of binding suggests that a lysine residue is involved in proteoglycan association with fibrillar A beta, whereas a protonated histidine appears to be needed for binding of the glycoconjugates to non-fibrillar peptide. Scatchard analysis of fibrillar A beta association with proteoglycans indicates a single affinity interaction, and the binding of both HSPG and CSPG to fibrillar A beta is completely inhibited by free glycosaminoglycan chains. This implies that these sulfated carbohydrate moieties are primarily responsible for proteoglycan.A beta interaction. The ability of proteoglycans to bind fibrillar A beta and inhibit its proteolytic degradation suggests a possible mechanism of senile plaque accumulation and persistence in Alzheimer's disease.
Bioorthogonally Cross-Linked Hydrogel Network with Precisely Controlled Disintegration Time over a Broad Range (2014)

Hydrogels with predictable degradation are highly desired for biomedical applications where timely disintegration of the hydrogel (e.g., drug delivery, guided tissue regeneration) is required. However, precisely controlling hydrogel degradation over a broad range in a predictable manner is challenging due to limited intrinsic variability in the degradation rate of liable bonds and difficulties in modeling degradation kinetics for complex polymer networks. More often than not, empirical tuning of the degradation profile results in undesired changes in other properties. Here we report a simple but versatile hydrogel platform that allows us to formulate hydrogels with predictable disintegration time from 2 to >250 days yet comparable macroscopic physical properties. This platform is based on a well-defined network formed by two pairs of four-armed polyethylene glycol macromers terminated with azide and dibenzocyclooctyl groups, respectively, via labile or stable linkages. The high-fidelity bioorthogonal reaction between the symmetric hydrophilic macromers enables robust cross-linking in water, phosphate-buffered saline, and cell culture medium to afford tough hydrogels capable of withstanding >90% compressive strain. Strategic placement of labile ester linkages near the cross-linking site within this superhydrophilic network, accomplished by adjustments of the ratio of the macromers used, enables broad tuning of the disintegration rates precisely matching with the theoretical predictions based on first-order linkage cleavage kinetics. This platform can be exploited for applications where a precise degradation rate is targeted.
A pilot study of rituximab in patients with recurrent, classic Hodgkin disease (2003)

The current data suggest that rituximab therapy in patients with recurrent, classic HD can alter serum IL-6 cytokine levels, can improve B symptoms, and may result in clinical remissions.
A low-power small-area ±7.28-ps-jitter 1-GHz DLL-based clock generator (2002)

In this paper, a delay-locked loop (DLL)-based clock generator is presented. Although a DLL-based clock generator requires a clean reference signal, it has several inherent advantages over conventional phase-locked-loop-based clock generators, i.e., no jitter accumulation, fast locking, stable loop operation, and easy integration of the loop filter. We propose a phase detector with a reset circuitry and a new frequency multiplier to overcome the limited locking range and frequency multiplication problems of the conventional DLL-based system. Fabricated in a 0.35-/spl mu/m CMOS process, our DLL-based clock generator occupies 0.07 mm/sup 2/ of area and consumes 42.9 mW of power. It operates in the frequency range of 120 MHz-1.1 GHz and has a measured cycle-to-cycle jitter of /spl plusmn/7.28 ps at 1 GHz. The die area, peak-to-peak, and r.m.s. jitter are the smallest compared to those of reported high-frequency clock multipliers.
Preparation, Structural Characteristics and Catalytic Properties of Large-Pore Rare Earth Element (Ce, La)/Al-Pillared Smectites (1996)

Abstract Ce/Al- and La/Al-pillared smectites were prepared by cation exchange of bentonite, saponite and laponite with hydrothermally treated (130–160 °C for 16–136 h) solutions containing mixtures of aluminumchlorohydrate (ACH) and Ce 3+ -/and La 3+ -salts. After calcination at 500 °C, the pillared products are characterized by basal spacings between 24.8 and 25.7 Å and surface areas of approximately 430 m 2 g −1 . The products are hydrothermally stable at 500 °C after 2 h in steam. The large basal spacings are due to the formation of a large Ce/La-bearing Al-polyoxocation, whose formation is favored by initially high Al concentrations ≥3.7 M and an OH/Al molar ratio of approximately 2.5. The Ce/Al or La/Al molar ratios can be as low as 1/30. 27 Al nuclear magnetic resonance (NMR) spectroscopy has shown that the polyoxocation has a higher Al tetrahedral /Al octahedral ratio than the Keggin structure Al 13 , which may partly explain the higher stability compared to normal Al-pillared clays. Hydroconversion of n-heptane indicated that the activity of the Pt-loaded pillared products is higher than that of a conventional Pt-loaded amorphous silica-alumina catalyst. Selectivity is strongly dependent on the type of starting clay and its acidity. In industrial hydrocracking of normal feedstock, a Ni/W-loaded Ce/Al-pillared bentonite catalyst showed rapid deactivation due to coke-formation reducing the surface area and the pore volume. Additionally, coke-formation is facilitated by the relatively high iron content of the pillared bentonite (3.43 wt% Fe 2 O 3 ).
β-Thalassemia (2005)

β-Thalassemia, which is caused by a decrease in the production of β-globin chains, affects multiple organs and is associated with considerable morbidity and mortality. Lifelong care is required, and the costs of proper treatment are substantial. This review discusses current approaches to the management of β-thalassemia.
Comparative Studies of Herpesvirus Papio (Baboon Herpesvirus) DNA and Epstein-Barr Virus DNA (1980)

An Epstein-Barr virus (EBV)-like herpesvirus has been isolated from a baboon cell line (594S/F9) by induction with the tumour promoter 12-O-tetradecanoyl-phorbol-13-acetate (TPA). The herpesvirus papio (HVP) DNA was mixed with B95 EBV DNA and was characterized by sedimentation in neutral glycerol gradient as 55S DNA, with a buoyant density of approx. 1.718 g/ml after equilibrium centrifugation in caesium chloride. DNA-DNA reassociation kinetics between B95 EBV and HVP DNA showed that HVP DNA shares about 40% homology with B95 EBV DNA. Blot hybridization of EcoRI fragments of HVP DNA with a 32P-B95 EBV DNA probe showed that most of the EcoRI fragments of HVP DNA were hybridized to B95 EBV DNA, suggesting that the homologous sequences were dispersed throughout the virus DNA.
Ku-0063794 is a specific inhibitor of the mammalian target of rapamycin (mTOR) (2009)

mTOR (mammalian target of rapamycin) stimulates cell growth by phosphorylating and promoting activation of AGC (protein kinase A/protein kinase G/protein kinase C) family kinases such as Akt (protein kinase B), S6K (p70 ribosomal S6 kinase) and SGK (serum and glucocorticoid protein kinase). mTORC1 (mTOR complex-1) phosphorylates the hydrophobic motif of S6K, whereas mTORC2 phosphorylates the hydrophobic motif of Akt and SGK. In the present paper we describe the small molecule Ku-0063794, which inhibits both mTORC1 and mTORC2 with an IC50 of approximately 10 nM, but does not suppress the activity of 76 other protein kinases or seven lipid kinases, including Class 1 PI3Ks (phosphoinositide 3-kinases) at 1000-fold higher concentrations. Ku-0063794 is cell permeant, suppresses activation and hydrophobic motif phosphorylation of Akt, S6K and SGK, but not RSK (ribosomal S6 kinase), an AGC kinase not regulated by mTOR. Ku-0063794 also inhibited phosphorylation of the T-loop Thr308 residue of Akt phosphorylated by PDK1 (3-phosphoinositide-dependent protein kinase-1). We interpret this as implying phosphorylation of Ser473 promotes phosphorylation of Thr308 and/or induces a conformational change that protects Thr308 from dephosphorylation. In contrast, Ku-0063794 does not affect Thr308 phosphorylation in fibroblasts lacking essential mTORC2 subunits, suggesting that signalling processes have adapted to enable Thr308 phosphorylation to occur in the absence of Ser473 phosphorylation. We found that Ku-0063794 induced a much greater dephosphorylation of the mTORC1 substrate 4E-BP1 (eukaryotic initiation factor 4E-binding protein 1) than rapamycin, even in mTORC2-deficient cells, suggesting a form of mTOR distinct from mTORC1, or mTORC2 phosphorylates 4E-BP1. Ku-0063794 also suppressed cell growth and induced a G1-cell-cycle arrest. Our results indicate that Ku-0063794 will be useful in delineating the physiological roles of mTOR and may have utility in treatment of cancers in which this pathway is inappropriately activated.
Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells (2002)

A suppressor tRNA Tyr and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-L-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNA Tyr gene was mutated, at three positions in the D arm, to generate the internal promoter for expression. However, this tRNA, together with the cognate TyrRS, failed to exhibit suppressor activity in mammalian cells. Then, we found that amber suppression can occur with the heterologous pair of E.coli TyrRS and Bacillus stearothermophilus suppressor tRNA Tyr , which naturally contains the promoter sequence. Furthermore, the efciency of this suppression was signicantly improved when the suppressor tRNA was expressed from a gene cluster, in which the tRNA gene was tandemly repeated nine times in the same direction. For incorporation of 3-iodo-L-tyrosine, its specic E.coli TyrRS variant, TyrRS(V37C195), which we recently created, was expressed in mammalian cells, together with the B.stearothermophilus suppressor tRNA Tyr , while 3-iodo-L-tyrosine was supplied in the growth medium. 3-Iodo-L-tyrosine was thus incorporated into the proteins at amber positions, with an occupancy of >95%. Finally, we demonstrated conditional 3-iodo-L-tyrosine incorporation, regulated by inducible expression of the TyrRS(V37C195) gene from a tetracycline-regulated promoter.
Block-based motion estimation algorithms — a survey (2013)

Abstract In the multi-view video coding, both temporal and inter-view redundancies can be exploited by using standard block-based motion estimation (BBME) technique. In this paper, an extensive review of BBME algorithms proposed within the last three decades is presented. Algorithms are divided into five categories: 1) based on the search position number reduction; 2) multiresolution; 3) based on the simplification of matching criterion; 4) fast full search; 5) computation-aware. Algorithms are compared in terms of their efficiency and computational complexity.
Arthritic calcitonin/α calcitonin gene-related peptide knockout mice have reduced nociceptive hypersensitivity (2001)

Peripheral inflammation induced with a knee joint injection of a mixture of kaolin/carrageenan (k/c) produces primary and secondary hyperalgesia. Inflammatory pain is thought to involve a variety of transmitters released from nerve terminals, including amino acids, substance P (SP) and calcitonin gene-related peptide (CGRP). In the present study, mice deficient in the calcitonin/alpha CGRP gene (CGRP(-/-)) displayed normal responses to noxious stimuli. However, the CGRP knockout mice failed to demonstrate development of secondary hyperalgesia after induction of knee joint inflammation in two tests that assess central sensitization, through testing at sites remote from the primary insult. Nociceptive behavioral responses were assessed using the hot-plate test and paw withdrawal latency (PWL) to radiant heat applied to the hindpaw. The CGRP(-/-) mice showed no signs of secondary hyperalgesia after development of knee joint inflammation, while the expected significant decrease in the PWL was observed in the CGRP(+/+) mice as control. The CGRP(-/-) mice also had a prolonged rather than a shortened response latency in the hot-plate test 4 h after knee joint injection of k/c. Immunohistological study showed that CGRP-like immunoreactivity (CGRP-LI) was absent in the spinal cord and dorsal root ganglia taken from the CGRP(-/-) mice. These results indicate that endogenous CGRP plays an important role in the plastic neurogenic changes occurring in response to peripheral inflammatory events including the development of nociceptive behaviors.
Shiga Toxin 2-Producing Acinetobacter haemolyticus Associated with a Case of Bloody Diarrhea (2006)

We report the first Shiga toxin 2-producing Acinetobacter haemolyticus strain that was isolated from the feces of a 3-month-old infant with bloody diarrhea. Usual enteropathogenic bacteria were not detected. This finding suggests that any Shiga toxin-producing microorganism capable of colonizing the human gut may have the potential to cause illness.
Community Structure and Co-operation in Biofilms (2000)

The study of biofilm considers the close association of micro-organisms with each other at interfaces and the consequent physiological adaptation to the proximity of other cells and surfaces. As such it is relevant to a variety of disciplines, including medicine, dentistry, bioremediation, biofouling, water technology, engineering and food science. Although the habitats studied, and their associated cellular communities, differ widely, some common elements exist such as method of attachment, coadhesion, regulation of biofilm phenotype and biofilm architecture. This book aims to distil the common principles of biofilm physiology and growth for all interested disciplines. It will appeal to the specialist biofilm researcher as well as to students wishing to introduce themselves to the topic.
A Review of Surrogate Assisted Multiobjective Evolutionary Algorithms (2016)

Multiobjective evolutionary algorithms have incorporated surrogate models in order to reduce the number of required evaluations to approximate the Pareto front of computationally expensive multiobjective optimization problems. Currently, few works have reviewed the state of the art in this topic. However, the existing reviews have focused on classifying the evolutionary multiobjective optimization algorithms with respect to the type of underlying surrogate model. In this paper, we center our focus on classifying multiobjective evolutionary algorithms with respect to their integration with surrogate models. This interaction has led us to classify similar approaches and identify advantages and disadvantages of each class.
Treatment Strategies in Follicular Lymphomas: Current Status and Future Perspectives (2005)

Although little progress has been made in the treatment of follicular lymphomas (FL) within the last few decades, several new therapeutic modalities have recently demonstrated promising activity. These include myeloablative therapy followed by autologous stem cell transplantation in younger patients in first remission revealing a significant prolongation of remission duration in three prospective randomized trials, whereas the impact on overall survival still needs to be determined. Adding the anti-CD20 antibody rituximab to conventional chemotherapy resulted in a significant increase in remission rate, remission duration and in two of four currently available prospective randomized studies even in a longer overall survival. A prolongation of remission duration was also seen when rituximab was administered as maintenance after cytoreductive therapy or by prolonged application as a single agent. Radioimmunotherapy (RIT) with radioisotopes coupled to monoclonal antibodies revealed encouraging data in several phase II studies. Prospective randomized studies are warranted, however, to define the impact of RIT on FL therapy. New therapeutic perspectives also emerge from increasing insights into the biology of the disease that unravel molecular targets for novel agents, some of which have entered clinical evaluation already.
Extended Life-Span Conferred by Cotransporter Gene Mutations in Drosophila (2000)

Aging is genetically determined and environmentally modulated. In a study of longevity in the adult fruit fly, Drosophila melanogaster, we found that five independent P-element insertional mutations in a single gene resulted in a near doubling of the average adult life-span without a decline in fertility or physical activity. Sequence analysis revealed that the product of this gene, named Indy (for I'm not dead yet), is most closely related to a mammalian sodium dicarboxylate cotransporter-a membrane protein that transports Krebs cycle intermediates. Indy was most abundantly expressed in the fat body, midgut, and oenocytes: the principal sites of intermediary metabolism in the fly. Excision of the P element resulted in a reversion to normal life-span. These mutations may create a metabolic state that mimics caloric restriction, which has been shown to extend life-span.
Immune Modulation by Altered Nutrient Metabolism: Nutritional Control of Immune-Induced Growth Depression (1993)

The ability of conjugated isomers of linoleic acid (CLA) to prevent reduced growth rate following endotoxin (lipopolysaccharide, LPS) injection was studied in two chick trials and one rat trial. Chicks (10 per treatment) were fed a corn and soybean meal-based diet with or without .5% CLA. At 21 days of age, chicks were weighed and injected i.p. with 1 mg/kg BW Escherichia coli LPS and sterile PBS. Body weights were again determined 24 h later. Antibody responses to SRBC were also determined. Rats fed .5% stearic acid or CLA for 4 wk (seven per treatment) were also injected with LPS, and BW change over a 24-h postinjection period was determined. Antibody responses to BSA, phytohemagglutinin foot pad swelling, and phagocytosis of elicited peritoneal macrophages were also determined. The CLA had no adverse effects on any immune variables measured in the chicks and rats. The CLA enhanced the phytohemagglutinin response and macrophage phagocytosis in rats. Chicks fed CLA and injected with LPS continued to grow, whereas those not fed CLA either failed to grow or lost weight following LPS injection. Both control and CLA-fed rats lost weight over the 24-h period after LPS injection; however, the loss of weight in rats fed CLA was only half of the weight loss of the control rats. Thus, CLA is effective in preventing the catabolic effects of immune stimulation.