gebhart/patrepeval huggingface dataset:
Blueberry Intake Alters Skeletal Muscle and Adipose Tissue Peroxisome Proliferator-Activated Receptor Activity and Reduces Insulin Resistance in Obese Rats (2011)

Metabolic syndrome can precede the development of type 2 diabetes and cardiovascular disease and includes phenotypes such as obesity, systemic inflammation, insulin resistance, and hyperlipidemia. A recent epidemiological study indicated that blueberry intake reduced cardiovascular mortality in humans, but the possible genetic mechanisms of this effect are unknown. Blueberries are a rich source of anthocyanins, and anthocyanins can alter the activity of peroxisome proliferator-activated receptors (PPARs), which affect energy substrate metabolism. The effect of blueberry intake was assessed in obesity-prone rats. Zucker Fatty and Zucker Lean rats were fed a higher-fat diet (45% of kcal) or a lower-fat diet (10% of kcal) containing 2% (wt/wt) freeze-dried whole highbush blueberry powder or added sugars to match macronutrient and calorie content. In Zucker Fatty rats fed a high-fat diet, the addition of blueberry reduced triglycerides, fasting insulin, homeostasis model index of insulin resistance, and glucose area under the curve. Blueberry intake also reduced abdominal fat mass, increased adipose and skeletal muscle PPAR activity, and affected PPAR transcripts involved in fat oxidation and glucose uptake/oxidation. In Zucker Fatty rats fed a low-fat diet, the addition of blueberry also significantly reduced liver weight, body weight, and total fat mass. Finally, Zucker Lean rats fed blueberry had higher body weight and reduced triglycerides, but all other measures were unaffected. In conclusion, whole blueberry intake reduced phenotypes of metabolic syndrome in obesity-prone rats and affected PPAR gene transcripts in adipose and muscle tissue involved in fat and glucose metabolism.
Molecular determinants of opioid analgesia: Modulation of presynaptic calcium channels (2001)

Abstract Opioid receptor agonists remain one of the most efficacious classes of analgesic drugs available for clinical use. Although multiple subclasses of opioid receptors have been identified (δ, κ, and μ), most opioid analgesics act at the μ receptor subtype to decrease cAMP formation, activate hyperpolarizing K + channels, and inhibit Ca 2+ channels. Here, we discuss the molecular interactions underlying opioid receptor‐mediated modulation of voltage‐dependent calcium channels. Opioid receptor activation results in binding of the G protein βγ complex to specific structural elements of the presynaptic calcium channel. The modulated calcium channel displays characteristic inhibition and kinetic slowing resulting in reduced Ca 2+ influx and diminished release of neurotransmitter. Mounting evidence suggests that desensitization of this opioid response involves regulators of G‐protein signaling (RGS), G‐protein coupled receptor kinases (GRK), and β‐arrestins. Further advances in our understanding of these subcellular events mediating opioid pain relief offer new prospects in the development of improved analgesic agents. Drug Dev. Res. 54:118–128, 2002. © 2002 Wiley‐Liss, Inc.
Gene Flow in Wheat at the Field Scale (2004)

In wheat (Triticum L.), large-scale field studies were conducted to assess the level of intra- and interspecific pollen-mediated gene movement that may exist at varying distances from a pollinator source. The objectives of this research were to measure gene flow rates from a blue-grained pollinator (T. aestivum cv. Purendo-38) to (i) red-grained spring wheat cv. CDC Teal (T. aestivum) over distances of 0.2 to 160 m, (ii) amber durum wheat cv. AC Navigator (T. turgidum L.) over distances of 0.2 to 260 m, and (iii) CDC Teal and AC Navigator over distances of 180 to 2760 m. In 2000 and 2001, 50- by 50-m blue-grained pollinator blocks were sown and surrounded by recipient fields of either CDC Teal or AC Navigator at Saskatoon, SK. At maturity, 0.5- by 4-m strips were harvested at specified distances between 0.2 and 160 m or 260 m along eight transects (N, E, S, W, NE, SE, SW, NW) radiating out from Purendo-38. In addition, random sampling was conducted in 2000 and 2001 from surrounding wheat fields to estimate gene flow rates over distances of 180 to 2760 m. Gene flow from Purendo-38 to recipient plants was identified by the expression of a light-blue pigment in the aleurone layer of F1 hybrid seed. Confirmed intra- and interspecific pollen-mediated gene flow rates remained below 0.5% and declined rapidly with distance from the pollinator. Elevated gene flow rates to the N, W, and NW of the pollinator were associated with prevalent winds in 2000, but not in 2001. In 2000, long distance intraspecific gene flow was confirmed at a frequency of 0.005% at a position 300 m northwest of the pollinator. No evidence of interspecific gene flow was observed at ≥40 m from the pollinator. The results suggest that gene flow occurrence in spring wheat is relatively low but that a tolerance level of 0% transgenic wheat in nontransgenic wheat grain is unrealistic.
Controlled release of insulin‐like growth factor 1 enhances urethral sphincter function and histological structure in the treatment of female stress urinary incontinence in a rat model (2017)

Periurethral administration of IGF-1-A-PLO-G microbeads facilitates recovery from SUI by promoting skeletal myogenesis and revascularisation. This therapy is promising, but detailed and longer term studies in animal models and humans are needed.
Comparative genomics among cyst nematodes reveals distinct evolutionary histories among effector families and an irregular distribution of effector‐associated promoter motifs (2022)

Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are essential for PCN control. However, the poor delineation of G. pallida pathotypes has hampered the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs (venom allergen-like proteins) diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCNs after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression ("DOG boxes") were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with the expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Resequencing of PCN populations with different virulence characteristics will allow for the linking of these characteristics to the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.
Linkage Disequilibrium between Chromosomes in the Human Genome: Test Statistics and Rapid Computation (2010)

Linkage disequilibrium (LD) refers to the statistical dependency of the DNA content at nearby locations of the chromosome. Numerous approaches to analyze genome data rely on the well documented fact that LD decays monotonously with the distance of the studied loci. This decay, though noisy and modi ed by a number of factors, can be attributed to the recombination process, a major source of genetic variation in diploid organisms.&#13;\n&#13;\nIn this work we take first steps toward analyzing the extent of LD between very distant loci, even loci from different chromosomes. This is in contrast to traditional "genome-wide" analyses which merely study the LD within each chromosome separately.&#13;\n&#13;\nWe design several measures of LD, and use them for analyzing the HapMap data. We also consider LD between supermarkers determined by haplotype clusters in windows of a few SNPs.&#13;\n&#13;\nWe report on suggestive pairs of loci where unusually large correlations are observed within all ethnic groups.&#13;\n&#13;\nWe describe how the computations can be arranged in a way that enables an all-pairs analysis of the data, that is, all pairs of loci across all the 22 autosomal chromosomes. This kind of "genome times genome" analysis is computationally very burdensome due to the sheer number of possible pairs. We show ways to make it feasible.
Obesity History and Daily Patterns of Physical Activity at Age 60–64 Years: Findings From the MRC National Survey of Health and Development (2017)

Obese older adults may require targeted interventions and additional support to improve their daily activity levels. As younger generations with greater lifetime exposure to obesity reach old age the proportion of adults achieving sufficient levels of activity to realize its associated health benefits is likely to decline.
Endotoxin-Induced Monocytic Microparticles Have Contrasting Effects on Endothelial Inflammatory Responses (2014)

Septic shock is a severe disease state characterised by the body's life threatening response to infection. Complex interactions between endothelial cells and circulating monocytes are responsible for microvasculature dysfunction contributing to the pathogenesis of this syndrome. Here, we intended to determine whether microparticles derived from activated monocytes contribute towards inflammatory processes and notably vascular permeability. We found that endotoxin stimulation of human monocytes enhances the release of microparticles of varying phenotypes and mRNA contents. Elevated numbers of LPS-induced monocytic microparticles (mMP) expressed CD54 and contained higher levels of transcripts for pro-inflammatory cytokines such as TNF, IL-6 and IL-8. Using a prothrombin time assay, a greater reduction in plasma coagulation time was observed with LPS-induced mMP than with non-stimulated mMP. Co-incubation of mMP with the human brain endothelial cell line hCMEC/D3 triggered their time-dependent uptake and significantly enhanced endothelial microparticle release. Unexpectedly, mMP also modified signalling pathways by diminishing pSrc (tyr416) expression and promoted endothelial monolayer tightness, as demonstrated by endothelial impedance and permeability assays. Altogether, these data strongly suggest that LPS-induced mMP have contrasting effects on the intercellular communication network and display a dual potential: enhanced pro-inflammatory and procoagulant properties, together with protective function of the endothelium.
Table S4 from Cancer-Associated Fibroblasts Promote Immunosuppression by Inducing ROS-Generating Monocytic MDSCs in Lung Squamous Cell Carcinoma (2023)

&lt;p&gt;Supplementary table 4&lt;/p&gt;
Transurethral Resection of Prostate in Benign Prostatic Hyperplasia Patients with Large Prostate Volume (2008)

PURPOSE: We investigated the safety and efficacy of transurethral resection of the prostate(TURP) in benign prostatic hyperplasia(BPH) more than 60cc by single surgeon for the relief of infravesical obstruction. MATERIALS AND METHODS: We evaluated 211 patients treated with TURP in BPH with large prostate by single surgeon. Each group was divided by prostate volume(group 1; 60-69.9, group 2; 70-79.9, group 3; 80-89.9, group 4; 90-99.9, group 5; &gt;100cc of prostate volume). Various parameters such as International Prostate Symptom Score(IPSS), maximal flow rate(Qmax.), postvoid residual volume(PVR), prostate volume, adenoma volume, resection time, resection prostate volume, irrigation fluid volume and complications were evaluated and compared. RESULTS: Age of each group was not significantly different. Prostate volume, adenoma volume, resection time, Resection volume, irrigation volume of each groups were different significantly. But, resection volume/resection time and irrigation volume/resection time were not different significantly. Mean resection volume/resection time was 1.34g/min, and mean irrigation volume/resection time was 315.8ml/min. And intraoperative and postoperative complications of each group were not different. Mean postoperative change of Hb was 2.0+/-1.1g/dl. Postoperative parameters(IPSS, Qmax, PVR) were improved significantly. Only 2 patients needed transfusion in group 5. No urinary incontinence and TUR syndrome in each group was observed. CONCLUSIONS: TURP by experienced surgeon is a safe and effective treatment in BPH patients with large prostates for relief of infravesical obstruction
Holographic data processing applications using photorefractive crystals (1981)

Abstract Optical holographic data processing systems and applications are described that use photorefractive electro-optic crystals such as lithium niobate. Powerful systems capable of performing numerical operations such as addition and multiplication in parallel on arrays of data are discussed.
US2011/0006406A1: Fabrication of Porogen Residue Free and Mechanically Robust Low-k Materials (2011)

A method is provided for producing a porogen-residue-free ultra low-k film with porosity higher than 50% and a high elastic modulus above 5 GPa. The method starts with depositing a SiCOH film using Plasma Enhanced Chemical Vapor Deposition (PE-CVD) or Chemical Vapor Deposition (CVD) onto a substrate and then first Perfonning an atomic hydrogen treatment at elevated wafer temperature in the range of 200 C up to 350 C to remove all the porogens and then performing a UV assisted thennal curing step.
Comparison of 6-s-cis- and 6-s-trans-Locked Analogs of 1α,25-Dihydroxyvitamin D3 Indicates That the 6-s-cis Conformation Is Preferred for Rapid Nongenomic Biological Responses and That Neither 6-s-cis- nor 6-s-trans-Locked Analogs Are Preferred for Genomic Biological Responses (1997)

The hormone 1alpha,25-dihydroxyvitamin D3 [1alpha,25(OH)2D3] generates biological responses via both genomic and rapid, nongenomic mechanisms. The genomic responses utilize signal transduction pathways linked to a nuclear receptor (VDRnuc) for 1alpha,25(OH)2D3, while the rapid responses are believed to utilize other signal transduction pathways that may be linked to a putative membrane receptor for 1alpha,25(OH)2D3. The natural seco steroid is capable of facile rotation about its 6,7 single carbon bond, which permits generation of a continuum of potential ligand shapes extending from the 6-s-cis (steroid like) to the 6-s-trans (extended). To identify the shape of conformer(s) that can serve as agonists for the genomic and rapid biological responses, we measured multiple known agonist activities of two families of chemically synthesized analogs that were either locked in the 6-s-cis (6C) or 6-s-trans (6T) conformation. We found that 6T locked analogs were inactive or significantly less active than 1alpha,25(OH)2D3 in both rapid responses (transcaltachia in perfused chick intestine, 45Ca2+ influx in ROS 17/2.8 cells) and genomic (osteocalcin induction in MG-63 cells, differentiation of HL-60 cells, growth arrest of MCF-7 cells, promoter transfection in COS-7 cells) assays. In genomic assays, 6C locked analogs bound poorly to the VDRnuc and were significantly less effective than 1alpha,25(OH)2D3 in the same series of assays designed to measure genomic responses. In contrast, the 6C locked analogs were potent agonists of both rapid response pathways and had activities equivalent to the conformationally flexibile 1alpha,25(OH)2D3; this represents the first demonstration that 6-s-cis locked analogs can function as agonists for vitamin D responses.
Effect of anti-P1A1 antibody on human platelets. I. The role of complement (1979)

Abstract We studied the interaction of complement with human platelets. Complement was activated by IgG anti-P1A1 antibody obtained from 3 patients with the post-transfusion purpura syndrome. We used a heparin- plasma buffer system that permits complement activation and also preserves platelet function. With this system complement activation was efficient, and platelet immune alteration was extensive. Anti-P1A1 antibody was effective only in the presence of complement, in which case both platelet lysis and serotonin release (release reaction) in the absence of lysis were observed. Platelet lysis, as assessed by 51Cr loss, required 10-fold more antibody than was necessary to induce platelet aggregation and release of 14C-serotonin. This platelet release reaction required an intact classic complement sequence through C6. The extent of platelet serotonin release parallelled the depletion of C1 and C4 from platelet-rich plasma. Concentrations of antibody insufficient to induce platelet aggregation and serotonin release could still activate C1 and deposit increased C3 on the platelet surface. These studies demonstrated that complement activation by anti-P1A1 antibody can alter human platelets in a nonlytic system. Several phases of complement-mediated human platelet alteration are possible, depending on the concentration of anti-P1A1 antibody.
A deep microfluidic absorbance detection cell replicated from a thickly stacked SU-8 dry film resist mold (2012)

Dry film resist SU-8 was used to make a thick mold for soft lithography of a poly(dimethylsiloxane) (PDMS) microfluidic chip with deep channels. The stacking of the SU-8 film enabled an ultra-thick (up to 500 μm) resist process on Si wafer. This process was fast and highly reproducible compared with the conventional liquid SU-8 process. The deep channel in the PDMS chip was utilized as a micro-flow cell for sensitive absorbance measurement. Sunset Yellow FCF dye was used to demonstrate absorption spectroscopy in the deep channel. Since the channel depth was proportional to the optical path length, which was proportional to the absorbance value, the PDMS chip achieved a detection limit (15.9 μM) comparable to U- or Z-shaped microfabricated absorbance detection cells in glass. Calibration curves for different solution concentrations were obtained with good R2 values (∼1).
Effects of the Factor Xa Inhibitor Apixaban on Venous Thrombosis and Hemostasis in Rabbits. (2006)

Abstract Apixaban is a small-molecule, potent, reversible and direct inhibitor of human coagulation factor Xa (FXa) (Ki = 0.08 nM) with greater than 30000-fold selectivity over other coagulation proteases. It is orally bioavailable in rats, dogs, chimpanzees and humans, and is currently in clinical development for prevention and treatment of thromboembolic diseases. The objective of this study was to compare antithrombotic and bleeding time effects of apixaban and warfarin in rabbits. We selected rabbits as the animal model because apixaban has similar potency in inhibiting human and rabbit FXa, but is less potent in inhibiting rat and dog FXa (Ki (nM): 0.16, rabbit; 1.3, rat; 1.8, dog). We induced the formation of venous thrombus by placing threads in the vena cava, and bleeding by the incision of cuticles in anesthetized rabbits. Apixaban was infused IV 60 min before the initiation of thrombosis. Warfarin was administered orally for 4 days before the study. Thrombus weight averaged 73±5 mg and bleeding time averaged 183±7 s in the vehicle group (n=6 per group). Apixaban and warfarin inhibited the formation of venous thrombus in a dose-dependent manner. The estimated IC50 for apixaban was 0.16±0.04 μM. At antithrombotic doses studied, apixaban did not alter blood pressure and heart rate, suggesting hemodynamic effects are not likely to be involved in its antithrombotic activity. At the antithrombotic ID80, apixaban and warfarin increased bleeding time by 9±4% and 516±24%, respectively (n=6 per group). At this dose, apixaban increased ex vivo activated partial thromboplastin time and prothrombin time to 1.4±0.1 and 1.7±0.1 times control, respectively, and warfarin increased prothrombin time to 4.5±0.1 times control. Apixaban at antithrombotic doses selectively inhibited ex vivo FXa but not thrombin activity. In summary, these findings demonstrate potent activity of apixaban as a selective FXa inhibitor exhibiting potential strong efficacy in prevention of venous thrombosis at doses that preserve hemostasis and produce less increases in systemic anticoagulation than warfarin.
The influence of the object-oriented language model on a supporting architecture (2002)

The MUSHROOM architecture is designed to efficiently support dynamic object-oriented languages such as Smalltalk. The authors describe the architecture, and how the object-oriented model of computation and the provision of a sophisticated computer led to various simplifications in the design and implementation of the architecture. Two particular features of the object-oriented model have been exploited in the architecture. Freedom of object identifier selection, allows for straightforward and efficient implementation in software of virtual-to-real address translation and for efficient object allocation, and the absence of address aliasing allows simple, virtually addressed caches to be used. A prototype implementation of this architecture is currently being commissioned.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fully integrated fused quartz acoustic horns for structural health monitoring (2019)

Non-destructive acoustic structural sensing is an imperative technology, applicable to many different fields such as aerospace and civil engineering. To maintain a high sensitivity or to mitigate acoustic loss, it is important to increase the signal-to-noise ratio by improving coupling efficiency from acoustic sources to the object under test, such as an acoustic waveguide. Here, a fully integrated fused quartz horn design is combined with a fused quartz acoustic waveguide. The resulting system is intended to demonstrate a high accuracy low cost alternative to current sensing systems and the present article report on the viability of using a merged acoustic horn and waveguide.