gebhart/patrepeval huggingface dataset:
Diesel Fuel Injection Pump Durability Test with Low Level Biodiesel Blends (2013)

This study documented information about the use of low-level blendsof biodiesel and petroleum diesel fuel (B1& B2). A 1-2% blend was selected todocument the lubricity benefits associated with the use of these fuels. A 1998Dodge pickup was fueled approximately 177,028 km (110,000 miles) miles on aB1 blend. Two Bosch injection pumps typically used in the Cummins B5.9Lengine were operated for 1000 hours under laboratory conditions at Iowa StateUniversity. One laboratory injection pump was fueled with diesel fuel. Thesecond laboratory injection pump was fueled with a B2 blend. The duty cycle forthe injection pump durability test was determined in conjunction with Cumminsand Bosch engineers. The engine oil was evaluated for levels of wear metals.
Safety Controller Synthesis Using Human Generated Trajectories (2014)

This paper focuses on the task of safety controller synthesis, that is, designing a controller that will take a system from any point within a compact set of initial states to a point inside a set of acceptable goal states, while never entering any state that is deemed unsafe. To do this we use a human generated trajectory-based approach. We introduce the control autobisimulation function, which is the analog of the control Lyapunov function for approximate bisimulation. We consider a class of hybrid systems and use this function to determine a set of admissible feedback control laws that guarantee trajectory robustness for underlying dynamics that are linear affine, feedback linearizable, and differentially flat. This property ensures that any trajectory of the closed-loop system that is initialized within some neighborhood of a nominal trajectory will stay within some tube of the nominal trajectory when given the same input. This feedback control and input can be used as the controller for some subset of the initial states. We demonstrate how to combine multiple trajectories into a synthesized controller that satisfies the safety problem.
Endogenous Retrovirus 3 – History, Physiology, and Pathology (2018)

Endogenous viral elements (EVE) seem to be present in all eukaryotic genomes. The composition of EVE varies between different species. The endogenous retrovirus 3 (ERV3) is one of these elements that is present only in humans and other Catarrhini. Conservation of ERV3 in most of the investigated Catarrhini and the expression pattern in normal tissues suggest a putative physiological role of ERV3. On the other hand, ERV3 has been implicated in the pathogenesis of auto-immunity and cancer. In the present review we summarize knowledge about this interesting EVE. We propose the model that expression of ERV3 (and probably other EVE loci) under pathological conditions might be part of a metazoan SOS response.
Supplementary Figure 1, Table 1 from Mechanism by Which Mcl-1 Regulates Cancer-Specific Apoptosis Triggered by mda-7/IL-24, an IL-10–Related Cytokine (2023)

Supplementary Figure 1, Table 1 from Mechanism by Which Mcl-1 Regulates Cancer-Specific Apoptosis Triggered by mda-7/IL-24, an IL-10–Related Cytokine
Light Scattering of TiO2 Nanoparticles Embedded in Polyurethane (2012)

A new approach of enhancing light scattering in polyurethane polymer through the effect of TiO2 nanoparticles (NP) is explored. The TiO2 NP with sizes of 360 nm, 410 nm and 500 nm were dispersed in polyurethane polymer in concentrations ranging from 0.25 wt% up to 2 wt%. Reflectivity and UV-visible absorption measurements were employed for studying the scattering and absorption properties of TiO2 NP.
Steamed Ginger May Enhance Insulin Secretion through KATP Channel Closure in Pancreatic β-Cells Potentially by Increasing 1-Dehydro-6-Gingerdione Content (2020)

Ginger (<i>Zingiber officinale</i> Roscoe) and its active compounds (gingerols, shogaols and paradols) have been reported as having beneficial functions for several diseases, including diabetes. In this study, we revealed that the steaming process could enhance the anti-diabetic potential of ginger. To confirm the anti-diabetic effect of steamed ginger extract (GG03), we assessed pancreatic islets impaired by alloxan in zebrafish and demonstrated anti-hyperglycemic efficacy in a mouse model. The EC<sub>50</sub> values of ginger extract (GE) and GG03 showed that the efficacy of GG03 was greater than that of GE. In addition, LC<sub>50</sub> values demonstrated that GG03 had lower toxicity than GE, and the comparison of the Therapeutic Index (TI) proved that GG03 is a safer functional food. Furthermore, our data showed that GG03 significantly lowered hyperglycemia in a diabetic mouse model. HPLC was performed to confirm the change in the composition of steamed ginger. Interestingly, GG03 showed a 375% increase in 1-dehydro-6-gingerdione (GD) compared with GE. GD has not yet been studied much pharmacologically. Thus, we identified the protective effects of GD in the damaged pancreatic islets of diabetic zebrafish. We further assessed whether the anti-diabetic mechanism of action of GG03 and GD involves insulin secretion. Our results suggest that GG03 and GD might stimulate insulin secretion by the closure of K<sub>ATP</sub> channels in pancreatic β-cells.
AAV9-mediated VEGF-B Gene Transfer Improves Systolic Function in Progressive Left Ventricular Hypertrophy (2012)

Mechanisms of the transition from compensatory hypertrophy to heart failure are poorly understood and the roles of vascular endothelial growth factors (VEGFs) in this process have not been fully clarified. We determined the expression profile of VEGFs and relevant receptors during the progression of left ventricular hypertrophy (LVH). C57BL mice were exposed to transversal aortic constriction (TAC) and the outcome was studied at different time points (1 day, 2, 4, and 10 weeks). A clear compensatory phase (2 weeks after TAC) was seen with following heart failure (4 weeks after TAC). Interestingly, VEGF-C and VEGF-D as well as VEGF receptor-3 (VEGFR-3) were upregulated in the compensatory hypertrophy and VEGF-B was downregulated in the heart failure. After treatment with adeno-associated virus serotype 9 (AAV9)-VEGF-B(186) gene therapy in the compensatory phase for 4 weeks the function of the heart was preserved due to angiogenesis, inhibition of apoptosis, and promotion of cardiomyocyte proliferation. Also, the genetic programming towards fetal gene expression, a known phenomenon in heart failure, was partly reversed in AAV9-VEGF-B(186)-treated mice. We conclude that VEGF-C and VEGF-D are associated with the compensatory LVH and that AAV9-VEGF-B(186) gene transfer can rescue the function of the failing heart and postpone the transition towards heart failure.
Transcriptome assessment of the Pompe (Gaa−/−) mouse spinal cord indicates widespread neuropathology (2016)

Pompe disease, caused by deficiency of acid alpha-glucosidase (GAA), leads to widespread glycogen accumulation and profound neuromuscular impairments. There has been controversy, however, regarding the role of central nervous system pathology in Pompe motor dysfunction. We hypothesized that absence of GAA protein causes progressive activation of neuropathological signaling, including pathways associated with cell death. To test this hypothesis, genomic data (Affymetrix Mouse Gene Array 2.0ST) from the midcervical spinal cord in 6 and 16 mo old Pompe (Gaa<sup>-/-</sup>) mice were evaluated (Broad Institute Molecular Signature Database), along with spinal cord histology. The midcervical cord was selected because it contains phrenic motoneurons, and phrenic-diaphragm dysfunction is prominent in Pompe disease. Several clinically important themes for the neurologic etiology of Pompe disease emerged from this unbiased genomic assessment. First, pathways associated with cell death were strongly upregulated as Gaa<sup>-/-</sup> mice aged, and motoneuron apoptosis was histologically verified. Second, proinflammatory signaling was dramatically upregulated in the Gaa<sup>-/-</sup> spinal cord. Third, many signal transduction pathways in the Gaa<sup>-/-</sup> cervical cord were altered in a manner suggestive of impaired synaptic function. Notably, glutamatergic signaling pathways were downregulated, as were "synaptic plasticity pathways" including genes related to neuroplasticity. Fourth, many genes and pathways related to cellular metabolism are dysregulated. Collectively, the data unequivocally confirm that systemic absence of GAA induces a complex neuropathological cascade in the spinal cord. Most importantly, the results indicate that Pompe is a neurodegenerative condition, and this underscores the need for early therapeutic intervention capable of targeting the central nervous system.
Maximizing efficiency and cost-effectiveness of Type 2 diabetes screening: the AusDiab study (2010)

Using a self-assessed diabetes risk score as an initial screening step, followed by a second risk score incorporating fasting plasma glucose, would maximize efficiency of identifying people with undiagnosed Type 2 diabetes and those at high risk of future diabetes.
Integrin-Kindlin3 requirements for microglial motility in vivo are distinct from those for macrophages (2017)

Microglia play a critical role in the development and homeostasis of the CNS. While mobilization of microglia is critical for a number of pathologies, understanding of the mechanisms of their migration in vivo is limited and often based on similarities to macrophages. Kindlin3 deficiency as well as Kindlin3 mutations of integrin-binding sites abolish both integrin inside-out and outside-in signaling in microglia, thereby resulting in severe deficiencies in cell adhesion, polarization, and migration in vitro, which are similar to the defects observed in macrophages. In contrast, while Kindlin3 mutations impaired macrophage mobilization in vivo, they had no effect either on the population of microglia in the CNS during development or on mobilization of microglia and subsequent microgliosis in a model of multiple sclerosis. At the same time, acute microglial response to laser-induced injury was impaired by the lack of Kindlin3-integrin interactions. Based on 2-photon imaging of microglia in the brain, Kindlin3 is required for elongation of microglial processes toward the injury site and formation of phagosomes in response to brain injury. Thus, while Kindlin3 deficiency in human subjects is not expected to diminish the presence of microglia within CNS, it might delay the recovery process after injury, thereby exacerbating its complications.
Abstract A5: Characterization of signaling pathways related to resistance of breast cancer cells against irreversible EGFR/HER/ErbB kinase inhibitors (2010)

Abstract Epidermal growth factor (EGF) receptor-related antigens (EGFR, ErbB1-4, HER1-4) represent emerging drug targets in oncology. However, resistance against ErbB-targeting drugs occurs frequently in cancer patients. Drug-resistant cells may exhibit drug-refractory phosphatidylinositol 3-kinase (PI3K) or mitogen-activated protein kinase (MAPK) signaling, but the relative impact and contribution of these two downstream pathways to drug resistance are still controversially discussed. We examined the effects of the two very potent, irreversibly binding ErbB receptor tyrosine kinase inhibitors (RTKIs) pelitinib (EKB-569) and canertinib (CI-1033) on PI3K- and MAPK activity in ErbB RTKI-sensitive and ErbB RTKI-resistant breast and ovarian cancer cells. Western blot analysis revealed that ErbB phosphorylation was abrogated by the inhibitors in both drug-sensitive and drug-resistant cells, whereas AKT- and GSK3β phosphorylation were drug-dependently downregulated only in drug-sensitive cells. ErbB RTKI sensitivity did not correlate with expression of wildtype PTEN or PIK3CA, nor was it associated with drug-dependent silencing of ERK1,2 in the breast and ovarian cancer cell lines examined. Moreover, exogenous AKT, but not MEK, significantly induced drug resistance. Our data demonstrate that blocking AKT phosphorylation is essential and sufficient, whereas abrogation of ERK phosphorylation is not required for ErbB RTKI anticancer efficacy. AKT phosphorylation may thus be a useful biomarker of ErbB RTKI sensitivity in breast and ovarian cancer cells. Supported by ‘MedizinischWissenschaftlicher Fonds des Bürgermeisters der Bundeshauptstadt Wien’ (#08037) and ‘Initiative Krebsforschung’, Medical Univ. Vienna. Citation Information: Clin Cancer Res 2010;16(7 Suppl):A5
AGE-RELATED DIFFERENCES IN THE EFFECTS OF CANDESARTAN AND AMLODIPINE ON LEFT VENTRICULAR HYPERTROPHY IN HIGH RISK HYPERTENSIVE PATIENTS - CASE-J SUB-ANALYSIS: PP.27.83 (2010)

Objective: Left ventricular hypertrophy (LVH) is now appreciated as an important risk factor for cardiovascular events. Recent studies have suggested that regression of LVH during antihypertensive treatment lead to a reduction in the incidence of cardiovascular events. However, there is little evidence for the relation between aging and the effect of antihypertensive drugs on regression of LVH. In the present study, we examined whether there exist age-related differences in the effects of candesartan and amlodipine on the regression of LVH as a sub-analysis of the CASE-J trial. Design and Method: Subjects were 404 high-risk hypertensive patients with LVH at baseline who underwent echocardiography at both baseline and three years after treatment. Left ventricular mass was calculated with Devereux□fs formula by echocardiography, normalized by body surface area and expressed as left ventricular mass index (LVMI). Effects of the two drugs on LVH were investigated stratified according to age (cut-off point: 65 years old). Results: The numbers of subjects were 205 in the candesartan group and 199 in the amlodipine group. There were no significant differences between the two groups with regard to background factors and blood pressure levels during the follow-up period. Reduction of LVMI after three years was 22.9 g/m2 in the candesartan group and 13.4 g/m2 in the amlodipine group (p = 0.023). Subgroup analysis by age revealed that reduction of LVMI in patients aged 65 years or more was 24.7 g/m2 in the candesartan group, significantly effective compared to the value 8.4 g/m2 in the amlodipine group (N = 95 v.s. N = 90; p = 0.009). However, no statistically significant difference was observed between the two groups in patients aged less than 65 years (−20.8 g/m2 v.s. −19.6 g/m2). Conclusions: Candesartan was more effective than amlodipine on regression of LVH. The effect of candesartan on regression of LVH was observed over wide age range, but the effect of amlodipine was attenuated in the elderly patients.
A feature agnostic approach for glaucoma detection in OCT volumes (2019)

Optical coherence tomography (OCT) based measurements of retinal layer thickness, such as the retinal nerve fibre layer (RNFL) and the ganglion cell with inner plexiform layer (GCIPL) are commonly employed for the diagnosis and monitoring of glaucoma. Previously, machine learning techniques have relied on segmentation-based imaging features such as the peripapillary RNFL thickness and the cup-to-disc ratio. Here, we propose a deep learning technique that classifies eyes as healthy or glaucomatous directly from raw, unsegmented OCT volumes of the optic nerve head (ONH) using a 3D Convolutional Neural Network (CNN). We compared the accuracy of this technique with various feature-based machine learning algorithms and demonstrated the superiority of the proposed deep learning based method. Logistic regression was found to be the best performing classical machine learning technique with an AUC of 0.89. In direct comparison, the deep learning approach achieved a substantially higher AUC of 0.94 with the additional advantage of providing insight into which regions of an OCT volume are important for glaucoma detection. Computing Class Activation Maps (CAM), we found that the CNN identified neuroretinal rim and optic disc cupping as well as the lamina cribrosa (LC) and its surrounding areas as the regions significantly associated with the glaucoma classification. These regions anatomically correspond to the well established and commonly used clinical markers for glaucoma diagnosis such as increased cup volume, cup diameter, and neuroretinal rim thinning at the superior and inferior segments.
Biodistribution of antisense nanoparticles in mammary carcinoma rat model (2010)

Efficient and specific delivery of antisenses (ASs) and protection of the sequences from degradation are critical factors for effective therapy. Sustained release nanoparticles (NP) offer increased resistance to nuclease degradation, increased amounts of AS uptake, and the possibility of control in dosing and sustained duration of AS administration. The biodegradable and biocompatible poly(D,L-lactic-co-glycolic acid) copolymer (PLGA) was utilized to encapsulate AS directed against osteopontin (OPN), which is a promising therapeutic target in mammary carcinoma. Whole body biodistribution of OPN AS NP was evaluated in comparison to naked AS, in intact and mammary carcinoma metastasis model bearing rats. Naked and NP encapsulated AS exhibited different biodistribution profiles. AS NP, in contrast to naked AS, tended to accumulate mostly in the spleen, liver, and at the tumor inoculation site. Drug levels in intact organs were negligible. The elimination of naked AS was faster, due to rapid degradation of the unprotected sequence. It is concluded that AS NP protect the AS from degradation, provide efficient AS delivery to the tumor tissue, and minimize AS accumulation in intact organs due to the AS sustained release profile as well as the favorable NP physicochemical properties.
Green Light Optimized Speed Advisory (GLOSA) with Traffic Preview (2022)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;By utilizing the vehicle to infrastructure communication, the conventional Green Light Optimized Speed Advisory (GLOSA) applications give speed advisory range for drivers to travel to pass at the green light. However, these systems do not consider the traffic between the ego vehicle and the traffic light location, resulting in inaccurate speed advisories. Therefore, the driver needs to intuitively adjust the vehicle's speed to pass at the green light and avoid traffic in these scenarios. Furthermore, inaccurate speed advisories may result in unnecessary acceleration and deceleration, resulting in poor fuel efficiency and comfort. To address these shortcomings of conventional GLOSA, in this study, we proposed the utilization of collaborative perception messages shared by smart infrastructures to create an enhanced speed advisory for the connected vehicle drivers and automated vehicles. Two different algorithms were designed by utilizing the available traffic preview (Signal Phase and Timing (SPAT), MAP, and Collaborative Perception Messages), predicted traffic preview from these messages, and measurements from onboard range sensors. While in the first algorithm, the vehicle is controlled with a rule-based approach, a reinforcement learning-based approach is used in the second algorithm. The designed algorithms are then simulated in a simulation environment created in a MATLAB Simulink. Our simulation results demonstrated the effectiveness of the developed algorithms with better fuel efficiency performance and more comfortable ride performance.&lt;/div&gt;&lt;/div&gt;
GEM-RL: Generalized Energy Management of Wearable Devices using Reinforcement Learning (2023)

Energy harvesting (EH) and management (EM) have emerged as enablers of self-sustained wearable devices. Since EH alone is not sufficient for self-sustainability due to uncertainties of ambient sources and user activities, there is a critical need for a user-independent EM approach that does not rely on expected EH predictions. We present a generalized energy management framework (GEM-RL) using multi-objective reinforcement learning. GEM-RL learns the trade-off between utilization and the battery energy level of the target device under dynamic EH patterns and battery conditions. It also uses a lightweight approximate dynamic programming (ADP) technique that utilizes the trained MORL agent to optimize the utilization of the device over a longer period. Thorough experiments show that, on average, GEM-RL achieves Pareto front solutions within 5.4% of the offline Oracle for a given day. For a 7-day horizon, it achieves utility up to 4% within the offline Oracle and up to 50% higher utility compared to baseline EM approaches. The hardware implementation on a wearable device shows negligible execution time (1.98 ms) and energy consumption (23.17 μJ) overhead.
Application of a pathogen microarray for the analysis of viruses and bacteria in clinical diagnostic samples from pigs (2015)

Many of the disease syndromes challenging the commercial swine industry involve the analysis of complex problems caused by polymicrobial, emerging or reemerging, and transboundary pathogens. This study investigated the utility of the Lawrence Livermore Microbial Detection Array (Lawrence Livermore National Laboratory, Livermore, California), designed to detect 8,101 species of microbes, in the evaluation of known and unknown microbes in serum, oral fluid, and tonsil from pigs experimentally coinfected with Porcine reproductive and respiratory syndrome virus (PRRSV) and Porcine circovirus-2 (PCV-2). The array easily identified PRRSV and PCV-2, but at decreased sensitivities compared to standard polymerase chain reaction detection methods. The oral fluid sample was the most informative, possessing additional signatures for several swine-associated bacteria, including Streptococcus sp., Clostridium sp., and Staphylococcus sp.
Structure‐Dependent Binding of Arylimidamides to the DNA Minor Groove (2013)

Heterocyclic diamidines are strong DNA minor-groove binders and have excellent antiparasitic activity. To extend the biological activity of these compounds, a series of arylimidamides (AIAs) analogues, which have better uptake properties in Leishmania and Trypanosoma cruizi than diamidines, was prepared. The binding of the AIAs to DNA was investigated by Tm , fluorescence displacement titration, circular dichroism, DNase I footprinting, biosensor surface plasmon resonance, X-ray crystallography and molecular modeling. These compounds form 1:1 complexes with AT sequences in the DNA minor groove, and the binding strength varies with substituent size, charge and polarity. These substituent-dependent structure and properties provide a SAR that can be used to estimate K values for binding to DNA in this series. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for AIAs.
Serum-soluble TRAIL levels in patients with severe persistent allergic asthma: Its relation to omalizumab treatment (2012)

Our study gives a different perspective on severe persistent allergic asthma and omalizumab treatment efficacy at the cell apoptosis-linked step by the serum sTRAIL levels.
DirectPath (2012)

With the widespread development of cloud computing and high speed communications, end users store or retrieve video, music, photo and other contents over the cloud or the local network for video-on-demand, wireless display and other usages. The traditional I/O model in a mobile platform consumes time and resources due to excessive memory access and copying when transferring content from a source device, e.g., network controller, to a destination device, e.g., hard disk. This model introduces unnecessary overhead and latency, negatively impacting the performance and energy consumption of content-intensive uses.