gebhart/patrepeval huggingface dataset:
Suppression of microRNA-29 Expression by TGF-β1 Promotes Collagen Expression and Renal Fibrosis (2011)

Synthesis and deposition of extracellular matrix (ECM) within the glomerulus and interstitium characterizes renal fibrosis, but the mechanisms underlying this process are incompletely understood. The profibrotic cytokine TGF-β1 modulates the expression of certain microRNAs (miRNAs), suggesting that miRNAs may have a role in the pathogenesis of renal fibrosis. Here, we exposed proximal tubular cells, primary mesangial cells, and podocytes to TGF-β1 to examine its effect on miRNAs and subsequent collagen synthesis. TGF-β1 reduced expression of the miR-29a/b/c/family, which targets collagen gene expression, and increased expression of ECM proteins. In both resting and TGF-β1-treated cells, ectopic expression of miR-29 repressed the expression of collagens I and IV at both the mRNA and protein levels by targeting the 3'untranslated region of these genes. Furthermore, we observed low levels of miR-29 in three models of renal fibrosis representing early and advanced stages of disease. Administration of the Rho-associated kinase inhibitor fasudil prevented renal fibrosis and restored expression of miR-29. Taken together, these data suggest that TGF-β1 inhibits expression of the miR-29 family, thereby promoting expression of ECM components. Pharmacologic modulation of these miRNAs may have therapeutic potential for progressive renal fibrosis.
Phosphorescence-Fluorescence ratio imaging for monitoring the oxygen status during photodynamic therapy (2004)

The effectiveness of photodynamic therapy is strongly dependent on the availabilty of oxygen. In the present paper we show that the ratio between photosensitiser phosphorescence and fluorescence is a parameter that can be used to monitor the competition between singlet oxygen production and other processes quenching the photosensitiser triplet state. We present a theoretical basis for the validity of this approach and a series of in vitro imaging experiments.
Human atherosclerosis. III. Immunocytochemical analysis of the cell composition of lesions of young adults. (1992)

There have been only limited immunocytochemical studies of the cell composition of the early lesions of human atherosclerosis, and none that incorporate a comprehensive panel of antibodies to various cell types and subsets. The authors thus performed a prospective study of 27 lesions from 16 different individuals ranging in age from 15 to 34 years. These were all lesions that appeared grossly as slightly raised, yellow fatty streaks in the posterior ascending aorta, but on histologic examination had varying degrees of round-cell, spindle-cell, and foam-cell accumulation. Using a panel of antibodies, including monoclonal antibodies specific for smooth muscle cells [HHF35], human macrophages [HAM56], endothelial cells [monoclonal antibodies to F. VIII related antigen], lymphocytes [anti-CD45, anti-CD20, anti-CD45RO, anti-T-cell receptor], it was revealed that the predominant cell type in these early lesions was the smooth muscle cell, including the vast majority of the foam cells, which tended to appear in the deeper regions of the lesions. There were variable numbers of smooth muscle cells and lymphocytes; the latter were exclusively T cells. It is concluded that in atherosclerotic lesions of young adults, which may represent various stages of fatty streak formation and advanced fatty streaks, smooth muscle cell accumulation may be an early event.
Some Metabolic Effects of Prolonged Feeding of Starch, Sucrose, Fructose and Carbohydrate-Free Diet in the Rat (1975)

Male rats of the ASL Wistar strain were fed from weaning on starch, fructose or carbohydrate-free diets for 4 and 12 weeks. In addition, further groups were fed for 24 weeks on starch, sucrose or carbohydrate-free diets. Livers were examined for gross composition, glucose-6-phosphatase activity and in vitro lipogenesis and glucose oxidation. Intestinal sucrase was also measured. Dietary fructose and the carbohydrate-free diet induced an enlargement of the livers after 12 weeks feeding, when expressed per 100g body weight, and at the same time, an increased fat content. Fructose caused an increase in liver glucose-6-phosphatase after 4 weeks, which persisted after 12 weeks, and a similar increase was observed after 24 weeks feeding on sucrose. Fructose produced an increase in intestinal sucrose after 4 weeks, but this did not persist and there was no increase evident after 12 weeks feeding, nor after 24 weeks feeding on sucrose. Fructose markedly depressed the in vitro lipogenesis and glucose oxidation in liver slices. This was evident after 4 weeks feeding and also after 12 weeks when the effect of age showed as a fall in both these parameters in the control group of animals. The carbohydrate-free diet caused an increase in liver glucose-6-phosphatase after 4 weeks, a smaller increase after 12 weeks, and there was no increase apparent when feeding was continued for 24 weeks. Apparently due to the absence of substrate, the intestinal sucrose activity fell to less than half after 4 weeks and to negligible levels after 12 and 24 weeks on carbohydrate-free diet. In vitro liver lipogenesis and glucose oxidation were depressed after 4 and 12 weeks in a similar way to the fructose diet. On both these diets the rise in liver glucose-6-phosphatase appeared to parallel the fall in liver lipogeneis and glucose oxidation.
Integrating E-Commerce and Data Mining: Architecture and Challenges (2000)

We show that the e-commerce domain can provide all the right ingredients for successful data mining and claim that it is a killer domain for data mining. We describe an integrated architecture, based on our expe-rience at Blue Martini Software, for supporting this integration. The architecture can dramatically reduce the pre-processing, cleaning, and data understanding effort often documented to take 80% of the time in knowledge discovery projects. We emphasize the need for data collection at the application server layer (not the web server) in order to support logging of data and metadata that is essential to the discovery process. We describe the data transformation bridges required from the transaction processing systems and customer event streams (e.g., clickstreams) to the data warehouse. We detail the mining workbench, which needs to provide multiple views of the data through reporting, data mining algorithms, visualization, and OLAP. We con-clude with a set of challenges.
Treatment of metastatic human papillomavirus-associated epithelial cancers with adoptive transfer of tumor-infiltrating T cells. (2018)

3004 Background: Adoptive T-cell therapy (ACT) is a promising cancer treatment modality. However, its study in epithelial cancers has been limited. Human papillomavirus (HPV)-associated cancers are difficult to treat epithelial malignancies for which better systemic treatments are needed. We conducted a clinical trial of ACT for the treatment of metastatic HPV-associated cancers. Methods: The clinical trial was a phase II design with two disease cohorts (cervical cancers and non-cervical cancers). Patients were treated with a single infusion of tumor-infiltrating lymphocytes (TIL), which were generated, when possible, from TIL subcultures with HPV-oncoprotein reactivity (HPV-TIL). HPV-TIL infusion was preceded by a lymphocyte-depleting conditioning regimen followed by systemic high-dose aldesleukin. Results: Objective tumor responses occurred in 5/18 (28%) patients in the cervical cancer cohort and 2/11 (18%) patients in the non-cervical cancer cohort. In the cervical cancer cohort, two patients experienced complete responses that are ongoing 53 and 67 months after treatment. Three patients experienced partial responses that were three months in duration. In the non-cervical cancer cohort, partial responses were observed in a patient with anal cancer (four months duration) and a patient with oropharyngeal cancer (five months duration). The latter patient had previously been treated with six systemic anti-cancer agents. Multiple thoracic metastases responded completely after HPV-TIL infusion. A brain metastasis developed five months after treatment and was surgically resected. He is without evidence of disease 51 months after treatment. Conclusions: HPV-TIL can mediate regression of metastatic HPV-associated cervical, oropharyngeal and anal epithelial cancers in some patients. These findings support the study of ACT for HPV-associated cancers and possibly other epithelial malignancies. Clinical trial information: NCT01585428.
Classical and recent advances in the treatment of inflammatory bowel diseases (2014)

Crohn's disease (CD) and ulcerative colitis (UC) are intestinal disorders that comprise the inflammatory bowel diseases (IBD). These disorders have a significant effect on the quality of life of affected patients and the increasing number of IBD cases worldwide is a growing concern. Because of the overall burden of IBD and its multifactorial etiology, efforts have been made to improve the medical management of these inflammatory conditions. The classical therapeutic strategies aim to control the exacerbated host immune response with aminosalicylates, antibiotics, corticosteroids, thiopurines, methotrexate and anti-tumor necrosis factor (TNF) biological agents. Although successful in the treatment of several CD or UC conditions, these drugs have limited effectiveness, and variable responses may culminate in unpredictable outcomes. The ideal therapy should reduce inflammation without inducing immunosuppression, and remains a challenge to health care personnel. Recently, a number of additional approaches to IBD therapy, such as new target molecules for biological agents and cellular therapy, have shown promising results. A deeper understanding of IBD pathogenesis and the availability of novel therapies are needed to improve therapeutic success. This review describes the overall key features of therapies currently employed in clinical practice as well as novel and future alternative IBD treatment methods.
Post-buckled precompressed subsonic micro-flight control actuators and surfaces (2008)

This paper describes a new class of flight control actuators using Post-Buckled Precompressed (PBP) piezoelectric elements to provide much improved actuator performance. These PBP actuator elements are modeled using basic large deflection Euler-beam estimations accounting for laminated plate effects. The deflection estimations are then coupled to a high rotation kinematic model which translates PBP beam bending to stabilator deflections. A test article using PZT-5H piezoceramic sheets built into an active bender element was fitted with an elastic band which induced much improved deflection levels. Statically the bender element was capable of producing unloaded end rotations on the order of ±2.6°. With axial compression, the end deflections were shown to increase nearly 4-fold. The PBP element was then fitted with a graphite-epoxy aeroshell which was designed to pitch around a tubular stainless steel main spar. Quasi-static bench testing showed excellent correlation between theory and experiment through ±25° of pitch deflection. Finally, wind tunnel testing was conducted at airspeeds up to 120kts (62m/s, 202ft/s). Testing showed that deflections up through ±20° could be maintained at even the highest flight speed. The stabilator showed no flutter or divergence tendencies at all flight speeds. At higher deflection levels, it was shown that a slight degradation deflection was induced by nose-down pitching moments generated by separated flow conditions induced by extremely high angles of attack.
Evaluation of the performance of antenna pattern correction under the influence of unknown antenna pattern changes (2002)

An assessment of the influence of antenna pattern changes in microwave radiation estimation taking into account antenna pattern correction (APC) has been conducted. In the usual case, the antenna pattern cannot be known exactly and its changes are unknown in space. Under such conditions, the APC process is not always stable. Therefore it is important to reduce the instability that is called 'ill-posedness in the inverse problem'. In the paper, the projection onto convex sets (POCS) method is introduced into the APC process and it is shown that the APC process becomes more stable by using POCS than the usual APC by numerical experiments. It can be concluded that the POCS method is recommended for the APC when the antenna pattern changes are unknown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A new wafer level package for improved electrical and reliability performance (2004)

Wafer level packages (WLPs) have demonstrated a very clear size and cost advantage vs. traditional wirebond technologies, especially for small components that have a high number of dice and I/O per wafer. The Kulicke & Soffa Flip Chip Division (FCD) introduced it's first WLP in 1998. This initial WLP utilized a bump on nitride structure (BON) which had good reliability but also high input capacitance. A new WLP has been developed by FCD. This new WLP has a solder bump on polymer (BOP) dielectric structure. A major driver for pursuing a BOP structure was to achieve minimal input capacitance for high speed applications. During development, a new polymer dielectric material was carefully selected based on reliability tests and manufacturability. Thermal Cycling (TC) test showed 30% better TC performance vs. the BON structure. The new WLP also passed 168 hours of autoclave and JEDEC Level 1 Preconditioning testing. In this paper, the advantages of this new WLP will be discussed in detail. In addition, reliability test results will be presented.
HP Caliper: a framework for performance analysis tools (2000)

HP Caliper, a framework for building dynamic instrumentation tools, lets you change program instructions on-the-fly with instrumentation probes. It offers a common framework for building performance analysis tools that can integrate hardware-supported performance measurement unit (PMU) sampling with dynamic instrumentation. This article describes Caliper's architecture, its public interfaces and its dynamic instrumentation algorithm.
Machine Vision Condition Monitoring of Railcar Structural Underframe Components (2009)

Monitoring the structural health of rolling stock is critical to ensuring safe and efficient railroad operation. The structural integrity of freight cars depends on the health of certain structural components within their underframes. These structural components serve two principal functions: supporting the car body and lading, and transmitting longitudinal buff and draft forces. Although railcars are engineered to withstand large static, dynamic and cyclical loads, various structural defects can still develop within their underframes. As a result, both the United States Department of Transportation (USDOT) Federal Railroad Administration (FRA) regulations and individual railroad mechanical department practices require periodic inspection of railcars to detect structural damage and defects. These inspections are conducted manually and rely heavily on the acuity, knowledge and endurance of qualified inspection personnel. Enhancements are possible through machine-vision technology, which uses computer algorithms to convert digital image data into useful information. This paper describes research investigating the feasibility of an automated inspection system capable of detecting structural defects in freight car underframes and presents an inspection approach using machine-vision techniques, including multi-scale image segmentation. Using field data from a preliminary image acquisition system, algorithms were developed to analyze images of railcar underframes and assess the condition of certain structural components. This technology, in conjunction with additional preventive maintenance systems, has the potential to provide more objective information on railcar condition, improve utilization of railcar inspection and repair resources, increase train and employee safety, and improve overall railroad network efficiency.
Analysis of TQCM surface contamination adsorbed during the Spacelab I Mission (1985)

The Temperature-Controlled Quartz Crystal Microbalance (TQCM) system was flown on the Spacelab I Mission as part of the Induced Environment Contamination Monitor to monitor surface contamination (SC) in the payload bay. SC on the five sensors of the TQCM was analyzed by means of IR spectroscopy, scanning electron spectroscopy, and energy dispersive X-ray fluorescence. The amount of SC ranged from 1.4 micrograms/sq cm for the -Z sensor to 39.9 micrograms/sq cm for the +X sensor. The IR analysis showed strong CH2, CH3, and carbonyl absorption bands, indicative of ester and polyester compounds found in adhesives, plasticizers, and tape. The particulates (mostly ranging from 1 micron to 20 microns in size) were mainly composed of Mg, Al, Al2O3, and Si, and probably originated in the solid rocket firings.
Ceramic Fiber Reinforced Piston for High Performance Diesel Engines (1983)

<div class="htmlview paragraph">A Ceramic Fiber Reinforced Aluminum Matrix Composite has been developed that has excellent wear resistance, seizure resistance against cast iron, good thermal conductivity and high strength at elevated temperatures, By strengthening top land and top ring groove of piston with the Aluminum Matrix Composites, a newly designed Diesel Engine attained excellent performance without sacrificing manufacturing cost and productivity.</div>
The Digestible Amino Acid Composition of Several Milk Proteins: Application of a New Bioassay (1998)

The aim of the present study was to determine the composition of amino acids that were truly digestible in the ileum. Several bovine milk products and two soy protein products were tested using the newly developed enzymatically hydrolyzed casein-ultrafiltration (UF) method. This method provides a novel approach for determining endogenous flows of amino acids at the terminal ileum, which are required for correcting apparent ileal digestibility values to true digestibility values. Digestibility was determined by sampling digesta of Sprague-Dawley male rats at the end of the small intestine (ileum). Chromic oxide was used as an indigestible marker. The traditional protein-free method for determining endogenous losses of amino acids was also used for comparison with the enzymatically hydrolyzed casein-UF method. Flows of endogenous amino acids at the terminal ileum of the rat following peptide alimentation were generally higher (1.8-fold) than those determined after a protein-free diet was fed. Compared with values for true amino acid digestibility, apparent values underestimated digestibility by 2 to 30%. True amino acid digestibility was high (79 to 102%) for all of the protein sources. The digestible amounts of methionine and lysine were 2 and 1.3 times higher, respectively, in dairy proteins than in soy proteins. The enzymatically hydrolyzed casein-UF method provides a physiological estimate of endogenous amino acid flow and appeared to be an appropriate method for correcting apparent digestibility values to true digestibility values. The data for true ileal digestibility of amino acids obtained using this technique demonstrated the high quality of bovine milk proteins.
On the detection of cosmological neutrinos by coherent scattering (1983)

There have been several proposals that the sea of cosmological relic neutrinos could be detected by the energy, momentum, or angular momentum transferred during their coherent interaction with matter. We show that all but one of these proposals is incorrect and that the one exception leads to an effect that is probably immeasurably small. We first review the existing limits on the cosmological neutrinos and describe the expectations from the standard hot big-bang model. We then prove a general theorem that if the time average of the neutrino flux is spatially homogeneous (which is expected for cosmological neutrinos), then to first order in the weak coupling the energy and momentum transfer to any microscopic or macroscopic target is zero. Similarly, the angular momentum transfer is zero unless the target has a nonzero polarization or current density (but in this case the effect is probably immeasurably small). No assumption is made concerning the isotropy of the neutrino flux. Finally, we reexamine the individual proposals using the language of geometrical optics and show where all but one of them was incorrect. In particular, we prove that the momentum and angular momentum transferred by refraction from a homogeneous incoming beam to a (microscopically) isotropic target vanish to order $n\ensuremath{-}1$, with $n$ the index of refraction.
New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae (2014)

Stop codon readthrough may be promoted by the nucleotide environment or drugs. In such cases, ribosomes incorporate a natural suppressor tRNA at the stop codon, leading to the continuation of translation in the same reading frame until the next stop codon and resulting in the expression of a protein with a new potential function. However, the identity of the natural suppressor tRNAs involved in stop codon readthrough remains unclear, precluding identification of the amino acids incorporated at the stop position. We established an in vivo reporter system for identifying the amino acids incorporated at the stop codon, by mass spectrometry in the yeast Saccharomyces cerevisiae. We found that glutamine, tyrosine and lysine were inserted at UAA and UAG codons, whereas tryptophan, cysteine and arginine were inserted at UGA codon. The 5' nucleotide context of the stop codon had no impact on the identity or proportion of amino acids incorporated by readthrough. We also found that two different glutamine tRNA(Gln) were used to insert glutamine at UAA and UAG codons. This work constitutes the first systematic analysis of the amino acids incorporated at stop codons, providing important new insights into the decoding rules used by the ribosome to read the genetic code.
Role of the Gut in Multiple Organ Failure: Bacterial Translocation and Permeability Changes (1996)

It is clear that increased gut permeability and bacterial translocation play a role in multiple organ failure (MOF). Failure of the gut barrier remains central to the hypothesis that toxins escaping from the gut lumen contribute to activation of the host's immune inflammatory defense mechanisms, subsequently leading to the autointoxication and tissue destruction seen in the septic response characteristic of MOF. However, the role of the gut is more than that of a sieve, which simply allows passage of bacteria and endotoxin from the gut lumen to the portal or systemic circulation. It appears, in addition, that the translocation of bacteria and endotoxin may lead to local activation of the immune inflammatory system and the local production of cytokines and other immune inflammatory mediators. These intestinally derived mediators may then exacerbate the systemic inflammatory response and potentially lead to a further increase in gut permeability. A vicious cycle of increased intestinal permeability, leading to toxic mediator release, resulting in a further increase in gut permeability is generated. Additionally, the systemic and local inflammatory cells that become activated in the gut contribute to the systemic response characteristic of the sepsis syndrome and MOF. Thus even if the immune inflammatory system, rather than the gut, is the "motor of" MOF, the gut remains one of the major pistons that turns the motor.