gebhart/patrepeval huggingface dataset:
Utilizing flow cytometry to monitor autophagy in living mammalian cells (2008)

Autophagy is a major intracellular catabolic pathway that takes part in diverse biological events including response to amino acid starvation, protein and organelle turnover, development, aging, pathogen infection and cell death. However, experimental methods to monitor this process in mammalian cells are limited due to lack of autophagic markers. Recently, MAP1-LC3 (LC3), a mammalian homologue of the ubiquitin-like (UBL) protein Atg8, was shown to selectively incorporate into autophagosome, thus serving as a unique bona fide marker of autophagosomes in mammals. However, current methods to quantify autophagic activity using LC3 are time-consuming, labor-intensive and require much experience for accurate interpretation. Here we took advantage of the Fluorescence Activated Cell Sorter (FACS) to quantify the turnover of GFP-LC3 as an assay to measure autophagic activity in living mammalian cells. We showed that during induction of autophagy by rapamycin, tunicamycin or starvation to amino acids, fluorescence intensity of GFP-LC3 is reduced in a time-dependent manner. This decrease occurred specifically in wild type LC3, but not in mutant LC3(G120A), and was inhibited by autophagic or lysosomal inhibitors, indicating that this signal is specific to selective autophagy-mediated delivery of LC3 into lysosomes. By utilizing this assay, we tested the minimal nutrient requirement for the autophagic process and determined its induction by deprivation of specific single amino acids. We conclude that this approach can be successfully applied to different cell-lines as a reliable and simple method to quantify autophagic activity in living mammalian cells.
Hydrolytic decomposition of glycosides in aqueous acids (2008)

A review is presented that collects the experimental results published on the acid catalyzed hydrolysis of alkyl and aryl pyranosides and furanosides over the last three decades. In aqueous acid, alkyl furanosides and pyranosides are hydrolysed via an oxocarbenium intermediate, which may be formed from the protonated substrate either by an exocyclic or endocyclic C-O bond cleavage. Both mechanisms lead eventually to the same products. Various methods have been used to distinguish between the pathways, and a lot of evidence exists to show that different pathways are followed depending on the structure of both the glycon moiety and the departing alcohol.
Support Vector Regression Machines (1996)

A new regression technique based on concept of support vectors is introduced. We compare support vector regression with a committee regression technique (bagging) based on regression trees and ridge regression done in feature space. On the basis of these experiments, it is expected that SVR will have advantages in high dimensionality space because SVR optimization does not depend on the dimension&amp;amp;y of input space. This is a longer version of the paper appear in Advances in Neural Processing Systems 9 (proceedings of the 1996 conference)
Classifying news stories using memory based reasoning (1992)

We describe a method for classifying news stories using Memory Based Reasoning (MBR) a k-nearest neighbor method), that does not require manual topic definitions. Using an already coded training database of about 50,000 stories from the Dow Jones Press Release News Wire, and SEEKER [Stanfill] (a text retrieval system that supports relevance feedback) as the underlying match engine, codes are assigned to new, unseen stories with a recall of about 80% and precision of about 70%. There are about 350 different codes to be assigned. Using a massively parallel supercomputer, we leverage the information already contained in the thousands of coded stories and are able to code a story in about 2 seconds. Given SEEKER, the text retrieval system, we achieved these results in about two person-months. We believe this approach is effective in reducing the development time to implement classification systems involving large number of topics for the purpose of classification, message routing etc.
Decoding Circulating Nucleic Acids in Human Serum Using Microfluidic Single Molecule Spectroscopy (2010)

Circulating nucleic acid (CNA) has been the focus of recent research as a noninvasive source of biomarker candidates. Among these markers, DNA fragment size has shown promise for discerning the source of CNA molecules in cancer and prenatal diagnostics. We have developed a one-step assay for analyzing circulating DNA size and quantity directly in human serum. Microfluidic cylindrical illumination confocal spectroscopy and fluorescence burst size analysis are used to individually count and size fluorescently-labeled CNA molecules as they are driven through a microfluidic constriction. First, single molecule sizing was performed on lambda Hind III digest DNA to obtain a size calibration curve. A linear relation between DNA length and burst size was seen from 564 bp to 27.5 kbp. Subsequently, the single molecule assay parameters were optimized. Finally, DNA sizing analysis was performed on serum samples from both early and late stage lung cancer patients. This assay was performed directly in patient serum using only a single reagent, a simple DNA intercalating dye, and without the need for DNA isolation or enzymatic amplification steps. This demonstrates that microfluidic single molecule spectroscopy can be a rapid, facile, and inexpensive alternative to the established PCR-based methods that have been used near exclusively for CNA analysis.
Synthesis, design and analysis of a novel variable lift cam follower system (2010)

This work proposes a novel variable lift cam follower system. Here follower lift varies according to input or camshaft speed. The system comprises a trapezoidal shape cam with ping finite spline curve as displacement profile. The height of the cam varies along the axis of the shaft and it slides in the axial direction so that the lift of the cam varies. Sliding motion of cam was executed by actuating mechanism and it works on principle of centrifugal actuation. When input speed varies, due to centrifugal force, actuator initiates linear axial movement of bush and cam on the shaft. This axial movement of cam varies the follower lift with respect to speed. Various components of proposed mechanism are designed and fabricated by proper processes and assembled together with suitable provisions. The system is tested experimentally and follower lift was measured using the computerised measuring system. Results show that the mechanism works properly and is useful to get variable lift. The proposed mechanism can be used in automotive engines as a valve train for variable valve actuation with necessary modifications.
Copy number alterations of c‐MYC and PTEN are prognostic factors for relapse after prostate cancer radiotherapy (2012)

Despite the use of PSA, Gleason score, and T-category as prognosticators in intermediate-risk prostate cancer, 20-40% of patients will fail local therapy. In order to optimize treatment approaches for intermediate-risk patients, additional genetic prognosticators are needed. Previous reports using array comparative genomic hybridization (aCGH) in radical prostatectomy cohorts suggested a combination of allelic loss of the PTEN gene on 10q and allelic gain of the c-MYC gene on 8q were associated with metastatic disease. We tested whether copy number alterations (CNAs) in PTEN (allelic loss) and c-MYC (allelic gain) were associated with biochemical relapse following modern-era, image-guided radiotherapy (mean dose 76.4 Gy). We used aCGH analyses validated by fluorescence in-situ hybridization (FISH) of DNA was derived from frozen, pre-treatment biopsies in 126 intermediate-risk prostate cancer patients. Patients whose tumors had CNAs in both PTEN and c-MYC had significantly increased genetic instability (percent genome alteration; PGA) compared to tumors with normal PTEN and c-MYC status (p < 0.0001). We demonstrate that c-MYC gain alone, or combined c-MYC gain and PTEN loss, were increasingly prognostic for relapse on multivariable analyses (hazard ratios (HR) of 2.58/p = 0.005 and 3.21/p = 0.0004; respectively). Triaging patients by the use of CNAs within pre-treatment biopsies may allow for better use of systemic therapies to target sub-clinical metastases or locally recurrent disease and improve clinical outcomes.
Most common surfactants employed in chemical enhanced oil recovery (2016)

Chemical enhanced oil recovery (EOR) and particularly surfactant injection has recently received a great deal of attention. The suggested recovery mechanisms after injecting surfactants include wettability alteration and IFT reduction. If a surfactant is properly selected according to the environmental variables-such as pressure, temperature, salinity, it can lead to more efficient enhanced recovery from an oil reservoir. On the other hand, poor selection of the surfactant can result in a low recovery and can even become detrimental to the reservoir due to undesirable wettability alteration and possible rock dissolution resulting in a chemical reaction with displacing fluid and blockage of the pore space. Also, choosing the wrong surfactant without considering the rock mineralogy may result in high adsorption on the pore surface of the rock and unnecessary waste of resources. It is also worthy to note that surfactants are some of the most expensive chemicals used during EOR. Extensive literature review suggests that anionic surfactant are the preferred surfactant category for EOR especially when it comes to sandstone reservoirs. Occasionally, in specific situations a better performance have been reported after injecting cationic, non-ionic or mixtures of both surfactants, particularly when dealing with carbonate reservoirs. This paper presents in detail a review of the most commonly applied surfactants in EOR studies and the optimum application criteria for of each type. To the best of the authors' knowledge, such detailed and comprehensive review is not available in the literature, presently.
Combination Therapy With Oral Sildenafil and Beraprost for Pulmonary Arterial Hypertension Associated With CREST Syndrome (2007)

Pulmonary arterial hypertension (PAH) is commonly associated with CREST (Calcinosis, Raynaud phenomenon, Esophageal motility disorders, Sclerodactyly, and Telangiectasia) syndrome. Sildenafil, an oral phosphodiesterase type-5 inhibitor, may offer benefits in the pharmacological management of PAH. However, little is known about the long-term hemodynamic effects of sildenafil, and the potential role of sildenafil in long-term combination with beraprost, an oral prostacyclin analogue, remains unclear. We therefore examined the hemodynamic effect of oral sildenafil alone and when coadministered with beraprost in a patient with PAH associated with CREST syndrome. Traces of the acute hemodynamic effects of beraprost (20 microg) disappeared after 2 hours. In contrast, the acute hemodynamic effects of sildenafil (50 mg) produced a greater reduction in PAP (31%) and PVR (40%), and these effects also disappeared after 5 hours. After 1 month of combination therapy of sildenafil (25 mg) twice daily and beraprost (20 microg) 3 times daily, the fall in pulmonary artery pressure and pulmonary vascular resistance was sustained (31% in both). Furthermore, the patient had significantly improved her 3-minute walk test and NYHA function class without significant adverse effects at the reported doses. The findings indicate that oral sildenafil is a potent pulmonary vasodilator that appears to act synergistically with oral beraprost to cause sustained pulmonary vasodilatation in a patient with PAH associated with CREST syndrome.
Energy Management and Control System: Desired Capabilities and Functionality (2005)

This document discusses functions and capabilities of a typical building/facility energy management and control systems (EMCS). The overall intent is to provide a building operator, manager or engineer with basic background information and recommended functions, capabilities, and good/best practices that will enable the control systems to be fully utilized/optimized, resulting in improved building occupant quality of life and more reliable, energy efficient facilities.
Borderline personality disorder and sensory processing impairment (2009)

Abstract Sensory processing disorder (SPD) is a term advocated by some occupational therapists to describe a range of problems that might be amenable to particular treatment strategies, and has mainly been applied within the fields of paediatrics and learning disability.In this article,the authors investigate whether there could be a common ground between borderline personality disorder (BPD) and SPD and describe an extension of the treatment strategies for SPD to those with BPD in their acute inpatient unit. Copyright © 2009 Wiley Interface Ltd
Studies on the reaction mechanism of a microbial lipase/acyltransferase using chemical modification and site-directed mutagenesis. (1991)

Aeromonas hydrophila releases a protein which is a member of the lipase superfamily, similar in reaction mechanism to the important mammalian plasma enzyme lecithin-cholesterol acyltransferase. We have used chemical modification and site-directed mutagenesis of the protein to identify amino acids which may be involved in catalysis. The enzyme was unaffected by phenylmethylsulfonyl fluoride, but it was almost completely inhibited by another serine-reactive compound, diethyl p-nitrophenyl phosphate. A serine selectively modified by this reagent was identified by sequencing the amino-terminal region of the protein. It was located at position 16, in the short consensus sequence shared by the enzyme with other lipases. When this serine was changed to asparagine the product was an enzymatically inert protein which nevertheless retained the surface activity of the wild-type enzyme, suggesting its ability to bind to substrate was not changed. Diethylpyrocarbonate treatment drastically reduced the rate of acyl transfer by the native enzyme, but this did not appear to be due to modification of an essential histidine, since inhibition was not reversed by addition of hydroxylamine. We have shown that only two of the histidines in the enzyme can be involved in catalysis (Hilton, S., McCubbin, W. D., Kay, C.M., and Buckley, J. T. (1990) Biochemistry, 29, 9072-9078). Replacing both of these with asparagines had little or no effect on enzyme activity. These results indicate that, in apparent contrast to other lipases, histidine does not participate in the reaction catalyzed by the microbial enzyme. Since catalysis was not inhibited by sulfhydryl reagents, we conclude that a free cysteine is also not required for activity. This may distinguish the microbial enzyme from the mammalian acyltransferase.
Fas Ligand on Tumor Cells Mediates Inactivation of Neutrophils (2003)

The expression of Fas ligand (FasL) on tumor cells (tumor FasL) has been implicated in their evasion of immune surveillance. In this study, we investigated the cellular mechanism for FasL-associated immune escape using melanoma B16F10-derived cells as a model. Transfectants carrying FasL-specific ribozymes expressed low levels of FasL (FasL(low) tumor cells) as compared with those carrying enhanced green fluorescent protein-N1 plasmids (FasL(high) tumor cells). When injected s.c. into C57BL/6 mice, FasL(low) tumor cells grew more slowly than did FasL(high) melanoma cells. FasL(high) tumor cells showed more intensive neutrophilic infiltration accompanied by multiple necrotizing areas than did FasL(low) tumor cells. The average size of FasL(low) tumors, but not of FasL(high) tumors, was significantly enhanced in mice depleted of neutrophils. Consistently, a local injection of LPS to recruit/activate neutrophils significantly delayed tumor formation by FasL(low) tumor cells, and slightly retarded that of FasL(high) tumor cells in both C57BL/6 and nonobese diabetic/SCID mice. Neutrophils killed FasL(low) melanoma cells more effectively than FasL(high) melanoma cells in vitro. The resistance of FasL(high) melanoma cells to being killed by neutrophils was correlated with impaired neutrophil activation, as demonstrated by reductions in gelatinase B secretion, reactive oxygen species production, and the surface expression of CD11b and the transcription of FasL. Local transfer of casein-enriched or PMA-treated neutrophils delayed tumor formation by melanoma cells. Taken together, inactivation of neutrophils by tumor FasL is an important mechanism by which tumor cells escape immune attack.
Overcharge performance of 3,7-disubstituted N-ethylphenothiazine derivatives in lithium-ion batteries (2013)

3,7-Disubstituted N-ethylphenothiazine derivatives were synthesized as redox shuttle candidates for lithium-ion batteries. Battery cycling results show that three derivatives prevent overcharge.
Prosthetic communication device. (1980)

A code-generating and display system is described which permits an individual who has lost vocal voluntary motor ability to communicate. The subject sustained severe brain damage in an automobile accident which left him without the power of speech or any significant motor ability, although he is not by definition quadriplegic. He lacks reliable control of eye blink, and the oral movements associated with sucking and blowing are severely impaired; thus, the usual foundations upon which prosthetic devices for quadriplegic patients are designed were not applicable in this case. The subject is confined to a bed, wheelchair, or an exercise table. The system described here has provided the subject with a simple and reliable means of communicating with his family and it permits him to communicate with persons who do not know the Morse code.
Thrombospondin modulates focal adhesions in endothelial cells. (1989)

We examined the effects of thrombospondin (TSP) in the substrate adhesion of bovine aortic endothelial cells. The protein was tested both as a substrate for cell adhesion and as a modulator of the later stages of the cell adhesive process. TSP substrates supported the attachment of some BAE cells, but not cell spreading or the formation of focal adhesion plaques. In contrast, cells seeded on fibrinogen or fibronectin substrates were able to complete the adhesive process, as indicated by the formation of focal adhesion plaques. Incubation of cells in suspension with soluble TSP before or at the time of seeding onto fibronectin substrates resulted in an inhibition of focal adhesion formation. Furthermore, the addition of TSP to fully adherent cells in situ or prespread on fibronectin substrates caused a reduction in the number of cells, which were positive for focal adhesions, although there was no significant effect on cell spreading. In a dose-dependent manner, TSP reduced the number of cells with adhesion plaques to approximately 60% of control levels. The distribution of remaining adhesion plaques in TSP-treated cells was also altered: plaques were primarily limited to the periphery of cells and were not present in the central cell body, as in control cells treated with BSA. The observed effects were specific for TSP and were not observed with platelet factor 4, beta-thromboglobulin, or fibronectin. The TSP-mediated loss of adhesion plaques was neutralized by the addition of heparin, fucoidan, other heparin-binding proteins, and by a monoclonal antibody to the heparin binding domain of TSP, but not by antibodies to the core or carboxy-terminal regions of TSP. The interaction of the heparin-binding domain of TSP with cell-associated heparan sulfate appears to be an important mechanistic component for this activity of TSP. These data indicate that TSP may have a role in destabilizing cell adhesion through prevention of focal adhesion formation and by loss of preformed focal adhesions.
Effects of food on pharmacokinetics of immediate release oral formulations of aspirin, dipyrone, paracetamol and NSAIDs – a systematic review (2015)

There is evidence that high, early plasma concentrations produces better early pain relief, better overall pain relief, longer lasting pain relief and lower rates of remedication. Taking analgesics with food may make them less effective, resulting in greater population exposure. It may be time to rethink research priorities and advice to professionals, patients and the public.
Homing of in vitro expanded Stro-1- or Stro-1+ human mesenchymal stem cells into the NOD/SCID mouse and their role in supporting human CD34 cell engraftment (2004)

The Stro-1 antigen potentially defines a mesenchymal stem cell (MSC) progenitor subset. We here report on the role of human ex vivo-expanded selected Stro-1(+) or Stro-1(-) MSC subsets on the engraftment of human CD34(+) cord blood cells in the nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mouse model. The data show that cotransplantation of expanded Stro-1(-) cells with CD34(+) cells resulted in a significant increase of human CD45, CD34, CD19, and CD11b cells detected in blood or in bone marrow (BM) and spleen as compared with the infusion of CD34(+) cells alone. Infusion into mice of expanded Stro-1(+) and Stro-1(-) cells (without CD34(+) cells) showed that the numbers of Stro-1(+)-derived (as assessed by DNA analysis of human beta-globin with quantitative polymerase chain reaction [PCR]) were higher than Stro-1(-)-derived cells in spleen, muscles, BM, and kidneys, while more Stro-1(-)-derived than Stro-1(+)-derived cells were found in lungs. The transduction of expanded Stro-1(+) cells with an enhanced green fluorescent protein (eGFP) gene did not modify their cytokine release and their homing in NOD/SCID mouse tissues. The difference between the hematopoietic support and the homing capabilities of expanded Stro-1(+) and Stro-1(-) cells may be of importance for clinical therapeutic applications: Stro-1(+) cells may rather be used for gene delivery in tissues while Stro-1(-) cells may rather be used to support hematopoietic engraftment.
Discretized Streams: A Fault-Tolerant Model for Scalable Stream Processing (2012)

Many "big data" applications need to act on data arriving in real time.However, current programming models for distributed stream processing are relatively low-level, often leaving the user to worry about consistency of state across the system and fault recovery.Furthermore, the models that provide fault recovery do so in an expensive manner, requiring either hot replication or long recovery times.We propose a new programming model, discretized streams (D-Streams), that offers a high-level functional API, strong consistency, and efficient fault recovery.D-Streams support a new recovery mechanism that improves efficiency over the traditional replication and upstream backup schemes in streaming databasesparallel recovery of lost state-and unlike previous systems, also mitigate stragglers.We implement D-Streams as an extension to the Spark cluster computing engine that lets users seamlessly intermix streaming, batch and interactive queries.Our system can process over 60 million records/second at sub-second latency on 100 nodes.