gebhart/patrepeval huggingface dataset:
Regulation of Proliferation-Survival Decisions during Tumor Cell Hypoxia (1998)

Hypoxia may influence tumor biology in paradoxically opposing ways: it is lethal as a direct stress trigger, yet hypoxic zones in solid tumors harbor viable cells which are particularly resistant to treatment and contribute importantly to disease relapse. To examine mechanisms underlying growth-survival decisions during hypoxia, we have compared genetically related transformed and untransformed fibroblast cells in vitro for proliferation, survival, clonogenicity, cell cycle, and p53 expression. Hypoxia induces G0/G1 arrest in primary fibroblasts but triggers apoptosis in oncogene-transformed derivatives. Unexpectedly, the mechanism of apoptosis is seen to require accumulated acidosis and is rescued by enhanced buffering. The direct effect of hypoxia under nonacidotic conditions is unique to transformed cells in that they override the hypoxic G0/G1 arrest of primary cells. Moreover, when uncoupled from acidosis, hypoxia enhances tumor cell viability and clonogenicity relative to normoxia. p53 is correspondingly upregulated in response to hypoxia-induced acidosis but downregulated during hypoxia without acidosis. Hypoxia may thus produce both treatment resistance and a growth advantage. Given strong evidence that hypoxic regions in solid tumors are often nonacidotic (G. Helmlinger, F. Yuan, M. Dellian, and R. K. Jain, Nat. Med. 3:177-182, 1997), this behavior may influence relapse and implicates such cells as potentially important therapeutic targets.
A 15ns 64K bipolar SRAM (1985)

THIS PAPER WILL DESCRIBE a 64K bipolar SRAM with a cell size of 190μ^2 and 2μ features that resulted in an overall die size of 28,608 square mils.
EVIDENCE-BASED USE OF EPLERENONE (2014)

Data of the negative effect of high concentrations of aldosterone in the blood for cardiovascular disease, which served as the theoretical basis for wider use in clinical practice of the drugs belonging to the class of aldosterone receptor blockers is presented. Evidence-based data on efficacy and safety of aldosterone receptor blockers, which were obtained in the course of several randomized clinical trials is performed. Particular attention is paid to aspects of the clinical use of selective aldosterone receptor blocker eplerenone, including current data, which makes reasonable extension of indications for its use in treating patients with chronic heart failure. Data on indications of eplerenone use in patients with hypertension, especially in the case of associated target organ damage is presented.
Monitoring gene therapy with cytosine deaminase: in vitro studies using tritiated-5-fluorocytosine. (1996)

5-Fluorocytosine transport may be a limiting factor for this therapeutic procedure. Quantitation with PET has to rely more on dynamic studies and modeling, including HPLC analysis of the plasma, than on nonmodeling approaches.
Real-Time Monitoring of Distillations by Near-Infrared Spectroscopy (2003)

A simple device is described to couple a fast-scanning acoustooptic tunable filter-based NIR spectrophotometer to a distillation apparatus for monitoring the condensed vapor in real time. The device consists of a small funnel whose glass neck (2-mm diameter) is bent into an "U" format to produce a flow cell of approximately 150-microL inner volume. A pair of optical fibers is used to deliver the monochromatic light and to collect the fraction passing through the glass tube. The end of the condenser of the distillation head touches the wall of the small funnel. The condensed liquid flows uncoupled from pressure changes in the interior of the distillation head. Absorbance spectra were obtained, during the distillation, as averages of 50 scans (4 s) every 5 s in the spectral range 950-1800 nm with nominal resolution of 2.0 nm. In the first experiments, the distillations were performed at constant power supplied to the sample (25 mL) in a microdistillation apparatus working without any type of reflux column. The usefulness of the real-time monitoring of distillation is demonstrated using some prepared binary mixtures and by comparing the distillation behavior of adulterated and regular gasoline samples. Data analysis and interpretation are facilitated by employing principal component analysis. The system accesses the composition of the condensate, which can separate and concentrate one or more compounds present in the original sample.
Differential expression of estrogen receptor-alpha and -beta messenger RNAs as a potential marker of ovarian carcinogenesis. (1998)

Although estrogen receptor (ER)-alpha is expressed in both benign and malignant ovarian tumors, the role of ER in ovarian carcinogenesis of epithelial tumors is still unknown. In view of the recent characterization of ER-beta, a second form of ER that seems to be highly expressed in ovaries, we reexamined this issue by studying the relative expression of ER-alpha and -beta in human ovarian tumor progression. We developed a competitive PCR assay based on coamplification of the two ERs in target nucleotide sequences displaying a high homology (exons 3 and 4). Coamplification experiments with varying amounts of plasmids containing ER-alpha and -beta cDNAs showed that this assay was reliable for discriminating as little as a 2-fold difference in the initial ER-alpha:ER-beta cDNA ratio. The relative expression of ER-alpha compared with ER-beta mRNAs was studied in human ovarian cancer cell lines (n = 5) and in normal ovaries (n = 6), then in human benign and malignant tumor samples including ovarian cysts (n = 24), borderline tumors (n = 3), and cancers (n = 10). In normal ovaries, ER-beta mRNA was the predominant ER form, whereas in ovarian cancer cell lines ER-alpha mRNA was markedly increased as compared with ER-beta. In benign and borderline tumors, ER-beta mRNA was detected in 78% of tumors, whereas ER-alpha mRNA was detected in 29%. In ovarian carcinomas, both ER-alpha and -beta mRNAs were expressed in 80% of tumors. The ER-alpha:ER-beta mRNA ratio was >1 in only one cyst sample (4%). In contrast, the ER-alpha:ER-beta mRNA ratio was markedly increased in ovarian cancers because 60% showed an ER-alpha:ER-beta mRNA >1. In situ hybridization experiments showed overlapping tissular distribution of ER-beta and -alpha expression in cancers and cysts, with a main localization in the epithelium and only a low level of expression in stromal cells. In summary, we found an increase in the ER-alpha:ER-beta mRNA ratio in ovarian carcinomas as compared with normal ovaries and cysts. These data suggest that overexpression of ER-alpha relative to ER-beta mRNA may be a marker of ovarian carcinogenesis.
Comparison of Brucella immunoglobulin M and G flow assays with serum agglutination and 2-mercaptoethanol tests in the diagnosis of brucellosis (2006)

The diagnostic value of Brucella IgM/IgG flow assays was evaluated in comparison with serum agglutination and 2-mercaptoethanol tests by testing a selection of serum samples submitted to the laboratory because of clinical suspicion of brucellosis. All 39 admission and 11 follow-up samples that agglutinated in the serum agglutination test tested positive in the flow assay, whereas all 20 serum agglutination negative samples with clinical suspicion of brucellosis, 23 control samples from healthy individuals and 20 control samples from cases with chronic hepatitis tested negative in the flow assay. The Brucella IgM and IgG flow assays were slightly more sensitive than the agglutination tests in discriminating between specific IgM and IgG antibodies. The Brucella IgM and IgG flow assays are easy-to-perform and quick assays that can be used for the diagnosis of brucellosis. The flow assays are very useful, especially in rural settings where brucellosis is widespread and where well-equipped laboratories to perform the laboratory tests are not readily available.
Illustrative Design Space Studies with Microarchitectural Regression Models (2007)

We apply a scalable approach for practical, comprehensive design space evaluation and optimization. This approach combines design space sampling and statistical inference to identify trends from a sparse simulation of the space. The computational efficiency of sampling and inference enables new capabilities in design space exploration. We illustrate these capabilities using performance and power models for three studies of a 260,000 point design space: (1) Pareto frontier analysis, (2) pipeline depth analysis, and (3) multiprocessor heterogeneity analysis. For each study, we provide an assessment of predictive error and sensitivity of observed trends to such error. We construct Pareto frontiers and find predictions for Pareto optima are no less accurate than those for the broader design space. We reproduce and enhance prior pipeline depth studies, demonstrating constrained sensitivity studies may not generalize when many other design parameters are held at constant values. Lastly, we identify efficient heterogeneous core designs by clustering per benchmark optimal architectures. Collectively, these studies motivate the application of techniques in statistical inference for more effective use of modern simulator infrastructure
Glycine ingestion improves subjective sleep quality in human volunteers, correlating with polysomnographic changes (2007)

In human volunteers who have been continuously experiencing unsatisfactory sleep, effects of glycine ingestion (3 g) before bedtime on subjective sleep quality were investigated, and changes in polysomnography (PSG) during sleep were analyzed. Effects on daytime sleepiness and daytime cognitive function were also evaluated. Glycine improved subjective sleep quality and sleep efficacy (sleep time/in-bed time), and shortened PSG latency both to sleep onset and to slow wave sleep without changes in the sleep architecture. Glycine lessened daytime sleepiness and improved performance of memory recognition tasks. Thus, a bolus ingestion of glycine before bedtime seems to produce subjective and objective improvement of the sleep quality in a different way than traditional hypnotic drugs such as benzodiazepines.
Threshold voltage adjustment on spherical, single-crystal silicon substrates by focused ion beam implantation (2006)

The development of spherical, rather than planar, imaging arrays would enable compact wide field-of-view cameras by reducing the size and complexity of the optical components. One approach is to fabricate the sensors and readout integrated circuits directly on a spherical shell machined from a single-crystal silicon substrate. Several significant advances in processing these substrates have already been reported. This article addresses one of the fundamental electronic issues: a threshold voltage correction procedure that accounts for the dependence of oxide thickness, fixed oxide charge, and interface trapped charge on crystallographic orientation and the variation of implant depth and projected dose on substrate geometry. Substrates with 15mm radius of curvature and 25mm diameter were machined from a B-doped (3Ωcm) (100) silicon ingot. The threshold voltage of as-formed capacitors varied from −0.4V in the center to −2.0V at a radius of 10mm. A 110keV B+ focused ion implantation system was used to adjust threshold voltage point by point with 1mm resolution. The authors demonstrate, for the first time, the ability to correct threshold voltage to within 0.12V over an 83° field of view.
Dense saliency-based spatiotemporal feature points for action recognition (2009)

Several spatiotemporal feature point detectors have been used in video analysis for action recognition. Feature points are detected using a number of measures, namely saliency, cornerness, periodicity, motion activity etc. Each of these measures is usually intensity-based and provides a different trade-off between density and informativeness. In this paper, we use saliency for feature point detection in videos and incorporate color and motion apart from intensity. Our method uses a multi-scale volumetric representation of the video and involves spatiotemporal operations at the voxel level. Saliency is computed by a global minimization process constrained by pure volumetric constraints, each of them being related to an informative visual aspect, namely spatial proximity, scale and feature similarity (intensity, color, motion). Points are selected as the extrema of the saliency response and prove to balance well between density and informativeness. We provide an intuitive view of the detected points and visual comparisons against state-of-the-art space-time detectors. Our detector outperforms them on the KTH dataset using nearest-neighbor classifiers and ranks among the top using different classification frameworks. Statistics and comparisons are also performed on the more difficult Hollywood human actions (HOHA) dataset increasing the performance compared to current published results.
Power–Velocity Process Design Charts for Powder Bed Additive Manufacturing (2017)

A current issue in metal-based additive manufacturing (AM) is achieving consistent, desired process outcomes in manufactured parts. When process outcomes such as strength, density, or precision need to meet certain specifications, changes in process variable selection can be made to meet these requirements. However, the changes required to achieve a better part performance may not be intuitive, particularly because process variable changes can simultaneously improve some outcomes while worsening others. There is great potential to design the additive manufacturing process, tailoring process variables based on user requirements for a given part. In this work, the tradeoffs between multiple process outcomes are formalized and the design problem is explored throughout the design space of process variables. Based on user input for each process outcome considered, P–V (power–velocity) process design charts are introduced, which map the process space and identify the best combination of process variables to achieve a user's desired outcome.
Bradykinin-Induced Chemotaxis of Human Gliomas Requires the Activation of K<sub>Ca</sub>3.1 and ClC-3 (2013)

Previous reports demonstrate that cell migration in the nervous system is associated with stereotypic changes in intracellular calcium concentration ([Ca(2+)](i)), yet the target of these changes are essentially unknown. We examined chemotactic migration/invasion of human gliomas to study how [Ca(2+)](i) regulates cellular movement and to identify downstream targets. Gliomas are primary brain cancers that spread exclusively within the brain, frequently migrating along blood vessels to which they are chemotactically attracted by bradykinin. Using simultaneous fura-2 Ca(2+) imaging and amphotericin B perforated patch-clamp electrophysiology, we find that bradykinin raises [Ca(2+)](i) and induces a biphasic voltage response. This voltage response is mediated by the coordinated activation of Ca(2+)-dependent, TRAM-34-sensitive K(Ca)3.1 channels, and Ca(2+)-dependent, 4,4'-diisothiocyanato-stilbene-2,2'-disulfonic acid (DIDS)-sensitive and gluconate-sensitive Cl(-) channels. A significant portion of these Cl(-) currents can be attributed to Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) activation of ClC-3, a voltage-gated Cl(-) channel/transporter, because pharmacological inhibition of CaMKII or shRNA-mediated knockdown of ClC-3 inhibited Ca(2+)-activated Cl(-) currents. Western blots show that K(Ca)3.1 and ClC-3 are expressed in tissue samples obtained from patients diagnosed with grade IV gliomas. Both K(Ca)3.1 and ClC-3 colocalize to the invading processes of glioma cells. Importantly, inhibition of either channel abrogates bradykinin-induced chemotaxis and reduces tumor expansion in mouse brain slices in situ. These channels should be further explored as future targets for anti-invasive drugs. Furthermore, these data elucidate a novel mechanism placing cation and anion channels downstream of ligand-mediated [Ca(2+)](i) increases, which likely play similar roles in other migratory cells in the nervous system.
SHAPEWAYS AND THE 3D PRINTING REVOLUTION (2014)

This serves as the first study to document the mechanisms of bone induction and fusion maturation between posterolateral arthrodeses treated with autograft versus rhOP-1. The histological data served to corroborate the radiographic and biomechanical findings, because the rhOP-1 treatments consistently demonstrated increased fusion rates and lower range of motion levels compared with the autograft group, particularly at the 8-week postoperative time period. The improvements in these fusion criteria for Osteogenic Protein-1 versus autograft were considered secondary to the differing mechanisms of bone induction. When implanted for posterolateral arthrodesis, rhOP-1 induces an intramembranous healing response, obviating the need for the cartilage intermediate phases found in endochondral bone development. The mechanism of increased speed and incidence of fusion using growth factors (rhOP-1) is delineated by this comprehensive study of preferential intramembranous ossification.
Pushing real time data usingHTML5 Web Sockets (2010)

The current browser landscape has no real support for server initiated push. Existing technologies such as Comet and AJAX emulate server push using "long-polling" and rely on maintaining two connections between client and browser for streaming. The latest HTML standard, HTML5, is introducing elements which will integrate web front-ends much tighter with server back-ends. Most importantly, web sockets are now being introduced and thereby allowing browser applications to receive asynchronous updates from the server side, so called server push. Web sockets de ne a full-duplex communication channel that operates over a single socket using HTML5 compliant browsers. Web sockets allow for true low latency applications and put less strain on the server.This paper is an attempt to create a web socket server according to the HTML5 web socket standard. The server will integrate with TickCapture[18] which is an existing system for back-testing and trading of algorithms written in various languages. TickCapture also allows for low latency presentation of real time market data and this data will be pushed through the web socket server to the clients using regular HTML5 compliant browsers.The nished system must provide good scalability so an in-depth study of scalability and load balancing techniques will be carried out to identify dierent solutions for my implementation.
<i>ethA</i> , <i>inhA</i> , and <i>katG</i> Loci of Ethionamide-Resistant Clinical <i>Mycobacterium tuberculosis</i> Isolates (2003)

Ethionamide (ETH) is a structural analog of the antituberculosis drug isoniazid (INH). Both of these drugs target InhA, an enzyme involved in mycolic acid biosynthesis. INH requires catalase-peroxidase (KatG) activation, and mutations in katG are a major INH resistance mechanism. Recently an enzyme (EthA) capable of activating ETH has been identified. We sequenced the entire ethA structural gene of 41 ETH-resistant Mycobacterium tuberculosis isolates. We also sequenced two regions of inhA and all or part of katG. The MICs of ETH and INH were determined in order to associate the mutations identified with a resistance phenotype. Fifteen isolates were found to possess ethA mutations, for all of which the ETH MICs were > or =50 microg/ml. The ethA mutations were all different, previously unreported, and distributed throughout the gene. In eight of the isolates, a missense mutation in the inhA structural gene occurred. The ETH MICs for seven of the InhA mutants were > or =100 microg/ml, and these isolates were also resistant to > or =8 microg of INH per ml. Only a single point mutation in the inhA promoter was identified in 14 isolates. A katG mutation occurred in 15 isolates, for which the INH MICs for all but 1 were > or =32 microg/ml. As expected, we found no association between katG mutation and the level of ETH resistance. Mutations within the ethA and inhA structural genes were associated with relatively high levels of ETH resistance. Approximately 76% of isolates resistant to > or =50 microg of ETH per ml had such mutations.
Beyond VEGF—The Weisenfeld Lecture (2016)

Future treatment of AMD should be based on biology, which will require continued elucidation of the pathogenic mechanisms of AMD development. Neuroprotection represents a potential therapeutic approach, and other promising targets include immune pathways (e.g., inflammation, complement, and inflammasomes) and lipid/lipoprotein accumulation. Finally, due to the heterogeneity of AMD, future progress in therapy will benefit from improved phenotyping and classification.
Rifampin Treatment of Prosthetic Valve Endocarditis Due to Staphylococcus epidermidis (1983)

Twenty-three patients with prosthetic valve endocarditis caused by methicillin-resistant Staphylococcus epidermidis were studied retrospectively for assessment of the role of rifampin treatment. Rifampin (900-1,200 mg daily) was administered in combination with either vancomycin or a beta-lactam antibiotic for an average of 38 days. Eight patients also received an aminoglycoside. Infection was cured in 16 (70%) of these patients; i.e., in 13 (87%) of 15 receiving rifampin plus vancomycin and in three (38%) of eight receiving rifampin plus a beta-lactam antibiotic (P = .025). The addition of rifampin to vancomycin regimens resulted in an increase in serum bactericidal activity. The selection of rifampin-resistant strains of S. epidermidis during treatment with a combination of antibiotics was noted in two patients with persistent infection. The rates of cure obtained with rifampin-beta-lactam combinations were similar to those obtained with beta-lactam agents alone; however, the cure rates obtained with rifampin plus vancomycin (with or without an aminoglycoside) were encouraging and merit further study.
Space efficiency in synopsis construction algorithms (2005)

Histograms and Wavelet synopses have been found to be useful in query optimization, approximate query answering and mining. Over the last few years several good synopsis algorithms have been proposed. These have mostly focused on the running time of the synopsis constructions, optimum or approximate, vis-a-vis their quality. However the space complexity of synopsis construction algorithms has not been investigated as thoroughly.
Formative evaluation of a prototype system for automated analysis of mass spectrometry data. (2005)

Mass Spectrometry (MS) is emerging as a breakthrough mass-throughput technology capable of producing powerful clinical diagnostic and prognostic models and of identifying important disease biomarkers. Few individuals possess the necessary skills to carry out MS analyses competently, and access to such individuals is limited in most settings, hindering progress in this field. We seek to ease this burden by creating a fully automated system (FAST-AIMS) capable of analyzing mass spectra to produce high-quality diagnostic and outcome prediction models and identify related biomarkers. In the present report we introduce the system and conduct a formative evaluation in which 6 users apply it to a challenging dataset. FAST-AIMS' performance is compared to that of an expert statistician as well as to a previously published analysis by an independent group. In our experiments FAST-AIMS when used by both MS-sophisticated users (n=4) and naïve users (n=2) achieves performance (a) comparable to our human expert, and (b) superior to the previously published manual analysis; in addition (c) the system's estimates future performance accurately, thus avoiding overfitting.
Whither corrosion? (1966)

IS IT NOT surprising that, although it is now over 100 years since Bessemer patented his process for the production of cheap steel, there is still no commercially available low-alloy steel whose corrosion resistance (except for minor improvements in resistance to some atmospheres) is significantly better than that of the steels available in the mid-nineteenth century? In fact it would not be impossible to find constructional engineers who consider modern steels not to have as much resistance as those of years ago.