gebhart/patrepeval huggingface dataset:
Evaluation of the Ras/B-Raf/SHP-2 Axis in B Cell Malignancies. (2004)

Abstract The Ras/Raf/MEK/MAPK pathway is a major regulator of tumor cell proliferation. Ras mutations have been known in many malignancies for several years, whereas more recent reports have shown that activating mutations of the BRAF gene are present in a large percentage of human malignant melanomas and thyroid carcinomas and in a substantial proportion of colon carcinomas (Nature2002;417:949–54). The vast majority of these mutations represent a T1796A change resulting in a V599E substitution within the activation segment of B-Raf. This mutant B-Raf kinase is constitutively active and results in inappropriate stimulation of downstream MAPK/ERKs and tumor cell proliferation. The PTPN11 gene encodes SHP-2 (Src homology 2 domain-containing protein tyrosine Phosphatase), a nonreceptor tyrosine protein tyrosine phosphatase (PTPase) that modulates Ras signaling. Germline mutations in PTPN11 are responsible for Noonan syndrome (NS), whereas somatic mutations have been detected in juvenile myelomonocytic leukemia (JMML). We investigated the presence of mutations in the Ras/B-Raf/SHP-2 axis in 25 lines from B-cell malignancies, including 19 multiple myeloma (MM) cell lines. DNA was isolated and B-Raf (exons 11 and 15), PTPN11 (3 and 13) and K-, N- and H-Ras sequences were amplified by PCR using specific flanking primers. The PCR products were purified and sequenced in automatic sequencer (ABI PRISM 3100 Genetic Analyzer; Applied Biosystems). Ras gene mutations were found in 11/25 (44%) of the studied cell lines. None of the previously described activating B-Raf mutations, including the most prevalent V599E, were found in our panel. Only one MM cell line demonstrated a C1332A substitution, which corresponds to a D444E change, which is predicted to have a minimal, if any, impact on kinase activity. A single PTPN11 G178C substitution, corresponding to a G60R change (previously described in NS and AML), was detected in another MM line. These data confirm the previously known role of Ras mutations in B-cell malignancies and identify a rare occurrence of a PTPN11 mutation in our panel. On the other hand, activating mutations of the B-Raf kinase are unlikely to play a significant part in the pathogenesis of B cell malignancies, in contrast to their prominent role in several types of solid tumors. In total, our data suggest that the Ras/Raf/MEK/MAPK can be overactive in these malignancies due to activating genetic events upstream of B-Raf, such as the previously described activating Ras mutations.
Predicting Speech Intelligibility and Quality from Model Auditory Nerve Fiber Mean-rate and Spike-timing Activity (2017)

This dissertation examines the prediction of speech intelligibility and quality using simulated auditory nerve fiber activity. The relationship of neural mean-rate and spike-timing activity to the perceptual salience of the envelope (ENV) and temporal fine-structure (TFS) of speech is indistinct. TFS affects neural temporal coding in two ways. TFS produces phase-locked spike-timing responses and narrowband cochlear filtering of TFS generates recovered ENV. These processes, with direct encoding of ENV to mean-rate responses, are the established transduction processes. We postulate that models based on mean-rate (over a time-window of approx. 6 to 16 ms) and spike-timing cues should produce accurate predictions of subjectively graded speech. Two studies are presented. The first study examined the contribution of mean-rate and spike-timing cues to predicting intelligibility. The relative level of mean-rate and spike-timing cues were manipulated using chimaerically vocoded speech. The Spectro-Temporal Modulation Index (STMI) and Neurogram SIMilarity (NSIM) were used to quantify the mean-rate and spike-timing activity. Linear regression models were developed using the STMI and NSIM. An interpretable model combining the STMI and the fine-timing NSIM demonstrated the most accurate predictions of the graded speech. The second study examined the contribution of mean-rate and spike-timing cues for predicting the quality of enhanced wideband speech. The mean-rate and fine-timing NSIM were used to quantify the mean-rate and spike-timing activity. Linear regression models were developed using the NSIM measures and optimization of the NSIM was investigated. A quality-optimized model with intermediate temporal resolution had the best predictive performance. The modelling approach used here allows for the study of normal and impaired hearing. It supports the design of hearing-aid processing algorithms and furthers the understanding how TFS cues might be applied in cochlear implant stimulation schemes.
Passive RFID tomographic imaging for device-free user localization (2012)

Localization of users is an important part of location aware systems and smart environments. It forms a major data source for superimposed intention recognition systems. In RF device-free localization (DFL), the person being tracked does not need to wear a RF transmitter or receiver in order to be located. Instead, they are tracked using the changes in signal strength measured on static links in a wireless network. This work presents a new algorithm for RF DFL using passive RFID networks. We formulate and show how a tomographic imaging algorithm provides both low computational complexity and highly accurate position estimates. Using measurements conducted in an indoor environment with various human positions, we find the algorithm can locate the human with as low as 30 cm mean location error.
Activation of NADPH oxidase by purine and pyrimidine nucleotides involves G proteins and is potentiated by chemotactic peptides (1989)

Human neutrophils and HL-60 leukaemic cells possess an NADPH oxidase which catalyses superoxide (O2-) formation and is activated by the chemotactic peptide, N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMet-Leu-Phe). In dibutyryl cyclic AMP-differentiated HL-60 cells, ATP and UTP in the presence of cytochalasin B activated O2- formation with EC50 values of 5 microM and efficacies amounting to 30% of that of fMet-Leu-Phe. The potency order of purine nucleotides in activating O2- generation was ATP = adenosine 5'-O-(3-thiotriphosphate) greater than ITP greater than dATP = ADP. Pyrimidine nucleotides activated NADPH oxidase in the potency order UTP greater than dUTP greater than CTP = TTP = UDP. Pertussis toxin completely prevented activation of NADPH oxidase by fMet-Leu-Phe and UTP, whereas the effect of ATP was only partially inhibited. ATP and UTP enhanced O2- generation induced by fMet-Leu-Phe by up to 8-fold, and primed the cells to respond to non-stimulatory concentrations of fMet-Leu-Phe. Activation of NADPH oxidase by UTP but not by ATP was inhibited by various activators of adenylate cyclase. In dimethyl sulphoxide-differentiated HL-60 cells and in human neutrophils, ATP and UTP per se did not activate NADPH oxidase, but they potentiated the effect of fMet-Leu-Phe. Our results suggest that purine and pyrimidine nucleotides act via purino- and novel pyrimidinoceptors respectively, which are coupled to guanine nucleotide-binding proteins leading to the activation of NADPH oxidase. As ATP and UTP are released from cells under physiological and pathological conditions, these nucleotides may play roles as intercellular signal molecules in the activation of O2- formation.
A Survey of Authentication and Communications Security in Online Banking (2016)

A survey was conducted to provide a state of the art of online banking authentication and communications security implementations. Between global regions the applied (single or multifactor) authentication schemes differ greatly, as well as the security of SSL/TLS implementations. Three phases for online banking development are identified. It is predicted that mobile banking will enter a third phase, characterized by the use of standard web technologies to develop mobile banking applications for different platforms. This has the potential to make mobile banking a target for attacks in a similar manner that home banking currently is.
Hot-carrier photodetector beyond spectral limit (2013)

The wavelength limit (λc) of detection in a conventional photodetector is limited to a characteristic energy (Δ) through the relationship: λc = hc/Δ, where Δ also determines the detector noise (dark current) and hence its performance such as the operating temperature. Here, we report an infrared photodetector with an extended operating range (responding beyond the standard spectral threshold) based on a hot-hole energy transfer mechanism. A detector with Δ = 0.32 eV showing a striking response up to 100 µm has been demonstrated, whereas without the hot-carrier effect the threshold should correspond to ∼3.9 µm. A detectivity of 7.8×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> cm Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> /W at 22 µm has been measured at 80 K.
Neural crest induction in <i>Xenopus</i>: evidence for a two-signal model (1998)

We have investigated the molecular interactions underlying neural crest formation in Xenopus. Using chordin overexpression to antagonize endogenous BMP signaling in whole embryos and explants, we demonstrate that such inhibition alone is insufficient to account for neural crest induction in vivo. We find, however, that chordin-induced neural plate tissue can be induced to adopt neural crest fates by members of the FGF and Wnt families, growth factors that have previously been shown to posteriorize induced neural tissue. Overexpression of a dominant negative XWnt-8 inhibits the expression of neural crest markers, demonstrating the necessity for a Wnt signal during neural crest induction in vivo. The requirement for Wnt signaling during neural crest induction is shown to be direct, whereas FGF-mediated neural crest induction may be mediated by Wnt signals. Overexpression of the zinc finger transcription factor Slug, one of the earliest markers of neural crest formation, is insufficient for neural crest induction. Slug-expressing ectoderm will generate neural crest in the presence of Wnt or FGF-like signals, however, bypassing the need for BMP inhibition in this process. A two-step model for neural crest induction is proposed.
Analysis of Lost Circulation During Drilling in Cooled Formations (2004)

Abstract A few of the lost circulation incidents that have occurred at the Statfjord field and the Veslefrikk field appeared to have been caused by drilling through cooled formations. These lost circulation incidents have been analyzed and compared with offset wells drilled with full returns. We have made plausible that the presented cases of lost circulation are caused by the fact that these wells have been drilled too close to a water injector. Injection data have been analyzed to determine the thermo-elastic stress changes around these injectors. To quantify the thermal cooling effect, downhole pressure data measured during the mud loss incident are analyzed. We found a significant reduction both in the breakdown pressure and minimum horizontal stress. When comparing these data with a thermo-elastic model, the theory predicts a much stronger effect than the interpreted downhole pressure measurements. Numerical simulations of near-wellbore thermal stress effects showed that differences between the mud temperature and the formation temperature could significantly increase the wellbore stresses toward compression. However, the combined near-wellbore thermal effects of formation cooling and a warm mud could not explain the discrepancy between the model and the interpreted stress measurements.
Enhanced Therapeutic Effects of Human iPS Cell Derived-Cardiomyocyte by Combined Cell-Sheets with Omental Flap Technique in Porcine Ischemic Cardiomyopathy Model (2017)

Transplant of human induced pluripotent stem cell derived cardiomyocytes (hiPS-CMs) cell-sheet is a promising approach for treating ischemic cardiomyopathy (ICM). However, poor blood supply to the transplanted cell-sheet is a concern related to the effectiveness and durability of the treatment. Herein, we hypothesized that the combined the omentum flap might enhance survival and the therapeutic effects of hiPS-CM cell-sheet transplant for ICM treatment. Treatment by Wnt signaling molecules in hiPS cells produced hiPS-CMs, which were magnetically labeled by superparamagnetic iron oxide (SPIO), followed by culture in the thermoresponsive dishes to generate hiPS-CMs cell-sheets. A porcine ICM model included 4 groups; sham operation, omentum flap only, cell-sheet only, or combination therapy. Ejection fraction (EF) was significantly greater in the cell-sheet only and combination group compared to the other groups during the follow-up period. At 3 months, the EF of the combination group was significantly greater than that of the cell-sheet only group. Consistently, the survival rate of the SPIO-labeled hiPS-CMs, as assessed by MRI, was significantly greater in the combination group than in the cell-sheet only group. This cell delivery system would be useful in optimizing the hiPS-CM cell-sheet transplant for treating severe heart failure.
Effects of Xuebijing injection on inflammatory response in patients with acute respiratory distress syndrome (2011)

Objective To evaluate the effects of Xuebijing injection on inflammatory response in patients with acute respiratory distress syndrome(ARDS) by the changes of the level of PCT in bronchoalveolar lavage fluid (BALF) and plasma so as well as serum tumor necrosis factor-α(TNF-α) 、interleukin-6(IL-6) and interleukin-8( IL-8). Methods Sixty patients treated at the intensive care unit(ICU) were recruited in this study;these subjects satisfied the diagnostic criteria for ARDS. They were randomly classified into two groups: study group ( 30 patients) in which patients were given Xuebijing injection 100ml and 5% Glucose injection 150 ml daily,and control group(30 patients) patients were given 5% Glucose injection 250ml daily. The changes of the level of PCT in BALF and plasma so as well as serum TNF-α,IL-6 and IL-8 were monitored before intervention and seven days later. Results The level of PCT in BALF and plasma before intervention were statistically higher than normal( t= 2.882、2.657 all P ＜0.01 )while decreased significantly seven days later ( all P ＜ 0.01 ) in study group but fewer change in control group ( all P ＞0.05 ). Levels of TNF-α,IL-6 and IL-8 were statistically higher than normal before intervention( all P ＜ 0.05 ) while decreased significantly seven days later( all P ＜0.01 )in study group but fewer change in control group( all P ＞0.05 ). The mortality of patients was 26.7% ( study group) and 33.3% ( control group) ( all P ＜ 0.05 ) respectively.Conclusion Xuebijing injection could lower the level of PCT in BALP and plasma of patients with ARDS,played the role of antiinflammatory and improving the oxygenation, and could to reduce the mortality of patients.

Key words: 
ARDS;  Bronchoalveolar lavage fluid;  Procalcitonin;  Cytokine;  Xuebijing injection
Desktop and Mobile Web Page Comparison: Characteristics, Trends, and Implications (2013)

The broad proliferation of mobile devices in recent years has drastically changed the means of accessing the World Wide Web. Describing a shift away from the desktop computer era for content consumption, predictions indicate that the main access of web-based content will come from mobile devices. Concurrently, the manner of content presentation has changed as well; web artifacts are allowing for richer media and higher levels of user interaction which is enabled through increasing access networks speeds. This article provides an overview of more than two years of high level web page characteristics by comparing the desktop and mobile client versions. Our study is the first long-term evaluation of differences as seen by desktop and mobile web browser clients. We showcase the main differentiating factors with respect to the number of web page object requests, their sizes, relationships, and web page object caching. We additionally highlight long-term trends and discuss their future implications.
Modern Machines for Dry Size Reduction in Fine Size Range. (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModern Machines for Dry Size Reduction in Fine Size Range.C. E. BerryCite this: Ind. Eng. Chem. 1946, 38, 7, 672–678Publication Date (Print):July 1, 1946Publication History Published online1 May 2002Published inissue 1 July 1946https://pubs.acs.org/doi/10.1021/ie50439a011https://doi.org/10.1021/ie50439a011research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Comparative study of various backup and monitoring techniques (2015)

With the rapid growth of data amount, it is very crucial to reduce the storage space that data occupies and the bandwidth consumption during network transmission. As an important means of information security, data backup technology has attained increasing attention. This paper proposes the types of data backup and a comparative study of the techniques available for data backup with their pros and cons.
Interstitial flow influences direction of tumor cell migration through competing mechanisms (2011)

Interstitial flow is the convective transport of fluid through tissue extracellular matrix. This creeping fluid flow has been shown to affect the morphology and migration of cells such as fibroblasts, cancer cells, endothelial cells, and mesenchymal stem cells. A microfluidic cell culture system was designed to apply stable pressure gradients and fluid flow and allow direct visualization of transient responses of cells seeded in a 3D collagen type I scaffold. We used this system to examine the effects of interstitial flow on cancer cell morphology and migration and to extend previous studies showing that interstitial flow increases the metastatic potential of MDA-MB-435S melanoma cells [Shields J, et al. (2007) Cancer Cell 11:526-538]. Using a breast carcinoma line (MDA-MB-231) we also observed cell migration along streamlines in the presence of flow; however, we further demonstrated that the strength of the flow as well as the cell density determined directional bias of migration along the streamline. In particular, we found that cells either at high seeding density or with the CCR-7 receptor inhibited migration against, rather than with the flow. We provide further evidence that CCR7-dependent autologous chemotaxis is the mechanism that leads to migration with the flow, but also demonstrate a competing CCR7-independent mechanism that causes migration against the flow. Data from experiments investigating the effects of cell concentration, interstitial flow rate, receptor activity, and focal adhesion kinase phosphorylation support our hypothesis that the competing stimulus is integrin mediated. This mechanism may play an important role in development of metastatic disease.
Studies on Iejimalide B: Preparation of the Seco Acid and Identification of the Molecule's “Achilles Heel” (2006)

Limitations of models in total synthesis are illustrated by a study towards the potent cytotoxic macrolide iejimalide B. Although the Yamaguchi protocol allowed for the esterification of elaborate segments, attempted macrolactonization of the seco acid met with failure (see scheme, Boc= tert-butyloxycarbonyl). The assembly of the seco acid involves some of the most advanced applications of the Julia olefination known to date.
The Neuropathology of a Chromosome 17-Linked Autosomal Dominant Parkinsonism and Dementia (“Pallido-Ponto-Nigral Degeneration”) (1998)

A group of similar autosomal dominant hereditary neurodegenerative disorders have been linked to chromosome 17 in thirteen kindreds. One of these disorders, known as pallido-ponto-nigral degeneration (PPND), is characterized by extensive degeneration of the globus pallidus and substantia nigra as well as accumulation of abnormally phosphorylated tau proteins. The authors now present comprehensive data on the cellular and molecular pathology of PPND, allowing its classification among chromosome 17-linked neurodegenerative disorders as well as its classification among sporadic and other familial tauopathies. First, we showed that PPND is characterized by abundant ballooned neurons in neocortical and subcortical regions as well as by tau-rich inclusions in the cytoplasm of neurons and oligodendroglia morphologically similar to those seen in corticobasal degeneration (CBD), but in a distribution pattern resembling progressive supranuclear palsy (PSP). Second, we demonstrated that antibodies to phosphorylation-independent (Alz50, 133, 304, Tau-2, T-46) as well as phosphorylation-dependent (AT8, PHF-6, 12E8, PHF-1, T3P, pS422) epitopes in human tau proteins stain these glial and neuronal inclusions as intensely as they stain CBD or PSP inclusions. Third, we probed PPND brain by Western blots using some of the same anti-tau antibodies to reveal 2 tau immunobands with molecular weights of 69 kD and 64 kD in gray and white matter extracts, as reported for both PSP and CBD. Finally, electron microscopy showed that these abnormal tau proteins formed flat twisted ribbons with a maximum diameter of 20 nanometers (nm) and a periodicity of about 200 nm, resembling those reported in CBD. Based on this, we conclude that PPND is a hereditary neurodegenerative disorder characterized by neuronal and glial tau-rich inclusions formed from aggregated filaments and hyperphosphorylated tau proteins and, hence, can be subcategorized into the tauopathy group of chromosome 17-linked neurodegenerative disorders. Further, since the morphologic and biochemical lesions of PPND overlap with those seen in sporadic CBD and PSP, we speculate that these disorders share common pathogenetic mechanisms.
Activation of the leu-500 promoter by adjacent transcription (1994)

The leu-500 mutation is an A-to-G point mutation in the -10 region of the promoter controlling the leuABCD operon of Salmonella typhimurium. Suppression of the leu-500 mutation in an S. typhimurium topA mutant has demonstrated the functional dependency of this mutated promoter on negative supercoiling. A plasmid bearing a minimal leu-500 promoter region (positions -80 to +87) failed to restore its expression in the S. typhimurium topA mutant. We showed that transcription-mediated local negative supercoiling can activate the leu-500 promoter on a plasmid. The coupled transcription and translation process is required for this activation, but peptide-mediated membrane anchorage may not be involved in this activation. Although the effect of negative supercoiling generated during transcription away from the promoter is limited to a short distance of 250 bp, it can activate the negative-supercoiling-dependent leu-500 promoter from positions either 5' or 3' of the leu-500 promoter. In the presence of a parallel-oriented lac promoter which transcribed away from the 3' end of the leu-500 promoter, transcriptional activation of the leu-500 promoter is a strong indication of cooperativity during the transcriptional initiation process.