gebhart/patrepeval huggingface dataset:
SOX2 Is the Determining Oncogenic Switch in Promoting Lung Squamous Cell Carcinoma from Different Cells of Origin (2016)

Lung squamous cell carcinoma (LSCC) is a devastating malignancy with no effective treatments, due to its complex genomic profile. Therefore, preclinical models mimicking its salient features are urgently needed. Here we describe mouse models bearing various combinations of genetic lesions predominantly found in human LSCC. We show that SOX2 but not FGFR1 overexpression in tracheobronchial basal cells combined with Cdkn2ab and Pten loss results in LSCC closely resembling the human counterpart. Interestingly, Sox2;Pten;Cdkn2ab mice develop LSCC with a more peripheral location when Club or Alveolar type 2 (AT2) cells are targeted. Our model highlights the essential role of SOX2 in commanding the squamous cell fate from different cells of origin and represents an invaluable tool for developing better intervention strategies.
Genome Sequence of the Shiga Toxin-Producing Escherichia coli Strain NCCP15657 (2012)

Shiga toxin-producing Escherichia coli causes bloody diarrhea and hemolytic-uremic syndrome and serious outbreaks worldwide. Here, we report the draft genome sequence of E. coli NCCP15657 isolated from a patient. The genome has virulence genes, many in the locus of enterocyte effacement (LEE) island, encoding a metalloprotease, the Shiga toxin, and constituents of type III secretion.
Impact of Swirl Flow on the Penetration Behaviour and Cooling Performance of a Starter Cooling Film in Modern Lean Operating Combustion Chambers (2014)

An experimental and numerical study is presented that deals with the impact of the swirled hot gas main flow on the penetration behaviour and cooling performance of a starter cooling film. Within modern combustion chambers designed for lean combustion the whole fuel/air mixing process is done by the fuel injectors without any additional mixing ports. Typically swirl stabilization is used within this kind of combustion chambers. The swirl flow interacts in a particular way with near wall cooling flows like starter cooling films which assure a proper wall cooling near the fuel injector. Experiments without combustion show the impact of the swirled main flow on the stability of the starter cooling film. Thermal analyses reveal a reduced cooling performance of the starter film near the stagnation area of the swirl flow. Laser optical measurement techniques reveal a significant reduced penetration of the starter cooling film close to the stagnation area. Numerical simulations show the reason for the reduced starter film performance in areas which cannot be accessed by optical measurement techniques. Based on experimental and numerical data different adaptive hole geometries where tested in combination with heat shield ribs in order to improve the starter film cooling performance. Results show that the combined application of heat shield ribs and adaptive cooling holes stabilize the starter cooling film and lead to a homogenous cooling performance.
SiO2/c-Si Bilayer Electron-Beam Resist Process for Nano-Fabrication (1996)

We have developed an SiO 2 /c-Si bilayer electron beam resist process in order to overcome the problems encountered in our previously developed SiO 2 /poly-Si resist system. The process parameters which include the electron beam exposure conditions, thicknesses of resist layers, etching of SiO 2 and c-Si by using buffered HF solution and NMD-3 solution, respectively, are optimized. The developed SiO 2 /c-Si EB resist system is used to produce a suspended mask structure with an opening of 12 nm width for the double angle deposition of Ti for our proposed ultrasmall metal-insulator-metal tunnel junction fabrication process. We have also demonstrated the successful lift-off of inorganic resist by removing underlying c-Si layer of 40 ×40 µ m 2 area using NMD-3 solution at 70° C, leaving an array of isolated Ti–TiO x –Ti dots, each having few hundred nm 2 area, on the substrate.
Photo-catalytic Degradation on B-, C-, N-, and F Element co-doped TiO 2 under Visible-light Irradiation (2010)

In this study, boron, carbon, nitrogen and fluorine co-doped photocatalysts using tetraethylammonium tetrafluoroborate (TEATFB) have been prepared by different heat treatment temperatures to decrease the band gap. To explore the visible light photocatalytic activity of the novel low‐zband gap photocatalyst, the removal of two dyes was investigated, namely, acridine orange and rhodamine B. XRD patterns demonstrate that the samples calcined at temperatures up to 800 clearly show anatase peaks. The XPS results show that all the doped samples contain N, C, B and F elements and the doped shows the shift in the band gap transition down to 2.98 eV as UV-DRS results. In these UV-Vis results, photocatalytic activity of the doped is 1.61 times better than undoped . Specially, excellent photoactivity results were obtained in the case of samples treated at 700 .
Experimental polarization state tomography using photon counting polarimeters (2006)

We report on the implementation of a photon counting polarimeter based on a scheme known to be optimal for obtaining the polarization vector of ensembles of spin-1/2 quantum systems. We show how to use this polarimeter to estimate the complete polarization state for generic multi-photon states. State reconstruction using the polarimeter is illustrated by actual measurements on prepared ensembles of one- and two-photon systems. The rate at which the estimated polarization state converges to an asymptote state is also measured and presented.
Feasibility Analysis of the Parametric Response Map as an Early Predictor of Treatment Efficacy in Head and Neck Cancer (2015)

Parametric response mapping of MR perfusion biomarkers could potentially guide treatment modification in patients with predicted treatment failure. Larger studies are needed to determine whether parametric response map analysis or percentage signal change in these perfusion parameters is the stronger predictor of survival.
Electrical percolation threshold of carbon black in a polymer matrix and its application to antistatic fibre (2019)

In this study, using three types of resins (each with unique material properties) as a matrix, and carbon black (CB) as a conductive additive, conductive fibres were fabricated through a melt-spinning process. An examination of the electrical conductivity revealed that a CB/polyethylene terephthalate (PET) composite had a low percolation value of 0.58 wt%, and thus the highest conductivity of the three resin types. These results indicate that CB/PET fibres could be used to manufacture antistatic fabrics.
Identification of factors required for intracellular survival of Pseudomonas aeruginosa (P3146) (2013)

Abstract Antibiotic resistance is becoming a greater threat to combating bacterial infections. Pathways directly responsible for infection, such as those involved in virulence or immune evasion, are likely to be good targets for novel approaches to treating infection; however, these approaches are currently not being pursued due to the lack of understanding of the requirements for bacterial survival within the host. Pseudomonas aeruginosa (PsA) is one of the most virulent opportunistic human pathogens and is often highly resistant to antibiotic therapy. Although it is traditionally considered an extracellular pathogen, PsA has been shown to invade and survive inside host cells. We hypothesize that this ability to survive intracellularly allows bacteria to become antibiotic insensitive, leading to the formation of reservoirs for recurrent infections. We have developed an in vitro infection model where we have identified genes required for intracellular survival in epithelial cells. We have also found strain specificity among clinical isolates in the kinetics of survival and in their ability to become antibiotic insensitive, suggesting a genetic basis for these differences. We are screening a PsA mutant library to find factors involved in intracellular survival that could be the basis for the development of novel anti-infectives.
Replacement of human sight-is it possible (1989)

Pioneering work by G.S. Brindley and W.S. Lewin (1968), and W.H. Dobelle (1974) laid the foundation of technical feasible visual prosthesis. The technique is simple in concept, and image is divided into an array of small elements or pixels. The number of pixels is reduced to the number of phosphenes made available by implantation of an array of electrodes on the surface of the visual cortex. The position of these phosphenes have been previously mapped in the visual field. There are, however, a number of problems to surmount; the minimum number of electrodes required for a useable image, implant power, implant packaging and the construction of the electrodes. The present author addresses these problems and describes the prostheses being designed and constructed at the Midland Centre for Neurosurgery. >
ChemInform Abstract: Synthesis of 11‐Amino‐Substituted 6,8‐Dimethyl‐12H‐(1)benzo(5,6) thiopyrano(2,3‐c)quinolin‐12‐ones as Benzo Analogues of Lucanthone. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An integrated DC current regulator with high EMI suppression (2007)

This paper presents an integrated DC current regulator using resistive trimming, which provides a high degree of immunity against conducted electromagnetic interference (EMI). While classic topologies generate erratic bias currents the moment EMI is injected into the circuit, this new topology continues to deliver the same reference DC current, whether or not EMI is present.
Mapping the deformability of natural and designed cellulosomes in solution (2022)

Our data quantifies variability of form and compactness of cellulosomal components in solution and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action.
Disposable shaker flasks (1963)

Abstract A disposable plastic tetrahedron bag is described which is suitable for holding a 50 ml. culture on a shaker table. Bags can be made out of polypropylene or Teflon and they are quite simple and inexpensive. The tetrahedrons make excellent use of the shaker table space and they give a threefold increase in aeration efficiency over Erlenmeyer flasks.
Endothelin‐1‐ and isoproterenol‐induced differential protein expression and signaling pathway in HL‐1 cardiomyocytes (2010)

It is well known that the two chemical compounds endothelin-1 (ET-1) and isoproterenol (ISO) can individually induce cardiac hypertrophy through G protein-coupled receptors in cardiomyocytes. However, the cardiac hypertrophy signaling pathway activated by ET-1 and ISO is not well defined. Therefore, we investigated the protein expression profile and signaling transduction in HL-l cardiomyocyte cells treated with ET-1 and ISO. Following separation of the cell lysates by using 2-DE and silver staining, we identified 16 protein spots that were differentially expressed as compared to the controls. Of these 16 spots, three changed only after treatment with ET-1, whereas four changed only after treatment with ISO, suggesting that these two stimuli could induce different signaling pathways. In order to reveal the differences between ET-1- and ISO-induced signaling, we studied the different events that occur at each step of the signaling pathways, when selected biocomponents were blocked by inhibitors. Our results indicated that ET-1 and ISO used different pathways for phosphorylation of glycogen synthase kinase-3β (GSK3β). ET-1 mainly used the mitogen-activated protein kinase and phosphatidylinositol-3-kinase/AKT pathways to activate GSK3β, whereas under ISO stimulation, only the phosphatidylinositol-3-kinase/AKT pathway was required to trigger the GSK3β pathway. Furthermore, the strength of the GSK3β signal in ISO-induced cardiac hypertrophy was stronger than that in ET-1-induced cardiac hypertrophy. We found that these two agonists brought about different changes in the protein expression of HL-1 cardiomyocytes through distinct signaling pathways even though the destination of the two signaling pathways was the same.
Apoptosis of hair follicle cells during doxorubicin-induced alopecia in rats. (1996)

Alopecia is a common side effect of cancer chemotherapy, and to date, little progress has been made in alopecia prevention or treatment. The present studies were undertaken to topographically localize the site of injury in the hair follicle after doxorubicin (DXR) administration and to investigate the mechanism of DXR-induced alopecia. Tissue samples of head and proximal neck skin obtained from newborn rats treated with DXR were histologically examined by light and electron microscopy and stained by the terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling method. Light microscopy revealed pyknotic cells in the matrix and in the upper bulb and a decrease in the number of mitotic cells. Terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate-digoxigenin nick-end labeling analysis evidenced cells with nuclear staining indicative of apoptosis, as confirmed by ultrastructural analysis. Kinetics studies indicated that even a single DXR treatment induced apoptosis and a decrease in mitotically active cells. Our data show that DXR treatment induces injury in a cell subset localized in the hair matrix. The successful prevention of drug-induced alopecia in patients may depend on the selective protection of these cells of the hair follicle.
Furazan Oxides. IV. Extensions of the Scope of the Haloalkoxy Substitution Reaction1a,b (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFurazan Oxides. IV. Extensions of the Scope of the Haloalkoxy Substitution Reaction1a,bFrank B. Mallory, Clelia S. Wood, and Barbara M. HurwitzCite this: J. Org. Chem. 1964, 29, 9, 2605–2609Publication Date (Print):September 1, 1964Publication History Published online1 May 2002Published inissue 1 September 1964https://pubs.acs.org/doi/10.1021/jo01032a029https://doi.org/10.1021/jo01032a029research-articleACS PublicationsRequest reuse permissionsArticle Views231Altmetric-Citations32LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Optical Solutions to Improve PDM-QPSK Resilience Against Cross-Channel Nonlinearities: A Comparison (2011)

We compare by simulation different optical methods to improve the resilience of coherent 112-Gb/s polarization-division multiplexing (PDM)-quadrature phase-shift keying (QPSK) wavelength-division-multiplexing (WDM) transmissions against cross-channel nonlinearities. Such methods consist of 1) increasing the line group velocity dispersion (GVD), or 2) the line polarization-mode dispersion (PMD), or 3) inserting in-line cross-phase modulation (XPM) suppressors. Such methods are tested using nonreturn-to-zero (NRZ), aligned return-to-zero (aRZ), and interleaved RZ (iRZ) pulse formats. We show that the nonlinearity-mitigating effect underlying all three methods is an increase of the interchannel decorrelation, obtained by either increasing walk-off (methods 1 and 3) or by depolarizing the WDM channels (method 2). Interchannel decorrelation improves performance and reduces the difference among the three pulse formats. We find that the best performance is achieved by iRZ-PDM-QPSK in a dispersion-managed link with an XPM suppressor at each span.
Impact of percent positive biopsy cores on cancer-specific mortality for patients with high-risk prostate cancer. (2018)

78 Background: A high percent positive biopsy cores (PBC), typically dichotomized at ≥50%, is prognostic of worse cancer-specific outcomes for patients with low- and intermediate-risk prostate cancer. The prognostic value of ≥50% PBC for patients with high-risk disease is poorly understood. We examined the association between ≥50% PBC and prostate cancer-specific mortality (PCSM) for patients with high-risk prostate cancer. Methods: We identified 7,569 men from the Surveillance, Epidemiology, and End Results program who were diagnosed with high-risk prostate cancer (Gleason 8-10, prostate-specific antigen &gt; 20 ng/mL, or cT3-T4 stage without evidence of nodal or metastatic disease) in 2010 or 2011 and had 6-24 cores sampled at biopsy. Multivariable Fine and Gray competing risks regression was utilized to examine the association between ≥50% PBC and PCSM, with adjustments for sociodemographic and clinicopathologic factors. Results: Median follow-up was 3.8 years (interquartile range 3.3-4.3 years). 56.2% of patients (4,253) had ≥50% PBC. The 4-year unadjusted cumulative incidences of PCSM were 2.0% (95% confidence interval [CI] 1.5-2.6%) and 5.6% (95% CI 4.9-6.4%) for patients with &lt; 50% and ≥50% PBC, respectively. On multivariable analysis, the presence of ≥50% PBC was associated with a significantly higher risk of PCSM (adjusted hazard ratio [AHR] 1.95, 95% CI 1.43-2.66, P&lt; 0.001). On subgroup analysis, ≥50% PBC was associated with a significantly higher risk of PCSM only for cT1-T2 disease (AHR 2.21, 95% CI 1.59-3.07, P&lt; 0.001) but not cT3-T4 disease (AHR 0.77, 95% CI 0.33-1.81, P= 0.547), with a significant interaction ( P interaction = 0.012). Conclusions: In this large, contemporary cohort of patients with high-risk prostate cancer, ≥50% PBC was independently associated with a two-fold increased risk of PCSM for patients with cT1-T2, but not cT3-T4, tumors. Percent PBC should be used to routinely risk stratify men with high-risk disease and identify patients who may benefit from intensification of therapy, such as adding docetaxel or abiraterone to radiotherapy with androgen deprivation therapy, to optimize cancer-specific outcomes.
Mask the Bias: Improving Domain-Adaptive Generalization of CTC-Based ASR with Internal Language Model Estimation (2023)

End-to-end ASR models trained on large amount of data tend to be implicitly biased towards language semantics of the training data. Internal language model estimation (ILME) has been proposed to mitigate this bias for autoregressive models such as attention-based encoder-decoder and RNN-T. Typically, ILME is performed by modularizing the acoustic and language components of the model architecture, and eliminating the acoustic input to perform log-linear interpolation with the text-only posterior. However, for CTC-based ASR, it is not as straightforward to decouple the model into such acoustic and language components, as CTC log-posteriors are computed in a non-autoregressive manner. In this work, we propose a novel ILME technique for CTC-based ASR models. Our method iteratively masks the audio timesteps to estimate a pseudo log-likelihood of the internal LM by accumulating log-posteriors for only the masked timesteps. Extensive evaluation across multiple out-of-domain datasets reveals that the proposed approach improves WER by up to 9.8% and OOV F1-score by up to 24.6% relative to Shallow Fusion, when only text data from target domain is available. In the case of zero-shot domain adaptation, with no access to any target domain data, we demonstrate that removing the source domain bias with ILME can still outperform Shallow Fusion to improve WER by up to 9.3% relative.
Editorial Peptides and Proteins View by Nanopores: Experiments, Simulations and Theory (2014)

International audience
Effects of Certain Antiallergic Drugs on Experimental Conjunctivitis in Guinea Pigs. (1995)

Effects of certain antiallergic drugs on experimental conjunctivitis were studied with guinea pigs. Chlorpheniramine, ketotifen and levocabastine were effective in inhibiting histamine- and antigen-induced conjunctivitis in guinea pigs. By contrast, amlexanox was only effective in inhibiting antigen-induced conjunctivitis. Topical application of antigen released 46.5 +/- 3.8% of histamine from the conjunctiva in sensitized guinea pigs. Both levocabastine and amlexanox were effective in inhibiting conjunctival histamine release induced by antigen application. Lacrimal histamine contents were also increased after challenge. The increase in the histamine content of tears was inhibited by pretreatment with levocabastine and amlexanox, but no significant effect was observed with chlorpheniramine and ketotifen. From these findings, it is concluded that certain antiallergic drugs, but not amlexanox, exhibited potent inhibition on experimental conjunctivitis in guinea pigs. In addition, it has been established that measurement of histamine in the conjunctiva and tears as well as observation of conjunctivitis syndromes are useful for evaluating the effectiveness of antiallergic drugs on various kinds of allergic conjunctivitis in clinical situations.
Rapidly scanning Fourier transform spectrometer based on a GHz repetition rate Yb-fiber laser pair (2009)

We demonstrate a rapidly scanning all-fiber Fourier transform spectrometer based on a temporal scanning all-optical delay line constructed with two mode-locked 1-GHz Yb fiber lasers. An effective mirror scan rate of 7.5 km/s is achieved.
A Methodology for Texture Feature-based Quality Assessment in Nucleus Segmentation of Histopathology Image (2017)

As image scanning technologies advance, large volumes of whole-slide tissue images will be available for research and clinical use. Efficient approaches for the assessment of quality and robustness of output from computerized image analysis workflows will become increasingly critical to extracting useful quantitative information from tissue images. Our work demonstrates the feasibility of machine-learning-based semi-automated techniques to assist researchers and algorithm developers in this process.