gebhart/patrepeval huggingface dataset:
The HA and NS Genes of Human H5N1 Influenza A Virus Contribute to High Virulence in Ferrets (2010)

Highly pathogenic H5N1 influenza A viruses have spread across Asia, Europe, and Africa. More than 500 cases of H5N1 virus infection in humans, with a high lethality rate, have been reported. To understand the molecular basis for the high virulence of H5N1 viruses in mammals, we tested the virulence in ferrets of several H5N1 viruses isolated from humans and found A/Vietnam/UT3062/04 (UT3062) to be the most virulent and A/Vietnam/UT3028/03 (UT3028) to be avirulent in this animal model. We then generated a series of reassortant viruses between the two viruses and assessed their virulence in ferrets. All of the viruses that possessed both the UT3062 hemagglutinin (HA) and nonstructural protein (NS) genes were highly virulent. By contrast, all those possessing the UT3028 HA or NS genes were attenuated in ferrets. These results demonstrate that the HA and NS genes are responsible for the difference in virulence in ferrets between the two viruses. Amino acid differences were identified at position 134 of HA, at positions 200 and 205 of NS1, and at positions 47 and 51 of NS2. We found that the residue at position 134 of HA alters the receptor-binding property of the virus, as measured by viral elution from erythrocytes. Further, both of the residues at positions 200 and 205 of NS1 contributed to enhanced type I interferon (IFN) antagonistic activity. These findings further our understanding of the determinants of pathogenicity of H5N1 viruses in mammals.
Automated Quality Monitoring in the Call Center with ASR and Maximum Entropy (2006)

This paper describes an automated system for assigning quality scores to recorded call center conversations. The system combines speech recognition, pattern matching, and maximum entropy classification to rank calls according to their measured quality. Calls at both end of the spectrum are flagged as "interesting" and made available for further human monitoring. In this process, pattern matching on the ASR transcript is used to answer a set of standard quality control questions such as "did the agent use courteous words and phrases," and to generate a question-based score. This is interpolated with the probability of a call being "bad," as determined by maximum entropy operating on a set of ASR-derived features such as "maximum silence length" and the occurrence of selected n-gram word sequences. The system is trained on a set of calls with associated manual evaluation forms. We present precision and recall results from IBM's North American Help Desk indicating that for a given amount of listening effort, this system triples the number of bad calls that are identified, over the current policy of randomly sampling calls
UVO Challenge on Video-based Open-World Segmentation 2021: 1st Place Solution (2021)

In this report, we introduce our (pretty straightforard) two-step "detect-then-match" video instance segmentation method. The first step performs instance segmentation for each frame to get a large number of instance mask proposals. The second step is to do inter-frame instance mask matching with the help of optical flow. We demonstrate that with high quality mask proposals, a simple matching mechanism is good enough for tracking. Our approach achieves the first place in the UVO 2021 Video-based Open-World Segmentation Challenge.
Les orthoréovirus : virus orphelins ou pathogènes chez l’homme ? (2008)

Les orthoreovirus, virus a ARN double brin segmente en dix fragments, representent les virus les plus repandus dans la nature. Trois principaux serotypes sont connus, nommes 1, 2 et 3. La denomination « reovirus » est l’acronyme de « respiratory enteric orphan virus », expression soulignant leur origine respiratoire et intestinale et le fait qu’ils n’ont pu etre relies de facon certaine a aucune maladie clinique bien definie. Neanmoins, des souches d’orthoreovirus ont ete isolees de divers cas de maladies symptomatiques chez l’homme, a savoir des maladies du systeme nerveux central telles que les encephalites et meningites entrainant parfois la mort du patient. Ces differents cas indiquent que les orthoreovirus pourraient etre des agents pathogenes a l’origine de maladies graves. L’infection par les orthoreovirus chez les animaux provoque egalement diverses pathologies. En effet, en fonction de la voie d’inoculation et du serotype de la souche inoculee, des encephalites ou des hepatites peuvent etre observees. Les segments d’ARN M2 et S1 semblent etre impliques dans le phenomene de neurovirulence et sont a la base de mecanismes cellulaires tels que l’entree du virus, la replication virale et l’apoptose. Toutefois, les mecanismes de virulence restent complexes.
Experimental Validation of a Single DC Bus Cascaded H-Bridge Multilevel Inverter for Multistring Photovoltaic Systems (2016)

For large-scale photovoltaic (PV) systems, the multistring configuration is becoming more and more attractive compared with the classical central inverter, since it results in better energy yield by realizing distributed maximum power point tracking. Among the existing solutions, an attractive topology consists in a single dc bus bar collector cascaded H-bridge (CHB) inverter. Through the use of a single dc bus bar collector, the CHB inverter presents inherent balanced operation while the multistring PV-system is fully decoupled from the grid-tie inverter. This paper proposes the experimental validation of this structure on a reduced-size single-phase laboratory prototype. Results confirm the interest of the proposed PV multistring architecture.
Pre-Estimation for Better Initial Guesses (2004)

Fast, assured convergence of iterative identification methods is important in many on-line applications, including systems that exploit indirect measurements, diagnostics, and model-based control. The transient response of a system can often be mapped directly to an estimate of the system model parameters. This initial estimate, or pre-estimate, can be evaluated in fixed time and may greatly accelerate subsequent iterative system identification procedures. A pre-estimation structure is developed and demonstrated with examples including single-tone frequency estimation and induction motor parameter identification.
Radiography of Implantable Devices (2021)

The pulse generator manufacturer and model can usually be identified from the chest radiograph. The chest X-ray remains an important tool in the preoperative and postoperative evaluation of a pacemaker, implantable cardioverter-defibrillator (ICD), or cardiac resynchronization therapy system. Additionally, the chest radiograph is essential when assessing the integrity of a cardiac implantable electronic device. If the radiograph has been stored digitally it is usually possible to manipulate the images to better delineate the leads. Currently used infrequently, but still functional in some patients, epicardial ICD systems usually have easily recognizable patches positioned over the heart, as well as epicardial or transvenous pacing leads for sensing and pacing purposes. ICD leads most commonly have an active fixation mechanism, but may be passive, and like pacing leads should have a gentle redundancy.
Development of an efficient marker‐free soybean transformation method using the novel bacterium Ochrobactrum haywardense H1 (2022)

We have discovered a novel bacterium, Ochrobactrum haywardense H1 (Oh H1), which is capable of efficient plant transformation. Ochrobactrum is a new host for Agrobacterium-derived vir and T-DNA-mediated transformation. Oh H1 is a unique, non-phytopathogenic species, categorized as a BSL-1 organism. We engineered Oh H1 with repurposed Agrobacterium virulence machinery and demonstrated Oh H1 can transform numerous dicot species and at least one monocot, sorghum. We generated a cysteine auxotrophic Oh H1-8 strain containing a binary vector system. Oh H1-8 produced transgenic soybean plants with an efficiency 1.6 times that of Agrobacterium strain AGL1 and 2.9 times that of LBA4404Thy-. Oh H1-8 successfully transformed several elite Corteva soybean varieties with T0 transformation frequency up to 35%. In addition to higher transformation efficiencies, Oh H1-8 generated high-quality, transgenic events with single-copy, plasmid backbone-free insertion at frequencies higher than AGL1. The SpcN selectable marker gene is excised using a heat shock-inducible excision system resulting in marker-free transgenic events. Approximately, 24.5% of the regenerated plants contained only a single copy of the transgene and contained no vector backbone. There were no statistically significant differences in yield comparing T3 null-segregant lines to wild-type controls. We have demonstrated that Oh H1-8, combined with spectinomycin selection, is an efficient, rapid, marker-free and yield-neutral transformation system for elite soybean.
SLADS-Net: Supervised Learning Approach for Dynamic Sampling using Deep Neural Networks (2018)

In scanning microscopy based imaging techniques, there is a need to develop novel data acquisition schemes that can reduce the time for data acquisition and minimize sample exposure to the probing radiation. Sparse sampling schemes are ideally suited for such applications where the images can be reconstructed from a sparse set of measurements. In particular, dynamic sparse sampling based on supervised learning has shown promising results for practical applications. However, a particular drawback of such methods is that it requires training image sets with similar information content which may not always be available. In this paper, we introduce a Supervised Learning Approach for Dynamic Sampling (SLADS) algorithm that uses a deep neural network based training approach. We call this algorithm SLADS-Net. We have performed simulated experiments for dynamic sampling using SLADS-Net in which the training images either have similar information content or completely different information content, when compared to the testing images. We compare the performance across various methods for training such as least-squares, support vector regression and deep neural networks. From these results we observe that deep neural network based training results in superior performance when the training and testing images are not similar. We also discuss the development of a pre-trained SLADS-Net that uses generic images for training. Here, the neural network parameters are pre-trained so that users can directly apply SLADS-Net for imaging experiments.
Supplementary Figure 3 from <i>TMPRSS2-ERG</i> Status Is Not Prognostic Following Prostate Cancer Radiotherapy: Implications for Fusion Status and DSB Repair (2023)

&lt;p&gt;Supplementary Figure 3 - PDF file 164K, A) Univariate Kaplan-Meier plots of biochemical relapse-free rates (bRFR) according to PSA levels in the aCGH-cohort. B) Univariate Kaplan-Meier plots of biochemical relapse-free rates (bRFR) according to T-category in the aCGH-cohort. C) Univariate Kaplan-Meier plots of biochemical relapse-free rates (bRFR) according to Gleason score in the aCGH-cohort. D) Univariate Kaplan-Meier plots of biochemical relapse-free rates (bRFR) according PSA levels in the IHC-cohort. E) Univariate Kaplan-Meier plots of biochemical relapse-free rates (bRFR) according to T category in the IHC-cohort. F) Univariate Kaplan-Meier plots of biochemical relapse-free rates (bRFR) according to Gleason score in the IHC-cohort&lt;/p&gt;
Hemonectin mediates adhesion of engrafted murine progenitors to a clonal bone marrow stromal cell line from Sl/Sld mice (1991)

Mutant Sl/Sld mice exhibit decreased marrow hematopoiesis. The defect is known to reside in the marrow microenvironment of these animals, which is reproduced in vitro by primary marrow explants as well as by cloned marrow stromal cell lines. Bone marrow progenitor cells are incapable of adhering to primary Sl/Sld stromal cells or cloned stromal cell lines derived from them to form cobblestone-islands and proliferate. The role of hemonectin, a marrow-specific adhesion protein in the defective hematopoiesis of the Sl/Sld mice, was studied. Indirect immunoperoxidase staining of marrow in situ from Sl/Sld mice showed little specific staining while specific staining was seen in a pericellular distribution in marrow from +/+ mice. Hemonectin expression in several cloned stromal cell lines from Sl/Sld mice was compared by immunoblotting with that in cloned stromal cell lines from normal +/+ littermates. Cell line Sld3, which has the least hematopoiesis supportive capacity in vitro, showed no detectable hemonectin by immunoblotting, while Sld1 and Sld2 showed detectable but greatly reduced amounts compared with normal +/+ 2.4, GBI/6, and D2XRII. Confluent cultures incubated with purified hemonectin and engrafted with enriched progenitors showed a significant increase in the cumulative number of cobbleston-islands and day 14 spleen colony-forming units (CFU-s) forming progenitors (39.15 +/- 3.6/dish; 16.3 +/- 3.1/dish, respectively), compared with untreated Sld3 cultures (cobblestone-islands 8.1 +/- 3.6/dish; CFU-s forming progenitors 8.8 +/- 0.05/dish). Hemonectin-mediated progenitor cell binding to the Sld3 stromal cells was specifically inhibited by antihemonectin but not by preimmune serum. These data support the role of hemonectin in early progenitor-stromal cell interactions.
Figure S1 from Vaccination with Designed Neopeptides Induces Intratumoral, Cross-reactive CD4<sup>+</sup> T-cell Responses in Glioblastoma (2023)

&lt;p&gt;Schematic outline of the personalized peptide vaccination. (A) Timeline of clinical events for a patient with glioblastoma in whom we applied a highly personalized peptide vaccination. I. Vaccine peptide design. Surgically resected primary glioblastoma and PBMCs were collected. Somatic mutants and over-/highly expressed genes in glioblastoma were identified as TSAs and TAAs by WES and RNA-seq, and the HLA genotype were identified with PBMCs by DNA sequencing. Potential vaccine peptides were predicted and selected from TSAs and TAAs based on HLA binding prediction. Peptide cocktails containing ~25 peptides for HLA class I or II molecules were prepared for vaccination. II. Peptide cocktail vaccination and testing. The patient was s.c. vaccinated with the peptide cocktails, and Imiquimod or XS15 + MontanideTM were used as the adjuvant. Meanwhile, the patient received treatment with pembrolizumab and bevacizumab. No dexamethasone was given throughout the periods of vaccination. PBMCs were collected after vaccination at the indicated time points and tested with vaccine peptides to examine the effect of immunotherapy. Surgically resected recurrent glioblastoma was collected after four vaccinations, and tumor-infiltrating lymphocytes (TILs) were isolated and tested with vaccine peptides. (B) HLA genotypes of the patient with glioblastoma, including HLA-A, HLA-B, HLA-DR, HLA-DP, and HLA-DQ alleles. n.a. indicates not available.&lt;/p&gt;
Time Delay Estimation via Minimum Entropy (2007)

Time delay estimation (TDE) is a basic technique for numerous applications where there is a need to localize and track a radiating source. The most important TDE algorithms for two sensors are based on the generalized cross-correlation (GCC) method. These algorithms perform reasonably well when reverberation or noise is not too high. In an earlier study by the authors, a more sophisticated approach was proposed. It employs more sensors and takes advantage of their delay redundancy to improve the precision of the time difference of arrival (TDOA) estimate between the first two sensors. The approach is based on the multichannel cross-correlation coefficient (MCCC) and was found more robust to noise and reverberation. In this letter, we show that this approach can also be developed on a basis of joint entropy. For Gaussian signals, we show that, in the search of the TDOA estimate, maximizing MCCC is equivalent to minimizing joint entropy. However, with the generalization of the idea to non-Gaussian signals (e.g., speech), the joint entropy-based new TDE algorithm manifests a potential to outperform the MCCC-based method
Supplementary Table 3 from Phase Ib Study of Buparlisib plus Trastuzumab in Patients with HER2-Positive Advanced or Metastatic Breast Cancer That Has Progressed on Trastuzumab-Based Therapy (2023)

&lt;p&gt;PDF file - 48K, Exposure to buparlisib and trastuzumab (safety set).&lt;/p&gt;
Direct imaging of transient interference in a single-mode waveguide using near-field scanning optical microscopy (2005)

Near-field scanning optical microscopy was used to image transient interference between the guided mode and a leaky mode induced in a single-mode waveguide due to a localized adlayer. The observed field response in the adlayer region as well as the period and decay length of the subsequent interference are in good agreement with beam propagation calculations. The transient interference impacts the element spacing in local evanescent array coupled sensors.
EphB2 stem-related and EphA2 progression-related miRNA-based networks in progressive stages of CRC evolution: clinical significance and potential miRNA drivers (2018)

EphB2 and EphA2 control stemness and differentiation in the intestinal mucosa, but the way they cooperate with the complex mechanisms underlying tumor heterogeneity and how they affect the therapeutic outcome in colorectal cancer (CRC) patients, remain unclear. MicroRNA (miRNA) expression profiling along with pathway analysis provide comprehensive information on the dysregulation of multiple crucial pathways in CRC.Through a network-based approach founded on the characterization of progressive miRNAomes centered on EphA2/EphB2 signaling during tumor development in the AOM/DSS murine model, we found a miRNA-dependent orchestration of EphB2-specific stem-like properties in earlier phases of colorectal tumorigenesis and the EphA2-specific control of tumor progression in the latest CRC phases. Furthermore, two transcriptional signatures that are specifically dependent on the EphA2/EphB2 signaling pathways were identified, namely EphA2, miR-423-5p, CREB1, ADAMTS14, and EphB2, miR-31-5p, mir-31-3p, CRK, CXCL12, ARPC5, SRC.EphA2- and EphB2-related signatures were validated for their expression and clinical value in 1663 CRC patients. In multivariate analysis, both signatures were predictive of survival and tumor progression.The early dysregulation of miRs-31, as observed in the murine samples, was also confirmed on 49 human tissue samples including preneoplastic lesions and tumors. In light of these findings, miRs-31 emerged as novel potential drivers of CRC initiation.Our study evidenced a miRNA-dependent orchestration of EphB2 stem-related networks at the onset and EphA2-related cancer-progression networks in advanced stages of CRC evolution, suggesting new predictive biomarkers and potential therapeutic targets.
Mechanism of substitution of acetone by alkenes in acetonepentacarbonyltungsten(O) (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of substitution of acetone by alkenes in acetonepentacarbonyltungsten(O)Mark Wrighton, George S. Hammond, and Harry B. GrayCite this: J. Am. Chem. Soc. 1971, 93, 23, 6048–6051Publication Date (Print):November 1, 1971Publication History Published online1 May 2002Published inissue 1 November 1971https://pubs.acs.org/doi/10.1021/ja00752a014https://doi.org/10.1021/ja00752a014research-articleACS PublicationsRequest reuse permissionsArticle Views234Altmetric-Citations14LEARN 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
(3,1) Drive PVDF acoustic displacement sensor (1996)

A (3,1) drive piezofilm vibration sensor is introduced. Operated above the lumped element resonance frequency of 600 Hz, the sensor delivers a voltage signal proportional to displacement over the frequency range of 2 kHz to 8 kHz. It is anticipated that the sensor response is flat above 8 kHz, but calibration has not been performed at higher frequencies. The sensor is very sensitive, detecting acoustic displacements as small as 10−5 nm. Because of its simple design the sensor is robust and easy to assemble.
Integrating genomic based information into clinical warfarin (Coumadin) management: an illustrative case report. (2008)

Warfarin is a well established oral anticoagulant for the treatment of thromboembolic disorders. Warfarin therapy is complicated by a narrow therapeutic index and marked inter-individual dose variability with therapeutic doses ranging from 1 mg to 10 mg/day. Recently genetic variation and resultant drug metabolizing polymorphisms have been found to contribute to warfarin dose variability with resultant hemorrhagic or thromboembolic complications. Cytochrome P4502C9 alters the rate of warfarin metabolism and clearance. A second enzyme, Vitamin K Epoxide Reductase Complex (VKORC) binds and reduces Vitamin K which is necessary for activation of clotting Factors II, VII, IX and X. The VKORC1 gene encodes for Vitamin K Epoxide Reductase Complex subunit 1, a key component of VKORC. The combination of physiologic factors (30%), CYP2C9 variations (20%) and VKORC1 variants (25%) accounts for approximately 75% of warfarin dose variability. This illustrative case report demonstrates the clinical importance of this new information. Clinicians need to incorporate these new genomic findings into appropriate management of warfarin dose anticoagulation.
Pilot study of ‘Scissorhands’ technique for gastric endoscopic submucosal dissection using novel gel and endoscopic scissors in a porcine model (with video) (2013)

The combined technique of endoscopic scissors for circumferential incision and viscous gel for submucosal dissection permitted easy, safe and efficient gastric ESD. Electrocautery may be avoided and its consequent adverse events (e.g. perforation).
Scientists on the Spot: A fraction of wisdom on heart failure (2021)

Dr Mahmoud Abdellatif from the Medical University of Graz (Austria), interviews Prof. Carolyn Lam, a Senior Consultant at theNationalHeart Centre Singapore (Singapore). Highlight: In this Onlife interview, Professor Carolyn Lam shares her expertise and major scientific findings on the subject of heart failure with preserved ejection fraction.