gebhart/patrepeval huggingface dataset:
Screening Clinical Cell Products for Replication Competent Retrovirus: The National Gene Vector Biorepository Experience (2018)

Replication-competent retrovirus (RCR) is a safety concern for individuals treated with retroviral gene therapy. RCR detection assays are used to detect RCR in manufactured vector, transduced cell products infused into research subjects, and in the research subjects after treatment. In this study, we reviewed 286 control (n = 4) and transduced cell products (n = 282) screened for RCR in the National Gene Vector Biorepository. The transduced cell samples were submitted from 14 clinical trials. All vector products were previously shown to be negative for RCR prior to use in cell transduction. After transduction, all 282 transduced cell products were negative for RCR. In addition, 241 of the clinical trial participants were also screened for RCR by analyzing peripheral blood at least 1 month after infusion, all of which were also negative for evidence of RCR infection. The majority of vector products used in the clinical trials were generated in the PG13 packaging cell line. The findings suggest that screening of the retroviral vector product generated in PG13 cell line may be sufficient and that further screening of transduced cells does not provide added value.
Anti-Aliased Non-periodic Source Separation (2017)

Summary In wavefield signal apparition, acquisition with periodic variations in source activation parameters shifts all or part of a signal cone out to, e.g., the Nyquist wavenumber, enabling perfect separation of simultaneous-source (sim-source) data in a diamond-shaped region below a certain temporal frequency. Cyclic convolution in the spatial frequency domain can be exploited to separate data with known non-periodic encoding functions. Such a separation comprises a least-squares reconstruction in the frequency-wavenumber (fk) domain. By applying the reconstruction in the S-transform domain and using an exact expression for NMO stretch, it is possible to perform anti-aliased source separation in conjunction with an invertible NMO or when pre-processing renders the encoding time and space-variant.
Integrated Ground-Based and Satellite Remote Sensing of the Earth’s Surface and Atmosphere in East and West Antarctica with Lidar and Radiometric Systems (2022)

We have developed remote ground-based and satellite methods and hardware and software for studying atmospheric aerosols, clouds, and the underlying surface in Eastern and Western Antarctica. The ground-based equipment includes: (1) a CIMEL solar spectrum photometer, which measures the spectrum of solar radiation transmitted and scattered by the atmosphere, (2) a multi-wavelength Raman lidar, which measures the vertical backscatter profile, (3) an albedometer, which measures the spectral albedo of the surface, primarily snow, and (4) a reflectometer, which measures the directional spectral reflectance of snow. The ground-based measurement data were integrated with data from satellite radiometers MODIS or OLCI and the satellite lidar CALIOP. A synergy of the manifold data results in retrieval of various atmosphere and surface characteristics such as the aerosol optical depth, profiles of concentration of the fine and coarse aerosol fractions, spatial distribution of the effective snow grain size, fraction of outcrops, etc.
1472: Factors Predictive of Biopsy-Proven Recurrence Following Radiotherapy for Prostate Cancer (2005)

sequences after gadolinium injection was performed. DCE-MRI slices orientation and thickness was the same as RP specimen sectionning according Stanford protocol. Systematic (10) and lesion directed biopsies were performed. MRI and histologic reconstruction maps allowed morphometric assesment of tumor location, contour, volume, malignant glandular density and Gleason grades. 14 consecutive patients with a diagnostic of cancer at biopsy were evaluated.
Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes (2020)

Anti-CRISPRs (Acrs) are small proteins that inhibit the RNA-guided DNA targeting activity of CRISPR-Cas enzymes. Encoded by bacteriophage and phage-derived bacterial genes, Acrs prevent CRISPR-mediated inhibition of phage infection and can also block CRISPR-Cas-mediated genome editing in eukaryotic cells. To identify Acrs capable of inhibiting <i>Staphylococcus aureus</i> Cas9 (SauCas9), an alternative to the most commonly used genome editing protein <i>Streptococcus pyogenes</i> Cas9 (SpyCas9), we used both self-targeting CRISPR screening and guilt-by-association genomic search strategies. Here we describe three potent inhibitors of SauCas9 that we name AcrIIA13, AcrIIA14, and AcrIIA15. These inhibitors share a conserved N-terminal sequence that is dispensable for DNA cleavage inhibition and have divergent C termini that are required in each case for inhibition of SauCas9-catalyzed DNA cleavage. In human cells, we observe robust inhibition of SauCas9-induced genome editing by AcrIIA13 and moderate inhibition by AcrIIA14 and AcrIIA15. We also find that the conserved N-terminal domain of AcrIIA13-AcrIIA15 binds to an inverted repeat sequence in the promoter of these Acr genes, consistent with its predicted helix-turn-helix DNA binding structure. These data demonstrate an effective strategy for Acr discovery and establish AcrIIA13-AcrIIA15 as unique bifunctional inhibitors of SauCas9.
Feature and distribution normalization schemes for statistical mismatch reduction in reverberant speech recognition (2007)

Reverberant noise has been a major concern in speech recognition systems. Many speech recognition systems, even with state-of-art features, fail to respond to reverberant effects and the recognition rate deteriorates. This paper explores the significance of normalization strategies in reducing statistical mismatches for robust speech recognition in reverberant environment. Most normalization works focused only on ambient noise and have yet been experimented on reverberant noise. In addition, we propose a new approach for the odd order cepstral moment normalization which is computationally more efficient and reduces the convergence rate in the algorithm. The proposed method is experimentally justified and corroborated by the performance of other normalization schemes. The results emphasize the significance of reducing statistical mismatches in feature space for reverberant speech recognition.
High pretilt four-domain twisted nematic liquid crystal display by microrubbing: Process, characterization, and optical simulation (2005)

A microrubbing (μ-rubbing) technique was utilized to create four-domain alignment in a liquid crystal display sample. A small metallic sphere under sufficient load was used to directly rub a homeotropic polyimide alignment layer to create a large surface pretilt angle. We demonstrate a 47-μm linewidth and a variable pretilt angle with respect to the substrate plane for different loads. The homeotropic polyimide surface was μ rubbed in such a way that neighboring alignment regions are rubbed in opposite directions. liquid crystal cells were constructed with two μ-rubbed substrates where the rubbing directions are orthogonal to each other. With this cell configuration we obtained four domains consisting of two left-handed and two right-handed twisted nematic subpixels. We report on the electro-optic performance properties, viewing angle characteristics, the relationship between pretilt angle versus load, and thermal aging study of the four-domain liquid crystal cell. The optical simulations of the liquid crystal director orientation, viewing angle characteristics, and the contrast ratio of the four domains are also presented. The experimental results are in agreement with the simulation results.
An 8-Pole Quazi-Eiliptic Function Filter Realized in 3 Dielectric Resonator Cavities (2005)

An eight-pole quazi-elliptic function filter with two pairs of transmission zeros (8-4) has been synthesized and experimentally realized in two triple-mode and one dual-mode dielectric resonator cavities. This was done by carefully selecting the optimum coupling topology. Subsequently the coupling matrix is generated using computer optimization program without using matrix rotation.
Architectural Considerations When Selecting a Neutral Form for Moving Images (2019)

Current thinking for the creation and distribution of moving images tends to lead to an unwarranted trust of mastering displays. If a mastering display (or projected image) and its ambient surround were to match the end use (as in 14 fl dark surround D-Cinema), then such trust is warranted. However, this is not typically the case in television, where the reference display and its ambient surround are unlikely to match the presentation viewing. Such variation in the presentation may also be part of future cinema presentation [e.g., with light-emitting diode (LED) walls]. This situation begs the question as to the nature of the image that would be mastered and distributed that could take into account the presentation variables in order to deliver a reasonable rendition of the mastered creative intent. Such a “neutral form” of the mastered image requires numerous considerations. We will examine the various candidate architectures for creating and utilizing a neutral form of moving images. We will also examine the meaning of “neutral,” which differs between measured neutrality (e.g., measured chromaticity invariance) versus appearance neutrality. Appearance neutrality might include such attributes as that the image looks as intended and is unbiased with respect to contrast and color (e.g., neutral gray appears neutral, and colors appear consistently natural). Although there are several viable choices for a neutral form, a strong case can be made for a graded scene-referred neutral form.
ChemInform Abstract: SYNTHESIS OF NATURALLY OCCURRING QUINONES. 14. SYNTHESIS OF 11‐DEOXYANTHRACYCLINONE PRECURSOR. A NEW STRATEGY TOWARD A TETRACYCLIC SYSTEM VIA TANDEM 1,4/(4+2) ADDITION (1984)

Abstract Aus dem Naphthol (Ia) wird über (Ib) und (II) das Acryloylnaphthochinon (III) hergestellt, das mit dem Pentadienyltrimethylstannan (IV) zu einem Gemisch aus den Verbindungen (V) und (VI) reagiert.
Natural World Distribution via Adaptive Confusion Energy Regularization (2021)

We introduce a novel and adaptive batch-wise regularization based on the proposed Batch Confusion Norm (BCN) to flexibly address the natural world distribution which usually involves fine-grained and long-tailed properties at the same time. The Fine-Grained Visual Classification (FGVC) problem is notably characterized by two intriguing properties, significant inter-class similarity and intra-class variations, which cause learning an effective FGVC classifier a challenging task. Existing techniques attempt to capture the discriminative parts by their modified attention mechanism. The long-tailed distribution of visual classification poses a great challenge for handling the class imbalance problem. Most of existing solutions usually focus on the class-balancing strategies, classifier normalization, or alleviating the negative gradient of tailed categories. Depart from the conventional approaches, we propose to tackle both problems simultaneously with the adaptive confusion concept. When inter-class similarity prevails in a batch, the BCN term can alleviate possible overfitting due to exploring image features of fine details. On the other hand, when inter-class similarity is not an issue, the class predictions from different samples would unavoidably yield a substantial BCN loss, and prompt the network learning to further reduce the cross-entropy loss. More importantly, extending the existing confusion energy-based framework to account for long-tailed scenario, BCN can learn to exert proper distribution of confusion strength over tailed and head categories to improve classification performance. While the resulting FGVC model by the BCN technique is effective, the performance can be consistently boosted by incorporating extra attention mechanism. In our experiments, we have obtained state-of-the-art results on several benchmark FGVC datasets, and also demonstrated that our approach is competitive on the popular natural world distribution dataset, iNaturalist2018.
Analysis of the Stability Mutant Ile96→Ala in Barnase, Based on Free Energy Simulations (1991)

Molecular dynamics simulations have been used to compute the difference in is replaced by Ala. They yield results (−3.42/−5.21 kcal/mol) that compared favorably with the experimental values (−3.3/−4.0 kcal/mol). The major contributions to the free energy difference arise from bonding terms involving degrees of freedom of the mutated sidechain, and from non‐bonded interactions of that sidechain with its environment in the folded protein. By comparison with simulations of an extended peptide in the absence of solvent, used as a reference state, it is shown that hydration effects play a minor role in the overall free energy balance of the Ile to Ala transformation.
The Experimental Studies of Improving the Aerodynamic Performance of a Turbine Exhaust System (2014)

Analysis and testing were conducted to optimize an axial diffuser–collector gas turbine exhaust. Two subsonic wind tunnel facilities were designed and built to support this program. A 1/12th scale test rig enabled rapid and efficient evaluation of multiple geometries. This test facility was designed to run continuously at an inlet Mach number of 0.41 and an inlet hydraulic diameter-based Reynolds number of 3.4 × 105. A 1/4th geometric scale test rig was designed and built to validate the data in the 1/12th scale rig. This blow-down rig facilitated testing at a nominally equivalent inlet Mach number, while the Reynolds number was matched to realistic engine conditions via back pressure. Multihole pneumatic pressure probes, particle image velocimetry (PIV), and surface oil flow visualization were deployed in conjunction with computational tools to explore physics-based alterations to the exhaust geometry. The design modifications resulted in a substantial increase in the overall pressure recovery coefficient of +0.07 (experimental result) above the baseline geometry. The optimized performance, first measured at 1/12th scale and obtained using computational fluid dynamics (CFD) was validated at the full scale Reynolds number.
Spectrum of Ocular Manifestations in CLN2-Associated Batten (Jansky-Bielschowsky) Disease Correlate with Advancing Age and Deteriorating Neurological Function (2013)

Ophthalmic manifestations of LINCL correlate closely with the degree of neurological function and the age of the patient. The newly established LINCL Ophthalmic Scale may serve as an objective marker of LINCL severity and disease progression, and may be valuable in the evaluation of novel therapeutic strategies for LINCL, including gene therapy.
A New and Versatile One‐Pot Synthesis of Indol‐2‐ones by a Novel Ugi‐Four‐Component‐Heck Reaction. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Targeting integrin alpha5 receptor in pancreatic stellate cells to diminish tumor-promoting effects in pancreatic cancer (2018)

Abstract Pancreatic stellate cells (PSCs) are the main precursors of cancer-associated fibroblasts (CAFs) in pancreatic ductal adenocarcinoma (PDAC), known to induce cancer aggressiveness. Integrin alpha5 (ITGA5), a fibronectin receptor, was found to be overexpressed by CAFs in stroma and linked to poor overall survival (log-rank p=0.022, n=137) of patients with PDAC. In vitro , knockdown of ITGA5 in human PSCs (hPSCs) inhibited their adhesion, migration, and proliferation and also inhibited TGF-β-mediated differentiation. In vivo , co-injection of PANC-1 tumor cells and hPSCs (sh-ITGA5) developed tumors with reduced fibrosis and slower growth rate compared to those composed of PANC-1 and hPSC (sh-Ctrl). Furthermore, we developed a ITGA5-antagonizing peptidomimetic (AV3) which inhibited TGFβ-mediated hPSC differentiation by blocking ITGA5/FAK pathway. In vivo , treatment with AV3 intraperitoneally attenuated tumor fibrosis and thereby enhanced the efficacy of gemcitabine in patient-derived xenografts in mice. Altogether, this study reports the therapeutic importance of ITGA5 in PDAC and provides novel therapeutic peptidomimetic to enhance the effect of chemotherapy.
Restricted spinal anaesthesia for ambulatory surgery: a pilot study (1999)

The increasing use of ambulatory surgery requires methods of anaesthesia that allow patients to be discharged soon after the operation is completed. Spinal anaesthesia is usually simple and quick, and the incidence of post-spinal headache has been reduced by using non-cutting small-gauge needles. Limiting the spread of spinal anaesthesia, as long as it still provides analgesia for surgery, should reduce the haemodynamic effects and speed recovery. Restricted spinal anaesthesia, intended to be unilateral using 0.18% hypobaric bupivacaine via a 25G or 27G Whitacre unidirectional needle, was compared with epidural anaesthesia (using a mixture of lignocaine and prilocaine) in 64 matched-pair patients undergoing ambulatory arthroscopy. Motor blockade, assessed for the specific myotomes L2 to S1, was significantly more unilateral in the spinal group. Two patients in the spinal group and nine patients in the epidural group were treated for hypotension (P < 0.05). One patient in the spinal group developed a post-spinal headache. One patient in the epidural group rated the anaesthesia poor.
Prostate Cancer (2010)

In the late 1980s and early 1990s, the number of newly diagnosed prostate cancers in the United States increased dramatically, surpassing lung cancer as the most common cancer in men. For example, the percentage of patients with low-risk disease has increased (45.3% in 1999-2001 vs. 29.8% in 1989-1992; P < .0001). In 2009, an estimated 192,280 new cases were diagnosed and prostate cancer was expected to account for 25% of new cancer cases in men. 1 Fortunately, the age-adjusted death rates from prostate cancer have also declined (-4.1% annually from 1994 to 2001).
DNA sequences in human nasopharyngeal carcinoma cells that specify susceptibility to tumor promoter-induced neoplastic transformation (1987)

Homologs of the recently described mouse pro genes, that transfer sensitivity to promotion of neoplastic transformation by tumor promoters, have been cloned from a genomic library of the human nasopharyngeal carcinoma (NPC) cell line CNE2. Both pro-1 and pro-2 homologs were identified by screening this library with mouse probes, but only the pro-1 homologs were able to confer sensitivity to TPA-induced transformation when transferred to promotion-insensitive mouse JB6 cells. This suggests a possible role for the putative pro-1 gene in the etiology of human NPC.
<title>Nanosatellites and MEMS fabrication by laser microprocessing</title> (2000)

By definition Nanosatellites are space systems that can weigh 1010 kg and can perform unique missions (e.g. global cloud cover monitoring, store-and-forward communications) acting either in constellation of distributed sensor-nodes or in a many-satellite platoon that flies in formation. The Aerospace Corporation has been exploring the application of microelectronics fabrication and advanced packaging technology to the development of a mass-producible nanosatellite. Particular attention is being directed at M<SUP>3</SUP> (Micromachining/MEMS/Microsystems) technology which appears to be important in the integration and manufacturing of these satellites. Laser direct-write processing techniques are being applied for rapid prototyping and to specific 3D fabrication steps where conventional microelectronics fabrication techniques fall short. In particular, a laser based technique has been developed that combines the rapid prototyping aspects of direct-write and the low cost/process uniformity aspects of batch processing. This technique has been used to develop various fluidic components and a microthruster subsystem in a photostructurable glass/ceramic material.
Combined PD-1, BRAF and MEK inhibition in BRAFV600E colorectal cancer: a phase 2 trial (2023)

While BRAF inhibitor combinations with EGFR and/or MEK inhibitors have improved clinical efficacy in BRAF<sup>V600E</sup> colorectal cancer (CRC), response rates remain low and lack durability. Preclinical data suggest that BRAF/MAPK pathway inhibition may augment the tumor immune response. We performed a proof-of-concept single-arm phase 2 clinical trial of combined PD-1, BRAF and MEK inhibition with sparatlizumab (PDR001), dabrafenib and trametinib in 37 patients with BRAF<sup>V600E</sup> CRC. The primary end point was overall response rate, and the secondary end points were progression-free survival, disease control rate, duration of response and overall survival. The study met its primary end point with a confirmed response rate (24.3% in all patients; 25% in microsatellite stable patients) and durability that were favorable relative to historical controls of BRAF-targeted combinations alone. Single-cell RNA sequencing of 23 paired pretreatment and day 15 on-treatment tumor biopsies revealed greater induction of tumor cell-intrinsic immune programs and more complete MAPK inhibition in patients with better clinical outcome. Immune program induction in matched patient-derived organoids correlated with the degree of MAPK inhibition. These data suggest a potential tumor cell-intrinsic mechanism of cooperativity between MAPK inhibition and immune response, warranting further clinical evaluation of optimized targeted and immune combinations in CRC. ClinicalTrials.gov registration: NCT03668431.
Synthesis and structure-activity studies of new 4"-O-acyltylosin derivatives of therapeutic interest. (1988)

Eleven 4''-O-acyltylosin derivatives were synthesized and subjected to a two-step screening system consisting of antimicrobial activity and esterase stability assays. The new derivatives were all active against macrolide-resistant Staphylococci and mycoplasmas, but only 4''-O-(4-methoxy)phenylacetyltylosin and 4''-O-(4-acetyl)phenylacetyltylosin showed better resistance to mouse liver esterase than 4''-O-phenylacetyltylosin (reference compound C).
Integrated system for Robot-Assisted in Prostate Biopsy in closed MRI Scanner (2008)

Prostate cancer biopsy is a routine medical procedure, yet conventional techniques suffer from low sensitivity attributed to suboptimal image guidance and needle placement. Targeting small lesions and foci (5 mm in diameter) is particularly prone to errors. We developed an integrated system to perform robot-assisted transperineal needle insertions into the prostate, under Magnetic Resonance Imaging (MRI) guidance. The system provides arbitrary needle trajectories and allows for simultaneous surveillance and correction of the needle path, based on intra-operative MRI. System functionality and data transfer and processing tests were conducted. Five lesions embedded in the gel phantom were targeted successfully, while communication delays (due to higher image frame rates) had no adverse affect on robot-software communication. The system was sufficiently resistant to high network loads and performed with an acceptable transfer rate.