gebhart/patrepeval huggingface dataset:
EBV-positive diffuse large B-cell lymphoma of the elderly in Peru: Report of 33 cases. (2011)

e18538 Background: EBV+ diffuse large B-cell lymphoma (DLBCL) of the elderly is a new entity included in the WHO Classification. It usually affects elderly patients and has a poor survival, and it is believed to be related to immunosenescence. The goal of this study was to evaluate clinical characteristics and survival of EBV+ DLBCL of the elderly from our institution. Methods: Between January 2002 and June 2008, 33 patients with EBV+ DLBCL of the elderly were identified and included in the analysis. All cases were positive for the presence of EBV-encoded RNA (EBER) by in situ hybridization and CD20 and/or Pax-5 expression by immunohistochemistry (IHC). Clinical data were reviewed retrospectively and patients’ biopsies were analyzed for the expression of BCL6, CD10, CD30 and MUM-1/IRF4. The survival analysis was performed using the Kaplan-Meier method. Results: The median age was 70 years (range 25-85 years); four patients were <50 years of age. B symptoms occurred in 14 (46%), ECOG >2 was seen in 19 (61%), and advanced stage in 16 patients (57%). The IPI score was high intermediate and high in 19 patients (61%). Extranodal disease occurred in 15 patients (48%); GI tract (n=6), oral cavity (n=3), soft tissue (n=2), CNS (n=2), lung (n=2), adrenal gland (n=1), peritoneum (n=1), and bone marrow (n=1). Interestingly, three patients (9%) were HTLV-1 carriers. By IHC, 21 patients (72%) had a non-germinal center (NGC) profile and nine cases (27%) were CD30+. Eight patients did not receive chemotherapy because of a poor performance status. From the 23 patients who received chemotherapy, 9 received R-chemotherapy with an ORR of 67% (5 complete responses and 1 partial response), and 14 received chemotherapy with an ORR of 29% (4 complete responses). Median overall survival (OS) for the whole group was 6 months. The median OS for patients who did not receive therapy was 1.5 months, 12 months for patients who received chemotherapy and 20 months for R-chemotherapy (p=0.001). Conclusions: EBV+ DLBCL of the elderly was associated with high IPI scores, poor performance status, frequent extranodal involvement, NGC profile, poor response to treatment and short survival rate. The role of rituximab-containing regimens in EBV+ DLBCL of the elderly needs further evaluation.
A Cascaded Microsecond-Pulse Generator for Discharge Applications (2014)

Gas discharges using pulsed power are a promising and efficient approach for producing low-temperature plasmas at atmospheric pressure. Pulsed power generators vary widely in performance and should be chosen according to the load and application requirements. In this paper, a microsecond-pulselength high voltage (HV) generator is developed for atmospheric-pressure plasma jets that use a cascade-type voltage circuit. The electrical parameters including voltage amplitude, pulse repetition frequency, and pulsewidth, are determined by the trigger system. The voltage amplitude can be up to 10 kV and the pulse repetition frequency varies from 1 Hz to 5 kHz. The unipolar output pulse can be either positive or negative, with either square or triangular wave profile that can also be controlled by the optical trigger system. When the output pulse is a square wave, the rising edge is about 100 ns, the falling edge is approximately 2~μs, and the pulsewidth at the top varies from 0.5 to 30 μs. When the output pulse is a triangular wave, the base of the pulse is from 7 to 62 μs, and the stepped rising edge is from 5 to 30 μs. The HV pulse generator is used for producing helium plasma jets into open air. Preliminary experimental data show the effects of the pulse voltage amplitude, pulse repetition frequency, and pulsewidth on plasma jets, and confirm that the generator can provide a good performance for driving cold plasma jets.
Protocol for 3D drug sensitivity and resistance testing of patient-derived cancer cells in 384-well plates (2022)

Establishment of drug testing of patient-derived cancer cells (PDCs) in physiologically relevant 3-dimensional (3D) culture is central for drug discovery and cancer research, as well as for functional precision medicine. Here, we describe the detailed protocol allowing the 3D drug testing of PDCs - or any type of cells of interest - in Matrigel in 384-well plate format using automation. We also provide an alternative protocol, which does not require supporting matrices. The cancer tissue is obtained directly from clinics (after surgery or biopsy) and processed into single cell suspension. Systematic drug sensitivity and resistance testing (DSRT) is carried out on the PDCs directly after cancer cell isolation from tissue or on cells expanded for a few passages. In the 3D-DSRT assay, the PDCs are plated in 384-well plates in Matrigel, grown as spheroids, and treated with compounds of interest for 72 h. The cell viability is directly measured using a luminescence-based assay. Alternatively, prior to the cell viability measurement, drug-treated cells can be directly subjected to automated high-content bright field imaging or stained for fluorescence (live) cell microscopy for further image analysis. This is followed by the quality control and data analysis. The 3D-DSRT can be performed within a 1-3-week timeframe of the clinical sampling of cancer tissue, depending on the amount of the obtained tissue, growth rate of cancer cells, and the number of drugs being tested. The 3D-DSRT method can be flexibly modified, e.g., to be carried out with or without supporting matrices with U-bottom 384-well plates when appropriate for the PDCs or other cell models used.
Correlations among visual analogue scale, neck disability index, shoulder joint range of motion, and muscle strength in young women with forward head posture (2017)

This study investigated the correlation between the neck disability index (NDI) and visual analogue scale (VAS), which are indicators of neck pain, shoulder joint range of motion (ROM), and muscle strength in women with a slight forward head posture. This study was carried out on 42 female college students attending Uiduk University in Gyeongju, Korea. The neck pain and disability index for each subject was measured using VAS and NDI, respectively. Two physiotherapists measured the shoulder joint ROM and muscle strengths of the subjects using a goniometer and a dynamometer, respectively. External rotation, internal rotation, and abduction of the shoulder joint were measured for each subject. A significant negative correlation between neck pain and shoulder joint ROM in external rotation and the muscle strength of the shoulder joint in abduction was found in the subjects. In addition, a significant positive correlation was observed between ROM in external rotation and muscle strength in abduction. This study showed a significant negative correlation between neck pain and ROM in external rotation as well as between neck pain and the muscle strength in abduction.
Enantioselective Formal Synthesis of (+)-Dihydrocorynantheine and (−)-Dihydrocorynantheol (2008)

The enantioselective construction of the 3-ethylindolo[2,3-a]quinolizidine moiety present in numerous indole alkaloids is reported, the key steps being a stereoselective cyclocondensation of (S)-tryptophanol with an appropriate racemic delta-oxoester and a regio- and stereoselective cyclization of the resulting oxazolopiperidones on the lactam carbonyl group. A new procedure for the removal of the hydroxymethyl auxiliary group, involving oxidation to an aldehyde, dehydration of the corresponding oxime, and reductive decyanation of the resulting alpha-aminonitrile, has been developed. The preparation of indoloquinolizidine 27 represents a formal total synthesis of (+)-dihydrocorynantheine, (-)-dihydrocorynantheol, and other indolo[2,3-a]quinolizidine and oxindole alkaloids bearing the same substitution pattern.
Abstract LB-102: Landscape analysis of the initial data release from AACR Project GENIE (2017)

Abstract AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) is a multi-phase, multi-year, international data-sharing consortium whose goal is to generate an evidence base for precision cancer medicine by integrating and linking clinical-grade cancer genomic data with clinical outcome data for tens of thousands of cancer patients treated at multiple institutions worldwide. The project fulfills an unmet need in oncology by providing the statistical power necessary to identify novel therapeutic targets, to understand genomic determinants of response to therapy, to design new biomarker-driven clinical trials and ultimately, to improve clinical decision-making and the care delivered to patients. Here we describe the goals, structure and data standards of the GENIE consortium and conclusions from a high-level analysis of the first public release of genomic and limited clinical data from approximately 19,000 patients treated at eight cancer centers obtained during this initial phase of the project. We also explore the clinical utility of these genomic data by examining rates of clinical actionability across multiple cancer types and by estimating patient enrollment rates to the NCI MATCH Trial. Based on yearly rates of sequencing at each of the eight founding institutions, together with the planned addition of new members, we estimate the GENIE database could grow to &amp;gt;100,000 samples within five years. Consistent with the goals of the proposed Cancer Moonshot National Cancer Data Ecosystem, GENIE is committed to the principles of generating interoperable, open access data that can be widely shared across the entire scientific community. Citation Format: Ethan Cerami, Alexander S. Baras, Justin Guinney, Eva Lepisto, Trevor J. Pugh, Nikolaus Schultz, Thomas Stricker, Shawn M. Sweeney, Laura J. van't Veer, Gerrit A. Meijer, Fabrice Andre, Victor E. Velculescu, Kenna R. Shaw, Mia A. Levy, Philippe L. Bedard, Barrett J. Rollins, Charles L. Sawyers, on behalf of the AACR Project GENIE Consortium. Landscape analysis of the initial data release from AACR Project GENIE [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-102. doi:10.1158/1538-7445.AM2017-LB-102
Group C Neisseria meningitidis variant polysaccharide vaccines in children (1981)

The currently United States-licensed group C Neisseria meningitidis vaccine, composed of the O-acetyl-positive capsular polysaccharide, is poorly immunogenic and does not afford protection from disease to infants and young children. Group C N. meningitidis O-acetyl-negative polysaccharide vaccine induces higher titers in adults than does the O-acetyl-positive vaccine. We compared the immunogenicity of these vaccines in 2-year-old children. Reactions were minimal and did not differ between the two vaccines. The postvaccination geometric mean titer was twofold greater in the O-acetyl-negative group (1.58 versus 0.73 micrograms of antibody per ml). The rates of decline in titer were similar in both groups. Further study regarding immunogenicity of and the anamnestic response to the O-acetyl-negative vaccine is warranted in the age group (less than 18 months) at highest risk for invasive meningococcal disease.
Anisotropic Mesh Generation with Particles. (1996)

Many important real-world problems require meshing, that is the approximation of a given geometry by a set of simpler elements such as triangles or quadrilaterals in two dimensions, and tetrahedra or hexahedra in three dimensions. Applications include finite element analysis and computer graphics. This work focuses on the former. A physically-based model of interacting &amp;quot;particles&amp;quot; is introduced to uniformly spread points over a 2-dimensional polygonal domain. The set of points is triangulated to form a triangle mesh. Delaunay triangulation is used because it guarantees a low computational cost and reasonably well-shaped elements. Several particle interaction (repulsion and attraction) models are investigated ranging from Gaussian energy potentials to Laplacian smoothing. Particle population control mechanisms are introduced to make the size of the mesh elements converge to the desired size. In most applications spatial mesh adaptivity is desirable. Triangles should not only adapt in si...
Ostrich Involvement in the Selection of H5N1 Influenza Virus Possessing Mammalian-Type Amino Acids in the PB2 Protein (2009)

Amino acids at positions 627 and 701 in the PB2 protein (PB2-627 and PB2-701, respectively) of avian influenza A viruses affect virus replication in some mammalian cells. Highly pathogenic H5N1 influenza viruses possessing mammalian-type PB2-627 were detected during the Qinghai Lake outbreak in 2005 and spread to Europe and Africa. Via a database search, we found a high rate of viral isolates from Ratitae, including ostrich, possessing mammalian-type PB2-627 or -701. Here, we report that H5N1 avian influenza viruses possessing mammalian-type amino acids in PB2-627 or -701 are selected during replication in ostrich cells in vitro and in vivo.
Solid-Phase Synthesis of the Cyclic Peptide Portion of Chlorofusin, an Inhibitor of p53-MDM2 Interactions (2003)

The first solid-phase synthesis of the chlorofusin peptide is described. The synthesis involved side-chain immobilization of N(alpha)-Fmoc-Asp-ODmab. Synthesis of the linear peptide, initially incorporating racemic Ade8 and unsubstituted ornithine in place of the chromophore-bearing residue, was followed by cyclization on resin and peptide release to give a mixture of diastereomers. Resynthesis identified (by HPLC) the second isomer as analogous to the natural product. Initial biological assays, using an immunofluorescence method, suggest that the compounds are not cytotoxic but do not inhibit the p53/mdm2 interaction. [structure: see text]
Data from A Transcriptional Profiling Study of CCAAT/Enhancer Binding Protein Targets Identifies Hepatocyte Nuclear Factor 3β as a Novel Tumor Suppressor in Lung Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;We showed previously that CCAAT/enhancer binding protein α (C/EBPα), a tissue-specific transcription factor, is a candidate tumor suppressor in lung cancer. In the present study, we have performed a transcriptional profiling study of C/EBPα target genes using an inducible cell line system. This study led to the identification of hepatocyte nuclear factor 3β (HNF3β), a transcription factor known to play a role in airway differentiation, as a downstream target of C/EBPα. We found down-regulation of HNF3β expression in a large proportion of lung cancer cell lines examined and identified two novel mutants of HNF3β, as well as hypermethylation of the HNF3β promoter. We also developed a tetracycline-inducible cell line model to study the cellular consequences of HNF3β expression. Conditional expression of HNF3β led to significant growth reduction, proliferation arrest, apoptosis, and loss of clonogenic ability, suggesting additionally that HNF3β is a novel tumor suppressor in lung cancer. This is the first study to show genetic abnormalities of lung-specific differentiation pathways in the development of lung cancer.&lt;/p&gt;&lt;/div&gt;
The effects of decanted sediments on embryogenesis in oysters (Crassostrea gigas) (2004)

Sediments act as sinks for contaminants of natural and anthropogenic origin, constituting a risk to the living organisms. In this study, sediments were collected from three sites on the coast of southwest France. The objective of this research was to determine the effects of sediments on embryonic development of bivalves and to identify precisely when the contaminants affect the embryos and induce them to develop in an abnormal way. The toxicity of decanted sediments and overlying waters were assessed using the oyster embryo bioassay. The physical characteristics and contaminant levels in the sediments were measured, including polycyclic aromatic hydrocarbon (PAH) and metal concentrations. Despite contaminant concentrations for PAH and metals only exceeding the effects range-low levels, all decanted sediments tested induced deleterious effects on the embryonic development of oysters, while no significant abnormalities were observed for overlying waters. The study results suggest that abnormal larvae mainly are caused by direct contact with contaminated sediments.
Identification of a Circulating MicroRNA Profile as a Biomarker of Metastatic Cutaneous Melanoma (2015)

No specific biomarkers for prognostication or evaluation of tumour load in melanoma have been reported to our knowledge. MicroRNAs (miRNAs) are strongly implicated in oncogenesis and tumour progression, and their circulating forms have been studied as potential biomarkers in oncology. The aim of this prospective study was to identify a melanoma-specific profile of plasma miRNAs. A screening phase, using RNA microarray, was conducted on plasma from 14 patients with metastatic melanoma and 5 healthy subjects. Selected miRNAs were analysed by RTqPCR in 2 independent training and validation cohorts including, respectively, 29 and 31 patients and 16 and 43 control subjects. A profile of 2 miRNAs (miR-1246 and miR-185) significantly associated with metastatic melanoma with a sensitivity of 90.5% and a specificity of 89.1% was identified. This plasma miRNA profile may become an accurate non-invasive biomarker for melanoma.
LSC 2013 abstract - Host defense against pneumonia: The role of the leptin/neutrophil axis? (2013)

Rationale: Respiratory infections are an important trigger of COPD exacerbations and a major risk factor for Acute Lung Injury. We have shown that leptin is a key mediator of neutrophil recruitment to the injured lung. However, the importance of leptin in the neutrophilic response to respiratory infection remains unknown. We hypothesize that leptin contributes to development of pulmonary neutrophilia in pneumonia and that defective leptin signaling impairs this response. Methods: Leptin staining was performed in human and murine lung tissue infected with bacterial or H1N1-influenza pneumonia and controls by immunohistochemistry. BAL neutrophilia was determined 24h after murine E.coli infection and o.p. aspiration of recombinant leptin or buffer. Human blood- and murine bone marrow-derived neutrophils were examined for phosphorylation of STAT3, Erk, p38, Akt, and GSK-3β after leptin stimulation. Results: Human and murine pneumonia lung samples showed increased leptin staining compared to controls. BAL neutrophil levels in E.coli infected mice significantly increased at 24h in mice treated with leptin compared to controls, whereas in db/db mice, these levels were decreased. In human and murine neutrophils stimulated with leptin ex vivo , increases in P-p38, P-Akt, and P-GSK3β were observed, whereas no P-STAT3 or P-Erk was found, suggesting that neutrophils signal to leptin primarily through the short form of the leptin receptor (ObRa). Conclusion: Pulmonary leptin is induced in the infected lung and is effective in neutrophil recruitment to the lung following infection. This response is impaired in ObRb deficient mice. Yet, a paradox is suggested by evidence that neutrophil leptin-response is primarily through ObRa.
Gold surface with sub-nm roughness realized by evaporation on a molecular adhesion monolayer (2006)

This letter describes a technique for realizing a gold (Au) surface with roughness at the atomic scale using techniques compatible with integrated device fabrication. The Au layer is electron-beam evaporated on a self-assembled monolayer of (3-Mercaptopropyl) trimethoxysilane on an oxidized silicon substrate and shows a root-mean-square surface roughness of ∼2Å over a 1μm2 area. The physical stability of the Au film toward commonly used chemicals and processes for photolithography and self-assembly, and its suitability for formation of well-ordered organic monolayers indicate that the films are well suited as substrates for future device fabrication in molecular electronics or other devices involving self-assembled monolayers.
Supplementary Table 3 from Cross-Species Functional Analysis of Cancer-Associated Fibroblasts Identifies a Critical Role for CLCF1 and IL-6 in Non–Small Cell Lung Cancer <i>In Vivo</i> (2023)

&lt;p&gt;XLS file - 68K, Onto-Express Analysis for Cellular Components&lt;/p&gt;
On-sky demonstration of the SuperSpec millimeter-wave spectrometer (Conference Presentation) (2018)

SuperSpec is an on-chip filter-bank spectrometer designed for wideband moderate-resolution spectroscopy at millimeter and submillimeter wavelengths. Employing TiN kinetic inductance detectors, the device has demonstrated noise performance suitable for photon noise limited ground-based observations at excellent millimeter-wave observing sites. In these proceedings we present a demonstration instrument featuring six independent single-polarization SuperSpec chips, covering 190-310 GHz with 300 channels. We summarize spectrometer performance, describe the cryostat and optical coupling, and present the readout and telescope control system. In an initial deployment to the Large Millimeter Telescope, we plan to observe submillimeter galaxies in [CII] emission at redshifts 5 &lt; z &lt; 9 and CO emission from lower-redshift galaxies. Real on-sky performance will inform the design of the next generation of instruments using large numbers of SuperSpec devices, which could include multi-object spectrometers or line intensity mapping experiments that target [CII] during the Epoch of Reionization.
Human Immunodeficiency Virus Type 1 Entry into Murine Cell Lines and Lymphocytes from Transgenic Mice Expressing a Glycoprotein 120-Binding Mutant Mouse CD4 (1996)

Human CD4, the receptor for the gp120 envelope glycoprotein of HIV-1, is the route for viral entry into CD4+ cells; other cellular factors may cooperate with CD4 to facilitate HIV-1 entry into human cells. Human CD4 expressed on murine cells does not readily mediate HIV-1 entry, which may reflect a functional incompatibility of human CD4 with murine cellular components. We postulated that a HIV-1 gp120-binding mutant murine CD4 (L3T4) possessing a minimal number of human amino acid residues could facilitate HIV-1 entry into rodent cells, unlike human CD4. This hypothesis led us to develop a series of murine L3T4 mutants that bear human CD4 gp120-binding region amino acid residues while retaining most L3T4 epitopes. HeLa cell transfectants expressing gp120-binding mutant L3T4 proteins could be infected with HIV-1. Three mouse cell lines expressing these L3T4 mutant proteins could also be infected with HIV-1 as determined by PCR techniques that detect viral DNA and spliced RNAs. Lectin-stimulated polymorphonuclear leukocytes from transgenic mice (SBL mouse) expressing a gp120-binding L3T4 mutant protein were infected with HIV-1 at the same frequency as lectin-stimulated human peripheral blood lymphocytes as determined by in situ PCR analyses. Supernatant p24gag and reverse transcriptase levels in HIV-infected mouse cell cultures, however, were routinely at background levels, unlike HIV-infected human cell cultures. Thus, gp120-binding mutant L3T4 proteins mediate viral entry in all mouse cells that were tested, but high-level viral replication is absent in these cells.