gebhart/patrepeval huggingface dataset:
Pembrolizumab in Microsatellite-Instability–High Advanced Colorectal Cancer (2020)

Pembrolizumab led to significantly longer progression-free survival than chemotherapy when received as first-line therapy for MSI-H-dMMR metastatic colorectal cancer, with fewer treatment-related adverse events. (Funded by Merck Sharp and Dohme and by Stand Up to Cancer; KEYNOTE-177 ClinicalTrials.gov number, NCT02563002.).
Cross-Talk Between Cognate and Noncognate RpoE Sigma Factors and Zn 2+ -Binding Anti-Sigma Factors Regulates Photooxidative Stress Response in Azospirillum brasilense (2013)

The two redox-sensitive ZAS anti-σ factors in A. brasilense may interact with their cognate as well as noncognate ECF σ factors to play an important role in redox homeostasis by facilitating recovery from the oxidative stress.
Lack of extensive mutations in the VH5 genes used in common B cell chronic lymphocytic leukemia. (1993)

B cell chronic lymphocytic leukemia (CLL) is a malignancy of the CD5+ B cells. Prior studies indicated that CLL B cells generally express immunoglobulin (Ig) VH and VL genes with little or no somatic mutations. However, a recent report indicated that VH251, one of three VH genes belonging to the VH5 subgroup (e.g., VH251, VH32, and VH15), not only is frequently rearranged in this disease, but also has extensive and selective mutations when expressed by CLL B cells. The extent and nature of these mutations contrasts markedly from the low level of mutations noted in VH5 genes used by normal B cells or other Ig V genes found expressed in CLL. To determine whether this difference reflects a unique property of VH251 or a previously unrecognized subgroup of CLL, we examined for VH5 Ig gene rearrangements in leukemia cells from 68 patients that satisfied clinical and diagnostic criteria for CD5+ B cell CLL. Southern blot hybridization studies with probes for VH251 and the JH locus revealed that only 7 (10%) of the 68 monoclonal CLL cell populations had undergone Ig gene rearrangement involving VH5 genes. Two (3%) were found to have functionally rearranged VH5 genes that shared > or = 98% sequence homology with 5-2R1, a VH251 gene isolated from a pre-B cell acute lymphocytic leukemia. The other five CLL (7%) had functionally rearranged VH5 genes that each shared > or = 99% nucleic acid sequence homology with a germline VH32 isolated from human sperm DNA. These data indicate that VH251 or VH32 also may be expressed by CD5+ CLL B cells with little or no somatic mutation. These findings contrast with a recently published study on VH5 gene expression in B CLL and contest the hypothesis that extensive somatic mutation is a common property of the VH5 genes used in this disease. Further work to define the clinical and/or phenotypic characteristics of patients with leukemia cells that express mutated versus nonmutated Ig V genes may reveal subsets of CLL that possibly differ in their cytogenesis, etiopathogenesis, and/or clinical behavior.
Localization of the BiP Molecular Chaperone with Respect to Endoplasmic Reticulum Foci Containing the Cystic Fibrosis Transmembrane Conductance Regulator in Yeast (2003)

Almost all secreted proteins pass through the endoplasmic reticulum (ER), an organelle that is equipped to tolerate and/or degrade misfolded proteins. We report here that yeast expressing the cystic fibrosis transmembrane conductance regulator (CFTR) concentrate the protein at defined sites in the ER membrane that are not necessarily enriched for the ER molecular chaperone BiP. We propose that these sites are Russell bodies, an ER subcompartment in which misfolded proteins are stored and can be targeted for degradation.
Newer treatments for non-Hodgkin's lymphoma: monoclonal antibodies. (1998)

Significant advances have been made in the application of monoclonal antibody-based therapies to the treatment of patients with lymphoma. The most promising areas appear to be the use of unconjugated monoclonal antibodies and the use of radiolabeled monoclonal antibodies. The recent approval by the US Food and Drug Administration (FDA) of rituximab (Rituxan), an unconjugated chimeric antibody against the CD20 antigen for the treatment of relapsed low-grade or follicular B-cell non-Hodgkin's lymphoma marked a milestone in the development of these antibody-based treatments. Other new drug applications to the FDA are pending using both unconjugated and radiolabeled monoclonal antibodies, and it is anticipated that further new treatment options based on monoclonal antibody technology will soon be available for the treatment of patients with non-Hodgkin's lymphoma. Forthcoming clinical trial results combining these new agents with current therapies are needed to determine if the addition of these new biologic agents to our armamentarium against lymphoma will alter the natural history of this disease for our patients. The most promising of these treatments and the comparison of these strategies are reviewed here.
Replication and packaging of coronavirus infectious bronchitis virus defective RNAs lacking a long open reading frame (1996)

The construction of a full-length clone of the avian coronavirus infectious bronchitis virus (IBV) defective RNA (D-RNA), CD-91 (9,080 nucleotides [Z. Penzes et al., Virology 203:286-293]), downstream of the bacteriophage T7 promoter is described. Electroporation of in vitro T7-transcribed CD-91 RNA into IBV helper virus-infected primary chick kidney cells resulted in the production of CD-91 RNA as a replicating D-RNA in subsequent passages. Three CD-91 deletion mutants were constructed--CD-44, CD-58, and CD-61--in which 4,639, 3,236, and 2,953 nucleotides, respectively, were removed from CD-91, resulting in the truncation of the CD-91 long open reading frame (ORF) from 6,465 to 1,311, 1,263, or 2,997 nucleotides in CD-44, CD-58, or CD-61, respectively. Electroporation of in vitro T7-transcribed RNA from the three constructs into IBV helper virus-infected cells resulted in the replication and packaging of CD-58 and CD-61 but not CD-44 RNA. The ORF of CD-61 was further truncated by the insertion of stop codons into the CD-61 sequence by PCR mutagenesis, resulting in constructs CD-61T11 (ORF: nucleotides 996 to 1,058, encoding 20 amino acids), CD-61T22 (ORF: nucleotides 996 to 2,294, encoding 432 amino acids), and CD-61T24 (ORF: nucleotides 996 to 2,450, encoding 484 amino acids), all of which were replicated and packaged to the same levels as observed for either CD-61 or CD-91. Analysis of the D-RNAs showed that the CD-91- or CD-61-specific long ORFs had not been restored. Our data indicate that IBV D-RNAs based on the natural D-RNA, CD-91, do not require a long ORF for efficient replication. In addition, a 1.4-kb sequence, corresponding to IBV sequence at the 5' end of the 1b gene, may be involved in the packaging of IBV D-RNAs or form part of a cis-acting replication element.
Molecular characterization of lymphatic endothelial cells (2002)

The lymphatic microvasculature is uniquely adapted for the continuous removal of interstitial fluid and proteins and is an important entry point for leukocytes and tumor cells. Specialized functions of lymphatics suggest differences in the molecular composition of the lymphatic and blood vascular endothelium. However, the extent to which the two cell types differ is still unclear, and few molecules that are truly specific to lymphatic endothelial cells have been identified to date. We have isolated primary lymphatic and blood microvascular endothelial cells from human skin by immunoselection with the lymphatic marker LYVE-1 and demonstrate that the two cell lineages express distinct sets of vascular markers and respond differently to growth factors and extracellular matrix. Comparative microarray analysis of gene-expression profiles revealed a number of unique molecular properties that distinguish lymphatic and blood vascular endothelium. The molecular profile of lymphatic endothelium seems to reflect characteristic functional and structural features of the lymphatic capillaries. Classification of the differentially expressed genes into functional groups revealed particularly high levels of genes implicated in protein sorting and trafficking, indicating a more active role of lymphatic endothelium in uptake and transport of molecules than previously anticipated. The identification of a large number of genes selectively expressed by lymphatic endothelium should facilitate the discovery of hitherto unknown lymphatic vessel markers and provide a basis for the analysis of the molecular mechanisms accounting for the characteristic functions of lymphatic capillaries.
The peregrine high‐performance RPC system (1993)

Abstract The Peregrine RPC system provides performance very close to the optimum allowed by the hardware limits, while still supporting the complete RPC model. Implemented on an Ethernet network of Sun‐3/60 workstations, a null RPC between two user‐level threads executing on separate machines requires 573μs. This time compares well with the fastest network RPC times reported in the literature, ranging from about 1100 to 2600 μs, and is only 309 μs above the measured hardware latency for transmitting the call and result packets in our environment. For large multi‐packet RPC calls, the Peregrine user‐level data transfer rate reaches 8.9 Mbit/s, approaching the Ethernet's 10 Mbit/s network transmission rate. Between two user‐level threads on the same machine, a null RPC requires 149 μs. This paper identifies some of the key performance optimizations used in Peregrine, and quantitatively assesses their benefits.
Selection of a Ribozyme That Functions as a Superior Template in a Self-Copying Reaction (1992)

The sunY ribozyme is derived from a self-splicing RNA group I intron. This ribozyme was chosen as a starting point for the design of a self-replicating RNA because of its small size. As a means of facilitating the self-replication process, the size of this ribozyme was decreased by the deletion of nonconserved structural domains; however, when such deletions were made, there were severe losses of enzymatic activity. In vitro genetic selection was used to identify mutations that reactivate a virtually inactive sunY deletion mutant. A selected mutant with five substitution mutations scattered throughout the primary sequence showed greater catalytic activity than the original ribozyme under the selection conditions. The sunY ribozyme and its small selected variant can both catalyze template-directed oligonucleotide assembly. The small size and reduced secondary structure of the selected variant results in an enhancement, relative to that of the original ribozyme, of its rate of self-copying. This engineered ribozyme is able to function effectively both as a catalyst and as a template in self-copying reactions.
Combined Total Genome Loss of Heterozygosity Scan of Breast Cancer Stroma and Epithelium Reveals Multiplicity of Stromal Targets (2004)

Recent breast cancer studies have highlighted the importance of interactions between cancer epithelium and tumor stroma. Recently, the focus of solid tumor investigations has shifted from mutations in carcinomatous epithelium to disturbances of tissue organization in cancer. The genetic basis of this microenvironment, however, remains to be clarified. To begin to resolve this problem, a total genome loss of heterozygosity (LOH) scan was done on epithelial and stromal DNA from 134 sporadic invasive breast carcinomas. In addition to detecting more frequent LOH at three loci in stroma than in epithelium, we found strong evidence that LOH frequencies were significantly elevated in specific regions of each chromosome. We detected 57 markers, which were preferentially lost either in stroma (n = 38) or epithelium (n = 19), relative to the background LOH frequencies on their respective chromosomes. This multiplicity of stromal cell LOH, and hence loss of genetic material, provides a possible mechanism for interpatient variation in host-stromal response to invading adenocarcinoma cells. This is consistent with a model in which initial, random LOH occurs equally among epithelium and stroma, but subsequent clonal selection is driven by factors, which appear to be distinctly different between malignant epithelial and surrounding stromal cells. Genetic alterations in stroma did not mimic those in epithelium, but they could play a different and parallel role in carcinogenesis and tumor progression, probably by modifying some features specific to breast cancer.
Hyolaryngeal excursion as the physiological source of swallowing accelerometry signals (2010)

Swallowing dysfunction, or dysphagia, is a serious condition that can result from any structural or neurological impairment (such as stroke, neurodegenerative disease or brain injury) that affects the swallowing mechanism. The gold-standard method of instrumental swallowing assessment is an x-ray examination known as the videofluoroscopic swallowing study, which involves radiation exposure. Consequently, there is interest in exploring the potential of less invasive methods, with lesser risks of biohazard, to accurately detect swallowing abnormalities. Accelerometry is one such technique, which measures the epidermal vibration signals on a patient's neck during swallowing. Determining the utility of accelerometry signals for detecting dysphagia requires an understanding of the physiological source of the vibrations that are measured on the neck during swallowing. The purpose of the current study was to determine the extent to which movement of the hyoid bone and larynx contributes to the vibration signal that is registered during swallowing accelerometry. This question was explored by mapping the movement trajectories of the hyoid bone and the arytenoid cartilages from lateral videofluoroscopy recordings collected during thin liquid swallowing, and comparing these trajectories to time-linked signals obtained from a dual-axis accelerometer placed on the neck, just anterior to the cricoid cartilage. Participants for this study included 43 adult patients referred for videofluoroscopic swallowing studies to characterize the nature and severity of suspected neurogenic dysphagia. A software program was created to allow frame-by-frame tracking of structural movement on the videofluoroscopy recordings. These movement data were then compared to the integrated acceleration data using multiple linear regressions. The results concur with previous studies, implicating hyolaryngeal excursion as the primary physiological source of swallowing accelerometry signals, with both the hyoid and the larynx contributing approximately equal amounts to the explained variance of the dependent variable, the integrated accelerometry signal.
100 GHz frequency step-tunable hybrid laser based on a vernier effect between a Fabry-Perot cavity and a sampled ﬁber Bragg grating (1999)

Frequency step-tunability is demonstrated in a hybrid fiber grating external cavity laser for the first time. This new configuration uses an in-fiber sampled Bragg grating (SBG) as the frequency selective element allowing the laser to be tuned by 100 GHz frequency steps from 1551.09 to 1556.66 nm. In this demonstration, the wavelength can be set to the eight strongest SBG reflection peaks giving a laser SMSR better than 25 dB and a linewidth of about 130 kHz.
Cascade molecules. Part 6. Synthesis and characterization of two-directional cascade molecules and formation of aqueous gels (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCascade molecules. Part 6. Synthesis and characterization of two-directional cascade molecules and formation of aqueous gelsGeorge R. Newkome, Gregory R. Baker, Sadao Arai, Mary Jane Saunders, Paul S. Russo, Kevin J. Theriot, Charles N. Moorefield, L. Edward Rogers, Joseph E. Miller, and Cite this: J. Am. Chem. Soc. 1990, 112, 23, 8458–8465Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/ja00179a034https://doi.org/10.1021/ja00179a034research-articleACS PublicationsRequest reuse permissionsArticle Views1680Altmetric-Citations214LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Infrared Spectra of Lignin and Related Compounds. II. Conifer Lignin and Model Compounds1,2 (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared Spectra of Lignin and Related Compounds. II. Conifer Lignin and Model Compounds1,2HERBERT L. HERGERTCite this: J. Org. Chem. 1960, 25, 3, 405–413Publication Date (Print):March 1, 1960Publication History Published online1 May 2002Published inissue 1 March 1960https://pubs.acs.org/doi/10.1021/jo01073a026https://doi.org/10.1021/jo01073a026research-articleACS PublicationsRequest reuse permissionsArticle Views1751Altmetric-Citations124LEARN 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
Pseudo Trust: Zero-Knowledge Based Authentication in Anonymous Peer-to-Peer Protocols (2007)

Most of the current trust models in peer-to-peer (P2P) systems are identity based, which means that in order for one peer to trust another, it needs to know the other peer's identity. Hence, there exists an inherent tradeoff between trust and anonymity. To the best of our knowledge, there is currently no P2P protocol that provides complete mutual anonymity as well as authentication and trust management. We propose a zero-knowledge authentication scheme called pseudo trust (PT), where each peer, instead of using its real identity, generates an unforgeable and verifiable pseudonym using a one-way hash function. A novel authentication scheme based on zero-knowledge proof is designed so peers can be authenticated without leaking any sensitive information. With the help of PT, most existing identity-based trust management schemes become applicable in mutual anonymous P2P systems. We analyze the levels of security and anonymity in PT, and evaluate its performance using trace-driven simulations and a prototype implementation. The strengths of pseudo trust include the lack of need for a centralized trusted party or CA, high scalability and security, low traffic and cryptography processing overheads, and man-in-middle attack resistance. We aim for the pseudo trust design to be included in the P2P trust and anonymity context.
Method for estimating quantum efficiency for CMOS image sensors (1998)

The standard method for measuring QE for a CCD sensor is not adequate for CMOS APS since it does not take into consideration the random offset, gain variations, and nonlinearity introduced by the APS readout circuits. The paper presents a new method to accurately estimate QE of an APS. Instead of varying illumination as in the CCD method, illumination is kept constant and the pixel output is continuously observed - sampling at regular intervals. This makes it possible to eliminate random offset. The experiment is repeated multiple times to obtain good estimates of the pixel output mean and variance at each sample time. The sensor response is approximated by a piecewise linear function and using the Poisson statistics of shot noise gain, charge and read noise are estimated for each line segment. This procedure is repeated at no illumination so that dark charge may be estimated and subtracted from the total charge estimates. The method can also be used to estimate readout noise and gain FPN. Results from 64 X 64 pixel APS test structures implemented in a 0.35 micrometers CMOS process are reported. Using 6 different chips and 16 pixels per chip QE equals 0.37, gain FPN equals 2 percent, dark charge equals 832e-, and readout noise equals 40e-, are estimated.
High lactate levels predict likelihood of metastases, tumor recurrence, and restricted patient survival in human cervical cancers. (2000)

Pathophysiological parameters such as vascular density and tissue oxygen pressure can influence tumor malignancy and patient survival. Observations from our group showed that metastatic spread of carcinomas of the uterine cervix and of head and neck cancers was closely correlated with the lactate concentration in the primary lesion. Because these results were obtained in a low number of patients, the present investigation was performed to verify such a correlation in a larger population. Cryobiopsies were taken at first diagnosis of cervical cancer from 34 patients. Tissue concentrations of ATP, glucose, and lactate in viable tumor regions of these biopsies were measured microscopically using the technique of imaging bioluminescence. There was no correlation between stage or grade and any of the metabolic parameters measured. ATP and glucose concentrations were not significantly different in metastatic and nonmetastatic primary tumors (P>0.05). However, lactate concentrations were significantly higher (P = 0.001) in tumors with metastatic spread (mean +/- SD, 10.0+/-2.9 micromol/g; n = 20) compared with malignancies in patients without metastases (6.3+/-2.8 micromol/g; n = 14). The majority of patients who suffered a recurrence of the disease (17 of a total of 22 patients) or died (15 of 20) within the observation period of up to 8 years belonged to the metastatic, i.e., high lactate group. A Kaplan-Meier analysis of the data showed that the overall and disease-free survival probabilities of patients having low tumor lactate values were significantly higher compared with patients with high tumor lactate concentrations (P = 0.015 and 0.014, respectively). We conclude that tumor lactate content may be used as a prognostic parameter in the clinic. Furthermore, these findings are in accordance with data from the literature showing that the presence of hypoxia in cervical tumors is associated with a poorer patient survival.