gebhart/patrepeval huggingface dataset:
Data from Transcriptomic Determinants of Response to Pembrolizumab Monotherapy across Solid Tumor Types (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;To explore relationships between biological gene expression signatures and pembrolizumab response.&lt;/p&gt;Experimental Design:&lt;p&gt;RNA-sequencing data on baseline tumor tissue from 1,188 patients across seven tumor types treated with pembrolizumab monotherapy in nine clinical trials were used. A total of 11 prespecified gene expression signatures [18-gene T-cell–inflamed gene expression profile (Tcell&lt;sub&gt;inf&lt;/sub&gt;GEP), angiogenesis, hypoxia, glycolysis, proliferation, MYC, RAS, granulocytic myeloid-derived suppressor cell (gMDSC), monocytic myeloid-derived suppressor cell (mMDSC), stroma/epithelial-to-mesenchymal transition (EMT)/TGFβ, and WNT] were evaluated for their relationship to objective response rate (per RECIST, version 1.1). Logistic regression analysis of response for consensus signatures was adjusted for tumor type, Eastern Cooperative Oncology Group performance status, and Tcell&lt;sub&gt;inf&lt;/sub&gt;GEP, an approach equivalent to evaluating the association between response and the residuals of consensus signatures after detrending them for their relationship with the Tcell&lt;sub&gt;inf&lt;/sub&gt;GEP (previously identified as a determinant of pembrolizumab response) and tumor type. Testing of the 10 prespecified non-Tcell&lt;sub&gt;inf&lt;/sub&gt;GEP consensus signatures for negative association [except proliferation (hypothesized positive association)] with response was adjusted for multiplicity.&lt;/p&gt;Results:&lt;p&gt;Covariance patterns of the 11 signatures (including Tcell&lt;sub&gt;inf&lt;/sub&gt;GEP) identified in Merck–Moffitt and The Cancer Genome Atlas datasets showed highly concordant coexpression patterns in the RNA-sequencing data from pembrolizumab trials. Tcell&lt;sub&gt;inf&lt;/sub&gt;GEP was positively associated with response; signatures for angiogenesis, mMDSC, and stroma/EMT/TGFβ were negatively associated with response to pembrolizumab monotherapy.&lt;/p&gt;Conclusions:&lt;p&gt;These findings suggest that features beyond IFNγ-related T-cell inflammation may be relevant to anti–programmed death 1 monotherapy response and may define other axes of tumor biology as candidates for pembrolizumab combinations.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/clincancerres/article/doi/10.1158/1078-0432.CCR-22-0015" target="_blank"&gt;See related commentary by Cho et al., p. 1479&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
A synthetic p-nitrophenyl esterase with remarkable substrate selectivity (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA synthetic p-nitrophenyl esterase with remarkable substrate selectivityWilmer K. Fife, Slawomir Rubinsztajn, and Martel ZeldinCite this: J. Am. Chem. Soc. 1991, 113, 22, 8535–8537Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://doi.org/10.1021/ja00022a059RIGHTS & PERMISSIONSArticle Views82Altmetric-Citations22LEARN 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 InReddit PDF (443 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Dissecting Structure of Prion Amyloid Fibrils by Hydrogen–Deuterium Exchange Ultraviolet Raman Spectroscopy (2012)

The molecular mechanisms underlying structural diversity of amyloid fibrils or prion strains formed within the same primary structure is considered to be one of the most enigmatic questions in prion biology. We report here on the direct characterization of amyloid structures using a novel spectroscopic technique, hydrogen–deuterium exchange ultraviolet Raman spectroscopy. This method enables us to assess the structural differences within highly ordered cross-β-cores of two amyloid states produced within the same amino acid sequence of full-length mammalian prion protein. We found that while both amyloid states consisted of β-structures, their cross-β-cores exhibited hydrogen bonding of different strengths. Moreover, Raman spectroscopy revealed that both amyloid states displayed equally narrow crystalline-like bands, suggesting uniform structures of cross-β-cores within each state. Taken together, these data suggest that highly polymorphous fibrils can display highly uniform structures of their cross-β-core and belong to the same prion strain.
Integrating petrophysical data to build a 3D‐earth model (2010)

This study presents the application of geostatistical methods to build a 3D earth model constrained by a large database of information that includes density logs measured from core samples of 32 boreholes, lithology, geochemistry (assay), gravity, magnetic and electromagnetic data. The database constituted part of an integrated study to delineate the lateral distribution of a Zn‐Pb‐Ag sulfide deposit. Massive sulfides exhibit high density contrasts with respect to a wide range of host rocks. The borehole‐derived density data provides the framework for building a heuristic 3D density model that honours the statistics of the density observations at sampled locations. This model can be further refined to accommodate the spatial correlation between rock densities and other existing rock properties such as metal concentration through cokriging. The cokriging process presented in this work is based on an established hierarchy between the rock physics variables. We used this geostatistical approach to locally characterize the 3D distribution of the rock mass of the Nash Creek base metal deposit, New Brunswick.
Study language models with specific user goals (2010)

Under different language contexts, people choose different terms or phrases to express their feelings and opinions. When a user is writing a paper or chatting with a friend, he/she applies a specific language model corresponding to the underlying goal. This paper presents a log-based study of analyzing the language models with specific goals. We exhibit the statistical information of terms and software programs, propose some methods to estimate the divergence of language models with specific user goals and measure the discrimination of these models. Experimental results show that the language models with different user goals have large divergence and different discrimination. These study conclusions can be applied to understand user needs and improve Human-Computer Interaction (HCI).
Classification of Traditional Chinese Medicine Cases based on Character-level Bert and Deep Learning (2019)

As one of the traditional cultures of our country, Traditional Chinese Medicine (TCM) has received more and more attention. As a valuable asset inherited from ancient times, TCM medical cases carry the core knowledge content of TCM. Accurate medical case classification is an important part of establishing a correct medical case diagnosis and treatment system, and is also an important part of medical assistance system. This paper proposes a new model to effectively classify medical cases. First, the multi-layer semantic expansion method is used to increase the semantic information of TCM medical cases in instance layer and attribute layer. Then, the character-level Bidirectional Encoder Representations from Transformers (Bert) model is used as a language model for text representation of the medical cases, and the results are as the input of the deep learning models. Finally, the optimized Text-Convolutional Neural Network (Text-CNN) model is used to classify TCM medical cases, and the reliability and accuracy of the whole model are verified through the comparison with the result of other text representation and classification methods.
Sex and Gender Considerations in Transplant Research: A Scoping Review (2019)

Despite a growing awareness of the need to integrate sex and gender in health research, education is required to ensure accurate and meaningful consideration of these concepts. We outline strategies for integrating sex and gender in allotransplantation and donation research during study design and analysis.
Prebolus quantitative MR heart perfusion imaging (2004)

The purpose of this study was to present the prebolus technique for quantitative multislice myocardial perfusion imaging. In quantitative MR perfusion studies the maximum contrast agent dose is limited by the requirement to determine the arterial input function (AIF). The prebolus technique consists of two consecutive contrast agent administrations. The AIF is determined from a first low-dose bolus, while a second, high-dose bolus allows the measurement of the myocardium with improved signal increase. The results of the prebolus technique using a multislice saturation recovery trueFISP sequence in healthy volunteers are presented. In comparison to a standard dose of 3 ml Gd-DTPA, perfusion values are maintained while the signal increase in the concentration time courses was considerably improved, accompanied by reduced standard deviations of the obtained perfusion values (0.72 +/- 0.13 ml/g/min for 1 ml/8 ml and 0.67 +/- 0.10 ml/g/min for 1 ml/12 ml Gd-DTPA, respectively).
A snapshot of SOSE in Victorian schools, 2003 (2004)

\n\t\t\t\t\tPresents a study on teaching Studies of Society and Environment (SOSE) in secondary schools in Victoria. Socio-demographic characteristics of SOSE teachers; Curriculum analysis; Attitudes of teachers and students toward SOSE; Challenges being faced by SOSE teachers; Implications of SOSE on Victorian education.&lt;br /&gt;\n\t\t\t\t
Study of the Energy Consumption of Borehole Systems with Rod Pumps on the Basis of Simulation of an Automated Electromechanical System (2021)

The late stage of field development is characterized by the need for new approaches to the operation and selection of equipment for operating production wells that ensure the production of oil and gas emulsion in difficult conditions at the lowest cost. This article examines the energy efficiency of downhole installations with sucker rod pumps. Experimental data of the research objects for which the PTs 80-6-02 chain drives have been selected, as well as the drive having the same performance of the PTs 80-6-02 balancing machine-pump are given. On the basis of the analysis and the developed model, the conclusion is drawn of the electricity consumption for oil production using electric centrifugal pump installations. Which significantly exceed the performance of similar chain-type drives due to the low efficiency and losses in the submersible electric pump. In addition, according to the analysis, it was revealed that in the process of performing 50 % of the cycle work, which is one stroke, the power consumption of the pumping unit is 15–20% higher than the power consumption of the chain drive. This allows us to say that from the point of view of electricity consumption in the considered modes of operation at this field and with the existing parameters, drives with a chain mechanism are more advanced in the operation processes relative to installations of sucker rod pumps.
A Study of the Determination of Cu(II) by Anodic Stripping Voltammetry on a Novel Nylon/Carbon Fiber Electrode (2004)

Abstract In this work we report a new electrode material formed by injection‐moulding of a conducting polymer consisting of carbon fibers in a Nylon matrix. This material is highly conductive, inexpensive, easy to mould in different shapes and requires minimal pretreatment. The electrode was tested as a mercury‐free sensor for the trace determination of Cu(II) by anodic stripping voltammetry (ASV). The deposition and stripping behavior of copper on the conducting material was initially studied by cyclic voltammetry and the chemical and instrumental parameters of the determination were investigated. The electrode has been shown to be suitable for the determination of Cu(II) in the range 8 μg L −1 to 30 mg L −1 (with deposition times ranging from 30 s to 10 min) with a relative standard deviation of 2.2% (at the 0.5 mg L −1 level) and a limit of detection of 8 μg L −1 Cu(II) for 10 min of accumulation (at a S/N ratio of 5). The electrode was, finally, applied to the determination of copper in tap‐water, pharmaceutical tablets and bovine serum with recoveries of 97.4, 94.9 and 93.4%, respectively
Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles (2021)

The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.
Genomic divergence of allopatric sibling species studied by molecular cytogenetics of their F1 hybrids (1992)

Despite their similar karyotype morphology and close taxonomic affinity, the genomes of allopatric sibling species, Gibasis karwinskyana and Gibasis consobrina , are clearly distinguished in metaphases of their F 1 hybrids by genomic in‐situ hybridization (GISH). The reduced ability of chromosomes from one species to bind labelled total DNA from the other involves almost the whole chromosome complement, and is equally pronounced in euchromatin and heterochromatin. The only region strongly conserved in the two species is an AT‐rich band proximal to each nucleolus organizer. Molecular differentiation is accompanied by chromosome pairing failure in the F 1 interspecific hybrids, although the reason remains open to question. The two species also differ in their numbers of detectable sites for rRNA genes. The greater number of such sites in G. consobrina may be linked with a propensity for interchange heterozygosity. The ability to discriminate rapidly and reliably between the chromosomes of close relatives with almost identical karyotypes makes GISH invaluable in preliminary studies of phytogeny. Detection of even small conserved chromosome bands using GISH confirms the sensitivity of the technique and demonstrates its potential use in evolutionary cytogenetics. This will allow rapid re‐evaluation of many important genetic systems exposed by classical cytogenetics in previous decades.
A Truncated NRIP1 Mutant Amplifies Microsatellite Instability of Colorectal Cancer by Regulating MSH2/MSH6 Expression, and Is a Prognostic Marker of Stage III Tumors (2021)

Microsatellite instability (MSI) is related to the alteration of mismatch repair (MMR) genes and plays a key role in colorectal cancer (CRC) pathogenesis. We previously reported that the transcription factor Nuclear Receptor Interacting Protein 1 (NRIP1) is involved in sporadic intestinal tumorigenesis. The aim of this study was to decipher its role in MSI CRC. By using different mouse models and engineered cell lines, we demonstrated that NRIP1 increased MSH2 and MSH6 MMR gene transcription and mRNA/protein levels. In human CRC cells, NRIP1 expression was associated with decreased MSI and the hypermutator phenotype, and with resistance to chemotherapy drugs. Using a cohort of 194 CRC patients, we detected in 22% of the cases a MSI-induced frameshift mutation in the NRIP1 coding sequence. This genetic alteration generates a truncated protein with a dominant negative activity that increased human CRC cell proliferation and impaired the regulation of MSH2 and MSH6 gene expression. Moreover, the NRIP1 mutant correlated with a decreased overall survival of patients with advanced CRC, especially when MLH1-deficient. By decreasing the expression of MSH2 and MSH6 gene expression, the NRIP1 variant may amplify MLH1-dependent CRC progression and behave as a new prognostic marker of advanced MSI CRC.
INVESTIGACIÓN CON RAYOS LÁSER (2007)

EN EL EDIFICIO DE CIENCIAS EXPERIMENTALES DE LA FACULTAD DE CIENCIAS DE LA UNAM SE ENCUENTRAN TRES LABORATORIOS CONJUNTOS: APTICA AVANZADA, L SERES Y LUMINISCENCIA, CUYO OBJETIVO FUNDAMENTAL COMPRENDE LA INVESTIGACION DE LOS ASPEECTOS CU NTICOS DE LA LUZ, CON EQUIPO QUE PERMITE EL REGISTRO, DIGITALIZACION Y ESTUDIO ESTADISTICO MEDIANTE SISTEMAS DE COMPUTO.
Characterization of in vivo tumorigenicity tests using severe immunodeficient NOD/Shi-scid IL2Rγnull mice for detection of tumorigenic cellular impurities in human cell-processed therapeutic products (2015)

The contamination of human cell-processed therapeutic products (hCTPs) with tumorigenic cells is one of the major concerns in the manufacturing and quality control of hCTPs. However, no quantitative method for detecting the tumorigenic cellular impurities is currently standardized. NOD/Shi-scid IL2Rγ<sup>null</sup> (NOG) mice have shown high xeno-engraftment potential compared with other well-known immunodeficient strains, e.g. nude mice. Hypothesizing that tumorigenicity test using NOG mice could be a sensitive and quantitative method to detect a small amount of tumorigenic cells in hCTPs, we examined tumor formation after subcutaneous transplantation of HeLa cells, as a model of tumorigenic cells, in NOG mice and nude mice. Sixteen weeks after inoculation, the 50% tumor-producing dose (TPD<sub>50</sub>) values of HeLa cells were stable at 1.3 × 10<sup>4</sup> and 4.0 × 10<sup>5</sup> cells in NOG and nude mice, respectively, indicating a 30-fold higher sensitivity of NOG mice compared to that of nude mice. Transplanting HeLa cells embedded with Matrigel in NOG mice further decreased the TPD<sub>50</sub> value to 7.9 × 10 cells, leading to a 5000-fold higher sensitivity, compared with that of nude mice. Additionally, when HeLa cells were mixed with 10<sup>6</sup> or 10<sup>7</sup> human mesenchymal stem cells as well as Matrigel, the TPD<sub>50</sub> values in NOG mice were comparable to those of HeLa cells alone with Matrigel. These results suggest that the <i>in vivo</i> tumorigenicity test using NOG mice with Matrigel is a highly sensitive and quantitative method to detect a trace amount of tumorigenic cellular impurities in human somatic cells, which can be useful in the quality assessment of hCTPs.
DF directed multipath equalization (2002)

This paper addresses the problem of equalizing a (narrow-band) multipath channel using data from an array of sensors. By exploiting the structure inherent in the data, it is shown that the number of multipath rays that can be uniquely identified is on the order of the number of data samples collected, rather than the number of sensors as in most direction finding applications. Two equalization algorithms are presented, both based on a frequency domain representation of the data and the availability of array calibration data. The performance of these algorithms is compared with that of several other recently developed equalization techniques, and is shown to be superior provided the calibration data is reasonably accurate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Target–aptamer binding triggered quadratic recycling amplification for highly specific and ultrasensitive detection of antibiotics at the attomole level (2015)

A novel electrochemical aptasensor for ultrasensitive detection of antibiotics by combining polymerase-assisted target recycling amplification with strand displacement amplification with the help of polymerase and nicking endonuclease has been reported. This work is the first time that target-aptamer binding triggered quadratic recycling amplification has been utilized for electrochemical detection of antibiotics.
Probing quantum walks through coherent control of high-dimensionally entangled photons (2020)

Control over the duration of a quantum walk is critical to unlocking its full potential for quantum search and the simulation of many-body physics. Here we report quantum walks of biphoton frequency combs where the duration of the walk, or circuit depth, is tunable over a continuous range without any change to the physical footprint of the system-a feature absent from previous photonic implementations. In our platform, entangled photon pairs hop between discrete frequency modes with the coupling between these modes mediated by electro-optic modulation of the waveguide refractive index. Through control of the phase across different modes, we demonstrate a rich variety of behavior: from walks exhibiting enhanced ballistic transport or strong energy confinement, to subspaces featuring scattering centers or local traps. We also explore the role of entanglement dimensionality in the creation of energy bound states, which illustrates the potential for these walks to quantify high-dimensional entanglement.
RECENT ADVANCES IN PATHOPHYSIOLOGY AND TREATMENT OF SPINAL CORD INJURY (2002)

Thirty years ago, patients with spinal cord injury (SCI) and their families were told "nothing can be done" to improve function. Since the SCI patient population is reaching normal life expectancy through better health care, it has become an obviously worthwhile enterprise to devote considerable research effort to SCI. Targets for intervention in SCI toward improved function have been identified using basic research approaches and can be simplified into a list: (1) reduction of edema and free-radical production, (2) rescue of neural tissue at risk of dying in secondary processes such as abnormally high extracellular glutamate concentrations, (3) control of inflammation, (4) rescue of neuronal/glial populations at risk of continued apoptosis, (5) repair of demyelination and conduction deficits, (6) promotion of neurite growth through improved extracellular environment, (7) cell replacement therapies, (8) efforts to bridge the gap with transplantation approaches, (9) efforts to retrain and relearn motor tasks, (10) restoration of lost function by electrical stimulation, and (11) relief of chronic pain syndromes. Currently, over 70 clinical trials are in progress worldwide. Consequently, in this millennium, unlike in the last, no SCI patient will have to hear "nothing can be done."