gebhart/patrepeval huggingface dataset:
Phase IIa trial of chimeric antigen receptor modified T cells directed against CD19 (CTL019) in patients with relapsed or refractory CD19+ lymphomas. (2015)

8516 Background: Autologous T cells expressing a chimeric antigen receptor with an external anti-CD19 single chain antibody domain and CD3ζ and 4-1BB signaling domains (CTL019 cells) mediate anti-tumor effects in patients (pts) with relapsed/refractory (r/r) CD19+ leukemias. We are conducting a phase IIa clinical trial of CTL019 cells in r/r CD19+ non-Hodgkin lymphomas. Methods: Eligible pts have CD19+ follicular lymphoma (FL), diffuse large B cell lymphoma (DLBCL), or mantle cell lymphoma (MCL) with anticipated survival less than 2 years. After collection of peripheral blood leukocytes, pts receive lymphodepleting chemotherapy based on histology and past therapies. One to 4 days after chemotherapy, pts receive 5 x 108CTL019 cells intravenously. Blood and marrow samples are collected for correlative studies. Response assessment is 3 months (mo) after infusion. Enrollment began February 2014; data reported are through January 2015. Results: Twenty-nine pts (19 DLBCL; 8 FL; 2 MCL) have enrolled. Median age is 56 (range: 25-77), male:female ratio 17:12, median prior therapies 4 (range: 1-8), and pts with prior ASCT 9 (31%). At enrollment, stages were: IV, 16 pts (55%); III, 5 pts (17%); II, 6 pts (21%); IE, 2 pts (7%); LDH was increased in 20 pts (69%). Eight pts are not evaluable for response (DLBCL 7; FL 1): 3 pts removed from study before T cell infusion due to progressive disease; 1 pt withdrew consent; 3 pts had inadequate T cell expansion; 1 pt received < protocol-specified cell dose. Twenty pts received CTL019 per protocol dose (12 DLBCL; 7 FL; 1 MCL). Pre-infusion chemotherapy regimens were EPOCH (2); cyclophosphamide (9); radiation + cyclophosphamide (2); bendamustine (6); cyclophosphamide-fludarabine (1). Cytokine release syndrome occurred in 15 pts (13 grade 2; 2 grade 3); neurologic toxicity in 3 pts: transient delirium (1 grade 2, 1 grade 3) and 1 possibly related, grade 5 encephalopathy. For 18 pts evaluable for response at 3 mo (12 DLBCL; 6 FL), overall response rate is 67% (DLBCL 50%; FL 100%). At median follow up 6 mo, progression-free survival for evaluable pts is 59% (DLBCL 37%; FL 100%). Conclusions: CTL019 cells induce durable responses in pts with r/r DLBCL and FL with acceptable toxicity. Clinical trial information: NCT02030834.
Supplementary Figures and Tables from Steroidogenic Enzyme AKR1C3 Is a Novel Androgen Receptor-Selective Coactivator that Promotes Prostate Cancer Growth (2023)

&lt;p&gt;Supplementary Figures and Tables - PDF file 898K, Supplementary Table ST1: AKR1C3 over-expression in HEK-293 cells reduces IC50 of androgens. Supplementary Table ST2: Finasteride increases the testosterone formation. Supplementary Figure S1: Over-expression of AKR1C3 increases LNCaP xenograft growth in intact mice. Supplementary Figure S2: AR target FKBP51, but not AR, protein expression is increased in LNCaP-AKR1C3 xenograft tumors. Supplementary Figure S3: AKR1C3 translocation to nucleus requires AR. Top panel. NIH3T3-AKR1C3 cells infected with adenovirus LacZ. Bottom panel. NIH3T3-AKR1C3 cells infected with adenovirus AR.Supplementary Figure S4: AKR1C3 migrates with AR. Supplementary Figure S5: Duolink assay demonstrates interaction between AR and AKR1C3 in LNCaP-AKR1C3 cells. Supplementary Figure S6: AKR1C3 synergizes with SRC-2 in AR transactivation assay. Supplementary Figure S7: AKR1C3 dependent- androgen induced- AR transactivation is not cell type dependent. Transient transactivation studies conducted in COS-1 cells Supplementary Figure S8: AKR1C3-dependent increase in transactivation is selective to AR. Supplementary Figure S9: R1881 induced- AKR1C3 dependent- AR transactivation is not observed with other AKR1C. Supplementary Figure-S10: Different domains mediate the enzymatic and activator functions of AKR1C3. Supplementary Figure S11: GTx-560 is specific for AKR1C3. Supplementary Figure S12: HEK-293-AKR1C3 enzyme activity. Supplementary Figure S14: GTx-560 inhibits AKR1C3-dependent A�dione-induced AR transactivation at all concentration of AKR1C3. Supplementary Figure S15: Expression of steroidogenic enzymes in VCaP cells&lt;/p&gt;
A simple method for measuring the random variation of an interferometer (2001)

A simple technique for measuring the random noise of an interferometric measurement is presented. The method is based on a filtering technique and the use of a low-pass convolution kernel. It is shown that the method gives a deterministic fraction of the real noise present in the experimental data. The evaluation of the probability density allows the determination of the enlarging constant for specifying the confidence level. Experimental results are reported in the case of moderately noisy and significantly noisy interferometric techniques: phase shifting interferometric testing of smooth surfaces and phase shifting speckle interferometry.
New Machinery Health Diagnostic Techniques Using High-Frequency Vibration (1973)

&lt;div class="htmlview paragraph"&gt;A technique is discussed for generating diagnostic information from the vibration signature of machinery in the high-frequency range (up to 100 kHz). The signal generation mechanism is discussed, as well as the diagnostically significant characteristics of the data and a method of extracting this information. Two specific cases are presented utilizing the techniques to illustrate its suitability for many of the common problems encountered in machinery.&lt;/div&gt;
Atomicity in electronic commerce (1997)

There is a tremendous demand to electronically buy and sell goods over networks. This field is called electronic commerce, and it has inspired a large variety of work. Unfortunately, much of this activity ignores traditional transaction processing concerns — chiefly atomicity. This paper discusses the role of atomicity in electronic commerce, pointing out various atomic flaws. Special attention is given to the atomicity problems of digital money proposals. Two examples of highly atomic electronic commerce systems, NetBill and cryptographic postage indicia, are presented.
Countercurrent Separation of Natural Products (2008)

An assessment of the technology and method development in countercurrent chromatography (CCC) and centrifugal partition chromatography (CPC), collectively referred to as countercurrent separation (CS), is provided. More than six decades of CS theory and applications are critically reviewed and developed into a practical guide to CS for natural products research. The necessary theoretical foundation is given for better use of CS in the separation of biological molecules of any size, small to large, and from any matrix, simple to complex. The three operational fundamentals of CS--instrumentation, biphasic solvent systems, and theory--are covered in a prismatic fashion. The goal of this review is to provide the necessary background and references for an up-to-date perspective of CS and to point out its potential for the natural products scientist for applications in natural products chemistry, metabolome, and proteome research involving organisms from terrestrial and marine sources.
Object-Coding for Resolution-Free Musical Audio (2007)

Object-based coding of audio represents the signal as a parameter stream for a set of sound-producing objects. Encoding in this manner can provide a resolution-free representation of an audio signal. Given a robust estimation of the object-parameters and a multi-resolution synthesis engine, the signal can be intelligently upsampled, extending the bandwidth and getting best use out of a high-resolution signal-chain. We present some initial findings on extending bandwidth using harmonic models.
Fabrication biocompatible de microcapsules par polymérisation ensemencée autour de microsphères d'agarose (1991)

Abstract A new process for microencapsulating cells is described. Cells in solution in agarose were extruded from a syringe into a paraffin‐oil containing medium. Solid microspheres were produced when the agarose gelled. A rigid interface around each bead was produced by polymerization of a latex‐seeded aqueous solution of a mixture of 5 wt.‐% acrylamide and 0,25 wt.‐% N , N ‐methylenediacrylamide. Cell viability was demonstrated by radioimmunoassay of prolactin liberated from encapsulated pituitary cells.
Dataset of prostate MRI annotated for anatomical zones and cancer (2022)

In the present work, we present a publicly available, expert-segmented representative dataset of 158 3.0 Tesla biparametric MRIs [1]. There is an increasing number of studies investigating prostate and prostate carcinoma segmentation using deep learning (DL) with 3D architectures [2], [3], [4], [5], [6], [7]. The development of robust and data-driven DL models for prostate segmentation and assessment is currently limited by the availability of openly available expert-annotated datasets [8], [9], [10]. The dataset contains 3.0 Tesla MRI images of the prostate of patients with suspected prostate cancer. Patients over 50 years of age who had a 3.0 Tesla MRI scan of the prostate that met PI-RADS version 2.1 technical standards were included. All patients received a subsequent biopsy or surgery so that the MRI diagnosis could be verified/matched with the histopathologic diagnosis. For patients who had undergone multiple MRIs, the last MRI, which was less than six months before biopsy/surgery, was included. All patients were examined at a German university hospital (Charité Universitätsmedizin Berlin) between 02/2016 and 01/2020. All MRI were acquired with two 3.0 Tesla MRI scanners (Siemens VIDA and Skyra, Siemens Healthineers, Erlangen, Germany). Axial T2W sequences and axial diffusion-weighted sequences (DWI) with apparent diffusion coefficient maps (ADC) were included in the data set. T2W sequences and ADC maps were annotated by two board-certified radiologists with 6 and 8 years of experience, respectively. For T2W sequences, the central gland (central zone and transitional zone) and peripheral zone were segmented. If areas of suspected prostate cancer (PIRADS score of ≥ 4) were identified on examination, they were segmented in both the T2W sequences and ADC maps. Because restricted diffusion is best seen in DWI images with high b-values, only these images were selected and all images with low b-values were discarded. Data were then anonymized and converted to NIfTI (Neuroimaging Informatics Technology Initiative) format.
Mutation detection using fluorescent hybridization probes and melting curve analysis (2001)

The LightCycler is a real-time PCR instrument that combines a thermocycler and a micro-volume fluorimeter. LightCycler technology is gaining popularity due to its ability to detect mutations quickly and accurately. Multiple base alterations are discriminated using hybridization probes and fluorescent melting curves. This review focuses on mutation detection and base discrimination by fluorescent hybridization probes. Assay designs for single base mutation detection and complex multiplex reactions are discussed. Types of mutations detected and reported applications are reviewed. Guidelines using melting curve analysis for the clinical laboratory are presented.
Discovery of Potent and Specific Dihydroisoxazole Inhibitors of Human Transglutaminase 2 (2014)

Transglutaminase 2 (TG2) is a ubiquitously expressed enzyme that catalyzes the posttranslational modification of glutamine residues on protein or peptide substrates. A growing body of literature has implicated aberrantly regulated activity of TG2 in the pathogenesis of various human inflammatory, fibrotic, and other diseases. Taken together with the fact that TG2 knockout mice are developmentally and reproductively normal, there is growing interest in the potential use of TG2 inhibitors in the treatment of these conditions. Targeted-covalent inhibitors based on the weakly electrophilic 3-bromo-4,5-dihydroisoxazole (DHI) scaffold have been widely used to study TG2 biology and are well tolerated in vivo, but these compounds have only modest potency, and their selectivity toward other transglutaminase homologues is largely unknown. In the present work, we first profiled the selectivity of existing inhibitors against the most pertinent TG isoforms (TG1, TG3, and FXIIIa). Significant cross-reactivity of these small molecules with TG1 was observed. Structure-activity and -selectivity analyses led to the identification of modifications that improved potency and isoform selectivity. Preliminary pharmacokinetic analysis of the most promising analogues was also undertaken. Our new data provides a clear basis for the rational selection of dihydroisoxazole inhibitors as tools for in vivo biological investigation.
Straylight considerations for NIR spectrographs (2008)

Modern NIR spectrographs aiming at the detection and spectral study of faint deep sky objects are potentially sensitive to performances-degrading straylight effects. In particular, the following straylight mechanisms have been identified: - ghost images, inherent to large aperture broadband camera in multi-band spectrographs, have often specific distribution which can (and needs to) be simulated when baffling is not possible; - scattered light generated at the surface of the component is also interesting in the NIR spectrum as it is often at the cross-over between a micro-roughness dominated behaviour and a particulate contamination dominated one; - the use of dispersing element such as diffraction grating brings its own straylight issues related to the control of non-evanescent orders and under incidence different from the one given by the main sequential optical path from telescope to detector; - finally, thermal background from local spectrograph environment or more remote observatory-level sources affects particularly the long wavelength end of the NIR spectrum (H and K bands typically) and in-band or out-of-band rejection is desirable as complementary or even alternative to potentially complex and costly full cryogenic operation. These different points are discussed and illustrated through case studies of several NIR multi-object spectrograph designs like the fibre-fed reflective grating with OH lines suppression FMOS (designed and built), the broadband multi-IFU slicer and slit grating KMOS (under development) and the fibre-fed grism-based SIDE (in conceptual design stage).
Fast H.264 Inter Mode Decision Based on Inter and Intra Block Conditions (2007)

In H.264 advanced video coding (AVC), the inter prediction with variable block sizes plays an important role to achieve compression efficiency. Although it actually raises the coding efficiency in H.264, it also increases the complexity due to the decision of the best inter mode. In this paper, we will propose a fast algorithm based on neighboring information and homogeneous condition to select the best mode effectively. For each macroblock, we first select the initial mode by using probability table and then use homogeneous condition analysis with motion vector relation to accelerate the inter mode decision process. Experimental results show that our proposed algorithm can save about 67~70% mode computation with negligible PSNR loss, which is very helpful for H.264 interframe coding.
CEC-CED Joint Knowledge and Skills Statement for All Becoming Teachers of Students Who Are Deaf or Hard of Hearing (1996)

In 1992, the National Council on Education of the Deaf (CED) and the Council for Exceptional Children (CEC) began a collaborative process in which new standards were jointly developed and approved by a representation of members from all organizations engaged in the preparation of teachers and in the delivery of services to deaf and hard of hearing learners, including educational, professional/administrative and consumer organizations. A Joint Standards Committee was appointed, and in 1992 enunciated mutually acceptable standards for the preparation of teachers of students who are deaf and hard of hearing. Fundamental to the entire standards development process was respect for the continuum of educational options available for children who are deaf and hard of hearing. The intent of this committee was to provide standards which were credible for all university and college teacher preparation programs and which could serve as a foundation for the development and maintenance of strong and viable programs according to the specific stated philosophy and practice of each. Information regarding the new standards and University/College Program Evaluation can be obtained from: Dr. Harold Johnson, Program Evaluation Chair, Kent State University, Room 405 White Hall, Kent, Ohio 44242.
Supplementary Figure 3 from EGFR Protein Expression in Non–Small Cell Lung Cancer Predicts Response to an EGFR Tyrosine Kinase Inhibitor—A Novel Antibody for Immunohistochemistry or AQUA Technology (2023)

&lt;p&gt;PDF file - 163KB&lt;/p&gt;
D34 Tool Path Modification for Overlapping Part of Tool Entry and Exit in End Milling (2010)

In a contour parallel toolpath used often in die machining/ part machining, a hollow-shaped machining error tends to appear at the overlapping part of tool entry and exit. In this study, we suggest the modification method of the tool exit in order to reduce such a hollow-shaped machining error. By an experiment, it is shown that a machining error is decreased compared with a conventional tool but it is still not sufficiently small by this method.
The mixture of poly(propylene-glycol)-block-poly(ethylene-glycol)-block-PPG with C12E5microemulsion (2013)

We study oil-in-water microemulsions, in particular dispersions of n-decane droplets coated with a monolayer of the surfactant C12E5 in a continuous phase of water. Upon addition of the tri-block poly(propylene-glycol)(PPG)-block-Poly(ethylene-glycol)(PEG)-block-PPG, the depletion interaction between the oil droplets of microemulsion is induced. At constant droplet size, we vary the polymer concentration and there is clear evidence for an increasing depletion interaction of the droplets from structural investigations with small-angle x-ray scattering and photon correlation spectroscopy (PCS). Our results show that the PEG does increase the depletion interaction more than the tri-block PPG-PEG-PPG.
Report on Color in Eggs (1957)

Journal Article Report on Color in Eggs Get access Richard H Forsythe Richard H Forsythe Associate Referee Henningsen, Inc., P.O. Box 2327, National Station, Springfield, Mo Search for other works by this author on: Oxford Academic Google Scholar Journal of Association of Official Agricultural Chemists, Volume 40, Issue 2, 1 May 1957, Pages 535–542, https://doi.org/10.1093/jaoac/40.2.535a Published: 24 January 2020
A random graph approach to NMR sequential assignment (2004)

Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics, and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding connectivity (e.g. through-bond atomic interactions) and amino acid type, typically using the former to determine strings of connected residues and the latter to map those strings to positions in the primary sequence. Significant ambiguity exists in both connectivity and amino acid type, and different algorithms have combined the information in two phases (find short unambiguous strings then align) or simultaneously (align while extending strings). This paper focuses on the information content available in connectivity alone, allowing for ambiguity rather than handling only unambiguous strings, and complements existing work on the information content in amino acid type.In this paper, we develop a novel random-graph theoretic framework for algorithmic analysis of NMR sequential assignment. Our random graph model captures the structure of chemical shift degeneracy (a key source of connectivity ambiguity). We then give a simple and natural randomized algorithm for finding an optimum sequential cover. The algorithm naturally and efficiently reuses substrings while exploring connectivity choices; it overcomes local ambiguity by enforcing global consistency of all choices. We employ our random graph model to analyze our algorithm, and show that it can provably tolerate a relatively large ambiguity while still giving expected optimal performance in polynomial time. To study the algorithm's performance in practice, we tested it on experimental data sets from a variety of proteins and experimental set-ups. The algorithm was able to overcome significant noise and local ambiguity and consistently identify significant sequential fragments.
Facile Peptides Functionalization of Lanthanide-Based Nanocrystals through Phosphorylation Tethering for Efficient in Vivo NIR-to-NIR Bioimaging (2016)

Peptide modification of nanoparticles is a challenging task for bioapplications. Here, we show that noncovalent surface engineering based on ligand exchange of peptides for lanthanide based upconversion and downconversion near-infrared (NIR) luminescent nanoparticles can be efficiently realized by modifying the hydroxyl functional group of a side grafted serine of peptides into a phosphate group (phosphorylation). By using the phosphorylated peptide with the arginine-glycine-aspartic acid (RGD) targeting motifs as typical examples, the modification allows improving the selectivity, sensitivity, and signal-to-noise ratio for the cancer targeting and bioimaging and reducing the toxicity derived from nonspecific interactions of nanoparticles with cells. The in vivo NIR bioimaging signal could even be detected at low injection amounts down to 20 μg per animal.
Targeted drug delivery into the human brain (2005)

More than 80 million people are being affected neurological diseases in the United States as per the NIH statistics. These diseases range from brain tumors to Parkinson’s disease, Alzheimer’s disease. Most of these disorders of the central nervous system (CNS) require large molecules drug therapy (using large molecular weight proteins such as trophic factors) as against a very few that are cured by just small molecules. The problem in delivering large molecules to the affected regions in the brain parenchyma is due to the presence of a network of tightly knit endothelial cells called as the Blood Brain Barrier (BBB). Due to the selective permeability of the BBB, large chemotherapeutic agents cannot pass through and thus cannot overcome the barrier. Diseases of the CNS such as Alzheimer’s, Parkinson’s, Autism, Multiple Sclerosis, Brain Cancer, Huntington’s disease etc need large molecules such as proteins that may include trophic factors such as glial derived neurotrophic factor (GDNF), Nerve Growth Factor (NGF), brain derived neurotrophic factor (BDNF). In addition, the type of drug chosen is specific to a particular kind of brain disorder and the therapeutic efficacy of a given drug may not be generic to all kinds of cerebral disorders. For example, for treating Parkinson’s disease hydrophilic drugs are generally used but are trapped in the BBB with the exception of Levodopa.