gebhart/patrepeval huggingface dataset:
Supplementary Data Table S.3 from Pathology-Driven Comprehensive Proteomic Profiling of the Prostate Cancer Tumor Microenvironment (2023)

&lt;p&gt;Incidence of biochemical recurrence in 133 patients from the validation cohort&lt;/p&gt;
Supplementary Figure Legend, Methods, Tables 1 - 2 from Earlier Detection of Breast Cancer with Ultrasound Molecular Imaging in a Transgenic Mouse Model (2023)

&lt;p&gt;PDF file - 116K, Table S1: Summary of Sensitivity, Specificity, Positive and Negative Predictive Values for Differentiating Benign (Normal, Hyperplasia) from Malignant (DCIS, Invasive Cancer) Pathologies Based on Different Imaging Signal Threshold Levels; Table S2a: Summary of Sensitivity, Specificity, Positive and Negative Predictive Values for Differentiating Benign (Normal, Hyperplasia) from DCIS Based on Different Imaging Signal Threshold Levels; Table S2b: Summary of Sensitivity, Specificity, Positive and Negative Predictive Values for Differentiating Benign (Normal, Hyperplasia) from Invasive Cancer Based on Different Imaging Signal Threshold Levels.&lt;/p&gt;
Substituted 2-Iminopiperidines as Inhibitors of Human Nitric Oxide Synthase Isoforms (1998)

A series of analogues of 2-iminopiperidine have been prepared and shown to be potent inhibitors of the human nitric oxide synthase (NOS) isoforms. Methyl substitutions on the 4-position (3) or 4- and 6-positions (8) afforded the most potent analogues. These compounds exhibited IC50 values of 0.1 and 0.08 microM, respectively, for hiNOS inhibition. Substitution with cyclohexylmethyl at the 6-position (13) afforded an inhibitor that showed the best selectivity for hiNOS versus heNOS (heNOS IC50/hiNOS IC50 = 64). Following oral administration, inhibitors were found to decrease serum nitrite/nitrate levels in an in vivo rat endotoxin assay. This series of 2-iminopiperidines were prepared via the described synthetic methodologies. The effect of ring substitutions on potency and selectivity for this class of cyclic amidines as NOS inhibitors is described.
HMM topology optimization for handwriting recognition (2002)

This paper addresses the problem of hidden Markov model (HMM) topology estimation in the context of on-line handwriting recognition. HMM have been widely used in applications related to speech and handwriting recognition with great success. One major drawback with these approaches, however, is that the techniques that they use for estimating the topology of the models (number of states, connectivity between the states and the number of Gaussians), are usually heuristically derived, without optimal certainty. This paper addresses this problem, by comparing a couple of commonly used heuristically derived methods to an approach that uses the Bayesian information criterion (BIC) for computing the optimal topology. Experimental results on discretely written letters show that using BIC gives comparable results to heuristic approaches with a model that has nearly 10% fewer parameters.
Effects of HER Family–targeting Tyrosine Kinase Inhibitors on Antibody-dependent Cell-mediated Cytotoxicity in HER2-expressing Breast Cancer (2020)

TKIs differentially alter tumor cell phenotype which can impact NK cell-mediated response to coadministered antibody therapies. mAb-induced ADCC response is relevant when rationalizing combinations for clinical investigation.
Supplementary Figure 3 from An Antimesothelin-Monomethyl Auristatin E Conjugate with Potent Antitumor Activity in Ovarian, Pancreatic, and Mesothelioma Models (2023)

&lt;p&gt;Supplementary Figure 3: In vivo efficacy data from Figure 6 replotted as mean tumor volumes {plus minus} SEM.&lt;/p&gt;
Ag-chalcogenide glass flexible radiation sensor: Impact of atomic ratio of Se on the TID influenced lateral diffusion of Ag (2016)

We report the results of our study on the impact of variable atomic ratio of Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Se <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> on the total ionization dose (TID) influenced lateral diffusion of Ag into chalcogenide glasses (ChG) in flexible radiation detection sensors.
Exploring the European Trichophaea-like discomycetes (Pezizales) using morphological, ecological and molecular data (2021)

Recent collections of unknown Trichophaea-like discomycetes made in Europe enabled the authors to explore the taxonomy of Trichophaea and allies, based on morphological, ecological and molecular data. Our 3-gene phylogeny confirms the paraphyly of the genus Trichophaea and designs a new systematics for this group of cup-fungi. Three new genera are published to accommodate several species previously assigned to Trichophaea or morphologically close genera: Perilachnea gen. nov. with Lachnea hemisphaerioides as type-species, Aurantiolachnea gen. nov. with Lachnea solsequia as type-species, and Parawilcoxina gen. nov. with P. inexpectata sp. nov. as type-species. Some species of the genus Paratrichophaea belong to the cleistothecial genus Lasiobolidium, and furthermore two new species, L. trachysporum and L. coprophilum, are described. Paratrichophaea macrocystis is also combined in Lasiobolidium. Finally, three new species of Chaetothiersia, C. laricina, C. cupressicola and C. eguttulata are described. A new species of Perilachnea, P. ochraceoflava, is outlined from Italy, and a new species of Trichophaeopsis, T. asturiensis, is described from Spain. A total of 15 species are described and illustrated herein.
Acute symptomatic seizures and hippocampus damage: DWI and MRS findings (2006)

The authors describe diffusion-weighted imaging (DWI) and magnetic resonance spectroscopy (MRS) changes in the hippocampus within 48 hours of acute symptomatic seizures or status epilepticus in 12 patients. DWI showed increased signal and a decreased apparent diffusion coefficient (ADC) in all patients, with corresponding lactate detected on MRS in six patients and EEG seizure activity in nine patients. On follow-up, the atrophic hippocampus had an increased ADC in six patients. DWI and MRS may predict development of hippocampal sclerosis.
Clonal lymphoid progenitor cell lines expressing the BCR/ABL oncogene retain full differentiative function. (1990)

The early stages of hematopoiesis have been difficult to study due to problems in obtaining homogeneous populations of progenitor cells that retain both self-renewal and differentiative capacities. We have developed an in vitro system in which transformation of murine bone-marrow cells with the BCR/ABL oncogene, a gene associated with stem-cell leukemias, leads to the outgrowth of clonal lines that have an early lymphoid progenitor cell phenotype. The progenitor cells retain immunoglobulin heavy and light chain genes in a germ-line configuration. These cells give rise in vitro to pre-B cells that have diverse diversity-joining (D-J) region rearrangements, and on transfer to mice with severe combined immune deficiency, differentiate to surface IgM+, immunoglobulin-secreting B cells that respond to T-cell help and function in an antigen-specific fashion. Although their growth is stimulated by BCR/ABL, the progenitor cells depend for continued growth on a stromal cell-derived soluble factor distinct from the pre-B-cell growth factor, interleukin 7. These findings show that BCR/ABL can promote proliferation of an early hematopoietic progenitor cell without preventing its differentiation. This system provides a means of studying the complete B-cell developmental process from clonal progenitor cell to end-stage plasma cell.
Childhood odontoid fractures evaluated with computerized tomography (1992)

A case is presented that illustrates the use of computerized tomography for the evaluation of an odontoid fracture in a child. Such a "fracture" may actually represent a "synchondrotic slip" of the odontoid and C-2 vertebral body between the neural arches of C-2. Treatment should almost always be conservative. Complete healing of the injury is expected.
A novel prototyping method for die-level monolithic integration of MEMS above-IC (2013)

This work presents a convenient and versatile prototyping method for integrating surface-micromachined microelectromechanical systems (MEMS) directly above IC electronics, at the die level. Such localized implementation helps reduce development costs associated with the acquisition of full-sized semiconductor wafers. To demonstrate the validity of this method, variants of an IC-compatible surface-micromachining MEMS process are used to build different MEMS devices above a commercial transimpedance amplifier chip. Subsequent functional assessments for both the electronics and the MEMS indicate that the integration is successful, validating the prototyping methodology presented in this work, as well as the suitability of the selected MEMS technology for above-IC integration.
R&D 100, 2016: Ultrafast X-ray Imager (2018)

The Ultrafast X-ray Imager is a solid-state camera capable of capturing a sequence of images with user-selectable exposure times as short as 2 billionths of a second. Using 3D semiconductor integration techniques to form a hybrid chip, this camera was developed to enable scientists to study the heating and compression of fusion targets in the quest to harness the energy process that powers the stars.
Metastasectomy Following Immunotherapy with Adoptive Cell Transfer for Patients with Advanced Melanoma (2016)

Surgery after immunotherapy is safe. Long PFS and OS can be achieved by metastasectomy in selected patients with progressive melanoma following treatment with ACT. Clinical variables important for patient selection for metastasectomy after immunotherapy remain largely undefined. Improvements in immunotherapeutic treatment strategies may increase the role of surgery for patients with advanced disease.
Thermally Conductive Composite Material With Percolating Microparticles Applied as Underfill (2017)

Efficient thermal management of large vertically stacked integrated circuits (ICs) requires a material with high thermal conductivity inside the micrometer-sized gaps between the IC dies. Such an underfill material can be obtained by adding thermally conductive filler particles at high loadings to the adhesive matrix material. However, viscosity requirements for the state-of-the-art capillary-driven filling of particle-loaded adhesives limit the particle fill fraction to values lower than those necessary to reach true percolation. Accordingly, heat transfer through the composite material is dominated by conduction through the adhesive matrix material. We propose using an alternative, sequential filling method to achieve percolation with particles down to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1~\mu \text{m}$ </tex-math></inline-formula> in diameter. The percolating thermal underfill (PTU) can be achieved by a centrifuge-assisted filling of micrometer-sized particles, followed by a backfilling of a low-viscosity epoxy with long open time acting as matrix material, and a final thermal curing step. In this paper, we present and discuss the fabrication and relevant process parameters of the PTU composite material in chip stacks with critical dimensions below <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$30~\mu \text{m}$ </tex-math></inline-formula> . The wet dispensing of alumina particles with a diameter distribution of 1– <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$15~\mu \text{m}$ </tex-math></inline-formula> is proposed for overcoming the agglomeration observed for dry particle filling. Thermal conductivities of up to 3 W/( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\hbox {m}\cdot \hbox {K}$ </tex-math></inline-formula> ) for the underfill system with a particle fill fraction of 61% were achieved, which is three times higher than those of commercially available capillary thermal underfills. Critical parameters in the formation of the percolating composite, such as the choice of filler material and its refinement, as well as the properties of the particle bed and the process parameters for the centrifugal filling, epoxy capillary backfilling, and composite curing are addressed.
Electrochemical DNA Hybridization Assay: Enzyme‐Labeled Detection of Mutation in p53 Gene (2011)

Abstract This paper discusses a new electrochemical DNA hybridization sensing approach based on the detection of a linked enzyme label. In this method we employ enzyme that is attached to a tethered ssDNA oligomer on the surface and the target analyte is a complementary ssDNA oligomer that does not require any pre‐treatment. The advantage of using of enzyme label is in its amplification of the registration of the hybridization event due to the catalytic reaction facilitated in the process. One particular novelty is associated with the use of enzymes that directly communicate with the electrode surface thus allowing for minimizing the need of additional reagents in the assay. The electrochemical assay was demonstrated when using mixed self‐assembled monolayers from thiolated oligonucleotide and 6‐mercapto 1‐hexanol on gold surfaces. Horseradish peroxidase (HRP) is attached to the surface tethered oligonucleotide using streptavidin‐biotin chemistry, and the enzyme successfully established direct electron transfer (DET) with the electrode or mediated electron transfer (MET) using a mediator. Hybridization results in increasing the angle of contact between electrode and DNA and also the stiffness of the ds DNA, which results in displacing the enzyme away from the electrode surface, and thereby reducing the occurrence of direct electron transfer between the enzyme and the electrode. The cyclic voltammetry showed a clear distinction in response between the complete complementary sequence and the two‐base mismatch sequence. Ellipsometric measurements show that the thickness of the thiol modified oligonucleotide on gold surfaces changes before and after hybridization for the complementary sequence, where as a minimal change in thickness was observed for the noncomplementary sequence. The model target analyte in this study was TP53 gene where a specific mutation is a marker for a list of cancers. Mutations of the TP53 gene have been demonstrated in tumors of the colon, breast, lung, ovary, bladder, and many other organs. Analysis of p53 mutations may provide useful information for the diagnosis, prognosis and therapy of cancer.
On the control of a high power backward-wave oscillator using quantifier elimination methods (1997)

This paper presents an experimental/theoretical study of methods to identify and control a repetitively-pulsed high power microwave source. A neural network was used to model the system and quantifier elimination (QE) theory is used to search for suitable operating conditions.
Annotation-free 3D segmentation of prostate glands enabled with deep-learning image translation (2021)

Glandular architecture is currently the basis for the Gleason grading of prostate biopsies. To visualize and computationally analyze glandular features in large 3D pathology datasets, we developed an annotation-free segmentation method for 3D prostate glands that relies upon synthetic 3D immunofluorescence (IF) enabled by generative adversarial networks. By using a fluorescent analog of H and E (cheap and fast stain) as an input, our strategy allows for accurate glandular segmentation that does not rely upon subjective and tedious human annotations or slow and expensive 3D immunolabeling. We aim to demonstrate that this 3D segmentation will enable improved prostate cancer prognostication.
Impact of transistor mismatch on the speed-accuracy-power trade-off of analog CMOS circuits (2002)

The influence of transistor mismatch on the trade-off between speed, accuracy and power consumption of basic building blocks and analog systems is investigated. The ratio (Speed Accuracy/sup 2/)/Power for a circuit or system in CMOS is shown to be only dependent on technological constants which express the matching quality of the technology. Moreover, the minimal power consumption of high speed analog systems in CMOS imposed by transistor mismatch is two orders higher than the limit imposed by thermal noise.
Mass preserving registration for lung CT (2009)

In this paper, we evaluate a novel image registration method on a set of expiratory-inspiratory pairs of computed tomography (CT) lung scans. A free-form multi resolution image registration technique is used to match two scans of the same subject. To account for the differences in the lung intensities due to differences in inspiration level, we propose to adjust the intensity of lung tissue according to the local expansion or compression. An image registration method without intensity adjustment is compared to the proposed method. Both approaches are evaluated on a set of 10 pairs of expiration and inspiration CT scans of children with cystic fibrosis lung disease. The proposed method with mass preserving adjustment results in significantly better alignment of the vessel trees. Analysis of local volume change for regions with trapped air compared to normally ventilated regions revealed larger differences between these regions in the case of mass preserving image registration, indicating that mass preserving registration is better at capturing localized differences in lung deformation.
Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3–MYC Interactions as a Target in Pancreatic Cancer (2016)

This provides initial preclinical evidence for an essential role of MYC-ERCC3 interactions in PDAC, and suggests a new mechanistic approach for disruption of critical survival signaling in MYC-dependent cancers. Clin Cancer Res; 22(24); 6153-63. ©2016 AACR.
P2‐155: Development and Validation of a Salivary TAU Biomarker in Alzheimer's Disease (2016)

Total tau (t-tau) and phosphorylated tau (p-tau) are abnormally elevated in the brain and cerebrospinal fluid (CSF) of Alzheimer's disease (AD) patients. Tau has also been found to be present in salivary gland tissue (Conrad et al. 2002) and saliva (Shi et al. 2011). Non-invasive and inexpensive biomarkers for AD are needed, and one possible source is saliva. Using unstimulated saliva and western blot analysis, we quantified the p-tau/t-tau ratio at different phosphorylation sites. We determined phosphorylation level at serine 404 (S404), serine 396 (S396) and threonine 181 (T181) as well as combined phosphorylation of serine 400, serine 403, and serine 404 (S400,S403,S404). We collected saliva from 41 AD subjects, diagnosed by clinicians at the Montreal Jewish General Hospital, and 44 cognitively normal elderly controls (NEC), aged 60 and over with a score of 25 or greater on the Montreal Cognitive Assessment (MoCA). As well, we collected saliva from 55 subjects with mild cognitive impairment (MCI) to determine its usefulness as an early biomarker. We also collected from 76 young controls to explore possible age-related differences. Finally, we collected from 16 frontotemporal dementia (FTD) patients, a condition where some subjects have tau pathology, and from 12 subjects with non-tau related neurological conditions, in order to better determine specificity of the test. We found that the p-tau/t-tau levels were significantly elevated in AD subjects compared to NEC at phosphorylation sites S396 and S404, ps<0.05. There was large variation in p-tau/t-tau levels in each diagnostic group. The large variation in levels of AD subjects suggests this test may not be useful as a diagnostic biomarker. However, our results demonstrate a significant difference in AD patients compared to cognitively healthy elderly subjects at two phosphorylation sites. Our work adds to the limited work on peripheral markers of AD. Future work should explore other phosphorylation sites, and should further investigate the mechanism for increased tau and p-tau in saliva.
Determination of Reaction Rate of In-situ Gelled Acids With Calcite Using the Rotating Disk Apparatus (2010)

In-situ gelled acids have been used extensively in matrix and acid fracturing for acid diversion, reducing the leak-off rate, and retarding the acid reaction for deep acid penetration. Although literature review shows that previous studies investigated the rate of dissolution of polymer-based acid, none has addressed in details the cross-linked polymer systems. Therefore, the aim of this work was to study the mass transport and the reaction rate kinetics of the reaction of HCl in-situ gelled acid and carbonate rocks.The reaction rate of 5 wt% in-situ gelled acid was measured using the rotating disk apparatus. Rock samples of 1.5 in. diameter and 1 in. length were utilized. The rate of reaction of in-situ gelled acid was investigated at different temperatures (150, 200, and 250°F) using different rock types (Austin Chalk, Edward limestone, and Pink Dessert limestone) at rotational speeds (100–1800) rpm. Calcium concentration was measured in the collected samples and was used to determine the acid reaction rate.Experimental results showed that the reaction rate is mass transfer limited up to a rotational speed of 1000 rpm and a surface reaction limited above this value. The diffusion coefficient of 5 wt% HCl in in-situ gelled acid was determined at 150°F and reported for such system for the first time. A power law kinetic model was used to determine the rate kinetics parameters. The reaction activation energy and the rate constant at 150, 200, and 250°F were reported. Effect of Fe+3 (cross-linker) on the reaction rate was studied and was found to decrease the dissolution rate of Pink Dessert limestone by a factor of two in a comparison with gelled acid with the same HCl concentration.
Investigation of the Proposed Interdomain Ribose Zipper in Hairpin Ribozyme Cleavage Using 2‘-Modified Nucleosides, (2001)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionInvestigation of the Proposed Interdomain Ribose Zipper in Hairpin Ribozyme Cleavage Using 2'-Modified Nucleosides,David J. Earnshaw, Michelle L. Hamm, Joseph A. Piccirilli, Alexander Karpeisky, Leo Beigelman, Bruce S. Ross, Muthiah Manoharan, and Michael J. GaitCite this: Biochemistry 2001, 40, 24, 7350Publication Date (Web):May 19, 2001Publication History Published online19 May 2001Published inissue 1 June 2001https://pubs.acs.org/doi/10.1021/bi015137whttps://doi.org/10.1021/bi015137wcorrectionACS PublicationsCopyright © 2001 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views249Altmetric-Citations-LEARN 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 PDF (10 KB) Get e-Alertsclose Get e-Alerts