gebhart/patrepeval huggingface dataset:
Quality control stress test for deep learning-based diagnostic model in digital pathology (2021)

Digital pathology provides a possibility for computational analysis of histological slides and automatization of routine pathological tasks. Histological slides are very heterogeneous concerning staining, sections' thickness, and artifacts arising during tissue processing, cutting, staining, and digitization. In this study, we digitally reproduce major types of artifacts. Using six datasets from four different institutions digitized by different scanner systems, we systematically explore artifacts' influence on the accuracy of the pre-trained, validated, deep learning-based model for prostate cancer detection in histological slides. We provide evidence that any histological artifact dependent on severity can lead to a substantial loss in model performance. Strategies for the prevention of diagnostic model accuracy losses in the context of artifacts are warranted. Stress-testing of diagnostic models using synthetically generated artifacts might be an essential step during clinical validation of deep learning-based algorithms.
Abstract 1507: Transcriptional profiles of CD14+ cells in situ in melanoma tumors reveal plasticity and localization dependent function (2019)

Abstract Mechanisms contributing to immunotherapy resistance in patients are the object of intense studies. Myeloid cells play a major role in tumors and include cells with different functions that can be grossly summarized as: (1) Antigen capture for presentation (dendritic cells, DCs) or for degradation (macrophages); (2) Tissue repair (macrophages) and (3) Effector function (mast cells, monocytes, granulocytes). However, the functional states of myeloid cells in human tumors are not completely understood. To study intact tumor microenvironments we have established a comprehensive approach for cellular and molecular analysis. Modular analysis of bulk RNAseq data of whole melanoma tissue sections stratified patient samples based on lymphocytic infiltrate but revealed inflammation and myeloid modules spread across samples. Polychromatic immunofluorescence and histocytometry showed that CD14+ cells represent the majority of the total tumor immune infiltrate. Furthermore, the majority of T cells present in melanoma tissue are in direct contact with CD14+ cells rather than melanoma cells. The distribution of CD14+ cells shows two distinct patterns: CD14+ cells within cancer nests (intratumoral) which are in close proximity to melanoma cells and are loaded with melanoma protein; CD14+ cells in the tissue surrounding cancer nests (stromal) which do not contain melanoma protein cargo and are organized in dense infiltrates. Using customized immunofluorescence-guided laser capture micro-dissection, we harvested CD14+ cells based on their tissue location and melanoma protein load for downstream analysis. We find that unsupervised clustering of transcriptomes groups cells by their tissue localization, i.e., intratumoral vs. stromal. Computational analysis, revealed distinct and replicable gene signatures associated with different pathways, in intratumoral and stromal CD14+ cells. Thus, the transcriptome differentiates the functional status of CD14+ cells related to their localization within tumor. Citation Format: Jan Martinek, Kyung In Kim, Te-Chia Wu, Victor Wang, Hannah M. Brookes, Lili Sun, Ananya Gulati, Joshy George, Philipp Henrich, Florentina Marches, Anthony Rongvaux, Michael Chiorazzi, Jeff Chuang, Paul Robson, Richard Flavell, Jacques Banchereau, Karolina Palucka. Transcriptional profiles of CD14+ cells in situ in melanoma tumors reveal plasticity and localization dependent function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1507.
Nephrostolithotomy: percutaneous techniques for urinary calculus removal (1982)

Recently the technique of percutaneous nephrostomy has been modified to allow the percutaneous extraction of urinary calculi. This communication describes experience with the percutaneous extraction of 63 calculi from the urinary tract. An overall success rate of 87%, a low incidence of complications (about 3%), a fast recovery, and sooner return to work are obtained. Several technical variants including grasping, fragmentation, flushing, and removal under direct vision have been used. In most cases, a combination of the different techniques has to be used in one patient. Essential to the technique is the introduction of large dilators into the kidney.
Dissecting the In Vivo Leukemogenic Potency of Bclxl (2014)

Overexpression of anti-apoptotic members of the BCL2 family has been found in all types of cancer. A member of the family, BCLxl (B-cell lymphoma extra-large), is known to be associated with the progression of leukemogenesis. In the present study, we focused on understanding the domains of BCLxl responsible for <i>in vivo</i> oncogenic potency. To this end, we utilized engineered BCLxl proteins with alternative transmembrane domains (TM) or chimeric BCLxl proteins containing domains from a less potent BCL2-like protein, BCLb. As expected, mice receiving MYC-only expressing bone marrow develop leukemia by 100 days, whereas co-expression of MYC with wild-type BCLxl led to aggressive myeloid leukemia with an average latency of ~25 days. Interestingly, mice injected with bone marrow co-expressing MYC and BCLxl targeted specifically to either mitochondria or ER also succumbed to leukemia with an average latency of ~25 days. Further, our study was extended to examine the role of the BH4 domain in driving potent leukemogenesis. Mice injected with bone marrow co-expressing MYC and BCLb succumb to leukemia in an average of ~55 days, but interestingly a BCLxl protein containing only the loop region of BCLb drove MYC-induced leukemogenesis with the same latency as wild-type BCLxl. These data suggest that the localization of exogenous BCLxl to either mitochondria or ER is not a steadfast dictator of <i>in vivo</i> oncogenic potency. Further, our findings suggest that the loop domain of BCLb and BCLxl is not responsible for dictating the <i>in vivo</i> leukemogeneic potency. This study provides further mechanistic details into the biochemical functions of BCLxl.
ChemInform Abstract: Studies on Transannular Rearrangement Pathways in the Bicyclo[4.4.1]undecane Ring System: A Novel Entry into the Bicyclo[4.2.1]nonene Ring System. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An algebraic characterization of 𝑘–colorability (2020)

We characterize <inline-formula content-type="math/mathml"> <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="k"> <mml:semantics> <mml:mi>k</mml:mi> <mml:annotation encoding="application/x-tex">k</mml:annotation> </mml:semantics> </mml:math> </inline-formula> –colorability of a simplicial graph via the intrinsic algebraic structure of the associated right-angled Artin group. As a consequence, we show that a certain problem about the existence of homomorphisms from right-angled Artin groups to products of free groups is NP–complete.
Binding and activation of plasminogen on the surface of osteosarcoma cells (1994)

Plasmin (Pm) is a broad action serine protease implicated in numerous physiological functions. In bone, Pm may play a role in growth, resorption, metastasis, and the activation of growth factors. The various components of the Pm system are known to bind and function on the cell surface of various cell types, but no pertinent data are available describing membrane-bound Pm or its zymogen, plasminogen (Pg), in either normal or neoplastic bone cells. We report here that Pg binds to the surface of the human osteosarcoma cell line MG-63 and is activated to Pm by endogenous urokinase plasminogen activator (uPA). These conclusions are based on experiments utilizing radiolabeled compounds and a cell surface proteolytic assay measuring amidolytic activity of Pm. 125I-Pg binding to cells was time dependent, saturable, reversible, and specific. Binding was characterized by a relatively low affinity (Kd approximately 0.9 microM) and a high capacity (approximately 7.5 x 10(6) sites/cell). The binding of 125I-Pg was associated with lysine binding sites of the plasminogen molecule. Activation of 125I-Pg to 125I-Pm occurred on the cell surface and was dependent upon cell bound uPA, as determined by inhibitory antibodies. Binding of Pg to MG-63 monolayers represented approximately 80% bound specifically to the cell surface and the remainder to the surrounding extra-cellular matrix. Either co-incubation with uPA or pre-incubation with Pm resulted in increased 125I-Pg binding to osteosarcoma cells. Cell surface Pm proteolytic activity was confirmed by an amidolytic chromogenic assay. Both Pm and Pg bound to cells with Pg being activated by endogenous uPA. Plasmin activated on the cell surface was partially protected from inhibition by alpha 2-antiPm (requiring Pm lysine binding site interaction) but inhibited by aprotinin, (interacting directly with the Pm catalytic site). Resistance of cell bound Pm to alpha 2-antiPm inhibition suggests that cell surface proteolysis can occur in the presence of a soluble Pm inhibitor known to exist in the extracellular space. Based on these results, we speculate that the various bone physiological processes implicating Pm may occur at or near the bone cell surface.
Immunogenicity of a plasmid DNA vaccine encoding chimeric idiotype in patients with B-cell lymphoma. (2002)

B-cell lymphomas express tumor-specific immunoglobulin, the variable regions of which [idiotype (Id)] can serve as a target for active immunotherapy. Promising results have been obtained in clinical studies of Id vaccination using Id proteins.However, Id protein is laborious and time-consuming to produce. DNA vaccination is an attractive alternative for delivering Id vaccines, because Id DNA can be rapidly isolated by PCR techniques. DNA coding for lymphoma Id can provide protective immunity in murine models. In the present study, we performed a Phase I/II clinical trial to study the safety and immunogenicity of naked DNA Id vaccines in 12 patients with follicular B-cell lymphoma. The DNA encoded a chimeric immunoglobulin molecule containing variable heavy and light chain immunoglobulin sequences derived from each patient's tumor, linked to the IgG2a and kappa mouse immunoglobulin (MsIg) heavy- and light-chain constant regions chains, respectively. Patients in remission after chemotherapy received three monthly i.m. injections of the DNA in three dose escalation cohorts of four patients each (200, 600, and 1800 micro g). After vaccination, 7 of 12 patients mounted either humoral (n = 4) or T-cell-proliferative (n = 4) responses to the MsIg component of the vaccine. In one patient, a T-cell response specific to autologous Id was also measured. Anti-Id antibodies were not detectable in any patient. A second series of vaccinations was then administered using a needle-free injection device (Biojector) to deliver 1800 micro g both i.m. and intradermally (i.d.); 9 of 12 patients had humoral (n = 6) and/or T-cell (n = 4) responses to MsIg. Six of 12 patients exhibited humoral and/or T-cell anti-Id responses; yet, these were cross-reactive with Id proteins from other patient's tumors. Subsequently, a third series of vaccinations was carried out using 500 micro g of human granulocyte-macrophage colony-stimulating factor DNA mixed with 1800 micro g of Id DNA. The proportion of patients responding to MsIg remained essentially unchanged (8 of 12), although humoral or T-cell responses were boosted in some cases. Throughout the study, no significant side effects or toxicities were observed. Despite the modest level of antitumor immune responses in this study, DNA vaccine technology retains potential advantages in developing anti-Id immunotherapies. Additional studies are warranted to optimize vaccine dose, routes of administration, vector designs, and prime-boost strategies. These results will help guide the design of such future DNA vaccine trials.
Energy Harvesting Using Galvanically Synthesized Piezoelectric ZnO Nanorods on Flexible Polymer Film (2015)

This paper reports advancement in bringing flexible piezoelectric nanogenerators (NGs) closer to being realized in a commercial market. We have adopted a method to synthesize piezoelectric ZnO nanorods (NRs) on any electrically conductive surface without a seed layer or a specially selected substrate with matching lattice spacing. By contacting a metal with a dissimilar electro-negativity, a galvanic cell is created in the electrolyte growth medium. We have demonstrated the performance of the as grown NRs on a thin NG using common PET film. The device produced voltages in excess of three times higher than a parallel fabricated reference sample under bending loads.
Analysis and Simulation of Double Resonant Path Converter with Variable Conversion Ratio (2020)

In this work, a resonant switched capacitor converter with two resonant paths is proposed. The target of this topology is to be used as sub-module converter in photovoltaic applications processing the generated power under partial shading, aiming at a small-sized, efficient solution. The topology achieves a variable voltage conversion ratio by altering its duty cycle. An explanation of its basic operation is initially offered, followed by a detailed analysis and exploration of the important metrics such as basic components' current and voltage stress. The analysis is then verified by simulations.
Control-Oriented Model for Camless Intake Process: Part I (1999)

Abstract The improvement of internal combustion engine is largely accomplished though the introduction of innovative actuators that allow optimization and control of the flow, mixing, and combustion processes. The realization of such a novel system depends on the existence of an operational controller that will stabilize the engine and allow experimental testing which, consequently, leads to further development of the actuator and the engine controller. This iterative process requires a starting point which is the development of a control-oriented model. Although not fully validated, the control-oriented model reveals issues associated with uncertainties, nonlinearities, and limitation of different subsystems. Moreover, it aides in defining the controller structure and the necessary parameters for the calibration of the closed loop system. In this paper (Part I) we describe the development process of a control-oriented model for a camless intake process.
Amperometric Aptasensor for Amyloid-β Oligomer Detection by Optimized Stem-Loop Structures with an Adjustable Detection Range (2019)

Amyloid-β oligomers (AβO) have become representative biomarkers for early diagnosis of Alzheimer’s disease. Here, we report on an aptasensor based on stem-loop probes for sensitive and specific detection of AβO by an amperometric transducer principle using alternating current voltammetry (ACV). Stem-loop probes with redox-active moieties are immobilized on a gold substrate as a receptor element. The signal transduction mechanism relies on redox ferrocene (Fc) reporting via charge transfer on a molecular recognition event involving a conformational change of the molecular beacon. The stem-loop structures were optimized by considering the aptamers’ stem length, spacer, and different ferrocene terminals. In addition, the sensor assembly and signal recording including aptamer concentration and ACV frequency dependence are discussed. Using the optimized stem-loop probe (B-3′ Fc), the aptasensor showed a decrease of the Fc peak current induced by AβO binding within the broad concentration range spanning 6 orders of magnitude. Furthermore, the detection limit of the sensor can be further decreased by optimizing the ACV frequency, however at the cost of a narrowed detection range. In this work, a label-free electrochemical aptasensor is demonstrated, which facilitates the quantification of the concentration of AβO with high selectivity and subpicomolar sensitivity, which may be conducive to improving the diagnosis and pharmacology studies of Alzheimer’s disease.
Perioperative Genomic Profiles Using Structure-Specific Oligonucleotide Probes (2009)

Significant genetic heterogeneity that may not be accounted for by taking a family medical history, or by obtaining routine laboratory test results, is present in most patients presenting for surgery and may be detected using a newly developed genotyping platform.
High-speed 1.5-µm self-aligned constricted mesa DFB lasers grown by MOCVD with highly doped p-sheet layers (1989)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Y. HIRAYAMA, H. FURUYAMA, M. MORINAGA, N. SUZUKI, T. NISHIBE, K. EGUCHI, and M. NAKAMURA, "High-speed 1.5-µm self-aligned constricted mesa DFB lasers grown by MOCVD with highly doped p-sheet layers," in Optical Fiber Communication Conference, Vol. 5 of 1989 OSA Technical Digest Series (Optica Publishing Group, 1989), paper TUC5. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Effects of sildenafil on invasive haemodynamics and exercise capacity in heart failure patients with preserved ejection fraction and pulmonary hypertension: a randomized controlled trial (2015)

Treatment with sildenafil did not reduce pulmonary artery pressures and did not improve other invasive haemodynamic or clinical parameters in our study population, characterized by HFpEF patients with predominantly isolated post-capillary pulmonary hypertension. (ClinicalTrials.gov, number NCT01726049).
Tachykinin receptor antagonists inhibit hyperpnea-induced bronchoconstriction in guinea pigs. (1993)

We tested the hypothesis that hyperpnea-induced bronchoconstriction (HIB) and hyperpnea-induced bronchovascular hyperpermeability (HIBVH) are mediated through stimulation of NK-1 and NK-2 receptors in guinea pigs. We first established the efficacy and selectivity of (+/-) CP-96,345 (3 mg/kg i.v.) and of SR-48,968 (300 micrograms/kg i.v.) as NK-1 and NK-2 antagonists, respectively. (+/-) CP-96,345 substantially attenuated bronchoconstriction and systemic vascular leak caused by administration of Sar9,Met(O2)11-Substance P (a specific NK-1 agonist), but had no effect upon bronchoconstriction induced by selective NK-2 stimulation with Nle10-Neurokinin A[4-10]. Conversely, SR-48,968 antagonized the bronchoconstrictor response to Nle10-NKA[4-10], right-shifting the dose-response curve by 2 log units, but had no effect on Sar9, Met(O2)11-SP-induced bronchoconstriction. Anesthetized, tracheostomized, opened-chest male Hartley guinea pigs were pretreated with (+/-) CP-96,345 (3 mg/kg i.v.), SR-48,968 (300 micrograms/kg i.v.), or their respective vehicles, and Evans blue dye (30 mg/kg i.v.) to label circulating albumin. 10 min isocapnic dry gas hyperpnea (12 ml/kg, 150 breaths/min) provoked HIB and HIBVH in vehicle-treated animals. (+/-) CP-96,345 reduced the magnitude of HIB by one-half (peak posthyperpnea RL 7.8 +/- 1.9 [SE] times prehyperpnea baseline versus 16.1 +/- 2.6, vehicle-treated; P < or = 0.0001, ANOVA); SR-48,968 blocked HIB more completely (peak posthyperpnea RL 5.1 +/- 1.7 [SE] times prehyperpnea baseline versus 19.3 +/- 2.8, vehicle-treated; P < 0.0001, ANOVA). Neither drug reduced HIBVH. We conclude that dry gas hyperpnea causes bronchoconstriction in guinea pigs through activation of tachykinin receptors. The differential effects of neurokinin receptor blockade on HIB and HIBVH demonstrate that hyperpnea-induced airflow obstruction is not primarily a consequence of hyperpnea-induced bronchovascular leak.
Composition and method for self-assembly and mineralization of peptide amphiphiles (2023)

The present invention is directed to a composition useful for making homogeneously mineralized self assembled peptide-amphiphile nanofibers and nanofiber gels. The composition is generally a solution comprised of a positively or negatively charged peptide-amphiphile and a like signed ion from the mineral. Mixing this solution with a second solution containing a dissolved counter-ion of the mineral and/or a second oppositely charged peptide amphiphile, results in the rapid self assembly of the peptide-amphiphiles into a nanofiber gel and templated mineralization of the ions. Templated mineralization of the initially dissolved mineral cations and anions in the mixture occurs with preferential orientation of the mineral crystals along the fiber surfaces within the nanofiber gel. One advantage of the present invention is that it results in homogenous growth of the mineral throughout the nanofiber gel. Another advantage of the present invention is that the nanofiber gel formation and mineralization reactions occur in a single mixing step and under substantially neutral or physiological pH conditions. These homogeneous nanostructured composite materials are useful for medical applications especially the regeneration of damaged bone in mammals. This invention is directed to the synthesis of peptide-amphiphiles with more than one amphiphilic moment and to supramolecular compositions comprised of such multi-dimensional peptide-amphiphiles. Supramolecular compositions can be formed by self assembly of multi-dimensional peptide-amphiphiles by mixing them with a solution comprising a monovalent cation.
All-Spectrum Cognitive Channelization around Narrowband and Wideband Primary Stations (2015)

In this paper we design, implement, and experimentally evaluate a wireless software-defined radio platform for cognitive channelization in the presence of narrowband or wideband primary stations. Cognitive channelization is achieved by jointly optimizing the transmission power and the waveform channel of the secondary users. The process of joint resource allocation requires no a-priori knowledge of the transmission characteristics of the primary user and maximizes the signal-to- interference-plus-noise ratio (SINR) at the output of the secondary receiver. This is achieved by designing waveforms that span the whole continuum of available/device-accessible spectrum, while satisfying a peak power constraint for the secondary users and an interference temperature (IT) constraint for the primary users. We build a four-node software-defined radio testbed and experimentally demonstrate in an indoor laboratory environment the theoretical concepts of all-spectrum cognitive channelization in terms of pre-detection SINR and bit-error-rate (BER) at both primary and secondary receivers.