gebhart/patrepeval huggingface dataset:
Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer (2023)

Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effective for many patients with lung cancer with EGFR mutations. However, not all patients are responsive to EGFR TKIs, including even those harboring EGFR-sensitizing mutations. In this study, we quantified the cells and cellular interaction features of the tumor microenvironment (TME) using routine H&E-stained biopsy sections. These TME features were used to develop a prediction model for survival benefit from EGFR TKI therapy in patients with lung adenocarcinoma and EGFR-sensitizing mutations in the Lung Cancer Mutation Consortium 1 (LCMC1) and validated in an independent LCMC2 cohort. In the validation data set, EGFR TKI treatment prolonged survival in the predicted-to-benefit group but not in the predicted-not-to-benefit group. Among patients treated with EGFR TKIs, the predicted-to-benefit group had prolonged survival outcomes compared with the predicted not-to-benefit group. The EGFR TKI survival benefit positively correlated with tumor-tumor interaction image features and negatively correlated with tumor-stroma interaction. Moreover, the tumor-stroma interaction was associated with higher activation of the hepatocyte growth factor/MET-mediated PI3K/AKT signaling pathway and epithelial-mesenchymal transition process, supporting the hypothesis of fibroblast-involved resistance to EGFR TKI treatment.
The Myxobacterial Metabolite Soraphen A Inhibits HIV-1 by Reducing Virus Production and Altering Virion Composition (2017)

Soraphen A is a myxobacterial metabolite that blocks the acetyl-coenzyme A carboxylase of the host and was previously identified as a novel HIV inhibitor. Here, we report that soraphen A acts by reducing virus production and altering the gp120 virion content, impacting entry capacity and infectivity. These effects are partially reversed by addition of palmitic acid, suggesting that inhibition of HIV envelope palmitoylation is one of the mechanisms of antiviral action.
Assaying Protein-DNA Interactions In Vivo and In Vitro Using Chromatin Immunoprecipitation and Electrophoretic Mobility Shift Assays (2007)

Many events in the viral life cycle involve protein binding to defined sequences on the viral chromosome. Chromatin immunoprecipitation allows the detection of the in vivo interaction of specific proteins with specific genomic regions. In this technique, living cells are treated with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules. The crosslink with formaldehyde is reversible and covers a short distance (2 A); the components that are crosslinked are therefore in close proximity. Nuclear fractions are isolated, and the genomic DNA is sheared to reduce the average DNA fragment size to around 500 bp. These nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. The DNA bound to the studied protein is enriched after the immunoprecipitation. After reversal of the crosslinking, the resulting DNA and proteins can be independently studied. The electrophoretic mobility shift assay provides a rapid method to study DNA-binding protein interactions in vitro. This assay is based on the observation that complexes of protein and DNA migrate through a nondenaturing polyacrylamide gel more slowly than free DNA fragments. The assay is performed by incubating a purified protein, or a complex mixture of proteins, with a 32P end-labeled DNA probe containing the protein-binding site. The reaction products are analyzed on a nondenaturing polyacrylamide gel. The specificity of the DNA-binding protein for the putative binding site is established by competition experiments using specific and nonspecific nonradiolabeled DNA probes. The components of the complexes can be identified with antibodies to the protein of interest.
A Study about the Propane Ammoxidation to Acrylonitrile with an Alumina-Supported Sb−V−O Catalyst (2006)

The propane ammoxidation reaction is investigated on an alumina-supported Sb−V−O catalyst with an Sb/V atomic ratio of 1 at nominal Sb + V monolayer coverage on alumina support. The roles of reaction temperature and of the partial pressure of reactants in the reaction are evaluated. Fresh and used catalyst is characterized by X-ray diffraction, Raman spectroscopy, and X-ray photoelectron spectroscopy. The effect of sudden changes in reaction feed is used to understand if the transient activation of the catalysts during the first hours on-stream is due to surface intermediates or to a change in the catalyst structure. A discussion is presented about the reaction network and the nature of the active phases.
The Impact of Transfer Setup on the Performance of Independent Wheelchair Transfers (2012)

The data will be used to revise the guidelines related to transfers and to enable designers and engineers to create an environment that is more accessible.
On the Basic Mechanisms of Infantile Spasms (2012)

Abstract We are at a very early stage in studying the basic mechanisms of infantile spasms. However, features of several promising animal models have been described, and more may be forthcoming in the near future. Technical challenges are substantial in studying seizures in infant rodents, but they are not insurmountable. The basic science and clinical communities need to evaluate each of the proposed animal models and develop minimal criteria for what they consider to be a valid animal model of this disorder. Once validated, models should provide an unprecedented opportunity to study the mechanisms responsible for this catastrophic epilepsy and hopefully provide new avenues for effective therapies.
Cu^2+-doped germano-silicate glass fiber with high resonant nonlinearity (2007)

We firstly report on the fabrication of Cu(2+)-doped germano-silicate glass fiber for nonlinear optical devices application by using modified chemical vapor deposition and solution doping processes. Broadband absorption near 700nm due to the 3d-shell electron transitions of Cu(2+) ions from the ground state to the excited states was observed. The resonant nonlinearity of the Cu(2+)-doped fiber was estimated to be 5.5x10(-17)m(2)/W by measuring the phase shift of the fringes obtained from the long-period fiber grating pair upon pumping with a laser diode at 980nm and non-resonant nonlinearities were also measured to be 4.114x10(-21)m(2)/W by the continuous wave self-phase modulation method.
SALT: Subspace Alignment as an Auxiliary Learning Task for Domain Adaptation (2019)

Unsupervised domain adaptation aims to transfer and adapt knowledge learned from a labeled source domain to an unlabeled target domain. Key components of unsupervised domain adaptation include: (a) maximizing performance on the target, and (b) aligning the source and target domains. Traditionally, these tasks have either been considered as separate, or assumed to be implicitly addressed together with high-capacity feature extractors. When considered separately, alignment is usually viewed as a problem of aligning data distributions, either through geometric approaches such as subspace alignment or through distributional alignment such as optimal transport. This paper represents a hybrid approach, where we assume simplified data geometry in the form of subspaces, and consider alignment as an auxiliary task to the primary task of maximizing performance on the source. The alignment is made rather simple by leveraging tractable data geometry in the form of subspaces. We synergistically allow certain parameters derived from the closed-form auxiliary solution, to be affected by gradients from the primary task. The proposed approach represents a unique fusion of geometric and model-based alignment with gradients from a data-driven primary task. Our approach termed SALT, is a simple framework that achieves comparable or sometimes outperforms state-of-the-art on multiple standard benchmarks.
Inflammatory stress in primary venous and aortic endothelial cells of type 1 diabetic mice (2009)

These data suggest that diabetes imparts diffuse endothelial perturbation in the arterial and venous endothelium.
The Impact of Aging Effects and Manufacturing Variation on SRAM Soft-Error Rate (2008)

This paper describes modeling and hardware results of how the soft-error rate (SER) of a 65-nm silicon-on-insulator SRAM memory cell changes over time, as semiconductor aging effects shift the SRAM cell behavior. This paper also describes how the SER changes in the presence of systematic and random manufacturing variation.
Scalable Modified Kneser-Ney Language Model Estimation (2013)

We present an efficient algorithm to estimate large modified Kneser-Ney models including interpolation. Streaming and sorting enables the algorithm to scale to much larger models by using a fixed amount of RAM and variable amount of disk. Using one machine with 140 GB RAM for 2.8 days, we built an unpruned model on 126 billion tokens. Machine translation experiments with this model show improvement of 0.8 BLEU point over constrained systems for the 2013 Workshop on Machine Translation task in three language pairs. Our algorithm is also faster for small models: we estimated a model on 302 million tokens using 7.7% of the RAM and 14.0 % of the wall time taken by SRILM. The code is open source as part of KenLM. 1
Identification of a De Novo Der(14) Chromosome by M-FISH Analysis (2002)

We used combinatorial-coded multicolor fluorescence in situ hybridization (M-FISH) for all 24 chromosomes to study a boy with a derivative chromosome of unknown origin. The proband had growth retardation, microcephaly, high forehead, broad nose, maxillary hypoplasia, high arched palate, bilateral hearing impairment and bilateral cryptorchidism. Cytogenetic analysis revealed a de novo der(14)(q32) in which a small additional material of unknown origin was attached to terminal 14q. The M-FISH results showed that the additional material on the der(14) was chromosome 2 in origin and thus the child has partial monosomy for 14q32.1→qter and partial trisomy for 2p24→pter. This case illustrates the usefulness of M-FISH to identify additional material in de novo situations where the segment is too small to guess the origin and test by conventional FISH analysis.
Type I Protein Secretion—Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family (2016)

A very large type I polypeptide begins to reel out from a ribosome; minutes later, the still unidentifiable polypeptide, largely lacking secondary structure, is now in some cases a thousand or more residues longer. Synthesis of the final hundred C-terminal residues commences. This includes the identity code, the secretion signal within the last 50 amino acids, designed to dock with a waiting ATP binding cassette (ABC) transporter. What happens next is the subject of this review, with the main, but not the only focus on hemolysin HlyA, an RTX protein toxin secreted by the type I system. Transport substrates range from small peptides to giant proteins produced by many pathogens. These molecules, without detectable cellular chaperones, overcome enormous barriers, crossing two membranes before final folding on the cell surface, involving a unique autocatalytic process.Unfolded HlyA is extruded posttranslationally, C-terminal first. The transenvelope "tunnel" is formed by HlyB (ABC transporter), HlyD (membrane fusion protein) straddling the inner membrane and periplasm and TolC (outer membrane). We present a new evaluation of the C-terminal secretion code, and the structure function of HlyD and HlyB at the heart of this nanomachine. Surprisingly, key details of the secretion mechanism are remarkably variable in the many type I secretion system subtypes. These include alternative folding processes, an apparently distinctive secretion code for each type I subfamily, and alternative forms of the ABC transporter; most remarkably, the ABC protein probably transports peptides or polypeptides by quite different mechanisms. Finally, we suggest a putative structure for the Hly-translocon, HlyB, the multijointed HlyD, and the TolC exit.
All-Pass-Filter-Based PLL Systems: Linear Modeling, Analysis, and Comparative Evaluation (2019)

All-pass filter (APF) passes all frequency components of a signal without altering their amplitude, but changes their phase. This feature has made the APF a versatile building block in different signal processing applications. The focus of this article is on APF-based phase-locked loops (PLLs), where the APF is required for creating a 90° phase shift at the fundamental frequency. Such a phase shift is needed for generating a fictitious orthogonal signal in single-phase applications and rejecting the grid voltage imbalance in three-phase systems. To the best of authors' knowledge, none of the APF-based PLLs have an accurate model yet. This gap in knowledge makes the analysis of these synchronization systems and identifying their advantages/disadvantages compared to state-of-the-art structures complicated. The main objective of this article is to bridge this knowledge gap.
Transarterial chemoembolization with miriplatin vs. epirubicin for unresectable hepatocellular carcinoma: a phase III randomized trial (2017)

JapicCTI-080632.
Erfolg endoskopischer Therapie bei traumatischen Gallengangsverletzungen (2004)

Einleitung: Für die endoskopische Diagnostik und Therapie von Gallengangsverletzungen durch stumpfe Bauchtraumata vor allem im Rahmen von Verkehrsunfällen (z.B. Steuerrad, Gurt) gibt es keine einheitlichen Richtlinien. Insbesondere die Abgrenzung zum chirurgischen Vorgehen ist unklar.
Effector form design for 1DOF planar actuation (2013)

Given a desired function for an effector, what is its appropriate shape? This paper formulates mechanical function as a product of both effector's shape and motion, and, assuming a fixed motion model, explores the role of shape in satisfying it. We assume that the desired mechanical function is expressed as a set of constraints on the geometry of contact, and develop the tools for transforming these constraints into an effector shape. A previous paper [1] addressed the special case of revolute or prismatic fingers. This paper develops the more general case, including all smooth 1DOF planar mechanisms. The technique is illustrated with the design of finger shapes to improve the stability of a planar grasp of an object.
Dietary fat interacts with QTLs controlling induction of<i>Pgc-1</i>α and<i>Ucp1</i>during conversion of white to brown fat (2003)

To identify novel regulatory factors controlling induction of the brown adipocyte-specific mitochondrial uncoupling protein (Ucp1) mRNA in the retroperitoneal white fat depot, we previously mapped quantitative trait loci (QTLs) that control this trait to chromosomes 2, 3, 8, and 19. Since the peroxisome proliferator activator receptor-gamma coactivator-1alpha (PGC-1alpha) regulates Ucp1 and other genes of energy metabolism, we have evaluated whether the QTLs controlling Ucp1 mRNA levels also modulate Pgc-1alpha mRNA levels by analysis of backcross progeny from the A/J and C57BL/6J strains of mice. The results indicate that a locus on chromosome 3 orchestrates expression of Pgc-1alpha and Ucp1 in retroperitoneal fat of mice fed a low-fat diet; however, the effect of this locus on Pgc-1alpha is lost, and a significant correlation between Ucp1 and Pgc-1alpha is severely reduced in mice fed a high-fat diet. An additional QTL located on chromosome 5 has also been identified for the selective regulation of Ucp1 mRNA levels. Similar to the effects of a high-fat diet on the chromosome 3 QTL, linkage of the chromosome 5 QTL is also lost in mice on a high-fat diet. Thus dietary fat has a profound influence on PGC-1alpha-regulated pathways controlling energy metabolism in white fat. The allelic variation observed in the regulation of Ucp1 and Pgc-1alpha expression in brown adipocytes of white fat but not interscapular brown fat suggests that fundamentally different regulatory mechanisms exist to control the thermogenic capacities of these tissues.
Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer’s disease (2018)

Our findings suggest that pleiotropy analysis is a useful approach to identifying novel genetic associations with complex diseases and their endophenotypes. Functional studies are needed to determine whether ECRG4 or HDAC9 is plausible as a therapeutic target.
Adenovirus-induced maturation of dendritic cells through a PI3 kinase-mediated TNF-α induction pathway (2004)

Systemic administration of adenovirus and adenovirus vectors induces a robust innate and adaptive immune response in a variety of animal models. In tumor necrosis factor (TNF)(-/-) mice, a diminished immune response to adenovirus (Ad) infection has been attributed to compromised dendritic cell (DC) maturation. In this report, we investigated the mechanisms responsible for Ad-mediated activation and maturation of DC. Ad infection induced high levels of TNF-alpha expression by murine bone marrow-derived DC, comparable to levels observed with lipopolysaccharide exposure. Ad-induced TNF-alpha production was necessary for DC maturation and acts in an autocrine manner. Unlike TNF-alpha production associated with exposure to lipopolysaccharide, Ad induction of TNF-alpha was not dependent on the MyD88 signaling pathway. In contrast, Ad-induced TNF-alpha production and DC maturation were dependent on signaling by phosphoinositide-3-OH kinase (PI3K), as determined by wortmannin and LY294002 blocking experiments. The adenovirus capsid protein penton contains a well characterized arginine-glycine-aspartic acid integrin-binding domain that stimulates PI3K in fibroblast cell lines. When this region of the penton was mutated, TNF-alpha expression and bone marrow-derived DC maturation were attenuated. We propose that integrin-mediated PI3K induction of NF-kappaB activates an autocrine TNF-alpha pathway required for DC maturation in response to Ad.
Magnetic resonance imaging of cardiomyocyte apoptosis with a novel magneto‐optical nanoparticle (2005)

The ability to image cardiomyocyte apoptosis in vivo with high-resolution MRI could facilitate the development of novel cardioprotective therapies. The sensitivity of the novel nanoparticle AnxCLIO-Cy5.5 for cardiomyocyte apoptosis was thus compared in vitro to that of annexin V-FITC and showed a high degree of colocalization. MRI was then performed, following transient coronary artery (LAD) occlusion, in five mice given AnxCLIO-Cy5.5 and in four mice given an identical dose (2 mg Fe/kg) of CLIO-Cy5.5. MR signal intensity and myocardial T2* were evaluated, in vivo, in hypokinetic regions of myocardium in the LAD distribution. Ex vivo fluorescence imaging was performed to confirm the in vivo findings. Myocardial T2* was significantly lower in the mice given AnxCLIO-Cy5.5 (8.1 versus 13.2 ms, P<0.01), and fluorescence target to background ratio was significantly higher (2.1 versus 1.1, P<0.01). This study thus demonstrates the feasibility of obtaining high-resolution MR images of cardiomyocyte apoptosis in vivo with the novel nanoparticle, AnxCLIO-Cy5.5.
Pseudophakic cystoid macular edema prevention and risk factors; prospective study with adjunctive once daily topical nepafenac 0.3% versus placebo (2017)

NIH ClincalTrials.gov retrospectively registered January 15, 2017, NCT03025945 .
Analysis of HSP90 and HSP70 expression in dogs before and after treatment with STA-1474. (2015)

&lt;p&gt;a) PBMCs were collected from normal control dogs (cont 1 and cont 2) and study dogs before and 24 hours after treatment with STA-1474 at 9.5 mg/kg over 8 hours. Protein lysates were generated and following SDS-PAGE, Western blotting was performed for HSP70. Blots were then stripped and reprobed for β-actin. b) Tumor biopsies and PBMCs were collected from dogs treated with 5 mg/kg STA-1474 over 1 hour before treatment and at 7 and 24 hours post treatment. Protein lysates were generated and an ELISA was performed to detect HSP70. Results are expressed as HSP70 protein (ng/ml) and percent of baseline. c) Protein lysates generated from the tumor biopsies described above were subjected to SDS-PAGE followed by Western blotting for HSP90. Blots were then stripped and re-probed for β-actin.&lt;/p&gt;
Heterocyclic liquid crystals designed for optical light emitting diode applications (1999)

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 R. J. Twieg, S. Gu, L. Sukhomlinova, G. G. Malliaras, R. Fan, and D. Culjkovic, "Heterocyclic Liquid Crystals Designed for Organic Light Emitting Diode Applications," in Organic Thin Films for Photonic Applications, OSA Technical Digest (Optica Publishing Group, 1999), paper SuD1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Smart-TV Based Integrated E-health Monitoring System with Agent Technology (2012)

An ageing population is now the leading concern for higher healthcare costs due to more cases of chronic illnesses. Telemedicine systems based on modern Information and Communication Technology (ICT) are expected to play a pivotal role in alleviating the pressure on health care services. Environmental factors have also profound impact on health condition of the patients. As a consequence monitoring of human health along with the environmental (where the patient is located) health enables the health care providers to comprehend more accurately about a patient's situation. In this paper we describe a novel integrated tele-monitoring framework (theoretical architecture) proposed to support both of the above functions simultaneously though a single framework. The proposed system also innovatively harnesses the power of emerging Smart-TV technology as a means of interaction between patient and the health care providers. To the best of our knowledge, this is the first of its kind.