gebhart/patrepeval huggingface dataset:
Differential expression of osteocalcin during the metastatic progression of prostate cancer (2009)

Osteocalcin expression is restricted to osteoblasts and serum osteocalcin level is elevated in metastatic bone tumors including prostate tumors, which predominantly metastasizes to the bone and causes typical osteoblastic lesions. Previously, we have reported that osteocalcin RNA is widely expressed but incompletely spliced in the prostate including prostate tumors. Considering that many studies using osteocalcin-driven gene therapy have been conducted to treat hormone refractory metastatic tumors, detailed mechanisms controlling osteocalcin expression needs to be clarified. We aim to learn how osteocalcin expression is regulated during the metastatic process of prostate cancer. We applied assays of immunohistochemistry and RNA in situ hybridization in prostate tumors acquired from prostate (15) and metastatic sites, 13 from lymph node and 14 from bone. RT-PCR analysis in various cultured prostate cells was also performed. As predicted, osteocalcin RNA was highly expressed in most prostate epithelial cells of tumors, regardless of metastatic status of the tumor. However, osteocalcin protein was undetectable in tumors acquired from the primary site or lymph nodes whereas protein was highly expressed in the majority of bone-metastasized prostate tumors. RT-PCR analysis demonstrated that there was more completely spliced form of osteocalcin RNA present in bone-derived prostate cancer cells. Our data suggest that osteocalcin RNA was expressed but not completely spliced in non-bone environment, ultimately resulting in improper production of osteocalcin protein. This study explains why serum osteocalcin level is increased in patients with bone-metastasized prostate cancers. Yet, it remains to be clarified what regulates bone-specific osteocalcin RNA splicing in prostate tumors.
Abstract 363: Therapeutic targeting of insulin receptor-A with a dual IGF-1R/IR inhibitor: Overcoming a potential escape mechanism from IGF-1R-specific signaling inhibition in insulin receptor-A transfected cancer cells (2010)

Abstract Type I Insulin-like Growth Factor Receptor (IGF-1R) is a tyrosine kinase receptor that is activated by binding to IGF-1 and IGF-II ligands; IGF-1R has been shown to play a role in cancer development and progression and therapies targeting IGF-1R have resulted in clinical benefit in cancer patients. Insulin Receptor (IR) which is closely related to IGF-1R, is expressed in normal tissues and tumors, and is expressed as two isoforms, IR-A and IR-B. IR-A exhibits mitogenic activity and is preferentially found in fetal tissue and cancer cells, whereas IR-B regulates glucose metabolism in response to insulin. Both IR isoforms bind insulin, and IR-A also binds IGF-II. Several cancer cell types that express IR-A also overexpress IGF-II, suggesting a possible autocrine loop that enhances tumor survival. Since IGF-1R antibodies bind specifically to IGF-1R and not to IR, IR signaling could represent a potential escape mechanism to antibody treatment through the IR-A pathway. BMS-754807, a small molecule inhibitor with dual activity against IGF-1R and IR, recently entered clinical development. It is anticipated that BMS-754807 can prevent or overcome therapeutic resistance resulting from increased IR-activated signaling. The goal of the presented studies was to demonstrate whether dual IGF-1R/IR inhibition by BMS-754807 may prevent IR-mediated resistance to IGF-1R inhibition. To test this hypothesis, a human rhabdomyosarcoma cell line, Rh41 expressing IGF-1R, but little IR, was engineered to express either IR-A (Rh41-IR-A) or IR-B (Rh41-IR-B). IR expression was confirmed by PCR analysis of specific IR isoforms. Rh41-IR-A cells showed phosphorylation of IR after stimulation with IGF-II and/or insulin. MAB391, a neutralizing monoclonal antibody to IGF-1R, inhibited the proliferation of parental Rh41 and Rh41-IR-B cells in vitro, but Rh41-IR-A cells exhibited no sensitivity to the IGF-1R mAb. Combination treatment with both IGF-1R and IR antibodies in Rh41-IR-A cells were strongly synergistic, suggesting dual receptor blocking is required for enhanced anti-tumor efficacy. Inhibition of IGF-1R and IR with BMS-754807 showed the same inhibitory activity in Rh41-IR-A cells as was observed in the parental Rh41 cells. Therefore, dual IGF-1R/IR inhibition by BMS-754807 treatment may overcome the ability of cancer cells to utilize the IR-A pathway and provide an advantage over IGF-1R specific antibodies in the treatment of cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 363.
Interactions of Fibroblasts with Different Morphologies Made of an Engineered Spider Silk Protein (2011)

Abstract Spider silk has been investigated for decades due to the intriguing mechanical and also biomedical properties of the silk fibers. Previously, it has been shown that recombinant silk proteins can also be processed into other morphologies. Here, we characterized scaffolds made of the recombinant spider silk protein eADF4(C16) concerning their surface interactions with fibroblasts. Studies of BALB/3T3 cells on hydrogels and films made of eADF4(C16) showed low cell adhesion without observable duplication. Electro‐spun non‐woven scaffolds made of eADF4(C16), however, enabled both their adhesion and proliferation. Since eADF4(C16) lacks specific motifs for cell attachment, fibroblasts cannot generate focal adhesions with the material's surface, and, therefore, other cell–interface interactions such as topographical anchorage or cell attachment mediated by adhesion of extracellular matrix proteins are discussed in this paper. On non‐woven meshes protrusion of filopodia and/or lamellipodia between individual fibers increase the surface contact area, which depends on the diameter of the fibers of the non‐woven meshes. In contrast, at flat (film) or microstructured surfaces (hydrogels) such interactions seem to be precluded.
ChemInform Abstract: Structural, Electronic, Optical and Vibrational Properties of Nanoscale Carbons and Nanowires: A Colloquial Review (2010)

Abstract Review: 230 refs.
OR2AT4 and OR1A2 counterregulate molecular pathophysiological processes of steroid-resistant inflammatory lung diseases in human alveolar macrophages (2022)

These are the first indications for utilizing olfactory receptors as therapeutic target molecules in treating steroid-resistant lung diseases with non-type 2 inflammation.
META-pipe - Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data (2016)

The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or exploited. Marine metagenomics (DNA shotgun sequencing), not only offers opportunities for studying structure and function of microbial communities, but also identification of novel biocatalysts and bioactive compounds. However, data analysis, management, storage, processing and interpretation are significant challenges in marine metagenomics due to the high diversity in samples and the size of the marine flagship projects. We provide a new pipeline, META-pipe, for marine metagenomics analysis. It offers pre- processing, assembly, taxonomic classification and functional analysis. To reduce the effort to develop and deploy it, we have integrated existing biological analysis frameworks, and compute and storage infrastructure resources. Our current META-pipe web service provides integration with identity provider services, distributed storage, computation on a Supercomputer, Galaxy workflows, and interactive data visualizations. We have evaluated the scalability and performance of the analysis pipeline. Our results demonstrate how to develop and deploy a pipeline on distributed compute and storage resources, and discusses important challenges related to this process.
Momentum considerations inside near-zero index materials (2022)

Near-zero index (NZI) materials, i.e., materials having a phase refractive index close to zero, are known to enhance or inhibit light-matter interactions. Most theoretical derivations of fundamental radiative processes rely on energetic considerations and detailed balance equations, but not on momentum considerations. Because momentum exchange should also be incorporated into theoretical models, we investigate momentum inside the three categories of NZI materials, i.e., inside epsilon-and-mu-near-zero (EMNZ), epsilon-near-zero (ENZ) and mu-near-zero (MNZ) materials. In the context of Abraham-Minkowski debate in dispersive materials, we show that Minkowski-canonical momentum of light is zero inside all categories of NZI materials while Abraham-kinetic momentum of light is zero in ENZ and MNZ materials but nonzero inside EMNZ materials. We theoretically demonstrate that momentum recoil, transfer momentum from the field to the atom and Doppler shift are inhibited in NZI materials. Fundamental radiative processes inhibition is also explained due to those momentum considerations inside three-dimensional NZI materials. Absence of diffraction pattern in slits experiments is seen as a consequence of zero Minkowski momentum. Lastly, consequence on Heisenberg inequality, microscopy applications and on the canonical momentum as generator of translations are discussed. Those findings are appealing for a better understanding of fundamental light-matter interactions at the nanoscale as well as for lasing applications.
PCSK9 expression in the ischaemic heart and its relationship to infarct size, cardiac function, and development of autophagy (2018)

PCSK9 is up-regulated in the ischaemic hearts and determines development of infarct size, cardiac function, and autophagy.
RNase H: Specificity, Mechanisms of Action, and Antiviral Target (2013)

The Ribonuclease (RNase) H is one of the four enzymes encoded by all retroviruses, including HIV. Its main activity is the hydrolysis of the RNA moiety in RNA-DNA hybrids. The RNase H ribonuclease is essential in the retroviral life cycle, since it generates and removes primers needed by the Reverse Transcriptase (RT) for initiation of DNA synthesis. Retroviruses lacking RNase H activity are noninfectious. Despite its importance, RNase H is the only enzyme of HIV not yet targeted by antiretroviral therapy. Here, we describe functions and mechanisms of RNase H during the HIV life cycle and describe a cleavage assay, which is suitable to determine RNase H activity in samples of various kinds. In this assay, an artificial, fluorescence-labeled RNA-DNA hybrid is cleaved in vitro by an RT/RNase H enzyme. Cleavage products are analyzed by denaturing polyacrylamide gel electrophoresis (PAGE). This assay may be used to detect the RNase H, assess the effect of inhibitors, or even activators, of the RNase H, as we have described, as candidates for novel antiretroviral agents.
Supported MoOx and WOx Solid Acids for Biomass Valorization: Interplay of Coordination Chemistry, Acidity, and Catalysis (2021)

Supported molybdenum oxide (MoOx) and tungsten oxide (WOx) materials are a vital class of solid acid catalysts for the chemical industry because of their nontoxic nature, strong acidity, remarkable stability in water, hydrogen, and oxygen atmospheres, and excellent reusability performance. These fascinating solid acids play a pivotal role in developing sustainable catalytic routes for renewable biomass processing to produce value-added fuels, chemicals, and platform molecules. The coordination chemistry of MoOx and WOx on the support materials (oxides, carbons, or zeolites) controls their acidic strength, active site accessibility, and catalytic activity. Hence, significant efforts have been made toward optimizing the conditions used for catalyst synthesis and biomass processing to tune the coordination chemistry of MoOx and WOx with the substrate molecules and, thus, their acid-activity/selectivity performance. This Review provides a comprehensive overview of supported MoOx and WOx solid acids for biomass valorization. The importance of the biomass and the role of solid acids for biomass valorization were emphasized, followed by a brief discussion of supported MoOx and WOx solid acids. Afterward, the interplay of coordination chemistry, acidic strength, and catalytic activity of supported MoOx and WOx solid acids was discussed. Finally, their catalytic applications for the valorization of several biomass substrates and their derivatives were summarized. This Review will provide valuable insights for developing advanced supported WOx and MoOx solid acids for catalytic biomass valorization and other challenging acid-catalyzed processes.
Tuning Pharmacokinetics to Improve Tumor Accumulation of a Prostate-Specific Membrane Antigen-Targeted Phototheranostic Agent (2018)

We describe a simple and effective bioconjugation strategy to extend the plasma circulation of a low molecular weight targeted phototheranostic agent, which achieves high tumor accumulation (9.74 ± 2.26%ID/g) and high tumor-to-background ratio (10:1). Long-circulating pyropheophorbide (LC-Pyro) was synthesized with three functional building blocks: (1) a porphyrin photosensitizer for positron-emission tomography (PET)/fluorescence imaging and photodynamic therapy (PDT), (2) a urea-based prostate-specific membrane antigen (PSMA) targeting ligand, and (3) a peptide linker to prolong the plasma circulation time. With porphyrin's copper-64 chelating and optical properties, LC-Pyro demonstrated its dual-modality (fluorescence/PET) imaging potential for selective and quantitative tumor detection in subcutaneous, orthotopic, and metastatic murine models. The peptide linker in LC-Pyro prolonged its plasma circulation time about 8.5 times compared to its truncated analog. High tumor accumulation of LC-Pyro enabled potent PDT, which resulted in significantly delayed tumor growth in a subcutaneous xenograft model. This approach can be applied to improve the pharmacokinetics of existing and future targeted PDT agents for enhanced tumor accumulation and treatment efficacy.
Nutrient effects on the hepatic production of somatomedin C (IGF,) in the milk-fed calf (1989)

The present study was aimed at determining the influence of nutrients supplied by a milk diet (glucose, amino acids, triglycerides) on hepatic somatomedin C (IGFi) production in vivo in four 30-d-old milk-fed calves fitted with chronically indwelling catheters in hepatic (HV), portal (PV) and mesenteric veins and in the hepatic artery (HA), and with electromagnetic flow-meters on HA and PV. Fasting for 16 h induced a decrease (P less than 0.01) in hepatic IGF1 production (nmol/kg body-weight (BW) for 6 h) (1.1 (SE 0.2) v. 6.6 (SE 0.7) in control animals). Infusion of glucose (1.8 g/kg BW for 4 h) or a mixture of amino acids (Azonutril; R. Bellon, Neuilly sur Seine; 62.5 mg nitrogen/kg BW for 3 h) in a mesenteric vein led to no significant effect on hepatic IGF1 production for 6 h (1.2 (SE 0.3) and 0.7 (SE 0.3) nmol/kg BW respectively) compared with fasted calves. Infusion of chylomicrons purified from milk-fed calves (10.5 mg/h per kg BW, i.e. 0.16 mg triglycerides/kg BW per min) enhanced significantly (P less than 0.01) the hepatic production of IGF1 (mean value for 6 h: 5.3 (SE 0.8) nmol/kg BW). Infusion of Intralipid (7 mg triglycerides/kg BW per min) induced a slight but significant hepatic IGF1 production which amounted to 3.5 (SE 0.4) nmol/kg BW (P less than 0.1 compared with chylomicron treatment) and it began only 5 h after starting the infusion. Neither triglyceride nor chylomicron infusion significantly modified hepatic blood flow. Thus, these results demonstrate for the first time the role of lipids in the regulation of hepatic IGF1 production in vivo.
Reperfused myocardial infarctions on T1‐ and susceptibility‐enhanced MRI: Evidence for loss of compartmentalization of contrast media (1994)

The purpose of this study was to characterize the contrast caused by a susceptibility MRI contrast agents, on spin echo T2-weighted imaging of reperfused myocardial infarction. Our interest in this model focused on the expected requirement that such agents be compartmentalized in the tissue to cause signal loss on spin echo images, a condition which may not be present in reperfused infarcted myocardium. Accordingly, nine rats were subjected to 2 h of left coronary artery occlusion followed by 3 +/- 0.5 h of reperfusion prior to administration of contrast media. Three sets of MR images were acquired: (a) baseline axial images at the midventricle, both T1-weighted (TR/TE = 300/20) and T2-weighted (TR/TE = 1500/60); (b) T1-weighted images after administering a T1-enhancing agent, Gd-DTPA-BMA (0.2 mmol/kg), to document that contrast media is delivered to the reperfused infarction; and (c) T2-weighted images after administering the susceptibility agent, Dy-DTPA-BMA (1.0 mmol/kg). Gadolinium-enhanced T1 images depicted reperfused infarction as regions with greatly enhanced signal intensity compared with uninfarcted myocardium, indicating that contrast agent was delivered to the infarcted zone. Dysprosium-enhanced T2 images depicted the injury as a region of persistent signal intensity relative to depletion of signal in normal myocardium, consistent with failure of the contrast agent to cause signal loss. Similar infarction sizes were observed for unenhanced T2-weighted images (33 +/- 5%), gadolinium-enhanced T1-weighted images (36 +/- 5%) and postmortem staining (30 +/- 6%); strong correlations (r > 0.9) were noted in comparisons of these data.(ABSTRACT TRUNCATED AT 250 WORDS)
MR Imaging Characterization of Microvessels in Experimental Breast Tumors by Using a Particulate Contrast Agent with Histopathologic Correlation (2001)

USPIO, a macromolecular particulate MR imaging contrast agent, can be applied successfully to characterize tumor microvessels in animals. USPIO-derived K(PS) correlated strongly with histopathologic tumor grade, MVD, and K(PS) values derived by using albumin-(Gd-DTPA)(30) in the same tumors.
Tris(phosphino)borato Silver(I) Complexes as Precursors for Metallic Silver Aerosol-Assisted Chemical Vapor Deposition (2008)

A series of light- and air-stable tris(phosphino)borato silver(I) complexes has been synthesized, structurally and spectroscopically characterized, and implemented in the growth of low resistivity metallic silver thin films by aerosol-assisted chemical vapor deposition (AACVD). Of the four complexes in the series, [RB(CH2PR'2) 3]AgPEt3 (R = Ph (1, 3), (n)Bu (2, 4); R' = Ph (1, 2), (i)Pr (3, 4), complexes 1 and 2 have been characterized by single-crystal X-ray diffraction. Complex 2 represents a significant improvement over previously available nonfluorinated Ag precursors, owing to ease of handling and efficient film deposition characteristics. Thermogravimetric analysis (TGA) shows that the thermolytic properties of these complexes can be significantly modified by altering the ligand structure. Polycrystalline cubic-phase Ag thin films were grown on glass, MgO(100), and 52100 steel substrates. Ag films of thicknesses 3 microm, grown at rates of 14-18 nm/min, exhibit low levels of extraneous element contamination by X-ray photoelectron spectroscopy (XPS). Atomic force microscopy (AFM) and scanning electron microscopy (SEM) indicate that film growth proceeds primarily via an island growth (Volmer-Weber) mechanism.
Learned Queries for Efficient Local Attention (2021)

Vision Transformers (ViT) serve as powerful vision models. Unlike convolutional neural networks, which dominated vision research in previous years, vision transformers enjoy the ability to capture long-range dependencies in the data. Nonetheless, an integral part of any transformer architecture, the self-attention mechanism, suffers from high latency and inefficient memory utilization, making it less suitable for high-resolution input images. To alleviate these shortcomings, hierarchical vision models locally employ self-attention on non-interleaving windows. This relaxation reduces the complexity to be linear in the input size; however, it limits the cross-window interaction, hurting the model performance. In this paper, we propose a new shift-invariant local attention layer, called query and attend (QnA), that aggregates the input locally in an overlapping manner, much like convolutions. The key idea behind QnA is to introduce learned queries, which allow fast and efficient implementation. We verify the effectiveness of our layer by incorporating it into a hierarchical vision transformer model. We show improvements in speed and memory complexity while achieving comparable accuracy with state-of-the-art models. Finally, our layer scales especially well with window size, requiring up-to x10 less memory while being up-to x5 faster than existing methods. The code is publicly available at \url{https://github.com/moabarar/qna}.
Venous thromboembolism in patients with myelodysplastic syndrome treated with lenalidomide: Incidence and risk factors (2008)

7084 Background: The frequency of venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE) among patients with myelodysplastic syndrome (MDS) has not been characterized. This analysis describes the frequency of and risk factors for VTE among MDS patients participating in clinical studies of lenalidomide. Methods: Demographic and clinical risk factors for VTE were assessed for 408 patients with a histologically confirmed diagnosis of MDS according to FAB criteria: 45 patients in a single-center, open-label, pilot dose-finding lenalidomide study and 363 patients with low- or intermediate-1-risk MDS without (N=215) or with (N=148) a del (5q) cytogenetic abnormality and red blood cell-transfusion-dependent anemia enrolled in multi-center single-arm open-label studies. Erythropoiesis-stimulating agents were excluded in all studies. Results: VTE occurred in 14 patients during study treatment (11 DVT; 4 PE), resulting in a cumulative incidence for first VTE of 3.4% (≤365 days, 2.9%). Nine patients experienced VTE within 6 months of starting study drug (range 5–590 days; median 112.5 days). There were no differences in median age (68 vs. 72; p = 0.19) or median MDS duration at baseline (1.75 years vs. 2.40; p = 0.37) between patients with and without VTE. No differences in gender, baseline IPSS score, FAB classification, ECOG scores or number of red blood cell units transfused during the 8-week baseline period were observed (p > 0.05, all comparisons). Review of safety information identified recognized risk factors for VTE in 12/14 patients, including hospitalization (n=3), VTE history (n=3), other peripheral vascular disease (n=2), congestive heart failure/atrial fibrillation (n=4), diabetes (n=4), overweight (n=1), stroke (n=1), prior malignancy (n=2), and hormone replacement therapy (n=1). Conclusions: The incidence of VTE among MDS patients treated with lenalidomide is low. Most patients with VTE had at least one additional risk factor. Recognition of additional risk factors for VTE, with consideration of thrombosis prophylaxis where clinically warranted, is important to improve clinical outcomes in MDS patients. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Celgene Corporation Celgene Corporation Celgene Corporation Celgene Corporation Celgene Corporation
How to Tell a Program from an Automobile (2016)

If I need an extra shift to supplement my wage I volunteer to work as a carer in the nursing home. I am still paid as a staff nurse but perform care assistant duties. Both nurses and carers are there to work together to meet patients' daily living, nursing, emotional and social needs so, in that sense, there is little difference. In fact I enjoy the freedom away from drug rounds, wound management and administration duties. I can get back to the heart of nursing: delivering direct care to patients.