gebhart/patrepeval huggingface dataset:
Diabetes Due to Secretion of an Abnormal Insulin (1980)

A 51-year-old, nonobese man with diabetes mellitus had marked hyperinsulinemia (70 to 120 muU per milliliter; 502 to 860 pmol per liter) and fasting hyperglycemia (140 to 170 mg per 100 ml; 7.8 to 9.4 mmol per liter). Plasma proinsulin, glucagon, growth hormone, and cortisol levels were normal; insulin antibodies and insulin-receptor antibodies were not detected. The patient showed relatively normal insulin sensitivity, and insulin receptors on circulating monocytes were within the normal range. Insulin from the patient's serum bound to IM-9 lymphocytes and rat adipocytes approximately 40 per cent as well as insulin standards. Its biologic activity on rat adipocytes averaged 15 per cent of that expected from its immunologic concentration. The impaired biologic activity of this patient's circulating insulin was probably due to a structural abnormality. Subsequent studies of the patient's insulin (fortuitously obtained from his pancreas during a laparotomy for a pancreatic cyst) have confirmed this conclusion. (N Engl J Med 302:129-135, 1980).
Diversity performance of Modulated Scattering Antenna Array with switched reflector (2010)

The previous researches on the modulated scattering antenna array (MSAA) have shown that the second-order intermodulation scattering signal is relatively low compared with the directly received signal. In this research, a switched reflector is used to solve this problem. The diversity performance of the MSAA with a switched reflector is investigated. It is shown that the diversity performance of the MSAA can be improved by mounting a switch on the reflector.
Filters in topology optimization based on Helmholtz‐type differential equations (2010)

Abstract The aim of this paper is to apply a Helmholtz‐type partial differential equation as an alternative to standard density filtering in topology optimization problems. Previously, this approach has been successfully applied as a sensitivity filter. The usual filtering techniques in topology optimization require information about the neighbor cells, which is difficult to obtain for fine meshes or complex domains and geometries. The complexity of the problem increases further in parallel computing, when the design domain is decomposed into multiple non‐overlapping partitions. Obtaining information from the neighbor subdomains is an expensive operation. The proposed filter technique requires only mesh information necessary for the finite element discretization of the problem. The main idea is to define the filtered variable implicitly as a solution of a Helmholtz‐type differential equation with homogeneous Neumann boundary conditions. The properties of the filter are demonstrated for various 2D and 3D topology optimization problems in linear elasticity, solved on serial and parallel computers. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Simulation-Based Design of Aircraft Electrical Power Systems (2011)

Early stage design provides the greatest opportunities to explore design alternatives and perform trade studies before costly design decisions are made. The goal of this research is to develop a simulation-based framework that enables architectural analysis of complex systems during the conceptual design phase. Using this framework, design teams can systematically explore architectural design decisions during the early stage of system development prior to the selection of specific components. The analysis performed at this earliest stage of design facilitates the development of more robust and reliable system architectures. Application of the presented method to the design of a representative aerospace electrical power system (EPS) demonstrates these capabilities.
Boosting Personalized Food Image Classifier by Sharing Food Records (2021)

Food image recognition tasks are generally addressed by using a closed dataset. In a real-world setting, however, the dataset is updated as the new class of food appears, and it is impossible to train a model that distinguishes all kinds of food in advance. Also, inter-class similarity and intra-class diversity make food image recognition tasks more challenging. Previous works have shown that a personalized classifier using an individual user's food records can deal with some of these problems. On top of that, we propose a personalized classifier that learns from not only the accumulating food records of the individual user but also the growing records of the entire user. To conduct a realistic experiment, we build a new dataset of daily food images using a food-logging application called FoodLog Athl. As a result, our proposed method significantly outperforms prior personalized classification methods for food image recognition in a realistic setting.
Novel assays monitoring direct glucocorticoid receptor protein activity exhibit high predictive power for ligand activity on endogenous gene targets (2022)

Abstract Exogenous glucocorticoids are widely used in the clinic for the treatment of inflammatory disorders and auto-immune diseases. Unfortunately, their use is hampered by many side effects and therapy resistance. Efforts to find more selective glucocorticoid receptor (GR) agonists and modulators (called SEGRAMs) that are able to separate anti-inflammatory effects via gene repression from metabolic effects via gene activation, have been unsuccessful so far. In this study, we characterized a set of functionally diverse GR ligands in A549 cells, first using a panel of luciferase-based reporter gene assays evaluating GR-driven gene activation and gene repression. We expanded this minimal assay set with novel luciferase-based read-outs monitoring GR protein levels, GR dimerization and GR Serine 211 (Ser211) phosphorylation status and compared their outcomes with compound effects on the mRNA levels of known GR target genes in A549 cells and primary hepatocytes. We found that luciferase reporters evaluating GR-driven gene activation and gene repression were not always reliable predictors for effects on endogenous target genes. Remarkably, our novel assay monitoring GR Ser211 phosphorylation levels proved to be the most reliable predictor for compound effects on almost all tested endogenous GR targets, both driven by gene activation and repression. The integration of this novel assay in existing screening platforms running both in academia and industry may therefore boost chances to find novel GR ligands with an actual improved therapeutic benefit.
Virus-encoded microRNA contributes to the molecular profile of EBV-positive Burkitt lymphomas (2015)

Burkitt lymphoma (BL) is an aggressive neoplasm characterized by consistent morphology and phenotype, typical clinical behavior and distinctive molecular profile. The latter is mostly driven by the MYC over-expression associated with the characteristic translocation (8;14) (q24; q32) or with variant lesions. Additional genetic events can contribute to Burkitt Lymphoma pathobiology and retain clinical significance. A pathogenetic role for Epstein-Barr virus infection in Burkitt lymphomagenesis has been suggested; however, the exact function of the virus is largely unknown.In this study, we investigated the molecular profiles (genes and microRNAs) of Epstein-Barr virus-positive and -negative BL, to identify specific patterns relying on the differential expression and role of Epstein-Barr virus-encoded microRNAs.First, we found significant differences in the expression of viral microRNAs and in selected target genes. Among others, we identified LIN28B, CGNL1, GCET2, MRAS, PLCD4, SEL1L, SXX1, and the tyrosine kinases encoding STK10/STK33, all provided with potential pathogenetic significance. GCET2, also validated by immunohistochemistry, appeared to be a useful marker for distinguishing EBV-positive and EBV-negative cases. Further, we provided solid evidences that the EBV-encoded microRNAs (e.g. BART6) significantly mold the transcriptional landscape of Burkitt Lymphoma clones.In conclusion, our data indicated significant differences in the transcriptional profiles of EBV-positive and EBV-negative BL and highlight the role of virus encoded miRNA.
SATE (Aryl) Phosphotriester Series. II. Stability Studies and Physicochemical Parameters (2003)

Abstract The stability of phosphotriester derivatives of 3′-azido-2′,3′-dideoxythymidine (AZT) bearing a S-pivaloyl-2-thioethyl (tBuSATE) group and various aryl residues derived from L-tyrosine was evaluated in biological media. The results demonstrate that such compounds give rise to intracellular delivery of the parent mononucleotide through esterase and phosphodiesterase hydrolytic steps, successively.
The use of acoustic radiation force decorrelation weighted pulse inversion (ADW-PI) in enhancing microbubble contrast (2015)

Nonlinear echo signals from microbubbles are commonly isolated and visualized using techniques such as pulse inversion (PI) or contrast pulse sequences (CPS). Although these methods function by suppressing the linear signal component, they are still susceptible to detection of a false-positive nonlinear signal arising from strong tissue interfaces. In this study, acoustic radiation force (ARF) was added to a PI imaging sequence to induce motion of specifically-targeted microbubbles in a mouse hind limb tumor. The interframe signal decorrelation from this induced motion was then used to isolate microbubble signal based on its decorrelation characteristics. Results demonstrate that this technique of decorrelation filtering significantly improves microbubble contrast-to-tissue ratio (CTR) by 1.5 dB, and thereby allows for higher levels of specificity. ARF was shown to be effective in further enhancing performance.
Cutinase gene disruption in Fusarium solani f sp pisi decreases its virulence on pea. (1994)

Fusarium solani f sp pisi (Nectria haematococca) isolate 77-2-3 with one cutinase gene produced 10 to 20% of the cutinase produced by isolate T-8 that has multiple cutinase genes, whereas cutinase gene-disrupted mutant 77-102 of isolate 77-2-3 did not produce cutinase. On the surface of pea stem segments, lesion formation was most frequent and most severe with T-8, less frequent and less severe with 77-2-3, and much less frequent and much milder with the gene-disrupted mutant. Microscopic examination of the lesions caused by the mutant strongly suggest that it penetrated the host mostly via the stomata. In seedling assays, 77-2-3 caused severe lesions on every seedling and stunted growth, whereas the mutant showed very mild lesions on one-third of the seedlings with no stunting. Thus, cutinase gene disruption resulted in a significant decrease in the pathogenicity of F. s. pisi on pea.
Data from Serial Diffusion MRI to Monitor and Model Treatment Response of the Targeted Nanotherapy CRLX101 (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Targeted nanotherapies are being developed to improve tumor drug delivery and enhance therapeutic response. Techniques that can predict response will facilitate clinical translation and may help define optimal treatment strategies. We evaluated the efficacy of diffusion-weighted magnetic resonance imaging to monitor early response to CRLX101 (a cyclodextrin-based polymer particle containing the DNA topoisomerase I inhibitor camptothecin) nanotherapy (formerly IT-101), and explored its potential as a therapeutic response predictor using a mechanistic model of tumor cell proliferation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Diffusion MRI was serially conducted following CRLX101 administration in a mouse lymphoma model. Apparent diffusion coefficients (ADCs) extracted from the data were used as treatment response biomarkers. Animals treated with irinotecan (CPT-11) and saline were imaged for comparison. ADC data were also input into a mathematical model of tumor growth. Histological analysis using cleaved-caspase 3, terminal deoxynucleotidyl transferase–mediated dUTP nick end labeling, Ki-67, and hematoxylin and eosin (H&amp;E) were conducted on tumor samples for correlation with imaging results.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; CRLX101-treated tumors at day 2, 4, and 7 posttreatment exhibited changes in mean ADC = 16 ± 9%, 24 ± 10%, 49 ± 17%, and size (TV) = −5 ± 3%, −30 ± 4%, and −45 ± 13%, respectively. Both parameters were statistically greater than controls [&lt;i&gt;p&lt;/i&gt;(ADC) ≤ 0.02, and &lt;i&gt;p&lt;/i&gt;(TV) ≤ 0.01 at day 4 and 7], and noticeably greater than CPT-11–treated tumors (ADC = 5 ± 5%, 14 ± 7%, and 18 ± 6%; TV = −15 ± 5%, −22 ± 13%, and −26 ± 8%). Model-derived parameters for cell proliferation obtained using ADC data distinguished CRLX101-treated tumors from controls (&lt;i&gt;P&lt;/i&gt; = 0.02).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Temporal changes in ADC specified early CRLX101 treatment response and could be used to model image-derived cell proliferation rates following treatment. Comparisons of targeted and nontargeted treatments highlight the utility of noninvasive imaging and modeling to evaluate, monitor, and predict responses to targeted nanotherapeutics. &lt;i&gt;Clin Cancer Res; 19(9); 2518–27. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Development and Characterization of a Fixed Repertoire of Blood Transcriptome Modules Based on Co-expression Patterns Across Immunological States (2019)

SUMMARY As the capacity for generating large scale data continues to grow the ability to extract meaningful biological knowledge from it remains a limitation. Here we describe the development of a new fixed repertoire of transcriptional modules. It is meant to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome profiling data. It is supported by customized resources, which include analysis workflows, fingerprint grid plots data visualizations, interactive web applications providing access to a vast number of module-specific functional profiling reports, reference transcriptional profiles and give users the ability to visualize of changes in transcript abundance across the modular repertoire at different granularity levels. A use case focusing on a set of six modules comprising interferon-inducible genes is also provided. Altogether we hope that this resource will also serve as a framework for improving over time our collective understanding of the immunobiology underlying blood transcriptome profiling data.
Anti-viral efficacy of a next-generation CD4-binding site bNAb in SHIV-infected animals in the absence of anti-drug antibody responses (2022)

Broadly neutralizing antibodies (bNAbs) against HIV-1 are promising immunotherapeutic agents for treatment of HIV-1 infection. bNAbs can be administered to SHIV-infected rhesus macaques to assess their anti-viral efficacy; however, their delivery into macaques often leads to rapid formation of anti-drug antibody (ADA) responses limiting such assessment. Here, we depleted B cells in five SHIV-infected rhesus macaques by pretreatment with a depleting anti-CD20 antibody prior to bNAb infusions to reduce ADA. Peripheral B cells were depleted following anti-CD20 infusions and remained depleted for at least 9 weeks after the 1<sup>st</sup> anti-CD20 infusion. Plasma viremia dropped by more than 100-fold in viremic animals after the initial bNAb treatment. No significant humoral ADA responses were detected for as long as B cells remained depleted. Our results indicate that transient B cell depletion successfully inhibited emergence of ADA and improved the assessment of anti-viral efficacy of a bNAb in a SHIV-infected rhesus macaque model.
Generation of 11-fs pulses from a self-mode-locked Ti:sapphire laser (1993)

By optimizing the intracavity dispersion compensation in a self-mode-locked Ti:sapphire laser, we have generated pulses of 10.95-fs duration. Dispersion within the laser cavity is reduced by use of a short 4.5-mm highly doped Ti:sapphire crystal and fused-silica prisms. The output from the laser has an average power of as much as 500 mW, with a wavelength centered at 780 nm and a bandwidth of 62 nm. Our results demonstrate that the exceptionally broad bandwidth of Ti:sapphire can be utilized to generate pulses that, to our knowledge, are shorter than has been possible with any other type of laser material to date.
Endocytic pathway of recombinant murine tumor necrosis factor in L-929 cells. (1988)

The fate of TNF after binding to the surface of L-929 cells was followed by using murine rTNF coupled to colloidal gold as a probe. A time-course study using electron microscopy was performed. Our results confirm previous indications obtained from biochemical studies suggesting that TNF is internalized by this cell type. They further directly show that internalization proceeds through the classical receptor-mediated endocytosis pathway, i.e., via clathrin-coated structures and endosomes before accumulation in secondary lysosomes.
The infrared structure and the origin of the starburst disk in NGC 1068 (1988)

We present a map at 10.8 microns made with good spatial resolution (4.4" x 4.1") of the infrared-luminous disk in the Seyfert galaxy NGC 1068. The relationship of the 10.8 micron emission with low-excitation, visible H II regions greatly strengthens the previous conclusion that the high infrared luminosity is reradiation from dust heated by young stars. The 10.8 micron emission is distributed across the central 3.5 kpc primarily in two very extended complexes, one located north of the nucleus and the other to the southwest. The two complexes coincide with the two dominant CO features and are located near the ends of a prominent bar evident in the near-infrared. Based on considerations of the rotation curve for the central region of NGC 1068, we show that the luminous starburst, the CO complexes, and the visually bright, inner spiral-like features probably result from a bar-driven density wave which also includes the effects of shock focusing. We conclude that the luminous Seyfert nucleus is not causally related to the extended starburst, except perhaps indirectly by the fueling of both the active galactic nucleus and the starburst with gas flowing in from the gas-rich galaxy disk.
The variation of the cell size and velocities of the supergranulation with heliographic latitude (1989)

Une analyse harmonique des champs de vitesse des supergranules solaires a differentes latitudes heliographiques est realisee. La variation des tailles des cellules des supergranules en fonction de la latitude est etudiee.
Jasmonic Acid Modulates Xylem Development by Controlling Expression of PIN-FORMED 7 (2019)

Jasmonic acid (JA) modulates plant development, growth, and responses to stress. Previously, we showed that in <i>Arabidopsis thaliana</i>, JA promotes the formation of extra xylem in roots, and mutant plants unable to express <i>PIN-FORMED 3</i> (<i>PIN3</i>) and <i>PIN7</i> formed extra xylem in the absence of exogenous JA. Those results suggested that JA modulates root xylem development by controlling PIN-mediated polar auxin transport. Consistent with this, treatment with an auxin transport inhibitor induced extra xylem formation. Here, we characterized the expression of <i>PIN3</i> and <i>PIN7</i> in JA-treated <i>Arabidopsis</i> plants. <i>PIN3</i> expression was not altered in response to JA; by contrast, <i>PIN7</i> expression was reduced by JA, which suggested that <i>PIN7</i> is involved in JA-mediated xylem development. Indeed, overexpressing <i>PIN7</i> suppressed the formation of extra xylem in response to JA. Based on these results, we propose that JA mediates xylem development by controlling polar auxin transport with PIN7 critically involved in this process.
The Recovery of Manganese from the Boleo Project Using Leach, Precipitation and Electrolytic Manganese Metal Production (2012)

This chapter contains sections titled: Introduction Manganese Carbonate Precipitation Conclusion Acknowledgements
Biosynthesis of vitamin B12: the structure of factor IV, the oxidized form of precorrin-4 (1993)

13 C Labelling and NMR experiments establish the structure of factor IV, the oxidized form of the tetramethylated intermediate on the biosynthetic pathway to precorrin-6x 2 in Pseudomonas denitrificans, thus demonstrating that the contraction of the macrocycle leads to an acetyl derivative at C-1.
Classifier-Agnostic Saliency Map Extraction (2019)

Extracting saliency maps, which indicate parts of the image important to classification, requires many tricks to achieve satisfactory performance when using classifier-dependent methods. Instead, we propose classifier-agnostic saliency map extraction. This allows to find all parts of the image that any classifier could use, not just one given in advance. This way we extract much higher quality saliency maps.
Reducing shoulder-surfing by using gaze-based password entry (2007)

Shoulder-surfing -- using direct observation techniques, such as looking over someone's shoulder, to get passwords, PINs and other sensitive personal information -- is a problem that has been difficult to overcome. When a user enters information using a keyboard, mouse, touch screen or any traditional input device, a malicious observer may be able to acquire the user's password credentials. We present EyePassword, a system that mitigates the issues of shoulder surfing via a novel approach to user input.
Comparative Transcriptomics Identifies Novel Genes and Pathways Involved in Post-Traumatic Osteoarthritis Development and Progression (2018)

Anterior cruciate ligament (ACL) injuries often result in post-traumatic osteoarthritis (PTOA). To better understand the molecular mechanisms behind PTOA development following ACL injury, we profiled ACL injury-induced transcriptional changes in knee joints of three mouse strains with varying susceptibility to OA: STR/ort (highly susceptible), C57BL/6J (moderately susceptible) and super-healer MRL/MpJ (not susceptible). Right knee joints of the mice were injured using a non-invasive tibial compression injury model and global gene expression was quantified before and at 1-day, 1-week, and 2-weeks post-injury using RNA-seq. Following injury, injured and uninjured joints of STR/ort and injured C57BL/6J joints displayed significant cartilage degeneration while MRL/MpJ had little cartilage damage. Gene expression analysis suggested that prolonged inflammation and elevated catabolic activity in STR/ort injured joints, compared to the other two strains may be responsible for the severe PTOA phenotype observed in this strain. MRL/MpJ had the lowest expression values for several inflammatory cytokines and catabolic enzymes activated in response to ACL injury. Furthermore, we identified several genes highly expressed in MRL/MpJ compared to the other two strains including <i>B4galnt2</i> and <i>Tpsab1</i> which may contribute to enhanced healing in the MRL/MpJ. Overall, this study has increased our knowledge of early molecular changes associated with PTOA development.
Self-Assembly of Proteolysis Targeting Chimeras Via Reversible Bioorthogonal Reactions (2022)

Targeted protein degradation (TPD) by PROteolysis TArgeting Chimeras (PROTACs) is of great interest for probe molecule and drug development. However, current bivalent PROTACs are rule-breaking molecules with sub-optimal cellular permeability, solubility, and other drug-like properties. In this study, we report a novel approach for TPD by Self-Assembled Proteolysis TArgeting Chimeras (SAPTACs) in which the target protein and E3 Ubiquitin ligase ligands assemble in cellulo via reversible, bioorthogonal reactions. SAPTACs that me-diate the degradation of the Von Hippel Landau (VHL) E3 Ubiquitin ligase are described. We show that pseu-do-homodimeric degraders for VHL can be assembled in situ through the interaction of VHL ligands linked to phenylboronic acid and catechol as well as to o-acetlyphenylboronic acid and an alkoxyamine. The efficiency of VHL degradation by these SAPTACs is linked to the strength of the reversible covalent interaction.