gebhart/patrepeval huggingface dataset:
Bayesian integrated testing strategy to assess skin sensitization potency: from theory to practice (2013)

Frameworks to predict in vivo effects by integration of in vitro, in silico and in chemico information using mechanistic insight are needed to meet the challenges of 21(st) century toxicology. Expert-based approaches that qualitatively integrate multifaceted data are practiced under the term 'weight of evidence', whereas quantitative approaches remain rare. To address this gap we previously developed a methodology to design an Integrated Testing Strategy (ITS) in the form of a Bayesian Network (BN). This study follows up on our proof of concept work and presents an updated ITS to assess skin sensitization potency expressed as local lymph node assay (LLNA) potency classes. Modifications to the ITS structure were introduced to include better mechanistic information. The parameters of the updated ITS were calculated from an extended data set of 124 chemicals. A detailed validation analysis and a case study were carried out to demonstrate the utility of the ITS for practical application. The improved BN ITS predicted correctly 95% and 86% of chemicals in a test set (n = 21) for hazard and LLNA potency classes, respectively. The practical value of using the BN ITS is far more than a prediction framework when all data are available. The BN ITS can develop a hypothesis using subsets of data as small as one data point and can be queried on the value of adding additional tests before testing is commenced. The ITS represents key steps of the skin sensitization process and a mechanistically interpretable testing strategy can be developed. These features are illustrated in the manuscript via practical examples.
Thermodynamically Leveraged Tandem Catalysis for Ester RC(O)O–R′ Bond Hydrogenolysis. Scope and Mechanism (2015)

Rapid and selective formal hydrogenolysis of aliphatic ester RC(O)O–R′ linkages is achieved by a tandem homogeneous metal triflate + supported palladium catalytic system. The triflate catalyzes the mildly exothermic, turnover-limiting O–R′ cleavage process, whereas the exothermic hydrogenation of the intermediate alkene further drives the overall reaction to completion.
Efficient and Accurate Label Propagation on Large Graphs and Label Sets (2013)

Abstract—Many web-based application areas must infer label distributions starting from a small set of sparse, noisy labels. Examples include searching for, recommending, and advertising against image, audio, and video content. These labeling problems must handle millions of interconnected entities (users, domains, content segments) and thousands of competing labels (interests, tags, recommendations, topics). Previous work has shown that graph-based propagation can be very effective at finding the best label distribution across nodes, starting from partial information and a weightedconnection graph. In their work on video recommendations, Baluja et al. [1] showed high-quality results using Adsorption, a normalized propagation process. An important step in the original formulation of Adsorption was re-normalization of the label vectors associated with each node, between every propagation step. That interleaved normalization forced computation of all label distributions, in synchrony, in order to allow the normalization to be correctly determined. Interleaved normalization also prevented use of standard linear-algebra methods, like stabilized bi-conjugate gradient descent (BiCGStab) and Gaussian elimination. This paper presents a method that replaces the interleaved normalization with a single pre-normalization, done once before the main propagation process starts, allowing use of selective label computation (label slicing) as well as large-matrix-solution methods. As a result, much larger graphs and label sets can be handled than in the original formulation and more accurate solutions can be found in fewer propagation steps. We also report results from using pre-normalized Adsorption in topic labeling for web domains, using label slicing and BiCGStab. Keywords-graph propagation, large-scale labeling, stabilized bi-conjugate gradient descent, Gaussian elimination, topic discovery, web domains. I.
Heat transfer measurements and computations of swept-shock-wave/boundary-layer interactions (1994)

An experimental research program providing basic knowledge and establishing new data on the heat transfer in swept shock wave/boundary-layer interactions is described. An equilibrium turbulent boundary-layer on a flat plate is subjected to impingement by swept planar shock waves generated by a sharp fin. Five different interactions with fin angles ranging from 10 to 20 deg at freestream Mach numbers of 3.0 and 4.0 produce a variety of interaction strengths from weak to very strong. A foil heater generates a uniform heat flux over the flat plate surface and miniature thin-film-resistance sensors mounted on it are used to measure the local surface temperature. The heat convection equation is then solved for the heat transfer distribution within an interaction, yielding a total uncertainty of about +/- 10 percent. These experimental data are compared with the results of numerical Navier-Stokes solutions which employ a kappa-epsilon turbulence model. Finally, a simplified form of the peak heat transfer correlation for fin interactions is suggested.
Correlation matching method for optical vortex detection using Shack-Hartmann wavefront sensor (2013)

We report a correlation matching algorithm for position detection of optical vortices using a Shack-Hartmann wavefront sensor. The accuracy experientially confirmed was 0.056, in units of lens-size of lenslet array used in the wavefront sensor.
X-ray phase-contrast tomosynthesis of a human ex vivo breast slice with an inverse Compton x-ray source (2016)

While the performance of conventional x-ray tube sources often suffers from the broad polychromatic spectrum, synchrotrons that could provide highly brilliant x-rays are restricted to large research facilities and impose high investment and maintenance costs. Lately, a new type of compact synchrotron sources has been investigated. These compact light sources (CLS) based on inverse Compton scattering provide quasi-monochromatic hard x-rays. The flux and brilliance yielded by a CLS currently lie between x-ray tube sources and third-generation synchrotrons. The relatively large partially coherent x-ray beam is well suited for the investigation of preclinical applications of grating-based phase-contrast and dark-field imaging. Here we present the first grating-based multimodal tomosynthesis images of a human breast slice acquired at a CLS to investigate the possibilities of improved breast cancer diagnostics.
Torsion points and height jumping in higher-dimensional families of\n abelian varieties (2016)

In 1983 Silverman and Tate showed that the set of points in a 1-dimensional\nfamily of abelian varieties where a section of infinite order has `small\nheight' is finite. We conjecture a generalisation to higher-dimensional\nfamilies, where we replace `finite' by `not Zariski dense'. We show that this\nconjecture would imply the Uniform Boundedness Conjecture for torsion points on\nabelian varieties. We then prove a few special cases of this new conjecture.\n
Improved Performance of Plasma-Assisted Molecular Beam Epitaxy Grown AlGaN/GaN High Electron Mobility Transistors with Gate-Recess and CF4-Treatment (2008)

High performance AlGaN/GaN high electron mobility transistors grown by plasma-assisted molecular beam epitaxy were fabricated. An integrated slant field-plate was used to suppress the DC-RF dispersion and enhance the breakdown. A recessed-gate structure was adopted to increase the cutoff frequency from 17.5 to 22 GHz. And a CF<sub>4</sub>-plasma treatment prior to gate metallization was found effective in reducing the gate leakage by one order of magnitude and improving the stability of the RF power operation. Treatment In a mixture of HF and HNO<sub>3</sub> acid was essential to ensure the effectiveness of the CF<sub>4</sub>-plasma treatment. Combination of these technologies yielded state-of-the-art MBE grown AlGaN/GaN HEMTs with stable high-power and high-efficiency operation. At 4-GHz frequency and 48-V bias, a CW power of 12 W/mm with 64% associated efficiency was achieved.
Oxidation Of Oximes To Ketones With Zeolite Supported Permanganate (1999)

Abstract A variety of aldoximes and ketoximes are oxidised to corresponding aldehydes and ketones in excellent yields by zeolite supported permanganate
Steric Effect of Alkylidene Groups of Furylfulgides on the Photochromic Behavior (1990)

Abstract Photoreactions of furylfulgides having a large alkylidene group (7-norbornylidene or 2-adamantylidene) were investigated. An adamantylidene fulgide with [1-(2,5-dimethyl-3-furyl)-2-methyl]propylidene group recorded 0.51 and 0.26 for coloring and bleaching quantum yields, respectively.
OR14-5 Challenges in implementing Hybrid Closed Loop Insulin Pump Therapy (medtronic 670g) In A 'Real World' Clinical Setting. (2019)

An observation study was conducted at Boston Children’s Hospital on patients with type 1 diabetes mellitus (T1DM) who elected to treat their diabetes with the FDA approved Medtronic 670G hybrid closed loop insulin pump. 83 pediatric and young adults were trained and started on the Medtronic 670G in automode between 5/30/17-9/7/18 (Age range 6-25 years). Average follow up time for the patient population was 8 months (range 3-18 months). 19% (16/83) of T1DM patients discontinued use of automode hybrid closed loop technology completely, often due to technical difficulties with the sensor or difficulties staying in automode. Calibration requirements, problems with sensor durability or adhesion, skin irritation and forced exits from automode were common areas of difficulty. 81% (67/83) continued to use automode although a wide range of percent time in automode was observed (10-90%). A subset of 58 patients who continued to use automode technology and who had available hemoglobin a1c data obtained within 6 months before and within 6 months after starting automode were analyzed . A mean decrease in hemoglobin A1c of 0.27% (95% confidence interval is -0.5, -0.03) was seen after an average of 97 days using automode closed loop technology (P=0.025). In conclusion, our data supports the observation that closed loop insulin delivery in subjects that are successful in using the technology improves glucose control (reduces HbA1c). Additional work is needed to understand barriers to successful implementation of technology.
Hydrolysis and Fermentation of Pericarp and Endosperm Fibers Recovered from Enzymatic Corn Dry‐Grind Process (2005)

ABSTRACT A modified dry‐grind corn process has been developed that allows recovery of both pericarp and endosperm fibers as coproducts at the front end of the process before fermentation. The modified process is called enzymatic milling (E‐Mill) dry‐grind process. In a conventional dry‐grind corn process, only the starch component of the corn kernel is converted into ethanol. Additional ethanol can be produced from corn if the fiber component can also be converted into ethanol. In this study, pericarp and endosperm fibers recovered in the E‐Mill dry‐grind process were evaluated as a potential ethanol feedstock. Both fractions were tested for fermentability and potential ethanol yield. Total ethanol yield recovered from corn by fermenting starch, pericarp, and endosperm fibers was also determined. Results show that endosperm fiber produced 20.5% more ethanol than pericarp fiber on a g/100 g of fiber basis. Total ethanol yield obtained by fermenting starch and both fiber fractions was 0.370 L/kg compared with ethanol yield of 0.334 L/kg obtained by fermenting starch alone.
The method for providing of parking location guidance service in a smart parking lot (2020)

We proposed a parking location guidance service method using deep learning model in a smart parking lot. License plate image detection and character recognition are required to guide the parking location, and both of these steps use machine learning methods. In particular, the edge system and the server are mounted with a learning model so as not to generate a lot of traffic by transmitting all vehicle images to the server, and the edge system cut only the license plate image using the vehicle license plate detection learning model and transmits it to the server. In the server mounted with the recognition learning model, only license plate images are collected to recognize license plate characters. Rather than performing both license plate image detection and license plate character recognition in the server, it will be much more efficient to cut the license plate image in the edge system and transmit only image information necessary for character recognition to the server as it can reduce the traffic load.
Cisplatin at clinically relevant concentrations enhances interleukin-2 synthesis by human primary blood lymphocytes (1999)

Cytotoxic drugs influence the expression of certain genes in cancer cells. Cisplatin has recently been shown to modulate interleukin (IL)-1 and tumor necrosis factor (TNF)-alpha production in macrophages. In this study, we wanted to investigate whether cisplatin interferes with the IL-2, IL-2 receptor (IL-2R), interferon (IFN)-gamma, and TNF-alpha expression in phytohemagglutinin-stimulated human peripheral blood lymphocytes. IL-2 was analyzed in a bioassay, while IFN-gamma and TNF-alpha were measured by ELISA. Northern blots were performed to quantify steady-state cytokine mRNA levels. Furthermore, T cell subsets and IL-2R surface expression were analyzed by means of flow cytometry. A maximum stimulatory effect on IL-2 production (1.8-fold increase) was observed with cisplatin at 5-10 microM while IFN-gamma and TNF-alpha synthesis and IL-2R density were unaffected. However, cisplatin-treated cells displayed enhanced IL-2, IL-2R, IFN-gamma and TNF-alpha mRNA levels compared to drug-free controls. Cisplatin did not prolong cytokine mRNA half-life as revealed with the transcriptional inhibitor actinomycin D. In contrast to an inhibited growth of CD4+ T lymphocytes, CD3+ CD8+ cell density was unaffected at intermediate cisplatin concentrations (10 microM). Bleomycin, carboplatin, doxorubicin, novobiocin or etoposide, which were included for comparison, did not interfere with IL-2 expression. Our data imply that cisplatin most likely stimulated cytokine transcription via a putative stress-induced signaling pathway.
Ultrasound-based combination therapy: potential in urologic cancer (2010)

Immune-sensitive urologic malignancies include prostate, kidney and bladder cancers. To date, most immunotherapeutic treatments have been applied to advanced metastatic disease. Limited efficacy in this setting is likely due to an excessive disease burden, which overwhelms the capacity of the immune system. Immunotherapy has not been widely utilized in a low-disease-burden state - a setting in which the immune system may be best suited to effectively mount a clinically meaningful response. The emergence of high-intensity focused ultrasound, and more recently, low-intensity focused ultrasound technologies, have demonstrated not only immune-stimulatory effects but also an interesting capacity to alter tissue architecture and cell membrane properties, which may be exploited to increase tumoral uptake of drugs and vaccines. In this article, we review the literature supporting the novel use of ultrasound combination therapy with adjunctive agents in the treatment of urologic malignancy.
Health Related Quality of Life Outcomes in Patients Treated for Metastatic Kidney Cancer: A Pilot Study (1997)

Patients undergoing nephrectomy and adjuvant tumor infiltrating lymphocytes plus interleukin-2 therapy for advanced renal cell carcinoma report better health related quality of life than those with other malignancies and better physical function than patients with congestive heart failure. However, health related quality of life is worse than in the general population and similar or worse than in patients with hypertension or type II diabetes. This surveyed population is selective and may represent the best responders among survivors of a highly toxic therapy. Nevertheless, quality and quantity of life should be addressed with patients when considering immunotherapy for metastatic kidney cancer.
Pancreatic secretory trypsin inhibitor (PSTI) isolated from pig intestine Influence on insulin and somatostatin release (1991)

Upon investigation of pig intestinal peptides for effects on the release of endocrine hormones from the isolated perfused rat pancreas, we reported earlier that glucose-stimulated insulin release was inhibited by PEC-60, a peptide with marked sequence similarity to PSTI (pancreatic secretory trypsin inhibitor). Continuing this study we found a polypeptide, which inhibited glucose-induced insulin release but enhanced glucose-induced somatostatin secretion. Determination of the amino acid sequence of this polypeptide revealed that it is identical to that of PSTI. Thus, PSTI modulates islet hormone release.
Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways (2022)

Abstract Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to- methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.
Synthetic Analogs of the Lewisb-Tetrasaccharideand their Binding to Griffonia Simplicifolia Lectin-PartI (2003)

The lewis b tetrasaccharide binds specifically to the Griffonia simplicifolia lectin GS-IV. In an effort to obtain tighter binding derivatives, we have synthesized a series of analogs of this tetrasaccharide and studied their binding to the lectin. This paper (part I in a series of two) describes the synthesis of and binding studies with analogs where the galactose unit (b) has been altered at the 6-position. Even though this position does not make direct contact with the protein in the crystal structure, the binding was very sensitive to these substitutions.
Cancer Detection using Infrared Transillumination (2007)

The viability of a new infrared imaging modality for the detection of breast cancer is tested via whole animal imaging studies. The potential of this technique for imaging human breast tissue is also demonstrated.
Identification of a small molecule inhibitor of Pseudomonas aeruginosa PvdQ acylase, an enzyme involved in siderophore pyoverdine synthesis (2013)

The bacteria Pseudomonas aeruginosa produces a peptide siderophore known as pyoverdine, which has a great affinity for iron and is used to acquire iron from the external environment. Several enzymes such as the PvdQ acylase are required for the biosynthesis of pyoverdine. Deletion of the PvdQ gene disrupts pyoverdine production and hinders P. aeruginosa proliferation. Bacteria defective in pyoverdine synthesis are not infectious implying that disrupting this siderophore production through PvdQ inhibition could be exploited as a putative target for the development of novel antibiotic compounds. This report describes the development of a small molecule inhibitor (ML318, CID 56604881) of PvdQ acylase. ML318 inhibits PvdQ in vitro with an IC50 of 6 nM, has no apparent toxicity in mammalian HeLa cells up to a concentration of 100 μM, and inhibits growth and pyoverdine production in P. aeruginosa exposed to iron-limiting conditions with an IC50 < 50 μM. ML318 can also significantly reduce the intracellular uptake of iron inside the bacteria. This probe is a useful tool for ongoing characterization of pyoverdine’s role in P. aeruginosa biology and could serve as a starting point for the development of a novel antibiotic.
The Effects of Lipidation on a TAT-Containing Peptide-Based Inhibitor of PSD-95 (2019)

Stability and cell permeability are critical parameters in the development of peptide therapeutics. Conjugation to fatty acids and cell-penetrating peptides, such as TAT (YGRKKRRQRRR), are established strategies to increase peptide stability and permeation, respectively. Here, we prepared lipidated analogues of a potent TAT-containing dimeric peptide-based inhibitor of the intracellular scaffolding protein PSD-95, an emerging drug target in ischaemic stroke. Lipidation increased peptide stability in vitro and in vivo. Combining both lipidation and conjugation to TAT improved brain/plasma ratios, but caused acute toxic effects due to the potent haemolytic activity of the TAT-lipid moiety.