gebhart/patrepeval huggingface dataset:
Outlook for Visual Analytics Research Funding (2007)

Visual Analytics has become a rapidly growing field of study. It is also a field that is addressing very significant real world problems in homeland security, business analytics, emergency management, genetics and bioinformatics, investigative analysis, medical analytics, and other areas. For both these reasons, it is attracting new funding and will continue to do so in the future. Visual analytics has also become an international field, with significant research efforts in Canada, Europe, and Australia, as well as the U.S. There is significant new research funding in Canada and Germany with other efforts being discussed, including a major program sponsored by the European Union. The contributors to this panel are some of the primary thought leaders providing research funding or involved in setting up the funding apparatus. We have asked them to present their needs, funding programs, and expectations from the research community. They all come from different perspectives, different missions, and different expectations. They will present their views of the range of activity in both the U.S. and internationally and discuss what is coming. Come learn about these programs, initiatives, and plans, and how you can contribute.
SSAGES: Software Suite for Advanced General Ensemble Simulations (2018)

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.
Importance of transducer position tracking for automated breast ultrasound: Initial assessments (2012)

Breast cancer causes the most cancer deaths in women all over the world. Given the unknown cause and invasive nature of the disease, early detection and treatment is crucial to the survival of the cancer patients. X-rays mammography is an effective screening tool for breast cancer but misses nearly half of them in women with dense breasts, in which case supplemental ultrasound (US) screening must be used. Recent development in 3D automated breast ultrasound (ABUS) provides a faster and potentially more accurate alternative to the conventional 2D hand-held US in detecting the tumors. Typically in these systems, a custom-built linear or curvilinear transducer is automatically swept over or rotated around the tissue to acquire a set of 2D images, from which a 3D high-resolution volume of the breast can be reconstructed. In this work, we study the importance of transducer position tracking in the ABUS volume reconstruction process. Our experiments show that an accurate localization of the images results in a more accurate volume reconstruction.
Analysis of a Parallel Branch in the Mitomycin Biosynthetic Pathway Involving the mitN-Encoded Aziridine N-Methyltransferase (2007)

Mitomycin C is a natural product with potent alkylating activity, and it is an important anticancer drug and antibiotic. mitN, one of three genes with high similarity to methyltransferases, is located within the mitomycin biosynthetic gene cluster. An inframe deletion in mitN of the mitomycin biosynthetic pathway was generated in Streptomyces lavendulae to produce the DHS5373 mutant strain. Investigation of DHS5373 revealed continued production of mitomycin A and mitomycin C in addition to the accumulation of a new mitomycin analog, 9-epi-mitomycin C. The mitN gene was overexpressed in Escherichia coli, and the histidine-tagged protein (MitN) was purified to homogeneity. Reaction of 9-epi-mitomycin C with MitN in the presence of S-adenosylmethionine yielded mitomycin E showing that the enzyme functions as an aziridine N-methyltransferase. Likewise, MitN was also shown to convert mitomycin A to mitomycin F under the same reaction conditions. We conclude that MitN plays an important role in a parallel biosynthetic pathway leading to the subclass of mitomycins with 9alpha-stereochemistry but is not involved directly in the biosynthesis of mitomycins A and C.
Separating Wheat from Chaff: Joining Biomedical Knowledge and Patient Data for Repurposing Medications (2019)

We present a system that jointly harnesses large-scale electronic health records data and a concept graph mined from the medical literature to guide drug repurposing—the process of applying known drugs in new ways to treat diseases. Our study is unique in methods and scope, per the scale of the concept graph and the quantity of data. We harness 10 years of nation-wide medical records of more than 1.5 million people and extract medical knowledge from all of PubMed, the world’s largest corpus of online biomedical literature. We employ links on the concept graph to provide causal signals to prioritize candidate influences between medications and target diseases. We show results of the system on studies of drug repurposing for hypertension and diabetes. In both cases, we present drug families identified by the algorithm which were previously unknown. We verify the results via clinical expert opinion and by prospective clinical trials on hypertension.
Development of Lipid-Based Nanoparticles for In Vivo Targeted Delivery of Imaging Agents into Breast Cancer Cells (2010)

Abstract : Breast cancer represents a unique disease in oncology, in that specific markers have been identified and are routinely used for diagnosis and targeted therapy. Targeted delivery of a combined imaging and therapy agent to cancer cells is an avenue to develop a new generation of effective and selective anticancer agents. The goal of this proposal is to develop novel nanoparticles for in vivo breast cancer targeting. The nanoparticles consist of a cholesterol ester core surrounded with a lipid monolayer shell containing an imaging agent and metal chelating groups that can attach proteins of interest through specific His6 tagging. We have synthesized nanoparticle building blocks as well as imaging agents consisting from the near infrared fluorophore pyropheophorbide a conjugated with core or shell lipids. Varying the core composition we have assembled a series of the nanoparticles with size from 8 nm for smallest one to 20 nm for largest nanoparticle. We have shown that the nanoparticles with cholesterol oleate core have supreme shelf-life and stability at the conditions close to physiological. We have prepared a number of lipid nanoparticles with His6-tagged targeting proteins, which were successfully tested in vitro for specific targeting of model cell lines. We have shown that due to multivalent nature of the targeting nanoparticles the wide spectrum of proteins from natural low affinity receptor ( 107 M-1) can be used in nanoparticle composition. Time course analysis of the nanoparticle binding to the cell surface revealed that the shell loaded imaging agent is much more effective than the core loaded one.
Microellipsometer with Radial Symmetry (2002)

We report on a novel microellipsometer that uses a spatially filtered high-numerical-aperture (NA) lens for large-angle ellipsometric illumination and high spatial resolution. A radially symmetric ellipsometric signal is achieved with two half-wave plates to produce a pure polarization rotation and a birefringent cube as a radial analyzer. This radial symmetry offers a better signal-to-noise ratio compared with other microellipsometer techniques. Ellipsometric measurement with a spatial resolution of 0.5 microm is performed with a He-Ne (632.8-nm) laser source and an objective lens with an NA of 0.8. Experimental data on SiO2 samples with different thicknesses are in good agreement with spectroscopic ellipsometer results. We acquired ellipsometric images of photoresist microstructure through scanning the sample. Surface profiles of the photoresist microstructure are derived from the ellipsometric data and compared with the results from a stylus profiler.
Table S2 from Selective Inhibition of the Second Bromodomain of BET Family Proteins Results in Robust Antitumor Activity in Preclinical Models of Acute Myeloid Leukemia (2023)

&lt;p&gt;Tumor growth inhibition in cell line-based xenograft models and supporting statistics.&lt;/p&gt;
A linearized modulator for high performance bandpass optical analog links (2002)

The spurious-free dynamic range of a sub-octave externally modulated optical analog link can be extended to as high as 138 dB-Hz with modest received optical power (only 2.3 mA average photocurrent!) and with very small noise figure penalty by using a simple linearized modulator design biased near its minimum transmission.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Morphometry and autoradiography of early hypertrophic changes in the ventricular myocardium of adult rat. A light microscopic study. (1975)

Quantitative autoradiographic localization of newly synthesized proteins was studied in the ventricular myocardium of adult rats 2 hours after the intravenous injection of 3H-leucine and 20 hours after the induction of hypertrophy by constriction of the abdominal aorta. Equal area samples of tissue from experimental and sham-operated controls were examined for differential grain counts and morphometric measurements by light microscopy. In comparison with control levels, the hypertrophic hearts show a 20 per cent increase in the average cross-sectional area of myocytes and a 43 per cent increase in the incorporation of amino acid into proteins. The higher concentration of labeled proteins is confined mainly to cardiac muscle cells, which show a 90 per cent increase in grain counts per cell cross-section, whereas no significant change is observed over the interstitium. A test of the specificity of the autoradiographic technique shows the expected reduction in tissue labeling following cycloheximide inhibition of protein synthesis, indicating that there is no significant amount of nonspecific binding of free amino acid during the paraformaldehyde-glutaraldehyde fixation procedure.
Decoupling Internalization, Acidification and Phagosomal-Endosomal/lysosomal Fusion during Phagocytosis of InlA Coated Beads in Epithelial Cells (2009)

Using this method, we found that the time scales for internalization, phagosomal acidification and phagosomal-endosomal/lysosomal fusion ranged from 23-32 min, 3-4 min and 74-120 min, respectively, for MDCK and Caco-2 epithelial cells. Both the static and real-time methods developed here are expected to be readily and broadly applicable, as they simply require fluorophore conjugation to a particle of interest, such as a pathogen or mimetic, in combination with common cell labeling dyes. As such, these methods hold promise for future measurements of receptor-mediated internalization in other cell systems, e.g. pathogen-host systems.
Dynamic Response Analysis of Composite Pipes Conveying Fluid in the Presence of Internal Wall Thinning (2020)

Pipes conveying fluids are primary components in almost all industries. Internal surface attack is inevitable in pipes and can be crucial to their structural integrity and dynamic response characteristics. In this study, the dynamic response analysis of composite pipes with internal surface discontinuity is investigated in the presence of fluid flow. The equations of motion are obtained using the extended Hamilton’s principle and discretized using the wavelet-based finite-element method (WBFEM). The internal surface defect is allowed to occupy any length along the pipe span, while its cross section can vary both in radial and angular directions. The dynamic response of the defected pipe is obtained by integrating the equations of motion forward in time using MATLAB solver ODE45. The developed dynamic model has been validated using ANSYS and some benchmark results are presented to underline the influence of the internal surface defect on dynamic response of composite pipes conveying fluid.
Proton Conduction in a Tyrosine‐Rich Peptide/Manganese Oxide Hybrid Nanofilm (2017)

Proton conduction is an essential process that regulates an integral part of several enzymatic catalyses and bioenergetics. Proton flows in biological entities are sensitively controlled by several mechanisms. To understand and manipulate proton conduction in biosystems, several studies have investigated bulk proton conduction in biomaterials such as polyaspartic acid, collagen, reflectin, serum albumin mats, and eumelanin. However, little is known about the bulk proton conductivity of short peptides and their sequence‐dependent behavior. Here, this paper focuses on a short tyrosine‐rich peptide that has redox‐active and cross‐linkable phenol groups. The spin‐coated peptide nanofilm is immersed in potassium permanganate solution to induce cross‐linking and oxidation, simultaneously leading to hybridization with manganese oxide (MnO x ). The peptide/MnO x hybrid nanofilm can efficiently transport protons, and its proton conductivity is ≈18.6 mS cm −1 at room temperature. This value is much higher than that of biomaterials and comparable to those of other synthetic proton‐conducting materials. These results suggest that peptide‐based hybrid materials can be a promising new class of proton conductor.
Bi-Directional X-Ray Phase-Contrast Mammography (2014)

Phase-contrast x-ray imaging is a promising improvement of conventional absorption-based mammography for early tumor detection. This potential has been demonstrated recently, utilizing structured gratings to obtain differential phase and dark-field scattering images. However, the inherently anisotropic imaging sensitivity of the proposed mono-directional approach yields only insufficient diagnostic information, and has low diagnostic sensitivity to highly oriented structures. To overcome these limitations, we present a two-directional x-ray phase-contrast mammography approach and demonstrate its advantages by applying it to a freshly dissected, cancerous mastectomy breast specimen. We illustrate that the two-directional scanning procedure overcomes the insufficient diagnostic value of a single scan, and reliably detects tumor structures, independently from their orientation within the breast. Our results indicate the indispensable diagnostic necessity and benefit of a multi-directional approach for x-ray phase-contrast mammography.
Aspergillus oryzaein solid-state and submerged fermentations (2002)

We report the progress of a multi-disciplinary research project on solid-state fermentation (SSF) of the filamentous fungus Aspergillus oryzae. The molecular and physiological aspects of the fungus in submerged fermentation (SmF) and SSF are compared and we observe a number of differences correlated with the different growth conditions. First, the aerial hyphae which occur only in SSFs are mainly responsible for oxygen uptake. Second, SSF is characterised by gradients in temperature, water activity and nutrient concentration, and inside the hyphae different polyols are accumulating. Third, pelleted growth in SmF and mycelial growth in SSF show different gene expression and protein secretion patterns. With this approach we aim to expand our knowledge of mechanisms of fungal growth on solid substrates and to exploit the biotechnological applications.
Surface Enrichment and Depletion Effects of Ions Dissolved in an Ionic Liquid: An X‐ray Photoelectron Spectroscopy Study (2006)

Surfaces of ionic liquids: Angle-dependent X-ray photoelectron spectroscopy (XPS) shows that the surface composition of a solution of [Pt(NH3)4]Cl2 in the ionic liquid 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIM][EtOSO3]) deviates considerably from the bulk composition. The [Pt(NH3)4]2+ cation is enriched on the surface at the expense of the [EMIM] cation (see picture), while the Cl− anion is depleted to below the XPS detection limit. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z602756_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Endoscopist-administered propofol sedation is safe - a prospective evaluation of 10,000 patients in an outpatient practice. (2012)

Due to improved patient satisfaction and its pharmacological benefits, more endoscopic procedures are carried out with the use of propofol. However, recent rulings in the USA challenge endoscopist-administered propofol sedation. We evaluated the safety of endoscopist-administered propofol sedation in a German outpatient practice.During a period of 65 months, we prospectively evaluated 10,000 patients who received endoscopic procedures. During 377 endoscopic procedures we performed extensive blood pressure observation. Propofol was administered via intermittent i.v. bolus titration by trained practice nurses under the supervision of the gastroenterologist. Oxygen saturation, heart rate and blood pressure were recorded constantly during the procedure and adverse cardiopulmonary events were monitored by the endoscopy team. A major respiratory event was defined as an episode of apnea or laryngospasm requiring assisted ventilation.13,764 endoscopic procedures were recorded in 10,000 patients (7,349 esophago-gastro-duodenoscopies (ESD), 6,415 colonoscopies); 9,654 patients were sedated with propofol (ESD: 115 +/- 35; colonoscopy: 155 +/- 52; combined: 199 +/- 55 mg) and 346 patients had endoscopic examination without sedation. 0.03% of the patients received mask ventilation due to apnea and in 0.39% minor events of hypoxemia (oxygen saturation < 90%) were recorded. Bradycardia and arterial hypotension occurred in 0.07% and 0.24% of the patients. Patients with adverse events were significantly older than patients without (P < 0.001).The low number of adverse events recorded in this prospective study concludes that endoscopist-administered propofol sedation is a safe procedure. It does not seem likely that additional support of an anaesthetist would further improve patient's safety, and particularly cost-efficiency.
Catalytic oxidation of aromatic hydrocarbons by a molecular iron–NHC complex (2017)

An iron–NHC complex bearing a tetradentate bis(N-heterocyclic carbene) ligand is applied as catalyst for the oxidation of methyl substituted arene substrates.
Repetitive and single shot pulse microwave six-port reflectometer (1990)

The six-port reflectometer technique is extended to make pulsed-RF measurements. It is shown that a time resolution on the order of 1 mu s is possible in both repetitive and single-shot mode of operation of the reflectometer. A proof of the principle of the method is carried out using passive and active loads. A simple method for the linearization of diode-detector response is presented. Because of its good time resolution, this method can be used to study thermal and burn-out effects in high-power solid-state amplifiers, or to characterize, for example, pulse devices used in phased-array radars. Its ability to operate in single-shot mode is in contrast to existing reflectometers. It is easily extendable to the millimeter-wave frequency range and can be used to make multiport measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Some Empirical Evidence on the Determinants of Trade Credit at the Industry Level of Aggregation (1974)

Anthony F. Herbst, Some Empirical Evidence on the Determinants of Trade Credit at the Industry Level of Aggregation, The Journal of Financial and Quantitative Analysis, Vol. 9, No. 3 (Jun., 1974), pp. 377-394
Myocardial extracellular volume imaging by CMR quantitatively characterizes myocardial infarction and subclinical myocardial fibrosis (2011)

Imaging of fibrosis by cardiovascular magnetic resonance (CMR) is performed using late gadolinium enhancement (LGE). However, LGE imaging only visualizes relative differences between “normal” myocardium and fibrosis or infarction. Recent developments in T1 mapping have made it practical to quantitatively image the extracellular volume fraction (ECV).
An 18.8-to-23.3 GHz ADPLL Based on Charge-Steering-Sampling Technique Achieving 75.9 fs RMS Jitter and –252 dB FoM (2023)

We propose a mm-wave all-digital PLL (ADPLL) based on a new concept of a charge-steering-sampling (CSS) digital phase detection (PD). The CSS-PD operation is formed by first, presetting the input capacitors of a SAR-ADC to $V_{\mathrm{D}\mathrm{D}}$, then discharging them during a reference pulse via a pseudo-differential-pair (pseudo-diff-pair”) directly driven by the oscillator. The differential-mode (DM) charge-residue, representing the phase error, is evaluated by the ADC for supporting the ADPLL operation. This new technique promotes a high PD gain, good isolation of the oscillator, and a multi-bit digital PD output simultaneously, fully benefiting from the advanced CMOS. Further, a digital loop filter (DLF) with a dead-zone (DZ) in the integral path is proposed to avoid any conflicts with the proportional path. Fabricated in 22-nm CMOS, the prototype achieves 75.9 fs RMS jitter, $\lt $-50dBc spur, and -252.4dB FoM from 18.8 to 23.3 GHz.
A streaming validation model for SOAP digital signature (2005)

The XML signature specification provides a rich and flexible message signature model for XML documents, and it has been adopted by SOAP applications to provide message-level security. However, the XML signature design introduces a number of complex processing steps, such as canonicalization and XPath filtering, that often lead to performance and scalability problems when encountering extremes of size and rate in the processing of XML. In this paper, we focus on the performance of validating large signed XML messages, as might be sent by a scientific application using grid Web services. We present the design and implementation of the GHPX/SSSV system for the streaming validation of SOAP digital signature. Our model consists of a streaming canonicalization and optimized SOAP signature validation. We present an empirical study of the performance characteristics of these streaming validation features. Based on our evaluations we conclude that the streaming validation model can not only provide high performance, but is also memory efficient.