gebhart/patrepeval huggingface dataset:
Molecular Similarity Analysis on Biologically Active Macrocyclic Bis(bibenzyls) (1996)

Conformational analysis of marchantin A (1), a bis(diarylether) type, and riccardin A (2), a diarylether-biphenyl type macrocyclic bis(bibenzyl) was carried out by systematic unbounded multiple minimum search (SUMM). Mobility of the macrocyclic rings was analysed by variable temperature 1H-NMR study. Molecular similarity analysis was performed on the minimum energy conformers of 1 and 2 comparing their steric, electrostatic and hydrophobic properties. Correlation between complexation properties and calmodulin inhibitor activity was established. Differences in steric and electrostatic profiles may be responsible for the reduced Ca2+ affinity and activity of 2.
Screening the Cellular Microenvironment: A Role for Microfluidics (2008)

The cellular microenvironment is an increasingly discussed topic in cell biology as it has been implicated in the progression of cancer and the maintenance of stem cells. The microenvironment of a cell is an organized combination of extracellular matrix (ECM), cells, and interstitial fluid that influence cellular phenotype through physical, mechanical, and biochemical mechanisms. Screening can be used to map combinations of cells and microenvironments to phenotypic outcomes in a way that can help develop more predictive in vitro models and to better understand phenotypic mechanisms from a systems biology perspective. This paper examines microenvironmental screening in terms of outcomes and benefits, key elements of the screening process, challenges for implementation, and a possible role for microfluidics as the screening platform. To assess microfluidics for use in microenvironmental screening, examples and categories of micro-scale and microfluidic technology are highlighted. Microfluidic technology shows promise for simultaneous control of multiple parameters of the microenvironment and can provide a base for scaling advanced cell-based experiments into automated high-throughput formats.
Assessing Experimental Uncertainty in Defined Approaches: Borderline Ranges for In Chemico and In Vitro Skin Sensitization Methods Determined from Ring Trial Data (2021)

Introduction: Prediction models of most toxicological assays translate continuous data to binary classifications (“positive” or “negative”) using cutoff values. Mostly these cutoffs do not consider data variability. Some OECD test guidelines, however, provide a range close to the cutoff. If a test result is in this range, a repetition of the test is proposed. Yet, these ranges were based on few data and not systematically derived. Materials and Methods: In the present study, we determined the borderline ranges from multilaboratory ring trial studies for five nonanimal methods addressing skin sensitization: Direct Peptide Reactivity Assay (OECD TG 442C), KeratinoSens® and LuSens (OECD TG 442D), and human cell line activation test (OECD TG 442E) as well as the kinetic direct peptide reactivity assay (update of OECD TG 442C). Results: We used a uniform statistical approach based on the log median absolute deviation. Implementing the proposed borderline ranges helps to assess certainty of both individual test results and of combinations of multiple data sources in a defined approach (DA) or an integrated approach. Conclusion: The OECD guideline on DAs for skin sensitization provides the first regulatory application of borderline ranges to the “2 out of 3” DA.
Immunostimulatory CpG treatment for genital HSV-2 infections (2003)

887 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Genome‐wide transcriptomic responses of a human isolate of Lactobacillus plantarum exposed to p‐coumaric acid stress (2012)

Contact with p-CA triggers responses that would be potentially beneficial for the intestinal function such as detoxification of dietary hydroxycinnamic acids and induction of a marked antioxidant response. Elicited responses indicated that contact with p-CA could provide preparedness to L. plantarum for adaptation to the gut environment. This knowledge facilitates the way to design methods to improve probiotic cell survival in this habitat.
Perfusion and transit-time quantification in the human liver using pseudo-continuous arterial spin labeling MR imaging (2016)

Purpose/Introduction: Arterial spin labeling (ASL) is a promising non-invasive approach for perfusion measurements1,2,3. However, liver perfusion imaging with ASL is limited by respiratory and cardiac motion artifacts. Background suppression (BS) can reduce the sensitivity of ASL measurements to physiological motion4. Furthermore, the quantification of liver perfusion is challenging due to the relative long blood transit-time and the short T1-relaxation time of the liver5. The aim of this study was to investigate the capability of pseudo-continuous ASL (pCASL) with BS to quantify the total liver perfusion and transit time of the blood delivery by varying the post-labeling delay. Subjects and Methods: Three healthy volunteers were examined on a 3T MR scanner (MAGNETOM Prisma, Siemens Healthcare) with body- and spine-array coils. Liver perfusion was measured using a pCASL echo-planar imaging sequence6.. Six sagittal slices were acquired with the following parameters: TR/TE, 9000/14 ms; slicethickness/ gap, 8/4 mm; in-plane resolution, 3 9 3 mm2; matrix, 82 9 100; bandwidth, 2380 Hz/Pixel; tagging flip angle, 25; and gradient strength 7 mT/m. Tag duration was set to 2000 ms and postlabeling delays (PLDs) were 700, 1500, 2000, 2500, 3000, 3500 ms. 32 label-control image pairs and anM0 image were acquired within 5 min. BS for liver tissue (T1 = 800 ms) was utilized by a double inversion approach. The tagging plane was placed perpendicular to the portal vein (Fig. 1). Images were acquired by employing a synchronized breathing protocol. Images with strong motion artefacts were discarded from subsequent analysis using MATLAB. A mask of liver parenchyma was created by segmenting averaged difference images. Mean perfusion and transit-time over the liver parenchyma mask were calculated based on a one-compartment perfusion model5,7,8. Results: pCASL with BS allowed for hepatic perfusion assessment in all participants. Perfusion-weighted images and the corresponding model fitting is depicted in Figure 2a+b. Liver perfusion values and transit-times are presented in Table 1. For comparison, the perfusion values at a single PLD calculated with simplified assumptions are shown. Model fitting provided a mean perfusion of 136 ml/100 g/min and a transit time of 1938 ms, whereas a perfusion of 73 ml/100 g/min was calculated based on a single PLD data.
Force Field Calculations on Five Membered Ring Aminoxyl Radicals (1993)

Two force fields (MM2 and Genmol) have been applied to the modeling of five membered ring aminoxyl radicals. For the six molecules which were investigated the geometry of the conformation with the lowest strain energy was in very good agreement with the X-ray geometry. However owing to the high flexibility of five membered rings other conformations were shown to have a strain energy close to the energy minimum.
Cooking up a storm (1999)

Microwaves are now being used in a variety of chemical laboratories. By improving the safety features of conventional microwave ovens to give them greater control and feedback capabilities, chemists have been able to increase the potential applications for this technology. Consequently, the ability of microwave ovens to enhance the rates of various physical and chemical reactions is now being exploited in areas such as combinatorial organic synthesis, extraction of organic environmental pollutants, and digestion of samples for elemental analysis.
Chirality Recognition of Selenium Compounds by NMR Spectroscopy in the Presence of a Chiral Dirhodium Complex (2005)

Abstract Diastereomeric adducts of chiral soft-base selenium ligands with the enantiopure dirhodium complex Rh* allows stereodifferentiation by NMR spectroscopy of various nuclei (dirhodium method). The individual adduct species can be identified by low-temperature NMR spectroscopy.
Model Predictive Control of High-Performance Braking Systems: A Force-Based Approach (2022)

In this letter, a Force-based Model Predictive Control (F-MPC) scheme for braking systems is proposed. The use of longitudinal force information for slip tracking shows two main advantages: 1) the closed-loop system becomes robust to different grip conditions without the need of a friction model, 2) the optimization problem can be formulated as a quadratic program, suitable for real-time implementation. The approach is tested on a full-fledged vehicle simulator coupled with a nonlinear actuator calibrated on a real electro-hydraulic brake. A comparison with state-of-the-art solutions highlights better transient and tracking performance under both nominal and uncertain friction conditions.
A novel measurement technique for demonstrating carbon nanotube FET operation at microwave frequencies (2005)

This paper reports a novel new measurement technique developed to measure microwave frequency performance of nanoscale devices. Typically, nanoscale devices are high impedance making them difficult to measure at RF. To circumvent this problem, we have developed a new technique in which we perform a two-tone test on a device operated in compression and observe the output at the difference frequency. We use this technique to verify the operation of a carbon nanotube based Field effect transistor (FET) at frequencies up to 23 GHz.
Supporting interactivity in automated 3D illustrations (1993)

An interactive intent-based illustration is a picture designed to satisfy an input communicative intent, and which can be interactively redesigned as it is viewed. We describe how the architecture of IBIS (Intent-Based Illustration System) automates the design of 3D interactive intent-based illustrations. The types of interaction that IBIS supports include changes in the world, as objects move and otherwise change state; changes in the communicative intent, as modified by the user or other programs; queries, in which the user can request additional information; and selfeva.luation, in which other programs can request IBIS to analyze various properties of the illustration, such as how well an illustration's communicative intent is satisfied or which graphical techniques it uses. We show how IBIS's design process and rule base make possible these forms of interaction.
Fragment-Based Discovery of Bromodomain Inhibitors Part 2: Optimization of Phenylisoxazole Sulfonamides (2011)

Bromodomains are epigenetic reader modules that regulate gene transcription through their recognition of acetyl-lysine modified histone tails. Inhibitors of this protein-protein interaction have the potential to modulate multiple diseases as demonstrated by the profound anti-inflammatory and antiproliferative effects of a recently disclosed class of BET compounds. While these compounds were discovered using phenotypic assays, here we present a highly efficient alternative approach to find new chemical templates, exploiting the abundant structural knowledge that exists for this target class. A phenyl dimethyl isoxazole chemotype resulting from a focused fragment screen has been rapidly optimized through structure-based design, leading to a sulfonamide series showing anti-inflammatory activity in cellular assays. This proof-of-principle experiment demonstrates the tractability of the BET family and bromodomain target class to fragment-based hit discovery and structure-based lead optimization.
High-Precision Adaptive Slope Compensation Circuit for System-on-Chip Power Management (2019)

In this work, a high precision adaptive slope compensation circuit is proposed used in DC-DC converter for System-on-Chip Power Management. Compared with the conventional adaptive slope compensation circuit, this work uses the comparator to sample the output voltage and the input voltage, so that the accuracy has been greatly improved. In this paper, the circuit is designed based on UMC 0.18-μm CMOS Technology and verified by Cadence simulation environment. Simulation results show that, the compensation precision of the slope can reach more than 96% when changes the input voltage with output voltage fixed or changes the output voltage while keeping input voltage constant.
Animal Genomics for Animal Health Report: Critical Needs, Problems to be Solved, Potential Solutions, and a Roadmap for Moving Forward (2008)

The first International Symposium on Animal Genomics for Animal Health, held at the World Organisation for Animal Health (OIE) Headquarter, 23-25 October, 2007, Paris, France, assembled more than 250 participants representing research organizations from 26 countries. The symposium included a roundtable discussion on critical needs, challenges and opportunities, and a forward look at the potential applications of animal genomics in animal health research. The aim of the roundtable discussion was to foster a dialogue between scientists working at the cutting edge of animal genomics research and animal health scientists. In an effort to broaden the perspective of the roundtable discussion, the organizers set out four priority areas to advance the use of genome-enabled technologies in animal health research. Contributions were obtained through open discussions and a questionnaire distributed at the start of the symposium. This symposium report provides detailed summaries ofthe outcome ofthe roundtable discussion for each of the four priority areas. For each priority, the problems needing to be solved, according to the views of the participants, are identified, including potential solutions, recommendations, and lastly, concrete steps that could be taken to address these problems. This report serves as a roadmap to steer research priorities in animal genomics research.
The histone deacetylase inhibitor AN-9 has selective toxicity to acute leukemia and drug-resistant primary leukemia and cancer cell lines (2002)

The novel prodrug of butyric acid, pivaloyloxymethyl butyrate (AN-9), a histone deacetylase inhibitor, shows great promise as an effective and relatively nontoxic anticancer agent for solid malignancies. However, little is known about its effects on hematopoietic malignancies. In this study, we show that 21 primary samples of acute leukemia were sensitive to the antiproliferative effects of AN-9, with a 50% inhibitory concentration (IC(50)) of 45.8 +/- 4.1 microM. In colony-forming assays, primary T-cell acute lymphoblastic leukemia (T-ALL) cells were 3-fold more sensitive to AN-9 than the normal hematopoietic progenitors, erythroid burst-forming units and granulocyte/monocyte colony-forming units. AN-9 induced apoptosis in the T-ALL cell line CEM. A common problem with cancer is chemoresistance, which is often typical of relapsed cancers. Remarkably, a T-ALL sample at diagnosis and an acute myeloid leukemia sample at relapse that were resistant to doxorubicin in vitro were sensitive to AN-9, with an IC(50) of 50 microM for both samples. More strikingly, samples from 2 infants with t(4;11) ALL obtained at diagnosis and relapse each were the most sensitive to AN-9, with IC(50) values of 25 microM and 17 microM, respectively. Furthermore, a doxorubicin-resistant clone of HL60, HL60/ADR, obtained by the transfection of the MDR-1 gene, was equally sensitive to AN-9 cytotoxicity as the parental cells. AN-9 induced the expression of p21 in an infant leukemia sample with 11q23 rearrangement, but not in T- or B-precursor ALL. Collectively, our results suggest that AN-9 is a selective agent for hematopoietic malignancies that can circumvent the mechanisms of chemoresistance limiting most conventional chemotherapy.
Fully stabilized GHz Yb-fiber laser frequency comb (2009)

Get PDF Email Share Share with Facebook Share on X Post on reddit Share with LinkedIn Add to Mendeley Add to BibSonomy Share with WeChat Get Citation Copy Citation Text I. Hartl, H. A. Mckay, R. Thapa, B. K. Thomas, A. Ruehl, L. Dong, and M. E. Fermann, "Fully stabilized GHz Yb-fiber laser frequency comb," in Advanced Solid-State Photonics, OSA Technical Digest Series (CD) (Optica Publishing Group, 2009), paper MF9. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Changes in Northern Elephant Seal Skeletal Muscle Following Thirty Days of Fasting and Reduced Activity (2020)

Northern elephant seals (NES, <i>Mirounga angustirostris</i>) undergo an annual molt during which they spend ∼40 days fasting on land with reduced activity and lose approximately one-quarter of their body mass. Reduced activity and muscle load in stereotypic terrestrial mammalian models results in decreased muscle mass and capacity for force production and aerobic metabolism. However, the majority of lost mass in fasting female NES is from fat while muscle mass is largely preserved. Although muscle mass is preserved, potential changes to the metabolic and contractile capacity are unknown. To assess potential changes in NES skeletal muscle during molt, we collected muscle biopsies from 6 adult female NES before the molt and after ∼30 days at the end of the molt. Skeletal muscle was assessed for respiratory capacity using high resolution respirometry, and RNA was extracted to assess changes in gene expression. Despite a month of reduced activity, fasting, and weight loss, skeletal muscle respiratory capacity was preserved with no change in OXPHOS respiratory capacity. Molt was associated with 162 upregulated genes including those favoring lipid metabolism. We identified 172 downregulated genes including those coding for ribosomal proteins and genes associated with skeletal muscle force transduction and glucose metabolism. Following ∼30 days of molt, NES skeletal muscle metabolic capacity is preserved although mechanotransduction may be compromised. In the absence of exercise stimulus, fasting-induced shifts in muscle metabolism may stimulate pathways associated with preserving the mass and metabolic capacity of slow oxidative muscle.
Approximate matching of persistent LExicon using search-engines for classifying Mobile app traffic (2016)

We present AMPLES, Approximate Matching of Persistent LExicon using Search-Engines, to address the Mobile-Application-Identification (MApId) problem in network traffic at a per-flow granularity. We transform MApId into an information-retrieval problem where lexical similarity of short-text-documents is used as a metric for classification tasks. Specifically, a network-flow, observed at an intercept-point, is treated as a semi-structured-text-document and modified into a flow-query. This query is then run against a corpus of documents pre-indexed in a search-engine. Each index-document represents an application, and consists of distinguishable identifiers from the metadata-file and URL-strings found in the application's executable-archive. The search-engine acts as a kernel function, generating a score distribution vis-'a-vis the index-documents, to determine a match. This extends the scope of MApId to fuzzy-classification mapping a flow to a family of apps when the score distribution is spread-out. Through experiments over an emulator-generated test-dataset (400 K applications and 13.5 million flows), we obtain over 80% flow coverage and about 85% application coverage with low false-positives (4%) and nearly no false-negatives. We also validate our methodology over a real network trace. Most importantly, our methodology is platform agnostic, and subsumes previous studies, most of which focus solely on the application coverage.
Generalized Degrees of Freedom of the Symmetric Cache-Aided MISO Broadcast Channel With Partial CSIT (2019)

We consider the cache-aided MISO broadcast channel (BC) in which a multi-antenna transmitter serves K single-antenna receivers, each equipped with a cache memory. The transmitter has access to partial knowledge of the channel state information. For a symmetric setting, in terms of channel strength levels, partial channel knowledge levels and cache sizes, we characterize the generalized degrees of freedom (GDoF) up to a constant multiplicative factor. The achievability scheme exploits the interplay between spatial multiplexing gains and coded-multicasting gain. On the other hand, a cut-set-based argument in conjunction with a GDoF outer bound for a parallel MISO BC under channel uncertainty is used for the converse. We further show that the characterized order-optimal GDoF is also attained in a decentralized setting, where no coordination is required for content placement in the caches.
Optical frequency combs using ultrafast diode lasers: Techniques and applications (2013)

This work reviews the authors' work in the generation of compact, electrically efficient sources of ultrastable optical frequency combs using semiconductor diode lasers and highlights several examples of their use in coherent optical signal processing applications.