gebhart/patrepeval huggingface dataset:
Fermentable Fibers or Oligosaccharides Reduce Urinary Nitrogen Excretion by Increasing Urea Disposal in the Rat Cecum (1995)

The availability of fermentable carbohydrates could influence the digestive degradation and disposal of blood urea. The effects of a poorly fermented cellulosic oat fiber, a soluble fermentable fiber (gum arabic) or one of two oligosaccharides (fructooligosaccharide or xylooligosaccharide) on nitrogen excretion were compared with a wheat starch-based control diet in male Wistar rats. The fibers and oligosaccharides were added to the semipurified diets at 7.5 g/100 g in place of wheat starch. The diets contained 13 g casein/100 g. Oat fiber did not cause an enlargement of the cecum. In contrast, gum arabic and the oligosaccharides elicited a 35-60% enlargement of the cecal wall and a 2 to 2.6-fold mean increase in the cecal pool of short chain fatty acids. Compared with rats fed the oat fiber-based diet, urea flux from blood to cecum was nearly 50% greater and more than 120% greater in those fed the gum arabic and oligosaccharide diets, respectively. In those groups, net nitrogen retention in the cecum more than doubled (nitrogen retention was calculated as the difference between net urea nitrogen flux into the cecum and ammonia nitrogen reabsorption). As a percentage of total excreted nitrogen, fecal nitrogen was 20% in the oat fiber group and 27-29% in the gum arabic and oligosaccharide groups, compared with only 10% in fiber-free controls. Results indicate that under these dietary conditions, the addition of oligosaccharides to the diet induced a 20 to 30% decrease in blood urea and renal and renal nitrogen excretion relative to the control, indicating a potential for oligosaccharide diet therapy in chronic renal disease.
Localized watermarking: methodology and application to operation scheduling (2003)

Recently, a number of techniques for IP protection have been introduced that rely on a selection of a global solution to an optimization problem according to a unique user-specific digital signature. Although such techniques may provide convincing proof of authorship with low hardware overhead, they fail to protect parts of design, do not provide an easy procedure for watermark detection, and are not capable of detecting the watermark when the design or its part is augmented in another larger design. Since these demands are of the highest interest for the IP business, we introduce localized watermarking as an IP protection technique that enables these features while satisfying the demand for low-cost and transparency. We propose a set of protocols that implement the new watermarking methodology at the operation scheduling design level. We have demonstrated that the difficulty of erasing or finding another signature in the synthesized design can be made arbitrarily computationally difficult. The watermarking method has been tested on a set of real-life benchmarks where high likelihood of authorship has been achieved with negligible overhead in solution quality.
Is the Glycoprotein Responsible for the Differences in Dispersal Rates between Lettuce Necrotic Yellows Virus Subgroups? (2022)

<i>Lettuce necrotic yellows virus</i> is a type of species in the <i>Cytorhabdovirus</i> genus and appears to be endemic to Australia and Aotearoa New Zealand (NZ). The population of lettuce necrotic yellows virus (LNYV) is made up of two subgroups, SI and SII. Previous studies demonstrated that SII appears to be outcompeting SI and suggested that SII may have greater vector transmission efficiency and/or higher replication rate in its host plant or insect vector. Rhabdovirus glycoproteins are important for virus-insect interactions. Here, we present an analysis of LNYV glycoprotein sequences to identify key features and variations that may cause SII to interact with its aphid vector with greater efficiency than SI. Phylogenetic analysis of glycoprotein sequences from NZ isolates confirmed the existence of two subgroups within the NZ LNYV population, while predicted 3D structures revealed the LNYV glycoproteins have domain architectures similar to Vesicular Stomatitis Virus (VSV). Importantly, changing amino acids at positions 244 and 247 of the post-fusion form of the LNYV glycoprotein altered the predicted structure of Domain III, glycosylation at N248 and the overall stability of the protein. These data support the glycoprotein as having a role in the population differences of LNYV observed between Australia and New Zealand.
Shape regulation of high-index facet nanoparticles by dealloying (2019)

Tetrahexahedral particles (~10 to ~500 nanometers) composed of platinum (Pt), palladium, rhodium, nickel, and cobalt, as well as a library of bimetallic compositions, were synthesized on silicon wafers and on catalytic supports by a ligand-free, solid-state reaction that used trace elements [antimony (Sb), bismuth (Bi), lead, or tellurium] to stabilize high-index facets. Both simulation and experiment confirmed that this method stabilized the {210} planes. A study of the PtSb system showed that the tetrahexahedron shape resulted from the evaporative removal of Sb from the initial alloy-a shape-regulating process fundamentally different from solution-phase, ligand-dependent processes. The current density at a fixed potential for the electro-oxidation of formic acid with a commercial Pt/carbon catalyst increased by a factor of 20 after transformation with Bi into tetrahexahedral particles.
A master oscillator power amplifier system based on external cavity mode-locking of a quantum-dot two-section diode laser (2005)

We study ultrashort, high power pulse generation from a master oscillator power amplifier system based on an external cavity QD mode-locked two-section diode laser and a multilayer QD-SOA. The compressed pulses are 1.2 psec in duration, with a pulse energy of 1.46 pJ, implying a peak power of 1.22 W.
On the Relationship between Redundancy and Decoding Error in Slepian-Wolf Coding (2006)

The relationship between redundancy and decoding error in Slepian-Wolf coding with one encoder is investigated. For any memoryless source-side information pair (X,Y) = {(X <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> ,Y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> )} <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">iinfin=1</sub> with finite alphabet, the redundancy R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> (epsi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ) of Slepian-Wolf coding is defined as the minimum of the difference between the compression rate of any Slepian-Wolf code resulting from coding X <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> with decoding error epsi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> , and the conditional entropy H(X|Y). When epsi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> denotes the block error probability in decoding, it is shown that under mild assumptions, R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> (epsi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> ) = thetas(radic(-(log epsi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n </sub> )/n)). When epsi <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sub> denotes the average symbol error in decoding, this relationship is further shown to hold for fixed-rate Slepian-Wolf coding
2-Methoxyestradiol and its derivatives inhibit store-operated Ca2+ entry in T cells: Identification of a new and potent inhibitor (2021)

T cell activation starts with formation of second messengers that release Ca<sup>2+</sup> from the endoplasmic reticulum (ER) and thereby activate store-operated Ca<sup>2+</sup> entry (SOCE), one of the essential signals for T cell activation. Recently, the steroidal 2-methoxyestradiol was shown to inhibit nuclear translocation of the nuclear factor of activated T cells (NFAT). We therefore investigated 2-methoxyestradiol for inhibition of Ca<sup>2+</sup> entry in T cells, screened a library of 2-methoxyestradiol analogues, and characterized the derivative 2-ethyl-3-sulfamoyloxy-17β-cyanomethylestra-1,3,5(10)-triene (STX564) as a novel, potent and specific SOCE inhibitor. STX564 inhibits Ca<sup>2+</sup> entry via SOCE without affecting other ion channels and pumps involved in Ca<sup>2+</sup> signaling in T cells. Downstream effects such as cytokine expression and cell proliferation were also inhibited by both 2-methoxyestradiol and STX564, which has potential as a new chemical biology tool.
All-optical production and trapping of metastable noble-gas atoms down to the single-atom regime (2014)

The determination of isotope ratios of noble gas atoms has many applications e.g. in physics, nuclear arms control, and earth sciences. For several applications, the concentration of specific noble gas isotopes (e.g. Kr and Ar) is so low that single atom detection is highly desirable for a precise determination of the concentration. As an important step in this direction, we demonstrate operation of a krypton Atom Trap Trace Analysis (ATTA) setup based on a magneto-optical trap (MOT) for metastable Kr atoms excited by all-optical means. Compared to other state-of-the-art techniques for preparing metastable noble gas atoms, all-optical production is capable of overcoming limitations regarding minimal probe volume and avoiding cross-contamination of the samples. In addition, it allows for a compact and reliable setup. We identify optimal parameters of our experimental setup by employing the most abundant isotope Kr-84, and demonstrate single atom detection within a 3D MOT.
Developing DRC plus rules through 2D pattern extraction and clustering techniques (2009)

As technology processes continue to shrink and aggressive resolution enhancement technologies (RET) and optical proximity correction (OPC) are applied, standard design rule constraints (DRC) sometimes fails to fully capture the concept of design manufacturability. DRC Plus augments standard DRC by applying fast 2D pattern matching to design layout to identify problematic 2D patterns missed by DRC. DRC Plus offers several advantages over other DFM techniques: it offers a simple pass/no-pass criterion, it is simple to document as part of the design manual, it does not require compute intensive simulations, and it does not require highly-accurate lithographic models. These advantages allow DRC Plus to be inserted early in the design flow, and enforced in conjunction with standard DRC. The creation of DRC Plus rules, however, remains a challenge. Hotspots derived from lithographic simulation may be used to create DRC Plus rules, but the process of translating a hotspot into a pattern is a difficult and manual effort. In this paper, we present an algorithmic methodology to identify hot patterns using lithographic simulation rather than hotspots. First, a complete set of pattern classes, which covers the entire design space of a sample layout, is computed. These pattern classes, by construction, can be directly used as DRC Plus rules. Next, the manufacturability of each pattern class is evaluated as a whole. This results in a quantifiable metric for both design impact and manufacturability, which can be used to select individual pattern classes as DRC Plus rules. Simulation experiment shows that hundreds of rules can be created using this methodology, which is well beyond what is possible by hand. Selective visual inspection shows that algorithmically generated rules are quite reasonable. In addition to producing DRC Plus rules, this methodology also provides a concrete understanding of design style, design variability, and how they affect manufacturability.
Exploring the Tunability and Dynamic Properties of MarR-PmarO Sensor System in Escherichia coli (2021)

Transcriptional factor-based biosensors (TFBs) have been widely used in dynamic pathway control or high-throughput screening. Here, we systematically explored the tunability of a salicylic acid responsive regulator MarR from <i>Escherichia coli</i> aiming to explore its engineering potential. The effect of endogenous MarR in <i>E. coli</i> on the MarR-PmarO biosensor system was investigated. Furthermore, to investigate the function of marO binding boxes in this biosensor system, a series of hybrid promoters were constructed by placing the marO binding boxes in the strong constitutive pL promoter. The engineered hybrid promoters became responsive to MarR and salicylic acid. To further study the influence of each nucleotide in the marO box on MarR binding, we employed dynamic modeling to simulate the interaction and binding energy between each nucleotide in the marO boxes with the corresponding residues on MarR. Guided by the results of the simulation, we introduced mutations to key positions on the hybrid promoters and investigated corresponding dynamic performance. Two promoter variants I12AII4T and I12AII14T that exhibited improved responsive strengths and shifted dynamic ranges were obtained, which can be beneficial for future metabolic engineering research.
miRWalk: An online resource for prediction of microRNA binding sites (2018)

miRWalk is an open-source platform providing an intuitive interface that generates predicted and validated miRNA-binding sites of known genes of human, mouse, rat, dog and cow. The core of miRWalk is the miRNA target site prediction with the random-forest-based approach software TarPmiR searching the complete transcript sequence including the 5'-UTR, CDS and 3'-UTR. Moreover, it integrates results other databases with predicted and validated miRNA-target interactions. The focus is set on a modular design and extensibility as well as a fast update cycle. The database is available using Python, MySQL and HTML/Javascript Database URL: http://mirwalk.umm.uni-heidelberg.de.
Differential effects of negative costimulatory molecules BTNL2 and PD-L1 on the activation of T cells when using MHC class I tetramer, MHC class II tetramer, or anti-CD3 immobilized on beads (90.6) (2009)

Abstract Immunologists have identified a growing list of negative costimulatory molecules in the B7 family of proteins. These molecules are defined in vitro by their capacity to inhibit purified T cell proliferation and cytokine production only when immobilized proximally to anti-CD3. We are interested in whether the negative costimulatory molecules behave differently when activating T cells in an antigen specific manner. The required proximal immobilization with TCR agonist can be achieved on beads loaded with MHC class I or class II tetramers and subsequent culture with appropriate transgenic T cells. In this poster, we show evidence that CD4 and CD8 T cells are inhibited differently when stimulated with peptide/MHC molecules compared to activation with anti-CD3. The two negative costimulatory molecules we are currently studying, BTNL2 and PDL1, block activation under different circumstances. Although both molecules can inhibit T cell responses to anti-CD3, PDL1 is more effective at inhibiting CD8 responses to MHC class I than CD4 responses to MHC class II. Conversely, BTNL2 inhibits CD4 T cells in the same system, but cannot block the CD8 response as well as PDL1. These studies imply that different negative costimulatory molecules may have cell specific roles and provide a system to investigate regulatory mechanisms that result in differential inhibition of CD8 and CD4 T cells.
Transcriptional evidence for the "Reverse Warburg Effect" in human breast cancer tumor stroma and metastasis: Similarities with oxidative stress, inflammation, Alzheimer's disease, and "Neuron-Glia Metabolic Coupling" (2010)

Caveolin-1 (-/-) null stromal cells are a novel genetic model for cancer-associated fibroblasts and myofibroblasts. Here, we used an unbiased informatics analysis of transcriptional gene profiling to show that Cav-1 (-/-) bone-marrow derived stromal cells bear a striking resemblance to the activated tumor stroma of human breast cancers. More specifically, the transcriptional profiles of Cav-1 (-/-) stromal cells were most closely related to the primary tumor stroma of breast cancer patients that had undergone lymph-node (LN) metastasis. This is consistent with previous morphological data demonstrating that a loss of stromal Cav-1 protein (by immuno-histochemical staining in the fibroblast compartment) is significantly associated with increased LN-metastasis. We also provide evidence that the tumor stroma of human breast cancers shows a transcriptional shift towards oxidative stress, DNA damage/repair, inflammation, hypoxia, and aerobic glycolysis, consistent with the "Reverse Warburg Effect". Finally, the tumor stroma of "metastasis-prone" breast cancer patients was most closely related to the transcriptional profiles derived from the brains of patients with Alzheimer's disease. This suggests that certain fundamental biological processes are common to both an activated tumor stroma and neuro-degenerative stress. These processes may include oxidative stress, NO over-production (peroxynitrite formation), inflammation, hypoxia, and mitochondrial dysfunction, which are thought to occur in Alzheimer?s disease pathology. Thus, a loss of Cav-1 expression in cancer-associated myofibroblasts may be a protein biomarker for oxidative stress, aerobic glycolysis, and inflammation, driving the "Reverse Warburg Effect" in the tumor micro-environment and cancer cell metastasis.
Scheduling and control co-design of networked induction motor control systems (2013)

This paper investigates the co-design of remote speed control and network scheduling for motion coordination of multiple induction motors through a shared communication network. An integrated feedback scheduling algorithm is designed to allocate the optimal sampling period and priority to each control loop to optimize the global performance of a networked control system (NCS), while satisfying the constraints of stability and schedulability. The rational gain of the network speed controllers is calculated using the Lyapunov theorem and online tuned by fuzzy logic to guarantee the robustness against complicated variations on the communication network. Furthermore, a state predictor is designed to compensate the time delay occurred in data transmission from the sensor to the controller, as a part of the networked controller. Simulation results are given to illustrate the effectiveness of the proposed control-and-scheduling co-design approach.
New tourniquet device concepts for battlefield hemorrhage control. (2011)

In order to solve the now most common cause of preventable death on the battlefield, junctional hemorrhage from the pelvic area, the planned approach is a systematic review of research, device and model development, and the fielding of a good device with appropriate training and doctrine.
Abstract 2912: Development of potent SHP2 inhibitors for in vivo studies (2012)

Abstract The Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) is a positive transducer of growth factor, cytokine, integrin, and hormone signaling pathways which regulates processes such as cell proliferation, differentiation, adhesion, migration, and apoptosis and plays a pivotal role in growth factor and cytokine signaling. Gain-of-function SHP2 mutations are associated with various kinds of leukemia, and solid tumors. This makes SHP2 an attractive target for anticancer therapy. We are developing SHP2 inhibitors as novel anticancer drugs. Previously, we have reported on SPI-112 and its methyl ester prodrug SPI-112Me. However, the poor solubility of SPI-112Me has become an obstacle for in vivo studies. In ongoing study, we generate SPI-112 analogs to further improve physicochemical properties of these SHP2 inhibitors, such as solubility and cell permeability. To this aim, we synthesized SPI-112 derivatives containing various phosphotyrosine mimics and their prodrugs. SPI-112 derivatives of SHP2 inhibitors having improved properties have been obtained in this effort. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2912. doi:1538-7445.AM2012-2912
Antimicrobial Photodynamic Therapy with Decacationic Monoadducts and Bisadducts of [70]Fullerene: In Vitro and In Vivo Studies (2013)

We propose that the attachment of an additional deca(tertiary-ethylenylamino)malonate arm to C70 allowed the moiety to act as a potent electron donor and increased the generation yield of hydroxyl radicals under UVA illumination.
Expression of an enzymatically active Yb3 glutathione S-transferase in Escherichia coli and identification of its natural form in rat brain. (1988)

Glutathione S-transferases containing Yb3 subunits are relatively uncommon forms that are expressed in a tissue-specific manner and have not been identified unequivocally or characterized. A cDNA clone containing the entire coding sequence of Yb3 glutathione S-transferase mRNA was incorporated into a pIN-III expression vector used to transform Escherichia coli. A fusion Yb3-protein containing 14 additional amino acid residues at its N terminus was purified to homogeneity. Recombinant Yb3 was enzymatically active with both 1-chloro-2,4-dinitrobenzene and 1,2-dichloro-4-nitrobenzene as substrates but lacked glutathione peroxidase activity. Substrate specificity patterns of recombinant Yb3 were more limited than those of glutathione S-transferase isoenzymes containing Yb1- or Yb2-type subunits. Peptides corresponding to unique amino acid sequences of Yb3 as well as a peptide from a region of homology with Yb1 and Yb2 subunits were synthesized. These synthetic peptides were used to raise antibodies specific to Yb3 and others that cross-reacted with all Yb forms. Immunoblotting was utilized to identify the natural counterpart of recombinant Yb3 among rat glutathione transferases. Brain and testis glutathione S-transferases were rich in Yb3 subunits, but very little was found in liver or kidney. Physical properties, substrate specificities, and binding patterns of the recombinant protein paralleled properties of the natural isoenzyme isolated from brain.