gebhart/patrepeval huggingface dataset:
2007 Best Paper Awards (2008)

Author’s Abstract. Researchers find that the successful implementation of information systems that span organizational boundaries enhances competitive advantage. However, the process by which networks of design and construction firms implement boundary-spanning technological changes remains poorly understood. In this paper I explore the implementation of threedimensional computer-aided design tools in 26 design and construction organizations. I analyze empirical data collected over a 7-month period to induce a set of antecedent constructs that enable the evolution from “printed sets of plans” to “virtual model” boundary objects. The findings highlight the importance of addressing regulative, technological, work, and organizational issues at the interfaces between design and construction firms when implementing boundary-spanning technological changes.
Developmental role for ACF1-containing nucleosome remodellers in chromatin organisation (2010)

The nucleosome remodelling complexes CHRAC and ACF of Drosophila are thought to play global roles in chromatin assembly and nucleosome dynamics. Disruption of the gene encoding the common ACF1 subunit compromises fly viability. Survivors show defects in chromatin assembly and chromatin-mediated gene repression at all developmental stages. We now show that ACF1 expression is under strict developmental control. The expression is strongly diminished during embryonic development and persists at high levels only in undifferentiated cells, including the germ cell precursors and larval neuroblasts. Constitutive expression of ACF1 is lethal. Cell-specific ectopic expression perturbs chromatin organisation and nuclear programmes. By monitoring heterochromatin formation during development, we have found that ACF1-containing factors are involved in the initial establishment of diversified chromatin structures, such as heterochromatin. Altering the levels of ACF1 leads to global and variegated deviations from normal chromatin organisation with pleiotropic defects.
Unified Model for Gas-Liquid Pipe Flow Via Slug Dynamics: Part 2 — Model Validation (2002)

In Zhang et al. [1], a unified hydrodynamic model is developed for prediction of gas-liquid pipe flow behavior based on slug dynamics. In this study, the new model is validated with extensive experimental data acquired with different pipe diameters, inclination angles, fluid physical properties, gas-liquid flow rates and flow patterns. Good agreement is observed in every aspect of the two-phase pipe flow.
Thiol-Activated HNO Release from a Ruthenium Antiangiogenesis Complex and HIF-1α Inhibition for Cancer Therapy (2016)

Metallonitrosyl complexes are promising as nitric oxide (NO) donors for the treatment of cardiovascular, endothelial, and pathogenic diseases, as well as cancer. Recently, the reduced form of NO(-) (protonated as HNO, nitroxyl, azanone, isoelectronic with O2) has also emerged as a candidate for therapeutic applications including treatment of acute heart failure and alcoholism. Here, we show that HNO is a product of the reaction of the Ru(II) complex [Ru(bpy)2(SO3)(NO)](+) (1) with glutathione or N-acetyl-L-cysteine, using met-myoglobin and carboxy-PTIO (2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) as trapping agents. Characteristic absorption spectroscopic profiles for HNO reactions with met-myoglobin were obtained, as well as EPR evidence from carboxy-PTIO experiments. Importantly, the product HNO counteracted NO-induced as well as hypoxia-induced stabilization of the tumor-suppressor HIF-1α in cancer cells. The functional disruption of neovascularization by HNO produced by this metallonitrosyl complex was demonstrated in an in vitro angiogenesis model. This behavior is consistent with HNO biochemistry and contrasts with NO-mediated stabilization of HIF-1α. Together, these results demonstrate for the first time thiol-dependent production of HNO by a ruthenium complex and subsequent destabilization of HIF-1α. This work suggests that the complex warrants further investigation as a promising antiangiogenesis agent for the treatment of cancer.
Effects of Catalyst Compositions on Deterioration of Reforming Catalysts in EGR of Gasoline Engines (2018)

Fuel reforming catalysts installed in the EGR system of gasoline engines are used to form hydrogen with steam reforming. However, deteriorations of the catalyst due to sulfur poisoning and carbon deposition are concerned for the practical use. In the present study, five catalysts consisting of different materials were examined to explore the catalysts that increase the hydrogen production and the tolerance. The experiments on variations of sulfur contents contained in the reformed fuels revealed that lanthanum (La) has a strong resistance to carbon deposition and adding platinum (Pt) or palladium (Pd) results in a high resistance to the sulfur poisoning.
CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq (2020)

lcRNA-seq coupled with CLEAR is widely used in our institution for profiling immune cells (circulating or tissue-infiltrating) for its transcript preservation characteristics. CLEAR fills an important niche in pre-processing lcRNA-seq data to facilitate transcriptome profiling and DEG analysis. We demonstrate the utility of CLEAR in analyzing rare cell populations in clinical samples and in murine neural DG region without sample pooling.
Bone marrow expands the repertoire of functional T cells targeting tumor-associated antigens in patients with resectable non-small-cell lung cancer (2019)

The efficacy of cancer immunotherapy may be improved by increasing the number of circulating tumor-reactive T cells. The bone marrow is a priming site and reservoir for such T cells. The characteristics of bone marrow-derived tumor-reactive T cells are poorly understood in patients with non-small-cell lung cancer (NSCLC). To compare the responsiveness of tumor antigen-reactive T cells from the bone marrow with matched peripheral blood samples in patients with resectable NSCLC, we used flow cytometry, cytokine capture assays and enzyme-linked immunospot assays to examine the responsiveness of T cells to 14 tumor antigens in matched bone marrow and peripheral blood samples from patients with resectable NSCLC or benign tumors and tumor-free patients. T cells with reactivity to tumor antigens were detected in the bone marrow of 20 of 39 (51%) NSCLC patients. The panel of tumor antigens recognized by bone marrow-derived T cells was distinct from that recognized by peripheral blood-derived T cells in NSCLC patients. Unlike for peripheral blood T cells, the presence of tumor-reactive T cells in the bone marrow did not correlate with recurrence-free survival after curative intent resection of NSCLC. T cells with reactivity to tumor antigens are common in the bone marrow of patients with NSCLC. Tumor-reactive T cells of the bone marrow have the potential to significantly broaden the total repertoire of tumor-reactive T cells in the body. To clarify the role of tumor-reactive T cells of the bone marrow in T cell-based immunotherapy approaches, clinical studies are needed (ClinicalTrials.gov: NCT02515760).
Chemical Mechanism Identification from Frequency Response to Small Temperature Modulation (2012)

The description of interactions between biochemical species and the elucidation of the corresponding chemical mechanisms encounter an increasing interest both for the comprehension of biological pathways at the molecular scale and for the rationalization of drug design. Relying on powerful experimental tools such as thermal microfluidics and fluorescence detection, we propose a methodology to determine the chemical mechanism of a reaction without fitting parameters. A mechanism consistent with the accessible knowledge is assumed, and the assumption is checked through an iterative protocol. The test is based on the frequency analysis of the response of a targeted reactive species to temperature modulation. We build specific functions of the frequency that are constant for the assumed mechanism and show that the graph of these functions can be drawn from appropriate data analysis. The method is general and can be applied to any complex mechanism. It is here illustrated in detail in the case of single relaxation time mechanisms.
Management of HIT II Patients with Hirudin Antibodies after Primary Therapy (2002)

Heparin, ein wasserlösliches, anionisches Glykosaminoglykan, ist das am häufigsten zur Antikoagulation eingesetzte Medikament. Das Grundgerüst des Moleküls ist eine alternierend aus Glukosamin, Glukuronsäure und Iduronsäure zusammengesetzte Polysaccharidkette, deren einzelne Untereinheiten durch Schwefelsäure verestert sind. Neben den hochmolekularen Heparinen mit Molekulargewichten zwischen 10 und 20 kDa (Kilodalton) werden heute zunehmend niedermolekulare Heparine (NMH) mit einem mittleren Molekulargewicht von vier bis sechs kDa verwendet, die durch Fraktionierung oder Depolymerisierung aus hochmolekularem Heparin erzeugt werden. Im Heparinmolekül finden sich mehrere Bindungsstellen für Proteine wie Antithrombin, Heparin-Kofaktor II und Plättchenfaktor 4 (PF 4).
Multiple Regulatory Elements in the Murine Stromelysin-3 Promoter (2000)

Stromelysin-3 (ST3) belongs to the matrix metalloproteinase (MMPs) family, a protease family involved in tissue remodeling. Although this family of enzymes is regulated by nuclear receptors, few hormone-responsive elements have been demonstrated in MMP promoters. In order to identify regulatory elements and/or factors that control the expression of the mouse st3 gene, we have analyzed genomic sequences encompassing 5 kilobase pairs of the ST3 promoter. Analysis of these sequences revealed several CCAAT/enhancer-binding proteins (C/EBP) and retinoic acid-responsive elements (RAREs), as well as one thyroid-responsive element. However, in contrast to most MMP promoters, no AP-1-binding sites were identified. Specific binding activities were demonstrated for all elements. Consistent with previous reports, retinoid X receptor is required for maximal binding to the ST3 RAREs and the TRE. The ST3-C/EBP element was shown to mediate dose-dependent promoter activation by C/EBPbeta. Among the RAREs, the proximal DR1-RARE was shown to be sufficient for ST3 promoter activation by ligand-bound retinoid receptors, whereas the two distal DR2-RAREs appear to be involved more in the control of base-line promoter activity. Accordingly, ST3 expression was induced by retinoic acid and was reduced in cells where specific retinoic acid receptors had been inactivated. The involvement of these conserved regulatory elements is discussed in the context of physiological or pathological situations associated with st3 expression. Our findings therefore assign to C/EBP, retinoids, and thyroid hormone important roles in the regulation of ST3 gene expression.
Fermentative Production of N-Methylglutamate From Glycerol by Recombinant Pseudomonas putida (2018)

<i>N</i>-methylated amino acids are present in diverse biological molecules in bacteria, archaea and eukaryotes. There is an increasing interest in this molecular class of alkylated amino acids by the pharmaceutical and chemical industries. <i>N</i>-alkylated amino acids have desired functions such as higher proteolytic stability, enhanced membrane permeability and longer peptide half-lives, which are important for the peptide-based drugs, the so-called peptidomimetics. Chemical synthesis of <i>N</i>-methylated amino acids often is limited by incomplete stereoselectivity, over-alkylation or the use of hazardous chemicals. Here, we describe metabolic engineering of <i>Pseudomonas putida</i> KT2440 for the fermentative production of <i>N</i>-methylglutamate from simple carbon sources and monomethylamine. <i>P. putida</i> KT2440, which is generally recognized as safe and grows with glucose and the alternative feedstock glycerol as sole carbon and energy source, was engineered for the production of <i>N</i>-methylglutamate using heterologous enzymes from <i>Methylobacterium extorquens</i>. About 3.9 g L<sup>-1</sup> <i>N</i>-methylglutamate accumulated within 48 h in shake flask cultures with minimal medium containing monomethylamine and glycerol. A fed-batch cultivation process yielded a <i>N-</i>methylglutamate titer of 17.9 g L<sup>-1</sup>.
TDM based reference signal multiplexing for Faster-than-Nyquist signaling using OFDM/OQAM (2014)

This paper proposes time division multiplexing (TDM) based reference signal (RS) multiplexing for non-orthogonal multiplexing employing Faster-than-Nyquist (FTN) signaling for orthogonal frequency division multiplexing (OFDM)/offset quadrature amplitude modulation (OQAM). Accurate channel estimation is essential for FTN signaling when using a turbo soft interference canceller (SIC). We propose dividing resource elements (REs) within a physical resource block (PRB) pair into orthogonal and non-orthogonal RE multiplexing regions based on TDM to decrease inter-symbol interference and inter-subcarrier interference to a substantially low level. The RSs for channel estimation are multiplexed in the REs in the orthogonal RE region. Based on link-level simulations, we show that TDM based RS multiplexing achieves accurate channel estimation such that the loss in the required average received signal-to-noise power ratio for satisfying the average block error rate of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> compared to the case with ideal channel estimation is suppressed to within approximately 2 dB.
Supplementary Figure 3 from Not all NOTCH Is Created Equal: The Oncogenic Role of NOTCH2 in Bladder Cancer and Its Implications for Targeted Therapy (2023)

&lt;p&gt;NOTCH2 silencing inhibited tumor progression through decreased cell proliferation and invasion.&lt;/p&gt;
New frontiers in the treatment of overactive bladder and incontinence. (2002)

In this article the author tries to forecast how urologists will treat the overactive bladder (OAB) in the next decade. He reviews drugs currently under development and also logical and exciting pharmacological targets that would be suitable targets for treating OAB in the future. The author also discusses intravesical therapy and alternative drug delivery methods, such as intravesical capsaicin and botulinum toxin. There are many advantages to advanced drug delivery systems, including the achievement of long-term therapeutic efficacy, decreased incidence and severity of side effects, and improved patient compliance. Special emphasis is placed on approaches to modulating bladder afferent nerve function to prevent OAB. Speculation on future techniques such as gene therapy can also be considered for treating OAB, because they may make it possible to access all of the genitourinary organs via minimally invasive techniques. Traditional anticholinergic therapies are limited in their effectiveness. There is great hope for future research and therapy for OAB and urinary incontinence.
Contribution of Host Defence Proteins and Peptides to Host-Microbiota Interactions in Chronic Inflammatory Lung Diseases (2018)

The respiratory tract harbours a variety of microorganisms, collectively called the respiratory microbiota. Over the past few years, alterations in respiratory and gut microbiota composition have been associated with chronic inflammatory diseases of the lungs. How these changes influence disease development and progression is an active field of investigation. Identifying and understanding host-microbiota interactions and factors contributing to these interactions could promote the development of novel therapeutic strategies aimed at restoring host-microbiota homeostasis. In this review, we discuss recent literature on host-microbiota interactions in the respiratory tract, with a specific focus on the influence of endogenous host defence peptides and proteins (HDPs) on the composition of microbiota populations in vivo and explore possible HDPs-related therapeutic approaches targeting microbiota dysbiosis in chronic inflammatory lung diseases.
FIB Chip Repair: Improving Success by Controlling Beam-Induced Damage and Thermal/Mechanical Stress (2004)

Abstract Focused Ion Beam (FIB) success has become more difficult as microchip process technology advances, requiring new techniques for damage control both during the microsurgery procedure and before the finished product can be electrically tested. Ultra thin gate dielectrics, shallower junctions, less ‘white space,’ and new materials surrounding active devices all create additional challenges for imaging, targeting, controlling instantaneous charge damage, and the removal of residual implanted charge. On the macro level, global thinning of bulk silicon housed in hybrid packages is causing new problems with thermal management and mechanical stress. Techniques and procedures used to control electrostatic discharge type damage become ever more critical when working on poorly buffered or isolated device elements, especially from the backside. Implanted gallium and residual charge perturb electrical characteristics, and must be dispersed prior to power-up thru carefully controlled bake steps. Left in place, these FIB-induced perturbations are likely to cause poor functionality or even latchup. The mechanical rigidity and thermal dissipation properties of newer, complex package types must also be restored post-FIB, otherwise cracked silicon or a thermal overload event might be the outcome. In this paper, we will attempt to address some of the common causes of FIB-induced failure on newer silicon and package technologies, and how they might be overcome. FIB techniques and preparatory processes must continue to evolve in order to deal effectively with the problems of direct beam damage, residual charge elimination, and sample stress management.
Pivotal Advance: PKCζ is required for migration of macrophages (2009)

The crosstalk, mediated by chemoattractants, between cancer cells and tumor-associated macrophages, plays an important role in tumor invasion and metastasis. Our previous study reported that atypical protein kinase C zeta (PKCzeta) regulates epidermal growth factor-induced chemotaxis of human breast cancer cells. In this study, we investigated the role of PKCzeta in CSF-1-induced chemotaxis of macrophages. Knockdown of PKCzeta by small interference RNA impaired CSF-1-induced chemotaxis of human acute monocytic leukemia cell line THP-1, which was probably a result of a decrease in CSF-1-induced phosphorylation of LIN-11, Is11, and MEC-3 protein domain kinase (LIMK)/cofilin and actin polymerization. Furthermore, silencing PKCzeta expression also impaired migration of mouse peritoneal macrophages. Scratch analysis indicated that PKCzeta was required for macrophage migration. Therefore, PKCzeta is required for CSF-1-induced chemotaxis of macrophages. Blocking activation of PKCzeta will be a novel strategy to inhibit cancer metastasis by blocking migration of cancer cells and macrophages.
High‐resolution MRI of mummified tissues using advanced short‐T<sub>2</sub> methodology and hardware (2020)

Mummy MRI is a potentially valuable tool for (paleo)pathological studies, as well as for investigations into ancient mummification processes. The results presented here show sufficient improvement in the depiction of mummified tissues to clear new paths for the exploration of this field.
Site-Selective Intramolecular Photocycloaddition of 2-Alkenyl-Substituted 1-Cyanonaphthalenes Depending on Additives, Solvents, and Substituents (2002)

Irradiation of 2,3-dimethylbut-2-enyl 1-cyano-2-naphthylmethyl ether in the presence of Eu(hfc)3 in benzene site-selectively afforded the (2π + 2π) intramolecular photocycloadduct at the 1,2-position on the naphthalene ring. On the other hand, allyl 1-cyano-2-naphthylmethyl ether in the presence of Mg(ClO4)2 in acetonitrile gave the photocycloadduct at the 3,4-position as a sole product.
Coupled-Resonator Optical Waveguides (CROWs) Based on Grating Resonators with Modulated Bandgap (2011)

We theoretically study CROWs based on modulated grating resonators. The defect sections between resonators control the coupling coefficients and frequency detuning. The transmission spectra of CROWs rely on a proper choice of the defect length.
Effect of the Exchanged Cation in an Algerian Montmorillonite Used as a Heterogeneous Catalyst for Biginelli Reaction (2021)

In this work, an Algerian montmorillonite (Mt) is exchanged by different cations from the transition metals family, namely: Cu2+, Ni2+, Cr3+, Co2+, Fe2+ and Fe3+, it is used as a heterogeneous catalyst for Biginelli reaction. The exchanged cations are known for their catalytic properties in homogeneous catalysis. The main purpose is to study the effect of the exchanged cations on the yield and the kinetics of the reaction. The characterization of montmorillonite was carried out by XRD, which allows us to follow the evolution of the basal spacing d001 as a function of the exchanged cation and to show that the exchange operation has not altered the montmorillonite structure. The cation exchange capacity (CEC) is determined by the titration of the exchanged cation by atomic absorption. The product of the reaction is characterized by NMR, IR and by the determination of the melting point. In addition, the importance of the introduction order of the reagents into the reaction medium has been demonstrated on the yield and the kinetics. Finally, the obtained results show that the exchanged montmorillonite is competitive with other costly heterogeneous and homogeneous catalysts.
Modeling communication and estimation processes of automated crash avoidance systems (2013)

We present a novel approach to modeling the combined estimation and networking processes of automated crash/collision avoidance systems (ACAS). The estimation and networking processes are two necessary components of the real-time situation awareness component of the system. The existing models for these two components are mostly based on stochastic modeling methods, describing each component separately and in abstract probabilistic terms. Such modeling methods lead to the loss of useful details. In our recent work we presented extended stochastic models using discrete-time Markov chains for the networking component and empirical statistical models for the estimation process. Although these models led to significantly improved designs for the situation awareness component of ACAS, it was observed that the extent of the improvement was limited. The limitation is due the fact that stochastic models are limited in describing the system which inherently has many deterministic features. In this paper we attempt to advance the approach to modeling the ACAS systems (and other similar systems) through developing a method to model the communication component based on Probabilistic Timed automata and also a Hybrid automata to combine and model the entire system (both estimation and communication/networking processes). This paper presents the new model and verifies it using simulations.