gebhart/patrepeval huggingface dataset:
High yield production of four-carbon dicarboxylic acids by metabolically engineered Escherichia coli (2017)

Several metabolic engineered Escherichia coli strains were constructed and evaluated for four-carbon dicarboxylic acid production. Fumarase A, fumarase B and fumarase C single, double and triple mutants were constructed in a ldhA adhE mutant background overexpressing the pyruvate carboxylase from Lactococcus lactis. All the mutants produced succinate as the main four-carbon (C4) dicarboxylic acid product when glucose was used as carbon source with the exception of the fumAC and the triple fumB fumAC deletion strains, where malate was the main C4-product with a yield of 0.61-0.67 mol (mole glucose)<sup>-1</sup>. Additionally, a mdh mutant strain and a previously engineered high-succinate-producing strain (SBS550MG-Cms pHL413-Km) were investigated for aerobic malate production from succinate. These strains produced 40.38 mM (5.41 g/L) and 50.34 mM (6.75 g/L) malate with a molar yield of 0.53 and 0.55 mol (mole succinate)<sup>-1</sup>, respectively. Finally, by exploiting the high-succinate production capability, the strain SBS550MG-Cms243 pHL413-Km showed significant malate production in a two-stage process from glucose. This strain produced 133 mM (17.83 g/L) malate in 47 h, with a high yield of 1.3 mol (mole glucose)<sup>-1</sup> and productivity of 0.38 g L<sup>-1</sup> h<sup>-1</sup>.
Deaza- and Deoxyadenosine Derivatives: Synthesis and Inhibition of Animal Viruses as Human Infection Models (2003)

N6-Cycloalkyl-2',3'-dideoxyadenosine derivatives and (2-chloro)-N6-cycloheptyl-3-deazaadenosine have been synthesized and tested, along with other (deaza)purine (deoxy)nucleosides from our chemical library, as inhibitors of virus replication against Bovine Herpes Virus 1 (BHV-1) and sheep Maedi/Visna Virus (MVV). Most compounds demonstrated good antireplicative activity against MVV, showing also low cell toxicity.
INTRANODAL TREATMENT WITH IFNΑ‐DENDRITIC CELLS AND RITUXIMAB INDUCES SYSTEMIC CLINICAL RESPONSE AND ENDOGENOUS VACCINATION AGAINST FOLLICULAR LYMPHOMA: FINAL RESULT OF A PHASE I STUDY (2019)

Purpose: This study was aimed at evaluating the feasibility, safety, immunological and clinical responses in patients with Follicular lymphoma (FL) treated with monocyte-derived dendritic cells generated in the presence of interferon-alpha and GM-CSF (IFN-DC) in combination with low doses of Rituximab (R). Experimental design: Firstly, we analyzed in vitro and in vivo the immunological properties of IFN-DC against FL. Thus, we performed a phase I trial in 8 refractory and relapsed FL patients based on sequential intranodal injections of low-dose of R and unloaded IFN-DC and report the safety, clinical and immunological results of the enrolled patients. Results: Preclinical studies indicated that IFN-DC can synergize with R leading to increased cytotoxicity and T cell tumor infiltration. The clinical evaluation showed that the combined treatment was totally safe. The overall response rate was 50%, PET-negative complete response rate 37% and remission is still ongoing in 2/4 of responding patients (median follow- up 26 months, range 11-47). Notably, following the combined therapy all patients showed induction/enhancement of T cell responses by CD107 degranulation or IFN-g ELISPOT assay against patient-specific tumor IGHV sequences. Conclusions: These results represent the proof-of-principle on the effectiveness of unloaded IFN-DC in inducing durable clinical responses and promoting induction of tumor specific peripheral T cells, thus suggesting the occurrence of an effective endogenous antitumor vaccination. The overall findings indicate that some unique properties of IFN-DC can be successfully exploited to induce/enhance antitumor responses, thus representing a valuable antitumor strategy for novel and more effective combination therapies in cancer patients. Translational relevance: The development of protocols of in situ cancer immunotherapy aimed at inducing an endogenous vaccination is currently regarded as a practical and promising antitumor strategy, with potential advantages with respect to the use of defined tumor antigens for inducing a broader antitumor immunity, potentially targeting also neoantigens emerging during tumor progression and therapies. This study represents the first evidence on the safety and clinical effectiveness of IFN-DC, a unique type of DC rapidly generated from monocytes under simple GMP conditions and endowed with special immunostimulatory properties. Combined with low doses of intranodal injection of R, IFN-DC induced clinical response in cancer patients and promoted the induction of tumor specific T cells. All this implies the occurrence of an endogenous antitumor vaccination possibly resulting in clinical response. The findings suggest that IFN-DC are a good candidate for a selective clinical use in combination therapies in cancer patients Keywords: dendritic cells; follicular lymphoma (FL); immune system.
Delayed Expulsion of the Nematode Trichinella spiralisIn Mice Lacking the Mucosal Mast Cell–Specific Granule Chymase, Mouse Mast Cell Protease-1 (2000)

Expulsion of gastrointestinal nematodes is associated with pronounced mucosal mast cell (MMC) hyperplasia, differentiation, and activation, accompanied by the systemic release of MMC granule chymases (chymotrypsin-like serine proteases). The beta-chymase mouse mast cell protease-1 (mMCP-1) is expressed predominantly by intraepithelial MMCs, and levels in the bloodstream and intestinal lumen are maximal at the time of worm expulsion in parasitized mice. To address the in vivo functions of MMC-specific beta-chymases, we have generated transgenic mice that lack the mMCP-1 gene. They were backcrossed onto a congenic BALB/c background to investigate the response to nematode infection. The deletion of the mMCP-1 gene is associated with significantly delayed expulsion of Trichinella spiralis and increased deposition of muscle larvae in BALB/c mice despite the presence of normal and sometimes increased numbers of MMCs. Neither worm fecundity nor worm burdens were altered in Nippostrongylus-infected mMCP-1(-/)- BALB/c mice. These data demonstrate, for the first time, that the ablation of an MMC-derived effector molecule compromises the expulsion process.
Selenium Biotransformation by the Salt Marsh Cordgrass Spartina alterniflora:  Evidence for Dimethylselenoniopropionate Formation (1999)

Phytoremediation of toxic inorganic selenium compounds by accumulation, assimilation, and volatilization is an ideal way to rid contaminated soils and sediments of these molecules. In this context, salt marsh cordgrass (Spartina alterniflora) was investigated for its potential to produce dimethylselenoniopropionate (DMSeP), which as we have shown can serve as a precursor for the enzymatic volatilization of the relatively nontoxic gas, dimethylselenide (DMSe). Plants grown in sand culture, under varying saline conditions amended with the environmentally toxic form of selenium (selenate) were analyzed for organoselenonium compounds. DMSeP was positively identified in plant tissue and partially purified plant extracts by alkaline degradation to DMSe, 1H and 77Se NMR, and by enzymatic cleavage by DMSP lyase to DMSe (and acrylate). DMSeP levels were highest in plants grown in high salt (full-strength seawater) and high selenium. Preliminary evidence suggests that cordgrass may also produce Se-methyl selenomethionine, the putative precursor of DMSeP. This appears to be the first report for the biological assimilation of selenate into DMSeP by a plant species. These findings suggest a possible mechanism for the volatilization of selenium, as DMSe, analogous to that of dimethylsulfide (DMS) production by the salt tolerant cordgrass, Spartina alterniflora.
Large enhancement in photoluminescence of ZnO grown on strain relaxed nanoporous GaN template by PLD (2014)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. Tang, L. Deng, J. Huang, I. P. Seetoh, K. K. Ansah-Antwi, T. Venkatesan, and S. J. Chua, "Large enhancement in photoluminescence of ZnO grown on strain relaxed nanoporous GaN template by PLD," in CLEO: 2014, OSA Technical Digest (online) (Optica Publishing Group, 2014), paper JTh2A.58. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Quantitative Measurement of Fiber Orientation and Fracture, Void and Weld-Lines in Short Fiber Reinforced Thermoplastic Composites (1989)

Mechanical properties of short fiber reinforced thermoplastics depend on fiber length and fiber orientation distribution produced during melt flow processing. The incorporation of short fibers into thermoplastic polymer melts increases their viscosity and the presence of fibers, increasing in length, results also in an increasing viscosity. Breakage of glass fibers during flow through a rheometer, also a serious problem in melt processing of short fiber reinforced thermoplastics, is demonstrated and analyzed. Short fibers greatly improve the mechanical properties of polymers, but may severely weaken molded parts at their weld-line. A quantitative determination of the glass fiber ori entation distribution in the weld-line region was done by analyzing photomicrographs of polished sections. Fiber orientation parallel to the weld-line, normal to the flow direction, causes a dramatic loss of tensile strength. Another factor playing an important role in fiber-filled thermoplastics is the associated void content. Unexpectedly high void volume fractions were estimated from density results. Reflected light micrographs of polished extrudates confirmed the existence of voids and their increasing content with increasing shear rate, fiber loading, fiber length and temperature.
Epigenetic markers in human gliomas: prospects for therapeutic intervention (2008)

Gliomas represent the most common CNS cancers in adults. Prognosis for patients harboring malignant gliomas is particularly dismal and, despite current treatment strategies comprising surgery, radiotherapy and chemotherapy, the median survival time after diagnosis is still in the range of just 12 months. In recent years, there has been an increased effort to identify tumor biomarkers that can be used as diagnostic tools, or markers for predicting therapeutic response and prognosis. Investigation of genetic changes has identified several such markers that have shown some success in predicting the most effective therapy. In recent years, however, it has become apparent that the biology of many cancers of the CNS is determined not only by their genetic profile but also their epigenetic profile. Epigenetic biomarkers show great potential in effectively predicting patient prognosis and response to therapy. The eventual application of epigenetic profiling of tumors may help to indicate the most effective tailored therapy for individual patients.
Femtosecond time-bin pulse transfer and retrieval on photon-echo-based quantum memory using quantum dots (2023)

We have developed a quantum memory using quantum dots with a photon echo method for the storage of ultraweak femtosecond pulses. This quantum memory has a large bandwidth of 7.2 THz, which can be achieved due to the large inhomogeneous broadening of quantum dots. We successfully demonstrated femtosecond timebin pulse transfer to photon-echo-based quantum memory using quantum dots. We also succeeded in measuring the retrieved time-bin pulses as a photon echo from the quantum memory using a pulse-pumped frequency upconversion single-photon detector (UCSPD) with a temporal resolution of 429 fs. It is found that the retrieved time-bin photon echo pulse maintains the sub-picosecond time duration and the relative phase.
Loran Coverage Availability Simulation Tool (2008)

The Loran coverage availability simulation tool (LCAST) was initially created for the 2004 Federal Aviation Administration (FAA) Loran technical evaluation report. The tool incorporated the then current models, algorithms and figures of merit being developed for the evaluation report. Models for noise, noise mitigation, signal strength, additional secondary factor (ASF), and envelope to cycle difference (ECD) were important inputs into LCAST. Algorithms include the integrity equation and cycle determination. Other figures of merit include station availability and continuity derived from historical data. These features allowed the tool to make our best estimate of the NPA availability and continuity coverage as well as HEA performance. Since the report, the tool has evolved to incorporate the ability to test new models being developed by the evaluation. Newer noise processing, cycle determination algorithm and ASF variation models have been added. The tool has been modified to test performance changes for different infrastructure scenarios, station selection algorithms and many more. This paper describes the LCAST. It details the design of the tool. It covers the models, algorithms and assumptions that are incorporated into the tool. It also presents some recent scenarios analyzed using LCAST.
Organocatalysts for the Controlled “Immortal” Ring‐Opening Polymerization of Six‐Membered‐Ring Cyclic Carbonates: A Metal‐Free, Green Process (2010)

Six-membered cyclic carbonates, namely trimethylene carbonate (TMC), 3,3-dimethoxytrimethylene carbonate (DMTMC) and 3-benzyloxytrimethylene carbonate (BTMC), undergo controlled "immortal" ring-opening polymerization (iROP) under mild conditions (bulk, 60-150 °C), by using organocatalysts, including an amine [4-N,N-dimethylaminopyridine (DMAP)], a guanidine [1,5,7-triazabicyclo-[4.4.0]dec-5-ene (TBD)], or a phosphazene [2-tert-butylimino-2-diethylamino-1,3-dimethylperhydro-1,3,2-diazaphosphorine (BEMP)], in the presence of an alcohol [benzyl alcohol (BnOH), 1,3-propanediol (PPD), glycerol (GLY)] that acts as both a co-initiator and a chain-transfer agent. Remarkably, such organocatalysts remain highly active in the iROP of technical-grade, unpurified TMC. Under optimized conditions, as much as 100,000 equivalents of TMC were fully converted by as little as 10 ppm of BEMP with the simultaneous growth of as many as 200 polymer chains, allowing the preparation of high molar mass poly(trimethylene carbonate)s (up to 45,800 g mol(-1)). These catalyst systems enable among the highest activities (TOF=55,800 h(-1)) and productivities (TON=95,000) ever reported for the ROP of TMC.
Potential distribution in three-dimensional periodic myocardium. I. Solution with two-scale asymptotic analysis (1990)

The use of two-scale asymptotic analysis allows development of a model of the steady-state potential distribution in three-dimensional cardiac muscle preserving the underlying cellular network. The myocardium is modeled as a periodic structure consisting of cylindrical cells embedded in extracellular fluid and connected by longitudinal and side junctions. The method is applicable to cardiac muscle of arbitrary extent since the periodicity of the tissue is dealt with analytically, and thus numerical computations require no more resources than a continuous volume conductor problem. The asymptotic analysis approach reveals that the potential in a periodic myocardium consists of two components. The large-scale component provides the baseline for the total solution and can be determined from the anisotropic monodomain model associated with the original periodic problem. The method provides the formula for calculating the conductivity of the equivalent monodomain model on the basis of cell geometry and conductivity distribution in the cardiac tissue. The small-scale component reflects the periodicity of the underlying structure and oscillates with periods determined by the dimensions of cardiac cells. The magnitude of these oscillations depends upon the gradient of the large-scale component. During stimulation with extracellular electrodes, the small-scale component determines both the shape and the magnitude of the transmembrane potential, while the influence of the large-scale component is negligible. Hence, the small-scale component merits closer attention in pacing and defibrillation studies, especially since the model based on two-scale asymptotic analysis provides an effective means of its computation.
Transient Dynamics of Rotating Flexible Structures-ModeIing (2005)

A method for modeling transient dynamics of rotating flexible components is presented. Such dynamic models are of practical importance for both design and control of several engineering applications. Some examples include flexible links of high-speed mechanisms, manipulator arms, airplane propellers, and flexible appendages of spinning spacecraft. This method is based on a nonlinear formulation of the Lagrangian form in conjunction with the finite element techniques. A mixed set of generalized coordinates that accounts for inertia coupling between reference motions and local elastic deformations is employed. Component mode substitution techniques are used for generating a finite set of selected modal coordinates. The formulation accounts for component mode changes due to the effect of reference rotational speed of the elastic component. Base motion excitations, including impulsive forces, are taken into consideration. Numerical results are presented for a beam with its midpoint fixed to a rotating base which is subjected to sinusoidal pulse excitation.
Aspartic Acid Residue 124 in the Third Transmembrane Domain of the Somatostatin Receptor Subtype 3 Is Essential for Somatostatin-14 Binding (1995)

A highly conserved aspartic acid residue present in the third membrane-spanning region of adrenergic and muscarinic receptors is directly involved in ligand binding. The five cloned somatostatin receptor subtypes also contain this residue at the same relative position. To test whether Asp-124 of the rat somatostatin receptor subtype 3 (SSTR3) is responsible for the binding of somatostain-14 (SST-14), this amino acid residue was replaced by an asparagine or a glutamic acid by polymerase chain reaction (PCR)-mediated site-directed mutagenesis. Expression and binding activity of the wild-type and mutant receptor constructs were studied in COS and HEK cells by ligand binding, UV cross-linking, Western blot, and immunocytochemical analysis. The Asn or Glu mutations result in a significant loss of SST-14 binding, although the mutant receptors are correctly transferred to the cell surface, demonstrating that Asp-124 is directly involved in binding of SST-14.
A Task-Based Approach to Adaptive and Multimodality Imaging (2008)

Multimodality imaging is becoming increasingly important in medical imaging. Since the motivation for combining multiple imaging modalities is generally to improve diagnostic or prognostic accuracy, the benefits of multimodality imaging cannot be assessed through the display of example images. Instead, we must use objective, task-based measures of image quality to draw valid conclusions about system performance. In this paper, we will present a general framework for utilizing objective, task-based measures of image quality in assessing multimodality and adaptive imaging systems. We introduce a classification scheme for multimodality and adaptive imaging systems and provide a mathematical description of the imaging chain along with block diagrams to provide a visual illustration. We show that the task-based methodology developed for evaluating single-modality imaging can be applied, with minor modifications, to multimodality and adaptive imaging. We discuss strategies for practical implementing of task-based methods to assess and optimize multimodality imaging systems.
Effects of Prone Position and Positive End-Expiratory Pressure on Noninvasive Estimators of ICP: A Pilot Study (2016)

Noninvasive ICP estimation may be useful in patients at risk of developing intracranial hypertension who require prone positioning.
Thickness Estimation with Optical Coherence Tomography and Statistical Decision Theory (2013)

We implement a maximum-likelihood (ML) estimator to interpret Optical Coherence Tomography (OCT) data, based on a Fourier-Domain OCT and a two-interface tear film model. We use the root mean square error as a figure of merit to quantify the system performance to estimate the tear film thickness. The impact of detector integration time is quantified. For an OCT system with a 1 μm axial resolution, the ML estimator can estimate up to 40 nm with a 10% relative error.
Understanding ternary PEMFC nanocatalyst atomic arrangement during growth and annealing: a Molecular Dynamics approach (2017)

International audience
Supplementary Data from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer (2023)

Supplementary Data from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer
Lightning activity for the July 10, 1996, storm during the Stratosphere‐Troposphere Experiment: Radiation, Aerosol, and Ozone‐A (STERAO‐A) experiment (2001)

We have analyzed the lightning activity recorded during the Stratosphere‐Troposphere Experiment: Radiation, Aerosols, and Ozone (STERAO‐A) July 10, 1996, storm by the Office National d'Etudes et de Recherches Aérospatiales (ONERA) lightning VHF interferometer and the National Lightning Detection Network (NLDN) system. Both cloud‐to‐ground and total lightning activity were observed and studied for the entire 5‐hour life of the storm. The July 10 storm was a multicellular complex, which became unicellular during the last hour. It primarily exhibited high intracloud activity with only 1.5% cloud‐to‐ground flashes. The maximum value of the total flash rate was 58 flashes per minute. Cloud‐to‐ground (CG) flashes occurred after some intracloud flashes with a delay ranging from 3 to 26 min for the different cells of the storm. Our study revealed that measured flash duration ranged from 23 μs to 1.8 s. Flash duration, averaged over 5‐min periods, increased during the storm life. Short‐duration flashes (&lt;1 ms) did not occur until 30 min after the initial flash in the storm when the 50 dBZ vertical profile reached 8 km mean sea level (msl). The short‐duration flashes were recorded in cells where high reflectivity reached high altitude. Detailed analysis showed that the ONERA and NLDN reports were temporally and spatially consistent in the measurement of the cloud‐to‐ground flashes. Finally, we developed a new technique to distinguish negative CG flashes from other flashes by identifying the VHF signature of the negative downward stepped leader‐return stroke process in the flash VHF signal.
Radical Cation of a Trimethylenemethane with a Nondegenerate Ground State (2005)

Upon ionization by gamma-irradiation in frozen CFCl(3), or by X-irradiation in an Ar matrix, 2,2,3,3-tetramethylmethylenecyclopropane (MCP-Me4) readily undergoes ring opening to yield the radical cation of 1,1,2,2-tetramethyltrimethylenemethane (TMM-Me4). The hyperfine-coupling constants for TMM-Me4(.+) are (mT) -1.99 (2H), +0.53 (6H), and +0.19 (6H), and the singly occupied orbital closely resembles one of the two degenerate nonbonding pi-MOs (NBMOs) of trimethylenemethane (TMM). Due to the expected effect of the methyl substituents, this "symmetric" NBMO, psi(2+) (b(1)), is energetically favored relative to its "antisymmetric" counterpart, psi(2-) (a(2)), so that the ground state assumes a structure with (2)B(1) symmetry in the C(2v) point group. Calculations show that the ring opening in the primary radical cation MCP-Me4(.+) to yield TMM-Me4(.+) is spontaneous, whereas in the parent system (MCP(.+) --> TMM(.+) a low barrier does exist. In contrast to the previously investigated case of the radical cation of tetramethyleneethane, the "electromer" of TMM-Me4(.+), in which the unpaired electron occupies psi(2-), cannot be attained photochemically.