gebhart/patrepeval huggingface dataset:
Thiolations, 99mTc Labelings, and Animal In Vivo Biodistributions of Divalent Monoclonal Antibody Fragments (1996)

A number of divalent monoclonal antibody fragments have been derivatized with a bifunctional reagent containing a latent thiol group, and the conjugates were thiol-deprotected by exposure to aqueous hydroxylamine. This two-step procedure enabled convenient 99mTc labeling of thiolated MAb divalent fragments, using either performed 99mTc-glucoheptonate or [99mTc] pertechnetate and single-vial lyophilized formulations of the conjugate and tin. Nonspecific incorporation of radiolabel was negligible, if any, when using nonthiolated antibodies. In animal biodistributions, in nude mice bearing LS174T human colon carcinoma xenografts, the 99mTc-labeled MAb divalent fragments studied were found to result in a 3-fold reduction in the kidney uptake of radioactivity at 24 h, compared to a 99mTc-Fab, and also to lead to improvements in other tumor:nontumor ratios.
Statistical analysis of a subspace method for blind channel identification (2002)

This paper considers the problem of blind channel estimation of multi-channel FIR filters. This is a problem arising in, for example, mobile communication systems using digital signalling. By using the orthogonality property between the noise subspace and the channel matrix, it has been shown in earlier work that the channel matrix is identifiable up to a multiplicative constant. In this article, the asymptotic properties of a subspace method using this orthogonality property is presented. An asymptotically correct weighting matrix is derived, demonstrating an attainable lower theoretical bound using the subspace estimate.
Wide-tuning (65 nm) Semi-cooled (50°C) Operation of a Tunable Laser based on a Novel Widely Tunable Filter (2011)

A tunable laser based on a medium wavelength selectivity tunable filter named a lateral-grating-assisted lateral-co-directional-coupler was developed. A wide tuning range of over 65 nm with SMSR of over 35 dB was demonstrated at 50°C.
One-pot synthesis of 1,3-butanediol by 1,4-anhydroerythritol hydrogenolysis over a tungsten-modified platinum on silica catalyst (2020)

Chemical production of 1,3-butanediol from biomass-derived compounds was first reported by 1,4-anhydroerythritol hydrogenolysis over a Pt–WO<sub>x</sub>/SiO<sub>2</sub> catalyst.
The Use of Skeletal Muscle Near Infrared Spectroscopy and a Vascular Occlusion Test at High Altitude (2013)

Microcirculatory function, central to tissue regulation of oxygen flux, may be altered by the chronic hypoxemia experienced at high altitude. We hypothesized that at high altitude, adaptations within skeletal muscle would result in reduced oxygen consumption and reduced microcirculatory responsiveness, detectable by near infrared spectroscopy (NIRS) during a vascular occlusion test (VOT). The VOT comprised 3 min of noninvasive arterial occlusion; thenar eminence tissue oxygenation (Sto2) was measured by NIRS during the VOT at sea level, 4900 m and 5600 m (after 7 and 17 days at altitude, respectively) in 12 healthy volunteers. Data were derived from Sto2 time-curves using specifically designed computer software. Mean (±SD) resting Sto2 was reduced at 4900 m and 5600 m (69.3 (± 8.2)% (p=0.001) and 64.2 (± 6.1)% (p<0.001) respectively) when compared to sea level (84.4 (± 6.0)%. The rate of Sto2 recovery after vascular occlusion (Sto2 upslope) was significantly reduced at 4900 m (2.4 (± 0.4)%/sec) and 5600 m (2.4 (± 0.8)%/sec) compared to sea level (3.7 (± 1.3)%/sec) (p=0.021 and p=0.032, respectively). There was no change from sea level in the rate of desaturation during occlusion (Sto2 downslope) at either altitude. The findings suggest that in resting skeletal muscle of acclimatizing healthy volunteers at high altitude, microvascular reactivity is reduced (Sto2 upslope after a short period of ischemia) but that oxygen consumption remains unchanged (Sto2 downslope).
Eukaryotes (2015)

The previous chapter described the procedures developed for studying the systems biology of metabolism in bacteria. In parallel, similar efforts have been undertaken for unicellular eukaryotes. The main challenge that arises is the presence of multiple intracellular compartments (organelles), that, in principle, can be dealt with during a reconstruction process, but in practice is difficult due to the scarcity of data of transporters that move metabolites in and out of organelles. The yeast Saccharomyces cerevisiae was the first eukaryote to undergo a genome-scale metabolic reconstruction in 2003. This achievement was followed by the reconstruction of other fungal species. A detailed reconstruction of photosynthetic green algae appeared in 2011. Reconstruction of metabolic networks in multicellular organisms have also appeared. The first version of the genome-scale human metabolic map was published in 2007, followed by parallel reconstruction efforts for other mammals. This global human map has since been customized for various cell and tissue types. Interacting models of multiple tissue types have appeared that, in principle, should be able to study systemic metabolism in humans. Therefore, it appears that the network reconstruction procedures that have developed for E. coli will extend to multicellular organisms; however, no model of metabolism in the elephant has yet appeared.
Chimie des processus biologiques (2015)

Enseignement Cours : Du CO2 aux carburants, un renversement salutaire Le développement des nouvelles technologies de l’énergie pour l’exploitation des énergies renouvelables, comme l’énergie solaire ou l’énergie éolienne diluées et intermittentes, nécessite celui des procédés de stockage de l’énergie. Une façon de stocker ces énergies est de les transformer en énergie chimique. L’exemple le plus classique est l’électrolyse de l’eau en hydrogène, ce dernier pouvant être en effet ensuite utilis...
Geometric methods for wavelet-based image compression (2003)

Natural images can be viewed as combinations of smooth regions, textures, and geometry. Wavelet-based image coders, such as the space-frequency quantization (SFQ) algorithm, provide reasonably efficient representations for smooth regions (using zerotrees, for example) and textures (using scalar quantization) but do not properly exploit the geometric regularity imposed on wavelet coefficients by features such as edges. In this paper, we develop a representation for wavelet coefficients in geometric regions based on the wedgelet dictionary, a collection of geometric atoms that construct piecewise-linear approximations to contours. Our <i>wedgeprint representation</i> implicitly models the coherency among geometric wavelet coefficients. We demonstrate that a simple compression algorithm combining wedgeprints with zerotrees and scalar quantization can achieve near-optimal rate-distortion performance <i>D(R) </i>~ (log <i>R</i>)<sup>2</sup>/<i>R</i><sup>2</sup> for the class of piecewise-smooth images containing smooth <i>C</i><sup>2</sup> regions separated by smooth <i>C</i><sup>2</sup> discontinuities. Finally, we extend this simple algorithm and propose a complete compression framework for natural images using a rate-distortion criterion to balance the three representations. Our Wedgelet-SFQ (WSFQ) coder outperforms SFQ in terms of visual quality and mean-square error.
Protein Nanoparticle Templates: Constrained Synthesis and Organization of Catalytically Active Metal Nanoparticles by Self‐Assembled Protein Templates (Adv. Mater. 34/2009) (2009)

Novel geometrical architectures of hybrid nanoparticle/protein complexes can be generated by chemically synthesizing monodisperse metal nanoparticles in situ in the presence of a stable, stress-related protein, report Silke Behrens, Oded Shoseyov, and co-workers on p. 3515. The particles are catalytically active and can reduce 4-nitrophenol, and are potentially useful as future biofunctional nanoparticle labels for catalytic signal amplification in optical assays.
Characterization of Drosophila embryos immobilized by fluidic microassembly (2004)

A technique for positioning and immobilization of Drosophila embryos in 2-D arrays for use in high throughput microinjection experiments has been characterized. The method is based on fluidic microassembly and immobilization yield, the number of misplaced embryos, and adhesion force of the embryos have been measured for samples with two different pad geomtries. For samples with 250 /spl mu/m/spl times/400 /spl mu/m sized pads an immobilization yield of 85% was achieved. The adhesion force of the embryos was estimated at 36 /spl mu/N/spl plusmn/22 /spl mu/N. A substantial amount of clustering was, however, observed. By reducing the pad size to 200 /spl mu/m/spl times/200 /spl mu/m and changing the pad pitch the number of misplaced embryos was reduced to less then 5%. The immobilization yield was, however, lower for these samples. The adhesion force of embryos immobilized at the smaller pads was estimated at 14 /spl mu/N/spl plusmn/5.5 /spl mu/N.
RLPlace: Using Reinforcement Learning and Smart Perturbations to Optimize FPGA Placement (2021)

Simulated annealing (SA) is one of the most common FPGA placement techniques, and is used both as a standalone algorithm and to improve an initial analytical placement. While SA-based placers can achieve high-quality results, they suffer from long runtimes. In this article, we introduce <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RLPlace</i> , a novel SA-based FPGA placer that utilizes both reinforcement learning (RL) and targeted perturbations (directed moves). The proposed moves target both wirelength and timing optimization and explore the solution space more efficiently than traditional random moves while preventing oscillation in the Quality of Results (QoR). RL techniques are used to dynamically select the most effective move types as optimization progresses. The experimental results show that <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RLPlace</i> outperforms the widely used VTR 8 placer across all runtime/quality tradeoff points, achieving better QoR placement solutions in less runtime. On average, across the Titan23 suite of large FPGA benchmarks, RLPlace can reduce CPU time by <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2.5\times $ </tex-math></inline-formula> with result quality comparable to VTR 8, or improve wirelength by 8% (at a high CPU time budget) −26% (at a low CPU time budget) versus VTR 8.0 given the same CPU time.
Hexakis(trimethylphosphine)molybdenum chemistry: dinitrogen, ethylene, butadiene, η-cyclopentadienyl, and related derivatives (1985)

Co-condensation of molybdenum atoms with trimethylphosphine gives octahedral [ Mo(PMe3)6](1) whose crystal structure has been determined. Treatment of (1) with dinitrogen, ethylene, carbon monoxide, iodine, or butadiene gives [Mo(N2)(PMe3)5], trans-[Mo(η-C2H4)2(PMe3)4]fac-[Mo(CO)3(PMe3)3], trans-[MoI2(PMe3)4], and cis-[Mo(η-C4H6)2(PMe3)2] respectively. Protonation of cis-[Mo(η-C4H6)2(PMe3)2] with tetrafluoroboric acid forms the compound cis-[[graphic omitted]CH2CHCHCH2)(η-C4H6)(PMe3)2]BF4. The presence of the Mo–H–C bond is shown by low-temperature n.m.r. spectra, and variable-temperature n.m.r. shows that the agostic hydrogen can scramble between the four terminal carbons of the two C4 ligands. The rate constants and activation parameters for the hydrogen-scrambling process have been determined and a mechanism is proposed. Reaction of cis-[Mo(η-C4H6)2(PMe3)2] with trifluoroacetic acid gives [Mo(η-MeC3H4)(η-C4H6)(PMe3)2(O2CCF3)]. Treatment of [Mo(PMe3)6] with cyclopentadiene forms [MoH(η-C5H5)(PMe3)3] which reacts with aqueous tetrafluoroboric acid giving [MoH2(η-C5H5)(PMe3)3]BF4 and [Mo(η-C5H5)(PMe3)2O]BF4. Reaction of [MoH(η-C5H5)(PMe3)3] with methyl iodide gives [MoH(η-C5H5)(PMe3)2I2].
Correction: Analysis of FOXP3+Regulatory T Cells That Display Apparent Viral Antigen Specificity during Chronic Hepatitis C Virus Infection (2012)

We reported previously that a proportion of natural CD25 + cells isolated from the PBMC of HCV patients can further upregulate CD25 expression in response to HCV peptide stimulation in vitro, and proposed that virus-specific regulatory T cells (Treg) were primed and expanded during the disease. Here we describe epigenetic analysis of the FOXP3 locus in HCVresponsive natural CD25 + cells and show that these cells are not activated conventional T cells expressing FOXP3, but hardwired Treg with a stable FOXP3 phenotype and function. Of ,46,000 genes analyzed in genome wide transcription profiling, about 1% were differentially expressed between HCV-responsive Treg, HCV-non-responsive natural CD25 + cells and conventional T cells. Expression profiles, including cell death, activation, proliferation and transcriptional regulation, suggest a survival advantage of HCV-responsive Treg over the other cell populations. Since no Treg-specific activation marker is known, we tested 97 NS3-derived peptides for their ability to elicit CD25 response (assuming it is a surrogate marker), accompanied by high resolution HLA typing of the patients. Some reactive peptides overlapped with previously described effector T cell epitopes. Our data offers new insights into HCV immune evasion and tolerance, and highlights the non-self specific nature of Treg during infection.
Dynamic Disorder and Stepwise Deactivation in a Chymotrypsin Catalyzed Hydrolysis Reaction (2007)

In situ observation of the catalytic activity of individual α-chymotrypsin enzymes reveals a novel pathway for spontaneous deactivation. Rather than deactivating abruptly in a one-step process, the enzyme seems to struggle for life; the activity decreases stepwise with intermittent inactive periods before deactivating irreversibly. During the active periods, dynamic disorder and memory effects are observed, originating from conformational fluctuations within the enzyme's structure.
Silicon Microfabricated Preconcentrator Design and Characterization (2020)

Abstract MEMS fabrication technology has been applied to build micro-GC systems for portable analysis and detection of volatile organic compounds for environmental monitoring, medical diagnostics and food safety and security (1). Pioneering work at Sandia National Laboratories developed - these miniature systems (2). Novel designs for pre-concentrators have been developed to provide efficient sample injection into these systems (3). We have integrated a 6m length micro-GC column with an ion trap mass spectrometer (4). To inject the sample into the column, our initial method was to use a syringe injection into a heated septum with Agilent 6890. However, for automated operation and method of sampling, pre-concentration of the volatile organic compounds is required, followed by rapid heating, for sample injection for analysis. A microfabricated pre-concentrator can fulfill this function by providing a high surface area in a compact platform with reduced thermal mass, compared to commercial desorption tubes. The design has an integrated platinum heater and was fabricated using standard photolithography, deep reactive ion etching and wafer bonding. To evaluate the performance, the pre-concentrator is mounted inside a commercial Agilent 6890 GC system. Liquid injections 0.02uL, using a syringe, with a 100:1 split, at a helium flow rate of 0.005 ml/min. The flow rate was increased during the desorption cycle, and the preconcentrator was heated by electrical current of providing approx. 5W to enable rapid heating to 180°C. This miniature pre-concentrator provides a small thermal mass design and was capable of fast desorption of several analytes with detection by FID. References [1] M. Akbar, M. Restaino, M. Agah, “Chip-scale gas chromatography: From injection through detection,” Microsystems Nanoengineering, Vol. 1, pg. 15938 (2015). [2] in J. J. Whiting, E. B. Myers, R. P. Manginell, M. W. Moorman, K. Pfeifer, J. M. Anderson, C. S. Fix, C. Washburn, A. Staton, D. Porter, D. Graf, D. R. Wheeler, J. Richards, K. E. Achuythan, M. Roukes, R. J. Simonson, "μChem Lab: twenty years of developing CBRNE detection systems with low false “μChemLab: twenty years of developing CBRNE detection systems with low false alarm rates”Proceedings of SPIE, Vo.l. 11010, Chemical, Biological, Radiological, Nuclear, and Explosives (CBRNE) Sensing XX, 1101012 (17 May 2019); doi: 10.1117/12.2518778. [3] Tian, Wei-Chang, H. K. L. Chan, Chia-Jung Lu, S. W. Pang, E. T. Zellers, “ Multiple-stage microfabricated preconcentrator-focuser for micro gas chromatography system,” J. Microelectromachanical Systems, Vol. 14, No. 3, pp 498-507 (2005). [4] Tzu-Hsuan Chang, D. Struk, M. Navaei, V. M. Doroshenko; V. Laiko; E. Moskovets; K. Novoselov, J. D. Dimandja, Peter J. Hesketh, “Separation of Volatile Organic Compounds using of MEMS-GC Integrated Heater for Ion Trap Mass Spectrometer,” Sensors and Actuators B, Vol. 307, pg. 127588 (2020).
An information centric networking approach to context-aware dissemination of services and information (2014)

Dissemination of information and advertising services to targeted nodes are important aspects in the performance of future large scale network systems. Context-awareness is a key ingredient in any ubiquitous and pervasive system and provides intelligence to the system, allowing computing devices to make appropriate and timely decisions on behalf of users. In this thesis, first the problem of access network selection based on the context of users to support intelligent services and applications that demand a certain quality of service level is addressed. As the contextual information are collected from various sources with uncertain quality, a decision methodology for access network selection that takes the quality of provided information into account is proposed and it is shown that it yields a more confident decision when the available information lack certainty. In addition, collected data that are uncertain and fuzzy in nature pose another problem for selecting services. Therefore, a service selection approach to leverage the context similarity among the users, services and applications to solve this problem is proposed. Information Centric Networking (ICN) is a shift in networking paradigm that is based on named data as the main token of networking instead of Internet Protocol (IP) addresses. Based on ICN, the problem of information dissemination is tackled by proposing the new notion of information topology and using the information about the spectral characteristics of the topology for an enhanced network coding scheme. The success of the proposed approach is demonstrated on the basis of achieving a better reliability and lowering the processing cost for the entire system. Furthermore, the feasibility of ICN for vehicular clouds is investigated and a method based on dimensionality reduction to reduce processing overhead is suggested. The proposed method enhances the control plane performance in support of real time applications in the presence of intermittent connectivity.
Experimental and computational analyses of electroabsorption in polar InGaN/GaN quantum zigzag heterostructures (2008)

Traditional quantum confined Stark effect is well known to lead to strong electroabsorption in multiple quantum well (MQW) structures, yielding only red-shift of the absorption edge with the externally applied electric field, independent of the direction of the applied field [1]. However, a little is known the electroabsorption behavior in IIInitride quantum structures grown on c-plane of their wurtzite crystal structure, which is substantially different than the electroabsorption of conventional quantum structures. Such III-N heterostructures exhibit strong polarization fields and discontinuity of such polarization fields at their heterointerfaces causes stimulation of large electrostatic fields in alternating directions for their wells and barriers [2]. Consequently, their energy band diagrams form a zigzag potential profile in conduction and valence bands, instead of those with square profiles. A natural and suitable approach for understanding these polarization fields and also developing insight to design related devices (e.g., electroabsorption modulators) is to study electroabsorption behavior as a function of the polarization field in such polar structures [3, 4]. To this end, we present a comparative, computational and experimental study of electroabsorption in our different designs of c-plane grown polar InGaN/GaN quantum structures with varying levels of polarization.
LMO2 Protein Expression Predicts Survival in Patients with Diffuse Large B-Cell Lymphoma in the Pre- and Post-Rituximab Treatment Eras. (2007)

Abstract Finding new prognostic markers in diffuse large B-cell lymphoma (DLBCL) is of importance because the disease is heterogeneous and current therapies fail to cure many affected patients. Previously, we showed that the expression of LMO2 mRNA was the strongest single predictor of superior outcome in patients with DLBCL in a multivariate model based on the expression of six genes (Lossos et al, NEJM 2004). Subsequently, we generated an anti-LMO2 monoclonal antibody and showed that LMO2 protein is expressed in a subset of germinal center-derived B-cell lymphomas including DLBCL, and that its expression predicted a superior outcome in DLBCL patients who were treated with anthracycline-based regimens (Natkunam et al, Blood 2006 &amp; 2007). We have now expanded this cohort to include DLBCL patients treated at five international medical centers and have also tested the prognostic impact of LMO2 in patients treated with the addition of rituximab to CHOP (R-CHOP), a regimen which was recently demonstrated to improve the outcome of DLBCL patients (Coiffier et al, NEJM 2002; Sehn et al, JCO 2005; Habermann et al, JCO 2006; Pfreundschuh et al, Lancet Oncol 2006). Immunohistochemistry for LMO2 was performed on tissue microarrays containing cores of diagnostic biopsy specimens from patients with de novo DLBCL treated with anthracycline-based chemotherapy (280 patients) or with R-CHOP (80 patients) who had been followed for clinical outcome. The results show that in the pre-rituximab group staining for LMO2 was strongly correlated with overall survival (OS) and progression-free survival (PFS) (p=0.0018 and p=0.00071, respectively). Similarly, in the post-rituximab group LMO2 protein expression was associated with a significantly longer OS (p=0.0048) and PFS (p=0.0087). In multivariate Cox regression analyses, the expression of the LMO2 protein was found to be independent of the clinical IPI and most strikingly, was more robust than the conventional IPI in predicting OS and PFS, particularly in the post-rituximab DLBCL group of patients (OS p = 0.03, PFS p = 0.01). The capacity of LMO2 protein to identify DLBCL patients with improved outcome in an IPI-independent manner indicates its potential role in risk stratification of this disease. We conclude that the prognostic value of LMO2 protein expression remains significant in the era of R-CHOP treatment and recommend its assessment in all newly diagnosed DLBCL patients to confirm these results and eventually to optimize patient management.