gebhart/patrepeval huggingface dataset:
A FACTOR VIII BINDING DOMAIN RESIDES WITHIN THE AMINO-TERMINAL 272 AMINO ACID RESIDUES OF VON WILLEBRAND FACTOR (1987)

We have identified a Factor VIII (FVIII) binding domain residing within the amino-terminal 272 amino acid residues of the mature von Willebrand Factor (vWF) subunit. Two dimensional crossed immunoelectrophoresis showed direct binding of purified human FVIII to purified human vWF. After proteolytic digestion of vWF with Staphylococcus aureus V8 protease, FVIII binding was seen only with the amino-terminal SP fragment III and not with the carboxy-terminal SP fragment II. A monoclonal anti-vWF antibody (C3) partially blocked FVIII binding to vWF and SP fragment III. FVIII also bound to vWF which had been adsorbed to polystyrene beads. This binding was inhibited in a dose dependent manner by whole vWF, SP fragment III, and by monoclonal antibody C3. Binding could not be inhibited by SP fragment I, which contains the middle portion of the vWF molecule, or by reduced and alkylated whole vWF. SP fragment II caused only minor inhibition. Trypsin cleavage of SP fragment III produced a 35-kDa fragment containing the amino-terminal 272 amino acid residues of vWF. This fragment reacted with monoclonal antibody C3 and inhibited the binding of FVIII to vWF in a dose dependent manner. The other major fragment obtained from this digestion was a two chain hetero-dimer composed of amino acid residues 273-511 and 674-728. This fragment did not inhibit FVIII binding. These studies demonstrate that a major FVIII binding site resides within the first 272 amino acid residues of vWF.
Development of solid state proton conductor gas sensor operative at ordinary temperature. (1986)

常温でも比較的高いイオン導電性を有するプロトン導電体(とくにアンチモン酸)を用いることにより, 空気中の微量のH2やCOを常温において検知できる新しいタイプのガスセンサーを試作した。本素子では, 応答信号として素子の短絡電流値を取りだすが, その応答性は良好で, たとえば常温において2000ppmH2(空気中)に対する90%応答時間は約10秒であった。また, その電流値(感度)はH2濃度にほぼ比例した。本素子の作動機構については,検知極上でH2の酸化反応(H2→2H++2e)により生成したH+がプロトン導電体中を移動して対極上でO2還元反応(1/2O2+2H++ 2e→H2O)により消費され, そのとき移動したH+量に見合った短絡電流が取りだせると考えられる。この機構は, 両反応に対する実際の分極曲線の測定, および開回路, 閉回路状態での各電極電位の挙動の観察により実験的に確かめられた。さらに本素子は, 多孔性のプロトン導電体膜(厚さ0.2mm)を用いることにより, 対極に空気を流す必要のない簡易で小型の素子に改良できた。この改良型素子のH2に対する応答特性は改良前のものとほぼ向様であり, また空気中の100ppm程度の微量COの検知も可能であることがわかった。
CNT EUV pellicle tunability and performance in a scanner-like environment (2021)

Research on carbon nanotube (CNT) films for the EUV pellicle application was initiated at imec in 2015 triggered by the remarkable optical, mechanical, and thermal properties of the CNT material. Today the advancement of the CNT material synthesis together with matured methods to fabricate thin CNT membranes make free-standing CNT films a very promising EUV pellicle candidate for high volume EUV lithography. Balancing the CNT material properties for the optimal pellicle performance in EUV scanners remains the ongoing research focus. Depending on the density and morphology of the CNTs within the film and individual CNT parameters, like number of walls, bundle size, metal catalyst content, purity etc., the optical and thermal properties of the CNT pellicle can be tuned. It is critical for the pellicle to be stable in the EUV lithography scanner environment which includes hydrogen plasma and heat loads associated with high powers beyond 250 W. Different types of CNTs, i.e. single-, double-, multi-walled CNTs and their combinations, are explored as building blocks of an optimized pellicle membrane. Optical properties of different pellicles and their ability to withstand high EUV powers in the hydrogen-based environment were tested. Transmission, spectroscopic and chemical composition mapping of the exposed free-standing CNT films are used to study the material changes that occur in the scanner-like environment. A solution is needed to extend the CNT pellicle lifetime and coating is discussed as a potential approach to protect the CNT material from hydrogen plasma damage.
A Toxic RNA Catalyzes the In Cellulo Synthesis of Its Own Inhibitor (2014)

Potent modulators of RNA function can be assembled in cellulo by using the cell as a reaction vessel and a disease-causing RNA as a catalyst. When designing small molecule effectors of function, a balance between permeability and potency must be struck. Low molecular weight compounds are more permeable whereas higher molecular weight compounds are more potent. The advantages of both types of compounds could be synergized if low molecular weight molecules could be transformed into potent, multivalent ligands by a reaction that is catalyzed by binding to a target in cells expressing a genetic defect. It was shown that this approach is indeed viable in cellulo. Small molecule modules with precisely positioned alkyne and azide moieties bind adjacent internal loops in r(CCUG)(exp), the causative agent of myotonic dystrophy type 2 (DM2), and are transformed into oligomeric, potent inhibitors of DM2 RNA dysfunction by a Huisgen 1,3-dipolar cycloaddition reaction, a variant of click chemistry.
Nickel recovery from spent nickel catalyst (2005)

A process for nickel recovery from a spent catalyst of definite composition has been developed using the hydro-metallurgical route. The processing steps includes direct sulphuric acid leaching followed by separation of iron as well as silica and other impurities. For a 152 microm particle size catalyst, extraction of about 98% nickel was achieved at 363 K in 2 h using a sulphuric acid concentration (v/v) of 8% and a pulp density of 10%. The dissolution of nickel followed diffusion-controlled leaching kinetics. Increase in temperature and sulphuric acid concentration resulted in increase in the nickel recovery. The activation energy for nickel dissolution was calculated to be 62.8 kJ mol(-1). Finally, nickel was recovered as value-added products such as sulphide and oxalate with overall recovery of 90 and 88% of nickel, respectively.
Epileptic seizure prediction using hybrid feature selection over multiple intracranial EEG electrode contacts: a report of four patients (2003)

Epileptic seizure prediction has steadily evolved from its conception in the 1970s, to proof-of-principle experiments in the late 1980s and 1990s, to its current place as an area of vigorous, clinical and laboratory investigation. As a step toward practical implementation of this technology in humans, we present an individualized method for selecting electroencephalogram (EEG) features and electrode locations for seizure prediction focused on precursors that occur within ten minutes of electrographic seizure onset. This method applies an intelligent genetic search process to EEG signals simultaneously collected from multiple intracranial electrode contacts and multiple quantitative features derived from these signals. The algorithm is trained on a series of baseline and preseizure records and then validated on other, previously unseen data using split sample validation techniques. The performance of this method is demonstrated on multiday recordings obtained from four patients implanted with intracranial electrodes during evaluation for epilepsy surgery. An average probability of prediction (or block sensitivity) of 62.5% was achieved in this group, with an average block false positive (FP) rate of 0.2775 FP predictions/h, corresponding to 90.47% specificity. These findings are presented as an example of a method for training, testing and validating a seizure prediction system on data from individual patients. Given the heterogeneity of epilepsy, it is likely that methods of this type will be required to configure intelligent devices for treating epilepsy to each individual's neurophysiology prior to clinical deployment.
Protein Engineering of Interferon Alphas (2005)

Interferon (IFN)-alphas constitute a family of proteins exhibiting high degree of homology in primary, secondary, and tertiary structure and display a high level of species specificity in their biological properties. However, small structural differences in these proteins may be responsible for a significant variety of biological actions. Understanding the structure and function of human IFN-alpha is very important. Recombinant techniques are important tools for the production and modification of IFN proteins. The first IFN hybrid, IFN-alpha1/alpha2 was constructed using recombinant technology in 1981. Subsequently, a number of IFN hybrids and mutants have been constructed, expressed and characterized. These hybrids and mutants have resulted in novel IFNs that either combine different biological properties from the parental proteins or have significantly different biological activity. Therefore, IFN hybrids and mutants have provided a powerful tool for studying the structure and function of these molecules. Also, these engineered IFNs may have important new therapeutic applications and may provide greater sights into understanding of the clinical activities of these molecules.
Scalability of reliable group communication using overlays (2004)

This study provides some new insights into the scalability of reliable group communication mechanisms using overlays. These mechanisms use individual TCP connections for packet transfers between end-systems. End-systems store incoming packets and forward them to downstream nodes using different unicast TCP connections. In this paper we assume that buffers in end-systems are large enough for the transfers. It is shown that the throughput of the reliable overlay group communication scales in the sense that for all multicast tree sizes and topologies, the group throughput is strictly positive under natural conditions. This is in contrast with the IP supported multicast paradigm where reliable protocols have vanishing throughput when the group size tends to infinity. The scalability of packet delay and buffer occupancy is then investigated. In the absence of additional control, the occupancy of the buffer and the latency in the end-systems explodes with time. It is then shown that proactive rate throttle mechanism implemented at the source leads to finite packet latency and buffer occupancy in any end-system of the network provided certain moment conditions are satisfied by cross traffic in the routers.
Bit-serial architecture for optical computing (1992)

The design of a complete, stored-program digital optical computer is described. A fully functional, proof-of-principle prototype can be achieved by using LiNbO(3) directional couplers as logic elements and fiber-optic delay lines as memory elements. The key design issues are computation in a realm where propagation delays are much greater than logic delays and implementation of circuits without fip-flops. The techniques developed to address these issues yield architectures that do not change as their clocking speed is scaled upward and the size is scaled downward proportionally; these are called speed-scalable architectures. Signal amplitude restoration and resynchronization are accomplished by the novel technique of switching in a fresh copy of the system clock. Device characteristics that are important to the proof-of-principle demonstration are discussed, including the special properties and limitations that are important when designing with them. Design principles are exemplified by the design of an n-bit counter. Following this, the design for a stored-program bit-serial computer is described. We estimate that the described prototype architecture can be operated in the 100-MHz region with off-the-shelf components, and in the O. 1-1-THz region with foreseeable future components.
Stereoselective Synthesis of HIV-1 Protease Inhibitor, DMP 323 (1996)

DMP 323, a potent HIV-1 protease inhibitor, has been synthesized by an efficient stereoselective process, amenable to large scale preparations. The core C(2) symmetric diol was synthesized by a stereoselective pinacol coupling of CBZ protected D-phenylalanine. Judicious selection of protecting groups allowed cyclic urea formation under mild conditions, enhanced the ease of bis-alkylation, and led to intermediates which were easily purified without chromatography. Additionally, a one-pot, high yield process was developed to prepare the alkylating agent, 4-[(triphenylmethoxy)methyl]benzyl chloride from 1,4-benzenedimethanol.
Exploiting Capabilities of Many Core Platforms in Reservoir Simulation (2011)

Abstract The forthcoming generation of many-core architectures suggests a strong paradigm shift in the way algorithms have been designed to achieve maximum performance in reservoir simulations. In this work, we propose a novel poly-algorithmic solver approach to develop hybrid CPU multicore and GPU computations for solving large sparse linear systems arising in realistic black oil and compositional flow scenarios. The GPU implementation exploits data parallelism through the simultaneous deployment of thousands of threads while reducing memory overhead per floating point operations involved in most BLAS kernels and in a suite of preconditioner options such as BILU(k), BILUT and multicoloring SSOR. On the other hand, multicore CPU computations are used to exploit functional parallelism to perform system partitioning and reordering, algebraic multigrid preconditioning, sparsification and model reduction operations in order to accelerate and reduce the number of GCR iterations. The efficient orchestration of these operations relies on carefully designing the heuristics depending on the timestep evolution, degree of nonlinearity and current system properties. Hence, we also propose several criteria to automatically decide the type of solver configuration to be employed at every time step of the simulation. To illustrate the potentials of the proposed solver approach, we perform numerical computations on state-of-the-art multicore CPU and GPU platforms. Computational experiments on a wide range of highly complex reservoir cases reveal that the solver approach yields significant speedups with respect to conventional CPU multicore solver implementations. The solver performance gain is of the order of 3x which impacts in about 2x the overall compositional simulation turnaround time. These results demonstrate the potential that many core solvers have to offer in improving the performance of near future reservoir simulations.
Retinal oxygen saturation evaluation by multi-spectral fundus imaging (2007)

Purpose: To develop a multi-spectral method to measure oxygen saturation of the retina in the human eye. Methods: Five Cynomolgus monkeys with normal eyes were anesthetized with intramuscular ketamine/xylazine and intravenous pentobarbital. Multi-spectral fundus imaging was performed in five monkeys with a commercial fundus camera equipped with a liquid crystal tuned filter in the illumination light path and a 16-bit digital camera. Recording parameters were controlled with software written specifically for the application. Seven images at successively longer oxygen-sensing wavelengths were recorded within 4 seconds. Individual images for each wavelength were captured in less than 100 msec of flash illumination. Slightly misaligned images of separate wavelengths due to slight eye motion were registered and corrected by translational and rotational image registration prior to analysis. Numerical values of relative oxygen saturation of retinal arteries and veins and the underlying tissue in between the artery/vein pairs were evaluated by an algorithm previously described, but which is now corrected for blood volume from averaged pixels (n > 1000). Color saturation maps were constructed by applying the algorithm at each image pixel using a Matlab script. Results: Both the numerical values of relative oxygen saturation and the saturation maps correspond to the physiological condition, that is, in a normal retina, the artery is more saturated than the tissue and the tissue is more saturated than the vein. With the multi-spectral fundus camera and proper registration of the multi-wavelength images, we were able to determine oxygen saturation in the primate retinal structures on a tolerable time scale which is applicable to human subjects. Conclusions: Seven wavelength multi-spectral imagery can be used to measure oxygen saturation in retinal artery, vein, and tissue (microcirculation). This technique is safe and can be used to monitor oxygen uptake in humans. This work is original and is not under consideration for publication elsewhere.
Gr-1+ CD11b+ Myeloid-derived Suppressor Cells Suppress Inflammation and Promote Insulin Sensitivity in Obesity (2011)

Activation of immune cells, including macrophages and CD8(+) T cells, contributes significantly to the advancement of obesity and its associated medical complications, such as atherosclerosis, insulin resistance, and type 2 diabetes. However, how the activation of these immune cells is regulated in vivo remains largely unexplored. Here we show that a group of immature myeloid cells with cell surface markers of Gr-1(+) CD11b(+) are highly enriched in peripheral tissues (i.e. liver and adipose tissues) during obesity. Down-regulation of these cells in obese animals significantly increases inflammation and impairs insulin sensitivity and glucose tolerance, whereas elevation of these cells via adoptive transfer has the opposite effects. Mechanistically, we show that under obese conditions, the Gr-1(+) cells suppress proliferation and induce apoptosis of CD8(+) T cells and are capable of skewing differentiation of macrophages into insulin-sensitizing, alternatively activated M2 macrophages. Taken together, our study demonstrates that immature myeloid cells provide a checks-and-balances platform to counter proinflammatory immune cells in the liver and adipose tissue during obesity to prevent overt immune responses.
Serum glial fibrillary acidic protein as a biomarker for intracerebral haemorrhage in patients with acute stroke (2005)

Serum GFAP can reliably detect ICH in the acute phase of stroke. Further evaluation of the usefulness of GFAP as an early diagnostic marker of ICH is now required, with the aim of optimising cause specific emergency management.
High-Frequency Magnetic Properties of Ca-Substituted Co<sub>2</sub>Z and Co<sub>2</sub>W Barium Hexaferrite Composites (2018)

A series of Ca-substituted Z-type hexaferrites having nominal composition Ba <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3-x</sub> Ca <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">24</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">41</sub> (x = 0-1.5) was studied for their high-frequency magnetic properties, including measurement of the permeability spectra and magnetic loss over a frequency range of 0.1-10 GHz. Analyses of crystal composition and microstructure reveal that hexaferrite composites consist of the Z-type phase and increasing amounts of the W-type phase were obtained as the Ca content was increased. Correspondingly, the permeability μ' displays a near linear decrease with x varying from 0 to 1.5, from ~8 to ~4.1 at 0.1 GHz. The relationship between permeability and variations in intrinsic magnetic parameters, i.e., saturation magnetization M <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> and coercivity H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> , follows the Globus model. Compared with the undoped Z-type hexaferrite, the sample with x = 0.2 has lower magnetic loss over a broad frequency range, and higher levels of Ca substitutions (x ≥ 1) lead to low magnetic loss at high frequencies. The dual-phase composite of Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Z and Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> W in proper ratio is an effective technique to improve the homogeneity of grain and microstructure, and thus reduce the high-frequency magnetic loss of the sintering hexaferrites.
Phase-sensitive optical coherence elastography at 15 million A-Lines per second (2015)

Shear-wave imaging optical coherence elastography (SWI-OCE) is an emerging method for 3D quantitative assessment of tissue local mechanical properties based on imaging and analysis of elastic wave propagation. Current methods for SWI-OCE involve multiple temporal optical coherence tomography scans (M-mode) at different spatial locations across tissue surface (B- and C-modes). This requires an excitation for each measurement position leading to clinically unacceptable long acquisition times up to tens of minutes. In this Letter, we demonstrate, for the first time, noncontact true kilohertz frame-rate OCE by combining a Fourier domain mode-locked swept source laser with an A-scan rate of ∼1.5 MHz and a focused air-pulse as an elastic wave excitation source. The propagation of the elastic wave in the sample was imaged at a frame rate of ∼7.3 kHz. Therefore, to quantify the elastic wave propagation velocity in a single direction, only a single excitation was needed. This method was validated by quantifying the elasticity of tissue-mimicking agar phantoms as well as of a porcine cornea ex vivo at different intraocular pressures. The results demonstrate that this method can reduce the acquisition time of an elastogram to milliseconds.
Guidelines for Optimizing Type S Non-Ribosomal Peptide Synthetases (2023)

Abstract Bacterial biosynthetic assembly lines, such as non-ribosomal peptide synthetases (NRPS) and polyketide synthases, are often subject of synthetic biology – because they produce a variety of natural products invaluable for modern pharmacotherapy. Acquiring the ability to engineer these biosynthetic assembly lines allows the production of artificial non-ribosomal peptides (NRP), polyketides, and hybrids thereof with new or improved properties. However, traditional bioengineering approaches have suffered for decades from their very limited applicability and, unlike combinatorial chemistry, are stigmatized as inefficient because they cannot be linked to the high-throughput screening platforms of the pharmaceutical industry. Although combinatorial chemistry can generate new molecules cheaper, faster, and in greater numbers than traditional natural product discovery and bioengineering approaches, it does not meet current medical needs because it covers only a limited biologically relevant chemical space. Hence, methods for high-throughput generation of new natural product-like compound libraries could provide a new avenue towards the identification of new lead compounds. To this end, prior to this work, we introduced an artificial synthetic NRPS type, referred to as type S NRPS, to provide a first-of-its-kind bicombinatorial approach to parallelized high-throughput NRP library generation. However, a bottleneck of these first two generations of type S NRPS was a significant drop in production yields. To address this issue, we applied an iterative optimization process that enabled titer increases of up to 55-fold compared to the non-optimized equivalents, restoring them to wild-type levels and beyond.