gebhart/patrepeval huggingface dataset:
Design of a Carbonic Anhydrase IX Active-Site Mimic To Screen Inhibitors for Possible Anticancer Properties (2009)

Recently, a convincing body of evidence has accumulated suggesting that the overexpression of carbonic anhydrase isozyme IX (CA IX) in some cancers contributes to the acidification of the extracellular matrix, which in turn promotes the growth and metastasis of the tumor. These observations have made CA IX an attractive drug target for the selective treatment of certain cancers. Currently, there is no available X-ray crystal structure of CA IX, and this lack of availability has hampered the rational design of selective CA IX inhibitors. In light of these observations and on the basis of structural alignment homology, using the crystal structure of carbonic anhydrase II (CA II) and the sequence of CA IX, a double mutant of CA II with Ala65 replaced by Ser and Asn67 replaced by Gln has been constructed to resemble the active site of CA IX. This CA IX mimic has been characterized kinetically using (18)O-exchange and structurally using X-ray crystallography, alone and in complex with five CA sulfonamide-based inhibitors (acetazolamide, benzolamide, chlorzolamide, ethoxzolamide, and methazolamide), and compared to CA II. This structural information has been evaluated by both inhibition studies and in vitro cytotoxicity assays and shows a correlated structure-activity relationship. Kinetic and structural studies of CA II and CA IX mimic reveal chlorzolamide to be a more potent inhibitor of CA IX, inducing an active-site conformational change upon binding. Additionally, chlorzolamide appears to be cytotoxic to prostate cancer cells. This preliminary study demonstrates that the CA IX mimic may provide a useful model to design more isozyme-specific CA IX inhibitors, which may lead to development of new therapeutic treatments of some cancers.
Determination of Electrode Sheet Resistance in Cathode Catalyst Layer by AC Impedance (2007)

Proton conduction resistance in the cathode electrode with various ionomer/carbon weight ratios (I/C-ratios) was characterized using AC impedance at different relative humidities (RH) in a H2/N2 cell. AC impedance data were analyzed by fitting sheet resistance, Rsheet, sheet capacitance, Csheet, and the high-frequency resistance, HFR, to a simplified transmission-line model with the assumption that the proton resistance and the pseudo-capacitance are distributed uniformly throughout the electrode. For given types of model membrane electrode assemblies (MEAs), a percolation threshold for proton conductivity in the electrode was observed at I/C-ratios of approximately &lt;0.6/1. The comparison to H2/O2 fuel cell performance shows that the ohmic loss in the catalyst layer can be quantified by this technique, and the parameter Rsheet extracted from the AC impedance spectra is indeed an intrinsic RH-dependent electrode property.
Continuous-wave and mode-locked laser operation of segmented grown Yb:KY(WO 4 ) 2 /KY(WO 4 ) 2 (2007)

The continuous-wave (cw) and passive mode-locked operation of a Ti:sapphire-pumped Yb doped KY(WO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> laser is reported in this paper. Laser performance in cw operation is studied in a Z-shaped four mirror cavity while in the mode-locked operation, a semiconductor saturable absorber and two SF10 prisms are additionally inserted in the cavity. Results show generation of optical pulses as short as 99 fs with up to 80% slope efficiency. The laser is tunable between 1024.4 nm and 1042.6 nm with pulse durations below 200 fs.
A novel compact beamformer for a high resolution sonar (2005)

A novel technique for implementing the CZT-beamformer for high-resolution sector scanning sonar which results in a very compact hardware is presented. A Delta-modulator is used to encode the spatially sampled sensor signals from a linear array in single-bit format, thus allowing the use of shift registers in place of analog bbd's. Another novel feature is the combination of bandpass sampling and spatial multiplexing into a single operation. The paper discusses this implementation of the CZT-beamformer, and provides simulation results and comparison with the conventional CZT-beamformer. These results demonstrate the potential of the novel technique for compact systems. A complete beamformer hardware has also been developed for a specific application.
Cooperative Multiagent Congestion Control for High-Speed Networks (2005)

An adaptive multiagent reinforcement learning method for solving congestion control problems on dynamic high-speed networks is presented. Traditional reactive congestion control selects a source rate in terms of the queue length restricted to a predefined threshold. However, the determination of congestion threshold and sending rate is difficult and inaccurate due to the propagation delay and the dynamic nature of the networks. A simple and robust cooperative multiagent congestion controller (CMCC), which consists of two subsystems: a long-term policy evaluator, expectation-return predictor and a short-term rate selector composed of action-value evaluator and stochastic action selector elements has been proposed to solve the problem. After receiving cooperative reinforcement signals generated by a cooperative fuzzy reward evaluator using game theory, CMCC takes the best action to regulate source flow with the features of high throughput and low packet loss rate. By means of learning procedures, CMCC can learn to take correct actions adaptively under time-varying environments. Simulation results showed that the proposed approach can promote the system utilization and decrease packet losses simultaneously.
Prediction of Vortex Penetration Depth in a Thermal Stratified Branch Pipe with Closed End (2003)

In a branch pipe with closed end, the cavity flow penetrates into the branch pipe from the main loop and the thermal boundary layer occurs because the cavity flow is a hot fluid, but the heat removal causes the colder fluid in the branch pipe. It is possible for the thermal stratification to affect the structural integrity. Therefore, it is necessary to establish the pipe design standard to suppress thermal fatigue. The pipe design standard consists of the maximum penetration depth L_<sv> and the minimum penetration depth L_<sh>. First of all, in order to establish the evaluation method for L_<sh>, the visualization test and the temperature fluctuation test were carried out. Theoretical formula of thermal stratification was introduced from the heat balance model. Using this model, the empirical equation was obtained from the map of fluid temperature fluctuation. The method can predict the vortex penetration depth by cavity flow in the horizontal branch pipe.
Asymmetric induction and racemisation in allenic sulphoxides (1976)

Menthyl sulphinates with Grignard reagents derived from α-acetylenic halides give mixtures of allenic and acetylenic sulphoxides. The extent of asymmetric induction in the allene groups is compared with that obtained in a simple alkyl sulphoxide by use of 1-methylheptylmagnesium bromide. Absolute configurations are assigned to the two chiral centres in the sulphoxides; that of the sulphinyl group follows from that of the sulphinate ester, and that of the allene system is derived from the sign of rotation of the allenic sulphone obtained by oxidation.Allenic sulphoxides undergo racemisation of the sulphinyl group under conditions in which the chirality of the allene system is unaffected. The activation parameters for the process in which the sulphinyl group is racemised provide evidence for sulphoxide–sulphenate equilibration, and this conclusion is supported by interception, with an amine, of an intermediate sulphenate ester.
Secure End-to-End Communication with Optimal Throughput in Unreliable Networks (2013)

We demonstrate the feasibility of end-to-end communication in highly unreliable networks. Modeling a network as a graph with vertices representing nodes and edges representing the links between them, we consider two forms of unreliability: unpredictable edge-failures, and deliberate deviation from protocol specifications by corrupt nodes. We present a robust routing protocol for end-to-end communication that is simultaneously resilient to both forms of unreliability. In particular, we prove rigorously that our protocol is SECURE against the actions of the corrupt nodes, achieves correctness (Receiver gets ALL of the messages from Sender, in order and without modification), and enjoys provably optimal throughput performance, as measured using competitive analysis. Furthermore, our protocol does not incur any asymptotic memory overhead as compared to other protocols that are unable to handle malicious interference of corrupt nodes. In particular, our protocol requires O(n^2) memory per processor, where n is the size of the network. This represents an O(n^2) improvement over all existing protocols that have been designed for this network model.
An Active Storage System for High Performance Computing (2008)

Traditionally, active storage devices execute custom application code on large amounts of data by utilizing the unused processing power of the storage nodes. For computation-intensive applications, the performance might be quite low due to insufficient processing power on the storage devices. In this paper we present a reconfigurable computing solution that can provide flexible, high-performance processing capabilities for the storage nodes. We have made a change over the existing active storage framework for object-based storage device by off loading computation-intensive request-driven services to a reconfigurable hardware accelerator. In the experiment, we use two applications (AES encryption and FFT) as the case studies, and the results show that the reconfigurable computing-based system can dramatically increase the performance comparing with the traditional software-based active storage systems.
Solvothermal Carbonization Route to Carbon Coating of Manganese Oxide for Supercapacitor Applications (2009)

Abstract not Available.
Table S1 from A Transposon Screen Identifies Loss of Primary Cilia as a Mechanism of Resistance to SMO Inhibitors (2023)

&lt;p&gt;Supplementary Table S1, related to Figure 1. A total of 182 transposon insertions were identified in 27 resistant clones. Provided as a separate Excel file&lt;/p&gt;
Shallow Aseismic Slip in the Delaware Basin Determined by Sentinel‐1 InSAR (2022)

Abstract The Delaware Basin, Texas is currently a hot‐spot of induced seismicity and ground deformation due to fluid extraction and injection associated with horizontal drilling techniques; however, the driving mechanism behind the seismicity and deformation remains under debate. Using vertical and east‐west horizontal surface deformation measurements derived from Sentinel‐1 interferometric synthetic aperture radar (InSAR), we show that the subsurface responds differently to oil and gas activity in the northern and southeastern portions of the basin. In the north, where there is little seismicity, deformation patterns display long‐wavelengths and equidimensional patterns. In contrast, the southeast region hosts most of the seismicity and displays spatial deformation patterns with narrow linear features that strike parallel to the maximum principal horizontal stress and to trends in seismicity, suggesting movement along normal faults. We model a linear deformation feature using edge dislocations and show that the InSAR observations can be reproduced by slip on normal faults contained within the Delaware Mountain Group (DMG), the formation that hosts local wastewater injection and the majority of earthquakes. Our model consists of three parallel, high‐angle normal faults, with two dipping toward one another in a graben structure. Slip magnitudes reach up to 25 cm and are spatially correlated with injection wells. Measured seismicity can only explain ∼2% of the fault motion predicted by our fault model, suggesting that slip leading to the deformation is predominantly aseismic. We conclude that seismic and aseismic fault motion in the southeastern Delaware Basin is likely driven by wastewater injection near critically‐stressed normal faults within the DMG.
Randomized phase II study of weekly carfilzomib 70 mg/m<sup>2</sup> and dexamethasone with or without cyclophosphamide in relapsed and/or refractory multiple myeloma patients (2023)

In this randomized phase II study (GEM-KyCyDex, clinicaltrials gov. Identifier: NCT03336073), the combination of weekly carfilzomib 70 mg/m2, cyclophosphamide and dexamethasone (KCd) was compared to carfilzomib and dexamethasone (Kd) in relapsed/refractory multiple myeloma (RRMM) after 1-3 prior lines (PL). One hundred and ninety-seven patients were included and randomized 1:1 to receive KCd (97 patients) or Kd (100 patients) in 28-day cycles until progressive disease or unacceptable toxicity occurred. Patient median age was 70 years, and the median number of PL was one (range, 1-3). More than 90% of patients had previously been exposed to proteasome inhibitors, approximetely 70% to immunomodulators, and approximetely 50% were refractory to their last line (mainly lenalidomide) in both groups. After a median follow-up of 37 months, median progression-free survival (PFS) was 19.1 and 16.6 months in KCd and Kd, respectively (P=0.577). Of note, in the post hoc analysis of the lenalidomide-refractory population, the addition of cyclophosphamide to Kd resulted in a significant benefit in terms of PFS: 18.4 versus 11.3 months (hazard ratio =1.7, 95% confidence interval: 1.1-2.7; P=0.043). The overall response rate and the percentage of patients who achieved complete response was around 70% and 20% in both groups. The addition of cyclophosphamide to Kd did not result in any safety signal, except for severe infections (7% vs. 2%). In conclusion, the combination of cyclophosphamide with Kd 70 mg/m2 weekly does not improve outcomes as compared with Kd alone in RRMM after 1-3 PL, but a significant benefit in PFS was observed with the triplet combination in the lenalidomide-refractory population. The administration of weekly carfilzomib 70 mg/m2 was safe and convenient, and, overall, the toxicity was manageable in both arms.
Encoder and list decoder of Reed-Solomon kernel based polar codes (2016)

In this paper, we propose the encoding and list decoding method of polar codes based on the four-dimensional Reed-Solomon (RS-4) kernel. In specific, an encoding table based method is employed to reduce the computational complexity of both encoder and decoder. In addition, a simplified method to update log-likelihood ratios (LLRs) which employs additions instead of exponential calculations is also proposed to further increase the decoding speed. In addition, we present a method to construct RS-4 polar codes using genie-aided simulations, where the symbol channel capacity is determined by the number of decoding errors. Through simulations, we show the decoding performance of the RS-4 polar codes and compare it with the binary polar codes.
Magnesium Oxide Nanoparticles Reinforced Electrospun Alginate-Based Nanofibrous Scaffolds with Improved Physical Properties (2017)

Mechanically robust alginate-based nanofibrous scaffolds were successfully fabricated by electrospinning method to mimic the natural extracellular matrix structure which benefits development and regeneration of tissues. Alginate-based nanofibres were electrospun from an alginate/poly(vinyl alcohol) (PVA) polyelectrolyte complex. SEM images revealed the spinnability of the complex composite nanofibrous scaffolds, showing randomly oriented, ultrafine, and virtually defects-free alginate-based/MgO nanofibrous scaffolds. Here, it is shown that an alginate/PVA complex scaffold, blended with near-spherical MgO nanoparticles (⌀ 45 nm) at a predetermined concentration (10% (w/w)), is electrospinnable to produce a complex composite nanofibrous scaffold with enhanced mechanical stability. For the comparison purpose, chemically cross-linked electrospun alginate-based scaffolds were also fabricated. Tensile test to rupture revealed the significant differences in the tensile strength and elastic modulus among the alginate scaffolds, alginate/MgO scaffolds, and cross-linked alginate scaffolds (<i>P</i> < 0.05). In contrast to cross-linked alginate scaffolds, alginate/MgO scaffolds yielded the highest tensile strength and elastic modulus while preserving the interfibre porosity of the scaffolds. According to the thermogravimetric analysis, MgO reinforced alginate nanofibrous scaffolds exhibited improved thermal stability. These novel alginate-based/MgO scaffolds are economical and versatile and may be further optimised for use as extracellular matrix substitutes for repair and regeneration of tissues.
Inhibition of HDAC6‐dependent carcinogenesis: Emerging, new therapeutic options besides belinostat (2008)

Dear Sir, The recent article by Qian et al. was highly interesting and enlightening.1 The authors have clearly shown that belinostat (PXD101) is a potent histone deacetylase (HDAC) inhibitor of prostate cancer. HDAC6 in particular is a key regulator of cellular migration as well as intercellular interactions and its inhibition can go a long way in down-regulation of systemic oncogenesis by modulating these cellular interactions. A number of potent HDAC6 inhibitors besides belinostat have been identified recently. Among these inhibitors some are specific for HDAC6. For instance, tubacin is a selective HDAC6 inhibitor.2 Biochemically it is a synthetic hydroxamic acid. Similarly, Dehmel et al. have recently identified certain trithiocarbonate derivatives (12ac) that are highly selective for HDAC63 while Itoh et al. have identified certain thiolate derivatives (16b) that demonstrate similar selectivity for HDAC6.4 Besides these selective HDAC6 inhibitors a number of broad spectrum HDAC inhibitors have been identified that inhibit other HDAC class I and II enzymes also. For instance, KD5170 is a nonhydroxamate broad-spectrum inhibitor that inhibits HDAC1 besides HDAC6.5 Vorinostat (suberoylanilide hydroxamic acid) is another broad-spectrum HDAC inhibitor, which inhibits HDAC6 also, especially so in tumors such as cutaneous T-cell lymphomas.6 Interestingly, the down-regulation of HDAC6 in tumors such as lung cancer tissue enhances the inhibitory effects of agents such as U0126,7 whereas similar HDAC6 inhibition in leukemia cells accentuates the sensitivity of tumor cells to inhibitors such as 17-allylamino-demothoxy geldanamycin.8 Similar synergistic results have been obtained when agents such as paclitaxel and bortezomib have been used in combination with attenuators of HDAC6 expression such as thiolate analogues.4 These synergistic effects clearly illustrate the massive chemotherapeutic potential of HDAC6 inhibitors. Without a doubt, HDAC6 has a major role to play in the evolution and progression of systemic cancers. The efficacy of belinostat in prostate cancer as illustrated by Qian et al. clearly highlights the potential of HDAC6 inhibitors. There is a clear need for more studies to further evaluate agents such as belinostat as well as a need for the development of further HDAC6 inhibitors which may very well change the future of oncology. Yours Sincerely, Shailendra Kapoor.
Compute-resource allocation for motion estimation in real-time video compression (2004)

We present a novel method for allocating computational resources in motion estimation for real time video compression that attempts to minimize prediction error over the whole image. The method makes decisions about how much compute power is allocated to motion estimation for each particular block based upon past observations of the input and output data of each task. We present results that demonstrate the ability of our method to improve the resulting quality of encoded video under a real-time computational constraint.
Angiogenesis and the multistage development of lung cancers. (2000)

As with other epithelial tumors, lung cancers develop after a series of morphological and molecular changes. The molecular alterations precede histopathological changes and commence in histologically normal epithelium [(1][1] [, 2)][2] . In the larger bronchi, the smoking-associated morphological
Real-Time Hierarchical Binary-Scene Voxelization (2009)

Volumetric representations provide the localization of shapes in space. When such representation is created on the fly from the geometry, it becomes very useful for a wide range of applications (constructive solid geometry (CSG), shape repair, collision detection, etc. Using the advanced functionalities provided by recent GPUs (geometry shaders, 32-bit integer texture format and bitwise operators), we show how to compute a robust scene voxelization and octree construction in a few milliseconds from any hardware-supported rasterizable geometry. Our hierarchical volumetric representation is thus especially well-suited for hierarchical computation of fully dynamic scenes.
IRAK-4 Mutation (Q293X): Rapid Detection and Characterization of Defective Post-Transcriptional TLR/IL-1R Responses in Human Myeloid and Non-Myeloid Cells (2006)

Innate immunodeficiency has recently been reported as resulting from the Q293X IRAK-4 mutation with consequent defective TLR/IL-1R signaling. In this study we report a method for the rapid allele-specific detection of this mutation and demonstrate both cell type specificity and ligand specificity in defective IL-1R-associated kinase (IRAK)-4-deficient cellular responses, indicating differential roles for this protein in human PBMCs and primary dermal fibroblasts and in LPS, IL-1beta, and TNF-alpha signaling. We demonstrate transcriptional and post-transcriptional defects despite NF-kappaB signaling and intact MyD88-independent signaling and propose that dysfunctional complex 1 (IRAK1/TRAF6/TAK1) signaling, as a consequence of IRAK-4 deficiency, generates specific defects in MAPK activation that could underpin this patient's innate immunodeficiency. These studies demonstrate the importance of studying primary human cells bearing a clinically relevant mutation; they underscore the complexity of innate immune signaling and illuminate novel roles for IRAK-4 and the fundamental importance of accessory proinflammatory signaling to normal human innate immune responses and immunodeficiencies.
Studies on Vitamin B<sub>1</sub> and Related Compounds. LIX (1954)

Allithiamine (III) is formed by the reaction of thiamine (XIII) and alicin (II), which is said to be the secondary component formed by the enzymatic decomposition of alliin (I) by alliinase. If this relationship be true, the formation of allithiamine (III) by reaction with thiamine will confirm the presence of alliin (I) in plants as the sulfur-containing component and, at the same time, the presence of allicin (II). This relationship will also hold for the methyl (VI) and propyl (XII) homologs of allithiamine.The fact that the above relationship is correct was confirmed by using synthesized S-alkyl-L-cysteine sulfoxide and alliinase isolated from a plant. In other words, the presence of S-methyl-(IV) and S-propyl-L-cysteine sulfoxide (X) can be assumed in Allium sativum L., besides alliin. In other Allium species, a minute amount of (X) can also be assumed to be present besides a large amount of alliin (I) and (IV).
A Dataflow Control Unit for C-to-Configurable Pipelines Compilation Flow (2004)

In the field of embedded systems, reconfigurable processors, composed of a standard processor core coupled with a reconfigurable device, are gaining more and more importance. Algorithm developers are facing the issue of mapping applications on configurable hardware, without a specific knowledge of the underlying architecture. In this paper, we present a modular data flow control unit for a reconfigurable datapath, which can be easily programmed starting from the C description of the required functionality.