gebhart/patrepeval huggingface dataset:
Selective Inhibition of Collagen Prolyl 4-Hydroxylase in Human Cells (2015)

Collagen is the most abundant protein in animals. Its overproduction is associated with fibrosis and cancer metastasis. The stability of collagen relies on post-translational modifications, the most prevalent being the hydroxylation of collagen strands by collagen prolyl 4-hydroxylases (CP4Hs). Catalysis by CP4Hs enlists an iron cofactor to convert proline residues to 4-hydroxyproline residues, which are essential for the conformational stability of mature collagen. Ethyl 3,4-dihydroxybenzoate (EDHB) is commonly used as a "P4H" inhibitor in cells, but suffers from low potency, poor selectivity, and off-target effects that cause iron deficiency. Dicarboxylates of 2,2'-bipyridine are among the most potent known CP4H inhibitors but suffer from a high affinity for free iron. A screen of biheteroaryl compounds revealed that replacing one pyridyl group with a thiazole moiety retains potency and enhances selectivity. A diester of 2-(5-carboxythiazol-2-yl)pyridine-5-carboxylic acid is bioavailable to human cells and inhibits collagen biosynthesis at concentrations that neither cause general toxicity nor disrupt iron homeostasis. These data anoint a potent and selective probe for CP4H and a potential lead for the development of a new class of antifibrotic and antimetastatic agents.
Ergodic and Outage Performance of Fading Broadcast Channels with 1-Bit Feedback (2010)

In this paper, the ergodic sum-rate and outage probability of a downlink single-antenna channel with K users are analyzed in the presence of Rayleigh flat fading, where limited channel state information (CSI) feedback is assumed. Specifically, only 1-bit feedback per fading block per user is available at the base station. We first study the ergodic sum-rate of the 1-bit feedback scheme, and consider the impact of feedback delay on the system. A closed-form expression for the achievable ergodic sum-rate is presented as a function of the fading temporal correlation coefficient. It is proved that the sum-rate scales as loglogK, which is the same scaling law achieved by the optimal non-delayed full CSI feedback scheme. The sum-rate degradation due to outdated CSI is also evaluated in the asymptotic regimes of either large K or low SNR. The outage performance of the 1-bit feedback scheme for both instantaneous and outdated feedback is then investigated. Expressions for the outage probabilities are derived, along with the corresponding diversity-multiplexing tradeoffs (DMT). It is shown that with instantaneous feedback, a power allocation based on the feedback bits enables to double the DMT compared to the case with short-term power constraint in which a dynamic power allocation is not allowed. But, with outdated feedback, the advantage of power allocation is lost, and the DMT reverts to that achievable with no CSI feedback. Nevertheless, for finite SNR, improvement in terms of outage probability can still be obtained.
Weaver: Language and runtime for software defined environments (2014)

Continuous delivery of software and related infrastructure environments is a challenging proposition. Typical enterprise environments, comprising distributed software and its supporting infrastructure, exhibit non-obvious, often implicit dependencies and requirements. Further increasing this challenge is that knowledge about configuration is fragmented and informally recorded. Given this situation, we propose Weaver, a domain-specific language designed to formally specify blueprints, desired state descriptions of environments. An associated runtime executes blueprints to create or modify environments through a set of target-specific platform providers that supply cloud-specific implementations. New and existing automation to implement and maintain the desired state can be associated with a blueprint specified in Weaver. Furthermore, Weaver supports the definition of conditions to validate a blueprint at design time and deployment time, as well as to continuously validate a deployed environment. We demonstrate the use of Weaver to deploy IBM Connections, an enterprise social software platform.
A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data (2011)

Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling.
Anti-HIV and anti-tumor activities of recombinant MAP30 from bitter melon (1995)

MAP30 is an anti-HIV plant protein that we have identified and purified to homogeneity from bitter melon (Momordica charantia). It is capable of acting against multiple stages of the viral life cycle, on acute infection as well as replication in chronically infected cells. In addition to antiviral action, MAP30 also possesses anti-tumor activity, topological inactivation of viral DNA, inhibition of viral integrase and cell-free ribosome-inactivation activities. We have cloned and expressed the MAP30 gene. The objective of this study is to characterize recombinant MAP30 (re-MAP30) and to determine its anti-HIV, anti-tumor and other activities. We report here that re-MAP30 inhibits HIV-1 and certain human tumors to the same extent as its native counterpart, natural MAP30 (nMAP30). The anti-HIV activity was measured by quantitative focal syncytium formation on CEM-ss cell monolayers, viral core protein p24 expression and viral-associated reverse transcriptase activity in HIV-1-infected H9 cells. The anti-tumor activity was measured by metabolic labeling of protein synthesis in tumor cells. In the dose range of the assay, re-MAP30 exhibits little toxicity to the uninfected viral target cells and other normal human cells. Identical to nMAP30, re-MAP30 is also active in topological inactivation of viral DNA, inhibition of viral DNA integration and cell-free ribosome inactivation. The cloning and expression of the gene encoding biologically active re-MAP30 provides an abundant source of homogeneous material for clinical investigations, as well as structure-function studies of this novel antiviral and anti-tumor agent.
Identification and Characterization of a Novel Lysophosphatidic Acid Receptor, p2y5/LPA6 (2009)

p2y5 is an orphan G protein-coupled receptor that is closely related to the fourth lysophosphatidic acid (LPA) receptor, LPA4. Here we report that p2y5 is a novel LPA receptor coupling to the G13-Rho signaling pathway. "LPA receptor-null" RH7777 and B103 cells exogenously expressing p2y5 showed [3H]LPA binding, LPA-induced [35S]guanosine 5'-3-O-(thio)triphosphate binding, Rho-dependent alternation of cellular morphology, and Gs/13 chimeric protein-mediated cAMP accumulation. LPA-induced contraction of human umbilical vein endothelial cells was suppressed by small interfering RNA knockdown of endogenously expressed p2y5. We also found that 2-acyl-LPA had higher activity to p2y5 than 1-acyl-LPA. A recent study has suggested that p2y5 is an LPA receptor essential for human hair growth. We confirmed that p2y5 is a functional LPA receptor and propose to designate this receptor LPA6.
Application of speech rate conversion technology to video editing : Allows up to 5 times normal speed playback while maintaining speech intelligibility (2001)

This paper describes an application of speech rate conversion technology to video editing. In video editing, it is common to search through the material at several times normal speed. The speech rate conversion technology maintains the original pitch and timbre of speech despite playing it back at a faster rate, which is varied adaptively to permit fast listening in real-time. In listening tests, users were able to comprehend speech played at up to 5 times normal speed which was incomprehensible without the adaptive rate conversion (even when pitch-shifted to restore the original pitch). A prototype editing system, which maintains the intelligibility of speech during variable-rate playback, has been applied to a non-linear editing system. The system can change the replay speed of MPEG1 or 2 audio and video simultaneously has been implemented on a personal computer.
<i>FASCIATED EAR4</i> Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize (2015)

Plant architecture is dictated by precise control of meristematic activity. In the shoot, an imbalance in positive or negative maintenance signals can result in a fasciated or enlarged meristem phenotype. fasciated ear4 (fea4) is a semidwarfed mutant with fasciated ears and tassels as well as greatly enlarged vegetative and inflorescence meristems. We identified FEA4 as a bZIP transcription factor, orthologous to Arabidopsis thaliana PERIANTHIA. FEA4 was expressed in the peripheral zone of the vegetative shoot apical meristem and in the vasculature of immature leaves and conspicuously excluded from the stem cell niche at the tip of the shoot apical meristem and from incipient leaf primordia. Following the transition to reproductive fate, FEA4 was expressed throughout the entire inflorescence and floral meristems. Native expression of a functional YFP:FEA4 fusion recapitulated this pattern of expression. We used chromatin immunoprecipitation-sequencing to identify 4060 genes proximal to FEA4 binding sites, including ones that were potentially bound and modulated by FEA4 based on transcriptional changes in fea4 mutant ears. Our results suggest that FEA4 promotes differentiation in the meristem periphery by regulating auxin-based responses and genes associated with leaf differentiation and polarity, potentially in opposition to factors such as KNOTTED1 and WUSCHEL.
Process for producing methane from carbon monoxide and steam. [preparation of promoted Ni catalyst supported on calcium phosphate] (1978)

A catalyst consisting essentially of nickel, a promoter selected from the group consisting of barium and uranium and a calcium phosphate support having a Ca:P atomic ratio in the range of 1.4:1 to 2.3:1, is formed by impregnating a calcium phosphate gel with suitable compounds of nickel and either barium or uranium. The resulting catalysts are useful for reacting carbon monoxide and steam and in steam reforming processes for producing methane.
<title>Robust detection of defects in imaging arrays</title> (2006)

As digital imagers continue to increase in size and pixel density, the detection of faults in the field becomes critical to delivering high quality output. Traditional schemes for defect detection utilize specialized hardware at the time of manufacture and are impractical for use in the field, while previously proposed software-based approaches tend to lead to quality-degrading false positive diagnoses. This paper presents an algorithm that utilizes statistical information extracted from a sequence of normally captured images to identify the location and type of defective pixels. Building on previous research, this algorithm utilizes data local to each pixel and Bayesian statistics to more accurately infer the likelihood of each defect, which successfully improves the detection time. Several defect types are considered, including pixels with one-half of the typical sensitivity and permanently stuck pixels. Monte Carlo simulations have shown that for defect densities of up to 0.5%, 50 ordinary images are sufficient to accurately identify all faults without falsely diagnosing good pixels as faulty. Testing also indicates that the algorithm can be extended to higher resolution imagers and to those with noisy stuck pixels, with only minimal cost to performance.
Distortion Behavior of Amplify-and-Forward Cooperative System with Layered Broadcast Coding (2010)

Cooperative system has been receiving considerable attention recently as an effective approach to improve transmission reliability in slow fading wireless channels. In this paper, we exploit cooperative diversity in multiple relay networks to improve the performance of Gaussian source transmission with layered broadcast coding. Specifically, we study the distortion performance of two amplify-and-forward (AF) schemes, namely, distributed beamforming and selection AF. First, we analyze their asymptotic performance in terms of the distortion exponent and the expected distortion. We then show that, under stringent delay constraint, there exist SNR thresholds below which the AF systems achieve lower distortion than the direct transmission system.
XID: Don't Care Identification of Test Patterns for Combinational Circuits (2004)

Given a test set for stuck-at faults of a combinational circuit or a full-scan sequential circuit, some of the primary input values may be changed to the opposite logic values without losing fault coverage. We can regard such input values as don't care (X). In this paper, we propose a method for identifying the X inputs of test vectors in a given test set. While there are many combinations of X inputs in the test set generally, the proposed method finds one including as many X inputs as possible, by using fault simulation and procedures similar to implication and justification of automatic test pattern generation (ATPG) algorithms. Experimental results for ISCAS benchmark circuits show that approximately 69% of the inputs of uncompacted test sets could be X on the average. Even for highly compacted test sets, the method found that approximately 48% of inputs are X.
Establishment of the Underlying Rationale and Description of a Cheap Nanofiltration-Based Method for Supplementing Desalinated Water with Magnesium Ions (2014)

The importance of supplying drinking water with a balanced mineral composition, including a minimal concentration of Mg(II) ions, has been recently acknowledged by many publications, as well as in official WHO guidelines. The issue is relevant to naturally occurring soft waters and lately to the rapidly increasing volume of supplied desalinated water. This paper presents an enhancement of a recently developed nanofiltration-based method for the selective separation of soluble Mg(II) species from seawater. The generated rich-Mg(II) brine is demonstrated to be suitable for supplementing soft waters with magnesium ions. The brine, generated using a commercial membrane (DS-5 DL, Osmonics) at various operational conditions is characterized by high Mg(II) concentrations (~8.5 g/L) and low Cl:Mg and Na:Mg molar concentration ratios (1.6 and 0.6, respectively, at 28-bar operation). A food-grade antiscalant is dosed to the feed seawater to prevent scaling; however, since the Mg(II) concentration in the brine is high, for attaining 10 mg Mg/L of desalinated water, the dilution ratio with the desalinated water is ~1:850, resulting in maximal additional concentrations of 0.024 antiscalant, 34.9 Cl(−I), 12.9 Na(I), 0.05 Sr(II) and 0.003 B (all concentrations in mg/L). The overall cost of 1 kg of Mg(II) separated by the presented process amounts to between $0.05 and $0.07, i.e., much cheaper than the estimated costs of alternative processes for Mg(II) addition to desalinated water.
High‐Speed Color‐Switching Silicon LEDs (2008)

Silicon-based light-emitting devices can be produced by patterning commercial silicon wafers into microscale metal–insulator–semiconductor diodes. In this image, a silicon LED switches from IR (false color – left) to off (middle) to visible (right).
Distral: Robust Multitask Reinforcement Learning (2017)

Most deep reinforcement learning algorithms are data inefficient in complex and rich environments, limiting their applicability to many scenarios. One direction for improving data efficiency is multitask learning with shared neural network parameters, where efficiency may be improved through transfer across related tasks. In practice, however, this is not usually observed, because gradients from different tasks can interfere negatively, making learning unstable and sometimes even less data efficient. Another issue is the different reward schemes between tasks, which can easily lead to one task dominating the learning of a shared model. We propose a new approach for joint training of multiple tasks, which we refer to as Distral (Distill & transfer learning). Instead of sharing parameters between the different workers, we propose to share a "distilled" policy that captures common behaviour across tasks. Each worker is trained to solve its own task while constrained to stay close to the shared policy, while the shared policy is trained by distillation to be the centroid of all task policies. Both aspects of the learning process are derived by optimizing a joint objective function. We show that our approach supports efficient transfer on complex 3D environments, outperforming several related methods. Moreover, the proposed learning process is more robust and more stable---attributes that are critical in deep reinforcement learning.
Antileukemic efficacy of a potent artemisinin combined with sorafenib and venetoclax (2021)

Artemisinins are active against human leukemia cell lines and have low clinical toxicity in worldwide use as antimalarials. Because multiagent combination regimens are necessary to cure fully evolved leukemias, we sought to leverage our previous finding that artemisinin analogs synergize with kinase inhibitors, including sorafenib (SOR), by identifying additional synergistic antileukemic drugs with low toxicity. Screening of a targeted antineoplastic drug library revealed that B-cell lymphoma 2 (BCL2) inhibitors synergize with artemisinins, and validation assays confirmed that the selective BCL2 inhibitor, venetoclax (VEN), synergized with artemisinin analogs to inhibit growth and induce apoptotic cell death of multiple acute leukemia cell lines in vitro. An oral 3-drug "SAV" regimen (SOR plus the potent artemisinin-derived trioxane diphenylphosphate 838 dimeric analog [ART838] plus VEN) killed leukemia cell lines and primary cells in vitro. Leukemia cells cultured in ART838 had decreased induced myeloid leukemia cell differentiation protein (MCL1) levels and increased levels of DNA damage-inducible transcript 3 (DDIT3; GADD153) messenger RNA and its encoded CCATT/enhancer-binding protein homologous protein (CHOP), a key component of the integrated stress response. Thus, synergy of the SAV combination may involve combined targeting of MCL1 and BCL2 via discrete, tolerable mechanisms, and cellular levels of MCL1 and DDIT3/CHOP may serve as biomarkers for action of artemisinins and SAV. Finally, SAV treatment was tolerable and resulted in deep responses with extended survival in 2 acute myeloid leukemia (AML) cell line xenograft models, both harboring a mixed lineage leukemia gene rearrangement and an FMS-like receptor tyrosine kinase-3 internal tandem duplication, and inhibited growth in 2 AML primagraft models.
THE USE OF PHOSPHORUS AND OTHER SOIL AMENDMENTS FOR IN SITU STABILIZATION OF SOIL LEAD (2000)

This study was conducted to evaluate the effects of P, Mn oxide, and time on bioavailable Pb in five metal-contaminated soils or mine spoils in the absence or the presence of plants, and to evaluate the effect of those treatments on phytoavailability of Pb, Cd, and Zn. The addition of P or Mn oxide reduced bioavailable Pb compared to control, as measured by a modified physiologically based extraction procedure (PBET). The maximum reduction in bioavailable Pb was always observed with the addition of P and manganese oxides together. X-ray diffractometry analyses support the PBET results, indicating that more “pyromorphite-like minerals ” may have formed in the presence of both P and Mn oxides. Synergistic effects from the presence of Mn oxide with P in reducing Pb bioavailability were still evident after extensive cropping of the soils. Several mechanisms, alone or in combination, may have been responsible for this synergistic effect. The concentrations of Pb, Cd, and Zn in sudax and Swiss chard plant tissues were reduced in the presence of soluble P, and soluble P or insoluble P with Mn oxides. This new improved in situ technique to remediate Pb-contaminated soil and mine wastes has advantages over standard methods. Key words: in situ stabilization, bioavailable PB, soil remediation
Fast Polar Decoders: Algorithm and Implementation (2014)

Polar codes provably achieve the symmetric capacity of a memoryless channel while having an explicit construction. The adoption of polar codes however, has been hampered by the low throughput of their decoding algorithm. This work aims to increase the throughput of polar decoding hardware by an order of magnitude relative to successive-cancellation decoders and is more than 8 times faster than the current fastest polar decoder. We present an algorithm, architecture, and FPGA implementation of a flexible, gigabit-per-second polar decoder.
Semiconductor all-optical buffers using quantum dots in resonator structures (2004)

A variable semiconductor all-optical buffer is proposed. The buffer uses electromagnetically-induced transparency in quantum dots. With resonator structures, the performance can be further improved. A device storing 168 bits in a 10 Gb/s system can be obtained at room temperature.
Electrical Extraction of Oil From Tar Sand (1977)

A new technique for the separation of bitumen from tar sand is described. In this technique an electrical current is passed through a quantity of tar sand which is positioned in a vessel beneath a column of water. The passage of current causes the tar sand and the lower portion of the water column to become violently agitated and to eject particles of bitumen and sand. The bitumen particles rise to the surface of the water where they combine to form a froth. The sand particles rise only a short distance and then fall back towards the bottom of the vessel. Figures for energy balance and for the composition of the extracted bitumen and the tailings are given for laboratory scale experiments. The technique is compared to the commercially used hot-water separation process.
Plasmid DNA Fingerprints Distinguish Pathotypes of<i>Xanthomonas campestris</i>pv.<i>citri,</i>the Causal Agent of Citrus Bacterial Canker Disease (1992)

Plasmid DNA was isolated from 54 strains of Xanthomonas campestris pv. citri, associated with different forms of citrus bacterial canker disease (CBCD). The number of plasmids per strain varied from one to five. A total of 24 plasmid bands with sizes from 7 to 100 kilobases (kb) were identified. Strains that had identical plasmid profiles were generally associated with the same form of CBCD. After digesting the plasmid DNA with each of three restriction endonucleases, 87 fragments with different sizes from about 1 to 30 kb were visualized (...)