gebhart/patrepeval huggingface dataset:
Xylitol Inhibits Growth and Blocks Virulence in Serratia marcescens (2021)

<i>Serratia marcescens</i> is an opportunistic nosocomial pathogen and causes wound and burn infections. It shows high resistance to antibiotics and its pathogenicity is mediated by an arsenal of virulence factors. Another therapeutic option to such infections is targeting quorum sensing (QS), which controls the expression of different <i>S. marcescens</i> virulence factors. Prevention of QS can deprive <i>S. marcescens</i> from its bacterial virulence without applying stress on the bacterial growth and facilitates the eradication of the bacteria by immunity. The objective of the current study is to explore the antimicrobial and antivirulence activities of xylitol against <i>S. marcescens</i>. Xylitol could inhibit the growth of <i>S. marcescens</i>. Sub-inhibitory concentrations of xylitol could inhibit biofilm formation, reduce prodigiosin production, and completely block protease activity. Moreover, xylitol decreased swimming motility, swarming motility and increased the sensitivity to hydrogen peroxide. The expression of <i>rsmA</i>, <i>pigP</i>, <i>flhC</i>, <i>flhD fimA</i>, fimC, <i>shlA bsmB</i>, and <i>rssB</i> genes that regulate virulence factor production was significantly downregulated by xylitol. In silico study showed that xylitol could bind with the SmaR receptor by hydrophobic interaction and hydrogen bonding, and interfere with the binding of the natural ligand with SmaR receptor. An in vivo mice survival test confirmed the ability of xylitol to protect mice against the virulence of <i>S. marcescens</i>. In conclusion, xylitol is a growth and virulence inhibitor in <i>S. marcescens</i> and can be employed for the treatment of <i>S. marcescens</i> wound and burn infections.
Construction and Working Mechanism of Sulfur Dioxide Sensor Utilizing Stabilized Zirconia and Metal Sulfate (1996)

An exploratory study was carried out to elucidate the fabrication principles of a potentiometric sensor utilizing stabilized zirconia (solid electrolyte) and a metal sulfate (auxiliary phase). Among the MgO‐, CaO‐, ‐stabilized zirconia (abbreviated as MSZ, CSZ, or YSZ) tested, only MSZ samples which contained 15 mole percent (m/o) MgO and were partially stabilized gave a stable sensor by being attached with , whereas almost fully stabilized MSZ (15 m/o MgO), partially stabilized MSZ (9 m/o MgO), CSZ (11 m/o CaO), or YSZ (8 m/o ) gave a stable device only when attached with a mixed auxiliary phase of . These facts indicated an active role by MgO, either segregated from the stabilized zirconia or added intentionally, for the devices. It is estimated that, together with and , MgO is an essential component of the interfacial compound which acts as an ionic bridge between stabilized zirconia ( conductor) and auxiliary phase ( conductor). The electromotive force (EMF) response of each device to followed Nernst's equation well for a two‐electron reaction per molecule, while the EMF dependence on oxygen concentration deviated slightly from the Nernstian behavior for the four‐electron reduction of . Such behavior is discussed based on the sensing mechanism proposed.
CXC chemokines, MIP‐2 and KC, induce P‐selectin‐dependent neutrophil rolling and extravascular migration in vivo (2001)

The purpose of this study was to examine the impact of CXC chemokines, i.e. macrophage inflammatory protein-2 (MIP-2) and KC, on leukocyte-endothelium interactions in detail and to evaluate the role of P-selectin by use of intravital microscopy in the mouse cremaster muscle. Administration of MIP-2 and KC provoked a dose (5 - 500 ng)- and time (0 - 4 h)-dependent increase in leukocyte rolling, adhesion and tissue recruitment. Neutrophils comprised more than 92% of the leukocyte response. Pretreatment with an antibody directed against P-selectin (RB40.34) significantly inhibited MIP-2- and KC-induced leukocyte rolling by more than 96%. This marked decrease in rolling abolished firm adhesion and extravascular accumulation of neutrophils (>89% reduction), suggesting that CXC chemokines induce P-selectin-dependent rolling, which in turn apparently is a precondition for the subsequent stationary adhesion and extravasation of neutrophils. Moreover, the extravascular recruitment of leukocytes was evaluated in whole-mounts of the cremaster muscle without preceding intravital microscopy. Using this approach, it was again observed that MIP-2- and KC-induced neutrophil accumulation was completely dependent onP-selectin function. In contrast to the CXC chemokines, administration of the classical chemoattractant formyl-methionyl leucyl phenylalanine (fMLP) did not provoke extravascular tissue accumulation of neutrophils. We could not detect gene expression of CXCR2 in murine endothelial cells, whereas neutrophils were positive, indicating that the stimulatory effect of CXC chemokines on leukocyte-endothelium interactions is not a direct effect on the endothelium but rather an indirect effect via activation of an intermediary tissue cell. However, challenge with MIP-2 and KC did not increase the number of degranulated mast cells. In conclusion, our data demonstrate that CXC chemokines induce all steps in the extravasation process of leukocytes, including rolling, adhesion and transmigration in vivo. Moreover, these results show that P-selectin plays a critical role in MIP-2 and KC provoked neutrophil recruitment as a critical mediator of initial leukocyte rolling. Additionally, our study suggest that a restricted action of MIP-2 and KC on neutrophils is far too simplistic to explain the complex mechanisms of action of CXC chemokines on neutrophil infiltration in vivo.
Incidences and Determinants of Functional Cure During Entecavir or Tenofovir Disoproxil Fumarate for Chronic Hepatitis B (2021)

HBsAg seroclearance rarely occurs in patients with chronic hepatitis B treated with ETV or TDF and is associated with low-level viremia, alanine aminotransferase flare, bilirubin level, and fatty liver.Functional cure of hepatitis B virus infection rarely occurred at an average annual rate of 0.22% during first-line oral antiviral treatment, with higher chances observed in patients with low-level viremia, high-level aminotransferase flare, elevation of serum bilirubin, and fatty liver.
Autoradiographical assessment of inflammation-targeting radioligands for atherosclerosis imaging: potential for plaque phenotype identification (2021)

Radioligands targeting inflammatory cell markers showed different levels of binding in atherosclerotic plaques and among plaque phenotypes. Different radioligands might be used for plaque detection and discerning early from vulnerable plaque. [<sup>111</sup>In]In-EC0800 and [<sup>111</sup>In]In-DANBIRT appear most suitable for plaque detection, while [<sup>67</sup>Ga]Ga-Pentixafor and [<sup>111</sup>In]In-DOTA-JR11 might be best suited for differentiation between plaque phenotypes.
Integration of Neuromorphic AI in Event-Driven Distributed Digitized Systems: Concepts and Research Directions (2022)

Increasing complexity and data-generation rates in cyber-physical systems and the industrial Internet of things are calling for a corresponding increase in AI capabilities at the resource-constrained edges of the Internet. Meanwhile, the resource requirements of digital computing and deep learning are growing exponentially, in an unsustainable manner. One possible way to bridge this gap is the adoption of resource-efficient brain-inspired "neuromorphic" processing and sensing devices, which use event-driven, asynchronous, dynamic neurosynaptic elements with colocated memory for distributed processing and machine learning. However, since neuromorphic systems are fundamentally different from conventional von Neumann computers and clock-driven sensor systems, several challenges are posed to large-scale adoption and integration of neuromorphic devices into the existing distributed digital-computational infrastructure. Here, we describe the current landscape of neuromorphic computing, focusing on characteristics that pose integration challenges. Based on this analysis, we propose a microservice-based framework for neuromorphic systems integration, consisting of a neuromorphic-system proxy, which provides virtualization and communication capabilities required in distributed systems of systems, in combination with a declarative programming approach offering engineering-process abstraction. We also present concepts that could serve as a basis for the realization of this framework, and identify directions for further research required to enable large-scale system integration of neuromorphic devices.
Link Performance Modeling of Interference Rejection Combining Receiver in System Level Evaluation for LTE-Advanced Downlink (2012)

The interference rejection combining (IRC) receiver, which can suppress inter-cell interference, is effective in improving the cell-edge user throughput. The IRC receiver is typically based on the minimum mean square error (MMSE) criteria, and requires a covariance matrix including the interference signals, in addition to a channel matrix from the serving cell. Therefore, in order to clarify the gain from the IRC receiver, the actual estimation error of these matrices should be taken into account. In a system performance evaluation, the link performance modeling of the IRC receiver, i.e., the output signal-to-interference-plus-noise power ratio (SINR) after IRC reception including the estimation errors, is very important in evaluating the actual performance of the IRC receiver in system level simulations. This is because these errors affect the suppression of the interference signals for the IRC receiver. Therefore, this paper investigates and proposes IRC receiver modeling schemes for the covariance matrix and channel estimation errors. As the modeling scheme for the covariance matrix, we propose a scheme that averages the conventional approximation using the complex Wishart distribution in the frequency domain to address issues that arise in a frequency selective fading channel. Furthermore, we propose a modeling scheme for the channel estimation error according to the ideal channel response of all cells and a channel estimation filter to address channel fading fluctuations. The results of simulations assuming the LTE/LTE-Advanced downlink with two transmitter and receiver antenna branches show that the proposed modeling scheme for the covariance matrix estimation error accurately approximates the performance of a realistic IRC receiver, which estimates the covariance matrix and channel matrix of the serving cell based on the demodulation reference signal (DM-RS), even in a frequency selective fading channel. The results also show that the proposed modeling scheme for the channel estimation error is a robust scheme in terms of the r.m.s. delay spread of a channel model compared to the scheme using the mean square error (MSE) statistic of the estimated channel coefficients based on a channel estimation filter.
Enabling application-specific integrated circuits on limited pattern constructs (2010)

Implementing sub-22nm designs using a limited set of pattern constructs can eliminate hotspot risk and can control systematic variability. Pattern regularity can incur a cell-level density penalty that is minimized or eliminated by co-optimization with circuits. More importantly, design with a limited set of pattern constructs can remove the limitations imposed by complex design rules, thus facilitating flexible synthesis of logic and memory blocks in place of hard IP.
Frozen protein arrays: A new method for arraying and detecting recombinant and native tissue proteins (2002)

DNA microarrays are powerful tools for high throughput analysis of gene expression; however, they do not measure protein expression. Current methods for producing protein arrays require sophisticated equipment or extensive protein modification. We developed a low overhead, customizable assay platform called frozen protein arrays that can detect native proteins in protein lysates. Frozen protein arrays were formed from a block of frozen histologic embedding compound containing an array of wells. The wells were filled with samples, which freeze and bond to the block. Cryosections were cut and transferred to nitrocellulose-coated slides. The reproducibility, linearity, and sensitivity was confirmed using frozen protein arrays filled with prostate specific antigen. Frozen protein arrays could detect native tissue proteins. The alpha1 subunit of NaK-ATPase was detected in rat kidneys with a coefficient of variation of 4.3-6.6%. Frozen protein array analysis indicated that the protein abundance decreased by 48.7% following renal ischemia, similar to the 40% decrease by Western blotting. We conclude that frozen protein arrays are a low cost, moderate size platform for arraying samples including protein lysates. Production of many identical frozen protein arrays is easy, inexpensive, and requires only small sample volumes. The method is gentle on proteins as they remain frozen during production.
Propellant Assisted Perforating -- An Effective Method for Reducing Formation Damage When Perforating (2001)

During the completion of a well the utilization of a propellant stimulation system immediately after or at the time of perforating has been demonstrated to provide sufficient stimulation energy to cleanup formation damage in the near wellbore region while remaining within the desired zone of interest. The focussed and virtually instantaneous nature of this technique means that it can be used in applications where more aggressive stimulation techniques may result in the increase of undesirable fluid production due to stimulation extension into adjoining regions. Propellant stimulation devices provide an inexpensive and effective method of dealing with near wellbore damage due to drilling, completion, or perforating in both producing and injecting environments.Standalone propellant stimulation techniques have been successfully utilized for a number of years in various areas of the world. The recent development of a propellant assisted perforating system means that the perforations and near wellbore region can be effectively stimulated at the instance of perforating. This advanced perforating system fuses perforating and propellant stimulation devices into a hybrid system - the well can be perforated and the near wellbore region stimulated all with one run in the hole. The development of propellant stimulation modeling software and high-speed electronic pressure recording devices has assisted in the development and verification of the technique's effectiveness in removing or reducing near wellbore damage.This paper will discuss the development history of this unique perforating and stimulation technique and the new analytical tools used in its advancement and ongoing application. A number of case histories are presented documenting the use and effectiveness of the stimulation method in a variety of environments and applications.
Quantum random bit generation using energy fluctuations in stimulated Raman scattering (2013)

Random number sequences are a critical resource in modern information processing systems, with applications in cryptography, numerical simulation, and data sampling. We introduce a quantum random number generator based on the measurement of pulse energy quantum fluctuations in Stokes light generated by spontaneously-initiated stimulated Raman scattering. Bright Stokes pulse energy fluctuations up to five times the mean energy are measured with fast photodiodes and converted to unbiased random binary strings. Since the pulse energy is a continuous variable, multiple bits can be extracted from a single measurement. Our approach can be generalized to a wide range of Raman active materials; here we demonstrate a prototype using the optical phonon line in bulk diamond.
A 10-GHz Global Clock Distribution Using Coupled (2003)

In this paper, a global clock network that incor- porates standing waves and coupled oscillators to distribute a high-frequency clock signal with low skew and low jitter is described. The key design issues involved in generating standing waves on a chip are discussed, including minimizing wire loss within an available technology. A standing-wave oscillator, which is a distributed oscillator that sustains ideal standing waves on lossy wires, is introduced. A clock grid architecture comprised of coupled standing-wave oscillators and differential low-swing clock buffers is presented, along with a compact circuit model for networks of oscillators. The measured results for a prototyped standing-wave clock grid operating at 10 GHz and fabricated in a 0.18- m 6M CMOS logic process are presented. A technique is proposed for on-chip skew measurements with subpicosecond precision.
Nuclear matrix proteins as proteomic markers of preneoplastic and cancer lesions : commentary re: G. Brunagel et al., nuclear matrix protein alterations associated with colon cancer metastasis to the liver. Clin. Cancer Res., 8: 3039-3045, 2002. (2002)

Only a pathologist can diagnose a cancer. This is accomplished by inspecting the visual features of the cancer cells, which include the marked variations in cellular structure termed pleomorphism. Disorganization and pleomorphism are a hallmark of cancer diagnosis and include highly variable
Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice (2015)

Mice lacking the growth hormone receptor (GHRKO) exhibit improved lifespan and healthspan due to loss of growth hormone signaling. Both the distribution and activity of brown and white adipose tissue (BAT and WAT) are altered in GHRKO mice, but the contribution of each tissue to age-related phenotypes has remained unclear. We therefore used whole-genome microarrays to evaluate transcriptional differences in BAT and WAT depots between GHRKO and normal littermates at six months of age. Our findings reveal a unique BAT transcriptome as well as distinctive responses of BAT to Ghr ablation. BAT from GHRKO mice exhibited elevated expression of genes associated with mitochondria and metabolism, along with reduced expression of genes expressed by monocyte-derived cells (dendritic cells [DC] and macrophages). Largely the opposite was observed in WAT, with increased expression of DC-expressed genes and reduced expression of genes associated with metabolism, cellular respiration and the mitochondrial inner envelope. These findings demonstrate divergent response patterns of BAT and WAT to loss of GH signaling in GHRKO mice. These patterns suggest both BAT and WAT contribute in different ways to phenotypes in GHRKO mice, with Ghr ablation blunting inflammation in BAT as well as cellular metabolism and mitochondrial biogenesis in WAT.
Triplet State Interactions between Nucleic Acid Bases in Solution at Room Temperature:  Intermolecular Energy and Electron Transfer (1996)

This study aims to provide information on the fate of triplet energy in DNA by considering the triplet-mediated reactions which occur between nucleic acid bases in solution, at room temperature. Following sensitization of base triplet states by acetone, the subsequent photophysics and photochemistry are highly dependent on the nature of the nucleotide pair under study. By establishing the direction of triplet energy transfer between pairs of mononucleotides, the relative triplet energy ordering was determined under physiologically relevant conditions, i.e. aqueous solution at room temperature. This order (C > U > G > A > T) is in agreement with that previously reported which was obtained at 77 K in rigid media. The absolute value for TMP triplet energy has been estimated as 310 kJ mol-1, based on triplet energy transfer studies involving acetophenone and 3-methoxyacetophenone. Determination of the triplet energy gaps between all mononucleotides, to within 1 kJ mol-1, has allowed an estimation of the absolute values of CMP (321 kJ mol-1), UMP (320 kJ mol-1), GMP (317 kJ mol-1), and AMP (314 kJ mol-1). The energy gaps between the triplet states are smaller than those reported at low temperature. This allows triplet energy transfer equilibria to be established in which a significant proportion of both triplets is present, unless thymine is present, in which case the dominant process is triplet energy transfer to the thymine. In any purine/pyrimidine (not thymine) pair, electron transfer from purine to pyrimidine is significant, producing the purine radical cation, which rapidly deprotonates to give the neutral radical. This process is most efficient for the guanosine−uracil combination and our evidence suggests that it is the purine triplet state which initiates the electron transfer. In the guanosine−adenosine system, there is no evidence of electron transfer and net triplet energy transfer is low due to a small triplet energy gap. This results in a relatively high proportion of both triplet states being observed in the equilibrium. These results show that DNA photochemistry should be highly sequence dependent and may have significance regarding the existence of “hot spots” in DNA photoproduct formation.
More Efficient Off-Policy Evaluation through Regularized Targeted Learning (2019)

We study the problem of off-policy evaluation (OPE) in Reinforcement Learning (RL), where the aim is to estimate the performance of a new policy given historical data that may have been generated by a different policy, or policies. In particular, we introduce a novel doubly-robust estimator for the OPE problem in RL, based on the Targeted Maximum Likelihood Estimation principle from the statistical causal inference literature. We also introduce several variance reduction techniques that lead to impressive performance gains in off-policy evaluation. We show empirically that our estimator uniformly wins over existing off-policy evaluation methods across multiple RL environments and various levels of model misspecification. Finally, we further the existing theoretical analysis of estimators for the RL off-policy estimation problem by showing their $O_P(1/\sqrt{n})$ rate of convergence and characterizing their asymptotic distribution.
Morphologic and histologic comparisons between in vivo and nuclear transfer derived porcine embryos (2007)

Nuclear transfer (NT) is an inefficient but invaluable tool of the biotechnology industry. This study looked at abnormalities associated with peri-implantation NT porcine embryos. Four experimental groups were examined: nonpregnant animals, in vivo pregnant animals, NT recipients, and manipulation control embryos (MC). Embryos (Day 10, 12, or 14) were evaluated for embryonic disc diameter, gross morphology, nucleoli density, and mitotic figure index. Day 12 (P < or = 0.03) and Day 14 (P < or = 0.01) NT embryos had increased numbers of nucleoli, and Day 14 NT embryos had an increased (P < or = 0.03) mitotic index compared to in vivo and MC embryos. In vivo produced Day 14 embryos had increased (P < or = 0.01) disk diameters when compared to other embryos except for MC Day 14, which also showed increases (P < or = 0.01) in disk diameter except when compared to in vivo produced Day 12 and Day 14 embryos. In vivo produced Day 12 had greater (P < or = 0.03) disk diameters when compared to NT and MC embryos except for MC Day 14, and in vivo produced Day 14 embryos, which had a significantly increased (P < or = 0.01) disk diameter. In vivo produced Day 14 embryos were morphologically more advanced (P < or = 0.01) than Day 14 NT and MC counterparts. NT embryos develop at a slower rate than their in vivo produced counterparts. The increase in nucleoli and mitotic index of NT embryos suggest the cell cycle may be affected or the NT embryos are employing other means to compensate for slow development. The techniques used during NT also appear to compromise embryo development.