gebhart/patrepeval huggingface dataset:
Isorhamnetin alleviates lipopolysaccharide-induced inflammatory responses in BV2 microglia by inactivating NF-κB, blocking the TLR4 pathway and reducing ROS generation (2018)

Isorhamnetin, which is a flavonoid predominantly found in fruits and leaves of various plants, including Hippophae rhamnoides L. and Oenanthe javanica (Blume) DC, is known to possess various pharmacological effects. However, the anti‑inflammatory potential of isorhamnetin remains poorly studied. Therefore, the present study aimed to investigate the inhibitory potential of isorhamnetin against inflammatory responses in lipopolysaccharide (LPS)‑stimulated BV2 microglia. To measure the effects of isorhamnetin on inflammatory mediators and cytokines, and reactive oxygen species (ROS) generation, the following methods were used: cell viability assay, griess assay, ELISA, reverse transcriptase‑polymerase chain reaction, flow cytometry, western blotting and immunofluorescence staining. The results revealed that isorhamnetin significantly suppressed LPS‑induced secretion of pro‑inflammatory mediators, including nitric oxide (NO) and prostaglandin E2, without exhibiting significant cytotoxicity. Consistent with these results, isorhamnetin inhibited LPS‑stimulated expression of regulatory enzymes, including inducible NO synthase and cyclooxygenase‑2 in BV2 cells. Isorhamnetin also downregulated LPS‑induced production and expression of pro‑inflammatory cytokines, such as tumor necrosis factor‑α and interleukin‑1β. The mechanism underlying the anti‑inflammatory effects of isorhamnetin was subsequently evaluated; this flavonoid inhibited the nuclear factor (NF)‑κB signaling pathway by disrupting degradation and phosphorylation of inhibitor κB‑α in the cytoplasm and blocking translocation of NF‑κB p65 into the nucleus. In addition, isorhamnetin effectively suppressed LPS‑induced expression of Toll‑like receptor 4 (TLR4) and myeloid differentiation factor 88. It also suppressed the binding of LPS with TLR4 in BV2 cells. Furthermore, isorhamnetin markedly reduced LPS‑induced generation of ROS in BV2 cells, thus indicating a strong antioxidative effect. Collectively, these results suggested that isorhamnetin may suppress LPS‑mediated inflammatory action in BV2 microglia through inactivating the NF‑κB signaling pathway, antagonizing TLR4 and eliminating ROS accumulation. Further studies are required to fully understand the anti‑inflammatory effects associated with the antioxidant capacity of isorhamnetin; however, the findings of the present study suggested that isorhamnetin may have potential benefits in inhibiting the onset and treatment of neuroinflammatory diseases.
CEO: Consistency of Encoding and Overhearing in Network Coding-Aware Routing (2013)

Network coding-aware routing attempts to find coding opportunities between an incoming flow and existing flows in wireless ad hoc networks. However, we find that a problem of most proposed coding-aware routing schemes is that they may misidentify the coding opportunities. Specifically, the opportunity misidentification may appear when a packet is about to be re-encoded. We call this the re-encoding problem. To solve this problem, we propose a principle called consistency of encoding and overhearing (CEO). By adhering to CEO, the encoding node is able to avoid misidentifying coding opportunities, thus ensuring the successful decoding of all encoded packets. In this letter, we first show the importance of CEO by analysis in a simple topology. Then, we introduce a distributed way to apply CEO to a coding-aware routing scheme, and show the improved network performance with CEO by simulation in different scenarios.
ChemInform Abstract: Dioxygen Activation in the Photochemistry of Some Oxo‐metalloporphyrin Complexes. (1987)

Abstract UV‐Irradiation of the peroxo‐complexes (I) induces elimination of O 2 and generation of the corresponding oxometalloporphyrins (II).
Correction to: RE‑MIND2: comparative effectiveness of tafasitamab plus lenalidomide versus polatuzumab vedotin/bendamustine/rituximab (pola‑BR), CAR‑T therapies, and lenalidomide/rituximab (R2) based on real‑world data in patients with relapsed/refractory diffuse large B‑cell lymphoma (2023)

Following the online publication of this paper, the authors have learned that the National Comprehensive Cancer Network (NCCN) requires some editorial changes relating to how their guidelines are referenced within the paper. The original article has been corrected.
Modeling, simulation, and analysis of active filter systems using generalized state space averaging method (2004)

In this paper, modeling and analysis of active filter systems based on the generalized state space averaging method is presented. The non-linear equations of the system are converted to a linear state space model. A fast and reliable approximation of the system is achieved in this method. Long execution time, divergence problem, and huge produced files, which are difficulties associated with the conventional modeling techniques of active filter systems, are not present in the proposed method. In addition, the developed models can be used for the purpose of control and stability assessment. The method is applicable to different topologies and control techniques. In this paper, modeling and simulation results are presented for typical single-phase shunt, single-phase series, and three-phase shunt active filter systems. Experimental results are also provided for the verification of the proposed approach.
X-ray computed tomography using projection x-ray microscope (2002)

We have applied projection X-ray microscope for three- dimensional (3D) structure analysis by means of cone-beam computed tomography. The projection images of small insect, Omiscus Porcellio, were recorded in every 1 degree for whole direction (360 degree) with a stepping motor controlled sample rotator. The images were recorded with cooled CCD camera (HAMAMATSU C4880) which detect X-ray directly. The 3D image was reconstructed from cone-beam projections using back-projection algorithm. The resolution of the reconstructed 3D image (256 x 256 x 256 pixels) was about 20 micrometers . The digestive organs were clearly visualized in 3D.
Toward model‐driven engineering of supramolecular copolymers (2014)

ABSTRACT The coassembly of two oligo‐( p ‐phenylene vinylene) (OPV) derivatives with different sizes and opposite chirality is studied. Short R ‐chiral ROPV 3 molecules experience a high energetic mismatch penalty when incorporated in helices formed by long S ‐chiral SOPV 4 molecules. In contrast, SOPV 4 easily coassembles into helices dominated by ROPV 3 . As a result, the coassembly behavior (i.e., mixing or phase separation of ROPV 3 and SOPV 4 within the assemblies) highly depends on the ratio between both molecular building blocks. By a combination of experiments and models, the assembly pathways are analyzed. Furthermore, the model allows identifying key parameters in the coassembly behavior, such as the cooperativity and the mismatch penalties. The model‐driven approach is anticipated to be generally applicable in the engineering of functional supramolecular copolymers. This article is dedicated to the 70th birthday of Jean Fréchet and we thank him for being a continuous source of inspiration for our group. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53 , 385–391
Effect of Rhesus D incompatibility on schizophrenia depends on offspring sex (2008)

Rhesus D incompatibility increases risk for schizophrenia, with some evidence that risk is limited to male offspring. The purpose of this study is to determine whether risk for schizophrenia due to Rhesus D incompatibility differs by offspring sex using a nuclear family-based candidate gene approach and a meta-analysis approach. The genetic study is based on a sample of 277 nuclear families with RHD genotype data on at least one parent and at least one child diagnosed with schizophrenia or related disorder. Meta-analysis inclusion criteria were (1) well-defined sample of schizophrenia patients with majority born before 1970, (2) Rhesus D incompatibility phenotype or genotype data available on mother and offspring, and by offspring sex. Two of ten studies, plus the current genetic study sample, fulfilled these criteria, for a total of 358 affected males and 226 affected females. The genetic study found that schizophrenia risk for incompatible males was significantly greater than for compatible offspring (p=0.03), while risk for incompatible and compatible females was not significantly different (p=.32). Relative risks for incompatible males and females were not significantly different from each other. Meta-analysis using a larger number of affected males and females supports their difference. Taken together, these results provide further support that risk of schizophrenia due to Rhesus D incompatibility is limited to incompatible males, although a weak female incompatibility effect cannot be excluded. Sex differences during fetal neurodevelopment should be investigated to fully elucidate the etiology of schizophrenia.
Femtosecond laser annealing effects on indium oxide nanowire transistors (2009)

We report the effects of annealing of the metal contacts to the nanowires using femtosecond laser pulses focused on the contact regions. The annealing induces significant shifts in the threshold voltage, and significantly reduces the drain conductance (gdS) of the nanowire transistors in the saturation region, along with modest improvements in the subthreshold slopes. Low frequency (1/f) noise measurements in these devices reveal that Hooge's constant is reduced following laser annealing presumably due to improved channel-metal interface and lowered Schottky barrier height.
Identification of DVA Interneuron Regulatory Sequences in Caenorhabditis elegans (2013)

We identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi-species phylogenetic comparisons.
The Incidence of Heterotopic Ossification After Hip Arthroscopy (2012)

The addition of indomethacin is effective in reducing the incidence of HO after hip arthroscopy and should be especially considered in male patients who undergo osteoplasty for correction of symptomatic FAI.
DSP-based DC servo acceleration control without speed sensor (2003)

A DC servo acceleration control system is proposed. When the servo motor is regulated by the proposed acceleration control system, the total servo system becomes the acceleration controlled system which is fixed to the nominal mechanical dynamics in the presence of parameter variations and force disturbance. Hence, both fast motion control and force control can be carried out easily. For the purpose of realizing this fast and accurate control, the proposed system is constructed by the software algorithm of a digital signal processor (DSP). Moreover, as the system uses only information from a position sensor, such as rotary encoder, it is economical and produces little noise at low motor speeds. Experimental and numerical examples show that the method is valid for both fast motion control and accurate force control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
AdaptDiffuser: Diffusion Models as Adaptive Self-evolving Planners (2023)

Diffusion models have demonstrated their powerful generative capability in many tasks, with great potential to serve as a paradigm for offline reinforcement learning. However, the quality of the diffusion model is limited by the insufficient diversity of training data, which hinders the performance of planning and the generalizability to new tasks. This paper introduces AdaptDiffuser, an evolutionary planning method with diffusion that can self-evolve to improve the diffusion model hence a better planner, not only for seen tasks but can also adapt to unseen tasks. AdaptDiffuser enables the generation of rich synthetic expert data for goal-conditioned tasks using guidance from reward gradients. It then selects high-quality data via a discriminator to finetune the diffusion model, which improves the generalization ability to unseen tasks. Empirical experiments on two benchmark environments and two carefully designed unseen tasks in KUKA industrial robot arm and Maze2D environments demonstrate the effectiveness of AdaptDiffuser. For example, AdaptDiffuser not only outperforms the previous art Diffuser by 20.8% on Maze2D and 7.5% on MuJoCo locomotion, but also adapts better to new tasks, e.g., KUKA pick-and-place, by 27.9% without requiring additional expert data. More visualization results and demo videos could be found on our project page.
Influence of Soft Tissue Preservation in Total Hip Arthroplasty: A 16-Year Experience. (2018)

The direct superior approach to the hip results in excellent stability with a dislocation rate of 0.17%. The patient's perception of pain and recovery is dramatically improved with preservation of the iliotibial band.
Substitutions in the protease (3Cpro) gene of poliovirus can suppress a mutation in the 5' noncoding region (1990)

The poliovirus mutant 5NC-11 has a 4-base insertion at position 70 within the 5' untranslated region and is deficient in RNA synthesis. Revertants from 5NC-11 were isolated, showing a partial recovery of wild-type levels of RNA synthesis. The 5' noncoding region of those revertants contained the mutation intact; mix-and-match experiments with the cDNA from these revertants revealed that a restricted region within the 3C gene was the site of the suppressing mutations in the revertants. The suppressors were point mutations, confirmed by introducing them into the 3C gene by site-directed mutagenesis. Although complementation studies indicated that the suppressors were cis active, we believe that protein changes rather than RNA sequence alterations are responsible for the suppression because RNA changes that did not alter protein sequence had no effect, whereas various protein alterations were suppressive. The results therefore imply that protein 3C interacts with the 5' end of the RNA and may play a role in RNA replication.
Monolithic integration of silicon electronics and photonics (2011)

A low power modulator is monolithically integrated with a radiation hardened CMOS driver. This integrated optoelectronic device demonstrates 1.68mW power consumption at 2Gbps.
Molecular Orientation of Membrane-Anchored Mucin Glycoprotein Mimics (2007)

Mucin glycoproteins contribute to a wide range of cell-surface phenomena. Their dense glycosylation is believed to confer structural rigidity as well as molecular extension beyond the glycocalyx, crucial to interaction with the cellular environment. However, controlled investigations of the relationships between glycosylation, rigidity, and extension of membrane-bound mucins or similar macromolecules are lacking, largely because of the absence of tractable experimental models. We have therefore made use of recently developed synthetic mucin mimetics, in which the core α-GalNAc monosaccharides of natural mucins are conjugated to a lipidated polymer backbone and anchored to fluid, solid-supported lipid membranes, and fluorescence interference contrast microscopy, an optical technique that provides nanometer-scale topographic information about objects near a reflective interface, to measure the orientation of the mucin mimics relative to the membrane plane. Data from two independent probes, fluorophores conjugated directly to the polymer backbone and fluorescent proteins bound to the sugar groups, unexpectedly show that the mucin mimic molecules lie flat along the membrane. Rigidity and core glycosylation are therefore insufficient to ensure molecular projection outward from a membrane surface.
Vaccines for Tuberculosis: Novel Concepts and Recent Progress (2005)

Three-quarters of a century after the introduction of Mycobacterium bovis BCG, the first tuberculosis vaccine, new vaccines for tuberculosis are finally entering clinical trials. This breakthrough is based not only on advances in proteomics and genomics which have made the construction of new vaccines possible, but also on a greatly expanded knowledge of the immunology of tuberculosis. Here we review our current understanding of how Mycobacterium tuberculosis subverts or survives the host's immune response to cause disease and why the current vaccination strategy, which relies on BCG, is only partially successful in countering the pathogen. This provides a background for describing the new generation of vaccines designed to supplement or replace the current vaccine and the different approaches they take to stimulate immunity against M. tuberculosis.
N-Chlorotaurine, a Long-Lived Oxidant Produced by Human Leukocytes, Inactivates Shiga Toxin of Enterohemorrhagic Escherichia coli (2012)

N-chlorotaurine (NCT), the main representative of long-lived oxidants produced by granulocytes and monocytes, is known to exert broad-spectrum microbicidal activity. Here we show that NCT directly inactivates Shiga toxin 2 (Stx2), used as a model toxin secreted by enterohemorrhagic Escherichia coli (EHEC). Bacterial growth and Stx2 production were both inhibited by 2 mM NCT. The cytotoxic effect of Stx2 on Vero cells was removed by ≥5.5 mM NCT. Confocal microscopy and FACS analyses showed that the binding of Stx2 to human kidney glomerular endothelial cells was inhibited, and no NCT-treated Stx2 entered the cytosol. Mass spectrometry displayed oxidation of thio groups and aromatic amino acids of Stx2 by NCT. Therefore, long-lived oxidants may act as powerful tools of innate immunity against soluble virulence factors of pathogens. Moreover, inactivation of virulence factors may contribute to therapeutic success of NCT and novel analogs, which are in development as topical antiinfectives.
Topoisomerase-I PS506 as a Dual Function Cancer Biomarker (2015)

Novel biomarkers for cancer diagnosis and therapy selection are urgently needed to facilitate early detection and improve therapy outcomes. We have previously identified a novel phosphorylation site at serine 506 (PS506) on topoisomerase-I (topo-I) and have shown that it is widely expressed in cell lines derived from several cancers, including lung cancer, but is low in cell lines derived from non-cancerous tissues. Here we have investigated how PS506 expression in lung tissue specimens correlates with their malignant status. We find that PS506 expression is significantly elevated in malignant tumors of non-small cell lung cancer (NSCLC) compared to adjacent, non-cancerous lung tissue and benign lung tumors. PS506 expression was up to 6-fold higher in malignant specimens than in paired non-malignant tissue. Using the well-characterized NIH/NCI 60-cell line panel, we correlate the most elevated expression levels of PS506 in lung, ovarian, and colon cancer cells lines with increased sensitivity to camptothecin, a plant alkaloid that targets topo-I. This is consistent with our earlier studies in a smaller sampling of cell lines and with our finding that PS506 increases topo-I DNA binding. Two widely used chemotherapeutic drugs for ovarian and colon cancer, topotecan and irinotecan, respectively, are derived from camptothecin. Irinotecan has also displayed efficacy in clinical trials of NSCLC. Our results suggest that elevated PS506 expression may correlate with clinical chemosensitivity to these agents in ovarian, colon, and NSCLC. PS506 may therefore serve as a biomarker for diagnosis or therapy selection.
Phagocyte subsets and lymphocyte clonal deletion behind ineffective immune response toStaphylococcus aureus (2015)

Lack of known mechanisms of protection against Staphylococcus aureus in humans is hindering development of efficacious vaccines. Preclinical as well as clinical data suggest that antibodies play an important role against S. aureus. For instance, certain hypogammaglobulinaemic patients are at increased risk of staphylococcal infections. However, development of effective humoral response may be dampened by converging immune-evasion mechanisms of S. aureus. We hypothesize that B-cell proliferation induced by staphylococcal protein A (SpA) and continuous antigen exposure, without the proper T-cell help and cytokine stimuli, leads to antigen-activated B-cell deletion and anergy. Recent findings suggest an important role of type I neutrophils (PMN-I) and conventionally activated macrophages (M1) against S. aureus, while alternatively activated macrophages (M2) favour biofilm persistence and sepsis. In addition, neutrophil-macrophage cooperation promotes extravasation and activation of neutrophils as well as clearance of bacteria ensnared in neutrophil extracellular traps. Activation of these processes is modulated by cytokines and T cells. Indeed, low CD4(+) T-cell counts represent an important risk factor for skin infections and bacteraemia in patients. Altogether, these observations could lead to the identification of predictive correlates of protection and ways for shifting the balance of the response to the benefit of the host through vaccination.
Online Estimation of Architectural Vulnerability Factor for Soft Errors (2008)

As CMOS technology scales and more transistors are packed on to the same chip, soft error reliability has become an increasingly important design issue for processors. Prior research has shown that there is significant architecture-level masking, and many soft error solutions take advantage of this effect. Prior work has also shown thatthe degree of such masking can vary significantly across workloads and between individual workload phases, motivating dynamic adaptation of reliability solutions for optimal cost and benefit. For such adaptation, it is important to be able to accurately estimate the amount ofmasking or the architecture vulnerability factor (AVF) online, while the program is running. Unfortunately, existing solutions for estimating AVF are often based on offline simulators and hard to implement in real processors. This paper proposes a novel way of estimating AVF online, using simple modifications to the processor. The estimation method applies to both logic and storage structures on the processor. Compared to previous methodsfor estimating AVF, our method does not require any offline simulation or calibration for different workloads. We tested our method with a widely used simulator from industry, for four processor structures and for 100 to 200 intervals of each of eleven SPEC benchmarks. The results show that our method provides acceptably accurate AVF estimates at runtime. The absoluteerror rarely exceeds 0.08 across all application intervals for all structures, and the mean absolute error for a given application and structure combination is always within 0.05.