gebhart/patrepeval huggingface dataset:
Evaluation of Blow/Fill/Seal extrusion through processing polymer contaminated with bacterial spores and endotoxin. (2004)

A study has been carried out to further the understanding of the extrusion process and its impact upon the quality of Blow/Fill/Seal product. Controlled challenges to the extrusion system, comprising low-density polyethylene granulate contaminated with characterized levels of Bacillus atrophaeus (ATCC 9372) endospores and Escherichia coli 055:B5 bacterial endotoxin, have been conducted. Batches of spore contaminated polymer, at challenge levels varying from 10(3) to 10(6) spores g(-1) polymer with derived D160 values ranging from 1.22 to 2.07 minutes, and endotoxin contaminated polymer, at challenge levels varying from 10(2) to 10(4) EU g(-1) polymer, were processed through a Blow/Fill/Seal machine employing Tryptone Soya Broth and Water for Injection as the fill mediums, respectively. Relationships have been established between the levels of challenge for each of spores and endotoxin and the extent of product contamination. The relationships allow for prediction of microbiological and pyrogenic quality based upon the microbiological and pyrogenic attributes of unprocessed polymeric granulate and for rationalized choices of polymeric granulate acceptance limits. It is stressed that the findings apply only to the particular Blow/Fill/Seal machine and to the specific conditions of machine operation.
Targeting MET Amplification as a New Oncogenic Driver (2014)

Certain genetically defined cancers are dependent on a single overactive oncogene for their proliferation and survival, a phenomenon known as "oncogene addiction". A new generation of drugs that selectively target such "driver oncogenes" manifests a clinical efficacy greater than that of conventional chemotherapy in appropriate genetically defined patients. MET is a proto-oncogene that encodes a receptor tyrosine kinase, and aberrant activation of MET signaling occurs in a subset of advanced cancers as result of various genetic alterations including gene amplification, polysomy, and gene mutation. Our preclinical studies have shown that inhibition of MET signaling either with the small-molecule MET inhibitor crizotinib or by RNA interference targeted to MET mRNA resulted in marked antitumor effects in cancer cell lines with MET amplification both in vitro and in vivo. Furthermore, patients with non-small cell lung cancer or gastric cancer positive for MET amplification have shown a pronounced clinical response to crizotinib. Accumulating preclinical and clinical evidence thus suggests that MET amplification is an "oncogenic driver" and therefore a valid target for treatment. However, the prevalence of MET amplification has not been fully determined, possibly in part because of the difficulty in evaluating gene amplification. In this review, we provide a rationale for targeting this genetic alteration in cancer therapy.
Design of a Self-powered Smart Mask for COVID-19 (2020)

Usage of a face mask has become mandatory in many countries after the outbreak of SARS-CoV-2, and its usefulness in combating the pandemic is a proven fact. There have been many advancements in the design of a face mask and the present treatise describes a face mask in which a simple textile triboelectric nanogenerator (TENG) serves the purpose of filtration of SARS-CoV-2. The proposed mask is designed with multilayer protection sheets, in which the first two layers act as triboelectric (TE) filter and the outer one is a smart filter. The conjugated effect of contact electrification, and electrostatic induction of the proposed smart mask are effective in inactivating the span of virus-ladden aerosols in a bidirectional way. Five pairs of triboseries fabrics i.e. nylon - polyester, cotton - polyester, poly(methyl methacrylate) - PVDF, lylon - PVDF and polypropylene - polyester have been optimized in this study in terms of their effective tribo-electric charge densities as 83.13, 211.48, 38.62, 69 and 74.25 nC/m2, respectively. This smart mask can be used by a wide range of people because of its simple mechanism, self-driven (harvesting mechanical energy from daily activities, e.g. breathing, talking, or other facial movements functionalities, and effective filtration efficiency and thus, it is expected to be potentially beneficial to slow down the devastating impact of COVID-19.
Homologous recombination-based genome editing by clade F AAVs is inefficient in the absence of a targeted DNA break (2019)

Abstract Adeno-associated virus (AAV) vectors are frequently used as donor templates for genome editing by homologous recombination. Although modification rates are typically under 1%, they are greatly enhanced by targeted double-stranded DNA breaks (DSBs). A recent report described clade F AAVs mediating high-efficiency homologous recombination-based editing in the absence of DSBs. The clade F vectors included AAV9 and a series isolated from human hematopoietic stem/progenitor cells (HSPCs). We evaluated these vectors by packaging homology donors into AAV9 and an AAVHSC capsid and examining their ability to insert GFP at the CCR5 or AAVS1 loci in human HSPCs and cell lines. As a control we used AAV6, which effectively edits HSPCs, but only when combined with a targeted DSB. Each AAV vector promoted GFP insertion in the presence of matched CCR5 or AAVS1 zinc finger nucleases (ZFNs), but none supported detectable editing in the absence of the nucleases. Rates of editing with ZFNs correlated with transduction efficiencies for each vector, implying no differences in the ability of donor sequences delivered by the different vectors to direct genome editing. Our results therefore do not support that clade F AAVs can perform high efficiency genome editing in the absence of a DSB.
Ligase Chain Reaction for Site-Directed In Vitro Mutagenesis (2003)

Before the advent of polymerase chain reaction (PCR) technology, many methods for site-directed mutagenesis basically relied on enzymatic extension of a mutagenic oligonucleotide annealed to a single-stranded template and amplification of the ligase-sealed double-stranded heteroduplex in an Escherichia coli host (1). Several techniques have been employed to enhance the frequency of clones containing the desired mutation by selecting against the parental strand through biological means or by in vitro manipulations (2–4).
Large format time-of-flight focal plane detector development (2005)

This paper reviews the progress of Advanced Scientific Concepts, Inc (ASC) large format flash ladar 3-D imaging systems for longer-range applications. Single-laser-pulse images are taken from a manned flight test at 1000 - 2000 ft demonstrating not only the 3-D mapping potential of the system but also its use in object identification. Gated images on the ground exemplify vehicle identification applications. Use of signal amplitude information in enhancing the 3-D image is also illustrated.
Molecular mechanisms of tumor suppression by LKB1 (2010)

The LKB1 tumor suppressor gene is frequently mutated in sporadic lung adenocarcinomas and cervical cancers and germline mutations are causative for Peutz-Jeghers syndrome characterized by gastrointestinal polyposis. The intracellular LKB1 kinase is implicated in regulating polarity, metabolism, cell differentiation, and proliferation - all functions potentially contributing to tumor suppression. LKB1 acts as an activating kinase of at least 14 kinases mediating LKB1 functions in a complex signaling network with partial overlaps. Regulation of the LKB1 signaling network is highly context dependent, and spatially organized in various cellular compartments. Also the mechanisms by which LKB1 activity suppresses tumorigenesis is context dependent, where recent observations are providing hints on the molecular mechanisms involved.
Solvent Extraction Studies of Lead Using Alamine 336 and Aliquat 336-S (1978)

Abstract New solvent extraction systems have been developed for the removal of lead ions from aqueous chloride solutions using the high-molecular-weight amines, Alamine 336 and Aliquat 336-S. The lead ions can be extracted with better than 80% efficiency using equal volumes of either 5% Alamine 336 or 5% Aliquat 336-S. The extractions are simple and rapid. The extracted lead can be stripped in both cases using EDTA
Effects of changes in roller compactor parameters on granulations produced by compaction (1992)

A Chilsonator (Model L-83, The Fitzpatrick Company, Elmhurst, IL) was studied to gain a better understanding of how compactor parameters influence product characteristics. The materials chosen for this study were Avicel PH 101, hydrous lactose and an acetaminophen blend. The blend consisted of 20% Avicel PH 101, 20% hydrous lactose and 60% acetaminophen crystals. The compactor parameters studied were the roll speed, horizontal feed speed and vertical feed speed. Various combinations of high, medium and low levels of these compactor parameters were tested. The system was modeled using a quadratic regression model. Changes in particle size distribution and recompressibility of the roller compacted granulations were used to monitor the effects of the changes in compactor parameter levels. The models differed for each of the materials evaluated. The response surface plots produced using the models helped in predicting the compactor parameter levels which would produce granulations with the necessary physical characteristics for successful tablet production.
Unified Uncertainty Analysis by the First Order Reliability Method (2008)

Two types of uncertainty exist in engineering. Aleatory uncertainty comes from inherent variations while epistemic uncertainty derives from ignorance or incomplete information. The former is usually modeled by the probability theory and has been widely researched. The latter can be modeled by the probability theory or nonprobability theories and is much more difficult to deal with. In this work, the effects of both types of uncertainty are quantified with belief and plausibility measures (lower and upper probabilities) in the context of the evidence theory. Input parameters with aleatory uncertainty are modeled with probability distributions by the probability theory. Input parameters with epistemic uncertainty are modeled with basic probability assignments by the evidence theory. A computational method is developed to compute belief and plausibility measures for black-box performance functions. The proposed method involves the nested probabilistic analysis and interval analysis. To handle black-box functions, we employ the first order reliability method for probabilistic analysis and nonlinear optimization for interval analysis. Two example problems are presented to demonstrate the proposed method.
Influenza Virus Infection Increases p53 Activity: Role of p53 in Cell Death and Viral Replication (2005)

ABSTRACT The induction of apoptotic cell death is a hallmark of influenza virus infection. Although a variety of cellular and viral proteins have been implicated in this process, to date no conserved cellular pathway has been identified. In this study, we report that the tumor suppressor protein p53 is essential for the induction of cell death in influenza virus-infected cells. In primary human lung cells, influenza virus increased p53 protein levels. This was also noted in the human lung cell line A549, along with the up-regulation of p53-dependent gene transcription. Reduction of p53 activity in A549 cells inhibited influenza virus-induced cell death as measured by trypan blue exclusion and caspase activity. These findings were not cell type specific. Influenza virus-induced cell death was absent in mouse embryo fibroblasts isolated from p53 knockout mice, which was not the case in wild-type mouse embryo fibroblasts, suggesting that p53 is a common cellular pathway leading to influenza virus-induced cell death. Surprisingly, inhibiting p53 activity led to elevated virus replication. Mechanistically, this may be due to the decrease in interferon signaling in p53-deficient cells, suggesting that functional p53 is involved in the interferon response to influenza infection. To our knowledge, these are the first studies demonstrating that p53 is involved in influenza virus-induced cell death and that inhibiting p53 leads to increased viral titers, potentially through modulation of the interferon response.
Backlog balancing flow control in high-speed data networks (2002)

The asynchronous transfer mode (ATM) has been accepted by the CCITT as the multiplexing and switching technique for the future B-ISDN. Flow control algorithms in high-speed networks are resources sharing policies implemented in a distributed manner. The open-loop control is too conservative, and may result in poor utilization of resources. On the other hand, the credit-based close-loop control would be too expensive to implement in practice. A simple rate-based flow control algorithm is proposed. The aim of flow control is to maximize the network utilization for achieving high throughput and tolerable delay for each virtual circuit (VC). In a resource sharing environment, this objective may also create network congestion when a cluster of aggressive VCs is contending for the same resource at a particular node. The basic idea of our flow control algorithm is to adjust the service rate of each node along the VC according to backlog discrepancies between neighboring nodes. The hand shaking procedure between any two consecutive nodes is carried out by a link-by-link feedback protocol. Each node will update its service rate periodically with a linear projection model on the flow dynamics and binary feedback information from downstream. Since the rate updating algorithm is designed to reduce the backlog discrepancy, it is expected that a nearly balanced backlog distribution throughout the VC can be achieved over the long run time. Furthermore, the problem of network congestion can be alleviated or totally avoided if all VCs in the network agree to comply with the some set of rules.
Fast lossless compression of whole slide pathology images using HEVC intra-prediction (2016)

The lossless compression of Whole Slide pathology Images (WSIs) using HEVC is investigated in this paper. Recently proposed intra-prediction algorithms based on differential pulse-code modulation (DPCM) and edge prediction provide significant bitrate improvements for a wide range of natural and screen content sequences, including WSIs. However, coding times remain relatively high due to the high number (35) of modes to be tested. In this paper, FastIn-tra, a novel method that requires testing only four modes is proposed. Among these four modes, FastIntra introduces a novel median edge predictor designed to accurately predict edges in different directionalities. Performance evaluations on various WSIs show average compression time reductions of 23.5% with important lossless coding improvements as compared to current block-wise intra-prediction and DPCM-based methods.
Vitamin B 12 -Stimulated Growth and Development of Jungermannia leiantha Grolle and Gymnocolea inflata (Huds.) Dum. (Hepaticae) (1985)

Exogenous vitamin B,2 supplied to axenically cultured gametophytes of Jungerman- nia leiantha Grolle (Jungermanniaceae) and Gymnocolea inflata (Huds.) Dum. (Lophoziaceae) significantly stimulated growth in both species. Pink-pigmented, facultative methylotrophic bacteria, which synthesize and accumulate vitamin B,2, have been regularlyfound associated with bryophytes. Our findings and those of others cited herein indicate that if the vitamin B2, synthesized by these bacteria, or from any other source, should become available, bryophytes and other embryophytes could benefit.
Expression of the Endothelial Leukocyte Adhesion Molecule‐1 (ELAM‐1) on Endothelial Cells in Experimental Gingivitis in Humans (1993)

In inflammatory conditions, mediators such as interleukin-1 (IL-1) are released by resident tissue cells as well as by infiltrating inflammatory cells. IL-1 activates endothelial cells causing them to express an adhesion molecule called endothelial leukocyte adhesion molecule-1 (ELAM-1). IL-1 is produced by macrophages, but can also be produced by activated keratinocytes. Here we present data from a study of experimentally induced gingivitis, showing the expression of ELAM-1 on endothelial cells even in tissue with little or only minor signs of clinical or histological inflammation. These results indicate that ELAM-1 is found on endothelial cells of the gingiva early in the course of experimental gingivitis, before overt clinical or histological evidence of inflammation is apparent.
Amphipathic Helices Support Function of Blood Coagulation Factor IXa (2000)

Blood coagulation factor IXa gains proteolytic efficiency upon binding to a phospholipid membrane. We have found that an amphipathic, membrane-binding peptide from the C2 domain of factor VIII, fVIII(2303)(-23), enhances proteolytic efficiency of factor IXa in the absence of phospholipid membranes. This enhancement is the result of a reduction in the K(M) for the substrate, factor X, with little effect on the k(cat). Enhanced function requires interaction of the gamma-carboxyglutamic acid (Gla) domains of factor IXa and factor X since (i) a synthetic peptide comprising the Gla domain of factor IXa and antibodies directed to the Gla domain of factor IXa inhibit this acceleration, (ii) the acceleration is Ca(II) dependent, and (iii) conversion of Gla-domainless factor X is not affected by the presence of fVIII(2303)(-23). The effect of fVIII(2303)(-23) on factor IXa parallels the enhanced function produced by phosphatidylserine-containing bilayers, and fVIII(2303)(-23) does not further enhance function of factor IXa when phospholipid vesicles are present. The critical feature of fVIII(2303)(-23) is apparently its amphipathic helix-forming structure [Gilbert, G. E., and Baleja, J. D. (1995) Biochemistry 34, 3022-3031] because other alpha-helical peptides such as a homologous peptide from the C2 domain of factor V and melittin have similar effects. Diastereomeric analogues of fVIII(2303)(-23) and melittin, which have reduced helical content, do not support factor IXa activity. A truncated peptide of fVIII(2303)(-23) with three C-terminal residues deleted retains alpha-helical content but loses capacity to enhance factor X cleavage, suggesting that a minimum length of alpha-helix is required. Although these results probably do not illuminate the physiologic function of the factor VIII peptide corresponding to fVIII(2303)(-23), they demonstrate a novel, membrane-mimetic role of amphipathic helical peptides in supporting function of factor IXa.
Timing performance of Hi-Rez detector for time-of-flight (TOF) PET (2006)

Positron emission tomography (PET)-based on time-of-flight (TOF) is desired to enhance the image quality by improving the noise variance in the reconstruction. This benchtop study evaluates the timing performance of the current Hi-Rez detector which is based on a 13/spl times/13 LSO array of 4 mm/spl times/4 mm/spl times/20 mm crystals and not optimized for TOF PET applications. A Hamamatsu R9779, fast, 51-mm-diameter PMT was used for some experiments in this study as a reference PMT and its time resolution was measured to be 160 ps with a plastic scintillator. The average crystal time resolution of two Hi-Rez detectors, coupled to a 2/spl times/2 array of Hamamatsu 25-mm-diameter R8619 PMTs at +1050 V, in coincidence was measured to be 733 ps. The average crystal energy resolutions for two detectors were measured 13.1% and 13.2%. The average crystal time resolution of two Hi-Rez detectors improved from 733 ps to 642 ps when the PMT voltage was increased to +1300 V. The Hi-Rez detector was originally optimized for good energy resolution to reduce scatter and high packing fraction to obtain high sensitivity and improved spatial resolution for clinical PET.
EVIDENCE THAT LARGE GRANULAR LYMPHOCYTES OF DONOR ORIGIN MEDIATE ACUTE GRAFT-VERSUS-HOST DISEASE (1989)

We have studied the phenotype of mononuclear cells infiltrating target organs of mice with acute graft-versus-host disease after bone marrow transplantation from H-2-identical donors. Infiltrating mononuclear cells with characteristics of large granular lymphocytes (LGL) were frequently found in close association with dead or dying epithelial cells in the skin, liver, and colon. The phenotype of these putative effector cells was Thy-1+, ASGM1+, Mac-1+, Lyt-1-, Lyt-2-, Ia-, which is characteristic of LGL. Differences in the Thy-1 allele between donor and host were used to demonstrate that these cells were of donor origin. Analysis of cytolytic function in GVHD splenocytes indicated high natural killer activity and low cytolytic T lymphocyte (CTL) activity. These findings suggest that an important effector cell in systemic acute graft-versus-host disease is a large granular lymphocyte of donor origin.
IC‐P‐039: Influence of the training library composition on a patch‐based label fusion method: Application to hippocampus segmentation on the ADNI dataset (2011)

The atrophy of medial temporal lobe structures is may serve as early biomarkers of Alzheimer's disease. The evaluation of hippocampus (HC) atrophy is estimated by volumetric studies requiring a segmentation step that can be very time consuming when done manually. This limitation can be overcome by using automatic segmentation methods. In this study, we propose to validate our nonlocal patch-based method [1] on the Alzheimer's Disease NeuroimagingInitiative (ADNI) database by segmenting the HC of Cognitively Normal (CN) subjects and patients with early Alzheimer's Disease (AD). We used images obtained from the ADNI database. For our experiments, we randomly selected 10 MRI of CN and 10 MRI of AD. The first experiment was designed to evaluate the accuracy of our segmentation method on a group constituting of CN and AD (8 CN and 8 AD). The second experiment was designed to investigate the impact of the composition of the training library. Three different training populations were built (i.e., the CN population: 8 CN, the AD population: 8 AD, and the mixed AD/ CN population: 4 CN and 4 AD). Through a leave-one-out procedure, our automatic segmentation method was applied on each of the 20 MRI scans. The quality of the obtained automatic segmentations was evaluated by estimating the Dice Kappa similarity index. For the first experiment, the median Dice Kappa values are presented in Table 1. The segmentation accuracy was significantly better (p-value = 0.002) for CN (median k = 0.883 for both HC) than for AD (median k = 0.838 for both HC). For the second experiment, Figure 1 and Table 2 show the Dice Kappa similarity index for both studied populations according to the training library composition. For both populations, the best median Kappa values were obtained with the mixed CN / AD training library (k = 0.875 for CN and k = 0.835 AD). First, we demonstrated that our patch-based method provides high segmentation accuracy for both CN and AD populations. Second, we showed that the characteristic of the training library has a significant impact on the segmentation accuracy. 1. Coupe, P., et al., Neuroimage, 2011. 54(2): p. 940-54. Kappa index distribution according to the composition of the training library for both studied populations.
Studies on Seven-membered Ring Compounds. III (1962)

Substitution reaction of 1-position in cyclohepta [b] pyrrol-8 (1H)-one derivatives (Ia-d) was examined and the reaction similar to that in indole compounds was found to be present. Reaction of (I) with acrylonitrile afforded 1-(2-cyanoethyl)-8H-cyclo-hepta [b] pyrrol-8 (1H)-one derivatives (IIa-c). Application of benzoyl chloride, ethyl bromoacetate, and aminoalkyl chloride to the sodium salt of (I), formed by reaction with sodium amide, afforded the corresponding 1-benzoyl-, 1-ethoxycarbonylmethyl-, and 1-aminoalkyl-8H-cyclohepta [b] pyrrol-8 (1H)-one derivatives. As the tricyclic and tetracyclic tropone derivatives corresponding to carboline derivative, Fischer's indole cyclization reaction of 1-methyl-4-piperidone 2-troponylhydrazone hydrochloride (IX) and 1-oxo-1, 2, 3, 4-tetrahydroquinolizinium bromide 2-troponylhydrazone (XII) was examined.