gebhart/patrepeval huggingface dataset:
Fourier Transform Infrared Spectrometry (1983)

The theory and instrumentation for Fourier transform infrared spectrometry are discussed. These instruments measure infrared spectra of the same quality as spectra measured on grating spectrometers in about one thousandth of the time. Their sensitivity advantage for spectra measured in equal times is between a factor of 10 and 100. Commercial spectrometers are now available from nine vendors in North America. Important areas of chemistry include atmospheric monitoring, surface chemistry, and on-line identification of chromatographically separated materials. Many new biochemical and biomedical applications are also becoming apparent, including investigations of phase transitions in lipids and studies of the biocompatibility of implant polymers.
Apolipoprotein A-I is required for cholesteryl ester accumulation in steroidogenic cells and for normal adrenal steroid production. (1996)

In addition to its ability to remove cholesterol from cells, HDL also delivers cholesterol to cells through a poorly defined process in which cholesteryl esters are selectively transferred from HDL particles into the cell without the uptake and degradation of the lipoprotein particle. The HDL-cholesteryl ester selective uptake pathway is known to occur in human, rabbit, and rodent hepatocytes where it may contribute to the clearance of plasma cholesteryl ester. The selective uptake pathway has been studied most extensively in steroidogenic cells of rodents in which it accounts for 90% or more of the cholesterol destined for steroid production or cholesteryl ester accumulation. In this study we have used apo A-I-, apo A-II-, and apo E-deficient mice created by gene targeting in embryonic stem cells to test the importance of the three major HDL proteins in determining cholesteryl ester accumulation in steroidogenic cells of the adrenal gland, ovary, and testis. apo E and apo A-II deficiencies were found to have only modest effects on cholesteryl ester accumulation. In contrast, apo A-I deficiency caused an almost complete failure to accumulate cholesteryl ester in steroidogenic cells. These results suggest that apo A-I is essential for the selective uptake of HDL-cholesteryl esters. The lack of apo A-I has a major impact on adrenal gland physiology causing diminished basal corticosteroid production, a blunted steroidogenic response to stress, and increased expression of compensatory pathways to provide cholesterol substrate for steroid production.
Differential Expression of Two β-Galactoside-Binding Lectins in the Reproductive Tracts of Pregnant Mice1 (1996)

Two beta-galactoside-binding proteins were isolated from uteroplacental complexes of pregnant mice and identified as the S-Lac lectins galectin-1 and galectin-3. The spatiotemporal pattern of appearance of those proteins was determined by immunocytochemistry. Galectin-1 was present in all tissue compartments of the uterus except the luminal and glandular epithelium. It was found in the uteri of animals from all preimplantation stages of pregnancy, as well as in those from nonpregnant, ovariectomized, or sexually immature animals. After implantation of the embryo, cells of the decidua basalis were labeled, as were granular metrial gland cells, all trophoblastic elements of the placenta, the myometrium, and nondecidualized endometrium. By contrast, there was little evidence of galectin-3 in the uteri of nonpregnant animals or during the preimplantation stages of pregnancy. However, immunoreactive material was observed in endometrial cells of the primary decidual zone immediately after implantation and at later stages of pregnancy in the decidua basalis, metrial gland, and all trophoblastic elements of the placenta. There was no evidence of galectin-3 in the myometrium or nondecidualized endometrium. After parturition, amounts of galectin-3 in the endometrium and metrial triangle appeared to decrease as the implantation sites were resorbed. These data suggested that the function of galectin-1 is one of tissue maintenance, whereas the function of galectin-3 is related specifically to pregnancy.
Signal-transducing protein phosphorylation cascades mediated by Ras/Rho proteins in the mammalian cell: the potential for multiplex signalling (1996)

The features of three distinct protein phosphorylation cascades in mammalian cells are becoming clear. These signalling pathways link receptor-mediated events at the cell surface or intracellular perturbations such as DNA damage to changes in cytoskeletal structure, vesicle transport and altered transcription factor activity. The best known pathway, the Ras-->Raf-->MEK-->ERK cascade [where ERK is extracellular-signal-regulated kinase and MEK is mitogen-activated protein (MAP) kinase/ERK kinase], is typically stimulated strongly by mitogens and growth factors. The other two pathways, stimulated primarily by assorted cytokines, hormones and various forms of stress, predominantly utilize p21 proteins of the Rho family (Rho, Rac and CDC42), although Ras can also participate. Diagnostic of each pathway is the MAP kinase component, which is phosphorylated by a unique dual-specificity kinase on both tyrosine and threonine in one of three motifs (Thr-Glu-Tyr, Thr-Phe-Tyr or Thr-Gly-Tyr), depending upon the pathway. In addition to activating one or more protein phosphorylation cascades, the initiating stimulus may also mobilize a variety of other signalling molecules (e.g. protein kinase C isoforms, phospholipid kinases, G-protein alpha and beta gamma subunits, phospholipases, intracellular Ca2+). These various signals impact to a greater or lesser extent on multiple downstream effectors. Important concepts are that signal transmission often entails the targeted relocation of specific proteins in the cell, and the reversible formation of protein complexes by means of regulated protein phosphorylation. The signalling circuits may be completed by the phosphorylation of upstream effectors by downstream kinases, resulting in a modulation of the signal. Signalling is terminated and the components returned to the ground state largely by dephosphorylation. There is an indeterminant amount of cross-talk among the pathways, and many of the proteins in the pathways belong to families of closely related proteins. The potential for more than one signal to be conveyed down a pathway simultaneously (multiplex signalling) is discussed. The net effect of a given stimulus on the cell is the result of a complex intracellular integration of the intensity and duration of activation of the individual pathways. The specific outcome depends on the particular signalling molecules expressed by the target cells and on the dynamic balance among the pathways.
TAK-701, a Humanized Monoclonal Antibody to Hepatocyte Growth Factor, Reverses Gefitinib Resistance Induced by Tumor-Derived HGF in Non–Small Cell Lung Cancer with an EGFR Mutation (2010)

Most non-small cell lung cancer (NSCLC) tumors with an activating mutation of the epidermal growth factor receptor (EGFR) are initially responsive to EGFR tyrosine kinase inhibitors (TKI) such as gefitinib but ultimately develop resistance to these drugs. Hepatocyte growth factor (HGF) induces EGFR-TKI resistance in NSCLC cells with such a mutation. We investigated strategies to overcome gefitinib resistance induced by HGF. Human NSCLC cells with an activating EGFR mutation (HCC827 cells) were engineered to stably express HGF (HCC827-HGF cells). HCC827-HGF cells secreted large amounts of HGF and exhibited resistance to gefitinib in vitro to an extent similar to that of HCC827 GR cells, in which the gene for the HGF receptor MET is amplified. A MET-TKI reversed gefitinib resistance in HCC827-HGF cells as well as in HCC827 GR cells, suggesting that MET activation induces gefitinib resistance in both cell lines. TAK-701, a humanized monoclonal antibody to HGF, in combination with gefitinib inhibited the phosphorylation of MET, EGFR, extracellular signal-regulated kinase, and AKT in HCC827-HGF cells, resulting in suppression of cell growth and indicating that autocrine HGF-MET signaling contributes to gefitinib resistance in these cells. Combination therapy with TAK-701 and gefitinib also markedly inhibited the growth of HCC827-HGF tumors in vivo. The addition of TAK-701 to gefitinib is a promising strategy to overcome EGFR-TKI resistance induced by HGF in NSCLC with an activating EGFR mutation.
Wireless Mobility Management with Prediction, Delay Reduction and Resource Management in 802.11 Networks (2014)

In 802.11 wireless infrastructure networks, as the mobile node moves from one access point to another, the active connections will not be badly dropped if the handoff is smooth and if there are sufficient resources reserved in the target access point. In a 5x5 grid of access points, within a 6x6 grid of regions, by location tracking and data mining, we predict the mobility pattern of mobile node with good accuracy. The pre-scanning of mobile nodes, along with pre-authenticating neighbouring access points and pre-reassociation is used to reduce the scan delay, authentication delay and re-association delay respectively. The model implements first stage reservation by using prediction results and does second stage reservation based on the packet content type, so that sufficient resources can be reserved when the mobile node does the handoff to the next access point. The overall mobility management scheme thus reduces the handoff delay. The performance simulations are done to verify the proposed model.
Search-based improvement of subsystem decompositions (2005)

The subsystem decomposition of a software system degrades gradually during its lifetime and therefore it gets harder and harder to maintain. As a result this decomposition needs to be reconditioned from time to time. The problem is to determine a suitable subsystem decomposition that can be used as a basis for future maintenance tasks. This paper describes a new methodology that computes such a subsystem decomposition by optimizing metrics and heuristics of good subsystem design. The main idea is to treat this task as a search problem and to solve it using a genetic algorithm.
Learning Spatio-Temporal Features with Two-Stream Deep 3D CNNs for Lipreading. (2019)

We focus on the word-level visual lipreading, which requires recognizing the word being spoken, given only the video but not the audio. State-of-the-art methods explore the use of end-to-end neural networks, including a shallow (up to three layers) 3D convolutional neural network (CNN) + a deep 2D CNN (e.g., ResNet) as the front-end to extract visual features, and a recurrent neural network (e.g., bidirectional LSTM) as the back-end for classification. In this work, we propose to replace the shallow 3D CNNs + deep 2D CNNs front-end with recent successful deep 3D CNNs --- two-stream (i.e., grayscale video and optical flow streams) I3D. We evaluate different combinations of front-end and back-end modules with the grayscale video and optical flow inputs on the LRW dataset. The experiments show that, compared to the shallow 3D CNNs + deep 2D CNNs front-end, the deep 3D CNNs front-end with pre-training on the large-scale image and video datasets (e.g., ImageNet and Kinetics) can improve the classification accuracy. Also, we demonstrate that using the optical flow input alone can achieve comparable performance as using the grayscale video as input. Moreover, the two-stream network using both the grayscale video and optical flow inputs can further improve the performance. Overall, our two-stream I3D front-end with a Bi-LSTM back-end results in an absolute improvement of 5.3% over the previous art on the LRW dataset.
Formation of a ternary complex by human XPA, ERCC1, and ERCC4(XPF) excision repair proteins. (1994)

The xeroderma pigmentosum complementation group A (XP-A) protein, XPA, has recently been expressed in Escherichia coli in a soluble and fully functional form. An affinity column was prepared by linking the XPA protein to a solid support. When HeLa cell-free extract capable of excision repair was applied to the column, > 99.9% of the proteins were in the flow-through. However, the flow-through fraction lacked excision activity. The activity was restored by adding the high salt (1 M KCl) eluate of the column to the flow-through fraction. The XPA protein-bound fraction was tested for specific proteins by an in vitro complementation assay with a panel of cell-free extracts from DNA repair-deficient human and rodent cell lines. The XPA-bound fraction complemented cell-free extracts of excision repair cross-complementing 1 (ERCC-1), ERCC-4 (XP-F), and XP-A mutants. We conclude that the XPA damage recognition protein makes a ternary complex with the ERCC1/ERCC4(XPF) heterodimer with a potential nuclease function.
A Common Pharmacophore for a Diverse Set of Colchicine Site Inhibitors Using a Structure-Based Approach (2005)

Modulating the structure and function of tubulin and microtubules is an important route to anticancer therapeutics, and therefore, small molecules that bind to tubulin and cause mitotic arrest are of immense interest. A large number of synthetic and natural compounds with diverse structures have been shown to bind at the colchicine site, one of the major binding sites on tubulin, and inhibit tubulin assembly. Using the recently determined X-ray structure of the tubulin:colchicinoid complex as the template, we employed docking studies to determine the binding modes of a set of structurally diverse colchicine site inhibitors. These binding models were subsequently used to construct a comprehensive, structure-based pharmacophore that in combination with molecular dynamics simulations confirms and extends our understanding of binding interactions at the colchicine site.
Interactions of cytokine gene polymorphisms in prostate cancer risk (2007)

Prostate cancer (CaP) is the second leading cause of cancer death in American men. Chronic inflammation has been one of several factors associated with the development of CaP. Single-nucleotide polymorphisms (SNPs) in cytokine genes have been associated with increased inflammation, increased cytokine production and possibly increased CaP risk. However, the effects of cytokine SNPs on CaP susceptibility have not been consistent. Using the genomic DNA collected in a CaP case-control study (557 cases and 547 controls), we pilot tested the interactions of nine functionally characterized SNPs of three cytokine genes in CaP risk using the multivariate adaptive regression splines (MARS)-logit models. African-Americans with the IL10-819TT genotype had a lower CaP risk [odds ratio (OR) = 0.27, 95% confidence interval (CI) = 0.07-1.01], but subjects with the genotype combination of IL1B-511CT/TT and IL10-592CC had a higher CaP risk (OR = 2.56, 95% CI = 1.09-6.02). In Caucasians, higher CaP risk was associated with the IL10-1082AG/GG genotype (OR = 3.62, 95% CI = 1.42-9.28), the genotype combination of IL10-1082AA plus IL1B-31TT/TC (OR = 2.92, 95% CI = 1.13-7.55) and the genotype combination of TNF-238GG plus IL10-592AA (OR = 2.14, 95% CI = 1.05-4.38). Our results highlight the importance of cytokine SNPs and their interactions in CaP risk.
Three-Dimensional Microtissue Assay for High-Throughput Cytotoxicity of Nanoparticles (2012)

Traditional in vitro nanotoxicity researches are conducted on cultured two-dimensional (2D) monolayer cells and thereby cannot reflect organism response to nanoparticle toxicities at tissue levels. This paper describes a new, high-throughput approach to test in vitro nanotoxicity in three-dimensional (3D) microtissue array, where microtissues are formed by seeding cells in nonsticky microwells, and cells are allowed to aggregate and grow into microtissues with defined size and shape. Nanoparticles attach and diffuse into microtissues gradually, causing radial cytotoxicity among cells, with more cells being killed on the outer layers of the microtissue than inside. Three classical toxicity assays [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] (MTT), glucose-6-phosphate dehydrogenase (G6DP), and calcein AM and ethidium homodimer (calcein AM/EthD-1)] have been adopted to verify the feasibility of the proposed approach. Results show that the nanotoxicities derived from this method are significantly lower than that from traditional 2D cultured monolayer cells (p < 0.05). Equipped with a microplate reader or a microscope, the nanotoxicity assay could be completed automatically without transferring the microtissue, ensuring the reliability of toxicity assay. The proposed approach provides a new strategy for high-throughput, simple, and accurate evaluation of nanoparticle toxicities by combining 3D microtissue array with a panel of classical toxicity assays.
Transplantation of Neural Progenitor and Stem Cells: Developmental Insights May Suggest New Therapies for Spinal Cord and Other CNS Dysfunction (1999)

Multipotent neural progenitors and stem cells may integrate appropriately into the developing and degenerating central nervous system. They may also be effective in the replacement of genes, cells, and nondiffusible factors in either a widespread or a more circumscribed manner, depending on the therapeutic demands of the clinical situation. In addition, they may be uniquely responsive to some types of neurodegenerative conditions. We believe that these various appealing capabilities are the normal expression of basic biologic properties and attributes of a stem cell. The therapeutic utility of some of those properties is illustrated in this review of ongoing work in our laboratory, particularly with regard to spinal dysfunction. In these examples, we believe we have tapped into a mechanism that underlies a remarkable degree of natural plasticity programmed into the nervous system at the cellular level, and we have now exploited those properties for therapeutic ends.
Identification and Characterization of Ich-3, a Member of the Interleukin-1β Converting Enzyme (ICE)/Ced-3 Family and an Upstream Regulator of ICE (1996)

We report here the isolation and characterization of a new member of the ice/ced-3 family of cell death genes, named ich-3. The predicted amino acid sequence of Ich-3 protein shares 54% identity with murine interleukin-1beta converting enzyme (ICE). Overexpression of ich-3 in Rat-1 and HeLa cells induces apoptosis, which can be inhibited by CrmA and Bcl-2. The mRNA and proteins of ich-3 are dramatically induced in vivo upon stimulation with lipopolysaccharide, an inducer of septic shock. The ich-3 gene product can be cleaved by cytotoxic T cells granule serine protease granzyme B, suggesting that Ich-3 may mediate apoptosis induced by granzyme B. Ich-3 does not process proIL-1beta directly but does promote proIL-1beta processing by ICE. These results suggest that Ich-3 may play a very important role in apoptosis and inflammatory responses and may be an upstream regulator of ICE.
Fluoroscopy as an Imaging Means for Computer-Assisted Surgical Navigation (1999)

AbstractObjective: Intraoperative fluoroscopy is a valuable tool for visualizing underlying bone and surgical tool positions in orthopedic procedures. Disadvantages of this technology include the need for continued radiation exposure for visual control, and cumbersome means of alignment. The purpose of this article was to highlight a new concept for a computer-assisted freehand navigation system that uses single intraoperatively acquired fluoroscopic images as a basis for real-time navigation of surgical toolsMaterials and Methods: Optoelectronic markers are placed on surgical tools, a patient reference, and the fluoroscope to track their position in space. Projection properties of the fluoro-scope are acquired through an initial precalibration procedure using a tracked radiopaque phantom grid. Corrections are applied to compensate for both the fluoroscope's image intensifier distortions and the mechanical bending of the C-arm frame. This enables real-time simulation of surgical tool positions simultaneously in several single-shot fluoroscopic images. In addition, through optoelec-tronically tracked digitization of a target viewpoint, the fluoroscope can be numerically aligned at precise angles relative to the patient without any X-ray exposureResults: This article shows the feasibility of this technology through its use in cadaver trials to perform the difficult task of distal locking of femoral nails.Key Words: C-armfluoroscopic image registrationcomputer-integrated surgerydistal lockingfemoral nail
Matrix Regulation of Lung Injury, Inflammation, and Repair: The Role of Innate Immunity (2006)

Mechanisms that regulate host defense after noninfectious tissue injury are incompletely understood. Our laboratory is interested in the role of the extracellular matrix glycosaminoglycan hyaluronan in the regulation of lung inflammation and fibrosis. We have identified key roles for two cell surface receptor systems that interact with hyaluronan to control lung inflammation and tissue repair. Hematopoietic CD44 is necessary to clear hyaluronan fragments that are produced after lung injury. Failure to clear hyaluronan fragments leads to unremitting inflammation. However, in the absence of CD44, alveolar macrophages continue to produce chemokines in response to hyaluronan fragments, implicating another receptor system in controlling macrophage effector function. We found that Toll-like receptors 2 and 4 (TLR2 and TLR4) are responsible for macrophage inflammatory gene expression in response to hyaluronan fragments. Although TLR2 and TLR4 initiate the innate immune response in noninfectious inflammation, they have a protective role against lung injury on alveolar epithelial cells.
On analyzing and improving COPE performance (2010)

COPE is a new architecture for unicasts in wireless mesh networks that employs opportunistic network coding to improve total throughput. Katti et al. showed through experiments that this system significantly improves the throughput of wireless networks with UDP traffic, and several attempts have been made to analyze the COPE performance. However, they are not completely satisfactory. In this paper, we give a new analysis of COPE, and argue that the key to COPE's success lies in the interaction between COPE and the MAC protocol. The local fairness enforced by the MAC protocol among competing nodes play an important role here. Based on the analysis, we also propose a simple modification to the COPE system that can further improve the network throughput.
A simple breath test for tuberculosis using ion mobility: A pilot study (2016)

Tuberculosis (TB) remains one of the world's major health burdens with 9.6 million new infections globally. Though considerable progress has been made in reduction of TB incidence and mortality, there is a continuous need for lower cost, simpler and more robust means of diagnosis. One method that may fulfil these requirements is in the area of breath analysis. In this study we analysed the breath of 21 patients with pulmonary or extra-pulmonary TB, recruited from a UK teaching hospital (University Hospital Coventry and Warwickshire) before or within 1 week of commencing treatment for TB. TB diagnosis was confirmed by reference tests (mycobacterial culture), histology or radiology. 19 controls were recruited to calculate specificity; these patients were all interferon-gamma release assay negative (T.SPOT(®).TB, Oxford Immunotec Ltd.). Whole breath samples were collected with subsequent chemical analysis undertaken by Ion Mobility Spectrometry. Our results produced a sensitivity of 81% and a specificity of 79% for all cases of TB (pulmonary and extra-pulmonary). Though lower than other studies analysing pulmonary TB alone, we believe that this technique shows promise, and a higher sensitivity could be achieved by further improving our sample capture methodology.