gebhart/patrepeval huggingface dataset:
Registration of physical space to laparoscopic image space for use in minimally invasive hepatic surgery (2000)

While laparoscopes are used for numerous minimally invasive (MI) procedures, MI liver resection and ablative surgery is infrequently performed. The paucity of cases is due to the restriction of the field of view by the laparoscope and the difficulty in determining tumor location and margins under video guidance. By merging MI surgery with interactive, image-guided surgery (IIGS), we hope to overcome localization difficulties present in laparoscopic liver procedures. One key component of any IIGS system is the development of accurate registration techniques to map image space to physical or patient space. This manuscript focuses on the accuracy and analysis of the direct linear transformation (DLT) method to register physical space with laparoscopic image space on both distorted and distortion-corrected video images. Experiments were conducted on a liver-sized plastic phantom affixed with 20 markers at various depths. After localizing the points in both physical and laparoscopic image space, registration accuracy was assessed for different combinations and numbers of control points (n) to determine the quantity necessary to develop a robust registration matrix. For n = 11, average target registration error (TRE) was 0.70 +/- 0.20 mm. We also studied the effects of distortion correction on registration accuracy. For the particular distortion correction method and laparoscope used in our experiments, there was no statistical significance between physical to image registration error for distorted and corrected images. In cases where a minimum number of control points (n = 6) are acquired, the DLT is often not stable and the mathematical process can lead to high TRE values. Mathematical filters developed through the analysis of the DLT were used to prospectively eliminate outlier cases where the TRE was high. For n = 6, prefilter average TRE was 17.4 +/- 153 mm for all trials; when the filters were applied, average TRE decreased to 1.64 +/- 1.10 mm for the remaining trials.
IL-7 Administration to Humans Leads to Expansion of CD8+ and CD4+ Cells but a Relative Decrease of CD4+ T-Regulatory Cells (2006)

Lymphopenia is a serious consequence of HIV infection and the administration of cancer chemotherapeutic agents. Although growth factors can be administered to patients to increase circulating neutrophils, there is no effective method to stimulate CD8+ lymphocyte production in humans, in vivo. This report is the first to describe the administration of recombinant interleukin-7 to humans and demonstrates the ability of this cytokine to mediate selective increases in CD4+ and CD8+ lymphocytes along with a decrease in the percentage of CD4+ T-regulatory cells. These studies suggest an important role for interleukin-7 in the treatment of patients with lymphopenia.
Speech recognition over the Internet using Java (1999)

A speech recognition system based on an Internet client-server model is presented in this paper. A Java applet records the voice at the client computer, sends the recorded speech file over the Internet, and the server computer recognizes the speech and displays the recognized text back to the user. Using this structure, an isolated digit recognition application was realized.
A Small Sun in an Etui: Possibilities in HCPV- (2006)

This paper discusses on possibilities of HCPV, including (1) cost (2) reliability (3) performance and (4) applications. The reduction of the cost is achieved by the reduction of the material itself. The material is not special. HCPV does not covered by special materials including pure Si, TCO, Ru-based dye, or Pt electrode or other materials using CVD or other vacuum process. HCPV modules are made without special tools. Local assembly is also possible. The weight of the 300 W HCPV module is 22 kg corresponding 0.07 kg/W. It is about 70% of the MC-Si flat-plate modules and less than half of the high efficiency tandem thin film modules. The recent 1-year field test done in Japan showed that the HCPV generated 1.6 times energy per area than that of the crystalline Si module (fixed installation). This implies that the HCPV has an advantage not only desert area but wet and cloudy area. Intensive reliability tests were done to the HCPV module. One of the keys is lifetime of the receiver against 20 years of accumulated concentrated UV flux in wet environment and other accelerated environment. Finally, the new applications of HCPV including rooftop installation and see-through design are discussed
Cationic liposomal delivery of plasmid to endothelial cells measured by quantitative flow cytometry (1996)

Cationic liposomes are potentially important gene transfer vehicles, capable of conjugating with anionic DNA by condensation. Flow cytometry was used to examine quantitatively the incorporation of DNA-liposome complex into murine capillary lung endothelial cells. The plasmid DNA, a pSV-β-galactosidase vector, was covalently labeled with ethidium monoazide by photoactivation. The cationic liposome consisted of egg phosphatidylcholine (90%), cholesterol (5%), and stearylamine (5%). The number of plasmid molecules contained within each cell as a function of exposure time was estimated from fluorescence intensity. Fluorescently labeled plasmid is detectable after 10 min and increases with continued exposure, but at a decreasing rate, up to 2160 min. After 2160 min each cell, on average, contains approximately 10,000 plasmid molecules. Following transfection, a single cell unimodal population was detected by flow cytometry, suggesting that all cells participate in transfection equally. Furthermore, cell cycle analysis indicates that the entry of DNA-liposome complex is independent of cell cycle. © 1996 John Wiley & Sons, Inc.
ATP-dependent remodeling and acetylation as regulators of chromatin fluidity (1999)

It has become widely accepted that modification of nucleosome structure is an important regulatory mechanism. The hypothesis that the acetylation of histones is involved in regulation was first formed over thirty years ago by Allfrey and colleagues (Allfrey et al. 1964). Subsequent genetic studies suggested that complexes that utilize ATP hydrolysis to alter chromatin structure might also play a regulatory role. In the past 5 years, numerous ATP-dependent remodeling complexes, acetyltransferases, and acetyltransferase complexes have been isolated and characterized. With the identification of these complexes, it is now possible to examine how these complexes modulate gene expression, and how the action of these complexes can be coordinated. The two major classes of chromatin modifying complexes that have been characterized differ in whether or not they use covalent modification to alter chromatin structure (recent reviews include Felsenfeld et al. 1996; Hartzog and Winston 1997; Tsukiyama and Wu 1997; Gregory and Horz 1998; Imhof and Wolffe 1998; Kadonaga 1998; Kuo and Allis 1998; Mizzen and Allis 1998; Pollard and Peterson 1998; Varga-Weisz and Becker 1998; Workman and Kingston 1998). The first class consists of histone acetyltransferase (HAT) and deacetylase complexes, which, respectively, add and remove acetyl groups from the amino termini of the four core histones; increased acetylation is usually (but not always) associated with activation of gene expression, whereas decreased acetylation is associated with repression of gene expression. The second class consists of ATP-dependent chromatin remodeling complexes, which alter chromatin structure by changing the location or conformation of the nucleosome. These structural changes are accomplished without covalent modification, and can be involved in either activation or repression. In addition to these two major classes of complexes, there are also other recently identified complexes such as FACT, DRIP/ARC, and SPT4/SPT5 that help the transcription machinery contend with nucleosome structure (Hartzog et al. 1998; LeRoy et al. 1998; Orphanides et al. 1998; Wada et al. 1998; Naar et al. 1999; Rachez et al. 1999). The mode of action of these other complexes is not yet understood. This review focuses on ATP-dependent remodeling complexes and how these complexes interact with acetylation complexes to regulate gene expression.
A memory controller with an integrated graphics processor (2002)

The paper describes the SX graphics accelerator. It is a programmable processor built into a workstation memory system. The goal of the SX is to achieve performance comparable to that of low end 2D and 3D graphics processors and to surpass low end imaging performance, at the lowest possible cost. The SX contains an integer vector processor, with an instruction set tailored to the needs of image processing and multimedia as well as 2D and 3D graphics. It can directly access data in both video and main memory, allowing accelerated processing on images up to 512 Mbyte in size. The SX offers a cost-effective method of providing a rich graphics and image processing capability compared to traditional workstation and accelerator approaches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Calcium Entry Mediated by GLR3.3, an Arabidopsis Glutamate Receptor with a Broad Agonist Profile (2006)

The amino acids glutamate (Glu) and glycine (Gly) trigger large, rapid rises in cytosolic Ca(2+) concentration and a concomitant rise in membrane potential (depolarization) in plants. The possibility that plant homologs of neuronal ionotropic glutamate receptors mediate these neuron-like ionic responses was tested in Arabidopsis (Arabidopsis thaliana) seedlings using a combination of Ca(2+) measurements, electrophysiology, and reverse genetics. The membrane depolarization triggered by Glu was greatly reduced or completely blocked in some conditions by mutations in GLR3.3, one of the 20 GLR genes in Arabidopsis. The same mutations completely blocked the associated rise in cytosolic Ca(2+). These results genetically demonstrate the participation of a glutamate receptor in the rapid ionic responses to an amino acid. The GLR3.3-independent component of the depolarization required Glu concentrations above 25 mum, did not display desensitization, and was strongly suppressed by increasing extracellular pH. It is suggested to result from H(+)-amino acid symport. Six amino acids commonly present in soils (Glu, Gly, alanine, serine, asparagine, and cysteine) as well as the tripeptide glutathione (gamma-glutamyl-cysteinyl-Gly) were found to be strong agonists of the GLR3.3-mediated responses. All other amino acids induced a small depolarization similar to the non-GLR, putative symporter component and in most cases evoked little or no Ca(2+) rise. From these results it may be concluded that sensing of six amino acids in the rhizosphere and perhaps extracellular peptides is coupled to Ca(2+) signaling through a GLR-dependent mechanism homologous to a fundamental component of neuronal signaling.
COMPARISON OF VAGINAL TOLERANCE TESTS OF SPERMICIDAL PREPARATIONS IN RABBITS AND MONKEYS (1969)

Summary. In order to decide whether the rabbit method or the rhesus monkey test is better suited for routine vaginal tolerance tests of spermicidal preparations, combined trials employing both techniques were carried out in the two laboratories in which the tests had been developed. A `double-blind' experimental design was used in which three unknown, coded compounds were tested jointly in both laboratories and evaluated independently and reciprocally after transatlantic exchange of the resulting histological material. Both test methods and the scoring systems employed in the assessment of findings are described and illustrated by representative photomicrographs. There was good agreement between both methods for two of the three preparations tested. For the third preparation, the rabbit test results were more consistent with the available clinical data than those of the monkey test. It was concluded that the rabbit technique is more sensitive than the monkey test. Since it has several obvious practical advantages over the latter, it is proposed that the rabbit vagina test should be generally adopted as the standard method for establishing the local tolerance of new spermicidal preparations for vaginal use.
Isolation and characterization of a macrophage-derived heparin-binding growth factor. (1990)

Human mononuclear cells were plated in culture, and the conditioned media of these cells were analyzed by heparin-Sepharose affinity chromatography. The fractions were tested for growth factor activity as measured by the stimulation of DNA synthesis in BALB/c 3T3 cells. After 2 d in culture, two peaks of heparin-binding growth factor (HBGF) activity were detected, one eluting with 0.5 M NaCl, which could be shown to be platelet-derived growth factor (PDGF)-like, and the other eluting with 1.0 M NaCl. After 7-11 d in culture, when monocytes had clearly differentiated into macrophages, greater than 95% of the HBGF activity in conditioned medium consisted of the 1.0 M NaCl elution peak. This activity, which was designated macrophage-derived HBGF (MD-HBGF), was found to be a cationic heat-resistant polypeptide with a molecular weight in the range of 14-25 kDa. Analysis using Western blots and specific neutralizing antisera, as well as comparative heparin affinity analysis, indicated that MD-HBGF was not identical to other heparin-binding 3T3 cell growth factors known to be produced by macrophages, such as PDGF (AB, AA, and BB forms), acidic fibroblast growth factor, and basic fibroblast growth factor. In addition to stimulating mitogenesis in 3T3 cells, MD-HBGF also stimulated the proliferation of vascular smooth muscle cells, but did not stimulate the proliferation of vascular endothelial cells.
Multiuser Detection (1998)

From the Publisher:
The development of multiuser detection techniques is one of the most important recent advances in communications technology. This self-contained and comprehensive book sets out the basic details of multiuser detection, starting with simple examples and progressing to state-of-the-art applications. The only prerequisites assumed are undergraduate-level probability, linear algebra, and digital communications. The book contains over 240 exercises and will be a suitable textbook for electrical engineering students. It will also be an ideal self-study guide for practicing engineers, as well as a valuable reference volume for researchers in communications, information theory, and signal processing.
Inducing α-Helices in Short Oligopeptides through Binding by an Artificial Hydrophobic Cavity (2010)

Short peptides were induced into alpha-helix conformations in water through enclathration to an artificial hydrophobic cavity. Peptides with two aromatic residues showed high affinity for the host, and these intermolecular aromatic-aromatic interactions specifically drove the helical folding of short peptides.
Liver X receptors as integrators of metabolic and inflammatory signaling (2006)

The liver X receptors (LXRs) are nuclear receptors that play central roles in the transcriptional control of lipid metabolism. LXRs function as nuclear cholesterol sensors that are activated in response to elevated intracellular cholesterol levels in multiple cell types. Once activated, LXRs induce the expression of an array of genes involved in cholesterol absorption, efflux, transport, and excretion. In addition to their function in lipid metabolism, LXRs have also been found to modulate immune and inflammatory responses in macrophages. Synthetic LXR agonists promote cholesterol efflux and inhibit inflammation in vivo and inhibit the development of atherosclerosis in animal models. The ability of LXRs to integrate metabolic and inflammatory signaling makes them particularly attractive targets for intervention in human metabolic disease.
Efficiency of Immunotoxin Cytotoxicity Is Modulated by the Intracellular Itinerary (2012)

Pseudomonas exotoxin-based immunotoxins, including LMB-2 (antiTac(F(v))-PE38), are proposed to traffic to the trans-Golgi network (TGN) and move by a retrograde pathway to the endoplasmic reticulum, where they undergo translocation to the cytoplasm, a step that is essential for cytotoxicity. The retrograde transport pathways used by LMB-2 are not completely understood, so it is unclear if transit through specific organelles is critical for maximal cytotoxic activity. In this study, we used Chinese hamster ovary (CHO) cell lines that express chimeric constructs of CD25, the Tac antigen, attached to the cytoplasmic domain of the TGN-targeted transmembrane proteins, TGN38 and furin. These chimeras are both targeted to the TGN, but the itineraries they follow are quite different. LMB-2 was incubated with the two cell lines, and the efficiency of cell killing was determined using cell viability and cytotoxicity assays. LMB-2 that is targeted through the endocytic recycling compartment to the TGN via Tac-TGN38 kills the cells more efficiently than immunotoxins delivered through the late endosomes by Tac-furin. Although the processing to the 37 kDa active fragment was more efficient in Tac-furin cells than in Tac-TGN38 cells, this was not associated with enhanced cytotoxicity - presumably because the toxin was also degraded more rapidly in these cells. These data indicate that trafficking through specific organelles is an important factor modulating toxicity by LMB-2.
p53 Functions as a Cell Cycle Control Protein in Osteosarcomas (1990)

Mutations in the p53 gene have been associated with a wide range of human tumors, including osteosarcomas. Although it has been shown that wild-type p53 can block the ability of E1a and ras to cotransform primary rodent cells, it is poorly understood why inactivation of the p53 gene is important for tumor formation. We show that overexpression of the gene encoding wild-type p53 blocks the growth of osteosarcoma cells. The growth arrest was determined to be due to an inability of the transfected cells to progress into S phase. This suggests that the role of the p53 gene as an antioncogene may be in controlling the cell cycle in a fashion analogous to the check-point control genes in Saccharomyces cerevisiae.
Beyond the technology: Software systems for proactive portfolio management (2000)

Software companies boast the latest in interactive technology to solve all the CRE director’s problems, but this is rarely the whole answer, part of the answer or even the answer at all. This paper explores and categorises the generic attributes of software systems and the many factors it is necessary to consider in their purchase and implementation. How systems can deal with performance measurement, management of the many tasks that need to be undertaken, togather with the complexities of project management, financial management and keeping track of outsourced activities are all important. Mere replication of existing management procedures does not generally provide the best benefits. Guidance is put forward which might assist in assessing the wider aspects of how information and knowledge are used. By reference to case study it is shown how such an approach can lead to a better, more practical end solution as well as avoiding many of the pitfalls of implementation. It is at that final hurdle of implementation that a high number of systems fail.
Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software (2019)

In recent years, many software packages for identifying structural variants (SVs) using whole-genome sequencing data have been released. When published, a new method is commonly compared with those already available, but this tends to be selective and incomplete. The lack of comprehensive benchmarking of methods presents challenges for users in selecting methods and for developers in understanding algorithm behaviours and limitations. Here we report the comprehensive evaluation of 10 SV callers, selected following a rigorous process and spanning the breadth of detection approaches, using high-quality reference cell lines, as well as simulations. Due to the nature of available truth sets, our focus is on general-purpose rather than somatic callers. We characterise the impact on performance of event size and type, sequencing characteristics, and genomic context, and analyse the efficacy of ensemble calling and calibration of variant quality scores. Finally, we provide recommendations for both users and methods developers.
Distinct Mechanisms Trigger Apoptosis in Human Immunodeficiency Virus Type 1-Infected and in Uninfected Bystander T Lymphocytes (1998)

Apoptosis is a main feature of AIDS pathogenesis and is thought to play a role in the progressive decrease of CD4+ T lymphocytes in infected individuals. To determine whether apoptosis occurs in infected and/or in uninfected peripheral blood T lymphocytes, we have used a recombinant human immunodeficiency virus type 1 (HIV-1) infectious clone expressing the green fluorescent protein (GFP). Using flow cytometry, we have determined the incidence of apoptosis by either terminal transferase dUTP nick end labeling or annexin-V assays in different cell subpopulations, i.e., in CD4+ or CD8+ T cells that were GFP positive or negative. After HIV-1 infection of purified peripheral blood lymphocytes, we observed that apoptosis occurred mostly in infected CD4+ peripheral blood lymphocytes. Remarkably, the presence of monocyte-derived macrophages in the culture increased dramatically the apoptosis of uninfected bystander T lymphocytes, while apoptosis in HIV-infected T lymphocytes was not changed. We therefore demonstrate that HIV-induced apoptosis results from at least two distinct mechanisms: (i) direct apoptosis in HIV-infected CD4+ T lymphocytes and (ii) indirect apoptosis in uninfected T cells mediated by antigen-presenting cells.
pH-Solubility relations of chenodeoxycholic and ursodeoxycholic acids: physical-chemical basis for dissimilar solution and membrane phenomena. (1980)

We examined by titration the electrochemical properties, apparent pK (pK'a), precipitation pH, and undissociated bile acid solubilities of chenodeoxycholic acid and its 7 beta epimer, ursodeoxycholic acid and their glycine conjugates as functions of a number of physical-chemical variables. Despite comparable pK'a values, ursodeoxycholic acid and its glycine conjugate precipitated from H2O(37 degrees C) at pH values of 8.0-8.1 and 6.5-7.4 whereas chenodeoxycholic acid and its glycine conjugate precipitated at pH values of 7.0-7.1 and 4.,-5.0, respectively. These differences were related to the low solubility of undissociated ursodeoxycholic acid in water (53 microM) and in ursodeoxycholic micelles (saturation ratio of anion:acid, 90-400:1) compared with the higher solubility of chenodeoxycholic acid in water and in chenodeoxycholate micelles (250 microM and 5-25:1, respectively). In model bile systems including those composed of conjugated ursodeoxycholate-chenodeoxycholate mixtures, ursodeoxycholic acid was less soluble than chenodeoxycholic acid and induced the mixtures to gel between pH 7.0 and 4.5-6.5. These results suggest that in vivo 1) the solubility and absorption of oral ursodeo;ycholic acid from the duodenum-jejunum may be limited, 2) ursodeoxycholic acid will precipitate in the colon at pH values less than 8.0 but chenodeoxycholic acid is soluble at pH values greater than 6.9 and hence is capable of eliciting a secretory diarrhea, 3) the precipitation pH of glycoursodeoxycholic acid, the predominant bile acid in bile during therapy with ursodeoxycholic acid, falls within the physiological range, thus it is poss;ble that this bile acid may short-circuit the entero-hepatic circulation and even precipitate from bile or gut luminal contents as crystals.