gebhart/patrepeval huggingface dataset:
Non-invasive observation of repeated adenoviral GFP gene delivery to the anterior segment of the monkey eyein vivo (2001)

Background Glaucoma is a group of chronic eye diseases often associated with an elevated intraocular pressure (IOP). If not controlled, the condition leads to blindness. The eye tissue responsible for maintaining aqueous humor resistance and thus normal IOP is the trabecular meshwork (TM). Adenoviral vectors are capable of transducing the TM in several rodent species. Because of the relevance of the non-human primate model in the study of glaucoma, gene transfer to the eyes of cynomolgus monkeys was investigated. Methods Four cynomolgus monkeys were injected with AdenoGFP into the anterior chamber: two monkeys received 109 pfu and the other two 107 pfu. One monkey received four consecutive injections into the same eye (107 pfu in each injection) over a 7-month period. In vivo gene transfer (fluorescence) and IOP were evaluated by standard clinical ophthalmic instruments (slit lamp biomicroscopy, gonioscopy and tonometry). Histopathology and cellular distribution were assessed postmortem. Results The first injection of the lower viral dose resulted in marked TM-preferred gene transfer visible non-invasively by in vivo gonioscopy. The expression of the transgene lasted for 3–4 weeks with little or no signs of clinical inflammation. Gene transfer was achieved on three sequential occasions (3–4 weeks each) but failed and induced substantial, albeit reversible, corneal abnormalities on the fourth occasion. Conclusions Gene transfer to the TM and cornea can be monitored non-invasively in non-human primates, allowing correlation of gene transfer with physiological parameters. Because of ocular immune privilege, repeated anterior chamber administrations of adenoviral vectors expressing appropriate genes may have therapeutic potential for glaucoma. Copyright © 2001 John Wiley & Sons, Ltd.
Cardiac output during exercise by the open circuit acetylene washin method: comparison with direct Fick (2000)

An open-circuit (OpCirc) acetylene uptake cardiac output (QT) method was modified for use during exercise. Two computational techniques were used. OpCirc1 was based on the integrated uptake vs. end-tidal change in acetylene, and OpCirc2 was based on an iterative finite difference modeling method. Six subjects [28-44 yr, peak oxygen consumption (VO(2)) = 120% predicted] performed cycle ergometry exercise to compare QT using OpCirc and direct Fick methods. An incremental protocol was repeated twice, separated by a 10-min rest, and subsequently subjects exercised at 85-90% of their peak work rate. Coefficient of variation of the OpCirc methods and Fick were highest at rest (OpCirc1, 7%, OpCirc2, 12%, Fick, 10%) but were lower at moderate to high exercise intensities (OpCirc1, 3%, OpCirc2, 3%, Fick, 5%). OpCirc1 and OpCirc2 QT correlated highly with Fick QT (R(2) = 0.90 and 0.89, respectively). There were minimal differences between OpCirc1 and OpCirc2 compared with Fick up to moderate-intensity exercise (<70% peak VO(2)); however, both techniques tended to underestimate Fick at >70% peak VO(2). These differences became significant for OpCirc1 only. Part of the differences between Fick and OpCirc methods at the higher exercise intensities are likely related to inhomogeneities in ventilation and perfusion matching (R(2) = 0.36 for Fick - OpCirc1 vs. alveolar-to-arterial oxygen tension difference). In conclusion, both OpCirc methods provided reproducible, reliable measurements of QT during mild to moderate exercise. However, only OpCirc2 appeared to approximate Fick QT at the higher work intensities.
AMERICANS CAN LEARN A LOT FROM EUROPEAN, JAPANESE SNOWFIGHTERS (1995)

The Federal Highway Administration, the American Association of State Highway and Transportation Officials, and the Transportation Research Board convened a panel of six managers responsible for snow and ice control operations from federal, state, county, and municipal levels. The panel toured Japan and Europe, focusing on international operations in snow and ice control. The panel returned with new knowledge of advanced international technologies with which they hope to create a domestic Winter Maintenance Program. This article describes various Japanese, German, and Austrian practices that cover broad topic areas, such as equipment, anti-icing operations, road weather information systems, weather forecasting services, public information systems, policy, roadway level-of-service criteria, visibility, and environmental issues.
Presurgical determination of estrogen receptor status using immunocytochemically stained fine needle aspirate smears in patients with breast cancer. (1987)

We have developed an immunocytochemical staining procedure (ERICA) using a monoclonal antibody to the estrogen receptor (ER) to determine ER status from samples obtained by fine needle aspiration of primary and recurrent breast cancer tissue (cyto-ERICA). ER status was assessable on 214 of 246 smeared aspirates from breast cancer patients. In 143 (66.8%) assessable smears positive nuclear staining was observed but was completely absent in 71 (33.2%) cases. In 107 cases we were able to compare results with those obtained with the quantifiable dextrancoated charcoal (DCC) radioligand binding technique using surgically excised material. We observed qualitative agreement in 53 of 62 (85.5%) of primary specimens and 16 of 16 (100%) recurrent samples compared to the subsequent DCC result on the same sample. Aspirates obtained from new secondary deposits were also assessed and in 16 of 19 (84.2%) cases results agreed with that established previously by DCC on the primary breast tumor. In a further 6 of 10 (60%) cases the cyto-ERICA result obtained from recurrent samples qualitatively agreed with that determined by DCC on a previous recurrent lesion. A comparison of staining of aspirates was also made against frozen tissue sections stained with the monoclonal antibody (tissue-ERICA). Where comparison was made of primary tumor specimens agreement was observed in 40 of 45 (88.9%) of cases while specimens from secondary lesions agreed qualitatively in 14 of 17 (82.3%) of cases. In a small number of samples where tissue-ERICA was performed on an earlier lesion to that aspirated for cyto-ERICA an agreement of 4 of 5 (80%) was observed. This technique shows good sensitivity in demonstrating ER in aspirate specimens, should therefore permit us to determine ER status before surgery for primary breast cancer, and may also mean that surgery for recurrent disease to determine receptor status is no longer necessary.
Mouse MHC class I tetramers that are unable to bind to CD8 reveal the need for CD8 engagement in order to activate naive CD8 T cells (2002)

Although the role of CD8 as a supplier of lck is unchallenged, its role in contributing to the formation of a stable complex between class I molecules and the TCR, as well as its role as an adhesion molecule, is less clear. To address the role of CD8/MHC-I interactions, we generated tetramers composed of H2-K(b) molecules with mutations in the alpha 3 domain of H2-K(b) that abolish CD8 binding. We show that the ability of tetramers to stain and activate CD8 T cells is strongly dependent on binding of CD8 to the same class I molecule engaged by the TCR. We characterize a mutation in the alpha 3 domain that results in H2-K(b) molecules capable of staining specific CD8 T cells with little ensuing activation. Although CD8 to some extent serves an adhesive function, this contribution is modest and does not substitute for lack of binding of CD8 to the class I molecule engaged by the TCR. We show that CD8 and the TCR associate in a process independent of binding of CD8 to class I. Our data support the notion that CD8 is required to form a stable complex between class I and the TCR.
Three-layer bubble-sorting-based nonManhattan channel routing (2000)

It is well known that a nonManhattan channel router can use fewer routing tracks, and is never worse than a Manhattan router in a channel. To my knowledge, a three-layer bubble-sorting-based nonManhattan channel routing problem is always solved by the solution in a two-layer bubble-sorintg-based nonManhattan channel routing problem. Recently, an O ( kn 2 ) heuristic algorithm [Chaudhary et al. 1991] and an O ( kn 2 ) optimal algorithm [Chen et al. 1994] have been proposed, where k is the number of two-layer routing tracks and n is the number of terminals in a bubble-sorintg-based nonManhattan channel. In this paper we propose an optimal three-layer bubble-sorintg-based nonManhattan routing algorithm to minimize the number of three-layer routing tracks. Furthermore, the time complexity of theis optimal algorithm is proven to be in O ( hn ) time, where h is the number of three-layer routing tracks and n is the number of terminals in a bubble-sorting-based nonManhattan channel.
Effects of Low Intensity Exercise Program with Telephone Coaching on Physical Fitness (2008)

Purpose: The purpose of this study was to determine the effects of low intensity exercise program with telephone coaching on the physical fitness of elderly people who are receiving home visiting nursing care. Method: This study was conducted using a non-equivalent control group pretest-posttest design. The participants were 61 elders. Elders (34) in the experimental group performed low intensity exercise and of these 16 received telephone coaching. The low intensity exercise program consisted of stretching, muscle strengthening with an elastic band, massage, and ball exercise, five days a week, for sixteen weeks. Data were collected from July 2007 to December 2007. -test, ANCOVA with SPSS WIN 11.0 program were used to analyse the data. Results: There were statistical differences in the right grasping power in the right hand (p=0.021), Raising behind of right arm (p=0.006), Raising behind of left arm (p=0.007). Conclusion: These results indicate, that a low intensity exercise program with telephone coaching can help improve physical fitness in elders receiving served home visiting nursing care.
Catalytic Enantioselective One-pot Aminoborylation of Aldehydes: A Strategy for Construction of Nonracemic α-Amino Boronates (2013)

We report a strategy for the conversion of aldehydes to enantiomerically enriched α-amino boronates through the intermediacy of in situ-generated silylimines. This transformation is brought about by Pt-catalyzed asymmetric addition of B2(pin)2 across the imine double bond. An attractive feature of the intermediate diboration adduct is that it can be acylated directly and provides convenient access to important N-acyl α-amino boronic ester derivatives.
Soluble TNF-Like Cytokine (TL1A) Production by Immune Complexes Stimulated Monocytes in Rheumatoid Arthritis (2007)

TNF-like cytokine (TL1A) is a newly identified member of the TNF superfamily of ligands that is important for T cell costimulation and Th1 polarization. However, despite increasing information about its functions, very little is known about expression of TL1A in normal or pathological states. In this study, we report that mononuclear phagocytes appear to be a major source of TL1A in rheumatoid arthritis (RA), as revealed by their strong TL1A expression in either synovial fluids or synovial tissue of rheumatoid factor (RF)-seropositive RA patients, but not RF-/RA patients. Accordingly, in vitro experiments revealed that human monocytes express and release significant amounts of soluble TL1A when stimulated with insoluble immune complexes (IC), polyethylene glycol precipitates from the serum of RF+/RA patients, or with insoluble ICs purified from RA synovial fluids. Monocyte-derived soluble TL1A was biologically active as determined by its capacity to induce apoptosis of the human erythroleukemic cell line TF-1, as well as to cooperate with IL-12 and IL-18 in inducing the production of IFN-gamma by CD4(+) T cells. Because RA is a chronic inflammatory disease with autoimmune etiology, in which ICs, autoantibodies (including RF), and various cytokines contribute to its pathology, our data suggest that TL1A could be involved in its pathogenesis and contribute to the severity of RA disease that is typical of RF+/RA patients.
Integrated power control and base station assignment (1995)

In cellular wireless communication systems, transmitted power is regulated to provide each user an acceptable connection while limiting the interference seen by other users. Previous work has focused on maximizing the minimum carrier to interference ratio (CIR) or attaining a common CIR over all radio links. However, previous work has assumed the assignment of mobiles to base stations is known and fixed. In this work, we integrate power control and base station assignment. In the context of a CDMA system, we consider the minimization of the total transmitted uplink power subject to maintaining an individual target CIR for each mobile. This minimization occurs over the set of power vectors and base station assignments. We show that this problem has special structure and identify synchronous and asynchronous distributed algorithms that find the optimal power vector and base station assignment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bile acid hydrophobicity is correlated with induction of apoptosis and/or growth arrest in HCT116 cells (2001)

Faecal bile acids have long been associated with colon cancer; highly hydrophobic bile acids, which induce apoptosis, have been implicated in the promotion of colon tumours. The moderately hydrophobic chemopreventive agent ursodeoxycholic acid (UDCA) does not induce apoptosis; rather, it causes colon-derived tumour cells to arrest their growth. To investigate the relationship between bile acid hydrophobicity and biological activity we examined 26 bile acids for their capacity to induce apoptosis or alter cell growth. We found that the rapidity with which, and the degree to which, bile acids could induce apoptosis or growth arrest was correlated with their relative hydrophobicities. Of the bile acids tested, only deoxycholic acid (DCA) and chenodeoxycholic acid, the most hydrophobic bile acids tested, could induce apoptosis in less than 12h in the human colon cancer cell line HCT116. The moderately hydrophobic bile acids hyoDCA, lagoDCA, norDCA, homoUDCA and isoUDCA induced growth arrest at 12h but longer incubations resulted in apoptosis. Conjugation of glycine or taurine to the bile acids decreased relative hydrophobicity and eliminated biological activity in our assays. In addition, we tested a subset of these bile acids for their ability to translocate across cell membranes. When 14C-labelled and 3H-labelled DCA, UDCA and lagoDCA were added to cell cultures, we found only minimal uptake by colon cells, whereas hepatocytes had considerably higher absorption. These experiments suggest that hydrophobicity is an important determinant of the biological activity exhibited by bile acids but that under our conditions these activities are not correlated with cellular uptake.
Requirement for Caspase-8 in NF-κB Activation by Antigen Receptor (2005)

Caspase-8, a proapoptotic protease, has an essential role in lymphocyte activation and protective immunity. We show that caspase-8 deficiency (CED) in humans and mice specifically abolishes activation of the transcription factor nuclear factor kappaB (NF-kappaB) after stimulation through antigen receptors, Fc receptors, or Toll-like receptor 4 in T, B, and natural killer cells. Caspase-8 also causes the alphabeta complex of the inhibitor of NF-kappaB kinase (IKK) to associate with the upstream Bcl10-MALT1 (mucosa-associated lymphatic tissue) adapter complex. Recruitment of the IKKalpha, beta complex, its activation, and the nuclear translocation of NF-kappaB require enzyme activity of full-length caspase-8. These findings thus explain the paradoxical association of defective apoptosis and combined immunodeficiency in human CED.
Cue-Based Networking Using Wireless Sensor Networks: A Video-over-IP Application (2008)

In this paper we present a new approach called cue-based networking that uses hints or cues about the physical environment to optimize networked application behavior. We define the notion of cues and describe how cues can be obtained using a wireless sensor network as the underlying platform. We identify both the research and system challenges that need to be addressed to realize benefits of the approach under a target application of video delivery over IP networks. In the process, we identify a key challenge of wireless sensor networks, namely the timeliness-robustness tradeoff. We design an adaptive algorithm that balances this tradeoff satisfying both timeliness and robustness requirements. Through an implementation of the video delivery application using the proposed algorithm in a real home environment, we highlight the practical benefits of the proposed approach.
PISCES: recent improvements to a PDB sequence culling server (2005)

PISCES is a database server for producing lists of sequences from the Protein Data Bank (PDB) using a number of entry- and chain-specific criteria and mutual sequence identity. Our goal in culling the PDB is to provide the longest list possible of the highest resolution structures that fulfill the sequence identity and structural quality cut-offs. The new PISCES server uses a combination of PSI-BLAST and structure-based alignments to determine sequence identities. Structure alignment produces more complete alignments and therefore more accurate sequence identities than PSI-BLAST. PISCES now allows a user to cull the PDB by-entry in addition to the standard culling by individual chains. In this scenario, a list will contain only entries that do not have a chain that has a sequence identity to any chain in any other entry in the list over the sequence identity cut-off. PISCES also provides fully annotated sequences including gene name and species. The server allows a user to cull an input list of entries or chains, so that other criteria, such as function, can be used. Results from a search on the re-engineered RCSB's site for the PDB can be entered into the PISCES server by a single click, combining the powerful searching abilities of the PDB with PISCES's utilities for sequence culling. The server's data are updated weekly. The server is available at http://dunbrack.fccc.edu/pisces.
The purification and properties of N-acetylglucosamine 6-phosphate deacetylase from Escherichia coli (1967)

1. N-Acetylglucosamine 6-phosphate deacetylase and 2-amino-2-deoxy-d-glucose 6-phosphate ketol-isomerase (deaminating) (EC 5.3.1.10, glucosamine 6-phosphate deaminase) of Escherichia coliK(12) have been separated by chromatography on DEAE-cellulose. 2. N-Acetylglucosamine 6-phosphate deacetylase has optimum pH8.5 and K(m) 0.8mm. Glucosamine 6-phosphate is a product of the reaction. There appear to be no essential cofactors. Glucosamine 6-phosphate and fructose 6-phosphate inhibit deacetylation. 3. Glucosamine 6-phosphate deaminase has optimum pH7.0 and K(m) 9.0mm. It is stimulated by N-acetylglucosamine 6-phosphate. 4. We propose that the deacetylase be termed 2-acetamido-2-deoxy-d-glucose 6-phosphate amidohydrolase (EC 3.5.1.-), with acetylglucosamine 6-phosphate deacetylase as a trivial name.
Improved cell-penetrating peptide–PNA conjugates for splicing redirection in HeLa cells and exon skipping in mdx mouse muscle (2008)

Steric blocking peptide nucleic acid (PNA) oligonucleotides have been used increasingly for redirecting RNA splicing particularly in therapeutic applications such as Duchenne muscular dystrophy (DMD). Covalent attachment of a cell-penetrating peptide helps to improve cell delivery of PNA. We have used a HeLa pLuc705 cell splicing redirection assay to develop a series of PNA internalization peptides (Pip) conjugated to an 18-mer PNA705 model oligonucleotide with higher activity compared to a PNA705 conjugate with a leading cell-penetrating peptide being developed for therapeutic use, (R-Ahx-R)(4). We show that Pip-PNA705 conjugates are internalized in HeLa cells by an energy-dependent mechanism and that the predominant pathway of cell uptake of biologically active conjugate seems to be via clathrin-dependent endocytosis. In a mouse model of DMD, serum-stabilized Pip2a or Pip2b peptides conjugated to a 20-mer PNA (PNADMD) targeting the exon 23 mutation in the dystrophin gene showed strong exon-skipping activity in differentiated mdx mouse myotubes in culture in the absence of an added transfection agent at concentrations where naked PNADMD was inactive. Injection of Pip2a-PNADMD or Pip2b-PNADMD into the tibealis anterior muscles of mdx mice resulted in approximately 3-fold higher numbers of dystrophin-positive fibres compared to naked PNADMD or (R-Ahx-R)(4)-PNADMD.
Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy (2016)

Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0-1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.
Esophageal adenocarcinoma associated with Barrett's esophagus: long-term management with laser ablation. (1995)

We report the use of neodymium:yttrium-aluminum-garnet (Nd:YAG) laser ablation to treat high-grade dysplasia and intramucosal esophageal adenocarcinoma associated with Barrett's esophagus in a patient who refused surgery. Throughout laser therapy, the patient received omeprazole 40 mg/day. After 1 1/2 yr, five laser treatments totaling 22,055 J given over a period of 13 months achieved squamous reepithelialization and absence of malignant transformation in the first area in which carcinoma was diagnosed. Squamous reepithelialization was maintained 1 yr later, confirming recent reports that photoablation plus omeprazole can achieve regression of Barrett's esophagus. During the last year of follow-up, a second contiguous area discovered to contain carcinoma was treated three times by photoablation, with a total of 13,164 J; biopsy showed only low-grade dysplasia in this area after two laser treatments totaling 8,108 J. No complications were seen during or after any of the laser sessions, and the patient remained asymptomatic 2 1/2 yr after the first photoablation and 3 yr after presentation.