gebhart/patrepeval huggingface dataset:
Causal ordering in reliable group communications (1993)

In this paper we present a solution to the causal reliable multicast problem. User processes generate separate sequences of messages and specify the causal relation among them according to some application need; the algorithm ensures that the messages within the same sequence are delivered to all active, i.e. both correct and faulty, processes in the group, or to none of them, and are processed according to their causal order. Messages belonging to different sequences can be concurrently processed.This problem has few solutions presented in literature; in common with a part of them, the algorithm we describe has the centralized approach and the use of history buffers to recover from omission failures. The differences mainly concern the mechanism we devised to recover from crash failures, that avoids resorting to specialized protocols. As a consequence, under failure conditions, the algorithm performs better than other proposals in terms of both network load and throughput without affecting the performances under reliable conditions. Further, it allows to implement the most general interpretation of causality and it does not require any particular service to the underlying transport protocol.
Enhancing In Vivo Survival of Adipose-Derived Stromal Cells Through Bcl-2 Overexpression Using a Minicircle Vector (2013)

Tissue regeneration using progenitor cell-based therapy has the potential to aid in the healing of a diverse range of pathologies, ranging from short-gut syndrome to spinal cord lesions. However, there are numerous hurdles to be overcome prior to the widespread application of these cells in the clinical setting. One of the primary barriers to effective stem cell therapy is the hostile environment that progenitor cells encounter in the clinical injury wound setting. In order to promote cellular survival, stem cell differentiation, and participation in tissue regeneration, relevant cells and delivery scaffolds must be paired with strategies to prevent cell death to ensure that these cells can survive to form de novo tissue. The Bcl-2 protein is a prosurvival member of a family of proteins that regulate the mitochondrial pathway of apoptosis. Using several strategies to overexpress the Bcl-2 protein, we demonstrated a decrease in the mediators of apoptosis in vitro and in vivo. This was shown through the use of two different clinical tissue repair models. Cells overexpressing Bcl-2 not only survived within the wound environment at a statistically significantly higher rate than control cells, but also increased tissue regeneration. Finally, we used a nonintegrating minicircle technology to achieve this in a potentially clinically applicable strategy for stem cell therapy.
Evaluation of VITEK 2 Rapid Identification and Susceptibility Testing System against Gram-Negative Clinical Isolates (2001)

A total of 281 strains of miscellaneous members of the family Enterobacteriaceae, Pseudomonas aeruginosa, and other gram-negative bacteria were evaluated by use of identification tests with the VITEK 2 system (bioMérieux) and an API identification system (bioMérieux). A total of 237 (95%) strains were correctly identified to the species level. Only six (2.1%) strains were misidentified, and eight (2.8%) strains were not identified. Among 14 strains with discrepant identifications, 8 (57.1%) strains were nonfermenters. The susceptibilities of 228 strains to 11 antibiotics including amikacin, netilmicin, tobramycin, gentamicin, ciprofloxacin, imipenem, meropenem, ceftazidime, cefepime, piperacillin, and piperacillin in combination with tazobactam were tested with the VITEK 2 AST-No. 12 card and by the broth microdilution (MB) method, according to NCCLS guidelines, as a reference. For the 2,508 organism-antibiotic combinations, the rates at which duplicate MICs correlated within +/-1 dilution ranged from 84.2 to 95.6%. Only 13 (0.5%) and 10 (0.4%) of the susceptibility tests gave major errors (resistant with the VITEK 2 system but sensitive by the MB method) and very major errors (sensitive with the VITEK 2 system but resistant by the MB method), respectively. Both VITEK 2 ID-GNB (an identification system) and VITEK 2 AST-No. 12 (a susceptibility testing system) card systems gave rapid, reliable, and highly reproducible results.
Contrast mechanisms in scanning ion microscope imaging for metals (1998)

The contrast of the secondary electron images in scanning ion microscopy (SIM) is compared with that in scanning electron microscopy (SEM) with ultrahigh vacuum for Al, Cu, Ag, and Au metals deposited on the Si(100) clean surface. The order of the secondary electron yields as a function of the atomic number (Z2) for ion bombardment is opposite to that for electron bombardment. The brightness of the secondary electron images observed by a focused Ga+ ion beam at 30 keV decreases with increasing Z2, while that by the electron beam increases with Z2. On the other hand, the order of the total secondary ion yields in SIM increases with Z2. The secondary electron image observed by a focused Ar+-ion beam at 3 keV shows the similar contrast to that of the Ga+-ion beam. The different Z2 dependence of the secondary electron yields between SEM and SIM was quantitatively confirmed by the total secondary electron spectra and is discussed based on the range profile below the surface, and it is concluded that the decrease of the secondary electron yields in SIM is attributed to the increase of the reflected ions at the surface with increasing Z2.
Bacterial expression of antibody fragments that block human rhinovirus infection of cultured cells. (1990)

Human rhinoviruses are the major causative agents of the common cold in humans and have been divided into major and minor groups based on receptor specificity. cDNAs encoding the light and heavy chains of a murine monoclonal antibody that recognizes the major group receptor were cloned, abundantly expressed in Escherichia coli, and renatured into Fab fragments that blocked virus binding and protected HeLa cell monolayers from rhinovirus infection. Elimination of the cysteines normally bridging the heavy and light chains yielded molecules indistinguishable from wild-type Fab fragments in virus binding assays. Single-chain antibodies with covalently linked light and heavy variable domains were also expressed and showed receptor binding and cell protection activities. These recombinant antibody fragments are potentially useful in preventing or treating common colds in humans.
Near-Specular Performance Of A Portable Scatterometer (1987)

A helium-neon portable scatterometer that was built and described previously has been modified. The intent was to obtain better data at angles very close to specular. We incorporated a twelve-element, linear array of silicon detectors in place of the first detector near the specular reflection direction, and removed the collimator to reduce the beam diameter. Attention was paid to scattered light from the instrument. A new scheme to orient the instrument to the sample surface using the array and the specular beam is described. Design details of the detection system capable of detecting signals ranging over five orders of magnitude and utilizing lock-in detection software are given. Results showing that the modification improved the scatterometer performance so that a Bidirectional Reflectance Distribution Function (BRDF) value of 1 sr -1 at one degree from specular can be measured with reasonable accuracy for a specular sample are discussed.
Enhanced susceptibility of S‐100B transgenic mice to neuroinflammation and neuronal dysfunction induced by intracerebroventricular infusion of human β‐amyloid (2005)

S-100B is an astrocyte-derived protein that is increased in focal areas of the brain most severely affected by neuropathological changes in Alzheimer's disease (AD). Cell-based and clinical studies have implicated S-100B in progression of a pathologic, glial-mediated pro-inflammatory state in the CNS. However, the relationship between S-100B levels and susceptibility to AD-relevant neuroinflammation and neuronal dysfunction in vivo has not been determined. To test the hypothesis that overexpression of S-100B increases vulnerability to beta-amyloid (Abeta)-induced damage, we used S-100B-overexpressing transgenic (Tg) and S-100B knockout (KO) mice in a mouse model that involves intracerebroventricular infusion of human oligomeric Abeta1-42. This model mimics many features of AD, including robust neuroinflammation, Abeta plaques, synaptic damage and neuronal loss in the hippocampus. S-100B Tg, KO, and wild-type (WT) mice were infused with Abeta for 28 days, sacrificed at 60 days, and hippocampal endpoints analyzed. We found that Tg mice showed increased vulnerability to Abeta-induced neuropathology relative to either WT or KO mice. Specifically, Tg mice exhibited enhanced glial activation and neuroinflammation, increased nitrotyrosine staining (a marker of glial-induced neuronal damage), and more pronounced loss of synaptic markers. Interestingly, Tg mice showed no significant differences in Abeta plaque burden compared with WT or KO mice, suggesting that, as in the human situation, the severity of neuronal dysfunction did not correlate with amyloid deposition. Our data are consistent with a model in which S-100B overexpression in AD enhances glial activation and leads to an augmented neuroinflammatory process that increases the severity of neuropathologic sequelae.
A cross-referencing-based droplet manipulation method for high-throughput and pin-constrained digital microfluidic arrays (2007)

Digital microfluidic biochips are revolutionizing high-throughput DNA sequencing, immunoassays, and clinical diagnostics. As high-throughput bioassays are mapped to digital microfluidic platforms, the need for design automation techniques for pin-constrained biochips is being increasingly felt. However, most prior work on biochips CAD has assumed independent control of the underlying electrodes using a large number of (electrical) input pins. The authors propose a droplet manipulation method based on a cross-referencing addressing method that uses row and columns to access electrodes. By mapping the droplet movement problem to the clique partitioning problem from graph theory, the proposed method allows simultaneous movement of a large number of droplets on a microfluidic array. This in turn facilitates high-throughput applications on a pin-constrained biochip. The authors use random synthetic benchmarks and a set of multiplexed bioassays to evaluate the proposed method
Osteopenia in pregnancy during long‐term heparin treatment: A radiological study post partum (1990)

Summary. Osteopenia, sometimes with compression fractures of the spine, is a side‐effect of long‐term heparin treatment. The frequency is unknown. In this study, 70 women were given subcutaneous heparin as therapy for, or prophylaxis against, thromboembolism during pregnancy. All, except two, were examined by X‐ray of the spine and hip first week post partum. The duration of treatment and the dosage of heparin varied. There were 12 (17%) with obvious Osteopenia, including two women with multiple fractures of the spine (3%). Re‐examination 6–12 months post partum showed that the changes were reversible in most cases. Another 18 women were examined about three years after heparin treatment during pregnancy. No obvious osteopenia was found among them or in a control group of 30 women examined in the first week post partum. The degree of osteopenia was not correlated with either the heparin dose or the duration of treatment. Women treated with heparin in consecutive pregnancies do not seem to have an increased risk of osteopenia.
Relative GPS Using DME/TACAN Data Link (1994)

A local area Relative GPS (RGPS) landing system is
described which has application to tactical or emergency
situations where an accurate site survey is not possible. The system is also unique in its use of existing TACAN ground and airborne equipment to provide a high integrity data link.

Data containing information on all satellites in view is up-linked to the aircraft, as well as enough siting data to support six simultaneous approaches. A relative solution using all common satellites is derived at the aircraft. Based on the calculated relative solution, aircraft guidance signals are generated which drive a CD1 display in real time. The up-link data is encoded onto ground-to-air DMlYlYACAN signals by pulse-position modulating a single data bit onto each existing DMlYlYACAN pulse pair. This data link has several advantages over Mode-S, VOR-band, and VHF alternatives: 

- Radiated signals meet existing ICAO specifications

- DMEYTACAN band is internationally designated for navigational use

- Existing ground equipment can be easily modified to encode the DGPS data during the transition to DGPS

- As DME/TACAN is phased out, DGPS-specific
ground equipment can be built at low cost
l Simultaneous dual use of existing ground
equipment

- Encoding DGPS data on existing TACAN or
DME has no effect on DMlYTACAN
performance

- Existing airborne TACAN and DME
interrogators and antennas can receive the DGPS
up-link data

- DME/TACAN data rate has room for future
expansion

E-Systems has implemented a complete RGPS system with
commercial-off-the-shelf GPS receivers and using a portable
ANflRN-41 TACAN transponder and a low-cost King KX-
64 general aviation DME interrogator. A special data link
error correction scheme was developed allowing full use of
the DME independent of GPS data reception. Statistical
analysis shows that the relative solution meets CAT-I
accuracy requirements, and the data link meets CAT I
integrity and continuity of service requirements in the
presence of worst-case interfering in-band signals from other DMEs, ATCRBS and TCAS transmissions. Flight test
results recorded in a Cessna 206 at the E-Systems DGPS test
facility in Tooele, Utah, will be presented.
Reversible Photocontrol of Peptide Helix Content:  Adjusting Thermal Stability of the Cis State (2004)

Cross-linking reagents based on an azobenzene core can be used to reversibly photoregulate secondary structure when introduced as intramolecular bridges in peptides and proteins. Photoisomerization of the azobenzene core in the trans to cis direction is triggered by photon absorption but isomerization from cis to trans occurs thermally as well as photochemically. The rate of the thermal process effectively determines the half-life of the cis form as well as the extent to which the trans form can be recovered. We designed and characterized a series of methanethiosulfonate (MTS)-bearing thiol-reactive azo-benzene-based cross-linkers. These cross-linkers are shown to permit photoregulation of helix content in a test peptide with half-lives for the cis conformation ranging from 11 s to 43 h at 25 degrees C. The cross-linkers described here thus broaden the range of reagents available for reversible photocontrol of peptide and protein conformation.
Antigenic Heterogeneity of Human Colorectal Cancer Cell Lines Analyzed by a Panel of Monoclonal Antibodies. I. Heterogeneous Expression of la-Like and HLA-Like Antigenic Determinants<xref ref-type="fn" rid="fn2">2</xref> (1982)

The pattern of reactivity of 10 monoclonal antibodies (MCA) developed against human lymphoid leukemia cells and tested with human T-cells, B-cells, as well T-lymphoma and B-lymphoma cell lines suggested that six of them detect la-like determinants, three detect HLA-like determinants, and the remaining one detects a non-Ia B-cell antigen. With the use of three binding assays, the six MCA that appeared to detect Ia-like determinants reacted strongly with the human colorectal cancer cell (CCC) line LoVo, and none of the three MCA that reacted with HLA-like determinants reacted with this cell line. Immunoprecipitation and polyacrylamide gel electrophoresis analysis confirmed the apparent specificities of the MCA for Ia-like and HLA molecules, demonstrated the presence of Ia-like molecules in LoVo, and failed to detect HLA in these cells. The cellular enzyme-linked immunosorbent assay was used for the testing of our anti-Ia and anti-HLA MCA with 15 other CCC lines. Marked heterogeneity was found in the expression of different Ia-like and HLA determinants defined by different or overlapping subsets of MCA, which suggested that these determinants might be present on different molecules or that different conformations of the same molecules exist in various CCC lines. Analysis of the surface phenotype of subclones of LoVo cells revealed the presence of stable variant cell subpopulations, which lost reactivity with four out of six of the anti-Ia-like MCA but retained at least one Ia-like molecule recognized by two of our MCA. All of the subclones maintained the HLA-negative phenotype. The possible immunologic and diagnostic consequences of the presence or absence of Ia-like or HLA markers on nonlymphoid tumor cells are discussed.
Expression of Tumor Suppressor Gene p16<sup>INK4</sup> Products in Primary Gastric Cancer (2000)

Recent studies have shown that the cyclin-dependent kinase (CDK) inhibitor p27(Kip1) represents an indicator for patients' outcome in several human malignancies including gastric cancer. However, the clinicopathologic value of another class of CDK inhibitor, p16(INK4), has not been determined. In a retrospective study, we examined the expression of p16(INK4) by immunohistochemical assay of 80 samples of primary gastric cancers and their adjacent nonneoplastic mucosas. Less than 10% of non-tumor gastric mucosal cells were p16(INK4) positive, whereas the expression of p16(INK4) in gastric cancer cells varied widely from 0 to 100% (mean, 24.5%). The expression of p16(INK4) was not seen in 11.3% (9/80) of the cancer cases, but in 65% (52/80) this protein was even overexpressed when compared with the nonneoplastic mucosa. A clinicopathologic survey indicated that a low or no expression of p16(INK4) was associated with poorly differentiated carcinoma (p = 0.0133), but the level of expression did not correlate with other parameters including patients' prognosis or with the expression of the pRb protein. In an effort to explore the underlying mechanism for the p16(INK4)-negative cases, a prospective study was also performed on 20 cases of gastric cancer to compare the level of the p16(INK4) protein with the methylation status of the p16(INK4) promoter. Gastric cancer tissues with methylation expressed significantly lower levels of the p16(INK4) protein (p = 0.0013) and two of them lacked p16(INK4) expression altogether, whereas all the cancer tissues without methylation expressed it. These findings suggest that the p16(INK4) protein may be associated with differentiation of gastric cancer tissues and that methylation of the p16(INK4) promoter may, in part, account for the loss of p16(INK4) expression.
Hitting the Surface--Softly (2001)

During the adsorption of a molecule on a surface, energy is lost from the molecule. This loss can occur through many loss channels, including the emission of ions or electrons, the formation of electron-hole pairs, and excitation of lattice vibrations. In his Perspective, [Auerbach][1] discusses the relative importance of these loss channels for high and low interaction energies. He highlights the report by [ Gergen et al .][2], who show that electron-hole pair formation is more important in low-energy adsorption than previously thought.

 [1]: http://www.sciencemag.org/cgi/content/full/294/5551/2488
 [2]: http://www.sciencemag.org/cgi/content/short/294/5551/2521
The XML log standard for digital libraries: analysis, evolution, and deployment (2003)

We describe current efforts and developments building on our proposal for an XML log standard format for digital library (DL) logging analysis and companion tools. Focus is given to the evolution of formats and tools, based on analysis of deployment in several DL systems and testbeds. Recent development of analysis tools also is discussed.
A pharmacological review of selective oestrogen receptor modulators (2000)

Selective oestrogen receptor modulators (SERMs) are structurally diverse non-steroidal compounds that bind to oestrogen receptors and produce oestrogen agonist effects in some tissues and oestrogen antagonist effects in others. SERMs are being evaluated for a number of oestrogen-related diseases, including post-menopausal osteoporosis, hormone-dependent cancers, and cardiovascular disease. Several compounds that exhibit a SERM profile are currently available for clinical use, including clomiphene, tamoxifen, and toremifene (which are triphenylethylenes) and raloxifene (a benzothiophene). Clomiphene is used for the induction of ovulation in sub-fertile women attempting pregnancy. Tamoxifen and toremifene are both used to treat breast cancer. Tamoxifen may have beneficial effects on bone mineral density and serum lipids. The effects of toremifene on serum lipids are similar to that of tamoxifen. Both compounds have stimulatory effects on the endometrium. Raloxifene, indicated for the treatment and prevention of post-menopausal osteoporosis, has beneficial effects on bone mineral density and serum lipids, but does not increase the risk of endometrial hyperplasia or endometrial cancer. Recently, raloxifene was shown to reduce the incidence of vertebral fractures in otherwise healthy women with osteoporosis; in the same study, a reduced incidence of breast cancer was also observed. Similar to oestrogens, SERMs increase the incidence of venous thromboembolism. Several newer compounds that exhibit a SERM profile are also in clinical development, including other triphenylethylenes (droloxifene, idoxifene) and benzothiophenes (LY353381.HCl), benzopyrans (EM-800), and naphthalenes (CP-336,156).
New ADRC for consumer digital VCR (1990)

A bit rate reduction method for consumer digital VCR must meet special requirements such as fast motion playback, slow motion playback, and electronic editing, while keeping robustness for consumer use. Adaptive quantizing is the suitable method to remove redundancies in data within each pixel level while keeping robustness for error propagation, which is essential to the capability of error concealment and multiple-dubbing. Considering these requirements, the authors developed the ADRC (adaptive dynamic range coding) method which can remove level redundancy according to the dynamic range of the block. They have improved the quantizing ability of ADRC and the efficiency of 3-dimensional processing. For a further improvement of compression efficiency, the spatio-temporal subsampling method is introduced to combine with the ADRC method. Using this new coding method, one can compress the Y, R-Y, B-Y component signal to 12.5 Mbps while maintaining picture quality. They have confirmed the efficiency of the new ADRC method by computer simulation.
Bilirubin oxidase from Myrothecium verrucaria: X-ray determination of the complete crystal structure and a rational surface modification for enhanced electrocatalytic O2 reduction (2011)

The blue multi-copper oxidase bilirubin oxidase (BOx) from the ascomycete plant pathogen Myrothecium verrucaria (Mv) efficiently catalyses the oxidation of bilirubin to biliverdin, with the concomitant reduction of O(2) to water, a reaction of considerable interest for low-temperature bio-fuel cell applications. We have solved the complete X-ray determined structure of Mv BOx at 2.4 Å resolution, using molecular replacement with the Spore Coat Protein A (CotA) enzyme from Bacillus subtilis (PDB code 1GSK) as a template. The structure reveals an unusual environment around the blue type 1 copper (T1 Cu) that includes two non-coordinating hydrophilic amino acids, asparagine and threonine. The presence of a long, narrow and hydrophilic pocket near the T1 Cu suggests that structure of the substrate-binding site is dynamically determined in vivo. We show that the interaction between the binding pocket of Mv BOx and its highly conjugated natural organic substrate, bilirubin, can be used to stabilise the enzyme on a pyrolytic graphite electrode, more than doubling its electrocatalytic activity relative to the current obtained by simple adsorption of the protein to the carbon surface.