gebhart/patrepeval huggingface dataset:
Intracellular Localization of Migration Inhibitory Factor-Related Protein (MRP) and Detection of Cell Surface MRP Binding Sites on Human Leukemia Cell Lines (1998)

The migration inhibitory factor-related proteins (MRPs) MRP-8 and MRP-14 were detected in differentiated human leukemia cell lines (THP-1 and HL-60) by immunocytochemical analysis. They were induced and colocalized in the cytoplasm and in lesser amounts in the nucleus when THP-1 and HL-60 cells were induced to differentiate by 1alpha,25-dihydroxyvitamin D3 or retinoic acid. In a search for a protein capable of binding MRPs, both MRPs were individually produced in insect cells (Sf21) infected with recombinant baculovirus. The purified recombinant MRPs were electrophoretically and antigenically indistinguishable from the native proteins, and their ability to form the MRP8/14 complex was retained. The presence of MRP binding sites was investigated by a binding assay using recombinant MRPs and specific monoclonal antibodies. MRP binding sites were detected on the cell membrane of the human leukemia cell lines THP-1, Raji, and MOLT-4. HL-60 cells treated with 1alpha, 25-dihydroxyvitamin D3 did not express MRP binding sites on the cell membrane, but a high level of MRPs accumulated in the cells. The occurrence of MRP binding sites on the cell surface of leukemia cell lines of monocyte and lymphocyte origin suggests that MRPs, released from neutrophils under certain conditions, may contribute to the activation and recruitment of effector cells to inflammatory lesions.
Methodologies in Assaying Prostate Cancer Stem Cells (2009)

The cancer stem cell (CSC) theory posits that only a small population of tumor cells within the tumor has the ability to reinitiate tumor development and is responsible for tumor homeostasis and progression. Tumor initiation is a defining property of putative CSCs, which have been reported in both blood malignancies and solid tumors. In order to test whether any given human tumor cell population has CSC properties, the relatively enriched single cells have to be put into a foreign microenvironment in a recipient animal to test their tumorigenic potential. Furthermore, various in vitro assays need be performed to demonstrate that the presumed CSCs have certain biological properties normally associated with the stem cells (SCs). Herein, we present a comprehensive review of the experimental methodologies that our lab has been using in assaying putative prostate cancer (PCa) SCs in culture, xenograft tumors, and primary tumor samples.
On the Accuracy of Spectrum-based Fault Localization (2007)

Spectrum-based fault localization shortens the test- diagnose-repair cycle by reducing the debugging effort. As a light-weight automated diagnosis technique it can easily be integrated with existing testing schemes. However, as no model of the system is taken into account, its diagnostic accuracy is inherently limited. Using the Siemens Set benchmark, we investigate this diagnostic accuracy as a function of several parameters (such as quality and quantity of the program spectra collected during the execution of the system), some of which directly relate to test design. Our results indicate that the superior performance of a particular similarity coefficient, used to analyze the program spectra, is largely independent of test design. Furthermore, near- optimal diagnostic accuracy (exonerating about 80% of the blocks of code on average) is already obtained for low-quality error observations and limited numbers of test cases. The influence of the number of test cases is of primary importance for continuous (embedded) processing applications, where only limited observation horizons can be maintained.
Efficient interprocedural analysis for program parallelization and restructuring (1988)

An approach to efficient interprocedural analysis for program parallelization and restructuring is presented. Such analysis is needed for parallelizing loops which contain procedure calls. Our approach captures call effect on data dependencies by propagating the precise information of array subscripts from the called procedure. This allows the optimizing compiler to choose an efficient yet precise data dependence test scheme depending on the complexity of array reference patterns. The other existing methods do not provide such flexibility, hence may suffer from either imprecision or inefficiency. The paper also discusses usage of classical summary information in several important transformations for program parallelization. Experimental results are reported.
ContainerVisor: Customized Control of Container Resources (2019)

Cloud platforms are increasingly using containers for lightweight virtualization. Unlike full system virtual machines (VMs) that each runs its own operating system, containers share a stateful operating system to reduce their memory footprint and execution overheads. However, mainstream operating systems are currently limited in their ability to customize a container's memory management, since they lack the necessary abstractions and mechanisms to accurately track and isolate a container's memory footprint. We propose a new abstraction, called the Container-Level Address Space (CLAS), that provides a unified view of a container's memory across all of its constituent processes. We present the design of ContainerVisor, a per-container resource management system that leverages CLAS to provide customized memory management services. We describe a ContainerVisor prototype on Linux for running unmodified applications and demonstrate three proof-of-concept customized services, namely process-level memory limits and reservations, container-specific page replacement policies, and privacy-aware memory de-allocation. Our evaluations show that ContainerVisor can provide these customized services within reasonable overheads.
Compariso n of Pasteuria penetrans from Meloidogyne incognita with a Related Mycelial and Endospore-forming Bacterial Parasite from Pratylenchus brachyurus1 (1988)

Major distinctions exist between members of the Pasteuria penetrans group occurring on the root- lesion nematode, Pratylenchus brachyurus, and the root-knot nematode, Meloidogyne incognita. These dissim- ilarities include highly restricted nematode host ranges, differences in the bacterial life stages in relation to those of the host nematodes, and disparities in ultrastructural morphology of their mature sporangia and endospores. The several stages of the bacterial parasite of the root-lesion nematode (RLP) occur in all the nematode's larval stages. The mature RLP sporangia are rhomboidal, and average 2.40 ± 0.24 ^m in diameter and 2.15 ± 0.19 nm in height. The endospores within the RLP sporangia are ellipsoidal or almost spherical, narrowly elliptic in section, having axes averaging 1.08 ± 0.21 by 1.29 ±0.1 4 ^m. By contrast, the mature bacterial stages from the root-knot nematode (RKP) occur only in the adult female nematode and not in the larvae. The RKP sporangia are cup-shaped, and average 3.42 ±0.18 ^m in diameter and 2.48 ± 0.22 pm in height. The RKP endospores, also ellipsoidal but broadly elliptic in section, have axes averaging 1.10 ± 0.11 by 1.42 ± 0.12 nm. These several differences strongly suggest that these 2 members of the P. penetrans group belong in separate taxa. Considerable morphological diversity was also evident from light-microscopic examination of members of the P. penetrans group occurring in archival nematode material (genera Dolichodorus, Heterodera, Hoplolaimus, Meloidogyne, Pratylenchus, Tylenchorhynchus, and Xiphinemd) from the USDA Nematode Collection.
Effects of lyophilization on human amniotic membrane (2008)

Lyophilization maintains the histological structure of HAM, but seems to cause greater reductions in total protein amount and growth factor concentration than cryopreservation.
A simple evolutionary algorithm for multi-objective optimization (SEAMO) (2003)

A simple steady-state, Pareto-based evolutionary algorithm is presented that uses an elitist strategy for replacement and a simple uniform scheme for selection. Throughout the genetic search, progress depends entirely on the replacement policy, and no fitness calculations, rankings, subpopulations, niches or auxiliary populations are required. Preliminary results presented in this paper show improvements on previously published results for some multiple knapsack problems.
Navigational Control Effect on Representing Virtual Environments (2003)

This present study investigated how users' navigational devices and modes of operation affect their ability to develop an accurate mental spatial representation of a virtual environment. Three input devices varying in their degree of egocentric calibration control were used for navigation: joystick, wand and headtracker, all of which were used in relative or absolute control mode, thus yielding six navigational method conditions. Participants were tested both in a non-ego-centric manner and in an ego-centric manner, and our hypotheses were that absolute and more ego-centric control devices would generate higher quality spatial mental representations than relative and non-egocentric devices. Experiment results showed that navigation control methods produce different amounts of exploration, and indicated an advantage for absolute mode devices in comparison to relative mode, but there was no benefit for ego-centric devices.
Exposure to methyl mercury results in serum autoantibodies to neurotypic and gliotypic proteins. (1996)

Environmental exposure to methylmercury (MeHg) continues to pose a threat to humans, making early detection of neurotoxic effects a pressing concern. An enzyme-linked immunosorbent assay (ELISA) to measure serum autoantibodies (lg) to neurotypic and gliotypic proteins [neurofilament triplet (NF68; NF160; NF200), myelin basic protein (MBP) and glial fibrillary acid protein (GFAP)] as markers of subclinical neurotoxicity was developed and tested in Fisher 344 rats exposed orally to 16 or 32 ppm MeHg. Both levels of MeHg resulted in serum lg to all 5 proteins, not normally seen in controls. For anti-NFs and anti-GFAP, lgM isotype predominated significantly (p < 0.05) over lgG. lg for MBP were of the lgG isotype, lgM were not detected. Significant differences (p < 0.05) between 16 and 32 ppm MeHg in levels of anti-NF 68 and GFAP, lgM, were evident at 7 days of exposure, but not at 14 days. Anti-NF 160, lgM, was significantly (p < 0.01) elevated in rats exposed to 32 ppm vs 16 ppm at 14 days. However, at both dose levels anti-NF 68 titers were the most elevated of the three NF proteins (p < 0.0001). For anti-NF 200 and anti-MBP it was the lgG isotype that was significantly (p < 0.01) elevated in the 32 ppm group at 7 days. GFAP levels as a marker of neurotoxicity were determined in the cortex, hippocampus and cerebellum. Exposure to 32ppm MeHg resulted in decreased (p < 0.05) levels in the cortex at 14 days. Both levels of MeHg resulted in increased GFAP in the cerebellum at 14 days. This study suggests that assay of autoantibodies against nervous system proteins may provide a means of assessing the early neurotoxic effects of environmental MeHg exposure.
Renal allograft implantation in respect of atypical vascular procedures (2003)

In minority of renal transplants it is unevitable to perform atypical vascular procedures of renal allograft implantation, which increases the risk of vascular complications, graft loss and lethality. In the presenting study, we retrospectively evaluated kinds of atypical vascular procedures in renal allograft implantation by donor type and the transplants outcome related to these procedures. From 1980 to 1998, a total of 463 patients (mean age 36.2+/-10.3), underwent renal transplantation (319 from living donor and 144 from cadaveric donor) at the Institute of Urology & Nephrology in Belgrade. Atypical vascular procedures of renal allograft implantation were representative for the some of the following cohorts: bypass grafting, endarterectomy, end to side both arterial and venous anastomotic site. A total of 45 patients (9.72%) underwent some of atypical vascular procedures (41 from living donor and 4 from cadaveric donor) (p<0.01). Among analyzed procedures, bypass grafting was performed in majority of cases (n=38). A total of 101 patients underwent endarterectomy. End to side both arterial and venous anastomotic site was done in two patients. Severe direct postoperative vascular complications following by lethal outcome appeared in 2 patients. Related to standardized, atypical vascular procedures had been of increased risk for appearance of severe vascular complication.
Compartment monitoring in tibial fractures. The pressure threshold for decompression. (1996)

We made a prospective study of 116 patients with tibial diaphyseal fractures who had continuous monitoring of anterior compartment pressure for 24 hours. Three patients had acute compartment syndrome (2.6%). In the first 12 hours of monitoring, 53 patients had absolute pressures over 30 mmHg and 30 had pressures over 40 mmHg, with four higher than 50 mmHg. Only one patient had a differential pressure (diastolic minus compartment pressure) of less than 30 mmHg; he had a fasciotomy. In the second 12-hour period 28 patients had absolute pressures over 30 mmHg and seven over 40 mmHg. Only two had differential pressures of less than 30 mmHg; they had fasciotomies. None of our 116 patients had any sequelae of the compartment syndrome at their latest review at least six months after injury. A threshold for decompression of 30 mmHg would have indicated that 50 patients (43%) would have required fasciotomy, and at a 40 mmHg threshold 27 (23%) would have been considered for an unnecessary fasciotomy. In our series, the use of a differential pressure of 30 mmHg as a threshold for fasciotomy led to no missed cases of acute compartment syndrome. We recommended that decompression should be performed if the differential pressure level drops to under 30 mmHg.
S-nitrosoglutathione (GSNO) is cytotoxic to intracellular amastigotes and promotes healing of topically treated Leishmania major or Leishmania braziliensis skin lesions (2013)

GSNO is cytotoxic to intracellular L. major amastigotes in vitro and had a healing effect on LCL caused by L. major and L. braziliensis in mice. These positive results on the topical therapeutic effect of GSNO in mouse leishmaniasis infections provide the experimental basis for a possible future trial in the treatment of human LCL.
Autologous tissue repair of large abdominal wall defects (2007)

The CST is the best documented procedure; it is associated with a high morbidity rate of 24.0 per cent and a recurrence rate of 18.2 per cent. Although the results of the da Silva technique are good (morbidity 5-20 per cent and reherniation 0-3 per cent), the poor methodological quality of the studies precludes firm conclusions. Repair with free fascia lata or dermal grafts is an alternative if the above techniques cannot be used, but wound complications affect 42 per cent of patients and recurrent hernia up to 29 per cent. Pedicled or free vascularized flaps are reserved for complex situations.
CD4 and CD8 T-Cell Responses to Mycobacterial Antigens in African Children (2010)

Mycobacteria-specific T-cell responses could be demonstrated in all groups of children, suggesting that the responses could be boosted by new TB vaccines currently in clinical trials.
Dynamic Speed Scaling to Manage Energy and Temperature (2004)

We first consider online speed scaling algorithms to minimize the energy used subject to the constraint that every job finishes by its deadline. We assume that the power required to run at speed s is P(s) = s/sup /spl alpha//. We provide a tight /spl alpha//sup /spl alpha// bound on the competitive ratio of the previously proposed optimal available algorithm. This improves the best known competitive ratio by a factor of 2/sup /spl alpha//. We then introduce an online algorithm, and show that this algorithm's competitive ratio is at most 2(/spl alpha//(/spl alpha/ - 1))/sup /spl alpha//e/sup /spl alpha//. This competitive ratio is significantly better and is approximately 2e/sup /spl alpha/+1/ for large /spl alpha/. Our result is essentially tight for large /spl alpha/. In particular, as /spl alpha/ approaches infinity, we show that any algorithm must have competitive ratio e/sup /spl alpha// (up to lower order terms). We then turn to the problem of dynamic speed scaling to minimize the maximum temperature that the device ever reaches, again subject to the constraint that all jobs finish by their deadlines. We assume that the device cools according to Fourier's law. We show how to solve this problem in polynomial time, within any error bound, using the ellipsoid algorithm.
The plant cell wall matrix harbors a precursor of defense signaling peptides (2005)

Proteins of plant cell walls serve as structural macromolecules and play important roles in morphogenesis and development but have not been reported to be the origins of peptide signals that activate genes for plant defense. We report here that the mRNA coding the tomato leaf polyprotein precursor of three hydroxyproline-rich glycopeptide defense signals (called LeHypSys I, II, and III) is synthesized in phloem parenchyma cells in response to wounding, systemin, and methyl jasmonate, and the nascent protein is sequestered in the cell wall matrix. These findings indicate that the plant cell wall can play an active role in defense as a source of peptide signals for systemic wound signaling.
Burdock Fermented by<i>Aspergillus awamori</i>Elevates Cecal<i>Bifidobacterium</i>, and Reduces Fecal Deoxycholic Acid and Adipose Tissue Weight in Rats Fed a High-Fat Diet (2013)

This study investigated the effects of dietary supplementation with burdock powder and Aspergillus awamori-fermented burdock powder at 5% on the intestinal luminal environment and body fat in rats fed a high-fat (HF) diet. Food intake and growth were unaffected by dietary manipulation. Consumption of the burdock and fermented burdock diets significantly elevated fecal IgA and mucins (indices of intestinal immune and barrier functions) and reduced fecal lithocholic acid (a risk factor for colon cancer) (p<0.05). The fermented burdock diet markedly elevated cecal Bifidobacterium and organic acids, including lactate, acetate, propionate, and butyrate, and reduced fecal deoxycholic acid (a risk factor for colon cancer) and perirenal adipose tissue weight (p<0.05), but the burdock diet did not. These results suggest that consumption of fermented burdock improves the intestinal luminal environment and suppresses obesity in rats fed a HF diet.
Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge (2008)

Amyloid proteins (fimbriae or other microbial surface-associated structures) are expressed by many types of bacteria, not yet identified, in biofilms from various habitats, where they likely are of key importance to biofilm formation and biofilm properties. As these amyloids are potentially of great importance to the floc properties in activated sludge wastewater treatment plants (WWTP), the abundance of amyloid adhesins in activated sludge flocs from different WWTP and the identity of bacteria producing these were investigated. Amyloid adhesins were quantified using a combination of conformationally specific antibodies targeting amyloid fibrils, propidium iodide to target all fixed bacterial cells, confocal laser scanning microscopy, and digital image analysis. The biovolume fraction containing amyloid adhesins ranged from 10 to 40% in activated sludge from 10 different WWTP. The identity of bacteria producing amyloid adhesins was determined using fluorescence in situ hybridization with oligonucleotide probes in combination with antibodies or thioflavin T staining. Among the microcolony-forming bacteria, amyloids were primarily detected among Alpha- and Betaproteobacteria and Actinobacteria. A more detailed analysis revealed that many denitrifiers (from Thauera, Azoarcus, Zoogloea, and Aquaspirillum-related organisms) and Actinobacteria-related polyphosphate-accumulating organisms most likely produced amyloid adhesins, whereas nitrifiers did not. Many filamentous bacteria also expressed amyloid adhesins, including several Alphaproteobacteria (e.g., Meganema perideroedes), some Betaproteobacteria (e.g., Aquaspirillum-related filaments), Gammaproteobacteria (Thiothrix), Bacteroidetes, Chloroflexi (e.g., Eikelboom type 1851), and some foam-forming Actinobacteria (e.g., Gordonia amarae). The results show that amyloid adhesins were an abundant component of activated sludge extracellular polymeric substances and seem to have unexpected, divers functions.
Structural basis for ligand recognition by RGD (Arg-Gly-Asp)-dependent integrins (2004)

Since the discovery of the RGD sequence motif as the essential cell attachment site in Fn (fibronectin), RGD-dependent ligand recognition by integrins has been the major focus of many integrin researches. Although many integrins recognize RGD-containing ligands, it is believed that residues outside the RGD motif provide specificity as well as high affinity for each integrin-ligand pair. These 'secondary' sites are generally assumed to interact directly with the alpha subunit of integrin, whereas the RGD motif binds primarily to the beta subunit. This necessitates that the integrin-ligand interface comprises a relatively large, or even scattered, area. Molecular electron microscopy and single-particle analysis were performed on a headpiece fragment of integrin alpha5beta1 in the presence and absence of bound ligand (Fn fragment), and revealed a marked shape change of the beta subunit hybrid and I-like domains that is linked with the ligand docking. Furthermore, electron microscopy images revealed a focal rather than a large contact area at the alpha5beta1-Fn interface, raising a question about '2-site docking model'. Kinetic analysis of real-time binding data showed that the synergy site greatly enhances kon but has little effect on the stability or koff of the complex, suggesting that the synergy site exerts its positive effect on alpha5beta1 binding by facilitating the initial encounter, rather than by contributing to the protein-protein interaction surface. Thus the ligand recognition mechanism by integrins needs further refinement through more structural analyses of the complexes as well as kinetic analysis of binding data.
D-Homo-steroids. Part I. Derivatives monosubstituted in ring D (1970)

D-Homo-5α-androstan-17a-one, -17-one, and -16-one, and the corresponding epimeric pairs of alcohols and acetates have been prepared. These are valuable reference compounds quasi-enantiomeric to derivatives monosubstituted in ring A. N.m.r. data are considered; o.r.d. and c.d. curves have been treated elsewhere.
Anodic oxidation of amines. VII. Oxidation of .BETA.-alkanolamines in aqueous buffer of pH 10. (1982)

The anodic oxidation of several different types of β-alkanolamines, R1R2C (OH) CR3R4NR5R6, was studied by cyclic voltammetry and controlled potential electrolysis in an aqueous carbonate buffer of pH 10 at a glassy carbon electrode. Upon oxidation, both the (α) C-(β) C and the C-N bonds are cleaved. Substituents R1-R4 affect the first oxidation potential and product distribution. The relative rates of the bond cleavages were estimated from the oxidation products. It was found that most of the amine cleaves through the (α) C-(β) C bond when at least one of the R groups is phenyl, nearly half cleaves through this bond when R is alkyl, and only about a tenth does so when R1-R4 are all hydrogen. The stability of the transient intermediates at the e-c step of the e-c-e process seems to affect the oxidation potentials and to govern the relative rates of the (α) C-(β) C bond cleavage. A scheme for the reaction processes is proposed.