Miracle-dz/UniFAR-FTUs huggingface dataset:
Flow-induced neointimal regression in baboon polytetrafluoroethylene grafts is associated with decreased cell proliferation and increased apoptosis.

OBJECTIVE We have previously shown that baboon grafts subjected to elevated shear stress exhibit an increase in luminal area through atrophy of the neointimal layer. This study was designed to investigate the smooth muscle cell (SMC) growth kinetics during early regression and evaluate the influence of nitric oxide (NO) in the regulation of this process. METHODS Sixteen baboons underwent bilateral polytetrafluorethylene aortoiliac graft placement. After development of a neointima over an 8-week period, blood flow through one graft was increased with placement of a downstream arteriovenous fistula. Grafts were harvested at 4 (n = 6), 7 (n = 5), and 14 (n = 5) days and assessed for neointimal cross-sectional area, SMC proliferation and apoptosis, and macrophage infiltration. High-flow grafts were compared with contralateral normal-flow controls. Eleven baboons underwent an identical experimental preparation to evaluate the effect of NO inhibition. Eight weeks after graft implantation, the animals were treated with an initial bolus (100 mg/kg) followed by continuous infusion (60 mg/kg/d) of either N(G)-nitro-L-arginine methyl ester (L-NAME; n = 6) or the inactive stereoisomer N(G)-nitro-D-arginine methyl ester (n = 5). Grafts were harvested at 7 days and evaluated with the experimental endpoints detailed previously. RESULTS Distal fistula placement resulted in a 3.8-fold increase in mean centerline velocity and wall shear stress. Grafts harvested during the initial 14 days after flow manipulation showed a progressive reduction in neointimal cross-sectional area. This change was associated with a decrease in subendothelial SMC proliferation and an increase in neointimal SMC apoptosis, the latter being in the region adjacent to the graft. Animals treated with L-NAME showed a 20% reduction in platelet cyclic guanosine monophosphate and a 17% reduction in serum nitrate/nitrite concentrations. Despite this inhibition of NO production, no effect on the flow-dependent changes in neointimal area, cell proliferation, or apoptosis was observed in the L-NAME-treated baboons. CONCLUSION The local hemodynamic environment within healing prosthetic grafts modulates neointimal SMC proliferation and apoptosis. An increase in graft flow leads to atrophy of the neointima.
N-terminally Truncated WT1 Protein with Oncogenic Properties Overexpressed in Leukemia*

WT1 was originally identified as an inactivated gene in Wilms tumor, a childhood kidney cancer. Alternative splicing of the WT1 transcript generates four major protein isoforms, each having different functional properties. Here we characterized a short transcript originating from a second promoter located within intron 1 of WT1. This 2.3-kb sWT1 transcript encodes a protein of ∼35–37 kDa that retains intact DNA-binding and transactivation domains but lacks the 147 amino acids at the N terminus required for transcriptional repression. We found sWT1 to be a more potent transcriptional activator than WT1 for cyclin E and insulin-like growth factor 1 receptor promoters, which are normally repressed by WT1. The expression patterns of the sWT1 and WT1 transcripts differed slightly in various organs; we found sWT1 protein in tissue samples from adult testis and fetal kidney, with low-level expression in adult kidney as well. The sWT1 transcript, but not the full-length transcript, was over-expressed in the leukemia samples tested. sWT1-specific small interfering RNA retarded the proliferation of leukemia cell line K562 in vitro. Finally, sWT1 cooperated with Ras in transforming primary fibroblasts in vitro. Further studies are needed to clarify the oncogenic behavior of this isoform and to determine the mechanism underlying its up-regulation in leukemia and other forms of cancer.
An Efficient Hashing-Based Scheme for RIB Management

In consideration of the exact matching characteristic of RIB lookups, we explore the applicability of hashing-based approaches for RIB management and evaluate their performance. Using real routing prefixes, we compare the efficiency of six different hash approaches mentioned in some papers about IP lookups: bit extraction from the routing prefix, CRC16 (cyclic redundancy checking polynomials), CRC32, Fletcher checksum, folding of prefix octets for using the exclusive-or operation and multiplication. This is the first comprehensive study of their performance using real core routing tables. We find that extracting the least significant bits from the routing prefix is a very efficient hash approach for RIB management. Then a RIB management scheme based on this hash approach is proposed. We use separate chaining as the collision resolution strategy, while not suffering from malloc/free overhead for frequent insertion or deletion. To keep the memory storage moderate, we set the hash table sizes based on the distribution of prefix lengths because it is not expected to change significantly with time. Through simulation, we find that this scheme can achieve very fast updates and fast lookups for routing prefixes while keep the memory storage moderate.
DNA Index in childhood acute lymphoblastic leukaemia: a karyotypic method to validate the flow cytometric measurement

The DNA index (DI) is a prognostic factor in childhood acute lymphoblastic leukemia (ALL). The accuracy of DI measurement is important for treatment stratification: hyperdiploidy with DI ≥ 1.16 is predictive of favorable prognosis whereas hypodiploidy is associated with poor prognosis. The aim of this study was to validate the accuracy of the DI measured by flow cytometry (FCM) by comparison with the karyotype. From samples of 112 childhood ALL, we created a formula to calculate a theoretical DNA index (tDI) based on the blast cell karyotype, taking into account the additional or missing chromosome material of the major clone. FCM DI correlated with tDI calculated from karyotype (R = 0.987) and with modal chromosome number (DI = 0.0202 × Modal NB + 0.0675 and R = 0.984). In three cases a hypodiploid blast cell population was detected by FCM, while only the duplicated clone was identified by the karyotype. The strong correlation between tDI and DI validates the accuracy of FCM quantification, which is technically fast on fresh or frozen samples. If the karyotype is essential to analyze chromosomal abnormalities, FCM provides complementary information in aneuploid ALLs, either by confirming the cytogenetic data or by detecting additional clones not identified when only using cytogenetic data.
Localisation of the benzimidazole fungicide binding site of Gibberella zeae β2-tubulin studied by site-directed mutagenesis.

BACKGROUND The efficacy of benzimidazole fungicides is often limited by resistance, and this is the case with the use of carbendazim for controlling Fusarium head blight caused by Gibberella zeae (Schwein.) Petch (anamorph Fusarium graminearum). Recent studies have shown that carbendazim resistance in field strains of G. zeae is associated with mutations in the β(2)-tubulin gene. The aims of the present study were to validate this mechanism and research the binding sites of carbendazim on β(2)-tubulin. RESULTS This work used site-directed mutagenesis followed by gene replacement to change the β(2)-tubulin gene of a carbendazim-sensitive field strain of G. zeae at residues 50, 167, 198 or 200. The transformants were confirmed and tested for their sensitivity to carbendazim. All the mutants were resistant to carbendazim, but the level of resistance differed depending on the mutation. Biological characteristics did not differ between the field strain and the site-directed mutants. A three-dimensional model of β(2)-tubulin was constructed, and the possible carbendazim binding site was analysed. CONCLUSION Mutations at codons 50, 167, 198 and 200 of G. zeae β(2)tub could cause resistance to carbendazim, and these codons may form a binding pocket.
A new control strategy for optimum efficiency operation of a synchronous reluctance motor

In this paper, an optimum efficiency control scheme of synchronous reluctance motors is presented. There exists a variety of combinations of d and q-axis current which provide a specific motor torque. The objective of the optimum efficiency controller is to seek a combination of d and q-axis current components, which provides minimum input power, that is, minimum losses at a certain operating point in steady state. A small amount of perturbation is added to the d-axis current reference for the purpose of searching a minimum input power operating point.
Establishing the evidence base for maintaining biodiversity and ecosystem function in the oil palm landscapes of South East Asia

The conversion of natural forest to oil palm plantation is a major current threat to the conservation of biodiversity in South East Asia. Most animal taxa decrease in both species richness and abundance on conversion of forest to oil palm, and there is usually a severe loss of forest species. The extent of loss varies significantly across both different taxa and different microhabitats within the oil palm habitat. The principal driver of this loss in diversity is probably the biological and physical simplification of the habitat, but there is little direct evidence for this. The conservation of forest species requires the preservation of large reserves of intact forest, but we must not lose sight of the importance of conserving biodiversity and ecosystem processes within the oil palm habitat itself. We urgently need to carry out research that will establish whether maintaining diversity supports economically and ecologically important processes. There is some evidence that both landscape and local complexity can have positive impacts on biodiversity in the oil palm habitat. By intelligent manipulation of habitat complexity, it could be possible to enhance not only the number of species that can live in oil palm plantations but also their contribution to the healthy functioning of this exceptionally important and widespread landscape.
TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis

Primates have evolved a variety of restriction factors that prevent retroviral replication. One such factor, TRIM5α, mediates a postentry restriction in many Old World primates. Among New World primates, Aotus trivirgatus exerts a similar early restriction mediated by TRIMCyp, a TRIM5–cyclophilin A (CypA) chimera resulting from a CypA retrotransposition between exons 7 and 8 of the TRIM5 gene. Macaca nemestrina do not express TRIM5α; therefore, we asked whether these animals and related Old World primates express TRIMCyp. RT-PCR of total RNA from M. nemestrina and Macaca fascicularis yielded three TRIMCyp amplification products, one of which is predicted to encode a TRIMCyp chimera containing a full-length CypA. Unlike A. trivirgatus, genomic sequencing of M. nemestrina and M. fascicularis identifies a CypA retrotransposition in the 3′ untranslated region of the TRIM5 locus. There is ≈78% homology between the predicted protein sequences of Old World and New World primate TRIMCyp, with most of the differences found in the TRIM5-derived sequence. Notably, exon 7 is absent from both M. nemestrina and M. fascicularis TRIMCyp. Neither M. nemestrina nor M. fascicularis TRIMCyp could restrict HIV-1 or simian immunodeficiency virus SIVmac in an in vitro infectivity assay. The discovery of TRIMCyp in both M. nemestrina and M. fascicularis indicates that TRIMCyp expression may be more common among Old World primates than previously believed. Convergent evolution of TRIMCyp in both Old World and New World primates suggests that TRIMCyp may have provided evolutionary advantages.
What Is the Biological Significance of Circulating Blood Levels of Metalloproteinases?

To the Editor: Nikkola et al. ([1][1]), examining pretreatment serum levels of matrix metalloproteinase 9 (MMP)-9 in 71 patients and MMP-1 and MMP-13 in 48 patients with advanced melanoma, showed that MMP-1, MMP-9, and MMP-13 “play important roles at different phases of metastatic melanoma spread
Chromatographic, ultracentrifugal, and related studies of fibrinogen "Baltimore".

Chromatographic, ultracentrifugal, and related studies of the fibrinogen of a patient with a congenital disorder of fibrinogen (fibrinogen "Baltimore" have provided evidence of structural differences from normal.Diethylaminoethyl-cellulose (DEAE-cellulose) gradient elution chromatography demonstrated two major peaks in the elution pattern of fibrinogen Baltimore as was the case for normal fibrinogen. However, the first peak of fibrinogen Baltimore was somewhat broader and more symmetrical and was eluted significantly later in the chromatogram than the corresponding peak of normal fibrinogen. Additionally, in some elution patterns, a shoulder on the ascending limb of peak 1 was present, suggesting the presence of chromatographically "normal" fibrinogen. Thrombin time determinations of eluted column fractions from a chromatogram of propositus fibrinogen supported this conclusion by demonstrating that fibrinogen from the ascending portion of peak 1 behaved functionally more like normal than that later in the chromatogram. Chromatograms of mixtures of propositus and normal fibrinogen confirmed the ability of this technique to distinguish normal from Baltimore fibrinogen. Chromatograms of fibrinogen isolated from two affected daughters displayed the characteristic increased anionic binding of peak 1 fibrinogen. Sedimentation velocity experiments indicated that the S(o) (20, [unk]) of fibrinogen Baltimore was slightly greater (8.13S vs. 7.85S) than that of normal fraction I-4. Differences in concentration dependence (- 0.65 c vs. - 1.30 c for normal) of the sedimentation coefficient could be attributable in part to spatial conformational differences. Molecular sieving experiments in acrylamide gels indicated that the molecular weight of propositus fraction I-2 was about the same as that of normal fibrinogen of comparable solubility (i.e. I-4, mol wt 325,000). Studies of the UV spectra, tyrosine/tryptophan ratios, sialic acid and hexose content, and N-terminal amino acids demonstrated no consistent significant differences from normal fraction I-4.
ZIP4 confers resistance to zinc deficiency-induced apoptosis in pancreatic cancer

Emerging evidence implicates the zinc importer ZIP4 as a critical factor that enhances pancreatic cancer proliferation; however, the role of ZIP4 in promoting pancreatic cancer progression by regulating apoptosis requires elucidation. To determine the effect of ZIP4 on apoptosis, we used cell lines where ZIP4 levels were upregulated or silenced in combination with Chelex 100 treatment to deplete intracellular zinc. Pancreatic cancer xenografts derived from those cells were also included. TUNEL and flow cytometry analysis were used to measure apoptosis and western blotting was used to analyze protein expression for PARP and multiple caspases. Cell cycle profiles were examined by flow cytometry. Zinc depletion by Chelex induced more apoptosis of pancreatic cancer cells in comparison to normal medium, where almost no apoptosis was observed. ZIP4 stably overexpressed MIA PaCa-2 (MIA-ZIP4) cells were more resistant to zinc depletion-induced apoptosis compared with vector control. Conversely, AsPC-1 (AsPC-shZIP4) cells with stable knockdown of ZIP4 were more sensitive to zinc deficiency than control. Resistance to apoptosis mediated by ZIP4 was accomplished by the caspase pathway. In vivo data also confirmed that ZIP4 overexpressed xenografts showed less apoptosis than controls. Cell cycle profiles indicate that silencing of ZIP4 leads to decreased cell population in S phase and G0/G1 arrest. These results described a previously uncharacterized role of ZIP4 in apoptosis resistance and elucidated a novel pathway through which ZIP4 regulates pancreatic cancer growth. This research provides additional evidence for ZIP4 and related signaling cascade as a molecular target for therapeutic intervention in pancreatic cancer.
Efficiency of solid state Photomultipliers in photon number resolution

Solid State Photomultipliers (SSPM) are widely recognized as new generation of photodetectors competitive with APD and PMT in various applications. SSPM advantages are high gain and ultra-low excess noise factor of internal amplification resulting in ability to detect single photons, high photon detection efficiency, fast response and good time resolution. SSPM drawbacks are high dark count rate, high probability of cross-talk and afterpulsing, and low dynamic range. Many applications in Nuclear Science and Medical Imaging for photodetector with scintillator require good energy resolution, which is represented with respect to photodetector itself by pulse height resolution or so-called Photon Number Resolution (PNR). The purpose of this study is to express SSPM PNR in analytical form taking into account excess noise factor of crosstalk and afterpulsing as well as nonlinearity of photoresponse due to limited number of pixels and finite reset time. Normalization of PNR relatively to ideal detector characterizes the intrinsic detector performance in terms of total excess noise factor of photodetection or, inversely, in terms of detective quantum efficiency, which seems to be very powerful tool for SSPM optimization and evaluation of SSPM applicability and competitiveness.
Estimation and testing of genotype and haplotype effects in case‐control studies: comparison of weighted regression and multiple imputation procedures

A popular approach for testing and estimating genotype and haplotype effects associated with a disease outcome is to conduct a population‐based case/control study, in which haplotypes are not directly observed but may be inferred probabilistically from unphased genotype data. A variety of methods exist to analyse the resulting data while accounting for the uncertainty in haplotype assignment, but most focus on the issue of testing the global null hypothesis that no genotype or haplotype effects exist. A more interesting question, once a region of disease association has been identified, is to estimate the relevant genotypic or haplotypic effects and to perform tests of complex null hypotheses such as the hypothesis that some loci, but not others, are associated with disease. Here I examine the assumptions behind, and the performance of, two classes of methods for addressing this question. The first is a weighted regression approach in which posterior probabilities of haplotype assignments are used as weights in a logistic regression analysis, generating a test based on either a weighted pseudo‐likelihood, or a weighted log‐likelihood. The second is a multiple imputation approach using either an improper procedure in which the posterior probabilities are used to generate replicate imputed data sets, or a proper data augmentation procedure. I compare these approaches to a simple expectation substitution (haplotype trend regression) approach. In simulations, all methods gave unbiased parameter estimation but the weighted pseudo‐likelihood, expectation substitution and multiple imputation methods had superior confidence interval coverage. For the weighted pseudo‐likelihood and expectation substitution methods it was necessary to estimate posterior haplotype assignment probabilities using the combined case/control data, whereas for the multiple imputation approaches it was necessary to estimate these probabilities in the case and control groups separately. Overall, multiple imputation was easiest approach to implement in standard statistical software and to extend to more complex models such as those that include gene‐gene or gene‐environment interactions. Genet. Epidemiol. 2006. © 2006 Wiley‐Liss, Inc.
Clock Drawing and Mini-Mental State Examination in Patients with Traumatic Brain Injury

The aim of this study was to compare the performances of patients with mild, moderate, and severe traumatic brain injury (TBI) on the Clock Drawing Test (CDT), the Mini-Mental State Examination (MMSE), and neuropsychological measures as well as to correlate these measures with outcome assessed by the Extended Glasgow Outcome Score. This study was conducted in an acute care early rehabilitation setting on 102 patients with mild, 30 with moderate, and 30 with severe TBI. Patients with moderate and severe TBI showed more impairment on the CDT compared with those with mild TBI. Similar results were obtained for the MMSE, F (2,159df) = 3.789, p = . 025. Finally, a receiver-operating characteristic analysis showed that the CDT and the Trail-Making Test-Part B (TMT-B) in combination have the potential for prediction of outcome in a TBI population. In conclusion, this combination of the CDT and the TMT-B seems to be useful for early assessment of TBI patients.
Unifying Map and Landmark Based Representations for Visual Navigation

This works presents a formulation for visual navigation that unifies map based spatial reasoning and path planning, with landmark based robust plan execution in noisy environments. Our proposed formulation is learned from data and is thus able to leverage statistical regularities of the world. This allows it to efficiently navigate in novel environments given only a sparse set of registered images as input for building representations for space. Our formulation is based on three key ideas: a learned path planner that outputs path plans to reach the goal, a feature synthesis engine that predicts features for locations along the planned path, and a learned goal-driven closed loop controller that can follow plans given these synthesized features. We test our approach for goal-driven navigation in simulated real world environments and report performance gains over competitive baseline approaches.
Nurses' experiences of practice and political reform in long-term aged care in Australia: implications for the retention of nursing personnel.

AIM The aim of the study was to explore registered nurses' experiences in long-term aged care in light of the political reform of aged care services in Australia. BACKGROUND In Australia, the aged care industry has undergone a lengthy period of political and structural reform. Despite reviews into various aspects of these reforms, there has been little consideration of the effect these are having on the practice experiences and retention of nursing staff in long-term care. METHODS In this critical hermeneutic study, 14 nurses from long-term care facilities in Australia were interviewed about their experiences during the reform period. RESULTS The data revealed a sense of tension and conflict between nurses' traditional values, roles and responsibilities and those supported by the reforms. Nurses struggled to re-negotiate both their practice roles and values as the reforms were implemented and the system evolved. Nursing management support was an important aspect in mediating the effect of reforms on nursing staff. CONCLUSION This research highlights both the tensions experienced by nurses in long-term aged care in Australia and the need to re-negotiate nursing roles, responsibilities and values within an evolving care system. This research supports a role for sensitive and proactive nursing management during periods of industry reform as a retention strategy for qualified nursing personnel.