Miracle-dz/UniFAR-FTUs huggingface dataset:
Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5′‐terminal Cy5 dyes

By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5′‐indocarbo‐cyanine 5 (5′‐Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5′‐Cy5‐labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5′‐Cy5‐labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5′‐carboxyfluorescein (5′‐FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5′‐labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5′‐Cy5‐labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5′‐Cy5‐labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3′ to 5′ exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.
Development of a semi-submersible autonomous surface vehicle for control of multiple autonomous underwater vehicles

A new autonomous surface vehicle (ASV) has been developed for control of multiple autonomous underwater vehicles (AUVs). Because it is semi-submersible type, the attitude in the sea surface waves is stable though the size is smaller than typical ASV. The cruising speed (3 kt) is confirmed in the testing basin. The operational concepts for control of multiple AUVs are discussed.
Contractile properties of atrial and ventricular myocardium of the heart of rainbow trout oncorhynchus mykiss: effects of thermal acclimation

Atrial and ventricular myocardium perform different tasks in the pumping work of the vertebrate heart, which are reflected in their contractile properties. Although atrial contraction is assumed to have an important role in the function of fish heart, the contractile properties of atrial and ventricular myocardium have not been directly compared in any fish species. The objective of this study was to clarify any contractile differences in the heart of teleost fish and, in particular, to elucidate the contribution of myofibrillar ATPase and intracellular Ca(2+) stores to the characteristics of atrial and ventricular contraction. Experiments were conducted on thermally acclimated rainbow trout Oncorhynchus mykiss to determine whether the effects of temperature adaptation are the same in atrial and ventricular tissue. It was shown that the rate of isometric contraction is much faster in atrial than in ventricular tissue of the fish heart and that acclimation to cold increases the rate of contraction in both cardiac compartments. The rapid contraction kinetics of the atrial tissue were associated with higher myofibrillar ATPase activity and faster Ca(2+) uptake rate of the sarcoplasmic reticulum (SR) compared with ventricular tissue. Similarly, the faster kinetics of contraction following cold acclimation could be attributed to enhancement of the myofibrillar and/or SR function. The atrio-ventricular and temperature-induced differences were also expressed in the recovery of force from inactivation, i.e. in the mechanical restitution. The refractory period and the rate constant of force restitution were shorter in atrial than in ventricular muscle tissue. Similar differences also existed between the tissues of cold-acclimated (CA, 4 degrees C) and warm-acclimated (WA, 17 degrees C) fish. The fast recovery of force from inactivation in the heart of the CA trout was, at least in part, due to more active SR. Furthermore, it was shown that the force of atrial contraction in the CA trout is sensitive to ryanodine (10 (&mgr;)mol l(-)(1)), a Ca(2+)-release channel blocker of SR, at physiological body temperature (4 degrees C) and at a physiological pacing rate (0.6 Hz). This finding indicates that the Ca(2+) stores of SR contribute to activation of cardiac contraction in the fish heart, and that the SR of fish heart is able to retain its Ca(2+) load at low body temperatures, i.e. the Ca(2+ )release channels of SR are not leaky in the cold. The present data show that in the atrial tissue of CA trout, the SR directly contributes to the cytosolic Ca(2+) and that in the atrium and ventricle of CA trout, the SR significantly accelerates the recovery of contractility from inactivation. The fast recovery from inactivation allows relatively high heart rates and therefore adequate cardiac outputs at low environmental temperatures for the cold-active rainbow trout.
Expression of multidrug resistance-associated proteins in paediatric soft tissue sarcomas before and after chemotherapy.

Expression of multidrug resistance (MDR) proteins is thought to significantly contribute to the different biological/clinical behaviour of soft tissue sarcomas (STS) of various histological types and clinicopathological stages, as they are responsible for active efflux of cytotoxic drugs from tumour cells. We investigated the expression of 3 MDR proteins, i.e., permeability glycoprotein 1 (P-gp), multidrug resistance-associated protein 1 (MRP1) and multidrug resistance 3 (MDR3), in 43 STS specimens from newly-diagnosed paediatric patients, 31 with rhabdomyosarcoma (RMS) and 12 with non-RMS STS. To assess the influence of chemotherapy on STS drug resistance, the number of MDR-associated protein-positive cells was determined in 15 patients on both primary lesions before chemotherapy and on residual tumour after chemotherapy. At least one of the MDR-associated proteins tested was detected in 84% of primary untreated STS specimens. In these specimens, MRP1 was detected in a high percentage (70%) of the cases, followed by MDR3 in 58% and P-gp in 44%. Many specimens showed co-expression of two different MDR proteins. Interestingly, MDR3 was significantly associated with the presence of PAX3/PAX7-FKHR transcripts in RMS (p<0.05). Moreover, expression of MRP1 and MDR3 was significantly more frequent in group III and IV tumours as compared with those of groups I and II (p<0.01). After chemotherapy MRP1, MDR3 and, to a lesser extent, P-gp expression was found to be increased in most of the samples. The frequent expression of these MDR-associated proteins in primary tumour cells before chemotherapy and the increase of their levels after chemotherapy, suggest that these proteins play a pivotal role in conferring drug resistance and in producing therapy-induced differentiation on STS.
Does diabetes mellitus influence the perioperative outcome or long term prognosis after resection of hepatocellular carcinoma?

OBJECTIVE:This study aims to evaluate whether diabetes mellitus has a significant influence on the perioperative outcome or long term prognosis after resection of hepatocellular carcinoma (HCC). METHODS:The clinicopathological data and postoperative morbidity and mortality of 62 diabetic and 463 nondiabetic patients who underwent resection of HCC between 1989 and 2000 were compared. The long term overall and disease-free survival results were also compared, and the prognostic impact of diabetes mellitus was assessed by multivariate analysis.RESULTS:The diabetic and nondiabetic groups were comparable in terms of the frequency of cirrhosis, liver function, type of resection, and tumor factors such as size and pTNM stage. Overall complication rate (38.7% vs 37.1%, p = 0.820), 30-day mortality (3.2% vs 3.0%, p = 0.583), and hospital mortality (6.4% vs 6.0%, p = 0.782) were similar in diabetic and nondiabetic patients. There was no significant difference in the overall survival (median = 43.5 vs 43.2 months, p = 0.438) or disease-free survival (median = 18.2 vs 15.0 months, p = 0.418). On multivariate analysis, only tumor pTNM stage, operative blood loss, and preoperative indocyanine green retention at 15 min were significant predictors of overall survival. Tumor pTNM stage, size, and operative blood loss were significant predictors of disease-free survival.CONCLUSIONS:This study indicates that diabetes mellitus does not increase the perioperative morbidity or mortality after resection of HCC, nor does it significantly influence the long term prognosis. Based on the current study data, diabetes mellitus should not be considered an unfavorable factor in the selection of patients for resection of HCC.
Motion-blurred SIFT invariants based on sampling in image deformation space and univariate search

Scale-invariant feature transform (SIFT) operator is a widely used algorithm to detect local features in images, yet applying this algorithm for motion-blurred image matching is difficult and inefficient. To resolve this issue, this study presents a motion-blurred invariant SIFT algorithm that is based on sample matching in an image deformation reconstructed space. First, the motion-blurred equation is deduced and its controlling parameters to reconstruct the deformation space are discretised. Second, the authors matched samples in the motion-blurred space with the blurred image to identify maximal matching points and optimal parameters. In order to improve the searching efficiency, the authors used a univariate search technique combined with a variable step hill-climbing method to determine the optimal matching. Together, the experimental results show that this improved algorithm has superior matching performance for motion-blurred images.
Gastric Sonography in the Fasted Surgical Patient: A Prospective Descriptive Study

BACKGROUND: Aspiration pneumonia remains a serious anesthetic-related complication. A reliable diagnostic tool to assess gastric volume is currently lacking. We recently demonstrated that gastric sonography can provide reliable qualitative and quantitative information about gastric content and volume in healthy volunteers. In the current study, we performed a prospective qualitative and quantitative analysis of the gastric antrum in 200 fasted patients undergoing elective surgery. METHODS: A standardized gastric scanning protocol was applied before anesthetic induction. Patients were classified following a 3-point grading system based solely on qualitative sonographic assessment of the antrum in the supine and right lateral decubitus positions. RESULTS: Eighty-six patients were classified as grade 0 (empty antrum); 107 patients as grade 1 (minimal fluid volume detected only in the right lateral decubitus position); and 7 patients were classified as grade 2 (antrum clearly distended with fluid visible in both supine and lateral positions). The 3-point grading system correlated with total gastric fluid volume as predicted by a previously reported mathematical model. Essentially grade 0 corresponds to a completely empty stomach, grade 1 corresponds to negligible fluid volumes (16 ± 36 mL) within normal ranges expected for fasted patients, and grade 2 correlates with significantly higher predicted gastric fluid volumes (180 ± 83 mL) beyond previously reported “safe” limits. One patient with a grade 2 antrum had an episode of significant regurgitation of gastric contents on emergence from anesthesia. CONCLUSION: We propose a 3-point grading system based exclusively on qualitative sonographic assessment of the gastric antrum that correlates well with predicted gastric volume. This grading system could be a promising “biomarker” to assess perioperative aspiration risk. Before it can be applied widely to clinical practice, this diagnostic tool needs to be further validated and characterized.
Wavelet Statistics of Sparse and Self-Similar Images

It is well documented that natural images are compressible in wavelet bases and tend to exhibit fractal properties. In this paper, we investigate statistical models that mimic these behaviors. We then use our models to make predictions on the statistics of the wavelet coefficients. Following an innovation modeling approach, we identify a general class of finite-variance self-similar sparse random processes. We first prove that spatially dilated versions of self-similar sparse processes are asymptotically Gaussian as the dilation factor increases. Based on this fundamental result, we show that the coarse-scale wavelet coefficients of these processes are also asymptotically Gaussian, provided the wavelet has enough vanishing moments. Moreover, we quantify the degree of Gaussianity by deriving the theoretical evolution of the kurtosis of the wavelet coefficients across scales. Finally, we apply our analysis to one- and two-dimensional signals, including natural images, and show that the wavelet coefficients .
Ranibizumab for neovascular age-related macular degeneration.

BACKGROUND Ranibizumab--a recombinant, humanized, monoclonal antibody Fab that neutralizes all active forms of vascular endothelial growth factor A--has been evaluated for the treatment of neovascular age-related macular degeneration. METHODS In this multicenter, 2-year, double-blind, sham-controlled study, we randomly assigned patients with age-related macular degeneration with either minimally classic or occult (with no classic lesions) choroidal neovascularization to receive 24 monthly intravitreal injections of ranibizumab (either 0.3 mg or 0.5 mg) or sham injections. The primary end point was the proportion of patients losing fewer than 15 letters from baseline visual acuity at 12 months. RESULTS We enrolled 716 patients in the study. At 12 months, 94.5% of the group given 0.3 mg of ranibizumab and 94.6% of those given 0.5 mg lost fewer than 15 letters, as compared with 62.2% of patients receiving sham injections (P<0.001 for both comparisons). Visual acuity improved by 15 or more letters in 24.8% of the 0.3-mg group and 33.8% of the 0.5-mg group, as compared with 5.0% of the sham-injection group (P<0.001 for both doses). Mean increases in visual acuity were 6.5 letters in the 0.3-mg group and 7.2 letters in the 0.5-mg group, as compared with a decrease of 10.4 letters in the sham-injection group (P<0.001 for both comparisons). The benefit in visual acuity was maintained at 24 months. During 24 months, presumed endophthalmitis was identified in five patients (1.0%) and serious uveitis in six patients (1.3%) given ranibizumab. CONCLUSIONS Intravitreal administration of ranibizumab for 2 years prevented vision loss and improved mean visual acuity, with low rates of serious adverse events, in patients with minimally classic or occult (with no classic lesions) choroidal neovascularization secondary to age-related macular degeneration. (ClinicalTrials.gov number, NCT00056836 [ClinicalTrials.gov].).
Incidental Abdominal Aneurysms

We evaluated the frequency and outcomes of abdominal aortic aneurysm (AAA) in Qatar. Data were collected retrospectively between 2004 and 2008 for all adult patients who underwent abdominal computed tomographic scanning for any reason. Patients with AAA were followed up for 3 years for aneurysmal rupture and mortality. Of the 13 115 patients screened, 61 (0.5%) patients had abdominal aneurysms. Most (82%) patients with AAA were male with mean age of 67 ± 12 years. The incidence of AAA substantially increased with age. Cardiovascular risk factors were prevalent among patients with AAA. The main location of AAA was infrarenal (67%), followed by thoracoabdominal (23%). The mean AAA diameter was 5.3 ± 2.5 cm. The rate of AAA rupture was 8% with a mortality rate of 60%; 80% of these were infrarenal, and 80% of them had a diameter of ≥5.5 cm. Overall mortality was 33%. This large study addressed the impact of screening for AAA in a population with high cardiovascular burden.
On the role of astroglial syncytia in self-repairing spiking neural networks

It has been shown that brain-like self-repair can arise from the interactions between neurons and astrocytes where endocannabinoids are synthesized and released from active neurons. This retrograde messenger feeds back to local synapses directly and indirectly to distant synapses via astrocytes. This direct/indirect feedback of the endocannabinoid retrograde messenger results in the modulation of the probability of release (PR) at synaptic sites. When synapses fail, there is a corresponding falloff in the firing activity of the associated neurons, and hence the strength of the direct feedback messenger diminishes. This triggers an increase in PR of healthy synapses, due to the indirect messenger from other active neurons, which is the catalyst for the repair process. In this paper, the repair process is implemented by developing a new learning rule that captures the spike-timing-dependent plasticity and Bienenstock, Cooper, and Munro learning rules. The rule is activated by the increase in PR and results in a potentiation of the weight values, which reestablishes the firing activity of neurons. In addition, this self-repairing mechanism is extended to network-level repair where astrocyte to astrocyte communications are implemented using a linear gap junction model. This facilitates the implementation of an astroglial syncytium involving multiple astrocytes, which relays the indirect feedback messenger to distant neurons: each astrocyte is bidirectionally coupled to neurons. A detailed and comprehensive set of results with analysis is presented demonstrating repair at both cellular and network levels.
A New K-anonymity Algorithm towards Multiple Sensitive Attributes

While k-anonymity algorithm has been used widely to prevent privacy disclosure in datasets published with single sensitive attribute. We improve k-anonymity algorithm to protect privacy in multiple sensitive attributes. Based on greedy strategy, we sort sensitive attributes and tuples first. We distribute tuples to equivalence classes evenly according to sensitive values in high degree. We use statistic information to cut off association among sensitive attributes to prevent positive and negative privacy disclosure. Information entropy is introduced as metric of diversity. Experiments on real dataset showed that our algorithm is effective and efficient.
Akt Protein Kinase Inhibits Non-apoptotic Programmed Cell Death Induced by Ceramide*

A growing body of evidence now suggests that programmed cell death (PCD) occurs via non-apoptotic mechanisms as well as by apoptosis. In contrast to apoptosis, however, the molecular mechanisms involved in the regulation of non-apoptotic PCD remain only poorly understood. Here we show that ceramide induces a non-apoptotic PCD with a necrotic-like morphology in human glioma cells. Characteristically, the cell death was not accompanied by loss of the mitochondrial transmembrane potential, cytosolic release of cytochrome c from mitochondria, or the activation of the caspase cascade. Consistent with these characteristics, this ceramide-induced cell death was inhibited neither by the overexpression of Bcl-xL nor by the pan-caspase inhibitor zVAD-fmk. However, strikingly, the ceramide-induced non-apoptotic cell death was inhibited by the activation of the Akt/protein kinase B pathway through the expression of a constitutively active version of Akt. The results for the first time indicate that the Akt kinase, known to play an essential role in survival factor-mediated inhibition of apoptotic cell death, is also involved in the regulation of non-apoptotic PCD.
C-Terminal Flap Endonuclease (rad27) Mutations: Lethal Interactions With a DNA Ligase I Mutation (cdc9-p) and Suppression by Proliferating Cell Nuclear Antigen (POL30) in Saccharomyces cerevisiae

During lagging-strand DNA replication in eukaryotic cells primers are removed from Okazaki fragments by the flap endonuclease and DNA ligase I joins nascent fragments. Both enzymes are brought to the replication fork by the sliding clamp proliferating cell nuclear antigen (PCNA). To understand the relationship among these three components, we have carried out a synthetic lethal screen with cdc9-p, a DNA ligase mutation with two substitutions (F43A/F44A) in its PCNA interaction domain. We recovered the flap endonuclease mutation rad27-K325* with a stop codon at residue 325. We created two additional rad27 alleles, rad27-A358* with a stop codon at residue 358 and rad27-pX8 with substitutions of all eight residues of the PCNA interaction domain. rad27-pX8 is temperature lethal and rad27-A358* grows slowly in combination with cdc9-p. Tests of mutation avoidance, DNA repair, and compatibility with DNA repair mutations showed that rad27-K325* confers severe phenotypes similar to rad27Δ, rad27-A358* confers mild phenotypes, and rad27-pX8 confers phenotypes intermediate between the other two alleles. High-copy expression of POL30 (PCNA) suppresses the canavanine mutation rate of all the rad27 alleles, including rad27Δ. These studies show the importance of the C terminus of the flap endonuclease in DNA replication and repair and, by virtue of the initial screen, show that this portion of the enzyme helps coordinate the entry of DNA ligase during Okazaki fragment maturation.
Clonal precursor of bone, cartilage, and hematopoietic niche stromal cells

Organs are composites of tissue types with diverse developmental origins, and they rely on distinct stem and progenitor cells to meet physiological demands for cellular production and homeostasis. How diverse stem cell activity is coordinated within organs is not well understood. Here we describe a lineage-restricted, self-renewing common skeletal progenitor (bone, cartilage, stromal progenitor; BCSP) isolated from limb bones and bone marrow tissue of fetal, neonatal, and adult mice. The BCSP clonally produces chondrocytes (cartilage-forming) and osteogenic (bone-forming) cells and at least three subsets of stromal cells that exhibit differential expression of cell surface markers, including CD105 (or endoglin), Thy1 [or CD90 (cluster of differentiation 90)], and 6C3 [ENPEP glutamyl aminopeptidase (aminopeptidase A)]. These three stromal subsets exhibit differential capacities to support hematopoietic (blood-forming) stem and progenitor cells. Although the 6C3-expressing subset demonstrates functional stem cell niche activity by maintaining primitive hematopoietic stem cell (HSC) renewal in vitro, the other stromal populations promote HSC differentiation to more committed lines of hematopoiesis, such as the B-cell lineage. Gene expression analysis and microscopic studies further reveal a microenvironment in which CD105-, Thy1-, and 6C3-expressing marrow stroma collaborate to provide cytokine signaling to HSCs and more committed hematopoietic progenitors. As a result, within the context of bone as a blood-forming organ, the BCSP plays a critical role in supporting hematopoiesis through its generation of diverse osteogenic and hematopoietic-promoting stroma, including HSC supportive 6C3(+) niche cells.