Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of chromosome breakpoints in neuroblastoma at sub‐kilobase resolution using fine‐tiling oligonucleotide array CGH

Understanding the genes and genetic pathways targeted by recurrent chromosomal imbalances in malignancy, along with the molecular mechanisms that generate the imbalances, are important problems in cancer biology. In this report, we demonstrate that oligonucleotide array CGH (oaCGH) analysis can routinely map chromosomal imbalance breakpoints at exon‐level resolution, including imbalances that are single copy number genomic alterations. Different tiling‐path array designs were used in this study: a whole‐genome array with a 6‐kb median probe spacing and fine‐tiling arrays for selected genomic regions with either 50‐ or 140‐bp median probe spacing. In both array formats, oligonucleotide probes were of isothermal design and were tiled through genic and inter‐genic regions. Whole‐genome oaCGH analysis of two neuroblastoma cell lines and three primary tumors led to the identification of 58 chromosomal breakpoints that generated 45 large‐scale partial chromosomal imbalances (>2 Mb). An unexpectedly high proportion (34%) of these breakpoint intervals mapped to regions containing segmental duplications. In addition, 88 smaller‐sized regions (<2 Mb) of imbalance were detected, the majority of which mapped to segmentally duplicated regions and may reflect constitutional copy number polymorphisms. The chromosomal breakpoints for 12 recurrent abnormalities exhibited in neuroblastoma tumors and cell lines, including MYCN amplicon boundaries, loss of 3p, loss of 11q, and gain of 17q, could be mapped to intervals ranging from 50 bp to 10 kb in size using high‐density fine‐tiling oligonucleotide microarrays. Fine‐tiling oaCGH analysis provides an unprecedented level of resolution, allowing detailed mapping of recurrent unbalanced chromosomal abnormalities. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience. wiley.com/jpages/1045‐2257/suppmat/index.html. © 2005 Wiley‐Liss, Inc.
Failure of prophylactic retinopexy in fellow eyes without a posterior vitreous detachment.

OBJECTIVE To describe adverse sequelae of retinal prophylaxis in fellow eyes of patients with rhegmatogenous retinal detachment. DESIGN Records were reviewed for 17 patients who had retinal breaks or detachment subsequent to prophylactic retinopexy applied to the fellow eye (without posterior vitreous detachment) at the time of primary rhegmatogenous retinal detachment surgery. Subsequent treatment included cryotherapeutic and laser retinopexy, scleral buckling, and vitrectomy. RESULTS Of the 17 patients, 12 were male (mean age, 49 years). Laser retinopexy alone was used in 6 cases. Sixteen (94%) developed retinal tears related to acute posterior vitreous detachment, of which 8 (47%) were at the edge of retinopexy and 8 (47%) were in the normal or untreated retina. Thirteen (76%) developed a retinal detachment, of which 11 (85%) did not involve the fovea. Median visual acuity following treatment was 0.18 logMAR (6/9 Snellen equivalent). CONCLUSIONS Prophylactic retinopexy in fellow eyes without posterior detachment is not completely successful and may cause breaks to develop at the edge of treated areas during subsequent acute posterior vitreous detachment. Patient education alone regarding the symptoms of retinal tear and detachment may be preferable to prophylactic retinopexy of the fellow eye in the absence of a posterior vitreous detachment.
Comparative Study of IS6110 Restriction Fragment Length Polymorphism and Variable-Number Tandem-Repeat Typing of Mycobacterium tuberculosis Isolates in the Netherlands, Based on a 5-Year Nationwide Survey

ABSTRACT In order to switch from IS6110 and polymorphic GC-rich repetitive sequence (PGRS) restriction fragment length polymorphism (RFLP) to 24-locus variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates in the national tuberculosis control program in The Netherlands, a detailed evaluation on discriminatory power and agreement with findings in a cluster investigation was performed on 3,975 tuberculosis cases during the period of 2004 to 2008. The level of discrimination of the two typing methods did not differ substantially: RFLP typing yielded 2,733 distinct patterns compared to 2,607 in VNTR typing. The global concordance, defined as isolates labeled unique or identically distributed in clusters by both methods, amounted to 78.5% (n = 3,123). Of the remaining 855 cases, 12% (n = 479) of the cases were clustered only by VNTR, 7.7% (n = 305) only by RFLP typing, and 1.8% (n = 71) revealed different cluster compositions in the two approaches. A cluster investigation was performed for 87% (n = 1,462) of the cases clustered by RFLP. For the 740 cases with confirmed or presumed epidemiological links, 92% were concordant with VNTR typing. In contrast, only 64% of the 722 cases without an epidemiological link but clustered by RFLP typing were also clustered by VNTR typing. We conclude that VNTR typing has a discriminatory power equal to IS6110 RFLP typing but is in better agreement with findings in a cluster investigation performed on an RFLP-clustering-based cluster investigation. Both aspects make VNTR typing a suitable method for tuberculosis surveillance systems.
Nanodiamond graphitization: a magnetic resonance study

We report on the first nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) study of the high-temperature nanodiamond-to-onion transformation. 1H, 13C NMR and EPR spectra of the initial nanodiamond samples and those annealed at 600, 700, 800 and 1800 ° C were measured. For the samples annealed at 600 to 800 ° C, our NMR data reveal the early stages of the surface modification, as well as a progressive increase in sp2 carbon content with increased annealing temperature. Such quantitative experimental data were recorded for the first time. These findings correlate with EPR data on the sensitivity of the dangling bond EPR line width to air content, progressing with rising annealing temperature, that evidences consequent graphitization of the external layers of the diamond core. The sample annealed at 1800 ° C shows complete conversion of nanodiamond particles into carbon onions.
Living without a diagnosis: the parental experience.

AIM the aim of this study was to explore the parental experiences of raising a child without a diagnosis. METHOD qualitative semistructured interviews were conducted with 14 parents recruited through a large Regional Genetics Centre in the United Kingdom. The interview guide was designed to examine issues such as when and why parents started searching for a diagnosis, whether they were still searching, and what psychosocial issues had arisen as a result of not having a diagnosis. Data were analyzed using the Grounded Theory method. RESULTS the parental experience can be viewed as a journey, which comprises of two distinct components: the inner, emotional experience, and the outer, sociological experience. Issues that comprise the emotional journey include the realization that there is a problem, the experience of testing, reasons for wanting a diagnosis, the emotional impact, and active coping mechanisms. Social issues include the experience with professionals, the various support networks accessed by parents, and issues such as education and housing. The issue of frustration was one that occurred throughout the journey. CONCLUSION although some of the experiences cited by parents are common to families raising a child with a diagnosed condition, lack of diagnosis adds a layer of complexity.
Enrichment for Plesiomonas shigelloides from stools

Bile peptone broth and alkaline peptone water (pH 8.5) were examined as enrichment media for the isolation of Plesiomonas shigelloides from stools, with salmonella-shigella agar as the isolation medium. After 423 parallel examinations in two different experiments, bile peptone broth enrichment for 24 h was observed to be six times more effective (P less than 0.01) than direct plating alone on salmonella-shigella agar. Bile peptone broth was found to be twice as effective as alkaline peptone water for the recovery of P. shigelloides from stools.
Kv1 channels selectively prevent dendritic hyperexcitability in rat Purkinje cells

Purkinje cells, the sole output of the cerebellar cortex, encode the timing signals required for motor coordination in their firing rate and activity pattern. Dendrites of Purkinje cells express a high density of P/Q‐type voltage‐gated calcium channels and fire dendritic calcium spikes. Here we show that dendritic subthreshold Kv1.2 subunit‐containing Kv1 potassium channels prevent generation of random spontaneous calcium spikes. With Kv1 channels blocked, dendritic calcium spikes drive bursts of somatic sodium spikes and prevent the cell from faithfully encoding motor timing signals. The selective dendritic function of Kv1 channels in Purkinje cells allows them to effectively suppress dendritic hyperexcitability without hindering the generation of somatic action potentials. Further, we show that Kv1 channels also contribute to dendritic integration of parallel fibre synaptic input. Kv1 channels are often targeted to soma and axon and the data presented support a major dendritic function for these channels.
Models for energy consumption of data structures and algorithms

This deliverable reports our early energy models for data structures and algorithms based on both micro-benchmarks and concurrent algorithms. It reports the early results of Task 2.1 on investigating and modeling the trade-off between energy and performance in concurrent data structures and algorithms, which forms the basis for the whole work package 2 (WP2). The work has been conducted on the two main EXCESS platforms: (1) Intel platform with recent Intel multi-core CPUs and (2) Movidius embedded platform.
Novel features of the ISC machinery revealed by characterization of Escherichia coli mutants that survive without iron–sulfur clusters

Biological assembly of iron–sulfur (Fe–S) clusters is mediated by complex systems consisting of multiple proteins. Escherichia coli possesses two distinct systems called the ISC and SUF machineries encoded by iscSUA‐hscBA‐fdx‐iscX and sufABCDSE respectively. Deletion of both pathways results in absence of the biosynthetic apparatus for Fe–S clusters, and consequent lethality, which has hampered detailed genetic studies. Here we report that modification of the isoprenoid biosynthetic pathway can offset the indispensability of the Fe–S cluster biosynthetic systems and show that the resulting Δisc Δsuf double mutants can grow without detectable Fe–S cluster‐containing proteins. We also constructed a series of mutants in which each isc gene was disrupted in the deletion background of sufABCDSE. Phenotypic analysis of the mutants revealed that Fdx, an essential electron‐transfer Fe–S protein in the ISC machinery, is dispensable under anaerobic conditions, which is similar to the situation with IscA. Furthermore, we found that several suppressor mutations in IscU, an Fe–S scaffold protein responsible for the de novo Fe–S cluster assembly, could bypass the essential role of the chaperone system HscA and HscB. These findings pave the way toward a detailed molecular analysis to understand the mechanisms involved in Fe–S cluster biosynthesis.
Importance of Volume and Concentration for Ropivacaine Interscalene Block in Preventing Recovery Room Pain and Minimizing Motor Block after Shoulder Surgery

Background:This three-staged study estimated the volume and concentration of interscalene ropivacaine that would prevent recovery room pain after shoulder surgery under general anesthesia. Methods:Stages 1/2: Interscalene catheter administration of ropivacaine was by a 10% incremental up–down sequential manner depending on the presence of recovery room pain in the previous patient. Stage 1: Ropivacaine (0.5% volume) was varied from 30 ml. Stage 2: Ropivacaine (20 ml, the ED(volume)95 estimate from stage 1) concentration was varied from 0.45%. Stage 3: Subjects were randomly assigned to receive 30 ml of ropivacaine, 0.5% (“conventional dose”), or 20 ml of ropivacaine, 0.375% (the estimated ED(volume+concentration)95 from stages 1/2). A postoperative elastomeric infusion of 0.2% ropivacaine (2 ml/h) was administered. Grip strength was measured in the recovery room and time to first pain at 24 h. Results:Stage 1 (n = 34): Ropivacaine 0.5% ED(volume)50/ED(volume)95 (95% CI) estimates were 2.7/20.5 ml (2.4–9.5/17.3–25.8). Stage 2 (n = 29): Ropivacaine 20 ml ED(concentration)50/ED(concentration)95 (95% CI) estimates were 0.15/0.34% (0.13–0.30/0.29–0.43). The ED(dose)50 was similar for stages 1/2 (13.5 vs. 30 mg), but the ED(dose)95 was higher for stage 1 (102.5 vs. 68 mg). Stage 3 (n = 40): Satisfaction (0–10) was modestly higher for the new/lower dose (median [interquartile range] = 10 [10–10] versus 9 [8–10], P = 0.007). Pooled data regression analysis showed that increasing ropivacaine concentration increased grip weakness but not block duration. Conclusions:Ropivacaine interscalene block requires a threshold volume and concentration, with concentration primarily determining motor block. When combined with continuous blockade, suprathreshold ropivacaine doses do not significantly prolong primary block duration but may compromise patient satisfaction.
Gross anatomy of the stomach of the dorcas gazelle (Gazella Dorcas, Linnaeus, 1758)

The macroscopic anatomy of the stomach in four adult dorcas gazelle was described. Four adult, two male and two female dorcas gazelle (Gazella dorcas) of the Frigya Zoological Park, Enfidha, Tunisie, were used in this study. The ruminal papillae were distributed unequally in the rumen, and were larger and more abundant within the atrium and in the two saccus cecus. The papillae were absent in dorsal part of the dorsal sac. The ruminal pillars had no papillae. The cellulae reticuli were divided and contained secondary and tertiary crests. The curvatura omasi measured 12.1±0.1 cm. A comparison with literature data for sand gazelles (Gazella subgutturosa marica) emphasises that differences between closely related species that fill similar niches cannot be expected to follow a clear pattern, but yield an inhomogenous picture, with some measurements more tending towards a specific feeding type in the one, and some other measurements tending more towards that feeding type in the other species.We concluded that the stomach morphology of the dorcas gazelle indicates the‘cattle-type’ morphophysiology representative for intermediate feeders.
Atherosclerosis in Patients with Rheumatoid Arthritis

Both Rheumatoid Arthritis (RA) and atherosclerosis are complex polygenic diseases. Previous studies have demonstrated that patients with RA are associated with up to 60% increased risk of cardiovascular disease related death. Nonetheless, the increased cardiovascular morbidity and mortality in patients with RA cannot be entirely explained by traditional risk factors, and likely to be multifactorial. The present article reviews the data supporting the association of RA with cardiovascular risk factors, possible mechanism for developing atherosclerosis and evaluates the potential strategies that may prevent premature atherosclerosis in these patients.
A Novel Scan Segmentation Design for Power Controllability and Reduction in At-Speed Test

The increasing power consumption during the chip testing process has become the bottleneck of chip production and testing for micro-nano VLSI circuits. Numerous low power design-for-testability (DfT) techniques have been proposed to deal with the test power problem, and segmented scan method was shown to be an efficient solution. We propose a new power-aware scan segment architecture, which can accurately control the power of shift and capture cycles at the same time. Since enabling only a subset of scan flip-flops to capture test responses in one cycle compromises the fault coverage, we propose a new method to reduce the fault coverage loss. First, we use a more accurate notion, spoiled nodes, instead of violation edges used in previous works to analyse the ependency of flip-flops, then we use simulated annealing(SA) mechanism to find the best combination of these flip-flops while considering the clock trees' impact. To the best of our knowledge, this is the first work to make shift and capture power in a controllable way with minimum fault coverage loss, small test-data volume and no extra hardware overhead for at-speed transition fault test. Extensive experiments have been performed on reference circuit ISCAS89 and IWLS2005 to verify the effectiveness of the proposed method.
Influence of Bovine Slurry Deposition on the Structure of Nodulating Rhizobium leguminosarum bv. viciae Soil Populations in a Natural Habitat

The population of nodulating R. leguminosarum bv. viciae in soil from a grass-covered valley area which had been used for bovine slurry deposition over a period of 5 years was analyzed. For these studies, a rapid and reproducible method based on enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to identify Rhizobium strains which had infected pea nodules. Soil samples were taken from different areas and further analyzed in plant tests to determine the impact of the application of slurry (polluted or nonpolluted), the slope position (summit or toe), and exposure (north or south). After comparison of all PCR fingerprint patterns, 24 strain groups were defined. Some strain groups from the nonpolluted soil were suppressed in the polluted samples, and new strain groups were detected in the slurry-polluted soil. After analyzing relationships between the strain groups, we determined the influences of local factors on the nodulating R. leguminosarum bv. viciae population. We show that one of those local parameters, slope position, had significantly greater impact on the composition of the Rhizobium population than the presence of slurry.
A diffuse, invaginating cone bipolar cell in primate retina

A bipolar cell type forming invaginating contacts with many cones was found by light and electron microscopy of Golgi preparations of the rhesus monkey retina. This diffuse, invaginating cone bipolar cell resembles, superficially, rod (“mop”) bipolars, and so may correspond to Polyak's “brush” bipolar. However, it differs from rod bipolars in that its dendrites are finer and they end in a single stratum containing cone pedicles in the outer plexiform layer (OPL). In the inner plexiform layer (IPL) its axon terminal is located sclerad (S4) to those of rod bipolars (S5), is thinner, and also more branched, and wider in span than rod bipolar axon terminals. Resectioning of Golgi‐impregnated diffuse, invaginating cone bipolars to study their connections in the OPL shows that their dendrites invaginate as many as seven cone pedicles, and terminate as central elements at the ribbon synaptic complex. Thus, the primate retina has multiple (diffuse) and single (midget) cone‐contacting bipolar cell pathways in both invaginating as well as flat varieties.
Empirical study on the determinants of CO2 emissions: evidence from OECD countries

This article empirically investigates the Environmental Kuznets Curve (EKC) for CO2 emissions in the cases of 11 OECD countries by taking into account the role of nuclear energy in electricity production. The autoregressive distributed lag approach to cointegration is employed as the estimation method. Our results indicate that energy consumption has a positive impact on CO2 emissions in most countries in the study. However, the impact of trade is not statistically significant. The results provide evidence for the role of nuclear power in reducing CO2 emissions only in some countries. Additionally, although the estimated long-run coefficients of income and its square satisfy the EKC hypothesis in Finland, Japan, Korea and Spain, only Finland's EKC turning point is inside the sample period of the study, providing poor evidence in support of the EKC hypothesis.
Pathologic findings from the National Surgical Adjuvant Breast and Bowel Project: prognostic significance of erbB-2 protein overexpression in primary breast cancer.

In order to investigate the prognostic significance of erbB-2 overexpression, immunohistochemical staining for the erbB-2 protein was performed on sections from paraffin blocks of 292 primary invasive breast cancers obtained from women enrolled in the National Surgical Adjuvant Breast and Bowel Project (NSABP) protocol B-06. Positive reaction indicative of erbB-2 overexpression was observed on tumor cells in 62 (21%) samples. Women whose cancers were judged to have erbB-2 overexpression had a significantly worse overall survival (P = .0012) with twice the mortality rate of women without detectable erbB-2 expression. No statistically significant effect was evident for disease-free survival (P = .22). In multivariate analysis, detection of erbB-2 overexpression was the second most predictive independent variable for survival after nodal status. Overexpression of erbB-2 was more common among tumors of poor nuclear grade (29%) than those of good nuclear grade (12%). The association of erbB-2 overexpression with decreased survival was evident only among women with tumors of good nuclear grade. In this subgroup, erbB-2 overexpression was associated with an approximately fivefold increase in mortality rate (P = .00001). The combined predictive value of erbB-2 overexpression and nuclear grade was evident regardless of their lymph node status. These results provide evidence that detection of erbB-2 overexpression may be an independent prognostic variable for patient survival. Moreover, when combined with evaluation of nuclear grade, it may be possible to use immunostaining for erbB-2 protein to identify patients at increased risk from within a relatively low-risk group.
Strike‐slip motion and double ridge formation on Europa

layer thickness of 2 km and shear velocity of 6 � 10 � 7 ms � 1 . Such a velocity is appropriate for diurnal (85 hour) tidal motion. The local increase in temperature may cause � 100 m uplift around the shear zone through thermal buoyancy. The stresses required to produce velocities of order 10 � 7 ms � 1 are similar to estimates for present-day tidal stresses on Europa (10 4 –10 5 Pa). Brittle layer thicknesses >2 km are unlikely to persist at active shear zones because of the effect of shear heating. Shear velocities greater than or equal to � 10 � 6 ms � 1 will give rise to melting at shallow depths. The removal of material by downwards percolation of meltwater may cause surface collapse along the shear zone; inward motion, leading to compression, may also result. The combination of thermally or compression-induced uplift and melt-related collapse may be responsible for the pervasive double ridges seen on Europa’s surface. INDEX TERMS: 5475 Planetology: Solid Surface Planets: Tectonics (8149); 6218 Planetology: Solar System Objects: Jovian satellites; 8120 Tectonophysics: Dynamics of lithosphere and mantle—general; 8160 Tectonophysics: Rheology—general; KEYWORDS: ice, shear zone, melting, viscosity, brittle-ductile transition
Studies of the respiratory activity of Histoplasma capsulatum. I. Aspects of the aerobic metabolism of the yeast phase.

veals that little is known of the respiratory activities of the dimorphic pathogenic fungi. Bernheim (1942) and Levine and Novak (1949, 1950a, 1950b) studied the yeast phase of Blastomyces dermatitidis, and Gale (1952) reported the effect of jS-propionolactone on the metabolism of the same fungal pathogen. Nickerson and Edwards (1949) examined the effect of temperature variation on the respiration of the mycelial and yeast phase of B. dermatitidis and B. brasiliensis. Data on the oxidative metabolism of the mycelial phase of Sporotrichum schenckii has been reported (Bacila et al, 1955). It was of interest, therefore, to investigate certain aspects of the respiratory activity of the yeast phase of the fungal pathogen, Histoplasma capsulatum.