Miracle-dz/UniFAR-FTUs huggingface dataset:
Ploidy Analysis and S‐Phase Fraction Determination by Flow Cytometry of Invasive Adenocarcinomas of the Breast

The results of flow cytometric analysis of ploidy and S-phase fraction for invasive breast cancers have been compared with various clinical and pathologic parameters by many investigators. Ploidy usually has been found to be associated with histologic type, tumor grade, and S-phase fraction values, but not with patient age, menopausal status, tumor size, axillary nodal status, estrogen receptor status, or progesterone receptor status. S-phase fraction values have correlated with histologic type, grade, estrogen receptor status, and progesterone receptor status, but not with menopausal status or axillary nodal status. Although in several studies ploidy and S-phase fraction have been compared with patient outcome, only a few of these reports have stratified data according to the histologic types and grades of the neoplasms. There is conflicting information regarding the value of ploidy analysis for women with either node-negative or node-positive breast carcinoma. Data from a few studies seem to indicate that S-phase fraction alone or in combination with ploidy may be more important prognostically than ploidy alone, although the results have not been uniform. More studies that examine ploidy, S-phase fraction, various important clinical and pathologic variables, and outcome for patients with invasive mammary cancer must be performed before the clinical importance of DNA analysis by flow cytometry becomes known.
Plate Tectonics: A Paradigm under Threat.

This paper looks at the challenges confronting plate tectonics— the ruling paradigm in the earth sciences. The classical model of thin litho- spheric plates moving over a global asthenosphere is shown to be implausi- ble. Evidence is presented that appears to contradict continental drift, seafloor spreading, and subduction, as well as the claim that the oceanic crust is relatively young. The problems posed by vertical tectonic movements are reviewed, including evidence for large areas of submerged continental crust in today's oceans. It is concluded that the fundamental tenets of plate tecton- ics might be wrong.
Parking Sensors: Analyzing and Detecting Parked Domains

A parked domain is an undeveloped domain which has no content other than automatically computed advertising banners and links, used to generate profit. Despite the apparent popularity of this practice, little is known about parked domains and domain parking services that assist domain owners in parking and monetizing unused domains. This paper presents and in-depth exploration of the ecosystem of domain parking services from a security point of view, focusing mostly on the consequences for everyday users who land on parked pages. By collecting data from over 8 million parked domains, we are able to map out the entities that constitute the ecosystem, thus allowing us to analyze the domain owners, parking services, and advertisement syndicators involved. We show that users who land on parked websites are exposed to malware, inappropriate content, and elaborate scams, such as fake antivirus warnings and costly remote “technicians”. At the same time, we find a significant number of parked domains to be abusing popular names and trademarks through typosquatting and through domain names confusingly similar to authoritative ones. Given the extent of observed abuse, we propose a set of features that are representative of parked pages and build a robust client-side classifier which achieves high accuracy with a negligible percentage of false positives.
A Segment-Based Speckle Filter Using Multisensoral Remote Sensing Imagery

In the proposed approach, the well-known enhanced Lee filter is modified to allow the integration of feature outlines-previously extracted from segmented optical images. The filter is applied to several ENVISAT ASAR images that cover urban, agricultural, and forest areas during different plant phenological stages. The performance of this segment-based speckle filter is compared to those of other filters using ratio images, visual interpretation, and statistical indexes. The approach reduces the loss of radiometry and spatial information. It performs comparable to more complex methods and outperforms common techniques
Effect of High Loss on Ignition-Fly Ash on Properties of Concrete Fully Immersed in Sulfate Solution

This paper presents the experimental results of an investigation on the engineering properties and durability of high loss on ignition-fly ash concrete fully immersed in 5% sodium sulfate solution. The fly ash used in this study is a raw material with the loss on ignition of 15.8%, which is much higher than the upper limitation of 6% as stipulated by ASTM C618. Eight concrete mixtures were designed with different water-to-binder ratios of 0.35 and 0.45. For each water-to-binder ratio, the fly ash was used to replace 0%, 10%, 20%, and 30% amount of cement. Test results show that the workability of fresh concrete increased, while its unit weight decreased with increasing the fly ash replacement level. In addition, the concrete mixtures with 10% and 20% fly ash content showed the higher compressive strength, especially at long-term ages, than that of the fly ash-free concrete mixture. Further, all of the fly ash concrete mixtures exhibited the good quality with ultrasonic pulse velocity values of higher than 4100 m/s.
Phosphorylation of AKT/PKB by CK2 is necessary for the AKT‐dependent up‐regulation of β‐catenin transcriptional activity

β‐Catenin is a key protein in the canonical Wnt signaling pathway and in many cancers alterations in transcriptional activity of its components are observed. This pathway is up‐regulated by the protein kinase CK2, but the underlying mechanism of this change is unknown. It has been demonstrated that CK2 hyperactivates AKT/PKB by phosphorylation at Ser129, and AKT phosphorylates β‐catenin at Ser552, which in turn, promotes its nuclear localization and transcriptional activity. However, the consequences of CK2‐dependent hyperactivation of AKT on β‐catenin activity and cell viability have not been evaluated. We assessed this regulatory process by manipulating the activity of CK2 and AKT through overexpression of wild‐type, constitutively active and dominant negative forms of these proteins as well as analyzing β‐catenin‐dependent transcriptional activity, survivin expression and viability in HEK‐293T cells. We observed that CK2α overexpression up‐regulated the β‐catenin transcriptional activity, which correlated to an increased nuclear localization of β‐catenin as well as survivin expression. Importantly, these effects were strongly reversed when an AKT‐S129A mutant was co‐expressed in the same cells, followed by a significant decrease in cell viability but no changes in β‐catenin stability. Taken together, the data suggest that the CK2α‐dependent up‐regulation of β‐catenin activity requires phosphorylation of AKT in human embryonic kidney cells. J. Cell. Physiol. 226: 1953–1959, 2011. © 2010 Wiley‐Liss, Inc.
Balance between Acetylation and Methylation of Histone H3 Lysine 9 on the E2F-Responsive Dihydrofolate Reductase Promoter

ABSTRACT Epigenetic marks that specify silent heterochromatic domains in eucaryotic genomes include methylation of histone H3 lysine 9. Strikingly, active loci in the vicinity of silent domains are sometimes characterized by acetylation of histone H3 lysine 9, suggesting that the balance between these two competitive modifications is important for the establishment of specific chromatin structures. Some euchromatic genes, targeted by the retinoblastoma protein Rb, are also believed to be regulated by histone H3 lysine 9 methylation. Here, we study the dihydrofolate reductase promoter, which is repressed in G0 and at the beginning of G1 by p107 or p130, two Rb-related proteins. We found that these two pocket proteins share with Rb the ability to associate with the histone methyl transferase SUV39H1. SUV39H1 can be recruited to the E2F transcription factor and functions as a transcriptional corepressor. With ChIP assays followed by real-time PCR, we showed that K9 of histone H3 evolves from a hypermethylated state in G0 to a hyperacetylated state at the G1/S transition. Taken together, these results indicate that the temporal regulation of euchromatic promoters may involve controlling the balance between methylation and acetylation of histone H3 lysine 9, a feature previously described for the spatial regulation of chromatin function.
Early weaning by maternal prolactin inhibition leads to higher neuropeptide Y and astrogliosis in the hypothalamus of the adult rat offspring

The suppression of prolactin production with bromocriptine (BRO) in the last 3 d of lactation reduces milk yield (early weaning) and increases the transfer of leptin through the milk, causing hyperleptinaemia in pups. In adulthood, several changes occur in the offspring as a result of metabolic programming, including overweight, higher visceral fat mass, hypothyroidism, hyperglycaemia, insulin resistance, hyperleptinaemia and central leptin resistance. In the present study, we investigated whether overweight rats programmed by early weaning with maternal BRO treatment have hypothalamic alterations in adulthood. We analysed the expression of neuropeptide Y (NPY), cocaine- and amphetamine-regulated transcript (CART), pro-opiomelanocortin (POMC) and α-melanocyte-stimulating hormone (α-MSH) by immunohistochemistry in the following hypothalamic nuclei: medial and lateral arcuate nucleus (ARC); paraventricular nucleus (PVN); lateral hypothalamus (LH). Additionally, we sought to determine whether these programmed rats exhibited hypothalamic inflammation as indicated by astrogliosis. NPY immunostaining showed a denser NPY-positive fibre network in the ARC and PVN (+82 % in both nuclei) of BRO offspring. Regarding the anorexigenic neuropeptides, no difference was found for CART, POMC and α-MSH. The number of astrocytes was higher in all the nuclei of BRO rats. The fibre density of glial fibrillary acidic protein was also increased in both medial and lateral ARC (6·06-fold increase and 9·13-fold increase, respectively), PVN (5·75-fold increase) and LH (2·68-fold increase) of BRO rats. We suggest that early weaning has a long-term effect on the expression of NPY as a consequence of developmental plasticity, and the presence of astrogliosis indicates hypothalamic inflammation that is closely related to overweight and hyperleptinaemia observed in our model.
Authentication analysis of red fruit (Pandanus Conoideus Lam) oil using FTIR spectroscopy in combination with chemometrics.

INTRODUCTION Red fruit (Pandanus conoideus Lam) is endemic plant of Papua, Indonesia and Papua New Guinea. The price of its oil (red fruit oil, RFO) is 10-15 times higher than that of common vegetable oils; consequently, RFO is subjected to adulteration with lower price oils. Among common vegetable oils, canola oil (CaO) and rice bran oil (RBO) have similar fatty acid profiles to RFO as indicated by the score plot of principal component analysis; therefore, CaO and RBO are potential adulterants in RFO. OBJECTIVE To develop FTIR spectroscopy in combination with chemometrics of partial least square regression (PLSR) and discriminant analysis (DA) for authentication of RFO from CaO and RBO. RESULTS The presence of CaO in RFO was better determined at frequency regions of 1200-1050 cm⁻¹; meanwhile, the combined frequency ranges of 1207-1078 and 1747-1600 cm⁻¹ were exploited for quantitative analysis of RBO with acceptable values of coefficient of determination (R²) and errors in calibration, prediction and during cross validation. DA based on Mahalanobis distance was able to discriminate between RFO and RFO adulterated with CaO and RBO. CONCLUSION FTIR spectroscopy combined with PLSR and DA can be successfully used for quantification and classification of oil adulterants in RFO. The developed method is rapid and environmentally friendly and sample preparation is easy.
A survey of the frequency of aminoglycoside antibiotic-resistant genotypes and phenotypes in Escherichia coli in broilers with septicaemia in Hebei, China

Abstract 1. The aim of this study was to investigate the occurrence of aminoglycoside resistance and the prevalence of 6 important modifying enzyme genes, i.e. (strA, strB, aph(3 ′)-IIa, aac(3)-IIa, aac(6 ′)-Ib and ant(3 ″)-Ia), in Escherichia coli strains in broilers with septicaemia in Hebei, China. 2. A total of 111 clinical isolates of E. coli were collected from 46 large-scale farms. Antimicrobial susceptibility tests, using the Kirby–Bauer disc diffusion method, were performed on all 111 isolates. In addition, all were screened for the presence of modifying enzyme genes using the polymerase chain reaction (PCR). 3. The results show that the rates of resistance were as follows: streptomycin: 97.3%, kanamycin: 97.0%, gentamicin: 95.5%, neomycin: 50.5%, amikacin: 46.0%, spectinomycin: 22.5%. Of the genes examined, strB (73.9%) was the most frequently identified gene in the phenotypic resistant isolates, followed in order by: ant(3 ″)-Ia, aac(3)-IIa, aac(6 ′)-Ib, aph(3 ′)-IIa and strA. 4. It is concluded that aminoglycoside resistance in E. coli from broilers with septicaemia remains a serious problem in Hebei, China. This emphasises the need to ban the non-therapeutic use of antibiotics, discourage their misuse and to be continually vigilant by providing appropriate scientific and technological support for the poultry industry.
Nonlinear dynamics of the elliptic instability

In this paper, we analyse by numerical simulations the nonlinear dynamics of the elliptic instability in the configurations of a single strained vortex and a system of two counter-rotating vortices. We show that although a weakly nonlinear regime associated with a limit cycle is possible, the nonlinear evolution far from the instability threshold is, in general, much more catastrophic for the vortex. In both configurations, we put forward some evidence of a universal nonlinear transition involving shear layer formation and vortex loop ejection, leading to a strong alteration and attenuation of the vortex, and a rapid growth of the vortex core size.
Potential Value of Aneurysm Sac Volume Measurements in Addition to Diameter Measurements after Endovascular Aneurysm Repair

Purpose: To investigate the value of aneurysm sac volume measurement in addition to diameter measurements based on computed tomographic angiography (CTA) after endovascular aneurysm repair (EVAR). Methods: Interrogation of a vascular database identified 56 patients (51 men; median age 77 years, range 59–92), 28 with an endoleak and 28 without, who had digital CTA data available at baseline (first postoperative scan) and at 1 and 2 years after EVAR. Total aneurysm volume, transverse maximum diameter (TMD), and orthogonal maximum diameter (OMD; perpendicular to the aortic center lumen line) were compared for all patients and between those with and without endoleak. Differences of 5% for volume and 5 mm for diameters were considered a significant change. Kappa statistics were used to compare measurements. Results: Volumetry detected aneurysm growth in 32 (24%) of 131 scans, which was reflected by TMD in 12 (38%) and by OMD in 14 (44%). Eighteen scans with increasing aneurysm volume were measured in patients with endoleaks, which was documented by TMD in 6 (33%) and by OMD in 8 (44%). Fourteen volume increases were measured in patients without endoleak; both TMD and OMD documented only 43%. Volumetry detected aneurysm shrinkage in 71 (54%) of 131 scans [detected by TMD in 38 (54%) and by OMD in 37 (52%)]. Thirty-two volume decreases were measured in patients with an endoleak, noted by TMD in 18 (56%) and OMD in 14 (44%). Thirty-nine scans showed decreasing volumes in patients without endoleaks; the TMD corresponded in 20 (51%) and the OMD in 23 (59%). The kappa agreements for volume increase were 0.42 (TMD) and 0.35 (OMD) and for volume decrease 0.48 (TMD) and 0.47 (OMD); different thresholds of change produced similar moderate-range kappa values (0.3–0.6). Conclusion: Volumetry detects sac size changes that are not reflected in diameter measurements. Vice versa, diameters can increase without a total volume increase, which might indicate a variety of morphological aneurysm changes. The agreement between volume and diameter measurements using different cutoff values is equally moderate. Volume measurements should be performed in addition to diameter measurements.
Friction stir weave welding (FSWW) of AA6061 aluminium alloy with a novel tool-path pattern

Abstract In this present work, a novel tool-path movement has been implemented in the friction stir welding of AA6061-T6 plates and termed as Friction stir weave welding (FSWW). The aim of this new process is to enhance the weld quality in terms of tensile strength and microstructure properties by the selection of effective process parameters, such as tool-path movements (Step size), spindle speed and weaving rate. The investigation results proved that the tensile strength of AA6061-T6 alloy joints were remarkably affected by the newly developed tool-path pattern. A three factor, three-level Box–Behnken design matrix was used to minimise the number of experiments. A response surface methodology technique was used for developing the objective function. TOPSIS technique was applied to optimise the FSWW process parameters. The optimised results were validated with the derived experimental results.
Web-based learning: effects on learning process and outcome

Educators have witnessed lately a proliferation of Web-based learning applications. These Web-learning environments have made learning much more convenient by stretching the spatial and temporal barriers. Their effectiveness, however, remains to be examined. In this research, the authors study the relative effectiveness of two different types of Web-learning environments: distributed passive learning (DPL) versus distributed interactive learning (DEL) environments. In the DPL environment, the Web is only used to deliver linear learning material, such as Word files and PowerPoint slides. In the DIL environment, however, the learning material is in hypertext format, providing the learner with more exploration and interactivity capabilities. The results of an empirical study show that the DIL environment is superior to the DPL environment in terms of both the learning process and the learning outcome.
Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.

Efforts to resolve Darwin's "abominable mystery"-the origin of angiosperms-have led to the conclusion that Gnetales and various fossil groups are sister to angiosperms, forming the "anthophytes. " Morphological homologies, however, are difficult to interpret, and molecular data have not provided clear resolution of relationships among major groups of seed plants. We introduce two sequence data sets from slowly evolving mitochondrial genes, cox1 and atpA, which unambiguously reject the anthophyte hypothesis, favoring instead a close relationship between Gnetales and conifers. Parsimony- and likelihood-based analyses of plastid rbcL and nuclear 18S rDNA alone and with cox1 and atpA also strongly support a gnetophyte-conifer grouping. Surprisingly, three of four genes (all but nuclear rDNA) and combined three-genome analyses also suggest or strongly support Gnetales as derived conifers, sister to Pinaceae. Analyses with outgroups screened to avoid long branches consistently identify all gymnosperms as a monophyletic sister group to angiosperms. Combined three- and four-gene rooted analyses resolve the branching order for the remaining major groups-cycads separate from other gymnosperms first, followed by Ginkgo and then (Gnetales + Pinaceae) sister to a monophyletic group with all other conifer families. The molecular phylogeny strongly conflicts with current interpretations of seed plant morphology, and implies that many similarities between gnetophytes and angiosperms, such as "flower-like" reproductive structures and double fertilization, were independently derived, whereas other characters could emerge as synapomorphies for an expanded conifer group including Gnetales. An initial angiosperm-gymnosperm split implies a long stem lineage preceding the explosive Mesozoic radiation of flowering plants and suggests that angiosperm origins and homologies should be sought among extinct seed plant groups.
Historical overview of transplantation.

Except for legends and claims of miracles, most histories of transplantation cover only the last 60 years because there were no earlier successes. However, the story of even this era has been documented in such rich detail that a full account would fill several volumes. Thus, this brief summary must be limited to highly selected "landmarks. " Some landmarks had an immediate impact, but the importance of others went unrecognized for decades. Some findings that deserved landmark status were overlooked or forgotten, whereas others of no biological significance had major impact. Placing these events in perspective is challenging. Several of transplantation's pioneers are still alive, and most of the others are within living memory. Virtually all of them have produced their own accounts. For the most part, they agree on what the "landmarks" are, but their differences in emphasis and perspective make an interesting story.
Early Embryogenesis-Specific Expression of the Rice Transposon Ping Enhances Amplification of the MITE mPing

Miniature inverted-repeat transposable elements (MITEs) are numerically predominant transposable elements in the rice genome, and their activities have influenced the evolution of genes. Very little is known about how MITEs can rapidly amplify to thousands in the genome. The rice MITE mPing is quiescent in most cultivars under natural growth conditions, although it is activated by various stresses, such as tissue culture, gamma-ray irradiation, and high hydrostatic pressure. Exceptionally in the temperate japonica rice strain EG4 (cultivar Gimbozu), mPing has reached over 1000 copies in the genome, and is amplifying owing to its active transposition even under natural growth conditions. Being the only active MITE, mPing in EG4 is an appropriate material to study how MITEs amplify in the genome. Here, we provide important findings regarding the transposition and amplification of mPing in EG4. Transposon display of mPing using various tissues of a single EG4 plant revealed that most de novo mPing insertions arise in embryogenesis during the period from 3 to 5 days after pollination (DAP), and a large majority of these insertions are transmissible to the next generation. Locus-specific PCR showed that mPing excisions and insertions arose at the same time (3 to 5 DAP). Moreover, expression analysis and in situ hybridization analysis revealed that Ping, an autonomous partner for mPing, was markedly up-regulated in the 3 DAP embryo of EG4, whereas such up-regulation of Ping was not observed in the mPing-inactive cultivar Nipponbare. These results demonstrate that the early embryogenesis-specific expression of Ping is responsible for the successful amplification of mPing in EG4. This study helps not only to elucidate the whole mechanism of mPing amplification but also to further understand the contribution of MITEs to genome evolution.