Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Ki67 Expression across Distinct Categories of Breast Cancer Specimens: A Population-Based Study of Matched Surgical Specimens, Core Needle Biopsies and Tissue Microarrays

Introduction Tumor cell proliferation in breast cancer is strongly prognostic and may also predict response to chemotherapy. However, there is no consensus on counting areas or cut-off values for patient stratification. Our aim was to assess the matched level of proliferation by Ki67 when using different tissue categories (whole sections, WS; core needle biopsies, CNB; tissue microarrays, TMA), and the corresponding prognostic value. Methods We examined a retrospective, population-based series of breast cancer (n = 534) from the Norwegian Breast Cancer Screening Program. The percentage of Ki67 positive nuclei was evaluated by visual counting on WS (n = 534), CNB (n = 154) and TMA (n = 459). Results The median percentage of Ki67 expression was 18% on WS (hot-spot areas), 13% on CNB, and 7% on TMA, and this difference was statistically significant in paired cases. Increased Ki67 expression by all evaluation methods was associated with aggressive tumor features (large tumor diameter, high histologic grade, ER negativity) and reduced patient survival. Conclusion There is a significant difference in tumor cell proliferation by Ki67 across different sample categories. Ki67 is prognostic over a wide range of cut-off points and for different sample types, although Ki67 results derived from TMA sections are lower compared with those obtained using specimens from a clinical setting. Our findings indicate that specimen specific cut-off values should be applied for practical use.
The ultraviolet properties of star-forming galaxies – I. HST WFC3 observations of very high redshift galaxies

The acquisition of deep near-IR imaging with Wide Field Camera 3 on the Hubble Space Telescope has provided the opportunity to study the very high redshift Universe. For galaxies up to z≈ 7.7 sufficient wavelength coverage exists to probe the rest-frame ultraviolet (UV) continuum without contamination from either Lyman α emission or the Lyman α break. In this work we use near-infrared (near-IR) imaging to measure the rest-frame UV continuum colours of galaxies at 4.7 < z < 7.7. We have carefully defined a colour–colour selection to minimize any inherent bias in the measured UV continuum slope for the drop-out samples. For the highest redshift sample (6.7 < z < 7.7), selected as zf850lp-band drop-outs, we find mean UV continuum colours approximately equal to zero (AB), consistent with a dust-free, solar metallicity, star-forming population (or a moderately dusty population of low metallicity). At lower redshift we find that the mean UV continuum colours of galaxies (over the same luminosity range) are redder, and that galaxies with higher luminosities are also slightly redder on average. One interpretation of this is that lower redshift and more luminous galaxies are dustier; however, this interpretation is complicated by the effects of the star formation history and metallicity and potentially the initial mass function on the UV continuum colours.
Computational Diversity in Complex Cells of Cat Primary Visual Cortex

A previous study has suggested that complex cells perform a MAX-like operation on their inputs: when two bar stimuli are presented within the receptive field, regardless of their relative separation, the cell's response is similar in amplitude to the larger of the responses elicited by the individual stimuli. This description of complex cells seems at odds with the classical energy model in which complex cells receive input from multiple simple cells with overlapping receptive fields. The energy model predicts, and experiments have confirmed, that bar stimuli should facilitate or suppress one another depending on their relative separation. We have recorded intracellularly from a population of complex cells and studied their responses to paired bar stimuli in detail. A wide range of behavior was observed, from the more classical separation-dependent interactions to purely MAX-like responses. We also found that the more MAX-like a cell was, the broader its spatial-frequency tuning as measured with drifting gratings. These observations are consistent with energy models in which classical complex cells receive input from simple cells with similar preferred spatial frequencies, and MAX-like complex cells receive input from simple cells with disparate preferred spatial frequencies. Generalized energy models, then, can account for diverse modes of computation in cortical complex cells.
A comparative analysis of Hindi word sense disambiguation and its approaches

Hindi language is written and spoken by majority of people in India. Like other natural languages, Hindi is also an ambiguous language which creates obstacle in usage of information technology properly. To use Hindi language efficiently and effectively on web, we require a tool to remove ambiguity from a single word, or from all words, called word sense disambiguation (WSD). In this paper we introduce the reader to the brief introduction of task, resources required for disambiguation, applications, brief review of previous works. We also compare and investigate different techniques and algorithms under these approaches which can be used for Hindi Word Sense Disambiguation (HWSD) task and finally, some open problems, conclusion and future directions are discussed on the basis of these comparisons.
A method to draw lessons from project postmortem databases

Postmortem project reviews often yield useful lessons learned. These project reviews are mostly recorded in plain text. This makes it difficult to derive useful overall findings from a set of such postmortem reviews, e.g. to monitor and guide a software process improvement program. We have developed a five-step method to transform the qualitative, natural language-type information present in those reports into quantitative information. This quantitative information can be analyzed statistically and related to other types of quantitative project-specific information. In this article, we discuss the method, and show the results of applying it in the setting of a large industrial software process improvement initiative. Through the application of the analysis method in the case study, improved questions for a new evaluation procedure were discovered. The analysis also showed that in this organization team cooperation and the architecture of the infrastructure had a major impact on project performance. Copyright © 2006 John Wiley & Sons, Ltd.
A Developed Restricted Rotation for Binary Trees Transformation

In this paper, we use four types of restricted rotations for tree transformation proposed by Wu et al [13] and develop their algorithm to transform weight sequences between any two binary trees. Converting a source tree to a destination tree, it is not necessary to rotate each pair of corresponding nodes whose weights are the same. From the proposed algorithm, we can also obtain an upper bound of n - 1 between any two binary trees.
Abnormal Ca2+ Spark/STOC Coupling in Cerebral Artery Smooth Muscle Cells of Obese Type 2 Diabetic Mice

Diabetes is a major risk factor for stroke. However, the molecular mechanisms involved in cerebral artery dysfunction found in the diabetic patients are not completely elucidated. In cerebral artery smooth muscle cells (CASMCs), spontaneous and local increases of intracellular Ca2+ due to the opening of ryanodine receptors (Ca2+ sparks) activate large conductance Ca2+-activated K+ (BK) channels that generate spontaneous transient outward currents (STOCs). STOCs have a key participation in the control of vascular myogenic tone and blood pressure. Our goal was to investigate whether alterations in Ca2+ spark and STOC activities, measured by confocal microscopy and patch-clamp technique, respectively, occur in isolated CASMCs of an experimental model of type-2 diabetes (db/db mouse). We found that mean Ca2+ spark amplitude, duration, size and rate-of-rise were significantly smaller in Fluo-3 loaded db/db compared to control CASMCs, with a subsequent decrease in the total amount of Ca2+ released through Ca2+ sparks in db/db CASMCs, though Ca2+ spark frequency remained. Interestingly, the frequency of large-amplitude Ca2+ sparks was also significantly reduced in db/db cells. In addition, the frequency and amplitude of STOCs were markedly reduced at all voltages tested (from −50 to 0 mV) in db/db CASMCs. The latter correlates with decreased BK channel β1/α subunit ratio found in db/db vascular tissues. Taken together, Ca2+ spark alterations lead to inappropriate BK channels activation in CASMCs of db/db mice and this condition is aggravated by the decrease in the BK β1 subunit/α subunit ratio which underlies the significant reduction of Ca2+ spark/STOC coupling in CASMCs of diabetic animals.
Designing and Annotating Metro Maps with Loop Lines

Schematic metro maps provide an effective means of simplifying the geographical configuration of public rapid transportation systems. Nonetheless, travelers still find it difficult to identify routes of a specific topology on the maps because it is usually hidden behind the conventional octilinear layout of the entire map. In this paper, we present an approach to designing schematic maps with loop lines, which are drawn as circles together with annotation labels for guiding different traveling purposes. Our idea here is to formulate the aesthetic criteria as mathematical constraints in the mixed-integer programming model, which allows us to either align stations on the loop line at a grid if they are interchange stations or noninterchange stations on a circle otherwise. We then distribute the annotation labels associated with stations on the loop line evenly to the four side boundary of the map domain in order to make full use of the annotation space, while maximally avoiding intersections between leader lines and the metro network by employing a flow network algorithm. Finally, we present several experimental results generated by our prototype system to demonstrate the feasibility of the proposed approach.
Fecal Indicators in Sand, Sand Contact, and Risk of Enteric Illness Among Beachgoers

Background: Beach sand can harbor fecal indicator organisms and pathogens, but enteric illness risk associated with sand contact remains unclear. Methods: In 2007, visitors at 2 recreational marine beaches were asked on the day of their visit about sand contact. Ten to 12 days later, participants answered questions about health symptoms since the visit. F+ coliphage, Enterococcus, Bacteroidales, fecal Bacteroides, and Clostridium spp. in wet sand were measured using culture and molecular methods. Results: We analyzed 144 wet sand samples and completed 4999 interviews. Adjusted odds ratios (aORs) were computed, comparing those in the highest tertile of fecal indicator exposure with those who reported no sand contact. Among those digging in sand compared with those not digging in sand, a molecular measure of Enterococcus spp. (calibrator cell equivalents/g) in sand was positively associated with gastrointestinal (GI) illness (aOR = 2.0 [95% confidence interval (CI) = 1.2–3.2]) and diarrhea (2.4 [1.4–4.2]). Among those buried in sand, point estimates were greater for GI illness (3.3 [1.3–7.9]) and diarrhea (4.9 [1.8–13]). Positive associations were also observed for culture-based Enterococcus (colony-forming units/g) with GI illness (aOR digging = 1.7 [1.1–2.7]) and diarrhea (2.1 [1.3–3.4]). Associations were not found among nonswimmers with sand exposure. Conclusions: We observed a positive relationship between sand-contact activities and enteric illness as a function of concentrations of fecal microbial pollution in beach sand.
On the Numerical Solution for Singularly Perturbed Second-order ODEs

In this article we consider the approximation of singularly perturbed boundary value problems using a local adaptive grid h-refinement for finite element method, the variation iteration method and the homotopy perturbation method. The solution to such problems contains boundary layers which overlap and interact and the numerical approximation must take this into account in order for the resulting scheme to converge uniformly with respect to the singular perturbation parameters. The results obtained by these methods are compared to the exact solutions for some model problems. It is found that the local adaptive grid h-refinement for finite element method is highly stable methods and always converges to the solution independently on the singular perturbation parameters.
A Robotics-Based Behavioral Paradigm to Measure Anxiety-Related Responses in Zebrafish

Zebrafish are gaining momentum as a laboratory animal species for the study of anxiety-related disorders in translational research, whereby they serve a fundamental complement to laboratory rodents. Several anxiety-related behavioral paradigms, which rest upon the presentation of live predatorial stimuli, may yield inconsistent results due to fatigue, habituation, or idiosyncratic responses exhibited by the stimulus itself. To overcome these limitations, we designed and manufactured a fully controllable robot inspired by a natural aquatic predator (Indian leaf fish, Nandus nandus) of zebrafish. We report that this robot elicits aversive antipredatorial reactions in a preference test and that data obtained therein correlate with data observed in traditional anxiety- and fear-related tests (light/dark preference and shelter-seeking). Finally, ethanol administration (0.25; 0.50; 1.00%) exerts anxiolytic effects, thus supporting the view that robotic stimuli can be used in the analysis of anxiety-related behaviors in zebrafish.
Engineering the Myocardial Niche in a Microscale Self-assembling Tissue-mimetic in vitro Model

Drugand cell-based strategies for treating heart disease, including myocardial infarction, face significant roadblocks on the path to the clinic, a primary obstacle being the lack of informationrich in vitro human model systems. Conventional model systems are hampered by at least one of three fundamental limitations which include a) the lack of an in vivo-like microenvironment specifically engineered for the input cell population, b) a relatively low-throughput assays, and c) the low-content nature of output parameters. Herein we describe an integrated computational, design, and experimental strategy for the rational design of a microfabricated high-content screening platform which we term the Cardiac MicroWire (CMW) system. Within this system, we recapitulate the basic microenvironment found in the heart, one which integrates cardiomyocytes, non-myocytes, the extracellular matrix, and dynamic electromechanical forces. CMW are morphologically reproducible, maintain high cardiac sarcomeric protein expression in a highly dense, aligned, and suspended 3-D extracellular matrix, exhibit normal electrophysiological responsiveness, can be generated hundreds at a time. Application of this system to CMW composed of human Embryonic Stem Cell-derived cardiomyocytes under a rapid (7-day) maturation regimen yielded CMW with a conduction velocity of 47.4 ± 12.4 cm/s, on par with healthy human heart tissue. These results highlight the CMW system’s potential as a powerful discovery tool for screening small molecules and transplantable cells toward heart regeneration therapies.
Overlapping Parietal Activity in Memory and Perception: Evidence for the Attention to Memory Model

The specific role of different parietal regions to episodic retrieval is a topic of intense debate. According to the Attention to Memory (AtoM) model, dorsal parietal cortex (DPC) mediates top–down attention processes guided by retrieval goals, whereas ventral parietal cortex (VPC) mediates bottom–up attention processes captured by the retrieval output or the retrieval cue. This model also hypothesizes that the attentional functions of DPC and VPC are similar for memory and perception. To investigate this last hypothesis, we scanned participants with event-related fMRI whereas they performed memory and perception tasks, each comprising an orienting phase (top–down attention) and a detection phase (bottom–up attention). The study yielded two main findings. First, consistent with the AtoM model, orienting-related activity for memory and perception overlapped in DPC, whereas detection-related activity for memory and perception overlapped in VPC. The DPC overlap was greater in the left intraparietal sulcus, and the VPC overlap in the left TPJ. Around overlapping areas, there were differences in the spatial distribution of memory and perception activations, which were consistent with trends reported in the literature. Second, both DPC and VPC showed stronger connectivity with medial-temporal lobe during the memory task and with visual cortex during the perception task. These findings suggest that, during memory tasks, some parietal regions mediate similar attentional control processes to those involved in perception tasks (orienting in DPC vs. detection in VPC), although on different types of information (mnemonic vs. sensory).
Genetic Heterogeneity of Self-Reported Ancestry Groups in an Admixed Brazilian Population

Background Population stratification is the main source of spurious results and poor reproducibility in genetic association findings. Population heterogeneity can be controlled for by grouping individuals in ethnic clusters; however, in admixed populations, there is evidence that such proxies do not provide efficient stratification control. The aim of this study was to evaluate the relation of self-reported with genetic ancestry and the statistical risk of grouping an admixed sample based on self-reported ancestry. Methods A questionnaire that included an item on self-reported ancestry was completed by 189 female volunteers from an admixed Brazilian population. Individual genetic ancestry was then determined by genotyping ancestry informative markers. Results Self-reported ancestry was classified as white, intermediate, and black. The mean difference among self-reported groups was significant for European and African, but not Amerindian, genetic ancestry. Pairwise fixation index analysis revealed a significant difference among groups. However, the increase in the chance of type 1 error was estimated to be 14%. Conclusions Self-reporting of ancestry was not an appropriate methodology to cluster groups in a Brazilian population, due to high variance at the individual level. Ancestry informative markers are more useful for quantitative measurement of biological ancestry.
Facial expression recognition using high order directional derivative local binary patterns

The most expressive manner which human can reveal his emotional states is facial expression. Automatic facial expression recognition is an emerging field of study having extensive applications among which the human-computer interaction (HCI) has received lots of attentions in recent years. The features extracted from facial images, in order to recognize facial expressions, play an essential role in effectiveness of the facial image descriptors. Local binary pattern (LBP) texture descriptors have been known as simple, yet efficient descriptors which are noticeably used for extracting facial patterns from images. Recently, a generalized form of local binary pattern has been introduced which can offer a more precise image description than simple LBP descriptors. Consequently, it would be expected that taking the advantage of using these new LBP texture descriptors will produce more promising results in comparison with use of simple local binary pattern descriptors. In this paper, a novel method has been proposed for image feature extraction using these new image texture descriptors (generalized LBP); then, the obtained results have been compared to the results produced when applying simple LBP descriptors. Furthermore, K-NN and SVM have been used as classifiers in the proposed approach. Finally, a comparison between the proposed method and the existing local binary pattern algorithms for facial expression recognition concludes the superiority of the proposed algorithm over its existing counterparts.
Intron size and genome size in plants.

It has long been known that genomes vary over a remarkable range of sizes in both plants (Bennett, Cox, and Leitch 1997) and animals (Gregory 2001). It also has become evident that across the broad phylogenetic sweep, genome size may be correlated with intron size (Deutsch and Long 1999; Vinogradov 1999; McLysaght et al. 2000), suggesting that some component of genome size evolution takes place within genes. Examples include humans and pufferfish (Fugu), where comparisons of 199 introns in 22 orthologous genes showed that introns in Fugu were on average eight times as small as those in humans, consistent with their ratio of genome sizes (McLysaght et al. 2000). Similarly, Deutsch and Long (1999) tabulated intron sizes across a broad phylogenetic spectrum of eukaryotes and noted a general but weak correlation with genome size, with humans having the most and longest introns (mean of 3.4 kbp) among the 10 taxa studied. Intron size is also correlated with genome size in Drosophila (Moriyama, Petrov, and Hartl 1998), showing that the correlation may extend to more recent divergences. At present there is little information on the correlation between genome and intron sizes in plants, although there are suggestions that plants with small genomes have smaller introns (Deutsch and Long 1999; Vinogradov 1999). Whereas broad comparisons across widely divergent taxa are now possible given completed draft sequences for the rice (Goff et al. 2002; Yu et al. 2002) and Arabidopsis (Arabidopsis Genome Initiative 2000) genomes, the divergence time between Poaceae and Brassicaceae is so large that the influence of genome size on intron size may be confounded by numerous other, unstudied covariables. It seems likely that more informative studies will involve closely related taxa that vary significantly in genome size but which share recent evolutionary history and a broad suite of life-history features. An additional advantage of comparing close relatives is that orthology among genes, and hence introns, may be more readily established. This latter point may be especially important, given the relative lability of copy-number for many gene families (Small and Wendel 2000). To exemplify this approach, we studied the relationship between intron size and genome size for or-