Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multi-Classifier System for Automatic Mitosis Detection in Breast Histopathology Images Using Deep Belief Networks

Mitotic count is an important diagnostic factor in breast cancer grading and prognosis. Detection of mitosis in breast histopathology images is very challenging mainly due to diffused intensities along object boundary and shape variation in different stages of mitosis. This paper demonstrates an accurate technique for detecting the mitotic cells in Hematoxyline and Eosin stained images by step by step refinement of segmentation and classification stages. Krill Herd Algorithm-based localized active contour model precisely segments cell nuclei from background stroma. A deep belief network based multi-classifier system classifies the labeled cells into mitotic and nonmitotic groups. The proposed method has been evaluated on MITOS data set provided for MITOS-ATYPIA contest 2014 and also on clinical images obtained from Regional Cancer Centre (RCC), Thiruvananthapuram, which is a pioneer institute specifically for cancer diagnosis and research in India. The algorithm provides improved performance compared with other state–of–the-art techniques with average F-score of 84.29% for the MITOS data set and 75% for the clinical data set from RCC.
Bifurcation-Based Stability Analysis of Photovoltaic-Battery Hybrid Power System

Photovoltaic-battery hybrid power system (PBHPS) is a good candidate for rural electrification in remote areas. In this system, multiple energy sources are combined together to power the user loads under various system structures. We identify and analyze the bifurcation process when the system enters unstable operation states. Then, a small signal stability criterion is derived for the system based on reasonable simplification of the bifurcation analysis. Furthermore, according to the nonlinear dynamics of the interconnected system with closed-loop control, a large-signal stability criterion is derived with mixed potential theory. The criterion that is straightforward with the dual-loop control can be considered and easily extended to multiple connected converter systems. The criterion is also coincident with the result of bifurcation analysis. Finally, the validity of proposed criteria is verified by simulation and experimental works in a practical PBHPS of 1 kW.
Loss of LDOC1 Expression by Promoter Methylation in Cervical Cancer Cells

Cervical cancer lacks reliable prognostic factors for both progression and chemotherapeutic responsiveness. The expression of the LDOC1 tumor suppressor candidate was therefore investigated. In four of six cervical cancer cell lines tested, expression of LDOC1 was silenced. Downregulation of LDOC1 could also be shown in biopsies of cervical cancer specimens. PCR-based promoter methylation analysis revealed a significant association between promoter methylation and the loss of LDOC1 expression, which could be reverted by DNA methyltransferase inhibitors. This indicates that silencing of LDOC1 is a frequent event in cervical cancer and may be of interest as a molecular marker in cervical cancer.
Efficient Document Filtering Using Vector Space Topic Expansion and Pattern-Mining: The Case of Event Detection in Microposts

Automatically extracting information from social media is challenging given that social content is often noisy, ambiguous, and inconsistent. However, as many stories break on social channels first before being picked up by mainstream media, developing methods to better handle social content is of utmost importance. In this paper, we propose a robust and effective approach to automatically identify microposts related to a specific topic defined by a small sample of reference documents. Our framework extracts clusters of semantically similar microposts that overlap with the reference documents, by extracting combinations of key features that define those clusters through frequent pattern mining. This allows us to construct compact and interpretable representations of the topic, dramatically decreasing the computational burden compared to classical clustering and k-NN-based machine learning techniques and producing highly-competitive results even with small training sets (less than 1'000 training objects). Our method is efficient and scales gracefully with large sets of incoming microposts. We experimentally validate our approach on a large corpus of over 60M microposts, showing that it significantly outperforms state-of-the-art techniques.
The KC Channel in the cbb3-Type Respiratory Oxygen Reductase from Rhodobacter capsulatus Is Required for Both Chemical and Pumped Protons

ABSTRACT The heme-copper superfamily of proton-pumping respiratory oxygen reductases are classified into three families (A, B, and C families) based on structural and phylogenetic analyses. Most studies have focused on the A family, which includes the eukaryotic mitochondrial cytochrome c oxidase as well as many bacterial homologues. Members of the C family, also called the cbb3-type oxygen reductases, are found only in prokaryotes and are of particular interest because of their presence in a number of human pathogens. All of the heme-copper oxygen reductases require proton-conducting channels to convey chemical protons to the active site for water formation and to convey pumped protons across the membrane. Previous work indicated that there is only one proton-conducting input channel (the KC channel) present in the cbb3-type oxygen reductases, which, if correct, must be utilized by both chemical protons and pumped protons. In this work, the effects of mutations in the KC channel of the cbb3-type oxygen reductase from Rhodobacter capsulatus were investigated by expressing the mutants in a strain lacking other respiratory oxygen reductases. Proton pumping was evaluated by using intact cells, and catalytic oxygen reductase activity was measured in isolated membranes. Two mutations, N346M and Y374F, severely reduced catalytic activity, presumably by blocking the chemical protons required at the active site. One mutation, T272A, resulted in a substantially lower proton-pumping stoichiometry but did not inhibit oxygen reductase activity. These are the first experimental data in support of the postulate that pumped protons are taken up from the bacterial cytoplasm through the KC channel.
Highlights of the 1998 National Youth Gang Survey

Of 3,018 recipients, 2,668 (88 percent) responded to the 1998 survey. Forty-eight percent of respondents reported active youth gangs in their jurisdictions in 1998, compared with 51 percent in 1997 and 53 percent in 1996. An estimated 4,464 jurisdictions in the United States experienced gang activity in 1998, compared with an estimated 4,712 jurisdictions in 1997 and 4,824 jurisdictions in 1996. For each area type, there was a decline between 1997 and 1998 in jurisdictions reporting gangs. The decline was from 786 of 1,098 (72 percent) to 736 of 1,049 (70 percent) for large cities, from 337 of 601 (56 percent) to 261 of 525 (50 percent) for suburban counties, from 125 of 375 (33 percent) to 117 of 368 (32 percent) for small cities, and from 164 of 692 (24 percent) to 139 of 648 (21 percent) for rural counties.
Intercultural Teaching Competence in the Disciplines: Teaching Strategies for Intercultural Learning

As universities continue to internationalize their curricula and recruit a growing number of international students, instructors facilitate learning in increasingly diverse classrooms. This chapter explores the application of Intercultural Teaching Competence (ITC) by faculty members across the disciplines at a large Canadian research university. Based on focus group interviews with instructors in eighteen disciplines, it provides varied and concrete examples of how instructors mobilize intercultural teaching competence to navigate diverse classrooms, promote perspective-taking and global learning goals among students, practice culturally relevant teaching, and validate different ways of knowing and communicating among students through assessment practices. Placing disciplines at the centre of the discussion in this way elucidates the extent to which ITC may be adapted to fit the contours of the academic field and allows readers to explore best practices for facilitating the development of intercultural competence among students in their disciplines. Finally, the implications of disciplinary differences in ITC are discussed for faculty development and curriculum support.
Expression and Activation of Matrix Metalloproteinase-2 and -9 in Rat Brain after Transient Focal Cerebral Ischemia

Matrix metalloproteinases (MMPs) degrade the extracellular matrix and carry out key functions during development and after injury. By means of zymography, Western blot and immunohistochemistry, we studied MMP-2 (gelatinase A) and MMP-9 (gelatinase B) in rat brain after focal cerebral ischemia. The control rat brain showed constitutive MMP-2 and, to a lesser extent, MMP-9, which were mainly present as prozymogens. MMP-2 protein was located in the cell body of neurons, glia, and endothelium, whereas MMP-9 was associated to neurons and myelinated fibre tracts. Ischemia greatly increased MMP activation in two temporal waves, in the first one, MMP-9 protein was induced from 4 h to 4 days, and also a small and short-lasting increase in MMP-2 was detected at 4 h. The second wave showed a massive increase in MMP-2 protein expression and activation by day 4, which was compatible with abundant MMP-2 in reactive microglia/macrophages. Our results are compatible with progressive induction of MMP-9 proform, likely in neurons, shortly after ischemia. For MMP-2, the results suggest a discrete production immediately after reperfusion, while a very enhanced expression and activation of MMP-2 attributable to microglia/macrophages occurs on day 4, and it might contribute to the phagocytic action of these reactive cells.
Population differentiation and behavioural association of the two ‘personality’ genes DRD4 and SERT in dunnocks (Prunella modularis)

Quantifying the variation in behaviour‐related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non‐native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two ‘personality’ genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced (New Zealand, NZ) population of dunnocks, Prunella modularis. The NZ population showed a significantly lower number of single nucleotide polymorphisms (SNPs) compared to the UK population. Standardized F’st estimates of the personality genes and neutral microsatellites indicate that selection (anthropogenic and natural) probably occurred during and post the introduction event. Notably, the largest genetic differentiation was found in the intronic regions of the genes. In the NZ population, we also examined the association between polymorphisms in DRD4 and SERT and two highly repeatable behavioural traits: flight‐initiation distance and mating status (promiscuous females and cobreeding males). We found 38 significant associations (for different allele effect models) between the two behavioural traits and the studied genes. Further, 22 of the tested associations showed antagonistic allele effects for males and females. Our findings illustrate how introduction events and accompanying ecological changes could influence the genetic diversity of behaviour‐related genes.
The Scientific Revolution—The Kidney and Nephrology in and about the Seventeenth Century (Part 1)

In the history of the evolution of the medical sciences, it is in the 17th century that the conscious, deliberate, and systematic study of the workings of the human body began. It was a product of the radical changing attitudes of this insurgent century when mathematical reasoning and mechanistic philosophy replaced the teleological outlook of earlier times. It was then that meticulous observation, reproducible quantification, experimental validation, and mathematical exactitude in the quest for truths launched the Scientific Revolution. The effect on medicine was a transformative change from a descriptive to an explanatory body of knowledge during the course of which rigorous anatomical dissections were used for the mechanical explanation of organ function, when morbid changes observed at postmortem began to be related to clinical features of disease, and when the secretive analytical methods of alchemy began to be refined for the study of chemical changes in living matter. Essentially what began with meticulous observations of anatomical features begat physiology and laid the foundations of pathology and chemistry. As a result, studies of organ structure, function, and changes in disease in general, and of the kidney in particular, were clarified and progressed at a rate never achieved theretofore.
Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake.

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169(T), was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169(T) grew in the presence of 0-3.0% (w/v) NaCl, at pH 5-10 and at 20-37 °C. The predominant quinone of strain HMD2169(T) was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169(T) was a representative of a lineage within the genus Chitinimonas. Strain HMD2169(T) was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169(T) is a representative of a novel species of the genus Chitinimonas, for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169(T) ( = KCTC 22839(T) = CECT 7703(T)).
LVB: parsimony and simulated annealing in the search for phylogenetic trees

UNLABELLED The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results. AVAILABILITY The software is available at http://www.rubic. reading.ac. uk/lvb/ SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION may be downloaded from http://www.rubic. reading.ac. uk/~daniel/
The ophthalmological complications of targeted agents in cancer therapy: what do we need to know as ophthalmologists?

Recently, there has been an increase in the use of targeted therapies for cancer treatments. Nevertheless, the ocular side‐effects of the commonly used targeted agents are generally under‐reported and not well studied in the literature. We conducted multiple searches in databases, including Medline, EMBASE, Cochrane Library and conference proceedings, using the following strings: ‘name of targeted therapeutic agent (both generic and commercial names)’ AND ‘eye OR ocular OR vision OR ophthalmological’. Various targeted agents have been found to be associated with ocular side‐effects due to their specific targeting of activities in the eye. Imatinib commonly causes periorbital oedema, epiphora and occasionally conjunctival haemorrhage. Cetuximab causes corneal lesions, meibomian gland dysfunction, periorbital and lid dermatitis, blepharitis and conjunctivitis. Erlotinib is related to various ocular toxicities, mainly on the ocular surface, and perifosine has been reported to be associated with severe keratitis. Bevacizumab could potentially disrupt intrinsic ocular circulation and lead to the development of thromboembolic events; there are rare reported cases of optic neuritis or optic neuropathy. Other targeted agents, such as trastuzumab, sunitinib and crizotinib, also have specific ocular toxicities. In conclusion, ocular effects of targeted agents are not uncommon in cancer patients receiving targeted therapy. Ophthalmologists should have high indexes of suspicion to diagnose and treat these complications promptly.
The North Carolina Charter School Choice: Selection Factors and Parental Decision Making

FEDEWA, MICHAEL JOSEPH. The North Carolina Charter School Choice: Selection Factors and Parental Decision Making. (Committee Chair: Dr. Robert Serow) The study discussed in this dissertation identified and examined the factors that influence a parent’s decision to choose a North Carolina charter school for their children. The study was conducted at 13 North Carolina Charter schools. Questionnaires were distributed to 2,325 parents, and 903 were completed. The questionnaire contained 14 questions that examined 16 factors that might influence parental decision-making. Frequency distributions were tabulated for each of the fourteen survey questions. A principal component and varimax analysis was conducted. The factors were grouped into three categories: (1) administration, (2) academic/instructional, and (3) student centered. Following this procedure, a multivariate analysis of variance (MANOVA) was applied to the data. This tested the three categories against the independent variables of race, parental income, and parent education level. A post hoc test (Tukey’s Studentized Range, HSD) was applied when appropriate. The category administration accounted for the greatest variance in the study. Factors in this category included sports programs, extracurricular activities, technology program, facilities, transportation, and food service. The category that accounted for the next largest portion of the variance in the study was academic/instructional factors. These factors included curriculum, people running the school, opportunities for parents to participate, the school’s expectation of parents, and academic standards. The category that accounted for the third largest portion of the variance in the model was student-centered factors. These factors included school size, class size, and individual attention provided by teachers. A multivariate analysis of variance (MANOVA) tested the three categories against independent variables of race, parental income levels, and education levels of parents. Post hoc testing was conducted when there was a significant main effect. This process led to the conclusion that minority parents place more value on administrative selection factors than majority parents. Furthermore, minority parents tend to place more value on academic/instructional selection factors than majority parents. Finally, parents that have professional or post graduate levels of education value administrative selection factors more than parents with lower levels of education. THE NORTH CAROLINA CHARTER SCHOOL CHOICE: SELECTION FACTORS AND PARENTAL DECISION-MAKING By MICHAEL J. FEDEWA A dissertation submitted to the graduate faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Doctor of Education DEPARTMENT OF EDUCATIONAL RESEARCH AND LEADERSHIP AND COUNSELOR EDUCATION
Predictors of Risk Perceptions of Childhood Injury among Parents of Preschoolers

This article assesses the relationship between parents' perceived risk of childhood injuries and familial, sociocultural, and situational variables. Data were obtained through a random digit dial telephone survey of 1,200 households with a preschool child in a southeastern metropolitan area. Perceived risks of childhood injury measures were based on social science theory and childhood injury epidemiology. Multiple item measures included dimensions of seriousness and likelihood for both injuries and hazards. When risk perceptions were viewed as individual items, parents underestimated the risk of some hazards and injuries and overestimated the risks of others, and parents whose children have sustained a recent injury had higher risk perception overall. When risk perceptions were viewed as summed scales, sociodemographic variables and parental safety behaviors were not significant predictors. Sociocultural factors of having a child previously injured, the parent reporting stress, having a household with self-reported risk factors, and the perception of the child as active and hard to manage are related to summed scales of risk perceptions, with some interactions by race of the parent. Findings illustrate the role of situational and sociocultural characteristics of respondents in risk perception research.
Broad-range Glycosidase Activity Profiling*

Plants produce hundreds of glycosidases. Despite their importance in cell wall (re)modeling, protein and lipid modification, and metabolite conversion, very little is known of this large class of glycolytic enzymes, partly because of their post-translational regulation and their elusive substrates. Here, we applied activity-based glycosidase profiling using cell-permeable small molecular probes that react covalently with the active site nucleophile of retaining glycosidases in an activity-dependent manner. Using mass spectrometry we detected the active state of dozens of myrosinases, glucosidases, xylosidases, and galactosidases representing seven different retaining glycosidase families. The method is simple and applicable for different organs and different plant species, in living cells and in subproteomes. We display the active state of previously uncharacterized glycosidases, one of which was encoded by a previously declared pseudogene. Interestingly, glycosidase activity profiling also revealed the active state of a diverse range of putative xylosidases, galactosidases, glucanases, and heparanase in the cell wall of Nicotiana benthamiana. Our data illustrate that this powerful approach displays a new and important layer of functional proteomic information on the active state of glycosidases.
Quantitative Site-specific Phosphorylation Dynamics of Human Protein Kinases during Mitotic Progression*

Reversible protein phosphorylation is a key regulatory mechanism of mitotic progression. Importantly, protein kinases themselves are also regulated by phosphorylation-dephosphorylation processes; hence, phosphorylation dynamics of kinases hold a wealth of information about phosphorylation networks. Here, we investigated the site-specific phosphorylation dynamics of human kinases during mitosis using synchronization of HeLa suspension cells, kinase enrichment, and high resolution mass spectrometry. In biological triplicate analyses, we identified 206 protein kinases and more than 900 protein kinase phosphorylation sites, including 61 phosphorylation sites on activation segments, and quantified their relative abundances across three specific mitotic stages. Around 25% of the kinase phosphorylation site ratios were found to be changed by at least 50% during mitotic progression. Further network analysis of jointly regulated kinase groups suggested that Cyclin-dependent kinase- and mitogen-activated kinase-centered interaction networks are coordinately down- and up-regulated in late mitosis, respectively. Importantly, our data cover most of the already known mitotic kinases and, moreover, identify attractive candidates for future studies of phosphorylation-based mitotic signaling. Thus, the results of this study provide a valuable resource for cell biologists and provide insight into the system properties of the mitotic phosphokinome.