Miracle-dz/UniFAR-FTUs huggingface dataset:
Papillary and neuroendocrine breast lesions: the WHO stance

In this review, we highlight adaptations in the WHO 2012 classification of papillary and neuroendocrine breast lesions as compared with the previous 2003 version. Consensus criteria for distinguishing atypical ductal hyperplasia from ductal carcinoma in situ within an intraductal papilloma are proposed. The absence of myoepithelial cells around the wall of an encapsulated papillary carcinoma, although raising consideration of an indolent tumour with minimal invasion, is currently regarded as in‐situ disease for staging purposes. The majority of solid papillary carcinomas are classified as in‐situ tumours, but lesions with irregular tumour islands within desmoplastic stroma may be considered to be invasive. The diagnosis of solid papillary carcinoma without further qualification as either in‐situ or invasive disease is discouraged. When invasive papillary carcinoma is seen in the breast, metastatic papillary carcinoma from other organ sites needs to be excluded. WHO 2012 classifies neuroendocrine breast tumours as well‐differentiated neuroendocrine tumour, small‐cell carcinoma, and invasive breast carcinoma with neuroendocrine differentiation. There is currently no clinical impact of identifying neuroendocrine differentiation in conventional invasive breast carcinomas, apart from acknowledging its frequent occurrence in subtypes such as the hypercellular variant of mucinous carcinoma and solid papillary carcinoma.
Molecular Analysis of Isoleucyl-tRNA Synthetase Mutations in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus with Low-Level Mupirocin Resistance

Emergence and spread of low-level mupirocin resistance in staphylococci have been increasingly reported in recent years. The aim of this study was to characterize missense mutations within the chromosomal isoleucyl-tRNA synthetase gene (ileS) among clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) with low-level mupirocin resistance. A total of 20 isolates of MRSA with low-level mupirocin resistance (minimal inhibitory concentration, 16-64 µg/mL) were collected from 79 patients in intensive care units for six months. The isolates were analyzed for isoleucyl-tRNA synthetase (IleS) mutations that might affect the binding of mupirocin to the three-dimensional structure of the S. aureus IleS enzyme. All isolates with low-level mupirocin resistance contained the known V588F mutation affecting the Rossman fold, and some of them additionally had previously unidentified mutations such as P187F, K226T, F227L, Q612H, or V767D. Interestingly, Q612H was a novel mutation that was involved in stabilizing the conformation of the catalytic loop containing the KMSKS motif. In conclusion, this study confirms that molecular heterogeneity in ileS gene is common among clinical MRSA isolates with low-level mupirocin resistance, and further study on clinical mutants is needed to understand the structural basis of low-level mupirocin resistance.
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes

The discovery of regulatory motifs embedded in upstream regions of plants is a particularly challenging bioinformatics task. Previous studies have shown that motifs in plants are short compared with those found in vertebrates. Furthermore, plant genomes have undergone several diversification mechanisms such as genome duplication events which impact the evolution of regulatory motifs. In this article, a systematic phylogenomic comparison of upstream regions is conducted to further identify features of the plant regulatory genomes, the component of genomes regulating gene expression, to enable future de novo discoveries. The findings highlight differences in upstream region properties between major plant groups and the effects of divergence times and duplication events. First, clear differences in upstream region evolution can be detected between monocots and dicots, thus suggesting that a separation of these groups should be made when searching for novel regulatory motifs, particularly since universal motifs such as the TATA box are rare. Second, investigating the decay rate of significantly aligned regions suggests that a divergence time of ∼100 mya sets a limit for reliable conserved non-coding sequence (CNS) detection. Insights presented here will set a framework to help identify embedded motifs of functional relevance by understanding the limits of bioinformatics detection for CNSs.
How the toughness in metallic glasses depends on topological and chemical heterogeneity

Significance This article reports and explains how the cavitation in metallic glasses is controlled by topological structure as well as chemical heterogeneity. It is shown that in the tough metal–metalloid Pd-Si metallic glass, cavitation initiation is controlled by both chemical separation and particular types of low coordination number (LCN) Pd-centered polyhedra. In contrast, cavitation in the brittle metal-metal Cu-Zr metallic glass is only governed by topological factors. A high-energy barrier to form LCN polyhedra and the process of chemical separation during cavitation initiation are believed to contribute to a higher metallic glass toughness, thereby allowing a larger plastic strain to fracture. To gain insight into the large toughness variability observed between metallic glasses (MGs), we examine the origin of fracture toughness through bending experiments and molecular dynamics (MD) simulations for two binary MGs: Pd82Si18 and Cu46Zr54. The bending experiments show that Pd82Si18 is considerably tougher than Cu46Zr54, and the higher toughness of Pd82Si18 is attributed to an ability to deform plastically in the absence of crack nucleation through cavitation. The MD simulations study the initial stages of cavitation in both materials and extract the critical factors controlling cavitation. We find that for the tougher Pd82Si18, cavitation is governed by chemical inhomogeneity in addition to topological structures. In contrast, no such chemical correlations are observed in the more brittle Cu46Zr54, where topological low coordination number polyhedra are still observed around the critical cavity. As such, chemical inhomogeneity leads to more difficult cavitation initiation in Pd82Si18 than in Cu46Zr54, leading to a higher toughness. The absence of chemical separation during cavitation initiation in Cu46Zr54 decreases the energy barrier for a cavitation event, leading to lower toughness.
Nested Monte-Carlo Search

Many problems have a huge state space and no good heuristic to order moves so as to guide the search toward the best positions. Random games can be used to score positions and evaluate their interest. Random games can also be improved using random games to choose a move to try at each step of a game. Nested Monte-Carlo Search addresses the problem of guiding the search toward better states when there is no available heuristic. It uses nested levels of random games in order to guide the search. The algorithm is studied theoretically on simple abstract problems and applied successfully to three different games: Morpion Solitaire, SameGame and 16×16 Sudoku.
Use of Fluorescent-Protein Tagging To Determine the Subcellular Localization of Mycoplasma pneumoniae Proteins Encoded by the Cytadherence Regulatory Locus

ABSTRACT Mycoplasma pneumoniae lacks a cell wall but has internal cytoskeleton-like structures that are assumed to support the attachment organelle and asymmetric cell shape of this bacterium. To explore the fine details of the attachment organelle and the cytoskeleton-like structures, a fluorescent-protein tagging technique was applied to visualize the protein components of these structures. The focus was on the four proteins—P65, HMW2, P41, and P24—that are encoded in the crl operon (for “cytadherence regulatory locus”), which is known to be essential for the adherence of M. pneumoniae to host cells. When the P65 and HMW2 proteins were fused to enhanced yellow fluorescent protein (EYFP), a variant of green fluorescent protein, the fused proteins became localized at the attachment organelle, enabling visualization of the organelles of living cells by fluorescence microscopy. The leading end of gliding M. pneumoniae cells, expressing the EYFP-P65 fusion, was observed as a focus of fluorescence. On the other hand, when the P41 and P24 proteins were labeled with EYFP, the fluorescence signals of these proteins were observed at the proximal end of the attachment organelle. Coexpression of the P65 protein labeled with enhanced cyan fluorescent protein clearly showed that the sites of localization of P41 and P24 did not overlap that of P65. The localization of P41 and P24 suggested that they are also cytoskeletal proteins that function in the formation of unknown structures at the proximal end of the attachment organelle. The fluorescent-protein fusion technique may serve as a powerful tool for identifying components of cytoskeleton-like structures and the attachment organelle. It can also be used to analyze their assembly.
Biomarkers for Early Detection of Colorectal Cancer and Polyps: Systematic Review

There is growing interest in early detection of colorectal cancer as current screening modalities lack compliance and specificity. This study systematically reviewed the literature to identify biomarkers for early detection of colorectal cancer and polyps. Literature searches were conducted for relevant papers since 2007. Human studies reporting on early detection of colorectal cancer and polyps using biomarkers were included. Methodologic quality was evaluated, and sensitivity, specificity, and the positive predictive value (PPV) were reported. The search strategy identified 3,348 abstracts. A total of 44 papers, examining 67 different tumor markers, were included. Overall sensitivities for colorectal cancer detection by fecal DNA markers ranged from 53% to 87%. Combining fecal DNA markers increased the sensitivity of colorectal cancer and adenoma detection. Canine scent detection had a sensitivity of detecting colorectal cancer of 99% and specificity of 97%. The PPV of immunochemical fecal occult blood test (iFOBT) is 1.26%, compared with 0.31% for the current screening method of guaiac fecal occult blood test (gFOBT). A panel of serum protein biomarkers provides a sensitivity and specificity above 85% for all stages of colorectal cancer, and a PPV of 0.72%. Combinations of fecal and serum biomarkers produce higher sensitivities, specificities, and PPVs for early detection of colorectal cancer and adenomas. Further research is required to validate these biomarkers in a well-structured population-based study. Cancer Epidemiol Biomarkers Prev; 23(9); 1712–28. ©2014 AACR.
Taking account of dependent species in management of the Southern Ocean krill fishery: estimating crabeater seal abundance off east Antarctica

Summary 1. The crabeater seal Lobodon carcinophaga is considered to be a key species in the krill-based foodweb of the Southern Ocean. Reliable estimates of the abundance of this species are necessary to allow the development of multispecies, predator‐prey models as a basis for management of the krill fishery in the Southern Ocean. 2. A survey of crabeater seal abundance was undertaken in 1500 000 km 2 of pack-ice off east Antarctica between longitudes 64‐150 ° E during the austral summer of 1999/2000. Sighting surveys, using double observer line transect methods, were conducted from an icebreaker and two helicopters to estimate the density of seals hauled out on the ice in survey strips. Satellite-linked dive recorders were deployed on a sample of seals to estimate the probability of seals being hauled out on the ice at the times of day when sighting surveys were conducted. Model-based inference, involving fitting a density surface, was used to infer densities in the entire survey region from estimates in the surveyed areas. 3. Crabeater seal abundance was estimated to be between 0·7 and 1·4 million animals (with 95% confidence), with the most likely estimate slightly less than 1 million. 4. Synthesis and applications. The estimation of crabeater seal abundance in Convention for the Conservation of Antarctic Marine Living Resources (CCAMLR) management areas off east Antarctic where krill biomass has also been estimated recently provides the data necessary to begin extending from single-species to multispecies management of the krill fishery. Incorporation of all major sources of uncertainty allows a precautionary interpretation of crabeater abundance and demand for krill in keeping with CCAMLR’s precautionary approach to management. While this study focuses on the crabeater seal and management of living resources in the Southern Ocean, it has also led to technical and theoretical developments in survey methodology that have widespread potential application in ecological and resource management studies, and will contribute to a more fundamental understanding of the structure and function of the Southern Ocean ecosystem.
Creating a New Product Development capability: the organisational enablers for moving up the value chain

The UK's innovative and productive performance remains a subject of considerable concern, not least because of its increasing productivity gap, but also because of concerns relating to manufacturing's reliance on gaining process efficiencies. Resolution of this position has been argued to involve a move up the value chain, through such means as New Product Development (NPD). Many examples of 'good' NPD practice exist within the literature. However, these examples and the associated determinants of NPD success principally focus on large organisations. In this paper, SMEs are argued as being different in their approach to developing new products, specifically focusing on their journey to create a NPD capability. This exploratory research incorporates two detailed case studies on UK based manufacturing SMEs in order to contribute to new knowledge and understanding, by identifying the key enablers to create a NPD capability.
Magnetic resonance scans should replace biopsies for the diagnosis of diffuse brain stem gliomas: a report from the Children's Cancer Group.

Children's Cancer Group Protocol CCG-9882 was designed to determine the effectiveness of hyperfractionated radiation for the treatment of children and young adults with brain stem gliomas. The study opened for the accrual of patients on September 21, 1988, and was closed on June 30, 1991. The first 54 children in the study were treated with irradiation doses of 100 cGy given twice daily to a total dosage of 7200 cGy. The next 66 children were treated with a similar daily regimens to a total of 7800 cGy. Tumors were diagnosed by clinical and radiographic criteria. Decisions about the need for surgery were left to the discretion of the treating neurosurgeon; tissue diagnosis did not alter the therapy in patients with diffuse infiltrating tumors. We reviewed the neuroradiology and neurosurgery reports as well as the pathological specimens of children entered on the study. By magnetic resonance (MR) imaging criteria, tumors involved the majority of the brain stem in 76% of cases; only three patients had tumors localized to the midbrain or medulla. Operations were performed on 56 of 120 patients (47%). Cerebrospinal fluid shunts were inserted in 27 (23%) of the children; insertion of a shunt was the only operation in 11, and a shunt was inserted in conjunction with a tumor operation in 16. Tumor operations were performed in 45 (38%) of the patients; 24 had stereotactic biopsies, and 21 had craniotomies. Of the 21 patients who had craniotomies, only biopsies were performed in 11; partial tumor resections were performed in 5 patients and subtotal resection in 5. (ABSTRACT TRUNCATED AT 250 WORDS)
S2E: a platform for in-vivo multi-path analysis of software systems

This paper presents S2E, a platform for analyzing the properties and behavior of software systems. We demonstrate S2E's use in developing practical tools for comprehensive performance profiling, reverse engineering of proprietary software, and bug finding for both kernel-mode and user-mode binaries. Building these tools on top of S2E took less than 770 LOC and 40 person-hours each. S2E's novelty consists of its ability to scale to large real systems, such as a full Windows stack. S2E is based on two new ideas: selective symbolic execution, a way to automatically minimize the amount of code that has to be executed symbolically given a target analysis, and relaxed execution consistency models, a way to make principled performance/accuracy trade-offs in complex analyses. These techniques give S2E three key abilities: to simultaneously analyze entire families of execution paths, instead of just one execution at a time; to perform the analyses in-vivo within a real software stack--user programs, libraries, kernel, drivers, etc.--instead of using abstract models of these layers; and to operate directly on binaries, thus being able to analyze even proprietary software. Conceptually, S2E is an automated path explorer with modular path analyzers: the explorer drives the target system down all execution paths of interest, while analyzers check properties of each such path (e.g., to look for bugs) or simply collect information (e.g., count page faults). Desired paths can be specified in multiple ways, and S2E users can either combine existing analyzers to build a custom analysis tool, or write new analyzers using the S2E API.
Efficacy of Tenofovir Disoproxil Fumarate Therapy in Nucleoside-Analogue Naive Iranian Patients Treated for Chronic Hepatitis B

Background: Tenofovir disoproxil fumarate (TDF) is a new effective treatment option for patients with chronic hepatitis B (CHB). Objectives: To evaluate TDF efficacy in nucleos(t)ide analogues (NAs)-naive Iranian patients with CHB. Patients and Methods: The NA-naive patients received TDF for at least six months. The primary endpoint was the proportion of patients achieving a complete virological response (CVR) during the treatment. Multivariate Cox regression analysis determined predictive factors independently associated with the time to CVR. The secondary endpoints were biochemical and serological responses, frequency of virological breakthrough, genotypic resistance development, safety and tolerability. Results: In all, 93 patients (64.5% hepatitis B e antigen [HBeAg]-negative) were eligible. Of these, 70 patients completed 24 months of treatment. The cumulative CVR rates in HBeAg-negative and HBeAg-positive patients were 87% versus 53% at 24 months, respectively. The multivariate Cox regression model showed only HBeAg positivity at baseline and a high baseline HBV DNA level were independent factors predicting a CVR. No patient achieved hepatitis B surface antigen (HBsAg) and HBeAg loss or seroconversion and no virologic breakthrough occurred. A new amino acid substitution (rtD263E) was observed to develop in 60% of patients with viremia. Conclusions: The cumulative CVR rates showed that patients with HBeAg-negative have better virologic respond than those with HBeAg-positive during the same period. The rtD263E mutation might be associated with partial resistance to TDF.
Clinical and Prognostic Importance of Serotyping Mycobacterium avium-Mycobacterium intracellulare Complex Isolates in Human Immunodeficiency Virus-Negative Patients

ABSTRACT We studied whether the serotypes of Mycobacterium avium-Mycobacterium intracellulare complex (MAC) isolates determine the prognosis for pulmonary MAC disease. We prospectively monitored a cohort of 68 patients with pulmonary MAC disease for whom the serotype-specific glycopeptidolipids in isolates were identified using thin-layer chromatography and fast atom bombardment mass-spectrometry in 1990 and 1995. Serovar 4 Mycobacterium avium was detected in 40/68 patients (58.8%). Other serotypes were serotypes 1 (five cases), 6 (three cases), 8 (seven cases), 9 (three cases), 14 (four cases), and 16 (six cases). Patients with serovar 4 were significantly (P < 0.01) younger (63.0 ± 9.8 years) than patients with other serotypes (71.8 ± 10.3). Patients who failed treatment had a significantly poorer prognosis than other patients. There were no cases of MAC-related death in the cured group. Chest radiographic findings progressively worsened in 36 (90%) of patients with serotype 4, and 14/36 died from respiratory failure caused by pulmonary Mycobacterium avium disease. The patients with serotype 4 had a significantly poorer prognosis than patients with other serotypes. These results show that both the outcome of chemotherapy and the serotypes of MAC isolates are important for assessing the prognosis of pulmonary MAC disease.
Islet Microvasculature in Islet Hyperplasia and Failure in a Model of Type 2 Diabetes

Gene expression profiling of islets from pre-diabetic male Zucker diabetic fatty (ZDF) rats showed increased expression of hypoxia-related genes, prompting investigation of the vascular integrity of the islets. The islet microvasculature was increased approximately twofold in young male ZDF rats by both morphometric analysis and quantifying mRNA levels of endothelial markers. ZDF rats at 12 weeks of age showed a significant reduction in the number of endothelial cells, which was prevented by pretreatment with pioglitazone. Light and electron microscopy of normoglycemic 7-week-old ZDF rats showed thickened endothelial cells with loss of endothelial fenestrations. By 12 weeks of age, there was disruption of the endothelium and intra-islet hemorrhage. Islets from 7- and 12-week-old ZDF rats showed an approximate three- and twofold increase in vascular endothelial growth factor (VEGF)-A mRNA and VEGF protein secretion, respectively, compared with lean controls. Thrombospondin-1 mRNA increased in 7- and 12-week-old rats by 2- and 10-fold, respectively, and was reduced by 50% in 12-week-old rats pretreated with pioglitazone. Islets from young male control rats induced migration of endothelial cells in a collagen matrix only after pretreatment with matrix metalloproteinase (MMP)-9. Islets from 7-week-old ZDF rats showed a fivefold increase in migration score compared with wild-type controls, even without MMP-9 treatment. Islets from 15-week-old ZDF rats did not induce migration; rather, they caused a significant rounding up of the duct-derived cells, suggesting a toxic effect. These data suggest that in the ZDF rat model of type 2 diabetes, an inability of the islet to maintain vascular integrity may contribute to β-cell failure.
The impact of ISO 9001 standard and the EFQM model: The view of the assessors

The aim of this article is to evaluate the impact of both the ISO 9000 standard and the European Foundation for Quality Management (EFQM) self-evaluation model, the total quality management model most employed in Europe. In order to directly compare the results obtained by the two models, we analyse them together in the same temporal frame, using the same methodology, but in a new way, utilising a sample of independent assessors of quality management models. To this end, we first performed a number of objective analyses of data regarding the impact of the models, data obtained from the ISO and EFQM international organisations themselves. We then conducted a survey of 107 experienced and independent quality-management assessors, followed by a personal interview of various stakeholders involved in the adoption of the models. The results obtained pertain to the different motivations of organisations for implementing ISO 9000 standards and the EFQM model, the obstacles detected in this implementation, the degree to which both are actually adopted and the results of the models. In this article, we also highlight the differences in the way that the two models are adopted.