Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species’ center of diversity. DOI: 10.7554/eLife.00731. 00
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

UNLABELLED Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks for a number of organisms. To grapple with these networks, we developed TopNet-like Yale Network Analyzer (tYNA), a Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks. It also allows one to manage a large number of private and public networks using a flexible tagging system, to filter them based on a variety of criteria, and to visualize them through an interactive graphical interface. A number of commonly used biological datasets have been pre-loaded into tYNA, standardized and grouped into different categories. AVAILABILITY The tYNA system can be accessed at http://networks.gersteinlab. org/tyna. The source code, JavaDoc API and WSDL can also be downloaded from the website. tYNA can also be accessed from the Cytoscape software using a plugin.
Duplicate Data Elimination in a SAN File System

Duplicate Data Elimination (DDE) is our method for identifying and coalescing identical data blocks in Storage Tank, a SAN file system. On-line file systems pose a unique set of performance and implementation challenges for this feature. Existing techniques, which are used to improve both storage and network utilization, do not satisfy these constraints. Our design employs a combination of content hashing, copy-on-write, and lazy updates to achieve its functional and performance goals. DDE executes primarily as a background process. The design also builds on Storage Tank’s FlashCopy function to ease implementation.1 We include an analysis of selected real-world data sets that is aimed at demonstrating the space-saving potential of coalescing duplicate data. Our results show that DDE can reduce storage consumption by up to 80% in some application environments. The analysis explores several additional features, such as the impact of varying file block size and the contribution of whole file duplication to the net savings.
Dietary vitamin A regulates wingless-related MMTV integration site signaling to alter the hair cycle

Alopecia areata (AA) is an autoimmune hair loss disease caused by a cell-mediated immune attack of the lower portion of the cycling hair follicle. Feeding mice 3–7 times the recommended level of dietary vitamin A accelerated the progression of AA in the graft-induced C3H/HeJ mouse model of AA. In this study, we also found that dietary vitamin A, in a dose dependent manner, activated the hair follicle stem cells (SCs) to induce the development and growth phase of the hair cycle (anagen), which may have made the hair follicle more susceptible to autoimmune attack. Our purpose here is to determine the mechanism by which dietary vitamin A regulates the hair cycle. We found that vitamin A in a dose-dependent manner increased nuclear localized beta-catenin (CTNNB1; a marker of canonical wingless-type Mouse Mammary Tumor Virus integration site family (WNT) signaling) and levels of WNT7A within the hair follicle bulge in these C3H/HeJ mice. These findings suggest that feeding mice high levels of dietary vitamin A increases WNT signaling to activate hair follicle SCs.
A Novel JSVM Approach for Automatic Image Annotation and Retrieval

This paper presents a novel image annotation framework for domains with large numbers of images. Automatic image annotation is such a domain, by which a computer system automatically assigns metadata in the form of captioning or keywords to a digital image. This application of computer vision technique is used in image retrieval system to organize and locate images of interest from a database. Many techniques have been proposed for image annotation in the last decade that has given reasonable performance on standard datasets In this work, we propose a new model for image annotation known as JSVM which treats annotation as a retrieval problem. In this work, we introduce an JSVM model for image annotation that treats annotation as a retrieval problem. The proposed technique utilizes low level image features and a simple combination of basic distances using JEC to find the nearest neighbors of a given image; the keywords are then assigned using SVM approach which aims to explore the combination of three different methods. First, the initial annotation of the data using flat wise and axis wise methods, and that takes the hierarchy into consideration by classifying consecutively its instances through position wise method. Finally, we make use of pair wise majority voting between methods by simply summing strings in order to produce a final annotation. The result of the proposed technique shows that this technique outperforms the current state of art methods on the standard datasets.
Population Pharmacokinetics of Tenofovir in Human Immunodeficiency Virus-Infected Patients Taking Highly Active Antiretroviral Therapy

ABSTRACT The influence of renal function on tenofovir pharmacokinetics was investigated in 193 human immunodeficiency virus (HIV)-infected patients by the use of a population approach performed with the nonlinear mixed effects modeling program NONMEM. Tenofovir pharmacokinetics was well described by a two-compartment open model in which the absorption and the distribution rate constants are equal. Typical population estimates of apparent central distribution volume (Vc/F), peripheral distribution volume (Vp/F), intercompartmental clearance (Q/F), and plasma clearance (CL/F) were 534 liters, 1,530 liters, 144 liters/h and 90.9 liters/h, respectively. Apparent plasma clearance was related to body weight/serum creatinine ratio (BW/SCR) and to the existence of a tubular dysfunction. Concomitant treatment with lopinavir/ritonavir was found to decrease tenofovir clearance. Individual Bayesian estimates of CL/F were used to calculate the tenofovir area under the concentration-time curve from time zero to 24 h (AUC0-24). In patients without tubular dysfunction, AUC0-24 values markedly decreased from 6.7 to 1.4 mg · h/liter for BW/SCR increasing from 0.44 to 1.73. The relevance of a dosage adjustment based on BW/SCR should be further evaluated.
Dual Priming Oligonucleotides for Broad-Range Amplification of the Bacterial 16S rRNA Gene Directly from Human Clinical Specimens

ABSTRACT Broad-range amplification and sequencing of the bacterial 16S rRNA gene directly from clinical specimens are offered as a diagnostic service in many laboratories. One major pitfall is primer cross-reactivity with human DNA which will result in mixed chromatograms. Mixed chromatograms will complicate subsequent sequence analysis and impede identification. In SYBR green real-time PCR assays, it can also affect crossing threshold values and consequently the status of a specimen as positive or negative. We evaluated two conventional primer pairs in common use and a new primer pair based on the dual priming oligonucleotide (DPO) principle. Cross-reactivity was observed when both conventional primer pairs were used, resulting in interpretation difficulties. No cross-reactivity was observed using the DPOs even in specimens with a high ratio of human to bacterial DNA. In addition to reducing cross-reactivity, the DPO principle also offers a high degree of flexibility in the design of primers and should be considered for any PCR assay intended for detection and identification of pathogens directly from human clinical specimens.
Human osteosarcoma cells resistant to detachment by an Arg-Gly-Asp- containing peptide overproduce the fibronectin receptor

MG-63 human osteosarcoma cells were selected for attachment and growth in the presence of increasing concentrations of a synthetic peptide containing the cell attachment-promoting Arg-Gly-Asp sequence derived from the cell-binding region of fibronectin. Cells capable of attachment and growth in 5-mM concentrations of a peptide having the sequence Gly-Arg-Gly-Asp-Ser-Pro overproduce the cell surface receptor for fibronectin. In contrast, these cells show no differences in the numbers of vitronectin receptor they express as compared with the parental MG-63 cells. In agreement with the resistance of the selected cells to detachment by the peptide, 25-fold more Arg-Gly-Asp-containing peptide is required to prevent the attachment of these cells to fibronectin-coated surfaces than is needed to inhibit the attachment of MG-63 cells to the same substrate. However, similar concentrations of this peptide inhibit attachment of both cell lines to vitronectin- coated surfaces. The increase in fibronectin receptor is due to an increase in the levels of mRNA encoding the fibronectin receptor. Because of the nature of the selection process, we reasoned that this increase might be due to amplification of the fibronectin receptor gene, but no increase in gene copy number was detected by Southern blot analysis. The peptide-resistant cells display a very different morphology from that of the MG-63 cells, one that has a greater resemblance to that of osteocytes. The resistant cells also grow much more slowly than the MG-63 cells. The increased fibronectin receptor and altered morphology and growth properties were stable for at least 3 mo in the absence of peptide. The enhanced expression of the fibronectin receptor on the resistant cells indicates that cells are capable of altering the amount of fibronectin receptor on their surface in response to environmental factors and that this may in turn affect the phenotypic properties of the cell.
AN OBJECT-ORIENTED RULE-BASED APPROACH TO DATA MODEL AND SCHEMA TRANSLATION

To achieve data sharing among heterogeneous database management systems, one essential step is the conversion of the schemata defined in the diverse data models used by these systems. A semantic preserving translation of different modeling constructs and constraints is necessary to ensure that the semantics of applications remain intact after the translation. In this paper, we present an object-oriented extensible core model (ORECOM) which is used as a neutral, intermediate model through which diverse modeling constructs and constraints are translated. The model provides very general and primitive structural constructs in the forms of objects and binary object associations for representing the structural properties of various high-level data models. It also provides behavioral constructs in the forms of operation specifications and semantic rules with triggers for capturing the semantic constraints of these high-level models. Different from the intermediate models used in the existing heterogeneous database management systems, ORECOM is developed for supporting the translation among object-oriented and semantically rich data models. It is extensible in the sense that new modeling constructs and constraints can be added by extending the primitives of ORECOM. This paper also describes the design and implementation of a data model and schema translation system which is being used to test the conversions between the constructs and constraints of data models such as IDEF-1X, NIAM, EXPRESS, and OSAM*. Applications of this system include schema sharing, database conversion, and semantics modification and extension of schema. The techniques and methodology developed in this system are also useful for schema integration and schema design.
Atmospheric Chemistry and Physics Contribution of Ammonium Nitrate to Aerosol Optical Depth and Direct Radiative Forcing by Aerosols over East Asia

This study focused on the contribution of ammo-nium nitrate (NH 4 NO 3) to aerosol optical depth (AOD) and direct radiative forcing (DRF) by aerosols over an East Asian domain. In order to evaluate the contribution, chemistry-transport model (CTM)-estimated AOD was combined with satellite-retrieved AOD, utilizing a data assimilation technique , over East Asia for the entire year of 2006. Using the assimilated AOD and CTM-estimated aerosol optical properties , the DRF by aerosols was estimated over East Asia via a radiative transfer model (RTM). Both assimilated AOD and estimated DRF values showed relatively good agreements with AOD and DRF by aerosols from AERONET. Based on these results, the contributions of NH 4 NO 3 to AOD and DRF by aerosols (AOD and DRF) were estimated for the four seasons of 2006 over East Asia. Both AOD and DRF showed seasonal variations over East Asia within the ranges between 4.7 % (summer) and 31.3 % (winter) and between 4.7 % (summer) and 30.7 % (winter), respectively, under clear-sky conditions, showing annual average contributions of 15.6 % and 15.3 %. Under all-sky conditions, DRF varied between 3.6 % (summer) and 24.5 % (winter), showing annual average contribution of 12.1 % over East Asia. These annual average contributions of NH 4 NO 3 to AOD and DRF are almost comparable to the annual average mass fractions of NH 4 NO 3 in PM 2.5 and PM 10 (17.0 % and 14.0 %, respectively). AOD and DRF were even larger in the locations where NH 3 and NO x emission rates are strong, such as the central East China (CEC) region and Sichuan Basin. For example, under clear-sky conditions, both AOD and DRF over the CEC region range between 6.9 % (summer) and 47.9 % (winter) and between 6.7 % (summer) and 47.5 % (winter), respectively. Based on this analysis, it was concluded that both AOD and DRF cannot be ignored in East Asian air quality and radiative forcing studies, particularly during winter.
ATTITUDES TO CYCLING: A QUALITATIVE STUDY AND CONCEPTUAL FRAMEWORK

It is known that attitudinal factors influence the willingness of individuals to use bicycles. A qualitative study was carried out to assess attitudes of cyclists and non-cyclists to cycling, with emphasis on exploring strategies that would encourage people to cycle. Thirteen focus groups were held, including two extended creativity sessions, in five towns. Projective techniques were used to de-layer responses and explore rationalisations and misperceptions. Stated preference exercises were also undertaken to verify and rank responses to cycle promotion strategies, including car restraint policies. A parallel study drew on experience from public health promotion and theories of motivation and behaviour change to devise a conceptual framework for interpreting and structuring the results from qualitative studies. Conclusions are drawn on the ways in which cycling should be promoted in the UK. (A)
Irrationality and pathologization of delusions

Pathological delusions are special because they are considered symptoms of illness; which judgment is made based on coexisting information that makes the delusions symptom-like, rather than based on delusions’ irrationality. When a delusion is judged pathological, we do not treat and evaluate the patient holding it as we treat and evaluate those who believe its content. The development of pathological delusions is a sign that an illness has worsened. Pathological delusions’ behavior sometimes resembles that of typical beliefs; however, this marks patients’ more distant departure from normality, and their illness’ further aggravation.
Role of Lipocalin-2-Chemokine Axis in the Development of Neuropathic Pain following Peripheral Nerve Injury*

Background: In the central nervous system, the role of LCN2 as a chemokine inducer has been previously reported. Results: Peripheral nerve injury increased LCN2 expression. Lcn2 deficiency attenuated pain hypersensitivity, microglial activation, and chemokine production. Chemokine expression and pain behavior were induced by LCN2. Conclusion: The LCN2-chemokine axis plays a critical role in the pathogenesis of neuropathic pain. Significance: LCN2 can be targeted for treatment of neuropathic pain. Lipocalin 2 (LCN2), which is also known as 24p3 and neutrophil gelatinase-associated lipocalin (NGAL), binds small, hydrophobic ligands and interacts with cell surface receptor 24p3R to regulate diverse cellular processes. In the present study, we examined the role of LCN2 in the pathogenesis of neuropathic pain using a mouse model of spared nerve injury (SNI). Lcn2 mRNA levels were significantly increased in the dorsal horn of the spinal cord after SNI, and LCN2 protein was mainly localized in neurons of the dorsal and ventral horns. LCN2 receptor 24p3R was expressed in spinal neurons and microglia after SNI. Lcn2-deficient mice exhibited significantly less mechanical pain hypersensitivity during the early phase after SNI, and an intrathecal injection of recombinant LCN2 protein elicited mechanical pain hypersensitivity in naive animals. Lcn2 deficiency, however, did not affect acute nociceptive pain. Lcn2-deficient mice showed significantly less microglial activation and proalgesic chemokine (CCL2 and CXCL1) production in the spinal cord after SNI than wild-type mice, and recombinant LCN2 protein induced the expression of these chemokines in cultured neurons. Furthermore, the expression of LCN2 and its receptor was detected in neutrophils and macrophages in the sciatic nerve following SNI, suggesting the potential role of peripheral LCN2 in neuropathic pain. Taken together, our results indicate that LCN2 plays a critical role in the development of pain hypersensitivity following peripheral nerve injury and suggest that LCN2 mediates neuropathic pain by inducing chemokine expression and subsequent microglial activation.
An antiglycolipid antibody inhibits Madin-Darby canine kidney cell adhesion to laminin and interferes with basolateral polarization and tight junction formation

Epithelial cells polarize not only in response to cell-cell contacts, but also to contacts with a substratum composed of extracellular matrix molecules. To probe the role of specific matrix constituents in epithelial cell polarization, we investigated the effects of an adhesion-blocking mAb, 12B12, on initial polarization of MDCK cells. The 12B12 antibody, raised against whole MDCK cells, blocks adhesion to laminin by 65% but has no effect on adhesion of cells to collagen type I. Taking advantage of this antibody's function-blocking activity, as well as the fact that MDCK cells secrete laminin, the role of endogenous laminin in polarization was examined by plating cells on collagen-coated substrata in the presence of the antibody. Under these conditions, cell spreading was reduced 1.5h after plating, and cells were flatter and had fewer microvilli after 24 h. Even though lateral cell membranes were closely apposed, transepithelial resistance in the presence of the antibody was significantly reduced relative to controls. When the polarization of specific apical and basolateral markers was examined both biochemically and immunocytochemically in the presence of the antibody, we observed that the apical marker polarized at normal rates while basolateral markers did not. Surprisingly, the 12B12 antibody was not directed against any known cell adhesion protein but reacted specifically with Forssman antigen, a glycosphingolipid. These results suggest that glycolipids may play a significant role in cell adhesion via laminin and in epithelial cell polarization.
Firm Growth : a Survey

We survey the phenomenon of the growth of firms drawing on literature from economics, management and sociology. We begin with a review of empirical "stylised facts" before discussing theoretical contributions. Firm growth is characterized by a predominant stochastic element, making it difficult to predict. Indeed, previous empirical research into the determinants of firm growth has had a limited success. We also observe that theoretical propositions concerning the growth of firms are often amiss. We conclude that progress in this area requires solid empirical work, perhaps making use of novel statistical techniques.
Aurora‐A over‐expression in high‐grade PIN lesions and prostate cancer

Over‐expression of Aurora‐A (Aurora 2 kinase, STK‐15), a protein found in centrosomes thought to be associated with genetic instability, has been previously documented in prostate cancer [Pihan et al.: Cancer Res 61(5):2212–2219, 2001]. It is unknown if this protein is also over‐expressed in high‐grade prostatic intraepithelial neoplasia (PIN) lesions.
Chapter V: Counseling

FOR THE first time in the history of these reviews, there is sufficient research in the process of counseling to justify a separate chapter dealing with the face to face situation thru which an effort to alter attitudes, choices, and behavior is made. The instruments of appraisal and diagnosis are covered in other sections. This chapter deals with the general formulations of significant hypotheses in counseling, with objective studies of the process involved in interviewing, with research regarding outcomes, and with a variety of new developments challenging further research.
Depression Scale Recognition from Audio, Visual and Text Analysis

Depression is a major mental health disorder that is rapidly affecting lives worldwide. Depression not only impacts emotional but also physical and psychological state of the person. Its symptoms include lack of interest in daily activities, feeling low, anxiety, frustration, loss of weight and even feeling of self-hatred. This report describes work done by us for Audio Visual Emotion Challenge (AVEC) 2017 during our second year BTech summer internship. With the increase in demand to detect depression automatically with the help of machine learning algorithms, we present our multimodal feature extraction and decision level fusion approach for the same. Features are extracted by processing on the provided Distress Analysis Interview Corpus-Wizard of Oz (DAIC-WOZ) database. Gaussian Mixture Model (GMM) clustering and Fisher vector approach were applied on the visual data; statistical descriptors on gaze, pose; low level audio features and head pose and text features were also extracted. Classification is done on fused as well as independent features using Support Vector Machine (SVM) and neural networks. The results obtained were able to cross the provided baseline on validation data set by 17% on audio features and 24.5% on video features.