Miracle-dz/UniFAR-FTUs huggingface dataset:
Clathrin Interaction and Subcellular Localization of Ce‐DAB‐1, an Adaptor for Protein Secretion in Caenorhabditis elegans

Growth factors must be secreted appropriately to co‐ordinate cell proliferation, specification and movement during development and to control cell numbers and migrations in adult animals. Previous results showed that the secretion of the Caenorhabditis elegans fibroblast growth factor homologue, EGL‐17, from vulval precursor cells in vivo involves the cytoplasmic adaptor protein Ce‐DAB‐1 and two lipoprotein receptors that bind Ce‐DAB‐1 and EGL‐17. Here, we confirm the Ce‐DAB‐1 requirement for EGL‐17 secretion using mutant animals. In vitro, Ce‐DAB‐1 binds to clathrin and APT‐4, the C. elegans homologue of the α‐adaptin subunit of adaptor protein 2 (AP2), and weakly to the γ‐appendage domains of APT‐1 (AP1γ‐adaptin) and APT‐9 (GGA protein). In tissue‐culture cells, Ce‐DAB‐1 localizes to various compartments, including AP2‐containing vesicles near the cell surface and perinuclear vesicles that contain AP1. The latter also contain Rab8, but not Rab5 or Rab11, as well as proteins en route from the trans Golgi network (TGN) to the surface. In vivo, EGL‐17 secretion was inhibited by depletion of apt‐1, apt‐9 or ce‐rab‐8 and partially inhibited by RNAi of ce‐rab‐5, consistent with an important role for these proteins in the secretion of EGL‐17 in vivo. These results suggest that Ce‐DAB‐1 might co‐ordinate the assembly of endocytic or secretory vesicles in vivo and may mediate EGL‐17 secretion directly, by recruiting clathrin to lipoprotein receptors at the TGN, or indirectly, by affecting lipoprotein receptor endocytosis and recycling.
A small sample study of the STEPP approach to assessing treatment–covariate interactions in survival data

A new, intuitive method has recently been proposed to explore treatment–covariate interactions in survival data arising from two treatment arms of a clinical trial. The method is based on constructing overlapping subpopulations of patients with respect to one (or more) covariates of interest and in observing the pattern of the treatment effects estimated across the subpopulations. A plot of these treatment effects is called a subpopulation treatment effect pattern plot. Here, we explore the small sample characteristics of the asymptotic results associated with the method and develop an alternative permutation distribution‐based approach to inference that should be preferred for smaller sample sizes. We then describe an extension of the method to the case in which the pattern of estimated quantiles of survivor functions is of interest. Copyright © 2009 John Wiley & Sons, Ltd.
An hypnotic technique for treating insomnia.

Abstract A technique for treating insomnia with short-term hypnotherapy is presented. 2 cases are presented to illustrate the clinical application of the technique. The treatment procedure, which incorporates the demand characteristics of the therapeutic setting, positive expectancies, a reduction in physiological arousal, and a reduction of excessive cognitive activity is discussed in terms of current theories of insomnia.
Re-Visiting the Theory and Practice Gap through the Lens of Student Teacher Dilemmas

This study concerns the dilemmas student teachers met during their field experiences: what they were and what coping strategies they used. Its purpose is to help staff and students better understand the challenges student teachers face as they move from university-based to school-based learning. Data reveal three main categories of dilemmas: teaching, professional identity and future career plans. When coping with dilemmas, participants turned to various people around them. They felt some of the dilemmas were beyond their control, thus, could not be resolved due to problems in the Turkish education system. Findings are discussed as related to professional learning.
Mixed H$_2$/H$_i$ region-based fuzzy controller design for continuous-time fuzzy systems

In this paper, Takagi-Sugeno (T-S) fuzzy control problem with minimizing H2/H∞ norm is studied. A new approach in designing fuzzy controller is called T-S region-based fuzzy controller (TSRFC), which is derived from the fuzzy region concept and the robust control technique. The fuzzy region concept is used to divide the general plant rules into several fuzzy regions and the robust control technique is used to stabilize all plant rules of each fuzzy region. A theorem in synthesizing TSRFC is derived from Lyapunov stability criterion, which is expressed in terms of LMIs. This proposed idea is greatly reduced the total number of LMIs and controller rules. For this reason, TSRFC is easy to implement with simple hardware. TSRFC is able to provide good performances as well as PDC-based designs even though the controller rules are reduced.
transcriptional response of Escherichia coli 1 O 157 : H 7 to cinnamaldehyde exposure 2 3 Running Title : Transcriptional response of E . coli to cinnamaldehyde 4 5 6 7

Title: Examination of the genome-wide transcriptional response of Escherichia coli 1 O157:H7 to cinnamaldehyde exposure 2 3 Running Title: Transcriptional response of E. coli to cinnamaldehyde 4 5 6 7 Jeyachchandran Visvalingam, Juan David Hernandez-Doria and Richard A Holley* 8 9 10 Department of Food Science, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, 11 Canada 12 Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, 13 Canada 14 15 16 17 18 Current Address: The University of Texas Southwestern Medical Center, Dallas, TX, US 19 20 *Corresponding author: R.A. Holley, Tel: +1 (204)474-9601; Fax: +1 (204) 474-7630; E21 mail: rick_holley@umanitoba.ca 22 23 Copyright © 2012, American Society for Microbiology. All Rights Reserved. Appl. Environ. Microbiol. doi:10.1128/AEM.02767-12 AEM Accepts, published online ahead of print on 26 November 2012
Priority-Based CCA Periods for Efficient and Reliable Communications in Wireless Sensor Networks

The IEEE 802.15. 4 standard utilizes the CSMA-CA mechanism to control nodes’ access to the shared wireless communication medium. CSMA-CA implements the Binary Exponential Backoff (BEB) algorithm by which a node refrains from sending any packet before the expiry of its backoff period. After that, the node is required to sense the medium for two successive time slots to assert that the medium is clear from any ongoing transmissions (this is referred to as Clear Channel Assessment (CCA)). Upon finding the medium busy, the node doubles its backoff period and repeats that process. While effective in reducing the likelihood of collisions, this approach takes no measures to preserve the priorities among the nodes contending to access the medium. In this paper we propose the Priority-Based BEB (PB-BEB) algorithm in which we enhance BEB such that nodes’ priority is preserved. We provide a simulation study to examine the performance of PB-BEB. Our simulations show that the latter not only outperforms BEB in terms of fairness, but also show promising results in terms other parameters like channel utilization, reliability, and power conservation.
The Wilms tumor suppressor WT1 directs stage‐specific quiescence and differentiation of human hematopoietic progenitor cells

WT1, a transcription factor implicated in both normal kidney differentiation and tumorigenesis, is also expressed in differentiating hematopoietic progenitors. Most human acute leukemias contain high levels of the wild‐type transcript, while a minority have point mutations, raising the possibility that this tumor suppressor might have a paradoxical oncogenic effect in some hematopoietic cells. Using high titer retroviral infection, we demonstrate that WT1 triggers rapid growth arrest and lineage‐specific differentiation in primary hematopoietic progenitors and differentiation‐competent leukemia cell lines, while it induces cellular quiescence in a primitive subset of primary precursors. Growth arrest by WT1 is associated with induction of p21CIP1, but expression of this cyclin‐dependent kinase inhibitor alone is insufficient for either cellular differentiation or primitive cell preservation. The effects of WT1 are enhanced by co‐expression of its naturally occurring isoforms, and are correlated with the physiological expression pattern of WT1 in vivo. Our observations suggest a role for WT1 in the differentiation of human hematopoietic cells, and provide a functional model that supports its capacity as a tumor suppressor in human acute leukemia.
Transparent pyroelectric sensors and organic field-effect transistors with fluorinated polymers: steps towards organic infrared detectors

Polymer electrets from the polyvinylidene family are highly suitable materials for plastic electronics. The high dielectric constant of such polymers in both the ferro- and non-ferroelectric phase is most suitably employed in gate dielectrics in organic field-effect transistors. The pyro- and piezoelectric response makes ferroelectric polymer electrets also an ideal choice for organic temperature, infrared radiation and pressure sensors. Here we report steps towards transparent organic pyroelectric infrared sensors: The infrared sensor element is based on poly (vinylidene fluoride), the top contact pentacene transistor on poly(vinylidene-fluoride tetrafluoroethylene hexafluoropropylene) and poly(vinyl cinnamate) as gate dielectric. Steps for combining the ferroelectric polymer sensors and transistors to a fully organic temperature and infrared sensing element are outlined. The sensor concept may be easily scaled up to the production of sensor arrays for thermal imaging
Optimized and quality improved incoherent optical fiber bundle calibration method for image transmission

Artificial vision, in spite of all theoretical and practical progress accomplished during last thirty years, still cannot be employed technically in some hazardous and strong industrial areas, where conditions are such that cameras would not operate properly. Alternatives on such problem are the quite recent IP65 and IP67 industrial cameras, and associated connectors, protected by an anticorrosive, waterproof, and high temperatures resistive carcass employing a dedicated electronic, in addition robust to almost 3G accelerations. Nevertheless, such cameras are still very expensive compared to conventional industrial cameras and would still not be enough in hardest conditions (explosive gas or dust environment) or in electromagnetic interferences environments. A good alternative in extreme conditions is the use of optical fiber bundle. Since such cable only transmits light, they intrinsically have electromagnetic interferences immunity and depending on the fiber material could be exposed to very high temperature (over 1000°C for sapphire fibers for example), could be employed in almost all corrosive environment, and are totally submersible. Nevertheless, the coherent optical fiber bundles are very expensive, and for large distances could be non-competitive facing the other hardware solutions. Thus, the best suitable option to develop a competitive system in those particular cases is the use of incoherent optical fiber bundle (IOFB), nowadays just employed for illumination tasks. Image transmission in this case is not direct but require a calibration step that we discuss in this paper. We propose in this work on a new calibration method of incoherent optical fiber bundle (IOFB) for image transmission purpose. First, we present the calibration method (an enhancement of previously published calibration methods), some resulting reconstructed images and a discussion on its quality improvement employing simple denoising methods. We finally depict the two new post calibration methods that efficiently refine the reconstruction Look Up Table (LUT) used for the output image reconstruction. Those two post calibration method are: correction of the input plan chromatics aberrations, and extraction of a unique pixel (almost centered) for each fibers.
CAN MEASUREMENT OF B‐TYPE NATRIURETIC PEPTIDE LEVELS IMPROVE CARDIOVASCULAR DISEASE PREVENTION?

1 The measurement of plasma levels of B‐type natriuretic peptide (BNP) and amino‐terminal pro‐BNP (NT‐proBNP) provides useful diagnostic information in patients with suspected heart failure and valuable prognostic information in patients with heart failure, acute coronary syndrome, valvular heart disease and other cardiac pathologies. 2 BNP‐ and NT‐proBNP‐guided heart failure therapy improves patient outcomes. 3 An increasing number of studies shows plasma BNP and NT‐proBNP levels predict all‐cause mortality and cardiovascular events including heart failure, myocardial infarction, stroke, atrial fibrillation and cardiovascular death in stable patients with or without known cardiovascular disease and provide information about cardiovascular risk additional to that provided by traditional risk factors. 4 Antihypertensive therapy reduces elevated NT‐proBNP levels in individuals at increased cardiovascular risk, thereby suggesting that change in NT‐proBNP levels provides a measure of risk reduction. 5 Thus, monitoring of BNP and NT‐proBNP levels offers the possibilities of improved targeting of individuals with increased cardiovascular risk and optimization of strategies for primary and secondary prevention of cardiovascular disease. 6 There is need for an outcome study to determine whether BNP‐ or NT‐proBNP‐guided therapy improves cardiovascular disease prevention.
Cellulomonas pakistanensis sp. nov., a moderately halotolerant Actinobacteria.

A rod-shaped, motile, facultatively anaerobic and moderately halotolerant plant-growth-promoting actinobacterial strain, designated NCCP-11(T), was isolated from paddy grains. To delineate its taxonomic position, the strain was subjected to a polyphasic characterization. Cells of strain NCCP-11(T) grew at 10-37 °C (optimum 28-32 °C), at pH 6-9 (optimum pH 7) and in 0-12% (w/v) NaCl (optimum 1-2%) in broth medium. Based on 16S rRNA gene sequence analysis, strain NCCP-11(T) showed highest similarity to the type strains of Cellulomonas hominis (98.99%) and Cellulomonas denverensis (98.09 %) and less than 97 % with other closely related taxa. The chemotaxonomic data [major menaquinone: MK-9(H4); cell-wall peptidoglycan: type A4β; major fatty acids: anteiso-C15 : 0, C16 : 0, C14 : 0 and anteiso-C17 : 0; major polar lipids: diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannosides and two unknown polar lipids] also supported the affiliation of strain NCCP-11(T) to the genus Cellulomonas. The level of DNA-DNA relatedness between strain NCCP-11(T) and the two type strains mentioned above was less than 42.7%. On the basis of DNA-DNA relatedness, physiological and biochemical characteristics and phylogenetic position, strain NCCP-11(T) can be differentiated from species of the genus Cellulomonas with validly published names and thus represents a novel species, for which the name Cellulomonas pakistanensis sp. nov. is proposed. The type strain is NCCP-11(T) ( = DSM 24792(T) = JCM 18755(T) = KCTC 19798(T)).
Permissive Dynamic Information Flow Analysis Technical Report # UCSC-SOE-09-34

A key challenge in dynamic information flow analysis is handling implicit flows, where code conditional on a private variable updates a public variable x. The naive approach of upgrading x to private results in x being partially-leaked, where its value contains private data but its label may be either private (on this execution) or public (on an alternative execution where the conditional update was not performed). Prior work proposed the no-sensitive-upgrade check, which handles implicit flows by prohibiting partially-leaked data, but attempts to update a public variable from a private context causes execution to get stuck. To overcome this limitation, we develop a sound yet flexible permissiveupgrade strategy. To prevent information leaks, partially-leaked data is permitted but carefully tracked, and it must be upgraded to private before being used in a conditional test. We present an automatic dynamic analysis technique for inferring these upgrade annotations and inserting them into the program source code. The combination of these techniques allows more programs to run to completion, while still guaranteeing termination-insensitive non-interference in a purely-dynamic manner.
Human brain endothelial cells (HUBEC) promote SCID repopulating cell expansion through direct contact

The objective of this study was to re-evaluate the previously published hematopoietic stem cell (HSC) expansion work using human brain endothelial cells (HUBEC). The expansion effect of contact and non-contact conditions was reported to be equivalent by others. However, we report here different results that the expansion can be achieved only with direct contact. We co-cultured human CD34+ cells with and without HUBEC contact for seven days with cytokines and the readouts were CD34+/CD38 − phenotype and SCID repopulating cell (SRC) frequency. Also tested was the inhibitory effect of Wnt receptor inhibitor Dkk-1 on HUBEC contact ex vivo expansion; whether an increased expression of Wnt3 occurs on the HUBEC surface; and detection of an increased nuclear localization of beta-catenin in CD34+/CD38 − cells in HUBEC contact culture condition. We conclude that the successful expansion by HUBEC contact culture is a candidate explanation based on the Wnt family protein, possibly Wnt3, expression on HUBEC.
Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity.

Controversy surrounds the apparent rising maximums of morphological complexity during eukaryotic evolution, with organisms increasing the number and nestedness of developmental areas as evidenced by morphological elaborations reflecting area boundaries. No "predictable drive" to increase this sort of complexity has been reported. Recent genetic data and theory in the general area of gene dosage effects has engendered a robust "gene balance hypothesis," with a theoretical base that makes specific predictions as to gene content changes following different types of gene duplication. Genomic data from both chordate and angiosperm genomes fit these predictions: Each type of duplication provides a one-way injection of a biased set of genes into the gene pool. Tetraploidies and balanced segments inject bias for those genes whose products are the subunits of the most complex biological machines or cascades, like transcription factors (TFs) and proteasome core proteins. Most duplicate genes are removed after tetraploidy. Genic balance is maintained by not removing those genes that are dose-sensitive, which tends to leave duplicate "functional modules" as the indirect products (spandrels) of purifying selection. Functional modules are the likely precursors of coadapted gene complexes, a unit of natural selection. The result is a predictable drive mechanism where "drive" is used rigorously, as in "meiotic drive. " Rising morphological gain is expected given a supply of duplicate functional modules. All flowering plants have survived at least three large-scale duplications/diploidizations over the last 300 million years (Myr). An equivalent period of tetraploidy and body plan evolution may have ended for animals 500 million years ago (Mya). We argue that "balanced gene drive" is a sufficient explanation for the trend that the maximums of morphological complexity have gone up, and not down, in both plant and animal eukaryotic lineages.
A synthetic cannabinoid, CP55940, inhibits lipopolysaccharide‐induced cytokine mRNA expression in a cannabinoid receptor‐independent mechanism in rat cerebellar granule cells

Objectives The inflammatory response plays an important role in the pathogenesis of many diseases in the central nervous system. Cannabinoids exhibit diverse pharmacological actions including anti‐inflammatory activity. In this study, we tried to elucidate possible effects of cannabinoids on lipopolysaccharide (LPS)‐induced expression of inflammatory cytokine mRNAs in rat cerebellar granule cells.
Myostatin Gene Mutated Mice Induced with TALE Nucleases

Myostain gene (MSTN) is expressed primarily in skeletal muscle, and negatively regulates skeletal muscle mass; it has been suggested that mice with MSTN inhibition have reduced adiposity and improved insulin sensitivity. Therefore, it is important to establish a fast and effective gene editing method. In this report, we established the myostatin mutated-mouse model by microinjection of Transcription Activator-Like Effector Nucleases (TALENs) mRNA within the mouse fertilized oocytes and achieved high rates of mutagenesis of the mouse MSTN in C57BL/6J. Six of 45 born mice carried target mutations and we appointed one as the parental mating with wild mouse to produce the F1 and backcross to produce the F2 generation. All the mutations of the mice were examined quickly and efficiently by high-resolution melting curve analysis (HRMA) and then verified by direct sequencing. We obtained the homozygous of the F2 generation which transmitted the mutant alleles to the progeny with 100% efficiency. Mutant mice exhibited increases in muscle mass comparable to those observed in wild-type mice. Therefore, combining TALEN-mediated gene targeting with HRMA technology is a superior method of constructing genetically modified mice through microinjection in the mouse fertilized oocytes with high efficiency and short time of selection.
Effects of different progestin regimens in hormone replacement therapy on blood coagulation factor VII and tissue factor pathway inhibitor.

BACKGROUND Long-term hormone replacement therapy (HRT) reduces cardiovascular risk, but an early increased risk was reported in women with coronary heart disease. In such women the arterial intima can express tissue factor, and changes in coagulation factor VII (factor VII) and tissue factor pathway inhibitor (TFPI) may be deleterious. METHODS We measured factor VII clotting activity, activated factor VII, and concentrations of factor VII and TFPI during 12 months in healthy post-menopausal women randomized to: (i). cyclic oral estrogen/progestin (n = 25); (ii). long-cycle oral estrogen/quarterly progestin (n = 32); (iii). continuous oral estrogen/progestin (n = 21); (iv). continuous oral estrogen/intrauterine progestin (n = 22); (v). no HRT (n = 26). Blood was collected at baseline, 3, 6 and 12 months. Additional sampling was done before progestin intake in the long cycle group. RESULTS No variations were observed in the reference group. There was a substantial decrease in TFPI concentrations in the HRT groups irrespective of the type of progestin. In women receiving long-cycle treatment, all factor VII measures increased during the unopposed estrogen periods, and the increase was reversed after progestin intake. The integrated response, AUC, for TFPI was significantly lower in the HRT groups compared with the reference group. CONCLUSION The observed changes may increase the early thrombotic risk associated with HRT use.
A Lagrangian Finite Element Analysis of Gravity Waves in Water of Variable Depth

The paper is concerned with the problem of gravitational wave propagation in water of variable depth. The problem is formulated in the Lagrangian description, and the ensuing equations are solved numerically by a finite element method. In computations a convecting mesh that follows the material fluid particles is used. As illustrations, results of numerical simulations carried out for plane gravity waves propagating over bottoms of simple geometry are presented. For parameters typical of a laboratory flume, the transformation of a transient wave, generated by a single movement of a piston-like wave maker, is investigated. The results show the evolution of the free-surface elevation, displaying steepening of the wave over sloping beds and its gradual attenuation in regions of uniform depth.
Clinical ecology

EDITOR,- The impression gained by Jon Nicholl and colleagues - “that the trauma centre is showing promising results is founded on the results put out by the trauma centre itself” - is correct.1 We work in the north west midlands trauma system and believe that we have a duty to audit our work and that the results of our internal audit should not …