Miracle-dz/UniFAR-FTUs huggingface dataset:
The Plasmid Complement of Lactococcus lactis UC509.9 Encodes Multiple Bacteriophage Resistance Systems

ABSTRACT Lactococcus lactis subsp. cremoris strains are used globally for the production of fermented dairy products, particularly hard cheeses. Believed to be of plant origin, L. lactis strains that are used as starter cultures have undergone extensive adaptation to the dairy environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids that specify technologically important phenotypic traits. Here, we present a detailed analysis of the eight plasmids of L. lactis UC509.9, an Irish dairy starter strain. Key industrial phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified, including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed phage resistance of L. lactis UC509.9. AbiB escape mutants were generated for phage sk1, which were found to carry mutations in orf6, which encodes the major capsid protein of this phage.
Elevated expression of Nkx‐2.5 in developing myocardial conduction cells

A number of different phenotypes emerge from the mesoderm‐derived cardiomyogenic cells of the embryonic tubular heart, including those comprising the cardiac conduction system. The transcriptional regulation of this phenotypic divergence within the cardiomyogenic lineage remains poorly characterized. A relationship between expression of the transcription factor Nkx‐2.5 and patterning to form cardiogenic mesoderm subsequent to gastrulation is well established. Nkx‐2.5 mRNA continues to be expressed in myocardium beyond the looped, tubular heart stage. To investigate the role of Nkx‐2.5 in later development, we have determined the expression pattern of Nkx‐2.5 mRNA by in situ hybridization in embryonic chick, fetal mouse, and human hearts, and of Nkx‐2.5 protein by immunolocalization in the embryonic chick heart. As development progresses, significant nonuniformities emerge in Nkx‐2.5 expression levels. Relative to surrounding force‐generating (“working”) myocardium, elevated Nkx‐2.5 mRNA signal becomes apparent in the specialized cells of the conduction system. Similar differences are found in developing chick, human, and mouse fetal hearts, and nuclear‐localized Nkx‐2.5 protein is prominently expressed in differentiating chick conduction cells relative to adjacent working myocytes. This tissue‐restricted expression of Nkx‐2.5 is transient and correlates with the timing of spatio‐temporal recruitment of cells to the central and the peripheral conduction system. Our data represent the first report of a transcription factor showing a stage‐dependent restriction to different parts of the developing conduction system, and suggest some commonality in this development between birds and mammals. This dynamic pattern of expression is consistent with the hypothesis that Nkx‐2.5, and its level of expression, have a role in regulation and/or maintenance of specialized fate selection by embryonic myocardial cells. Anat Rec 263:307–313, 2001. © 2001 Wiley‐Liss, Inc.
Optimal Report Strategies for WBANs Using a Cloud-Assisted IDS

Applying an Intrusion Detection System (IDS) to Wireless Body Area Networks (WBANs) becomes a costly task for body sensors due to their limited resources. To solve this problem, a cloud-assisted IDS framework is proposed. We adopt a new distributed-centralized mode, where IDS agents residing in body sensors will be triggered to launch. All IDS agents are only responsible for reporting the monitored events, not intrusion decision that is processed in the cloud platform. We then employ the signaling game to construct an IDS Report Game (IDSRG) depicting interactions between a body sensor and its opponent. The pure- and mixed-strategy Bayesian Nash Equilibriums (BNEs) of the stage IDSRG are achieved, respectively. As two players interact continually, we develop the stage IDSRG into a dynamic multistage game in which the belief can be updated dynamically. Upon the current belief, the Perfect Bayesian Equilibrium (PBE) of the dynamic multistage IDSRG is attained, which helps the IDS-sensor select the optimal report strategy. We afterward design a PBE-based algorithm to make the IDS-sensor decide when to report the monitored events. Experiments show the effectiveness of the dynamic multistage IDSRG in predicting the type and optimal strategy of a malicious body sensor.
Saccharomyces cerevisiae RAD2 gene: isolation, subcloning, and partial characterization

A plasmid (pNF2000) containing a 9.7-kilobase pair DNA insert that complements the UV sensitivity of rad2-1, rad2-2, and rad2-4 mutants of Saccharomyces cerevisiae has been isolated from a yeast genomic library. Genetic analysis of strains derived by transformation of rad2 mutants with an integrating plasmid containing a 9.3-kilobase pair fragment from pNF2000 shows that the fragment integrates exclusively at the chromosomal rad2 gene. We therefore conclude that this plasmid contains the RAD2 gene. The 9.3-kilobase pair fragment was partially digested with Sau3A and cloned into a multicopy yeast vector designed for easy retrieval of Sau3A inserts. The smallest subclone that retains the RAD2 gene is 4.5 kilobase pairs. This fragment was partially digested with Sau3A and cloned into an integrating plasmid. These plasmids were isolated and integrated into a heterozygous rad2/RAD2 strain. Plasmids containing internal fragments of the RAD2 gene were identified because they yielded UV-sensitive transformants due to disruption of the RAD2 gene. Sporulation of diploids transformed with integrating plasmids containing internal fragments of RAD2 gave rise to four viable haploids per tetrad, indicating that unlike the RAD3 gene of S. cerevisiae, the RAD2 gene is not essential for the viability of haploid cells under normal growth conditions. Measurements of the RNA transcript by RNA-DNA hybridization with the internal fragment as the probe indicate a size of approximately 3.2 kilobases.
Interpreting coagulation assays

The interpretation of coagulation assays requires knowledge of the principal clotting pathways. The activated partial thromboplastin time is sensitive to all hemostatic factors except FVII, whereas the prothrombin time reflects levels of prothrombin and FV, FVII, and FX. Using the two tests in concert is helpful in identifying hemophilia, the coagulopathy of liver disease, and disseminated intravascular coagulation. In addition, the activated partial thromboplastin time and prothrombin time are used for monitoring anticoagulant therapy with heparin and warfarin, respectively. Measurement of D-dimer is informative in patients suspected of having thrombotic disorders and determining the risk of thrombosis recurrence. Mixing tests distinguish clotting factor deficiencies from circulating anticoagulants such as heparin, the lupus anticoagulant, and antibodies directed against specific clotting factors. The modified Bethesda assay detects and provides an indication of the strength of FVIII inhibitors. However, interpreting the results of coagulation assays is not always straightforward, and expert consultation is occasionally required to resolve difficult clinical situations.
CHARMing Clinical Pathways - Modeling of Clinical Pathways based on the Goal-Oriented Ontological Framework CHARM

Much procedural knowledge in the medical domain, such as clinical practice guidelines, nursing manuals, and clinical pathways (abbreviated to CPs), is documented and shared. This paper concentrates on the CP, which represents a standard time-sequence of actions carried out by clinical staff for each disease. With the aim not of replacing the conventional form of CPs in a clinical setting but of facilitating description and revision of knowledge by knowledge managers, we have proposed CHARM, which is a goal-oriented, tree-structured model based on an ontology of actions. The aim of the work described in this paper is to confirm the practical ability of CHARM to represent medical actions in CPs in a computer-interpretable way, using eight real CPs in Osaka University Hospital. CHARM trees in terms of actions defined clearly in the ontology explicitly represent goals of actions, i.e., why the actions should be needed, and so on, which are implicit in the conventional CPs. We also confirmed the benefits of CHARM for describing/revising CPs by the knowledge mangers in a comparison of the actions in CPs, such as finding commonality among CPs, easy comparison of CPs from a goal-oriented perspective, and explanation of the reasons for differences.
Is telephone screening feasible? Accuracy and cost-effectiveness of identifying people medically eligible for home- and community-based services.

PURPOSE To determine the accuracy of a telephone-screening system to identify persons eligible for home- and community-based long-term care. DESIGN AND METHODS Data from Michigan telephone screens were compared to data from in-person assessments using the Minimum Data Set for Home Care (MDS-HC). Weighted kappa statistics measured the level of agreement between the two assessments. RESULTS Overall, recommendations based on the telephone screen produced a marginal match compared to recommendations based on in-person assessment. "False positives" (individuals scoring as more impaired on the telephone screen than in person) occurred in 27% of all cases, while "false negatives" (individuals scoring as less impaired on the telephone screen) only occurred among 6% of the callers. Neither individual screen questions, source of information, location of the individual, timing between screen and assessment, nor temporal changes accounted for mismatches. Telephone screens resulted in an 11% savings over the cost of providing in-person assessments to all program seekers. IMPLICATIONS The telephone screen has utility as a broad targeting mechanism that allows agencies to avoid costly in-person assessments for all program seekers. Evidence does not support use of the telephone screen alone to determine either medical eligibility or a specific level of care.
Role of autophagy, SQSTM1, SH3GLB1, and TRIM63 in the turnover of nicotinic acetylcholine receptors

Removal of ubiquitinated targets by autophagosomes can be mediated by receptor molecules, like SQSTM1, in a mechanism referred to as selective autophagy. While cytoplasmic protein aggregates, mitochondria, and bacteria are the best-known targets of selective autophagy, their role in the turnover of membrane receptors is scarce. We here showed that fasting-induced wasting of skeletal muscle involves remodeling of the neuromuscular junction (NMJ) by increasing the turnover of muscle-type CHRN (cholinergic receptor, nicotinic/nicotinic acetylcholine receptor) in a TRIM63-dependent manner. Notably, this process implied enhanced production of endo/lysosomal carriers of CHRN, which also contained the membrane remodeler SH3GLB1, the E3 ubiquitin ligase, TRIM63, and the selective autophagy receptor SQSTM1. Furthermore, these vesicles were surrounded by the autophagic marker MAP1LC3A in an ATG7-dependent fashion, and some of them were also positive for the lysosomal marker, LAMP1. While the amount of vesicles containing endocytosed CHRN strongly augmented in the absence of ATG7 as well as upon denervation as a model for long-term atrophy, denervation-induced increase in autophagic CHRN vesicles was completely blunted in the absence of TRIM63. On a similar note, in trim63−/− mice denervation-induced upregulation of SQSTM1 and LC3-II was abolished and endogenous SQSTM1 did not colocalize with CHRN vesicles as it did in the wild type. SQSTM1 and LC3-II coprecipitated with surface-labeled/endocytosed CHRN and SQSTM1 overexpression significantly induced CHRN vesicle formation. Taken together, our data suggested that selective autophagy regulates the basal and atrophy-induced turnover of the pentameric transmembrane protein, CHRN, and that TRIM63, together with SH3GLB1 and SQSTM1 regulate this process.
Pilot Activities : LEGO WeDo at Primary School

In this thesis we study the first-contact situation in which 3rd grade pupils in primary school encounter LEGO WeDo for the first time. We compare reactions and the work of two groups of 3rd graders – only one of these groups had previously worked with virtual robotic software and developed their logical and algorithmic thinking. We look for signs that signify using virtual robotic software considerably influenced their ability to solve problems in a LEGO WeDo programming language. We also use these pilot lessons to prove our introductory activities with LEGO WeDo and we make several enhancements for the next iteration. We have made several interesting observations that will serve us as foundations for our next research.
Investigation on compressed wavefront sensing in freeform surface measurements

In this paper, conventional modal wavefront reconstruction is compared with compressed wavefront sensing to reconstruct freeform surface profiles using the Shack-Hartmann wavefront sensor. The modal wavefront reconstruction represents the phase or the wavefront in the Zernike domain. The compressed wavefront sensing method based on the sparse Zernike representation (SPARZER) represents the phase slopes in the Zernike domain. The effectiveness of compressed wavefront sensing in freeform surface profile measurements is investigated.
Therapeutics , Targets , and Chemical Biology DOG 1 Regulates Growth and IGFBP 5 in Gastrointestinal Stromal Tumors

Gastrointestinal stromal tumors (GIST) are characterized by activating mutations of KIT or platelet-derived growth factor receptor a(PDGFRA), which can be therapeutically targeted by tyrosine kinase inhibitors (TKI) such as imatinib. Despite long-lasting responses, most patients eventually progress after TKI therapy. The calcium-dependent chloride channel DOG1 (ANO1/TMEM16A), which is strongly and specifically expressed in GIST, is used as a diagnostic marker to differentiate GIST from other sarcomas. Here, we report that loss of DOG1 expression occurs together with loss of KIT expression in a subset of GIST resistant to KIT inhibitors, and we illustrate the functional role of DOG1 in tumor growth, KIT expression, and imatinib response. Although DOG1 is a crucial regulator of chloride balance in GIST cells, we found that RNAi-mediated silencing or pharmacologic inhibition of DOG1 did not alter cell growth or KIT signaling in vitro. In contrast, DOG1 silencing delayed the growth ofGIST xenografts in vivo. Expression profiling of explanted tumors afterDOG1blockade revealed a strong upregulation in the expression of insulin-like growth factor-binding protein 5 (IGFBP5), a potent antiangiogenic factor implicated in tumor suppression. Similar results were obtained after selection of imatinib-resistant DOG1and KIT-negative cells derived from parental DOG1 and KIT-positive GIST cells, where a 5,000-fold increase in IGFBP5 mRNA transcripts were documented. In summary, our findings establish the oncogenic activity of DOG1 in GIST involving modulation of IGF/IGF receptor signaling in the tumor microenvironment through the antiangiogenic factor IGFBP5. Cancer Res; 73(12); 1–10. 2013 AACR.
Chromatin , Gene , and RNA Regulation CPEB 1 Regulates the Expression of MTDH / AEG-1 and Glioblastoma Cell Migration

Cytoplasmic polyadenylation element-binding protein 1 (CPEB1) is an mRNA-binding protein present in both neurons and glia. CPEB1 is capable of both repressing mRNA translation and activating it depending upon its phosphorylation state. CPEB1-boundmRNAs are held in translational dormancy until CPEB1 is phosphorylated, leading to the cytoplasmic polyadenylation of the bound mRNA that triggers translation. Here, we show that CPEB1 can bind to and regulate translation of the mRNA-encoding metadherin (MTDH, also known as AEG-1 and Lyric) in the rat glioblastoma cell lineCNS1.MTDH/AEG-1 is being revealed as a critical signalingmolecule in tumor progression, playing roles in invasion, metastasis, and chemoresistance. By using a mutant of CPEB1 that cannot be phosphorylated (thereby holding target mRNAs in translational arrest), we show that inhibiting CPEB1mediated translation blocks MTDH/AEG-1 expression in vitro and inhibits glioblastomas tumor growth in vivo. CPEB1-mediated translation is likely to impact several signaling pathways thatmaypromote tumor progression, but we present evidence suggesting a role in directed cell migration in glioblastoma cells. In addition, reporter mRNA containing CPEB1-binding sites is transported to the leading edge of migrating cells and translated, whereas the samemRNAwith point mutations in the binding sites is synthesized perinuclearly. Our findings show that CPEB1 is hyperactive in rat glioblastoma cells and is regulating an important cohort ofmRNAswhose increased translation is fueling the progression of tumor proliferation and dispersal in the brain. Thus, targeting CPEB1-mediated mRNA translation might be a sound therapeutic approach. Mol Cancer Res; 11(2); 149–60. 2012 AACR.
Big Data Analytics to Predict Breast Cancer Recurrence on SEER Dataset using MapReduce Approach

traditional data analytic might not have the capacity to handle enormous amount of data. Due to the rapid growth of information, solutions need to be contemplated and provided in order to handle and extract value and knowledge from these data sets. Moreover, decision makers should have the capacity to increase significant bits of knowledge from such fluctuated and quickly evolving information. Such esteem can be given utilizing big data analytic, which is the utilization of advanced analytic techniques on big data using MapReduce approach. This paper examines to develop a high performance platform to efficiently analyse big SEER (Surveillance, Epidemiology, and End Results) breast cancer data set using MapReduce to find the recurrence of breast cancer. Keywordscancer; Big data, Classification; Data analytics, MapReduce, SEER.
Susceptibility of fetal guinea pig brain cell cultures to replicating guinea pig cytomegalovirus infection is increased with increasing fetal age: infection of astrocytes

Guinea pig brain cell cultures were established from fetuses at 25, 31, and 37 days of gestation (DG). After 7 days in vitro, the cultures were infected with guinea pig cytomegalovirus (GPCMV). Based on cytopathic effect, immunofluorescence staining for GPCMV by using virus-specific antiserum, and the amount of virus recovered, cultures established from fetuses at 25 DG were least susceptible to replicating infection, and cultures established from fetuses at 37 DG were most susceptible. Using cell-type-specific markers, it was determined that the increase in susceptibility to replicating infection paralleled an increase in the number of differentiated cells. Astrocytes were the most abundant cell type identified and were susceptible to replicating GPCMV infection, whereas neurons were not.
Consistent, Two-Stage Sampled Distribution Regression via Mean Embedding

We focus on the distribution regression problem: regressing to a real-valued response from a probability distribution. Although there exist a large number of similarity measures between distributions, very little is known about their generalization performance in specific learning tasks. Learning problems formulated on distributions have an inherent two-stage sampled difficulty: in practice only samples from sampled distributions are observable, and one has to build an estimate on similarities computed between sets of points. To the best of our knowledge, the only existing method with consistency guarantees for distribution regression requires kernel density estimation as an intermediate step (which suffers from slow convergence issues in high dimensions), and the domain of the distributions to be compact Euclidean. In this paper, we provide theoretical guarantees for a remarkably simple algorithmic alternative to solve the distribution regression problem: embed the distributions to a reproducing kernel Hilbert space, and learn a ridge regressor from the embeddings to the outputs. Our main contribution is to prove the consistency of this technique in the two-stage sampled setting under mild conditions (on separable, topological domains endowed with kernels). For a given total number of observations, we derive convergence rates as an explicit function of the problem difficulty. As a special case, we answer a 15-year-old open question: we establish the consistency of the classical set kernel [Haussler, 1999; Gartner et. al, 2002] in regression, and cover more recent kernels on distributions, including those due to [Christmann and Steinwart, 2010].
NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

Universally conserved factors from NusG family bind at the upstream fork junction of transcription elongation complexes and modulate RNA synthesis in response to translation, processing, and folding of the nascent RNA. Escherichia coli NusG enhances transcription elongation in vitro by a poorly understood mechanism. Here we report that E. coli NusG slows Gre factor-stimulated cleavage of the nascent RNA, but does not measurably change the rates of single nucleotide addition and translocation by a non-paused RNA polymerase. We demonstrate that NusG slows RNA cleavage by inhibiting backtracking. This activity is abolished by mismatches in the upstream DNA and is independent of the gate and rudder loops, but is partially dependent on the lid loop. Our comprehensive mapping of the upstream fork junction by base analogue fluorescence and nucleic acids crosslinking suggests that NusG inhibits backtracking by stabilizing the minimal transcription bubble. DOI: http://dx.doi. org/10.7554/eLife.18096. 001
Exploring non-equilibrium many-body physics with alkaline earth atoms and polar molecules

Among of the ultimate goals of modern science is the understanding of emergent complex properties of matter in the strongly interacting regime from simple constituents and their interactions. This understanding can lead towards the development of new materials and devices with novel functionalities both at the level of basic research and for numerous technological applications. Richard Feynman's pioneering ideas of quantum simulation constitute a promising path to reach such goals. A major push to implement them has been possible thanks to advances in cooling and trapping atoms in optical lattices. These systems are not only a defect-free replica of electrons in crystalline lattices but, in addition satisfy the requirement of full controllability.
ROAD SAFETY VALUATION UNDER A STATED CHOICE FRAMEWORK

The value of fatal risk reductions is a vital input for road safety cost-benefit analysis and has been traditionally estimated by means of contingent valuation in spite of the growing criticism surrounding this approach. Furthermore, many scholars believe that risk-money trade-offs are not well understood because of the difficulty of internalising tiny risks; the authors have applied the Stated Choice (SC) approach to tackle this problem. To assess the robustness of SC, the authors conducted an external validity test based on the results of three different studies. They found that people can internalise risk, expressed as fatal crashes, in a consistent way from an economic point of view. Finally they offer a hypothesis to explain the differences between their values and figures obtained in developed countries, highlighting the importance of conducting local studies rather than transferring imported values. © 2006 LSE and the University of Bath