Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global Nosocomial Dominance

ABSTRACT The management of infections due to Klebsiella pneumoniae has been complicated by the emergence of antimicrobial resistance, especially to carbapenems. Resistance to carbapenems in K. pneumoniae involves multiple mechanisms, including the production of carbapenemases (e.g., KPC, NDM, VIM, OXA-48-like), as well as alterations in outer membrane permeability mediated by the loss of porins and the upregulation of efflux systems. The latter two mechanisms are often combined with high levels of other types of β-lactamases (e.g., AmpC). K. pneumoniae sequence type 258 (ST258) emerged during the early to mid-2000s as an important human pathogen and has spread extensively throughout the world. ST258 comprises two distinct lineages, namely, clades I and II, and it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Incompatibility group F plasmids with blaKPC have contributed significantly to the success of ST258. The optimal treatment of infections due to carbapenemase-producing K. pneumoniae remains unknown. Some newer agents show promise for treating infections due to KPC producers; however, effective options for the treatment of NDM producers remain elusive.
IRES-Mediated Protein Translation Overcomes Suppression by the p14ARF Tumor Suppressor Protein

Internal ribosome entry sites (IRES elements) have attracted interest in cancer gene therapy because they can be used in the design of gene transfer vectors that provide bicistronic co-expression of two transgene products under the control of a single promoter. Unlike cellular translation of most mRNAs, a process that requires a post-translational 5' modification of the mRNA known as the cap structure, IRES-mediated translation is independent of the cap structure. The cellular conditions that may intervene to modulate IRES-mediated, cap-independent versus cap-dependent translation, however, remain poorly understood, although they could be critical to the choice of gene transfer vectors. Here we have compared the effects of the p14ARF (Alternate Reading Frame) tumor suppressor, a translational suppressor frequently overexpressed in cancer, on cap-dependent translation versus cap-independent translation from the EMCV viral IRES often used in bicistronic gene transfer vectors. We find that ectopic overexpression of p14ARF suppresses endogenous and ectopic cap-dependent protein translation, consistent with other studies. However, p14ARF has little or no effect on transgene translation initiated within an IRES element. This suggests that transgenes placed downstream of an IRES element will retain efficient translation of their gene products in the presence of high levels of ectopic or endogenous p14ARF, a finding that could be particularly relevant to therapeutic gene therapy strategies for cancer.
Stack-based typed assembly language

This paper presents STAL, a variant of Typed Assembly Language with constructs and types to support a limited form of stack allocation. As with other statically-typed low-level languages, the type system of STAL ensures that a wide class of errors cannot occur at run time, and therefore the language can be adapted for use in certifying compilers where security is a concern. Like the Java Virtual Machine Language (JVML), STAL supports stack allocation of local variables and procedure activation records, but unlike the JVML, STAL does not pre-suppose fixed notions of procedures, exceptions, or calling conventions. Rather, compiler writers can choose encodings for these high-level constructs using the more primitive RISC-like mechanisms of STAL. Consequently, some important optimizations that are impossible to perform within the JVML, such as tail call elimination or callee-saves registers, can be easily expressed within STAL.
Chemical Linkage to Injected Tissues Is a Distinctive Property of Oxidized Avidin

We recently reported that the oxidized avidin, named AvidinOX®, resides for weeks within injected tissues as a consequence of the formation of Schiff's bases between its aldehyde groups and tissue protein amino groups. We also showed, in a mouse pre-clinical model, the usefulness of AvidinOX for the delivery of radiolabeled biotin to inoperable tumors. Taking into account that AvidinOX is the first oxidized glycoprotein known to chemically link to injected tissues, we tested in the mouse a panel of additional oxidized glycoproteins, with the aim of investigating the phenomenon. We produced oxidized ovalbumin and mannosylated streptavidin which share with avidin glycosylation pattern and tetrameric structure, respectively and found that neither of them linked significantly to cells in vitro nor to injected tissues in vivo, despite the presence of functional aldehyde groups. The study, extended to additional oxidized glycoproteins, showed that the in vivo chemical conjugation is a distinctive property of the oxidized avidin. Relevance of the high cationic charge of avidin into the stable linkage of AvidinOX to tissues is demonstrated as the oxidized acetylated avidin lost the property. Plasmon resonance on matrix proteins and cellular impedance analyses showed in vitro that avidin exhibits a peculiar interaction with proteins and cells that allows the formation of highly stable Schiff's bases, after oxidation.
The distribution and effect of non-native earthworms on soil structure in northern Michigan

Brooke Callaghan Olivia Mitchinson Jonathan Ruiz Courtney Whitcher University of Michigan Biological Station EEB 381 June 15, 2017 Joel Heinen Understanding the change in abundance of exotic earthworms and their effect on soil structure is crucial in assessing their influence on different microhabitats. Studies comparing the effect of earthworm species on environments in northern Michigan remain limited. To address this, we conducted experiments in plots of different soil compositions to survey the abundance and distribution of earthworms. Four earthworm species have been found in present-day microhabitats of northern Michigan: Lumbricus rubellus, Lumbricus terrestris, Dendrobaena octaedra and Aporrectodea spp. We found that there were significantly more earthworms in nutrient rich soils than in sandy soil environments. In addition, a thick 0-A horizon mixture correlated with greater earthworm abundance. This study will allow for greater understanding of the influence and abundance of non-native earthworms in different microhabitats. I grant the Regents of the University of Michigan the non-exclusive right to retain, reproduce, and distribute my paper, titled in electronic formats and at no cost throughout the world. The University of Michigan may make and keep more than one copy of the Paper for purposes of security, backup, preservation and access, and may migrate the Paper to any medium or format for the purpose of preservation and access in the future.
Do we Still Need Gold Standards for Evaluation?

The availability of a huge mass of textual data in electronic format has increased the need for fast and accurate techniques for textual data processing. Machine learning and statistical approaches have been increasingly used in NLP since a decade, mainly because they are quick, versatile and efficient. However, despite this evolution of the field, evaluation still rely (most of the time) on a comparison between the output of a probabilistic or statistical system on the one hand, and a non-statistic, most of the time hand-crafted, gold standard on the other hand. In this paper, we take the example of the acquisition of subcategorization frames from corpora as a practical example. Our study is motivated by the fact that, even if a gold standard is an invaluable resource for evaluation, a gold standard is always partial and does not really show how accurate and useful results are.
Multiwavelength generation in a Raman fiber laser with sampled Bragg grating

Simultaneous continuous-wave multiwavelength operation of a Raman fiber laser is demonstrated with sampled Bragg grating (SBG) at room temperature. The characteristics of multiwavelength fiber ring laser can be easily controlled by adjusting the parameters of the SBG, including the sampling period and the sampling length. In the proposed fiber laser, stable four oscillating wavelengths with 100- and 50-GHz spacing has been achieved, respectively, as well as five oscillating ones with a wavelength spacing of only 25 GHz by varying the sampling period of the SBG.
Leveraging Human Inputs in Interactive Machine Learning for Human Robot Interaction

A key challenge of HRI is allowing robots to be adaptable, especially as robots are expected to penetrate society at large and to interact in unexpected environments with non-technical users. One way of providing this adaptability is to use Interactive Machine Learning, i.e. having a human supervisor included in the learning process who can steer the action selection and the learning in the desired direction. We ran a study exploring how people use numeric rewards to evaluate a robot's behaviour and guide its learning. From the results we derive a number of challenges when designing learning robots: what kind of input should the human provide? How should the robot communicate its state or its intention? And how can the teaching process by made easier for human supervisors?
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription

Although microRNAs (miRNAs) are important regulators of gene expression, the transcriptional regulation of miRNAs themselves is not well understood. We employed an integrative computational pipeline to dissect the transcription factors (TFs) responsible for altered miRNA expression in ovarian carcinoma. Using experimental data and computational predictions to define miRNA promoters across the human genome, we identified TFs with binding sites significantly overrepresented among miRNA genes overexpressed in ovarian carcinoma. This pipeline nominated TFs of the p53/p63/p73 family as candidate drivers of miRNA overexpression. Analysis of data from an independent set of 253 ovarian carcinomas in The Cancer Genome Atlas showed that p73 and p63 expression is significantly correlated with expression of miRNAs whose promoters contain p53/p63/p73 family binding sites. In experimental validation of specific miRNAs predicted by the analysis to be regulated by p73 and p63, we found that p53/p63/p73 family binding sites modulate promoter activity of miRNAs of the miR-200 family, which are known regulators of cancer stem cells and epithelial–mesenchymal transitions. Furthermore, in chromatin immunoprecipitation studies both p73 and p63 directly associated with the miR-200b/a/429 promoter. This study delineates an integrative approach that can be applied to discover transcriptional regulatory mechanisms in other biological settings where analogous genomic data are available.
Object Detection Using Generalization and Efficiency Balanced Co-Occurrence Features

In this paper, we propose a high-accuracy object detector based on co-occurrence features. Firstly, we introduce three kinds of local co-occurrence features constructed by the traditional Haar, LBP, and HOG respectively. Then the boosted detectors are learned, where each weak classifier corresponds to a local image region with a co-occurrence feature. In addition, we propose a Generalization and Efficiency Balanced (GEB) framework for boosting training. In the feature selection procedure, the discrimination ability, the generalization power, and the computation cost of the candidate features are all evaluated for decision. As a result, the boosted detector achieves both high accuracy and good efficiency. It also shows performance competitive with the state-of-the-art methods for pedestrian detection and general object detection tasks.
A Proposed Experimental Methodology for Assessing the Effects of Biophysical Properties and Energy Content on Live Fuel Flammability

The effectiveness of fire management tactics and safety of firefighters strongly depend on the reliability of fire behaviour predictions that is currently limited by a lack of understanding of the flammability of live fuel. Until now fire modeling has been primarily based on the flammability of dead fuel using the assumption that combustion of the live fuel has a very limited effect on fire behaviour. However, the analysis of the existing data revealed that live fuel constituted from 48% to 60% of fuel consumed during the passage of a flame-front, meaning that live fuel plays a significant role in determining frontal fire intensity and fire behaviour. Introducing a new definition of flammability and a test method for flammability assessment, this study identifies how and to what extent live fuel and its properties may affect frontal flame intensity. By evaluating flammability directly in a flame, the proposed oxygen consumption calorimetry method better represents the high-intensity combined radiative and convective heat transfer prior to ignition as well as the conditions of oxygen deficiency and high concentrations of water vapor within the flame-front. The flammability of live fuel consumed within the flame-front was defined as energy release contribution to the frontal flame and represented the energy-generation component of the energy balance of the flame-front rather than just an energy content of separate fuel elements. The flammability was measured as the change in energy release from the flame resulting from interaction with live fuel during average flame-front residence time. Assessing the flammability of fresh shoots rather than just foliage allowed for better representation of the live plant
H(2) cooling of primordial gas triggered by UV irradiation

We investigate the formation of molecular hydrogen (H_2) in a primordial H+He gas cloud irradiated by a power-law UV flux. We find that at high densities (>1 cm^{-3}) and low temperatures (<10^4 K), the background radiation enhances the formation of H_2 and results in molecular cooling dominating over photoionization heating. This process could accelerate the collapse and fragmentation of dense objects at high redshifts.
Covering Points of a Digraph with Point-Disjoint Paths and Its Application to Code Optimization

A point-disjoint path cover of a directed graph is a collection of point-disjoint paths (some paths possibly having zero length) which covers all the points. A path cover which minimizes the number of paths corresponds to an optimal sequence of the steps of a computer program for efficient coding and documentation. The minimization problem for the general directed graph is hard in the sense of being NP-complete. In the case of cycle-free digraphs, however, the problem is polynomial, for it is shown that it can be reduced to the maximum-matching problem. A heuristic given here for finding a near optimal path cover for the general case is based upon applying the maximum-matching algorithm to the subgraphs of an interval decomposition.
Canonical Transient Receptor Potential Channel (TRPC) 3 and TRPC6 Associate with Large-Conductance Ca2+-Activated K+ (BKCa) Channels: Role in BKCa Trafficking to the Surface of Cultured Podocytes

Large-conductance (BKCa type) Ca2+-activated K+ channels encoded by the Slo1 gene and various canonical transient receptor potential channels (TRPCs) are coexpressed in many cell types, including podocytes (visceral epithelial cells) of the renal glomerulus. In this study, we show by coimmunoprecipitation and GST pull-down assays that BKCa channels can associate with endogenous TRPC3 and TRPC6 channels in differentiated cells of a podocyte cell line. Both types of TRPC channels colocalize with Slo1 in podocytes and in human embryonic kidney (HEK) 293T cells transiently coexpressing the TRPC channels with Slo1. In HEK293T cells, coexpression of TRPC6 increased surface expression of a Slo1 subunit splice variant (Slo1VEDEC) that is typically retained in intracellular compartments, as assessed by cell-surface biotinylation assays and confocal microscopy. Corresponding currents through BKCa channels were also increased with TRPC6 coexpression, as assessed by whole-cell and excised inside-out patch recordings. By contrast, coexpression of TRPC3 had no effect on the surface expression of BKCa channels in HEK293T cells or on the amplitudes of currents in whole cells or excised patches. In podocytes, small interfering RNA knockdown of endogenous TRPC6 reduced steady-state surface expression of endogenous Slo1 channels, but knockdown of TRPC3 had no effect. TRPC6, but not TRPC3 knockdown also reduced voltage-evoked outward current through podocyte BKCa channels. These data indicate that TRPC6 and TRPC3 channels can bind to Slo1, and this colocalization may allow them to serve as a source of Ca2+ for the activation of BKCa channels. TRPC6 channels also play a role in the regulation of surface expression of a subset of podocyte BKCa channels.
Photoemission study of the valence-band electronic structure in FexO, Fe3O4, and alpha -Fe2O3 single crystals.

Valence-band photoemission spectra have been measured from cleaved stoichiometric iron oxide single crystals using synchrotron radiation. The total photoelectron yield is observed to increase dramatically at photon energies above the Fe 3p\ensuremath{\rightarrow}3d excitation threshold, and the resonant onset correlates directly with the oxidation state of the Fe cations. Features in the total yield profiles are interpreted in terms of atomic multiplets. The phenomenon of resonant photoemission is used to distinguish the Fe 3d-derived valence states from the overlapping unhybridized O 2p states in each of the oxides. By use of cleaved single crystals, the subtle differences in the valence-band photoemission features associated with ferrous (${\mathrm{Fe}}^{2+}$) and ferric (${\mathrm{Fe}}^{3+}$) cations have been determined. The measured energy distribution of the photoemission final states in single crystal \ensuremath{\alpha}-${\mathrm{Fe}}_{2}$${\mathrm{O}}_{3}$ are in good agreement with recent measurements and configuration-interaction cluster calculations by Fujimori et al., which take into account ligand-to-metal charge transfer. Constant-initial-state spectra measured across the 3p\ensuremath{\rightarrow}3d threshold in each oxide indicate that most of the photoemission intensity near the top of the valence band is derived from hybridized cation-3d--ligand-2p states, whereas the emission at higher binding energies results from primarily 3${d}^{n\mathrm{\ensuremath{-}}1}$ final states. On this basis, each of the iron oxides is classified as a charge-transfer rather than a Mott-Hubbard insulator.
Qualitative properties of certain piecewise deterministic Markov processes

We study a class of Piecewise Deterministic Markov Processes with state space Rd x E where E is a finite set. The continuous component evolves according to a smooth vector field that is switched at the jump times of the discrete coordinate. The jump rates may depend on the whole position of the process. Working under the general assumption that the process stays in a compact set, we detail a possible construction of the process and characterize its support, in terms of the solutions set of a differential inclusion. We establish results on the long time behaviour of the process, in relation to a certain set of accessible points, which is shown to be strongly linked to the support of invariant measures. Under Hormander-type bracket conditions, we prove that there exists a unique invariant measure and that the processes converges to equilibrium in total variation. Finally we give examples where the bracket condition does not hold, and where there may be one or many invariant measures, depending on the jump rates between the flows.
More Examples

Some important examples and explications of Grothendieck duality which should have been included in Chapter 5 of [C1] were overlooked. Several such topics are treated here. One question which can be asked about the trace map H(X,ΩX/k) → k for a proper smooth scheme X of pure dimension n over a field k is how it relates to the trace map for a smooth divisor. Generalizing a little, one can ask whether there is an analogous statement if one replace “smooth” with “CM”. This matter is addressed in the relative case in §1, and the answer winds up involving a sign of (−1)n−1. In a different direction, one can ask how the Grothendieck trace map for a proper smooth variety over C is related to a “topological” trace map defined in terms of topological Poincaré duality, as in [C1, (2.3.4)]. They do not agree, but instead are off by a sign of (−1). In the projective case, one can analyze this problem quite pleasantly by using Bertini’s theorem, induction, and the divisor compatibility treated in §1, once one has also worked out the analytic analogue of §1. We work out such an analogue in §2, and the answer winds up involving a sign of (−1), a contrast with the sign of (−1)n−1 in the algebraic case, and it is this discrepancy of −1 that ultimately leads to the sign of (−1) when comparing the Grothendieck and topological traces in the projective algebraic case (since each of the n hyperplane slices contributes a sign of −1 in the comparison, but everything agrees in dimension 0). Despite naive impressions, our sign of (−1) in the analytic/algebraic trace comparison is consistent with the lack of such a sign in the analytic/algebraic comparison given in the appendix to [D]. The explanation for the consistency is given in the pp. 33, 36 remarks in [C2]. The analytic/algebraic comparison in the general proper case can be reduced to the projective case (and even just the case of projective spaces! ) by using local cohomology, as we explain in §3. Finally, in §4 we work out the comparison between the residue map and the Chern class map for line bundles on curves (where the Chern class is viewed with values in the ground field rather than in Z). I am grateful to deJong, Ogus, and Serre for asking me questions about these topics, and to P. Sastry and Y. Tong for convincing me that one could use local cohomology to replace the use of alterations in the comparison of the analytic/algebraic traces.
On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics

Ordinary differential equations (ODE) are a powerful tool for modeling dynamic processes with wide applications in a variety of scientific fields. Over the last 2 decades, ODEs have also emerged as a prevailing tool in various biomedical research fields, especially in infectious disease modeling. In practice, it is important and necessary to determine unknown parameters in ODE models based on experimental data. Identifiability analysis is the first step in determing unknown parameters in ODE models and such analysis techniques for nonlinear ODE models are still under development. In this article, we review identifiability analysis methodologies for nonlinear ODE models developed in the past one to two decades, including structural identifiability analysis, practical identifiability analysis and sensitivity-based identifiability analysis. Some advanced topics and ongoing research are also briefly reviewed. Finally, some examples from modeling viral dynamics of HIV, influenza and hepatitis viruses are given to illustrate how to apply these identifiability analysis methods in practice.