Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques

Abstract Background: The aim of this study was to investigate whether the diagnosis of infective endocarditis (IE) could be improved using molecular tools in addition to standard microscopy and cultivation methods. Methods: Cultivation was performed on blood or tissue samples as recommended in the modified Duke criteria. The molecular tools included a broad-range polymerase chain reaction (PCR)-based denaturant gradient gel electrophoresis and a more detailed identification by constructing clone libraries followed by sequencing. Results: Of 14 patients, 12 were positive by blood or tissue cultivation and all were monomicrobial. Molecular methods showed the presence of DNA from multiple bacterial species in 6 of the samples and indicated a larger variety of bacteria in the different samples than identified by cultivation. For 8 of the patients there was a good correlation between the results of cultivation and molecular methods, and for these samples the identified bacteria are known to be frequently involved with IE. Many of the additional bacteria only identified by the molecular methods are not reported as common causes of IE. Conclusions: Application of molecular tools in addition to cultivation indicated that polymicrobial infections might be of importance in IE. However, the significance of the more unknown microorganisms needs to be investigated further.
Attachment 1 Health Effects of Exposure to Methyl Tertiary Butyl Ether ( MTBE )

Methyl tertiary butyl ether (MTBE) (CAS No. 1634-04-4) is a volatile organic compound used almost exclusively as an oxygenate in unleaded gasoline to improve combustion efficiency. In the past it also had limited use as a therapeutic drug for dissolving cholesterol gallbladder stones. Currently, MTBE is added at 11% by volume to almost all of the gasoline used in California, although on March 25, 1999 Governor Gray Davis signed Executive Order D-5-99 requiring that its use in fuel in California be discontinued by December 31, 2002. Due to its use as a fuel additive, MTBE is produced in high volume; it was the second most-produced chemical in the U.S. in 1997.
Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9

Significance Using the recently introduced Cas9/sgRNA technique, we have developed a method for specifically targeting Drosophila germ-line cells to generate heritable mutant alleles. We have established transgenic lines that stably express Cas9 in the germ line and compared different promoters and scaffolds of sgRNA in terms of their efficiency of mutagenesis. An overall mutagenesis rate of 74.2% was achieved with this optimized system, as determined by the number of mutant progeny out of all progeny screened. We also evaluated the off-targets associated with the method and established a Web-based resource, as well as a searchable, genome-wide database of predicted sgRNAs appropriate for genome engineering in flies. Our results demonstrate that this optimized Cas9/sgRNA system in Drosophila is efficient, specific, and cost-effective and can be readily applied in a semi-high-throughput manner. The ability to engineer genomes in a specific, systematic, and cost-effective way is critical for functional genomic studies. Recent advances using the CRISPR-associated single-guide RNA system (Cas9/sgRNA) illustrate the potential of this simple system for genome engineering in a number of organisms. Here we report an effective and inexpensive method for genome DNA editing in Drosophila melanogaster whereby plasmid DNAs encoding short sgRNAs under the control of the U6b promoter are injected into transgenic flies in which Cas9 is specifically expressed in the germ line via the nanos promoter. We evaluate the off-targets associated with the method and establish a Web-based resource, along with a searchable, genome-wide database of predicted sgRNAs appropriate for genome engineering in flies. Finally, we discuss the advantages of our method in comparison with other recently published approaches.
Moe in epithelial cell survival . Rho 1 regulates apoptosis via activation of the JNK signaling pathway at the plasma membrane

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 189 No. 2 311–323 www.jcb. org/cgi/doi/10.1083/jcb.200912010 JCB 311 Correspondence to Richard G. Fehon: rfehon@uchicago.edu Abbreviations used in this paper: Bsk, Basket; CA, constitutively active; CRIB, Cdc42 and Rac interactive binding; Dia, Diaphanous; DN, dominant negative; Egr, Eiger; enGal4, engrailed-Gal4; ERM, ezrin/radixin/moesin; GAP, GTPase-activating protein; GDI, GDP dissociation inhibitor; Hep, Hemipterous; IP, immunoprecipitation; JNKKK, JNK kinase kinase; MLK, mixed lineage kinase; Moe, Moesin; POSH, Plenty of SH3s; Puc, Puckered; RHG, reaper, hid, and grim; Rok, Rho kinase; Slpr, Slipper; Wgn, Wengen; Wnd, Wallenda. Introduction
The TP-Index: a dynamic and efficient indexing mechanism for temporal databases

To support temporal operators efficiently, indexing based on temporal attributes must be supported. The authors propose a dynamic and efficient index scheme called the time polygon (TP-index) for temporal databases. In the scheme, temporal data are mapped into a two-dimensional temporal space, where the data can be clustered based on time. The date space is then partitioned into time polygons where each polygon corresponds to a data page. The time polygon directory can be organized as a hierarchical index. The index handles long duration temporal data elegantly and efficiently. The performance analysis indicates that the time polygon index is efficient both in storage utilization and query search. <<ETX>>
Query Representation with Global Consistency on User Click Graph

The Internet of Things aggregates large-scale query logs. A query log is generally represented as a bipartite graph on a query set and a URL set. Most of the traditional methods used the raw click frequency to weigh the link between a query and a URL on the click graph. In order to address the disadvantages of raw click frequency, researchers proposed the entropy-biased model, which incorporates raw click frequency with inverse query frequency of the URL as the weighting scheme for query representation. In this paper, we observe that the inverse query frequency can be considered a global property of the URL on the click graph, which is more informative than raw click frequency, which can be considered a local property of the URL. Based on this insight, we develop the global consistency model for query representation, which utilizes the click frequency and the inverse query frequency of a URL in a consistent manner. Furthermore, we propose a new scheme called inverse URL frequency as an effective way to capture the global property of a URL. Experiments have been conducted on the AOL search engine log data. The result shows that our global consistency model achieved better performance than the current models.
Drug Carrier for Photodynamic Cancer Therapy

Photodynamic therapy (PDT) is a non-invasive combinatorial therapeutic modality using light, photosensitizer (PS), and oxygen used for the treatment of cancer and other diseases. When PSs in cells are exposed to specific wavelengths of light, they are transformed from the singlet ground state (S0) to an excited singlet state (S1–Sn), followed by intersystem crossing to an excited triplet state (T1). The energy transferred from T1 to biological substrates and molecular oxygen, via type I and II reactions, generates reactive oxygen species, (1O2, H2O2, O2*, HO*), which causes cellular damage that leads to tumor cell death through necrosis or apoptosis. The solubility, selectivity, and targeting of photosensitizers are important factors that must be considered in PDT. Nano-formulating PSs with organic and inorganic nanoparticles poses as potential strategy to satisfy the requirements of an ideal PDT system. In this review, we summarize several organic and inorganic PS carriers that have been studied to enhance the efficacy of photodynamic therapy against cancer.
A Hybrid CPU-GPU Accelerated Framework for Fast Mapping of High-Resolution Human Brain Connectome

Recently, a combination of non-invasive neuroimaging techniques and graph theoretical approaches has provided a unique opportunity for understanding the patterns of the structural and functional connectivity of the human brain (referred to as the human brain connectome). Currently, there is a very large amount of brain imaging data that have been collected, and there are very high requirements for the computational capabilities that are used in high-resolution connectome research. In this paper, we propose a hybrid CPU-GPU framework to accelerate the computation of the human brain connectome. We applied this framework to a publicly available resting-state functional MRI dataset from 197 participants. For each subject, we first computed Pearson’s Correlation coefficient between any pairs of the time series of gray-matter voxels, and then we constructed unweighted undirected brain networks with 58 k nodes and a sparsity range from 0.02% to 0.17%. Next, graphic properties of the functional brain networks were quantified, analyzed and compared with those of 15 corresponding random networks. With our proposed accelerating framework, the above process for each network cost 80∼150 minutes, depending on the network sparsity. Further analyses revealed that high-resolution functional brain networks have efficient small-world properties, significant modular structure, a power law degree distribution and highly connected nodes in the medial frontal and parietal cortical regions. These results are largely compatible with previous human brain network studies. Taken together, our proposed framework can substantially enhance the applicability and efficacy of high-resolution (voxel-based) brain network analysis, and have the potential to accelerate the mapping of the human brain connectome in normal and disease states.
Spatial generalization of optimal control for robot manipulators

This paper presents a diffusion-based learning approach to generalize optimal control of a robot manipulator over a bounded work space. Generally, optimal control requires to solve a two point boundary value problem with respect to increase and decrease of time and is very difficult to be solved analytically. In our approach, we first assume that, for some sets of initial and desired terminal conditions of the robots positions we already have the numerical optimal solutions (for example, using some complex numerical computation techniques). Then by using radial basis function network we parameterize these control inputs by a set of weight matrixes. Finally, we apply our diffusion-based algorithm to generalize these weight matrixes for different terminal position conditions. This approach greatly reduced computation cost for the robot to find its optimal control. In addition, since diffusion-based algorithm is a parallel distributed learning approach which only requires local interaction between the nodes of a learning network (a lattice), it can be realized by resent IC hardware technology easily. Computer simulations of a 2-DOF robot arm show the effectiveness of our approach.
Morphometric and molecular characterization of populations of Pratylenchus kumamotoensis and P. pseudocoffeae (Nematoda, Pratylenchidae) newly recorded in Korea

Abstract At least 70 species of root-lesion nematodes, Pratylenchus spp. , have been identified worldwide, many of which are serious pests of various agricultural crop plants. In Korea, only 14 species have been recorded in vegetable and fruit fields. Here, we report two new records of root-lesion nematode species in Korea based on morphometric and molecular methods. Soil samples were collected from chrysanthemum cultivars in various regions. Morphometric diagnosis showed that two new records for Korea: Pratylenchus kumamotoensis in Chilgok County and Pratylenchus pseudocoffeae in Geumsan County. In addition, molecular diagnosis using the two sequences of the internal transcribed spacer (ITS) and the D2–D3 region of ribosomal DNA showed that these two species were most similar with those from Japan, Costa Rica and USA. The similarities of the ITS and D2–D3 sequences were 99.85 and 99.74%, respectively, for Pratylenchus kumamotoensis and 99.99 with Costa Rica populations and 99.86% with USA populations, respectively, for Pratylenchus pseudocoffeae. To our knowledge, this is the first report of two species in Korea.
Telling Stories: A Thematic Narrative Analysis of Eight Women's PhD Experiences

This research examined eight women’s stories about their PhD experiences to explore their lived experience of this journey and if gender was a consideration in their PhD journey. The aims of this thesis were firstly, to provide a more in-depth understanding of women’s decisions to participate in doctoral education; and secondly, to provide a more in-depth understanding of women’s experiences in undertaking doctoral degrees and the factors that increase their chances of successful completion. Using thematic narrative analysis, the study found that motivation to do a PhD is multi-faceted. In some instances the motivations were complementary, such as a personal interest in the topic and/or the discipline and wanting to begin or build an academic career. In some cases they were incongruent – being awarded a prestigious scholarship was motivation for one woman to start her degree, but the departmental pressure and expectations that went along with it were de-motivating.
Exploring Body Image and Body Mass Index of Male and Female Special Olympics Athletes

Individuals with intellectual disabilities are largely marginalized within society and are understudied as a group (Reel & Bucciere, 2011). Although there have been numerous body image studies with able-bodied athletes, this study represents the first attempt to explore body image of male and female Special Olympics athletes. Athletes (N = 103) were 18–61 years of age (M = 33.34; SD = 11.20) and represented mild to moderate severity for diagnosable intellectual disabilities. Height and weight were measured to determine body mass index (BMI). Body image was verbally assessed via individual interviews using the Figure Ratings Scale and open-ended items. Female athletes had a significantly higher BMI (M = 33.02, SD = 9.28) than male athletes (M = 28.24, SD = 7.38). The BMI means for the female and male athletes met the classifications for obese and overweight, respectively. There was also a negative relationship between body satisfaction and BMI in the overall sample (r = -.46), male athletes only (r = -.51).
Efficient Methods for Biomedical Named Entity Recognition

In recent years, conditional random fields (CRFs) have shown good performance in named entity recognition tasks. However, a direct application of it to biomedical named entity recognition incurs a very high training cost. In this paper, we evaluate two alternatives to training a CRF with a traditional single-phase maximum likelihood training method. One is to use an online training method and the other is to divide the named entity recognition task into two tasks. For the cascaded method, we propose to include a "margin" in the model that leads to better recognition results. Both methods give better performance with substantial decrease in training time. In particular, the cascaded method outperforms the best system in the JNLPBA shared task.
Sparse Locality Preserving Embedding

Principal component analysis (PCA) is an unsupervised linear method of variables technique used in data compression, classification, and visualization[1]. The essence of PCA is to extract principal components, linear combinations of input variables that together best account for the variance in a data set. Linear discriminant analysis (LDA) is a favored tool for supervised linear classification in many areas because of its simplicity and robustness[2]. The goal of LDA is to provide low dimensional projections of data onto the most discriminative directions. Locality preserving projection (LPP) is a recently proposed method[3], which can be regarded as the linearization of Laplacian EigenMap[4]. When applied to face recognition tasks, LPP is also called LaplacianFaces. The idea behind LPP is that it considers the manifold structure of the data set, and preserves the locality of data in the embedding space. LPP has shown the superiority in terms of image indexing and face recognition. One of the major disadvantages of these three methods is that the derived projections are linear combinations of all the original features. Hence the learned results are difficult to interpret. In this paper, we propose a novel algorithm, called sparse locality preserving embedding (SpLPE), which is based on lasso regression framework for learning sparse projections by incorporating c 1 penalty with conventional locality preserving projections. The affinity graph constructed in LPP encodes both discriminant and geometrical structure in the data[3]. Once the Laplacian matrix is computed, we recast the generalized eigenvalue problem of LPP in the lasso regression framework to obtain sparse basis functions. The proposed SpLPE is a combination of locality preserving with sparsity. Additionally, our algorithm can be performed in either supervised or unsupervised mode.
Expression profile of the RNA‐binding protein gene hermes during chicken embryonic development

The hermes gene encodes an RNA‐binding protein containing an RNA‐recognition motif. Its expression has been described previously in Xenopus and in the developing heart of very young chicken embryos. We have analyzed the expression of cHermes in later heart development, where expression is maintained in the myocardium, and also in previously undescribed sites. cHermes expression first appears in the somites in the first terminally differentiated myocytes of both the epaxial and the hypaxial myotome. Expression is also seen in the primordium of the allantois and continues in the developing allantoic sac. cHermes expression in the pronephric and mesonephric kidneys coincides temporally and spatially with the appearance of the vascular components of the glomeruli. In addition, cHermes expression was seen in the mesoderm of the gut and in the notochord. Developmental Dynamics 233:1045–1051, 2005. © 2005 Wiley‐Liss, Inc.
On the spectrum of sum and product of non-hermitian random matrices

In this note, we revisit the work of T. Tao and V. Vu on large non-hermitian random matrices with independent and identically distributed (i.i.d.) entries with mean zero and unit variance. We prove under weaker assumptions that the limit spectral distribution of sum and product of non-hermitian random matrices is universal. As a byproduct, we show that the generalized eigenvalues distribution of two independent matrices converges almost surely to the uniform measure on the Riemann sphere.
β‐Arrestin2 Regulates the Differential Response of Cortical and Trabecular Bone to Intermittent PTH in Female Mice

Cytoplasmic arrestins regulate PTH signaling in vitro. We show that female β‐arrestin2−/− mice have decreased bone mass and altered bone architecture. The effects of intermittent PTH administration on bone microarchitecture differed in β‐arrestin2−/− and wildtype mice. These data indicate that arrestin‐mediated regulation of intracellular signaling contributes to the differential effects of PTH at endosteal and periosteal bone surfaces.
C2A: Controlled conservative advancement for continuous collision detection of polygonal models

We present a simple and fast algorithm to perform continuous collision detection between polygonal models undergoing rigid motion for interactive applications. Our approach can handle all triangulated models and makes no assumption about the underlying geometry and topology. The algorithm uses the notion of conservative advancement (CA), originally developed for convex polytopes [1], [2]. We extend this formulation to general models using swept sphere volume hierarchy and present a compact formulation to compute the motion bounds along with a novel controlling scheme. We have implemented the algorithm and highlight its performance on various benchmarks. In practice, our algorithm can perform continuous collision queries in few milli-seconds on models composed of tens of thousands of triangles.
Self-enhancing Confabulation: Revisiting the Motivational Hypothesis

We report a patient who developed spontaneous confabulation following surgical clipping of an anterior communicating artery aneurysm. An autobiographical memory test was used to measure the emotional valence of the patient's self-representations in true and false memories. We found that his confabulations included significantly more positive self-representations than his true memories and that the overall valence of his confabulations was more positive than that of his true memories and than that of the memories of five healthy control participants of the same age and educational attainment. It is proposed that while cognitive dysfunction may explain how confabulations are formed, emotional factors may explain which specific confabulations are constructed.
Recent patents on therapeutic applications of the transcription factor decoy approach

Introduction: Transcription is considered as an important target of drugs employed in biomedicine. Therefore, novel strategies to inhibit the biological effects of transcription factors (TFs) are of interest, such as targeting promoters with triple-helix-forming oligonucleotides and antisense targeting of mRNAs coding for TFs. Areas covered: The objective of this review is to describe studies considering inhibition of TF functions with molecules mimicking TF binding sites (transcription factor decoy approach, TFD) and to summarize the patents on possible clinical applications of this approach. Expert opinion: Treatment of cells with TFD molecules leads to inhibition (or activation) of genes regulated by the target transcription factors. The studies and patents on this specific issue have taken in great consideration the delivery strategy, which is a very important parameter. The TFD strategy has been proven effective in vivo. The stability of the TFD molecules in vivo should be carefully considered, as well as the possible toxicity and/or possible effects on innate and adaptive immune response. In order to improve clinical parameters, many patents suggest the use of the TFD molecules in combination with drugs already employed in therapy. We are expecting in the near future relevant clinical trials based on the TFD strategy.
Reliability Generalization: Exploring Variance in Measurement Error Affecting Score Reliability Across Studies

Because tests are not reliable, it is important to explore score reliability in virtually all studies. The present article proposes and illustrates a new method-reliability generalization-that can be used in a meta-analysis application similar to validity generalization. Reliability generalization characterizes (a) the typical reliability of scores for a given test across studies, (b) the amount of variability in reliability coefficients for given measures, and (c) the sources of variability in reliability coefficients across studies. The use of reliability generalization is illustrated here by analyzing 87 reliability coefficients reported for the two scales of the Bem Sex Role Inventory (BSRI).