Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of two genes with prepilin-like leader sequences involved in type 4 fimbrial biogenesis in Pseudomonas aeruginosa

Type 4 fimbriae are surface filaments produced by a range of bacterial pathogens for colonization of host epithelial surfaces. In Pseudomonas aeruginosa, they are involved in adhesion as well as in a form of surface translocation called twitching motility, and sensitivity to infection by fimbria-specific bacteriophage. Analysis of the 2.5-kb intergenic region between the previously defined pilR and pilV genes on P. aeruginosa genomic SpeI fragment E has identified three new genes, fimT, fimU, and dadA*. The predicted 18.5-kDa products of the fimT and fimU genes contain prepilin-like leader sequences, whereas the third gene, dadA*, encodes a protein similar to the D-amino acid dehydrogenase of Escherichia coli. Isogenic mutants constructed by allelic exchange demonstrated that the fimU gene was required for fimbrial biogenesis and twitching motility, whereas the fimT and dada* mutants retained wild-type phenotypes. However, overexpression of the fimT gene was found to be able to functionally replace the lack of a fimU gene product, suggesting a subtle role in fimbrial biogenesis. The identification of these proteins increases the similarity between type 4 fimbrial biogenesis and the supersystems involved in macromolecular traffic, such as extracellular protein secretion and DNA uptake, all of which now possess multiple protein species that possess prepilin-like leader sequences.
Opinion Holder and Target Extraction based on the Induction of Verbal Categories

We present an approach for opinion role induction for verbal predicates. Our model rests on the assumption that opinion verbs can be divided into three different types where each type is associated with a characteristic mapping between semantic roles and opinion holders and targets. In several experiments, we demonstrate the relevance of those three categories for the task. We show that verbs can easily be categorized with semi-supervised graphbased clustering and some appropriate similarity metric. The seeds are obtained through linguistic diagnostics. We evaluate our approach against a new manually-compiled opinion role lexicon and perform in-context classification.
Liver ablation guidance with acoustic radiation force impulse imaging: challenges and opportunities

Previous studies have established the feasibility of monitoring radiofrequency (RF) ablation procedures with acoustic radiation force impulse (ARFI) imaging. However, questions remained regarding the utility of the technique in clinically realistic scenarios and at scanning depths associated with abdominal imaging in adults. We address several of these issues and detail recent progress towards the clinical relevance of the ARFI technique. Results from in vitro bovine tissues and an in vivo ovine model are presented. Additional experiments were conducted with a tissue-mimicking phantom and parallel receive tracking techniques in order to further support the clinical feasibility of the method. Thermal lesions created during RF ablation are visualized with high contrast in both in vitro and in vivo hepatic tissues, and radial lesion growth can be monitored throughout the duration of the procedure. ARFI imaging is implemented on a diagnostic ultrasonic scanner, and thus may be a convenient option to guide RF ablation procedures, particularly when electrode insertion is also performed with sonographic guidance.
Low temperature S0 biomineralization at a supraglacial spring system in the Canadian High Arctic

Elemental sulfur (S0) is deposited each summer onto surface ice at Borup Fiord pass on Ellesmere Island, Canada, when high concentrations of aqueous H2S are discharged from a supraglacial spring system. 16S rRNA gene clone libraries generated from sulfur deposits were dominated by β‐Proteobacteria, particularly Ralstonia sp. Sulfur‐cycling micro‐organisms such as Thiomicrospira sp. , and ε‐Proteobacteria such as Sulfuricurvales and Sulfurovumales spp. were also abundant. Concurrent cultivation experiments isolated psychrophilic, sulfide‐oxidizing consortia, which produce S0 in opposing gradients of Na2S and oxygen. 16S rRNA gene analyses of sulfur precipitated in gradient tubes show stable sulfur‐biomineralizing consortia dominated by Marinobacter sp. in association with Shewanella, Loktanella, Rubrobacter, Flavobacterium, and Sphingomonas spp. Organisms closely related to cultivars appear in environmental 16S rRNA clone libraries; none currently known to oxidize sulfide. Once consortia were simplified to Marinobacter and Flavobacteria spp. through dilution‐to‐extinction and agar removal, sulfur biomineralization continued. Shewanella, Loktanella, Sphingomonas, and Devosia spp. were also isolated on heterotrophic media, but none produced S0 alone when reintroduced to Na2S gradient tubes. Tubes inoculated with a Marinobacter and Shewanella spp. co‐culture did show sulfur biomineralization, suggesting that Marinobacter may be the key sulfide oxidizer in laboratory experiments. Light, florescence and scanning electron microscopy of mineral aggregates produced in Marinobacter experiments revealed abundant cells, with filaments and sheaths variably mineralized with extracellular submicron sulfur grains; similar biomineralization was not observed in abiotic controls. Detailed characterization of mineral products associated with low temperature microbial sulfur‐cycling may provide biosignatures relevant to future exploration of Europa and Mars.
Enhanced lipid—but not carbohydrate—supported mitochondrial respiration in skeletal muscle of PGC‐1α overexpressing mice

Skeletal muscle mitochondrial dysfunction has been linked to several disease states as well as the process of aging. A possible factor involved is the peroxisome proliferator‐activated receptor (PPAR) γ co‐activator 1α (PGC‐1α), a major player in the regulation of skeletal muscle mitochondrial metabolism. However, it is currently unknown whether PGC‐1α, besides stimulating mitochondrial proliferation, also affects the functional capacity per mitochondrion. Therefore, we here tested whether PGC‐1α overexpression, besides increasing mitochondrial content, also leads to intrinsic mitochondrial adaptations. Skeletal muscle mitochondria from 10 male, muscle‐specific PGC‐1α overexpressing mice (PGC‐1αTg) and 8 wild‐type (WT) mice were isolated. Equal mitochondrial quantities were then analyzed for their oxidative capacity by high‐resolution respirometry, fuelled by a carbohydrate‐derived (pyruvate) and a lipid (palmitoyl‐CoA plus carnitine) substrate. Additionally, mitochondria were tested for reactive oxygen species (superoxide) production and fatty acid (FA)‐induced uncoupling. PGC‐1αTg mitochondria were characterized by an improved intrinsic mitochondrial fat oxidative capacity as evidenced by pronounced increase in ADP‐stimulated respiration (P < 0.001) and maximal uncoupled respiration (P < 0.001) upon palmitoyl‐CoA plus carnitine. Interestingly, intrinsic mitochondrial capacity on a carbohydrate‐derived substrate tended to be reduced. Furthermore, the sensitivity to FA‐induced uncoupling was diminished in PGC‐1αTg mitochondria (P = 0.02) and this was accompanied by a blunted reduction in mitochondrial ROS production upon FAs in PGC‐1αTg versus WT mitochondria (P = 0.04). Uncoupling protein 3 (UCP3) levels were markedly reduced in PGC‐1αTg mitochondria (P < 0.001). Taken together, in addition to stimulating mitochondrial proliferation in skeletal muscle, we show here that overexpression of PGC‐1α leads to intrinsic mitochondrial adaptations that seem restricted to fat metabolism. J. Cell. Physiol. 227: 1026–1033, 2012. © 2011 Wiley Periodicals, Inc.
Attentive Computing 27 Attentive Computing

Although the purpose of technological progress of humanity is open for debate, it can be concluded that the outcome of advancements should enhance the quality of life in general. This enhancement does not only depend on new functionalities provided by advancements but also depends on strategies to present these functionalities. Presentation strategies are particularly important for technologies that are used ubiquitously found in many modern digital computing systems.
Rapid determination of orotic acid in urine by liquid chromatography-electrospray tandem mass spectrometry.

Orotic acid (ORA) is an important biochemical marker for uridine monophosphate synthase deficiency, an autosomal recessive disease characterized by macrocytic hypochromic megaloblastic anemia, growth retardation, orotic aciduria, and crystalluria (1). In addition, patients with urea cycle diseases excrete increased amounts of urinary ORA (2). Thus, ORA aciduria is observed in patients with ornithine carbamoylasetransferase deficiency (OCTD), an X-linked disorder, and could reveal heterozygosity after a protein load, and in citrullinemia, argininosuccinic aciduria, and argininemia (2)(3). Currently there are two widely accepted approaches to the determination of urinary ORA, stable-isotope-dilution gas chromatography–mass spectrometry (GC/MS), and ion-exchange HPLC methods with ultraviolet detection, each of which has difficulties and limitations (4)(5)(6)(7). Ito et al.(8) recently described a liquid chromatography–electrospray tandem mass spectrometry (LC-ESI-MS/MS) method for a large number of urinary metabolites, including ORA. In the present work we describe a more specific, high-throughput, sensitive stable-isotope-dilution LC-ESI-MS/MS method for the determination of urinary ORA. ORA was purchased from Sigma, and [1,3-15N2]orotic acid used as internal standard (IS) was obtained from Cambridge Isotope Laboratories. Acetonitrile and glacial acetic used for HPLC were purchased from Fisher Scientific. Syringe-driven membrane filter units were of LCR type (0.45 μm pore size) obtained from Millipore. Glass autosampler vials (2-mL capacity) and 300-μL vial inserts were purchased from Agilent. Urine samples were from pediatric patients investigated for metabolic diseases. Adult urine samples were from healthy laboratory personnel. All urine samples were stored at −20 °C until analysis. MS/MS analysis was carried out on a Micromass QuattroLC triple quadrupole mass spectrometer interfaced with a Z-spray ESI source and equipped with a Jasco HPLC pump Model PU-980 and a Jasco Model AS-950 autosampler. The ESI source was operated in the negative-ion mode with the source kept at 150 …
Identification of simultaneous mutation of fibrinogen α chain and protein C genes in a Japanese kindred

Summary. Afibrinogenaemia usually induces a bleeding tendency during infancy, whereas protein C deficiency increases susceptibility to thrombosis in children or adolescence. Mutations of these genes have been, therefore, established as independent risk factors for coagulation disorders. We describe the homozygous mutation of the fibrinogen α chain gene and additional heterozygous mutation of the protein C gene in a male infant who showed prolonged umbilical bleeding after birth. On examination, the plasma fibrinogen was undetectable, and the activity and antigen level of protein C were reduced. The patient showed no fibrinogen Aα chain as well as Bβ and γ chains by Western blotting. The sequencing analysis showed the homozygous deletion of 1238 bases from intron 3 at position 2008 to intron 4 at position 3245 in the fibrinogen α chain gene. Both parents were heterozygous carriers of this mutation. In this patient, an additional mutation was also detected in the protein C gene: the heterozygous deletion of exon 7 at position 6161–6163 or 6164–6166, resulting the deletion of one amino acid (Lys150 or 151). His mother was also a carrier of this mutation. As the simultaneous mutation of the fibrinogen α chain and protein C genes has not been previously reported, the influence of the interaction between these two mutations on the clinical manifestations of this patient should be carefully monitored for a long period.
Topical Review on Protein-Protein Interaction Techniques Techniques for the Analysis of Protein-Protein Interactions in Vivo 1 [ OPEN ]

Identifying key players and their interactions is fundamental for understanding biochemical mechanisms at the molecular level. The ever-increasing number of alternative ways to detect protein-protein interactions (PPIs) speaks volumes about the creativity of scientists in hunting for the optimal technique. PPIs derived from single experiments or high-throughput screens enable the decoding of binary interactions, the building of large-scale interaction maps of single organisms, and the establishment of crossspecies networks. This review provides a historical view of the development of PPI technology over the past three decades, particularly focusing on in vivo PPI techniques that are inexpensive to perform and/or easy to implement in a state-of-the-art molecular biology laboratory. Special emphasis is given to their feasibility and application for plant biology as well as recent improvements or additions to these established techniques. The biology behind each method and its advantages and disadvantages are discussed in detail, as are the design, execution, and evaluation of PPI analysis. We also aim to raise awareness about the technological considerations and the inherent flaws of these methods, which may have an impact on the biological interpretation of PPIs. Ultimately, we hope this review serves as a useful reference when choosing the most suitable PPI technique.
Places and Spaces: The Role of Metonymy in Organizational Talk

Cultural meaning making as reflected in, and constituted by, organizational talk is an established field of interest in organizational analysis. However, the discursive mechanics of the process whereby this cultural meaning making is created and maintained are less well understood. The premise of this paper is that taken-for-granted assumptions embedded in organizational talk can be explored through the analysis of metonymy, a trope which is under explored in the linguistic turn in organization studies. This lack of focus on metonymy is, we believe, related to the fundamentally conventional nature of the trope in use, which expresses ideas, values and relationships that seem natural, normal and routine but which are culturally bound. We address this gap and carry out a metonymical analysis of organizational talk about physical places and spaces in one organization, to show how cultural norms and meanings are reflected, maintained, and potentially changed in these figures of speech. We show how metonymic chains based on buildings can reflect, reify and simplify the symbolic order of the organization, how these symbolic meanings can be transferred on to other inanimate objects and the constructions thereby spread, how people can be constructed within this symbolic chain, and how these metonymic chains can be invoked to potentially confirm, challenge or change the organizational order.
Automatic recognition of emotion from voice: a rough benchmark

Automatic recognition of a speaker’s emotions is a natural objective for research, but is difficult to gauge the level of performance that is currently attainable. We describe a study that offers a rough benchmark. Speech data came from five passages of about 100 syllables each. They had been selected following pilot studies because they were effective at evoking specific emotion fear, anger, happiness, sadness, and neutrality. 40 subjects were recorded reading them. A battery of 32 potentially relevant features was extracted using our ASSESS system. They were broadly speaking prosodic, derived from contours tracing the movement of intensity and pitch. They were input to statistical decision mechanisms, of two types. Discriminant analysis uses linear combinations of variables to separate samples that belong to different categories. There are reasons to suspect that linear combination will not be appropriate, so neural net classifiers were also considered. An automatic relevance determination procedure was used to identify the most relevant parameters. Discriminant analysis outperformed the neural networks. Using 90% of the data for training, and testing on the remaining 10%, a classification rate of 55 % (+/0.08%) was achieved. The most useful predictors covered a variety of properties – intensity (relative to the start of the passage) and its spread; pitch spread; durations of silences, rises in intensity, and syllables; and a property related to the shape of ‘tunes’, the number of inflections in the F0 contour per tune. Many more variables were less important, but nevertheless contributed.
Stimulation of the Midbrain Periaqueductal Gray Modulates Preinspiratory Neurons in the Ventrolateral Medulla in the Rat In Vivo

The midbrain periaqueductal gray (PAG) is involved in many basic survival behaviors that affect respiration. We hypothesized that the PAG promotes these behaviors by changing the firing of preinspiratory (pre‐I) neurons in the pre‐Bötzinger complex, a cell group thought to be important in generating respiratory rhythm. We tested this hypothesis by recording single unit activity of pre‐Bötzinger pre‐I neurons during stimulation in different parts of the PAG. Stimulation in the dorsal PAG increased the firing of pre‐I neurons, resulting in tachypnea. Stimulation in the medial part of the lateral PAG converted the pre‐I neurons into inspiratory phase‐spanning cells, resulting in inspiratory apneusis. Stimulation in the lateral part of the lateral PAG generated an early onset of the pre‐I neuronal discharge, which continued throughout the inspiratory phase, while at the same time attenuating diaphragm contraction. Stimulation in the ventral part of the lateral PAG induced tachypnea but inhibited pre‐I cell firing, whereas stimulation in the ventrolateral PAG inhibited not only pre‐I cells but also the diaphragm, leading to apnea. These findings show that PAG stimulation changes the activity of the pre‐Bötzinger pre‐I neurons. These changes are in line with the different behaviors generated by the PAG, such as the dorsal PAG generating avoidance behavior, the lateral PAG generating fight and flight, and the ventrolateral PAG generating freezing and immobility. J. Comp. Neurol. 521: 3083–3098, 2013. © 2013 Wiley Periodicals, Inc.
ARCS, the Arcminute Radio Cluster-lens Search — I. Selection criteria and initial results

We present the results of an unbiased radio search for gravitational lensing events with image separations between 15 and 60 arcsec, which would be associated with clusters of galaxies with masses >1013–14 M⊙. A parent population of 1023 extended radio sources stronger than 35 mJy with stellar optical identifications was selected using the FIRST radio catalogue at 1.4 GHz and the APM optical catalogue. The FIRST catalogue was then searched for companions to the parent sources stronger than 7 mJy and with separation in the range 15 to 60 arcsec. Higher-resolution observations of the resulting 38 lens candidates were made with the VLA at 1.4 and 5 GHz, and with MERLIN at 5 GHz in order to test the lens hypothesis in each case. None of our targets was found to be a gravitational lens system. These results provide the best current constraint on the lensing rate for this angular scale, but improved calculations of lensing rates from realistic simulations of the clustering of matter on the relevant scales are required before cosmologically significant constraints can be derived from this null result. We now have an efficient, tested observational strategy with which it will be possible to make an order-of-magnitude larger unbiased search in the near future.
Differences in the Antigenic Profile and Infectivity of Murine Macrophages of Leishmania (Viannia) Parasites

Abstract The antigenic profile and infectivity were compared between 3 recent Leishmania (Viannia) isolates from the Amazonian region (Instituto Nacional de Pesquisas da Amazonia [INPA] strains) and 3 World Health Organization (WHO) reference species (Leishmania guyanensis, Leishmania braziliensis, and Leishmania naiffi). Differences were observed in the peak and extent of promastigote growth. The WHO reference strains exhibited significantly higher exponential growth as promastigotes than INPA strains. In the immunoblot analyses, the INPA strains revealed several specific peptide fragments, as well as the greatest recognition frequencies by sera from Leishmania sp. –infected patients; among the latter, antigens derived from L. naiffi were the most frequently recognized. In vitro infection was carried out using mice peritoneal macrophages; all strains were able to enter the macrophages, but only L. amazonensis was able to reproduce. A striking observation was that L. naiffi exhibited the longest survival time inside the macrophages. Our data strongly suggest the application of recently isolated parasites as sources of antigen for diagnosis procedures. Moreover, L. naiffi species possesses several characteristics relevant for its use as a source of novel antigens to be explored in the design of diagnostic tools and vaccines.
Semantic Compositionality in Tree Kernels

Kernel-based learning has been largely applied to semantic textual inference tasks. In particular, Tree Kernels (TKs) are crucial in the modeling of syntactic similarity between linguistic instances in Question Answering or Information Extraction tasks. At the same time, lexical semantic information has been studied through the adoption of the so-called Distributional Semantics (DS) paradigm, where lexical vectors are acquired automatically from large corpora. Notice how methods to account for compositional linguistic structures (e.g. grammatically typed bi-grams or complex verb or noun phrases) have been proposed recently by defining algebras on lexical vectors. The result is an extended paradigm called Distributional Compositional Semantics (DCS). Although lexical extensions have been already proposed to generalize TKs towards semantic phenomena (e.g. the predicate argument structures as for role labeling), currently studied TKs do not account for compositionality, in general. In this paper, a novel kernel called Compositionally Smoothed Partial Tree Kernel is proposed to integrate DCS operators into the tree kernel evaluation, by acting both over lexical leaves and non-terminal, i.e. complex compositional, nodes. The empirical results obtained on a Question Classification and Paraphrase Identification tasks show that state-of-the-art performances can be achieved, without resorting to manual feature engineering, thus suggesting that a large set of Web and text mining tasks can be handled successfully by the kernel proposed here.
A proposed sentiment analysis tool for modern Arabic using human-based computing

Sentiment analysis is the process of identifying the polarity of sentiments held in opinions found in pieces of text and classifying them as positive, negative or neutral. In this paper, we propose the implementation of a sentiment analysis tool that is conducted over text found in Arabic new media including web forums, comments on newspaper articles and other websites with evaluative content. The expected input of the tool, which is informal Colloquial Arabic, is characterized to be of highly non-structured nature and subject to trends used to express sentiments. Our solution is a novel technique that merges the area of human computation with the task of natural language processing.