Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Argonaute on Gene Expression in Thermus thermophilus

Background Eukaryotic Argonaute proteins mediate RNA-guided RNA interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. Recently, it has become evident that prokaryotic Argonaute homologs mediate DNA-guided DNA interference, and play a role in host defense. Argonaute of the bacterium Thermus thermophilus (TtAgo) targets invading plasmid DNA during and after transformation. Using small interfering DNA guides, TtAgo can cleave single and double stranded DNAs. Although TtAgo additionally has been demonstrated to cleave RNA targets complementary to its DNA guide in vitro, RNA targeting by TtAgo has not been demonstrated in vivo. Methods To investigate if TtAgo also has the potential to control RNA levels, we analyzed RNA-seq data derived from cultures of four T. thermophilus strain HB27 variants: wild type, TtAgo knockout (Δago), and either strain transformed with a plasmid. Additionally we determined the effect of TtAgo on expression of plasmid-encoded RNA and plasmid DNA levels. Results In the absence of exogenous DNA (plasmid), TtAgo presence or absence had no effect on gene expression levels. When plasmid DNA is present, TtAgo reduces plasmid DNA levels 4-fold, and a corresponding reduction of plasmid gene transcript levels was observed. We therefore conclude that TtAgo interferes with plasmid DNA, but not with plasmid-encoded RNA. Interestingly, TtAgo presence stimulates expression of specific endogenous genes, but only when exogenous plasmid DNA was present. Specifically, the presence of TtAgo directly or indirectly stimulates expression of CRISPR loci and associated genes, some of which are involved in CRISPR adaptation. This suggests that TtAgo-mediated interference with plasmid DNA stimulates CRISPR adaptation.
Utility of Stellate Ganglion Block in Atypical Facial Pain: A Case Report and Consideration of Its Possible Mechanisms

We present this report of a young patient with chronic severe atypical facial pain who was successfully controlled with stellate ganglion block under ultrasound guidance. The patient had a history of severe disabling, unilateral, facial neuropathic pain with minimal response to analgesic medications. Upon assessment the patient had features suggestive of trigeminal neuralgia, although postherpetic neuralgia could not be ruled out. As a diagnostic test intervention, stellate ganglion block was tried under ultrasound guidance. The patient showed significant improvement in pain control and functional disability lasting beyond 10 weeks. Subsequent blocks reinforced the analgesia. Atypical facial pain has several differential diagnoses. The involvement of sympathetic system in its causation or sustenance is uncertain. Stellate ganglion block achieves sympathetic block of cervicofacial structures, and its blockade has been shown to affect chronic pain conditions. Although its mechanism is not clear, one has to consider its possible role in conditions of stress apart from directly controlling the sympathetic activity. There is certainly a role in exploring the potential benefits of stellate ganglion block in such clinical conditions. The technique of stellate block under ultrasound is also described, as it influences the safety and precision of the block.
Near-IR observations of NGC 6822: AGB stars, distance, metallicity and structure

Observations in the IJK s wave bands covering the central 20 � × 20 � of the Local Group galaxy NGC 6822 have been made with the William Herschel Telescope in La Palma. They have allowed us to characterize, for the first time in the near-infrared across the whole galaxy, its late-type stellar population (i.e. red giant and asymptotic giant branch stars) and to derive from the ratio between carbon-rich and oxygen-rich asymptotic giant branch stars an indication about spatial variations in metallicity. These amount to about 1.56 dex, twice of what has been previously found within each Magellanic Cloud using the same technique. We have calibrated our photometry on the DENIS (I-band) and 2MASS (J and Ks bands) data and obtained a distance modulus of (m − M)0 = 23.34 ± 0.12 from the position of the tip of the RGB. The large scale distribution of late-type stars suggests that either the galaxy is viewed under a high inclination angle or it has a non-negligible thickness.
Testing the limits of data-driven learning: language proficiency and training

Abstract The potential for corpora in language learning has attracted a significant amount of attention in recent years, including in the form of data-driven learning (DDL). Careful not to appear to over-promote the field, enthusiasts have urged caution in its application, in particular with regard to lower-level learners, and have argued that extensive learner-training in corpus techniques is an essential condition for DDL to be successful. Such limits seem eminently reasonable, but there is a notable dearth of empirical studies to support them. This paper describes a simple experiment to see how lower-level learners cope with corpus data with no prior training. The language focus here is on linking adverbials in English, which are renowned to be difficult to teach using traditional methods. The subjects are 132 first-year students at an engineering college in France of roughly intermediate and lower levels of English. They were divided into random groups to compare their ability to deal with the target items using traditional sources (extracts from a bilingual dictionary or a grammar/usage manual) or corpus data (short contexts or truncated concordances). Performance was tested prior to the experiment, subsequently to check ability to use the different information sources as a reference, and later to test recall. No evidence was found that traditional sources promote better recall, and corpus data seemed to be more effective for reference purposes. While the results of any single experiment must be treated with caution, these findings suggest the need for more empirical studies to complement the theoretical arguments and qualitative data which currently dominate the discussions of DDL.
Brca 2 is involved in meiosis in Arabidopsis thaliana as suggested by its interaction with Dmc 1

Two BRCA2-like sequences are present in the Arabidopsis genome. Both genes are expressed in flower buds and encode nearly identical proteins, which contain four BRC motifs. In a yeast two-hybrid assay, the Arabidopsis Brca2 proteins interact with Rad51 and Dmc1. RNAi constructs aimed at silencing the BRCA2 genes at meiosis triggered a reproducible sterility phenotype, which was associated with dramatic meiosis alterations. We obtained the same phenotype upon introduction of RNAi constructs aimed at silencing the RAD51 gene at meiosis in dmc1 mutant plants. The meiotic figures we observed strongly suggest that homologous recombination is highly disturbed in these meiotic cells, leaving aberrant recombination events to repair the meiotic double-strand breaks. The ‘brca2’ meiotic phenotype was eliminated in spo11 mutant plants. Our experiments point to an essential role of Brca2 at meiosis in Arabidopsis. We also propose a role for Rad51 in the dmc1 context. The EMBO Journal (2004) 23, 1392–1401. doi:10.1038/ sj.emboj. 7600146; Published online 4 March 2004 Subject Categories: plant biology; genome stability & dynamics
Effects of Reading Attitude on Reading Achievement of Students in Grades One through Six.

No Child Left Behind (2001) and Individuals with Disabilities Education Act (2004) has put pressure on all teachers to develop proficient readers. In order to do just this, develop proficient readers, teachers must understand the effects that reading attitude has on reading achievement for all students. Research states that individuals with a positive attitude toward reading typically achieve at a higher level than those students with a poor attitude toward reading (Sainsbury & Schagen, 2004). However, there is a limited amount of research that has provided insight into how factors of socioeconomic status, gender, and disability may play a part in both attitudes and achievement in reading. This study examined whether socioeconomic status, gender, and/or disability played a role in the reading attitudes of students in grades one through six. The study also evaluated whether students’ attitude toward reading changed depending on their grade level.
A simple non-contact vital sensing method using Doppler sensors applicable to multiple targets

This paper proposed a new very simple method for non-contact vital sensing using Doppler sensors. It is emphasized that the proposed method can cope with multiple bodies even if they are closely located. The proposed method enables us to estimate (1) The number of signal (NOS), (2) the fundamental waveform, (3) the period, and (4) Direction of arrival (DOA), for each of the incoming signals. In addition, the proposed method is computationally effective so that it is advantageous for the hardware implementation. Some numerical examples are provided for performance verification.
Demonstrating causal links between fMRI time series using time-lagged correlation

An autoregressive modelling-based technique, Granger analysis, has increasingly been used for measuring causal connections between brain regions in fundamental magnetic resonance imaging brain imaging (fMRI). This paper summarises the possibilities and limitations of applying Granger analysis to fMRI. It also describes a replication of a previous theoretical study, and an application to spatial working memory currently under way. Previous researchers have described methods for detecting time-lagged correlation between neural activations in brain regions of interest (ROI)–often variants of ‘Grangercausality analysis’ (GCA). With appropriate caveats, GCA can draw inferences from time-lagged correlation about effective connectivity between ROIs in a way other popular methods do not. We replicated an existing theoretical model using a different non-linear function, and different method of combining a haemodynamic response function. We then examined whether GCA can estimate the direction of causation in brain regions shown to act together in spatial working memory tasks. Independent Component Analysis (ICA) was used to identify independent spatial components. Then, GCA tested the interactions between those components. The method identified causal relationships on replicated, artificially simulated data and in between extracted components in the data. Work is now underway to determine the implications of these relationships. Keywords—Granger causality analysis; independent component analysis; effective connectivity; fMRI; time-lagged correlation
SYSTEMATICS OF AMARYLLIDACEAE BASED ON CLADISTIC ANALYSIS OF PLASTID RBCL AND TRNL-F SEQUENCE DATA 1

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n 5 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.
Morphologically Constrained GRFs: Applications to Texture Synthesis and Analysis

A new class of Gibbs random fields (GRFs) is proposed capable of modeling geometrical constraints in images by means of mathematical morphology. The proposed approach, known as morphologically constrained GRFs, models images by means of their size density. Since the size density is a multiresolution statistical summary, morphologically constrained GRFs explicitly incorporate multiresolution information into image modeling. Important properties are studied and their implication to texture synthesis and analysis is discussed. Statistical inference can be easily implemented by means of mathematical morphology. This allows the design of a computationally simple morphological Bayes classifier which produces excellent results in classifying natural textures.
Overexpression of Protein-tyrosine Phosphatase-1B in Adipocytes Inhibits Insulin-stimulated Phosphoinositide 3-Kinase Activity without Altering Glucose Transport or Akt/Protein Kinase B Activation*

Previous studies suggested that protein-tyrosine phosphatase 1B (PTP1B) antagonizes insulin action by catalyzing dephosphorylation of the insulin receptor (IR) and/or other key proteins in the insulin signaling pathway. In adipose tissue and muscle of obese humans and rodents, PTP1B expression is increased, which led to the hypothesis that PTP1B plays a role in the pathogenesis of insulin resistance. Consistent with this, mice in which the PTP1B gene was disrupted exhibit increased insulin sensitivity. To test whether increased expression of PTP1B in an insulin-sensitive cell type could contribute to insulin resistance, we overexpressed wild-type PTP1B in 3T3L1 adipocytes using adenovirus-mediated gene delivery. PTP1B expression was increased ∼3–5-fold above endogenous levels at 16 h, ∼14-fold at 40 h, and ∼20-fold at 72 h post-transduction. Total protein-tyrosine phosphatase activity was increased by 50% at 16 h, 3–4-fold at 40 h, and 5–6-fold at 72 h post-transduction. Compared with control cells, cells expressing high levels of PTP1B showed a 50–60% decrease in maximally insulin-stimulated tyrosyl phosphorylation of IR and insulin receptor substrate-1 (IRS-1) and phosphoinositide 3-kinase (PI3K) activity associated with IRS-1 or with phosphotyrosine. Akt phosphorylation and activity were unchanged. Phosphorylation of p42 and p44 MAP kinase (MAPK) was reduced ∼32%. Overexpression of PTP1B had no effect on basal, submaximally or maximally (100 nm) insulin-stimulated glucose transport or on the EC50 for transport. Our results suggest that: 1) insulin stimulation of glucose transport in adipocytes requires ≤45% of maximal tyrosyl phosphorylation of IR or IRS-1 and <50% of maximal activation of PI3K, 2) a novel PI3K-independent pathway may play a role in insulin-induced glucose transport in adipocytes, and 3) overexpression of PTP1B alone in adipocytes does not impair glucose transport.
The moderating role of brand reputation and moral obligation

Purpose – The purpose of this paper is twofold: first, to examine the influences of theory of planned behavior (TPB) constructs (i.e. attitude, subjective norm, and perceived behavioral control (PBC)) on individuals’ volunteer intention for future sporting events, and second, to investigate the moderating effects of brand reputation and moral obligation in the relationships between TPB constructs and volunteer intention. Design/methodology/approach – The sample consisted of 107 volunteers at the 2009 NCAA Men's Basketball Tournament. Moderated hierarchical multiple regression analysis was used to test the hypothesized relationships of the model. Findings – Subjective norm and PBC were significantly associated with volunteer intention. Brand reputation was found to be a moderator in the relationships between attitude and volunteer intention and between subjective norm and volunteer intention, and moral obligation moderated the relationship between PBC and volunteer intention. Practical implications – Sport.
Reduction of uranium by Desulfovibrio desulfuricans

The possibility that sulfate-reducing microorganisms contribute to U(VI) reduction in sedimentary environments was investigated. U(VI) was reduced to U(IV) when washed cells of sulfate-grown Desulfovibrio desulfuricans were suspended in a bicarbonate buffer with lactate or H2 as the electron donor. There was no U(VI) reduction in the absence of an electron donor or when the cells were killed by heat prior to the incubation. The rates of U(VI) reduction were comparable to those in respiratory Fe(III)-reducing microorganisms. Azide or prior exposure of the cells to air did not affect the ability of D. desulfuricans to reduce U(VI). Attempts to grow D. desulfuricans with U(VI) as the electron acceptor were unsuccessful. U(VI) reduction resulted in the extracellular precipitation of the U(IV) mineral uraninite. The presence of sulfate had no effect on the rate of U(VI) reduction. Sulfate and U(VI) were reduced simultaneously. Enzymatic reduction of U(VI) by D. desulfuricans was much faster than nonenzymatic reduction of U(VI) by sulfide, even when cells of D. desulfuricans were added to provide a potential catalytic surface for the nonenzymatic reaction. The results indicate that enzymatic U(VI) reduction by sulfate-reducing microorganisms may be responsible for the accumulation of U(IV) in sulfidogenic environments. Furthermore, since the reduction of U(VI) to U(IV) precipitates uranium from solution, D. desulfuricans might be a useful organism for recovering uranium from contaminated waters and waste streams.
Diagnostic Significance of Intracystic Nodules on MRI in Rathke's Cleft Cyst

Background and Purpose. To explore strategies for the diagnosis and treatment of Rathke's cleft cyst (RCC). Methods. The medical records of 24 patients with sellar RCC were retrospectively reviewed. Two patients had concomitant pituitary adenoma, 2 underwent transcranial surgery, and 22 underwent transsphenoidal surgery. The clinical features, especially the findings of intracystic nodules on MRI, were evaluated and compared with the pathological findings. Results. Preoperatively, only 2 patients were diagnosed with RCC or suspected RCC. Pre- and postoperative MRI images revealed 10 intracystic nodules in 9 (37.5%) patients. Two nodules had bull's eyelike changes. The signal intensity of the intracystic nodules varied on T1- and T2-weighted images. Not all nodules on T2-weighted images were visualized. Postoperative MRI revealed recurrence or residual lesion in 5 patients; none had new symptoms and a second surgery was not required. Conclusions. Identifying intracystic nodules is important in patients with sellar cystic lesions. Bull's eyelike change in an intracystic nodule on MRI, which is reported here for the first time, potentially might have value for confirming the diagnosis.
Generalized Prediction Model for Detection of Psychiatric Disorders

Computer aided diagnosis of mental disorders like Attention Deficit Hyperactivity Disorder (ADHD) and Autism is a primary step towards automated detection and prognosis of these psychiatric diseases. This dissertation applies analyses based on learning models that use structural texture and functional connectivity to diagnose ADHD and also Autism, from (structural) 3-dimensional magnetic resonance imaging (MRI) and 4-dimensional restingstate functional magnetic resonance imaging (fMRI) scans of subjects. One model learns texture-based filters that are used to extract features from MRI scans. Using these learned features, the model achieves 0.6257 (baseline 0.5497) accuracy on the ADHD-200 hold-out dataset for differentiating between healthy control vs ADHD patients and also achieves 0.6173 (baseline 0.5157) accuracy on the ABIDE (Autism) hold-out test for differentiating between healthy control vs Autism patients. Our next model examines temporal sequence of fMRI activation levels at various brain locations in order to make a diagnosis from fMRI scans. This incorporates spatial nonstationary independent component analysis of the fMRI scans in order to extract the uncorrelated components and decomposes fMRI scans into common spatial components and corresponding time courses. Using individual time courses of 45 independent components as features, our algorithm learns a classifier that yields an accuracy of 0.6491 on the ADHD-200 hold-out dataset, and 0.6233 accuracy on the ABIDE hold-out test. This result is higher (0.0231 for ADHD and 0.0233 for Autism) than previously published accuracies on these datasets using fMRI scans. Finally a combination of multimodal features yields 0.6725 diagnosis accuracy on ADHD-200 and 0.6431 accuracy on ABIDE. This result is significantly higher (0.0465 for ADHD with one sided p = 0.01 and 0.0431 for Autism with one sided p = 1.6172e-06) than previously published hold-out accuracies on these datasets using only imaging data. Our results indicate that combining multimodal features yields good classification accuracy for diagnosis of ADHD and Autism, which is an important step towards computer aided diagnosis of these psychiatric diseases.
Observations of the Hubble Deep Field South with the Infrared Space Observatory– I. Observations, data reduction and mid-infrared source counts

We present results from a deep mid-infrared survey of the Hubble Deep Field South (HDF-S) region performed at 6.7 and 15 μm with the ISOCAM instrument on board the Infrared Space Observatory (ISO). The final map in each band was constructed by the co-addition of four independent rasters, registered using bright sources securely detected in all rasters, with the absolute astrometry being defined by a radio source detected at both 6.7 and 15 μm. We sought detections of bright sources in a circular region of radius 2.5 arcmin at the centre of each map, in a manner that simulations indicated would produce highly reliable and complete source catalogues using simple selection criteria. Merging source lists in the two bands yielded a catalogue of 35 distinct sources, which we calibrated photometrically using photospheric models of late-type stars detected in our data. We present extragalactic source count results in both bands, and discuss the constraints that they impose on models of galaxy evolution, given the volume of space sampled by this galaxy population.
Locality differences of sickness absence in the context of health and social conditions of the inhabitants

Background and aim: Earlier research has suggested that local communities develop different sickness absence practices, expressed in variation in the absence figures. This study aimed to test the hypothesis that the work places residing in a locality share similar sickness absence practice. Methods: Register data from the major public sector employers and from private industrial employers were used to compare the absence in two localities. Results: There were significant differences by locality in both branches and both in short and in long sickness absences. Population-level statistics showed a corresponding locality difference in recipients of sickness allowance benefits and in primary healthcare visits, but not in indicators of mortality and morbidity. Social problems were more common in the locality with high rate of absence. Conclusion: Area-specific practice, or habitus, as an independent determinant of sickness absence is discussed and an explicitly sociological context is recommended for debates about ‘‘best sickness absence practices’’ and corresponding intervention measures.