Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific versus Non-Specific Immune Responses in an Invertebrate Species Evidenced by a Comparative de novo Sequencing Study

Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5′-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5′-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs) of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences) belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance of gene duplication and acquisition of paralog functional diversity in the evolution of specific invertebrate immune responses.
Oxyhalides: A new class of high-TC multiferroic materials

Researchers discover a new class of magnetoelectric multiferroics with high critical temperature. Magnetoelectric multiferroics have attracted enormous attention in the past years because of their high potential for applications in electronic devices, which arises from the intrinsic coupling between magnetic and ferroelectric ordering parameters. The initial finding in TbMnO3 has triggered the search for other multiferroics with higher ordering temperatures and strong magnetoelectric coupling for applications. To date, spin-driven multiferroicity is found mainly in oxides, as well as in a few halogenides. We report multiferroic properties for synthetic melanothallite Cu2OCl2, which is the first discovery of multiferroicity in a transition metal oxyhalide. Measurements of pyrocurrent and the dielectric constant in Cu2OCl2 reveal ferroelectricity below the Néel temperature of ~70 K. Thus, melanothallite belongs to a new class of multiferroic materials with an exceptionally high critical temperature. Powder neutron diffraction measurements reveal an incommensurate magnetic structure below TN, and all magnetic reflections can be indexed with a propagation vector [0.827(7), 0, 0], thus discarding the claimed pyrochlore-like “all-in–all-out” spin structure for Cu2OCl2, and indicating that this transition metal oxyhalide is, indeed, a spin-induced multiferroic material.
Introduction of Culex Toxicity into Bacillus thuringiensis Cry4Ba by Protein Engineering

ABSTRACT Bacillus thuringiensis mosquitocidal toxin Cry4Ba has no significant natural activity against Culex quinquefasciatus or Culex pipiens (50% lethal concentrations [LC50], >80,000 and >20,000 ng/ml, respectively). We introduced amino acid substitutions in three putative loops of domain II of Cry4Ba. The mutant proteins were tested on four different species of mosquitoes, Aedes aegypti, Anopheles quadrimaculatus, C. quinquefasciatus, and C. pipiens. Putative loop 1 and 2 exchanges eliminated activity towards A. aegypti and A. quadrimaculatus. Mutations in a putative loop 3 resulted in a final increase in toxicity of >700-fold and >285-fold against C. quinquefasciatus (LC50 ≅ 114 ng/ml) and C. pipiens (LC50 ⩬ 37 ng/ml), respectively. The enhanced protein (mutein) has very little negative effect on the activity against Anopheles or Aedes. These results suggest that the introduction of short variable sequences of the loop regions from one toxin into another might provide a general rational design approach to enhancing B. thuringiensis Cry toxins.
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A fluorescent reporter of caspase activity for live imaging

There is a growing interest in the mechanisms that control the apoptosis cascade during development and adult life. To investigate the regulatory events that trigger apoptosis in whole tissues, we have devised a genetically encoded caspase sensor that can be detected in live and fixed tissue by standard confocal microscopy. The sensor comprises two fluorophores, mRFP, monomeric red fluorescent protein (mRFP) and enhanced green fluorescent protein (eGFP), that are linked by an efficient and specific caspase-sensitive site. Upon caspase activation, the sensor is cleaved and eGFP translocates to the nucleus, leaving mRFP at membranes. This is detected before other markers of apoptosis, including anti–cleaved caspase 3 immunoreactivity. Moreover, the sensor does not perturb normal developmental apoptosis and is specific, as cleavage does not occur in Drosophila embryos that are unable to activate the apoptotic cascade. Importantly, dying cells can be recognized in live embryos, thus opening the way for in vivo imaging. As expected from the high conservation of caspases, it is also cleaved in dying cells of chick embryos. It is therefore likely to be generally useful to track the spatiotemporal pattern of caspase activity in a variety of species.
Selective information dissemination in P2P networks: problems and solutions

We study the problem of selective dissemination of information in P2P networks. We present our work on data models and laiguages for textual information dissemination and discuss a relemnt P2P architecture that motivates our efforts. We also survey our results on the computational complexity of three related algorithmic problems (query satisfiability, entailment and filtering) and present efficient algorithms for the most crucial of these problems (filtering). Finally, we discuss the features of P2P-DIET, a super-peer system we have implemented at the Technical Lniversity of Crete, that realizes our vision and is able to support both ad-hoc querying and selective information dissemination scenarios in a P2P framework.
Correlates of reward-predictive value in learning-related hippocampal neural activity

We use point process likelihood models to explain the spiking activity of individual hippocampal pyramidal neurons as a function of task-relevant covariates and their Temporal Difference (TD) reward-predictive value during reinforcement learning. Our results suggest that CA1 and CA3 neurons may signal information about the reward-predictive value of task-relevant signals pertinent to the acquisition of behavioral strategies that maximize reward, with more CA1 but not CA3 neurons doing so during novel versus familiar experiences.
Chromosome analysis of solid tumors. I. Twenty‐eight nonepithelial tumors

Of 25 nonepithelial solid cancers at least two appeared to have classically diploid stemlines. Of aneuploid tumors a few showed the same karyotype in every cell whereas other tumors showed unequivocal karyotype variation from cell to cell. One tumor contained a stemline marker apparently identical with one previously observed in Burkitt's lymphosarcoma. A number of tumors exhibited prominent secondary constriction patterns. Occasional cells showed broken chromosomes and multiradial forms. Two of three lymph nodes, diagnosed histologically as hyperplastic lymph nodes, showed classically diploid cells. A third showed unequivocal chromosome abnormalities.
How should we evaluate supervised hashing?

Hashing produces compact representations for documents, to perform tasks like classification or retrieval based on these short codes. When hashing is supervised, the codes are trained using labels on the training data. This paper first shows that the evaluation protocols used in the literature for supervised hashing are not satisfactory: we show that a trivial solution that encodes the output of a classifier significantly outperforms existing supervised or semi-supervised methods, while using much shorter codes. We then propose two alternative protocols for supervised hashing: one based on retrieval on a disjoint set of classes, and another based on transfer learning to new classes. We provide two baseline methods for image-related tasks to assess the performance of (semi-)supervised hashing: without coding and with unsupervised codes. These baselines give a lower- and upper-bound on the performance of a supervised hashing scheme.
MJO Propagation Shaped by Zonal Asymmetric Structures: Results from 24 GCM Simulations

AbstractEastward propagation is an essential characteristic of the Madden–Julian oscillation (MJO). Yet, simulation of MJO propagation in general circulation models (GCMs) remains a major challenge and understanding the causes of propagation remains controversial. The present study explores why the GCMs have diverse performances in MJO simulation by diagnosis of 24 GCM simulations. An intrinsic linkage is found between MJO propagation and the zonal structural asymmetry with respect to the MJO convective center. The observed and realistically simulated MJO eastward propagations are characterized by stronger Kelvin easterly waves than Rossby westerly waves in the lower troposphere, which is opposite to the Gill pattern where Rossby westerly waves are 2 times stronger than Kelvin easterly waves. The GCMs simulating stronger Rossby westerly waves tend to show a stationary MJO. MJO propagation performances are robustly correlated with the quality of simulated zonal asymmetries in the 850-hPa equatorial zonal w.
Fitness of Escherichia coli mutants with reduced susceptibility to tigecycline

Objectives The objective of this study was to determine the fitness of Escherichia coli mutants with reduced susceptibility to tigecycline after exposure to adverse conditions in vitro and in vivo. Methods Survival in response to low pH, bile salts, oxidative stress and human serum was examined for E. coli mutants with reduced susceptibility to tigecycline due to single mutations that caused increased efflux (marR, lon) or impaired LPS (rfaC, rfaE, lpcA). An in vitro competition assay was used to determine growth fitness defects. Competitive fitness was assessed using mouse infection models. MICs, exponential growth rates and expression levels of efflux-related genes were measured for genetically reconstructed double and triple mutants. Results The LPS mutants were 48–85-fold more susceptible to bile salts compared with the ERN mutants and the WT. As shown by in vitro competitions, the fitness reduction was 0.3%–13% for ERN mutants and ∼24% for LPS mutants. During in vivo survival experiments, LPS mutants were outcompeted by the WT strain in the thigh infection model. Constructed double ERN and LPS mutants showed additive and synergistic increases in tigecycline MICs. Conclusions Generally, reduced susceptibility to tigecycline caused a decrease in fitness under stressful in vitro and in vivo conditions with ERN mutants being fitter than LPS mutants. When combined, ERN mutations caused a synergistic increase in the MIC of tigecycline. These findings could explain why clinical resistance to tigecycline in E. coli is mainly associated with up-regulation of the AcrAB efflux system.
Familial risk of early and late onset cancer: nationwide prospective cohort study

Objective To determine whether familial risk of cancer is limited to early onset cases. Design Nationwide prospective cohort study. Setting Nationwide Swedish Family-Cancer Database. Participants All Swedes born after 1931 and their biological parents, totalling >12.2 million individuals, including >1.1 million cases of first primary cancer. Main outcome measures Familial risks of the concordant cancers by age at diagnosis. Results The highest familial risk was seen for offspring whose parents were diagnosed at an early age. Familial risks were significantly increased for colorectal, lung, breast, prostate, and urinary bladder cancer and melanoma, skin squamous cell carcinoma, and non-Hodgkin’s lymphoma, even when parents were diagnosed at age 70-79 or 80-89. When parents were diagnosed at more advanced ages (≥90), the risk of concordant cancer in offspring was still significantly increased for skin squamous cell carcinoma (hazard ratio 1.9, 95% confidence interval 1.4 to 2.7), colorectal (1.6, 1.2 to 2.0), breast (1.3, 1.0 to 1.6), and prostate cancer (1.3, 1.1 to 1.6). For offspring with a cancer diagnosed at ages 60-76 whose parents were affected at age <50, familial risks were not significantly increased for nearly all cancers. Conclusion Though the highest familial risks of cancer are seen in offspring whose parents received a diagnosis of a concordant cancer at earlier ages, increased risks exist even in cancers of advanced ages. Familial cancers might not be early onset in people whose family members were affected at older ages and so familial cancers might have distinct early and late onset components.
Acoustic startle in alcohol-naïve male rats predicts subsequent voluntary alcohol intake and alcohol preference.

AIMS Acoustic startle response in rats is used to model sensorimotor reactivity. The aim of the study was to determine whether acoustic startle response in alcohol-naïve rats predicts subsequent increased voluntary alcohol drinking or alcohol preference. METHODS Startle responses to 90, 95 and 100 decibel (dB) white noise stimuli presented in counterbalanced semi-randomized order were tested in alcohol-naïve young adult male Wistar rats before voluntary alcohol intake was established with an intermittent alcohol access (IAA) model. RESULTS Startle amplitude in response to 95 or 100 dB stimuli was positively correlated with subsequent alcohol intake and alcohol preference following 3 months of IAA. Rats with high (median split) pre-IAA startle amplitude in response to 95 or 100 dB stimuli developed increased alcohol intake as well as increased alcohol preference following 3 months of IAA, relative to rats with low pre-IAA startle amplitude. CONCLUSION Startle response to moderate acoustic stimuli can be a predictive index of vulnerability to developing increased alcohol drinking.
Relationships between static foot alignment and dynamic plantar loads in runners with acute and chronic stages of plantar fasciitis: a cross-sectional study

BACKGROUND: The risk factors for the development of plantar fasciitis (PF) have been associated with the medial longitudinal arch (MLA), rearfoot alignment and calcaneal overload. However, the relationships between the biomechanical variables have yet to be determined. OBJECTIVE: The goal of this study was to investigate the relationships between the MLA, rearfoot alignment, and dynamic plantar loads in runners with unilateral PF in acute and chronic phases. METHOD: Cross-sectional study which thirty-five runners with unilateral PF were evaluated: 20 in the acute phase (with pain) and 15 with previous chronic PF (without pain). The MLA index and rearfoot alignment were calculated using digital images. The contact area, maximum force, peak pressure, and force-time integral over three plantar areas were acquired with Pedar X insoles while running at 12 km/h, and the loading rates were calculated from the vertical forces. RESULTS: The multiple regression analyses indicated that both the force-time integral (R 2=0.15 for acute phase PF; R 2=0.17 for chronic PF) and maximum force (R 2=0.35 for chronic PF) over the forefoot were predicted by an elevated MLA index. The rearfoot valgus alignment predicted the maximum force over the rearfoot in both PF groups: acute (R 2=0.18) and chronic (R 2=0.45). The rearfoot valgus alignment also predicted higher loading rates in the PF groups: acute (R 2=0.19) and chronic (R 2=0.40). CONCLUSION: The MLA index and the rearfoot alignment were good predictors of plantar loads over the forefoot and rearfoot areas in runners with PF. However, rearfoot valgus was demonstrated to be an important clinical measure, since it was able to predict the maximum force and both loading rates over the rearfoot.
Recognizing Textual Entailment

Since 2005, researchers have worked on a broad task called Recognizing Textual Entailment (RTE), which is designed to focus efforts on general textual inference capabilities, but without constraining participants to use a specific representation or reasoning approach. There have been promising developments in this sub-field of Natural Language Processing (NLP), with systems showing steady improvement, and investigations of a range of approaches to the problem. A number of researchers appear to have converged on some defining characteristics of the problem, and on characteristics of practical approaches to solving it. RTE solutions have been shown to be of practical use in other NLP applications, and other grand Natural Language Understanding (NLU) challenges, such as Learning by Reading [27] and Machine Reading [43] have emerged that will require similar problems to be solved. It is an exciting time to be working in this area. Textual Inference is a key capability for improving performance in a wide range of NLP tasks, particularly those which can benefit from integrating background knowledge. Performance of Question-Answering systems, which can be thought of as potentially the next generation of search engines, is limited, especially outside the class of factoid questions; and the task of extracting facts of interest (such as “People who have worked for Company X”) from a collection of plain text documents (such as newspaper articles) may require significant abstraction, synthesis, and application of world knowledge on the part of a human reader – and therefore
Spatial genetic structure and clonal diversity in an alpine population of Salix herbacea (Salicaceae).

BACKGROUND AND AIMS Many alpine plant species combine clonal and sexual reproduction to minimize the risks of flowering and seed production in high mountain regions. The spatial genetic structure and diversity of these alpine species is strongly affected by different clonal strategies (phalanx or guerrilla) and the proportion of generative and vegetative reproduction. METHODS The clonal structure of the alpine plant species Salix herbacea was investigated in a 3 x 3 m plot of an alpine meadow using microsatellite (simple sequence repeat; SSR) analysis. The data obtained were compared with the results of a random amplified polymorphic DNA (RAPD) analysis. KEY RESULTS SSR analysis, based on three loci and 16 alleles, revealed 24 different genotypes and a proportion of distinguishable genotypes of 0.18. Six SSR clones were found consisting of at least five samples, 17 clones consisting of more than two samples and seven single genotypes. Mean clone size comprising at least five samples was 0.96 m(2), and spatial autocorrelation analysis showed strong similarity of samples up to 130 cm. RAPD analysis revealed a higher level of clonal diversity but a comparable number of larger clones and a similar spatial structure. CONCLUSIONS The spatial genetic structure as well as the occurrence of single genotypes revealed in this study suggests both clonal and sexual propagation and repeated seedling recruitment in established populations of S. herbacea and is thus suggestive of a relaxed phalanx strategy.
Porcine model to compare real-time intraocular pressure during LASIK with a mechanical microkeratome and femtosecond laser.

PURPOSE To compare real-time intraocular pressure (IOP) during laser in situ keratomileusis (LASIK) in porcine eyes using two types of microkeratomes. METHODS An interventional, prospective study of two microkeratomes: a Moria 2 (Moria group) and an IntraLase femtosecond laser (IntraLase Corp., Irvine, CA; IntraLase group). These devices were used to create lamellar corneal flaps in freshly enucleated porcine eyes. The IOP changes induced by the procedures were recorded with a reusable blood pressure transducer connected to the anterior chamber by direct cannulation. RESULTS Seven porcine eyes were studied in each group. The IOP increased during the suctioning phase, reaching a mean of 122.52 +/- 30.40 and 160.52 +/- 22.73 mm Hg during the cutting phase in the Moria group (the total time in this group was 36.42 +/- 7.48 seconds; suctioning required 21.42 +/- 7.48 seconds and the cutting phase, 15 +/- 2.88 seconds). In the IntraLase group, the IOP reached 89.24 +/- 24.26 mm Hg during the suctioning phase and 119.33 +/- 15.88 mm Hg during the intrastromal laser application (the total time was 92.85 +/- 13.49 seconds; suctioning required 40.00 +/- 9.57 seconds and the cutting phase 52.85 +/- 5.66 seconds). Both IOPs during both phases differed significantly between the two groups (P = 0.01 for all comparisons). CONCLUSIONS Real-time IOP can be measured during LASIK using a transducer connected to the anterior chamber. The results showed a significant increase in IOP during the procedure in both groups, although with the IntraLase the IOP seemed to increase to a lesser extent than with the conventional mechanical microkeratome.
Vitamin D receptor BsmI polymorphism and osteoporosis risk in post-menopausal women

Introduction Many studies have suggested that the vitamin D receptor polymorphism BsmI might be associated with the risk of osteoporosis development in post-menopausal women. However, the results have been inconsistent. The aim of this meta-analysis was to derive a more precise evaluation of the relationship. Material and methods Published literature from PubMed, EMBASE and the CNKI database was searched. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of any association. Results Ten case-control studies were included with a total of 1,403 osteoporosis cases and 2,144 healthy controls. In the overall analysis, no significant association was found between BsmI polymorphism and osteoporosis risk (BB vs. bb: OR = 0.76, 95% CI = 0.39–1.48; BB vs. Bb: OR = 0.90, 95% CI = 0.71–1.15; dominant model: OR = 1.20, 95% CI = 0.74–1.93; recessive model: OR = 0.83, 95% CI = 0.53–1.30). In the subgroup analysis by ethnicity, the results showed similar result that BsmI polymorphism m had no association with osteoporosis. Conclusions Results from the current meta-analysis suggest that vitamin D receptor BsmI polymorphism may not be a risk factor for osteoporosis in post-menopausal women.