Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphological variation of Aphidius ervi Haliday (Hymenoptera: Braconidae) associated with different aphid hosts

Background Parasitoids are frequently used in biological control due to the fact that they are considered host specific and highly efficient at attacking their hosts. As they spend a significant part of their life cycle within their hosts, feeding habits and life history of their host can promote specialization via host-race formation (sequential radiation). The specialized host races from different hosts can vary morphologically, behaviorally and genetically. However, these variations are sometimes inconspicuous and require more powerful tools in order to detect variation such as geometric morphometrics analysis. Methods We examined Aphidius ervi, an important introduced biological control agent in Chile associated with a great number of aphid species, which are exploiting different plant hosts and habitats. Several combinations (biotypes) of parasitoids with various aphid/host plant combinations were analyzed in order to obtain measures of forewing shape and size. To show the differences among defined biotypes, we chose 13 specific landmarks on each individual parasitoid wing. The analysis of allometric variation calculated in wing shape and size over centroid size (CS), revealed the allometric changes among biotypes collected from different hosts. To show all differences in shape of forewings, we made seven biotype pairs using an outline-based geometric morphometrics comparison. Results The biotype A. pis_pea (Acyrthosiphon pisum on pea) was the extreme wing size in this study compared to the other analyzed biotypes. Aphid hosts have a significant influence in the morphological differentiation of the parasitoid forewing, splitting biotypes in two groups. The first group consisted of biotypes connected with Acyrthosiphon pisum on legumes, while the second group is composed of biotypes connected with aphids attacking cereals, with the exception of the R. pad_wheat (Rhopalosiphum padi on wheat) biotype. There was no significant effect of plant species on parasitoid wing size and shape. Discussion Although previous studies have suggested that the genotype of parasitoids is of greater significance for the morphological variations of size and shape of wings, this study indicates that the aphid host on which A. ervi develops is the main factor to alter the structure of parasitoid forewings. Bigger aphid hosts implied longer and broader forewings of A. ervi.
Genome Characterization of the Oleaginous Fungus Mortierella alpina

Mortierella alpina is an oleaginous fungus which can produce lipids accounting for up to 50% of its dry weight in the form of triacylglycerols. It is used commercially for the production of arachidonic acid. Using a combination of high throughput sequencing and lipid profiling, we have assembled the M. alpina genome, mapped its lipogenesis pathway and determined its major lipid species. The 38.38 Mb M. alpina genome shows a high degree of gene duplications. Approximately 50% of its 12,796 gene models, and 60% of genes in the predicted lipogenesis pathway, belong to multigene families. Notably, M. alpina has 18 lipase genes, of which 11 contain the class 2 lipase domain and may share a similar function. M. alpina's fatty acid synthase is a single polypeptide containing all of the catalytic domains required for fatty acid synthesis from acetyl-CoA and malonyl-CoA, whereas in many fungi this enzyme is comprised of two polypeptides. Major lipids were profiled to confirm the products predicted in the lipogenesis pathway. M. alpina produces a complex mixture of glycerolipids, glycerophospholipids and sphingolipids. In contrast, only two major sterol lipids, desmosterol and 24(28)-methylene-cholesterol, were detected. Phylogenetic analysis based on genes involved in lipid metabolism suggests that oleaginous fungi may have acquired their lipogenic capacity during evolution after the divergence of Ascomycota, Basidiomycota, Chytridiomycota and Mucoromycota. Our study provides the first draft genome and comprehensive lipid profile for M. alpina, and lays the foundation for possible genetic engineering of M. alpina to produce higher levels and diverse contents of dietary lipids.
Guaranteed cost output feedback control design of discrete-time uncertain fuzzy system

This study deals with guaranteed cost control problem for discrete time nonlinear systems with parameter uncertainties. The Takagi and Sugeno (T-S) fuzzy model with parameter uncertainties is employed to represent an uncertain discrete time nonlinear system. Based on the structural information in rule base, a piecewise output feedback controller design method is introduced. Sufficient condition for the existence of guaranteed cost output feedback controllers is derived Further more, by means of a convex optimization with linear matrix inequality (LMI) constraints, a simple but practical algorithm is applied to design the output feedback controller which minimizes the guaranteed cost of the closed-loop uncertain system. Numerical example is given to demonstrate the effectiveness of the proposed method.
Individual and Collective User Behavior in Crowdsourcing Services

We study profiles of user behavior in selecting tasks and the resulting profits in online crowdsourcing services. Specifically, we focus on (1) understanding the individual user behavior as well as the underlying collective behavior, (2) understanding the effects of competition among users on the resulting profits and (3) the evolution of user behavior with experience. Our analysis is based on data from a popular crowdsourcing service covering thousands of workers and jobs posted over a period of more than a year. We found two distinct characteristics when looking at individual worker behavior versus the collective behavior of the community. On the one hand, we show evidence of a market segmentation where individual workers tend to direct their effort to tasks from specific ranges of rewards, reflecting their level of skill. On the other hand, the contribution of the community as a whole spreads more evenly across the entire range of rewards and this contribution exhibits a diminishing increase with the value of the reward. Furthermore, we found significant correlations between different measures of competition among users and the resulting profit and characterized how the user’s performance improves with experience. Our results would provide valuable insights to the designers of crowdsourcing services and may inform the design of novel features such as task recommendation based on user skill.
Role of Src Homology Domain Binding in Signaling Complexes Assembled by the Murid γ-Herpesvirus M2 Protein*

Background: The M2 γ-herpesvirus protein exploits B cell signaling pathways to promote viral latency. Results: M2 binds several SH2- and SH3-containing signaling proteins using phosphotyrosine motifs and a proline-rich region, respectively. Conclusion: These interactions affect the juxtamembranar localization of M2 as well as downstream signaling events. Significance: M2 may be used as a model to understand modulation of B cells by γ-herpesvirus infection. γ-Herpesviruses express proteins that modulate B lymphocyte signaling to achieve persistent latent infections. One such protein is the M2 latency-associated protein encoded by the murid herpesvirus-4. M2 has two closely spaced tyrosine residues, Tyr120 and Tyr129, which are phosphorylated by Src family tyrosine kinases. Here we used mass spectrometry to identify the binding partners of tyrosine-phosphorylated M2. Each M2 phosphomotif is shown to bind directly and selectively to SH2-containing signaling molecules. Specifically, Src family kinases, NCK1 and Vav1, bound to the Tyr(P)120 site, PLCγ2 and the SHP2 phosphatase bound to the Tyr(P)129 motif, and the p85α subunit of PI3K associated with either motif. Consistent with these data, we show that M2 coordinates the formation of multiprotein complexes with these proteins. The effect of those interactions is functionally bivalent, because it can result in either the phosphorylation of a subset of binding proteins (Vav1 and PLCγ2) or in the inactivation of downstream targets (AKT). Finally, we show that translocation to the plasma membrane and subsequent M2 tyrosine phosphorylation relies on the integrity of a C-terminal proline-rich SH3 binding region of M2 and its interaction with Src family kinases. Unlike other γ-herpesviruses, that encode transmembrane proteins that mimic the activation of ITAMs, murid herpesvirus-4 perturbs B cell signaling using a cytoplasmic/membrane shuttling factor that nucleates the assembly of signaling complexes using a bilayered mechanism of phosphotyrosine and proline-rich anchoring motifs.
Dicer-2 Processes Diverse Viral RNA Species

RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double-stranded (ds)RNA precursors by Dicer and guide the RNA-induced silencing complex (RISC) to targets. Although principles governing small RNA sorting into RISC have been uncovered, the spectrum of RNA species that can be targeted by Dicer proteins, particularly the viral RNAs present during an infection, are poorly understood. Dicer-2 potently restricts viral infection in insects by generating virus-derived siRNAs from viral RNA. To better characterize the substrates of Dicer-2, we examined the virus-derived siRNAs produced during the Drosophila antiviral RNAi response to four different viruses using high-throughput sequencing. We found that each virus was uniquely targeted by the RNAi pathway; dicing substrates included dsRNA replication intermediates and intramolecular RNA stem loops. For instance, a putative intergenic RNA hairpin encoded by Rift Valley Fever virus generates abundant small RNAs in both Drosophila and mosquito cells, while repetitive sequences within the genomic termini of Vaccinia virus, which give rise to abundant small RNAs in Drosophila, were found to be transcribed in both insect and mammalian cells. Moreover, we provide evidence that the RNA species targeted by Dicer-2 can be modulated by the presence of a viral suppressor of RNAi. This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi.
Hypothermia rescues hippocampal CA1 neurons and attenuates down-regulation of the AMPA receptor GluR2 subunit after forebrain ischemia

Brief forebrain ischemia in rodents induces selective and delayed neuronal death, particularly of hippocampal CA1 pyramidal neurons. Neuronal death is preceded by down-regulation specific to CA1 of GluR2, the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor subunit that limits Ca2+ influx. This alteration is hypothesized to cause neurodegeneration by permitting a lethal influx of Ca2+ and/or Zn2+ through newly formed GluR2-lacking AMPA receptors. Two days of mild hypothermia induced 1 h after ischemia potently and lastingly protects against ischemic injury. We examined molecular mechanisms underlying hypothermia-induced neuroprotection. We report that hypothermia rescues most hippocampal CA1 neurons from ischemia-induced cell death and attenuates ischemia-induced down-regulation of mRNA encoding the AMPA receptor subunit GluR2. Ischemia induced a marked down-regulation of GluR2 mRNA and a small down-regulation of GluR1 mRNA in CA1 at 2 days, as assessed by quantitative in situ hybridization. The ischemia-induced changes in gene expression were cell-specific in that GluR2 was not significantly altered in CA3 or dentate gyrus. After ischemia treated by hypothermia GluR2 mRNA expression was modestly reduced at 2 days and exhibited complete recovery to control levels at 7 days. Hypothermia prevented ischemia induced changes in GluR1 mRNA expression. These findings suggest that intervention at the level of transcriptional regulation of the GluR2 gene may be a mechanism by which prolonged postischemic cooling rescues CA1 neurons otherwise “destined to die. ”
Long-term glucocorticoid effect on bone mineral density in patients with congenital adrenal hyperplasia due to 21-hydroxylase deficiency.

INTRODUCTION Patients with 21-hydroxylase deficiency (21OHD) assume a lifelong glucocorticoid (GC) therapy. Excessive GC treatment increases the risk of osteoporosis and bone fractures, even though the role of substitutive therapy is not fully established: we analyzed the effect of GC dose on bone metabolism and bone mineral density (BMD) over time in patients with 21OHD. METHODS We studied bone metabolism markers and BMD in 38 adult patients with 21OHD (19-47 years, 24 females and 14 males) and 38 matched healthy control. In 15 patients, BMD data were available at both baseline and after a long-term follow-up. RESULTS BMD was lower in patients than in controls at lumbar spine (0.961±0.1g/cm(2) vs 1.02±0.113g/cm(2), P=0.014) and femur neck (0.736±0.128g/cm(2) vs 0.828±0.103g/cm(2), P=0.02); otherwise, after height correction, only femoral neck BMD was lower in patients (0.458±0.081g/cm(2) vs 0.498±0.063g/cm(2), P=0.028). In those 21OHD subjects with at least 10 years follow-up, we observed an increase in lumbar BMD (P=0.0429) and a decrease in femur neck BMD values (P=0.004). Cumulative GC dose was not related to bone metabolism or BMD. No patient experienced clinical fragility fractures. CONCLUSIONS BMD values are decreased in patients with 21OHD, which are in part explained by decreased height, but not by the dose of glucocorticoids. Nevertheless, bone status should be carefully monitored in patients with 21OHD.
Expression of muscarinic receptor subtypes in tree shrew ocular tissues and their regulation during the development of myopia

Purpose Muscarinic receptors are known to regulate several important physiologic processes in the eye. Antagonists to these receptors such as atropine and pirenzepine are effective at stopping the excessive ocular growth that results in myopia. However, their site of action is unknown. This study details ocular muscarinic subtype expression within a well documented model of eye growth and investigates their expression during early stages of myopia induction. Methods Total RNA was isolated from tree shrew corneal, iris/ciliary body, retinal, choroidal, and scleral tissue samples and was reverse transcribed. Using tree shrew-specific primers to the five muscarinic acetylcholine receptor subtypes (CHRM1-CHRM5), products were amplified using polymerase chain reaction (PCR) and their identity confirmed using automated sequencing. The expression of the receptor proteins (M1-M5) were also explored in the retina, choroid, and sclera using immunohistochemistry. Myopia was induced in the tree shrew for one or five days using monocular deprivation of pattern vision, and the expression of the receptor subtypes was assessed in the retina, choroid, and sclera using real-time PCR. Results All five muscarinic receptor subtypes were expressed in the iris/ciliary body, retina, choroid, and sclera while gene products corresponding to CHRM1, CHRM3, CHRM4, and CHRM5 were present in the corneal samples. The gene expression data were confirmed by immunohistochemistry with the M1-M5 proteins detected in the retina, choroid, and sclera. After one or five days of myopia development, muscarinic receptor gene expression remained unaltered in the retinal, choroidal, and scleral tissue samples. Conclusions This study provides a comprehensive profile of muscarinic receptor gene and protein expression in tree shrew ocular tissues with all receptor subtypes found in tissues implicated in the control of eye growth. Despite the efficacy of muscarinic antagonists at inhibiting myopia development, the genes of the muscarinic receptor subtypes are neither regulated early in myopia (before measurable axial elongation) nor after significant structural change.
The Deleterious Influence of Tenofovir-Based Therapies on the Progression of Atherosclerosis in HIV-Infected Patients

We investigated the potential differential effects of antiretroviral therapies on unbalanced chemokine homeostasis and on the progression of atherosclerosis in HIV-infected patients. A two-year prospective study was performed in 67 consecutive HIV-infected patients initiating antiretroviral therapy with abacavir/lamivudine or tenofovir/emtricitabine. Circulating levels of inflammatory biomarkers, progression of subclinical atherosclerosis and expression levels of selected chemokines genes in circulating leukocytes were assessed. Control subjects showed significantly lower plasma concentrations of CRP, tPA, IL-6, and MCP-1 than HIV-infected patients at a baseline. After two years of followup, the observed decreases in plasma inflammatory biomarker levels were only significant for MCP-1, tPA, and IL-6. The decrease in plasma MCP-1 concentration was associated with the progression of atherosclerosis, and this effect was negligible only in patients receiving TDF-based therapy. Multivariate analysis confirmed that treatment with TDF was positively and significantly associated with a higher likelihood of subclinical atherosclerosis progression. However, the expression levels of selected genes in blood cells only showed associations with the viral load and total and HDL-cholesterol levels. Current antiretroviral treatments may partially attenuate the influence of HIV infection on certain inflammatory pathways, though patients receiving TDF therapy must be carefully monitored with respect to the presence and/or progression of atherosclerosis.
A Two-Layer Model of Natural Stimuli Estimated with Score Matching

We consider a hierarchical two-layer model of natural signals in which both layers are learned from the data. Estimation is accomplished by score matching, a recently proposed estimation principle for energy-based models. If the first-layer outputs are squared and the second-layer weights are constrained to be nonnegative, the model learns responses similar to complex cells in primary visual cortex from natural images. The second layer pools a small number of features with similar orientation and frequency, but differing in spatial phase. For speech data, we obtain analogous results. The model unifies previous extensions to independent component analysis such as subspace and topographic models and provides new evidence that localized, oriented, phase-invariant features reflect the statistical properties of natural image patches.
Electrophoretic analysis of genetic diversity in natural house fly (Musca domestica L.) populations from the western and southern coasts of Turkey

In this study genetic variation was determined with isozyme analysis in 8 natural house fly (Musca domestica L.) populations from the western and southern coasts of Turkey, a part of the southern Palearctic region. For this purpose, 7 isozyme systems (ACP, AOX, CAT, HBDH, HXK, MDH, and SOD) were resolved using the native polyacrylamide gel electrophoresis (native-PAGE) technique. A total of 9 loci and 20 alleles were detected. The proportion of polymorphic loci in populations ranged from 44.44% to 66.67%. The overall mean number of effective alleles per locus (Ne) was 1.314 ± 0.454. The mean estimated expected heterozygosity (He) of populations was 0.177 ± 0.228. A very high proportion (93.70%) of genetic diversity was due to variation within populations while a relatively small portion (6.30%) was due to variation among populations. The average level of gene flow (Nm) was calculated to be 3.7182 per generation among all populations studied. The gene flow detected among the Aegean populations (Nm = 6.4451) was 2 times higher than the gene flow detected among the Mediterranean populations (Nm = 3.3331). Our results confirmed the high levels of genetic diversity in house flies reported earlier, supporting the notion that the southern Palearctic region, particularly the Middle East, is the most likely location for the origin of M. domestica.
High-Sensitivity Metamaterial-Inspired Sensor for Microfluidic Dielectric Characterization

A new metamaterial-inspired microwave microfluidic sensor is proposed in this paper. The main part of the device is a microstrip coupled complementary split-ring resonator (CSRR). At resonance, a strong electric field will be established along the sides of CSRR producing a very sensitive area to a change in the nearby dielectric material. A micro-channel is positioned over this area for microfluidic sensing. The liquid sample flowing inside the channel modifies the resonance frequency and peak attenuation of the CSRR resonance. The dielectric properties of the liquid sample can be estimated by establishing an empirical relation between the resonance characteristics and the sample complex permittivity. The designed microfluidic sensor requires a very small amount of sample for testing since the cross-sectional area of the sensing channel is over five orders of magnitude smaller than the square of the wavelength. The proposed microfluidic sensing concept is compatible with lab-on-a-chip platforms owing to its compactness.
European Centre for Medium-Range Weather Forecasts

In the late 1960s, a number of European scientists had the vision that forecasting the weather up to 10 days ahead would be possible. Such medium-range weather forecasts would be of enormous benefit for the protection, safety and economic development of society. As a result, European governments agreed to combine their individual resources and establish an intergovernmental organisation with the goal of developing, improving and operationally producing medium-range weather forecasts. Today, ECMWF is an intergovernmental organisation supported by 34 countries in and around Europe. It was established in 1975 to pool together resources in Europe to provide high quality weather forecasts for the benefit of European citizens. Since then it has become the world leader in global numerical weather prediction. What are ECMWF’s objectives?
Language Modeling for limited-data domains

With the increasing focus of speech recognition and natural language processing applications on domains with limited amount of in-domain training data, enhanced system performance often relies on approaches involving model adaptation and combination. In such domains, language models are often constructed by interpolating component models trained from partially matched corpora. Instead of simple linear interpolation, we introduce a generalized linear interpolation technique that computes context-dependent mixture weights from features that correlate with the component confidence and relevance for each n-gram context. Since the n-grams from partially matched corpora may not be of equal relevance to the target domain, we propose an n-gram weighting scheme to adjust the component n-gram probabilities based on features derived from readily- available corpus segmentation and metadata to de-emphasize out-of-domain n grams. In scenarios without any matched data for a development set, we examine unsupervised and active learning techniques for tuning the interpolation and weighting parameters. Results on a lecture transcription task using the proposed generalized linear interpolation and n-gram weighting techniques yield up to a 1.4% absolute word error rate reduction over a linearly-interpolated baseline language model. As more sophisticated models are only as useful as they are practical, we developed the MIT Language Modeling (MITLM) toolkit, designed for efficient iterative parameter optimization, and released it to the research community. With a compact vector-based n-gram data structure and optimized algorithm implementations, the toolkit not only improves the running time of common tasks by up to 40x, but also enables the efficient parameter tuning for language modeling techniques that were previously deemed impractical. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)