Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a Cost-Effective Method for Capripoxvirus Genotyping Using Snapback Primer and dsDNA Intercalating Dye

Sheep pox virus (SPPV), goat pox virus (GTPV) and lumpy skin disease virus (LSDV) are very closely related viruses of the Capripoxvirus (CaPV) genus of the Poxviridae family. They are responsible for sheep pox, goat pox and lumpy skin disease which affect sheep, goat and cattle, respectively. The epidemiology of capripox diseases is complex, as some CaPVs are not strictly host-specific. Additionally, the three forms of the disease co-exist in many sub-Saharan countries which complicates the identification of the virus responsible for an outbreak. Genotyping of CaPVs using a low-cost, rapid, highly specific, and easy to perform method allows a swift and accurate identification of the causative agent and significantly assists in selecting appropriate control and eradication measures, such as the most suitable vaccine against the virus during the outbreaks. The objective of this paper is to describe the design and analytical performances of a new molecular assay for CaPV genotyping using unlabelled snapback primers in the presence of dsDNA intercalating EvaGreen dye. This assay was able to simultaneously detect and genotype CaPVs in 63 samples with a sensitivity and specificity of 100%. The genotyping was achieved by observing the melting temperature of snapback stems of the hairpins and those of the full-length amplicons, respectively. Fourteen CaPVs were genotyped as SPPVs, 25 as GTPVs and 24 as LSDVs. The method is highly pathogen specific and cross platform compatible. It is also cost effective as it does not use fluorescently labelled probes, nor require high-resolution melting curve analysis software. Thus it can be easily performed in diagnostic and research laboratories with limited resources. This genotyping method will contribute significantly to the early detection and genotyping of CaPV infection and to epidemiological studies.
Short- and long-term outcomes of critically ill patients with cancer and prolonged ICU length of stay.

BACKGROUND Data on patients with cancer who have a prolonged length of stay (LOS) in the ICU are scarce. The aim of the present study was to evaluate the characteristics and the outcomes of cancer patients with life-threatening complications with an ICU stay > or = 21 days. METHODS A cohort study performed at a 10-bed oncology medical-surgical ICU from May 2000 to December 2005. Prolonged ICU LOS was defined as an ICU stay > or = 21 days. RESULTS During the period, 1,090 patients were admitted to the ICU and 163 patients (15%) had a prolonged ICU LOS. These patients, however, accounted for 48% (5,828/12,224) of the total ICU bed-days. The hospital and 6-month mortality rates were 50% and 60%, respectively, and similar to patients with ICU LOS < 21 days (51% and 61%, respectively). ICU-acquired events and complications were common, and the most frequent were infections (90%), mechanical ventilation (99%), and need for vasopressors (88%). The number of organ failures, older age, and poor performance status were the main outcome predictors. The median long-term follow-up after hospital discharge was 537 days (range, 193 to 1,119 days), and 29 patients (18%) were alive. CONCLUSIONS Fifteen percent of critically ill patients with cancer had a prolonged ICU LOS. Short- and long-term survival rates were reasonable, and the prognosis was better than expected a priori. In our opinion, the length of ICU admission per se should not be used in the clinical decisions regarding the continuation of treatment in these patients.
Dust in an Extremely Metal-Poor Galaxy: Mid-infrared Observations ofSBS 0335–052

The metal-deficient (Z=Z☉/41) blue compact dwarf galaxy SBS 0335-052 was observed with ISOCAM between 5 and 17 μm. With an L12μm/LB ratio of 2.15, the galaxy is unexpectedly bright in the mid-infrared for such a low-metallicity object. The mid-infrared spectrum shows no sign of the unidentified infrared bands, which we interpret as an effect of the destruction of their carriers by the very high UV energy density in SBS 0335-052. The spectral energy distribution (SED) is dominated by a very strong continuum, which makes the ionic lines of [S IV] and [Ne III] very weak. From 5 to 17 μm, the SED can be fitted with a graybody spectrum, modified by an extinction law similar to that observed toward the Galactic center, with an optical depth of AV ~19-21 mag. Such a large optical depth implies that a large fraction (as much as ~75%) of the current star formation activity in SBS 0335-052 is hidden by dust with a mass between 3 × 103 and 5 × 105 M☉. Silicate grains that are present as silicate extinction bands at 9.7 and 18 μm can account for the unusual shape of the MIR spectrum of SBS 0335-052. It is remarkable that such a nearly primordial environment contains as much dust as galaxies that are 10 times more metal-rich. If the hidden star formation in SBS 0335-052 is typical of young galaxies at high redshifts, then the cosmic star formation rate derived from UV/optical fluxes would be underestimated.
Inhibition of prenylated KRAS in a lipid environment

RAS mutations lead to a constitutively active oncogenic protein that signals through multiple effector pathways. In this chemical biology study, we describe a novel coupled biochemical assay that measures activation of the effector BRAF by prenylated KRASG12V in a lipid-dependent manner. Using this assay, we discovered compounds that block biochemical and cellular functions of KRASG12V with low single-digit micromolar potency. We characterized the structural basis for inhibition using NMR methods and showed that the compounds stabilized the inactive conformation of KRASG12V. Determination of the biophysical affinity of binding using biolayer interferometry demonstrated that the potency of inhibition matches the affinity of binding only when KRAS is in its native state, namely post-translationally modified and in a lipid environment. The assays we describe here provide a first-time alignment across biochemical, biophysical, and cellular KRAS assays through incorporation of key physiological factors regulating RAS biology, namely a negatively charged lipid environment and prenylation, into the in vitro assays. These assays and the ligands we discovered are valuable tools for further study of KRAS inhibition and drug discovery.
Comparative epidemiology of pandemic and seasonal influenza A in households.

BACKGROUND There are few data on the comparative epidemiology and virology of the pandemic 2009 influenza A (H1N1) virus and cocirculating seasonal influenza A viruses in community settings. METHODS We recruited 348 index patients with acute respiratory illness from 14 outpatient clinics in Hong Kong in July and August 2009. We then prospectively followed household members of 99 patients who tested positive for influenza A virus on rapid diagnostic testing. We collected nasal and throat swabs from all household members at three home visits within 7 days for testing by means of quantitative reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay and viral culture. Using hemagglutination-inhibition and viral-neutralization assays, we tested baseline and convalescent serum samples from a subgroup of patients for antibody responses to the pandemic and seasonal influenza A viruses. RESULTS Secondary attack rates (as confirmed on RT-PCR assay) among household contacts of index patients were similar for the pandemic influenza virus (8%; 95% confidence interval [CI], 3 to 14) and seasonal influenza viruses (9%; 95% CI, 5 to 15). The patterns of viral shedding and the course of illness among index patients were also similar for the pandemic and seasonal influenza viruses. In a subgroup of patients for whom baseline and convalescent serum samples were available, 36% of household contacts who had serologic evidence of pandemic influenza virus infection did not shed detectable virus or report illness. CONCLUSIONS Pandemic 2009 H1N1 virus has characteristics that are broadly similar to those of seasonal influenza A viruses in terms of rates of viral shedding, clinical illness, and transmissibility in the household setting.
Hydromechanical signaling between the ciliate Mesodinium pulex and motile protist prey

The raptorial ciliate Mesodinium pulex (Claparede & Lachmann, 1858) was fed 3 differ- ent prey species: Rhodomonas salina, Heterocapsa rotundata and Gymnodinium simplex. Each prey displayed different motility patterns, including dramatic and effective escape responses. M. pulex only fed while motionless and responded only to motile prey by either an attack or an escape. Both the attack and escape responses are associated with a strong directional component in M. pulex. M. pulex responded to motile prey when the critical fluid velocity exceeded ~15 to 42 µm s -1 , depending on prey species. These values are similar to hydromechanical signal thresholds found in marine metazoans. Prey-induced escape responses in M. pulex are associated with fast-swimming prey such as G. simplex. Deformation rates calculated in these specialized cases exceed the reported critical deformation rate for escape in ciliated protists, suggesting that fast-swimming prey mimic an approaching predator. Microscopic observations indicate that the band of equatorial cirri encircling M. pulex is the principal detector of motile prey. We propose that M. pulex exhibits a specialized fluid velocity-sensitive mechanoreceptor analogous to the fluid motion mechanoreceptors found in meta- zoans. M. pulex fails to ingest the cryptophytic prey R. salina. Our observations suggest that this is due to mismatch between the capturing organelles of the ciliate and surface properties of the prey. Dinoflagellate prey are more effectively ingested, but a high percentage escaped from M. pulex. Pre-capture escape responses may be triggered by ciliate-generated hydromechanical signals and facilitated by the strong swimming ability of the flagellates. Hydromechanical signaling can affect the outcome of predator-prey interactions and may select for distinctive morphological and behavioral features in planktonic protists.
Chemotherapy-free treatment in patients with follicular lymphoma

The outcome of patients with follicular lymphoma (FL) has improved over the last two decades through the introduction of anti-CD20 monoclonal antibodies, usually used in combination with chemotherapy. However, patients with FL still experience multiple relapses, requiring several lines of treatment. Early toxicity of chemotherapy is a significant concern and as the life expectancy of patients with FL is increasing, late toxicities become an increasingly important concern. Progress made in understanding the biology of FL, especially dysregulation of intracellular pathways and immunological antitumor responses, recently allowed for the development of innovative chemo-free therapeutic approaches. In this report, different options such as new anti-CD20 antibodies, antibodies targeting other cell surface antigens, bi-specific antibodies, immunomodulation, idiotype vaccine and other targeted therapies are presented. The article also highlights how, although promising in early phase studies, the cost–effectiveness of new agents will have to be justified in Phase III trials. Furthermore, chemo-free regimen might not mean toxicity-free treatment and monitoring of early and late toxicities is required.
Acupoint Injection of Autologous Stromal Vascular Fraction and Allogeneic Adipose-Derived Stem Cells to Treat Hip Dysplasia in Dogs

Stem cells isolated from adipose tissue show great therapeutic potential in veterinary medicine, but some points such as the use of fresh or cultured cells and route of administration need better knowledge. This study aimed to evaluate the effect of autologous stromal vascular fraction (SVF, n = 4) or allogeneic cultured adipose-derived stem cells (ASCs, n = 5) injected into acupuncture points in dogs with hip dysplasia and weak response to drug therapy. Canine ASCs have proliferation and differentiation potential similar to ASCs from other species. After the first week of treatment, clinical evaluation showed marked improvement compared with baseline results in all patients treated with autologous SVF and three of the dogs treated with allogeneic ASCs. On days 15 and 30, all dogs showed improvement in range of motion, lameness at trot, and pain on manipulation of the joints, except for one ASC-treated patient. Positive results were more clearly seen in the SVF-treated group. These results show that autologous SVF or allogeneic ASCs can be safely used in acupoint injection for treating hip dysplasia in dogs and represent an important therapeutic alternative for this type of pathology. Further studies are necessary to assess a possible advantage of SVF cells in treating joint diseases.
Multi-attention Network for One Shot Learning

One-shot learning is a challenging problem where the aim is to recognize a class identified by a single training image. Given the practical importance of one-shot learning, it seems surprising that the rich information present in the class tag itself has largely been ignored. Most existing approaches restrict the use of the class tag to finding similar classes and transferring classifiers or metrics learned thereon. We demonstrate here, in contrast, that the class tag can inform one-shot learning as a guide to visual attention on the training image for creating the image representation. This is motivated by the fact that human beings can better interpret a training image if the class tag of the image is understood. Specifically, we design a neural network architecture which takes the semantic embedding of the class tag to generate attention maps and uses those attention maps to create the image features for one-shot learning. Note that unlike other applications, our task requires that the learned attention generator can be generalized to novel classes. We show that this can be realized by representing class tags with distributed word embeddings and learning the attention map generator from an auxiliary training set. Also, we design a multiple-attention scheme to extract richer information from the exemplar image and this leads to substantial performance improvement. Through comprehensive experiments, we show that the proposed approach leads to superior performance over the baseline methods.
ECOLOGICAL GENETICS OF GYNODIOECY IN SILENE VULGARIS: RELATIVE FITNESS OF FEMALES AND HERMAPHRODITES DURING THE COLONIZATION PROCESS

Recent theoretical models have addressed the influence of metapopulation dynamics on the fitness of females and hermaphrodites in gynodioecious plants. In particular, selection is thought to favor hermaphrodites during population establishment because that sex should be less prone to pollen limitation, especially if self‐fertilization is possible. However, inbreeding depression could limit this advantage. In this experimental study of Silene vulgaris, a weedy gynodioecious plant, the fitness of females and hermaphrodites was estimated from seed production in both mixed‐sex populations and for individuals isolated from these populations by 20, 40, 80, or 160 m. In mixed populations females display statistically significant greater per capita seed production owing to higher capsule production and higher rates of seed germination. The fitness of both sexes declines with increasing isolation, but at different rates, such that in the 160‐m treatment hermaphrodites are by far the more fit sex. Allozyme studies suggest that this differential decline is because the selfing rate in hermaphrodites increases as a function of isolation, at least partially compensating for a decline in the availability of outcross pollen. Overall, the negative effects of pollen limitation on females far outweighs the negative effects of inbreeding depression following selfing in hermaphrodites. Thus, extinction/recolonization dynamics would appear to favor hermaphrodites as long as seed dispersal events exceed some critical distance.
Optimum Shape Design for Unsteady Flows with Time-Accurate Continuous and Discrete Adjoint Methods

This paper presents an adjoint method for the optimal control of unsteady flows. The goal is to develop the continuous and discrete unsteady adjoint equations and their corresponding boundary conditions for the time-accurate method. First, this paper presents the complete formulation of the time-dependent optimal design problem. Second, we present the time-accurate unsteady continuous and discrete adjoint equations. Third, we present results that demonstrate the application of the theory to a two-dimensional oscillating airfoil. The results are compared with a multipoint approach to illustrate the added benefit of performing full unsteady optimization.
Cortical Dynamics Subserving Visual Apparent Motion

Motion can be perceived when static images are successively presented with a spatial shift. This type of motion is an illusion and is termed apparent motion (AM). Here we show, with a voltage sensitive dye applied to the visual cortex of the ferret, that presentation of a sequence of stationary, short duration, stimuli which are perceived to produce AM are, initially, mapped in areas 17 and 18 as separate stationary representations. But time locked to the offset of the 1st stimulus, a sequence of signals are elicited. First, an activation traverses cortical areas 19 and 21 in the direction of AM. Simultaneously, a motion dependent feedback signal from these areas activates neurons between areas 19/21 and areas 17/18. Finally, an activation is recorded, traveling always from the representation of the 1st to the representation of the next or succeeding stimuli. This activation elicits spikes from neurons situated between these stimulus representations in areas 17/18. This sequence forms a physiological mechanism of motion computation which could bind populations of neurons in the visual areas to interpret motion out of stationary stimuli.
Secreted Frizzled-Related Protein 4 (SFRP4) is Elevated in Patients with Diabetes Mellitus

Abstract Recently, SFRP4 was identified as a molecular link between islet inflammation and defective insulin secretion. Gene co-expression analysis detected a molecule associated with type 2 diabetes mellitus (T2D), elevated HbA1c, and reduced insulin secretion in mice as well as in a pilot sample of humans. To our knowledge SFRP4 has never been investigated in patients with different types of diabetes. We included 179 patients: 46 with type 1 diabetes (T1D), 30 age matched healthy controls for patients with T1D (CO-T1D), 55 with T2D, 37 with latent autoimmune diabetes of the adult (LADA) and 30 healthy controls (CO) for patients with T2D and LADA. Apart from anthropometric data, lipids and renal parameters were assessed. SFRP4 levels were measured by a commercial ELISA. Patients with diabetes had significant higher SFRP4 levels than CO: T2D vs. CO: 37.1±26.7 vs. 8.8±3.0 ng/ml, p<0.001; LADA vs. CO: 15.6±6.2 vs. 8.7±3.0 ng/ml, p<0.001; T1D vs. CO-T1D: 24.6±17.9 vs. 16.9±4.5 ng/ml, p=0.011. SFRP4 levels were correlated with age, BMI, HbA1c, HDL-cholesterol, and triglycerides. A multivariate model revealed HDL-cholesterol, triglycerides and BMI as predictors for SFRP4. This is the first study demonstrating that SFRP4 is significantly increased in patients with different types of diabetes suggesting that this protein is generally involved in islet dysfunction and potentially subclinical inflammation irrespective of type of diabetes.
About the Chemical Evolution of dSphs (and the peculiar Globular Cluster ω Cen)

Abstract We present three dimensional hydrodynamical simulations aimed at studying the dynamical and chemical evolution of the interstellar medium (ISM) in isolated dwarf spheroidal galaxies (dSphs). This evolution is driven by the explosion of Type II and Type Ia supernovae, whose different contribution on both the dynamics and chemical enrichment is taken into account. Radiative losses are effective in radiating away the huge amount of energy released by SNe explosions, and the dSph is able to retain most of the gas allowing a long period (≥ 2 − 3 Gyr) of star formation, as usually observed in this kind of galaxies. We are able to reproduce the stellar metallicity distribution function (MDF) as well as the peculiar chemical properties of strongly O-depleted stars observed in several dSphs. The model also naturally predicts two different stellar populations, with an anti-correlation between [Fe/H] and velocity dispersion, similarly to what observed in the Sculptor and Fornax dSphs. These results derive from the inhomogeneous pollution of the SNe Ia, a distinctive characteristic of our model. We also applied the model to the peculiar globular cluster (GC) ω Cen in the hypothesis that it is the remnant of a formerly larger stellar system, possibly a dSph.
Some remarks on morphisms between Fano threefolds

Let X, Y be Fano threefolds of Picard number one and such that the ample generators of Picard groups are very ample. Let X be of index one and Y be of index two. It is shown that the only morphisms from X to Y are double coverings. In fact nearly the whole paper is the analysis of the case where Y is the linear section of the Grassmannian G(1,4), since the other cases were more or less solved in another article. This remaining case is treated with the help of Debarre's connectedness theorem for inverse images of Schubert cycles.
Enhanced Amyloidogenic Processing of the β-Amyloid Precursor Protein in Gene-targeted Mice Bearing the Swedish Familial Alzheimer's Disease Mutations and a “Humanized” Aβ Sequence*

The processing of the β-amyloid precursor protein (APP) in vivo has been characterized in a novel animal model that recapitulates, in part, the APP genotype of a familial form of Alzheimer's disease (AD). A gene-targeting strategy was used to introduce the Swedish familial AD mutations and convert mouse Aβ to the human sequence. The mutant APP is expressed at normal levels in brain, and cleavage at the mutant β-secretase site is both accurate and enhanced. Furthermore, human Aβ production is significantly increased to levels 9-fold greater than those in normal human brain while nonamyloidogenic processing is depressed. The results on Aβ production extend similar findings obtained in cell culture to the brain of an animal and substantiate Aβ as a etiological factor in Swedish familial AD. These animals provide several distinguishing features over others created by conventional transgenic methodologies. The spatial and temporal expression patterns of human Aβ are expected to be faithfully reproduced because the gene encoding the mutant APP remains in its normal chromosomal context. Thus, the neuropathological consequences of human Aβ overproduction can be evaluated longitudinally in the absence of potential mitigating effects of APP overexpression or presence of the mouse Aβ peptide.