Miracle-dz/UniFAR-FTUs huggingface dataset:
Limits of a rapid identification of common Mediterranean sandflies using polymerase chain reaction-restriction fragment length polymorphism

A total of 131 phlebotomine Algerian sandflies have been processed in the present study. They belong to the species Phlebotomus bergeroti, Phlebotomus alexandri, Phlebotomus sergenti, Phlebotomus chabaudi, Phlebotomus riouxi, Phlebotomus perniciosus, Phlebotomus longicuspis, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus chadlii, Sergentomyia fallax, Sergentomyia minuta, Sergentomyia antennata, Sergentomyia schwetzi, Sergentomyia clydei, Sergentomyia christophersi and Grassomyia dreyfussi. They have been characterised by sequencing of a part of the cytochrome b (cyt b), t RNA serine and NADH1 on the one hand and of the cytochrome C oxidase I of the mitochondrial DNA (mtDNA) on the other hand. Our study highlights two sympatric populations within P. sergenti in the area of its type-locality and new haplotypes of P. perniciosus and P. longicuspis without recording the specimens called lcx previously found in North Africa. We tried to use a polymerase chain reaction-restriction fragment length polymorphism method based on a combined double digestion of each marker. These method is not interesting to identify sandflies all over the Mediterranean Basin.
Autophagy and the cvt Pathway Both Depend onAUT9

ABSTRACT In growing cells of the yeast Saccharomyces cerevisiae, proaminopeptidase I reaches the vacuole via the selective cytoplasm-to-vacuole targeting (cvt) pathway. During nutrient limitation, autophagy is also responsible for the transport of proaminopeptidase I. These two nonclassical protein transport pathways to the vacuole are distinct in their characteristics but in large part use identical components. We expanded our initial screen foraut− mutants and isolated aut9-1cells, which show a defect in both pathways, the vacuolar targeting of proaminopeptidase I and autophagy. By complementation of the sporulation defect of homocygous diploid aut9-1 mutant cells with a genomic library, in this study we identified and characterized the AUT9 gene, which is allelic withCVT7. aut9-deficient cells have no obvious defects in growth on rich media, vacuolar biogenesis, and acidification, but like other mutant cells with a defect in autophagy, they exhibit a reduced survival rate and reduced total protein turnover during starvation. Aut9p is the first putative integral membrane protein essential for autophagy. A biologically active green fluorescent protein-Aut9 fusion protein was visualized at punctate structures in the cytosol of growing cells.
Physically-Based Depth of Field in Augmented Reality

We present a novel method for rendering and compositing video in augmented reality. We focus on calculating the physically correct result of the depth of field caused by a lens with finite sized aperture. In order to correctly simulate light transport, ray-tracing is used and in a single pass combined with differential rendering to compose the final augmented video. The image is fully rendered on GPUs, therefore an augmented video can be produced at interactive frame rates in high quality. Our method runs on the fly, no video postprocessing is needed. In addition we evaluated the user experiences with our rendering system with the hypothesis that a depth of field effect in augmented reality increases the realistic look of composited video. Results with 30 users show that 90% perceive videos with a depth of field considerably more realistic.
ATM regulates 3-methylpurine-DNA glycosylase and promotes therapeutic resistance to alkylating agents.

UNLABELLED Alkylating agents are a first-line therapy for the treatment of several aggressive cancers, including pediatric glioblastoma, a lethal tumor in children. Unfortunately, many tumors are resistant to this therapy. We sought to identify ways of sensitizing tumor cells to alkylating agents while leaving normal cells unharmed, increasing therapeutic response while minimizing toxicity. Using an siRNA screen targeting over 240 DNA damage response genes, we identified novel sensitizers to alkylating agents. In particular, the base excision repair (BER) pathway, including 3-methylpurine-DNA glycosylase (MPG), as well as ataxia telangiectasia mutated (ATM), were identified in our screen. Interestingly, we identified MPG as a direct novel substrate of ATM. ATM-mediated phosphorylation of MPG was required for enhanced MPG function. Importantly, combined inhibition or loss of MPG and ATM resulted in increased alkylating agent-induced cytotoxicity in vitro and prolonged survival in vivo. The discovery of the ATM-MPG axis will lead to improved treatment of alkylating agent-resistant tumors. SIGNIFICANCE Inhibition of ATM and MPG-mediated BER cooperate to sensitize tumor cells to alkylating agents, impairing tumor growth in vitro and in vivo with no toxicity to normal cells, providing an ideal therapeutic window.
Comparative evaluation of the API 20S system and the automicrobic system gram-positive identification card for species identification of streptococci

Two commercial methods, the API 20S system (API; Analytab Products, Inc., Plainview, N.Y.) and the Gram-Positive Identification Card (GPI; Vitek Systems, Inc., Hazelwood, Mo.), were evaluated without additional tests for the identification of 241 streptococcus strains. Organisms included 60 beta-hemolytic strains, 36 group D strains, 26 Streptococcus pneumoniae strains, and 119 viridans streptococcus strains. API correctly identified to species 68.3% of beta-hemolytic strains, 86.1% of group D strains, 53.9% of S. pneumoniae strains, and 12.6% of viridans streptococci. This method provided excellent identification of group A and B and S. faecalis strains. Overall, API correctly identified 41.9% of strains to species, with 41.1% good likelihood but low selectivity, 15.8% incorrect, and 1.2% not identified. GPI correctly identified to species 58.3% of beta-hemolytic strains, 97.2% of group D strains, 80.8% of S. pneumoniae strains, and 57.2% of viridans streptococci. Group A, B, and D strains were all accurately identified by this system. Overall, GPI correctly identified to species 66.0% of strains, with 8.7% correct preliminary identification, 20.8% incorrect, and 4.6% not identified. Both methods represent a worthwhile advance in streptococcal identification. Neither system, however, can be recommended for species identification of the viridans group at this time.
Gene ranking using bootstrapped P-values

Recent research has shown that it is possible to find genes involved in the pathogenesis of a particular condition on the basis of microarray experiments. Genes which are differentially expressed, for example between healthy and diseased tissues, are likely to be relevant to the disease under study. Some of the properties of microarray datasets make the task of finding these genes a challenging one. This paper proposes a gene-ranking algorithm whose main novelty is the use of bootstrapped P-values. We present an analysis of the algorithm, showing how it takes account of small-sample variability in observed values of the test statistic, in a way conventional statistical tests cannot. Experimental results show that our algorithm outperforms the widely-used two-sample t-test on challenging artificial data. Gene ranking is then performed on two well-known microarray datasets, with encouraging results. For example, a number of genes from one of the datasets, whose differential expression was subsequently confirmed by a more reliable biochemical analysis, are found to be ranked higher by the bootstrapped algorithm than by the conventional t-test, suggesting that the proposed algorithm may be better able to exploit the limited data available to infer biologically useful information.
Early anti‐inflammatory treatment reduces lipid peroxidation and protein nitration after spinal cord injury in rats

We investigated mechanisms by which a monoclonal antibody (mAb) against the CD11d subunit of the leukocyte integrin CD11d/CD18 improves neurological recovery after spinal cord injury (SCI) in the rat. The effects of an anti‐CD11d mAb treatment were assessed on ED‐1 expression (estimating macrophage infiltration), myeloperoxidase activity (MPO, approximating neutrophil infiltration), lipid peroxidation, inducible nitric oxide synthase (iNOS) and nitrotyrosine (indicating protein nitration) expression in the spinal cord lesion after severe clip‐compression injury. Protein expression was evaluated by western blotting and immunocytochemistry. Lipid peroxidation was assessed by thiobarbituric acid reactive substances (TBARS) production. After anti‐CD11d mAb treatment, decreased ED‐1 expression at 6–72 h after SCI indicated reduced macrophage infiltration. MPO activity (units/g tissue) was reduced significantly from 114 ± 11 to 75 ± 8 (− 34%) at 6 h and from 38 ± 2 to 22 ± 4 (− 42%) at 72 h. After SCI, anti‐CD11d mAb treatment significantly reduced TBARS from 501 ± 61 to 296 ± 17 nm (− 41%) at 6 h and to approximately uninjured values (87 nm) at 72 h. The mAb treatment also attenuated the expression of iNOS and formation of nitrotyrosine at 6–72 h after SCI. These data indicate that anti‐CD11d mAb treatment blocks intraspinal neutrophil and macrophage infiltration, reducing the intraspinal concentrations of reactive oxygen and nitrogen species. These effects likely underlie improved tissue preservation and neurological function resulting from the mAb treatment.
Susceptibility to coccidiosis: effect of strain of mouse on reproduction of Eimeria vermiformis

SUMMARY The reproduction of Eimeria vermiformis in different strains of phenotypically normal mice and in mice with various immunological characteristics or defects was compared. In some strains of phenotypically normal mice there were marked differences in oocyst production, both in terms of numbers and in the duration of patency, allowing the strains to be classified as resistant or susceptible to infection with E. vermiformis. These differences were apparent only in primary infections; both types of strain were equally resistant to reinfection. Amongst the strains of mice with immunological deficiencies, reproduction of the parasite was greatest in the athymic (nu/nu) mutants and these mice were completely susceptible to reinfection. Strains of mice with lowered or defective antibody production, or with defective neutrophils and low NK cell activity (bg/bg) were more susceptible than the relevant controls to primary infection but all developed substantial immunity to reinfection. Asplenic (Dh/+) mutants were remarkably resistant to infection.
Age-Related Mercury Contamination and Relationship with Luteinizing Hormone in a Long-Lived Antarctic Bird

Seabirds, as long-lived top predators, accumulate contaminants such as mercury (Hg), an established endocrine disruptor. In long lived species hormonal secretion varies with age; therefore, Hg-induced endocrine disruption may be exacerbated in some age classes. Here we investigated relationships between blood total Hg and luteinizing hormone (LH, a key pituitary hormone for the onset of breeding), in pre-laying known-age (11–45 years old) snow petrels (Pagodroma nivea) from Adélie Land, Antarctica. We predicted that 1) blood Hg would increase with advancing age as a consequence of bio-accumulation; and that 2) increasing blood Hg would be related to decreased concentrations of LH in the most Hg-contaminated individuals. Hg concentrations were higher in females than in males (p<0.001), and contrary to our prediction, decreased with advancing age in males (p = 0.009) and tended to do so in females (p = 0.06). The analysis of stable isotopes (δ13C and δ15N) suggested that this unexpected pattern could originate from age and sex-related variations in trophic niche, and hence Hg exposure. Regarding LH, our prediction was only supported in young birds (≤23 years) where baseline LH was inversely correlated with Hg concentrations (p = 0.04). Hg burden did not predict baseline LH or GnRH-induced LH in birds that were more than 23 years old. These results show that age and contaminants may interfere with major endocrine mechanisms and, together with other recent studies, support the view that Hg could be connected to LH secretion and could then impair the fitness of long-lived birds.
Degradation of graphite/bismaleimide laminates with multiple embedded fiber optic sensors

This paper summarizes the reduction in mechanical properties of graphite/bismaleimide (Gr/BMI) laminates due to the presence of multiple embedded fiber-optic sensors. Previous work has shown that small quantities of optical fibers embedded parallel to the loading direction have only a negligible effect on the tension behavior of laminated structures. This work establishes the significance of larger quantities of embedded optical fibers on the tensile and compressive behavior of composite laminates. Experimental strength and modulus data from six test groups of seven tension and seven compression specimens are compared to a control group. All specimens were fabricated from G40-600/5245C Gr/BMI pre-preg tape to form a [°3/9o2/°]s stacking sequence. The quantity of optical fibers embedded parallel to the loading direction was varied in the different test groups. Uniaxial compression testing using an IITRI fixture and uniaxial tension testing were performed in accordance with ASTM Standards. Catastrophic failure was induced by fiber fracture. Results indicate that large quantities of embedded optical fibers reduce the static tensile strength up to 4% and stiffness up to 9%, while reducing the static compressive strength up to 24% and stiffness up to 20%. It is concluded that large quantities of embedded optical fibers result in significant degradation of the compressive strength of laminated composite structures, but do not significantly affect the tensile behavior.
Dynamic Facial Expressions Evoke Distinct Activation in the Face Perception Network: A Connectivity Analysis Study

Very little is known about the neural structures involved in the perception of realistic dynamic facial expressions. In the present study, a unique set of naturalistic dynamic facial emotional expressions was created. Through fMRI and connectivity analysis, a dynamic face perception network was identified, which is demonstrated to extend Haxby et al.'s [Haxby, J. V. , Hoffman, E. A. , & Gobbini, M. I. The distributed human neural system for face perception. Trends in Cognitive Science, 4, 223–233, 2000] distributed neural system for face perception. This network includes early visual regions, such as the inferior occipital gyrus, which is identified as insensitive to motion or affect but sensitive to the visual stimulus, the STS, identified as specifically sensitive to motion, and the amygdala, recruited to process affect. Measures of effective connectivity between these regions revealed that dynamic facial stimuli were associated with specific increases in connectivity between early visual regions, such as the inferior occipital gyrus and the STS, along with coupling between the STS and the amygdala, as well as the inferior frontal gyrus. These findings support the presence of a distributed network of cortical regions that mediate the perception of different dynamic facial expressions.
The Cardioprotective Effects of Fish Oil During Pressure Overload Are Blocked by High Fat Intake: Role Of Cardiac Phospholipid Remodeling

Supplementation with eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) from fish oil may prevent development of heart failure through alterations in cardiac phospholipids that favorably impact inflammation and energy metabolism. A high-fat diet may block these effects in chronically stressed myocardium. Pathological left ventricle (LV) hypertrophy was generated by subjecting rats to pressure overload by constriction of the abdominal aorta. Animals were fed: (1) standard diet (10% of energy from fat), (2) standard diet with EPA+DHA (2.3% of energy intake as EPA+DHA), (3) high fat (60% fat); or (4) high fat with EPA+DHA. Pressure overload increased LV mass by ≈40% in both standard and high-fat diets without fish oil. Supplementation with fish oil increased their incorporation into cardiac phospholipids, and decreased the proinflammatory fatty acid arachidonic acid and urine thromboxane B2 with both the standard and high-fat diet. Linoleic acid and tetralinoloyl cardiolipin (an essential mitochondrial phospholipid) were decreased with pressure overload on standard diet, which was prevented by fish oil. Animals fed high-fat diet had decreased linoleic acid and tetralinoloyl cardiolipin regardless of fish oil supplemention. Fish oil limited LV hypertrophy on the standard diet, and prevented upregulation of fetal genes associated with heart failure (myosin heavy chain-β and atrial natriuetic factor). These beneficial effects of fish oil were absent in animals on the high-fat diet. In conclusion, whereas treatment with EPA+DHA prevented tetralinoloyl cardiolipin depletion, LV hypertrophy, and abnormal genes expression with pressure overload, these effects were absent with a high-fat diet.
A Framework for Decision-Theoretic Planning I: Combining the Situation Calculus, Conditional Plans, Probability and Utility

This paper shows how we can combine logical representations of actions and decision theory in such a manner that seems natural for both. In partitular we assume an axiomatization of the domain in terms of situation calculus, using what is essentially Reiter's solution to the frame problem, in terms of the completion of the axioms defining the state change. Uncertainty is handled in terms of the independent choice logic, which allows for independent choices and a logic program that gives the consequences of the choices. As part of the consequences are a specification of the utility of (final) states. The robot adopts robot plans, similar to the GOLOG programming language. Within this logic, we can define the expected utility of a conditional plan, based on the axiomadzation of the actions, the uncertainty and the utility. The 'planning' problem is to find the plan with the highest expected utility. This is related to recent structured representations for POMDPs; here we use stochastic situation calculus rules to specify the state transition function and the reward/value function. Finally we show that with stochastic frame axioms, actions representations in probabilistic STRIPS are exponentially larger than using the representation proposed here.
Mitochondrial DNA Aberrations of Bone Marrow Cells from Patients with Aplastic Anemia

This study was undertaken primarily to test the hypothesis that mitochondrial DNA (mtDNA) mutations may be associated with aplastic anemia. Complete mtDNA nucleotide sequence was analyzed in nine and eight bone marrow specimens from Korean patients with aplastic anemia and healthy individuals, respectively. We found a large number of polymorphisms as well as apparent new mutations in both patients and controls throughout the entire mtDNA genome; 12 mutations harbored amino acid changes in patients and none of the mutations in controls produced amino acid changes. There were heteroplasmic mutations and more nonsynonymous mtDNA changes observed in patients, so the mean number of mtDNA aberrations of bone marrow cells showed statistically significant difference overall between patients (mean=25.6) and controls (mean=12.8) (p=0.019). Our data may support an association of mtDNA aberrations with aplastic anemia.
Recommendations for switching antipsychotics . A position statement of the Spanish Society of Psychiatry and the Spanish Society of Biological Psychiatry

a Programa Esquizofrènia Clínic, Servei de Psiquiatria, Hospital Clínic, IDIBAPS, Universitat de Barcelona, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Spain b Programa de Trastornos Bipolares, Instituto Clínico de Neurociencias, Hospital Clínic, Universitat de Barcelona, IDIBAPS, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Spain c Servicio de Psiquiatría, Hospital Universitario Ramón y Cajal, Universidad de Alcalá, IRYCIS, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain d Instituto de Neurociencias, Centro de Investigaciones Biomédicas (CIBM), Universidad de Granada, Granada, Spain e Departamento de Farmacología, Universidad de Alcalá, Alcalá de Henares, Madrid, Spain f Área de Psiquiatría, Departamento de Medicina, Universidad de Oviedo, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Oviedo, Spain
Definitive treatment of primary vaginal cancer with radiotherapy: multi-institutional retrospective study of the Korean Radiation Oncology Group (KROG 12-09)

Objective To assess the outcome of the treatment of primary vaginal cancer using definitive radiotherapy (RT) and to evaluate the prognostic factors of survival. Methods The medical records of nine institutions were retrospectively reviewed to find the patients with vaginal cancer treated with definitive RT with or without chemotherapy. A total of 138 patients met the inclusion criteria. None had undergone curative excision. Results The median follow-up time of the survivors was 77.6 months and the median survival time was 46.9 months. The 5-year overall survival, cancer-specific survival (CSS), and progression-free survival (PFS) rates were 68%, 80%, and 68.7%, respectively. In the survival analysis, the multivariate analysis showed that a lower the International Federation of Gynecology and Obstetrics (FIGO) stage and prior hysterectomy were favorable prognostic factors of CSS, and a lower FIGO stage and diagnosed prior to year 2000 were favorable prognostic factors of PFS. In the subgroup analysis of the patients with available human papillomavirus (HPV) results (n=27), no statistically significant relationship between the HPV status and recurrence or survival was found. Grade 3 or 4 acute and late toxicity were present in 16 and 9 patients, respectively. The FIGO stage and the tumor size were predictors of severe late toxicity. Conclusion The data clearly showed that a higher FIGO stage was correlated with a worse survival outcome and higher severe late toxicity. Therefore, precise RT and careful observation are crucial in advanced vaginal cancer. In this study, the HPV status was not related to the survival outcome, but its further investigation is needed.
A Graphical Representation of the Failure Surface of a Composite

This note concerns the graphical descriptions of a general failure theory recently presented in [1]. While numerical analyses are incomplete it was felt that a discussion of some preliminary evidence is timely and in order. The objective of this work is to represent the failure criteria of anisotropic materials in three dimensional space and then draw certain conclusions from numerical analyses and comparisons of the plotted surfaces. In light of our analysis, which will be presented briefly, we feel that three-dimensional representations are essential for the failure surface of anisotropic materials and should replace the more common specialized cases of plane curves. This is a simple task since recently developed computer techniques offer this capability. Once analytical perspective has been gained by determining the lengths of the axes and the center of the coordinate system of the surface, from three-dimensional plots, it is possible to specialize the surface by cutting it with the plane of interest. The theory presently under investigation is of the form: