Miracle-dz/UniFAR-FTUs huggingface dataset:
Sustainable exploitation of biomass for bioenergy from Marginal Lands (SEEMLA)

The main objective of the H2020 funded EU project SEEMLA (acronym for Sustainable Exploitation of Biomass for Bioenergy from Marginal Lands in Europe) is the establishment of suitable innovative land-use strategies for a sustainable production of plant-based energy on marginal lands while improving general ecosystem services. The use of marginal lands (MagL) could contribute to the mitigation of the fast growing competition between traditional food production and production of renewable bio-resources on arable lands. SEEMLA focuses on the promotion of re-conversion of MagLs for the production of bioenergy through the direct involvement of farmers and forester, the strengthening of local small-scale supply chains, and the promotion of plantations of bioenergy plants on MagLs. Life cycle assessment is performed in order to analyse possible impacts on the environment. A soil quality rating tool is applied to define and classify MagL. Suitable perennial and woody bioenergy crops are selected to be grown in pilot areas in the partner countries Ukraine, Greece and Germany. SEEMLA is expected to contribute to an increasing demand of biomass for bioenergy production in order to meet the 2020 targets and beyond.
Supersymmetric (non-)abelian bundles in the type-I and SO(32) heterotic string

We discuss perturbative four-dimensional compactifications of both the SO(32) heterotic and the type-I string on smooth Calabi-Yau manifolds endowed with general non-abelian and abelian bundles. We analyse the generalized Green-Schwarz mechanism for multiple anomalous U(1) factors and derive the generically non-universal one-loop threshold corrections to the gauge kinetic function as well as the one-loop corrected Fayet-Iliopoulos terms. The latter can be interpreted as a stringy one-loop correction to the Donaldson-Uhlenbeck-Yau condition. Applying S-duality, for the type-I string we obtain the perturbative ? -stability condition for non-abelian bundles on curved spaces. Some simple examples are given, and we qualitatively discuss some generic phenomenological aspects of this kind of string vacua. In particular, we point out that in principle an intermediate string scale scenario with TeV scale large extra dimensions might be possible for the heterotic string.
Interactions and Potential Implications of Plasmodium falciparum-Hookworm Coinfection in Different Age Groups in South-Central Côte d'Ivoire

Background Given the widespread distribution of Plasmodium and helminth infections, and similarities of ecological requirements for disease transmission, coinfection is a common phenomenon in sub-Saharan Africa and elsewhere in the tropics. Interactions of Plasmodium falciparum and soil-transmitted helminths, including immunological responses and clinical outcomes of the host, need further scientific inquiry. Understanding the complex interactions between these parasitic infections is of public health relevance considering that control measures targeting malaria and helminthiases are going to scale. Methodology A cross-sectional survey was carried out in April 2010 in infants, young school-aged children, and young non-pregnant women in south-central Côte d'Ivoire. Stool, urine, and blood samples were collected and subjected to standardized, quality-controlled methods. Soil-transmitted helminth infections were identified and quantified in stool. Finger-prick blood samples were used to determine Plasmodium spp. infection, parasitemia, and hemoglobin concentrations. Iron, vitamin A, riboflavin, and inflammation status were measured in venous blood samples. Principal Findings Multivariate regression analysis revealed specific association between infection and demographic, socioeconomic, host inflammatory and nutritional factors. Non-pregnant women infected with P. falciparum had significantly lower odds of hookworm infection, whilst a significant positive association was found between both parasitic infections in 6- to 8-year-old children. Coinfected children had lower odds of anemia and iron deficiency than their counterparts infected with P. falciparum alone. Conclusions/Significance Our findings suggest that interaction between P. falciparum and light-intensity hookworm infections vary with age and, in school-aged children, may benefit the host through preventing iron deficiency anemia. This observation warrants additional investigation to elucidate the mechanisms and consequences of coinfections, as this information could have important implications when implementing integrated control measures against malaria and helminthiases.
Genomic and functional analysis of leukemic transformation of myeloproliferative neoplasms

Significance Myeloproliferative neoplasms (MPN) are chronic hematopoietic disorders characterized by clonal proliferation of mature myeloid elements. A subset of MPNs transforms to acute myeloid leukemia (AML). The mechanisms and pathways that contribute to transformation from MPN to AML have not been well delineated. We have characterized the somatic mutational spectrum of post-MPN AML and demonstrate that somatic tumor protein 53 (TP53) mutations are common in JAK2V617F-mutant, post-MPN AML but not in chronic-phase MPN. We demonstrate that expression of JAK2V617F combined with Tp53 loss in a murine model leads to fully penetrant AML in vivo. We have characterized this model and used it to test therapeutic strategies. These data reveal novel insights into the pathogenesis of, and potential therapeutic strategies for, leukemic transformation. Patients with myeloproliferative neoplasms (MPNs) are at significant, cumulative risk of leukemic transformation to acute myeloid leukemia (AML), which is associated with adverse clinical outcome and resistance to standard AML therapies. We performed genomic profiling of post-MPN AML samples; these studies demonstrate somatic tumor protein 53 (TP53) mutations are common in JAK2V617F-mutant, post-MPN AML but not in chronic-phase MPN and lead to clonal dominance of JAK2V617F/TP53-mutant leukemic cells. Consistent with these data, expression of JAK2V617F combined with Tp53 loss led to fully penetrant AML in vivo. JAK2V617F-mutant, Tp53-deficient AML was characterized by an expanded megakaryocyte erythroid progenitor population that was able to propagate the disease in secondary recipients. In vitro studies revealed that post-MPN AML cells were sensitive to decitabine, the JAK1/2 inhibitor ruxolitinib, or the heat shock protein 90 inhibitor 8-(6-iodobenzo[d][1.3]dioxol-5-ylthio)-9-(3-(isopropylamino)propyl)-9H-purine-6-amine (PU-H71). Treatment with ruxolitinib or PU-H71 improved survival of mice engrafted with JAK2V617F-mutant, Tp53-deficient AML, demonstrating therapeutic efficacy for these targeted therapies and providing a rationale for testing these therapies in post-MPN AML.
General and Specific Alterations in Programming of Global Viral Gene Expression during Infection by VP16 Activation-Deficient Mutants of Herpes Simplex Virus Type 1

ABSTRACT During productive infection by herpes simplex virus 1 (HSV-1), viral gene expression occurs in a temporally regulated cascade in which transcription of the viral immediate-early (IE) genes is strongly stimulated by the virion protein VP16. We have employed an oligonucleotide microarray to examine the effect of VP16 mutations on the overall pattern of viral gene expression following infection of HeLa cells. This microarray detects essentially all HSV-1 transcripts with relative and absolute levels correlating well with known kinetics of expression. This analysis revealed that deletion of the VP16 activation domain sharply reduced overall viral gene expression; moreover, the pattern of this reduced expression varied greatly from the pattern of a wild-type (wt) infection. However, when this mutant virus was delivered at a high multiplicity of infection or in the presence of the cellular stress inducer hexamethylene bisacetamide, expression was largely restored to the wt levels and pattern. Infection with virions that deliver wt VP16 protein at the start of infection but synthesize only truncated VP16 resulted in a normal kinetic cascade. This suggests that newly synthesized VP16 does not play a significant role in the expression of later classes of transcripts. The VP16 activation domain comprises two subregions. Deletion of the C-terminal subregion resulted in minimal changes in the level and profile of gene expression compared to a normal (wt) cascade. In contrast, deletion of the N-terminal subregion reduced the overall expression levels and skewed the relative levels of IE transcripts but did not significantly alter the kinetic pattern of early and late transcript expression. We conclude that the general activation of IE gene transcription by VP16, but not the specific ratios of IE transcripts, is necessary for the subsequent ordered expression of viral genes. Moreover, this report establishes the feasibility of microarray analysis for globally assessing viral gene expression programs as a function of the conditions of infection.
Disintegration/dissolution profiles of copies of Fosamax (alendronate)

SUMMARY Objective: Poor quality has been reported for some generics and other copies of original products. We performed a pilot study to compare the disintegration/dissolution profiles of FOSAMAX (alendronate) 70 mg tablets with those of copies of FOSAMAX that were manufactured outside the United States. Research design and methods: We used the standard United States Pharmacopeia (USP) disintegration method to evaluate FOSAMAX 70mg tablets and 13 copies. At least 12 (n = 12) dosage units were tested for each product (except Fosmin, n = 10). The dissolution profiles of FOSAMAX and one representative copy were also compared. Results: Nine copies (Osteomax, Defixal, Fosmin, Endronax, Osteomix, Genalmen, Fixopan, Osteoplus, and Fosval) disintegrated two- to tenfold faster than FOSAMAX. Three other copies (Neobon, Regenesis, and Ostenan) disintegrated at least five-fold slower than FOSAMAX. Neobon is a softgel capsule, so special consideration was given to this different dosage form. One copy (Arendal) did not fall into either category but exhibited potentially large inter- and intra-lot variability. Dissolution of alendronate from Regenesis lagged behind that from FOSAMAX. Conclusion: Slower disintegration may reduce efficacy because bisphosphonates must be taken in the fasting state and contact with food or even certain beverages severely reduces bioavailability. Faster disintegration (or the use of gel-caps or other alterations to the drug formulation) could increase the risk of esophagitis, an adverse event associated with prolonged contact of the esophagus with bisphosphonates. These disintegration and dissolution results suggest that important differences may exist between FOSAMAX and its copies with regard to bioavailability, pharmacokinetics, and clinical efficacy and safety profiles. Additional testing is warranted to evaluate the pharmacokinetics and clinical safety of these copies.
OpenIMAJ and ImageTerrier: Java libraries and tools for scalable multimedia analysis and indexing of images

OpenIMAJ and ImageTerrier are recently released open-source libraries and tools for experimentation and development of multimedia applications using Java-compatible programming languages. OpenIMAJ (the Open toolkit for Intelligent Multimedia Analysis in Java) is a collection of libraries for multimedia analysis. The image libraries contain methods for processing images and extracting state-of-the-art features, including SIFT. The video and audio libraries support both cross-platform capture and processing. The clustering and nearest-neighbour libraries contain efficient, multi-threaded implementations of clustering algorithms. The clustering library makes it possible to easily create BoVW representations for images and videos. OpenIMAJ also incorporates a number of tools to enable extremely-large-scale multimedia analysis using distributed computing with Apache Hadoop. ImageTerrier is a scalable, high-performance search engine platform for content-based image retrieval applications using features extracted with the OpenIMAJ library and tools. The ImageTerrier platform provides a comprehensive test-bed for experimenting with image retrieval techniques. The platform incorporates a state-of-the-art implementation of the single-pass indexing technique for constructing inverted indexes and is capable of producing highly compressed index data structures.
Acute stress response in gilthead sea bream (Sparus aurata L.) is time-of-day dependent: Physiological and oxidative stress indicators

Since fish show daily rhythms in most physiological functions, it should not be surprising that stressors may have different effects depending on the timing of exposure. In this study, we investigated the influence of time of day on the stress responses, at both physiological and cellular levels, in gilthead sea bream (Sparus aurata L.) submitted to air exposure for 30 s and then returned to their tank. One hour after air exposure, blood, hypothalamus and liver samples were taken. Six fish per experimental group (control and stressed) were sampled every 4 h during a 24-h cycle. Fish were fed in the middle of the light cycle (ML) and locomotor activity rhythms were recorded using infrared photocells to determine their daily activity pattern of behaviour, which showed a peak around feeding time in all fish. In the control group, cortisol levels did not show daily rhythmicity, whereas in the stressed fish, a daily rhythm of plasma cortisol was observed, being the average values higher than in the control group, with increased differences during the dark phase. Blood glucose showed daily rhythmicity in the control group but not in the stressed one which also showed higher values at all sampling points. In the hypothalamus of control fish, a daily rhythm of corticotropin-releasing hormone (crh) gene expression was observed, with the acrophase at the beginning of the light phase. However, in the stressed fish, this rhythm was abolished. The expression of crh-binding protein (crhbp) showed a peak at the end of the dark phase in the control group, whereas in the stressed sea bream, this peak was found at ML. Regarding hepatic gene expression of oxidative stress biomarkers: (i) cytochrome c oxidase 4 showed daily rhythmicity in both control and stressed fish, with the acrophases located around ML, (ii) peroxiredoxin (prdx) 3 and 5 (prdx5) only presented daily rhythmicity of expression in the stressed fish, with the acrophase located at the beginning of the light cycle and (iii) uncoupling protein 1 showed significant differences between sampling points only in the control group, with significantly higher expression at the beginning of the dark phase. Taken together, these results indicate that stress response in gilthead sea bream is time-dependent as cortisol level rose higher at night, and that different rhythmic mechanisms interplay in the control of neuroendocrine and cellular stress responses.
Structure of the Escherichia coli ProQ RNA-binding protein

The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.
An intelligent positioning approach: RSSI-based indoor and outdoor localization scheme in Zigbee networks

In this paper, we study the positioning schemes in Zigbee sensor networks. Basing on different conditions of indoor and outdoor environment, we propose two different types of positioning approaches. Considering the arrangement of the building, the indoor schemes cluster the localization area into many subzones, while the outdoor schemes use the estimated distance to determine the position of the sensed node. Our approaches bases on the receiving strength of the signal and does not need any location fingerprinting process in advance or location database. We also conduct field tests to see the performance of the proposed schemes. The results of the experiments show that our methods can achieve good accuracy no matter in indoor or outdoor environments.
Membranous Replication Factories Induced by Plus-Strand RNA Viruses

In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments.
Dexmedetomidine versus Magnesium Sulfate in Anesthesia for Cochlear Implantation Surgery in Pediatric Patients

Context: Cochlear implantation surgery represents a great advance in ENT surgeries. Special anesthetic managements were required to provide bloodless surgical field and monitoring of the facial nerve. Aims: We aimed to compare both dexmedetomidine and magnesium sulfate as regards their efficacy in inducing deliberate hypotension and providing better quality of the surgical field during cochlear implantation in pediatrics. Settings and Design: Prospective, randomized double-blinded study. Subjects and Methods: Forty-six pediatric patients aging 1.5–2.5 years of either sex with American Society of Anesthesiologists physical status classes I and II were randomized into dexmedetomidine (D) group (n = 23) and magnesium sulfate (M) group (n = 23). In the D group, after induction of anesthesia but before the surgery, a bolus dose of 0.4 μg/kg slowly infused over 10 min, then continuous infusion by a rate of 0.4 μg/kg/h until the end of surgery. In M group, after induction of anesthesia but before the surgery, magnesium sulfate 10% (50 mg/kg) was given slowly, then continuous infusion by a rate of 10 mg/kg/h during the whole surgery. Intraoperative hemodynamics, quality of surgical field, fentanyl consumption, blood loss, operative time, FLACC pain scores, and adverse effects were compared in both groups. Statistical Analysis Used: Data were presented as mean ± standard deviation, ranges, numbers, and percentages as appropriate. Comparison of demographic data and time of surgery was done by Student's t-test. Two-way analysis of variance with correction for repeated measurements was used for heart rate and blood pressure comparison. Mann–Whitney U-test was used for nonparametric measurements. Results: Surgical field score and blood loss were better in D group than M group. Fentanyl consumption was less in D group than M group. Heart rate and mean atrial blood pressure were lower in D group except in the initial times than M group.Conclusions: In our study, both drugs were effective in achieving hypotensive anesthesia in pediatrics; however, dexmedetomidine proved to have superior effect on the surgical field and blood loss compared to magnesium sulfate with no intra- and post-operative complications for cochlear implantation surgery.
Opposite effects of 5-HT/AKH and octopamine on the crop contractions in adult Drosophila melanogaster: Evidence of a double brain-gut serotonergic circuitry

This study showed that in adult Drosophila melanogaster, the type of sugar—either present within the crop lumen or in the bathing solution of the crop—had no effect on crop muscle contraction. What is important, however, is the volume within the crop lumen. Electrophysiological recordings demonstrated that exogenous applications of serotonin on crop muscles increases both the amplitude and the frequency of crop contraction rate, while adipokinetic hormone mainly enhances the crop contraction frequency. Conversely, octopamine virtually silenced the overall crop activity. The present study reports for the first time an analysis of serotonin effects along the gut-brain axis in adult D. melanogaster. Injection of serotonin into the brain between the interocellar area shows that brain applications of serotonin decrease the frequency of crop activity. Based on our results, we propose that there are two different, opposite pathways for crop motility control governed by serotonin: excitatory when added in the abdomen (i.e., directly bathing the crop) and inhibitory when supplied within the brain (i.e., by injection). Finally, our results point to a double brain-gut serotonergic circuitry suggesting that not only the brain can affect gut functions, but the gut can also affect the central nervous system. On the basis of our results, and data in the literature, a possible mechanism for these two discrete serotonergic functions is suggested.
Hedgehog controls hepatic stellate cell fate by regulating metabolism.

BACKGROUND & AIMS The pathogenesis of cirrhosis, a disabling outcome of defective liver repair, involves deregulated accumulation of myofibroblasts derived from quiescent hepatic stellate cells (HSCs), but the mechanisms that control transdifferentiation of HSCs are poorly understood. We investigated whether the Hedgehog (Hh) pathway controls the fate of HSCs by regulating metabolism. METHODS Microarray, quantitative polymerase chain reaction, and immunoblot analyses were used to identify metabolic genes that were differentially expressed in quiescent vs myofibroblast HSCs. Glycolysis and lactate production were disrupted in HSCs to determine if metabolism influenced transdifferentiation. Hh signaling and hypoxia-inducible factor 1α (HIF1α) activity were altered to identify factors that alter glycolytic activity. Changes in expression of genes that regulate glycolysis were quantified and localized in biopsy samples from patients with cirrhosis and liver samples from mice following administration of CCl(4) or bile duct ligation. Mice were given systemic inhibitors of Hh to determine if they affect glycolytic activity of the hepatic stroma; Hh signaling was also conditionally disrupted in myofibroblasts to determine the effects of glycolytic activity. RESULTS Transdifferentiation of cultured, quiescent HSCs into myofibroblasts induced glycolysis and caused lactate accumulation. Increased expression of genes that regulate glycolysis required Hh signaling and involved induction of HIF1α. Inhibitors of Hh signaling, HIF1α, glycolysis, or lactate accumulation converted myofibroblasts to quiescent HSCs. In diseased livers of animals and patients, numbers of glycolytic stromal cells were associated with the severity of fibrosis. Conditional disruption of Hh signaling in myofibroblasts reduced numbers of glycolytic myofibroblasts and liver fibrosis in mice; similar effects were observed following administration of pharmacologic inhibitors of Hh. CONCLUSIONS Hedgehog signaling controls the fate of HSCs by regulating metabolism. These findings might be applied to diagnosis and treatment of patients with cirrhosis.