Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual isotope and isotopomer signatures of nitrous oxide from fungal denitrification--a pure culture study.

RATIONALE The contribution of fungal denitrification to the emission of the greenhouse gas nitrous oxide (N2O) from soil has not yet been sufficiently investigated. The intramolecular (15)N site preference (SP) of N2O could provide a tool to distinguish between N2O produced by bacteria or fungi, since in previous studies fungi exhibited much higher SP values than bacteria. METHODS To further constrain isotopic evidence of fungal denitrification, we incubated six soil fungal strains under denitrifying conditions, with either NO3(-) or NO2(-) as the electron acceptor, and measured the isotopic signature (δ(18)O, δ(15)Nbulk and SP values) of the N2O produced. The nitrogen isotopic fractionation was calculated and the oxygen isotope exchange associated with particular fungal enzymes was estimated. RESULTS Five fungi of the order Hypocreales produced N2O with a SP of 35.1 ± 1.7 ‰ after 7 days of anaerobic incubation independent of the electron acceptor, whereas one Sordariales species produced N2O from NO2(-) only, with a SP value of 21.9 ± 1.4 ‰. Smaller isotope effects of (15)Nbulk were associated with larger N2O production. The δ(18)O values were influenced by oxygen exchange between water and denitrification intermediates, which occurred primarily at the nitrite reduction step. CONCLUSIONS Our results confirm that SP of N2O is a promising tool to differentiate between fungal and bacterial N2O from denitrification. Modelling of oxygen isotope fractionation processes indicated that the contribution of the NO2(-) and NO reduction steps to the total oxygen exchange differed among the various fungal species studied. However, more information is needed about different biological orders of fungi as they may differ in denitrification enzymes and consequently in the SP and δ(18)O values of the N2O produced.
Causes and pattern of missing permanent teeth among Kenyans.

OBJECTIVE To determine the causes and pattern of missing permanent teeth among Kenyans. DESIGN A descriptive cross-sectional study. SETTING Five districts in Kenya. SUBJECTS Seven hundred and twenty two persons aged 6-85 years (346 males and 376 females). METHODS This study was undertaken in October 2001 during the National Dental Health Action Month organised by the Kenya Dental Association. Six centres in five districts were identified and subjects randomly selected. Intra- oral examination was done visually and results were recorded on specially designed clinical examination forms. RESULTS The mean number of missing teeth in the population was 1.60. Among those with missing teeth, the mean number of missing teeth was 3.35. The most commonly missing teeth were lower molars followed by upper molars. No record of complete edentulousness in both jaws was encountered. Dental caries was the commonest cause of tooth loss (52.6%), followed by periodontal disease (27.6%). Extractions, as a form of traditional practice, accounted for 12.3% of total tooth loss. Orthodontic treatment and trauma accounted for 2.2% and 2.0% respectively of total tooth loss. The upper and lower posteriors were the commonest teeth lost due to dental caries and periodontal disease. Teeth lost due to trauma were mostly upper anteriors, whereas those extracted due to traditional practices were exclusively lower anteriors. CONCLUSION The findings of this study show that the commonly lost teeth are molars and the principal cause of tooth loss is dental caries followed by periodontal disease. Overall, very few extractions had been done for orthodontic reasons.
Satellite-Based Method for Estimating the Spatial Distribution of Crop Evapotranspiration: Sensitivity to the Priestley-Taylor Coefficient

This work discusses an operational method for actual evapotranspiration (ET) retrieval from remote sensing, considering a minimum quantity of ancillary data. The method consists in a graphical approach based on the Priestley-Taylor (PT) equation, where the dry soil and non-limiting water conditions are defined by land surface temperature (LST) and vegetation index (VI) space, both retrieved from remote sensing. Using ET tower flux measurements and Landsat 5 TM images of an irrigation scheme in southeast Spain, a sensitivity analysis of ET spatial distribution was performed for the period 2009–2011 with respect to: (i) the shape (trapezoidal or rectangular) of the LST-VI space; and (ii) the value of the PT coefficient, α. The results from ground truth validation were satisfactory, both shapes providing similar performances in estimating ET, with root mean square error ~30 W/m2 and relative difference ~10% with respect to tower-based measurements. Importantly, the best fit with ground data was found for α close to 1, a somewhat different value from the commonly used value of 1.27, indicating that substantial error might arise when using the latter value. Overall, our study underlines the importance of a more precise knowledge of the actual value of α coefficient when using ET retrieval methods based on the LST-VI space.
c-ETS1 Facilitates G1/S-phase Transition by Up-regulating Cyclin E and CDK2 Genes and Cooperates with Hepatitis B Virus X Protein for Their Deregulation*

Recent studies on the molecular mechanisms responsible for cell cycle deregulation in cancer have puzzled out the role of oncogenes in mediating unscheduled cellular proliferation. This is reminiscence of their activity as proto-oncogenes that drives scheduled cell cycle progression under physiological conditions. Working on the cell cycle regulatory activity of proto-oncogene, we observed that c-ETS1 transcriptionally up-regulated both cyclin E and CDK2 genes, the master regulators of G1/S-phase transition. The process was mediated by kinetic coherence of c-ETS1 expression and its recruitment to both promoters during G1/S-phase transition. Furthermore, enforced expression of c-ETS1 helped G0-arrested cells to progress into G1/S-phases apparently due to the activation of cyclin E/CDK2 genes. Physiological induction of c-ETS1 by EGF showed the remodeling of mononucleosomes bound to the c-ETS1 binding site on both promoters during their activation. The exchange of HDAC1 with histone acetyltransferase-p300 was contemporaneous to the chromatin remodeling with consequent increase in histone H3K9 acetylation. Furthermore, the ATP-dependent chromatin remodeler hBRM1 recruitment was also associated with nucleosome remodeling and promoter occupancy of phospho-Ser5 RNA polymerase II. Intriguingly, the activity of the HBx viral oncoprotein was dependent on c-ETS1 in a hepatotropic manner, which led to the activation of cyclin E/CDK2 genes. Thus, cyclin E and CDK2 genes are key physiological effectors of the c-ETS1 proto-oncogene. Furthermore, c-ETS1 is indispensable for the hepatotropic action of HBx in cell cycle deregulation.
Gender Inequality and Marketisation Hypothesis in Sub-Saharan Africa

The marketisation hypothesis states that the growth of the services sector reduces gender inequality. Women have a comparative advantage in service jobs and consequently benefit more than men as the services sector grows. In recent years, the African service sector has grown considerably, however, gender inequality on the continent is still relatively high. Using a new dataset on gender inequality and panel data analysis, we study the relationship between service sector shares and gender inequality in 31 sub-Saharan African countries during the 1990-2014 period. Consistent with predictions of the hypothesis, services sector shares significantly reduce gender inequality and the results are robust after the inclusion of a wide range of controls. However, we find that this relationship is non-linear, suggesting that the size of the services sector reaches a threshold before we observe improvements in gender inequality.
The Fix Is In: Properly Backing Out Backfill Bias

Researchers have long known about backfill bias in hedge fund databases. The most common treatments include either retaining all backfilled returns or truncating a fixed number of returns from each return series. However, we show that truncation largely preserves backfilled returns and document that either of these backfill treatments can lead to biased empirical findings, including cross-sectional results. Thus, our findings show that the best practice for empirical tests is to remove returns prior to the listing date. Because most databases do not have listing dates, we propose a novel method to infer unavailable listing dates. Received August 19, 2018; editorial decision December 4, 2018 by Editor Wei Jiang.
Localization of the herpes simplex virus type 1 65-kilodalton DNA-binding protein and DNA polymerase in the presence and absence of viral DNA synthesis

Using indirect immunofluorescence, well-characterized monoclonal and polyclonal antibodies, and temperature-sensitive (ts) mutants of herpes simplex virus type 1, we demonstrated that the 65-kilodalton DNA-binding protein (65KDBP), the major DNA-binding protein (infected cell polypeptide 8 [ICP8]), and the viral DNA polymerase (Pol) colocalize to replication compartments in the nuclei of infected cells under conditions which permit viral DNA synthesis. When viral DNA synthesis was blocked by incubation of the wild-type virus with phosphonoacetic acid, the 65KDBP, Pol, and ICP8 failed to localize to replication compartments. Instead, ICP8 accumulated nearly exclusively to prereplication sites, while the 65KDBP was only diffusely localized within the nuclei. Although some of the Pol accumulated in prereplication sites occupied by ICP8 in the presence of phosphonoacetic acid, a significant amount of Pol also was distributed throughout the nuclei. Examination by double-labeling immunofluorescence of DNA- ts mutant virus-infected cells revealed that the 65KDBP also did not colocalize with ICP8 to prereplication sites at temperatures nonpermissive for virus replication. These results are in disagreement with the hypothesis that ICP8 is the major organizational protein responsible for attracting other replication protein to prereplication sites in preparation for viral DNA synthesis (A. de Bruyn Kops and D. M. Knipe, Cell 55:857-868, 1988), and they suggest that other viral proteins, perhaps in addition to ICP8, or replication fork progression per se are required to organize the 65KDBP.
The European Union–West Africa Economic Partnership Agreement: Small impact and new questions

ABSTRACT Despite recent modifications, the Economic Partnership Agreement (EPA) between the European Union (EU) and West African (WA) countries is still being criticized for its potential detrimental effects on WA countries. This paper provides updated evidence on the impact of the EPA on these countries. A dynamic multi-country, multi-sector computable general equilibrium trade model with modeling of the dual–dual economy and with a consistent tariff aggregator is used to simulate a series of new scenarios that include updated information on the agreement. We also go beyond estimating macro-level economic effects to analyze the impacts on poverty. The policy simulation results show that the implementation of the EPA between the EU and WA countries would have marginal but positive impacts on Burkina Faso and Côte d'Ivoire and negative impacts on Benin, Ghana, Nigeria, Senegal, and Togo. The impact on poverty indicators in Ghana and Nigeria would be marginal. From the perspective of WA countries, this study supports the view that recent EU concessions are not sufficient and that domestic fiscal reforms are needed in WA countries themselves.
Non-Rayleigh Distributions in Underwater Acoustic Reverberation in a Patchy Environment

In this communication, two main causes for the probability distribution function (pdf) of reverberation amplitude to deviate from the Rayleigh model are identified: (1) sonar configuration and (2) environmental variability. If the total environment may be considered as a patchwork of local environments that are resolvable by the sonar system, but not reliably distinguishable due to positional inaccuracies and overlap in the range of reverberation amplitude values, then the resulting ensemble may have a pdf that is a mixture of the pdfs of the local components. The number of components in a mixture of Rayleigh models is examined, using the measurements and results of Abraham and Lyons [J. Acoust. Soc. Amer. , vol. 106, pp. 1307-1315, 1999]. The patchiness of the environment determines the number of components and their proportions in the mixture, while the sonar configuration determines the kernel of the pdf. Finally, the issue of stationarity is discussed as it applies to a patchy environment. It is concluded that although the reverberation from a patchy environment is, strictly speaking, nonstationary, the perception of stationarity may be achieved if the components in the mixture recur with some regularity, and if the sampling window is wide enough in space and/or time to include a sufficient number of recurrences of all components.
Coping among the caregivers of patients with schizophrenia

Coping is understood as the process of managing external or internal demands that are considered as taxing or exceeding the resources of the person. There is no formal classification of coping strategies, and these are understood as adaptive versus maladaptive and problem focuses versus emotion-focused. Understanding the commonly used coping strategies in a particular group of subjects can provide valuable insights for designing interventions to reduce the stress. In this review, we look at the literature which is available with regards to the coping strategies used by the caregivers of patients with schizophrenia. Findings suggest that caregivers of patients with schizophrenia use mixed type of coping mechanisms to deal with the stress of caregiving. The coping strategies are shown to have association with variables such as caregiver burden, caregiving experience, expressed emotions, social support, psychological morbidity in the caregivers, quality of life of caregivers and psychopathology in patients. One of the major limitations of the literature is that there is a lot of variability in the assessment instruments used across different studies to assess coping.
Axonal connections of a forebrain nucleus involved with vocal learning in zebra finches

Connections of a telencephalic vocal‐control nucleus, the lateral magnocellular nucleus of the anterior neostriatum (lMAN), were studied in adult male zebra finches. Anterograde transport of horseradish peroxidase (alone or conjugated to wheat germ agglutinin) revealed that neurons in lMAN project to another forebrain song‐control nucleus, the robust nucleus of the archistriatum (RA). RA is known to project onto the hypoglossal motor neurons that innervate the vocal organ. Retrograde transport of HRP from lMAN labeled a large thalamic nucleus, the medial portion of the dorsolateral nucleus of the thalamus (DLM). DLM in turn receives input from another nucleus of the song‐control system, area X of the parolfactory lobe. We confirmed results of previous studies showing that area X receives a projection from the ventral area of Tsai (AVT) in the midbrain. In addition, we replicated results of previous experiments with canaries showing that the song‐control nucleus HVc (caudal nucleus of the ventral hyperstriatum) receives input from three sources: the medial magnocellular nucleus of the anterior neostriatum (mMAN), the interfacial nucleus (NIf), and the uvae‐form nucleus (Uva) of the thalamus. HVc neurons project to area X and to RA. In summary, there is a path from AVT in the midbrain, to area X, to DLM, and then to lMAN; HVc projects to X and hence indirectly to lMAN. We do not yet know the afferent connections of AVT. Thus, lMAN receives indirect input from a variety of other sources, including other regions known to be involved with vocal control.
Air—water exchange of polycyclic aromatic hydrocarbons in the New York—New Jersey, USA, Harbor Estuary

Polycyclic aromatic hydrocarbons (PAHs, n = 36) were measured in the gas and particle phases in the atmosphere and the dissolved and particle phases in the waters of the New York—New Jersey Harbor Estuary, USA, during a weeklong intensive field campaign in July 1998. Mean total (gas + particulate) phenanthrene and pyrene concentrations were 3.3 and 0.33 ng/m3, respectively, over Raritan Bay, and 14 and 1.1 ng/m3, respectively, over New York Harbor. Similar PAH profiles (p values < 0.01) in the atmospheric gas phase and the dissolved phase in water demonstrate the close coupling of the air and water compartments. Air—water exchange fluxes of PAHs estimated using shore‐based air data lead to erroneous flux estimates when compared to those derived using over‐water air samples. The gross absorptive air—water flux dominates atmospheric loadings (wet, dry particle, gas absorption) to the estuary for PAHs of molecular weight < 234 g/mol. Dry particle deposition is increasingly more important for the higher‐molecular‐weight, particle‐bound PAH species. Gross volatilization dominates gross absorption for the majority of PAHs in the New York—New Jersey Harbor Estuary.
Influence of different softstart polymerization techniques on marginal adaptation of Class V restorations.

PURPOSE To investigate the influence of different curing methods used to achieve softstart polymerization on the marginal adaptation of a resin-based composite in Class V restoration. MATERIALS AND METHODS Class V cavities, with the gingival wall located 1 mm below the cemento-enamel junction, were prepared on buccal and lingual surface of 80 extracted premolar teeth. The teeth were randomly divided into 8 groups of 10 teeth. The cavities were restored with a combination of resin-based composite (Z100) and adhesive (Single Bond) in different softstart-polymerization techniques or placement techniques. Softstart-polymerization obtained from either softstart mode (Elipar Highlight) or the modified methods using standard curing unit (Spectrum 900 and XL3000), bulk or incremental filling techniques were also used. After thermocycling between 5 degrees C and 55 degrees C for 500 cycles, the specimens were immersed in 2% methylene blue dye at 37 degrees C for 6 hours. Longitudinal sections of the specimens were scored for marginal dye penetration under the microscope. Kruskal-Wallis and Mann-Whitney tests were used for statistical analysis. RESULTS There was no statistically significant difference of dye penetration among techniques at enamel or dentin margins (P > 0.05). Dye penetration observed at dentin margins was significantly higher than that observed at enamel margins (P < 0.05) except for the group restored with a combination of incremental technique and softstart-polymerization using Spectrum curing unit. There was no statistically significant difference of microleakage between buccal and lingual cavities at enamel or dentin margins (P > 0.05).
Transfer of very low density lipoprotein-associated phospholipids to activated human platelets Published, JLR Papers in Press, November 17, 2005.

LDL-associated phospholipids (PLs) may be transferred into platelets. In this work, we characterized the role of VLDLs as PL donors. VLDL transferred radiolabeled PLs to platelets in a temperature- and concentration-dependent manner. LPL stimulated this process through its action on VLDL lipolysis, because it was abolished by tetrahydrolipstatin. LPL also stimulated the platelet production of thromboxane B2 (TXB2). Both LPL actions were inhibited in the presence of fatty acid-free albumin, suggesting that they were attributable to fatty acids generated during VLDL lipolysis. To study the relationship between PL transfers and platelet activation, we performed incubations in the presence of HDL, a physiological acceptor of PL released from VLDL. HDL antagonized the transfer of PL from VLDL to platelets but had no effect on the production of TXB2, suggesting that PL transfers were driven by platelet activation. Confirming this idea, thrombin stimulated both the production of TXB2 and the transfers of PL. In conclusion, VLDL can transfer PL to platelets. These transfers are stimulated by LPL and thrombin through their action on platelet activation. They might be enhanced in pathologies characterized by increased VLDL concentrations.
Simulation of LSPR Sensor Based on Exposed-Core Grapefruit Fiber With a Silver Nanoshell

A localized surface plasmon resonance (LSPR) sensor based on exposed-core grapefruit fiber (EC-GF) with a silver nanoshell (SNS) is presented. The SNS, composed of a dielectric core coated with a thin silver layer, is placed at the exposed section of the EC-GF as the sensing channel to avoid the metal coating, and then deposited with the analyte to avert the liquid filling. Two orthogonal polarized resonance peaks (x-polarized and y-polarized) can be observed due to the birefringence and each polarization exhibits multipolar plasmon resonances, which can realize the cross reference. Due to the good features of the SNS, the position of the LSPR band can be tuned in a broad range, from 2100 to 4020 nm, making the proposed sensor of great importance for biosensing. An extremely high sensitivity 7903.03 nm/RIU is obtained in the sensing range of 1.33–1.42, almost twice as high as the same type works. The influence of the SNS structure on the sensor's performance is also investigated numerically.
Colony Development and Reproductive Success of Bumblebees in an Urban Gradient

Approximately 35% of all crop production is dependent on animal-mediated pollination. Many wild bee species are declining rapidly across North America and Europe, a potential consequence of land-use change driven by agricultural intensification and urbanization. In this study we assessed the impact of urbanization on the reproductive success and population growth rate of bumblebees in an urbanization gradient. We placed experimental nests in ten sites; all except one were community gardens, ranging from a 0–99% degree of urbanization. Reproductive success and colony size were positively correlated with cumulative weight gain of the nests (p 0.05). Growth rate was strongly negatively affected by the abundance of wax moth larvae (p < 0.05) and positively correlated with parasite diversity (p < 0.05) and the number of foragers entering the nest (p < 0.01). With this study we show that not only bottom-up but also top-down effects are equally important for pollinator population dynamics.
Increased Number of Fetal Nucleated Red Blood Cells in the Placentas of Term or Near-Term Stillborn and Neonates Correlates with the Presence of Diffuse Intradural Hemorrhage in the Perinatal Period

Release of nucleated red blood cells (nRBCs) into the peripheral blood occurs in stillbirths/neonates with a probable hypoxic mode of death and antenatal stress. We correlated the number of nRBCs in the placenta with the occurrence of intradural (IDH) and subdural hemorrhage (SDH) and the potential link with fetal hypoxia. Two groups of 22 cases each of nonmacerated term or near-term (≥36 weeks of gestational age) stillborn or newborns dying in the 1st day of life were studied. One group had IDH (with or without SDH) and the other did not have IDH or SDH. In each case, the number of nRBCs was determined in 10 consecutive placental fields at ×40. Data were analyzed with Fisher exact test, receiver operating characteristic (ROC) curve analysis, and logistic regression. There was a significant association between the diffuse IDH and increased number of nRBCs (Fisher exact test P = 0.0165). An ROC curve analysis showed that the cut-off number of nRBCs with the highest accuracy was 2.15 nRBCs/high-power field, with 79% sensitivity and 67% specificity. The presence of diffuse IDH was associated with SDH (Fisher exact test, P = 0.002). The absence of hypoxic brain change was associated with the absence of diffuse IDH (odds ratio 0.308; P = 0.039). We established a significant correlation between the release of nRBCs into the placental circulation and the occurrence of diffuse IDH and between diffuse IDH and the presence of SDH.