Miracle-dz/UniFAR-FTUs huggingface dataset:
SCIAMACHY stratospheric aerosol extinction profile retrieval using the OMPS/LP algorithm

Abstract. The Ozone Mapper and Profiler Suite, Limp Profiler (OMPS/LP) algorithm is used to retrieve ozone concentration and aerosol extinction profiles using a series of 120 SCIAMACHY limb measurements collocated with SAGE II solar occultation events. The primary goal of the study is to ascertain the capability of the OMPS/LP retrieval algorithm to accurately retrieve the vertical distribution of stratospheric aerosol extinction coefficient so as to better account for aerosol effects in the ozone profiling retrieval process. Using simulated radiances, we show that the aerosol extinction coefficient can be retrieved from limb scatter measurements within 5% and a standard deviation better than 15%, which is more than sufficient to improve the OMPS/LP ozone products to be used as Environmental Data Records. We also illustrate the ability of SCIAMACHY limb measurements to retrieve stratospheric aerosol extinction profiles with accuracy comparable to other instruments. The retrieved aerosol extinction profiles agree with collocated SAGE II measurements on average to within 25%, with a standard deviation of 35%.
Brief communication: Y-chromosome haplotypes in Egypt.

We analyzed Y-chromosome haplotypes in the Nile River Valley in Egypt in 274 unrelated males, using the p49a,f TaqI polymorphism. These individuals were born in three regions along the river: in Alexandria (the Delta and Lower Egypt), in Upper Egypt, and in Lower Nubia. Fifteen different p49a,f TaqI haplotypes are present in Egypt, the three most common being haplotype V (39.4%), haplotype XI (18.9%), and haplotype IV (13.9%). Haplotype V is a characteristic Arab haplotype, with a northern geographic distribution in Egypt in the Nile River Valley. Haplotype IV, characteristic of sub-Saharan populations, shows a southern geographic distribution in Egypt.
Salivary Biomarkers in Caries Affected and Caries Free Children

1 Department of Community Dentistry, Faculty of Dentistry, Mansoura University, Egypt. 2 Department of Preventive Dentistry, Faculty of Dentistry, Umm Al-Qura University, Saudi Arabia. 3 Department of Microbiology and Immunology, Faculty of Medicine, Suez Canal University, Egypt. 4 Department of Basic and Clinical Oral Sciences, Faculty of Dentistry, Umm Al-Qura University, Saudi Arabia. International Journal of Dentistry and Oral Science (IJDOS) ISSN: 2377-8075
Variability and Uncertainty of 18F-FDG PET Imaging Protocols for Assessing Inflammation in Atherosclerosis: Suggestions for Improvement

PET with 18F-FDG shows promise for the evaluation of metabolic activities in atherosclerotic plaques. Although recommendations regarding the acquisition and measurement protocols to be used for 18F-FDG PET imaging of atherosclerosis inflammation have been published, there is no consensus regarding the most appropriate protocols, and the image reconstruction approach has been especially overlooked. Given the small size of the targeted lesions, the reconstruction and measurement methods might strongly affect the results. We determined the differences in results due to the protocol variability and identified means of increasing the measurement reliability. Methods: An extensive literature search was performed to characterize the variability in atherosclerosis imaging and quantification protocols. Highly realistic simulations of atherosclerotic carotid lesions based on real patient data were designed to determine how the acquisition and processing protocol parameters affected the measured values. Results: In 49 articles, we identified 53 different acquisition protocols, 51 reconstruction protocols, and 46 quantification methods to characterize atherosclerotic lesions from 18F-FDG PET images. The most important parameters affecting the measurement accuracy were the number of iterations used for reconstruction and the postfiltering applied to the reconstructed images, which could together make the measured standardized uptake values (SUVs) vary by a factor greater than 3. Image sampling, acquisition duration, and metrics used for the measurements also affected the results to a lesser extent (SUV varying by a factor of 1.3 at most). For an acceptable SUV variability, the lowest bias in SUV was observed using an 8-min acquisition per bed position; ordered-subset expectation maximization reconstruction with at least 120 maximum likelihood expectation maximization equivalent iterations, including a point spread function model using a 1 mm3 voxel size; and no postfiltering. Because of the partial-volume effect, measurement bias remained greater than 60%. The use and limitations of the target–to–blood activity ratio metrics are also presented and discussed. Conclusion: 18F-FDG PET protocol harmonization is needed in atherosclerosis imaging. Optimized protocols can significantly reduce the measurement errors in wall activity estimates, but PET systems with higher spatial resolution and advanced partial-volume corrections will be required to accurately assess plaque inflammation from 18F-FDG PET.
Loss of RUNX1 is associated with aggressive lung adenocarcinomas

The mammalian runt‐related factor 1 (RUNX1) is a master transcription factor that regulates lineage specification of hematopoietic stem cells. RUNX1 translocations result in the development of myeloid leukemias. Recently, RUNX1 has been implicated as a tumor suppressor in other cancers. We postulated RUNX1 expression may be associated with lung adenocarcinoma etiology and/or progression. We evaluated the association of RUNX1 mRNA expression with overall survival data from The Cancer Genome Atlas (TCGA), a publically available database. Compared to high expression levels, Low RUNX1 levels from lung adenocarcinomas were associated with a worse overall survival (Hazard Ratio = 2.014 (1.042–3.730 95% confidence interval), log‐rank p = 0.035) compared to those that expressed high RUNX1 levels. Further immunohistochemical examination of 85 surgical specimens resected at the University of Vermont Medical Center identified that low RUNX1 protein expression was associated with larger tumors (p = 0.038). Gene expression network analysis was performed on the same subset of TCGA cases that demonstrated differential survival by RUNX1 expression. This analysis, which reveals regulatory relationships, showed that reduced RUNX1 levels were closely linked to upregulation of the transcription factor E2F1. To interrogate this relationship, RUNX1 was depleted in a lung cancer cell line that expresses high levels of RUNX1. Loss of RUNX1 resulted in enhanced proliferation, migration, and invasion. RUNX1 depletion also resulted in increased mRNA expression of E2F1 and multiple E2F1 target genes. Our data implicate loss of RUNX1 as driver of lung adenocarcinoma aggression, potentially through deregulation of the E2F1 pathway.
The influence of ENSO on air‐sea interaction in the Atlantic

Observations and model experiments are used to investigate the influence of El Niño/the Southern Oscillation (ENSO) on air‐sea interaction in the north Atlantic, Gulf of Mexico and Caribbean Sea. In one experiment, observed sea surface temperatures (SSTs) in the tropical Pacific are specified as boundary conditions in an atmospheric general circulation model (AGCM), while SSTs over the remainder of the global oceans are simulated by a mixed layer model. The observed warming in the tropical North Atlantic and cooling in the Gulf of Mexico in the winter/spring after ENSO peaks is well simulated by the model. Prior to the basin wide warming, latent heat fluxes generate negative SST anomalies in the Caribbean during August–October. Ocean‐atmosphere coupling outside of the tropical Pacific significantly enhances the warm season atmospheric response to ENSO in the Caribbean region.
The “readers” of unacetylated p53 represent a new class of acidic domain proteins

ABSTRACT Acetylation of non-histone proteins plays important roles in regulating protein functions but the mechanisms of action are poorly understood. Our recent study uncovered a previously unknown mechanism by which C-terminal domain (CTD) acetylation of p53 serves as a “switch” to determine the interaction between a unique group of acidic domain-containing proteins and p53, as well as revealed that acidic domains may act as a novel class of “readers” for unacetylated p53. However, the properties of acidic domain “readers” are not well elucidated yet. Here, we identified that the charge effect between acidic domain “readers” and the p53 CTD is necessary for their interaction. Both the length and the amino acid composition of a given acidic domain contributed to its ability to recognize the p53 CTD. Finally, we summarized the characteristic features of our identified acidic domains, which would distinguish this kind of “readers” from other types of acidic amino acid-containing domains.
A Case of Jejunal Intussusception caused by Burkitt Lymphoma in an Acquired Immunodeficiency Syndrome Patient

Non-Hodgkin's lymphoma of B-cell type is the second most common neoplasm after Kaposi's sarcoma among patients with human immunodeficiency virus infection. Most non-Hodgkin's lymphoma cases that are associated with acquired immunodeficiency syndrome (AIDS) involve extranodal sites, especially the digestive tract and the central nervous system. We report a case of multiple jejunal intussusception caused by Burkitt lymphoma in a 42-year-old AIDS patient. Upper gastrointestinal endoscopy and surgical biopsy were performed and a complete diagnostic study including histological and immunohistochemical analyses showed Burkitt lymphoma.
Loss of SigB in Listeria monocytogenes Strains EGD-e and 10403S Confers Hyperresistance to Hydrogen Peroxide in Stationary Phase under Aerobic Conditions

ABSTRACT SigB is the main stress gene regulator in Listeria monocytogenes affecting the expression of more than 150 genes and thus contributing to multiple-stress resistance. Despite its clear role in most stresses, its role in oxidative stress is uncertain, as results accompanying the loss of sigB range from hyperresistance to hypersensitivity. Previously, these differences have been attributed to strain variation. In this study, we show conclusively that unlike for all other stresses, loss of sigB results in hyperresistance to H2O2 (more than 8 log CFU ml−1 compared to the wild type) in aerobically grown stationary-phase cultures of L. monocytogenes strains 10403S and EGD-e. Furthermore, growth at 30°C resulted in higher resistance to oxidative stress than that at 37°C. Oxidative stress resistance seemed to be higher with higher levels of oxygen. Under anaerobic conditions, the loss of SigB in 10403S did not affect survival against H2O2, while in EGD-e, it resulted in a sensitive phenotype. During exponential phase, minor differences occurred, and this result was expected due to the absence of sigB transcription. Catalase tests were performed under all conditions, and stronger catalase results corresponded well with a higher survival rate, underpinning the important role of catalase in this phenotype. Furthermore, we assessed the catalase activity in protein lysates, which corresponded with the catalase tests and survival. In addition, reverse transcription-PCR (RT-PCR) showed no differences in transcription between the wild type and the ΔsigB mutant in various oxidative stress genes. Further investigation of the molecular mechanism behind this phenotype and its possible consequences for the overall phenotype of L. monocytogenes are under way. IMPORTANCE SigB is the most important stress gene regulator in L. monocytogenes and other Gram-positive bacteria. Its increased expression during stationary phase results in resistance to multiple stresses. However, despite its important role in general stress resistance, its expression is detrimental for the cell in the presence of oxidative stress, as it promotes hypersensitivity against hydrogen peroxide. This peculiar phenotype is an important element of the physiology of L. monocytogenes, and it might help us explain the behavior of this organism in environments where oxidative stress is present.
Defining the Most Appropriate Delivery Mode in Women with Inflammatory Bowel Disease: A Systematic Review

Introduction: High cesarean section (CS) rates are observed in patients with inflammatory bowel disease (IBD), but limited data are available to support this decision. We conducted a comprehensive review to evaluate the most appropriate mode of delivery in women with IBD according to disease phenotype and activity, as well as surgical history. Materials and Methods: We searched MEDLINE (source PubMed) and international conference abstracts, and included all studies that evaluated digestive outcome after delivery in patients with IBD. Results: A total of 41 articles or abstracts were screened, and 18 studies were considered in this review, with sample sizes ranging from 4 to 229 patients and follow-up ranging from 2 months to 7.7 years. Pooled CS rates in patients without Perianal Crohn's disease (PCD), healed PCD or active PCD, were 27%, 43%, and 46%, respectively. Regarding the median rate of new PCD (3.0% [IQR, 1.5–11.5] versus 6.5% [0–19.7]) or PCD recurrence (13.5% [3.2–32.7] versus 45% [0–58]), no increase was observed in patients with vaginal delivery compared to CS, but for patients with an active disease, worsening of symptoms was noted in two-thirds of cases. Episiotomy, perianal tears, and instrumental delivery did not influence the incidence of PCD. In patients with ileal pouch anal anastomosis, uncomplicated vaginal delivery seemed to moderately influence pouch function, with no significant difference in terms of overall continence, daytime, or night-time stool frequency, or incontinence. However, these parameters seemed negatively impacted by a complicated vaginal delivery. Conclusions: New long-term data from well-designed studies are needed, but our review suggests that systematic CS in patients suffering from IBD should probably be limited to women at risk of perineal tears and obstetric injuries, with an active PCD, or with ileal pouch anal anastomosis.
A novel method for diagnosing seasonal to inter-annual surface ocean carbon dynamics from bottle data using neural networks

The ocean's role in modulating the observed 1–7 Pg C yr −1 inter-annual variability in atmospheric CO 2 growth rate is an important, but poorly constrained process due to current spatio-temporal limitations in ocean carbon measurements. Here, we investigate and develop a non-linear empirical approach to predict inorganic CO 2 concentrations (total carbon dioxide ( C T ) and total alkalinity ( A T )) in the global ocean mixed layer from hydrographic properties (temperature, salinity, dissolved oxygen and nutrients). The benefit of this approach is that once the empirical relationship is established, it can be applied to hydrographic datasets that have better spatio-temporal coverage, and therefore provide an additional constraint to diagnose ocean carbon dynamics globally. Previous empirical approaches have employed multiple linear regressions (MLR) and relied on ad hoc geographic and temporal partitioning of carbon data to constrain complex global carbon dynamics in the mixed layer. Synthesizing a new global C T / A T carbon bottle dataset consisting of ~33 000 measurements in the open ocean mixed layer, we develop a neural network based approach to better constrain the non-linear carbon system. The approach classifies features in the global biogeochemical dataset based on their similarity and homogeneity in a self-organizing map (SOM; Kohonen, 1988). After the initial SOM analysis, which includes geographic constraints, we apply a local linear optimizer to the neural network, which considerably enhances the predictive skill of the new approach. We call this new approach SOMLO, or self-organizing multiple linear output. Using independent bottle carbon data, we compare a traditional MLR analysis to our SOMLO approach to capture the spatial C T and A T distributions. We find the SOMLO approach improves predictive skill globally by 19% for C T , with a global capacity to predict C T to within 10.9 μmol kg −1 (9.2 μmol kg −1 for A T ). The non-linear SOMLO approach is particularly powerful in complex but important regions like the Southern Ocean, North Atlantic and equatorial Pacific, where residual standard errors were reduced between 25 and 40% over traditional linear methods. We further test the SOMLO technique using the Bermuda Atlantic time series (BATS) and Hawaiian ocean time series (HOT) datasets, where hydrographic data was capable of explaining 90% of the seasonal cycle and inter-annual variability at those multi-decadal time-series stations.
Effect of Kappa Number Variation on Modified Pulping of Eucalyptus

This work evaluated the impact of brownstock pulp kappa number variations on modified pulping process, oxygen delignification, bleaching, and the physical characteristics on bleached pulp. Wood chips of 6-year-old Eucalyptus grandis x Eucalyptus urophylla from Brazil were used. A modified pulping process was performed with the purpose of achieving two delignification levels on brownstock pulp: kappa 18 and kappa 15. Pulps were submitted to oxygen delignification and elemental chlorine-free (ECF) bleaching to achieve 89.5 ± 0.5% of ISO brightness. Subsequently, pulps were refined in four levels (0, 750, 1500, and 3000 rotations) for physical mechanical tests. Delignification increased after increasing the cooking H factor and alkali charge. As a result, delignification negatively impacted the pulping yields (from 56.1% to 55.0%) and the pulp viscosity (from 1,317 cm³/g to 1,227 cm³/g). Pulps with an initial kappa of 15 presented more efficient oxygen delignification and lower consumption of bleaching reagents. The final viscosity of these pulps were lower (899 cm³/g against 963 cm³/g), however, than that of the pulps with an initial kappa of 18. Furthermore, the pulps with a higher unbleached kappa demanded less refining energy and had lower capillarity. The other physical properties were not influenced by the brownstock delignification level.
omparative proteomic analysis provides new insights into the regulation of arbon metabolism during leaf senescence of rice grown under field conditions

In rice (Oryza sativa), approximately 60–100% of the carbon in mature grains originates from CO2 assimilation during the grain-filling period, with the flag leaf as the most important contributor to the dry weight accumulation in grains. It is therefore important to understand molecular mechanisms of flag leaf senescence. To investigate the regulation of the metabolic network during leaf senescence, changes in protein expression were analyzed using a comparative proteomic approach during senescence of flag leaves in rice grown under field conditions. A total of 170 differentially expressed proteins during senescence of flag leaves were identified by mass spectrometry. Of these, there were 48 down-regulated proteins and 122 up-regulated proteins, corresponding to total 124 unique proteins. These identified proteins are involved hotosynthesis
Lianas Abundance is Positively Related with the Avian Acoustic Community in Tropical Dry Forests

Dry forests are important sources of biodiversity where lianas are highly abundant given their ability to grow during times of drought and as a result of secondary growth processes. Lianas provide food and shelter for fauna such as birds, but there are no studies assessing the influence of liana abundance on birds in dry forests. Here we evaluate the influence of liana abundance on the avian acoustic community in the dry forests of Costa Rica at Santa Rosa National Park. We selected forest sites with different levels of liana abundance and set up automated sound recorders for data collection, analysis and estimation of the avian acoustic community. When the number of lianas increases, the avian acoustic community becomes more complex. Lianas could provide important direct and indirect resources for birds such as structure for shelter, protection, nesting and roosting, and food. The positive relationship that lianas have with birds is particularly important in dry forests where lianas are becoming highly abundant due to the level of forest disturbance and climate change, especially for some bird species that are restricted to this ecosystem. By validating the number of bird species detected in the recordings with the acoustic complexity index, we found that a higher acoustic complexity means higher species richness.
Predictors of low back pain in nursing home workers after implementation of a safe resident handling programme

Objectives Healthcare workers have high rates of low back pain (LBP) related to handling patients. A large chain of nursing homes experienced reduced biomechanical load, compensation claims and costs following implementation of a safe resident handling programme (SRHP). The aim of this study was to examine whether LBP similarly declined and whether it was associated with relevant self-reported occupational exposures or personal health factors. Methods Worker surveys were conducted on multiple occasions beginning with the week of first SRHP introduction (baseline). In each survey, the outcome was LBP during the prior 3 months with at least mild severity during the past week. Robust Poisson multivariable regression models were constructed to examine correlates of LBP cross-sectionally at 2 years (F3) and longitudinally at 5–6 years (F5) post-SRHP implementation among workers also in at least one prior survey. Results LBP prevalence declined minimally between baseline and F3. The prevalence was 37% at F3 and cumulative incidence to F5 was 22%. LBP prevalence at F3 was positively associated with combined physical exposures, psychological job demands and prior back injury, while frequent lift device usage and ‘intense’ aerobic exercise frequency were protective. At F5, the multivariable model included frequent lift usage at F3 (relative risk (RR) 0.39 (0.18 to 0.84)) and F5 work–family imbalance (RR=1.82 (1.12 to 2.98)). Conclusions In this observational study, resident lifting device usage predicted reduced LBP in nursing home workers. Other physical and psychosocial demands of nursing home work also contributed, while frequent intense aerobic exercise appeared to reduce LBP risk.
Diffuse interface modelling of soluble surfactants in two-phase flow

Phase field models for two-phase flow with a surfactant soluble in possibly both fluids are derived from balance equations and an energy inequality so that thermodynamic consistency is guaranteed. Via a formal asymptotic analysis, they are related to sharp interface models. Both cases of dynamic as well as instantaneous adsorption are covered. Flexibility with respect to the choice of bulk and surface free energies allows to realise various isotherms and relations of state between surface tension and surfactant. Some numerical simulations display the effectiveness of the presented approach.
A decade of evolving composites: regression- and meta-analysis

Purpose – The purpose of this paper is to assess the impact of seven variables that emerge from forensic research on facial-composite construction and naming using contemporary police systems: EvoFIT, Feature and Sketch. Design/methodology/approach – The paper involves regression- and meta-analyses on composite-naming data from 23 studies that have followed procedures used by police practitioners for forensic face construction. The corpus for analyses contains 6,464 individual naming responses from 1,069 participants in 41 experimental conditions. Findings – The analyses reveal that composites constructed from the holistic EvoFIT system were over four-times more identifiable than composites from “Feature” (E-FIT and PRO-fit) and Sketch systems; Sketch was somewhat more effective than Feature systems. EvoFIT was more effective when internal features were created before rather than after selecting hair and the other (blurred) external features. Adding questions about the global appearance of the face (as pa.