Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk of Lymphoma in Patients With Inflammatory Bowel Disease Treated With Anti-tumour Necrosis Factor Alpha Agents: A Systematic Review and Meta-analysis

Background and Aims The association between anti-tumor necrosis factor alpha agents and the risk of lymphoma in patients with inflammatory bowel disease has already been sufficiently reported. However, the results of these studies are inconsistent. Hence, this analysis was conducted to investigate whether anti-tumor necrosis factor alpha agents can increase the risk of lymphoma in inflammatory bowel disease patients. Methods MEDLINE, EMBASE and the Cochrane Library were searched to identify relevant studies which evaluated the risk of lymphoma in inflammatory bowel disease patients treated with anti-tumor necrosis factor alpha agents. A random-effects meta-analysis was performed to calculate the pooled incidence rate ratios as well as risk ratios. Results Twelve studies comprising 285811 participants were included. The result showed that there was no significantly increased risk of lymphoma between anti-tumor necrosis factor alpha agents exposed and anti-tumor necrosis factor alpha agents unexposed groups (random effects: incidence rate ratio [IRR], 1.43 95%CI, 0.91-2.25, p= 0.116; random effects: risk ratio [RR], 0.83 95%CI, 0.47-1.48, p=0.534). However, monotherapy of anti-tumor necrosis factor alpha agents (random effects: IRR=1.65, 95%CI, 1.16-2.35; p=0.006; random effects: RR=1.00, 95%CI, 0.39-2.59; p=0.996) or combination therapy (random effects: IRR=3.36, 95%CI, 2.23-5.05; p< 0.001; random effects: RR=1.90, 95%CI, 0.66-5.44; p=0.233) can significantly increase the risk of lymphoma. Conclusions Exposition of anti-tumor necrosis factor alpha agents in patients with inflammatory bowel disease is not associated with a higher risk of lymphoma. Combination therapy and anti-tumor necrosis factor alpha agents monotherapy can significantly increase the risk of lymphoma in patients with inflammatory bowel disease.
AMR Parsing as Graph Prediction with Latent Alignment

Abstract meaning representations (AMRs) are broad-coverage sentence-level semantic representations. AMRs represent sentences as rooted labeled directed acyclic graphs. AMR parsing is challenging partly due to the lack of annotated alignments between nodes in the graphs and words in the corresponding sentences. We introduce a neural parser which treats alignments as latent variables within a joint probabilistic model of concepts, relations and alignments. As exact inference requires marginalizing over alignments and is infeasible, we use the variational autoencoding framework and a continuous relaxation of the discrete alignments. We show that joint modeling is preferable to using a pipeline of align and parse. The parser achieves the best reported results on the standard benchmark (74.4% on LDC2016E25).
Comparison of Human Milk Fatty Acid Composition of Women From Cambodia and Australia

Background: Human milk is a rich source of omega-3 long-chain polyunsaturated fatty acids, which are postulated to be important for brain development. There is a lack of data on the human milk fatty acid composition of Cambodian women compared with data from Western women. Research Aim: The aim of this study was to determine the human milk fatty acid composition of women living in Cambodia and compare it with that of women living in Australia. Method: Human milk samples from Cambodian (n = 67) and Australian (n = 200) mothers were collected at 3 to 4 months postpartum. Fatty acid composition was analyzed using capillary gas chromatography followed by Folch extraction with chloroform/methanol (2:1 v/v), and fat content was measured gravimetrically. Result: Compared with Australian participants, human milk from Cambodian participants contained a significantly lower level of total fat (2.90 vs. 3.45 g/dL, p = .028), lower percentages of linoleic acid (9.30% vs. 10.66%, p < .0001) and α-linolenic acid (0.42% vs. 0.95%, p < .0001), but higher percentages of arachidonic acid (0.68% vs. 0.38%, p < .0001) and docosahexaenoic acid (0.40% vs. 0.23%, p < .0001). Conclusion: Differences in human milk fatty acid composition between Cambodian and Australian participants may be explained by differences in the dietary patterns between the two populations.
The energy and carbon footprint of the global ICT and E&M sectors 2010 - 2015

This article presents estimations of the energy and carbon footprint of the Information and Communication Technology (ICT) and Entertainment & Media (E&M) sectors globally for 2010–2015 including a forecast to 2020. It builds on three previous global studies (2007, 2011, and 2018) and a Swedish study (2015) by the same authors. The study is based on an extensive dataset which combines primary and secondary data for operational (use stage) energy consumption and life cycle greenhouse gas emissions (CO2e) for the included sub-sectors, including energy and carbon footprint data from about 100 of the major global manufacturers, operators, and ICT and E&M service providers. The data set also includes sales statistics and forecasts for equipment to estimate product volumes in addition to published LCA studies and primary manufacturing data to estimate the embodied carbon footprint of products. The result shows that the ICT and E&M sectors have turned their previously growing footprints into shrinking ones despite a continuous increase in subscriptions and data traffic. Furthermore, the results of this study are also indicating that these footprints are significantly smaller than previously forecasted.
Return Level Estimation of Extreme Rainfall over the Iberian Peninsula: Comparison of Methods

Different ways to estimate future return levels (RLs) for extreme rainfall, based on extreme value theory (EVT), are described and applied to the Iberian Peninsula (IP). The study was done for an ensemble of high quality rainfall time series observed in the IP during the period 1961–2010. Two approaches, peaks-over-threshold (POT) and block maxima (BM) with the generalized extreme value (GEV) distribution, were compared in order to identify which is the more appropriate for the estimation of RLs. For the first approach, which identifies trends in the parameters of the asymptotic distributions of extremes, both all-days and rainy-days-only datasets were considered because a major fraction of values of daily rainfall over the IP is zero. For the second approach, rainy-days-only data were considered showing how the mean, variance and number of rainy days evolve. The 20-year RLs expected for 2020 were estimated using these methods for three seasons: autumn, spring and winter. The GEV is less reliable than the POT because fixed blocks lead to the selection of non-extreme values. Future RLs obtained with the POT are greater than those estimated with the GEV, mainly because some gauges show significant positive trends for the number of rainy days. Autumn, rather than winter, is currently the season with the heaviest rainfall for some regions.
Prevalence and Intensity of Helminth Parasites of African Catfish Clarias gariepinus in Lake Manzala, Egypt

The African catfish, Clarias gariepinus, is generally considered to be one of the most important tropical catfish species for aquaculture purposes. Parasitological investigation was performed in two hundred naturally collected fish samples during the period of February to December 2014. The prevalence of gastrointestinal helminth parasites infecting C. gariepinus was investigated. A total of 249 helminth parasites belonging to four genera were recovered from 130 (65%) examined fish samples. They were digenea Orientocreadium batrachoides, cestode Polyonchobothrium clariae, and nematode Procamallanus laevionchus and Camallanus polypteri. Majority of the recorded parasites were found in the intestine. Female fish samples had higher prevalence rate 72 (90%) than males 58 (48.33%), and there was no significant difference (P > 0.05) in infestation rate between the two sexes. The relationship of host size (weight/length) and parasite infection showed that there was no significant difference in the parasitic infection among three classes, although fish of larger sizes had more infections. In addition, this study determines the effect of fish age on the prevalence and intensity of gastrointestinal parasites.
Postnatal development of cholinergic input to the thalamic reticular nucleus of the mouse

The thalamic reticular nucleus (TRN), a shell‐like structure comprised of GABAergic neurons, gates signal transmission between thalamus and cortex. While TRN is innervated by axon collaterals of thalamocortical and corticothalamic neurons, other ascending projections modulate activity during different behavioral states such as attention, arousal, and sleep‐wake cycles. One of the largest arise from cholinergic neurons of the basal forebrain and brainstem. Despite its integral role, little is known about how or when cholinergic innervation and synapse formation occurs. We utilized genetically modified mice, which selectively express fluorescent protein and/or channelrhodopsin‐2 in cholinergic neurons, to visualize and stimulate cholinergic afferents in the developing TRN. Cholinergic innervation of TRN follows a ventral‐to‐dorsal progression, with nonvisual sensory sectors receiving input during week 1, and the visual sector during week 2. By week 3, the density of cholinergic fibers increases throughout TRN and forms a reticular profile. Functional patterns of connectivity between cholinergic fibers and TRN neurons progress in a similar manner, with weak excitatory nicotinic responses appearing in nonvisual sectors near the end of week 1. By week 2, excitatory responses become more prevalent and arise in the visual sector. Between weeks 3–4, inhibitory muscarinic responses emerge, and responses become biphasic, exhibiting a fast excitatory, and a long‐lasting inhibitory component. Overall, the development of cholinergic projections in TRN follows a similar plan as the rest of sensory thalamus, with innervation of nonvisual structures preceding visual ones, and well after the establishment of circuits conveying sensory information from the periphery to the cortex.
Formulation of and numerical studies with the Dutch Atmospheric Large-Eddy Simulation (DALES)

This discussion paper is/has been under review for the journal Geoscientific Model Development (GMD). Please refer to the corresponding final paper in GMD if available. Formulation of and numerical studies with the Dutch Atmospheric Large-Eddy Simulation (DALES) T. Heus, C. C. van Heerwaarden, H. J. J. Jonker, A. Pier Siebesma, S. Axelsen, K. van den Dries, O. Geoffroy, A. F. Moene, D. Pino, S. R. de Roode, and J. Vilà-Guerau de Arellano Royal Netherlands Meteorological Institute, De Bilt, The Netherlands Meteorology and Air Quality Section, Wageningen University, Wageningen, The Netherlands Department of Multi-Scale Physics, Delft University of Technology, Delft, The Netherlands Institute for Marine and Atmospheric Research Utrecht, Utrecht University, Utrecht, The Netherlands Applied Physics Department, Technical University of Catalonia, and Institute for Space Studies of Catalonia (IEEC/CSIC), Barcelona, Spain Max Planck Institute for Meteorology, Bundesstraße 53, 20146 Hamburg, Germany
A Wall Boundary Condition for the Simulation of a Turbulent Non-Newtonian Domestic Slurry in Pipes

The concentration (using a lesser amount of water) of domestic slurry promotes resource recovery (nutrients and biomass) while saving water. This article is aimed at developing numerical methods to support engineering processes such as the design and implementation of sewerage for concentrated domestic slurry. The current industrial standard for computational fluid dynamics-based analyses of turbulent flows is Reynolds-averaged Navier–Stokes (RANS) modelling. This is assisted by the wall function approach proposed by Launder and Spalding, which permits the use of under-refined grids near wall boundaries while simulating a wall-bounded flow. Most RANS models combined with wall functions have been successfully validated for turbulent flows of Newtonian fluids. However, our experiments suggest that concentrated domestic slurry shows a Herschel–Bulkley-type non-Newtonian behaviour. Attempts have been made to derive wall functions and turbulence closures for non-Newtonian fluids; however, the resulting laws or equations are either inconsistent across experiments or lack relevant experimental support. Pertinent to this study, laws or equations reported in literature are restricted to a class of non-Newtonian fluids called power law fluids, which, as compared to Herschel–Bulkley fluids, yield at any amount of applied stress. An equivalent law for Herschel–Bulkley fluids that require a minimum-yield stress to flow is yet to be reported in literature. This article presents a theoretically derived (with necessary approximations) law of the wall for Herschel–Bulkley fluids and implements it in a RANS solver using a specified shear approach. This results in a more accurate prediction of the wall shear stress experienced by a circular pipe with a turbulent Herschel–Bulkley fluid flowing through it. The numerical results are compared against data from our experiments and those reported in literature for a range of Reynolds numbers and rheological parameters that are relevant to the prediction of pressure losses in a sewerage transporting non-Newtonian domestic slurry. Nonetheless, the application of this boundary condition could be extended to areas such as chemical and food engineering, wherein turbulent non-Newtonian flows can be found.
Bacterial Silver Resistance Gained by Cooperative Interspecies Redox Behavior

ABSTRACT Silver has emerged as an important therapeutic option for wound infections in recent years due to its broad-spectrum antimicrobial activity. The silver cation (Ag+), but not the bulk metal (Ag0), is highly toxic for most microorganisms, although resistance due to genetic modification or horizontal gene transfer does occur. Pseudomonas aeruginosa, however, achieves silver resistance by producing the redox-active metabolite pyocyanin that reduces Ag+ to nontoxic Ag0. Pyocyanin also possesses broad-spectrum antimicrobial activity. Many microbial species reduce pyocyanin, which reduces molecular oxygen to antimicrobial hydrogen peroxide. In this study, it was hypothesized that both Ag+ and oxygen would act as competing terminal electron acceptors for pyocyanin, thus acting as a universal microbial protectant from Ag+ while avoiding hydrogen peroxide formation. Escherichia coli and Staphylococcus aureus efficiently reduced pyocyanin and generated hydrogen peroxide, while Ag+ markedly reduced the amount of hydrogen peroxide produced. Although unable to reduce directly Ag+ to Ag0 on their own, E. coli and S. aureus did so when pyocyanin was present, resulting in increased survival when exposed to Ag+. Coincubation experiments with either E. coli or S. aureus with P. aeruginosa demonstrated increased survival for those species to Ag+, but only if pyocyanin was present. These data demonstrate that microorganisms that display no intrinsic silver resistance may survive and proliferate under potentially toxic conditions, provided their environment contains a suitable redox-active metabolite-producing bacterium. Chronic wounds are often polymicrobial in nature, with pyocyanin-producing P. aeruginosa bacteria frequently being present; therefore, redox-based silver resistance may compromise treatment efforts.
Hepatitis B virus (HBV) reactivation—The potential role of direct‐acting agents for hepatitis C virus (HCV)

Hepatitis C virus (HCV) is known to inhibit hepatitis B virus (HBV) replication in patients with HBV/HCV coinfection. Reactivation of HBV in patients treated for HCV with direct‐acting agents (DAAs) has emerged recently as an important clinical consideration. A growing number of case reports and case series support the association between new HCV treatments and HBV reactivation. Yet, very little is known about the specific viral characteristics that facilitate reactivation as functional characterization of the reactivated HBV has been conducted only rarely. This review provides the most recent data on HBV reactivation in the context of DAA initiation and highlights the existing viral genomic data from reactivating viruses. Current functional studies of HBV reactivation are largely limited by the retrospective identification of cases, no standardization of genomic regions that are studied with respect to HBV reactivation, and the lack of inclusion of nonreactivating controls to establish specific viral mutations that are associated with HBV reactivation. Importantly, none of these sequencing studies included cases of HBV reactivation after initiation of DAAs.
Aerobic Oxidation of 5-(Hydroxymethyl)furfural Cyclic Acetal Enables Selective Furan-2,5-dicarboxylic Acid Formation with CeO2 -Supported Gold Catalyst.

The utilization of 5-(hydroxymethyl)furfural (HMF) for the large-scale production of essential chemicals has been largely limited by the formation of solid humin as a byproduct, which prevents the operation of stepwise batch-type and continuous flow-type processes. The reaction of HMF with 1,3-propanediol produces an HMF acetal derivative that exhibits excellent thermal stability. Aerobic oxidation of the HMF acetal with a CeO2 -supported Au catalyst and Na2 CO3 in water gives a 90-95 % yield of furan 2,5-dicarboxylic acid, an increasingly important commodity chemical for the biorenewables industry, from concentrated solutions (10-20 wt %) without humin formation. The six-membered acetal ring suppresses thermal decomposition and self-polymerization of HMF in concentrated solutions. Kinetic studies supported by DFT calculations identify two crucial steps in the reaction mechanism, that is, the partial hydrolysis of the acetal into 5-formyl-2-furan carboxylic acid involving OH- and Lewis acid sites on CeO2 , and subsequent oxidative dehydrogenation of the in situ generated hemiacetal involving Au nanoparticles. These results represent a significant advance over the current state of the art, overcoming an inherent limitation of the oxidation of HMF to an important monomer for biopolymer production.
Specific Binding to Differentially Expressed Human Carcinoembryonic Antigen-Related Cell Adhesion Molecules Determines the Outcome of Neisseria gonorrhoeae Infections along the Female Reproductive Tract

The gonococcal Opa proteins are an antigenically variable family of surface adhesins that bind human carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), CEACAM3, CEACAM5, and/or CEACAM6, cell surface glycoproteins that are differentially expressed on a broad spectrum of human cells and tissues. While they are presumed to be important for infection, the significance of various Opa-CEACAM-mediated cellular interactions in the context of the genital tract has remained unclear. ABSTRACT The gonococcal Opa proteins are an antigenically variable family of surface adhesins that bind human carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), CEACAM3, CEACAM5, and/or CEACAM6, cell surface glycoproteins that are differentially expressed on a broad spectrum of human cells and tissues. While they are presumed to be important for infection, the significance of various Opa-CEACAM-mediated cellular interactions in the context of the genital tract has remained unclear. Here, we observed that CEACAM1 and CEACAM5 are differentially expressed on epithelia lining the upper and lower portions of the human female genital tract, respectively. Using transgenic mouse lines expressing human CEACAMs in a manner that reflects this differential pattern, we considered the impact of Opa-CEACAM interactions during uncomplicated lower genital tract infections versus during pelvic inflammatory disease. Our results demonstrate that Opa-CEACAM5 binding on vaginal epithelia facilitates the long-term colonization of the lower genital tract, while Opa protein binding to CEACAM1 on uterine epithelia enhances gonococcal association and penetration into these tissues. While these Opa-dependent interactions with CEACAM-expressing epithelial surfaces promote infection, Opa binding by neutrophil-expressed CEACAMs counterbalances this by facilitating more effective gonococcal clearance. Furthermore, during uterine infections, CEACAM-dependent tissue invasion aggravates disease pathology by increasing the acute inflammatory response. Together, these findings demonstrate that the outcome of infection is determined by both the cell type-specific expression of human CEACAMs and the CEACAM specificity of the Opa variants expressed, which combine to determine the level of gonococcal association with the genital mucosa versus the extent of CEACAM-dependent inflammation and gonococcal clearance by neutrophils.
Weaning Time in Preterm Infants: An Audit of Italian Primary Care Paediatricians

Introduction: According to the 2016 Italian National Institute of Statistics (Istat) data in Italy, about 6.7% of all newborns are born prematurely. Due to the lack of data on current complementary feeding in preterm infants in Italy, the aim of the survey was to evaluate individual attitudes of primary care paediatricians, concerning the introduction of complementary foods in preterm infants. Methods: An internet-based survey was conducted among primary care paediatricians, working in Italy, regarding (1) timing of the introduction of complementary foods to preterm newborns; (2) type of complementary foods introduced; (3) vitamin D and iron supplementations. Results: A total of 347 primary care Italian paediatricians answered the questionnaire; 44% of responders based the timing of the introduction of solid food exclusively on an infant’s age, 18% on an infant’s neurodevelopmental status and 4% on the body weight; the remaining 34% based the timing on two or more of these aspects. The type of complementary foods did not comply with an evidence-based sequence; 98% of participants promoted vitamin D supplementation and 89% promoted iron supplementation with great diversity in timing and doses. Conclusions: Due to limited evidence, there is a great heterogeneity in the attitudes of primary care paediatricians concerning the introduction of complementary foods to preterm newborns. Further research is needed to provide evidence-based guidelines regarding weaning preterm newborns.
Short-Term Soy Protein Isolate Feeding Prevents Liver Steatosis and Reduces Serum ALT and AST Levels in Obese Female Zucker Rats

Non-alcoholic fatty liver disease is a common liver disorder worldwide and is associated with obesity. We investigated effects of obesity and short-term intake of soy protein with isoflavones (SPI) on body weight change, energy intake, liver steatosis, and serum aspartate aminotransferase (AST), alanine aminotransferase (ALT), and leptin levels. Seventeen lean and seventeen obese (fa/fa) female Zucker rats were randomly assigned to either casein or SPI diet for 8 weeks. Body weight was recorded twice weekly; feed intake was measured weekly. Livers were examined histologically, and serum AST, ALT, and leptin levels were measured. Obese soy-fed (OS) rats gained more weight but had lower liver steatosis than obese casein-fed (OC) rats. Energy intake for OS versus OC rats were only different at weeks 2 and 3. Serum AST and ALT levels were lower in OS versus OC rats. Obesity increased serum leptin levels for both diets. In summary, short-term SPI intake reduced liver steatosis, and the only time points at which the mean energy intakes of OS and OC rats differed were at weeks 2 and 3, where OS rats had a higher mean energy intake, which may have accounted for the increased body weight in OS rats.