Miracle-dz/UniFAR-FTUs huggingface dataset:
Winter is coming: Pathogen emergence in seasonal environments

Many infectious diseases exhibit seasonal dynamics driven by periodic fluctuations of the environment. Predicting the risk of pathogen emergence at different points in time is key for the development of effective public health strategies. Here we study the impact of seasonality on the probability of emergence of directly transmitted pathogens under different epidemiological scenarios. We show that when the period of the fluctuation is large relative to the duration of the infection, the probability of emergence varies dramatically with the time at which the pathogen is introduced in the host population. In particular, we identify a new effect of seasonality (the winter is coming effect) where the probability of emergence is vanishingly small even though pathogen transmission is high. We use this theoretical framework to compare the impact of different control strategies on the average probability of emergence. We show that, when pathogen eradication is not attainable, the optimal strategy is to act intensively in a narrow time interval. Interestingly, the optimal control strategy is not always the strategy minimizing R0, the basic reproduction ratio of the pathogen. This theoretical framework is extended to study the probability of emergence of vector borne diseases in seasonal environments and we show how it can be used to improve risk maps of Zika virus emergence.
Grazing management for more resilient mixed livestock farming systems on native grasslands of southern South America

Droughts in southern South America affect grazing systems in many ways. They reduce biomass productivity; decrease livestock feed intake, weight and reproductive performance; increase farmers’ costs; and reduce farm income. It was hypothesized that simple grazing management variables affect the resilience of grazing systems to droughts at the paddock and farm scales. The effects of grazing management on herbage and animal production were assessed at paddock level, and how technological and structural variables relate to the production and economic performances at farm level. Results of a grazing experiment controlling herbage allowance at paddock level showed that resistance of herbage accumulation and animal live weight to drought was significantly higher for paddocks with higher pre-drought herbage allowance than for those managed to low herbage allowance treatments. A strong positive linear relationship was found between pre-drought herbage height and resistance of herbage accumulation rate (p
A review of the threats to adult survival for swallows (Family: Hirundinidae)

ABSTRACT Capsule: For declining migratory birds, including many aerial insectivores, such as swallows, there is evidence that adult survival is a demographic process with strong effects on population trends. Aims: The aim was to identify and quantify the effect of threats affecting adult survival and potentially driving population declines for five well-studied swallow species: Barn Swallow Hirundo rustica, Cliff Swallow Petrochelidon pyrrhonota, Tree Swallow Tachycineta bicolor, Sand Martin Riparia riparia, and Purple Martin Progne subis. Methods: We reviewed the literature to identify the threats to adult survival, quantified the magnitude of the effect and identified whether threats had a direct or indirect effect on survival. Results: We identified habitat change, weather, competition, incidental loss, contaminants, insect availability, disease, and predation as threats to adult survival in swallows, although for many of these threats there was limited information to quantify their impact. However, weather, particularly cold snaps and precipitation, had negative effects on survival for many populations of four species, either directly or indirectly through effects on insect availability. When there was a relationship, weather was associated with a 13–53% decrease in survival. Conclusion: Based on the available research, weather conditions throughout the annual cycle is a key threat to adult survival for several swallow species. However, future research on the threats to these species should consider examining the effect of insect availability and the effect of threats during the non-breeding period on survival. Finally, we suggest that new research should be devoted to understanding the importance of adult survival for declining bird populations.
Resveratrol Improves Boar Sperm Quality via 5′AMP-Activated Protein Kinase Activation during Cryopreservation

Mammalian sperm is highly susceptible to the reactive oxygen species (ROS) stress caused by biochemical and physical modifications during the cryopreservation process. 5′AMP-activated protein kinase (AMPK) is involved in regulating both cell metabolism and cellular redox status. The aim of the present study was to investigate whether the resveratrol protects boar sperm against ROS stress via activation of AMPK during cryopreservation. Boar sperm was diluted with the freezing medium supplemented with resveratrol at different concentrations (0, 25, 50, 75, 100, and 125 μM). It was observed that the addition of 50 μM resveratrol significantly improved the postthaw sperm progressive motility, membrane integrity, acrosome integrity, mitochondrial activity, glutathione (GSH) level, activities of enzymatic antioxidants (glutathione peroxidase (GPx), superoxide dismutase (SOD), and catalase), and the phosphorylation of AMPK. Meanwhile, the lipid peroxidation, ROS levels, and apoptosis of postthaw sperm were reduced in the presence of 50 μM resveratrol. Furthermore, when fresh boar sperm was incubated with the medium in the presence of 50 μM resveratrol and 30 μM Compound C (an AMPK inhibitor), the effects of the resveratrol were partly counteracted by the Compound C. These observations suggest that the resveratrol protects boar sperm via promoting AMPK phosphorylation. In conclusion, the addition of resveratrol to the freezing extenders protects boar sperm against ROS damage via promoting AMPK phosphorylation for decreasing the ROS production and improving the antioxidative defense system of postthaw sperm. These findings provide novel insights into understanding the mechanisms of resveratrol on how to protect boar sperm quality contrary to the ROS production during cryopreservation.
An Epidemiological and Diagnostic Study of Anaplasma ovis Parasite in Native Goats in Anbar Province- Iraq

This study was conducted to investigate the epidemiology of Anaplasma ovis parasite in the native goat of some areas in Anbar province (Ramadi, Fallujah, Khalidiya, Hit and Baghdadi), by collecting 156 blood samples of both sexes andm different ages ranging from one month to nine years for the period from March 2017 to February 2018, the parasite was diagnosed with microscopic examination using Giemsa stain. The results showed a total infection rate 34.6%, the infection rate in females was 38.8% higher than that of males 29.5% and significant differences (p≤ 0.05). The highest rate of infection (40, 39.5%) was observed for the age group 4-5 years and 6-7 years respectively. The highest rate was 75% in April and lowest rate 18.1% in February. The study also included a number of hematological parameters, which showed a decrease in total erythrocyte count (RBC), hemoglobin concentration (Hb), packed cell volume (PCV) in the infected goats.
Species‐specific responses to wetland mitigation among amphibians in the Greater Yellowstone Ecosystem

Habitat loss and degradation are leading causes of biodiversity declines, therefore assessing the capacity of created mitigation wetlands to replace habitat for wildlife has become a management priority. We used single season occupancy models to compare the occurrence of larvae of four species of pond‐breeding amphibians in wetlands created for mitigation, wetlands impacted by road construction, and unimpacted reference wetlands along a highway corridor in the Greater Yellowstone Ecosystem, United States. Created wetlands were shallow and had less aquatic vegetation and surface area than impacted and reference wetlands. Occupancy of barred tiger salamander (Ambystoma mavortium) and boreal chorus frog (Pseudacris maculata) larvae was similar across wetland types, whereas boreal toads (Anaxyrus boreas) occurred more often in created wetlands than reference and impacted wetlands. However, the majority of created wetlands (>80%) dried partially or completely before amphibian metamorphosis occurred in both years of our study, resulting in heavy mortality of larvae and, we suspect, little to no recruitment. Columbia spotted frogs (Rana luteiventris), which require emergent vegetation that is not common in newly created wetlands, occurred commonly in impacted and reference wetlands but were found in only one created wetland. Our results show that shallow created wetlands with little aquatic vegetation may be attractive breeding areas for some amphibians, but may result in high mortality and little recruitment if they fail to hold water for the entire larval period.
Context-Dependent Decision Making in a Premotor Circuit

Cognitive capacities afford contingent associations between sensory information and behavioral responses. We studied this problem using an olfactory delayed match to sample task whereby a sample odor specifies the association between a subsequent test odor and rewarding action. Multi-neuron recordings revealed representations of the sample and test odors in olfactory sensory and association cortex, which were sufficient to identify the test odor as match/non-match. Yet, inactivation of a downstream premotor area (ALM), but not orbitofrontal cortex, confined to the epoch preceding the test odor, led to gross impairment. Olfactory decisions that were not context dependent were unimpaired. Therefore, ALM may not receive the outcome of a match/non-match decision from upstream areas but contextual information—the identity of the sample—to establish the mapping between test odor and action. A novel population of pyramidal neurons in ALM layer 2 may mediate this process.
Bacteriological Monitoring of Inanimate Surfaces and Equipment in Some Referral Hospitals in Assiut City, Egypt

Hospital-acquired infections represent a serious public health problem in all countries. It is clear that monitoring of the hospital environment is an essential element in the control and a part of the policy for preventing nosocomial infections. It allows a better understanding of the microbial ecology for the purpose of conducting preventive and corrective actions. The aims of this work were to determine the percentage of bacterial contamination of environmental samples and to identify potential nosocomial pathogens isolated from environments of seven referral hospitals from 2009 to 2015. By using the swab technique, 12863 samples were collected. Qualitative and quantitative cultures were performed. The organisms were primarily identified by colony morphology, microscopy of Gram stain, and standard biochemical tests. 25.6% of total samples showed contamination (93% was monomicrobial and 7.0% was polymicrobial). The predominant species was coagulase-negative staphylococcus (CNS) (32%), followed by methicillin-resistant S. aureus (MRSA) (26%) and then K. pneumonia (10.6%). The percentage of contamination varied among the covered hospitals and according to the year of monitoring with highly statistically significant difference (p value < 0.001). Direct contact with environmental surfaces or equipment transmits the majority of nosocomial infection. Major nosocomial pathogens have been identified. Hospital managers and healthcare bodies must be aware of the reality of the concept of environmental bacterial tanks and the need for respect of biocleaning procedures and choice of biocleaning tools.
Albumin inhibits the activation of hepatic stellate cells by suppressing TGF-β/Smad3 signaling via IL-1β

Activated hepatic stellate cells (HSCs) play a key role in liver fibrosis and inactivating HSCs has been considered a promising therapeutic approach. We previously showed that albumin and its derivative, retinol binding protein (RBP)-albumin domain III fusion protein (named R-III), inhibit HSC activation. Here, we investigate the mode of action of albumin and R-III. NF-κB in activated HSCs was evenly distributed in the cytoplasm, but albumin expression and R-III treatment (albumin/R-III) induced NF-κB nuclear translocation via retinoic acid (RA) sequestration, resulting in increased expression of interleukin-1β (IL-1β). In an IL-1β dependent manner, albumin/R-III inhibited Smad3 nuclear translocation via TAK1-, JNK-mediated Smad3 linker phosphorylation and decreased expression of Smad3 target genes, such as α-smooth muscle actin and collagen type I. Mutation of the Smad3 linker phosphorylation sites abolished R-III effects on Smad3. In conclusion, our data suggest that the anti-fibrotic effects of albumin/R-III are due to RA sequestration which downregulates RAR-mediated signaling and also TGF-β/Smad3 signaling. This mechanistic elucidation of albumin function in HSCs provides clues to understanding the frequent albumin mutations found in hepatocellular carcinoma.
Diagnosis of malaria in pregnancy: A comparison of microscopy with rapid diagnostic tests

Malaria in pregnancy in Nigeria is a serious life threatening infection to the pregnant mother and the fetus. A study was conducted to test the effectiveness of rapid diagnostic tests in the parasitological diagnosis of malaria in pregnant women in the absence of reliable microscopy facilities. Blood samples of 500 pregnant women were tested for malaria parasite by Giemsa stained smear and Malaria Pf rapid diagnostic test (RDT). Thirty percent of the samples were positive by microscopy while 27% were positive by the RDT. The younger pregnant women (20 to 25 years) and women in the second trimester of pregnancy (13 to 24 weeks) have more malaria prevalence than other age groups. The sensitivity of the Malaria Pf test was 86.7%, the specificity was 98.6%. The positive predictive value was 96.3% and the negative predictive value was 94.5%. In the absence of good quality microscopy facilities, and experienced laboratory personnel, the Malaria Pf test should be employed as a viable alternative to ensure a reliable parasite based diagnosis of malaria in pregnant women for prompt and accurate treatment.
Uncovering the dynamic mechanisms of the Pseudomonas aeruginosa quorum sensing and virulence networks using Boolean modelling

Introduction Pseudomonas aeruginosa is an opportunistic pathogen with an extraordinary metabolic adaptability and a large repertoire of virulence factors that allow it to cause acute and chronic infections. Treatment of P. aeruginosa infections often fail due to its antibiotic resistance mechanisms, thus novel strategies aim at targeting virulence factors instead of growth-related features. However, there is currently not a clear understanding of the dynamic nature inherent to the wiring of its virulence networks. Results In this study, we manually reconstructed the signalling and transcriptional regulatory networks of 12 acute (incl. pyocin and elastase) and 8 chronic virulence factors (incl. biofilm), and the 4 quorum sensing (QS) systems of P. aeruginosa. Using Boolean modelling (BM), we unveiled the important roles that stochasticity and node connectivity play in the networks’ inherent dynamicity and robustness. We showed that both the static interactions, as well as the time when the interactions take place, are important features in the QS network. In addition, we found that the virulence factors of the acute networks are under strict repression, or under an activation that is non-strict or oscillatory, while the chronic networks favour the repression of the virulence factor, with only moderate activation under certain conditions. Conclusion In conclusion, our in silico-modelling framework provided us with a system-level view of the P. aeruginosa virulence and QS networks to gain new insights into the various mechanisms that support its pathogenicity and response to stressors targeting these networks. Thus, we suggest that BM provides an invaluable tool to guide the design of new treatments against P. aeruginosa.
Ultrasound and Microbubble Gene Delivery for Targeting Altered Placental MicroRNAs in Preeclampsia

Ultrasound (US) and microbubble (MB) gene delivery has attracted growing interest as a clinically applicable gene therapy (GT). Though preclinical studies have investigated the system in various tissues, there is limited research in targeting the placenta. This is a potential therapeutic strategy for preeclampsia (PE), which has an underlying genetic basis and ineffective management strategies. Differentially expressed placental microRNAs (miRNAs) in PE may represent suitable targets for GT. Microbubbles (SonoVue) and plasmid (pGL3 or pGL4.13) were administered systemically to CD1 mice, followed by exposure of the heart to US (H14, 1.8 M.I., 1cm focal depth, 2 minutes), using Siemens Acuson Sequoia-512 system and 15L8 probe. Luciferase assays were performed to evaluate gene transfection. Significantly differentially expressed placental miRNAs in PE patients were identified as candidates based on detection by three or more screening studies. Expression of candidate miRNAs was measured by qRT-PCR in PE rat model placentas. In trial 1, low levels of luciferase activity were detected in the heart of treatment mouse 1, 2 and 3. In trial 2, luciferase activity was evident in the atria of treatment mouse 2. In trial 3, higher luciferase activity was detected in the ventricles of the treatment mouse and activity was also detected in the atria. The literature review identified eight candidate miRNAs. MiR-223 (1.46-fold increase) and miR-181a (0.81-fold decrease) were significantly differentially expressed in PE rat model placentas. MiR-223 and -181a may represent targets for US and MB gene delivery. Future studies will apply the US and MB gene delivery protocol for translation to targeting the placenta in our PE rodent model.
Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

Whole-genome resequencing provides information of great relevance for crop genetics, evolution, and breeding. Here, we present the first whole-genome resequencing study using seven eggplant (Solanum melongena) and one wild relative (Solanum incanum) accessions. These eight accessions were selected for displaying a high phenotypic and genetic diversity and for being the founder parents of an eggplant multiparent advanced generation intercrosses population. By resequencing at an average depth of 19.8× and comparing to the high-quality reference genome “67/3” over 10 million high-reliable polymorphisms were discovered, of which over 9 million (84.5%) were single nucleotide polymorphisms and more than 700,000 (6.5%) InDels. However, while for the S. melongena accessions, the variants identified ranged from 0.8 to 1.3 million, over 9 million were detected for the wild S. incanum. This confirms the narrow genetic diversity of the domesticated eggplant and suggests that introgression breeding using wild relatives can efficiently contribute to broadening the genetic basis of this crop. Differences were observed among accessions for the enrichment in genes regulating important biological processes. By analyzing the distribution of the variants, we identified the potential footprints of old introgressions from wild relatives that can help to unravel the unclear domestication and breeding history. The comprehensive annotation of these eight genomes and the information provided in this study represents a landmark in eggplant genomics and allows the development of tools for eggplant genetics and breeding.
Prostate cancer biology & genomics

Prostate Cancer is now the second biggest cause of cancer mortality in the UK. Media coverage has been rising, with some attributing to a rise in the cases diagnosed and treated in the NHS down to the “Fry and Turnbull effect”. Our understanding of prostate cancer has increased tremendously in the past decades, with advances in molecular biology and genomics driving the way to new treatments and diagnostics. This Special Edition of Translational Andrology and Urology 2019: Prostate Cancer Biology and Genomics aims to review the current state of prostate cancer genomics, proteomics, diagnostics and treatment.
High-energy diets for reproductive rabbit does: effect of energy source.

The main energy diets developed and evaluated in recent decades for reproductive rabbit does are reviewed, with the emphasis on the effect of the energy source (animal fat, vegetable oil, and cereal starch) used. During gestation, energy supplementation of diets usually produces a decrease in feed intake due to energy intake regulation, but in some cases females are unable to regulate their feed intake with high-starch diets, leading to excessive energy intake. This overfeeding can cause fattening of does, sometimes related to greater pup mortality at birth. During lactation, reproductive rabbit does clearly increase their energy intake when fed with fat-enriched diets. This energy supplement is mainly utilized to increase their milk energy production (higher milk yield with a higher energy content), and higher litter growth and survival is consequently observed with fat-enriched diets. However, higher milk yield of these does is usually related to a greater negative energy balance and lower fertility values. In lactating does given cereal starch-enriched diets, primiparous rabbit does, whose voluntary intake is physically limited, usually show a higher energy intake, whereas multiparous does even decrease their energy intake. In any case, milk yield and composition of does given starch-enriched diets are not improved and may even worsen, negatively affecting litter performance and survival. However, does fed high-starch diets frequently present better energy balance during lactation as a consequence of their lower milk yield (lower lactation strain). Therefore, the addition of animal fat to the diet seems to improve the utilization of ingested energy for milk production, whereas the inclusion of higher dietary starch content can decrease the negative energy balance that reproductive rabbit does usually experience. The results obtained with vegetable oil-added diets are between those observed for animal fat- and starch-supplemented diets, showing similar milk production and litter performance but with lower body reserve depletion.
Whole digesta properties as influenced by feed processing explain variation in gastrointestinal transit times in pigs

Abstract Physicochemical properties of diets are believed to play a major role in the regulation of digesta transit in the gastrointestinal tract. Starch, being the dominant nutrient in pig diets, strongly influences these properties. We studied transport of digesta solids and liquids through the upper gastrointestinal tract of ninety pigs in a 3 × 3 factorial arrangement. Dietary treatments varied in starch source (barley, maize and high-amylose maize) and form (isolated starch, ground cereal and extruded cereal). Mean retention times (MRT) of digesta solids ranged 129–225 min for the stomach and 86–124 min for the small intestine (SI). The MRT of solids consistently exceeded that of liquids in the stomach, but not in the SI. Solid digesta of pigs fed extruded cereals remained 29–75 min shorter in the stomach compared with pigs fed ground cereals (P < 0·001). Shear stress of whole digesta positively correlated with solid digesta MRT in the stomach (r 0·33, P < 0·001), but not in the SI. The saturation ratio (SR), the actual amount of water in stomach digesta as a fraction of the theoretical maximum held by the digesta matrix, explained more variation in digesta MRT than shear stress. The predictability of SR was hampered by the accumulation of large particles in the stomach. In addition, the water-holding capacity of gelatinised starch leads to a decreased SR of diets, but not of stomach digesta, which was caused by gastric hydrolysis of starch. Both of these phenomena hinder the predictability of gastric retention times based on feed properties.