Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of sleeve gastrectomy on sperm quality and fertility on non-obese diabetes diet model rat

Background In people with diabetes, the effect of sleeve gastrectomy on impaired sperm parameters, hormonal profile and testis tissue remains controversial to some extent. The context and purpose of the study Effects of sleeve gastrectomy on hormonal profile, sperm parameters, and testis tissue in infertile men with type II diabetes mellitus (TIIDM). This study included thirty two TIIDM that were scheduled with and without sleeve gastrectomy. All rats were taken a sperm analysis, a testis tissue and a serum hormone profile before, 8 weeks after surgery. Results There was a significant correlation between weight loss after sleeve gastrectomy and decreased in glucose profile (p < 0.05). As regards the hormonal profile, testosterone improved significantly after 8 weeks following sleeve gastrectomy. There was a significant increase in sperm count (p < 0.05), and improved sperm morphology during the follow-up after sleeve gastrectomy, also showed that significant changes as improved in testis tissue after surgery. Conclusion Sleeve gastrectomy significantly improves testosterone deficiency, testis tissue and sperm count in TIIDM rats. More prospective clinical studies are needed to show how bariatric surgery affects infertility affected by TIIDM patients.
Nucleocapsid condensation drives Ebola viral factory maturation and dispersion

Replication and genome encapsidation of many negative-sense RNA viruses take place in virus-induced membrane-less organelles termed viral factories (VFs). While liquid properties of VFs are believed to control the transition from genome replication to encapsidation, the nucleocapsid assembly, VF maturation and interactions with the cellular environment remain elusive. Here we apply in situ cryo-correlative light and electron tomography to follow nucleocapsid assembly and changes in VF morphology and their liquid properties during Ebola virus infection. We show that Ebola viral nucleocapsids transition from loosely packed helical assemblies in early VFs to condensed cylinders that arrange into highly organized parallel bundles later in infection. Early VFs associate with intermediate filaments and are devoid of other host material, but become progressively accessible to cellular components. Our data suggest that this process is coupled to VF solidification and dispersion, and that changes in liquid properties of VFs promote nucleocapsid transport to budding sites. Highlights - Cryo-ET reveals the molecular architecture of Ebola virus replication compartments - Loosely coiled nucleocapsids transition to condensed cylinders forming bundles - Nucleocapsid condensation drives dispersion of viral factories promoting viral egress - Intermediate filaments associate with and are critical for virus factory formation
Early inflammatory response mediated by Angiotensin II in cardiac arteries of normotensive mice

To verify if a low dose of angiotensin II (Ang II) can induce an inflammatory response in cardiac arteries, even though blood pressure remains at normal values. Were used C57Bl/6J male mice treated with a low dose of Ang II (30ng/kg IP) and AT1R blockers. Blood pressure was recorded after 10, 30, 60min, 2 and 6hours after Saline or Ang II injection. Time curve (30 and 60min, 2, 6, 12, 24, and 48hours after treatment) for expression of inflammatory markers was evaluated in cardiac arteries (TGF-β, IL-1β, IL-6, TNF-α and ICAM-1) by immunohistochemistry and western blot. Serum TNF-α and IL-6 were analyzed by ELISA. Although Ang II did not alter blood pressure, local TGF-α and IL-6 presented an early increase in cardiac arteries. IL-1β and ICAM-1 participated in a late response to Ang II (12 hours). Ang II group showed a systemic increase of IL-6 30 to 60 minutes after treatment. AT1 and AT2 receptor blockers (losartan, 20mg/kg, and PD123.319, 15mg/kg) were given alone or concomitant to Ang II. This combination showed that Ang II increases TGF-β and IL-6 by acting on the AT1 receptor in a fast response. IL-1β regulation by Ang II seems to be mediated by both AT1 and AT2 receptors. The results suggest that, independently of hemodynamic influences, Ang II, acting on AT1R, leads to the expression of inflammatory markers in cardiac vessels. AT2 receptor seems to be involved in the counterbalance of AT1R during modulation of IL-1β production in cardiac arteries.
Single cell RNA-seq reveals protracted germ line X chromosome reactivation dynamics directed by a PRC2 dependent mechanism

Initiating soon after PGC specification, female germ cells undergo reactivation of the silenced X chromosome during genome wide reprogramming. However, the kinetics and dynamics of XCR in vivo have remained poorly understood. To address this here we perform a global appraisal of XCR using high-dimensional techniques. Using F1 B6 v CAST mouse embryos, we perform a detailed assessment, applying single-cell RNA-seq and chromatin profiling on germ cells purified from E10.5 to E16.5. While scRNA-seq profile showed that male and female germ cells are transcriptionally indistinct at E11.5, they are sexually dimorphic by E12.5, diverging further through development to E16.5. With allelic resolution, we show that the reactivating X chromosome is only partly active at E10.5, then reactivates gradually and reaches near parity in output to the constitutively active X chromosome at ∼E16.5 when developing oogonia are meiosis prophase I. Crucially, we show that sexually dimorphic dosage compensation patterns observed in germ cells, occur in tandem with an increase in the allelic proportion from the reactivating X chromosome. While Xist is extinguished from E10.5, the epigenetic memory of earlier XCI in female cells persists much longer, likely from self-sustained PRC2 complex (Ezh2 / Eed / Suz12) function. The reactivating X chromosome is enriched in the epigenetic silencing mark H3K27me3 at E13.5, which is removed by E16.5 permitting gene expression. Our findings link XCR, along with functional regulation of PRC2 in promoting female meiosis.
Mitochondrial One-Carbon Metabolism is Required for TGF-β-Induced Glycine Synthesis and Collagen Protein Production

A hallmark of Idiopathic Pulmonary Fibrosis is the TGF-β-dependent activation of lung fibroblasts, leading to excessive deposition of collagen proteins and progressive scarring. We have previously shown that synthesis of collagen by lung fibroblasts requires de novo synthesis of glycine, the most abundant amino acid in collagen protein. TGF-β upregulates the expression of the enzymes of the de novo serine/glycine synthesis pathway in lung fibroblasts through mTORC1 and ATF4- dependent transcriptional programs. SHMT2, the final enzyme of the de novo serine/glycine synthesis pathway, transfers a one-carbon unit from serine to tetrahydrofolate (THF), producing glycine and 5,10-methylene-THF (meTHF). meTHF is converted back to THF in the mitochondrial one-carbon (1C) pathway through the sequential actions of MTHFD2 (which converts meTHF to 10-formyl-THF), and either MTHFD1L, which produces formate, or ALDH1L2, which produces CO2. It is unknown how the mitochondrial 1C pathway contributes to glycine biosynthesis or collagen protein production in fibroblasts, or fibrosis in vivo. Here, we demonstrate that TGF-β induces the expression of MTHFD2, MTHFD1L, and ALDH1L2 in human lung fibroblasts. MTHFD2 expression was required for TGF-β-induced cellular glycine accumulation and collagen protein production. Combined knockdown of both MTHFD1L and ALDH1L2 also inhibited glycine accumulation and collagen protein production downstream of TGF-β; however knockdown of either protein alone had no inhibitory effect, suggesting that lung fibroblasts can utilize either enzyme to regenerate THF. Pharmacologic inhibition of MTHFD2 recapitulated the effects of MTHFD2 knockdown in lung fibroblasts and ameliorated fibrotic responses after intratracheal bleomycin instillation in vivo. Our results provide insight into the metabolic requirements of lung fibroblasts and provide support for continued development of MTHFD2 inhibitors for the treatment of IPF and other fibrotic diseases.
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type 2 diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.
Astrocyte-to-microglia communication via Sema4B-Plexin-B2 modulates injury-induced reactivity of microglia

After central nervous system injury, a rapid cellular and molecular response is induced. This response can be both beneficial and detrimental to neuronal survival in the first few days and increases the risk for neurodegeneration if persistent. Semaphorin4B (Sema4B), a transmembrane protein primarily expressed by cortical astrocytes, has been shown to play a role in neuronal cell death following injury. Our study shows that after cortical stab wound injury, cytokine expression is attenuated in Sema4B knockout mice and microglia/macrophage reactivity is altered. In vitro, Sema4B enhances the reactivity of microglia following injury, suggesting astrocytic Sema4B functions as a ligand. Moreover, injury-induced microglia reactivity is attenuated in the presence of Sema4B knockout astrocytes compared to heterozygous astrocytes. In vitro, experiments indicate Plexin-B2 is the Sema4B receptor on microglia. Consistent with this, in microglia/macrophage-specific Plexin-B2 knockout mice, similar to Sema4B knockout mice, microglial/macrophage reactivity and neuronal cell death are attenuated after cortical injury. Finally, in Sema4B/Plexin-B2 double heterozygous mice, microglial/macrophage reactivity is also reduced after injury, thus supporting the idea that both Sema4B and Plexin-B2 are part of the same signaling pathway. Taken together, we propose a model in which following injury, astrocytic Sema4B enhances the response of microglia/macrophages via Plexin-B2, leading to increased reactivity. Significance statement In this study, we show that in the brain cortex, Sema4B, a protein mainly expressed by astrocytes, plays a crucial role in enhancing the reactivity of microglia/macrophages via Plexin-B2. These findings reveal new molecular signaling instigated by astrocytes toward microglia/macrophages in the context of central nervous system (CNS) injury, shedding new light on the complex interplay between astrocytes and microglia/macrophages. Taken together, our findings suggest that targeting the Sema4B/Plexin-B2 pathway could be a promising therapeutic approach for reducing microglia reactivity and improving the adaptive response in the context of CNS injury.
Thermal imaging can reveal variation in stay-green functionality of wheat canopies under temperate conditions

Canopy temperature (CT) is often interpreted as representing leaf activity traits such as photosynthetic rates, gas exchange rates, or stomatal conductance. Accordingly, CT measurements may provide a basis for high throughput assessments of the productivity of wheat canopies during early grain filling, which would allow distinguishing functional from dysfunctional stay-green. However, whereas the usefulness of CT as a fast surrogate measure of sustained vigor under soil drying is well established, its potential to quantify leaf activity traits under high-yielding conditions is less clear. To better understand sensitivity limits of CT measurements under high yielding conditions, we generated within-genotype variability in stay-green functionality by means of differential short-term pre-anthesis canopy shading that modified the sink:source balance. We quantified the effects of these modifications on stay-green properties through a combination of gold standard physiological measurements of leaf activity and newly developed methods for organ-level senescence monitoring based on timeseries of high-resolution imagery and deep-learning-based semantic image segmentation. In parallel, we monitored CT by means of a pole-mounted thermal camera that delivered continuous, ultra-high temporal resolution CT data. Our results show that differences in leaf activity stemming from differences in stay-green functionality translate into measurable differences in CT in the absence of major confounding factors. Differences amounted to approximately 0.8°C and 1.5°C for a very high-yielding source-limited genotype, and a medium-yielding sink-limited genotype, respectively. The gradual nature of the effects of shading on CT during the stay-green phase underscore the importance of a high measurement frequency and a time-integrated analysis of CT, whilst modest effect sizes confirm the importance of restricting screenings to a limited range of morphological and phenological diversity.
Implementing of RCPs Scenarios for the Prediction of Evapotranspiration in Egypt

This study investigates the projected changes in evapotranspiration in Egypt, with a focus on the Delta, Middle and Upper Egypt regions. Maximum and minimum air temperature were statistically downscaled and compared with current climate (defined as the period 1971–2000). FAO-56 Penman-Monteith equation was used to estimate ETo using climatic data Evapotranspiration is estimated based on the predicted maximum and minimum temperature under four Representative Concentration Pathway (RCP) scenarios (RCP2.6 – RCP4.5 – RCP6.0 and RCP8.5) during three time series (2011-2040, 2041-2070 and 2071-2100) Other climate factors i.e., radiation, relative humidity and wind speed, used from current climate data. The obtained results revealed that maximum and minimum air temperatures increased under all RCPs scenarios compared to current data. Moreover, the RCP8.5 had the highest maximum and minimum air temperature compared to the other RCPs scenarios. It was found that for all future periods the annual evapotranspiration will increase for all agro-meteorological zones by uneven values. Results also revealed that ETo increased significantly in different tested time series compared to current ETo values. The values of ETo for the 2071-2100 period were higher than that for the 2011-2040 period or mid-term (20412070) period. The highest ETo values was predicted in this study by RCP8.5 during the 2071 – 2100 time series in the Upper Egypt region. Original Research Article Abdrabbo; IJPSS, 6(1): 50-63, 2015; Article no.IJPSS. 2015.096 51
Discovery of the FeO orange bands in the terrestrial night airglow spectrum obtained with OSIRIS on the Odin spacecraft

An unidentified pseudo‐continuum in the 600 nm region is observed in the upper mesosphere with the limb‐scanning OSIRIS imaging spectrograph on‐board the Odin spacecraft. Averages of low latitude spectra at a series of tangent limb altitudes from 75 to 105 km are assembled and matched with synthetic spectra of the known night airglow emission band systems to isolate the underlying airglow continuum. The upper limit of the NO + O → NO2* air afterglow continuum component in the observed 600 nm pseudo‐continuum is estimated to be 5% at low latitudes. The spectral profile of the unidentified 600 nm residual airglow continuum is very similar to published laboratory measurements of the ‘orange bands’ of FeO. The volume emission rate altitude profile of this 600 nm airglow continuum, derived from averaged limb radiance profiles, is very similar in shape and in altitude to the concurrently observed Na vertical profile suggesting related source mechanisms.
Computed Tomography Dose Level in Selected Five Principal Hospitals in Ethiopia

BACKGROUND: X-ray Computed Tomography dose levels have been varying among modalities and scanning body regions due to the absence of incessant routine follow-up. Thus, the study aimed to compute the dose index discrepancies in Ethiopia for the most recurring scan protocols (head, chest, abdomen, and pelvis). METHODS: A purposive sampling method was employed to select the hospitals due to the rare existence of functional CT scanners in Ethiopia. From the selected hospitals, a total of 1,385 (249 heads, 804 chests, 132 abdomens, and 200 pelvis) were collected in terms of standard dose metric values in the period of December 2019-March 2020. Patients’ DLP was computed into mean value using IBM SPSS Statistics 20 software. From the mean DLP, we can compute the effective dose. RESULTS: Patients’ dose level disparity was observed in this study though it is below the ICRP standard level for all body regions except for pelvis DLP (593.37 mGy-cm) at Black Lion. The dose level for the head and chest are computed within the recommended level at all hospitals. Effective doses for the pelvis at four hospitals (Teklehaimanot, Black Lion, ALERT, Paul’s, and Ayder hospitals) were computed as 6.45, 8.90, 5.08, 6.54, and 6.84 mSv respectively, and the effective doses for abdomen at Ayder Hospital was obtained to be 8.90 mSv, which is above the recommended value. CONCLUSION: X-ray CT scanners are somewhat properly functioning although some sort of justification and optimization for pelvis and abdomen examinations are strongly recommended to implement as low as reasonably achievable principle.
Design, Synthesis and Bioactivity Evaluation of Heterocycle-Containing Mono- and Bisphosphonic Acid Compounds

Fosmidomycin (FOS) is a naturally occurring compound active against the 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) enzyme in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, and using it as a template for lead structure design is an effective strategy to develop new active compounds. In this work, by replacing the hydroxamate unit of FOS with pyrazole, isoxazole and the related heterocycles that also have metal ion binding affinity, while retaining the monophosphonic acid in FOS or replacing it with a bisphosphonic acid group, heterocycle-containing mono- and bisphosphonic acid compounds as FOS analogs were designed. The key steps involved in the facile synthesis of these FOS analogs included the Michael addition of diethyl vinylphosphonate or tetraethyl vinylidenebisphosphonate to β-dicarbonyl compounds and the subsequent cyclic condensation with hydrazine or hydroxylamine. Two additional isoxazolinone-bearing FOS analogs were synthesized via the Michaelis–Becker reaction with diethyl phosphite as a key step. The bioactivity evaluation on model plants demonstrated that several compounds have better herbicidal activities compared to FOS, with the most active compound showing a 3.7-fold inhibitory activity on Arabidopsis thaliana, while on the roots and stalks of Brassica napus L. and Echinochloa crus-galli in a pre-emergence inhibitory activity test, the activities of this compound were found to be 3.2- and 14.3-fold and 5.4- and 9.4-fold, respectively, and in a post-emergency activity test on Amaranthus retroflexus and Echinochloa crus-galli, 2.2- and 2.0-fold inhibition activities were displayed. Despite the significant herbicidal activity, this compound exhibited a DXR inhibitory activity lower than that of FOS but comparable to that of other non-hydroxamate DXR inhibitors, and the dimethylallyl pyrophosphate rescue assay gave no statistical significance, suggesting that a different target might be involved in the inhibiting process. This work demonstrates that using bioisosteric replacement can be considered as a valuable strategy to discover new FOS analogs that may have high herbicidal activities.
A VERTEBRATE FAUNA FROM THE MIDDLE DEVONIAN YAHATINDA FORMATION OF SOUTHWESTERN CANADA

Abstract The Yahatinda Formation of southern Alberta and British Columbia consists of a series of channels cut into lower Paleozoic rocks and represents deposition in marine to littoral environments across a major regional unconformity. The age of the beds is late Givetian based on spore assemblages and plant macrofossils. A vertebrate fauna from the formation is described here for the first time and includes Heterostraci (two new species of tuberculated pteraspidids), Placodermi (an antiarch and the arthrodire Holonema together with indeterminate arthrodires), Osteolepiformes, and Porolepiformes. This report documents for the first time that pteraspidids, considered to be organisms characteristic of the Lower Devonian elsewhere, lingered to the end of the Middle Devonian in western North America. This fauna is similar to others occurring further south in the western United States.