bluuebunny/crossref_metadata_2025 huggingface dataset:
T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
Authors: Paz Michelle Almeida da , Taher Leila
Published: June 2022

BackgroundDespite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome’s regulatory landscape, many challenges remain. In particular, because of their repetitive nature, the sequencing reads derived from transposable elements (TEs) pose a real bioinformatics challenge, to the point that standard analysis pipelines typically ignore reads whose genomic origin cannot be unambiguously ascertained.ResultsWe show that discarding ambiguously mapping reads may lead to a systematic underestimation of the number of reads associated with young TE families/subfamilies. We also provide evidence suggesting that the strategy of randomly permuting the location of the read mappings (or the TEs) that is often used to compute the background for enrichment calculations at TE families/subfamilies can result in both false positive and negative enrichments. To address these problems, we present the Transposable Element Enrichment Estimator (T3E), a tool that makes use of ChIP-seq data to characterise the epigenetic profile of associated TE families/subfamilies. T3E weights the number of read mappings assigned to the individual TE copies of a family/subfamily by the overall number of genomic loci to which the corresponding reads map, and this is done at the single nucleotide level. In addition, T3E computes ChIP-seq enrichment relative to a background estimated based on the distribution of the read mappings in the input control DNA. We demonstrated the capabilities of T3E on 23 different ChIP-seq libraries. T3E identified enrichments that were consistent with previous studies. Furthermore, T3E detected context-specific enrichments that are likely to pinpoint unexplored TE families/subfamilies with individual TE copies that have been frequently exapted as cis-regulatory elements during the evolution of mammalian regulatory networks. ConclusionsT3E is a novel open-source computational tool (available for use at: https://github.com/michelleapaz/T3E) that overcomes some of the pitfalls associated with the analysis of ChIP-seq data arising from the repetitive mammalian genome and provides a framework to shed light on the epigenetics of entire TE families/subfamilies.
Chimpanzees, dung beetles and seed dispersal: implications for habitat conservation of the West African chimpanzee Pan troglodytes verus in Taï National Park, Côte d'Ivoire
Authors: KOFFI Kouadio Kan Sylvestre , DOSSO Kanvaly , BAROT Sebastien , WITTIG Roman M. , ARISTOPHANOUS Marios , MORETTO Philippe , KONE Inza , TIHO Seydou
Published: June 2022

Seed dispersal is a key stage in the life cycle of plants, thus in forest regeneration, especially in the tropics. Chimpanzees are known as important seed dispersers and dung beetles play critical roles in secondary dispersal thus increasing the chance for seed post-dispersal success. Hence, understanding secondary seed dispersal by dung beetles is critical to our understanding of forest dynamics. The aim of this study was to evaluate the effects of successive dispersal by chimpanzees and by dung beetles on the surface dispersal and burial of the seeds of four plant species: (Dacryodes klaineana (Pierre) H.J. Lam, Diospyros mannii Hiern, Pycnanthus angolensis (Welw.) Warb. and Uapaca guineensis Muell) at three nesting site in the Taï National Park. To investigate this, 28 seeds i.e. seven seeds per plant species (N = 75, average ± SD: 28.24 ± 3.06 seeds) were introduced into 85 g of chimpanzee faecal matter. This set was exposed on the forest floor for 48h following an average faecal radius of 5 cm (N = 40, average ± SD: 5 ± 1.06 cm). From the observations made, it emerges an essentially surface dispersion, ie 45.6% of the seeds dispersed against 6.3% of seeds buried. The highest rate of vertically dispersed seeds, ie 10.31%, and average depth of burial, ie 7.45 cm, were quantified in the southern nesting sites. This distribution of seeds would not only be linked to the time of deposition of the faecal matter, but also and above all to the size of the secondary disperser.
Engineered an accessory enzymatic system of cellulase for simultaneous saccharification and co-fermentation
Authors: Liu Han , Wang Xuxin , Liu Yanping , Kang Zhuoran , Lu Jiaqi , Ye Yutong , Wang Zhipeng , Zhuang Xinshu , Tian Shen
Published: June 2022

The enhanced hydrolysis of xylan-type hemicellulose is important to maximize ethanol production yield and substrate utilization rate in lignocellulose-based simultaneous saccharification and co-fermentation system. In this study, we conduct d-integration CRISPR Cas9 to achieve multicopy chromosomal integration with high efficiency of reductase-xylitol dehydrogenase pathway in Saccharomyces cerevisiae. Subsequently, we devise a CBP-enabling S. cerevisiae consortium, in which every engineered yeast strain could secrete or display different assembly component to be adaptive assembled on the surface of scaffoldin-displaying yeast cell for synergistic catalysis and co-fermentation from steam-exploded Pennisetum purpureum. Despite the accumulation of xylitol, the maximum ethanol titer of genetic engineered yeast strain reached 12.88 g/l with the cellulose conversion of 91.21% and hemicellulose conversion of 55.25% under 30 ºC after 96 h with the addition of commercial cellulase. The elaborated cellulosomal organization toward genetic engineering of an industrially important microorganism presents a designed approach for advanced lignocellulolytic potential and improved capability of biofuel processing.
Prolong the shelf-life and quality attributes of ready-to-eat pomegranate arils using PLA/ZnO nanoparticle/ Zataria multiflora essential oil nanocomposite film
Authors: Heydari-Majd Mojtaba , Monjazeb-Marvdashti Leila , Bratovcic Amra , Abdolshahi Anna , Shadan Mohammad Reza , Yazdani-Dehnavi Marzieh
Published: June 2022

The dried pomegranate (Punica granatum L.) arils have several health benefits and are in demand worldwide. Therefore, in the current study, the wrapping effects of Poly L-lactide (PLA) activated with zinc oxide nanoparticles (ZnO NPs, 1.5% w/w) and Zataria multiflora Boiss. essential oil (ZEO, 1 and 1.5% w/w) was studied on pomegranate arils' storage-life extension in cold storage. The arils were analyzed periodically for properties of physiochemical (weight loss, pH, total soluble solids, color measurement, antioxidant activity and sensory attributes) and microbial (total aerobic bacteria and total fungi counts). Results showed that the ZEO causes to decrease and ZnO causes to increase of pH during storage. Also, the active films were more effective than the control film in maintaining TTS and preventing weight loss of arils. The PLA/ZnO/1.5% ZEO sample had the highest phenolic content (∼520 mg/100 ml in juice) and antioxidant activity (∼90%) on day 15. Nevertheless, the effect of ZEO on the color properties of arils was more than ZnO, and 0.5 and 1.5% ZEO-PLA, showed the highest a* (55.14) and b* (31.30) with fresh arils, respectively. The microbial test results showed that ZEO was more effective in controlling bacterial growth than ZnO. Based on atomic absorption spectrophotometer measurement, minimal amounts (∼29 mg Kg− 1 sample) of Zn2 + ions released into arils were observed. Generally, the active PLA could be used as a safe and effective way to prolong the storage life of arils in refrigerated conditions.
Prediction model of total agricultural carbon emissions in Henan Province based on neural network and nonlinear surface fitting
Authors: Pan Yisha , Wang Chongyang , Yu Beichen , Wang Yidi , Yang Zhiwen , Ren Kangde
Published: June 2022

Controlling carbon dioxide emissions and taking the road of green development are inevitable choices for the sustainable development of the earth. The prediction of agricultural carbon emissions is of guiding significance to accelerate the pace of reducing carbon emissions and is beneficial to guide green technology innovation. Based on six influencing factors such as chemical fertilizer, pesticide and agricultural film, this paper uses neural network model and nonlinear surface fitting method to carry out regression and prediction of total carbon emissions, and the conclusions are as follows: 1) In terms of the return of the carbon emissions and forecast, the absolute value of multilayer perceptron model residual |δi|∈[0,0.03], the radial basis function model of the absolute value of residuals |δi|∈[0,0.19], the former has better effect than the latter, this is because, the former on the various factors affecting more fully utilized; 2) Set up the prediction model of nonlinear curved surface fitting based on the complex plane, and established the carbon emissions for influence factors in the complex plane expressions: Z=z1+jz2, and by calculation |Z| can be clearly predicted each year, under the influence of various factors, prediction of carbon emissions. 3) The correlation coefficients between the prediction results of the neural network and the nonlinear surface fitting prediction model and the original data exceed 0.9, indicating that the two methods are used in the regression and prediction of total carbon emissions.
Explosive Separation Properties of Double-hole Charge Structure
Authors: Wang Meng , Zhu Yu , Chen Gang , Su Hong , Xuan Haijun , He Zekan , Wan Zhao
Published: June 2022

In order to explore the critical charge diameter for explosive separation of titanium alloy plates under the structure of double-hole charge. In this paper, based on the SPH algorithm in the AUTODYN software, a numerical model of the explosion separation of titanium alloy plates was established, and numerical simulations were carried out for different charge aperture models.According to the strength criterion and the simulation calculation results, the fracture judgment was carried out, and the fracture mechanism of the double opening separation was analyzed, and the law of the damage to the plate by the diameter of the charging hole was explored. According to the simulation results, the results show that the test results are highly consistent with the simulation results. When the double hole charge structure is used for explosive separation, the size of the charge aperture not only directly affects the effect of explosive separation, but also affects the flying off kinetic energy after plate fracture. Under the influence of various factors, the plate breaks from the hole wall from inside to outside, and finally breaks into a seam to complete the separation. With the increase of the charge hole diameter, the damage condition of the titanium alloy plate increases almost linearly, that is, the larger the charge hole diameter, the more serious the damage to the titanium alloy plate.
The Utility of Intraoperative Endoscopy to Assist Novice Surgeons in the Detection of Gastric Stenosis during Laparoscopic Sleeve Gastrectomy
Authors: Chen I-Sung , Tsai Ming-Shian , Chen Jian-Han , Chen Chung-Yen , Chen I-Lin , Tai Chi-Ming
Published: June 2022

Laparoscopic sleeve gastrectomy (LSG) is a commonly performed bariatric surgery, but is associated with gastric stenosis and leaks. Herein, we report our experience of intraoperative endoscopy (IOE) to evaluate stenosis and leaks during LSG. LSG was performed by three surgeons. Patients who underwent LSG and IOE between January 2016 and March 2020 were enrolled and assigned to two groups: group 1 (1st-30th LSG case for each surgeon) and group 2 (>30th LSG for each surgeon). Patients’ anthropometric and biochemical data pre- and post-LSG, as well as IOE findings and follow-up esophagogastroduodenoscopy records were reviewed. In total, 352 patients were enrolled including 90 patients in group 1 and 262 patients in group 2. Three out of 352 patients (0.9%) were found to have stenosis by IOE, which was related to tightly gastropexy stitch or reinforcement stitch, all of which were in group 1. Stenosis was resolved after removal of the stitch during LSG. The incidence of gastric stenosis detected by IOE was 3.3% (3/90) and 0% (0/262) in group 1 and group 2, respectively (P=0.003). No leakage was found in this study and no patient developed clinical or endoscopic stenosis after LSG. In conclusion, IOE can help detect gastric stenosis during LSG, especially for novice surgeons, and the stenosis could be resolved during operation.
Prefeasibility analysis of low-scale biorefineries: annatto and açai case
Authors: Poveda-Giraldo Jhonny Alejandro , Piedrahita-Rodríguez Sara , Salgado-Aristizabal Natalia , Moreno Haminton Salas , Alzate Carlos Ariel Cardona
Published: June 2022

The industrial applicability of exotic and wild fruits has been investigated as stand-alone processes framed to obtain a single main product. However, their combination and the valorization of the processing residues in a biorefinery scheme have not been explored. Therefore, this work aims to assess the technical and economic feasibility of low-scale biorefineries based on annatto and açai as raw materials. Therefore, the actual processing of both fruits was carried out experimentally. For annatto, the extraction of dye paste was performed, obtaining mass yields of up to 58.4% by working with ground seed. Regarding the açai, pulp was obtained with a polyphenol content of 23.56 mg of gallic acid equivalent per gram of sample. The residues generated in both processes were used as substrates for biogas production, achieving biomethane yields between 186–533 mL per gram of volatile solids. These results were the basis for the design and simulation of process scale-up in low-scale biorefinery contexts. Five scenarios were evaluated, involving the production of annatto dye paste, açai pulp, biogas from exhausted annatto seeds, slurry and seeds of açai, and feedstock integration. As the main energy result, it was found that the individual production of açai pulp can fully supply the required energy of the process through the self-generation index. From the economic perspective, it was found that there is economic feasibility working with flows below the regional and national production in Colombia for all scenarios.
Identification of N7-methylguanosine-related patterns and characterization of the tumor microenvironment in hepatocellular carcinoma
Authors: Yu Jianfa , Wang Shuang , Shi Rui , Yang Long , Lang Qi , Zhang Yamin
Published: June 2022

Background: N7-methylguanosine (m7G) is an essential epigenetic modification and there is increasing evidence that it is closely associated with tumorigenesis progression. However, the expression pattern of m7G-related genes in hepatocellular carcinoma (HCC) remains systematically analyzed.Methods: We downloaded HCC genetic and transcriptomic data from TCGA and GEO datasets. Unsupervised clustering methods identified different m7G-related gene subtypes, and then an m7G_score for predicting overall survival and characterizing the tumor microenvironment (TME) was constructed. Eventually, a highly accurate nomogram was constructed based on the score.Results: In this study, two m7G-related gene subtypes were obtained by unsupervised clustering analysis of 18 m7G-related genes, and the relationship between different subtypes and clinicopathological features and TME was systematically evaluated.Conclusion: N7-methylguanosine-related patterns are closely related to the clinical characteristics and tumor microenvironment of HCC patients, providing a new perspective on the treatment of HCC patients. Meanwhile, m7G_score can improve the clinical applicability with HCC patients.
The negative impact of opioids on cancer patients treated with immune checkpoint inhibitors: A systematic review and meta-analysis
Authors: Gao Ziming , Ju Mingguang , Liu Xiaofang , Zhou Heng , Wang Ruiying , Zheng Chen , Dong Daosong , Zhu Zhi , Li Kai
Published: June 2022

Background
As one of the most effective analgesics, opioids are essential for patients with cancer-related pain, even in the context of the opioid abuse crisis. The current meta-analysis aimed to identify whether concomitant exposure to opioids can affect the efficacy of ICIs and lead to a worse prognosis.
Methods
PubMed, Embase, and the Cochrane Library were searched Based on the PRISMA checklist, through April 2022, for the following terms: ("opioids" OR "concomitant medication") AND ("Neoplasm" OR "Carcinoma" OR "Cancer" OR "Tumor") AND ("Immunotherapy" OR "Immune Checkpoint Inhibitor" OR "PD-L1 Inhibitor" OR "PD-1 Inhibitor" OR "CTLA-4 Inhibitor"). The outcomes considered were overall survival (OS) and progression-free survival (PFS) calculated using the random-effects or fixed-effects model.
RESULTS
After screening 531 studies, a total of 7 articles involving 2690 patients were eligible for quantitative analysis. The use of opioids was negatively correlated with OS (HR = 1.75, 95%CI = 1.32–2.31, P < .001; I2 = 81%, P < .001) and significantly reduced the PFS (HR = 1.61, 95%CI = 1.41–1.83, P < .001; I2 = 0%, P = .63) of patients treated with ICIs. Similar results were obtained in each subgroup analysis. While NSAIDs could lead to poor OS (HR = 1.25, 95% CI = 1.03–1.51, P = 0.02) but not PFS (HR = 1.11, 95% CI = 0.89–1.39, P = 0.36) for ICIs patients. And sensitivity analyses confirmed the reliability of the results.
CONCLUSIONS
Opioids significantly reduced OS and PFS in patients receiving ICI therapy. Thus, the use of different types of opioids should be considered with caution, and it is necessary to actively develop alternative treatments.
Analysis of the top coal stability of the large section open-off cut under the gob in thick seams slicing mining
Authors: Chai Jing , Liu Yongliang , Gao Shigang , Yang Jianfeng , Zhang Dingding , Du Wengang , Ma Chenyang , Han Zhicheng
Published: June 2022

The reserved thickness of top coal has an important influence on the stability of a large section open-off cut under gob in the thick seams slicing mining. The destabilization extremum conditions of the open-off cut top coal were derived from by elastic-plastic theory, and the optical fiber sensing technology was utilized to monitor the top coal deformation law with different thicknesses (3, 3.5, and 4m) in the physical similar simulation experiment in the paper. The results show that the top coal thickness is greater than 3.4m without tension cracks. In the vertical direction, the top coal of the LSOOC is divided into mining and excavation disturbance zones under the influence of the upper slice coal mining and the excavation disturbance. In the direction of the span of the open-off cut, the top coal can be divided into the roof fall risk zone and the warning zone. The deformation changes from exponential to linear to logarithmic in the roof fall risk zone, and it changes from linear to logarithmic in the roof fall warning zone as the number of excavations increases. The sinking amount in the two zones is smaller as the thickness of the top coal becomes larger. It is comprehensively determined that the thickness of the top coal of open-off cut is set as 3.5m, the stability is moderate, and the field application shows that the integrity of the top coal is good after support, and the maximum off-layer value is 6mm, which can satisfy the production requirements.
Pharmacological Activities and Characterization of Phenolic and Flavonoid Compounds in Solenostemma argel Extract
Authors: Soliman Mohamed S. M. , Abdella Asmaa , Khidr Yehia A. , Osman Hassan G. O. , Aladadh Mohamed Abdullah , Elsanhoty Rafaat M.
Published: June 2022

Solenostemma argel is a desert medicinal plant indigenous to African countries. The goal of this work was to investigate the pharmacological properties of phenolic and flavonoid compounds present in the Solenostemma argel. Aerial parts (leaves and flowers) of Solenostemma argel were tested for antibacterial activity, antioxidant activity, cell viability and cytotoxic effects, and anti-inflammatory activity. Phenolic and flavonoid contents (HPLC), and volatile constituents (GC-MS) were also characterized. The antioxidant activity of Solenostemma argel extract increased from (34.47%) at a concentration of 10 µg/mL to (98.47%) at a concentration of 1280 µg/mL. The most sensitive organism was S. aureus with the highest inhibition zone and lowest MIC, with acetone extract. Whereas C. tropicalis was the most resistant, with the lowest inhibition zone. MTT assay indicated that the methanolic extract of Solenostemma argel had significant cytotoxic effects on the A549, Caco-2, and MDAMB-231 cell lines, respectively. The anti-inflammatory activity showed at lower concentrations of methanolic extract, and those effects were compared with indomethacin as a standard. Gallic was the most abundant phenolic acid, followed by syringic, p-coumaric, caffeic and ferulic acids, respectively. The Catechin and Quersestin, Luteolin and rutin flavonoids were also found in the methanolic extract. GC-mass analysis showed that aerial parts of Solenostemma argel were rich in 2-(5-methyl-5 vinyl tetrahydro-2-furanyl)-2-propanol (11.63%), hexanoic acid methyl ester (10.93%), 3-dioxolane,4-methyl-2-pentadecyl (9.69%), phenol, 2-(1,1-dimethylethyl) (8.50%). It can be concluded that methanolic extract of Solenostemma argel could be used as an available source of natural bioactive constituents with consequent health benefits such as antioxidants, anti-inflammation, anticancer and antimicrobial effects.
A Gibbs sampler for multi-species occupancy models
Authors: Clark Allan Ernest , Altwegg Res
Published: June 2022

Multi-species occupancy (MSO) models use detection-nondetection data from several species observed at different locations to estimate the probability that a particular species occupies a particular geographical region. The models are particularly useful for estimating the occupancy probabilities associated with rare species since they are seldom observed when undertaking field surveys. In this paper, we develop Gibbs sampling algorithms that can be used to fit various Bayesian MSO models to detection-nondetection data. Bayesian analysis of these models can be undertaken using statistical packages such as JAGS, Stan and NIMBLE , however, since these packages were not developed specifically to fit occupancy models, one often experiences long run-times when undertaking analysis. In a single season (single species) nonspatial and spatial occupancy modelling context, Clark and Altwegg (2019), show that special purpose Gibbs samplers can produce posterior chains that mix faster and have larger expected sampling rates (Holmes & Held, 2006) than those obtained using JAGS and Stan. These results suggest that such algorithms could potentially lead to significant reductions in the run-times of MSO models. This paper illustrates how to fit MSO models when the detection and occupancy processes are modelled using logistic link functions and apply these methods to a camera-trapping study undertaken by 1 Drouilly, Clark, and O’Riain (2018). Variable selection is undertaken using a reversible-jump Markov chain Monte Carlo (Barker & Link, 2013) algorithm. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using Stan, resulting in faster run-times and has a larger expected sampling rate than Stan when analysing the above-referenced data set.
A Head-to-Head comparison of fast-SENC and Feature Tracking to LV long axis strain for assessment of myocardial deformation in chest pain patients
Authors: Siry Deborah , Riffel Johannes , Salatzki Janek , André Florian , Weberling Lukas Damian , Ochs Marco , Atia Noura A. , Hillier Elizabeth , Albert David , Katus Hugo A. , Giannitsis Evangelos , Frey Norbert , Friedrich Matthias Gero
Published: June 2022

BackgroundMyocardial strain imaging has gained importance in cardiac magnetic resonance (CMR) imaging in recent years as an even more sensitive marker of early left ventricular dysfunction than left-ventricular ejection fraction (LVEF). fSENC (fast strain encoded imaging) and FT (Feature Tracking) both allow for reproducible assessment of myocardial strain. However, left-ventricular long axis strain (LVLAS) might enable an equally sensitive measurement of myocardial deformation as global longitudinal or circumferential strain in a more rapid and simple fashion. MethodsIn this study we compared the diagnostic performance of fSENC, FT and LVLAS for identification of cardiac illness (ACS, cardiac-non-ACS) in patients presenting with chest pain (initial hscTnT 5- 52 ng/l). Patients were prospectively recruited from the chest pain unit in Heidelberg. The CMR scan was performed within 1h after patient presentation. Analysis of LVLAS was compared to the GLS and GCS as measured by fSENC and FT. ResultsIn total 40 patients were recruited (ACS n=6, cardiac-non-ACS n=6, non-cardiac n=28). LVLAS was comparable to fSENC for differentiation between healthy myocardium and myocardial illness (GLS-fSENC AUC: 0.882; GCS-fSENC AUC: 0.899; LVLAS AUC: 0.771; GLS-FT AUC: 0.740; GCS-FT: 0.688). There was significant variability between the three techniques. Intra- and inter-observer variability (OV) was excellent for fSENC and FT, whilst for LVLAS the agreement was lower and levels of variability higher (intra-OV: Pearson >0.7, ICC>0.8; inter-OV: Pearson>0.65, ICC>0.8; CoV > 25%). ConclusionsAlthough there was significant bias between the three deformation parameters, reproducibility was excellent for both FT and fSENC. Whilst LVLAS demonstrated lower levels of agreement and higher variability, it was comparable to FT and fSENC for identification of myocardial illness and might be used as a rapid supporting parameter for assessment of left-ventricular function.
A Viroporin from SARS-CoV-2 Reduces the Infectivity of Human Immunodeficiency Virus type 1 (HIV-1)
Authors: Henke Wyatt , Waisner Hope , Arachchige Sachith Polpitiya , Kalamvoki Maria , Stephens Edward
Published: June 2022

Background: Viroporins are virally encoded ion channels that are involved in virus assembly and release. Human immunodeficiency virus type 1 (HIV-1) and influenza A virus encode for viroporins. The human coronavirus SARS-CoV-2 encodes for at least two viroporin proteins, a small 75 amino acid transmembrane protein known as the envelope (E) protein and a larger 370 amino acid protein known as Orf3a. Here, we compared the HIV-1 virus infectivity in the presence of four different β-coronavirus E proteins. Results: We observed that the SARS-CoV-2 and SARS-CoV E proteins reduced the release of infectious HIV-1 yields by approximately 100-fold while MERS-CoV or HCoV-OC43 E proteins restricted HIV-1 infectivity to a lesser extent. Mechanistically, we show that the E proteins reduced the levels of HIV-1 protein synthesis in cells and that that the E protein neither affected reverse transcription nor genome integration. However, SARS-CoV-2 E protein activated the ER-stress pathway associated with the phosphorylation of eIF-2α, which is known to attenuate protein synthesis in cells. Other ever-expressed proteins (HSV-1 gD, HIV-1 gp160 and EGFP) did not cause phosphorylation of eIF-2α. Finally, we show that unlike the Vpu protein of HIV-1 and the Spike protein of SARS-CoV-2, the four E proteins and the SARS-CoV-2 N protein did not significantly down-regulate bone marrow stromal cell antigen 2 (BST-2). Conclusions: The results of this study indicate that while viroporins from homologous viruses can enhance virus release, that we show a viroporin from a heterologous virus can suppress HIV-1 protein synthesis and virus release.
Diabetes during the COVID-19 pandemic: are people getting access to the right level of care?
Authors: Meyerowitz-Katz Gideon , Ferdousi Shahana , Maberly Glen , Astell-Burt Thomas
Published: June 2022

Introduction Avoidance of health services, in particular hospital and community services, is problematic for people with diabetes. Evidence has demonstrated that such missed attendances are associated with worse health, faster declines in functioning, and higher rates of mortality long-term. This paper investigated the impact of the pandemic on healthcare access across community and hospital care, including Virtual Care (VC) using several large datasets of GP and hospital services in western Sydney. Methods A retrospective cohort study using a time-series database of 173,805 HbA1c tests done at Blacktown and Mt Druitt hospitals and 1.8 million recorded consultations at GP clinics in the region was undertaken. Results The average rate of diabetes in ED fell from 17.8% pre-pandemic to 11% after January 2020 (p < 0.001). This rate varied substantially over time, and correlated well with large outbreaks of COVID-19 in the state. Conversely, attendances of people with diabetes to GP clinics, especially using VC services, increased substantially over the pandemic period. Discussion During the pandemic there was a substantial avoidance of hospital care by patients with diabetes. However, this may have been replaced by VC offered in the community for those with less severe diseases.
Impact of Kidney Function and Kidney Volume on Intracranial Aneurysms in Patients with Autosomal Dominant Polycystic Kidney Disease
Authors: Kataoka Hiroshi , Akagawa Hiroyuki , Yoshida Rie , Iwasa Naomi , Ushio Yusuke , Akihisa Taro , Sato Masayo , Manabe Shun , Makabe Shiho , Kawachi Keiko , Hoshino Junichi , Tsuchiya Ken , Nitta Kosaku , Mochizuki Toshio
Published: June 2022

Background
To date, only a personal or family history of intracranial aneurysm/subarachnoid hemorrhage (IA/SAH) has been established as a risk factor for IA in autosomal dominant polycystic kidney disease (ADPKD). Recently, an association between splicing/frameshift mutations, which are reportedly associated with declining kidney function/increased total kidney volume (TKV), and IAs in patients with ADPKD was reported.
Objective
To confirm the association between kidney function/volume and IAs in patients with ADPKD.
Methods
This study included 519 patients with ADPKD. Kidney function, TKV, and general risk factors for IA were assessed for associations with IA formation.
Results
At baseline IA screening, the median age, estimated glomerular filtration rate, and TKV were 44 years, 54.5 mL/min/1.73 m2, and 1054.3 mL, respectively. A family IA/SAH history was confirmed in 18.1% patients, and 54.3% patients had hypertension. IA point prevalence was 12.5%. During a clinical follow-up of 3104 patient-years, de novo IA was detected in 29 patients (0.93% patient-years). IA period prevalence was 18.1% (median age, 60 years). Multivariable logistic regression analyses demonstrated that TKV ≥ 1000 mL (odds ratio [OR] = 2.81), height-adjusted TKV ≥ 500 mL (OR = 2.81), Mayo 1D–1E (OR = 2.52), and chronic kidney disease stages 3–5 (OR = 2.31) were significantly associated with IA formation.
Conclusions
IAs in patients with ADPKD may be associated with risk factors for IAs in the general population as well as declining kidney function and increased kidney volume. Kidney disease progression may contribute to effective IA screening and treatment planning in patients with ADPKD.
Visualizing bacterial quorum sensing and quorum quenching interaction on Medicago roots
Authors: Rosier Amanda , Bais Harsh P.
Published: June 2022

Background
Defining interactions of bacteria in the rhizosphere (area near and on the plant root) is important to understand how they affect plant health. Some rhizosphere bacteria, including plant growth promoting rhizobacteria (PGPR) engage in the intraspecies communication known as quorum sensing (QS). Many use the extracellular autoinducer signal molecule N-acyl homoserine lactone (AHL) and other rhizobacteria, including PGPR, can interfere or disrupt QS through quorum quenching (QQ). Traditional AHL biosensor assays used for screening and identifying QS and QQ bacteria interactions fail to account for the role of the plant root.
Methods
Medicago spp. seedlings germinated on Lullien’s agar are transferred to soft-agar plates containing the broad-range AHL biosensor Agrobacterium tumefaciens KYC55 and X-gal substrate. Cultures of QS and QQ bacteria as well as pure AHLs and QQ protein are applied to the plant roots and incubated for 3 days.
Results
We show that this expanded use of an AHL biosensor successfully allowed for visualization of QS/QQ interactions localized at the plant root. KYC55 detected pure AHLs as well as AHLs from live bacteria cultures grown directly on the media. We also showed clear detection of QQ interactions occurring in the presence of the plant root.
Conclusions
Our novel tri-trophic system using an AHL biosensor is useful to study QS interspecies interactions in the rhizosphere.
Expression of hexokinase-2 (HK2), glutaminase-1 (GLS1) and fatty acid synthase (FASN) in gastric cancer and their prognostic significance
Authors: García-Martínez Elisa , Lino-Silva Leonardo S. , Romo-Pérez Adriana , Chavez-Blanco Alma , Dominguez-Gomez Guadalupe , Taja-Chayeb Lucia , Lopez-Basave Horacio N , Padilla-Rosciano Alejandro E , Diaz-Romero Consuelo , Trejo-Becerril Catalina , González-Fierro Aurora , Duenas-González Alfonso
Published: June 2022

PurposeThe malignant metabolic phenotype characterized by high rates of glycolysis, glutaminolysis and de novo synthesis of fatty acids is also observed in gastric carcinoma. These alterations can be used as therapeutical opportunities with the use of drug inhibitors targeting key enzymes for the metabolism of glucose, glutamine and fatty acid synthesis. MethodsHere we analyzed the immunohistochemical expression of Hexokinase-2 (HK2), Glutaminase-1 (GLS1) and fatty acid synthase (FASN) key enzymes for glycolysis, glutaminolysis and de novo fatty acid synthesis in 92 tumor samples of diffuse gastric carcinoma. Clinicopathological variables, treatment and follow-up data were obtained from files. ResultsHK2 overexpressed in 19 (20.7%), GLS1 in 28 (30.4%) and FASN in 21 (22.8%). Ten (10.9%) patients co-overexpressed HK2/FASN and 8 (8.7%) patients the three enzymes (HK2/GLS1/FASN). Enzyme overexpression either single or combined but no GLS1, correlated with higher stage and disease progression. At a median follow-up time of 31.8 months (2-116). All patients with combined expression died. The co-overexpression of both HK2/FASN and HK2/GLS/FASN was associated with shorter progression free survival whereas only the triple expression with overall survival (median 11.1 vs. 20.4, p=0.01). Nonetheless, stage was the only independent variable for overall survival. ConclusionIn our knowledge, this is the first study to demonstrate that HK2, GLS1 and FASN are concurrently overexpressed which provide support for further studies evaluating the antitumor effects of inhibitors of glycolysis, glutaminolysis and de novo synthesis of fatty acids for metabolic therapy of gastric cancer.
Diffuse alveolar hemorrhage caused by sevoflurane: case report and literature review
Authors: Zhu Yao , Shang Guansheng , Qin Yiwei , Gu Shengyan , Wang Fengling , Huang Jin
Published: June 2022

Diffuse alveolar hemorrhage (DAH), as an exclusion diagnosis in the clinic, is often occult but with serious consequences. DAH can be caused by many immune factors such as systemic lupus erythematosus (SLE) and antiphospholipid syndrome, or non-immune factors such as cocaine, marijuana, infection and radiotherapy. This paper reports a case of DAH caused by sevoflurane during anesthesia. The patient was a 31-year-old healthy male. After the oxygenation decreased during operation, the resuscitation was delayed in the anesthesia resuscitation room. At the same time, severe acute cor pulmonale occurred, which caused hemodynamic disorder and a progressive decrease in oxygenation. After active treatment, the patient recovered. In addition, DAH caused by sevoflurane and other factors was reviewed in this paper.
The Impact of Pathogenic BRCA1/2 Tumor Mutation Status on Advanced Stage-High Grade Serous Epithelial Ovarian Cancer Survival Outcome
Authors: Sutrisno Sutrisno , Purbadi Sigit , Tjahjadi Hartono , Werdhani Retno Asti , Khonsa Oni , Sembiring Ruth Emalian , Effendi Iwan Kurnia , Gultom Fajar Lamhot , Marleen Stella , Sugiharto Sony , Hendrasti Ardiana , Maharani Nastiti
Published: June 2022

Objective: To evaluate the impact of pathogenic BRCA1/2 tumor mutation on advanced stage-high grade serous epithelial ovarian cancer (HGSOC) survival outcome. Methods: A total of 68 from 144 patients were diagnosed with FIGO 2014 stage IIB-IV HGSOC between January 1st 2015, until March 31st 2021, at Dr. Cipto Mangunkusumo National Central Referral Hospital, Persahabatan Central Referral Hospital, and MRCCC Central Referral Hospital Siloam Jakarta, underwent NGS tumor BRCA1/2 gene testing and were included in this cohort historical study. We compared patient’s overall survival outcomes to pathogenic BRCA1/2 tumor mutational status. The patient’s clinicopathological characteristic factors that might affect patient’s survival outcomes were also investigated. Results: In the group with pathogenic BRCA1/2 tumor mutation, the likelihood of dying was 86% ​​lower (adjusted RR 0.149; 95%CI 0.046-0.475; p-value=0.001), and the median survival was better (median 46 months; 95%CI 34.009-57.991; p value=0.001) than the group without pathogenic BRCA1/2 tumor mutations (median 23 months; 95%CI 15.657-30.343; p value=0.001). The multivariate analyses identified pathogenic BRCA1/2 tumor mutation as an independent favorable prognostic factor for survival outcome (adjusted RR 0.149; 95%CI 0.046-0.475; p-value=0.001).Conclusions: In advanced stage-HGSOC patients, the pathogenic BRCA1/2 tumor mutations group have a better prognosis with longer survival outcomes than those without pathogenic BRCA1/2 tumor mutations.
Early Signs of Neuroinflammation in the Postnatal Wobbler Mice Model of Amyotrophic Lateral Sclerosis
Authors: Meyer Maria , Lima Analia , Deniselle Maria Claudia Gonzalez , De Nicola Alejandro F.
Published: June 2022

The Wobbler mouse is an accepted model of sporadic amyotrophic lateral sclerosis. The spinal cord of clinically symptomatic animals (3-5 months old) show vacuolar motoneuron degeneration, inflammation and gliosis accompanied by motor impairment. However, data are not conclusive concerning pathological changes appearing early after birth. To answer this question, we used postnatal day (PND) 6 genotyped Wobbler pups to determine abnormalities of glia and neurons at this early age period. We found astrogliosis, microgliosis with morphophenotypic changes pointing to active ameboid microglia, enhanced expression of the proinflammatory markers TLR4, NFkB, TNFα and inducible nitric oxide synthase. The astrocytic enzyme glutamine synthase and the glutamate-aspartate transporter GLAST were also reduced in PND 6 Wobbler pups, suggesting excitotoxicity due to impaired glutamate homeostasis. At the neuronal level, PND 6 Wobblers showed swollen soma, increased choline acetyltransferase immunofluorescence staining and low expression of the neuronal nuclear antigen NeuN. However, vacuolated motoneurons, a typical signature of older clinically symptomatic Wobbler mice were absent in the spinal cord of PND 6 Wobblers. The results suggest predominance of neuroinflammation and abnormalities of microglia and astrocytes at this early period of Wobbler life, accompanied by some neuronal changes. Data support the non-cell autonomous hypothesis of the Wobbler disorder, and bring useful information with regards to intervening molecular inflammatory mechanisms at the beginning stage of human motoneuron degenerative diseases.
Comprehensive Analysis of a Cuproptosis-Related Gene Index in Pancreatic Adenocarcinoma with Significant Implications on Prognosis and Immunotherapy as well as Chemotherapy Efficacy
Authors: Huang Xufeng , Zhou Shujing , Liu Ying , Tóth János , András Hajdu
Published: June 2022

Background
A novel type of cell death induced by intracellular copper accumulation, principally different from other known ones such as autophagy, ferroptosis, and pyroptosis, was discovered and referred to as “Cuproptosis” recently. As the underlying mechanism was newly identified, its potential connection to pancreatic adenocarcinoma (PAAD) is still an open issue. However, interestingly, one of the 10 Cuproptosis-related genes, CDKN2A, was previously reported as a driver mutation gene in pancreatic adenocarcinoma. Therefore, it raised our interest to develop a Cuproptosis-related gene index (CRGI) for better overall survival (OS) estimation, explore the corresponding relationship with tumor immunology, and discuss the chemotherapy efficacy of commonly used anti-cancerous drugs relevant to CRGI.
Methods
Gene expression profiles and matched clinical data were curated from publicly accessible sources from which the CRGI was developed. Immunogenic properties were investigated according to the immune checkpoints, potential response to the immunotherapy, cancer immunity cycle, etc. The sensitivity to chemotherapy agents was evaluated through the IC50 curve. The consensus clustering approach was implemented to robustly identify the CRGI-based molecular subtypes and explore the immunotherapy and chemotherapy efficacies.
Results
A novel gene signature derived from Cuproptosis was established. Compared with those signatures originating from other cell death mechanisms, it exerted a more robust yet more accurate predictive performance. Besides, the result of correlation analysis unraveled the distinct differences in tumor immunology between the high- and low-risk groups. Through in-depth analysis of the IC50 curve of each drug, the predictive chemotherapy efficacy of 32 commonly used anti-cancerous drugs was also found various in high- and low-risk groups. The analysis of molecular subtypes has further confirmed these ideas.
Conclusion
In the present study, we highlighted the outstanding achievement of CRGI in PAAD prognostic prediction and its association with tumor immunology. These findings may benefit future immunotherapy- and chemotherapy-based interventions.
Brucine-induced neurotoxicity by targeting caspase 3: Involvement of PPARγ/NF- κB/apoptosis signaling pathway
Authors: Lei Yaying , Hou Fangqin , Wu Xiaoyu , Yi Yang , Xu Fan , Gong Qihai , Gao Jianmei
Published: June 2022

Brucine, a weak alkaline indole alkaloid, is one of the main bioactive and toxic constituents of Strychnos nux-vomica L., which exerts multiple pharmacological activities, such as anti-tumor, anti-inflammatory, analgesic effect. However, its potential toxic effects limited its clinical application, especially central nervous system toxicity. The present study was designed to investigate the neurotoxicity and mechanism of brucine. Our results showed that brucine significantly induced Neuro-2a cells and primary astrocytes death, as evidenced by MTT assay and LDH release. Moreover, transcriptome analysis indicated that PPAR/NF-κB and apoptosis signaling pathways were involved in the brucine-induced cytotoxicity in Neuro-2a cells. Subsequently, in fact, brucine evidently inhibited PPARγ, promoted phosphorylation of NF-κB. Furthermore, PPARγ inhibitor aggravated the neurotoxicity, while, NF-κB inhibitor substantially reversed brucine-induced neurotoxicity. Moreover, brucine also significantly induced neuronal apoptosis and triggered increase in ratio of Bax/Bcl-2, level of cleaved caspase-3, as well as its activity as evidenced by TUNEL staining and Western blot. Furthermore, molecular docking analysis predicted that brucine directly bound to caspase 3. Intriguingly, a caspase 3 inhibitor (Z-DEVE-FMK) largely abolished the neurotoxicity of brucine. Our results reveal that brucine-induced neurotoxicity via activation of PPARγ/NF-κB/caspase 3-dependent apoptosis pathway. These findings will provide a novel strategy against brucine-induced neurotoxicity.
Dynamic transcriptome profiling of salt-responsive long noncoding RNAs in quinoa
Authors: Luo Chuping , He Bing , Shi Pibiao , Pang Bingwen , Cheng Junjie , Hu Fengqin , Qi Weicong , Lv Yuanda
Published: June 2022

Background Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long noncoding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. Results In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. Conclusions This study is the first report on genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.
Diabetes-Related Complications and Mortality in Patients with Atrial Fibrillation Receiving Different Oral Anticoagulants
Authors: Shakeel Reem , Munir Sheheryar , Mazhar Naqash
Published: June 2022

Introduction: Globally, cardiovascular disease is the main contributor to mortality, accounting for about 17.5 million deaths, or 46.2% of deaths from non-communicable diseases. Objectives: The main objective of the study is to find the diabetes-related complications and mortality in patients with atrial fibrillation receiving different oral anticoagulants. Material and methods: This cross-sectional study was conducted in Services Institute of medical sciences, Lahore during June 2021 to December 2021. The data were collected from 120 diabetic patients who diagnosed with AF. After permission from hospital ethical committee, total 120 patients meeting the inclusion and exclusion criteria was enrolled in the study. Detailed history of DM and physical examination was done to meet the inclusion and exclusion criteria. Results: The data was collected from 120 patients. Out of 120 participants, 60 were treated with warfarin while 60 were considered as control group. Median age was 26 years in the group I and 25.3 years in the group II (p=0.705). Female cases counted for 41 (86%) and 19 (14%) in I and II groups, respectively. Conclusion: It is concluded that patients with AF and diabetes have a high overall cardiovascular risk. Non–vitamin K antagonist oral anticoagulants were associated with lower hazards of diabetes complications and mortality than warfarin in patients with AF and DM.
Sudanese Communications GEO Satellite: A case study on SUDASAT
Authors: Ahmed Mayada A M , Saeed Rashid A
Published: June 2022

recently, and to cater to increased needs for communicating through satellite, there has been a growing interest in the marketplace as well as in the research community to develop advanced applications utilizing satellite communications systems. Satellite communications are becoming a common trend in Arab countries. A growing body of literature has focused on developing Geostationary Satellite (GEO) satellites. However, International Telecommunications Union (ITU) have the main coordination for all GEO satellite around the world. The present paper seeks to address the main timelines which relate to a Sudanese satellite. This research study is focused on GEO SUDASAT to offer a variety of communications applications in Sudan. The obtained data is provided from Space Capture ITU software. In this paper, we investigate a proposal for a Sudanese satellite called SUDASAT. The main goal of this paper is to define the SUDASAT technical information which consists of satellite orbital position, the main earth station, and its look angles, the coverage area, launch vehicle, satellite manufacturer and the suitable platform, EIRP, G/T, frequency bands, and several transponders.