bluuebunny/crossref_metadata_2025 huggingface dataset:
Experiences of Honours Research Students and Supervisors During the COVID-19 Pandemic: A Pilot Study Framed by Self-Determination Theory
Authors: Kumar Natasha N. , Summerell Elizabeth , Spehar Branka , Cranney Jacquelyn
Published: October 2021

This study evaluated the impact of the COVID-19 pandemic in a sample of Honours students (n = 21) and Honours supervisors (n = 41) at a major Australian university. Data were collected from voluntary, online, anonymous surveys, which included ratings of the pandemic’s impact on their 1) experience of Honours research activities, and 2) sense of relatedness, competence, autonomy, and wellbeing. Self-determination theory (SDT), which posits that the psychological needs of relatedness, competence, and autonomy lead to a sense of wellbeing, provided a theoretical framework for understanding student and supervisor experience during the pandemic. Both students and supervisors indicated significant impact of the pandemic on the students’ research projects, and the degree of perceived impact did not differ between students and supervisors. There was no relationship between the severity of impact and student or supervisor wellbeing. Student wellbeing was low, but the hypotheses that student SDT needs would not be met were only partly supported. Overall, the extent to which Honours students’ SDT needs were met predicted wellbeing; the outcome was similar for supervisors. Our hypothesis that SDT needs and wellbeing would be higher for supervisors than for students was supported. The theoretical and practical implications of these findings are discussed, including recommendations for Honours programs as we move through the current pandemic.
The Value of Anti-Müllerian Hormone in the Prediction of Spontaneous Pregnancy: A Systematic Review and Meta-Analysis
Authors: Lin Chenxi , Jing Miaomiao , Zhu Wenjun , Tu Xiaoyu , Chen Qi , Wang Xiufang , Zheng Youbing , Zhang Runju
Published: October 2021

Objective

To determine whether serum anti-Müllerian hormone (AMH) level is a predictor of clinical pregnancy in women trying to achieve a natural conception.

Methods

The PubMed, Embase, and Cochrane Library databases were searched for articles published until August 2020. Studies that met the inclusion and exclusion criteria were included in the meta-analysis; no language limitations were imposed. Quality was appraised using the Quality Assessment of Diagnostic Accuracy Studies-2 checklist. Heterogeneity due to the threshold effect was identified; thus, we plotted a summary receiver operating characteristic curve and calculated its area under the summary receiver operating characteristic curve (AUC) and Cochran’s Q index to assess whether AMH level is a predictor of spontaneous pregnancy. Publication bias and sensitivity were also assessed.

Results

Eleven studies (4,388 women) were ultimately included in this meta-analysis. The AUC and Cochran’s Q indices were 0.5932 and 0.5702, respectively. For women younger than 35 years, the AUC was 0.6355 and the Q index was 0.6025. For those older than 35 years, the AUC was 0.5536 and the Q index was 0.5403. Subgroup analyses by study type and population characteristics showed results similar to the overall outcome. No publication bias was identified, and the sensitivity analysis confirmed the robustness of the final result.

Conclusions

Serum AMH levels have poor predictive value for natural pregnancy. The predictive value of AMH was poor in the younger and older subgroups. Our findings suggest that low serum AMH levels are not associated with reduced fertility.

Introduction

This study investigated the predictive value of anti-Müllerian hormone (AMH) level for natural pregnancy. Other than age, few factors can predict the chances of natural fertility. AMH is an established biomarker of ovarian reserve that is widely used to predict oocyte yield in cases of in vitro fertilization (IVF) and menopause. In clinical practice, the applications of AMH are increasing. However, its predictive value for natural conception remains controversial. In this study, since AMH is closely related with ovarian reserve, we evaluated whether it has predictive value for natural pregnancy. Our findings will fine-tune the clinical application of AMH in pre-pregnancy counseling. The topic should be of wide interest to investigators in the reproductive endocrinology and gynecology fields.

Systematic Review Registration

PROSPERO 2020 CRD42020216265, Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020216265.
Medical Significance of Uterine Corpus Endometrial Carcinoma Patients Infected With SARS-CoV-2 and Pharmacological Characteristics of Plumbagin
Authors: Li Yongming , Yu Songzuo , Li Yu , Liang Xiao , Su Min , Li Rong
Published: October 2021

Background

Clinically, evidence shows that uterine corpus endometrial carcinoma (UCEC) patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may have a higher death-rate. However, current anti-UCEC/coronavirus disease 2019 (COVID-19) treatment is lacking. Plumbagin (PLB), a pharmacologically active alkaloid, is an emerging anti-cancer inhibitor. Accordingly, the current report was designed to identify and characterize the anti-UCEC function and mechanism of PLB in the treatment of patients infected with SARS-CoV-2 via integrated in silico analysis.

Methods

The clinical analyses of UCEC and COVID-19 in patients were conducted using online-accessible tools. Meanwhile, in silico methods including network pharmacology and biological molecular docking aimed to screen and characterize the anti-UCEC/COVID-19 functions, bio targets, and mechanisms of the action of PLB.

Results

The bioinformatics data uncovered the clinical characteristics of UCEC patients infected with SARS-CoV-2, including specific genes, health risk, survival rate, and prognostic index. Network pharmacology findings disclosed that PLB-exerted anti-UCEC/COVID-19 effects were achieved through anti-proliferation, inducing cytotoxicity and apoptosis, anti-inflammation, immunomodulation, and modulation of some of the key molecular pathways associated with anti-inflammatory and immunomodulating actions. Following molecular docking analysis, in silico investigation helped identify the anti-UCEC/COVID-19 pharmacological bio targets of PLB, including mitogen-activated protein kinase 3 (MAPK3), tumor necrosis factor (TNF), and urokinase-type plasminogen activator (PLAU).

Conclusions

Based on the present bioinformatic and in silico findings, the clinical characterization of UCEC/COVID-19 patients was revealed. The candidate, core bio targets, and molecular pathways of PLB action in the potential treatment of UCEC/COVID-19 were identified accordingly.
Hepatic Steatosis Contributes to the Development of Muscle Atrophy via Inter-Organ Crosstalk
Authors: Pasmans Kenneth , Adriaens Michiel E. , Olinga Peter , Langen Ramon , Rensen Sander S. , Schaap Frank G. , Olde Damink Steven W. M. , Caiment Florian , van Loon Luc J. C. , Blaak Ellen E. , Meex Ruth C. R.
Published: October 2021

Individuals with hepatic steatosis often display several metabolic abnormalities including insulin resistance and muscle atrophy. Previously, we found that hepatic steatosis results in an altered hepatokine secretion profile, thereby inducing skeletal muscle insulin resistance via inter-organ crosstalk. In this study, we aimed to investigate whether the altered secretion profile in the state of hepatic steatosis also induces skeletal muscle atrophy via effects on muscle protein turnover. To investigate this, eight-week-old male C57BL/6J mice were fed a chow (4.5% fat) or a high-fat diet (HFD; 45% fat) for 12 weeks to induce hepatic steatosis, after which the livers were excised and cut into ~200-µm slices. Slices were cultured to collect secretion products (conditioned medium; CM). Differentiated L6-GLUT4myc myotubes were incubated with chow or HFD CM to measure glucose uptake. Differentiated C2C12 myotubes were incubated with chow or HFD CM to measure protein synthesis and breakdown, and gene expression via RNA sequencing. Furthermore, proteomics analysis was performed in chow and HFD CM. It was found that HFD CM caused insulin resistance in L6-GLUT4myc myotubes compared with chow CM, as indicated by a blunted insulin-stimulated increase in glucose uptake. Furthermore, protein breakdown was increased in C2C12 cells incubated with HFD CM, while there was no effect on protein synthesis. RNA profiling of C2C12 cells indicated that 197 genes were differentially expressed after incubation with HFD CM, compared with chow CM, and pathway analysis showed that pathways related to anatomical structure and function were enriched. Proteomics analysis of the CM showed that 32 proteins were differentially expressed in HFD CM compared with chow CM. Pathway enrichment analysis indicated that these proteins had important functions with respect to insulin-like growth factor transport and uptake, and affect post-translational processes, including protein folding, protein secretion and protein phosphorylation. In conclusion, the results of this study support the hypothesis that secretion products from the liver contribute to the development of muscle atrophy in individuals with hepatic steatosis.
Early Follicular Phase Human Chorionic Gonadotropin Addition May Improve the Outcomes of In Vitro Fertilization/Intracytoplasmic Sperm Injection in Patients With “Unpredictable” Poor Response to Gonadotropin-Releasing Hormone Antagonist Protocol
Authors: Zhang Chunhui , Wu Fangrong , Wu Zexuan , Sun Bolan , Chen Cheng , Qian Weiping
Published: October 2021

Purpose

To compare the effects of early and mid-late follicular phase administration of 150 IU of human chorionic gonadotropin (hCG) on gonadotropin-releasing hormone (GnRH) antagonist protocol in “unpredictable” poor ovarian response (POR) women undergoing in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) treatment.

Methods

A retrospective single-center cohort study was conducted on 67 patients with “unpredictable” POR in their first IVF/ICSI cycle receiving GnRH antagonist protocol. Patients were treated with a second IVF/ICSI cycle using the same GnRH antagonist protocol with the same starting dose of recombinant follicle-stimulating hormone (rFSH) as the first cycle; a daily dose of 150 IU of hCG was administrated on either stimulation day 1 (Group A, n = 35) or day 6 (Group B, n = 32). The number of oocytes retrieved, number of usable embryos, serum level of estradiol (E2) on day of hCG trigger, and clinical pregnant outcomes were studied.

Results

The addition of 150 IU of hCG on either the first day or sixth day of stimulation increases the serum level of E2, luteinizing hormone (LH), and hCG on the day of hCG trigger. Only the use of 150 IU of hCG on the first stimulation day improved the number of oocytes retrieved, mature of oocytes, and usable embryos, but not the addition of hCG on stimulation day 6. Implantation rate, clinical pregnancy rate, and ongoing pregnancy rate showed an increasing trend in patients receiving 150 IU of hCG in the early phase compared with mid-late phase, even thought there was no statistically significant difference.

Conclusions

Our study demonstrated that adding 150 IU of hCG in subsequent GnRH antagonist cycle in “unpredictable” poor responders is associated with the improvement of response to stimulation. Furthermore, early follicular phase addition of 150 IU of hCG significantly increased the number of oocytes retrieved and usable embryos than did the mid-late addition of the same dose.
Basal and Calcium-Stimulated Procalcitonin for the Diagnosis of Medullary Thyroid Cancers: Lights and Shadows
Authors: Censi Simona , Di Stefano Marta , Repaci Andrea , Benvenuti Teresa , Manso Jacopo , Pagotto Uberto , Iacobone Maurizio , Barollo Susi , Bertazza Loris , Galuppini Francesca , Benna Clara , Pennelli Gianmaria , Plebani Mario , Faggian Diego , Colombo Carla , Fugazzola Laura , Mian Caterina
Published: October 2021

Background

Procalcitonin (proCt) was recently proposed as an alternative or in addition to calcitonin (Ct) in medullary thyroid cancer (MTC) diagnostics.

Methods

Serum basal Ct (bCt) and proCt (bproCt) levels were measured before surgery from a consecutive series of patients with (n=43) and without (n=75) MTC, retrospectively collected in Padua. Serum bproCt, bCt and stimulated proCt and Ct (sproCt and sCt) were measured in another consecutive series of 33 patients seen at three tertiary-level institutions undergoing a calcium stimulation test prior to surgery, 20 of them with a final diagnosis of MTC, and 13 with non-MTC nodular disease.

Results

Median bproCt levels were higher in MTC than in non-MTC. A positive correlation was found for bproCt with bCt (P<0.01, R2 = 0.75), and with tumor size (P<0.01, R2 = 0.39). The cut-off for bproCt differentiating between MTC and non-MTC patients was >0.07 ng/ml (sensitivity: 85.7%, specificity: 98.9%, positive predictive value [PPV]: 98.2%, negative predictive value [NPV]: 90.6%, P<0.01). While bproCt was >0.07 ng/ml in 38/39 (97.4%) patients with MTC >10 mm, it was above said cut-off only in 15/23 (65.2%) patients with tumors ≤10 mm. A sproCt >0.19 ng/ml was able to identify MTC [sensitivity: 90.0%, specificity:100.0%, PPV: 100.0%, NPV: 86.7% (P<0.01)].

Conclusions

Our data suggest that bproCt can be a good adjunct to Ct for MTC diagnostic purposes. In consideration of its high specificity, it can be used in combination with Ct in MTC diagnostics, particularly in the case of mildly elevated basal Ct levels.
A Theoretical Model of Sequential Combinatorial Games of Subsidies and Penalties: From Waste to Renewable Energy
Authors: Dou Yijie , Zhang Tong , Meng Xin
Published: October 2021

Subsidies and penalties are two main regulation methods adopted by authorities to promote the development of renewable energy. Due to the possibility of subsidy fraud, it is necessary to explore effective ways to combine these two policies. In this article, subsidy and penalty policies are incorporated into a sequential game theory model to explore the impact of different regulatory mechanisms on the promotion of renewable energy from recycled resources. We take biodiesel production from used cooking oil (UCO) as an example. UCO can be converted into environmentally friendly biodiesel or mixed with fresh cooking oil, resulting in inferior cooking oil containing harmful carcinogens but with huge profits. There are two mechanisms in the sequential combination model, spot checks after subsidy and subsidy after spot checks. Under both cases, fines are imposed if fraud is found during spot checks. The amounts of subsidies and fines also need to be determined. We show that the effects of subsidies depend on the implementation of the timing. The ex-ante subsidies have no effect. When spot checks are performed first, the larger subsidies will increase the probability of producing inferior cooking oil due to lower probability of spot checks. While combined with penalties, the ex-post subsidies have a positive effect on biodiesel production, that is, there exists synergy effect of penalty and subsidy on renewable energy production. In an infinitely repeated game, the shutdown threat of a grim trigger strategy (GTS) is much easier to induce biodiesel production than the penalty threat of a tit-for-tat strategy (TFT). When penalties are large enough, TFT can achieve the same goal of legal production effectively as GTS. The sooner illegal production is observed, the lower penalties are required to induce the processor to produce legally. Compared to subsidies, penalties are more effective in encouraging processors to produce renewable energy rather than illegal products. Moreover, our simulation results suggest that higher fines or profits from legal production are more likely to stimulate renewable energy production than subsidies. Our findings enrich our knowledge of the link between government regulations and the promotion of renewable energy.
Applications of Thermal Energy Storage in Solar Organic Rankine Cycles: A Comprehensive Review
Authors: Salem Mohamed , Fahim Alavi Morteza , Mahariq Ibrahim , Accouche Oussama , El Haj Assad Mamdouh
Published: October 2021

Organic Rankine Cycles (ORCs) are promising approaches for generating power from medium or low temperature heat sources. In this regard, ORCs can be used to indirectly produce power from solar energy. Due to intermittent nature of solar energy, storage unit should be coupled with solar ORCs to improve the output power and operating hours. In this article, studies on solar ORCs integrated with various types of storage units were reviewed; the main findings of such studies were extracted and provided. Based on the findings, several factors such as the temperature and pressure at the inlet of the turbine, as well as the operating condition affect the performance of solar ORCs with thermal storage unit just like the conventional ORCs. In addition, the optimum size of the storage unit in the solar ORCs was found to depend on the operating condition. From the financial perspective, it can be noted that the storage unit affects the corresponding indicators. Moreover, the improvement rate in the ORCs by applying storage units could be affected by the configuration of the system.
Occurrence of Multidrug-Resistant Listeria monocytogenes in Environmental Waters: A Menace of Environmental and Public Health Concern
Authors: Kayode Adeoye John , Semerjian Lucy , Osaili Tareq , Olapade Ola , Okoh Anthony Ifeanyi
Published: October 2021

The occurrence and antibiogram profiles ofListeria monocytogenesin environmental waters in the Eastern Cape Province, South Africa, were investigated. Seventy-eight samples from rivers, wastewater, and irrigation water were collected at different geographical locations within the province from February to September 2019. The procedure of the International Organization for Standardization EN ISO 11290:2017 part 1 and 2 was adopted for the isolation of Lm. The counts of presumptive Lm ranged from 2.0 × 103 CFU/100 ml to 3.6 × 105 CFU/100 ml. About 39.74% of the samples were positive for Lm, and the isolates were confirmed as serotype 1/2a (78.95%) and serotype 4b (21.05%). About 68.42% of the isolates demonstrated biofilm-forming potentials. Ten virulence determinants including theplcA, inlA, andinlBwere detected in all the isolates; however,inlC(85.97%),inlJ(80.70%),actA(59.65%),prfA(92.98%),plcB(89.47%),hly(80.70%), andmpl(73.68%) were less prevalent. The antibiogram profiles of confirmed Lm isolates revealed high susceptibilities (>50%) to all antibiotics ranging from 52.63% (cefotetan) to 100% (ampicillin) except for sulfamethoxazole (35.09%), erythromycin (26.32%), streptomycin (38.60%), oxytetracycline (45.61%), and amoxicillin (49.12%). Conversely, high resistance rates against sulfamethoxazole (63.16%), oxytetracycline (54.39%), and amoxicillin (50.88%) were observed. Isolates exhibited 52 resistance patterns against 22 antibiotics tested ranging from 1 to 15 antibiotics, and 82.46% showed multidrug-resistance phenotypes against the antibiotics. The antibiotic resistance index (ARI) of river water (0.18) was less than the permissible (0.2) Krumperman threshold, whereas that of irrigation and wastewater were higher than the Krumperman threshold. The multiple/antibiotic resistance index ((M)ARI) of each of the isolates ranged from 0.05–0.68. Resistance determinants (21) encoding resistance against sulphonamides, β-lactamase, phenicols, aminoglycosides, and tetracyclines were detected among the phenotypically resistant Lm isolates investigated which justifies the phenotypic resistance observed in this study. The abundance of resistance determinants in Lm recovered from environmental waters in this study suggests that the aquatic environments may serve as a channel for the dissemination of antimicrobial-resistant Lm to other niches including the food chain.
Hierarchical Functional Response of a Forager on a Wetland Landscape
Authors: DeAngelis Donald L. , Yurek Simeon , Tennenbaum Stephen , Lee Hyo Won
Published: October 2021

We show that for some foragers the form that a functional response takes depends on the temporal and spatial scales considered. In representing the consumption rate of an organism, it may be necessary to use a hierarchy of functional responses. Consider, for example, a wading bird foraging in wetland landscape characterized by a spatial distribution of potential foraging sites, such as ponds. At the smallest time scale of minutes or hours, during which a wading bird is foraging within a single site, the functional response will reflect the local density of prey, as well as features of the site that affect the feeding rate, such as water depth. At this short time scale, which is determined by the giving up time of the wading bird in a particular site, prey density may be relatively constant. The food intake from a particular pond is then the product of the time spent before giving-up time and moving to another site and the rate of prey consumption at that site. A prey-centered functional response is most appropriate for describing the prey consumption rate. We propose that over the longer time scale of a day, during which a wading bird may visit several foraging sites, the type of functional response can be considered to be patch centered. That is, it is influenced by the spatial configuration of sites with available prey and the wading bird’s strategy of choosing among different sites and decisions on how long to stay in any given sites. Over the time scale of a day, if the prey densities stay relatively constant, the patch-centered functional response for a constant environment is adequate. However, on the longer time scale of a breeding season, in which changing water levels result in temporal changes in the availability of prey in sites, a third hierarchical level may be relevant. At that scale, the way in which the landscape pattern changes through time, and how the wading bird responds, influences the functional response. This hierarchical concept applies to a colony of breeding wading birds foraging in wetlands such as the Everglades.
Dendrochronology in European Russia in the Early 21st Century: State of the Art
Authors: Solomina Olga , Matskovsky Vladimir
Published: October 2021

In this review, we have focused on the following key points: (1) living trees in European Russia and their climatic sensitivity. Species suitable for tree-ring analyses, their age limits, spatial distribution of temperature- and drought-sensitive trees, and the available tree-ring chronologies. (2) Extension of the living-tree chronologies using archeological and architectural samples. Dendrochronological dating of archeological and cultural monuments. (3) Tree-ring-based climatic reconstructions in European Russia. European Russia drought atlas. (4) Climatic and environmental reconstructions in the Northern Caucasus. (5) Dendroecology. We also briefly summarized the problems and prospects of tree-ring research in European Russia.
Correlative Localization Analysis Between mRNA and Enhanced Green Fluorescence Protein-Fused Protein by a Single-Molecule Fluorescence in situ Hybridization Using an egfp Probe in Aspergillus oryzae
Authors: Morita Yuki , Katakura Yoshinori , Takegawa Kaoru , Higuchi Yujiro
Published: October 2021

Although subcellular localization analysis of proteins fused with enhanced green fluorescence protein (EGFP) has been widely conducted in filamentous fungi, little is known about the localization of messenger RNAs (mRNAs) encoding the EGFP-fused proteins. In this study, we performed single-molecule fluorescence in situ hybridization (smFISH) using an egfp probe to simultaneously visualize EGFP-fused proteins and their mRNAs in the hyphal cells of the filamentous fungus Aspergillus oryzae. We investigated the subcellular localization of mRNAs encoding cytoplasmic EGFP, an actin marker protein Lifeact tagged with EGFP, and several EGFP-fused proteins AoSec22, AoSnc1, AoVam3, and AoUapC that localize to the endoplasmic reticulum (ER), the apical vesicle cluster Spitzenkörper, vacuolar membrane, and plasma membrane, respectively. Visualization of these mRNAs by smFISH demonstrated that each mRNA exhibited distinct localization patterns likely depending on the mRNA sequence. In particular, we revealed that mRNAs encoding Lifeact-EGFP, EGFP-AoSec22, EGFP-AoVam3, and AoUapC-EGFP, but not cytoplasmic EGFP and EGFP-AoSnc1, were preferentially localized at the apical cell, suggesting certain mechanisms to regulate the existence of these transcripts among hyphal regions. Our findings provide the distinct localization information of each mRNA in the hyphal cells of A. oryzae.
Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries
Authors: Bendixsen Devin P. , Peris David , Stelkens Rike
Published: October 2021

The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecificSaccharomycesyeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.
A Novel Six Autophagy-Related Genes Signature Associated With Outcomes and Immune Microenvironment in Lower-Grade Glioma
Authors: Lin Tao , Cheng Hao , Liu Da , Wen Lei , Kang Junlin , Xu Longwen , Shan Changguo , Chen Zhijie , Li Hainan , Lai Mingyao , Zhou Zhaoming , Hong Weiping , Hu Qingjun , Li Shaoqun , Zhou Cheng , Geng Jiwu , Jin Xin
Published: October 2021

Since autophagy and the immune microenvironment are deeply involved in the tumor development and progression of Lower-grade gliomas (LGG), our study aimed to construct an autophagy-related risk model for prognosis prediction and investigate the relationship between the immune microenvironment and risk signature in LGG. Therefore, we identified six autophagy-related genes (BAG1, PTK6, EEF2, PEA15, ITGA6, and MAP1LC3C) to build in the training cohort (n = 305 patients) and verify the prognostic model in the validation cohort (n = 128) and the whole cohort (n = 433), based on the data from The Cancer Genome Atlas (TCGA). The six-gene risk signature could divide LGG patients into high- and low-risk groups with distinct overall survival in multiple cohorts (all p < 0.001). The prognostic effect was assessed by area under the time-dependent ROC (t-ROC) analysis in the training, validation, and whole cohorts, in which the AUC value at the survival time of 5 years was 0.837, 0.755, and 0.803, respectively. Cox regression analysis demonstrated that the risk model was an independent risk predictor of OS (HR > 1, p < 0.05). A nomogram including the traditional clinical parameters and risk signature was constructed, and t-ROC, C-index, and calibration curves confirmed its robust predictive capacity. KM analysis revealed a significant difference in the subgroup analyses’ survival. Functional enrichment analysis revealed that these autophagy-related signatures were mainly involved in the phagosome and immune-related pathways. Besides, we also found significant differences in immune cell infiltration and immunotherapy targets between risk groups. In conclusion, we built a powerful predictive signature and explored immune components (including immune cells and emerging immunotherapy targets) in LGG.
hGATA1 Under the Control of a μLCR/β-Globin Promoter Rescues the Erythroid but Not the Megakaryocytic Phenotype Induced by the Gata1low Mutation in Mice
Authors: Martelli Fabrizio , Verachi Paola , Zingariello Maria , Mazzarini Maria , Vannucchi Alessandro M. , Lonetti Annalisa , Bacci Barbara , Sarli Giuseppe , Migliaccio Anna Rita
Published: October 2021

The phenotype of mice carrying the Gata1low mutation that decreases expression of Gata1 in erythroid cells and megakaryocytes, includes anemia, thrombocytopenia, hematopoietic failure in bone marrow and development of extramedullary hematopoiesis in spleen. With age, these mice develop myelofibrosis, a disease sustained by alterations in stem/progenitor cells and megakaryocytes. This study analyzed the capacity of hGATA1 driven by a μLCR/β-globin promoter to rescue the phenotype induced by the Gata1low mutation in mice. Double hGATA1/Gata1low/0 mice were viable at birth with hematocrits greater than those of their Gata1low/0 littermates but platelet counts remained lower than normal. hGATA1 mRNA was expressed by progenitor and erythroid cells from double mutant mice but not by megakaryocytes analyzed in parallel. The erythroid cells from hGATA1/Gata1low/0 mice expressed greater levels of GATA1 protein and of α- and β-globin mRNA than cells from Gata1low/0 littermates and a reduced number of them was in apoptosis. By contrast, hGATA1/Gata1low/0 megakaryocytes expressed barely detectable levels of GATA1 and their expression of acetylcholinesterase, Von Willebrand factor and platelet factor 4 as well as their morphology remained altered. In comparison with Gata1+/0 littermates, Gata1low/0 mice contained significantly lower total and progenitor cell numbers in bone marrow while the number of these cells in spleen was greater than normal. The presence of hGATA1 greatly increased the total cell number in the bone marrow of Gata1low/0 mice and, although did not affect the total cell number of the spleen which remained greater than normal, it reduced the frequency of progenitor cells in this organ. The ability of hGATA1 to rescue the hematopoietic functions of the bone marrow of the double mutants was confirmed by the observation that these mice survive well splenectomy and did not develop myelofibrosis with age. These results indicate that hGATA1 under the control of µLCR/β-globin promoter is expressed in adult progenitors and erythroid cells but not in megakaryocytes rescuing the erythroid but not the megakaryocyte defect induced by the Gata1low/0 mutation.
Animal Models of Ehlers–Danlos Syndromes: Phenotype, Pathogenesis, and Translational Potential
Authors: Vroman Robin , Malfait Anne-Marie , Miller Rachel E. , Malfait Fransiska , Syx Delfien
Published: October 2021

The Ehlers–Danlos syndromes (EDS) are a group of heritable connective tissues disorders mainly characterized by skin hyperextensibility, joint hypermobility and generalized tissue fragility. Currently, 14 EDS subtypes each with particular phenotypic features are recognized and are caused by genetic defects in 20 different genes. All of these genes are involved in the biosynthesis and/or fibrillogenesis of collagens at some level. Although great progress has been made in elucidating the molecular basis of different EDS subtypes, the pathogenic mechanisms underlying the observed phenotypes remain poorly understood, and consequentially, adequate treatment and management options for these conditions remain scarce. To date, several animal models, mainly mice and zebrafish, have been described with defects in 14 of the 20 hitherto known EDS-associated genes. These models have been instrumental in discerning the functions and roles of the corresponding proteins during development, maturation and repair and in portraying their roles during collagen biosynthesis and/or fibrillogenesis, for some even before their contribution to an EDS phenotype was elucidated. Additionally, extensive phenotypical characterization of these models has shown that they largely phenocopy their human counterparts, with recapitulation of several clinical hallmarks of the corresponding EDS subtype, including dermatological, cardiovascular, musculoskeletal and ocular features, as well as biomechanical and ultrastructural similarities in tissues. In this narrative review, we provide a comprehensive overview of animal models manifesting phenotypes that mimic EDS with a focus on engineered mouse and zebrafish models, and their relevance in past and future EDS research. Additionally, we briefly discuss domestic animals with naturally occurring EDS phenotypes. Collectively, these animal models have only started to reveal glimpses into the pathophysiological aspects associated with EDS and will undoubtably continue to play critical roles in EDS research due to their tremendous potential for pinpointing (common) signaling pathways, unveiling possible therapeutic targets and providing opportunities for preclinical therapeutic interventions.
Using Summary Statistics to Model Multiplicative Combinations of Initially Analyzed Phenotypes With a Flexible Choice of Covariates
Authors: Wolf Jack M. , Westra Jason , Tintle Nathan
Published: October 2021

While the promise of electronic medical record and biobank data is large, major questions remain about patient privacy, computational hurdles, and data access. One promising area of recent development is pre-computing non-individually identifiable summary statistics to be made publicly available for exploration and downstream analysis. In this manuscript we demonstrate how to utilize pre-computed linear association statistics between individual genetic variants and phenotypes to infer genetic relationships between products of phenotypes (e.g., ratios; logical combinations of binary phenotypes using “and” and “or”) with customized covariate choices. We propose a method to approximate covariate adjusted linear models for products and logical combinations of phenotypes using only pre-computed summary statistics. We evaluate our method’s accuracy through several simulation studies and an application modeling ratios of fatty acids using data from the Framingham Heart Study. These studies show consistent ability to recapitulate analysis results performed on individual level data including maintenance of the Type I error rate, power, and effect size estimates. An implementation of this proposed method is available in the publicly available R package pcsstools.
A Novel Meiosis-Related lncRNA, Rbakdn, Contributes to Spermatogenesis by Stabilizing Ptbp2
Authors: Liu Wensheng , Zhao Yinan , Liu Xiaohua , Zhang Xiaoya , Ding Jiancheng , Li Yang , Tian Yingpu , Wang Haibin , Liu Wen , Lu Zhongxian
Published: October 2021

Spermatocyte meiosis is the cornerstone of mammalian production. Thousands of long noncoding RNAs (lncRNAs) have been reported to be functional in various cellular processes, but the function of lncRNAs in meiosis remains largely unknown. Here, we profiled lncRNAs in spermatocytes at stage I of meiosis and identified a testis-specific lncRNA, Rbakdn, as a vital regulator of meiosis. Rbakdn is dynamically expressed during meiosis I, and Rbakdn knockdown inhibits meiosis in vitro. Furthermore, Rbakdn knockdown in testes in mice by intratesticular injection disturbs meiosis, reduces testicular volume, and increases apoptosis of spermatocytes, resulting in vacuolation of the seminiferous tubules. Rbakdn can bind to Ptbp2, an RNA-binding protein that is important in the regulation of the alternative splicing of many genes in spermatogenesis. Rbakdn knockdown leads to a decrease in Ptbp2 through the ubiquitination degradation pathway, indicating that Rbakdn maintains the stability of Ptbp2. In conclusion, our study identified an lncRNA, Rbakdn, with a crucial role in meiosis.
Vps54 Regulates Lifespan and Locomotor Behavior in Adult Drosophila melanogaster
Authors: Wilkinson Emily C. , Starke Emily L. , Barbee Scott A.
Published: October 2021

Vps54 is an integral subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). A destabilizing missense mutation in Vps54 causes the age-progressive motor neuron (MN) degeneration, muscle weakness, and muscle atrophy observed in the wobbler mouse, an established animal model for human MN disease. It is currently unclear how the disruption of Vps54, and thereby the GARP complex, leads to MN and muscle phenotypes. To develop a new tool to address this question, we have created an analogous model in Drosophila by generating novel loss-of-function alleles of the fly Vps54 ortholog (scattered/scat). We find that null scat mutant adults are viable but have a significantly shortened lifespan. Like phenotypes observed in the wobbler mouse, we show that scat mutant adults are male sterile and have significantly reduced body size and muscle area. Moreover, we demonstrate that scat mutant adults have significant age-progressive defects in locomotor function. Interestingly, we see sexually dimorphic effects, with scat mutant adult females exhibiting significantly stronger phenotypes. Finally, we show that scat interacts genetically with rab11 in MNs to control age-progressive muscle atrophy in adults. Together, these data suggest that scat mutant flies share mutant phenotypes with the wobbler mouse and may serve as a new genetic model system to study the cellular and molecular mechanisms underlying MN disease.
The Ubiquitin Conjugating Enzyme UbcD1 is Required for Notch Signaling Activation During Drosophila Wing Development
Authors: Zhang Fengchao , Chen Yao , Shen Jie , Zhang Junzheng
Published: October 2021

Notch signaling pathway plays crucial roles in animal development. Protein ubiquitination contributes to Notch signaling regulation by governing the stability and activity of major signaling components. Studies in Drosophila have identified multiple ubiquitin ligases and deubiquitinating enzymes that modify Notch ligand and receptor proteins. The fate of ubiquitinated substrates depend on topologies of the attached ubiquitin chains, which are determined by the ubiquitin conjugating enzymes (E2 enzymes). However, which E2 enzymes participate in Notch signal transduction remain elusive. Here, we report that the E2 enzyme UbcD1 is required for Notch signaling activation during Drosophila wing development. Mutations of UbcD1 lead to marginal nicks in the adult wing and reduction of Notch signaling targets expression in the wing imaginal disc. Genetic analysis reveal that UbcD1 functions in the signaling receiving cells prior to cleavage of the Notch protein. We provide further evidence suggesting that UbcD1 is likely involved in endocytic trafficking of Notch protein. Our results demonstrate that UbcD1 positively regulates Notch signaling and thus reveal a novel role of UbcD1 in development.
Defining the Role of Nuclear Factor (NF)-κB p105 Subunit in Human Macrophage by Transcriptomic Analysis of NFKB1 Knockout THP1 Cells
Authors: Somma Domenico , Kok Fatma O. , Kerrigan David , Wells Christine A. , Carmody Ruaidhrí J.
Published: October 2021

Since its discovery over 30 years ago the NF-ĸB family of transcription factors has gained the status of master regulator of the immune response. Much of what we understand of the role of NF-ĸB in immune development, homeostasis and inflammation comes from studies of mice null for specific NF-ĸB subunit encoding genes. The role of inflammation in diseases that affect a majority of individuals with health problems globally further establishes NF-ĸB as an important pathogenic factor. More recently, genomic sequencing has revealed loss of function mutations in the NFKB1 gene as the most common monogenic cause of common variable immunodeficiencies in Europeans. NFKB1 encodes the p105 subunit of NF-ĸB which is processed to generate the NF-ĸB p50 subunit. NFKB1 is the most highly expressed transcription factor in macrophages, key cellular drivers of inflammation and immunity. Although a key role for NFKB1 in the control of the immune system is apparent from Nfkb1-/- mouse studies, we know relatively little of the role of NFKB1 in regulating human macrophage responses. In this study we use the THP1 monocyte cell line and CRISPR/Cas9 gene editing to generate a model of NFKB1-/- human macrophages. Transcriptomic analysis reveals that activated NFKB1-/- macrophages are more pro-inflammatory than wild type controls and express elevated levels of TNF, IL6, and IL1B, but also have reduced expression of co-stimulatory factors important for the activation of T cells and adaptive immune responses such as CD70, CD83 and CD209. NFKB1-/- THP1 macrophages recapitulate key observations in individuals with NFKB1 haploinsufficiency including decreased IL10 expression. These data supporting their utility as an in vitro model for understanding the role of NFKB1 in human monocytes and macrophages and indicate that of loss of function NFKB1 mutations in these cells is an important component in the associated pathology.
Seminal Plasma and Seminal Plasma Exosomes of Aged Male Mice Affect Early Embryo Implantation via Immunomodulation
Authors: Wang Dandan , Jueraitetibaike Kadiliya , Tang Ting , Wang Yanbo , Jing Jun , Xue Tongmin , Ma Jinzhao , Cao Siyuan , Lin Ying , Li Xiaoyan , Ma Rujun , Chen Xi , Yao Bing
Published: October 2021

Seminal plasma (SP), particularly SP exosomes (sExos), alters with age and can affect female mouse uterine immune microenvironment. However, the relationship between fertility decline in reproductively older males, and SP and sExos age-related changes, which may compromise the uterine immune microenvironment, remains unclear. The present study demonstrated that the implantation rate of female mice treated with SP from reproductively older male mice (aged-SP group) was lower than that of those treated with SP from younger male mice (young-SP group). RNA-sequencing analysis revealed altered levels of dendritic cell (DC)-related cytokines and chemokines in the uteri of the former group compared with those of the latter group. In vivo and in vitro experiments demonstrated a weaker inhibitory effect of aged SP on DC maturation than of young SP upon stimulation. After isolating and characterizing sExos from young and advanced-age male mice, we discovered that insemination of a subset of the aged-SP group with sExos from young male mice partially recovered the implantation rate decline. Additional in vivo and in vitro experiments revealed that sExos extracted from age male mice exerted a similar effect on DC maturation as SP of aged mice, indicating an age-related sExos inhibitory effect. In conclusion, our study demonstrated that age-related alterations of sExos may be partially responsible for lower implantation rates in the aged-SP group compared with those in the young-SP group, which were mediated by uterine immunomodulation. These findings provide new insights for clinical seminal adjuvant therapy.
Diminished Peripheral CD29hi Cytotoxic CD4+ T Cells Are Associated With Deleterious Effects During SIV Infection
Authors: Olwenyi Omalla A. , Johnson Samuel D. , Pandey Kabita , Thurman Michellie , Acharya Arpan , Buch Shilpa J. , Fox Howard S. , Podany Anthony T. , Fletcher Courtney V. , Byrareddy Siddappa N.
Published: October 2021

Cytotoxic CD4+ T cells (CD4+ CTLs) limit HIV pathogenesis, as evidenced in elite controllers (a subset of individuals who suppress the virus without the need for therapy). CD4+ CTLs have also been shown to kill HIV-infected macrophages. However, little is known about their contribution towards HIV persistence, how they are affected following exposure to immune modulators like morphine, and what factors maintain their frequencies and function. Further, the lack of robust markers to identify CD4+ CTLs in various animal models limits understanding of their role in HIV pathogenesis. We utilized various PBMC samples obtained from SIV infected and cART treated rhesus macaques exposed to morphine or saline and subjected to flow cytometry evaluations. Thereafter, we compared and correlated the expression of CD4+ CTL-specific markers to viral load and viral reservoir estimations in total CD4+ T cells. We found that CD29 could be reliably used as a marker to identify CD4+ CTLs in rhesus macaques since CD29hi CD4+ T cells secrete higher cytotoxic and proinflammatory cytokines following PMA/ionomycin or gag stimulation. In addition, this immune cell subset was depleted during untreated SIV infection. Strikingly, we also observed that early initiation of cART reconstitutes depleted CD29hi CD4+ T cells and restores their function. Furthermore, we noted that morphine exposure reduced the secretion of proinflammatory cytokines/cytotoxic molecules in CD29hi CD4+ T cells. Lastly, increased functionality of CD29hi CD4+ T cells as depicted by elevated levels of either IL-21 or granzyme B hi T Bet+ gag specific responses were linked to limiting the size of the replication-competent reservoir during cART treatment. Collectively, our data suggest that CD4+ CTLs are crucial in limiting SIV pathogenesis and persistence.
Traditional Farming Lifestyle in Old Older Mennonites Modulates Human Milk Composition
Authors: Seppo Antti E. , Choudhury Rakin , Pizzarello Catherine , Palli Rohith , Fridy Sade , Rajani Puja Sood , Stern Jessica , Martina Camille , Yonemitsu Chloe , Bode Lars , Bu Kevin , Tamburini Sabrina , Piras Enrica , Wallach David S. , Allen Maria , Looney R. John , Clemente Jose C. , Thakar Juilee , Järvinen Kirsi M.
Published: October 2021

Background

In addition to farming exposures in childhood, maternal farming exposures provide strong protection against allergic disease in their children; however, the effect of farming lifestyle on human milk (HM) composition is unknown.

Objective

This study aims to characterize the maternal immune effects of Old Order Mennonite (OOM) traditional farming lifestyle when compared with Rochester (ROC) families at higher risk for asthma and allergic diseases using HM as a proxy.

Methods

HM samples collected at median 2 months of lactation from 52 OOM and 29 ROC mothers were assayed for IgA1 and IgA2 antibodies, cytokines, endotoxin, HM oligosaccharides (HMOs), and targeted fatty acid (FA) metabolites. Development of early childhood atopic diseases in children by 3 years of age was assessed. In addition to group comparisons, systems level network analysis was performed to identify communities of multiple HM factors in ROC and OOM lifestyle.

Results

HM contains IgA1 and IgA2 antibodies broadly recognizing food, inhalant, and bacterial antigens. OOM HM has significantly higher levels of IgA to peanut, ovalbumin, dust mites, and Streptococcus equii as well TGF-β2, and IFN-λ3. A strong correlation occurred between maternal antibiotic use and levels of several HMOs. Path-based analysis of HMOs shows lower activity in the path involving lactoneohexaose (LNH) in the OOM as well as higher levels of lacto-N-neotetraose (LNnT) and two long-chain FAs C-18OH (stearic acid) and C-23OH (tricosanoic acid) compared with Rochester HM. OOM and Rochester milk formed five different clusters, e.g., butyrate production was associated with Prevotellaceae, Veillonellaceae, and Micrococcaceae cluster. Development of atopic disease in early childhood was more common in Rochester and associated with lower levels of total IgA, IgA2 to dust mite, as well as of TSLP.

Conclusion

Traditional, agrarian lifestyle, and antibiotic use are strong regulators of maternally derived immune and metabolic factors, which may have downstream implications for postnatal developmental programming of infant’s gut microbiome and immune system.