bluuebunny/crossref_metadata_2025 huggingface dataset:
Relative Importance for Lincoln’s Sparrow (Melospiza lincolnii) Occupancy of Vegetation Type versus Noise Caused by Industrial Development
Authors: Sánchez Natalie V. , Sandoval Luis , Hedley Richard W. , St. Clair Colleen C. , Bayne Erin M.
Published: March 2022

Anthropogenic noise can create an acoustic environment detrimental for animals that communicate using acoustic signals. Currently, most studies of noise and wildlife come from traffic noise in cities. Less is known about the effects of noise created by industry in natural areas. Songbirds far from cities, but influenced by industry, could be affected by noise, but also are likely to be impacted by changes in vegetation conditions related to industrial development. We described the importance of industrial noise (from facilities and transportation) on occupancy of Lincoln’s Sparrow (Melospiza lincolnii) relative to habitat change caused by vegetation alteration and edge effects. Lincoln’s Sparrows naturally breed in varying seral stages and types of boreal forest. To test the influence of industrial noise, we selected three areas in Northern Alberta, Canada with high, medium, and low levels of industrial development and varying road density. At each area, we deployed a systematic arrangement of autonomous recording units (280 units in total, separated by 600 m) for 3 consecutive days. To measure noise, we developed a method that used the relative noise values extracted from the recordings of 8 frequency-octave bands. We obtained three noise measurements: noise with high energy in the low part of the spectrum (mean 0.5–1 kHz), masking level noise (mean 2–8 kHz), and noise in all frequency octave bands (mean 0.5–16 kHz). Proportion of chronic noise sources explained the highest variation of noise in the environment, and less by traffic noise. We found Lincoln’s Sparrow had a higher occupancy in areas with higher proportion of industrial disturbances, shrubs and grass, and decreased in noisy areas. Masking level noise had a negative effect on Lincoln’s Sparrow occupancy in areas with industrial disturbances, relative to areas with similar changes in vegetation structure, but no noise. Masking noise could indicate limitation in communication as noise increases. Our study amplifies the findings of others that future research should consider not only anthropogenic changes to vegetation in human-altered landscapes, but also human-caused changes to acoustic environments.
Demographic Consequences of Small-Scale Fisheries for Two Sex-Changing Groupers of the Tropical Eastern Pacific
Authors: Chong-Montenegro Carolina , Kindsvater Holly K.
Published: March 2022

The effects of fishing on the demography and population ecology of sex-changing fishes are largely unknown, despite the fact that their fisheries provide important economic and nutritional resources in coastal communities throughout the tropics, especially in Latin America. Species with female-first sex change often have naturally skewed sex ratios in the adult population, and fishing pressure can alter this natural bias, limiting egg production and fertilization success. How fishing alters demography and population vital rates depends on which sizes and sexes are selected. We consider two types of fishery selectivity “asymptotic (selecting the largest fish) and plate-sized (selecting fish between in a narrow, but small, size range)” that to represent fisheries for two important fish species of the Tropical Eastern Pacific, the Pacific goliath grouper (Epinephelus quinquefasciatus) and the endemic sailfin grouper (Mycteroperca olfax) of the Galapagos Islands, known locally as bacalao. Each of these large, long-lived species support small scale fisheries of significant value, but there is limited information on fishing effort, selectivity, or population trends. Using a population model, we estimate how the biology of these species contributes to their risk of overexploitation under different possible scenarios of fishing and reproductive biology. Specifically, we consider how variation in growth rates and fertilization rates interact with selectivity to affect age structure and sex ratios. We compare two metrics of population status: the spawning potential ratio (SPR), and the relative standing biomass after fishing (BF/B0). In our modeled populations, when fertilization rates were reduced, fishing rapidly decreased the spawning potential of both species, but did not affect biomass at moderate levels of fishing mortality. However, we predict low fertilization success, fast somatic growth, and asymptotic selectivity of fisheries for sex-changing species decreases both spawning potential and biomass, even at low levels of exploitation, suggesting these factors can cause rapid depletion of sex-changing species. Our findings highlight key gaps in our knowledge of spawning behavior and fertilization success of sex-changing fishes that must be filled if we are to sustainably manage these culturally and economically significant fisheries.
Transcriptome Analysis Reveals miR-302a-3p Affects Granulosa Cell Proliferation by Targeting DRD1 in Chickens
Authors: Liu Yufang , Zhou Zuyang , Zhang Hui , Han Haiyin , Yang Junqi , Li Wenting , Wang Kejun
Published: March 2022

Egg production is an important economic trait in laying chickens as higher yields bring higher profits. Small yellow follicle (SYFL) development is a key determinant of chicken reproductive performance; however, the majority of SYFLs are not selected during the process of chicken reproduction and thus, atresia occurs. Although there have been numerous omic studies focused on egg production, the molecular mechanisms involved are still not well-understood. In this study, we used high-throughput technology to analyze the differences between the SYFL mRNA transcriptomes of high– (H) and low–egg-yielding (L) Taihang layer hens, with the aim of identifying the potential candidate genes involved in controlling the rate of egg production. We constructed six cDNA libraries, three from H and three from L Taihang hens and then performed high-throughput sequencing. Comparison of the H and L groups showed 415 differentially expressed genes (DEGs). In the high-yield group, 226 were upregulated and 189 were downregulated. Differentially enriched biological functions and processes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis. Ten of the candidate DEGs we identified (DRD1, MC5R, PCK1, CTSA, TGFBR3, AGO4, SLIT2, RGS1, SCNN1B, and ZP3) have been identified in previous studies as being involved in the development of small yellow follicles. DRD1 was significantly enriched in the gap junction pathway, which is an important pathway in chicken granulosa cells (GCs) to pass nutrition to an oocyte. Homology analysis showed that DRD1 was highly conserved in numerous species, indicating that it may be a productive target for improving egg production. Evidence from bioinformatics analysis revealed that gga-miR-302a-3p putatively targets the 3′UTR region of DRD1. We then identified the functions of gga-miR-302a-3p in follicular granulosa cell proliferation by targeting DRD1. RT-qPCR analysis showed that DRD1 and miR-302a-3p expression were inversely related in the SYLs of high and low egg-yielding chickens. Luciferase assays showed that miR-302a-3p targets the 3′UTR of DRD1, and overexpression of miR-302a-3p significantly inhibits the expression of DRD1 in chicken GCs (p < 0.01). Functional experiments revealed that by targeting DRD1, miR-302a-3p acts as an inhibitor of GC proliferation. Taken together, we concluded that miR-302a-3p affects chicken GC proliferation by targeting DRD1. Our data expanded the knowledge base of genes whose functions are important in egg production and the molecular mechanisms of high-yield egg production in chicken small yellow follicles.
Distinct Expression Patterns of Interleukin-22 Receptor 1 on Blood Hematopoietic Cells in SARS-CoV-2 Infection
Authors: Albayrak Nurhan , Orte Cano Carmen , Karimi Sina , Dogahe David , Van Praet Anne , Godefroid Audrey , Del Marmol Véronique , Grimaldi David , Bondue Benjamin , Van Vooren Jean-Paul , Mascart Françoise , Corbière Véronique
Published: March 2022

The new pandemic virus SARS-CoV-2 is characterized by uncontrolled hyper-inflammation in severe cases. As the IL-22/IL-22R1 axis was reported to be involved in inflammation during viral infections, we characterized the expression of IL-22 receptor1, IL-22 and IL-22 binding protein in COVID-19 patients. Blood samples were collected from 19 non-severe and 14 severe patients on the day they presented (D0), at D14, and six months later, and from 6 non-infected controls. The IL-22R1 expression was characterized by flow cytometry. Results were related to HLA-DR expression of myeloid cells, to plasma concentrations of different cytokines and chemokines and NK cells and T lymphocytes functions characterized by their IFN-γ, IL-22, IL-17A, granzyme B and perforin content. The numbers of IL-22R1+ classical, intermediate, and non-classical monocytes and the proportions of IL-22R1+ plasmacytoid DC (pDC), myeloid DC1 and DC2 (mDC1, mDC2) were higher in patients than controls at D0. The proportions of IL-22R1+ classical and intermediate monocytes, and pDC and mDC2 remained high for six months. High proportions of IL-22R1+ non-classical monocytes and mDC2 displayed HLA-DRhigh expression and were thus activated. Multivariate analysis for all IL-22R1+ myeloid cells discriminated the severity of the disease (AUC=0.9023). However, correlation analysis between IL-22R1+ cell subsets and plasma chemokine concentrations suggested pro-inflammatory effects of some subsets and protective effects of others. The numbers of IL-22R1+ classical monocytes and pDC were positively correlated with pro-inflammatory chemokines MCP-1 and IP-10 in severe infections, whereas IL-22R1+ intermediate monocytes were negatively correlated with IL-6, IFN-α and CRP in non-severe infections. Moreover, in the absence of in vitro stimulation, NK and CD4+ T cells produced IFN-γ and IL-22, and CD4+ and CD8+ T cells produced IL-17A. CD4+ T lymphocytes also expressed IL-22R1, the density of its expression defining two different functional subsets. In conclusion, we provide the first evidence that SARS-CoV-2 infection is characterized by an abnormal expression of IL22R1 on blood myeloid cells and CD4+ T lymphocytes. Our results suggest that the involvement of the IL-22R1/IL-22 axis could be protective at the beginning of SARS-CoV-2 infection but could shift to a detrimental response over time.
Quantitative Comparison of the Clinical Efficacy of 6 Classes Drugs for IgA Nephropathy: A Model-Based Meta-Analysis of Drugs for Clinical Treatments
Authors: Yu Jiesen , Luo Jieren , Zhu Haoxiang , Sui Zichao , Liu Hongxia , Li Lujin , Zheng Qingshan
Published: March 2022

Introduction

There is a wide variety of drugs for the clinical treatment of immunoglobulin A (IgA) nephropathy; however, previous studies have failed to clarify the quantitative differences in the efficacy of various drugs. In this study, we aimed to quantitatively compare the clinical efficacy of 6 classes of drugs with different pharmacological mechanisms for the treatment of IgA nephropathy and to identify relevant influencing factors.

Methods

Clinical trials of drugs for the treatment of IgA nephropathy were obtained from public databases. The change in daily urinary protein excretion from baseline was used as the efficacy index, and the time–effect model was established using a model-based meta-analysis method. Based on the final model, the typical efficacy was simulated, and the differences in efficacy were compared.

Results

A total of 40 studies with 2288 subjects were included in this study. The results showed that the time–effect relationship of the placebo and 6 classes of drugs was consistent with the Emax model. The placebo reduced urinary protein excretion by up to 0.44 g/day, and it took more than 27 months to reach half of its maximum effect. The onset of the 6 classes of drugs were the same; they all reached half of their maximum effect after 5.59 months. More importantly, we found a significant influence of urinary protein baseline on drug efficacy, as indicated by an increase of 0.63 g/day in the theoretical maximum effect of drugs for every 1 g/day increase in urinary protein baseline. After correcting for the urinary protein baseline, the order of efficacy of the 6 classes of drugs was as follows: corticosteroids > immunosuppressants > other drugs > renin–angiotensin system blockers > antiplatelet agents > N-3 fatty acids.

Conclusion

This study provides the first comprehensive quantitative analysis of the differences in the efficacy of 6 classes of drugs with different pharmacological mechanisms for treating IgA nephropathy. The results of this study provide an important reference for the rational clinical use of drugs for IgA nephropathy, and also provide a reliable efficacy standard for the development of new drugs for IgA nephropathy.
Alarmin Cytokines as Central Regulators of Cutaneous Immunity
Authors: Hasegawa Tatsuya , Oka Tomonori , Demehri Shadmehr
Published: March 2022

Skin acts as the primary interface between the body and the environment. The skin immune system is composed of a complex network of immune cells and factors that provide the first line of defense against microbial pathogens and environmental insults. Alarmin cytokines mediate an intricate intercellular communication between keratinocytes and immune cells to regulate cutaneous immune responses. Proper functions of the type 2 alarmin cytokines, thymic stromal lymphopoietin (TSLP), interleukin (IL)-25, and IL-33, are paramount to the maintenance of skin homeostasis, and their dysregulation is commonly associated with allergic inflammation. In this review, we discuss recent findings on the complex regulatory network of type 2 alarmin cytokines that control skin immunity and highlight the mechanisms by which these cytokines regulate skin immune responses in host defense, chronic inflammation, and cancer.
Spatial and Temporal Variations of Cockle (Cerastoderma spp.) Populations in Two Portuguese Estuarine Systems With Low Directed Fishing Pressure
Authors: Santos Cátia , Cabral Sara , Carvalho Frederico , Sousa António , Goulding Thomas , Ramajal João , Medeiros João Paulo , Silva Gilda , Angélico Maria Manuel , Gaspar Miguel B. , Brito Ana C. , Costa José Lino , Chainho Paula
Published: March 2022

Cockles are amongst the most exploited bivalve species in Portugal, playing an important ecological and socioeconomic role in coastal ecosystems. Two sympatric species of cockles, Cerastoderma edule (Linnaeus, 1758) and Cerastoderma glaucum (Bruguière, 1789–1792) may co-occur in estuaries and coastal lagoons in mixed populations along the European Atlantic coast, namely in Portugal, France and the United Kingdom. The increasing importance of shellfish harvesting in Portugal requires a good knowledge of cockle stocks and temporal variability in stock levels to better inform sustainable management practices. Therefore, this study aimed at assessing spatial and temporal variations in cockle populations in two Portuguese estuarine systems where the species are exploited at low levels. Sampling was carried out using a clam dredge, covering the entire potential area of occurrence of cockles in the Tagus and Sado estuaries at around the same time of the year in each of the three sampling years (2015, 2018, and 2019). The abundance, spatial distribution and population structure of cockles were examined at each system. Moreover, several water and sediment parameters were measured to understand the influence of environmental conditions on the spatial distribution and abundance of cockles. The results obtained showed that cockles occur mostly in the intermediate areas of both estuarine systems and are more abundant in the Tagus estuary. Depth, average sediment grain size and the species Ruditapes philippinarum were the factors that better explained the probability of species occurrence. The population structure analysis indicated that natural mortality is constraining the cockle communities given the low abundance of adult individuals with marketable size in both estuaries. This study highlights the need for appropriate management measures to ensure the sustainability of these bivalve population stocks that have significant socioeconomic importance for local populations.
Clinical Characteristics and Early Visual Outcomes of Highly Myopic Cataract Eyes: The Shanghai High Myopia Study
Authors: He Wenwen , Yao Yunqian , Zhang Keke , Du Yu , Qi Jiao , Zhang Yinglei , Zhang Shaohua , Zhao Zhennan , Cai Lei , Fan Qi , Jiang Yongxiang , Yang Jin , Zhu Xiangjia , Lu Yi
Published: March 2022

Purpose: To report ocular characteristics and early visual outcomes of highly myopic cataract eyes, and to analyze the risk factors of low vision.

Methods: A total of 2,027 eyes of 1,400 cataract patients with axial length (AL) ≥ 26 mm undergoing cataract surgery in Eye & ENT Hospital of Fudan University, who were registered in the Shanghai High Myopia Study, were analyzed. Routine pre-operative ophthalmic examinations were performed and macular scan of optical coherence tomography (OCT) were obtained. Macular complications, central foveal thickness (CFT) and subfoveal choroidal thickness (SFCT) were evaluated from OCT images. Ocular and surgical history and perioperative complications were also recorded. Uncorrected and best-corrected visual acuity (UCVA/BCVA) 1 month post-operatively and its influencing factors were evaluated.

Results: The average AL of all involved eyes was 29.52 ± 2.26 mm, and 39.7% of which were with an AL > 30 mm and 26.4% of which were with a corneal astigmatism more than 1.5 D. Nuclear cataract accounted for the largest proportion (70.6%). The rate of overall macular complications was 27.6%. Postoperative UCVA and BCVA were 0.70 ± 0.46 and 0.25 ± 0.32 logMAR, respectively. BCVA improved significantly after surgery (vs. P < 0.001) and affected by the elongation of AL (P < 0.001) and thinning of CFT and SFCT (both P < 0.001). The risk factors of post-operative low vision (BCVA < 20/66) were macular atrophy, lamellar macular hole, high corneal astigmatism, long AL, thin SFCT and junior surgeons, odds ratios ranging from 1.54 to 54.87 (all P < 0.05).

Conclusion: Cataract surgery could improve the VA of highly myopic eyes. Eye with macular complications, higher corneal astigmatism, longer AL, thinner SFCT, and who was treated by a junior surgeon, may have a high risk of low vision after surgery.
Could Emergency Diseases Surveillance Systems Be Transitioned to Routine Surveillance Systems? A Proposed Transition Strategy for Early Warning, Alert, and Response Network
Authors: Asghar Rana Jawad , Abubakar Abdinasir , Buliva Evans , Tayyab Muhammad , Elnossery Sherein
Published: March 2022

In humanitarian emergencies, traditional disease surveillance systems either do not exist to begin with or come under stress due to a huge influx of internal or external migrants. However, cramped camps with an unreliable supply of safe water and weak sanitation systems are the ideal setting for major disease outbreaks of all kinds. The Early Warning, Alert and Response Network (EWARN) has been supported by the WHO since the late 1990s to ensure health system capacity to identify and control risks early before they become major epidemics. These systems have been proven to be an excellent asset in reducing morbidity and mortality in humanitarian crises around the world. However, there is also a global challenge of transitioning them back to a regular or national monitoring system in their respective countries. This article is the result of in-country consultations arranged by the Eastern Mediterranean office of the World Health Organization. In these consultations, the unique local conditions and limitations of different countries were discussed to identify a way forward for transitioning these emergency disease surveillance systems into regular systems. After these discussions, different options were presented which could be further modified according to local needs. As there has not been any documented evidence of a successful transition of any emergency surveillance system, it is difficult to discuss or determine the gold standard for transition. As with any public health program being practiced in the field, local decision-making with some broad guidelines will be the best approach available. This article provides these guidelines and practical steps which could be further modified according to country needs.
Enhancement of Online Education to the Teaching Paradigm: Taking Academic Medical Postgraduate Cultivation as an Example
Authors: Su Bin
Published: March 2022

Background

The COVID-19 pandemic posed enormous challenges to postgraduate teaching in 2020. Large-scale and continuous online teaching explorations were introduced to cope with this difficult situation, which incidentally shifted the paradigm of postgraduate teaching.

Purpose

A review of the online teaching of local medical schools for postgraduates was performed to identify the success factors in realizing the practice.

Methods

We retrieved medical postgraduate online teaching publications mainly from the local database, the China National Knowledge Infrastructure (CNKI), via the keywords stated below and then performed a retrospective analysis.

Results

We analyzed key success factors in improving online learning engagement that were considered exclusive to offline classroom teaching, including emotional interaction, the immediacy of communication, and enthusiasm for participation. With these positive effects, the integration of online and offline teaching advantages is beneficial for the initiative of academic medical postgraduates and promotes the construction and development of medical postgraduate education.

Conclusion

Online education can overcome the limitations of time, space, and teaching frequency, with great advantages in terms of flexibility and mobility over traditional classroom teaching. It can effectively cope with difficulties in the education of academic medical postgraduates in challenging times. In the post-pandemic era, blended online and offline teaching approaches continue and will become the new normal pedagogy for the training of medical postgraduate students.
Effects and Long-Term Outcomes of a Modified Triple-P Procedure in Patients With Severe PAS: A Retrospective Cohort Study
Authors: Zhao Huidan , Zhao Xianlan , Chen Chen , Tao Ya , Guo Ruixia
Published: March 2022

Background

The distinguished Triple-P procedure has been reported as a conservative surgical alternative to peripartum hysterectomy for placental accreta spectrum (PAS). In this study, we modified the procedure combined with prophylactic abdominal aorta balloon occlusion and/or tourniquet and evaluated the effect and long-term outcomes.

Methods

This was a retrospective study involving pregnant patients with clinically confirmed severe PAS (including placenta increta and percreta) between January 1st, 2017 and June 30th, 2020 in the First Affiliated Hospital of Zhengzhou University. A total of 334 pregnant women were recruited in this study. The 142 women that were subjected to modified Triple P Procedure were regarded as the observation group while 194 pregnant women that were treated with other sutures were regarded as the control group. Demographic characteristics, placental accreta spectrum score (PAS score), estimated blood loss (EBL), operative time, blood transfusion rate and volume, neonatal weight, post-operative hospital stays and costs were evaluated. Short-term complications, including fever, hematoma, thrombus, bladder rupture and intensive care unit (ICU) transfer rate, as well as long-term outcomes including breast feeding, menstruation, intrauterine adhesion, and chronic abdominal pain among others were followed up in the outpatient clinic and by phone calls.

Results

For all cases, EBL was lower in the observation group than in the control group, 1,200 (687–1,812) ml and 1,300 (800–2,500) ml, respectively. The difference was statistically significant (P < 0.05). Operative time were statistically significantly shorter in the observation group [99.5 (84.0–120.0) min and 109.0 (83.8–143.0) min, P < 0.05]. Lengths of postoperative hospital stays were 4 (4–7) and 5 (4–7) days in the observation and control group, which was significantly shorter in the observation group (P < 0.05). There were no significant differences in PAS scores, blood transfusion volume, neonatal weight, fever, hematoma, thrombus, bladder rupture and ICU transfer rates between the two groups. All patients, except one in control group, had preserved uterus. There were no statistically significant differences in short-term and long-term complications between two groups.

Conclusion

In summary, when combined with tourniquet and/or prophylactic abdominal aorta balloon occlusion, modified Triple-P procedure may be effective in reducing intraoperative blood loss and hysterectomy in patients with placenta increta/percreta. It is a safe and effective surgical alternative to peripartum hysterectomy. However, the complications associated with interventional radiology service should be evaluated furthermore.
Identification of an Immune Classification and Prognostic Genes for Lung Adenocarcinoma Based on Immune Cell Signatures
Authors: Deng Lili , Long Fei , Wang Ting , Dai Ling , Chen Huajian , Yang Yujun , Xie Guoming
Published: March 2022

Objective

Current advances in immunotherapy requires accurate tumor sub-classification due to the heterogeneity of lung adenocarcinoma (LUAD). This study aimed to develop a LUAD sub-classification system based on immune cell signatures and identified prognostic gene markers.

Methods

Signatures related to the prognosis of TCGA-LUAD and 4 GSE cohorts were screened and intersected from 184 previously published immune cell signatures. The LUAD samples in the TCGA were clustered by ConsensusClusterPlus. Molecular characteristics, immune characteristics and sensitivity to immunotherapies/chemotherapies were compared. LDA score was established through Linear Discriminant Analysis (LDA). Co-expression module was constructed by Weighted Gene Co-Expression Network Analysis (WGCNA).

Results

Four LUAD subtypes with different molecular and immune characteristics were identified. Significant differences in prognosis among the four subtypes were observed. The IS1 subtype with the worst prognosis showed the highest number of TMB, mutant genes, IFN γ score, angiogenesis score and immune score. Twenty co-expression modules were generated by WGCNA. Blue module, sky blue module and light yellow module were significantly correlated with LUAD prognosis. The hub genes (CCDC90B, ARNTL2, RIPK2, SMCO2 and ADA and NBN) showing great prognostic significance were identified from the blue module. A total of 8 hub genes (NLRC3, CLEC2D, GIMAP5, CXorf65, PARP15, AKNA, ZC3H12D, and ARRDC5) were found in the light yellow module. Except for CXorf65, the expression of the other seven genes were significantly correlated with LUAD prognosis.

Conclusion

This study determined four LUAD subtypes with different molecular and immune characteristics and 13 genes closely related to the prognosis of LUAD. The current findings could help understand the heterogeneity of LUAD immune classes.
Dietary Supplementation With Fine-Grinding Wheat Bran Improves Lipid Metabolism and Inflammatory Response via Modulating the Gut Microbiota Structure in Pregnant Sow
Authors: Wang Zijie , Chen Yifan , Wang Wenhui , Huang Caiyun , Hu Yongfei , Johnston Lee , Wang Fenglai
Published: March 2022

This study investigated the effects of fine-grinding wheat bran on pregnant sow body condition, lipid metabolism, inflammatory response, and gut microbiota. In this study, wheat bran was crushed into three particle sizes. A total of 60 Landrace × Yorkshire second parity sows were allotted to two groups: CWB (a diet containing coarse wheat bran with particle size of 605 μm) and FWB (a diet containing fine wheat bran with particle size of 438 μm). Fine-grinding wheat bran had higher soluble dietary fiber concentration, swelling capacity, water-holding capacity, and fermentability than coarse wheat bran. Pregnant sows fed FWB throughout pregnancy had lower body weight and fat deposition than sows fed CWB. And the piglet body weight at birth of the FWB group was remarkably increased. Serum concentrations of lipids (triglycerides, total cholesterol, and free fatty acid), interleukin 6, leptin, and resistin were decreased on day 90 of pregnancy by fine wheat bran supplementation. Feeding FWB significantly decreased abundance of Firmicutes and dramatically increased the abundance of Bacteroidetes at phylum level. At genus level, the abundance of Terrisporobacter was decreased in FWB feeding sows, but the abundance of Parabacteroides was increased. Fecal total short-chain fatty acids, propionate, and butyrate contents were markedly increased in the FWB group. The results suggested that the physicochemical properties of finely ground wheat bran had been improved. Dietary supplementation with fine wheat bran changed the gut microbiota structure and enhanced the short-chain fatty acids level, which improved the maternal body condition, metabolic and inflammatory status, and reproductive performance in sows.
Physiological and Biochemical Responses of Bicarbonate Supplementation on Biomass and Lipid Content of Green Algae Scenedesmus sp. BHU1 Isolated From Wastewater for Renewable Biofuel Feedstock
Authors: Singh Rahul Prasad , Yadav Priya , Kumar Ajay , Hashem Abeer , Al-Arjani Al-Bandari Fahad , Abd_Allah Elsayed Fathi , Rodríguez Dorantes Angélica , Gupta Rajan Kumar
Published: March 2022

In the present study, different microalgae were isolated from wastewater environment and evaluated for higher growth and lipid accumulation. The growth adaptability of all the isolated microalgae were tested for carbon source with supplementation of sodium bicarbonate in BG-11 N+ medium. Further based on the uptake rate of sodium bicarbonate and growth behavior, microalgal strains were selected for biofuel feedstock. During the study, growth parameters of all the isolates were screened after supplementation with various carbon sources, in which strain Scenedesmus sp. BHU1 was found highly effective among all. The efficacy of Scenedesmus sp. BHU1 strain under different sodium bicarbonate (4–20 mM) concentration, in which higher growth 1.4 times greater than control was observed at the concentration 12 mM sodium bicarbonate. In addition, total chlorophyll content (Chl-a + Chl-b), chlorophyll fluorescence (Fv/Fm, Y(II), ETR max, and NPQmax), and biomass productivity were found to be 11.514 μg/ml, 0.673, 0.675, and 31.167 μmol electrons m−2 s−1, 1.399, 59.167 mg/L/day, respectively, at the 12 mM sodium bicarbonate. However, under optimum sodium bicarbonate supplementation, 56.920% carbohydrate and 34.693% lipid content were accumulated, which showed potential of sodium bicarbonate supplementation in renewable biofuel feedstock by using Scenedesmus sp. BHU1 strain.
Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent
Authors: Wambui Joseph , Stevens Marc J. A. , Cernela Nicole , Stephan Roger
Published: March 2022

The spoilage of vacuum-packed meat by Clostridium estertheticum complex (CEC), which is accompanied by or without production of copious amounts of gas, has been linked to the acetone–butyrate–ethanol fermentation, but the mechanism behind the variable gas production has not been fully elucidated. The reconstruction and comparison of intra- and interspecies metabolic pathways linked to meat spoilage at the genomic level can unravel the genetic basis for the variable phenotype. However, this is hindered by unavailability of CEC genomes, which in addition, has hampered the determination of genetic diversity and its drivers within CEC. Therefore, the current study aimed at determining the diversity of CEC through comprehensive comparative genomics. Fifty CEC genomes from 11 CEC species were compared. Recombination and gene gain/loss events were identified as important sources of natural variation within CEC, with the latter being pronounced in genomospecies2 that has lost genes related to flagellar assembly and signaling. Pan-genome analysis revealed variations in carbohydrate metabolic and hydrogenases genes within the complex. Variable inter- and intraspecies gas production in meat by C. estertheticum and Clostridium tagluense were associated with the distribution of the [NiFe]-hydrogenase hyp gene cluster whose absence or presence was associated with occurrence or lack of pack distention, respectively. Through comparative genomics, we have shown CEC species exhibit high genetic diversity that can be partly attributed to recombination and gene gain/loss events. We have also shown genetic basis for variable gas production in meat can be attributed to the presence/absence of the hyp gene cluster.
Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers’ Diarrhoea
Authors: Bird Matthew T. , Greig David R. , Nair Satheesh , Jenkins Claire , Godbole Gauri , Gharbia Saheer E.
Published: March 2022

Increasing levels of antimicrobial resistance (AMR) have been documented in Escherichia coli causing travellers’ diarrhoea, particularly to the third-generation cephalosporins. Diarrhoeagenic E. coli (DEC) can act as a reservoir for the exchange of AMR genes between bacteria residing in the human gut, enabling them to survive and flourish through the selective pressures of antibiotic treatments. Using Oxford Nanopore Technology (ONT), we sequenced eight isolates of DEC from four patients’ specimens who had all recently returned to the United Kingdome from Pakistan. Sequencing yielded two DEC harbouring blaCTX-M-15 per patient, all with different sequence types (ST) and belonging to five different pathotypes. The study aimed to determine whether blaCTX-M-15 was located on the chromosome or plasmid and to characterise the drug-resistant regions to better understand the mechanisms of onward transmission of AMR determinants. Patients A and C both had one isolate where blaCTX-M-15 was located on the plasmid (899037 & 623213, respectively) and one chromosomally encoded (899091 & 623214, respectively). In patient B, blaCTX-M-15 was plasmid-encoded in both DEC isolates (786605 & 7883090), whereas in patient D, blaCTX-M-15 was located on the chromosome in both DEC isolates (542093 & 542099). The two blaCTX-M-15-encoding plasmids associated with patient B were different although the blaCTX-M-15-encoding plasmid isolated from 788309 (IncFIB) exhibited high nucleotide similarity to the blaCTX-M-15-encoding plasmid isolated from 899037 (patient A). In the four isolates where blaCTX-M-15 was chromosomally encoded, two isolates (899091 & 542099) shared the same insertion site. The blaCTX-M-15 insertion site in isolate 623214 was described previously, whereas that of isolate 542093 was unique to this study. Analysis of Nanopore sequencing data enables us to characterise the genomic architecture of mobile genetic elements encoding AMR determinants. These data may contribute to a better understanding of persistence and onward transmission of AMR determinants in multidrug-resistant (MDR) E. coli causing gastrointestinal and extra-intestinal infections.
Vaccination to Prevent Pseudomonas aeruginosa Bloodstream Infections
Authors: Hart Robert J. , Morici Lisa A.
Published: March 2022

The bacterium Pseudomonas aeruginosa (Pa) is ubiquitous in the environment and causes opportunistic infections in humans. Pa is increasingly becoming one of the most difficult to treat microorganisms due to its intrinsic and acquired resistance to multiple antibiotics. The World Health Organization estimates that at least 700,000 people die each year from drug resistant microbial infections and have listed Pa as one of three bacterial species for which there is the most critical need for the development of novel therapeutics. Pa is a common cause of bloodstream infections (BSI) and bacterial sepsis. With nearly 49 million sepsis cases and 11 million deaths worldwide, an effective vaccine against Pa could prevent the morbidity and mortality resulting from Pa BSI and lessen our dependence on antibiotics. We reviewed the current landscape of Pa vaccines in pre-clinical and clinical stages over the last two decades. It is readily apparent that Pa vaccine development efforts have been largely directed at the prevention of pulmonary infections, likely due to Pa’s devastating impact on individuals with cystic fibrosis. However, the increase in nosocomial infections, BSI-related sepsis, and the emergence of widespread antibiotic resistance have converged as a major threat to global public health. In this perspective, we draw attention to potential Pa vaccine candidates and encourage a renewed effort for prophylactic vaccine development to prevent drug-resistant Pa BSI.
Species-Resolved Metagenomics of Kindergarten Microbiomes Reveal Microbial Admixture Within Sites and Potential Microbial Hazards
Authors: Lam TzeHau , Chew Dillon , Zhao Helen , Zhu Pengfei , Zhang Lili , Dai Yajie , Liu Jiquan , Xu Jian
Published: March 2022

Microbiomes on surfaces in kindergartens, the intermediate transfer medium for microbial exchange, can exert significant impact on the hygiene and wellbeing of young children, both individually and as a community. Here employing 2bRAD-M, a novel species-resolved metagenomics approach for low-biomass microbiomes, we surveyed over 100 samples from seven frequently contacted surfaces by children, plus individual children’s palms, in two kindergartens. Microbiome compositions, although kindergarten-specific, were grouped closely based on the type of surface within each kindergarten. Extensive microbial admixture were found among the various sampled sites, likely facilitated by contact with children’s hands. Notably, bacterial species with potential human health concerns and potentially antibiotic-resistant, although found across all sampled locations, were predominantly enriched on children’s hands instead of on the environmental sites. This first species-resolved kindergarten microbiome survey underscores the importance of good hand hygiene practices in kindergartens and provides insights into better managing hygiene levels and minimizing spread of harmful microbes in susceptible indoor environments.
Metabolism-Related Signature Analysis Uncovers the Prognostic and Immunotherapeutic Characteristics of Renal Cell Carcinoma
Authors: Zhang Jianye , Zhang Qi , Shi Yue , Wang Ping , Gong Yanqing , He Shiming , Li Zhihua , Feng Ninghan , Wang Yang , Jiang Peng , Ci Weimin , Li Xuesong , Zhou Liqun
Published: March 2022

Renal cell carcinoma (RCC) is one of the most common urological cancers. RCC has a poor prognosis and is considered a metabolic disease. It has been reported that many metabolic pathways are associated with the development of RCC. However, the prognostic value of metabolism-related genes in RCC is unclear. We herein aimed to establish a scoring system based on the gene expression profile of metabolic genes to evaluate the response to immunotherapy and predict the prognosis of RCC. In this study, we collected multicentre RCC data and performed integrated analysis to characterize the role of tumour metabolism in RCC and explore the relationship between metabolism and prognosis and immune therapy. Based on transcriptomic data, metabolism-related genes were used for nonnegative matrix factorization clustering. We obtained three subclasses of RCC (M1, M2, and M3), and they are associated with different prognoses and immune infiltrate levels. Then, based on the pathway activity of 113 metabolism-related gene signatures, we classified patients into three distinct metabolism-related signatures. Finally, we provide a metabolism-related pathway score (MRPScore) that is significantly associated with RCC prognosis and the response to immunotherapy. Taken together, in this study, we established an RCC classification system based on metabolic gene expression profiles that could further the understanding of the diversity of RCC. We also present the MRPScore, which may be used as an indicator to predict the response to clinical immune therapy.
Alzheimer’s Disease: An Update and Insights Into Pathophysiology
Authors: Abubakar Murtala Bello , Sanusi Kamaldeen Olalekan , Ugusman Azizah , Mohamed Wael , Kamal Haziq , Ibrahim Nurul Husna , Khoo Ching Soong , Kumar Jaya
Published: March 2022

Alzheimer’s disease (AD) is an irreversible brain disorder associated with slow, progressive loss of brain functions mostly in older people. The disease processes start years before the symptoms are manifested at which point most therapies may not be as effective. In the hippocampus, the key proteins involved in the JAK2/STAT3 signaling pathway, such as p-JAK2-Tyr1007 and p-STAT3-Tyr705 were found to be elevated in various models of AD. In addition to neurons, glial cells such as astrocytes also play a crucial role in the progression of AD. Without having a significant effect on tau and amyloid pathologies, the JAK2/STAT3 pathway in reactive astrocytes exhibits a behavioral impact in the experimental models of AD. Cholinergic atrophy in AD has been traced to a trophic failure in the NGF metabolic pathway, which is essential for the survival and maintenance of basal forebrain cholinergic neurons (BFCN). In AD, there is an alteration in the conversion of the proNGF to mature NGF (mNGF), in addition to an increase in degradation of the biologically active mNGF. Thus, the application of exogenous mNGF in experimental studies was shown to improve the recovery of atrophic BFCN. Furthermore, it is now coming to light that the FGF7/FGFR2/PI3K/Akt signaling pathway mediated by microRNA-107 is also involved in AD pathogenesis. Vascular dysfunction has long been associated with cognitive decline and increased risk of AD. Vascular risk factors are associated with higher tau and cerebral beta-amyloid (Aβ) burden, while synergistically acting with Aβ to induce cognitive decline. The apolipoprotein E4 polymorphism is not just one of the vascular risk factors, but also the most prevalent genetic risk factor of AD. More recently, the research focus on AD shifted toward metabolisms of various neurotransmitters, major and minor nutrients, thus giving rise to metabolomics, the most important “omics” tool for the diagnosis and prognosis of neurodegenerative diseases based on an individual’s metabolome. This review will therefore proffer a better understanding of novel signaling pathways associated with neural and glial mechanisms involved in AD, elaborate potential links between vascular dysfunction and AD, and recent developments in “omics”-based biomarkers in AD.
The Relative Importance of Vascular Risk Factors on Early Cognitive Aging Varies Only Slightly Between Men and Women
Authors: Bonberg Nadine , Wulms Niklas , Berger Klaus , Minnerup Heike
Published: March 2022

Objective

To investigate the sex-specific course and impact of vascular risk factors on cognitive aging in a rather young and healthy community-dwelling cohort.

Methods

We used data from a population-based cohort study, collected three times during 6 years, comprising 1,911 examinations from 798 participants aged 35–66 years at baseline. Cognitive performance on the Color-Word-Interference-Test, the Trail Making Tests (TMT) A&B, the Word Fluency Test, a 12-item word list, the Purdue Pegboard Test and a principal component global score were used as outcomes in linear mixed models. We evaluated (1) sex differences in cognitive trajectories, (2) the mediating role of hypertension, diabetes, smoking and obesity [body mass index (BMI) > 30] on sex differences and (3) in sex-stratified analyses, potential sex-specific effects of these risk factors on cognition.

Results

For all cognitive tests, we observed cognitive decline with age. Rates of decline slightly differed across sexes, showing a later but steeper decline for women in tests of memory (word list) and word fluency, but a steeper decline for men in tests of psychomotor speed and mental set shifting (TMT A&B) in older age. Women generally scored better on cognitive tests, but the slightly higher prevalence of classical vascular risks factors in men in our cohort could not explain these sex differences. Sex-stratified analyses revealed a generally small, concordantly negative, but quantitatively slightly different impact of diabetes, smoking and obesity on cognitive functions but mixed effects for arterial hypertension, depending on the blood pressure values, the treatment status and the duration of arterial hypertension.

Conclusion

Cognitive sex differences in this rather young and healthy cohort could not be explained by a differing prevalence of vascular risks factors across sexes. The association of cardiovascular risk factors with cognition, however, slightly differed between men and women, whereby effects were generally small. Whereas longtime diabetes, obesity and smoking had a sex-specific, but concordantly negative impact on psychomotor speed, executive and motor functions, we found some opposing effects for arterial hypertension. Our results can help to identify sex-specific susceptibilities to modifiable risk factors, to attract attention to potential information bias and to stimulate further research into alternative causes and mechanism of sex differences in cognitive aging.
Therapeutic Devices for Motor Symptoms in Parkinson’s Disease: Current Progress and a Systematic Review of Recent Randomized Controlled Trials
Authors: Fujikawa Joji , Morigaki Ryoma , Yamamoto Nobuaki , Oda Teruo , Nakanishi Hiroshi , Izumi Yuishin , Takagi Yasushi
Published: March 2022

Background

Pharmacotherapy is the first-line treatment option for Parkinson’s disease, and levodopa is considered the most effective drug for managing motor symptoms. However, side effects such as motor fluctuation and dyskinesia have been associated with levodopa treatment. For these conditions, alternative therapies, including invasive and non-invasive medical devices, may be helpful. This review sheds light on current progress in the development of devices to alleviate motor symptoms in Parkinson’s disease.

Methods

We first conducted a narrative literature review to obtain an overview of current invasive and non-invasive medical devices and thereafter performed a systematic review of recent randomized controlled trials (RCTs) of these devices.

Results

Our review revealed different characteristics of each device and their effectiveness for motor symptoms. Although invasive medical devices are usually highly effective, surgical procedures can be burdensome for patients and have serious side effects. In contrast, non-pharmacological/non-surgical devices have fewer complications. RCTs of non-invasive devices, especially non-invasive brain stimulation and mechanical peripheral stimulation devices, have proven effectiveness on motor symptoms. Nearly no non-invasive devices have yet received Food and Drug Administration certification or a CE mark.

Conclusion

Invasive and non-invasive medical devices have unique characteristics, and several RCTs have been conducted for each device. Invasive devices are more effective, while non-invasive devices are less effective and have lower hurdles and risks. It is important to understand the characteristics of each device and capitalize on these.