bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid and Visual Detection of SARS-CoV-2 Using Multiplex Reverse Transcription Loop-Mediated Isothermal Amplification Linked With Gold Nanoparticle-Based Lateral Flow Biosensor
Authors: Chen Xu , Zhou Qingxue , Li Shijun , Yan Hao , Chang Bingcheng , Wang Yuexia , Dong Shilei
Published: July 2021

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that has caused the outbreak of coronavirus disease 2019 (COVID-19) all over the world. In the absence of appropriate antiviral drugs or vaccines, developing a simple, rapid, and reliable assay for SARS-CoV-2 is necessary for the prevention and control of the COVID-19 transmission.

Methods

A novel molecular diagnosis technique, named multiplex reverse transcription loop-mediated isothermal amplification, that has been linked to a nanoparticle-based lateral flow biosensor (mRT-LAMP-LFB) was applied to detect SARS-CoV-2 based on the SARS-CoV-2 RdRp and N genes, and the mRT-LAMP products were analyzed using nanoparticle-based lateral flow biosensor. The mRT-LAMP-LFB amplification conditions, including the target RNA concentration, amplification temperature, and time were optimized. The sensitivity and specificity of the mRT-LAMP-LFB method were tested in the current study, and the mRT-LAMP-LFB assay was applied to detect the SARS-CoV-2 virus from clinical samples and artificial sputum samples.

Results

The SARS-CoV-2 specific primers based on the RdRp and N genes were valid for the establishment of mRT-LAMP-LFB assay to detect the SARS-CoV-2 virus. The multiple-RT-LAMP amplification condition was optimized at 63°C for 30 min. The full process, including reaction preparation, viral RNA extraction, RT-LAMP, and product identification, could be achieved in 80 min. The limit of detection (LoD) of the mRT-LAMP-LFB technology was 20 copies per reaction. The specificity of mRT-LAMP-LFB detection was 100%, and no cross-reactions to other respiratory pathogens were observed.

Conclusion

The mRT-LAMP-LFB technique developed in the current study is a simple, rapid, and reliable method with great specificity and sensitivity when it comes to identifying SARS-CoV-2 virus for prevention and control of the COVID-19 disease, especially in resource-constrained regions of the world.
Phenotypic and Functional Signatures of Peripheral Blood and Spleen Compartments of Cynomolgus Macaques Infected With T. cruzi: Associations With Cardiac Histopathological Characteristics
Authors: Sathler-Avelar Renato , Vitelli-Avelar Danielle Marquete , Mattoso-Barbosa Armanda Moreira , Pascoal-Xavier Marcelo Antônio , Elói-Santos Silvana Maria , Costa-Rocha Ismael Artur da , Teixeira-Carvalho Andréa , Dick Edward J. , VandeBerg Jane F. , VandeBerg John L. , Martins-Filho Olindo Assis
Published: July 2021

We performed a detailed analysis of immunophenotypic features of circulating leukocytes and spleen cells from cynomolgus macaques that had been naturally infected with Trypanosoma cruzi, identifying their unique and shared characteristics in relation to cardiac histopathological lesion status. T. cruzi-infected macaques were categorized into three groups: asymptomatic [CCC(-)], with mild chronic chagasic cardiopathy [CCC(+)], or with moderate chronic chagasic cardiopathy [CCC(++)]. Our findings demonstrated significant differences in innate and adaptive immunity cells of the peripheral blood and spleen compartments, by comparison with non-infected controls. CCC(+) and CCC(++) hosts exhibited decreased frequencies of monocytes, NK and NKT-cell subsets in both compartments, and increased frequencies of activated CD8+ T-cells and GranA+/GranB+ cells. While a balanced cytokine profile (TNF/IL-10) was observed in peripheral blood of CCC(-) macaques, a predominant pro-inflammatory profile (increased levels of TNF and IFN/IL-10) was observed in both CCC(+) and CCC(++) subgroups. Our data demonstrated that cardiac histopathological features of T. cruzi-infected cynomolgus macaques are associated with perturbations of the immune system similarly to those observed in chagasic humans. These results provide further support for the validity of the cynomolgus macaque model for pre-clinical research on Chagas disease, and provide insights pertaining to the underlying immunological mechanisms involved in the progression of cardiac Chagas disease.
Living With Elephants: Evidence-Based Planning to Conserve Wild Elephants in a Megadiverse South East Asian Country
Authors: Wong Ee Phin , Campos-Arceiz Ahimsa , Zulaikha Natasha , Chackrapani Praveena , Quilter Aida Ghani , de la Torre J. Antonio , Solana-Mena Alicia , Tan Wei Harn , Ong Lisa , Rusli Muhammad Amin , Sinha Sinchita , Ponnusamy Vanitha , Lim Teck Wyn , Or Oi Ching , Aziz Ahmad Fitri , Hii Ning , Tan Ange Seok Ling , Wadey Jamie , Loke Vivienne P. W. , Zawawi Abdullah , Idris Muhammad Munir , Abdul Patah Pazil , Abdul Rahman Mohd Taufik , Saaban Salman
Published: July 2021

Theory of Change (ToC) and Social Return of Investment (SROI) are planning tools that help projects craft strategic approaches in order to create the most impact. In 2018, the Management & Ecology of Malaysian Elephants (MEME) carried out planning exercises using these tools to develop an Asian elephant conservation project with agriculture communities. First, a problem tree was constructed together with stakeholders, with issues arranged along a cause-and-effect continuum. There were 17 main issues identified, ranging from habitat connectivity and fragmentation, to the lack of tolerance toward wild elephants. All issues ultimately stemmed from a human mindset that favors human-centric development. The stakeholders recognize the need to extend conservation efforts beyond protected areas and move toward coexistence with agriculture communities for the survival of the wild elephants. We mapped previous Human-Elephant Conflict (HEC) management methods and other governmental policies in Malaysia against the problem tree, and provided an overview of the different groups of stakeholders. The ToC was developed and adapted for each entity, while including Asian elephants as a stakeholder in the project. From the SROI estimation, we extrapolated the intrinsic value of the wild Asian elephant population in Johor, Malaysia, to be conservatively worth at least MYR 7.3 million (USD 1.8 million) per year. From the overall calculations, the potential SROI value of the project is 18.96 within 5 years, meaning for every ringgit invested in the project, it generates MYR 18.96 (USD 4.74) worth of social return value. There are caveats with using these value estimations outside of the SROI context, which was thoroughly discussed. The SROI provides projects with the ability to justify to funders the social return values of its activities, which we have adapted to include the intrinsic value of an endangered megafauna. Moreover, SROI encourages projects to consider unintended impacts (i.e., replacement, displacement, and deadweight), and acknowledge contributions from stakeholders. The development of the problem tree and ToCviaSROI approach, can help in clarifying priorities and encourage thinking out of the box. For this case study, we presented the thinking process, full framework and provided evidences to support the Theory of Change.
Review of COVID-19 Myocarditis in Competitive Athletes: Legitimate Concern or Fake News?
Authors: Khan Zulqarnain , Na Jonathan S. , Jerome Scott
Published: July 2021

Since the first reported case of COVID-19 in December 2019, the global landscape has shifted toward an unrecognizable paradigm. The sports world has not been immune to these ramifications; all major sports leagues have had abbreviated seasons, fan attendance has been eradicated, and athletes have opted out of entire seasons. For these athletes, cardiovascular complications of COVID-19 are particularly concerning, as myocarditis has been implicated in a significant portion of sudden cardiac death (SCD) in athletes (up to 22%). Multiple studies have attempted to evaluate post-COVID myocarditis and develop consensus return-to-play (RTP) guidelines, which has led to conflicting information for internists and primary care doctors advising these athletes. We aim to review the pathophysiology and diagnosis of viral myocarditis, discuss the heterogeneity regarding incidence of COVID myocarditis among athletes, and summarize the current expert recommendations for RTP. The goal is to provide guidance for practitioners who will be managing and advising athletes in the COVID era.
Numerical Analysis of Sand Bed Degrading and Sediment Transport Rate Under Tailings Dam Break
Authors: Tian Zhong , Yang Hao , Wang Wei , Cao DeSheng
Published: July 2021

Dam-breaking accidents in tailings ponds may result in loss of tailings, damage to the downstream bridges and houses, flooding of farmland and roads, hazards to the local environment, and even loss of property and lives. Therefore, research on dam breaks in tailings reservoirs and prediction of subsequent impacts are of great significance. This paper describes theoretical and numerical analyses of the retrogressive erosion model and calculations of the sand bed surface profile and sediment transport rate following tailings dam break events. The calculation results show that the degrading rate of the bed surface in the reservoir area reaches a maximum when the breach is formed and then rapidly decreases to a stable value. Farther away from the breach, the peak degrading rate of the bed surface is lower. The time of the peak tailings outflow rate is related to the formation of the breach. A larger breach has a shorter formation time and a greater peak flow.
Academic Integrity in Online Assessment: A Research Review
Authors: Holden Olivia L. , Norris Meghan E. , Kuhlmeier Valerie A.
Published: July 2021

This paper provides a review of current research on academic integrity in higher education, with a focus on its application to assessment practices in online courses. Understanding the types and causes of academic dishonesty can inform the suite of methods that might be used to most effectively promote academic integrity. Thus, the paper first addresses the question of why students engage in academically dishonest behaviours. Then, a review of current methods to reduce academically dishonest behaviours is presented. Acknowledging the increasing use of online courses within the postsecondary curriculum, it is our hope that this review will aid instructors and administrators in their decision-making process regarding online evaluations and encourage future study that will form the foundation of evidence-based practices.
Pituitary Metastasis of Lung Neuroendocrine Carcinoma Mimicking Pituitary Adenoma:Case Report and Literature Review
Authors: Liu Xiaohai , Wang Renzhi , Li Mingchu , Chen Ge
Published: July 2021

Pituitary metastasis is an unusual situation in clinical practice, while the incidence is increasing with age. Breast cancer for women and lung cancer for men were the most frequent primary origins of pituitary metastasis. Diagnosing asymptomatic patients with unknown primary malignant origin is difficult, thus pituitary metastasis may be diagnosed as primary pituitary adenoma. Here, we report a case of a 65-year-old patient with visual changes and diabetes insipidus, showing an extensive mass in the sellar region which was initially thought to be a primary pituitary adenoma. Patient corticotropic deficits were corrected, and transnasal transsphenoidal surgery was adopted, leading to total tumor resection. Tumor texture during surgical procedure was similar to that of pituitary adenoma. However, the histopathological and immunohistochemistry results suggested it as a pituitary metastasis from lung neuroendocrine tumor. Postoperative chest CT scan confirmed a pulmonary mass consistent with primary neoplasm. Abdominal CT further detected multiple metastases in liver, pancreas, and colon. Despite intensive treatment, the patient continued to show decreased level of consciousness due to cachexia, resulting in death 1 week after surgery. This case highlights the importance of differential diagnosis of invasive lesions of the sellar region, especially in individuals over 60 years of age with diabetes insipidus.
Considerations When Applying the Consumer Functional Response Measured Under Artificial Conditions
Authors: Griffen Blaine D.
Published: July 2021

Since its creation, considerable effort has been given to improving the utility of the consumer functional response. To date, the majority of efforts have focused on improving mathematical formulation in order to include additional ecological processes and constraints, or have focused on improving the statistical analysis of the functional response to enhance rigor and to more accurately match experimental designs used to measure the functional response. In contrast, relatively little attention has been given to improving the interpretation of functional response empirical results, or to clarifying the implementation and extrapolation of empirical measurements to more realistic field conditions. In this paper I explore three concepts related to the interpretation and extrapolation of empirically measured functional responses. First, I highlight the need for a mechanistic understanding when interpreting foraging patterns and highlight pitfalls that can occur when we lack understanding between the shape of the functional response curve and the mechanisms that give rise to that shape. Second, I discuss differences between experimental and real-world field conditions that must be considered when trying to extrapolate measured functional responses to more natural conditions. Third, I examine the importance of the time scale of empirical measurements, and the need to consider tradeoffs that alter or limit foraging decisions under natural conditions. Clearly accounting for these three conceptual areas when measuring functional responses and when interpreting and attempting to extrapolate empirically measured functional responses will lead to more accurate estimates of consumer impacts under natural field conditions, and will improve the utility of the functional response as a heuristic tool in ecology.
Seasonality of Biennial Burning Has No Adverse Effects on Mature Longleaf Pine Survival or Productivity
Authors: Willis John L. , Sharma Ajay , Kush John S.
Published: July 2021

Emulating natural disturbance has become an increasingly important restoration strategy. In the fire-maintained woodlands of the southeastern United States, contemporary restoration efforts have focused on approximating the historical fire regime by burning at short intervals. Due to concerns over escape and damage to mature trees, most prescribed burning has occurred in the dormant season, which is inconsistent with the historical prevalence of lightning-initiated fire in the region. This discordance between contemporary prescribed burning and what is thought to be the historical fire regime has led some to question whether dormant season burning should remain the most common management practice; however, little is known about the long-term effects of repeated growing season burning on the health and productivity of desirable tree species. To address this question, we report on a long-term experiment comparing the effects of seasonal biennial burning (winter, spring, and summer) and no burning on the final survival status, height, diameter, and volume growth of 892 mature longleaf pine (Pinus palustris) over 23 years in three mature even-aged stands in southern Alabama, United States. Overall, longleaf pine survival across all treatments averaged 81 ± 2% [s.e]. Among seasonal burn treatments, survival was highest in the spring burns (82 ± 4%) but did not vary significantly from any other treatment (summer – 79 ± 4%, winter – 81 ± 4%, unburned – 84 ± 4%). However, survival was statistically influenced by initial diameter at breast height, as survival of trees in the largest size class (30 cm) was 40% higher than trees in the smallest size class (5 cm). Productivity of longleaf pine was not significantly different among treatment averages in terms of volume (38.9–44.1 ± 6.0 m3 ha–1), diameter (6.0–6.7 ± 0.3 cm), and height (2.5–3.4 ± 0.4 m) growth. Collectively, our results demonstrate that burning outside the dormant season will have little impact on mature longleaf pine survival and growth. This finding has important implications for the maintenance of restored southeastern woodlands, as interest in burning outside the dormant season continues to grow.
Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds
Authors: Lyu Guangqi , Feng Chunyu , Zhu Shiyu , Ren Shuang , Dang Wanyi , Irwin David M. , Wang Zhe , Zhang Shuyi
Published: July 2021

Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the “Mame Shiba Inu” breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including FST, Hp and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.
Perinatal Mental Health Care for Women With Severe Mental Illness During the COVID-19 Pandemic in India—Challenges and Potential Solutions Based on Two Case Reports
Authors: Nagendrappa Sachin , Vinod Pratibha , Pai Naveen Manohar , Ganjekar Sundarnag , Desai Geetha , Kishore M. Thomas , Thippeswamy Harish , Vaiphei Kimneihat , Chandra Prabha S.
Published: July 2021

The ongoing COVID-19 pandemic in India has created several challenges in the care of women with perinatal mental illness. Access to healthcare has been disrupted by lockdowns, travel restrictions, and the unavailability of outpatient services. This report aims to discuss the challenges faced by women with severe mental illnesses during the perinatal period with the help of two case reports. Accordingly, we have highlighted the role of COVID-19 infection as a traumatic event during childbirth and its role in triggering a psychotic episode in women with vulnerabilities; difficulties faced by women with postpartum psychosis in accessing perinatal psychiatry services; and the challenges of admission into an inpatient Mother-Baby Unit (MBU). Further, we have discussed potential solutions from the perspectives of Lower and Middle-income (LAMI) countries that need to be extended beyond the pandemic. They include offering video consultations, reviewing hospital policies, and evolving strategies to mitigate traumatic experiences for pregnant and postpartum women with severe mental illnesses in both obstetric and psychiatric care.
Brain Metastases Status and Immunotherapy Efficacy in Advanced Lung Cancer: A Systematic Review and Meta-Analysis
Authors: Hu Hao , Xu Zhi-Yong , Zhu Qian , Liu Xi , Jiang Si-Cong , Zheng Ji-Hua
Published: July 2021

Background

Brain metastases (BMs) indicate poor outcomes and are commonly excluded in immunotherapy clinical trials in advanced lung cancer; moreover, the effect of BM status on immunotherapy efficacy is inconsistent and inconclusive. Therefore, we conducted a meta-analysis to assess the influence of BM status on immunotherapy efficacy in advanced lung cancer.

Methods

Electronic databases and all major conference proceedings were searched without language restrictions according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. We extracted randomized clinical trials on lung cancer immunotherapy that had available overall survival (OS) and/or progression-free survival (PFS) data based on the BM status. All analyses were performed using random effects models.

Results

Fourteen randomized clinical trials with 9,089 patients were identified. Immunotherapy conferred a survival advantage to BM patients [OS-hazard ratio (HR), 0.72; 95% confidence interval (CI), 0.58–0.90; P = 0.004; and PFS-HR, 0.68; 95% CI, 0.52–0.87, P = 0.003]. Non-BM patients could also derive a survival benefit from immunotherapy (OS-HR, 0.76; 95% CI, 0.71–0.80; P <0.001; and PFS-HR, 0.68; 95% CI, 0.56–0.82, P <0.001). The pooled ratios of OS-HRs and PFS-HRs reported in BM patients versus non-BM patients were 0.96 (95% CI, 0.78–1.18; P = 0.72) and 0.97 (95% CI, 0.79–1.20; P = 0.78), respectively, indicating no statistically significant difference between them. Subsequent sensitivity analyses did not alter the results. Subgroup analyses according to tumor type, line of therapy, immunotherapy type, study design, and representation of BM patients reconfirmed these findings.

Conclusion

We demonstrated that BM status did not significantly influence the immunotherapy efficacy in lung cancer, suggesting that both BM and non-BM patients could obtain comparable benefits.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/, identifier (CRD42020207446).
Safety and Immunogenicity of ChAd63/MVA Pfs25-IMX313 in a Phase I First-in-Human Trial
Authors: de Graaf Hans , Payne Ruth O. , Taylor Iona , Miura Kazutoyo , Long Carol A. , Elias Sean C. , Zaric Marija , Minassian Angela M. , Silk Sarah E. , Li Lee , Poulton Ian D. , Baker Megan , Draper Simon J. , Gbesemete Diane , Brendish Nathan J. , Martins Filipa , Marini Arianna , Mekhaiel David , Edwards Nick J. , Roberts Rachel , Vekemans Johan , Moyle Sarah , Faust Saul N. , Berrie Eleanor , Lawrie Alison M. , Hill Fergal , Hill Adrian V. S. , Biswas Sumi
Published: July 2021

Background

Transmission blocking vaccines targeting the sexual-stages of the malaria parasite could play a major role to achieve elimination and eradication of malaria. The Plasmodium falciparum Pfs25 protein (Pfs25) is the most clinically advanced candidate sexual-stage antigen. IMX313, a complement inhibitor C4b-binding protein that forms heptamers with the antigen fused to it, improve antibody responses. This is the first time that viral vectors have been used to induce antibodies in humans against an antigen that is expressed only in the mosquito vector.

Methods

Clinical trial looking at safety and immunogenicity of two recombinant viral vectored vaccines encoding Pfs25-IMX313 in healthy malaria-naive adults. Replication-deficient chimpanzee adenovirus serotype 63 (ChAd63) and the attenuated orthopoxvirus modified vaccinia virus Ankara (MVA), encoding Pfs25-IMX313, were delivered by the intramuscular route in a heterologous prime-boost regimen using an 8-week interval. Safety data and samples for immunogenicity assays were taken at various time-points.

Results

The reactogenicity of the vaccines was similar to that seen in previous trials using the same viral vectors encoding other antigens. The vaccines were immunogenic and induced both antibody and T cell responses against Pfs25, but significant transmission reducing activity (TRA) was not observed in most volunteers by standard membrane feeding assay.

Conclusion

Both vaccines were well tolerated and demonstrated a favorable safety profile in malaria-naive adults. However, the transmission reducing activity of the antibodies generated were weak, suggesting the need for an alternative vaccine formulation.

Trial Registration

Clinicaltrials.gov NCT02532049.
Complement C4, Infections, and Autoimmune Diseases
Authors: Wang Hongbin , Liu Mengyao
Published: July 2021

Complement C4, a key molecule in the complement system that is one of chief constituents of innate immunity for immediate recognition and elimination of invading microbes, plays an essential role for the functions of both classical (CP) and lectin (LP) complement pathways. Complement C4 is the most polymorphic protein in complement system. A plethora of research data demonstrated that individuals with C4 deficiency are prone to microbial infections and autoimmune disorders. In this review, we will discuss the diversity of complement C4 proteins and its genetic structures. In addition, the current development of the regulation of complement C4 activation and its activation derivatives will be reviewed. Moreover, the review will provide the updates on the molecule interactions of complement C4 under the circumstances of bacterial and viral infections, as well as autoimmune diseases. Lastly, more evidence will be presented to support the paradigm that links microbial infections and autoimmune disorders under the condition of the deficiency of complement C4. We provide such an updated overview that would shed light on current research of complement C4. The newly identified targets of molecular interaction will not only lead to novel hypotheses on the study of complement C4 but also assist to propose new strategies for targeting microbial infections, as well as autoimmune disorders.
Gut Microbiota, Probiotics, and Their Interactions in Prevention and Treatment of Atopic Dermatitis: A Review
Authors: Fang Zhifeng , Li Lingzhi , Zhang Hao , Zhao Jianxin , Lu Wenwei , Chen Wei
Published: July 2021

Atopic dermatitis (AD) is a public health concern and is increasing in prevalence in urban areas. Recent advances in sequencing technology have demonstrated that the development of AD not only associate with the skin microbiome but gut microbiota. Gut microbiota plays an important role in allergic diseases including AD. The hypothesis of the “gut-skin” axis has been proposed and the cross-talk mechanism between them has been gradually demonstrated in the research. Probiotics contribute to the improvement of the intestinal environment, the balance of immune responses, regulation of metabolic activity. Most studies suggest that probiotic supplements may be an alternative for the prevention and treatment of AD. This study aimed to discuss the effects of probiotics on the clinical manifestation of AD based on gut microbial alterations. Here we reviewed the gut microbial alteration in patients with AD, the association between gut microbiota, epidermal barrier, and toll-like receptors, and the interaction of probiotics and gut microbiota. The potential mechanisms of probiotics on alleviating AD via upregulation of epidermal barrier and regulation of immune signaling had been discussed, and their possible effective substances on AD had been explored. This provides the supports for targeting gut microbiota to attenuate AD.
Diversity and Consequences of Social Network Structure in Toothed Whales
Authors: Weiss Michael N. , Ellis Samuel , Croft Darren P.
Published: July 2021

Toothed whales (suborder Odontoceti) are highly social, large brained mammals with diverse social systems. In recent decades, a large body of work has begun investigating these dynamic, complex societies using a common set of analytical tools: social network analysis. The application of social network theory to toothed whales enables insight into the factors that underlie variation in social structure in this taxon, and the consequences of these structures for survival, reproduction, disease transmission, and culture. Here, we perform a systematic review of the literature regarding toothed whale social networks to identify broad patterns of social network structure across species, common drivers of individual social position, and the consequences of network structure for individuals and populations. We also identify key knowledge gaps and areas ripe for future research. We recommend that future studies attempt to expand the taxonomic breadth and focus on standardizing methods and reporting as much as possible to allow for comparative analyses to test evolutionary hypotheses. Furthermore, social networks analysis may provide key insights into population dynamics as indicators of population health, predictors of disease risk, and as direct drivers of survival and reproduction.
The Next Wave of Passive Acoustic Data Management: How Centralized Access Can Enhance Science
Authors: Wall Carrie C. , Haver Samara M. , Hatch Leila T. , Miksis-Olds Jennifer , Bochenek Rob , Dziak Robert P. , Gedamke Jason
Published: July 2021

Passive acoustic data collection has grown exponentially over the past decade resulting in petabytes of data that document our ocean soundscapes. This effort has resulted in two big data challenges: (1) the curation, management, and global dissemination of passive acoustic datasets and (2) efficiently extracting critical information and comparing it to other datasets in the context of ecosystem-based research and management. To address the former, the NOAA National Centers for Environmental Information recently established an archive for passive acoustic data. This fast-growing archive currently contains over 100 TB of passive acoustic audio files mainly collected from stationary recorders throughout waters in the United States. These datasets are documented with standards-based metadata and are freely available to the public. To begin to address the latter, through standardized processing and centralized stewardship and access, we provide a previously unattainable comparison of first order sound level-patterns from archived data collected across three distinctly separate long-term passive acoustic monitoring (PAM) efforts conducted at regional and national scales: NOAA/National Park Service Ocean Noise Reference Station Network, the Atlantic Deepwater Ecosystem Observatory Network, and the Sanctuary Soundscape Monitoring Project. Nine sites were selected from these projects covering the Alaskan Arctic, Northeast and Central Pacific, Gulf of Mexico, Caribbean Sea, and Mid and Northwest Atlantic. Sites could generally be categorized into those strongly influenced by anthropogenic noise (e.g., vessel traffic) and those that were not. Higher sound levels, specifically for lower frequencies (<125 Hz), and proximity to densely populated coastal zones were common characteristics of sites influenced by anthropogenic noise. Conversely, sites with lower overall sound levels and away from dense populations resulted in soundscape patterns influenced by biological sources. Seasonal variability in sound levels across selected decidecade bands was apparent for most sites and often represented changes in the presence or behavior of sound-producing species. This first order examination of levels across projects highlights the utility of these initial metrics to identify patterns that can then be examined in more detail. Finally, to help the PAM community collectively and collaboratively move forward, we propose the next frontier for scalable data stewardship, access, and processing flow.
Peritoneal Protein Loss Is Not Associated With Sarcopenia in Peritoneal Dialysis Patients
Authors: Do Jun Young , Kim A Young , Kang Seok Hui
Published: July 2021

Introduction: Maintenance of a peritoneal membrane is essential for maintaining long-term peritoneal dialysis (PD). Peritoneal protein loss (PPL) is basically the loss of an essential nutrient, which may lead to malnutrition. We aimed to evaluate the association between PPL and sarcopenia in PD patients.

Methods: We conducted a cross-sectional study from September 2017 to November 2020 on all PD patients (n = 199). Finally, the patients were divided into tertiles based on the PPL level as follows: low, middle, and high. PPL (mg/day), appendicular lean mass (ALM) using dual-energy X-ray absorptiometry, and handgrip strength (HGS) were evaluated. Sarcopenia was defined using cut-off values from the Asian Working Group for Sarcopenia.

Results: The median PPL (interquartile range, interval) in the low, middle, and high tertiles were 4,229 (904, 1,706–5,111), 6,160 (760, 5,118–7,119), and 8,543 (2,284, 7,145–24,406) mg/day, respectively. HGS in the low, middle, and high tertiles was 23.4 ± 9.2, 23.8 ± 8.9, and 23.6 ± 8.3 kg, respectively (P = 0.967). The ALM index in the low, middle, and high tertiles was 6.0 ± 1.3, 6.0 ± 1.2, and 6.5 ± 1.1 kg/m2, respectively (P = 0.061). Multivariate analyses did not reveal significant differences in HGS and ALM index in among tertiles. The proportions of patients with sarcopenia in the low, middle, and high tertiles was 24 (36.4%), 19 (28.4%), and 21 (31.8%), respectively (P = 0.612).

Conclusion: The present study showed that PPL is not independently associated with muscle mass, strength, and sarcopenia in PD patients.
Scoring System to Evaluate the Performance of ICU Ventilators in the Pandemic of COVID-19: A Lung Model Study
Authors: Hu Xingshuo , Xie Fei , Wang Kaifei , Gu Hongjun , Mo Guoxin , Wen Ruoxuan , Zhao Ying , Yang Qingyun , Möller Knut , Zhao Zhanqi , Xie Lixin
Published: July 2021

Ventilators in the intensive care units (ICU) are life-support devices that help physicians to gain additional time to cure the patients. The aim of the study was to establish a scoring system to evaluate the ventilator performance in the context of COVID-19. The scoring system was established by weighting the ventilator performance on five different aspects: the stability of pressurization, response to leaks alteration, performance of reaction, volume delivery, and accuracy in oxygen delivery. The weighting factors were determined with analytic hierarchy process (AHP). Survey was sent out to 66 clinical and mechanical experts. The scoring system was built based on 54 valid replies. A total of 12 commercially available ICU ventilators providing non-invasive ventilation were evaluated using the novel scoring system. A total of eight ICU ventilators with non-invasive ventilation mode and four dedicated non-invasive ventilators were tested according to the scoring system. Four COVID-19 phenotypes were simulated using the ASL5000 lung simulator, namely (1) increased airway resistance (IR) (10 cm H2O/L/s), (2) low compliance (LC) (compliance of 20 ml/cmH2O), (3) low compliance plus increased respiratory effort (LCIE) (respiratory rate of 40 and inspiratory effort of 10 cmH2O), (4) high compliance (HC) (compliance of 50 ml/cmH2O). All of the ventilators were set to three combinations of pressure support and positive end-expiratory pressure levels. The data were collected at baseline and at three customized leak levels. Significant inaccuracies and variations in performance between different non-invasive ventilators were observed, especially in the aspect of leaks alteration, oxygen and volume delivery. Some ventilators have stable performance in different simulated phenotypes whereas the others have over 10% scoring differences. It is feasible to use the proposed scoring system to evaluate the ventilator performance. In the COVID-19 pandemic, clinicians should be aware of possible strengths and weaknesses of ventilators.
Construction of a Nomogram for Predicting Survival in Elderly Patients With Lung Adenocarcinoma: A Retrospective Cohort Study
Authors: You Haisheng , Teng Mengmeng , Gao Chun Xia , Yang Bo , Hu Sasa , Wang Taotao , Dong Yalin , Chen Siying
Published: July 2021

Elderly patients with non-small-cell lung cancer (NSCLC) exhibit worse reactions to anticancer treatments. Adenocarcinoma (AC) is the predominant histologic subtype of NSCLC, is diverse and heterogeneous, and shows different outcomes and responses to treatment. The aim of this study was to establish a nomogram that includes the important prognostic factors based on the Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2015. We collected 53,694 patients of older than 60 who have been diagnosed with lung AC from the SEER database. Univariate and multivariate Cox regression analyses were used to screen the independent prognostic factors, which were used to construct a nomogram for predicting survival rates in elderly AC patients. The nomogram was evaluated using the concordance index (C-index), calibration curves, net reclassification index (NRI), integrated discrimination improvement (IDI), and decision-curve analysis (DCA). Elderly AC patients were randomly divided into a training cohort and validation cohort. The nomogram model included the following 11 prognostic factors: age, sex, race, marital status, tumor site, histologic grade, American Joint Committee for Cancer (AJCC) stage, surgery status, radiotherapy status, chemotherapy status, and insurance type. The C-indexes of the training and validation cohorts for cancer-specific survival (CSS) (0.832 and 0.832, respectively) based on the nomogram model were higher than those of the AJCC model (0.777 and 0.774, respectively). The CSS discrimination performance as indicated by the AUC was better in the nomogram model than the AJCC model at 1, 3, and 5 years in both the training cohort (0.888 vs. 0.833, 0.887 vs. 0.837, and 0.876 vs. 0.830, respectively) and the validation cohort (0.890 vs. 0.832, 0.883 vs. 0.834, and 0.880 vs. 0.831, respectively). The predicted CSS probabilities showed optimal agreement with the actual observations in nomogram calibration plots. The NRI, IDI, and DCA for the 1-, 3-, and 5-year follow-up examinations verified the clinical usability and practical decision-making effects of the new model. We have developed a reliable nomogram for determining the prognosis of elderly AC patients, which demonstrated excellent discrimination and clinical usability and more accurate prognosis predictions. The nomogram may improve clinical decision-making and prognosis predictions for elderly AC patients.
Effect of a Multispecies Probiotic Mixture on the Growth and Incidence of Diarrhea, Immune Function, and Fecal Microbiota of Pre-weaning Dairy Calves
Authors: Wu Yanyan , Wang Lili , Luo Ruiqing , Chen Hongli , Nie Cunxi , Niu Junli , Chen Cheng , Xu Yongping , Li Xiaoyu , Zhang Wenjun
Published: July 2021

The effects of different doses of a multispecies probiotic (MSP) mixture on growth performance, the incidence of diarrhea rate and immune function, and fecal microbial diversity and structure were evaluated in pre-weaning Holstein dairy calves at WK2, WK4, WK6, and WK8. Forty Chinese Holstein female newborn calves were randomly assigned to four treatments with 10 calves in each group, C (control group), T1 (0.5 g MSP/calf/day, T2 (1 g MSP/calf/day), and T3 (2 g MSP/calf/day) groups. The experimental period was 56 days. Feed intake and health scoring were recorded every day until the end of the experiment. Fecal contents and blood samples were sampled at WK2, WK4, WK6, and WK8. Growth performance, incidence of diarrhea, and total serum concentrations (IgA, IgG, and IgM) were analyzed. Bacterial 16S rRNA and fungal ITS genes were high-throughput sequenced for fecal microbiota. The relationships among the populations of the principal fecal microbiota at WK2 and the growth performance or serum immunoglobulin concentrations were analyzed using Pearson’s rank correlation coefficients. The MSP supplementation reduced the incidence of diarrhea in the first 4 weeks of life, and serum IgA, IgG, and IgM concentrations increased between WK2 and WK8 in the T3 group. There was an increase in growth performance and reduction in the incidence of diarrhea until WK4 after birth in T3 group, compared with the control, T1, and T2 groups. The results of fecal microbiota analysis showed that Firmicutes and Bacteroides were the predominant phyla, with Blautia, Ruminococcaceae_UCG-005, norank_f__Muribaculaceae, Bacteroides, Subdoligranulum, and Bifidobacterium being the dominant genera in calf feces. Aspergillus, Thermomyces, and Saccharomyces were the predominant fungal phyla. Compared with the control, in T1 and T2 groups, the MSP supplementation reduced the relative abundance of Bacteroidetes and increased the relative abundance of Bifidobacterium, Lactobacillus, Collinsella, and Saccharomyces at WK2 in group T3. Thus, the fecal microbial composition and diversity was significantly affected by the MSP mixture during the first 2 weeks of the calves’ life. MSP mixtures reduced the incidence of diarrhea in pre-weaning calves (during the first 4 weeks of life). There was a significant improvement in growth performance, reduction in calf diarrhea, balance in the fecal microbiota, and an overall improvement in serum immunity, compared with the control group. We, therefore, recommend adding 2 g/day of multispecies probiotic mixture supplementation in diets of dairy calves during their first 4 weeks of life before weaning.
Deciphering the Bacillus amyloliquefaciens B9601-Y2 as a Potential Antagonist of Tobacco Leaf Mildew Pathogen During Flue-Curing
Authors: Pan Zuxian , Munir Shahzad , Li Yongmei , He Pengbo , He Pengfei , Wu Yixin , Xie Yan , Fu Zongwei , Cai Yongzhan , He Yueqiu
Published: July 2021

Tobacco leaf mildew caused by Rhizopus oryzae (Mucorales, Zygomycota) is an important and devastating post-harvest disease during flue-cured tobacco period, and also is known to cause diseases of fruits and vegetables. In this study, assessment of several candidate biological control agents were first tested in vitro to determine their antifungal activities and potential strains were further applied to tobacco leaves to prevent pathogen colonization during the tobacco-curing process. In vitro screening of 36 bacteria and the isolates of one fungus were performed for their antifungal activities against R. oryzae using dual culture method. Potential five isolates viz. Bacillus amyloliquefaciens B9601-Y2 (Y2), B. amyloliquefaciens YN201728 (YN28), Pseudomonas sp. (Pb), and B. amyloliquefaciens YN201732 (YN32) and T. harzianum B (Th-B) from total screened isolates have shown remarkable results for controlling the mycelial growth of R. oryzae. Finally, out of these five isolates, B. amyloliquefaciens B9601-Y2 potentially reduced the mycelial growth of fungal pathogen with great inhibitory effect. In order to get a better understanding of the biocontrol effect of B9601-Y2 in a flue-curing barn, various suspension density tests with two application methods involving spraying and soaking were examined. Two application methods of B. amyloliquefaciens B9601-Y2 had 98.60 and 98.15% control effects, respectively. In curing barn, the incidence in the treatment group was significantly reduced and tobacco leaves did not get mildew. Altogether, the study demonstrated that candidate bacterial strain B. amyloliquefaciens B9601-Y2 is a potential antagonist for the management of tobacco leaf mildew during flue-curing.
The Multiple Regulatory Relationship Between RNA-Chaperone Hfq and the Second Messenger c-di-GMP
Authors: Fu Yang , Yu Zhaoqing , Zhu Li , Li Zhou , Yin Wen , Shang Xiaodong , Chou Shan-Ho , Tan Qi , He Jin
Published: July 2021

RNA chaperone protein Hfq is an important post-transcriptional regulator in bacteria, while c-di-GMP is a second messenger signaling molecule widely distributed in bacteria. Both factors have been found to play key roles in post-transcriptional regulation and signal transduction pathways, respectively. Intriguingly, the two factors show some common aspects in the regulation of certain physiological functions such as bacterial motility, biofilm formation, pathogenicity and so on. Therefore, there may be regulatory relationship between Hfq and c-di-GMP. For example, Hfq can directly regulate the activity of c-di-GMP metabolic enzymes or alter the c-di-GMP level through other systems, while c-di-GMP can indirectly enhance or inhibit thehfqgene expression through intermediate factors. In this article, after briefly introducing the Hfq and c-di-GMP regulatory systems, we will focus on the direct and indirect regulation reported between Hfq and c-di-GMP, aiming to compare and link the two regulatory systems to further study the complicated physiological and metabolic systems of bacteria, and to lay a solid foundation for drawing a more complete global regulatory network.
The Role and Regulatory Network of the CiaRH Two-Component System in Streptococcal Species
Authors: He Li-Yuan , Le Yao-Jin , Guo Zhong , Li Sha , Yang Xiao-Yan
Published: July 2021

Pathogenic streptococcal species are responsible for a broad spectrum of human diseases ranging from non-invasive and localized infections to more aggressive and life-threatening diseases, which cause great economic losses worldwide. Streptococci possess a dozen two-component systems (TCSs) that play important roles in the response to different environmental changes and adjust the expression of multiple genes to successfully colonize and infect host cells. In this review, we discuss the progress in the study of a conserved TCS named CiaRH in pathogenic or opportunistic streptococci including Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus mutans, Streptococcus gordonii, Streptococcus sanguinis, and Streptococcus suis, focusing on the function and regulatory networks of CiaRH, which will provide a promising strategy for the exploration of novel antistreptococcal therapies. This review highlights the important role of CiaRH and provides an important basis for the development of antistreptococcal drugs and vaccines.
Hydrologic Alteration and Enhanced Microbial Reductive Dissolution of Fe(III) (hydr)oxides Under Flow Conditions in Fe(III)-Rich Rocks: Contribution to Cave-Forming Processes
Authors: Calapa Kayla A. , Mulford Melissa K. , Rieman Tyler D. , Senko John M. , Auler Augusto S. , Parker Ceth W. , Barton Hazel A.
Published: July 2021

Previous work demonstrated that microbial Fe(III)-reduction contributes to void formation, and potentially cave formation within Fe(III)-rich rocks, such as banded iron formation (BIF), iron ore and canga (a surficial duricrust), based on field observations and static batch cultures. Microbiological Fe(III) reduction is often limited when biogenic Fe(II) passivates further Fe(III) reduction, although subsurface groundwater flow and the export of biogenic Fe(II) could alleviate this passivation process, and thus accelerate cave formation. Given that static batch cultures are unlikely to reflect the dynamics of groundwater flow conditions in situ, we carried out comparative batch and column experiments to extend our understanding of the mass transport of iron and other solutes under flow conditions, and its effect on community structure dynamics and Fe(III)-reduction. A solution with chemistry approximating cave-associated porewater was amended with 5.0 mM lactate as a carbon source and added to columns packed with canga and inoculated with an assemblage of microorganisms associated with the interior of cave walls. Under anaerobic conditions, microbial Fe(III) reduction was enhanced in flow-through column incubations, compared to static batch incubations. During incubation, the microbial community profile in both batch culture and columns shifted from a Proteobacterial dominance to the Firmicutes, including Clostridiaceae, Peptococcaceae, and Veillonellaceae, the latter of which has not previously been shown to reduce Fe(III). The bacterial Fe(III) reduction altered the advective properties of canga-packed columns and enhanced permeability. Our results demonstrate that removing inhibitory Fe(II) via mimicking hydrologic flow of groundwater increases reduction rates and overall Fe-oxide dissolution, which in turn alters the hydrology of the Fe(III)-rich rocks. Our results also suggest that reductive weathering of Fe(III)-rich rocks such as canga, BIF, and iron ores may be more substantial than previously understood.