bluuebunny/crossref_metadata_2025 huggingface dataset:
Riparian Zones—From Policy Neglected to Policy Integrated
Authors: Urbanič Gorazd , Politti Emilio , Rodríguez-González Patricia María , Payne Robin , Schook Derek , Alves Maria Helena , Anđelković Ana , Bruno Daniel , Chilikova-Lubomirova Mila , Di Lonardo Sara , Egozi Roey , Garófano-Gómez Virginia , Gomes Marques Inês , González del Tánago Marta , Gültekin Yaşar Selman , Gumiero Bruna , Hellsten Seppo , Hinkov Georgi , Jakubínský Jiří , Janssen Philippe , Jansson Roland , Kelly-Quinn Mary , Kiss Timea , Lorenz Stefan , Martinez Romero Roberto , Mihaljević Zlatko , Papastergiadou Eva , Pavlin Urbanič Maja , Penning Ellis , Riis Tenna , Šibík Jozef , Šibíková Mária , Zlatanov Tzvetan , Dufour Simon
Published: April 2022

1. Riparian zones are vital areas of interaction between land and rivers and are often degraded by several pressures such as urbanisation, intensive agriculture and river engineering works. 2. This policy brief provides five key policy messages and recommendations to be considered by policy-makers, scientists, managers, and stakeholders to enhance riparian zone management. 3. Adopting an integrated socio-economic and environmentally dynamic view will ensure the sustainable management of riparian zones. 4. In light of climate change, it is critically important to conserve and/or restore the ecological integrity of riparian zones. 5. European Union Directives and national-scale legislation and regulations need updating to ensure coordinated implementation of riparian zone-related policies. 6. Stakeholder knowledge exchange, policy co-creation and adaptive management are key to enhancing riparian zone functions.
Impact of Meteorological Conditions and Human Activities on Air Quality During the COVID-19 Lockdown in Northeast China
Authors: Wang Taihao , Du Huadong , Zhao Zezheng , Zhang Jiping , Zhou Chengjun
Published: April 2022

During the lockdown implemented to curb the spread of COVID-19, human activities have drastically reduced, providing a valuable opportunity to study and compare the impact of meteorological conditions and human activities on air quality. In this study, large-scale weather circulation, local meteorological conditions, and the impact of human activities are comprehensively considered, and changes in the concentration of major air pollutants in the northeast during this period are systematically studied. The large-scale weather circulation patterns that mainly affect the northeast region are divided into nine types by using the T-mode Principal components analysis objective circulation classification method. It is found that the northeast region is located at the edge of weak high pressure (Types 1, 2, and 7) and at the rear of high pressure (Type 4) and has higher concentrations of PM2.5, NO2, SO2, and CO; in cyclonic weather systems, low vortices (Types 3 and 5) and under the influence of the updraft (Type 6) in front of the trough, the ozone concentration is higher. The changes in the concentrations of PM2.5, NO2, CO, SO2, and O3 in the three cities, namely Shenyang, Changchun, and Harbin, during the lockdown period are compared, and it is found that the concentrations of PM2.5, NO2, CO, and SO2 have a tendency to first decrease and then increase, while the changes of O3 concentration are cyclical and increased significantly during this period. This demonstrates that pollutants such as PM2.5, NO2, CO, and SO2 are more susceptible to human activities and local meteorological conditions, and changes in O3 concentration are more closely related to changes in weather circulation types. Finally, the FLEXPART-WRF model is used to simulate the pollution process of nine circulation types, which confirms that particulate pollution in the northeast is mainly affected by local emissions and local westward sinking airflow.
Impacts of a Near-Peer Urban Ecology Research Mentoring Program on Undergraduate Mentors
Authors: Aloisio Jason M. , Roberts Su-Jen , Becker-Klein Rachel , Dunifon Sarah , Lewis J. D. , Clark J. Alan , Munshi-South Jason , Tingley Karen
Published: April 2022

Environmental educators have used guided-inquiry in natural and supportive learning environments for decades, but comparatively little programming and research has focused on experiences in urban environments, including in constructed ecosystems like green roofs, or impacts on older youth and adults. To address this gap, we designed a tiered, near-peer research mentoring program called Project TRUE (Teens Researching Urban Ecology) and used a mixed-methods approach to evaluate impacts on undergraduates serving as research mentors. During the 11-week program, undergraduates conducted independent urban ecology research projects in a variety of New York City green spaces, including green roofs. They mentored a team of high school students working on their research projects, providing support throughout design, data collection, and dissemination. Our results indicate that these types of hands-on experiences can effectively support youth in learning research and mentoring skills and applying them to effectively manage and support high school students. Furthermore, 18 months after participation, mentors reported a sustained influence on their professional development, career paths, and science interest, especially in the context of their appreciation for nature. These results suggest that tiered, near-peer urban ecology research mentoring programs that utilizes urban green spaces, such as green roofs, can be an effective environmental education tool, especially in densely populated urban areas lacking traditional green space.
Individual Variation in Response to Novel Food in Captive Capuchin Monkeys (Sapajus spp.)
Authors: Ventricelli Marialba , Gratton Paolo , Sabbatini Gloria , Addessi Elsa , Sgaraglia Giulia , Rufo Fabrizio , Sirianni Giulia
Published: April 2022

How animals respond to novelty may have important outcomes in terms of fitness. On the one hand, aversion to novel stimuli may reduce the risks of consuming potentially toxic food or encountering predators. On the other hand, the propensity to approach novel stimuli may allow individuals to explore novel food sources and more flexibly adapt to novel challenges. Different species and individuals may find different ways to balance the costs and benefits that novelty posits. To date, however, little is known on how response to novel food varies across individuals of the same species depending on their previous experience with novelty, risk attitude and presence of higher-ranking conspecifics. In this study, we assessed individual variation in response to novel food by testing captive capuchin monkeys (Sapajus spp.) in an unconstrained social context, where all individuals in a group were able to access the testing area on a voluntary basis. We provided familiar and novel food to 23 study subjects belonging to four social groups differing in (i) previous experience with novel food, (ii) risk attitude (as assessed by a previous risky decision-making task), and (iii) dominance rank. We predicted that, as individuals may generalize their previous experience to novel contexts, those with more previous experience with novel food would be less neophobic than those with less experience. Moreover, if neophobia is a facet of the individual’s risk attitude, we predicted that more risk-prone individuals would be less neophobic than less risk-prone ones. Finally, individuals might flexibly modify their food choices according to the presence of conspecifics; in this respect, we predicted that, in response to monopolization of preferred resources by higher-ranking individuals, lower-ranking individuals would prefer familiar over novel food in the absence of higher-ranking individuals, but would modify their preference in favor of novel food in the presence of higher-ranking individuals. None of these predictions were supported by our results. We observed, however, that neophobia, measured as the latency to retrieve a food item, was more pronounced in lower-ranking than higher-ranking individuals, and that males showed a generally stronger bias than females toward a quicker retrieval of familiar food.
Naked Mole-Rat Social Phenotypes Vary in Investigative and Aggressive Behavior in a Laboratory Partner Preference Paradigm
Authors: Toor Ilapreet , Maynard Rashoun , Peng Xinye , Beery Annaliese K. , Holmes Melissa M.
Published: April 2022

Here we employed the partner preference test (PPT) to examine how naked mole-rat non-breeding individuals of different behavioral phenotypes make social decisions. Naked mole-rats from six colonies were classified into three behavioral phenotypes (soldiers, dispersers, and workers) using a battery of behavioral tests. They then participated in a 3 h long PPT, where they could freely interact with a tethered familiar or tethered unfamiliar conspecific. By comparing the three behavioral phenotypes, we tested the hypothesis that the PPT can be used to interrogate social decision-making in this species, revealing individual differences in behavior that are consistent with discrete social phenotypes. We also tested whether a shorter, 10 min version of the paradigm is sufficient to capture group differences in behavior. Overall, soldiers had higher aggression scores toward unfamiliar conspecifics than both workers and dispersers at the 10 min and 3 h comparison times. At the 10 min comparison time, workers showed a stronger preference for the familiar animal’s chamber, as well as for investigating the familiar conspecific, compared to both dispersers and soldiers. At the 3 h time point, no phenotype differences were seen with chamber or investigation preference scores. Overall, all phenotypes spent more time in chambers with another animal vs. being alone. Use of the PPT in a comparative context has demonstrated that the test identifies species and group differences in affiliative and aggressive behavior toward familiar and unfamiliar animals, revealing individual differences in social decision-making and, importantly, capturing aspects of species-specific social organization seen in nature.
Differential Expression Characterisation of the Heat Shock Proteins DnaJB6, DnaJshv, DnaJB13, and DnaJB14 in Apis cerana cerana Under Various Stress Conditions
Authors: Li Guilin , Zhang Shuxin , Wang Hongfang , Liang Li , Liu Zhenguo , Wang Ying , Xu Baohua , Zhao Hang
Published: April 2022

As key pollinators, bees are frequently exposed to multiple environmental stresses and have developed crucial mechanisms by which they adapt to these stressors. However, the molecular bases mediated at the gene level remain to be discovered. Here, we found four heat shock protein DnaJB subfamily genes, DnaJB6, DnaJshv, DnaJB13, and DnaJB14, from Apis cerana cerana, that all have J domains in their protein sequences. The expression levels of DnaJB6 and DnaJshv were upregulated by different degrees of heat stress, and the transcript level of DnaJB14 was gradually upregulated as the degree of heat stress increased, while the mRNA level of DnaJB13 was downregulated at multiple time points during heat stress treatment. The mRNA levels of all four DnaJBs were upregulated by cold and UV stress. In addition, the expression levels of DnaJB6, DnaJshv and DnaJB13 were reduced under abamectin, imidacloprid, cypermethrin, bifenthrin, spirodiclofen, and methomyl stresses. The transcript level of DnaJB14 was decreased by imidacloprid, cypermethrin, spirodiclofen, and methomyl exposure but increased by abamectin and bifenthrin exposure. These results indicate that the demand of A. cerana cerana for these four DnaJBs differs under various stress conditions. To further explore the role of DnaJBs in the stress response, we successfully silenced DnaJshv and DnaJB14. The content of protein carbonyl was increased, while the content of VC, the enzymatic activities of CAT, GST, and SOD, the mRNA levels of many antioxidant-related genes, and the total antioxidant capacity were reduced after knockdown of DnaJshv and DnaJB14 in A. cerana cerana. These results indicate that silencing DnaJshv and DnaJB14 increases oxidative damage and decreases the antioxidant ability of A. cerana cerana. Taken together, our results demonstrate that DnaJB6, DnaJshv, DnaJB13, and DnaJB14 are differentially expressed under stress conditions and play crucial roles in response to various stressors, possibly through the antioxidant signalling pathway. These findings will be conducive to understanding the molecular basis of bee responses to environmental stresses and are beneficial for improving bee protection.
Assessing the Spatiotemporal Heterogeneity of Terrestrial Temperature as a Proxy to Microclimate and Its Relationship With Urban Hydro-Biophysical Parameters
Authors: Mallick Javed , Alsubih Majed , Ahmed Mohd. , Almesfer Mohammed K. , Kahla Nabil Ben
Published: April 2022

Rapid urban land use and land cover changes have become a major environmental issue because of their ecological effects, including loss of green space and urban heat islands. Effective monitoring and management techniques are required. The Saudi Arabian twin city of Abha-Khamis Mushyet was selected as a case study for this research. As a result, the current study aimed to statistically and spatially investigate the relationship between land surface temperature (LST) and land use land cover based urban biophysical parameters such as normalized difference built-up index (NDBI), normalized difference vegetation index (NDVI), and normalized difference water index (NDWI). This study used random forest (RF) to classify LULC in 1990, 2000, and 2018. We also validated the LULC maps in a novel way. Using mono window algorithm techniques, we extracted LST for three periods. The dynamics of LULC, LST, and biophysical parameters were investigated using standard statistical graphs such as the heat map and the Sankey diagram. The correlation coefficient and the global bivariate Moran’ I approach were used to determine the association between LST and urban biophysical parameters. The relationship was then established in greater detail by categorizing the entire pixel into percentile classes and employing parallel coordinate plots. Finally, the association was built using GeoDA software and a conditional map. The LULC maps revealed a 334.4 percent increase in urban areas between 1990 and 2018. The built-up region is the largest stable LULC, with an 83.6 percent transitional probability matrix between 1990 and 2018. While 17.9%, 21.8%, 12.4%, and 10.5% of agricultural land, scrubland, exposed rocks, and water bodies were converted to built-up areas, respectively. The LST has increased rapidly over time because of LULC changes. The link between LST and urban biophysical parameters revealed that NDBI had a positive relationship, whereas NDWI and NDVI had a negative relationship. As a result, this study could be very important because it could help decision makers figure out how to lessen the effects of urban heat islands because of changes in LULC.
Ensemble-AHTPpred: A Robust Ensemble Machine Learning Model Integrated With a New Composite Feature for Identifying Antihypertensive Peptides
Authors: Lertampaiporn Supatcha , Hongsthong Apiradee , Wattanapornprom Warin , Thammarongtham Chinae
Published: April 2022

Hypertension or elevated blood pressure is a serious medical condition that significantly increases the risks of cardiovascular disease, heart disease, diabetes, stroke, kidney disease, and other health problems, that affect people worldwide. Thus, hypertension is one of the major global causes of premature death. Regarding the prevention and treatment of hypertension with no or few side effects, antihypertensive peptides (AHTPs) obtained from natural sources might be useful as nutraceuticals. Therefore, the search for alternative/novel AHTPs in food or natural sources has received much attention, as AHTPs may be functional agents for human health. AHTPs have been observed in diverse organisms, although many of them remain underinvestigated. The identification of peptides with antihypertensive activity in the laboratory is time- and resource-consuming. Alternatively, computational methods based on robust machine learning can identify or screen potential AHTP candidates prior to experimental verification. In this paper, we propose Ensemble-AHTPpred, an ensemble machine learning algorithm composed of a random forest (RF), a support vector machine (SVM), and extreme gradient boosting (XGB), with the aim of integrating diverse heterogeneous algorithms to enhance the robustness of the final predictive model. The selected feature set includes various computed features, such as various physicochemical properties, amino acid compositions (AACs), transitions, n-grams, and secondary structure-related information; these features are able to learn more information in terms of analyzing or explaining the characteristics of the predicted peptide. In addition, the tool is integrated with a newly proposed composite feature (generated based on a logistic regression function) that combines various feature aspects to enable improved AHTP characterization. Our tool, Ensemble-AHTPpred, achieved an overall accuracy above 90% on independent test data. Additionally, the approach was applied to novel experimentally validated AHTPs, obtained from recent studies, which did not overlap with the training and test datasets, and the tool could precisely predict these AHTPs.
Correlation of Cytokine Release Syndrome With Prognosis After Chimeric Antigen Receptor T Cell Therapy: Analysis of 54 Patients With Relapsed or Refractory Multiple Myeloma
Authors: Wang Xue , Zhao Lina , Wang Jing , Yao Yue , Wang Jiaojiao , Ji Shengwei , Hua Tian , Wang Shiyuan , Cheng Hai , Shi Ming , Li Zhenyu , Zeng Lingyu , Zheng Junnian , Xu Kailin , Cao Jiang
Published: April 2022

Although chimeric antigen receptor T (CAR-T) cell therapy has proven to be effective in treating relapsed or refractory multiple myeloma (R/R MM), the severity of cytokine release syndrome (CRS) can affect patient survival and the risk factors for CRS remain an intractable issue. We enrolled 54 patients with R/R MM following combined infusion of anti-CD19 and anti-B-cell maturation antigen (BCMA) CAR-T cells. The results showed the overall response rate was 94% (51/54) after CAR-T cell infusion, with a 100% incidence of CRS, including 47 patients with grade 1-2 (mild) CRS and 7 patients with grade 3-5 (severe) CRS. In the mild CRS group, the median progression-free survival (PFS) was 18.2 months (95% CI, 6.5 to 30.1) and the median overall survival (OS) was not reached yet. In the severe CRS group, median PFS and median OS were 1.9 months (95% CI, 0.2 to 3.8). Further analysis demonstrated that severe CRS had a shorter median PFS and OS than mild CRS (p=0.029, p=0.020). Bone marrow tumor burden was found to be independently associated with CRS. The grade of CRS was positively correlated with six serum cytokines levels including G-CSF, IL-6, IL-8, IP-10, MIP-1a and RANTES. In conclusion, early detection and management of CRS are imperative for the prevention of life-threatening complications and improvement in the survival of patients of CAR-T cell therapy.

Clinical Trial Registration

www.chictr.org.cn, identifier ChiCTR-OIC-17011272.
Virological and Clinical Determinants of the Magnitude of Humoral Responses to SARS-CoV-2 in Mild-Symptomatic Individuals
Authors: Pradenas Edwards , Ubals Maria , Urrea Víctor , Suñer Clara , Trinité Benjamin , Riveira-Muñoz Eva , Marfil Silvia , Ávila-Nieto Carlos , Rodríguez de la Concepción María Luisa , Tarrés-Freixas Ferran , Laporte Josep , Ballana Ester , Carrillo Jorge , Clotet Bonaventura , Mitjà Oriol , Blanco Julià
Published: April 2022

Background

Evidence on the determinants of the magnitude of humoral responses and neutralizing titers in individuals with mild COVID-19 is scarce.

Methods

In this cohort study of mild COVID-19 patients, we assessed viral load (VL) by RT-qPCR at two/three time points during acute infection, and anti-SARS-CoV-2 antibodies by ELISA and plasma neutralizing responses using a pseudovirus assay at day 60.

Results

Seventy-one individuals (65% female, median 42 years old) were recruited and grouped into high viral load (VL) >7.5 Log10 copies/mL (n=20), low, VL ≤7.5 Log10 copies/mL (n=22), or as Non-early seroconverters with a positive PCR (n=20), and healthy individuals with a negative PCR (n=9). Individuals with high or low VL showed similar titers of total neutralizing antibodies at day 60, irrespective of maximal VL or viral dynamics. Non-early seroconverters had lower antibody titers on day 60, albeit similar neutralizing activity as the groups with high or low VL. Longer symptom duration and older age were independently associated with increased humoral responses.

Conclusions

In mild SARS-CoV-2-infected individuals, the duration of symptoms and age (but not VL) contribute to higher humoral responses.
Complement System and Alarmin HMGB1 Crosstalk: For Better or Worse
Authors: Gaboriaud Christine , Lorvellec Marie , Rossi Véronique , Dumestre-Pérard Chantal , Thielens Nicole M.
Published: April 2022

Our immune system responds to infectious (PAMPs) and tissue damage (DAMPs) signals. The complement system and alarmin High-Mobility Group Box 1 (HMGB1) are two powerful soluble actors of human host defense and immune surveillance. These systems involve molecular cascades and amplification loops for their signaling or activation. Initially activated as alarm raising systems, their function can be finally switched towards inflammation resolution, where they sustain immune maturation and orchestrate repair mechanisms, opening the way back to homeostasis. However, when getting out of control, these defense systems can become deleterious and trigger serious cellular and tissue damage. Therefore, they can be considered as double-edged swords. The close interaction between the complement and HMGB1 pathways is described here, as well as their traditional and non-canonical roles, their functioning at different locations and their independent and collective impact in different systems both in health and disease. Starting from these systems and interplay at the molecular level (when elucidated), we then provide disease examples to better illustrate the signs and consequences of their roles and interaction, highlighting their importance and possible vicious circles in alarm raising and inflammation, both individually or in combination. Although this integrated view may open new therapeutic strategies, future challenges have to be faced because of the remaining unknowns regarding the molecular mechanisms underlying the fragile molecular balance which can drift towards disease or return to homeostasis, as briefly discussed at the end.
Case Report: Maintenance Nivolumab in Complete Responder After Multimodality Therapy in Metastatic Pancreatic Adenocarcinoma
Authors: Yang Shih-Hung , Lee Jen-Chieh , Chen Bang-Bin , Kuo Sung-Hsin , Hsu Chiun , Bai Li-Yuan
Published: April 2022

Maintenance therapy is rarely considered in pancreatic ductal adenocarcinoma (PDAC). We describe the case of a 57-year-old man with metastatic PDAC treated with an initially full but subsequently de-escalated dose of combination chemotherapy due to intolerance to neurotoxicity. After a complete response to combined radiofrequency ablation for the liver metastasis and radiotherapy for the pancreatic tumor was achieved, chemotherapy was terminated and maintenance therapy was applied: nivolumab plus cytokine-induced killer cell therapy initially and then a de-escalated dosing interval of nivolumab monotherapy subsequently. No adverse events occurred during nivolumab therapy for more than 2 years, and the patient remains disease-free. To date, this is the first report of maintenance nivolumab after successful multimodality therapy in metastatic PDAC.
Distal Consequences of Mucosal Infections in Intestinal and Lung Inflammation
Authors: Melo-González Felipe , Sepúlveda-Alfaro Javiera , Schultz Bárbara M. , Suazo Isidora D. , Boone David L. , Kalergis Alexis M. , Bueno Susan M.
Published: April 2022

Infectious diseases are one of the leading causes of morbidity and mortality worldwide, affecting high-risk populations such as children and the elderly. Pathogens usually activate local immune responses at the site of infection, resulting in both protective and inflammatory responses, which may lead to local changes in the microbiota, metabolites, and the cytokine environment. Although some pathogens can disseminate and cause systemic disease, increasing evidence suggests that local infections can affect tissues not directly invaded. In particular, diseases occurring at distal mucosal barriers such as the lung and the intestine seem to be linked, as shown by epidemiological studies in humans. These mucosal barriers have bidirectional interactions based mainly on multiple signals derived from the microbiota, which has been termed as the gut-lung axis. However, the effects observed in such distal places are still incompletely understood. Most of the current research focuses on the systemic impact of changes in microbiota and bacterial metabolites during infection, which could further modulate immune responses at distal tissue sites. Here, we describe how the gut microbiota and associated metabolites play key roles in maintaining local homeostasis and preventing enteric infection by direct and indirect mechanisms. Subsequently, we discuss recent murine and human studies linking infectious diseases with changes occurring at distal mucosal barriers, with particular emphasis on bacterial and viral infections affecting the lung and the gastrointestinal tract. Further, we discuss the potential mechanisms by which pathogens may cause such effects, promoting either protection or susceptibility to secondary infection.
Establishment of a lncRNA-Based Prognostic Gene Signature Associated With Altered Immune Responses in HCC
Authors: Li Xiawei , Zhang Zhiqian , Liu Mingcheng , Fu Xing , A Jun , Chen Guoan , Wu Shian , Dong Jin-Tang
Published: April 2022

Hepatocellular carcinoma (HCC) is a common malignancy with higher mortality, and means are urgently needed to improve the prognosis. T cell exclusion (TCE) plays a pivotal role in immune evasion, and lncRNAs represent a large group of tumor development and progression modulators. Using the TCGA HCC dataset (n=374), we identified 2752 differentially expressed and 702 TCE-associated lncRNAs, of which 336 were in both groups. As identified using the univariate Cox regression analysis, those associated with overall survival (OS) were subjected to the LASSO-COX regression analysis to develop a prognosis signature. The model, which consisted of 11 lncRNAs and was named 11LNCPS for 11-lncRNA prognosis signature, was validated and performed better than two previous models. In addition to OS and TCE, higher 11LNCPS scores had a significant correlation with reduced infiltrations of CD8+ T cells and dendritic cells (DCs) and decreased infiltrations of Th1, Th2, and pro B cells. As expected, these infiltration alterations were significantly associated with worse OS in HCC. Analysis of published data indicates that HCCs with higher 11LNCPS scores were transcriptomically similar to those that responded better to PDL1 inhibitor. Of the 11LNCPS lncRNAs, LINC01134 and AC116025.2 seem more crucial, as their upregulations affected more immune cell types’ infiltrations and were significantly associated with TCE, worse OS, and compromised immune responses in HCC. LncRNAs in the 11LNCPS impacted many cancer-associated biological processes and signaling pathways, particularly those involved in immune function and metabolism. The 11LNCPS should be useful for predicting prognosis and immune responses in HCC.
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment
Authors: Bridges Kate , Miller-Jensen Kathryn
Published: April 2022

Recent advances in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq), have permitted high throughput transcriptional profiling of a wide variety of biological systems. As scRNA-seq supports inference of cell-cell communication, this technology has and continues to anchor groundbreaking studies into the efficacy and mechanism of novel immunotherapies for cancer treatment. In this review, we will highlight methods developed to infer inter- and intracellular signaling from scRNA-seq and discuss how they have contributed to studies of immunotherapeutic intervention in the tumor microenvironment (TME). However, a central challenge remains in validating the hypothesized cell-cell interactions. Therefore, this review will also cover strategies for integration of these scRNA-seq-derived interaction networks with existing experimental and computational approaches. Integration of these networks with imaging, protein secretion measurements, and network analysis and mathematical modeling tools addresses challenges that remain with scRNA-seq to enhance studies of immunosuppressive and immunotherapy-altered signaling in the TME.
CD45RB Glycosylation and Ig Isotype Define Maturation of Functionally Distinct B Cell Subsets in Human Peripheral Blood
Authors: Koers Jana , Pollastro Sabrina , Tol Simon , Pico-Knijnenburg Ingrid , Derksen Ninotska I. L. , van Schouwenburg Pauline A. , van der Burg Mirjam , van Ham S. Marieke , Rispens Theo
Published: April 2022

Glycosylation of CD45RB (RB+) has recently been identified to mark antigen-experienced B cells, independent of their CD27 expression. By using a novel combination of markers including CD45RB glycosylation, CD27 and IgM/IgD isotype expression we segregated human peripheral blood B cell subsets and investigated their IGHV repertoire and in vitro functionality. We observed distinct maturation stages for CD27-RB+ cells, defined by differential expression of non-switched Ig isotypes. CD27-RB+ cells, which only express IgM, were more matured in terms of Ig gene mutation levels and function as compared to CD27-RB+ cells that express both IgM and IgD or cells that were CD27-RB-. Moreover, CD27-RB+IgM+ cells already showed remarkable rigidity in IgM isotype commitment, different from CD27-RB+IgMD+ and CD27-RB- cells that still demonstrated great plasticity in B cell fate decision. Thus, glycosylation of CD45RB is indicative for antigen-primed B cells, which are, dependent on the Ig isotype, functionally distinct.
Study on the Activity Laws of Fishing Vessels in China’s Sea Areas in Winter and Spring and the Effects of the COVID-19 Pandemic Based on AIS Data
Authors: Guan Yanan , Zhang Jie , Zhang Xi , Li Zhongwei , Meng Junmin , Liu Genwang , Bao Meng , Cao Chenghui
Published: April 2022

Using AIS data to mine the dynamic characteristics of fishery resource exploitation helps to carry out scientific management of fishery and realize the sustainable development of marine resources. We proposed a framework that integrates multiple AIS data processing and analysis modules, which can efficiently divide fishing voyages, determine the fishing activities and identify fishing types, and provide near real-time analysis results on the number of fishing vessels, fishing duration, voyages and so on. The framework was applied to 1.68 billion AIS trajectory data points of approximately 588,000 fishing vessels. We selected China’s sea areas overall and six fishing grounds as the research area, explored the characteristics of fishing vessel activities in winter and spring of 2019, and analyzed the impact of COVID-19 on winter-spring fishing in China in 2020. In 2019, our results showed that the number of fishing vessels in China’s sea areas gradually increased over time, with the Chinese New Year holiday affecting fishing activities at the corresponding time but having little impact on the entire month. We found that the changing laws of the fishing duration and voyages in the inshore fishing grounds were similar to those of the number of fishing vessels, which increased to varying degrees over time. Gillnetters were the most numerous fishing vessel type operating in the inshore fishing grounds with increased in spring, while seiners had an absolute advantage in the Xisha-Zhongsha fishing ground. In 2020, during the occurrence period of COVID-19, the fishing activities in China’s sea areas was almost unaffected. During the outbreak period, the number, distribution range, activity intensity, and fishing duration of fishing vessels all experienced a relatively large decline. After the epidemic was effectively controlled, they were rapidly increased. In addition, we found that compared with the Government Response Stringency Index, the number of fishing vessels and the number of new confirmed cases showed a more obvious negative correlation. By processing, mining and analyzing AIS data with high spatial-temporal granularity, this study can provide data support for the reasonable development of fishery resources, and help fishery practitioners make wise decisions when responding to unexpected emergencies (e.g. pandemics).
The Microbiome of Suaeda monoica and Dipterygium glaucum From Southern Corniche (Saudi Arabia) Reveals Different Recruitment Patterns of Bacteria and Archaea
Authors: Jalal Rewaa S. , Sheikh Hassan I. , Alotaibi Mohammed T. , Shami Ashwag Y. , Ashy Ruba A. , Baeshen Naseebh N. , Abulfaraj Aala A. , Baz Lina , Refai Mohammed , Baeshen Nabih A. , Fadhlina Anis , Arifullah Mohammed , Baeshen Mohammed N.
Published: April 2022

Soil and plant interact differently in response to the same stress (e.g., salinity) and recruit certain bacteria. The southern corniche (Saudi Arabia) has limited plant growth, which could be due to the high temperature and salinity. The study aimed to determine the soil microbiome of selected plants and the interactions between soil and these plants.Suaeda monoicaandDipterygium glaucumsoil samples were collected from the crust (surface) and rhizosphere, while soil with no plant growth from the nearby area was used as control. High-throughput hypervariable V3–V4 region of the 16S rRNA gene was used to evaluate the shifts in soil microbiome due to growth of plant growth. The analysis detected up to 16% archaeal strains inS. monoica-associated samples, whileD. glaucumand control samples contained 100% bacterial strains. The top 10 phyla composition of the soil samples were Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadota, Bacteroidota, Halobacterota, Cyanobacteria, Cloroflexi, Planctomycetota, and Myxococcota. The V3–V4 region analysis successfully clustered the 5 samples into 3 clusters (control,D. glaucum, andS. monoica) at higher-order classification but not at the species level due to unidentified bacteria. The main differences between soil samples were due to halophyteS. monoicasamples containing high amounts of halophilic archaea and halophilic bacteria. This showed that selected plants interacted differently with the soil. EC- and KO-based analyses of functional genes and pathways showed that 5 pathways were specific to control, 11 pathways were observed only inD. glaucumsamples, 12 pathways were expressed inS. monoicasamples only, and 9 pathways were common in all samples. The study also detected numerous relatively novel genera in high abundance such asAliifodinibius,Pontibacter, andLacunisphaera. This showed that the soil in the sampling area is not well explored and that novel species could be isolated from the soil samples and used for future research.
Radium-Derived Water Mixing and Associated Nutrient in the Northern South China Sea
Authors: Liu Jianan , Du Jinzhou , Wu Ying , Liu Sumei
Published: April 2022

Nutrients play an important role as biogenic elements in modulating marine productivity, and water mixing usually facilitates the transportation of nutrients in the coastal ocean. In this study, the distributions of naturally occurring radioisotopes 226Ra and 228Ra in the surface and water column of the northern South China Sea (NSCS) have been investigated to estimate oceanic mixing and nutrient supplies. We identified three masses of the South China Sea Warm Current (SCSWC), the South China Sea Branch of the Kuroshio (SCSBK), and shelf water in the summer of June 2015, but only SCSWC and SCSBK were observed in the spring of March 2017. The fraction of the SCSBK in summer was estimated to be an average of 0.25 ± 0.16, which was lower than that in the spring of 0.57 ± 0.32 in our study area. The horizontal mixing from the Pearl River plume revealed eddy diffusion of (1.2 ± 0.79) × 105 cm2/s and advection velocity ω of 0.25 ± 0.16 cm/s in the slope region. In the water column, the best-fit exponential curve gradient of 228Ra led to a vertical diffusion coefficient of 0.43 ± 0.33 cm2/s that went down to the subsurface of the upper 1,000 m, and an upward vertical diffusion coefficient was revealed as 18 ± 9.9 cm2/s from the near-bottom. Combining the nutrient distributions, horizontal mixing from the Pearl River plume carried (5.6 ± 4.9) × 102 mmol N/m2/d, 2.2 ± 2.0 mmol P/m2/d, and (4.1 ± 3.9) × 102 mmol Si/m2/d in the very surface layer, suggesting that shelf water plays a significant role in the nutrient sources of the slope of the NSCS during June 2015. The upward vertical mixing supplied 2.7 ± 1.6 mmol N/m2/d, 0.18 ± 0.11 mmol P/m2/d, and 15 ± 8.4 mmol Si/m2/d to the upper layer, which appeared more important than atmospheric deposition and rivaled submarine groundwater discharge.
Connectivity of Striped Marlin From the Central North Pacific Ocean
Authors: Lam Chi Hin , Tam Clayward , Lutcavage Molly E.
Published: April 2022

Striped marlin, Kajikia audax, have been in overfished condition in the Western and Central North Pacific, and overfishing is still occurring, prompting an urgent need to devise conservation and management measures based on the best, current information on biology and ecology of this species. Despite conventional tagging efforts off Hawaii, striped marlin movements are not known across the broader Pacific, and little research has been conducted since 2005. To address this gap, 31 popup satellite archival tags (PSAT) were deployed on striped marlin (138-192 cm eye fork length) between 2016 and 2019 via the Hawaii-based longline fleet. To complement tagging efforts, 148 fin clips were also collected for genetic analyses during June-August 2017. Tag attachments ranged from 1-365 days (median = 74), where mechanical failures and non-reporting tags lowered expected data returns. Striped marlin tracks revealed extensive spatial use of the Central Pacific, spanning 15°S to 43°N and 122 to 170°W, showing diverse seasonal dispersal patterns and individual movements, and some coincided in time and space with known spawning grounds. Genetic profiles of 55 Hawaii-landed striped marlin were assigned to two genetic groups: Australia, New Zealand and Hawaii (n = 19), and Hawaii alone (n=36), suggesting the Hawaii-based longline fleet interacted with individuals from multiple populations.

A year-long track confirmed migration between the Central North Pacific and Australia (>9,400 km), and combined with genetic results, is the first to document regional connectivity. By combining tools from conventional and electronic tags, biological sampling, and genomic techniques, a more holistic understanding emerges, suggesting that striped marlin should be collectively managed. Under global warming scenarios and changing pelagic ecosystems, integrative knowledge is critical for designing effective management strategies for rebuilding sustainable populations across the Pacific Ocean.
Insights Into the Electronic Properties of PbBi Atomic Layers on Ge(111) and Si(111) Surfaces
Authors: Mihalyuk A. N. , Vekovshinin Y. E. , Bondarenko L. V. , Tupchaya A. Y. , Utas T. V. , Gruznev D. V. , Eremeev S. V. , Zotov A. V. , Saranin A. A.
Published: April 2022

Co-adsorption of Pb and Bi onto Si(111) and Ge(111) surfaces has been found to result in formation of atomic-layer PbBi compounds having similar structures. These are two co-existing crystalline PbBi phases with 23×23 and 2 × 2 periodicities. Using density functional theory calculations, we found that these two phases present insulating and highly anisotropic metallic systems, respectively. However, electronic structure of the metallic 2 × 2-PbBi phase on Ge(111) appears qualitatively different from that on the Si(111). We investigated electronic properties of the PbBi compound considering the effects induced by the different supporting substrates, namely Si(111) and Ge(111). As a part of comparative study, we made the chemical-bonding analysis and examined a free-standing PbBi layer inspecting the dependence of its spectral characteristics on the compressive/tensile strain. We believe that the present findings will play an important role in the development of new electronic devices fabricated in the ultimate two-dimensional limit.
T-Cell Subsets and Interleukin-10 Levels Are Predictors of Severity and Mortality in COVID-19: A Systematic Review and Meta-Analysis
Authors: Alshammary Amal F. , Alsughayyir Jawaher M. , Alharbi Khalid K. , Al-Sulaiman Abdulrahman M. , Alshammary Haifa F. , Alshammary Heba F.
Published: April 2022

Background

Many COVID-19 patients reveal a marked decrease in their lymphocyte counts, a condition that translates clinically into immunodepression and is common among these patients. Outcomes for infected patients vary depending on their lymphocytopenia status, especially their T-cell counts. Patients are more likely to recover when lymphocytopenia is resolved. When lymphocytopenia persists, severe complications can develop and often lead to death. Similarly, IL-10 concentration is elevated in severe COVID-19 cases and may be associated with the depression observed in T-cell counts. Accordingly, this systematic review and meta-analysis aims to analyze T-cell subsets and IL-10 levels among COVID-19 patients. Understanding the underlying mechanisms of the immunodepression observed in COVID-19, and its consequences, may enable early identification of disease severity and reduction of overall morbidity and mortality.

Methods

A systematic search was conducted covering PubMed MEDLINE, Scopus, Web of Science, and EBSCO databases for journal articles published from December 1, 2019 to March 14, 2021. In addition, we reviewed bibliographies of relevant reviews and the medRxiv preprint server for eligible studies. Our search covered published studies reporting laboratory parameters for T-cell subsets (CD4/CD8) and IL-10 among confirmed COVID-19 patients. Six authors carried out the process of data screening, extraction, and quality assessment independently. The DerSimonian-Laird random-effect model was performed for this meta-analysis, and the standardized mean difference (SMD) and 95% confidence interval (CI) were calculated for each parameter.

Results

A total of 52 studies from 11 countries across 3 continents were included in this study. Compared with mild and survivor COVID-19 cases, severe and non-survivor cases had lower counts of CD4/CD8 T-cells and higher levels of IL-10.

Conclusion

Our findings reveal that the level of CD4/CD8 T-cells and IL-10 are reliable predictors of severity and mortality in COVID-19 patients. The study protocol is registered with the International Prospective Register of Systematic Reviews (PROSPERO); registration number CRD42020218918.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020218918, identifier: CRD42020218918.
Veno-Venous Extracorporeal Membrane Oxygenation in Minipigs as a Robust Tool to Model Acute Kidney Injury: Technical Notes and Characteristics
Authors: Szabó-Biczók Antal , Varga Gabriella , Varga Zoltán , Bari Gábor , Vigyikán Gyöngyvér , Gajda Ámos , Vida Noémi , Hodoniczki Ádám , Rutai Attila , Juhász László , Nászai Anna , Gyöngyösi Máté , Turkevi-Nagy Sándor , Érces Dániel , Boros Mihály
Published: April 2022

Objective

Veno-venous extracorporeal membrane oxygenation (vv-ECMO) can save lives in severe respiratory distress, but this innovative approach has serious side-effects and is accompanied by higher rates of iatrogenic morbidity. Our aims were, first, to establish a large animal model of vv-ECMO to study the pathomechanism of complications within a clinically relevant time frame and, second, to investigate renal reactions to increase the likelihood of identifying novel targets and to improve clinical outcomes of vv-ECMO-induced acute kidney injury (AKI).

Methods

Anesthetized Vietnamese miniature pigs were used. After cannulation of the right jugular and femoral veins, vv-ECMO was started and maintained for 24 hrs. In Group 1 (n = 6) ECMO was followed by a further 6-hr post-ECMO period, while (n = 6) cannulation was performed without ECMO in the control group, with observation maintained for 30 h. Systemic hemodynamics, blood gas values and hour diuresis were monitored. Renal artery flow (RAF) was measured in the post-ECMO period with an ultrasonic flowmeter. At the end of the experiments, renal tissue samples were taken for histology to measure myeloperoxidase (MPO) and xanthine oxidoreductase (XOR) activity and to examine mitochondrial function with high-resolution respirometry (HRR, Oroboros, Austria). Plasma and urine samples were collected every 6 hrs to determine neutrophil gelatinase-associated lipocalin (NGAL) concentrations.

Results

During the post-ECMO period, RAF dropped (96.3 ± 21 vs. 223.6 ± 32 ml/min) and, similarly, hour diuresis was significantly lower as compared to the control group (3.25 ± 0.4 ml/h/kg vs. 4.83 ± 0.6 ml/h/kg). Renal histology demonstrated significant structural damage characteristic of ischemic injury in the tubular system. In the vv-ECMO group NGAL levels, rose significantly in both urine (4.24 ± 0.25 vs. 2.57 ± 0.26 ng/ml) and plasma samples (4.67 ± 0.1 vs. 3.22 ± 0.2 ng/ml), while tissue XOR (5.88 ± 0.8 vs. 2.57 ± 0.2 pmol/min/mg protein) and MPO (11.93 ± 2.5 vs. 4.34 ± 0.6 mU/mg protein) activity was elevated. HRR showed renal mitochondrial dysfunction, including a significant drop in complex-I-dependent oxidative capacity (174.93 ± 12.7 vs. 249 ± 30.07 pmol/s/ml).

Conclusion

Significantly decreased renal function with signs of structural damage and impaired mitochondrial function developed in the vv-ECMO group. The vv-ECMO-induced acute renal impairment in this 30-hr research protocol provides a good basis to study the pathomechanism, biomarker combinations or possible therapeutic possibilities for AKI.