bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution Characteristics of Quaternary Channel Systems and Their Controlling Factors in the Qiongdongnan Basin, South China Sea
Authors: Meng Miaomiao , Liang Jinqiang , Kuang Zenggui , Ren Jinfeng , He Yulin , Deng Wei , Gong Yuehua
Published: June 2022

The study of deepwater channels is important for the understanding of the sedimentary evolution mechanism and the sedimentary process of the marginal sea. In 2019, thick pore-filling gas hydrate with high saturation was firstly discovered in the Quaternary sands of the Qiongdongnan Basin (QDNB), which expanded the reservoir types of gas hydrates in the South China Sea. However, the distribution of sand-related channels is not well characterized, which limits the ability to predict sand reservoirs with gas hydrate. Using integrated 2D/3D seismic, multi-beam, well logging, and coring data, the current study documents the distribution characteristics of channel systems in the Quaternary strata and discusses their controlling factors. The integrated analysis shows that the channel-related sedimentary facies include channel-filling facies, levee facies, crevasse splay facies, and lobes facies. A total of six periods of channel systems is identified in the Quaternary strata. There are obvious distribution differences between the Channel 1 and Channel 3 systems when comparing the western, middle, and eastern sections: the channels in the western and eastern sections are mainly dominated by near straight V-shaped channels, while the middle section mainly consists of large braided channels, where channel-levee sedimentary facies developed. Compared with the distribution of the Central Canyon that developed in the Miocene, the Channel 1 and Channel 3 systems in the western section show southward migration since the Miocene. The distribution and evolution of Quaternary channels were likely collectively controlled by seafloor morphology, tectonic movement, sea-level fluctuations, and provenance supply. Tectonic movement controls seafloor morphology, which directly controls the flow of channels and their distribution characteristics; provenance supply determines the scale and sedimentary characteristics of each channel. The periodic changes in sea-level determine the evolution of multi-stage channel systems. This study has implications for the prediction of gas hydrate–bearing sands in the Quaternary QDNB and deepens our understanding of the Quaternary tectonic and sedimentary evolution in the QDNB.
Anti-Müllerian Hormone Signal Transduction involved in Müllerian Duct Regression
Authors: Cate Richard L.
Published: June 2022

Over seventy years ago it was proposed that the fetal testis produces a hormone distinct from testosterone that is required for complete male sexual development. At the time the hormone had not yet been identified but was invoked by Alfred Jost to explain why the Müllerian duct, which develops into the female reproductive tract, regresses in the male fetus. That hormone, anti-Müllerian hormone (AMH), and its specific receptor, AMHR2, have now been extensively characterized and belong to the transforming growth factor-β families of protein ligands and receptors involved in growth and differentiation. Much is now known about the downstream events set in motion after AMH engages AMHR2 at the surface of specific Müllerian duct cells and initiates a cascade of molecular interactions that ultimately terminate in the nucleus as activated transcription factors. The signals generated by the AMH signaling pathway are then integrated with signals coming from other pathways and culminate in a complex gene regulatory program that redirects cellular functions and fates and leads to Müllerian duct regression.
Dual Roles of Prolactin and Vasoinhibin in Inflammatory Arthritis
Authors: Clapp Carmen , Ortiz Georgina , García-Rodrigo Jose F. , Ledesma-Colunga María G. , Martínez-Díaz Oscar F. , Adán Norma , Martínez de la Escalera Gonzalo
Published: June 2022

The term inflammatory arthritis defines a family of diseases, including rheumatoid arthritis (RA), caused by an overactive immune system, and influenced by host aspects including sex, reproductive state, and stress. Prolactin (PRL) is a sexually dimorphic, reproductive, stress-related hormone long-linked to RA under the general assumption that it aggravates the disease. However, this conclusion remains controversial since PRL has both negative and positive outcomes in RA that may depend on the hormone circulating levels, synthesis by joint tissues, and complex interactions at the inflammatory milieu. The inflamed joint is rich in matrix metalloproteases that cleave PRL to vasoinhibin, a PRL fragment with proinflammatory effects and the ability to inhibit the hyperpermeability and growth of blood vessels. This review addresses this field with the idea that explanatory mechanisms lie within the PRL/vasoinhibin axis, an integrative framework influencing not only the levels of systemic and local PRL, but also the proteolytic conversion of PRL to vasoinhibin, as vasoinhibin itself has dual actions on joint inflammation. In this review, we discuss recent findings from mouse models suggesting the upregulation of endogenous vasoinhibin by the pro-inflammatory environment and showing dichotomous actions and signaling mechanisms of PRL and vasoinhibin on joint inflammation that are cell-specific and context-dependent. We hypothesize that these opposing actions work together to balance the inflammatory response and provide new insights for understanding the pathophysiology of RA and the development of new treatments.
What Does the Future Hold for Páramo Plants? A Modelling Approach
Authors: Peyre Gwendolyn
Published: June 2022

Understanding the effects of climate change on tropicalpine biota remains a scientific challenge today. The Andean páramo is the largest and most diverse tropicalpine biogeographical region in the world, and also one of the most threatened as it is prone to accelerated environmental changes. My goal was to predict changes in the distribution ranges of the diverse and highly endemic páramo flora on the mid-term (50 years). First, I predicted distribution changes in páramo plant species under novel climates and considering dispersal constraints. Second, I looked for consensus areas of species losses vs. gains in the páramo, expecting to identify a gradient of increasing relative richness with elevation over time. Last, I evaluated the behavior of plant species regarding their climatic refugia since the Last Glacial Maximum (LGM) to establish if they likely remain or transcend them. Based on VegParamo vegetation data and CHELSA bioclimatic information, I performed species distribution models for a 664 species pool, that were then contrasted between the present, future (2070) and past (LGM). About 8.3% of the entire species pool (55 species) were predicted to be extirpated from the páramo by 2070, including 22 species endemics. On average, páramo plants gained 15.52% of additional distribution by 2070 (18.81% for endemics). Models predicted the most area gains for the northern páramos of Colombia and Venezuela, and the highest losses for the eastern Ecuadorian and Peruvian mountains. Moreover, area gains were more pronounced at high elevations, suggesting a future accelerated colonization process toward the northern Andean summits. Finally, only 21.41% of the species’ 2070 distribution coincided with their LGM (19.75% for endemics), and the largest climatic refugia since the LGM were found in southern Ecuador and Peru. This study is pioneer in predicting future distribution shifts for páramo plant species overall and provides solid bases to support climate change research and adaptation strategies in the tropical Andes.
Transcriptome Analysis of Pennisetum glaucum (L.) R. Br. Provides Insight Into Heat Stress Responses
Authors: Maibam Albert , Lone Showkat Ahmad , Ningombam Sunil , Gaikwad Kishor , Amitha Mithra S. V. , Singh Madan Pal , Singh Sumer Pal , Dalal Monika , Padaria Jasdeep Chatrath
Published: June 2022

Pennisetum glaucum (L.) R. Br., being widely grown in dry and hot weather, frequently encounters heat stress at various stages of growth. The crop, due to its inherent capacity, efficiently overcomes such stress during vegetative stages. However, the same is not always the case with the terminal (flowering through grain filling) stages of growth, where recovery from stress is more challenging. However, certain pearl millet genotypes such as 841-B are known to overcome heat stress even at the terminal growth stages. Therefore, we performed RNA sequencing of two contrasting genotypes of pearl millet (841-B and PPMI-69) subjected to heat stress (42°C for 6 h) at flowering stages. Over 274 million high quality reads with an average length of 150 nt were generated, which were assembled into 47,310 unigenes having an average length of 1,254 nucleotides, N50 length of 1853 nucleotides, and GC content of 53.11%. Blastx resulted in the annotation of 35,628 unigenes, and functional classification showed 15,950 unigenes designated to 51 Gene Ontology terms. A total of 13,786 unigenes were allocated to 23 Clusters of Orthologous Groups, and 4,255 unigenes were distributed to 132 functional Kyoto Encyclopedia of Genes and Genomes database pathways. A total of 12,976 simple sequence repeats and 305,759 SNPs were identified in the transcriptome data. Out of 2,301 differentially expressed genes, 10 potential candidate genes were selected based on log2 fold change and adjusted p value parameters for their differential gene expression by qRT-PCR. We were able to identify differentially expressed genes unique to either of the two genotypes, and also, some DEGs common to both the genotypes were enriched. The differential expression patterns suggested that 841-B 6 h has better ability to maintain homeostasis during heat stress as compared to PPMI-69 6 h. The sequencing data generated in this study, like the SSRs and SNPs, shall serve as an important resource for the development of genetic markers, and the differentially expressed heat responsive genes shall be used for the development of transgenic crops.
Transposable Elements in Pluripotent Stem Cells and Human Disease
Authors: Ma Gang , Babarinde Isaac A. , Zhou Xuemeng , Hutchins Andrew P.
Published: June 2022

Transposable elements (TEs) are mobile genetic elements that can randomly integrate into other genomic sites. They have successfully replicated and now occupy around 40% of the total DNA sequence in humans. TEs in the genome have a complex relationship with the host cell, being both potentially deleterious and advantageous at the same time. Only a tiny minority of TEs are still capable of transposition, yet their fossilized sequence fragments are thought to be involved in various molecular processes, such as gene transcriptional activity, RNA stability and subcellular localization, and chromosomal architecture. TEs have also been implicated in biological processes, although it is often hard to reveal cause from correlation due to formidable technical issues in analyzing TEs. In this review, we compare and contrast two views of TE activity: one in the pluripotent state, where TEs are broadly beneficial, or at least mechanistically useful, and a second state in human disease, where TEs are uniformly considered harmful.
Good Cop, Bad Cop: The Different Roles of SRPKs
Authors: Nikolakaki Eleni , Sigala Ioanna , Giannakouros Thomas
Published: June 2022

SR Protein Kinases (SRPKs), discovered approximately 30 years ago, are widely known as splice factor kinases due to their decisive involvement in the regulation of various steps of mRNA splicing. However, they were also shown to regulate diverse cellular activities by phosphorylation of serine residues residing in serine-arginine/arginine-serine dipeptide motifs. Over the last decade, SRPK1 has been reported as both tumor suppressor and promoter, depending on the cellular context and has been implicated in both chemotherapy sensitivity and resistance. Moreover, SRPK2 has been reported to exhibit contradictory functions in different cell contexts promoting either apoptosis or tumor growth. The aim of the current review is to broaden and deepen our understanding of the SRPK function focusing on the subcellular localization of the kinases. There is ample evidence that the balance between cytoplasmic and nuclear SRPK levels is tightly regulated and determines cell response to external signals. Specific cell states coupled to kinase levels, spatial specific interactions with substrates but also changes in the extent of phosphorylation that allow SRPKs to exhibit a rheostat-like control on their substrates, could decide the proliferative or antiproliferative role of SRPKs.
A Molecular Analysis of Memory B Cell and Antibody Responses Against Plasmodium falciparum Merozoite Surface Protein 1 in Children and Adults From Uganda
Authors: Gonzales S. Jake , Clarke Kathleen N. , Batugedara Gayani , Garza Rolando , Braddom Ashley E. , Reyes Raphael A. , Ssewanyana Isaac , Garrison Kendra C. , Ippolito Gregory C. , Greenhouse Bryan , Bol Sebastiaan , Bunnik Evelien M.
Published: June 2022

Memory B cells (MBCs) and plasma antibodies against Plasmodium falciparum (Pf) merozoite antigens are important components of the protective immune response against malaria. To gain understanding of how responses against Pf develop in these two arms of the humoral immune system, we evaluated MBC and antibody responses against the most abundant merozoite antigen, full-length Pf merozoite surface protein 1 (PfMSP1FL), in individuals from a region in Uganda with high Pf transmission. Our results showed that PfMSP1FL-specific B cells in adults with immunological protection against malaria were predominantly IgG+ classical MBCs, while children with incomplete protection mainly harbored IgM+ PfMSP1FL-specific classical MBCs. In contrast, anti-PfMSP1FL plasma IgM reactivity was minimal in both children and adults. Instead, both groups showed high plasma IgG reactivity against PfMSP1FL, with broadening of the response against non-3D7 strains in adults. The B cell receptors encoded by PfMSP1FL-specific IgG+ MBCs carried high levels of amino acid substitutions and recognized relatively conserved epitopes on the highly variable PfMSP1 protein. Proteomics analysis of PfMSP119-specific IgG in plasma of an adult revealed a limited repertoire of anti-MSP1 antibodies, most of which were IgG1 or IgG3. Similar to B cell receptors of PfMSP1FL-specific MBCs, anti-PfMSP119 IgGs had high levels of amino acid substitutions and their sequences were predominantly found in classical MBCs, not atypical MBCs. Collectively, these results showed evolution of the PfMSP1-specific humoral immune response with cumulative Pf exposure, with a shift from IgM+ to IgG+ B cell memory, diversification of B cells from germline, and stronger recognition of PfMSP1 variants by the plasma IgG repertoire.
Adrenomedullin Expression Is Associated With the Severity and Poor Prognosis of Interstitial Lung Disease in Dermatomyositis Patients
Authors: Ye Lifang , Zuo Yu , Chen Fang , Xu Yuetong , Zhang Puli , Yang Hongxia , Peng Qinglin , Wang Guochun , Shu Xiaoming
Published: June 2022

Objective

To evaluate adrenomedullin mRNA levels in the peripheral blood mononuclear cells (PBMCs) of patients with dermatomyositis (DM) as well as their correlation with the severity of interstitial lung disease (ILD).

Methods

A total of 41 DM patients and seven immune-mediated necrotizing myopathy (IMNM) patients were recruited, in addition to 21 healthy controls (HCs). The adrenomedullin mRNA levels in PBMCs were measured via quantitative reverse-transcription real-time polymerase chain reaction (qRT-PCR). The associations between adrenomedullin expression levels and major clinical, laboratory, pulmonary function parameters and the prognosis of patients with DM-related ILD (DM-ILD) were analyzed. Immunohistochemical analysis was performed on lung tissues of DM-ILD patients to determine adrenomedullin expression.

Results

Adrenomedullin mRNA levels in PBMCs were significantly higher in DM patients than in IMNM patients and HCs (p = 0.022 and p<0.001, respectively). Among DM patients, the levels were significantly higher in those with rapidly progressive ILD (RP-ILD) than in those with chronic ILD (p = 0.002) or without ILD (p < 0.001). The adrenomedullin mRNA levels in DM-ILD were positively correlated with serum ferritin (r =0.507, p =0.002), lactate dehydrogenase (LDH) (r =0.350, p =0.045), and lung visual analog scale (VAS) (r=0.392, p=0.021) and were negatively correlated with pulmonary function test parameters, including predicted forced vital capacity (FVC)% (r = −0.523, p = 0.025), forced expiratory volume in 1 s (FEV1)% (r = -0.539, p = 0.020), and diffusing capacity of carbon monoxide (DLco)% (r = -0.495, p = 0.036). Immunohistochemical analysis of adrenomedullin confirmed higher expression in the alveolar epithelial cells and macrophages of DM patients with RP-ILD. Among the DM patients with ILD, the six decedents exhibited higher adrenomedullin levels than the 28 survivors (p = 0.042). The cumulative survival rate was significantly lower (62.5% vs. 100%, P = 0.005) in patients with an adrenomedullin level > 0.053 than in those with a level <0.053.

Conclusions

Adrenomedullin levels are upregulated in DM patients with RP-ILD and are associated with ILD severity and poor prognosis. Adrenomedullin may be a potential prognostic biomarker in DM patients with ILD, although need further investigation.
Uncovering the Mast Cell Response to Mycobacterium tuberculosis
Authors: Torres-Atencio Ivonne , Campble Ariadne , Goodridge Amador , Martin Margarita
Published: June 2022

The immunologic mechanisms that contribute to the response to Mycobacterium tuberculosis infection still represent a challenge in the clinical management and scientific understanding of tuberculosis disease. In this scenario, the role of the different cells involved in the host response, either in terms of innate or adaptive immunity, remains key for defeating this disease. Among this coordinated cell response, mast cells remain key for defeating tuberculosis infection and disease. Together with its effector’s molecules, membrane receptors as well as its anatomical locations, mast cells play a crucial role in the establishment and perpetuation of the inflammatory response that leads to the generation of the granuloma during tuberculosis. This review highlights the current evidences that support the notion of mast cells as key link to reinforce the advancements in tuberculosis diagnosis, disease progression, and novel therapeutic strategies. Special focus on mast cells capacity for the modulation of the inflammatory response among patients suffering multidrug resistant tuberculosis or in co-infections such as current COVID-19 pandemic.
mRNA Vaccines: The Dawn of a New Era of Cancer Immunotherapy
Authors: Deng Zhuoya , Tian Yuying , Song Jianxun , An Guangwen , Yang Penghui
Published: June 2022

mRNA therapy is a novel anticancer strategy based on in vitro transcription (IVT), which has potential for the treatment of malignant tumors. The outbreak of the COVID-19 pandemic in the early 21st century has promoted the application of mRNA technologies in SARS-CoV-2 vaccines, and there has been a great deal of interest in the research and development of mRNA cancer vaccines. There has been progress in a number of key technologies, including mRNA production strategies, delivery systems, antitumor immune strategies, etc. These technologies have accelerated the progress and clinical applications of mRNA therapy, overcoming problems encountered in the past, such as instability, inefficient delivery, and weak immunogenicity of mRNA vaccines. This review provides a detailed overview of the production, delivery systems, immunological mechanisms, and antitumor immune response strategies for mRNA cancer vaccines. We list some mRNA cancer vaccines that are candidates for cancer treatment and discuss clinical trials in the field of tumor immunotherapy. In addition, we discuss the immunological mechanism of action by which mRNA vaccines destroy tumors as well as challenges and prospects for the future.
Comprehensive Analysis of Senescence Characteristics Defines a Novel Prognostic Signature to Guide Personalized Treatment for Clear Cell Renal Cell Carcinoma
Authors: Zhou Peng , Liu Zheng , Hu Henglong , Lu Yuchao , Xiao Jun , Wang Yanan , Xun Yang , Xia Qidong , Liu Chenqian , Hu Jia , Wang Shaogang
Published: June 2022

Accumulating evidence has suggested the impact of senescence on tumor progression, but no report has yet described how senescence shapes the tumor microenvironment of clear cell renal cell carcinoma (ccRCC). The objective of this study was to delineate the senescence features of ccRCC and its role in shaping the tumor microenvironment through a comprehensive analysis of multiple datasets, including 2,072 ccRCC samples. Unsupervised consensus clustering identified three senescence subtypes, and we found that the senescence-activated subtype survived the worst, even in the condition of targeted therapy and immunotherapy. The activated senescence program was correlated to increased genomic instability, unbalanced PBMR1/BAP1 mutations, elevated immune cell infiltration, and enhanced immune inhibitory factors (cancer-associated fibroblasts, immune suppression, immune exclusion, and immune exhaustion signaling). A senescence score based on nine senescence-related genes (i.e., P3H1, PROX1, HJURP, HK3, CDKN1A, AR, VENTX, MAGOHB, and MAP2K6) was identified by adaptive lasso regression and showed robust prognostic predictive power in development and external validation cohorts. Notably, we found that the senescence score was correlated to immune suppression, and the low-score subgroup was predicted to respond to anti–PD-1 therapy, whereas the high-score subgroup was predicted to respond to Sunitinib/Everolimus treatment. Collectively, senescence acted as an active cancer hallmark of ccRCC, shaped the immune microenvironment, and profoundly affected tumor prognosis and drug treatment response.
One Stone, Two Birds: N6-Methyladenosine RNA Modification in Leukemia Stem Cells and the Tumor Immune Microenvironment in Acute Myeloid Leukemia
Authors: Ouyang Xianfeng , Gong Yuping
Published: June 2022

Acute myeloid leukemia is the most common acute leukemia in adults, with accumulation of abundant blasts and impairment of hematogenic function. Despite great advances in diagnosis and therapy, the overall survival of patients with acute myeloid leukemia remains poor. Leukemia stem cells are the root cause of relapse and chemoresistance in acute myeloid leukemia. The tumor immune microenvironment is another trigger to induce recurrence and drug resistance. Understanding the underlying factors influencing leukemia stem cells and the tumor immune microenvironment is an urgent and unmet need. Intriguingly, N6-methyladenosine, the most widespread internal mRNA modification in eukaryotes, is found to regulate both leukemia stem cells and the tumor immune microenvironment. Methyltransferases and demethylases cooperatively make N6-methyladenosine modification reversible and dynamic. Increasing evidence demonstrates that N6-methyladenosine modification extensively participates in tumorigenesis and progression in various cancers, including acute myeloid leukemia. In this review, we summarize the current progress in studies on the functions of N6-methyladenosine modification in acute myeloid leukemia, especially in leukemia stem cells and the tumor immune microenvironment. We generalize the landscape of N6-methyladenosine modification in self-renewal of leukemia stem cells and immune microenvironment regulation, as well as in the initiation, growth, proliferation, differentiation, and apoptosis of leukemia cells. In addition, we further explore the clinical application of N6-methyladenosine modification in diagnosis, prognostic stratification, and effect evaluation. Considering the roles of N6-methyladenosine modification in leukemia stem cells and the tumor immune microenvironment, we propose targeting N6-methyladenosine regulators as one stone to kill two birds for acute myeloid leukemia treatment.
C1QTNF3 is Upregulated During Subcutaneous Adipose Tissue Remodeling and Stimulates Macrophage Chemotaxis and M1-Like Polarization
Authors: Micallef Peter , Vujičić Milica , Wu Yanling , Peris Eduard , Wang Ying , Chanclón Belén , Ståhlberg Anders , Cardell Susanna L. , Wernstedt Asterholm Ingrid
Published: June 2022

The adipose tissue undergoes substantial tissue remodeling during weight gain-induced expansion as well as in response to the mechanical and immunological stresses from a growing tumor. We identified the C1q/TNF-related protein family member C1qtnf3 as one of the most upregulated genes that encode secreted proteins in tumor-associated inguinal adipose tissue - especially in high fat diet-induced obese mice that displayed 3-fold larger tumors than their lean controls. Interestingly, inguinal adipose tissue C1qtnf3 was co-regulated with several macrophage markers and chemokines and was primarily expressed in fibroblasts while only low levels were detected in adipocytes and macrophages. Administration of C1QTNF3 neutralizing antibodies inhibited macrophage accumulation in tumor-associated inguinal adipose tissue while tumor growth was unaffected. In line with this finding, C1QTNF3 exerted chemotactic actions on both M1- and M2-polarized macrophages in vitro. Moreover, C1QTNF3 treatment of M2-type macrophages stimulated the ERK and Akt pathway associated with increased M1-like polarization as judged by increased expression of M1-macrophage markers, increased production of nitric oxide, reduced oxygen consumption and increased glycolysis. Based on these results, we propose that macrophages are recruited to adipose tissue sites with increased C1QTNF3 production. However, the impact of the immunomodulatory effects of C1QTNF3 in adipose tissue remodeling warrants future investigations.
Reducing the Fuel Use Intensity of Fisheries: Through Efficient Fishing Techniques and Recovered Fish Stocks
Authors: Bastardie Francois , Hornborg Sara , Ziegler Friederike , Gislason Henrik , Eigaard Ole Ritzau
Published: June 2022

Understanding the drivers of greenhouse gas emissions in food production systems is becoming urgent. For wild capture fisheries, fuel use during the fishing phase generally dominates emissions and is highly variable between fisheries. Fuel use is also essential for the economy of the fisheries, but fuel-intensive fisheries can still be profitable due to fuel subsidies, in particular, if the target species is of high value. Developing an innovative bottom-up approach based on detailed catch and spatial fishing effort data, in the absence of direct fuel data, we analysed the fuel use intensity (fuel use per kg landed) and economic efficiency (landing value per litre fuel used) of Danish capture fisheries for the period 2005-2019. An overall decline in fishing effort did not significantly affect the overall fuel use intensity and efficiency, which was stable for most of the fleet segments and marine species. Robust differences in fuel use intensity among individual fisheries, reflected differential spatial accessibility and vulnerability of target species to fishing. In addition, different fishing techniques targeting the same set of species showed differences in fuel use per unit landed. Danish seining and gillnets had a lower fuel use intensity and higher economic efficiency than demersal trawling; and purse seining than pelagic trawling. The variability between stocks and fleets also indicates that there is generally potential for improvement in overall efficiency from improved stock status. Short-term management actions to promote the best available fuel-efficient fishing techniques combined with additional long-term actions to secure the recovery of stocks have the potential to reduce fishery greenhouse gas emissions. Sustainable fisheries and normative environmental management are crucial to developing incentives towards reducing fuel use whenever the fishing sector industry and science work jointly at implementing solutions, as incentives for the industry to reduce fuel use are limited as long as the fishing activity is profitable.
Calcification, Dissolution and Test Properties of Modern Planktonic Foraminifera From the Central Atlantic Ocean
Authors: Zarkogiannis Stergios D. , Iwasaki Shinya , Rae James William Buchanan , Schmidt Matthew W. , Mortyn P. Graham , Kontakiotis George , Hertzberg Jennifer E. , Rickaby Rosalind E. M.
Published: June 2022

The mass of well-preserved calcite in planktonic foraminifera shells provides an indication of the calcification potential of the surface ocean. Here we report the shell weight of 8 different abundant planktonic foraminifera species from a set of core-top sediments along the Mid-Atlantic Ridge. The analyses showed that near the equator, foraminifera shells of equivalent size weigh on average 1/3 less than those from the middle latitudes. The carbonate preservation state of the samples was assessed by high resolution X-ray microcomputed tomographic analyses of Globigerinoides ruber and Globorotalia truncatulinoides specimens. The specimen preservation was deemed good and does not overall explain the observed shell mass variations. However, G. ruber shell weights might be to some extent compromised by residual fine debris internal contamination. Deep dwelling species possess heavier tests than their surface-dwelling counterparts, suggesting that the weight of the foraminifera shells changes as a function of the depth habitat. Ambient seawater carbonate chemistry of declining carbonate ion concentration with depth cannot account for this interspecies difference. The results suggest a depth regulating function for plankton calcification, which is not dictated by water column acidity.
Bacterial Metabolic Response to Change in Phytoplankton Communities and Resultant Effects on Carbon Cycles in the Amundsen Sea Polynya, Antarctica
Authors: Kim Bomina , Kim Sung-Han , Min Jun-Oh , Lee Youngju , Jung Jinyoung , Kim Tae-Wan , Lee Jae Seong , Yang Eun Jin , Park Jisoo , Lee SangHoon , Hyun Jung-Ho
Published: June 2022

We investigated changes in heterotrophic bacterial metabolic activities and associated carbon cycles in response to a change in dominant phytoplankton communities during two contrasting environmental conditions in austral summer in the Amundsen Sea polynya (ASP), Antarctica: the closed polynya condition in 2014 (ANA04) and the open polynya condition in 2016 (ANA06). In ANA04, Phaeocystis antarctica predominated phytoplankton biomass, comprising 78% of total phytoplankton carbon biomass, whereas diatoms and Dictyocha speculum accounted for 45% and 48% of total phytoplankton carbon biomass, respectively, in ANA06. Bacterial production (BP) showed a significant positive correlation with only chlorophyll-a (Chl-a, rho = 0.66, p < 0.001) in P. antarctica-dominated ANA04, whereas there were significant positive relationships of BP with various organic carbon pools, such as chromophoric dissolved organic matter (CDOM, rho = 0.84, p < 0.001), Chl-a (rho = 0.59, p < 0.001), and dissolved organic carbon (DOC, rho = 0.51, p = 0.001), in ANA06 when diatoms and D. speculum co-dominated. These results indicate that BP depended more on DOC directly released from P. antarctica in ANA04, but was supported by DOC derived from various food web processes in the diatom-dominated system in ANA06. The BP to primary production (BP : PP) ratio was three-fold higher in P. antarctica-dominated ANA04 (BP: PP = 0.09), than in diatom- and D. speculum-co-dominated ANA06 (BP : PP = 0.03). These results suggested that the microbial loop is more significant in Phaeocystis-dominated conditions than in diatom-dominated conditions. In addition, the decreases in BP : PP ratio and bacterial respiration with increasing diatom proportion in the surface mixed layer indicated that the change from P. antarctica to diatom predominance enhanced biological carbon pump function by increasing particulate organic carbon export efficiency. Consequently, our results suggest that bacterial metabolic response to shifts in phytoplankton communities could ultimately affect larger-scale ecological and biogeochemical processes in the water column of the ASP.
Virtual Learning Environment of the Brazilian Health System (AVASUS): Efficiency of Results, Impacts, and Contributions
Authors: Valentim Ricardo A. M. , de Oliveira Carlos A. P. , Oliveira Eloiza S. G. , Ribeiro Eduardo L. , da Costa Soneide M. , Morais Ione R. D. , Fernandes Felipe R. dos S. , Caitano Alexandre R. , Gusmão Cristine M. G. , Cunha-Oliveira Aliete , Rêgo Maria C. F. D. , Coutinho Karilany D. , Barros Daniele M. S. , Ceccim Ricardo B.
Published: June 2022

The Virtual Learning Environment of the Brazilian Health System (AVASUS) is a free and open distance education platform of the Ministry of Health (MS). AVASUS is a scalable virtual learning environment that has surpassed 800,000 users, 2 million enrollments, and 310 courses in its catalog. The objective of this paper was to assess the impacts of the educational offerings on health services and AVASUS course participants' professional practice. This study analyzed data from AVASUS, the Brazilian National Registry of Health Care Facilities (CNES), the Brazilian Occupational Classification (CBO), and a questionnaire applied to 720-course participants from five regions of Brazil. After acquiring and extracting data, computational methods were used for the evaluation process. Only the responses of 462 participants were considered for data analysis, as they had a formal link to CNES. The results showed that respondents recommended 76.2% of AVASUS courses to peers. Accordingly, the quality of educational offerings motivated 81.3% of such recommendations. In addition, 75.6% of course participants who answered the questionnaire also indicated that AVASUS course contents contribute to enhancing existing health services in the health facilities where they work. Finally, 24.6% of all responses mentioned that courses available in AVASUS were essential in offering new health services in such facilities.
Non-cancer Causes of Death Following Initial Synchronous Bone Metastasis in Cancer Patients
Authors: Xu Yao , Abdelazeem Basel , Abbas Kirellos Said , Lin Yile , Wu Haixiao , Zhou Fei , Peltzer Karl , Chekhonin Vladimir P. , Li Shu , Li Huiyang , Ma Wenjuan , Zhang Chao
Published: June 2022

Purpose

To investigate the non-cancer causes of death (COD) in cancer patients with synchronous bone metastasis (BM) that is based on the Surveillance, Epidemiology, and End Results (SEER) database.

Methods

The retrospective cohort study included malignant cancer patients with synchronous BM diagnosed from 2010 to 2018 in the SEER database. The frequencies and proportion of non-cancer COD were calculated and analyzed in different genders, ages, and races subgroups.

Results

A total of 97,997 patients were deceased and included into the current study and 6,782 patients were died of non-cancer causes with a male predominance (N = 4,515, 66.6%). Around half of deaths (N = 3,254, 48.0%) occurred within 6 months after diagnosis while 721 patients were deceased after 3 years. Lung and bronchus cancer, prostate cancer, breast cancer, kidney and renal pelvis cancer, and liver cancer were proved to be the top five cancer types resulting in non-cancer caused death. Cardiovascular and cerebrovascular diseases were the leading non-cancer cause of death (N = 2,618), followed by COPD and associated conditions (N = 553) and septicemia, infectious and parasitic diseases (N = 544). Sub-analyses stratified by gender, age and race were performed and the similar results with slightly difference were observed.

Conclusions

Cardiovascular and cerebrovascular diseases were the main non-cancer cause of death in cancer patients with synchronous BM. Other non-cancer causes included COPD, septicemia, infectious and parasitic diseases, and so on. These findings should be considered by physicians. Physicians can counsel cancer patients with BM regarding survivorship with death causes screening and focus on prevention of non-cancer deaths.
Indirect Application of Intense Pulsed Light Induces Therapeutic Effects on Experimental Murine Meibomian Gland Dysfunction
Authors: Xie Luoying , Song Wenjing , Dong Wenhui , Li Yingsi , Chen Shudi , Sun Xiaona , Huang Meiting , Cheng Yu , Gao Yuan , Yang Songlin , Yan Xiaoming
Published: June 2022

Purpose

To investigate the indirect effects of intense pulsed light (IPL) on morphological and pathological changes of the meibomian glands (MGs) in apolipoprotein E knockout (ApoE–/–) mice and explore the underlying mechanisms.

Methods

ApoE–/– mice were treated with or without IPL three times below the lower eyelids and MGs were not directly exposed to irradiation. The eyelids and ocular surface were observed under a stereoscope. The morphology of MGs was examined by photographing and hematoxylin and eosin staining. Lipid droplets in MGs were examined by Oil Red O staining. The ultrastructure of meibocytes and mitochondria was observed under transmission electron microscopy. The relative gene and protein expression in MGs of upper eyelids was determined by immunostaining, Western blot, and qRT–PCR.

Results

Three IPL treatments decreased the toothpaste-like plugging of orifices and thickening and irregularity of the upper and lower eyelid margins in ApoE–/– mice. The morphology of some MGs improved after IPL treatments, accompanied by increased proliferation of acinar basal cells and decreased ductal keratinization. Furthermore, the accumulation of hyperchromatic lipid droplets in the acini increased, and the lipid droplets distributed in the cells around the acini were round and small. Compared with untreated ApoE–/– mice, oxidative stress and apoptosis were downregulated by IPL treatment, accompanied by the improvements in mitochondrial structure. Further research showed that IPL treatments reduced the levels of tumor necrosis factor-alpha (TNF-α), interleukin (IL)-17A, IL-6 in MGs and inactivated nuclear factor kappa B (NF-κ B).

Conclusion

Collectively, the results demonstrate that indirect effects of IPL can improve the structure and function of MGs and mitigate the progression of MGD, which may be related to the indirect effects of photobiomodulation.
Chest L-Transformer: Local Features With Position Attention for Weakly Supervised Chest Radiograph Segmentation and Classification
Authors: Gu Hong , Wang Hongyu , Qin Pan , Wang Jia
Published: June 2022

We consider the problem of weakly supervised segmentation on chest radiographs. The chest radiograph is the most common means of screening and diagnosing thoracic diseases. Weakly supervised deep learning models have gained increasing popularity in medical image segmentation. However, these models are not suitable for the critical characteristics presented in chest radiographs: the global symmetry of chest radiographs and dependencies between lesions and their positions. These models extract global features from the whole image to make the image-level decision. The global symmetry can lead these models to misclassification of symmetrical positions of the lesions. Thoracic diseases often have special disease prone areas in chest radiographs. There is a relationship between the lesions and their positions. In this study, we propose a weakly supervised model, called Chest L-Transformer, to take these characteristics into account. Chest L-Transformer classifies an image based on local features to avoid the misclassification caused by the global symmetry. Moreover, associated with Transformer attention mechanism, Chest L-Transformer models the dependencies between the lesions and their positions and pays more attention to the disease prone areas. Chest L-Transformer is only trained with image-level annotations for lesion segmentation. Thus, Log-Sum-Exp voting and its variant are proposed to unify the pixel-level prediction with the image-level prediction. We demonstrate a significant segmentation performance improvement over the current state-of-the-art while achieving competitive classification performance.
Infection Strategies and Pathogenicity of Biotrophic Plant Fungal Pathogens
Authors: Mapuranga Johannes , Zhang Na , Zhang Lirong , Chang Jiaying , Yang Wenxiang
Published: June 2022

Biotrophic plant pathogenic fungi are widely distributed and are among the most damaging pathogenic organisms of agriculturally important crops responsible for significant losses in quality and yield. However, the pathogenesis of obligate parasitic pathogenic microorganisms is still under investigation because they cannot reproduce and complete their life cycle on an artificial medium. The successful lifestyle of biotrophic fungal pathogens depends on their ability to secrete effector proteins to manipulate or evade plant defense response. By integrating genomics, transcriptomics, and effectoromics, insights into how the adaptation of biotrophic plant fungal pathogens adapt to their host populations can be gained. Efficient tools to decipher the precise molecular mechanisms of rust–plant interactions, and standardized routines in genomics and functional pipelines have been established and will pave the way for comparative studies. Deciphering fungal pathogenesis not only allows us to better understand how fungal pathogens infect host plants but also provides valuable information for plant diseases control, including new strategies to prevent, delay, or inhibit fungal development. Our review provides a comprehensive overview of the efforts that have been made to decipher the effector proteins of biotrophic fungal pathogens and demonstrates how rapidly research in the field of obligate biotrophy has progressed.
Antimicrobial Peptide Expression at the Ocular Surface and Their Therapeutic Use in the Treatment of Microbial Keratitis
Authors: Shannon Allison H. , Adelman Sara A. , Hisey Erin A. , Potnis Sanskruti S. , Rozo Vanessa , Yung Madeline W. , Li Jennifer Y. , Murphy Christopher J. , Thomasy Sara M. , Leonard Brian C.
Published: June 2022

Microbial keratitis is a common cause of ocular pain and visual impairment worldwide. The ocular surface has a relatively paucicellular microbial community, mostly found in the conjunctiva, while the cornea would be considered relatively sterile. However, in patients with microbial keratitis, the cornea can be infected with multiple pathogens includingStaphylococcus aureus,Pseudomonas aeruginosa, andFusariumsp. Treatment with topical antimicrobials serves as the standard of care for microbial keratitis, however, due to high rates of pathogen resistance to current antimicrobial medications, alternative therapeutic strategies must be developed. Multiple studies have characterized the expression and activity of antimicrobial peptides (AMPs), endogenous peptides with key antimicrobial and wound healing properties, on the ocular surface. Recent studies and clinical trials provide promise for the use of AMPs as therapeutic agents. This article reviews the repertoire of AMPs expressed at the ocular surface, how expression of these AMPs can be modulated, and the potential for harnessing the AMPs as potential therapeutics for patients with microbial keratitis.
Gene Regulatory Network Inference and Gene Module Regulating Virulence in Fusarium oxysporum
Authors: Cano Regnier , Lenz Alexandre Rafael , Galan-Vasquez Edgardo , Ramirez-Prado Jorge H. , Perez-Rueda Ernesto
Published: June 2022

In this work, we inferred the gene regulatory network (GRN) of the fungus Fusarium oxysporum by using the regulatory networks of Aspergillus nidulans FGSC A4, Neurospora crassa OR74A, Saccharomyces cerevisiae S288c, and Fusarium graminearum PH-1 as templates for sequence comparisons. Topological properties to infer the role of transcription factors (TFs) and to identify functional modules were calculated in the GRN. From these analyzes, five TFs were identified as hubs, including FOXG_04688 and FOXG_05432, which regulate 2,404 and 1,864 target genes, respectively. In addition, 16 communities were identified in the GRN, where the largest contains 1,923 genes and the smallest contains 227 genes. Finally, the genes associated with virulence were extracted from the GRN and exhaustively analyzed, and we identified a giant module with ten TFs and 273 target genes, where the most highly connected node corresponds to the transcription factor FOXG_05265, homologous to the putative bZip transcription factor CPTF1 of Claviceps purpurea, which is involved in ergotism disease that affects cereal crops and grasses. The results described in this work can be used for the study of gene regulation in this organism and open the possibility to explore putative genes associated with virulence against their host.
Shared Microbial Taxa Respond Predictably to Cyclic Time-Varying Oxygen Limitation in Two Disparate Soils
Authors: Hall Steven J. , Huang Wenjuan , Napieralski Stephanie A. , Roden Eric
Published: June 2022

Periodic oxygen (O2) limitation in humid terrestrial soils likely influences microbial composition, but whether communities share similar responses in disparate environments remains unclear. To test if specific microbial taxa share consistent responses to anoxia in radically different soils, we incubated a rainforest Oxisol and cropland Mollisol under cyclic, time-varying anoxic/oxic cycles in the laboratory. Both soils are known to experience anoxic periods of days to weeks under field conditions; our incubation treatments consisted of anoxic periods of 0, 2, 4, 8, or 12 d followed by 4 d of oxic conditions, repeated for a total of 384 d. Taxa measured by 16S rRNA gene sequences after 48 d and 384 d of experimental treatments varied strongly with increasing anoxic period duration, and responses to anoxia often differed between soils at multiple taxonomic levels. Only 19% of the 30,356 operational taxonomic units (OTUs) occurred in both soils, and most OTUs did not respond consistently to O2treatments. However, the OTUs present in both soils were disproportionally abundant, comprising 50% of sequences, and they often had a similar response to anoxic period duration in both soils (p < 0.0001). Overall, 67 OTUs, 36 families, 15 orders, 10 classes, and two phyla had significant and directionally consistent (positive or negative) responses to anoxic period duration in both soils. Prominent OTUs and taxonomic groups increasing with anoxic period duration in both soils included actinomycetes (Micromonosporaceae), numerousRuminococcaceae, possible metal reducers (Anaeromyxobacter) or oxidizers (CandidatusKoribacter), methanogens (Methanomicrobia), and methanotrophs (Methylocystaceae). OTUs decreasing with anoxic duration in both soils included nitrifiers (Nitrospira) and ubiquitous unidentifiedBradyrhizobiaceaeandMicromonosporaceae. Even within the same genus, different OTUs occasionally showed strong positive or negative responses to anoxic duration (e.g.,Dactylosporangiumin theActinobacteria), highlighting a potential for adaptation or niche partitioning in variable-O2environments. Overall, brief anoxic periods impacted the abundance of certain microbial taxa in predictable ways, suggesting that microbial community data may partially reflect and integrate spatiotemporal differences in O2availability within and among soils.