bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Pore Size and Crosslinking Methods on the Immobilization of Myoglobin in SBA-15
Authors: Miao Hengmin , Li Maosheng , Sun Xiaochun , Xia Jikun , Li Yanqing , Li Jiao , Wang Fang , Xu Jiakun
Published: January 2022

A series of stable mesoporous silica sieves (SBA-15) with different pore sizes (9.8, 7.2, and 5.5 nm) were synthesized using a hydrothermal method. The resulting mesoporous material was then utilized for protein immobilization using myoglobin (Mb) as the target protein. The effects of pore size and adsorption methods on the immobilization efficiency of Mb in a mesoporous material were studied. The SBA-15 with a pore size of 7.2 nm showed the best loading capacity, reaching 413.8 mg/g. The SBA-15 with a pore size of 9.8 nm showed the highest retained catalytic ability (92.36%). The immobilized enzyme was more stable than the free enzyme. After seven consecutive assay cycles, Mb adsorbed by SBA-15 (Mb/SBA-15) and Mb adsorbed by SBA-15 and crosslinked with glutaraldehyde (Mb/G/SBA-15) retained 36.41% and 62.37% of their initial activity, respectively.
Cell-Free Fat Extract Prevents Tail Suspension–Induced Bone Loss by Inhibiting Osteocyte Apoptosis
Authors: Xu Mingming , Du Jingke , Cui Junqi , Zhang Shuangyan , Zhang Shuhong , Deng Mingwu , Zhang Wenjie , Li Hanjun , Yu Zhifeng
Published: January 2022

Introduction: As the space field has developed and our population ages, people engaged in space travel and those on prolonged bed rest are at increasing risk for bone loss and fractures. Disuse osteoporosis occurs frequently in these instances, for which the currently available anti-osteoporosis agents are far from satisfactory and have undesirable side effects. CEFFE is a cell-free fraction isolated from nanofat that is enriched with a variety of growth factors, and we aim to investigate its potential therapeutic effects on disuse osteoporosis.

Methods: A tail suspension–induced osteoporosis model was applied in this study. Three weeks after tail suspension, CEFFE was intraperitoneally injected, and PBS was used as a control. The trabecular and cortical bone microstructures of the tibia in each group were assessed by μCT after 4 weeks of administration. Osteocyte lacunar-canalicularity was observed by HE and silver staining. In vitro, MLO-Y4 cell apoptosis was induced by reactive oxygen species (ROSUP). TUNEL staining and flow cytometry were used to detect apoptosis. CCK-8 was used to detect cell proliferation, and Western blotting was used to detect MAPK signaling pathway changes.

Results: CEFFE increased the bone volume (BV/TV) and trabecular number (Tb.N) of the trabecular bone and increased the thickness of the cortical bone. HE and silver staining results showed that CEFFE reduced the number of empty lacunae and improved the lacuna-canalicular structure. CEFFE promoted osteocyte proliferative capacity in a dose-dependent manner. CEFFE protected MLO-Y4 from apoptosis by activating the serine/threonine-selective protein kinase (ERK) signaling pathways.

Conclusion: CEFFE attenuated immobilization-induced bone loss by decreasing osteocyte apoptosis. CEFFE increased the survival of osteocytes and inhibited osteocyte apoptosis by activating the ERK signaling pathway in vitro.
Investigating the Influence of the Building Material on the Indoor Air Quality in Apartment in Dubai
Authors: Arar Mohammad , Jung Chuloh , Qassimi Nahla Al
Published: January 2022

The residents of Dubai spend more than 90% of their time indoors and this lifestyle makes them easily exposed to Sick Building Syndrome (SBS). Even though Dubai Municipality strictly apply the IAQ (Indoor Air Quality) stipulation, indiscreet use of unproven finishing materials has been increased to deteriorate the health of residents in Dubai. The objective of this paper is to investigate the degree of influence of building material on indoor air pollutants concentration by measurement and prediction. As a methodology, indoor pollutants concentration was measured and investigated, variables were extracted through emission intensity experiments, and the indoor concentration was predicted by applying the double exponential decay model. The result had shown that electronic products, furniture, and textile products become new sources of indoor air pollution. The difference in emission patterns of wallpaper and flooring is confirmed via the emission rate test. It is statistically proven that Formaldehyde (CH2O) and VOCs showed a difference in the cumulative emission amount within 100 h but after that, it was confirmed that the difference in emission amount between materials became very small. In case of CH2O, the cumulative emission of the flooring material is greater than that of the wallpaper. This study will serve as a basic data to explore the cause of indoor air pollutants in daily life to reduce SBS symptoms in Dubai.
Circulating NAD+ Metabolism-Derived Genes Unveils Prognostic and Peripheral Immune Infiltration in Amyotrophic Lateral Sclerosis
Authors: Li Cheng , Zhu Yu , Chen Wenzhi , Li Menghua , Yang Mi , Shen Ziyang , Zhou Yiyi , Wang Lulu , Wang Huan , Li Shu , Ma Jiacheng , Gong Mengni , Xu Renshi
Published: January 2022

Background: Nicotinamide adenine dinucleotide (NAD+) metabolism has drawn more attention on neurodegeneration research; however, the role in Amyotrophic Lateral Sclerosis (ALS) remains to be fully elucidated. Here, the purpose of this study was to investigate whether the circulating NAD+ metabolic-related gene signature could be identified as a reliable biomarker for ALS survival.

Methods: A retrospective analysis of whole blood transcriptional profiles and clinical characteristics of 454 ALS patients was conducted in this study. A series of bioinformatics and machine-learning methods were combined to establish NAD+ metabolic-derived risk score (NPRS) to predict overall survival for ALS patients. The associations of clinical characteristic with NPRS were analyzed and compared. Receiver operating characteristic (ROC) and the calibration curve were utilized to assess the efficacy of prognostic model. Besides, the peripheral immune cell infiltration was assessed in different risk subgroups by applying the CIBERSORT algorithm.

Results: Abnormal activation of the NAD+ metabolic pathway occurs in the peripheral blood of ALS patients. Four subtypes with distinct prognosis were constructed based on NAD+ metabolism-related gene expression patterns by using the consensus clustering method. A comparison of the expression profiles of genes related to NAD+ metabolism in different subtypes revealed that the synthase of NAD+ was closely associated with prognosis. Seventeen genes were selected to construct prognostic risk signature by LASSO regression. The NPRS exhibited stronger prognostic capacity compared to traditional clinic-pathological parameters. High NPRS was characterized by NAD+ metabolic exuberant with an unfavorable prognosis. The infiltration levels of several immune cells, such as CD4 naive T cells, CD8 T cells, neutrophils and macrophages, are significantly associated with NPRS. Further clinicopathological analysis revealed that NPRS is more appropriate for predicting the prognostic risk of patients with spinal onset. A prognostic nomogram exhibited more accurate survival prediction compared with other clinicopathological features.

Conclusions: In conclusion, it was first proposed that the circulating NAD+ metabolism-derived gene signature is a promising biomarker to predict clinical outcomes, and ultimately facilitating the precise management of patients with ALS.
Analysis of miRNAs Involved in Mouse Heart Injury Upon Coxsackievirus A2 Infection
Authors: Wu Zhaoke , Zhu Shenshen , Qian Juanfeng , Hu Yanmin , Ji Wangquan , Li Dong , Zhu Peiyu , Liang Ruonan , Jin Yuefei
Published: January 2022

Coxsackievirus A2 (CVA2) has recently been constantly detected, and is associated with viral myocarditis in children. Our previous study demonstrated that CVA2 led to heart damage in a neonatal murine model. However, the molecular mechanism of heart injury caused by CVA2 remains largely unknown. Emerging evidence suggests the significant functions of miRNAs in Coxsackievirus infection. To investigate potential miRNAs involved in heart injury caused by CVA2, our study, for the first time, conducted a RNA-seq in vivo employing infected mice hearts. In total, 87, 101 and 76 differentially expressed miRNAs were identified at 3 days post infection (dpi), 7 dpi and 7 dpi vs 3 dpi. Importantly, above 3 comparison strategies shared 34 differentially expressed miRNAs. These results were confirmed by quantitative PCR (qPCR). Next, we did GO, KEGG, and miRNA-mRNA integrated analysis of differential miRNAs. The dual-luciferase reporter assay confirmed the miRNA-mRNA pairs. To further confirm the above enriched pathways and processes, we did Western blotting and immunofluorescence staining. Our results suggest that inflammatory responses, T cell activation, apoptosis, autophagy, antiviral immunity, NK cell infiltration, and the disruption of tight junctions are involved in the pathogenesis of heart injury caused by CVA2. The dysregulated miRNAs and pathways recognized in the current study can improve the understanding of the intricate interactions between CVA2 and the heart injury, opening a novel avenue for the future study of CVA2 pathogenesis.
Diverse Mechanisms of Protective Anti-Pneumococcal Antibodies
Authors: Gingerich Aaron D. , Mousa Jarrod J.
Published: January 2022

The gram-positive bacteriumStreptococcus pneumoniaeis a leading cause of pneumonia, otitis media, septicemia, and meningitis in children and adults. Current prevention and treatment efforts are primarily pneumococcal conjugate vaccines that target the bacterial capsule polysaccharide, as well as antibiotics for pathogen clearance. While these methods have been enormously effective at disease prevention and treatment, there has been an emergence of non-vaccine serotypes, termed serotype replacement, and increasing antibiotic resistance among these serotypes. To combatS. pneumoniae, the immune system must deploy an arsenal of antimicrobial functions. However,S. pneumoniaehas evolved a repertoire of evasion techniques and is able to modulate the host immune system. Antibodies are a key component of pneumococcal immunity, targeting both the capsule polysaccharide and protein antigens on the surface of the bacterium. These antibodies have been shown to play a variety of roles including increasing opsonophagocytic activity, enzymatic and toxin neutralization, reducing bacterial adherence, and altering bacterial gene expression. In this review, we describe targets of anti-pneumococcal antibodies and describe antibody functions and effectiveness againstS. pneumoniae.
Acute Lesion Imaging in Predicting Chronic Tissue Injury in the Ventricles
Authors: El Hajjar Abdel Hadi , Huang Chao , Zhang Yichi , Mekhael Mario , Noujaim Charbel , Dagher Lilas , Nedunchezhian Saihariharan , Pottle Christopher , Kholmovski Eugene , Ayoub Tarek , Dhorepatil Aneesh , Barakat Michel , Yamaguchi Takano , Chelu Mihail , Marrouche Nassir
Published: January 2022

Background

Chronic lesion formation after cardiac tissue ablation is an important indicator for procedural outcome. Moreover, there is a lack of knowledge regarding the features that predict chronic lesion formation.

Objective

The aim of this study is to determine whether acute lesion visualization using late gadolinium enhanced magnetic resonance imaging (LGE-MRI) can reliably predict chronic lesion size.

Methods

Focal lesions were created in left and right ventricles of canine models using either radiofrequency (RF) ablation or cryofocal ablation. Multiple ablation parameters were used. The first LGE-MRI was acquired within 1–5 h post-ablation and the second LGE-MRI was obtained 47–82 days later. Corview software was used to perform lesion segmentations and size calculations.

Results:

Fifty-Five lesions were created in different locations in the ventricles. Chronic volume size decreased by a mean of 62.5 % (95% CI 58.83–67.97, p < 0.0005). Similar regression of lesion volume was observed regardless of ablation location (p = 0.32), ablation technique (p = 0.94), duration (p = 0.37), power (p = 0.55) and whether lesions were connected or not (p = 0.35). There was no significant difference in lesion volume reduction assessed at 47–54 days and 72–82 days after ablation (p = 0.31). Chronic lesion volume was equal to 0.32 of the acute lesion volumes (R2 = 0.75).

Conclusion

Chronic tissue injury related to catheter ablation can be reliably modeled as a linear function of the acute lesion volume as assessed by LGE-MRI, regardless of the ablation parameters.
Case Report: Management of a 10-Year-Old Patient Who Presented With Infective Endocarditis and Stanford Type A Aortic Dissection
Authors: Liang Yanxiao , Wan Mingzhi , Wang Lijie , Yang Ni , Li Dongyu
Published: January 2022

A 10-year-old girl presented with a chief complaint of cyclic vomiting since the last 12 h and chest pain since the last 6 h. She was diagnosed with Stanford type A aortic dissection. Intraoperatively, the aortic valve was found to be bi-lobed, and infective endocarditis associated with aortic valve perforation and rupture of the aortic sinus aneurysm, was also observed. Therefore, she underwent aortic valve replacement due to an enlarged aortic root and aortic sinus repair. The perioperative recovery was good. A large amount of bloody pericardial effusion was found in this child pre-operatively. Therefore, early surgical intervention was necessary. Acute aortic dissection rarely occurs in children. There are no clinical guidelines for the management of pediatric aortic dissection. However, if a large pericardial effusion exists, emergency surgery is necessary and effective. The treatment of the valve should be based on the actual situation. It is best to give priority to valve molding, although valve replacement is required in the majority of cases for infective endocarditis.
Lipoprotein(a) Induces Vesicular Cardiovascular Calcification Revealed With Single-Extracellular Vesicle Analysis
Authors: Rogers Maximillian A. , Atkins Samantha K. , Zheng Kang H. , Singh Sasha A. , Chelvanambi Sarvesh , Pham Tan H. , Kuraoka Shiori , Stroes Erik S. G. , Aikawa Masanori , Aikawa Elena
Published: January 2022

Lipoprotein(a) (Lp[a]) blood levels >50 mg/dL is a major cardiovascular disease risk factor in humans. Lp(a) associates with increased cardiovascular calcification, a critical pathology with no clinically available drug therapies. The mechanisms through which Lp(a) increases cardiovascular calcification risk remain undefined. We hypothesized that Lp(a) promotes the release of calcifying extracellular vesicles (EVs) that contribute to formation of microcalcification in cardiovascular tissues. Here, we show Lp(a) increased calcification in both primary human smooth muscle cells (SMCs) and valvular interstitial cells (VICs), potentially through inflammation-related mechanisms that were suppressed with E06 antibody that neutralizes pro-inflammatory oxidized phospholipids. Incubating human SMCs and VICs with Lp(a) altered the composition of EVs, increasing CD29+/tetraspanin− microvesicle release, demonstrated with a tailored single-EV microarray assay that can distinguish multivesicular body-derived exosomes and plasma membrane budded microvesicles at a single-vesicle level. Lp(a) stimulation led to release of SMC and VIC EVs that readily calcified in acellular 3D-collagen hydrogels mimicking formation of ectopic microcalcification occurring in extracellular matrix of human atherosclerotic arteries and stenotic aortic valves. Our study mechanistically demonstrates that Lp(a) partially mediates cardiovascular calcification formation via inducing the release of calcifying EVs. Additionally, we provide a customized method to assess calcifying EVs at a single-vesicle level that can be more broadly applied to assist in quantitatively differentiating exosome and microvesicle EV subpopulations.
Cardio-Oncology in the COVID Era (Co & Co): The Never Ending Story
Authors: Bisceglia Irma , Canale Maria Laura , Gallucci Giuseppina , Turazza Fabio Maria , Lestuzzi Chiara , Parrini Iris , Russo Giulia , Maurea Nicola , Quagliariello Vincenzo , Oliva Stefano , Di Fusco Stefania Angela , Lucà Fabiana , Tarantini Luigi , Trambaiolo Paolo , Moreo Antonella , Geraci Giovanna , Gabrielli Domenico , Gulizia Michele Massimo , Oliva Fabrizio , Colivicchi Furio
Published: January 2022

The pathophysiology of some non-communicable diseases (NCDs) such as hypertension, cardiovascular disease (CVD), diabetes, and cancer includes an alteration of the endothelial function. COVID-19 is a pulmonary and vascular disease with a negative impact on patients whose damaged endothelium is particularly vulnerable. The peculiar SARS-CoV-2-induced “endothelitis” triggers an intriguing immune-thrombosis that affects both the venous and arterial vascular beds. An increased liability for infection and an increased likelihood of a worse outcome have been observed during the pandemic in patients with active cancer and in cancer survivors. “Overlapping commonalities” between COVID-19 and Cardio-Oncology have been described that include shared phenotypes of cardiovascular toxicities such as left ventricular dysfunction, ischemic syndromes, conduction disturbances, myocarditis, pericarditis and right ventricular failure; shared pathophysiologic mechanisms such as inflammation, release of cytokines, the renin-angiotensin-aldosterone-pathway, coagulation abnormalities, microthrombosis and endothelial dysfunction. For these features and for the catalyst role of NCDs (mainly CVD and cancer), we should refer to COVID-19 as a “syndemic.” Another challenging issue is the persistence of the symptoms, the so-called “long COVID” whose pathogenesis is still uncertain: it may be due to persistent multi-organ viral attacks or to an abnormal immune response. An intensive vaccination campaign is the most successful pharmacological weapon against SARS-CoV-2, but the increasing number of variants has reduced the efficacy of the vaccines in controlling SARS-CoV-2 infections. After a year of vaccinations we have also learned more about efficacy and side-effects of COVID-19 vaccines. An important byproduct of the COVID-19 pandemic has been the rapid expansion of telemedicine platforms across different care settings; this new modality of monitoring cancer patients may be useful even in a post pandemic era. In this paper we analyze the problems that the cardio-oncologists are facing in a pandemic scenario modified by the extensive vaccination campaign and add actionable recommendations derived from the ongoing studies and from the syndemic nature of the infection.
Generalizable Framework for Atrial Volume Estimation for Cardiac CT Images Using Deep Learning With Quality Control Assessment
Authors: Abdulkareem Musa , Brahier Mark S. , Zou Fengwei , Taylor Alexandra , Thomaides Athanasios , Bergquist Peter J. , Srichai Monvadi B. , Lee Aaron M. , Vargas Jose D. , Petersen Steffen E.
Published: January 2022

Objectives

Cardiac computed tomography (CCT) is a common pre-operative imaging modality to evaluate pulmonary vein anatomy and left atrial appendage thrombus in patients undergoing catheter ablation (CA) for atrial fibrillation (AF). These images also allow for full volumetric left atrium (LA) measurement for recurrence risk stratification, as larger LA volume (LAV) is associated with higher recurrence rates. Our objective is to apply deep learning (DL) techniques to fully automate the computation of LAV and assess the quality of the computed LAV values.

Methods

Using a dataset of 85,477 CCT images from 337 patients, we proposed a framework that consists of several processes that perform a combination of tasks including the selection of images with LA from all other images using a ResNet50 classification model, the segmentation of images with LA using a UNet image segmentation model, the assessment of the quality of the image segmentation task, the estimation of LAV, and quality control (QC) assessment.

Results

Overall, the proposed LAV estimation framework achieved accuracies of 98% (precision, recall, and F1 score metrics) in the image classification task, 88.5% (mean dice score) in the image segmentation task, 82% (mean dice score) in the segmentation quality prediction task, and R2 (the coefficient of determination) value of 0.968 in the volume estimation task. It correctly identified 9 out of 10 poor LAV estimations from a total of 337 patients as poor-quality estimates.

Conclusions

We proposed a generalizable framework that consists of DL models and computational methods for LAV estimation. The framework provides an efficient and robust strategy for QC assessment of the accuracy for DL-based image segmentation and volume estimation tasks, allowing high-throughput extraction of reproducible LAV measurements to be possible.
Deciphering Degassing and Source Effects in Cl Isotopes in Melt Inclusions: The Possible Role of Amphibole in the Magma Source of Stromboli (Aeolian Island Arc)
Authors: Bouvier Anne-Sophie , Rose-Koga Estelle F. , Chapuis Alexis
Published: January 2022

Chlorine isotopes have emerged as a new geochemical tool over the past 15 years. Most of the data consist of bulk rock data, with a minority carried out in situ on melt inclusions using secondary ion mass spectrometry. More data are necessary to understand the relationship between δ37Cl measured in melt inclusions and that in bulk rocks from the same volcanic center. Here we have analyzed a suite of melt inclusions entrapped in olivine Fo63-85, as well as some from clinopyroxene crystals, from a single hand-sample from the Vancori unit of Stromboli, Aeolian Islands. The 27 selected melt inclusions have major element compositions ranging from high potassium alkali basalt to evolved shoshonite. Their δ37Cl vary from −2.6 ± 0.1‰ to +1.2 ± 0.2‰, a far larger range than for Stromboli bulk rocks. In this dataset, the δ37Cl variation in melt inclusions is not related to Cl degassing, or to fractional crystallization. Instead, correlations between δ37Cl and S/Cl, K2O and trace element ratios suggest mixing of two Cl endmembers with distinct δ37Cl signatures. A first endmember is characterized by high potassium alkali basalt compositions, high Ba/La (∼28), high S/Cl, and high δ37Cl (>1‰), confirming the influence in the mantle source of an aqueous fluid and providing a new constraint on its composition: that it derives from the breakdown of amphibole. The second endmember has a more evolved composition, high La/Yb, low S/Cl, and low δ37Cl (<−2‰), identifying the influence of a solute-rich component derived from subducted sediments. The δ37Cl data thus help refine the two sources initially identified from bulk rock studies and δ37Cl proves to be a potential tracer for amphibole.
Sedimentary Anthropogenic Carbon Signals From the Western Pacific Margin for the Last Century
Authors: Lee Jay , Yang Rick J. , Lin Hui-Ling , Chen Yi-Chi , Cai-Li Ren-Yi , Ren Haojia , Liu James T.
Published: January 2022

The declining trend of the δ13C of tropical corals over the last century was about −0.01‰ year−1, according to global coral records. The decrease was attributable to the significant input of anthropogenic CO2 (13C Suess effect) to the atmosphere. Previous studies of δ13C in corals suggested that the signal of the anthropogenic carbon in the Pacific and Indian Oceans were weaker than that in the Atlantic Ocean. However, biases relating to environments in which corals grew caused concerns. To investigate the anthropogenic carbon signal in the Western Pacific, foraminiferal records in a suite of 13 box cores with good age control were obtained from the continental slope off southwestern Taiwan between 2004 and 2006. δ18O values of planktonic foraminifera (Globigerinoides sacculifer or so-called Trilobatus sacculifer) in collected cores were relatively stable at −2.5‰ to −2‰ in the last century, but foraminiferal δ13C had a gradual secular decline after the 1900s. The decline trend of δ13C began to intensify after the 1960s, and its rate was similar to that observed in the Atlantic. Similar decline trends of δ13C were also found in coral records at regions where the human activity is high (Liuqiu) and low (Dongsha). Our findings indicate that the anthropogenic carbon signal in the Western Pacific was not weaker than that recorded in the Atlantic, and the nearshore sediment can supplement the lack of δ13C records in corals, which are deficient when the environment is not suitable to grow.
Geochemical Characteristics and Origin of Tight Gas in Member Two of the Upper Triassic Xujiahe Formation in Western Sichuan Depression, Sichuan Basin, SW China
Authors: Wu Xiaoqi , Liu Quanyou , Chen Yingbin , Yang Jun , Zeng Huasheng , Li Huaji
Published: January 2022

Natural gas in the tight sandstone reservoirs in Member two of the Upper Triassic Xujiahe Formation in the Western Sichuan Depression of the Sichuan Basin has complex geochemical characteristics, and the origin and source of the tight gas are revealed based on the geochemical analysis and comparison in this study. The tight gas has the dryness coefficient of 0.950–0.994, which is positively correlated with the CH4 content. The gaseous alkanes display positive carbon isotopic series, with the δ13C1 and δ13C2 values ranging from −35.6‰ to −30.3‰ and from −29.1‰ to −21.0‰, respectively, and the δD1 values range from −176‰ to −155‰. Genetic identification based on the carbon and hydrogen isotopic compositions indicates that a small amount of tight gas is typically coal-derived gas, whereas most of the tight-gas samples have experienced mixing by oil-associated gas. Geochemical comparisons suggest that the tight gas displays distinct differences with the typical oil-associated gas in Member four of the Middle Triassic Leikoupo Formation in the Chuanxi gas field and the typical coal-derived gas in Member five of Xujiahe Formation in the Xinchang gas field. It is also apparently different from the typical coal-derived gas in Member two of Xujiahe Formation in both Zhongba and Qiongxi gas fields. Among the tight gas in Member two of the Xujiahe Formation from the Western Sichuan Depression, the coal-derived gas is generated mainly by the humic mudstone in the Upper Triassic Ma’antang and Xiaotangzi formations, with assistance of the humic mudstone in Member two of the Xujiahe Formation, whereas the oil-associated gas is derived from the sapropelic limestone in the Ma’antang Formation.
The Potential of Bison Restoration as an Ecological Approach to Future Tribal Food Sovereignty on the Northern Great Plains
Authors: Shamon Hila , Cosby Olivia G. , Andersen Chamois L. , Augare Helen , BearCub Stiffarm Jonny , Bresnan Claire E. , Brock Brent L. , Carlson Ervin , Deichmann Jessica L. , Epps Aaron , Guernsey Noelle , Hartway Cynthia , Jørgensen Dennis , Kipp Willow , Kinsey Daniel , Komatsu Kimberly J. , Kunkel Kyran , Magnan Robert , Martin Jeff M. , Maxwell Bruce D. , McShea William J. , Mormorunni Cristina , Olimb Sarah , Rattling Hawk Monica , Ready Richard , Smith Roxann , Songer Melissa , Speakthunder Bronc , Stafne Grant , Weatherwax Melissa , Akre Thomas S.
Published: January 2022

Future climate projections of warming, drying, and increased weather variability indicate that conventional agricultural and production practices within the Northern Great Plains (NGP) will become less sustainable, both ecologically and economically. As a result, the livelihoods of people that rely on these lands will be adversely impacted. This is especially true for Native American communities, who were relegated to reservations where the land is often vast but marginal and non-tribal operators have an outsized role in food production. In addition, NGP lands are expected to warm and dry disproportionately relative to the rest of the United States. It is therefore critical to identify models of sustainable land management that can improve ecological function and socio-economic outcomes for NGP communities, all while increasing resilience to a rapidly changing climate. Efforts led by Native American Nations to restore North American Plains bison (Bison bison bison) to tribal lands can bring desired socio-ecological benefits to underserved communities while improving their capacity to influence the health of their lands, their people, and their livelihoods. Ecological sustainability will depend on the restoration of bison herds and bison’s ability to serve as ecosystem engineers of North America’s Plains. The historically broad distribution of bison suggests they can adapt to a variety of conditions, making them resilient to a wide range of management systems and climates. Here we review bison’s ecological, cultural, and economic value using four case studies from tribal communities within the NGP. We discuss the potential contributions of bison to food sovereignty, sustainable economies, and conservation of a working landscape with limited protections and significant risk of conversion. The ecological role of bison within this setting has potential due to cultural acceptance and the vast availability of suitable lands; however, it is critical to address tribal needs for funding support, enhanced community capacity, and solving complex landownership for these goals to be achieved.
Comparison of Capture Hi-C Analytical Pipelines
Authors: Aljogol Dina , Thompson I. Richard , Osborne Cameron S. , Mifsud Borbala
Published: January 2022

It is now evident that DNA forms an organized nuclear architecture, which is essential to maintain the structural and functional integrity of the genome. Chromatin organization can be systematically studied due to the recent boom in chromosome conformation capture technologies (e.g., 3C and its successors 4C, 5C and Hi-C), which is accompanied by the development of computational pipelines to identify biologically meaningful chromatin contacts in such data. However, not all tools are applicable to all experimental designs and all structural features. Capture Hi-C (CHi-C) is a method that uses an intermediate hybridization step to target and select predefined regions of interest in a Hi-C library, thereby increasing effective sequencing depth for those regions. It allows researchers to investigate fine chromatin structures at high resolution, for instance promoter-enhancer loops, but it introduces additional biases with the capture step, and therefore requires specialized pipelines. Here, we compare multiple analytical pipelines for CHi-C data analysis. We consider the effect of retaining multi-mapping reads and compare the efficiency of different statistical approaches in both identifying reproducible interactions and determining biologically significant interactions. At restriction fragment level resolution, the number of multi-mapping reads that could be rescued was negligible. The number of identified interactions varied widely, depending on the analytical method, indicating large differences in type I and type II error rates. The optimal pipeline depends on the project-specific tolerance level of false positive and false negative chromatin contacts.
Identification of Heterotic Groups and Patterns Based on Genotypic and Phenotypic Characteristics Among Rice Accessions of Diverse Origins
Authors: Hussain Izhar , Ali Sajid , Liu Wuge , Awais Muhammad , Li Jinhua , Liao Yilong , Zhu Manshan , Fu Chongyun , Liu Dilin , Wang Feng
Published: January 2022

Identification of the right parental combinations to maximize heterosis is the major goal of hybrid breeding, which could be achieved through identification of heterotic groups. The main objective of this study was to identify promising heterotic groups for future rice breeding programs. A collection of 359 rice genotypes of diverse origins of China and abroad, composed of inbreds, maintainers, restorers, and temperature-sensitive genic male sterile (TGMS) lines were genotyped using 10K SNP chips. The SNP data set was subjected to genomic analyses for estimation of genetic divergence and diversity. Significant variations were observed in the germplasm with the identification of six different genetic groups. These lines were assigned to the genetic groups independent of their origin. Taking an account of commercially used heterotic groups present in each cluster, three cytoplasmic male sterile (CMS) lines and 14 inbred and restorer lines with moderate to high genetic distances selected from five heterotic patterns were crossed and obtained 42 F1 hybrids. A total of 14 hybrids were found with significant maximum mid- and better-parent heterosis, namely, TaifengA × Guang122, TaifengA × Wushansimiao, and TaifengA × Minghui63 for earliness; Guang8A × Huazhan for dwarf stature; and Guang8A × Huanghuzhan-1, TaifengA × Yuexiangzhan, Guang8A × Minhui3301, TianfengA × Guang122, Guang8A × Yahui2115, TianfengA × Huanghuazhan, TianfengA × Minghui63, TianfengA × Minhui3301, TaifengA × Gui99, and Guang8A × Yuenongsimiao for yield and yield-related traits. Mid-parent and better-parent heterotic F1 hybrids were in positive correlation with the genetic distances as that manifested by commercially used heterotic groups, encouraging the use of genotypic data for identification of heterotic groups. Our study provides an informative strategy for the development of early maturing, lodging resistant and high-yielding commercial hybrids and cultivars in future heterosis breeding programs.
GATA3 Truncation Mutants Alter EMT Related Gene Expression via Partial Motif Recognition in Luminal Breast Cancer Cells
Authors: Saotome Mika , Poduval Deepak Balakrishnan , Nair Renju , Cooper Mikhala , Takaku Motoki
Published: January 2022

GATA3 is known to be one of the most frequently mutated genes in breast cancer. More than 10% of breast tumors carry mutations in this gene. However, the functional consequence of GATA3 mutations is still largely unknown. Clinical data suggest that different types of GATA3 mutations may have distinct roles in breast cancer characterization. In this study, we have established three luminal breast cancer cell lines that stably express different truncation mutants (X308 splice site deletion, C321 frameshift, and A333 frameshift mutants) found in breast cancer patients. Transcriptome analysis identified common and distinct gene expression patterns in these GATA3 mutant cell lines. In particular, the impacts on epithelial-to-mesenchymal transition (EMT) related genes are similar across these mutant cell lines. Chromatin localization of the mutants is highly overlapped and exhibits non-canonical motif enrichment. Interestingly, the A333 frameshift mutant expressed cells displayed the most significant impact on the GATA3 binding compared to X308 splice site deletion and C321fs mutants expressed cells. Our results suggest the common and different roles of GATA3 truncation mutations during luminal breast cancer development.
The Inhibitory Receptor Siglec-8 Interacts With FcεRI and Globally Inhibits Intracellular Signaling in Primary Mast Cells Upon Activation
Authors: Korver Wouter , Wong Alan , Gebremeskel Simon , Negri Gian Luca , Schanin Julia , Chang Katherine , Leung John , Benet Zachary , Luu Thuy , Brock Emily C. , Luehrsen Kenneth , Xu Alan , Youngblood Bradford A.
Published: January 2022

Immunomodulation of mast cell (MC) activity is warranted in allergic and inflammatory diseases where MCs have a central role in pathogenesis. Targeting Siglec-8, an inhibitory receptor on MCs and eosinophils, has shown promising activity in preclinical and clinical studies. While the intracellular pathways that regulate Siglec-8 activity in eosinophils have been well studied, the signaling mechanisms that lead to MC inhibition have not been fully elucidated. Here, we evaluate the intracellular signaling pathways of Siglec-8-mediated inhibition in primary MCs using an anti-Siglec-8 monoclonal antibody (mAb). Phospho-proteomic profiling of FcεRI-activated MCs revealed Siglec-8 mAb-treatment globally inhibited proximal and downstream kinases, leading to attenuated MC activation and degranulation. In fact, Siglec-8 was found to directly interact with FcεRI signaling molecules. Siglec-8 inhibition was dependent on both cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs) that interact with the SH2 containing protein phosphatase Shp-2 upon Siglec-8 phosphorylation. Taken together, these data support a model in which Siglec-8 regulates proximal FcεRI-induced phosphorylation events through phosphatase recruitment and interaction with FcεRIγ, resulting in global inhibition of MCs upon Siglec-8 mAb engagement.
Exploring the Potential of Forecasting Fish Distributions in the North East Atlantic With a Dynamic Earth System Model, Exemplified by the Suitable Spawning Habitat of Blue Whiting
Authors: Miesner Anna K. , Brune Sebastian , Pieper Patrick , Koul Vimal , Baehr Johanna , Schrum Corinna
Published: January 2022

Local oceanographic variability strongly influences the spawning distribution of blue whiting (Micromesistius poutassou). Here, we explore the potential of using a dynamic Earth System Model (ESM) to forecast the suitable spawning habitat of blue whiting to assist management. Retrospective forecasts of temperature and salinity with the Max Planck Institute ESM (MPI-ESM) show significant skill within blue whiting’s spawning region and spawning depth (250–600 m) during the peak months of spawning. While persistence forecasts perform well at shorter lead times (≤2 years), retrospective forecasts with MPI-ESM are clearly more skilful than persistence in predicting salinity at longer lead times. Our results indicate that retrospective forecasts of the suitable spawning habitat of blue whiting based on predicted salinity outperform those based on calibrated species distribution models. In particular, we find high predictive skill for the suitable spawning habitat based on salinity predictions around one year ahead in the area of Rockall-Hatton Plateau. Our approach shows that retrospective forecasts with MPI-ESM show a better ability to differentiate between the presence and absence of suitable habitat over Rockall Plateau compared to persistence. Our study highlights that physical-biological forecasts based on ESMs could be crucial for developing distributional forecasts of marine organisms in the North East Atlantic.
Cadmium Substitution Effect on Microstructure and Magnetic Properties of Mg-Cu-Zn Ferrites
Authors: Beyranvand Morteza , Zahedi Ahmad , Gholizadeh Ahmad
Published: January 2022

The microstructure, optical, and magnetic properties of CdxMg0.3-xCu0.2Zn0.5Fe2O4 ferrites prepared by the citrate auto-combustion method were investigated. The samples were analyzed by X-ray diffraction, scanning electron microscopy, UV-Vis spectroscopy, https://soh.iums.ac.ir/uploads/uv-vis_-_2.pptx X-ray energy-dispersive spectroscopy, Fourier-transform infrared spectroscopy, and vibrating sample magnetometer. Rietveld refinement of XRD patterns shows a single-phase cubic structure (space group Fd3¯m) for the samples with x up to 0.20, while the impurity phase of CdO is observed in the samples with x = 0.25, 0.30. As the substitution content increases, the presence of non-magnetic Cd2+ ions in the octahedral site and the migration of Fe3+ions from the octahedral site to the tetrahedral site decreases the saturation magnetization of the samples. Comparison of the bandgap energy of the samples shows an increasing trend with Cd substitution for x up to 0.20 and then decreases, which can be interpreted in terms of changes in the electronic structure of the samples. Improvement in dielectric properties of the samples with increase of Cd2+ content for x up to 0.20 may be attributed to easier transfer and electron exchange between Fe3+and M2+ ions.
Potential Application of 4D Technology in Fabrication of Orthodontic Aligners
Authors: Elshazly Tarek M. , Keilig Ludger , Alkabani Yasmine , Ghoneima Ahmed , Abuzayda Moosa , Talaat Wael , Talaat Sameh , Bourauel Christoph P.
Published: January 2022

Objectives: To investigate and quantify forces generated by three-dimensional-printed aligners made of shape memory polymers (four-dimensional [4D] aligner).

Methods: Clear X v1.1 material was used in this study. On a custom-made typodont model, correction of maxillary central incisor (tooth 21) malposition by 4D aligners with thicknesses of 0.8 and 1.0 mm was measured by superimposition of subsequent scans. Maximum deflection forces generated by foil sheet specimens were measured at different temperatures in three-point bending (3-PB) tests. In a biomechanical system (orthodontic measurement and simulation system [OMSS]), forces generated on movements of tooth 21 by the 4D aligners were measured at different temperatures.

Results: 4D aligners succeeded to achieve a significant tooth movement (2.5 ± 0.5 mm) on the typodont, with insignificant difference between different thicknesses. In the 3-PB test, the maximum deflection forces measured at 20, 30, 37, 45, and 55°C, were 3.8 ± 1.1, 2.5 ± 0.9, 1.7 ± 0.6, 1.0 ± 0.4, and 0.5 ± 0.4 N, respectively. Forces delivered on palatal displacement of tooth 21 at 37, 45, and 55°C by 0.8-mm aligners were 0.3 ± 0.1, 0.2 ± 0.1, and 0.7 ± 0.2 N, respectively, whereas those by 1.0-mm aligners were 0.3 ± 0.1, 0.3 ± 0.1, and 0.6 ± 0.2 N, respectively. A good concordance with movement on the typodont model was shown in OMSS.

Conclusion: An initial study of 4D-printed aligner shows its ability to move a tooth by biocompatible orthodontic forces, after a suitable thermal stimulus within the oral temperature range.
A Natural History of Disease Framework for Improving the Prevention, Management, and Research on Post-viral Fatigue Syndrome and Other Forms of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
Authors: O'Boyle Shennae , Nacul Luis , Nacul Flavio E. , Mudie Kathleen , Kingdon Caroline C. , Cliff Jacqueline M. , Clark Taane G. , Dockrell Hazel M. , Lacerda Eliana M.
Published: January 2022

We propose a framework for the treatment, rehabilitation, and research into Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) using a natural history of disease approach to outline the distinct disease stages, with an emphasis on cases following infection to provide insights into prevention. Moving away from the method of subtyping patients based on the various phenotypic presentations and instead reframing along the lines of disease progression could help with defining the distinct stages of disease, each of which would benefit from large prospective cohort studies to accurately describe the pathological mechanisms taking place therein. With a better understanding of these mechanisms, management and research can be tailored specifically for each disease stage. Pre-disease and early disease stages call for management strategies that may decrease the risk of long-term morbidity, by focusing on avoidance of further insults, adequate rest to enable recovery, and pacing of activities. Later disease stages require a more holistic and tailored management approach, with treatment—as this becomes available—targeting the alleviation of symptoms and multi-systemic dysfunction. More stringent and standardised use of case definitions in research is critical to improve generalisability of results and to create the strong evidence-based policies for management that are currently lacking in ME/CFS.
A New Method for the Sputum Cytology Test Without Direct Contact to Specimens During COVID-19 Pandemic
Authors: Cui Junqi , Wang Xia , Rao Yamin , Ji Tianhai , Li Long
Published: January 2022

Background

Coronavirus disease 2019 (COVID-19) pandemic continues to spread across the world. Specimens of blood, body fluids and excreta received in the department of pathology undoubtedly increased the risk of infection, especially in some hospitals that are short of professional protection capability. Here we provided a new simple way for the sputum cytology test during the COVID-19 pandemic.

Methods

Sputum samples from 30 patients with lung cancer were collected and divided into two groups, including the control group and the experimental group. Samples of the control group were processed in the biological safety cabinet, while the experimental group was put into the sealed specimen bag directly and pretreated with 75% medical alcohol. Then the cell morphology and tumor cell identification were analyzed by cell smears and liquid-based cell staining. The expression of cell antigens was determined by immunohistochemical staining.

Result

Our result showed that both sputum samples in two groups exhibited complete cell structure and clear morphology according to the cell smear and liquid-based cell staining. In addition, the immunohistochemical result showed that cell antigens, including cytokeratin (CK), leukocyte common antigen (LCA), and thyroid transcription factor-1 (TTF1), were specifically expressed in the cell membrane, cytoplasm, and nucleus, respectively. The tumor cells were distributed diffusely, and cell antigens were located accurately after pretreatment with 75% medical alcohol and were consistent with that of the control group.

Conclusion

Using 75% medical alcohol to pretreat sputum specimens has no obvious impact on cell morphology and antigens expression. Our study provided a new method for the sputum cytology test with no direct contact so as to protect medical staff against the virus during COVID-19 outbreak.
Differential COVID-19 Symptoms Given Pandemic Locations, Time, and Comorbidities During the Early Pandemic
Authors: Wang Yang , Zhang Fengwei , Byrd J. Brian , Yu Hong , Ye Xianwei , He Yongqun
Published: January 2022

Background

COVID-19 pandemic is disaster to public health worldwide. Better perspective on COVID's features early in its course–prior to the development of vaccines and widespread variants–may prove useful in the understanding of future pandemics. Ontology provides a standardized integrative method for knowledge modeling and computer-assisted reasoning. In this study, we systematically extracted and analyzed clinical phenotypes and comorbidities in COVID-19 patients found at different countries and regions during the early pandemic using an ontology-based bioinformatics approach, with the aim to identify new insights and hidden patterns of the COVID-19 symptoms.

Results

A total of 48 research articles reporting analysis of first-hand clinical data from over 40,000 COVID-19 patients were surveyed. The patients studied therein were diagnosed with COVID-19 before May 2020. A total of 18 commonly-occurring phenotypes in these COVID-19 patients were first identified and then classified into different hierarchical groups based on the Human Phenotype Ontology (HPO). This meta-analytic approach revealed that fever, cough, and the loss of smell and taste were ranked as the most commonly-occurring phenotype in China, the US, and Italy, respectively. We also found that the patients from Europe and the US appeared to have more frequent occurrence of many nervous and abdominal symptom phenotypes (e.g., loss of smell, loss of taste, and diarrhea) than patients from China during the early pandemic. A total of 22 comorbidities, such as diabetes and kidney failure, were found to commonly exist in COVID-19 patients and positively correlated with the severity of the disease. The knowledge learned from the study was further modeled and represented in the Coronavirus Infectious Disease Ontology (CIDO), supporting semantic queries and analysis. Furthermore, also considering the symptoms caused by new viral variants at the later stages, a spiral model hypothesis was proposed to address the changes of specific symptoms during different stages of the pandemic.

Conclusions

Differential patterns of symptoms in COVID-19 patients were found given different locations, time, and comorbidity types during the early pandemic. The ontology-based informatics provides a unique approach to systematically model, represent, and analyze COVID-19 symptoms, comorbidities, and the factors that influence the disease outcomes.