bluuebunny/crossref_metadata_2025 huggingface dataset:
Blue Swimming Crab (Portunus pelagicus, Linnaeus 1758) Capture Fishery Practices in Tigbauan, Iloilo, Central Philippines
Authors: TORING-FARQUERABAO Maria Liza , TAHILUDDIN Albaris
Published: March 2022

Blue swimming crab (BSC) (Portunus pelagicus) is an economically significant aquatic species contributing to the Philippine economy. Tigbauan, a coastal municipality in Iloilo, central Philippines, has been practicing BSC capture fishery for decades. However, there is a limited existing study on BSC fishing practices in this particular area. Thus, this study aimed to assess the status of the BSC capture fishery in Tigbauan, Iloilo. A household survey was done in October 2019 for the five crabbing villages (barangays) in the area using a semi-structured questionnaire. Results showed that most crabbers (83.4%) were still living below the country poverty threshold. Although some crabbers were engaged in other livelihood opportunities, the marginal contribution from these earnings to the household income was still inadequate to supplement the fundamental and other family needs. Limiting their chances to other sources of income may be due to their lack of formal education. Fishing gears used by locals were crab pots locally known as panggal and crab entangling net or bottom-set gillnet locally known as pukot. Crabbing operation varied in each village and was done regularly and even twice a day in peak season time. The instances of catching gravid females were high. Hence, threatening the status of wild stocks. Rampant trawling and dragging activities in the municipality also became a big problem for the crabbers and contributed to the catch decline. Strict implementation of the existing ordinances must be carried out and focused on the biology, seasonality, and stock enhancement to formulate an effective management framework plan.
İklim Değişikliğinin Tahıl Virüs Hastalıkları Üzerine Etkisi
Authors: AKBAŞ Birol , MORCA Ali Ferhan , COŞKAN Sevgi
Published: March 2022

İklim değişikliğinin tüm ekosistemler üzerinde etkisini arttırarak, küresel ve bölgesel ölçeklerde hissedilir bir şekilde ortaya çıkması tahmin edilmektedir. Toprak ve su rejimleri değişime uğrayarak, tarım arazilerini verimsizleştirmesi, zararlı-hastalıkların çoğalmasına sebep olması ve tüm tarımsal ekosistemleri tahrip etmesi beklenmektedir. İklim değişikliklerinin bitkisel üretimde verim ve kalite kaybına yol açacak olması, kayıpların nedeninin doğru bir şekilde anlaşılmasını engellemektedir. Dolayısıyla orta ve uzun vadede etkinliği artacağı düşünülen hastalıkların oluşturacağı risk dikkate alınmalıdır. Bu konuda çok yönlü birçok çalışma yapılması gereklidir. Aksi takdirde verimdeki düşüşler gibi olumsuzlukların çevre koşullarındaki değişimden kaynaklı olduğuna odaklanılarak viral patojenler gibi biyotik faktörler göz ardı edilecektir. Bu derlemede, stres altında kalan tarımsal ekolojide, tahıl hastalıklarının önemli bir zararlı organizma grubu olan viral patojenlerin gelecekte oluşturabileceği riskler değerlendirilmiştir. Özellikle böcek ve akar vektörü ile taşınan Barley yellow dwarf virus (BYDV), Wheat dwarf virus (WDV) ve Wheat streak mosaic virus (WSMV) gibi virüslerin yakın gelecekte Türkiye’de tahıl ekiliş alanlarında etkisini arttırabileceği öngörülürken, Soil-borne wheat mosaic virus (SBWMV), Barley yellow mosaic virus (BaYMV) gibi plazmodioforidler ile taşınan virüslerin etkinliğinin lokasyona göre değişkenlik göstereceği öngörülmektedir. Dolayısıyla iklim değişikliğinin lokasyona ve vektöre bağlı olarak bazı tahıl virüslerinin etkinliğini arttırırken bazılarının etkinliğini azaltacağı yönündedir.
Kısa Süreli Polen Muhafaza Yöntemleri Kullanılarak Sera Şartlarında Mısır Bitkilerinde Tohumluk Üretimi
Authors: YÜKSEL Nur , KÖSTEKÇİ Melih , TURCAN Ahmet Serdar , KAHRIMAN Fatih
Published: March 2022

Bu çalışma, sera şartlarında yetiştirilen mısır hat ve hibritlerinin farklı polen muhafaza yöntemleri ile tohum üretimini incelemek amacıyla yürütülmüştür. Araştırmada altı farklı genotip (IHO, B73, HYA, HYAxB73, MAY66, IND2) materyal olarak kullanılmıştır. Sera denemesi 2020 yılı Eylül-Mart ayları arasında yürütülmüştür. Her materyalden en az 30 fide yetiştirilerek saksılara şaşırtılmıştır. Polen muhafaza yöntemi olarak üç ayrı yöntem (Tepe püskülü muhafaza, +4 °C polen muhafaza, -20 °C polen muhafaza) kıyaslanmış ve 3’er gün aralıklarla 9 günlük sürede tozlanma işlemleri gerçekleştirilmiştir. Her tozlanma işleminden önce kullanılan polen örneğinde canlılık testi yapılarak muhafaza yöntemlerine göre polen canlılığındaki değişimi izlenmiştir. Ayrıca sera şartlarında bitkilerin gelişimlerini izlemek amacıyla bitki boyu (cm), tepe püskülü boyu (cm) ve tepe püskülü yan dal sayısı (adet) ölçümleri alınmıştır. Çalışma sonuçları mısır genotiplerinden sera şartlarında toplanan polen örneklerinin canlılık süresinin kullanılan yönteme göre değiştiğini göstermiştir. Tohum bağlama ve sera şartlarında gelişim bakımından da genotipler arasında önemli farklılıklar olduğu belirlenmiştir.
ANALISIS POTENSI DAERAH RAWAN ABRASI PANTAI BERDASARKAN PARAMETER FISIKA OSEANOGRAFI DI PESISIR UTARA DAN TIMUR LAUT PULAU WAWONII, SULAWESI TENGGARA
Authors: Hartomo La Ode Ibnu , Asmadin . , Pratikino A. Ginong
Published: March 2022

Berdasarkan data risiko bencana Kabupaten Konawe Kepulauan pada kawasan rawan abrasi terdapat tiga dari tujuh kecamatan di pulau seluas 650 Km2 telah mengalami abrasi yang membuat garis pantai semakin menjauh ke darat. Tujuan penelitian ini yaitu untuk mengetahui karakteristik pantai, kondisi parameter Fisika Oseanografi serta mengetahui potensi daerah rawan abrasi pantai di pesisir Utara dan Timur Laut Pulau Wawonii. Pengambilan data dilaksanakan pada bulan Agustus 2020 bertempat di perairan pesisir  pantai Wawonii Utara dan Timur Laut Konawe Kepulauan dengan 4 titik stasiun. Metode penelitian untuk mengetahui karakteristik pantai dan potensi daerah rawan abrasi pantai menggunakan metode pembobotan atau scoring. Kondisi parameter fisika oseanografi berupa gelombang dan arus menggunakan metode peramalan gelombang berdasarkan data arah dan kecepatan angin bersumber dari ECMWF. Hasil penelitian menunjukkan bahwa pada kedua lokasi studi memiliki tipe substrat yang sama yaitu berpasir, keseluruhan bentuk pantai relatif datar, dan jarang atau tidak ditemukannya habitat mangrove. Perairan Wawonii Utara memiliki tinggi gelombang signifikan relatif lebih kecil yaitu 0.54 m dengan periode 4.29 s. Perairan Wawonii Timur Laut menunjukkan tinggi gelombang signifikan sebesar 3.17 m dengan periode gelombang 11.52 s. Kedua perairan memiliki tipe arus sejajar pantai (longshore current). Pada Wawonii Utara kedua titik lokasinya memiliki tingkat kerawanan abrasi dalam kategori sedang dengan skor nilai 13 dan 15 sedangkan pada Wawonii Timur Laut termasuk dalam kategori tinggi dengan skor nilai masing-masing 17 dan 17.Kata Kunci: Wilayah Pesisir, abrasi, Daerah Rawan Abrasi, Fisika Oseanografi, Pulau Wawonii
POLA ARUS PERMUKAAN LAUT DI BAGIAN TERLUAR TELUK KENDARI DAN PERAIRAN SEKITARNYA
Authors: Nurlin . , Asmadin . , Takwir Amadhan
Published: March 2022

permukaan umumnya bersumber dari gerakan angin. Penelitian ini bertujuan untuk mengetahui pengaruh angin terhadap pergerakan arus permukaan di bagian terluar Teluk Kendari dan Perairan sekitarnya pada musim yang berbeda. Data yang dikumpulkan pada penelitian ini terdiri dari 2 jenis data yaitu data primer meliputi data arus dan angin serta data sekunder meliputi data pasang surut. Metode penelitian untuk mengukur kecepatan arus permukaan menggunakan metode Euler. Metode  untuk memperhitungkan  nilai  dan  arah  kecepatan  angin  menggunakan  metode  Wind  Rose. Metode untuk memperhitungkan  gerak  osilasi  pasang  surut  secara  periodik  menggunakan  Metode  Admiralty. Hasil  penelitian menunjukkan bahwa pola pergerakan arus  permukaan  laut  di bagian terluar Teluk Kendari dan Perairan sekitarnya pada setiap musimnya memiliki nilai kecepatan arus laut permukaan tertinggi terjadi pada musim timur yaitu 0.26 m/s dengan arah dari Timur menuju ke Barat dan nilai terendah terjadi pada musim peralihan II yaitu 0.01 m/s dengan arah dari Barat menuju ke Timur. Perubahan arah dan kecepatan angin di bagian terluar Teluk Kendari dan Perairan sekitarnya tidak memberikan pengaruh sepenuhnya terhadap perubahan arah dan kecepatan arus permukaan pada setiap musimnnya. Selain angin diduga ada faktor lain yang memengaruhi perubahan arah dan kecepatan arus permukaan, seperti pasang surut, gaya coriolis dan bentuk topografi pada Perairan Teluk Kendari bagian luar dan sekitarnya.Kata Kunci:, Arus, Angin, Pasut, Teluk Kendari
Comparative Study of Traditional Single-Needle Electrospinning and Novel Spiral-Vane Electrospinning: Influence on the Properties of Poly(caprolactone)/Gelatin Nanofiber Membranes
Authors: Xu Qi , Liu Wei , Yi Bingcheng
Published: March 2022

Spiral-vane electrospinning (SVE), a novel needleless electrospinning, was proven effective in obtaining high-throughput production of nanofibers. However, the properties of the electrospun nanofibers produced by SVE remain relatively underexplored, especially in comparison with those made by traditional single-needle electrospinning (SNE). Hence, for the comparative study of SNE and SVE in this study, the difference in the preparation mechanism was first analyzed using numerical simulation, followed by the experimental analysis of the effects of spinneret types on the quality and biocompatibility of electrospun poly(caprolactone)/gelatin (PCL/Gel) nanofibers. The values predicted by the electric field results were consistent with the experimental data, showing that the PCL/Gel nanofibers prepared by SVE have higher yields than SNE. Although the different spinnerets (i.e., needle and spiral vane) had little effect on the surface chemistry, thermal stability, and composition of the PCL/Gel nanofibers, they had great effects on the fiber diameter distribution and mechanical properties in which SVE-electrospun nanofibers have the wider diameter distribution and higher softness. Furthermore, the SVE-electrospun nanofibers were also proven to exhibit good biocompatibility for cell growth of human adipose-derived stem cells (hADSCs) and cell–fiber interactions. Summarily, compared to the traditional SNE, SVE-electrospun nanofibers exhibited many merits including high-throughput yield, good air permeability, and compliance, which provide a facile and effective platform for the improvement of nanofiber applications in biomedical fields (e.g., tissue engineering, cosmetic, and medical textiles).
c-Abl Activation Linked to Autophagy-Lysosomal Dysfunction Contributes to Neurological Impairment in Niemann-Pick Type A Disease
Authors: Marín Tamara , Dulcey Andrés E. , Campos Fabián , de la Fuente Catalina , Acuña Mariana , Castro Juan , Pinto Claudio , Yañez María José , Cortez Cristian , McGrath David W. , Sáez Pablo J. , Gorshkov Kirill , Zheng Wei , Southall Noel , Carmo-Fonseca Maria , Marugán Juan , Alvarez Alejandra R. , Zanlungo Silvana
Published: March 2022

Niemann-Pick type A (NPA) disease is a fatal lysosomal neurodegenerative disorder caused by the deficiency in acid sphingomyelinase (ASM) activity. NPA patients present severe and progressive neurodegeneration starting at an early age. Currently, there is no effective treatment for this disease and NPA patients die between 2 and 3 years of age. NPA is characterized by an accumulation of sphingomyelin in lysosomes and dysfunction in the autophagy-lysosomal pathway. Recent studies show that c-Abl tyrosine kinase activity downregulates autophagy and the lysosomal pathway. Interestingly, this kinase is also activated in other lysosomal neurodegenerative disorders. Here, we describe that c-Abl activation contributes to the mechanisms of neuronal damage and death in NPA disease. Our data demonstrate that: 1) c-Abl is activated in-vitro as well as in-vivo NPA models; 2) imatinib, a clinical c-Abl inhibitor, reduces autophagy-lysosomal pathway alterations, restores autophagy flux, and lowers sphingomyelin accumulation in NPA patient fibroblasts and NPA neuronal models and 3) chronic treatment with nilotinib and neurotinib, two c-Abl inhibitors with differences in blood-brain barrier penetrance and target binding mode, show further benefits. While nilotinib treatment reduces neuronal death in the cerebellum and improves locomotor functions, neurotinib decreases glial activation, neuronal disorganization, and loss in hippocampus and cortex, as well as the cognitive decline of NPA mice. Our results support the participation of c-Abl signaling in NPA neurodegeneration and autophagy-lysosomal alterations, supporting the potential use of c-Abl inhibitors for the clinical treatment of NPA patients.
Clinical Characteristics and Long-Term Outcomes of Patients With Differing Haemoglobin Levels Undergoing Semi-Urgent and Elective Percutaneous Coronary Intervention in an Asian Population
Authors: Soh Rodney Yu-Hang , Sia Ching-Hui , Djohan Andie Hartanto , Lau Rui-Huai , Ho Pei-Ying , Neo Jonathan Wen-Hui , Ho Jamie Sin-Ying , Sim Hui-Wen , Yeo Tiong-Cheng , Tan Huay-Cheem , Chan Mark Yan-Yee , Loh Joshua Ping-Yun
Published: March 2022

Introduction

This study aimed to investigate the impact of anaemia on long-term clinical outcomes in patients who underwent semi-urgent and elective percutaneous coronary intervention (PCI) in an Asian population. Although the effects of anaemia on outcomes in Asian patients are well studied for acute coronary syndrome, its impact on Asian patients undergoing semi-urgent and elective PCI is unclear.

Methods

This was a retrospective cohort study of patients who underwent semi-urgent and elective PCI from January 1, 2014, to December 31, 2015, at a tertiary academic centre. A total of 1,685 patients were included. They were stratified into three groups: normal (≥12 g/dL), intermediate (10–11.9 g/dL), and low (<10 g/dL) haemoglobin levels. Demographics, risk factors, and end-points including the 5-point major adverse cardiac and cerebrovascular events (MACCE) (all-cause death, subsequent stroke, myocardial infarction, congestive cardiac failure, and target lesion revascularisation), cardiovascular death, and bleeding events were analysed.

Results

Patients in intermediate and low haemoglobin level groups were older with more comorbidities. Compared to the normal haemoglobin level group, low haemoglobin level group patients were associated with an increased risk of composite endpoints of all-cause death, subsequent stroke, myocardial infarction, congestive cardiac failure, and target lesion revascularisation [adjusted hazard ratio (aHR) 1.89, 95% confidence interval (CI):1.22, 2.92; p = 0.004]. This was driven by the increased risk of target lesions revascularisation observed in the low haemoglobin level group compared to the normal haemoglobin level group (aHR 17.74, 95% CI: 1.74, 180.80; p = 0.015). The patients in the low haemoglobin level group were also associated with a higher risk of bleeding events compared to the normal haemoglobin level group (aHR 7.18, 95% CI: 1.13, 45.40; p = 0.036).

Conclusion

In our Asian cohort, patients with anaemia undergoing PCI were associated with a higher comorbid burden. Despite adjustments for comorbidities, these patients had higher mortality and worse cardiovascular outcomes following contemporary PCI.
Case Report: Myocarditis Associated With COVID-19 mRNA Vaccination Following Myocarditis Associated With Campylobacter Jejuni
Authors: Kojima Nobuko , Tada Hayato , Okada Hirofumi , Yoshida Shohei , Sakata Kenji , Usui Soichiro , Ikeda Hiroko , Okajima Masaki , Kawashiri Masa-aki , Takamura Masayuki
Published: March 2022

We herein present our experience with a case involving a 17-year-old Japanese boy suffering from acute myocarditis after his second coronavirus disease-2019 (COVID-19) messenger RNA (mRNA) vaccine shot. The patients had a history of myocarditis associated with Campylobacter jejuni 3 years prior. This has been the first-ever documented case of myocarditis associated with COVID-19 mRNA vaccination in a patient with a history of myocarditis. We present a series of images and blood biomarkers for different types of myocarditis that developed in this single patient.
Beat-Level Interpretation of Intra-Patient Paradigm Based on Object Detection
Authors: Kang Man , Wang Xue-Feng , Xiao Jing , Tian He , Ren Tian-Ling
Published: March 2022

Electrocardiogram (ECG), as a product that can most directly reflect the electrical activity of the heart, has become the most common clinical technique used for the analysis of cardiac abnormalities. However, it is a heavy and tedious burden for doctors to analyze a large amount of ECG data from the long-term monitoring system. The realization of automatic ECG analysis is of great significance. This work proposes a beat-level interpretation method based on the automatic annotation algorithm and object detector, which abandons the previous mode of separate R peak detection and heartbeat classification. The ground truth of the QRS complex is automatically annotated and also regarded as the object the model can learn like category information. The object detector unifies the localization and classification tasks, achieving an end-to-end optimization as well as decoupling the high dependence on the R peak. Compared with most advanced methods, this work shows superior performance. For the interpretation of 12 heartbeat types in the MIT-BIH dataset, the average accuracy is 99.60%, the average sensitivity is 97.56%, and the average specificity is 99.78%. This method can be used as a clinical auxiliary tool to help doctors diagnose arrhythmia after receiving large-scale database training.
The Long-Term Effects of Non-Pharmacological Interventions on Diabetes and Chronic Complication Outcomes in Patients With Hyperglycemia: A Systematic Review and Meta-Analysis
Authors: Zhou Rongrong , Cui Yashan , Zhang Yuehong , De Jin , An Xuedong , Duan Yingying , Zhang Yuqing , Kang Xiaomin , Lian Fengmei
Published: March 2022

Objective

This study aimed at examining the long-term effects of non-pharmacological interventions on reducing the diabetes incidence among patients with prediabetes and chronic complications events among patients with hyperglycemia (pre-diabetes and diabetes) by performing a systematic review and meta-analysis of randomized controlled trials (RCTs).

Methods

PubMed, MEDLINE, EMBASE, the Cochrane Library, and the Web of Science Core Collection were searched for studies published between January 1990 and November 2021, looking for RCTs to evaluate the effects of non-pharmacological interventions on preventing the incidence of diabetes and chronic complications in comparison with medical therapy, placebo, or usual diabetes care. Two independent reviews extracted relevant data and quality assessment. Any discrepancies were resolved by a third reviewer.

Results

In total, 20 articles involved 16 RCTs (follow-up ranged from 2 to 30 years) were included. Pooled analysis of intervention studies demonstrated clearly that non-pharmacological interventions have a significant effect on reducing the diabetes events in patients with prediabetes (RR 0.62; 95% CI 0.54, 0.71). Pooled analysis of extended follow-up studies showed that non-pharmacological interventions could effectively reduce the diabetes incidence in patients with prediabetes (RR 0.78; 95% CI 0.63, 0.96). Meta-regression and subgroup analysis indicates that the diabetes incidence of the long-term group (duration > 3 years) was clearly reduced by 0.05% compared with the relatively short-term group (duration ≤ 3 years). The incidence of microvascular complications in patients with hyperglycemia was effectively lowered by non-pharmacological interventions (RR 0.60; 95% CI 0.43, 0.83).

Conclusion

Non-pharmacological interventions have a long-term effect on reducing the diabetes incidence among prediabetic patients and effectively preventing microvascular complications on hyperglycemia.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/.
Accurate Modeling Simulation and Experimental Study of Hybrid Multi-Terminal UHVDC Transmission System
Authors: Xing Chao , Cai Wang , Che Yanbo , Bi Guihong , Chen Shilong , Gao Jingye , Wang Long
Published: March 2022

This study researches on the Wudongde hybrid multi-terminal Ultra High-Voltage Direct Current Transmission (UHVDC) project (referred to as Wudongde transmission project in short) from the electromagnetic transient model and simulation and establishes an accurate simulation model of the hybrid multi-terminal UHVDC transmission system with the Power Systems Computer-Aided Design (PSCAD). The hybrid multi-terminal UHVDC transmission system consists of the primary system and the control system. The simulation model of the primary system adopts the parameters of the Wudongde transmission project, and the simulation model of the control system refers to the control system benchmark model of HVDC transmission and 9-terminal DC grid in the International Council on Large Electric Systems (CIGRE). According to the characteristics of the hybrid multi-terminal UHVDC control system, the benchmark model of HVDC transmission and 9-terminal DC grid control system in the CIGRE is modified accordingly, and a simulation model of the control system applicable to the hybrid multi-terminal UHVDC transmission system is established. The accuracy and credibility of the model are verified through the comparison of the recording waveform and the simulating waveform of the steady-state and transient operation. The simulating and field recording waveforms show that the model can accurately simulate the Wudongde transmission project and be used as an effective tool for further studying the electromagnetic transient characteristics of the hybrid multi-terminal UHVDC transmission system.
Heat Transfer Characteristics and Pressure Drop of U-type Channel in Vacuum Distillation Process for Titanium Sponge
Authors: Yang Kangquan , Zhang Chengqi , Yuan Hui , Wu Fuzhong
Published: March 2022

Blockage of the U-type channel exacerbates the intermittency of production, and clarifying the channel heat transfer characteristics and pressure drop is an effective way to address this problem. The channel heat transfer and flow characteristics of the fluid in the channel are experimentally investigated in this study. According to the experiments, the heat transfer coefficient is between 59.95 and 200.29 W/m2⋅K and increases with the flow velocity and fluid temperature. Because the pressure drop is usually accompanied by a change in the energy loss of the fluid, the energy loss is evaluated experimentally. The results demonstrate that the friction loss in the straight tube section accounts for 80% of the energy loss. A bent tube of 90° is recommended instead of a right-angle tube to reduce the pressure drop. A dimensionless relation regarding the Nusselt number is presented to predict the heat transfer characteristics. We provided proposals to address the problem of blockage of the U-type channel, this is helpful to reduce production energy consumption and improve the quality of titanium sponge.
Identification of GGT5 as a Novel Prognostic Biomarker for Gastric Cancer and its Correlation With Immune Cell Infiltration
Authors: Wang Yuli , Fang Yuan , Zhao Fanchen , Gu Jiefei , Lv Xiang , Xu Rongzhong , Zhang Bo , Fang Zhihong , Li Yan
Published: March 2022

Gastric cancer (GC) is a common malignant tumor of the digestive system. Recent studies revealed that high gamma-glutamyl-transferase 5 (GGT5) expression was associated with a poor prognosis of gastric cancer patients. In the present study, we aimed to confirm the expression and prognostic value of GGT5 and its correlation with immune cell infiltration in gastric cancer. First, we compared the differential expression of GGT5 between gastric cancer tissues and normal gastric mucosa in the cancer genome atlas (TCGA) and GEO NCBI databases using the most widely available data. Then, the Kaplan-Meier method, Cox regression, and univariate logistic regression were applied to explore the relationships between GGT5 and clinical characteristics. We also investigated the correlation of GGT5 with immune cell infiltration, immune-related genes, and immune checkpoint genes. Finally, we estimated enrichment of gene ontologies categories and relevant signaling pathways using GO annotations, KEGG, and GSEA pathway data. The results showed that GGT5 was upregulated in gastric cancer tissues compared to normal tissues. High GGT5 expression was significantly associated with T stage, histological type, and histologic grade (p < 0.05). Moreover, gastric cancer patients with high GGT5 expression showed worse 10-years overall survival (p = 0.008) and progression-free intervals (p = 0.006) than those with low GGT5 expression. Multivariate analysis suggested that high expression of GGT5 was an independent risk factor related to the worse overall survival of gastric cancer patients. A nomogram model for predicting the overall survival of GC was constructed and computationally validated. GGT5 expression was positively correlated with the infiltration of natural killer cells, macrophages, and dendritic cells but negatively correlated with Th17 infiltration. Additionally, we found that GGT5 was positively co-expressed with immune-related genes and immune checkpoint genes. Functional analysis revealed that differentially expressed genes relative to GGT5 were mainly involved in the biological processes of immune and inflammatory responses. In conclusion, GGT5 may serve as a promising prognostic biomarker and a potential immunological therapeutic target for GC, since it is associated with immune cell infiltration in the tumor microenvironment.
Identification of Tissue-Specific Expressed Hub Genes and Potential Drugs in Rheumatoid Arthritis Using Bioinformatics Analysis
Authors: Xing Xuewu , Xia Qun , Gong Baoqi , Shen Zhongyang , Zhang Yingze
Published: March 2022

Background: Rheumatoid arthritis (RA) is a common autoimmune disease characterized by progressive, destructive polyarthritis. However, the cause and underlying molecular events of RA are not clear. Here, we applied integrated bioinformatics to identify tissue-specific expressed hub genes involved in RA and reveal potential targeted drugs.

Methods: Three expression profiles of human microarray datasets involving fibroblast-like synoviocytes (FLS) were downloaded from the Gene Expression Omnibus (GEO) database, the differentially expressed mRNAs (DEGs), miRNAs (DEMs), and lncRNAs (DELs) between normal and RA synovial samples were screened using GEO2R tool. BioGPS was used to identified tissue-specific expressed genes. Functional and pathway enrichment analyses were performed for common DEGs using the DAVID database, and the protein-protein interaction (PPI) network of common DEGs was constructed to recognize hub genes by the STRING database. Based on receiver operating characteristic (ROC) curve, we further investigated the prognostic values of tissue-specific expressed hub genes in RA patients. Connectivity Map (CMap) was run to identify novel anti-RA potential drugs. The DEM–DEG pairs and ceRNA network containing key DEMs were established by Cytoscape.

Results: We obtain a total of 418 DEGs, 23 DEMs and 49 DELs. 64 DEGs were verified as tissue-specific expressed genes, most derive from the hematologic/immune system (20/64, 31.25%). GO term and KEGG pathway enrichment analysis showed that DEGs focused primarily on immune-related biological process and NF-κB pathway. 10 hub genes were generated via using MCODE plugin. Among them, SPAG5, CUX2, and THEMIS2 were identified as tissue-specific expressed hub genes, these 3 tissue-specific expressed hub genes have superior diagnostic value in the RA samples compared with osteoarthritis (OA) samples. 5 compounds (troleandomycin, levodopa, trichostatin A, LY-294002, and levamisole) rank among the top five in connectivity score. In addition, 5 miRNAs were identified to be key DEMs, the lncRNA–miRNA–mRNA network with five key DEMs was formed. The networks containing tissue-specific expressed hub genes are as follows: ARAP1-AS2/miR-20b-3p/TRIM3, ARAP1-AS2/miR-30c-3p/FRZB.

Conclusion: This study indicates that screening for identify tissue-specific expressed hub genes and ceRNA network in RA using integrated bioinformatics analyses could help us understand the mechanism of development of RA. Besides, SPAG5 and THEMIS2 might be candidate biomarkers for diagnosis of RA. LY-294002, trichostatin A, and troleandomycin may be potential drugs for RA.
The Political Ecology of COVID-19 and Compounded Uncertainties in Marginal Environments
Authors: Mehta Lyla , Parthasarathy D. , Pickard Justin , Srivastava Shilpi
Published: March 2022

In this paper, we use a political ecology lens to look at how COVID-19 adds to a set of existing uncertainties and challenges faced by vulnerable people in the marginal environments of coastal India. Over the last few decades, local people have been systematically dispossessed from resource commons in the name of industrial, urban and infrastructure development or conservation efforts, leading to livelihood loss. We build on our current research in the TAPESTRY (https://tapestry-project.org/) project in coastal Kutch and Mumbai to demonstrate how the pandemic has laid bare structural inequalities and unequal access to public goods and natural resources. The impacts of COVID-19 have intersected with ongoing food, water and climate crises in these marginal environments, threatening already fragile livelihoods, and compounding uncertainties and vulnerabilities. Extreme weather events such as cyclones, droughts, heatwaves and floods in the last couple of decades have also compounded the problems faced in these regions, affecting seasonal migration patterns. We demonstrate how responses from “above” have been inadequate, failing to address problems, or arriving too late. Authoritarian leaders have used the pandemic to “other” and victimise certain groups and polarise society along religious lines. Lockdowns and covid restrictions have been used to surreptitiously complete environmentally destructive infrastructure projects, while avoiding resistance and opposition from affected local communities, who have also been subject to increased surveillance and restrictions on movement. While state responses have often been unpredictable and inadequate, there has been an outburst of local forms of mutual aid, solidarity, and civic action. There are also many examples of resilience at the local level, especially amongst communities that have largely relied on subsistence production. Despite the acute suffering, COVID-19 has also prompted civic groups, activists, and local communities to reflect on the possibilities for reimagining transformative pathways towards just and sustainable futures.
A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance
Authors: Ovchinnikov Victor , Karplus Martin
Published: March 2022

The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine,e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.
Diversity and Distribution of Cyatholaimidae (Chromadorida: Nematoda): A Taxonomic and Systematic Review of the World Records
Authors: Cunha Beatriz P. , Fonseca Gustavo , Amaral A. Cecilia Z.
Published: March 2022

Nematoda is a very species-rich phylum that has successfully adapted to almost all types of ecosystems. Despite their abundance and ecological importance, the taxonomic knowledge of nematodes is still limited and the identification of species is not trivial. In Cyatholaimidae, a relatively common and abundant family of free-living nematodes, the identification of organisms is challenging due to the overlap of some generic diagnoses and the absence of updated systematic reviews. Here we systematically reviewed the knowledge about the family diversity, providing a list of valid species, the diagnostic characters to genus level, and the geographical and habitat distribution of species. The review systematized a total of 619 records. The occurrences were classified into biogeographic ecoregions and habitats. Cyatholaimidae includes 211 valid species, classified in 20 genera. The genera can be differentiated based on six diagnostics characters, namely: pattern of cuticle ornamentation; number of longitudinal rows of pore-complex in cuticle; structures of the buccal cavity; presence/absence of pharyngeal bulb; pre-cloacal supplements aspect; and the shape of gubernaculum. Cyatholaimidae includes mainly marine species, mostly occurring in the Coastal Zone. Four and three species were registered in freshwater and terrestrial habitats, respectively, all classified in the genus Paracyatholaimus. About 38% of the valid species occur in more than one type of habitat, under very different environmental conditions, suggesting a broad niche. The occurrence of congeneric species in different habitats types indicates that, throughout the evolutionary history of the family, multiple ecological shift events have occurred. The family occurs worldwide in 74 ecoregions, and the majority of the records and species are in the North Sea and Western Mediterranean. Most species are endemic to one ecoregion, and examples of broadly distributed ones may be a result of misidentifications or cases of long-distance dispersal, especially for those associated with biological substrates.
Experimental Study on Microstructure Evolution and Fractal Features of Expansive Soil Improved by MICP Method
Authors: Su Huanyu , Xiao Hongbin , Li Zhenyu , Tian Xuwen , Luo Shenping , Yu Xinpei , Ouyang Qianwen
Published: March 2022

Experimental study on one-dimensional consolidation and scanning electron microscope imaging of expansive soil improved by MICP method has been carried out, by using WG type consolidator and electron scanning microscope. Theoretical analysis on microstructure evolution process of improved expansive soil has been carried out based on fractal theory and damage theory. Through the research, the influence mechanism of cementation and filling effect of calcium carbonate precipitation on the microstructure of improved soil samples such as particle size and pore characteristics is revealed. Based on fractal theory, a porosity calculation model of improved expansive soil has been established considering microstructure damage of soil. Furthermore, a fractal calculation theory of consolidation deformation of improved expansive soil has been proposed. The relevant calculation parameters have also been determined. The rationality of this calculation theory is verified by comparing the calculated results with the tested results. With these research results, a theoretical foundation for further research on microstructure evolution of expansive soil improved by MICP method has been laid. A new train of thought for quantitative research on the water stability and swell–shrink characteristics as well as strength characteristics of improved expansive soil has been provided.
MMPs Regulate Neuronal Substance P After a Painful Equibiaxial Stretch in a Co-Culture Collagen Gel Model Simulating Injury of an Innervated Ligament
Authors: Ita Meagan E. , Winkelstein Beth A.
Published: March 2022

Chronic joint pain is a major health problem that can result from abnormal loading of the innervated ligamentous capsule that surrounds synovial joints. The matrix metalloproteinases-1 (MMP-1) and MMP-9 are hypothesized pain mediators from stretch-induced injuries since they increase in pathologic joint tissues and are implicated in biomechanical and nociceptive pathways that underlay painful joint injuries. There is also emerging evidence that MMP-1 and MMP-9 have mechanistic interactions with the nociceptive neuropeptide substance P. Yet, how a ligament stretch induces painful responses during sub-failure loading and whether MMP-1 or MMP-9 modulates nociception via substance P are unknown. We used a neuron–fibroblast co-culture collagen gel model of the capsular ligament to test whether a sub-failure equibiaxial stretch above the magnitude for initiating nociceptive responses in neurons also regulates MMP-1 and MMP-9. Pre-stretch treatment with the MMP inhibitor ilomastat also tested whether inhibiting MMPs attenuates the stretch-induced nociceptive responses. Because of the role of MMPs in collagen remodeling, collagen microstructural kinematics were measured in all tests. Co-culture gels were incubated for one week in either normal conditions, with five days of ilomastat treatment, or with five days of a vehicle control solution before a planar equibiaxial stretch that imposed strains at magnitudes that induce pain in vivo and increase nociceptive modulators in vitro. Force, displacement, and strain were measured, and polarized light imaging captured collagen fiber kinematics during loading. At 24 h after stretch, immunolabeling quantified substance P, MMP-1, and MMP-9 protein expression. The same sub-failure equibiaxial stretch was imposed on all co-cultures, inducing a significant re-organization of collagen fibers (p ≤ 0.031) indicative of fiber realignment. Stretch induces a doubling of substance P expression in normal and vehicle-treated co-cultures (p = 0.038) that is prevented with ilomastat treatment (p = 0.114). Although MMP-1 and MMP-9 expression are unaffected by the stretch in all co-culture groups, ilomastat treatment abolishes the correlative relationships between MMP-1 and substance P (p = 0.002; R2 = 0.13) and between MMP-1 and MMP-9 (p = 0.007; R2 = 0.11) that are detected without an inhibitor. Collectively, these findings implicate MMPs in a painful ligamentous injury and contribute to a growing body of work linking MMPs to nociceptive-related signaling pathways and/or pain.
Limited Genomics Training Among Physicians Remains a Barrier to Genomics-Based Implementation of Precision Medicine
Authors: Schaibley Valerie M. , Ramos Irma N. , Woosley Raymond L. , Curry Steven , Hays Sean , Ramos Kenneth S.
Published: March 2022

The field of precision medicine has undergone significant growth over the past 10 years. Despite increasing applications of clinical genetic and genomic testing, studies consistently report limited knowledge of genetics and genomics among healthcare providers. This study explored barriers to the implementation of precision medicine by surveying physicians working in a large academic medical center. We assessed prior training in genetics, use of genetic testing in the clinic, desire for additional resources in genetics and genomic medicine and perceived barriers to successful integration of precision medicine. Only 20% of respondents reported moderate or extensive training in genetics. Physicians with limited or no training in genetics were less likely to have ordered a genetic test for any purpose. Furthermore, 41% of physicians responded that their lack of training identifying appropriate genetic tests and how to interpret genetic testing results was the most significant barrier to ordering genetic testing for their patients. These findings suggest that future efforts to realize the promise of precision medicine should focus on the integration of training programs for non-genetics trained healthcare providers.
Differentiation Between Malignant and Benign Pulmonary Nodules by Using Automated Three-Dimensional High-Resolution Representation Learning With Fluorodeoxyglucose Positron Emission Tomography-Computed Tomography
Authors: Lai Yung-Chi , Wu Kuo-Chen , Tseng Neng-Chuan , Chen Yi-Jin , Chang Chao-Jen , Yen Kuo-Yang , Kao Chia-Hung
Published: March 2022

Background

The investigation of incidental pulmonary nodules has rapidly become one of the main indications for 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET), currently combined with computed tomography (PET-CT). There is also a growing trend to use artificial Intelligence for optimization and interpretation of PET-CT Images. Therefore, we proposed a novel deep learning model that aided in the automatic differentiation between malignant and benign pulmonary nodules on FDG PET-CT.

Methods

In total, 112 participants with pulmonary nodules who underwent FDG PET-CT before surgery were enrolled retrospectively. We designed a novel deep learning three-dimensional (3D) high-resolution representation learning (HRRL) model for the automated classification of pulmonary nodules based on FDG PET-CT images without manual annotation by experts. For the images to be localized more precisely, we defined the territories of the lungs through a novel artificial intelligence-driven image-processing algorithm, instead of the conventional segmentation method, without the aid of an expert; this algorithm is based on deep HRRL, which is used to perform high-resolution classification. In addition, the 2D model was converted to a 3D model.

Results

All pulmonary lesions were confirmed through pathological studies (79 malignant and 33 benign). We evaluated its diagnostic performance in the differentiation of malignant and benign nodules. The area under the receiver operating characteristic curve (AUC) of the deep learning model was used to indicate classification performance in an evaluation using fivefold cross-validation. The nodule-based prediction performance of the model had an AUC, sensitivity, specificity, and accuracy of 78.1, 89.9, 54.5, and 79.4%, respectively.

Conclusion

Our results suggest that a deep learning algorithm using HRRL without manual annotation from experts might aid in the classification of pulmonary nodules discovered through clinical FDG PET-CT images.
Relationship Between C-Reactive Protein/Serum Albumin Ratio, Neutrophil/Lymphocyte Ratio, and ANCA-Associated Vasculitis Activity: A Retrospective Single Center Cohort Study
Authors: Tian Yao , Liu Na , Yin Hui , Duan Lihua
Published: March 2022

Objectives

To evaluate the role of C-reactive protein/albumin ratio (CAR), neutrophil/lymphocyte ratio (NLR), and mean platelet volume (MPV) in newly diagnosed AAV patients and examine their clinical significance.

Methods

Data from 79 untreated newly diagnosed AAV patients were collected and 76 health examination subjects were included in the healthy control group. All clinical characteristics of AAV patients were extracted from their medical records. The NLR, CAR, and MPV levels of AAV patients and the healthy controls were compared and the correlation between these markers and clinical characteristics was analyzed. Patients were then divided into two groups based on the 2003 Birmingham Vasculitis Activity Score (BVAS). The correlation between NLR, CAR, and MPV and disease activity was analyzed and their effects on the cumulative survival rate were analyzed.

Results

Compared with the healthy control group, elevated CAR, NLR, and MPV were observed in AAV patients. CAR (r = 0.701, P < 0.0001) and NLR (r = 0.369, P < 0.05) were positively correlated with the BVAS while MPV did not show any significant correlation (P = 0.85). The optimal cutoff value for disease activity evaluation using CAR was 0.80 (sensitivity: 85% and specificity: 82%, P < 0.05). The optimal cutoff value for disease activity evaluation using NLR was 5.15 (sensitivity: 66% and specificity: 72%, P < 0.05). Kaplan–Meier survival analysis revealed that the all-cause mortality rate was higher in patients with CAR ≥ 0.8 than in patients with CAR < 0.8 (P < 0.05). Patients with low NLR also showed a lower cumulative survival rate (P < 0.05).

Conclusions

NLR and CAR can reflect the inflammatory response and disease activity in AAV patients, while MPV is not significantly correlated with disease activity in AAV patients. The all-cause mortality rate was higher in patients with high CAR and NLR than in patients with low CAR and NLR.
Redox and Calcium Alterations of a Müller Cell Line Exposed to Diabetic Retinopathy-Like Environment
Authors: Rosato Clarissa , Bettegazzi Barbara , Intagliata Pia , Balbontin Arenas Maria , Zacchetti Daniele , Lanati Antonella , Zerbini Gianpaolo , Bandello Francesco , Grohovaz Fabio , Codazzi Franca
Published: March 2022

Diabetic retinopathy (DR) is a common complication of diabetes mellitus and is the major cause of vision loss in the working-age population. Although DR is traditionally considered a microvascular disease, an increasing body of evidence suggests that neurodegeneration is an early event that occurs even before the manifestation of vasculopathy. Accordingly, attention should be devoted to the complex neurodegenerative process occurring in the diabetic retina, also considering possible functional alterations in non-neuronal cells, such as glial cells. In this work, we investigate functional changes in Müller cells, the most abundant glial population present within the retina, under experimental conditions that mimic those observed in DR patients. More specifically, we investigated on the Müller cell line rMC-1 the effect of high glucose, alone or associated with activation processes and oxidative stress. By fluorescence microscopy and cellular assays approaches, we studied the alteration of functional properties, such as reactive oxygen species production, antioxidant response, calcium homeostasis, and mitochondrial membrane potential. Our results demonstrate that hyperglycaemic-like condition per se is well-tolerated by rMC-1 cells but makes them more susceptible to a pro-inflammatory environment, exacerbating the effects of this stressful condition. More specifically, rMC-1 cells exposed to high glucose decrease their ability to counteract oxidative stress, with consequent toxic effects. In conclusion, our study offers new insights into Müller cell pathophysiology in DR and proposes a novel in vitro model which may prove useful to further investigate potential antioxidant and anti-inflammatory molecules for the prevention and/or treatment of DR.