bluuebunny/crossref_metadata_2025 huggingface dataset:
Key features of tests for detection of SARS-CoV2 antibodies
Authors: Berestovskaya V. S. , Vavilova T. V. , Gubanova A. V. , Chernysh N. Yu.
Published: June 2021

On March 11, 2020, the World Health Organization recognized the outbreak of the disease COVID-19 (Coronavirus Disease 2019) and the spread of the new coronavirus (SARS-CoV-2), which caused this disease, as a pandemic. The SARS-CoV-2 virus stimulates the production of antigen-specific antibodies for which commercial tests have been developed. The issue of diagnosing antibodies to SARS-CoV-2 became especially acute together with the beginning of mass vaccination of the population. Due to the fact that the reading of the result depends on the test format, it is necessary to understand how the antigenic target, the composition of the immunoglobulins and the way of expressing the result affect its interpretation. When analyzing the literature, it was found that with COVID-19, antibodies to the nucleocapsid antigen of SARS-CoV-2 can be detected somewhat earlier than antibodies to the spike antigen; virus-neutralizing antibodies are directed to the receptor-binding domain, seroconversion of immunoglobulins M and G begins simultaneously, and tests for total antibodies are potentially more sensitive due to the ability to capture antibodies with various features of the immune response. The problem of incomparability of quantitative results obtained on different systems is also noted. These factors must be taken into account when choosing a test for detecting antibodies to SARS-CoV-2, which will adequately solve a specific clinical and epidemiological problem.
Place of serological test-systems for detection of antibodies to SARS-CoV2 in emergency cardiac surgery
Authors: Petrova O. V. , Tverdokhlebova D. K. , Nikulina D. M. , Tarasov D. G.
Published: June 2021

The article reveals the need for a comprehensive laboratory assessment of testing for antibodies to SARS-CoV-2. In progress it is focused on the possible product of laboratory testing studies of false-positive results caused by the presence of human serum antibodies in that cross reacting with SARS-CoV-2 proteins. It is concluded that in order to reduce the proportion of false positive results of the study require the use of confirmatory test.
Multimodal differential diagnostics of viral pneumonia in SARS‑CoV‑2 pandemic conditions (clinical case)
Authors: Borsukov A. V. , Morozova T. G. , Venidiktova D. Yu. , Tikhankova A. V. , Gorbatenko O. A. , Kovalyov А. A. , Tagil A. O. , Eryomkina A. V. , Bezmenova T. S.
Published: June 2021

Objective. To demonstrate the capabilities of a comprehensive instrumental multimodal differential diagnosis of viral pneumonia in the context of the COVID-19 pandemic.

Material and methods. A clinical case of a patient with complicated viral pneumonia and a detailed description of the clinical picture, laboratory information, instrumental research data using minimally invasive interventions, followed by cytological and bacteriological examination, is presented.

Results. While the patient was in the hospital, a comprehensive study was performed with a targeted assessment of the state of the chest organs and using minimally invasive diagnostic methods. The signs of bilateral pneumonia (probably of viral etiology, possibly corresponding to COVID-19 infection) revealed by ultrasound and MDCT of the chest organs were the basis for patient’s hospitalization.

Conclusion. The multimodal instrumental approach allows to obtain a more complete picture of the pathological process in patients with viral pneumonia in a short time and minimizing radiation and determine the further tactical position in the treatment of this category of patients.
Determination of reference ranges for automated platelet aggregometry on Sysmex CS‑5100 analyzer
Authors: Kovalchuk Yu. P. , Kadinskaya M. I. , Pimenov M. S. , Efimova I. Yu.
Published: June 2021

Measurement of platelet function by light transmission aggregometry (LTA) using a special device – an aggregometer requires significant time and is time-consuming. In this study, an automated LTA procedure was evaluated to establish the reference ranges. On the Sysmex CS-5100 analyzer, aggregation measurements were performed using several agonists at a certain concentration: ADP (2 µmol/L); arachidonic acid (1 mmol/L); collagen (2 µg/ml); ristocetin (1.2 mg/ml); epinephrine (5 µmol/L). For each agonist, the maximum and final aggregation, the Lag phase and the Area under the aggregation curve were measured. Reference ranges for a standard panel of activators were determined on 40 samples of healthy subjects in the concentrations recommended by the International Society on Thrombosis and Haemostasis. A standard panel of agonists can be used on Sysmex CS series analyzers: ADP, arachidonic acid; collagen; ristocetin, epinephrine, so these devices can replace specialized aggregometers or perform platelet aggregation where this investigation is not currently performed.
EDTA‑dependent pseudothrombocytopenia in child (clinical case report)
Authors: Sokolova N. A. , Savina M. I. , Shokhina O. S.
Published: June 2021

Ethylenediaminetetraacetic acid (EDTA)-dependent pseudothrombocytopenia is the phenomenon of a spurious low platelet count due to antiplatelet antibodies that cause platelet clumping in blood anticoagulated with EDTA. The aggregation of platelets in EDTA-dependent pseudothrombocytopenia is usually prevented by other anticoagulants, such as sodium citrate. EDTA-dependent pseudothrombocytopenia has never been associated with hemorrhagic diathesis or platelet dysfunction. In this article, a 2,5-year-old boy with EDTA-dependent pseudothrombocytopenia is presented because of rare presentation. We report that EDTA can induce platelet clumping, and thus spuriously low platelet counts. However, aggregation of platelets was not detected in blood samples with sodium citrate, and platelet count was normal.
Laboratory markers of premature aging and metabolic syndrome in liquidators of consequences of Chernobyl accident
Authors: Alkhutova N. A. , Kovyazina N. А. , Rybnikov V. Yu.
Published: June 2021

In this paper, the metabolic syndrome (MS) is considered as a manifestation of an excessive adaptive response of the body, which underlies premature aging. It is relevant to search for new early markers of MS formation in LPA in the context of modern ideas about the role of universal mechanisms of adaptation and stress-induced premature aging in its pathogenesis. The data obtained by the authors allow us to consider the relative androgen deficiency as a predictor of the formation of MS in LPA. The results of the study demonstrate that the levels of triiodothyronine and DHEAS serve as early markers of the formation of MS, while the testosterone/estradiol ratio is a universal laboratory indicator of accelerated aging of the body and MS.
Visualisation System of COVID-19 Data in Malaysia
Authors: KHAN REHMAN ULLAH , SYAMIMI NOR SYAZA , MAMBANG CLADIA SIMBUT ANAK , THOMAS IVY ANAK , WEE TZI NI
Published: June 2021

Pandemics are highly unlikely events, therefore, we need a system to understand the statistics about the pandamic. Machine learning algorithms can analyse the data and then we can plan for handling the pandamic. To date, many people are suffering because of the lack of reliable information system. The problem is that there is no integrated system to use the data and plan for pandemic management to minimise social panic. This study aims to provide a system, using COVID-19 data as a sample to visualise and analyse cases, deaths, discharged ICU cases updates in Malaysia as a whole state wise of COVID-19 daily statistics. The results provide visualisation and case comparison among states in Malaysia to easily and quickly understand the situation. This will help and assist the management in decision-making.
Implementation Strategy of Digital Marketing Tourism Bus Rental Satisfaction in the New Era of Normality
Authors: Savitri Shela Indah , Kharisma Indri , Hadistia Ananda
Published: June 2021

Purpose of study to find out and describe the attitudes and responses of businessman regarding the PO Juragan 99 tourism bus rental business in the new era of normality, to find out and describe the related digital marketing strategies in the PO Juragan 99 tourism bus rental and to find out and describe the extent of the implications of the digital marketing strategy on bus rental PO Juragan 99 in the new era of normality to achieve customer satisfaction This study uses a qualitative method. The qualitative method by Miles which consists of three streams of activity occurring simultaneously, which includes data reduction, data presentation, and drawing conclusions or verification used in this study. Primary data is the main data or base used in this reasearch. The main data obtained from this research is primary data because it is directly from the respondent's data. Data taken from interviews, observation and documentation. Data analysis was performed using 4 (four) stages, namely data collection, data reduction, data presentation and conclusion drawing. The output produced in this study is a journal. Theoretically, the results of this research will add to the repertoire of knowledge, especially in the field of developing digital marketing strategies for businessman.
Problems Experienced by Family Physicians in Sivas during the Pandemic Period and Its Relationship with COVID-19 Fear
Authors: Karahan Seher , Agadayi Ezgi , Yilmaz Irfan Gazi
Published: June 2021

Aim: To determine the COVID-19 fear level of family physicians during the pandemic working in Sivas and its relationship to their experienced problems.

Methods: This descriptive study was delivered to 225 family physicians in Sivas between December-January 2021 via an online survey containing 24 questions of participants' sociodemographic data, the problems they experienced in family medicine, and the COVID-19 Fear Scale. Descriptive statistics and logistic regression analysis were used to analyze thedata.

Results: A total of 138 family physicians whose mean age was 37.6±7.3, with 52.2 % males and 47.8% females, included. Participants’ 16.7% had the COVID-19 infection. COVID-19 Fear Scale mean score of 18.3±6.5, appearing significantly higher in females (19.6±5.8) than in males (17.2±6.9). 28.3% of subjects needed taking professional psychological support, on which increase of working period in family medicine and COVID-19 Fear Scale Score and being single had a positive effect. Also, 86.2% experienced primary health care services problems, most frequently ranked as cancer screening, mobile service, and chronic illness follow-up.

Conclusion: Necessary psychosocial support should be provided to all healthcare workers, especially family physicians, during the pandemic. So, we recommend authorities take proper precautions to continue without interruption for primary preventive health services.

Keywords: COVID-19, fear, family practice, COVID-19, fear, primary care physicians
Active Botanical Biofiltration in Built Environment to Maintain Indoor Air Quality
Authors: Mannan Mehzabeen , Al-Ghamdi Sami G.
Published: June 2021

The implementation of sustainable solutions for maintaining indoor air quality has become a particular concern to the building community. Research on green technologies for indoor air has highlighted the potential of active botanical biofiltration (ABB) systems, where the air is circulated through the plant root zone as well as the growing medium for maximum phytoremediation effect. ABB has been found beneficial for pollutant removal along with the potential for increasing humidity and air cooling. Assessment in laboratory condition revealed the removal efficiency of ABB systems ranged from 54 to 85% for total suspended particulate matters where gaseous pollutants such as formaldehyde and toluene removal efficiencies were 90% and over 33%, respectively, in real environment. Moreover, the esthetic value of ABB acts as an added benefit for positive mental effects. However, very limited data is available to date that demonstrates the pollutant removal efficiency of ABB systems in realistic indoor environments, and the mechanisms behind this emerging technology are still poorly understood. The purpose of this mini review study is to present a quantitative assessment of the recent advancement of ABB systems and indoor air quality. Finally, the limitations of ABB systems and research gaps are highlighted for future improvement.
3D-STED Super-Resolution Microscopy Reveals Distinct Nanoscale Organization of the Hematopoietic Cell-Specific Lyn Substrate-1 (HS1) in Normal and Leukemic B Cells
Authors: Sampietro Marta , Zamai Moreno , Díaz Torres Alfonsa , Labrador Cantarero Veronica , Barbaglio Federica , Scarfò Lydia , Scielzo Cristina , Caiolfa Valeria R.
Published: June 2021

HS1, the hematopoietic homolog of cortactin, acts as a versatile actin-binding protein in leucocytes. After phosphorylation, it is involved in GTPase and integrin activation, and in BCR, TCR, and CXCR4 downstream signaling. In normal and leukemic B cells, HS1 is a central cytoskeletal interactor and its phosphorylation and expression are prognostic factors in chronic lymphocytic leukemia (CLL) patients. We here introduce for the first time a super-resolution imaging study based on single-cell 3D-STED microscopy optimized for revealing and comparing the nanoscale distribution of endogenous HS1 in healthy B and CLL primary cells. Our study reveals that the endogenous HS1 forms heterogeneous nanoclusters, similar to those of YFP-HS1 overexpressed in the leukemic MEC1 cell line. HS1 nanoclusters in healthy and leukemic B cells form bulky assemblies at the basal sides, suggesting the recruitment of HS1 for cell adhesion. This observation agrees with a phasor-FLIM-FRET and STED colocalization analyses of the endogenous MEC1-HS1, indicating an increased interaction with Vimentin at the cell adhesion sites. In CLL cells isolated from patients with poor prognosis, we observed a larger accumulation of HS1 at the basal region and a higher density of HS1 nanoclusters in the central regions of the cells if compared to good-prognosis CLL and healthy B cells, suggesting a different role for the protein in the cell types analyzed. Our 3D-STED approach lays the ground for revealing tiny differences of HS1 distribution, its functionally active forms, and colocalization with protein partners.
Effects of Matrix pH on Spontaneous Transient Depolarization and Reactive Oxygen Species Production in Mitochondria
Authors: Aklima Jannatul , Onojima Takumi , Kimura Sawako , Umiuchi Kanji , Shibata Takahiro , Kuraoka Yusho , Oie Yoshiki , Suganuma Yoshiki , Ohta Yoshihiro
Published: June 2021

Reactive oxygen species (ROS) oxidize surrounding molecules and thus impair their functions. Since mitochondria are a major source of ROS, suppression of ROS overproduction in the mitochondria is important for cells. Spontaneous transient depolarization of individual mitochondria is a physiological phenomenon widely observed from plants to mammals. Mitochondrial uncoupling can reduce ROS production; therefore, it is conceivable that transient depolarization could reduce ROS production. However, transient depolarization has been observed with increased ROS production. Therefore, the exact contribution of transient depolarization to ROS production has not been elucidated. In this study, we examined how the spontaneous transient depolarization occurring in individual mitochondria affected ROS production. When the matrix pH increased after the addition of malate or exposure of the isolated mitochondria to a high-pH buffer, transient depolarization was stimulated. Similar stimulation by an increased matrix pH was also observed in the mitochondria in intact H9c2 cells. Modifying the mitochondrial membrane potential and matrix pH by adding K+ in the presence of valinomycin, a K+ ionophore, clarified that an increase in the matrix pH is a major cause of ROS generation. When we added ADP in the presence of oligomycin to suppress the transient depolarization without decreasing the matrix pH, we observed the suppression of mitochondrial respiration, increased matrix pH, and enhanced ROS production. Based on these results, we propose a model where spontaneous transient depolarization occurs during increased proton influx through proton channels opened by increased matrix pH, leading to the suppression of ROS production. This study improves our understanding of mitochondrial behavior.
HFS-SLPEE: A Novel Hierarchical Feature Selection and Second Learning Probability Error Ensemble Model for Precision Cancer Diagnosis
Authors: Meng Yajie , Jin Min
Published: June 2021

The emergence of high-throughput RNA-seq data has offered unprecedented opportunities for cancer diagnosis. However, capturing biological data with highly nonlinear and complex associations by most existing approaches for cancer diagnosis has been challenging. In this study, we propose a novel hierarchical feature selection and second learning probability error ensemble model (named HFS-SLPEE) for precision cancer diagnosis. Specifically, we first integrated protein-coding gene expression profiles, non-coding RNA expression profiles, and DNA methylation data to provide rich information; afterward, we designed a novel hierarchical feature selection method, which takes the CpG-gene biological associations into account and can select a compact set of superior features; next, we used four individual classifiers with significant differences and apparent complementary to build the heterogeneous classifiers; lastly, we developed a second learning probability error ensemble model called SLPEE to thoroughly learn the new data consisting of classifiers-predicted class probability values and the actual label, further realizing the self-correction of the diagnosis errors. Benchmarking comparisons on TCGA showed that HFS-SLPEE performs better than the state-of-the-art approaches. Moreover, we analyzed in-depth 10 groups of selected features and found several novel HFS-SLPEE-predicted epigenomics and epigenetics biomarkers for breast invasive carcinoma (BRCA) (e.g., TSLP and ADAMTS9-AS2), lung adenocarcinoma (LUAD) (e.g., HBA1 and CTB-43E15.1), and kidney renal clear cell carcinoma (KIRC) (e.g., IRX2 and BMPR1B-AS1).
Synthesis of New 1H-1,2,3-Triazole Analogs in Aqueous Medium via “Click” Chemistry: A Novel Class of Potential Carbonic Anhydrase-II Inhibitors
Authors: Avula Satya Kumar , Khan Majid , Halim Sobia Ahsan , Khan Ajmal , Al-Riyami Samia Ahmed , Csuk Rene , Das Biswanath , Al-Harrasi Ahmed
Published: June 2021

A series of novel 1H-1,2,3-triazole analogs (9a–j) were synthesized via “Click” chemistry and Suzuki–Miyaura cross-coupling reaction in aqueous medium. The compounds were evaluated for their carbonic anhydrase-II enzyme inhibitory activity in vitro. The synthesis of triazole 7a was accomplished using (S)-(-) ethyl lactate as a starting material. This compound (7a) underwent Suzuki–Miyaura cross-coupling reaction with different arylboronic acids in aqueous medium to afford the target molecules, 9a–j in good yields. All newly synthesized compounds were characterized by 1H NMR, 13C NMR, FT-IR, HRMS, and where applicable 19F NMR spectroscopy (9b, 9e, 9h, and 9j). The new compounds have shown moderate inhibition potential against carbonic anhydrase-II enzyme. A preliminary structure-activity relationship suggested that the presence of polar group at the 1H-1,2,3-triazole substituted phenyl ring in these derivatives (9a–j) has contributed to the overall activity of these compounds. Furthermore, via molecular docking, it was deduced that the compounds exhibit inhibitory potential through direct binding with the active site residues of carbonic anhydrase-II enzyme. This study has unraveled a new series of triazole derivatives as good inhibitors against carbonic anhydrase-II.
The Research of G–Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes
Authors: Zhu Yanhong , Li Zhongkui , Wang Pengfei , Qiu Qi–Ming , Ma Hongwei , Li Hui
Published: June 2021

A detailed understanding of the mismatched base-pairing interactions in DNA will help reveal genetic diseases and provide a theoretical basis for the development of targeted drugs. Here, we utilized mononucleotide fragment to simulate mismatch DNA interactions in a local hydrophobic microenvironment. The bipyridyl-type bridging ligands were employed as a mild stabilizer to stabilize the GG mismatch containing complexes, allowing mismatch to be visualized based on X-ray crystallography. Five single crystals of 2′-deoxyguanosine–5′–monophosphate (dGMP) metal complexes were designed and obtained via the process of self-assembly. Crystallographic studies clearly reveal the details of the supramolecular interaction between mononucleotides and guest intercalators. A novel guanine–guanine base mismatch pattern with unusual (high anti)–(high anti) type of arrangement around the glycosidic angle conformations was successfully constructed. The solution state 1H–NMR, ESI–MS spectrum studies, and UV titration experiments emphasize the robustness of this g–motif in solution. Additionally, we combined the methods of single-crystal and solution-, solid-state CD spectrum together to discuss the chirality of the complexes. The complexes containing the g–motif structure, which reduces the energy of the system, following the solid-state CD signals, generally move in the long-wave direction. These results provided a new mismatched base pairing, that is g–motif. The interaction mode and full characterizations of g–motif will contribute to the study of the mismatched DNA interaction.
Prognostic Value of Right Ventricular 3D Speckle-Tracking Strain and Ejection Fraction in Patients With HFpEF
Authors: Meng Yuanli , Zhu Shuangshuang , Xie Yuji , Zhang Yanting , Qian Mingzhu , Gao Lang , Li Meng , Lin Yixia , Wu Wenqian , Wang Jing , Yang Yali , Lv Qing , Zhang Li , Li Yuman , Xie Mingxing
Published: June 2021

Background: Right ventricular longitudinal strain of free wall (RV FWLS) assessed by two-dimensional speckle-tracking echocardiography (2D-STE) is recognized as an independent predictor of poor prognosis in patients with heart failure with preserved ejection fraction (HFpEF). However, the prognostic implications of three-dimensional STE (3D-STE) parameters in patients with HFpEF have not been well-established. The purpose of our study was to determine whether 3D-STE parameters were the more powerful predictors of poor outcomes in HFpEF patients compared with 2D-STE indices.

Methods: Eighty-one consecutive patients with HFpEF were studied by 2D-STE and 3D-STE. RV volumes, ejection fraction (EF) and 3D-RVFWLS were measured by 3D-STE. 2D-RVFWLS was determined by 2D-STE. Patients were followed for the primary end point of heart failure (HF)-related hospitalization and death for HF.

Results: After a median follow-up period of 17 months, 39 (48%) patients reached the end point of cardiovascular events. Compared with HFpEF patients without end-point events, those with end-point events had lower RVEF and 3D-RVFWLS (P < 0.05). Separate multivariate Cox regression analyses revealed that 3D-RVFWLS (HR 5.73; 95% CI 2.77–11.85; P < 0.001), RVEF (HR 3.47; 95% CI 1.47–8.21; P = 0.005), and 2D-RVFWLS (HR 3.17; 95% CI 1.54–6.53; P = 0.002) were independent predictors of adverse outcomes. The models with 3D-RVFWLS (AIC = 246, C-index = 0.75) and RVEF (AIC = 247, C-index = 0.76) had similar predictive performance for future clinical events as with 2D-RVFWLS (AIC = 248, C-index = 0.74).

Conclusions: 3D-STE parameters are powerful predictors of poor outcomes, providing a similar predictive value as 2D-STE indices in patients with HFpEF. These findings support the potential of RV 3D-STE to identify HFpEF patients at higher risk for adverse cardiac events.
Submarine Active Faults and Morpho-Tectonics Around the Iberian Margins: Seismic and Tsunamis Hazards
Authors: Somoza Luis , Medialdea Teresa , Terrinha Pedro , Ramos Adrià , Vázquez Juan-Tomás
Published: June 2021

The aim of this work is to make a synthesis at regional scale focused on the geophysical characterization of submarine faults around the Iberian margin to identify active structures and analyze their development in the framework of the present plate organization. Most of these submarine faults show seabed morphological expressions mapped with high-resolution swath bathymetry data, high-resolution parametric sub-bottom profiles and multichannel seismic profiles. Present active tectonics, deformation, seismicity, and tsunami-affected coastal areas is mainly focused on south Iberia at the Eurasian and Nubia plate boundary. Submarine active faults in these areas are represented by long strike-slip fault systems and arcuate fold-thrust systems. Their development takes place in response to present NW-SE convergence between the Eurasian and Nubia plates. We propose a strain partitioning model of the plate boundary into simple and pure shear zones to explain the distribution and mechanisms of active submarine faults along the Gulf of Cádiz, Gibraltar Arc and Alborán Sea in response to the present-day shear stress orientation. Nevertheless, deformation is also focused in the NW Iberian margin. Thus, along the Galician and Portuguese margin, several submarine faults mapped as thrust fault systems with high-seismic activity along the Iberian ocean-continent transition reflect the re-activation of former structures. We suggest that submarine active faults in the NW and W Iberia are also the response to the eastwards transfer of short-offset transform faults of the Mid Atlantic Ridge into the oceanic Iberian along a weakness as the former plate boundary between the oceanic Iberia and Eurasia domains. The distribution and activity of submarine faults mapped in this work from geophysical and bathymetric data are in good agreement with geodetic data and focal mechanisms.
Monochromatic Long-Period Seismicity Prior to the 2012 Earthquake Swarm at Little Sitkin Volcano, Alaska
Authors: Haney Matthew M. , Buurman Helena , Holtkamp Stephen , McNutt Stephen R.
Published: June 2021

Detection of the earliest stages of unrest is one of the most challenging and yet critically needed aspects of volcano monitoring. We investigate a sequence of five unusual long-period (LP) earthquakes that occurred in the days prior to the onset of a months-long volcano-tectonic (VT) earthquake swarm beneath Little Sitkin volcano in the Aleutian Islands during late 2012. The long-period earthquakes had two distinctive characteristics: their signals were dominated by a monochromatic spectral peak at approximately 0.57 Hz and they had impulsive P and S-wave arrivals on a seismometer located on Amchitka Island 80 km to the southeast of the volcano. In each case, the monochromatic earthquakes ended with a higher-frequency event after approximately 2 min of duration. We find evidence that the five monochromatic LP earthquakes resulted from the resonance of a tabular magma body at middle crustal depths (15 km) on the western side of Little Sitkin. Based on the resonant frequency and quality factor of the monochromatic LP earthquakes, we infer the magma body to have a lateral extent of 500 m and a thickness of 9 m. We interpret that a magmatic intrusion excited the monochromatic LP earthquakes and subsequently increased the stress beneath the volcano, leading to the onset of the shallow (<10 km depth) VT swarm five days later.
Covid-19 (in) a Class of Its Own: Student and Teacher Musings Regarding Their Learnings and Well-Being when Moving a Large Blended First Year Class Virtually Overnight
Authors: Trafford Julie , Haxell Ailsa , Lau Kelvin , Carlson Gema , Rebelo da Silva Ana Patricia , Hart Andrew , De Freitas Thais Regina , Rope Sheridan
Published: June 2021

Covid-19 is (in) a class of its own in its influence on human lives and livelihoods globally, precipitating steep learning and psychological well-being curves for university teachers and students. This has impacted dramatically on the conditions under which higher education has had to function in regard to research and what is now referred to as ‘emergency online education’. As staff face unprecedented challenges, so too do students. Given that the consequences of these times are likely to be felt well into the future, it is important to capture what is happening now. We therefore present this perspective piece comprising 13 musings co-authored by students and educators regarding our experiences of two lockdowns within Aotearoa New Zealand in 2020 representative of the disrupted university in its adjustment to learning and teaching. In contributing to calls to develop a post-pandemic pedagogy for higher education, and better support staff and student well-being, we draw on methods that would multiply questions and invoke possibilities, as an impetus for reimagining higher education. Making use of a cogenerative dialoguing process, these musings enable multiple voices to be heard and considered. A non-representational lens enables us to explore the what and how of Covid-19 creating disruption and uncertainty for students’ and educators, influencing their psychological well-being and higher education pedagogy and practices, and becoming a contextually relevant taonga (treasure) of experiences that might inform future educational activities.
Clinical Characteristics and Risk of Diabetic Complications in Data-Driven Clusters Among Type 2 Diabetes
Authors: Xing Lin , Peng Fangyu , Liang Qian , Dai Xiaoshuang , Ren Junli , Wu Han , Yang Shufen , Zhu Yaxin , Jia Lijing , Zhao Shancen
Published: June 2021

Background

This study aimed to cluster newly diagnosed patients and patients with long-term diabetes and to explore the clinical characteristics, risk of diabetes complications, and medication treatment related to each cluster.

Research Design and Methods

K-means clustering analysis was performed on 1,060 Chinese patients with type 2 diabetes based on five variables (HbA1c, age at diagnosis, BMI, HOMA2-IR, and HOMA2-B). The clinical features, risk of diabetic complications, and the utilization of elven types of medications agents related to each cluster were evaluated with the chi-square test and the Tukey–Kramer method.

Results

Four replicable clusters were identified, severe insulin-resistant diabetes (SIRD), severe insulin-deficient diabetes (SIDD), mild obesity-related diabetes (MOD), and mild age-related diabetes (MARD). In terms of clinical characteristics, there were significant differences in blood pressure, renal function, and lipids among clusters. Furthermore, individuals in SIRD had the highest prevalence of stages 2 and 3 chronic kidney disease (CKD) (57%) and diabetic peripheral neuropathy (DPN) (67%), while individuals in SIDD had the highest risk of diabetic retinopathy (32%), albuminuria (31%) and lower extremity arterial disease (LEAD) (13%). Additionally, the difference in medication treatment of clusters were observed in metformin (p = 0.012), α-glucosidase inhibitor (AGI) (p = 0.006), dipeptidyl peptidase 4 inhibitor (DPP-4) (p = 0.017), glucagon-like peptide-1 (GLP-1) (p <0.001), insulin (p <0.001), and statins (p = 0.006).

Conclusions

The newly diagnosed patients and patients with long-term diabetes can be consistently clustered into featured clusters. Each cluster had significantly different patient characteristics, risk of diabetic complications, and medication treatment.
General Optimization Model of Modular Equipment Selection and Serialization for Shale Gas Field
Authors: Hong Bingyuan , Li Xiaoping , Cui Xuemeng , Gao Jingjing , Li Yu , Gong Jing , Liu Huanying
Published: June 2021

The potential technical and economic advantages and flexible operability of modular equipment make it increasing widely used in gas field production and development. In addition to considering the manufacturing process, the selection and serialization of modular equipment should be made according to the productivity prediction of a gas well, so as to meet the field demand to the greatest extent and enhance the flexibility of gathering and transportation system. This article proposes a method to determine the use planning of modular equipment in shale gas field. Considering the processing capacity, processing cost, floor area, construction cost of modular equipment, and the changes of market supply and demand, an optimization model is established. On the basis of the abovementioned model, the method of serialization of modular equipment is proposed. The effectiveness of the model is verified by an actual case study. It is proved that the model can optimize the layout of modular equipment, make the modular equipment run efficiently and economically, reduce costs, and increase efficiency. This study provides a reference for optimizing the equipment management strategy and promoting green production practice of shale gas production.
Dynamics of Community Biomass and Soil Nutrients in the Process of Vegetation Succession of Abandoned Farmland in the Loess Plateau
Authors: Gu Menghe , Liu Shulin , Duan Hanchen , Wang Tao , Gu Zhong
Published: June 2021

The interaction between vegetation and soil is important for vegetation restoration and reconstruction during the succession of abandoned farmland. We chose four kinds of abandoned farmlands with the time of 1, 6, 12, and 22 years to experiment in the Loess Plateau. The community composition, community biomass, and soil nutrients of the four kinds of abandoned farmlands were studied by the method of temporal–spatial alternation, and the interaction effects among vegetation, biomass, soil nutrients, and abandonment time were analyzed. The results showed there were 33 species belonging to 13 families during the succession and 15 species of Gramineae and Compositae, accounting for 47% of the total community species. The succession trend of abandoned farmland was as follows: The vegetation was the weed community of Heteropappus altaicus + Artemisia capillaris in the beginning of the abandonment stage and became the weed community of Tragus racemosus + Enneapogon borealis after 6 years of abandonment. Then, Leymus secalinus became the dominant population in the community after 12 years of abandonment. When the succession lasted for 22 years, the vegetation became a common advantageous community of Stipa breviflora and Cleistogenes songorica. Soil moisture (SM) was positively correlated with soil nutrients and negatively correlated with abandonment time and community biomass. Soil organic matter (SOM), soil total nitrogen (STN), and alkali hydrolyzable nitrogen (AHN) were the highest in 0–10 cm soil layer, showing obvious surface accumulation. The three decreased with the soil layer, and there was a positive correlation among them. The abandonment time had a positive effect on the above-ground biomass (AGB) and below-ground biomass (BGB) and a negative effect on the SOM, STN, and AHN. The root/shoot ratio (R/S) was positively correlated with SOM and negatively correlated with abandonment time. With the progress of succession, the hierarchical differentiation of the community was gradually obvious, and the community structure begun to complicate. The community better adapted to the arid environment and toward the local top community succession.
Will Climate Change Exacerbate the Economic Damage of Flood to Agricultural Production? A Case Study of Rice in Ha Tinh Province, Vietnam
Authors: Giang Pham Quy , Vy Tran Trung
Published: June 2021

In developing countries in general and in Vietnam in particular, flood induced economic loss of agriculture is a serious concern since the livelihood of large populations depends on agricultural production. The objective of this study was to examine if climate change would exacerbate flood damage to agricultural production with a case study of rice production in Huong Son District of Ha Tinh Province, North-central Vietnam. The study applied a modeling approach for the prediction. Extreme precipitation and its return periods were calculated by the Generalized Extreme Value distribution method using historical daily observations and output of the MRI-CGCM3 climate model. The projected extreme precipitation data was then employed as an input of the Mike Flood model for flood modeling. Finally, an integrated approach employing flood depth and duration and crop calendar was used for the prediction of potential economic loss of rice production. Results of the study show that in comparison with the baseline period, an increase of 49.14% in the intensity of extreme precipitation was expected, while the frequency would increase 5 times by 2050s. As a result, the seriousness of floods would increase under climate change impacts as they would become more intensified, deeper and longer, and consequently the economic loss of rice production would increase significantly. While the level of peak flow was projected to rise nearly 1 m, leading the area of rice inundated to increase by 12.61%, the value of damage would rise by over 21% by 2050s compared to the baseline period. The findings of the present study are useful for long-term agricultural and infrastructural planning in order to tackle potential flooding threats to agricultural production under climate change impacts.
Comparison of Resampling Algorithms to Address Class Imbalance when Developing Machine Learning Models to Predict Foodborne Pathogen Presence in Agricultural Water
Authors: Weller Daniel Lowell , Love Tanzy M. T. , Wiedmann Martin
Published: June 2021

Recent studies have shown that predictive models can supplement or provide alternatives to E. coli-testing for assessing the potential presence of food safety hazards in water used for produce production. However, these studies used balanced training data and focused on enteric pathogens. As such, research is needed to determine 1) if predictive models can be used to assess Listeria contamination of agricultural water, and 2) how resampling (to deal with imbalanced data) affects performance of these models. To address these knowledge gaps, this study developed models that predict nonpathogenic Listeria spp. (excluding L. monocytogenes) and L. monocytogenes presence in agricultural water using various combinations of learner (e.g., random forest, regression), feature type, and resampling method (none, oversampling, SMOTE). Four feature types were used in model training: microbial, physicochemical, spatial, and weather. “Full models” were trained using all four feature types, while “nested models” used between one and three types. In total, 45 full (15 learners*3 resampling approaches) and 108 nested (5 learners*9 feature sets*3 resampling approaches) models were trained per outcome. Model performance was compared against baseline models where E. coli concentration was the sole predictor. Overall, the machine learning models outperformed the baseline E. coli models, with random forests outperforming models built using other learners (e.g., rule-based learners). Resampling produced more accurate models than not resampling, with SMOTE models outperforming, on average, oversampling models. Regardless of resampling method, spatial and physicochemical water quality features drove accurate predictions for the nonpathogenic Listeria spp. and L. monocytogenes models, respectively. Overall, these findings 1) illustrate the need for alternatives to existing E. coli-based monitoring programs for assessing agricultural water for the presence of potential food safety hazards, and 2) suggest that predictive models may be one such alternative. Moreover, these findings provide a conceptual framework for how such models can be developed in the future with the ultimate aim of developing models that can be integrated into on-farm risk management programs. For example, future studies should consider using random forest learners, SMOTE resampling, and spatial features to develop models to predict the presence of foodborne pathogens, such as L. monocytogenes, in agricultural water when the training data is imbalanced.
Bioinformatics-Based Identification of Tumor Microenvironment-Related Prognostic Genes in Pancreatic Cancer
Authors: Chen Shaojie , Huang Feifei , Chen Shangxiang , Chen Yinting , Li Jiajia , Li Yaqing , Lian Guoda , Huang Kaihong
Published: June 2021

Objective

Growing evidence has highlighted that the immune and stromal cells that infiltrate in pancreatic cancer microenvironment significantly influence tumor progression. However, reliable microenvironment-related prognostic gene signatures are yet to be established. The present study aimed to elucidate tumor microenvironment-related prognostic genes in pancreatic cancer.

Methods

We applied the ESTIMATE algorithm to categorize patients with pancreatic cancer from TCGA dataset into high and low immune/stromal score groups and determined their differentially expressed genes. Then, univariate and LASSO Cox regression was performed to identify overall survival-related differentially expressed genes (DEGs). And multivariate Cox regression analysis was used to screen independent prognostic genes and construct a risk score model. Finally, the performance of the risk score model was evaluated by Kaplan-Meier curve, time-dependent receiver operating characteristic and Harrell’s concordance index.

Results

The overall survival analysis demonstrated that high immune/stromal score groups were closely associated with poor prognosis. The multivariate Cox regression analysis indicated that the signatures of four genes, including TRPC7, CXCL10, CUX2, and COL2A1, were independent prognostic factors. Subsequently, the risk prediction model constructed by those genes was superior to AJCC staging as evaluated by time-dependent receiver operating characteristic and Harrell’s concordance index, and both KRAS and TP53 mutations were closely associated with high risk scores. In addition, CXCL10 was predominantly expressed by tumor associated macrophages and its receptor CXCR3 was highly expressed in T cells at the single-cell level.

Conclusions

This study comprehensively investigated the tumor microenvironment and verified immune/stromal-related biomarkers for pancreatic cancer.
Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues
Authors: Overbey Eliah G. , Ng Theros T. , Catini Pietro , Griggs Lisa M. , Stewart Paul , Tkalcic Suzana , Hawkins R. David , Drechsler Yvonne
Published: June 2021

While the chicken (Gallus gallus) is the most consumed agricultural animal worldwide, the chicken transcriptome remains understudied. We have characterized the transcriptome of 10 cell and tissue types from the chicken using RNA-seq, spanning intestinal tissues (ileum, jejunum, proximal cecum), immune cells (B cells, bursa, macrophages, monocytes, spleen T cells, thymus), and reproductive tissue (ovary). We detected 17,872 genes and 24,812 transcripts across all cell and tissue types, representing 73% and 63% of the current gene annotation, respectively. Further quantification of RNA transcript biotypes revealed protein-coding and lncRNAs specific to an individual cell/tissue type. Each cell/tissue type also has an average of around 1.2 isoforms per gene, however, they all have at least one gene with at least 11 isoforms. Differential expression analysis revealed a large number of differentially expressed genes between tissues of the same category (immune and intestinal). Many of these differentially expressed genes in immune cells were involved in cellular processes relating to differentiation and cell metabolism as well as basic functions of immune cells such as cell adhesion and signal transduction. The differential expressed genes of the different segments of the chicken intestine (jejunum, ileum, proximal cecum) correlated to the metabolic processes in nutrient digestion and absorption. These data should provide a valuable resource in understanding the chicken genome.
Using Genetic Variants to Evaluate the Causal Effect of Plasma Phospholipid Fatty Acids on Breast Cancer and Prostate Cancer: A Mendelian Randomization Study
Authors: Yang Ze , Li Jingjia , Sun Yandi , Qu Zihao , Lin Yindan , Zhang Lihong , He Qian , Jia Xueyao , Ahmad Mashaal , Zhang Xueyun , Luo Yan
Published: June 2021

Background

Observational studies indicate that phospholipid fatty acids (FAs) have an impact on the etiology in cancers, but the results are conflicting. We aimed to investigate the causal association of phospholipid FAs with breast cancer and prostate cancer.

Methods

Fourteen single nucleotide polymorphisms (SNPs) were selected as instrumental variables to predict the level of 10 phospholipid FAs from Genome-wide association studies (GWAS). We obtained the summary statistics for the latest and largest GWAS datasets for breast cancer (113,789 controls and 133,384 cases) and prostate cancer (61,106 controls and 79,148 cases) from the Breast Cancer Association Consortium (BCAC) and Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium. Two-sample Mendelian randomization analysis was applied.

Results

The results demonstrate that the 10 individual plasma phospholipid FAs are not significantly associated with breast cancer risk and prostate cancer risk.

Conclusion

The evidence is insufficient to support the causal association of the 10 individual plasma phospholipid FAs with breast cancer and prostate cancer.
Segregation Analysis of Genotyped and Family-Phased, Long Range MHC Classical Class I and Class II Haplotypes in 5 Families With Type 1 Diabetes Proband in the United Arab Emirates
Authors: Tay Guan K. , Al Naqbi Halima , Mawart Aurélie , Baalfaqih Zahrah , Almaazmi Anoud , Deeb Asma , Alsafar Habiba
Published: June 2021

The classical Human Leucocyte Antigen (HLA) class II haplotypes of the Major Histocompatibility Complex (MHC) that are associated with type 1 diabetes (T1D) were identified in five families from the United Arab Emirates (UAE). Segregation analyses were performed on these 5 families with the disease, 3 with one child and 2 with 2 children diagnosed with T1D. Three HLA-DR4 haplotypes were identified: HLA- DRB1∗04:01:01-DQB1∗03:02:01:01; HLA- DRB1∗04:02:01- DQB1∗03:02:01; and HLA -DRB1∗04:05:01-DQB1∗02:02:01:02. All have previously been identified to be associated with T1D in studies of the Arabian population. In the 10 parents from the 5 families, 9 had at least one HLA-DR4 and HLA-DR3 haplotype which potentially increases the risk of T1D. Of these 9 parents, 3 were heterozygous for HLA-DR4/HLA-DR3 and one was homozygous for HLA-DR3. Two haplotypes that were identified here extend to the HLA class I region were previously designated AH8.2 (HLA -A∗26-B∗08-DRB1∗03) and AH50.2 (HLA -C∗06-B∗50-DRB1∗03:01-DQ∗02) and associated with diabetes in neighboring North Indian populations. This study provides examples of MHC haplotype analysis in pedigrees to improve our understanding of the genetics of T1D in the understudied population of the UAE.