bluuebunny/crossref_metadata_2025 huggingface dataset:
CALCULATED EVALUATION OF THE DEGREE OF SUBSOLIDUS STRUCTURE COMPLEXITY OF THE PHYSICO-CHEMICAL THREE-COMPONENT SYSTEMS
Authors: Sergey Mikhailovich Logvinkov  , Oksana Nikolaevna Borisenko  , Nataliіa Sergeevna Tsapko  , Galina Nikolaevna Shabanova  , Alla Nikolaevna Korohodska  , Vita Nikolaevna Shumejko  , Olena Gaponova
Published: July 2022

The study of state diagrams of multicomponent physicochemical systems is the most science-intensive task of materials science. Without knowledge about the structure of the state diagrams of such systems, it is impossible for technologists to predict the phase composition of materials during their production and use of products from them; the systematic analysis of the results of experimental studies to optimize the properties of the materials being developed becomes much more complicated. In refractory technology, the defining stage of production is solid-phase sintering, which makes the information on the subsolidus structure of state diagrams of physicochemical systems represented by a set of components in accordance with the planned phase composition of materials particularly important. Three-component systems, the simple components of which are refractory oxides, constitute the physicochemical basis of most mass-produced refractories and their subsolidus structure is quite clearly displayed in the concentration triangle of the system by a set of triangles, the vertices of which are the points of the composition of the compounds. The study is devoted to the establishment of an analytical relationship between the number of double and triple compounds and the number of all possible segments of connecting lines between the points of the composition of the connections, as well as the points of intersection of the compounds between themselves. During the research, the general principles of systems analysis, logical methods and terminology of physicochemical analysis of multicomponent systems, as well as information on elementary mathematics from the sections on numerical series, the basics of combinatorics and algebra were used. The corresponding analytical expressions make it possible to calculate the quantitative classification characteristics in the taxonomy of multicomponent systems by the degree of complexity of the structure of their subsolidus regions, in particular, when comparing the complexity of studies of three-component oxide systems and their typification. The formulas obtained were tested for calculations using examples of specific oxide systems. The research results allow one to obtain important quantitative characteristics for assessing the degree of complexity of the subsolidus structure of three-component systems.
Sediment Provenance Studies of the Calcasieu Ship Channel, Louisiana : A Synopsis Report
Authors: Perkey David W. , Priestas Anthony M. , Corbino Jeffrey M. , Brown Gary L. , Hartman Michael A. , Tarpley Danielle R. N. , Phu V. Loung
Published: July 2022

To maintain the navigability of the Calcasieu Ship Channel (CSC), the US Army Corps of Engineers annually dredges millions of cubic yards of sediment from the inland channel. To assess sources of channel shoaling, a previous study examined river and bankline erosion as inputs. Results from that study accounted for approximately 20% of dredged volumes. Through the support of the Regional Sediment Management Program, a follow-up investigation reviewed prior sediment budgets, identified potential missing sediment sources, modeled potential sediment pathways, and utilized geochemical fingerprinting to discern primary shoaling sources to the channel. The missing sediment sources from the original budget include coastally derived sediment from the Gulf of Mexico and terrestrially derived sediment from Lake Calcasieu and surrounding wetlands. Results from geochemical fingerprinting of various potential sediment sources indicate the Calcasieu River and the Gulf of Mexico are primary contributors of sediment to the CSC, and sediments sourced from bankline erosion, Lake Calcasieu bed, and interior wetlands are secondary in nature. These results suggest that engineering solutions to control shoaling in the CSC should be focused on sources originating from the Gulf of Mexico and river headwaters as opposed to Lake Calcasieu, channel banklines, and surrounding wetlands.
Discussion of Laya et al. (2021), Dissolution of ooids in seawater-derived fluids - an example from Lower Permian re-sedimented carbonates, West Texas, USA [Sedimentology 68(6), 2671-2706]
Authors: Granier Bruno R.C. , Kendall Christopher G. St.
Published: July 2022

This discussion reassesses earlier interpretations of calcareous turbidites from the subsurface Spraberry Formation of the Happy Field (Garza County, NW Texas). It is based on routine petrographic analyses with a standard microscope. The succession of diagenetic products in this deep water setting were a little initial cementation by low magnesian calcite (LMC) and then the partial or complete leaching of both aragonite and high magnesian calcite (HMC) allochems facilitated by the presence of a residual primary intergranular porosity. This contradicts Laya et al.'s (2021) claim that cementation left no residual intergranular porosity so further leaching of the ooids would not have been possible. Instead the study made for this discussion with the same thin sections found residual primary intergranular porosity remains as evidenced by some of their photomicrographs. Most thin sections with porous grainstones have 1) collapsed molds that exhibit evidence of little initial cementation and 2) measured permeability values that range from some mD to some tens of mD. Isopachous LMC cements occur in almost all thin sections lining the margins of most intergranular pores. As these cements do not fully fill the pores, there is permeable well-connected residual primary porosity with no significant LMC cement in the secondary moldic porosity. Compaction affects the allochems and, where these are partially leached, intergranular and moldic porosities. Dissolution of aragonite (a major component) and HMC (possibly a minor component) was probably not coeval. The order of paragenetic sequence of this discussion study was: 1) LMC cementation; 2) aragonite leaching facilitated by oxidation of the organic matter in the "biocrystals" of bioclasts and oolitic cortices; 3) compactional brecciation, which was first mechanical, and then chemical causing local collapse of the molds of some of the largest pores. It was governed by cementation initially in a shallow burial diagenetic setting and then leaching whereas chemical compaction marks a slightly deeper burial diagenetic setting. The final event was marked by oil migration into the Happy Field reservoirs, freezing the calcium carbonate diagenesis. The theory of Laya et al. (2021) of the leaching of ooids in directly "seawater-derived fluids" is unsupported by the paragenetic sequence described above.
A larger benthic foraminiferal zonation for the Eocene of the Caribbean and central American region
Authors: Mitchell Simon F. , Robinson Edward , Özcan Ercan , Jiang Mark M. , Robinson Natalie
Published: July 2022

We have undertaken a study of the larger benthic foraminifera (LBF) of the Eocene of Jamaica that involved collecting free specimens and calibrating their occurrence against chronostratigraphy using calcareous nannofossils identified from sample splits or adjacent samples. The results have been plotted stratigraphically and allow a detailed zonation of the Eocene (14 zones) to be developed based largely on lepidocyclinids and similar forms. The zonation can be shown to be applicable to the Americas extending from northern South America, to Central America, the Caribbean and southern North America. The LBF biostratigraphy is based on the evolution of various groups. Three zones are recognized in the Ypresian, six zones in the Lutetian, three zones in the Bartonian, and two zones in the Priabonian. In order to classify the LBF we have revised the important groups used for the zonation scheme that occur in the Eocene and figure numerous examples. Our revision rearranges described genera into evolutionary, monophyletic clades to which we give the hierarchy of family and subfamily. We provide remarks on published taxa explaining how they are recognized and describe all the new taxa (two families, one subfamily, four genera and five species). The following families, genera and species are new: Butterliniana gen. nov., Helicosteginidae fam. nov., Helicostegina minor sp. nov., Helicostegina jamaicensis sp. nov., Helicostegina jeannemairae sp. nov., Pseudolepidinidae fam. nov., Orbitoininae subfam. nov., Planorbitoinella gen. nov., Polyorbitoinella gen. nov., Polyorbitoinella lilyfieldensis sp. nov., Orbitoina wrighti sp. nov., and Nephronummulites gen. nov.
A Prognostic Model for Death in COVID-19 Patients Presenting to the Emergency Room: The Added Value of Computed Tomography.
Authors: Besutti Giulia , Ottone Marta , Fasano Tommaso , Pattacini Pierpaolo , Iotti Valentina , Spaggiari Lucia , Bonacini Riccardo , Nitrosi Andrea , Bonelli Efrem , Canovi Simone , Colla Rossana , Zerbini Alessandro , Massari Marco , Lattuada Ivana , Ferrari Anna Maria , Rossi Paolo Giorgi ,   Reggio Emilia COVID-19 Working group
Published: July 2022

Objective: The added value of CT in prognostic models for coronavirus disease 2019 (COVID-19) patients is unclear. The aim of this study was to develop a prognostic model for death in COVID-19 patients using clinical and CT variables.Methods: Consecutive patients who presented to the emergency room between February 27 and March 23, 2020 for suspected COVID-19, underwent chest CT, and had a positive swab within 10 days were included in this retrospective study. Age, sex, comorbidities, days from symptom onset, and laboratory data were retrieved from institutional information systems. CT disease extension was visually graded as < 20%, 20-39%, 40-59%, or ≥ 60%. The association between clinical and CT variables with death was estimated with univariable and multivariable Cox proportional hazards models; model performance was assessed using k-fold cross-validation for the area under the ROC curve (CvAUC).Results: Of the 866 included patients (median age 59.8, women 39.2%), 93 (10.74%) died. Clinical variables significantly associated with death in multivariable model were age, male sex, HDL cholesterol, dementia, heart failure, vascular diseases, time from symptom onset, neutrophils, LDH, and oxygen saturation level (SO2). CT disease extension was also independently associated with death (HR=7.56, 95% CI=3.49; 16.38 for ≥ 60% extension). CvAUCs were 0.927 (bootstrap bias corrected-95%CI=0.899-0.947) for the clinical model and 0.936 (bootstrap bias corrected-95%CI=0.912-0.953) when adding CT extension.Conclusions: A prognostic model based on clinical variables is highly accurate in predicting death in COVID-19 patients. Adding CT disease extension to the model scarcely improves its accuracy.
Unique Glutelin Expression Patterns and Seed Endosperm Structure Facilitate Glutelin Accumulation in Polyploid Rice Seed
Authors: Gan Lu , Huang Baosheng , Song Zhaojian , Zhang Yachun , Zhang Yujie , Chen Si , Tong Liqi , Wei Zhisong , Yu Lingxiang , Luo Xiangbo , Zhang Xianhua , Cai Detian , He Yuchi
Published: July 2022

Background: Polyploidy is an evolutionary trajectory in plants, which is prevalent in nature and confers advantages, such as robust growth, fruit enlargement, and enhancement of stress tolerance and nutrient content. Total protein and glutelin contents in tetraploid rice seeds increased significantly when compared with contents in diploid rice. Additionally, rice is not only a food resource but also a source of high-quality protein. Therefore, enhancing glutelin by polyploidization is an attractive strategy for enhancing the nutritional value of rice seeds and presents a great potential for enhancing the commercial value of rice.Results: To enhance the nutritional value of rice, we developed tetraploid rice and evaluated the contents of various nutrient elements in mature seeds. The results revealed a significant increase in protein contents, including the total seed storage proteins, glutelins, and amino acids in tetraploid rice when compared to those in diploid rice. Tandem mass tag-based quantitative proteomic analyses of seeds revealed that glutelins regulated by GluA-1, GluA-2, GluA-3, GluB-2, GluB-4, GluB-5, and GluD-1 in 9311-4x were significantly up-regulated (≥ 1.5 fold), which were further verified by immunoblot analyses. In addition, temporal expression patterns of various glutelin subunits in rice seeds with various ploidy levels were investigated to determine the effect of polyploidization on the synthesis and accumulation of glutelins. Quantitative real-time PCR and immunoblot analyses revealed that the expression patterns of glutelin genes in tetraploid rice (9311-4x) varied from those in diploid rice (9311-2x) at different filling stages, such as the initial time, duration, and relative levels of the genes. Cytohistological analyses revealed that the thickness of aleurone cell layers increased significantly by 32% in tetraploid rice, the structures of PSVs in sub-aleurone cells were more diverse and abundant than in diploid rice. Conclusion: Genome duplication influenced the molecular and cytological characteristics of rice seed, resulting in an increase in glutelin content and total storage proteins, which could provide new insights into the enhancement of the nutritional quality of rice seeds by polyploid breeding.
The Gut Microbiome as a Promising Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma
Authors: Otoshi Takehiro , Nagano Tatsuya , Park Jonguk , Hosomi Koji , Yamashita Tomoya , Tachihara Motoko , Tabata Tokiko , Sekiya Reina , Tanaka Yugo , Kobayashi Kazuyuki , Mizuguchi Kenji , Itoh Tomoo , Maniwa Yoshimasa , Kunisawa Jun , Nishimura Yoshihiro
Published: July 2022

Background: The gut microbiome plays an important role in the immune system and has attracted attention as a new biomarker of various diseases, including cancer. As such, in this study, we examined the relationship between the gut microbiome and lung cancer progression. In addition, we assessed the correlation between the gut microbiome and epidermal growth factor receptor (EGFR) mutation status.Methods: Female never-smokers diagnosed with lung adenocarcinoma were consecutively enrolled between May 2018 and August 2019. Fecal samples were collected within 1 month before or after diagnosis and before administration of any lung cancer treatment. Principal coordinate analyses were performed using Bray-Curtis distance matrices to investigate the effects of clinical variables (age, body mass index, Tumor-Node-Metastasis stage, T category, N category, M category, primary tumor size, performance status, and EGFR mutation status) on the gut microbial community. A correlation analysis was also performed to determine the strength of association between the dominant taxonomy (comprising ≥1% of the relative abundance of bacterial DNA sequences) and clinical variables.Results: A total of 37 patients were enrolled. T category and primary tumor size were significantly correlated with the gut microbial community (p=0.018 and 0.041, respectively). At the genus level, a significant positive correlation was observed between the relative abundance of Faecalibacterium and both T category (correlation coefficient, R=0.51, p=0.0013) and primary tumor size (R=0.37, p=0.024), whereas a significant negative correlation was observed between the relative abundances of Fusicatenibacter and Bacteroides and T category (R=−0.35, p=0.034 and R=−0.32, p=0.05, respectively) and primary tumor size (R=−0.36, p=0.029 and R=−0.41, p=0.012, respectively). EGFR mutation status had no statistically significant effect on the gut microbial community (p=0.11). However, the relative abundances of Bifidobacterium and Faecalibacterium were significantly higher in EGFR mutation–negative patients than EGFR mutation–positive patients (p=0.012 and 0.041), whereas the relative abundance of Blautia was significantly lower in EGFR mutation–negative patients (p=0.036).Conclusions: This is the first study identifying the gut microbiome as a promising biomarker of lung cancer progression. Further elucidation of the role of the gut microbiome in lung cancer progression could facilitate development of new treatments for lung cancer.
Developing a Tailored Implementation Action Plan for A Suicide Prevention Clinical Intervention in an Australian Mental Health Service: A Qualitative Study Using the EPIS Framework.
Authors: Zbukvic Isabel , Rheinberger Demee , Rosebrock Hannah , Lim Jaclyn , McGillivray Lauren , Mok Katherine , Stamate Eve , McGill Katie , Shand Fiona , Torok Michelle , Moullin Joanna C
Published: July 2022

Background: Tailoring implementation strategies to local contexts is a promising approach to supporting implementation and sustainment of evidence-based practices in health settings. While there is increasing research on tailored implementation of mental health interventions, implementation research on suicide prevention interventions is limited. This study aimed to evaluate implementation and subsequently develop a tailored action plan to support implementation, sustainment and scale-up of an evidence-based suicide prevention intervention - Collaborative Assessment and Management of Suicidality (CAMS) - in an Australian public mental health service.Methods: This study took place within a larger randomised stepped-wedge design suicide prevention trial. Approximately 150 mental health staff working within a regional and remote community Local Health District in Australia were trained in CAMS. Semi-structured interviews and focus groups with frontline staff and clinical leaders were conducted to examine barriers and facilitators to using CAMS. Data were analysed using a reflexive thematic analysis approach and mapped to the Exploration, Preparation, Implementation and Sustainment (EPIS) framework. This was followed by stakeholder engagement to design a tailored implementation action plan based on a ‘tailored blueprint’ methodology.Results: A total of 22 barriers to implementing CAMS were identified. Based on the perceived impact on implementation fidelity and the feasibility of addressing identified barriers, six barriers were prioritised for addressing through an implementation plan. These barriers were mapped to evidence-based implementation strategies and, in collaboration with local health district staff, goals and actionable steps for each strategy were generated. This information was combined into a tailored implementation plan to support the sustainable use of CAMS as part of routine care within this mental health service. Conclusions: This study provides an example of a collaborative approach to tailoring strategies for implementation on a large scale. Novel insights were obtained into the challenges of evaluating the implementation process and barriers to implementing an evidence-based suicide prevention treatment approach within a geographically large and varied mental health service in Australia.Trial registration: This study was conducted as part of the LifeSpan suicide prevention trial. Trial registration for LifeSpan in Australia New Zealand Clinical Trials Register, ID: ACTRN12617000457347. Prospectively registered on 28 March 2017.
Correlation-driven organic 3D topological insulator with relativistic fermions
Authors: Nomoto Tetsuya , Imajo Shusaku , Akutsu Hiroki , Nakazawa Yasuhiro , Kohama Yoshimitsu
Published: July 2022

Exploring new topological phenomena and functionalities induced by strong electron correlation has been a central issue in modern condensed-matter physics. One example is a topological insulator (TI) state and its functionality driven by the Coulomb repulsion rather than a spin-orbit coupling. Here, we report a ‘correlation-driven’ TI state realized in an organic zero-gap system α-(BETS)2I3. The surface metallic state that emerges at low temperatures exhibits characteristic transport properties of a gapless Dirac semimetal, evidencing the presence of a topological surface state in this compound. Moreover, we observe a topological phase switching between the TI state and non-equilibrium Dirac semimetal state by a dc current, which is a unique functionality of a correlation-driven TI state. Our findings demonstrate that correlation-driven TIs are promising candidates not only for practical electronic devices but also as a field for discovering new topological phenomena and phases.
Does Medicaid Broaden the Choices of Patients with Low Socioeconomic Status? An Analysis of Bypassing Behaviors in Brooklyn
Authors: Lee Jae Bok
Published: July 2022

Background: Many governments worldwide have committed to extending choices in public service delivery. However, the extent to which policies ensure equity is unclear. We investigated whether Medicaid programs in the United States improve hospital accessibility among patients with low socioeconomic status, compared to those with non-low socioeconomic status who are non-Medicaid recipients or uninsured.Methods: We employed a difference-in-difference-in-differences approach using a rich dataset of information on inpatients and their choice of hospitals from Statewide Planning Research and Cooperative System and information on hospitals from the American Hospital Association in Brooklyn, New York, from 2003 to 2009Results: The findings indicated that Medicaid has failed to broaden the range of the hospital choices for patients with low socioeconomic status, assessed in terms of bypassing behaviors. Conclusions: Medicaid is a public program that offers choices driven by purchasing power. The findings of this study imply that this program has some limitations in alleviating existing socioeconomic inequities in available hospital choices.
A Combination Approach of Pseudotime Analysis And Mathematical Modeling For Understanding The Drug-Resistant Mechanisms
Authors: Magi Shigeyuki , Ki Sewon , Ukai Masao , Domínguez-Hüttinger Elisa , Naito Atsuhiko , Suzuki Yutaka , Okada Mariko
Published: July 2022

Cancer cells acquire drug resistance through the following nonresistant, pre-resistant, and resistant stages. Although the molecular mechanism of drug resistance is well investigated, the process of drug resistance acquisition remains largely unknown. Here we elucidate the molecular mechanisms underlying the process of drug resistance acquisition by sequential analysis of gene expression patterns in tamoxifen-treated breast cancer cells. Single-cell RNA-sequencing indicates that tamoxifen-resistant cells can be subgrouped into two, one showing altered gene expression related to metabolic regulation. The other showed high expression levels of adhesion-related molecules and histone-modifying enzymes. Pseudotime analysis showed a cell transition trajectory to the two resistant subgroups that stem from a shared pre-resistant state. An ordinary differential equation model based on the trajectory fitted well with the experimental results of cell growth. Based on the established model, it was predicted and experimentally validated that inhibition of transition to both resistant subtypes would prevent the appearance of tamoxifen resistance.
Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study
Authors: Bao Renren , Mei Qing , Yang Tianjun , Zhang Lei , Zhu Chunyan , Fan Xiaoqin , Wang Yinzhong , Tong Fei , He Yuxi , Fang Xiaowei , Geng Shike , Yang Yu , Sheng Ximei , Pan Aijun
Published: July 2022

Objectives: To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used. Methods: In this retrospective, nested, case-control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n=53) were matched at a ratio of 1 to 2 (n=106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient’s prognosis of the two groups were compared. Results: An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P=0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P=0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P=0.024). However, there were no significant differences in ICU mortality or 28-day mortality. Conclusions: We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.
Sirt1 regulates microglial activation and inflammation following oxygen-glucose deprivation/reoxygenation injury by targeting the Shh/Gli-1 signaling pathway
Authors: Liao Hongyan , Huang Jiagui , Liu Jie , Zhu Huimin , Chen Yue , Li Xuemei , Wen Jun , Yang Qin
Published: July 2022

Background: Cerebral ischemic injury leads to over-activation of microglia, which release pro-inflammatory factors that deteriorate neurological function during the acute phase of stroke. Thus, inhibiting microglial over-activation is crucial for reducing ischemic injury. Sirtuin 1 (Sirt1) has been shown to play a critical role in stroke, neurodegenerative diseases and aging. However, the effect of Sirt1 on the regulation of microglial activation following cerebral ischemic injury, as well as the underlying mechanism, remain unclear. The aim of the present study was to examine the effect of Sirt1 on oxygen-glucose deprivation/reoxygenation (OGD/R)-treated N9 microglia following treatment with the Sirt1 agonists resveratrol and SRT1720 and the Sirt1 antagonist sirtinol. Methods: Cell viability, Apoptosis, activation and inflammatory responses of microglia, expressions and activity of Shh signaling pathway proteins were detected by Cell Counting Kit 8, Flow Cytometry, immunocytochemistry, ELISA, and Western blotting, respectively.Results: The results demonstrated that treatment with resveratrol or SRT1720 could inhibit the activation of microglia and inflammation during OGD/R. Moreover, these treatments also led to the translocation of the GLI family zinc finger-1 (Gli-1) protein from the cytoplasm to the nucleus and upregulated the expression of Sonic hedgehog (Shh), Patched homolog-1 (Ptc-1), smoothened frizzled class receptor and Gli-1. By contrast, the inhibition of Sirt1 using sirtinol had the opposite effect. Conclusions: These findings suggested that Sirt1 may regulate microglial activation and inflammation by targeting the Shh/Gli-1 signaling pathway following OGD/R injury.
Low Energy Consumption Routing Protocol for Oil and Gas Pipeline Internet of Things
Authors: Liu Miao , Liu Yangyang , Yao Rong , Sun Zhenxing
Published: July 2022

For ensuring effective monitoring oil and gas pipelines deployed in the field or arears with poor environment, the wireless sensor network with flexibility, scalability and ease installation has become the basis of the Oil and Gas Pipeline Internet of Things (OGP-IoT). The energy limitation of sensor nodes is the key factor to restrict the performance of OGP-IoT. In addition, the end-to-end delay of the network determines the response time of OGP-IoT to pipeline accidents. It is also the key parameter to improve the real-time performance of OGP-IoT. For solving the problems of energy limitation and end-to-end delay, the Pipeline Internet of Things—Low Energy Consumption Routing Protocol (PIoT-LERP) is proposed in the paper. It can realize the energy balance of the Internet of Things by taking the remaining energy of nodes and the distance between nodes and aggregation nodes as the index of selecting candidate forwarding nodes. So, the life of network is extended and the end-to-end delay of the network is reduced by decreasing the number of data transmission hops. The simulation results show that PIoTLERP can effectively improve the network performance by extending the network life and reducing the network delay comparing with the classical opportunistic routing protocols ExOR and RE-OR.
A novel method for handling missing data in health care real-world study: Optimal Intact Subset Method
Authors: Wu Jingxian , Chang huan , Tong Rongsheng , Wu Xingwei
Published: July 2022

Background
Handling missing data is indispensable in health care real-world data processing. Deleting or imputing missing data may introduce error or lead to multicollinearity. Therefore, we tried to explore a novel missing data processing method to avoid the above issues.
Method
By exploring an optimal deleting way of columns and rows with missing data, we developed a missing data processing method which can retain most information of original datasets. Traditionally, the goal can be realized by traversing all possible deleting combinations. But the computational cost is too high to use in large datasets. Therefore, we established an Optimal Intact Subset Method (OIS.Method) by using an indicator containing missing information of both columns and rows to determine an optimal deleting order of columns. OIS.Method can ascertain the optimal deleting way and simplify computing meanwhile. In order to validate the effectiveness of OIS.Method, we compared OIS.Method with five other data-imputation methods in 700 classification datasets (simulated datasets 1) generated by computer. In order to simulate real-world datasets, we generated simulated datasets 2: introducing redundant variables in simulated datasets 1. We also compared OIS.Method with control methods on that. Finally, we validated OIS.Method in two real-world classification tasks: 1. predict the risk of hypotension during dialysis, 2. predict the risk of drug adverse reaction in elderly patients with type 2 diabetes.
Results
In simulated datasets 1, we found that OIS.Method performed well when the distribution of missing data was unbalanced among columns. In simulated datasets 2, the comprehensive performance of OIS.Method was better in all evaluating dimensions. In two real-world datasets, OIS.Method could acquire better classification performance. We used the area under ROC curve (AUC) to evaluate it: OIS.Method VS Simple Impute VS Random Forest VS Modified Random Forest, 0.8179 ± 0.0005VS0.8116 ± 0.0002VS0.8087 ± 0.0009VS0.8093 ± 0.0014 in task1, and 0.7028VS0.6963VS0.6957VS0.6699 in task2.
Conclusions
Our study provided a novel method for handing missing data in real-world study. Compared with other existing missing data processing methods, the calculation of OIS.Method is smaller, and OIS.Method can reflect the true data situation of original datasets. Moreover, OIS.Method is well-suited for real-world datasets with large sample size and multiple variables.
Insilco Vaccine Design of spike and hemagglutinin esterase proteins of Bovine Coronavirus
Authors: Awadelkareem Eman Ali , S Hamdoun
Published: July 2022

Background: Bovine coronavirus (BCoV) is a widespread, fatal illness in cattle that has a large economic impact in particularly disease-prone hosts. BCoV does not have an effective vaccine. As a result, the objective of this study was to use immunoinformatics and computational tools to design a multi-epitope vaccine against Spike and haemagglutinin proteins of Bovine coronavirus. BCoV proteins were also subjected to protein analysis.Methods: A variety of tools of bioinformatics were used for data analysis. Conserved B and T cell epitopes against BCoV target proteins were predicted using the Immune Epitope Database (IEDB). Proteins were characterized utilizing a variety of servers, including Protparam, PSIPRED and the GOR IV servers. The antigenicity, allergenicity, and toxicity of the anticipated epitopes were assessed as well. Results: Several MHCI epitopes were predicted from S and HE proteins. As top epitopes, the peptides 77NMALKGTLL85 and 56SYMDLNPAL65 were proposed from Spike and hemagglutinin proteins, respectively. These epitopes exhibited high scores of antigenicity, no allergenicity, no toxicity, and a strong connection to Bola alleles.Moreover, three epitopes (1204YYYPE1208, 379TCQPQ384, and 720QLQPINY726) from Spike glycoprotein were selected as surface, linear, and antigenic epitopes using B cell scales. The methods dropped to anticipate effective and safe epitope (s) to cover all B cell scales from HE protein. Conclusion: Three B cell epitopes (1204YYYPE1208, 379TCQPQ384, and 720QLQPINY726) were predicted from Spike protein (S) of BCoV only. MHC I epitopes of S and HE proteins of BCoV (77NMALKGTLL85 and 56SYMDLNPAL65) were shown to have a strong link to Bola alleles, as well as high antigenicity and safety. The predicted epitopes' activity should be tested experimentally as a multi-epitope vaccine against BCoV using in vitro and in vivo trials.
Accumulation of Toxic and Essential Elements in Patients with Gastrointestinal Carcinoma from Pakistan
Authors: Qayyum Muhammad Abdul , Mahmood Mian H.R. , Muddassir Khawaja , shahzad Muhammad , Shad Naveed Akhtar , Hussain Nazim , Ahmad Muhammad
Published: July 2022

The authors have requested that this preprint be removed from Research Square.
Elongin BC complex negatively regulates AXL and marks a differentiated phenotype in melanoma
Authors: Peeper Daniel , Schieven Sebastiaan , Traets Joleen , Vliet Alex , Baalen Martijn , Song Ji-Ying , Kuilman Thomas
Published: July 2022

High expression of the receptor tyrosine kinase AXL is implicated in epithelial-to-mesenchymal transition, cancer progression and therapy resistance. For example, AXL is abundant in BRAF mutant melanomas progressing on targeted BRAF/MEK inhibition. Therefore, AXL is thought to represent an attractive therapeutic target. This notwithstanding, little is known about the mechanisms governing expression of AXL. Here, we describe a fluorescence-activated cell sorting (FACS)-based whole genome-wide CRISPR-Cas9 screen to uncover regulators of AXL expression. We identified several genes, inactivation of which led to increased AXL expression. Most remarkable was the identification of five components that associate with the Elongin B/C heterodimer. The Elongin B/C heterodimer engages in multiple protein-protein interactions, including the transcription factor complex subunit Elongin A, the von Hippel-Lindau (VHL) tumor suppressor protein, and members of the SOCS-box protein family. The screen identified ELOB, ELOC, SOCS5, UBE2F and RNF7, each of which we demonstrate to serve as an inhibitor of AXL expression. Although the AXL promoter contains hypoxia response elements and Elongin B/C are found in the VHL complex, Elongin B/C unexpectedly regulate AXL independently of hypoxia. Instead, we demonstrate that the Elongin BC complex interacts with AXL through ELOB, and contributes to proteasomal AXL turnover. RNA-sequencing analysis of several melanoma datasets revealed a negative association between Elongin B/C and dedifferentiation. This was confirmed by immunohistochemistry in patient-derived melanoma xenografts. These results uncover the Elongin BC complex as a key determinant of AXL expression in melanoma, and that this correlates with a differentiated state.
Environmental Impact Assessment of Air-Purifying Paver Blocks Using Photocatalysis and Sensors Technology
Authors: Partheeban Pachaivannan , Christopher Chella Gifta , Anuradha Baskaran , Keerthana Sureshbabu , Haripriya Nagaraju
Published: July 2022

Air pollution is a major problem in India, and vehicular emissions cause about 27% of air pollution in urban areas. The major pollutants released from vehicles are carbon monoxide, carbon dioxide, nitrous oxide, photochemical oxidants, etc. The present investigation emphasizes the utilization of power plant waste materials effectively to replace the natural fine aggregate, leads to a new dimension of manufacturing concrete paver blocks. M-sand is replaced by bottom ash from 50–100%, and natural coarse aggregate is replaced with recycled coarse aggregates. Materials such as titanium dioxide (TiO2) and recycled glass particles are also incorporated to improve the photodegradation of air pollutants. Concrete paver blocks were prepared and tested, and the compressive strength of the various mixes were compared with other research works. Real-time air quality is monitored using an Internet of Things (IoT) device developed to assess the performance of paver blocks laid on the roadside. The results concluded that bottom ash could be replaced with natural fine aggregate and recycled coarse aggregate can be replaced with natural coarse aggregate. Real time study results of air quality monitoring IoT device concluded that the pollution concentrations have been reduced up to 50%.
Widely-conserved transcription factors regulate symbiosis-specific NCR genes
Authors: Zhang Senlei , Wang Ting , Lima Rui , Pettkó-Szandtner Aladár , Kereszt Attila , Downie J. Allan , Kondorosi Eva
Published: July 2022

Symbiotic nitrogen fixation by rhizobium bacteria within the cells of legume root nodules alleviates the need for nitrogen fertilizers. Nitrogen fixation requires the endosymbionts to differentiate into bacteroids and this can be reversible or terminal. The latter is controlled by the plant, is more beneficial and has evolved in a large clade of the legume family. The plant effectors of terminal differentiation are Nodule-specific Cysteine-Rich NCR peptides, which are absent in legumes such as soybean where there is no terminal differentiation of rhizobia. It was assumed that NCRs coevolved with specific transcription factors, but our work demonstrates that expression of NCR genes does not require NCR-specific transcription factors. Introduction of the Medicago truncatula NCR169 gene under its own promoter into soybean roots resulted in nodule-specific expression of NCR169, leading to bacteroid changes associated with terminal differentiation. We identified two AT-Hook Motif Nuclear Localized (AHL) transcription factors from both M. truncatula and soybean nodules that bound to AT-rich sequences in the NCR169 promoter inducing its expression. Whereas mutation of NCR169 arrested bacteroid development at a late stage, the absence of MtAHL1 or MtAHL2 completely blocked bacteroid differentiation indicating that they also regulate other NCR genes required for development of nitrogen-fixing nodules. Regulation of NCRs by orthologous transcription factors in non-IRLC legumes opens the possibility of increasing the efficiency of nitrogen fixation in legumes lacking NCRs.
Characteristics of Visual Function in Children with Cerebral Palsy and Mental Retardation in Urban Beijing
Authors: Tao Jun , Hao Rui , Guo Yatu , Zhang Wei
Published: July 2022

BackgroundMost children with cerebral palsy and mental retardation cannot express independently, parents or guardians usually ignored the visual impairment. To investigate the ocular development and characteristics of visual function of children with cerebral palsy and mental retardation in special schools in Beijing's Chaoyang District.MethodsA total of 160 children (320 eyes) with cerebral palsy and mental retardation, including 86 boys and 74 girls, aged between 6 and 18 years old were included in this study. Subjective far vision, objective far vision (electrophysiological sweep VEP), near stereopsis, diopter, anterior segment, and fundus were examined. Statistical analysis was performed on the data obtained from children of different age groups, genders, degrees of intellectual impairment, and different etiology.Results156 eyes (54.93%) were greater than or equal to 20/40 for subjective far vision, 259 eyes (84.09%) were greater than or equal to 20/40 for objective far vision, 214 eyes with ametropia (70.39%), 94 eyes with astigmatism (30.92%), 8 eyes with hyperopia (2.63%), 112 eyes with myopia (36.84%), and 8 children with glasses, which was a correction rate of 7.69%, 192 eyes needed glasses to correct, which is an uncorrected rate of 92.31%. 64 children had strabismus (40%), 8 children had a color weakness (5%), and 24 children had nystagmus (15%). 72 children (64.29%) had 100″and less, while 40 children (35.71%) had between 200″ and 900″in the near stereopsis test. There were no significant differences in subjective far vision, objective far vision, corrected vision, diopter, and near stereopsis acuity among various degrees of mental retardation,various pathogenys and two age groups.ConclusionThe prevalence of abnormal visual function in children with cerebral palsy and intellectual disability was significantly higher than in typically developing children. Some of children with cerebral palsy and intellectual disability may have visual pathway damage, in a condition known as central visual impairment. Severe intellectual disability caused by craniocerebral diseases had the worst visual function, which undoubtedly demands significant attention of caregivers and the entire society.Fund Program: National Natural Science Foundation of China (81800861)Key Programme: Tianjin Key Research and Development Plan Science and Technology Support (19YFZCSY00990)
Xerostomia in Dialysis Patients – Oral Care to Reduce Hyposalivation, Dental Biofilms and Gingivitis in Patients with Terminal Renal Insufficiency: A Randomized Clinical Study
Authors: Egbring Leonie C. , Lang Tomas , Kreft Burkhard , Gaengler Peter , Weich Karl W.
Published: July 2022

Objectives Dialysis patients suffer from xerostomia based on hyposalivation even in stimulated saliva testing. It was, therefore, the aim (i) to evaluate an optimized oral hygiene system with an oral care gel on oral dryness, dental plaque control and number of gingivitis teeth, (ii) to document the efficacy in a randomized controlled trial with dental indices and (iii) to record the individual oral health related quality of life.MethodsAfter ethical approval (EC-UWH 103/2019) 44 dialysis patients signed informed consent and were divided into two groups followed up for four weeks. Subjects of the verum group A were taking daily oral care gel OROFAN® based on biopolymers with mild antibacterial and saliva stimulating action. They were compared to control group B executing routine oral hygiene with conventional dentifrice and toothbrushes. Oral Health Impact Profile was documented at baseline and at end of study.ResultsTwenty two subjects were allocated to group A and to group B. At baseline there were no statistical differences concerning renal insufficiency (years on dialysis, complications), systemic diseases, dental background (caries experience, periodontal diseases, plaque index, number of gingivitis teeth). All subjects exhibited hyposalivation (< 0.7-1.0 ml/min).The control group B showed no statistical differences from baseline to end of study in dry mouth parameters, in all dental plaque and inflammation indices, and in the Oral Health Impact Profile. In contrast, verum group A exhibited highly significant (p<0.001) decrease of xerostomia frequency, of number of gingivitis teeth and of plaque index. Oral Health Impact Profile improved considerably (p<0.01).Significance of ResultsTerminally ill patients may gain better oral health and, consequently, improved quality of live by rather simple oral care including long lasting, eatable anti-inflammatory oral hygiene gel and dentist`s devotion.
Improving genetic risk prediction across diverse population by disentangling ancestry representations
Authors: Gyawali Prashnna , Guen Yann Le , Liu Xiaoxia , Tang Hua , Zou James , He Zihuai
Published: July 2022

Risk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from participants with similar (mostly European) ancestry. This can lead to biases in the risk predictors resulting in poor generalization when applied to minority populations and admixed individuals such as African Americans. To address this bias, largely due to the prediction models being confounded by the underlying population structure, we propose a novel deep-learning framework that leverages data from diverse population and disentangles ancestry from the phenotype-relevant information in its representation. The ancestry disentangled representation can be used to build risk predictors that perform better across minority populations. We applied the proposed method to the analysis of Alzheimer’s disease genetics. Comparing with standard linear and nonlinear risk prediction methods, the proposed method substantially improves risk prediction in minority populations, including admixed individuals, without needing self-reported ancestry information.
Exciton-assisted low-energy magnetic excitations in a photoexcited Mott insulator on the square lattice
Authors: Tsutsui Kenji , Shinjo Kazuya , Sota Shigetoshi , Tohyama Takami
Published: July 2022

Photoexcitation of a Mott insulator on a square lattice has weakened the intensity of both single- and two-magnon as observed in time-resolved resonant-inelastic x-ray scattering and time-resolved Raman scattering. However, the spectral change in low-energy regions below the magnons has not been clarified so far. To uncover the nature of photoinduced low-energy magnetic excitations of the Mott insulator, we numerically investigate transient magnetic dynamics in a photoexcited half-filled Hubbard model on the square lattice. After turning off a pump pulse tuned for an absorption edge, new magnetic signals clearly emerge well below magnon energy in both single- and two-magnon excitations. We find that the low-energy excitations are predominantly created via excitonic states at the absorption edge. These exciton-assisted magnetic excitations may provide a possible explanation for low-energy spectral weight in a recent time-resolved two-magnon Raman scattering experiment for insulating YBa2Cu3O6.1.
LncRNA MALAT1/calpain-1 axis in ATO/hypoxia induced hERG channel deficiency
Authors: Li Baoxin , Yan Caichuan , Li Yuexin , Li Yang , Zhang Yuhao , Guo Jiamengyi , Yu Wenting , Ren Jiacheng , Zhang Yuxin , Zhao Xin
Published: July 2022

The KCNH2 encoded hERG potassium channel is responsible for the drugs or pathological conditions induced long QT syndrome. The density of hERG ion channels on plasma membrane is governed by various factors including epigenetic alterations like non-coding RNA. Here, we found that LncRNA MALAT1 was aberrant elevated in the HEK293-hERG cell line in the presence of ATO or under hypoxia condition. Mechanistically, MALAT1 directly binds to calpain-1and limits its the ubiquitination degradation, which leading to the enhancement of calpain-1 mediated hERG channel cleavage. Consistently, silencing of MALAT1 or calpain-1 greatly abrogated the forced protein expression of calpain-1 and the reduction of hERG channel. In addition, the enhanced expression of MALAT1 may attribute to the increased acetylation level of transcription factor foxo1. Meanwhile, tanshinoneⅡA and propranolol have a certain reversal effect on the reduction of hERG caused by ATO/hypoxia. Collectively, MALAT1 could govern the density of hERG channel, at least partially, by regulating the stability of calpain-1 enzyme, which confers a novel theoretical understanding of the disadvantage caused by cardiotoxic drugs or pathological conditions.