bluuebunny/crossref_metadata_2025 huggingface dataset:
Physical recovery of COVID‐19 pneumosepsis intensive care survivors compared with non‐COVID pneumosepsis intensive care survivors during post–intensive care hospitalization: The RECOVID retrospective cohort study
Authors: Moonen Hanneke Pierre Franciscus Xaverius , Strookappe Bert , van Zanten Arthur Raymond Hubert
Published: August 2021

Background

Coronavirusdisease 2019 (COVID‐19) pneumosepsis survivors are at a high risk of developing intensive care unit (ICU)–acquired weakness (ICUAW) because of high incidence of acute respiratory distress syndrome and the common need for prolonged invasive ventilation. It remains unknown whether regular postpneumosepsis physical rehabilitation strategies are suitable for this extraordinary patient category.

Methods

We retrospectively compared the physical recovery of COVID‐19 and non‐COVID pneumosepsis ICU survivors during post‐ICU hospitalization, defined as the difference in performance on the Medical Research Council Sum‐Score (MRC‐SS), Chelsea Critical Care Physical Assessment tool (CPAx), and percentage of predicted handgrip strength (POP‐HGS). An analysis of covariance model was built using age, sex, Barthel index, body mass index, admission Acute Physiology And Chronic Health Evaluation II score, adequacy of protein delivery during ICU stay, and ward length of stay as covariates.

Results

Thirty‐five COVID‐19 ICU patients could be compared with 21 non‐COVID pneumosepsis ICU survivors. All patients scored ≤48 on the MRC‐SS at ICU discharge, indicating ICUAW. When controlling for covariates, COVID‐19 patients performed worse on all physical assessments upon ICU discharge, but had improved more at hospital discharge on the MRC‐SS (ɳ2 = 0.214, P =.002) and CPAx (ɳ2 = 0.153, P =.011). POP‐HGS remained lower in COVID‐19 patients throughout hospital stay.

Conclusion

COVID‐19 ICU survivors are vulnerable to ICUAW, but they show better tendency towards physical rehabilitation than non‐COVID pneumosepsis ICU survivors during the post‐ICU hospitalization period regarding MRC‐SS and CPAx. COVID‐19 ICU patients might benefit from early, more intensive physical therapy.
LAGOS‐US LOCUS v1.0: Data module of location, identifiers, and physical characteristics of lakes and their watersheds in the conterminous U.S.
Authors: Cheruvelil Kendra Spence , Soranno Patricia A. , McCullough Ian M. , Webster Katherine E. , Rodriguez Lauren K. , Smith Nicole J.
Published: August 2021

Macroscale studies of aquatic ecosystems are needed to address many contemporary broad‐scale problems related to global change, particularly to inform national‐scale environmental policies. In this data paper, we fill two important gaps in data availability for lakes at the scale of the conterminous U.S., the lack of: (1) high‐resolution geographic representations of lakes and their watersheds and (2) an open data platform to connect disparate U.S. national‐scale lake datasets. We describe the LAGOS‐US LOCUS v1.0 data module that includes a detailed User Guide, which is part of the LAGOS‐US extensible research‐ready open data platform. This platform can be used to study the 479,950 lakes and reservoirs larger than or equal to 1 ha across the entire conterminous U.S. at multiple scales of space and time. The LOCUS module includes spatially‐explicit information on lakes and their watersheds, including location information, physical characteristics, and identifiers of other important national‐scale datasets.
Analysis of the corrosion failure causes of shale gas surface pipelines
Authors: Wu Hua , Huang Chencheng , Wen Ninghua , Mao Ting , Tao Shiping , Wang Maomao
Published: August 2021

A shale gas gathering and transportation pipeline in a good block in Sichuan Province started leaking after less than a year of operation. To investigate the causes of corrosion of the sulfate‐reducing bacteria (SRB), optical microscopy, scanning electron microscopy, and X‐ray diffraction were used to analyze the corrosion and perforation of the shale gas surface pipeline in conjunction with bacterial corrosion simulation experiments. The results showed that the pipeline material (L360N) conformed to the requirements of the American Petroleum Institute 5 L standard and that extracellular polymeric substances were present in the corrosion pits. The corrosion products mainly included FeCO3, FeS, CaCO3, MgCO3, and Fe mineralization. At 40°C, the uniform corrosion rate of L360N in the simulation experiment was 0.234 mm/a, and the local corrosion rate was 0.458 mm/a. SRB, saprophytes, and iron bacteria were detected in the on‐site water medium and corrosion products, indicating that the main causes of shale gas pipeline corrosion are bacterial and CO2 corrosion.
Investigation and modelling of edge corrosion of e‐coated galvanized steel with respect to the spatial edge orientation
Authors: Kapfer Konstantin , Mandel Marcel , Mittelbach Andreas , Krüger Lutz
Published: August 2021

The effect of the spatial orientation of e‐coated hot dip galvanized test sheets on edge corrosion is investigated. Therefore paint delamination from corrosion sample edges at different steps in time of samples at different angles relative to the horizontal during a corrosion test is analysed. Two general relations are found: Horizontally oriented edges exhibit significantly increased coating delamination compared with vertically oriented edges. This is due to increased exposure to the electrolyte, resulting from the pinning of electrolyte droplets along the upper edge. With increasing angular displacement relative to the ground, electrolyte exposure and edge delamination decrease. The edges of the upward‐facing specimen side showed a higher delamination width compared with the downward‐facing side at the same angle. These results are supported by electrochemical impedance spectroscopy and a wetting test. Ultimately, a semi‐empirical model to numerically predict the edge delamination over time, incorporating electrochemical impedance spectroscopy and polarization curves, is presented.
Multiple rogue wave solutions and the linear superposition principle for a (3 + 1)‐dimensional Kadomtsev–Petviashvili–Boussinesq‐like equation arising in energy distributions
Authors: Manafian Jalil
Published: August 2021

The multiple exp‐function method and multiple rogue wave solutions method are employed for searching the multiple soliton solutions to the (3 + 1)‐dimensional Kadomtsev–Petviashvili–Boussinesq‐like (KP‐Boussinesq‐like) equation. The obtained solutions contain the first‐order, second‐order, third‐order, and fourth‐order wave solutions. At the critical point, the second‐order derivative and Hessian matrix for only one point are investigated, and the lump solution has one maximum value. Moreover, we employ the linear superposition principle to determineN‐soliton wave solutions of the KP‐Boussinesq‐like equation. The physical phenomena of these gained multiple soliton solutions are analyzed and indicated in figures by selecting suitable values.
Study on the explicit solutions of the Benney–Luke equation via the variational direct method
Authors: Wang Kang‐Jia , Wang Guo‐Dong
Published: August 2021

In this current work, we main to find the abundant explicit solutions of the Benney–Luke equation by a novel approach, which is called the variational direct method (VDM). The VDM based on the variational theory and Ritz‐like method can reduce the order of the differential equation to make the equation simpler and obtain the optimal solution by the stationary conditions. The explicit solutions in terms of dark solitary, dark‐like solitary, kinky‐dark solitary, and periodic wave solutions are presented through the numerical results in the form of 3‐D plot, 2‐D curve, and 2‐D contour. The results show that the VDM is simple, straightforward, and powerful, which is expected to open new perspectives for the traveling wave theory.
Morin Acts as a USP7 Inhibitor to Hold Back the Migration of Rheumatoid Arthritis Fibroblast‐Like Synoviocytes in a “Prickle1‐mTORC2” Dependent Manner
Authors: Yang Ling , Cao Na , Miao Yumeng , Dai Yue , Wei Zhifeng
Published: July 2021

Introduction

The aim of this study is to investigate the effect and detailed mechanisms of morin, an anti‐arthritis compound widely distributed in foods of plant origin, on the pathological migration of fibroblast‐like synoviocytes (FLS).

Methods and Results

The migration of FLS collected from arthritis rats and MH7A cells is induced by platelet‐derived growth factor, and an arthritis model in rats is established by Freund's complete adjuvant. The results show that morin remarkably restrains FLS migration but slightly affects FLS apoptosis and proliferation. Moreover, in the progression of FLS migration, focal adhesion (FA) turnover is inhibited by morin via lowering the activation of Paxillin and focal adhesion kinase (FAK) and internalization of integrin β1. Morin disrupts the formation of mTOR complex 2 (mTORC2) and the activation of AKT (S473) and PKCα (S657), and MHY1485 reverses morin‐limited FLS migration. Of note, the protein stability of Prickle1, a binding factor of Rictor, is reduced by morin, and MG132 but not Baf A1 shows a repressive effect. Finally, the target protein is identified as ubiquitin‐specific protease 7 (USP7) but not USP9X. USP7 overexpressing plasmid weakens morin‐affected protein and ubiquitination of Prickle1, and mechanisms are confirmed in vivo by using an overexpressing plasmid and inhibitor.

Conclusion

Morin restricts FLS migration and arthritis by intervening in “USP7‐Prickle1‐mTORC2” signaling and FA turnover.
Procyanidin B1 and p‐Coumaric Acid from Highland Barley Grain Showed Synergistic Effect on Modulating Glucose Metabolism via IRS‐1/PI3K/Akt Pathway
Authors: Liu Ze‐Hua , Li Bo
Published: August 2021

Introduction

Phenolic extract in highland barley grain has showed hypoglycemic effect, while little information is available about the active compounds and whether there exist additive or synergistic effect on modulating glucose metabolism.

Methods and Results

Procyanidin B1 (PB) and p‐coumaric acid (CA) are the active compounds in highland barley grain and show synergistic effect on improving glucose uptake and glycogen synthesis by upregulating glucose transporter (GLUT4) and downregulating glycogen synthase kinase‐3β (GSK‐3β) protein expression, respectively. The mechanism may be attributed to target insulin receptor (IRβ) and regulate insulin receptor substrate‐1 (IRS‐1)/phosphatidylinositol 3‐kinase (PI3K)/ protein kinase B (Akt) pathway. Furthermore, PB + CA exhibits synergistic effect on restoring glucose intolerance and insulin resistance, and improving hepatic glycogen synthesis in impaired glucose tolerance (IGT) mice. The postprandial blood glucose (PBG), homeostasis model assessment (HOMA)‐IR values and serum insulin contents in PB + CA‐treated IGT mice with dosage of 300 mg kg‐1 BW are reversed to normal levels. Additionally, PC + CA shows additive effect on inhibiting gluconeogenesis in vitro and in vivo.

Conclusion

PB + CA in highland barley grain synergistically modulate glucose metabolism. These results may provide evidence of whole highland barley grain diet achieve superior effect on restoring IGT than isolated components.
A novel use of biomechanical model‐based deformable image registration (DIR) for assessing colorectal liver metastases ablation outcomes
Authors: Anderson Brian M. , Lin Yuan‐Mao , Lin Ethan Y. , Cazoulat Guillaume , Gupta Sanjay , Kyle Jones A. , Odisio Bruno C. , Brock Kristy K.
Published: August 2021

Purpose

Colorectal cancer is the third most common form of cancer in the United States, and up to 60% of these patients develop liver metastasis. While hepatic resection is the curative treatment of choice, only 20% of patients are candidates at the time of diagnosis. While percutaneous thermal ablation (PTA) has demonstrated 24%–51% overall 5‐year survival rates, assurance of sufficient ablation margin delivery (5 mm) can be challenging, with current methods of 2D distance measurement not ensuring 3D minimum margin. We hypothesized that biomechanical model‐based deformable image registration (DIR) can reduce spatial uncertainties and differentiate local tumor progression (LTP) patients from LTP‐free patients.

Methods

We retrospectively acquired 30 patients (16 LTP and 14 LTP‐free) at our institution who had undergone PTA and had a contrast‐enhanced pre‐treatment and post‐ablation CT scan. Liver, disease, and ablation zone were manually segmented. Biomechanical model‐based DIR between the pre‐treatment and post‐ablation CT mapped the gross tumor volume onto the ablation zone and measured 3D minimum delivered margin (MDM). An in‐house cone‐tracing algorithm determined if progression qualitatively collocated with insufficient 5 mm margin achieved.

Results

Mann–Whitney U test showed a significant difference (p < 0.01) in MDM from the LTP and LTP‐free groups. A total of 93% (13/14) of patients with LTP had a correlation between progression and missing 5 mm of margin volume.

Conclusions

Biomechanical DIR is able to reduce spatial uncertainty and allow measurement of delivered 3D MDM. This minimum margin can help ensure sufficient ablation delivery, and our workflow can provide valuable information in a clinically useful timeframe.
Weight Loss, Survival, and Fatty Acid Composition in Overwintered Juvenile Coppernose Bluegill Lepomis macrochirus purpurescens Cultured in Outdoor Tanks Using Different Feeding Regimens
Authors: Roy Luke A. , Rawles Steven D. , Quintero Herbert E. , Kelly Anita M. , Park Jeonghwan , Webster Carl D.
Published: August 2021

Commercial producers raising centrarchids in Arkansas routinely report winter mortality. Juvenile centrarchids are susceptible to harsh winter conditions. The Coppernose Bluegill Lepomis macrochirus purpurescens is a popular sport fish for recreational fishing, and there are no recommended best management practices for winter feeding of this species. An outdoor trial was conducted to investigate the effect of different feeding regimens on performance of Coppernose Bluegill in the winter of 2014–2015. Four feeding regimens were implemented that included feeding twice per week (2×/week), once per week (1×/week), twice per month (2×/month), or once per month (1×/month). Twenty-five Coppernose Bluegill (initial weight = 2.59 ± 0.19 g) were stocked per tank (16 tanks, 4 replicates). Temperatures ranged from 0°C to 16°C during the trial. After 95 d, there were no differences (P > 0.05) in final weight or weight loss. Fish that were fed 2×/week or 1×/week had higher survival (P < 0.05) than those fed 2×/month or 1×/month. Fatty acid profiles of initial fish were distinctly different from the postwinter profiles of fed fish, although winter feeding frequency did not appear to influence fatty acid profiles in Coppernose Bluegill. Levels of saturates were higher in initial fish than in postwinter fish. The monounsaturated fatty acids 16:1 and 18:1(n-9) were higher in initial fish than in postwinter fish. Initial fish contained lower levels of 18:2(n-6), 20:4, and 22:6(n-3) than postwinter fish. Total polyunsaturated fatty acids (PUFAs) and n-3 and n-6 levels were also lower in initial fish than in postwinter fish, while the ratio of n-6/n-3 fatty acids did not differ significantly among initial and postwinter fed fish. Data indicate that (1) overwintering and infrequently fed Coppernose Bluegill preferentially conserve PUFAs and (2) feeding 1 × /week or 2 × /week may be a beneficial strategy for sport fish producers to increase survival of Coppernose Bluegill during the winter in temperate regions of the USA.
Predicting the return of bladder function following vaginal native tissue repair using data from a suprapubic catheter regimen
Authors: Hines Katherine N. , McKenzie Collin , Overholt Tyler , Mirzazadeh Majid , Matthews Catherine A. , Schachar Jeffrey , Russel Greg , Lentz Samuel
Published: August 2021

Aims

To evaluate time to return of normal voiding function following native tissue vaginal reconstruction and evaluate risk factors for postoperative urinary retention (POUR).

Methods

A retrospective cohort analysis of women undergoing vaginal reconstruction and suprapubic catheter with standardized regimen for voiding trials. Postvoid residual <150 ml at 4 h post catheter clamping was used as surrogate marker for return of bladder function. Univariate and multivariate regression analyses were used to identify risk factors for return of bladder function >4 days after surgery.

Results

Between 2013 and 2018, 148 women underwent surgery, 124 were analyzed. Mean age was 67 years (±11.1), 62.9% (n = 78) had greater than or equal to stage 3 prolapse. Mean time to return of bladder function: 4.1 days (±3.1). Significant risk factors for >4 days to return of bladder function on univariate analysis included (mean ± SD): surgery length (150.4 min ±44.6) (odds ratio [OR], 1.24; confidence interval [CI], 1.12, 1.38); anesthesia length (228.1 min ±53.5) (OR, 1.12; CI: 1.04, 1.23); length of stay (2.2 days ±2.7) (OR, 2.43; CI: 1.11, 5.35); hysterectomy (OR, 3.10; CI: 1.39, 6.90); estimated blood loss (124.4 ml ±64.8) (OR, 1.39; CI: 1.04, 1.87). Postmenopausal status was protective (OR, 0.17; CI: 0.03, 0.92.). On multivariate analysis, significant findings were diabetes mellitus (OR, 0.18; CI: 0.04, 0.93) and surgery length (OR, 1.21; CI: 1.06, 1.38).

Conclusions

Hysterectomy, surgical length and estimated blood loss were significantly associated with delayed return of bladder function after native tissue vaginal reconstruction. This data can help clinicians tailor postoperative voiding trials after failed initial attempt.
Nebulized plasma‐activated water has an effective antimicrobial effect on medically relevant microbial species and maintains its physicochemical properties in tube lengths from 0.1 up to 1.0 m
Authors: Chiappim William , Sampaio Aline , Miranda Felipe , Petraconi Gilberto , da Silva Sobrinho Argemiro , Cardoso Paulo , Kostov Konstantin , Koga‐Ito Cristiane , Pessoa Rodrigo
Published: August 2021

This study applies a proof of concept for future applications in controlling the microbiota in tubes and tracheal appliances used in the respiratory tract. Therefore, the physical–chemical parameters of the plasma‐activated and nebulized water (NPAW) are measured in a nebulizer tube with different lengths between 0.1 and 3.0 m. The pH values and oxidation–reduction potential (ORP) do not change during nebulization of PAW over a 1.0 m tube. However, for longer lengths, there is an increase in pH and a decrease in ORP. At 3.0 m, the pH increases approximately 16% compared with the 1.0 m position with a 20% decrease in the ORP values. Hydrogen peroxide (H2O2) measured quantitatively using test strips presents values between 0.5 and 2.0 mg/L for condensed NPAW in different tube lengths between 0.1 and 3.0 m, and maintains the approximate value of 2.0 mg/L in tubes up to 1.0 m, with a reduction proportional to the increase in the length of the tube. The antimicrobial efficacy of NPAW applied for 15 min shows the inactivation of Staphylococcus aureus and Escherichia coli but without significant inactivation of Candida albicans.
Cyclic etching of silicon oxide using NF3/H2 remote plasma and NH3 gas flow
Authors: Gill You Jung , Kim Doo San , Gil Hong Seong , Kim Ki Hyun , Jang Yun Jong , Kim Ye Eun , Yeom Geun Young
Published: August 2021

Selective isotropic cyclic dry etching of silicon oxide (SiO2) was investigated using a three‐step cyclic process composed of hydrogen fluoride (HF) adsorption by NF3/H2 remote plasma and reaction with NH3 gas flow to form ammonium fluorosilicate ((NH4)2SiF6), and desorption by heating. The variation of the ratio of NF3:H2 (2:1 to 1:3) and adsorption time (10–180 s) showed the highest etch selectivity of SiO2 over Si3N4 at 1:2 ratio of NF3:H2 and with the adsorption time of 20 s. The etch selectivity higher than 40 was observed with 20 s of adsorption time with a 1:2 ratio of NF3:H2 remote plasma and the total etch depth was linearly increased with the increase of cycles with the SiO2 EPC of ~7.5 nm/cycle.
Flexible parametric copula modeling approaches for clustered survival data
Authors: Kwon Sookhee , Ha Il Do , Shih Jia‐Han , Emura Takeshi
Published: August 2021

Copula‐based survival regression models, which consist of a copula function and marginal distribution (i.e., marginal survival function), have been widely used for analyzing clustered multivariate survival data. Archimedean copula functions are useful for modeling such dependence. For the likelihood inference, one‐stage and two‐stage estimation methods have been usually used. The two‐stage procedure can give inefficient estimation results because of separate estimation of the marginal and copula's dependence parameters. The more efficient one‐stage procedure has been mainly developed under a restrictive parametric assumption of marginal distribution due to complexity of the full likelihood with unknown marginal baseline hazard functions. In this paper, we propose a flexible parametric Archimedean copula modeling approach using a one‐stage likelihood procedure. In order to reduce the complexity of the full likelihood, the unknown marginal baseline hazards are modeled based on a cubic M‐spline basis function that does not require a specific parametric form. Simulation results demonstrate that the proposed one‐stage estimation method gives a consistent estimator and also provides more efficient results over existing one‐ and two‐stage methods. The new method is illustrated with three clinical data sets. The Appendix provides an R function so that the proposed method becomes directly accessible to interested readers.
Confidence intervals for exposure‐adjusted rate differences in randomized trials
Authors: Scosyrev Emil , Pethe Abhijit
Published: August 2021

Exposure‐adjusted event rate is a quantity often used in clinical trials to describe average event count per unit of person‐time. The event count may represent the number of patients experiencing first (incident) event episode, or the total number of event episodes, including recurring events. For inference about difference in the exposure‐adjusted rates between interventions, many methods of interval estimation rely on the assumption of Poisson distribution for the event counts. These intervals may suffer from substantial undercoverage both, asymptotically due to extra‐Poisson variation, and in the settings with rare events even when the Poisson assumption is satisfied. We review asymptotically robust methods of interval estimation for the rate difference that do not depend on distributional assumptions for the event counts, and propose a modification of one of these methods. The new interval estimator has asymptotically nominal coverage for the rate difference with an arbitrary distribution of event counts, and good finite sample properties, avoiding substantial undercoverage with small samples, rare events, or over‐dispersed data. The proposed method can handle covariate adjustment and can be implemented with commonly available software. The method is illustrated using real data on adverse events in a clinical trial.
Transplantation of Human Autologous Synovial Mesenchymal Stem Cells with Trisomy 7 into the Knee Joint and 5 Years of Follow-up
Authors: Mizuno Mitsuru , Endo Kentaro , Katano Hisako , Amano Naoki , Nomura Masaki , Hasegawa Yoshinori , Ozeki Nobutake , Koga Hideyuki , Takasu Naoko , Ohara Osamu , Morio Tomohiro , Sekiya Ichiro
Published: August 2021

Mesenchymal stem cells (MSCs) can show trisomy 7; however, the safety of these cells has not been fully investigated. The purposes of this study were to determine the ratio of patients whose synovial MSCs were transplanted clinically, to intensively investigate MSCs with trisomy 7 from a safety perspective, and to follow up the patients for 5 years after transplantation. Synovial MSCs at passage 0 were transplanted into a knee for degenerative meniscus tears in 10 patients, and the patients were checked at 5 years. The synovial MSCs were evaluated at passages 0 to 15 by G-bands and digital karyotyping, and trisomy 7 was found in 3 of 10 patients. In those three patients, 5% to 10% of the synovial MSCs showed trisomy 7. The mRNA expressions of representative oncogenes and genes on chromosome 7 did not differ between MSCs with and without trisomy 7. Whole-genome sequencing and DNA methylation analysis showed similar results for MSCs with and without trisomy 7. Transplantation of human synovial MSCs with trisomy 7 into eight mouse knees did not result in tumor formation under the skin or in the knees after 8 weeks in any mouse, whereas transplanted HT1080 cells formed tumors. In vitro chondrogenic potentials were similar between MSCs with and without trisomy 7. Five-year follow-ups revealed no serious adverse events in all 10 human patients, including 3 who had received MSCs with trisomy 7. Overall, our findings indicated that synovial MSCs with trisomy 7 were comparable with MSCs without trisomy 7 from a safety perspective.
Add the Finishing Touch: Molecular Engineering of Conjugated Small Molecule for High‐Performance AIE Luminogen in Multimodal Phototheranostics
Authors: Li Dan , Li Youmei , Wu Qian , Xiao Peihong , Wang Lei , Wang Dong , Tang Ben Zhong
Published: August 2021

Phototheranostics based on luminogens with aggregation‐induced emission (AIE) characteristics is captivating increasing research interest nowadays. However, AIE luminogens are inherently featured by inferior absorption coefficients (ε) resulting from the distorted molecular geometry. Besides, molecular innovation of long‐wavelength light‐excitable AIE luminogens with highly efficient phototheranostic outputs is an appealing yet significantly challenging task. Herein, on the basis of a fused‐ring electron acceptor–donator–acceptor (A–D–A) type molecule (IDT) with aggregation‐caused quenching (ACQ) properties, molecular engineering smoothly proceeds and successfully yields a novel AIE luminogen (IDT‐TPE) via simply modifying tetraphenylethene (TPE) moieties on the sides of IDT backbone. The AIE tendency endows IDT‐TPE nanoparticles with enhanced fluorescence brightness and far superior fluorescence imaging performance to IDT nanoparticles for mice tumors. Moreover, IDT‐TPE nanoparticles exhibit near‐infrared light‐excitable features with a high ε of 8.9 × 104 m−1 cm−1, which is roughly an order of magnitude higher than that of most previously reported AIE luminogens. Combining with their reactive oxygen species generation capability and extremely high photothermal conversion efficiency (59.7%), IDT‐TPE nanoparticles actualize unprecedented performance in multimodal phototheranostics. This study thus brings useful insights into the development of versatile phototheranostic materials with great potential for practical cancer theranostics.
Time to infer miRNA sponge modules
Authors: Zhang Junpeng , Liu Lin , Xu Taosheng , Zhang Wu , Li Jiuyong , Rao Nini , Le Thuc Duy
Published: August 2021

Inferring competing endogenous RNA (ceRNA) or microRNA (miRNA) sponge modules is a challenging and meaningful task for revealing ceRNA regulation mechanism at the module level. Modules in this context refer to groups of miRNA sponges which have mutual competitions and act as functional units for achieving biological processes. The recent development of computational methods based on heterogeneous data provides a novel way to discern the competitive effects of miRNA sponges on human complex diseases. This article aims to provide a comprehensive perspective of miRNA sponge module discovery methods. We first review the publicly available databases of cancer‐related miRNA sponges, as the miRNA sponges involved in human cancers contribute to the discovery of cancer‐associated modules. Then we review the existing computational methods for inferring miRNA sponge modules. Furthermore, we conduct an assessment on the performance of the module discovery methods with the pan‐cancer dataset, and the comparison study indicates that it is useful to infer biologically meaningful miRNA sponge modules by directly mapping heterogeneous data to the competitive modules. Finally, we discuss the future directions and associated challenges in developing in silico methods to infer miRNA sponge modules.

This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Small Molecule‐RNA Interactions

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Threat‐Based State and Transition Models Predict Sage‐Grouse Occurrence while Promoting Landscape Conservation
Authors: Doherty Kevin E. , Boyd Chad S. , Kerby Jay D. , Sitz Angela L. , Foster Lee J. , Cahill Matt C. , Johnson Dustin D. , Sparklin Bill D.
Published: August 2021

A recent collaboration between federal, state and private partners in southeast Oregon developed mental models to distill complex plant‐based community ecology for management. The mental models were then turned into a simplified, habitat‐classification system that addressed landscape‐level threats to the sagebrush ecosystem. The simplified, habitat‐classification system formed the foundation of Threat‐based State and Transition Models (TBSTM). We quantitatively linked greater sage‐grouse (Centrocercus urophasianus, hereafter sage‐grouse) lek occurrence to a landscape‐level habitat classification based upon the TBSTM framework. We investigated whether TBSTM classifications were able to spatially predict locations of sage‐grouse breeding areas equivalently to landcover variables that have been studied for over a decade. We showed the TBSTM framework was able to predict the locations of sage‐grouse accurately (R2 = 0.70, AUC = 0.91, Correctly Classified = 83%). Model fit statistics were similar to the model built with traditional land cover variables (R2 = 0.65, AUC = 0.89, Correctly Classified = 80%). The high degree of model fit for the TBSTM framework allows conservation practitioners a direct, quantifiable, and biological link to understand outcomes of transitioning habitats from various threat states to sagebrush‐dominated landscapes with a perennial understory across large landscapes. Sage‐grouse are well known to respond to landscape‐level amounts of habitat and exhibit low tolerance to threats. We documented similar responses between threats such as the percentage of conifers within 560‐m and the conifer threat bin at the same spatial scale. Our work also quantified the importance of having a healthy perennial‐grass understory and perennial‐grass patches in conjunction with sagebrush cover across large landscapes. Our work suggests that understory grass communities at landscape scales may be limiting grouse occurrence in certain parts of Oregon. © 2021 The Authors. Wildlife Society Bulletin published by Wiley Periodicals LLC on behalf of The Wildlife Society.
‘Choice Is Yours’: Anatomy of a Lesson Plan from University V
Authors: Costello Eamon , Girme Prajakta
Published: August 2021

This chapter aims to explore education as posthuman practice via the anatomy of a lesson plan. The lesson is narrated through the methodological device of speculative fiction. It is a fabulation set in the future but with roots that tangle with the past. Dark histories and futures are set to flicker here. Deception, de-identification and datafication lurk everywhere. If you are squeamish, you may wish to read no further. The datafication of people, their reduction to numbers, bytes and, most fatally of all, words, is laid out here in gory detail. If you do wish to read on, however, then you need nothing: just come as you are, and be assured as always that as the reader, choice is yours.
Historical Metamodels of Agency
Authors: Bryant Peter T.
Published: August 2021

Each major period of civilized humanity exhibits dominant metamodels of agentic form and function, which vary in terms of capability and supportive technology. The chapter identifies three such periods. The first is premodernity, which predates the European Enlightenment and industrialization. It was characterized by stable social systems, in which agentic form and functioning were replicative. Whereas in modernity, capabilities and technologies greatly advance, and the dominant agentic metamodel is one of adaptation and developmental learning. In the contemporary period, a new digitalized agentic metamodel is emerging, reflecting the close collaboration of human and artificial agents as augmented agents. It will be dynamic, generative, and transformative. It also poses new questions and problematics, especially about the supervision of digitalized capabilities and potentialities.
Problem-Solving
Authors: Bryant Peter T.
Published: August 2021

Human and artificial agents are both intelligent problem solvers. Therefore, problem-solving will be central to their collaboration. Among notable developments in this domain is the capability for artificial agents to sample and search in a very farsighted fashion, or to be hyperopic, which is the technical term for farsighted vision, the opposite of myopia. This inverts the dominant concern of prior theory, which focuses on limited, bounded capabilities in problem-solving and decision-making. This shift poses significant opportunities and risks for augmented agents. Human processing will likely remain naturally myopic and limited, while artificial processing is increasingly hyperopic and powerful. Given these differences, digitally augmented problem-solving could be extremely divergent and dysfunctional, for example, by sampling and searching in a hyperopic fashion, while guided by persistent human myopia. Alternatively, one agent might dominate the other, leading to extreme convergence and possibly the digital domination of problem-solving.
Cognitive Empathy
Authors: Bryant Peter T.
Published: August 2021

Human beings try to interpret and read other minds. This is the process of cognitive empathizing, which can be implicit and intuitive, or explicit and deliberate. The process also qualifies as a form of complex problem-solving, where the focal problem is another person’s mental states. Hence, cognitive empathizing by digitally augmented agents will exhibit the characteristics discussed in the preceding chapter, regarding digitalized problem-solving. It follows, therefore, that augmented agents might combine human myopia and bias, with overly farsighted, artificial sampling and search of other minds. Augmented agents will then misread other minds, often viewing them as unrealistic, irrational, or deviant. This chapter examines the origins and implications of these effects, especially for interpersonal trust and cooperation.
Self-Regulation
Authors: Bryant Peter T.
Published: August 2021

To monitor and manage the dilemmas of digitalization, augmented agents must self-regulate in a collaborative fashion. Artificial agents are advancing rapidly in these respects and some are fully self-generative. They are increasingly capable of complex, fast, sensitive self-regulation. In consequence, augmented agents will have the potential for effective self-regulation and self-supervision. However, human self-regulation is often simplified and sluggish and lacks sensitivity. People rely on habit, routine, and docility, and often with good reasons. Yet, as noted, artificial agents are increasingly hyperactive and hypersensitive, compared to humans. When both agents combine, therefore, artificial self-regulatory functioning could be complex, fast, and precise, while human functioning is relatively simple, sluggish, and heuristic. The result could be self-regulatory divergence or convergence and possibly dysfunction. Further implications then follow for self-efficacy, task engagement, and motivational strength.
Self-Generation
Authors: Bryant Peter T.
Published: August 2021

Autonomous agents are self-generative, meaning they can manage their own development and reproduction without external direction. For artificial agents, self-generation entails the composition of algorithmic systems and metamodels. For humans, it involves the composition of life narratives and identities. That said, many people have few self-generative options because they lack the required resources, opportunities, and capabilities. Digitalization supports remedial efforts in this regard. Digital augmentation strengthens capabilities and expands potentialities. Many people already enjoy these benefits. Yet there is also evidence of the opposite. Some individuals and groups are excluded, while others resist digital augmentation or feel blocked and incapable of absorbing these opportunities. Instead, they either persist with singular, traditional life paths, or flounder in the face of complexity, or surrender choice and submit to digital determination. As this chapter explains, such responses erode self-generation and put human flourishing at risk.
Existence and orbital stability of standing waves to a nonlinear Schrödinger equation with inverse square potential on the half-line
Authors: Csobo Elek
Published: August 2021

In our work, we establish the existence of standing waves to a nonlinear Schrödinger equation with inverse-square potential on the half-line. We apply a profile decomposition argument to overcome the difficulty arising from the non-compactness of the setting. We obtain convergent minimizing sequences by comparing the problem to the problem at “infinity” (i.e., the equation without inverse square potential). Finally, we establish orbital stability/instability of the standing wave solution for mass subcritical and supercritical nonlinearities respectively.
Standardized assessment of bone micromorphometry around teeth following orthodontic tooth movement
Authors: Trelenberg-Stoll Viktoria , Wolf Michael , Busch Caroline , Drescher Dieter , Becker Kathrin
Published: August 2021

Purpose

Volumetric quantitative analyses of bone micromorphometry changes following orthodontic tooth movements are hardly standardizable. The present study aimed at validating and applying a novel microcomputed tomography (CT)-based approach that enables the segmentation of teeth and definition of a standardized volume of interest (VOI) around the roots to assess local bone micromorphometry.

Methods

The jaws of 3 untreated and 14 orthodontically treated mice (protraction of the upper right molar for 11 days with 0.5 N; untreated left upper molar) were scanned with a micro-CT. The first molars and the alveolar bone were segmented, and a standardized VOI was defined around the teeth. The bone volume per total volume (BV/TV) was assessed within the VOI, and BV/TV values were compared between contralateral sites in both untreated (method validation) and treated animals (method application).

Results

The intraclass correlation coefficient of 0.99 revealed high reliability of the method. In the untreated animals, Bland–Altman analysis confirmed comparable BV/TV fractions (mean difference: −1.93, critical difference: 1.91, Wilcoxon: p = 0.03). In the orthodontically treated animals, BV/TV values were significantly lower at the test compared to the control site (test: 33.23% ± 5.74%, control: 41.33% ± 4.91%, Wilcoxon: p < 0.001).

Conclusion

Within the limits of the study, the novel approach demonstrated the applicability to evaluate bone micromorphometry around teeth subjected to orthodontic treatment.
Epidemiology, classification and treatment of olecranon fractures in adults: an observational study on 2462 fractures from the Swedish Fracture Register
Authors: Brüggemann Anders , Mukka Sebastian , Wolf Olof
Published: August 2021

Purpose

This nationwide study aims to describe the epidemiology, fracture classification and current treatment regimens of olecranon fractures in adults.

Methods

We performed a descriptive study based on registered data from the Swedish Fracture Register (SFR). All non-pathological olecranon fractures reported between 1 January 2014 and 31 December 2018 in patients aged ≥ 18 years were included. Data on age, sex, injury mechanism, fracture classification (according to the modified Mayo classification system), primary treatment and seasonal variation were analyzed. We compared patients < 65 with those > 65 years regarding injury mechanism, distribution of fracture types and subsequent treatment.

Results

In total, 2462 olecranon fractures were identified in the SFR. Median age was 66 years and 65% were women. Of all fractures, 303 (12%) were proximal avulsion, 1044 (42%) simple central, 717 (29%) comminuted central and 398 (16%) distal olecranon fractures. Nonoperative treatment was performed in 21% of the patients < 65 and 35% of the patients > 65 years. Tension band wiring was used for most simple central fractures. Plate fixation was used in almost half of the operatively treated fractures classified as unstable comminuted central and distal olecranon fractures. Men show a higher proportion of high-energy trauma than women in both age groups.

Conclusion

Isolated fractures of the olecranon occur after a low-energy trauma, especially in older women (> 65 years). Non-operative treatment is common in uncomplicated fractures and operative treatment in more complex fractures nationwide. A shift to plate fixation in the more unstable fracture patterns is observed. These results may help health care providers and clinicians gain a better understanding of isolated olecranon fractures.
An IBD-based mixed model approach for QTL mapping in multiparental populations
Authors: Li Wenhao , Boer Martin P. , Zheng Chaozhi , Joosen Ronny V. L. , van Eeuwijk Fred A.
Published: August 2021

Key message

The identity-by-descent (IBD)-based mixed model approach introduced in this study can detect quantitative trait loci (QTLs) referring to the parental origin and simultaneously account for multilevel relatedness of individuals within and across families. This unified approach is proved to be a powerful approach for all kinds of multiparental population (MPP) designs.

Multiparental populations (MPPs) have become popular for quantitative trait loci (QTL) detection. Tools for QTL mapping in MPPs are mostly developed for specific MPPs and do not generalize well to other MPPs. We present an IBD-based mixed model approach for QTL mapping in all kinds of MPP designs, e.g., diallel, Nested Association Mapping (NAM), and Multiparental Advanced Generation Intercross (MAGIC) designs. The first step is to compute identity-by-descent (IBD) probabilities using a general Hidden Markov model framework, called reconstructing ancestry blocks bit by bit (RABBIT). Next, functions of IBD information are used as design matrices, or genetic predictors, in a mixed model approach to estimate variance components for multiallelic genetic effects associated with parents. Family-specific residual genetic effects are added, and a polygenic effect is structured by kinship relations between individuals. Case studies of simulated diallel, NAM, and MAGIC designs proved that the advanced IBD-based multi-QTL mixed model approach incorporating both kinship relations and family-specific residual variances (IBD.MQMkin_F) is robust across a variety of MPP designs and allele segregation patterns in comparison to a widely used benchmark association mapping method, and in most cases, outperformed or behaved at least as well as other tools developed for specific MPP designs in terms of mapping power and resolution. Successful analyses of real data cases confirmed the wide applicability of our IBD-based mixed model methodology.
The effect of drought stress of sorghum grains on the textural features evaluated using machine learning
Authors: Ropelewska Ewa , Nazari Leyla
Published: July 2021

This study aimed to determine the discriminatory power of textural features to differentiate the sorghum grains subjected to normal, mild deficit, and severe deficit irrigation. The studies were carried out with the use of image processing, discrimination analysis, analysis of variance and cluster analysis using the selected texture parameters calculate for images from individual color channels L, a, b, R, G, B, U, V, S, X, Y and Z. The results indicated that different levels of irrigation can discriminate the sorghum grain with an accuracy of up to about 100%. Most of the genotypes for each level of irrigation were different in the terms of values of textural features and formed separate homogeneous groups. Drought is one of the limiting factors contributing to a decrease in sorghum grain productivity and nutritional quality, especially when it is cultivated in a marginal area. Therefore, low-quality grains produced under water stress should be recognized before they enter into the food and feed chain. The application of image analysis based on textures of sorghum grain images proved to be useful for the discrimination of sorghum grains subjected to drought stress. The applied procedure provided the fast, objective results that may be applied in practice for screening distinguishing the sorghum grains with different irrigation levels.
The importance of Cu ×  Pb interactions to Lentinula edodes yield, major/trace elements accumulation and antioxidants
Authors: Gąsecka Monika , Siwulski Marek , Budzyńska Sylwia , Magdziak Zuzanna , Niedzielski Przemysław , Budka Anna , Kalač Pavel , Mleczek Mirosław
Published: July 2021

Due to the use of various substrates
in the production of edible mushrooms which may contain metals, including Cu and Pb, it is important to understand the influence of mutual interactions between them in the process of their accumulation in fruit bodies. For this reason, the effects of Cu, Pb, and Cu × Pb on yield, accumulation of five major elements (Ca, K, Mg, Na and P), trace elements (Cu, Pb and Fe) and some bioactive compounds in Lentinula edodes fruit bodies were studied. Both the metals were added in doses of 0.1 and 0.5 mM (Cu0.1, Cu0.5, Pb0.1, Pb0.5 and their combinations). The addition of the metals resulted in a reduction in size, amount and finally yield of fruit bodies. Depending on the presence of Cu and or Pb and their concentration in the substrate, both antagonism and synergism may occur. The influence on the accumulation of other determining elements was also recorded. Among phenolic compounds, phenolic acids and flavonoids were detected. 2,5-Dihydroxybenzoic acid dominated in fruit bodies in the control variant, Pb0.1, Pb0.5 and all experimental variants enriched with Cu + Pb, while gallic acid was the major phenolic after Cu0.1 and Cu0.5 addition. Only protocatechuic acid content increased in all combinations. A significant decrease of all aliphatic acid contents in comparison to the control variant was observed in the Cu0.1 and Pb0.1 variants. Significant stimulation of aliphatic acid synthesis was recorded in Cu0.5 and Pb0.5 variants and in the mixture of both the metals. The additions pointed to the possible role of the determined molecules in detoxification mechanisms.
The relationship between acidification (pH) and meat quality traits of polish white breed pigs
Authors: Jankowiak Hanna , Cebulska Aleksandra , Bocian Maria
Published: July 2021

The paper presents the results of a study on the relationship between acidification (pH) and standard quality characteristics of the meat of Polish Large White × Polish Landrace pig crossbreds. The meat for the study was obtained from 184 F1Polish Large White × Polish Landrace fatteners from a herd free of the stress-sensitivity gene. The obtained results were analysed in groups formed according to the meat’s measured pH45values (≤ 6.3; 6.3–6.7; > 6.7) and pHuvalues (≤ 5.3; 5.3–5.6; > 5.6). Increasing measured pH45values were paralleled by greater water-holding capacity and plasticity, lower drip loss, darker colour L* as assessed visually and with equipment, and greater content of muscle pigments (P < 0.01) of the evaluated meat. Higher pHuvalues had a more pronounced impact on WHC, free drip loss, tenderness, water content, and colour parameters: a*, b*, chroma C* (P < 0.01), and hue angle ho(P < 0.05). The obtained simple correlations between pH45and pHuacidity and meat-quality characteristics indicate that the measured pH45value was correlated more closely than ultimate acidification (P < 0.01) with visually assessed colour intensity, tactilely assessed meat hardness, colour lightness L* (P < 0.01), hue angle ho(P < 0.05), and muscle pigment content. On the other hand, pHuwas more strongly correlated with water-holding capacity, drip loss, meat tenderness as well as water and protein content (P < 0.01).