bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiologically-based strategies for the detection of emerging plant pathogens
Authors: Mastin Alexander J. , van den Bosch Frank , Bourhis Yoann , Parnell Stephen 
Published: June 2022

AbstractEmerging pests and pathogens of plants are a major threat to natural and managed ecosystems worldwide. Whilst it is well accepted that surveillance activities are key to both the early detection of new incursions and the ability to identify pest-free areas, the performance of these activities must be evaluated to ensure they are fit for purpose. This requires consideration of the number of potential hosts inspected or tested as well as the epidemiology of the pathogen and the detection method used. In the case of plant pathogens, one particular concern is whether the visual inspection of plant hosts for signs of disease is able to detect the presence of these pathogens at low prevalences, given that it takes time for these symptoms to develop. One such pathogen is the ST53 strain of the vector-borne bacterial pathogen Xylella fastidiosa in olive hosts, which was first identified in southern Italy in 2013. Additionally, X. fastidiosa ST53 in olive has a rapid rate of spread, which could also have important implications for surveillance. In the current study, we evaluate how well visual surveillance would be expected to perform for this pathogen and investigate whether molecular testing of either tree hosts or insect vectors offer feasible alternatives. Our results identify the main constraints to each of these strategies and can be used to inform and improve both current and future surveillance activities.
Robust model selection using the out-of-bag bootstrap in linear regression
Authors: Rabbi Fazli , Khalil Alamgir , Khan Ilyas , Almuqrin Muqrin A. , Khalil Umair , Andualem Mulugeta 
Published: June 2022

AbstractOutlying observations have a large influence on the linear model selection process. In this article, we present a novel approach to robust model selection in linear regression to accommodate the situations where outliers are present in the data. The model selection criterion is based on two components, the robust conditional expected prediction loss, and a robust goodness-of-fit with a penalty term. We estimate the conditional expected prediction loss by using the out-of-bag stratified bootstrap approach. In the presence of outliers, the stratified bootstrap ensures that we obtain bootstrap samples that are similar to the original sample data. Furthermore, to control the undue effect of outliers, we use the robust MM-estimator and a bounded loss function in the proposed criterion. Specifically, we observe that instead of minimizing the penalized loss function or the conditional expected prediction loss separately, it is better to minimize them simultaneously. The simulation and real-data based studies confirm the consistent and satisfactory behavior of our bootstrap model selection procedure in the presence of response outliers and covariate outliers.
Reducing the energy cost of walking with low assistance levels through optimized hip flexion assistance from a soft exosuit
Authors: Kim Jinsoo , Quinlivan Brendan T. , Deprey Lou-Ana , Arumukhom Revi Dheepak , Eckert-Erdheim Asa , Murphy Patrick , Orzel Dorothy , Walsh Conor J. 
Published: June 2022

AbstractAs we age, humans see natural decreases in muscle force and power which leads to a slower, less efficient gait. Improving mobility for both healthy individuals and those with muscle impairments/weakness has been a goal for exoskeleton designers for decades. In this work, we discover that significant reductions in the energy cost required for walking can be achieved with almost 50% less mechanical power compared to the state of the art. This was achieved by leveraging human-in-the-loop optimization to understand the importance of individualized assistance for hip flexion, a relatively unexplored joint motion. Specifically, we show that a tethered hip flexion exosuit can reduce the metabolic rate of walking by up to 15.2 ± 2.6%, compared to locomotion with assistance turned off (equivalent to 14.8% reduction compared to not wearing the exosuit). This large metabolic reduction was achieved with surprisingly low assistance magnitudes (average of 89 N, ~ 24% of normal hip flexion torque). Furthermore, the ratio of metabolic reduction to the positive exosuit power delivered was 1.8 times higher than ratios previously found for hip extension and ankle plantarflexion. These findings motivated the design of a lightweight (2.31 kg) and portable hip flexion assisting exosuit, that demonstrated a 7.2 ± 2.9% metabolic reduction compared to walking without the exosuit. The high ratio of metabolic reduction to exosuit power measured in this study supports previous simulation findings and provides compelling evidence that hip flexion may be an efficient joint motion to target when considering how to create practical and lightweight wearable robots to support improved mobility.
Effect of distributed Bragg reflectors on photoluminescence properties of CH3NH3PbI3 film
Authors: Jiang Feng , Xiao Zhiguang , Dong Mengqi , Song Jiawen , Wang Yinong 
Published: June 2022

AbstractThe nanoporous (NP) GaN distributed Bragg reflector (DBR) was prepared by using electrochemical etching. Then the NP-GaN DBR was pretreated by using ozone treatment. Atomic force microscopy and X-ray diffraction (XRD) were used to investigate the influence of ozone treatment on the structure of the substrates. The hybrid organic–inorganic CH3NH3PbI3 perovskite films were grown on the NP-GaN DBR and reference substrates by using a one-step solution method. The XRD and field emission scanning electron microscopy test results indicate the high quality of the prepared CH3NH3PbI3 perovskite films. The photoluminescence intensity of the prepared CH3NH3PbI3 perovskite film on the NP-GaN DBR substrate is ~ 3.5 times higher than that of the film on the reference substrate, with a 3.6 nm spectral blue-shift. The enhancement should be contributable to amplify spontaneous emission by resonant cavity, while the blue-shift could be contributable to stoichiometric difference of the films on different substrates.
Overexpression of satellite RNAs in heterochromatin induces chromosomal instability and reflects drug sensitivity in mouse cancer cells
Authors: Tamaki Sawako , Suzuki Koichi , Abe Iku , Endo Yuhei , Kakizawa Nao , Watanabe Fumiaki , Saito Masaaki , Tsujinaka Shingo , Miyakura Yasuyuki , Ohta Satoshi , Tago Kenji , Yanagisawa Ken , Konishi Fumio , Rikiyama Toshiki 
Published: June 2022

AbstractOverexpression of satellite RNAs in heterochromatin induces chromosomal instability (CIN) through the DNA damage response and cell cycle checkpoint activation. Although satellite RNAs may be therapeutic targets, the associated mechanisms underlying drug sensitivity are unknown. Here, we determined whether satellite RNAs reflect drug sensitivity to the topoisomerase I inhibitor camptothecin (CPT) via CIN induction. We constructed retroviral vectors expressing major satellite and control viruses, infected microsatellite stable mouse colon cancer cells (CT26) and MC38 cells harboring microsatellite instability, and assessed drug sensitivity after 48 h. Cells overexpressing satellite RNAs showed clear features of abnormal segregation, including micronuclei and anaphase bridging, and elevated levels of the DNA damage marker γH2AX relative to controls. Additionally, overexpression of satellite RNAs enhanced MC38 cell susceptibility to CPT [half-maximal inhibitory concentration: 0.814 μM (control) vs. 0.332 μM (MC38 cells with a major satellite), p = 0.003] but not that of CT26. These findings imply that MC38 cells, which are unlikely to harbor CIN, are more susceptible to CIN-induced CPT sensitivity than CT26 cells, which are characterized by CIN. Furthermore, CPT administration upregulated p53 levels but not those of p21, indicating that overexpression of major satellite transcripts likely induces CPT-responsive cell death rather than cellular senescence.
Identification of soil particle size distribution in different sedimentary environments at river basin scale by fractal dimension
Authors: Wang Yanyan , He Yujiang , Zhan Jiang , Li Zhiping 
Published: June 2022

AbstractThe geomorphology of river basin is complex, and its soil sedimentary characteristics are poorly defined. To study the spatial variability of soil structure in different sedimentary environments at the basin scale, 356 sets of soil samples were collected from five typical sedimentary environments in the Yellow River Basin and the Haihe River Basin, including the upper and lower reaches of the rivers, mountain-front plains, central alluvial plains and eastern coastal plains. The particle size distribution (PSD) of the soil samples was obtained using a laser particle size analyzer, and the fractal dimension (D) of the soil structure was derived by applying fractal theory. The PSD, D and the correlation between them were analyzed by the Pearson correlation method for typical sedimentary environments in two basins. The results show that: (1) The main soil types in the typical geological environments in the basin are sand, loamy sand, sandy loam, silty loam, and silty soil. The soil particle size in the upper and lower reaches of the rivers was higher than that in the plain areas. (2) In the plane, The D value descended in different regions in the following order: the mountain-front plain > the eastern coastal plain > the upper Yellow River > the central alluvial plain > the lower Yellow River. In the vertical direction for both rivers, the D value showed a decreasing trend with increasing burial depth. (3) The model results showed a cubic polynomial correlation between D values and PSD, which was closely related to the non-uniformity of particle size during sorting and deposition. The soil PSD and fractal characteristics are effective tools for the quantitative evaluation of soil structure in various sedimentary environments in the basin.
Multi-block data integration analysis for identifying and validating targeted N-glycans as biomarkers for type II diabetes mellitus
Authors: Adua Eric , Afrifa-Yamoah Ebenezer , Peprah-Yamoah Emmanuel , Anto Enoch Odame , Acheampong Emmanuel , Awuah-Mensah Kwaafo Akoto , Wang Wei 
Published: June 2022

AbstractPlasma N-glycan profiles have been shown to be defective in type II diabetes Mellitus (T2DM) and holds a promise to discovering biomarkers. The study comprised 232 T2DM patients and 219 healthy individuals. N-glycans were analysed by high-performance liquid chromatography. The multivariate integrative framework, DIABLO was employed for the statistical analysis. N-glycan groups (GPs 34, 32, 26, 31, 36 and 30) were significantly expressed in T2DM in component 1 and GPs 38 and 20 were related to T2DM in component 2. Four clusters were observed based on the correlation of the expressive signatures of the 39 N-glycans across T2DM and controls. Cluster A, B, C and D had 16, 16, 4 and 3 N-glycans respectively, of which 11, 8, 1 and 1 were found to express differently between controls and T2DM in a univariate analysis $$(p < 0.05)$$

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. Multi-block analysis revealed that trigalactosylated (G3), triantennary (TRIA), high branching (HB) and trisialylated (S3) expressed significantly highly in T2DM than healthy controls. A bipartite relevance network revealed that HB, monogalactosylated (G1) and G3 were central in the network and observed more connections, highlighting their importance in discriminating between T2DM and healthy controls. Investigation of these N-glycans can enhance the understanding of T2DM.
Risk coefficient model of necroptosis-related lncRNA in predicting the prognosis of patients with lung adenocarcinoma
Authors: Chen HuiWei , Xie Zhimin , Li QingZhu , Qu GenYi , Tan NianXi , Zhang YuLong 
Published: June 2022

AbstractModel algorithms were used in constructing the risk coefficient model of necroptosis-related long non-coding RNA in identifying novel potential biomarkers in the prediction of the sensitivity to chemotherapeutic agents and prognosis of patients with lung adenocarcinoma (LUAD). Clinic and transcriptomic data of LUAD were obtained from The Cancer Genome Atlas. Differently expressed necroptosis-related long non-coding RNAs got identified by performing both the univariate and co-expression Cox regression analyses. Subsequently, the least absolute shrinkage and selection operator technique was adopted in constructing the nrlncRNA model. We made a comparison of the areas under the curve, did the count of the values of Akaike information criterion of 1-year, 2-year, as well as 3-year receiver operating characteristic curves, after which the cut-off value was determined for the construction of an optimal model to be used in identifying high risk and low risk patients. Genes, tumor-infiltrating immune cells, clinical correlation analysis, and chemotherapeutic agents data of both the high-risk and low-risk subgroups were also performed. We identified 26 DEnrlncRNA pairs, which were involved in the Cox regression model constructed. The curve areas under survival periods of 1 year, 2 years, and 3 years of patients with LUAD were 0.834, 0.790, and 0.821, respectively. The cut-off value set was 2.031, which was used in the identification of either the high-risk or low-risk patients. Poor outcomes were observed in patients belonging to the high-risk group. The risk score was the independent predictor of the LUAD outcome (p < 0.001). The expression levels of immune checkpoint and infiltration of specific immune cells were anticipated by the gene risk model. The high-risk group was found to be highly sensitive to docetaxel, erlotinib, cisplatin, and paclitaxel. The model established through nrlncRNA pairs irrespective of the levels of expression could give a prediction on the LUAD patients’ prognosis and assist in identifying the patients who might gain more benefit from chemotherapeutic agents.
Seasonal variations of the relationships between measures of training monotony and strain in professional soccer players
Authors: Nobari Hadi , Martins Alexandre Duarte , Oliveira Rafael , Ardigò Luca Paolo 
Published: June 2022

AbstractThe purposes of this study were (a) to determine the variations in internal and external measures of training monotony (TM) and strain (TS) in professional soccer players according to periods of the season and playing positions, and (b) to analyze the relationships between internal and external measures of TM and TS. Twenty male professional players (age = 29.4 ± 4.4 years) were followed for 20 weeks through session rating of perceived exertion (s-RPE), total distance (TD), high-speed running distance (HSRD) and sprint distance (SpD). Regardless of measure, highest mean TM and TS scores were observed in mid-season and end-season. In general, wingers and strikers tended to have greater values in TM. Midfielders exhibited greater TS of TD and SpD. Correlation results for TM revealed that s-RPE was positively associated with SpD in early-season (r = 0.608) and negatively associated in mid-season (r = − 0.506). Regarding the TS, result demonstrated that s-RPE is negatively associated with HSRD in early-season (r = − 0.464) and positively associated in mid-season (r = 0.476). In general, there different meanings in correlations between internal and external measures across the season. On the one hand, our findings highlighted that TM and TS of professional soccer players is sensitive to period of the season and player’s position, but on other hand, correlation analyses proved that changes in one external/internal measure does not cause changes in another external/internal measure which support the constant monitoring of these values across the season.
Six genetically linked mutations in the CD36 gene significantly delay the onset of Alzheimer's disease
Authors: Šerý Omar , Zeman Tomáš , Sheardová Kateřina , Vyhnálek Martin , Marková Hana , Laczó Jan , Lochman Jan , Kralik Petr , Vrzalová Kamila , Dziedzinska Radka , Balcar Vladimir J. , Hort Jakub 
Published: June 2022

AbstractThe risk of Alzheimer’s disease (AD) has a strong genetic component, also in the case of late-onset AD (LOAD). Attempts to sequence whole genome in large populations of subjects have identified only a few mutations common to most of the patients with AD. Targeting smaller well-characterized groups of subjects where specific genetic variations in selected genes could be related to precisely defined psychological traits typical of dementia is needed to better understand the heritability of AD. More than one thousand participants, categorized according to cognitive deficits, were assessed using 14 psychometric tests evaluating performance in five cognitive domains (attention/working memory, memory, language, executive functions, visuospatial functions). CD36 was selected as a gene previously shown to be implicated in the etiology of AD. A total of 174 polymorphisms were tested for associations with cognition-related traits and other AD-relevant data using the next generation sequencing. Several associations between single nucleotide polymorphisms (SNP’s) and the cognitive deficits have been found (rs12667404 with language performance, rs3211827 and rs41272372 with executive functions, rs137984792 with visuospatial performance). The most prominent association was found between a group of genotypes in six genetically linked and the age at which the AD patients presented with, or developed, a full-blown dementia. The identified alleles appear to be associated with a delay in the onset of LOAD. In silico studies suggested that the SNP’s alter the expression of CD36 thus potentially affecting CD36-related neuroinflammation and other molecular and cellular mechanisms known to be involved in the neuronal loss leading to AD. The main outcome of the study is an identification of a set of six new mutations apparently conferring a distinct protection against AD and delaying the onset by about 8 years. Additional mutations in CD36 associated with certain traits characteristic of the cognitive decline in AD have also been found.
PALB2 or BARD1 loss confers homologous recombination deficiency and PARP inhibitor sensitivity in prostate cancer
Authors: Dillon Kasia M. , Bekele Raie T. , Sztupinszki Zsofia , Hanlon Timothy , Rafiei Shahrzad , Szallasi Zoltan , Choudhury Atish D. , Mouw Kent W. 
Published: June 2022

AbstractPARP inhibitors were recently approved for treatment of molecularly-defined subsets of metastatic castrate-resistant prostate cancer (mCRPC) patients. Although the PARP inhibitor olaparib was approved for use in patients with a mutation in one of fourteen genes, the mutation frequency of the genes varies widely in mCRPC and the impact of the less commonly altered genes on PARP inhibitor sensitivity is uncertain. We used functional approaches to directly test the impact of PALB2 and BARD1 loss on homologous recombination (HR) function and PARP inhibitor sensitivity in prostate cancer cell lines. PALB2 or BARD1 loss led to decreased HR function as measured by loss of radiation-induced Rad51 foci formation as well as decreased HR capacity in a cell-based reporter assay. PALB2 or BARD1 loss also significantly increased sensitivity to the PARP inhibitors olaparib and rucaparib across a panel of prostate cancer cell lines. These data support PALB2 and BARD1 loss as markers of clinically relevant PARP inhibitor sensitivity and highlight the potential to use functional approaches to complement and extend findings from clinical trials of targeted agents.
A systematic review of engagement reporting in remote measurement studies for health symptom tracking
Authors: White Katie M. , Williamson Charlotte , Bergou Nicol , Oetzmann Carolin , de Angel Valeria , Matcham Faith , Henderson Claire , Hotopf Matthew 
Published: June 2022

AbstractRemote Measurement Technologies (RMTs) could revolutionise management of chronic health conditions by providing real-time symptom tracking. However, the promise of RMTs relies on user engagement, which at present is variably reported in the field. This review aimed to synthesise the RMT literature to identify how and to what extent engagement is defined, measured, and reported, and to present recommendations for the standardisation of future work. Seven databases (Embase, MEDLINE and PsycINFO (via Ovid), PubMed, IEEE Xplore, Web of Science, and Cochrane Central Register of Controlled Trials) were searched in July 2020 for papers using RMT apps for symptom monitoring in adults with a health condition, prompting users to track at least three times during the study period. Data were synthesised using critical interpretive synthesis. A total of 76 papers met the inclusion criteria. Sixty five percent of papers did not include a definition of engagement. Thirty five percent included both a definition and measurement of engagement. Four synthetic constructs were developed for measuring engagement: (i) engagement with the research protocol, (ii) objective RMT engagement, (iii) subjective RMT engagement, and (iv) interactions between objective and subjective RMT engagement. The field is currently impeded by incoherent measures and a lack of consideration for engagement definitions. A process for implementing the reporting of engagement in study design is presented, alongside a framework for definition and measurement options available. Future work should consider engagement with RMTs as distinct from the wider eHealth literature, and measure objective versus subjective RMT engagement.Registration: This review has been registered on PROSPERO [CRD42020192652].
An imaging flow cytometry-based methodology for the analysis of single extracellular vesicles in unprocessed human plasma
Authors: Woud Wouter W. , van der Pol Edwin , Mul Erik , Hoogduijn Martin J. , Baan Carla C. , Boer Karin , Merino Ana 
Published: June 2022

AbstractExtracellular vesicles (EVs) are tissue-specific particles released by cells containing valuable diagnostic information in the form of various biomolecules. To rule out selection bias or introduction of artefacts caused by EV isolation techniques, we present a clinically feasible, imaging flow cytometry (IFCM)–based methodology to phenotype and determine the concentration of EVs with a diameter ≤400 nm in human platelet-poor plasma (PPP) without prior isolation of EVs. Instrument calibration (both size and fluorescence) were performed with commercial polystyrene beads. Detergent treatment of EVs was performed to discriminate true vesicular events from artefacts. Using a combination of markers (CFSE & Tetraspanins, or CD9 & CD31) we found that >90% of double-positive fluorescent events represented single EVs. Through this work, we provide a framework that will allow the application of IFCM for EV analysis in peripheral blood plasma in a plethora of experimental and potentially diagnostic settings. Additionally, this direct approach for EV analysis will enable researchers to explore corners of EVs as cellular messengers in healthy and pathological conditions.
Xtrapol8 enables automatic elucidation of low-occupancy intermediate-states in crystallographic studies
Authors: De Zitter Elke , Coquelle Nicolas , Oeser Paula , Barends Thomas R. M. , Colletier Jacques-Philippe 
Published: June 2022

AbstractUnstable states studied in kinetic, time-resolved and ligand-based crystallography are often characterized by a low occupancy, which hinders structure determination by conventional methods. To automatically extract structural information pertaining to these states, we developed Xtrapol8, a program which (i) applies various flavors of Bayesian-statistics weighting to generate the most informative Fourier difference maps; (ii) determines the occupancy of the intermediate states by use of methods hitherto not available; (iii) calculates extrapolated structure factors using the various proposed formalisms while handling the issue of negative structure factor amplitudes, and (iv) refines the corresponding structures in real and reciprocal-space. The use of Xtrapol8 could accelerate data processing in kinetic and time-resolved crystallographic studies, and as well foster the identification of drug-targetable states in ligand-based crystallography.