bluuebunny/crossref_metadata_2025 huggingface dataset:
The Physical-Biogeochemical Responses to a Subsurface Anticyclonic Eddy in the Northwest Pacific
Authors: Ding Ya-nan , Yu Fei , Ren Qiang , Nan Feng , Wang Ran , Liu Yansong , Tang Ying
Published: January 2022

Due to the unique physical processes of mesoscale eddies, the physical and biogeochemical properties within the subsurface anticyclonic eddy (SSAE) and in the surrounding water are distinct. Analyses using satellite and model data have revealed distinct seasonal variations in the central potential density structure of a long-standing SSAE south of Japan; this SSAE exhibits a normal concave isopycnals structure from January to April and a convex lens isopycnals structure from May to December, and these variations may be related to the subduction of low-potential vorticity (PV) mode water. In contrast to the idea of the self-sustained oscillation mechanism, the strength of the SSAE was enhanced due to the eddy kinetic energy provided by dramatic increasing of the positive baroclinic conversion rate during the Kuroshio path transition period from the non-large meander (NLM) path to the large meander (LM) path. Twofold to threefold enhancement of chlorophyll (CHL) was detected in the subsurface CHL maximum layers at the core of the SSAE, and this enhancement was related to the injection of nutrients into the euphotic layer due to winter mixing and the convex of isopycnals. During the period from May to December, elevated CHL and dissolved oxygen (DO) levels and reduced nitrate levels were observed along the periphery of the eddy below the maximum subsurface CHL anomaly depth. The combined result of these two processes: (1) the central downward displaced isopycnals caused by intensified SSAE, and (2) winter mixing deepened to the nutricline due to the thickened mixed layer depth (MLD) and weakened stratification in winter 2017 (during the NLM period) may have led to numerous nutrients and CHL enrichments throughout the mixed layer, thus generating a CHL bloom in the following April. The SSAE intensified in winter 2018 (during the LM period), whereas the shallower MLD and stronger stratification limited the depth of CHL downward displacement.
Validity and Reliability of Pre-matriculation and Institutional Assessments in Predicting USMLE STEP 1 Success: Lessons From a Traditional 2 x 2 Curricular Model
Authors: Puri Nitin , McCarthy Michael , Miller Bobby
Published: January 2022

Purpose

We have observed that students' performance in our pre-clerkship curriculum does not align well with their United States Medical Licensing Examination (USMLE) STEP1 scores. Students at-risk of failing or underperforming on STEP1 have often excelled on our institutional assessments. We sought to test the validity and reliability of our course assessments in predicting STEP1 scores, and in the process, generate and validate a more accurate prediction model for STEP1 performance.

Methods

Student pre-matriculation and course assessment data of the Class of 2020 (n = 76) is used to generate a stepwise STEP1 prediction model, which is tested with the students of the Class of 2021 (n = 71). Predictions are developed at the time of matriculation and subsequently at the end of each course in the programing language R. For the Class of 2021, the predicted STEP1 score is correlated with their actual STEP1 scores, and data agreement is tested with means-difference plots. A similar model is generated and tested for the Class of 2022.

Results

STEP1 predictions based on pre-matriculation data are unreliable and fail to identify at-risk students (R2 = 0.02). STEP1 predictions for most year one courses (anatomy, biochemistry, physiology) correlate poorly with students' actual STEP1 scores (R2 = 0.30). STEP1 predictions improve for year two courses (microbiology, pathology, and pharmacology). But integrated courses with customized NBMEs provide more reliable predictions (R2 = 0.66). Predictions based on these integrated courses are reproducible for the Class of 2022.

Conclusion

MCAT and undergraduate GPA are poor predictors of student's STEP1 scores. Partially integrated courses with biweekly assessments do not promote problem-solving skills and leave students' at-risk of failing STEP1. Only courses with integrated and comprehensive assessments are reliable indicators of students' STEP1 preparation.
The Efficacy and Safety of Janus Kinase Inhibitors for Patients With COVID-19: A Living Systematic Review and Meta-Analysis
Authors: Zhang Xueyang , Shang Lianhan , Fan Guohui , Gu Xiaoying , Xu Jiuyang , Wang Yeming , Huang Lixue , Cao Bin
Published: January 2022

Background

Cytokine storm observed in patients with severe Coronavirus Disease 2019 (COVID-19) contributes to poor clinical outcomes and increased mortality. Janus kinases (JAKs) are important mediators in the cytokine storm. Therefore, we conduct a living systematic review and meta-analysis of the literature investigating efficacy and safety of JAK inhibitors for patients with COVID-19.

Methods

Databases were searched up to December 1, 2021 for interventional and observational studies comparing JAK inhibitor treatment with concurrent control in patients with COVID-19. Efficacy and safety outcomes were evaluated by pooled risk ratio (RR).

Results

Of 3,170 records retrieved, 15 studies were eligible and 13 were evaluated in the meta-analysis (n = 3,977). Based on data from three randomized controlled trials (RCTs), baricitinib treatment significantly decreased mortality by day 28 in hospitalized patients with COVID-19 (RR = 0.64, 95% CI 0.51–0.80) without increasing the incidence of adverse outcomes. In subgroup analysis, patients who required supplemental oxygen (RR = 0.62, 95% CI 0.41–0.95) or high-flow oxygen/non-invasive ventilation (RR = 0.59, 95% CI 0.42–0.85) at baseline benefited most. Pooled analysis of all eligible studies for JAK inhibitors (baricitinib, ruxolitinib, tofacitinib, and nezulcitinib) demonstrated a significant decrease in mortality (RR = 0.62, 95% CI 0.49–0.78) with no increase in the risk of adverse events.

Conclusion

Baricitinib probably decreases mortality in hospitalized adult patients with COVID-19, especially for patients who required supplemental oxygen or high-flow oxygen/non-invasive ventilation at baseline. The efficacy and safety of other JAK inhibitors, such as ruxolitinib, tofacitinib, and nezulcitinib, await more evidence.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021261414, identifier: CRD42021261414.
COVID GEAS: COVID-19 National Survey in Patients With Systemic Autoimmune Diseases
Authors: Gracia Borja Del Carmelo , Sáez Luis , Pallarés Lucio , Velilla Jose , Marín Adela , Martinez-Lostao Luis , Simeón Carmen Pilar , Fanlo Patricia
Published: January 2022

Objectives

COVID-19 outcomes in population with systemic autoimmune diseases (SAD) remain poorly understood. The aim was to examine demographic and clinical factors associated with COVID-19 infection in people with rheumatic disease.

Methods

Two phases cross-sectional survey of individuals with rheumatic disease in April 2020 and October 2020. COVID infection, severity of disease, age, sex, smoking status, underlying rheumatic disease diagnosis, comorbidities and rheumatic disease medications taken immediately prior to infection were analyzed.

Results

A total of 1,529 individuals with autoimmunity disease diagnosis were included. Out of 50 positive patients, 21 required telephone medical assistance, 16 received assessment by primary care physician, 9 were evaluated in Emergency Department and 4 patient required hospitalization. Multivariate analysis was performed without obtaining differences in any of the systemic autoimmune diseases. Regarding the treatments, significant differences were found (p 0.011) in the treatment with anti-TNF-alpha agents with OR 3.422 (1.322–8.858) and a trend to significance (p 0.094) was observed in patients receiving mycophenolate treatment [OR 2.016 (0.996–4-081)].

Conclusions

Anti-TNF-alpha treatment was associated with more than 3-fold risk of suffering from SARS-CoV-2 infection, although in all cases infection was mild. Cumulative incidence in patients with SAD was up to 5 times higher than general population but with great differences between autoimmune diseases.
Prediction Models for Sepsis-Associated Thrombocytopenia Risk in Intensive Care Units Based on a Machine Learning Algorithm
Authors: Jiang Xuandong , Wang Yun , Pan Yuting , Zhang Weimin
Published: January 2022

Sepsis-associated thrombocytopenia (SAT) is a common complication in the intensive care unit (ICU), which significantly increases the mortality rate and leads to poor prognosis of diseases. Machine learning (ML) is widely used in disease prediction in critically ill patients. Here, we aimed to establish prediction models for platelet decrease and severe platelet decrease in ICU patients with sepsis based on four common ML algorithms and identify the best prediction model. The research subjects were 1,455 ICU sepsis patients admitted to Dongyang People's Hospital affiliated with Wenzhou Medical University from January 1, 2015, to October 31, 2019. Basic clinical demographic information, biochemical indicators, and clinical outcomes were recorded. The prediction models were based on four ML algorithms: random forest, neural network, gradient boosting machine, and Bayesian algorithms. Thrombocytopenia was found to occur in 732 patients (49.7%). The mechanical ventilation time and length of ICU stay were longer, and the mortality rate was higher for the thrombocytopenia group than for the non-thrombocytopenia group. The models were validated on an online international database (Medical Information Mart for Intensive Care III). The areas under the receiver operating characteristic curves (AUCs) of the four models for the prediction of thrombocytopenia were between 0.54 and 0.72. The AUCs of the models for the prediction of severe thrombocytopenia were between 0.70 and 0.77. The neural network and gradient boosting machine models effectively predicted the occurrence of SAT, and the Bayesian models had the best performance in predicting severe thrombocytopenia. Therefore, these models can be used to identify such high-risk patients at an early stage and guide individualized clinical treatment, to improve the prognosis of diseases.
Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau
Authors: Chen Yuying , Liu Yongqin , Liu Keshao , Ji Mukan , Li Yang
Published: January 2022

Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.
Curvularia coatesiae XK8, a Potential Bioadsorbent Material for Adsorbing Cd(II) and Sb(III) Compound Pollution: Characteristics and Effects
Authors: Di Zhao , Chaoyang Li , Mengxi Zheng , Yunlin Zhao , Zhenggang Xu , Guiyan Yang
Published: January 2022

Soil heavy metal pollution is a common problem in mining areas. The soil of the Xikuangshan located in Lengshuijiang, Hunan Province, China contains various excessive heavy metals, especially antimony and cadmium. Previous studies have shown that heavy metal-tolerant microorganisms screened from mining areas have the potential to adsorb heavy metals. In this study, we screened out a cadmium and antimony tolerant fungus named XK8 from the slags collected from the Xikuangshan. Then, we explored the single and binary biosorption characteristics of Cd(II) and Sb(III) on it. In our results, the fungus XK8 was identified as Curvularia coatesiae XK8 by ITS sequencing analysis. Under the optimal conditions, in binary biosorption of the XK8, the main effect of the initial cadmium concentration on the cadmium removal rate of XK8 is negative, while the main effect of the initial antimony concentration, biosorption time, and initial pH on the cadmium removal rate of XK8 is positive. The initial pH has the greatest impact on the biosorption of cadmium on XK8, followed by the biosorption time; moreover, the effects of both are stronger than the coexisting ions. SAS analysis shows that under the optimal conditions, the theoretical maximum cadmium removal rate of XK8 is 100%, and the actual removal rate is 67.57%. Compared to the single biosorption with binary biosorption, the maximum biosorption capacity of XK8 for cadmium in the composite biosorption system increased to 23.6 mg g–1. It shows that under the background of high antimony, Sb(III) has a promoting effect on the biosorption of Cd(II) on XK8. In summary, a cadmium and antimony tolerant fungus with strong cadmium biosorption ability under the background of high antimony was screened out. It provides a potential microbial material for the bioremediation of heavy metal pollution.
Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea Surface Waters
Authors: Cordone Angelina , D’Errico Giuseppe , Magliulo Maria , Bolinesi Francesco , Selci Matteo , Basili Marco , de Marco Rocco , Saggiomo Maria , Rivaro Paola , Giovannelli Donato , Mangoni Olga
Published: January 2022

Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. However, the number of studies reporting the simultaneous diversity of the phytoplankton and bacterioplankton in Antarctic waters are limited. Here, we report data on the bacterial diversity in relation to phytoplankton community structure in the surface waters of the Ross Sea during the Austral summer 2017. Our results show partially overlapping bacterioplankton communities between the stations located in the Terra Nova Bay (TNB) coastal waters and the Ross Sea Open Waters (RSOWs), with a dominance of members belonging to the bacterial phyla Bacteroidetes and Proteobacteria. In the TNB coastal area, microbial communities were characterized by a higher abundance of sequences related to heterotrophic bacterial genera such as Polaribacter spp., together with higher phytoplankton biomass and higher relative abundance of diatoms. On the contrary, the phytoplankton biomass in the RSOW were lower, with relatively higher contribution of haptophytes and a higher abundance of sequences related to oligotrophic and mixothrophic bacterial groups like the Oligotrophic Marine Gammaproteobacteria (OMG) group and SAR11. We show that the rate of diversity change between the two locations is influenced by both abiotic (salinity and the nitrogen to phosphorus ratio) and biotic (phytoplankton community structure) factors. Our data provide new insight into the coexistence of the bacterioplankton and phytoplankton in Antarctic waters, suggesting that specific rather than random interaction contribute to the organic matter cycling in the Southern Ocean.
Biocontrol Activity of Nonpathogenic Strains of Fusarium oxysporum: Colonization on the Root Surface to Overcome Nutritional Competition
Authors: Iida Yuichiro , Ogata Aya , Kanda Hiroki , Nishi Oumi , Sushida Hirotoshi , Higashi Yumiko , Tsuge Takashi
Published: January 2022

Fusarium oxysporum is a soil-borne fungal pathogen that causes vascular wilts in a wide variety of crops. Certain nonpathogenic strains of F. oxysporum are known to protect crops against F. oxysporum pathogens. We assessed the biocontrol activities of nonpathogenic mutants of F. oxysporum ff. spp. melonis and lycopersici generated by disruption of the FOW2 gene, which encodes a Zn(II)2Cys6-type transcriptional regulator essential for their pathogenicity. Pre-inoculation of melon or tomato roots with strain ΔFOW2 conidia markedly reduced disease incidence caused by the parental wild-type strain in a concentration-dependent manner of conidial suspensions of ΔFOW2 strains. The biocontrol effect caused by the ΔFOW2 pre-inoculation lasted for at least 7 days. Pre-inoculation of melon roots with the wild-type or ΔFOW2 strain of F. oxysporum f. sp. lycopersici and nonpathogenic F. oxysporum strain also led to biocontrol activity against F. oxysporum f. sp. melonis, indicating that the biocontrol activity of ΔFOW2 strains is due to its nonpathogenic nature, not to the FOW2 disfunction. Conidial germination and hyphal elongation of only the wild-type strain were inhibited on melon root surface pre-inoculated with conidia of strains nonpathogenic to melon plants. Expression of defense-related genes was not significantly induced in roots and aboveground parts of melon seedlings preinoculated with ΔFOW2 conidia. Carbon source competition assay showed that nonpathogenic strains competed with the wild-type strain for a carbon source in soil. Strain ΔFOW2 also competed with the oomycete pathogen Pythium aphanidermatum for carbon source and protected melon plants from P. aphanidermatum. Our results suggest that the biocontrol activity of the nonpathogenic F. oxysporum strains used in this study mainly depends on their extensive colonization of the root surface and outcompeting pathogens for nutrients.
A Transient Metabolic State in Melanoma Persister Cells Mediated by Chemotherapeutic Treatments
Authors: Karki Prashant , Angardi Vahideh , Mier Juan C. , Orman Mehmet A.
Published: January 2022

Persistence is a transient state that poses an important health concern in cancer therapy. The mechanisms associated with persister phenotypes are highly diverse and complex, and many aspects of persister cell physiology remain to be explored. We applied a melanoma cell line and panel of chemotherapeutic agents to show that melanoma persister cells are not necessarily preexisting dormant cells; in fact, they may be induced by cancer chemotherapeutics. Our metabolomics analysis and phenotype microarray assays further demonstrated a transient upregulation in Krebs cycle metabolism in persister cells. We also verified that targeting electron transport chain activity can significantly reduce melanoma persister levels. The reported metabolic remodeling feature seems to be a conserved characteristic of melanoma persistence, as it has been observed in various melanoma persister subpopulations derived from a diverse range of chemotherapeutics. Elucidating a global metabolic mechanism that contributes to persister survival and reversible switching will ultimately foster the development of novel cancer therapeutic strategies.
Modeling the MreB-CbtA Interaction to Facilitate the Prediction and Design of Candidate Antibacterial Peptides
Authors: Awuni Elvis
Published: January 2022

Protein-protein interactions (PPIs) have emerged as promising targets for PPI modulators as alternative drugs because they are essential for most biochemical processes in living organisms. In recent years, a spotlight has been put on the development of peptide-based PPI inhibitors as the next-generation therapeutics to combat antimicrobial resistance taking cognizance of protein-based PPI-modulators that interact with target proteins to inhibit function. Although protein-based PPI inhibitors are not effective therapeutic agents because of their high molecular weights, they could serve as sources for peptide-based pharmaceutics if the target-inhibitor complex is accessible and well characterized. The Escherichia coli (E. coli) toxin protein, CbtA, has been identified as a protein-based PPI modulator that binds to the bacterial actin homolog MreB leading to the perturbation of its polymerization dynamics; and consequently has been suggested to have antibacterial properties. Unfortunately, however, the three-dimensional structures of CbtA and the MreB-CbtA complex are currently not available to facilitate the optimization process of the pharmacological properties of CbtA. In this study, computer modeling strategies were used to predict key MreB-CbtA interactions to facilitate the design of antiMreB peptide candidates. A model of the E. coli CbtA was built using the trRosetta software and its stability was assessed through molecular dynamics (MD) simulations. The modeling and simulations data pointed to a model with reasonable quality and stability. Also, the HADDOCK software was used to predict a possible MreB-CbtA complex, which was characterized through MD simulations and compared with MreB-MreB dimmer. The results suggest that CbtA inhibits MreB through the competitive mechanism whereby CbtA competes with MreB monomers for the interprotofilament interface leading to interference with double protofilament formation. Additionally, by using the antiBP software to predict antibacterial peptides in CbtA, and the MreB-CbtA complex as the reference structure to determine important interactions and contacts, candidate antiMreB peptides were suggested. The peptide sequences could be useful in a rational antimicrobial peptide hybridization strategy to design novel antibiotics. All-inclusive, the data reveal the molecular basis of MreB inhibition by CbtA and can be incorporated in the design/development of the next-generation antibacterial peptides targeting MreB.
Compromised Astrocyte Swelling/Volume Regulation in the Hippocampus of the Triple Transgenic Mouse Model of Alzheimer’s Disease
Authors: Tureckova Jana , Kamenicka Monika , Kolenicova Denisa , Filipi Tereza , Hermanova Zuzana , Kriska Jan , Meszarosova Lenka , Pukajova Barbora , Valihrach Lukas , Androvic Peter , Zucha Daniel , Chmelova Martina , Vargova Lydia , Anderova Miroslava
Published: January 2022

In this study, we aimed to disclose the impact of amyloid-β toxicity and tau pathology on astrocyte swelling, their volume recovery and extracellular space (ECS) diffusion parameters, namely volume fraction (α) and tortuosity (λ), in a triple transgenic mouse model of Alzheimer’s disease (3xTg-AD). Astrocyte volume changes, which reflect astrocyte ability to take up ions/neurotransmitters, were quantified during and after exposure to hypo-osmotic stress, or hyperkalemia in acute hippocampal slices, and were correlated with alterations in ECS diffusion parameters. Astrocyte volume and ECS diffusion parameters were monitored during physiological aging (controls) and during AD progression in 3-, 9-, 12- and 18-month-old mice. In the hippocampus of controls α gradually declined with age, while it remained unaffected in 3xTg-AD mice during the entire time course. Moreover, age-related increases in λ occurred much earlier in 3xTg-AD animals than in controls. In 3xTg-AD mice changes in α induced by hypo-osmotic stress or hyperkalemia were comparable to those observed in controls, however, AD progression affected α recovery following exposure to both. Compared to controls, a smaller astrocyte swelling was detected in 3xTg-AD mice only during hyperkalemia. Since we observed a large variance in astrocyte swelling/volume regulation, we divided them into high- (HRA) and low-responding astrocytes (LRA). In response to hyperkalemia, the incidence of LRA was higher in 3xTg-AD mice than in controls, which may also reflect compromised K+ and neurotransmitter uptake. Furthermore, we performed single-cell RT-qPCR to identify possible age-related alterations in astrocytic gene expression profiles. Already in 3-month-old 3xTg-AD mice, we detected a downregulation of genes affecting the ion/neurotransmitter uptake and cell volume regulation, namely genes of glutamate transporters, α2β2 subunit of Na+/K+-ATPase, connexin 30 or Kir4.1 channel. In conclusion, the aged hippocampus of 3xTg-AD mice displays an enlarged ECS volume fraction and an increased number of obstacles, which emerge earlier than in physiological aging. Both these changes may strongly affect intercellular communication and influence astrocyte ionic/neurotransmitter uptake, which becomes impaired during aging and this phenomenon is manifested earlier in 3xTg-AD mice. The increased incidence of astrocytes with limited ability to take up ions/neurotransmitters may further add to a cytotoxic environment.
Machine Learning-Based Assessment of Cognitive Impairment Using Time-Resolved Near-Infrared Spectroscopy and Basic Blood Test
Authors: Oyama Katsunori , Sakatani Kaoru
Published: January 2022

We have demonstrated that machine learning allows us to predict cognitive function in aged people using near-infrared spectroscopy (NIRS) data or basic blood test data. However, the following points are not yet clear: first, whether there are differences in prediction accuracy between NIRS and blood test data; second, whether there are differences in prediction accuracy for cognitive function in linear models and non-linear models; and third, whether there are changes in prediction accuracy when both NIRS and blood test data are added to the input layer. We used a linear regression model (LR) for the linear model and random forest (RF) and deep neural network (DNN) for the non-linear model. We studied 250 participants (mean age = 73.3 ± 12.6 years) and assessed cognitive function using the Mini Mental State Examination (MMSE) (mean MMSE scores = 22.9 ± 6.1). We used time-resolved NIRS (TNIRS) to measure absolute concentrations of hemoglobin and optical pathlength at rest in the bilateral prefrontal cortices. A basic blood test was performed on the same day. We compared predicted MMSE scores and grand truth MMSE scores; prediction accuracies were evaluated using mean absolute error (MAE) and mean absolute percentage error (MAPE). We found that (1) the DNN-based prediction using TNIRS data exhibited lower MAE and MAPE compared with those using blood test data, (2) the difference in MAPE between TNIRS and blood test data was only 0.3%, (3) adding TNIRS data to the blood test data of the input layer only improved MAPE by 1.0% compared to the use of blood test data alone, whereas the use of the blood test data alone exhibited the prediction accuracy with 81.8% sensitivity and 91.3% specificity (N = 202, repeated five-fold cross validation). Given these findings and the benefits of using blood test data (low cost and large-scale screening possible), we concluded that the DNN model using blood test data is still the most suitable for mass screening.
Cognitive Workload of Tugboat Captains in Realistic Scenarios: Adaptive Spatial Filtering for Transfer Between Conditions
Authors: Miklody Daniel , Blankertz Benjamin
Published: January 2022

Changing and often class-dependent non-stationarities of signals are a big challenge in the transfer of common findings in cognitive workload estimation using Electroencephalography (EEG) from laboratory experiments to realistic scenarios or other experiments. Additionally, it often remains an open question whether actual cognitive workload reflected by brain signals was the main contribution to the estimation or discriminative and class-dependent muscle and eye activity, which can be secondary effects of changing workload levels. Within this study, we investigated a novel approach to spatial filtering based on beamforming adapted to changing settings. We compare it to no spatial filtering and Common Spatial Patterns (CSP). We used a realistic maneuvering task, as well as an auditoryn-backsecondary task on a tugboat simulator as two different conditions to induce workload changes on professional tugboat captains. Apart from the typical within condition classification, we investigated the ability of the different classification methods to transfer between then-backcondition and the maneuvering task. The results show a clear advantage of the proposed approach over the others in the challenging transfer setting. While no filtering leads to lowest within-condition normalized classification loss on average in two scenarios (22 and 10%), our approach using adaptive beamforming (30 and 18%) performs comparably to CSP (33 and 15%). Importantly, in the transfer from one to another setting, no filtering and CSP lead to performance around chance level (45 to 53%), while our approach in contrast is the only one capable of classifying in all other scenarios (34 and 35%) with a significant difference from chance level. The changing signal composition over the scenarios leads to a need to adapt the spatial filtering in order to be transferable. With our approach, the transfer is successful due to filtering being optimized for the extraction of neural components and additional investigation of their scalp patterns revealed mainly neural origin. Interesting findings are that rather the patterns slightly change between conditions. We conclude that the approaches with low normalized loss depend on eye and muscle activity which is successful for classification within conditions, but fail in the classifier transfer since eye and muscle contributions are highly condition-specific.
Adaptive Whisking in Mice
Authors: Chakrabarti Shubhodeep , Nambiar Jithin , Schwarz Cornelius
Published: January 2022

Rodents generate rhythmic whisking movements to explore their environment. Whisking trajectories, for one, appear as a fixed pattern of whisk cycles at 5–10 Hz driven by a brain stem central pattern generator. In contrast, whisking behavior is thought to be versatile and adaptable to behavioral goals. To begin to systematically investigate such behavioral adaptation, we established a whisking task, in which mice altered the trajectories of whisking in a goal-oriented fashion to gain rewards. Mice were trained to set the whisker to a defined starting position and generate a protraction movement across a virtual target (no touch-related tactile feedback). By ramping up target distance based on reward history, we observed that mice are able to generate highly specific whisking patterns suited to keep reward probability constant. On a sensorimotor level, the behavioral adaptation was realized by adjusting whisker kinematics: more distant locations were targeted using higher velocities (i.e., pointing to longer force generation), rather than by generating higher acceleration (i.e., pointing to stronger forces). We tested the suitability of the paradigm of tracking subtle alteration in whisking motor commands using small lesions in the rhythmic whisking subfield (RW) of the whisking-related primary motor cortex. Small contralateral RW lesions generated the deterioration of whisking kinematics with a latency of 12 days post-lesion, a change that was readily discriminated from changes in the behavioral adaptation by the paradigm.
Associations Between Independent Assessments of Child Appetite Self-Regulation: A Narrative Review
Authors: Papaioannou Maria A. , Micheli Nilda , Power Thomas G. , Fisher Jennifer O. , Hughes Sheryl O.
Published: January 2022

A variety of eating behaviors among children have been associated with obesity risk and are thought to broadly reflect child appetite self-regulation (ASR). While ASR is thought to occur on cognitive, emotional, motivational, biological, and behavioral levels, the inter-relatedness of ASR constructs as assessed by different methods/measures is not well-characterized. This narrative review describes the correspondence between different methods/measures of child ASR constructs as assessed by self-report questionnaires and/or observational tasks and their relationship to child standardized body mass index (BMIz). Research involving at least two different methods/measures is presented including observational tasks such as the Eating in the Absence of Hunger task, compensation trials, and eating rate, as well as various child eating behavior self-report questionnaires. Keyword searches in the PubMed and PsycINFO databases for articles published between 2000 and July 2021 identified 21,042 articles. Eighteen articles met the inclusion criteria and examined at least two of the targeted measures. Studies comparing questionnaire data with other questionnaire data showed the most evidence of significant associations (r values ranging from −0.45 to 0.49), whereas studies comparing questionnaires with observational tasks mostly showed weak (r values ranging from −0.17 to 0.19) or not significant associations, with only few studies finding moderate associations (r values ranging from −0.38 to 0.33). Studies comparing different observational tasks showed no significant associations. Overall, studies comparing self-report questionnaires showed the most correspondence, whereas those comparing observational tasks showed no correspondence. Studies across methods (questionnaires with tasks) showed less correspondence. Significant associations were found between ASR constructs and child BMIz across five studies using self-report questionnaires and two studies using observational tasks. Future research is needed to clearly define the various ASR constructs, their expected correspondence, and the strength of that correspondence, as well as the relations between ASR constructs and child weight among youth with and without overweight/obesity.
Serum Inflammatory Biomarkers Contribute to the Prognosis Prediction in High-Grade Glioma
Authors: Chen Xiao-Yong , Pan Ding-Long , Xu Jia-Heng , Chen Yue , Xu Wei-Feng , Chen Jin-Yuan , Wu Zan-Yi , Lin Yuan-Xiang , You Hong-Hai , Ding Chen-Yu , Kang De-Zhi
Published: January 2022

Background

To evaluate the prognostic value of serum inflammatory biomarkers and develop a risk stratification model for high-grade glioma (HGG) patients based on clinical, laboratory, radiological, and pathological factors.

Materials and Methods

A retrospective study of 199 patients with HGG was conducted. Patients were divided into a training cohort (n = 120) and a validation cohort (n = 79). The effects of potential associated factors on the overall survival (OS) time were investigated and the benefits of serum inflammatory biomarkers in improving predictive performance was assessed. Univariable and multivariable Cox regression analyses, the least absolute shrinkage and selection operator (LASSO) regression analysis, and support vector machines (SVM) were used to select variables for the final nomogram model.

Results

After multivariable Cox, LASSO, and SVM analysis, in addition to 3 other clinico-pathologic factors, platelet-to-lymphocyte ratio (PLR) >144.4 (hazard ratio [HR], 2.05; 95% confidence interval [CI], 1.25–3.38; P = 0.005) were left for constructing the predictive model. The model with PLR exhibited a better predictive performance than that without them in both cohorts. The nomogram based on the model showed an excellent ability of discrimination in the entire cohort (C-index, 0.747; 95%CI, 0.706–0.788). The calibration curves showed good consistency between the predicted and observed survival probability.

Conclusion

Our study confirmed the prognostic value of serum inflammatory biomarkers including PLR and established a comprehensive scoring system for the OS prediction in HGG patients.
Identification of Circular RNA-Based Immunomodulatory Networks in Colorectal Cancer
Authors: Feng Zongfeng , Li Leyan , Tu Yi , Shu Xufeng , Zhang Yang , Zeng Qingwen , Luo Lianghua , Wu Ahao , Chen Wenzheng , Cao Yi , Li Zhengrong
Published: January 2022

Background

Circular RNAs (circRNAs) have been recently proposed as hub molecules in various diseases, especially in tumours. We found that circRNAs derived from ribonuclease P RNA component H1 (RPPH1) were highly expressed in colorectal cancer (CRC) samples from Gene Expression Omnibus (GEO) datasets.

Objective

We sought to identify new circRNAs derived from RPPH1 and investigate their regulation of the competing endogenous RNA (ceRNA) and RNA binding protein (RBP) networks of CRC immune infiltration.

Methods

The circRNA expression profiles miRNA and mRNA data were extracted from the GEO and The Cancer Genome Atlas (TCGA) datasets, respectively. The differentially expressed (DE) RNAs were identified using R software and online server tools, and the circRNA–miRNA–mRNA and circRNA–protein networks were constructed using Cytoscape. The relationship between targeted genes and immune infiltration was identified using the GEPIA2 and TIMER2 online server tools.

Results

A ceRNA network, including eight circRNAs, five miRNAs, and six mRNAs, was revealed. Moreover, a circRNA–protein network, including eight circRNAs and 49 proteins, was established. The targeted genes, ENOX1, NCAM1, SAMD4A, and ZC3H10, are closely related to CRC tumour-infiltrating macrophages.

Conclusions

We analysed the characteristics of circRNA from RPPH1 as competing for endogenous RNA binding miRNA or protein in CRC macrophage infiltration. The results point towards the development of a new diagnostic and therapeutic paradigm for CRC.
Case Report: Durable Clinical Response to Third-Line Pyrotinib After Resistance to Trastuzumab in a Gastric Cancer Patient
Authors: Wu Junyi , Li Lei , Qin Jun , Yan Zhengqing , Chen Shiqing , Jin Tao , Xu Junming
Published: January 2022

Background

Trastuzumab plus chemotherapy remains the standard first-line treatment strategy for HER2-positive gastric cancer (GC). Trastuzumab resistance, on the other hand, remains a significant issue. There are a few effective anti-HER2 agents for patients who develop resistance to trastuzumab.

Case Presentation

A 49-year-old female was diagnosed with stage IV GC with liver and lung metastasis in July 2017. She underwent gastrostomy, and the immunohistochemistry (IHC) result of postoperative tissue demonstrated HER2 (3+). She received first-line treatment of trastuzumab (440 mg), oxaliplatin (200 mg), and S-1 (40 mg). After treatment for 6 months, the patient achieved complete response (CR) with PFS up to 21 months. After progression, she subsequently received trastuzumab (440 mg) plus oxaliplatin (200 mg) as second-line treatment. However, the patient developed resistance to trastuzumab after 12 months of treatment. She started to receive third-line treatment of irinotecan (200 mg d1) and capecitabine (60 mg bid) plus pyrotinib (400 mg/day). After 2 months of treatment, the tumor is evaluated as partial response with PFS of 12 months.

Conclusions

We presented a patient with HER2-positive GC who benefited from the pyrotinib-based treatment after two lines of trastuzumab-based therapies failed. Further research is required to validate such conclusions.
A New Strategy to Identify ceRNA-Based CCDC144NL-AS1/SERPINE1 Regulatory Axis as a Novel Prognostic Biomarker for Stomach Adenocarcinoma via High Throughput Transcriptome Data Mining and Computational Verification
Authors: Huang Zhihong , Liu Xinkui , Wu Chao , Lu Shan , Antony Stalin , Zhou Wei , Zhang Jingyuan , Wu Zhishan , Tan Yingying , Fan Xiaotian , You Leiming , Jing Zhiwei , Wu Jiarui
Published: January 2022

Stomach adenocarcinoma (STAD) is one of the most malignant cancers that endanger human health. There is growing evidence that competitive endogenous RNA (ceRNA) regulatory networks play an important role in various human tumors. However, the complexity and behavioral characteristics of the ceRNA network in STAD are still unclear. In this study, we constructed a ceRNA regulatory network to identify the potential prognostic biomarkers associated with STAD. The expression profile of lncRNA, miRNA, and mRNA was downloaded from The Cancer Genome Atlas (TCGA). After performing bioinformatics analysis, the CCDC144NL-AS1/hsa-miR-145-5p/SERPINE1 ceRNA network associated to STAD prognosis of STAD was obtained. The CCDC144NL-AS1/SERPINE1 axis in the ceRNA network was identified by correlation analysis and considered as a clinical prognosis model by Cox regression analysis. In addition, methylation analysis indicated that the abnormal upregulation of CCDC144NL-AS1/SERPINE1 axis might be related to the aberrant methylation of some sites, and immune infiltration analysis suggested that CCDC144NL-AS1/SERPINE1 axis probably influences the alteration of tumor immune microenvironment and the occurrence and development of STAD. In particular, the CCDC144NL-AS1/SERPINE1 axis based on the ceRNA network constructed in the present study might be an important novel factor correlating with the diagnosis and prognosis of STAD.
Feasibility of Shear Wave Elastography Imaging for Evaluating the Biological Behavior of Breast Cancer
Authors: Liu Chaoxu , Zhou Jin , Chang Cai , Zhi Wenxiang
Published: January 2022

Objective

To explore the feasibility of shear wave elastography (SWE) parameters for assessing the biological behavior of breast cancer.

Materials and Methods

In this prospective study, 224 breast cancer lesions in 216 female patients were examined by B-mode ultrasound and shear wave elastography in sequence. The maximum size (Smax) of the lesion was measured by B-mode ultrasound, and then shear wave elastography was performed on this section to obtain relevant parameters, including maximum elasticity (Emax), mean elasticity (Emean), standard deviation of elasticity (SD), and the area ratio of shear wave elastography to B-mode ultrasound (AR). The relationship between SWE parameters and pathological type, histopathological classification, histological grade, lymphovascular invasion status (LVI), axillary lymph node status (ALN), and immunohistochemistry of breast cancer lesions was performed according to postoperative pathology.

Results

In the univariate analysis, the pathological type and histopathological classification of breast cancer were not significantly associated with SWE parameters; with an increase in the histological grade of invasive ductal carcinoma (IDC), SD (p = 0.016) and Smax (p = 0.000) values increased. In the ALN-positive group, Smax (p = 0.004) was significantly greater than in the ALN-negative group; Smax (p = 0.003), Emax (p = 0.034), and SD (p = 0.045) were significantly higher in the LVI-positive group than in the LVI-negative group; SD (p = 0.043, p = 0.047) and Smax (p = 0.000, p = 0.000) were significantly lower in the ER+ and PR+ groups than in the ER- and PR- groups, respectively; AR (p = 0.032) was significantly higher in the ER+ groups than in the ER- groups, and Smax (p = 0.002) of the HER2+ group showed higher values than that of the HER2- group; Smax (p = 0.000), SD (p = 0.006), and Emax (p = 0.004) of the Ki-67 high-expression group showed significantly higher values than those of the Ki-67 low-expression group. In the multivariate analysis, Ki-67 was an independent factor of Smax (p = 0.005), Emax (p = 0.004), and SD (p = 0.006); ER was an independent influencing factor of Smax (p = 0.000) and AR (p = 0.032). LVI independently influences Smax (p = 0.006).

Conclusions

The SWE parameters Emax, SD, and AR can be used to evaluate the biological behavior of breast cancer.
Role of Long Non-Coding RNA LINC00641 in Cancer
Authors: Han Xue , Zhang Shitai
Published: January 2022

Long non-coding RNAs (lncRNAs) are non-protein coding RNAs with more than 200 nucleic acids in length. When lncRNAs are located in the nucleus, they regulate chromosome structure, participate in chromatin remodeling, and act as transcription regulators. When lncRNAs are exported to the cytoplasm, they regulate mRNA stability, regulate translation, and interfere with post-translational modification. In recent years, more and more evidences have shown that lncRNA can regulate the biological processes of tumor proliferation, apoptosis, invasion and metastasis, and can participate in a variety of tumor signaling pathways. Long-gene non-protein coding RNA641 (LINC00641), located on human chromosome 14q11.2, is differentially expressed in a variety of tumors and is related to overall survival and prognosis, etc. Interfering the expression of LINC00641 can lead to changes in tumor cell proliferation, invasion, metastasis, apoptosis and other biological behaviors. Therefore, LINC00641 is a promising new biomarker and potential clinical therapeutic target. In this review, the biological functions, related mechanisms and clinical significance of LINC00641 in many human cancers are described in detail.
Chromosomal Aberrations in Blood Lymphocytes as Predictors of Respiratory Function After Stereotactic Lung Irradiation
Authors: Kocsis Zsuzsa S. , Farkas Gyöngyi , Bajcsay András , Kun-Gazda Márta , Lövey József , Ostoros Gyula , Pócza Tamás , Herein András , Ladányi Katalin , Székely Gábor , Markóczy Zsolt , Takácsi-Nagy Zoltán , Polgár Csaba , Juranyi Zsolt
Published: January 2022

Due to the profound difference in radiosensitivity of patients and various side effects caused by this phenomenon, a radiosensitivity marker is needed. Prediction by a marker may help personalise the treatment. In this study, we tested chromosomal aberrations (CA) of in vitro irradiated blood as predictor of pulmonary function decrease of nonsmall cell lung cancer (NSCLC) patients and also compared it with the CAs in the blood of irradiated patients. Peripheral blood samples were taken from 45 lung cancer patients before stereotactic radiotherapy (SBRT) and immediately after the last fraction and 3, 6, 9, 12, 15, 18, 21, and 24 months later. Respiratory function measurements were performed at the same time. Diffusing capacity of lung for carbon monoxide (DLCO), forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1s), and FEV1s/FVC (FEV1%) were monitored. Metaphase preparations of lymphocytes were made with standard procedures, and chromosome aberrations were analysed. In our cohort, the 36-month local relapse-free survival was 97.4%, and the distant metastasis-free survival was 71.5% at 36 months. There was no change in the mean of the pulmonary function tests (PFTs) after the therapy. However, there was a considerable variability between the patients. Therefore, we subtracted the baseline and normalised the PFT values. There were significant decreases at 12–24 months in relative FEV1s and relative FEV1%. The tendentious decrease of the PFTs could be predicted by the in vitro chromosome aberration data. We also found connections between the in vitro and in vivo CA values (i.e., dicentrics plus rings after 3 Gy irradiation predicts dicentric-plus-ring value directly after the radiotherapy/V54 Gy (p = 0.001 24.2%)).

We found that—after further validation—chromosome aberrations resulted from in vitro irradiation before radiotherapy can be a predictive marker of pulmonary function decrease after lung irradiation.