bluuebunny/crossref_metadata_2025 huggingface dataset:
Gravity compensation of a 2R1T mechanism with remote center of motion for minimally invasive transnasal surgery applications
Authors: Aldanmaz Ataol Behram , Ayit Orhan , Kiper Gökhan , Dede Mehmet İsmet Can
Published: May 2022

This work addresses the gravity balancing of a 2R1T (2 rotations – 1 translation) mechanism with remote center of motion. A previously developed balancing solution is modified and applied to a prototype, and test results are presented. The mechanism is an endoscope holder for minimally invasive transnasal pituitary gland surgery. In this surgery, the endoscope is inserted through a nostril of the patient through a natural path to the pituitary gland. During the surgery, it is vital for the manipulator to be statically balanced so that in case of a motor failure, the patient is protected against any harmful motion of the endoscope. Additionally, static balancing takes the gravitational load from the actuators and hence facilitates the control of the mechanism. The mechanism is a 2URRR-URR type parallel manipulator with three legs. The payload mass is distributed to the legs on the sides. By using counter-masses for two links of each leg, the center of mass of each leg is lumped on the proximal link which simplifies the problem of balancing of a two degree-of-freedom inverted pendulum. The two proximal links with the lumped mass are statically balanced via springs. Dynamic simulations indicate that when the mechanism is statically balanced, generated actuator torques are reduced by 93.5%. Finally, the balancing solution is implemented on the prototype of the manipulator. The tests indicate that the manipulator is statically balanced within its task space when the actuators are disconnected. When the actuators are connected, the torque requirements decrease by about 37.8% with balancing.
Religiosity, impulsivity, and compulsivity in university students
Authors: Grant Jon E. , Blum Austin W. , Chamberlain Samuel R. , Lust Katherine
Published: May 2022

Objectives

Prior research suggests that religiosity may be associated with healthier levels of mental health in certain domains (eg, higher self-esteem and lower rates of substance use problems). However, very little is known about religiosity and impulsive plus compulsive tendencies. This study examined associations between religiosity and impulsive and compulsive behaviors and traits among university students.

Methods

Nine thousand, four hundred and forty-nine students received a 156-item anonymous online survey which assessed religiosity, alcohol and drug use, mental health issues, and impulsive and compulsive traits. Two groups of interest were defined: those with high religiosity, and those with low religiosity, based on z-scores. The two groups were compared on the measures of interest.

Results

Three thousand, five hundred and seventy-two university students (57.1% female) responded to the survey. Those with high levels of organizational religious activity, as well as those with high levels of intrinsic or subjective religiosity, differed from their fellow students in having better self-esteem, being less likely to have alcohol or drug problems, and generally being less impulsive in terms of attention and planning. Compulsivity did not differ between groups. Associations were of small effect size except for the link between religiosity and lower impulsivity, which was of medium effect size.

Conclusion

This study shows a link between higher religiosity and lower impulsivity, as well as higher levels of mental health across several domains. Whether these associations are causal—and if so, the direction of such causality—requires rigorous longitudinal research.
Breaking the Impasse: Rethinking Refugee Integration through the Equality Act 2010 in the United Kingdom
Authors: Walkey Claire , Brown Philip , Martin Philip
Published: May 2022

Integration is widely considered to be difficult to define and even harder to facilitate. Whist the integration of migrants to the United Kingdom (UK) remains a ‘hot topic’ in policy, politics and public opinion it is also the subject of numerous attempts to conceptualise and measure it. In this article we draw on empirical research undertaken with a wide range of organisations working between refugees and powerful national organisations which perform everyday ‘integration work’. We present a possible framework for operationalising and enriching the day-to-day work of the integration of refugees. We explore this work through the lens of the Equality Act 2010. In so doing, we aim to demonstrate that more closely aligning ‘integration work’ within the framework of the Equality Act provides both greater conceptual and operational clarity about how to enhance the integration of refugees in the UK.
Cell-TypeAnalyzer: A flexible Fiji/ImageJ plugin to classify cells according to user-defined criteria
Authors: Cayuela López Ana , Gómez-Pedrero José A. , Blanco Ana M. O. , Sorzano Carlos Oscar S.
Published: May 2022

Fluorescence microscopy techniques have experienced a substantial increase in the visualization and analysis of many biological processes in life science. We describe a semiautomated and versatile tool called Cell-TypeAnalyzer to avoid the time-consuming and biased manual classification of cells according to cell types. It consists of an open-source plugin for Fiji or ImageJ to detect and classify cells in 2D images. Our workflow consists of (a) image preprocessing actions, data spatial calibration, and region of interest for analysis; (b) segmentation to isolate cells from background (optionally including user-defined preprocessing steps helping the identification of cells); (c) extraction of features from each cell; (d) filters to select relevant cells; (e) definition of specific criteria to be included in the different cell types; (f) cell classification; and (g) flexible analysis of the results. Our software provides a modular and flexible strategy to perform cell classification through a wizard-like graphical user interface in which the user is intuitively guided through each step of the analysis. This procedure may be applied in batch mode to multiple microscopy files. Once the analysis is set up, it can be automatically and efficiently performed on many images. The plugin does not require any programming skill and can analyze cells in many different acquisition setups.
Twins’ Continuing Tales: New Evidence Reshapes Thinking/Appreciation and Recognition: Honoring Colleagues, Honoring Twins; Remembering Colleagues, Remembering Twins / In the Media: Ukrainian Twins in Wartime; Twins Born in Different Years; Identical Twin Surrogate; A Quaternary Family; Abducted Twins in Serbia
Authors: Segal Nancy L.
Published: May 2022

Twin research proceeds at a rapid pace, with new findings constantly modifying our knowledge and thoughts about many issues. In the present article, this concept is applied to the writing of books and articles about twins, with special emphasis on the author’s recent experience. My lead essay in most contributions to the News, Views and Comment section of this journal is usually followed by a review of current research findings; however, significant events necessitated a departure from this format. At this time, it is important to both honor and remember colleagues and twins, both past and present. The final entry in this article highlights media events that variously pose biological and social implications for our field. They include the hardships of Ukrainian twins during wartime; twins born in different years; identical twin surrogacy, a quaternary family and abducted twins in Serbia.
Evaluation of COAMPS Boundary Layer Refractivity Forecast Accuracy for 2–40 GHz Electromagnetic Wave Propagation
Authors: Xu Luyao , Yardim Caglar , Haack Tracy
Published: May 2022

In this paper, the performance of the Coupled Ocean‐Atmosphere Mesoscale Prediction System (COAMPS®) electromagnetic (EM) propagation forecast is assessed using numerous metrics such as forecast lengths, frequencies, ranges, and spatial resolutions. The modeled PL (Propagation Loss) for 2–40 GHz based on the COAMPS ®predicted refractivity profiles is evaluated by 1 month of range‐dependent measurements, which were collected during Coupled Air‐Sea Processes and Electromagnetic ducting Research (CASPER) East Campaign. PL data were collected using a shore‐to‐ship radio link, near the coast of Duck, NC. Mesoscale atmospheric refractivity predictions for the CASPER East operational area are provided by COAMPS®. Propagation loss predictions are computed from these refractivity profiles via a parabolic wave equation propagation code. The results show a good agreement between the COAMPS®‐predicted and the measured propagation loss for the northwest Atlantic region. The analyses show that the prediction error varies from 3 to 8 dB as the frequency increases from 2 to 40 GHz. In addition, COAMPS® successfully tracked the changes in the refractivity field even when the forecast length increased from 0 to 48 hr, with only a marginal degradation in EM prediction accuracy within the first 12 hr. Higher horizontal range resolution does not result in significant improvement in EM predictions as long as there are at least 2 M‐profiles that allows the EM propagation code to capture the first order horizontal variation. Low‐resolution, high order nested COAMPS® fields still produce good EM forecasts for this particular geometry.
Telehealth Provision of Parent–Child Interaction Therapy During the COVID-19 Pandemic: A Case Report
Authors: Bono Madeline H.
Published: May 2022

Objective: To present a case report detailing the trajectory of a caregiver-targeted intervention – Parent-Child Interaction Therapy (PCIT) – delivered via telehealth to a five-year-old pediatric brain cancer survivor with externalizing behaviors during the COVID-19 pandemic. Method: The patient’s medical and developmental history are presented. The patient’s case conceptualization and intervention rationale are discussed. The course of the patient’s PCIT treatment is described. Results: After 10 PCIT sessions following an intake session, the frequency of the patient’s externalizing behaviors was reduced, and the patient’s mother reported feeling more competent and less distressed. At a six-month follow-up, the patient’s mother reported maintenance of treatment gains. Conclusions: Telehealth-delivered PCIT shows promise as a parent-directed intervention that can reduce parental distress and the frequency of externalizing behaviors in young children. The intervention was seen by a medically complex patient’s family as feasible and acceptable for meeting their behavioral health needs during a public health emergency. Further research into PCIT’s implementation possibilities may help to bridge present treatment gaps for young children with externalizing behaviors across a variety of settings.

Implications for Impact Statement

This case study describes the processes and outcomes of a caregiver-directed therapy – Parent-Child Interaction Therapy (PCIT) – delivered remotely to a mother and her child, a five-year-old pediatric brain cancer survivor. The positive outcomes in this case support that telehealth-delivered PCIT is effective for medically complex patients. This case highlights how parent-targeted telehealth interventions can address barriers to health care-accessibility.
Understanding Solicitous Parenting and Pain Acceptance in Pediatric Patients With Abdominal Pain
Authors: Wagoner Scott T. , Deacy Amanda D. , Friesen Craig A. , Schurman Jennifer V.
Published: May 2022

Objective:

The current study sought to explore how solicitous parenting predicts patient engagement in valued activities (i.e., activity engagement) and prioritization of controlling pain (i.e., pain willingness), two factors of pain acceptance. We also examined how solicitous parenting and abdominal pain severity interact to predict these two factors.

Method:

Participants were 119 pediatric patients seen for an initial evaluation in a multidisciplinary abdominal pain clinic. Patients met criteria for a Rome functional gastrointestinal disorder, and, as part of standard care, patients and their caregivers completed questionnaires assessing solicitous parenting, pain acceptance, and abdominal pain severity.

Results:

Greater negatively reinforcing solicitous parenting predicted lower activity engagement and pain willingness. Further, positively reinforcing solicitous parenting did not add significant variance in predicting activity engagement or pain willingness after accounting for variance predicted by negatively reinforcing solicitous parenting. Last, while negatively reinforcing solicitous parenting and abdominal pain severity did not interact to predict activity engagement or pain willingness, abdominal pain severity predicted significant variance in each facet of pain acceptance even after accounting for negatively reinforcing solicitous parenting.

Conclusions:

Results suggest that patients experiencing negatively reinforcing solicitous parenting may engage in valued activities less and be less willing to tolerate pain while prioritizing other life goals. Findings highlight the importance of monitoring parenting behavior and identifying goals that will encourage patient action in the face of increased pain severity.

Implications for Impact Statement

This study suggests that how parents respond to their child’s abdominal pain relates to how the child views pain and acts while in pain.
Ultraviolet phosphorescent carbon nanodots
Authors: Song Shi-Yu , Liu Kai-Kai , Cao Qing , Mao Xin , Zhao Wen-Bo , Wang Yong , Liang Ya-Chuan , Zang Jin-Hao , Lou Qing , Dong Lin , Shan Chong-Xin
Published: May 2022

Phosphorescent carbon nanodots (CNDs) have generated enormous interest recently, and the CND phosphorescence is usually located in the visible region, while ultraviolet (UV) phosphorescent CNDs have not been reported thus far. Herein, the UV phosphorescence of CNDs was achieved by decreasing conjugation size and in-situ spatial confinement in a NaCNO crystal. The electron transition from the px to the sp2 orbit of the N atoms within the CNDs can generate one-unit orbital angular momentum, providing a driving force for the triplet excitons population of the CNDs. The confinement caused by the NaCNO crystal reduces the energy dissipation paths of the generated triplet excitons. By further tailoring the size of the CNDs, the phosphorescence wavelength can be tuned to 348 nm, and the room temperature lifetime of the CNDs can reach 15.8 ms. As a demonstration, the UV phosphorescent CNDs were used for inactivating gram-negative and gram-positive bacteria through the emission of their high-energy photons over a long duration, and the resulting antibacterial efficiency reached over 99.9%. This work provides a rational design strategy for UV phosphorescent CNDs and demonstrates their novel antibacterial applications.
Developing momentum in vanishing index photonics
Authors: Kinsey Nathaniel
Published: May 2022

Refractive index invariably describes the speed at which light passes through materials, and subsequently its perceived momentum. But what happens to these quantities as the index becomes zero? A new work explores this question, highlighting how momentum in near-zero-index materials affects linear optical processes.
Resting state functional brain networks associated with emotion processing in frontotemporal lobar degeneration
Authors: Canu Elisa , Calderaro Davide , Castelnovo Veronica , Basaia Silvia , Magno Maria Antonietta , Riva Nilo , Magnani Giuseppe , Caso Francesca , Caroppo Paola , Prioni Sara , Villa Cristina , Pain Debora , Mora Gabriele , Tremolizzo Lucio , Appollonio Ildebrando , Poletti Barbara , Silani Vincenzo , Filippi Massimo , Agosta Federica
Published: May 2022

This study investigated the relationship between emotion processing and resting-state functional connectivity (rs-FC) of the brain networks in frontotemporal lobar degeneration (FTLD). Eighty FTLD patients (including cases with behavioral variant of frontotemporal dementia, primary progressive aphasia, progressive supranuclear palsy syndrome, motor neuron disease) and 65 healthy controls underwent rs-functional MRI. Emotion processing was tested using the Comprehensive Affect Testing System (CATS). In patients and controls, correlations were investigated between each emotion construct and rs-FC changes within critical networks. Mean rs-FC of the clusters significantly associated with CATS scoring were compared among FTLD groups. FTLD patients had pathological CATS scores compared with controls. In controls, increased rs-FC of the cerebellar and visuo-associative networks correlated with better scores in emotion-matching and discrimination tasks, respectively; while decreased rs-FC of the visuo-spatial network was related with better performance in the affect-matching and naming. In FTLD, the associations between rs-FC and CATS scores involved more brain regions, such as orbitofrontal and middle frontal gyri within anterior networks (i.e., salience and default-mode), parietal and somatosensory regions within visuo-spatial and sensorimotor networks, caudate and thalamus within basal-ganglia network. Rs-FC changes associated with CATS were similar among all FTLD groups. In FTLD compared to controls, the pattern of rs-FC associated with emotional processing involves a larger number of brain regions, likely due to functional specificity loss and compensatory attempts. These associations were similar across all FTLD groups, suggesting a common physiopathological mechanism of emotion processing breakdown, regardless the clinical presentation and pattern of atrophy.
Tumor suppressor p53 restrains cancer cell dissemination by modulating mitochondrial dynamics
Authors: Phan Trinh T. T. , Lin Yu-Chun , Chou Yu-Ting , Wu Chien-Wei , Lin Lih-Yuan
Published: May 2022

Tumor suppressor p53 plays a central role in preventing tumorigenesis. Here, we unravel how p53 modulates mitochondrial dynamics to restrain the metastatic properties of cancer cells. p53 inhibits the mammalian target of rapamycin complex 1 (mTORC1) signaling to attenuate the protein level of mitochondrial fission process 1 (MTFP1), which fosters the pro-fission dynamin-related protein 1 (Drp1) phosphorylation. This regulatory mechanism allows p53 to restrict cell migration and invasion governed by Drp1-mediated mitochondrial fission. Downregulating p53 expression or elevating the molecular signature of mitochondrial fission correlates with aggressive tumor phenotypes and poor prognosis in cancer patients. Upon p53 loss, exaggerated mitochondrial fragmentation stimulates the activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) signaling resulting in epithelial-to-mesenchymal transition (EMT)-like changes in cell morphology, accompanied by accelerated matrix metalloproteinase 9 (MMP9) expression and invasive cell migration. Notably, blocking the activation of mTORC1/MTFP1/Drp1/ERK1/2 axis completely abolishes the p53 deficiency-driven cellular morphological switch, MMP9 expression, and cancer cell dissemination. Our findings unveil a hitherto unrecognized mitochondria-dependent molecular mechanism underlying the metastatic phenotypes of p53-compromised cancers.
Validation of disease-specific biomarkers for the early detection of bronchopulmonary dysplasia
Authors: Kindt Alida S. D. , Förster Kai M. , Cochius-den Otter Suzan C. M. , Flemmer Andreas W. , Hauck Stefanie M. , Flatley Andrew , Kamphuis Juliette , Karrasch Stefan , Behr Jürgen , Franz Axel , Härtel Christoph , Krumsiek Jan , Tibboel Dick , Hilgendorff Anne
Published: May 2022

Objective

To demonstrate and validate the improvement of current risk stratification for bronchopulmonary dysplasia (BPD) early after birth by plasma protein markers (sialic acid-binding Ig-like lectin 14 (SIGLEC-14), basal cell adhesion molecule (BCAM), angiopoietin-like 3 protein (ANGPTL-3)) in extremely premature infants.

Methods and results

Proteome screening in first-week-of-life plasma samples of n = 52 preterm infants <32 weeks gestational age (GA) on two proteomic platforms (SomaLogic®, Olink-Proteomics®) confirmed three biomarkers with significant predictive power: BCAM, SIGLEC-14, and ANGPTL-3. We demonstrate high sensitivity (0.92) and specificity (0.86) under consideration of GA, show the proteins’ critical contribution to the predictive power of known clinical risk factors, e.g., birth weight and GA, and predicted the duration of mechanical ventilation, oxygen supplementation, as well as neonatal intensive care stay. We confirmed significant predictive power for BPD cases when switching to a clinically applicable method (enzyme-linked immunosorbent assay) in an independent sample set (n = 25, p < 0.001) and demonstrated disease specificity in different cohorts of neonatal and adult lung disease.

Conclusion

While successfully addressing typical challenges of clinical biomarker studies, we demonstrated the potential of BCAM, SIGLEC-14, and ANGPTL-3 to inform future clinical decision making in the preterm infant at risk for BPD.

Trial registration

Deutsches Register Klinische Studien (DRKS) No. 00004600; https://www.drks.de.

Impact

The urgent need for biomarkers that enable early decision making and personalized monitoring strategies in preterm infants with BPD is challenged by targeted marker analyses, cohort size, and disease heterogeneity.

We demonstrate the potential of the plasma proteins BCAM, SIGLEC-14, and ANGPTL-3 to identify infants with BPD early after birth while improving the predictive power of clinical variables, confirming the robustness toward proteome assays and proving disease specificity.

Our comprehensive analysis enables a phase-III clinical trial that allows full implementation of the biomarkers into clinical routine to enable early risk stratification in preterms with BPD.
Altered hippocampus and amygdala subregion connectome hierarchy in major depressive disorder
Authors: Jacob Yael , Morris Laurel S. , Verma Gaurav , Rutter Sarah B. , Balchandani Priti , Murrough James W.
Published: May 2022

The hippocampus and amygdala limbic structures are critical to the etiology of major depressive disorder (MDD). However, there are no high-resolution characterizations of the role of their subregions in the whole brain network (connectome). Connectomic examination of these subregions can uncover disorder-related patterns that are otherwise missed when treated as single structures. 38 MDD patients and 40 healthy controls (HC) underwent anatomical and diffusion imaging using 7-Tesla MRI. Whole-brain segmentation was performed along with hippocampus and amygdala subregion segmentation, each representing a node in the connectome. Graph theory analysis was applied to examine the importance of the limbic subregions within the brain network using centrality features measured bynode strength(sum of weights of the node’s connections),Betweenness(number of shortest paths that traverse the node), andclustering coefficient(how connected the node’s neighbors are to one another and forming a cluster). Compared to HC, MDD patients showed decreased node strength of the right hippocampus cornu ammonis (CA) 3/4, indicating decreased connectivity to the rest of the brain, and decreased clustering coefficient of the right dentate gyrus, implying it is less embedded in a cluster. Additionally, within the MDD group, the greater the embedding of the right amygdala central nucleus (CeA) in a cluster, the greater the severity of depressive symptoms. The altered role of these limbic subregions in the whole-brain connectome is related to diagnosis and depression severity, contributing to our understanding of the limbic system involvement in MDD and may elucidate the underlying mechanisms of depression.
Pirtobrutinib inhibits wild-type and mutant Bruton’s tyrosine kinase-mediated signaling in chronic lymphocytic leukemia
Authors: Aslan Burcu , Kismali Gorkem , Iles Lakesla R. , Manyam Ganiraju C. , Ayres Mary L. , Chen Lisa S. , Gagea Mihai , Bertilaccio Maria Teresa Sabrina , Wierda William G. , Gandhi Varsha
Published: May 2022

Pirtobrutinib (LOXO-305), a reversible inhibitor of Bruton’s tyrosine kinase (BTK), was designed as an alternative strategy to treat ibrutinib-resistant disease that develops due to C481 kinase domain mutations. The clinical activity of pirtobrutinib has been demonstrated in CLL, but the mechanism of action has not been investigated. We evaluated pirtobrutinib in 4 model systems: first, MEC-1, a CLL cell line overexpressing BTKWT, BTKC481S, or BTKC481R; second, murine models driven by MEC-1 overexpressing BTKWT or BTKC481S; third, in vitro incubations of primary CLL cells; and finally, CLL patients during pirtobrutinib therapy (NCT03740529, ClinicalTrials.gov). Pirtobrutinib inhibited BTK activation as well as downstream signaling in MEC-1 isogenic cells overexpressing BTKWT, BTKC481S, or BTKC481R. In mice, overall survival was short due to aggressive disease. Pirtobrutinib treatment for 2 weeks led to reduction of spleen and liver weight in BTKWT and BTKC481S cells, respectively. In vitro incubations of CLL cells harboring wild-type or mutant BTK had inhibition of the BCR pathway with either ibrutinib or pirtobrutinib treatment. Pirtobrutinib therapy resulted in inhibition of BTK phosphorylation and downstream signaling initially in all cases irrespective of their BTK profile, but these effects started to revert in cases with other BCR pathway mutations such as PLCG2 or PLEKHG5. Levels of CCL3 and CCL4 in plasma were marginally higher in patients with mutated BTK; however, there was a bimodal distribution. Both chemokines were decreased at early time points and mimicked BCR pathway protein changes. Collectively, these results demonstrate that pirtobrutinib is an effective BTK inhibitor for CLL harboring wild-type or mutant BTK as observed by changes in CCL3 and CCL4 biomarkers and suggest that alterations in BCR pathway signaling are the mechanism for its clinical effects. Long-term evaluation is needed for BTK gatekeeper residue variation along with pathologic kinase substitution or mutations in other proteins in the BCR pathway.
Ixovex-1, a novel oncolytic E1B-mutated adenovirus
Authors: Anwar Mohiemen , Arendt Maja-Louise , Ramachandran Mohanraj , Carlsson Anette , Essand Magnus , Akusjärvi Göran , Alusi Ghasan , Öberg Daniel
Published: May 2022

There is a great demand for improved oncolytic viruses that selectively replicate within cancer cells while sparing normal cells. Here, we describe a novel oncolytic adenovirus, Ixovex-1, that obtains a cancer-selective replication phenotype by modulating the level of expression of the different, alternatively spliced E1B mRNA isoforms. Ixovex-1 is a recombinant adenovirus that carries a single point mutation in the E1B-93R 3’ splice acceptor site that results in overexpression of the E1B-156R splice isoform. In this paper, we studied the characteristics of this novel oncolytic adenovirus by validating its in vitro behaviour in a panel of normal cells and cancer cells. We additionally studied its anti-tumour efficacy in vivo. Ixovex-1 significantly inhibited tumour growth and prolonged survival of mice in an immune-deficient lung carcinoma tumour implantation model. In complementation experiments, overexpression of E1B-156R was shown to increase the oncolytic index of both Ad5wt and ONYX-015. In contrast to prior viruses of similar type, Ixovex-1 includes a functional E3B region for better in vivo efficacy. Throughout this study, the Ixovex-1 virus has been proven to be superior in competency compared to a virus with multiple deletions.
Emerging functions of circular RNA in the regulation of adipocyte metabolism and obesity
Authors: Zhang Yuanyuan , Tian Zhichen , Ye Haibo , Sun Xiaomei , Zhang Huiming , Sun Yujia , Mao Yongjiang , Yang Zhangping , Li Mingxun
Published: May 2022

As noncoding RNAs, circular RNAs (circRNAs) are covalently enclosed endogenous biomolecules in eukaryotes that have tissue specificity and cell specificity. circRNAs were once considered a rare splicing byproduct. With the development of high-throughput sequencing, it has been confirmed that they are expressed in thousands of mammalian genes. To date, only a few circRNA functions and regulatory mechanisms have been verified. Adipose is the main tissue for body energy storage and energy supply. Adipocyte metabolism is a physiological process involving a series of genes and affects biological activities in the body, such as energy metabolism, immunity, and signal transmission. When adipocyte formation is dysregulated, it will cause a series of diseases, such as atherosclerosis, obesity, fatty liver, and diabetes. In recent years, many noncoding RNAs involved in adipocyte metabolism have been revealed. This review provides a comprehensive overview of the basic structure and biosynthetic mechanism of circRNAs, and further discusses the circRNAs related to adipocyte formation in adipose tissue and liver. Our review will provide a reference for further elucidating the genetic regulation mechanism of circRNAs involved in adipocyte metabolism.
Calibration after bootstrap for accurate uncertainty quantification in regression models
Authors: Palmer Glenn , Du Siqi , Politowicz Alexander , Emory Joshua Paul , Yang Xiyu , Gautam Anupraas , Gupta Grishma , Li Zhelong , Jacobs Ryan , Morgan Dane
Published: May 2022

Obtaining accurate estimates of machine learning model uncertainties on newly predicted data is essential for understanding the accuracy of the model and whether its predictions can be trusted. A common approach to such uncertainty quantification is to estimate the variance from an ensemble of models, which are often generated by the generally applicable bootstrap method. In this work, we demonstrate that the direct bootstrap ensemble standard deviation is not an accurate estimate of uncertainty but that it can be simply calibrated to dramatically improve its accuracy. We demonstrate the effectiveness of this calibration method for both synthetic data and numerous physical datasets from the field of Materials Science and Engineering. The approach is motivated by applications in physical and biological science but is quite general and should be applicable for uncertainty quantification in a wide range of machine learning regression models.
Influence of diet on acute endocannabinoidome mediator levels post exercise in active women, a crossover randomized study
Authors: Forteza Fabiola , Bourdeau-Julien Isabelle , Nguyen Guillaume Q. , Guevara Agudelo Fredy Alexander , Rochefort Gabrielle , Parent Lydiane , Rakotoarivelo Volatiana , Feutry Perrine , Martin Cyril , Perron Julie , Lamarche Benoît , Flamand Nicolas , Veilleux Alain , Billaut François , Di Marzo Vincenzo , Raymond Frédéric
Published: May 2022

The extended endocannabinoid system, also termed endocannabinoidome, participates in multiple metabolic functions in health and disease. Physical activity can both have an acute and chronic impact on endocannabinoid mediators, as does diet. In this crossover randomized controlled study, we investigated the influence of diet on the peripheral response to acute maximal aerobic exercise in a sample of active adult women (n = 7) with no underlying metabolic conditions. We compared the impact of 7-day standardized Mediterranean diet (MedDiet) and control diet inspired by Canadian macronutrient intake (CanDiet) on endocannabinoidome and short-chain fatty acid metabolites post maximal aerobic exercise. Overall, plasmatic endocannabinoids, their congeners and some polyunsaturated fatty acids increased significantly post maximal aerobic exercise upon cessation of exercise and recovered their initial values within 1 h after exercise. Most N-acylethanolamines and polyunsaturated fatty acids increased directly after exercise when the participants had consumed the MedDiet, but not when they had consumed the CanDiet. This impact was different for monoacylglycerol endocannabinoid congeners, which in most cases reacted similarly to acute exercise while on the MedDiet or the CanDiet. Fecal microbiota was only minimally affected by the diet in this cohort. This study demonstrates that endocannabinoidome mediators respond to acute maximal aerobic exercise in a way that is dependent on the diet consumed in the week prior to exercise.
Gaseous NO2 induces various envelope alterations in Pseudomonas fluorescens MFAF76a
Authors: Chautrand Thibault , Depayras Ségolène , Souak Djouhar , Kondakova Tatiana , Barreau Magalie , Kentache Takfarinas , Hardouin Julie , Tahrioui Ali , Thoumire Olivier , Konto-Ghiorghi Yoan , Barbey Corinne , Ladam Guy , Chevalier Sylvie , Heipieper Hermann J. , Orange Nicole , Duclairoir-Poc Cécile
Published: May 2022

Anthropogenic atmospheric pollution and immune response regularly expose bacteria to toxic nitrogen oxides such as NO•and NO2. These reactive molecules can damage a wide variety of biomolecules such as DNA, proteins and lipids. Several components of the bacterial envelope are susceptible to be damaged by reactive nitrogen species. Furthermore, the hydrophobic core of the membranes favors the reactivity of nitrogen oxides with other molecules, making membranes an important factor in the chemistry of nitrosative stress. Since bacteria are often exposed to endogenous or exogenous nitrogen oxides, they have acquired protection mechanisms against the deleterious effects of these molecules. By exposing bacteria to gaseous NO2, this work aims to analyze the physiological effects of NO2on the cell envelope of the airborne bacteriumPseudomonas fluorescensMFAF76a and its potential adaptive responses. Electron microscopy showed that exposure to NO2leads to morphological alterations of the cell envelope. Furthermore, the proteomic profiling data revealed that these cell envelope alterations might be partly explained by modifications of the synthesis pathways of multiple cell envelope components, such as peptidoglycan, lipid A, and phospholipids. Together these results provide important insights into the potential adaptive responses to NO2exposure inP. fluorescensMFAF76a needing further investigations.
Density-functional-theory simulations of the water and ice adhesion on silicene quantum dots
Authors: Duan Tianpei , Wu Wei , Choy Kwang-Leong
Published: May 2022

The absorption of water and ice on silicon is important to understand for many applications and safety concerns for electronic devices as most of them are fabricated using silicon. Meanwhile, recently silicene nanostructures have attracted much attention due to their potential applications in electronic devices such as gas or humidity sensors. However, for the moment, the theoretical study of the interaction between water molecules and silicene nanostructures is still rare although there is already theoretical work on the effect of water molecules on the silicene periodic structure. The specific conditions such as the finite size effect, the edge saturation of the silicene nanostructure, and the distance between the water/ice and the silicene at the initial onset of the contact have not been carefully considered before. Here we have modelled the absorption of a water molecule and a square ice on the silicene nanodot by using hybrid-exchange density-functional theory, complemented by the Van der Waals forces correction. Three different sizes of silicene nanodots have been chosen for simulations, namely $$3\times 3$$

3
×
3

, $$4\times 4$$

4
×
4

, and $$5\times 5$$

5
×
5

, with and without the hydrogen saturation on the edge. Our calculations suggest that the silicene nanodots chosen here are both hydrophilic and ice-philic. The water molecule and the square ice have tilted angles towards the silicene nanodot plane at ~ 70º and ~ 45º, respectively, which could be owing to the zig–zag structure on silicene. The absorption energies are size dependent for unsaturated silicene nanodots, whereas almost size independent for the hydrogen saturated cases. Our work on the single water molecule absorption energy on silicene nanodots is qualitatively in agreement with the previous theoretical and experimental work. However, the ice structure on silicene is yet to be validated by the relevant experiments. Our calculation results not only further complement the current paucity of water-to-silicene-nanostructure contact mechanisms, but also lead to the first study of square-ice contact mechanisms for silicene. Our findings presented here could be useful for the future design of semiconducting devices based on silicene nanostructures, especially in the humid and low-temperature environments.
Metabolome dynamics during wheat domestication
Authors: Ben-Abu Yuval , Itsko Mark
Published: May 2022

One of the most important crops worldwide is wheat. Wheat domestication took place about 10,000 years ago. Not only that its wild progenitors have been discovered and phenotypically characterized, but their genomes were also sequenced and compared to modern wheat. While comparative genomics is essential to track genes that contribute to improvement in crop yield, comparative analyses of functional biological end-products, such as metabolites, are still lacking. With the advent of rigorous mass-spectrometry technologies, it is now possible to address that problem on a big-data scale. In attempt to reveal classes of metabolites, which are associated with wheat domestication, we analyzed the metabolomes of wheat kernel samples from various wheat lines. These wheat lines represented subspecies of tetraploid wheat along primary and secondary domestications, including wild emmer, domesticated emmer, landraces durum, and modern durum. We detected that the groups of plant metabolites such as plant-defense metabolites, antioxidants and plant hormones underwent significant changes during wheat domestication. Our data suggest that these metabolites may have contributed to the improvement in the agricultural fitness of wheat. Closer evaluation of specific metabolic pathways may result in the future in genetically-engineered high-yield crops.
6-Bromo-2-naphthol from Silene armeria extract sensitizes Acinetobacter baumannii strains to polymyxin
Authors: Kang Mingyeong , Kim Wonjae , Lee Jaebok , Jung Hye Su , Jeon Che Ok , Park Woojun
Published: May 2022

The overuse of antibiotics has led to the emergence of multidrug-resistant bacteria, which are resistant to various antibiotics. Combination therapies using natural compounds with antibiotics have been found to have synergistic effects against several pathogens. Synergistic natural compounds can potentiate the effects of polymyxins for the treatment of Acinetobacter baumannii infection. Out of 120 types of plant extracts, only Silene armeria extract (SAE) showed a synergistic effect with polymyxin B (PMB) in our fractional inhibitory concentration and time-kill analyses. The survival rate of G. mellonella infected with A. baumannii ATCC 17978 increased following the synergistic treatment. Interestingly, the addition of osmolytes, such as trehalose, canceled the synergistic effect of SAE with PMB; however, the underlying mechanism remains unclear. Quadrupole time-of-flight liquid chromatography-mass spectrometry revealed 6-bromo-2-naphthol (6B2N) to be a major active compound that exhibited synergistic effects with PMB. Pretreatment with 6B2N made A. baumannii cells more susceptible to PMB exposure in a time- and concentration-dependent manner, indicating that 6B2N exhibits consequential synergistic action with PMB. Moreover, the exposure of 6B2N-treated cells to PMB led to higher membrane leakage and permeability. The present findings provide a promising approach for utilizing plant extracts as adjuvants to reduce the toxicity of PMB in A. baumannii infection.
Machine learning-assisted lens-loaded cavity response optimization for improved direction-of-arrival estimation
Authors: Abbasi Muhammad Ali Babar , Akinsolu Mobayode O. , Liu Bo , Yurduseven Okan , Fusco Vincent F. , Imran Muhammad Ali
Published: May 2022

This paper presents a millimeter-wave direction of arrival estimation (DoA) technique powered by dynamic aperture optimization. The frequency-diverse medium in this work is a lens-loaded oversized mmWave cavity that hosts quasi-random wave-chaotic radiation modes. The presence of the lens is shown to confine the radiation within the field of view and improve the gain of each radiation mode; hence, enhancing the accuracy of the DoA estimation. It is also shown, for the first time, that a lens loaded-cavity can be transformed into a lens-loaded dynamic aperture by introducing a mechanically controlled mode-mixing mechanism inside the cavity. This work also proposes a way of optimizing this lens-loaded dynamic aperture by exploiting the mode mixing mechanism governed by a machine learning-assisted evolutionary algorithm. The concept is verified by a series of extensive simulations of the dynamic aperture states obtained via the machine learning-assisted evolutionary optimization technique. The simulation results show a 25$$\%$$%improvement in the conditioning for the DoA estimation using the proposed technique.
Classification and reconstruction of spatially overlapping phase images using diffractive optical networks
Authors: Mengu Deniz , Veli Muhammed , Rivenson Yair , Ozcan Aydogan
Published: May 2022

Diffractive optical networks unify wave optics and deep learning to all-optically compute a given machine learning or computational imaging task as the light propagates from the input to the output plane. Here, we report the design of diffractive optical networks for the classification and reconstruction of spatially overlapping, phase-encoded objects. When two different phase-only objects spatially overlap, the individual object functions are perturbed since their phase patterns are summed up. The retrieval of the underlying phase images from solely the overlapping phase distribution presents a challenging problem, the solution of which is generally not unique. We show that through a task-specific training process, passive diffractive optical networks composed of successive transmissive layers can all-optically and simultaneously classify two different randomly-selected, spatially overlapping phase images at the input. After trained with ~ 550 million unique combinations of phase-encoded handwritten digits from the MNIST dataset, our blind testing results reveal that the diffractive optical network achieves an accuracy of > 85.8% for all-optical classification of two overlapping phase images of new handwritten digits. In addition to all-optical classification of overlapping phase objects, we also demonstrate the reconstruction of these phase images based on a shallow electronic neural network that uses the highly compressed output of the diffractive optical network as its input (with e.g., ~ 20–65 times less number of pixels) to rapidly reconstruct both of the phase images, despite their spatial overlap and related phase ambiguity. The presented phase image classification and reconstruction framework might find applications in e.g., computational imaging, microscopy and quantitative phase imaging fields.
An efficient Planet Optimization Algorithm for solving engineering problems
Authors: Sang-To Thanh , Hoang-Le Minh , Wahab Magd Abdel , Cuong-Le Thanh
Published: May 2022

In this study, a meta-heuristic algorithm, named The Planet Optimization Algorithm (POA), inspired by Newton's gravitational law is proposed. POA simulates the motion of planets in the solar system. The Sun plays the key role in the algorithm as at the heart of search space. Two main phases, local and global search, are adopted for increasing accuracy and expanding searching space simultaneously. A Gauss distribution function is employed as a technique to enhance the accuracy of this algorithm. POA is evaluated using 23 well-known test functions, 38 IEEE CEC benchmark test functions (CEC 2017, CEC 2019) and three real engineering problems. The statistical results of the benchmark functions show that POA can provide very competitive and promising results. Not only does POA require a relatively short computational time for solving problems, but also it shows superior accuracy in terms of exploiting the optimum.
Identification and validation of QTLs for tuber quality related traits in greater yam (Dioscorea alata L.)
Authors: Ehounou Adou Emmanuel , Cormier Fabien , Maledon Erick , Nudol Elie , Vignes Hélène , Gravillon Marie Claire , N’guetta Assanvo Simon Pierre , Mournet Pierre , Chaïr Hâna , Kouakou Amani Michel , Arnau Gemma
Published: May 2022

TwoDioscorea alatapopulations were generated by hand pollination between contrasted diploid genitors. Population A (74F × Kabusa) was composed of 121 progenies while population B (74F × 14M) involved 193 progenies. These two populations were assessed over two consecutive years regarding important tuber quality traits. Analysis of variance showed that the genotype had the greatest influence on the phenotypic scores. Also for some traits, effect of the year_replicate was strong. The heritabilities of most traits were high. Based on these data and a reference high-density genetic map of greater yam, a total of 34 quantitative trait loci (QTLs) were detected on 8 of the 20 yam chromosomes. They corresponded to five of each of the following traits: tuber size, shape regularity, tubercular roots, skin texture, tuber flesh oxidation, six for oxidation ratio and three for flesh colour. The fraction of total phenotypic variance attributable to a single QTL ranged from 11.1 to 43.5%. We detected significant correlations between traits and QTL colocalizations that were consistent with these correlations. A majority of QTLs (62%) were found on linkage group LG16, indicating that this chromosome could play a major role in genetic control of the investigated traits. In addition, an inversion involving this chromosome was detected in the Kabusa male. Nine QTLs were validated on a diversity panel, including three for tuber size, three for shape regularity, two for skin texture and one for tubercular roots. The approximate physical localization of validated QTLs allowed the identification of various candidates genes. The validated QTLs should be useful for breeding programs using marker-assisted selection to improve yam tuber quality.
Destructive coastal sea level oscillations generated by Typhoon Maysak in the Sea of Japan in September 2020
Authors: Medvedev Igor P. , Rabinovich Alexander B. , Šepić Jadranka
Published: May 2022

Typhoon Maysak (Julian in the Philippines) was a powerful tropical cyclone that strongly impacted coastal regions of the Sea of Japan on 2–4 September 2020. Destructive winds, violent storm waves, and intense rainfall occurred in Japan, on the Korean Peninsula, and in Far-Eastern Russia. Devastating coastal floods caused severe damage to coastal infrastructure and to ships and boats anchored in harbours and were responsible for numerous deaths. Our study indicates that the main reason for the destructive floods was the superposition of storm surge, extreme seiches (meteorological tsunamis), and surf beats. At various sites, different types of sea level oscillations prevailed depending on the atmospheric forcing, local topographic properties, and resonant shelf/coastal zone features. The principal forcing factors of these oscillations were atmospheric pressure and wind stress, but the exact generation mechanism of each specific type of oscillation was strongly site dependent. The uniqueness of the sea level response at each site is the main challenge in our understanding of the generation process and to the mitigation of the hazardous consequences of possible future events.