bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of hypoxia on the proteomic signature of pig adipose-derived stromal/stem cells (pASCs)
Authors: Bukowska Joanna , Słowińska Mariola , Cierniak Patrycja , Kopcewicz Marta , Walendzik Katarzyna , Frazier Trivia , Gawrońska-Kozak Barbara
Published: November 2020

Human adipose-derived stem cells (ASCs) have potential to improve wound healing; however, their equivalents from domestic animals have received less attention as an alternative cell-based therapy for animals or even humans. Hypoxia is essential for maintaining stem cell functionality in tissue-specific niches. However, a cellular response to low oxygen levels has not been demonstrated in pig ASCs. Hence, the goal of our study was to characterize ASCs isolated from the subcutaneous fat of domestic pigs (pASCs) and examine the effect of hypoxia on their proteome and functional characteristics that might reproduce pASCs wound healing ability. Analysis of immunophenotypic and functional markers demonstrated that pASCs exhibited characteristics of mesenchymal stem cells. Proteomic analysis revealed 70 differentially abundant proteins between pASCs cultured under hypoxia (1% O2) or normoxia (21% O2). Among them, 42 proteins were enriched in the cells exposed to low oxygen, whereas 28 proteins showed decrease expression following hypoxia. Differentially expressed proteins were predominantly involved in cell metabolism, regulation of focal and intracellular communication, and attributed to wound healing. Functional examination of hypoxic pASCs demonstrated acquisition of contractile abilities in vitro. Overall, our results demonstrate that hypoxia pre-conditioning impacts the pASC proteome signature and contractile function in vitro and hence, they might be considered for further cell-based therapy study on wound healing.
Motor learning in real-world pool billiards
Authors: Haar Shlomi , van Assel Camille M. , Faisal A. Aldo
Published: November 2020

The neurobehavioral mechanisms of human motor-control and learning evolved in free behaving, real-life settings, yet this is studied mostly in reductionistic lab-based experiments. Here we take a step towards a more real-world motor neuroscience using wearables for naturalistic full-body motion-tracking and the sports of pool billiards to frame a real-world skill learning experiment. First, we asked if well-known features of motor learning in lab-based experiments generalize to a real-world task. We found similarities in many features such as multiple learning rates, and the relationship between task-related variability and motor learning. Our data-driven approach reveals the structure and complexity of movement, variability, and motor learning, enabling an in-depth understanding of the structure of motor learning in three ways: First, while expecting most of the movement learning is done by the cue-wielding arm, we find that motor learning affects the whole body, changing motor-control from head to toe. Second, during learning, all subjects decreased their movement variability and their variability in the outcome. Subjects who were initially more variable were also more variable after learning. Lastly, when screening the link across subjects between initial variability in individual joints and learning, we found that only the initial variability in the right forearm supination shows a significant correlation to the subjects’ learning rates. This is in-line with the relationship between learning and variability: while learning leads to an overall reduction in movement variability, only initial variability in specific task-relevant dimensions can facilitate faster learning.
Characterization of a new cell line from ornamental fish Amphiprion ocellaris (Cuvier, 1830) and its susceptibility to nervous necrosis virus
Authors: Yashwanth B. S. , Goswami Mukunda , Kooloth Valappil Rajendran , Thakuria Dimpal , Chaudhari Aparna
Published: November 2020

Amphiprion ocellaris(ocellaris clownfish) is one of the most commercially important marine ornamental fish. A cell line designated as OCF was developed for the first time from the caudal fin of this fish species. The cell line was maintained in Leibovitz’s—15 medium supplemented with 15% FBS (Fetal Bovine Serum) and was successfully subcultured up to 34 passages. The cell line was authenticated by sequencing mitochondrial cytochrome C oxidase subunit I (COI) and 16S rRNA genes. The growth rate of the OCF cell line was maximum in medium containing 20% FBS and 1% of 0.2 M NaCl at 28 °C. Chromosome analysis revealed 48 diploid chromosomes. The OCF cell line was transfected with the pMaxGFP plasmid vector with 7% efficiency and GFP expression was observed. The OCF cell line was used for testing nervous necrosis virus (NNV) susceptibility. Cytopathic effect (CPE) was observed in terms of plaque formation after virus inoculation. Nested PCR confirmed the susceptibility of the OCF cell line to NNV. The cell line was successfully cryopreserved by a slow freezing procedure at − 80 °C with a revival efficiency of 70–75%. The study revealed that the OCF cell line would be useful for virological studies. In addition, the cell line would play an important role as an in vitro tool for carrying out toxicological and biotechnological studies.
Multilevel and spatial analyses of childhood malnutrition in Uganda: examining individual and contextual factors
Authors: Amegbor Prince M. , Zhang Zhaoxi , Dalgaard Rikke , Sabel Clive E.
Published: November 2020

In this study, we examine the concepts of spatial dependence and spatial heterogeneity in the effect of macro-level and micro-level factors on stunting among children aged under five in Uganda. We conducted a cross-sectional analysis of 3624 Ugandan children aged under five, using data from the 2016 Ugandan Demographic and Health Survey. Multilevel mixed-effect analysis, spatial regression methods and multi-scale geographically weight regression (MGWR) analysis were employed to examine the association between our predictors and stunting as well as to analyse spatial dependence and variability in the association. Approximately 28% of children were stunted. In the multilevel analysis, the effect of drought, diurnal temperature and livestock per km2 on stunting was modified by child, parent and household factors. Likewise, the contextual factors had a modifiable effect on the association between child’s sex, mother’s education and stunting. The results of the spatial regression models indicate a significant spatial error dependence in the residuals. The MGWR suggests rainfall and diurnal temperature had spatial varying associations with stunting. The spatial heterogeneity of rainfall and diurnal temperature as predictors of stunting suggest some areas in Uganda might be more sensitive to variability in these climatic conditions in relation to stunting than others.
Medicinal potential of mycelium and fruiting bodies of an arboreal mushroom Fomitopsis officinalis in therapy of lifestyle diseases
Authors: Fijałkowska Agata , Muszyńska Bożena , Sułkowska-Ziaja Katarzyna , Kała Katarzyna , Pawlik Anna , Stefaniuk Dawid , Matuszewska Anna , Piska Kamil , Pękala Elżbieta , Kaczmarczyk Piotr , Piętka Jacek , Jaszek Magdalena
Published: November 2020

Fomitopsis officinalis is a medicinal mushroom used in traditional European eighteenth and nineteenth century folk medicine. Fruiting bodies of F. officinalis were collected from the natural environment of Świętokrzyskie Province with the consent of the General Director for Environmental Protection in Warsaw. Mycelial cultures were obtained from fragments of F. officinalis fruiting bodies. The taxonomic position of the mushroom mycelium was confirmed using the PCR method. The presence of organic compounds was determined by HPLC–DAD analysis. Bioelements were determined by AF-AAS. The biochemical composition of the tested mushroom material was confirmed with the FTIR method. Antioxidant properties were determined using the DPPH method, and the antiproliferative activity was assessed with the use of the MTT test. The presence of indole compounds (l-tryptophan, 6-methyl-d,l-tryptophan, melatonin, 5-hydroxy-l-tryptophan), phenolic compounds (p-hydroxybenzoic acid, gallic acid, catechin, phenylalanine), and sterols (ergosterol, ergosterol peroxide) as well as trace elements was confirmed in the mycelium and fruiting bodies of F. officinalis. Importantly, a high level of 5-hydroxy-l-tryptophan in in vitro mycelium cultures (517.99 mg/100 g d.w) was recorded for the first time. The tested mushroom extracts also showed antioxidant and antiproliferative effects on the A549 lung cancer cell line, the DU145 prostate cancer cell line, and the A375 melanoma cell line.
17α-ethynylestradiol prevents the natural male-to-female sex change in gilthead seabream (Sparus aurata L.)
Authors: García Hernández M. Pilar , Cabas Isabel , Rodenas M. Carmen , Arizcun Marta , Chaves-Pozo Elena , Power Deborah M. , García Ayala Alfonsa
Published: November 2020

Exposure to 17α-ethynylestradiol (EE2, 5 μg/g food) impairs some reproductive events in the protandrous gilthead seabream and a short recovery period does not allow full recovery. In this study, spermiating seabream males in the second reproductive cycle (RC) were fed a diet containing 5 or 2.5 μg EE2/g food for 28 days and then a commercial diet without EE2 for the remaining RC. Individuals were sampled at the end of the EE2 treatment and then at the end of the RC and at the beginning of the third RC, 146 and 333 days after the cessation of treatment, respectively. Increased hepatic transcript levels of the gene coding for vitellogenin (vtg) and plasma levels of Vtg indicated both concentrations of EE2 caused endocrine disruption. Modifications in the histological organization of the testis, germ cell proliferation, plasma levels of the sex steroids and pituitary expression levels of the genes coding for the gonadotropin β-subunits, fshβ and lhβ were detected. The plasma levels of Vtg and most of the reproductive parameters were restored 146 days after treatments. However, although 50% of the control fish underwent sex reversal as expected at the third RC, male-to female sex change was prevented by both EE2 concentrations.
High prevalence of undiagnosed comorbidities among adolescents with obesity
Authors: Leong Karen S. W. , Jayasinghe Thilini N. , Wilson Brooke C. , Derraik José G. B. , Albert Benjamin B. , Chiavaroli Valentina , Svirskis Darren M. , Beck Kathryn L. , Conlon Cathryn A. , Jiang Yannan , Schierding William , Vatanen Tommi , Holland David J. , O’Sullivan Justin M. , Cutfield Wayne S.
Published: November 2020

Metabolic diseases are increasing among adolescents with obesity. Although the reported prevalence of metabolic syndrome is approximately 30% worldwide, its prevalence is largely unknown among New Zealand adolescents. Therefore, we assessed the health of adolescents with obesity (BMI ≥ 30 kg/m2) enrolled in a randomised clinical trial (Gut Bugs Trial), to identify the prevalence of undiagnosed comorbidities. Assessments included anthropometry, 24-h ambulatory blood pressure monitoring, and insulin sensitivity. We report on baseline data (pre-randomisation) on 87 participants (14–18 years; 59% females), with mean BMI 36.9 ± 5.3 kg/m2 (BMI SDS 3.33 ± 0.79). Approximately 40% of participants had undiagnosed metabolic syndrome, which was twice as common among males. Half (53%) had pre-diabetes and 92% a reduction in insulin sensitivity. Moreover, 31% had pre-hypertension/hypertension, 69% dyslipidaemia, and 25% abnormal liver function. Participants with class III obesity had a greater risk of metabolic syndrome than those with classes I/II [relative risk 1.99 (95% CI 1.19, 3.34)]. Risks for pre-hypertension/hypertension and inflammation were also greater among those with class III obesity. We identified a high prevalence of undiagnosed comorbidities among adolescents with obesity in New Zealand. As adolescent obesity tracks into adulthood, early interventions are needed to prevent progression to overt cardiometabolic diseases.
Using quantitative trait in adults with ADHD to test predictions of dual-process theory
Authors: Persson Emil , Heilig Markus , Tinghög Gustav , Capusan Andrea J.
Published: November 2020

Dual-process theory is a widely utilized modelling tool in the behavioral sciences. It conceptualizes decision-making as an interaction between two types of cognitive processes, some of them fast and intuitive, others slow and reflective. We make a novel contribution to this literature by exploring differences between adults with clinically diagnosed ADHD and healthy controls for a wide range of behaviors. Given the clinical picture and nature of ADHD symptoms, we had a strong a priori reason to expect differences in intuitive vs reflective processing; and thus an unusually strong case for testing the predictions of dual-process theory. We found mixed results, with overall weaker effects than expected, except for risk taking, where individuals with ADHD showed increased domain sensitivity for gains vs losses. Some of our predictions were supported by the data but other patterns are more difficult to reconcile with theory. On balance, our results provide only limited empirical support for using dual-process theory to understand basic social and economic decision-making.
JavaCyte, a novel open-source tool for automated quantification of key hallmarks of cardiac structural remodeling
Authors: Winters J. , von Braunmuhl M. Edler , Zeemering S. , Gilbers M. , Brink T. Ten , Scaf B. , Guasch E. , Mont L. , Batlle M. , Sinner M. , Hatem S. , Mansour M. K. , Fabritz L. , Sommerfeld L. C. , Kirchhof P. , Isaacs A. , Stoll M. , Schotten U. , Verheule S.
Published: November 2020

Many cardiac pathologies involve changes in tissue structure. Conventional analysis of structural features is extremely time-consuming and subject to observer bias. The possibility to determine spatial interrelations between these features is often not fully exploited. We developed a staining protocol and an ImageJ-based tool (JavaCyte) for automated histological analysis of cardiac structure, including quantification of cardiomyocyte size, overall and endomysial fibrosis, spatial patterns of endomysial fibrosis, fibroblast density, capillary density and capillary size. This automated analysis was compared to manual quantification in several well-characterized goat models of atrial fibrillation (AF). In addition, we tested inter-observer variability in atrial biopsies from the CATCH-ME consortium atrial tissue bank, with patients stratified by their cardiovascular risk profile for structural remodeling. We were able to reproduce previous manually derived histological findings in goat models for AF and AV block (AVB) using JavaCyte. Furthermore, strong correlation was found between manual and automated observations for myocyte count (r = 0.94, p < 0.001), myocyte diameter (r = 0.97, p < 0.001), endomysial fibrosis (r = 0.98, p < 0.001) and capillary count (r = 0.95, p < 0.001) in human biopsies. No significant variation between observers was observed (ICC = 0.89, p < 0.001). We developed and validated an open-source tool for high-throughput, automated histological analysis of cardiac tissue properties. JavaCyte was as accurate as manual measurements, with less inter-observer variability and faster throughput.
RNA sequencing as an alternative tool for detecting measurable residual disease in core-binding factor acute myeloid leukemia
Authors: Kim TaeHyung , Moon Joon Ho , Ahn Jae-Sook , Ahn Seo-Yeon , Jung Sung-Hoon , Yang Deok-Hwan , Lee Je-Jung , Shin Myung-Geun , Choi Seung Hyun , Lee Ja-yeon , Tyndel Marc S. , Lee Hui Young , Kim Kyoung Ha , Cai Yu , Lee Yoo Jin , Sohn Sang Kyun , Min Yoo Hong , Cheong June-Won , Kim Hyeoung-Joon , Zhang Zhaolei , Kim Dennis Dong Hwan
Published: November 2020

DNA sequencing-based measurable residual disease (MRD) detection has shown to be clinically relevant in AML. However, the same methodology cannot be applied to fusion gene-driven subtypes of AML such as core-binding factor AML (CBF-AML). Here in this study, we evaluated the effectiveness of using DNA and RNA sequencing in MRD detection and in tracking clonal dynamics in CBF-AML. Using RNA-seq, we were able to quantify expression levels of RUNX1-RUNX1T1 and CBFB-MYH11 at diagnosis and their levels of reduction during remission (P < 6.3e−05 and P < 2.2e−13). The level of reduction of RUNX1-RUNX1T1 as measured by RNA-seq and qPCR were highly correlated (R2 = 0.74, P < 5.4e−05). A decision tree analysis, based on 3-log reduction of RUNX1-RUNX1T1 and cKIT-D816mut at diagnosis, stratified RUNX1-RUNX1T1 AML patients into three subgroups. These three subgroups had 2-year overall survival rates at 87%, 74%, and 33% (P < 0.08) and 2-year relapse incidence rates at 13%, 42%, and 67% (P < 0.05). On the other hand, although low residual allelic burden was common, it was not associated with long-term outcome, indicating that mutation clearance alone cannot be interpreted as MRD-negative. Overall, our study demonstrates that the clinical utility of RNA sequencing as a potential tool for MRD monitoring in fusion gene-driven AML such as RUNX1-RUNX1T1 AML.
Galectin-3 gene deletion results in defective adipose tissue maturation and impaired insulin sensitivity and glucose homeostasis
Authors: Blasetti Fantauzzi Claudia , Iacobini Carla , Menini Stefano , Vitale Martina , Sorice Gian Pio , Mezza Teresa , Cinti Saverio , Giaccari Andrea , Pugliese Giuseppe
Published: November 2020

Adiposopathy is a pathological adipose tissue (AT) response to overfeeding characterized by reduced AT expandability due to impaired adipogenesis, which favors inflammation, insulin resistance (IR), and abnormal glucose regulation. However, it is unclear whether defective adipogenesis causes metabolic derangement also independently of an increased demand for fat storage. As galectin-3 has been implicated in both adipocyte differentiation and glucose homeostasis, we tested this hypothesis in galectin-3 knockout (Lgal3−/−) mice fed a standard chow. In vitro, Lgal3−/− adipocyte precursors showed impaired terminal differentiation (maturation). Two-month-old Lgal3−/− mice showed impaired AT maturation, with reduced adipocyte size and expression of adipogenic genes, but unchanged fat mass and no sign of adipocyte degeneration/death or ectopic fat accumulation. AT immaturity was associated with AT and whole-body inflammation and IR, glucose intolerance, and hyperglycemia. Five-month-old Lgal3−/− mice exhibited a more mature AT phenotype, with no difference in insulin sensitivity and expression of inflammatory cytokines versus WT animals, though abnormal glucose homeostasis persisted and was associated with reduced β-cell function. These data show that adipogenesis capacity per se affects AT function, insulin sensitivity, and glucose homeostasis independently of increased fat intake, accumulation and redistribution, thus uncovering a direct link between defective adipogenesis, IR and susceptibility to diabetes.
Risk prediction for malignant intraductal papillary mucinous neoplasm of the pancreas: logistic regression versus machine learning
Authors: Kang Jae Seung , Lee Chanhee , Song Wookyeong , Choo Wonho , Lee Seungyeoun , Lee Sungyoung , Han Youngmin , Bassi Claudio , Salvia Roberto , Marchegiani Giovanni , Wolfgang Cristopher L. , He Jin , Blair Alex B. , Kluger Michael D. , Su Gloria H. , Kim Song Cheol , Song Ki-Byung , Yamamoto Masakazu , Higuchi Ryota , Hatori Takashi , Yang Ching-Yao , Yamaue Hiroki , Hirono Seiko , Satoi Sohei , Fujii Tsutomu , Hirano Satoshi , Lou Wenhui , Hashimoto Yasushi , Shimizu Yasuhiro , Del Chiaro Marco , Valente Roberto , Lohr Matthias , Choi Dong Wook , Choi Seong Ho , Heo Jin Seok , Motoi Fuyuhiko , Matsumoto Ippei , Lee Woo Jung , Kang Chang Moo , Shyr Yi-Ming , Wang Shin-E. , Han Ho-Seong , Yoon Yoo-Seok , Besselink Marc G. , van Huijgevoort Nadine C. M. , Sho Masayuki , Nagano Hiroaki , Kim Sang Geol , Honda Goro , Yang Yinmo , Yu Hee Chul , Do Yang Jae , Chung Jun Chul , Nagakawa Yuichi , Seo Hyung Il , Choi Yoo Jin , Byun Yoonhyeong , Kim Hongbeom , Kwon Wooil , Park Taesung , Jang Jin-Young
Published: November 2020

Most models for predicting malignant pancreatic intraductal papillary mucinous neoplasms were developed based on logistic regression (LR) analysis. Our study aimed to develop risk prediction models using machine learning (ML) and LR techniques and compare their performances. This was a multinational, multi-institutional, retrospective study. Clinical variables including age, sex, main duct diameter, cyst size, mural nodule, and tumour location were factors considered for model development (MD). After the division into a MD set and a test set (2:1), the best ML and LR models were developed by training with the MD set using a tenfold cross validation. The test area under the receiver operating curves (AUCs) of the two models were calculated using an independent test set. A total of 3,708 patients were included. The stacked ensemble algorithm in the ML model and variable combinations containing all variables in the LR model were the most chosen during 200 repetitions. After 200 repetitions, the mean AUCs of the ML and LR models were comparable (0.725 vs. 0.725). The performances of the ML and LR models were comparable. The LR model was more practical than ML counterpart, because of its convenience in clinical use and simple interpretability.
New evidence on the earliest domesticated animals and possible small-scale husbandry in Atlantic NW Europe
Authors: Crombé Philippe , Aluwé Kim , Boudin Mathieu , Snoeck Christophe , Messiaen Liesbeth , Teetaert Dimitri
Published: November 2020

The distribution of the first domesticated animals and crops along the coastal area of Atlantic NW Europe, which triggered the transition from a hunter-gatherer-fisher to a farmer-herder economy, has been debated for many decades among archaeologists. While some advocate a gradual transition in which indigenous hunter-gatherers from the very beginning of the 5th millennium cal BC progressively adopted Neolithic commodities, others are more in favor of a rapid transition near the end of the 5th millennium caused by a further northwest migration of farmers-herders colonizing the lowlands. Here, radiocarbon dated bones from sheep/goat and possibly also cattle are presented which provide the first hard evidence of an early introduction of domesticated animals within a hunter-gatherer context in NW Belgium, situated ca. 80 km north of the agro-pastoral frontier. Based on their isotope signal it is suggested that these first domesticates were probably not merely obtained through exchange with contemporaneous farmers but were kept locally, providing evidence of small-scale local stockbreeding in the lowlands maybe as early as ca. 4800/4600 cal BC. If confirmed by future in-depth isotope analyses, the latter testifies of intense contact and transmission of knowledge in this early contact period, which is also visible in the material culture, such as the lithic and pottery technology. It also implies direct and prolonged involvement of farmer-herders, either through visiting specialists or intermarriage, which follows recent genetic evidence demonstrating much more hunter-gatherer ancestry in early farmer’s genes in western Europe compared to central and SE Europe.
Fire-scarred fossil tree from the Late Triassic shows a pre-fire drought signal
Authors: Byers Bruce A. , DeSoto Lucía , Chaney Dan , Ash Sidney R. , Byers Anya B. , Byers Jonathan B. , Stoffel Markus
Published: November 2020

Exploring features of wood anatomy associated with fire scars found on fossil tree trunks is likely to increase our knowledge of the environmental and ecological processes that occurred in ancient forests and of the role of fire as an evolutionary force. In Petrified Forest National Park, Arizona, where Late Triassic fossil trees are exposed, we found 13 examples of fossil logs with external features resembling modern fire scars. One specimen with the unambiguous external features of a fire scar was collected for analysis of its fossilized wood. A light-colored band composed of compressed and distorted tracheids was associated with the scarring event. Cell lumen diameter and cell wall thickness in the pre-scarring fossilized wood show a response similar to that described in modern trees experiencing drought conditions. Tracheids in the post-scarring wood are initially smaller, and then become larger than average following a recovery period, as is often observed in modern conifers following fire. The responses in external morphology and wood anatomy to drought and fire were similar to those of some modern trees and support the view that some forests may have experienced conditions favoring the evolution of fire-adapted traits for more than 200 million years.
Long term visuo-vestibular mismatch in freely behaving mice differentially affects gaze stabilizing reflexes
Authors: França de Barros Filipa , Schenberg Louise , Tagliabue Michele , Beraneck Mathieu
Published: November 2020

The vestibulo-ocular reflex (VOR) and the optokinetic reflex (OKR) work synergistically to stabilize gaze in response to head movements. We previously demonstrated that a 14-day visuo-vestibular mismatch (VVM) protocol applied in freely behaving mice decreased the VOR gain. Here, we show for the first time that the OKR gain is also reduced and report on the recovery dynamics of both VOR and OKR after the end of the VVM protocol. Using sinusoidally-modulated stimulations, the decreases in VOR and OKR were found to be frequency-selective with larger reductions for frequencies < 0.5 Hz. Constant-velocity OKR stimulation tests demonstrated that the persistent components of the OKR were not modified while the transient, initial responses were. To identify the signals driving VOR and OKR reductions, we compared the responses of mice exposed to a high-contrast and no-contrast VVM. Despite being more robust in the high-contrast conditions, reductions were largely comparable and recovered with a similar time course. An analysis that directly compared VOR and OKR responses revealed that, alterations in the VOR were of significantly larger amplitude with significantly slower dynamics of recovery. Our findings are evidence for a frequency-selective influence of visual signals in the tuning of gaze stabilizing reflexes in normal mice.
Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance
Authors: Aono Alexandre Hild , Costa Estela Araujo , Rody Hugo Vianna Silva , Nagai James Shiniti , Pimenta Ricardo José Gonzaga , Mancini Melina Cristina , dos Santos Fernanda Raquel Camilo , Pinto Luciana Rossini , Landell Marcos Guimarães de Andrade , de Souza Anete Pereira , Kuroshu Reginaldo Massanobu
Published: November 2020

Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and for sugarcane, brown rust resistance is a desirable characteristic due to the large economic impact of the disease. Although marker-assisted selection for rust resistance has been successful, the genes involved are still unknown, and the associated regions vary among cultivars, thus restricting methodological generalization. We used genotyping by sequencing of full-sib progeny to relate genomic regions with brown rust phenotypes. We established a pipeline to identify reliable SNPs in complex polyploid data, which were used for phenotypic prediction via machine learning. We identified 14,540 SNPs, which led to a mean prediction accuracy of 50% when using different models. We also tested feature selection algorithms to increase predictive accuracy, resulting in a reduced dataset with more explanatory power for rust phenotypes. As a result of this approach, we achieved an accuracy of up to 95% with a dataset of 131 SNPs related to brown rust QTL regions and auxiliary genes. Therefore, our novel strategy has the potential to assist studies of the genomic organization of brown rust resistance in sugarcane.
Dynamic and static properties of stadium-shaped antidot arrays
Authors: Saavedra E. , Corona R. M. , Vidal-Silva N. , Palma J. L. , Altbir D. , Escrig J.
Published: November 2020

In this work we performed a detailed numerical analysis on the static and dynamic properties of magnetic antidot arrays as a function of their geometry. In particular, we explored how by varying the shape of these antidot arrays from circular holes to stadium-shaped holes, we can effectively control the magnetic properties of the array. Using micromagnetic simulations we evidenced that coercivity is very sensitive to the shape of antidots, while the remanence is more robust to these changes. Furthermore, we studied the dynamic susceptibility of these systems, finding that it is possible to control both the position and the number of resonance peaks simply by changing the geometry of the holes. Thus, this work provides useful insights on the behavior of antidot arrays for different geometries, opening routes for the design and improvement of two-dimensional technologies.
Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia
Authors: Nishizawa Ayako , Kumada Kazuki , Tateno Keiko , Wagata Maiko , Saito Sakae , Katsuoka Fumiki , Mizuno Satoshi , Ogishima Soichi , Yamamoto Masayuki , Yasuda Jun , Sugawara Junichi
Published: November 2020

Preeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.
Detection of cell-free foetal DNA fraction in female-foetus bearing pregnancies using X-chromosomal insertion/deletion polymorphisms examined by digital droplet PCR
Authors: Zednikova Iveta , Pazourkova Eva , Lassakova Sona , Vesela Barbora , Korabecna Marie
Published: November 2020

In families with X-linked recessive diseases, foetal sex is determined prenatally by detection of Y-chromosomal sequences in cell-free foetal DNA (cffDNA) in maternal plasma. The same procedure is used to confirm the cffDNA presence during non-invasive prenatal RhD incompatibility testing but there are no generally accepted markers for the detection of cffDNA fraction in female-foetus bearing pregnancies. We present a methodology allowing the detection of paternal X-chromosomal alleles on maternal background and the confirmation of female sex of the foetus by positive amplification signals. Using digital droplet PCR (ddPCR) we examined X-chromosomal INDEL (insertion/deletion) polymorphisms: rs2307932, rs16397, rs16637, rs3048996, rs16680 in buccal swabs of 50 females to obtain the population data. For all INDELs, we determined the limits of detection for each ddPCR assay. We examined the cffDNA from 63 pregnant women bearing Y-chromosome negative foetuses. The analysis with this set of INDELs led to informative results in 66.67% of examined female-foetus bearing pregnancies. Although the population data predicted higher informativity (74%) we provided the proof of principle of this methodology. We successfully applied this methodology in prenatal diagnostics in a family with Wiscott–Aldrich syndrome and in pregnancies tested for the risk of RhD incompatibility.
Stromal vapors for real-time molecular guidance of breast-conserving surgery
Authors: Vaysse Pierre-Maxence , Kooreman Loes F. S. , Engelen Sanne M. E. , Kremer Bernd , Olde Damink Steven W. M. , Heeren Ron M. A. , Smidt Marjolein L. , Porta Siegel Tiffany
Published: November 2020

Achieving radical tumor resection while preserving disease-free tissue during breast-conserving surgery (BCS) remains a challenge. Here, mass spectrometry technologies were used to discriminate stromal tissues reported to be altered surrounding breast tumors, and build tissue classifiers ex vivo. Additionally, we employed the approach for in vivo and real-time classification of breast pathology based on electrosurgical vapors. Breast-resected samples were obtained from patients undergoing surgery at MUMC+. The specimens were subsequently sampled ex vivo to generate electrosurgical vapors analyzed by rapid evaporative ionization mass spectrometry (REIMS). Tissues were processed for histopathology to assign tissue components to the mass spectral profiles. We collected a total of 689 ex vivo REIMS profiles from 72 patients which were analyzed using multivariate statistical analysis (principal component analysis-linear discriminant analysis). These profiles were classified as adipose, stromal and tumor tissues with 92.3% accuracy with a leave-one patient-out cross-validation. Tissue recognition using this ex vivo-built REIMS classification model was subsequently tested in vivo on electrosurgical vapors. Stromal and adipose tissues were classified during one BCS. Complementary ex vivo analyses were performed by REIMS and by desorption electrospray ionization mass spectrometry (DESI-MS) to study the potential of breast stroma to guide BCS. Tumor border stroma (TBS) and remote tumor stroma (RTS) were classified by REIMS and DESI-MS with 86.4% and 87.8% accuracy, respectively. We demonstrate the potential of stromal molecular alterations surrounding breast tumors to guide BCS in real-time using REIMS analysis of electrosurgical vapors.
Potential miRNA biomarkers for the diagnosis and prognosis of esophageal cancer detected by a novel absolute quantitative RT-qPCR method
Authors: Lin Zhiyuan , Chen Yongquan , Lin Yanling , Lin Huayue , Li Hongwei , Su Xiaosong , Fang Zanxi , Wang Jiajia , Wei Qingchun , Teng Jing , Zhang Zhongying
Published: November 2020

miRNAs are expected to become potential biomarkers in the diagnosis and prognosis of Esophageal cancer (EC). Through a series of screening, miR-34a-5p, miR-148a-3p and miR-181a-5p were selected as EC-associated miRNAs. Based on AllGlo probe, a novel absolute quantitative RT-qPCR method with high sensitivity, specificity and accuracy was established for detecting miRNAs. Then the clinical significance of these 3 miRNAs was explored with 213 patients (166 cases with EC and 47 cases with benign diseases) and 170 normal controls. Compared with normal controls, the level of miR-34a-5p increased while miR-148a-3p and miR-181a-5p decreased in EC and benign patients (P < 0.001), and the level of miR-181a-5p in early EC patients was significantly lower (P < 0.001). According to logistic regression analysis, combined detection of miR-34a-5p, miR-148a-3p and Cyfra21-1 provided the highest diagnosis efficiency of 85.07% with sensitivity and specificity reaching 85.45% and 84.71%. Compared with preoperative samples, the level of miR-34a-5p decreased while miR-148a-3p and miR-181a-5p increased in postoperative samples (P < 0.001). Collectively, this first developed, novel absolute quantitative RT-qPCR method exhibits high application value in detecting miRNAs, miR-34a-5p, miR-148a-3p and miR-181a-5p may serve as potential biomarkers in the diagnosis and prognosis of EC, and miR-181a-5p probably could serve as a new biomarker for early EC.
Serological follow-up of SARS-CoV-2 asymptomatic subjects
Authors: Milani Gregorio Paolo , Dioni Laura , Favero Chiara , Cantone Laura , Macchi Chiara , Delbue Serena , Bonzini Matteo , Montomoli Emanuele , Bollati Valentina ,   the UNICORN Consortium, Albetti Benedetta , Bandi Claudio , Bellini Tommaso , Buscaglia Marco , Cantarella Carlo , Carugno Michele , Casartelli Sergio , D’Alessandro Sarah , De Chiara Francesca , Eberini Ivano , Ferrari Luca , Ferraroni Monica , Galastri Laura , Galli Cristina , Hoxha Mirjam , Iodice Simona , La Vecchia Carlo , Manenti Alessandro , Manini Ilaria , Marchi Serena , Mariani Jacopo , Pariani Elena , Pesatori Angela Cecilia , Rota Federica , Ruscica Massimiliano , Schioppo Tommaso , Tarantini Letizia , Trombetta Claudia Maria , Vicenzi Marco , Zanchetta Giuliano
Published: November 2020

SARS-CoV-2 symptoms are non-specific and can range from asymptomatic presentation to severe pneumonia. Asymptomatic subjects carrying SARS-CoV-2 often remain undiagnosed and it is still debated whether they develop immunoglobulins (Ig) and how long they persist. The aim of this study was to investigate the development and persistence of antibodies against SARS-CoV-2 in asymptomatic subjects infected by the virus. This follow-up study was performed on the 31 asymptomatic subjects who presented a positive nasal swab or serology against SARS-CoV-2 (Ig against Spike-RBD) in the first part of the UNICORN study (March 2020) aimed at attesting previous or current contacts with the virus in the personnel of the University of Milan. Eight weeks after the first Ig measure, these subjects were invited to donate a second blood sample for testing serum antibodies (IgM, IgG and total antibodies) and to fill-in a structured questionnaire. About 80% of asymptomatic subjects did not present circulating immunoglobulins against SARS-CoV-2 after 8 weeks from a positive nasal swab against the virus. Moreover, in more than 40% of these subjects, no Ig against SARS-CoV-2 were detected at any time. Finally, about two third of subjects with immunoglobulins at baseline did not present IgG against SARS-CoV-2 after 8 weeks. The majority of subjects who developed an asymptomatic SARS-CoV-2 infection do not present antibodies against the RBD-spike protein after 8 weeks of follow-up. These data should be taken into account for the interpretation of the serological evidences on SARS-CoV-2 that are emerging nowadays.
Direct observation of the specific heat of Majorana quasiparticles in superfluid3He-B
Authors: Bunkov Yu. M. , Gazizulin R. R.
Published: November 2020

The existence of Majorana quasiparticles was predicted in the edge state in topological insulators, especially in the p-wave superfluid medium $${^3}$$

3

He-B. Due to its purity and coherent quantum state, $${^3}$$

3

He-B is an ideal platform for searching for Majorana fermions in condensed matter systems. In the limit of extremely low temperatures, the density of Bogolyubov quasiparticles and the heat capacity of $${^3}$$

3

He-B decrease exponentially. In this article, we present the first observation of the deviation of its heat capacity from exponential dependence in the limit of record low cooling. We found an additional heat capacity that more than doubled the heat capacity of bulk $${^3}$$

3

He-B and changes as T$$^2$$

2

. The additional heat capacity is in good agreement with the predicted heat capacity of 2D gas of Majorana. This observation is a direct proof of the existence of Majorana quasiparticles in $${^3}$$

3

He-B.
Graphene/PVA buckypaper for strain sensing application
Authors: Mehmood Ahsan , Mubarak N. M. , Khalid Mohammad , Jagadish Priyanka , Walvekar Rashmi , Abdullah E. C.
Published: November 2020

Strain sensors in the form of buckypaper (BP) infiltrated with various polymers are considered a viable option for strain sensor applications such as structural health monitoring and human motion detection. Graphene has outstanding properties in terms of strength, heat and current conduction, optics, and many more. However, graphene in the form of BP has not been considered earlier for strain sensing applications. In this work, graphene-based BP infiltrated with polyvinyl alcohol (PVA) was synthesized by vacuum filtration technique and polymer intercalation. First, Graphene oxide (GO) was prepared via treatment with sulphuric acid and nitric acid. Whereas, to obtain high-quality BP, GO was sonicated in ethanol for 20 min with sonication intensity of 60%. FTIR studies confirmed the oxygenated groups on the surface of GO while the dispersion characteristics were validated using zeta potential analysis. The nanocomposite was synthesized by varying BP and PVA concentrations. Mechanical and electrical properties were measured using a computerized tensile testing machine, two probe method, and hall effect, respectively. The electrical conducting properties of the nanocomposites decreased with increasing PVA content; likewise, electron mobility also decreased while electrical resistance increased. The optimization study reports the highest mechanical properties such as tensile strength, Young’s Modulus, and elongation at break of 200.55 MPa, 6.59 GPa, and 6.79%, respectively. Finally, electrochemical testing in a strain range of ε ~ 4% also testifies superior strain sensing properties of 60 wt% graphene BP/PVA with a demonstration of repeatability, accuracy, and preciseness for five loading and unloading cycles with a gauge factor of 1.33. Thus, results prove the usefulness of the nanocomposite for commercial and industrial applications.
Effects of biochar and biofertilizer on cadmium-contaminated cotton growth and the antioxidative defense system
Authors: Zhu Yongqi , Wang Haijiang , Lv Xin , Zhang Yutong , Wang Weiju
Published: November 2020

Consistent use of large amounts of fertilizers, pesticides, and mulch can cause the accumulation of harmful substances in cotton plants. Among these harmful substances, cadmium (Cd), an undegradable element, stands out as being particularly highly toxic to plants. The objective of this study was to evaluate the ability of biochar (3%) and biofertilizer (1.5%) to decrease Cd uptake, increase cotton dry weight, and modulate the activities of photosynthetic and peroxidase (POD), superoxide dismutase (SOD), catalase enzyme (CAT) in cotton (Gossypium hirsutumL.) grown in Cd-contaminated soil (0, 1, 2, or 4 mg Cd kg−1soil) in pots. These studies showed that, as expected, exogenous Cd adversely affects cotton chlorophyll and photosynthesis. However, biochar and biofertilizer increased cotton dry weight by an average of 16.82% and 32.62%, respectively. Meanwhile, biochar and biofertilizer decreased the accumulation of Cd in cotton organs, and there was a significant reduction in the amount of Cd in bolls (P < 0.05). Biochar and biofertilizer have a positive impact on cotton chlorophyll content, net photosynthesis, stomatal conductance, transpiration rate, and intercellular CO2concentration. Thus, the addition of biochar and biofertilizer promote cotton growth. However, biochar and biofertilizer increased the SOD activity of leaves (47.70% and 77.21%), CAT activity of leaves (35.40% and 72.82%), SOD activity of roots (33.62% and 39.37%), and CAT activity of roots (36.91% and 60.29%), respectively, and the addition of biochar and biofertilizer decreased the content of MDA and electrolyte leakage rate. Redundancy analyses showed that biochar and biofertilizer also improved SOD and POD activities by reducing the heavy metal-induced oxidative stress in cotton and reducing Cd uptake in cotton organs. Therefore, biochar and biofertilizer have a positive effect on the growth of cotton.
Multispectral imaging detects gastritis consistently in mouse model and in humans
Authors: Bazin Thomas , Martinez-Herrera Sergio Ernesto , Jobart-Malfait Aude , Benezeth Yannick , Boffety Matthieu , Julié Catherine , Emile Jean-François , Michel Valérie , Goudail François , Touati Eliette , Marzani Franck , Lamarque Dominique
Published: November 2020

Gastritis constitutes the initial step of the gastric carcinogenesis process. Gastritis diagnosis is based on histological examination of biopsies. Non-invasive real-time methods to detect mucosal inflammation are needed. Tissue optical properties modify reemitted light, i.e. the proportion of light that is emitted by a tissue after stimulation by a light flux. Analysis of light reemitted by gastric tissue could predict the inflammatory state. The aim of our study was to investigate a potential association between reemitted light and gastric tissue inflammation. We used two models and three multispectral analysis methods available on the marketplace. We used a mouse model of Helicobacter pylori infection and included patients undergoing gastric endoscopy. In mice, the reemitted light was measured using a spectrometer and a multispectral camera. We also exposed patient’s gastric mucosa to specific wavelengths and analyzed reemitted light. In both mouse model and humans, modifications of reemitted light were observed around 560 nm, 600 nm and 640 nm, associated with the presence of gastritis lesions. These results pave the way for the development of improved endoscopes in order to detect real-time gastritis without the need of biopsies. This would allow a better prevention of gastric cancer alongside with cost efficient endoscopies.
Occurrence and risks of antibiotics in an urban river in northeastern Tibetan Plateau
Authors: Kuang Yuzhu , Guo Xiaoyu , Hu Jingrun , Li Si , Zhang Ruijie , Gao Qiang , Yang Xi , Chen Qian , Sun Weiling
Published: November 2020

There is a dearth of information on the occurrence and risks of antibiotics in the urban rivers from plateau areas. This study investigated 83 antibiotics in water and sediments of an urban river and effluents of sewage treatment plants (E-STPs) in Xining, Qinghai (northeastern Tibetan Plateau). Fifty-three antibiotics were detected, and the concentrations of individual antibiotics varied in the range of undetected (ND)-552 ng/L in water, ND-164 ng/g in sediments, and ND-3821 ng/L in E-STPs. Seasonal differences of antibiotic concentrations were significant for water samples (p < 0.05) but insignificant for sediments (p > 0.05). In urban area, E-STP is the main source of antibiotics in the river, while runoff from manured cropland contributes partially to antibiotics in the river in the suburban area. The antibiotic compositions in water were different from those in sediments, but were similar to those in E-STPs. Notably, because of strong solar radiation and long sunshine hours in the plateau area, low levels of quinolones, which are sensitive to photolysis, were observed in river water. Moreover, norfloxacin and enrofloxacin, observed in urban river from other regions of China, were not detected in the Huangshui River water. The occurrence of ofloxacin, erythromycin, roxithromycin, clarithromycin, and trimethoprim in E-STPs may induce a possible risk to antibiotic resistance evolution. Trimethoprim, anhydroerythromycin, sulfamethoxazole, sulfapyridine, and clindamycin in river water could pose low to medium risks to aquatic organisms. Further investigation on the occurrence and distribution of antibiotic resistance genes in the Huangshui River is urgently needed.