bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation metrics and validation of presence-only species distribution models based on distributional maps with varying coverage
Authors: Konowalik Kamil , Nosol Agata
Published: January 2021

We examine how different datasets, including georeferenced hardcopy maps of different extents and georeferenced herbarium specimens (spanning the range from 100 to 85,000 km2) influence ecological niche modeling. We check 13 of the available environmental niche modeling algorithms, using 30 metrics to score their validity and evaluate which are useful for the selection of the best model. The validation is made using an independent dataset comprised of presences and absences collected in a range-wide field survey of Carpathian endemic plantLeucanthemum rotundifolium(Compositae). Our analysis of models’ predictive performances indicates that almost all datasets may be used for the construction of a species distributional range. Both very local and very general datasets can produce useful predictions, which may be more detailed than the original ranges. Results also highlight the possibility of using the data from manually georeferenced archival sources in reconstructions aimed at establishing species’ ecological niches. We discuss possible applications of those data and associated problems. For the evaluation of models, we suggest employing AUC, MAE, and Bias. We show an example of how AUC and MAE may be combined to select the model with the best performance.
Association between low body mass index and increased 28-day mortality of severe sepsis in Japanese cohorts
Authors: Oami Takehiko , Karasawa Satoshi , Shimada Tadanaga , Nakada Taka-aki , Abe Toshikazu , Ogura Hiroshi , Shiraishi Atsushi , Kushimoto Shigeki , Saitoh Daizoh , Fujishima Seitaro , Mayumi Toshihiko , Shiino Yasukazu , Tarui Takehiko , Hifumi Toru , Otomo Yasuhiro , Okamoto Kohji , Umemura Yutaka , Kotani Joji , Sakamoto Yuichiro , Sasaki Junichi , Shiraishi Shin-ichiro , Takuma Kiyotsugu , Tsuruta Ryosuke , Hagiwara Akiyoshi , Yamakawa Kazuma , Masuno Tomohiko , Takeyama Naoshi , Yamashita Norio , Ikeda Hiroto , Ueyama Masashi , Fujimi Satoshi , Gando Satoshi ,   JAAM FORECAST Group, Tasaki Osamu , Mizobata Yasumitsu , Funakoshi Hiraku , Okuyama Toshiro , Yamashita Iwao , Kanai Toshio , Yamada Yasuo , Aibiki Mayuki , Sato Keiji , Yamashita Susumu , Yamashita Susumu , Yoshida Kenichi , Kasaoka Shunji , Kon Akihide , Rinka Hiroshi , Kato Hiroshi , Okudera Hiroshi , Narimatsu Eichi , Fujiwara Toshifumi , Sugita Manabu , Shichinohe Yasuo , Nakae Hajime , Iiduka Ryouji , Nakamura Mitsunobu , Murata Yuji , Sato Yoshitake , Ishikura Hiroyasu , Myojo Yasuhiro , Tsujita Yasuyuki , Kinoshita Kosaku , Yamaguchi Hiroyuki , Sakurai Toshihiro , Miyatake Satoru , Saotome Takao , Yasuda Susumu , Mizushima Yasuaki
Published: January 2021

Current research regarding the association between body mass index (BMI) and altered clinical outcomes of sepsis in Asian populations is insufficient. We investigated the association between BMI and clinical outcomes using two Japanese cohorts of severe sepsis (derivation cohort, Chiba University Hospital, n = 614; validation cohort, multicenter cohort, n = 1561). Participants were categorized into the underweight (BMI < 18.5) and non-underweight (BMI ≥ 18.5) groups. The primary outcome was 28-day mortality. Univariate analysis of the derivation cohort indicated increased 28-day mortality trend in the underweight group compared to the non-underweight group (underweight 24.4% [20/82 cases] vs. non-underweight 16.0% [85/532 cases]; p = 0.060). In the primary analysis, multivariate analysis adjusted for baseline imbalance revealed that patients in the underweight group had a significantly increased 28-day mortality compared to those in the non-underweight group (p = 0.031, adjusted odds ratio [OR] 1.91, 95% confidence interval [CI] 1.06–3.46). In a repeated analysis using a multicenter validation cohort (underweight n = 343, non-underweight n = 1218), patients in the underweight group had a significantly increased 28-day mortality compared to those in the non-underweight group (p = 0.045, OR 1.40, 95% CI 1.00–1.97). In conclusion, patients with a BMI < 18.5 had a significantly increased 28-day mortality compared to those with a BMI ≥ 18.5 in Japanese cohorts with severe sepsis.
Assessment of real life eating difficulties in Parkinson’s disease patients by measuring plate to mouth movement elongation with inertial sensors
Authors: Kyritsis Konstantinos , Fagerberg Petter , Ioakimidis Ioannis , Chaudhuri K. Ray , Reichmann Heinz , Klingelhoefer Lisa , Delopoulos Anastasios
Published: January 2021

Parkinson’s disease (PD) is a neurodegenerative disorder with both motor and non-motor symptoms. Despite the progressive nature of PD, early diagnosis, tracking the disease’s natural history and measuring the drug response are factors that play a major role in determining the quality of life of the affected individual. Apart from the common motor symptoms, i.e., tremor at rest, rigidity and bradykinesia, studies suggest that PD is associated with disturbances in eating behavior and energy intake. Specifically, PD is associated with drug-induced impulsive eating disorders such as binge eating, appetite-related non-motor issues such as weight loss and/or gain as well as dysphagia—factors that correlate with difficulties in completing day-to-day eating-related tasks. In this work we introduce Plate-to-Mouth (PtM), an indicator that relates with the time spent for the hand operating the utensil to transfer a quantity of food from the plate into the mouth during the course of a meal. We propose a two-step approach towards the objective calculation of PtM. Initially, we use the 3D acceleration and orientation velocity signals from an off-the-shelf smartwatch to detect the bite moments and upwards wrist micromovements that occur during a meal session. Afterwards, we process the upwards hand micromovements that appear prior to every detected bite during the meal in order to estimate the bite’s PtM duration. Finally, we use a density-based scheme to estimate the PtM durations distribution and form the in-meal eating behavior profile of the subject. In the results section, we provide validation for every step of the process independently, as well as showcase our findings using a total of three datasets, one collected in a controlled clinical setting using standardized meals (with a total of 28 meal sessions from 7 Healthy Controls (HC) and 21 PD patients) and two collected in-the-wild under free living conditions (37 meals from 4 HC/10 PD patients and 629 meals from 3 HC/3 PD patients, respectively). Experimental results reveal an Area Under the Curve (AUC) of 0.748 for the clinical dataset and 0.775/1.000 for the in-the-wild datasets towards the classification of in-meal eating behavior profiles to the PD or HC group. This is the first work that attempts to use wearable Inertial Measurement Unit (IMU) sensor data, collected both in clinical and in-the-wild settings, towards the extraction of an objective eating behavior indicator for PD.
Modified recombinant human erythropoietin with potentially reduced immunogenicity
Authors: Susantad Thanutsorn , Fuangthong Mayuree , Tharakaraman Kannan , Tit-oon Phanthakarn , Ruchirawat Mathuros , Sasisekharan Ram
Published: January 2021

Recombinant human erythropoietin (rHuEPO) is a biopharmaceutical drug given to patients who have a low hemoglobin related to chronic kidney disease, cancer or anemia. However, some patients repeatedly receiving rHuEPO develop anti-rHuEPO neutralizing antibodies leading to the development of pure red cell aplasia (PRCA). The immunogenic antibody response activated by rHuEPO is believed to be triggered by T-cells recognizing EPO epitopes bound to MHC molecules displayed on the cell surface of APCs. Previous studies have reported an association between the development of anti-rHuEpo-associated PRCA and the HLA-DRB1*09 gene, which is reported to be entrenched in the Thai population. In this study, we used computational design to screen for immunogenic hotspots recognized by HLA-DRB1*09, and predicted seventeen mutants having anywhere between one through four mutations that reduce affinity for the allele, without disrupting the structural integrity and bioactivity. Five out of seventeen mutants were less immunogenic in vitro while retaining similar or slightly reduced bioactivity than rHuEPO. These engineered proteins could be the potential candidates to treat patients who are rHuEpo-dependent and express the HLA-DRB1*09 allele.
Targeted metabolomics analysis of postoperative delirium
Authors: Tripp Bridget A. , Dillon Simon T. , Yuan Min , Asara John M. , Vasunilashorn Sarinnapha M. , Fong Tamara G. , Metzger Eran D. , Inouye Sharon K. , Xie Zhongcong , Ngo Long H. , Marcantonio Edward R. , Libermann Towia A. , Otu Hasan H.
Published: January 2021

Postoperative delirium is the most common complication among older adults undergoing major surgery. The pathophysiology of delirium is poorly understood, and no blood-based, predictive markers are available. We characterized the plasma metabolome of 52 delirium cases and 52 matched controls from the Successful Aging after Elective Surgery (SAGES) cohort (N = 560) of patients ≥ 70 years old without dementia undergoing scheduled major non-cardiac surgery. We applied targeted mass spectrometry with internal standards and pooled controls using a nested matched case-control study preoperatively (PREOP) and on postoperative day 2 (POD2) to identify potential delirium risk and disease markers. Univariate analyses identified 37 PREOP and 53 POD2 metabolites associated with delirium and multivariate analyses achieved significant separation between the two groups with an 11-metabolite prediction model at PREOP (AUC = 83.80%). Systems biology analysis using the metabolites with differential concentrations rendered “valine, leucine, and isoleucine biosynthesis” at PREOP and “citrate cycle” at POD2 as the most significantly enriched pathways (false discovery rate < 0.05). Perturbations in energy metabolism and amino acid synthesis pathways may be associated with postoperative delirium and suggest potential mechanisms for delirium pathogenesis. Our results could lead to the development of a metabolomic delirium predictor.
De novo assembled salivary gland transcriptome and expression pattern analyses for Rhipicephalus evertsi evertsi Neuman, 1897 male and female ticks
Authors: Pienaar Ronel , de Klerk Daniel G. , de Castro Minique H. , Featherston Jonathan , Mans Ben J.
Published: January 2021

Ticks secrete proteins in their saliva that change over the course of feeding to modulate the host inflammation, immune responses, haemostasis or may cause paralysis. RNA next generation sequencing technologies can reveal the complex dynamics of tick salivary glands as generated from various tick life stages and/or males and females. The current study represents 15,115 Illumina sequenced contigs of the salivary gland transcriptome from male and female Rhipicephalus evertsi evertsi ticks of early, mid and late feeding stages from 1320 separate assemblies using three short read assemblers. The housekeeping functional class contributed to the majority of the composition of the transcriptome (80%) but with lower expression (51%), while the secretory protein functional class represented only 14% of the transcriptome but 46% of the total coverage. Six percent had an unknown status contributing 3% of the overall expression in the salivary glands. Platelet aggregation inhibitors, blood clotting inhibitors and immune-modulators orthologous to the ancestral tick lineages were confirmed in the transcriptome and their differential expression during feeding in both genders observed. This transcriptome contributes data of importance to salivary gland biology and blood feeding physiology of non-model organisms.
Multi-energy spectral photon-counting computed tomography (MARS) for detection of arthroplasty implant failure
Authors: Lau Lawrence Chun Man , Lee Wayne Yuk Wai , Butler Anthony P. H. , Chernoglazov Alex I. , Chung Kwong Yin , Ho Kevin Ki Wai , Griffith James , Butler Philip H. , Yung Patrick Shu Hang
Published: January 2021

To determine whether state-of-the-art multi-energy spectral photon-counting computed tomography (MARS) can detect knee arthroplasty implant failure not detected by standard pre-operative imaging techniques. A total knee arthroplasty (TKA) removed from a patient was reviewed. The extracted prosthesis [NexGen Legacy Posterior Stabilized (LPS) TKA] was analyzed as were pre-operative imaging examination and compared with a MARS-CT examination obtained of the extracted TKA prosthesis. Radiographs, fluoroscopy, ultrasound and MRI preoperatively did not reveal the cause of the implant failure. MARS CT images of the extracted prosthesis clearly showed the presence of posteromedial polyethylene and tibial tray wear which is compatible with the clinical appearance of the extracted TKA. MARS can identify polyethylene insert and metallic tibial tray wear as a cause of TKA failure, that could not be identified with on standard pre-operative imaging. Although clinical MARS CT system is still under development, this case does illustrate its potential clinical usefulness. This is the first study to document how MARS CT imaging can detect orthopedic implant failure not detected by standard current imaging techniques. This system has a potential clinical application in orthopedic patients.
Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike
Authors: Brassac Jonathan , Muqaddasi Quddoos H. , Plieske Jörg , Ganal Martin W. , Röder Marion S.
Published: January 2021

Total spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.
A framework of current based defibrillation improves defibrillation efficacy of biphasic truncated exponential waveform in rabbits
Authors: Li Weiming , Li Jingru , Wei Liang , Wang Jianjie , Peng Li , Wang Juan , Yin Changlin , Li Yongqin
Published: January 2021

Defibrillation is accomplished by the passage of sufficient current through the heart to terminate ventricular fibrillation (VF). Although current-based defibrillation has been shown to be superior to energy-based defibrillation with monophasic waveforms, defibrillators with biphasic waveforms still use energy as a therapeutic dosage. In the present study, we propose a novel framework of current-based, biphasic defibrillation grounded in transthoracic impedance (TTI) measurements: adjusting the charging voltage to deliver the desired current based on the energy setting and measured pre-shock TTI; and adjusting the pulse duration to deliver the desired energy based on the output current and intra-shock TTI. The defibrillation efficacy of current-based defibrillation was compared with that of energy-based defibrillation in a simulated high impedance rabbit model of VF. Cardiac arrest was induced by pacing the right ventricle for 60 s in 24 New Zealand rabbits (10 males). A defibrillatory shock was applied with one of the two defibrillators after 90 s of VF. The defibrillation thresholds (DFTs) at different pathway impedances were determined utilizing a 5-step up-and-down protocol. The procedure was repeated after an interval of 5 min. A total of 30 fibrillation events and defibrillation attempts were investigated for each animal. The pulse duration was significantly shorter, and the waveform tilt was much lower for the current-based defibrillator. Compared with energy-based defibrillation, the energy, peak voltage, and peak current DFT were markedly lower when the pathway impedance was > 120 Ω, but there were no differences in DFT values when the pathway impedance was between 80 and 120 Ω for current-based defibrillation. Additionally, peak voltage and the peak current DFT were significantly lower for current-based defibrillation when the pathway impedance was < 80 Ω. In sum, a framework of adjusting the charging voltage and shock duration to deliver constant energy for low impedance and constant current for high impedance via pre-shock and intra-shock impedance measurements, greatly improved the defibrillation efficacy of high impedance by lowering the energy DFT.
Obesity alters the collagen organization and mechanical properties of murine cartilage
Authors: Collins Amber T. , Hu Guoli , Newman Hunter , Reinsvold Michael H. , Goldsmith Monique R. , Twomey-Kozak John N. , Leddy Holly A. , Sharma Deepika , Shen Leyao , DeFrate Louis E. , Karner Courtney M.
Published: January 2021

Osteoarthritis is a debilitating disease characterized by cartilage degradation and altered cartilage mechanical properties. Furthermore, it is well established that obesity is a primary risk factor for osteoarthritis. The purpose of this study was to investigate the influence of obesity on the mechanical properties of murine knee cartilage. Two-month old wild type mice were fed either a normal diet or a high fat diet for 16 weeks. Atomic force microscopy-based nanoindentation was used to quantify the effective indentation modulus of medial femoral condyle cartilage. Osteoarthritis progression was graded using the OARSI system. Additionally, collagen organization was evaluated with picrosirius red staining imaged using polarized light microscopy. Significant differences between diet groups were assessed usingttests with p < 0.05. Following 16 weeks of a high fat diet, no significant differences in OARSI scoring were detected. However, we detected a significant difference in the effective indentation modulus between diet groups. The reduction in cartilage stiffness is likely the result of disrupted collagen organization in the superficial zone, as indicated by altered birefringence on polarized light microscopy. Collectively, these results suggest obesity is associated with changes in knee cartilage mechanical properties, which may be an early indicator of disease progression.
Black spicules from a new interstitial opheliid polychaete Thoracophelia minuta sp. nov. (Annelida: Opheliidae)
Authors: Jimi Naoto , Fujimoto Shinta , Takehara Mami , Imura Satoshi
Published: January 2021

The phylum Annelida exhibits high morphological diversity coupled with its extensive ecological diversity, and the process of its evolution has been an attractive research subject for many researchers. Its representatives are also extensively studied in fields of ecology and developmental biology and important in many other biology related disciplines. The study of biomineralisation is one of them. Some annelid groups are well known to form calcified tubes but other forms of biomineralisation are also known. Herein, we report a new interstitial annelid species with black spicules, Thoracophelia minuta sp. nov., from Yoichi, Hokkaido, Japan. Spicules are minute calcium carbonate inclusions found across the body and in this new species, numerous black rod-like inclusions of calcium-rich composition are distributed in the coelomic cavity. The new species can be distinguished from other known species of the genus by these conspicuous spicules, shape of branchiae and body formula. Further, the new species’ body size is apparently smaller than its congeners. Based on our molecular phylogenetic analysis using 18S and 28S sequences, we discuss the evolutionary significance of the new species’ spicules and also the species' progenetic origin.
A subset of liver resident natural killer cells is expanded in hepatitis C-infected patients with better liver function
Authors: Doyle Erin H. , Aloman Costica , El-Shamy Ahmed , Eng Francis , Rahman Adeeb , Klepper Arielle L. , Haydel Brandy , Florman Sander S. , Fiel M. Isabel , Schiano Thomas , Branch Andrea D.
Published: January 2021

Viral hepatitis leads to immune-mediated liver injury. The rate of disease progression varies between individuals. We aimed to phenotype immune cells associated with preservation of normal liver function during hepatitis C virus (HCV) infection. Clinical data and specimens were obtained from 19 HCV-infected patients undergoing liver transplantation. Liver and peripheral blood mononuclear cells were isolated and eight subsets of innate immune cells were delineated by multiparameter flow cytometry. Cytokine assays and microarrays were performed. Intrahepatic CD56Bright/CD16-natural killer (NK) cells comprised the only subset correlating with better liver function, i.e., lower bilirubin (p = 0.0002) and lower model for end stage of liver disease scores (p = 0.03). The signature of liver NK cells from HCV-infected patients included genes expressed by NK cells in normal liver and by decidual NK cells. Portal vein blood had a higher concentration of interleukin (IL)-10 than peripheral blood (p = 0.03). LMCs were less responsive to toll-like receptor (TLR) stimulation than PBMCs, with fewer pro-inflammatory gene-expression pathways up-regulated after in vitro exposure to lipopolysaccharide and a TLR-7/8 agonist. Hepatic CD56Bright/CD16-NK cells may be critical for maintaining liver homeostasis. Portal vein IL-10 may prime inhibitory pathways, attenuating TLR signaling and reducing responsiveness to pro-inflammatory stimuli.
Amikacin and bacteriophage treatment modulates outer membrane proteins composition in Proteus mirabilis biofilm
Authors: Maszewska Agnieszka , Moryl Magdalena , Wu Junli , Liu Bin , Feng Lu , Rozalski Antoni
Published: January 2021

Modification of outer membrane proteins (OMPs) is the first line of Gram-negative bacteria defence against antimicrobials. Here we point to Proteus mirabilis OMPs and their role in antibiotic and phage resistance. Protein profiles of amikacin (AMKrsv), phage (Brsv) and amikacin/phage (AMK/Brsv) resistant variants of P. mirabilis were compared to that obtained for a wild strain. In resistant variants there were identified 14, 1, 5 overexpressed and 13, 5, 1 downregulated proteins for AMKrsv, Brsv and AMK/Brsv, respectively. Application of phages with amikacin led to reducing the number of up- and downregulated proteins compared to single antibiotic treatment. Proteins isolated in AMKrsv are involved in protein biosynthesis, transcription and signal transduction, which correspond to well-known mechanisms of bacteria resistance to aminoglycosides. In isolated OMPs several cytoplasmic proteins, important in antibiotic resistance, were identified, probably as a result of environmental stress, e.g. elongation factor Tu, asparaginyl-tRNA and aspartyl-tRNA synthetases. In Brsv there were identified: NusA and dynamin superfamily protein which could play a role in bacteriophage resistance. In the resistant variants proteins associated with resistance mechanisms occurring in biofilm, e.g. polyphosphate kinase, flagella basal body rod protein were detected. These results indicate proteins important in the development of P. mirabilis antibiofilm therapies.
Partial substitution of anthracite for coke breeze in iron ore sintering
Authors: Zhang Xin , Zhong Qiang , Liu Chen , Rao Mingjun , Peng Zhiwei , Li Guanghui , Jiang Tao
Published: January 2021

In the sintering of iron ores, the partial substitution of anthracite for coke breeze has been considered to be an effective way of reducing pollutant emissions and production cost. In this study, the basic characteristics of anthracite and coke breeze were compared and the sintering performance at different substitution ratios of anthracite for coke breeze was investigated. The porosity of anthracite is lower than that of coke breeze, but its density and combustion reactivity are higher. The substitution of anthracite for coke breeze has no influence on the granulation effect of the sintering blend. As the anthracite proportion increased, the sintering speed and productivity increased and the sintering yield and tumbler index decreased. As the substitution ratio increased from 0 to 60%, the melting temperature duration and the melt quantity index decreased from 2.59 to 2.03 min and from 3218.28 to 2405.75 °C·min, respectively, leading to insufficient sintering mineralization and bad sintering indexes. For an anthracite substitution ratio of 40%, the sintering speed, sintering productivity, sintering yield and tumbler index were 22.34 mm min−1, 1.49 t·(m2 h)−1, 71.65% and 63.59%, respectively, which entirely satisfies the production requirements. Furthermore, hematite (Fe2O3), calcium ferrite (CaO–Fe2O3), and compound calcium ferrite (CaO–SiO2–Fe2O3) were the major mineral phases, which were embedded with an interwoven structure.
Implicit motor learning within three trials
Authors: Ruttle Jennifer E. , ’t Hart Bernard Marius , Henriques Denise Y. P.
Published: January 2021

In motor learning, the slow development of implicit learning is traditionally taken for granted. While much is known about training performance during adaptation to a perturbation in reaches, saccades and locomotion, little is known about the time course of the underlying implicit processes during normal motor adaptation. Implicit learning is characterized by both changes in internal models and state estimates of limb position. Here, we measure both as reach aftereffects and shifts in hand localization in our participants, after every training trial. The observed implicit changes were near asymptote after only one to three perturbed training trials and were not predicted by a two-rate model’s slow process that is supposed to capture implicit learning. Hence, we show that implicit learning is much faster than conventionally believed, which has implications for rehabilitation and skills training.
lncRNA expression profiles and associated ceRNA network analyses in epicardial adipose tissue of patients with coronary artery disease
Authors: Wang Qian-Chen , Wang Zhen-Yu , Xu Qian , Chen Xu-Liang , Shi Rui-Zheng
Published: January 2021

Epicardial adipose tissue (EAT) contributes to the pathophysiological process of coronary artery disease (CAD). The expression profiles of long non-coding RNAs (lncRNA) in EAT of patients with CAD have not been well characterized. We conducted high-throughput RNA sequencing to analyze the expression profiles of lncRNA in EAT of patients with CAD compared to patients without CAD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were executed to investigate the principal functions of the significantly dysregulated mRNAs. We confirmed a dysregulated intergenic lncRNA (lincRNA) (LINC00968) by real-time quantitative PCR (RT-qPCR). Subsequently, we constructed a ceRNA network associated with LINC00968, which included 49 mRNAs. Compared with the control group, lncRNAs and genes of EAT in CAD were characterized as metabolic active and pro-inflammatory profiles. The sequencing analysis detected 2539 known and 1719 novel lncRNAs. Then, we depicted both lncRNA and gene signatures of EAT in CAD, featuring dysregulation of genes involved in metabolism, nuclear receptor transcriptional activity, antigen presentation, chemokine signaling, and inflammation. Finally, we identified a ceRNA network as candidate modulator in EAT and its potential role in CAD. We showed the expression profiles of specific EAT lncRNA and mRNA in CAD, and a selected non-coding associated ceRNA regulatory network, which taken together, may contribute to a better understanding of CAD mechanism and provide potential therapeutic targets.

Trial registration Chinese Clinical Trial Registry, No. ChiCTR1900024782.
Self-agglomerated collagen patterns govern cell behaviour
Authors: Dede Eren Aysegul , Eren E. Deniz , Wilting Twan J. S. , de Boer Jan , Gelderblom Hanneke , Foolen Jasper
Published: January 2021

Reciprocity between cells and their surrounding extracellular matrix is one of the main drivers for cellular function and, in turn, matrix maintenance and remodelling. Unravelling how cells respond to their environment is key in understanding mechanisms of health and disease. In all these examples, matrix anisotropy is an important element, since it can alter the cell shape and fate. In this work, the objective is to develop and exploit easy-to-produce platforms that can be used to study the cellular response to natural proteins assembled into diverse topographical cues. We demonstrate a robust and simple approach to form collagen substrates with different topographies by evaporating droplets of a collagen solution. Upon evaporation of the collagen solution, a stain of collagen is left behind, composed of three regions with a distinct pattern: an isotropic region, a concentric ring pattern, and a radially oriented region. The formation and size of these regions can be controlled by the evaporation rate of the droplet and initial collagen concentration. The patterns form topographical cues inducing a pattern-specific cell (tenocyte) morphology, density, and proliferation. Rapid and cost-effective production of different self-agglomerated collagen topographies and their interfaces enables further study of the cell shape-phenotype relationship in vitro. Substrate topography and in analogy tissue architecture remains a cue that can and will be used to steer and understand cell function in vitro, which in turn can be applied in vivo, e.g. in optimizing tissue engineering applications.
Early infection-induced natural antibody response
Authors: Kubelkova Klara , Hudcovic Tomas , Kozakova Hana , Pejchal Jaroslav , Macela Ales
Published: January 2021

There remains to this day a great gap in understanding as to the role of B cells and their products—antibodies and cytokines—in mediating the protective response to Francisella tularensis, a Gram-negative coccobacillus belonging to the group of facultative intracellular bacterial pathogens. We previously have demonstrated that Francisella interacts directly with peritoneal B-1a cells. Here, we demonstrate that, as early as 12 h postinfection, germ-free mice infected with Francisella tularensis produce infection-induced antibody clones reacting with Francisella tularensis proteins having orthologs or analogs in eukaryotic cells. Production of some individual clones was limited in time and was influenced by virulence of the Francisella strain used. The phylogenetically stabilized defense mechanism can utilize these early infection-induced antibodies both to recognize components of the invading pathogens and to eliminate molecular residues of infection-damaged self cells.
A quantitative model of cellular decision making in direct neuronal reprogramming
Authors: Merlevede Adriaan , Legault Emilie M. , Drugge Viktor , Barker Roger A. , Drouin-Ouellet Janelle , Olariu Victor
Published: January 2021

The direct reprogramming of adult skin fibroblasts to neurons is thought to be controlled by a small set of interacting gene regulators. Here, we investigate how the interaction dynamics between these regulating factors coordinate cellular decision making in direct neuronal reprogramming. We put forward a quantitative model of the governing gene regulatory system, supported by measurements of mRNA expression. We found that nPTB needs to feed back into the direct neural conversion network most likely via PTB in order to accurately capture quantitative gene interaction dynamics and correctly predict the outcome of various overexpression and knockdown experiments. This was experimentally validated by nPTB knockdown leading to successful neural conversion. We also proposed a novel analytical technique to dissect system behaviour and reveal the influence of individual factors on resulting gene expression. Overall, we demonstrate that computational analysis is a powerful tool for understanding the mechanisms of direct (neuronal) reprogramming, paving the way for future models that can help improve cell conversion strategies.
A novel and facile green synthesis method to prepare LDH/MOF nanocomposite for removal of Cd(II) and Pb(II)
Authors: Soltani Roozbeh , Pelalak Rasool , Pishnamazi Mahboubeh , Marjani Azam , Albadarin Ahmad B. , Sarkar Shaheen M. , Shirazian Saeed
Published: January 2021

To date, many nanoadsorbents have been developed and used to eliminate heavy metal contamination, however, one of the challenges ahead is the preparation of adsorbents from processes in which toxic organic solvents are used in the least possible amount. Herein, we have developed a new carboxylic acid-functionalized layered double hydroxide/metal–organic framework nanocomposite (LDH/MOF NC) using a simple, effective, and green in situ method. UiO-66-(Zr)-(COOH)2 MOF nanocrystals were grown uniformly over the whole surface of COOH-functionalized Ni50Co50-LDH ultrathin nanosheets in a green water system under a normal solvothermal condition at 100 °C. The synthesized LDH/MOF NC was used as a potential adsorbent for removal of toxic Cd(II) and Pb(II) from water and the influence of important factors on the adsorption process was monitored. Various non-linear isotherm and kinetic models were used to find plausible mechanisms involved in the adsorption, and it was found that the Langmuir and pseudo-first-order models show the best agreement with isotherm and kinetic data, respectively. The calculated maximum adsorption capacities of Cd(II) and Pb(II) by the LDH/MOF NC were found to be 415.3 and 301.4 mg g−1, respectively, based on the Langmuir model (pH = 5.0, adsorbent dose = 0.02 g, solution volume = 20 mL, contact time = 120 min, temperature = 25 ℃, shaking speed 200 rpm).
PMCA4 inhibition does not affect cardiac remodelling following myocardial infarction, but may reduce susceptibility to arrhythmia
Authors: Stafford Nicholas , Zi Min , Baudoin Florence , Mohamed Tamer M. A. , Prehar Sukhpal , De Giorgio Daria , Cartwright Elizabeth J. , Latini Roberto , Neyses Ludwig , Oceandy Delvac
Published: January 2021

Ischaemic heart disease is the world’s leading cause of mortality. Survival rates from acute myocardial infarction (MI) have improved in recent years; however, this has led to an increase in the prevalence of heart failure (HF) due to chronic remodelling of the infarcted myocardium, for which treatment options remain poor. We have previously shown that inhibition of isoform 4 of the plasma membrane calcium ATPase (PMCA4) prevents chronic remodelling and HF development during pressure overload, through fibroblast mediated Wnt signalling modulation. Given that Wnt signalling also plays a prominent role during remodelling of the infarcted heart, this study investigated the effect of genetic and functional loss of PMCA4 on cardiac outcomes following MI. Neither genetic deletion nor pharmacological inhibition of PMCA4 affected chronic remodelling of the post-MI myocardium. This was the case when PMCA4 was deleted globally, or specifically from cardiomyocytes or fibroblasts. PMCA4-ablated hearts were however less prone to acute arrhythmic events, which may offer a slight survival benefit. Overall, this study demonstrates that PMCA4 inhibition does not affect chronic outcomes following MI.
Capture and return of sexual genomes by hybridogenetic frogs provides clonal genome enrichment in a sexual species
Authors: Doležálková-Kaštánková Marie , Mazepa Glib , Jeffries Daniel L. , Perrin Nicolas , Plötner Marcela , Plötner Jörg , Guex Gaston-Denis , Mikulíček Peter , Poustka Albert J. , Grau Jose , Choleva Lukáš
Published: January 2021

Hybridogenesis is a reproductive tool for sexual parasitism. Hybridogenetic hybrids use gametes from their sexual host for their own reproduction, but sexual species gain no benefit from such matings as their genome is later eliminated. Here, we examine the presence of sexual parasitism in water frogs through crossing experiments and genome-wide data. We specifically focus on the famous Central-European populations where Pelophylax esculentus males (hybrids of P. ridibundus and P. lessonae) live with P. ridibundus. We identified a system where the hybrids commonly produce two types of clonal gametes (hybrid amphispermy). The haploid lessonae genome is clonally inherited from generation to generation and assures the maintenance of hybrids through a process, in which lessonae sperm fertilize P. ridibundus eggs. The haploid ridibundus genome in hybrids received from P. ridibundus a generation ago, is perpetuated as clonal ridibundus sperm and used to fertilize P. ridibundus eggs, yielding female P. ridibundus progeny. These results imply animal reproduction in which hybridogenetic taxa are not only sexual parasites, but also participate in the formation of a sexual taxon in a remarkable way. This occurs through a process by which sexual gametes are being captured, converted to clones, and returned to sexual populations in one generation.
Estimating epidemiological parameters using diagnostic testing data from low pathogenicity avian influenza infected turkey houses
Authors: Bonney Peter J. , Malladi Sasidhar , Ssematimba Amos , Spackman Erica , Torchetti Mia Kim , Culhane Marie , Cardona Carol J.
Published: January 2021

Limiting spread of low pathogenicity avian influenza (LPAI) during an outbreak is critical to reduce the negative impact on poultry producers and local economies. Mathematical models of disease transmission can support outbreak control efforts by estimating relevant epidemiological parameters. In this article, diagnostic testing data from each house on a premises infected during a LPAI H5N2 outbreak in the state of Minnesota in the United States in 2018 was used to estimate the time of virus introduction and adequate contact rate, which determines the rate of disease spread. A well-defined most likely time of virus introduction, and upper and lower 95% credibility intervals were estimated for each house. The length of the 95% credibility intervals ranged from 11 to 22 with a mean of 17 days. In some houses the contact rate estimates were also well-defined; however, the estimated upper 95% credibility interval bound for the contact rate was occasionally dependent on the upper bound of the prior distribution. The estimated modes ranged from 0.5 to 6.0 with a mean of 2.8 contacts per day. These estimates can be improved with early detection, increased testing of monitored premises, and combining the results of multiple barns that possess similar production systems.
Possible diverse contribution of coronary risk factors to left ventricular systolic and diastolic cavity sizes
Authors: Suzuki Kenichiro , Inoue Yasunori , Ogawa Kazuo , Nagoshi Tomohisa , Minai Kosuke , Ogawa Takayuki , Kawai Makoto , Yoshimura Michihiro
Published: January 2021

It is generally believed that risk factors damage the coronary arteries, cause myocardial ischemia, and consequently change the shape of the heart. On the other hand, each of the risk factors may also have a negative effect on the heart. However, it is very difficult to examine the effects of each of these risk factors independently. Therefore, it is necessary to select an appropriate statistical method and apply it efficiently. In this study, the effects of coronary risk factors on left ventricular size and cardiac function were investigated using structure equation modeling (SEM), and were shown as Bayesian SEM-based frequency polygons using selected two-dimensional contours. This study showed that each risk factor directly affected the shape of the heart. Because vascular risk and heart failure risk are likely to evolve at the same time, managing risk factors is very important in reducing the heart failure pandemic.
Ultrasound probe tilt impedes the needle-beam alignment during the ultrasound-guided procedures
Authors: Mao Qingxiang , He Haitao , Lu Yuangang , Hu Yi , Wang Zhen , Gan Maoxiang , Yan Hong , Chen Liyong
Published: January 2021

The objective of this study was to identify the factors that complicate the needle visualization in ultrasound-guided in-plane needling procedures. Forty-nine residents were recruited and randomized to insert the simulated blood vessel with four different views including Neutral (the long axis of the probe along the visual axis and the ultrasonic beam vertical to the surface of gel phantom), 45°-rotation (45° angle between the long axis of probe and the operator’s visual axis), 45°-tilt (45° angle between the ultrasonic beam and the surface of gel phantom) and 45°-rotation plus 45°-tilt of probe. Number of needle redirections, insertion time, and needle visibility were documented and compared for each procedure. When the residents faced with 45°-tilt view, the needle redirections (2 vs 0) and insertion time increased significantly (39 vs 16) compared with that of the Neutral view. When faced with 45°-rotation plus 45°-tilt view, the residents’ performance decreased further as compared with that of the 45°-tilt view and the Neutral view. However, there was no performance difference between the Neutral view and 45°-rotation view. In conclusion, during ultrasound-guided in-plane procedures, tilting the ultrasound probe may increase the difficulty of needle-beam alignment.
A risk marker of tribasic hemagglutinin cleavage site in influenza A (H9N2) virus
Authors: Zhang Jiahao , Ma Kaixiong , Li Bo , Chen Yiqun , Qiu Ziwen , Xing Jinchao , Huang Jinyu , Hu Chen , Huang Yifan , Li Huanan , Liu Dingxiang , Liao Ming , Qi Wenbao
Published: January 2021

Low pathogenic avian influenza A(H9N2) virus is endemic worldwide and continually recruit internal genes to generate human-infecting H5N1, H5N6, H7N9, and H10N8 influenza variants. Here we show that hemagglutinin cleavage sites (HACS) of H9N2 viruses tended to mutate towards hydrophilic via evolutionary transition, and the tribasic HACS were found at high prevalence in Asia and the Middle East. Our finding suggested that the tribasic H9N2 viruses increased the viral replication, stability, pathogenicity and transmission in chickens and the virulence of mice compared to the monobasic H9N2 viruses. Notably, the enlarged stem-loop structures of HACS in the RNA region were found in the increasing tribasic H9N2 viruses. The enlarged HACS RNA secondary structures of H9N2 viruses did not influence the viral replication but accelerated the frequency of nucleotide insertion in HACS. With the prevailing tendency of the tribasic H9N2 viruses, the tribasic HACS in H9N2 viruses should be paid more attention.
High throughput estimates of Wolbachia, Zika and chikungunya infection in Aedes aegypti by near-infrared spectroscopy to improve arbovirus surveillance
Authors: Santos Lilha M. B. , Mutsaers Mathijs , Garcia Gabriela A. , David Mariana R. , Pavan Márcio G. , Petersen Martha T. , Corrêa-Antônio Jessica , Couto-Lima Dinair , Maes Louis , Dowell Floyd , Lord Anton , Sikulu-Lord Maggy , Maciel-de-Freitas Rafael
Published: January 2021

Deployment ofWolbachiato mitigate dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) transmission is ongoing in 12 countries. One way to assess the efficacy ofWolbachiareleases is to determine invasion rates within the wild population ofAedes aegyptifollowing their release. Herein we evaluated the accuracy, sensitivity and specificity of the Near Infrared Spectroscopy (NIRS) in estimating the time post death, ZIKV-, CHIKV-, andWolbachia-infection in trapped dead femaleAe. aegyptimosquitoes over a period of 7 days. Regardless of the infection type, time post-death of mosquitoes was accurately predicted into four categories (fresh, 1 day old, 2–4 days old and 5–7 days old). Overall accuracies of 93.2, 97 and 90.3% were observed when NIRS was used to detect ZIKV, CHIKV andWolbachiain deadAe. aegyptifemale mosquitoes indicating NIRS could be potentially applied as a rapid and cost-effective arbovirus surveillance tool. However, field data is required to demonstrate the full capacity of NIRS for detecting these infections under field conditions.
Solid-state colorimetric polydiacetylene liposome biosensor sensitized by gold nanoparticles
Authors: Kim Jayoung , Moon Byeong-Seok , Hwang Eunhee , Shaban Samy , Lee Wonjung , Pyun Do-Gi , Lee Dong Hyun , Kim Dong-Hwan
Published: January 2021

Solid-state polydiacetylene liposome biosensors are sensitized by gold nanoparticles to exhibit clear colorimetric response from blue to red upon biomolecular binding. This hybrid system will pave the way for portable colorimetric biosensors.
Correction: Determination of sulfonamides in blood using acetonitrile–salt aqueous two-phase extraction coupled with high-performance liquid chromatography and liquid chromatography-tandem mass spectrometry
Authors: Yu Wei , Liu Zhongling , Gao Shiqian , Cui Shusen , Yang Xiao , Qiu Wei , Zhang Hanqi , Yu Aimin , Huan Yanfu
Published: January 2021

Correction for ‘Determination of sulfonamides in blood using acetonitrile-salt aqueous two-phase extraction coupled with high-performance liquid chromatography and liquid chromatography–tandem mass spectrometry’ by Wei Yu et al., Anal. Methods, 2013, 5, 5983–5989, DOI: 10.1039/C3AY40902C.
The intramolecular reaction of acetophenone N-tosylhydrazone and vinyl: Brønsted acid-promoted cationic cyclization toward polysubstituted indenes
Authors: Wang Zhixin , Li Yang , Chen Fan , Qian Peng-Cheng , Cheng Jiang
Published: January 2021

In the presence of TsNHNH2, a Brønsted acid-promoted intramolecular cyclization of o-(1-arylvinyl) acetophenone derivatives was developed, leading to polysubstituted indenes with complexity and diversity in moderate to excellent yields.
Introduction to (photo)electrocatalysis for renewable energy
Authors: Dey Abhishek , Houle Frances A. , Lubner Carolyn E. , Sevilla Marta , Shaw Wendy J.
Published: January 2021

(Photo)electrocatalysis holds the promise to enable the broad implementation of renewable energies. The articles highlighted in this issue emphasize advances in types and activity of catalysts and electrode materials for a variety of reactions and technologies.
Electrocatalytic nitrogen reduction on the transition-metal dimer anchored N-doped graphene: performance prediction and synergetic effect
Authors: Ma Dongwei , Wang Yuanyuan , Liu Liangliang , Jia Yu
Published: January 2021

Present studies highlight the important role of the heteronuclear members for the development of the double-atom catalysts, and further provide a strategy to design efficient heteronuclear double-atom catalysts from the large chemical composition space for the electrocatalytic NRR.
The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals
Authors: Hentschel Lorena , Hansen Jan , Egelhaaf Stefan U. , Platten Florian
Published: January 2021

Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.
Modulating oxidation state of Ni/CeO2 catalyst for steam methane reforming: a theoretical prediction with experimental verification
Authors: Wu Chan , Xiao Zhourong , Wang Li , Li Guozhu , Zhang Xiangwen , Wang Lichang
Published: January 2021

Rational design of partially oxidized Ni/CeO2 with both high activity and good stability by DFT for efficient methane steam reforming.