bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia
Authors: Ingle Danielle J. , Ambrose Rebecca L. , Baines Sarah L. , Duchene Sebastian , Gonçalves da Silva Anders , Lee Darren Y. J. , Jones Miriam , Valcanis Mary , Taiaroa George , Ballard Susan A. , Kirk Martyn D. , Howden Benjamin P. , Pearson Jaclyn S. , Williamson Deborah A.
Published: August 2021

Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
IceR improves proteome coverage and data completeness in global and single-cell proteomics
Authors: Kalxdorf Mathias , Müller Torsten , Stegle Oliver , Krijgsveld Jeroen
Published: August 2021

Label-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficient and user-friendly quantification workflow that combines high identification rates of data-dependent acquisition with low missing value rates similar to data-independent acquisition. Specifically, IceR uses ion current information for a hybrid peptide identification propagation approach with superior quantification precision, accuracy, reliability and data completeness compared to other quantitative workflows. Applied to plasma and single-cell proteomics data, IceR enhanced the number of reliably quantified proteins, improved discriminability between single-cell populations, and allowed reconstruction of a developmental trajectory. IceR will be useful to improve performance of large scale global as well as low-input proteomics applications, facilitated by its availability as an easy-to-use R-package.
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics
Authors: Oftadeh Omid , Salvy Pierre , Masid Maria , Curvat Maxime , Miskovic Ljubisa , Hatzimanikatis Vassily
Published: August 2021

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the most accurate models of biological systems include Expression and Thermodynamics FLux (ETFL), which efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To adapt this model for Saccharomyces cerevisiae, we developed yETFL, in which we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the ability of yETFL to predict maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the presented formulation can be extended to a wide range of eukaryotic organisms to the benefit of academic and industrial research.
The cytokines HGF and CXCL13 predict the severity and the mortality in COVID-19 patients
Authors: Perreau Matthieu , Suffiotti Madeleine , Marques-Vidal Pedro , Wiedemann Aurelie , Levy Yves , Laouénan Cédric , Ghosn Jade , Fenwick Craig , Comte Denis , Roger Thierry , Regina Jean , Vollenweider Peter , Waeber Gerard , Oddo Mauro , Calandra Thierry , Pantaleo Giuseppe
Published: August 2021

The objective of the present study was to identify biological signatures of severe coronavirus disease 2019 (COVID-19) predictive of admission in the intensive care unit (ICU). Over 170 immunological markers were investigated in a ‘discovery’ cohort (n = 98 patients) of the Lausanne University Hospital (LUH-1). Here we report that 13 out of 49 cytokines were significantly associated with ICU admission in the three cohorts (P < 0.05 to P < 0.001), while cellular immunological markers lacked power in discriminating between ICU and non-ICU patients. The cytokine results were confirmed in two ‘validation’ cohorts, i.e. the French COVID-19 Study (FCS; n = 62) and a second LUH-2 cohort (n = 47). The combination of hepatocyte growth factor (HGF) and C-X-C motif chemokine ligand 13 (CXCL13) was the best predictor of ICU admission (positive and negative predictive values ranging from 81.8% to 93.1% and 85.2% to 94.4% in the 3 cohorts) and occurrence of death during patient follow-up (8.8 fold higher likelihood of death when both cytokines were increased). Of note, HGF is a pleiotropic cytokine with anti-inflammatory properties playing a fundamental role in lung tissue repair, and CXCL13, a pro-inflammatory chemokine associated with pulmonary fibrosis and regulating the maturation of B cell response. Up-regulation of HGF reflects the most powerful counter-regulatory mechanism of the host immune response to antagonize the pro-inflammatory cytokines including CXCL13 and to prevent lung fibrosis in COVID-19 patients.
Metagenomic analysis revealed the potential role of gut microbiome in gout
Authors: Chu Yongliang , Sun Silong , Huang Yufen , Gao Qiang , Xie Xuefeng , Wang Peng , Li Junxia , Liang Lifeng , He Xiaohong , Jiang Yiqi , Wang Maojie , Yang Jianhua , Chen Xiumin , Zhou Chu , Zhao Yue , Ding Fen , Zhang Yi , Wu Xiaodong , Bai Xueyuan , Wu Jiaqi , Wei Xia , Chen Xianghong , Yue Zhen , Fang Xiaodong , Huang Qingchun , Wang Zhang , Huang Runyue
Published: August 2021

Emerging evidence indicates an association between gut microbiome and arthritis diseases including gout. However, how and which gut bacteria affect host urate degradation and inflammation in gout remains unclear. Here we performed a metagenome analysis on 307 fecal samples from 102 gout patients and 86 healthy controls. Gout metagenomes significantly differed from those of healthy controls. The relative abundances of Prevotella, Fusobacterium, and Bacteroides were increased in gout, whereas those of Enterobacteriaceae and butyrate-producing species were decreased. Functionally, gout patients had greater abundances for genes in fructose, mannose metabolism and lipid A biosynthesis, and lower for genes in urate degradation and short chain fatty acid production. A three-pronged association between metagenomic species, functions and clinical parameters revealed that decreased abundances of species in Enterobacteriaceae were associated with reduced amino acid metabolism and environmental sensing, which together contribute to increased serum uric acid and C-reactive protein levels in gout. A random forest classifier based on three gut microbial genes showed high predictivity for gout in both discovery and validation cohorts (0.91 and 0.80 accuracy), with high specificity in the context of other chronic disorders. Longitudinal analysis showed that uric-acid-lowering and anti-inflammatory drugs partially restored gut microbiota after 24-week treatment. Comparative analysis with obesity, type 2 diabetes, ankylosing spondylitis and rheumatoid arthritis indicated that gout metagenomes were more similar to those of autoimmune than metabolic diseases. Our results suggest that gut dysbiosis was associated with dysregulated host urate degradation and systemic inflammation and may be used as non-invasive diagnostic markers for gout.
Contractile behavior of the gastrocnemius medialis muscle during running in simulated hypogravity
Authors: Richter Charlotte , Braunstein Bjoern , Staeudle Benjamin , Attias Julia , Suess Alexander , Weber Tobias , Mileva Katya N. , Rittweger Joern , Green David A. , Albracht Kirsten
Published: August 2021

Vigorous exercise countermeasures in microgravity can largely attenuate muscular degeneration, albeit the extent of applied loading is key for the extent of muscle wasting. Running on the International Space Station is usually performed with maximum loads of 70% body weight (0.7 g). However, it has not been investigated how the reduced musculoskeletal loading affects muscle and series elastic element dynamics, and thereby force and power generation. Therefore, this study examined the effects of running on the vertical treadmill facility, a ground-based analog, at simulated 0.7 g on gastrocnemius medialis contractile behavior. The results reveal that fascicle−series elastic element behavior differs between simulated hypogravity and 1 g running. Whilst shorter peak series elastic element lengths at simulated 0.7 g appear to be the result of lower muscular and gravitational forces acting on it, increased fascicle lengths and decreased velocities could not be anticipated, but may inform the development of optimized running training in hypogravity. However, whether the alterations in contractile behavior precipitate musculoskeletal degeneration warrants further study.
Lost photon enhances superresolution
Authors: Mikhalychev A. B. , Novik P. I. , Karuseichyk I. L. , Lyakhov D. A. , Michels D. L. , Mogilevtsev D. S.
Published: August 2021

Quantum imaging can beat classical resolution limits, imposed by the diffraction of light. In particular, it is known that one can reduce the image blurring and increase the achievable resolution by illuminating an object by entangled light and measuring coincidences of photons. If an n-photon entangled state is used and the nth-order correlation function is measured, the point-spread function (PSF) effectively becomes $$\sqrt{n}$$

n

times narrower relatively to classical coherent imaging. Quite surprisingly, measuring n-photon correlations is not the best choice if an n-photon entangled state is available. We show that for measuring (n − 1)-photon coincidences (thus, ignoring one of the available photons), PSF can be made even narrower. This observation paves a way for a strong conditional resolution enhancement by registering one of the photons outside the imaging area. We analyze the conditions necessary for the resolution increase and propose a practical scheme, suitable for observation and exploitation of the effect.
Early Pleistocene faunivorous hominins were not kleptoparasitic, and this impacted the evolution of human anatomy and socio-ecology
Authors: Domínguez-Rodrigo Manuel , Baquedano Enrique , Organista Elia , Cobo-Sánchez Lucía , Mabulla Audax , Maskara Vivek , Gidna Agness , Pizarro-Monzo Marcos , Aramendi Julia , Galán Ana Belén , Cifuentes-Alcobendas Gabriel , Vegara-Riquelme Marina , Jiménez-García Blanca , Abellán Natalia , Barba Rebeca , Uribelarrea David , Martín-Perea David , Diez-Martin Fernando , Maíllo-Fernández José Manuel , Rodríguez-Hidalgo Antonio , Courtenay Lloyd , Mora Rocío , Maté-González Miguel Angel , González-Aguilera Diego
Published: August 2021

Humans are unique in their diet, physiology and socio-reproductive behavior compared to other primates. They are also unique in the ubiquitous adaptation to all biomes and habitats. From an evolutionary perspective, these trends seem to have started about two million years ago, coinciding with the emergence of encephalization, the reduction of the dental apparatus, the adoption of a fully terrestrial lifestyle, resulting in the emergence of the modern anatomical bauplan, the focalization of certain activities in the landscape, the use of stone tools, and the exit from Africa. It is in this period that clear taphonomic evidence of a switch in diet with respect to Pliocene hominins occurred, with the adoption of carnivory. Until now, the degree of carnivorism in early humans remained controversial. A persistent hypothesis is that hominins acquired meat irregularly (potentially as fallback food) and opportunistically through klepto-foraging. Here, we test this hypothesis and show, in contrast, that the butchery practices of early Pleistocene hominins (unveiled through systematic study of the patterning and intensity of cut marks on their prey) could not have resulted from having frequent secondary access to carcasses. We provide evidence of hominin primary access to animal resources and emphasize the role that meat played in their diets, their ecology and their anatomical evolution, ultimately resulting in the ecologically unrestricted terrestrial adaptation of our species. This has major implications to the evolution of human physiology and potentially for the evolution of the human brain.
Biochemical and structural studies of target lectin SapL1 from the emerging opportunistic microfungus Scedosporium apiospermum
Authors: Martínez-Alarcón Dania , Balloy Viviane , Bouchara Jean-Philippe , Pieters Roland J. , Varrot Annabelle
Published: August 2021

Scedosporium apiospermum is an emerging opportunistic fungal pathogen responsible for life-threatening infections in humans. Host–pathogen interactions often implicate lectins that have become therapeutic targets for the development of carbohydrate mimics for antiadhesive therapy. Here, we present the first report on the identification and characterization of a lectin from S. apiospermum named SapL1. SapL1 was found using bioinformatics as a homolog to the conidial surface lectin FleA from Aspergillus fumigatus known to play a role in the adhesion to host glycoconjugates present in human lung epithelium. In our strategy to obtain recombinant SapL1, we discovered the importance of osmolytes to achieve its expression in soluble form in bacteria. Analysis of glycan arrays indicates specificity for fucosylated oligosaccharides as expected. Submicromolar affinity was measured for fucose using isothermal titration calorimetry. We solved SapL1 crystal structure in complex with α-methyl-L-fucoside and analyzed its structural basis for fucose binding. We finally demonstrated that SapL1 binds to bronchial epithelial cells in a fucose-dependent manner. The information gathered here will contribute to the design and development of glycodrugs targeting SapL1.
Comparative analysis of freshwater phytoplankton communities in two lakes of Burabay National Park using morphological and molecular approaches
Authors: Malashenkov Dmitry V. , Dashkova Veronika , Zhakupova Kymbat , Vorobjev Ivan A. , Barteneva Natasha S.
Published: August 2021

We analyzed phytoplankton assemblages’ variations in oligo-mesotrophic Shchuchie and Burabay lakes using traditional morphological and next-generation sequencing (NGS) approaches. The total phytoplankton biodiversity and abundance estimated by both microscopy and NGS were significantly higher in Lake Burabay than in Lake Shchuchie. NGS of 16S and 18S rRNA amplicons adequately identify phytoplankton taxa only on the genera level, while species composition obtained by microscopic examination was significantly larger. The limitations of NGS analysis could be related to insufficient coverage of freshwater lakes phytoplankton by existing databases, short algal sequences available from current instrumentation, and high homology of chloroplast genes in eukaryotic cells. However, utilization of NGS, together with microscopy allowed us to perform a complete taxonomic characterization of phytoplankton lake communities including picocyanobacteria, often overlooked by traditional microscopy. We demonstrate the high potential of an integrated morphological and molecular approach in understanding the processes of organization in aquatic ecosystem assemblages.
Effects of airway management and tidal volume feedback ventilation during pediatric resuscitation in piglets with asphyxial cardiac arrest
Authors: Manrique Gema , Pérez Gema , Butragueño-Laiseca Laura , García Miriam , Slöcker María , González Rafael , Herrera Laura , Mencía Santiago , del Castillo Jimena , Solana María José , Sanz Débora , Cieza Raquel , Fernández Sarah N. , López Jorge , Urbano Javier , López-Herce Jesús
Published: August 2021

To compare the effect on the recovery of spontaneous circulation (ROSC) of early endotracheal intubation (ETI) versus bag-mask ventilation (BMV), and expiratory real-time tidal volume (VTe) feedback (TVF) ventilation versus without feedback or standard ventilation (SV) in a pediatric animal model of asphyxial cardiac arrest. Piglets were randomized into five groups: 1: ETI and TVF ventilation (10 ml/kg); 2: ETI and TVF (7 ml/kg); 3: ETI and SV; 4: BMV and TVF (10 ml/kg) and 5: BMV and SV. Thirty breaths-per-minute guided by metronome were given. ROSC, pCO2, pO2, EtCO2 and VTe were compared among groups. Seventy-nine piglets (11.3 ± 1.2 kg) were included. Twenty-six (32.9%) achieved ROSC. Survival was non-significantly higher in ETI (40.4%) than BMV groups (21.9%), p = 0.08. No differences in ROSC were found between TVF and SV groups (30.0% versus 34.7%, p = 0.67). ETI groups presented lower pCO2, and higher pO2, EtCO2 and VTe than BMV groups (p < 0.05). VTe was lower in TVF than in SV groups and in BMV than in ETI groups (p < 0.05). Groups 1 and 3 showed higher pO2 and lower pCO2 over time, although with hyperventilation values (pCO2 < 35 mmHg). ETI groups had non significantly higher survival rate than BMV groups. Compared to BMV groups, ETI groups achieved better oxygenation and ventilation parameters. VTe was lower in both TVF and BMV groups. Hyperventilation was observed in intubated animals with SV and with 10 ml/kg VTF.
Detection of three pandemic causing coronaviruses from non-respiratory samples: systematic review and meta-analysis
Authors: Mishra Chandan , Meena Suneeta , Meena Jitendra Kumar , Tiwari Suman , Mathur Purva
Published: August 2021

SARS-CoV-2 has posed an unprecedented challenge to the world. Pandemics have been caused previously by viruses of this family like Middle East Respiratory Corona Virus (MERS CoV), Severe Acute Respiratory Syndrome Corona Virus (SARS CoV). Although these viruses are primarily respiratory viruses, but they have been isolated from non-respiratory samples as well. Presently, the detection rate of SARS‐CoV‐2 RNA from different clinical specimens using Real Time Reverse Transcriptase Polymerized Chain Reaction (qRT‐PCR) after onset of symptoms is not yet well established. Therefore, the aim of this systematic review was to establish the profile of detecting SARS‐CoV‐2, MERS CoV, SARS CoV from different types of clinical specimens other than the respiratory using a standard diagnostic test (qRT‐PCR). A total of 3429 non-respiratory specimens were recorded: SARS CoV (total sample—802), MERS CoV (total sample—155), SARS CoV-2 (total sample—2347). Out of all the samples studied high positive rate was seen for saliva with 96.7% (14/14; 95% CI 87.6–100.0%) for SARS CoV and 57.5% (58/250; 95% CI − 1.2 to 116.2%) for SARS CoV-2, while low detection rate in urine samples for SARS CoV-2 with 2.2% (8/318; 95% CI 0.6–3.7%) and 9.6% (12/61; 95% CI − 0.9 to 20.1%) for SARS CoV but there was relatively higher positivity in urine samples for MERS CoV with detection rate of 32.4% (2/38; 95% CI − 37.3 to 102.1%). In Stool sample positivity was 54.9% (396/779; 95% CI 41.0–68.8%), 45.2% (180/430; 95% CI 28.1–62.3%) and 34.7% (4/38; 95% CI − 29.5 to 98.9%) for SARS CoV-2, MERS CoV, and SARS CoV, respectively. In blood sample the positivity was 33.3% (7/21; 95% CI 13.2–53.5%), 23.7% (42/277; 95% CI 10.5–36.9%) and 2.5% (2/81; 95% CI 0.00–5.8%) for MERS CoV, SARS CoV-2 and SARS CoV respectively. SARS‐CoV‐2 along with previous two pandemic causing viruses from this family, were highly detected stool and saliva. A low positive rate was recorded in blood samples. Viruses were also detected in fluids along with unusual samples like semen and vaginal secretions thus highlighting unique pathogenic potential of SARS‐CoV‐2.
An effective model of endogenous clocks and external stimuli determining circadian rhythms
Authors: Breitenbach Tim , Helfrich-Förster Charlotte , Dandekar Thomas
Published: August 2021

Circadian endogenous clocks of eukaryotic organisms are an established and rapidly developing research field. To investigate and simulate in an effective model the effect of external stimuli on such clocks and their components we developed a software framework for download and simulation. The application is useful to understand the different involved effects in a mathematical simple and effective model. This concerns the effects of Zeitgebers, feedback loops and further modifying components. We start from a known mathematical oscillator model, which is based on experimental molecular findings. This is extended with an effective framework that includes the impact of external stimuli on the circadian oscillations including high dose pharmacological treatment. In particular, the external stimuli framework defines a systematic procedure by input-output-interfaces to couple different oscillators. The framework is validated by providing phase response curves and ranges of entrainment. Furthermore, Aschoffs rule is computationally investigated. It is shown how the external stimuli framework can be used to study biological effects like points of singularity or oscillators integrating different signals at once. The mathematical framework and formalism is generic and allows to study in general the effect of external stimuli on oscillators and other biological processes. For an easy replication of each numerical experiment presented in this work and an easy implementation of the framework the corresponding Mathematica files are fully made available. They can be downloaded at the following link: https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/circadian/.
Identification of intima-to-media signals for flow-induced vascular remodeling using correlative gene expression analysis
Authors: Kolega John , Poppenberg Kerry E. , Lim Hee-Woong , Gutierrez Liza C. , Veeturi Sricharan S. , Siddiqui Adnan H. , Rajabzadeh-Oghaz Hamidreza , Tutino Vincent M.
Published: August 2021

Changes in blood flow can induce arterial remodeling. Intimal cells sense flow and send signals to the media to initiate remodeling. However, the nature of such intima-media signaling is not fully understood. To identify potential signals, New Zealand white rabbits underwent bilateral carotid ligation to increase flow in the basilar artery or sham surgery (n = 2 ligated, n = 2 sham). Flow was measured by transcranial Doppler ultrasonography, vessel geometry was determined by 3D angiography, and hemodynamics were quantified by computational fluid dynamics. 24 h post-surgery, the basilar artery and terminus were embedded for sectioning. Intima and media were separately microdissected from the sections, and whole transcriptomes were obtained by RNA-seq. Correlation analysis of expression across all possible intima-media gene pairs revealed potential remodeling signals. Carotid ligation increased flow in the basilar artery and terminus and caused differential expression of 194 intimal genes and 529 medial genes. 29,777 intima-media gene pairs exhibited correlated expression. 18 intimal genes had > 200 medial correlates and coded for extracellular products. Gene ontology of the medial correlates showed enrichment of organonitrogen metabolism, leukocyte activation/immune response, and secretion/exocytosis processes. This demonstrates correlative expression analysis of intimal and medial genes can reveal novel signals that may regulate flow-induced arterial remodeling.
Validity of the Gender Dysphoria diagnosis and incidence trends in Sweden: a nationwide register study
Authors: Indremo Malin , White Richard , Frisell Thomas , Cnattingius Sven , Skalkidou Alkistis , Isaksson Johan , Papadopoulos Fotios C.
Published: August 2021

The aim of this study was to examine the validity of the Gender Dysphoria (GD) diagnoses in the Swedish National Patient Register (NPR), to discuss different register-based definitions of GD and to investigate incidence trends. We collected data on all individuals with registered GD diagnoses between 2001 and 2016 as well as data on the coverage in the NPR. We regarded gender confirming medical intervention (GCMI) as one proxy for a clinically valid diagnosis and calculated the positive predictive value (PPV) for receiving GCMI for increasing number of registered GD diagnoses. We assessed crude and coverage-adjusted time trends of GD during 2004–2015 with a Poisson regression, using assigned sex and age as interaction terms. The PPV for receiving GCMI was 68% for ≥ 1 and 79% for ≥ 4 GD-diagnoses. The incidence of GD was on average 35% higher with the definition of ≥ 1 compared to the definition of ≥ 4 diagnoses. The incidence of GD, defined as ≥ 4 diagnoses increased significantly during the study period and mostly in the age categories 10–17 and 18–30 years, even after adjusting for register coverage. We concluded that the validity of a single ICD code denoting clinical GD in the Swedish NPR can be questioned. For future research, we propose to carefully weight the advantages and disadvantages of different register-based definitions according to the individual study’s needs, the time periods involved and the age-groups under study.
Impact of elevation and slope aspect on floristic composition in wadi Elkor, Sarawat Mountain, Saudi Arabia
Authors: Fadl Mohamed A. , Al-Yasi Hatim M. , Alsherif Emad A.
Published: August 2021

The current research was carried out in Wadi Elkor, one of the Sarawat Mountains regions, which is a special location from an environmental standpoint and one of the only places in Saudi Arabia where a range of Palaearctic flora co-exists with Afrotropical species. The study aimed to determine the floristic composition as well as the effects of slope aspect and elevation on species, life forms, and phytogeographical elements distribution. The study area is located in Wadi Elkor, a valley in the Sarawat Mountains that cuts off the Al-Hada escarpment, 47 km southeast of Makkah City, Saudi Arabia. We conducted the research at three different locations, each with a different elevation and slope aspect. Based on floristic composition, Ward classification moreover Jaccard comparisons were performed. A total of 189 species was discovered, divided into 131 genera and 43 families. The current study identified Argyrolobium rarum Dumme as a new vascular plant in Saudi Arabia's terrestrial flora. In the current study, the Gramineae, Leguminosae, and Compositae families contributed 29% of the total plant species, whereas 14 families were represented by one species each. Solanum was the most numerous genus, with seven species, followed by Acacia and Pulicaria, each with six species, while Commicarpos and Euphorbia, each with four species. At an elevation of 1060 m above sea level, the north facing slope had the most plants, genera, and families. Therophytes had the most species, accounting for 44%, followed by Chamaephytes, which accounted for 26%. Hemicryptophytes accounted for 12% of the total, while phanerophytes accounted for 10%. In the studied area, the bioregional Saharo-Sindian and Sudano-Zambesian groups were the most well-represented (41%). The floristic composition, as well as the distribution of life forms and phytogeographical components, were found to be significantly affected by the elevation and slope aspects. The study showed that slope aspect and elevation both affected the distribution of plant species, with elevation being the most influential of the two variables.
Machine learning screening of bile acid-binding peptides in a peptide database derived from food proteins
Authors: Imai Kento , Shimizu Kazunori , Honda Hiroyuki
Published: August 2021

Bioactive peptides (BPs) are protein fragments that exhibit a wide variety of physicochemical properties, such as basic, acidic, hydrophobic, and hydrophilic properties; thus, they have the potential to interact with a variety of biomolecules, whereas neither carbohydrates nor fatty acids have such diverse properties. Therefore, BP is considered to be a new generation of biologically active regulators. Recently, some BPs that have shown positive benefits in humans have been screened from edible proteins. In the present study, a new BP screening method was developed using BIOPEP-UWM and machine learning. Training data were initially obtained using high-throughput techniques, and positive and negative datasets were generated. The predictive model was generated by calculating the explanatory variables of the peptides. To understand both site-specific and global characteristics, amino acid features (for site-specific characteristics) and peptide global features (for global characteristics) were generated. The constructed models were applied to the peptide database generated using BIOPEP-UWM, and bioactivity was predicted to explore candidate bile acid-binding peptides. Using this strategy, seven novel bile acid-binding peptides (VFWM, QRIFW, RVWVQ, LIRYTK, NGDEPL, PTFTRKL, and KISQRYQ) were identified. Our novel screening method can be easily applied to industrial applications using whole edible proteins. The proposed approach would be useful for identifying bile acid-binding peptides, as well as other BPs, as long as a large amount of training data can be obtained.
Rapid geographical indication of peppercorn seeds using corona discharge mass spectrometry
Authors: Charoensumran Preeyarad , Rauytanapanit Monrawat , Sricharoen Nontawat , Smith Barry L. , Wongravee Kanet , Maher Simon , Praneenararat Thanit
Published: August 2021

With increasing demands for more rapid and practical analyses, various techniques of ambient ionization mass spectrometry have gained significant interest due to the speed of analysis and abundance of information provided. Herein, an ambient ionization technique that utilizes corona discharge was applied, for the first time, to analyze and categorize whole seeds of black and white peppers from different origins. This setup requires no solvent application nor gas flow, thus resulting in a very simple and rapid analysis that can be applied directly to the sample without any prior workup or preparation. Combined with robust data pre-processing and subsequent chemometric analyses, this analytical method was capable of indicating the geographical origin of each pepper source with up to 98% accuracies in all sub-studies. The simplicity and speed of this approach open up the exciting opportunity for onsite analysis without the need for a highly trained operator. Furthermore, this methodology can be applied to a variety of spices and herbs, whose geographical indication or similar intellectual properties are economically important, hence it is capable of creating tremendous impact in the food and agricultural industries.
Effect of EPSPS gene copy number and glyphosate selection on fitness of glyphosate-resistant Bassia scoparia in the field
Authors: Lim Charlemagne Ajoc , Jha Prashant , Kumar Vipan , Dyer Alan T.
Published: August 2021

The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. With the continued use of glyphosate in GR sugar beet, the effect of increasing glyphosate rates (applied as single or sequential applications) on the fitness of GR B. scoparia individuals with variable EPSPS gene copies was tested under field conditions. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2214 g ae ha−1 or higher prevented seed production in B. scoparia plants with 2–4 (low levels of resistance) and 5–6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2–6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.
Validating deep learning inference during chest X-ray classification for COVID-19 screening
Authors: Sadre Robbie , Sundaram Baskaran , Majumdar Sharmila , Ushizima Daniela
Published: August 2021

The new coronavirus unleashed a worldwide pandemic in early 2020, and a fatality rate several times that of the flu. As the number of infections soared, and capabilities for testing lagged behind, chest X-ray (CXR) imaging became more relevant in the early diagnosis and treatment planning for patients with suspected or confirmed COVID-19 infection. In a few weeks, proposed new methods for lung screening using deep learning rapidly appeared, while quality assurance discussions lagged behind. This paper proposes a set of protocols to validate deep learning algorithms, including our ROI Hide-and-Seek protocol, which emphasizes or hides key regions of interest from CXR data. Our protocol allows assessing the classification performance for anomaly detection and its correlation to radiological signatures, an important issue overlooked in several deep learning approaches proposed so far. By running a set of systematic tests over CXR representations using public image datasets, we demonstrate the weaknesses of current techniques and offer perspectives on the advantages and limitations of automated radiography analysis when using heterogeneous data sources.
The relationship between cholinergic system brain structure and function in healthy adults and patients with mild cognitive impairment
Authors: Peter Jessica , Mayer Isabella , Kammer Thomas , Minkova Lora , Lahr Jacob , Klöppel Stefan , Grothe Michel J. , Orth Michael
Published: August 2021

We assessed the structure–function relationship of the human cholinergic system and hypothesized that structural measures are associated with short-latency sensory afferent inhibition (SAI), an electrophysiological measure of central cholinergic signal transmission. Healthy volunteers (n = 36) and patients with mild cognitive impairment (MCI, n = 20) underwent median nerve SAI and 3T structural MRI to determine the volume of the basal forebrain and the thalamus. Patients with MCI had smaller basal forebrain (p < 0.001) or thalamus volumes (p < 0.001) than healthy volunteers. Healthy SAI responders (> 10% SAI) had more basal forebrain volume than non-responders (p = 0.004) or patients with MCI (p < 0.001). More basal forebrain volume was associated with stronger SAI in healthy volunteers (r = 0.33, p < 0.05) but not patients with MCI. There was no significant relationship between thalamus volumes and SAI. Basal forebrain volume is associated with cholinergic function (SAI) in healthy volunteers but not in MCI patients. The in-vivo investigation of the structure–function relationship could further our understanding of the human cholinergic system in patients with suspected or known cholinergic system degeneration.
Targeted activity of the small molecule kinase inhibitor Pz-1 towards RET and TRK kinases
Authors: Moccia Marialuisa , Yang Donglin , Lakkaniga Naga Rajiv , Frett Brendan , McConnell Nicholas , Zhang Lingtian , Brescia Annalisa , Federico Giorgia , Zhang Lingzhi , Salerno Paolo , Santoro Massimo , Li Hong-yu , Carlomagno Francesca
Published: August 2021

We have recently described Pz-1, a benzimidazole-based type-2 RET and VEGFR2 inhibitor. Based on a kinome scan, here we show that Pz-1 is also a potent (IC50 < 1 nM) TRKA/B/C inhibitor. Pz-1 potently inhibited proliferation of human cancer cells carrying either RET- or TRKA oncoproteins (IC50 ~ 1 nM), with a negligible effect against RET- and TRKA-negative cells. By testing mutations, known to mediate resistance to other compounds, RET G810R/S, but not L730I/V, E732K, V738A and Y806N, showed some degree of resistance to Pz-1. In the case of TRKA, G595R and F589L, but not G667C, showed some degree of resistance. In xenograft models, orally administered Pz-1 almost completely inhibited RET- and TRKA-mutant tumours at 1–3 mg/kg/day but showed a reduced effect on RET/TRKA-negative cancer models. The activity, albeit reduced, on RET/TRKA-negative tumours may be justified by VEGFR2 inhibition. Tumours induced by NIH3T3 cells transfected by RET G810R and TRKA G595R featured resistance to Pz-1, demonstrating that RET or TRKA inhibition is critical for its anti-tumourigenic effect. In conclusion, Pz-1 represents a new powerful kinase inhibitor with distinct activity towards cancers induced by oncogenic RET and TRKA variants, including some mutants displaying resistance to other drugs.
Solar cell design using graphene-based hollow nano-pillars
Authors: Raad Shiva Hayati , Atlasbaf Zahra
Published: August 2021

In this paper, the full solar spectrum coverage with an absorption efficiency above 96% is attained by shell-shaped graphene-based hollow nano-pillars on top of the refractory metal substrate. The material choice guarantees the high thermal stability of the device along with its robustness against harsh environmental conditions. To design the structure, constitutive parameters of graphene material in the desired frequency range are investigated and its absorption capability is illustrated by calculating the attenuation constant of the electromagnetic wave. It is observed that broadband absorption is a consequence of wideband retrieved surface impedance matching with the free-space intrinsic impedance due to the tapered geometry. Moreover, the azimuthal and longitudinal cavity resonances with different orders are exhibited for a better understanding of the underlying wideband absorption mechanism. Importantly, the device can tolerate the oblique incidence in a wide span around 65°, regardless of the polarization. The proposed structure can be realized by large-area fabrication techniques.
Hyperspectral data as a biodiversity screening tool can differentiate among diverse Neotropical fishes
Authors: Kolmann M. A. , Kalacska M. , Lucanus O. , Sousa L. , Wainwright D. , Arroyo-Mora J. P. , Andrade M. C.
Published: August 2021

Hyperspectral data encode information from electromagnetic radiation (i.e., color) of any object in the form of a spectral signature; these data can then be used to distinguish among materials or even map whole landscapes. Although hyperspectral data have been mostly used to study landscape ecology, floral diversity and many other applications in the natural sciences, we propose that spectral signatures can be used for rapid assessment of faunal biodiversity, akin to DNA barcoding and metabarcoding. We demonstrate that spectral signatures of individual, live fish specimens can accurately capture species and clade-level differences in fish coloration, specifically among piranhas and pacus (Family Serrasalmidae), fishes with a long history of taxonomic confusion. We analyzed 47 serrasalmid species and could distinguish spectra among different species and clades, with the method sensitive enough to document changes in fish coloration over ontogeny. Herbivorous pacu spectra were more like one another than they were to piranhas; however, our method also documented interspecific variation in pacus that corresponds to cryptic lineages. While spectra do not serve as an alternative to the collection of curated specimens, hyperspectral data of fishes in the field should help clarify which specimens might be unique or undescribed, complementing existing molecular and morphological techniques.
Fabrication and characterization of scaffolds containing different amounts of allantoin for skin tissue engineering
Authors: Nokoorani Yeganeh Dorri , Shamloo Amir , Bahadoran Maedeh , Moravvej Hamideh
Published: August 2021

Using the skin tissue engineering approach is a way to help the body to recover its lost skin in cases that the spontaneous healing process is either impossible or inadequate, such as severe wounds or burns. In the present study, chitosan/gelatin-based scaffolds containing 0.25, 0.5, 0.75, and 1% allantoin were created to improve the wounds’ healing process. EDC and NHS were used to cross-link the samples, which were further freeze-dried. Different in-vitro methods were utilized to characterize the specimens, including SEM imaging, PBS absorption and degradation tests, mechanical experiments, allantoin release profile assessment, antibacterial assay, and cell viability and adhesion tests. The results indicated that the scaffolds’ average pore sizes were approximately in the range of 390–440 µm, and their PBS uptake amounts were about 1000% to 1250% after being soaked in PBS for 24 h. Around 70% of the specimens were degraded in 6 days, but they were not fully degraded after 21 days. Besides, the samples showed antibacterial activity against S. aureus and E. coli bacteria. In general, the MTT cell viability test indicated that the cells’ density increased slightly or remained the same during the experiment. SEM images of cells seeded on the scaffolds indicated appropriate properties of the scaffolds for cell adhesion.
Metabolome profiling and molecular docking analysis revealed the metabolic differences and potential pharmacological mechanisms of the inflorescence and succulent stem of Cistanche deserticola
Authors: Sun Xiao , Zheng Yan , Tian Lixia , Miao Yujing , Zeng Tiexin , Jiang Yuan , Pei Jin , Ahmad Bashir , Huang Linfang
Published: August 2021

Flow chart for exploring the metabolic and pharmacological characteristics of different parts of Cistanche deserticola.
Determination of certain VOCs in paints and architectural coatings by dynamic headspace gas chromatography-mass spectrometry
Authors: Alderman Nicholas P. , Courville Matthew , Tokarczyk Ryszard
Published: August 2021

A quantitative method for the determination of VOCs in paints was developed in support of Environment and Climate Change Canada's Automotive Refinishing Product and Architectural Coatings VOC Concentration Limits regulations.
A simple unlabeled human chorionic gonadotropin biosensor based on a peptide aptamer
Authors: Li Huanhuan , Cai Tongji , Ren Yi , Huang Jing , Jiang Hanbing , Hou Yucui , Tang Chunhua , Yang Jie , Zhao Jia , Yu Peng
Published: August 2021

As an essential biochemical indicator in the fields of pregnancy and oncology, HCG can be evaluated using colloidal gold immunochromatographic paper and quantified using a biochemical analyzer based on the principle of the antibody sandwich method.
From organotin hydrides to heteronuclear main group metal compounds: isolation of the first neutral bismuth/tin clusters
Authors: Steller Beate G. , Flock Michaela , Fischer Roland C.
Published: August 2021

From conversions of diaryltindihydrides, Ar2SnH2, and bismuth(iii) amide, Bi[N(SiMe3)2]3, the first representatives of mixed, uncharged Bi/Sn clusters, Bi8Sn3Ar6 were isolated.
Hollow fibers: from fabrication to applications
Authors: Tian Ye , Wang Zhaoyang , Wang Liqiu
Published: August 2021

This article features the state-of-the-art progress in the field of hollow fibers, covering fabrication methods, types, applications and prospects of their future development.
The synthesis and formation mechanism of nonpolar InN nanoplates
Authors: Song Wenqing , Li Tao , Zhang Lei , Zhu Wenhui , Wang Liancheng
Published: August 2021

High-crystal-quality nonpolar indium nitride (InN) nanoplates were synthesized via deploying controllable chemical vapor deposition (CVD) technology using the M-plane of GaN nanowires (NWs) as a template.
Kinetic Monte Carlo simulations of self-organization of Ge islands on Si(001)
Authors: Ghosh Paramita , Gupta Nidhi , Dhankhar Monika , Ranganathan Madhav
Published: August 2021

Kinetic Monte Carlo simulations of the growth of Ge on Si(001) indicate self-assembled quantum dot formation via nucleation at 500 K and instability at 600 K.
Dimension effect on ferroelectricity: a first-principles study on GeS nanoribbons
Authors: Su Haishan , Hu Ting , Kan Erjun
Published: August 2021

H-terminated armchair GeSNRs exhibit large in-plane polarization along the ribbon direction which converges to the value of 2D GeS as the width increases, while out-of-plane polarization only arises in those with n = odd number.
Exploration on the drug solubility enhancement in aqueous medium with the help of endo-functionalized molecular tubes: a computational approach
Authors: Paul Rabindranath , Paul Sandip
Published: August 2021

Drug solubility enhancement in aqueous medium with the help of endo-functionalized molecular tubes.
Temperature-dependent dynamics of endohedral fullerene Sc2@C80(CH2Ph) studied by EPR spectroscopy
Authors: Kandrashkin Yuri E. , Zaripov Ruslan B. , Liu Fupin , Büchner Bernd , Kataev Vladislav , Popov Alexey A.
Published: August 2021

Variable-temperature EPR spectroscopy of Sc2@C80(CH2Ph) reveals different dynamic regime of the molecule and cluster rotation.
Recent advances in electrochemical oxidative cross-coupling with hydrogen evolution involving radicals
Authors: Yuan Yong , Yang Jie , Lei Aiwen
Published: August 2021

This tutorial review provides an overview of the most recent developments in electrochemical oxidative cross-coupling with hydrogen evolution involving radicals.
Metal–organic frameworks of linear trinuclear cluster secondary building units: structures and applications
Authors: Chao Meng-Yao , Li Qing , Zhang Wen-Hua , Young David J.
Published: August 2021

Metal–organic frameworks sustained by linear trinuclear secondary building units have been summarized with their property and applications highlighted.
Preparation and characterization of soybean insoluble dietary fiber and its prebiotic effect on dyslipidemia and hepatic steatosis in high fat-fed C57BL/6J mice
Authors: Wang Sainan , Sun Wanling , Swallah Mohammed Sharif , Amin Khalid , Lyu Bo , Fan Hongliang , Zhang Zhao , Yu Hansong
Published: August 2021

Insoluble dietary fiber extracted from soybean residue had a loose and porous structure, polysaccharide groups, and typical crystalline cellulose I structure. It played a role in regulating lipid metabolism by promoting fatty acid oxidation and inhibiting lipid accumulation.
Correction: Inhibition of NLRP3 inflammasome activation and pyroptosis with the ethyl acetate fraction of Bungeanum ameliorated cognitive dysfunction in aged mice
Authors: Zhao Meihuan , Dai Yuan , Li Ping , Wang Jie , Ma Tengyun , Xu Shijun
Published: August 2021

Correction for ‘Inhibition of NLRP3 inflammasome activation and pyroptosis with the ethyl acetate fraction of Bungeanum ameliorated cognitive dysfunction in aged mice’ by Meihuan Zhao et al., Food Funct., 2021, DOI: 10.1039/D1FO00876E.
Selective lignin fractionation using CO2-expanded 2-methyltetrahydrofuran (2-MTHF)
Authors: Weidener Dennis , Klose Holger , Graf von Westarp William , Jupke Andreas , Leitner Walter , Domínguez de María Pablo , Grande Philipp M.
Published: August 2021

Expanding the portfolio. Lignin fractionation with CO2-expanded 2-MTHF to narrow size distribution and properties depending on the CO2 pressure.