bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractEmerging 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

AbstractVigorous 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

AbstractQuantum 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

AbstractHumans 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

AbstractScedosporium 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

AbstractWe 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

AbstractTo 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

AbstractSARS-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

AbstractCircadian 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

AbstractChanges 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

AbstractThe 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

AbstractThe 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

AbstractBioactive 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.