bluuebunny/crossref_metadata_2025_split huggingface dataset:
Desulfovibrio diazotrophicasp. nov., a sulphate reducing bacterium from the human gut capable of nitrogen fixation
Authors: Sayavedra Lizbeth , Li Tianqi , Batista Marcelo Bueno , Seah Brandon K.B. , Booth Catherine , Zhai Qixiao , Chen Wei , Narbad Arjan 
Published: July 2020

AbstractSulphate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, genome sequencing, and physiological characterisation of a novel SRB species belonging to the classDeltaproteobacteria(QI0027T). Phylogenomic analysis revealed that the QI0027Tstrain belongs to the genusDesulfovibriowith its closest relative beingDesulfovibrio legallii. Metagenomic sequencing of stool samples from 45 individuals, as well as comparison with 1690Desulfovibrionaceaemetagenome-assembled genomes, revealed the presence of QI0027Tin at least 22 further individuals. QI0027Tencoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027Toverexpressed 45 genes in nitrogen limiting conditions as compared to cultures supplemented with ammonia, including nitrogenases, an urea uptake system and the urease enzyme complex. To the best of our knowledge, this is the firstDesulfovibriohuman isolate for which nitrogen fixation has been demonstrated. This isolate was namedDesulfovibrio diazotrophicasp. nov., referring to its ability to fix nitrogen (‘diazotroph’).ImportanceAnimals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen. These strategies range from amino acid transporters to stable associations with beneficial microbes that can provide fixed nitrogen. Although frequently thought as a nutrient-rich environment, nitrogen fixation can occur in the human gut of some populations, but so far it has been attributed mainly toClostridiaandKlebsiellabased on sequencing. We have cultivated a novelDesulfovibriofrom human gut origin which encoded, expressed and actively used nitrogen fixation genes, suggesting that some sulphate reducing bacteria could also play a role in the availability of nitrogen in the gut.
Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies
Authors: McAulay Kathrine , Bryan Andrew , Greninger Alexander L. , Grill Francisca , Lake Douglas , Kaleta Erin J. , Grys Thomas E. 
Published: July 2020

AbstractCoronavirus disease 2019 (COVID-19) is a potentially life-threatening respiratory infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), for which numerous serologic assays are available. In a CLIA laboratory setting, we used a retrospective sample set (n = 457) to evaluate two lateral flow immunoassays (LFIAs; two iterations of Rapid Response™ COVID-19 Test Cassette, BTNX Inc.) and a subset of to evaluate SARS-COV-2 IgG/IgM Rapid Test, ACON Laboratories (n = 200); and Standard Q COVID-19 IgM/IgG Duo, SD BIOSENSOR (n = 155) for their capacity to detect of SARS-CoV-2 IgG. In a cohort of primarily hospitalized patients with RT-PCR confirmed COVID-19, the BTNX assays demonstrated 95% and 92% agreement with the Abbott SARS-CoV-2 IgG assay and sensitivity was highest at ≥ 14 days from symptom onset [BTNX kit 1, 95%; BTNX kit 2, 91%]. ACON and SD assays demonstrated 99% and 100% agreement with the Abbott assay at ≥ 14 days from symptom onset. Specificity was measured using 74 specimens collected prior to SARS-CoV-2 circulation in the United States and 31 “cross-reactivity challenge” specimens, including those from patients with a history of seasonal coronavirus infection and was 98% for BTNX kit 1 and ACON and 100% for BTNX kit 2 and SD. Taken with data from EUA assays, these results suggest that LFIAs may provide adequate results for rapid detection of SARS-CoV-2. Replicating these results in fingerstick blood in outpatient populations, would further support the possibility that LFIAs may be useful to increase access to serologic testing
Accelerated aortic stiffness is associated with brain structure, perfusion and cognition in the Whitehall II Imaging Sub-study
Authors: Suri Sana , Chiesa Scott T. , Zsoldos Enikő , Mackay Clare E. , Filippini Nicola , Griffanti Ludovica , Mahmood Abda , Singh-Manoux Archana , Shipley Martin J , Brunner Eric J , Kivimäki Mika , Deanfield John E. , Ebmeier Klaus P. 
Published: July 2020

AbstractBackgroundAortic stiffness is closely linked with cardiovascular diseases, but recent studies suggest that it is also a risk factor for cognitive decline and dementia. However, the brain changes underlying this risk are unclear. We examined whether aortic stiffening in the transition from mid to late-life affects brain structure and cognition.Methods and FindingsAortic pulse wave velocity was measured in 2007-09 (Phase 9) and at a 4-year follow-up in 2012-13 (Phase 11) in the Whitehall II Imaging Sub-study cohort. Between 2012-2016 (Imaging Phase), participants received a multi-modal 3T brain magnetic resonance imaging (MRI) scans and cognitive tests. Participants were selected if they had no clinical diagnosis of dementia and no gross brain structural abnormalities. Voxel-based analyses were used to assess grey matter volume, white matter microstructure (fractional anisotropy and diffusivity), cerebral blood flow, and white matter lesions. Cognitive outcomes were performance on verbal memory, semantic fluency, working memory and executive function tests. Of 544 participants, 445 (81.8%) were men. The mean (SD) age was 63.9 (5.2) years at the baseline Phase 9 examination, 67.9 (5.3) years at Phase 11 and 69.8 (5.2) years at the Imaging Phase. Voxel-based analysis revealed that accelerated aortic stiffening in mid-to-late life was associated with poor white matter integrity, viz. lower fractional anisotropy in 4.2% of white matter and higher radial diffusivity in 6.7% of white matter, including the corpus callosum, corona radiata, superior longitudinal fasciculus and corticospinal tracts. Accelerated aortic stiffening was also related to lower cerebral perfusion in 1.1% of grey matter including the parietal, frontal, and occipital cortices. No associations with grey matter volume or white matter lesions were observed. Further, higher baseline aortic stiffness was associated with poor semantic fluency (B=-0.48, 95%CI −0.77 to −0.19, p<0.005) and verbal learning outcomes (B=-0.36, 95%CI - 0.60 to −0.13, p<0.005).ConclusionsFaster aortic stiffening in mid-to-late life is associated with poor brain white matter microstructural integrity and reduced cerebral perfusion, likely due to increased transmission of pulsatile energy to the delicate cerebral microvasculature. Strategies to prevent arterial stiffening prior to this point may be required to offer cognitive benefit in older age.
Spatial engineering ofE. coliwith addressable phase-separated RNAs
Authors: Guo Haotian , Ryan Joseph C. , Mallet Adeline , Song Xiaohu , Pabst Victor , Decrulle Antoine , Lindner Ariel B. 
Published: July 2020

AbstractBiochemical processes often require spatial regulation and specific microenvironments. The general lack of organelles in bacteria limits the potential of bioengineering complex intracellular reactions. Here we demonstrate Transcriptionally Engineered Addressable RNA Solvent droplets (TEARS) as synthetic microdomains within theEscherichia coli.TEARS are assembled from RNA-binding protein recruitment domains fused to poly-CAG repeats that spontaneously drive liquid-liquid phase separation from the bulk cytoplasm. Targeting TEARS with fluorescent proteins revealed multilayered structures and a non-equilibrium mechanism controlling their composition and reaction robustness. We show that TEARS provide organelle-like bioprocess isolation for sequestering biochemical pathways, controlling metabolic branch points, buffering mRNA translation rates and scaffolding protein-protein interactions. TEARS are a simple and versatile tool for spatially controllingE. colibiochemistry.
Reintroduced nativePopulus nigrain restored floodplain reduces spread of exotic poplar species
Authors: Broeck An Vanden , Cox Karen , Van Braeckel Alexander , Neyrinck Sabrina , De Regge Nico , Van Looy Kris 
Published: July 2020

1.AbstractExoticPopulustaxa pose a threat to the success of riparian forest restoration in floodplain areas. We evaluated the impact of exoticPopulustaxa on softwood riparian forest development along the river Common Meuse after introducing nativePopulus nigraand after the re-establishment of the natural river dynamics. We sampled 154 poplar seedlings that spontaneously colonised restored habitat and assessed their taxonomy based on diagnostic chloroplast and nuclear microsatellite markers. Furthermore, by using a paternity analysis on 72 seedlings resulting from six open pollinatedP. nigrafemales, we investigated natural hybridization between frequently planted cultivated poplars and nativeP. nigra. The majority of the poplar seedlings from the gravel banks analyzed where identified asP. nigra; only 2% of the sampled seedlings exhibited genes of exotic poplar species. Similarly, the majority of the seedlings from the open pollinated progenies were identified asP. nigra. For three seedlings (4%), paternity was assigned to a cultivar ofP. xcanadensis. Almost two decades after reintroducingP. nigra, the constitution of the seed and pollen pools changed in the study area in favour of reproduction of the native species and at the expense of the exotic poplar species. This study indicates that, although significant gene flow form exotic poplars is observed in European floodplains, restoration programmes of the nativeP. nigracan vigorously outcompete the exotic gene flows and strongly reduce the impact of exoticPopulustaxa on the softwood riparian forest development.
High-resolution structures of malaria parasite actomyosin and actin filaments
Authors: Vahokoski Juha , Calder Lesley J. , Lopez Andrea J. , Molloy Justin E. , Rosenthal Peter B. , Kursula Inari 
Published: July 2020

AbstractMalaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodiumspp.) that cause the disease depend upon an unconventional actomyosin motor for both gliding motility and host cell invasion. The motor system, often referred to as the glideosome complex, remains to be understood in molecular terms and is an attractive target for new drugs that might block the infection pathway. Here, we present the first high-resolution structure of the actomyosin motor complex fromPlasmodium falciparum. Our structure includes the malaria parasite actin filament (PfAct1) complexed with the myosin motor (PfMyoA) and its two associated light-chains. The high-resolution core structure reveals thePfAct1:PfMyoA interface in atomic detail, while at lower-resolution, we visualize thePfMyoA light-chain binding region, including the essential light chain (PfELC) and the myosin tail interacting protein (PfMTIP). Finally, we report a barePfAct1 filament structure at an improved resolution, which gives new information about the nucleotide-binding site, including the orientation of the ATP/ADP sensor, Ser15, and the presence of a channel, which we propose as a possible phosphate exit path after ATP hydrolysis.Significance statementWe present the first structure of the malaria parasite motor complex; actin 1 (PfAct1) and myosin A (PfMyoA) with its two light chains. We also report a high-resolution structure of filamentousPfAct1 that reveals new atomic details of the ATPase site, including a channel, which may provide an exit route for phosphate and explain why phosphate release is faster inPfAct1 compared to canonical actins.PfAct1 goes through no conformational changes uponPfMyoA binding. OurPfMyoA structure also superimposes with a recent crystal structure ofPfMyoA alone, though there are small but important conformational changes at the interface. Our structures serve as an excellent starting point for drug design against malaria, which is one of the most devastating infectious diseases.
Guide RNA categorization enables target site choice in Tn7-CRISPR-Cas transposons
Authors: Petassi Michael T. , Hsieh Shan-Chi , Peters Joseph E. 
Published: July 2020

SummaryCRISPR-Cas defense systems have been coopted multiple times in nature for guide RNA-directed transposition by Tn7-like elements. Prototypic Tn7 uses dedicated proteins for two targeting pathways, one targeting a neutral and conserved attachment site in the chromosome and a second directing transposition into mobile plasmids facilitating cell-to-cell transfer. We show that Tn7-CRISPR-Cas elements evolved a system of guide RNA categorization to accomplish the same two-pathway lifestyle. Selective regulation of specialized guide RNAs allows long-term memory for access to chromosomal sites upon entry into a new host, while conventional CRISPR features maintain the ability to continually acquire guide RNAs to new plasmid and phage targets. Transposon-encoded guide RNAs are also privatized to be recognized only by the transposon-adapted system working with selective regulation to guard against toxic self-targeting by endogenous CRISPR-Cas defense systems. This information reveals new avenues to engineer guide RNAs for enhanced CRISPR-Cas functionality for genome modification.
Urine metabolomics of rats with chronic atrophic gastritis
Authors: Zu Guo-Xiu , Sun Qian-Qian , Chen Jian , Liu Xi-Jian , Sun Ke-Yun , Zhang Liang-Kun , li Ling , Han Tao , Huang Ha I-Liang 
Published: July 2020

AbstractBackground/Aim: To use liquid chromatography-mass spectrometry (LC-MS) to identify endogenous differential metabolites in the urine of rats with chronic atrophic gastritis (CAG). Materials and Methods: Methylnitronitrosoguanidine (MNNG) was used to produce a CAG model in Wistar rats, and HE staining was used to determine the pathological model. LC-MS was used to detect the differential metabolic profiles in rat urine. Diversified analysis was performed by the statistical method. Results: Compared with the control group, the model group had 68 differential metabolites, 25 that were upregulated and 43 that were downregulated. The main metabolic pathways were D-glutamine and D-glutamic acid metabolism, histidine metabolism and purine metabolism. Conclusion: By searching for differential metabolites and metabolic pathways in the urine of CAG rats, this study provides effective experimental data for the pathogenesis and clinical diagnosis of CAG.
Multi-ethnic transcriptome-wide association study of prostate cancer
Authors: Fiorica Peter N. , Schubert Ryan , Morris John D. , Sami Mohammed Abdul , Wheeler Heather E. 
Published: July 2020

AbstractThe genetic risk for prostate cancer has been governed by a few rare variants with high penetrance and over 150 commonly occurring variants with lower impact on risk; however, most of these variants have been identified in studies containing exclusively European individuals. People of non-European ancestries make up less than 15% of prostate cancer GWAS subjects. Across the globe, incidence of prostate cancer varies with population due to environmental and genetic factors. The discrepancy between disease incidence and representation in genetics highlights the need for more studies of the genetic risk for prostate cancer across diverse populations. To better understand the genetic risk for prostate cancer across diverse populations, we performed PrediXcan and GWAS in a cohort of 4,769 self-identified African American (2,463 cases and 2,306 controls), 2,199 Japanese American (1,106 cases and 1,093 controls), and 2,147 Latin American (1,081 cases and 1,066 controls) individuals from the Multiethnic Genome-wide Scan of Prostate Cancer. We used prediction models from 46 tissues in GTEx version 8 and five models from monocyte transcriptomes in the Multi-Ethnic Study of Artherosclerosis. Across the three populations, we predicted 19 gene-tissue pairs, including five unique genes, to be significantly (lfsr< 0.05) associated with prostate cancer. One of these genes,NKX3-1, replicated in a larger European cohort. At the SNP level, 110 SNPs met genome-wide significance in the African American cohort while 123 SNPs met significance in the Japanese American cohort. Fine mapping revealed three significant independent loci in the African American cohort and two significant independent loci in the Japanese American cohort. These identified loci confirm findings from previous GWAS of prostate cancer in diverse cohorts while PrediXcan-identified genes suggest potential new directions for prostate cancer research in populations across the globe.
Molecular Logic of Cellular Diversification in the Mammalian Cerebral Cortex
Authors: Di Bella Daniela J. , Habibi Ehsan , Yang Sun-Ming , Stickels Robert R. , Brown Juliana , Yadollahpour Payman , Chen Fei , Macosko Evan Z. , Regev Aviv , Arlotta Paola 
Published: July 2020

ABSTRACTThe neocortex has an unparalleled diversity of cell types, which are generated during development through a series of temporally orchestrated events that are under tight evolutionary constraint and are critical for proper cortical assembly and function. However, the molecular logic that governs the establishment and organization of cortical cell types remains elusive, largely due to the large number of cell classes undergoing dynamic cell-state transitions over extended developmental timelines. Here, we have generated a comprehensive single-cell RNA-seq and single-cell ATAC-seq atlas of the developing mouse neocortex, sampled every day throughout embryonic corticogenesis. We computationally reconstruct developmental trajectories across the diversity of cortical cell classes, and infer the gene regulatory programs that accompany their lineage bifurcation decisions and their differentiation trajectories. Finally, we demonstrate how this developmental map pinpoints the origin of lineage-specific developmental abnormalities linked to aberrant corticogenesis in mutant animals. The data provides the first global picture of the regulatory mechanisms governing cellular diversification in the neocortex.
Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity
Authors: Gor Mian-Chee , Vezina Ben , McMahon Róisín M. , King Gordon J. , Panjikar Santosh , Rehm Bernd H. A. , Martin Jennifer L. , Smith Andrew T. 
Published: July 2020

AbstractPlantacyclin B21AG is a circular bacteriocin produced byLactobacillus plantarumB21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens,Listeria monocytogenesandClostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from food gradeLactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 17 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed Phe8Ala and Trp45Ala mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. Lys19Ala mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.
Asymptomatic Genu Recurvatum Reshapes Lower Limb Sagittal Joint and Elevation Angles During Gait at Different Speeds
Authors: Dierick Frédéric , Schreiber Céline , Lavallée Pauline , Buisseret Fabien 
Published: July 2020

AbstractPurposeThe main objective of this study is to characterize the lower limb sagittal joint and elevation angles during walking in participants with asymptomatic genu recurvatum and compare it with control participants without knee deformation. The secondary objective is to study the influence of walking speed on these kinematic variables.MethodsThe spatio-temporal parameters and kinematics of the lower limb were recorded using an optoelectronic motion capture system in 26 partici-pants (n = 13 with genu recurvatum and n = 13 controls). The participants walked on an instrumented treadmill during five minutes at three different speeds: slow, medium and fast.ResultsParticipants with genu recurvatum showed several significant differences with controls: a narrower step width, a greater maximum hip joint extension angle, a greater knee joint extension angle at mid stance, a lower maximum knee joint flexion angle during the swing phase, and a greater ankle joint extension angle at the end of the gait cycle. Participants with genu recurvatum had a greater minimum thigh elevation angle, a greater maximum foot elevation angle, and a change in the orientation of the covariance plane. Walking speed had a significant effect on nearly all lower limb joint, elevation angle, and covariance plane parameters.ConclusionOur findings show that genu recurvatum reshapes lower limb sagittal joint and elevation angles during walking at different speeds but preserves the covariation of elevation angles along a plane during both stance and swing phases and the rotation of this plane with increasing speed.
Compact four-port vertically polarized UWB monopole antenna for MIMO communications
Authors: J. Premalatha , D. Sheela 
Published: July 2020

Purpose
This paper aims to present the design of a compact vertically polarized four-element UWB antenna suitable for MIMO communications.

Design/methodology/approach
The unit cell antenna is constructed using a square ring radiator excited through a stepped impedance feed. The proposed antenna covers the Ultra-wideband (UWB) spectrum ranging from 2.2 to 12.3 GHz. The isolation between the unit cell antennas in the array is enhanced using a simple microstrip line resonator. The decoupling element is connected to the ground through a via.

Findings
The proposed scheme offers at least 16 dB improvement in the port-to-port coupling. Furthermore, the four-element antenna array is constructed using a specific interlocking scheme. The proposed antenna array’s Multiple Input Multiple Output (MIMO) performance metrics are analyzed.

Originality/value
By suitably selecting the excitation port, directional radiation patterns can be realized. The combined radiation pattern covers 360 degrees. A prototype antenna array is fabricated, and the simulation results are verified using real-time experiments. The proposed antenna is a suitable candidate for shark fin housing in automotive communications.