bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth
Authors: Zuñiga Cristal , Li Tingting , Guarnieri Michael T. , Jenkins Jackson P. , Li Chien-Ting , Bingol Kerem , Kim Young-Mo , Betenbaugh Michael J. , Zengler Karsten 
Published: July 2020

AbstractMicrobial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
Strategies to enable large-scale proteomics for reproducible research
Authors: Poulos Rebecca C. , Hains Peter G. , Shah Rohan , Lucas Natasha , Xavier Dylan , Manda Srikanth S. , Anees Asim , Koh Jennifer M. S. , Mahboob Sadia , Wittman Max , Williams Steven G. , Sykes Erin K. , Hecker Michael , Dausmann Michael , Wouters Merridee A. , Ashman Keith , Yang Jean , Wild Peter J. , deFazio Anna , Balleine Rosemary L. , Tully Brett , Aebersold Ruedi , Speed Terence P. , Liu Yansheng , Reddel Roger R. , Robinson Phillip J. , Zhong Qing 
Published: July 2020

AbstractReproducible research is the bedrock of experimental science. To enable the deployment of large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time and across instruments and develop computational methods for improving quantitative accuracy. We perform 1560 data independent acquisition (DIA)-MS runs of eight samples containing known proportions of ovarian and prostate cancer tissue and yeast, or control HEK293T cells. Replicates are run on six mass spectrometers operating continuously with varying maintenance schedules over four months, interspersed with ~5000 other runs. We utilise negative controls and replicates to remove unwanted variation and enhance biological signal, outperforming existing methods. We also design a method for reducing missing values. Integrating these computational modules into a pipeline (ProNorM), we mitigate variation among instruments over time and accurately predict tissue proportions. We demonstrate how to improve the quantitative analysis of large-scale DIA-MS data, providing a pathway toward clinical proteomics.
Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms
Authors: Selleck Christopher , Pedroso Marcelo Monteiro , Wilson Liam , Krco Stefan , Knaven Esmée Gianna , Miraula Manfredi , Mitić Nataša , Larrabee James A. , Brück Thomas , Clark Alice , Guddat Luke W. , Schenk Gerhard 
Published: July 2020

AbstractGenes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.
Mini-canaloplasty as a modified technique for the surgical treatment of open-angle glaucoma
Authors: Rękas Marek , Konopińska Joanna , Byszewska Anna , Mariak Zofia 
Published: July 2020

AbstractAuthors present a modified surgical technique for canaloplasty without preparing the classical trabeculo-Descemet’s membrane (TDM) and having to close sutures. Twelve patients with open-angle glaucoma (OAG) (aged 58–77 years) received the modified technique, which does not require the deep scleral flap to be excised, an intrascleral lake to be created, or TDM dissection. After accessing the Schlemm’s canal (SC), cannulation and placement of the sutures are made similar to those in the classical canaloplasty. The conjunctiva is closed via bipolar diathermy. The mean intraocular pressure (IOP) before surgery was 18.0 ± 8 mmHg, and the mean number of anti-glaucoma medications taken was 3 ± 1. Mean IOP at the end of the observation period (18.0 ± 6.0 months) was reduced by 23% (15.5 ± 4.1 mmHg), while the mean number of medications taken was reduced to 0.25 ± 1.0. In all eyes, the SC was successively opened, with no cheese-wiring. Adverse events included microhyphaema, mild corneal oedema, and folds in the TDM. The eyes recovered spontaneously within a few days after the procedure. The mini-canaloplasty technique may reduce the risk of complications associated with classical canaloplasty while effectively lowering the IOP in patients with OAG.
Enhanced mechanical and wear properties of Al6061 alloy nanocomposite reinforced by CNT-template-grown core–shell CNT/SiC nanotubes
Authors: Yoo Sung Chan , Kang Byungchul , Van Trinh Pham , Phuong Doan Dinh , Hong Soon Hyung 
Published: July 2020

AbstractNovel one-dimensional template-grown coaxial SiC@carbon nanotubes (SiC@CNTs) were fabricated using a chemical vapor deposition method. To facilitate the formation of SiC on CNT template, a molecular-level mixing process was used to coat the surface of commercial multiwalled carbon nanotubes (MWCNTs) by Fe2O3. These Fe-CNTs were transformed into SiC@CNT nanotubes, which were then mixed with Al6061 alloy and consolidated by spark plasma sintering to obtain Al6061-SiC@CNT nanocomposites. The addition of 5 vol% SiC@CNT resulted in 58% enhancement in Young’s modulus and 46% enhancement in yield strength. Furthermore, the friction coefficient was reduced by 31% and the specific wear rate was reduced by 45%. The enhancement effect of Al6061-SiC@CNT on the mechanical and tribological properties was much greater than those of traditional nanoparticles, nanowires, and whiskers of SiCs. The extraordinary strengthening behavior of SiC@CNT, when compared with that of other SiC analogues, is attributed to the coaxial structure consisting of a SiC shell and CNT core. This coaxial structure enhanced the mechanical and tribological properties beyond that attainable with traditional SiC-derived reinforcements.
Automated application of low energy electron irradiation enables inactivation of pathogen- and cell-containing liquids in biomedical research and production facilities
Authors: Fertey Jasmin , Thoma Martin , Beckmann Jana , Bayer Lea , Finkensieper Julia , Reißhauer Susann , Berneck Beatrice Sarah , Issmail Leila , Schönfelder Jessy , Casado Javier Portillo , Poremba Andre , Rögner Frank-Holm , Standfest Bastian , Makert Gustavo R. , Walcher Lia , Kistenmacher Ann-Kathrin , Fricke Stephan , Grunwald Thomas , Ulbert Sebastian 
Published: July 2020

AbstractIonizing radiation is widely used to inactivate pathogens. It mainly acts by destroying nucleic acids but causes less damage to structural components like proteins. It is therefore highly suited for the sterilization of biological samples or the generation of inactivated vaccines. However, inactivation of viruses or bacteria requires relatively high doses and substantial amounts of radiation energy. Consequently, irradiation is restricted to shielded facilities—protecting personnel and the environment. We have previously shown that low energy electron irradiation (LEEI) has the same capacity to inactivate pathogens in liquids as current irradiation methods, but generates much less secondary X-ray radiation, which enables the use in normal laboratories by self-shielded irradiation equipment. Here, we present concepts for automated LEEI of liquids, in disposable bags or as a continuous process. As the electrons have a limited penetration depth, the liquid is transformed into a thin film. High concentrations of viruses (Influenza, Zika virus and Respiratory Syncytial Virus), bacteria (E. coli, B. cereus) and eukaryotic cells (NK-92 cell line) are efficiently inactivated by LEEI in a throughput suitable for various applications such as sterilization, vaccine manufacturing or cell therapy. Our results validate the premise that for pathogen and cell inactivation in liquids, LEEI represents a suitable and versatile irradiation method for standard biological research and production laboratories.
The role of ADC values within the normal-appearing brain in the prognosis of multiple sclerosis activity during interferon-β therapy in the 3-year follow-up: a preliminary report
Authors: Zacharzewska-Gondek Anna , Pokryszko-Dragan Anna , Budrewicz Sławomir , Sąsiadek Marek , Trybek Grzegorz , Bladowska Joanna 
Published: July 2020

AbstractPredictors of multiple sclerosis (MS) activity during disease-modifying treatment are being extensively investigated. The aim of this study was to assess the prognosis of NEDA (no evidence of disease activity) status during IFN-β (interferon-β) treatment, using apparent diffusion coefficient (ADC) measurements obtained at initial MRI (magnetic resonance imaging). In 87 MS patients treated with IFN-β, ADC values were calculated for 13 regions of normal-appearing white and grey matter (NAWM, NAGM) based on MRI performed with a 1.5 T magnet before (MS0, n = 45) or after one year of therapy (MS1, n = 42). Associations were evaluated between ADC, conventional MRI findings, demographic and clinical factors and NEDA status within the following 3 years using logistic, Cox and multinomial logistic regression models. NEDA rates in the MS0 group were 64.4%, 46.5% and 33.3% after the 1st, 2nd and 3rd year of treatment, respectively and in MS1 patients 71.4% and 48.7% for the periods 1st–2nd and 1st–3rd years of treatment, respectively. ADC values in the NAWM regions contributed to loss of NEDA and its clinical and radiological components, with a 1–3% increase in the risk of NEDA loss (p = 0.0001–0.0489) in both groups. ADC measurements may have an additional prognostic value with regard to NEDA status.
Precision-based exercise as a new therapeutic option for children and adolescents with haematological malignancies
Authors: Lanfranconi Francesca , Zardo W. , Moriggi T. , Villa E. , Radaelli G. , Radaelli S. , Paoletti F. , Bottes E. , Miraglia T. , Pollastri L. , Vago P. , Nichelli F. , Jankovic M. , Biondi A. , Balduzzi A. 
Published: July 2020

AbstractChildren and adolescents with haematological malignancies (PedHM) are characterized by a severe loss of exercise ability during cancer treatment, lasting throughout their lives once healed and impacting their social inclusion prospects. The investigation of the effect of a precision-based exercise program on the connections between systems of the body in PedHM patients is the new frontier in clinical exercise physiology. This study is aimed at evaluating the effects of 11 weeks (3 times weekly) of combined training (cardiorespiratory, resistance, balance and flexibility) on the exercise intolerance in PedHM patients. Two-hundred twenty-six PedHM patients were recruited (47% F). High or medium frequency participation (HAd and MAd) was considered when a participant joined; > 65% or between 30% and < 64% of training sessions, respectively. The “up and down stairs'' test (TUDS), “6 min walking” test (6MWT), the “5 Repetition Maximum strength” leg extension and arm lateral raise test (5RM-LE and 5RM-ALR), flexibility (stand and reach), and balance (stabilometry), were performed and evaluated before and after training. The TUDS, the 5RM-LE and 5RM-ALR, and the flexibility exercises showed an increase in HAd and MAd groups (P < 0.05), while the 6MWT and balance tests showed improvement only in HAd group (P < 0.0001). These results support the ever-growing theory that, in the case of the treatment of PedHM, ‘exercise is medicine’ and it has the potential to increase the patient’s chances of social inclusion.
Variations in storm-induced bed level dynamics across intertidal flats
Authors: de Vet P. L. M. , van Prooijen B. C. , Colosimo I. , Steiner N. , Ysebaert T. , Herman P. M. J. , Wang Z. B. 
Published: July 2020

AbstractHydrodynamic forces on intertidal flats vary over a range of temporal and spatial scales. These spatiotemporal inhomogeneities have implications for intertidal flat morphodynamics and ecology. We determine whether storm events are capable of altering the long-term morphological evolution of intertidal flats, and unravel the contributions of tidal flow, wind-driven flow, waves, and water depth on inhomogeneities in bed level dynamics (bed level changes over ~days) across these areas. We complement decades of bed level measurements on eight intertidal flats in two estuaries in the Netherlands with an extensive 1-month field campaign on one of those flats. Across this intertidal flat, the hydrodynamics and morphodynamics of a storm event were captured, including the post-storm recovery. We show that individual events can persistently alter the morphological evolution of intertidal flats; magnitudes of some bed level changes are even comparable to years of continuous evolution. The morphological impacts of events are largely controlled by the relative timing of the forcing processes, and not solely by their magnitudes. Spatiotemporal variations in bed level dynamics of intertidal flats are driven by a combination of: (1) the inhomogeneous distributions of the hydrodynamic forcing processes (including the under-explored role of the wind); and (2) the linear proportionality between bed level dynamics and the local bed slope.
A glycomics and proteomics study of aging and Parkinson’s disease in human brain
Authors: Raghunathan Rekha , Hogan John D. , Labadorf Adam , Myers Richard H. , Zaia Joseph 
Published: July 2020

AbstractPrevious studies on Parkinson’s disease mechanisms have shown dysregulated extracellular transport of α-synuclein and growth factors in the extracellular space. In the human brain these consist of perineuronal nets, interstitial matrices, and basement membranes, each composed of a set of collagens, non-collagenous glycoproteins, proteoglycans, and hyaluronan. The manner by which amyloidogenic proteins spread extracellularly, become seeded, oligomerize, and are taken up by cells, depends on intricate interactions with extracellular matrix molecules. We sought to assess the alterations to structure of glycosaminoglycans and proteins that occur in PD brain relative to controls of similar age. We found that PD differs markedly from normal brain in upregulation of extracellular matrix structural components including collagens, proteoglycans and glycosaminoglycan binding molecules. We also observed that levels of hemoglobin chains, possibly related to defects in iron metabolism, were enriched in PD brains. These findings shed important new light on disease processes that occur in association with PD.
Distribution patterns, carbon sources and niche partitioning in cave shrimps (Atyidae: Typhlatya)
Authors: Chávez-Solís E. M. , Solís C. , Simões N. , Mascaró M. 
Published: July 2020

AbstractCave shrimps of the Typhlatya genus are common and widespread in fresh, brackish and marine groundwater throughout the Yucatan Peninsula (Mexico). These species are ideal models to test niche partitioning within sympatric species in oligotrophic systems. Nevertheless, their food sources remain unidentified, and despite their frequency and functional importance, distribution and abundance patterns of these species within caves have not been fully recognized. Here, we describe the abundance of three Typhlatya species in different temporal and spatial scales, investigate changes in water conditions, and potential sources of carbon as an indication of food origin. Species composition and abundance varied markedly in space and time revealing patterns that differed from one system to another and in relation to environmental parameters. Isotope analysis showed that each species reflects a particular δ13C and Δ14C fingerprint, suggesting they feed in different proportions from the available carbon sources. Overall, our findings suggest a niche partitioning of habitat and feeding sources amongst the three Typhlatya species investigated, where environmental characteristics and physiological differences could play an important role governing their distribution patterns.
Early evidence of sheep lambing de-seasoning in the Western Mediterranean in the sixth millennium BCE
Authors: Tornero Carlos , Balasse Marie , Bréhard Stéphanie , Carrère Isabelle , Fiorillo Denis , Guilaine Jean , Vigne Jean-Denis , Manen Claire 
Published: July 2020

AbstractToday, sheep farmers in the Western Mediterranean de-season their ewes to achieve autumnal births. This strategy contrasts sharply with spring lambing further north, and provides benefits in terms of out-of-season availability of animal products. These competences are closely linked to specific sheep physiology and favorable Western Mediterranean climatic conditions. It is not known exactly how far back in the past the ability to de-season Mediterranean sheep breeds extends. This study shows that this practice existed seven millennia ago in Southern France, at an early stage of the major agricultural expansion of the Neolithic into the Western Mediterranean. To achieve this reproductive management regime, three prerequisites were required: (i) the ability of sheep to give birth in autumn, constituting early evidence for the genetic selection of specimens with prolonged reproductive fertility; (ii) intentional management of female and male interactions within the herd, which would have required good knowledge of the timing of the fertility cycle in ewes, and; (iii) adequate pasture resources to support lactation in the autumn, possibly favored by autumnal rains, substantiating previous paleoclimatological data for the existence of a Mediterranean-type precipitation regime at that time. Moreover, we also show that winter foddering of sheep occurred, using forest resources, and that this maintained good body weights for spring mating. These findings add pivotal information about shepherding practices and the socio-economic abilities of Early Neolithic communities, which allowed for the extension of their areas of influence from the Eastern Mediterranean area to the West during the Early Neolithic agricultural expansion in Europe.
Plasma polymerized nanoparticles effectively deliver dual siRNA and drug therapy in vivo
Authors: Michael Praveesuda , Lam Yuen Ting , Filipe Elysse C. , Tan Richard P. , Chan Alex H. P. , Lee Bob S. L. , Feng Nicolas , Hung Juichien , Cox Thomas R. , Santos Miguel , Wise Steven G. 
Published: July 2020

AbstractMultifunctional nanocarriers (MNCs) promise to improve therapeutic outcomes by combining multiple classes of molecules into a single nanostructure, enhancing active targeting of therapeutic agents and facilitating new combination therapies. However, nanocarrier platforms currently approved for clinical use can still only carry a single therapeutic agent. The complexity and escalating costs associated with the synthesis of more complex MNCs have been major technological roadblocks in the pathway for clinical translation. Here, we show that plasma polymerized nanoparticles (PPNs), synthesised in reactive gas discharges, can bind and effectively deliver multiple therapeutic cargo in a facile and cost-effective process compatible with up scaled commercial production. Delivery of siRNA against vascular endothelial growth factor (siVEGF) at extremely low concentrations (0.04 nM), significantly reduced VEGF expression in hard-to-transfect cells when compared with commercial platforms carrying higher siRNA doses (6.25 nM). PPNs carrying a combination of siVEGF and standard of care Paclitaxel (PPN-Dual) at reduced doses (< 100 µg/kg) synergistically modulated the microenvironment of orthotopic breast tumors in mice, and significantly reduced tumor growth. We propose PPNs as a new nanomaterial for delivery of therapeutics, which can be easily functionalised in any laboratory setting without the need for additional wet-chemistry and purification steps.
The role of biomass burning states in light absorption enhancement of carbonaceous aerosols
Authors: Wu Yu , Cheng Tianhai , Pan Xiaole , Zheng Lijuan , Shi Shuaiyi , Liu Hang 
Published: July 2020

AbstractCarbonaceous aerosols, which are emitted from biomass burning, significantly contribute to the Earth’s radiation balance. Radiative forcing caused by biomass burning has been poorly qualified, which is largely attributed to uncertain absorption enhancement values (Eabs) of black carbon (BC) aerosols. Laboratory measurements and theoretical modelling indicate a significant value of Eabs; but this enhancement is observed to be negligible in the ambient environment, implying that models may overestimate global warming due to BC. Here, we present an aggregate model integrating BC aerosol ensembles with different morphologies and mixing states and report a quantitative analysis of the BC Eabs from different combustion states during biomass burning. We show that the BC Eabs produced by flaming combustion may be up to two times more than those produced by smouldering combustion, suggesting that the particle morphology and mixing state of freshly emitted BC aerosols is an important source of the contrasting values of Eabs. The particle morphology of freshly emitted BC aerosols is widely assumed to be bare in models, which is rare in the ambient environment and leads to small estimates of Eabs by field observations. We conclude that the exact description of freshly emitted carbonaceous aerosols plays an important role in constraining aerosol radiative forcing.