bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-organ imaging demonstrates the heart-brain-liver axis in UK Biobank participants
Authors: McCracken Celeste , Raisi-Estabragh Zahra , Veldsman Michele , Raman Betty , Dennis Andrea , Husain Masud , Nichols Thomas E. , Petersen Steffen E. , Neubauer Stefan 
Published: December 2022

AbstractMedical imaging provides numerous insights into the subclinical changes that precede serious diseases such as heart disease and dementia. However, most imaging research either describes a single organ system or draws on clinical cohorts with small sample sizes. In this study, we use state-of-the-art multi-organ magnetic resonance imaging phenotypes to investigate cross-sectional relationships across the heart-brain-liver axis in 30,444 UK Biobank participants. Despite controlling for an extensive range of demographic and clinical covariates, we find significant associations between imaging-derived phenotypes of the heart (left ventricular structure, function and aortic distensibility), brain (brain volumes, white matter hyperintensities and white matter microstructure), and liver (liver fat, liver iron and fibroinflammation). Simultaneous three-organ modelling identifies differentially important pathways across the heart-brain-liver axis with evidence of both direct and indirect associations. This study describes a potentially cumulative burden of multiple-organ dysfunction and provides essential insight into multi-organ disease prevention.
Understanding variability in petroleum jet fuel life cycle greenhouse gas emissions to inform aviation decarbonization
Authors: Jing Liang , El-Houjeiri Hassan M. , Monfort Jean-Christophe , Littlefield James , Al-Qahtani Amjaad , Dixit Yash , Speth Raymond L. , Brandt Adam R. , Masnadi Mohammad S. , MacLean Heather L. , Peltier William , Gordon Deborah , Bergerson Joule A. 
Published: December 2022

AbstractA pressing challenge facing the aviation industry is to aggressively reduce greenhouse gas emissions in the face of increasing demand for aviation fuels. Climate goals such as carbon-neutral growth from 2020 onwards require continuous improvements in technology, operations, infrastructure, and most importantly, reductions in aviation fuel life cycle emissions. The Carbon Offsetting Scheme for International Aviation of the International Civil Aviation Organization provides a global market-based measure to group all possible emissions reduction measures into a joint program. Using a bottom-up, engineering-based modeling approach, this study provides the first estimates of life cycle greenhouse gas emissions from petroleum jet fuel on regional and global scales. Here we show that not all petroleum jet fuels are the same as the country-level life cycle emissions of petroleum jet fuels range from 81.1 to 94.8 gCO2e MJ−1, with a global volume-weighted average of 88.7 gCO2e MJ−1. These findings provide a high-resolution baseline against which sustainable aviation fuel and other emissions reduction opportunities can be prioritized to achieve greater emissions reductions faster.
Multi-dimensional data transmission using inverse-designed silicon photonics and microcombs
Authors: Yang Ki Youl , Shirpurkar Chinmay , White Alexander D. , Zang Jizhao , Chang Lin , Ashtiani Farshid , Guidry Melissa A. , Lukin Daniil M. , Pericherla Srinivas V. , Yang Joshua , Kwon Hyounghan , Lu Jesse , Ahn Geun Ho , Van Gasse Kasper , Jin Yan , Yu Su-Peng , Briles Travis C. , Stone Jordan R. , Carlson David R. , Song Hao , Zou Kaiheng , Zhou Huibin , Pang Kai , Hao Han , Trask Lawrence , Li Mingxiao , Netherton Andy , Rechtman Lior , Stone Jeffery S. , Skarda Jinhee L. , Su Logan , Vercruysse Dries , MacLean Jean-Philippe W. , Aghaeimeibodi Shahriar , Li Ming-Jun , Miller David A. B. , Marom Dan M. , Willner Alan E. , Bowers John E. , Papp Scott B. , Delfyett Peter J. , Aflatouni Firooz , Vučković Jelena 
Published: December 2022

AbstractThe use of optical interconnects has burgeoned as a promising technology that can address the limits of data transfer for future high-performance silicon chips. Recent pushes to enhance optical communication have focused on developing wavelength-division multiplexing technology, and new dimensions of data transfer will be paramount to fulfill the ever-growing need for speed. Here we demonstrate an integrated multi-dimensional communication scheme that combines wavelength- and mode- multiplexing on a silicon photonic circuit. Using foundry-compatible photonic inverse design and spectrally flattened microcombs, we demonstrate a 1.12-Tb/s natively error-free data transmission throughout a silicon nanophotonic waveguide. Furthermore, we implement inverse-designed surface-normal couplers to enable multimode optical transmission between separate silicon chips throughout a multimode-matched fibre. All the inverse-designed devices comply with the process design rules for standard silicon photonic foundries. Our approach is inherently scalable to a multiplicative enhancement over the state of the art silicon photonic transmitters.
Ocean variability beneath Thwaites Eastern Ice Shelf driven by the Pine Island Bay Gyre strength
Authors: Dotto Tiago S. , Heywood Karen J. , Hall Rob A. , Scambos Ted A. , Zheng Yixi , Nakayama Yoshihiro , Hyogo Shuntaro , Snow Tasha , Wåhlin Anna K. , Wild Christian , Truffer Martin , Muto Atsuhiro , Alley Karen E. , Boehme Lars , Bortolotto Guilherme A. , Tyler Scott W. , Pettit Erin 
Published: December 2022

AbstractWest Antarctic ice-shelf thinning is primarily caused by ocean-driven basal melting. Here we assess ocean variability below Thwaites Eastern Ice Shelf (TEIS) and reveal the importance of local ocean circulation and sea-ice. Measurements obtained from two sub-ice-shelf moorings, spanning January 2020 to March 2021, show warming of the ice-shelf cavity and an increase in meltwater fraction of the upper sub-ice layer. Combined with ocean modelling results, our observations suggest that meltwater from Pine Island Ice Shelf feeds into the TEIS cavity, adding to horizontal heat transport there. We propose that a weakening of the Pine Island Bay gyre caused by prolonged sea-ice cover from April 2020 to March 2021 allowed meltwater-enriched waters to enter the TEIS cavity, which increased the temperature of the upper layer. Our study highlights the sensitivity of ocean circulation beneath ice shelves to local atmosphere-sea-ice-ocean forcing in neighbouring open oceans.
Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers
Authors: Eliaz D. , Paul S. , Benyamin D. , Cernescu A. , Cohen S. R. , Rosenhek-Goldian I. , Brookstein O. , Miali M. E. , Solomonov A. , Greenblatt M. , Levy Y. , Raviv U. , Barth A. , Shimanovich U. 
Published: December 2022

AbstractSilk is a unique, remarkably strong biomaterial made of simple protein building blocks. To date, no synthetic method has come close to reproducing the properties of natural silk, due to the complexity and insufficient understanding of the mechanism of the silk fiber formation. Here, we use a combination of bulk analytical techniques and nanoscale analytical methods, including nano-infrared spectroscopy coupled with atomic force microscopy, to probe the structural characteristics directly, transitions, and evolution of the associated mechanical properties of silk protein species corresponding to the supramolecular phase states inside the silkworm’s silk gland. We found that the key step in silk-fiber production is the formation of nanoscale compartments that guide the structural transition of proteins from their native fold into crystalline β-sheets. Remarkably, this process is reversible. Such reversibility enables the remodeling of the final mechanical characteristics of silk materials. These results open a new route for tailoring silk processing for a wide range of new material formats by controlling the structural transitions and self-assembly of the silk protein’s supramolecular phases.
Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria
Authors: Zhao Weishu , Zhong Bozitao , Zheng Lirong , Tan Pan , Wang Yinzhao , Leng Hao , de Souza Nicolas , Liu Zhuo , Hong Liang , Xiao Xiang 
Published: December 2022

AbstractAncestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.
Structure of a RecT/Redβ family recombinase in complex with a duplex intermediate of DNA annealing
Authors: Caldwell Brian J. , Norris Andrew S. , Karbowski Caroline F. , Wiegand Alyssa M. , Wysocki Vicki H. , Bell Charles E. 
Published: December 2022

AbstractSome bacteriophage encode a recombinase that catalyzes single-stranded DNA annealing (SSA). These proteins are apparently related to RAD52, the primary human SSA protein. The best studied protein, Redβ from bacteriophage λ, binds weakly to ssDNA, not at all to dsDNA, but tightly to a duplex intermediate of annealing formed when two complementary DNA strands are added to the protein sequentially. We used single particle cryo-electron microscopy (cryo-EM) to determine a 3.4 Å structure of a Redβ homolog from a prophage of Listeria innocua in complex with two complementary 83mer oligonucleotides. The structure reveals a helical protein filament bound to a DNA duplex that is highly extended and unwound. Native mass spectrometry confirms that the complex seen by cryo-EM is the predominant species in solution. The protein shares a common core fold with RAD52 and a similar mode of ssDNA-binding. These data provide insights into the mechanism of protein-catalyzed SSA.
Antibodies targeting the neuraminidase active site inhibit influenza H3N2 viruses with an S245N glycosylation site
Authors: Stadlbauer Daniel , McMahon Meagan , Turner Hannah L. , Zhu Xueyong , Wan Hongquan , Carreño Juan Manuel , O’Dell George , Strohmeier Shirin , Khalil Zain , Luksza Marta , van Bakel Harm , Simon Viviana , Ellebedy Ali H. , Wilson Ian A. , Ward Andrew B. , Krammer Florian 
Published: December 2022

AbstractContemporary influenza A H3N2 viruses circulating since 2016 have acquired a glycosylation site in the neuraminidase in close proximity to the enzymatic active site. Here, we investigate if this S245N glycosylation site, as a result of antigenic evolution, can impact binding and function of human monoclonal antibodies that target the conserved active site. While we find that a reduction in the inhibitory ability of neuraminidase active site binders is measurable, this class of broadly reactive monoclonal antibodies maintains protective efficacy in vivo.
Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling
Authors: Drake Zachary C. , Seffernick Justin T. , Lindert Steffen 
Published: December 2022

AbstractCovalent labeling (CL) in combination with mass spectrometry can be used as an analytical tool to study and determine structural properties of protein-protein complexes. However, data from these experiments is sparse and does not unambiguously elucidate protein structure. Thus, computational algorithms are needed to deduce structure from the CL data. In this work, we present a hybrid method that combines models of protein complex subunits generated with AlphaFold with differential CL data via a CL-guided protein-protein docking in Rosetta. In a benchmark set, the RMSD (root-mean-square deviation) of the best-scoring models was below 3.6 Å for 5/5 complexes with inclusion of CL data, whereas the same quality was only achieved for 1/5 complexes without CL data. This study suggests that our integrated approach can successfully use data obtained from CL experiments to distinguish between nativelike and non-nativelike models.
Photoprogrammable circularly polarized phosphorescence switching of chiral helical polyacetylene thin films
Authors: Huang Zizhao , He Zhenyi , Ding Bingbing , Tian He , Ma Xiang 
Published: December 2022

AbstractThe developments of pure organic room-temperature phosphorescence (RTP) materials with circularly polarized luminescence (CPL) have significantly facilitated the future integration and systemization of luminescent material in fundamental science and technological applications. Here, a type of photoinduced circularly polarized RTP materials are constructed by homogeneously dispersing phosphorescent chiral helical substituted polyacetylenes into a processable poly(methyl methacrylate) (PMMA) matrix. These substituted polyacetylenes play vital roles in the propagation of CPL and present prominently optical characteristics with high absorption and luminescent dissymmetric factors up to 0.029 (gabs) and 0.019 (glum). The oxygen consumption properties of the films under UV light irradiation endow materials with dynamic chiro-optical functionality, which can leverage of light to precisely control and manipulate the circularly polarized RTP properties with the remarkable advantages of being contactless, wireless and fatigue-resistant. Significantly, the distinct materials with dynamic properties can be used as anti-counterfeiting materials involving photoprogrammability.
Characterization and in vitro anticancer potential of exopolysaccharide extracted from a freshwater diatom Nitzschia palea (Kütz.) W.Sm. 1856
Authors: Sanniyasi Elumalai , Patrick Antony Prakash Rejoy , Rajagopalan Kreedika , Gopal Rajesh Kanna , Damodharan Rajesh 
Published: December 2022

AbstractDiatoms are photoautotrophic microalgae classified under class Bacillariophyceae, engulfed by hard silicate frustules, which give mechanical support and protection from bacterial infections. They exude polysaccharides extracellularly that help them with their gliding motion (locomotion). However, the bioactivity of such compounds was least explored from freshwater diatoms. In the present study, a single species of pennate diatom identified as Nitzschia palea was isolated and molecularly characterized by 18S rRNA smaller subunit gene (partial) sequencing and submitted to GenBank NCBI and accession number retrieved as ON360983. Based on logarithmic growth curve analysis, the exponential phase was obtained from 3rd to 4th day of diatom culture. The exopolysaccharide was extracted by the hot-water extraction method, and characterized by FT-IR. The total yield of exopolysaccharide from Nitzschia palea was estimated as 1.56 mg in 100 mL of culture after 7 days of incubation. The estimated carbohydrate content was 51.35 µg/100 µL. The monosaccharide constituents were determined by acid hydrolysis of exopolysaccharide, silylation (derivatization), followed by GC–MS analysis and tabulated. The extracted exopolysaccharide was evaluated for its anti-cancer potential against the Human Adenocarcinoma lung cancer cell line (A549) and the estimated IC50 value was 62.64 µg/mL. Acridine orange staining assay and DNA fragmentation assay also confirmed the apoptotic activity of exopolysaccharide derived from the diatom Nitzschia palea.
Transcriptomic and proteomic pathways of diabetic and non-diabetic mitochondrial transplantation
Authors: Doulamis Ilias P. , Nomoto Rio S. , Tzani Aspasia , Hong Xuechong , Duignan Thomas , Celik Aybuke , del Nido Pedro J. , McCully James D. 
Published: December 2022

AbstractReduced mitochondrial function increases myocardial susceptibility to ischemia–reperfusion injury (IRI) in diabetic hearts. Mitochondrial transplantation (MT) ameliorates IRI, however, the cardioprotective effects of MT may be limited using diabetic mitochondria. Zucker Diabetic Fatty (ZDF) rats were subjected to temporary myocardial RI and then received either vehicle alone or vehicle containing mitochondria isolated from either diabetic ZDF or non-diabetic Zucker lean (ZL) rats. The ZDF rats were allowed to recover for 2 h or 28 days. MT using either ZDF- or ZL-mitochondria provided sustained reduction in infarct size and was associated with overlapping upregulation of pathways associated with muscle contraction, development, organization, and anti-apoptosis. MT using either ZDF- or ZL-mitochondria also significantly preserved myocardial function, however, ZL- mitochondria provided a more robust long-term preservation of myocardial function through the mitochondria dependent upregulation of pathways for cardiac and muscle metabolism and development. MT using either diabetic or non-diabetic mitochondria decreased infarct size and preserved functional recovery, however, the cardioprotection afforded by MT was attenuated in hearts receiving diabetic compared to non-diabetic MT.
Multifrequency-based sharpening of focal volume
Authors: Riis Thomas , Kubanek Jan 
Published: December 2022

AbstractSystems that emit electromagnetic or sonic waves for diagnostic or interventional applications often have constraints on the size of their aperture, and thus produce an elongated focus in the axial dimension. This extended depth of focus limits imaging resolution and spatial specificity of the delivered energy. Here, we have developed a method that substantially minimizes the depth of focus. The method superimposes beams of distinct frequencies in space and time to create constructive interference at target and amplify deconstructive interference everywhere else, thus sharpening the focus. The method does not require labeling of targets or other manipulations of the medium. Using simulations, we found that the method tightens the depth of focus even for systems with a narrow bandwidth. Moreover, we implemented the method in ultrasonic hardware and found that a 46.1% frequency fractional bandwidth provides an average 7.4-fold reduction in the focal volume of the resulting beams. This method can be readily applied to sharpen the focus of interventional systems and is expected to also improve the axial resolution of existing imaging systems.
Co-application of ACC deaminase-producing rhizobial bacteria and melatonin improves salt tolerance in common bean (Phaseolus vulgaris L.) through ion homeostasis
Authors: Alinia Mozhgan , Kazemeini Seyed A. , Dadkhodaie Ali , Sepehri Mozhgan , Mahjenabadi Vahid A. Jahandideh , Amjad Syeda F. , Poczai Peter , El-Ghareeb Doaa , Bassouny Mohamed A. , Abdelhafez Ahmed A. 
Published: December 2022

AbstractA comprehensive body of scientific evidence indicates that rhizobial bacteria and melatonin enhance salt tolerance of crop plants. The overall goal of this research was to evaluate the ability of Rhizobium leguminoserum bv phaseoli to suppress salinity stress impacts in common bean treated with melatonin. Treatments included bacterial inoculations (inoculated (RI) and non-inoculated (NI)), different salinity levels (non-saline (NS), 4 (S1) and 8 (S2) dS m−1 of NaCl) and priming (dry (PD), melatonin (PM100) and hydro (PH) priming) with six replications in growing media containing sterile sand and perlite (1:1). The results showed that the bacterial strain had the ability to produce indole acetic acid (IAA), ACC deaminase and siderophore. Plants exposed to salinity stress indicated a significant decline in growth, yield, yield components, nitrogen fixation and selective transport (ST), while showed a significant increase in sodium uptake. However, the combination of PM100 and RI treatments by improving growth, photosynthesis rate and nitrogen fixation positively influenced plant performance in saline conditions. The combined treatment declined the negative impacts of salinity by improving the potassium translocation, potassium to sodium ratio in the shoot and root and ST. In conclusion, the combination of melatonin and ACC deaminase producing rhizobium mitigated the negative effects of salinity. This result is attributed to the increased ST and decreased sodium uptake, which significantly reduced the accumulation of sodium ions in shoot.
Broadband photodetection using one-step CVD-fabricated MoS2/MoO2 microflower/microfiber heterostructures
Authors: Mouloua D. , Rajput N. S. , Saitzek S. , Kaja K. , Hoummada K. , El Marssi M. , El Khakani M. A. , Jouiad M. 
Published: December 2022

AbstractMolybdenum disulfide (MoS2) has been combined so far with other photodetecting semiconductors as an enhancing agent owing to its optical and electronic properties. Existing approaches demonstrated MoS2-incorporated photodetector devices using complex and costly fabrication processes. Here, we report on simplified one-step on the chemical vapor deposition (CVD) based synthesis of a unique microfiber/microflower MoS2-based heterostructure formed by capturing MoO2 intermediate material during the CVD process. This particular morphology engenders a material chemical and electronic interplay exalting the heterostructure absorption up to ~ 98% over a large spectral range between 200 and 1500 nm. An arsenal of characterization methods were used to elucidate the properties of these novel heterostructures including Raman spectroscopy, X-ray diffraction, X-ray photoelectron spectrometry, high-resolution transmission and scanning electron microscopies, and Kelvin probe force microscopy. Our findings revealed that the MoS2 and the MoO2 crystallize in the hexagonal and monoclinic lattices, respectively. The integration of the MoS2/MoO2 heterostructures into functional photodetectors revealed a strong photoresponse under both standard sun illumination AM1.5G and blue light excitation at 450 nm. Responsivity and detectivity values as high as 0.75 mA W−1 and 1.45 × 107 Jones, respectively, were obtained with the lowest light intensity of 20 mW cm−2 at only 1 V bias. These results demonstrate the high performances achieved by the unique MoS2/MoO2 heterostructure for broadband light harvesting and pave the way for their adoption in photodetection applications.