bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-stringency blueprint of the human proteome
Authors: Adhikari Subash , Nice Edouard C. , Deutsch Eric W. , Lane Lydie , Omenn Gilbert S. , Pennington Stephen R. , Paik Young-Ki , Overall Christopher M. , Corrales Fernando J. , Cristea Ileana M. , Van Eyk Jennifer E. , Uhlén Mathias , Lindskog Cecilia , Chan Daniel W. , Bairoch Amos , Waddington James C. , Justice Joshua L. , LaBaer Joshua , Rodriguez Henry , He Fuchu , Kostrzewa Markus , Ping Peipei , Gundry Rebekah L. , Stewart Peter , Srivastava Sanjeeva , Srivastava Sudhir , Nogueira Fabio C. S. , Domont Gilberto B. , Vandenbrouck Yves , Lam Maggie P. Y. , Wennersten Sara , Vizcaino Juan Antonio , Wilkins Marc , Schwenk Jochen M. , Lundberg Emma , Bandeira Nuno , Marko-Varga Gyorgy , Weintraub Susan T. , Pineau Charles , Kusebauch Ulrike , Moritz Robert L. , Ahn Seong Beom , Palmblad Magnus , Snyder Michael P. , Aebersold Ruedi , Baker Mark S. 
Published: October 2020

AbstractThe Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP’s tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
16.8% Monolithic all-perovskite triple-junction solar cells via a universal two-step solution process
Authors: Wang Junke , Zardetto Valerio , Datta Kunal , Zhang Dong , Wienk Martijn M. , Janssen René A. J. 
Published: October 2020

AbstractPerovskite semiconductors hold a unique promise in developing multijunction solar cells with high-efficiency and low-cost. Besides design constraints to reduce optical and electrical losses, integrating several very different perovskite absorber layers in a multijunction cell imposes a great processing challenge. Here, we report a versatile two-step solution process for high-quality 1.73 eV wide-, 1.57 eV mid-, and 1.23 eV narrow-bandgap perovskite films. Based on the development of robust and low-resistivity interconnecting layers, we achieve power conversion efficiencies of above 19% for monolithic all-perovskite tandem solar cells with limited loss of potential energy and fill factor. In a combination of 1.73 eV, 1.57 eV, and 1.23 eV perovskite sub-cells, we further demonstrate a power conversion efficiency of 16.8% for monolithic all-perovskite triple-junction solar cells.
Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution
Authors: Liang Jinyang , Wang Peng , Zhu Liren , Wang Lihong V. 
Published: October 2020

AbstractSimultaneous and efficient ultrafast recording of multiple photon tags contributes to high-dimensional optical imaging and characterization in numerous fields. Existing high-dimensional optical imaging techniques that record space and polarization cannot detect the photon’s time of arrival owing to the limited speeds of the state-of-the-art electronic sensors. Here, we overcome this long-standing limitation by implementing stereo-polarimetric compressed ultrafast photography (SP-CUP) to record light-speed high-dimensional events in a single exposure. Synergizing compressed sensing and streak imaging with stereoscopy and polarimetry, SP-CUP enables video-recording of five photon tags (x, y, z: space; t: time of arrival; and ψ: angle of linear polarization) at 100 billion frames per second with a picosecond temporal resolution. We applied SP-CUP to the spatiotemporal characterization of linear polarization dynamics in early-stage plasma emission from laser-induced breakdown. This system also allowed three-dimensional ultrafast imaging of the linear polarization properties of a single ultrashort laser pulse propagating in a scattering medium.
Detection of haplotype-dependent allele-specific DNA methylation in WGBS data
Authors: Abante J. , Fang Y. , Feinberg A. P. , Goutsias J. 
Published: October 2020

AbstractIn heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole-genome bisulfite sequencing (WGBS) data perform statistically independent marginal analysis at individual cytosine-phosphate-guanine (CpG) sites, thus ignoring correlations in the methylation state, or carry-out a joint statistical analysis of methylation patterns at four CpG sites producing unreliable statistical evidence. Here, we employ the one-dimensional Ising model of statistical physics and develop a method for detecting allele-specific methylation (ASM) events within segments of DNA containing clusters of linked single-nucleotide polymorphisms (SNPs), called haplotypes. Comparisons with existing approaches using simulated and real WGBS data show that our method provides an improved fit to data, especially when considering large haplotypes. Importantly, the method employs robust hypothesis testing for detecting statistically significant imbalances in mean methylation level and methylation entropy, as well as for identifying haplotypes for which the genetic variant carries significant information about the methylation state. As such, our ASM analysis approach can potentially lead to biological discoveries with important implications for the genetics of complex human diseases.
Metal chalcogenide hollow polar bipyramid prisms as efficient sulfur hosts for Na-S batteries
Authors: Aslam Muhammad Kashif , Seymour Ieuan D. , Katyal Naman , Li Sha , Yang Tingting , Bao Shu-juan , Henkelman Graeme , Xu Maowen 
Published: October 2020

AbstractSodium sulfur batteries require efficient sulfur hosts that can capture soluble polysulfides and enable fast reduction kinetics. Herein, we design hollow, polar and catalytic bipyramid prisms of cobalt sulfide as efficient sulfur host for sodium sulfur batteries. Cobalt sulfide has interwoven surfaces with wide internal spaces that can accommodate sodium polysulfides and withstand volumetric expansion. Furthermore, results from in/ex-situ characterization techniques and density functional theory calculations support the significance of the polar and catalytic properties of cobalt sulfide as hosts for soluble sodium polysulfides that reduce the shuttle effect and display excellent electrochemical performance. The polar catalytic bipyramid prisms sulfur@cobalt sulfide composite exhibits a high capacity of 755 mAh g−1 in the second discharge and 675 mAh g−1 after 800 charge/discharge cycles, with an ultralow capacity decay rate of 0.0126 % at a high current density of 0.5 C. Additionally, at a high mass loading of 9.1 mg cm−2, sulfur@cobalt sulfide shows high capacity of 545 mAh g−1 at a current density of 0.5 C. This study demonstrates a hollow, polar, and catalytic sulfur host with a unique structure that can capture sodium polysulfides and speed up the reduction reaction of long chain sodium polysulfides to solid small chain polysulfides, which results in excellent electrochemical performance for sodium-sulfur batteries.
Cryopreservation impairs 3-D migration and cytotoxicity of natural killer cells
Authors: Mark Christoph , Czerwinski Tina , Roessner Susanne , Mainka Astrid , Hörsch Franziska , Heublein Lucas , Winterl Alexander , Sanokowski Sebastian , Richter Sebastian , Bauer Nina , Angelini Thomas E. , Schuler Gerold , Fabry Ben , Voskens Caroline J. 
Published: October 2020

AbstractNatural killer (NK) cells are important effector cells in the immune response to cancer. Clinical trials on adoptively transferred NK cells in patients with solid tumors, however, have thus far been unsuccessful. As NK cells need to pass stringent safety evaluation tests before clinical use, the cells are cryopreserved to bridge the necessary evaluation time. Standard degranulation and chromium release cytotoxicity assays confirm the ability of cryopreserved NK cells to kill target cells. Here, we report that tumor cells embedded in a 3-dimensional collagen gel, however, are killed by cryopreserved NK cells at a 5.6-fold lower rate compared to fresh NK cells. This difference is mainly caused by a 6-fold decrease in the fraction of motile NK cells after cryopreservation. These findings may explain the persistent failure of NK cell therapy in patients with solid tumors and highlight the crucial role of a 3-D environment for testing NK cell function.
GPAHex-A synthetic biology platform for Type IV–V glycopeptide antibiotic production and discovery
Authors: Xu Min , Wang Wenliang , Waglechner Nicholas , Culp Elizabeth J. , Guitor Allison K. , Wright Gerard D. 
Published: October 2020

AbstractGlycopeptide antibiotics (GPAs) are essential for the treatment of severe infectious diseases caused by Gram-positive bacteria. The emergence and spread of GPA resistance have propelled the search for more effective GPAs. Given their structural complexity, genetic intractability, and low titer, expansion of GPA chemical diversity using synthetic or medicinal chemistry remains challenging. Here we describe a synthetic biology platform, GPAHex (GPA Heterologous expression), which exploits the genes required for the specialized GPA building blocks, regulation, antibiotic transport, and resistance for the heterologous production of GPAs. Application of the GPAHex platform results in: (1) a 19-fold increase of corbomycin titer compared to the parental strain, (2) the discovery of a teicoplanin-class GPA from an Amycolatopsis isolate, and (3) the overproduction and characterization of a cryptic nonapeptide GPA. GPAHex provides a platform for GPA production and mining of uncharacterized GPAs and provides a blueprint for chassis design for other natural product classes.
Monitoring of inhaler use at home with a smartphone video application in a pilot study
Authors: Dhadge Nagesh , Shevade Madhuragauri , Kale Nisha , Narke Govinda , Pathak Dhananjay , Barne Monica , Madas Sapna , Salvi Sundeep 
Published: October 2020

AbstractInhalation therapy is the basis of the pharmacological management of asthma and COPD. Most patients are trained on the correct use of inhalers by health professionals but after that do patients continue to take them correctly at home remains largely unknown. Video recording of the inhalation technique using a smartphone can be used to evaluate the inhaler technique at home. Through this pilot study, we aimed to understand whether inhaler training given to patients in the outpatient clinic translates into good inhalation practices at home by a video application platform using a smartphone. We recruited 70 newly diagnosed asthma and COPD patients and a pulmonologist trained them to use their inhaler until they were able to use it correctly. Videos of inhaler use were captured by a relative or a friend at home and then sent to an independent reviewer via WhatsApp on Days 1, 7, 14 and 28 (±2). Each step of the inhaler technique was evaluated based on a predetermined checklist with a rating scale of 0 to 10 (10 for all steps done correctly). Out of 70 patients recruited, 30 (42%) sent all videos. We found that, although all patients performed all the steps correctly in the clinic, none of them performed all steps correctly at home even on Day 1 itself of the inhaler use. On Day 1, the steps score reduced from 10 to 6.9 with a downward trend until Day 28. The most common mistakes from Day 1 onwards were incorrect inspiratory flow rates and not gargling after the inhaler use. Also, most patients showed partially effective inhalation as per our scoring method. Remote video monitoring of inhaler use in the home environment is possible with a mobile video application that gives us a better insight into the most common inhaler mistakes performed by patients at home. Inhaler errors start appearing immediately on Day 1 after the training, and incorrect inspiratory flow rates and forgetting to do gargles are common errors. Early detection of inhaler errors at home may be possible through this method.
Rabies virus-based COVID-19 vaccine CORAVAX™ induces high levels of neutralizing antibodies against SARS-CoV-2
Authors: Kurup Drishya , Wirblich Christoph , Ramage Holly , Schnell Matthias J. 
Published: October 2020

AbstractThe recently emerged coronavirus SARS-CoV-2, the causative agent of COVID-19, is rapidly spreading in the world. The exponentially expanding threat of SARS-CoV-2 to global health highlights the urgent need for a vaccine. Herein we show the rapid development of a novel, highly efficient, and safe COVID-19 vaccine using a rabies virus-based vector that has proven to be an efficient vaccine against several emerging infectious diseases. This study reports that both a live and an inactivated rabies virus containing the SARS-CoV-2 spike S1 protein induces potent virus-neutralizing antibodies at much higher levels than seen in the sera of convalescent patients. In summary, the results provided here warrant further development of this safe and established vaccine platform against COVID-19.
TILES-2018, a longitudinal physiologic and behavioral data set of hospital workers
Authors: Mundnich Karel , Booth Brandon M. , L’Hommedieu Michelle , Feng Tiantian , Girault Benjamin , L’Hommedieu Justin , Wildman Mackenzie , Skaaden Sophia , Nadarajan Amrutha , Villatte Jennifer L. , Falk Tiago H. , Lerman Kristina , Ferrara Emilio , Narayanan Shrikanth 
Published: October 2020

AbstractWe present a novel longitudinal multimodal corpus of physiological and behavioral data collected from direct clinical providers in a hospital workplace. We designed the study to investigate the use of off-the-shelf wearable and environmental sensors to understand individual-specific constructs such as job performance, interpersonal interaction, and well-being of hospital workers over time in their natural day-to-day job settings. We collected behavioral and physiological data fromn = 212 participants through Internet-of-Things Bluetooth data hubs, wearable sensors (including a wristband, a biometrics-tracking garment, a smartphone, and an audio-feature recorder), together with a battery of surveys to assess personality traits, behavioral states, job performance, and well-being over time. Besides the default use of the data set, we envision several novel research opportunities and potential applications, including multi-modal and multi-task behavioral modeling, authentication through biometrics, and privacy-aware and privacy-preserving machine learning.
Individual Brain Charting dataset extension, second release of high-resolution fMRI data for cognitive mapping
Authors: Pinho Ana Luísa , Amadon Alexis , Gauthier Baptiste , Clairis Nicolas , Knops André , Genon Sarah , Dohmatob Elvis , Torre Juan Jesús , Ginisty Chantal , Becuwe-Desmidt Séverine , Roger Séverine , Lecomte Yann , Berland Valérie , Laurier Laurence , Joly-Testault Véronique , Médiouni-Cloarec Gaëlle , Doublé Christine , Martins Bernadette , Salmon Eric , Piazza Manuela , Melcher David , Pessiglione Mathias , van Wassenhove Virginie , Eger Evelyn , Varoquaux Gaël , Dehaene Stanislas , Hertz-Pannier Lucie , Thirion Bertrand 
Published: October 2020

AbstractWe present an extension of the Individual Brain Charting dataset –a high spatial-resolution, multi-task, functional Magnetic Resonance Imaging dataset, intended to support the investigation on the functional principles governing cognition in the human brain. The concomitant data acquisition from the same 12 participants, in the same environment, allows to obtain in the long run finer cognitive topographies, free from inter-subject and inter-site variability. This second release provides more data from psychological domains present in the first release, and also yields data featuring new ones. It includes tasks on e.g. mental time travel, reward, theory-of-mind, pain, numerosity, self-reference effect and speech recognition. In total, 13 tasks with 86 contrasts were added to the dataset and 63 new components were included in the cognitive description of the ensuing contrasts. As the dataset becomes larger, the collection of the corresponding topographies becomes more comprehensive, leading to better brain-atlasing frameworks. This dataset is an open-access facility; raw data and derivatives are publicly available in neuroimaging repositories.
A disposable, ultra-fine endoscope for non-invasive, close examination of the intraluminal surface of the peritoneal dialysis catheter and peritoneal cavity
Authors: Nakayama Masaaki , Hamada Chieko , Yokoyama Keitaro , Tanno Yudo , Matsuo Nanae , Nakata Junichiro , Ishibashi Yoshio , Okuzawa Atsushi , Sakamoto Kazuhiro , Nara Tamaki , Kakuta Takatoshi , Nangaku Masaomi , Yokoo Takashi , Suzuki Yusuke , Miyata Toshio 
Published: October 2020

AbstractThe ability to visualize intraluminal surface of peritoneal dialysis (PD) catheter and peritoneal cavity could allow elucidation of the cases of outflow problems, and provide information on changes to the peritoneal membrane leading to encapsulating peritoneal sclerosis. A non-invasive examination that allows those monitoring in need is desirable. We have developed a disposable ultra-fine endoscope that can be inserted into the lumen of the existing PD catheter, allowing observation of the luminal side of the catheter and peritoneal cavity from the tip of the PD catheter, with minimum invasion in practice. In a pre-clinical study in pigs and a clinical study in 10 PD patients, the device provided detailed images, enabling safe, easy observation of the intraluminal side of the entire catheter, and of the morphology and status of the peritoneal surface in the abdominal cavity under dwelling PD solution. Since this device can be used repeatedly during PD therapy, clinical application of this device could contribute to improved management of clinical issues in current PD therapy, positioning PD as a safer, more reliable treatment modality for end-stage renal disease.
The role of kinship and demography in shaping cooperation amongst male lions
Authors: Chakrabarti Stotra , Kolipakam Vishnupriya , Bump Joseph K. , Jhala Yadvendradev V. 
Published: October 2020

AbstractThe influence of kinship on animal cooperation is often unclear. Cooperating Asiatic lion coalitions are linearly hierarchical; male partners appropriate resources disproportionately. To investigate how kinship affect coalitionary dynamics, we combined microsatellite based genetic inferences with long-term genealogical records to measure relatedness between coalition partners of free-ranging lions in Gir, India. Large coalitions had higher likelihood of having sibling partners, while pairs were primarily unrelated. Fitness computations incorporating genetic relatedness revealed that low-ranking males in large coalitions were typically related to the dominant males and had fitness indices higher than single males, contrary to the previous understanding of this system based on indices derived from behavioural metrics alone. This demonstrates the indirect benefits to (related) males in large coalitions. Dominant males were found to ‘lose less’ if they lost mating opportunities to related partners versus unrelated males. From observations on territorial conflicts we show that while unrelated males cooperate, kin-selected benefits are ultimately essential for the maintenance of large coalitions. Although large coalitions maximised fitness as a group, demographic parameters limited their prevalence by restricting kin availability. Such demographic and behavioural constraints condition two-male coalitions to be the most attainable compromise for Gir lions.
A nonlinear rotation-free shell formulation with prestressing for vascular biomechanics
Authors: Nama Nitesh , Aguirre Miquel , Humphrey Jay D. , Figueroa C. Alberto 
Published: October 2020

AbstractWe implement a nonlinear rotation-free shell formulation capable of handling large deformations for applications in vascular biomechanics. The formulation employs a previously reported shell element that calculates both the membrane and bending behavior via displacement degrees of freedom for a triangular element. The thickness stretch is statically condensed to enforce vessel wall incompressibility via a plane stress condition. Consequently, the formulation allows incorporation of appropriate 3D constitutive material models. We also incorporate external tissue support conditions to model the effect of surrounding tissue. We present theoretical and variational details of the formulation and verify our implementation against axisymmetric results and literature data. We also adapt a previously reported prestress methodology to identify the unloaded configuration corresponding to the medically imaged in vivo vessel geometry. We verify the prestress methodology in an idealized bifurcation model and demonstrate the significance of including prestress. Lastly, we demonstrate the robustness of our formulation via its application to mouse-specific models of arterial mechanics using an experimentally informed four-fiber constitutive model.
Thermal insulation property of graphene/polymer coated textile based multi-layer fabric heating element with aramid fabric
Authors: Kim Hyelim , Kim Han Seong , Lee Sunhee 
Published: October 2020

AbstractThis study investigated the thermal insulation properties based on electrical heating test of graphene-based multi-layer fabric heating elements to confirm the possibility of application for fabric heating element for protective clothing. Four layers were designed as layers of outer, filler, electrical heating textile, and lining. The outer fabrics used two different densities of aramid woven fabrics (LD_ARW and HD_ARW), an aramid knit (AR_KT), and nonwoven (AR_NW). Fabricated graphene/polymer coated electrical heating textile (GR) exhibits a surface temperature of about 85 °C, a current of 0.12 A, and a power of 3 W when 30 V is applied. As composed with 4-layer, the surface temperature of LD_ARW and HD_ARW used as the outer for sample indicated less than 50 °C, due to their excellent heat resistance property; whereas, when AR_KT and AR_NW were used, the temperature was about 50 °C. This is because their fine fibers form high porosity that can entrap air. As a result of the thermal insulation properties, the temperature difference of each layer was in the order ΔT(GR-N3) < ΔT(GR-Lining) < ΔT(GR-Outer). In particular, when AR_NW was used as the outer fabric, ΔT(GR-Outer)was decreased by about 10 °C, compared with that of the other outer fabric. By the effect of relative humidity under dry 25% RH and comfortable 55% RH, the temperature difference was decreased under 55% RH; thus, the thermal insulation property was improved under comfortable humidity condition. Therefore, the best thermal insulation performance was exhibited when AR_NW was used as outer under 55% RH, and it is expected to expand its application to fabric heating element for protective clothing.