bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward instrument combination for boundary layer classification
Authors: Rieutord Thomas , Martinet Pauline , Paci Alexandre 
Published: November 2022

AbstractTo handle the complexity of the atmospheric boundary layer (ABL) and make accurate feature detection (top height, low‐level jets, inversions, etc.), a prior necessary step is to identify the type of boundary layer. This study proposes a new method to identify the boundary layer type through unsupervised classification and the synergistic use of ground‐based remote sensing. Unsupervised classification is used to lighten the human supervision. The new classification was applied to a 1‐day case study collected during wintertime in the Arve River valley near Chamonix–Mont‐Blanc during the Passy‐2015 field experiment. The ABL classification obtained from microwave radiometer and ceilometer observations (ground‐based remote sensors [GBReS]) combination is compared with high‐frequency radiosoundings (RS) data and the French convective scale AROME model outputs. Classifications from RS and GBReS broadly agree, demonstrating the good behavior of the method, AROME leading to different results at night. The difference of AROME is likely due to the different nature of the data (model fields are smoother and include forecasting errors). The results show the ability of unsupervised classification to segment relevant objects in the boundary layer and the benefit to use a combination of GBReS.
Ancient endosymbiont‐mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes
Authors: Shimpi Gaurav G. , Bentlage Bastian 
Published: November 2022

AbstractIn contrast to bilaterian animals, non‐bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter‐domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.
Generation of reference cell lines, media, and a process platform for CHO cell biomanufacturing
Authors: Cordova Lauren T. , Dahodwala Hussain , Elliott Kathryn S. , Baik Jongyoun , Odenewelder Daniel C. , Nmagu Douglas , Skelton Bradley A. , Uy Lisa , Klaubert Stephanie R. , Synoground Benjamin F. , Chitwood Dylan G. , Dhara Venkata Gayatri , Naik Harnish Mukesh , Morris Caitlin S. , Yoon Seongkyu , Betenbaugh Michael , Coffman Jon , Swartzwelder Frank , Gillmeister Michael P. , Harcum Sarah W. , Lee Kelvin H. 
Published: November 2022

AbstractDue to the favorable attributes of Chinese hamster ovary (CHO) cells for therapeutic proteins and antibodies biomanufacturing, companies generate proprietary cells with desirable phenotypes. One key attribute is the ability to stably express multi‐gram per liter titers in chemically defined media. Cell, media, and feed diversity has limited community efforts to translate knowledge. Moreover, academic, and nonprofit researchers generally cannot study “industrially relevant” CHO cells due to limited public availability, and the time and knowledge required to generate such cells. To address these issues, a university‐industrial consortium (Advanced Mammalian Biomanufacturing Innovation Center, AMBIC) has acquired two CHO “reference cell lines” from different lineages that express monoclonal antibodies. These reference cell lines have relevant production titers, key performance outcomes confirmed by multiple laboratories, and a detailed technology transfer protocol. In commercial media, titers over 2 g/L are reached. Fed‐batch cultivation data from shake flask and scaled‐down bioreactors is presented. Using productivity as the primary attribute, two academic sites aligned with tight reproducibility at each site. Further, a chemically defined media formulation was developed and evaluated in parallel to the commercial media. The goal of this work is to provide a universal, industrially relevant CHO culture platform to accelerate biomanufacturing innovation.
Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria
Authors: Koteska Diana , Marter Pia , Huang Sixing , Pradella Silke , Petersen Jörn , Schulz Stefan 
Published: November 2022

AbstractVolatiles released by the apicomplexan alga Chromera velia CCAP1602/1 and their associated bacteria have been investigated. A metagenome analysis allowed the identification of the most abundant heterotrophic bacteria of the phycosphere, but the isolation of additional strains showed that metagenomics underestimated the complexity of the algal microbiome, However, a culture‐independent approach revealed the presence of a planctomycete that likely represents a novel bacterial family. We analysed algal and bacterial volatiles by open‐system‐stripping analysis (OSSA) on Tenax TA desorption tubes, followed by thermodesorption, cryofocusing and GC‐MS‐analysis. The analyses of the alga and the abundant bacterial strains Sphingopyxis litoris A01A‐101, Algihabitans albus A01A‐324, “Coraliitalea coralii” A01A‐333 and Litoreibacter sp. A01A‐347 revealed sulfur‐ and nitrogen‐containing compounds, ketones, alcohols, aldehydes, aromatic compounds, amides and one lactone, as well as the typical algal products, apocarotenoids. The compounds were identified by gas chromatographic retention indices, comparison of mass spectra and syntheses of reference compounds. A major algal metabolite was 3,4,4‐trimethylcyclopent‐2‐en‐1‐one, an apocarotenoid indicating the presence of carotenoids related to capsanthin, not reported from algae so far. A low overlap in volatiles bouquets between C. velia and the bacteria was found, and the xenic algal culture almost exclusively released algal components.
A word of caution: Early failure of Magmaris® bioresorbable stent after pulmonary artery stenting
Authors: Haddad Raymond N. , Adel Hassan Ahmed , AL Soufi Mahmoud , Kasem Mohamed 
Published: November 2022

AbstractBioresorbable scaffolds (BRS) have been advocated as the fourth revolution in interventional cardiology medical devices with promising technology to improve the treatment of coronary artery disease with an event‐free future. We describe the first reported use and early collapse of the Magmaris® Resorbable Magnesium Scaffold (RMS) stent (BIOTRONIK AG, Switzerland) to relieve left pulmonary artery severe stenosis in a newborn after the Norwood procedure. The stent collapse was detected 2 weeks after implantation and urgently treated with a balloon‐expandable stent. This complication raises the alarm about the need to keep implanted RMS under scrutiny. The possibility of faster scaffold resorption in small babies or lack of sufficient radial force of RMS to resist acute vessel recoil has led to ineffective relief of branch pulmonary artery stenosis and failure to enable a safe short‐term bridge to Stage II palliation.
Inclusion of the Mother Liquor of Three Different Salt Crystals Formed via Industrial Crystallization Processes
Authors: Tsushima Ippei , Kubota Kohei , Katogi Kento , Nakamoto Kanami , Maeda Kouji , Arafune Koji , Itoh Kazuhiro , Yamamoto Takuji , Taguchi Syogo , Miki Hideo 
Published: November 2022

AbstractThree different salt crystals (K2SO4, KCl, and Na2SO4·10H2O) were produced via batch cooling and continuous crystallization using a bench‐scale crystallization device, in order to elucidate the mechanism of inclusion of the mother liquor as a function of crystal size. The inclusion ratio of the mother liquor was higher at small sizes and decreased with crystal growth. All results were represented by the previously proposed model of core‐aggregation and shell‐growth processes for the three different salt crystals. Crystals with small Vickers hardness aggregated with each other, and the inclusion ratio of the mother liquor of aggregated grown crystals was high for all three salt crystals tested herein.
Resolving the Chemical Formula of Nesquehonite via NMR Crystallography, DFT Computation, and Complementary Neutron Diffraction
Authors: Cui Jinlei , Prisk Timothy R. , Olmsted David L. , Su Vicky , Asta Mark , Hayes Sophia E. 
Published: November 2022

AbstractNesquehonite is a magnesium carbonate mineral relevant to carbon sequestration envisioned for carbon capture and storage of CO2. Its chemical formula remains controversial today, assigned as either a hydrated magnesium carbonate [MgCO3 ⋅ 3H2O], or a hydroxy‐ hydrated‐ magnesium bicarbonate [Mg(HCO3)OH ⋅ 2H2O]. The resolution of this controversy is central to understanding this material‘s thermodynamic, phase, and chemical behavior. In an NMR crystallography study, using rotational‐echo double‐resonance 13C{1H} (REDOR), 13C−1H distances are determined with precision, and the combination of 13C static NMR lineshapes and density functional theory (DFT) calculations are used to model different H atomic coordinates. [MgCO3 ⋅ 3H2O] is found to be accurate, and evidence from neutron powder diffraction bolsters these assignments. Refined H positions can help understand how H‐bonding stabilizes this structure against dehydration to MgCO3. More broadly, these results illustrate the power of NMR crystallography as a technique for resolving questions where X‐ray diffraction is inconclusive.
Simulation of Compression Heat Pump Cycles Using NH3/H2O Mixtures to Estimate Their Working Domains
Authors: Loth Maximilian , Kabelac Stephan 
Published: November 2022

AbstractA computer‐aided process design methodology is used to determine the limits of NH3/H2O mixtures in different heat pump cycles from 20 °C to 150 °C. The evaluation is based on a defined parameter set consisting of the coefficient of performance, total heat transfer area and volumetric heat capacity. Simple cycles with two heat flows were chosen to meet good process integration capabilities. The results are shown in a sink outlet/temperature lift matrix considering current technical limits. R1366mzz(Z) in a standard compression cycle with internal heat exchanger serves as a benchmark. To provide temperatures up to 150 °C the lift of the heat pump has to increase to about 80 K of which only the wet compressions cycle with NH3/H2O is capable of. The working domains of NH3/H2O and R1366mzz(Z) are similar, when a two‐stage compression for NH3/H2O is applied.
A continuous flow reactor for the flexible production of different formulations: CFD‐aided design
Authors: Bacci di Capaci Riccardo , Bellagotti Filippo , Pannocchia Gabriele , Brunazzi Elisabetta , Galletti Chiara 
Published: November 2022

AbstractThe increasing need to improve the sustainability of industrial processes requires more flexible and intensified solutions. For this purpose, nowadays lots of efforts are made to switch from batch to continuous processes, the latter being able to ensure the same processing history to all fluid elements, with a consequent better control of the operating conditions and product quality. The present work aims at developing a continuous flow reactor for the production of several fine chemicals, including medical‐surgical aids, but also other substances for specific industrial sectors. The plant is basically an inline reactor equipped with various static mixers and side inlets, and it is conceived to ensure on‐site production. This is an important feature also in light of the recent COVID‐19 pandemic, which asked for flexible and distributed production of chemicals. Numerical simulations based on computational fluid dynamics are employed to study the performance, in terms of pressure drops and degree of mixing, of different static mixers, that is, the Lightnin Inliner Series 50 and Ross low pressure drop (LPD), combining various elements of mixing and injections in different operating conditions in both laminar and turbulent regimes. The results highlighted how numerical simulations may represent a valid tool for supporting the detailed design of such flow reactors by allowing the evaluation of the optimal design solutions.
Sarcopenia identified by computed tomography imaging using a deep learning–based segmentation approach impacts survival in patients with newly diagnosed multiple myeloma
Authors: Nandakumar Bharat , Baffour Francis , Abdallah Nadine H. , Kumar Shaji K. , Dispenzieri Angela , Buadi Francis K. , Dingli David , Lacy Martha Q. , Hayman Suzanne R. , Kapoor Prashant , Leung Nelson , Fonder Amie , Hobbs Miriam , Hwa Yi Lisa , Muchtar Eli , Warsame Rahma , Kourelis Taxiarchis V. , Go Ronald S. , Kyle Robert A. , Gertz Morie A. , Rajkumar S. Vincent , Klug Jason , Korfiatis Panagiotis , Gonsalves Wilson I. 
Published: November 2022

BackgroundSarcopenia increases with age and is associated with poor survival outcomes in patients with cancer. By using a deep learning–based segmentation approach, clinical computed tomography (CT) images of the abdomen of patients with newly diagnosed multiple myeloma (NDMM) were reviewed to determine whether the presence of sarcopenia had any prognostic value.MethodsSarcopenia was detected by accurate segmentation and measurement of the skeletal muscle components present at the level of the L3 vertebrae. These skeletal muscle measurements were further normalized by the height of the patient to obtain the skeletal muscle index for each patient to classify them as sarcopenic or not.ResultsThe study cohort consisted of 322 patients of which 67 (28%) were categorized as having high risk (HR) fluorescence in situ hybridization (FISH) cytogenetics. A total of 171 (53%) patients were sarcopenic based on their peri‐diagnosis standard‐dose CT scan. The median overall survival (OS) and 2‐year mortality rate for sarcopenic patients was 44 months and 40% compared to 90 months and 18% for those not sarcopenic, respectively (p < .0001 for both comparisons). In a multivariable model, the adverse prognostic impact of sarcopenia was independent of International Staging System stage, age, and HR FISH cytogenetics.ConclusionsSarcopenia identified by a machine learning–based convolutional neural network algorithm significantly affects OS in patients with NDMM. Future studies using this machine learning–based methodology of assessing sarcopenia in larger prospective clinical trials are required to validate these findings.
Perception of brightness when the eyes are closed
Authors: Sakai Hideki 
Published: November 2022

AbstractTo describe the lighting environment during sleep accurately, it is necessary to know the extent to which light is still perceived when the eyelids are closed. In this study, we measured the perception of equivalent brightness under closed‐eye and open‐eye conditions in binocular photopic vision. The light sources used were monochromatic red (peak wavelength 630 nm), yellow (593 nm), green (515 nm), and blue (460 nm) LEDs, as well as a white LED (Tcp = 4188 K, Ra = 93). A total of 33 subjects (Asian adults aged 22 years on average) with eyelids of approximately the same color were recruited. The average effective transmittances of their closed eyes were 52.4% ± 31.5% for red, 26.2% ± 18.2% for yellow, 21.6% ± 16.7% for green, 4.5% ± 3.9% for blue, and 42.7% ± 24.8% for white light. These values were up to 10 times higher than eyelid transmittances reported previously, so eyelid transmittance cannot by itself explain perceived closed‐eye brightness. There were also significant individual differences. As it is unlikely that the physical transmittances of the eyelids differed from subject to subject, psychological factors may be responsible. This phenomenon should be further investigated in the future.
Self‐Organization of Lipid‐Porphyrin Conjugates at the Air/Water Interface
Authors: Cressey Paul , Abuillan Wasim , Ibrahim Nada , Alhoussein Jana , Konovalov Oleg , Zheng Gang , Makky Ali 
Published: November 2022

AbstractLipid‐porphyrin conjugates are versatile compounds which can self‐assemble into liposome‐like structures with multifunctional properties. Most of the conjugates that have been described so far, consisted in grafting pyropheophorbide‐a (Pyro‐a) or other porphyrin derivatives through the esterification of the hydroxyl group in the sn‐2 position of a lysophosphatidylcholine. However, despite the versatility of these conjugates, less is known about the impact of the lipid backbone structure on their 2D phase behavior at the air/water interface and more precisely on their fine structures normal to the interface as well as on their in‐plane organization. Herein, we synthesized a new lipid‐porphyrin conjugate (PyroLSM) based on the amide coupling of Pyro‐a to a lysosphingomyelin backbone (LSM) and we compared its interfacial behavior to that of Pyro‐a and Pyro‐a conjugated lysophosphatidylcholine (PyroLPC) using Langmuir balance combined to a variety of other physical techniques. Our results provided evidence on the significant impact of the lipid backbone on the lateral packing of the conjugates as well as on the shape and size of the formed domains. Compared to Pyro‐a and PyroLPC monolayers, PyroLSM exhibited the highest lateral packing which highlights the role of the lipid backbone in controlling their 2D organization which in turn may impact the photophysical properties of their assemblies.
ConVarT: Search Engine for Missense Variants Between Humans and Other Organisms
Authors: Pir Mustafa S. , Cevik Sebiha , Kaplan Oktay I. 
Published: November 2022

AbstractConVarT (https://convart.org/) is a search engine for searching for conjugate variants between humans and other species. The search engine is based on matching conjugate variants called MatchVars between species. Matching equivalent variants requires correct alignment of orthologous proteins with the use of multiple sequence alignments (MSA). Indeed, the ConVarT pipeline has performed over a million MSAs and integrated variants and variant‐specific annotations (pathogenicity, phenotypic variants; etc.) into the corresponding positions on MSAs. When a clinically relevant variant is discovered whose functional relevance is unknown, ConVarT offers clinician scientists the possibility to search for a MatchVar in other species and to look for functional data on that variant. Fortunately, ConVarT enables users to paste a protein sequence in FASTA format to search for human orthologous proteins. A pairwise sequence alignment (PSA) is then performed between the provided protein sequence and the human orthologous protein, allowing users to visualize human variants on the PSA. Here, we describe the step‐by‐step usage of ConVarT. © 2022 Wiley Periodicals LLC.Basic Protocol 1: Searching matching variants (MatchVar) with gene/protein identifiers.Basic Protocol 2: Searching with a FASTA sequence.Alternate Protocol: Search with gene name in multiple species.Basic Protocol 3: Search genes associated with a disease.
An ingenious methodology of deriving single‐FTFN‐based canonic grounded‐capacitor SRCOs
Authors: Senani Raj , Bhaskar Data Ram , Gupta Shanti Swaroop , Kumar Pragati , Sharma Ravindra Kumar 
Published: November 2022

SummaryIn the past, several new active elements have been employed to realize single‐resistance‐controlled oscillators (SRCO) of which the four‐terminal‐floating‐nullors (FTFN) have attracted considerable attention in the literature. In this paper, an ingenious methodology of deriving single‐FTFN‐based canonic grounded‐capacitor (GC) SRCOs has been presented. It is shown that such oscillators can be systematically evolved from a class of earlier known op‐amp‐based SRCOs through the application of two theorems pertaining to RC‐nullor oscillators published earlier. The presented methodology not only yields all the previously known (four) single‐FTFN‐based canonic GC SRCOs but also reveals a number of (12) new circuits, which have not been known in the open literature earlier. The viability of the evolved oscillator circuits has been confirmed through SPICE simulations, and some simulation results have been given.
Perturbation responses in co‐evolved model meta‐communities
Authors: Abernethy Gavin M. 
Published: November 2022

AbstractA spatially explicit eco‐evolutionary model assembles simulated meta‐communities which are subjected to species and community perturbation experiments to determine factors affecting the stability of the global ecosystem. Spatial structure and resource variety increase the persistence of the ensembles against the removal of an individual species, yet they remain vulnerable to re‐invasion by an existing member of the meta‐community if it is introduced to all patches with minimal population. Optimal reserve placement strategies are identified for maximally preserving global biodiversity from the effects of sequences of patch disruption, and targeted reserve placement that shields the most or the rarest biodiversity is usually effective. However, if disturbed populations are permitted to re‐settle in neighboring patches, then reserves should also be situated remotely to isolate their residents from invasion.
A functional analysis of personal autonomy: How restricting ‘what’, ‘when’ and ‘how’ affects experienced agency and goal motivation
Authors: Zhang Chao , Sankaran Supraja , Aarts Henk 
Published: November 2022

AbstractPersonal autonomy is central to people's experiences of agency and abilities to actively take part in society. To address the challenges of supporting autonomy, we propose a functional model of autonomy, according to which the experience of agency is a function of the opportunity to determine what to do, when to act and how to act in goal‐pursuit. We tested the model in three experiments where the three goal‐pursuit components could be constrained by another person or an artificial intelligence (AI) agent. Results showed that removing any of the three components from one's own decisions reduced experienced agency (Study 1a and 1b) and lowered motivation to pursue goals in organisational contexts (Study 2). In comparison to the strong and robust main effects, interactions between the components and the effects of the source of restriction (human vs. AI) were negligible. Implications for personal autonomy, algorithmic decision‐making and behaviour change interventions are discussed.
Electrochemical Sensing Platform Integrated with Solid‐state Reference Electrode Based on Indium Tin Oxide Interdigitated Array Electrodes
Authors: Bae Je Hyun , Jeon Hyeri , Yang Hyun Ju , Kang Chung Mu , Han Donghoon 
Published: November 2022

AbstractWe present a new strategy for the fabrication of a fully integrated electrochemical platform. The three‐electrode system consists of an indium tin oxide interdigitated array as working electrode, a solid‐state reference electrode, and an electrodeposited Pt counter electrode that are placed in microfluidic channel. By controlling the electrodeposition conditions, such as the applied potential and time, the stability and uniformity of the films can be optimized. A solid‐state reference electrode was fabricated on the nanoporous Pt via electropolymerization of poly‐1,3‐phenylenediamine. This system provides a simple method for the fabrication of three‐electrode system and opens the possibility for an electroanalytical platform.