bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caveats on COVID-19 herd immunity threshold: the Spain case
Authors: García-García David , Morales Enrique , Fonfría Eva S. , Vigo Isabel , Bordehore Cesar 
Published: January 2022

AbstractAfter a year of living with the COVID-19 pandemic and its associated consequences, hope looms on the horizon thanks to vaccines. The question is what percentage of the population needs to be immune to reach herd immunity, that is to avoid future outbreaks. The answer depends on the basic reproductive number,R0, a key epidemiological parameter measuring the transmission capacity of a disease. In addition to the virus itself,R0also depends on the characteristics of the population and their environment. Additionally, the estimate ofR0depends on the methodology used, the accuracy of data and the generation time distribution. This study aims to reflect on the difficulties surroundingR0estimation, and provides Spain with a threshold for herd immunity, for which we considered the different combinations of all the factors that affect theR0of the Spanish population. Estimates ofR0range from 1.39 to 3.10 for the ancestral SARS-CoV-2 variant, with the largest differences produced by the method chosen to estimateR0. With these values, the herd immunity threshold (HIT) ranges from 28.1 to 67.7%, which would have made 70% a realistic upper bound for Spain. However, the imposition of the delta variant (B.1.617.2 lineage) in late summer 2021 may have expanded the range ofR0to 4.02–8.96 and pushed the upper bound of the HIT to 90%.
Association between the recognition of muscle mass and exercise habits or eating behaviors in female college students
Authors: Mase Tomoki , Ohara Kumiko , Momoi Katsumasa , Nakamura Harunobu 
Published: January 2022

AbstractThis study aimed to examine the association between muscle mass and perception of body shape, desired body shape, physical strength, exercise habits, and eating behaviors. Height, weight, and body composition in 270 female university students were measured. The questionnaire on body shape perception, desired body shape, dieting experience, current, and past exercise habits, exercise preference, and eating behaviors were administered. The analysis of covariance with body fat mass as the covariate found that the skeletal muscle index (SMI) was different among each group on each of body perception or desired body shape (all, p < 0.001). In the post hoc test on body shape perception, the SMI in “obese” was significantly more than that in “slim” (p < 0.001) and “normal” (p < 0.001). In the desired body shape, the SMI in “become thin” was more than that in “maintain as current shape” (p < 0.001). Further, a significant difference was found among the categories of diet experience, with body fat mass as the covariate. In the post hoc test, the SMI in “yes” was more than that in “no” (p < 0.001). These results indicate that not only body fat mass but skeletal muscle mass drives young females’ desire for thinness even with exercise advantages.
System analysis of the sequencing quality of human whole exome samples on BGI NGS platform
Authors: Belova Vera , Pavlova Anna , Afasizhev Robert , Moskalenko Viktoriya , Korzhanova Margarita , Krivoy Andrey , Cheranev Valery , Nikashin Boris , Bulusheva Irina , Rebrikov Denis , Korostin Dmitriy 
Published: January 2022

AbstractHuman exome sequencing is a classical method used in most medical genetic applications. The leaders in the field are the manufacturers of enrichment kits based on hybridization of cRNA or cDNA biotinylated probes specific for a genomic region of interest. Recently, the platforms manufactured by the Chinese company MGI Tech have become widespread in Europe and Asia. The reliability and quality of the obtained data are already beyond any doubt. However, only a few kits compatible with these sequencers can be used for such specific tasks as exome sequencing. We developed our own solution for library pre-capture pooling and exome enrichment with Agilent probes. In this work, using a set of the standard benchmark samples from the Platinum Genome collection, we demonstrate that the qualitative and quantitative parameters of our protocol which we called “RSMU_exome” exceed those of the MGI Tech kit. Our protocol allows for identifying more SNV and indels, generates fewer PCR duplicates, enables pooling of more samples in a single enrichment procedure, and requires less raw data to obtain results comparable with the MGI Tech's protocol. The cost of our protocol is also lower than that of MGI Tech's solution.
Being in a crowd bonds people via physiological synchrony
Authors: Baranowski-Pinto G. , Profeta V. L. S. , Newson M. , Whitehouse H. , Xygalatas D. 
Published: January 2022

AbstractCollective events can generate intense emotions, shape group identities, and forge strong bonds. Do these effects extend to remote participation, and what are the psychological mechanisms underpinning their social power? We monitored psycho-physiological activity among groups of basketball fans who either attended games in-person (in a stadium) or watched games live on television in small groups. In-person attendance was associated with greater synchronicity in autonomic nervous system activation at the group level, which resulted in more transformative experiences and contributed to stronger identity fusion. Our findings suggest that the social effects of sports depend substantially on the inter-personal dynamics unfolding among fans, rather than being prompted simply by watching the game itself. Given the increasing prevalence of virtual experiences, this has potentially wide-reaching implications for many domains of collective human interaction.
Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes
Authors: Potapova Nadezhda A. , Kondrashov Alexey S. , Mirkin Sergei M. 
Published: January 2022

AbstractGenomic inversions come in various sizes. While long inversions are relatively easy to identify by aligning high-quality genome sequences, unambiguous identification of microinversions is more problematic. Here, using a set of extra stringent criteria to distinguish microinversions from other mutational events, we describe microinversions that occurred after the divergence of humans and chimpanzees. In total, we found 59 definite microinversions that range from 17 to 33 nucleotides in length. In majority of them, human genome sequences matched exactly the reverse-complemented chimpanzee genome sequences, implying that the inverted DNA segment was copied precisely. All these microinversions were flanked by perfect or nearly perfect inverted repeats pointing to their key role in their formation. Template switching at inverted repeats during DNA replication was previously discussed as a possible mechanism for the microinversion formation. However, many of definite microinversions found by us cannot be easily explained via template switching owing to the combination of the short length and imperfect nature of their flanking inverted repeats. We propose a novel, alternative mechanism that involves repair of a double-stranded break within the inverting segment via microhomology-mediated break-induced replication, which can consistently explain all definite microinversion events.
Top-emitting 940-nm thin-film VCSELs transferred onto aluminum heatsinks
Authors: Moon Sunghyun , Yun Yeojun , Lee Minhyung , Kim Donghwan , Choi Wonjin , Park Ji-Yong , Lee Jaejin 
Published: January 2022

AbstractThin-film vertical cavity surface emitting lasers (VCSELs) mounted onto heatsinks open up the way toward low-power consumption and high-power operation, enabling them to be widely used for energy saving high-speed optical data communication and three-dimensional sensor applications. There are two conventional VCSEL polarity structures: p-on-n and n-on-p polarity. The former is more preferably used owing to the reduced series resistance of n-type bottom distributed Bragg reflection (DBR) as well as the lower defect densities of n-type GaAs substrates. In this study, the p-on-n structures of thin-film VCSELs, including an etch stop layer and a highly n-doped GaAs ohmic layer, were epitaxially grown in upright order by using low-pressure metalorganic chemical vapor deposition (LP-MOCVD). The p-on-n structures of thin-film VCSELs were transferred onto an aluminum heatsink via a double-transfer technique, allowing the top-emitting thin-film VCSELs to keep the p-on-n polarity with the removal of the GaAs substrate. The threshold current (Ith) and voltage (Vth) of the fabricated top-emitting thin-film VCSELs were 1 mA and 2.8 V, respectively. The optical power was 7.7 mW at a rollover point of 16.1 mA.
Self-referenced method for the Judd–Ofelt parametrisation of the Eu3+ excitation spectrum
Authors: Ćirić Aleksandar , Marciniak Łukasz , Dramićanin Miroslav D. 
Published: January 2022

AbstractJudd–Ofelt theory is a cornerstone of lanthanides’ spectroscopy given that it describes 4fn emissions and absorptions of lanthanide ions using only three intensity parameters. A self-referenced technique for computing Judd–Ofelt intensity parameters from the excitation spectra of Eu3+-activated luminescent materials is presented in this study along with an explanation of the parametrisation procedure and free user-friendly web application. It uses the integrated intensities of the 7F0 → 5D2, 7F0 → 5D4, and 7F0 → 5L6 transitions in the excitation spectrum for estimation and the integrated intensity of the 7F0 → 5D1 magnetic dipole transition for calibration. This approach facilitates an effortless derivation of the Ω6 intensity parameter, which is challenging to compute precisely by Krupke’s parametrisation of the emission spectrum and, therefore, often omitted in published research papers. Compared to the parametrisation of absorption spectra, the described method is more accurate, can be applied to any material form, and requires a single excitation spectrum.
Innate immune deficiencies are associated with severity and poor prognosis in patients with COVID-19
Authors: Peyneau Marine , Granger Vanessa , Wicky Paul-Henri , Khelifi-Touhami Dounia , Timsit Jean-François , Lescure François-Xavier , Yazdanpanah Yazdan , Tran-Dinh Alexy , Montravers Philippe , Monteiro Renato C. , Chollet-Martin Sylvie , Hurtado-Nedelec Margarita , de Chaisemartin Luc 
Published: January 2022

AbstractCOVID-19 can cause acute respiratory distress syndrome, leading to death in many individuals. Evidence of a deleterious role of the innate immune system is accumulating, but the precise mechanisms involved remain unclear. In this study, we investigated the links between circulating innate phagocytes and severity in COVID-19 patients. We performed in-depth phenotyping of neutrophil and monocyte subpopulations and measured soluble activation markers in plasma. Additionally, anti-microbial functions (phagocytosis, oxidative burst, and NETosis) were evaluated on fresh cells from patients. Neutrophils and monocytes had a strikingly disturbed phenotype, and elevated concentrations of activation markers (calprotectin, myeloperoxidase, and neutrophil extracellular traps) were measured in plasma. Critical patients had increased CD13low immature neutrophils, LOX-1 + and CCR5 + immunosuppressive neutrophils, and HLA-DRlow downregulated monocytes. Markers of immature and immunosuppressive neutrophils were strongly associated with severity. Moreover, neutrophils and monocytes of critical patients had impaired antimicrobial functions, which correlated with organ dysfunction, severe infections, and mortality. Together, our results strongly argue in favor of a pivotal role of innate immunity in COVID-19 severe infections and pleads for targeted therapeutic options.
Cyclic production of biocompatible few-layer graphene ink with in-line shear-mixing for inkjet-printed electrodes and Li-ion energy storage
Authors: Carey Tian , Alhourani Abdelnour , Tian Ruiyuan , Seyedin Shayan , Arbab Adrees , Maughan Jack , Šiller Lidija , Horvath Dominik , Kelly Adam , Kaur Harneet , Caffrey Eoin , Kim Jong M. , Hagland Hanne R. , Coleman Jonathan N. 
Published: January 2022

AbstractThe scalable production of two-dimensional (2D) materials is needed to accelerate their adoption to industry. In this work, we present a low-cost in-line and enclosed process of exfoliation based on high-shear mixing to create aqueous dispersions of few-layer graphene, on a large scale with a Yw ~ 100% yield by weight and throughput of ϕ ~ 8.3 g h−1. The in-line process minimises basal plane defects compared to traditional beaker-based shear mixing which we attribute to a reduced Reynolds number, Re ~ 105. We demonstrate highly conductive graphene material with conductivities as high as σ ∼ 1.5 × 104 S m−1 leading to sheet-resistances as low as Rs ∼ 2.6 Ω □−1 (t ∼ 25 μm). The process is ideal for formulating non-toxic, biocompatible and highly concentrated (c ∼ 100 mg ml−1) inks. We utilise the graphene inks for inkjet printable conductive interconnects and lithium-ion battery anode composites that demonstrate a low-rate lithium storage capability of 370 mAh g−1, close to the theoretical capacity of graphite. Finally, we demonstrate the biocompatibility of the graphene inks with human colon cells and human umbilical vein endothelial cells at high c ∼ 1 mg ml−1 facilitating a route for the use of the graphene inks in applications that require biocompatibility at high c such as electronic textiles.
SERPINB3 (SCCA1) inhibits cathepsin L and lysoptosis, protecting cervical cancer cells from chemoradiation
Authors: Wang Songyan , Luke Cliff J. , Pak Stephen C. , Shi Victoria , Chen Liyun , Moore Jonathan , Andress Arlise P. , Jayachandran Kay , Zhang Jin , Huang Yi , Platik Marina , Apicelli Anthony A. , Schwarz Julie K. , Grigsby Perry W. , Silverman Gary A. , Markovina Stephanie 
Published: January 2022

AbstractThe endogenous lysosomal cysteine protease inhibitor SERPINB3 (squamous cell carcinoma antigen 1, SCCA1) is elevated in patients with cervical cancer and other malignancies. High serum SERPINB3 is prognostic for recurrence and death following chemoradiation therapy. Cervical cancer cells genetically lacking SERPINB3 are more sensitive to ionizing radiation (IR), suggesting this protease inhibitor plays a role in therapeutic response. Here we demonstrate that SERPINB3-deficient cells have enhanced sensitivity to IR-induced cell death. Knock out of SERPINB3 sensitizes cells to a greater extent than cisplatin, the current standard of care. IR in SERPINB3 deficient cervical carcinoma cells induces predominantly necrotic cell death, with biochemical and cellular features of lysoptosis. Rescue with wild-type SERPINB3 or a reactive site loop mutant indicates that protease inhibitory activity is required to protect cervical tumor cells from radiation-induced death. Transcriptomics analysis of primary cervix tumor samples and genetic knock out demonstrates a role for the lysosomal protease cathepsin L in radiation-induced cell death in SERPINB3 knock-out cells. These data support targeting of SERPINB3 and lysoptosis to treat radioresistant cervical cancers.
Lysoptosis is an evolutionarily conserved cell death pathway moderated by intracellular serpins
Authors: Luke Cliff J. , Markovina Stephanie , Good Misty , Wight Ira E. , Thomas Brian J. , Linneman John M. , Lanik Wyatt E. , Koroleva Olga , Coffman Maggie R. , Miedel Mark T. , Gong Qingqing , Andress Arlise , Campos Guerrero Marlene , Wang Songyan , Chen LiYun , Beatty Wandy L. , Hausmann Kelsey N. , White Frances V. , Fitzpatrick James A. J. , Orvedahl Anthony , Pak Stephen C. , Silverman Gary A. 
Published: January 2022

AbstractLysosomal membrane permeabilization (LMP) and cathepsin release typifies lysosome-dependent cell death (LDCD). However, LMP occurs in most regulated cell death programs suggesting LDCD is not an independent cell death pathway, but is conscripted to facilitate the final cellular demise by other cell death routines. Previously, we demonstrated that Caenorhabditis elegans (C. elegans) null for a cysteine protease inhibitor, srp-6, undergo a specific LDCD pathway characterized by LMP and cathepsin-dependent cytoplasmic proteolysis. We designated this cell death routine, lysoptosis, to distinguish it from other pathways employing LMP. In this study, mouse and human epithelial cells lacking srp-6 homologues, mSerpinb3a and SERPINB3, respectively, demonstrated a lysoptosis phenotype distinct from other cell death pathways. Like in C. elegans, this pathway depended on LMP and released cathepsins, predominantly cathepsin L. These studies suggested that lysoptosis is an evolutionarily-conserved eukaryotic LDCD that predominates in the absence of neutralizing endogenous inhibitors.
TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth
Authors: Sepporta Maria-Vittoria , Praz Viviane , Balmas Bourloud Katia , Joseph Jean-Marc , Jauquier Nicolas , Riggi Nicolò , Nardou-Auderset Katya , Petit Audrey , Scoazec Jean-Yves , Sartelet Hervé , Renella Raffaele , Mühlethaler-Mottet Annick 
Published: January 2022

AbstractThe embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis colonization in immunocompromised mice. Moreover, TWIST1 knockout tumors display a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings confirm TWIST1 as promising therapeutic target in NB.
Asymbiotic mass production of the arbuscular mycorrhizal fungus Rhizophagus clarus
Authors: Tanaka Sachiko , Hashimoto Kayo , Kobayashi Yuuki , Yano Koji , Maeda Taro , Kameoka Hiromu , Ezawa Tatsuhiro , Saito Katsuharu , Akiyama Kohki , Kawaguchi Masayoshi 
Published: January 2022

AbstractArbuscular mycorrhizal (AM) symbiosis is a mutually beneficial interaction between fungi and land plants and promotes global phosphate cycling in terrestrial ecosystems. AM fungi are recognised as obligate symbionts that require root colonisation to complete a life cycle involving the production of propagules, asexual spores. Recently, it has been shown that Rhizophagus irregularis can produce infection-competent secondary spores asymbiotically by adding a fatty acid, palmitoleic acid. Furthermore, asymbiotic growth can be supported using myristate as a carbon and energy source for their asymbiotic growth to increase fungal biomass. However, the spore production and the ability of these spores to colonise host roots were still limited compared to the co-culture of the fungus with plant roots. Here we show that a combination of two plant hormones, strigolactone and jasmonate, induces the production of a large number of infection-competent spores in asymbiotic cultures of Rhizophagus clarus HR1 in the presence of myristate and organic nitrogen. Inoculation of asymbiotically-generated spores promoted the growth of host plants, as observed for spores produced by symbiotic culture system. Our findings provide a foundation for the elucidation of hormonal control of the fungal life cycle and the development of inoculum production schemes.
Computational complexity continuum within Ising formulation of NP problems
Authors: Kalinin Kirill P. , Berloff Natalia G. 
Published: January 2022

AbstractA promising approach to achieve computational supremacy over the classical von Neumann architecture explores classical and quantum hardware as Ising machines. The minimisation of the Ising Hamiltonian is known to be NP-hard problem yet not all problem instances are equivalently hard to optimise. Given that the operational principles of Ising machines are suited to the structure of some problems but not others, we propose to identify computationally simple instances with an ‘optimisation simplicity criterion’. Neuromorphic architectures based on optical, photonic, and electronic systems can naturally operate to optimise instances satisfying this criterion, which are therefore often chosen to illustrate the computational advantages of new Ising machines. As an example, we show that the Ising model on the Möbius ladder graph is ‘easy’ for Ising machines. By rewiring the Möbius ladder graph to random 3-regular graphs, we probe an intermediate computational complexity between P and NP-hard classes with several numerical methods. Significant fractions of polynomially simple instances are further found for a wide range of small size models from spin glasses to maximum cut problems. A compelling approach for distinguishing easy and hard instances within the same NP-hard class of problems can be a starting point in developing a standardised procedure for the performance evaluation of emerging physical simulators and physics-inspired algorithms.
Challenging the sustainability of urban beekeeping using evidence from Swiss cities
Authors: Casanelles-Abella Joan , Moretti Marco 
Published: January 2022

AbstractUrban beekeeping is booming, heightening awareness of pollinator importance but also raising concerns that its fast growth might exceed existing resources and negatively impact urban biodiversity. To evaluate the magnitude of urban beekeeping growth and its sustainability, we analysed data on beehives and available resources in 14 Swiss cities in 2012–2018 and modelled the sustainability of urban beekeeping under different scenarios of available floral resources and existing carrying capacities. We found large increases in hives numbers across all cities from an average 6.48 hives per km2 (3139 hives in total) in 2012 to an average 8.1 hives per km2 (6370 in total) in 2018 and observed that available resources are insufficient to maintain present densities of beehives, which currently are unsustainable.
Effects of First Language Background and Learning Experience in Perceiving Mandarin Lexical Tones: Learners and Nonlearners From English- and Japanese-Speaking Backgrounds
Authors: Tsukada Kimiko , Idemaru Kaori 
Published: January 2022

Purpose:
This research compared individuals from two first language (L1) backgrounds (English and Japanese) to determine how they may differ in their perception of Mandarin tones (Tones 1 vs. 2 [T1–T2], Tones 1 vs. 3 [T1–T3], Tones 1 vs. 4 [T1–T4], Tones 2 vs. 3 [T2–T3], Tones 2 vs. 4 [T2–T4], Tones 3 vs. 4 [T3–T4]) on account of their L1.

Method:

The participants included two groups of
learners of Mandarin
(23 English speakers, 18 Japanese speakers), two groups of
nonlearners of Mandarin
(24 English speakers, 21 Japanese speakers), and a
control group
of 10 Mandarin speakers. A four-alternative forced-choice discrimination task that included 360 trials was presented in three blocks of 120 trials.

Results:
The native Mandarin group was more accurate in their tonal discrimination of all six tone pairs than all the nonnative groups. While Japanese nonlearners generally outperformed English nonlearners in their overall perception of Mandarin lexical tones, L1-based differences were less extensive for the two groups of learners. Both learner groups were least accurate on T2–T3 and most accurate on T3–T4.

Conclusion:
The results suggest that with classroom experience, English speakers can overcome their initial disadvantage and learn lexical tones in a new language as successfully as speakers of Japanese with classroom experience.