bluuebunny/crossref_metadata_2025_split huggingface dataset:
X-ray study of ferroic octupole order producing anomalous Hall effect
Authors: Kimata Motoi , Sasabe Norimasa , Kurita Kensuke , Yamasaki Yuichi , Tabata Chihiro , Yokoyama Yuichi , Kotani Yoshinori , Ikhlas Muhammad , Tomita Takahiro , Amemiya Kenta , Nojiri Hiroyuki , Nakatsuji Satoru , Koretsune Takashi , Nakao Hironori , Arima Taka-hisa , Nakamura Tetsuya 
Published: September 2021

AbstractRecently found anomalous Hall, Nernst, magnetooptical Kerr, and spin Hall effects in the antiferromagnets Mn3X (X = Sn, Ge) are attracting much attention for spintronics and energy harvesting. Since these materials are antiferromagnets, the origin of these functionalities is expected to be different from that of conventional ferromagnets. Here, we report the observation of ferroic order of magnetic octupole in Mn3Sn by X-ray magnetic circular dichroism, which is only predicted theoretically so far. The observed signals are clearly decoupled with the behaviors of uniform magnetization, indicating that the present X-ray magnetic circular dichroism is not arising from the conventional magnetization. We have found that the appearance of this anomalous signal coincides with the time reversal symmetry broken cluster magnetic octupole order. Our study demonstrates that the exotic material functionalities are closely related to the multipole order, which can produce unconventional cross correlation functionalities.
A scalable workflow to characterize the human exposome
Authors: Hu Xin , Walker Douglas I. , Liang Yongliang , Smith Matthew Ryan , Orr Michael L. , Juran Brian D. , Ma Chunyu , Uppal Karan , Koval Michael , Martin Greg S. , Neujahr David C. , Marsit Carmen J. , Go Young-Mi , Pennell Kurt D. , Miller Gary W. , Lazaridis Konstantinos N. , Jones Dean P. 
Published: September 2021

AbstractComplementing the genome with an understanding of the human exposome is an important challenge for contemporary science and technology. Tens of thousands of chemicals are used in commerce, yet cost for targeted environmental chemical analysis limits surveillance to a few hundred known hazards. To overcome limitations which prevent scaling to thousands of chemicals, we develop a single-step express liquid extraction and gas chromatography high-resolution mass spectrometry analysis to operationalize the human exposome. We show that the workflow supports quantification of environmental chemicals in human plasma (200 µL) and tissue (≤100 mg) samples. The method also provides high resolution, sensitivity and selectivity for exposome epidemiology of mass spectral features without a priori knowledge of chemical identity. The simplicity of the method can facilitate harmonization of environmental biomonitoring between laboratories and enable population level human exposome research with limited sample volume.
Quantum fluids of light in all-optical scatterer lattices
Authors: Alyatkin S. , Sigurdsson H. , Askitopoulos A. , Töpfer J. D. , Lagoudakis P. G. 
Published: September 2021

AbstractOne of the recently established paradigms in condensed matter physics is examining a system’s behaviour in artificial potentials, giving insight into phenomena of quantum fluids in hard-to-reach settings. A prominent example is the matter-wave scatterer lattice, where high energy matter waves undergo transmission and reflection through narrow width barriers leading to stringent phase matching conditions with lattice band formation. In contrast to evanescently coupled lattice sites, the realisation of a scatterer lattice for macroscopic matter-wave fluids has remained elusive. Here, we implement a system of exciton-polariton condensates in a non-Hermitian Lieb lattice of scatterer potentials. By fine tuning the lattice parameters, we reveal a nonequilibrium phase transition between distinct regimes of polariton condensation: a scatterer lattice of gain guided polaritons condensing on the lattice potential maxima, and trapped polaritons condensing in the potential minima. Our results pave the way towards unexplored physics of non-Hermitian fluids in non-stationary mixtures of confined and freely expanding waves.
Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control
Authors: Cottee Matthew A. , Beckwith Sean L. , Letham Suzanne C. , Kim Sarah J. , Young George R. , Stoye Jonathan P. , Garfinkel David J. , Taylor Ian A. 
Published: September 2021

AbstractExcessive replication of Saccharomyces cerevisiae Ty1 retrotransposons is regulated by Copy Number Control, a process requiring the p22/p18 protein produced from a sub-genomic transcript initiated within Ty1 GAG. In retrotransposition, Gag performs the capsid functions required for replication and re-integration. To minimize genomic damage, p22/p18 interrupts virus-like particle function by interaction with Gag. Here, we present structural, biophysical and genetic analyses of p18m, a minimal fragment of Gag that restricts transposition. The 2.8 Å crystal structure of p18m reveals an all α-helical protein related to mammalian and insect ARC proteins. p18m retains the capacity to dimerise in solution and the crystal structures reveal two exclusive dimer interfaces. We probe our findings through biophysical analysis of interface mutants as well as Ty1 transposition and p18m restriction in vivo. Our data provide insight into Ty1 Gag structure and suggest how p22/p18 might function in restriction through a blocking-of-assembly mechanism.
Identification of the factor XII contact activation site enables sensitive coagulation diagnostics
Authors: Heestermans Marco , Naudin Clément , Mailer Reiner K. , Konrath Sandra , Klaetschke Kristin , Jämsä Anne , Frye Maike , Deppermann Carsten , Pula Giordano , Kuta Piotr , Friese Manuel A. , Gelderblom Mathias , Sickmann Albert , Preston Roger J. S. , Nofer Jerzy-Roch , Rose-John Stefan , Butler Lynn M. , Salomon Ophira , Stavrou Evi X. , Renné Thomas 
Published: September 2021

AbstractContact activation refers to the process of surface-induced activation of factor XII (FXII), which initiates blood coagulation and is captured by the activated partial thromboplastin time (aPTT) assay. Here, we show the mechanism and diagnostic implications of FXII contact activation. Screening of recombinant FXII mutants identified a continuous stretch of residues Gln317–Ser339 that was essential for FXII surface binding and activation, thrombin generation and coagulation. Peptides spanning these 23 residues competed with surface-induced FXII activation. Although FXII mutants lacking residues Gln317–Ser339 were susceptible to activation by plasmin and plasma kallikrein, they were ineffective in supporting arterial and venous thrombus formation in mice. Antibodies raised against the Gln317–Ser339 region induced FXII activation and triggered controllable contact activation in solution leading to thrombin generation by the intrinsic pathway of coagulation. The antibody-activated aPTT allows for standardization of particulate aPTT reagents and for sensitive monitoring of coagulation factors VIII, IX, XI.
A Replication stress biomarker is associated with response to gemcitabine versus combined gemcitabine and ATR inhibitor therapy in ovarian cancer
Authors: Konstantinopoulos Panagiotis A. , da Costa Alexandre André B. A. , Gulhan Doga , Lee Elizabeth K. , Cheng Su-Chun , Hendrickson Andrea E. Wahner , Kochupurakkal Bose , Kolin David L. , Kohn Elise C. , Liu Joyce F. , Stover Elizabeth H. , Curtis Jennifer , Tayob Nabihah , Polak Madeline , Chowdhury Dipanjan , Matulonis Ursula A. , Färkkilä Anniina , D’Andrea Alan D. , Shapiro Geoffrey I. 
Published: September 2021

AbstractIn a trial of patients with high grade serous ovarian cancer (HGSOC), addition of the ATR inhibitor berzosertib to gemcitabine improved progression free survival (PFS) compared to gemcitabine alone but biomarkers predictive of treatment are lacking. Here we report a candidate biomarker of response to gemcitabine versus combined gemcitabine and ATR inhibitor therapy in HGSOC ovarian cancer. Patients with replication stress (RS)-high tumors (n = 27), defined as harboring at least one genomic RS alteration related to loss of RB pathway regulation and/or oncogene-induced replication stress achieve significantly prolonged PFS (HR = 0.38, 90% CI, 0.17–0.86) on gemcitabine monotherapy compared to those with tumors without such alterations (defined as RS-low, n = 30). However, addition of berzosertib to gemcitabine benefits only patients with RS-low tumors (gemcitabine/berzosertib HR 0.34, 90% CI, 0.13–0.86) and not patients with RS-high tumors (HR 1.11, 90% CI, 0.47–2.62). Our findings support the notion that the exacerbation of RS by gemcitabine monotherapy is adequate for lethality in RS-high tumors. Conversely, for RS-low tumors addition of berzosertib-mediated ATR inhibition to gemcitabine is necessary for lethality to occur. Independent prospective validation of this biomarker is required.
Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern
Authors: Yang Wan , Shaman Jeffrey 
Published: September 2021

AbstractTo support COVID-19 pandemic planning, we develop a model-inference system to estimate epidemiological properties of new SARS-CoV-2 variants of concern using case and mortality data while accounting for under-ascertainment, disease seasonality, non-pharmaceutical interventions, and mass-vaccination. Applying this system to study three variants of concern, we estimate that B.1.1.7 has a 46.6% (95% CI: 32.3–54.6%) transmissibility increase but nominal immune escape from protection induced by prior wild-type infection; B.1.351 has a 32.4% (95% CI: 14.6–48.0%) transmissibility increase and 61.3% (95% CI: 42.6–85.8%) immune escape; and P.1 has a 43.3% (95% CI: 30.3–65.3%) transmissibility increase and 52.5% (95% CI: 0–75.8%) immune escape. Model simulations indicate that B.1.351 and P.1 could outcompete B.1.1.7 and lead to increased infections. Our findings highlight the importance of preventing the spread of variants of concern, via continued preventive measures, prompt mass-vaccination, continued vaccine efficacy monitoring, and possible updating of vaccine formulations to ensure high efficacy.
Examining the effects of cigarette smoke on mouse lens through a multi OMIC approach
Authors: Khan Shahid Y. , Ali Muhammad , Jang Yura , Ryu Taekyung , Schwab Andrew J. , Ingram Brian O. , Cable Peter H. , Na Chan Hyun , Handa James T. , Riazuddin S. Amer 
Published: September 2021

AbstractHere, we report a multi OMIC (transcriptome, proteome, and metabolome) approach to investigate molecular changes in lens fiber cells (FC) of mice exposed to cigarette smoke (CS). Pregnant mice were placed in a whole-body smoke chamber and a few days later pups were born, which were exposed to CS for 5 hours/day, 5 days/week for a total of 3½ months. We examined the mice exposed to CS for CS-related cataractogenesis after completion of the CS exposure but no cataracts were observed. Lenses of CS-exposed and age-matched, untreated control mice were extracted and lens FC were subjected to multi OMIC profiling. We identified 348 genes, 130 proteins, and 14 metabolites exhibiting significant (p < 0.05) differential levels in lens FC of mice exposed to CS, corresponding to 3.6%, 4.3%, and 5.0% of the total genes, protein, and metabolites, respectively identified in this study. Our multi OMIC approach confirmed that only a small fraction of the transcriptome, the proteome, and the metabolome was perturbed in the lens FC of mice exposed to CS, which suggests that exposure of CS had a minimal effect on the mouse lens. It is worth noting that while our results confirm that CS exposure does not have a substantial impact on the molecular landscape of the mouse lens FC, we cannot rule out that CS exposure for longer durations and/or in combination with other morbidities or environmental factors would have a more robust effect and/or result in cataractogenesis.
Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2
Authors: López-Cortés Georgina I. , Palacios-Pérez Miryam , Zamudio Gabriel S. , Veledíaz Hannya F. , Ortega Enrique , José Marco V. 
Published: September 2021

AbstractAs the SARS-CoV-2 has spread and the pandemic has dragged on, the virus continued to evolve rapidly resulting in the emergence of new highly transmissible variants that can be of public health concern. The evolutionary mechanisms that drove this rapid diversity are not well understood but neutral evolution should open the first insight. The neutral theory of evolution states that most mutations in the nucleic acid sequences are random and they can be fixed or disappear by purifying selection. Herein, we performed a neutrality test to better understand the selective pressures exerted over SARS-CoV-2 spike protein from homologue proteins of Betacoronavirus, as well as to the spikes from human clinical isolates of the virus. Specifically, Tyr and Asn have higher occurrence rates on the Receptor Binding Domain (RBD) and in the overall sequence of spike proteins of Betacoronavirus, whereas His and Arg have lower occurrence rates. The in vivo evolutionary phenomenon of SARS-CoV-2 shows that Glu, Lys, Phe, and Val have the highest probability of occurrence in the emergent viral particles. Amino acids that have higher occurrence than the expected by the neutral control, are favorable and are fixed in the sequence while the ones that have lower occurrence than expected, influence the stability and/or functionality of the protein. Our results show that most unique mutations either for SARS-CoV-2 or its variants of health concern are under selective pressures, which could be related either to the evasion of the immune system, increasing the virus’ fitness or altering protein – protein interactions with host proteins. We explored the consequences of those selected mutations in the structure and protein – protein interaction with the receptor. Altogether all these forces have shaped the spike protein and the continually evolving variants.
Ene-reductase transformation of massoia lactone to δ-decalactone in a continuous-flow reactor
Authors: Szczepańska Ewa , Colombo Danilo , Tentori Francesca , Olejniczak Teresa , Brenna Elisabetta , Monti Daniela , Boratyński Filip 
Published: September 2021

AbstractThe demand for natural food flavorings increases every year. Biotransformation has become an attractive approach to obtain natural products. In this work, enantiomerically pure (R)-(+)-δ-decalactone was obtained by reduction of the C=C double bond of natural massoia lactone in a continuous-flow reactor. Of 13 different ene-reductases isolated, purified and tested, OYE3 was found to be the most efficient biocatalyst. The selected biocatalyst, either in the form of purified enzyme, cell lysate, whole cells or immobilized cells, was tested in the batch system as well as in the packed-bed flow bioreactor. The biotransformation performed in batch mode, using Ca2+-alginate immobilized cells of Escherichia coli BL21(DE3)/pET30a-OYE3, furnished the desired product with complete conversion in 30 min. The process was intensified using a continuous-flow reactor-membrane filtration system (flow 0.1 mL/min, substrate concentration 10 mM, pH 7, 24 °C) with cell lysate as biocatalyst combined with a cofactor regeneration system, which allowed obtaining > 99% bioconversion of massoia lactone.
Destruction mechanisms of ozone over SARS-CoV-2
Authors: Ataei-Pirkooh Angila , Alavi Ali , Kianirad Mehran , Bagherzadeh Kowsar , Ghasempour Alireza , Pourdakan Omid , Adl Reza , Kiani Seyed Jalal , Mirzaei Mehdi , Mehravi Bita 
Published: September 2021

AbstractIn this pandemic SARS-CoV-2 crisis, any attempt to contain and eliminate the virus will also stop its spread and consequently decrease the risk of severe illness and death. While ozone treatment has been suggested as an effective disinfection process, no precise mechanism of action has been previously reported. This study aimed to further investigate the effect of ozone treatment on SARS-CoV-2. Therefore, virus collected from nasopharyngeal and oropharyngeal swab and sputum samples from symptomatic patients was exposed to ozone for different exposure times. The virus morphology and structure were monitored and analyzed through Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), Atomic Absorption Spectroscopy (AAS), and ATR-FTIR. The obtained results showed that ozone treatment not only unsettles the virus morphology but also alters the virus proteins’ structure and conformation through amino acid disturbance and Zn ion release from the virus non-structural proteins. These results could provide a clearer pathway for virus elimination and therapeutics preparation.
Proliferative diabetic retinopathy transcriptomes reveal angiogenesis, anti-angiogenic therapy escape mechanisms, fibrosis and lymphatic involvement
Authors: Korhonen Ani , Gucciardo Erika , Lehti Kaisa , Loukovaara Sirpa 
Published: September 2021

AbstractProliferative diabetic retinopathy (PDR) is a sight-threatening diabetic complication in urgent need of new therapies. In this study we identify potential molecular mechanisms and target candidates in the pathogenesis of PDR fibrovascular tissue formation. We performed mRNA sequencing of RNA isolated from eleven excised fibrovascular membranes of type 1 diabetic PDR patients and two non-diabetic patients with rhegmatogenous retinal detachment with proliferative vitreoretinopathy. We determined differentially expressed genes between these groups and performed pathway and gene ontology term enrichment analyses to identify potential underlying mechanisms, pathways, and regulators. Multiple pro-angiogenic processes, including VEGFA-dependent and -independent pathways, as well as processes related to lymphatic development, epithelial to mesenchymal transition (EMT), wound healing, inflammation, fibrosis, and extracellular matrix (ECM) composition, were overrepresented in PDR. Overrepresentation of different angiogenic processes may help to explain the transient nature of the benefits that many patients receive from current intravitreal anti-angiogenic therapies, highlighting the importance of combinatorial treatments. Enrichment of genes and pathways related to lymphatic development indicates that targeting lymphatic involvement in PDR progression could have therapeutic relevance. Together with overrepresentation of EMT and fibrosis as well as differential ECM composition, these findings demonstrate the complexity of PDR fibrovascular tissue formation and provide avenues for the development of novel treatments.
A genetic risk score using human chromosomal-scale length variation can predict schizophrenia
Authors: Toh Christopher , Brody James P. 
Published: September 2021

AbstractStudies indicate that schizophrenia has a genetic component, however it cannot be isolated to a single gene. We aimed to determine how well one could predict that a person will develop schizophrenia based on their germ line genetics. We compared 1129 people from the UK Biobank dataset who had a diagnosis of schizophrenia to an equal number of age matched people drawn from the general UK Biobank population. For each person, we constructed a profile consisting of numbers. Each number characterized the length of segments of chromosomes. We tested several machine learning algorithms to determine which was most effective in predicting schizophrenia and if any improvement in prediction occurs by breaking the chromosomes into smaller chunks. We found that the stacked ensemble, performed best with an area under the receiver operating characteristic curve (AUC) of 0.545 (95% CI 0.539–0.550). We noted an increase in the AUC by breaking the chromosomes into smaller chunks for analysis. Using SHAP values, we identified the X chromosome as the most important contributor to the predictive model. We conclude that germ line chromosomal scale length variation data could provide an effective genetic risk score for schizophrenia which performs better than chance.
The importance of environmental microbes for Drosophila melanogaster during seasonal macronutrient variability
Authors: Davies Lucy Rebecca , Loeschcke Volker , Schou Mads F. , Schramm Andreas , Kristensen Torsten N. 
Published: September 2021

AbstractExperiments manipulating the nutritional environment and the associated microbiome of animals have demonstrated their importance for key fitness components. However, there is little information on how macronutrient composition and bacterial communities in natural food sources vary across seasons in nature and on how these factors affect the fitness components of insects. In this study, diet samples from an orchard compost heap, which is a natural habitat for many Drosophila species and other arthropods, were collected over 9 months covering all seasons in a temperate climate. We developed D. melanogaster on diet samples and investigated stress resistance and life-history traits as well as the microbial community of flies and compost. Nutrient and microbial community analysis of the diet samples showed marked differences in macronutrient composition and microbial community across seasons. However, except for the duration of development on these diet samples and Critical Thermal maximum, fly stress resistance and life-history traits were unaffected. The resulting differences in the fly microbial community were also more stable and less diverse than the microbial community of the diet samples. Our study suggests that when D. melanogaster are exposed to a vastly varying nutritional environment with a rich, diverse microbial community, the detrimental consequences of an unfavourable macronutrient composition are offset by the complex interactions between microbes and nutrients.
Interhemispheric asymmetry during NREM sleep in the dog
Authors: Reicher Vivien , Kis Anna , Simor Péter , Bódizs Róbert , Gácsi Márta 
Published: September 2021

AbstractFunctional hemispheric asymmetry was evidenced in many species during sleep. Dogs seem to show hemispheric asymmetry during wakefulness; however, their asymmetric neural activity during sleep was not yet explored. The present study investigated interhemispheric asymmetry in family dogs using non-invasive polysomnography. EEG recordings during 3-h-long afternoon naps were carried out (N = 19) on two occasions at the same location. Hemispheric asymmetry was assessed during NREM sleep, using bilateral EEG channels. To include periods with high homeostatic sleep pressure and to reduce the variance of the time spent in NREM sleep between dogs, the first two sleep cycles were analysed. Left hemispheric predominance of slow frequency range was detected in the first sleep cycle of sleep recording 1, compared to the baseline level of zero asymmetry as well as to the first sleep cycle of sleep recording 2. Regarding the strength of hemispheric asymmetry, we found greater absolute hemispheric asymmetry in the second sleep cycle of sleep recording 1 and 2 in the frequency ranges of alpha, sigma and beta, compared to the first sleep cycle. Differences between sleep recordings and consecutive sleep cycles might be indicative of adaptation-like processes, but do not closely resemble the results described in humans.