bluuebunny/crossref_metadata_2025_split huggingface dataset:
A revised SNP-based barcoding scheme for typing
Mycobacterium tuberculosis
complex isolates
Authors: Shitikov Egor , Bespiatykh Dmitry 
Published: June 2023

ABSTRACT

The development of whole-genome sequencing technologies is gradually leading to a more detailed description of the population structure of the
Mycobacterium tuberculosis
complex (MTBC). In this study, we correlated previously published classifications on a collection of more than 10,000 genomes and proposed a new, comprehensive nomenclature that unifies the existing ones. In total, we identified 169 lineages and sublineages of
M. tuberculosis
/
M. africanum
and 9 animal-adapted species. For the purpose of organizing these genotypes in a more streamlined manner, we stratified them into five hierarchical levels. To represent the classification and compare it with the reference, we compiled a confirmatory data set of 670 high-quality isolates, which includes all genotypes and species of MTBC, and this confirmatory data set can serve as a basis for further studies. We proposed a set of 213 robust barcoding single-nucleotide polymorphisms and a suitable workflow for reliable differentiation of genotypes and species within the complex. This work integrates the results of all the major systematized studies to date to provide an understanding of the global diversity of the MTBC population structure. The results of this work may ultimately help to reliably determine the pathogen genotype and associate it with traits that reflect its prevalence, virulence, vaccination, and treatment efficiency, as well as to reliably find natural features revealed during its spread.

IMPORTANCE

Through years of research into the
Mycobacterium tuberculosis
complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes.
Recent Data of Multidisciplinary Studies of the Major Pleistocene Climatic Events: Glaciations, Formation of Ice-Dammed Lakes, and Their Catastrophic Drainage in Altai (Mountains of Southern Siberia)
Authors: Agatova A. R. , Nepop R. K. , Moska P. , Nikitenko B. L. , Bronnikova M. A. , Zhdanova A. N. , Zazovskaya E. P. , Karpukhina N. V. , Kuzmina O. B. , Nepop A. R. , Ovchinnikov I. Yu. , Petrozhitskiy A. V. , Uspenskaya O. N. 
Published: June 2023

Abstract
The use of geological–geomorphological and geochronological (14C, OSL) methods allowed establishing that the bordering mountains of the Chuya basin (Russian Altai) were affected by glaciation as early as the Middle Pleistocene, about 160–180 ka (MIS 6). However, the ice-dammed lake with the highest (up to 2100 m a.s.l.) strandlines in the Chuya and Kurai basins existed later than 90–80 ka, i.e., in the Late Pleistocene. This chronological benchmark limits the influence of the catastrophic outburst floods of the largest lakes on the accumulation of the Inya formation in the Chuya and Katun river valleys. It is confirmed that a large ice-dammed lake existed and had a water level of at least 1730 m a.s.l. in MIS 2 in the Kurai basin. The lake drained no later than 16 ka. Synchronously (about 17–16 ka) the accumulation of diluvial–lacustrine cyclites began in the Inya mouth. It was found that the accumulation of the Saldzhar formation in the Katun River valley between the mouths of the Chuya and Sema rivers was long-lasting during the entire MIS 2 not only as a result of flood events, but also due to gradual hydrological processes. It is necessary to revise the concept adopted by SibRISC in 2018. This concept assumes (i) the absence of ice-dammed lakes in intermont basins of Russian Altai in MIS 2 and (ii) the accumulation of the Inya and Saldzhar catafluvial formations, as well as the high and medium terraces they deposited in the valleys of the Chuya and Katun rivers before 90 ka.
Caryochroite, a Rare Mineral from the Titanosilicate Group: Crystal Structure, Crystal Chemistry, and Thermal Properties
Authors: Soboleva S. V. , Boeva N. M. , Kartashov P. M. , Bortnikov N. S. 
Published: June 2023

Abstract
The crystal structure of the rare mineral caryochroite is determined for the first time using X-ray diffractometry and electron microdiffraction data. The new idealized crystal formula of the mineral is [Na(Sr0.5Ca0.5)Mg]3[Fe$$_{8}^{{3 + }}$$Mn($${\text{Fe}}_{{0.5}}^{{2 + }}{{\square }_{{0.5}}}$$)]10(Ti2Si12)O37(OH)14(Н2О)3. The parameters of the monoclinic unit cell refined by the least square method are a 16.550(3), b 5.281(2), c 24.25(3) Å, β 93.0°, Z = 2, space group P2/n. The crystal structure of caryochroite is a new type of Ti–Si lattice responsible for the large structural channels, which are able to enclose the exchange cations and a high amount of water components (OH groups and H2O molecules).
Trend and Phasing of Carbonate Accumulation in the History of the Earth
Authors: Kuznetsov V. G. 
Published: June 2023

Abstract
In the geological history of the Earth, there has been a significant change in the composition and areas of carbonate accumulation, which reflects the general evolution of the formation of carbonate deposits, paleogeographic and geochemical settings, and different stages of this evolution. At the Archean–Proterozoic boundary, acidic conditions in water reservoirs changed to moderately acidic, which resulted in the appearance of iron carbonates. The second milestone is the Siderian–Rhyacian boundary, when intensive assimilation of CO2 led to the development of alkaline conditions in water reservoirs and the accumulation of Mg carbonates. Carbonate accumulation itself occurred in the inland water reservoirs. The third milestone is the Vendian–Cambrian boundary, when skeletal fauna appeared, and carbonate accumulation became largely biogenic. Along with the basins of the continental block, there appeared new oceanic areas of carbonate accumulation, where the skeletons of nekton organisms became a significant supplier of material. The fourth milestone—the Paleozoic–Mesozoic—was the beginning of the accumulation of the proper oceanic deep-water carbonate sediments. The fifth milestone is associated with the Cretaceous period, when oceanic carbonate accumulation sharply increased due to accumulation of planktonic organisms.
A Tectonic Scheme for the Amerasia Basin of the Arctic Ocean
Authors: Chernykh A. A. , Yakovenko I. V. , Kaminskiy V. D. , Glebovskiy V. Yu. , Korneva M. S. , Bashev I. A. 
Published: June 2023

Abstract
A tectonic scheme of the Amerasia Basin was created for the first time on a 1 : 2 500 000 scale on the basis of integrated analysis of geological and geophysical data. The structural framework of the scheme was developed according to the mapping of the basement surface using reflection seismic sections; the surface was detailed on the basis of potential fields. The results of three-dimensional gravity modeling according to calculation of the Moho depths and consolidated earth crust thickness were used as the basic indicators of the origin of the crust. Tectonic elements of different ranks and kinematics were identified on the seismic sections and traced according to the potential fields. The created scheme is the most detailed out of those published previously. It demonstrates the features of the tectonic structure of individual geostructures and their nature and allows us to draw conclusions about the evolution of the Amerasia Basin.
Can we do better? A qualitative study in the East of England investigating patient experience and acceptability of using the faecal immunochemical test in primary care
Authors: Snudden Claudia M , Calanzani Natalia , Archer Stephanie , Honey Stephanie , Pannebakker Merel M , Faher Anissa , Chang Aina , Hamilton Willie , Walter Fiona M 
Published: June 2023

ObjectivesThe faecal immunochemical test (FIT) is increasingly used in UK primary care to triage patients presenting with symptoms and at different levels of colorectal cancer risk. Evidence is scarce on patients’ views of using FIT in this context. We aimed to explore patients’ care experience and acceptability of using FIT in primary care.DesignA qualitative semi-structured interview study. Interviews were conducted via Zoom between April and October 2020. Transcribed recordings were analysed using framework analysis.SettingEast of England general practices.ParticipantsConsenting patients (aged ≥40 years) who presented in primary care with possible symptoms of colorectal cancer, and for whom a FIT was requested, were recruited to the FIT-East study. Participants were purposively sampled for this qualitative substudy based on age, gender and FIT result.Results44 participants were interviewed with a mean age 61 years, and 25 (57%) being men: 8 (18%) received a positive FIT result. Three themes and seven subthemes were identified. Participants’ familiarity with similar tests and perceived risk of cancer influenced test experience and acceptability. All participants were happy to do the FIT themselves and to recommend it to others. Most participants reported that the test was straightforward, although some considered it may be a challenge to others. However, test explanation by healthcare professionals was often limited. Furthermore, while some participants received their results quickly, many did not receive them at all with the common assumption that ‘no news is good news’. For those with a negative result and persisting symptoms, there was uncertainty about any next steps.ConclusionsWhile FIT is acceptable to patients, elements of communication with patients by the healthcare system show potential for improvement. We suggest possible ways to improve the FIT experience, particularly regarding communication about the test and its results.
Pericoronary adipose tissue density is increased in patients with recent spontaneous coronary dissection
Authors: Wolny Rafał R , Kwieciński Jacek , Zalewska Joanna , Michałowska Ilona , Kruk Mariusz , Kepka Cezary , Prejbisz Aleksander , Pręgowski Jerzy , Chwała Alicja , Skowroński Jarosław , Kobierska Agata , Ciesielski Radosław , Januszewicz Andrzej , Witkowski Adam , Adlam David , Dey Damini , Kądziela Jacek 
Published: June 2023

ObjectiveInflammatory activity is one of the potential mechanisms of spontaneous coronary artery dissection (SCAD). Recently, the pericoronary adipose tissue attenuation (PCAT) derived from CT angiography (CTA) has been established as a method for measuring vascular inflammation. We aimed to characterise the pancoronary and vessel-specific PCAT in patients with and without recent SCAD.MethodsThe study comprised patients with SCAD referred to a tertiary centre between 2017 and 2022 who underwent CTA and were compared with individuals with no prior SCAD. PCAT was analysed on end-diastolic CTA reconstructions along proximal 40 mm of all major coronary vessels as well as the SCAD-related vessel. We analysed 48 patients with recent SCAD (median 6.1 (IQR 3.5–14.9) months since SCAD, 95.8% female) and 48 patients in the group without SCAD.ResultsPancoronary PCAT was higher in patients with SCAD compared with those without SCAD (−80.6±7.9 vs −85.3 HU±6.1, p=0.002). Vessel-specific PCAT in patients with SCAD compared with patients without SCAD was higher for both the RCA (−80.9±9.5 vs −87.1±6.9 HU, p=0.001) and the LCA (−80.3±7.8 vs −83.4±7.2 HU, p=0.04). In patients with SCAD, PCAT of the SCAD-related vessel was not significantly different from averaged PCAT of unaffected vessels (−81.2±9.2 vs −80.6±7.6, p=0.74). There was no association between PCAT and the interval from SCAD to CTA.ConclusionsPatients with recent SCAD have higher PCAT compared with patients without SCAD, suggesting an increased perivascular inflammatory activity. This association is not restricted to the dissected vessel.
2,5-dimethylcelecoxib alleviated NK and T-cell exhaustion in hepatocellular carcinoma via the gastrointestinal microbiota-AMPK-mTOR axis
Authors: Pan Banglun , Chen Zhanfei , Zhang Xiaoxia , Wang Zengbin , Yao Yuxin , Wu Xiaoxuan , Qiu Jiacheng , Lin Hua , Yu Liumin , Tu Haijian , Tang Nanhong 
Published: June 2023

Background2,5-dimethylcelecoxib (DMC), a derivative of celecoxib, is an inhibitor of microsomal prostaglandin E synthase-1 (mPGES-1). Our previous studies have demonstrated that DMC inhibits the expression of programmed death-ligand 1 on hepatocellular carcinoma (HCC) cells to prevent tumor progression. However, the effect and mechanism of DMC on HCC infiltrating immune cells remain unclear.MethodsIn this study, single-cell-based high-dimensional mass cytometry was performed on the tumor microenvironment of HCC mice treated with DMC, celecoxib and MK-886 (a known mPGES-1 inhibitor). Moreover, 16S ribosomal RNA sequencing was employed to analyze how DMC improved the tumor microenvironment of HCC by remodeling the gastrointestinal microflora.ResultsWe found that (1) DMC significantly inhibited the growth of HCC and improved the prognosis of the mice, and this depended on the stronger antitumor activity of natural killer (NK) and T cells; (2) compared with celecoxib and MK-886, DMC significantly enhanced the cytotoxic and stem-like potential, and inhibited exhaustion of NK and T cells; (3) mechanistically, DMC inhibited the expression of programmed cell death protein-1 and upregulated interferon-γ expression of NK and T cells via the gastrointestinal microbiota (Bacteroides acidifaciens, Odoribacter laneus, and Odoribacter splanchnicus)-AMPK-mTOR axis.ConclusionsOur study uncovers the role of DMC in improving the tumor microenvironment of HCC, which not only enriches the relationship between the mPGES-1/prostaglandin E2 pathway and the antitumor function of NK and T cells, but also provide an important strategic reference for multitarget or combined immunotherapy of HCC.Cite Now
Dominant negative variants inIKZF2cause ICHAD syndrome, a new disorder characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay
Authors: Mohajeri Arezoo , Vaseghi-Shanjani Maryam , Rosenfeld Jill A , Yang Gui Xiang , Lu Henry , Sharma Mehul , Lin Susan , Salman Areesha , Waqas Meriam , Sababi Azamian Mahshid , Worley Kim C , Del Bel Kate L , Kozak Frederick K , Rahmanian Ronak , Biggs Catherine M , Hildebrand Kyla J , Lalani Seema R , Nicholas Sarah K , Scott Daryl A , Mostafavi Sara , van Karnebeek Clara , Henkelman Erika , Halparin Jessica , Yang Connie L , Armstrong Linlea ,   Undiagnosed Diseases Network,   Care4Rare Canada Consortium, Turvey Stuart E , Lehman Anna 
Published: June 2023

BackgroundHelios (encoded byIKZF2), a member of the Ikaros family of transcription factors, is a zinc finger protein involved in embryogenesis and immune function. Although predominantly recognised for its role in the development and function of T lymphocytes, particularly the CD4+regulatory T cells (Tregs), the expression and function of Helios extends beyond the immune system. During embryogenesis, Helios is expressed in a wide range of tissues, making genetic variants that disrupt the function of Helios strong candidates for causing widespread immune-related and developmental abnormalities in humans.MethodsWe performed detailed phenotypic, genomic and functional investigations on two unrelated individuals with a phenotype of immune dysregulation combined with syndromic features including craniofacial differences, sensorineural hearing loss and congenital abnormalities.ResultsGenome sequencing revealedde novoheterozygous variants that alter the critical DNA-binding zinc fingers (ZFs) of Helios. Proband 1 had a tandem duplication of ZFs 2 and 3 in the DNA-binding domain of Helios (p.Gly136_Ser191dup) and Proband 2 had a missense variant impacting one of the key residues for specific base recognition and DNA interaction in ZF2 of Helios (p.Gly153Arg). Functional studies confirmed that both these variant proteins are expressed and that they interfere with the ability of the wild-type Helios protein to perform its canonical function—repressingIL2transcription activity—in a dominant negative manner.ConclusionThis study is the first to describe dominant negativeIKZF2variants. These variants cause a novel genetic syndrome characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay.
Antithrombin III levels in critically ill surgical patients: do they correlate with VTE?
Authors: Bhatti Umar F , Dhillon Navpreet K , Mason Russell , Wang Andrew , Hashim Yassar M , Barmparas Galinos , Ley Eric J 
Published: June 2023

ObjectiveAntithrombin III (ATIII) deficiency may result from hereditary or acquired reduction in ATIII levels and is associated with an increase in venous thromboembolism (VTE) in the general population. VTE is a potentially preventable complication in the critically ill surgical patients. The objective of this study was to evaluate the relation between ATIII levels and VTE in surgical intensive care unit (SICU) patients.MethodsAll patients admitted to the SICU from January 2017 to April 2018 who had ATIII levels drawn were included in the study. An ATIII level below 80% of normal was considered low. The rate of VTE during the same admission was compared among patients with normal and low levels of ATIII. Prolonged length of stay (LOS >10 days) and mortality were also measured.ResultsOf the 227 patients included, 59.9% were male. The median age was 60 years. Overall, 66.9% of patients had low ATIII levels. Trauma patients had a higher rate of normal ATIII levels, whereas those weighing more than 100 kg had a higher rate of low ATIII levels. Patients with low ATIII levels had higher VTE rates compared with those with normal ATIII levels (28.9% vs. 16%, p=0.04). Patients with low ATIII levels also had prolonged LOS (76.3% vs. 60%, p=0.01) and increased mortality (21.7% vs. 6.7%, p<0.01). Trauma patients with VTE were more likely to have normal ATIII levels (38.5% in low ATIII cohort vs. 61.5% VTE in normal ATIII cohort, p<0.01).ConclusionCritically ill surgical patients with low ATIII levels have higher incidence of VTE, longer LOS, and higher mortality. In contrast, critically ill trauma patients may have high incidence of VTE even with normal ATIII levels.Level of evidenceIII.
Evaluating seedbank stimulants for wild oat and volunteer cereal management on the Canadian Prairies
Authors: Sharpe Shaun M. , Kaye Taylor , Tidemann Breanne D. 
Published: June 2023

Wild oat is a widespread threat to annual crop production on the Canadian Prairies. Infestations are difficult to manage due to a persistent seedbank, complex dormancy, a long emergence window, herbicide resistance, and seed shatter corresponding to crop harvest timings. The study objective was to evaluate the efficacy of potassium nitrate (KNO3) and pyroligneous acid for promoting germination and emergence of wild oat and volunteer wheat, barley, and oat. A total of 24 repeated experiments were conducted using freshly produced seeds to ensure adequate endodormancy. Wheat and barley demonstrated no endodormancy following seed formation and rapidly emerged with moisture. All species imbibed but did not germinate in Petri dishes within pyroligneous acid solutions of 5%–100%. Dormancy release was observed within 0.1% and 1% pyroligneous acid solutions. KNO3 did not stimulate germination or emergence for any species and was inhibitory at 125 kg N ha−1. Pyroligneous acid increased wild oat emergence with 50% and 100% solutions applied at 200 L ha−1 in the first study and with 10% solutions in the second study. Emergence inhibition was noted for oat, barley, and wheat with pyroligneous acid applications. This research further confirms that pyroligneous acid may stimulate wild oat emergence and confirms activity on freshly matured seed.
Accessing compton form factors at the electron ion collider in China: an impact study on $${\textbf {Im}} {\mathcal E}$$
Authors: Cao Xu , Zhang Jinlong 
Published: June 2023

AbstractWe estimate the impact of asymmetry measurements of Deeply Virtual Compton Scattering (DVCS) with transversely polarized proton beam taken at a future Electron Ion Collider in China (EicC) on the extraction of Compton Form Factors (CFFs). The CFFs extracted from an analysis based on artificial neural-network approach are reweighted by means of pseudo-data generated in the expected kinematic region of EicC. We find a remarkable improvement in the extraction of CFF $$Im {\mathcal E}$$

I
m
E

, especially at the range of parton momentum fraction $$x \sim $$

x
∼

0.01, thus hinting for a future experimental probe of the parton orbital angular momentum. This work casts a glance at a practical implementation of Bayesian reweighting method on CFFs’ impact study.
Imprints of Casimir wormhole in Einstein Gauss–Bonnet gravity with non-vanishing complexity factor
Authors: Zubair M. , Farooq Mushayydha 
Published: June 2023

AbstractThis article investigates Casimir wormhole solutions in Einstein Gauss–Bonnet (EGB) gravity. We are familiar that Null energy conditions (NEC) need not be satisfied for a stable wormhole due to the existence of exotic matter. As the Casimir effect acts as a negative energy source, it can be treated as a classical applicant for the exotic matter to discuss the stable dynamics of the wormhole. This work explores the Casimir effects with the Generalized Uncertainty Principle (GUP) on wormhole geometry in EGB gravity by confining our results for $$D=5$$

D
=
5

. We have examined two GUP procedures, e.g., Kempf, Mangano, Mann (KMM) and Dentournay, Gabriel, and Spindel (DGS). We have developed shape functions for Casimir wormholes, and GUP corrected Casimir wormholes and studied their existence. In addition, we investigate the behavior of the Gauss–Bonnet (GB) Coupled parameter and minimal uncertainty (MU) parameter on the Equation of state (EOS) parameter. The active gravitational mass and embedding diagrams for all developed shape functions are analysed. Moreover, the violation of the NEC by an exotic matter, the equilibrium forces, and the complexity factor of Casimir wormholes and GUP-corrected Casimir wormholes have also been explored.
Small Circles of Empowerment
Authors: Bocheńska Joanna , Hamelink Wendelmoet , Salih Kaziwa , Keskin Hüseyin Rodi 
Published: June 2023

Abstract
This article investigates the activities of Kurdish women aimed at protecting and revitalising Kurdish language, which include collecting and publishing folklore, translating into Kurdish, and writing literature in Kurdish. Throughout the 20th century, countries like Turkey, Syria, Iran, and Iraq, in varying degrees, imposed restrictions on the use of Kurdish. Our primary focus is on Turkey because this country has been most repressive toward Kurdish language since the establishment of the Republic in 1923, but also due to a recent increased visibility of women language activists and folklore collectors. According to Fishman, language revitalisation does not only pertain to caring for a language but brings about a complete, self-defining way of life. Through language revitalisation, Kurdish women not only build an alternative to the state policy of denial, they also win respect and freedom within their communities. Drawing from Martha Nussbaum’s capability approach and from Sara Ahmed’s understanding of how emotions function through language and its circulation, we demonstrate how collecting and publishing Kurdish language and culture in ‘small circles’ enables Kurdish women to assert their citizenship rights.