bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the chloroplast genome and phylogenetic evolution of three species of Syringa
Authors: Yang Chengjun , Wang Kai , Zhang Hang , Guan Qingjie , Shen Jian 
Published: November 2022

Abstract
Background
By the time our study was completed, the chloroplast genomes of Syringa oblata, S. pubescents subsp. Microphylla, and S. reticulate subsp. Amurensis had not been sequenced, and their genetic background was not clear.

The research content
In this study, the chloroplast genomes of Syringa oblata, S. pubescents subsp. Microphylla, S. reticulate subsp. Amurensis, and five other species of Syringa were sequenced for a comparative genomics analysis, inverted repeat (IR) boundary analysis, collinearity analysis, codon preference analysis and a nucleotide variability analysis. Differences in the complete chloroplast genomes of 30 species of Oleaceae were compared with that of S. oblata as the reference species, and Ginkgo biloba was used as the out group to construct the phylogenetic tree.

Results
The results showed that the chloroplast genomes of S. oblata, S. pubescents subsp. Microphylla, and S. reticulate subsp. Amurensis were similar to those of other angiosperms and showed a typical four-segment structure, with full lengths of 155,569, 160,491, 155,419, and protein codes of 88, 95, and 87, respectively. Because the IR boundary of S. pubescents subsp. Microphylla was significantly expanded to the large single copy (LSC) region, resulting in complete replication of some genes in the IR region, the LSC region of S. pubescents subsp. Microphylla was significantly shorter than those of S. oblate and S. reticulate subsp. Amurensis. Similar to most higher plants, these three species have a preference for their codons ending with A/T.

Conclusions
We consider the genus Syringa to be a synphyletic group. The nucleotide variability and phylogenetic analyses showed that Syringa differentiated before Ligustrum and Ligustrum developed from Syringa. We propose removing the existing section division and directly dividing Syringa into five series.
Breaking Landauer's bound in a spin-encoded quantum computer
Authors: Wang Frank Zhigang 
Published: November 2022

AbstractIt is commonly recognized that Landauer's bound holds in (irreversible) quantum measurement. In this study, we overturned this common sense by extracting a single spin from a spin–spin magnetic interaction experiment to demonstrate that Landauer’s bound can be broken quantitatively by a factor of $$10^{4} \sim 10^{10}$$

10
4

∼

10
10

via quantum spin tunneling. It is the quantum limit ($$\hbar /2 \approx 10^{ - 34} \;{\text{J}} \cdot {\text{s}}$$

ħ
/
2
≈

10

-
34

J
·
s

), rather than Landauer’s bound, that governs the performance of a spin qubit. An optically-manipulated spin-encoded quantum computer is designed, in which energy bound well below $$k_{B} T$$

k
B

T

to erase a spin qubit at the expense of a long spin relaxation time is theoretically sensible and experimentally verified. This work may represent the last piece of the puzzle in quantum Landauer erasure in terms of a single spin being the smallest and the closest to the quantum limit.
Co-occurrence of antibiotic and metal resistance in long-term sewage sludge-amended soils: influence of application rates and pedo-climatic conditions
Authors: Mokni-Tlili Sonia , Hechmi Sarra , Ouzari Hadda-Imene , Mechergui Najet , Ghorbel Manel , Jedidi Naceur , Hassen Abdennaceur , Hamdi Helmi 
Published: November 2022

AbstractUrban sewage sludge (USS) is increasingly being used as an alternative organic amendment in agriculture. Because USS originates mostly from human excreta, partially metabolized pharmaceuticals have also been considered in risk assessment studies after reuse. In this regard, we investigated the cumulative effect of five annual USS applications on the spread of antibiotic-resistant bacteria (ARB) and their subsequent resistance to toxic metals in two unvegetated soils. Eventually, USS contained bacterial strains resistant to all addressed antibiotics with indices of resistance varying between 0.25 for gentamicin to 38% for ampicillin and azithromycin. Sludge-amended soils showed also the emergence of resistome for all tested antibiotics compared to non-treated controls. In this regard, the increase of sludge dose generally correlated with ARB counts, while soil texture had no influence. On the other hand, the multi-antibiotic resistance (MAR) of 52 isolates selected from USS and different soil treatments was investigated for 10 most prescribed antibiotics. Nine isolates showed significant MAR index (≥ 0.3) and co-resistance to Cd, As and Be as well. However, events including an extreme flash flood and the termination of USS applications significantly disrupted ARB communities in all soil treatments. In any case, this study highlighted the risks of ARB spread in sludge-amended soils and a greater concern with the recent exacerbation of antibiotic overuse following COVID-19 outbreak.
Neither friend, nor device
Authors: Wassmer Marlene , Schwarzenegger Christian 
Published: November 2022

AbstractWith smart speakers diffusing into society, artificial intelligence is moving from the imaginative reservoirs of dystopian storytelling into vernacular living. How do users perceive communication with it? Are Alexa and Siri considered simple devices, sentient assistants, or even artificial friends? Based on nine qualitative interviews with former smart speaker users in Germany, this study analyzes smart speaker use and related personal epistemologies within a media repertoire perspective. By presenting six interrelated action-guiding principles explaining smart speaker use and people’s ambivalent sensemaking, we argue that smart speakers appear neither as friends nor as mere neutral devices to their users. The identified principles explain the peripheral role of smart speakers within media repertoires as handy but suspicious gimmicks. For future smart speaker adoption, whether smart assistants are interpreted as simple-minded, exploitative gimmicks or relevant, reliable, and trustworthy companions will be crucial.
Insight into the Neuroprotective Effect of Genistein-3′-Sodium Sulfonate Against Neonatal Hypoxic-Ischaemic Brain Injury in Rats by Bioinformatics
Authors: Xie Ting , Shuang Liyan , Liu Gaigai , Zhao Shanshan , Yuan Zhidong , Cai Hao , Jiang Lixia , Huang Zhihua 
Published: November 2022

Abstract
Therapeutic hypothermia (TH) is the only intervention approved for the treatment of neonatal hypoxic-ischaemic encephalopathy (HIE), but its treatment window is narrow (within 6 h after birth), and its efficacy is not ideal. Thus, alternative treatments are urgently needed. Our previous studies showed that genistein-3′-sodium sulfonate (GSS), a derivative of genistein (Gen), has a strong neuroprotective effect in rats with ischaemic stroke, but its role in HIE is unclear. A hypoxia–ischaemia (HI) brain injury model was established in neonatal male Sprague‒Dawley (SD) rats. Twenty-four hours after reperfusion, rats treated with GSS were assessed for cerebral infarction, neurological function, and neuronal damage. RNA-Seq and bioinformatics analysis were used to explore differentially expressed genes (DEGs) and regulated signalling pathways, which were subsequently validated by Western blotting and immunofluorescence. In this study, we found that GSS not only significantly reduced the size of brain infarcts and alleviated nerve damage in rats with HIE but also inhibited neuronal loss and degeneration in neonatal rats with HIE. A total of 2170 DEGs, of which 1102 were upregulated and 1068 were downregulated, were identified in the GSS group compared with the HI group. In an analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) categories, the downregulated DEGs were significantly enriched in the pathways “Phagosome”, “NF-κB signalling”, and “Complement and coagulation cascades”, amongst others. Meanwhile, the upregulated DEGs were significantly enriched in the pathways “Neurodegeneration”, “Glutamatergic synapse”, and “Calcium signalling pathway”, amongst others. These results indicate that GSS intervenes in the process of HIE-induced brain injury by participating in multiple pathways, which suggests potential candidate drugs for the treatment of HIE.
Graphical Abstract
In silico and in vitro analysis of the impact of single substitutions within EXO-motifs on Hsa-MiR-1246 intercellular transfer in breast cancer cell
Authors: Rybarczyk Agnieszka , Lehmann Tomasz , Iwańczyk-Skalska Ewa , Juzwa Wojciech , Pławski Andrzej , Kopciuch Kamil , Blazewicz Jacek , Jagodziński Paweł P. 
Published: November 2022

AbstractMiR-1246 has recently gained much attention and many studies have shown its oncogenic role in colorectal, breast, lung, and ovarian cancers. However, miR-1246 processing, stability, and mechanisms directing miR-1246 into neighbor cells remain still unclear. In this study, we aimed to determine the role of single-nucleotide substitutions within short exosome sorting motifs — so-called EXO-motifs: GGAG and GCAG present in miR-1246 sequence on its intracellular stability and extracellular transfer. We applied in silico methods such as 2D and 3D structure analysis and modeling of protein interactions. We also performed in vitro validation through the transfection of fluorescently labeled miRNA to MDA-MB-231 cells, which we analyzed by flow cytometry and fluorescent microscopy. Our results suggest that nucleotides alterations that disturbed miR-1246 EXO-motifs were able to modulate miRNA-1246 stability and its transfer level to the neighboring cells, suggesting that the molecular mechanism of RNA stability and intercellular transfer can be closely related.
Molecular background of Leber congenital amaurosis in a Polish cohort of patients—novel variants discovered by NGS
Authors: Skorczyk-Werner Anna , Sowińska-Seidler Anna , Wawrocka Anna , Walczak-Sztulpa Joanna , Krawczyński Maciej Robert 
Published: November 2022

AbstractLeber congenital amaurosis (LCA) is the most severe form of inherited retinal dystrophies and the most frequent cause of congenital blindness in children. To date, 25 genes have been implicated in the pathogenesis of this rare disorder. Performing an accurate molecular diagnosis is crucial as gene therapy is becoming available. This study aimed to report the molecular basis of Leber congenital amaurosis, especially novel and rare variants in 27 Polish families with a clinical diagnosis of LCA fully confirmed by molecular analyses. Whole exome sequencing or targeted next-generation sequencing (NGS) of inherited retinal dystrophies-associated (IRD) genes was applied to identify potentially pathogenic variants. Bidirectional Sanger sequencing and quantitative PCR (qPCR) were carried out for validation and segregation analysis of the variants identified within the families. We identified 28 potentially pathogenic variants, including 11 novel, in 8 LCA genes: CEP290, CRB1, GUCY2D, NMNAT1, RPGRIP1, CRX, LRAT1, and LCA5. This study expands the mutational spectrum of the LCA genes. Moreover, these results, together with the conclusions from our previous studies, allow us to point to the most frequently mutated genes and variants in the Polish cohort of LCA patients.
Pre-service teachers' use of ICT to collaborate to complete assessment tasks
Authors: Slater Eileen V. , Barwood Donna , Cordery Zina 
Published: November 2022

AbstractThis research explored the use of ICT products by n = 123 pre-service teachers to complete collaborative assessments. Students responded to a questionnaire relating to the use, benefits and limitations, and what would better enable the use of ICT for collaborative assessment purposes. The ICT products favoured by students did not support some key elements necessary for online collaboration, through either student use or product functionality. Poor Internet access was a commonly cited limitation with the effect of reducing access to available ICT skills training. Suggestions for changes to course structure and content and further research are made.
Effective practices during emergency school lockdowns: shared experiences of four Australian schools
Authors: Kearney M. , Schuck S. , Fergusson J. , Perry R. 
Published: November 2022

AbstractThis study investigates common features of a set of diverse schools’ responses to the initial school lockdown period during the pandemic in 2020, with a focus on practices supporting learning, inclusion and wellbeing. It comprises a collective case study of four Australian schools that were selected based on their reputation for impactful support of students and teachers during the emergency remote teaching period. Methods included interviews and focus groups with school leaders, teachers and students. The schools had widely differing contexts, technology access and student needs. Despite these varied contexts, the findings provided important insights into common practices supporting effective remote teaching. Emerging principles of effective practice illuminate ways forward to mitigate the significant risks accompanying emergency remote teaching, and guide practices in a variety of school contexts.
Immunocompromised Patients with Protracted COVID-19: a Review of “Long Persisters”
Authors: Dioverti Veronica , Salto-Alejandre Sonsoles , Haidar Ghady 
Published: November 2022

Abstract

Purpose of Review
Certain immunocompromised individuals are at risk for protracted COVID-19, in which SARS-CoV-2 leads to a chronic viral infection. However, the pathogenesis, diagnosis, and management of this phenomenon remain ill-defined.

Recent Findings
Herein, we review key aspects of protracted SARS-CoV-2 infection in immunocompromised individuals, or the so-called long persisters, and describe the clinical presentation, risk factors, diagnosis, and treatment modalities of this condition, as well as intra-host viral evolution. Based on the available data, we also propose a framework of criteria with which to approach this syndrome.

Summary
Protracted COVID-19 is an uncharacterized syndrome affecting patients with B-cell depletion; our proposed diagnostic approach and definitions will inform much needed future research.
A Tattoo on my Brain
Authors: Gibbs Daniel , Barker Teresa H. 
Published: November 2022

Dr Daniel Gibbs is one of 50 million people worldwide with an Alzheimer's disease diagnosis. Unlike most patients with Alzheimer's, however, Dr Gibbs worked as a neurologist for twenty-five years, caring for patients with the very disease now affecting him. Also unusual is that Dr Gibbs had begun to suspect he had Alzheimer's several years before any official diagnosis could be made. Forewarned by genetic testing showing he carried alleles that increased the risk of developing the disease, he noticed symptoms of mild cognitive impairment long before any tests would have alerted him. In this highly personal account, Dr Gibbs documents the effect his diagnosis has had on his life and explains his advocacy for improving early recognition of Alzheimer's. Weaving clinical knowledge from decades caring for dementia patients with his personal experience of the disease, this is an optimistic tale of one man's journey with early-stage Alzheimer's disease. Soon to be a documentary film on MTV/Paramount +.
New insight into the tectonic setting of fault-bounded Indian Gondwana coal basins from U–Pb detrital zircon provenance ages of the Bokaro and Jharia basins, central east India
Authors: Jeffrey Laura Leigh , Beukes Nicolas , Vorster Clarisa , Mukhopadhyay Joydip 
Published: November 2022

AbstractA detrital zircon U–Pb laser ablation–inductively coupled plasma–quadrupole mass spectrometry (LA-ICP-QMS) provenance study was undertaken on samples selected from the Lower Gondwana successions preserved in the fault-bounded Bokaro and Jharia basins in India to investigate the provenance of the sediment and determine whether the strata were deposited in isolated syn-depositional graben basins or formed part of a wider regional depositional system. A total of 730 concordant U–Pb detrital zircon ages revealed six distinct age fractions: (i) a latest Neoproterozoic to earliest Cambrian age fraction (530 to 510 Ma), which tails down in some samples to older Neoproterozoic ages (650 to 630 Ma); (ii) a major age fraction with an age peak of earliest Neoproterozoic (950 Ma), accompanied in some samples by a twin Mesoproterozoic peak (1000 Ma); (iii) a middle Mesoproterozoic age fraction (1330 to 1300 Ma); (iv) a prominent earliest Mesoproterozoic zircon age fraction (1600 Ma); (v) a less well-defined late Palaeoproterozoic zircon age fraction (2100 to 1700 Ma, or 1600 Ma); and (vi) an Archaean zircon age fraction that typically comprises two zircon age fractions, namely zircons with early Neoarchaean ages (2800 to 2750 Ma) coupled with zircons with ages older than 3100 Ma. Comparison of these newly obtained age fractions with detrital zircon age data presented by Veevers & Saeed (2009) shows similarities with the Gondwana strata of the Mahanadi and Pranhita–Godavari basins, implying that strata preserved in the fault-bounded Gondwana basins in central east India formed part of a much wider regional depositional system and that they were not deposited in isolated half-graben or graben basins. Potential source regions to the Gondwana strata of the Bokaro and Jharia basins include the Eastern Ghats Mobile Belt and rock units in Antarctica.
Seminal quality comparison of first and second cryopreserved ejaculates of Alpine kid goats by flow cytometry
Authors: Novaes Marco Aurélio Schiavo , Almeida Palloma Porto , Souza Netto Domingos Lollobrigida de , de Carvalho Victor Hugo Rabelo , Lovatti João Vitor Ribeiro , da Silveira Joana Diniz , Leite Giulia Berzoini Costa , Torres Ciro Alexandre Alves 
Published: November 2022

SummaryDiscarding the first ejaculate is recommended as an alternative for improving seminal quality after long sexual resting, especially when semen should be used for cryopreservation. However, when the males are not in sexual resting the necessity to discarding the first ejaculate is still unknown. Therefore, this study aimed to compare by flow cytometry the quality of the first and second ejaculates. Ten kids and uniform goats between 5 and 6 months of age were used in a completely randomized design. Semen collection was carried out every 4 days, until a total of five ejaculates per animal in each treatment was completed. The fresh and frozen semen collected were processed and analyzed using macroscopic and microscopic parameters, resistance test, hypo-osmotic medium test, and flow cytometry (FC). The FC parameters were production of reactive oxygen species, plasma and acrosomal membrane integrity, and lipid peroxidation of the plasma membrane. The ejaculates did not differ for the resistance test, the reactivity in the hypo-osmotic medium and for the macroscopic and microscopic seminal parameters, except for sperm volume and concentration. The first ejaculate had a higher percentage of minor and total defects. None of the FC parameters analyzed differed between the first and second ejaculates. The first and second ejaculates demonstrated similar seminal qualities, so for Alpine kid goats without a sexual resting period, discarding the first ejaculate it is not recommended.
Coseismic Folding During Ramp Failure at the Front of the Sulaiman Fold‐and‐Thrust Belt
Authors: Javed Muhammad Tahir , Barbot Sylvain , Javed Farhan , Ali Aamir , Braitenberg Carla 
Published: November 2022

AbstractThe Sulaiman Fold Thrust (SFT) in Central Pakistan formed during the India‐Eurasia collision in the late Cenozoic. However, the mechanics of shortening of the brittle crust at time scales of seismic cycles is still poorly understood. Here, we use radar interferometry to analyze the deformation associated with the 2015 magnitude (Mw) 5.7 Dajal blind earthquake at the eastern boundary of the SFT. We use kinematic inversions to determine the distribution of slip on the frontal ramp and of flexural slip along active axial surfaces for the forward‐ and backward‐verging two end‐member models: a double fault‐bend‐fold system and a fault‐propagation‐fold. In both models, a décollement branches into a shallow ramp at approximately 7.5 km depth with coseismic folding in the hanging wall. The Dajal earthquake ruptured the base of the Boundary Thrust buried under the sediment from the Indus‐River floodplain, representing fault‐bend or fault‐propagation folding some 30 km off its nearest surface exposure.
Investigating the Role of Amazonian Mesoscale Wind Patterns and Strength on the Spatial Distribution of Martian Bedrock Exposures
Authors: Gary‐Bicas C. E. , Michaels T. I. , Rogers A. D. , Fenton L. K. , Warner N. H. , Cowart A. C. 
Published: November 2022

AbstractThe Martian highlands contain Noachian‐aged areally‐extensive (>225 km2) bedrock exposures that have been mapped using thermal and visible imaging datasets. Given their age, crater density and impact gardening should have led to the formation of decameter scale layers of regolith that would overlie and bury these outcrops if composed of competent materials like basaltic lavas. However, many of these regions lack thick regolith layers and show clear exposures of bedrock materials with elevated thermal inertia values compared to the global average. Hypothesized reasons for the lack of regolith include: (a) relatively weaker material properties than lavas, where friable materials are comminuted and deflated during wind erosion, (b) long‐term protection from regolith development through burial and later exhumation through one or more surface processes, and (c) spatially concentrated aeolian erosion and wind energetics on well‐lithified basaltic substrates. To test the third hypothesis, we used the Mars Regional Atmospheric Modeling System to calculate wind erosive strength at 10 regions throughout the Martian highlands and compared it to their thermophysical properties by using thermal infrared data derived from the Thermal Emission Spectrometer to understand the effect that Amazonian mesoscale wind patterns may have on the exposure of bedrock. We also investigated the effect of planet obliquity, Ls of perihelion, and atmospheric mean pressure on wind erosion potential. We found no evidence for increased aeolian activity over bedrock‐containing regions relative to surrounding terrains, including at the mafic floor unit at Jezero crater (Máaz formation), supporting the first or second hypotheses for these regions.
Leveraging the CYGNSS Spaceborne GNSS‐R Observations to Detect Ionospheric Irregularities Over the Oceans: Method and Verification
Authors: Ren Xiaodong , Liu Hang , Mei Dengkui , Yang Pengxin , Zhang Zhiyu , Freeshah Mohamed , Zhang Xiaohong 
Published: November 2022

AbstractThe Global Navigation Satellite System (GNSS) has significantly facilitated the detection of ionospheric irregularities. Nevertheless, the ground‐based GNSS stations are inhomogeneously distributed around the world with large gaps, especially in the vast ocean regions. This adversely affects the interpretation of the spatio‐temporal variation characteristics of the ionospheric irregularities. In this study, ionospheric irregularities over the regions of the equatorial, and low‐latitude ocean during a G4‐class strong geomagnetic storm were investigated by utilizing the spaceborne GNSS reflectometry (GNSS‐R) technique. We derived and validated the ionospheric regularities index S4R from the signal‐to‐noise ratio measurements of the spaceborne GNSS‐R. Meanwhile, we utilized the ionospheric irregularities data from ground‐based (GNSS and ionosonde) and space‐based (Swarm and FORMOSAT‐3/COSMIC) instruments to evaluate and analyze the CYGNSS‐derived S4R. All comparisons and validations conducted within this study illustrate that the spaceborne GNSS‐R measurements provide complementary data and realize the timely observation as well as confirmation of the ionospheric irregularities at the same location over the oceans. It is expected to benefit the application of spaceborne GNSS‐R in ionospheric irregularities monitoring and applications over the ocean area.