bluuebunny/crossref_metadata_2025 huggingface dataset:
Stability investigation of Eu3+ doped CaF2 thin film with ZnO coating under electron beam irradiation
Authors: Abdallah R. A. A. , Kroon R. E. , Coetsee E. , Hasabeldaim E. H. H. , Swart H. C.
Published: March 2024

Eu3+ ion doped CaF2 thin film was successfully prepared using the hydrothermal method and coated by a spin coating technique. A thin layer of ZnO was deposited on the Eu3+ doped CaF2 thin film by pulsed laser technique. Incorporation of the dopant into the CaF2 crystal was confirmed by x-ray powder diffraction and x-ray photoelectron spectroscopy (XPS). Excitation of the film at 227 nm produced the characteristic emissions of Eu3+ ions. The stability of the film under electron beam bombard was studied using Auger electron spectroscopy, cathodoluminescence (CL), and XPS. The CL and Auger peak-to-peak heights (APPHs) data were collected concurrently using the same electron beam. The APPH of Ca and O increased, while that of F decreased, which indicated the conversion of CaF2 to CaO. The CL emission decreased initially during degradation and stabilized beyond 48 C/cm2 for the film with the ZnO coating. XPS analysis also indicated the dissociation of the fluoride compounds and subsequent formation of oxide compounds such as CaO and EuO after electron beam degradation.
Relativistic acceleration in noninertial frames of a line of objects
Authors: Dobson Chris
Published: March 2024

A general solution to the problem of relativistic acceleration of point objects in the noninertial frame of any of the objects is given in one spatial dimension. The objects are initially at rest in a common inertial frame and accelerate until they are at rest in a second inertial frame. The starting time and position of each object, the acceleration rate of each object, and the number of objects are arbitrary. The solution gives the position and velocity of each object in the noninertial frame of the host object, and the proper time of each, as functions of the proper time of the host. The method is based on system states for a pair of objects, and it is found that there are nine series of states which cover all cases, including those in which objects are separated from the host by its Rindler horizon. The familiar problems of acceleration of an elastic rod and a (Born) rigid rod are treated, and a number of examples are given of spaceflight sequences for multiple craft in tandem.
Experimentation on stochastic trajectories: From Brownian motion to inertial confined dynamics
Authors: Brigante Azul María , Révora Corina , Volonnino Gabriel Fernando , Perez Marcos Damián , Pasquini Gabriela , Capeluto María Gabriela
Published: March 2024

Statistical physics courses typically employ abstract language that describes objects too small to be seen, making the topic challenging for students to understand. In this work, we introduce a simple experiment that allows conceptualizing some of the underlying ideas of stochastic processes through direct experimentation. Students analyze stochastic trajectories of beads in a bouncing bed of smaller beads subjected to an external periodic drive. The analysis of the trajectories involves the application of a vast toolkit of statistical estimators that are useful in many fields of physics.
Employing an operator form of the Rodrigues formula to calculate wavefunctions without differential equations
Authors: Noonan Joseph R. , Shah Maaz ur Rehman , Xu Luogen , Freericks James K.
Published: March 2024

The factorization method of Schrödinger shows us how to determine the energy eigenstates without needing to determine the wavefunctions in position or momentum space. A strategy to convert the energy eigenstates to wavefunctions is well known for the one-dimensional simple harmonic oscillator by employing the Rodrigues formula for the Hermite polynomials in position or momentum space. In this work, we illustrate how to generalize this approach in a representation-independent fashion to find the wavefunctions of other problems in quantum mechanics that can be solved by the factorization method. We examine three problems in detail: (i) the one-dimensional simple harmonic oscillator; (ii) the three-dimensional isotropic harmonic oscillator; and (iii) the three-dimensional Coulomb problem. This approach can be used in either undergraduate or graduate classes in quantum mechanics.
Molecular rheology of nanoconfined oligomer melts
Authors: Yıldırım A. B. , Erbaş A. , Biancofiore L.
Published: March 2024

We use nonequilibrium atomistic molecular dynamics simulations of unentangled melts of linear and star oligomer chains (C25H52) to study the steady-state viscoelastic response under confinement within nanoscale hematite (α−Fe2O3) channels. We report (i) the negative (positive) first (second) normal stress difference and (ii) the presence of viscoelastic tension at low Wi. With the aim of uncovering the molecular mechanism of viscoelasticity, we link these effects to bond alignment such that absorbed chains near the surface can carry the elastic force exerted on the walls, which decays as the chains become more aligned in the flow direction. This alignment is observed to be independent of the film thickness but enhanced as the shear rate increases or the surface attraction weakens.
Structure and function of the
Arabidopsis
ABC transporter ABCB19 in brassinosteroid export
Authors: Ying Wei , Wang Yaowei , Wei Hong , Luo Yongming , Ma Qian , Zhu Heyuan , Janssens Hilde , Vukašinović Nemanja , Kvasnica Miroslav , Winne Johan M. , Gao Yongxiang , Tan Shutang , Friml Jiří , Liu Xin , Russinova Eugenia , Sun Linfeng
Published: March 2024

Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In
Arabidopsis thaliana
, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.
A milder reaction to feed the world
Authors: Rupprechter Günther
Published: March 2024

Surface science defies the complexity of ammonia synthesis
Johannes Zaanen (1957–2024)
Authors: Phillips Philip W.
Published: March 2024

Oracle of condensed matter physics
Can quantum tech give telescopes sharper vision?
Authors: Clery Daniel
Published: March 2024

Quantum memories and networks could help combine light from widely separated mirrors
A novel hybridization capture method for direct whole genome sequencing of clinical specimens to inform Legionnaires’ disease investigations
Authors: Weeber Phillip , Singh Navjot , Lapierre Pascal , Mingle Lisa , Wroblewski Danielle , Nazarian Elizabeth J. , Haas Wolfgang , Weiss Don , Musser Kimberlee A.
Published: March 2024

The unprecedented precision and resolution of whole genome sequencing (WGS) can provide definitive identification of infectious agents for epidemiological outbreak tracking. WGS approaches, however, are frequently impeded by low pathogen DNA recovery from available primary specimens or unculturable samples. A cost-effective hybrid capture assay for
Legionella pneumophila
WGS analysis directly on primary specimens was developed. DNA from a diverse range of sputum and autopsy specimens PCR-positive for
L. pneumophila
serogroup 1 (LPSG1) was enriched with this method, and WGS was performed. All tested specimens were determined to be enriched for
Legionella
reads (up to 209,000-fold), significantly improving the discriminatory power to compare relatedness when no clinical isolate was available. We found the WGS data from some enriched specimens to differ by less than five single-nucleotide polymorphisms (SNPs) when compared to the WGS data of a matched culture isolate. This testing and analysis retrospectively provided previously unconfirmed links to environmental sources for clinical specimens of sputum and autopsy lung tissue. The latter provided the additional information needed to identify the source of these culture-negative cases associated with the South Bronx 2015 Legionnaires’ disease (LD) investigation in New York City. This new method provides a proof of concept for future direct clinical specimen hybrid capture enrichment combined with WGS and bioinformatic analysis during outbreak investigations.

IMPORTANCE

Legionnaires’ disease (LD) is a severe and potentially fatal type of pneumonia primarily caused by inhalation of
Legionella
-contaminated aerosols from man-made water or cooling systems. LD remains extremely underdiagnosed as it is an uncommon form of pneumonia and relies on clinicians including it in the differential and requesting specialized testing. Additionally, it is challenging to obtain clinical lower respiratory specimens from cases with LD, and when available, culture requires specialized media and growth conditions, which are not available in all microbiology laboratories. In the current study, a method for
Legionella pneumophila
using hybrid capture by RNA baiting was developed, which allowed us to generate sufficient genome resolution from
L. pneumophila
serogroup 1 PCR-positive clinical specimens. This new approach offers an additional tool for surveillance of future LD outbreaks where isolation of
Legionella
is not possible and may help solve previously unanswered questions from past LD investigations.
Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression
Authors: Fijalkowski Igor , Snauwaert Valdes , Van Damme Petra
Published: March 2024

In recent years, it has become evident that the true complexity of bacterial proteomes remains underestimated. Gene annotation tools are known to propagate biases and overlook certain classes of truly expressed proteins, particularly proteoforms—protein isoforms arising from a single gene. Recent (re-)annotation efforts heavily rely on ribosome profiling by providing a direct readout of translation to fully describe bacterial proteomes. In this study, we employ a robust riboproteogenomic pipeline to conduct a systematic census of expressed N-terminal proteoform pairs, representing two isoforms encoded by a single gene raised by annotated and alternative translation initiation, in
Salmonella
. Intriguingly, conditional-dependent changes in relative utilization of annotated and alternative translation initiation sites (TIS) were observed in several cases. This suggests that TIS selection is subject to regulatory control, adding yet another layer of complexity to our understanding of bacterial proteomes.

IMPORTANCE

With the emerging theme of genes within genes comprising the existence of alternative open reading frames (ORFs) generated by translation initiation at in-frame start codons, mechanisms that control the relative utilization of annotated and alternative TIS need to be unraveled and our molecular understanding of resulting proteoforms broadened. Utilizing complementary ribosome profiling strategies to map ORF boundaries, we uncovered dual-encoding ORFs generated by in-frame TIS usage in
Salmonella
. Besides demonstrating that alternative TIS usage may generate proteoforms with different characteristics, such as differential localization and specialized function, quantitative aspects of conditional retapamulin-assisted ribosome profiling (Ribo-RET) translation initiation maps offer unprecedented insights into the relative utilization of annotated and alternative TIS, enabling the exploration of gene regulatory mechanisms that control TIS usage and, consequently, the translation of N-terminal proteoform pairs.
Host-derived protease promotes aggregation of
Staphylococcus aureus
by cleaving the surface protein SasG
Authors: Crosby Heidi A. , Keim Klara , Kwiecinski Jakub M. , Langouët-Astrié Christophe J. , Oshima Kaori , LaRivière Wells B. , Schmidt Eric P. , Horswill Alexander R.
Published: March 2024

Staphylococcus aureus
is one of the leading causes of hospital-acquired infections, many of which begin following attachment and accumulation on indwelling medical devices or diseased tissue. These infections are often linked to the establishment of biofilms, but another often overlooked key characteristic allowing
S. aureus
to establish persistent infection is the formation of planktonic aggregates. Such aggregates are physiologically similar to biofilms and protect pathogens from innate immune clearance and increase antibiotic tolerance. The cell-wall-associated protein SasG has been implicated in biofilm formation via mechanisms of intercellular aggregation but the mechanism in the context of disease is largely unknown. We have previously shown that the expression of cell-wall-anchored proteins involved in biofilm formation is controlled by the ArlRS-MgrA regulatory cascade. In this work, we demonstrate that the ArlRS two-component system controls aggregation, by repressing the expression of
sasG
by activation of the global regulator MgrA. We also demonstrate that SasG must be proteolytically processed by a non-staphylococcal protease to induce aggregation and that strains expressing functional full-length
sasG
aggregate significantly upon proteolysis by a mucosal-derived host protease found in human saliva. We used fractionation and N-terminal sequencing to demonstrate that human trypsin within saliva cleaves within the A domain of SasG to expose the B domain and induce aggregation. Finally, we demonstrated that SasG is involved in virulence during mouse lung infection. Together, our data point to SasG, its processing by host proteases, and SasG-driven aggregation as important elements of
S. aureus
adaptation to the host environment.

IMPORTANCE

Here, we demonstrate that the
Staphylococcus aureus
surface protein SasG is important for cell-cell aggregation in the presence of host proteases. We show that the ArlRS two-component regulatory system controls SasG levels through the cytoplasmic regulator MgrA. We identified human trypsin as the dominant protease triggering SasG-dependent aggregation and demonstrated that SasG is important for
S. aureus
lung infection. The discovery that host proteases can induce
S. aureus
aggregation contributes to our understanding of how this pathogen establishes persistent infections. The observations in this study demonstrate the need to strengthen our knowledge of
S. aureus
surface adhesin function and processing, regulation of adhesin expression, and the mechanisms that promote biofilm formation to develop strategies for preventing chronic infections.
The role of host traits and geography in shaping the gut microbiome of insectivorous bats
Authors: Dai Wentao , Leng Haixia , Li Jun , Li Aoqiang , Li Zhongle , Zhu Yue , Li Xiaolin , Jin Longru , Sun Keping , Feng Jiang
Published: March 2024

The gut microbiome is a symbiotic microbial community associated with the host and plays multiple important roles in host physiology, nutrition, and health. A number of factors have been shown to influence the gut microbiome, among which diet is considered to be one of the most important; however, the relationship between diet composition and gut microbiota in wild mammals is still not well recognized. Herein, we characterized the gut microbiota of bats and examined the effects of diet, host taxa, body size, gender, elevation, and latitude on the gut microbiota. The cytochrome C oxidase subunit I (COI) gene and 16S rRNA gene amplicons were sequenced from the feces of eight insectivorous bat species in southern China, including
Miniopterus fuliginosus
,
Aselliscus stoliczkanus
,
Myotis laniger
,
Rhinolophus episcopus
,
Rhinolophus osgoodi
,
Rhinolophus ferrumequinum
,
Rhinolophus affinis,
and
Rhinolophus pusillus
. The results showed that the composition of gut microbiome and diet exhibited significant differences among bat species. Diet composition and gut microbiota were significantly correlated at the order, family, genus, and operational taxonomic unit levels, while certain insects had a marked effect on the gut microbiome at specific taxonomic levels. In addition, elevation, latitude, body weight of bats, and host species had significant effects on the gut microbiome, but phylosymbiosis between host phylogeny and gut microbiome was lacking. These findings clarify the relationship between gut microbiome and diet and contribute to improving our understanding of host ecology and the evolution of the gut microbiome in wild mammals.

IMPORTANCE

The gut microbiome is critical for the adaptation of wildlife to the dynamic environment. Bats are the second-largest group of mammals with short intestinal tract, yet their gut microbiome is still poorly studied. Herein, we explored the relationships between gut microbiome and food composition, host taxa, body size, gender, elevation, and latitude. We found a significant association between diet composition and gut microbiome in insectivorous bats, with certain insect species having major impacts on gut microbiome. Factors like species taxa, body weight, elevation, and latitude also affected the gut microbiome, but we failed to detect phylosymbiosis between the host phylogeny and the gut microbiome. Overall, our study presents novel insights into how multiple factors shape the bat’s gut microbiome together and provides a study case on host-microbe interactions in wildlife.
Inoculation with
Stutzerimonas stutzeri
strains decreases N₂O emissions from vegetable soil by altering microbial community composition and diversity
Authors: Gao Nan , Zhang Huanhuan , Hu Chun , Li Qing , Li Linmei , Lei Peng , Xu Hong , Shen Weishou
Published: March 2024

Inoculation with plant growth-promoting rhizobacteria (PGPR) strains has promoted plant growth and decreased nitrous oxide (N₂O) emissions from agricultural soils simultaneously. However, limited PGPR strains can mitigate N₂O emissions from agricultural soils, and the microbial ecological mechanisms underlying N₂O mitigation after inoculation are poorly understood. In greenhouse pot experiments, the effects of inoculation with
Stutzerimonas stutzeri
NRCB010 and NRCB025 on tomato growth and N₂O emissions were investigated in two vegetable agricultural soils with contrasting textures. Inoculation with NRCB010 and NRCB025 significantly promoted tomato growth in both soils. Moreover, inoculation with NRCB010 decreased the N₂O emissions from the fine- and coarse-textured soils by 38.7% and 52.2%, respectively, and inoculation with NRCB025 decreased the N₂O emissions from the coarse-textured soil by 76.6%. Inoculation with NRCB010 and NRCB025 decreased N₂O emissions mainly by altering soil microbial community composition and the abundance of nitrogen-cycle functional genes. The N₂O-mitigating effect might be partially explained by a decrease in the (
amoA + amoB
)/(
nosZ
I +
nosZ
II) and (
nirS + nirK
)/(
nosZ
I +
nosZ
II) ratios, respectively. Soil pH and organic matter were key variables that explain the variation in abundance of N-cycle functional genes and subsequent N₂O emission. Moreover, the N₂O-mitigating effect varied depending on soil textures and individual strain after inoculation. This study provides insights into developing biofertilizers with plant growth-promoting and N₂O-mitigating effects.

IMPORTANCE

Plant growth-promoting rhizobacteria (PGPR) have been applied to mitigate nitrous oxide (N₂O) emissions from agricultural soils, but the microbial ecological mechanisms underlying N₂O mitigation are poorly understood. That is why only limited PGPR strains can mitigate N₂O emissions from agricultural soils. Therefore, it is of substantial significance to reveal soil ecological mechanisms of PGPR strains to achieve efficient and reliable N₂O-mitigating effect after inoculation. Inoculation with
Stutzerimonas stutzeri
strains decreased N₂O emissions from two soils with contrasting textures probably by altering soil microbial community composition and gene abundance involved in nitrification and denitrification. Our findings provide detailed insight into soil ecological mechanisms of PGPR strains to mitigate N₂O emissions from vegetable agricultural soils.
First report of multidrug-resistant carbapenemase-producing
Aeromonas caviae
co-harboring
mcr-3.43
and
mcr-7.2
Authors: Xu Tingting , Song Jingjie , Liu Jialong , Huang Lili , Li Zhao , Zhou Kai
Published: March 2024

Hospital sewage serves as a crucial reservoir for antibiotic resistance genes. As colistin and carbapenems are the last-resort antibiotics, the emergence of their resistance genes has become a significant concern in clinical settings. In this study, we found that two novel
mcr
alleles (
mcr-3
.43 and
mcr-7
.2) with two carbapenemase genes (
bla
NDM-1
and
bla
KPC-2
) were encoded in a single
Aeromonas caviae
strain isolated from hospital sewage. Our phylogenetic analysis revealed that the
mcr-3.43
gene clustered with
mcr-3.17
(with 95.55% amino acid identity), while the
mcr-7.2
gene clustered with
mcr-7.1
(with 68.68% amino acid identity). BLAST search against GenBank showed that
mcr-7.2
was exclusively detected in
Aeromonas
spp. Mobile genetic elements were not found in the genetic context of
mcr-7.2
, suggesting that the dissemination of
mcr-7.2
in
Aeromonas
spp. may be dependent on vertical transfer or recombination. The
bla
NDM-1
was adjacent to a recombinase gene and flanked by two IS
91
elements, indicating a potential mobilization mechanism mediated by recombination and/or ISs. The
bla
KPC-2
gene was located on an IncU plasmid and adjacent to an IS
Kpn6
. In summary, our study provides evidence for
Aeromonas
spp. as one of the potential reservoirs of colistin and carbapenem resistance genes.

IMPORTANCE

The study discovered two novel
mcr
genes (
mcr-3.43
and
mcr-7.2
) and two carbapenemase genes (
bla
NDM-1
and
bla
KPC-2
) in a single
Aeromonas caviae
strain retrieved from hospital sewage. Using phylogenetic analysis and comparative data evaluation, the study revealed the genetic relatedness and dissemination potential of the detected resistance genes. With the exclusive discovery that
mcr-7.2
is only present in
Aeromonas
spp. and the lack of mobile genetic elements in its genetic context, there is a strong indication of limited dissemination. The identification of these four resistance genes in a single strain of
Aeromonas
provided valuable insights into their potential presence in this genus. This study revealed that hospital sewage functions as a significant reservoir for antibiotic resistance genes, including colistin and carbapenem resistance genes.
Broad host range phages target global
Clostridium perfringens
bacterial strains and clear infection in five-strain model systems
Authors: Thanki Anisha M. , Osei Emmanuel K. , Whenham Natasha , Salter Michael G. , Bedford Mike R. , Masey O’Neill Helen V. , Clokie Martha R. J.
Published: March 2024

Clostridium perfringens
is a prevalent bacterial pathogen in poultry, and due to the spread of antimicrobial resistance, alternative treatments are needed to prevent and treat infection. Bacteriophages (phages), viruses that kill bacteria, offer a viable option and can be used therapeutically to treat
C. perfringens
infections. The aim of this study was to isolate phages against
C. perfringens
strains currently circulating on farms across the world and establish their virulence and development potential using host range screening, virulence assays, and larva infection studies. We isolated 32 phages of which 19 lysed 80%–92% of our global
C. perfringens
poultry strain collection (
n
= 97). The virulence of these individual phages and 32 different phage combinations was quantified in liquid culture at multiple doses. We then developed a multi-strain
C. perfringens
larva infection model, to mimic an effective poultry model used by the industry. We tested the efficacy of 16/32 phage cocktails in the larva model. From this, we identified that our phage cocktail consisting of phages CPLM2, CPLM15, and CPLS41 was the most effective at reducing
C. perfringens
colonization in infected larvae when administered before bacterial challenge. These data suggest that phages do have significant potential to prevent and treat
C. perfringens
infection in poultry.

IMPORTANCE

Clostridium perfringens
causes foodborne illness worldwide, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry,
C. perfringens
infection causes necrotic enteritis, and associated mortality rates can be up to 50%. However, treating infections is difficult as the bacterium is becoming antibiotic-resistant. Furthermore, the poultry industry is striving toward reduced antibiotic usage. Bacteriophages (phages) offer a promising alternative, and to progress this approach, robust suitable phages and laboratory models that mimic
C. perfringens
infections in poultry are required. In our study, we isolated phages targeting
C. perfringens
and found that many lyse
C. perfringens
strains isolated from chickens worldwide. Consistent with other published studies, in the model systems we assayed here, when some phages were combined as cocktails, the infection was cleared most effectively compared to individual phage use.
Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum
Authors: Blais Marie-Amélie , Vincent Warwick F. , Vigneron Adrien , Labarre Aurélie , Matveev Alex , Coelho Lígia Fonseca , Lovejoy Connie
Published: March 2024

Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22–3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.

IMPORTANCE

Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.
Oman as a fragment of Ediacaran eastern Gondwana
Authors: Gómez-Pérez Irene , Morton Andrew , Rawahi Hussam Al , Frei Dirk
Published: March 2024

Comprehensive U-Pb detrital zircon geochronology of Ediacaran sandstones from Oman indicates that they originated from Neoproterozoic basement with a peak magmatic age of ca. 850–780 Ma (Tonian), with lesser Paleoproterozoic and Ediacaran sources and renewed magmatic input starting at ca. 550 Ma. Comparison with detrital zircons from the Arabian-Nubian and NW Indian Shields supports an eastern Gondwana affinity for the Ediacaran succession of Oman. Tonian basement sediment sources are present in Oman. Sources for older Paleoproterozoic zircons (ca. 2500 and 1800 Ma) are not found in Oman but are known from the cratonic Indian Shield. The signal of the main magmatic events of the juvenile Arabian-Nubian Shield, peaking at ca. 640–620 Ma, is rare or absent in the Ediacaran rock succession of Oman. However, deformed Ediacaran clastic units with an Arabian-Nubian Shield affinity occur in western Oman. Influx of latest Ediacaran–early Cambrian zircons (550–525 Ma) is interpreted as due to final Cambrian Angudan/Malagasy orogeny-related magmatism.

These results, together with new ages for volcano-sedimentary terranes in the subsurface of SW Oman and seismic observations, support the interpretation that the Ediacaran succession of Oman was deposited along the western, passive margin of the Greater Indian Shield, on the eastern (east and west in this paper refer to present-day coordinates) side of the Mozambique Ocean. Oman then collided with the Arabian-Nubian Shield in the early Cambrian, when the Angudan/Malagasy orogeny led to final consolidation of Gondwana. Our data support the inference that the youngest and final suture between the Indian and Arabian Shields lies in the subsurface of Oman along the early Cambrian western deformation front.
Disconformity-controlled hydrothermal dolomitization and cementation during basin evolution: Upper Triassic carbonates, UAE
Authors: Mansurbeg H. , Alsuwaidi M. , Morad D. , Morad S. , Tiepolo M. , Shahrokhi S. , Al-Aasm I.S. , Koyi H.
Published: March 2024

Petrography, fluid-inclusion microthermometry, stable isotope analyses, and radiometric (206Pb/238U) dating of Upper Triassic dolostones, saddle dolomite, and quartz and calcite cements were used to constrain the timing and conditions of dolomitization and cementation in the context of the tectonic evolution of a basin in the northern United Arab Emirates. Dolomitization (ca. 152.4 Ma) and precipitation of saddle dolomite (ca. 146.8 Ma), calcite (ca. 144.6 Ma), and quartz cements are attributed to focused synrifting flow of hot basinal brines into grain-supported limestones in which permeability was enhanced by incursion of meteoric waters beneath a disconformity surface. Another calcite cement generation (ca. 99.7 Ma) was formed by flow of hot brines during tectonic compression related to the obduction of Oman ophiolites in the Late Cretaceous. Thus, this paper provides new insights into (1) stratigraphic controls on and timing of hydrothermal (hot basinal brines) dolomitization, (2) the origin of closely associated intraformational limestones and dolostones, and (3) linkages between diagenesis and thermochemical modifications of basinal brines during tectonic evolution of sedimentary basins.
Nasogastric tube placement perforating the nasopharynx causing mediastinal passage and feeding into the pleural space
Authors: Zafran Muhammad , Crook Rebecca , Tuck Alexander , Banerjee Atmadeep
Published: March 2024

A mid-60s female with known primary progressive multiple sclerosis was admitted to our hospital with aspiration pneumonia. Due to reduced consciousness, a nasogastric (NG) tube was inserted for feeding. A chest x-ray (CXR) report from a thoracic radiologist confirmed an atypical tip position due to a hiatus hernia but concluded it was almost certainly within the stomach. However, after deteriorating on feed commencement, a CT scan of the chest confirmed the tube had perforated the nasopharynx and run parallel to the oesophagus through the mediastinum into the right pleural space. The patient subsequently developed an empyema and pneumothorax, requiring multiple therapeutic interventions and a prolonged hospital stay. This case demonstrates how the routine insertion of an NG tube can lead to serious complications. Additionally, position check CXRs can be difficult to interpret, so the decision to use the tube must be made cautiously by the clinical team.
Ewing sarcoma of the cervix: an unusual site of presentation
Authors: Hernández-García Jesús Guillermo , Pinto García Luis José , Marché Fernández Osvaldo Alexis , Diaz-Garcia Juan Daniel
Published: March 2024

Ewing sarcoma is an exceedingly rare form of cancer that affects the cervix. It falls within the spectrum of neoplastic diseases known as Ewing’s family of tumours, typically observed in osseous tissues. A woman in her 40s, experiencing symptoms of leucorrhoea and transvaginal bleeding that commenced 3 months before her consultation, was referred to our gynaecological oncology clinic with a preliminary diagnosis of ovarian teratoma. A colposcopy procedure was conducted unveiling a complete loss of cervical anatomy with friable and malodorous tissue. Pelvic ultrasound identified a lesion of uncertain origin in the cervix, suggestive of malignancy. Histopathological assessment of cervical biopsy specimens confirmed the presence of a small, round, blue cell neoplasm consistent with Ewing sarcoma. She underwent chemotherapy and pelvic radiotherapy, achieving complete remission 9 months after diagnosis, without experiencing any systemic adverse effects or sequelae.
Gestational alloimmune liver disease with alpha thalassaemia in a neonate
Authors: Banait Nishant , Varanasi Sai Vamshi , Nayak Abinash , Talukder Kushal
Published: March 2024

A term baby presented with cholestatic jaundice since birth. She was diagnosed as gestational alloimmune liver disease-neonatal haemochromatosis (GALD-NH) on evaluation. The baby received intravenous immunoglobulin (IVIG) and recovered gradually from the illness. She was also diagnosed with alpha thalassaemia during the course of evaluation, confirmed by genetic testing. NH is a very rare disorder that results in fetal loss or neonatal death due to liver failure. NH is now known to be a phenotypic expression of GALD. Worldwide, NH is seen in less than one in a million pregnancies. The mortality rate of GALD has traditionally been around 80% with almost all babies needing liver transplantation, with advent of maternal and neonatal IVIG treatment, this has reduced significantly. There is no reported case of GALD-NH treated successfully with IVIG from India. Here, we report an interesting case of GALD-NH with alpha thalassaemia.
Cardiac fibroma presenting as hypoplastic left heart syndrome in a foetus: causal or coincidental?
Authors: Sundari Abinaya , Gurusamy Umamaheshwari
Published: March 2024

Primary cardiac tumours are very rare. Cardiac tumours in the perinatal period are even more uncommon with a prevalence of 0.0017% to 0.28% in autopsy series. The majority of benign cardiac tumours are cardiac rhabdomyomas, followed by cardiac fibromas. Another rare congenital heart disease is hypoplastic left heart syndrome (HLHS). Here we present a 21-week-old foetus diagnosed antenatally with HLHS on foetal echocardiogram. An autopsy done on the foetus following medical termination of pregnancy revealed a cardiac fibroma in the ventricular septum. It is very uncommon to have a combination of two congenital heart diseases. An extensive literature review revealed only three cases that had rhabdomyoma and associated HLHS. This case presented with cardiac fibroma which in early gestation would have resulted in left ventricular outflow obstruction leading to the development of HLHS. Small cardiac tumours which are difficult to detect by echocardiogram in early gestation can lead to the development of HLHS. A thorough and hierarchical autopsy examination of such cases can help in a better understanding of the relationship between HLHS and cardiac tumours.
Hepatic veno-occlusive disease complicated with extreme hyperammonaemia (920 µmol/L) treated with defibrotide, lactulose, rifampin and haemodialysis
Authors: Kabat Maciej , Gill Sarvarinder , Kim Kevin , Omidvari Karan , Lee Robert
Published: March 2024

Hepatic veno-occlusive disease (VOD)/sinusoidal obstructive syndrome (SOS) is a severe complication that can occur following haematopoietic stem cell transplant (HSCT) with high-intensity conditioning chemotherapy regimens. Severe VOD/SOS, often characterised by multiorgan failure, is associated with a high mortality rate. This case report details the complex clinical course of a male patient in his mid-20s, recently diagnosed with B cell acute lymphoblastic leukaemia, who underwent allogeneic HSCT. Based on the 2023 European Society for Blood and Marrow Transplantation (EBMT) criteria, the patient developed very severe VOD/SOS, prompting immediate treatment with defibrotide. Unexpectedly, he developed profound hyperammonaemia exceeding 900 µmol/L, leading to encephalopathy and cerebral oedema. Despite aggressive interventions including defibrotide, lactulose, rifampin and haemodialysis, the patient passed away due to cerebral oedema and pulseless electrical activity arrest. We theorise the hyperammonaemia is disproportionate to his hepatic dysfunction and is possibly secondary to an acquired defect of the urea synthesis consistent with idiopathic hyperammonaemia, a rare complication in patients receiving intense conditioning chemotherapy.
Income disparities in loss in life expectancy after colon and rectal cancers: a Swedish register-based study
Authors: Syriopoulou Elisavet , Osterman Erik , Miething Alexander , Nordenvall Caroline , Andersson Therese Marie-Louise
Published: March 2024

Background

Differences in the prognosis after colorectal cancer (CRC) by socioeconomic position (SEP) have been reported previously; however, most studies focused on survival differences at a particular time since diagnosis. We quantified the lifetime impact of CRC and its variation by SEP, using individualised income to conceptualise SEP.

Methods

Data included all adults with a first-time diagnosis of colon or rectal cancers in Sweden between 2008 and 2021. The analysis was done separately for colon and rectal cancers using flexible parametric models. For each cancer and income group, we estimated the life expectancy in the absence of cancer, the life expectancy in the presence of cancer and the loss in life expectancy (LLE).

Results

We found large income disparities in life expectancy after a cancer diagnosis, with larger differences among the youngest patients. Higher income resulted in more years lost following a cancer diagnosis. For example, 40-year-old females with colon cancer lost 17.64 years if in the highest-income group and 13.68 years if in the lowest-income group. Rectal cancer resulted in higher LLE compared with colon cancer. Males lost a larger proportion of their lives. All patients, including the oldest, lost more than 30% of their remaining life expectancy. Based on the number of colon and rectal cancer diagnoses in 2021, colon cancer results in almost double the number of years lost compared with rectal cancer (24 669 and 12 105 years, respectively).

Conclusion

While our results should be interpreted in line with what individualised income represents, they highlight the need to address inequalities.
Inflammation biomarkers in the intracranial blood are associated with outcome in patients with ischemic stroke
Authors: Dargazanli Cyril , Blaquière Marine , Moynier Marinette , de Bock Frédéric , Labreuche Julien , ter Schiphorst Adrien , Derraz Imad , Radu Răzvan Alexandru , Gascou Gregory , Lefevre Pierre Henri , Rapido Francesca , Fendeleur Julien , Arquizan Caroline , Bourcier Romain , Marin Philippe , Machi Paolo , Cagnazzo Federico , Hirtz Christophe , Costalat Vincent , Marchi Nicola
Published: March 2024

Background

Performing endovascular treatment (EVT) in patients with acute ischemic stroke (AIS) allows a port of entry for intracranial biological sampling.

Objective

To test the hypothesis that specific immune players are molecular contributors to disease, outcome biomarkers, and potential targets for modifying AIS.

Methods

We examined 75 subjects presenting with large vessel occlusion of the anterior circulation and undergoing EVT. Intracranial blood samples were obtained by microcatheter aspiration, as positioned for stent deployment. Peripheral blood samples were collected from the femoral artery. Plasma samples were quality controlled by electrophoresis and analyzed using a Mesoscale multiplex for targeted inflammatory and vascular factors.

Results

We measured 37 protein biomarkers in our sample cohort. Through multivariate analysis, adjusted for age, intravenous thrombolysis, pretreatment National Institutes of Health Stroke Scale and Alberta Stroke Program Early CT scores, we found that post-clot blood levels of interleukin-6 (IL-6) were significantly correlated (adjusted P value <0.05) with disability assessed by the modified Rankin Scale (mRS) score at 90 days, with medium effect size. Chemokine (C-C) ligand 17 CCL17/TARC levels were inversely correlated with the mRS score. Examination of peripheral blood showed that these correlations did not reach statistical significance after correction. Intracranial biomarker IL-6 level was specifically associated with a lower likelihood of favorable outcome, defined as a mRS score of 0–2.

Conclusions

Our findings show a signature of blood inflammatory factors at the cerebrovascular occlusion site. The correlations between these acute-stage biomarkers and mRS score outcome support an avenue for add-on and localized immune modulatory strategies in AIS.
Identification of suspicious behavior through anomalies in the tracking data of fishing vessels
Authors: Rodríguez Jorge P. , Irigoien Xabier , Duarte Carlos M. , Eguíluz Víctor M.
Published: March 2024

Automated positioning devices can generate large datasets with information on the movement of humans, animals and objects, revealing patterns of movement, hot spots and overlaps among others. However, in the case of Automated Information Systems (AIS), attached to vessels, observed strange behaviors in the tracking datasets may come from intentional manipulation of the electronic devices. Thus, the analysis of anomalies can provide valuable information on suspicious behavior. Here, we analyze anomalies of fishing vessel trajectories obtained with the Automatic Identification System. The map of silent anomalies, those that occur when positioning data are absent for more than 24 hours, shows that they are most likely to occur closer to land, with 87.1% of anomalies observed within 100 km of the coast. This behavior suggests the potential of identifying silence anomalies as a proxy for illegal activities. With the increasing availability of high-resolution positioning of vessels and the development of powerful statistical analytical tools, we provide hints on the automatic detection of illegal activities that may help optimize the management of fishing resources.
Dynamical behavior of soliton solutions to the fractional phi-four model via two analytical techniques
Authors: Ahmad Jamshad , Younas Tayyaba
Published: March 2024

This study explores solutions for a mathematical equation called the time-space fractional phi-four equation using two methods: the Sardar-subequation method and the modified extended auxiliary equation method. The phi-four equation is connected to the Klein–Gordon model and is important in different scientific areas like biology and nuclear physics. Understanding its solutions is crucial. By using a specific wave transformation, the equation is changed into a simpler form for analysis. The methods proposed give a variety of solutions, such as Kink, bright singular, dark, combo dark bright, periodic, and singular periodic solutions. Each solution we find using these methods has specific rules that determine when it’s correct. We carefully choose specific values for the parameters to help us understand more about the solutions. This helps us see the detailed features of the solutions and improves our understanding of how the model behaves in the real world. These methods create a strong framework for studying solitons, which are specific types of mathematical solutions. The study compares the outcomes of these methods with earlier ones to get a complete understanding. Graphical illustrations are used to visually represent some of these solutions, helping us grasp their characteristics. Visual representations in two- and three-dimensional figures add originality to the findings. Importantly, these methods can be applied to solve similar problems with fractional derivatives in various scientific contexts. In summary, this research not only deepens our understanding of the phi-four equation but also introduces powerful methods with broad applications in fractional differential equations.
Impact of truncated M-fractional derivative on the new types of exact solitons to the (4+1)-dimensional DSKP model
Authors: Junjua Moin-ud-Din , Mostafa Almetwally M. , AlQahtani Nouf F. , Bekir Ahmet
Published: March 2024

This research explores different types of exact wave solitons of nonlinear (4+1)-dimensional Davey–Stewartson–Kadomtsev–Petviashvili (DSKP) model along truncated M-fractional by applying the Sardar sub-equation and generalized Kudryashov methods. This model describes the interactions among internal waves. This model is used to represent the nonlinear natural occurrence. The obtained results involve dark, singular, bright, periodic and other solitons. The gained results satisfy the concerned model and are represented by 2D, 3D and contour graphs. The gained results are not present in the literature due to the use of fractional derivative. Impacts of truncated M-fractional derivative on gained results are also represented by graphs. Hence, our gained results are fruitful in the future study for these models. Finally, we conclude that the applied techniques are simple, fruitful and reliable to solve the other models in mathematical physics.
Deep Residual Network and Wavelet Transform-Based Non-Local Means Filter for Denoising Low-Dose Computed Tomography
Authors: Sehgal Rashmita , Kaushik Vandana Dixit
Published: March 2024

Image denoising helps to strengthen the image statistics and the image processing scenario. Because of the inherent physical difficulties of various recording technologies, images are prone to the emergence of some noise during image acquisition. In the existing methods, poor illumination and atmospheric conditions affect the overall performance. To solve these issues, in this paper Political Taylor-Anti Coronavirus Optimization (Political Taylor-ACVO) algorithm is developed by integrating the features of Political Optimizer (PO) with Taylor series and Anti Coronavirus Optimization (ACVO). The input medical image is subjected to noisy pixel identification step, in which the deep residual network (DRN) is used to discover noise values and then pixel restoration process is performed by the created Political Taylor-ACVO algorithm. Thereafter image enhancement mechanism strategy is done using vectorial total variation (VTV) norm. On the other hand, original image is applied to discrete wavelet transform (DWT) such that transformed result is fed to non-local means (NLM) filter. An inverse discrete wavelet transform (IDWT) is utilized to the filtered outcome for generating the denoised image. Finally, image enhancement result is fused with denoised image computed through filtering model to compute fused output image. The proposed model observed the value for Peak signal-to-noise ratio (PSNR) of 29.167 dB, Second Derivative like Measure of Enhancement (SDME) of 41.02 dB, and Structural Similarity Index (SSIM) of 0.880 for Gaussian noise.