bluuebunny/crossref_metadata_2025 huggingface dataset:
PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides
Authors: Ramos-Llorens Marc , Bello-Madruga Roberto , Valle Javier , Andreu David , Torrent Marc
Published: June 2024

The alarming rise of antibiotic-resistant bacterial infections is driving efforts to develop alternatives to conventional antibiotics. In this context, antimicrobial peptides (AMPs) have emerged as promising candidates for their ability to target a broad range of microorganisms. However, the development of AMPs with optimal potency, selectivity, and/or stability profiles remains a challenge. To address it, computational tools for predicting AMP properties and designing novel peptides have gained increasing attention. PyAMPA is a novel platform for AMP discovery. It consists of five modules, namely AMPScreen, AMPValidate, AMPSolve, AMPMutate, and AMPOptimize, that allow high-throughput proteome inspection, candidate screening, and optimization through point-mutation and genetic algorithms. The platform also offers additional tools for predicting and evaluating AMP properties, including antimicrobial and cytotoxic activity, and peptide half-life. By providing innovative and accessible inroads into AMP motifs in proteomes, PyAMPA will enable advances in AMP development and potential translation into clinically useful molecules. PyAMPA is available at:
https://github.com/SysBioUAB/PyAMPA

IMPORTANCE

This paper introduces PyAMPA, a new bioinformatics platform designed for the discovery and optimization of antimicrobial peptides (AMPs). It addresses the urgent need for new antimicrobials due to the rise of antibiotic-resistant infections. PyAMPA, with its five predictive modules -AMPScreen, AMPValidate, AMPSolve, AMPMutate and AMPOptimize, enables high-throughput screening of proteomes to identify potential AMP motifs and optimize them for clinical use. Its unique approach, combining prediction, design, and optimization tools, makes PyAMPA a robust solution for developing new AMP-based therapies, offering a significant advance in combatting antibiotic resistance.
Comparative genomic analysis of an emerging Pseudomonadaceae member,
Thiopseudomonas alkaliphila
Authors: Burcham Zachary M.
Published: June 2024

Thiopseudomonas alkaliphila
, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how
T. alkaliphila
functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of
T. alkaliphila
includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in
T. alkaliphila
genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of
T. alkaliphila
, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.

IMPORTANCE

As the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact.
Thiopseudomonas alkaliphila
is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification,
T. alkaliphila
has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that
T. alkaliphila
is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting
T. alkaliphila
may operate as an undescribed opportunistic pathogen.
Resistance to ceftazidime–avibactam and other new β-lactams in
Pseudomonas aeruginosa
clinical isolates: a multi-center surveillance study
Authors: Valzano Felice , La Bella Gianfranco , Lopizzo Teresa , Curci Anna , Lupo Laura , Morelli Elisabetta , Mosca Adriana , Marangi Marianna , Melfitano Raffaela , Rollo Tiziana , De Nittis Rosella , Arena Fabio
Published: June 2024

New β-lactam–β-lactamase inhibitor combinations represent last-resort antibiotics to treat infections caused by multidrug-resistant
Pseudomonas aeruginosa
. Carbapenemase gene acquisition can limit their spectrum of activity, and reports of resistance toward these new molecules are increasing. In this multi-center study, we evaluated the prevalence of resistance to ceftazidime–avibactam (CZA) and comparators among
P. aeruginosa
clinical isolates from bloodstream infections, hospital-acquired or ventilator-associated pneumonia, and urinary tract infections, circulating in Southern Italy. We also investigated the clonality and content of relevant β-lactam resistance mechanisms of CZA-resistant (CZA
R
) isolates. A total of 120
P
.
aeruginosa
isolates were collected. CZA was among the most active β-lactams, retaining susceptibility in the 81.7% of cases, preceded by cefiderocol (95.8%) and followed by ceftolozane–tazobactam (79.2%), meropenem–vaborbactam (76.1%), imipenem–relebactam (75%), and aztreonam (69.6%). Among non-β-lactams, colistin and amikacin were active against 100% and 85.8% of isolates respectively. In CZA
R
strains subjected to whole-genome sequencing (
n
= 18), resistance was mainly due to the expression of metallo-β-lactamases (66.6% VIM-type and 5.5% FIM-1), followed by PER-1 (16.6%) and GES-1 (5.5%) extended-spectrum β-lactamases, mostly carried by international high-risk clones (ST111 and ST235). Of note, two strains producing the PER-1 enzyme were resistant to all β-lactams, including cefiderocol. In conclusion, the CZA resistance rate among
P. aeruginosa
clinical isolates in Southern Italy remained low. CZA
R
isolates were mostly metallo-β-lactamases producers and belonging to ST111 and ST253 epidemic clones. It is important to implement robust surveillance systems to monitor emergence of new resistance mechanisms and to limit the spread of
P. aeruginosa
high-risk clones.

IMPORTANCE

Multidrug-resistant
Pseudomonas aeruginosa
infections are a growing threat due to the limited therapeutic options available. Ceftazidime–avibactam (CZA) is among the last-resort antibiotics for the treatment of difficult-to-treat
P. aeruginosa
infections, although resistance due to the acquisition of transferable β-lactamase genes is increasing. With this work, we report that CZA represents a highly active antipseudomonal β-lactam compound (after cefiderocol), and that metallo-β-lactamases (VIM-type) and extended-spectrum β-lactamases (GES and PER-type) production is the major factor underlying CZA resistance in isolates from Southern Italian hospitals. In addition, we reported that such resistance mechanisms were mainly carried by the international high-risk clones ST111 and ST235.
High-pressure, low-temperature metamorphism preserved in the Indus-Yarlung suture zone of the eastern Himalaya: Overprinting at amphibolite facies and comparison with occurrences in the western Himalaya
Authors: Li Wangchao , Yin Changqing , Yakymchuk Chris , Ding Lin , Li Shun , Qian Jiahui , Gao Peng , Zhang Yanling
Published: June 2024

Eclogite and blueschist are important monitors of subduction zone processes and can record complex polymetamorphic histories during the protracted evolution of subduction systems. However, the rarity of such high-pressure, low-temperature metamorphic rocks in the Indus-Yarlung suture zone of the Himalaya hinders our understanding of the convergence of India and Asia. Here, we examine high-pressure, low-temperature metamorphic rocks from the Milin area of the eastern Indus-Yarlung suture zone. A comprehensive microtextural, mineral chemistry, and phase-equilibrium modeling investigation shows that low-temperature eclogite-facies metapelites with different parageneses (garnet-mica schists) experienced a cold subduction history along a low-thermal gradient, with peak pressures of ~1.6 GPa at ~550 °C. This represents an approximate thermal gradient of ~10 °C km−1. After peak pressure, these rocks underwent a two-step exhumation history with initial exhumation accompanying heating at ~590–600 °C and ~0.8–1.0 Gpa; this was followed by the second stage of exhumation to lower amphibolite-facies conditions. We interpret these low-temperature eclogite-facies metapelites to represent sedimentary rocks that overlaid Neo-Tethyan oceanic crust during subduction. Exhumation paths of high-pressure, low-temperature rocks in the eastern Indus-Yarlung suture zone include an amphibolite-facies overprint, which is absent from high-pressure, low-temperature rocks in the western Indus-Yarlung suture zone. This result is caused by the different timing of exhumation relative to the terminal collision of India and Asia.
Hydrological phenomena related to elevation head on the Arabian Plate
Authors: Stewart S.A.
Published: June 2024

Arabian Plate geology consists of exposed basement in the west overlain by a Phanerozoic sequence in the east that reaches 10 km in thickness and incorporates the Zagros fold-and-thrust belt on the northeast margin of the plate. The Phanerozoic wedge results from Neogene to Recent plate tilt and consequent uplift and erosion, exposing most of the Phanerozoic formations at outcrop, becoming progressively older from the east coast of Saudi Arabia, to the Arabian Shield at an altitude of ~900 m. Reservoirs in this Phanerozoic sequence that have top and base seals but are laterally extensive and open to the land surface have active hydrodynamics, with flow driven up to 1000 km northeastward into the basin by elevation head, discharging into the Arabian Gulf via topseal failures deep in the basin. Deep wells and seismic reflection data originally acquired for hydrocarbon exploration have been repurposed to investigate the basin-scale hydrogeology. This data has revealed previously undescribed phenomena including intra-reservoir haloclines separating fresh and saline water layers more than 1000 m below sea level, and quantified regional hydraulic gradients and an area of over 60,000 km2 where the vadose zone is up to 450 in thickness. Hydraulic gradients have been measured by wells at ~1 m/km in several different reservoirs.
The role of Fe(II)-silicate gel in the generation of Archean and Paleoproterozoic chert
Authors: Tostevin Rosalie , Sevgen Serhat
Published: June 2024

Chert is abundant in Archean and Paleoproterozoic rocks and is commonly densely packed with authigenic Fe(II)-silicate nanoparticles such as greenalite, indicating a close relationship between iron and silica deposition. We investigate the relationship between Fe(II)-silicate minerals and dissolved silica during precipitation, settling, and diagenesis using anoxic synthesis, sorption, and heating experiments. Excess silica is associated with the solid during precipitation, resulting in high molar Si/Fe ratios (<1.52) that exceed that of stoichiometric greenalite (0.67). At pH 8–8.5, silica sorbs to the surface, reaching sorption densities of 0.68 mmol Si per mmol Fe(II)-silicate. Furthermore, excess Si is released upon heating as the Fe(II)-silicate gel crystallizes. We suggest that Fe(II)-silicate minerals acted as an effective Si shuttle between the water column and the sediments in Archean and Paleoproterozoic marine environments, providing sites for the growth of early diagenetic chert, consistent with observations from the sedimentary record. Our results explain the exceptional preservation of greenalite in early chert and indicate that these minerals could provide a robust archive of marine geochemical data.
Determining the age and origin of a Tertiary karstic system by in situ U-Pb geochronology on speleothems
Authors: Moreau Kévin , Brigaud Benjamin , Andrieu Simon , Briais Justine , Quesnel Florence
Published: June 2024

Dating the onset of ancient (>1 Ma) karstification is a challenge. One approach is to date the earliest calcite cements in speleothems. We show the benefits of in situ U-Pb dating directly on thin sections from ancient (ca. 30 Ma) thin (<1 mm) speleothems in the karstified Lower Oligocene lacustrine-palustrine carbonates of the Paris Basin (France), which cannot be dated using other methods. We dated 32 calcite rafts (a type of speleothem), one geopetal cement, and 10 calcite cements precipitated along the karstic walls. The ages of the calcite rafts and cements at 29 ± 1 Ma (Lower Oligocene) fall within the age range of the host deposits (≈29 Ma) previously deduced from palaeontological evidence. We demonstrate that cementation of the carbonate host rock, its dissolution, and the speleothem precipitation occurred within 2 m.y. after deposition. Ostracods and intraclasts trapped within Rupelian calcite rafts clearly indicate that the karst developed deep underground shortly before a phase of lacustrine-palustrine sedimentation at the surface. This very early dissolution episode is attributed to the uplift of the Paris Basin as a result of the far-field intraplate deformation induced by the alpine orogenesis. This study shows that in situ U-Pb geochronology on ancient calcite rafts is a promising technique for the indirect dating of karstification and, more broadly, for dating geodynamic events and diagenetic evolution of sedimentary basins.
Paediatric opioid poisoning in the UK: a retrospective analysis of clinical enquiries to the National Poisons Information Service
Authors: Yard Hannah Elisabeth , Thompson John P , Gray Laurence , Coulson James M , Bradberry Sally M , Sandilands Euan , Thanacoody Ruben , Tuthill David
Published: June 2024

Objective

To evaluate a decade of reported paediatric opioid poisoning cases in the UK.

Methods

The National Poisons Information Service (NPIS) telephone enquiries database (UK Poisons Information Database) was searched for calls regarding opioid poisoning in children under 18 years from 2012 to 2021. The NPIS online clinical guidance database TOXBASE was searched for accesses relating to opioids for both adults and children. The Office of National Statistics provided paediatric data for hospital admissions and deaths in those aged under 20 years old due to opioids.

Results

The NPIS received 426 774 telephone enquiries from 2012 to 2021 from across the UK, 3600 in relation to opioid exposures regarding children under 18 years. Annual telephone enquiries regarding paediatric opiate poisoning reduced year on year, from around 450 to 300 calls/year. A rise in all age TOXBASE annual accesses relating to opioids from 71 642 in 2012 to 87 498 in 2021 was noted, a total of 838 455 during the study period. Hospital admissions from opioid poisoning remained consistent, with around 1500 admissions/year. Deaths were uncommon, but averaged 18 deaths annually. Co-codamol was the most reported substance to NPIS, with 1193 calls (36.5%), followed by codeine with 935 (26.1%).

Conclusions

Opioid poisoning in children is not uncommon. There is a general downward trend in telephone enquiries to NPIS, but many childhood exposures may have been dealt with through consultations via TOXBASE, where accesses relating to opioids have increased. Unfortunately, children still die from opioid exposure each year in the UK and this figure has changed little during 2012–2021.
Development of a survey to support assessment of safety learning systems
Authors: Mahmoud Hassan Assem , Mulpuru Sunita , Thavorn Kednapa , McIsaac Daniel , Forster Alan J
Published: June 2024

Background

Patient safety learning systems play a critical role in supporting safety culture in healthcare organisations. A lack of explicit standards leads to inconsistent implementation across organisations, causing uncertainty about their roles and impact. Organisations can address inconsistent implementation by using a self-assessment tool based on agreed-on best practices. Therefore, we aimed to create a survey instrument to assess an organisation’s approach to learning from safety events.

Methods

The foundation for this work was a recent systematic review that defined features associated with the performance of a safety learning system. We organised features into themes and rephrased them into questions (items). Face validity was checked, which included independent pre-testing to ensure comprehensibility and parsimony. It also included clinical sensibility testing in which a representative sample of leaders in quality at a large teaching hospital (The Ottawa Hospital) answered two questions to judge each item for clarity and necessity. If more than 20% of respondents judged a question unclear or unnecessary, we modified or removed that question accordingly. Finally, we checked the internal consistency of the questionnaire using Cronbach’s alpha.

Results

We initially developed a 47-item questionnaire based on a prior systematic review. Pre-testing resulted in the modification of 15 of the questions, 2 were removed and 2 questions were added to ensure comprehensiveness and relevance. Face validity was assessed through yes/no responses, with over 80% of respondents confirming the clarity and 85% the necessity of each question, leading to the retention of all 47 questions. Data collected from the five-point responses (strongly disagree to strongly agree) for each question were used to assess the questionnaire’s internal consistency. The Cronbach’s alpha was 0.94, indicating a high internal consistency.

Conclusion

This self-assessment questionnaire is evidence-based and on preliminary testing is deemed valid, comprehensible and reliable. Future work should assess the range of survey responses in a large sample of respondents from different hospitals.
Rethinking empathy: professional work with persons with PIMD
Authors: Hanisch Halvor , Skarsaune Synne Kristin Nese
Published: June 2024

This article combines ethnographic interpretations with analyses of the conceptual history of empathy. Moving beyond the more common notions, which often rely in psychological theories and terminologies, the conceptual-historical analyses trace its roots to 18th and 19th century notions of ‘
Einfühlung
’. As the ethnographic work follows the professional work with two young women with profound intellectual and multiple disabilities, the article makes a fivefold argument. First, we argue that empathy is often considered a matter of individual cognition but should be rethought as an embodied process of feeling-into. Second, we argue that this process is characterised by incompleteness—and hence must acknowledge that empathy is always partial, always on the way to understanding. Third, we argue that this incompleteness forces us to think about the underlying ‘connecting force’, and that the conceptual history suggests that we should think about this force as a form of love. Fourth, we suggest that this ‘love’ is highly embodied, and that this suggests that theoretical notions of empathy should relate to notions of kinship. Fifth, we suggest that the combination of this love (affection, appreciation), embodied kinship and incompleteness suggests a final rethinking, namely the notion of empathy as a form of longing.
Oligoclonal bands
Authors: Willis Mark D , Kreft Karim L , Dancey Bethan
Published: June 2024

Oligoclonal bands (OCBs) represent the presence of intrathecal immunoglobulin G (IgG) as detected by isoelectric focusing and immunofixation. Cerebrospinal fluid (CSF) analysed alongside a paired serum sample gives five different immunofixation patterns. These are: type 1—the normal physiological state with no intrathecal IgG synthesis; type 2—evidence for intrathecal IgG synthesis, with CSF-restricted OCBs; type 3—evidence for intrathecal IgG synthesis, with CSF-restricted OCBs, but with additional, identical bands in the CSF and serum; type 4—absence of intrathecal IgG synthesis, but with identical OCBs in CSF and serum; and type 5—absence of intrathecal IgG synthesis, with a monoclonal band in CSF and serum. Analysis of these patterns can help to diagnose a range of neurological conditions, including multiple sclerosis. However, it is important to interpret OCB results alongside other CSF tests and their clinical context.
Spontaneous resolution of
Trichomonas vaginalis
infection in men
Authors: Van Gerwen Olivia T. , Aaron Kristal J. , Schroeder Julia , Kissinger Patricia J. , Muzny Christina A.
Published: June 2024

Objectives

We aimed to investigate the early natural history of
Trichomonas vaginalis
in men recently testing positive for this infection by a nucleic acid amplification test (NAAT). We hypothesised that 50% of men would spontaneously resolve their infection (in the absence of treatment) on repeat
T. vaginalis
NAAT.

Methods

Men ages ≥18 years at the Jefferson County Health Department Sexual Health Clinic testing positive for
T. vaginalis
by NAAT during standard-of-care (SOC) within the past 30 days and presenting to the clinic for treatment were approached. At enrolment, participants completed a questionnaire, provided urine for repeat
T. vaginalis
NAAT, and were treated with 2 g oral metronidazole. Those with a repeat positive enrolment NAAT were seen for a 4-week test-of-cure (TOC) visit. At TOC, men provided urine for repeat NAAT. We determined the proportion of men with spontaneous resolution of
T. vaginalis
and evaluated predictors of spontaneous resolution. In those with a repeat positive enrolment
T. vaginalis
NAAT, we evaluated the proportion with persistent infection at TOC as a secondary outcome.

Results

Between October 2021 and January 2023, 53 men with a recent positive SOC
T. vaginalis
NAAT were approached; 37 (69.8%) participated. The mean participant age was 32.9 years (SD 9.9); all identified as Black. The majority (97.3%) reported sex with women only; 35.1% reported sex with >1 partner in the last month. At enrolment, 26/37 (70.3%) had a repeat positive
T. vaginalis
NAAT in the absence of treatment after an average of 8.4 days (SD 5.9). Sexual partner gender, number of recent sexual partners, genital symptoms, unprotected sex with any partner and recent antibiotic use were not associated with spontaneous resolution. Of the 26 men attending a TOC visit, 17 (65.4%) returned and all except one (94.1%) were cured.

Conclusion

Most men do not spontaneously clear
T. vaginalis
infection during early repeat testing.
Neighbourhood inequities in the availability of retailers selling tobacco products: a systematic review
Authors: Kong Amanda Y , Lee Joseph G L , Halvorson-Fried Sarah M , Sewell Kerry B , Golden Shelley Diane , Henriksen Lisa , Herbert Lily , Ribisl Kurt M
Published: June 2024

Objective

To examine inequities in tobacco retailer availability by neighbourhood-level socioeconomic, racial/ethnic and same-sex couple composition.

Data sources

We conducted a 10 November 2022 search of PubMed, PsycINFO, Global Health, LILACS, Embase, ABI/Inform, CINAHL, Business Source Complete, Web of Science and Scopus.

Study selection

We included records from Organisation for Economic Co-operation and Development member countries that tested associations of area-level measures of tobacco retailer availability and neighbourhood-level sociodemographic characteristics. Two coders reviewed the full text of eligible records (n=58), including 41 records and 205 effect sizes for synthesis.

Data extraction

We used dual independent screening of titles, abstracts and full texts. One author abstracted and a second author confirmed the study design, location, unit of analysis, sample size, retailer data source, availability measure, statistical approach, sociodemographic characteristic and unadjusted effect sizes.

Data synthesis

Of the 124 effect sizes related to socioeconomic inequities (60.5% of all effect sizes), 101 (81.5%) indicated evidence of inequities. Of 205 effect sizes, 69 (33.7%) tested associations between retailer availability and neighbourhood composition of racially and ethnically minoritised people, and 57/69 (82.6%) documented inequities. Tobacco availability was greater in neighbourhoods with more Black, Hispanic/Latine and Asian residents (82.8%, 90.3% and 40.0% of effect sizes, respectively). Two effect sizes found greater availability with more same-sex households.

Conclusions

There are stark inequities in tobacco retailer availability. Moving beyond documenting inequities to partnering with communities to design, implement, and evaluate interventions that reduce and eliminate inequities in retail availability is needed to promote an equitable retail environment.

PROSPERO registration number

CRD42019124984.
Long-term impact of ivacaftor on mortality rate and health outcomes in people with cystic fibrosis
Authors: Merlo Christian A , Thorat Teja , DerSarkissian Maral , McGarry Lisa J , Nguyen Catherine , Gu Yuqian M , Healy Joe , Rubin Jaime L , Brookhart M Alan
Published: June 2024

Background

Ivacaftor (IVA) has been shown to improve lung function and other clinical outcomes in people with cystic fibrosis (CF). A decade of real-world IVA availability has enabled the examination of long-term outcomes with this treatment. This retrospective, longitudinal cohort study investigated the impact of IVA on mortality rate and health outcomes among people with CF in the US.

Methods

Data from the US CF Foundation Patient Registry from January 2010 to December 2019 were analysed. The IVA-treated cohort included people with a CF transmembrane conductance regulator (CFTR) gating mutation (excludingR117H); age-matched comparator cohort included people with aF508deland a minimal functionCFTRmutation who had no prior CFTR modulator treatment. Baseline characteristics were balanced between cohorts using standardised mortality ratio weighting generated from propensity scores. Outcomes of interest were overall survival, lung transplant, percent predicted forced expiratory volume in 1 s (ppFEV1), body mass index (BMI), pulmonary exacerbations (PEx), outpatient visits and hospitalisations.

Findings

Over a maximum follow-up of 7.9 years, the IVA-treated cohort (N=736) had lower rates of mortality (hazard ratio [HR] (95% CI): 0.22 (0.09 to 0.45)), lung transplant (HR: 0.11 (95% CI 0.02 to 0.28)), PEx (rate ratio: 0.49 (95% CI 0.42 to 0.55)) and all-cause hospitalisations (rate ratio: 0.50 (95% CI 0.43 to 0.56)) as well as better lung function (mean difference in ppFEV1: 8.46 (95% CI 7.34 to 9.75)) and higher BMI/BMIz-scores (mean difference 1.20 (95% CI 0.92 to 1.71) kg/m2and 0.27 (95% CI 0.25 to 0.40), respectively) than the comparator cohort (N=733).

Interpretation

Our analysis suggests that IVA provides sustained clinical benefits in people with CF over a follow-up period of approximately 8 years. These findings reinforce the existing real-world evidence that IVA can slow disease progression and decrease the healthcare burden of CF over the long term.
Paleoenvironmental and chemostratigraphic implications of variations in geochemical proxies across the Upper Jurassic–Lower cretaceous boundary: a case study from the Flemish Pass Basin
Authors: Bingham-Koslowski N. , Azmy K. , Layton-Matthews D.
Published: June 2024

The Jurassic–Cretaceous boundary is the only Phanerozoic period-level boundary that lacks a golden spike on the geological timescale despite significant global geological and environmental change during this time related to the opening of the Atlantic Ocean. Paleoenvironmental proxy profiles (total organic carbon, δ34S, δ15N, Fe, Mn, Ce/Ce*, Th/U, δ13Corg, P, Ni, Zn, Cu, and B/Ga) for core 3 of the Baccalieu I-78 well in the Flemish Pass Basin, offshore eastern Canada, exhibit a geochemical anomaly between 3288.5 and 3289 m, overlapping with the biostratigraphic placement of the Jurassic–Cretaceous boundary. Collectively the geochemical analyses are interpreted to indicate that the anomaly is associated with a fall in relative sea level, followed by a rise, which led to restricted circulation, stratification, and widespread anoxia. This anoxia, coupled with an arid climate, further resulted in reduced weathering, limited nutrient supply, and an overall reduction in primary productivity. The results of this study, in conjunction with previous biostratigraphic studies on core 3, suggest that the Jurassic–Cretaceous boundary in Baccalieu I-78 likely falls within the geochemical anomaly, specifically between 3228.5 and 3288.85 m. Furthermore, the paleoenvironmental interpretations derived in this study agree with published reports on global sea level and climate trends around the Jurassic–Cretaceous boundary, implying the influence of global, rather than regional, factors on deposition. This suggests that geochemical proxies may be useful in providing additional paleoenvironmental insights and helping to constrain stratigraphic boundaries, particularly in intervals that lack significant lithological or biological change.
The response of trophic interaction networks to multiple stressors along a large-scale latitudinal range in the Southern Hemisphere
Authors: Marina Tomás I. , Saravia Leonardo A. , Rodriguez Iara D. , Funes Manuela , Cordone Georgina , Doyle Santiago R. , Silvestro Anahí , Galván David E. , Kortsch Susanne , Momo Fernando R.
Published: June 2024

Ecological networks offer valuable insights into community structure, key species identification, and ecosystem management. Understanding how these networks respond to global change stressors is of increasing interest, especially along geographical gradients. This review summarizes potential stressor responses in marine food webs from the Southwest Atlantic to the Antarctic (45–78°S), encompassing areas such as San Jorge Gulf, Beagle Channel, Burdwood Bank, Scotia Sea, Potter Cove, and the Weddell Sea in Antarctica. The objectives are (1) to describe the structure of marine food webs along this latitudinal axis using a network approach; (2) to identify predominant global change-related stressors affecting each ecosystem; and (3) to summarize observed food web changes and hypothesize on stressor impacts. The effects of stressors were primarily reviewed at the species level. Alternative hypotheses for each study area were formulated considering (a) main stressors; (b) impacted parameters; (c) node-level species properties; and (d) network-level food web properties. Global warming emerges as the most common stressor among the studied areas across the latitudinal gradient, except in the Beagle Channel and Burdwood Bank, where alien species introduction and fisheries are more influential. We offer a series of alternative hypotheses on how warming may affect the food webs. This review emphasizes the benefits of using a network approach to understand and predict stressor effects in Southern Hemisphere marine ecosystems. This approach provides a holistic understanding of ecosystems, which enhances our ability to identify key species and their interactions, offering insights for ecosystem management and conservation in the face of global change stressors.
Hamiltonian, geometric momentum and force operators for a spin zero particle on a curve: physical approach
Authors: Shikakhwa M. S. , Chair N.
Published: June 2024

The Hamiltonian for a spin zero particle that is confined to a 1D curve embedded in the 3D space is constructed. Confinement is achieved by starting with the particle living in a small tube surrounding the curve, and assuming an infinitely strong normal force that squeezes the thickness of the tube to zero, eventually pinning the particle to the curve. We follow the new approach that we applied to confine a particle to a surface, in that we start with an expression for the 3D momentum operators whose components along and normal to the curve directions are separately Hermitian. The kinetic energy operator expressed in terms of the momentum operator in the normal direction is then a Hermitian operator in this case. When this operator is dropped and the thickness of the tube surrounding the curve is set to zero, one automatically gets the Hermitian curve Hamiltonian that contains the geometric potential term as expected. It is demonstrated that the origin of this potential lies in the ordering or symmetrization of the original 3D momentum operators in order to render them Hermitian. The Hermitian momentum operator for the particle as it is confined to the curve is also constructed and is seen to be similar to what is known as the geometric momentum of a particle confined to a surface in that it has a term proportional to the curvature that is along the normal to the curve. The force operator of the particle on the curve is also derived, and is shown to reduce, for a curve with a constant curvature and torsion, to a -apparently- single component normal to the curve that is a symmetrization of the classical expression plus a quantum term. All the above quantities are then derived for the specific case of a particle confined to a cylindrical helix embedded in 3D space.
Improving Gold and Palladium Ohmic Contacts of Carbyne-Based Devices
Authors: Tomov Rade , Aleksandrova Mariya
Published: June 2024

The effects of the sequence of technology steps of electrical contact formation between carbyne layers and metal electrodes (gold, platinum) on contact parameters were explored. Enhancements in contact parameters were achieved through thermal annealing of the samples. Contact parameters were measured by transmission line method (TLM) and impedance spectroscopy after annealing at atmospheric conditions. Lowering of contact resistivity and sheet resistance of the carbyne layer after annealing was observed for temperatures up to 150[Formula: see text]C for palladium contacts and up to 100[Formula: see text]C for gold contacts. It was found that exceeding these temperatures is not recommended, as higher annealing temperatures led to a reduction in the sheet resistance of the carbyne layer. Based on these findings, it can be concluded that the electrical losses at metal contacts of carbyne-based devices, with Au or Pd metallization, can be reduced through annealing. This is particularly critical in carbyne-based gas sensors, where decreasing contact resistance enhances sensitivity.
Frobenius pairs arising from Morita rings
Authors: Liang Li , Ma Yajun , Yang Gang
Published: June 2024

This paper is to study how to construct Frobenius pairs over a Morita ring [Formula: see text]. Given Frobenius pairs [Formula: see text] and [Formula: see text] in [Formula: see text] and [Formula: see text], respectively, we construct Frobenius pairs [Formula: see text] and [Formula: see text] in [Formula: see text] under some conditions. As an application, we establish a sufficient and necessary condition of Gorenstein projective modules over the Morita ring [Formula: see text].
A SUPERVISED ONLINE CROWD ANALYSIS NETWORK WITH DUAL-TASK DEEP LEARNING IDEA IN HEALTHCARE APPLICATION
Authors: WANG JUNLI , LENG WENHAO , WANG SHITONG , ZHANG TAO , JIN JIALI
Published: June 2024

As the most active research branch in the field of artificial intelligence, deep learning has gradually become a research hotspot in the medical field in recent years, and has achieved some success in medical image and signal processing, biomedical and healthcare, medical information mining and retrieval, showing great application prospects. Aiming at the problem of the uneven distribution of data in biomedical and healthcare area under smart city, this paper proposes a novel supervised network by a dual-task deep learning scheme. First, we optimize the early distribution by supervising the features of the early stage, which helps the shallow network to determine the distribution of data, and avoids the gradient disappearance and slow convergence. Then, a novel supervised network framework is proposed to focus on the prediction accuracy and generate crowd response maps that reflect the importance of different features. The final distribution revising module uses high-frequency semantic information to further supervise the predicted distribution. The noise data suppression module is proposed to suppress the misjudgment on fake biomedical data. Experimental results on four commonly healthcare used datasets show that our proposed deep learning model performs better in the biomedical data analysis and density distribution, and outperforms the state-of-the-art methods.
Unsteady chemically reactive Maxwell nanofluid flow through a porous elastic surface with Cattaneo–Christov model
Authors: Ahmad Manzoor , Bibi Qudsia , Taj Muhammad , Khan Sami Ullah , Butt Faisal Mehmood , Bhatti M. M.
Published: June 2024

Novel nanomaterial applications claim distinct uses in thermal engineering, cooling processes, heat transfer devices, and automobile industries, among others. Motivated research uses modified heat and mass flux theories to present thermal observations for the unsteady flow of magnetized Maxwell nanofluid, confined by porous bidirectionally stretched surfaces. The heat transfer model’s extension is based on Joule heating and heat source effects. The Cattaneo–Christov theories govern the expansion of mass and heat transfer. We analyze thermal problems under zero-mass diffusion constraints. The use of proper variables simplifies mathematical modeling into a dimensionless form. The Homotopy Analysis Method (HAM) solves the dimensionless system. The paper highlights the convergence criteria for the HAM procedure. Graphics underline the problem’s physical perspective. We observe that the Deborah number enhances heat and mass transfer. The temperature profile decreases when the parameter becomes unstable.
Unbiased Feature Learning with Causal Intervention for Visible-Infrared Person Re-Identification
Authors: Yuan Bowen , Lu Jiahao , You Sisi , Bao Bing-Kun
Published: June 2024

Visible-infrared person re-identification (VI-ReID) aims to match individuals across different modalities. Existing methods can learn class-separable features but still struggle with modality gaps within class due to the modality-specific information, which is discriminative in one modality but not present in another (e.g., a black striped shirt). The presence of the interfering information creates a spurious correlation with the class label, which hinders alignment across modalities. To this end, we propose an Unbiased feature learning method based on Causal inTervention for VI-ReID from three aspects. Firstly, through the proposed structural causal graph, we demonstrate that modality-specific information acts as a confounder that restricts the intra-class feature alignment. Secondly, we propose a causal intervention method to remove the confounder using an effective approximation of backdoor adjustment, which involves adjusting the spurious correlation between features and labels. Thirdly, we incorporate the proposed approximation method into the basic VI-ReID model. Specifically, the confounder can be removed by adjusting the extracted features with a set of weighted pre-trained class prototypes from different modalities, where the weight is adapted based on the features. Extensive experiments on the SYSU-MM01 and RegDB datasets demonstrate that our method outperforms state-of-the-art methods. Code is available at
https://github.com/NJUPT-MCC/UCT
.
DAG-YOLO: A Context-Feature Adaptive fusion Rotating Detection Network in Remote Sensing Images
Authors: Guo Zhenjiang , He Xiaohai , Yang Yu , Qing Linbo , Chen Honggang
Published: June 2024

Object detection in remote sensing image (RSI) research has seen significant advancements, particularly with the advent of deep learning. However, challenges such as orientation, scale, aspect ratio variations, dense object distribution, and category imbalances remain. To address these challenges, we present DAG-YOLO, a
one-stage context-feature adaptive weighted fusion network
that incorporates through three innovative parts. First, we integrate
1D Gaussian Angle-coding
with YOLOv5 to convert the angle regression task into a classification task, establishing a more robust rotating object detection baseline, GLR-YOLO. Second, we introduce the Dual Branch Context Adaptive Modeling module, which enhances feature extraction capabilities by capturing global context information. Third, we design an adaptive detect head with the Adaptive Global Feature Aggregation and Reweighting (AGFAR) module. AGFAR addresses feature inconsistency among different output layers of the Feature Pyramid Network, retaining useful semantic information and elevating detection accuracy. Extensive experiments on public datasets DOTA-v1.0, DOTA-v1.5, and UCAS-AOD showcase mAP scores of 77.75%, 73.79%, and 90.27%, respectively. Our proposed method has the best performance among the current mainstream SOTA methods, which proves its effectiveness in RSI object detection.
Auxiliary Feature Fusion and Noise Suppression for HOI Detection
Authors: Chan Sixian , Zeng Xianpeng , Wang Xinhua , Hu Jie , Bai Cong
Published: June 2024

In recent years, one-stage HOI (Human–Object Interaction) detection methods tend to divide the original task into multiple sub-tasks by using a multi-branch network structure. However, there is no sufficient attention to information communication between these branches. The inference approach in the cascaded structure is singular, while fully parallel methods will disrupt the associations between different pieces of information. Besides, noise interference may occur during the fusion of different features and thus affect the detection performance. To address these issues, this article proposes a one-stage three-branch parallel HOI detection method, which treats HOI as three separate sub-tasks (human detection, object detection, and interaction detection) and leverages three distinct reasoning relationships to generate richer relational information.
Firstly
, an auxiliary feature fusion (AFF) module is introduced, which integrates features originally extracted independently to form fused features enriched with supplementary information. This approach strengthens communication between branches in the network while handling the three sub-tasks concurrently, thereby facilitating the exchange of more contextual information.
Secondly
, to mitigate noise interference generated during the fusion process, a fusion noise suppression (FNS) module is introduced, which effectively suppresses noise and enhances the model’s performance in interaction detection tasks.
Finally
, experiments are conducted on two major benchmark datasets, and experimental results show that our HOI detection method is superior to previous methods. Also, ablation studies confirm the effectiveness of all the components in our proposed method.
RGB LED for Communication, Harvesting and Sensing in IoT Applications
Authors: Mir Muhammad Sarmad Shahab
Published: June 2024

RGB LED bulbs have entered the market as a promising alternative to traditional phosphor-coating LEDs to meet illumination standards. In this article, we introduce and propose solutions to address the challenges of RGB LED lighting for the Internet of Things applications, performing communication, harvesting energy, and sensing tasks. Through experiments, we demonstrate that we can use RGB LEDs for multiple tasks. We can achieve a bandwidth in the order of 50 kHz and distances of around 3.5 m using commercial RGB LED bulbs as transceivers, without using any dedicated photodetector. RGB LED links are composed of three main colors, and we show that red is the best color both for communicating to another receiving RGB LED bulb, as well as for harvesting with a solar cell; green and blue can instead be exploited for standard-compliant lighting and/or sensing purposes. We evaluate the system in two proofs of concept and provide insights for operating RGB LEDs for multiple tasks including vertical farming.
Text-Driven Video Prediction
Authors: Song Xue , Chen Jingjing , Zhu Bin , Jiang Yu-Gang
Published: June 2024

Current video generation models usually convert signals indicating appearance and motion received from inputs (e.g., image and text) or latent spaces (e.g., noise vectors) into consecutive frames, fulfilling a stochastic generation process for the uncertainty introduced by latent code sampling. However, this generation pattern lacks deterministic constraints for both appearance and motion, leading to uncontrollable and undesirable outcomes. To this end, we propose a new task called Text-driven Video Prediction (TVP). Taking the first frame and text caption as inputs, this task aims to synthesize the following frames. Specifically, appearance and motion components are provided by the image and caption separately. The key to addressing the TVP task depends on fully exploring the underlying motion information in text descriptions, thus facilitating plausible video generation. In fact, this task is intrinsically a cause-and-effect problem, as the text content directly influences the motion changes of frames. To investigate the capability of text in causal inference for progressive motion information, our TVP framework contains a Text Inference Module (TIM), producing step-wise embeddings to regulate motion inference for subsequent frames. In particular, a refinement mechanism incorporating global motion semantics guarantees coherent generation. Extensive experiments are conducted on Something-Something V2 and Single Moving MNIST datasets. Experimental results demonstrate that our model achieves better results over other baselines, verifying the effectiveness of the proposed framework.
Study of Process Variation in Nanotube Tunnel Field Effect Transistor
Authors: Gedam Anju , Acharya Bibhudendra , Mishra Guru Prasad
Published: June 2024

In the nanoscale, the process parameters and device dimension variation extensively affect the electrical performance of the device. Therefore, an inclusive study for the prediction of the overall device behavior is extremely necessary. In this manuscript, process variations caused by random dopant fluctuation (RDFs), variation of oxide thickness, and workfunction during fabrication are analyzed in junctionless nanotube TFET. The work quantitatively evaluates the impact of process variability on the various electrical parameters like energy band diagram, electric field, carrier concentration, and drain current of the nanotube TFET structure. The device simulation has been carried out with a 3-D SILVACO ATLAS simulator.
Perinatal asphyxia leads to acute kidney damage and increased renal susceptibility in adulthood
Authors: Lakat Tamas , Fekete Andrea , Demeter Kornel , Toth Akos R. , Varga Zoltan K. , Patonai Attila , Kelemen Hanga , Budai Andras , Szabo Miklos , Szabo Attila J. , Kaila Kai , Denes Adam , Mikics Eva , Hosszu Adam
Published: June 2024

This article demonstrates that perinatal asphyxia leads to subclinical kidney injury that permanently increases renal susceptibility to subsequent ischemic injury. We identified major molecular pathways involved in perinatal asphyxia-induced renal complications, highlighting potential targets of therapeutic approaches. In addition, random forest analysis revealed a model that classifies perinatal asphyxia with 95.5% accuracy that may provide a strong foundation for further biomarker research. These findings underscore the importance of multiorgan follow-up for perinatal asphyxia-affected patients.