bluuebunny/crossref_metadata_2025 huggingface dataset:
Process Evaluation of a Scaled-Up School-Based Physical Activity Program for Adolescents: Physical Activity 4 Everyone
Authors: Mclaughlin Matthew , Duff Jed , Campbell Elizabeth , McKenzie Tom , Davies Lynda , Wolfenden Luke , Wiggers John , Sutherland Rachel
Published: June 2024

Background: Physical Activity 4 Everyone (PA4E1) is a whole-school physical activity program, with demonstrated efficacy (2012–2014). PA4E1 was adapted (scaled-up) and tested in a scale-up trial (2017–2020). This process evaluation study of the scale-up trial had 2 aims. First, to describe the acceptability, appropriateness, and feasibility of PA4E1 in the scale-up trial, from the perspective of school staff involved in the program management and delivery. Second, to generate themes that may explain school staff assessments of acceptability, appropriateness, and feasibility. Methods: Data were collected at various time points throughout the 2-year implementation phase. Online surveys were collected from In-School Champions, Head Physical Education teachers, Principals, and Physical Education teachers (quantitative data). Focus groups and interviews were conducted with In-School Champions, Principals, and Physical Education teachers (qualitative data). Existing published data on website engagement, adaptations, modifications, and the scale-up trial primary outcome (implementation of physical activity practices) were triangulated with the quantitative and qualitative during analysis, to generate themes. Results: School staff delivering PA4E1 reported it was highly acceptable, appropriate, and feasible. Seven themes were generated relating to acceptability, appropriateness, and feasibility. The themes related to how the program was funded, the delivery modes of implementation support, the identification of easy-wins, the recruitment of the right in-school champion, facilitating principal buy-in, mitigating the impact of school staff turnover, and engaging the whole school. Conclusions: Recommendations are made to inform future adaptations for PA4E1 and potentially school-based physical activity programs more generally. The findings may inform future scalability assessments of the suitability of programs for scale-up.
Small variations in ice composition and layer thickness explain bright reflections below martian polar cap without liquid water
Authors: Lalich Daniel E. , Hayes Alexander G. , Poggiali Valerio
Published: June 2024

Abnormally bright radar reflections below the Martian south polar layered deposit were originally interpreted as evidence of subglacial liquid water. However, unlike on Earth, conditions beneath the Martian ice are too cold to create or maintain meltwater. In this work, we use radar reflectivity simulations to show that the strong reflections can instead be caused by constructive interference between dusty ice layers that are more closely spaced than the radar resolution. Unlike previous hypotheses, interference does not require anomalous subsurface conditions or exotic materials to be present beneath the ice. In addition, interference between thin layers can explain the variable power of radar returns beneath the entire ice sheet and does not require different mechanisms to be responsible for reflections in different regions.
Mortality attributable to PM
2.5
from wildland fires in California from 2008 to 2018
Authors: Connolly Rachel , Marlier Miriam E. , Garcia-Gonzales Diane A. , Wilkins Joseph , Su Jason , Bekker Claire , Jung Jihoon , Bonilla Eimy , Burnett Richard T. , Zhu Yifang , Jerrett Michael
Published: June 2024

In California, wildfire risk and severity have grown substantially in the last several decades. Research has characterized extensive adverse health impacts from exposure to wildfire-attributable fine particulate matter (PM
2.5
), but few studies have quantified long-term outcomes, and none have used a wildfire-specific chronic dose-response mortality coefficient. Here, we quantified the mortality burden for PM
2.5
exposure from California fires from 2008 to 2018 using Community Multiscale Air Quality modeling system wildland fire PM
2.5
estimates. We used a concentration-response function for PM
2.5
, applying ZIP code–level mortality data and an estimated wildfire-specific dose-response coefficient accounting for the likely toxicity of wildfire smoke. We estimate a total of 52,480 to 55,710 premature deaths are attributable to wildland fire PM
2.5
over the 11-year period with respect to two exposure scenarios, equating to an economic impact of $432 to $456 billion. These findings extend evidence on climate-related health impacts, suggesting that wildfires account for a greater mortality and economic burden than indicated by earlier studies.
Multiplexed CRISPR-Cas9 mutagenesis of rice
PSBS1
noncoding sequences for transgene-free overexpression
Authors: Patel-Tupper Dhruv , Kelikian Armen , Leipertz Anna , Maryn Nina , Tjahjadi Michelle , Karavolias Nicholas G. , Cho Myeong-Je , Niyogi Krishna K.
Published: June 2024

Understanding CRISPR-Cas9’s capacity to produce native overexpression (OX) alleles would accelerate agronomic gains achievable by gene editing. To generate OX alleles with increased RNA and protein abundance, we leveraged multiplexed CRISPR-Cas9 mutagenesis of noncoding sequences upstream of the rice
PSBS1
gene. We isolated 120 gene-edited alleles with varying non-photochemical quenching (NPQ) capacity in vivo—from knockout to overexpression—using a high-throughput screening pipeline. Overexpression increased OsPsbS1 protein abundance two- to threefold, matching fold changes obtained by transgenesis. Increased PsbS protein abundance enhanced NPQ capacity and water-use efficiency. Across our resolved genetic variation, we identify the role of 5′UTR indels and inversions in driving knockout/knockdown and overexpression phenotypes, respectively. Complex structural variants, such as the 252-kb duplication/inversion generated here, evidence the potential of CRISPR-Cas9 to facilitate significant genomic changes with negligible off-target transcriptomic perturbations. Our results may inform future gene-editing strategies for hypermorphic alleles and have advanced the pursuit of gene-edited, non-transgenic rice plants with accelerated relaxation of photoprotection.
Brucella
NpeA is a secreted Type IV effector containing an N-WASP-binding short linear motif that promotes niche formation
Authors: Giménez Agostina , Del Giudice Mariela G. , López Paula V. , Guaimas Francisco , Sámano-Sánchez Hugo , Gibson Toby J. , Chemes Lucía B. , Arregui Carlos O. , Ugalde Juan E. , Czibener Cecilia
Published: June 2024

The modulation of actin polymerization is a common theme among microbial pathogens. Even though microorganisms show a wide repertoire of strategies to subvert the activity of actin, most of them converge in the ones that activate nucleating factors, such as the Arp2/3 complex.
Brucella
spp. are intracellular pathogens capable of establishing chronic infections in their hosts. The ability to subvert the host cell response is dependent on the capacity of the bacterium to attach, invade, avoid degradation in the phagocytic compartment, replicate in an endoplasmic reticulum-derived compartment and egress. Even though a significant number of mechanisms deployed by
Brucella
in these different phases have been identified and characterized, none of them have been described to target actin as a cellular component. In this manuscript, we describe the identification of a novel virulence factor (NpeA) that promotes niche formation. NpeA harbors a short linear motif (SLiM) present within an amphipathic alpha helix that has been described to bind the GTPase-binding domain (GBD) of N-WASP and stabilizes the autoinhibited state. Our results show that NpeA is secreted in a Type IV secretion system-dependent manner and that deletion of the gene diminishes the intracellular replication capacity of the bacterium.
In vitro
and
ex vivo
experiments demonstrate that NpeA binds N-WASP and that the short linear motif is required for the biological activity of the protein.

IMPORTANCE

The modulation of actin-binding effectors that regulate the activity of this fundamental cellular protein is a common theme among bacterial pathogens. The neural Wiskott–Aldrich syndrome protein (N-WASP) is a protein that several pathogens target to hijack actin dynamics. The highly adapted intracellular bacterium
Brucella
has evolved a wide repertoire of virulence factors that modulate many activities of the host cell to establish successful intracellular replication niches, but, to date, no effector proteins have been implicated in the modulation of actin dynamics. We present here the identification of a virulence factor that harbors a short linear motif (SLiM) present within an amphipathic alpha helix that has been described to bind the GTPase-binding domain (GBD) of N-WASP stabilizing its autoinhibited state. We demonstrate that this protein is a Type IV secretion effector that targets N-WASP-promoting intracellular survival and niche formation.
Draft genome sequence of
Vibrio
sp. PBL-C16, isolated from Batu Laut Beach in Selangor, Malaysia
Authors: Kahar Ummirul Mukminin , Goh Kian Mau , Zakaria Iffah Izzati , Radzlin Nurfatini , Mohd Ruslan Izzatul Husna , Azizan Suha
Published: June 2024

Vibrio
sp. PBL-C16 is a bacterium that was isolated from Batu Laut Beach in Selangor, Malaysia. Here, we present a high-quality annotated draft genome of strain PBL-C16 and suggest its potential glycoside hydrolase enzymes for polysaccharide degradation.
IgA multiple myeloma-associated mediastinal spinal plasmacytoma presenting as spinal cord compression
Authors: Prathivadhi-Bhayankaram Sruti , Marar Rosalyn , Atiya Samir , Krishnan Mridula
Published: June 2024

Multiple myeloma associated with extramedullary plasmacytoma at initial presentation is rare. We describe a case of a man in his 30s who initially presented with symptoms of spinal cord compression. Further imaging revealed a mediastinal tumour, with a biopsy confirming plasmacytoma. Immunofixation revealed IgA lambda paraprotein. Bone marrow biopsy demonstrated atypical T-cell cytotoxic proliferation and trilineage hypoplasia. The patient was diagnosed with extramedullary plasmacytoma with active IgA multiple myeloma. The patient received mediastinal radiation to the tumour, followed by anti-myeloma therapy. This diagnosis is critical as managing a solitary plasmacytoma drastically differs from an extramedullary plasmacytoma with active multiple myeloma.
Transparency interventions to improve health system outcomes in low and middle-income countries: a narrative systematic review
Authors: Gholami Masoomeh , Takian Amirhossein , Kabir Mohammad Javad , Olyaeemanesh Alireza , Mohammadi Mehrdad
Published: June 2024

Objectives

This study aimed to identify the types of transparency interventions in the health systems of the low-income and middle-income countries and the outcomes of such interventions in those systems.

Method

We searched major medical databases including PubMed, Embase and Scopus, for any kind of interventional study on transparency in health systems. We also looked for additional sources of information in organisational websites, grey literature and reference checking. Using the PRISMA algorithm for identifying related studies, we included 24 articles.

Results

Our initial search, from 1980 to August 2021, retrieved 407 articles, 24 of which were narratively analysed. Response to a problem (mostly corruption) was the main reason for the initiation of a transparency intervention. Transparency interventions differed in terms of types, performance methods, collaboration partners and outcomes. They help improve the health system mostly in the short term and in some cases, long term.

Conclusion

Although our findings revealed that transparency initiatives could reduce some problems such as counterfeit drugs and corruption, and improve health indicators in a short term, still their sustainability remains a concern. Health systems need robust interventions with clearly defined and measured outcomes, especially sustainable outcomes to tackle corruption fundamentally.
Cohort profile: longitudinal and population comparison of children who are HIV-exposed uninfected and children who are HIV unexposed in Kenya (HOPE study)
Authors: Njuguna Irene N , King'e Maureen , Moraa Helen , Kumar Manasi , Benki-Nugent Sarah , Wagner Anjuli Dawn , McGrath Christine J , Dorsey Shannon , Ndegwa Serah , Onyango Alvin , Wamalwa Dalton , John-Stewart Grace
Published: June 2024

Purpose

Globally, the number of children/adolescents exposed to HIV but uninfected (HIV-exposed uninfected, HEU) is growing. The HEU outcomes: population-evaluation and screening strategies study was designed to provide population-level evidence of the impact of HIV and recent antiretroviral therapy regimen exposure on neurodevelopmental, hearing and mental health outcomes from infancy to adolescence.

Participants

The study includes a prospective mother–infant cohort and cross-sectional child/youth–caregiver cohorts conducted in Kenya.

Between 2021 and 2022, the study enrolled 2000 mother–infant pairs (1000 HEU and 1000 HIV-unexposed uninfected (HUU)) for longitudinal follow-up. Infants were eligible if they were aged 4–10 weeks and healthy. Mothers were eligible if their HIV status was known and were ≥18 years. Study visits are 6 monthly until the child reaches age 3 years.

Cross-sectional cohorts spanning ages 3–18 years started enrolment in 2022. Target enrolment is 4400 children/youth (4000 HEU and 400 HUU). Children and youth are eligible if they are HIV negative, maternal HIV status and timing of diagnosis is known, and caregivers are ≥18 years.

Data on infant/child/youth growth, neurodevelopment, mental health, morbidity and hearing are collected at enrolment using standardised tools. Dry blood spots samples are collected for telomere length assessment at baseline and yearly for the longitudinal cohort. Growth z-scores, neurodevelopmental scores, telomere length and prevalence of developmental and hearing problems will be compared between HEU/HUU populations.

Findings to date

Full cohort enrolment for the longitudinal cohort is complete and participants are in follow-up. At 1 year of age, comparing HEU to HUU neurodevelopment using the Malawi developmental assessment tool, we found that HEU infants had higher language scores and comparable scores in fine motor, gross motor and social scores. The cross-sectional cohort has enrolled over 2000 participants and recruitment is ongoing.

Future plans

Longitudinal cohort follow-up and enrolment to the cross-sectional study will be completed in June 2024.
Evaluating a Modified Use of the Kaiser Permanente Early-onset Sepsis Risk Calculator to Reduce Antibiotic Exposure: a Retrospective Study
Authors: Alhindi Mohammed Yasir , Almalki Faisal Ghazi , Al Saif Saif , Almalahi Abdulaziz , Alsaegh Mawaddah Hesham , Mustafa Ahmed , AlQurashi Mansour Abdullah
Published: June 2024

Background

Early-onset neonatal sepsis (EONS) remains an important disease entity due to very serious adverse outcomes if left untreated. Lack of diagnostic tools in identifying healthy from diseased neonates, and clinicians’ fear of the missing positive-culture sepsis babies, or babies with clinical sepsis have led to overtreating and unnecessary antibiotic exposure. Kaiser Permanente EONS risk calculator is an internally validated tool that can predict EONS. This sepsis risk calculator (SRC) classifies neonates into three subgroups: (1) ill-appearing, (2) equivocal and (3) well-appearing. We propose a modification to this tool that aims to use it solely for well-appearing babies. This modification represents a more conservative approach to decrease antibiotic exposure and offers an alternative for those hesitant to fully implement this tool.

Methods

This is a dual-centre retrospective study where data were extracted from the electronic medical records. Our primary outcome was to validate the modified use of the SRC with a two-by-two table. Specificity, negative predictive value and expected antibiotic reduction were used to evaluate the tool’s feasibility.

Result

Among 770 babies suspected of EONS, the feasibility of the modified use was tested. The expected antibiotic exposure reduction rate on the modification was 40.4% overall. The proposed modification resulted in a specificity and negative predictive value of 99.28% (95% CI: 97.92% to 99.85%) and 99.5% (95% CI: 99% to 99.8%), respectively.

Conclusion

The modified use of the sepsis risk calculator has shown that it can safely reduce antibiotic exposure in well-appearing babies. The modified use is used as a ‘rule out’ test that can identify very low risk of EONS babies, and safely minimise antibiotic exposure. Further prospective studies are needed to examine the efficacy of this use, and quality improvement projects are required to evaluate its applicability in different clinical settings.
Characterizations of multi-kingdom gut microbiota in immune checkpoint inhibitor-treated hepatocellular carcinoma
Authors: Zhu Chengpei , Zhang Chenchen , Wang Shanshan , Xun Ziyu , Zhang Dongya , Lan Zhou , Zhang Longhao , Chao Jiashuo , Liang Yajun , Pu Zilun , Ning Cong , Sang Xinting , Yang Xiaobo , Wang Hanping , Jiang Xianzhi , Zhao Haitao
Published: June 2024

Background

The association between gut bacteria and the response to immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) has been studied; however, multi-kingdom gut microbiome alterations and interactions in ICI-treated HCC cohorts are not fully understood.

Methods

From November 2018 to April 2022, patients receiving ICI treatment for advanced HCC were prospectively enrolled. Herein, we investigated the multi-kingdom microbiota characterization of the gut microbiome, mycobiome, and metabolome using metagenomic, ITS2, and metabolomic data sets of 80 patients with ICI-treated HCC.

Results

Our findings demonstrated that bacteria and metabolites differed significantly between the durable clinical benefit (DCB) and non-durable clinical benefit (NDB) groups, whereas the differences were smaller for fungi. The overall diversity of bacteria and fungi before treatment was higher in the DCB group than in the NDB group, and the difference in diversity began to change with the use of immunotherapy after 6–8 weeks. We also explored the alterations of gut microbes in the DCB and NDB groups, established 18 bacterial species models as predictive biomarkers for predicting whether immunotherapy is of sustained benefit (area under the curve=75.63%), and screened two species of bacteria (Actinomyces_sp_ICM47, andSenegalimassilia_anaerobia) and one metabolite (galanthaminone) as prognostic biomarkers for predicting survival in patients with HCC treated with ICI.

Conclusions

In this study, the status and characterization of the multi-kingdom microbiota, including gut bacteria, fungi, and their metabolites, were described by multiomics sequencing for the first time in patients with HCC treated with ICI. Our findings demonstrate the potential of bacterial taxa as predictive biomarkers of ICI clinical efficacy, and bacteria and their metabolites as prognostic biomarkers.
Using Defence Engagement (Health) to progress the Women Peace and Security agenda
Authors: Kinkaid Victoria , Masti M , Whitaker J , Russell A , McCrae L
Published: June 2024

Since the unanimous passing of United Nations Security Council Resolution 1325, which calls on member states to address gender inequality, many countries and the wider North Atlantic Treaty Organisation community have championed the Women Peace and Security agenda to empower women and reduce violence within fragile states. When women are empowered and actively involved in decision-making, there is less violence, and more peace and stability in that society, which benefits all members.

Defence Medical Services are uniquely positioned to progress this agenda, particularly through its Defence Engagement activities. The UK’s military medical community has more women in leadership than the wider military community. Our personnel can and should be used to model and empower military healthcare workers in partner nations. This paper forms part of a special issue ofBMJ Military Healthdedicated to Defence Engagement.
Plasma effects on resonant phenomena
Authors: Pradhan Anil
Published: June 2024

The effect of autoionizing resonances in atomic systems and processes is reviewed. Theoretical framework for treating resonances in the coupled channel approximation using the R-matrix method, as well as approximations related to plasma applications are described. The former entails large-scale atomic computations, and the latter is based on a new method for including collisional, Stark, thermal, and other broadening mechanisms. We focus particularly on the problem of opacities calculations in high-energy-density plasmas such as stellar interiors and inertial confinement fusion devices. The treatment is generally relevant to radiative and collisional processes as the cross sections become energy-temperature-density dependent. While the computational difficulty increases considerably, the reaction rates are significantly affected. The related issue of the Boltzmann–Saha equation-of-state and its variants in local thermodynamic equilibrium is also explored as the intermediary between atomic data on the one hand and plasma environments on the other.
Dynamics and Chaos of Convective Fluid Flow
Authors: Guo Siyu , Luo Albert C. J.
Published: June 2024

In this paper, a mathematical model of fluid flows in a convective thermal system is developed, and a five-dimensional dynamical system is developed for the investigation of the convective fluid dynamics. The analytical solutions of periodic motions to chaos of the convective fluid flows are developed for steady-state vortex flows, and the corresponding stability and bifurcations of periodic motions in the five-dimensional dynamical system are studied. The harmonic frequency-amplitude characteristics for periodic flows are obtained, which provide energy distribution in the parameter space. Analytical homoclinic orbits for the convective fluid flow systems are developed for the asymptotic convection through the infinite-many homoclinic orbits in the five-dimensional dynamical system. The dynamics of fluid flows in the convective thermal systems are revealed, and one can use such methodology to predict atmospheric and oceanic phenomena through thermal convections.
Role of Brand Familiarity on the Influence of Electronic Word-of-Mouth and Customers’ Behavioral Intentions
Authors: Ojiaku Obinna C. , Nwaizugbo Ireneus Chukwudi , Osarenkhoe Aihie
Published: June 2024

Despite the increased confidence in e-commerce, consumers remain skeptical when shopping online and therefore rely on electronic word-of-mouth generated by other consumers to aid their brand or store choice. Because eWOM can have detrimental or beneficial effects on brands and is beyond the control of firms, measuring the extent to which consumers use this information source to inform their decisions is a major challenge facing scholars and practitioners. This study examines the influence of eWOM on customers’ behavioral intentions and tests the role of brand familiarity. Five hypotheses are developed and tested based on the accessibility-diagnosticity theory and the elaboration likelihood model. A sample of 432 participants was recruited from a university in Southeastern Nigeria to participate in a [Formula: see text] between-subject factorial experiment. The results show that the positive or negative sentiments conveyed in eWOM messages and the familiarity of a brand affect customers’ behavioral intentions independently, and that the volume of eWOM messages interacts with brand familiarity to impact these behavioral intentions such that unfamiliar brands benefit more from high volume than familiar retailers do. The implication is that firms can overcome the problem of familiarity and performance risk by motivating and displaying as many eWOM communications as possible in their social media and advertisements.
Dark matter from evaporating primordial black holes in the early universe
Authors: Chattopadhyay Pratik , Chaudhuri Arnab , Khlopov Maxim Yu.
Published: June 2024

Primordial Black Holes (PBHs) could dominate in the early universe and, evaporating before Big bang Nucleosynthesis, provide new freeze in mechanism of dark matter (DM) production. The proposed scenario is considered for two possible mechanisms of PBH formation and the corresponding continuous PBH mass spectra so that the effect of non-single PBH mass spectrum is taken into account in the results of PBH evaporation, by which PBH dominance in the early universe ends. We specify the conditions under which the proposed scenario can explain production of dark matter in very early universe.
PDM relativistic quantum oscillator in Einstein–Maxwell–Lambda space-time
Authors: Ahmed Faizuddin , Bouzenada Abdelmalek
Published: June 2024

In this paper, we study the relativistic dynamics of quantum oscillator fields within the context of a position-dependent mass (PDM) system in the background of a curved space-time. The chosen curved space-time is generated by a magnetic field incorporating a non-zero cosmological constant called Einstein–Maxwell–Lambda solution. To analyze PDM quantum oscillator fields, we introduce a modification into the Klein–Gordon equation by substituting the four-momentum vector [Formula: see text], where various four-vectors are defined by [Formula: see text], [Formula: see text] with [Formula: see text], and [Formula: see text] is the mass oscillator frequency. The radial wave equation for the modified Klein–Gordon equation is derived and subsequently solve for two distinct scalar multipliers: (i) [Formula: see text] and (ii) [Formula: see text], where [Formula: see text] and [Formula: see text]. The resultant approximate energy levels and wave function for quantum oscillator fields are demonstrated to be influenced by the cosmological constant and the geometrical topology parameter which breaks the degeneracy of the energy spectrum. Furthermore, we observed noteworthy modifications in the approximate energy levels and wave function when compared to the results derived in the flat space.
Sustainable Built Environments and the Water, Energy, and Food Nexus: Toward an Interdisciplinary Approach to Urban Resilience
Authors: ELZEIN Zeina
Published: June 2024

Urban resilience has been a research focus, particularly with the pandemic impact on urban infrastructure, service provision and accessibility to core resources. This paper explores the need for interdisciplinary approaches to the built environment that integrate water, energy, and food resources. The study goes through articles on water, energy and food nexus and urban resilience in the past 10 years. It identifies the key research focus, gaps and needs for future research. Recommendations for future studies include the allocation of funds to ensure vulnerable communities have access to resources, sustainable operation of urban agriculture practices, circular economy and reuse, and engagement of experts, local authorities and communities in decision-making and training. The study recommends using quantitative assessment to identify the impact of urban agriculture and urban water management practices on the environment and include socio-economic aspects in assessment models. Finally, participatory approaches and integrating technology are recommended for promoting sustainable resilient communities.
Construction of New Bivariate Semilinear Copulas Based on the Ali–Mikhail–Haq, Farlie–Gumbel–Morgenstern and Plackett Families
Authors: Correia Átila P. , Suzuki Adriano K. , Ferreira Paulo H. , Viola Márcio L. L.
Published: June 2024

Copulas are quite a popular, flexible, and useful tool for multivariate modeling in many fields of applications, including finance and insurance, actuarial sciences, biomedical studies, geostatistics, and hydrology. In this paper, we use the concept of diagonal function to build new bivariate copulas based on the well known and important Ali–Mikhail–Haq (AMH), Farlie–Gumbel–Morgenstern (FGM) and Plackett families. We also study some dependence properties of the newly constructed semilinear copulas, namely, the Spearman’s [Formula: see text] coefficient. In particular, we find that the range of this rank correlation coefficient varies between weak and moderate values for the transformed AMH and FGM families, although it varies between moderate and strong values for the transformed Plackett families. Moreover, in all cases, the Spearman’s [Formula: see text] coefficient reaches negative and positive values. Finally, we present a synthetic data generation algorithm, as well as a classical method of estimation of the copula association parameter [Formula: see text] for each of the six transformed bivariate families.
Learning a Subspace and Clustering Simultaneously with Manifold Regularized Nonnegative Matrix Factorization
Authors: Nie Feiping , Chen Huimin , Huang Heng , Ding Chris H. Q. , Li Xuelong
Published: June 2024

With the incredible growth of high-dimensional data such as microarray gene expression data and web blogs from internet, the researchers are desirable to develop new clustering techniques to address the critical problem created by irrelevant dimensions. Properties of Nonnegative Matrix Factorization (NMF) as a clustering method were studied by relating its formulation to other methods such as K-means clustering. In this paper, by introducing clustering indicator constraints on NMF and incorporating manifold regularization to preserve geometric structures, we propose a novel manifold regularized NMF method that can simultaneously learn subspace and do clustering. As a result, our clustering results can directly assign cluster label to data points. Extensive experimental results show that our method outperforms related other methods.
Efficient SpMM Accelerator for Deep Learning: Sparkle and Its Automated Generator
Authors: Xu Shiyao , Jiang Jingfei , Xu Jinwei , Qian Xifu
Published: June 2024

Deep learning (DL) technology has made breakthroughs in a wide range of intelligent tasks, such as vision, language, recommendation systems, and so on. Sparse matrix multiplication (SpMM) is the key computation kernel of most sparse models. Conventional computing platforms, such as CPUs, GPUs, and AI chips with regular processing units, are unable to effectively support sparse computation due to their fixed structure and instruction sets. This work extends Sparkle, an accelerator architecture, which is developed specifically for processing SpMM in DL. During the balanced data loading process, some modifications are implemented to enhance the flexibility of the Sparkle architecture. Additionally, a Sparkle generator is proposed to accommodate diverse resource constraints and facilitate adaptable deployment. Leveraging Sparkle’s structural parameters and template-based design methods, the generator enables automatic Sparkle circuit generation under varying parameters. An instantiated Sparkle accelerator is implemented on the Xilinx xqvu11p FPGA platform with a specific configuration. Compared to the state-of-the-art SpMM accelerator SIGMA, the Sparkle accelerator instance improves the sparse computing efficiency by about 10 to 20

\(\%\)

. Furthermore, the Sparkle instance achieved 7.76

\(\times\)

higher performance over the Nvidia Orin NX GPU. More instances of accelerators with different parameters were evaluated, demonstrating that the Sparkle architecture can effectively accelerate SpMM.
Turn on, Tune in, and Listen up: Maximizing Side-Channel Recovery in Cross-Platform Time-to-Digital Converters
Authors: Drewes Colin , Sheaves Tyler , Weng Olivia , Ryan Keegan , Hunter Bill , McCarty Christopher , Kastner Ryan , Richmond Dustin
Published: June 2024

Voltage fluctuation sensors measure minute changes in an FPGA power distribution network, allowing attackers to extract information from concurrently executing computations. Previous voltage fluctuation sensors make assumptions about the co-tenant computation and require the attacker have
a priori
access or system knowledge to tune the sensor parameters statically. Additionally, prior voltage fluctuation sensors make use of proprietary vendor intellectual property and do not provide guidance on sensor migration to other vendors. We present the open-source design of the Tunable Dual-Polarity Time-to-Digital Converter, which introduces three dynamically tunable parameters that optimize signal measurement, including the transition polarity, sample window, frequency, and phase. We show that a properly tuned sensor improves co-tenant classification accuracy by 2.5

\(\times\)

over prior work and increases the ability to identify the co-tenant computation and its microarchitectural implementation. Across 13 varying applications, our techniques yield an 80% classification accuracy that generalizes beyond a single board. Our sensor improves the ability of a correlation power analysis attack to rank correct subkey values by 2

\(\times\)

. As an extension to our prior work, we show that the voltage fluctuation sensor is portable to multiple FPGA vendors, and we demonstrate implementations on both Xilinx and Intel FPGA systems.
Exploring Trade-offs in Explainable AI
Authors: Brown Dene , Hawe Glenn
Published: June 2024

Machine Learning (ML) models are increasingly used in systems that involve physical human interaction or decision-making systems that impact human health and safety. Ensuring that these systems are safe and reliable is an important topic of current AI research.

For many ML models it is unclear how a prediction (output) is arrived at from the provided features (input). Critical systems cannot blindly trust the predictions of such "black box" models, but instead need additional reassurance via insight into the model's reasoning. A range of methods exist within the field of Explainable AI (XAI) to make the reasoning of black box ML models more understandable and transparent.

The explanations provided by XAI methods may be evaluated in a number of (competing) ways. In this paper, we investigate the trade-off between selected metrics for an XAI method called UnRAvEL, which is similar to the popular LIME approach. Our results show that by weighting the terms within the acquisition function used in UnRAvEL, different trade-offs can be achieved.
Towards a Catalog of Prompt Patterns to Enhance the Discipline of Prompt Engineering
Authors: Schmidt Douglas C. , Spencer-Smith Jesse , Fu Quchen , White Jules
Published: June 2024

The rapid advent of Large Language Models (LLMs), such as ChatGPT and Claude, is revolutionizing various fields, from education and healthcare to the engineering of reliable software systems. These LLMs operate through "prompts," which are natural language inputs that users employ to query and leverage the models' capabilities. Given the novelty of LLMs, the understanding of how to effectively use prompts remains largely anecdotal, based on isolated use cases. This fragmented approach limits the reliability and utility of LLMs, especially when they are applied in mission-critical software environments. To harness the full potential of LLMs in such crucial contexts, therefore, we need a systematic, disciplined approach to "prompt engineering" that guides interactions with and evaluations of these LLMs.
Mode Change Management for Adaptive Cyber-physical Systems
Authors: García-Gordillo Miguel , Valls Joan J. , Coronel Javier , Sáez Sergio
Published: June 2024

Cyber-physical systems are usually integrated with a highly changing environment. Because of the variability of their environment, these systems need to adapt their behaviour at runtime to achieve the expected results. In the case of distributed solutions, this behaviour must be consistent across the continuum, increasing the complexity of the design due to the need to synchronise the different components distributed in the multiple nodes.

A multimode application approach could be used to solve this need, assuming it is implemented as a distributed system. The approach involves applications with multiple behaviours (or operational modes) and a mechanism to change from one mode to another.

This article describes an operational mode change management solution based on that approach and the reference architecture presented in the TRANSACT project. This architecture integrates CPS end devices at the edge of the network with edge computing servers and cloud computing facilities. Static and dynamic views are included to describe the solution, and specific use case scenarios are added for better understanding.
A Bioarchaeological Perspective: What's in a Name?
Authors: Buikstra Jane E.
Published: June 2024

This article explores the history of bioarchaeology from the beginning of the twentieth century, proxied by representation in publications as reported annually by the editors-in-chief of the American Journal of Physical/Biological Anthropology. Embedded within this history is the career trajectory of Jane E. Buikstra, who coined the term in relationship to the study of archaeologically recovered human remains in 1976.
New Technologies in Search and Seizure
Authors: Brank Eve M. , Groscup Jennifer L. , Sircy Kayla R.
Published: June 2024

The Fourth Amendment and court cases interpreting it provide guidelines for how law enforcement should legally approach searching for and taking evidence in criminal investigations. Though it originally applied to physical intrusion by law enforcement, current—and likely future—intrusions are more virtual in nature. Law enforcement officers no longer need to walk onto someone's property to search for criminal activity because various technologies now provide similar or more in-depth information. Technological innovations have stretched the bounds of the Fourth Amendment. Although public opinion cannot answer the policy implications, it can speak to what the public reasonably expects of the police. In general, limited research demonstrates that the public has concerns about the way law enforcement officers can use technology in their investigations, but those concerns are not strong enough to decrease individuals’ technology use.
The Use of Caenorhabditis elegans as a Model for Plant-Parasitic Nematodes: What Have We Learned?
Authors: Coke Mirela C. , Bell Christopher A. , Urwin P.E.
Published: June 2024

Nematoda is a diverse phylum that is estimated to contain more than a million species. More than 4,100 of these species have the ability to parasitize plants and cause agricultural losses estimated at US $173 billion annually. This has led to considerable research into their biology to minimize crop losses via control methods. At the infancy of plant-parasitic nematode molecular biology, researchers compared nematode genomes, genes, and biological processes to the model nematode species Caenorhabditis elegans, which is a free-living bacterial feeder. This well-annotated and researched model nematode assisted the molecular biology research, e.g., with genome assemblies, of plant-parasitic nematodes. However, as research into these plant parasites progressed, the necessity of relying on the free-living relative as a reference has reduced. This is partly driven by revealing the considerable divergence between the two types of nematodes both genomically and anatomically, forcing comparisons to be redundant as well as the increased quality of molecular plant nematology proposing more suitable model organisms for this clade of nematode. The major irregularity between the two types of nematodes is the unique anatomical structure and effector repertoire that plant nematodes utilize to establish parasitism, which C. elegans lacks, therefore reducing its value as a heterologous system to investigate parasitic processes. Despite this, C. elegans remains useful for investigating conserved genes via its utility as an expression system because of the current inability to transform plant-parasitic nematodes. Unfortunately, owing to the expertise that this requires, it is not a common and/or accessible tool. Furthermore, we believe that the application of C. elegans as an expression system for plant nematodes will be redundant once tools are established for stable reverse-genetics in these plant parasites. This will remove the restraints on molecular plant nematology and allow it to excel on par with the capabilities of C. elegans research.
The Molecular Maze of Potyviral and Host Protein Interactions
Authors: Pollari Maija E. , Aspelin William W.E. , Wang Linping , Mäkinen Kristiina M.
Published: June 2024

The negative effects of potyvirus diseases on the agricultural industry are extensive and global. Understanding how protein-protein interactions contribute to potyviral infections is imperative to developing resistant varieties that help counter the threat potyviruses pose. While many protein-protein interactions have been reported, only a fraction are essential for potyviral infection. Accumulating evidence demonstrates that potyviral infection processes are interconnected. For instance, the interaction between the eukaryotic initiation factor 4E (eIF4E) and viral protein genome-linked (VPg) is crucial for both viral translation and protecting viral RNA (vRNA). Additionally, recent evidence for open reading frames on the reverse-sense vRNA and for nonequimolar expression of viral proteins has challenged the previous polyprotein expression model. These discoveries will surely reveal more about the potyviral protein interactome. In this review, we present a synthesis of the potyviral infection cycle and discuss influential past discoveries and recent work on protein-protein interactions in various infection processes.
Interactions Between 3D Surface Shape and Material Perception
Authors: Marlow Phillip J. , Anderson Barton L.
Published: June 2024

Our visual systems are remarkably adept at deriving the shape and material properties of surfaces even when only one image of a surface is available. This ability implies that a single image of a surface contains potent information about both surface shape and material. However, from a computational perspective, the problem of deriving surface shape and material is formally ill posed. Any given image could be due to many combinations of shape, material, and illumination. Early computational models required prior knowledge about two of the three scene variables to derive the third. However, such models are biologically implausible because our visual systems are tasked with extracting all relevant scene variables from images simultaneously. This review describes recent progress in understanding how the visual system solves this problem by identifying complex forms of image structure that support its ability to simultaneously derive the shape and material properties of surfaces from images.
How Shape Perception Works, in Two Dimensions and Three Dimensions
Authors: Nielsen Kristina J. , Connor Charles E.
Published: June 2024

The ventral visual pathway transforms retinal images into neural representations that support object understanding, including exquisite appreciation of precise 2D pattern shape and 3D volumetric shape. We articulate a framework for understanding the goals of this transformation and how they are achieved by neural coding at successive ventral pathway stages. The critical goals are (a) radical compression to make shape information communicable across axonal bundles and storable in memory, (b) explicit coding to make shape information easily readable by the rest of the brain and thus accessible for cognition and behavioral control, and (c) representational stability to maintain consistent perception across highly variable viewing conditions. We describe how each transformational step in ventral pathway vision serves one or more of these goals. This three-goal framework unifies discoveries about ventral shape processing into a neural explanation for our remarkable experience of shape as a vivid, richly detailed aspect of the natural world.
Comparison of Airborne Antibiotic Resistance Genes in the Chicken Farm during Winter and Summer
Authors: Song Lu , Ma Jinbiao , Jiang Guanyu , Wang Can , Zhang Yuan , Chen Hong , Huang Ru-jin
Published: June 2024

Information regarding the abundance and dissemination of airborne antibiotic resistance genes (ARGs) in chicken farms and their correlations with airborne bacteria is limited. In this study, we investigated the bacterial communities and quantified the ARGs and mobile genetic elements (MGEs) in fecal and air samples in summer and winter. The concentrations of nearly all the airborne ARG and MGE subtypes in winter are three or four orders of magnitude higher than those in summer. Findings reveal that the indoor air of a chicken farm is a reservoir of ARGs. Based on the fecal samples, bacteria might be easily distributed in the air in the intensive chicken farm during winter. The mobility of target ARGs during winter might be stronger than during summer. These results may improve the understanding of airborne ARG transmission and its distribution characteristics and provide a reference for assessing the risks arising from chicken farms. More effort is needed to prevent and control the potential health risks induced by airborne ARGs.
Multidecadal High Mortality Disease Events in Australian Domestic Geese Associated with a Novel Alphaherpesvirus, Designated Anatid Alphaherpevirus 2
Authors: Kelly-Bosma Mirrim , Ossedryver Selina , Bowater Rachel Olive , Butler Jeff , Reid Tristan , Suen Willy W. , Underwood Darren , Latimore Shaylie , Izzard Leonard , Joseph Ancy , Mileto Patrick , Stevens Vittoria , Wang Jianning , Mackie Tessa , Mastakov Alexandr , Doneley Robert , Allavena Rachel , Neave Matthew J.
Published: June 2024

Herpesviruses are ubiquitous viruses which infect a wide range of hosts. Novel herpesviruses are being increasingly detected in free‐ranging bird populations and there are growing concerns for cross‐species infection and spillover events. Herein, multiple sporadic outbreaks of mortality caused by a herpesvirus are described in domestic geese in Queensland, Australia. Goose herpesvirus was initially detected in 1989 in south‐east Queensland, and this article details four further recent outbreaks and reports novel genome sequencing and phylogeny of the preliminarily designated anatid alphaherpesvirus 2 (AnHV‐2). Affected flocks were housed outdoors and comingled with other domesticated and wild anseriforms and other birds which were unaffected by disease. Affected geese displayed anorexia, lethargy, weakness, vomiting, and diarrhoea prior to death within 12–24 hr of the onset of clinical signs. Post‐mortem examinations showed variable hepatic necrosis, splenic necrosis, fibrinonecrotising enteritis, lymphoid necrosis, necrotising thymitis, necrotising adrenalitis, and vasculitis. Intranuclear inclusion bodies were observed in hepatocytes, biliary epithelium, small intestinal mucosal epithelium, thymus, endothelial cells, ovarian stromal cells, adrenal cortical cells, and neuronal cell bodies in peripheral nerve ganglia. Transmission electron microscopy visualised herpesviral particles in virus culture supernatant, and within the nuclei of hepatocytes, biliary epithelium, and endothelial cells in case tissues. The genome sequence of this herpesvirus, designated anatid alphaherpesvirus 2 (AnHV‐2), is described. While investigating goose mortalities, archived isolate from a swan with suspected herpesvirus infection was tested and genome sequencing identified a further novel herpesvirus, proposed anatid alphaherpesvirus 3 (AnHV‐3). The AnHV‐2 and AnHV‐3 genomes were more similar to each other, with a nucleotide identity of 76.1%, than to reference genome sequences. Phylogenetically, the new genomes formed a distinct clade within the alphaherpesvirus genus Mardivirus. We sequenced four AnHV‐2 genomes from different cases and these did not display consistent divergence over time or distance. Expanded surveillance and outbreak testing are recommended, facilitated by the development of a specific real‐time PCR for the rapid detection of AnHV‐2.