bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum walks-based simple authenticated quantum cryptography protocols for secure wireless sensor networks
Authors: Alanezi Ahmad , Abd El-Latif Ahmed A , Kolivand Hoshang , Abd-El-Atty Bassem
Published: December 2023

Wireless sensor networks (WSNs) play a crucial role in various applications, ranging from environmental monitoring to industrial automation that require high levels of security. With the development of quantum technologies, many security mechanisms may be hacked due to the promising capabilities of quantum computation. To address this challenge, quantum protocols have emerged as a promising solution for enhancing the security of wireless sensor communications. One of the common types of quantum protocols is quantum key distribution (QKD) protocols, which are investigated to allow two participants with fully quantum capabilities to share a random secret key, while semi-quantum key distribution (SQKD) protocols are designed to perform the same task using fewer quantum resources to make quantum communications more realizable and practical. Quantum walk (QW) plays an essential role in quantum computing, which is a universal quantum computational paradigm. In this work, we utilize the advantages of QW to design three authenticated quantum cryptographic protocols to establish secure channels for data transmission between sensor nodes: the first one is authenticated quantum key distribution (AQKD), the second one is authenticated semi-quantum key distribution (ASQKD) with one of the two participants having limited quantum capabilities, and the last one is ASQKD but both legitimate users possess limited quantum resources. The advantages of the proposed protocols are that the partners can exchange several different keys with the same exchanged qubits, and the presented protocols depend on a one-way quantum communication channel. In contrast, all previously designed SQKD protocols rely on two-way quantum communication. Security analyses prove that the presented protocols are secure against various well-known attacks and highly efficient. The utilization of the presented protocols in wireless sensor communications opens up new avenues for secure and trustworthy data transmission, enabling the deployment of resilient WSNs in critical applications. This work also paves the way for future exploration of quantum-based security protocols and their integration into WSNs for enhanced data protection.
Three-dimensional bound states of cylindrical quantum heterostructures with position-dependent mass carriers
Authors: Christiansen H R , Lima R M
Published: December 2023

We present a comprehensive spectral analysis of cylindrical quantum heterostructures by considering effective electronic carriers with position-dependent mass for five different kinetic-operator orderings. We obtain the bound energy eigenstates of particles in a three-dimensional cylindrical nanowire under a confining hyperbolic potential with both open and closed boundary conditions in the radial and the axial directions. In the present model we consider carriers with continuous mass distributions within the dot with abrupt mass discontinuities at the barriers, moving in a quantum dot that connects different substances. Continuity of mass and potential at the interfaces with the external layers result as a particular case. Our approach is mostly analytical and allows a precise comparison among von Roos ordering classes.
Thermal quantum coherence of two–qutrit Heisenberg XXZ model with Herring-Flicker coupling and Dzyaloshinskii-Moriya interaction under magnetic field
Authors: Adnane Brahim , Moqine Younes , Belouad Abdelhadi , El Bouâzzaoui Choubabi , Houça Rachid
Published: December 2023

In this study, we use the concept of l
1-norm coherence to characterize the entanglement of a two–qutrit Heisenberg XXZ model for subject to a uniform magnetic field and z–axis Dzyaloshinskii–Moriya interaction with Herring-Flicker coupling. We show that the temperature, magnetic field, DM interaction, and distance of Herring-Flicker coupling can all control the entanglement. However, the state system becomes less entangled at high temperatures or strong magnetic fields and vice versa. Our findings suggest that entanglement rises when the z–axis DM interaction increases. Additionally, we show that plateau behavior in the entanglement between spins (1, 1) occurs in the XXZ Heisenberg spin system and is influenced by the magnetic field, demonstrating that thermal agitation can weaken entanglement plateaus. Moreover, by setting the strengths coupling of the spin, we quickly recover the isotropic XY and XXX Heisenberg models. Finally, Herring-Flicker coupling affects the degree of entanglement. When Herring-Flicker coupling and temperature are at small values, the degree of entanglement is at its highest. Still, when Herring-Flicker coupling is at substantial values, the degree of entanglement tends to stabilize.
A scalable system to measure contrail formation on a per-flight basis
Authors: Geraedts Scott , Brand Erica , Dean Thomas R , Eastham Sebastian , Elkin Carl , Engberg Zebediah , Hager Ulrike , Langmore Ian , McCloskey Kevin , Yue-Hei Ng Joe , Platt John C , Sankar Tharun , Sarna Aaron , Shapiro Marc , Goyal Nita
Published: December 2023

Persistent contrails make up a large fraction of aviation's contribution to global warming. We describe a scalable, automated detection and matching (ADM) system to determine from satellite data whether a flight has made a persistent contrail. The ADM system compares flight segments to contrails detected by a computer vision algorithm running on images from the GOES-16 Advanced Baseline Imager. We develop a flight matching algorithm and use it to label each flight segment as a match or non-match. We perform this analysis on 1.6 million flight segments. The result is an analysis of which flights make persistent contrails several orders of magnitude larger than any previous work. We assess the agreement between our labels and available prediction models based on weather forecasts. Shifting air traffic to avoid regions of contrail formation has been proposed as a possible mitigation with the potential for very low cost/ton-CO2e. Our findings suggest that imperfections in these prediction models increase this cost/ton by about an order of magnitude. Contrail avoidance is a cost-effective climate change mitigation even with this factor taken into account, but our results quantify the need for more accurate contrail prediction methods and establish a benchmark for future development.
Initiative to reduce unnecessary routine daily testing of complete blood counts across 11 safety net hospitals
Authors: Cho Hyung J , Israilov Sigal , Tsega Surafel , Alaiev Dan , Talledo Joseph , Chandra Komal , Alarcon Manchego Peter , Zaurova Milana , Petrilli Christopher M , Krouss Mona
Published: December 2023

Objectives

National societies recommend against performing routine daily laboratory testing without a specific indication. Unnecessary testing can lead to patient harm, such as hospital-acquired anemia. The objective of this study was to reduce repeat complete blood counts (CBCs) after initial testing.

Methods

This was a quality improvement initiative implemented across 11 safety net hospitals in New York City. A best practice advisory (BPA) was implemented that asked the user to remove a CBC if the last 2 CBCs within 72 hours had normal white blood cell and platelet counts and unchanged hemoglobin levels. The outcome measure was the rate of CBCs per 1000 patient days preintervention (January 8, 2020, to December 22, 2020) to postintervention (December 23, 2020, to December 7, 2021). The process measure was the acceptance rate of the BPA, defined as the number of times the repeat CBC order was removed through the BPA divided by the total number of times the BPA triggered.

Results

Across 11 hospitals, repeat CBC testing decreased by 12.3% (73.05 to 64.04 per 1000 patient days, P < .001). Six of the 11 hospitals exhibited statistically significant decreases, ranging from a 10% to 48.9% decrease of repeat CBCs. The overall BPA action rate was 20.0% (24,029 of 119,944 repeat CBCs).

Conclusions

This low-effort, electronic health record–based intervention can effectively reduce unnecessary laboratory testing.
Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering
Authors: Zheng Jiahao , Yang Yuedong , Dai Zhiming
Published: December 2023

Single-cell Hi-C (scHi-C) technology enables the investigation of 3D chromatin structure variability across individual cells. However, the analysis of scHi-C data is challenged by a large number of missing values. Here, we present a scHi-C data imputation model HiC-SGL, based on Subgraph extraction and graph representation learning. HiC-SGL can also learn informative low-dimensional embeddings of cells. We demonstrate that our method surpasses existing methods in terms of imputation accuracy and clustering performance by various metrics.
Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes
Authors: Zou Min , Li Honghao , Su Dongqing , Xiong Yuqiang , Wei Haodong , Wang Shiyuan , Sun Hongmei , Wang Tao , Xi Qilemuge , Zuo Yongchun , Yang Lei
Published: December 2023

Pancreatic cancer is a globally recognized highly aggressive malignancy, posing a significant threat to human health and characterized by pronounced heterogeneity. In recent years, researchers have uncovered that the development and progression of cancer are often attributed to the accumulation of somatic mutations within cells. However, cancer somatic mutation data exhibit characteristics such as high dimensionality and sparsity, which pose new challenges in utilizing these data effectively. In this study, we propagated the discrete somatic mutation data of pancreatic cancer through a network propagation model based on protein–protein interaction networks. This resulted in smoothed somatic mutation profile data that incorporate protein network information. Based on this smoothed mutation profile data, we obtained the activity levels of different metabolic pathways in pancreatic cancer patients. Subsequently, using the activity levels of various metabolic pathways in cancer patients, we employed a deep clustering algorithm to establish biologically and clinically relevant metabolic subtypes of pancreatic cancer. Our study holds scientific significance in classifying pancreatic cancer based on somatic mutation data and may provide a crucial theoretical basis for the diagnosis and immunotherapy of pancreatic cancer patients.
Urinary glyphosate levels and association with mortality in the 2013–16 National Health and Nutrition Examination Survey
Authors: Untalan Matthew , Ivic-Pavlicic Tara , Taioli Emanuela
Published: December 2023

Objectives

Glyphosate is the most commonly used herbicide in the USA; however, its safety is still under debate. We assessed glyphosate levels and their association with overall mortality in a representative sample of the US adult population from the 2013 to 2016 National Health and Nutrition Examination Survey.

Methods

We extracted data on urinary glyphosate (N = 2910) measured by ion chromatography isotope-dilution tandem mass spectrometry. Associations between glyphosate concentrations and demographic, lifestyle and other exposures were analyzed. Data were linked to public-use Mortality Files for 2019.

Results

The mean (STD) glyphosate level was 0.53 (0.59) ng/ml, with 25.7% of the subjects having glyphosate levels at or below the detection limit. At multivariate analysis, age and creatinine were associated with glyphosate urinary levels (both P < 0.0001). There was a borderline association between glyphosate levels and mortality (HRadj 1.33; 95% CI 0.99–1.77 P = 0.06). When 3,5,6-trichloropyridinol was excluded from the Cox model, glyphosate exhibits a significant association with mortality (HRadj 1.33; 95% CI 1.00–1.77; P = 0.0532).

Conclusions

These nationally representative data suggest that recent exposure to glyphosate could be associated with increased mortality. More studies are necessary to understand population-level risk associated with the product, given its widespread use in agriculture.
Functional and anatomical connectivity predict brain stimulation’s mnemonic effects
Authors: Ezzyat Youssef , Kragel James E , Solomon Ethan A , Lega Bradley C , Aronson Joshua P , Jobst Barbara C , Gross Robert E , Sperling Michael R , Worrell Gregory A , Sheth Sameer A , Wanda Paul A , Rizzuto Daniel S , Kahana Michael J
Published: December 2023

Closed-loop direct brain stimulation is a promising tool for modulating neural activity and behavior. However, it remains unclear how to optimally target stimulation to modulate brain activity in particular brain networks that underlie particular cognitive functions. Here, we test the hypothesis that stimulation’s behavioral and physiological effects depend on the stimulation target’s anatomical and functional network properties. We delivered closed-loop stimulation as 47 neurosurgical patients studied and recalled word lists. Multivariate classifiers, trained to predict momentary lapses in memory function, triggered the stimulation of the lateral temporal cortex (LTC) during the study phase of the task. We found that LTC stimulation specifically improved memory when delivered to targets near white matter pathways. Memory improvement was largest for targets near white matter that also showed high functional connectivity to the brain’s memory network. These targets also reduced low-frequency activity in this network, an established marker of successful memory encoding. These data reveal how anatomical and functional networks mediate stimulation’s behavioral and physiological effects, provide further evidence that closed-loop LTC stimulation can improve episodic memory, and suggest a method for optimizing neuromodulation through improved stimulation targeting.
Anonymization of face images with Contrastive Learning
Authors: Xu Xintong , Cui Run , Huang Chanying , Yan Kedong
Published: December 2023

Photos or videos taken by individuals often carry sensitive details such as facial identities, which has led to an escalating societal interest in privacy protection measures. We suggest an improved face identity transformer that offers password-protected anonymization and de-anonymization of photo-realistic facial images in visual data. Our face identity transformer is designed to (1) erase facial identity information after anonymization, (2) restore the original face when a correct password is provided and (3) generate an incorrect but realistic face when given an incorrect password. The processes of image anonymization and de-anonymization are facilitated through a password scheme, a multi-task learning objective and generative adversarial networks comprising InfoGAN and contrastive learning. In-depth experiments indicate that our methodology can execute anonymization and de-anonymization based on password conditions whilst reducing training time and enhancing image quality compared to existing anonymization procedures. Additionally, it maintains a recognition rate as low as 4.8% for anonymized images without sacrificing the face detection rate of the original method.
Design of the formalized and integrated Alzheimer’s Disease Ontology and its application in retrieving textual data via text mining
Authors: Zhang Bide , Lage-Rupprecht Vanessa , Wegner Philipp , Sargsyan Astghik , Gebel Stephan , Jacobs Marc , Klein Jürgen , Hofmann-Apitius Martin , Tom Kodamullil Alpha
Published: December 2023

As one of the leading causes for dementia in the population, it is imperative that we discern exactly why Alzheimer’s disease (AD) has a strong molecular association with beta-amyloid and tau. Although a clear understanding about etiology and pathogenesis of AD remains unsolved, scientists worldwide have dedicated significant efforts to discovering the molecular interactions linked to the pathological characteristics and potential treatments. Knowledge representations, such as domain ontologies encompassing our current understanding about AD, could greatly assist and contribute to disease research. This paper describes the construction and application of the integrated Alzheimer’s Disease Ontology (ADO), combining selected concepts from the former version of the ADO and the Alzheimer’s Disease Mapping Ontology (ADMO). In addition to the existing entities available from these knowledge models, essential knowledge about AD from public sources, such as newly discovered risk factor genes and novel treatments, was also integrated. The ADO can also be leveraged in text mining scenarios given that it is conceptually enriched with domain-specific knowledge as well as their relations. The integrated ADO consists of 39 855 total axioms. The ontology covers many aspects of the AD domain, including risk factor genes, clinical features, treatments and experimental models. The ontology complies with the Open Biological and Biomedical Ontology principles and was accepted by the foundry. In this paper, we illustrate the role of the presented ontology in extracting textual information from the SCAIView database and key measures in an ADO-based corpus.

Database URL:  https://academic.oup.com/database
Peoples, Inhabitants and Workers: Colonialism in the Treaty of Rome
Authors: Eklund Hanna
Published: December 2023

In 1957, when the Treaty of Rome was signed, founding the European Economic Community (EEC), which later became the European Union (EU), four out of six of the original member states were colonial powers. This article uses archival material from the Treaty of Rome negotiations to interrogate ways in which the colonial politics of the time shaped the drafting of legal categories describing individuals: those of peoples, inhabitants and workers. As the Treaty of Rome ‘associated’ colonized territories to the EEC, this article shows how the treaty simultaneously arranged its legal categories to exclude individuals who lived in colonized territories from legal benefits and representation. This article situates the EU as an example of a post-World War II international organization, with its founding legal texts shaped by colonialism.
John Sheppard and the Ewens: a closer look
Authors: Smart Jason
Published: December 2023

The known musical career of John Sheppard spans just 15 years. In 1543, when he was probably still in his late twenties, he was appointed informator choristarum of Magdalen College, Oxford. At his death in 1558, at about the age of 43, he was a Gentleman of the Chapel Royal, perhaps having been appointed on leaving Oxford in 1548. A recent article draws attention to the fact that, early in the reign of Queen Mary, Sheppard and his family were involved in a legal action concerning a group of properties in the parish of St Clement Danes, Middlesex. Deeper investigation of this dispute reveals where Sheppard’s geographical ties lay shortly before his Oxford appointment. It allows us to pinpoint with a high degree of confidence when and where his first marriage took place and to understand a little of the young couple’s circumstances. A separate action, in which he appeared as a joint plaintiff with his Chapel Royal colleague Luke Caustell, is less revealing, but potentially points to a connection with the same geographical region of England.
Antibacterial activity of solid surfaces is critically dependent on relative humidity, inoculum volume, and organic soiling
Authors: Kaur Harleen , Rosenberg Merilin , Kook Mati , Danilian Dmytro , Kisand Vambola , Ivask Angela
Published: December 2023

Antimicrobial surface materials potentially prevent pathogen transfer from contaminated surfaces. Efficacy of such surfaces is assessed by standard methods using wet exposure conditions known to overestimate antimicrobial activity compared to dry exposure. Some dry test formats have been proposed but semi-dry exposure scenarios e.g. oral spray or water droplets exposed to ambient environment, are less studied. We aimed to determine the impact of environmental test conditions on antibacterial activity against the model species Escherichia coli and Staphylococcus aureus. Surfaces based on copper, silver, and quaternary ammonium with known or claimed antimicrobial properties were tested in conditions mimicking microdroplet spray or larger water droplets exposed to variable relative air humidity in the presence or absence of organic soiling. All the environmental parameters critically affected antibacterial activity of the tested surfaces from no effect in high-organic dry conditions to higher effect in low-organic humid conditions but not reaching the effect size demonstrated in the ISO 22169 wet format. Copper was the most efficient antibacterial surface followed by silver and quaternary ammonium based coating. Antimicrobial testing of surfaces using small droplet contamination in application-relevant conditions could therefore be considered as one of the worst-case exposure scenarios relevant to dry use surfaces.
The “Mother of All Protests” Meets Israeli Older Persons: When Age and Gender Intersect in Political Protests
Authors: Ayalon Liat , Okun Sarit
Published: December 2023

Objectives

The Israeli government’s announcement of a judicial overhaul has resulted in ongoing protests and strikes starting in early 2023. The present study examines the intersection between age and gender in political protests.

Methods

The present qualitative study is based on interviews with 13 men and 17 women over the age of 65 who participated in the protests. We conducted qualitative thematic analysis comparing and contrasting categories within and between interviews, while taking the gender perspective into account.

Results

The study highlights patterns of gendered but also older-age protesting practices. Whereas men fought for the sake of past generations, women protested mainly for the sake of their children and grandchildren. In addition, men tended to capitalize on their past achievements as fighters, whereas women emphasized their current achievements as grandmothers.

Discussion

Our findings suggest that under some circumstances, even stereotypical devalued attributes (e.g., being a grandmother) can be used as powerful tools to attract supporters and fight for a cause. Older men, on the other hand, tend to hold on to their past achievements as fighters, at the top of the hegemonic hierarchy to ensure their power and status in current protests. To ensure the appeal of political protests, heterogeneity in motives and protesting styles should be acknowledged.
Partisan YouTube use and evaluation of knowledge in Korea and the United States: a fresh perspective via the Dunning–Kruger effect
Authors: Lee Hoon , Kim Hyeonwoo , Yeon Jiyoung
Published: December 2023

This study investigates how partisan YouTube use can paint biased evaluations of one’s own as well as others’ knowledge. Understanding of these relationships is enriched by a fresh theoretical perspective via the Dunning–Kruger effect, suggesting that people, especially those who perform poorly, tend to overestimate their own competence. Using South Korea and the United States as two different contexts, we also attend to how cultures moderate these relationships. Findings based on two independent surveys in these countries shed light on the role of partisan YouTube use in shaping people’s hyperbolic self-evaluations and contrasted assessments of in- and out-group members. Furthermore, these trends are more pronounced among those with relatively a low level of actual knowledge. Finally, using partisan YouTube for news is strongly associated with group-based evaluations of knowledge in Korea, whereas it yields significant relationships only with self-evaluations of knowledge in the United States.
Impact of Sickle Cell Awareness Day on online health information seeking in Africa using Google Trends
Authors: Parry Emma , Ayinla-Jimoh Idayat , Shepherd Thomas A
Published: December 2023

The United Nations Council Assembly recognized sickle cell disease (SCD) as a global public health problem due to its increasing burden, particularly in sub-Saharan Africa. To raise awareness, a resolution was adopted, designating June 19th as SCD awareness day. However, the impact of this awareness day on online health information seeking behaviour (OHISB) in African countries is not well understood, especially in Nigeria, Ghana and Uganda where SCD prevalence is high. To assess the impact, the study used Google Trends data as a measure of OHISB for SCD. The analysis covered the 60 days before the awareness day, the awareness day itself, and the 60 days afterward. Time series analysis was conducted using joinpoint regression to identify significant changes in OHISB trends. The results indicated that the impact of the Sickle Cell Awareness Day on OHISB varied across African countries and did not consistently inspire significant changes in information seeking behaviour. This suggests the need for more targeted awareness campaigns to improve public knowledge of SCD in Africa. It also highlights the importance of revising the current awareness day or creating alternative health awareness initiatives that adopt a long-term approach and address the specific health needs of the African population. Furthermore, due to limitations in using Google Trends data in some African countries with insufficient data, future research should explore other sources of internet data or conduct surveys to gain a more comprehensive understanding of the impact of the Sickle Cell Awareness Day on OHISB in Africa.
Media coverage of commercial industry activities impacting Aboriginal and Torres Strait Islander health, 2018–2022
Authors: Crocetti Alessandro Connor , Cubillo (Larrakia) Beau , Hill (Torres Strait Islander) Karen , Carter (Yorta Yorta) Morgan , Paradies (Wakaya) Yin , Backholer Kathryn , Browne Jennifer
Published: December 2023

This study aimed to examine the extent and nature of Australian news media coverage of commercial industry activities that explicitly speak to Aboriginal and Torres Strait Islander contexts. We undertook content and framing analysis of Australian newspaper and online media articles published between January 2018 and March 2022 that included terms related to ‘Indigenous’, ‘commercial’ and ‘health’. Analysis focused on the nature of coverage, framing of responsibility, patterns over time and stakeholder representation. Forty-six media articles were included in the analysis. Half of these articles related to the actions of three companies (Woolworths, WAM Clothing and Rio Tinto). Most articles described negative health and well-being impacts of commercial activity, while four described positive impacts. The most common voice represented in media articles was from industry (n = 25). Aboriginal or Torres Strait Islander voices were represented in 21 articles. This analysis highlights how commercial activities in Australia are reported to negatively influence Aboriginal and Torres Strait Islander health and well-being, and that industry voices are more commonly represented in the media related to these issues.
The impact of maternal pertussis vaccination recommendation on infant pertussis incidence and mortality in the USA: an interrupted time series analysis
Authors: Psaras Catherine , Regan Annette , Nianogo Roch , Arah Onyebuchi A , Seamans Marissa J
Published: December 2023

Background

Pertussis is a contagious respiratory disease. Maternal tetanus–diphtheria–acellular pertussis vaccination during pregnancy has been recommended by the United States Centres for Disease Control (US CDC) Advisory Committee on Immunization Practices (ACIP) for unvaccinated pregnant women since October 2011 to prevent infection among infants; in 2012, ACIP extended this recommendation to every pregnancy, regardless of previous vaccination status. The population-level effect of these recommendations on infant pertussis is unknown. This study aimed to examine the impact of the 2011/2012 ACIP pertussis recommendation on pertussis incidence and mortality among US infants.

Methods

We used monthly data on pertussis deaths among infants aged <1 year between January 2005 and December 2017 in the CDC Death Data and yearly infant pertussis incidence data from the CDC National Notifiable Disease Surveillance System to perform an interrupted time series analysis, accounting for the passage of the Affordable Care Act.

Results

This study included 156 months of data. A potential decline in trend in infant pertussis incidence was noted during the post-recommendations period. No appreciable differences in trend were found in population-level infant pertussis mortality after the guideline changes in both adjusted and unadjusted models. Results were similar for all mortality sensitivity analyses.

Conclusions

The 2011/2012 ACIP maternal pertussis vaccination recommendations were not associated with a population-level change in the trend in mortality, but were potentially associated with a decrease in incidence in the USA between 2005 and 2017.
Existence of unattainable states for Schrödinger type flows on the half-line
Authors: Özsarı Türker , Kalimeris Konstantinos
Published: December 2023

We prove that the solutions of the Schrödinger and biharmonic Schrödinger equations do not have the exact boundary controllability property on the half-line by showing that the associated adjoint models lack observability. We consider the framework of $L^2$ boundary controls with data spaces $H^{-1}(\mathbb{R}_+)$ and $H^{-2}(\mathbb{R}_+)$ for the classical and biharmonic Schrödinger equations, respectively. The lack of controllability on the half-line contrasts with the corresponding dynamics on a finite interval for a similar regularity setting. Our proof is based on an argument that uses the sharp fractional time trace estimates for solutions of the adjoint models. We also make several remarks on the connection of controllability and temporal regularity of spatial traces.
Analysis of In-Patient Evolution of Escherichia coli Reveals Potential Links to Relapse of Bone and Joint Infections
Authors: Thiriet-Rupert Stanislas , Josse Jérôme , Perez-Pascual David , Tasse Jason , Andre Camille , Abad Lélia , Lebeaux David , Ghigo Jean-Marc , Laurent Frédéric , Beloin Christophe
Published: December 2023

Bone and joint infections (BJIs) are difficult to treat and affect a growing number of patients, in which relapses are observed in 10–20% of case. These relapses, which call for prolonged antibiotic treatment and increase resistance emergence risk, may originate from ill-understood adaptation of the pathogen to the host. Here, we investigated 3 pairs of Escherichia coli strains from BJI cases and their relapses to unravel adaptations within patients. Whole-genome comparison presented evidence for positive selection and phenotypic characterization showed that biofilm formation remained unchanged, contrary to what is usually described in such cases. Although virulence was not modified, we identified the loss of 2 virulence factors contributing to immune system evasion in one of the studied strains. Other strategies, including global growth optimization and colicin production, likely allowed the strains to outcompete competitors. This work highlights the variety of strategies allowing in-patient adaptation in BJIs.
ACC1-mediated fatty acid biosynthesis intrinsically controls thymic iNKT cell development
Authors: Kanno Toshio , Miyako Keisuke , Endo Takeru , Yokoyama Satoru , Asou Hikari K , Yamada Kazuko , Ohara Osamu , Nakayama Toshinori , Kimura Motoko Y , Endo Yusuke
Published: December 2023

To meet the energetic requirements associated with activation, proliferation, and survival, T cells switch their metabolic signatures from energetically quiescent to activated. However, little is known about the role of metabolic pathway controlling the development of invariant natural killer T (iNKT) cells. In the present study, we found that acetyl-CoA carboxylase 1 (ACC1), a rate-limiting enzyme for the fatty acid biosynthesis pathway, plays an essential role in the development of iNKT cells in the thymus. Mice lacking T-cell specific ACC1 showed a reduced number of iNKT cells with an increased proportion of iNKT cells at immature stages 0 and 1. Furthermore, mixed bone marrow (BM) chimera experiments revealed that T-cell intrinsic ACC1 expression was selectively important for the development of thymic iNKT cells, especially for the differentiation of the NKT1 cell subset. Our single-cell RNA-sequencing (scRNA-seq) data and functional analysis demonstrated that ACC1 is responsible for survival of developing iNKT cells. Thus, these findings highlighted a novel role of ACC1 in controlling thymic iNKT cell development mediated by the control of cell survival.
Comparative genomic analysis reveals niche adaption of Lactobacillus acidophilus
Authors: Liu Xudong , Wu Zhinan , Hu Tongyuan , Lin Xiaoqian , Liang Hewei , Li Wenxi , Jin Xin , Xiao Liang , Fang Xiaodong , Zou Yuanqiang
Published: December 2023

Aims

Lactobacillus acidophilus has been extensively applied in plentiful probiotic products. Although several studies have been performed to investigate the beneficial characteristics and genome function of L. acidophilus, comparative genomic analysis remains scarce. In this study, we collected 74 L. acidophilus genomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis.

Methods and results

This study revealed the potential correlation of the genomic diversity and niche adaptation of L. acidophilus from different perspectives. The pan-genome of L. acidophilus was found to be open, with metabolism, information storage, and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to the adaptation of the animal gut. SNP analysis showed the differences of the utilization of vitamin B12 in cellular of L. acidophilus strains from animal gut and others.

Conclusions

This work provides new insights for the genomic diversity analysis of L. acidophilus and uncovers the ecological adaptation of the specific strains.
Potential of yeasts as biocontrol agents against Fusarium graminearum in vitro and on corn
Authors: de Oliveira Andressa Jacqueline , Ono Mario Augusto , Suguiura Igor Massahiro de Souza , Zucareli Claudemir , Garcia Emanueli Bastos , Olchanheski Luiz Ricardo , Ono Elisabete Yurie Sataque
Published: December 2023

Aims

The antifungal effect of the yeast species Kluyveromyces marxianus, Meyerozyma caribbica, and Wickerhamomyces anomalus was evaluated against two Fusarium graminearum strains (FRS 26 and FSP 27) in vitro and on corn seeds.

Methods and results

The antifungal effect of the yeasts against F. graminearum was evaluated using scanning electron microscopy and extracellular chitinase and glucanase production to further elucidate the biocontrol mode of action. In addition, the germination percentage and vigor test were investigated after applying yeast on corn seeds. All the yeast strains inhibited fungal growth in vitro (57.4%–100.0%) and on corn seeds (18.9%–87.2%). In co-culture with antagonistic yeasts, F. graminearum showed collapsed hyphae and turgidity loss, which could be related to the ability of yeasts to produce chitinases and glucanases. The three yeasts did not affect the seed corn germination, and W. anomalus and M. caribbica increased corn seed growth parameters (germination percentage, shoot and root length, and shoot dry weight).

Conclusion

Meyerozyma caribbica and W. anomalus showed satisfactory F. graminearum growth inhibition rates and did not affect seed growth parameters. Further studies are required to evaluate the application of these yeasts to the crop in the field.
Developing and evaluating pediatric phecodes (Peds-Phecodes) for high-throughput phenotyping using electronic health records
Authors: Grabowska Monika E , Van Driest Sara L , Robinson Jamie R , Patrick Anna E , Guardo Chris , Gangireddy Srushti , Ong Henry H , Feng QiPing , Carroll Robert , Kannankeril Prince J , Wei Wei-Qi
Published: December 2023

Objective

Pediatric patients have different diseases and outcomes than adults; however, existing phecodes do not capture the distinctive pediatric spectrum of disease. We aim to develop specialized pediatric phecodes (Peds-Phecodes) to enable efficient, large-scale phenotypic analyses of pediatric patients.

Materials and Methods

We adopted a hybrid data- and knowledge-driven approach leveraging electronic health records (EHRs) and genetic data from Vanderbilt University Medical Center to modify the most recent version of phecodes to better capture pediatric phenotypes. First, we compared the prevalence of patient diagnoses in pediatric and adult populations to identify disease phenotypes differentially affecting children and adults. We then used clinical domain knowledge to remove phecodes representing phenotypes unlikely to affect pediatric patients and create new phecodes for phenotypes relevant to the pediatric population. We further compared phenome-wide association study (PheWAS) outcomes replicating known pediatric genotype-phenotype associations between Peds-Phecodes and phecodes.

Results

The Peds-Phecodes aggregate 15 533 ICD-9-CM codes and 82 949 ICD-10-CM codes into 2051 distinct phecodes. Peds-Phecodes replicated more known pediatric genotype-phenotype associations than phecodes (248 vs 192 out of 687 SNPs, P < .001).

Discussion

We introduce Peds-Phecodes, a high-throughput EHR phenotyping tool tailored for use in pediatric populations. We successfully validated the Peds-Phecodes using genetic replication studies. Our findings also reveal the potential use of Peds-Phecodes in detecting novel genotype-phenotype associations for pediatric conditions. We expect that Peds-Phecodes will facilitate large-scale phenomic and genomic analyses in pediatric populations.

Conclusion

Peds-Phecodes capture higher-quality pediatric phenotypes and deliver superior PheWAS outcomes compared to phecodes.
A bright triple transient that vanished within 50 min
Authors: Solano Enrique , Marcy Geoffrey W , Villarroel Beatriz , Geier Stefan , Streblyanska Alina , Lombardi Gianluca , Bär Rudolf E , Andruk Vitaly N
Published: December 2023

We report on three optically bright, ∼16th mag, point sources within 10 arcsec of each other that vanished within 1 h, based on two consecutive exposures at Palomar Observatory on 1952 July 19 (POSS I Red and Blue). The three point sources have continued to be absent in telescope exposures during 71 yr with detection thresholds of ∼21st mag. We obtained two deep exposures with the 10.4-m Gran Telescopio Canarias on 2023 April 25 and 27 in r and g band, both reaching magnitude 25.5 (3σ). The three point sources are still absent, implying they have dimmed by more than 10 mag within an hour back in 1952. When bright in 1952, the most isolated transient source has a profile nearly the same as comparison stars, implying the sources are subarcsec in angular size and they exhibit no elongation due to movement. This triple transient has observed properties similar to other cases where groups of transients (‘multiple transients’) have appeared and vanished in a small region within a plate exposure. The explanation for these three transients and the previously reported cases remains unclear. Models involving background objects that are optically luminous for less than 1 h coupled with foreground gravitational lensing seem plausible. If so, a significant population of massive objects with structure serving as the lenses, to produce three images, are required to explain the subhour transients.
High dust content of a quiescent galaxy at z ∼ 2 revealed by deep ALMA observation
Authors: Lee Minju M , Steidel Charles C , Brammer Gabriel , Förster-Schreiber Natascha , Renzini Alvio , Liu Daizhong , Herrera-Camus Rodrigo , Naab Thorsten , Price Sedona H , Übler Hannah , Arriagada-Neira Sebastián , Magdis Georgios
Published: December 2023

We report the detection of cold dust in an apparently quiescent massive galaxy (log (M⋆/M⊙) ≈ 11) at z ∼ 2 (G4). The source is identified as a serendipitous 2 mm continuum source in a deep ALMA observation within the field of Q2343-BX610, a z = 2.21 massive star-forming disc galaxy. Available multiband photometry of G4 suggests redshift of z ∼ 2 and a low specific star formation rate (sSFR), log (SFR/M⋆)[yr−1] ≈ −10.2, corresponding to ≈1.2 dex below the z = 2 main sequence (MS). G4 appears to be a peculiar dust-rich quiescent galaxy for its stellar mass (log (Mdust/M⋆) = −2.71 ± 0.26), with its estimated mass-weighted age (∼1–2 Gyr). We compile z ≳ 1 quiescent galaxies in the literature and discuss their age–ΔMS and log (Mdust/M⋆)–age relations to investigate passive evolution and dust depletion scale. A long dust depletion time and its morphology suggest morphological quenching along with less efficient feedback that could have acted on G4. The estimated dust yield for G4 further supports this idea, requiring efficient survival of dust and/or grain growth, and rejuvenation (or additional accretion). Follow-up observations probing the stellar light and cold dust peak are necessary to understand the implication of these findings in the broader context of galaxy evolutionary studies and quenching in the early universe.
The magnetically quiet solar surface dominates HARPS-N solar RVs during low activity
Authors: Lakeland Ben S , Naylor Tim , Haywood Raphaëlle D , Meunier Nadège , Rescigno Federica , Dalal Shweta , Mortier Annelies , Thompson Samantha J , Cameron Andrew Collier , Dumusque Xavier , López-Morales Mercedes , Pepe Francesco , Rice Ken , Sozzetti Alessandro , Udry Stéphane , Ford Eric , Ghedina Adriano , Lodi Marcello
Published: December 2023

Using images from the Helioseismic and Magnetic Imager aboard the Solar Dynamics Observatory, we extract the radial velocity (RV) signal arising from the suppression of convective blueshift and from bright faculae and dark sunspots transiting the rotating solar disc. We remove these rotationally modulated magnetic-activity contributions from simultaneous RVs observed by the HARPS-N (High Accuracy Radial velocity Planet Searcher for the Northern hemisphere) solar feed to produce an RV time series arising from the magnetically quiet solar surface (the ‘inactive-region RVs’). We find that the level of variability in the inactive-region RVs remains constant over the almost 7-yr baseline and shows no correlation with well-known activity indicators. With an root-mean-square scatter of roughly 1 ${\rm m\, s}^{-1}$, the inactive-region RV time series dominates the total RV variability budget during the decline of solar cycle 24. Finally, we compare the variability amplitude and time-scale of the inactive-region RVs with simulations of supergranulation. We find consistency between the inactive-region RV and simulated time series, indicating that supergranulation is a significant contribution to the overall solar RV variability, and may be the main source of variability towards solar minimum. This work highlights supergranulation as a key barrier to detecting Earth twins.
Common computations for metacognition and meta-metacognition
Authors: Zheng Yunxuan , Recht Samuel , Rahnev Dobromir
Published: December 2023

Recent evidence shows that people have the meta-metacognitive ability to evaluate their metacognitive judgments of confidence. However, it is unclear whether meta-metacognitive judgments are made by a different system and rely on a separate set of computations compared to metacognitive judgments. To address this question, we asked participants (N = 36) to perform a perceptual decision-making task and provide (i) an object-level, Type-1 response about the identity of the stimulus; (ii) a metacognitive, Type-2 response (low/high) regarding their confidence in their Type-1 decision; and (iii) a meta-metacognitive, Type-3 response (low/high) regarding the quality of their Type-2 rating. We found strong evidence for the existence of Type-3, meta-metacognitive ability. In a separate condition, participants performed an identical task with only a Type-1 response followed by a Type-2 response given on a 4-point scale. We found that the two conditions produced equivalent results such that the combination of binary Type-2 and binary Type-3 responses acts similar to a 4-point Type-2 response. Critically, while Type-2 evaluations were subject to metacognitive noise, Type-3 judgments were made at no additional cost. These results suggest that it is unlikely that there is a distinction between Type-2 and Type-3 systems (metacognition and meta-metacognition) in perceptual decision-making and, instead, a single system can be flexibly adapted to produce both Type-2 and Type-3 evaluations recursively.
Analysis of treatment sequence and outcomes in patients with relapsed malignant peripheral nerve sheath tumors
Authors: Zhang Lindy , Lemberg Kathryn M , Calizo Ana , Varadhan Ravi , Siegel Alan H , Meyer Christian F , Blakeley Jaishri O , Pratilas Christine A
Published: December 2023

Background

Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas originating from cellular components within the nerve sheath. The incidence of MPNST is highest in people with neurofibromatosis type 1 (NF1), and MPNST is the leading cause of death for these individuals. Complete surgical resection is the only curative therapeutic option, but is often unfeasible due to tumor location, size, or presence of metastases. Evidence-based choices of chemotherapy for recurrent/refractory MPNST remain elusive. To address this gap, we conducted a retrospective analysis of our institutional experience in treating patients with relapsed MPNST in order to describe patient outcomes related to salvage regimens.

Methods

We conducted a retrospective electronic health record analysis of patients with MPNST who were treated at Johns Hopkins Hospital from January 2010 to June 2021. We calculated time to progression (TTP) based on salvage chemotherapy regimens.

Results

Sixty-five patients were included in the analysis. Upfront therapy included single or combined modalities of surgery, chemotherapy, or radiotherapy. Forty-eight patients received at least 1 line of chemotherapy, which included 23 different regimens (excluding active clinical studies). Most patients (n = 42, 87.5%) received a combination of doxorubicin, ifosfamide, or etoposide as first-line chemotherapy. Salvage chemotherapy regimens and their TTP varied greatly, with irinotecan/temozolomide-based regimens having the longest average TTP (255.5 days, among 4 patients).

Conclusions

Patients with advanced or metastatic MPNST often succumb to their disease despite multiple lines of therapy. These data may be used as comparative information in decision-making for future patients and clinical trials.