bluuebunny/crossref_metadata_2025 huggingface dataset:
The rise, fall, and resurgence of phage therapy for urinary tract infection
Authors: Zulk Jacob J. , Patras Kathryn A. , Maresso Anthony W.
Published: January 2024

In the face of rising antimicrobial resistance, bacteriophage therapy, also known as phage therapy, is seeing a resurgence as a potential treatment for bacterial infections including urinary tract infection (UTI). Primarily caused by uropathogenic
Escherichia coli
, the 400 million UTI cases annually are major global healthcare burdens and a primary cause of antibiotic prescriptions in the outpatient setting. Phage therapy has several potential advantages over antibiotics including the ability to disrupt bacterial biofilms and synergize with antimicrobial treatments with minimal side effects or impacts on the microbiota. Phage therapy for UTI treatment has shown generally favorable results in recent animal models and human case reports. Ongoing clinical trials seek to understand the efficacy of phage therapy in individuals with asymptomatic bacteriuria and uncomplicated cystitis. A possible challenge for phage therapy is the development of phage resistance in bacteria during treatment. While resistance frequently develops
in vitro
and
in vivo
, resistance can come with negative consequences for the bacteria, leaving them susceptible to antibiotics and other environmental conditions and reducing their overall virulence. “Steering” bacteria toward phage resistance outcomes that leave them less fit or virulent is especially useful in the context of UTI where poorly adherent or slow-growing bacteria are likely to be flushed from the system. In this article, we describe the history of phage therapy in treating UTI and its current resurgence, the state of its clinical use, and an outlook on how well-designed phage therapy could be used to “steer” bacteria toward less virulent and antimicrobial-susceptible states.
Critical roles of
Rickettsia parkeri
outer membrane protein B (OmpB) in the tick host
Authors: Tongluan Natthida , Engström Patrik , Jirakanwisal Krit , Langohr Ingeborg M. , Welch Matthew D. , Macaluso Kevin R.
Published: January 2024

Rickettsia parkeri
is a pathogen of public health concern and transmitted by the Gulf Coast tick,
Amblyomma maculatum
. Rickettsiae are obligate intracellular bacteria that enter and replicate in diverse host cells. Rickettsial outer membrane protein B (OmpB) functions in bacterial adhesion, invasion, and avoidance of cell-autonomous immunity in mammalian cell infection, but the function of OmpB in arthropod infection is unknown. In this study, the function of
R. parkeri
OmpB was evaluated in the tick host.
R. parkeri
wild-type and

R. parkeri ompB
STOP
::tn

(non-functional OmpB) were capillary fed to naïve
A. maculatum
ticks to investigate dissemination in the tick and transmission to vertebrates. Ticks exposed to
R. parkeri
wild-type had greater rickettsial loads in all organs than ticks exposed to

R. parkeri ompB
STOP
::tn

at 12 h post-capillary feeding and after 1 day of feeding on host. In rats that were exposed to

R. parkeri ompB
STOP
::tn

-infected ticks, dermal inflammation at the bite site was less compared to
R. parkeri
wild-type-infected ticks.
In vitro
,

R. parkeri ompB
STOP
::tn

cell attachment to tick cells was reduced, and host cell invasion of the mutant was initially reduced but eventually returned to the level of
R. parkeri
wild-type by 90 min post-infection.

R. parkeri ompB
STOP
::tn

and
R. parkeri
wild-type had similar growth kinetics in the tick cells, suggesting that OmpB is not essential for
R. parkeri
replication in tick cells. These results indicate that
R. parkeri
OmpB functions in rickettsial attachment and internalization to tick cells and pathogenicity during tick infection.
Harnessing preexisting influenza virus-specific immunity increases antibody responses against SARS-CoV-2
Authors: Dulin Harrison , Barre Ramya S. , Xu Duo , Neal Arrmund , Vizcarra Edward , Chavez Jerald , Ulu Arzu , Yang Myeon-Sik , Khan Siddiqur Rahman , Wuang Keidy , Bhakta Nikhil , Chea Chanvoraboth , Wilson Emma H. , Martinez-Sobrido Luis , Hai Rong
Published: January 2024

Increased globalization and changes in human interactions with wild animals has increased the likelihood of the emergence of novel viruses with pandemic potential. Vaccines can be effective in preventing severe disease caused by pandemic viruses. However, it takes time to develop protective immunity via prime-boost vaccination. More effective vaccine designs should quickly induce protective immunity. We propose leveraging preexisting immunity to a different pathogen to boost protection against emerging viruses. We targeted SARS-CoV-2 as a representative pandemic virus and generated a fusion protein vaccine that combines the nucleoprotein from influenza A virus and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Our vaccine design significantly increased the production of RBD-specific antibodies in mice that had previously been exposed to influenza virus, compared to those without previous exposure. This enhanced immunity reduced SARS-CoV-2 replication in mice. Our results offer a vaccine design that could be valuable in a future pandemic setting.
Functional metabolomics of the human scalp: a metabolic niche for
Staphylococcus epidermidis
Authors: Nothias Louis-Félix , Schmid Robin , Garlet Allison , Cameron Hunter , Leoty-Okombi Sabrina , André-Frei Valérie , Fuchs Regine , Dorrestein Pieter C. , Ternes Philipp
Published: January 2024

Systems biology research on host-associated microbiota focuses on two fundamental questions: which microbes are present and how do they interact with each other, their host, and the broader host environment? Metagenomics provides us with a direct answer to the first part of the question: it unveils the microbial inhabitants, e.g., on our skin, and can provide insight into their functional potential. Yet, it falls short in revealing their active role. Metabolomics shows us the chemical composition of the environment in which microbes thrive and the transformation products they produce. In particular, untargeted metabolomics has the potential to observe a diverse set of metabolites and is thus an ideal complement to metagenomics. However, this potential often remains underexplored due to the low annotation rates in MS-based metabolomics and the necessity for multiple experimental chromatographic and mass spectrometric conditions. Beyond detection, prospecting metabolites’ functional role in the host/microbiome metabolome requires identifying the biological processes and entities involved in their production and biotransformations. In the present study of the human scalp, we developed a strategy to achieve comprehensive structural and functional annotation of the metabolites in the human scalp environment, thus diving one step deeper into the interpretation of “omics” data. Leveraging a collection of openly accessible software tools and integrating microbiome data as a source of functional metabolite annotations, we finally identified the specific metabolic niche of
Staphylococcus epidermidis
, one of the key players of the human skin microbiome.
Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making
Authors: Ban Shibo , Cheng Wei , Wang Xi , Niu Jiao , Wu Qun , Xu Yan
Published: January 2024

This work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality.
Adaptive laboratory evolution reveals regulators involved in repressing biofilm development as key players in
Bacillus subtilis
root colonization
Authors: Pomerleau Maude , Charron-Lamoureux Vincent , Léonard Lucille , Grenier Frédéric , Rodrigue Sébastien , Beauregard Pascale B.
Published: January 2024

In this study, we aimed to enhance the abilities of the plant-beneficial bacterium
Bacillus subtilis
to colonize plant roots in the presence of competing
Pseudomonas
bacteria. To achieve this, we conducted adaptive laboratory experiments, allowing
Bacillus
to evolve in a defined environment. We successfully obtained strains of
Bacillus
that were more effective at colonizing plant roots than the ancestor strain. To identify the genetic changes driving this improvement, we sequenced the genomes of these evolved strains. Interestingly, mutations that facilitated the formation of robust biofilms on roots were predominant. Many of these evolved
Bacillus
isolates also displayed the remarkable ability to outcompete
Pseudomonas
species. Our research sheds light on the mutational paths selected in
Bacillus subtilis
to thrive in root environments and offers exciting prospects for improving beneficial traits in plant growth-promoting microorganisms. Ultimately, this could pave the way for the development of more effective biofertilizers and sustainable agricultural practices.
Genetic mutation in
Escherichia coli
genome during adaptation to the murine intestine is optimized for the host diet
Authors: Tsukimi Tomoya , Obana Nozomu , Shigemori Suguru , Arakawa Kazuharu , Miyauchi Eiji , Yang Jiayue , Song Isaiah , Ashino Yujin , Wakayama Masataka , Soga Tomoyoshi , Tomita Masaru , Ohno Hiroshi , Mori Hirotada , Fukuda Shinji
Published: January 2024

The gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as
Escherichia coli
live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in
E. coli
are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the
E. coli
K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
Gold(I) ion and the phosphine ligand are necessary for the anti-
Toxoplasma gondii
activity of auranofin
Authors: Ma C. I. , Tirtorahardjo J. A. , Schweizer S. S. , Zhang J. , Fang Z. , Xing L. , Xu M. , Herman D. A. , Kleinman M. T. , McCullough B. S. , Barrios A. M. , Andrade R. M.
Published: January 2024

Auranofin, an FDA-approved drug for rheumatoid arthritis, has emerged as a promising antiparasitic medication in recent years. The gold(I) ion in auranofin is postulated to be responsible for its antiparasitic activity. Notably
,
aurothiomalate and aurothioglucose also contain gold(I), and, like auranofin, they were previously used to treat rheumatoid arthritis. Whether they have antiparasitic activity remains to be elucidated. Herein, we demonstrated that auranofin and similar derivatives, but not aurothiomalate and aurothioglucose, inhibited the growth of
Toxoplasma gondii in vitro
. We found that auranofin affected the
T. gondii
biological cycle (lytic cycle) by inhibiting
T. gondii’s
invasion and triggering its egress from the host cell. However, auranofin could not prevent parasite replication once
T. gondii
resided within the host. Auranofin treatment induced apoptosis in
T. gondii
parasites
,
as demonstrated by its reduced size and elevated phosphatidylserine externalization (PS). Notably, the gold from auranofin enters the cytoplasm of
T. gondii,
as demonstrated by scanning transmission electron microscopy-energy dispersive X-ray spectroscopy (STEM-EDS) and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS).

IMPORTANCE

Toxoplasmosis, caused by
Toxoplasma gondii
, is a devastating disease affecting the brain and the eyes, frequently affecting immunocompromised individuals. Approximately 60 million people in the United States are already infected with
T. gondii
, representing a population at-risk of developing toxoplasmosis. Recent advances in treating cancer, autoimmune diseases, and organ transplants have contributed to this at-risk population's exponential growth. Paradoxically, treatments for toxoplasmosis have remained the same for more than 60 years, relying on medications well-known for their bone marrow toxicity and allergic reactions. Discovering new therapies is a priority, and repurposing FDA-approved drugs is an alternative approach to speed up drug discovery. Herein, we report the effect of auranofin, an FDA-approved drug, on the biological cycle of
T. gondii
and how both the phosphine ligand and the gold molecule determine the anti-parasitic activity of auranofin and other gold compounds. Our studies would contribute to the pipeline of candidate anti-
T. gondii
agents.
Unveiling the super tolerance of
Candida nivariensis
to oxidative stress: insights into the involvement of a catalase
Authors: Qi Yanhua , Qin Qijian , Liao Guiyan , Tong Lige , Jin Cheng , Wang Bin , Fang Wenxia
Published: January 2024

Yeast cells involved in fermentation processes face various stressors that disrupt redox homeostasis and cause cellular damage, making the study of oxidative stress mechanisms crucial. In this investigation, we isolated a resilient yeast strain,
Candida nivariensis
GXAS-CN, capable of thriving in the presence of high concentrations of H
2
O
2
. Transcriptomic analysis revealed the up-regulation of multiple antioxidant genes in response to oxidative stress. Deletion of the catalase gene
Cncat
significantly impacted H
2
O
2
-induced oxidative stress. Enzymatic analysis of recombinant
Cn
Cat highlighted its highly efficient catalase activity and its essential role in mitigating H
2
O
2
. Furthermore, over-expression of
Cn
Cat in
Saccharomyces cerevisiae
improved oxidative resistance by reducing intracellular ROS accumulation. The presence of multiple stress-responsive transcription factor binding sites at the promoters of antioxidative genes indicates their regulation by different transcription factors. These findings demonstrate the potential of utilizing the remarkably tolerant
C. nivariensis
GXAS-CN or enhancing the resistance of
S. cerevisiae
to improve the efficiency and cost-effectiveness of industrial fermentation processes.

IMPORTANCE

Enduring oxidative stress is a crucial trait for fermentation strains. The importance of this research is its capacity to advance industrial fermentation processes. Through an in-depth examination of the mechanisms behind the remarkable H
2
O
2
resistance in
Candida nivariensis
GXAS-CN and the successful genetic manipulation of this strain, we open the door to harnessing the potential of the catalase
Cn
Cat for enhancing the oxidative stress resistance and performance of yeast strains. This pioneering achievement creates avenues for fine-tuning yeast strains for precise industrial applications, ultimately leading to more efficient and cost-effective biotechnological processes.
The mechanism of action of auranofin analogs in
B. cenocepacia
revealed by chemogenomic profiling
Authors: Maydaniuk Dustin T. , Martens Brielle , Iqbal Sarah , Hogan Andrew M. , Lorente Cobo Neil , Motnenko Anna , Truong Dang , Liyanage Sajani H. , Yan Mingdi , Prehna Gerd , Cardona Silvia T.
Published: January 2024

Drug repurposing efforts led to the discovery of bactericidal activity in auranofin, a gold-containing drug used to treat rheumatoid arthritis. Auranofin kills Gram-positive bacteria by inhibiting thioredoxin reductase, an enzyme that scavenges reactive oxygen species (ROS). Despite the presence of thioredoxin reductase in Gram-negative bacteria, auranofin is not always active against them. It is not clear whether the lack of activity in several Gram-negative bacteria is due to the cell envelope barrier or the presence of other ROS protective enzymes such as glutathione reductase (GOR). We previously demonstrated that chemical analogs of auranofin (MS-40 and MS-40S), but not auranofin, are bactericidal against the Gram-negative
Burkholderia cepacia
complex. Here, we explore the targets of auranofin, MS-40, and MS-40S in
Burkholderia cenocepacia
and elucidate the mechanism of action of the auranofin analogs by a genome-wide, randomly barcoded transposon screen (BarSeq). Auranofin and its analogs inhibited the
B. cenocepacia
thioredoxin reductase and induced ROS but did not inhibit the bacterial GOR. Genome-wide, BarSeq analysis of cells exposed to MS-40 and MS-40S compared to the ROS inducers arsenic trioxide, diamide, hydrogen peroxide, and paraquat revealed common and unique mediators of drug susceptibility. Furthermore, deletions of
gshA
and
gshB
that encode enzymes in the glutathione biosynthetic pathway led to increased susceptibility to MS-40 and MS-40S. Overall, our data suggest that the auranofin analogs kill
B. cenocepacia
by inducing ROS through inhibition of thioredoxin reductase and that the glutathione system has a role in protecting
B. cenocepacia
against these ROS-inducing compounds.

IMPORTANCE

The Burkholderia cepacia complex is a group of multidrug-resistant bacteria that can cause infections in the lungs of people with the autosomal recessive disease, cystic fibrosis. Specifically, the bacterium Burkholderia cenocepacia can cause severe infections, reducing lung function and leading to a devastating type of sepsis, cepacia syndrome. This bacterium currently does not have an accepted antibiotic treatment plan because of the wide range of antibiotic resistance. Here, we further the research on auranofin analogs as antimicrobials by finding the mechanism of action of these potent bactericidal compounds, using a powerful technique called BarSeq, to find the global response of the cell when exposed to an antimicrobial.
Unveiling the structure-emulsifying function relationship of truncated recombinant forms of the SA01-OmpA protein opens up a new vista in bioemulsifiers
Authors: Mohseni Sani Naeema , Talaee Mahbubeh , Akbari Ali , Ashoori Faranak , Zamani Javad , Kermani Ali A. , Shahbani Zahiri Hossein , Presley John , Vali Hojatollah , Akbari Noghabi Kambiz
Published: January 2024

The emulsifying ability of SA01-OmpA (outer membrane protein A from
Acinetobacter
sp. SA01) was found to be constrained by challenges like low production efficiency and high costs associated with protein recovery from
E. coli
inclusion bodies, as described in our previous study. The present study sought to benefit from the advantages of the targeted truncating of SA01-OmpA protein, taking into account the reduced propensity of protein expression as inclusion bodies and cytotoxicity. Here, the structure and activity relationship of two truncated recombinant forms of SA01-OmpA protein was unraveled through a hybrid approach based on experimental data and computational methodologies, representing an innovative bioemulsifier with advantageous emulsifying activity. The recombinant truncated SA01-OmpA variants were cloned and heterologously expressed in
E. coli
host cells and subsequently purified. The results showed increased emulsifying activity of N-terminally truncated SA01-OmpA (NT-OmpA) compared to full-length SA01-OmpA. Molecular dynamics (MD) simulations analysis demonstrated a direct correlation between the C-terminally truncated SA01-OmpA (CT-OmpA) and its expression as inclusion bodies. Analysis of the structure-activity relationship of truncated variants of SA01-OmpA revealed that, compared to the full-length protein, deletion of the β-barrel portion from the N-terminal of SA01-OmpA increased the emulsifying activity of NT-OmpA while lowering its expression as inclusion bodies. Contrary to the full-length protein, the N-terminally truncated SA01-OmpA was not as cytotoxic, according to the MTT assay, FCM analysis, and AO/EB staining. The findings of this extensive study advance our knowledge of SA01-OmpA at the molecular level as well as the design and development of efficient bioemulsifiers.

IMPORTANCE

Previous research (Shahryari et al. 2021, mSystems 6: e01175-20) introduced and characterized the SA01-OmpA protein as a multifaceted protein with a variety of functions, including maintaining cellular homeostasis under oxidative stress conditions, biofilm formation, outer membrane vesicles (OMV) biogenesis, and beneficial emulsifying capacity. By truncating the SA01-OmpA protein, the current study presents a unique method for developing protein-type bioemulsifiers. The findings indicate that the N-terminally truncated SA01-OmpA (NT-OmpA) has the potential to fully replace full-length SA01-OmpA as a novel bioemulsifier with significant emulsifying activity. This study opens up a new frontier in bioemulsifiers, shedding light on a possible relationship between the structure and activity of SA01-OmpA truncated forms.
Lack of leisure time physical activity and variations in cardiovascular mortality across US communities: a comprehensive county-level analysis (2011–2019)
Authors: Abohashem Shady , Nasir Khurram , Munir Malak , Sayed Ahmed , Aldosoky Wesam , Abbasi Taimur , Michos Erin D , Gulati Martha , Rana Jamal S
Published: January 2024

Objectives

To investigate the associations between county-level proportions of adults not engaging in leisure-time physical activity (no LTPA) and age-adjusted cardiovascular mortality (AACVM) rates in the overall US population and across demographics.

Methods

Analysing 2900 US counties from 2011 to 2019, we used the Centers for Disease Control and Prevention (CDC) databases to obtain annual AACVM rates. No LTPA data were sourced from the CDC’s Behavioural Risk Factor Surveillance System survey and county-specific rates were calculated using a validated multilevel regression and poststratification modelling approach. Multiple regression models assessed associations with county characteristics such as socioeconomic, environmental, clinical and healthcare access factors. Poisson generalised linear mixed models were employed to calculate incidence rate ratios (IRR) and additional yearly deaths (AYD) per 100 000 persons.

Results

Of 309.9 million residents in 2900 counties in 2011, 7.38 million (2.4%) cardiovascular deaths occurred by 2019. County attributes such as socioeconomic, environmental and clinical factors accounted for up to 65% (adjusted R2=0.65) of variance in no LTPA rates. No LTPA rates associated with higher AACVM across demographics, notably among middle-aged adults (standardised IRR: 1.06; 95% CI (1.04 to 1.07)), particularly women (1.09; 95% CI (1.07 to 1.12)). The highest AYDs were among elderly non-Hispanic black individuals (AYD=68/100 000).

Conclusions

Our study reveals a robust association between the high prevalence of no LTPA and elevated AACVM rates beyond other social determinants. The most at-risk groups were middle-aged women and elderly non-Hispanic black individuals. Further, county-level characteristics accounted for substantial variance in community LTPA rates. These results emphasise the need for targeted public health measures to boost physical activity, especially in high-risk communities, to reduce AACVM.
Aulukluki neqkat: centering care of salmon and relational research in Indigenous fisheries in the Kuskokwim River, Alaska
Authors: Esquible Janessa , Hoffman Avery , Lowrey Danielle , Ropati Destiny , Cleveland Jacqueline , Williams Mike , Samuelson Jonathan , Justin Wilson , Christiansen Freddie , Black Jessica , Donkersloot Rachel , Stevens Carrie , Woods Brooke , Chya Dehrich , Carothers Courtney
Published: January 2024

This Indigenous-led project aims to better understand historical and contemporary ways in which Alaska Native Peoples steward salmon and the values connected to salmon stewardship. Indigenous Peoples have stewarded Alaska lands and waters for thousands of years yet have been largely excluded from western science and management systems. In this project, we utilize a participatory approach that allows for the equitable valuing of ideas and knowledges to document the breadth and depth of Yup'ik and Athabascan knowledge and governance systems in southwestern Alaska. We reshape research methodologies by centering Indigenous frameworks and methodologies, including circle dialogues and multi-generational interviews led by Indigenous scholars and students in their home communities and regions. In this paper, we share the Yup'ik and Athabascan values, knowledge, management, and governance mechanisms that can improve the long-term sustainability and equity of Alaska salmon systems. This research elevates the voices of Alaska Native salmon stewards and experts from the Kuskokwim Bay and the Kuskokwim River. We elaborate on five key themes that emerged from this research, including traditional Indigenous ways of life, Indigenous stewardship, self-determination, food and livelihood sovereignty, and ecosystem changes, and identify a more equitable and sustainable path forward for salmon and people in Alaska.
Enhancing winter road maintenance with explainable AI: SHAP analysis for interpreting machine learning models in road friction estimation
Authors: Ding Xueru , Kwon Tae J.
Published: January 2024

Effective winter road maintenance relies on precise road friction estimation. Machine learning (ML) models have shown significant promise in this; however, their inherent complexity makes understanding their inner workings challenging. This paper addresses this issue by conducting a comparative analysis of road friction estimation models using four ML methods, including regression tree, random forest, eXtreme Gradient Boosting (XGBoost), and support vector regression (SVR). We then employ the SHapley Additive exPlanations (SHAP) explainable artificial intelligence (AI) to enhance model interpretability. Our analysis on an Alberta dataset reveals that the XGBoost model performs best with an accuracy of 91.39%. The SHAP analysis illustrates the logical relationships between predictor features and friction within all three tree-based models, but it also uncovers inconsistencies within the SVR model, potentially attributed to insufficient feature interactions. Thus, this paper not only showcase the role of explainable AI in improving the ML interpretability of models for road friction estimation, but also provides practical insights that could improve winter road maintenance decisions.
Potential replacement understory woody plants for Robinia pseudoacacia plantations: species composition and vertical distribution pattern
Authors: Yang Haijiao , Wang Zhibin
Published: January 2024

Black locust ( Robinia pseudoacacia L.) plantations on the Loess Plateau have become multigenerational sprouting forests with an obvious trend toward degradation. The species composition and vertical distribution pattern of understory woody plants were investigated in mature stands located at the top (T_GS) and bottom (B_GS) of a slope in the gully region to explore whether there may be replacement species for black locust. The species composition of T_GS and B_GS clearly differed, and species diversity indices in B_GS were significantly greater than those in T_GS. These differences in species composition were mainly attributed to elevation, leaf area index, and basal area of total canopy trees. In T_GS, Rubus corchorifolius and Rosa xanthina had an absolute advantage in terms of the number of individuals in the vertical space of (0, 100] cm and (100, 300] cm, respectively. In B_GS, Acanthopanax senticosus was dominant at (0, 200] cm, and Broussonetia papyrifera and Celtis sinensis began to dominate at >200 cm. These results suggest that shrub species ( Rubus corchorifolius and Rosa xanthina) and tree species ( Broussonetia papyrifera and Celtis sinensis) should be prioritized when mixed with black locust in T_GS and B_GS, respectively, to gradually replace black locust on the Loess Plateau.
What relational event models can reveal: Commentary on Thomas Grund’s “Dynamics of Denunciation: The Limits of a Scandal”
Authors: Jones Pete
Published: January 2024

This article provides a commentary on Thomas Grund’s International Conference on Computational Social Science 2021 keynote “Dynamics of Denunciation: The Limits of a Scandal”. The keynote presents results from research investigating the relational dynamics underpinning the denunciations provided in testimonies relating to a Canadian political scandal. Grund uses relational event models to test hypotheses about the social mechanisms driving the denunciations. Although denunciation should depend only on who is guilty and not on who has said what up to that point, Grund’s study finds evidence in support of a number of relational mechanisms influencing the denunciation process. Grund argues that the apparent influence of past denunciations on testimonies reveals the limits of the inquiry process itself and what it can reveal about a scandal. This article reviews Grund’s talk and puts the work in a broader context of using approaches rooted in event history modelling and social network theory to illuminate the processes defining social interaction data. It highlights ways in which the keynote can inform the development of computational social science approaches to analysing such data, and argues that the value of such an analysis has implications for scholarship beyond the social sciences.
SEEUNRS: Semantically Enriched Entity-Based Urdu News Recommendation System
Authors: Kanwal Safia , Malik Muhammad Kamran , Nawaz Zubair , Mehmood Khawar
Published: January 2024

The advancement in the production, distribution, and consumption of news has fostered easy access to the news with fair challenges. The main challenge is to present the right news to the right audience. The news recommendation system is one of the technological solutions to this problem. Much work has been done on news recommendation systems for the major languages of the world, but trivial work has been done for resource-poor languages like Urdu. Another significant hurdle in the development of an efficient news recommendation system is the scarcity of an accessible and suitable Urdu dataset. To this end, an Urdu news mobile application was used to collect the news data and user feedback for 1 month. After refinement, the first-ever Urdu dataset of 100 users and 23,250 news was curated for the Urdu news recommendation system. In addition,
SEEUNRS
, a semantically enriched entity-based Urdu news recommendation system, is proposed. The proposed scheme exploits the hidden features of a news article and entities to suggest the right article to the right audience. Results have shown that the presented model has an improvement of 6.9% in the F1 measure from traditional recommendation system techniques.
Identifying and Explaining Safety-critical Scenarios for Autonomous Vehicles via Key Features
Authors: Neelofar Neelofar , Aleti Aldeida
Published: January 2024

Ensuring the safety of autonomous vehicles (AVs) is of utmost importance, and testing them in simulated environments is a safer option than conducting in-field operational tests. However, generating an exhaustive test suite to identify critical test scenarios is computationally expensive, as the representation of each test is complex and contains various dynamic and static features, such as the AV under test, road participants (vehicles, pedestrians, and static obstacles), environmental factors (weather and light), and the road’s structural features (lanes, turns, road speed, etc.). In this article, we present a systematic technique that uses
Instance Space Analysis (ISA)
to identify the significant features of test scenarios that affect their ability to reveal the unsafe behaviour of AVs. ISA identifies the features that best differentiate safety-critical scenarios from normal driving and visualises the impact of these features on test scenario outcomes (safe/unsafe) in two dimensions. This visualisation helps to identify untested regions of the instance space and provides an indicator of the quality of the test suite in terms of the percentage of feature space covered by testing. To test the predictive ability of the identified features, we train five Machine Learning classifiers to classify test scenarios as safe or unsafe. The high precision, recall, and F1 scores indicate that our proposed approach is effective in predicting the outcome of a test scenario without executing it and can be used for test generation, selection, and prioritisation.
A Selective Separation of Platinum Group Metals from the Fe-PGM Alloy Using Electrodeposition Combined with Electrochemical Dealloying
Authors: Łoś Przemysław , Jacek-Krakus Sabina , Markowicz Justyna , Łabuz Adrian , Sobianowska-Turek Agnieszka , Zygmunt Michał , Janosz Michał , Fornalczyk Agnieszka
Published: January 2024

In the European automotive industry, a considerable volume of recalled car catalysts stems from diesel vehicles, characterized by their high silicon carbide (SiC) content. Processing such materials poses notable challenges compared to gasoline vehicle catalysts. The presence of SiC demands additional time and energy in electric arc furnace processing, with SiC’s high melting point and strong reducing properties complicating separation. The Fe-PGM alloy obtained after pyrometallurgical treatment of these SiC-rich catalysts presents hurdles for hydrometallurgical processing. With high silicon content, the alloy resists corrosion in sulfuric acid, impeding solubility and hindering progress in the recovery process. This article explores an innovative approach for selectively extracting platinum group metals (Pt, Pd, Rh) from Si-rich Fe-PGM alloys. Traditional hydrometallurgical methods struggle due to the alloy’s near-immunity to acid leaching. The study presents chemical leaching results and proposes electrodeposition combined with electrochemical dealloying as a feasible solution. This method, aiming for selective metal separation, seeks to enhance recovery process profitability by producing pure metals.
Acute cardiovascular effects of 4th generation electronic cigarettes and combusted cigarettes: implications for harm reduction
Authors: Nguyen Randy , Ruedisueli Isabelle , Lakhani Karishma , Ma Joyce , Middlekauff Holly R.
Published: January 2024

We found that nicotine, not the non-nicotine constituents in tobacco cigarette (TC) or electronic cigarette (EC) emissions, may be the instigator of the acute, potentially adverse, changes in hemodynamics and heart rate variability (HRV) that were recorded several minutes after tobacco product use. Furthermore, acute EC use produced an abnormal HRV pattern associated with increased cardiac risk in people who chronically smoke ECs and produced similar hemodynamic increases compared with acute TC use in people who chronically smoke TCs, including people who are dual users.
Effects of aging and lifelong aerobic exercise on expression of innate immune components in skeletal muscle of women
Authors: Perkins Ryan K. , Lavin Kaleen M. , Raue Ulrika , Jemiolo Bozena , Trappe Scott W. , Trappe Todd A.
Published: January 2024

We recently reported that aging increases basal expression of many Toll-like receptors (TLRs) in men and lifelong aerobic exercise does not prevent this effect. In addition, a resistance exercise (RE) challenge increased the expression of many TLRs. Here we show that basal TLR expression is minimally influenced by aging in women and findings support the sexual dimorphism of immunity, with women having greater basal skeletal muscle TLR expression and a differential response to unaccustomed exercise than men.
Exercise microdosing for skeletal muscle health applications to spaceflight
Authors: Voss Adam C. , Chambers Toby L. , Gries Kevin J. , Jemiolo Bozena , Raue Ulrika , Minchev Kiril , Begue Gwenaelle , Lee Gary A. , Trappe Todd A. , Trappe Scott W.
Published: January 2024

Declines in skeletal muscle health are a concern for astronauts on long-duration spaceflights. The current findings add to the growing body of exercise countermeasures data, suggesting that small doses of specific exercise can be beneficial for certain aspects of skeletal muscle health. This information can be used in conjunction with other components of existing exercise programs for astronauts and might translate to other areas focused on skeletal muscle health (e.g., sports medicine, rehabilitation, aging).
Hypohydration attenuates increases in creatinine clearance to oral protein loading and the renal hemodynamic response to exercise pressor reflex
Authors: Chapman Christopher L. , Holt Sadie M. , O’Connell Cameron T. , Brazelton Shaun C. , Medved Hannah N. , Howells William A. B. , Reed Emma L. , Needham Karen Wiedenfeld , Halliwill John R. , Minson Christopher T.
Published: January 2024

Insufficient hydration is prevalent among free living adults. This study found that hypohydration induced by 24-h fluid deprivation engaged renal functional reserve and that oral protein loading did not further increase creatinine clearance. Hypohydration also attenuated the ability to increase renal vascular resistance during the exercise pressor reflex. In addition, hypohydration neither enhanced nor impaired urine-concentrating ability during oral protein loading. These data support the importance of mitigating hypohydration in free living adults.
Newborn Pulse Oximetry Screening for Detecting Congenital Heart Disease: Experience at a Tertiary Care Center
Authors: Bulbul Ziad R. , Younis Nour K. , Malaeb Farah , Hussein Haytham Bou , Arabi Mariam , Bitar Fadi
Published: January 2024

Background. Congenital heart disease (CHD) remains the number one birth defect worldwide. Pulse oximetry screening (POS) is a widely used CHD screening modality effective in detecting critical lesions. This study is aimed at assessing the accuracy and cost-effectiveness of POS in a cohort of term well-babies admitted to a regular nursery in a tertiary care center. Methods. We reviewed the charts of term babies admitted to our regular nursery over a period of one year. The results of POS and the findings of echocardiography were collected. Similarly, we explored the records of our fetal echocardiography program to identify the fetuses screened for CHD during the same period. Results. 900 term babies were born and admitted to newborn nursery at our center, and 69 fetuses were evaluated by our fetal cardiology team during the study period. None of our term babies had a positive POS at birth or 24 hours of age. However, 56 babies had a cardiac echo before hospital discharge due to suspicious findings on physical examination or a family history of CHD. A simple noncritical CHD was noted in 10 of them. Additionally, 53 babies underwent echocardiography within the first five years of life; a simple CHD was noted in 6 of them. In parallel, 21 of our fetuses were found to have CHD: 16 simple CHD and 5 critical CHD (CCHD). Conclusion. Despite its cost-effectiveness and efficacy in screening for CCHD, POS is suboptimal for detecting simple CHD. In the absence of a proper prenatal screening and fetal echocardiography program, POS remains a cost-effective modality for detecting CCHD.
Partial Support in Chronic Heart Failure
Authors: Meyns Bart , Droogne Walter , Jacobs Steven
Published: January 2024

Partial left ventricular assist device (LVAD) support offers several advantages in treating chronic heart failure. It also raises concerns about insufficient support, worsening symptoms, and impediment of myocardial recovery. The clinical trial results for the CircuLite device (Medtronic) have shown that close monitoring can ensure improved outcomes for partial support. Another study on the ovine model demonstrated that partial and full support have similar effects regarding reverse remodeling. Thus, patients receiving partial LVAD support need regular follow-up care. Clinical assessment of symptoms and organ function must be used alongside objective judgment of patients’ needs to ensure support levels are appropriately adjusted.
Treatment of Refractory Ventricular Tachycardia with Radiofrequency Ablation and Temporary Mechanical Circulatory Support
Authors: Singh Som , Margenat Alejandro , Boone David , Condoure Ellen , Hariharan Ramesh
Published: January 2024

Catheter-based radiofrequency ablation has long been recognized as an effective treatment for refractory ventricular tachycardia (VT). A 57-year-old male with severe coronary artery disease underwent percutaneous mechanical circulatory support because of worsening cardiogenic shock after failed revascularization attempts. Despite aggressive medical management, the patient experienced refractory VT episodes, leading to the decision to proceed with radiofrequency catheter ablation. Notably, the Impella 5.5 device (Abiomed) provided critical left ventricular support during the ablation procedure. This case underscores the potential benefits of Impella support during radiofrequency ablation of complex ventricular arrhythmias.
Organization of Somatosensory Cortex in the South American Rodent Paca (Cuniculus paca)
Authors: Freire Marco Aurelio M. , Franca João G. , Picanco-Diniz Cristovam W. , Manger Paul R. , Kaas Jon H. , Pereira Antonio
Published: January 2024

Introduction: The study of non-laboratory species has been part of a broader effort to establish the basic organization of the mammalian neocortex, as these species may provide unique insights relevant to cortical organization, function, and evolution. Methods: In the present study, the organization of three somatosensory cortical areas of the medium-sized (5–11 kg body mass) Amazonian rodent, the paca (Cuniculus paca), was determined using a combination of electrophysiological microelectrode mapping and histochemical techniques (cytochrome oxidase and NADPH diaphorase) in tangential sections. Results: Electrophysiological mapping revealed a somatotopically organized primary somatosensory cortical area (S1) located in the rostral parietal cortex with a characteristic foot-medial/head-lateral contralateral body surface representation similar to that found in other species. S1 was bordered laterally by two regions housing neurons responsive to tactile stimuli, presumably the secondary somatosensory (S2) and parietal ventral (PV) cortical areas that evinced a mirror-reversal representation (relative to S1) of the contralateral body surface. The limits of the putative primary visual (V1) and primary auditory (A1) cortical areas, as well as the complete representation of the contralateral body surface in S1, were determined indirectly by the histochemical stains. Like the barrel field described in small rodents, we identified a modular arrangement located in the face representation of S1. Conclusions: The relative location, somatotopic organization, and pattern of neuropil histochemical reactivity in the three paca somatosensory cortical areas investigated are similar to those described in other mammalian species, providing additional evidence of a common plan of organization for the somatosensory cortex in the rostral parietal cortex of mammals.
Analysis of Cochlear Morphology for Cochlear Implantation Using Three-Dimensional Reconstruction of Computed Tomography Images
Authors: Jun Beomcho , Song Sunwha
Published: January 2024

Introduction: Preoperative evaluation of cochlear morphology is important for successful cochlear implantation. This study analyzed the cochlear canal by three-dimensional reconstructions of temporal bones using computed tomography (CT). Methods: Fifty temporal bones from 25 patients aged 42–74 years were evaluated. The inner spaces of the bony cochlea were reconstructed using a surface rendering technique on the CT images. Eight angular points (P0–P7) every 90° were selected from 0° to 630° from the center of the round window using the reconstructed cochlear canal images. The radius (R) and thickness (T) of the cochlear canal at each point were measured. The cochlear canal length (CoCL) was estimated using an equation based on the radius at each point. The cochlear width and height based on multiplanar CT images were also measured and compared with the length and volume of the cochlear canal. Results: The mean CoCL from 0° to 630° was 31.5 mm, and the cochlear volume was 55.9 mm3. The CoCL to P7 was correlated with the cochlear volume (r = 0.77), coiling ratios (R4/R0, r = 0.47; R5/R1, r = 0.384), cochlear width (long) (r = 0.539), cochlear height (r = 0.385), and total thickness at each point (r = 0.475). The cochlear volume was correlated with CoCL (630°) (r = 0.77), coiling ratio (R4/R0, r = 0.367), cochlear width (long) (r = 0.616), cochlear height (r = 0.447), and total T (r = 0.566). Conclusion: Preoperative evaluation using three-dimensional reconstruction can elucidate the size and shape of the cochlear canal before cochlear implantation.
A study on microclimate monitoring and control inside greenhouse using fans automation
Authors: Ardiansah Irfan , Vergian Nusantara Endryaz , Harnesa Putri Selly , Hara Permana Ryan
Published: January 2024

Efficient microclimate management is crucial in enhancing crop yields in greenhouses. Factors like temperature, relative humidity, and ultraviolet (UV) index significantly impact crop quality. The absence of adequate ventilation mechanisms in greenhouses presents a challenge for temperature regulation. This study proposes a solution for tropical greenhouses by designing a system that automatically activates fans when temperatures rise above 30 °C. This system regulates temperature and cultivates optimal growth conditions for crops. It is supported by a web page that enables monitoring and adjustment of microclimate data. To accommodate individual crop requirements, the minimum temperature threshold for fan activation can be modified, enhancing the system's adaptability. The impact of the UV index on greenhouse temperature is also considered. The automation system decreases the temperature by around ±3 °C when the UV index hits 10. Nonetheless, its cooling impact wanes beyond the UV index of 10. A greenhouse automation system, equipped with fans and internet access, proves quite useful for agricultural environment management. It tackles the temperature control issue and offers varied solutions.
Development of a novel optimization algorithm for a microstrip patch antenna array
Authors: A. Galleto Jr Fredelino , Don M. Africa Aaron , Jyllian A. Abello Ara , Miguel B. Lalusin Joaquin
Published: January 2024

Microstrip patch antennas are typically used because they have a low profile and cost. The main theme of this study is to present a novel 2×2 microstrip antenna array design using rough set theory. In designing the 2×2 microstrip antenna array, an FR4 dielectric substrate was used to improve the performance. The rough set theory was used to optimize the microstrip antenna parameters. The FR4 dielectric substrate compared better to the microstrip patch antenna array wherein no substrate was used. The antenna with no substrate used had the energy that is radiating underneath which contributed to the sidelobes of the radiation pattern whereas the use of the substrate reduced the energy radiated at the substrate. Furthermore, the gains of the two were also simultaneously evaluated and it showed that the microstrip antenna array with the dielectric substrate had better gain than the one without. This 2×2 microstrip array antenna design may be used for applications such as mobile communications since it is small in size and performs well.