bluuebunny/crossref_metadata_2025 huggingface dataset:
Eco-microbiology: discovering biochemical enhancers of PET biodegradation by
Piscinibacter sakaiensis
Authors: Piedra Felipe-Andrés , Salazar Miguel A. , Abouelniaj Sara , Rahman Raayed , Clark Justin C. , Han Yimo , Wang Zhao , Maresso Anthony
Published: February 2025

The scale of plastic pollution boggles the mind. Nearly 400 megatons of virgin plastics are produced annually, with an environmental release rate of 80%, and plastic waste, including microplastics and nanoplastics, is associated with a plethora of problems. The naturally evolved abilities of plastic-degrading microbes offer a starting point for generating sustainable and eco-centric solutions to plastic pollution—a field of endeavor we term eco-microbiology. Here, we developed an iterative discovery procedure coupling faster polyethylene terephthalate (PET)-dependent bioactivity screens with longer-term PET biodegradation assays to find biochemical boosters of PET consumption by the bacterium
Piscinibacter sakaiensis
. We discovered multiple hits supporting the enhancement of PET biodegradation, with a 0.39% dilution of growth medium #802, a rich medium similar to Luria-Bertani broth, on average more than doubling the rate of PET biodegradation both alone and in combination with 0.125% ethylene glycol. In addition, we identified other chemical species (sodium phosphate, L-serine, GABA) worth further exploring, especially in combination with growth medium #802, for enhanced PET biodegradation by
P. sakaiensis
. This work represents an important step toward the creation of a low-cost PET fermentation process needed to help solve PET plastic pollution.

IMPORTANCE

Plastic pollution is an urgent issue. Adding to the well-known problems of bulk plastic litter, shed microplastics and nanoplastics are globally distributed, found in diverse organisms including human foodstuffs and tissues, and increasingly associated with chronic disease. Solutions are needed and the microbial world offers abundant help via naturally evolved consumers of plastic waste. We are working to accelerate polyethylene terephthalate (PET) plastic biodegradation by
Piscinibacter sakaiensis
, a recently described bacterium that evolved to slowly but completely consume PET, one of the most common types of plastic pollution. We used a combination of PET-dependent bioactivity screens and biodegradation tests to find stimulators of PET biodegradation. Out of hundreds, we found a small number of biochemical conditions that more than double the PET biodegradation rate. Our work provides a foundation for further studies to realize a fermentation process needed to help solve PET plastic pollution.
HilD-regulated chemotaxis proteins contribute to
Salmonella
Typhimurium colonization in the gut
Authors: Cooper Kendal G. , Kari Laszlo , Chong Audrey , Tandon Naman , Doran Kathleen , Gomes Da Silva Lidiane , Cockrell Diane C. , Baylink Arden , Steele-Mortimer Olivia
Published: February 2025

In the enteric pathogen
Salmonella
Typhimurium, invasion and motility are coordinated by HilD, a master regulator that activates expression of genes encoding the type III secretion system 1 and some motility genes, including the chemotaxis gene
mcpC
. Previously, we have shown that McpC induces smooth swimming, which is important for type III secretion system 1-dependent invasion of epithelial cells. Here, we have studied another
Salmonella
-specific chemotaxis gene,
mcpA
, and demonstrate that it is also HilD regulated. Whereas HilD induction of
mcpC
occurs by direct derepression of H-NS,
mcpA
induction requires neither H-NS derepression nor the flagellar-specific sigma factor
fliA
; instead it occurs through a HilD-SprB regulatory cascade, providing experimental confirmation of previous transcriptional regulatory mapping. McpA and McpC contain methyl-accepting domains characteristic of bacterial chemoreceptors, and McpA also contains a chemoreceptor zinc-binding (CZB) protein domain found in a variety of bacterial proteins, many of which are involved in signaling or regulatory roles. Here, we show that, in a mouse model for acute
Salmonella
colitis, both
mcpA
and
mcpC
deletion mutants are outcompeted by wild-type
Salmonella
Typhimurium in the gut lumen. CZB domains bind Zn
2+
through a conserved cysteine residue and are thought to perform redox-sensing through redox-initiated alterations in zinc homeostasis. We found that the conserved cysteine is required for McpA function in the mouse gut, thus demonstrating a virulence role for the CZB Zn
2+
-binding site during infection.

IMPORTANCE

The gut-adapted bacterium
Salmonella
Typhimurium causes inflammatory diarrhea via a process that involves active invasion of intestinal epithelial cells, secretion of inflammatory molecules, and recruitment of immune cells. Although bacterial motility and invasion of host cells are coordinated, how directed movement facilitates luminal survival and growth or invasion at the mucosal surface is not understood. Chemotaxis is the process by which bacteria control movement toward attractants and away from repellents. Previously, we identified a
Salmonella
-specific chemoreceptor, McpC, that is co-expressed with the invasion machinery and promotes smooth swimming for optimal host cell invasion. Here, we investigated another chemoreceptor, McpA, also regulated with invasion-associated genes and show it contributes to luminal expansion rather than invasion of epithelial cells. McpA activity requires a conserved Zn
2+
-binding domain, thought to be involved in sensing inflammation. This work demonstrates that coordination of invasion and chemotaxis plays a significant role in the gut.
Acinetobacter baumannii
OmpA hinders host autophagy via the CaMKK2-reliant AMPK-pathway
Authors: Woo Kyungho , Kim Dong Ho , Park Ho-Sung , Oh Man Hwan , Lee Je Chul , Choi Chul Hee
Published: February 2025

Outer membrane protein A (OmpA) plays a vital role in the interactions between
Acinetobacter baumannii
and host cells. Autophagy is a defense mechanism that hinders the intracellular replication of bacteria, thereby safeguarding cells against microbial infections. While it has been observed that
A. baumannii
triggers cellular autophagy, the precise role of its virulence protein OmpA in this process remains uncertain. In this study, we investigated the effects of
A. baumannii
OmpA (AbOmpA) on autophagy and explored the underlying molecular mechanisms. We found that AbOmpA exerted its autophagy-suppressive effect through inhibition of CaMKK2 phosphorylation. Compared to the wild-type strain, the
ompA
-deletion mutant strain displayed considerably enhanced autophagy induction,
via
the AMPK-ULK1 pathway. AbOmpA hindered starvation-induced autophagy, while
A. baumannii
-Omp33 (AbOmp33) and
Escherichia coli
-OmpA (EcOmpA) did not. Importantly, we confirmed that exogenous AbOmpA suppressed autophagy through the CaMKK2-AMPK-ULK1 pathway during
A. baumannii
infection. These findings reveal a novel mechanism for AbOmpA-mediated autophagy evasion, providing new insights into the pathogenesis of
A. baumannii
infection.

IMPORTANCE

Acinetobacter baumannii
is a significant clinical pathogen notorious for causing infections in hospitals. Its outer membrane protein A acts as a virulence factor and helps the bacteria evade host defenses. Autophagy is a defense mechanism that hinders the intracellular replication of bacteria. While it has been observed that
A. baumannii
triggers cellular autophagy, the precise role of its AbOmpA in this process remains uncertain. Our studies demonstrate the AbOmpA of
A. baumannii
inhibits the cellular defense process, autophagy, through the CaMKK2-AMPK-ULK1 signaling cascade, thereby enhancing bacterial survival. This insight into how AbOmpA bypasses autophagy sheds light on
A. baumannii
infection's novel virulence strategy and suggests possible treatments.
Reduced prevalence of phage defense systems in
Pseudomonas aeruginosa
strains from cystic fibrosis patients
Authors: van den Berg Daan F. , Brouns Stan J. J.
Published: February 2025

Cystic fibrosis is a genetic disorder that affects mucus clearance, particularly of the lungs. As a result, cystic fibrosis patients often experience infections from bacteria, which contribute to the disease progression.
Pseudomonas aeruginosa
is one of the most common opportunistic pathogens associated with cystic fibrosis. The presence of
P. aeruginosa
complicates the treatment due to its high antibiotic resistance. Thus, research is ongoing to treat these infections with bacterial viruses instead, known as bacteriophages. Notably,
P. aeruginosa
clinical strains possess a variety of phage defense mechanisms that may limit the effectiveness of phage therapy. In this study, we compared the defense system repertoire of
P. aeruginosa
strains isolated from cystic fibrosis patients with those from non-cystic fibrosis patients. Our findings reveal that
P. aeruginosa
strains isolated from cystic fibrosis patients have fewer phage defense mechanisms per strain than from non-cystic fibrosis patients, suggesting altered phage selection pressures in strains colonizing CF patient lungs.

IMPORTANCE

Cystic fibrosis patients often experience chronic
Pseudomonas aeruginosa
lung infections, which are challenging to treat with antibiotics and contribute to disease progression and eventual respiratory failure. Phage therapy is being explored as an alternative treatment strategy for these infections. However, assessing strain susceptibility to phage treatment is essential for ensuring efficacy. To address this, we investigated whether CF-associated clinical
P. aeruginosa
strains have a distinct phage defense repertoire compared with those isolated from other lung patients. We observed that CF-associated
P. aeruginosa
strains have significantly fewer phage defenses, possibly affecting the susceptibility of these strains to phage infection.
Low-dose interleukin 2 therapy halts the progression of post-streptococcal autoimmune complications in a rat model of rheumatic heart disease
Authors: Rafeek Rukshan Ahamed Mohamed , Ketheesan Natkunam , Good Michael F. , Pandey Manisha , Lepletier Ailin
Published: February 2025

Acute rheumatic fever (ARF) is an autoimmune disease triggered by antibodies and T cells targeting the group A
Streptococcus
(GAS, Strep A) bacterium, often leading to rheumatic heart disease (RHD) and Sydenham’s chorea. Long-term monthly penicillin injections are recognized as a cornerstone of public health programs to prevent Strep A reinfection and progression of ARF. However, compliance is poor, and better tools are required to slow disease progression. Preclinical evidence suggests that this can be achieved. Using a rat model that replicates post-streptococcal autoimmune complications, we explored the potential of low-dose interleukin-2 (LD-IL-2) as an immunotherapeutic intervention for ARF/RHD. In this model, injections of recombinant M protein from Strep A type 5 (rM5) to Lewis rats induce cardiac tissue inflammation, conduction abnormalities, and cross-reactive antibodies against cardiac and brain proteins central to disease pathogenesis. In animals injected with rM5 and treated with LD-IL-2, no cardiac functional or histological changes was observed. LD-IL-2 therapy effectively reduced the production of cross-reactive antibodies raised against host proteins and significantly increased regulatory T cells in the mediastinal lymph nodes. These novel findings suggest that LD-IL-2 will be an effective immunotherapeutic agent for treating ARF and has the potential to replace the standard monthly penicillin injections.

IMPORTANCE

Post-streptococcal autoimmune syndromes, including acute rheumatic fever, rheumatic heart disease, and Sydenham’s chorea, represent a significant yet often under-recognized health and economic burden. This is especially true in low-income countries and among Indigenous populations in high-income nations, where the disease burden is most severe. These conditions arise from an autoimmune response to group A
Streptococcus
infections, leading to long-term health complications, disability, and premature death. Despite their widespread impact, no vaccine is currently available to prevent reinfections, and no specific therapy exists to treat the resulting autoimmune process. This study uses a rat model of rheumatic heart disease to evaluate the potential of low-dose interleukin 2 therapy in improving clinical outcomes and reducing the incidence of autoimmune diseases triggered by streptococcal infections.
Draft genome sequence of the
Serratia liquefaciens
strain UNJFSC002, isolated from the soil of a potato field of the Bicentenaria variety
Authors: Rodriguez-Grados Pedro M. , Arbizu Carlos I. , Castillo Gianmarco , Camel Vladimir , Conteras-Liza Sergio
Published: February 2025

In this study, we present the draft genome assembly of the
Serratia liquefaciens
strain UNJFSC002, isolated from the experimental potato field of the Bicentenaria variety at the Universidad Nacional José Faustino Sánchez Carrión, Lima, Peru.
Complete genome sequence of three methicillin-resistant
Staphylococcus aureus
ST630 strains isolated from cattle in Algeria
Authors: Belhout Chahrazed , Fernandez Javier E. , Perreten Vincent
Published: February 2025

Methicillin-resistant
Staphylococcus aureus
(MRSA) sequence type 630 (ST630) is an emerging clone causing infections in humans. We report the complete genomes of three MRSA ST630 from cattle. The 2.8 Mbp genomes contained several antimicrobial resistance and virulence genes and were related to those of previously detected human-associated MRSA ST630.
Complete genome of the mutualistic symbiont “
Candidatus
Carsonella ruddii” from a Japanese island strain of the Asian citrus psyllid
Diaphorina citri
Authors: Mizutani Masaki , Fujikawa Takashi , Fukatsu Takema , Kakizawa Shigeyuki
Published: February 2025

The complete genome, 173,958 bp in size, of “
Candidatus
Carsonella ruddii” DC-OKEB1
,
an obligate bacterial endosymbiont of the Asian citrus psyllid
Diaphorina citri
, was determined. The genome sequence provides valuable information for comparative and evolutionary aspects of the intimate insect–microbe mutualism.
Draft genome sequence of
Streptomyces
sp. Sce081 isolated from the nest of wasp
Sceliphron destillatorium
(Illiger, 1807)
Authors: Pytel-Huta Sofiia , Kachor Anna , Zatushevsky Andriy , Samborskyy Markiyan , Rebets Yuriy
Published: February 2025

Actinobacteria are often involved in ecological interactions with insects.
Streptomyces
sp. Sce081 with notable antifungal activity was isolated from the nest of wasp
Sceliphron destillatorium
(Illiger, 1807). Here, we report the draft sequence and analysis of the
Streptomyces
sp. Sce081 genome.
Estimated size of the total genome and protein space of viruses
Authors: Lu Congyu , Wu Yifan , Zhang Zheng , Mao Longfei , Ge Xingyi , Wu Aiping , Sun Fengzhu , Jiang Yongqiang , Peng Yousong
Published: February 2025

Recent metagenomic studies have identified a vast number of viruses. However, the systematic assessment of the true genetic diversity of the whole virus community on our planet remains to be investigated. Here, we explored the genome and protein space of viruses by simulating the process of virus discovery in viral metagenomic studies. Among multiple functions, the power function was found to best fit the increasing trends of virus diversity and was, therefore, used to predict the genetic space of viruses. The estimate suggests that there are at least 8.23e+08 viral operational taxonomic units and 1.62e+09 viral protein clusters on Earth when assuming the saturation of the virus genetic space, taking into account the balance of costs and the identification of novel viruses. It is noteworthy that less than 3% of the viral genetic diversity has been uncovered thus far, emphasizing the vastness of the unexplored viral landscape. To saturate the genetic space, a total of 3.08e+08 samples would be required. Analysis of viral genetic diversity by ecosystem yielded estimates consistent with those mentioned above. Furthermore, the estimate of the virus genetic space remained robust when accounting for the redundancy of sampling, sampling time, sequencing platform, and parameters used for protein clustering. This study provides a guide for future sequencing efforts in virus discovery and contributes to a better understanding of viral diversity in nature.

IMPORTANCE

Viruses are the most abundant and diverse biological entities on Earth. In recent years, a large number of viruses have been discovered based on sequencing technology. However, it is not clear how many kinds of viruses exist on Earth. This study estimates that there are at least 823 million types of viruses and 1.62 billion types of viral proteins. Remarkably, less than 3% of this large diversity has been uncovered to date. These findings highlight the enormous potential for discovering new viruses and reveal a significant gap in our current understanding of the viral world. This study calls for increased attention and resources to be directed toward viral discovery and metagenomics and provides a guide for future sequencing efforts, enhancing our knowledge of viral diversity in nature for ecology, biology, and public health.
Studies of Composite Protective Coatings of an Ancient Ship from Phanagoria (1st Century BC)
Authors: Greshnikov E. A. , Olkhovskiy S. V. , Chernova O. F. , Kamaev A. V. , Antipin A. M. , Svetogorov R. D. , Mandrykina A. V. , Kondratev O. A. , Tereschenko E. Yu. , Yatsishina E. B.
Published: February 2025

Samples of the internal and external coatings of the hull of a warship that sank in the seaport of Phanagoria (modern Taman Bay) in the 1st century BC are studied. As a result of the application of a complex of complementary natural-science methods (optical microscopy, X-ray diffractometry, scanning electron microscopy with energy dispersive X-ray microanalysis, gas chromatography with mass-selective detection), it is found that the internal wooden part of the ship was treated with a “mastic,” based on clay mixed with wool and down. The outer surface of the ship’s sheathing board was coated by realgar mixed with wax and pine resin. Thus the recipes used for the waterproofing, fireproofing, and bioprotection of warships used by sailors of the Pontic Kingdom more than 2000 years ago are presented.
Glass Imports to Southwestern Crimea in the 13th Century AD Based on Findings from a Hillfort of the Eski-Kermen Plateau
Authors: Khairedinova E. A. , Rumyantseva O. S. , Ismagulov A. M. , Bilida E. Yu. , Shalyavina N. B. , Saifutyarov R. R. , Tereschenko E. Yu.
Published: February 2025

The chemical composition of glass of 19 items (mostly vessels) from the Eski-Kermen plateau in southwestern Crimea has been studied with LA-ICP-MS and SEM-EDX techniques. The findings originate from the destruction layer of the late 13th century AD as well as from two churches and a manor of a noble citizen. The studied samples are made of Eastern Mediterranean plant ash glass, mainly of the Levantine origin, and of glass with high concentrations of boron and lithium, which origin is associated with Western Anatolia. It does not necessarily imply that the vessels themselves originate from these glassmaking regions, because raw glass, at least Eastern Mediterranean (Levantine), was a long-distance trade commodity and could have been imported into Byzantium or elsewhere. Glass of presumably Western Anatolian origin is heterogeneous in composition and likely originate from glassmaking centers that used raw materials from different sources. Most glass of this group features signs of the extensive recycling. The glass with a high B and Li content appears in Esky-Kermen in the 10th century AD at the latest. According to an earlier study of window glass composition from the site, its emergence here before the 13th century remained doubtful. Two early Islamic marvered vessels are made of glass with elevated content of boron and lithium, featuring signs of recycling. Such examples have already been recorded earlier among glassware made in this style from Pergamon and Branichevo in Serbia. This raises the question of possible manufacturing centers for some vessels with marvered décor.
Laryngeal squamous cell carcinoma disguised as asthma
Authors: Corcoran Jason , Merry Ty , Ali Kabeer , Reddy Pramod
Published: February 2025

Head and neck squamous cell carcinoma (HNSCC) with laryngeal involvement can lead to significant airway obstruction and compromise. This case report details a female patient in her 60s with a history of asthma who presented with refractory dyspnoea and persistent hoarseness, initially attributed to asthma. After multiple emergency room visits and treatment with bronchodilators and steroids, further investigation revealed an exophytic mass in the larynx, diagnosed as SCC. Despite normal pulmonary function tests, imaging indicated significant airway narrowing. The patient underwent a tracheostomy to secure her airway and was subsequently referred for curative surgery. This case underscores the importance of considering HNSCC in patients with unexplained respiratory symptoms, regardless of smoking history, and highlights the need for thorough investigation to prevent complications from advanced disease. Early multidisciplinary intervention is crucial in managing such cases effectively.
Benchmarking open-source large language models on Portuguese Revalida multiple-choice questions
Authors: Bruneti Severino João Victor , Basei de Paula Pedro Angelo , Berger Matheus Nespolo , Loures Filipe Silveira , Todeschini Solano Amadori , Roeder Eduardo Augusto , Veiga Maria Han , Guedes Murilo , Marques Gustavo Lenci
Published: February 2025

Objective

The study aimed to evaluate the top large language models (LLMs) in validated medical knowledge tests in Portuguese.

Methods

This study compared 31 LLMs in the context of solving the national Brazilian medical examination test. The research compared the performance of 23 open-source and 8 proprietary models across 399 multiple-choice questions.

Results

Among the smaller models, Llama 3 8B exhibited the highest success rate, achieving 53.9%, while the medium-sized model Mixtral 8×7B attained a success rate of 63.7%. Conversely, larger models like Llama 3 70B achieved a success rate of 77.5%. Among the proprietary models, GPT-4o and Claude Opus demonstrated superior accuracy, scoring 86.8% and 83.8%, respectively.

Conclusions

10 out of the 31 LLMs attained better than human level of performance in the Revalida benchmark, with 9 failing to provide coherent answers to the task. Larger models exhibited superior performance overall. However, certain medium-sized LLMs surpassed the performance of some of the larger LLMs.
Thrombus iodine-based perviousness is associated with recanalisation and functional outcomes in endovascular thrombectomy
Authors: Tian Chao , Liu Song , Fu Lejun , Guo Jingjing , Cao Chen , Sun Yu , Ren Tao , Wang Huiying , Wang Sifei , Luo Leilei , Wang Luotong , Wei Ming , Xia Shuang , Jin Song , Han Tong , Hao Nina
Published: February 2025

Background

Dual-energy CT (DECT) provides several novel methods to assess thrombus perviousness. We aimed to evaluate whether the novel thrombus perviousness measured with DECT is associated with improved recanalisation and better functional outcomes in acute ischaemic stroke (AIS) patients with endovascular thrombectomy (EVT).

Methods

108 AIS patients with middle cerebral artery occlusion who underwent DECT angiography on admission and received EVT treatment between April 2020 and September 2023 were retrospectively analysed. Thrombus attenuation increase (TAI) was evaluated on routine CT angiography and non-contrast CT, and DECT quantitative parameters of thrombus, including iodine concentration (IC) and normalised IC (NIC) were measured. Multivariable logistic regression analysis was used to evaluate the association of thrombus characteristics with arterial occlusive lesion scale and 90-day modified Rankin Scale.

Results

NIC was significantly associated with successful recanalisation (OR 1.372 (95% CI 1.194 to 1.625); p<0.001) and good functional outcome (OR 1.252 (95% CI 1.114 to 1.446); p<0.001). NIC yielded higher performance, with area under curve (AUC) of 0.789 and 0.740, in the prediction of recanalisation and functional outcome than TAI (AUCs=0.635 and 0.592). Compared with low-level NIC thrombus, high-level NIC was associated with 11.4 and 15.4 times higher likelihood of successful recanalisation and good functional outcome. Moreover, NIC was a significant indicator to differentiate large artery atherosclerosis from cardioembolism stroke with high specificity and positive predictive value.

Conclusions

Higher DECT-derived NIC is associated with increased odds of successful recanalisation and good functional outcome for EVT patients, and it yielded higher prediction performance than TAI.
A comprehensive study of particle dynamics, thermal fluctuations with Barrow entropy, and greybody factors of quantum-improved charged black holes
Authors: Fatima Ghulam , Zhu Tao , Javed Faisal , Waseem Arfa , Mustafa G.
Published: February 2025

This study examines the characteristics and behavior of quantum-improved charged black holes, focusing on the relationships between mass, charge, and the quantum-improved parameter. We explore the consequences of these characteristics on the structure of a black hole’s horizon, particularly investigating the ways that variations in charge and mass modify the horizon radius and size of innermost stable circular orbits. A thorough thermodynamic analysis indicates substantial impacts on corrected energies, including Helmholtz free energy, enthalpy, internal energy, and Gibbs free energy, in the context of Barrow entropy, emphasizing stable and unstable configurations across various quantum correction parameter ranges. Additionally, we analyze wave behavior near the cosmic horizon and its correlation with effective potential, illustrating whether wave frequency influences the gravitational absorption function and the transmission properties of scalar fields near quantum-improved charged black holes. Our findings highlight the complex interaction between black hole dynamics and quantum parameters, facilitating a more profound comprehension of black hole thermodynamics and their significance in curved space-time quantum field theory.
Are there ‘true substrates’ in turbidite depositional settings?
Authors: Uchman Alfred , Wetzel Andreas
Published: February 2025

True substrates in the strict sense are difficult to recognize in turbiditic deposits because it is hard to prove no sedimentary stasis before the deposition of sandstone beds. However, preservation of some graphoglyptid trace fossils, especially
Paleodictyon
, can help to approach solving this problem. If the shafts of
Paleodictyon
are preserved as series of knobs arranged in a hexagonal pattern on the lower bedding surfaces, there is no erosion, or erosion was minimal. Also cast scratch circles produced by rotating objects carving the sea floor or microbial mats can be evidence of true substrates. In addition, hardgrounds, or mineral crusts have the potential to represent true substrates in the deep-sea settings.
Salvage Anthropology and Low-Resource NLP: What Computer Science Should Learn from the Social Sciences
Authors: Widder David Gray , Kneese Tamara
Published: February 2025

This forum focuses on the conditions and futures of the labor underpinning technology production and maintenance. We welcome standalone articles as well as interviews and conversations about all tech labor within the global supply chain of digital technologies.
--- Seyram Avle and Sarah Fox, Editors
Dani Kalarikalayil Raju
Authors: Raju Dani Kalarikalayil
Published: February 2025

This section of the magazine features SIGCHI Chapters volunteers who are having an impact on the ground for HCI globally. ---
Jeni Paay and Elizabeth F. Churchill, Editors
How Computational Theorists Deal with Electrode Potential
Authors: Anderson Alfred B
Published: February 2025

For many years since Gurney introduced quantum mechanics to electrochemistry, models and calculations assumed bonding and other properties at the electrochemical interface may be calculated with adequate accuracy at the potential of zero charge (PZC) and that the effect of potential lies solely in controlling the energy of the electron involved in the transfer, which comes from or goes to an external energy level. The energy of the electron is assigned to the Fermi energy, Ef, of the electrode for the particular potential being modeled. This is done in the Butler-Volmer theory as well as in several quantum mechanical modeling procedures that are introduced here. Though the PZC in fact changes as the identity, amount, and structures of molecules chemically bonded to the electrode are varied during calculations using these models, there is no control of the electrode potential in the calculations. The past two decades have seen the development of computer codes that can incorporate controlled incremental surface charging with polarizable electrolyte models that compensate it, resulting in zero net interface charge. Calculations using these codes provide accurate predictions of the potential-dependent energies of reactants and products, reversible potentials, and electron transfer activation energies.
A Roadmap to Precision Immunotherapy for Early-Stage Non–Small Cell Lung Cancer
Authors: Vaccaro Alessandra , Rahal Zahraa , Kadara Humam , Cascone Tina
Published: February 2025

Immunotherapy has revolutionized the treatment of early-stage non–small cell lung cancer; yet many patients fail to achieve long-lasting benefit, partially because of incomplete or inconsistent biomarker predictions. Integrative multiomics, combining tumor-intrinsic, immune microenvironment, and systemic factors, offer a more comprehensive framework for precision immunotherapy, enabling improved patient stratification, treatment selection and outcomes.
The association between changes in peer pressure and changes in alcohol and cannabis use: a prospective cohort study among men during emerging adulthood
Authors: Gmel Gerhard , Marmet Simon , Wicki Matthias , Studer Joseph , Dietze Paul
Published: February 2025

Introduction: Cross-sectional studies have shown that peer influence to use a substance are associated with increased rates of substance use, but there are few longitudinal studies of this relationship or studies investigating whether peer influence to not use substances are associated with decreases in rates of substance use. The present study looks at both directions of influence and compares alcohol with cannabis use.
Methods: Two-wave longitudinal study, separated 15.8 months; cross-domain coupling model to disentangle effects of peer influence and peer selection; GEE models to analyse changes in pressure to use and not to use alcohol or cannabis.
6,528 young men from six mandatory military recruitment centres in Lausanne, Windisch and Mels in Switzerland completed at least one questionnaire at baseline (age at baseline: 20.00) or follow-up. Questionnaires were completed outside of the army and independent of recruitment for military or social service.
Volume of drinking, heavy episodic drinking, cannabis use frequency, and three items of the misconduct subscale of the Peer Pressure Inventory (pressure to use or not cannabis, pressure to drink or not, and pressure to get drunk or not) were measured.
Results: Peer pressure and peer selection operated bidirectionally for alcohol use. For cannabis use, peer selection was about 5-times stronger than peer pressure. Increases in pressure to use a substance were associated with increased substance use and decreases in pressure with decreases in use.
Conclusions: Peer pressure continue to operate after adolescence into emerging adulthood, but the strength of effects of peer pressure and peer selection depends on the substance. Peer pressure may have putatively positive effects when pressure is towards non-use of a substance.
The Evolution of Sally Rooney’s Writing in Intermezzo
Authors: Angelo Barbara Moreira Bom
Published: February 2025

Rooney, Sally. Intermezzo. New York: Farrar, Straus and Giroux, 2024. 431 pp.
Introduction
Authors: Bolfarine Mariana , Izarra Laura P.Z.
Published: February 2025

Introduction the ABEI Journal number 26 volume 2.
Effect of Early Life Trauma Exposure on Vascular Dysfunction in Black Men and Women
Authors: Spikes Telisa A. , Thorpe Roland J. , Michopoulos Vasiliki , Wharton Whitney , Pelkmans Jordan , Dunbar Sandra B. , Mehta Puja K. , Pemu Priscilla , Taylor Herman , Quyyumi Arshed
Published: February 2025

Background

Psychosocial stressors such as childhood trauma have been associated with an increased risk of hypertension. The impact of childhood trauma on vascular dysfunction in Black adults remains less clear. We examined the association between childhood trauma and vascular function in Black adults.

Methods and Results

Childhood trauma exposure and vascular function were assessed in a cohort of healthy Black participants without known cardiovascular disease (n=404) from a large metropolitan city. Childhood trauma was assessed using the Early Trauma Inventory Short Form with higher scores indicative of higher traumatic life events assessed before age 18 years. Outcomes of central augmentation index (CAIx) and carotid femoral pulse wave velocity were measured as indices of wave reflections and arterial stiffness using applanation tonometry (Sphygmocor Inc.), and central pulse pressure (CPP) was calculated as the difference between the central aortic systolic and diastolic blood pressures. Relationships between Early Trauma Inventory Short Form and outcomes were assessed using multivariate‐adjusted and sex‐stratified linear regression models. The mean age of the cohort was 53 (SD=10.3), 61% women. Cumulative childhood trauma was not associated with CAIx, central pulse pressure, or carotid femoral pulse wave velocity in the minimal or fully adjusted models for sociodemographic, sex, clinical factors, medical history, health behaviors, and depression. Significant trauma × sex interactions were identified for CAIx (
P
=0.003) and central pulse pressure (
P
=0.025). Childhood trauma was associated with lower CAIx (
β
=−0.55% [95% CI, −1.07 to −0.03] in men, but higher CAIx (
β
=0.35% [95% CI, 0.08–0.63]) and central pulse pressure (
β
=0.23 mm Hg [95% CI, 0.01–0.43]) in women.

Conclusions

Childhood trauma is independently associated with impaired arterial compliance in Black women.
Sex‐Related Differences in the Prognostic Role of Acetylcholine Provocation Testing
Authors: Rinaldi Riccardo , Russo Michele , Occhipinti Giovanni , Laudani Claudio , Torre Ilaria , Colucci Michele , Gurgoglione Filippo Luca , Animati Francesco Maria , Lenkowicz Jacopo , Tudor Andrada Mihaela , Liuzzo Giovanna , Sanna Tommaso , Leone Antonio Maria , Niccoli Giampaolo , Lanza Gaetano A. , Trani Carlo , Burzotta Francesco , Crea Filippo , Montone Rocco A.
Published: February 2025

Background

Intracoronary provocation testing with acetylcholine (ACh) is helpful to diagnose and risk‐stratify patients with ischemia with nonobstructed coronary arteries (NOCA) and myocardial infarction with NOCA. This study explored potential sex‐related disparities on the prognostic significance of ACh provocative testing.

Methods

Consecutive patients with ischemia with NOCA and those with myocardial infarction with NOCA who underwent ACh provocation testing were enrolled. The primary end point was the incidence of major adverse cardiovascular and cerebrovascular events at follow‐up. Co‐primary end points were angina recurrence and quality of life assessed by 12‐month Seattle Angina Questionnaire (SAQ) summary score.

Results

A total of 519 patients (mean age, 61.4±12.1 years; 275 [53.0%] women and 244 [47%] men) were enrolled: 346 (66.7%) with ischemia with NOCA and 173 (33.3%) with myocardial infarction with NOCA. A positive ACh test was observed in 274 (52.8%) patients, with a lower prevalence of epicardial spasm (82 [56.2%] versus 106 [82.8%]) and a higher prevalence of microvascular spasm (64 [43.8%] versus 22 [17.2%]) in women compared with men (
P
>0.001). After a median 22‐month follow‐up, major adverse cardiovascular and cerebrovascular events occurred in 53 (10.2%) patients, without significant sex differences (
P
>0.05). Men with a positive ACh test had a significantly higher rate of major adverse cardiovascular and cerebrovascular events (22 [17.2%] versus 5 [4.3%],
P
=0.002) compared with those with a negative test; no difference was observed in women (
P
>0.05) (
P
for interaction=0.003). Women with a positive test experienced a higher rate of angina recurrence (61 [41.8%] versus 32 [24.8%],
P
=0.005) and a lower SAQ summary score (82 [interquartile range, 72–90] versus 86 [interquartile range, 78–100],
P
<0.001) compared with those with a negative result; no difference was observed in men (
P
>0.05).

Conclusions

This study revealed the importance of recognizing sex‐specific differences in the prognostic value of ACh testing for proper management of coronary vasomotor disorders.
Excessive Hypercholesterolemia in Pregnancy Impairs Later‐Life Maternal Vascular Function in Rats
Authors: de Oliveira Amanda A. , Elder Emma , Graton Murilo E. , Spaans Floor , Wooldridge Amy L. , Quon Anita , Kirschenman Raven , Cooke Christy‐Lynn M. , Davidge Sandra T.
Published: February 2025

Background

Preeclampsia is a risk factor for the development of later‐life cardiovascular disease. However, the underlying mechanisms are poorly understood. Excessive hypercholesteremia in pregnancy induces a preeclampsia‐like phenotype, but whether this also impacts maternal vascular function later in life has not been fully characterized.

Methods and Results

Sprague Dawley rats received a control diet (CD) or a high‐cholesterol (HCD) diet from gestational day 6 to 20, after which maternal vascular function was assessed 3 months postpartum. Exposure to an HCD in pregnancy reduced later‐life endothelium‐dependent vasodilation in carotid arteries (−15.24±3.27%), which was mediated via prostaglandin H synthase 2. There were no differences in vasodilation between CD and HCD postpartum rats in the mesenteric arteries, coronary arteries, or aortas. Vasoconstriction to phenylephrine increased in carotid arteries (61.02±21.48%) and reduced in aortas (−23.24±6.19%) of the HCD postpartum group versus CD dams, without differences in mesenteric and coronary arteries. The increased vasoconstriction in carotid arteries was due to lower nitric oxide modulation of constriction. Moreover, carotid artery myogenic response was reduced (−37.68±10.07%) and stiffness was increased (19.67±6.21%) in the HCD postpartum rats compared with CD along with decreased elastin density (−20.85±4.52%). The impact of the HCD on vascular function did not occur in age‐matched never‐pregnant female rats.

Conclusions

Excessive hypercholesterolemia in pregnancy impairs later‐life maternal vascular function in rats with varying impacts across different vascular beds. Understanding mechanisms for
pregnancy‐specific
excessive hypercholesterolemia provides avenues for targeted intervention strategies to reduce the burden of cardiovascular disease in women who had a complicated pregnancy.
Open and Citizen Science in Light of New European Research Policies
Authors: Adam Frane , Gorišek Maruša
Published: February 2025

This article discusses the meaning of open science, and in particular the concept of citizen science, in a broader socio-political and scientific context. The authors highlight the ambivalence of these concepts and the lack of critical reflection on the possible (unwanted) negative implications of the establishment of these ideas. The authors address these issues using an international comparative analysis based primarily on documentation and secondary data analysis. Research approaches in the sense of open science and citizen science can, in many cases, be useful for researchers as well as for cognitively active citizens. They can enable the enrichment of knowledge and the potential for (social) innovation. However, there are also risks and unwanted side effects that diminish the relevance and status of scientific research. It is particularly dangerous to create illusions about the potential of ad hoc citizen science projects and their outstanding, immediate results. The campaign for open science may serve as a cover-up for some of the problems and anomalies in the realm of science. The authors also see danger in the potential erosion of the autonomy of science and diverting attention from some of the more pressing problems in science.
Exploring consumer perception of edible insects in Korea using text mining
Authors: Kang K. , Kim Y.
Published: February 2025

Food security is a critical issue derived from the limitations of protein production systems, promoting the exploration of edible insects as alternative protein sources. While perception surveys are essential to a research planning process to address entomophobia, they are costly and time-consuming. Analysing text data on social media using text mining has been suggested for innovative perception surveys in the era of big data. This study analysed articles about edible insects from blogs and online communities to understand the Korean public’s perception. The comprehensive results of word frequency and similarity analysis showed that Koreans are steadily interested in edible insects as future food and in farms, industries, and businesses of edible insects in Korea. Additionally, the public’s perception of health benefits or drying processing methods of edible insects was identified over the years. Results of topic modeling, though less intuitive than word frequency and similarity analysis, provided complementary insights such as future, alternative, health effect, usage, and application of edible insects. The text mining results (TMR) were validated because similar results on TMR and perception survey results (PSR) were obtained. TMR provided insights into unpredictable words or topics, such as domestic markets and health issues, which were not captured by PSR. In conclusion, the public’s perception and new meanings of edible insects were derived using text mining, and the applicability of this novel and cost-effective method as a perception survey was confirmed through this research.
New Insights into Middle Nubian Ceramic Traditions at Elephantine: An Attempt for a Better Understanding of Cultural Complexities in Upper Egypt and Nubia
Authors: Schröder Marie-Kristin
Published: February 2025

The Middle Nubian ‘C-Group’, ‘Kerma’, and ‘Pan-Grave’ cultures have commonly been believed to be contemporaneous for most of their occurrence, but recent research on Nubian-style ceramics from the settlement at Elephantine Island indicate that this contemporaneity must be reconsidered. This paper presents the results of the ceramic analysis of the Nubian-style corpus from recent excavations in the Northwestern town at Elephantine with a focus on intra- and intercultural ceramic finds. Although site-specific pottery formations at Elephantine allow for a more neutral way of addressing ceramic assemblages, comparisons with ceramics from sites in Lower and Upper Nubia enable us to differentiate between Nubian traditions. The domestic and funerary ceramic assemblages of the C-Group culture are significant for redefining the cultural complexities of the Middle Nubian traditions. This paper sheds light on the ceramic tradition of the C-Group in comparison to those of the Pan-Grave horizon, Kerma culture as well as pharaonic traditions.
Nubian Style Pottery from the New Kingdom Town of Sai Island
Authors: Budka Julia
Published: February 2025

The pottery corpus from the city on Sai Island, one of the characteristic colonial towns in New Kingdom Nubia, comprises a majority of Egyptian style vessels and Nubian style ceramics as well as ‘hybrid’ pieces. This paper presents the Eighteenth Dynasty Nubian pottery from Sai city, focussing primarily on quantities, shapes, wares and parallels from various sites in context, and discusses its social and cultural implications. A key concern is how much Sai represents an elite urban phenomenon that differs from rural contexts in the hinterland of the city.

The Nubian style pottery as an integral part of the corpus of Sai attests to social practices of a local group with a specific cultural identity. The community practices reflected in the pottery show that the legacy of the Kerma empire was never completely abandoned but adapted in relation to the new political, social and religious circumstances in a colonial context.
Fuzzy Boundaries or Hard Borders? Cultural Groupings in Second Millennium bc Nubia from the View of Linguistic Evidence
Authors: Cooper Julien
Published: February 2025

The region of Sudan and Nubia has always been witness to a complicated nexus of linguistic groupings, frequently exhibiting episodes of linguistic shifts, migration, and extinction. From Nilo-Saharan languages like Meroitic, to Afroasiatic languages like Beja, the region of the Second Millennium bce Middle Nile was certainly not homogenous ethno-linguistically. Linguistic enigmas provide further confusion, like the unknown languages of Lower Nubia that correlate to A- and C-Group material horizons. This paper describes the limits of the evidence in organizing linguistic groupings of ancient Nubia and critiques the issue as to whether these linguistic blocs correlate to geographic boundaries of specific material cultures. Does homogeneity in the archaeological record demonstrate similar homogeneity in linguistic identity? How do we expect nomadic pastoralists, seasonal movements, and migrations to affect this linguistic map? With a focus on pragmatic arguments and the use of later linguistic evidence, this paper reflects on the peopling of the Middle Nile region.
2. Introduction to building your research 'kitchen'
Authors: Lane Stuart , Lave Rebecca
Published: February 2025

Here we provide an overview of the chapters in Section 1 of the Field Guide, using the metaphor of research as a kitchen in which the cook (the researcher) chooses the recipe (the research design) they want to make and the ingredients (particular methods) they want to use.
3. Framing, disciplines and mixing methods in environmental research
Authors: Lane Stuart , Lave Rebecca
Published: February 2025

The academy is built upon disciplines which both enable and constrain what we do, so defining the methods we choose to use and how we use them; and in turn determining the knowledge produced by our research. In this Chapter, we define this process as one of framing and illustrate different kinds of framing using examples from Section 2 of The Field Guide. We describe how frames can be mixed in four different ways, in cross-disciplinary, multi-disciplinary, interdisciplinary and transdisciplinary settings. The mixing of methods in each of these may allow research questions to be answered in different ways. Across them, the extent to which methods are modified, how they are combined and who is involved in combining them will change. But behind them all is a single theme which is where what is mixed and how is framed by what is being researched rather than how disciplines say it should be researched. This can make mixing methods a challenge as it may sit uncomfortably with disciplinary norms; but also because mixing methods may challenge the traditional and supposed separation of the researcher and what is being researched.
4. Mixed methods in tension
Authors: Biermann Christine , Gibbes Cerian
Published: February 2025

Mixing methods helps environmental researchers to engage with the complexity present in the interconnected biophysical and social world. At the same time, tensions often arise as biophysical and social methods (and the results they yield) are put into conversation with one another. This chapter explores the productive tensions that researchers engage with when pursuing mixed methods environmental research. These include tensions around resolution and scale of analysis, epistemologies, values embedded in particular methods, and more. We argue that mixed methods approaches are valuable not in spite of the tensions they engender, but indeed because of these tensions, as they require a more reflexive research practice and in turn allow for a richer understanding of the world.