bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key role of adsorption site abundance in the direct electrochemical co-detection of estradiol and dopamine
Authors: Delmo Naela , Pande Ishan , Peltola Emilia 
Published: August 2024

Abstract
Estradiol (E2) is a hormone that influences various aspects of women’s health. Beyond its reproductive functions, E2 impacts neurotransmitter systems such as dopamine (DA). Vertically aligned carbon nanofibers (VACNFs) have shown good sensitivity, selectivity against ascorbic acid (AA) and uric acid (UA), biocompatibility, and reduced fouling in DA sensing. In this study, we explore the use of Ti-Ni-CNF electrodes with CNFs grown for 5 min and 30 min for the direct electrochemical co-detection of E2 and DA. The longer growth time led to a 142% increase in average CNF length and a 36% larger electroactive surface area. In E2 detection, the electrodes demonstrate a wide linear range of 0.05–10 µM and sensitivity of 0.016 and 0.020 µA/µM for Ti-Ni-CNF-5 min and Ti-Ni-CNF-30 min, respectively. The sensor performance remains largely unaffected even in the presence of other steroid hormones such as progesterone and testosterone. Co-detection of equimolar E2 and DA shows promising peak separation of 0.34 ± 0.01 V and repeatability after 10 measurements. A notable improvement in the E2/DA peak current ratio, from 0.53 ± 0.07 to 0.81 ± 0.16, was achieved with the increased CNF length. Our results demonstrate the influence of adsorption sites in electrochemical detection, especially for analytes such as E2 and DA that both rely on adsorption for oxidation. While detecting small and fluctuating physiological concentrations remains a challenge, these findings can be used in choosing and fabricating electrode materials for more accurate and accessible continuous hormone measurements, including the possibility of multianalyte sensing platforms.

Graphic abstract
Whole genome sequence and characterisation of Streptococcus suis 3112, isolated from snakeskin gourami, Trichopodus pectoralis
Authors: Aiewsakun Pakorn , Ruangchai Wuthiwat , Jaemsai Bharkbhoom , Bodharamik Thavin , Meemetta Watcharachai , Senapin Saengchan 
Published: August 2024

Abstract
Background
Streptococcus suis (S. suis) is an important swine and human pathogen. A recent study reported the first isolate of S. suis capable of infecting fish, designated as S. suis strain 3112. The bacterium was isolated from snakeskin gourami (Trichopodus pectoralis), an economically important fish species native to Southeast Asia, and it was previously shown that it can infect and cause lethal streptococcosis in the fish.

Results
In this study, we present the complete genome of S. suis 3112. Molecular sequence analysis revealed that it belongs to serotype 6, sequence type 2340. Phylogenetic analysis showed that the bacterium clustered with healthy-pig S. suis isolates, suggestive of an ultimate swine (as opposed to human) origin of the bacterium. Two fluoroquinolone resistance genes are present in the bacterial genome, namely patA and patB. Our results showed that both genes are expressed in our bacterium, and the bacterium is resistant to norfloxacin, but is still sensitive to other fluoroquinolones, including ciprofloxacin, enrofloxacin, and sparfloxacin. Additionally, the bacterium is sensitive to β-lactams, tetracyclines, sulphonamides, and an aminoglycoside.

Conclusions
This study reports and describes the complete genome of S. suis 3112, the first isolate of S. suis known to infect fish, and provides further insights into the bacterial isolate, particularly regarding its drug resistance profile. These results will facilitate further investigations of the comparative genomics and pathogenic characteristics of S. suis, as well as the development of control strategies against this newly-identified fish pathogen.
Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches
Authors: Hashempour Ava , Khodadad Nastaran , Akbarinia Shokufeh , Ghasabi Farzane , Ghasemi Younes , Nazar Mohamad Matin Karbalaei Ali , Falahi Shahab 
Published: August 2024

AbstractSubstantial advances have been made in the development of promising HIV vaccines to eliminate HIV-1 infection. For the first time, one hundred of the most submitted HIV subtypes and CRFs were retrieved from the LANL database, and the consensus sequences of the eleven HIV proteins were obtained to design vaccines for human and mouse hosts. By using various servers and filters, highly qualified B-cell epitopes, as well as HTL and CD8 + epitopes that were common between mouse and human alleles and were also located in the conserved domains of HIV proteins, were considered in the vaccine constructs. With 90% coverage worldwide, the human vaccine model covers a diverse allelic population, making it widely available. Codon optimization and in silico cloning in prokaryotic and eukaryotic vectors guarantee high expression of the vaccine models in human and E. coli hosts. Molecular dynamics confirmed the stable interaction of the vaccine constructs with TLR3, TLR4, and TLR9, leading to a substantial immunogenic response to the designed vaccine. Vaccine models effectively target the humoral and cellular immune systems in humans and mice; however, experimental validation is needed to confirm these findings in silico.
A longitudinal assessment of heat exposure and biomarkers of kidney function on heat shock protein 70 and antibodies among agricultural workers
Authors: Butler-Dawson Jaime , Johnson Richard J. , Krisher Lyndsay , Jaramillo Diana , Cruz Alex , Pilloni Daniel , Brindley Stephen , Rodriguez-Iturbe Bernardo , Sanchez-Lozada Laura Gabriela , Dally Miranda , Newman Lee S. 
Published: August 2024

Abstract
Background
Exposure to extreme heat impacts millions of people worldwide and outdoor workers are among the populations most affected by hot temperatures. Heat stress induces several biological responses in humans, including the production of heat shock proteins (HSP) and antibodies against HSP (anti-HSP) which may play a central role in the body’s cellular response to a hot environment.

Objective
This longitudinal study investigated the impact of elevated temperatures and humidity on the presence of HSP70 and anti-HSP70 and examined relationships with markers of kidney function in an at-risk workforce under conditions of extreme heat and exertion in Guatemala.

Methods
We collected ambient temperature and relative humidity data as well as biomarkers and clinical data from 40 sugarcane workers at the start and the end of a 6-month harvest. We used generalized mixed-effects models to estimate temperature effects on HSP70 and anti-HSP70 levels. In addition, we examined trends between HSP70 and anti-HSP70 levels and markers of kidney function across the harvest.

Results
At the end of the harvest, temperatures were higher, and workers had, on average, higher levels of HSP70 and anti-HSP70 compared to the beginning of the season. We observed significant increasing trends with temperature indices, heat index, and HSP70 levels. Maximum temperature was associated with HSP70 increments after controlling for age, systolic and diastolic blood pressure (β: 0.21, 95% Confidence Interval: 0.09, 0.33). Kidney function decline across the harvest was associated with both higher levels of anti-HSP70 levels at the end of the harvest as well as greater increases in anti-HSP70 levels across the harvest.

Conclusions
These results suggest that workplace heat exposure may increase the production of HSP70 and anti-HSP70 levels and that there may be a relationship between increasing anti-HSP70 antibodies and the development of renal injury. HSP70 holds promise as a biomarker of heat stress in exposed populations.
Mortality from pulmonary hypertension in Europe 2001-2019
Authors: Hartley Adam , Singh Harpreet , Jani Chinmay , Salciccioli Justin D. , Shalhoub Joseph , Howard Luke S. , Marshall Dominic C. 
Published: August 2024

Abstract
Background
The incidence of Pulmonary Hypertension (PH) and Pulmonary Arterial Hypertension (PAH) is believed to be on the rise and is associated with poor outcomes.

Methods
We extracted age-standardized mortality rates (ASMRs) for decedents ≥ 18 years of age from the World Health Organization Mortality Database, using International Classification of Diseases 10th edition codes for PH and PAH, covering the period from 2001 to 2019. The UK and European Union countries with at least 1,000,000 inhabitants and at least 75% of available data points over the study period were included.

Results
Between 2001 and 2019, in countries with available data, the median ASMR for PH increased by + 1.19 per 1,000,000 (+ 22.51%) in females and + 0.36 per 1,000,000 (+ 6.06%) in males. Out of 19 countries, 13 demonstrate an increase in female PH ASMR, and 12 reported an increase in male PH ASMR. In contrast, median PAH ASMR decreased by -0.29 per 1,000,000 (-28.74%) in females and remained relatively unchanged in males, with a minor increase of + 0.01 per 1,000,000 (+ 1.07%). Notably, there was significant inter-country heterogeneity, with countries such as Hungary, Romania, and Poland displaying results incongruous with the rest of Europe.

Conclusions
While publicly available mortality statistics for PH may be unreliable, these data suggest an overall increase in mortality across Europe from 2001 to 2019. However, mortality from PAH has shown a decrease in females and a modest increase in males. This underscores the urgent need for robust and high-quality mortality reporting, including international registries, for both PH and PAH.
Genome-wide association study for metabolic syndrome reveals APOA5 single nucleotide polymorphisms with multilayered effects in Koreans
Authors: Park Young Jun , Moon Sungji , Choi Jaeyong , Kim Juhyun , Kim Hyun-Jin , Son Ho-Young , Im Sun-Wha , Kim Jong-Il 
Published: August 2024

Abstract
Background and purpose
Genome-wide association studies (GWAS) of metabolic syndrome (MetS) have predominantly focused on non-Asian populations, with limited representation from East Asian cohorts. Moreover, previous GWAS analyses have primarily emphasized the significance of top single nucleotide polymorphisms (SNPs), poorly explaining other SNP signals in linkage disequilibrium. This study aimed to reveal the interaction between rs651821 and rs2266788, the principal variants of apolipoprotein A5 (APOA5), within the most significant loci identified through GWAS on MetS.

Methods
GWAS on MetS and its components was conducted using the data from the Korean Genome and Epidemiology Study (KoGES) city cohort comprising 58,600 individuals with available biochemical, demographic, lifestyle factors, and the most significant APOA5 locus was analyzed further in depth.

Results
According to GWAS of MetS and its diagnostic components, a significant association between the APOA5 SNPs rs651821/rs2266788 and MetS/triglycerides/high-density lipoprotein phenotypes was revealed. However, a conditional analysis employing rs651821 unveiled a reversal in the odds ratio for rs2266788. Therefore, rs651821 and rs2266788 emerged as independent and opposing signals in the extended GWAS analysis, i.e., the multilayered effects. Further gene-environment interaction analyses regarding lifestyle factors such as smoking, alcohol consumption, and physical activity underscored these multilayered effects.

Conclusion
This study unveils the intricate interplay between rs651821 and rs2266788 derived from MetS GWAS. Removing the influence of lead SNP reveals an independent protective signal associated with rs2266788, suggesting a multilayered effect between these SNPs. These findings underline the need for novel perspectives in future MetS GWAS.
Development of a biomarker prediction model for post-trauma multiple organ failure/dysfunction syndrome based on the blood transcriptome
Authors: Duran Ivan , Banerjee Ankita , Flaherty Patrick J. , Que Yok-Ai , Ryan Colleen M. , Rahme Laurence G. , Tsurumi Amy 
Published: August 2024

Abstract
Background
Multiple organ failure/dysfunction syndrome (MOF/MODS) is a major cause of mortality and morbidity among severe trauma patients. Current clinical practices entail monitoring physiological measurements and applying clinical score systems to diagnose its onset. Instead, we aimed to develop an early prediction model for MOF outcome evaluated soon after traumatic injury by performing machine learning analysis of genome-wide transcriptome data from blood samples drawn within 24 h of traumatic injury. We then compared its performance to baseline injury severity scores and detection of infections.

Methods
Buffy coat transcriptome and linked clinical datasets from blunt trauma patients from the Inflammation and the Host Response to Injury Study (“Glue Grant”) multi-center cohort were used. According to the inclusion/exclusion criteria, 141 adult (age ≥ 16 years old) blunt trauma patients (excluding penetrating) with early buffy coat (≤ 24 h since trauma injury) samples were analyzed, with 58 MOF-cases and 83 non-cases. We applied the Least Absolute Shrinkage and Selection Operator (LASSO) and eXtreme Gradient Boosting (XGBoost) algorithms to select features and develop models for MOF early outcome prediction.

Results
The LASSO model included 18 transcripts (AUROC [95% CI]: 0.938 [0.890–0.987] (training) and 0.833 [0.699–0.967] (test)), and the XGBoost model included 41 transcripts (0.999 [0.997–1.000] (training) and 0.907 [0.816–0.998] (test)). There were 16 overlapping transcripts comparing the two panels (0.935 [0.884–0.985] (training) and 0.836 [0.703–0.968] (test)). The biomarker models notably outperformed models based on injury severity scores and sex, which we found to be significantly associated with MOF (APACHEII + sex—0.649 [0.537–0.762] (training) and 0.493 [0.301–0.685] (test); ISS + sex—0.630 [0.516–0.744] (training) and 0.482 [0.293–0.670] (test); NISS + sex—0.651 [0.540–0.763] (training) and 0.525 [0.335–0.714] (test)).

Conclusions
The accurate assessment of MOF from blood samples immediately after trauma is expected to aid in improving clinical decision-making and may contribute to reduced morbidity, mortality and healthcare costs. Moreover, understanding the molecular mechanisms involving the transcripts identified as important for MOF prediction may eventually aid in developing novel interventions.
Policy brief Belgian EBCP mirror group Artificial Intelligence in cancer care
Authors: Cauët Emilie , Schittecatte Gabrielle , Van Den Bulcke Marc ,   BE-EBCP mirror group ‘Artificial Intelligence, Albarani Valentina , Allaoui El Maati , Antoine-Poirel Hélène , Baatout Sarah , Broeckx Glenn , Chavez Marcela , Coche Emmanuel , Croes Romaric , De Broe Sofie , Demetter Pieter , De Witte Chloë , Delsupehe Louis , Deman Frederik , Dendooven Amelie , Dhont Jennifer , Ertaylan Gokhan , Gevaert Thierry , Gijssels Stefan , Hasaers Koen , Haustermans Karin , Hovelinck Rudy , Hustinx Roland , Jodogne Sébastien , Lahousse Lies , Lauwers Steven , Lejeune Stephane , Leloup Arthur , Lippens Evi , Macq Benoit , Maes Brigitte , Meca Carlos , Rommel Ward , Salgado Roberto , Schelfhout Bart , Schreurs Wim , Sys Gwen , Van De Voorde Lien , Van Den Bulck Isabelle , Van Lint Johan , Van Roose Wim , Van Steen Kristel , Vandermeulen Ad , Volders Pieter-Jan , Yogeswaran Suresh 
Published: August 2024

AbstractArtificial Intelligence (AI) is already a reality in health systems, bringing benefits to patients, healthcare providers, and other stakeholders in the health care. To further leverage AI in health, Belgium is advised to make policy-level decisions about how to fund, design and undertake actions focussing on data access and inclusion, IT-infrastructure, legal and ethical frameworks, public and professional trust, in addition to education and interpretation. EU initiatives, such as European Health data space (EHDS), the Genomics Data Infrastructure (GDI) and the EU Cancer Imaging Infrastructure (EUCAIM) are building EU data infrastructures. To continue these positive developments, Belgium should continue to invest and support existing European data infrastructures. At the national level, a clear vision and strategy need to be developed and infrastructures need to be harmonized at the European level.
Nitrogen deposition enhances the competitive advantage of invasive plant species over common native species through improved resource acquisition and absorption
Authors: Xiang Chixuan , Wang Xiao , Chen Yanni , Liu Lele , Li Mingyan , Wang Tong , Sun Yingkun , Li Haimei , Guo Xiao 
Published: August 2024

Abstract
Background
Previous studies into the interactions between native and invasive species under nitrogen (N) deposition have often overlooked the presence of co-occurring native species, a factor that could influence the outcomes of interspecific competition. Furthermore, publication bias may lead researchers to focus on rare native species with limited adaptability. In this study, we examined how two levels of N deposition affected the physiological and ecological traits and the interspecies interactions between three invasive and three common native species.

Results
N deposition promoted the growth of both invasive and native species. The relative dominance index (RDI) of invasive species was consistently higher than that of native species. Invasive species had an advantage over common native species in using the increased N effectively. The biomass distribution of invasive species was biased toward the aboveground parts, indicating competition for light resources.

Conclusions
N deposition conferred a stronger competitive advantage to invasive species than to native species, suggesting that the distribution range of invasive species may expand further under increased N deposition.
Systematic transcriptomic analysis of childhood medulloblastoma identifies N6-methyladenosine-dependent lncRNA signatures associated with molecular subtype, immune cell infiltration, and prognosis
Authors: Joshi Kandarp , Yuan Menglang , Katsushima Keisuke , Saulnier Olivier , Ray Animesh , Amankwah Ernest , Stapleton Stacie , Jallo George , Taylor Michael D. , Eberhart Charles G. , Perera Ranjan J. 
Published: August 2024

AbstractMedulloblastoma, the most common malignant pediatric brain tumor, is classified into four main molecular subgroups, but group 3 and group 4 tumors are difficult to subclassify and have a poor prognosis. Rapid point-of-care diagnostic and prognostic assays are needed to improve medulloblastoma risk stratification and management. N6-methyladenosine (m6A) is a common RNA modification and long non-coding RNAs (lncRNAs) play a central role in tumor progression, but their impact on gene expression and associated clinical outcomes in medulloblastoma are unknown. Here we analyzed 469 medulloblastoma tumor transcriptomes to identify lncRNAs co-expressed with m6A regulators. Using LASSO-Cox analysis, we identified a five-gene m6A-associated lncRNA signature (M6LSig) significantly associated with overall survival, which was combined in a prognostic clinical nomogram. Using expression of the 67 m6A-associated lncRNAs, a subgroup classification model was generated using the XGBoost machine learning algorithm, which had a classification accuracy > 90%, including for group 3 and 4 samples. All M6LSig genes were significantly correlated with at least one immune cell type abundance in the tumor microenvironment, and the risk score was positively correlated with CD4+ naïve T cell abundance and negatively correlated with follicular helper T cells and eosinophils. Knockdown of key m6A writer genes METTL3 and METTL14 in a group 3 medulloblastoma cell line (D425-Med) decreased cell proliferation and upregulated many M6LSig genes identified in our in silico analysis, suggesting that the signature genes are functional in medulloblastoma. This study highlights a crucial role for m6A-dependent lncRNAs in medulloblastoma prognosis and immune responses and provides the foundation for practical clinical tools that can be rapidly deployed in clinical settings.
Hydrogeochemical and microbial characterization of a Middle Triassic carbonate aquifer (Muschelkalk) in Berlin and geochemical simulation of its use as a high-temperature aquifer thermal energy storage
Authors: Virchow Lioba , Siever-Wenzlaff Christian , Blöcher Guido , Alibrandi Armando , Kallmeyer Jens , Zimmer Martin , Wiersberg Thomas , Thielke Christoph , Schleicher Anja , Regenspurg Simona 
Published: August 2024

AbstractThe geological formation of the Muschelkalk is widespread in the center of the North German Basin (NGB) and is increasingly attracting interest for application of geothermal energy extraction or high-temperature aquifer thermal energy storage (HT-ATES). This study investigates the Middle Triassic “Rüdersdorfer Schaumkalk”, which was the former injection horizon of the natural gas storage facility in Berlin, Germany. For the first time, detailed chemical and microbiological analyses of formation water of this Lower Muschelkalk limestone formation were conducted and hydrogeochemically characterized. In addition, a hydrogeochemical model was developed to quantify the potential reactions during HT-ATES focusing on calcite dissolution and precipitation. The main objectives of this study are: (1) to determine the origin of the water from the three wells targeting the Muschelkalk aquifer, (2) to understand changes in hydrochemistry after system operation, and (3) to evaluate the long-term sustainability of a potential HT-ATES system with increasing temperature. The target formation is encountered by several wells at about 525 m below the surface with an average thickness of 30 m. Two hydraulic lifting tests including physical, chemical, and microbial groundwater as well as gas monitoring were carried out. In addition, several downhole samples of formation fluid were collected from the aquifer at in situ pressure and temperature conditions. Fluid analysis of the saline formation water indicate a seawater origin within the Muschelkalk with subsequent evaporation and various water–rock interactions with anhydrite/gypsum, dolomite, and calcite. With a salinity of 130 g/L, dominated by Na–Cl, a slightly acidic pH between 6 and 7, and a low gas content of 3%, the formation water fits to other saline deep formation waters of the NGB. Gas concentrations and microbial communities like sulfate-reducing bacteria and methanogenic archaea in the produced water indicate several geochemical alterations and microbial processes like corrosion and the forming of biogenic methane. Geochemical simulations of calcite equilibrium over 10 HT-ATES cycles indicated a pronounced propensity for calcite precipitation up to 31 mg/kgw, within the heat exchanger. At the same time, these models predicted a significant potential for calcite dissolution, with rates up to 21 mg/kgw, in both the cold and hot reservoirs. The results from the carbonate aquifer characterized in this study can be transferred to other sites in the NGB affected by salt tectonics and have provided information on the microbiological-chemical processes to be expected during the initial use of old wells.