bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of HRM-Analysis of the Melting Curves Obtained after Amplification of VNTR-Loci for Identification and Differentiation of Brucella Strains
Authors: Anisimova E. A. , Mirgazov D. A. , Dodonova E. A. , Elizarova I. A. , Pankova E. V. , Osyanin K. A. 
Published: January 2024

The aim of the present study was to evaluate the effectiveness of analysis of the high resolution melting curves obtained after amplification of VNTR loci for the identification and differentiation of Brucella strains.Materials and methods. 16 strains of Brucella species – B. canis (n=1), B. abortus (n=9), B. melitensis (n=2), B. suis (n=4) – of different geographical origin were used as objects of the research. The MLVA-typing was performed using conventional PCR followed by separation of amplicons in agarose gel and real-time PCR with post-amplification analysis of the curves of VNTR loci melting in the presence of intercalating dye SybrGreen. Bioinformatics analysis was conducted with the help of Vector NTI 9.1, Mega 11 software (MUSCLE algorithm). Phylogenetic analysis was carried out applying UPGMA method using the Mega 11 program.Results and discussion. MLVA approach based on the analysis of the melting point curves of the obtained after amplification of VNTR-loci PCR fragments has shown that each of the 16 strains of Brucella is characterized by a unique melting temperature profile. PCR followed by electrophoresis has demonstrated that despite the high variability of the used VNTR sequences (h=0.48…0.74), only post-amplification melting curves of the Bru7, Bru9, Bru18, Bru21 loci had sufficient information content to determine the genetic polymorphism of the studied Brucella strains. Based on the results of phylogenetic analysis of the Bru7, Bru9, Bru18, Bru21 sequences, it has been found that the majority of the studied Brucella strains are distributed in the dendrogram in accordance with their taxonomic and geographical position. Thus, HRM analysis of melting curves obtained after amplification of the Bru7, Bru9, Bru18, Bru21 loci has the potential to be used for differentiating Brucella strains.
MLVA25 and CRISPR Genotypes of <I>Yersinia pestis</I> Strains from the Caspian Sandy Plague Focus
Authors: Goryunova P. A. , Eroshenko G. A. , Balykova A. N. , Kovrizhnikov A. V. , Shevchenko K. S. , Kukleva L. M. , Naryshkina E. A. , Chervyakova N. S. , Kutyrev V. V. 
Published: January 2024

The aim of the work was to study the genetic diversity and spatial-temporal structure of Yersinia pestis in the Caspian sandy plague focus using MLVA25 and CRISPR typing methods.Materials and methods. 98 Y. pestis strains isolated in the territory of the Caspian sandy plague focus in 1925–2015 were used in the study. Whole genome sequencing was performed on Ion GeneStudio S5 System (ThermoFisher Scientific) and MGI (DNBSEQ-G50RS) platforms. Fragment sequencing was conducted using “ABI PRISM 3500XL”. The search for VNTR and CRISPR loci with subsequent alignment of nucleotide sequences was carried out in the MEGA X program. The obtained sequences were entered into the created database in the Bionumerics v7.6 (Applied Maths) software. The phylogenetic tree was constructed using the UPGMA method.Results and discussion. According to the results of MLVA25 and CRISPR analysis, 98 Y. pestis strains are divided into 60 genotypes (CS1 – CS60). Variability by 23 VNTR loci has been discovered. 7 new CRISPR spacers are described: 5 in YPa and 2 in YPb (size 31–33 bp, GC composition 34–58 %). The described spacers are designated as a108, a109, a110, a111, a112, b53, b54. The interrelation of changes in the copy number of VNTR loci depending on the place and time of isolation of strains has been revealed. The data obtained can be used to carry out molecular-genetic certification of the territory of the Caspian sandy plague focus and to study the routes and patterns of evolution and spatiotemporal circulation of Y. pestis populations in the Caspian plague foci.
Correlation Study of Rupture Risk in Intracranial Unruptured Aneurysms: Integration of Mannose-binding lectin、Hydrodynamics and Morphology
Authors: Dai Junxia , Li Zhiwei , Lin Qun , Cai Jianyong , Chen Xiaoxiang 
Published: January 2024

Abstract
Background
The purpose of this study is to explore the interconnection between Mannose-Binding Lectin (MBL) and fluid dynamics in the context of rupture risk associated with intracranial unruptured aneurysms.
Methods
68 cases of intracranial unruptured aneurysms were selected from patients treated at Wenzhou Central Hospital between June 2020 and December 2022. Based on MBL concentrations, cases were categorized into three groups: <0.80 mg/L for the low concentration group, 0.80–1.10 mg/L for the moderate concentration group, and > 1.10 mg/L for the high concentration group. Geometric and computational fluid dynamics were employed to calculate morphological and hemodynamic parameters. PHASES score was calculated for each case to estimate rupture risk. Univariate and multivariate logistic regression analyses were conducted to investigate the relationship between morphological-hemodynamic patterns and MBL, as well as their association with rupture risk.
Results
Among them, there were 30 cases in the low concentration group (44.1%), 25 cases in the moderate concentration group (36.8%), and 13 cases in the high concentration group (19.1%). Size ratio, wall shear stress, velocity, low wall shear stress, and relative residence time (RRT) were identified as independent risk factors associated with elevated serum MBL concentration in intracranial unruptured aneurysms. With an increase in PHASES score, there is a significant rise in size-related parameters and the frequency of irregular shapes. Additionally, lower and oscillatory wall shear stress is observed, along with a lower intra-aneurysmal flow velocity and prolonged residence time, indicative of altered hemodynamic patterns. Simultaneously, there is a decrease in the proportion of low MBL concentrations, while the proportions of moderate and high MBL concentrations in aneurysms show a significant increase(P < 0.001).
Conclusions
The serum MBL concentration levels in patients with intracranial unruptured aneurysms are closely associated with their aneurysmal morphology and hemodynamics. Intracranial unruptured aneurysms at higher risk of rupture tend to exhibit larger and irregular shapes, characterized by fluid dynamics with low and variable wall shear stress. Additionally, these aneurysms show elevated serum MBL concentrations.
Climate Change Effects on the Sundarban Mangrove Ecosystem and Tiger Population Dynamics in the Indian Region
Authors: Barik Parthasarathi , Gouda KC 
Published: January 2024

Abstract
In this study, we investigate the impact of climate change, encompassing both natural and anthropogenic scenarios, on the Sundarban mangrove ecosystem—the world's largest natural low-lying mangrove habitat—and its implications for the Royal Bengal Tiger habitat. Situated along the Ganges River between India and Bangladesh, the Sundarban spans approximately 9,600 square km. Employing a multi-source approach, we analyze climate parameters from satellite and real observations, alongside data on mangrove and tiger populations from various sources. Our findings reveal a concerning decrease in mangrove coverage in the present decade, attributed to climate change factors such as rising temperatures, coastal storms, sea-level rise, high humidity, and inadequate rainfall, particularly during the monsoon period. Simultaneously, the Royal Bengal Tiger population in the region has dwindled from 250 in 1960 to a current estimation of 70–80, with the decline attributed to poaching, climate change, and habitat loss. The analysis underscores the interconnectedness of climate, mangrove health, and tiger population, indicating a pressing need for conservation efforts. The study provides critical insights for researchers and policymakers, enhancing our understanding of the complex dynamics between climate change and coastal biodiversity, with significant implications for mangrove ecosystems and tiger habitats. Furthermore, it emphasizes the potential migration of tiger populations from Sundarban to alternative regions due to habitat loss, emphasizing the urgency of addressing climate-induced threats to preserve these vital ecosystems.
A stochastic evolutionary game model of green credit participation behavior among banks and enterprises
Authors: Sun Hao , Feng Yuan 
Published: January 2024

Abstract
With the growing severity of environmental problems, green credit has become an important means of promoting low-carbon development, however, the motivation of banks and enterprises to participate in green credit is insufficient. In order to effectively guide banks and enterprises to actively participate in green credit, we constructed a stochastic evolutionary game model for banks and enterprises to participate in green credit, and analyzed the dynamic game relationship between banks and enterprises. Due to the uncertainty of the external environment, we introduce Gaussian white noise in the replicated dynamic equations, and finally, we use numerical simulation to describe the dynamic evolution trend of the two-dimensional game system. The results show that the stochastic disturbances from external uncertainties amplify the fluctuation range of the game between banks and enterprises and shortening the time to achieve a stable strategy. As enterprises’ fulfillment levels improve, the strategic choices of both banks and enterprises gradually converge to (implement, participate), with banks converging more swiftly. When the government provides certain subsidies, both banks and enterprises tend to opt for green credit, however, after subsidies reach a certain threshold, increasing them no longer significantly impacts strategic choices. An escalation in carbon trading prices also spurs enterprises to choose green credit.
Evaluating Treatment and Care Outcomes for Neuromuscular Diseases in a Pediatric Intermediate Care Setting
Authors: Brisca Giacomo , Strati Marina F. , Canzoneri Francesca , Mariani Marcello , Pirlo Daniela , Romanengo Marta , Tardini Giacomo , Brolatti Noemi , Buratti Silvia , Pedemonte Marina , Striano Pasquale , Bruno Claudio , Moscatelli Andrea 
Published: January 2024

Abstract
Background
Neuromuscular disorders (NMDs) represent a complex group requiring specialized care, often straddling the needs between general pediatric wards and Intensive Care Units (ICUs). Our research focuses on the role of a newly established pediatric Intermediate Care Unit (IMCU) in this context.
Methods
We conducted a single-center retrospective observational study, encompassing patients with NMDs admitted to the newly established pediatric IMCU at IRCCS Istituto Giannina Gaslini, Genoa, Italy, from January 2021 to June 2023. The study assessed demographics, clinical characteristics, therapeutic management, length of stay, and outcomes including mortality 28 days post-discharge.
Results
Sixty-three patients (median age 12, female 58.7%) were included. The majority of admissions were due to neurological issues (39.7%) and respiratory complications (22%), with a significant proportion of patients requiring initiation or potentiation of respiratory support (59%). Factors such as the presence of tracheostomy (p = 0.021), the need for antibiotics (p = 0.025), and parenteral nutrition (p = 0.026) were associated with ICU admissions while steroid treatment (p = 0.047) increased IMCU stay.
Conclusions
The establishment of the IMCU has shown promising results in managing NMDs patients, serving as a crucial step-down unit for ICU patients and a step-up unit for those with worsening conditions in low-intensity care units. It has led to decreased ICU admissions and shorter ICU stays, suggesting potential healthcare costs and patient comfort benefits. The study underscores the importance of pediatric IMCUs in providing specialized care for children with NMDs, balancing the need for intensive monitoring and treatment in a less intensive setting than an ICU.
LightGBM-Based Stochastic Modeling for River Dust-Raising Alert
Authors: Ho Chih Chao , Chang Chih Hsiung 
Published: January 2024

Abstract
To enhance the accuracy of Taiwan's existing river dust-raising alert system, which exclusively depends on wind speed predictions, this study combines hydrological, meteorological, air quality information with LightGBM to establish a stochastic model for forecasting PM10 exceedance probabilities. The flexible probability information can effectively reduce the risk of poor decision-making caused by concentration deterministic forecast errors. LightGBM, a boosting-based ensemble learning algorithm, employs a depth-constrained leaf-wise growth strategy, speeding up training, reducing memory consumption, and shortening training time. The results of model training and validation demonstrate good performance in terms of accuracy, recall, and specificity metrics. This signifies that the model effectively predicts the occurrence of actual dust-raising events. In comparison to the current dust-raising alert mechanism, the model can significantly reduce unnecessary dust alerts and lightening the workforce's burden. Moreover, this model effectively forecasts dust events under low to moderate wind speed conditions, providing decision-makers with crucial support data for proactive dust control deployment.
Single-cell RNA-seq reveals TCR clonal expansion and a high frequency of transcriptionally distinct double-negative T cells in NOD mice
Authors: Robben Michael , Islam Md ZOhorul , Zimmerman Sam , Weidanz Jon , Ordovas-Montanes Jose , Kostic Aleksandar , Luber Jacob 
Published: January 2024

Abstract
T cells primarily drive the autoimmune destruction of pancreatic beta cells in Type 1 diabetes (T1D). However, the profound yet uncharacterized diversity of the T cell populations in vivo has hindered obtaining a clear picture of the T cell changes that occur longitudinally during T1D onset. This study aimed to identify T cell clonal expansion and distinct transcriptomic signatures associated with T1D progression in Non-Obese Diabetic (NOD) mice. Here we profiled the transcriptome and T cell receptor (TCR) repertoire of T cells at single-cell resolution from longitudinally collected peripheral blood and pancreatic islets of NOD mice using single-cell RNA sequencing technology. Surprisingly, we detected a considerable high frequency of islet-matching T cell clones in the peripheral circulation and blood-matching T cell clones in the islets. Our analysis showed that transcriptional signatures of the T cells are associated with the matching status, suggesting potential future applications of T cell clonal biomarkers for early prediction of diabetic onset using peripheral T cells. In addition, we discovered a high frequency of transcriptionally distinct double negative (DN) T cells that likely play a major role in creating an immunosuppressive environment in the pancreas that protects from inflammatory damage. This study provides a single-cell level transcriptome and TCR repertoire atlas of T cells in NOD mice and opens the door for more research into the causes of type 1 diabetes and inflammatory autoimmune disease using mouse models.
Arctic Climate Feedback Response to Local Sea-Ice Concentration and Remote Sea Surface Temperature Changes in PAMIP Simulations
Authors: Jenkins Matthew T. , Dai Aiguo , Deser Clara 
Published: January 2024

Abstract

Local and remote processes have been suggested to drive Arctic amplification (AA) – the enhanced warming of the Arctic region relative to other areas under increased greenhouse gases. We use Polar Amplification Model Intercomparison Project (PAMIP) simulations with changes in Arctic sea-ice with fixed global sea surface temperature (SST), or changes in global SST with fixed Arctic sea-ice to untangle the climate response to Arctic sea-ice loss or SST-induced warming, respectively. In response to Arctic sea-ice loss, the surface albedo feedback activates in summer mainly to increase oceanic heat uptake, leading to weak summertime warming. During winter, Arctic sea-ice loss greatly enhances oceanic heat release, which produces Arctic bottom-heavy warming and triggers positive lapse rate and cloud feedbacks, leading to large AA. In contrast, enhanced atmospheric energy convergence into the Arctic becomes the dominant contributor to relatively small AA under global SST-induced warming. Water vapor feedback contributes to Arctic warming but opposes AA due to larger tropical than Arctic moistening under SST-induced warming with fixed Arctic sea-ice. We also find top-heavy to uniform (bottom-heavy) Arctic warming and moistening in the Arctic mid-upper (lower) troposphere in the SST (Arctic sea-ice) perturbation runs, producing a negative-neutral (positive) Arctic lapse rate feedback, respectively. Lastly, we show that the responses to global SST or polar SIC perturbations are linearly separable. Our results suggest that large AA is caused primarily by sea-ice loss and resultant local changes in surface fluxes, while increased poleward energy transport can only produce weak AA under fixed sea ice.
Fabricating Pentaazatetraethylene Modified Sulfonated Polyacrylamide for Dye Adsorption from Aqueous Media: Isotherms and Kinetics Models
Authors: Karimi Seyed Yaghoub , Marofi Safar , Zare Mohamad Ali 
Published: January 2024

Abstract
In this study, pentaazatetraethylene modified sulfonated polyacrylamide (PAm-SO3-N5) was synthesized and used as a novel efficient adsorbent to remove Calmagite from aqueous media. To this end, a central composite design (CCD) was applied to reduce the number of reaction variables (i.e., adsorbent concentration, temperature, initial concentration, and pH) on Calmagite removal. The results showed that calmagite was entirely adsorbed by the PAm-SO3-N5 within 30 min. In addition, a pseudo-second-order (PSO) model was prepared as the optimum formula to fit the kinetics information. The modeling results revealed that film diffusion and adsorption are rate-limiting stages to remove the dyes. Using a Langmuir isotherm to fit the equilibrium data, the highest equilibrium adsorption was calculated to be 1,732.5 mg/g. In the present study, the ΔH value indicates that the adsorption is of chemical type. Also, the negative sign of ΔS° shows that PAm-SO3-N5 removes Calmagite during a relatively stable process with randomness in the system. The increase in ΔG° values with increasing temperature indicates a descending trend in the feasibility degree of Calmagite adsorption. Eventually, recycling the adsorbent for 7 cycles to adsorb calmagite dye showed no remarkable activity loss.
Repeatability of 18F-FDG uptake in metastatic bone lesions of breast cancer patients and implications for accrual to clinical trials
Authors: Muzi Mark , Peterson Lanell M. , Specht Jennifer M. , Hippe Daniel S. , Novakova-Jiresova Alena , Lee Jean H. , Kurland Brenda F. , Mankoff David A. , Obuchowski Nancy , Linden Hannah M. , Kinahan Paul E. 
Published: January 2024

Abstract
BACKGROUND
Standard measures of response such as Response Evaluation Criteria in Solid Tumors are ineffective for bone lesions, often making breast cancer patients with bone-dominant metastases ineligible for clinical trials with potentially helpful therapies. In this study we prospectively evaluated the test-retest uptake variability of 2-deoxy-2-[18F]fluoro-D-glucose (18F-FDG) in a cohort of breast cancer patients with bone-dominant metastases to determine response criteria. The thresholds for 95% specificity of change versus no-change were then applied to a second cohort of breast cancer patients with bone-dominant metastases.
In this study, nine patients with 38 bone lesions were imaged with 18F-FDG in the same calibrated scanner twice within 14 days. Tumor uptake was quantified as the maximum tumor voxel normalized by dose and body weight (SUVmax) and the mean of a 1-cc maximal uptake volume normalized by dose and lean-body-mass (SULpeak). The asymmetric repeatability coefficients with confidence intervals of SUVmax and SULpeak were used to determine limits of 18F-FDG uptake variability. A second cohort of 28 breast cancer patients with bone-dominant metastases that had 146 metastatic bone lesions was imaged with 18F-FDG before and after standard-of-care therapy for response assessment.
RESULTS
The mean relative difference of SUVmax in 38 bone tumors of the first cohort was 4.3%. The upper and lower asymmetric limits of the repeatability coefficient were 19.4% and -16.3%, respectively. The 18F-FDG repeatability coefficient confidence intervals resulted in the following patient stratification for the second patient cohort: 11-progressive disease, 5-stable disease, 7-partial response, and 1-complete response with three inevaluable patients. The asymmetric repeatability coefficients response criteria changed the status of 3 patients compared to standard the standard Positron Emission Tomography Response Criteria in Solid Tumors of ±30% SULpeak.
CONCLUSIONS
In evaluating bone tumor response for breast cancer patients with bone-dominant metastases using 18F-FDG uptake, the repeatability coefficients from test-retest studies show that reductions of more than 17% and increases of more than 20% are unlikely to be due to measurement variability. Serial 18F-FDG imaging in clinical trials investigating bone lesions from these patients, such as the ECOG-ACRIN EA1183 trial, benefit from confidence limits that allow interpretation of response.
Visualization of blood-brain barrier disruption in septic mice with the new method based on in vivo imaging technology
Authors: Zhang Haisong , Ai Yuhang , Zhang Xiaolei , Deng Fuxing , Jiang Shiwei , Xie Shucai , Peng Milin , Chen Wei , Hu Jiyun , Deng Songyun , Zhang Lina 
Published: January 2024

Abstract
Objectives
Dynamic monitoring of the blood-brain barrier (BBB) functional status in septic mice can helps to explore the pathological mechanisms. Therefore, we proposed a new method for monitoring BBB permeability and apply it to the detection of sepsis models.
Methods
The new method involves the construction of an optical cranial window and in vivo imaging. We performed dynamic monitoring of BBB permeability and cerebral blood flow (CBF) in cecal ligation puncture (CLP) and endotoxemia (LPS) mice.
Results
The sensitivity and accuracy of this method were higher than those of Evans blue evaluation. The increase of BBB permeability in CLP group mice was relatively mild and correlated with overall survival (OS), and the damage was irreversible. Contrarily, BBB damage in the LPS group was more acute and severe, unrelated to OS, but recoverable. The CBF decreased significantly in both model mouse groups 24 hours after modeling, but only the CBF proportion decrease in the LPS group was significantly correlated with the increased value of BBB permeability. Within 24 hours after both models were established, the decrease in blood flow in the digestive organs occurred earlier than in the brain and kidneys, and the decrease in small intestine blood flow in the LPS group progressed faster.
Conclusion
We have successfully demonstrated the feasibility of our novel method to detect BBB permeability in mice. Our results revealed a significant difference in the BBB permeability change trend between the CLP and LPS model mice when survival curves were consistent. Notably, the CLP model mice demonstrated a closer resemblance to clinical patients. Our findings suggest that early-stage brain tissue hypoperfusion has a greater impact on BBB function damage in endotoxemia mice, which is related to the faster progression of blood flow redistribution.