bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of extraction-free protocols for SARS-CoV-2 detection using a commercial rRT-PCR assay
Authors: Kang Minhee , Jeong Eunjung , Kim Ji-Yeon , Yun Sun Ae , Jang Mi-Ae , Jang Ja-Hyun , Kim Tae Yeul , Huh Hee Jae , Lee Nam Yong 
Published: November 2023

AbstractIn the ongoing global fight against coronavirus disease 2019 (COVID-19), the sample preparation process for real-time reverse transcription polymerase chain reaction (rRT-PCR) faces challenges due to time-consuming steps, labor-intensive procedures, contamination risks, resource demands, and environmental implications. However, optimized strategies for sample preparation have been poorly investigated, and the combination of RNase inhibitors and Proteinase K has been rarely considered. Hence, we investigated combinations of several extraction-free protocols incorporating heat treatment, sample dilution, and Proteinase K and RNase inhibitors, and validated the effectiveness using 120 SARS-CoV-2 positive and 62 negative clinical samples. Combining sample dilution and heat treatment with Proteinase K and RNase inhibitors addition exhibited the highest sensitivity (84.26%) with a mean increase in cycle threshold (Ct) value of + 3.8. Meanwhile, combined sample dilution and heat treatment exhibited a sensitivity of 79.63%, accounting for a 38% increase compared to heat treatment alone. Our findings highlight that the incorporation of Proteinase K and RNase inhibitors with sample dilution and heat treatment contributed only marginally to the improvement without yielding statistically significant differences. Sample dilution significantly impacts SARS-CoV-2 detection, and sample conditions play a crucial role in the efficiency of extraction-free methods. Our findings may provide insights for streamlining diagnostic testing, enhancing its accessibility, cost-effectiveness, and sustainability.
Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints
Authors: Apenteng Ofosuhene O. , Aarestrup Frank M. , Vigre Håkan 
Published: November 2023

AbstractCurrent surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier. Here, we simulate the results of an AMR surveillance program based on metagenomics in the Danish pig population. We modelled both an increase in the occurrence of ARGs and an introduction of a new ARG in a few farms and the subsequent spread to the entire population. To make the simulation realistic, the total cost of the surveillance was constrained, and the sampling schedule was set at one pool per month with 5, 20, 50, or 100 samples. Our simulations demonstrate that a pool of 20–50 samples and a sequencing depth of 250 million fragments resulted in the shortest time to detection in both scenarios, with a time delay to detection of change of $$>\hspace{0.17em}$$

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15 months in all scenarios. Compared with culture-based surveillance, our simulation indicates that there are neither significant reductions nor increases in time to detect a change using metagenomics. The benefit of metagenomics is that it is possible to monitor all known resistance in one sampling and laboratory procedure in contrast to the current monitoring that is based on the phenotypic characterisation of selected indicator bacterial species. Therefore, overall changes in AMR in a population will be detected earlier using metagenomics due to the fact that the resistance gene does not have to be transferred to and expressed by an indicator bacteria before it is possible to detect.
Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics
Authors: Jaisamut Kitipong , Pitiwararom Rachtipan , Sukawutthiya Poonyapat , Sathirapatya Tikumphorn , Noh Hasnee , Worrapitirungsi Wikanda , Vongpaisarnsin Kornkiat 
Published: November 2023

AbstractThe evolutionary dynamics of mitochondrial DNA within the Thai population were comprehensively explored with a specific focus on the influence of South Asian admixture. A total of 166 samples were collected through randomized sampling, ensuring a diverse representation. Our findings unveil substantial genetic and haplogroup diversity within the Thai population. We have identified 164 haplotypes categorized into 97 haplogroups, with a notable inclusion of 20 novel haplogroups. The distribution of haplogroups exhibited variations across different populations and countries. The central Thai population displayed a high diversity of haplogroups from both the M and N clades. Maternal lineage affinities were discerned between several Mainland Southeast Asia (MSEA) and South Asian populations, implying ancestral genetic connections and a substantial influence of South Asian women in establishing these relationships. f4-statistics indicates the presence of a Tibeto-Burman genetic component within the Mon population from Thailand. New findings demonstrate two phases of population expansion occurring 22,000–26,000 and 2500–3800 years ago, coinciding with the Last Glacial Maximum, and Neolithic demographic transition, respectively. This research significantly enhances our understanding of the maternal genetic history of Thailand and MSEA, emphasizing the influence of South Asian admixture. Moreover, it underscores the critical role of prior information, such as mutation rates, within the Bayesian framework for accurate estimation of coalescence times and inferring demographic history.
Different cultivation systems and foliar application of calcium nanoparticles affect the growth and physiological characteristics of pennyroyal (Mentha pulegium L.)
Authors: Roosta Hamid Reza , Samadi Arman , Bikdeloo Mahdi 
Published: November 2023

AbstractThe aim of this study was to investigate the impact of different cultivation systems (soil cultivation, hydroponic cultivation in greenhouse conditions, and hydroponic vertical cultivation in plant factory under different LED lights) and foliar spraying of nano calcium carbonate on pennyroyal plants. Nano calcium carbonate was applied to the plants at a 7-day interval, three times, one month after planting. Results showed that the greenhouse cultivation system with calcium carbonate foliar spraying produced the highest amount of shoot and root fresh mass in plants. Additionally, foliar spraying of calcium carbonate increased internode length and leaf area in various cultivation systems. Comparing the effects of different light spectrums revealed that red light increased internode length while decreasing leaf length, leaf area, and plant carotenoids. Blue light, on the other hand, increased the leaf area and root length of the plants. The hydroponic greenhouse cultivation system produced plants with the highest levels of chlorophyll, carotenoids, and phenolic compounds. White light-treated plants had less iron and calcium than those exposed to other light spectrums. In conclusion, pennyroyal plants grown in greenhouses or fields had better growth than those grown in plant factories under different light spectrums. Furthermore, the calcium foliar application improved the physiological and biochemical properties of the plants in all the studied systems.
Decentralized collaborative optimal scheduling for EV charging stations based on multi‐agent reinforcement learning
Authors: Li Hang , Han Bei , Li Guojie , Wang Keyou , Xu Jin , Khan Muhammad Waseem 
Published: November 2023

AbstractCharging behaviours of electric vehicles (EVs) exhibit substantial randomness, making accurate prediction or modelling challenging. Furthermore, as the number of EVs continues to increase, charging stations are diversifying their offerings to accommodate distinct charging characteristics, addressing a wide spectrum of EV charging needs. Previous research mostly focused on the randomness of EVs while neglecting the heterogeneity in charging infrastructure. Therefore, this paper introduces a decentralized collaborative optimal method for EV charging stations, taking into account the varying facility types and the power limitations. First, a decentralized collaborative framework is proposed. The energy boundary model and the average laxity of EVs contribute to transforming the optimization problem into a Markov Decision Process (MDP) with uncertain transitions. Then, multi‐agent deep deterministic policy gradient multi‐individuals (MADDPG‐MI) algorithm is developed to train several heterogeneous agents presenting different types of charging facilities. Each agent makes decisions for multiple homogenous charging piles. Numerous simulation studies validate that the proposed method can effectively reduce charging costs and manages in scenarios involving either homogeneous or multiple heterogeneous charging facilities. Moreover, the MADDPG‐MI algorithm demonstrates performance consistency among multiple decision‐making units while consuming lower training resources offering enhanced scalability.
A visual faulty feeder detection method for power distribution network based on spatial image generation and deep learning
Authors: Guo Wei , Shi Yuntao 
Published: November 2023

AbstractIn the case of a single‐phase grounding fault in the distribution network, the transient zero‐sequence current (TZSC) tends to be non‐linear and non‐stationary. The faulty line selection is relatively difficult. The distributed power access further brings many difficulties to faulty line selection. This work proposes a novel method of faulty line selection using spatial image generation and deep learning. At first, the optimal smooth denoising model can be used to smooth the zero‐sequence current for each line, reducing the external environment electromagnetic interference. Then, the treated zero‐sequence current is mapped into the colorful floral hoop image by using symmetrized Hilbert transform pattern (SHTP). The SHTP transforms the one‐dimensional time domain signal into the two‐dimensional space domain image, enhancing invisible information and obtaining more abundant feature information. Finally, the deep features of the SHTP floral hoop image are extracted by means of deep learning method. In order to improve the faulty line selection universality, a mixed sample library containing three different topologies is established, including the 10 kV radial distribution network, IEEE‐13 node model, IEEE‐34 node model and StarSim platform. The comparisons show that the proposed method has a more noticeable visualization effect on fault features, higher classification precision rate, and better anti‐noise performance.
Evolution and prognostic value of left ventricular deformation and myocardial work parameters in transthyretin amyloid cardiomyopathy
Authors: Antonelli Jerome , Neveu Antoine , Kosmala Wojciech , L’Official Guillaume , Curtis Elizabeth , Oger Emmanuel , Donal Erwan 
Published: November 2023

AbstractAimsWild-type transthyretin amyloid cardiomyopathy (ATTR-CM) is an increasingly recognized condition. It remains challenging to estimate the extent of disease and the prognosis for most patients. Myocardial work is a sensitive echocardiographic approach that improves the characterization of myocardial damage. We investigate the parameters of myocardial deformation and work in ATTR-CM patients and their changes over time.Methods and resultsWe analysed clinical, electrocardiographic, biological, and echocardiographic characteristics in 113 patients [median age 82 (77–85), 90.4% male] diagnosed with wild-type ATTR-CM based on international consensus at a single centre. We compared the data at baseline and 18-month follow-up. Thirty-four patients died and 12 were hospitalized for heart failure at a median follow-up of 935 days (interquartile range 691–1159 days). Left ventricular end-diastolic diameter, left atrial strain during reservoir phase (LASRES), left ventricular longitudinal strain, global work index (GWI), global constructive work significantly decreased from baseline to 18 months, while left ventricular wall thickness increased. Left ventricular ejection fraction, right ventricular free wall strain (FWS), global wasted work (GWW), and global work efficiency did not alter significantly. Strain parameters were identified as prognostic on baseline evaluation using a multivariate analysis: GWI, GWW, FWS, and LASRES. They were significantly associated with the risk of death and hospitalization for heart failure.ConclusionMulti-chamber strain assessment may improve the surveillance of patients with ATTR-CM, and myocardial work parameters may improve clinical risk stratification in this population.
The prevalence and significance of the EIF2AK4 variants in the patients with pulmonary arterial hypertension
Authors: Momoi M , Hiraide T , Shinya Y , Sato K , Inami T , Fukuda K , Kataoka M 
Published: November 2023

Abstract

Background
Eukaryotic translation initiation factor 2 alpha kinase 4 (EIF2AK4) has been reported to be the causative gene of pulmonary veno-occlusive disease (PVOD).[1] Although some patients with pulmonary arterial hypertension (PAH) also carry the EIF2AK4 variants, its importance remains unclear.

Purpose
The purpose of this study was to evaluate the prevalence and significance of EIF2AK4 variants in patients with PAH.

Methods
The whole exome sequencing were performed in total 162 patients with idiopathic or heritable PAH. The clinical data including the high-resolution CT scanning, pulmonary function test, laboratory data at diagnosis, and therapeutic response to pulmonary vasodilator were evaluated.

Results
We identified the heterozygous variants of EIF2AK4 in 6 (3.7%) patients. Among them, 2 patients also had bone morphogenetic protein receptor type 2 (BMPR2) variants which were defined as pathogenic by American College of Medical Genetics and Genomics classification. The other 4 patients did not have known PAH associated gene variants. Although the typical findings of PVOD such as interlobular septal thickening and enlarged mediastinal lymph nodes, were not identified by the CT scanning, the median percent diffusing capacity for carbon monoxide of patients with EIF2AK4 heterozygous variants was reduced to 45.6%. In addition, 4 of 6 patients received prostacyclin injection therapy because oral combination therapy was ineffective, and 2 patients died. Moreover, none of the 6 patients reached mean pulmonary arterial pressure≤30 mmHg despite the combination therapy. We also identified homozygous EIF2AK4 variants in 2 patients with PAH. They did not have the known causative variants of PAH. CT scanning at diagnosis did not detect any characteristic of PVOD in either of the two patients. Although the pulmonary vasodilator was initiated without induction of pulmonary edema, one patient was refractory to the therapy.

Conclusions
The genetic analysis is crucial for accurate diagnosis even in patients diagnosed with PAH because heterozygous or homozygous variants in EIF2AK4 could be involved in the disease pathology.
Retrospective analysis of confirmed cases of pulmonary veno-occlusive disease: a single tertiary referral center study
Authors: Gonzalez Bonilla H M , Frantz R P , Cajigas H R , Borlaug B A , Bratt A , Krowka M J , Dubrock H M , Reddy Y N V , Kane G C , Anand V 
Published: November 2023

Abstract

Background
Pulmonary veno-occlusive disease (PVOD) is a rare cause of pulmonary hypertension that primarily results in intimal fibrosis of the pulmonary venules and veins, the venous lesions are often associated with changes in interlobular septa, lung parenchyma, and pulmonary arterioles and arteries.

Purpose
We sought to study the clinical characteristics of patients with confirmed PVOD at a single large referral center.

Methods
We retrospectively reviewed data from a total of 675 patients with pulmonary hypertension (identified by ICD codes or search of text) from 2017 and 2022 from a database obtained from electronic medical records at our institution. Patients with group 2 pulmonary hypertension were excluded. Only 29 cases were confirmed by histology or genetic testing.

Results
Out of the 29 patients confirmed with PVOD, 28 (96.5%) had a characteristic histology (lung biopsy (55.1%), explanted lung for transplant (27.5%) and autopsy (13.7%)) and 1 (3.4%) had a positive genetic test for EIF2AK4 biallelic mutation. The age at diagnosis was 53±16 years, 14 (48.2%) were men, 2 (6.8%) had systemic scleroderma, 2 (6.8%) had psoriasis, 2 (6.8%) were exposed to cytotoxic agents, 16 (55.1%) were smokers and 2 (6.8%) had a family history of pulmonary hypertension. All patients had computed tomography of the chest but only 12 (41.3%) had all 3 typical features found in PVOD (ground glass opacities, interlobular septal thickening, and lymphadenopathy). The most common feature was interlobular septal thickening in 26 (89.6%), followed by ground glass opacities present in 25 (86.2%) and lymphadenopathy in 12 (41.3%) of the patients. At diagnosis, mean pulmonary artery pressure was 45±15 mmHg and pulmonary vascular resistance was 9±6 WU. The median DLCO was 41 (34-58) %. On echocardiogram, 14 (48.2%) had severely enlarged right ventricle (RV), RV function was ≥moderately reduced in 17 (58.6%), RV systolic pressure was 63±20 mmHg and 6 (20.6%) had pericardial effusion. Out of 21 (72.4%) patients who received pulmonary vasodilators, 4 (13.7%) received single agent. 10 (34.4%) received 2 agents, 6 (20.6%) 3 agents, and 1 (3.4%) received 4 agents. 35.7% of these treated patients reported an improvement or initial worsening of symptoms with subsequent improvement afterwards. 18 (62%) patients with PVOD died, 12 (41.3%) had a lung transplant and 6 (20.6%) were still alive without the transplant until the day data was collected. Mean duration from diagnosis to death and lung transplantation was 446 ± 405 days and 274±479 days respectively.

Conclusion
PVOD is a rare and lethal cause of pulmonary hypertension. When suspected, a trial of medical therapy should be initiated carefully. The evaluation for lung transplant should be considered early given its high mortality.
Of mice and men: transcriptome-based clustering reveals molecular heterogeneity among mouse atherosclerosis models and partially reflects the diversity of human plaques
Authors: Brouwer E , Michal M , Pasterkamp G 
Published: November 2023

Abstract

Background
Mice are frequently used as model organisms to study atherosclerosis, but many treatments effective in mice do not successfully translate to humans. In a recent study, we clustered 654 human plaques based on transcriptomic data and described the categorisation into five distinct plaque types. We now hypothesise that the reasons for the failures of translating results from mouse models can be partially explained by the fact that mouse models do not reflect all the phenotypic variability we observe in human plaques.

Methods
We used transcriptomic data from the aortic samples (from arch to mid abdomen) of 102 different strains of inbred mice (n = 366). Those mice are F1 progenies from the Hybrid Mouse Diversity Panel (HMDP) crossed with C57BL/6J carrying dominant ApoE-Leiden and CETP transgenes. The gene expression data were normalised and batch effect was removed and clustered by a shared nearest neighbour modularity optimization-based clustering algorithm. Differential gene expression between the clusters was performed to reveal the difference in the biology of the clusters. The clusters were linked to physiological measurements and correlated to human transcriptomic-based plaque clusters.

Results
Transcriptional profiles of atherosclerotic lesions in mice could be categorised into four distinct clusters with specific gene expression fingerprints. The different clusters have a different activity for some pathways, including smooth muscle cell related pathways and metabolic pathways. Comparison with human clusters revealed that most mice strains (n = 287, 78%) correlated best with human plaque type #3 which is enriched in both inflammatory and fibrosis-related genes. This cluster represents about 20% of all human lesions but was found to be associated with severe cardiovascular events. A few mouse strains showed the highest correlations with two other human plaque types (e.g. BUB/Bnj for plaque type #1 and LG/J for plaque type #4), while the human plaque types #0 and #2 were much less reflected in analysed mouse models. Interestingly inflammatory pathways, important drivers in differentiating human clusters, only showed minor differences through all mice clusters.

Conclusions
Transcriptomic profiling of atherosclerotic lesions reveals that mice associate only partly with the human plaque phenotypes. The best associations were observed with those human plaques that correlate with a more severe clinical phenotype. The existence of different types of lesions observed in humans should be taken into account when choosing a mouse model to study atherosclerosis.
Dynamics of indicators of central hemodynamics and arterial wall rigidity during the background of combination therapy with amlodipine/ valsartan in patients with arterial hypertension
Authors: Yuldasheva A , Abdullaeva G J , Khamidullaeva G A , Masharipov S H M , Ibragimova I A 
Published: November 2023

Abstract

Aim
Assess the impact of antihypertensive therapy of the double fixed combination of amlodipine/valsartan on the parameters of central hemodynamics and elastic properties of arteries in patients with arterial hypertension.

Materials and methods
During the 3-month follow-up period, 30 patients with arterial hypertension were examined at our cardiology center. Women - 53.3%, men - 46.7%. The average age of the respondents was 54.7±11.3 years. The average duration of AH was 9.5±7.1 years. Patients with previously uncontrolled hypertension were prescribed combination therapy with the inclusion of amlodipine/valsartan, if necessary, the dose was titrated every 2 weeks. All patients initially and 3 months later underwent applanation tonometry using the SphygmoCor device. Central systolic blood pressure (cSBP), central diastolic blood pressure (cDBP), central pulse pressure (cPP), aortic augmentation (AA), augmentation index (AIx), pulse wave velocity (PWV) were measured, resulting in a conclusion about the state of arterial stiffness . Results are presented as M±SD.

Results
An analysis of the dynamics of central hemodynamic parameters and vascular stiffness during 3-month combination therapy with amlodipine/valsartan showed a significant decrease in such indicators as cSBP, cDAP, CPD, AA, as well as pulse wave velocity. Thus, the cSBP index initially amounted to 155.2±22.6 mm Hg. and in dynamics - 131.6±18.3 mm Hg. (p&lt;0.001); the cDAP index was 84.2±12.7 mm Hg. vs. 78.4±8.2 mm Hg respectively (p&lt;0.02); the CPP index was 71.0±19.8 mm Hg. vs. 53.2±18.1 mm Hg. respectively (p&lt;0.001); the AA index was 18.3±16.5 mm Hg. vs. 11.9±6.3 mm Hg. respectively (p&lt;0.02); PWV was 9.9±2.7 m/s versus 8.2±2.7 m/s, respectively (p&lt;0.001).

Conclusions
According to the results of 3-month combination therapy, indicators of central hemodynamics and the state of elastic properties of arteries are significantly improved, which is potentially associated with a decrease in the risk of developing cardiovascular complications in patients with hypertension.