bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome
Authors: Lubna  , Asaf Sajjad , Khan Ibrahim , Jan Rahmatullah , Asif Saleem , Bilal Saqib , Kim Kyung-Min , AL-Harrasi Ahmed 
Published: June 2024

AbstractIn this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa’s plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.
Man versus machine: cost and carbon emission savings of 4G-connected Artificial Intelligence technology for classifying species in camera trap images
Authors: Smith James , Wycherley Ashleigh , Mulvaney Josh , Lennane Nathan , Reynolds Emily , Monks Cheryl-Ann , Evans Tom , Mooney Trish , Fancourt Bronwyn 
Published: June 2024

AbstractTimely and accurate detection and identification of species are crucial for monitoring wildlife for conservation and management. Technological advances, including connectivity of camera traps to mobile phone networks and artificial intelligence (AI) algorithms for automated species identification, can potentially improve the timeliness and accuracy of species detection and identification. Adoption of this new technology, however, is often seen as cost-prohibitive as it has been difficult to calculate the cost savings or qualitative benefits over the life of the program. We developed a decision tool to quantify potential cost savings associated with incorporating the use of mobile phone network connectivity and AI technologies into monitoring programs. Using a feral cat eradication program as a case study, we used our decision tool to quantify technology-related savings in costs and carbon emissions, and compared the accuracy of AI species identification to that of experienced human observers. Over the life of the program, AI technology yielded cost savings of $0.27 M and when coupled with mobile phone network connectivity, AI saved $2.15 M and 115,838 kg in carbon emissions, with AI algorithms outperforming human observers in both speed and accuracy. Our case study demonstrates how advanced technologies can improve accuracy and cost-effectiveness and improve monitoring program efficiencies.
Associations of tissue factor and tissue factor pathway inhibitor with organ dysfunctions in septic shock
Authors: Lehner Georg Franz , Tobiasch Anna Katharina , Perschinka Fabian , Mayerhöfer Timo , Waditzer Markus , Haller Viktoria , Zassler Birgit , Maier Sarah , Ulmer Hanno , Joannidis Michael 
Published: June 2024

AbstractCoagulopathy, microvascular alterations and concomitant organ dysfunctions are hallmarks of sepsis. Attempts to attenuate coagulation activation with an inhibitor of tissue factor (TF), i.e. tissue factor pathway inhibitor (TFPI), revealed no survival benefit in a heterogenous group of sepsis patients, but a potential survival benefit in patients with an international normalized ratio (INR) < 1.2. Since an increased TF/TFPI ratio determines the procoagulant activity specifically on microvascular endothelial cells in vitro, we investigated whether TF/TFPI ratio in blood is associated with INR alterations, organ dysfunctions, disseminated intravascular coagulation (DIC) and outcome in septic shock. Twenty-nine healthy controls (HC) and 89 patients with septic shock admitted to a tertiary ICU were analyzed. TF and TFPI in blood was analyzed and related to organ dysfunctions, DIC and mortality. Patients with septic shock had 1.6-fold higher levels of TF and 2.9-fold higher levels of TFPI than HC. TF/TFPI ratio was lower in septic shock compared to HC (0.003 (0.002–0.005) vs. 0.006 (0.005–0.008), p < 0.001). Non-survivors had higher TFPI levels compared to survivors (43038 (29354–54023) vs. 28041 (21675–46582) pg/ml, p = 0.011). High TFPI levels were associated with acute kidney injury, liver dysfunction, DIC and disease severity. There was a positive association between TF/TFPI ratio and troponin T (b = 0.531 (0.309–0.754), p < 0.001). A high TF/TFPI ratio is exclusively associated with myocardial injury but not with other organ dysfunctions. Systemic TFPI levels seem to reflect disease severity. These findings point towards a pathophysiologic role of TF/TFPI in sepsis-induced myocardial injury.
A genomic instability-associated lncRNA signature for predicting prognosis and biomarkers in lung adenocarcinoma
Authors: Lin Chunxuan , Lin Kunpeng , Li Pan , Yuan Hai , Lin Xiaochun , Dai Yong , Zhang Yingying , Xie Zhijun , Liu Taisheng , Wei Chenggong 
Published: June 2024

AbstractGenomic instability (GI) was associated with tumorigenesis. However, GI-related lncRNA signature (GILncSig) in lung adenocarcinoma (LUAD) is still unknown. In this study, the lncRNA expression data, somatic mutation information and clinical survival information of LUAD were downloaded from The Cancer Genome Atlas (TCGA) and performed differential analysis. Functional and prognosis analysis revealed that multiple GI-related pathways were enriched. By using univariate and multivariate Cox regression analysis, 5 GI-associated lncRNAs (AC012085.2, FAM83A-AS1, MIR223HG, MIR193BHG, LINC01116) were identified and used to construct a GILncSig model. Mutation burden analysis indicated that the high-risk GI group had much higher somatic mutation count and the risk score constructed by the 5 GI-associated lncRNAs was an independent predictor for overall survival (OS) (P < 0.05). Overall, our study provides valuable insights into the involvement of GI-associated lncRNAs in LUAD and highlights their potential as therapeutic targets.
Evaluation of dose delivery based on deformed CT using a commercial software for lung cancer
Authors: Chen Jihong , Chen Kaiqiang , OuYang Min , Wang Guohua , Bai Penggang , You Hongqiang 
Published: June 2024

AbstractThis study employed a commercial software velocity to perform deformable registration and dose calculation on deformed CT images, aiming to assess the accuracy of dose delivery during the radiotherapy for lung cancers. A total of 20 patients with lung cancer were enrolled in this study. Adaptive CT (ACT) was generated by deformed the planning CT (pCT) to the CBCT of initial radiotherapy fraction, followed by contour propagation and dose recalculation. There was not significant difference between volumes of GTV and CTV calculated from the ACT and pCT. However, significant differences in dice similarity coefficient (DSC) and coverage ratio (CR) between GTV and CTV were observed, with lower values for GTV volumes below 15 cc. The mean differences in dose corresponding to 95% of the GTV, GTV-P, CTV, and CTV-P between ACT and pCT were − 0.32%, 4.52%, 2.17%, and 4.71%, respectively. For the dose corresponding to 99%, the discrepancies were − 0.18%, 8.35%, 1.92%, and 24.96%, respectively. These differences in dose primarily appeared at the edges of the target areas. Notably, a significant enhancement of dose corresponding to 1 cc for spinal cord was observed in ACT, compared with pCT. There was no statistical difference in the mean dose of lungs and heart. In general, for lung cancer patients, anatomical motion may result in both CTV and GTV moving outside the original irradiation region. The dose difference within the original target area was small, but the difference in the planning target area was considerable.
Potential diagnostic biomarkers for immunogenic cell death in elderly female patients with ischemic stroke: identification and analysis
Authors: Qin Lihua , Li Sheng , Cao Xi , Huang Tengjia , Liu Yixin , Chen Ouying 
Published: June 2024

AbstractIschemic stroke (IS) is of increasing concern given the aging population and prevalence of unhealthy lifestyles, with older females exhibiting higher susceptibility. This study aimed to identify practical diagnostic markers, develop a diagnostic model for immunogenic cell death (ICD)-associated IS, and investigate alterations in the immune environment caused by hub genes. Differentially expressed genes associated with ICD in IS were identified based on weighted gene co-expression network analysis and the identification of significant modules. Subsequently, machine learning algorithms were employed to screened hub genes, which were further assessed using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis. A nomogram mode lwas then constructed for IS diagnosis, and its diagnostic value was assessed using a receiver operating characteristic curve. Finally, alterations in immune cell infiltration were assessed within patients with IS, and the pan-cancer expression patterns of hub genes were evaluated. Three hub genes associated with ICD (PDK4, CCL20, and FBL) were identified. The corresponding nomogram model for IS diagnosis could effectively identify older female patients with IS (area under the curve (AUC) = 0.9555). Overall, the three hub genes exhibit good diagnostic value (AUC > 0.8). CCL20 and FBL are significantly associated with the extent of immune cells infiltration. Moreover, a strong link exists between hub gene expression and pan-cancer prognosis. Cumulatively, these results indicate that ICD-related hub genes critically influence IS progression in older females, presenting novel diagnostic and therapeutic targets for personalized treatment.
Bile acids and the gut microbiome are involved in the hyperthermia mediated by 3,4-methylenedioxymethamphetamine (MDMA)
Authors: Rana Srishti , Canfield Jeremy R. , Ward Christopher S. , Sprague Jon E. 
Published: June 2024

AbstractHyperthermia induced by phenethylamines, such as 3,4–methylenedioxymethamphetamine (MDMA), can lead to life-threatening complications and death. Activation of the sympathetic nervous system and subsequent release of norepinephrine and activation of uncoupling proteins have been demonstrated to be the key mediators of phenethylamine-induced hyperthermia (PIH). Recently, the gut microbiome was shown to also play a contributing role in PIH. Here, the hypothesis that bile acids (BAs) produced by the gut microbiome are essential to PIH was tested. Changes in the serum concentrations of unconjugated primary BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) and secondary BA deoxycholic acid (DCA) were measured following MDMA (20 mg/kg, sc) treatment in antibiotic treated and control rats. MDMA-induced a significant hyperthermic response and reduced the serum concentrations of three BAs 60 min post-treatment. Pretreatment with antibiotics (vancomycin, bacitracin and neomycin) in the drinking water for five days resulted in the depletion of BAs and a hypothermic response to MDMA. Gut bacterial communities in the antibiotic-treated group were distinct from the MDMA or saline treatment groups, with decreased microbiome diversity and alteration in taxa. Metagenomic functions inferred using the bioinformatic tool PICRUSt2 on 16S rRNA gene sequences indicated that bacterial genes associated to BA metabolism are less abundant in the antibiotic-MDMA treated group. Overall, these findings suggest that gut bacterial produced BAs might play an important role in MDMA-induced hyperthermia.
Non-destructive evaluation method for track slabs damaged by impact of ice blocks detached from high-speed trains
Authors: Song Xiaolin , Fu Xuanran , Xiao Dingjun , Yi Cai 
Published: June 2024

AbstractIn winter snowy or rainy weather, the phenomenon of icing under rolling stock during high-speed operation is significantly severe, posing a potential risk of detachment and impact on track structures due to the presence of ice blocks with substantial mass and velocity. Therefore, it is crucial to develop an efficient method for characterizing and evaluating this impact damage in order to assess the service life of the track. To address this issue, the indoor ice impact tests were conducted on track slab models, and a comprehensive analysis was performed on non-destructive testing data before and after the impact test, including 3D surface morphology assessment, surface hardness and wave velocity measurements. Additionally, in order to verify the effectiveness of the nondestructive testing method, the frozen-thawed and not frozen-thawed track slab models were tested and their results were compared. The experimental results revealed that when impacted by ice blocks at a velocity of 100 m/s, small dimples formed on the surface of track slab models with the maximum depth measured at 0.0694 mm. There was a maximum increase rate in surface hardness amounting to 11.61%, and a maximum decrease rate in wave velocity measuring at 6.52%. Furthermore, the impact damage of the two models has been evaluated, the not frozen-thawed track slab model exhibited minor damage after impact, whereas the frozen-thawed track slab model demonstrated moderate damage in the contact region and minor damage outside of that region. The proposed non-destructive testing method effectively enables assessing the impact damage inflicted upon slab models while providing valuable insights for maintenance and repair strategies related to track slabs.
Fluorescence-based reagent and spectrum-based optical reader for lactoferrin detection in tears: differentiating Sjögren’s syndrome from non-Sjögren’s dry eye syndrome
Authors: Tsai Chia-Ying , Hong Chitsung , Hsu Min-Yen , Lai Tso-Ting , Huang Ching-Wen , Lu Cheng-Yo , Chen Wei-Li , Cheng Chao-Min 
Published: June 2024

AbstractIdentification of an early biomarker and effective testing device to differentiate dry eye disease secondary to autoimmune disease (Sjögren’s syndrome dry eye disease) from non-Sjögren’s dry eye disease are prerequisites for appropriate treatment. We aimed to demonstrate the capacity of a new photo-detection device to evaluate tear lactoferrin levels as a tool for differentiating systemic conditions associated with dry eye disease. Patients with non-Sjögren’s and Sjögren’s syndrome dry eye disease (n = 54 and n = 52, respectively) and controls (n = 11) were enrolled. All participants completed the Ocular Surface Disease Index questionnaire. Tear collection was performed with Schirmer test, and tear break-up time was examined using a slit lamp. Tear lactoferrin was evaluated using our newly developed photo-detection device. The average lactoferrin concentration was significantly lower in samples from patients with non-Sjögren’s dry eye disease (0.337 ± 0.227 mg/mL, n = 54) and Sjögren’s syndrome dry eye disease (0.087 ± 0.010 mg/mL, n = 52) than in control samples (1.272 ± 0.54 mg/mL, n = 11) (p < 0.0001). Further, lactoferrin levels were lower in patients with Sjögren’s syndrome dry eye disease than in those with non-Sjögren’s dry eye disease (p < 0.001). Our cost-effective, antibody-free, highly sensitive photo-detection device for evaluating tear lactoferrin levels can assist ophthalmologists in differentiating different types of dry eye diseases.
Bionanocomposite MIL-100(Fe)/Cellulose as a high-performance adsorbent for the adsorption of methylene blue
Authors: Abbasi Shahla , Nezafat Zahra , Javanshir Shahrzad , Aghabarari Behzad 
Published: June 2024

AbstractWorld production of dyes is estimated at more than 800,000 t·yr−1. The purpose of this research falls within the scope of the choice of an effective, local, and inexpensive adsorbent to remove dyes from wastewater. Adsorptive elimination of dyes by commonly accessible adsorbents is inefficient. The metal–organic frameworks (MOFs) are an important class of porous materials offering exceptional properties as adsorbents by improving separation efficiency compared to existing commercial adsorbents. However, its powder form limits its applications. One way to overcome this problem is to trap them in a flexible matrix to form a hierarchical porous composite. Therefore, in this work, we prepared MIL-100 (Fe) embedded in a cellulose matrix named MIL-100(Fe)/Cell, and used it as an adsorbent of methylene blue (MB) dye. According to the BET analysis, the specific surface area of the synthesized MOF is 294 m2/g which is related to the presence of the cellulose as efficient and green support. The structure of this composite is approximately hexagonal. Adsorption was studied as a function of contact time, adsorbent mass and pollutant load (concentration), and pH, and the effect of each of them on absorption efficiency was optimized. The MIL-100(Fe)/Cell was capable of removing 98.94% of MB dye with an initial concentration of 150 mg/L within 10 min at pH = 6.5 and room temperature. The obtained maximum adsorption capacity was 384.615 mg/g. The adsorption isotherm is consistent with the Langmuir models. The mechanism of MB adsorption proceeds through п-п and electrostatic interactions.
Extended supercooled storage of red blood cells
Authors: Isiksacan Ziya , William Nishaka , Senturk Rahime , Boudreau Luke , Wooning Celine , Castellanos Emily , Isiksacan Salih , Yarmush Martin L. , Acker Jason P. , Usta O. Berk 
Published: June 2024

AbstractRed blood cell (RBC) transfusions facilitate many life-saving acute and chronic interventions. Transfusions are enabled through the gold-standard hypothermic storage of RBCs. Today, the demand for RBC units is unfulfilled, partially due to the limited storage time, 6 weeks, in hypothermic storage. This time limit stems from high metabolism-driven storage lesions at +1-6 °C. A recent and promising alternative to hypothermic storage is the supercooled storage of RBCs at subzero temperatures, pioneered by our group. Here, we report on long-term supercooled storage of human RBCs at physiological hematocrit levels for up to 23 weeks. Specifically, we assess hypothermic RBC additive solutions for their ability to sustain supercooled storage. We find that a commercially formulated next-generation solution (Erythro-Sol 5) enables the best storage performance and can form the basis for further improvements to supercooled storage. Our analyses indicate that oxidative stress is a prominent time- and temperature-dependent injury during supercooled storage. Thus, we report on improved supercooled storage of RBCs at −5 °C by supplementing Erythro-Sol 5 with the exogenous antioxidants, resveratrol, serotonin, melatonin, and Trolox. Overall, this study shows the long-term preservation potential of supercooled storage of RBCs and establishes a foundation for further improvement toward clinical translation.
Onset of Mid-Pleistocene glaciation in the Eastern Himalayan syntaxis
Authors: Wang Ping , Hu Gang , Wang Huiying , Ge Yukui , Ma Yan , Yu Ziying , Wang Xin , Fox Matthew 
Published: June 2024

AbstractThe Tibetan Plateau contains the largest numbers of glaciers outside the polar regions, yet the initiation times of glacial advances remain unclear. The potential relics of original moraines might be preserved in the sedimentary basins. Here, we present sedimentological and geochronological data from five boreholes located upstream of the Tsangpo Gorge, Eastern Himalayan Syntaxis. Our findings reveal that fluvial sediment accumulation began over 2.5 million of years ago due to enhanced rock uplift downstream, and extensive glacial advances occurred after ~0.75 million of years. Notably, the earliest extensive glacial advance (~0.75 million of years) is considerably younger than the formation of the Tsangpo Gorge (>2.5 million of years). Following the initiation of this glacial advance, the Eastern Himalayan Syntaxis experienced rapid exhumation of approximately 1.3–1.6 kilometers. Such geomorphological processes and exhumation history suggest that rock uplift, rather than glacial damming, played a pivotal role in maintaining the stability of the knickpoints on the southeastern margins of the Tibetan Plateau.
AXES-SDSS: Comparison of SDSS galaxy groups with all-sky X-ray extended sources
Authors: Damsted S. , Finoguenov A. , Lietzen H. , Mamon G. A. , Comparat J. , Tempel E. , Dmitrieva I. , Clerc N. , Collins C. , Gozaliasl G. , Eckert D. 
Published: June 2024

Context. Advances in cosmological studies require us to improve our understanding of the baryonic content of galaxy groups. The key baryonic components of groups are galaxies and hot gas, while key non-baryonic mass tracers are the velocity dispersion of galaxies and the distribution of galaxies within the group.
Aims. We revisit the picture of X-ray emission of groups through the study of systematic differences in the optical properties of groups, with and without X-ray emission, and we study the effect of the large-scale density field on scaling relations.
Methods. We present the identification of X-ray galaxy groups using a combination of ROSAT All Sky Survey (RASS) and Sloan Digital Sky Survey (SDSS) data. We include a new X-ray reanalysis of RASS, covering very extended (up to a size of half a degree) sources, and we account for differences in the limiting sensitivity with respect to compact and very extended X-ray emission. We applied a screening of the identified X-ray sources, based on the optical properties, to achieve 95% clean catalogues. We used a mock SDSS survey to understand the performance of our FoF group finder and applied the CLEAN algorithm to revise group mass estimates and achieve a clean membership catalogue.
Results. X-ray groups exhibit less scatter in the scaling relations and selecting the groups based on the extended X-ray emission leads to an additional scatter reduction. Most of the scatter for the optical groups is associated with a small (6%) fraction of outliers, primarily associated with low optical-luminosity groups found in dense regions of the cosmic web. These groups are primary candidates for the contaminants in the optical group catalogues. We find that removing only those groups from the optical group sample using optically measured properties leads to a substantial reduction in the scatter of the scaling relations of the optical groups. We report a dependence of both the X-ray and optical luminosity of groups on large-scale density, which we associate with the assembly bias. These results motivate an introduction of an additional characterization of galaxy clusters and shed light on the physical origin of anomalous clustering of galaxy clusters, found by the Dark Energy Survey (DES).