bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea
Authors: Lücker Sebastian , Sakoula Dimitra , Schatteman Arne , Blom Pieter , Jetten Mike , Kessel Maartje van , Lehtovirta-Morley Laura 
Published: September 2023

Abstract
Recently, an activity-based labelling protocol for the in situ detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of a universal activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this universal activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.
Phytoremediation potential of plants growing spontaneously on abandoned coal mine wastes
Authors: Sanami Nateq Lashkari , Ghorbani Jamshid , Vahabzadeh Ghorban , Hodjati Seyed Mohammad , Motesharezadeh Babak 
Published: September 2023

Abstract

Coal mining activities cause drastic perturbation of vegetation, soil and diffuse heavy metal to environment. Hence, identification of heavy metals tolerant species is essential for ecological restoration of mine impacted lands. This study aimed to assess the concentration of heavy metals in soils and the phytoremediation potential of 13 dominant plants naturally growing on abandoned coal waste dumps in northern Iran. Plant roots and shoots and the corresponding soils were sampled and then prepared, dried and milled in the laboratory. The results showed that metals concentration varied among plants and for each species between root and shoot. Majority of plants accumulated greater metals in aboveground biomass than belowground biomass, which indicates their effective metal translocating capacity. Artemisia scoparia and Capparis spinosa were contained the highest concentrations of Cu in shoot with 41.06 and 42.48 mg/kg, and TF>1 indicating the capacity for phytoextraction. The accumulation of Arsenic in the shoots and roots of Sylibum marianum was higher than normal. Cynodon dactylon and Hordeum vulgare were the only plants that accumulated >100 mg/kg Zn in the roots and can be recommended for phytostabilization. S. marianum and Chenopodium album potentially can be considered as Cd-accumulator. Kochia prostrate with BCF and TF < 1 for most detected metals is the only excluder species. The only indicator species for Vanadium was S. marianum with a transfer factor of 2.01. S. marianum and Glaucium fimbriligerum showed a tolerance mechanism to Strontium. The findings confirmed the potential of these plants in translocating of metal(loid)s from roots to the aerial parts.
Serum LH Levels on hCG Trigger Day Affect IVF Outcomes Intensified by Poor Ovarian Reserve and Advanced Age
Authors: Chen Xia , Wei Siyi , Yue Lin , Xu Zhihui , Wu Dandan , Xu Jian 
Published: September 2023

Abstract
Objective
To assess the impact of luteinizing hormone (LH) level of hCG trigger day on in-vitro fertilization (IVF) outcomes after fresh embryo transfers, and whether the effects are associated with women’ ovarian reserve and age.
Methods
Totally 1,423 women who underwent GnRH antagonist protocol for controlled ovarian stimulation at their first IVF cycle were included and stratified by LH level on hCG trigger day, 0.86 IU/L(10th ), 1.3 IU/L (25th ), 1.94 IU/L (50th ), 3.07 IU/L (75th ), 4.75 IU/L (90th ).
Results
LH level among 1.3-<1.94 IU/L presented the highest live birth rate (LBR, 52.3%) and lowest early pregnancy loss rate (ePLR, 10.5%), while LH < 0.86 IU/L had the lowest LBR (40.4%) and highest ePLR (15.6%). We further stratified the population into three groups, low LH (< 1.3 IU/L), normal LH (1.3-<4.75 IU/L) and high LH (≥ 4.75 IU/L). Multivariate regression analysis indicated that low LH was associated with lower chances of LBR (Adjusted odds ratio (AOR) 0.66, 95% CI 0.51 to 0.85), combined with increased risks of ePLR (AOR 1.51, 1.06 to 2.15). Additionally, the absolute risk difference for LBR was up to -16.3% between low LH and normal LH group among the poor ovarian reserve (AMH < 1.2 ng/ml), much greater than that among normal ovarian reserve (-10.0%). The same trend was showed in women ≥ 35 years age.
Conclusions
Either declined or elevated LH levels on hCG day were associated with adverse IVF outcomes. Compared with normal LH, low LH decreased the LBR and increased the ePLR, and the effects were exacerbated by poor ovarian reserve and advanced age.
Development and validation of a prognostic model for 4 years risk of Peripheral arterial disease restenosis following endovascular therapy
Authors: Meng Yizhe , Liu Jianping 
Published: September 2023

Abstract
Objectives: This study sought to investigate factors associated with restenosis after endovascular therapy (EVT) and established a novel nomogram integrating the Trans-Atlantic Inter-Society Consensus (TASC) II classification and clinicopathological characteristics to establish easy-to-use and efficient prognostic tool to predict the probability of risk of restenosis following EVT in subjects with PAD.
Background: EVT’s common use, risk factors of restenosis have not been systematically studied. Arterial restenosis after EVT is a difficult problem to solve, requiring further attempts at revascularization with associated poorer clinical outcomes and increased cost.
Methods: Between January 2018 and December 2021, we studied 240 limbs from 486 original patients who were diagnosed Peripheral arterial disease (PAD). Predictors for restenosis in patients with PAD were assessed using a Cox proportional hazards model. A nomogram was constructed by using variables defined in the all data, which was validated in predictive discriminative, accuracy and clinical application.
Results: In the study, optimal independent factors included older age (hazard ratio [HR], 0.97; 95% CI: 0.94–1.00); poor BTK runoff (hazard ratio [HR], 2.41; 95% CI: 1.36–4.29); and TASC Ⅱ Class D in the femoropopliteal artery vs others classes (hazard ratio [HR], 2.59; 95% CI: 1.32–5.08), which were included in the nomogram predicting the vascular restenosis risk (all P < 0.05). The C-index values for restenosis risk in PAD with EVT were 0.732. Calibration curves indicated good consistency between predicted and actual outcomes. DCA confirmed the clinical utility of the diagnostic model.
Conclusions: In conclusion, the current study constructed an easy-going nomogram that plays a convincing role in the evaluation of the risk of progression of the restenosis risk in PAD patients following EVT. Meanwhile, FIB and Cr also are interesting idea to study the predictors in restenosis. Anyway, further study with larger sample sizes and multiple centers are essential to verify our conclusions.
Numerical simulation on performance improvement for blood cell separation under sheath-assisted dielectrophoresis
Authors: Hu Sheng , Wang Yang-cheng , Tong Rui-jie 
Published: September 2023

Abstract
Dielectrophoresis (DEP), known as an attractive and frugal technique, can be used to manipulate biological or non-biological particles in microfluidics. This paper presents a three-dimensional sheath-assisted microfluidic chip for focusing cells and separating red blood cells (RBCs) from white blood cells (WBCs) in continuous flow. Based on the control variables, a simulation model using COMSOL Multiphysics 6.0 is calculated to obtain the favorable flow rate ratio under an electric potential as low as 14 Vpp, at the frequency of 175 kHz. Both RBCs and WBCs respond to negative dielectrophoresis forces and the performance of the separation process are analyzed by evaluating the purity and separation efficiency. The results reveal that the optimal flow rate ratio of the device is suitable to effectively separate RBCS from WBCs with high purity and cell separation efficiency factors up to 88% and 97%, at the throughput of 8 µL/h. The current research provides valuable insights into the design of microchip devices for the effective and selective separation regarding different cells in biological applications.
From Spectacle to Sustainability: Navigating Waste Management Challenges in Mega-Sporting Events of the Modern Era
Authors: Zafari Zahra , Golzary Abooali 
Published: September 2023

Abstract
In modern times, sports play a significant role in people's lives, serving as major global events. While sports can have a positive impact on health and quality of life, they can also have negative effects on the environment and people's health in specific circumstances. The production of massive amounts of waste during events like the Olympics and the World Cup is a major concern. Improper waste management can lead to land and water pollution, harm ecosystems, destroy biodiversity, and negatively impact human health. The amount of waste produced by stadiums around the world varies depending on factors such as population density, lifestyle, levels of consumption, and commercial activities near the stadiums. Weather conditions, seasons, and changes in people's behavior can also influence waste production. Understanding the variety of stadium waste (production rate, quantity, quality, source, etc.) and the characteristics of the host city is essential to design and implement sustainable waste management systems. Inefficient waste management can result in resource depletion, visual pollution, high management costs, and adverse effects on human health. This study aims to investigate different waste management strategies for mega-sporting events during the last two decades. The findings demonstrate that governments and event organizers have increasingly focused on implementing effective waste management systems. Going forward, organizers should prioritize smart waste management strategies to manage the waste stream generated by these events.
Neo-adjuvant chemotherapy plus immunotherapy in resectable N1/N2 NSCLC
Authors: Du Chengli , Chen Yunhao , Zhou Yuwei , Zheng Difang , Zhao Jiangang , Tang Jie , Wu Yihe , Tu Zhengliang 
Published: September 2023

Abstract
Background
Locally advanced non-small cell lung cancer (NSCLC) with N1/N2 lymph node metastasis is challenging with poor survival. Neo-adjuvant chemo-immunotherapy has gained benefits in a proportion of these patients. However no specific biomarker has been proved to predict the effect before therapy. In addition, the relationship of nodal status and survival after neo-adjuvant chemo-immunotherapy is still not well stated.
Methods
A total of 75 resectable NSCLC patients with N1/N2 stage who received neo-adjuvant chemo-immunotherapy plus surgery were retrospectively studied. The clinical characteristics, surgical information and safety parameters were collected. The correlations of major pathological response (MPR) and pathological complete response (pCR) with clinical data were analyzed. The progression free disease(PFS) and overall survival(OS) were evaluated with pathological response and nodal status.
Results
Of the 75 patients, 69 (92%) patients experienced treatment related adverse effects, while grade 3–4 adverse effects occurred in 8 (10%) patients. All the patients received surgical R0 resection with a MPR rate of 60% and a pCR rate of 36%. 67% of N1 patients and 77% of N2 patients had nodal clearance after neo-adjuvant treatment. A significant difference was observed between pathological response with age, histology and multiple lymph node metastasis. The PFS was better in the MPR cohort. The PFS was 90.1% and 83.6% at the nodal clearance group at the time of 12 and 18 months, compared with 70.1% and 63.7% at the nodal residual group.
Conclusions
The neo-adjuvant chemo-immunotherapy for locally advanced NSCLC with nodal positive was safe and feasible. The patients with elder age and squamous-cell carcinoma (SCC) were more likely to have better pathological response, while multiple nodal metastasis was a negative predictor. The clearance of lymph node resulted in significantly longer PFS and OS.
Floristic classification is not a predictor of species-specific evolutionary patterns
Authors: Fahey Patrick , Dimon Richard , Merwe Marlien van der , Bragg Jason , Rossetto Maurizio 
Published: September 2023

Abstract

The relationship between intra-specific and inter-specific patterns and processes over evolutionary time is key to ecological investigations. We examine this relationship from a novel perspective, focussing on the association between floristic classifications, a summary of inter-specific processes, and intra-specific genetic structuring. Applying an innovative, multispecies, and standardised population genomic approach we test the relationship between vegetation mapping schemes and landscape-level estimates of gene flow across a large, environmentally heterogenous region. We show that intra-specific genetic variation shows limited correspondence to vegetation classifications and is better explained by distance between sampled populations and the location of biogeographical features which limit gene flow. However, vegetation classification schemes with contiguous mapping classes were more predictive of genetic lineages than geographically non-contiguous schemes. The size of mapping units was found to be important, as most local vegetation types contained only single intra-specific genetic lineages, while these genetic lineages spanned hundreds of km’s across multiple vegetation types. We conclude that floristic classifications are not closely correlated with intra-specific genetic patterns, showing that intra-specific genetic processes are independent of inter-specific floristic assembly processes. This study also showcases the depth of understanding that can be developed using large, multispecies genetic datasets.
Does Excessive Physical Activity Increase the Risk of Sarcopenia? A Cross-sectional Study of Older Adults in Taiwan
Authors: Tsai Chi-Hsuan , Liao Yung , Chang Shao-Hsi 
Published: September 2023

Abstract

Objectives: The updated World Health Organization 2020 guidelines strongly recommend an optimal physical activity level of 150-300 min/week for older adults. However, few studies have examined the relationship between different levels of physical activity and sarcopenia. Therefore, the purpose of this study was to investigate the cross-sectional association between physical activity levels and the risk of sarcopenia in older adults.
Methods: A nationwide cross-sectional telephone survey of older adults (≥65 years) was conducted in Taiwan from October 2019 to January 2020. Older adults were interviewed to collect data on their self-reported level of physical activity (measured by the Taiwanese version of the IPAQ-SF), sarcopenia risk (measured by the SARC-F questionnaire), and sociodemographics. Chi-square tests and binary logistic regression models were applied.
Results: A total of 1068 older adults were surveyed. Compared with the optimal physical activity level recommendations in the WHO guidelines and after adjusting for potential confounders, older adults with insufficient physical activity levels (<150 min/week) were more likely to have a higher risk of sarcopenia (OR: 3.18; CI: 1.63-6.22), whereas older adults with excessive physical activity levels (≥300 min/week) were more likely to have a lower risk of sarcopenia (OR: 0.38; CI: 0.19-0.75).
Conclusions: The findings of this study highlight that inconsistent with the 2020 WHO guidelines, going beyond the recommended range of physical activity seems to be effective for sarcopenia prevention in older adults. Future research should further explore whether excessive physical activity levels could result in other health benefits.
Status of primary macronutrients and their connection to the chemical composition of the soil in Varanasi's vegetable-growing region
Authors: University Pramod Kumar Sharma Banaras Hindu , Universitry Kshirod Chandra Sahoo GIET 
Published: September 2023

Abstract
Plant nutrition is the key factor for crop growth particularly primary macronutrients. A lot of work conducted on cereals instead of vegetable growing areas. The major macronutrient status of the Shanshahpur village in Varanasi, Uttar Pradesh, a region known for its vegetable cultivation, was the subject of the current study. 50 samples were taken from each interplanted vegetable in the farmer's field to test for all primary macronutrients, i.e.N, P & K respectively. The pH of soil sample ranges from 6.03–8.72 in which maximum samples under alkaline category. The EC of soil sample suitable for vegetable growing which contain less amount of salt. The organic carbon content in medium range which favourable for crop growth. From 110 to 377 Kgha− 1 of accessible nitrogen was found in the surface soil of the village of Shanshahpur, with 84 percent falling into the low category. The accessible phosphorus level in the vegetable producing areas were in the medium to high range, with a mean value of 15.95 Kgha− 1 and a range of 10 to 34 Kgha− 1. The available potassium levels in the soils varied from 202 to 358 Kgha− 1, largely in the high to medium range. The available nitrogen was shown to strongly correlate (r = 0.15) with soil pH. The amount of accessible nitrogen (r = 0.26) and the amount of organic carbon (r=-0.23) were adversely linked with the electrical conductivity of soil. With regard to available nitrogen content, organic carbon content in vegetable-growing regions was very significant (r = 0.99***). The association was favourable (r = 0.16) between organic matter and available phosphorus.
Optimizing Deep Learning-Based Segmentation of Densely Packed Cells using Cell Surface Markers
Authors: Han Sunwoo , Phasouk Khamsone , Zhu Jia , Fong Youyi 
Published: September 2023

Abstract
Background: Spatial molecular profiling depends on accurate cell segmentation. Identification and quantitation of individual cells in dense tissues, e.g. highly inflamed tissue caused by viral infection or immune reaction, remains a challenge.
Methods: We first assess the performance of 18 deep learning-based cell segmentation models, either pre-trained or trained by us using two public image sets, on a set of immunofluorescence images stained with immune cell surface markers in skin tissue obtained during human herpes simplex virus (HSV) infection. We then further train eight of these models using up to 10,000+ training instances from the current image set. Finally, we seek to improve performance by tuning parameters of the most successful method from the previous step.
Results: The best model before fine-tuning achieves a mean Average Precision (mAP) of 0.516. Prediction performance improves substantially after training. The best model is the cyto model from Cellpose. After training, it achieves an mAP of 0.694; with further parameter tuning, the mAP reaches 0.711.
Conclusion: Selecting the best model among the existing approaches and further training the model with images of interest produce the most gain in prediction performance. The performance of the resulting model compares favorably to human performance. The imperfection of the final model performance can be attributed to the moderate signal-to-noise ratio i the imageset.
Microwave in situ inactivation technique for the treatment of giant cell tumor of bone: a systematic review and meta-analysis
Authors: Jiang Xiang , Xia Pingguang , Yu Aixi 
Published: September 2023

Abstract
Introduction Giant cell tumor of bone (GCTB) necessitates a distinct treatment approach compared to benign and malignant bone tumors due to its invasive nature. Intralesional curettage, with adequate margin control, is an established and effective treatment option that is widely accepted. The efficacy of microwave in situ inactivation (MIST) or microwave ablation (MWA) technology, which is commonly used as an adjuvant, needs to be evaluated. The objective of this study was to systematically review the treatment options of microwave in situ inactivation for GCTB. Materials and methods A systematic review of published literature was conducted to analyze the treatment of giant cell tumor of bone with microwave ablation. The literature search was performed using various online databases such as EMBASE, the Cochrane Library, PubMed, Web of Science, and Medline. The effectiveness of MIST in treating GCTB and any associated complications were evaluated through the summary of the literature. Results The included literature presents findings from five studies, which collectively reported a total of 221 cases. The effectiveness of MIST was assessed in terms of the Musculoskeletal Tumor Society (MSTS) score over an average 18-month follow-up period. The results showed a significant improvement, with a mean difference of 26.65 (95% CI: 24.91–28.39, p < 0.00001). Subgroup analysis specifically focusing on distal femur and distal radius lesions demonstrated excellent outcomes with satisfactory control of overall complications. Conclusions Existing evidence suggests that the combination of MIST and effective intralesional curettage achieves satisfactory short-to-medium-term treatment outcomes for giant cell tumors of the bone. This approach offers significant advantages in key aspects, including postoperative mobility and preservation of joint function, control of local recurrence, prevention of joint degeneration, and reduction in metastasis and mortality rates.