bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asgard archaea defense systems and their roles in the origin of eukaryotic immunity
Authors: Leão Pedro , Little Mary , Appler Kathryn , Sahaya Daphne , Aguilar-Pine Emily , Currie Kathryn , Finkelstein Ilya , De Anda Valerie , Baker Brett 
Published: October 2023

Abstract

Immune systems are integral to survival against viral infection. Recently, dozens of new anti-viral systems have been characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes. However, little is known about these defense mechanisms in archaea. Here, we identified 2,610 complete defense systems in archaea related to eukaryotes, the Asgardarchaeota. These comprise 89 unique systems, including argonaute, NLR, mokosh, viperin, lassamu, and CBASS. Asgard viperin (asVip) and argonaute (asAgo) proteins are present at high frequencies compared to bacteria and have structural homology to eukaryotes. Phylogenetic analyses revealed asVips are ancestral eukaryotic proteins. Heterologous expression of asVips in bacteria, including the lineage closest to eukaryotes, Hodarchaeales, showed robust anti-phage activity. Eukaryotic- and bacterial-argonaute proteins appear to have originated in Asgardarchaeota, and preserve ancient structural characteristics. AsAgos have argonaute-PIWI domains which are key components of the RNA interference (RNAi) in eukaryotes. Characterization of hundreds of defense systems in the Asgardarchaeota revealed these archaea played important roles in the innovation of viral protection in eukaryotes. Given their relationship to eukaryotes, these defense systems may have applications in biomedicine and biotechnology.
Development of insecticidal nano-composite solution to control termite losses in peach
Authors: Zarish Sana , Raja Naveed Iqbal , Abbasi Fozia 
Published: October 2023

Abstract
Peach (Prunus persica L.) be a part of family Rosacea, although Aaru is its local name. Pakistan ranked 25th in peach production. In Pakistan, peach is a prime stone fruit after plum. It is summer fruit but can be used in winter season after drying its fruit. It also contains medicinal properties because it carries various phenolic compounds in fruit. Termites are one of the most important insect that damage the peach tree and due to their attack tree should be hollowed, leaves become wilt and ultimately becomes in the form of plant death. Termites attack on plants can be control by a unique innovative technique which is nanotechnology. Nanotechnology is the 21st century science executes output of various nanoparticles possessing range amid 1 to 100 nm. Among these, Ag/ZnO nanoparticles are very important due to raised surface area to volume ratio and catalytic efficiency. Bimetallic nanoparticles may increase water uptake, nutrient use efficiency, hence may improve plant growth and their yield by changing physio-morphic and biochemical attributes. Green bimetallic Ag/ZnO nanoparticles will be synthesized from salts reduced by Moringaoleifera Lam. Ag/ZnO nanoparticles will be characterized by UV-Visible Spectroscopy, SEM, FTIR and EDX. Nanocomposite Ag/ZnO with various concentrations i.e 100ppm, 200ppm, 300ppm, 400ppm, 500ppmand have two control (T + no treatment and T- 500ppm Ag/ZnO salt). Effect will be analyzed for physiological (membrane stability index, chlorophyll content, relative water content), biochemical (SOD, POD, catalase, proline content, protein content, sugar content). All the obtained data will be analyzed through ANOVA by using SPSS 16.1 program.
Specific colorimetric LAMP assay for the detection of maize bushy stunt phytoplasma in corn through comparative genomics
Authors: Egito Isabella Cristina Santos , Alves Angelica Rodrigues , Carvalho Ian Carlos Bispo , Ferreira Luciellen Costa , Rossato Maurício 
Published: October 2023

Abstract

Brazil stands out for being the third largest corn producer in the world, in addition to having self-sufficiency in national supply. Even with the high production, the country has, throughout its extension, climatic conditions that favor the attack of several pathogens. Maize red stunt, caused by maize bushy stunt phytoplasma (MBSP), is one of the most harmful diseases to the crop, therefore, there is a demand for detection methods that are fast and accurate. Loop-mediated isothermal amplification (LAMP) is one of these methods, being fast, sensitive, with high specificity and can be used in field analysis. The goal of the present work was the development of a LAMP protocol, through comparative genomics, for MBSP in maize. To design the sets of primers, MBSP genome sequence and other sequences of other pathogens were used in the RUCS software to select only core unique sequences. Three sets of primers presented the desired criteria and were synthetized. The most promising primer set, MBSP-LP, was used to test the LAMP assay together with the Warmstart colorimetric LAMP 2X master mix (NEB) Kit. The collection of 51 samples of corn with and without symptoms was tested with a typical nested-PCR and compared with the proposed LAMP assay. Considering the presence and absence of symptoms, there was confirmation that the symptomatic plants were positive for LAMP in a greater proportion than for nested-PCR. The proposed LAMP assay proved to be sensitive, detecting up to 0.1 fg µL-1 of DNA. The use of plant material directly in the reaction was evaluated for changing the color of the master mix and also for inhibiting the reaction. It was identified that there are no inhibitors in the maize plant tissue, being possible to use this LAMP with plant tissue without the DNA extraction step.
Lack of mitochondrial complex I assembly factor NDUFAF2 results in a distinctive infantile-onset brainstem neurodegenerative disease with early lethality
Authors: Hanna Firas Abu , Zehavi Yoav , Cohen-Barak Eran , Khayat Morad , warwar Nasim , shreter Roni , Rodenburg Richard J , SPIEGEL RONEN 
Published: October 2023

Abstract
Background Congenital disorders of the mitochondrial respiratory chain are a heterogeneous group of inborn errors of metabolism. Among them, NADH:ubiquinone oxidoreductase (complex I, CI) deficiency is the most common. Biallelic pathogenic variants in NDUFAF2, encoding the nuclear assembly CI factor NDUFAF2, were initially reported to cause progressive encephalopathy beginning in infancy. Since the initial report in 2005, less than a dozen patients with NDUFAF2-related disease have been reported.
Methods Clinical, biochemical, and neuroradiological features of four new patients were collected. Enzymatic activities of the five respiratory-chain complexes were determined in isolated fibroblast mitochondria by spectrophotometric methods. Western blot analyses were conducted with anti-human NDUFAF2 antibody; antibody against the mitochondrial marker VDAC1 was used as a loading control. Genetic studies were performed by chromosome microarray analysis using Affymetrix CytoScan 750K arrays.
Results The patients presented with infantile-onset growth retardation, ophthalmological impairments with nystagmus, strabismus, and optic atrophy, and further progressed to life-threatening episodes of apnea triggered by trivial febrile illnesses with gradual loss of acquired developmental milestones. Serial magnetic-resonance imaging studies showed a progressive pattern of abnormal T2-weighted hyperintense signals involving primarily the brainstem, the upper cervical cord, and later, the basal ganglia and thalami. Magnetic-resonance spectroscopy in one patient showed an increased lactate peak. Disease progression was marked by ventilatory dependency and early lethality. The patients harbored a homozygous 142-kb partial interstitial deletion that omits exons 2–4 of NDUFAF2. Mitochondrial CI activity was significantly decreased. Western blot analysis disclosed the absence of NDUFAF2 protein compared to normal controls. In addition, we reviewed all 10 previously reported NDUFAF2-deficient cases to better characterize the disease.
Conclusions Biallelic loss-of-function mutations in NDUFAF2 result in a distinctive phenotype in the spectrum of Leigh syndrome with clinical and neuroradiological features that are primarily attributed to progressive brainstem damage.
Genome-wide association study suggests that CPQ influences the Omicron variant COVID-19 severity
Authors: Hou Can , Zeng Yu , Zhang Yanan , Yang Lei , Yang Huazhen , Chen Wenwen , Qu Yuanyuan , Bu Fengxiao , Valdimarsdóttir Unnur A. , Fang Fang , Li Qian , Song Jie , Song Huan 
Published: October 2023

Abstract
Host genetic background has been indicated in the severity of coronavirus disease 2019 (COVID-19) with multiple genetic variants identified, either across or in specific populations. However, previous host genetic studies of COVID-19 were either pre-Omicron era or conducted on various mutants of SARS-CoV-2, and few were performed among non-European populations. To investigate the genetic variation contributing to the severity of infections with SARS-CoV-2 Omicron variant, we performed a genome-wide association study among 5,151 Chinese individuals newly infected with SARS-CoV-2 since January 2022 (269 severe cases and 4,882 mild cases). We identified a novel genomic locus on chromosome 8q22.1 (rs7817424, P-value = 4.60×10−8) in the CPQ gene that is involved in hydrolysis of circulating peptides. Gene mapping approach using colocalization of eQTL, pQTL and sQTL data and similarity-based gene prioritization suggested CPQ as the risk gene. Multiple analyses using single-cell RNA sequencing data, in combination with transcription factor binding motif analyses support a role of the CPQ gene in the manifestation of severe symptoms of the Omicron variant, which might be through involvement in the NF-κB pathway activation. Future confirmatory studies are warranted and may help identify mechanistic targets for therapeutic development.
Assessing Excess Mortality of Baby Boomers from the COVID-19 Pandemic: Taiwan Naïve Omicron Infection Study
Authors: Lin Ting-Yu , Hsu Chen-Yang , Yen Amy Ming-Fang , Chen Sam Li-Sheng , Chen Hsiu-Hsi 
Published: October 2023

Abstract
Background: Asia's elderly Baby Boomer demographic (born between 1946 and 1964) faced a huge problem during the COVID-19 pandemic due to increased all-cause mortality. We aimed to provide a unique Taiwan situation regarding the impact of Baby Boomers on excess mortalities from all causes relative to non-Baby Boomers throughout distinct times of SARS-CoV-2 mutations during the COVID-19 pandemic.
Methods: The Poisson time series design with Bayesian directed acyclic graphic approach was proposed to build the background mortality prior to the COVID-19 pandemic in 2015-2019. It was then used for predicting the expected all-cause deaths compared to the reported figures during the COVID-19 pandemic period based on Taiwan residents, a naïve Omicron infection cohort.
Results: Baby Boomers experienced a 2% (95% CI: 1%-3%) negative excess in 2020 (Wuhan/D614G) and a 4% (95% CI: 2%-5%) excess in 2021 (Alpha/Delta), relative to non-Baby Boomers, due to a rising mortality trend for Baby Boomers, but remained constant for non-Baby Boomers. Baby Boomer and non-Baby Boomer mortality rates soared to 9% (95% CI: 7%-10%) and 10% (95% CI: 9%-11%), respectively. Surprisingly, Baby Boomers aged 58-76 experienced the same 9% excess mortality as non-Baby Boomers aged 77 and beyond. Non-COVID-19 deaths were more prevalent among Baby Boomers than non-Baby Boomers (33% vs. 29%).
Conclusion: Baby Boomers were more likely to die from COVID-19 and had more non-COVID-19 deaths than older non-Baby Boomers. For this vulnerable population, adequate access to medical care and medical capacity require more consideration.
Energy sustainability and carbon dioxide emissions mitigation Options for South Africa’s Road Transport Sector
Authors: Ntuli Menzi Nazi , Eloka-Eboka Andrew C , Mwangi Festus MAINA , Ewim Daniel Raphael Ejike , Dioha Michael O 
Published: October 2023

Abstract
Background
The transport sector in South Africa is responsible for around 11% of the country's carbon dioxide emissions, with road transport contributing an overwhelming 90% of this total, as noted by the South African Green Transport Energy of South Africa. As part of its commitment to global climate pacts, South Africa aims to reduce emissions from its road transport sector. Yet, studies focused on reducing energy consumption and related emissions in this sector have been sparse.
Results
Utilizing a bottom-up accounting modelling framework, this research investigated five low-carbon transition scenarios alongside a business-as-usual (BAU) scenario for road transport. These scenarios comprised Fuel and Technology Switching (FTS), Modal Shift (MS), Logistics Improvement (LI), Energy Efficient (EEF), and a Combined Mitigation (CMT). The BAU scenario was established as a benchmark to demonstrate energy demand and emissions in the absence of changes to current practices or policies. According to our model, under the BAU scenario, there will be a 61% surge in final energy demand, from 769 petajoules (PJ) in 2020 to 1240 PJ by 2050, accompanied by a proportional increase in emissions. The study revealed that the implementation of any of the alternative low-carbon scenarios could yield a reduced energy demand by 2050. Significantly, a combined approach, integrating multiple low-carbon policies, can achieve more substantial reductions in energy demand and CO2 emissions than applying single policies separately.
Conclusions
This study emphasizes the importance of crafting province-specific solutions, acknowledging that challenges and contexts vary between provinces. Furthermore, lessening energy reliance not only diminishes the nation's fuel import bills but also improves air quality and aids in achieving low emission targets.
Metagenomics next generation sequencing for diagnosis of invasive fungal diseases in patients with hematological diseases
Authors: Chen Xi , Lian Yun , Song Yuhua , Long Qiqiang 
Published: October 2023

Abstract
PURPOSE: To investigate the clinical characteristics and risk factors of invasive fungal disease (IFD) in patients with hematological disorders.
METHODS: From January 2022 to January 2023, seventy patients with blood diseases hospitalized at the Second Hospital of Nanjing who were suspected of infection with IFD underwent mNGS and fungal pathogen detection. The clinical characteristics and laboratory data of 32 fungal infected individuals (IFD group) and 38 non-IFD groups were compared. SPSS and R software were used for the statistical analysis of risk factors associated with IFD.
RESULTS: Using the results of conventional fungal cultures as a “gold standard”, the sensitivity, specificity, positive predictive value, and negative predictive value of mNGS for the evaluation of fungal pathogen infections in patients with hematological disorders were found to be 100% (10/10), 63.3% (38/60), 31.3% (10/32), and 100% (38/38), respectively. Multivariate logistic regression analysis revealed six independent risk factors associated with IFD in patients with hematological disorders: CD4+T cell count < 400 cells/µL (odds ratio (OR)=7.43, p=3.79x10-4), elevated C-reactive protein (OR=3.71, p=0.01), elevated interleukin (IL)-6 (OR=6.5, p=2.93x10-4), elevated IL-10 (OR=3.03, p=0.041), hypoproteinemia (OR=7.04, p=0.025), and neutropenia persisting for >10 days (OR=3.03, p=0.002).
CONCLUSION: mNGS has high sensitivity in detecting IFD in patients with hematological diseases. CD4+cell count below 400/ul, increased level of C-reactive protein, IL-6, and IL-10, hypoalbuminemia, and neutropenia lasting for more than 10 days are independent risk factors for IFD in patients with hematological diseases.
The combined application of the frailty index and prognostic nutritional index for short-term prognosis after colorectal surgery
Authors: Huang Lihong , Li Zhifa , Liang Zhiwei , Wu Xiaobing , Song Shixi , Qin Haifeng , Li Ziqiao , Chen Huixian , Xie Yingjun , Chen Rong 
Published: October 2023

Abstract
Objective
Cooperative physiological reserve function is closely related to postoperative mortality and adverse outcomes. Elderly patients with colorectal cancer should undergo preoperative geriatric assessment (GA). To construct a PNI-MFI-5 scoring system based on the prognostic nutrition index (PNI) and 5-factor Modified Frailty Index (MFI-5), we evaluated elderly patients before surgery and explored its value in predicting poor prognosis after colorectal cancer surgery.
Methods
A total of 213 elderly patients who underwent radical resection of colorectal cancer were selected. The critical values of PNI and MFI-5 and their correlation were determined by receiver operating characteristic (ROC) curves, and the relationship between the PNI-MFI-5 score and clinical parameters of colorectal cancer was analysed. A Cox regression model was used to determine the relationship between the PNI-MFI-5 score and poor postoperative prognosis, and an ROC curve was used to determine the predictive efficiency of PNI-MFI-5.
Results
There was a significant correlation between preoperative PNI and preoperative MFI-5 score (r = -0.14, p < 0.05). The PNI-MFI-5 scores increased significantly in advanced age (P < 0.003), ASA grade 3–4 (p < 0.001), preoperative anaemia (p < 0.001), preoperative hypoproteinaemia (p < 0.001) and tumour diameter ≥ 5 cm (p < 0.001). A total of 73 patients had adverse outcome events, of which postoperative hypoproteinaemia accounted for the highest proportion, followed by pulmonary infection. With increasing grade, postoperative pulmonary infection (OR = 2.374, p < 0.001), anastomotic leakage (OR = 2.390, p < 0.001), septicemia (OR = 4.198, p < 0.001), hypoproteinaemia (OR = 3.075, p < 0.001), and cardio-cerebrovascular accident (OR = 3.742) occurred. The risk of postoperative adverse outcome events, such as death at 30 days after the operation (OR = 4.198, p < 0.05), increased. Further univariate and multivariate analyses showed that only the PNI-MFI-5 score (OR = 2.540, 95% CI 1.498–4.307 score pendant 0.001) was an independent predictor of adverse outcome events after CRC. The prediction efficiency of PNI-MFI-5 was higher, and the area under the curve of the PNI-MFI-5 score (AUC = 0.724, P < 0.001) was larger than that of the MFI-5 score (AUC = 0.678, 95% CI 0.602–0.753 (P < 0.001) and PNI (AUC = 0.667, 95% CI 0.585–0.748, P < 0.001).
Conclusion
The perioperative risk model of the PNI-MFI-5 score system was constructed to accurately predict the risk of postoperative adverse outcomes in patients with colorectal cancer.
Estimating alcohol and tobacco consumption of university students and urban population in Ho Chi Minh city by wastewater-based epidemiology
Authors: Do Thi Thuy Quyen , Tran Thi Yen Nhi , Nguyen Thi Thanh Nhon , To Thi Hien 
Published: October 2023

Abstract
This study employed wastewater-based epidemiology (WBE) to assess alcohol and tobacco consumption of university students and urban residents in Ho Chi Minh City, Vietnam. Ethyl sulfate and cotinine were chosen to be the markers of alcohol and tobacco use, respectively. The estimation showed that on average a student consumed between 0.69 ± 0.13 mL of pure alcohol and 1.2 ± 0.2 mg nicotine per day. These values were significantly lower when compared to the consumption rates among urban residents, which were 2.41 ± 0.34 mL of pure alcohol and 4.34 ± 0.60 mg nicotine per day per person aged 15 and above. The estimated alcohol consumption in this study was substantially lower than previous survey-based reports, however, the tobacco consumption rate closely aligned with the findings of surveys conducted among current smokers. The degradation of biomaker within household on-site septic tanks was thought to take account for the low alcohol comsuption estimation. Further research is necessary to consider the correction factors of WBE method in the context of sewage system.
Optimized, automated and cGMP-compliant synthesis of the HER2 targeting [68Ga]Ga-ABY-025 tracer
Authors: Jussing Emma , Ferrat Mélodie , Moein Mohammad M , Alfredéen Henrik , Tegnebratt Tetyana , Bratteby Klas , Samén Erik , Feldwisch Joachim , Altena Renske , Axelsson Rimma , Tran Thuy A 
Published: October 2023

Abstract
Background

The Affibody molecule, ABY-025, has demonstrated utility to
detect human epidermal growth factor receptor 2 (HER2) in vivo,
either radiolabelled with indium-111 (111In) or
gallium-68 (68Ga). Using the latter, 68Ga, is
preferred due to its use in positron emission tomography with
superior resolution and quantifying capabilities in the clinical
setting compared to 111In. For an ongoing phase II study
(NCT05619016) evaluating ABY-025 for detecting HER2-low lesions and
selection of patients for HER2-targeted treatment, the aim was to
optimize an automated and cGMP-compliant radiosynthesis of
[68Ga]Ga-ABY-025.

[68Ga]Ga-ABY-025 was produced on a synthesis module, Modular-Lab PharmTracer (Eckert & Ziegler), commonly used for 68Ga-labelings. The radiotracer has previously been radiolabeled on this module, but to streamline the production, the method was optimized. Steps requiring manual interactions to the radiolabeling procedure were minimized including a convenient and automated pre-concentration of the 68Ga-eluate and a simplified automated final formulation procedure. Every part of the radiopharmaceutical production was carefully developed to gain robustness and to avoid any operator bound variations to the manufacturing. The optimized production method was successfully applied for 68Ga-labeling of another radiotracer, verifying its versatility as a universal and robust method for radiosynthesis of Affibody-based peptides.

Results

A simplified and optimized automated cGMP-compliant radiosynthesis method of [68Ga]Ga-ABY-025 was developed. With a decay corrected radiochemical yield of 44.5 ± 2.2%, a radiochemical purity (RCP) of 99 ± 1%, and with an RCP stability of 98 ± 1% at 2 hours after production, the method was found highly reproducible. The production method also showed comparable results when implemented for radiolabeling another similar peptide.

Conclusion

The improvements made for the radiosynthesis of [68Ga]Ga-ABY-025, including introducing a pre-concentration of the 68Ga-eluate, aimed to utilize the full potential of the 68Ge/68Ga generator radioactivity output, thereby reducing radioactivity wastage. Furthermore, reducing the number of manually performed preparative steps prior to the radiosynthesis, not only minimized the risk of potential human/operator errors but also enhanced the process’ robustness. The successful application of this optimized radiosynthesis method to another similar peptide underscores its versatility, suggesting that our method can be adopted for 68Ga-labeling radiotracers based on Affibody molecules in general.
Trial registration: NCT, NCT05619016, Registered 7 November 2022, https://clinicaltrials.gov/study/NCT05619016?term=HER2&cond=ABY025&rank=1