bluuebunny/crossref_metadata_2025_split huggingface dataset:
Template and target-site recognition by human LINE-1 in retrotransposition
Authors: Thawani Akanksha , Ariza Alfredo Jose Florez , Nogales Eva , Collins Kathleen 
Published: December 2023

AbstractThe long interspersed element-1 (LINE-1, hereafter L1) retrotransposon has generated nearly one-third of the human genome and serves as an active source of genetic diversity and human disease1. L1 spreads through a mechanism termed target-primed reverse transcription, in which the encoded enzyme (ORF2p) nicks the target DNA to prime reverse transcription of its own or non-self RNAs2. Here we purified full-length L1 ORF2p and biochemically reconstituted robust target-primed reverse transcription with template RNA and target-site DNA. We report cryo-electron microscopy structures of the complete human L1 ORF2p bound to structured template RNAs and initiating cDNA synthesis. The template polyadenosine tract is recognized in a sequence-specific manner by five distinct domains. Among them, an RNA-binding domain bends the template backbone to allow engagement of an RNA hairpin stem with the L1 ORF2p C-terminal segment. Moreover, structure and biochemical reconstitutions demonstrate an unexpected target-site requirement: L1 ORF2p relies on upstream single-stranded DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break. Our research provides insights into the mechanism of ongoing transposition in the human genome and informs the engineering of retrotransposon proteins for gene therapy.
Mucosal boosting enhances vaccine protection against SARS-CoV-2 in macaques
Authors: McMahan Katherine , Wegmann Frank , Aid Malika , Sciacca Michaela , Liu Jinyan , Hachmann Nicole P. , Miller Jessica , Jacob-Dolan Catherine , Powers Olivia , Hope David , Wu Cindy , Pereira Juliana , Murdza Tetyana , Mazurek Camille R. , Hoyt Amelia , Boon Adrianus C. M. , Davis-Gardner Meredith , Suthar Mehul S. , Martinot Amanda J. , Boursiquot Mona , Cook Anthony , Pessaint Laurent , Lewis Mark G. , Andersen Hanne , Tolboom Jeroen , Serroyen Jan , Solforosi Laura , Costes Lea M. M. , Zahn Roland C. , Barouch Dan H. 
Published: December 2023

AbstractA limitation of current SARS-CoV-2 vaccines is that they provide minimal protection against infection with current Omicron subvariants1,2, although they still provide protection against severe disease. Enhanced mucosal immunity may be required to block infection and onward transmission. Intranasal administration of current vaccines has proven inconsistent3–7, suggesting that alternative immunization strategies may be required. Here we show that intratracheal boosting with a bivalent Ad26-based SARS-CoV-2 vaccine results in substantial induction of mucosal humoral and cellular immunity and near-complete protection against SARS-CoV-2 BQ.1.1 challenge. A total of 40 previously immunized rhesus macaques were boosted with a bivalent Ad26 vaccine by the intramuscular, intranasal and intratracheal routes, or with a bivalent mRNA vaccine by the intranasal route. Ad26 boosting by the intratracheal route led to a substantial expansion of mucosal neutralizing antibodies, IgG and IgA binding antibodies, and CD8+ and CD4+ T cell responses, which exceeded those induced by Ad26 boosting by the intramuscular and intranasal routes. Intratracheal Ad26 boosting also led to robust upregulation of cytokine, natural killer, and T and B cell pathways in the lungs. After challenge with a high dose of SARS-CoV-2 BQ.1.1, intratracheal Ad26 boosting provided near-complete protection, whereas the other boosting strategies proved less effective. Protective efficacy correlated best with mucosal humoral and cellular immune responses. These data demonstrate that these immunization strategies induce robust mucosal immunity, suggesting the feasibility of developing vaccines that block respiratory viral infections.
Proximity induced band gap opening in topological-magnetic heterostructure (Ni80Fe20/p-TlBiSe2/p-Si) under ambient condition
Authors: Singh Roshani , Maurya Gyanendra Kumar , Gautam Vidushi , Kumar Rachana , Kumar Mahesh , Suresh K. G. , Panigrahi Brahmaranjan , Murapaka Chandrasekhar , Haldar Arbinda , Kumar Pramod 
Published: December 2023

AbstractThe broken time reversal symmetry states may result in the opening of a band gap in TlBiSe2 leading to several interesting phenomena which are potentially relevant for spintronic applications. In this work, the quantum interference and magnetic proximity effects have been studied in Ni80Fe20/p-TlBiSe2/p-Si (Magnetic/TI) heterostructure using physical vapor deposition technique. Raman analysis shows the symmetry breaking with the appearance of A21u mode. The electrical characteristics are investigated under dark and illumination conditions in the absence as well as in the presence of a magnetic field. The outcomes of the examined device reveal excellent photo response in both forward and reverse bias regions. Interestingly, under a magnetic field, the device shows a reduction in electrical conductivity at ambient conditions due to the crossover of weak localization and separation of weak antilocalization, which are experimentally confirmed by magnetoresistance measurement. Further, the photo response has also been assessed by the transient absorption spectroscopy through analysis of charge transfer and carrier relaxation mechanisms. Our results can be beneficial for quantum computation and further study of topological insulator/ferromagnet heterostructure and topological material based spintronic devices due to high spin orbit coupling along with dissipationless conduction channels at the surface states.
The impact of difficult embryo transfer on the success of IVF: a systematic review and meta-analysis
Authors: Galati Giulia , Reschini Marco , Mensi Laura , Di Dio Camilla , Somigliana Edgardo , Muzii Ludovico 
Published: December 2023

AbstractThe procedure of embryo transfer (ET) must be as gentle as possible since any traumatism may cause uterine contractility that interferes with the implantation. However, this ideal conduct is not always possible, and additional measures may be necessary (difficult ET). Different studies have evaluated the impact of difficult ET on the clinical pregnancy rate (CPR), but results were not univocal. The present systematic review and meta-analysis was aimed to provide a precise estimate of the possible detrimental effects of difficult ET on CPR. The study protocol was registered online (PROSPERO number: CRD42023387197). An electronic database search was performed to identify articles published until September 2022. The primary outcome was CPR. Fifteen studies fulfilled the inclusion criteria. Difficult ET significantly reduced the CPR (OR 0.70; 95%CI: 0.64–0.76; p < 0.0001. All pre-planned subgroup analyses according to study design (retrospective vs prospective studies), historical period (studies published before and after 2010), type of catheter, frequency of difficult cases (> or < 19%) and pregnancy rate (> or < 38%) confirmed the significant association. Difficult ET is associated with a significant reduction of CPR. Further studies are warranted to understand how to prevent or manage this common clinical situation.
Filtering property of myelinated internode can change neural information representability and might trigger a compensatory action during demyelination
Authors: Das Sarbani , Maharatna Koushik 
Published: December 2023

AbstractIn this paper, for the first time, we showed that an Internode Segment (INS) of a myelinated axon acts as a lowpass filter, and its filter characteristics depend on the number of myelin turns. Consequently, we showed how the representability of a neural signal could be altered with myelin loss in pathological conditions involving demyelinating diseases. Contrary to the traditionally held viewpoint that myelin geometry of an INS is optimised for maximising Conduction Velocity (CV) of Action Potential (AP), our theory provides an alternative viewpoint that myelin geometry of an INS is optimised for maximizing representability of the stimuli a fibre is meant to carry. Subsequently, we show that this new viewpoint could explain hitherto unexplained experimentally observed phenomena such as, shortening of INS length during demyelination and remyelination, and non-uniform distribution of INS in the central nervous system fibres and associated changes in diameter of nodes of ranvier along an axon. Finally, our theory indicates that a compensatory action could take place during demyelination up to a certain number of loss of myelin turns to preserve the neural signal representability by simultaneous linear scaling of the length of an INS and the inner radius of the fibre.
The geodynamic origin of Los Humeros volcanic field in Mexico: insights from numerical simulations
Authors: Bayona A. , Manea V. C. , Manea M. , Yoshioka S. , Moreno E. , Suenaga N. 
Published: December 2023

AbstractCompared to normal arc-related volcanic eruptions, the formation of a volcanic caldera is a relatively atypical event. During caldera formation a series of large volumes of magma are erupted, reducing the structural support for the rock above the magma chamber and creating a large depression at the surface called caldera. Los Humeros volcanic field (LHVF) represents one of the largest volcanic calderas in Mexico. It is located some 400 km from the trench at the eastern edge of the Trans Mexican Volcanic Belt where the depth to the Cocos slab is more than 300 km. In this study we employ high-resolution two-dimensional thermomechanical numerical simulations of magma intrusions and a horizontal tectonic strain rate to better understand the influence of crustal deformation for the formation of Los Humeros caldera. A minimum number of three thermal anomaly pulses of hydrated mantle material (with diameter of 15 km or more) and a regional strain rate of 7.927 × 10–16 s−1 are required for magma to reach the surface. Modeling results show that regional extension coupled with deep thermal anomalies (with a temperature excess of ΔT ≥ 100 °C) that come in a specific chain-type sequence produce surface deformation patterns similar to LHVF. We propose an asthenospheric sub-slab deep source (> 300 km depth) for the thermal anomalies where previous studies showed the existence of a gap or tear in the Cocos slab.
Risk assessment of hollow-bearing trees in urban forests
Authors: Suchocka Marzena , Jelonek Tomasz , Błaszczyk Magdalena , Wińska-Krysiak Marzena , Kubus Marcin , Ziemiański Maciej , Kalaji Hazem M. 
Published: December 2023

AbstractThe paper is a study of risk assessment posed by trees in selected urban woodlands (urban forests) of Warsaw. Two groups of trees were analysed and compared: exhibiting signs of maturity and ageing (hollow-bearing trees with open or hidden cavities and/or caries) and with no signs of decay. 373 individual trees growing near routes frequently or continuously used for recreational purposes were examined using Roloff's vitality classification, and tree risk assessment method, complemented by instrumental studies: a resistance resistograph, pulling tests, and sonic tomography (SoT). The collected data was analysed using the Chi-square test. The results indicate that it is not possible to conclude unequivocally that the presence of hollows in aged trees significantly increases the risk of falling. According to the safety factor results from the SoT and pulling tests, no correlation was demonstrated between the presence of hollow trees and an increase in risk class. The highest proportion of hollow trees (89.42%) was in the low risk group for trunk fracture and uprooting. The results also indicate the coherence of the diagnostic methods to be necessary for providing sufficient information to assess the statics and, ultimately, as our study showed, the protection of hollow trees.
Plasmodium sporozoite excystation involves local breakdown of the oocyst capsule
Authors: Saeed Sadia , Tremp Annie Z. , Dessens Johannes T. 
Published: December 2023

AbstractPlasmodium oocysts develop on the abluminal side of the mosquito midgut in relatively small numbers. Oocysts possess an extracellular cell wall—the capsule—to protect them from the insect's haemolymph environment. To further maximise transmission, each oocyst generates hundreds of sporozoites through an asexual multiplication step called sporogony. Completion of transmission requires sporozoite egress from the capsule (excystation), but this process remains poorly understood. In this study, we fused the parasite-encoded capsule protein Cap380 with green fluorescent protein in a transgenic P. berghei line, allowing live fluorescence imaging of capsules throughout sporogony and sporozoite excystation. The results show that capsules progressively weaken during sporulation ultimately resulting in sporozoite exit through small holes. Prior to formation of the holes, local thinning of the capsule was observed. Our findings support an excystation model based on local, rather than global, weakening of the capsule likely facilitated by local re-orientation of sporozoites and apical secretion.
Cognitive impairment experienced by Chinese breast cancer survivors
Authors: Chen Dan , Mackenzie Lynette , Hossain Syeda Zakia , Wang Jing-Xin , Jiang Ping-Lan , Wang Yuanxiao , Qin Lanhui , Zhen Jun , Jia Jie 
Published: December 2023

AbstractTo identify cognitive function in Chinese breast cancer survivors. Research questions were: is cognitive function was associated with breast cancer and/or chemotherapy treatment and/or psychological functioning:? and did women with breast cancer experience more cognitive and psychological issues than age-matched women without cancer? Breast cancer survivors with chemotherapy (n = 106, mean age = 50.2 ± 9.5), breast cancer survivors without chemotherapy (n = 100, mean age = 50.5 ± 10.0) and matched healthy controls (n = 96, mean age = 47.9 ± 9.1) completed a battery of cognitive and psychosocial functioning. Demographic characteristics were also collected. The Perceived Cognitive Impairment score for cancer groups was significantly higher than for the healthy group (p = 0.04), but not between the cancer groups. Processing speed was significantly slower in the cancer groups than in the healthy group (both p < 0.001), but not between the cancer groups. Age, living status and education were significantly associated with the FACT-Cog (all p < 0.05). The correlations between the FACT-Cog score and BSI score were strong (r = 0.60 p < 0.01), and between the HADS anxiety and depression scales were strong (r = 0.53 and 0.50, p < 0.01) but correlations were weaker between performance based cognitive tests and measures of psychological functioning. Breast cancer groups indicated more cognitive impairment and reduced psychological functioning compared to the healthy group. However, there was no differences between the breast cancer groups. Chinese breast cancer survivors experienced excess cognitive impairment not associated with usual ageing. Assessment and intervention to address cognitive impairment should be made available to breast cancer survivors.
Granite dust application to hemp – variety-specific impacts on growth and cannabinoid production
Authors: Hillier N. K. , Voscort L. , Zamlynny L. , Hillier W. , Faraone N. 
Published: December 2023

AbstractThe hemp industry has grown exponentially with the recent legalization of Cannabis sativa in Canada. With this new market expansion, there is an increased need for hemp plants, particularly for production of cannabinoids. Growing concerns regarding pesticide residues in commodities for human consumption, as well as global demand for fertilizer has increased consumer demand for natural products as alternatives to synthetic agrochemicals and pest management strategies. The objective of this study was to investigate the potential for using different composite granite dusts applied as soil amendments in improving C. sativa growth, and cannabinoid production (specifically, cannabidiol and cannabidiolic acid). We selected three varieties of industrial hemp with low yield production of cannabidiol (Fibranova, CFX-2, and Katani) and one variety with high yield production of cannabidiol (Cherry Blossom). Varieties were planted in potting soil amended with zero, five or ten percent granite dust mixture, and assayed for growth characteristics, and cannabinoid composition. Among tested cannabis varieties, results suggest that improvements to flower growth (> 44% mass) and cannabinoid production (> 2.5 fold or > 145%) from application of granite dust were evident in one variety of fibre hemp, CFX-2. Overall, this work suggests there may be selective benefits to soil applications of granite dust composites to improve hemp propagation, and that degree of improvement to cannabinoid production vary between varieties of hemp.
PKM2 is a potential prognostic biomarker and related to immune infiltration in lung cancer
Authors: Yin Lan , Shi Jiaying , Zhang Jingfei , Lin Xinyu , Jiang Wenhao , Zhu Yingchuan , Song Yue , Lu Yilu , Ma Yongxin 
Published: December 2023

AbstractPyruvate kinase M2 (PKM2), a subtype of pyruvate kinase, plays a crucial role as a key enzyme in the final step of glycolysis. It is involved in regulating the tumor microenvironment and accelerating tumor progression. However, the relationship between PKM2 expression and the prognosis and immune infiltration remains unclear in lung cancer. In this study, we analyzed PKM2 expression in pan-cancer, and investigated its association with prognosis and immune cell infiltration of lung cancer by using multiple online databases, including Gent2, Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), PrognoScan, Kaplan–Meier plotter, and The Human Protein Atlas (HPA). The results showed that PKM2 expression is elevated in tumor tissues compared with the adjacent normal tissues of most cancers, including lung cancer. Prognostic analysis indicated that high expression of PKM2 was associated with poorer prognosis in overall lung cancer patients, especially in lung adenocarcinoma (LUAD). Notably, PKM2 exhibited a strong correlation with B cells and CD4+ T cells in LUAD; and with B cells, CD8+ T cells, CD4+ cells, and macrophages in lung squamous cell carcinoma (LUSC). Furthermore, PKM2 expression displayed a significant negative correlation with the expression of immune cell markers in both LUAD and LUSC. These findings suggested that PKM2 could serve as a promising prognostic biomarker for lung cancer and provided insights into its essential role in modulating the immune cell infiltration.
Tracking industry pollution sources and health risks in China
Authors: Sing Tien Foo , Wang Wenwen , Zhan Changwei 
Published: December 2023

AbstractAgglomeration of firms significantly increases pollution emission intensity and brings unintended consequences to public health. We develop the pollution emission indices using the firm-level pollutant emission data in China to track pollution intensities at the source using the locally weighted regression approach. Our constant-quality pollutant emission indices for three pollutants (wastewater discharge, COD, and SO2) and the pollution emission heatmaps show decreasing trends for the three pollutants from 1998 to 2012. We also show significant spatial clustering and regional variations in pollution emission trends. Industrial pollution mitigations in China's Eastern and Central regions have been neglected for decades since 2021, when driving economic growth took priority. The regime shifts in pollution controls from the 10th (2000–2005) to the 11th (2006–2010) Five-Year Plan period show the effects of tightening pollution emission controls. Failure to cut pollution emissions at source causes health consequences to residents living and working in nearby polluting industries. The latent environmental hazard could be a ticking time bomb, which could not be delinked from the emergence of cancer villages in the regions. Therefore, enforcing strict and uniform pollution controls and setting clear emission limits at sources can eliminate free-rider problems by polluting firms.
The impact of perioperative fluid therapy on the short-term outcomes after laparoscopic colorectal cancer surgery with ERAS protocol: a prospective observational study
Authors: Pisarska-Adamczyk Magdalena , Torbicz Grzegorz , Gajewska Natalia , Małczak Piotr , Major Piotr , Pędziwiatr Michał , Wysocki Michał 
Published: December 2023

AbstractThe main goals of the Enhanced recovery after surgery (ERAS) protocol are focused on shortening the length of hospital stay (LOS), expediting convalescence, and reducing morbidity. A balanced perioperative fluid therapy is among the significant interventions incorporated by the ERAS protocol. The article contains extensive discussion surrounding the impact of this individual intervention on short-term outcomes. The aim of this study was to assess the impact of perioperative fluid therapy on short-term outcomes in patients after laparoscopic colorectal cancer surgery. The analysis included consecutive patients, who had undergone laparoscopic colorectal cancer operations between 2013 and 2020. Patients were divided into two groups: restricted (≤ 2500 ml) or excessive (> 2500 ml) perioperative fluid therapy. A standardized ERAS protocol was implemented in all patients. The study outcomes included recovery parameters and the morbidity rate, LOS and 30 days readmission rate. There were 361 and 80 patients in groups 1 and 2, respectively. There were no statistically significant differences between the groups in terms of demographic parameters and factors related to the surgical procedure. Logistic regression showed that restricted fluid therapy as a single intervention was associated with improvement in tolerance of diet on 1st postoperative day (OR 2.18, 95% CI 1.31–3.62, p = 0.003), accelerated mobilization on 1st postoperative day (OR 2.43, 95% CI 1.29–4.61, p = 0.006), lower risk of postoperative morbidity (OR 0.58, 95%CI 0.36–0.98, p = 0.046), shorter LOS (OR 0.49, 95% CI 0.29–0.81, p = 0.005) and reduced readmission rate (OR 0.48, 95% CI 0.23–0.98, p = 0.045). A balanced perioperative fluid therapy on the day of surgery may be associated with faster convalescence, lower morbidity rate, shorter LOS and lower 30 days readmission rate.
Unidirectional alignment and orientation pinning mechanism of h-BN nucleation on Ir(111) via reactive probe atomic force microscopy
Authors: Pan Jinliang , Wu Tongwei , Ma Chao , Wu Yangfan , Zheng Yi , Hu Kui , Sun Luye , Ma Sumei , Liu Mengxi , Zhang Yanning , Qiu Xiaohui 
Published: December 2023

AbstractThe epitaxial growth of wafer-scale single-crystalline two-dimensional materials requires precise control over the crystallographic orientation and morphology of clusters formed during the initial stages of nucleation. However, there is limited knowledge about the critical nucleus and its growth mechanism for h-BN on high-symmetry surfaces of transition metals. In this study, we provide atomic insights into h-BN nucleation on Ir(111) using scanning tunneling microscopy and noncontact atomic force microscopy, corraborated by density functional theory (DFT) calculations. The atomic-resolved structural characterization reveals that the smallest h-BN cluster, exhibiting a non-1:1 stoichiometric ratio of boron and nitrogen atoms, maintains a triangular shape with zigzag-type edges. Through force spectroscopy, individual B and N atoms within the cluster, as well as the N-termination edge, are clearly identified, indicating the atomic-scale elemental sensitivity of the chemical-reactive metallic tip. While DFT calculations suggest that the NtopBfcc configuration is thermodynamically favored for larger clusters, a predominant crystalline orientation is observed for nuclei of various sizes, unequivocally attributed to the NtopBhcp registry. This orientation pinning behavior presents opportunities for large-scale growth of binary and ternary materials by impeding rotational alignment of nuclei in the early stages of nucleation.