bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epizootic hemorrhagic disease virus oral infection affects midge reproduction and is vertically transmitted to offspring in the biting midge, Culicoides sonorensis (Diptera: Ceratopogonidae)
Authors: Erram Dinesh , McGregor Bethany , Acevedo Carolina , Alto Barry , Burkett-Cadena Nathan 
Published: May 2024

Abstract

Epizootic hemorrhagic disease virus (EHDV: Reoviridae: Orbivirus) is a Culicoides-borne pathogen that affects a variety of ruminants, causing significant economic losses and/or ecological impacts in animal agriculture/wildlife populations worldwide. In this study, we examined the effect of EHDV serotype-2 oral infection on the survival and reproduction of Culicoides sonorensis Wirth and Jones (a confirmed vector of EHDV in North America), and the potential vertical transmission of EHDV-2 (from infected female to its offspring) in this midge species. Culicoides sonorensis females were fed on defibrinated bovine blood with EHDV-2 (5.5 log10 PFU/ml) or without EHDV-2 (control). Adult survival/longevity, oviposition rates, number of eggs deposited, egg hatch rates (fertility), larval survival, larval stage duration, eclosion rates, and sex-ratios of the progeny were recorded and compared between the two groups. In addition, the progeny (eggs and F1 generation adults) of the EHDV-2 infected females were processed for viral detection through RT-qPCR and plaque assays. Survival/longevity of the blood-fed adults, oviposition rates, number of eggs deposited, larval stage duration, eclosion rates, and sex-ratios were not significantly different between the two groups. However, egg hatch rates were significantly lower in the EHDV-2 infected group (35.8 ± 5.2%) than the uninfected group (74.5 ± 6.8%), but larval survival rates were higher in the EHDV-2 infected group (59.8 ± 4.9%) compared to the control group (34.1 ± 6.5%). EHDV-2 was detected in the eggs (3.4%, 1/29 females tested, Cq value 22.1) and F1 adult progeny (1.7%, 1/58 adults tested, Cq value 23.5) of the orally exposed females through RT-qPCR as well as plaque assays. Our findings suggest that EHDV-2 infection has no major impact on C. sonorensis survival/longevity or oviposition but has a significant negative effect on midge fecundity/fertility. Our study also provides evidence for the vertical transmission of EHDV-2 from an infected adult female to its offspring in C. sonorensis. However, salivary transmission of EHDV-2 from the vertically infected progeny and its significance in the epidemiology of hemorrhagic disease are currently unknown and remain to be examined in further studies. Overall, these findings collectively indicate that Orbivirus infection can negatively affect vector reproduction and that vertical transmission is a probable mechanism of overwintering of EHDV in North America.
Analysis of the effect of HIV-1 subtype-specific Tat polymorphisms on Tat-TAR interaction
Authors: Zhamalbekova Alnara , Abidi Syed Hani 
Published: May 2024

Abstract

Introduction: HIV Tat is responsible for HIV replication activation and interacts with the TAR RNA element for its function. Genetic polymorphisms in the Tat sequence can affect the interaction between Tat and TAR. Previous studies, focusing on HIV subtypes B and C, found that substitutions such as C31S, R57S, and Q63E can alter the binding conformations of Tat and TAR. However, it is not known if polymorphisms in other HIV subtypes can also affect Tat-TAR interactions. This study, therefore, aims to identify subtype-specific polymorphisms in TAR and their effect on Tat-TAR interactions.
Methods: HIV Tat sequences from subtypes A, A1, A2, A3, A4, A6, A7, A8, B, C, D, CRF01_AE, and CRF02_AG was retrieved from the HIV Los Alamos Database. The sequences were aligned and used to generate consensus sequences, subsequently to identify subtype-specific Tat polymorphisms. The sequences were used to generate 3D models of Tat, which were used in molecular docking and molecular dynamic simulations analyses (performed using HDOCK and Desmond tools, respectively) to identify the effect of subtype-specific polymorphisms on binding affinity and interaction with TAR element.
Results: Our results show that subtypes A7, A2, and D showed higher affinity to TAR (with a docking score range of -171.36 to -231.79 and free energy binding range of -111.66 to -123.94 kJ/mol). The subtype-specific polymorphisms that may have increased affinity were Lysine 29 (K29) and Proline 36 (P36). On the contrary, subtype A3 had the weakest binding affinity to TAR with a docking score of -177.78 and free energy of binding value of -54.15 kJ/mol. This lowered affinity may be attributed to subtype-specific polymorphisms such as Alanine 29 (29A) and Proline 59 (59P).
Conclusion: The results of the study suggest that subtype-specific polymorphisms can affect Tat-TAR interactions allowing certain subtypes to interact much more strongly with TAR as compared to others. This finding may have implications in the subtype-specific disease pathogenesis mediated by the Tat protein.
Extracting relevant patterns from GNSS observations to mitigate multipath in RTK deformation monitoring
Authors: Yiyang Jiang , Jinfeng Wang 
Published: May 2024

Abstract

Employing high precise positioning ability, the Global Navigation Satellite Systems (GNSS) could accurately capture subtle deformations in bridges, supplying critical data for structural health monitoring. However, GNSS antennas placed on bridges often encounter multipath interference generated by bridge deck and water surface reflections, compromising the quality of observation data and positioning accuracy. Through the analysis of GNSS data collected from an operational bridge, we discovered a strong correlation between pseudorange multipath and carrier multipath components. Subsequently, through a series of steps including phase adjustment, decorrelation, and resolution, we successfully mitigated the multipath within residuals, and then reconstructed the corrected residuals into displacements; in addition, the method does not require advance deployment of GNSS equipment to collect calibration information. In terms of positioning results, this method improves by 69.8% compared to the original kinematic resolution and by 32% compared to the least squares method. The residuals of each satellite are reduced by 33.2% compared to kinematic resolution, effectively weakening the multipath interference in carrier phase observations and significantly improving positioning accuracy.
Nab-paclitaxel plus platinum versus paclitaxel plus platinum as first-line therapy in patients with metastatic or recurrent cervical cancer
Authors: liu yuan , Fang Shan-shan , Zhao Run-sheng , Liu Bo , Jin Yi-qiang , Li Quan 
Published: May 2024

Abstract

Purpose
This study aimed to assess the efficacy and safety of nanoparticle albumin-bound paclitaxel (nab-paclitaxel) plus platinum versus paclitaxel plus platinum as first-line therapy in patients with metastatic or recurrent cervical cancer.
Methods
Between October 2020 and March 2022, consecutive patients with diagnosed with metastatic or recurrent cervical cancer were retrospectively recruited in our hospital. Fifty-four patients were treated with nab-paclitaxel plus cisplatin or carboplatin. Twenty-four patients were treated with paclitaxel plus cisplatin or carboplatin. The two groups were compared for objective response rate (ORR), progression-free survival (PFS), overall survival (OS), and safety. Univariate Cox proportional hazards regression was used to identify the prognostic factors for survival in patients with cervical cancer.
Results
The nab-paclitaxel group showed a higher ORR (72.2% vs 45.8%; P=0.025) than the paclitaxel group. The median PFS was significantly longer in the nab-paclitaxel group than in the paclitaxel group (12 vs 7 months; P=0.041). The median OS was not reached in the nab-paclitaxel group and 15 months in the paclitaxel group, with no statistical difference (P=0.077). The univariate analysis showed that distant organ metastasis and poor ORR were associated with worse PFS and OS (P<0.05). The most common toxicity was hematological adverse events, including grade 3-4 neutropenia, grade 3 anemia and thrombocytopenia in both groups and no statistical differences were observed between the groups (all P>0.05).
Conclusion
Compared with paclitaxel plus platinum, nab-paclitaxel plus platinum may be an effective and tolerable option as first-line therapy for patients with metastatic or recurrent cervical cancer.
Maximizing Tree Diversity in Cocoa Agroforestry: Taking advantage of Planted, Spontaneous, and Remnant Trees
Authors: Kouamé Isaac Konan , N'Guessan Anny Estelle , Dago Marie Ruth , Kouassi Aimé , N'dja Justin Kassi , Aussenac Raphaël , Guei Stéphane , Jagoret Patrick , Traoré Soulemane , Hérault Bruno 
Published: May 2024

Abstract

Cocoa production stands as the primary driver of biodiversity loss in West Africa. In response to this challenge, agroforestry emerges as a promising solution to restore forest cover and preserve biodiversity in agricultural landscapes. Despite distributions of millions of trees to farmers through various sustainability initiatives, survival rates of planted trees have been disappointing in cocoa fields. However, many non-planted trees currently exist in cocoa fields, including trees from spontaneous regeneration and remnants from previous forests. Our study aims to explore the origins of tree biodiversity in current Ivorian cocoa fields and identify the key socio-environmental determinants. Across 150 cocoa fields, more than 10,000 trees were botanically identified, allowing estimation of diversity and complementarity levels between planted, spontaneous, and remnant cohorts, linked to socio-environmental variables within a Bayesian modelling framework. Results revealed that remnant and spontaneous trees exhibited much greater diversity than planted trees, with the latter showing important complementarity with the other cohorts. Moreover, the diversity of each tree cohort was influenced by a distinct set of environmental factors such as climate and soil composition, highlighting the need to consider the unique history and location of each cocoa field to support agroforestry development. Effective biodiversity maximisation thus relies on preserving remnant trees, vital sources of propagules for natural regeneration, while carefully selecting spontaneous trees and complementary introducing planted trees. Furthermore, recognizing the farmer's identity as a key factor shaping observed biodiversity underscores the importance of raising awareness among farmers and offering tree recognition training, particularly for young trees.
Equilibrium exclusive dealing in oligopoly
Authors: Ziss Steffen 
Published: May 2024

Abstract

This paper considers a setting in which upstream oligopolists delegate the retailing of their differentiated products to a set of undifferentiated retailing agents. The downstream market structure is assumed to consist of a set of independent agents that exclusively sell the product of a single manufacturer and a common agent that sells the product of many manufacturers. A three-stage game is considered. In the first stage the manufacturers choose whether to market their products using an independent agent or the common agent. In the second stage the manufacturers set the terms of the two-part tariff contract offered to their agents. In the final stage agents engage in either differentiated Bertrand or differentiated Cournot competition. If the agents engage in differentiated Cournot competition then the model shows that either all manufacturers employ independent agents, or they all employ the common agent. Which of these two equilibria emerge depend on the degree of product substitutability and on the number of manufacturers. If the agents engage in differentiated Bertrand competition, then a third type of equilibrium also emerges in which some firms employ the common agent and others employ independent agents.
Utility of the Dynamic Duo of Ck19 and Cd56 in Cytological Diagnosis of Thyroid Nodules
Authors: Auzumeedi Srikanth , Philpose Rashmi Tresa , Rajampeta Shalini , Mahek Adeenah , Mohammed Abdul Aleem 
Published: May 2024

Abstract

Purpose: Thyroid nodules are a common finding in everyday clinical practice, however only a small percentage is malignant. A cytologic examination is directed toward establishing a precise diagnosis to distinguish malignant or suspicious nodules requiring surgical treatment from those that can be medically managed. Fine-needle aspiration (FNA) is the first choice for diagnostic evaluation of thyroid nodules. It can be a screening test for a large population of patients with nodules, a small group of whom should be considered for surgery. Various ancillary tests have been proposed to help more accurately classify thyroid FNA to prevent unnecessary surgery.The present study was undertaken to evaluate utility of immunoexpression of CK19, and CD56 in the diagnosis of thyroid nodules.
Methods: This was a prospective study conducted over a period of 4 years, in tertiary care referral hospital from 2014 August to 2018. A total of 108 cases were included in the study and the fine needle aspiration cytology smears were subjected to CK19, CD56 immunocytochemistry in 98 cases for evaluation based on adequacy criteria.
Results: CD56 expression was lost in 96.29% of papillary thyroid carcinomas with a sensitivity of discriminating malignant from benign thyroid lesion was 83.87% and specificity of 94.44%. CK19 expression in PTCs with a sensitivity of 92.0% and specificity of 83.3% was noted.
Conclusion: CK19 and CD56 are useful in differentiating benign and malignant thyroid neoplasms, particularly true for differentiating papillary thyroid carcinoma and benign thyroid lesions. Thus, combination of positive marker (CK19) and negative marker (CD56) increases the accuracy of diagnosis of malignancy in cytology with immunocytochemistry.
A novel recombinant begomovirus isolated in Southeast Asia breaks the Ty-1-mediated resistance in tomato
Authors: Pohan Nadya Syafira , Kanae Okuno , Okabe Shoko , Kesumawati Elly , Koeda Sota 
Published: May 2024

Abstract

Infections by begomoviruses have threatened the global production of multiple crops, including Solanaceae species. Recombination, a phenomenon frequently observed in begomoviruses, has profound effects on virus populations, enabling them to adapt to changing environmental conditions. We previously isolated pepper yellow leaf curl Aceh virus (PepYLCAV) from pepper (Capsicum annuum), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum) plants in Aceh Province, Indonesia and determined it is a recombinant of the widely distributed pepper yellow leaf curl Indonesia virus (PepYLCIV). To compare PepYLCAV with its major putative parent PepYLCIV in terms of virulence, multiple solanaceous plants (Nicotiana benthamiana, pepper, and tomato) were inoculated with the two viruses. Disease symptom severity, growth inhibition, and viral DNA accumulation were greater for the infection with PepYLCAV than for the infection with PepYLCIV. Furthermore, the inoculation with PepYLCAV revealed the Ty-1-mediated resistance of the begomovirus-resistant tomato cultivar was compromised, resulting in moderate symptoms, which were not detected in the plants infected with PepYLCIV. According to the polymerase chain reaction-based re-analysis of samples collected from fields in Indonesia from 2012 to 2019, PepYLCAV rather than PepYLCIV has been the predominant species since 2017. In conclusion, PepYLCAV, which is a novel recombinant bipartite begomovirus that is more virulent and widespread than its major putative parent (PepYLCIV), can overcome the Ty-1-mediated resistance of commercial F1 hybrid tomato cultivars.
Computed Tomography Assessment of the Conus Medullaris and the Dural Sac Termination in Adult Sheep: Anatomical Implications for Lumbosacral and Sacrococcygeal Injections
Authors: Gutiérrez-Bautista Álvaro , García-Roselló Mireia , Redondo José Ignacio , Moreno-Barragán Mar , García-Vitoria Carles 
Published: May 2024

Abstract

This study aimed to provide information about the conus medullaris (CM) and dural sac (DS) termination points in sheep. Thirteen adult Merino-mixed sheep were anaesthetised and underwent lumbosacral computed tomography (CT) myelography. A spinal injection was administered using a Tuohy needle while the sheep were in sternal recumbency. After confirming the presence of cerebrospinal fluid, 0.4 ml kg-1 iodinated contrast media was injected, and a CT scan was conducted. The analysis focused on determining the vertebrae at which the CM and DS ended. The results showed that in eight cases, the conus ended at the first sacral vertebra, while in five sheep, the termination point was identified at the level of the second sacral vertebra. DS termination occurred in the 3rd sacral vertebra in one animal, the 4th sacral vertebra in another sheep, the 1st caudal vertebra in six cases, and the 2nd caudal vertebra in five cases. The findings highlight the need for caution during lumbosacral injections in sheep, as the CM concludes caudally to this space. It is also essential to be aware that the DS persists caudal to the sacrococcygeal space for safe epidural injections in this region.
Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat
Authors: Luo Xiao , Li Yichen , Chen Enlian , Xu Jialu , Zhang Wenhai , Zeng Xiangxiang , Liu Yuansheng 
Published: May 2024

Abstract

Error self-correction is a pivotal first step in the analysis of long-read sequencing data. However, most existing methods for this purpose are primarily tailored for noisy sequencing data with error rates exceeding 5%, often collapsing true variants in repeats and haplotypes. Alternatively, some methods are heavily optimized for PacBio HiFi reads, leaving a gap in methods specifically designed for Nanopore R10 reads basecalled with high accuracy or super accuracy models, which typically have error rates below 2%. Here, we introduce DeChat, a novel approach specifically designed for Nanopore R10 reads. DeChat enables repeat- and haplotype-aware error correction, leveraging the strengths of both de Bruijn graphs and variant-aware multiple sequence alignment to create a synergistic approach. This approach avoids read overcorrection, ensuring that variants in repeats and haplotypes are preserved while sequencing errors are accurately corrected. Benchmarking experiments reveal that reads corrected using DeChat exhibit substantially fewer errors, ranging from several times to two orders of magnitude lower, compared to the current state-of-the-art approaches. Furthermore, the application of DeChat for error correction significantly improves genome assembly across various aspects. DeChat is implemented as a highly efficient, standalone, and user-friendly software and is publicly available at https://github.com/LuoGroup2023/DeChat
Global burden of ischemic stroke attributable to high body-mass index in 204 countries and territories, 1990–2019
Authors: Guo Xiucai , Zhang Ziping , Yin Xueyan , Xu Qirong , Li Feng , Zhu Feng 
Published: May 2024

Abstract

Background
A high body mass index (hBMI) is one of the major risk factors for ischemic stroke (IS), although independent estimates of the global burden and trend of IS attributable to hBMI are unclear.
Methods
Study data was extracted from the Global Burden of Diseases, Injuries, and Risk Factors Study and analyzed by age, sex, year, and geographical location. The socio-demographic index (SDI) and the human development index (HDI) were used as indicators of national socioeconomic status; Geographic distribution and trend were assessed by calculating the estimated annual percentage change (EAPC); Associations between age-standardized death rate (ASMR) or disability-adjusted life years rate (DALY) and socioeconomic status were analyzed.
Results
Deaths and DALYs increased worldwide from 1990 to 2019, with increases of 79.18% for the former and 96.03% for the latter; the ASMR and ASDR decreased, with ASMR and ASDR-related EAPCs of -1.06 (95% CI: -1.19–-0.92) and − 0.46 (95% CI: -0.60–-0.35), respectively; Women had a higher number of deaths and DALYs, and the majority of deaths and DALYs were shared by those aged ≥ 70. The highest burden rates were shared by Eastern Europe, Central Asia and North Africa and the Middle East; ASMR-related EAPC was associated with ASMR in 1990 (R=-0.36, P < 0.001) and SDI in 2019 in different countries (R=-0.67, P < 0.001), respectively; these patterns were similar to what ASDR had; the HDI in 2019 was associated with ASMR-related EAPC (R=-0.72, P < 0.001) and ASDR-related EAPC in different countries (R= -0.71, P < 0.001).
Conclusions
The number of deaths and DALY of ischemic stroke attributable to hBMI worldwide had increased substantially from 1990 to 2019. Successful population-wide initiatives targeting hBMI may mitigate a wide range of burdens on this disease. Taking into account variations in SDI burden, future prevention and control strategies must be developed and implemented according to country-specific development status.
Non-resonant invariant foliations of quasi-periodically forced systems
Authors: Szalai Robert 
Published: May 2024

Abstract

We show the existence and uniqueness of invariant foliations about invariant tori in analytic discrete-time dynamical systems. The parametrisation method is used prove the result. Our theory is a foundational block of data-driven model order reduction, that can only be carried out using invariant foliations. The theory is illustrated by two mechanical examples, where instantaneous frequencies and damping ratios are calculated about the invariant tori.
MSC codes 34A34 34C45 37M21 37C86
The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion
Authors: Zhang Jianjun , Hu Xin , Zhu Bo , Vokes Natalie , Fukuoka Junya , Alvarez Frank Rojas , Heeke Simon , Moreira Andre , Solis Luisa , Haymaker Cara , Velcheti Vamsidhar , Sterman Daniel , Pass Harvey , Cheng Chao , Lee Jack , Zhang Jianhua , Wei Zhubo , Wu Jia , Li Xiuning , Ostrin Edwin , Toumazis Iakovos , Gibbons Don , Su Dan , Fukuoka Junya , Antonoff Mara , Gerber David , Li Chenyang , Kadara Humam , Wang Linghua , Davis Mark , Heymach John , Hanash Samir , Wistuba Ignacio , Dubinett Steven , Alexandrov Ludmil , Lippman Scott , Spira Avrum , Futreal Andrew , Reuben Alexandre 
Published: May 2024

Abstract

Studying lung adenocarcinoma (LUAD) early carcinogenesis is challenging, primarily due to the lack of LUAD precursors specimens. We amassed multi-omics data from 213 LUAD and LUAD precursors to identify molecular features underlying LUAD precancer evolution. We observed progressively increasing mutations, chromosomal aberrations, whole genome doubling and genomic instability from precancer to invasive LUAD, indicating aggravating chromosomal instability (CIN). Telomere shortening, a crucial genomic alteration linked to CIN, emerged at precancer stage. Moreover, later-stage lesions demonstrated increasing cancer stemness and decreasing alveolar identity, suggesting epithelial de-differentiation during early LUAD carcinogenesis. The innate immune cells progressively diminished from precancer to invasive LUAD, concomitant with a gradual recruitment of adaptive immune cells (except CD8+ and gamma-delta T cells that decreased in later stages) and upregulation of numerous immune checkpoints, suggesting LUAD precancer evolution is associated with a shift from innate to adaptive immune response and immune evasion mediated by various mechanisms.