bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of Tuberculosis After Achieving Human Immunodeficiency Virus Virological Suppression on Antiretroviral Therapy: A Danish Nationwide Prospective Cohort Study
Authors: Virdee Amrit Kaur , Knudtzen Fredrikke Christie , Llibre Josep M , Omland Lars Haukali , Obel Niels , Stærke Nina Breinholt , Åhsberg Johanna , Ørsted Iben , Kronborg Gitte , Mohey Rajesh , Montejo Maria del Pilar Fernandez , Johansen Isik Somuncu , Martin-Iguacel Raquel 
Published: October 2024

Abstract

Background
In countries with low tuberculosis burden, the risk of tuberculosis in people living with human immunodeficiency virus (HIV; PWH) once HIV virological suppression is achieved is not fully understood.

Methods
In a nationwide cohort, we included all adult PWH from the Danish HIV Cohort initiating antiretroviral therapy (ART) (1995–2017) without prior tuberculosis disease. We used Kaplan–Meier estimation and Poisson regression to calculate the tuberculosis incidence rate (IR) after 6 months of ART, along with associated risk factors and mortality rates.

Results
Among 6849 PWH initiating ART (median follow-up, 7.4 years), 84 developed tuberculosis (IR, 1.4/1000 person-years [PY]), 54 of them &gt;6 months after ART initiation (IR, 0.97/1000 PY [95% confidence interval [CI]: 1.17–1.79); 1.95/1000 PY [1.34–2.76] in non–Danish born, 0.36/1000 PY [.21–.62] in Danish born without injection drug use (IDU), and 2.95/1000 PY [1.53–5.66] in Danish born with IDU). Danish-born individuals with suppressed viremia and no IDU or known tuberculosis exposures had the lowest risk (IR, 0.05/1000 PY). In the adjusted analysis, being non–Danish born (adjusted IR ratio, 4.27 [95% CI: 2.36–7.72]), IDU (4.95 [2.55–9.62]), and previous AIDS-defining events (2.05 [1.06–3.94]) raised the tuberculosis risk, while suppressed HIV RNA levels (0.58 [.34–.99]) reduced it. The overall mortality rate for HIV/tuberculosis coinfected after ART was high, at 48.9/1000 PY (95% CI: 30.4–78.7).

Conclusions
The tuberculosis risk remains elevated in PWH beyond 6 months after ART initiation, especially among migrants, those with IDU, those without suppressed HIV RNA, and those exposed to areas highly endemic for tuberculosis or with social risk determinants of health. Conversely, PWH without these risk factors have a tuberculosis risk similar to the general population and would not require targeted tuberculosis screening strategies.
Superiority Trials in Invasive Aspergillosis: A Harsh Reality Check With the IA-DUET (HOVON502) Trial
Authors: Lamberink Hanne , Huygens Sammy , Aerts Robina , Lagrou Katrien , van Leeuwen-Segarceanu Elena , Lodewyck Tom , Nieuwenhuizen Laurens , Corsten Maarten F , Moors Ine , Servais Sophie , De Greef Julien , Hites Maya , Demandt Astrid , Schauwvlieghe Alexander , Maertens Johan , Rijnders Bart 
Published: October 2024

Abstract
The IA-DUET study aimed to compare azole-echinocandin combination therapy with azole monotherapy for invasive aspergillosis. Recruitment was hindered by patient ineligibility, competing studies, and guidelines favoring combination therapy when azole resistance was unknown. The low IA-attributable mortality suggests future trials may benefit from cluster randomization or composite endpoints to enhance efficiency.
Clonality Determination by Detecting Unmodified Monoclonal Serum Free Light Chains Using On-Probe Extraction Coupled with Liquid Chromatography-High-Resolution Mass Spectrometry
Authors: Yeung Priscilla S W , Liu Yajing , Yang Samuel , Ruan Ashley , Kerr Christina R , Wong Carolyn V , Shi Run-Zhang , Iberri David J , Luo Ruben Y 
Published: October 2024

Abstract

Background
Serum free light chains (FLCs) are an essential clinical biomarker for the diagnosis and monitoring of patients with plasma cell neoplasms. The current widely used immunoassay methods quantify total serum FLCs, which include monoclonal FLCs as well as FLCs in the polyclonal background. Patients with chronic diseases, inflammatory disorders, or renal dysfunction can have elevated total FLCs that lead to ambiguous results. These patients may benefit from a direct measurement of monoclonal FLCs. The purpose of this study was to develop a method that couples on-probe extraction (OPEX) with liquid chromatography-high-resolution mass spectrometry (LC-HR-MS), abbreviated to OPEX-MS, to directly determine the clonality of FLCs.

Methods
OPEX immunocapture was performed using microprobes loaded with anti-kappa or anti-lambda light chain antibodies. Captured proteins were separated by reversed-phase LC and analyzed by HR-MS.

Results
Four cohorts of samples from unique patients were tested based on immunoassay FLC results. The LC-HR-MS analysis in the OPEX-MS method provides both a unique retention time along with deconvoluted masses of FLC monomers and dimers for each clone. The study found that 16 out of 49 (33%) kappa FLC elevated samples as well as 83 out of 100 (83%) dual kappa and lambda FLC elevated samples did not have monoclonal FLCs, which is consistent with the knowledge that there is often no clonal population in samples with mildly elevated FLC immunoassay results.

Conclusions
The OPEX-MS method can serve as a complementary approach to directly determine clonality in patients with difficult-to-interpret FLC immunoassay results.
Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes
Authors: Guo Shuming , Huang Zhuo , Zhang Yanming , He Yukun , Chen Xiangju , Wang Wenjuan , Li Lansheng , Kang Yu , Gao Zhancheng , Yu Jun , Du Zhenglin , Chu Yanan 
Published: October 2024

Abstract
Whole-exome sequencing (WES) data are frequently used for cancer diagnosis and genome-wide association studies (GWAS), based on high-coverage read mapping, informative variant calling, and high-quality reference genomes. The center position of the currently used genome assembly, GRCh38, is now challenged by two newly published telomere-to-telomere (T2T) genomes, T2T-CHM13 and T2T-YAO, and it becomes urgent to have a comparative study to test population specificity using the three reference genomes based on real case WES data. Here, we report our analysis along this line for 19 tumor samples collected from Chinese patients. The primary comparison of the exon regions among the three references reveals that the sequences in up to ∼ 1% of target regions in T2T-YAO are widely diversified from GRCh38 and may lead to off-target in sequence capture. However, T2T-YAO still outperforms GRCh38 by obtaining 7.41% of more mapped reads. Due to more reliable read-mapping and closer phylogenetic relationship with the samples than GRCh38, T2T-YAO reduces half of variant calls of clinical significance which are mostly benign, while maintaining sensitivity in identifying pathogenic variants. T2T-YAO also outperforms T2T-CHM13 in reducing calls of Chinese-specific variants. Our findings highlight the critical need for employing population-specific reference genomes in genomic analysis to ensure accurate variant analysis and the significant benefits of tailoring these approaches to the unique genetic background of each ethnic group.
Natural variation in MdNAC5 contributes to fruit firmness and ripening divergence in apple
Authors: Liu Li , Wang Yuanji , Guo Jianhua , Han Ziqi , Yu Kaixuan , Song Yaxiao , Chen Hongfei , Gao Hua , Yang Yazhou , Zhao Zhengyang 
Published: October 2024

Abstract
Fruit firmness is an important trait for characterizing the quality and value of apple. It also serves as an indicator of fruit maturity, as it is a complex trait regulated by multiple genes. Resequencing techniques can be employed to elucidate variations in such complex fruit traits. Here, the whole genomes of 294 F1 hybrids of ‘Fuji’ and ‘Cripp's Pink’ were resequenced, and a high-density binmap was constructed using 5014 bin markers with a total map distance of 2213.23 cM and an average map distance of 0.44 cM. Quantitative trait loci (QTLs) of traits related to fruit were mapped, and an A-T allele variant identified in the coding region of MdNAC5 was found to potentially regulate fruit firmness and ripening. The overexpression of MdNAC5A resulted in higher production of methionine and 1-aminocyclopropanecarboxylic acid compared to MdNAC5T, leading to reduced fruit firmness and accelerated ripening in apples and tomatoes. Furthermore, the activities of MdNAC5A and MdNAC5T were enhanced through their differential binding to the promoter regions of MdACS1 and MdERF3. Spatial variations in MdNAC5A and MdNAC5T caused changes in MdACS1 expression following their interaction with MdERF3. Ultimately, utilizing different MdNAC5 alleles offers a strategy to manipulate fruit firmness in apple breeding.
Bounded Pluriharmonic Functions and Holomorphic Functions on Teichmüller Space
Authors: Miyachi Hideki 
Published: October 2024

Abstract
In this paper, we discuss the boundary behavior of bounded pluriharmonic functions and bounded holomorphic functions on the Teichmüller space. We will show a version of the Fatou theorem that every bounded pluriharmonic function admits the radial limits along the Teichmüller geodesic rays, and a version of the F. and M. Riesz theorem that the radial limit of a non-constant bounded holomorphic function is not constant on any non-null measurable set on the Bers boundary in terms of the pluriharmonic measure. As a corollary, we obtain the non-ergodicity of the action of the Torelli group for a closed surface of genus $g\ge 2$ on the space of projective measured foliations.
Armed attacks against merchant vessels: ‘Looking behind the Flag’ to find the victim State
Authors: Cavalcanti de Mello Filho Eduardo 
Published: October 2024

Abstract
This article argues that a non-flag State can be considered the victim of an armed attack against one or more merchant vessels and thus entitled to the right of self-defence under Article 51 of the Charter of the United Nations. This argument gains momentum in light of the recent Houthi attacks in the Red Sea against ships with diverse nationalities. Traditionally, attacks on merchant vessels have been considered attacks on the flag State due to the latter’s economic interests in the vessels. However, given the prevalence of open ship registries, today over 70 per cent of world tonnage is registered under foreign flags. Consequently, the jus ad bellum concerning armed attacks against merchant vessels necessitates a reassessment. The first section of this article revisits the traditional understanding that only the flag State can be considered the victim of an armed attack on merchant vessels. Hinting at the popularization of open registries, this article then clarifies how the laws of the sea and naval warfare have dealt with this phenomenon. It is remarked that ‘looking behind the flag’, especially in naval warfare, has become inevitable. This realization is then transposed to the jus ad bellum. In doing so, this article examines key references concerning armed attacks against merchant vessel: the Oil Platforms judgment by the International Court of Justice and the 1974 Definition of Aggression. This article also engages with directly relevant State practice. Ultimately, this article demonstrates that these references support the need for the reassessment advanced here.
Potential global distributions of an important aphid pest, Rhopalosiphum padi: insights from ensemble models with multiple variables
Authors: Yang Mingsheng , Yu Jiayi , Wang Yongli , Dewer Youssef , Huo Yiqi , Wang Zhengbing , Zhang Hongfei , Shao Xinliang , Ma Feilong , Shangguan Xinxin , Xu Kedong , Shang Suqin , Ma Keshi 
Published: October 2024

Abstract
Species distribution modeling is extensively used for predicting potential distributions of invasive species. However, an ensemble modeling approach has been less frequently used particularly pest species. The bird cherry-oat aphid Rhopalosiphum padi L. is an important pest of wheat (Triticum aestivum L.) worldwide and causes 30% yield losses. Here, we developed a series of ensemble models with multiple variables to predict the habitat suitability of this pest at a global scale. The current suitable habitat for R. padi is mainly distributed in East Asia, South Asia, Europe, southern North America, southern South America, eastern Australia, and New Zealand. The highly suitable regions are primarily distributed in east of China, Japan, most of North America, southeastern South America, most of Europe, and southeastern edge of Australia. In future scenarios, the suitable habitats will undergo a significant contraction overall northward, and no moderately nor highly suitable habitats are predicted for this pest in other areas. Our findings indicate that a high risk of R. padi outbreaks currently exists for the highly suitable regions mentioned above, especially with wheat cultivation, but the capacity of R. padi to cause such outbreaks will weaken in the future. Climate-associated factors are significantly more important than land use, elevation and host-plant factors, and the BIO11 (mean temperature of the coldest quarter), in particular, predominated in shaping projections of R. padi’s distribution. The predicted distribution pattern and key ecological factors affecting this pattern identified herein could provide important guidance for developing management policies targeting this economically important pest.
The Conditional Autoregressive F-Riesz Model for Realized Covariance Matrices
Authors: Opschoor Anne , Lucas André , Rossini Luca 
Published: October 2024

Abstract
We introduce a new model for the dynamics of fat-tailed (realized) covariance-matrix-valued time-series using the F-Riesz distribution. The model allows for heterogeneous tail behavior across the coordinates of the covariance matrix via two vector-valued degrees of freedom parameters, thus generalizing the familiar Wishart and matrix-F distributions. We show that the filter implied by the new model is invertible and that a two-step targeted maximum likelihood estimator is consistent. Applying the new F-Riesz model to U.S. stocks, both tail heterogeneity and tail fatness turn out to be empirically relevant: they produce significant in-sample and out-of-sample likelihood increases, ex-post portfolio standard deviations that are in the global minimum variance model confidence set, and economic differences that are either in favor of the new model or competitive with a range of benchmark models.
Realized Random Graphs, with an Application to the Interbank Network
Authors: Buccheri Giuseppe , Mazzarisi Piero 
Published: October 2024

Abstract
We introduce a new inferential methodology for dynamic network models driven by latent state variables. The main idea is to obtain a noisy representation of the state variables dynamics by computing a sequence of cross-sectional estimates of the network model at each point in time. The dynamic modeling of these cross-sectional estimates, that we name realized random graphs, transforms the original nonlinear state-space network model into a linear time-series model that can be easily estimated. Under the assumption of a mixed-membership blockmodel structure, the model parameters and the unobservable state variables can be consistently estimated when both the size of the network and the time-series length are large. By allowing for an extremely rich parameterization of the model in high dimensions, the proposed methodology describes the heterogeneous topology of real-world networks. We corroborate our findings by using this novel framework to estimate and forecast the dynamic common factors driving the evolution of the Italian electronic market of interbank deposits, and we show that the interbank lending rate is a key factor determining the network topology.
Tilianin obtained from Agastache mexicana inhibits monoamine oxidase and modifies depressive behavior in rats
Authors: Rodríguez-Wilson Edgar , Estrada-Soto Samuel , Rubio-Osornio Moisés , Tristán-López Luis , Navarrete-Vázquez Gabriel , Gutiérrez-Hernández Abraham , Montes Sergio 
Published: October 2024

Abstract

Background
Agastache mexicana is used in traditional medicine to treat anxiety, insomnia, pain, among others. In a previous study, the methanolic extract exerted anxiolytic and sedative effects, as observed behaviorally, associated with one of its major components, tilianin.

Objective
To assess the effect produced by the extracts and tilianin obtained from Agastache mexicana on depressive-induced behavior model and on the activity of monoamine oxidases (MAOs).

Methods
The depression experimental model consisted of the forced swimming test in rats. MAOs activity was evaluated in cortex and hippocampus from the tilianin and Agastache extracts treated rats using specific inhibitors for each isoform. The quantification of monoamines was carried out using an High Performance Liquid Chromatography method.

Results
An increase in the swimming time was observed in rodents treated with doses of 16 (226.6 ± 5.5 seconds) and 50 mg/kg (237.8 ± 5.7 seconds) of tilianin, methanolic (260.4 ± 3 seconds), and hydroalcoholic extracts (249.6 ± 2.6 seconds) at 100 mg/kg. MAOs activity was significantly decreased in brain tissue from animals treated with 16 and 50 mg/kg of tilianin, methanolic, and hydroalcoholic extracts at 100 mg/kg.

Conclusions
The tilianin effect on monoamine oxidases inhibition is confirmed, suggesting its potential use in the treatment of certain neurological disorders.
Surgical resection of late extrahepatic metastasis of hepatocellular carcinoma 11 years after initial diagnosis: case report and literature review
Authors: Baz Carolina , Nudotor Richard , Ian Bussey , Garg Ravin , Gibson Glen 
Published: October 2024

Abstract
Hepatocellular carcinoma (HCC) is the second most common cause of cancer mortality worldwide. Liver resection is considered the pillar of curative treatment, although it is usually reserved for early-stage localized disease since the presence of metastases carries a poor prognosis. Despite advances in imaging, surgical techniques, and systemic therapy, the recurrence rate after oncologic resection remains high, even with localized disease. In the setting of extrahepatic HCC recurrence, there is no consensus regarding the best treatment strategy. Nevertheless, while the development of metastasis can be considered an expression of systemic disease, surgical resection may prolong survival. We report the case of a patient with a history of an oncologic hepatic resection for HCC, successfully treated with resection of an isolated peritoneal cavity metastasis. This case demonstrates that an aggressive approach involving the resection of extrahepatic HCC metastasis should be considered in select patients with the intention of achieving prolonged survival.
Successful surgical repair of a huge left ventricular pseudoaneurysm after repair of left ventricular rupture during mitral valve replacement
Authors: Hayashi Kyoka , Ushioda Ryohei , Maruoka Jun , Shimizu Kaname , Shirakura Kentaro , Mochizuki Nobuhiro , Setogawa Yuki , Okubo Ryo , Hiroyuki Miyamoto , Takahashi Shougo , Kunioka Shingo , Tsutsui Masahiro , Hiroyuki Kamiya 
Published: October 2024

Abstract
A 78-year-old man underwent pericardial patch repair for left ventricular (LV) rupture during mitral valve replacement. After the first operation, a huge (&gt;10 cm) LV pseudoaneurysm was detected, necessitating reoperation. LV rupture is a rare but often fatal complication of mitral valve replacement. Although repair of LV rupture during mitral valve replacement has been reported, the development of pseudoaneurysm after such repair is exceedingly rare. In this case, we successfully treated a huge LV pseudoaneurysm using two pericardial patches to sandwich the rupture hole from the inside.
Multi-scale phenotyping of senescence-related changes in roots of rapeseed in response to nitrate limitation
Authors: James Maxence , Masclaux-Daubresse Céline , Balliau Thierry , Marmagne Anne , Chardon Fabien , Trouverie Jacques , Etienne Philippe 
Published: October 2024

Abstract
Root senescence remains largely unexplored. In this study, the time-course of the morphological, metabolic, and proteomic changes occurring with root aging were investigated, providing a comprehensive picture of the root senescence program. We found novel senescence-related markers for the characterization of the developmental stage of root tissues. The rapeseed root system is unique in that it consists of the taproot and lateral roots. Our study confirmed that the taproot, which transiently accumulates large quantities of starch and proteins, is specifically dedicated to nutrient storage and remobilization, while the lateral roots are mainly dedicated to nutrient uptake. Proteomic data from the taproot and lateral roots highlighted the different senescence-related events that control nutrient remobilization and nutrient uptake capacities. Both the proteome and enzyme activities revealed senescence-induced proteases and nucleotide catabolic enzymes that deserve attention as they may play important roles in nutrient remobilization efficiency in rapeseed roots. Taking advantage of publicly available transcriptomic and proteomic data on senescent Arabidopsis leaves, we provide a novel lists of senescence-related proteins specific or common to root organs and/or leaves.
Wanted dead or alive: epistemic logic for impure simplicial complexes
Authors: van Ditmarsch Hans , Kuznets Roman 
Published: October 2024

Abstract
We propose a logic of knowledge for impure simplicial complexes. Impure simplicial complexes represent synchronous distributed systems under uncertainty over which processes are still active (are alive) and which processes have failed or crashed (are dead). Our work generalizes the logic of knowledge for pure simplicial complexes, where all processes are alive, by Goubault et al. In our semantics, given a designated face in a complex, a formula can only be true or false there if it is defined. The following are undefined: dead processes cannot know or be ignorant of any proposition, and live processes cannot know or be ignorant of factual propositions involving processes they know to be dead. The semantics are therefore three-valued, with undefined as the third value. We propose an axiomatization that is a version of the modal logic S5. We also show that impure simplicial complexes correspond to certain Kripke models where agents’ accessibility relations are equivalence relations on a subset of the domain only.