bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium tuberculosis
epidemiology in Oman: whole-genome sequencing uncovers transmission pathways
Authors: Babiker Hamza A , Al-Jardani Amina , Al-Azri Saleh , Petit Robert A. , Saad Eltaib , Al-Mahrouqi Sarah , Mohamed Reham A.H. , Al-Hamidhi Salama , Balkhair Abdullah A. , Al Kharusi Najma , Al Balushi Laila , Al Zadjali Samiya , Pérez-Pardal Lucía , Beja-Pereira Albano , Babiker Ahmed 
Published: September 2023

ABSTRACT

Tuberculosis (TB) originating from expatriates that hail from high TB-burden countries is hypothesized to play a role in continued TB transmission in Oman. Here, we used whole-genome sequencing (WGS) to assess national TB transmission dynamics. The annual incidence per 100,000 population per year was calculated for nationals and expatriates. A convenience sample of
Mycobacterium tuberculosis
(MTB) isolates from 2018 to 2019 was sequenced and analyzed with publicly available TB sequences from Bangladesh, Tanzania, the Philippines, India, and Pakistan. Relatedness was assessed by generating core-genome single nucleotide polymorphism (SNP) distances. The incidence of TB was five cases per 100,000 persons in 2018 and seven cases per 100,000 persons in 2020 (

R
2

= 0.34,
P
= 0.60). Incidence among nationals was 3.9 per 100,000 persons in 2018 and 3.5 per 100,000 persons in 2020 (

R
2

= 0.20
, P
= 0.70), and incidence among expatriates was 7.2 per 100,000 persons in 2018 and 12.7 per 100,000 persons in 2020 (

R
2

= 0.74,
P
= 0.34). Sixty-eight local MTB isolates were sequenced and analyzed with 393 global isolates. Isolates belonged to nine distinct spoligotypes. Two isolates, originating from an expatriate and an Omani national, were grouped into a WGS-based cluster (SNP distance < 12), which was corroborated by an epidemiological investigation. Relatedness of local and global isolates (SNP distance < 100) was also seen. The relatedness between MTB strains in Oman and those in expatriate countries of origin can aid inform TB control policy. Our results provide evidence that WGS can complement epidemiological analysis to achieve the End TB strategy goal in Oman.

IMPORTANCE

Tuberculosis (TB) incidence in Oman remains above national program control targets. TB transmission originating from expatriates from high TB-burden countries has been hypothesized to play a role. We used whole-genome sequencing (WGS) to assess TB transmission dynamics between expatriates and Omani nationals to inform TB control efforts. Available
Mycobacterium tuberculosis
isolates from 2018 to 2019 underwent WGS and analysis with publicly available TB sequences from Bangladesh, the Philippines, India, and Pakistan to assess for genetic relatedness. Our analysis revealed evidence of previously unrecognized transmission between an expatriate and an Omani national, which was corroborated by epidemiological investigation. Analysis of local and global isolates revealed evidence of distant relatedness between local and global isolates. Our results provide evidence that WGS can complement classic public health surveillance to inform targeted interventions to achieve the End TB strategy goal in Oman.
Lactobacillus gallinarum-derived metabolites boost anti-PD1 efficacy in colorectal cancer by inhibiting regulatory T cells through modulating IDO1/Kyn/AHR axis
Authors: Fong Winnie , Li Qing , Ji Fenfen , Liang Wei , Lau Harry Cheuk Hay , Kang Xing , Liu Weixin , To Kenneth Kin-Wah , Zuo Zhong , Li Xiaoxing , Zhang Xiang , Sung Joseph JY , Yu Jun 
Published: September 2023

ObjectiveGut microbiota is a key player in dictating immunotherapy response. We aimed to explore the immunomodulatory effect of probioticLactobacillus gallinarumand its role in improving anti-programmed cell death protein 1 (PD1) efficacy against colorectal cancer (CRC).DesignThe effects ofL. gallinarumin anti-PD1 response were assessed in syngeneic mouse models and azoxymethane/dextran sulfate sodium-induced CRC model. The change of immune landscape was identified by multicolour flow cytometry and validated by immunohistochemistry staining and in vitro functional assays. Liquid chromatography-mass spectrometry was performed to identify the functional metabolites.ResultsL. gallinarumsignificantly improved anti-PD1 efficacy in two syngeneic mouse models with different microsatellite instability (MSI) statuses (MSI-high for MC38, MSI-low for CT26). Such effect was confirmed in CRC tumourigenesis model.L. gallinarumsynergised with anti-PD1 therapy by reducing Foxp3+CD25+regulatory T cell (Treg) intratumoural infiltration, and enhancing effector function of CD8+T cells.L. gallinarum-derived indole-3-carboxylic acid (ICA) was identified as the functional metabolite. Mechanistically, ICA inhibited indoleamine 2,3-dioxygenase (IDO1) expression, therefore suppressing kynurenine (Kyn) production in tumours. ICA also competed with Kyn for binding site on aryl hydrocarbon receptor (AHR) and antagonised Kyn binding on CD4+T cells, thereby inhibiting Treg differentiation in vitro. ICA phenocopiedL. gallinarumeffect and significantly improved anti-PD1 efficacy in vivo, which could be reversed by Kyn supplementation.ConclusionL. gallinarum-derived ICA improved anti-PD1 efficacy in CRC through suppressing CD4+Treg differentiation and enhancing CD8+T cell function by modulating the IDO1/Kyn/AHR axis.L. gallinarumis a potential adjuvant to augment anti-PD1 efficacy against CRC.
Longitudinal radiological follow-up of individual level non-ischemic cerebral enhancing lesions following endovascular aneurysm treatment
Authors: Guetarni Zakaria , Bernard Remy , Boulouis Grégoire , Labeyrie Marc-Antoine , Biondi Alessandra , Velasco Stéphane , Saliou Guillaume , Bartolini Bruno , Daumas-Duport Benjamin , Bourcier Romain , Janot Kevin , Herbreteau Denis , Michelozzi Caterina , Premat Kevin , Redjem Hocine , Escalard Simon , Bricout Nicolas , Thouant Pierre , Arteaga Charles , Pierot Laurent , Tahon Florence , Boubagra Kamel , Ikka Leon , Chabert Emmanuel , Lenck Stephanie , Guédon Alexis , Consoli Arturo , Saleme Suzana , Forestier Géraud , Di Maria Federico , Ferré Jean-Christophe , Anxionnat René , Eugene Francois , Kerleroux Basile , Dargazanli Cyril , Sourour Nader-Antoine , Clarençon Frédéric , Shotar Eimad 
Published: September 2023

BackgroundNon-ischemic cerebral enhancing (NICE) lesions following aneurysm endovascular therapy are exceptionally rare, with unknown longitudinal evolution.ObjectiveTo evaluate the radiological behavior of individual NICE lesions over time.MethodsPatients included in a retrospective national multicentric inception cohort were analyzed. NICE lesions were defined, using MRI, as delayed onset punctate, nodular, or annular foci enhancements with peri-lesion edema, distributed in the vascular territory of the aneurysm treatment, with no other confounding disease. Lesion burden and the longitudinal behavior of individual lesions were assessed.ResultsTwenty-two patients were included, with a median initial lesion burden of 36 (IQR 17–54) on the first MRI scan. Of the 22 patients with at least one follow-up MRI scan, 16 (73%) had new lesions occurring mainly within the first 200 weeks after the date of the procedure. The median number of new lesions per MRI was 6 (IQR 2–16). Among the same 22 patients, 7 (32%) had recurrent lesions. The median persistent enhancement of a NICE lesion was 13 weeks (IQR 6–30). No factor was predictive of early regression of enhancement activity with lesion regression kinetics mainly being patient-dependent.ConclusionsThe behavior of individual NICE lesions was found to be highly variable with an overall patient-dependent regression velocity.
Feasibility and workflow analysis of IV-DSA-based augmented reality-guided brain arteriovenous malformation resection in a hybrid operating room: i-Flow tailored method
Authors: Huang Chih-Wei , Lee Chung-Hsin , Chung Kai-Chen , Tsuei Yuang-Seng 
Published: September 2023

Augmented reality (AR) has emerged as a promising technology in various medical fields.1 2 In the context of brain arteriovenous malformation (bAVM) surgery, AR offers the potential to enhance surgical visualization and improve procedural accuracy.3 4 5 6 This report aims to explore the application of digital subtraction angiography (DSA) from an IV contrast injection (IV-DSA) in AR-guided resection of bAVMs in a neurosurgical hybrid operating room.The workflow of IV-DSA-based AR-guided surgery for the resection of bAVMs consists of four main components: (1) acquiring source images through i-Flow tailored or multiphase scans (Siemens, Germany); (2) labelling targets in the workstation using Smartbrush software (Brainlab, Westchester, Illinois, USA); (3) using the Brainlab Curve navigation system; and (4) merging microscopic AR fusion using Zeiss Kinevo (AG, Germany). In video 1 we show the entire workflow and introduce i-Flow tailored IV-DSA data acquisition in the hybrid operating room. In summary, IV-DSA-based augmented reality is an innovative technique for bAVM surgery.Video 1-i-flow tailored iv-DSA
Genotype and environment interaction on the wood quality of Eucalyptus spp. for energy purposes
Authors: da Cunha Thammi Queuri Gomes , Lima Pedro Augusto Fonseca , Santos Alyne Chaveiro , Novaes Evandro , Sette-Junior Carlos Roberto 
Published: September 2023

The objective of this study was to evaluate the wood chemical and energetic characteristics of Eucalyptus spp. clones planted in three sites in the Midwest of Brazil. Thus, five clones from Eucalyptus spp. were planted in different sites aiming to determine the qualitative characteristics of the wood resulting from the variation in the tree growth environment and the genetic material. The same clones were planted in the three sites to determine the genotype × environment interaction. The trees were then sampled at 5 years after planting for their physical–chemical and energetic characterization. The results showed that the wood characteristics vary in different proportions according to the clone, just as the growth environment of the trees alters the behavior of the clones for the same characteristics. The edaphic variables affected the wood characteristics, inferring that the water content in the soil has more effect on the wood properties than the water content in the air, mainly on wood basic density. The results of this study indicate that using the appropriate genotype related to the environment conditions determines the wood characteristics, since the wood properties are strongly influenced by the edaphoclimatic variables.
The impact of ionizing radiation compared to drug-induced immunological changes
Authors: Hussien Soha M. 
Published: September 2023

Ionizing radiation (IR) activates several signaling pathways. This study shows the impact of acute low-dose IR on crucial cytokines involved in cell-mediated immunity. The immunomodulatory effects of 0.25 and 0.5 Gray (Gy) gamma rays and standard immunomodulatory drugs (cyclophosphamide) on blood counts and significant pro-inflammatory cytokines implicated in various inflammatory conditions were tested in 20 rats. Examined was the effect of acute low doses on critical cytokines, which could be utilized as an alternative to current immunosuppressive drugs. One day post-irradiation, serum levels of interferon-gamma (INF-γ), tumor necrosis factor-alpha, and interleukin-2/1-beta were measured. A 0.25 Gy exposure did not affect the detected cytokines or blood cell count compared to the nonirradiated group. On the other hand, 0.5 Gy raises the majority of the immunologically examined cytokines except for INF-γ. Except for INF-γ, cyclophosphamide reduces all of the cytokines examined. As a result, low-dose IR has a less negative influence on essential inflammatory cytokines, permitting its use. More research is needed to determine how low amounts could be used in different immunological disorders.
Simulation and background characterisation of the SABRE South experiment
Authors: Barberio E. , Baroncelli T. , Bignell L. J. , Bolognino I. , Brooks G. , Dastgiri F. , D’Imperio G. , Di Giacinto A. , Duffy A. R. , Froehlich M. , Fu G. , Gerathy M. S. M. , Hill G. C. , Krishnan S. , Lane G. J. , Lawrence G. , Leaver K. T. , Mahmood I. , Mariani A. , McGee P. , McKie L. J. , McNamara P. C. , Mews M. , Melbourne W. J. D. , Milana G. , Milligan L. J. , Mould J. , Nuti F. , Pettinacci V. , Scutti F. , Slavkovská Z. , Spinks N. J. , Stanley O. , Stuchbery A. E. , Taylor G. N. , Tomei C. , Urquijo P. , Vignoli C. , Williams A. G. , Zhong Y. Y. , Zurowski M. J. 
Published: September 2023

AbstractSABRE (Sodium iodide with Active Background REjection) is a direct detection dark matter experiment based on arrays of radio-pure NaI(Tl) crystals. The experiment aims at achieving an ultra-low background rate and its primary goal is to confirm or refute the results from the DAMA/LIBRA experiment. The SABRE Proof-of-Principle phase was carried out in 2020–2021 at the Gran Sasso National Laboratory (LNGS), in Italy. The next phase consists of two full-scale experiments: SABRE South at the Stawell Underground Physics Laboratory, in Australia, and SABRE North at LNGS. This paper focuses on SABRE South and presents a detailed simulation of the detector, which is used to characterise the background for dark matter searches including DAMA/LIBRA-like modulation. We estimate an overall background of 0.72 cpd/kg/$$\hbox {keV}_{\hbox {{ee}}}$$

keV
ee

in the energy range 1–6 $$\hbox {keV}_{\hbox {{ee}}}$$

keV
ee

primarily due to radioactive contamination in the crystals. Given this level of background and considering that the SABRE South has a target mass of 50 kg, we expect to exclude (confirm) DAMA/LIBRA modulation at $$4~(5)\sigma $$

4

(
5
)
σ

within 2.5 years of data taking.
Outcomes of Revision Unlinked Total Elbow Arthroplasty for Rheumatoid Elbow
Authors: KODAMA Akira , MIZUSEKI Takaya , ADACHI Nobuo 
Published: September 2023

Background: Although unlinked total elbow arthroplasty (TEA) is a treatment option for end-stage rheumatoid arthritis (RA) of the elbow, its long-term outcomes were inferior. Moreover, revision TEA could be technically challenging. The unlinked TEA procedure comprises the ease of implant removal at revision and advantage of bone preservation. This study evaluated the clinical outcomes in patients who underwent revision TEA using primary unlinked TEA for rheumatoid elbows. It also aimed to determine whether selecting the unlinked prosthesis for the primary TEA would make revision more accessible and successful. Methods: We retrospectively reviewed data of 13 consecutive patients (14 elbows) who underwent revision TEAs for implant failure due to different aetiologies, excluding septic loosening. Three different unlinked TEA implants were used: the Kudo type-5 with all-polyethylene (AP) ulnar component, Kudo type-5 with metal-backed (MB) ulnar component and K-Now TEA. We evaluated the patients’ pre- and postoperative outcomes, including the range of motion, pain score and Mayo Elbow Performance Index (MEPI). Results: Among the 14 elbows, 11 were revised using the Kudo type-5 ulnar component (nine and two with AP and MB ulnar component, respectively), and three using the K-Now. We found that each model of TEA had different tendencies to indication for revision surgery. Three more resulted in further failure. The clinical outcomes were assessed in the 11 surviving elbows. Eight of the 11 elbows showed no pain at the final follow-up. However, the remaining three showed only mild pain. The MEPI revealed that seven cases were excellent, two were good and two were fair. Conclusions: The mode of implant failure was largely dependent on the implant design. Furthermore, partial revision with the same implant design was sufficient in managing implant failure in the early phase. However, conversion from unlinked to linked design could be recommended in patients with progressive failure or instability. Level of Evidence: Level IV (Therapeutic)
Post-traumatic Non-haemophilic Haemosiderotic Synovitis of the Elbow: A Case Report
Authors: HOSOKAWA Takafumi , TAJIKA Tsuyoshi , YAMADA Hiroaki , CHIKUDA Hirotaka 
Published: September 2023

Haemosiderotic synovitis (HS) is a rare synovial proliferative disease secondary to haemarthrosis, often with articular cartilage destruction. It is most frequently reported in patients with haemophiliacs, and the knee joint is most frequently affected. However, there are no reports on the elbow joint without haemophiliacs. A 60-year-old woman who had undergone osteosynthesis for a left radial head fracture 8 years earlier came to our clinic with left elbow pain. X-rays and CT scans showed osteopenia and osteoarthritic changes throughout the elbow joint. MRI revealed joint effusion and synovial membrane hyperplasia. Surgical synovectomy and screw removal were performed. The pathological diagnosis of the synovial membrane was HS. Postoperatively, the pain was relieved, osteopenia improved and there was no recurrence of symptoms. This is the first report of non-haemophilic HS of the elbow; post-traumatic HS caused elbow arthropathy, which was improved by screw removal and synovectomy. Level of Evidence: Level V (Therapeutic)
The tectonics of introversion and extroversion: redefining interior and exterior oceans in the supercontinent cycle
Authors: Martin Erin Lee , Cawood Peter A. , Murphy J. Brendan , Nance R. Damian , Heron Phillip J. 
Published: September 2023

Abstract
Supercontinent amalgamation is described by the end-member kinematic processes of introversion – closure of interior oceans; extroversion – closure of exterior oceans; or orthoversion – amalgamation 90° from the centroid of the previous supercontinent. However, supercontinent formations are often ascribed to contradictory mechanisms; for example, Pangaea has been argued to have formed by introversion from Pannotia/Gondwana, and extroversion from Rodinia. Conflicting interpretations arise partly from attempting to define oceans as interior or exterior based on palaeogeography or the age of the oceanic lithosphere relative to the time of supercontinent breakup. We define interior and exterior oceans relative to the external subduction ring, and associated accretionary orogens that surround amalgamated supercontinents. All oceans within the continental dominated cell and internal to the subduction ring are interior oceans. The exterior ocean is separated from the interior oceans by the subduction ring and bordered by external accretionary orogens. Wilson cycle tectonics dominate the interior continental cell, conversely, subduction of the exterior ocean is doubly vergent and lacks continent–continent collision. For the exterior ocean to close, the subduction ring must collapse upon itself, leading to the collision of external accretionary orogens. Employing this definition, Rodinia formed by extroversion, but all other supercontinents formed by introversion.
From Asset Flow to Status, Action, and Intention Discovery: Early Malice Detection in Cryptocurrency
Authors: Cheng Ling , Zhu Feida , Wang Yong , Liang Ruicheng , Liu Huiwen 
Published: September 2023

Cryptocurrency has been subject to illicit activities probably more often than traditional financial assets due to the pseudo-anonymous nature of its transacting entities. An ideal detection model is expected to achieve all three critical properties of early detection, good interpretability, and versatility for various illicit activities. However, existing solutions cannot meet all these requirements, as most of them heavily rely on deep learning without interpretability and are only available for retrospective analysis of a specific illicit type. To tackle all these challenges, we propose Intention Monitor for early malice detection in Bitcoin, where the on-chain record data for a certain address are much scarcer than other cryptocurrency platforms.
We first define asset transfer paths with the Decision Tree based feature Selection and Complement to build different feature sets for different malice types. Then, the Status/Action Proposal module and the Intention-VAE module generate the status, action, intent-snippet, and hidden intent-snippet embedding. With all these modules, our model is highly interpretable and can detect various illegal activities. Moreover, well-designed loss functions further enhance the prediction speed and the model’s interpretability. Extensive experiments on three real-world datasets demonstrate that our proposed algorithm outperforms the state-of-the-art methods. Furthermore, additional case studies justify that our model not only explains existing illicit patterns but also can find new suspicious characters.
Nationwide, Multioperator Self-Exclusion and Psychiatric Comorbidity in Patients with Gambling Disorder: A Retrospective Chart Review Study from a Regional Treatment Unit
Authors: Miles M. , Rothschild J. , Åkesson G. , Håkansson A. 
Published: September 2023

Gambling disorder is an addictive disorder that has been shown to have a detrimental effect on an individual’s health, social, and financial situations. Voluntary self-exclusion is one way for patients to reduce harm in gambling disorder, but breaching one’s self-exclusion appears to be common. In January 2019, Sweden launched a nationwide, multioperator self-exclusion instrument called Spelpaus (literally “game break”). Spelpaus is unique to Sweden, and there is limited research on the use of this type of nationwide, multioperator self-exclusion services, also in relation to gambling disorder and mental health. There is a reason to follow the clinical picture of treatment seeking for gambling disorder over time, and this study aims to explore clinical characteristics of patients seeking clinical gambling disorder treatment, including sex distribution and mental health comorbidity, as well as the use of Spelpaus amongst patients with gambling disorder and how frequently users gambled despite ongoing self-exclusion, in relation to sex and psychiatric comorbidities. A retrospective chart study was carried out on patients presenting to a regional gambling disorder treatment unit. Information regarding self-exclusions using Spelpaus, gambling despite self-exclusion, and the method of gambling despite self-exclusion as well as psychiatric comorbidities were extracted from medical records. Females were markedly more likely to report overall psychiatric comorbidities (48% vs. 25% among males,

p

< 0.001), affective, neurotic/anxiety-related (

p

< 0.001), and behavioral/emotional (

p

= 0.028) diagnoses and more likely to have two or more diagnoses excluding gambling disorder (

p

= 0.001). From 120 patients from whom information regarding self-exclusion was present, 114 (95%) had chosen to self-exclude. From the 114 self-excluders, 67 reported to have gambled despite self-exclusion, with unregistered websites being the most common method. Self-exclusion was not significantly related to sex (

p

= 0.146) or to psychiatric comorbidities (

p

= 0.178). In conclusion, psychiatric comorbidity was particularly common in female gambling disorder patients and gambling despite self-exclusion was common. Gambling regulations should be improved to help self-excluders avoid being able to gamble on unlicensed gambling operators. Further research should focus on sex differences and the association with psychiatric comorbidities.