bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing Mycobacteria and Algorithm-determined Resistant Tuberculosis Treatment (SMARTT): a study protocol for a phase IV pragmatic randomized controlled patient management strategy trial
Authors: Van Rie Annelies , De Vos Elise , Costa Emilyn , Verboven Lennert , Ndebele Felex , Heupink Tim H. , Abrams Steven ,   SMARTT team, Maraba Noriah , Makkan Heeran , Beattie Trevor , Sibeko Zandile Rachel , Bohlela S’thabiso , Segwaba Pulane , Ogunbayo Emmanuel Ayodeji , Mhlambi Nomadlozi , Wells Felicia , Rigouts Leen , Maartens Gary , Conradie Francesca , Black John , Potgieter Sam , Fanampe Boitumelo , Van der Spoel Van Dyk Anneke , Charalambous Salome , Churchyard Gavin , Warren Rob 
Published: October 2022

Abstract
Background
Rifampicin-resistant tuberculosis (RR-TB) remains an important global health problem. Ideally, the complete drug-resistance profile guides individualized treatment for all RR-TB patients, but this is only practised in high-income countries. Implementation of whole genome sequencing (WGS) technologies into routine care in low and middle-income countries has not become a reality due to the expected implementation challenges, including translating WGS results into individualized treatment regimen composition.

Methods
This trial is a pragmatic, single-blinded, randomized controlled medical device trial of a WGS-guided automated treatment recommendation strategy for individualized treatment of RR-TB. Subjects are 18 years or older and diagnosed with pulmonary RR-TB in four of the five health districts of the Free State province in South Africa. Participants are randomized in a 1:1 ratio to either the intervention (a WGS-guided automated treatment recommendation strategy for individualized treatment of RR-TB) or control (RR-TB treatment according to the national South African guidelines). The primary effectiveness outcome is the bacteriological response to treatment measured as the rate of change in time to liquid culture positivity during the first 6 months of treatment. Secondary effectiveness outcomes include cure rate, relapse rate (recurrence of RR-TB disease) and TB free survival rate in the first 12 months following RR-TB treatment completion. Additional secondary outcomes of interest include safety, the feasibility of province-wide implementation of the strategy into routine care, and health economic assessment from a patient and health systems perspective.

Discussion
This trial will provide important real-life evidence regarding the feasibility, safety, cost, and effectiveness of a WGS-guided automated treatment recommendation strategy for individualized treatment of RR-TB. Given the pragmatic nature, the trial will assist policymakers in the decision-making regarding the integration of next-generation sequencing technologies into routine RR-TB care in high TB burden settings.

Trial registration
ClinicalTrials.gov NCT05017324. Registered on August 23, 2021.
Eligibility screening older research participants using remote cognitive assessment—experiences and reflections from a primary care randomised controlled trial
Authors: Brundle Caroline , Heaven Anne , Clegg Andrew 
Published: October 2022

Abstract
Background
The COVID-19 pandemic forced many research teams to adjust the way they conduct studies, including moving to remote delivery of some or all of their recruitment and data collection processes. The Montreal Cognitive Assessment (MoCA) is widely used in research and is available in multiple formats for different groups and assessment settings. Here, we reflect on our experiences of administering the MoCA Blind/Telephone as part of the initial telephone eligibility check for participation in a randomised controlled trial with community-dwelling older people with frailty.

Main body
In response to COVID-19, a number of changes were made to the trial’s screening and recruitment procedures, to minimise the amount of time the researchers would spend in the participants’ homes when recruitment began in May 2021. One of the changes was for the researchers to conduct a cognitive assessment for eligibility during an initial telephone call, rather than during the subsequent home visit for consent and baseline data collection. We found that in comparison with conducting the assessment in-person, telephone administration caused uncertainty for the researchers about whether participants were struggling to answer questions due to cognition or hearing impairment. Some participants experienced practical difficulties when combining holding a telephone and completing one of the assessment items. It was hard for the researchers to judge the emotional impact that undertaking the assessment was having on the older people on the telephone, without visual warning signs of fatigue or mood. We discuss the potential impact of these issues on trial recruitment and participant engagement, and the feasibility of videoconferencing as an alternative method of conducting the MoCA.

Conclusion
The MoCA is a useful tool when cognitive impairment is part of screening and data collection and it is helpful to have the option to use the test remotely. However, as we have found, telephone testing is not always straightforward. Researchers should weigh up the pros and cons for each individual study, especially those involving older adults. If choosing remote methods, consider the practicality of using videoconferencing and think about the possible impact of telephone assessment on the relationship with the (potential) research participants.

Trial registration
Personalised care planning for older people with frailty ISRCTN16123291 28/08/2020.
MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning
Authors: Li Chang , Zhi Degui , Wang Kai , Liu Xiaoming 
Published: October 2022

AbstractMultiple computational approaches have been developed to improve our understanding of genetic variants. However, their ability to identify rare pathogenic variants from rare benign ones is still lacking. Using context annotations and deep learning methods, we present pathogenicity prediction models, MetaRNN and MetaRNN-indel, to help identify and prioritize rare nonsynonymous single nucleotide variants (nsSNVs) and non-frameshift insertion/deletions (nfINDELs). We use independent test sets to demonstrate that these new models outperform state-of-the-art competitors and achieve a more interpretable score distribution. Importantly, prediction scores from both models are comparable, enabling easy adoption of integrated genotype-phenotype association analysis methods. All pre-computed nsSNV scores are available athttp://www.liulab.science/MetaRNN. The stand-alone program is also available athttps://github.com/Chang-Li2019/MetaRNN.
Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns
Authors: Lian Kjersti , Furulund Betty M. N. , Tveita Anders A. , Haugen Peik , Johansen Steinar D. 
Published: October 2022

Abstract
Background
Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes.

Results
A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3′ polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3′ overhang at the intron insertion site.

Conclusions
The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus.
New mechanism for mesenchymal stem cell microvesicle to restore lung permeability: intracellular S1P signaling pathway independent of S1P receptor-1
Authors: Ye Lifang , Song Jieqiong , Zheng Yijun , Zhong Ming , Liu Jun , Zhu Duming , Hu Shuling 
Published: October 2022

Abstract
Background
Microvesicles (MVs) derived from human bone marrow mesenchymal stem cell (MSC) were demonstrated to restore lung protein permeability and attenuate acute lung injury. In our previous study, we found that MSC MV increased sphingosine-1-phosphate (S1P) kinase1 mRNA levels in injured human lung microvascular endothelial cells (HLMVEC) significantly. However, the role of S1P signaling in MSC MV to restore lung protein permeability is unknown.

Methods
In this study, we hypothesized that MSC MV might restore lung permeability in part through increasing intracellular S1P signaling pathway in injured HLMVEC independent of S1P receptors. We used the transwell co-culture system to study the effect of MSC MV on protein permeability of Lipopolysaccharide (LPS) damaged HLMVEC.

Results
Our results showed that LPS significantly increased the permeability of HLMVEC to FITC-dextran (70 kDa) within 24 h. MSC MV restores this permeability and, to a large extent, prevents the cytoskeleton protein F-actin from recombining into “actin stress fibers,” and restores the positions of tight junctions and adhesion junctions in the damaged HLMVEC. This therapeutic effect of MSC MV was related to the increase in the S1P level in injured HLMVEC and was not eliminated when adding the antagonist of S1P receptor, suggesting that MSC MV to restore lung permeability was independent of S1P receptors on HLMVEC. Laser confocal further observed that Ca2+ mobilization and Rac1 activation in LPS injured HLMVEC were increased in parallel with the increase in intracellular S1P level after MSC MV treatment.

Conclusions
In short, MSC MV partially restored protein permeability across HLMVEC through the intracellular S1P signaling pathway independent of S1P receptor-1.
Inhibition of sphingolipid metabolism in osteosarcoma protects against CD151-mediated tumorigenicity
Authors: Wang Hongsheng , Jin Xinmeng , Zhang Yangfeng , Wang Zhuoying , Zhang Tao , Xu Jing , Shen Jiakang , Zan Pengfei , Sun Mengxiong , Wang Chongren , Hua Yingqi , Ma Xiaojun , Sun Wei 
Published: October 2022

AbstractOsteosarcoma is the most common primary bone tumor, with a poor prognosis owing to the lack of efficient molecular-based targeted therapies. Previous studies have suggested an association between CD151 and distinct consequences in osteosarcoma tumorigenicity. However, the potential of CD151 as a therapeutic target has not yet been sufficiently explored. Here, we performed integrated transcriptomic and metabolomic analyses of osteosarcoma and identified sphingolipid metabolism as the top CD151-regulated pathway. CD151 regulates sphingolipid metabolism primarily through SPTCL1, the first rate-limiting enzyme in sphingolipid biosynthesis. Mechanistically, depletion of CD151 enhanced c-myc polyubiquitination and subsequent degradation. c-myc is vital for the transcriptional activation of SPTLC1. Functionally, sphingolipid synthesis and the SPTLC1 inhibitor, myriocin, significantly suppressed the clonogenic growth of CD151-overexpression cells. Importantly, myriocin selectively restrained CD151-high expression tumor growth in preclinical patient-derived xenograft models. Collectively, these data establish that CD151 is a key mediator of sphingolipid metabolism and provide a new approach to developing novel CD151-based targeted therapies for osteosarcoma.
Epidemiological and etiological characteristics of mild hand, foot and mouth disease in children under 7 years old, Nanjing, China, 2010–2019
Authors: Wang Junjun , Ding Songning , Xie Weijia , Wang Taiwu , Qin Ying , Zheng Jiandong , Yang Xiaokun , Zhao Hongting , Peng Zhibin , Ma Tao 
Published: October 2022

Abstract
Background
Mild hand, foot and mouth disease (HFMD) cases make up a relatively high proportion of HFMD while have often been overlooked. This study aimed to investigate the epidemiological and etiological characteristics of mild HFMD in Nanjing.

Methods
Data on mild HFMD cases, during 2010–2019 in Nanjing, were collected from the China Information System for Disease Control and Prevention. This study mainly focused on mild cases aged < 7 years. Descriptive analysis was used to summarize epidemiological and etiological characteristics of mild cases. Flexible spatial scan statistic was used to detect spatial clusters of mild cases.

Results
A total of 175,339 mild cases aged < 7 years were reported, accounting for 94.4% of all mild cases. There was a higher average annual incidence of mild HFMD in children aged < 7 years (4,428 cases/100,000) compared with children aged ≥ 7 years (14 cases/100,000, P < 0.001), and especially children aged 1-year-old (7,908 cases/100,000). Mild cases showed semi-annual peaks of activity, including a major peak (April to July) and a minor peak (September to November). The average annual incidence was higher in males (5,040 cases/100,000) than females (3,755 cases/100,000). Based on the cumulative reported cases, the most likely cluster was detected, including Yuhuatai District, Jiangning District, Jiangbei new Area, and Pukou District. The annual distribution of enterovirus serotypes showed a significant difference. During 2010–2016, Enterovirus 71 (EV71), Coxsackievirus A16 (Cox A16), and other non-EV71/Cox A16 EVs, accounted for 29.1%, 34.6%, 36.3% of all the enterovirus test positive cases, respectively. Moreover, during 2017–2019, Cox A6, Cox A16, EV71, and other non-EV71/Cox A16/Cox A6 EVs, accounted for 47.3%, 32.5%, 10.7%, 9.5%, respectively.

Conclusions
Children under 7 years old are at higher risk of mild HFMD. Regions with high risk are mainly concentrated in the areas surrounding central urban areas. Cox A16 and Cox A6 became the dominant serotypes and they alternated or were co-epidemic. Our findings could provide valuable information for improving the regional surveillance, prevention and control strategies of HFMD.
HaNDL syndrome: a reversible cerebral vasoconstriction triggered by an infection? A case report and a case-based review
Authors: Fiamingo Giuseppe , Canavero Isabella , Gastaldi Matteo , Coloberti Elisa , Buongarzone Gabriele , Ghiotto Natascia , Bacila Ana , Costa Alfredo , Ravaglia Sabrina 
Published: October 2022

Abstract
Background
The syndrome of transient Headache and Neurological Deficits with cerebrospinal fluid (CSF) Lymphocytosis (HaNDL) is classified among secondary headaches attributed to “non-infectious, inflammatory intracranial disease”. Despite its classification among secondary headaches, the current definition of HaNDL does not contemplate a causal agent. Thus, the aetiology, as well as the pathogenesis of both the headache and the transient focal deficits, remains unknown.

Case presentation
We describe a 29-year-old healthy male developing episodes of thunderclap headaches associated with recurrence of hemiparesis/hemi-paraesthesia; CSF showed lymphocytosis 200/mm3 and increased albumin; brain MRI revealed widespread leptomeningeal enhancement and a non-enhancing, circular diffusion restriction in the splenium of corpus callosum. Screening for neurotropic pathogens detected Epstein-Barr (EBV) DNA in serum and CSF, interpreted as a primary EBV infection once the seroconversion of EBV nuclear antigen (EBNA) IgM to IgG was proven on follow-up. Transcranial Doppler detected, during headache, increased flow velocity in middle cerebral arteries, possibly indicating vasospasm. Oral nimodipine was administered, with prompt clinical recovery, resolution of CSF/MRI abnormalities, and normalization of flow velocities in middle cerebral arteries.

Case-based review
Although the definition of HaNDL does not contemplate a viral trigger or abnormal brain imaging, we found other literature cases of HaNDL associated with direct or indirect signs of CNS infection.

Conclusions
At least in a proportion of patients, a viral aetiology may have a role in HaNDL. Whatever the aetiology, we suggest that the pathogenic mechanism may rely on the (viral or other) agent ultimately triggering cerebral vasoconstriction, which would explain both focal symptoms and headache. Calcium channel blockers might be a therapeutic option.
Tumor microenvironment and immunotherapy of oral cancer
Authors: Liu Chang , Wang Min , Zhang Haiyang , Li Chunyan , Zhang Tianshou , Liu Hong , Zhu Song , Chen Jie 
Published: October 2022

AbstractOral cancer is one of the most common malignant tumors of the head and neck, not only affects the appearance, but also affects eating and even endangers life. The clinical treatments of oral cancer mainly include surgery, radiotherapy, and chemotherapy. However, unsatisfactory therapeutic effect and toxic side effects are still the main problems in clinical treatment. Tumor microenvironment (TME) is not only closely related to the occurrence, growth, and metastasis of tumor but also works in the diagnosis, prevention, and treatment of tumor and prognosis. Future studies should continue to investigate the relationship of TME and oral cancer therapy. This purpose of this review was to analyze the characteristics of oral cancer microenvironment, summarize the traditional oral cancer therapy and immunotherapy strategies, and finally prospect the development prospects of oral cancer immunotherapy. Immunotherapy targeting tumor microenvironment is expected to provide a new strategy for clinical treatment of oral cancer.
Ink-lithographic fabrication of silver-nanocrystal-based multiaxial strain gauge sensors through the coffee-ring effect for voice recognition applications
Authors: Ahn Junhyuk , Choi Hyung Jin , Bang Junsung , Son Gayeon , Oh Soong Ju 
Published: October 2022

AbstractHuman voice recognition techniques have remarkable potential for clinical applications because information from acoustic signals can reflect human body conditions. This paper reports the fabrication of Ag nanocrystal (NC)-based multiaxial wearable strain gauge sensors by ink-lithography for voice recognition systems. Benefiting from the one-step-device-fabrication strategy of ink-lithography, which can yield Ag NC patterns with specific dimensions and endow physical properties, the Ag NC-based multiaxial strain sensors can be fabricated on an ultrathin substrate (~ 6 μm). Additionally, the coffee-ring effect can be induced onto the Ag NC patterns to realize high sensitivity and angle dependence (gauge factors $${G}_{0^\circ }$$

G

0
∘

= 11.7 ± 1.2 and $${G}_{90^\circ }$$

G

90
∘

= 105.5 ± 20.1); moreover, the voice onset time for voice recognition can be detected by the sensors. These features assist in distinguishing between voiced and voiceless plosive contrasts via measurements of contact-based voice onset time differences and can act as a cornerstone for further advancements in wearable sensors as well as voice recognition and analysis.
Graphical Abstract
Small nuclei identification with a hemispherical brain PET
Authors: Takahashi Miwako , Akamatsu Go , Iwao Yuma , Tashima Hideaki , Yoshida Eiji , Yamaya Taiga 
Published: October 2022

Abstract
Background
To confirm the performance of the first hemispherical positron emission tomography (PET) for the brain (Vrain) that we developed to visualise the small nuclei in the deep brain area, we compared 18F-fluorodeoxyglucose (FDG) brain images with whole-body PET images.

Methods
Ten healthy male volunteers (aged 22–45 years) underwent a representative clinical whole-body PET, followed by Vrain each for 10 min. These two scans were initiated 30 min and 45 min after FDG injection (4.1 ± 0.5 MBq/kg), respectively. First, we visually identified the small nuclei and then compared their standardised uptake values (SUVs) with the participants’ age. Next, the SUVs of each brain region, which were determined by applying a volume-of-interest template for anatomically normalised PET images, were compared between the brain images with the Vrain and those with the whole-body PET images.

Results
Small nuclei, such as the inferior colliculus, red nucleus, and substantia nigra, were more clearly visualised in Vrain than in whole-body PET. The anterior nucleus and dorsomedial nucleus in the thalamus and raphe nucleus in the brainstem were identified in Vrain but not in whole-body PET. The SUVs of the inferior colliculus and dentate gyrus in the cerebellum positively correlated with age (Spearman’s correlation coefficient r = 0.811, p = 0.004; r = 0.738, p = 0.015, respectively). The SUVs of Vrain were slightly higher in the mesial temporal and medial parietal lobes than those in whole-body PET.

Conclusions
This was the first time that the raphe nuclei, anterior nuclei, and dorsomedial nuclei were successfully visualised using the first hemispherical brain PET.

Trial registration

Japan Registry of Clinical Trials, jRCTs032210086, Registered 13 May 2021, https://jrct.niph.go.jp/latest-detail/jRCTs032210086.
Modulation of bioactive calcium phosphate micro/nanoparticle size and shape during in situ synthesis of photo-crosslinkable gelatin methacryloyl based nanocomposite hydrogels for 3D bioprinting and tissue engineering
Authors: Bhattacharyya Amitava , Janarthanan Gopinathan , Kim Taeyang , Taheri Shiva , Shin Jisun , Kim Jihyeon , Bae Hyun Cheol , Han Hyuk-Soo , Noh Insup 
Published: October 2022

Abstract

Background
The gelatin-methacryloyl (GelMA) polymer suffers shape fidelity and structural stability issues during 3D bioprinting for bone tissue engineering while homogeneous mixing of reinforcing nanoparticles is always under debate.

Method
In this study, amorphous calcium phosphates micro/nanoparticles (CNP) incorporated GelMA is synthesized by developing specific sites for gelatin structure-based nucleation and stabilization in a one-pot processing. The process ensures homogenous distribution of CNPs while different concentrations of gelatin control their growth and morphologies. After micro/nanoparticles synthesis in the gelatin matrix, methacrylation is carried out to prepare homogeneously distributed CNP-reinforced gelatin methacryloyl (CNP GelMA) polymer. After synthesis of CNP and CNP GelMA gel, the properties of photo-crosslinked 3D bioprinting scaffolds were compared with those of the conventionally fabricated ones.

Results
The shape (spindle to spherical) and size (1.753 μm to 296 nm) of the micro/nanoparticles in the GelMA matrix are modulated by adjusting the gelatin concentrations during the synthesis. UV cross-linked CNP GelMA (using Irgacure 2955) has significantly improved mechanical (three times compressive strength), 3D printability (160 layers, 2 cm self-standing 3D printed height) and biological properties (cell supportiveness with osteogenic differentiation). The photo-crosslinking becomes faster due to better methacrylation, facilitating continuous 3D bioprinting or printing.

Conclusion
For 3D bioprinting using GelMA like photo cross-linkable polymers, where structural stability and homogeneous control of nanoparticles are major concerns, CNP GelMA is beneficial for even bone tissue regeneration within short period.

Graphical Abstract