bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and validation of cellular senescence patterns to predict clinical outcomes and immunotherapeutic responses in lung adenocarcinoma
Authors: Lin Weihao , Wang Xin , Xu Zhenyi , Wang Zhen , Liu Tiejun , Cao Zheng , Feng Xiaoli , Gao Yibo , He Jie
Published: December 2021

Background

Aging and senescence can alter immune cell fitness and influence the efficacy of lung cancer treatments, especially immunotherapy. However, the correlations between cellular senescence and tumor microenvironment are still not clearly clarified and the value of cellular senescence-related genes in evaluating the immune infiltration and clinical outcomes of lung adenocarcinoma (LUAD) need further investigated.

Methods

We identified three cellular senescence clusters by NMF algorithm and correlated the cellular senescence clusters with the immune landscape in LUAD patients. A prognostic scoring system was established using random survival forest algorithm and validated in 4 external cohorts. Multivariate Cox regression analysis was performed to evaluate the prognostic value of the scoring system. Expression of LYPD3 was evaluated by immunohistochemistry in LUAD samples.

Results

Based on the mRNA expression profiles of 278 cellular senescence-related genes, three cellular senescence clusters with distinct prognosis were identified. We characterized three cellular senescence clusters by differences in biological processes, EMT score, expression of immunomodulatory genes, extent of intratumor heterogeneity and response to immunotherapy. Meanwhile, a cellular senescence-related scoring system (CSS) was established and validated as an independent prognostic factor and immunotherapy predictor of LUAD. Patients with low CSS was characterized by prolonged survival time. In response to anti-cancer drugs, patients with low CSS exhibited higher sensitivities to molecular drugs, such as Roscovitine (CDKs inhibitor), Lenaidornide (TNF-α inhibitor), MK2206 (Akt 1/2/3 inhibitor), and especially increased response to anti-PD-1/L1 immunotherapy.

Conclusions

This study demonstrated the correlations between cellular senescence patterns and tumor immune landscape in LUAD, which enhanced our understanding of the tumor immune microenvironment and provided new insights for improving the outcome of immunotherapy for LUAD patients.
Camera-based heart rate estimation for hospitalized newborns in the presence of motion artifacts
Authors: Chen Qiong , Wang Yalin , Liu Xiangyu , Long Xi , Yin Bin , Chen Chen , Chen Wei
Published: December 2021

Background

Heart rate (HR) is an importantvital signfor evaluating the physiological condition of a newborn infant. Recently, for measuring HR, novel RGB camera-based non-contact techniques have demonstrated their specific superiority compared with other techniques, such as dopplers and thermal cameras. However, they still suffered poor robustness in infants’ HR measurements due to frequent body movement.

Methods

This paper introduces a framework to improve the robustness of infants’ HR measurements by solving motion artifact problems. Our solution is based on the following steps: morphology-based filtering, region-of-interest (ROI) dividing, Eulerian video magnification and majority voting. In particular, ROI dividing improves ROI information utilization. The majority voting scheme improves the statistical robustness by choosing the HR with the highest probability. Additionally, we determined the dividing parameter that leads to the most accurate HR measurements. In order to examine the performance of the proposed method, we collected 4 hours of videos and recorded the corresponding electrocardiogram (ECG) of 9 hospitalized neonates under two different conditions—rest stillandvisible movements.

Results

Experimental results indicate a promising performance: the mean absolute error duringrest stillandvisible movementsare 3.39 beats per minute (BPM) and 4.34 BPM, respectively, which improves at least 2.00 and 1.88 BPM compared with previous works. The Bland-Altman plots also show the remarkable consistency of our results and the HR derived from the ground-truth ECG.

Conclusions

To the best of our knowledge, this is the first study aimed at improving the robustness of neonatal HR measurement under motion artifacts using an RGB camera. The preliminary results have shown the promising prospects of the proposed method, which hopefully reduce neonatal mortality in hospitals.
Tumor antigens and immune subtypes guided mRNA vaccine development for kidney renal clear cell carcinoma
Authors: Xu Hang , Zheng Xiaonan , Zhang Shiyu , Yi Xianyanling , Zhang Tianyi , Wei Qiang , Li Hong , Ai Jianzhong
Published: December 2021

Current treatment strategy for kidney renal clear cell carcinoma (KIRC) is limited. Tumor-associated antigens, especially neoantigen-based personalized mRNA vaccines represent new strategies and manifest clinical benefits in solid tumors, but only a small proportion of patients could benefit from them, which prompts us to identify effective antigens and suitable populations to facilitate mRNA vaccines application in cancer therapy. Through performing expression, mutation, survival and correlation analyses in TCGA-KIRC dataset, we identified four genes including DNA topoisomerase II alpha (TOP2A), neutrophil cytosol factor 4 (NCF4), formin-like protein 1 (FMNL1) and docking protein 3 (DOK3) as potential KIRC-specific neoantigen candidates. These four genes were upregulated, mutated and positively associated with survival and antigen-presenting cells in TCGA-KIRC. Furthermore, we identified two immune subtypes, named renal cell carcinoma immune subtype 1 (RIS1) and RIS2, of KIRC. Distinct clinical, molecular and immune-related signatures were observed between RIS1 and RIS2. Patients of RIS2 had better survival outcomes than those of RIS1. Further comprehensive immune-related analyses indicated that RIS1 is immunologically “hot” and represent an immunosuppressive phenotype, whereas RIS2 represents an immunologically “cold” phenotype. RIS1 and RIS2 also showed differential features with regard to tumor infiltrating immune cells and immune checkpoint-related genes. Moreover, the immune landscape construction identified the immune cell components of each KIRC patient, predicted their survival outcomes, and assisted the development of personalized mRNA vaccines. In summary, our study identified TOP2A, NCF4, FMNL1 and DOK3 as potential effective neoantigens for KIRC mRNA vaccine development, and patients with RIS2 tumor might benefit more from mRNA vaccination.
Recent advances of fluorescent biosensors based on cyclic signal amplification technology in biomedical detection
Authors: Qu Hongke , Fan Chunmei , Chen Mingjian , Zhang Xiangyan , Yan Qijia , Wang Yumin , Zhang Shanshan , Gong Zhaojian , Shi Lei , Li Xiayu , Liao Qianjin , Xiang Bo , Zhou Ming , Guo Can , Li Guiyuan , Zeng Zhaoyang , Wu Xu , Xiong Wei
Published: December 2021

The cyclic signal amplification technology has been widely applied for the ultrasensitive detection of many important biomolecules, such as nucleic acids, proteins, enzymes, adenosine triphosphate (ATP), metal ions, exosome, etc. Due to their low content in the complex biological samples, traditional detection methods are insufficient to satisfy the requirements for monitoring those biomolecules. Therefore, effective and sensitive biosensors based on cyclic signal amplification technology are of great significance for the quick and simple diagnosis and treatment of diseases. Fluorescent biosensor based on cyclic signal amplification technology has become a research hotspot due to its simple operation, low cost, short time, high sensitivity and high specificity. This paper introduces several cyclic amplification methods, such as rolling circle amplification (RCA), strand displacement reactions (SDR) and enzyme-assisted amplification (EAA), and summarizes the research progress of using this technology in the detection of different biomolecules in recent years, in order to provide help for the research of more efficient and sensitive detection methods.

Graphical Abstract
Assessing the impact of knowledge communication and dissemination strategies targeted at health policy-makers and managers: an overview of systematic reviews
Authors: Chapman Evelina , Pantoja Tomas , Kuchenmüller Tanja , Sharma Tarang , Terry Robert F.
Published: December 2021

Background

The use of research evidence as an input for health decision-making is a need for most health systems. There are a number of approaches for promoting evidence use at different levels of the health system, but knowledge of their effectiveness is still scarce. The objective of this overview was to evaluate the effectiveness of knowledge communication and dissemination interventions, strategies or approaches targeting policy-makers and health managers.

Methods

This overview of systematic reviews used systematic review methods and was conducted according to a predefined and published protocol. A comprehensive electronic search of 13 databases and a manual search in four websites were conducted. Both published and unpublished reviews in English, Spanish or Portuguese were included. A narrative synthesis was undertaken, and effectiveness statements were developed, informed by the evidence identified.

Results

We included 27 systematic reviews. Three studies included only a communication strategy, while eight only included dissemination strategies, and the remaining 16 included both. None of the selected reviews provided “sufficient evidence” for any of the strategies, while four provided some evidence for three communication and four dissemination strategies. Regarding communication strategies, the use of tailored and targeted messages seemed to successfully lead to changes in the decision-making practices of the target audience. Regarding dissemination strategies, interventions that aimed at improving only the reach of evidence did not have an impact on its use in decisions, while interventions aimed at enhancing users’ ability to use and apply evidence had a positive effect on decision-making processes. Multifaceted dissemination strategies also demonstrated the potential for changing knowledge about evidence but not its implementation in decision-making.

Conclusions

There is limited evidence regarding the effectiveness of interventions targeting health managers and policy-makers, as well as the mechanisms required for achieving impact. More studies are needed that are informed by theoretical frameworks or specific tools and using robust methods, standardized outcome measures and clear descriptions of the interventions. We found that passive communication increased access to evidence but had no effect on uptake. Some evidence indicated that the use of targeted messages, knowledge-brokering and user training was effective in promoting evidence use by managers and policy-makers.
The use of food swaps to encourage healthier online food choices: a randomized controlled trial
Authors: Jansen Laura , van Kleef Ellen , Van Loo Ellen J.
Published: December 2021

Background

Online grocery stores offer opportunities to encourage healthier food choices at the moment that consumers place a product of their choice in their basket. This study assessed the effect of a swap offer, Nutri-Score labeling, and a descriptive norm message on the nutrient profiling (NP) score of food choices in an online food basket. Additionally explored was whether these interventions made it more motivating and easier for consumers to select healthier foods and whether potential effects were moderated by consumer health interest.

Methods

Hypotheses were tested with a randomized controlled trial (RCT) in a simulated online supermarket. Dutch participants (n = 550) chose their preferred product out of six product options for four different categories (breakfast cereals, crackers, pizza, and muesli bars). Participants were randomly allocated to one of eight groups based on the interventions in a 2 (Nutri-Score: present, not present) X 2 (swap offer: present, not present) X 2 (norm message: present, not present) between subject design. The primary outcome was the difference in combined NP score of product choices, for which a lower score represented a healthier product.

Results

Swap offer (B = − 9.58, 95% CI: [− 12.026; − 7.132], Ƞ2 = 0.098) and Nutri-Score labeling (B = − 3.28, 95% CI: [− 5.724; −.829], Ƞ2 = 0.013) significantly improved the combined NP score compared to the control condition (NP score M = 18.03, SD = 14.02), whereas a norm message did not have a significant effect (B = − 1.378, 95% CI [− 3.825; 1.070], Ƞ2 = 0.002). No evidence was found that interventions made it more motivating or easier for consumers to select healthier food, but situational motivation significantly influenced the healthiness score of food choices for both swap offer (b = − 3.40, p < .001) and Nutri-Score (b = − 3.25, p < .001). Consumer health interest only significantly moderated the influence of Nutri-Score on ease of identifying the healthy food option (b = .23, p = .04).

Conclusions

Swap offer and Nutri-Score labeling were effective in enhancing healthy purchase behavior in the online store environment.

Trial registration

This study was retrospectively registered in the ISRCTN database on 02-09-2021 (ISRCTN80519674).
The maintained attention assessment in patients affected by Myalgic encephalomyelitis/chronic fatigue syndrome: a reliable biomarker?
Authors: Murga Iñigo , Aranburu Larraitz , Gargiulo Pascual A. , Gómez-Esteban Juan-Carlos , Lafuente José-Vicente
Published: December 2021

The maintained attention is the cause of great functional limitations in CFS/ME, a disease that mainly affects women in the central period of life. Cognitive function is explored using the Montreal Cognitive Assessment, the maintained attention using the Toulouse-Piéron test with which the Global Index of Attention and Perception (GIAP) is obtained, the fatigue using the visual analog scale and the perception of effort using the modified Borg scale. The final sample were 84 patients (66 women/18 men) who met diagnostic criteria (Fukuda-1994, Carruthers-2011) and 22 healthy controls (14 women/8 men). Most of patients maintain normal cognitive function, showing low or very low attention score in the 70% of patients with a marked cognitive fatigue compared to the control group (p < 0.05). There were no significant differences between genders in GIAP or fatigue for CFS/ME; however, sick women perceive cognitive effort higher than men. Deficits in sustained attention and the perception of fatigue, so effort after performing the proposed test are a sensitive and reliable indicator that allows us to substantiate a clinical suspicion and refer patients for further studies in order to confirm or rule out CFS/ME.
Automated and accurate assessment for postural abnormalities in patients with Parkinson’s disease based on Kinect and machine learning
Authors: Zhang Zhuoyu , Hong Ronghua , Lin Ao , Su Xiaoyun , Jin Yue , Gao Yichen , Peng Kangwen , Li Yudi , Zhang Tianyu , Zhi Hongping , Guan Qiang , Jin LingJing
Published: December 2021

Background

Automated and accurate assessment for postural abnormalities is necessary to monitor the clinical progress of Parkinson’s disease (PD). The combination of depth camera and machine learning makes this purpose possible.

Methods

Kinect was used to collect the postural images from 70 PD patients. The collected images were processed to extract three-dimensional body joints, which were then converted to two-dimensional body joints to obtain eight quantified coronal and sagittal features (F1-F8) of the trunk. The decision tree classifier was carried out over a data set established by the collected features and the corresponding doctors’ MDS-UPDRS-III 3.13 (the 13th item of the third part of Movement Disorder Society-Sponsored Revision of the Unified Parkinson’s Disease Rating Scale) scores. An objective function was implanted to further improve the human–machine consistency.

Results

The automated grading of postural abnormalities for PD patients was realized with only six selected features. The intraclass correlation coefficient (ICC) between the machine’s and doctors’ score was 0.940 (95%CI, 0.905–0.962), meaning the machine was highly consistent with the doctors’ judgement. Besides, the decision tree classifier performed outstandingly, reaching 90.0% of accuracy, 95.7% of specificity and 89.1% of sensitivity in rating postural severity.

Conclusions

We developed an intelligent evaluation system to provide accurate and automated assessment of trunk postural abnormalities in PD patients. This study demonstrates the practicability of our proposed method in the clinical scenario to help making the medical decision about PD.
Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach
Authors: Zeng Jian , Wang Yan , Zhang Ju , Yang Shixing , Zhang Wen
Published: December 2021

Members of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.
Capsule-dependent impact of MAPK signalling on host cell invasion and immune response during infection of the choroid plexus epithelium by Neisseria meningitidis
Authors: Herold Rosanna , Scholtysik René , Moroniak Selina , Weiss Christel , Ishikawa Hiroshi , Schroten Horst , Schwerk Christian
Published: December 2021

Background

The Gram-negative bacterium Neisseria meningitidis (Nm) can cause meningitis in humans, but the host signalling pathways manipulated by Nm during central nervous system (CNS) entry are not completely understood.

Methods

We investigate the role of the mitogen-activated protein kinases (MAPK) Erk1/2 and p38 in an in vitro model of the blood-cerebrospinal fluid barrier (BCSFB) based on human epithelial choroid plexus (CP) papilloma (HIBCPP) cells during infection with Nm serogroup B (NmB) and serogroup C (NmC) strains. A transcriptome analysis of HIBCPP cells following infection with Nm by massive analysis of cDNA ends (MACE) was done to further characterize the cellular response to infection of the barrier.

Results

Interestingly, whereas NmB and NmC wild type strains required active Erk1/2 and p38 pathways for infection, invasion by capsule-deficient mutants was independent of Erk1/2 and, in case of the NmB strain, of p38 activity. The transcriptome analysis of HIBCPP cells following infection with Nm demonstrated specific regulation of genes involved in the immune response dependent on Erk1/2 signalling. Gene ontology (GO) analysis confirmed loss of MAPK signalling after Erk1/2 inhibition and revealed an additional reduction of cellular responses including NFκB and JAK-STAT signalling. Interestingly, GO terms related to TNF signalling and production of IL6 were lost specifically following Erk1/2 inhibition during infection with wild type Nm, which correlated with the reduced infection rates by the wild type in absence of Erk1/2 signalling.

Conclusion

Our data point towards a role of MAPK signalling during infection of the CP epithelium by Nm, which is strongly influenced by capsule expression, and affects infection rates as well as the host cell response.
In search of traces of the mandrake myth: the historical, and ethnobotanical roots of its vernacular names
Authors: Dafni Amots , Blanché Cesar , Khatib Salekh Aqil , Petanidou Theodora , Aytaç Bedrettin , Pacini Ettore , Kozuharova Ekaterina , Geva-Kleinberger Aharon , Shahvar Soli , Dajic Zora , Klug Helmut W. , Benítez Guillermo
Published: December 2021

Background

Mandrake (Mandragoraspp.) is one of the most famous medicinal plant in western cultures since Biblical times and throughout written history. In many cultures, mandrake is related to magic and witchcraft, which is said to have a psychosomatic effect (especially when mandrake contains narcotic compounds) in addition to the pharmacological influence, as occurs with other narcotic magical plants. Due to its unique properties and related myths, it is not surprising that this plant has many names in many languages.

Methods

This paper presents an attempt to reconstruct the historical, ethnobotanical, and folkloristic roots of 292 vernacular names ofMandragoraspp. in forty-one languages. We used the plant’s morphological data, philology, myths and legends, medicinal properties and uses, as well as historical evidence and folkloric data, to explain meaning, origin, migration, and history of the plant’s names.

Results

The names were classified into the following main categories: Derivatives ofmandragora(19 languages),alraun(7) and ofyabroukh(5). The salient groups of the plant’s vernacular names are related to: Anthropomorphism (33 names in 13 languages); Similarity to other plants (28/9); Supernatural agents (28/9); Narcotic effects (21/8); Leaves, fruits, and seeds (21/8); Aphrodisiac properties (17/10); Use of a dog (15/9); Gallows (14/5); Black magic, sorcery, witchcraft (13/8), and Medicinal use (11/7).

Conclusions

This frequency distribution of the mandrake’s vernacular names reflects its widespread reputation as related to the doctrine of signatures, beliefs in its supernatural, natural, and mythic powers, and to a lesser extent, its uses in magic and medicine. A spatiotemporal analysis of the mandrake’s names supports the old idea that the pulling ceremonies for this plant originated in the Near East and that various other myths related to this plant may have originated in different places and periods.
A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set
Authors: Schaller David , Hellmuth Marc , Stadler Peter F.
Published: December 2021

Background

The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf setLis known to be solvable in linear time. Existing approaches refine one input tree using information of the others and then test whether the results are isomorphic.

Results

AnO(k|L|) algorithm, , for constructing the common refinementTofkinput trees with a common leaf setLis proposed that explicitly computes the parent function ofTin a bottom-up approach.

Conclusion

is simpler to implement than other asymptotically optimal algorithms for the problem and outperforms the alternatives in empirical comparisons.

Availability

An implementation of in Python is freely available athttps://github.com/david-schaller/tralda.
Long-term safety and effectiveness of velaglucerase alfa in Gaucher disease: 6-year interim analysis of a post-marketing surveillance in Japan
Authors: Sagara Rieko , Ishigaki Masahide , Otsuka Manami , Murayama Kei , Ida Hiroyuki , Fernandez Jovelle
Published: December 2021

Background

Gaucher disease (GD) is caused by reduced lysosomal enzyme β-glucocerebrosidase activity. Heterogeneous genotypes and phenotypes have been observed within GD types and across ethnicities. Enzyme replacement therapy is generally recommended for patients with type 1 GD, the least severe form of GD. In Japan, velaglucerase alfa has a broad indication covering type 1, 2 or 3 GD. 

Methods

All patients with type 1, 2, or 3 GD administered velaglucerase alfa 60 U/kg every 2 weeks via intravenous infusion after its launch date in Japan in 2014, were enrolled in a non-interventional, observational post-marketing surveillance (PMS). Individual patient data were reported via case report forms (CRFs). Key safety endpoints investigated included the incidence of infusion-related reactions (IRRs), the safety of velaglucerase alfa in patients with types 2 and 3 GD, from patients under one year of age to elderly patients (≥ 65 years of age). Long-term efficacy was also assessed. 

Results

In total, 53 patients with GD were registered. CRFs were available for 41 (77.4%) patients at the 6-year interim analysis. Fourteen adverse drug reactions (ADRs) were reported in seven patients. All reported ADRs occurred in patients with type 2 GD. ADRs were reported by 63.6% (7/11) of patients with type 2 GD. Ten ADRs were reported in five patients aged < 4 years. No elderly patients experienced any ADR during the surveillance period. Five ADRs occurring in three (10.0%) patients were classified as IRRs, with one case of vomiting (moderate severity) resulting in treatment discontinuation. Ten serious adverse events were reported in five (16.7%) patients. Three fatal events were considered to be unrelated to treatment with velaglucerase alfa. Platelet counts increased after the administration of velaglucerase alfa and were generally maintained within the normal range over the administration period. Among eleven patients tested for neutralizing anti-velaglucerase alfa antibodies, two (18.2%) were assessed as positive results. 

Conclusion

PMS data from patients with types 1–3 GD in Japan indicate that long-term treatment with velaglucerase alfa was well-tolerated and associated with increased platelet counts, which is consistent with observations made in studies outside of Japan.

Trial registration: NCT03625882 registered July 2014.
Challenges to the implementation and adoption of physical distancing measures against COVID-19 by internally displaced people in Mali: a qualitative study
Authors: Ag Ahmed Mohamed Ali , Ly Birama Apho , Diarra Niélé Hawa , Traore Fatoumata Bintou , Diarra Djeneba , Kande Inna Fatoumata , Dembele Mahamadou , Doumbia Seydou , Alami Hassane
Published: December 2021

Background

For almost a decade now, Mali has been facing a security crisis that led to the displacement of thousands of people within the country. Since March 2020, a health crisis linked to the COVID-19 pandemic also surfaced. To overcome this health crisis, the government implemented some physical distancing measures but their adoption proved difficult, particularly among internally displaced people (IDPs). The objective of this study is to identify the challenges relating to the implementation and adoption of physical distancing measures and to determine the main mitigation measures taken by IDPs to adjust to these new policies.

Methods

An exploratory qualitative research was conducted in Bamako and Ségou, two of the ten regions of Mali. The study counted 68 participants including 50 IDPs, seven administrative and health authorities, and 11 humanitarian actors. Sampling was guided by the principle of saturation and diversification, and data was collected through semi-structured individual interviews (n = 36) and focus groups (n = eight). Analysis was based on thematic content analysis through NVivo software.

Results

The main challenges identified concerning the implementation and adoption of physical distancing measures include the proximity in which IDPs live, their beliefs and values, the lack of toilets and safe water on sites, IDPs habits and economic situation, humanitarian actors’ lack of financial resources and authority, and social pressure from religious leaders. Implemented mitigation measures include the building of new shelters or their compartmentalization, the creation of income-generating activities and food banks, psychosocial support, promoting awareness of IDPs, and nightly police patrols and surveillance to discourage IDPs from going out. Finally, a call for action is suggested for the actors involved in IDPs support and management.

Conclusions

The study demonstrates the difficulty for IDPs to follow most of the physical distancing measures and informs about the risk of disease spreading among IDPs with its potential consequences. It also shows the inability of mitigation measures to control the outbreak and suggests actions to be considered.
A novel red fluorescence dopamine biosensor selectively detects dopamine in the presence of norepinephrine in vitro
Authors: Nakamoto Chihiro , Goto Yuhei , Tomizawa Yoko , Fukata Yuko , Fukata Masaki , Harpsøe Kasper , Gloriam David E. , Aoki Kazuhiro , Takeuchi Tomonori
Published: December 2021

Dopamine (DA) and norepinephrine (NE) are pivotal neuromodulators that regulate a broad range of brain functions, often in concert. Despite their physiological importance, untangling the relationship between DA and NE in the fine control of output function is currently challenging, primarily due to a lack of techniques to allow the observation of spatiotemporal dynamics with sufficiently high selectivity. Although genetically encoded fluorescent biosensors have been developed to detect DA, their poor selectivity prevents distinguishing DA from NE. Here, we report the development of a red fluorescent genetically encoded GPCR (G protein-coupled receptor)-activation reporter for DA termed ‘R-GenGAR-DA’. More specifically, a circular permutated red fluorescent protein (cpmApple) was replaced by the third intracellular loop of human DA receptor D1 (DRD1) followed by the screening of mutants within the linkers between DRD1 and cpmApple. We developed two variants: R-GenGAR-DA1.1, which brightened following DA stimulation, and R-GenGAR-DA1.2, which dimmed. R-GenGAR-DA1.2 demonstrated a reasonable dynamic range (ΔF/F0 = − 43%), DA affinity (EC50 = 0.92 µM) and high selectivity for DA over NE (66-fold) in HeLa cells. Taking advantage of the high selectivity of R-GenGAR-DA1.2, we monitored DA in presence of NE using dual-color fluorescence live imaging, combined with the green-NE biosensor GRABNE1m, which has high selectivity for NE over DA (> 350-fold) in HeLa cells and hippocampal neurons grown from primary culture. Thus, this is a first step toward the multiplex imaging of these neurotransmitters in, for example, freely moving animals, which will provide new opportunities to advance our understanding of the high spatiotemporal dynamics of DA and NE in normal and abnormal brain function.
The interphalangeal angle as a novel radiological measurement tool for Morton's neuroma – a matched case‐control study
Authors: Zaleski Martin , Tondelli Timo , Hodel Sandro , Rigling Dominic , Wirth Stephan
Published: December 2021

Background

The aim of this retrospective study was to examine if a correlation between Morton's Neuroma (MN) and an increased interphalangeal angle (IPA) or intermetatarsal angle (IMA) can be found in preoperative weightbearing dorsal‐plantar X‐rays of the foot.

Methods

Forty‐five patients with forty‐nine MN in the interspaces 2/3 or 3/4 and 49 controls were recruited for this study. Every MN was matched with an asymptomatic control without history of metatarsalgia. The diagnosis was made by clinical examination, magnetic resonance imaging (MRI) and positive histopathology after operative resection. IMA 1/5, 2/3, 2/4, 2/5, 3/4 and IPA 2/3, 3/4 were measured for both groups.

Results

The IPA 3/4 was significantly enlarged by 2.8 degrees (p < 0.001) with Area under the curve (AUC) 0.75 (p < 0.001), sensitivity of 73% and specificity of 67% in feet with MN compared to controls. The IMA 3/4 was significantly enlarged by 1 degree (p < 0.048) with AUC 0.64 (p < 0.031), sensitivity of 71% and specificity of 43% in feet with MN compared to controls. No difference between IMA 2/4, 2/5, 1/5 or correlation between IPA or IMA and the size of the MN in the MRI was found.

Conclusion

The results confirm the clinical observation of an increased IPA in patients with MN. An increased IPA should therefore be considered in the diagnosis of MN.
The effect of different vitrification protocols on cell survival in human ovarian tissue: a pilot study
Authors: Marschalek J. , Egarter C. , Nouri K. , Dekan S. , Ott J. , Frank M. , Pietrowski D.
Published: December 2021

Background

Vitrification has superseded the slow freezing method for cryopreservation of oocytes, embryos, and sperm, but there are as yet no standard protocols for its use in ovarian tissue cryopreservation (OTC). Published protocols diverge mainly with regard to the extent of supplementation of dimethyl sulfoxide (DMSO) to the vitrification medium, and to the use of an open or closed vitrification system.

We investigated the viability of cells after vitrification/warming, using ovarian tissue of transgender patients, by means of Fluorescence Activated Cells Sorting (FACS), and histomorphological analyses using a DMSO-containing (P1) and a DMSO-free protocol (P2) in an open or closed vitrification setting.

Results

Twelve ovarian samples were donated from female-to-male transgender patients: 6 were vitrified according to protocol 1, the other 6 according to protocol 2. The amount of viable cells was 90.1% (P1) and 88.4% (P2) before vitrification. After vitrification and subsequent warming, viable cells were reduced to 82.9% (P1, p = 0.093) and 72.4% (P2, p = 0.019). When comparing the closed and the open systems, the decline in cell viability from pre- to post-vitrification was significant only for the latter (p = 0.037). Histological examination reveals no significant differences with respect to degenerated follicles before or after vitrification.

Conclusion

These results led us to conclude that a protocol containing DMSO results in a higher viability of ovarian cells than a protocol that uses ethylene glycol as cryoprotective agent in vitrification. The use of an open vitrification system led to significant decline in the rate of viable cells.

Trial registration

NCT03649087, retrospectively registered 28.08.2018.
Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing
Authors: Kim Heon Seok , Grimes Susan M. , Hooker Anna C. , Lau Billy T. , Ji Hanlee P.
Published: December 2021

We developed a single-cell approach to detect CRISPR-modified mRNA transcript structures. This method assesses how genetic variants at splicing sites and splicing factors contribute to alternative mRNA isoforms. We determine how alternative splicing is regulated by editing target exon-intron segments or splicing factors by CRISPR-Cas9 and their consequences on transcriptome profile. Our method combines long-read sequencing to characterize the transcript structure and short-read sequencing to match the single-cell gene expression profiles and gRNA sequence and therefore provides targeted genomic edits and transcript isoform structure detection at single-cell resolution.
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
Authors: Huang Sihao , Zhang Wen , Katanski Christopher D. , Dersh Devin , Dai Qing , Lolans Karen , Yewdell Jonathan , Eren A. Murat , Pan Tao
Published: December 2021

Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu) that utilizes native content training, machine learning modeling, and single-read linkage analysis. Biologically, we find interferon inducible Ψ modifications in interferon-stimulated gene transcripts which are consistent with a role of Ψ in enabling efficacy of mRNA vaccines.
Effects of a periodized circuit training protocol delivered by telerehabilitation compared to face-to-face method for knee osteoarthritis: a protocol for a non-inferiority randomized controlled trial
Authors: Aily Jéssica Bianca , de Almeida Aline Castilho , de Noronha Marcos , Mattiello Stela Marcia
Published: December 2021

Background

Regular exercise is an effective method for reducing pain and disability in patients with knee osteoarthritis (OA), as well as improving body composition. Thus, a combination of both resistance and aerobic training (circuit training) has shown to be promising for this population. However, access to physical therapy is limited by physical distance, social isolation, and/or treatment costs. Remote rehabilitation seems to be an effective way to minimize these barriers, but the benefits are dependent on the participants’ adherence to the interventions provided at a distance. The objectives of this protocol are to compare the effects of a periodized circuit training applied via telerehabilitation with the same protocol applied in the face-to-face model for individuals with knee OA.

Methods

This study presents a single-blinded protocol for a non-inferiority randomized controlled trial. One hundred participants diagnosed with knee OA (grades II and III Kellgren and Lawrence system), aged 40 years or more, and BMI < 30 kg/m2 will be randomly divided into two groups: telerehabilitation (TR) and face-to-face (FtF) circuit training. The FtF group will perform a 14-week periodized circuit training protocol supervised by a physical therapist, 3 times a week. The TR group will perform the same exercise protocol at home, at least 3 times a week. In addition, the TR group will be able to follow the execution and orientations of the exercises by DVD, a website, and online file sharing tools, and they will receive periodic phone calls in order to motivate, clarify, and inform some aspects of knee OA. The primary outcomes are changes in self-reported pain intensity (visual analog scale (VAS)) and physical function (Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC)), with a primary end-point of 14 weeks and a secondary end-point of 26 weeks. Secondary outcomes include changes in other clinical outcomes, in morphological characteristics, adherence, acceptability, and treatment perspective.

Discussion

A circuit training through telerehabilitation may contribute to developing early intervention in the causative and potentiating factors of the knee OA, verifying the effects of a low-cost, non-pharmacological and non-invasive treatment.

Trial registration

Brazilian Registry of Clinical Trials (ReBEC) ID: RBR-662hn2. Registered on 31 March 2019. Link: http://www.ensaiosclinicos.gov.br; Universal Trial Number (UTN) of World Health Organization: U1111-1230-9517.
Combined effects of vitamin D supplementation and endurance exercise training on insulin resistance in newly diagnosed type 2 diabetes mellitus patients with vitamin D deficiency: study protocol for a randomized controlled trial
Authors: Xiang Mi , Sun Xiaomin , Wei Junxiang , Cao Zhen-Bo
Published: December 2021

Background

Although approximately 50% of Chinese with type 2 diabetes mellitus (T2DM) patients have vitamin D deficiency, studies regarding vitamin D supplementation on insulin resistance (IR) have mainly focused on non-Asians. Endurance exercise training (ET) enhances insulin-mediated glucose metabolism, which plays a critical role in T2DM prevention and control. However, the combined effects of vitamin D supplementation and ET on IR in T2DM patients are unclear. The objectives of this study is to investigate the synergistic effect of vitamin D supplementation combined with exercise training intervention on IR in T2DM patients.

Methods and analysis

We propose a 3-month randomized controlled trial among 60 T2DM patients aged 40–65, newly diagnosed with T2DM ≤ 1 year, and with stable HbA1c level (≤ 8.0%) in the past 3 months. The participants will be randomly allocated to the vitamin D group, vitamin D combined with exercise training group, exercise training group, and control group (CG) using a computer-generated random number sequence. At baseline, participants will undergo a medical review, anthropometric measurements, dual X-ray absorptiometry, a 75-g oral glucose tolerance test (OGTT), ankle-brachial index measurements, and physical fitness measurements and will complete related lifestyle questionnaires. Fasting blood lipid and glucose levels were also measured. In a 3-month intervention period, vitamin D intervention group will receive a dose of 1000 IU daily; exercise group will perform a 1-h endurance exercise 3 times per week (maximal heart rate, 60–80%), and the control group will receive apparently identical tablets. Additionally, all participants will be advised to maintain their normal diet and physical activities during the intervention. All measurements will be repeated at 3-month follow-up after the intervention with the primary outcome measure expressed as a change from baseline in insulin sensitivity and secretion. Secondary outcome measures will compare the changes in anthropometry, ankle-brachial index, and physical fitness factors (e.g., peak oxygen uptake, hand grip strength). Data will be managed and analyzed using the Statistical Package for the Social Sciences.

Discussion

This is the first study to conduct a randomized trial to clearly determine the independent and combined effects of vitamin D supplementation and endurance exercise trial on IR in Chinese T2DM patients as measured by OGTT. The findings from the proposed study will not only provide new evidences that vitamin D supplementation plays an important role in IR management but also develop a simple and efficient method to improve IR-associated metabolic diseases for T2DM patients.

Trial registration

Chinese Clinical Trial Registry ChiCTR1800015383, Registered on 28 March 2018
Ethionine-mediated reduction of S-adenosylmethionine is responsible for the neural tube defects in the developing mouse embryo-mediated m6A modification and is involved in neural tube defects via modulating Wnt/β-catenin signaling pathway
Authors: Zhang Li , Cao Rui , Li Dandan , Sun Yuqing , Zhang Juan , Wang Xiuwei , Khan Ajab , Liu Zhizhen , Niu Bo , Xu Jun , Xie Jun
Published: December 2021

Neural tube defects (NTDs) remain one of the most life-threatening birth defects affecting infants. Most patients with NTDs eventually develop lifelong disability, which cause significant morbidity and mortality and seriously reduce the quality of life. Our previous study has found that ethionine inhibits cell viability by disrupting the balance between proliferation and apoptosis, and preventing neural stem cells from differentiating into neurons and astrocytes. However, how ethionine participates in the pathogenesis of neural tube development through N6-methyladenosine (m6A) modification remains unknown. This study aims to investigate METTL3- and ALKBH5-mediated m6A modification function and mechanism in NTDs. Herein, our results demonstrate that SAM play not only a compensatory role, it also leads to changes of m6A modification in neural tube development and regulation. Additionally, these data implicate that METTL3 is enriched in HT-22 cells, and METTL3 knockdown reduces cell proliferation and increases apoptosis through suppressing Wnt/β-catenin signaling pathway. Significantly, overexpression of ALKBH5 can only inhibit cell proliferation, but cannot promote cell apoptosis. This research reveals an important role of SAM in development of NTDs, providing a good theoretical basis for further research on NTDs. This finding represents a novel epigenetic mechanism underlying that the m6A modification has profound and lasting implications for neural tube development.
Gut microbiota imbalance in colorectal cancer patients, the risk factor of COVID-19 mortality
Authors: Cai Changjing , Zhang Xiangyang , Liu Yihan , Shen Edward , Feng Ziyang , Guo Cao , Han Ying , Ouyang Yanhong , Shen Hong
Published: December 2021

Background

COVID-19 pandemic is sweeping across the world. Previous studies have shown that gut microbiota is associated with COVID-19, and operational taxonomic unit (OTU) composed of Blautia genus, Lactobacillus genus, and Ruminococcus genus of Firmicutes is correlated with the severity of COVID-19. Gut microbiota imbalance in colorectal cancer patients may lead to the variation of OTU.

Results

Based on the GMrepo database, the gut microbiota of 1374 patients with colorectal neoplasms and 27,329 healthy people was analyzed to investigate the differences in the abundance of microbes between colorectal neoplasms patients and healthy people. Furthermore, We collected feces samples from 12 patients with colorectal cancer and 8 healthy people in Xiangya hospital for metabolomic analysis to investigate the potential mechanisms. Our study showed that the abundance of Blautia and Ruminococcus was significantly increased in colorectal neoplasms, which may increase the severity of COVID-19. The gender and age of patients may affect the severity of COVID-19 by shaping the gut microbiota, but the BMI of patients does not.

Conclusions

Our work draws an initial point that gut microbiota imbalance is a risk factor of COVID-19 mortality and gut microbiota may provide a new therapeutic avenue for colorectal cancer patients.
Self-Administered Gerocognitive Examination: longitudinal cohort testing for the early detection of dementia conversion
Authors: Scharre Douglas W. , Chang Shu ing , Nagaraja Haikady N. , Wheeler Natalie C. , Kataki Maria
Published: December 2021

Background

Significant cognitive changes as individuals’ age are not being identified in a timely manner, delaying diagnosis and treatments. Use of brief, multi-domain, self-administered, objective cognitive assessment tools may remove some barriers in assessing and identifying cognitive changes. We compared longitudinal Self-Administered Gerocognitive Examination (SAGE) test scores to non-self-administered Mini-Mental State Examination (MMSE) scores in 5 different diagnostic subgroups.

Methods

A cohort study evaluating annual rates of change was performed on 665 consecutive patients from Ohio State University Memory Disorders Clinic. Patients with at least two visits 6 months apart evaluated with SAGE and MMSE and classified according to standard clinical criteria as subjective cognitive decline (SCD), mild cognitive impairment (MCI), or Alzheimer’s disease (AD) dementia were included. The pattern of change in SAGE scores was compared to MMSE. One way and repeated measures ANOVA and linear regression models were used.

Results

Four hundred twenty-four individuals (40 SCD, 94 MCI non-converters to dementia, 70 MCI converters to dementia (49 to AD dementia and 21 to non-AD dementia), 220 AD dementia) met inclusion criteria. SAGE and MMSE scores declined respectively at annual rates of 1.91 points/year (p < 0.0001) and 1.68 points/year (p < 0.0001) for MCI converters to AD dementia, and 1.82 points/year (p < 0.0001) and 2.38 points/year (p < 0.0001) for AD dementia subjects. SAGE and MMSE scores remained stable for SCD and MCI non-converters. Statistically significant decline from baseline scores in SAGE occurred at least 6 months earlier than MMSE for MCI converters to AD dementia (14.4 vs. 20.4 months), MCI converters to non-AD dementia (14.4 vs. 32.9 months), and AD dementia individuals (8.3 vs. 14.4 months).

Conclusions

SAGE detects MCI conversion to dementia at least 6 months sooner than MMSE. Being self-administered, SAGE also addresses a critical need of removing some barriers in performing cognitive assessments. Limitations of our single-site cohort study include potential referral and sampling biases. Repetitively administering SAGE and identifying stability or decline may provide clinicians with an objective cognitive biomarker impacting evaluation and management choices.