bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth differentiation factor 1-induced tumour plasticity provides a therapeutic window for immunotherapy in hepatocellular carcinoma
Authors: Cheng Wei , Li Hao-Long , Xi Shao-Yan , Zhang Xiao-Feng , Zhu Yun , Le Xing  , Mo Yan-Xuan , Li Mei-Mei , Kong Fan-En , Zhu Wen-Jie , Chen Xiao-Gang , Cui Hui-Qing , Cao Zhi-Ming , Gong Yuan-Feng , Tang Yun-Qiang , Zhang Yan , Guan Xin-Yuan , Ma Ning-Fang , Liu Ming 
Published: December 2021

AbstractTumour lineage plasticity is an emerging hallmark of aggressive tumours. Tumour cells usually hijack developmental signalling pathways to gain cellular plasticity and evade therapeutic targeting. In the present study, the secreted protein growth and differentiation factor 1 (GDF1) is found to be closely associated with poor tumour differentiation. Overexpression of GDF1 suppresses cell proliferation but strongly enhances tumour dissemination and metastasis. Ectopic expression of GDF1 can induce the dedifferentiation of hepatocellular carcinoma (HCC) cells into their ancestral lineages and reactivate a broad panel of cancer testis antigens (CTAs), which further stimulate the immunogenicity of HCC cells to immune-based therapies. Mechanistic studies reveal that GDF1 functions through the Activin receptor-like kinase 7 (ALK7)-Mothers against decapentaplegic homolog 2/3 (SMAD2/3) signalling cascade and suppresses the epigenetic regulator Lysine specific demethylase 1 (LSD1) to boost CTA expression. GDF1-induced tumour lineage plasticity might be an Achilles heel for HCC immunotherapy. Inhibition of LSD1 based on GDF1 biomarker prescreening might widen the therapeutic window for immune checkpoint inhibitors in the clinic.
The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer
Authors: Banavar Guruduth , Ogundijo Oyetunji , Toma Ryan , Rajagopal Sathyapriya , Lim Yen Kai , Tang Kai , Camacho Francine , Torres Pedro J. , Gline Stephanie , Parks Matthew , Kenny Liz , Perlina Ally , Tily Hal , Dimitrova Nevenka , Amar Salomon , Vuyisich Momchilo , Punyadeera Chamindie 
Published: December 2021

AbstractDespite advances in cancer treatment, the 5-year mortality rate for oral cancers (OC) is 40%, mainly due to the lack of early diagnostics. To advance early diagnostics for high-risk and average-risk populations, we developed and evaluated machine-learning (ML) classifiers using metatranscriptomic data from saliva samples (n = 433) collected from oral premalignant disorders (OPMD), OC patients (n = 71) and normal controls (n = 171). Our diagnostic classifiers yielded a receiver operating characteristics (ROC) area under the curve (AUC) up to 0.9, sensitivity up to 83% (92.3% for stage 1 cancer) and specificity up to 97.9%. Our metatranscriptomic signature incorporates both taxonomic and functional microbiome features, and reveals a number of taxa and functional pathways associated with OC. We demonstrate the potential clinical utility of an AI/ML model for diagnosing OC early, opening a new era of non-invasive diagnostics, enabling early intervention and improved patient outcomes.
Deep nasal sinus cavity microbiota dysbiosis in Parkinson’s disease
Authors: Pal Gian , Ramirez Vivian , Engen Phillip A. , Naqib Ankur , Forsyth Christopher B. , Green Stefan J. , Mahdavinia Mahboobeh , Batra Pete S. , Tajudeen Bobby A. , Keshavarzian Ali 
Published: December 2021

AbstractOlfactory dysfunction is a pre-motor symptom of Parkinson’s disease (PD) that appears years prior to diagnosis and can affect quality of life in PD. Changes in microbiota community in deep nasal cavity near the olfactory bulb may trigger the olfactory bulb-mediated neuroinflammatory cascade and eventual dopamine loss in PD. To determine if the deep nasal cavity microbiota of PD is significantly altered in comparison to healthy controls, we characterized the microbiota of the deep nasal cavity using 16S rRNA gene amplicon sequencing in PD subjects and compared it to that of spousal and non-spousal healthy controls. Correlations between microbial taxa and PD symptom severity were also explored. Olfactory microbial communities of PD individuals were more similar to those of their spousal controls than to non-household controls. In direct comparison of PD and spousal controls and of PD and non-spousal controls, significantly differently abundant taxa were identified, and this included increased relative abundance of putative opportunistic-pathobiont species such as Moraxella catarrhalis. M. catarrhalis was also significantly correlated with more severe motor scores in PD subjects. This proof-of-concept study provides evidence that potential pathobionts are detected in the olfactory bulb and that a subset of changes in the PD microbiota community could be a consequence of unique environmental factors associated with PD living. We hypothesize that an altered deep nasal microbiota, characterized by a putative pro-inflammatory microbial community, could trigger neuroinflammation in PD.
Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis
Authors: Rahbar Mohammad Reza , Jahangiri Abolfazl , Khalili Saeed , Zarei Mahboubeh , Mehrabani-Zeinabad Kamran , Khalesi Bahman , Pourzardosht Navid , Hessami Anahita , Nezafat Navid , Sadraei Saman , Negahdaripour Manica 
Published: December 2021

AbstractSpike glycoprotein (Sgp) is liable for binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the host receptors. Since Sgp is the main target for vaccine and drug designing, elucidating its mutation pattern could help in this regard. This study is aimed at investigating the correspondence of specific residues to the SgpSARS-CoV-2 functionality by explorative interpretation of sequence alignments. Centrality analysis of the Sgp dissects the importance of these residues in the interaction network of the RBD-ACE2 (receptor-binding domain) complex and furin cleavage site. Correspondence of RBD to threonine500 and asparagine501 and furin cleavage site to glutamine675, glutamine677, threonine678, and alanine684 was observed; all residues are exactly located at the interaction interfaces. The harmonious location of residues dictates the RBD binding property and the flexibility, hydrophobicity, and accessibility of the furin cleavage site. These species-specific residues can be assumed as real targets of evolution, while other substitutions tend to support them. Moreover, all these residues are parts of experimentally identified epitopes. Therefore, their substitution may affect vaccine efficacy. Higher rate of RBD maintenance than furin cleavage site was predicted. The accumulation of substitutions reinforces the probability of the multi-host circulation of the virus and emphasizes the enduring evolutionary events.
Opisthenar microvessel area as a sensitive predictive index of arterial stiffness in hypertensive patients
Authors: Guo Zhen Yi , Chen Chen , Jin Xin , Zhao Zai Hao , Cui Lan , Zhang Yin Hua 
Published: December 2021

AbstractWe aimed to analyze whether opisthenar microvessel area (OMA, measured with Optical Coherence Tomography (OCT) angiography) was associated with blood pressure (BP), arterial stiffness and whether OMA can predict arterial stiffness in hypertensive (HTN) patients. Results from 90 participants showed that BP, brachial-ankle pulse wave velocity (baPWV) and ankle brachial index (ABI) were significantly higher but OMA (in control, with cold- and warm-stimulation, NT, CST, HST and the differences, CSD, HSD) were significantly reduced in HTN group (n = 36) compared to non-HTN (n = 54). NT, CST, HST and HSD showed negative correlations with baPWV and ABI in all participants, female (n = 47) and male group (n = 43), but the correlation was absent when the participants were divided into HTN and non-HTN. Logistic Regression analysis showed that only baPWV was a significant risk factor for HSD (OR 19.7, 95%CI 4.959–78.733, p < 0.0001) but not the age, BMI, smoking, drinking or exercise status (p > 0.05). Receiver Operating Characteristics analysis for HSD was 0.781, 0.804, 0.770, respectively. HSD < 9439.5 μm2 predicted high BP and arterial stiffness (95% CI in all participants: baPWV, 0.681–0.881, SBP, 0.709–0.900, DBP, 0.672–0.867, p < 0.001). These results suggest that OMA is a sensitive index to predict arterial stiffness in HTN population.
An altered microbiome in a Parkinson’s disease model Drosophila melanogaster has a negative effect on development
Authors: Parker-Character Jade , Hager David R. , Call Tanner B. , Pickup Zachary S. , Turnbull Scott A. , Marshman Evan M. , Korch Shaleen B. , Chaston John M. , Call Gerald B. 
Published: December 2021

AbstractParkinson’s disease (PD) is the second most common neurodegenerative disease, besides Alzheimer’s Disease, characterized by multiple symptoms, including the well-known motor dysfunctions. It is well-established that there are differences in the fecal microbiota composition between Parkinson’s disease (PD) patients and control populations, but the mechanisms underlying these differences are not yet fully understood. To begin to close the gap between description and mechanism we studied the relationship between the microbiota and PD in a model organism, Drosophila melanogaster. First, fecal transfers were performed with a D. melanogaster model of PD that had a mutation in the parkin (park25) gene. Results indicate that the PD model feces had a negative effect on both pupation and eclosion in both control and park25 flies, with a greater effect in PD model flies. Analysis of the microbiota composition revealed differences between the control and park25 flies, consistent with many human studies. Conversely, gnotobiotic treatment of axenic embryos with feces-derived bacterial cultures did not affect eclosure. We speculate this result might be due to similarities in bacterial prevalence between mutant and control feces. Further, we confirmed a bacteria-potentiated impact on mutant and control fly phenotypes by measuring eclosure rate in park25 flies that were mono-associated with members of the fly microbiota. Both the fecal transfer and the mono-association results indicate a host genotype-microbiota interaction. Overall, this study concludes functional effects of the fly microbiota on PD model flies, providing support to the developing body of knowledge regarding the influence of the microbiota on PD.
Comparing data driven and physics inspired models for hopping transport in organic field effect transistors
Authors: Lakshminarayanan Madhavkrishnan , Dutta Rajdeep , Repaka D. V. Maheswar , Jayavelu Senthilnath , Leong Wei Lin , Hippalgaonkar Kedar 
Published: December 2021

AbstractThe past few decades have seen an uptick in the scope and range of device applications of organic semiconductors, such as organic field-effect transistors, organic photovoltaics and light-emitting diodes. Several researchers have studied electrical transport in these materials and proposed physical models to describe charge transport with different material parameters, with most disordered semiconductors exhibiting hopping transport. However, there exists a lack of a consensus among the different models to describe hopping transport accurately and uniformly. In this work, we first evaluate the efficacy of using a purely data-driven approach, i.e., symbolic regression, in unravelling the relationship between the measured field-effect mobility and the controllable inputs of temperature and gate voltage. While the regressor is able to capture the scaled mobility well with mean absolute error (MAE) ~ O(10–2), better than the traditionally used hopping transport model, it is unable to derive physically interpretable input–output relationships. We then examine a physics-inspired renormalization approach to describe the scaled mobility with respect to a scale-invariant reference temperature. We observe that the renormalization approach offers more generality and interpretability with a MAE of the ~ O(10–1), still better than the traditionally used hopping model, but less accurate as compared to the symbolic regression approach. Our work shows that physics-based approaches are powerful compared to purely data-driven modelling, providing an intuitive understanding of data with extrapolative ability.
Closely related gull species show contrasting foraging strategies in an urban environment
Authors: Lato K. A. , Madigan D. J. , Veit R. R. , Thorne L. H. 
Published: December 2021

AbstractThe expansion of urban landscapes has both negative and positive effects on wildlife. Understanding how different species respond to urbanization is key to assessing how urban landscapes influence regional wildlife behavior and ecosystem structure. Gulls are often described as strong urban adapters, but few studies have explored species-specific differences in habitat use. Here, we use GPS tracking in conjunction with stable isotope analysis (SIA) to quantify the habitat use and trophic ecology of great black-backed gulls (Larus marinus) and herring gulls (L. argentatus) in an urbanized area. Non-Metric Multidimensional Scaling (NMDS) of foraging locations revealed significant differences in the habitat use between species. Great black-backed gulls foraged primarily in marine habitats and herring gulls foraged primarily in specific urban habitats (e.g., landfills, dumpsters) and showed higher site fidelity in terms of the proportion of foraging sites revisited. Further, great black-backed gulls had significantly higher δ15N and δ13C than herring gulls, reflecting the use of marine, rather than urban, food sources. This study highlights the variability in urban habitat utilization among closely related species, assesses stable isotope signatures of urban diets in wild birds, and discusses ecological implications of the relative contribution of urban and marine foraging.
Response triggering by an acoustic stimulus increases with stimulus intensity and is best predicted by startle reflex activation
Authors: Maslovat Dana , Sadler Christin M. , Smith Victoria , Bui Allison , Carlsen Anthony N. 
Published: December 2021

AbstractIn a simple reaction time task, the presentation of a startling acoustic stimulus has been shown to trigger the prepared response at short latency, known as the StartReact effect. However, it is unclear under what conditions it can be assumed that the loud stimulus results in response triggering. The purpose of the present study was to examine how auditory stimulus intensity and preparation level affect the probability of involuntary response triggering and the incidence of activation in the startle reflex indicator of sternocleidomastoid (SCM). In two reaction time experiments, participants were presented with an irrelevant auditory stimulus of varying intensities at various time points prior to the visual go-signal. Responses were independently categorized as responding to either the auditory or visual stimulus and those with or without SCM activation (i.e., SCM+/−). Both the incidence of response triggering and proportion of SCM+ trials increased with stimulus intensity and presentation closer to the go-signal. Data also showed that participants reacted to the auditory stimulus at a much higher rate on trials where the auditory stimulus elicited SCM activity versus those that did not, and a logistic regression analysis confirmed that SCM activation is a reliable predictor of response triggering for all conditions.
Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans
Authors: Suarez-Pajes Eva , Díaz-García Claudio , Rodríguez-Pérez Héctor , Lorenzo-Salazar Jose M. , Marcelino-Rodríguez Itahisa , Corrales Almudena , Zheng Xiuwen , Callero Ariel , Perez-Rodriguez Eva , Garcia-Robaina Jose C. , González-Montelongo Rafaela , Flores Carlos , Guillen-Guio Beatriz 
Published: December 2021

AbstractDespite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10–4, OR [95% CI] = 0.47 [0.29– 0.73]).
Hole doping effect of MoS2 via electron capture of He+ ion irradiation
Authors: Han Sang Wook , Yun Won Seok , Kim Hyesun , Kim Yanghee , Kim D.-H. , Ahn Chang Won , Ryu Sunmin 
Published: December 2021

AbstractBeyond the general purpose of noble gas ion sputtering, which is to achieve functional defect engineering of two-dimensional (2D) materials, we herein report another positive effect of low-energy (100 eV) He+ ion irradiation: converting n-type MoS2 to p-type by electron capture through the migration of the topmost S atoms. The electron capture ability via He+ ion irradiation is valid for supported bilayer MoS2; however, it is limited at supported monolayer MoS2 because the charges on the underlying substrates transfer into the monolayer under the current condition for He+ ion irradiation. Our technique provides a stable and universal method for converting n-type 2D transition metal dichalcogenides (TMDs) into p-type semiconductors in a controlled fashion using low-energy He+ ion irradiation.
The structure of the superior and inferior parietal lobes predicts inter-individual suitability for virtual reality
Authors: Hosoda Chihiro , Futami Kyosuke , Hosokawa Kenchi , Isogaya Yuko , Terada Tsutomu , Maruya Kazushi , Okanoya Kazuo 
Published: December 2021

AbstractThe global virtual reality (VR) market is significantly expanding and being challenged with an increased demand owing to COVID-19. Unfortunately, VR is not useful for everyone due to large interindividual variability existing in VR suitability. To understand the neurobiological basis of this variability, we obtained neural structural and functional data from the participants using 3T magnetic resonance imaging. The participants completed one of two tasks (sports training or cognitive task) using VR, which differed in the time scale (months/minutes) and domain (motor learning/attention task). Behavioral results showed that some participants improved their motor skills in the real world after 1-month training in the virtual space or obtained high scores in the 3D attention task (high suitability for VR), whereas others did not (low suitability for VR). Brain structure analysis revealed that the structural properties of the superior and inferior parietal lobes contain information that can predict an individual’s suitability for VR.
Dengue NS1 antigen kit shows high sensitivity for detection of recombinant dengue virus-2 NS1 antigen spiked with Aedes aegypti mosquitoes
Authors: Abraham Philip Raj , R Bharathy , N Pradeep Kumar , Kumar Ashwani 
Published: December 2021

AbstractDengue, caused by the dengue virus (DENV) is a significant vector-borne disease. In absence of a specific treatment and vaccine, dengue is becoming a rising threat to public health. Currently, control of dengue mainly focuses on the surveillance of the mosquito vectors. Improved surveillance methods for DENV in mosquito populations would be highly beneficial to the public health. However, current methods of DENV detection in mosquitoes requires specialized equipment and expensive reagents and highly trained personnel. As an alternative, commercially available dengue NS1 antigen ELISA kits could be used for detection of DENV infection inAedes aegyptimosquitoes. In this study, we explored the utility of commercially available Dengue NS1 antigen kit (J. Mitra & Co. Pvt. Ltd) for the detection of recombinant dengue virus-2 (rDENV-2) NS1 protein and serum of dengue infected patient spiked withAe. aegyptimosquito pools. The kit was found to be highly sensitive and specific towards detection of all serotypes of DENV. Further, it could detect as low as 750 femto gram rDENV-2 NS1 protein. It was also observed that rDENV-2 NS1 antigen spiked with blood-fed and unfed mosquito pools could be detected. In addition, the kit also detected dengue infected patient serum spiked withAe. aegyptimosquito pools. Overall, the Dengue NS1 antigen kit displayed high sensitivity towards detection of recombinant as well as serum NS1 protein spiked withAe. aegyptimosquito pools and could be considered for the dengue virus surveillance after a field evaluation inAe. aegyptimosquitoes.
Machine learning of native T1 mapping radiomics for classification of hypertrophic cardiomyopathy phenotypes
Authors: Antonopoulos Alexios S. , Boutsikou Maria , Simantiris Spyridon , Angelopoulos Andreas , Lazaros George , Panagiotopoulos Ioannis , Oikonomou Evangelos , Kanoupaki Mikela , Tousoulis Dimitris , Mohiaddin Raad H. , Tsioufis Konstantinos , Vlachopoulos Charalambos 
Published: December 2021

AbstractWe explored whether radiomic features from T1 maps by cardiac magnetic resonance (CMR) could enhance the diagnostic value of T1 mapping in distinguishing health from disease and classifying cardiac disease phenotypes. A total of 149 patients (n = 30 with no heart disease, n = 30 with LVH, n = 61 with hypertrophic cardiomyopathy (HCM) and n = 28 with cardiac amyloidosis) undergoing a CMR scan were included in this study. We extracted a total of 850 radiomic features and explored their value in disease classification. We applied principal component analysis and unsupervised clustering in exploratory analysis, and then machine learning for feature selection of the best radiomic features that maximized the diagnostic value for cardiac disease classification. The first three principal components of the T1 radiomics were distinctively correlated with cardiac disease type. Unsupervised hierarchical clustering of the population by myocardial T1 radiomics was significantly associated with myocardial disease type (chi2 = 55.98, p < 0.0001). After feature selection, internal validation and external testing, a model of T1 radiomics had good diagnostic performance (AUC 0.753) for multinomial classification of disease phenotype (normal vs. LVH vs. HCM vs. cardiac amyloid). A subset of six radiomic features outperformed mean native T1 values for classification between myocardial health vs. disease and HCM phenocopies (AUC of T1 vs. radiomics model, for normal: 0.549 vs. 0.888; for LVH: 0.645 vs. 0.790; for HCM 0.541 vs. 0.638; and for cardiac amyloid 0.769 vs. 0.840). We show that myocardial texture assessed by native T1 maps is linked to features of cardiac disease. Myocardial radiomic phenotyping could enhance the diagnostic yield of T1 mapping for myocardial disease detection and classification.