bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systems biology analysis of lung fibrosis-related genes in the bleomycin mouse model
Authors: Toren Dmitri , Yanai Hagai , Abu Taha Reem , Bunu Gabriela , Ursu Eugen , Ziesche Rolf , Tacutu Robi , Fraifeld Vadim E 
Published: September 2021

AbstractTissue fibrosis is a major driver of pathology in aging and is involved in numerous age-related diseases. The lungs are particularly susceptible to fibrotic pathology which is currently difficult to treat. The mouse bleomycin-induced fibrosis model was developed to investigate lung fibrosis and widely used over the years. However, a systematic analysis of the accumulated results has not been performed. We undertook a comprehensive data mining and subsequent manual curation, resulting in a collection of 213 genes (available at the TiRe database, www.tiredb.org), which when manipulated had a clear impact on bleomycin-induced lung fibrosis. Our meta-analysis highlights the age component in pulmonary fibrosis and strong links of related genes with longevity. The results support the validity of the bleomycin model to human pathology and suggest the importance of a multi-target therapeutic strategy for pulmonary fibrosis treatment.
Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies
Authors: Rehman Atta Ur , Sepahi Neda , Bedoni Nicola , Ravesh Zeinab , Salmaninejad Arash , Cancellieri Francesca , Peter Virginie G. , Quinodoz Mathieu , Mojarrad Majid , Pasdar Alireza , Asad Ali Ghanbari , Ghalamkari Saman , Piran Mehran , Piran Mehrdad , Superti-Furga Andrea , Rivolta Carlo 
Published: September 2021

AbstractInherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
Tumor distribution affects bladder recurrence but not survival outcome of multifocal upper tract urothelial carcinoma treated with radical nephroureterectomy
Authors: Sheu Zai-Lin , Huang Chi-Ping , Chang Chao-Hsiang , Chen Chung-Hsin , Hong Jian-Hua , Weng Han-Yu , Tai Ta-Yao , Chung Shiu-Dong , Lo Chi-Wen , Hsueh Thomas Y. , Tsai Yao-Chou , Jiang Yuan-Hong , Chiang Bing-Juin , Chen Yung-Tai , Lin Jen-Tai , Lin Wei-Yu , Jou Yeong-Chin , Tseng Jen-Shu , Wu Chia-Chang , Wu Wen‑Jeng , Yeh Hsin‑Chih 
Published: September 2021

AbstractTumor multifocality and location are prognostic factors for upper tract urothelial carcinoma (UTUC). However, confounding effects can appear when these two factors are analyzed together. Therefore, we aimed to investigate the impact of tumor distribution on the outcomes of multifocal UTUC after radical nephroureterectomy. From the 2780 UTUC patients in the Taiwan UTUC Collaboration Group, 685 UTUC cases with multifocal tumors (defined as more than one tumor lesion in unilateral upper urinary tract) were retrospectively included and divided into three groups: multiple renal pelvic tumors, multiple ureteral tumors, and synchronous renal pelvic and ureteral tumors included 164, 152, and 369 patients, respectively. We found the prevalence of carcinoma in situ was the highest in the synchronous group. In multivariate survival analyses, tumor distribution showed no difference in cancer-specific and disease-free survival, but there was a significant difference in bladder recurrence-free survival. The synchronous group had the highest bladder recurrence rate. In summary, tumor distribution did not influence the cancer-specific outcomes of multifocal UTUC, but synchronous lesions led to a higher rate of bladder recurrence than multiple renal pelvic tumors. We believe that the distribution of tumors reflects the degree of malignant involvement within the urinary tract, but has little significance for survival or disease progression.
Modified double dumbbell-shaped split-ring resonator-based negative permittivity metamaterial for satellite communications with high effective medium ratio
Authors: Hossain Md Bellal , Faruque Mohammad Rashed Iqbal , Islam Sikder Sunbeam , Islam Mohammad Tariqul 
Published: September 2021

AbstractMetamaterial with negative permittivity demonstrate excellent performance in cutting-edge technology. Thus, this study modified the double dumbbell-shaped split-ring resonator (MDD-SRR) based negative permittivity for satellite communications. The proposed MDD-SRR unit cell comprises a square-shaped split-ring resonator and two dumbbell-shaped rings. Some parts of the outer square ring were extended to enlarge the electrical length which altered the inductance of the metamaterial unit cell. The dimension of the proposed unit cell is 9 × 9 × 1.524 mm3, fabricated on a Rogers RT6002 (lossy) substrate material. Based on the results, five resonances for the transmission coefficient were achieved at frequencies of 2.896 GHz, 8.11 GHz, 9.76 GHz, 12.48 GHz and 13.49 GHz, including the S, X and Ku band satellite communication frequency bands through numerical simulation in a high-frequency electromagnetic simulator Computer Simulation Technology (CST) microwave studio. Negative permittivity at frequencies ranging from 2.896–3.76 GHz, 8.11–8.592 GHz, 9.76–10.784 GHz, 12.496–12.768 GHz, 13.504–14.4 GHz, were observed and extracted using the Robust and Nicolson–Ross–Weir (NRW) methods. Meanwhile, an effective medium ratio (EMR) measured at 11.51 to 2.896 GHz specified the goodness of the metamaterial unit cell for satellite communication with higher bandwidth and gain. The simulated, circuit model and measured results that were compared for validation purposes indicated that the simulation results, the equivalent circuit model results and measured results occupied each other. Moreover, the numerical simulation of the double dumbbell-shaped metamaterial unit cell was performed using a High-Frequency Structure Simulator (HFSS) to confirm the results. To evaluate the parametric study, the proposed unit cell was subjected to change different substrate types, change of split gap of rings, change of direction of electromagnetic field propagation, and structural optimization. In conclusion, the S, X and Ku-bands in the proposed metamaterial are competent for satellite communications as they are also investigated using an array of a unit cell.
Benefits from one session of deep and slow breathing on vagal tone and anxiety in young and older adults
Authors: Magnon Valentin , Dutheil Frédéric , Vallet Guillaume T. 
Published: September 2021

AbstractAnxiety is recognized as a major health issue and is quite prevalent among older adults. An efficient way to manage anxiety is abdominal breathing. Breathing exercises seem to reduce anxiety and to increase parasympathetic activity assessed by HRV indexes. Yet, the effect of abdominal breathing on physiological stress (HRV) and anxiety in older adults remains poorly understood. Therefore, the aim of this study is to test the effects of deep and slow breathing (DSB, low inhale/exhale ratio) on physiological stress and anxiety in older adults (n = 22) in comparison with younger ones (n = 25). DSB increased significantly HFpower and reduced state anxiety in both younger and older adults. Interestingly, the increased in HF power was significantly higher among older adults than younger ones. As expected, the ratio inhale/exhale being not equal, RMSSD did not increase following DSB. Thus, we provide evidence suggesting that DSB is more beneficial to older adults than younger ones to restore vagal outflow. Despite future work being required, those results provide relevant clinical application leads to manage state anxiety among older adults and to promote successfull aging.
One dollar incentive improves tuberculosis treatment outcomes in programmatic settings in rural Uganda
Authors: Baluku Joseph Baruch , Nakazibwe Bridget , Twinomugisha Bright , Najjuuko Rebecca , Isabella Nyirazihawe , Nassozi Sylvia , Namiiro Sharon , Katagira Winceslaus , Byonanebye Dathan Mirembe , Sekaggya-Wiltshire Christine , Muchiri Joseph , Ndungu Elizabeth , Anguzu Godwin , Mayanja-Kizza Harriet , Andia-Biraro Irene 
Published: September 2021

AbstractThe study aim was to determine the association of a one United States dollar (USD) dollar incentive and tuberculosis (TB) treatment outcomes among people with TB receiving treatment at a rural hospital in Uganda under programmatic settings. We conducted a quasi-experiment in which people with TB were randomised (1:1 ratio) to receive either a one USD incentive at months 0, 2, 5 and 6 (Dollar arm) or routine care (Routine arm). A second control group (Retrospective controls) consisted of participants who had a treatment outcome in the preceding 6 months. Treatment outcomes were compared between the intervention and control groups using Pearson’s chi-square and Fisher’s exact tests. The association between the incentive and treatment outcomes was determined using Poisson regression analysis with robust variances. Between November 2018 and October 2019, we enrolled 180 participants (60 in the Dollar arm and 120 in the Control group). TB cure (33.3% vs. 20.8%, p = 0.068) and treatment success (70.0% vs. 59.2% p = 0.156) were higher in the Dollar arm than the Control group, while loss-to-follow-up was lower in the Dollar arm (10.0% vs. 20.8% p = 0.070). Participants in the Dollar arm were more likely to be cured (adjusted incidence rate ratio (aIRR): 1.59, 95% CI 1.04–2.44, p = 0.032) and less likely to be lost to follow-up (aIRR: 0.44, 95% CI 0.20–0.96, p = 0.040). A one-dollar incentive was associated with higher TB cure and lower loss-to-follow-up among people with TB in rural Uganda.
Vicarious ratings of social touch the effect of age and autistic traits
Authors: Haggarty Connor J. , Moore David J. , Trotter Paula D. , Hagan Rachel , McGlone Francis P. , Walker Susannah C. 
Published: September 2021

AbstractTactile sensitivities are common in Autism Spectrum Conditions (autism). Psychophysically, slow, gentle stroking touch is typically rated as more pleasant than faster or slower touch. Vicarious ratings of social touch results in a similar pattern of velocity dependent hedonic ratings as directly felt touch. Here we investigated whether adults and children’s vicarious ratings vary according to autism diagnosis and self-reported autistic traits. Adults’ scoring high on the AQ rated stroking touch on the palm as less pleasant than a Low AQ group. However, in contrast to our hypothesis, we did not find any effect of autism diagnosis on children’s touch ratings despite parental reports highlighting significant somatosensory sensitivities. These results are discussed in terms of underpinning sensory and cognitive factors.
Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC
Authors: Ohshiro Takahito , Konno Masamitsu , Asai Ayumu , Komoto Yuki , Yamagata Akira , Doki Yuichiro , Eguchi Hidetoshi , Ofusa Ken , Taniguchi Masateru , Ishii Hideshi 
Published: September 2021

AbstractEpitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. We have proposed a single-molecule quantum sequencer for mapping RNA base modifications in microRNAs (miRNAs), such as N6-methyladenosine (m6A) or 5-methylcytidine (5mC), which are related to cancer cell propagation and suppression. Here, we investigated 5mC and m6A in hsa-miR-200c-5p extracted from colorectal cancer cells and determined their methylation sites and rates; the data were comparable to those determined by mass spectrometry. Furthermore, we evaluated the methylation ratio of cytidine and adenosine at each site in the sequences and its relationship. These results suggest that the methylation ratio of cytidine and adenosine is facilitated by the presence of vicinal methylation. Our work provides a robust new tool for sequencing various types of RNA base modifications in their RNA context.
Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis
Authors: Wang Zhong-Yi , Keogh Adrian , Waldt Annick , Cuttat Rachel , Neri Marilisa , Zhu Shanshan , Schuierer Sven , Ruchti Alexandra , Crochemore Christophe , Knehr Judith , Bastien Julie , Ksiazek Iwona , Sánchez-Taltavull Daniel , Ge Hui , Wu Jing , Roma Guglielmo , Helliwell Stephen B. , Stroka Deborah , Nigsch Florian 
Published: September 2021

AbstractFibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide. Previous studies of nonalcoholic steatohepatitis (NASH) with fibrosis were largely restricted to bulk transcriptome profiles. Thus, our understanding of this disease is limited by an incomplete characterization of liver cell types in general and hepatic stellate cells (HSCs) in particular, given that activated HSCs are the major hepatic fibrogenic cell population. To help fill this gap, we profiled 17,810 non-parenchymal cells derived from six healthy human livers. In conjunction with public single-cell data of fibrotic/cirrhotic human livers, these profiles enable the identification of potential intercellular signaling axes (e.g., ITGAV–LAMC1, TNFRSF11B–VWF and NOTCH2–DLL4) and master regulators (e.g., RUNX1 and CREB3L1) responsible for the activation of HSCs during fibrogenesis. Bulk RNA-seq data of NASH patient livers and rodent models for liver fibrosis of diverse etiologies allowed us to evaluate the translatability of candidate therapeutic targets for NASH-related fibrosis. We identified 61 liver fibrosis-associated genes (e.g., AEBP1, PRRX1 and LARP6) that may serve as a repertoire of translatable drug target candidates. Consistent with the above regulon results, gene regulatory network analysis allowed the identification of CREB3L1 as a master regulator of many of the 61 genes. Together, this study highlights potential cell–cell interactions and master regulators that underlie HSC activation and reveals genes that may represent prospective hallmark signatures for liver fibrosis.
Refractive lens power and lens thickness in children (6–16 years old)
Authors: Lu Tailiang , Song Jike , Wu Qiuxin , Jiang Wenjun , Tian Qingmei , Zhang Xiuyan , Xu Jing , Wu Jianfeng , Hu Yuanyuan , Sun Wei , Bi Hongsheng 
Published: September 2021

AbstractTo examine the refractive lens power (RLP) and lens thickness and their associated factors in children from North-Western China. Children from two schools (primary school and junior high school) in the North-Western Chinese province of Qinghai underwent a comprehensive ophthalmic examination including biometry and cycloplegic refractometry. The RLP was calculated using Bennett’s equation. The study included 596 (77.9%) individuals (mean age: 11.0 ± 2.8 years; range: 6–16 years) with a mean axial length of 23.65 ± 1.24 mm (range: 20.02–27.96 mm). Mean lens thickness was 3.30 ± 0.16 mm (range: 2.85–3.99 mm) and mean RLP was 24.85 ± 1.98D (range: 19.40–32.97). In univariate analysis, girls as compared to boys had a significantly thicker lens and greater RLP, shorter axial length, smaller corneal curvature radius and shorter corneal curvature radius (all P < 0.001). Both sexes did not differ significantly in refractive error (P = 0.11) and corneal thickness (P = 0.16). RLP was positively associated with refractive error (correlation coefficient r = 0.33; P < 0.001) and lens thickness (r = 0.62; P < 0.001) and negatively with axial length (r =  − 0.70; P < 0.001). In univariate analysis, RLP decreased significantly with older age in the age group from age 6–13, while it plateaued thereafter, with no significant difference between boys and girls. In multivariate regression analysis, a higher RLP was associated with younger age (P < 0.001; standard regression coefficient β =  − 0.07), female sex (P < 0.001; β =  − 0.08), shorter axial length (P < 0.001; β =  − 0.48) and higher lens thickness (P < 0.001; β = 0.42). In Chinese children, RLP with a mean of 24.85 ± 1.98D decreases with older age, male sex, longer axial length, and thinner lens thickness. Changes in RLP and axial length elongation are important players in the emmetropization and myopization.
Acute and subacute macular and peripapillary angiographic changes in choroidal and retinal blood flow post-intravitreal injections
Authors: Arumuganathan Nadhini , Wiest Maximilian Robert Justus , Toro Mario Damiano , Hamann Timothy , Fasler Katrin , Zweifel Sandrine Anne 
Published: September 2021

AbstractWhether post injectional acute intraocular pressure (IOP) increase is associated with decreased peripapillary and macular perfusion is still under debate. Here, we investigated early changes in the choroidal and retinal blood flow using OCTA imaging in a cohort of patients undergoing anti-VEGF intravitreal injections (IVI) for macular edema following retinal vein occlusion and diabetic retinopathy. In this prospective single-center, observational study, the pre- and post-IVI changes in retinal perfusion were examined via assessment of vessel length density (VLD) and vessel density (VD) in deep and superficial capillary segmentations (DCP and SCP), foveal avascular zone (FAZ) in SCP, as well as flow signal deficits in the choriocapillaris segmentation. Mean IOP significantly changed over the study course (p = 0.000; ANOVA). Measurements at 5 min post-IVI (33.48 ± 10.84 mmHg) differed significantly from baseline (17.26 ± 2.41 mmHg, p = 0.000), while measurements from one day, one week, and one-month post-IVI did not (p = 0.907, p = 1.000 and p = 1.000 respectively). In comparison to baseline, no changes in OCTA parameters, including FAZ, VD, VLD, and FV, were detected 5 min post-IVI. No significant alterations in OCTA parameters were observed during study course. Increased IOP spikes were detected post-IVI; however, no potential permanent ischemic retinal damage was suspected.
A Random Forest approach to identify metrics that best predict match outcome and player ranking in the esport Rocket League
Authors: Smithies Tim D. , Campbell Mark J. , Ramsbottom Niall , Toth Adam J. 
Published: September 2021

AbstractNotational analysis is a popular tool for understanding what constitutes optimal performance in traditional sports. However, this approach has been seldom used in esports. The popular esport “Rocket League” is an ideal candidate for notational analysis due to the availability of an online repository containing data from millions of matches. The purpose of this study was to use Random Forest models to identify in-match metrics that predicted match outcome (performance indicators or “PIs”) and/or in-game player rank (rank indicators or “RIs”). We evaluated match data from 21,588 Rocket League matches involving players from four different ranks. Upon identifying goal difference (GD) as a suitable outcome measure for Rocket League match performance, Random Forest models were used alongside accompanying variable importance methods to identify metrics that were PIs or RIs. We found shots taken, shots conceded, saves made, and time spent goalside of the ball to be the most important PIs, and time spent at supersonic speed, time spent on the ground, shots conceded and time spent goalside of the ball to be the most important RIs. This work is the first to use Random Forest learning algorithms to highlight the most critical PIs and RIs in a prominent esport.
Towards optimization of plant cell detection in suspensions using impedance-based analyses and the unified equivalent circuit model
Authors: Kadan-Jamal Kian , Jog Aakash , Sophocleous Marios , Georgiou Julius , Avni Adi , Shacham-Diamand Yosi 
Published: September 2021

AbstractAn improved approach for comparative study of plant cells for long term and continuous monitoring using electrical impedance spectroscopy is demonstrated for tomato and tobacco plant cells (MSK8 and BY2) in suspensions. This approach is based on the locations and magnitudes of defining features in the impedance spectra of the recently reported unified equivalent circuit model. The ultra-wide range (4 Hz to 20 GHz) impedance spectra of the cell lines were measured using custom probes, and were analyzed using the unified equivalent circuit model, highlighting significant negative phase peaks in the ~ 1 kHz to ~ 10 MHz range. These peaks differ between the tomato and tobacco cells, and since they can be easily defined, they can potentially be used as the signal for differentiating between different cell cultures or monitoring them over time. These findings were further analysed, showing that ratios relating the resistances of the media and the resistance of the cells define the sensitivity of the method, thus affecting its selectivity. It was further shown that cell agglomeration is also an important factor in the impedance modeling in addition to the overall cell concentration. These results can be used for optimizing and calibrating electrical impedance spectroscopy-based sensors for long term monitoring of cell lines in suspension for a given specific cell and media types.
Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination
Authors: Li Heqin , Yue Haiwang , Xie Junliang , Bu Junzhou , Li Li , Xin Xueying , Zhao Yanming , Zhang Haiyan , Yang Li , Wang Jianhua , Jiang Xuwen 
Published: September 2021

AbstractAbiotic stresses, including cold and drought, negatively affect maize (Zea mays L.) seed field emergence and later yield and quality. In order to reveal the molecular mechanism of maize seed resistance to abiotic stress at seed germination, the global transcriptome of high- vigour variety Zhongdi175 exposed to cold- and drought- stress was analyzed by RNA-seq. In the comparison between the control and different stressed sample, 12,299 differentially expressed genes (DEGs) were detected, of which 9605 and 7837 DEGs were identified under cold- and drought- stress, respectively. Functional annotation analysis suggested that stress response mediated by the pathways involving ribosome, phenylpropanoid biosynthesis and biosynthesis of secondary metabolites, among others. Of the obtained DEGs (12,299), 5,143 genes are common to cold- and drought- stress, at least 2248 TFs in 56 TF families were identified that are involved in cold and/or drought treatments during seed germination, including bHLH, NAC, MYB and WRKY families, which suggested that common mechanisms may be originated during maize seed germination in response to different abiotic stresses. This study will provide a better understanding of the molecular mechanism of response to abiotic stress during maize seed germination, and could be useful for cultivar improvement and breeding of high vigour maize cultivars.