bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human adipose-derived stromal/stem cells expressing doublecortin improve cartilage repair in rabbits and monkeys
Authors: Ge Dongxia , O’Brien Michael J. , Savoie Felix H. , Gimble Jeffrey M. , Wu Xiying , Gilbert Margaret H. , Clark-Patterson Gabrielle L. , Schuster Jason D. , Miller Kristin S. , Wang Alun , Myers Leann , You Zongbing 
Published: November 2021

AbstractLocalized cartilage lesions in early osteoarthritis and acute joint injuries are usually treated surgically to restore function and relieve pain. However, a persistent clinical challenge remains in how to repair the cartilage lesions. We expressed doublecortin (DCX) in human adipose-derived stromal/stem cells (hASCs) and engineered hASCs into cartilage tissues using an in vitro 96-well pellet culture system. The cartilage tissue constructs with and without DCX expression were implanted in the knee cartilage defects of rabbits (n = 42) and monkeys (n = 12). Cohorts of animals were euthanized at 6, 12, and 24 months after surgery to evaluate the cartilage repair outcomes. We found that DCX expression in hASCs increased expression of growth differentiation factor 5 (GDF5) and matrilin 2 in the engineered cartilage tissues. The cartilage tissues with DCX expression significantly enhanced cartilage repair as assessed macroscopically and histologically at 6, 12, and 24 months after implantation in the rabbits and 24 months after implantation in the monkeys, compared to the cartilage tissues without DCX expression. These findings suggest that hASCs expressing DCX may be engineered into cartilage tissues that can be used to treat localized cartilage lesions.
Diversity and molecular network patterns of symptom phenotypes
Authors: Shu Zixin , Wang Jingjing , Sun Hailong , Xu Ning , Lu Chenxia , Zhang Runshun , Li Xiaodong , Liu Baoyan , Zhou Xuezhong 
Published: November 2021

AbstractSymptom phenotypes have continuously been an important clinical entity for clinical diagnosis and management. However, non-specificity of symptom phenotypes for clinical diagnosis is one of the major challenges that need be addressed to advance symptom science and precision health. Network medicine has delivered a successful approach for understanding the underlying mechanisms of complex disease phenotypes, which will also be a useful tool for symptom science. Here, we extracted symptom co-occurrences from clinical textbooks to construct phenotype network of symptoms with clinical co-occurrence and incorporated high-quality symptom-gene associations and protein–protein interactions to explore the molecular network patterns of symptom phenotypes. Furthermore, we adopted established network diversity measure in network medicine to quantify both the phenotypic diversity (i.e., non-specificity) and molecular diversity of symptom phenotypes. The results showed that the clinical diversity of symptom phenotypes could partially be explained by their underlying molecular network diversity (PCC = 0.49, P-value = 2.14E-08). For example, non-specific symptoms, such as chill, vomiting, and amnesia, have both high phenotypic and molecular network diversities. Moreover, we further validated and confirmed the approach of symptom clusters to reduce the non-specificity of symptom phenotypes. Network diversity proposes a useful approach to evaluate the non-specificity of symptom phenotypes and would help elucidate the underlying molecular network mechanisms of symptom phenotypes and thus promotes the advance of symptom science for precision health.
An interpretable machine learning model based on a quick pre-screening system enables accurate deterioration risk prediction for COVID-19
Authors: Jia Lijing , Wei Zijian , Zhang Heng , Wang Jiaming , Jia Ruiqi , Zhou Manhong , Li Xueyan , Zhang Hankun , Chen Xuedong , Yu Zheyuan , Wang Zhaohong , Li Xiucheng , Li Tingting , Liu Xiangge , Liu Pei , Chen Wei , Li Jing , He Kunlun 
Published: November 2021

AbstractA high-performing interpretable model is proposed to predict the risk of deterioration in coronavirus disease 2019 (COVID-19) patients. The model was developed using a cohort of 3028 patients diagnosed with COVID-19 and exhibiting common clinical symptoms that were internally verified (AUC 0.8517, 95% CI 0.8433, 0.8601). A total of 15 high risk factors for deterioration and their approximate warning ranges were identified. This included prothrombin time (PT), prothrombin activity, lactate dehydrogenase, international normalized ratio, heart rate, body-mass index (BMI), D-dimer, creatine kinase, hematocrit, urine specific gravity, magnesium, globulin, activated partial thromboplastin time, lymphocyte count (L%), and platelet count. Four of these indicators (PT, heart rate, BMI, HCT) and comorbidities were selected for a streamlined combination of indicators to produce faster results. The resulting model showed good predictive performance (AUC 0.7941 95% CI 0.7926, 0.8151). A website for quick pre-screening online was also developed as part of the study.
Complex energies of the coherent longitudinal optical phonon–plasmon coupled mode according to dynamic mode decomposition analysis
Authors: Sakata Itsushi , Sakata Takuya , Mizoguchi Kohji , Tanaka Satoshi , Oohata Goro , Akai Ichiro , Igarashi Yasuhiko , Nagano Yoshihiro , Okada Masato 
Published: November 2021

AbstractIn a dissipative quantum system, we report the dynamic mode decomposition (DMD) analysis of damped oscillation signals. We used a reflection-type pump-probe method to observe time-domain signals, including the coupled modes of long-lived longitudinal optical phonons and quickly damped plasmons (LOPC) at various pump powers. The Fourier transformed spectra of the observed damped oscillation signals show broad and asymmetric modes, making it difficult to evaluate their frequencies and damping rates. We then used DMD to analyze the damped oscillation signals by precisely determining their frequencies and damping rates. We successfully identified the LOPC modes. The obtained frequencies and damping rates were shown to depend on the pump power, which implies photoexcited carrier density. We compared the pump-power dependence of the frequencies and damping rates of the LOPC modes with the carrier density dependence of the complex eigen-energies of the coupled modes by using the non-Hermitian phenomenological effective Hamiltonian. Good agreement was obtained between the observed and calculated dependences, demonstrating that DMD is an effective alternative to Fourier analysis which often fails to estimate effective damping rates.
Genetically predicted sex hormone binding globulin and ischemic heart disease in men and women: a univariable and multivariable Mendelian randomization study
Authors: Zhao Jie V. , Schooling C. Mary 
Published: November 2021

AbstractMen are more vulnerable to ischemic heart disease (IHD) than women, possibly due to testosterone. Correspondingly, sex hormone binding globulin (SHBG) which lowers circulating testosterone might protect men against IHD. SHBG may also affect IHD independent of testosterone, which has not previously been examined. To assess the sex-specific role of SHBG in IHD, in univariable Mendelian randomization (MR), we used sex-specific, genome-wide significant genetic variants to predict SHBG, and examined their association with IHD in the UK Biobank. We also replicated using genetic instruments from Japanese men and applied to Biobank Japan. To assess the role of SHGB independent of testosterone in men, we used multivariable MR controlling for testosterone. Genetically predicted SHBG was associated with lower IHD risk in men [odds ratio (OR) 0.78 per standard deviation, 95% confidence interval (CI) 0.70 to 0.87], and the association was less clear in women. The estimates were similar in Japanese. The inverse association remained after controlling for testosterone in men (OR 0.79, 95% CI 0.71 to 0.88). SHBG might lower the risk of IHD in men, with a role independent of testosterone. Exploring intervention strategies that increase SHBG is important for targeting IHD treatments.
Proteomic profiling of human amnion for preterm birth biomarker discovery
Authors: Bruschi Maurizio , Bartolucci Martina , Petretto Andrea , Buffelli Francesca , Kajana Xhuliana , Parodi Alessandro , Carbone Riccardo , Fulcheri Ezio , Ramenghi Luca Antonio , Panfoli Isabella , Candiano Giovanni 
Published: November 2021

AbstractSpontaneous preterm birth (PTB) complicates about 12% of pregnancies worldwide, remaining the main cause of neonatal morbidity and mortality. Spontaneous preterm birth PTBs is often caused by microbial-induced preterm labor, mediated by an inflammatory process threatening both maternal and newborn health. In search for novel predictive biomarkers of PTB and preterm prelabor rupture of the membranes (pPROM), and to improve understanding of infection related PTB, we performed an untargeted mass spectrometry discovery study on 51 bioptic mid zone amnion samples from premature babies. A total of 6352 proteins were identified. Bioinformatics analyses revealed a ranked core of 159 proteins maximizing the discrimination between the selected clinical stratification groups allowing to distinguish conditions of absent (FIR 0) from maximal Fetal Inflammatory Response (FIR 3) stratified in function of Maternal Inflammatory Response (MIR) grade. Matrix metallopeptidase-9 (MMP-9) was the top differentially expressed protein. Gene Ontology enrichment analysis of the core proteins showed significant changes in the biological pathways associated to inflammation and regulation of immune and infection response. Data suggest that the conditions determining PTB would be a transversal event, secondary to the maternal inflammatory response causing a breakdown in fetal-maternal tolerance, with fetal inflammation being more severe than maternal one. We also highlight matrix metallopeptidase-9 as a potential predictive biomarker of PTB that can be assayed in the maternal serum, for future investigation.
Functional and structural phenotyping of cardiomyocytes in the 3D organization of embryoid bodies exposed to arsenic trioxide
Authors: Rebuzzini Paola , Civello Cinzia , Fassina Lorenzo , Zuccotti Maurizio , Garagna Silvia 
Published: November 2021

AbstractChronic exposure to environmental pollutants threatens human health. Arsenic, a world-wide diffused toxicant, is associated to cardiac pathology in the adult and to congenital heart defects in the foetus. Poorly known are its effects on perinatal cardiomyocytes. Here, bioinformatic image-analysis tools were coupled with cellular and molecular analyses to obtain functional and structural quantitative metrics of the impairment induced by 0.1, 0.5 or 1.0 µM arsenic trioxide exposure on the perinatal-like cardiomyocyte component of mouse embryoid bodies, within their 3D complex cell organization. With this approach, we quantified alterations to the (a) beating activity; (b) sarcomere organization (texture, edge, repetitiveness, height and width of the Z bands); (c) cardiomyocyte size and shape; (d) volume occupied by cardiomyocytes within the EBs. Sarcomere organization and cell morphology impairment are paralleled by differential expression of sarcomeric α-actin and Tropomyosin proteins and of acta2, myh6 and myh7 genes. Also, significant increase of Cx40, Cx43 and Cx45 connexin genes and of Cx43 protein expression profiles is paralleled by large Cx43 immunofluorescence signals. These results provide new insights into the role of arsenic in impairing cytoskeletal components of perinatal-like cardiomyocytes which, in turn, affect cell size, shape and beating capacity.
Exogenous application of silicon improves the performance of wheat under terminal heat stress by triggering physio-biochemical mechanisms
Authors: Mustafa Talha , Sattar Abdul , Sher Ahmad , Ul-Allah Sami , Ijaz Muhammad , Irfan Muhammad , Butt Madiha , Cheema Mumtaz 
Published: November 2021

AbstractDue to climate change, temperature in late February and early March raised up which cause heat stress at reproductive stage (terminal growth phase of wheat crop) which has become the major causative factor towards low wheat production in arid and semiarid regions. Therefore; strategies need to be adopted for improving terminal heat stress tolerance in wheat. In this study, we assessed whether foliar application of silicon (Si) (2 and 4 mM) at terminal growth phase i.e. heading stage of wheat imposed to heat stress (37 ± 2 °C) under polythene tunnel could improve the performance of wheat. Results of the study revealed that heat stress significantly reduced the photosynthetic pigments (chlorophyll a, b and a + b and carotenoids) leading to a lower grain yield. However, a 4 mM Si application (foliar applied) at heading stage prominently increased the chlorophyll a, b and a + b and carotenoids of flag leaf by improving the activities of enzymatic antioxidants (catalase, peroxidase and superoxide dismutase) and osmoprotectants (soluble sugar protein and proline) under terminal heat stress. Improvements in the performance of wheat (chlorophyll contents, carotenoids, soluble sugar and proteins and proline and yield) with foliar application of Si were also observed under control conditions. Correlation analysis revealed strong association (r > 0.90) of chlorophyll contents and carotenoids with grain and biological yield. Negative correlation (−0.81 < r > −0.63) of physio-biochemical components (antioxidants, proline, soluble sugars and proteins) with yield revealed that under heat stress these components produced in more quantities to alleviate the effects of heat, and Si application also improved these physio biochemical components. In crux, foliar application of Si alleviates the losses in the performance of wheat caused by terminal heat stress by improving the antioxidant mechanism and production of osmoprotectants.
Site specific incidence rate of virulence related genes of enteroaggregative Escherichia coli and association with enteric inflammation and growth in children
Authors: Das Rina , Palit Parag , Haque Md. Ahshanul , Mahfuz Mustafa , Faruque A. S. G. , Ahmed Tahmeed 
Published: November 2021

AbstractThere is a lack of information highlighting the possible association between strain carrying genes of enteroaggregative Escherichia coli (EAEC) and environmental enteric dysfunction (EED) and on linear growth during childhood. Strain carrying genes of EAEC from stool samples collected from 1705 children enrolled in the MAL-ED birth cohort were detected by TaqMan Array Cards. We measured site-specific incidence rate by using Poisson regression models, identified the risk factors and estimated the associations of strain carrying genes of EAEC with the composite EED score and linear growth at 24 months of age. Overall highest incidence rate (43.3%) was found among children having infection with the aggR gene, which was the greatest in Tanzania (56.7%). Low maternal education, lack of improved floor, and ownership of domestic cattle were found to be risk factors for EAEC infection. In the multivariate models, after adjusting the potential covariates, strain carrying genes of EAEC showed strong positive associations with the EED scores and with poor linear growth at 24 months of age. Our analyses may lay the cornerstone for a prospective epidemiologic investigation for a potential vaccine development aimed at reducing the burden of EAEC infections and combat childhood malnutrition.
Visualization of radiocesium distribution in surface layer of seafloor around Fukushima Daiichi Nuclear Power Plant
Authors: Sanada Yukihisa , Urabe Yoshimi , Misonou Toshiharu , Shiribiki Takehiko , Nakanishi Takahiro , Watanabe Yusuke , Tsuruta Tadahiko 
Published: November 2021

AbstractLarge quantities of volatile radionuclides were released into the atmosphere and the hydrosphere following the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident on March, 2011. Monitoring of radiocesium in sediment is important for evaluating the behavior of radiocesium in the environment and its effect on aquatic organisms. In this study, the radiocesium distribution in the surface sediment around the FDNPP was visualized as a radiocesium concentration map using periodical survey data from a towed gamma-ray detection system. The uncertainty of the radiocesium map was evaluated via comparison with a large amount of sediment core sample data. The characteristics of the radiocesium distribution were examined considering the seafloor topography and a geological map, which were obtained via acoustic wave survey. The characteristics of the formation of 137Cs anomaly at the estuaries were analyzed using a contour map of 137Cs concentration combined with water depth. Validation of the created map showed that it was comparable with actual sediment core samples. The map generated using the towed radiation survey depicted the 137Cs concentration distribution as the position resolution of a 1 km mesh. Finally, the 137Cs concentration decreased with time in consideration of such uncertainty.
Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex
Authors: Zhu Lizhe , Jiang Hanlun , Cao Siqin , Unarta Ilona Christy , Gao Xin , Huang Xuhui 
Published: November 2021

AbstractDespite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo2). Interestingly, we found that the slowest mode of motion therein is not the gRNA-target base-pairing, but the coordination of the target phosphate groups with a set of positively charged residues of hAgo2. Moreover, the ability of Helix-7 to approach the PIWI and MID domains was found to reduce the effective volume accessible to the target mRNA and therefore facilitate both the backbone coordination and base-pair formation. Further mutant simulations revealed that alanine mutation of the D358 residue on Helix-7 enhanced a trap state to slow down the loading of target mRNA. Similar trap state was also observed when wobble pairs were introduced in g6 and g7, indicating the role of Helix-7 in suppressing non-canonical base-paring. Our study pointed to a general mechanism for mRNA recognition by eukaryotic Agos and demonstrated the promise of qMSM in investigating complex conformational changes of biomolecular systems.
The lowest-energy structure of the gold cluster Au10: planar vs. nonplanar?
Authors: Nhat Pham Vu , Si Nguyen Thanh , Hang Nguyen Thi Nhat , Nguyen Minh Tho 
Published: November 2021

A plausible coexistence of both planar and non-planar isomers of Au10 at the onset of 2D–3D structural transition of pure gold clusters.
Type Iax supernovae from deflagrations in Chandrasekhar mass white dwarfs
Authors: Lach F. , Callan F. P. , Bubeck D. , Röpke F. K. , Sim S. A. , Schrauth M. , Ohlmann S. T. , Kromer M. 
Published: November 2021

Context. Due to the ever increasing number of observations during the past decades, Type Ia supernovae are nowadays regarded as a heterogeneous class of optical transients consisting of several subtypes. One of the largest of these subclasses is the class of Type Iax supernovae. They have been suggested to originate from pure deflagrations in carbon-oxygen Chandrasekhar mass white dwarfs because the outcome of this explosion scenario is in general agreement with their subluminous nature.
Aims. Although a few deflagration studies have already been carried out, the full diversity of the class has not been captured yet. This, in particular, holds for the faint end of the subclass. We therefore present a parameter study of single-spot ignited deflagrations in Chandrasekhar mass white dwarfs varying the location of the ignition spark, the central density, the metallicity, and the composition of the white dwarf. We also explore a rigidly rotating progenitor to investigate whether the effect of rotation can spawn additional trends.
Methods. We carried out three-dimensional hydrodynamic simulations employing the LEAFS code. Subsequently, detailed nucleosynthesis results were obtained with the nuclear network code YANN. In order to compare our results to observations, we calculated synthetic spectra and light curves with the ARTIS code.
Results. The new set of models extends the range in brightness covered by previous studies to the lower end. Our single-spot ignited explosions produce 56Ni masses from 5.8 × 10−3 to 9.2 × 10−2 M⊙. In spite of the wide exploration of the parameter space, the main characteristics of the models are primarily driven by the mass of 56Ni and form a one-dimensional sequence. Secondary parameters seem to have too little impact to explain the observed trend in the faint part of the Type Iax supernova class. We report kick velocities of the gravitationally bound explosion remnants from 6.9 to 369.8 km s−1. The magnitude as well as the direction of the natal kick is found to depend on the strength of the deflagration.
Conclusions. This work corroborates the results of previous studies of deflagrations in Chandrasekhar mass white dwarfs. The wide exploration of the parameter space in initial conditions and viewing angle effects in the radiative transfer lead to a significant spread in the synthetic observables. The trends in observational properties toward the faint end of the class are, however, not reproduced. This motivates a quantification of the systematic uncertainties in the modeling procedure and the influence of the 56Ni-rich bound remnant to get to the bottom of these discrepancies. Moreover, while the pure deflagration scenario remains a favorable explanation for bright and intermediate luminosity Type Iax supernovae, our results suggest that other mechanisms also contribute to this class of events.