bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome wide methylation profiling of selected matched soft tissue sarcomas identifies methylation changes in metastatic and recurrent disease
Authors: Vargas Ana Cristina , Gray Lesley-Ann , White Christine L. , Maclean Fiona M. , Grimison Peter , Ardakani Nima Mesbah , Bonar Fiona , Algar Elizabeth M. , Cheah Alison L. , Russell Peter , Mahar Annabelle , Gill Anthony J. 
Published: January 2021

AbstractIn this study we used the Illumina Infinium Methylation array to investigate in a cohort of matched archival human tissue samples (n = 32) from 14 individuals with soft tissue sarcomas if genome-wide methylation changes occur during metastatic and recurrent (Met/Rec) disease. A range of sarcoma types were selected for this study: leiomyosarcoma (LMS), myxofibrosarcoma (MFS), rhabdomyosarcoma (RMS) and synovial sarcoma (SS). We identified differential methylation in all Met/Rec matched samples, demonstrating that epigenomic differences develop during the clonal evolution of sarcomas. Differentially methylated regions and genes were detected, not been previously implicated in sarcoma progression, including at PTPRN2 and DAXX in LMS, WT1-AS and TNXB in SS, VENTX and NTRK3 in pleomorphic RMS and MEST and the C14MC / miR-379/miR-656 in MFS. Our overall findings indicate the presence of objective epigenetic differences across primary and Met/Rec human tissue samples not previously reported.
Microbiota analysis and transient elastography reveal new extra-hepatic components of liver steatosis and fibrosis in obese patients
Authors: Lanthier Nicolas , Rodriguez Julie , Nachit Maxime , Hiel Sophie , Trefois Pierre , Neyrinck Audrey M. , Cani Patrice D. , Bindels Laure B. , Thissen Jean-Paul , Delzenne Nathalie M. 
Published: January 2021

AbstractObesity could lead to metabolic dysfunction-associated fatty liver disease (MAFLD), which severity could be linked to muscle and gut microbiota disturbances. Our prospective study enrolled 52 obese patients whose MAFLD severity was estimated by transient elastography. Patients with severe steatosis (n = 36) had higher ALAT values, fasting blood glucose levels as well as higher visceral adipose tissue area and skeletal muscle index evaluated by computed tomography. Patients with fibrosis (n = 13) had higher ASAT values, increased whole muscle area and lower skeletal muscle density index. In a multivariate logistic regression analysis, myosteatosis was the strongest factor associated with fibrosis. Illumina sequencing of 16S rRNA gene amplicon was performed on fecal samples. The relative abundance of fecal Clostridium sensu stricto was significantly decreased with the presence of liver fibrosis and was negatively associated with liver stiffness measurement and myosteatosis. In addition, 19 amplicon sequence variants were regulated according to the severity of the disease. Linear discriminant analysis effect size (LEfSe) also highlighted discriminant microbes in patients with fibrosis, such as an enrichment of Enterobacteriaceae and Escherichia/Shigella compared to patients with severe steatosis without fibrosis. All those data suggest a gut-liver-muscle axis in the pathogenesis of MAFLD complications.
Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2
Authors: Liu Jibin , Cheng Anchun , Wang Mingshu , Liu Mafeng , Zhu Dekang , Yang Qiao , Wu Ying , Jia Renyong , Chen Shun , Zhao Xinxin , Zhang Shaqiu , Huang Juan , Ou Xumin , Mao Sai , Gao Qun , Wen Xingjian , Zhang Ling , Liu Yunya , Yu Yanling , Tian Bin , Pan Leichang , Ur Rehman Mujeeb , Chen Xiaoyue 
Published: January 2021

AbstractRiemerella anatipestifer is a major pathogenic microorganism in poultry causing serositis with significant mortality. Serotype 1 and 2 were most pathogenic, prevalent, and liable over the world. In this study, the intracellular metabolites in R. anatipestifer strains RA-CH-1 (serotype 1) and RA-CH-2 (serotype 2) were identified by gas chromatography-mass spectrometer (GC–MS). The metabolic profiles were performed using hierarchical clustering and partial least squares discriminant analysis (PLS-DA). The results of hierarchical cluster analysis showed that the amounts of the detected metabolites were more abundant in RA-CH-2. RA-CH-1 and RA-CH-2 were separated by the PLS-DA model. 24 potential biomarkers participated in nine metabolisms were contributed predominantly to the separation. Based on the complete genome sequence database and metabolite data, the first large-scale metabolic models of iJL463 (RA-CH-1) and iDZ470 (RA-CH-2) were reconstructed. In addition, we explained the change of purine metabolism combined with the transcriptome and metabolomics data. The study showed that it is possible to detect and differentiate between these two organisms based on their intracellular metabolites using GC–MS. The present research fills a gap in the metabolomics characteristics of R. anatipestifer.
Effects of vestibular neurectomy and neural compensation on head movements in patients undergoing vestibular schwannoma resection
Authors: Zobeiri Omid A. , Mischler Gavin M. , King Susan A. , Lewis Richard F. , Cullen Kathleen E. 
Published: January 2021

AbstractThe vestibular system is vital for maintaining balance and stabilizing gaze and vestibular damage causes impaired postural and gaze control. Here we examined the effects of vestibular loss and subsequent compensation on head motion kinematics during voluntary behavior. Head movements were measured in vestibular schwannoma patients before, and then 6 weeks and 6 months after surgical tumor removal, requiring sectioning of the involved vestibular nerve (vestibular neurectomy). Head movements were recorded in six dimensions using a small head-mounted sensor while patients performed the Functional Gait Assessment (FGA). Kinematic measures differed between patients (at all three time points) and normal subjects on several challenging FGA tasks, indicating that vestibular damage (caused by the tumor or neurectomy) alters head movements in a manner that is not normalized by central compensation. Kinematics measured at different time points relative to vestibular neurectomy differed substantially between pre-operative and 6-week post-operative states but changed little between 6-week and > 6-month post-operative states, demonstrating that compensation affecting head kinematics is relatively rapid. Our results indicate that quantifying head kinematics during self-generated gait tasks provides valuable information about vestibular damage and compensation, suggesting that early changes in patient head motion strategy may be maladaptive for long-term vestibular compensation.
A pre-operative prognostic score for the selection of patients for salvage surgery after recurrent head and neck squamous cell carcinomas
Authors: Lupato Valentina , Polesel Jerry , La Torre Fabio Biagio , Fanetti Giuseppe , Fratta Elisabetta , Gobitti Carlo , Baldassarre Gustavo , Vaccher Emanuela , Franchin Giovanni , Giacomarra Vittorio 
Published: January 2021

AbstractSalvage surgery in recurrent head and neck squamous cell carcinoma has a poor outcome, both in terms of survival and quality of life. Therefore, the identification of pre-operative prognostic factors to improve the selection of patients who could benefit the most from salvage surgery is clinically relevant. The present study is a single-center retrospective analysis of 164 patients treated with salvage surgery after recurrence of head and neck cancer. Progression free survival and overall survival were calculated through Kaplan–Meier method. Hazard risk (HR) and corresponding confidence intervals (CI) were estimated through Cox proportional hazard model, adjusting for potential confounders. Significant predictors were combined into a prognostic score, attributing one point to each factor. Progression-free survival and overall survival were respectively 50.3% and 56.5% at 2 years, and 36.6% and 44.2% at 5 years. Four pre-operative factors were independently associated with poor prognosis: age > 70 years (HR = 2.18; 95% CI 1.27–3.73), initial stage IV (HR = 2.37; 95% CI 1.18–4.76), disease free interval < 12 months (HR = 1.72; 95% CI 1.01–2.94), and loco-regional recurrence (HR = 2.22; 95% CI 1.22–4.04). No post operative factor was associated with oncologic outcomes. Patients with 3–4 unfavorable factors showed a 5-year overall survival of 0.0% compared to 65.7% in those with 0–1 unfavorable factors (HR = 5.61; 95% CI 2.89–10.92). Despite the low number of patients, 3–4 unfavorable factors were associated to worse prognosis in all sub-sites. In conclusion, age > 70 years, initial stage IV, disease-free interval < 12 months, and loco-regional recurrence are strong independent pre-operative predictors of poor outcome in patients undergoing salvage surgery. Patients with two or more of these factors should be informed about the low success rate after salvage surgery and alternative treatments should be considered.
The evaluation of pituitary damage associated with cardiac arrest: An experimental rodent model
Authors: Okuma Yu , Aoki Tomoaki , Miyara Santiago J. , Hayashida Kei , Nishikimi Mitsuaki , Takegawa Ryosuke , Yin Tai , Kim Junhwan , Becker Lance B. , Shinozaki Koichiro 
Published: January 2021

AbstractThe pituitary gland plays an important endocrinal role, however its damage after cardiac arrest (CA) has not been well elucidated. The aim of this study was to determine a pituitary gland damage induced by CA. Rats were subjected to 10-min asphyxia and cardiopulmonary resuscitation (CPR). Immunohistochemistry and ELISA assays were used to evaluate the pituitary damage and endocrine function. Samples were collected at pre-CA, and 30 and 120 min after cardio pulmonary resuscitation. Triphenyltetrazolium chloride (TTC) staining demonstrated the expansion of the pituitary damage over time. There was phenotypic validity between the pars distalis and nervosa. Both CT-proAVP (pars nervosa hormone) and GH/IGF-1 (pars distalis hormone) decreased over time, and a different expression pattern corresponding to the damaged areas was noted (CT-proAVP, 30.2 ± 6.2, 31.5 ± 5.9, and 16.3 ± 7.6 pg/mg protein, p < 0.01; GH/IGF-1, 2.63 ± 0.61, 0.62 ± 0.36, and 2.01 ± 0.41 ng/mg protein, p < 0.01 respectively). Similarly, the expression pattern between these hormones in the end-organ systems showed phenotypic validity. Plasma CT-proAVP (r = 0.771, p = 0.025) and IGF-1 (r = −0.775, p = 0.024) demonstrated a strong correlation with TTC staining area. Our data suggested that CA induces pathological and functional damage to the pituitary gland.
Design of fractional evolutionary processing for reactive power planning with FACTS devices
Authors: Muhammad Yasir , Akhtar Rizwan , Khan Rahimdad , Ullah Farman , Raja Muhammad Asif Zahoor , Machado J. A. Tenreiro 
Published: January 2021

AbstractReactive power dispatch is a vital problem in the operation, planning and control of power system for obtaining a fixed economic load expedition. An optimal dispatch reduces the grid congestion through the minimization of the active power loss. This strategy involves adjusting the transformer tap settings, generator voltages and reactive power sources, such as flexible alternating current transmission systems (FACTS). The optimal dispatch improves the system security, voltage profile, power transfer capability and overall network efficiency. In the present work, a fractional evolutionary approach achieves the desired objectives of reactive power planning by incorporating FACTS devices. Two compensation arrangements are possible: the shunt type compensation, through Static Var compensator (SVC) and the series compensation through the Thyristor controlled series compensator (TCSC). The fractional order Darwinian Particle Swarm Optimization (FO-DPSO) is implemented on the standard IEEE 30, IEEE 57 and IEEE 118 bus test systems. The power flow analysis is used for determining the location of TCSC, while the voltage collapse proximity indication (VCPI) method identifies the location of the SVC. The superiority of the FO-DPSO is demonstrated by comparing the results with those obtained by other techniques in terms of measure of central tendency, variation indices and time complexity.
Engineering calcium signaling of astrocytes for neural–molecular computing logic gates
Authors: Barros Michael Taynnan , Doan Phuong , Kandhavelu Meenakshisundaram , Jennings Brendan , Balasubramaniam Sasitharan 
Published: January 2021

AbstractThis paper proposes the use of astrocytes to realize Boolean logic gates, through manipulation of the threshold of $$\hbox {Ca}^{2+}$$

Ca

2
+

ion flows between the cells based on the input signals. Through wet-lab experiments that engineer the astrocytes cells with pcDNA3.1-hGPR17 genes as well as chemical compounds, we show that both AND and OR gates can be implemented by controlling $$\hbox {Ca}^{2+}$$

Ca

2
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signals that flow through the population. A reinforced learning platform is also presented in the paper to optimize the $$\hbox {Ca}^{2+}$$

Ca

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activated level and time slot of input signals $$T_b$$

T
b

into the gate. This design platform caters for any size and connectivity of the cell population, by taking into consideration the delay and noise produced from the signalling between the cells. To validate the effectiveness of the reinforced learning platform, a $$\hbox {Ca}^{2+}$$

Ca

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signalling simulator was used to simulate the signalling between the astrocyte cells. The results from the simulation show that an optimum value for both the $$\hbox {Ca}^{2+}$$

Ca

2
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activated level and time slot of input signals $$T_b$$

T
b

is required to achieve up to 90% accuracy for both the AND and OR gates. Our method can be used as the basis for future Neural–Molecular Computing chips, constructed from engineered astrocyte cells, which can form the basis for a new generation of brain implants.
UV-C mediated accumulation of pharmacologically significant phytochemicals under light regimes in in vitro culture of Fagonia indica (L.)
Authors: Abbasi Bilal Haider , Khan Taimoor , Khurshid Razia , Nadeem Muhammad , Drouet Samantha , Hano Christophe 
Published: January 2021

AbstractFagonia indica(L.) is an important medicinal plant with multitude of therapeutic potentials. Such application has been attributed to the presence of various pharmacological important phytochemicals. However, the inadequate biosynthesis of such metabolites in intact plants has hampered scalable production. Thus, herein, we have established an in vitro based elicitation strategy to enhance such metabolites in callus culture ofF. indica. Cultures were exposed to various doses of UV radiation (UV-C) and grown in different photoperiod regimes and their impact was evaluated on biomass accumulation, biosynthesis of phytochemicals along antioxidant expression. Cultures grown under photoperiod (16L/8D h) after exposure to UV-C (5.4 kJ/m2) accumulated optimal biomass (438.3 g/L FW; 16.4 g/L DW), phenolics contents (TPC: 11.8 μgGAE/mg) and flavonoids contents (TFC: 4.05 μgQE/mg). Similarly, HPLC quantification revealed that total production (6.967 μg/mg DW) of phytochemicals wherein kaempferol (1.377 μg/mg DW), apigenin (1.057 μg/mg DW), myricetin (1.022 μg/mg DW) and isorhamnetin (1.022 μg/mg DW) were recorded highly accumulated compounds in cultures at UV-C (5.4 kJ/m2) dose than other UV-C radiations and light regimes.. The antioxidants activities examined as DPPH (92.8%), FRAP (182.3 µM TEAC) and ABTS (489.1 µM TEAC) were also recorded highly expressed by cultures under photoperiod after treatment with UV-C dose 5.4 kJ/m2. Moreover, same cultures also expressed maximum % inhibition towards phospholipase A2 (sPLA2: 35.8%), lipoxygenase (15-LOX: 43.3%) and cyclooxygenases (COX-1: 55.3% and COX-2: 39.9%) with 1.0-, 1.3-, 1.3- and 2.8-fold increased levels as compared with control, respectively. Hence, findings suggest that light and UV can synergistically improve the metabolism ofF. indicaand could be used to produce such valuable metabolites on commercial scale.
Synthesis, characterization, and imaging of radiopaque bismuth beads for image-guided transarterial embolization
Authors: Negussie Ayele H. , de Ruiter Quirina M. B. , Britton Hugh , Donahue Danielle R. , Boffi Quentin , Kim Young-Seung , Pritchard William F. , Moonen Chrit , Storm Gert , Lewis Andrew L. , Wood Bradford J. 
Published: January 2021

AbstractCurrent therapy for hypervascular cancers, e.g., hepatocellular carcinoma, includes occlusion of the tumor blood supply by arterial infusion of embolic microspheres (beads) suspended in iodine-based contrast under fluoroscopic guidance. Available radiopaque, imageable beads use iodine as the radiopacifier and cannot be differentiated from contrast. This study aimed to synthesize and characterize imageable beads using bismuth as the radiopacifier that could be distinguished from iodine contrast based upon the difference in the binding energy of k-shell electrons (k-edge). Radiodense bismuth beads were successfully synthesized some with uniform bismuth distribution across the beads. The beads were spherical and could be infused through clinical microcatheters. The bismuth beads could be imaged with clinical dual-energy computed tomography (CT), where iodine-based contrast could be distinguished from the microspheres. The ability to separate iodine from bismuth may enhance the diagnostic information acquired on follow-up CT, identifying the distribution of the embolic beads separately from the contrast. Furthermore, with sequential use of iodine- and bismuth-based beads, the two radiopaque beads could be spatially distinguished on imaging, which may enable the development of dual drug delivery and dual tracking.
3D imaging using scanning diffractometry
Authors: Siavashani Morteza J. , Naghedi Iman , Abbasian Vahid , Akhlaghi Ehsan A. , Charsooghi Mohammad A. , Tavassoly Mohammad Taghi , Moradi Ali-Reza 
Published: January 2021

AbstractImaging of cells is a challenging problem as they do not appreciably change the intensity of the illuminating light. Interferometry-based methods to do this task suffer from high sensitivity to environmental vibrations. We introduce scanning diffractometry as a simple non-contact and vibration-immune methodology for quantitative phase imaging. Fresnel diffractometry by a phase step has led to several applications such as high-precision measurements of displacement. Additional scanning may lead to 3D imaging straightforwardly. We apply the technique to acquire 3D images of holographic grating, red blood cell, neuron, and sperm cell. Either visibility of the diffraction fringes or the positions of extrema may be used for phase change detection. The theoretical analysis through the Fresnel diffraction from one-dimensional phase step is presented and the experimental results are validated with digital holographic microscopy. The presented technique can be suggested to serve as a robust device for 3D phase imaging and biomedical measurements.
Parametric shift from rational to irrational decisions in mice
Authors: Schneider Nathan A. , Ballintyn Benjamin , Katz Donald , Lisman John , Pi Hyun-Jae 
Published: January 2021

AbstractIn the classical view of economic choices, subjects make rational decisions evaluating the costs and benefits of options in order to maximize their overall income. Nonetheless, subjects often fail to reach optimal outcomes. The overt value of an option drives the direction of decisions, but covert factors such as emotion and sensitivity to sunk cost are thought to drive the observed deviations from optimality. Many questions remain to be answered as to (1) which contexts contribute the most to deviation from an optimal solution; and (2) the extent of these effects. In order to tackle these questions, we devised a decision-making task for mice, in which cost and benefit parameters could be independently and flexibly adjusted and for which a tractable optimal solution was known. Comparing mouse behavior with this optimal solution across parameter settings revealed that the factor most strongly contributing to suboptimal performance was the cost parameter. The quantification of sensitivity to sunk cost, a covert factor implicated in our task design, revealed it as another contributor to reduced optimality. In one condition where the large reward option was particularly unattractive and the small reward cost was low, the sensitivity to sunk cost and the cost-led suboptimality almost vanished. In this regime and this regime only, mice could be viewed as close to rational (here, ‘rational’ refers to a state in which an animal makes decisions basing on objective valuation, not covert factors). Taken together, our results suggest that “rationality” is a task-specific construct even in mice.
Patterns and risk of HIV-1 transmission network among men who have sex with men in Guangxi, China
Authors: Pang Xianwu , Wei Hui , Huang Jinghua , He Qin , Tang Kailing , Fang Ningye , Zhou Xinjuan , Zhu Qiuying , Wu Xiuling , Lan Guanghua , Shen Zhiyong , Lin Mei , Liang Shujia 
Published: January 2021

AbstractThe prevalence of HIV-1 in Guangxi is very high, and the rate of HIV-1 infection among men who have sex with men (MSM) has been increasing. Therefore, it is necessary to explore the patterns and risk factors of HIV transmission in Guangxi. For this purpose, individuals diagnosed with HIV-1 during 2013–2018 in Guangxi were recruited. Phylogenetic relationship, transmission clusters, and genotypic drug resistance analyses were performed based on HIV-1 pol sequences. Related factors were analysed to assess for their association with HIV-1 transmission. CRF07_BC (50.4%) and CRF01_AE (33.4%) were found to be the predominant subtypes. The analysed 1633 sequences (50.15%, Guangxi; 49.85%, other provinces) were segregated into 80 clusters (size per cluster, 2–704). We found that 75.3% of the individuals were in three clusters (size ˃ 100), and 73.8% were high-risk spreaders (links ≥ 4). Infection time, marital status, and subtype were significantly associated with HIV-1 transmission. Additionally, 80.2% of recent infections were linked to long-term infections, and 46.2% were linked to other provinces. A low level of transmitted drug resistance was detected (4.8%). Our findings indicated superclusters and high-risk HIV-1 spreaders among the MSM in Guangxi. Effective strategies blocking the route of transmission should be developed.
Future thermal regimes for epaulette sharks (Hemiscyllium ocellatum): growth and metabolic performance cease to be optimal
Authors: Wheeler Carolyn R. , Rummer Jodie L. , Bailey Barbara , Lockwood Jamie , Vance Shelby , Mandelman John W. 
Published: January 2021

AbstractClimate change is affecting thermal regimes globally, and organisms relying on their environment to regulate biological processes face unknown consequences. In ectotherms, temperature affects development rates, body condition, and performance. Embryonic stages may be the most vulnerable life history stages, especially for oviparous species already living at the warm edge of their distribution, as embryos cannot relocate during this developmental window. We reared 27 epaulette shark (Hemiscyllium ocellatum) embryos under average summer conditions (27 °C) or temperatures predicted for the middle and end of the twenty-first century with climate change (i.e., 29 and 31 °C) and tracked growth, development, and metabolic costs both in ovo and upon hatch. Rearing sharks at 31 °C impacted embryonic growth, yolk consumption, and metabolic rates. Upon hatch, 31 °C-reared sharks weighed significantly less than their 27 °C-reared counterparts and exhibited reduced metabolic performance. Many important growth and development traits in this species may peak after 27 °C and start to become negatively impacted nearing 31 °C. We hypothesize that 31 °C approximates the pejus temperature (i.e., temperatures at which performance of a trait begin to decline) for this species, which is alarming, given that this temperature range is well within ocean warming scenarios predicted for this species’ distribution over the next century.