bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual head models for estimating the TMS-induced electric field in rat brain
Authors: Koponen Lari M. , Stenroos Matti , Nieminen Jaakko O. , Jokivarsi Kimmo , Gröhn Olli , Ilmoniemi Risto J. 
Published: October 2020

AbstractIn transcranial magnetic stimulation (TMS), the initial cortical activation due to stimulation is determined by the state of the brain and the magnitude, waveform, and direction of the induced electric field (E-field) in the cortex. The E-field distribution depends on the conductivity geometry of the head. The effects of deviations from a spherically symmetric conductivity profile have been studied in detail in humans. In small mammals, such as rats, these effects are more pronounced due to their less spherical head, proportionally much thicker neck region, and overall much smaller size compared to the TMS coils. In this study, we describe a simple method for building individual realistically shaped head models for rats from high-resolution X-ray tomography images. We computed the TMS-induced E-field with the boundary element method and assessed the effect of head-model simplifications on the estimated E-field. The deviations from spherical symmetry have large, non-trivial effects on the E-field distribution: for some coil orientations, the strongest stimulation is in the brainstem even when the coil is over the motor cortex. With modelling prior to an experiment, such problematic coil orientations can be avoided for more accurate targeting.
Seasonal synchronization of foodborne outbreaks in the United States, 1996–2017
Authors: Simpson Ryan B. , Zhou Bingjie , Naumova Elena N. 
Published: October 2020

AbstractModern food systems represent complex dynamic networks vulnerable to foodborne infectious outbreaks difficult to track and control. Seasonal co-occurrences (alignment of seasonal peaks) and synchronization (similarity of seasonal patterns) of infections are noted, yet rarely explored due to their complexity and methodological limitations. We proposed a systematic approach to evaluate the co-occurrence of seasonal peaks using a combination of L-moments, seasonality characteristics such as the timing (phase) and intensity (amplitude) of peaks, and three metrics of serial, phase-phase, and phase-amplitude synchronization. We used public records on counts of nine foodborne infections abstracted from CDC’s FoodNet Fast online platform for the US and ten representative states from 1996 to 2017 (264 months). Based on annualized and trend-adjusted Negative Binomial Harmonic Regression (NBHR) models augmented with the δ-method, we determined that seasonal peaks ofCampylobacter,Salmonella, and Shiga toxin-producingEscherichia Coli(STEC) were tightly clustered in late-July at the national and state levels. Phase-phase synchronization was observed betweenCryptosporidiumandShigella,Listeria, andSalmonella(ρ = 0.51, 0.51, 0.46; p < 0.04). Later peak timing of STEC was associated with greater amplitude nationally (ρ = 0.50, p = 0.02) indicating phase-amplitude synchronization. Understanding of disease seasonal synchronization is essential for developing reliable outbreak forecasts and informing stakeholders on mitigation and preventive measures.
Blood pool activity on F-18 FDG PET/CT as a possible imaging biomarker of metabolic syndrome
Authors: Bang Ji-In , Moon Chang Mo , Kim Hye Ok , Kang Seo Young , Yoon Hai-Jeon , Kim Bom Sahn 
Published: October 2020

AbstractAssociation of blood pool (BP) and adipose tissue activity from F-18 fluorodeoxyglucose positron-emission tomography/computed tomography (FDG PET/CT) with the parameters of metabolic syndrome (MetS) and different MetS/obesity types were investigated. 245 subjects underwent FDG PET/CT scan for health check-ups were investigated retrospectively. Associations of BP (BP SUV: SUVmax, SUVmean), visceral (VAT SUV), and subcutaneous adipose tissue (SAT SUV) activity with parameters of MetS, body mass index (BMI), and lipid profiles were analyzed. MetS/obesity types were subdivided into metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO). BP SUV was higher in subjects with MetS (t-test, P < 0.005), and was associated with MetS from multivariable binary logistic regression (OR 5.232 P = 0.010). BP SUV was statistically higher in MUO than in MHO (P < 0.05) along with blood pressure, triglycerides, and HDL-cholesterol. Multivariable binary logistic regression analysis showed MUO had higher blood pressure and BP SUV, while lower HDL-cholesterol relative to MHO after adjusting for triglycerides.
Towards shifted position-diffuse reflectance imaging of anatomically correctly scaled human microvasculature
Authors: Späth Moritz , Hohmann Martin , Roider Clemens , Lengenfelder Benjamin , Stelzle Florian , Wirtz Stefan , Klämpfl Florian 
Published: October 2020

AbstractDue to significant advantages, the trend in the field of medical technology is moving towards minimally or even non-invasive examination methods. In this respect, optical methods offer inherent benefits, as does diffuse reflectance imaging (DRI). The present study attempts to prove the suitability of DRI—when implemented alongside a suitable setup and data evaluation algorithm—to derive information from anatomically correctly scaled human capillaries (diameter: $$10\,\upmu \hbox {m}$$

10

μ
m

, length: $$45\,\upmu \hbox {m}$$

45

μ
m

) by conducting extensive Monte–Carlo simulations and by verifying the findings through laboratory experiments. As a result, the method of shifted position-diffuse reflectance imaging (SP-DRI) is established by which average signal modulations of up to 5% could be generated with an illumination wavelength of $$\lambda =424\,\hbox {nm}$$

λ
=
424

nm

and a core diameter of the illumination fiber of $$50\,\upmu \hbox {m}$$

50

μ
m

. No reference image is needed for this technique. The present study reveals that the diffuse reflectance data in combination with the SP-DRI normalization are suitable to localize human capillaries within turbid media.
Cir-ITCH inhibits gastric cancer migration, invasion and proliferation by regulating the Wnt/β-catenin pathway
Authors: Peng Yang , Wang Hong Hong 
Published: October 2020

AbstractCircular RNAs (circRNAs) are differentially expressed in various tumours, but the expression and regulatory mechanisms of circular RNA ITCH (cir-ITCH) in gastric cancer remain unclear. For this reason, in the present study, we assessed the expression of cir-ITCH and the associated regulatory mechanism of cir-ITCH in gastric cancer. Through RTq-PCR assays, we observed that cir-ITCH expression was attenuated in gastric cancer cell lines and tissues, with cir-ITCH expression in gastric cancer tissues with lymph node metastasis being considerably lower than that observed in gastric cancer tissues without lymph node metastasis. In addition, we demonstrated that cir-ITCH or linear ITCH may be a useful marker for gastric cancer prognosis by Kaplan–Meier survival analysis. We also showed that cir-ITCH overexpression could increase linear ITCH expression through miR-17 via RNA immunoprecipitation (RIP) and luciferase reporter assays. Moreover, in vivo and in vitro experimental results showed that cir-ITCH can act as a tumour suppressor to prevent gastric cancer tumourgenesis by sponging miR-17. The Wnt/β-catenin pathway plays a crucial role during the carcinogenesis of cancers, and we observed that cir-ITCH could negatively regulate Wnt/β-catenin signalling, which could be restored by miR-17. In summary, cir-ITCH was shown to prevent gastric cancer tumourgenesis through the Wnt/β-catenin signalling pathway by sequestering miR-17.
KRAS K104 modification affects the KRASG12D-GEF interaction and mediates cell growth and motility
Authors: Chen Chih-Chieh , Hsu Chia-Yi , Lin Hsiao-Yun , Zeng Hong-Qi , Cheng Kuang-Hung , Wu Chia-Wei , Tsai Eing-Mei , Hsieh Tsung-Hua 
Published: October 2020

AbstractMutant RAS genes play an important role in regulating tumors through lysine residue 104 to impair GEF-induced nucleotide exchange, but the regulatory role of KRAS K104 modification on the KRASG12D mutant remains unclear. Therefore, we simulated the acetylation site on the KRASG12D three-dimensional protein structure, including KRASG12D, KRASG12D/K104A and KRASG12D/K104Q, and determined their trajectories and binding free energy with GEF. KRASG12D/K104Q induced structural changes in the α2- and α3-helices, promoted KRAS instability and hampered GEF binding (ΔΔG = 6.14 kJ/mol). We found decreased binding to the Raf1 RBD by KRASG12D/K104Q and reduced cell growth, invasion and migration. Based on whole-genome cDNA microarray analysis, KRASG12D/K104Q decreased expression of NPIPA2, DUSP1 and IL6 in lung and ovarian cancer cells. This study reports computational and experimental analyses of Lys104 of KRASG12D and GEF, and the findings provide a target for exploration for future treatment.
Genome targeting by hybrid Flp-TAL recombinases
Authors: Voziyanova Eugenia , Li Feng , Shah Riddhi , Voziyanov Yuri 
Published: October 2020

AbstractGenome engineering is a rapidly evolving field that benefits from the availability of different tools that can be used to perform genome manipulation tasks. We describe here the development of the Flp-TAL recombinases that can target genomic FRT-like sequences in their native chromosomal locations. Flp-TAL recombinases are hybrid enzymes that are composed of two functional modules: a variant of site-specific tyrosine recombinase Flp, which can have either narrow or broad target specificity, and the DNA-binding domain of the transcription activator-like effector, TAL. In Flp-TAL, the TAL module is responsible for delivering and stabilizing the Flp module onto the desired genomic FRT-like sequence where the Flp module mediates recombination. We demonstrate the functionality of the Flp-TAL recombinases by performing integration and deletion experiments in human HEK-293 cells. In the integration experiments we targeted a vector to three genomic FRT-like sequences located in the β-globin locus. In the deletion experiments we excised ~ 15 kilobases of DNA that contained a fragment of the integrated vector sequence and the neighboring genome sequence. On average, the efficiency of the integration and deletion reactions was about 0.1% and 20%, respectively.
Identification of epigenetic variation associated with synchronous pod maturity in mungbean (Vigna radiata L.)
Authors: Ha Jungmin , Kwon Hakyung , Cho Kang-Heum , Yoon Min Young , Kim Moon Young , Lee Suk-Ha 
Published: October 2020

AbstractCytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.
Assessment of removal and adsorption enhancement of high-flux hemodialyzers in convective therapies by a novel in vitro uremic matrix
Authors: Gomez Miquel , Bañon-Maneus Elisenda , Arias-Guillén Marta , Maduell Francisco 
Published: October 2020

AbstractAdsorption properties of hemodialyzers are traditionally retrieved from diffusive treatments and mainly focused on inflammatory markers and plasma proteins. The possible depurative enhancement of middle and high molecular weight solutes, as well as protein-bound uremic toxins by adsorption in convective treatments, is not yet reported. We used discarded plasma exchanges from uremic patients and out-of-date erythrocytes as a novel in vitro uremic precursor matrix to assess removal and adsorption patterns of distinct material and structure but similar surface hemodialyzers in hemodialysis and on-line hemodiafiltration treatments. We further related the obtained results to the possible underlying membrane pore blocking mechanisms. Convection improved removal but slightly enhanced adsorption in the cellulosic and synthetic dialyzers tested. The polymethylmethacrylate hemodialyzer obtained the highest extracted ($$M_{ext}$$

M

ext

) and adsorbed ($$M_{ads}$$

M

ads

) mass values when submitted to hemodiafiltration for all molecules analyzed including albumin ($$M_{ext}=15.8\pm 3.9$$

M

ext

=
15.8
±
3.9

g, $$M_{ads}=44.3\pm 11.5$$

M

ads

=
44.3
±
11.5

mg), whereas the polyamide membrane obtained substantial lower results even for this molecule ($$M_{ext}=2.2\pm 1.2$$

M

ext

=
2.2
±
1.2

g, $$M_{ads}=4.2\pm 0.7$$

M

ads

=
4.2
±
0.7

mg) under the same treatment parameters. Hemodiafiltration in symmetric and enlarged pore hemodialyzers enhances removal and adsorption by internal pore deposition (intermediate pore-blocking) for middle and high molecular weight toxins but leads to substantial and deleterious albumin depuration.
Integral correlation for uneven and differently sampled data, and its application to the Law Dome Antarctic climate record
Authors: Roberts Jason L. , Jong Lenneke M. , McCormack Felicity S. , Curran Mark A. , Moy Andrew D. , Etheridge David M. , Greenbaum Jamin S. , Young Duncan A. , Phipps Steven J. , Xue Wenyue , van Ommen Tas D. , Blankenship Donald D. , Siegert Martin J. 
Published: October 2020

AbstractWe present a new simple and efficient method for correlation of unevenly and differently sampled data. This new method overcomes problems with other methods for correlation with non-uniform sampling and is an easy modification to existing correlation based codes. To demonstrate the usefulness of this new method to real-world examples, we apply the method with good success to two glaciological examples to map the ages from a well-dated ice core to a nearby core, and by tracing isochronous layers within the ice sheet measured from ice-penetrating radar between the two ice core sites.
Transcriptome analysis of alternative splicing in the pathogen life cycle in human foreskin fibroblasts infected with Trypanosoma cruzi
Authors: Jung Hyeim , Han Seonggyun , Lee Younghee 
Published: October 2020

AbstractTrypanosoma cruzi is an intracellular protozoan parasite that causes Chagas disease as a zoonotic pathogen. The parasite has been shown to remodel expression in the host transcriptome under different conditions. Although alternative splicing (AS) is involved in virtually every biological function in eukaryotes, including cellular differentiation and responses to immune reactions, host AS events that occur as a result of T. cruzi infection have yet to be explored. In this study, we bioinformatically investigated the transcriptome AS dynamics of T. cruzi (Y strain) infected human foreskin fibroblasts using RNA-Seq data captured over four timepoints (4, 24, 48, and 72 h post infection (hpi)). We identified 1768, 399, 250, and 299 differentially expressed exons (AS exons) at 4, 24, 48, and 72 hpi, respectively, showing that host AS mechanism may have a significant role in the intracellular life cycle of the parasite. We present an exon skipping event in HDAC7, which is a candidate gene that is important in the parasite’s cell cycle. To sum up, this bioinformatics analysis of transcriptome may provide new potential insight into AS regulation in human foreskin fibroblast (HFF) cells infected by T. cruzi and into its implication to the parasite life cycle. Moreover, identified AS genes may provide new potential molecular candidates for improving treatment.
CmLOX10 positively regulates drought tolerance through jasmonic acid -mediated stomatal closure in oriental melon (Cucumis melo var. makuwa Makino)
Authors: Xing Qiaojuan , Liao Jingjing , Cao Songxiao , Li Meng , Lv Tinghui , Qi Hongyan 
Published: October 2020

AbstractDrought stress severely impairs plant growth and production. Lipoxygenase (LOX), a master regulator for lipid peroxidation, is critical for direct or indirect response to abiotic stresses. Here, we found that drought stress induced the transcription of CmLOX10 in leaves of oriental melon seedlings. Reverse genetic approaches and physiological analyses revealed that silencing CmLOX10 increased drought susceptibility and stomatal aperture in oriental melon seedlings, and that ectopic overexpression of CmLOX10 in Arabidopsis enhanced drought tolerance and decreased the stomatal aperture. Moreover, the transcription of jasmonic acid (JA)-related genes and JA accumulation were significantly induced in CmLOX10-overexpressed Arabidopsis, which were reversely suppressed in CmLOX10-silenced seedlings during the stage of drought stress. Foliar application of JA further verified that JA enhanced drought tolerance and induced stomatal closure in leaves of melon seedlings. In addition, the feedback regulation of CmLOX10 was induced by JA signaling, and the expression level of CmMYC2 was increased by JA and drought treatment. Yeast one-hybrid analysis showed that CmMYC2 directly bound to the promoter of CmLOX10. In summary, we identified the important roles of CmLOX10 in the regulation of drought tolerance in oriental melon seedlings through JA- mediated stomatal closure and JA signaling-mediated feedback through CmMYC2.
Experimental study on the influence of locked-in stress on the uniaxial compressive strength and elastic modulus of rocks
Authors: Liu Xin , Geng Hansheng , Xu Hongfa , Yang Yinhao , Ma Linjian , Dong Lu 
Published: October 2020

AbstractThe rock contains many inclusions which produce high locked-in stress under the ground stress. In order to study the influence of locked-in stress on the mechanical properties of rocks, the rock-like materials and nitrile rubber particles are used to make a test block of the rock-like model which contains inclusions. The rubber particles will expand as the test block is heated, which creates locked-in stress in the inclusions. Uniaxial compression tests of similar model blocks with different locked-in stresses and different inclusion contents were performed by using a water bath and MTS-5T uniaxial compression testing machine. The results show that the peak strength and elastic modulus decreased with the increasement of locked-in stress and inclusion content. In the meantime, the relationship among the peak strength, the elastic modulus of the test piece, the locked-in stress and the inclusion content were obtained with the help of a mathematical fitting analysis of the quantitative formula. Furthermore, the expression and value curve of the joint impact factor are calculated. This paper evaluates the importance of the locked-in stress in the mechanical properties of the rock-like material and provide a guide for other researchers to further investigate the locked-in stress in rocks.
Hafnium isotope constraints on the nature of the mantle beneath the Southern Lau basin (SW Pacific)
Authors: Yan Quanshu , Straub Susanne , Castillo Paterno , Zhang Haitao , Tian Liyan , Shi Xuefa 
Published: October 2020

AbstractNew Hf isotope data provide new insights into the nature of the mantle beneath the southern Lau basin, adding new constraints on the displacement process of the Pacific mid-ocean ridge basalt (MORB)-type mantle by the Indian MORB-type mantle. The Hf isotopic ratios (176Hf/177Hf) of submarine lavas from the eastern Lau spreading center (ELSC) range from 0.283194 (εHf = 14.92) to 0.283212 (εHf = 15.54), with an average value of 0.283199 (εHf = 15.11) whereas those from the Valu Fa ridge (VFR) vary from 0.283221 (εHf = 15.88) to 0.283200 (εHf = 15.14), with an average of 0.283214 (15.61), indicating that ELSC lavas have a slightly more radiogenic Hf isotopic composition than VFR lavas. In contrast to the results from previous studies, the new Hf analyses combined with previous Nd isotope data clearly show that both VFR and ELSC have the distinct Hf–Nd isotope composition of the so-called DUPAL isotopic anomaly in the Indian MORB-type mantle. The DUPAL isotopic signature at VFR demonstrates for the first time that the inflow of the Indian MORB-type mantle has reached the southern tip of tectonic propagation in the southern Lau basin.
Flowering season of vernal herbs is shortened at elevated temperatures with reduced precipitation in early spring
Authors: Nam Bo Eun , Kim Jae Geun 
Published: October 2020

AbstractVernal herbs are exposed to the risk of climate change under spring frost and canopy closure. Although vernal herbs contribute to the biodiversity of the understorey layer in temperate forests, few studies assessed the effect of climate change on the phenology of the herbs. To examine phenological shifts in flowering seasons of vernal herb species caused by climate change, a greenhouse experiment was conducted using four species (Adonis amurensis, Hepatica nobilis var. japonica, Viola phalacrocarpa, and Pulsatilla cernua) under two temperature conditions (ambient or elevated temperature) and two precipitation conditions (convective or reduced precipitation). Experimental warming advanced overall aspects of the flowering timing including the first and last day of flowering. The growth of flowering stalk was also promoted by elevated temperature. Effects of decreased precipitation varied among species, which advanced the last day of the flowering of the later flowering species. Consequently, a decrease in overall flowering period length was observed. These results indicate that overall, climate change results in a shortening of the flowering season of vernal herb species, specifically at a higher temperature and under conditions of less precipitation.
BTEX biodegradation by Bacillus amyloliquefaciens subsp. plantarum W1 and its proposed BTEX biodegradation pathways
Authors: Wongbunmak Akanit , Khiawjan Sansanee , Suphantharika Manop , Pongtharangkul Thunyarat 
Published: October 2020

AbstractBenzene, toluene, ethylbenzene and (p-, m- and o-) xylene (BTEX) are classified as main pollutants by several environmental protection agencies. In this study, a non-pathogenic, Gram-positive rod-shape bacterium with an ability to degrade all six BTEX compounds, employed as an individual substrate or as a mixture, was isolated. The bacterial isolate was identified as Bacillus amyloliquefaciens subsp. plantarum strain W1. An overall BTEX biodegradation (as individual substrates) by strain W1 could be ranked as: toluene > benzene, ethylbenzene, p-xylene > m-xylene > o-xylene. When presented in a BTEX mixture, m-xylene and o-xylene biodegradation was slightly improved suggesting an induction effect by other BTEX components. BTEX biodegradation pathways of strain W1 were proposed based on analyses of its metabolic intermediates identified by LC–MS/MS. Detected activity of several putative monooxygenases and dioxygenases suggested the versatility of strain W1. Thus far, this is the first report of biodegradation pathways for all of the six BTEX compounds by a unique bacterium of the genus Bacillus. Moreover, B. amyloliquefaciens subsp. plantarum W1 could be a good candidate for an in situ bioremediation considering its Generally Recognized as Safe (GRAS) status and a possibility to serve as a plant growth-promoting rhizobacterium (PGPR).