bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling of variables in cellular infection reveals CXCL10 levels are regulated by human genetic variation and the Chlamydia-encoded CPAF protease
Authors: Schott Benjamin H. , Antonia Alejandro L. , Wang Liuyang , Pittman Kelly J. , Sixt Barbara S. , Barnes Alyson B. , Valdivia Raphael H. , Ko Dennis C. 
Published: October 2020

AbstractSusceptibility to infectious diseases is determined by a complex interaction between host and pathogen. For infections with the obligate intracellular bacterium Chlamydia trachomatis, variation in immune activation and disease presentation are regulated by both host genetic diversity and pathogen immune evasion. Previously, we discovered a single nucleotide polymorphism (rs2869462) associated with absolute abundance of CXCL10, a pro-inflammatory T-cell chemokine. Here, we report that levels of CXCL10 change during C. trachomatis infection of cultured cells in a manner dependent on both host and pathogen. Linear modeling of cellular traits associated with CXCL10 levels identified a strong, negative correlation with bacterial burden, suggesting that C. trachomatis actively suppresses CXCL10. We identified the pathogen-encoded factor responsible for this suppression as the chlamydial protease- or proteasome-like activity factor, CPAF. Further, we applied our modeling approach to other host cytokines in response to C. trachomatis and found evidence that RANTES, another T-cell chemoattractant, is actively suppressed by Chlamydia. However, this observed suppression of RANTES is not mediated by CPAF. Overall, our results demonstrate that CPAF suppresses CXCL10 to evade the host cytokine response and that modeling of cellular infection parameters can reveal previously unrecognized facets of host–pathogen interactions.
A systematic investigation of human DNA preservation in medieval skeletons
Authors: Parker Cody , Rohrlach Adam B. , Friederich Susanne , Nagel Sarah , Meyer Matthias , Krause Johannes , Bos Kirsten I. , Haak Wolfgang 
Published: October 2020

AbstractAncient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
Apoptotic effect of novel pyrazolone-based derivative [Cu(PMPP-SAL)(EtOH)] on HeLa cells and its mechanism
Authors: Reheman Delizhaer , Zhao Jing , Guan Shan , Xu Guan-Cheng , Li Yi-Jie , Sun Su-Rong 
Published: October 2020

AbstractPyrazolone complexes have strong anti-tumor and antibacterial properties, but the anti-tumor mechanism of pyrazolone-based copper complexes has not been fully understood. In this study, the possible mechanism and the inhibitory effect of a novel pyrazolone-based derivative compound [Cu(PMPP-SAL)(EtOH)] on human cervical cancer cells (HeLa cells) was investigated. [Cu(PMPP-SAL)(EtOH)] effectively inhibited proliferation of HeLa cells in vitro with an IC50 value of 2.082 after treatment for 72 h. Cell cycle analysis showed apoptosis was induced by blocking the cell cycle in the S phase. [Cu(PMPP-SAL)(EtOH)] promoted the loss of mitochondrial membrane potential, release of cytochrome c, PARP cleavage, and activation of caspase-3/9 in HeLa cells. Additionally, [Cu(PMPP-SAL)(EtOH)] inhibited the PI3K/AKT pathway and activated the P38/MAPK, and JNK/MAPK pathways. [Cu(PMPP-SAL)(EtOH)] also inhibited the phosphorylation of Iκ-Bα in the NF-κB pathway activated by TNF-α, thus restricting the proliferation of HeLa cells which were activated by TNF-α. In conclusion, [Cu(PMPP-SAL)(EtOH)] inhibited the growth of HeLa cells and induced apoptosis possibly via the caspase-dependent mitochondria-mediated pathway. These results suggest that [Cu(PMPP-SAL)(EtOH)] can be a potential candidate for the treatment of cervical cancer.
Inkjet printed self-healable strain sensor based on graphene and magnetic iron oxide nano-composite on engineered polyurethane substrate
Authors: Hassan Gul , Khan Muhammad Umair , Bae Jinho , Shuja Ahmed 
Published: October 2020

AbstractIn recent years, self-healing property has getting tremendous attention in the future wearable electronic. This paper proposes a novel cut-able and highly stretchable strain sensor utilizing a self-healing function from magnetic force of magnetic iron oxide and graphene nano-composite on an engineered self-healable polyurethane substrate through commercialized inkjet printer DMP-3000. Inducing the magnetic property, magnetic iron oxide is applied to connect between graphene flacks in the nano-composite. To find the best nano-composite, the optimum graphene and magnetic iron oxide blending ratio is 1:1. The proposed sensor shows a high mechanical fracture recovery, sensitivity towards strain, and excellent self-healing property. The proposed devices maintain their performance over 10,000 times bending/relaxing cycles, and 94% of their function are recovered even after cutting them. The device also demonstrates stretchability up to 54.5% and a stretching factor is decreased down to 32.5% after cutting them. The gauge factor of the device is 271.4 at 35%, which means its sensitivity is good. Hence, these results may open a new opportunity towards the design and fabrication of future self-healing wearable strain sensors and their applied electronic devices.
Evaluation of surgical procedures of mouse urethra by visualization and the formation of fistula
Authors: Hyuga Taiju , Hashimoto Daiki , Matsumaru Daisuke , Kumegawa Shinji , Asamura Shinichi , Suzuki Kentaro , Katayama Kei-ichi , Nakamura Shigeru , Nakai Hideo , Yamada Gen 
Published: October 2020

AbstractVisualization of the surgically operated tissues is vital to improve surgical model animals including mouse. Urological surgeries for urethra include series of fine manipulations to treat the increasing number of birth defects such as hypospadias. Hence visualization of the urethral status is vital. Inappropriate urethral surgical procedure often leads to the incomplete wound healing and subsequent formation of urethro-cutaneous fistula or urethral stricture. Application of indocyanine green mediated visualization of the urethra was first performed in the current study. Indocyanine green revealed the bladder but not the urethral status in mouse. Antegrade injection of contrast agent into the bladder enabled to detect the urethral status in vivo. The visualization of the leakage of contrast agent from the operated region was shown as the state of urethral fistula in the current hypospadias mouse model and urethral stricture was also revealed. A second trial for contrast agent was performed after the initial operation and a tendency of accelerated urethral stricture was observed. Thus, assessment of post-surgical conditions of urogenital tissues can be improved by the current analyses on the urethral status.
Shear strength characteristics of a sand clay liner
Authors: Dafalla Muawia , Shaker Abdullah , Elkady Tamer , Almajed Abdullah , Al-Shamrani Mosleh 
Published: October 2020

AbstractThis study investigated shear strength behaviour of compacted sand–clay mixtures used as liners, with 10%, 20%, and 30% clay contents. A natural high-plasticity and highly expansive clay found in the eastern province of Saudi Arabia was used. A series of consolidated undrained triaxial tests and pore water pressure measurements of saturated samples with various clay contents and confining pressures was conducted using a computer-controlled Bishop and Wesley triaxial cell. The unit was equipped with pressure volume controllers and a pressure transducer for measuring sample volume changes and excess pore water pressure. The experimental test results indicate that clay content and confining pressure significantly affect stress strain response curves, pore water pressure generation curves, and steady-state shear strength. Sand–clay mixtures with clay content less than 10% showed a tendency toward contractive behaviour. The failure line slope increased in accordance with clay content increase. The deviator stress versus axial strain of saturated sand–clay mixtures indicated a hyperbolic trend. The stress ratio versus axial strain representation was more informative for the shear strength behaviour assessment. Clay content did not significantly affect critical-state friction angle. Scanning electron microscope images of the sand-clay mixtures with different clay contents are presented.
Chia seeds as a potential cognitive booster in the APP23 Alzheimer’s disease model
Authors: Schreyer Stefanie , Klein Charlotte , Pfeffer Anna , Rasińska Justyna , Stahn Laura , Knuth Karlotta , Abuelnor Basim , Panzel Alina Elisabeth Catharina , Rex André , Koch Stefan , Hemmati-Sadeghi Shabnam , Steiner Barbara 
Published: October 2020

AbstractGlucose hypometabolism potentially contributes to Alzheimer’s disease (AD) and might even represent an underlying mechanism. Here, we investigate the relationship of diet-induced metabolic stress and AD as well as the therapeutic potential of chia seeds as a modulator of glucose metabolism in the APP23 mouse model. 4–6 (pre-plaque stage, PRE) and 28–32 (advanced-plaque stage, ADV) weeks old APP23 and wild type mice received pretreatment for 12 weeks with either sucrose-rich (SRD) or control diet, followed by 8 weeks of chia seed supplementation. Although ADV APP23 mice generally showed functioning glucose homeostasis, they were more prone to SRD-induced glucose intolerance. This was accompanied by elevated corticosterone levels and mild insulin insensitivity. Chia seeds improved spatial learning deficits but not impaired cognitive flexibility, potentially mediated by amelioration of glucose tolerance, attenuation of corticosterone levels and reversal of SRD-induced elevation of pro-inflammatory cytokine levels. Since cognitive symptoms and plaque load were not aggravated by SRD-induced metabolic stress, despite enhanced neuroinflammation in the PRE group, we conclude that impairments of glucose metabolism do not represent an underlying mechanism of AD in this mouse model. Nevertheless, chia seeds might provide therapeutic potential in AD as shown by the amelioration of cognitive symptoms.
Extended harmonic mapping connects the equations in classical, statistical, fluid, quantum physics and general relativity
Authors: Zhai Xiaobo , Huang Changyu , Ren Gang 
Published: October 2020

AbstractOne potential pathway to find an ultimate rule governing our universe is to hunt for a connection among the fundamental equations in physics. Recently, Ren et al. reported that the harmonic maps with potential introduced by Duan, named extended harmonic mapping (EHM), connect the equations of general relativity, chaos and quantum mechanics via a universal geodesic equation. The equation, expressed as Euler–Lagrange equations on the Riemannian manifold, was obtained from the principle of least action. Here, we further demonstrate that more than ten fundamental equations, including that of classical mechanics, fluid physics, statistical physics, astrophysics, quantum physics and general relativity, can be connected by the same universal geodesic equation. The connection sketches a family tree of the physics equations, and their intrinsic connections reflect an alternative ultimate rule of our universe, i.e., the principle of least action on a Finsler manifold.
Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists
Authors: Naranpanawa D. N. U. , Chandrasekara C. H. W. M. R. B. , Bandaranayake P. C. G. , Bandaranayake A. U. 
Published: October 2020

AbstractRecent advances in next-generation sequencing technologies have paved the path for a considerable amount of sequencing data at a relatively low cost. This has revolutionized the genomics and transcriptomics studies. However, different challenges are now created in handling such data with available bioinformatics platforms both in assembly and downstream analysis performed in order to infer correct biological meaning. Though there are a handful of commercial software and tools for some of the procedures, cost of such tools has made them prohibitive for most research laboratories. While individual open-source or free software tools are available for most of the bioinformatics applications, those components usually operate standalone and are not combined for a user-friendly workflow. Therefore, beginners in bioinformatics might find analysis procedures starting from raw sequence data too complicated and time-consuming with the associated learning-curve. Here, we outline a procedure for de novo transcriptome assembly and Simple Sequence Repeats (SSR) primer design solely based on tools that are available online for free use. For validation of the developed workflow, we used Illumina HiSeq reads of different tissue samples of Santalum album (sandalwood), generated from a previous transcriptomics project. A portion of the designed primers were tested in the lab with relevant samples and all of them successfully amplified the targeted regions. The presented bioinformatics workflow can accurately assemble quality transcriptomes and develop gene specific SSRs. Beginner biologists and researchers in bioinformatics can easily utilize this workflow for research purposes.
Screening for energetic compounds based on 1,3-dinitrohexahydropyrimidine skeleton and 5-various explosopheres: molecular design and computational study
Authors: Duan Binghui , Liu Ning , Lu Xianming , Mo Hongchang , Zhang Qian , Liu Yingzhe , Wang Bozhou 
Published: October 2020

AbstractIn this paper, twelve 1,3-dinitrohexahydropyrimidine-based energetic compounds were designed by introducing various explosopheres into hexahydropyrimidine skeleton. Their geometric and electronic structures, heats of formation (HOFs), energetic performance, thermal stability and impact sensitivity were discussed. It is found that the incorporation of electron-withdrawing groups (–NO2, –NHNO2, –N3, –CH(NO2)2, –CF(NO2)2, –C(NO2)3) improves HOFs of the derivatives and all the substituents contribute to enhancing the densities and detonation properties (D, P) of the title compounds. Therein, the substitution of –C(NO2)3 features the best energetic performance with detonation velocity of 9.40 km s−1 and detonation pressure of 40.20 GPa. An analysis of the bond dissociation energies suggests that N–NO2 bond may be the initial site in the thermal decompositions for most of the derivatives. Besides, –ONO2 and –NF2 derivatives stand out with lower impact sensitivity. Characters with striking detonation properties (D = 8.62 km s−1, P = 35.08 GPa; D = 8.81 km s−1, P = 34.88 GPa), good thermal stability, and acceptable impact sensitivity (characteristic height H50 over 34 cm) lead novel compounds 5,5-difluoramine-1,3-dinitrohexahydropyrimidine (K) and 5-fluoro-1,3,5-trinitrohexahydropyrimidine (L) to be very promising energetic materials. This work provides the theoretical molecular design and a reasonable synthetic route of L for further experimental synthesis and testing.
Universal non-Markovianity detection in hybrid open quantum systems
Authors: Svozilík Jiří , Hidalgo-Sacoto Raúl , Arkhipov Ievgen I. 
Published: October 2020

AbstractA universal characterization of non-Markovianity for any open hybrid quantum systems is presented. This formulation is based on the negativity volume of the generalized Wigner function, which serves as an indicator of the quantum correlations in any composite quantum systems. It is shown, that the proposed measure can be utilized for any single or multi-partite quantum system, containing any discrete or continuous variables. To demonstrate its power in revealing non-Markovianity in such quantum systems, we additionally consider a few illustrative examples.
Sex differences in type of exercise associated with depression in South Korean adults
Authors: Kim Hyunkyu , Jeong Wonjeong , Kwon Junhyun , Kim Youseok , Jang Sung-In , Park Eun-Cheol 
Published: October 2020

AbstractExercise has been considered as treatment and a preventive modality to alleviate depressive symptoms, but sex differences regarding specific types of exercise in association with depression have not been clearly elucidated. Here, we investigated sex differences in the association between exercise type and depression in Korean adults. Data from the Korea National Health and Nutrition Examination Survey (KNHANES) were used for this study. A total of 13,914 participants who had filled in a Patient Health Questionnaire-9 (PHQ-9) were included. The subjects’ exercise status had been evaluated with questions on strength exercise and walking, and answers were analysed in the current study using multivariate logistic regression. Male participants who reported having done strength exercise more than once in a week were less likely to be depressed after adjusting for covariates assumed to affect depression levels [adjusted odds ratio (OR) 0.60, 95% CI 0.40–0.92]. In women, walking more than once during the previous week was associated with lower depression levels after covariate adjustments (adjusted OR 0.54, CI 0.34–0.87). This study identifies the relationship between exercise and the presence of depressive symptoms and finds sex differences in the types of exercise that correlate with depression in Korean adults.
Substrate utilisation of cultured skeletal muscle cells in patients with CFS
Authors: Tomas Cara , Elson Joanna L. , Newton Julia L. , Walker Mark 
Published: October 2020

AbstractChronic fatigue syndrome (CFS) patients often suffer from severe muscle pain and an inability to exercise due to muscle fatigue. It has previously been shown that CFS skeletal muscle cells have lower levels of ATP and have AMP-activated protein kinase dysfunction. This study outlines experiments looking at the utilisation of different substrates by skeletal muscle cells from CFS patients (n = 9) and healthy controls (n = 11) using extracellular flux analysis. Results show that CFS skeletal muscle cells are unable to utilise glucose to the same extent as healthy control cells. CFS skeletal muscle cells were shown to oxidise galactose and fatty acids normally, indicating that the bioenergetic dysfunction lies upstream of the TCA cycle. The dysfunction in glucose oxidation is similar to what has previously been shown in blood cells from CFS patients. The consistency of cellular bioenergetic dysfunction in different cell types supports the hypothesis that CFS is a systemic disease. The retention of bioenergetic defects in cultured cells indicates that there is a genetic or epigenetic component to the disease. This is the first study to use cells derived from skeletal muscle biopsies in CFS patients and healthy controls to look at cellular bioenergetic function in whole cells.
DDX3 DEAD-box RNA helicase (Hel67) gene disruption impairs infectivity of Leishmania donovani and induces protective immunity against visceral leishmaniasis
Authors: Pandey Satish Chandra , Pande Veena , Samant Mukesh 
Published: October 2020

AbstractVisceral leishmaniasis (VL) is a vector-borne disease caused by the digenetic protozoan parasiteLeishmania donovanicomplex. So far there is no effective vaccine available against VL. The DDX3 DEAD-box RNA Helicase (Hel67) is 67 kDa protein which is quite essential for RNA metabolism, amastigote differentiation, and infectivity inL. major and L. infantum. To investigate the role ofHel67in theL. donovani, we createdL. donovanideficient in theHel67. Helicase67 null mutants (LdHel67−/−) were not able to differentiate as axenic amastigotes and were unable to infect the hamster. So, we have analyzed the prophylactic efficacy of theLdHel67−/−null mutant in hamsters. TheLdHel67−/−null mutant based candidate vaccine exhibited immunogenic response and a higher degree of protection againstL. donovaniin comparison to the infected control group. Further, the candidate vaccine displayed antigen-specific delayed-type hypersensitivity (DTH) as well as strong antibody response and NO production which strongly correlates to long term protection of candidate vaccine against the infection. This study confirms the potential ofLdHel67−/−null mutant as a safe and protective live attenuated vaccine candidate against visceral leishmaniasis.
Objective analysis of perfluoropropane tamponade area after pars plana vitrectomy using ultra-widefield fundus stereographic projection images
Authors: Choi Mihyun , Hong Suji , Yun Cheolmin , Kim Seong-Woo 
Published: October 2020

AbstractTo objectively analyze the gas tamponade area in patients with different concentrations of perfluoropropane (C3F8) after pars plana vitrectomy (PPV), retrospective analysis was performed in patients diagnosed with retinal detachment or macular hole and underwent PPV with C3F8 tamponade of two concentrations (14% and 20%). The ultra-widefield fundus (UWF) images at one and 10 days and four weeks postoperatively were corrected using stereographic projection to adjust peripheral distortion. The gas–fluid interface curvatures were delineated using UWF stereographic projection images, and the gas–fluid area ratio and estimated gas area were calculated at each concentration. Among 65 eyes, 30 were in the 14% group and 35 were in the 20% group. The gas–fluid area ratio was 0.71 in the 14% group and 0.83 in the 20% group at 10 days (p = 0.046) and 0.27 and 0.45, respectively, at four weeks postoperatively (p < 0.001). The estimated gas area was 52.56 and 60.82 mm2 at 10 days (p = 0.025) and 19.83 and 33.86 mm2 at four weeks (p < 0.001). The gas tamponade areas were objectively shown to be greater under the 20% concentration than the 14% concentration of C3F8 at 10 days and 4 weeks postoperatively using UWF stereographic projection images.
Quantitative analysis of choroidal vasculature in polypoidal choroidal vasculopathy using ultra-widefield indocyanine green angiography
Authors: Ryu Gahyung , Moon Cheolwon , van Hemert Jano , Sagong Min 
Published: October 2020

AbstractPolypoidal choroidal vasculopathy (PCV) is a common choroidal vascular disease particularly in Asians. However, the underlying pathogenesis of PCV is still yet to be fully elucidated, and the correlation between choroidal vasculature and treatment response of PCV are poorly understood. Accordingly, we sought to find clues to understand the pathogenesis and prognosis of PCV by quantitatively evaluating choroidal vasculature from the entire fundus using ultra-widefield (UWF) indocyanine green angiography (ICGA). In this study, 32 eyes from 29 patients with treatment naïve PCV and 30 eyes from 30 healthy control participants were enrolled. Choroidal vascular density (CVD) of PCV eyes was higher than normal eyes in majority regions including the periphery. CVD was positively correlated with choroidal thickness and choroidal hyperpermeability, supporting that the pathogenesis of PCV may include choroidal congestion and dilatation. Thicker choroid and higher CVD were also correlated with poor treatment response after anti-VEGF injections. The CVD, quantified from UWF ICGA can also be used as an effective image biomarker to predict the treatment response in PCV.