bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of key genes involved in the biosynthesis of triterpenic acids in the mint family
Authors: Aminfar Zahra , Rabiei Babak , Tohidfar Masoud , Mirjalili Mohammad Hossein 
Published: November 2019

AbstractTriterpenic acids (TAs), a large group of natural compounds with diverse biological activity, are produced by several plant taxa. Betulinic, oleanolic, and ursolic acids are the most medicinally important TAs and are mainly found in plants of the mint family. Metabolic engineering is strongly dependent on identifying the key genes in biosynthetic pathways toward the products of interest. In this study, gene expression tracking was performed by transcriptome mining, co-expression network analysis, and tissue-specific metabolite-expression analysis in order to identify possible key genes involved in TAs biosynthetic pathways. To this end, taxa-specific degenerate primers of six important genes were designed using an effective method based on the MEME algorithm in a phylogenetically related group of sequences and successfully applied in three members of the Lamiaceae (Rosmarinus officinalis, Salvia officinalis, and Thymus persicus). Based on the results of in-depth data analysis, genes encoding squalene epoxidase and oxido squalene cyclases are proposed as targets for boosting triterpene production. The results emphasize the importance of identifying key genes in triterpene biosynthesis, which may facilitate genetic manipulation or overexpression of target genes.
Laparoscopic Resection of Residual Retroperitoneal Tumor Mass in Advanced Nonseminomatous Testicular Germ Cell Tumors; a Feasible and Safe Oncological Procedure
Authors: Öztürk Çiğdem , Been Lukas B. , van Ginkel Robert J. , Gietema Jourik A. , Hoekstra Harald J. 
Published: November 2019

AbstractTen-year oncological experience of the University Medical Center Groningen with conventional laparotomy (C-RRRTM) and laparoscopy (L-RRRTM) is described concerning resection of residual retroperitoneal tumor masses (RRTM) in a large series of patients with advanced nonseminomatous testicular germ cell tumors (NSTGCT). 150 consecutive patients with disseminated NSTGCT required adjunctive surgery after combination chemotherapy. L-RRRTM was scheduled in 89 and C-RRRTM in 61 patients. Median residual tumor diameter was 20 mm in the L-RRRTM versus 42 mm in the C-RRRTM group (p < 0.001). Conversion rate was 15% in the L-RRRTM group. Perioperative complications occurred in 5 patients (6%) in the L-RRRTM and 7 (12%, NS) in the C-RRRTM group. Median duration of L-RRRTM was 156 minutes vs. 221 minutes for C-RRRTM (p < 0.001). 17/89 patients in the L-RRRTM group had postoperative complications versus 18/61 patients in the C-RRRTM group (NS). Median postoperative stay in the L-RRRTM group was 2 vs. 6 days in the C-RRRTM group (p < 0.001). During a median follow-up of 79 months, 27 patients had recurrences: 8 (9%) in the L-RRRTM group and 19 (31%) in the C-RRRTM group (p < 0.001). Laparoscopic resection of RRTM for advanced NSTGCT is feasible and an oncologically safe option in appropriately selected patients.
Contrasting global, regional and local patterns of genetic structure in gray reef shark populations from the Indo-Pacific region
Authors: Boissin E. , Thorrold S. R. , Braun C. D. , Zhou Y. , Clua E. E. , Planes S. 
Published: November 2019

AbstractHuman activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (FST = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.
Evidence that fodipir (DPDP) binds neurotoxic Pt2+ with a high affinity: An electron paramagnetic resonance study
Authors: Stehr Jan Eric , Lundström Ingemar , Karlsson Jan Olof G. 
Published: November 2019

AbstractOxaliplatin typically causes acute neuropathic problems, which may, in a dose-dependent manner, develop into a chronic form of chemotherapy-induced peripheral neuropathy (CIPN), which is associated with retention of Pt2+ in the dorsal root ganglion. A clinical study by Coriat and co-workers suggests that co-treatment with mangafodipir [Manganese(II) DiPyridoxyl DiPhosphate; MnDPDP] cures ongoing CIPN. These authors anticipated that it is the manganese superoxide dismutase mimetic activity of MnDPDP that explains its curative activity. However, this is questionable from a pharmacokinetic perspective. Another, but until recently undisclosed possibility is that Pt2+ outcompetes Mn2+/Ca2+/Zn2+ for binding to DPDP or its dephosphorylated metabolite PLED (diPyridoxyL EthylDiamine) and transforms toxic Pt2+ into a non-toxic complex, which can be readily excreted from the body. We have used electron paramagnetic resonance guided competition experiments between MnDPDP (10logKML ≈ 15) and K2PtCl4, and between MnDPDP and ZnCl2 (10logKML ≈ 19), respectively, in order to obtain an estimate the 10logKML of PtDPDP. Optical absorption spectroscopy revealed a unique absorption line at 255 nm for PtDPDP. The experimental data suggest that PtDPDP has a higher formation constant than that of ZnDPDP, i.e., higher than 19. The present results suggest that DPDP/PLED has a high enough affinity for Pt2+ acting as an efficacious drug in chronic Pt2+-associated CIPN.
The effect of local species composition on the distribution of an avian invader
Authors: Magory Cohen Tali , Dor Roi 
Published: November 2019

AbstractEstimating the potential distribution of invasive species has been primarily achieved by employing species distribution models (SDM). Recently introduced joint species distribution models (JSDM) that include species interactions are expected to improve model output. Here we compare the predictive ability of SDM and JSDM by modelling the distribution of one of the most prolific avian invaders in the world, the common myna (Acridotheres tristis), in a recent introduction in Israel. Our results indicate that including information on the local species composition did not improve model accuracy, possibly because of the unique characteristics of this species that include broad environmental tolerance and behavior flexibility. However, the JSDM provided insights into co-occurrence patterns of common mynas and their local heterospecifics, suggesting that at this time point, there is no evidence of species exclusion by common mynas. Our findings suggest that the invasion potential of common mynas depends greatly on urbanization and less so on the local species composition and reflect the major role of anthropogenic impact in increasing the distribution of avian invaders.
Caldera-forming eruptions of mushy magma modulated by feedbacks between ascent rate, gas retention/loss and bubble/crystal framework interaction
Authors: Okumura Satoshi , L. de Silva Shanaka , Nakamura Michihiko , Sasaki Osamu 
Published: November 2019

AbstractCaldera-forming eruptions of mushy silicic magma are among the most catastrophic natural events on Earth. In such magmas, crystals form an interlocking framework when their content reaches critical thresholds, resulting in the dramatic increase in viscous resistance to flow. Here, we propose a new mechanism for the ascent of mushy magma based on microstructural observations of crystal-rich silicic pumices and lavas from the Central Andes and decompression experiments. Microstructural data include spherical vesicles and jigsaw-puzzle association of broken crystals in pumices, whereas there is limited breakage of crystals in lavas. These observations insinuate that shearing of magma during ascent was limited. Decompression experiments reveal contrasting interaction between growing gas bubbles and the crystal framework in crystal-rich magma. Under slow decompression typical of effusive eruptions, gas extraction is promoted, whereas under rapid decompression, bubbles are retained and the crystal framework collapses. This feedback between decompression rate, retention of gas bubbles, and integrity of the crystal framework leads to strong non-linearity between magma decompression rate and eruption explosivity. We extend these findings to caldera-forming eruptions of crystal-rich magma where large overpressures are induced by caldera-collapse, resulting in magma plug-flow, rapid decompression facilitated by shear-localization at conduit margins, and explosive eruption.
The HIV protease inhibitor darunavir prevents kidney injury via HIV-independent mechanisms
Authors: Gao Xiaobo , Rosales Alan , Karttunen Heidi , Bommana Geetha M. , Tandoh Buadi , Yi Zhengzi , Habib Zainab , D’Agati Vivette , Zhang Weijia , Ross Michael J. 
Published: November 2019

AbstractHIV-associated nephropathy (HIVAN) is a rapidly progressive kidney disease that is caused by HIV infection of renal epithelial cells with subsequent expression of viral genes, including vpr. Antiretroviral therapy ameliorates HIVAN without eradicating HIV from the kidneys and the mechanism by which it protects kidneys is poorly understood. Since HIV protease inhibitors have “off target” cellular effects, we studied whether darunavir, the most commonly prescribed protease inhibitor, protects kidneys from HIV-induced injury via mechanisms independent of HIV protease and viral replication. Renal epithelial cells were transduced with lentiviruses encoding HIV (lacking protease and reverse transcriptase), Vpr, or vector control. Darunavir attenuated HIV and Vpr-induced activation of Stat3, Src, Erk, and cytokines, which are critical for HIVAN pathogenesis. We then studied HIV-transgenic mice, which develop HIVAN in the absence of HIV protease or reverse transcriptase. Mice were treated with darunavir, zidovudine, darunavir + zidovudine, or control. Darunavir and darunavir + zidovudine reduced albuminuria and histologic kidney injury and normalized expression of dysregulated proteins. RNA-seq analyses demonstrated that darunavir suppressed HIV-induced upregulation of immune response genes in human kidney cells. These data demonstrate that darunavir protects against HIV-induced renal injury via mechanisms that are independent of inhibition of HIV protease.
Machine-learning based reconstructions of primary and secondary climate variables from North American and European fossil pollen data
Authors: Salonen J. Sakari , Korpela Mikko , Williams John W. , Luoto Miska 
Published: November 2019

AbstractWe test several quantitative algorithms as palaeoclimate reconstruction tools for North American and European fossil pollen data, using both classical methods and newer machine-learning approaches based on regression tree ensembles and artificial neural networks. We focus on the reconstruction of secondary climate variables (here, January temperature and annual water balance), as their comparatively small ecological influence compared to the primary variable (July temperature) presents special challenges to palaeo-reconstructions. We test the pollen–climate models using a novel and comprehensive cross-validation approach, running a series ofh-block cross-validations usinghvalues of 100–1500 km. Our study illustrates major benefits of this variableh-block cross-validation scheme, as the effect of spatial autocorrelation is minimized, while the cross-validations with increasinghvalues can reveal instabilities in the calibration model and approximate challenges faced in palaeo-reconstructions with poor modern analogues. We achieve well-performing calibration models for both primary and secondary climate variables, with boosted regression trees providing the overall most robust performance, while the palaeoclimate reconstructions from fossil datasets show major independent features for the primary and secondary variables. Our results suggest that with careful variable selection and consideration of ecological processes, robust reconstruction of both primary and secondary climate variables is possible.
Mechanism and Consequences of The Impaired Hif-1α Response to Hypoxia in Human Proximal Tubular HK-2 Cells Exposed to High Glucose
Authors: García-Pastor Coral , Benito-Martínez Selma , Moreno-Manzano Victoria , Fernández-Martínez Ana B. , Lucio-Cazaña Francisco Javier 
Published: November 2019

AbstractRenal hypoxia and loss of proximal tubular cells (PTC) are relevant in diabetic nephropathy. Hypoxia inhibits hypoxia-inducible factor-1α (HIF-1α) degradation, which leads to cellular adaptive responses through HIF-1-dependent activation of gene hypoxia-responsive elements (HRE). However, the diabetic microenvironment represses the HIF-1/HRE response in PTC. Here we studied the mechanism and consequences of impaired HIF-1α regulation in human proximal tubular HK-2 cells incubated in hyperglycemia. Inhibition at different levels of the canonical pathway of HIF-1α degradation did not activate the HIF-1/HRE response under hyperglycemia, except when proteasome was inhibited. Further studies suggested that hyperglycemia disrupts the interaction of HIF-1α with Hsp90, a known cause of proteasomal degradation of HIF-1α. Impaired HIF-1α regulation in cells exposed to hyperglycemic, hypoxic diabetic-like milieu led to diminished production of vascular endothelial growth factor-A and inhibition of cell migration (responses respectively involved in tubular protection and repair). These effects, as well as impaired HIF-1α regulation, were reproduced in normoglycemia in HK-2 cells incubated with microparticles released by HK-2 cells exposed to diabetic-like milieu. In summary, these results highlight the role of proteasome-dependent mechanisms of HIF-1α degradation on diabetes-induced HK-2 cells dysfunction and suggest that cell-derived microparticles may mediate negative effects of the diabetic milieu on PTC.
People with autism perceive drastic illusory changes for repeated verbal stimuli
Authors: Itoi Chihiro , Kato Nobumasa , Kashino Makio 
Published: November 2019

AbstractA core symptom of autism spectrum disorder (ASD) is restricted and repetitive behavior, characterized partly by insistence on sameness and excessively focused interest. This behavior has often been interpreted as a manifestation of anxiety and fear triggered by resistance to change. The implicit assumption underlying this interpretation is that perception per se (such as the judgment of sameness and changes in sensory stimuli) is not different between ASD and typically developed (TD) individuals, but that only the emotional response to the same amount of perceived change is. However, few studies have examined how individuals with ASD actually perceive a repeated presentation of the same sensory stimulus. To explore this issue, we conducted a listening test to compare perception of a repeated sound pattern, namely a spoken word, between ASD and TD groups. Prolonged listening to a repeated word without a pause may induce perceptual changes, which is known as the verbal transformation effect. We discovered that individuals with ASD tend to perceive more drastic changes or differences for the same repeated auditory pattern. This suggests that such variable perception incites individuals with ASD to persist for sameness.
Numerical Simulations of MitraClip Placement: Clinical Implications
Authors: Kamakoti Ramji , Dabiri Yaghoub , Wang Dee Dee , Guccione Julius , Kassab Ghassan S. 
Published: November 2019

AbstractMitral regurgitation (MR) is the most common type of valvular heart disease in patients over the age of 75 in the US. Despite the prevalence of mitral regurgitation in the elderly population, however, almost half of patients identified with moderate-severe MR are turned down for traditional open heart surgery due to frailty and other existing co-morbidities. MitraClip (MC) is a recent percutaneous approach to treat mitral regurgitation by placement of MC in the center of the mitral valve to reduce MR. There are currently no computational simulations to elucidate the role of MC on both the fluid and solid mechanics of the mitral valve. Here, we use the Smoothed Particle Hydrodynamics (SPH) approach to study various positional placements of the MC in the mitral valve and its impact on reducing MR. SPH is a particle based (meshless) approach that handles flow through narrow regions quite efficiently. Fluid and surrounding anatomical structure interactions is handled via contact and hence can be used for studying fluid-structure interaction problems such as blood flow with surrounding tissues/structure. This method is available as part of the Abaqus/Explicit solver. Regurgitation was initiated by removing targeted chordae tendineae that are attached to specified leaflets of the mitral valve and, subsequently, MC implants are placed in various locations, starting from the region near where the chordae tendineae were removed and moving away from the location towards the center of the valve. The MC implant location closest to where the chordae tendineae were removed showed the least amount of residual MR post-clip implantation amongst all other locations of MC implant considered. These findings have important implications for strategic placement of the MC depending on the etiology of MR to optimize clinical outcome.
Microbial communities and soil chemical features associated with commercial production of the medicinal mushroom Ganoderma lingzhi in soil
Authors: Ke Le-Qin , Li Pu-Dong , Xu Jian-Ping , Wang Qiu-Shuang , Wang Liang-Liang , Wen Hui-Ping 
Published: November 2019

AbstractCrop production, including mushroom farming, may cause significant changes to the underlying substrates which in turn, can influence crop quality and quantity during subsequent years. Here in this study, we analyzed the production of the medicinal mushroom Ganoderma lingzhi and the associated soil microbial communities and soil chemical features over 24 months from April 2015 to April 2017. This Basidiomycete mushroom, known as Lingzhi in China, is commonly found on dead trees and wood logs in temperate and subtropical forests. Its economic and medicinal importance have propelled the development of a diversity of cultivation methods. The dominant method uses wood logs as the main substrate, which after colonization by Lingzhi mycelia, are buried in the soil to induce fruiting. The soil microbial communities over the 24 months were analyzed using the Illumina HiSeq platform targeting a portion of the bacterial 16S rRNA gene and the fungal internal transcribed spacer 1 (ITS1). Overall, a significant reduction of Lingzhi yield was observed over our experimentation period. Interestingly, temporal changes in soil microbial compositions were detected during the 24 months, with the fungal community showing more changes than that of bacteria in terms of both species richness and the relative abundance of several dominant species after each fruiting. The soil chemical features also showed significant changes, with decreasing soil nitrogen and phosphorus concentrations and increasing soil pH and iron content after each fruiting. We discuss the implications of our results in sustainable Lingzhi production in soil.
Comparison of whole blood and spleen transcriptional signatures over the course of an experimental malaria infection
Authors: Talavera-López Carlos , Bediako Yaw , Lin Jing-wen , Joseph Valletta John , Recker Mario , Langhorne Jean 
Published: November 2019

AbstractAlthough the spleen is broadly accepted as the major lymphoid organ involved in generating immune responses to the erythrocytic stages of the malaria parasite, Plasmodium, human splenic tissue is not readily available in most cases. As a result, most studies of malaria in humans rely on peripheral blood to assess cellular immune responses to malaria. The suitability of peripheral blood as a proxy for splenic immune responses is however unknown. Here, we have simultaneously analysed the transcriptomes of whole blood and spleen over 12 days of erythrocytic stage Plasmodium chabaudi infection in C57BL/6 mice. Using both unsupervised and directed approaches, we compared gene expression between blood and spleen over the course of infection. Taking advantage of publicly available datasets, we used machine learning approaches to infer cell proportions and cell-specific gene expression signatures from our whole tissue transcriptome data. Our findings demonstrate that spleen and blood are quite dissimilar, sharing only a small amount of transcriptional information between them, with transcriptional differences in both cellular composition and transcriptional activity. These results suggest that while blood transcriptome data may be useful in defining surrogate markers of protection and pathology, they should not be used to predict specific immune responses occurring in lymphoid organs.
Identification of candidate ATP-binding cassette transporter gene family members in Diaphorina citri (Hemiptera: Psyllidae) via adult tissues transcriptome analysis
Authors: Wang Zhengbing , Tian Fajun , Cai Lijun , Zhang Jie , Liu Jiali , Zeng Xinnian 
Published: November 2019

AbstractThe ATP-binding cassette (ABC) transporters exist in all living organisms and play major roles in various biological functions by transporting a wide variety of substrates across membranes. The functions of ABC transporters in drug resistance have been extensively studied in vertebrates; however, they are rarely characterized in agricultural pests. The Asian citrus psyllid, Diaphorina citri, is one of the most damaging pests of the Citrus genus because of its transmission of Huanglongbing, also known as Yellow Dragon disease. In this study, the next-generation sequencing technique was applied to research the ABC transporters of D. citri. Fifty-three ABC transporter genes were found in the RNA-Seq data, and among these ABC transporters, 4, 4, 5, 2, 1, 4, 18 and 15 ABC proteins belonged to the ABCA-ABCH subfamilies, respectively. Different expression profiles of 52 genes between imidacloprid-resistant and imidacloprid-susceptible strains were studied by qRT-PCR; 5 ABCGs and 4 ABCHs were significantly upregulated in the imidacloprid-resistant strain. In addition, five of the nine upregulated genes were widely expressed in adult tissues in spatial expression analysis. The results suggest that these genes may play key roles in this phenotype. In general, this study contributed to our current understanding of D. citri resistance to insecticides.