bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pathway for multivariate analysis of ecological communities using copulas
Authors: Anderson Marti J. , de Valpine Perry , Punnett Andrew , Miller Arden E. 
Published: March 2019

AbstractWe describe a new pathway for multivariate analysis of data consisting of counts of species abundances that includes two key components: copulas, to provide a flexible joint model of individual species, and dissimilarity‐based methods, to integrate information across species and provide a holistic view of the community. Individual species are characterized using suitable (marginal) statistical distributions, with the mean, the degree of over‐dispersion, and/or zero‐inflation being allowed to vary among a priori groups of sampling units. Associations among species are then modeled using copulas, which allow any pair of disparate types of variables to be coupled through their cumulative distribution function, while maintaining entirely the separate individual marginal distributions appropriate for each species. A Gaussian copula smoothly captures changes in an index of association that excludes joint absences in the space of the original species variables. A permutation‐based filter with exact family‐wise error can optionally be used a priori to reduce the dimensionality of the copula estimation problem. We describe in detail a Monte Carlo expectation maximization algorithm for efficient estimation of the copula correlation matrix with discrete marginal distributions (counts). The resulting fully parameterized copula models can be used to simulate realistic ecological community data under fully specified null or alternative hypotheses. Distributions of community centroids derived from simulated data can then be visualized in ordinations of ecologically meaningful dissimilarity spaces. Multinomial mixtures of data drawn from copula models also yield smooth power curves in dissimilarity‐based settings. Our proposed analysis pathway provides new opportunities to combine model‐based approaches with dissimilarity‐based methods to enhance understanding of ecological systems. We demonstrate implementation of the pathway through an ecological example, where associations among fish species were found to increase after the establishment of a marine reserve.
Molecular characterization of nodule worm in a community of Bornean primates
Authors: Frias Liesbeth , Stark Danica J. , Salgado Lynn Milena , Nathan Senthilvel , Goossens Benoit , Okamoto Munehiro , MacIntosh Andrew J. J. 
Published: March 2019

AbstractStrongyles are commonly reported parasites in studies of primate parasite biodiversity. Among them, nodule worm species are often overlooked as a serious concern despite having been observed to cause serious disease in nonhuman primates and humans. In this study, we investigated whether strongyles found in Bornean primates are the nodule worm Oesophagostomum spp., and to what extent these parasites are shared among members of the community. To test this, we propose two hypotheses that use the parasite genetic structure to infer transmission processes within the community. In the first scenario, the absence of parasite genetic substructuring would reflect high levels of parasite transmission among primate hosts, as primates’ home ranges overlap in the study area. In the second scenario, the presence of parasite substructuring would suggest cryptic diversity within the parasite genus and the existence of phylogenetic barriers to cross‐species transmission. By using molecular markers, we identify strongyles infecting this primate community as O. aculeatum, the only species of nodule worm currently known to infect Asian nonhuman primates. Furthermore, the little to no genetic substructuring supports a scenario with no phylogenetic barriers to transmission and where host movements across the landscape would enable gene flow between host populations. This work shows that the parasite's high adaptability could act as a buffer against local parasite extinctions. Surveys targeting human populations living in close proximity to nonhuman primates could help clarify whether this species of nodule worm presents the zoonotic potential found in the other two species infecting African nonhuman primates.
Facile Synthesis and Self‐Assembly of Zinc (2‐Diethoxyphosphorylethynyl)porphyrins
Authors: Mitrofanov Alexander Yu. , Rousselin Yoann , Khrustalev Victor N. , Cheprakov Andrey V. , Bessmertnykh‐Lemeune Alla , Beletskaya Irina P. 
Published: March 2019

AbstractInvited for the cover of this issue are Alla Lemeune, Alexander Yu. Mitrofanov, Irina P. Beletskaya and co‐workers from the International Associated Laboratory of Macrocyclic Systems and Related Materials (LIA LAMREM) of CNRS and RAS supported by RFBR and included the ICMUB, Université Bourgogne Franche‐Comté (Dijon, France), Frumkin Institute of Physical Chemistry and Electrochemistry, Peoples’ Friendship University and Lomonosov Moscow State University (Moscow, Russia). The cover image shows the biomimetic self‐organization of (phosphorylethynyl)porphyrins.
Host defense triggers rapid adaptive radiation in experimentally evolving parasites
Authors: Bush Sarah E. , Villa Scott M. , Altuna Juan C. , Johnson Kevin P. , Shapiro Michael D. , Clayton Dale H. 
Published: March 2019

AbstractAdaptive radiation occurs when the members of a single lineage evolve different adaptive forms in response to selection imposed by competitors or predators. Iconic examples include Darwin's finches, Caribbean anoles, and Hawaiian silverswords, all of which live on islands. Although adaptive radiation is thought to be an important generator of biodiversity, most studies concern groups that have already diversified. Here, we take the opposite approach. We experimentally triggered diversification in the descendants of a single population of host-specific parasites confined to different host “islands.” We show rapid adaptive divergence of experimentally evolving feather lice in response to preening, which is a bird's main defense against ectoparasites. We demonstrate that host defense exerts strong phenotypic selection for crypsis in lice transferred to different colored rock pigeons (Columba livia). During four years of experimental evolution (∼60 generations), the lice evolved heritable differences in color. Strikingly, the observed color differences spanned the range of phenotypes found among congeneric lice adapted to other species of birds. To our knowledge, this is the first real-time demonstration that microevolution is fast enough to simulate millions of years of macroevolutionary change. Our results further indicate that host-mediated selection triggers rapid divergence in the adaptive radiation of parasites, which are among the most diverse organisms on Earth.
Suggestions for plant parameters to monitor potential CO2 leakage from carbon capture and storage (CCS) sites
Authors: Kim You Jin , He Wenmei , Yoo Gayoung 
Published: March 2019

AbstractPotential CO2 leakage from carbon capture and storage (CCS) facilities should be monitored and managed carefully. Biomonitoring technologies for CO2 leakage using plants could be very effective, especially in areas near transport pipelines, because of the extensive areas that they can cover. A greenhouse study was conducted to investigate whether early changes in plant parameters could be an effective indicator to detect leaked CO2. Corn (Zea mays), which was reported to be a CO2‐tolerant species, was selected to identify specific indicators of CO2 leakage. The mean soil CO2 concentration for soil treated with CO2 was 20–40%, which is similar to the concentration that could occur near transport pipelines through slow‐insidious seepage. In the soil treated with CO2, the number of yellow leaves at the canopy level was significantly increased from the sixth day of CO2 injection compared to the control. The chlorophyll content in green leaves was significantly reduced on the eighth day from CO2 injection. The soil water content in the treated soil was increased from the sixth day of injection due to reduced root adsorption. The results of this study implied that early changes in parameters of CO2‐tolerant species such as canopy‐level discoloration and chlorophyll content could be used as CO2‐specific indicators for the detection of soil CO2 leakage. We suggested that canopy‐level monitoring is a promising, useful technique for soil CO2 leakage in extensive areas, such as near CO2 transport pipelines. In addition, rhizosphere‐level parameters, such as soil water content, could be good subsidiary indicators together with the large‐scale collection of baseline data and statistical analysis. © 2019 Society of Chemical Industry and John Wiley & Sons, Ltd.
Particulates in the ascending gas caused by the 2013 Ya'an earthquake: A new matter released by earthquake
Authors: Liu Rui , Cao Jianjin , Luo Songying , Liao Yipeng , Chen Jie 
Published: March 2019

Earthquakes can be destructive, killing many people and causing great financial loss. Costs from earthquakes are increasing rapidly, and thus seismic research is an important tool for reducing loss. Traditional studies of earthquakes have mainly been based on geophysics (seismic waves, geomagnetism, and geoelectricity), hydrogeology, and geogas. However, earthquakes can also release numerous particulates, which can be carried by ascending gas to reach the surface. These particulates provide us with abundant and direct information about earthquake activity and can serve as a new medium for studying earthquakes. In this study, we first find, using a transmission electron microscope (TEM), that ascending gas in the soil of the 2013 Ya'an earthquake region carries many particulates. These particulates are usually 20–600 nm and are composed of amorphous crystal, monocrystalline, and polycrystalline structures. In addition, these particulates contain O, Na, Mg, Al, Si, P, S, Cl, K, Ca, Cr, Fe, Zn, Ba, Hg, Ti, Mn, Ni, Cu, Cd, Sn, Sb, Cs, Pt, and Pb. Compared to the background areas (Yuhe and Hongzi Village and the Fengguanshan inactive fault), particulates carried by ascending gas in the Ya'an earthquake region have many abnormal elements (element associations), including Ti, Mn, Ni, Cd, Sn, Sb, Pt, and Pb. This finding confirms our hypothesis that earthquakes can release particulates carried by ascending gas that reach the surface. In addition, the elements occurring in these particulates indicate that earthquakes can trigger element activation and migration in the form of particulates. As particulates carried by ascending gas in the earthquake region are significantly different from those in the background areas, they can be used to predict earthquakes. The particulates in our study are significantly different from particulates carried by ascending gas from ruptures caused by the Wenchuan earthquake; therefore, we first propose that particulates in ascending gas from earthquake regions may exhibit a close relationship with the magnitudes and hypocentre depths of earthquakes and can be used to predict earthquakes with larger magnitudes and deeper hypocentre depths.
MicroRNA‐503 contributes to podocyte injury via targeting E2F3 in diabetic nephropathy
Authors: Zha Fangfang , Bai Lin , Tang Bo , Li Ji , Wang Yakun , Zheng PengXi , Ji Tingting , Bai Shoujun 
Published: March 2019

AbstractDiabetic nephropathy (DN) is serious diabetic complication with capillary injury. Podocyte injury exerts a crucial effect on DN pathogenesis. MicroRNA‐503 (miR‐503) has been reported in various diseases including DN. Here, we investigated the detailed mechanism of miR‐503 in the podocyte injury of DN. The functional role of miR‐503 was investigated in cultured podocytes and diabetic rats. Podocyte injury was evaluated by migration and apoptosis experiments in podocytes and we observed that high glucose elevated miR‐503 in a time and dose‐dependent manner. Meanwhile, E2F transcription factor 3 (E2F3), as a crucial regulator in multiple diseases, was predicted as a potential target of miR‐503 here. It was shown that E2F3 was greatly decreased in podocytes incubated with high glucose and miR‐503 modulated its expression negatively. In addition, downregulation of E2F3 contributed to podocyte injury, which was reversed by miR‐503 inhibitors in vitro. Furthermore, we proved that increase of miR‐503 resulted in an unfavorable renal function in diabetic rats via targeting E2F3. These revealed for the first time that the overexpression of miR‐503 promoted podocyte injury via targeting E2F3 in diabetic nephropathy and miR‐503/E2F3 axis might represent a pathological mechanism of diabetic nephropathy progression.
miRNA‐301b‐3p accelerates migration and invasion of high‐grade ovarian serous tumor via targeting CPEB3/EGFR axis
Authors: Liu Fengying , Zhang Guilian , Lv Shiming , Wen Xinmian , Liu Peishu 
Published: March 2019

AbstractHigh‐grade ovarian serous carcinoma (HGS‐OvCa), a type of ovarian cancer with poor prognosis due to distant metastasis, is urgently in need of new therapeutic targets. microRNAs (miRNAs), a class of small noncoding RNAs, perform significant roles in tumor progression. Mounting evidence has revealed the aberrant expression of miRNA in various cancers, one of which is HGS‐OvCa. Present study planned to investigate that miRNA‐301b‐3p accelerates migration and invasion of high‐grade ovarian serous tumor via targeting CPEB3/EGFR axis. Upregulation of miR‐301b‐3p was uncovered in HGS‐OvCa tissues and cell lines, and was identified to be associated with metastasis. The Kaplan‐Meier analysis confirmed the association of miR‐301b‐3p with poor prognosis of HGS‐OvCa patients. Transwell assay validated the oncogenic effect of miR‐301b‐3p on migration and invasion of HGS‐OvCa cells. Cytoplasmic polyadenylation element binding protein 3 (CPEB3) was then identified as a target of miR‐301b‐3p. It was also discovered that CPEB3 was downregulated in HGS‐OvCa tissues and cell lines. The Spearman correlation curve presented the negative correlation of CPEB3 expression with miR‐301b‐3p. Furthermore, rescue assays proved that miRNA‐301b‐3p regulated the invasion and migration through CPEB3. Western blot and qRT‐PCR analysis showed that miRNA‐301b‐3p induced epidermal growth factor receptor and downstream metastasis‐related proteins, p38, and extracellular signal‐regulated kinase 1/2 (ERK1/2), through CPEB3. To be concluded, these results indicated that miRNA‐301b‐3p accelerated migration and invasion of high‐grade ovarian serous tumor via targeting CPEB3/EGFR axis.
XRCC4, which is inhibited by PFDA, regulates DNA damage repair and cell chemosensitivity
Authors: Liu Fengyan , Fan Ziyan , Song Ning , Han Mingyong , Yan Ming , Guo Liang‐Hong , Jihui Jia , Liu Shili 
Published: March 2019

AbstractThe mechanism of environmental pollution promoting gastric cancer incidence and difficulty of treatment is not fully understood. In the present article, perfluorodecanoic acid (PFDA), a common persistent environmental pollutant, was used to treat the gastric cell lines and mice to test its genotoxicity. The γ‐H2AX immunoblot and plasmid fragment PCR results showed that PFDA had a promotion effect on the DNA double‐strand breaks (DSBs) in human and mouse cells. Subsequent results showed that PFDA significantly altered the sensitivity of cells to chemotherapy. Microarray data showed that the expressions of some important DNA repair genes were changed. Further investigation discovered that PFDA inhibition of DNA repair was mediated by X‐ray repair cross complementing 4 (XRCC4). The cells deficient in XRCC4 generally exhibited reduced proliferation and premature aging in culture; however, our results indicated that PFDA induced p53 inhibition rescued cells from the apoptosis that was triggered by nonhomologous end‐joining (NHEJ) inactivation, and overexpression of p53 expression in PFDA‐treated cells enhanced their apoptosis. Finally, T‐cell specific factor 4 was suggested by the results as an upstream regulator of XRCC4. This article revealed for the first time that perfluorinated chemicals affect chemotherapeutic sensitivity and the NHEJ pathway, and p53 reduction rescues cells from death.
Reduced PDGF‐AA in subchondral bone leads to articular cartilage degeneration after strenuous running
Authors: Yao Zilong , Chen Peisheng , Wang Shengnan , Deng Ganming , Hu Yanjun , Lin Qingrong , Zhang Xianrong , Yu Bin 
Published: March 2019

AbstractTo identify the effects of running on articular cartilage and subchondral bone remodeling, C57BL/6 mice were randomly divided into three groups: control, moderate‐, and strenuous running. Magnetic resonance imaging showed bone marrow lesions in the knee subchondral bone in the strenuous‐running group in contrast with the other two groups. The microcomputed tomography analysis showed promoted bone formation in the subchondral bone in mice subjected to strenuous running. Histological and immunohistochemistry results indicated that terminal differentiation of chondrocytes and degeneration of articular cartilage were enhanced but, synthesis of platelet‐derived growth factor‐AA (PDGF‐AA) in the subchondral bone was suppressed after strenuous running. In vitro, excessive mechanical treatments suppressed the expression of PDGF‐AA in osteoblasts, and the condition medium from mechanical‐treated osteoblasts stimulated maturation and terminal differentiation of chondrocytes. These results indicate that strenuous running suppresses the synthesis of PDGF‐AA in subchondral bone, leading to downregulated PDGF/Akt signal in articular cartilage and thus cartilage degeneration.
Combination therapy with dacarbazine and statins improved the survival rate in mice with metastatic melanoma
Authors: Tsubaki Masanobu , Takeda Tomoya , Obata Naoya , Kawashima Keishi , Tabata Mitsuki , Imano Motohiro , Satou Takao , Nishida Shozo 
Published: March 2019

AbstractMalignant melanoma is a highly aggressive skin cancer, and the overall median survival in patients with metastatic melanoma is only 6–9 months. Although molecular targeted therapies have recently been developed and have improved the overall survival, melanoma patients may show no response and acquisition of resistance to these drugs. Thus, other molecular approaches are essential for the treatment of metastatic melanoma. In the present study, we investigated the effect of cotreatment with dacarbazine and statins on tumor growth, metastasis, and survival rate in mice with metastatic melanomas. We found that cotreatment with dacarbazine and statins significantly inhibited tumor growth and metastasis via suppression of the RhoA/RhoC/LIM domain kinase/serum response factor/c‐Fos pathway and enhanced p53, p21, p27, cleaved caspase‐3, and cleaved poly(ADP‐ribose) polymerase 1 expression in vivo. Moreover, the cotreatment significantly improved the survival rate in metastasis‐bearing mice. Importantly, treatment with dacarbazine plus 100 mg/kg simvastatin or fluvastatin prevented metastasis‐associated death in 4/20 mice that received dacarbazine + simvastatin and in 8/20 mice that received dacarbazine + fluvastatin (survival rates, 20% and 40%, respectively). These results suggested that cotreatment with dacarbazine and statins may thus serve as a new therapeutic approach to control tumor growth and metastasis in melanoma patients.
Enhanced phycocyanin and protein content of Arthrospira by applying neutral density and red light shading filters: a small‐scale pilot experiment
Authors: Kilimtzidi Evmorfia , Cuellar Bermudez Sara , Markou Giorgos , Goiris Koen , Vandamme Dries , Muylaert Koenraad 
Published: March 2019

AbstractBACKGROUNDThe cyanobacterium Arthrospira contains proteins and the blue pigment phycocyanin that can be used as a natural colourant in the food industry. The aim of this study was to investigate a strategy for increasing the yield of phycocyanin and protein from Arthrospira cultures by shading the cultures with neutral density and red light filters. Experiments were conducted under three different irradiance conditions: (i) laboratory tests under relatively low light intensities (100 μmol m−2 s−1), (ii) laboratory tests under relatively high light intensities (516 μmol m−2 s−1) and (iii) scaled‐up tests under natural conditions by cultivating Arthrospira in raceway ponds in a greenhouse.RESULTSIn all cases, shading of cultures with red filters resulted in biomass with increased phycocyanin content achieving a maximum of 134, 71 and 121 mg g−1 under low light intensity, high light intensity and natural conditions, respectively. Under high light intensity and natural conditions, shaded cultures displayed phycocyanin of higher purity and increased protein content, which reached up to 43 and 65%, respectively.CONCLUSIONSShading of Arthrospira cultures by low‐cost polyester red light filters may be an effective way for enhancing phycocyanin production and improving its purity in outdoor ‘spirulina farms’. © 2019 Society of Chemical Industry
Abdominal Ultrasonography: Improved Image Quality with the Combined Use of a Diet and Laxatives
Authors: Vogel Huibert J. Ph. , Schipper Jaap , Hermans Jo 
Published: March 2019

Intestinal contents (gas and food particles) are well known to cause problems in abdominal ultrasonography by inducing confusing and inconclusive images. We prospectively studied the effect on the combination of a 2‐day low‐calorie, low gasforming diet with laxatives on abdominal sonographic image quality.For a total group of 100 consecutive outpatients, 50 patients (diet‐laxative or DL group) were randomly assigned to follow the preparation of a diet and laxatives, and 50 patients (control or C group) served as a control group without any special preparation. The sonographic imaging quality of abdominal organs and retroperitoneal structures was assessed without knowledge of which group the patients were assigned to. The DL group patients showed a significant improvement in visibility of the extrahepatic common bile duct (p = 0.009), head and body of the pancreas (p = 0.015 and 0.004, respectively), para‐aortic region (p = 0.001), and the iliac vessels (p = 0.0005).The combined use of a low‐calorie, low gas‐forming diet and laxatives improves the abdominal sonographic image quality of the above‐mentioned structures to such an extent that the sonographer will be able to make more pertinent statements about the presence or absence of pathology.
Echographic Diagnosis of Omphalocele in the First Trimester of Pregnancy
Authors: Pagliano Marco , Mossetti Massimo , Ragno Patrizia 
Published: March 2019

Ultrasound represent an invaluable modality for the early diagnosis of structural alterations of the fetus, and facilitates a correct prognosis and effective therapeutic action.Omphalocele is the herniation of the abdominal organs at the insertion of the umbilical cord. It develops between 8 and 11 weeks, menstrual age.The echographic diagnosis of omphalocele is easily carried out during the second trimester of pregnancy; however, a careful examination of the fetus is necessary for a differential diagnosis in the first trimester of pregnancy.Examining the international literature we found that the earliest reported diagnosis of omphalocele was carried out at the 12th week, menstrual age.The following is a report of a case of omphalocele identified at 10.9 weeks, menstrual age.
A Case of Scrotal Birth Trauma: Sonographic Evaluation
Authors: Weinberg Brighita , Rodriguez Luis R. , Diakoumakis Evangelos E. 
Published: March 2019

Real‐time sonography has been proven to be useful in the evaluation of the traumatized scrotum, especially since in many instances the clinical assessment is quite limited. Testicular rupture is accurately diagnosed, thus leading to prompt surgical intervention. Hematoceles and areas of focal alteration in the texture of the testis corresponding to intratesticular infarction or hemorrhage can be identified.We report a case of a neonate with a deep scrotal injury from birth trauma that was diagnosed by sonography.