bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid diagnosis of MDR and XDR tuberculosis with the MeltPro TB assay in China
Authors: Pang Yu , Dong Haiyan , Tan Yaoju , Deng Yunfeng , Cai Xingshan , Jing Hui , Xia Hui , Li Qiang , Ou Xichao , Su Biyi , Li Xuezheng , Zhang Zhiying , Li Junchen , Zhang Jiankang , Huan Shitong , Zhao Yanlin 
Published: May 2016

AbstractNew diagnostic methods have provided a promising solution for rapid and reliable detection of drug-resistant TB strains. The aim of this study was to evaluate the performance of the MeltPro TB assay in identifying multidrug-resistant (MDR-) and extensively drug-resistant tuberculosis (XDR-TB) patients from sputum samples. The MeltPro TB assay was evaluated using sputum samples from 2057 smear-positive TB patients. Phenotypic Mycobacterial Growth Indicator Tube (MGIT) 960 drug susceptibility testing served as a reference standard. The sensitivity of the MeltPro TB assay was 94.2% for detecting resistance to rifampicin and 84.9% for detecting resistance to isoniazid. For second-line drugs, the assay showed a sensitivity of 83.3% for ofloxacin resistance, 75.0% for amikacin resistance, and 63.5% for kanamycin resistance. However, there was a significant difference for detecting kanamycin resistance between the two pilot sites in sensitivity, which was 53.2% in Guangdong and 81.5% in Shandong (P = 0.015). Overall, the MeltPro TB assay demonstrated good performance for the detection of MDR- and XDR-TB, with a sensitivity of 86.7% and 71.4%, respectively. The MeltPro TB assay is an excellent alternative for the detection of MDR- and XDR-TB cases in China, with high accuracy, short testing turn-around time, and low unit price compared with other tests.
A platinum-based hybrid drug design approach to circumvent acquired resistance to molecular targeted tyrosine kinase inhibitors
Authors: Wei Yuming , Poon Daniel C. , Fei Rong , Lam Amy S. M. , Au-Yeung Steve C. F. , To Kenneth K. W. 
Published: May 2016

AbstractThree molecular targeted tyrosine kinase inhibitors (TKI) were conjugated to classical platinum-based drugs with an aim to circumvent TKI resistance, predominately mediated by the emergence of secondary mutations on oncogenic kinases. The hybrids were found to maintain specificity towards the same oncogenic kinases as the original TKI. Importantly, they are remarkably less affected by TKI resistance, presumably due to their unique structure and the observed dual mechanism of anticancer activity (kinase inhibition and DNA damage). The study is also the first to report the application of a hybrid drug approach to switch TKIs from being efflux transporter substrates into non-substrates. TKIs cannot penetrate into the brain for treating metastases because of efflux transporters at the blood brain barrier. The hybrids were found to escape drug efflux and they accumulate more than the original TKI in the brain in BALB/c mice. Further development of the hybrid compounds is warranted.
Theoretical approach to resonant inelastic x-ray scattering in iron-based superconductors at the energy scale of the superconducting gap
Authors: Marra Pasquale , van den Brink Jeroen , Sykora Steffen 
Published: May 2016

AbstractWe develop a phenomenological theory to predict the characteristic features of the momentum-dependent scattering amplitude in resonant inelastic x-ray scattering (RIXS) at the energy scale of the superconducting gap in iron-based super-conductors. Taking into account all relevant orbital states as well as their specific content along the Fermi surface we evaluate the charge and spin dynamical structure factors for the compounds LaOFeAs and LiFeAs, based on tight-binding models which are fully consistent with recent angle-resolved photoemission spectroscopy (ARPES) data. We find a characteristic intensity redistribution between charge and spin dynamical structure factors which discriminates between sign-reversing and sign-preserving quasiparticle excitations. Consequently, our results show that RIXS spectra can distinguish between s± and s++ wave gap functions in the singlet pairing case. In addition, we find that an analogous intensity redistribution at small momenta can reveal the presence of a chiral p-wave triplet pairing.
Asymmetric magnetic proximity effect in a Pd/Co/Pd trilayer system
Authors: Kim Dong-Ok , Song Kyung Mee , Choi Yongseong , Min Byoung-Chul , Kim Jae-Sung , Choi Jun Woo , Lee Dong Ryeol 
Published: May 2016

AbstractIn spintronic devices consisting of ferromagnetic/nonmagnetic systems, the ferromagnet-induced magnetic moment in the adjacent nonmagnetic material significantly influences the spin transport properties. In this study, such magnetic proximity effect in a Pd/Co/Pd trilayer system is investigated by x-ray magnetic circular dichroism and x-ray resonant magnetic reflectivity, which enables magnetic characterizations with element and depth resolution. We observe that the total Pd magnetic moments induced at the top Co/Pd interface are significantly larger than the Pd moments at the bottom Pd/Co interface, whereas transmission electron microscopy and reflectivity analysis indicate the two interfaces are nearly identical structurally. Such asymmetry in magnetic proximity effects could be important for understanding spin transport characteristics in ferromagnetic/nonmagnetic systems and its potential application to spin devices.
The nuclear receptor LXR modulates interleukin-18 levels in macrophages through multiple mechanisms
Authors: Pourcet Benoit , Gage Matthew C. , León Theresa E. , Waddington Kirsty E. , Pello Oscar M. , Steffensen Knut R. , Castrillo Antonio , Valledor Annabel F. , Pineda-Torra Inés 
Published: May 2016

AbstractIL-18 is a member of the IL-1 family involved in innate immunity and inflammation. Deregulated levels of IL-18 are involved in the pathogenesis of multiple disorders including inflammatory and metabolic diseases, yet relatively little is known regarding its regulation. Liver X receptors or LXRs are key modulators of macrophage cholesterol homeostasis and immune responses. Here we show that LXR ligands negatively regulate LPS-induced mRNA and protein expression of IL-18 in bone marrow-derived macrophages. Consistent with this being an LXR-mediated process, inhibition is abolished in the presence of a specific LXR antagonist and in LXR-deficient macrophages. Additionally, IL-18 processing of its precursor inactive form to its bioactive state is inhibited by LXR through negative regulation of both pro-caspase 1 expression and activation. Finally, LXR ligands further modulate IL-18 levels by inducing the expression of IL-18BP, a potent endogenous inhibitor of IL-18. This regulation occurs via the transcription factor IRF8, thus identifying IL-18BP as a novel LXR and IRF8 target gene. In conclusion, LXR activation inhibits IL-18 production through regulation of its transcription and maturation into an active pro-inflammatory cytokine. This novel regulation of IL-18 by LXR could be applied to modulate the severity of IL-18 driven metabolic and inflammatory disorders.
Identification of PKD2 mutations in human preimplantation embryos in vitro using a combination of targeted next-generation sequencing and targeted haplotyping
Authors: Chen Song-Chang , Xu Xiao-Li , Zhang Jun-Yu , Ding Guo-Lian , Jin Li , Liu Bei , Sun Dong-Mei , Mei Chang-Lin , Yang Xiao-Nan , Huang He-Feng , Xu Chen-Ming 
Published: May 2016

AbstractHere, we evaluate the applicability of a new method that combines targeted next-generation sequencing (NGS) with targeted haplotyping in identifying PKD2 gene mutations in human preimplantation embryos in vitro. To achieve this goal, a proband family with a heterozygous deletion of c.595_595 + 14delGGTAAGAGCGCGCGA in exon 1 of the PKD2 gene was studied. A total of 10 samples were analyzed, including 7 embryos. An array-based gene chip was designed to capture all of the exons of 21 disease-related genes, including PKD2. We performed Sanger sequencing combined with targeted haplotyping to evaluate the feasibility of this new method. A total of 7.09 G of data were obtained from 10 samples by NGS. In addition, 24,142 informative single-nucleotide polymorphisms (SNPs) were identified. Haplotyping analysis of several informative SNPs of PKD2 that we selected revealed that embryos 3, 5, and 6 did not inherit the mutation haplotypes of the PKD2 gene, a finding that was 100% accurate and was consistent with Sanger sequencing. Our results demonstrate that targeted NGS combined with targeted haplotyping can be used to identify PKD2 gene mutations in human preimplantation embryos in vitro with high sensitivity, fidelity, throughput and speed.
Co-circulation of H5N6, H3N2, H3N8 and Emergence of Novel Reassortant H3N6 in a Local Community in Hunan Province in China
Authors: Li Xuyong , Yang Jiayun , Liu Bin , Jia Yane , Guo Jing , Gao Xue , Weng Shaoting , Yang Maijuan , Wang Liang , Wang Lin-Fa , Cui Jie , Chen Hualan , Zhu Qiyun 
Published: May 2016

AbstractMultiple infections of avian influenza viruses (AIVs) in poultry or wild birds contribute to the continued evolution of H5 subtype viruses in nature and provide potential recombination of AIVs of different origins. In this study, we carried out surveillance of AIVs in ducks, geese and the environment of a community in Hunan province, China, from 2014–2015. We isolated multiple co-circulated AIVs including H3N2, H3N8 and H5N6, and, most importantly, a novel reassortant: H3N6. Phylogenetic analyses suggest that H3N6 is highly likely derived from H5N6, which has recently been shown to have zoonotic potential with human infections. Studies with mammalian cell lines and a mouse model indicate that four selected AIVs of duck or goose origin can infect MDCK and A549 cells but have low pathogenicity in mice. We propose that a potential co-circulation of multiple subtypes including H5N6 in local area may result in the production of novel subtypes such as H3N6 by gene reassortment.
Multilocus phylogenetic analyses reveal unexpected abundant diversity and significant disjunct distribution pattern of the Hedgehog Mushrooms (Hydnum L.)
Authors: Feng Bang , Wang Xiang-Hua , Ratkowsky David , Gates Genevieve , Lee Su See , Grebenc Tine , Yang Zhu L. 
Published: May 2016

AbstractHydnum is a fungal genus proposed by Linnaeus in the early time of modern taxonomy. It contains several ectomycorrhizal species which are commonly consumed worldwide. However, Hydnum is one of the most understudied fungal genera, especially from a molecular phylogenetic view. In this study, we extensively gathered specimens of Hydnum from Asia, Europe, America and Australasia, and analyzed them by using sequences of four gene fragments (ITS, nrLSU, tef1α and rpb1). Our phylogenetic analyses recognized at least 31 phylogenetic species within Hydnum, 15 of which were reported for the first time. Most Australasian species were recognized as strongly divergent old relics, but recent migration between Australasia and the Northern Hemisphere was also detected. Within the Northern Hemisphere, frequent historical biota exchanges between the Old World and the New World via both the North Atlantic Land Bridge and the Bering Land Bridge could be elucidated. Our study also revealed that most Hydnum species found in subalpine areas of the Hengduan Mountains in southwestern China occur in northeastern/northern China and Europe, indicating that the composition of the mycobiota in the Hengduan Mountains reigion is more complicated than what we have known before.
Computational investigation of dynamical transitions in Trp-cage miniprotein powders
Authors: Kim Sang Beom , Gupta Devansh R. , Debenedetti Pablo G. 
Published: May 2016

AbstractWe investigate computationally the dynamical transitions in Trp-cage miniprotein powders, at three levels of hydration: 0.04, 0.26 and 0.4 g water/g protein. We identify two distinct temperatures where transitions in protein dynamics occur. Thermal motions are harmonic and independent of hydration level below Tlow ≈ 160 K, above which all powders exhibit harmonic behavior but with a different and enhanced temperature dependence. The second onset, which is often referred to as the protein dynamical transition, occurs at a higher temperature TD that decreases as the hydration level increases and at the lowest hydration level investigated here (0.04 g/g) is absent in the temperature range we studied in this work (T ≤ 300 K). Protein motions become anharmonic at TD and their amplitude increases with hydration level. Upon heating above TD, hydrophilic residues experience a pronounced enhancement in the amplitude of their characteristic motions in hydrated powders, whereas it is the hydrophobic residues that experience the more pronounced enhancement in the least hydrated system. The dynamical transition in Trp-cage is a collective phenomenon, with every residue experiencing a transition to anharmonic behavior at the same temperature.
Suppression of rolling circle amplification by nucleotide analogs in circular template for three DNA polymerases
Authors: Tang Suming , Wei Hua , Hu Tianyu , Jiang Jiquan , Chang Jinglin , Guan Yifu , Zhao Guojie 
Published: May 2016

Abstract
Among wide applications of nucleotide analogs, their roles in enzyme catalytic reactions are significant in both fundamental and medical researches. By introducing analogs into circular templates, we succeeded in determining effects of four analogs on RCA efficiency for three different DNA polymerases. Results showed an obvious suppression effect for 2′-OMeRNA modification, which might be due to the size of the C2′-modified moieties. 2′-F RNA, LNA and PS had little interference, suggesting good analog candidates for application in RCA. Different polymerases and nucleobases made a little difference according to analogs we used. These results are useful for understanding polymerase catalytic mechanism and analogs applications in RCA reaction.
A new species of arboreal rat, genus Oecomys (Rodentia, Cricetidae) from Chaco
Authors: Pardiñas Ulyses F. J. , Teta Pablo , Salazar-Bravo Jorge , Myers Phil , Galliari Carlos A. 
Published: May 2016

AbstractA new species of rodent is added to the highly diverse genus Oecomys (Cricetidae, Sigmodontinae, Oryzomyini) based on specimens collected in the Argentinian provinces of Chaco and Formosa. The new species is characterized by a derived carotid circulatory pattern, a feature shared with O. concolor, O. mamorae, and O. sydandersoni. A unique combination of morphological, morphometric, and molecular characters, however, provides unambiguous evidence of its validity as a separate entity. Individuals of the new species are larger than other representatives of Oecomys, and their skulls have wide and cuneate interorbital regions with well-developed supraorbital shelves, long incisive foramina, long palates, absent alisphenoid struts, and broad Eustachian tubes. This new Oecomys appears to be endemic to the Humid Chaco, an ecoregion listed as Vulnerable due to the human impact. Preliminary observations suggest that several specimens from Eastern Paraguay and the Brazilian Pantanal could also be assigned to the new species described herein.Una nueva especie es adicionada al altamente diverso género de roedores Oecomys (Cricetidae, Sigmodontinae, Oryzomyini), sobre la base de especímenes coleccionados en las provincias Argentinas de Chaco y Formosa. La nueva especie se caracteriza por un patrón de circulación carotídea derivado, un rasgo compartido con O. concolor, O. mamorae y O. sydandersoni. Sin embargo, la combinación única de caracteres morfológicos, morfométricos y moleculares provee evidencia inequívoca sobre su validez como una entidad separada. Individuos de la nueva especie son de mayor tamaño en comparación con otros Oecomys y sus cráneos tienen una región interorbitaria ancha y acuñada con plataformas supraorbitarias bien desarrolladas, forámenes incisivos largos, paladares largos, ausencia de las barras alisfenoideas y tubos de Eustaquio anchos. Este nuevo Oecomys parece ser endémico del Chaco Húmedo, una ecorregión considerada como Vulnerable debido al impacto antrópico. Observaciones preliminares sugieren que varios especímenes de Paraguay Oriental y del Pantanal Brasilero podrían también ser asignados a la nueva especie aquí descrita.
From epigenetic landscape to phenotypic fitness landscape: evolutionary effect of pathogens on host traits
Authors: Cortez Mark Jayson V. , Rabajante Jomar F. , Tubay Jerrold M. , Babierra Ariel L. 
Published: May 2016

AbstractThe epigenetic landscape illustrates how cells differentiate into different types through the control of gene regulatory networks. Numerous studies have investigated epigenetic gene regulation but there are limited studies on how the epigenetic landscape and the presence of pathogens influence the evolution of host traits. Here we formulate a multistable decision-switch model involving many possible phenotypes with the antagonistic influence of parasitism. As expected, pathogens can drive dominant (common) phenotypes to become inferior, such as through negative frequency-dependent selection. Furthermore, novel predictions of our model show that parasitism can steer the dynamics of phenotype specification from multistable equilibrium convergence to oscillations. This oscillatory behavior could explain pathogen-mediated epimutations and excessive phenotypic plasticity. The Red Queen dynamics also occur in certain parameter space of the model, which demonstrates winnerless cyclic phenotype-switching in hosts and in pathogens. The results of our simulations elucidate how epigenetic landscape is associated with the phenotypic fitness landscape and how parasitism facilitates non-genetic phenotypic diversity.
Shear-induced nitric oxide production by endothelial cells
Authors: Sriram K. , Laughlin J. G. , Rangamani P. , Tartakovsky D. M. 
Published: May 2016

AbstractWe present a biochemical model of the wall shear stress (WSS)-induced activation of endothelial nitric oxide synthase (eNOS) in an endothelial cell (EC). The model includes three key mechanotransducers: mechanosensing ion channels, integrins and G-protein-coupled receptors. The reaction cascade consists of two interconnected parts. The first is rapid activation of calcium, which results in formation of calcium-calmodulin complexes, followed by recruitment of eNOS from caveolae. The second is phosphoryaltion of eNOS by protein kinases PKC and AKT. The model also includes a negative feedback loop due to inhibition of calcium influx into the cell by cyclic guanosine monophosphate (cGMP). In this feedback, increased nitric oxide (NO) levels cause an increase in cGMP levels, so that cGMP inhibition of calcium influx can limit NO production. The model was used to predict the dynamics of NO production by an EC subjected to a step increase of WSS from zero to a finite physiologically relevant value. Among several experimentally observed features, the model predicts a highly nonlinear, bipha-sic transient behavior of eNOS activation and NO production: a rapid initial activation due to the very rapid influx of calcium into the cytosol (occurring within 1 to 5 minutes) is followed by a sustained period of activation due to protein kinases.AcronymsAKT, protein kinase B; [Ca2+]c, [Ca2+]s, [Ca2+]eand [Ca2+]b, cytosolic, stored, external and buffer concentrations of calcium ions, respectively; Ca3-CaM and Ca4-CaM, calcium-calmodulin complexes with 3 and 4 calcium ions bound to CaM, respectively; CaM, calmodulin; CCE, capacitative calcium entry; cGMP, cyclic guanosine monophosphate; EC, endothelial cell; ECM, extracellular matrix; eNOS, endothelial nitric oxide synthase; eNOScav, eNOS bound to caveolin; eNOS*, eNOS-CaM complex phosphorylated at Ser-1197; eNOS0, caveolin-bound eNOS phosphorylated at Thr-495; ER, endoplasmic reticulum; FAK, focal adhesion kinase; G, active G proteins; Gt, total G proteins; GPCR, G-protein-coupled receptors; Hsp90, heat shock protein 90; GTP, guanosine triphosphate; IP3, inositol triphosphate; L-Arg, L-form of arginine; MSIC, mechanosensing ion channel; NO, nitric oxide; O2, oxygen; PIP2, phosphatidylinositol 4,5-bisphosphate; PIP3, phos-phatidylinositol (3,4,5)-triphosphate; PI3K, phosphatidylinositide 3-kinases; PKC, protein kinase C; RBC, red blood cell; sGC, soluble guanylate cyclase; WSS, wall shear stress
The role of accrual estimation errors to determine accrual and earnings quality
Authors: Izadi Zadeh Darjezi Javad 
Published: May 2016

Purpose
Managers, investors and security analysts all pay special attention to the bottom line of income statements and they miss significant information included in accruals about the quality of earnings. A considerable portion of the earnings-quality literature examines the possibility of using the accruals to shift reported income among fiscal periods. One of the main roles of working-capital accruals is to adjust the recognition of cash flows. This paper aims to focus on earnings quality by examining the working-capital accruals quality using the method of Dechow and Dichev (2002).

Design/methodology/approach
Following the Dechow and Dichev (2002) model, the result of this paper shows that accrual quality is related to the absolute magnitude of accruals negatively. Also, the standard deviation of accruals, cash flows, sales and earnings is positively related to firm size. The result demonstrates and suggests that these observable firm characteristics can be used as instruments for measuring accrual quality. According to this framework, the author expects that the larger the unsigned abnormal accrual measure, the lower the earnings quality. Therefore, firms with low accrual quality have more accruals that are unrelated to cash flow realisations and so have more noise and less persistence in their earnings.

Findings
After examining earnings and accrual quality, this paper finds that average UK company behaviour was quite similar to the behaviour found earlier in the USA. This paper’s findings show that greater volatility of sales, cash flow, accruals and earnings results in a lower accrual quality. Without a doubt, some of the analysis in this paper, especially that using different equations to calculate working-capital accruals, leads us to a valuable improvement of the earlier studies.

Originality/value
In this paper, the author follows the method of Dechow and Dichev (2002) and define accrual quality as the extent to which accruals map into cash-flow insights based on the UK data. To find the quality of working-capital accruals, the author uses the standard deviation of the residuals as accrual quality that resulted from the author’s firm-specific OLS regressions of working-capital accruals based on last, current and one-year-ahead operating cash flow. Unlike prior research, to avoid a restriction to working-capital accruals, we use different equations to cover more items of working-capital accruals.