bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus sequence typing of Candida albicans isolates from the oral cavities of patients undergoing haemodialysis
Authors: Gong Yan-Bing , Jin Bo , Qi He , Zhang Rong , Zhang Xiu-Ying , Yuan Ping , Zhao Tong-Xiang , Geng Xing-Hua , Zhang Min , Zheng Jian-Ling 
Published: October 2018

AbstractThis study evaluates the prevalence, diversity, and genetic profiles ofCandida albicansisolates recovered from the oral cavities of haemodialysis patients. Oral swab samples were obtained from haemodialysis patients (n = 126) and healthy control subjects (n = 233) andCandidaspecies were characterised. There was no significant difference between the haemodialysis and control groups in the prevalence of yeast carriers (23.6%vs. 31.0%, respectively) orC. albicanscarriers (19.8%vs. 21.0%, respectively).C. albicanswas the most populous species in both cohorts, followed byC. parapsilosis.C. parapsilosisandC. glabratawere more prevalent in the haemodialysis group than in the control group (C. parapsilosis5.6%vs. 0.9% andC. glabrata3.2%vs. 0.4%, respectively;P < 0.05).C. albicansisolates were analysed by multilocus sequence typing and the results were used to construct a phylogenetic tree. Most haemodialysis isolates were placed into Clade 4 (20.0%) and Clade 19 (16.0%) and most control isolates into Clade 8 (17%) and Clade 4 (14.9%). Differences in the strain abundance in each clade were not statistically significant between the two groups. Moreover, there was no significant association between the health status or diagnosis and either the sequence types or clades.
High-precision gas refractometer by comb-mode-resolved spectral interferometry
Authors: Yang Lijun , Li Yan , Wei Haoyun 
Published: October 2018

AbstractHigh-accuracy knowledge of gas refractivity is typically crucial for optical interferometry, precise optical systems, and calculable pressure standard development. Here, we demonstrate an absolute gas refractometer by spectral interferometry and a high-resolution spectrometer. The spectral interferometry relies on a comb with fiber Fabry–Pérot filtering cavity, and a double-spaced vacuum cell. The spectrometer employs a virtually imaged phased array, diffraction grating and near-infrared camera to fully resolve the comb modes. Finally, by means of fast-Fourier-transform, the group refractivity can be derived from the spectrally resolved interferograms of the two beams propagating in the inside and outside of the vacuum cell. To confirm the feasibility and performance of the gas refractometer, the measurement of ambient air was conducted. The proposed scheme has a combined uncertainty of 1.3 × 10−9 for air and a single measurement only takes 10 ms, which is applicable for gas refractivity monitoring and compensating in real time.
A bacteria-derived tail anchor localizes to peroxisomes in yeast and mammalian cells
Authors: Lutfullahoğlu-Bal Güleycan , Seferoğlu Ayşe Bengisu , Keskin Abdurrahman , Akdoğan Emel , Dunn Cory D. 
Published: October 2018

AbstractProkaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.
Enhanced food-related responses in the ventral medial prefrontal cortex in narcolepsy type 1
Authors: van Holst Ruth Janke , Janssen Lieneke K. , van Mierlo Petra , Lammers Gert Jan , Cools Roshan , Overeem Sebastiaan , Aarts Esther 
Published: October 2018

AbstractNarcolepsy type 1 is a chronic sleep disorder caused by a deficiency of the orexin (hypocretin) neuropeptides. In addition to sleep regulation, orexin is important for motivated control processes. Weight gain and obesity are common in narcolepsy. However, the neurocognitive processes associated with food-related control and overeating in narcolepsy are unknown. We explored the neural correlates of general and food-related attentional control in narcolepsy-type-1 patients (n = 23) and healthy BMI-matched controls (n = 20). We measured attentional bias to food words with a Food Stroop task and general executive control with a Classic Stroop task during fMRI. Moreover, using multiple linear regression, we assessed the relative contribution of neural responses during Food Stroop and Classic Stroop to spontaneous snack intake. Relative to healthy controls, narcolepsy patients showed enhanced ventral medial prefrontal cortex responses and connectivity with motor cortex during the Food Stroop task, but attenuated dorsal medial prefrontal cortex responses during the Classic Stroop task. Moreover, the former activity but not the latter, was a significant predictor of spontaneous snack intake. These findings demonstrate that narcolepsy, characterized by orexin deficiency, is associated with decreased dorsal medial prefrontal cortex responses during general executive control and enhanced ventral medial prefrontal cortex responses during food-driven attention.
Involvement of the capsular GalXM-induced IL-17 cytokine in the control of Cryptococcus neoformans infection
Authors: LaRocque-de-Freitas Isabel Ferreira , Rocha Juliana Dutra B. , Nunes Marise Pinheiro , Oliveira Priscila Angelica V. , Nascimento Danielle de Oliveira , Freire-de-Lima Leonardo , Takiya Christina Maeda , Morrot Alexandre , Decote-Ricardo Debora , Previato Jose Osvaldo , DosReis George A. , Mendonça-Previato Lucia , Freire-de-Lima Celio Geraldo 
Published: October 2018

AbstractCryptococcus neoformans is an opportunistic fungus that can cause lethal brain infections in immunosuppressed individuals. Infection usually occurs via the inhalation of a spore or desiccated yeast which can then disseminate from the lung to the brain and other tissues. Dissemination and disease is largely influence by the production of copious amounts of cryptococcal polysaccharides, both which are secreted to the extracellular environment or assembled into a thick capsule surrounding the cell body. There are two important polysaccharides: glucuronoxylomannan (GXM) and galactoxylomannan, also called as glucuronoxylomanogalactan (GXMGal or GalXM). Although GXM is more abundant, GalXM has a more potent modulatory effect. In the present study, we show that GalXM is a potent activator of murine dendritic cells, and when co-cultured with T cells, induces a Th17 cytokine response. We also demonstrated that treating mice with GalXM prior to infection with C. neoformans protects from infection, and this phenomenon is dependent on IL-6 and IL-17. These findings help us understand the immune biology of capsular polysaccharides in fungal pathogenesis.
Progressive hearing loss in vitamin A-deficient mice which may be protected by the activation of cochlear melanocyte
Authors: Gi Mia , Shim Dae Bo , Wu Ling , Bok Jinwoong , Song Mee Hyun , Choi Jae Young 
Published: October 2018

AbstractVitamin A deficiency (VAD) produces various pathologic phenotypes in humans and animals. However, evidence regarding the effect of VAD on hearing function has been inconsistent. In this study, we evaluated the effect of VAD on hearing function in two mouse models of VAD. Hearing ability was evaluated on the basis of auditory brainstem response from 3 to 20 weeks after birth in C57BL/6 (pigmented) and imprinting control region (albino) mice. The two mice strains were divided into the VAD (purified vitamin A-free diet from 7 days after pregnancy) and control (normal diet) groups. Albino VAD mice exhibited hearing loss after 6 weeks and became deaf at 18 weeks. Histological findings revealed degenerative changes in outer hair cells and neuronal loss in the spiral ganglion in albino VAD mice. In contrast, pigmented VAD mice, except those with middle-ear infection, showed no significant hearing loss. Interestingly, pigmented VAD mice exhibited melanocyte activation in the stria vascularis and upregulation of tyrosinase. Recovery of hearing after noise exposure was poorer in pigmented VAD mice than in control mice. In conclusion, complete VAD might be related to age-related or noise-induced hearing loss in mice, protection against which might involve melanocyte activation.
AtHKT1 gene regulating K+ state in whole plant improves salt tolerance in transgenic tobacco plants
Authors: Wang Li , Liu Yuhui , Feng Shoujiang , Wang Zhuoyu , Zhang Jinwen , Zhang Junlian , Wang Di , Gan Yantai 
Published: November 2018

AbstractThe status of K+ is important for plant health. However, little is known about if high-affinity potassium transporter HKTs may help K+ retention under salt stress. Here, we determined the effect of Arabidopsis thaliana transporter gene (AtHKT1) on the K+ status, Na+-induced toxicity, and salt tolerance in tobacco (Nicotiana tabacum L.). Six AtHKT1 transformed tobacco lines (T1, T2, … T6) were contrasted with a non-transgenic plantlet at the whole-plant and molecule levels. AtHKT1 gene was expressed in the xylems of stem, root and leaf vein in the transgenic tobacco, with the line T3 having highest expression. At Day 15, in the 200 mmol L−1 NaCl stress treatment, the transgenic plants remained a healthy K+ status, while the control plants decreased K+ content by 70% and Na+ contents in leaves and stems were 1.7 times that in the transgenic line. The AtHKT1 expression enhanced the activities of SOD, CAT and POD, raised chlorophyll and soluble sugar contents and root activity, and decreased MDA and proline contents and electrolyte leakage destruction. The constitutive over-expression of AtHKT1 that helps maintain a healthy K+ status while reducing Na+ toxicity may serve as a possible mechanism in maximizing productivity of tobacco under salt stress.
β-Glucuronidases of opportunistic bacteria are the major contributors to xenobiotic-induced toxicity in the gut
Authors: Dashnyam Punsaldulam , Mudududdla Ramesh , Hsieh Tung-Ju , Lin Ting-Chien , Lin Hsien-Ya , Chen Peng-Yuan , Hsu Chia-Yi , Lin Chun-Hung 
Published: October 2018

AbstractGut bacterial β-D-glucuronidases (GUSs) catalyze the removal of glucuronic acid from liver-produced β-D-glucuronides. These reactions can have deleterious consequences when they reverse xenobiotic metabolism. The human gut contains hundreds of GUSs of variable sequences and structures. To understand how any particular bacterial GUS(s) contributes to global GUS activity and affects human health, the individual substrate preference(s) must be known. Herein, we report that representative GUSs vary in their ability to produce various xenobiotics from their respective glucuronides. To attempt to explain the distinct substrate preference, we solved the structure of a bacterial GUS complexed with coumarin-3-β-D-glucuronide. Comparisons of this structure with other GUS structures identified differences in loop 3 (or the α2-helix loop) and loop 5 at the aglycone-binding site, where differences in their conformations, hydrophobicities and flexibilities appear to underlie the distinct substrate preference(s) of the GUSs. Additional sequence, structural and functional analysis indicated that several groups of functionally related gut bacterial GUSs exist. Our results pinpoint opportunistic gut bacterial GUSs as those that cause xenobiotic-induced toxicity. We propose a structure-activity relationship that should allow both the prediction of the functional roles of GUSs and the design of selective inhibitors.
Biological interactions of biocompatible and water-dispersed MoS2 nanosheets with bacteria and human cells
Authors: Kaur Jasneet , Singh Manjot , Dell‘Aversana Carmela , Benedetti Rosaria , Giardina Paola , Rossi Manuela , Valadan Mohammadhassan , Vergara Alessandro , Cutarelli Anna , Montone Angela Michela Immacolata , Altucci Lucia , Corrado Federica , Nebbioso Angela , Altucci Carlo 
Published: October 2018

AbstractTwo dimensional materials beyond graphene such as MoS2 and WS2 are novel and interesting class of materials whose unique physico-chemical properties can be exploited in applications ranging from leading edge nanoelectronics to the frontiers between biomedicine and biotechnology. To unravel the potential of TMD crystals in biomedicine, control over their production through green and scalable routes in biocompatible solvents is critically important. Furthermore, considering multiple applications of eco-friendly 2D dispersions and their potential impact onto live matter, their toxicity and antimicrobial activity still remain an open issue. Herein, we focus on the current demands of 2D TMDs and produce high-quality, few-layered and defect-free MoS2 nanosheets, exfoliated and dispersed in pure water, stabilized up to three weeks. Hence, we studied the impact of this material on human cells by investigating its interactions with three cell lines: two tumoral, MCF7 (breast cancer) and U937 (leukemia), and one normal, HaCaT (epithelium). We observed novel and intriguing results, exhibiting evident cytotoxic effect induced in the tumor cell lines, absent in the normal cells in the tested conditions. The antibacterial action of MoS2 nanosheets is then investigated against a very dangerous gram negative bacterium, such as two types of Salmonellas: ATCC 14028 and wild-type Salmonella typhimurium. Additionally, concentration and layer-dependent modulation of cytotoxic effect is found both on human cells and Salmonellas.
Improving genetic transformation rates in honeybees
Authors: Otte M. , Netschitailo O. , Kaftanoglu O. , Wang Y. , Page R. E. , Beye M. 
Published: November 2018

AbstractFunctional genetic studies in honeybees have been limited by transformation tools that lead to a high rate of transposon integration into the germline of the queens. A high transformation rate is required to reduce screening efforts because each treated queen needs to be maintained in a separate honeybee colony. Here, we report on further improvement of the transformation rate in honeybees by using a combination of different procedures. We employed a hyperactive transposase protein (hyPBaseapis), we tripled the amount of injected transposase mRNAs and we injected embryos into the first third (anterior part) of the embryo. These three improvements together doubled the transformation rate from 19% to 44%. We propose that the hyperactive transposase (hyPBaseapis) and the other steps used may also help to improve the transformation rates in other species in which screening and crossing procedures are laborious.
Laminar profile of task-related plasticity in ferret primary auditory cortex
Authors: Francis Nikolas A. , Elgueda Diego , Englitz Bernhard , Fritz Jonathan B. , Shamma Shihab A. 
Published: October 2018

AbstractRapid task-related plasticity is a neural correlate of selective attention in primary auditory cortex (A1). Top-down feedback from higher-order cortex may drive task-related plasticity in A1, characterized by enhanced neural representation of behaviorally meaningful sounds during auditory task performance. Since intracortical connectivity is greater within A1 layers 2/3 (L2/3) than in layers 4–6 (L4–6), we hypothesized that enhanced representation of behaviorally meaningful sounds might be greater in A1 L2/3 than L4–6. To test this hypothesis and study the laminar profile of task-related plasticity, we trained 2 ferrets to detect pure tones while we recorded laminar activity across a 1.8 mm depth in A1. In each experiment we analyzed high-gamma local field potentials (LFPs) and multi-unit spiking in response to identical acoustic stimuli during both passive listening and active task performance. We found that neural responses to auditory targets were enhanced during task performance, and target enhancement was greater in L2/3 than in L4–6. Spectrotemporal receptive fields (STRFs) computed from both high-gamma LFPs and multi-unit spiking showed similar increases in auditory target selectivity, also greatest in L2/3. Our results suggest that activity within intracortical networks plays a key role in the underlying neural mechanisms of selective attention.
Temporal changes of Sall4 lineage contribution in developing embryos and the contribution of Sall4-lineages to postnatal germ cells in mice
Authors: Tahara Naoyuki , Kawakami Hiroko , Zhang Teng , Zarkower David , Kawakami Yasuhiko 
Published: October 2018

AbstractMutations in the SALL4 gene cause human syndromes with defects in multiple organs. Sall4 expression declines rapidly in post-gastrulation mouse embryos, and our understanding of the requirement of Sall4 in animal development is still limited. To assess the contributions of Sall4 expressing cells to developing mouse embryos, we monitored temporal changes of the contribution of Sall4 lineages using a Sall4 GFP-CreERT2 knock-in mouse line and recombination-dependent reporter lines. By administering tamoxifen at various time points we observed that the contributions of Sall4 lineages to the axial level were rapidly restricted from the entire body to the posterior part of the body. The contribution to forelimbs, hindlimbs, craniofacial structures and external genitalia also declined after gastrulation with different temporal dynamics. We also detected Sall4 lineage contributions to the extra-embryonic tissues, such as the yolk sac and umbilical cord, in a temporal manner. These Sall4 lineage contributions provide insights into potential roles of Sall4 during mammalian embryonic development. In postnatal males, long-term lineage tracing detected Sall4 lineage contributions to the spermatogonial stem cell pool during spermatogenesis. The Sall4 GFP-CreERT2 line can serve as a tool to monitor spatial-temporal contributions of Sall4 lineages as well as to perform gene manipulations in Sall4-expressing lineages.
Conversion of an amide to a high-energy thioester by Staphylococcus aureus sortase A is powered by variable binding affinity for calcium
Authors: Wang Xiao , Chen Jia-Liang , Otting Gottfried , Su Xun-Cheng 
Published: October 2018

AbstractThioesters are key intermediates in biology, which often are generated from less energy-rich amide precursors. Staphylococcus aureus sortase A (SrtA) is an enzyme widely used in biotechnology for peptide ligation. The reaction proceeds in two steps, where the first step involves the conversion of an amide bond of substrate peptide into a thioester intermediate with the enzyme. Here we show that the free energy required for this step is matched by an about 30-fold increase in binding affinity of a calcium ion at the calcium binding site of SrtA, which is remote from the thioester bond. The magnitude of this allosteric effect highlights the importance of calcium for the activity of SrtA. The increase in calcium binding affinity upon binding of substrate not only achieves catalytic formation of an energy-rich intermediate in the absence of nucleotide triphosphates or any tight non-covalent enzyme-substrate interactions, but is also accompanied by accumulation of the labile thioester intermediate, which makes it directly observable in nuclear magnetic resonance (NMR) spectra.
Machine learning predicts individual cancer patient responses to therapeutic drugs with high accuracy
Authors: Huang Cai , Clayton Evan A. , Matyunina Lilya V. , McDonald L. DeEtte , Benigno Benedict B. , Vannberg Fredrik , McDonald John F. 
Published: October 2018

AbstractPrecision or personalized cancer medicine is a clinical approach that strives to customize therapies based upon the genomic profiles of individual patient tumors. Machine learning (ML) is a computational method particularly suited to the establishment of predictive models of drug response based on genomic profiles of targeted cells. We report here on the application of our previously established open-source support vector machine (SVM)-based algorithm to predict the responses of 175 individual cancer patients to a variety of standard-of-care chemotherapeutic drugs from the gene-expression profiles (RNA-seq or microarray) of individual patient tumors. The models were found to predict patient responses with >80% accuracy. The high PPV of our algorithms across multiple drugs suggests a potential clinical utility of our approach, particularly with respect to the identification of promising second-line treatments for patients failing standard-of-care first-line therapies.
The dissolution of temporal distance increases risk-taking: experimental evidence
Authors: Muda Rafał , Niszczota Paweł , Augustynowicz Paweł , Markiewicz Łukasz 
Published: November 2018

AbstractEarlier research shows that delaying the realization of a lottery (temporal distance) increases risk tolerance. Presumably, this happens because temporal distance protects one from encountering the negative emotions produced when facing risk. However, no study has tested whether people that made a choice in the presence of temporal distance would actually change their decision later on (in the absence of temporal distance), towards the safer choice. To test this, 137 participants were subject to actual temporal distance, consisting of a four-week waiting period. To explore how each participant behaved “in the heat of the moment” (in the absence of temporal distance), we assessed their electrodermal activity and analysed self-description measures of susceptibility to affect. Participants had to choose between 40 lottery pairs (they could win up to the equivalent of about $400 US; the expected payout for each participant was about $12). Results showed that, contrary to expectations, participants tended to choose riskier lotteries after the waiting period. The results of an additional experiment suggest that this is not the result of prior exposure to the same set of lotteries, however, interestingly, an exploratory analysis showed that the main effect was driven by the behaviour of male participants. We discuss possible explanations for our surprising main finding and its implications for studies on temporal distance.
Quasi-phase-matched third harmonic generation in organic multilayers
Authors: Kim Jiung , Kumar CH. S. S. Pavan , Cha Myoungsik , Choi Heejoo , Kim Kyung-Jo , Peyghambarian N. 
Published: October 2018

AbstractWe report the first realization of quasi-phase-matched (QPM) third harmonic generation in isotropic polymer films. Spin-coated thin films of ethyl-violet molecules dispersed in a polymer host (EV) were used as cubic nonlinear optical media because of their transparency at both the fundamental (1230 nm) and the third harmonic (410 nm) wavelengths. A passive layer of a UV-curable material was formed to compensate the phase shift between the two light waves after propagating through each EV layer. We fabricated a series of samples with 1~4 EV layers (0~3 alternatingly coated passive layers). The third harmonic output power showed a quadratic increase with the number of layers, providing a strong evidence for successful quasi-phase-matching. A conversion efficiency of 0.15% was observed with a 190 fs pulse input.