bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double Interferometer Design for Independent Wavefront Manipulation in Spectral Domain Optical Coherence Tomography
Authors: Kanngiesser Jonas , Rahlves Maik , Roth Bernhard 
Published: October 2019

AbstractSpectral domain optical coherence tomography (SD-OCT) is a highly versatile method which allows for three dimensional optical imaging in scattering media. A number of recent publications demonstrated the technique to benefit from structured illumination and beam shaping approaches, e.g. to enhance the signal-to-noise ratio or the penetration depth with samples such as biological tissue. We present a compact and easy to implement design for independent wavefront manipulation and beam shaping at the reference and sample arm of the interferometric OCT device. The design requires a single spatial light modulator and can be integrated to existing free space SD-OCT systems by modifying the source arm only. We provide analytical and numerical discussion of the presented design as well as experimental data confirming the theoretical analysis. The system is highly versatile and lends itself for applications where independent phase or wavefront control is required. We demonstrate the system to be used for wavefront sensorless adaptive optics as well as for iterative optical wavefront shaping for OCT signal enhancement in strongly scattering media.
Electrophysiological responses of relatedness to consecutive word stimuli in relation to an actively recollected target word
Authors: Dijkstra Karen , Farquhar Jason , Desain Peter 
Published: October 2019

AbstractIn this paper, we investigate the robustness of electrophysiological responses of relatedness to multiple consecutive word stimuli (probes), in relation to an actively recollected target word. Such relatedness information could be used by a Brain Computer Interface to infer the active semantic concept on a user’s mind, by integrating the knowledge of the relationship between the multiple probe words and the ‘unknown’ target. Such a BCI can take advantage of the N400: an event related potential that is sensitive to semantic content of a stimulus in relation to an established semantic context. However, it is unknown whether the N400 is suited for the multiple probing paradigm we propose, as other intervening words might distract from the established context (i.e., the target word). We perform an experiment in which we present up to ten words after an initial target word, and find no attenuation of the strength of the N400 in grand average ERPs and no decrease in classification accuracy for probes occurring later in the sequences. These results are groundwork for developing a BCI that infers the concept on a user’s mind through repeated probing, however, low single trial decoding accuracy, and high subject variability may limit practical applicability.
Upper-tropospheric bridging of wintertime surface climate variability in the Euro-Atlantic region and northern Asia
Authors: Schlichtholz Pawel 
Published: October 2019

AbstractA remarkable feature of interannual climate variability is a robust link of wintertime anomalies of surface air temperature (SAT) in northern Asia to pan-Atlantic SAT variations associated with the North Atlantic Oscillation (NAO). Here statistical analyses of data from the era of satellite observations (1979–2017) are used to show that about 80% of the variance of the winter (December-March) mean area-averaged SAT anomalies in northern Asia can be explained by the anomalous surface circulation associated with an NAO-like mode of sea level pressure variability over extratropical Eurasia. These SAT anomalies are related equally strongly to the “Lake Baikal” vortex representing variations of the upper-tropospheric circulation over northern Asia. Support is given for the scenario that this vortex drives SAT anomalies in northern Asia via surface-reaching displacements of isentropic surfaces and that it is coupled to climate variability in the Euro-Atlantic sector via interactions between the North Atlantic storm track, quasi-stationary planetary waves, and zonal-mean zonal winds. The results underpin the importance of a lesser-known zonal wavenumber-3 structure of disturbances trapped over Eurasia by the polar front jet rather than the better-known zonal wavenumber-5 structure of disturbances trapped by the subtropical jet for NAO teleconnections.
All-optical majority gate based on an injection-locked laser
Authors: von Lerber Tuomo , Lassas Matti , Lyubopytov Vladimir S. , Ylinen Lauri , Chipouline Arkadi , Hofmann Klaus , Küppers Franko 
Published: October 2019

AbstractAn all-optical computer has remained an elusive concept. To construct a practical computing primitive equivalent to an electronic Boolean logic, one should utilize nonlinearity that overcomes weaknesses that plague many optical processing schemes. An advantageous nonlinearity provides a complete set of logic operations and allows cascaded operations without changes in wavelength or in signal encoding format. Here we demonstrate an all-optical majority gate based on a vertical-cavity surface-emitting laser (VCSEL). Using emulated signal coupling, the arrangement provides Bit Error Ratio (BER) of 10−6 at the rate of 1 GHz without changes in the wavelength or in the signal encoding format. Cascaded operation of the injection-locked laser majority gate is simulated on a full adder and a 3-bit ripple-carry adder circuits. Finally, utilizing the spin-flip model semiconductor laser rate equations, we prove that injection-locked lasers may perform normalization operations in the steady-state with an arbitrary linear state of polarization.
Stable reference genes for RT-qPCR analysis of gene expression in the Musa acuminata-Pseudocercospora musae interaction
Authors: Rego Erica Cristina Silva , Pinheiro Tatiana David Miranda , Antonino Jose Dijair , Alves Gabriel Sergio Costa , Cotta Michelle Guitton , Fonseca Fernando Campos De Assis , Miller Robert Neil Gerard 
Published: October 2019

AbstractLeaf pathogens are limiting factors in banana (Musaspp.) production, withPseudocercosporaspp. responsible for the important Sigatoka disease complex. In order to investigate cellular processes and genes involved in host defence responses, quantitative real-time PCR (RT-qPCR) is an analytical technique for gene expression quantification. Reliable RT-qPCR data, however, requires that reference genes for normalization of mRNA levels in samples are validated under the conditions employed for expression analysis of target genes. We evaluated the stability of potential reference genesACT1,α-TUB,UBQ1,UBQ2,GAPDH,EF1α,APTandRAN. Total RNA was extracted from leaf tissues ofMusa acuminatagenotypes Calcutta 4 (resistant) and Cavendish Grande Naine (susceptible), both subjected toP.musaeinfection. Expression stability was determined with NormFinder, BestKeeper, geNorm and RefFinder algorithms.UBQ2andRANwere the most stable across allM.acuminatasamples, whereas when considering inoculated and non-inoculated leaf samples,APTandUBQ2were appropriate for normalization in Calcutta 4, withRANandα-TUBmost stable in Cavendish Grande Naine. This first study of reference genes for relative quantification of target gene expression in theM.acuminata-P.musaeinteraction will enable reliable analysis of gene expression in this pathosystem, benefiting elucidation of disease resistance mechanisms.
Maternal energy insufficiency affects testicular development of the offspring in a swine model
Authors: Lin Yan , Xu Xue-Yu , Wu De , Lin Hao , Fang Zheng-Feng , Feng Bin , Xu Sheng-Yu , Che Lian-Qiang , Li Jian , Zhuo Yong , Wu Cai-Mei , Zhang Jun-Jie , Dong Hong-Jun 
Published: October 2019

AbstractWe determined the effects of insufficient maternal energy on testicular development in offspring in a swine model. Thirty-six sows were divided into control (CON) and low-energy diet (LE) groups during gestation. We observed that the number of Sertoli, germ, and Leydig cells in the offspring of the CON group were significantly higher than those in the LE group at 28 and 120 d after birth. Furthermore, the percentage of apoptotic testis cells was significantly higher in the offspring of the LE group than in the CON group. Transcriptome analysis of differentially expressed mRNAs and long noncoding RNAs in offspring testes indicated that these RNAs were mainly involved in lipid metabolism, apoptosis, cell proliferation, and some pivotal regulatory pathways. Results revealed that AMPK–PI3K–mTOR, MAPK, and oxidative phosphorylation signaling pathways play an important role in mediating the programming effect of insufficient maternal energy on testicular development, and that this effect occurs mainly at an early stage in life. mRNA and protein expression analyses confirmed the importance of certain signaling pathways in the regulation of testicular development. This study provides insights into the influence and possible mechanism underlying the effect of inadequate maternal energy intake on testicular development in the offspring.
Associations between Neonatal Serum Bilirubin and Childhood Obesity in Term Infants
Authors: Zou Lile , Yu Huan , He Yuan , Luo Lijuan , Dong Wenbin , Zhang Jun , Lei Xiaoping , Wieg Christian 
Published: October 2019

AbstractInverse correlations between serum bilirubin level and obesity had been reported in adults. We aimed to investigate the associations between neonatal hyperbilirubinemia and childhood obesity. Data was obtained from the U.S. Collaborative Perinatal Project (CPP), a multicenter study from 1959 to 1976. Data of serum bilirubin in term newborns were used to observe the association with obesity at age of 7 years. Logistic regression models were performed to calculate adjusted odds ratios (aORs) for obesity. For children from the same mother sharing similar factors, Generalized Estimating Equation (GEE) model was used to correct for intracluster correlation. Relative to newborns with total serum bilirubin (TSB) < 3 mg/dl, there are lower risks for obesity in those with 3 mg/dl ≤ TSB < 6 mg/dl (aOR 0.91; 95%CI 0.81, 1.02), 6 mg/dl ≤ TSB < 9 mg/dl (aOR 0.88; 95%CI 0.78, 0.99), 9 mg/dl ≤ TSB<13 mg/dl (aOR 0.83; 95%CI 0.71, 0.98). By stratifying for subtypes of bilirubin, the inverse correlations only existed in exposure to unconjugated bilirubin. By using the GEE model correcting for intracluster correlations, the results are consistent. In summary, exposure to bilirubin up to 13 mg/dl is inversely associated with obesity at the age of 7 years in term infants.
Phase Space Reconstruction Based CVD Classifier Using Localized Features
Authors: Vemishetty Naresh , Gunukula Ramya Lakshmi , Acharyya Amit , Puddu Paolo Emilio , Das Saptarshi , Maharatna Koushik 
Published: October 2019

AbstractThis paper proposes a generalized Phase Space Reconstruction (PSR) based Cardiovascular Diseases (CVD) classification methodology by exploiting the localized features of the ECG. The proposed methodology first extracts the ECG localized features including PR interval, QRS complex, and QT interval from the continuous ECG waveform using features extraction logic, then the PSR technique is applied to get the phase portraits of all the localized features. Based on the cleanliness and contour of the phase portraits CVD classification will be done. This is first of its kind approach where the localized features of ECG are being taken into considerations unlike the state-of-art approaches, where the entire ECG beats have been considered. The proposed methodology is generic and can be extended to most of the CVD cases. It is verified on the PTBDB and IAFDB databases by taking the CVD including Atrial Fibrillation, Myocardial Infarction, Bundle Branch Block, Cardiomyopathy, Dysrhythmia, and Hypertrophy. The methodology has been tested on 65 patients’ data for the classification of abnormalities in PR interval, QRS complex, and QT interval. Based on the obtained statistical results, to detect the abnormality in PR interval, QRS complex and QT interval the Coefficient Variation (CV) should be greater than or equal to 0.1012, 0.083, 0.082 respectively with individual accuracy levels of 95.3%, 96.9%, and 98.5% respectively. To justify the clinical significance of the proposed methodology, the Confidence Interval (CI), the p-value using ANOVA have been computed. The p-value obtained is less than 0.05, and greater F-statistic values reveal the robust classification of CVD using localized features.
Low-grade glioma harbors few CD8 T cells, which is accompanied by decreased expression of chemo-attractants, not immunogenic antigens
Authors: Weenink Bas , Draaisma Kaspar , Ooi Han Z. , Kros Johan M. , Sillevis Smitt Peter A. E. , Debets Reno , French Pim J. 
Published: October 2019

AbstractIn multiple tumor types, prediction of response to immune therapies relates to the presence, distribution and activation state of tumor infiltrating lymphocytes (TILs). Although such therapies are, to date, unsuccessful in gliomas, little is known on the immune contexture of TILs in these tumors. We assessed whether low and high-grade glioma (LGG and HGG, grade II and IV respectively) differ with respect to number, location and tumor reactivity of TILs; as well as expression of molecules involved in the trafficking and activation of T cells. Intra-tumoral CD8 T cells were quantified by flow cytometry (LGG: n = 12; HGG: n = 8) and immunofluorescence (LGG: n = 28; HGG: n = 28). Neoantigen load and expression of Cancer Germline Antigens (CGAs) were assessed using whole exome sequencing and RNA-seq. TIL-derived DNA was sequenced and the variable domain of the TCRβ chain was classified according to IMGT nomenclature. QPCR was used to determine expression of T cell-related genes. CD8 T cell numbers were significantly lower in LGG and, in contrast to HGG, mainly remained in close vicinity to blood vessels. This was accompanied by lower expression of chemo-attractants CXCL9, CXCL10 and adhesion molecule ICAM1. We did not observe a difference in the number of expressed neoantigens or CGAs, nor in diversity of TCR-Vβ gene usage. In summary, LGG have lower numbers of intra-tumoral CD8 T cells compared to HGG, potentially linked to decreased T cell trafficking. We have found no evidence for distinct tumor reactivity of T cells in either tumor type. The near absence of TILs in LGG suggest that, at present, checkpoint inhibitors are unlikely to have clinical efficacy in this tumor type.
DNA-PKcs and ATM epistatically suppress DNA end resection and hyperactivation of ATR-dependent G2-checkpoint in S-phase irradiated cells
Authors: Mladenov Emil , Fan Xiaoxiang , Paul-Konietzko Katja , Soni Aashish , Iliakis George 
Published: October 2019

AbstractWe previously reported that cells exposed to low doses of ionizing radiation (IR) in the G2-phase of the cell cycle activate a checkpoint that is epistatically regulated by ATM and ATR operating as an integrated module. In this module, ATR interphases exclusively with the cell cycle to implement the checkpoint, mainly using CHK1. The ATM/ATR module similarly regulates DNA end-resection at low IR-doses. Strikingly, at high IR-doses, the ATM/ATR coupling relaxes and each kinase exerts independent contributions to resection and the G2-checkpoint. DNA-PKcs links to the ATM/ATR module and defects cause hyper-resection and hyperactivation of G2-checkpoint at all doses examined. Surprisingly, our present report reveals that cells irradiated in S-phase utilize a different form of wiring between DNA-PKcs/ATM/ATR: The checkpoint activated in G2-phase is regulated exclusively by ATR/CHK1; similarly at high and low IR-doses. DNA end-resection supports ATR-activation, but inhibition of ATR leaves resection unchanged. DNA-PKcs and ATM link now epistatically to resection and their inhibition causes hyper-resection and ATR-dependent G2-checkpoint hyperactivation at all IR-doses. We propose that DNA-PKcs, ATM and ATR form a modular unit to regulate DSB processing with their crosstalk distinctly organized in S- and G2- phase, with strong dependence on DSB load only in G2-phase.
Immobilisation of living coral embryos and larvae
Authors: Randall Carly J. , Giuliano Christine , Mead David , Heyward Andrew J. , Negri Andrew P. 
Published: October 2019

AbstractEmbedding and immobilisation of living cells and microorganisms is used in a variety of research and commercial applications. Here we report the successful extended immobilisation of coral larvae in a low-gelling temperature agarose. Embryos and larvae of five broadcast-spawning Scleractinian species were immobilised in agarose gel and tested in a series of exploratory survival and settlement assays. The optimal developmental stage for immobilisation was after ciliation at approximately 24 hours post-fertilisation, after which, survival of immobilised larvae of all species was nearly 100%. In long-term assays, 50% of Montipora digitata larvae survived immobilised for 89 days. Furthermore, immobilised larvae of multiple species, that were released from the agarose, generally remained capable of settlement. These results demonstrate that the immobilisation of the early life-history stages of corals is possible for a variety of applications in basic and applied science.
Association of oral health status with the CD4+ cell count in children living with HIV in Phnom Penh, Cambodia
Authors: Kikuchi Kimiyo , Furukawa Yusuke , Tuot Sovannary , Pal Khuondyla , Huot Chantheany , Yi Siyan 
Published: October 2019

AbstractThe association between oral and overall health, and particularly between dental and immune health, in children living with HIV remains unclear. This study examined the association between the decayed, missing and filled teeth (DMFT) score and CD4+ cell counts in 142 children living with HIV aged 8–15 years (male, 51%) from Phnom Penh, Cambodia. Other indicators of oral health (e.g., debris index, salivary flow, salivary pH and oral health-related quality of life) and overall health (e.g., nutritional status and quality of life) were also evaluated. DMFT scores were negatively associated with the CD4+ cell count in male children (β: −0.13, 95% confidence interval [CI]: −0.25, −0.02). In all children, positive associations were observed between salivary pH and CD4+ count (β: −0.645, 95% CI: 0.02, 1.25) and between salivary flow and height-for-age Z-score (β: 1.22, 95% CI: 0.50, 1.95). The debris index was negatively associated with the height-for-age Z-score (β: −2.04, 95% CI: −3.38, −0.71). In summary, oral health was associated with immune and nutritional status. Oral health policies for children living with HIV should be emphasised, and further studies should evaluate the mechanism underlying the relationship between oral and overall health.
A one-step tRNA-CRISPR system for genome-wide genetic
interaction mapping in mammalian cells
Authors: Zhao Yulei , Tyrishkin Kathrin , Sjaarda Calvin , Khanal Prem , Stafford Jeff , Rauh Michael , Liu Xudong , Babak Tomas , Yang Xiaolong 
Published: October 2019

AbstractMapping genetic interactions in mammalian cells is limited due to
technical obstacles. Here we describe a method called TCGI (tRNA-CRISPR for genetic
interactions) to generate a high-efficient, barcode-free and scalable pairwise
CRISPR libraries in mammalian cells for identifying genetic interactions. We have
generated a genome- wide library to identify genes genetically interacting with TAZ
in cell viability regulation. Validation of candidate synergistic genes reveals the
screening accuracy of 85% and TAZ-MCL1 is characterized as combinational drug
targets for non-small cell lung cancer treatments. TCGI has dramatically improved
the current methods for mapping genetic interactions and screening drug targets for
combinational therapies.
Noninvasive intravital high-resolution imaging of pancreatic neuroendocrine tumours
Authors: Balan Mirela , Trusohamn Marta , Ning Frank Chenfei , Jacob Stefan , Pietras Kristian , Eriksson Ulf , Berggren Per-Olof , Nyqvist Daniel 
Published: October 2019

AbstractPreclinical trials of cancer drugs in animal models are important for drug development. The Rip1Tag2 (RT2) transgenic mouse, a model of pancreatic neuroendocrine tumours (PNET), has provided immense knowledge about PNET biology, although tumour progression occurs in a location inaccessible for real-time monitoring. To overcome this hurdle we have developed a novel platform for intravital 3D imaging of RT2 tumours to facilitate real-time studies of cancer progression. Pre-oncogenic islets retrieved from RT2 mice were implanted into the anterior chamber of the eye (ACE) of host mice, where they engrafted on the iris, recruited blood vessels and showed continuous growth. Noninvasive confocal and two-photon laser-scanning microscopy through the transparent cornea facilitated high-resolution imaging of tumour growth and angiogenesis. RT2 tumours in the ACE expanded up to 8-fold in size and shared hallmarks with tumours developing in situ in the pancreas. Genetically encoded fluorescent reporters enabled high-resolution imaging of stromal cells and tumour cell migration. Sunitinib treatment impaired RT2 tumour angiogenesis and growth, while overexpression of the vascular endothelial growth factor (VEGF)-B increased tumour angiogenesis though tumour growth was impaired. In conclusion, we present a novel platform for intravital high-resolution and 3D imaging of PNET biology and cancer drug assessment.
Microbial metabolite deoxycholic acid controls Clostridium perfringens-induced chicken necrotic enteritis through attenuating inflammatory cyclooxygenase signaling
Authors: Wang Hong , Latorre Juan D. , Bansal Mohit , Abraha Mussie , Al-Rubaye Bilal , Tellez-Isaias Guillermo , Hargis Billy , Sun Xiaolun 
Published: October 2019

AbstractNecrotic enteritis (NE) caused by Clostridium perfringens infection has reemerged as a prevalent poultry disease worldwide due to reduced usage of prophylactic antibiotics under consumer preferences and regulatory pressures. The lack of alternative antimicrobial strategies to control this disease is mainly due to limited insight into the relationship between NE pathogenesis, microbiome, and host responses. Here we showed that the microbial metabolic byproduct of secondary bile acid deoxycholic acid (DCA), at as low as 50 µM, inhibited 82.8% of C. perfringens growth in Tryptic Soy Broth (P < 0.05). Sequential Eimeria maxima and C. perfringens challenges significantly induced NE, severe intestinal inflammation, and body weight (BW) loss in broiler chickens. These negative effects were diminished (P < 0.05) by 1.5 g/kg DCA diet. At the cellular level, DCA alleviated NE-associated ileal epithelial death and significantly reduced lamina propria cell apoptosis. Interestingly, DCA reduced C. perfringens invasion into ileum (P < 0.05) without altering the bacterial ileal luminal colonization. Molecular analysis showed that DCA significantly reduced inflammatory mediators of Infγ, Litaf, Il1β, and Mmp9 mRNA accumulation in ileal tissue. Mechanism studies revealed that C. perfringens induced (P < 0.05) elevated expression of inflammatory mediators of Infγ, Litaf, and Ptgs2 (Cyclooxygenases-2 (COX-2) gene) in chicken splenocytes. Inhibiting the COX signaling by aspirin significantly attenuated INFγ-induced inflammatory response in the splenocytes. Consistent with the in vitro assay, chickens fed 0.12 g/kg aspirin diet protected the birds against NE-induced BW loss, ileal inflammation, and intestinal cell apoptosis. In conclusion, microbial metabolic product DCA prevents NE-induced BW loss and ileal inflammation through attenuating inflammatory response. These novel findings of microbiome protecting birds against NE provide new options on developing next generation antimicrobial alternatives against NE.