bluuebunny/crossref_metadata_2025_split huggingface dataset:
CAESNet: Convolutional AutoEncoder based Semi-supervised Network for improving multiclass classification of endomicroscopic images
Authors: Tong Li , Wu Hang , Wang May D 
Published: June 2019

Abstract

Objective
This article presents a novel method of semisupervised learning using convolutional autoencoders for optical endomicroscopic images. Optical endomicroscopy (OE) is a newly emerged biomedical imaging modality that can support real-time clinical decisions for the grade of dysplasia. To enable real-time decision making, computer-aided diagnosis (CAD) is essential for its high speed and objectivity. However, traditional supervised CAD requires a large amount of training data. Compared with the limited number of labeled images, we can collect a larger number of unlabeled images. To utilize these unlabeled images, we have developed a Convolutional AutoEncoder based Semi-supervised Network (CAESNet) for improving the classification performance.

Materials and Methods
We applied our method to an OE dataset collected from patients undergoing endoscope-based confocal laser endomicroscopy procedures for Barrett’s esophagus at Emory Hospital, which consists of 429 labeled images and 2826 unlabeled images. Our CAESNet consists of an encoder with 5 convolutional layers, a decoder with 5 transposed convolutional layers, and a classification network with 2 fully connected layers and a softmax layer. In the unsupervised stage, we first update the encoder and decoder with both labeled and unlabeled images to learn an efficient feature representation. In the supervised stage, we further update the encoder and the classification network with only labeled images for multiclass classification of the OE images.

Results
Our proposed semisupervised method CAESNet achieves the best average performance for multiclass classification of OE images, which surpasses the performance of supervised methods including standard convolutional networks and convolutional autoencoder network.

Conclusions
Our semisupervised CAESNet can efficiently utilize the unlabeled OE images, which improves the diagnosis and decision making for patients with Barrett’s esophagus.
PARP inhibitors for BRCA wild type ovarian cancer; gene alterations, homologous recombination deficiency and combination therapy
Authors: Matsumoto Koji , Nishimura Meiko , Onoe Takuma , Sakai Hideki , Urakawa Yusaku , Onda Takashi , Yaegashi Nobuo 
Published: June 2019

Abstract
After a brief summary of the current status of poly-ADP ribose polymerase (PARP) inhibitors for ovarian cancer, we summarize the current status of PARP inhibitors for BRCA wild type ovarian cancer, especially regarding gene alterations other than BRCA, homologous recombination deficiency (HRD), and combinations. Discussion of gene alterations other than BRCA include the results of multiple gene panels studying homologous recombination repair deficiency genes and cancer susceptibility genes, and influences of these alterations on efficacy of PARP inhibitors and cancer susceptibility. Discussions of HRD include the results of phase three trials using HRD assay, the definition of HRD assays, and the latest assays. Discussions of combinations include early phase trial results and ongoing trials combining PARP inhibitors with immune checkpoint inhibitors, anti-angiogenic agents, and triplets.
Spectroscopic and photometric studies of four W UMa-type eclipsing binaries
Authors: Long Liu , Zhang Li-Yun , Han Xianming L , Lu Hong-Peng , Pi Qing-feng , Yue Qiang 
Published: June 2019

Abstract
We performed new photometric and spectroscopic studies on four W UMa-type eclipsing binaries (V400 Lyr, V574 Lyr, V1033 Her and V1062 Her). The main aims were to determine the orbital parameters and period variations of these four systems. We classified V574 Lyr, V1033 Her and V1062 Her spectral types based on LAMOST spectra, and used a spectra subtraction technique to measure the properties of the H α, H β and Ca ii H&K lines. We updated the ephemerides of these four systems, and conducted analyses of period variation for three systems (V574 Lyr, V1033 Her and V1062 Her). The period of V400 Lyr shows a continuous decrease, while that of V1033 Her continuously increases. Meanwhile, V574 Lyr and V1062 Her show a cyclic variation, caused by the light-time effect via the third body or magnetic activity cycle. The orbital and star-spot parameters of these four systems were obtained using the Wilson–Devinney program. This is the first time that precise orbital parameters have been obtained for V574 Lyr and V1062. We also concluded that these four objects are shallow contact eclipsing binaries with a cool spot on the primary. We found star-spot variabilities of about one month for V574 Lyr, and on long (years) time-scales for V1033 Her and V1062 Her. There are also obvious variations in the differences of light-curve maxima between 0.25 and 0.75 phases.
Tidal disruption event discs around supermassive black holes: disc warp and inclination evolution
Authors: Zanazzi J J , Lai Dong 
Published: June 2019

ABSTRACT
After the tidal disruption event (TDE) of a star around a supermassive black hole (SMBH), the bound stellar debris rapidly forms an accretion disc. If the accretion disc is not aligned with the spinning SMBH’s equatorial plane, the disc will be driven into Lense–Thirring precession around the SMBH’s spin axis, possibly affecting the TDE’s light curve. We carry out an eigenmode analysis of such a disc to understand how the disc’s warp structure, precession, and inclination evolution are influenced by the disc’s and SMBH’s properties. We find an oscillatory warp may develop as a result of strong non-Keplarian motion near the SMBH. The global disc precession frequency matches the Lense–Thirring precession frequency of a rigid disc around a spinning black hole within a factor of a few when the disc’s accretion rate is high, but deviates significantly at low accretion rates. Viscosity aligns the disc with the SMBH’s equatorial plane over time-scales of days to years, depending on the disc’s accretion rate, viscosity, and SMBH’s mass. We also examine the effect of fallback material on the warp evolution of TDE discs, and find that the fallback torque aligns the TDE disc with the SMBH’s equatorial plane in a few to tens of days for the parameter space investigated. Our results place constraints on models of TDE emission which rely on the changing disc orientation with respect to the line of sight to explain observations.
The lifetime of binary black holes in Sérsic galaxy models
Authors: Biava Nadia , Colpi Monica , Capelo Pedro R , Bonetti Matteo , Volonteri Marta , Tamfal Tomas , Mayer Lucio , Sesana Alberto 
Published: June 2019

Abstract
In the local Universe, black holes of $10^{5-6}\, {\rm M_\odot }$ are hosted in galaxies displaying a variety of stellar profiles and morphologies. These black holes are the anticipated targets of LISA, the Laser Interferometer Space Antenna that will detect the low-frequency gravitational-wave signal emitted by binary black holes in this mass interval. In this paper, we infer upper limits on the lifetime of binary black holes of $10^{5-6}\, {\rm M_\odot }$ and up to $10^8\, {\rm M_\odot }$, forming in galaxy mergers, exploring two underlying stellar density profiles, by Dehnen and by Prugniel & Simien, and by exploiting local scaling relations between the mass of the black holes and several quantities of their hosts. We focus on the phase of the dynamical evolution when the binary is transitioning from the hardening phase ruled by the interaction with single stars to the phase driven by the emission of gravitational waves. We find that different stellar profiles predict very distinct trends with binary mass, with lifetimes ranging between fractions of a Gyr to more than 10 Gyr, and with a spread of about one order of magnitude, given by the uncertainties in the observed correlations, which are larger in the low-mass tail of the observed black hole population.
Testing the scale-dependent hemispherical asymmetry with the 21-cm power spectrum from the epoch of reionization
Authors: Li Botao , Chen Zhaoting , Cai Yi-Fu , Mao Yi 
Published: June 2019

Abstract
Hemispherical power asymmetry has emerged as a new challenge to cosmology in early Universe. While the cosmic microwave background (CMB) measurements indicated the asymmetry amplitude A ≃ 0.07 at the CMB scale $k_{\rm CMB}\simeq 0.0045\, {\rm Mpc}^{-1}$, the high-redshift quasar observations found no significant deviation from statistical isotropy. This conflict can be reconciled in some scale-dependent asymmetry models. We put forwards a new parametrization of scale-dependent asymmetric power spectrum, inspired by a multispeed inflation model. The 21-cm power spectrum from the epoch of reionization can be used to constrain the scale-dependent hemispherical asymmetry. We demonstrate that an optimum, multifrequency observation by the Square Kilometre Array (SKA) Phase 2 can impose a constraint on the amplitude of the power asymmetry anomaly at the level of ΔA ≃ 0.2 at $0.056 \lesssim k_{\rm 21cm} \lesssim 0.15 \, {\rm Mpc}^{-1}$. This limit may be further improved by an order of magnitude as ΔA ≃ 0.01 with a cosmic variance limited experiment such as the Omniscope.
MORC2 regulates DNA damage response through a PARP1-dependent pathway
Authors: Zhang Lin , Li Da-Qiang 
Published: June 2019

AbstractMicrorchidia family CW-type zinc finger 2 (MORC2) is a newly identified chromatin remodeling enzyme with an emerging role in DNA damage response (DDR), but the underlying mechanism remains largely unknown. Here, we show that poly(ADP-ribose) polymerase 1 (PARP1), a key chromatin-associated enzyme responsible for the synthesis of poly(ADP-ribose) (PAR) polymers in mammalian cells, interacts with and PARylates MORC2 at two residues within its conserved CW-type zinc finger domain. Following DNA damage, PARP1 recruits MORC2 to DNA damage sites and catalyzes MORC2 PARylation, which stimulates its ATPase and chromatin remodeling activities. Mutation of PARylation residues in MORC2 results in reduced cell survival after DNA damage. MORC2, in turn, stabilizes PARP1 through enhancing acetyltransferase NAT10-mediated acetylation of PARP1 at lysine 949, which blocks its ubiquitination at the same residue and subsequent degradation by E3 ubiquitin ligase CHFR. Consequently, depletion of MORC2 or expression of an acetylation-defective PARP1 mutant impairs DNA damage-induced PAR production and PAR-dependent recruitment of DNA repair proteins to DNA lesions, leading to enhanced sensitivity to genotoxic stress. Collectively, these findings uncover a previously unrecognized mechanistic link between MORC2 and PARP1 in the regulation of cellular response to DNA damage.
A Novel Bacterial Nitrate Transporter Composed of Small Transmembrane Proteins
Authors: Maeda Shin-ichi , Aoba Risa , Nishino Yuma , Omata Tatsuo 
Published: June 2019

AbstractA putative silent gene of the freshwater cyanobacterium Synechococcus elongatus strain PCC 7942, encoding a small protein with two transmembrane helices, was named nrtS, since its overexpression from an inducible promoter conferred nitrate uptake activity on the nitrate transport-less NA4 mutant of S. elongatus. Homologs of nrtS, encoding proteins of 67–118 amino acid residues, are present in a limited number of eubacteria including mostly cyanobacteria and proteobacteria, but some others, e.g. the actinobacteria of the Mycobacterium tuberculosis complex, also have the gene. When expressed in NA4, the nrtS homolog of the γ-proteobacterium Marinomonas mediterranea took up nitrate with higher affinity for the substrate as compared with the S. elongatus NrtS (Km of 0.49 mM vs. 2.5 mM). Among the 61 bacterial species carrying the nrtS homolog, the marine cyanobacterium Synechococcus sp. strain PCC 7002 is unique in having two nrtS genes (nrtS1 and nrtS2) located in tandem on the chromosome. Coexpression of the two genes in NA4 resulted in nitrate uptake with a Km (NO3−) of 0.15 mM, while expression of either of the two resulted in low-affinity nitrate uptake activity with Km values of >3 mM, indicating that NrtS1 and NrtS2 form a heteromeric transporter complex. The heteromeric transporter was shown to transport nitrite as well. A Synechococcus sp. strain PCC 7002 mutant defective in the nitrate transporter (NrtP) showed a residual activity of nitrate uptake, which was ascribed to the NrtS proteins. Blue-native PAGE and immunoblotting analysis suggested a hexameric structure for the NrtS proteins.
Phototropins Mediate Chloroplast Movement in Phalaenopsis aphrodite (Moth Orchid)
Authors: Lin Yi-Jyun , Chen Yu-Chung , Tseng Kuan-Chieh , Chang Wen-Chi , Ko Swee-Suak 
Published: June 2019

AbstractChloroplast movement is important for plants to avoid photodamage and to perform efficient photosynthesis. Phototropins are blue light receptors in plants that function in chloroplast movement, phototropism, stomatal opening, and they also affect plant growth and development. In this study, full-length cDNAs of two PHOTOTROPIN genes, PaPHOT1 and PaPHOT2, were cloned from a moth orchid Phalaenopsis aphrodite, and their functions in chloroplast movement were investigated. Phylogenetic analysis showed that PaPHOT1 and PaPHOT2 orthologs were highly similar to PHOT1 and PHOT2 of the close relative Phalaenopsis equestris, respectively, and clustered with monocots PHOT1 and PHOT2 orthologs, respectively. Phalaenopsis aphrodite expressed a moderate level of PaPHOT1 under low blue light of 5 μmolï¿½m−2ï¿½s−1 (BL5) and a high levels of PaPHOT1 at >BL100. However, PaPHOT2 was expressed at low levels at <BL50 but expressed at high levels at > BL100. Analysis of light-induced chloroplast movements using the SPAD method indicated that orchid accumulated chloroplasts at <BL10. The chloroplast avoidance response was detectable at >BL25 and significant chloroplast avoidance movement was observed at >BL100. Virus-induced gene silencing of PaPHOTs in orchids showed decreased gene expression of PaPHOTs and reduced both chloroplast accumulation and avoidance responses. Heterologous expression of PaPHOT1 in Arabidopsis phot1phot2 double mutant recovered chloroplast accumulation response at BL5, but neither PaPHOT1 nor PaPHOT2 was able to restore mutant chloroplast avoidance at BL100. Overall, this study showed that phototropins mediate chloroplast movement in Phalaenopsis orchid is blue light-dependent but their function is slightly different from Arabidopsis which might be due to gene evolution.
Reducing the use of screen electronic devices in the evening is associated with improved sleep and daytime vigilance in adolescents
Authors: Perrault Aurore A , Bayer Laurence , Peuvrier Mathias , Afyouni Alia , Ghisletta Paolo , Brockmann Celine , Spiridon Mona , Hulo Vesely Sophie , Haller Dagmar M , Pichon Swann , Perrig Stephen , Schwartz Sophie , Sterpenich Virginie 
Published: June 2019

AbstractThe use of screen electronic devices in the evening negatively affects sleep. Yet, sleep is known to be essential for brain maturation and a key factor for good academic performance, and thus is particularly critical during childhood and adolescence. Although previous studies reported associations between screen time and sleep impairment, their causal relationship in adolescents remains unclear. Using actigraphy and daily questionnaires in a large sample of students (12 to 19 years old), we assessed screen time in the evening and sleep habits over 1 month. This included a 2 week baseline phase, followed by a 40 min sleep education workshop and a 2 week interventional phase, in which participants were asked to stop using screen devices after 9 pm during school nights. During the interventional phase, we found that the reduction of screen time after 9 pm correlated with earlier sleep onset time and increased total sleep duration. The latter led to improved daytime vigilance. These findings provide evidence that restricting screen use in the evening represents a valid and promising approach for improving sleep duration in adolescents, with potential implications for daytime functioning and health.
Retesting for verification of HIV diagnosis before antiretroviral therapy initiation in Harare, Zimbabwe: Is there a gap between policy and practice?
Authors: Dupwa Beatrice , Kumar Ajay M V , Tripathy Jaya Prasad , Mugurungi Owen , Takarinda Kudakwashe C , Dzangare Janet , Bara Hilda , Mukeredzi Innocent 
Published: June 2019

Abstract

Background
WHO recommends retesting of HIV-positive patients before starting antiretroviral therapy (ART). There is no evidence on implementation of retesting guidelines from programmatic settings. We aimed to assess implementation of HIV retesting among clients diagnosed HIV-positive in the public health facilities of Harare, Zimbabwe, in June 2017.

Methods
This cohort study involved analysis of secondary data collected routinely by the programme.

Results
Of 1729 study participants, 639 (37%) were retested. Misdiagnosis of HIV was found in six (1%) of the patients retested—all were infants retested with DNA-PCR. There was no HIV misdiagnosis among adults. Among those retested, 95% were retested on the same day and two-thirds were tested by a different provider as per national guidelines. Among those retested and found positive, 95% were started on ART, while none of those with negative retest results were started on ART. Of those not retested, about half (51%) were started on ART. The median (IQR) time to ART initiation from diagnosis was 0 (0–1) d.

Conclusion
The implementation of HIV-retesting policy in Harare was poor. While most HIV retest positives were started on ART, only half non-retested received ART. Future research is needed to understand the reasons for non-retesting and non-initiation of ART among those not retested.
Dynamics of Race Structures of the Rice Blast Pathogen Population in Heilongjiang Province, China From 2006 Through 2015
Authors: Zhang Yaling , Wang Jinyan , Yao Yongxiang , Jin Xuehui , Correll James , Wang Ling , Pan Qinghua 
Published: June 2019

Rice blast caused by the fungus Magnaporthe oryzae is one of the most destructive diseases of rice. Its control through the deployment of host resistance genes would be facilitated by understanding the pathogen’s race structure. Here, dynamics of race structures in this decade in Heilongjiang province were characterized by Chinese differential cultivars. Two patterns of dynamics of the race structures emerged: both race diversity and population-specific races increased gradually between 2006 and 2011, but they increased much more sharply between 2011 and 2015, with concomitant falls in both the population-common races and dominant races. Four races (ZD1, ZD3, ZD5, and ZE1) were among the top three dominant races over the whole period, indicating that the core of the race structure remained stable through this decade. On the host side, the composition of resistance in the cultivar differential set could be divided in two: the three indica-type entries of the differential set expressed a higher level of resistance to the population of M. oryzae isolates tested than did the four japonica-type entries. The cultivars Tetep and Zhenlong 13 as well as two additional resistance genes α and ε were confirmed as the most promising donors of blast resistance for the local rice improvement programs. [Formula: see text]Copyright © 2019 The Author(s). This is an open-access article distributed under the CC BY-NC-ND 4.0 International license .
Exposure to Heat Wave During Pregnancy and Adverse Birth Outcomes
Authors: Wang Jiajia , Tong Shilu , Williams Gail , Pan Xiaochuan 
Published: June 2019

Background:
Several studies have investigated the acute effects of high ambient temperature or extreme weather on preterm birth and stillbirth. However, little was known about whether there are any particular stages during which high ambient temperature or heat wave exposure is most harmful to fetal growth. The aim of this study was to examine the effects of heat wave exposure in different gestational months on the risk of preterm birth and stillbirth.

Methods:
Based on all singleton birth records between 2000 and 2010 and the corresponding environmental data in Brisbane, Australia, we explored relationships between heat wave exposure in different months of pregnancy and preterm birth or stillbirth. Six heat wave definitions were used in this study. After controlling for confounding factors, hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated using extended Cox proportional hazards regression models with time-dependent covariates.

Results:
For most heat wave definitions, the adjusted HRs of preterm birth varied by different gestational months and ranged from 1.08 (HR = 1.08; 95% CI = 1.00, 1.18) to 1.53 (HR = 1.53; 95% CI = 1.41, 1.68). Heat wave exposure in early pregnancy was more likely to increase the risk of stillbirth compared with heat wave exposure in late pregnancy.

Conclusions:
Overall, we found relationships between preterm birth and heat wave exposure in all months of pregnancy based on most heat wave definitions. We did not find a specifically high period of susceptibility during pregnancy for preterm birth associated with heat wave exposure. However, earlier gestational months might be key exposure windows for heat-wave–affected stillbirth.
Neurodevelopmental Trajectory During Infancy and Diagnosis of Autism Spectrum Disorder as an Outcome at 32 Months of Age
Authors: Nishimura Tomoko , Takei Nori , Tsuchiya Kenji J. 
Published: June 2019

Background:
Little is known about the extent to which neurodevelopmental trajectories in infancy predict a later diagnosis of autism spectrum disorder (ASD).

Methods:
We investigated the association between the neurodevelopmental trajectory classes identified using a latent class growth analysis and the distal clinical outcome. Participants included 952 infants from the Hamamatsu Birth Cohort for Mothers and Children (HBC study). Neurodevelopment was measured using the Mullen Scales of Early Learning, which contains five subscales (gross motor, fine motor, visual reception, receptive language, and expressive language), at seven time points from 1 to 24 months of age. ASD was diagnosed in 3.1% of the children at 32 months of age. The clinical outcome was included in our analysis model.

Results:
Five neurodevelopmental classes were identified: high normal (11.5%), normal (49.2%), low normal (21.2%), delayed (14.1%), and markedly delayed (4.0%). The probability of a diagnosis of ASD in the markedly delayed class was highest (32.6%) when compared with the other classes. The probabilities of receiving a diagnosis of ASD in the delayed and low normal classes were 6.4% and 4.0%, respectively, whereas the probabilities in the normal and high normal classes were both 0%.

Conclusions:
A diagnosis of ASD may be predicted by the neurodevelopmental trajectories during infancy, which can be evaluated both routinely and objectively in clinical settings. In this representative population, children diagnosed with ASD showed early signs in neurodevelopmental domains during the first 2 years of life.