bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of task-specific optical systems using broadband diffractive neural networks
Authors: Luo Yi , Mengu Deniz , Yardimci Nezih T. , Rivenson Yair , Veli Muhammed , Jarrahi Mona , Ozcan Aydogan 
Published: December 2019

AbstractDeep learning has been transformative in many fields, motivating the emergence of various optical computing architectures. Diffractive optical network is a recently introduced optical computing framework that merges wave optics with deep-learning methods to design optical neural networks. Diffraction-based all-optical object recognition systems, designed through this framework and fabricated by 3D printing, have been reported to recognize hand-written digits and fashion products, demonstrating all-optical inference and generalization to sub-classes of data. These previous diffractive approaches employed monochromatic coherent light as the illumination source. Here, we report a broadband diffractive optical neural network design that simultaneously processes a continuum of wavelengths generated by a temporally incoherent broadband source to all-optically perform a specific task learned using deep learning. We experimentally validated the success of this broadband diffractive neural network architecture by designing, fabricating and testing seven different multi-layer, diffractive optical systems that transform the optical wavefront generated by a broadband THz pulse to realize (1) a series of tuneable, single-passband and dual-passband spectral filters and (2) spatially controlled wavelength de-multiplexing. Merging the native or engineered dispersion of various material systems with a deep-learning-based design strategy, broadband diffractive neural networks help us engineer the light–matter interaction in 3D, diverging from intuitive and analytical design methods to create task-specific optical components that can all-optically perform deterministic tasks or statistical inference for optical machine learning.
Meta-analytic method reveal a significant association of theBDNF Val66Met variant with smoking persistence
based on a large samples
Authors: Zhao Hailong , Xiong Shuicai , Li Zhiwei , Wu Xuebiao , Li Lijuan 
Published: December 2019

AbstractAlthough numerous genetic studies have reported the link between
Val66Met in BDNF gene with smoking, the findings
remain controversial, mainly due to small-to-moderate sample sizes. The main aim of
current investigation is to explore whether the variant of Val66Met has any genetic
functions in the progress of smoking persistence. The Val-based dominant genetic
model considering Val/* (namely, Val/Val + Val/Met) and Met/Met as two genotypes
with comparison of the frequency of each genotype in current smokers and never
smokers. There were seven genetic association articles including eight independent
datasets with 10,160 participants were chosen in current meta-analytic
investigation. In light of the potent effects of ethnicity on homogeneity across
studies, we carried out separated meta-analyses according to the ancestry origin by
using the wide-used tool of Comprehensive Meta-analysis software (V 2.0). Our
meta-analyses results indicated that the Val66Met polymorphism was significantly
linked with smoking persistence based on either all the chosen samples (N = 10,160; Random and fixed models: pooled OR = 1.23;
95% CI = 1.03–1.46; P value = 0.012) or Asian
samples (N = 2,095; Fixed model: pooled
OR = 1.25; 95% CI = 1.01–1.54; P value = 0.044;
Random model: pooled OR = 1.25; 95% CI = 1.001–1.56; P value = 0.049). No significant clue of bias in publications or
heterogeneity across studies was detected. Thus, we conclude that the Val66Met
(rs6265) variant conveys genetic susceptibility to maintaining smoking, and smokers
who carry Val/* genotypes have a higher possibility of maintaining smoking than
those having Met/Met genotype.
PRMT1 suppresses ATF4-mediated endoplasmic reticulum response in cardiomyocytes
Authors: Jeong Myong-Ho , Jeong Hyeon-Ju , Ahn Byeong-Yun , Pyun Jung-Hoon , Kwon Ilmin , Cho Hana , Kang Jong-Sun 
Published: December 2019

AbstractEndoplasmic reticulum (ER) stress signaling plays a critical role in the control of cell survival or death. Persistent ER stress activates proapoptotic pathway involving the ATF4/CHOP axis. Although accumulating evidences support its important contribution to cardiovascular diseases, but its mechanism is not well characterized. Here, we demonstrate a critical role for PRMT1 in the control of ER stress in cardiomyocytes. The inhibition of PRMT1 augments tunicamycin (TN)-triggered ER stress response in cardiomyocytes while PRMT1 overexpression attenuates it. Consistently, PRMT1 null hearts show exacerbated ER stress and cell death in response to TN treatment. Interestingly, ATF4 depletion attenuates the ER stress response induced by PRMT1 inhibition. The methylation-deficient mutant of ATF4 with the switch of arginine 239 to lysine exacerbates ER stress accompanied by enhanced levels of proapoptotic cleaved Caspase3 and phosphorylated-γH2AX in response to TN. The mechanistic study shows that PRMT1 modulates the protein stability of ATF4 through methylation. Taken together, our data suggest that ATF4 methylation on arginine 239 by PRMT1 is a novel regulatory mechanism for protection of cardiomyocytes from ER stress-induced cell death.
A point mutation resulting in a 13 bp deletion in the coding sequence of Cldf leads to a GA-deficient dwarf phenotype in watermelon
Authors: Wei Chunhua , Zhu Chunyu , Yang Liping , Zhao Wei , Ma Rongxue , Li Hao , Zhang Yong , Ma Jianxiang , Yang Jianqiang , Zhang Xian 
Published: December 2019

AbstractThe dwarf architecture is an important and valuable agronomic trait in watermelon breeding and has the potential to increase fruit yield and reduce labor cost in crop cultivation. However, the molecular basis for dwarfism in watermelon remains largely unknown. In this study, a recessive dwarf allele (designated asCldf(Citrullus lanatus dwarfism)) was fine mapped in a 32.88 kb region on chromosome 09 using F2segregation populations derived from reciprocal crossing of a normal line M08 and a dwarf line N21. Gene annotation of the corresponding region revealed that theCla015407gene encoding a gibberellin 3β-hydroxylase functions as the best possible candidate gene forCldf. Sequence analysis showed that the fourth polymorphism site (a G to A point mutation) at the 3′ AG splice receptor site of the intron leads to a 13 bp deletion in the coding sequence ofCldfin dwarf line N21 and thus results in a truncated protein lacking the conserved domain for binding 2-oxoglutarate. In addition, the dwarf phenotype ofCldfcould be rescued by exogenous GA3application. Phylogenetic analysis suggested that the small multigene familyGA3ox(GA3 oxidase) in cucurbit species may originate from three ancient lineages in Cucurbitaceae. All these data support the conclusion thatCldfis a GA-deficient mutant, which together with the cosegregated marker can be used for breeding new dwarf cultivars.
Functional identification of lncRNAs in sweet cherry (Prunus avium) pollen tubes via transcriptome analysis using single-molecule long-read sequencing
Authors: Li Yang , Wu Chuanbao , Liu Chunsheng , Yu Jie , Duan Xuwei , Fan Wenqi , Wang Jing , Zhang Xiaoming , Yan Guohua , Li Tianzhong , Zhang Kaichun 
Published: December 2019

AbstractSweet cherry (Prunus avium) is a popular fruit with high nutritional value and excellent flavor. Although pollen plays an important role in the double fertilization and subsequent fruit production of this species, little is known about its pollen tube transcriptome. In this study, we identified 16,409 transcripts using single-molecule sequencing. After filtering 292 transposable elements, we conducted further analyses including mRNA classification, gene function prediction, alternative splicing (AS) analysis, and long noncoding RNA (lncRNA) identification to gain insight into the pollen transcriptome. The filtered transcripts could be matched with 3,438 coding region sequences from the sweet cherry genome. GO and KEGG analyses revealed complex biological processes during pollen tube elongation. A total of 2043 AS events were predicted, 7 of which were identified in different organs, such as the leaf, pistil and pollen tube. Using BLASTnt and the Coding-Potential Assessment Tool (CPAT), we distinguished a total of 284 lncRNAs, among which 154 qualified as natural antisense transcripts (NATs). As the NATs could be the reverse complements of coding mRNA sequences, they might bind to coding sequences. Antisense transfection assays showed that the NATs could regulate the expression levels of their complementary sequences and even affect the growth conditions of pollen tubes. In summary, this research characterizes the transcripts of P. avium pollen and lays the foundation for elucidating the physiological and biochemical mechanisms underlying sexual reproduction in the male gametes of this species.
RhMYB108, an R2R3-MYB transcription factor, is involved in ethylene- and JA-induced petal senescence in rose plants
Authors: Zhang Shuai , Zhao Qingcui , Zeng Daxing , Xu Jiehua , Zhou Hougao , Wang Fenglan , Ma Nan , Li Yonghong 
Published: December 2019

AbstractRose (Rosa hybrida) plants are major ornamental species worldwide, and their commercial value greatly depends on their open flowers, as both the quality of fully open petals and long vase life are important. Petal senescence can be started and accelerated by various hormone signals, and ethylene is considered an accelerator of petal senescence in rose. To date, however, the underlying mechanism of signaling crosstalk between ethylene and other hormones such as JA in petal senescence remains largely unknown. Here, we isolated RhMYB108, an R2R3-MYB transcription factor, which is highly expressed in senescing petals as well as in petals treated with exogenous ethylene and JA. Applications of exogenous ethylene and JA markedly accelerated petal senescence, while the process was delayed in response to applications of 1-MCP, an ethylene action inhibitor. In addition, silencing of RhMYB108 alter the expression of SAGs such as RhNAC029, RhNAC053, RhNAC092, RhSAG12, and RhSAG113, and finally block ethylene- and JA-induced petal senescence. Furthermore, RhMYB108 was identified to target the promoters of RhNAC053, RhNAC092, and RhSAG113. Our results reveal a model in which RhMYB108 functions as a receptor of ethylene and JA signals to modulate the onset of petal senescence by targeting and enhancing senescence-associated gene expression.
Molecular and structural insights into an asymmetric proteolytic complex (ClpP1P2) from Mycobacterium smegmatis
Authors: Nagpal Jyotsna , Paxman Jason J. , Zammit Jessica E. , Thomas Adam A. , Truscott Kaye N. , Heras Begoña , Dougan David A. 
Published: December 2019

AbstractThe ClpP protease is found in all kingdoms of life, from bacteria to humans. In general, this protease forms a homo-oligomeric complex composed of 14 identical subunits, which associates with its cognate ATPase in a symmetrical manner. Here we show that, in contrast to this general architecture, the Clp protease from Mycobacterium smegmatis (Msm) forms an asymmetric hetero-oligomeric complex ClpP1P2, which only associates with its cognate ATPase through the ClpP2 ring. Our structural and functional characterisation of this complex demonstrates that asymmetric docking of the ATPase component is controlled by both the composition of the ClpP1 hydrophobic pocket (Hp) and the presence of a unique C-terminal extension in ClpP1 that guards this Hp. Our structural analysis of MsmClpP1 also revealed openings in the side-walls of the inactive tetradecamer, which may represent sites for product egress.
Dual Action of Sulfated Hyaluronan on Angiogenic Processes in Relation to Vascular Endothelial Growth Factor-A
Authors: Koehler Linda , Ruiz-Gómez Gloria , Balamurugan Kanagasabai , Rother Sandra , Freyse Joanna , Möller Stephanie , Schnabelrauch Matthias , Köhling Sebastian , Djordjevic Snezana , Scharnweber Dieter , Rademann Jörg , Pisabarro M. Teresa , Hintze Vera 
Published: December 2019

AbstractPathological healing characterized by abnormal angiogenesis presents a serious burden to patients’ quality of life requiring innovative treatment strategies. Glycosaminoglycans (GAG) are important regulators of angiogenic processes. This experimental and computational study revealed how sulfated GAG derivatives (sGAG) influence the interplay of vascular endothelial growth factor (VEGF)165 and its heparin-binding domain (HBD) with the signaling receptor VEGFR-2 up to atomic detail. There was profound evidence for a HBD-GAG-HBD stacking configuration. Here, the sGAG act as a “molecular glue” leading to recognition modes in which sGAG interact with two VEGF165-HBDs. A 3D angiogenesis model demonstrated the dual regulatory role of high-sulfated derivatives on the biological activity of endothelial cells. While GAG alone promote sprouting, they downregulate VEGF165-mediated signaling and, thereby, elicit VEGF165-independent and -dependent effects. These findings provide novel insights into the modulatory potential of sGAG derivatives on angiogenic processes and point towards their prospective application in treating abnormal angiogenesis.
Role of zinc substitution in magnetic hyperthermia properties of magnetite nanoparticles: interplay between intrinsic properties and dipolar interactions
Authors: Hadadian Yaser , Ramos Ana Paula , Pavan Theo Z. 
Published: December 2019

AbstractOptimizing the intrinsic properties of magnetic nanoparticles for magnetic hyperthermia is of considerable concern. In addition, the heating efficiency of the nanoparticles can be substantially influenced by dipolar interactions. Since adequate control of the intrinsic properties of magnetic nanoparticles is not straightforward, experimentally studying the complex interplay between these properties and dipolar interactions affecting the specific loss power can be challenging. Substituting zinc in magnetite structure is considered as an elegant approach to tune its properties. Here, we present experimental and numerical simulation results of magnetic hyperthermia studies using a series of zinc-substituted magnetite nanoparticles (ZnxFe1-xFe2O4, x = 0.0, 0.1, 0.2, 0.3 and 0.4). All experiments were conducted in linear regime and the results were inferred based on the numerical simulations conducted in the framework of the linear response theory. The results showed that depending on the nanoparticles intrinsic properties, interparticle interactions can have different effects on the specific loss power. When dipolar interactions were strong enough to affect the heating efficiency, the parameter σ = KeffV/kBT (Keff is the effective anisotropy and V the volume of the particles) determined the type of the effect. Finally, the sample x = 0.1 showed a superior performance with a relatively high intrinsic loss power 5.4 nHm2kg−1.
Stress-controlled decomposition routes in cubic AlCrN films assessed by in-situ high-temperature high-energy grazing incidence transmission X-ray diffraction
Authors: Meindlhumer M. , Klima S. , Jäger N. , Stark A. , Hruby H. , Mitterer C. , Keckes J. , Daniel R. 
Published: December 2019

AbstractThe dependence of decomposition routes on intrinsic microstructure and stress in nanocrystalline transition metal nitrides is not yet fully understood. In this contribution, three Al0.7Cr0.3N thin films with residual stress magnitudes of −3510, −4660 and −5930 MPa in the as-deposited state were in-situ characterized in the range of 25–1100 °C using in-situ synchrotron high-temperature high-energy grazing-incidence-transmission X-ray diffraction and temperature evolutions of phases, coefficients of thermal expansion, structural defects, texture as well as residual, thermal and intrinsic stresses were evaluated. The multi-parameter experimental data indicate a complex intrinsic stress and phase changes governed by a microstructure recovery and phase transformations taking place above the deposition temperature. Though the decomposition temperatures of metastable cubic Al0.7Cr0.3N phase in the range of 698–914 °C are inversely proportional to the magnitudes of deposition temperatures, the decomposition process itself starts at the same stress level of ~−4300 MPa in all three films. This phenomenon indicates that the particular compressive stress level functions as an energy threshold at which the diffusion driven formation of hexagonal Al(Cr)N phase is initiated, provided sufficient temperature is applied. In summary, the unique synchrotron experimental setup indicated that residual stresses play a decisive role in the decomposition routes of nanocrystalline transition metal nitrides.
Markov versus quantum dynamic models of belief change during evidence monitoring
Authors: Busemeyer Jerome R. , Kvam Peter D. , Pleskac Timothy J. 
Published: December 2019

AbstractTwo different dynamic models for belief change during evidence monitoring were evaluated: Markov and quantum. They were empirically tested with an experiment in which participants monitored evidence for an initial period of time, made a probability rating, then monitored more evidence, before making a second rating. The models were qualitatively tested by manipulating the time intervals in a manner that provided a test for interference effects of the first rating on the second. The Markov model predicted no interference, whereas the quantum model predicted interference. More importantly, a quantitative comparison of the two models was also carried out using a generalization criterion method: the parameters were fit to data from one set of time intervals, and then these same parameters were used to predict data from another set of time intervals. The results indicated that some features of both Markov and quantum models are needed to accurately account for the results.
Mid-Cretaceous amber inclusions reveal morphogenesis of extinct rachis-dominated feathers
Authors: Carroll Nathan R. , Chiappe Luis M. , Bottjer David J. 
Published: December 2019

AbstractWe describe three-dimensionally preserved feathers in mid-Cretaceous Burmese amber that share macro-morphological similarities (e.g., proportionally wide rachis with a “medial stripe”) with lithic, two-dimensionally preserved rachis-dominated feathers, first recognized in the Jehol Biota. These feathers in amber reveal a unique ventrally concave and dorsoventrally thin rachis, and a dorsal groove (sometimes pigmented) that we identify as the “medial stripe” visible in many rachis-dominated rectrices of Mesozoic birds. The distally pennaceous portion of these feathers shows differentiated proximal and distal barbules, the latter with hooklets forming interlocking barbs. Micro-CT scans and transverse sections demonstrate the absence of histodifferentiated cortex and medullary pith of the rachis and barb rami. The highly differentiated barbules combined with the lack of obvious histodifferentiation of the barb rami or rachis suggests that these feathers could have been formed without the full suite and developmental interplay of intermediate filament alpha keratins and corneous beta-proteins that is employed in the cornification process of modern feathers. This study thus highlights how the development of these feathers might have differed from that of their modern counterparts, namely in the morphogenesis of the ventral components of the rachis and barb rami. We suggest that the concave ventral surface of the rachis of these Cretaceous feathers is not homologous with the ventral groove of modern rachises. Our study of these Burmese feathers also confirms previous claims, based on two-dimensional fossils, that they correspond to an extinct morphotype and it cautions about the common practice of extrapolating developmental aspects (and mechanical attributes) of modern feathers to those of stem birds (and their dinosaurian outgroups) because the latter need not to have developed through identical pathways.
BioSphincters to treat Fecal Incontinence in Nonhuman Primates
Authors: Dadhich Prabhash , Bohl Jaime L. , Tamburrini Riccardo , Zakhem Elie , Scott Christie , Kock Nancy , Mitchell Erin , Gilliam John , Bitar Khalil N. 
Published: December 2019

AbstractLoss of anorectal resting pressure due to internal anal sphincter (IAS) dysfunctionality causes uncontrolled fecal soiling and leads to passive fecal incontinence (FI). The study is focused on immediate and long-term safety and potential efficacy of bioengineered IAS BioSphincters to treat passive FI in a clinically relevant large animal model of passive FI. Passive FI was successfully developed in Non-Human Primates (NHPs) model. The implantation of autologous intrinsically innervated functional constructs resolved the fecal soiling, restored the resting pressure and Recto Anal Inhibitory Reflex (RAIR) within 1-month. These results were sustained with time, and efficacy was preserved up to 12-months. The histological studies validated manometric results with the regeneration of a well-organized neuro-muscular population in IAS. The control groups (non-treated and sham) remained affected by poor anal hygiene, lower resting pressure, and reduced RAIR throughout the study. The pathological assessment of implants, blood, and the vital organs confirmed biocompatibility without any adverse effect after implantation. This regenerative approach of implanting intrinsically innervated IAS BioSphincters has the potential to offer a better quality of life to the patients suffering from FI.
Metabolic shift induced by synthetic co-cultivation promotes high yield of chain elongated acids from syngas
Authors: Diender Martijn , Parera Olm Ivette , Gelderloos Marten , Koehorst Jasper J. , Schaap Peter J. , Stams Alfons J. M. , Sousa Diana Z. 
Published: December 2019

AbstractBio-catalytic processes for sustainable production of chemicals and fuels receive increased attention within the concept of circular economy. Strategies to improve these production processes include genetic engineering of bio-catalysts or process technological optimization. Alternatively, synthetic microbial co-cultures can be used to enhance production of chemicals of interest. It remains often unclear however how microbe to microbe interactions affect the overall production process and how this can be further exploited for application. In the present study we explored the microbial interaction in a synthetic co-culture of Clostridium autoethanogenum and Clostridium kluyveri, producing chain elongated products from carbon monoxide. Monocultures of C. autoethanogenum converted CO to acetate and traces of ethanol, while during co-cultivation with C. kluyveri, it shifted its metabolism significantly towards solventogenesis. In C. autoethanogenum, expression of the genes involved in the central carbon- and energy-metabolism remained unchanged during co-cultivation compared to monoculture condition. Therefore the shift in the metabolic flux of C. autoethanogenum appears to be regulated by thermodynamics, and results from the continuous removal of ethanol by C. kluyveri. This trait could be further exploited, driving the metabolism of C. autoethanogenum to solely ethanol formation during co-cultivation, resulting in a high yield of chain elongated products from CO-derived electrons. This research highlights the important role of thermodynamic interactions in (synthetic) mixed microbial communities and shows that this can be exploited to promote desired conversions.