Alternating minimization algorithms for graph regularized tensor completion

We consider a low-rank tensor completion (LRTC) problem which aims to recover a tensor from incomplete observations. LRTC plays an important role in many applications such as signal processing, computer vision, machine learning, and neuroscience. A widely used approach is to combine the tensor completion data fitting term with a regularizer based on a convex relaxation of the multilinear ranks of the tensor. For the data fitting function, we model the tensor variable by using the Canonical Polyadic (CP) decomposition and for the low-rank promoting regularization function, we consider a graph Laplacian-based function which exploits correlations between the rows of the matrix unfoldings. For solving our LRTC model, we propose an efficient alternating minimization algorithm. Furthermore, based on the Kurdyka-{\L}ojasiewicz property, we show that the sequence generated by the proposed algorithm globally converges to a critical point of the objective function. Besides, an alternating direction method of multipliers algorithm is also developed for the LRTC model. Extensive numerical experiments on synthetic and real data indicate that the proposed algorithms are effective and efficient

Understanding binary phase separation towards Cu-C nanocrystalline-amorphous composites

The nanocrystalline-amorphous textures are commonly observed in the coatings synthesized by energetic deposition. We report a binary phase separation towards Cu-C nanocrystalline-amorphous composites by the FCVA deposition. The experimental results highlight that the average size of Cu nanocrystallines mainly depends on the C2H2 content. By performing a MD simulation using the LAMMPS, we theoretically explained how the initial reagent concentration fundamentally determines Cu nanocrystalline's final morphology and size during phase separation. This finding may give insight into the formation of nanocrystalline-amorphous structures by energetic deposition.Comment: 12 pages,5 figure

Up-regulation of hypoxia inducible factor-1α by cobalt chloride correlates with proliferation and apoptosis in PC-2 cells

<p>Abstract</p> <p>Background</p> <p>The exact mechanism of the effects of hypoxia on the proliferation and apoptosis in carcinoma cells is still conflicting. This study investigated the variation of hypoxia-inducible factor-1α(HIF-1α) expression and the apoptosis effect of hypoxia stimulated by cobalt chloride (CoCl₂) in pancreatic cancer PC-2 cells.</p> <p>Methods</p> <p>PC-2 cells were cultured with different concentration (50-200 μmol/L) of CoCl₂after 24-120 hours to simulate hypoxia in vitro. The proliferation of PC-2 cells was examined by MTT assay. The cellular morphology of PC-2 cells were observed by light inverted microscope and transmission electron microscope(EM). The expression of HIF-1α on mRNA and protein level was measured by semi-quantitive RT-PCR and Western blot analysis. Apoptosis of PC-2 cells were demonstrated by flow cytometry with Annexin V-FITC/PI double staining.</p> <p>Results</p> <p>MTT assay showed that the proliferation of PC-2 cells were stimulated in the first 72 h, while after treated over 72 h, a dose- dependent inhibition of cell growth could be observed. By using transmission electron microscope, swollen chondrosomes, accumulated chromatin under the nuclear membrane and apoptosis bodies were observed. Flow cytometer(FCM) analysis showed the apoptosis rate was correlated with the dosage of CoCl₂. RT-PCR and Western blot analysis indicated that hypoxia could up-regulate the expression of HIF-1α on both mRNA and protein levels.</p> <p>Conclusion</p> <p>Hypoxic microenvironment stimulated by CoCl₂could effectively induce apoptosis and influence cell proliferation in PC-2 cells, the mechanism could be related to up-expression of HIF-1α.</p

Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

<p>Abstract</p> <p>Background</p> <p>With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies.</p> <p>Results</p> <p>Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, <it>Phyllostachys heterocycla </it>cv. <it>pubescens</it>, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study.</p> <p>Conclusion</p> <p>Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.</p

Monocyte-Derived Macrophages Orchestrate Multiple Cell-Type Interactions To Repair Necrotic Liver Lesions in Disease Models

The liver can fully regenerate after partial resection, and its underlying mechanisms have been extensively studied. The liver can also rapidly regenerate after injury, with most studies focusing on hepatocyte proliferation; however, how hepatic necrotic lesions during acute or chronic liver diseases are eliminated and repaired remains obscure. Here, we demonstrate that monocyte-derived macrophages (MoMFs) were rapidly recruited to and encapsulated necrotic areas during immune-mediated liver injury and that this feature was essential in repairing necrotic lesions. At the early stage of injury, infiltrating MoMFs activated the Jagged1/notch homolog protein 2 (JAG1/NOTCH2) axis to induce cell death-resistant SRY-box transcription factor 9+ (SOX9+) hepatocytes near the necrotic lesions, which acted as a barrier from further injury. Subsequently, necrotic environment (hypoxia and dead cells) induced a cluster of complement 1q-positive (C1q+) MoMFs that promoted necrotic removal and liver repair, while Pdgfb+ MoMFs activated hepatic stellate cells (HSCs) to express α-smooth muscle actin and induce a strong contraction signal (YAP, pMLC) to squeeze and finally eliminate the necrotic lesions. In conclusion, MoMFs play a key role in repairing the necrotic lesions, not only by removing necrotic tissues, but also by inducing cell death-resistant hepatocytes to form a perinecrotic capsule and by activating α-smooth muscle actin-expressing HSCs to facilitate necrotic lesion resolution

Co-benefits for net carbon emissions and rice yields through improved management of organic nitrogen and water

Returning organic nutrient sources (for example, straw and manure) torice fields is inevitable for coupling crop–livestock production. However,an accurate estimate of net carbon (C) emissions and strategies tomitigate the abundant methane (CH4) emission from rice fields suppliedwith organic sources remain unclear. Here, using machine learning and aglobal dataset, we scaled the field findings up to worldwide rice fields toreconcile rice yields and net C emissions. An optimal organic nitrogen (N)management was developed considering total N input, type of organicN source and organic N proportion. A combination of optimal organic Nmanagement with intermittent flooding achieved a 21% reduction in netglobal warming potential and a 9% rise in global rice production comparedwith the business-as-usual scenario. Our study provides a solution forrecycling organic N sources towards a more productive, carbon-neutral andsustainable rice–livestock production system on a global scale