A statistical perspective on algorithm unrolling models for inverse problems

We consider inverse problems where the conditional distribution of the observation ${\bf y}$ given the latent variable of interest ${\bf x}$ (also known as the forward model) is known, and we have access to a data set in which multiple instances of ${\bf x}$ and ${\bf y}$ are both observed. In this context, algorithm unrolling has become a very popular approach for designing state-of-the-art deep neural network architectures that effectively exploit the forward model. We analyze the statistical complexity of the gradient descent network (GDN), an algorithm unrolling architecture driven by proximal gradient descent. We show that the unrolling depth needed for the optimal statistical performance of GDNs is of order $\log(n)/\log(\varrho_n^{-1})$, where $n$ is the sample size, and $\varrho_n$ is the convergence rate of the corresponding gradient descent algorithm. We also show that when the negative log-density of the latent variable ${\bf x}$ has a simple proximal operator, then a GDN unrolled at depth $D'$ can solve the inverse problem at the parametric rate $O(D'/\sqrt{n})$. Our results thus also suggest that algorithm unrolling models are prone to overfitting as the unrolling depth $D'$ increases. We provide several examples to illustrate these results

Primerjalna študija genetske raznovrstnosti talnih bakterij in gliv v različnih sukcesijah vegetacije na krasu v provinci Guizhou, Kitajska

To study the soil genetic diversity of bacteria and fungi in different vegetation successions (grassland, shrubbery, primary forest and secondary forest) from the karst area, the Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) technology was applied. The results showed that: (1) the diversity of bacterial communities and the fungal communities in karst area were higher than non karst area in each vegetation succession. Compared with the survey from bacterial (the Shannon index was 2.97 in primary forest, 2.91 in secondary forest, 3.18 in shrubbery, 3.14 in grassland and 2.68 in non karst), fungal diversity between karst areas (the Shannon index was 3.56 in primary forest, 3.78 in secondary forest, 3.73 in shrubbery and 3.70 in grassland) and non karst areas (the Shannon index was 3.08) was more evident, which may be related to the alterations of the composition of plant community and the source of carbon in soil with the vegetation succession of karst ecosystem; (2) The comparation of bacterial diversity index and the richness comprehensively evaluated as follows: shrubbery > grassland > primary forest > nsecondary forest. The diversity index and the richness of fungal communities was as follows: secondary forest > shrubbery > grassland > primary forest. The results suggest that the fungal communities have been greatly changed via vegetation successions, but the diversity index and the richness of the bacterial communities have not been seriously affected. The results provide scientific basis for understanding karst surface ecosystem, which contributes to the future aim of protecting the karst from desertification.Za proučevanje genetske pestrosti talnih bakterij in gliv v različnih sukcesijah vegetacije (travišče, grmičevje, primarni gozd in sekundarni gozd) na krasu je bila uporabljena tehnologija verižne reakcije s polimerazo-denaturirajoča gradientna gelska elektroforeza (PCR-DGGE). Rezultati raziskave so pokazali, da: (1) je bila v vsaki sukcesiji vegetacije pestrost bakterijskih in glivnih združb na kraškem območju višja kot na nekraškem. V primerjavi z bakterijsko raznovrstnostjo (Shannonov indeks je bil 2,97 v primarnem gozdu, 2,91 v sekundarnem gozdu, 3,18 v tleh grmičevja, 3,14 v tleh travišč in 2,68 v nekraškem območju) je bila raznovrstnost gliv med kraškimi območji (Shannonov indeks je bil v primarnem gozdu 3,56, 3,78 v sekundarnem gozdu, 3,73 v tleh grmičevja in 3,70 v tleh travišč) in nekraškimi (Shannonov indeks je bil 3,08) jasneje izražena. To je lahko povezano s spremembami v sestavi rastlinske združbe in vira ogljika v tleh glede na stanje sukcesije v vegetaciji kraškega ekosistema. (2) Primerjava kazalnikov bakterijske raznovrstnosti in abundance je bila celostno ovrednotena in sledi takole: grmičevje > travišče > primarni gozd > sekundarni gozd. Kazalnika raznovrstnosti in abundance glivnih združb kažeta sledeči trend: sekundarni gozd > grmičevje > travišče > primarni gozd. Rezultati izkazujejo, da so se glivne združbe precej spremenile zaradi sukcesije v vegetaciji, vendar pa na drugi strani ni bilo bistvenega vpliva na kazalnika bakterijske raznovrstnosti in abundance. Rezultati med drugim dajejo tudi znanstveno podlago za razumevanje delovanja kraškega površinskega ekosistema, kar ključno prispeva k cilju zaščite krasa pred dezertifikacijo (širjenjem puščav)

Millennial-scale variations in sedimentary oxygenation in the western subtropical North Pacific and its links to North Atlantic climate

The deep-ocean carbon cycle, especially carbon sequestration and outgassing, is one of the mechanisms to explain variations in atmospheric CO2 concentrations on millennial and orbital timescales. However, the potential role of subtropical North Pacific subsurface waters in modulating atmospheric CO2 levels on millennial timescales is poorly constrained. An increase in the respired CO2 concentration in the glacial deep-ocean due to biological pump generally corresponds to deoxygenation in the ocean interior. This link thus offers a chance to study oceanic ventilation and coeval export productivity based on redox-controlled sedimentary geochemical parameters. Here, we investigate a suite of geochemical proxies in a sediment core from the Okinawa Trough to understand sedimentary oxygenation variations in the subtropical North Pacific over the last 50 000 years (50 ka). Our results suggest that enhanced mid-depth western subtropical North Pacific (WSTNP) sedimentary oxygenation occurred during cold intervals and after 8.5 ka, while oxygenation decreased during the Bölling-Alleröd (B/A) and Preboreal. The enhanced oxygenation during cold spells is linked to the North Pacific IntermediateWater (NPIW), while interglacial increase after 8.5 ka is linked to an intensification of the Kuroshio Current due to strengthened northeast tradewinds over the tropics. The enhanced formation of the NPIW during Heinrich Stadial 1 (HS1) was likely driven by the perturbation of sea ice formation and sea surface salinity oscillations in the high-latitude North Pacific. The diminished sedimentary oxygenation during the B/A due to a decreased NPIW formation and enhanced export production, indicates an expansion of the oxygen minimum zone in the North Pacific and enhanced CO2 sequestration at mid-depth waters, along with the termination of atmospheric CO2 concentration increase. We attribute the millennial-scale changes to an intensified NPIW and enhanced abyss flushing during deglacial cold and warm intervals, respectively, closely related to variations in North Atlantic Deep Water formation

Relationship between histone demethylase LSD family and development and prognosis of gastric cancer

Objectiveto elucidate the correlation between histone demethylase and gastric cancerResearch objecthistone demethylase and gastric cancerResultsAs one of the important regulatory mechanisms in molecular biology and epigenetics, histone modification plays an important role in gastric cancer including downstream gene expression regulation and epigenetics effect. Both histone methyltransferase and histone demethylases are involved in the formation and maintaining different of histone methylation status, which in turn through a variety of vital molecules and signaling pathways involved in the recognition of histone methylation modification caused by the downstream biological process, eventually participate in the regulation of chromatin function, and with a variety of important physiological activities, especially closely related to the occurrence of gastric cancer and embryonic development.ConclusionThis paper intends to review the research progress in this field from the aspects of histone methylation modification and the protein structure, catalytic mechanism and biological function of the important histone demethylases LSD1 and LSD2, in order to provide the theoretical reference for further understanding and exploration of histone demethylases in development and prognosis of gastric cancer

Halophyte Nitraria billardieri CIPK25 promotes photosynthesis in Arabidopsis under salt stress

The calcineurin B-like (CBL)-interacting protein kinases (CIPKs), a type of plant-specific genes in the calcium signaling pathway, function in response to adverse environments. However, few halophyte derived CIPKs have been studied for their role in plant physiological and developmental adaptation during abiotic stresses, which inhibits the potential application of these genes to improve environmental adaptability of glycophytes. In this study, we constructed Nitraria billardieri CIPK25 overexpressing Arabidopsis and analyzed the seedling development under salt treatment. Our results show that Arabidopsis with NbCIPK25 expression exhibits more vigorous growth than wild type plants under salt condition. To gain insight into the molecular mechanisms underlying salt tolerance, we profiled the transcriptome of WT and transgenic plants via RNA-seq. GO and KEGG analyses revealed that upregulated genes in NbCIPK25 overexpressing seedlings under salt stress are enriched in photosynthesis related terms; Calvin-cycle genes including glyceraldehyde-3-phosphate dehydrogenases (GAPDHs) are significantly upregulated in transgenic plants, which is consistent with a decreased level of NADPH (GAPDH substrate) and increased level of NADP+. Accordingly, NbCIPK25 overexpressing plants exhibited more efficient photosynthesis; soluble sugar and proteins, as photosynthesis products, showed a higher accumulation in transgenic plants. These results provide molecular insight into how NbCIPK25 promotes the expression of genes involved in photosynthesis, thereby maintaining plant growth under salt stress. Our finding supports the potential application of halophyte-derived NbCIPK25 in genetic modification for better salt adaptation

Circulating tumor DNA clearance predicts prognosis across treatment regimen in a large real-world longitudinally monitored advanced non-small cell lung cancer cohort

Background: Although growth advantage of certain clones would ultimately translate into a clinically visible disease progression, radiological imaging does not reflect clonal evolution at molecular level. Circulating tumor DNA (ctDNA), validated as a tool for mutation detection in lung cancer, could reflect dynamic molecular changes. We evaluated the utility of ctDNA as a predictive and a prognostic marker in disease monitoring of advanced non-small cell lung cancer (NSCLC) patients.Methods: This is a multicenter prospective cohort study. We performed capture-based ultra-deep sequencing on longitudinal plasma samples utilizing a panel consisting of 168 NSCLC-related genes on 949 advanced NSCLC patients with driver mutations to monitor treatment responses and disease progression. The correlations between ctDNA and progression-free survival (PFS)/overall survival (OS) were performed on 248 patients undergoing various treatments with the minimum of 2 ctDNA tests.Results: The results of this study revealed that higher ctDNA abundance (P=0.012) and mutation count (P=8.5x10(-4)) at baseline are associated with shorter OS. We also found that patients with ctDNA clearance, not just driver mutation clearance, at any point during the course of treatment were associated with longer PFS (P=2.2x10(-1)6, HR 0.28) and OS (P=4.5x10(-6), HR 0.19) regardless of type of treatment and evaluation schedule.Conclusions: This prospective real-world study shows that ctDNA clearance during treatment may serve as predictive and prognostic marker across a wide spectrum of treatment regimens

Genome and pan-genome assembly of asparagus bean (Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation

Asparagus bean (Vigna unguiculata ssp. sesquipedialis) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and Vigna occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean

Self-Assembled Polymeric Micellar Nanoparticles as Nanocarriers for Poorly Soluble Anticancer Drug Ethaselen

A series of monomethoxy poly(ethylene glycol)-poly(lactide) (mPEG-PLA) diblock copolymers were synthesized, and mPEG-PLA micelle was fabricated and used as a nanocarrier for solubilization and delivery of a promising anticancer drug ethaselen. Ethaselen was efficiently encapsulated into the micelles by the dialysis method, and the solubility of ethaselen in water was remarkably increased up to 82 μg/mL before freeze-drying. The mean diameter of ethaselen-loaded micelles ranged from 51 to 98 nm with a narrow size distribution and depended on the length of PLA block. In vitro hemolysis study indicated that mPEG-PLA copolymers and ethaselen-loaded polymeric micelles had no hemolytic effect on the erythrocyte. The enhanced antitumor efficacy and reduced toxic effect of ethaselen-loaded polymeric micelle when compared with ethaselen-HP-β-CD inclusion were observed at the same dose in H22human liver cancer cell bearing mouse models. These suggested that mPEG-PLA polymeric micelle nanoparticles had great potential as nanocarriers for effective solubilization of poorly soluble ethaselen and further reducing side effects and toxicities of the drug

Thyroid Disruption by Di-n-Butyl Phthalate (DBP) and Mono-n-Butyl Phthalate (MBP) in Xenopus laevis

BACKGROUND: Di-n-butyl phthalate (DBP), a chemical widely used in many consumer products, is estrogenic and capable of producing seriously reproductive and developmental effects in laboratory animals. However, recent in vitro studies have shown that DBP and mono-n-butyl phthalate (MBP), the major metabolite of DBP, possessed thyroid hormone receptor (TR) antagonist activity. It is therefore important to consider DBP and MBP that may interfere with thyroid hormone system. METHODOLOGY/PRINCIPAL FINDINGS: Nieuwkoop and Faber stage 51 Xenopus laevis were exposed to DBP and MBP (2, 10 or 15 mg/L) separately for 21 days. The two test chemicals decelerated spontaneous metamorphosis in X. laevis at concentrations of 10 and 15 mg/L. Moreover, MBP seemed to possess stronger activity. The effects of DBP and MBP on inducing changes of expression of selected thyroid hormone response genes: thyroid hormone receptor-beta (TRβ), retinoid X receptor gamma (RXRγ), alpha and beta subunits of thyroid-stimulating hormone (TSHα and TSHβ) were detected by qPCR at all concentrations of the compounds. Using mammalian two-hybrid assay in vitro, we found that DBP and MBP enhanced the interactions between co-repressor SMRT (silencing mediator for retinoid and thyroid hormone receptors) and TR in a dose-dependent manner, and MBP displayed more markedly. In addition, MBP at low concentrations (2 and 10 mg/L) caused aberrant methylation of TRβ in head tissue. CONCLUSIONS: The current findings highlight potential disruption of thyroid signalling by DBP and MBP and provide data for human risk assessment