Image Clustering via the Principle of Rate Reduction in the Age of Pretrained Models

The advent of large pre-trained models has brought about a paradigm shift in both visual representation learning and natural language processing. However, clustering unlabeled images, as a fundamental and classic machine learning problem, still lacks effective solution, particularly for large-scale datasets. In this paper, we propose a novel image clustering pipeline that leverages the powerful feature representation of large pre-trained models such as CLIP and cluster images effectively and efficiently at scale. We show that the pre-trained features are significantly more structured by further optimizing the rate reduction objective. The resulting features may significantly improve the clustering accuracy, e.g., from 57\% to 66\% on ImageNet-1k. Furthermore, by leveraging CLIP's image-text binding, we show how the new clustering method leads to a simple yet effective self-labeling algorithm that successfully works on unlabeled large datasets such as MS-COCO and LAION-Aesthetics. We will release the code in https://github.com/LeslieTrue/CPP.Comment: 21 pages, 13 figure

Coupled evolution of nitrogen cycling and redoxcline dynamics on the Yangtze Block across the Ediacaran-Cambrian transition

The authors acknowledge funding support from the NSF FESD and Earth-Life Transitions programs (T.L.), the NASA Astrobiology Institute under Cooperative Agreement No. NNA15BB03A issued through the Science Mission Directorate (T.L.), the key project of the Natural Science Foundation of China (C.-F.C.) (No. 41730424), and the program of China Scholarships Council (Y.C.) (No. 201504910582). Nitrogen and carbon isotope analyses were funded by startup funds from Virginia Tech to B.C.G.The Ediacaran-Cambrian transition is characterized by the evolution of complex eukaryotes and rapid diversification of metazoans. However, linkages between environmental triggers and evolutionary patterns remain unclear. Here, we present high-resolution records of carbon and nitrogen isotopic data (δ13C, δ15N) for a drill core extending from the early Ediacaran Doushantuo Formation to the early Cambrian Jiumenchong Formation, located on the slope of the Yangtze Block. Our data show that sedimentary bulk nitrogen isotope values (δ15Nbulk) decrease progressively from the early Ediacaran to the early Cambrian, broadly concurrent with nitrogen isotope data from other sections throughout the Yangtze Block. During the early Ediacaran, however, δ15Nbulk values from our study are higher (maximum 11.2‰) compared to those from more restricted coeval sections, suggesting a higher degree of denitrification in our slope section. The early Ediacaran δ15Nbulk data from the Yangtze Block may thus provide indirect evidence for an upwelling system that led to a shallower redoxcline in slope environments of the Upper Yangtze region. Widespread light δ15Nbulk values from the early Cambrian (minimum −7.5‰) paired with excess silicate-bound nitrogen throughout much of the Yangtze Block are most parsimoniously interpreted as non-quantitative assimilation of ammonium (NH4+) with relatively high concentrations of NH4+ accumulating in the deep basin. Overall, the spatial and temporal trends in nitrogen cycling across the Yangtze Block suggest that fixed nitrogen was more bioavailable in the Ediacaran-Cambrian Yangtze Basin compared to previously studied Mesoproterozoic sections, although nitrogen speciation in the photic zone may have varied with time. Environmental factors such as oxygen levels and nitrogen bioavailability may have shaped the evolutionary trajectory of life on the Yangtze Block and potentially elsewhere across the Ediacaran-Cambrian transition.PostprintPeer reviewe

Sign-reversal of the in-plane resistivity anisotropy in hole-doped iron pnictides

The in-plane anisotropy of the electrical resistivity across the coupled orthorhombic and magnetic transitions of the iron pnictides has been extensively studied in the parent and electron-doped compounds. All these studies universally show that the resistivity $\rho_{a}$ across the long orthorhombic axis $a_{O}$ - along which the spins couple antiferromagnetically below the magnetic transition temperature - is smaller than the resistivity $\rho_{b}$ of the short orthorhombic axis $b_{O}$, i. e. $\rho_{a}<\rho_{b}$. Here we report that in the hole-doped compounds Ba$_{1-x}$K$_{x}$Fe$_{2}$As$_{2}$, as the doping level increases, the resistivity anisotropy initially becomes vanishingly small, and eventually changes sign for sufficiently large doping, i. e. $\rho_{b}<\rho_{a}$. This observation is in agreement with a recent theoretical prediction that considers the anisotropic scattering of electrons by spin-fluctuations in the orthorhombic/nematic state.Comment: This paper has been replaced by the new version offering new explanation of the experimental results first reported her

AFM, SEM and TEM Studies on Porous Anodic Alumina

Porous anodic alumina (PAA) has been intensively studied in past decade due to its applications for fabricating nanostructured materials. Since PAA’s pore diameter, thickness and shape vary too much, a systematical study on the methods of morphology characterization is meaningful and essential for its proper development and utilization. In this paper, we present detailed AFM, SEM and TEM studies on PAA and its evolvements with abundant microstructures, and discuss the advantages and disadvantages of each method. The sample preparation, testing skills and morphology analysis are discussed, especially on the differentiation during characterizing complex cross-sections and ultrasmall nanopores. The versatility of PAAs is also demonstrated by the diversity of PAAs’ microstructure

Fabrication of Porous Anodic Alumina with Ultrasmall Nanopores

Anodization of Al foil under low voltages of 1–10 V was conducted to obtain porous anodic aluminas (PAAs) with ultrasmall nanopores. Regular nanopore arrays with pore diameter 6–10 nm were realized in four different electrolytes under 0–30°C according to the AFM, FESEM, TEM images and current evolution curves. It is found that the pore diameter and interpore distance, as well as the barrier layer thickness, are not sensitive to the applied potentials and electrolytes, which is totally different from the rules of general PAA fabrication. The brand-new formation mechanism has been revealed by the AFM study on the samples anodized for very short durations of 2–60 s. It is discovered for the first time that the regular nanoparticles come into being under 1–10 V at the beginning of the anodization and then serve as a template layer dominating the formation of ultrasmall nanopores. Under higher potentials from 10 to 40 V, the surface nanoparticles will be less and less and nanopores transform into general PAAs

Rapamycin Upregulates Connective Tissue Growth Factor Expression in Hepatic Progenitor Cells Through TGF-β-Smad2 Dependent Signaling

Rapamycin (sirolimus) is a mTOR kinase inhibitor and is widely used as an immunosuppressive drug to prevent graft rejection in organ transplantation currently. However, some recent investigations have reported that it had profibrotic effect in the progression of organ fibrosis, and its precise role in the liver fibrosis is still poorly understood. Here we showed that rapamycin upregulated connective tissue growth factor (CTGF) expression at the transcriptional level in hepatic progenitor cells (HPCs). Using lentivirus-mediated small hairpin RNA (shRNA) we demonstrated that knockdown of mTOR, Raptor, or Rictor mimicked the effect of rapamycin treatment. Mechanistically, inhibition of mTOR activity with rapamycin resulted in a hyperactive PI3K-Akt pathway, whereas this activation inhibited the expression of CTGF in HPCs. Besides, rapamycin activated the TGF-β-Smad signaling, and TGF-β receptor type I (TGFβRI) serine/threonine kinase inhibitors completely blocked the effects of rapamycin on HPCs. Moreover, Smad2 was involved in the induction of CTGF through rapamycin-activated TGF-β-Smad signaling as knockdown completely blocked CTGF induction, while knockdown of Smad4 expression partially inhibited induction, whereas Smad3 knockdown had no effect. Rapamycin also induced ROS generation and latent TGF-β activation which contributed to TGF-β-Smad signaling. In conclusion, this study demonstrates that rapamycin upregulates CTGF in HPCs and suggests that rapamycin has potential fibrotic effect in liver

Nomogram constructed by immunological and inflammatory indicators for predicting prognosis of patients with esophageal squamous cell carcinoma treated with neoadjuvant chemoradiotherapy plus surgery

ObjectivesAt present, esophageal squamous cell carcinoma (ESCC) patients accepting neoadjuvant chemoradiotherapy (nCRT) plus surgery lack corresponding prognostic indicators. This study aimed to construct a prognostic prediction model for ESCC patients undergoing nCRT and surgery based on immune and inflammation-related indicators.MethodsWe retrospectively analyzed the levels of serum immune- and inflammation-related indicators of ESCC patients before receiving nCRT plus surgery in the training cohort (99 patients) and validation cohort (67 patients), which were collected from 2007 to 2020. Univariate and multivariate Cox survival analyses were conducted to evaluate the indicators to set up a nomogram associated with the patients’ overall survival (OS). The prediction accuracy and discriminative ability of the nomogram were measured by the concordance index (C-index), decision curve, calibration curve, integrated discrimination improvement (IDI), and net reclassification improvement (NRI).ResultsUnivariate and multivariate Cox analyses demonstrated that immune globin A (IgA) and C-reactive protein (CRP) were independent risk factors. A nomogram based on IgA, CRP, and cTNM stage was established for predicted OS in the training cohort and validated in the validation cohort. The C-index of the nomogram was 0.820 (95% CI: 0.705–0.934), which was higher than that of the cTNM stage (0.655 (95% CI: 0.546–0.764), p &lt; 0.05) in the training cohort, and similar results were observed in the validation cohort (0.832 (95% CI: 0.760–0.903 vs 0.635 (95% CI: 0.509–0.757), p &lt; 0.001). Furthermore, the prediction accuracy and net benefit of the nomogram verified by the calibration curve, decision curve, NRI, and IDI were satisfactory in the training and validation cohorts.ConclusionThe newly constructed nomogram concluding serum IgA, CRP, and cTNM stage might be helpful in the prognosis prediction for ESCC patients receiving nCRT plus surgery

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines, 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD. In the present study, to unravel the potential genetic mechanisms underlying resistance to MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using quantitative real-time PCR (qPCR), all of which were successfully confirmed. Finally, qPCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying resistance and susceptibility to MD in view of its function and overlaps with data from previous study. Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.https://doi.org/10.1186/s12863-020-00884-

A Macromolecular Approach to Eradicate Multidrug Resistant Bacterial Infections while Mitigating Drug Resistance Onset

Polymyxins remain the last line treatment for multidrug-resistant (MDR) infections. As polymyxins resistance emerges, there is an urgent need to develop effective antimicrobial agents capable of mitigating MDR. Here, we report biodegradable guanidinium-functionalized polycarbonates with a distinctive mechanism that does not induce drug resistance. Unlike conventional antibiotics, repeated use of the polymers does not lead to drug resistance. Transcriptomic analysis of bacteria further supports development of resistance to antibiotics but not to the macromolecules after 30 treatments. Importantly, high in vivo treatment efficacy of the macromolecules is achieved in MDR A. baumannii-, E. coli-, K. pneumoniae-, methicillin-resistant S. aureus-, cecal ligation and puncture-induced polymicrobial peritonitis, and P. aeruginosa lung infection mouse models while remaining non-toxic (e.g., therapeutic index—ED50/LD50: 1473 for A. baumannii infection). These biodegradable synthetic macromolecules have been demonstrated to have broad spectrum in vivo antimicrobial activity, and have excellent potential as systemic antimicrobials against MDR infections

Commelina danxiaensis (Commelinaceae), a new species from Guangdong, China

Commelina danxiaensis (Commelinaceae), a remarkable new species from Mount Danxia, Guangdong Province, China, is described and illustrated. This species is similar to C. communis in inflorescences and flowers but readily distinguishable in its nearly erect stems, larger flowers, and different petal colouration