Lossy Kernelization for (Implicit) Hitting Set Problems

We re-visit the complexity of polynomial time pre-processing (kernelization) for the d-Hitting Set problem. This is one of the most classic problems in Parameterized Complexity by itself, and, furthermore, it encompasses several other of the most well-studied problems in this field, such as Vertex Cover, Feedback Vertex Set in Tournaments (FVST) and Cluster Vertex Deletion (CVD). In fact, d-Hitting Set encompasses any deletion problem to a hereditary property that can be characterized by a finite set of forbidden induced subgraphs. With respect to bit size, the kernelization complexity of d-Hitting Set is essentially settled: there exists a kernel with ?(k^d) bits (?(k^d) sets and ?(k^{d-1}) elements) and this it tight by the result of Dell and van Melkebeek [STOC 2010, JACM 2014]. Still, the question of whether there exists a kernel for d-Hitting Set with fewer elements has remained one of the most major open problems in Kernelization. In this paper, we first show that if we allow the kernelization to be lossy with a qualitatively better loss than the best possible approximation ratio of polynomial time approximation algorithms, then one can obtain kernels where the number of elements is linear for every fixed d. Further, based on this, we present our main result: we show that there exist approximate Turing kernelizations for d-Hitting Set that even beat the established bit-size lower bounds for exact kernelizations - in fact, we use a constant number of oracle calls, each with "near linear" (?(k^{1+?})) bit size, that is, almost the best one could hope for. Lastly, for two special cases of implicit 3-Hitting set, namely, FVST and CVD, we obtain the "best of both worlds" type of results - (1+?)-approximate kernelizations with a linear number of vertices. In terms of size, this substantially improves the exact kernels of Fomin et al. [SODA 2018, TALG 2019], with simpler arguments

Live Poultry Exposures, Hong Kong and Hanoi, 2006

Since 1997, the largest epidemic of highly pathogenic avian influenza (H5N1) ever recorded has caused 172 human and several billion bird deaths. Recently administered questionnaires determined that live poultry exposures have declined by ≈63% in Hong Kong since 2004 and that, in Vietnam, domestic backyard exposures to poultry are likely more important than retail exposures

Compact approximation stencils based on integrated flat radial basis functions

This paper presents improved ways of constructing compact integrated radial basis function (CIRBF) stencils, based on extended precision, definite integrals, higher-order IRBFs and minimum number of derivative equations, to enhance their performance over large values of the RBF width. The proposed approaches are numerically verified through second-order linear differential equations in one and two variables. Significant improvements in the matrix condition number, solution accuracy and convergence rate with grid refinement over the usual approaches are achieved

Statistical Analsysis to Evaluate Heavy Metal Pollution in the Air Obatained by Moss Technique in Hanoi and its Surrounding Region

The aim of this paper was the application of statistical analysis including principal component analysis to evaluate heavy metal pollution obtained by moss technique in the air of Ha Noi and its surrounding areas and to evaluate potential pollution sources. The concentrations of 33 heavy metal elements in 27 samples of Barbula Indica moss in the investigated region collected in December of 2016 in the investigated area have been examined using multivariate statistical analysis. Five factors explaining 80% of the total variance were identified and their potential sources have been discussed

Improvement of catalytic performance of lignin peroxidase for the enhanced degradation of lignocellulose biomass based on the imbedded electron-relay in long-range electron transfer route

Background: Although lignin peroxidase is claimed as a key enzyme in enzyme-catalyzed lignin degradation, in vitro enzymatic degradation of lignin was not easily observed in lab-scale experiments. It implies that other factors may hinder the enzymatic degradation of lignin. Irreversible interaction between phenolic compound and lignin peroxidase was hypothesized when active enzyme could not be recovered after the reaction with degradation product (guaiacol) of lignin phenolic dimer. Results: In the study of lignin peroxidase isozyme H8 from white-rot fungi Phanerochaete chrysosporium (LiPH8), W251 site was revealed to make the covalent coupling with one moiety of monolignolic radical (guaiacol radical) by LC-MS/MS analysis. Hypothetical electron-relay containing W251 residue was newly suggested based on the observation of repressed radical coupling and remarkably lower electron transfer rate for W215A mutant. Furthermore, the retardation of the suicidal radical coupling between the W251 residue and the monolignolic radical was attempted by supplementing the acidic microenvironment around the W251 residue to engineer radical-robust LiPH8. Among many mutants, mutant A242D showed exceptional catalytic performances by yielding 21.1- and 4.9-fold higher increases of k(cat) and k(cat)/K-M values, respectively, in the oxidation of non-phenolic model lignin dimer. Conclusions: A mechanism-based suicide inhibition of LiPH8 by phenolic compounds was firstly revealed and investigated in this work. Radical-robust LiPH8 was also successfully engineered by manipulating the transient radical state of radical-susceptible electron-relay. Radical-robust LiPH8 will play an essential role in degradation of lignin, which will be consequently linked with improved production of sugars from lignocellulose biomass.open

Ocular adverse events after COVID-19 vaccination

Purpose The COVID-19 pandemic has galvanized the development of new vaccines at an unprecedented pace. Since the widespread implementation of vaccination campaigns, reports of ocular adverse effects after COVID-19 vaccinations have emerged. This review summarizes ocular adverse effects possibly associated with COVID-19 vaccination, and discusses their clinical characteristics and management. Methods Narrative Literature Review. Results Ocular adverse effects of COVID-19 vaccinations include facial nerve palsy, abducens nerve palsy, acute macular neuroretinopathy, central serous retinopathy, thrombosis, uveitis, multiple evanescent white dot syndrome, Vogt-Koyanagi-Harada disease reactivation, and new-onset Graves' Disease. Studies in current literature are primarily retrospective case series or isolated case reports - these are inherently weak in establishing association or causality. Nevertheless, the described presentations resemble the reported ocular manifestations of the COVID-19 disease itself. Hence, we hypothesize that the human body's immune response to COVID-19 vaccinations may be involved in the pathogenesis of the ocular adverse effects post-COVID-19 vaccination. Conclusion Ophthalmologists and generalists should be aware of the possible, albeit rare, ocular adverse effects after COVID-19 vaccination.Ophthalmic researc

Discrete seasonal hydroclimate reconstructions over northern Vietnam for the past three and a half centuries

We present a 350-year hydroclimatic year (HY) index for northern Vietnam derived from three discrete seasonal reconstructions from tree rings: an index of autumn rainfall from the earlywood widths of Chinese Douglas fir (Pseudotsuga sinensis), the first such record from this species, and two nearby published Palmer Drought Severity Index (PDSI) reconstructions from cypress (Fokienia hodginsii) tree rings for spring and summer, respectively. Autumn rainfall over the study region constitutes only around 9% of the annual total, but its variability is strongly linked to the strength of the atmospheric gradient over Asia during the transition from the boreal summer to winter monsoons. Deficit or surplus of autumn rainfall enhances or mitigates, respectively, the impact of the annual winter dry season on trees growing on porous karst hillsides. The most protracted HY drought (dry across all seasons) occurred at the turn of the twentieth century at a time of relative quiet, but a mid-to-late eighteenth century multi-year HY drought coincided with a period of great societal turmoil across mainland Southeast Asia and the Tay Son Rebellion in northern Vietnam. A mid-nineteenth century uprising accompanied by a smallpox epidemic, crop failure and famine, occurred during the worst autumn drought of the past two and a half centuries but only moderate drought in spring and summer. The “Great Vietnamese Famine” of the mid-twentieth century was dry only in autumn, with a wet spring and an average summer

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides

To meet the growing demand for synthetic genes more robust, scalable and inexpensive gene assembly technologies must be developed. Here, we present a protocol for high-quality gene assembly directly from low-cost marginal-quality microarray-synthesized oligonucleotides. Significantly, we eliminated the time- and money-consuming oligonucleotide purification steps through the use of hybridization-based selection embedded in the assembly process. The protocol was tested on mixtures of up to 2000 oligonucleotides eluted directly from microarrays obtained from three different chip manufacturers. These mixtures containing <5% perfect oligos, and were used directly for assembly of 27 test genes of different sizes. Gene quality was assessed by sequencing, and their activity was tested in coupled in vitro transcription/translation reactions. Genes assembled from the microarray-eluted material using the new protocol matched the quality of the genes assembled from >95% pure column-synthesized oligonucleotides by the standard protocol. Both averaged only 2.7 errors/kb, and genes assembled from microarray-eluted material without clonal selection produced only 30% less protein than sequence-confirmed clones. This report represents the first demonstration of cost-efficient gene assembly from microarray-synthesized oligonucleotides. The overall cost of assembly by this method approaches 5¢ per base, making gene synthesis more affordable than traditional cloning

In silico-designed lignin peroxidase from Phanerochaete chrysosporium shows enhanced acid stability for depolymerization of lignin

Background: The lignin peroxidase isozyme H8 from the white-rot fungus Phanerochaete chrysosporium (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lignin. However, native LiPH8 is unstable under acidic pH conditions. This characteristic is a barrier to lignin depolymerization, as repolymerization of phenolic products occurs simultaneously at neutral pH. Because repolymerization of phenolics is repressed at acidic pH, a highly acid-stable LiPH8 could accelerate the selective depolymerization of recalcitrant lignin. Results: The engineered LiPH8 was in silico designed through the structural superimposition of surface-active site-harboring LiPH8 from Phanerochaete chrysosporium and acid-stable manganese peroxidase isozyme 6 (MnP6) from Ceriporiopsis subvermispora. Effective salt bridges were probed by molecular dynamics simulation and changes to Gibbs free energy following mutagenesis were predicted, suggesting promising variants with higher stability under extremely acidic conditions. The rationally designed variant, A55R/N156E-H239E, demonstrated a 12.5-fold increased half-life under extremely acidic conditions, 9.9-fold increased catalytic efficiency toward veratryl alcohol, and a 7.8-fold enhanced lignin model dimer conversion efficiency compared to those of native LiPH8. Furthermore, the two constructed salt bridges in the variant A55R/N156E-H239E were experimentally confirmed to be identical to the intentionally designed LiPH8 variant using X-ray crystallography (PDB ID: 6A6Q). Conclusion: Introduction of strong ionic salt bridges based on computational design resulted in a LiPH8 variant with markedly improved stability, as well as higher activity under acidic pH conditions. Thus, LiPH8, showing high acid stability, will be a crucial player in biomass valorization using selective depolymerization of lignin