Tertiary Alphabet for the Observable Protein Structural Universe

Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective mapping between sequence and structure. We demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones. Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Finally, locations of TERMs in protein chains can be predicted from sequence alone based on sequence signatures emergent from TERM instances in the PDB. For multisegment motifs, this method identifies spatially adjacent fragments that are not contiguous in sequence—a major bottleneck in structure prediction. Although all TERMs recur in diverse proteins, some appear specialized for certain functions, such as interface formation, metal coordination, or even water binding. Structural biology has benefited greatly from previously observed degeneracies in structure. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities toward better understanding, design, and prediction of protein structure

POSITIVE SOLUTION OF CRITICAL HARDY-SOBOLEV ELLIPTIC SYSTEMS WITH THE BOUNDARY SINGULARITY

Abstract. In this paper, we are concerned with the existence of positive solutions to the system where N−2 , N 3 . We show that if Ω = R N + , problem (0.1) possesses a least energy solution and if Ω is bounded, 0 ∈ ∂ Ω , there exists λ * > 0 such that problem (0.1) has at least a positive solution provided 0 < λ < λ *

A novel pollution pattern: Highly chlorinated biphenyls retained in Black-crowned night heron (Nycticorax nycticorax) and Whiskered tern (Chlidonias hybrida) from the Yangtze River Delta

AbstractContamination of organochlorine pesticides (OCPs), polychlorinated diphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), hydroxylated polybrominated diphenyl ethers (OH-PBDEs) and their methylated counterparts (MeO-PBDEs) were determined in Black-crowned night heron (Nycticorax nycticorax) and Whiskered tern (Chlidonias hybrida) from two drinking water sources, e.g. Tianmu lake and East Tai lake in Yangtze River Delta, China. A novel PCBs contamination pattern was detected, including 11% and 6.9% highly chlorinated biphenyls (PCBs with eight to ten chlorines) in relation to total PCB concentrations in the Black-crowned night heron and Whiskered tern eggs, respectively. The predominating OCPs detected in the present study were 4,4′-DDE, with concentration range 280–650 ng g−1 lw in Black-crowned night heron and 240–480 ng g−1 lw in Whiskered tern, followed by β-HCH and Mirex. 6-MeO-BDE-90 and 6-MeO-BDE-99 are the two predominant congeners of MeO-PBDEs whereas 6-OH-BDE-47 contributes mostly to the OH-PBDEs in both species. Contamination level was considered as median or low level compared global data

Zero-shot Clinical Entity Recognition using ChatGPT

In this study, we investigated the potential of ChatGPT, a large language model developed by OpenAI, for the clinical named entity recognition task defined in the 2010 i2b2 challenge, in a zero-shot setting with two different prompt strategies. We compared its performance with GPT-3 in a similar zero-shot setting, as well as a fine-tuned BioClinicalBERT model using a set of synthetic clinical notes from MTSamples. Our findings revealed that ChatGPT outperformed GPT-3 in the zero-shot setting, with F1 scores of 0.418 (vs.0.250) and 0.620 (vs. 0.480) for exact- and relaxed-matching, respectively. Moreover, prompts affected ChatGPT's performance greatly, with relaxed-matching F1 scores of 0.628 vs.0.541 for two different prompt strategies. Although ChatGPT's performance was still lower than that of the supervised BioClinicalBERT model (i.e., relaxed-matching F1 scores of 0.628 vs. 0.870), our study demonstrates the great potential of ChatGPT for clinical NER tasks in a zero-shot setting, which is much more appealing as it does not require any annotation.Comment: 7 pages, 5 tables, 1 figur

Turbulent flame propagation with pressure oscillation in the end gas region of confined combustion chamber equipped with different perforated plates

Experiments were conducted in a newly designed constant volume combustion chamber with a perforated plate by varying the initial conditions. Hydrogen-air mixtures were used and the turbulent flame, shock wave, and the processes of flame-shock interactions were tracked via high-speed Schlieren photography. The effects of hole size and porosities on flame and shock wave propagation, intensity of the shock wave and pressure oscillation in closed combustion chamber were analyzed in detail. The effect of interactions between the turbulent flame and reflected shock or acoustic wave on the turbulent flame propagation was comprehensively studied during the present experiment. The results demonstrated that flame front propagation velocity and pressure oscillation strongly depend on the hole size and porosities of the perforated plate. The flame front propagation velocity in the end gas region increases as hole size increases and porosity decreases. The flame front propagation intensity in the end region of a confined space is strongly relevant to two competing effects: the initial turbulent formation and turbulent flame development. The experimental results indicated that an oscillating flame is associated with both the reflected shock wave and the acoustic wave. Meanwhile, different turbulent flame propagations and combustion modes were observed

Chinese Parental Awareness of Children's COVID-19 Protective Measures

[[abstract]]Objectives: In this research our aim was to investigate Chinese parents’ awareness of pediatric COVID-19 in relation to protecting their children. Methods: A cross-sectional study was conducted in Fujian provinces in China using a Web-based questionnaire to survey parents of children aged 6 to 16 years old. Results: The sample included 1222 participants. Overall, 99.2% of participants were aware of respiratory transmission of COVID-19, and 75.6% also believed fecal-oral transmission to be possible. Although 98.3% of participants claimed to know how to wear and remove masks properly, some parents were unaware of good handwashing techniques and answered incorrectly regarding cough etiquette. Parents also seemed uncertain about pediatric COVID-19 symptoms. Awareness scores significantly differed across parental role, educational attainment levels, and social-economic levels (p value < .005), with fathers, more educated parents, and those of higher income showing greater levels of awareness. Conclusion: Research results suggest an urgent need for parental education regarding COVID-19 in children, especially regarding handwashing techniques and cough etiquette; educational outreach for both parents and schoolchildren is critical.[[notice]]補正完

Existence of critical elliptic systems with boundary singularities

In this paper, we are concerned with the existence of positive solutions of the following nonlinear elliptic system involving critical Hardy-Sobolev exponent \begin{equation*}\label{eq:1}(*) \left\{ \begin{array}{lll} -\Delta u= \frac{2\alpha}{\alpha+\beta}\frac{u^{\alpha-1}v^\beta}{|x|^s}-\lambda u^p, & \quad {\rm in}\quad \Omega,\\[2mm] -\Delta v= \frac{2\beta}{\alpha+\beta}\frac{u^\alpha v^{\beta-1}}{|x|^s}-\lambda v^p, & \quad {\rm in}\quad \Omega,\\[2mm] u\gt 0, v\gt 0, &\quad {\rm in}\quad \Omega,\\[2mm] u=v=0, &\quad {\rm on}\quad \partial\Omega, \end{array} \right. \end{equation*} where $N\geq 4$ and $\Omega$ is a $C^1$ bounded domain in $\mathbb{R}^N$ with $0\in\partial\Omega$. $0\lt s \lt 2$, $\alpha+\beta=2^*(s)=\frac{2(N-s)}{N-2}$, $\alpha,\beta\gt 1$, $\lambda\gt 0$ and $1 \lt p\lt \frac{N+2}{N-2}$. The case when 0 belongs to the boundary of $\Omega$ is closely related to the mean curvature at the origin on the boundary. We show in this paper that problem $(*)$ possesses at least a positive solution

Contribution à la modélisation de l'endommagement anisotrope et de la variation de la perméabilité des roches fragiles

LILLE1-BU (590092102) / SudocSudocFranceF

A Modification of the Imperialist Competitive Algorithm with Hybrid Methods for Multi-Objective Optimization Problems

This paper proposes a modification of the imperialist competitive algorithm to solve multi-objective optimization problems with hybrid methods (MOHMICA) based on a modification of the imperialist competitive algorithm with hybrid methods (HMICA). The rationale for this is that there is an obvious disadvantage of HMICA in that it can only solve single-objective optimization problems but cannot solve multi-objective optimization problems. In order to adapt to the characteristics of multi-objective optimization problems, this paper improves the establishment of the initial empires and colony allocation mechanism and empire competition in HMICA, and introduces an external archiving strategy. A total of 12 benchmark functions are calculated, including 10 bi-objective and 2 tri-objective benchmarks. Four metrics are used to verify the quality of MOHMICA. Then, a new comprehensive evaluation method is proposed, called “radar map method”, which could comprehensively evaluate the convergence and distribution performance of multi-objective optimization algorithm. It can be seen from the four coordinate axes of the radar maps that this is a symmetrical evaluation method. For this evaluation method, the larger the radar map area is, the better the calculation result of the algorithm. Using this new evaluation method, the algorithm proposed in this paper is compared with seven other high-quality algorithms. The radar map area of MOHMICA is at least 14.06% larger than that of other algorithms. Therefore, it is proven that MOHMICA has advantages as a whole

Impact of NaOH on the Hydrothermal Oxidation of Guaiacol for the Production of Value-Added Products

In this study, the impact of NaOH on the hydrothermal oxidation of guaiacol was investigated. It was found that NaOH significantly accelerated the production of formic acid and acetic acid with H2O2 or CuO as the oxidant. With the strong oxidant, H2O2, the highest acetic acid yield (15.73%) and formic acid (5.64%) were obtained at 300 °C for 90 s with NaOH 1.0 mol·L−1 and a 100% H2O2 oxygen supply. In comparison, with CuO as the oxidant, the highest values of acetic acid (13.42%) and formic acid (4.21%) were acquired at 250 °C for 6 h with NaOH 1.0 mol·L−1. Formic acid and acetic acid were generated through the oxidation of intermediates, such as levulinic acid, fumaric acid, maleic acid, etc. These results demonstrated that NaOH catalytic hydrothermal oxidation has potential for the production of value-added chemicals from biomass materials. When CuO is used as the oxidant, this process could also be used as a green method for copper smelting along with the utilization of lignin biomass