A structured iterative division approach for non-sparse regression models and applications in biological data analysis.

In this paper, we focus on the modeling problem of estimating data with non-sparse structures, specifically focusing on biological data that exhibit a high degree of relevant features. Various fields, such as biology and finance, face the challenge of non-sparse estimation. We address the problems using the proposed method, called structured iterative division. Structured iterative division effectively divides data into non-sparse and sparse structures and eliminates numerous irrelevant variables, significantly reducing the error while maintaining computational efficiency. Numerical and theoretical results demonstrate the competitive advantage of the proposed method on a wide range of problems, and the proposed method exhibits excellent statistical performance in numerical comparisons with several existing methods. We apply the proposed algorithm to two biology problems, gene microarray datasets, and chimeric protein datasets, to the prognostic risk of distant metastasis in breast cancer and Alzheimer's disease, respectively. Structured iterative division provides insights into gene identification and selection, and we also provide meaningful results in anticipating cancer risk and identifying key factors.

Association between body roundness index and prevalence of kidney stone in the U.S: a study based on the NHANES database.

OBJECTIVE: This study aimed to evaluate the potential association between the body roundness index (BRI) and kidney stone prevalence in adults in the United States. METHODS: A cohort of participants from the National Health and Nutrition Examination Survey (NHANES) database spanning 2007-2018 were gathered for analysis. Logistic regression analyses, subgroup assessments, and calculations were employed to examine the potential link between BRI and kidney stone prevalence. RESULTS: The study included 30,990 participants aged > 20 years, of which 2,891 declared a kidney stone history. After modulating all relevant confounding factors, each unit increase in the BRI was linked to a 65% increase in kidney stone prevalence (OR = 1.65, 95% CI: 1.47, 1.85). Sensitivity analyses conducted by categorizing the BRI into three groups revealed a 59% increase in kidney stone prevalence in the highest tertile BRI group compared to the lowest one (OR = 1.59, 95% CI: 1.42, 1.79). Furthermore, dose-response curves depicted a positive near-linear correlation between the BRI and the risk of kidney stone prevalence. CONCLUSION: These findings suggest a clinically noteworthy positive correlation between higher BRI values and kidney stone prevalence among the studied US adult population. However, it is essential to acknowledge that the observed relationship does not establish a causal link.

Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery.

Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.

Local linear approximation with Laplacian smoothing penalty and application in biology.

Highly correlated structures appear in various fields, such as biology, biochemistry, and finance, with challenges of dimensionality and sparse estimation. To solve this problem, we propose an algorithm called local linear approximation with the Laplacian smoothing penalty (LLA-LSP). This method produces an accurate and smooth estimate that incorporates the correlation structure among predictors. We compare and discuss the difference between the Laplacian smoothing penalty and the total variance penalty. We prove that this algorithm converges to the oracle solution in a few iterations with a large probability. Numerical results show that the LLA-LSP has good performance in both variable selection and estimation. We apply the proposed algorithm to two biological datasets, a gene expression dataset and a chemical protein dataset, and provide meaningful insights.

Upregulated LINC00319 aggravates neuronal injury induced by oxygen-glucose deprivation via modulating miR-200a-3p.

Ischemic stroke is one of the main causes of physical disability and mortality worldwide. Long non-coding RNAs (lncRNAs) are reported to be dysregulated in various biological progressions and serve important roles in pathological processes of cerebral ischemia. However, their biological actions and potential mechanisms in the progression of ischemic stroke remain unknown. The present study aimed to investigate the functions of LINC00319 on ischemic brain injury. It was identified that LINC00319 was significantly upregulated in the Gene Expression Omnibus profile of ischemic stroke. Furthermore, LINC00319 overexpression elevated caspase-3 activity and increased the apoptotic rate of neuronal cells, as well as decreased cell viability and glucose uptake. It was also demonstrated that LINC00319 participated in oxygen-glucose deprivation (OGD)-induced cerebral ischemic injury. LINC00319 could competitively bind with microRNA (miR)-200a-3p and decrease its expression. Moreover, miR-200a-3p could partly offset the negative effects of LINC00319 overexpression on neuronal injury caused by OGD. Collectively, the present results suggested that LINC00319 promoted apoptosis and aggravated neuronal injury induced by OGD by regulating miR-200a-3p, which may be important for ischemic stroke treatment.

Mathermycin, an anti-cancer molecule that targets cell surface phospholipids.

Mathermycin, a lantipeptide isolated from marine actinomycete Marinactinospora thermotolerans, is an antibiotic that has been shown to disrupt bacterial plasma membrane. We now provide evidences that mathermycin can also disrupt cancer, but not normal, cell plasma membranes through targeting phosphatidylethanolamine (PE), which is located only in the inner leaflet of the plasma membrane in normal cells but in both the inner and outer leaflets of the membrane in tumor cells. Our data shows that mathermycin inhibits the metabolic activity and induces mainly necrotic death of all cancer cell lines with EC50 between 4.2 and 16.9 µM, while normal cell lines have EC50 between 113 and 129 µM. The cytotoxicity of mathermycin could be inhibited by exogenous PE, but not phosphoserine and phosphocholine. The formation of mathermycin-PE complexes was confirmed by in silico analysis, HPLC and MS spectrometer. Furthermore, mathermycin exhibited similar cytotoxicity toward cancer and multidrug resistant cancer cells, which could be due to its ability to inhibit mitochondrial function, as shown by our data from the Seahorse™ metabolic analyzer. This study demonstrates that mathermycin is a potentially effective class of anti-tumor chemotherapeutics that do not easily develop resistance due to a mechanism of action targeting PE.

Novel Lime Calcination System for CO2 Capture and Its Thermal-Mass Balance Analysis.

In conventional lime calcination processes, because of fuel combustion in the kiln, the carbon dioxide (CO2) from limestone decomposition is mixed with the flue gas, which results in energy requirement for gas separation in the carbon capture process. Here, a novel lime calcination system with carrier gas (CO2) heating and air cooling is proposed to avoid the mixing problem of the CO2 and the flue gas. This system consists of a new shaft kiln with four processing zones and a furnace system, where fuel combustion, limestone reaction, and lime cooling are carried out separately. Therefore, while obtaining qualified lime products, the CO2 from limestone decomposition can be captured without a gas separation process, which accounts for 70% of the total carbon emission in lime production. Furthermore, a thermal-mass balance model was developed for the new system. Based on the model calculation, the energy consumption level of the new system was clarified via a case study. Moreover, parametric analyses were performed to examine the influence of the coefficient of excess air, the coefficient of lost carrier gas, and the calorific value of coal gas on the system performance such as the energy consumption and the CO2 captured.

Why jumped is so difficult: tense/aspect marking in Mandarin-English bilingual children.

Learning to mark for tense in a second language is notoriously difficult for speakers of a tenseless language like Chinese. In this study we test two reasons for these difficulties in Chinese-English sequential bilingual children: (1) morphophonological transfer (i.e., avoidance of complex codas), and (2) interpretation of -ed as an aspect marker of completion, like the Mandarin -le. Mandarin-English bilingual children and age-matched monolinguals did a cartoon retell task. The verbs used in the stories were coded for accuracy in English, telicity, and suppliance of -ed or -le. The results were consistent with morphophonological transfer: the bilingual children were more accurate with irregular past forms in English than regular forms. The results were also consistent with the bilingual children's interpretation of -ed as an aspect marker: most of their production of -ed was on telic verbs. We discuss possible reasons for the children's interpretation of -ed as an aspect marker.

Shellmycin A-D, Novel Bioactive Tetrahydroanthra-γ-Pyrone Antibiotics from Marine Streptomyces sp. Shell-016.

Four novel bioactive tetrahydroanthra-γ-pyrone compounds, shellmycin A-D (1-4), were isolated from the marine Streptomyces sp. shell-016 derived from a shell sediment sample collected from Binzhou Shell Dike Island and Wetland National Nature Reserve, China. The structures of these four compounds were established by interpretation of 1D and 2D NMR and HR-MS data, in which the absolute configuration of 1 was confirmed by single crystal X-ray diffraction, and compound 3 and 4 are a pair of stereoisomers. Compound 1-4 exhibited cytotoxic activity against five cancer cell lines with the IC50 value from 0.69 µM to 26.3 µM. Based on their structure-activity relationship, the putative biosynthetic pathways of these four compounds were also discussed.

Maize factors ZmUBP15, ZmUBP16 and ZmUBP19 play important roles for plants to tolerance the cadmium stress and salt stress.

Ubiquitin-Specific Protease16 (UBP16) has been described involved in cadmium stress and salt stress in Arabidopsis, however nothing is known about the functions of its homologs in maize. In this study, we investigate the functions of ZmUBP15, ZmUBP16 and ZmUBP19, three Arabidopsis UBP16 homologs in maize. Our results indicate that ZmUBP15, ZmUBP16 and ZmUBP19 are ubiquitously expressed throughout plant development, and ZmUBP15, ZmUBP16 and ZmUBP19 proteins are mainly localized in plasma membrane. Complementation analyses show that over-expression of ZmUBP15 or ZmUBP16 can rescue the defective phenotype of ubp16-1 in cadmium stress. In addition, over-expression of ZmUBP15, ZmUBP16 or ZmUBP19 can increase the plant tolerance to cadmium stress. These results indicate that ZmUBP15, ZmUBP16 and ZmUBP19 are required for plant to tolerance the cadmium stress. Consistent with this point, cadmium-related genes are markedly up-regulated in seedlings over-expressing ZmUBP15, ZmUBP16 or ZmUBP19. Furthermore, our data indicate that ZmUBP15, ZmUBP16 and ZmUBP19 partially rescue the salt-stress phenotype of ubp16-1. Thus, our research uncover the functions of three novel maize proteins, ZmUBP15, ZmUBP16 and ZmUBP19, which are required for plants in response to cadmium stress and salt stress.

Evaluating the Effectiveness of the Health Management Program for the Elderly on Health-Related Quality of Life among Elderly People in China: Findings from the China Health and Retirement Longitudinal Study.

The world's rapidly aging population brings serious challenges which could be addressed by changes in behaviour and policy that promote good health in older age. However, these cheap and simple interventions are not available in many countries. China is one of the fastest-ageing countries in the world. The health management programs for the elderly in basic public health services was introduced by the government to promote the health of the elderly in China and address the challenges related to ageing. However, the effectiveness of the program is uncertain. So, we use a propensity score matching difference-in-difference (PSM-DID) model to analyse the causal effect of the health management program for the elderly in basic public health services on the health-related quality of life (HRQoL) of the elderly in China. The result shows that the program has improved the physical health of the elderly but has had no significant impact on mental health. Expanding the program to cover mental health could further benefit the HRQoL of the elderly. The program is a cost-effective approach to tackle the challenges of ageing and is a good example for other developing countries facing the same ageing challenges.