Plasma proteomic landscape and patient stratification in response to severe infection

Rationale: A dysregulated host response to infection can cause life-threatening organ dysfunction, presenting as the clinical syndrome of sepsis. Sepsis is an unmet global health challenge, with substantial clinical and molecular heterogeneity hindering the development of targeted therapies. Subphenotypes in sepsis have been identified at the clinical and molecular levels, especially using the leukocyte transcriptome. Due to the limited throughput of proteome profiling, there has not been a comprehensive analysis of the sepsis plasma proteome that enables understanding of the individual response. In severe COVID-19, a maladaptive immune response to SARS-CoV-2 infection can also lead to organ failure and adverse outcome. This thesis characterises the proteomic landscape in sepsis and COVID-19 to investigate disease mechanisms and inter-individual variation in the response. Methods: The plasma proteome was profiled using high-throughput mass spectrometry for 2622 samples from 1612 individuals, including ICU sepsis patients with community acquired pneumonia or faecal peritonitis and non-septic controls. Higher-depth proteomics and cytokine data were also generated for subsets of the sepsis patients to complement the analysis. For understanding the COVID-19 blood proteome, 395 plasma and serum samples from patients and controls were analysed. Results: Various aspects of the immune response distinguished sepsis from control conditions, highlighting alterations in innate immunity, acute-phase response, neutrophil function and extracellular matrix organisation, with sepsis-specific proteins identified. Three sepsis patient subgroups based on the plasma proteome were identified and validated in independent samples. The subgroups were associated with differential clinical severity and distinct molecular characteristics, including one subgroup showing greater activity in immune pathways and predictive of higher mortality. The proteomic and previously defined leukocyte transcriptomic patient subgroups exhibited significant interaction, shared and distinct molecular mechanisms, and improved risk stratification when combined. Proteomic features of COVID-19 severity were identified, including acute-phase response, complement cascade, tissue necrosis and shifted lipoprotein metabolism. Conclusion: This thesis has identified key biological processes of the sepsis response and clinically informative patient subgroups at the plasma proteome level, highlighting opportunities for patient stratification and development of a precision medicine approach

Organophosphate Ester Flame Retardants and Plasticizers in ocean sediments from the North Pacific to the Arctic Ocean

The occurence of organophosphate ester (OPE) flame retardants and plasticizers in surface sediment from the North Pacific to Arctic Ocean was observed for the first time during the fourth National Arctic Research Expedition of China in the summer of 2010. The samples were analyzed for three halogenated OPEs [tris(2-chloroethyl) phosphate (TCEP), tris(1-chloro-2-propyl) phosphate (TCPP), and tris(dichloroisopropyl) phosphate], three alkylated OPEs [triisobutyl phosphate (TiBP), tri-n-butyl phosphate, and tripentyl phosphate], and triphenyl phosphate. Σ7OPEs (total concentration of the observed OPEs) was in the range of 159–4658 pg/g of dry weight. Halogenated OPEs were generally more abundant than the nonhalogenated OPEs; TCEP and TiBP dominated the overall concentrations. Except for that of the Bering Sea, Σ7OPEs values increased with increasing latitudes from Bering Strait to the Central Arctic Ocean, while the contributions of halogenated OPEs (typically TCEP and TCPP) to the total OPE profile also increased from the Bering Strait to the Central Arctic Ocean, indicating they are more likely to be transported to the remote Arctic. The median budget of 52 (range of 17–292) tons for Σ7OPEs in sediment from the Central Arctic Ocean represents only a very small amount of their total production volume, yet the amount of OPEs in Arctic Ocean sediment was significantly larger than the sum of polybrominated diphenyl ethers (PBDEs) in the sediment, indicating they are equally prone to long-range transport away from source regions. Given the increasing level of production and usage of OPEs as substitutes of PBDEs, OPEs will continue to accumulate in the remote Arctic

FollowBench: A Multi-level Fine-grained Constraints Following Benchmark for Large Language Models

The ability to follow instructions is crucial for Large Language Models (LLMs) to handle various real-world applications. Existing benchmarks primarily focus on evaluating pure response quality, rather than assessing whether the response follows constraints stated in the instruction. To fill this research gap, in this paper, we propose FollowBench, a Multi-level Fine-grained Constraints Following Benchmark for LLMs. FollowBench comprehensively includes five different types (i.e., Content, Situation, Style, Format, and Example) of fine-grained constraints. To enable a precise constraint following estimation on diverse difficulties, we introduce a Multi-level mechanism that incrementally adds a single constraint to the initial instruction at each increased level. To assess whether LLMs' outputs have satisfied every individual constraint, we propose to prompt strong LLMs with constraint-evolution paths to handle challenging open-ended instructions. By evaluating ten closed-source and open-source popular LLMs on FollowBench, we highlight the weaknesses of LLMs in instruction following and point towards potential avenues for future work. The data and code are publicly available at https://github.com/YJiangcm/FollowBench.Comment: 19 pages, 9 figures, 14 table

Polycyclic aromatic hydrocarbons in ocean sediments from the North Pacific to the Arctic Ocean

Abstract Eighteen polycyclic aromatic hydrocarbons (PAHs) were measured in surficial sediments along a marine transect from the North Pacific into the Arctic Ocean. The highest average Σ18PAHs concentrations were observed along the continental slope of the Canada Basin in the Arctic (68.3 ± 8.5 ng g−1 dw), followed by sediments in the Chukchi Sea shelf (49.7 ± 21.2 ng g−1 dw) and Bering Sea (39.5 ± 11.3 ng g−1 dw), while the Bering Strait (16.8 ± 7.1 ng g−1 dw) and Central Arctic Ocean sediments (13.1 ± 9.6 ng g−1 dw) had relatively lower average concentrations. The use of principal components analysis with multiple linear regression (PCA/MLR) indicated that on average oil related or petrogenic sources contributed ∼42% of the measured PAHs in the sediments and marked by higher concentrations of two methylnaphthalenes over the non-alkylated parent PAH, naphthalene. Wood and coal combustion contributed ∼32%, and high temperature pyrogenic sources contributing ∼26%. Petrogenic sources, such as oil seeps, allochthonous coal and coastally eroded material such as terrigenous sediments particularly affected the Chukchi Sea shelf and slope of the Canada Basin, while biomass and coal combustion sources appeared to have greater influence in the central Arctic Ocean, possibly due to the effects of episodic summertime forest fires

N-Glycosylation-Defective Splice Variants of Neuropilin-1 Promote Metastasis by Activating Endosomal Signals

Neuropilin-1 (NRP1) is an essential transmembrane receptor with a variety of cellular functions. Here, we identify two human NRP1 splice variants resulting from the skipping of exon 4 and 5, respectively, in colorectal cancer (CRC). Both NRP1 variants exhibit increased endocytosis/recycling activity and decreased levels of degradation, leading to accumulation on endosomes. This increased endocytic trafficking of the two NRP1 variants, upon HGF stimulation, is due to loss of N-glycosylation at the Asn150 or Asn261 site, respectively. Moreover, these NRP1 variants enhance interactions with the Met and β1-integrin receptors, resulting in Met/β1-integrin co-internalization and co-accumulation on endosomes. This provides persistent signals to activate the FAK/p130Cas pathway, thereby promoting CRC cell migration, invasion and metastasis. Blocking endocytosis or endosomal Met/β1-integrin/FAK signaling profoundly inhibits the oncogenic effects of both NRP1 variants. These findings reveal an important role for these NRP1 splice variants in the regulation of endocytic trafficking for cancer cell dissemination

Clinical efficacy of Osteoking in knee osteoarthritis therapy: a prospective, multicenter, non-randomized controlled study in China

BackgroundOsteoking has been extensively used for the treatment of knee osteoarthritis (KOA). However, it is lack of high-quality evidence on the clinical efficacy of Osteoking against KOA and the comparison with that of nonsteroidal anti-inflammatory drugs (NSAIDs).AimsTo evaluate the efficacy and safety of Osteoking in treating KOA.MethodsIn the current study, a total of 501 subjects were recruited from 20 medical centers, and were divided into the Osteoking treatment group (n = 428) and the NSAIDs treatment group (n = 73). The Propensity Score Matching method was used to balance baseline data of different groups. Then, the therapeutic effects of Osteoking and NSAIDs against KOA were evaluated using VAS score, WOMAC score, EQ-5D-3L and EQ-VAS, while the safety of the two treatment were both assessed based on dry mouth, dizziness, diarrhea, etc.ResultsAfter 8 weeks of treatment, the Osteoking group was compared with the NSAIDs group, the VAS score [2.00 (1.00, 3.00) vs. 3.00 (2.00, 4.00)], WOMAC pain score [10.00 (8.00, 13.00) vs. 11.00 (8.00, 16.00) ], WOMAC physical function score [32.00 (23.00, 39.00) vs. 39.07 ± 16.45], WOMAC total score [44.00 (31.00, 55.00) vs. 53.31 ± 22.47) ], EQ-5D-3L score [0.91 (0.73, 0.91) vs. 0.73 (0.63, 0.83) ] and EQ-VAS score [80.00 (79.00, 90.00) vs. 80.00 (70.00, 84.00) ] were improved by the treatment of Osteoking for 8 weeks more effectively than that by the treatment of NSAIDs. After 8 weeks of treatment with Osteoking, the VAS scores of KOA patients with the treatment of Osteoking for 8 weeks were reduced from 6.00 (5.00, 7.00) to 2.00 (1.00, 3.00) (p < 0.05), which was better than those with the treatment of NSAIDs starting from 2 weeks during this clinical observation. Importantly, further subgroup analysis revealed that the treatment of Osteoking was more suitable for alleviating various clinical symptoms of KOA patients over 65 years old, with female, KL II-III grade and VAS 4-7 scores, while the clinical efficacy of NSAIDs was better in KOA patients under 65 years old and with VAS 8–10 scores. Of note, there were no differences in adverse events and adverse reactions between the treatment groups of the two drugs.ConclusionOsteoking may exert a satisfying efficacy in relieving joint pain and improving life quality of KOA patients without any adverse reactions, especially for patients with KL II-III grades and VAS 4–7 scores.Clinical Trial Registration:https://www.chictr.org.cn/showproj.html?proj=55387, Identifier ChiCTR200003447

Does Serum Uric Acid Mediate Relation between Healthy Lifestyle and Components of Metabolic Syndrome?

A healthy lifestyle is related to metabolic syndrome (MetS), but the mechanism is not fully understood. This study aimed to examine the association of components of MetS with lifestyle in a Chinese population and potential mediation role of serum uric acid (SUA) in the association between lifestyle behaviors and risk of components of MetS. Data were derived from a baseline survey of the Shaanxi urban cohort in the Regional Ethnic Cohort Study in northwest China. The relationship between components of MetS, healthy lifestyle score (HLS), and SUA was investigated by logistic or linear regression. A counterfactual-based mediation analysis was performed to ascertain whether and to what extent SUA mediated the total effect of HLS on components of MetS. Compared to those with 1 or less low-risk lifestyle factors, participants with 4–5 factors had 43.6% lower risk of impaired glucose tolerance (OR = 0.564; 95%CI: 0.408~0.778), 60.8% reduction in risk of high blood pressure (OR = 0.392; 95%CI: 0.321~0.478), 69.4% reduction in risk of hypertriglyceridemia (OR = 0.306; 95%CI: 0.252~0.372), and 47.3% lower risk of low levels of HDL cholesterol (OR = 0.527; 95%CI: 0.434~0.641). SUA mediated 2.95% (95%CI: 1.81~6.16%) of the total effect of HLS on impaired glucose tolerance, 14.68% (95%CI: 12.04~18.85%) on high blood pressure, 17.29% (95%CI: 15.01~20.5%) on hypertriglyceridemia, and 12.83% (95%CI: 10.22~17.48%) on low levels of HDL cholesterol. Increased HLS tends to reduce risk of components of MetS partly by decreasing the SUA level, which could be an important mechanism by which lifestyle influences MetS

Is Increasing Diet Diversity of Animal-Source Foods Related to Better Health-Related Quality of Life among Chinese Men and Women?

Diet plays a crucial role in regulating individuals’ lifestyles and is closely related to health. The intake of animal-sourced foods (ASF) provides the human body with high-quality protein and various micronutrients. This study aimed to investigate whether the diversity of animal foods has a positive impact on the health-related quality of life (HRQoL) among residents. The data came from the Shaanxi baseline survey of the Northwest Chinese Regional Ethnic Cohort Study, which recruited more than 100 thousand participants aged 35 to 74 from five provinces between June 2018 and May 2019. A total of 39,997 participants in Shaanxi (mean age: 50 years; 64% women) were finally included in this current study. The animal source food diet diversity score (ASFDDS) was established based on the frequency of consuming pork, mutton, beef, poultry, seafood, eggs, pure milk, and yogurt. The physical component score (PCS) and mental component score (MCS), ranging from 0 to 100 on the 12-Item Short Form Survey (SF-12), were used to assess participants’ HRQoL. Better PCS/MCS was defined as scores higher than the 90th percentile. The results showed that men had a higher intake of ASF and ASFDDS than women. After adjusting for potential confounders, compared with those who never or rarely consumed animal foods, the likelihood of having better PCS and MCS increased by 16% (OR = 1.16, 95%CI: 1.01–1.34) and 24% (OR = 1.24, 95%CI: 1.03–1.448), respectively, in men with an ASFDDS ≥ 2. In women, a 34% increase (OR = l.34, 95%CI: 116–l.54) likelihood for better PCS was observed for an ASFDDS ≥ 2, but no association was observed for MCS. Increasing each specific animal source’s food intake was associated with better PCS after adjusting for all covariates. However, for MCS, positive associations were only observed in seafood consumption among men and eggs among women. Restricted cubic splines showed a substantial dose-response association between intake frequency of animal-source foods and PCS, both in men and women. The study suggests that a diverse intake of animal-sourced foods can potentially improve the HRQoL of Chinese adults

An immune dysfunction score for stratification of patients with acute infection based on whole-blood gene expression

Dysregulated host responses to infection can lead to organ dysfunction and sepsis, causing millions of global deaths each year. To alleviate this burden, improved prognostication and biomarkers of response are urgently needed. We investigated the use of whole-blood transcriptomics for stratification of patients with severe infection by integrating data from 3149 samples from patients with sepsis due to community-acquired pneumonia or fecal peritonitis admitted to intensive care and healthy individuals into a gene expression reference map. We used this map to derive a quantitative sepsis response signature (SRSq) score reflective of immune dysfunction and predictive of clinical outcomes, which can be estimated using a 7- or 12-gene signature. Last, we built a machine learning framework, SepstratifieR, to deploy SRSq in adult and pediatric bacterial and viral sepsis, H1N1 influenza, and COVID-19, demonstrating clinically relevant stratification across diseases and revealing some of the physiological alterations linking immune dysregulation to mortality. Our method enables early identification of individuals with dysfunctional immune profiles, bringing us closer to precision medicine in infection.peer-reviewe