Noninvasive, microbiome-based diagnosis of inflammatory bowel disease.

Despite recent progress in our understanding of the association between the gut microbiome and inflammatory bowel disease (IBD), the role of microbiome biomarkers in IBD diagnosis remains underexplored. Here we developed a microbiome-based diagnostic test for IBD. By utilization of metagenomic data from 5,979 fecal samples with and without IBD from different geographies and ethnicities, we identified microbiota alterations in IBD and selected ten and nine bacterial species for construction of diagnostic models for ulcerative colitis and Crohn's disease, respectively. These diagnostic models achieved areas under the curve >0.90 for distinguishing IBD from controls in the discovery cohort, and maintained satisfactory performance in transethnic validation cohorts from eight populations. We further developed a multiplex droplet digital polymerase chain reaction test targeting selected IBD-associated bacterial species, and models based on this test showed numerically higher performance than fecal calprotectin in discriminating ulcerative colitis and Crohn's disease from controls. Here we discovered universal IBD-associated bacteria and show the potential applicability of a multibacteria biomarker panel as a noninvasive tool for IBD diagnosis.

Loading Dyes into Chiral Cd/Zn-Metal-Organic Frameworks for Efficient Full-Color Circularly Polarized Luminescence.

Host-guest chemistry of chiral metal-organic frameworks (MOFs) has endowed them with circularly polarized luminescence (CPL), it is still limited for MOFs to systematically tune full-color CPL emissions and sizes. This work directionally assembles the chiral ligands, metal sites and organic dyes to prepare a series of crystalline enantiomeric D/L-Cd/Zn-n MOFs (n = 1 ~ 5, representing the adding amount of dyes), where D/L-Cd/Zn with the formula of Cd2(D/L-Cam)2(TPyPE) and Zn2(D/L-Cam)2(TPyPE) (D/L-Cam = D/L-camphoric acid, TPyPE = 4,4',4'',4'''-(1,2-henediidenetetra-4,1-phenylene)tetrakis[pyridine]) were used as the chiral platforms.  The framework-dye-enabled emission and through-space chirality transfer facilitate D/L-Cd/Zn-n bright full-color CPL activity. The ideal yellow CPL of D-Cd-5 and D-Zn-4, with |glum| as 4.9 × 10-3 and 1.3 × 10-3 and relatively high photoluminescence quantum yield of 40.79% and 45.40%, are further assembled into a white CPL light-emitting diode. The crystal sizes of D/L-Cd/Zn-n were found to be strongly correlated to the types and additional amounts of organic dyes, that the positive organic dyes allow for the preparation of > 7 mm bulks and negative dyes account for sub-20 µm particles. This work opens a new avenue to fabricate full-color emissive CPL composites and provides a potentially universal method for controlling the size of optical platforms.

ABCDE assessment for palliative care truth-telling dilemmas: a case study.

BACKGROUND: In Indonesia, the diagnosis of a serious illness is often mediated through the patient's family, reflecting the cultural importance of family involvement in the patient's care and collective decision-making. AIM: To use a case study to show the difficulty that healthcare professionals face telling the patient the truth about their condition in Indonesia. METHOD: The Kagawa-Singer and Blackhall ABCDE framework was used during truth-telling dilemmas to assess patients' and families' attitudes (A), beliefs (B), contexts (C), decision-making styles (D) and environments (E). FINDINGS: Studies have shown that family involvement in health-related communications can alleviate the stress associated with the disclosure of a serious illness. Palliative care nurses must acknowledge the importance of family in the patient's cultural context, by involving them in the disclosure of a diagnosis and disease trajectory by integrating every element of the ABCDE model in palliative care.

The multinomial mixed-effect regression model for predicting PCOC phases in hospice patients.

PURPOSE: The Palliative Care Outcomes Collaboration (PCOC) aims to enhance patient outcomes systematically. However, identifying crucial items and accurately determining PCOC phases remain challenging. This study aims to identify essential PCOC data items and construct a prediction model to accurately classify PCOC phases in terminal patients. METHODS: A retrospective cohort study assessed PCOC data items across four PCOC phases: stable, unstable, deteriorating, and terminal. From July 2020 to March 2023, terminal patients were enrolled. A multinomial mixed-effect regression model was used for the analysis of multivariate PCOC repeated measurement data. RESULTS: The dataset comprised 1933 terminally ill patients from 4 different hospice service settings. A total of 13,219 phases of care were analyzed. There were significant differences in the symptom assessment scale, palliative care problem severity score, Australia-modified Karnofsky performance status, and resource utilization groups-activities of daily living among the four PCOC phases of care. Clinical needs, including pain and other symptoms, declined from unstable to terminal phases, while psychological/spiritual and functional status for bed mobility, eating, and transfers increased. A robust prediction model achieved areas under the curves (AUCs) of 0.94, 0.94, 0.920, and 0.96 for stable, unstable, deteriorating, and terminal phases, respectively. CONCLUSIONS: Critical PCOC items distinguishing between PCOC phases were identified, enabling the development of an accurate prediction model. This model enhances hospice care quality by facilitating timely interventions and adjustments based on patients' PCOC phases.

The ubiquitin E3 ligase RZFP1 affects drought tolerance in poplar by mediating the degradation of the protein phosphatase PP2C-9.

Abscisic acid signaling has been implicated in plant responses to water deficit-induced osmotic stress. However, the underlying molecular mechanism remains unelucidated. This study identified the RING-type E3 ubiquitin ligase RING ZINC FINGER PROTEIN1 (PtrRZFP1) in poplar (Populus trichocarpa), a woody model plant. PtrRZFP1 encodes a ubiquitin E3 ligase that participates in protein ubiquitination. PtrRZFP1 mainly functions in the nucleus and endoplasmic reticulum and is activated by drought and abscisic acid. PtrRZFP1-overexpressing transgenic poplars (35S:PtrRZFP1) showed greater tolerance to drought, whereas PtrRZFP1-knockdown lines (KD-PtrRZFP1) showed greater sensitivity to drought. Under treatment with polyethylene glycol and abscisic acid, PtrRZFP1 promoted the production of NO and H2O2 in stomatal guard cells, ultimately enhancing stomatal closure and improving drought tolerance. Additionally, PtrRZFP1 physically interacted with the clade A Protein Phosphatase 2C protein PtrPP2C-9, a core regulator of abscisic acid signaling, and mediated its ubiquitination and eventual degradation through the ubiquitination-26S proteasome system, indicating that PtrRZFP1 positively regulates the abscisic acid signaling pathway. Furthermore, the PtrPP2C-9-overexpression line was insensitive to abscisic acid and more sensitive to drought than the wild-type plants, whereas the opposite phenotype was observed in 35S:PtrRZFP1 plants. In general, PtrRZFP1 negatively regulates the stability of PtrPP2C-9 to mediate poplar drought tolerance. The results of this study provide a theoretical framework for the targeted breeding of drought-tolerant traits in perennial woody plants.

6-Thioguanine nucleotide levels are associated with infliximab but not adalimumab levels in inflammatory bowel disease patients on combination therapy.

BACKGROUND: Thiopurine co-therapy with anti-tumour necrosis factor-alpha (anti-TNFα) agents is associated with higher anti-TNFα drug levels and reduced immunogenicity in inflammatory bowel disease (IBD). AIMS: We aimed to evaluate the association between 6-thioguanine nucleotide (6-TGN) and anti-TNFα levels and the optimal 6-TGN threshold level associated with higher anti-TNFα levels in combination therapy. METHODS: We performed a retrospective cross-sectional multicentre study of patients with IBD on combination anti-TNFα and thiopurine maintenance therapy between January 2015 and August 2021. Primary outcomes were infliximab and adalimumab levels. Secondary outcomes were antibodies to infliximab (ATI) or adalimumab (ATA). Univariable and multivariable linear regression were performed to identify variables associated with anti-TNFα levels. Receiver operator characteristic curves were used to define the optimal 6-TGN cut-off levels associated with therapeutic anti-TNFα levels. RESULTS: The study included 743 paired 6-TGN and anti-TNFα levels (640 infliximab and 103 adalimumab). 6-TGN levels were associated with infliximab levels, but not adalimumab levels, on univariable and multivariable regression. The optimal 6-TGN cut-off associated with therapeutic infliximab levels (≥5 mcg/mL) was 261 pmol/8 × 108 red blood cell (RBC) (area under the curve (AUC) = 0.57) for standard infliximab dosing and 227.5 pmol/8 × 108 RBC (AUC = 0.58) for escalated dosing. For therapeutic adalimumab levels (≥7.5 mcg/mL), the 6-TGN cut-off was 218.5 pmol/8 × 108 RBC (AUC = 0.59) for standard adalimumab dosing and 237.5 pmol/8 × 108 RBC (AUC = 0.63) for escalated dosing. CONCLUSION: 6-TGN levels were weakly associated with infliximab but not adalimumab levels in combination therapy. 6-TGN levels in the lower end of the therapeutic range (230-260 pmol/8 × 108 RBC) may be adequate to maintain higher infliximab levels, particularly with escalated infliximab dosing.

Management of Crohn's disease in Taiwan: consensus guideline of the Taiwan Society of Inflammatory Bowel Disease updated in 2023.

Crohn's disease (CD) is a chronic, fluctuating inflammatory condition that primarily affects the gastrointestinal tract. Although the incidence of CD in Taiwan is lower than that in Western countries, the severity of CD presentation appears to be similar between Asia and the West. This observation indicates the urgency for devising revised guidelines tailored to the unique reimbursement system, and patient requirements in Taiwan. The core objectives of these updated guidelines include the updated treatment choices and the integration of the treat-to-target strategy into CD management, promoting the achievement of deep remission to mitigate complications and enhance the overall quality of life. Given the diversity in disease prevalence, severity, insurance policies, and access to medical treatments in Taiwan, a customized approach is imperative for formulating these guidelines. Such tailored strategies ensure that international standards are not only adapted but also optimized to local contexts. Since the inception of its initial guidelines in 2017, the Taiwan Society of Inflammatory Bowel Disease (TSIBD) has acknowledged the importance of continuous revisions for incorporating new therapeutic options and evolving disease management practices. The latest update leverages international standards and recent research findings focused on practical implementation within the Taiwanese healthcare system.

Management of ulcerative colitis in Taiwan: consensus guideline of the Taiwan Society of Inflammatory Bowel Disease updated in 2023.

Ulcerative colitis (UC) is a chronic inflammation of the gastrointestinal tract and is characterized by alternating periods of inflammation and remission. Although UC incidence is lower in Taiwan than in Western countries, its impact remains considerable, demanding updated guidelines for addressing local healthcare challenges and patient needs. The revised guidelines employ international standards and recent research, emphasizing practical implementation within the Taiwanese healthcare system. Since the inception of the guidelines in 2017, the Taiwan Society of Inflammatory Bowel Disease has acknowledged the need for ongoing revisions to incorporate emerging therapeutic options and evolving disease management practices. This updated guideline aims to align UC management with local contexts, ensuring comprehensive and context-specific recommendations, thereby raising the standard of care for UC patients in Taiwan. By adapting and optimizing international protocols for local relevance, these efforts seek to enhance health outcomes for patients with UC.

Chromosome-level genome assembly of an oligophagous leaf beetle Ophraella communa (Coleoptera: Chrysomelidae).

The leaf beetle Ophraella communa LeSage (Coleoptera: Chrysomelidae) is an effective biological control agent of the common ragweed. Here, we assembled a chromosome-level genome of the O. communa by combining Illumina, Nanopore, and Hi-C sequencing technologies. The genome size of the final genome assembly is 733.1 Mb, encompassing 17 chromosomes, with an improved contig N50 of 7.05 Mb compared to the original version. Genome annotation reveals 25,873 protein-coding genes, with functional annotations available for 22,084 genes (85.35%). Non-coding sequence annotation identified 204 rRNAs, 626 tRNAs, and 1791 small RNAs. Repetitive elements occupy 414.41 Mb, constituting 57.76% of the genome. This high-quality genome is fundamental for advancing biological control strategies employing O. communa.

[Progress in enrichment methods for protein N-phosphorylation].

Protein phosphorylation is one of the most common and important post-translational modifications that regulates almost all life processes. In particular, protein phosphorylation regulates the development of major diseases such as tumors, neurodegenerative diseases, and diabetes. For example, excessive phosphorylation of Tau protein can cause neurofibrillary tangles, leading to Alzheimer's disease. Therefore, large-scale methods for identifying protein phosphorylation must be developed. Rapid developmentin efficient enrichment methods and biological mass spectrometry technologies have enabled the large-scale identification of low-abundance protein O-phosphorylation modifications in, allowing for a more thorough study of their biological functions. The N-phosphorylation modifications that occur on the side-chain amino groups of histidine, arginine, and lysine have recently received increased attention. For example, the biological function of histidine phosphorylation in prokaryotes has been well studied; this type of modification regulates signal transduction and sugar metabolism. Two mammalian pHis kinases (NME1 and NME2) and three pHis phosphatases (PHPT1, LHPP, and PGAM5) have been successfully identified using various biological methods. N-Phosphorylation is involved in multiple biological processes, and its functions cannot be ignored. However, N-phosphorylation is unstable under acidic and thermal conditions owing to the poor chemical stability of the P-N bond. Unfortunately, the current O-phosphorylation enrichment method, which relies on acidic conditions, is unsuitable for N-phosphorylation enrichment, resulting in a serious lag in the large-scale identification of protein N-phosphorylation. The lack of enrichment methods has also seriously hindered studies on the biological functions of N-phosphorylation. Therefore, the development of efficient enrichment methods that target protein N-phosphorylation is an urgent undertaking. Research on N-phosphorylation proteome enrichment methods is limited, hindering functional research. Thus, summarizing such methods is necessary to promote further functional research. This article introduces the structural characteristics and reported biological functions of protein N-phosphorylation, reviews the protein N-phosphorylation modification enrichment methods developed over the past two decades, and analyzes the advantages and disadvantages of each method. In this study, both antibody-based and nonantibody-dependent methods are described in detail. Owing to the stability of the molecular structure of histidine, the antibody method is currently limited to histidine phosphorylation enrichment research. Future studies will focus on the development of new enrichment ligands. Moreover, research on ligands will promote studies on other nonconventional phosphorylation targets, such as two acyl-phosphates (pAsp, pGlu) and S-phosphate (pCys). In summary, this review provides a detailed analysis of the history and development directions of N-phosphorylation enrichment methods.

Validation of Database Autopsy for Review of Pregnancy-Associated Deaths in Canada.

The database autopsy method was developed to determine probable causes of maternal deaths in the Canadian Institute for Health Information's hospital discharge abstract database; however, the method has yet to be validated. Using immediate cause of death information from Québec's hospitalization database as the gold standard, this study assessed the validity and reliability of the database autopsy method for pregnancy-associated deaths. The method had high sensitivity and specificity for identifying the most common causes of these deaths, as well as high interobserver agreement. We conclude that the database autopsy method is valid and reliable overall.

A randomised controlled test in virtual reality of the effects on paranoid thoughts of virtual humans' facial animation and expression.

Virtual reality (VR) is increasingly used in the study and treatment of paranoia. This is based on the finding that people who mistakenly perceive hostile intent from other people also perceive similar threat from virtual characters. However, there has been no study of the programming characteristics of virtual characters that may influence their interpretation. We set out to investigate how the animation and expressions of virtual humans may affect paranoia. In a two-by-two factor, between-groups, randomized design, 122 individuals with elevated paranoia rated their perceptions of virtual humans, set in an eye-tracking enabled VR lift scenario, that varied in facial animation (static or animated) and expression (neutral or positive). Both facial animation (group difference = 102.328 [51.783, 152.872], p < 0.001, η p 2 = 0.125) and positive expressions (group difference = 53.016 [0.054, 105.979], p = 0.049, η p 2 = 0.033) led to less triggering of paranoid thoughts about the virtual humans. Facial animation (group difference = 2.442 [- 4.161, - 0.724], p = 0.006, η p 2 = 0.063) but not positive expressions (group difference = 0.344 [- 1.429, 2.110], p = 0.681, η p 2 = 0.001) significantly increased the likelihood of neutral thoughts about the characters. Our study shows that the detailed programming of virtual humans can impact the occurrence of paranoid thoughts in VR. The programming of virtual humans needs careful consideration depending on the purpose of their use.

PuERF008-PuFAD2 module regulates aroma formation via the fatty acid pathway in response to calcium signaling in 'Nanguo' pear.

Calcium acts as a secondary messenger in plants and is essential for plant growth and development. However, studies on the pathway of aroma synthesis in 'Nanguo' pear (Pyrus ussriensis Maxim.) are scarce. In this study, a bioinformatics analysis of transcriptomic data from calcium-treated 'Nanguo' pear was performed, which identified two fatty acid desaturases, PuFAD2 and PuFAD3, and eight AP2/ERF transcription factors, all exhibiting the same expression patterns. Transient expression experiments showed overexpression of PuFAD2 and PuFAD3 significantly increased the levels of aromatic substrates linoleic acid, hexanal, linolenic acid, and (E)-2-hexenal, but RNAi (RNA interference) had the opposite expression. Promoter sequences analysis revealed that PuFAD2 and PuFAD3 have ERE (estrogen response element) motifs on their promoters. The strongest activation of PuFAD2 by PuERF008 was verified using a dual-luciferase reporting system. Additionally, yeast one-hybrid and electrophoretic mobility shift assays revealed PuERF008 could active PuFAD2. Transient overexpression and RNAi analyses of PuERF008 showed a strong correlation with the expression of PuFAD2. This study provides insights into the process of aroma biosynthesis in 'Nanguo' pear and offers a theoretical basis for elucidating the role of calcium signaling in aroma synthesis.

Is systemic lupus erythematosus linked to Immunoglobulin G4 Autoantibodies?

Systemic lupus erythematosus (SLE) is a systemic autoimmune disorder characterized by a hyperactive immune system with multiple abnormalities in B-cell proliferation, antibody production, T-cell regulation, and immune complex (IC) formation. In humans, Immunoglobulin (Ig) G is found in four subclasses. IgG1-IgG4, which are distinguished by both structural and biological differences. Fab-arm Exchange (FAE), specific biases in the IgG4 response repertoire, and a decreased capacity to induce effector functions mediated by interactions in the fragment crystallizable (Fc) region are just a few of the distinctive characteristics of IgG4. The recent finding of the presence of double-stranded DNA (dsDNA) and antinuclear antibody (ANA)-IgG4 has raised attention to this IgG subclass and its possible role in SLE. IgG4 was previously believed to just have anti-inflammatory effects by inhibiting immune responses, but recent studies have shown that these antibodies can also play a role in the onset and development of some clinical disorders. To consider the clinical effects of IgG4 presence, it is necessary to discuss its characteristics, which could underlie the potential role it can play in SLE. Therefore, this study aimed to comprehensively review the role of IgG4 in SLE to elucidate the collective incidence of high IgG4 levels reported in some SLE patients.

Assisted Reproductive Technology During COVID-19: A Population-Based Study Of Pregnancy Outcomes.

We assessed the impact of the COVID-19 pandemic on the pregnancy outcomes of patients who used assisted reproductive technology. We conducted a population-based cohort study of 443,101 patients who conceived naturally or with assisted reproductive technology between December 2015 and July 2021 and had a delivery in hospitals of Quebec, Canada. The main exposure measure was use of assisted reproductive technology before or during the pandemic. Outcomes included preeclampsia, preterm birth, and other pregnancy complications. We used adjusted log-binomial regression models to estimate risk ratios (RR) and 95% confidence intervals (CI) for the association of assisted reproductive technology with adverse pregnancy outcomes compared with natural conception before vs. during the pandemic. In secondary analyses, we examined the association of COVID-19 infection with pregnancy outcomes among women who used assisted reproductive technology. Compared with natural conception, assisted reproductive technology was associated with an increased risk of preeclampsia (RR 1.43; 95% CI 1.21-1.68), preterm birth (RR 2.07; 95% CI 1.84-2.33), and low birth weight (RR 1.94; 95% CI 1.72-2.20) during the pandemic. However, the same risks were also present before the pandemic. Compared with no infection, COVID-19 infection was not associated with adverse outcomes among women who conceived with assisted reproductive technology. This study suggests that the COVID-19 pandemic did not significantly impact the pregnancy outcomes of women who underwent assisted reproductive procedures in Quebec. The findings are reassuring for patients concerned about the potential reproductive effects of the pandemic.

Chromosome-level genome assembly of the two-spotted spider mite Tetranychus urticae.

The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a notorious pest in agriculture that has developed resistance to almost all chemical types used for its control. Here, we assembled a chromosome-level genome for the TSSM using Illumina, Nanopore, and Hi-C sequencing technologies. The assembled contigs had a total length of 103.94 Mb with an N50 of 3.46 Mb, with 87.7 Mb of 34 contigs anchored to three chromosomes. The chromosome-level genome assembly had a BUSCO completeness of 94.8%. We identified 15,604 protein-coding genes, with 11,435 genes that could be functionally annotated. The high-quality genome provides invaluable resources for the genetic and evolutionary study of TSSM.

Chromosome-level genome assembly of the western flower thrips Frankliniella occidentalis.

The western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) is a global invasive species that causes increasing damage by direct feeding on crops and transmission of plant viruses. Here, we assemble a previously published scaffold-level genome into a chromosomal level using Hi-C sequencing technology. The assembled genome has a size of 302.58 Mb, with a contig N50 of 1533 bp, scaffold N50 of 19.071 Mb, and BUSCO completeness of 97.8%. All contigs are anchored on 15 chromosomes. A total of 16,312 protein-coding genes are annotated in the genome with a BUSCO completeness of 95.2%. The genome contains 492 non-coding RNA, and 0.41% of interspersed repeats. In conclusion, this high-quality genome provides a convenient and high-quality resource for understanding the ecology, genetics, and evolution of thrips.

Stem Cell Division and Its Critical Role in Mammary Gland Development and Tumorigenesis: Current Progress and Remaining Challenges.

The origin of breast cancer (BC) has traditionally been a focus of medical research. It is widely acknowledged that BC originates from immortal mammary stem cells and that these stem cells participate in two division modes: symmetric cell division (SCD) and asymmetrical cell division (ACD). Although both of these modes are key to the process of breast development and their imbalance is closely associated with the onset of BC, the molecular mechanisms underlying these phenomena deserve in-depth exploration. In this review, we first outline the molecular mechanisms governing ACD/SCD and analyze the role of ACD/SCD in various stages of breast development. We describe that the changes in telomerase activity, the role of polar proteins, and the stimulation of ovarian hormones subsequently lead to two distinct consequences: breast development or carcinogenesis. Finally, gene mutations, abnormalities in polar proteins, modulation of signal-transduction pathways, and alterations in the microenvironment disrupt the balance of BC stem cell division modes and cause BC. Important regulatory factors such as mammalian Inscuteable mInsc, Numb, Eya1, PKCα, PKCθ, p53, and IL-6 also play significant roles in regulating pathways of ACD/SCD and may constitute key targets for future research on stem cell division, breast development, and tumor therapy.

Nuclear and mitochondrial genomes of the plum fruit moth Grapholita funebrana.

The plum fruit moth Grapholita funebrana (Tortricidae, Lepidoptera) is an important pest of many wild and cultivated stone fruits and other plants in the family Rosaceae. Here, we assembled its nuclear and mitochondrial genomes using Illumina, Nanopore, and Hi-C sequencing technologies. The nuclear genome size is 570.9 Mb, with a repeat rate of 51.28%, and a BUCSO completeness of 97.7%. The karyotype for males is 2n = 56. We identified 17,979 protein-coding genes, 5,643 tRNAs, and 94 rRNAs. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomes provide resources to understand the genetics, ecology, and genome evolution of the tortricid moths.