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Background: Systemic lupus erythematosus (SLE) is distinguished by an extensive range of clinical heterogeneity with unpredictable disease flares and organ damage. This research investigates the potential of aberrant signatures on T cell genes, soluble Co-IRs/ligands, and Co-IRs expression on T cells as biomarkers for lupus disease parameters., Methods: Comparative transcriptome profiling analysis of non-renal and end-stage renal disease (ESRD) phenotypes of SLE was performed using CD4 + and CD8 + cDNA microarrays of sorted T cells. Comparing the expression of Co-IRs on T cells and serum soluble mediators among healthy and SLE phenotypes., Results: SLE patients with ESRD were downregulated CD38, PLEK, interferon-γ, CX3CR1, FGFBP2, and SLCO4C1 transcripts on CD4 + and CD8 + T cells simultaneously and NKG7, FCRL6, GZMB/H, FcγRIII, ITGAM, Fas ligand, TBX21, LYN, granulysin, CCL4L1, CMKLR1, HLA-DRβ, KIR2DL3, and KLRD1 in CD8 T cells. Pathway enrichment and PPI network analyses revealed that the overwhelming majority of Differentially Expressed Genes (DEGs) have been affiliated with novel cytotoxic, antigen presentation, and chemokine-cell migration signature pathways. CD8 + GZMK + T cells that are varied in nature, including CD161 + Mucosal-associated invariant T (MAIT) cells and CD161- aged-associated T (Taa) cells and CD161-GZMK + GZMB + T cells might account for a higher level of GZMK in CD8 + T cells associated with ESRD. SLE patients have higher TIGIT + , PD1 + , and lower CD127 + cell percentages on CD4 + T cells, higher TIM3 + , TIGIT + , HLA-DR + cell frequency, and lower MFI expression of CD127, CD160 in CD8 T cells. Co-IRs expression in T cells was correlated with soluble PD-1, PDL-2, and TIM3 levels, as well as SLE disease activity, clinical phenotypes, and immune-therapy responses., Conclusion: The signature of dysfunctional pathways defines a distinct immunity pattern in LN ESRD patients. Expression levels of Co-IRs in peripheral blood T cells and serum levels of soluble PD1/PDL-2/TIM3 can serve as biomarkers for evaluating clinical parameters and therapeutic responses., (© 2024. The Author(s).)

Introduction: Natural killer/T cell lymphoma (NKTL) is an aggressive malignancy associated with poor prognosis. This is largely due to limited treatment options, especially for relapsed patients. Immunotherapies like immune checkpoint inhibitors (ICI) and anti-CD38 therapies have shown promising but variable clinical efficacies. Combining these therapies has been suggested to enhance efficacy., Methods: We conducted a case study on a relapsed NKTL patient treated sequentially with anti-CD38 followed by ICI (anti-PD1) using cytometry analyses., Results and Discussion: Our analysis showed an expected depletion of peripheral CD38+ B cells following anti-CD38 treatment. Further analysis indicated that circulating anti-CD38 retained their function for up to 13 weeks post-administration. Anti-PD1 treatment triggered re-activation and upregulation of CD38 on the T cells. Consequently, these anti-PD1-activated T cells were depleted by residual circulating anti-CD38, rendering the ICI treatment ineffective. Finally, a meta-analysis confirmed this counterproductive effect, showing a reduced efficacy in patients undergoing combination therapy. In conclusion, our findings demonstrate that sequential anti-CD38 followed by anti-PD1 therapy leads to a counterproductive outcome in NKTL patients. This suggests that the treatment sequence is antithetic and warrants re-evaluation for optimizing cancer immunotherapy strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lee, Lim, Tang, Tan, Koh, Puan, Wang, Lim, Tan, Chng, Lim, Ong and Rotzschke.)

As the principal ligand for NKG2D, MICA elicits the recruitment of subsets of T cells and NK cells in innate immunity. MICA gene variants greatly impact the functionality and expression of MICA in humans. The current study evaluated whether MICA polymorphisms distinctively influence the pathogenesis of psoriasis (PSO), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE) in Taiwanese subjects. The distributions of MICA alleles and levels of serum soluble NKG2D were compared between healthy controls and patients with PSO, RA, and SLE, respectively. The binding capacities and cell surface densities of MICA alleles were assessed by utilizing stable cell lines expressing four prominent Taiwanese MICA alleles. Our data revealed that MICA *010 was significantly associated with risks for PSO and RA (P FDR = 1.93 × 10 -15 and 0.00112, respectively), while MICA *045 was significantly associated with predisposition to SLE (P FDR = 0.0002). On the other hand, MICA *002 was associated with protection against RA development (P FDR = 4.16 × 10 -6 ), while MICA *009 was associated with a low risk for PSO (P FDR = 0.0058). MICA *002 exhibited the highest binding affinity for NKG2D compared to the other MICA alleles. Serum concentrations of soluble MICA were significantly elevated in SLE patients compared to healthy controls ( p = 0.01). The lack of cell surface expression of the MICA *010 was caused by its entrapment in the endoplasmic reticulum. As a prevalent risk factor for PSO and RA, MICA *010 is deficient in cell surface expression and is unable to interact with NKG2D. Our study suggests that MICA alleles distinctively contribute to the pathogenesis of PSO, RA, and SLE in Taiwanese people.

Aims: To explore stakeholders' perceptions of a facilitator's role in supporting carers when embedding iSupport for Dementia psychoeducation program, in care services., Methods: A qualitative descriptive study design was applied. Data were collected from workshops and interviews with carers of people living with dementia (PLWD)and with health and social care professionals from two tertiary hospitals and two community aged care organisations across three Australian states between October 2021 and March 2022. A thematic analysis was used to analyse data. The COREQ guideline was followed to report our findings., Results: A total of 30 family carers and 45 health and social care professionals participated in the study. Three main themes and seven subthemes were identified from the data. We described the main themes as (1) the facilitator's role at the time of dementia diagnosis, (2) the facilitator's role throughout the everyday dementia care journey and (3) the facilitator's role during transition moments., Conclusions: Caring for family members with dementia is demanding and stressful for carers. Embedding a facilitator-enabled iSupport for Dementia program in hospital and community aged care settings has the potential to mitigate sources of stress associated with care recipient factors, carer factors and care service factors, and improve the health and well-being of carers and those for whom they care., Relevance to Clinical Practice: Our findings will inform the establishment of iSupport facilitators appointed by dementia care providers in hospital and community care settings and help determine their roles and responsibilities in delivering the iSupport program. Our findings relate to nurse-led and coordinated dementia care in hospital and community aged care settings., Patient or Public Contribution: This study was co-designed with stakeholders from two aged care organisations and two tertiary hospitals. The study participants were staff employed by these organisations and carers of PLWD who were service users., (© 2023 The Authors. Journal of Clinical Nursing published by John Wiley & Sons Ltd.)

Objective: Distress is prevalent among lymphoma patients/survivors. Current processes of distress identification rely on self-reporting by patients/survivors, which may be limited by their willingness to report symptoms. To help identify patients/survivors at greater risk, this systematic review aims to comprehensively review factors that may contribute to distress in lymphoma patients/survivors., Methods: PubMed was systematically searched for peer-reviewed primary articles (1997-2022) consisting of standardised keywords "lymphoma" and "distress." Information from 41 articles was integrated via narrative synthesis., Results: Consistent risk factors of distress include younger age, relapsed disease, and greater comorbidities and symptom burden. Active treatment and the transition from treatment to post-treatment could be challenging phases. Adequate social support, adaptive adjustment to cancer, engaging in work and healthcare professionals' support may mitigate distress. There is some evidence that older age may be associated with greater depression and life changes/experiences may shape how individuals cope with lymphoma. Gender and marital status were not robust predictors of distress. Other clinical, psychological and socioeconomic factors are understudied or have mixed findings., Conclusions: While several factors of distress align with that of other cancers, more research is needed to identify significant factors of distress in lymphoma patients/survivors. The identified factors may support clinicians in identifying distressed lymphoma patients/survivors and providing interventions where necessary. The review also highlights avenues for future research and a need to routinely collect data on distress and its factors in registries., (© 2023 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.)

Caregivers of People with dementia (PwD) commonly experience burdens and other mental health issues, e.g., depression and anxiety. At present, there are limited studies that examine the relationships between caregiver psychological factors and caregiver burden, and depressive and anxiety symptoms. Therefore, this study's objectives were to examine the relationships between psychological flexibility and mindfulness in caregivers of PwD, and to determine the predictors of these three outcomes. This was a cross-sectional study conducted in the geriatric psychiatry clinic of Kuala Lumpur Hospital, Malaysia, and the sample ( n = 82) was recruited via a universal sampling method over three months. The participants completed a questionnaire that consisted of the sociodemographics of the PwD and caregivers, illness characteristics of the PwD, Acceptance and Action Questionnaire-II (AAQ-II), Mindful Attention Awareness Scale (MAAS), Zarit Burden Interview Scale (ZBI), Patient Health Questionnaire-9 (PHQ-9) and Generalized Anxiety Disorder-7 (GAD-7). The results show that despite significant relationships between psychological flexibility and mindfulness and lower levels of caregiver burden, and depressive and anxiety symptoms ( p < 0.01), only psychological inflexibility ( p < 0.01) remained as a significant predictor of the three outcomes. Therefore, in conclusion, intervention programs that target the awareness of the caregiver's psychological inflexibility should be implemented to alleviate these adverse outcomes in dementia caregivers.

Severe SARS-CoV-2 infection can trigger uncontrolled innate and adaptive immune responses, which are commonly associated with lymphopenia and increased neutrophil counts. However, whether the immune abnormalities observed in mild to severely infected patients persist into convalescence remains unclear. Herein, comparisons were drawn between the immune responses of COVID-19 infected and convalescent adults. Strikingly, survivors of severe COVID-19 had decreased proportions of NKT and Vδ2 T cells, and increased proportions of low-density neutrophils, IgA+/CD86+/CD123+ non-classical monocytes and hyperactivated HLADR+CD38+ CD8+ T cells, and elevated levels of pro-inflammatory cytokines such as hepatocyte growth factor and vascular endothelial growth factor A, long after virus clearance. Our study suggests potential immune correlates of "long COVID-19", and defines key cells and cytokines that delineate true and quasi-convalescent states., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Lim, Puan, Wang, Teng, Loh, Tan, Carissimo, Chan, Poh, Lee, Fong, Yeo, Chee, Amrun, Chang, Tay, Torres-Ruesta, Leo Fernandez, How, Andiappan, Lee, Duan, Tan, Yan, Kalimuddin, Lye, Leo, Ong, Young, Renia, Ng, Lee and Rötzschke.)

Covid-19 pandemic and the public health measure have forced an en masse transition to remote therapy from physical sessions. Remote psychodynamic psychotherapy is not a new treatment modality, but its effectiveness in holding the analytic frame has been concerned by some therapists. We would like to highlight some of the therapeutic processes involved with remote psychodynamic psychotherapy, via the help of a narrative experience of a psychiatry trainee who was novice to this delivery method of therapy. Reflections on these concerns have been made in line with the experiences highlighted., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Predicting the functional consequences of single point mutations has relevance to protein function annotation and to clinical analysis/diagnosis. We developed and tested Packpred that makes use of a multi-body clique statistical potential in combination with a depth-dependent amino acid substitution matrix (FADHM) and positional Shannon entropy to predict the functional consequences of point mutations in proteins. Parameters were trained over a saturation mutagenesis data set of T4-lysozyme (1,966 mutations). The method was tested over another saturation mutagenesis data set (CcdB; 1,534 mutations) and the Missense3D data set (4,099 mutations). The performance of Packpred was compared against those of six other contemporary methods. With MCC values of 0.42, 0.47, and 0.36 on the training and testing data sets, respectively, Packpred outperforms all methods in all data sets, with the exception of marginally underperforming in comparison to FADHM in the CcdB data set. A meta server analysis was performed that chose best performing methods of wild-type amino acids and for wild-type mutant amino acid pairs. This led to an increase in the MCC value of 0.40 and 0.51 for the two meta predictors, respectively, on the Missense3D data set. We conjecture that it is possible to improve accuracy with better meta predictors as among the seven methods compared, at least one method or another is able to correctly predict ∼99% of the data., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Tan, Kanitkar, Kwoh and Madhusudhan.)

MICA (major histocompatibility complex class I chain-related gene A) interacts with NKG2D on immune cells to regulate host immune responses. We aimed to determine whether MICA alleles are associated with AS susceptibility in Taiwanese. MICA alleles were determined through haplotype analyses of major MICA coding SNP (cSNP) data from 895 AS patients and 896 normal healthy controls in Taiwan. The distributions of MICA alleles were compared between AS patients and normal healthy controls and among AS patients, stratified by clinical characteristics. ELISA was used to determine soluble MICA (sMICA) levels in serum of AS patients and healthy controls. Stable cell lines expressing four major MICA alleles ( MICA * 002 , MICA * 008 , MICA * 010 and MICA * 019 ) in Taiwanese were used for biological analyses. We found that MICA*019 is the only major MICA allele significantly associated with AS susceptibility (P FDR = 2.25 × 10 -115 ; OR, 14.90; 95% CI, 11.83-18.77) in Taiwanese. In addition, the MICA*019 allele is associated with syndesmophyte formation (P FDR = 0.0017; OR, 1.69; 95% CI, 1.29-2.22) and HLA-B27 positivity (P FDR = 1.45 × 10 -33 ; OR, 28.79; 95% CI, 16.83-49.26) in AS patients. Serum sMICA levels were significantly increased in AS patients as compared to healthy controls. Additionally, MICA*019 homozygous subjects produced the highest levels of sMICA, compared to donors with other genotypes. Furthermore, in vitro experiments revealed that cells expressing MICA*019 produced the highest level of sMICA, as compared to other major MICA alleles. In summary, the MICA * 019 allele, producing the highest levels of sMICA, is a significant risk factor for AS and syndesmophyte formation in Taiwanese. Our data indicate that a high level of sMICA is a biomarker for AS.

An extensive database study of hydrogen bonds in different protein environments showed systematic variations in donor-acceptor-acceptor antecedent angle ( Ĥ ) and donor-acceptor distance. Protein environments were characterized by depth (distance of amino acids from bulk solvent), secondary structure, and whether the donor/acceptor belongs to the main chain (MC) or side chain (SC) of amino acids. The MC-MC hydrogen bonds (whether in secondary structures or not) have Ĥ angles tightly restricted to a value of around 155°, which was distinctly different from other Ĥ angles. Quantum chemical calculations attribute this characteristic MC-MC Ĥ angle to the nature of the electron density distribution around the planar peptide bond. Additional classical simulations suggest a causal link between MC-MC Ĥ angle and the conformation of secondary structures in proteins. We also showed that donor-acceptor distances are environment dependent, which has implications on protein stability. Our results redefine hydrogen bond geometries in proteins and suggest useful refinements to existing molecular mechanics force fields., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Author(s).)

Few longitudinal studies are capable of identifying criminal career profiles using both self-report and official court data beyond the 30s. The current study aims to identify criminal career profiles across three developmental periods using self-report data, validate these profiles with official court records and determine early childhood predictors. Data came from the Seattle Social Development Project (n = 808). Latent Class Analysis was used to examine criminal careers from self-reported data during adolescence (aged 14-18), early adulthood (aged 21-27) and middle adulthood (aged 30-39). Official court records were used to validate the classes. Childhood risk and promotive factors measured at ages 11-12 were used to predict classes. Findings revealed four career classes: non-offending (35.6%), adolescence-limited (33.2%), adult desister (18.3%) and life-course/persistent (12.9%). Official court records are consistent with the description of the classes. Early life school and family environments as well as having antisocial beliefs and friends differentiate membership across the classes. The results of this study, with a gender-balanced and racially diverse sample, bolster the current criminal career knowledge by examining multiple developmental periods into the 30s using both self-report and official court data., (© 2020 John Wiley & Sons Ltd.)

Osteoarthritis (OA), one of the most common joint disease, affects more than 80% of the population aged 70 or over. Mesenchymal stem cells (MSCs) show multi-potent differentiation and self-renewal capability, and, after exposure to an inflammatory environment, also exhibit immunosuppressive properties. In this study, we have used a model of lipopolysaccharide (LPS)-stimulated chondrocytes to evaluate MSC anti-inflammatory efficacy. The anti-inflammatory mechanism was tested in two cell-contained culture systems: (i) MSC-chondrocyte indirect contact system and (ii) MSC-chondrocyte direct contact system, and one cytokine-only culture system: MSC-conditioned medium (CM) system. Results showed that MSCs reduced chondrocyte inflammation through both paracrine secretion and cell-to-cell contact. The inflammation-associated, and free-radical-related genes were down-regulated significantly in the direct contact system on 24 h, however, the TNF-α. IL-6 were upregulated and aggrecan, COLII were downregulated on 72 h in direct contact system. Moreover, we found CM produced by MSC possess well therapeutic effect on inflammatory chondorcyte, and the 10-fold concentrated MSC-conditioned medium could down-regulated chondorcyte synthesis inflammation-associated, and free-radical-related genes, such as TNF-α, IL-1β, IL-6 and iNOS even treated for 72 h. In conclusion, MSC-CM showed great potential for MSC-based therapy for OA., Competing Interests: The authors have declared that no competing interests exist.

Recently, we reported that the histone methyltransferase, EZH2, controls leukocyte migration through interaction with the cytoskeleton remodeling effector, VAV, and direct methylation of the cytoskeletal regulatory protein, Talin. However, it is unclear whether this extranuclear, epigenetic-independent function of EZH2 has a profound impact on the initiation of cellular transformation and metastasis. Here, we show that EZH2 increases Talin1 methylation and cleavage, thereby enhancing adhesion turnover and promoting accelerated tumorigenesis. This transforming capacity is abolished by targeted disruption of EZH2 interaction with VAV. Furthermore, our studies demonstrate that EZH2 in the cytoplasm is closely associated with cancer stem cell properties, and that overexpression of EZH2, a mutant EZH2 lacking its nuclear localization signal (EZH2ΔNLS), or a methyl-mimicking Talin1 mutant substantially promotes JAK2-dependent STAT3 activation and cellular transformation. Taken together, our results suggest a critical role for the VAV interaction-dependent, extranuclear action of EZH2 in neoplastic transformation.

The 20 naturally occurring amino acids have different environmental preferences of where they are likely to occur in protein structures. Environments in a protein can be classified by their proximity to solvent by the residue depth measure. Since the frequencies of amino acids are different at various depth levels, the substitution frequencies should vary according to depth. To quantify these substitution frequencies, we built depth dependent substitution matrices. The dataset used for creation of the matrices consisted of 3696 high quality, non redundant pairwise protein structural alignments. One of the applications of these matrices is to predict the tolerance of mutations in different protein environments. Using these substitution scores the prediction of deleterious mutations was done on 3500 mutations in T4 lysozyme and CcdB. The accuracy of the technique in terms of the Matthews Correlation Coefficient (MCC) is 0.48 on the CcdB testing set, while the best of the other tested methods has an MCC of 0.40. Further developments in these substitution matrices could help in improving structure-sequence alignment for protein 3D structure modeling., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Drug-induced cardiotoxicity is the one of the most common causes of drug withdrawal from market. A major barrier in managing the risk of drug-induced cardiotoxicity has been the lack of relevant models to study cardiac safety. Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have great potential in drug discovery and cardiotoxcity screens as they display many characteristics of the human myocardium and offer unlimited supply. This unit describes how to use pluripotent stem cells derived cardiomyocytes to study drug-induced cardiotoxicty using doxorubicin as an example. We present a workflow that explains procedure for editing hPSC using the CRISPR/Cas9 system and for differentiation of hPSC into cardiomyocytes. We also report protocols to study drug effect on ROS production, intracellular calcium concentration, formation of DNA double strand breaks, gene expression and electrophysiological properties of hPSC-CMs. © 2017 by John Wiley & Sons, Inc., (Copyright © 2017 by John Wiley & Sons, Inc.)

Alpha1,2-fucosyltransferases, FUT1 and FUT2, which transfer fucoses onto the terminal galactose of N-acetyl-lactosamine via α1,2-linkage have been shown to be highly expressed in various types of cancers. A few studies have shown the involvement of FUT1 substrates in tumor cell proliferation and migration. Lysosome-associated membrane protein 1, LAMP-1, has been reported to carry alpha1,2-fucosylated Lewis Y (LeY) antigens in breast cancer cells, however, the biological functions of LeY on LAMP-1 remain largely unknown. Whether or not its family member, LAMP-2, displays similar modifications and functions as LAMP-1 has not yet been addressed. In this study, we have presented evidence supporting that both LAMP-1 and 2 are substrates for FUT1, but not FUT2. We have also demonstrated the presence of H2 and LeY antigens on LAMP-1 by a targeted nanoLC-MS(3) and the decreased levels of fucosylation on LAMP-2 by MALDI-TOF analysis upon FUT1 knockdown. In addition, we found that the expression of LeY was substantial in less invasive ER+/PR+/HER- breast cancer cells (MCF-7 and T47D) but negligible in highly invasive triple-negative MDA-MB-231 cells, of which LeY levels were correlated with the levels of LeY carried by LAMP-1 and 2. Intriguingly, we also observed a striking change in the subcellular localization of lysosomes upon FUT1 knockdown from peripheral distribution of LAMP-1 and 2 to a preferential perinuclear accumulation. Besides that, knockdown of FUT1 led to an increased rate of autophagic flux along with diminished activity of mammalian target of rapamycin complex 1 (mTORC1) and enhanced autophagosome-lysosome fusion. This may be associated with the predominantly perinuclear distribution of lysosomes mediated by FUT1 knockdown as lysosomal positioning has been reported to regulate mTOR activity and autophagy. Taken together, our results suggest that downregulation of FUT1, which leads to the perinuclear localization of LAMP-1 and 2, is correlated with increased rate of autophagic flux by decreasing mTOR signaling and increasing autolysosome formation.

Severe acute respiratory syndrome (SARS) led to a life-threatening form of atypical pneumonia in late 2002. Following that, Middle East Respiratory Syndrome (MERS-CoV) has recently emerged, killing about 36% of patients infected globally, mainly in Saudi Arabia and South Korea. Based on a scaffold we reported for inhibiting neuraminidase (NA), we synthesized the analogues and identified compounds with low micromolar inhibitory activity against 3CL(pro) of SARS-CoV and MERS-CoV. Docking studies show that a carboxylate present at either R(1) or R(4) destabilizes the oxyanion hole in the 3CL(pro). Interestingly, 3f, 3g and 3m could inhibit both NA and 3CL(pro) and serve as a starting point to develop broad-spectrum antiviral agents., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Acculturation strategy, a significant predictor of immigrant adaptation, has been under-studied with Asian Americans, in particular, Asian American youth. Using person-oriented latent profile analysis, this study identified acculturation strategies among Korean American early adolescents living in the Midwest. Two-hundred ninety-one families were interviewed in 2007 that included 220 youth (mean age 13, 47.7 % female), along with 272 mothers and 164 fathers (N = 656). They were re-interviewed in 2008 (N = 588). The study found three distinct acculturation strategies: separation (11.8 %, n = 26), integrated bicultural (66.9 %, n = 150), and modest bicultural (21.3 %, n = 44). Integrated bicultural youth reported the strongest sense of ethnic identity and the most favorable characteristics, providing empirical support for the benefit of biculturalism. The findings further suggest that separation may not be as detrimental as previously thought, and modest bicultural-biculturalism that is not fully developed-may in fact be less desirable among Korean American youth.

The most severe form of virus-induced inflammation at the ocular surface is epidemic keratoconjunctivitis (EKC), often caused by group D human adenoviruses (HAdVs). We investigated the dynamics and mechanisms of changes in natural killer (NK) cell types in the human ocular mucosal surface in situ over the course of infection. In the acute phase of infection, the mature CD56(dim)NK cells that comprise a major subpopulation in the normal human conjunctiva are replaced by CD56(bright)NK cells recruited to the ocular surface by chemokines produced by the infected epithelium, and NKG2A-expressing CD56(dim) and CD56(bright) NK cells become the major subpopulations in severe inflammation. These NK cells attracted to the mucosal surface are however incapable of mounting a strong antiviral response because of upregulation of the inhibitory ligand human leukocyte antigen-E (HLA-E) on infected epithelium. Furthermore, group D HAdVs downregulate ligands for activating NK cell receptors, thus rendering even the mature NKG2A(-)NK cells unresponsive, an immune-escape mechanism distinct from other adenoviruses. Our findings imply that the EKC-causing group D HAdVs utilize these multiple pathways to inhibit antiviral NK cell responses in the initial stages of the infection.

High-throughput screening was performed on ∼6800 compounds to identify KR-72039 as an inhibitor of H1N1 and H5N1 neuraminidases (NAs). Structure-activity relationship studies led to 3e, which inhibited H5N1 NA with an IC50 of 2.8 μM and blocked viral replication. Docking analysis shows that compounds bind to loop-430 around the NA active site. Compound 3l additionally inhibited H7N9 NA, making it a dual inhibitor of N1- and N2-type NAs.

Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Aim: This study was performed to determine the accuracy of ultrasound (USG) as compared to mammography (MMG) in detecting breast cancer., Methods: This was a review of patients who had breast imaging and biopsy during an 18-month period. Details of patients who underwent breast biopsy were obtained from the department biopsy record books and imaging request forms. Details of breast imaging findings and histology of lesions biopsied were obtained from the hospital Integrated Radiology Information System (IRIS). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of USG and MMG were calculated with histology as the gold standard., Results: A total of 326 breast lesions were biopsied. Histology results revealed the presence of 74 breast cancers and 252 benign lesions. USG had a sensitivity of 82%, specificity of 84%, PPV = 60%, NPV = 94% and an accuracy of 84%. MMG had a sensitivity of 49%, specificity of 89%, PPV = 53%, NPV = 88% and an accuracy of 81%. A total of 161 lesions which were imaged with both modalities were analyzed to determine the significance in the differences in sensitivity and specificity between USG and MMG. Sensitivity of USG (75%) was significantly higher than sensitivity of MMG (44%) (X(2)1=6.905, p=0.014). Specificity of MMG (91%) was significantly higher than specificity of USG (79%) (X(2)1=27.114, p<0.001). Compared with MMG, the sensitivity of USG was 50% (95% CI 10%-90%) higher in women aged less than 50 years (X(2)1=0.000, p=1.000) and 27% (95% CI 19%-36%) higher in women aged 50 years and above (X(2)1=5.866, p=0.015). Compared with MMG, the sensitivity of USG was 40% (95% CI 10%-70%) higher in women with dense breasts (X(2)1=0.234, p=0.628) and 27% (95% CI 9%-46%) higher in women with non-dense breasts (X(2)1=4.585, p=0.032)., Conclusion: Accuracy of USG was higher compared with MMG. USG was more sensitive than MMG regardless of age group. However, MMG was more specific in those aged 50 years and older. USG was more sensitive and MMG was more specific regardless of breast density. In this study, 20% of breast cancers detected were occult on MMG and seen only on USG.

This study examined the interplay of parental racial-ethnic socialization and youth multidimensional cultural orientations to investigate how they indirectly and directly influence youth depressive symptoms and antisocial behaviors. Using data from the Korean American Families (KAF) Project (220 youths, 272 mothers, and 164 fathers, N = 656), this study tested the relationships concurrently, longitudinally, and accounting for earlier youth outcomes. The main findings include that racial-ethnic socialization is significantly associated with mainstream and ethnic cultural orientation among youth, which in turn influences depressive symptoms (but not antisocial behaviors). More specifically, parental racial-ethnic identity and pride discourage youth mainstream orientation, whereas cultural socialization in the family, as perceived by youth, increases ethnic orientation. These findings suggest a varying impact of racial-ethnic socialization on the multidimensional cultural orientations of youth. Korean language proficiency of youth was most notably predictive of a decrease in the number of depressive symptoms concurrently, longitudinally, and after controlling for previous levels of depressive symptoms. English language proficiency was also associated with a decrease in depressive symptoms, implying a benefit of bilingualism.

Background: In the application of microarray data, how to select a small number of informative genes from thousands of genes that may contribute to the occurrence of cancers is an important issue. Many researchers use various computational intelligence methods to analyzed gene expression data., Results: To achieve efficient gene selection from thousands of candidate genes that can contribute in identifying cancers, this study aims at developing a novel method utilizing particle swarm optimization combined with a decision tree as the classifier. This study also compares the performance of our proposed method with other well-known benchmark classification methods (support vector machine, self-organizing map, back propagation neural network, C4.5 decision tree, Naive Bayes, CART decision tree, and artificial immune recognition system) and conducts experiments on 11 gene expression cancer datasets., Conclusion: Based on statistical analysis, our proposed method outperforms other popular classifiers for all test datasets, and is compatible to SVM for certain specific datasets. Further, the housekeeping genes with various expression patterns and tissue-specific genes are identified. These genes provide a high discrimination power on cancer classification.

Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to the closest bulk water. We consider the non-bulk waters to occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation of cavity sizes is statistically superior to estimates made by CASTp and VOIDOO, and on par with McVol over a data set of 40 cavities. Our calculated cavity volumes correlated best with the experimentally determined destabilization of 34 mutants from five proteins. Some of the cavities identified are capable of binding small molecule ligands. In this study, we have enhanced our depth-based predictions of binding sites by including evolutionary information. We have demonstrated that on a database (LigASite) of ∼200 proteins, we perform on par with ConCavity and better than MetaPocket 2.0. Our predictions, while less sensitive, are more specific and precise. Finally, we use depth (and other features) to predict pKas of GLU, ASP, LYS and HIS residues. Our results produce an average error of just <1 pH unit over 60 predictions. Our simple empirical method is statistically on par with two and superior to three other methods while inferior to only one. The DEPTH server (http://mspc.bii.a-star.edu.sg/depth/) is an ideal tool for rapid yet accurate structural analyses of protein structures.

Objective: Labisia pumila var. alata, commonly known as 'Kacip Fatimah' or 'Selusuh Fatimah' in Southeast Asia, is traditionally used by members of the Malay community because of its post-partum medicinal properties. Its various pharmaceutical applications cause an excessive harvesting and lead to serious shortage in natural habitat. Thus, this in vitro propagation study investigated the effects of different plant growth regulators (PGRs) on in vitro leaf and stem explants of L. pumila., Methods: The capabilities of callus, shoot, and root formation were evaluated by culturing both explants on Murashige and Skoog (MS) medium supplemented with various PGRs at the concentrations of 0, 1, 3, 5, and 7 mg/L., Results: Medium supplemented with 3 mg/L indole-3-butyric acid (IBA) showed the optimal callogenesis from both leaf and stem explants with (72.34 ± 19.55)% and (70.40 ± 14.14)% efficacy, respectively. IBA was also found to be the most efficient PGR for root induction. A total of (50.00 ± 7.07)% and (77.78 ± 16.47)% of root formation were obtained from the in vitro stem and leaf explants after being cultured for (26.5 ± 5.0) and (30.0 ± 8.5) d in the medium supplemented with 1 and 3 mg/L of IBA, respectively. Shoot formation was only observed in stem explant, with the maximum percentage of formation ((100.00 ± 0.00)%) that was obtained in 1 mg/L zeatin after (11.0 ± 2.8) d of culture., Conclusions: Callus, roots, and shoots can be induced from in vitro leaf and stem explants of L. pumila through the manipulation of types and concentrations of PGRs.

Objective: To compare the efficacy difference in the treatment of supraspinous ligament injury between floating acupuncture at Tianying point and the conventional warm needling therapy., Methods: Ninety patients were randomized into a floating acupuncture group and a warm needling group, 45 cases in each one. In the floating acupuncture group, the floating needling technique was adopted at Tianying point. In the warm needling group, the conventional warm needling therapy was applied at Tianying point as the chief point in the prescription. The treatment was given 3 times a week and 6 treatments made one session. The visual analogue scale (VAS) was adopted for pain comparison before and after treatment of the patients in two groups and the efficacy in two groups were assessed., Results: The curative and remarkably effective rate was 81.8% (36/44) in the floating acupuncture group and the total effective rate was 95.5% (42/44), which were superior to 44.2% (19/43) and 79.1% (34/43) in the warm needling group separately (P < 0.01, P < 0.05). VAS score was lower as compared with that before treatment of the patients in two groups (both P < 0.01) and the score in the floating acupuncture group was lower than that in the warm needling group after treatment (P < 0.01). Thirty-six cases were cured and remarkably effective in the floating acupuncture group after treatment, in which 28 cases were cured and remarkably effective in 3 treatments, accounting for 77.8 (28/36), which was apparently higher than 26.3 (5/19) in the warm-needling group (P < 0.01)., Conclusion: The floating acupuncture at Tianying point achieves the quick and definite efficacy on supraspinous ligament injury and presents the apparent analgesic effect. The efficacy is superior to the conventional warm-needling therapy.

This study compared the effects of implanting two interpenetrating polymer networks (IPNs) into rabbit corneas. The first (Implant 1) was based on PEG-diacrylate, the second (Implant 2) was based on PEG-diacrylamide. There were inserted into deep stromal pockets created using a manual surgical technique for either 3 or 6 months. The implanted corneas were compared with normal and sham-operated corneas through slit lamp observation, anterior segment optical coherence tomography, in vivo confocal scanning and histological examination. Corneas with Implant 1 (based on PEG-diacrylate) developed diffuse haze, ulcers and opacities within 3 months, while corneas with Implant 2 (based on PEG-diacrylamide) remained clear at 6 months. They also exhibited normal numbers of epithelial cell layers, without any immune cell infiltration, inflammation, oedema or neovascularisation at post-operative 6 month. Morphological studies showed transient epithelial layer thinning over the hydrogel inserted area and elevated keratocyte activity at 3 months; however, the epithelium thickness and keratocyte morphology were improved at 6 months. Implant 2 exhibited superior in vivo biocompatibility and higher optical clarity than Implant 1. PEG-diacrylamide-based IPN hydrogel is therefore a potential candidate for corneal inlays to correct refractive error.

SARS-CoV (severe acute respiratory syndrome-associated coronavirus) caused infection of ~8000 people and death of ~800 patients around the world during the 2003 outbreak. In addition, picornaviruses such as enterovirus, coxsackievirus and rhinovirus also can cause life-threatening diseases. Replication of picornaviruses and coronaviruses requires 3Cpro (3C protease) and 3CLpro (3C-like protease) respectively, which are structurally analogous with chymotrypsin-fold, but the former is a monomer and the latter is dimeric due to an extra third domain for dimerization. Subtle structural differences in the S2 and S3 pockets of these proteases make inhibitors selective, but some dual inhibitors have been discovered. Our findings as summarized in the present review provide new potential anti-coronavirus and anti-picornavirus therapeutic agents and a clue to convert 3CLpro inhibitors into 3Cpro inhibitors and vice versa.

Our server, CLICK: http://mspc.bii.a-star.edu.sg/click, is capable of superimposing the 3D structures of any pair of biomolecules (proteins, DNA, RNA, etc.). The server makes use of the Cartesian coordinates of the molecules with the option of using other structural features such as secondary structure, solvent accessible surface area and residue depth to guide the alignment. CLICK first looks for cliques of points (3-7 residues) that are structurally similar in the pair of structures to be aligned. Using these local similarities, a one-to-one equivalence is charted between the residues of the two structures. A least square fit then superimposes the two structures. Our method is especially powerful in establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants. CLICK has been extensively benchmarked and compared with other popular methods for protein and RNA structural alignments. In most cases, CLICK alignments were statistically significantly better in terms of structure overlap. The method also recognizes conformational changes that may have occurred in structural domains or subdomains in one structure with respect to the other. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server.

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight <1.5  KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of ∼0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

A series of pyrazolone compounds as possible SARS-CoV 3CL protease inhibitors were designed, synthesized, and evaluated by in vitro protease assay using fluorogenic substrate peptide in which several showed potent inhibition against the 3CL protease. Interestingly, one of the inhibitors was also active against 3C protease from coxsackievirus B3. These inhibitors could be potentially developed into anti-coronaviral and anti-picornaviral agents., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

Breast cancer resistance protein (BCRP/ABCG2) is a membrane-bound efflux transporter important in cellular detoxification and multidrug resistance. Some aryl hydrocarbon receptor (AHR) agonists were reported to induce BCRP expression in human colon carcinoma cells. However, a direct involvement of AHR transcriptional regulation remains unexplored. In this study, we show that BCRP induction by AHR ligands occurs in human intestinal, liver, and mammary carcinoma cells and in primary colonocytes and hepatocytes. Increased BCRP transporter activity consistent with gene induction was also evident in the Caco2 subclone C2bbe1 cells. Using RNA interference and ectopic expression techniques to manipulate cellular AHR status, we confirmed AHR dependence of ABCG2 gene regulation. By gene promoter analysis, chromatin immunoprecipitation, and electrophoretic mobility shift assays, an active, proximal dioxin-response element at -194/-190 base pairs upstream of the transcription start site of the human ABCG2 gene was identified. Despite a common observation in human-derived cells, our in vitro and in vivo studies supported by phylogenetic footprinting analysis did not find that mouse Abcg2 is subject to AHR regulation. We conclude that AHR is a direct transcriptional regulator of human BCRP and provide an unprecedented role of AHR in cellular adaptive response and cytoprotection by up-regulating an important ATP-binding cassette efflux transporter.

A series of 2-(benzylthio)-6-oxo-4-phenyl-1,6-dihydropyrimidine as SARS-CoV 3CL protease inhibitors were developed and their potency was evaluated by in vitro protease inhibitory assays. Two candidates had encouraging results for the development of new anti-SARS compounds., (Copyright 2010 Elsevier Ltd. All rights reserved.)

A study of residents at the Silver Jubilee Home for the Aged was conducted to determine the prevalence, awareness and control of hypertension in this elderly community in Penang, Malaysia. Prevalence of hypertension was 36%, with 81% of patients being initially aware of this diagnosis. This relatively low hypertension prevalence rate may be because residents have a fairly sheltered lifestyle with less social stress and a daily routine that incorporates adequate exercise. Similarly, the high hypertension awareness rate compared to reported figures in the community may be because residents are more regularly monitored by the attending medical care-givers. At the beginning of the study, only 34% of hypertensive patients were well controlled with a blood pressure less than 140/90 mm Hg. This proportion rose to 53% at the end of study period. Compliance is better at a residential home because medication is served by their care-givers and cost is absorbed in this charitable organization. Our study suggests that hypertension awareness and control can be reasonable for the elderly in a residential home.

Objective: To observe the effect of electroacupuncture (EA) of "Baihui" (GV 20) and "Yamen" (GV 15) on the permeability of blood-brain barrier for exogenous nerve growth factor (NGF) and its relevance to PKC pathway in cerebral ischemia (CI) rats., Methods: Forty-eight SD rats were randomized into sham-operation (sham), model, NGF, EA, NGF + EA, and NGF + H7 + EA groups. CI model was established by repeated occlusion of the bilateral carotid arteries and reperfusion. NGF (10 microg/kg) was administrated by intravenous injection (vena caudalis); while H 7 [1-(5-isoquinolinesulfonyl)-2-mehtylpoperazine, an inhibitor of protein kinase C (PKC), 1 mg/kg] was given by intraperitoneal injection. EA (100 Hz, 2 mA) was applied to "Baihui" (GV 20) and "Yamen" (GV 15) for 20 min. NGF content in the brain tissue was assayed by enzyme-labeled immunosorbent assay (ELISA)., Results: In comparison with sham group, cerebral NGF content had no apparent change in model group (P > 0.05). Comparison among the abovementioned 6 groups showed that cerebral NGF level in NGF + EA group was significantly higher than those in sham, model, EA and NGF groups (P < 0.01). No significant differences were found among sham, model, NGF, EA and NGF+ H7 + EA groups and between NGF + EA and NGF + H7 + EA groups in cerebral NGF contents (P > 0.05)., Conclusion: EA of GV 20 and GV 15 can raise the permeability of blood-brain barrier for NGF to increase its level in the cerebral tissue in CI rats, favoring the regeneration and repair of nerves, which has no clear relevance to PKC pathway.

Clinical use of retinoic acids (RA) is hindered by toxicity possibly related to oxidative stress. Recently, RA at relatively low concentrations was shown to inhibit NRF2 and the expression of its target antioxidative genes. This raises the possibility that RA toxicity may result from cellular inability to cope with resultant oxidative stress. Using in vitro cell and in vivo mouse models, we report that RA, specifically all-trans-RA (atRA) at concentrations implicated in toxicity, can activate NRF2 and induce NRF2 target genes, particularly the subunits of the rate-limiting enzyme of glutathione biosynthesis, glutamate cysteine ligase (GCLM/GCLC). RNA interference-mediated silencing of NRF2, but not of retinoid X receptor-alpha and -beta, reduced basal and atRA-induced GCLM/GCLC gene expression. Moreover, RA increased nuclear accumulation of NRF2, antioxidant response element (ARE) reporter activity, and NRF2 occupancy at AREs. 4-Hydroxynonenal, a lipid peroxidation product, was increased by RA. Inhibition of MEK1/ERK mitogen-activated protein kinases significantly suppressed atRA-induced NRF2 activation and ARE-regulated gene expression, reducing cell resistance against toxic concentrations of RA. NRF2-silenced cells were vulnerable to atRA-induced mitochondrial toxicity and apoptosis. In conclusion, toxic RA activates NRF2, thereby triggering an adaptive response against the resultant oxidative stress. NRF2 enhancement as a therapeutic target of retinoid toxicity awaits further investigation.

Oxidative stress, causing necrotic and apoptotic cell death, is associated with bile acid toxicity. Using liver (HepG2, Hepa1c1c7, and primary human hepatocytes) and intestinal (C2bbe1, a Caco-2 subclone) cells, we demonstrated that toxic bile acids, such as lithocholic acid (LCA) and chenodeoxycholic acid, induced the nuclear factor (erythroid-2 like) factor 2 (Nrf2) target genes, especially the rate-limiting enzyme in glutathione (GSH) biosynthesis [glutamate cysteine ligase modulatory subunit (GCLM) and glutamate cysteine ligase catalytic subunit (GCLC)] and thioredoxin reductase 1. Nrf2 activation and induction of Nrf2 target genes were also evident in vivo in the liver of CD-1 mice treated 7 to 8 h or 4 days with LCA. Silencing of Nrf2 via small-interfering RNA suppressed basal and bile acid-induced mRNA levels of the above-mentioned genes. Consistent with this, overexpression of Nrf2 enhanced, but dominant-negative Nrf2 attenuated, Nrf2 target gene induction by bile acids. The activation of Nrf2-antioxidant responsive element (ARE) transcription machinery by bile acids was confirmed by increased nuclear accumulation of Nrf2, enhanced ARE-reporter activity, and increased Nrf2 binding to ARE. It is noteworthy that Nrf2 silencing increased cell susceptibility to LCA toxicity, as evidenced by reduced cell viability and increased necrosis and apoptosis. Concomitant with GCLC/GCLM induction, cellular GSH was significantly increased in bile acid-treated cells. Cotreatment with N-acetyl-l-cysteine, a GSH precursor, ameliorated LCA toxicity, whereas cotreatment with buthionine sulfoximine, a GSH synthesis blocker, exacerbated it. In summary, this study provides molecular evidence linking bile acid toxicity to oxidative stress. Nrf2 is centrally involved in counteracting such oxidative stress by enhancing adaptive antioxidative response, particularly GSH biosynthesis, and hence cell survival.

We report the discovery of an osmosensitive transcriptional control of human CYP3A4, CYP3A7, and CYP3A5. Ambient hypertonicity (350-450 mOsmol/kg) increased mRNA expressions of the CYP3A by approximately 10- to 20-fold in human-intestinal C(2)bbe1 cells, followed by an increase of CYP3A protein. Hypotonicity, on the other hand, suppressed CYP3A mRNA levels, indicating that physiological isotonic conditions may regulate the basal expression of CYP3A. Similar responses to ambient tonicity were observed in other human-derived cell lines (intestinal LS180 and hepatic HepG2) and human primary colonic cells. The 11-base pair tonicity-responsive enhancer (TonE) is an osmosensitive regulator that is activated by the transcription factor, the nuclear factor of activated T-cells 5 (NFAT5). Luciferase-based reporter assays of 13 consensus TonE motifs within +/-10 kilobases (kb) from the transcription start sites of CYP3A showed that only the CYP3A7 intron 2 region ( approximately 5 kb downstream from the transcription start site), which contains two TonE motifs (+5076/+5086 and + 5417/+5427), was responsive to hypertonicity stimuli. This observation was confirmed upon cotransfection with an NFAT5 expression vector, small interfering RNA, or dominant-negative NFAT5. Deletion and mutation analyses suggested that the TonE (+5417/+5427) is indispensable for the enhancer activity. NFAT5 binding to the CYP3A7 intron 2 TonE motif was demonstrated with electrophoretic mobility shift assay and in a native cell context by chromatin immunoprecipitation. We conclude that transcription of human CYP3A is influenced by ambient tonicity. The physiological significance of the tonic regulation of CYP3A enzymes remains to be determined.