CD8+ T-cell responses towards conserved influenza B virus epitopes across anatomical sites and age

Influenza B viruses (IBVs) cause substantive morbidity and mortality, and yet immunity towards IBVs remains understudied. CD8+ T-cells provide broadly cross-reactive immunity and alleviate disease severity by recognizing conserved epitopes. Despite the IBV burden, only 18 IBV-specific T-cell epitopes restricted by 5 HLAs have been identified currently. A broader array of conserved IBV T-cell epitopes is needed to develop effective cross-reactive T-cell based IBV vaccines. Here we identify 9 highly conserved IBV CD8+ T-cell epitopes restricted to HLA-B*07:02, HLA-B*08:01 and HLA-B*35:01. Memory IBV-specific tetramer+CD8+ T-cells are present within blood and tissues. Frequencies of IBV-specific CD8+ T-cells decline with age, but maintain a central memory phenotype. HLA-B*07:02 and HLA-B*08:01-restricted NP30-38 epitope-specific T-cells have distinct T-cell receptor repertoires. We provide structural basis for the IBV HLA-B*07:02-restricted NS1196-206 (11-mer) and HLA-B*07:02-restricted NP30-38 epitope presentation. Our study increases the number of IBV CD8+ T-cell epitopes, and defines IBV-specific CD8+ T-cells at cellular and molecular levels, across tissues and age.

Automated lead toxicity prediction using computational modelling framework

Background

Lead, an environmental toxicant, accounts for 0.6% of the global burden of disease, with the highest burden in developing countries. Lead poisoning is very much preventable with adequate and timely action. Therefore, it is important to identify factors that contribute to maternal BLL and minimise them to reduce the transfer to the foetus. Literacy and awareness related to its impact are low and the clinical establishment for biological monitoring of blood lead level (BLL) is low, costly, and time-consuming. A significant contribution to an infant's BLL load is caused by maternal lead transfer during pregnancy. This acts as the first pathway to the infant's lead exposure. The social and demographic information that includes lifestyle and environmental factors are key to maternal lead exposure.

Results

We propose a novel approach to build a computational model framework that can predict lead toxicity levels in maternal blood using a set of sociodemographic features. To illustrate our proposed approach, maternal data comprising socio-demographic features and blood samples from the pregnant woman is collected, analysed, and modelled. The computational model is built that learns from the maternal data and then predicts lead level in a pregnant woman using a set of questionnaires that relate to the maternal's social and demographic information as the first point of testing. The range of features identified in the built models can estimate the underlying function and provide an understanding of the toxicity level. Following feature selection methods, the 12-feature set obtained from the Boruta algorithm gave better prediction results (kNN = 76.84%, DT = 74.70%, and NN = 73.99%).

Conclusion

The built prediction model can be beneficial in improving the point of care and hence reducing the cost and the risk involved. It is envisaged that in future, the proposed methodology will become a part of a screening process to assist healthcare experts at the point of evaluating the lead toxicity level in pregnant women. Women screened positive could be given a range of facilities including preliminary counselling to being referred to the health centre for further diagnosis. Steps could be taken to reduce maternal lead exposure; hence, it could also be possible to mitigate the infant's lead exposure by reducing transfer from the pregnant woman.

Broad spectrum SARS-CoV-2-specific immunity in hospitalized First Nations peoples recovering from COVID-19

Indigenous peoples globally are at increased risk of COVID-19-associated morbidity and mortality. However, data that describe immune responses to SARS-CoV-2 infection in Indigenous populations are lacking. We evaluated immune responses in Australian First Nations peoples hospitalized with COVID-19. Our work comprehensively mapped out inflammatory, humoral and adaptive immune responses following SARS-CoV-2 infection. Patients were recruited early following the lifting of strict public health measures in the Northern Territory, Australia, between November 2021 and May 2022. Australian First Nations peoples recovering from COVID-19 showed increased levels of MCP-1 and IL-8 cytokines, IgG-antibodies against Delta-RBD and memory SARS-CoV-2-specific T cell responses prior to hospital discharge in comparison with hospital admission, with resolution of hyperactivated HLA-DR+ CD38+ T cells. SARS-CoV-2 infection elicited coordinated ASC, Tfh and CD8+ T cell responses in concert with CD4+ T cell responses. Delta and Omicron RBD-IgG, as well as Ancestral N-IgG antibodies, strongly correlated with Ancestral RBD-IgG antibodies and Spike-specific memory B cells. We provide evidence of broad and robust immune responses following SARS-CoV-2 infection in Indigenous peoples, resembling those of non-Indigenous COVID-19 hospitalized patients.

Robust and prototypical immune responses toward COVID-19 vaccine in First Nations peoples are impacted by comorbidities

High-risk groups, including Indigenous people, are at risk of severe COVID-19. Here we found that Australian First Nations peoples elicit effective immune responses to COVID-19 BNT162b2 vaccination, including neutralizing antibodies, receptor-binding domain (RBD) antibodies, SARS-CoV-2 spike-specific B cells, and CD4+ and CD8+ T cells. In First Nations participants, RBD IgG antibody titers were correlated with body mass index and negatively correlated with age. Reduced RBD antibodies, spike-specific B cells and follicular helper T cells were found in vaccinated participants with chronic conditions (diabetes, renal disease) and were strongly associated with altered glycosylation of IgG and increased interleukin-18 levels in the plasma. These immune perturbations were also found in non-Indigenous people with comorbidities, indicating that they were related to comorbidities rather than ethnicity. However, our study is of a great importance to First Nations peoples who have disproportionate rates of chronic comorbidities and provides evidence of robust immune responses after COVID-19 vaccination in Indigenous people.

A Study of Maternal and Umbilical Cord Blood Lead Levels in Pregnant Women

Lead is a highly toxic element which can cross the placental barrier and enter the fetus during pregnancy. Parental lead exposure has adverse effect on infant as well as on maternal health. As part of our program to investigate the lead poisoning in human population we investigated the maternal blood lead levels (MBLL) and umbilical cord blood lead (UBLL) levels in 200 pregnant women and collected their socio-demographic details. In the study we found high lead levels in both maternal and umbilical cord blood samples. The results showed 47.5% maternal blood (n = 95) detected with lead while 38.5% umbilical cord blood (n = 77) samples had lead concentration higher than that of reference range of ≤ 5 µg/dL. We also found that the Spearman's correlation coefficient (rs) revealed a strong positive correlation between the MBLL and UBLL (rs = 0.63). The results from socio-demographic questionnaire demonstrated that the recent home painting (p = 0.002) and residing close proximity to traffic congestion (p = 0.05) were significantly associated with MBLL. Education, mother age, fuel and water sources were not significantly associated with MBLL. Iron and calcium deficiency along with tiredness, lethargy, abdominal pain were also reported in women having high lead level > 5 µg/dL. Concludingly, on the basis of results obtained it may be stated that we found elevated BLLs in both pregnant women as well as in umbilical cord blood. The prevalence of elevated lead levels in mothers will expose the fetus to lead through placental barriers mobilization and it can have long term adverse effects on the developing fetus. Therefore, it is recommended that screening of blood lead levels be carried out in high-risk women based on their social, occupational, environmental, and individual factors. In addition, stringent regulations on lead-based products are also required from government agencies/authorities to reduce environmental lead burden and toxicity. Moreover, public awareness programs should be organized on hazardous effect of lead.

SARS-CoV-2-specific T cell memory with common TCRαβ motifs is established in unvaccinated children who seroconvert after infection

As the establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell memory in children remains largely unexplored, we recruited convalescent COVID-19 children and adults to define their circulating memory SARS-CoV-2-specific CD4+ and CD8+ T cells prior to vaccination. We analyzed epitope-specific T cells directly ex vivo using seven HLA class I and class II tetramers presenting SARS-CoV-2 epitopes, together with Spike-specific B cells. Unvaccinated children who seroconverted had comparable Spike-specific but lower ORF1a- and N-specific memory T cell responses compared with adults. This agreed with our TCR sequencing data showing reduced clonal expansion in children. A strong stem cell memory phenotype and common T cell receptor motifs were detected within tetramer-specific T cells in seroconverted children. Conversely, children who did not seroconvert had tetramer-specific T cells of predominantly naive phenotypes and diverse TCRαβ repertoires. Our study demonstrates the generation of SARS-CoV-2-specific T cell memory with common TCRαβ motifs in unvaccinated seroconverted children after their first virus encounter.

Robust and prototypical immune responses towards COVID-19 BNT162b2 vaccines in Indigenous people

SARS-CoV-2 has led to >270 million infections and >5 million deaths globally. Indigenous people are disproportionately affected by infectious diseases, therefore also more susceptible to the COVID-19 pandemic. There are an estimated 476 million indigenous people globally, including an estimated 798,365 Aboriginal and Torres Strait Islander in Australia. With the high vulnerability to COVID-19, this knowledge is urgently needed to better protect indigenous populations.

We evaluated a breadth of immune responses in indigenous (n=57) and non-indigenous (n=49) individuals after COVID-19 vaccination. We tested RBD antibodies, spike/RBD-probe-specific B cells, peptide stimulations with activation-induced marker (AIM) assay and intracellular cytokine staining.

We found 22% and 34% seroconversion rates after 1st dose of BNT162b2 vaccine for Indigenous and non-indigenous individuals, respectively, which increased to 100% at 1-mth after 2nd dose for both groups. RBD-specific IgG levels in indigenous individuals at 1-mth after 2nd dose positively correlated with their body mass index. At 1-mth after the 2nd COVID-19 vaccination, CD4+ and CD8+ T cell responses via AIM expression and IFN-γ+TNF+ production was comparable between indigenous and non-indigenous individuals. We are also going to assess the longevity of antibodies and T cells.

Therefore, COVID-19 vaccination induced similar immune responses in indigenous and non-indigenous individuals.

A Multi-Task Learning Framework for Automated Segmentation and Classification of Breast Tumors From Ultrasound Images

Breast cancer is one of the most fatal diseases leading to the death of several women across the world. But early diagnosis of breast cancer can help to reduce the mortality rate. So an efficient multi-task learning approach is proposed in this work for the automatic segmentation and classification of breast tumors from ultrasound images. The proposed learning approach consists of an encoder, decoder, and bridge blocks for segmentation and a dense branch for the classification of tumors. For efficient classification, multi-scale features from different levels of the network are used. Experimental results show that the proposed approach is able to enhance the accuracy and recall of segmentation by 1.08%, 4.13%, and classification by 1.16%, 2.34%, respectively than the methods available in the literature.

Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein

CD8⁺ T cells play an important role in vaccination and immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although numerous SARS-CoV-2 CD8⁺ T cell epitopes have been identified, the molecular basis underpinning T cell receptor (TCR) recognition of SARS-CoV-2-specific T cells remains unknown. The T cell response directed toward SARS-CoV-2 spike protein–derived S^269–277 peptide presented by the human leukocyte antigen (HLA)-A∗02:01 allomorph (hereafter the HLA-A2^S269–277 epitope) is, to date, the most immunodominant SARS-CoV-2 epitope found in individuals bearing this allele. As HLA-A2^S269–277-specific CD8⁺ T cells utilize biased TRAV12 gene usage within the TCR α-chain, we sought to understand the molecular basis underpinning this TRAV12 dominance. We expressed four TRAV12⁺ TCRs which bound the HLA-A2^S269–277 complex with low micromolar affinity and determined the crystal structure of the HLA-A2^S269–277 binary complex, and subsequently a ternary structure of the TRAV12⁺ TCR complexed to HLA-A2^S269–277. We found that the TCR made extensive contacts along the entire length of the S^269–277 peptide, suggesting that the TRAV12⁺ TCRs would be sensitive to sequence variation within this epitope. To examine this, we investigated cross-reactivity toward analogous peptides from existing SARS-CoV-2 variants and closely related coronaviruses. We show via surface plasmon resonance and tetramer studies that the TRAV12⁺ T cell repertoire cross-reacts poorly with these analogous epitopes. Overall, we defined the structural basis underpinning biased TCR recognition of CD8⁺ T cells directed at an immunodominant epitope and provide a framework for understanding TCR cross-reactivity toward viral variants within the S^269–277 peptide.

SARS-CoV-2-specific CD8+ T-cell responses and TCR signatures in the context of a prominent HLA-A*24:02 allomorph

In‐depth understanding of human T‐cell‐mediated immunity in coronavirus disease 2019 (COVID‐19) is needed if we are to optimize vaccine strategies and immunotherapies. Identification of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) T‐cell epitopes and generation of peptide–human leukocyte antigen (peptide–HLA) tetramers facilitate direct ex vivo analyses of SARS‐CoV‐2‐specific T cells and their T‐cell receptor (TCR) repertoires. We utilized a combination of peptide prediction and in vitro peptide stimulation to validate novel SARS‐CoV‐2 epitopes restricted by HLA‐A*24:02, one of the most prominent HLA class I alleles, especially in Indigenous and Asian populations. Of the peptides screened, three spike‐derived peptides generated CD8⁺IFNγ⁺ responses above background, S_1208–1216 (QYIKWPWYI), S_448–456 (NYNYLYRLF) and S_193–201 (VFKNIDGYF), with S₁₂₀₈ generating immunodominant CD8⁺IFNγ⁺ responses. Using peptide–HLA‐I tetramers, we performed direct ex vivo tetramer enrichment for HLA‐A*24:02‐restricted CD8⁺ T cells in COVID‐19 patients and prepandemic controls. The precursor frequencies for HLA‐A*24:02‐restricted epitopes were within the range previously observed for other SARS‐CoV‐2 epitopes for both COVID‐19 patients and prepandemic individuals. Naïve A24/SARS‐CoV‐2‐specific CD8⁺ T cells increased nearly 7.5‐fold above the average precursor frequency during COVID‐19, gaining effector and memory phenotypes. Ex vivo single‐cell analyses of TCRαβ repertoires found that the A24/S₄₄₈⁺CD8⁺ T‐cell TCRαβ repertoire was driven by a common TCRβ chain motif, whereas the A24/S₁₂₀₈⁺CD8⁺ TCRαβ repertoire was diverse across COVID‐19 patients. Our study provides an in depth characterization and important insights into SARS‐CoV‐2‐specific CD8⁺ T‐cell responses associated with a prominent HLA‐A*24:02 allomorph. This contributes to our knowledge on adaptive immune responses during primary COVID‐19 and could be exploited in vaccine or immunotherapeutic approaches.

Modelling mobile-based technology adoption among people with dementia

The work described in this paper builds upon our previous research on adoption modelling and aims to identify the best subset of features that could offer a better understanding of technology adoption. The current work is based on the analysis and fusion of two datasets that provide detailed information on background, psychosocial, and medical history of the subjects. In the process of modelling adoption, feature selection is carried out followed by empirical analysis to identify the best classification models. With a more detailed set of features including psychosocial and medical history information, the developed adoption model, using kNN algorithm, achieved a prediction accuracy of 99.41% when tested on 173 participants. The second-best algorithm built, using NN, achieved 94.08% accuracy. Both these results have improved accuracy in comparison to the best accuracy achieved (92.48%) in our previous work, based on psychosocial and self-reported health data for the same cohort. It has been found that psychosocial data is better than medical data for predicting technology adoption. However, for the best results, we should use a combination of psychosocial and medical data where it is preferable that the latter is provided from reliable medical sources, rather than self-reported.

CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity

To better understand primary and recall T cell responses during coronavirus disease 2019 (COVID-19), it is important to examine unmanipulated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells. By using peptide-human leukocyte antigen (HLA) tetramers for direct ex vivo analysis, we characterized CD8⁺ T cells specific for SARS-CoV-2 epitopes in COVID-19 patients and unexposed individuals. Unlike CD8⁺ T cells directed toward subdominant epitopes (B7/N₂₅₇, A2/S₂₆₉, and A24/S_1,208) CD8⁺ T cells specific for the immunodominant B7/N₁₀₅ epitope were detected at high frequencies in pre-pandemic samples and at increased frequencies during acute COVID-19 and convalescence. SARS-CoV-2-specific CD8⁺ T cells in pre-pandemic samples from children, adults, and elderly individuals predominantly displayed a naive phenotype, indicating a lack of previous cross-reactive exposures. T cell receptor (TCR) analyses revealed diverse TCRαβ repertoires and promiscuous αβ-TCR pairing within B7/N₁₀₅⁺CD8⁺ T cells. Our study demonstrates high naive precursor frequency and TCRαβ diversity within immunodominant B7/N₁₀₅-specific CD8⁺ T cells and provides insight into SARS-CoV-2-specific T cell origins and subsequent responses.

Effect of Mindfulness Meditation on Intraocular Pressure and Trabecular Meshwork Gene Expression: A Randomized Controlled Trial

PURPOSE

To evaluate the effect of mindfulness meditation (MM) on intraocular pressure (IOP) and trabecular meshwork (TM) gene expression in patients with medically uncontrolled primary open angle glaucoma (POAG).

DESIGN

Parallel arm, single-masked, randomized controlled trial.

METHODS

Sixty POAG patients with IOP ≥21 mm Hg taking maximal topical medication and scheduled for trabeculectomy were included in this study at a tertiary eye care center in India. Thirty patients (Group 1) underwent 3 weeks of 45-minute daily MM sessions in addition to medical therapy while Group 2 continued medical therapy only. Primary outcome was change in IOP (ΔIOP) after 3 weeks of MM. Secondary outcomes were probability of success, percentage of reduction in IOP, effect on diurnal variations of IOP, changes in quality of life (QoL), and changes in gene expression patterns in TM.

RESULTS

At 3 weeks, a significant decrease in IOP was seen in Group 1 (20.16 ± 3.3 to 15.05 ± 2.4mm Hg; P = .001), compared to Group 2 (21.2 ± 5.6 to 20.0 ± 5.8mm Hg; P = .38). ΔIOP was significantly higher in Group 1 than in Group 2 (5.0 ± 1.80 vs. 0.20 ± 3.03mm Hg; P = .001). Analysis of gene expression revealed significant upregulation of nitric oxide synthetase (NOS1 and NOS3) and neuroprotective genes with downregulation of proinflammatory genes in Group 1 in comparison to Group 2 (P = .001).

CONCLUSIONS

MM was associated with significant decrease in IOP and changes in TM gene expression, indicating its direct impact on ocular tissues.

Suboptimal SARS-CoV-2-specific CD8+ T cell response associated with the prominent HLA-A*02:01 phenotype

An improved understanding of human T cell-mediated immunity in COVID-19 is important for optimizing therapeutic and vaccine strategies. Experience with influenza shows that infection primes CD8+ T cell memory to peptides presented by common HLA types like HLA-A2, which enhances recovery and diminishes clinical severity upon reinfection. Stimulating peripheral blood mononuclear cells from COVID-19 convalescent patients with overlapping peptides from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to the clonal expansion of SARS-CoV-2-specific CD8+ and CD4+ T cells in vitro, with CD4+ T cells being robust. We identified two HLA-A*02:01-restricted SARS-CoV-2-specfic CD8+ T cell epitopes, A2/S269-277 and A2/Orf1ab3183-3191 Using peptide-HLA tetramer enrichment, direct ex vivo assessment of A2/S269+CD8+ and A2/Orf1ab3183+CD8+ populations indicated that A2/S269+CD8+ T cells were detected at comparable frequencies (∼1.3 × 10-5) in acute and convalescent HLA-A*02:01+ patients. These frequencies were higher than those found in uninfected HLA-A*02:01+ donors (∼2.5 × 10-6), but low when compared to frequencies for influenza-specific (A2/M158) and Epstein-Barr virus (EBV)-specific (A2/BMLF1280) (∼1.38 × 10-4) populations. Phenotyping A2/S269+CD8+ T cells from COVID-19 convalescents ex vivo showed that A2/S269+CD8+ T cells were predominantly negative for CD38, HLA-DR, PD-1, and CD71 activation markers, although the majority of total CD8+ T cells expressed granzymes and/or perforin. Furthermore, the bias toward naïve, stem cell memory and central memory A2/S269+CD8+ T cells rather than effector memory populations suggests that SARS-CoV-2 infection may be compromising CD8+ T cell activation. Priming with appropriate vaccines may thus be beneficial for optimizing CD8+ T cell immunity in COVID-19.

Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism

Effective colonization of host cells by some Gram-positive bacteria often involves using lengthy, adhesive macromolecular structures called sortase-dependent pili. Among commensals, the gut-adapted Lactobacillus rhamnosus GG strain encodes the operons for two varieties of these pili (SpaCBA and SpaFED), with each structure consisting of backbone, tip, and basal pilin subunits. Although the tertiary structure was recently solved for the backbone subunit (SpaA) of the SpaCBA pilus, no structural information exists for its counterpart in the SpaFED pilus. Here, we report several crystal structures for the SpaD backbone pilin, two of which capture the N-terminal domain in either the closed (linear) or open (bent) conformation. To our knowledge, this is the first observation of the bent conformation in Gram-positive pilin structures. Based on this bent conformation, we suggest a three-stage model, which we call the expose-ligate-seal mechanism, for the docking and assembly of backbone pilins into the sortase-dependent pilus.

Priyanka Chaurasia et al. report crystal structures of the SpaD backbone pilin from a gut-adapted bacteria, Lactobacillus rhamnosus. The observed bent conformation of the N-terminal domain has not been seen in other Gram-positive pilin structures.

Technology adoption and prediction tools for everyday technologies aimed at people with dementia

A wide range of assistive technologies have been developed to support the elderly population with the goal of promoting independent living. The adoption of these technology based solutions is, however, critical to their overarching success. In our previous research we addressed the significance of modelling user adoption to reminding technologies based on a range of physical, environmental and social factors. In our current work we build upon our initial modeling through considering a wider range of computational approaches and identify a reduced set of relevant features that can aid the medical professionals to make an informed choice of whether to recommend the technology or not. The adoption models produced were evaluated on a multi-criterion basis: in terms of prediction performance, robustness and bias in relation to two types of errors. The effects of data imbalance on prediction performance was also considered. With handling the imbalance in the dataset, a 16 feature-subset was evaluated consisting of 173 instances, resulting in the ability to differentiate between adopters and non-adopters with an overall accuracy of 99.42 %.

New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit

Thus far, all solved structures of pilin-proteins comprising sortase-assembled pili are from pathogenic genera and species. Here, we present the first crystal structure of a pilin subunit (SpaA) from a non-pathogen host (Lactobacillus rhamnosus GG). SpaA consists of two tandem CnaB-type domains, each with an isopeptide bond and E-box motif. Intriguingly, while the isopeptide bond in the N-terminal domain forms between lysine and asparagine, the one in the C-terminal domain atypically involves aspartate. We also solved crystal structures of mutant proteins where residues implicated in forming isopeptide bonds were replaced. Expectedly, the E-box-substituted E139A mutant lacks an isopeptide bond in the N-terminal domain. However, the C-terminal E269A substitution gave two structures; one of both domains with their isopeptide bonds present, and another of only the N-terminal domain, but with an unformed isopeptide bond and significant conformational changes. This latter crystal structure has never been observed for any other Gram-positive pilin. Notably, the C-terminal isopeptide bond still forms in D295N-substituted SpaA, irrespective of E269 being present or absent. Although E-box mutations affect SpaA proteolytic and thermal stability, a cumulative effect perturbing normal pilus polymerization was unobserved. A model showing the polymerized arrangement of SpaA within the SpaCBA pilus is proposed.

Purification, crystallization and preliminary X-ray diffraction analysis of SpaD, a backbone-pilin subunit encoded by the fimbrial spaFED operon in Lactobacillus rhamnosus GG

SpaD is the predicted backbone-pilin subunit of the SpaFED pilus, whose loci are encoded by the fimbrial spaFED operon in Lactobacillus rhamnosus GG, a Gram-positive gut-adapted commensal strain with perceived probiotic benefits. In this study, soluble recombinant SpaD protein was overproduced in Escherichia coli and then purified by Ni2+-chelating affinity and gel-filtration chromatography. After limited proteolysis with α-chymotrypsin, good-quality crystals of SpaD were obtained which diffracted beyond 2.0 Å resolution. These crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=50.11, b=83.27, c=149.65 Å. For phasing, sodium iodide-derivatized crystals were prepared using the halide quick-soaking method and diffraction data were collected in-house to a resolution of 2.2 Å. An interpretable electron-density map was successfully obtained using single-wavelength anomalous diffraction (SAD).

A duration-based online reminder system

Purpose

– The purpose of this paper is to discuss an online sensor-based support system which the authors believe can be useful in such scenarios. Persons with a cognitive impairment, such as those with Alzheimer’s disease, suffer from deficiencies in cognitive skills which reduce their independence; such patients can benefit from the provision of further assistance such as reminders for carrying out instrumental activities of daily living (IADLs).

Design/methodology/approach

– The system proposed processes data from a network of sensors that have the capability of sensing user interactions and on-going IADLs in the living environment itself. A probabilistic learning model is built that computes joint probability distributions over different activities representing users’ behavioural patterns in performing activities. This probability model can underpin an intervention framework that prompts the user with the next step in the IADL when inactivity is being observed. This prompt for the next step is inferred from the conditional probability taken into consideration the IADL steps that have already been completed, in addition to contextual information relating to the time of day and the amount of time already spent on the activity. The originality of the work lies in combining partially observed sensor sequences and duration data associated with the IADLs. The prediction of the next step is then adjusted as further steps are completed and more time is spent towards the completion of the activity, thus updating the confidence that the prediction is correct. A reminder is only issued when there has been sufficient inactivity on the part of the patient and the confidence is high that the prediction is correct.

Findings

– The results of this study verify that by including duration information the prediction accuracy of the model is increased and the confidence level for the next step in the IADL is also increased. As such, there is approximately a 10 per cent rise in the prediction performance in the case of single sensor activation in comparison to an alternative approach which did not consider activity durations.

Practical implications

– Duration information to a certain extent has been widely ignored by activity recognition researchers and has received a very limited application within smart environments.

Originality/value

– This study concludes that incorporating progressive duration information into partially observed sensor sequences of IADLs has the potential to increase performance of a reminder system for patients with a cognitive impairment, such as Alzheimer’s disease.

A duration-based online reminder system

Purpose

– This paper aims to discuss an online sensor-based support system which is believed to be useful for persons with a cognitive impairment, such as those with Alzheimer’s disease, suffering from deficiencies in cognitive skills which reduce their independence. Such patients can benefit from the provision of further assistance such as reminders for carrying out instrumental activities of daily living (iADLs).

Design/methodology/approach

– The system proposed processes data from a network of sensors that have the capability of sensing user interactions and ongoing iADLs in the living environment itself. A probabilistic learning model is built that computes joint probability distributions over different activities representing users’ behavioural patterns in performing activities. This probability model can underpin an intervention framework that prompts the user with the next step in the iADL when inactivity is being observed. This prompt for the next step is inferred from the conditional probability, taking into consideration the iADL steps that have already been completed, in addition to contextual information relating to the time of day and the amount of time already spent on the activity. The originality of the work lies in combining partially observed sensor sequences and duration data associated with the iADLs. The prediction of the next step is then adjusted as further steps are completed and more time is spent towards the completion of the activity; thus, updating the confidence that the prediction is correct. A reminder is only issued when there has been sufficient inactivity on the part of the patient and the confidence is high that the prediction is correct.

Findings

– The results verify that by including duration information, the prediction accuracy of the model is increased, and the confidence level for the next step in the iADL is also increased. As such, there is approximately a 10 per cent rise in the prediction performance in the case of single-sensor activation in comparison to an alternative approach which did not consider activity durations. Thus, it is concluded that incorporating progressive duration information into partially observed sensor sequences of iADLs has the potential to increase performance of a reminder system for patients with a cognitive impairment, such as Alzheimer’s disease.

Originality/value

– Activity duration information can be a potential feature in measuring the performance of a user and distinguishing different activities. The results verify that by including duration information, the prediction accuracy of the model is increased, and the confidence level for the next step in the activity is also increased. The use of duration information in online prediction of activities can also be associated to monitoring the deterioration in cognitive abilities and in making a decision about the level of assistance required. Such improvements have significance in building more accurate reminder systems that precisely predict activities and assist its users, thus, improving the overall support provided for living independently.

Histone methylation and ubiquitination with their cross-talk and roles in gene expression and stability

Methylation of lysine residues of histones is associated with functionally distinct regions of chromatin, and, therefore, is an important epigenetic mark. Over the past few years, several enzymes that catalyze this covalent modification on different lysine residues of histones have been discovered. Intriguingly, histone lysine methylation has also been shown to be cross-regulated by histone ubiquitination or the enzymes that catalyze this modification. These covalent modifications and their cross-talks play important roles in regulation of gene expression, heterochromatin formation, genome stability, and cancer. Thus, there has been a very rapid progress within past several years towards elucidating the molecular basis of histone lysine methylation and ubiquitination, and their aberrations in human diseases. Here, we discuss these covalent modifications with their cross-regulation and roles in controlling gene expression and stability.

What causes cancer gallbladder?: a review

Gallbladder cancer is a common malignancy of the biliary tract. It is the fifth common malignancy of the gastrointestinal tract in United States and third in Northern India. Despite such high prevalence, there is scanty published literature about this disease in indexed journals. Therefore, this article is intended to provide a brief overview of gallbladder cancer risk factors, based mainly on published evidence from analytical epidemiology and recent research findings of biologists and practising oncologists. Furthermore, an attempt has been made to establish an association between different causative factors and the occurrence of the disease.

Nucleosome positioning and periodicity of satellite DNA in the liver of aging rats. Nucleosome positioning and periodicity of satellite DNA

The positioning of nucleosomes has been analysed by comparing the pattern of cutting sites of a probing reagent on chromatin and naked DNA. For this purpose, high molecular weight DNA and nuclei from the liver of young (18 +/- 2 weeks) and old (100 +/- 5 weeks) Wistar male rats were digested with micrococcal nuclease (MNase) and hybridized with 32P-labelled rat satellite DNA probe. A comparison of the ladder generated by MNase with chromatin and nuclei indicates long range organization of the satellite chromatin fiber with distinct non-random positioning of nucleosomes. However, the positioning of nucleosomes on satellite DNA does not vary with age. For studying the periodicity and subunit structure of satellite DNA, high molecular weight DNA from the liver of young and old rats were digested with different restriction enzymes. Surprisingly, no noteworthy age-related change is visible in the periodicity and subunit structural organization of the satellite DNA. These results suggest that the nucleosome positioning and the periodicity of liver satellite DNA do not vary with age.

Nuclease susceptibility of the rat liver satellite DNA-containing chromatin decreases with age

Nuclease susceptibility of the satellite DNA-containing chromatin of the liver of young (18 +/- 2 weeks) and old (100 +/- 5 weeks) rats was analysed using nick-translated rat 185 bp satellite I DNA fragment cloned in pBR322. With increasing concentration of DNaseI and micrococcal nuclease (MNase), multimeric forms of the satellite ladder gradually disappear in both the ages. The rate of disappearance is faster in young rats as compared to old ones. Such age-dependent decrease in the susceptibility of satellite DNA-containing chromatin reflects its condensation towards heterochromatization in old age.

Nucleosomal organization of the rat liver satellite DNA-containing chromatin during aging

Nucleosomal organization of the satellite DNA-containing chromatin of the liver of young (18 +/- 2 weeks) and old (100 +/- 5 weeks) rats was examined by nucleases and satellite I DNA probe. The satellite DNA-containing chromatin exhibits lower accessibility to endogenous endonucleases in old rats. The nucleosomal repeat length of this chromatin as investigated from digestion with endogenous endonucleases and MNase differs remarkably from bulk chromatin, though it does not alter with age. However, age-dependent loss of satellite DNA is apparent from hybridization results. Furthermore, DNase I analysis of the satellite DNA-containing chromatin at nucleosomal level reveals a relatively loose organization in young rats than old ones. It also shows an altered 10 bp periodicity as compared to bulk chromatin in both ages. These findings establish organizational differences between rat liver bulk and satellite DNA-containing chromatin. They further show that repeat length and altered 10 bp periodicity are similar in young and old, but accessibility to nucleases declines with age.

Age-related analysis of EcoRI generated satellite DNA-containing chromatin of rat liver

EcoRI digestion of nuclei and their subsequent lysis with EDTA solubilizes 45% and 36% of chromatin DNA from the liver of young (18 +/- 2 weeks) and old (100 +/- 5 weeks) rats, respectively. After hybridization with 185 bp rat satellite I DNA, these soluble fractions are found to be enriched in specific DNA sequences such as satellite DNA. Besides regular repeat pattern, a major portion of the satellite chromatin forms higher order organization. Digestion kinetics confirms condensation of satellite DNA-containing chromatin similar to that of bulk chromatin in old age. Furthermore, densitometric scanning of the slot-blot of soluble chromatin fractions reveals loss of satellite DNA in the old. However, an increase in the linker histone H1 and its subfraction H1zero in the satellite DNA-enriched fraction of chromatin from old rats suggests greater compaction. These results provide the first evidence that the satellite DNA-containing chromatin differs in the liver of young and old rats.