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Cancer remains one of the leading causes of death globally. New immunotherapies that harness the patient’s immune system to fight cancer show promise, but their development requires analyzing the diversity of immune cells called T-cells. T-cells have receptors that recognize and bind to cancer cells. Sequencing these T-cell receptors allows to provide insights into their immune response, but extracting useful information is challenging. In this study, we propose a new computational method, TCellR2Vec, to select key features from T-cell receptor sequences for classifying different cancer types. We extracted features like amino acid composition, charge, and diversity measures and combined them with other sequence embedding techniques. For our experiments, we used a dataset of over 50,000 T-cell receptor sequences from five cancer types, which showed that TCellR2Vec improved classification accuracy and efficiency over baseline methods. These results demonstrate TCellR2Vec’s ability to capture informative aspects of complex T-cell receptor sequences. By improving computational analysis of the immune response, TCellR2Vec could aid the development of personalized immunotherapies tailored to each patient’s T-cells. This has important implications for creating more effective cancer treatments based on the individual’s immune system.

Data visualization plays a crucial role in gaining insights from high-dimensional datasets. ISOMAP is a popular algorithm that maps high-dimensional data into a lower-dimensional space while preserving the underlying geometric structure. However, ISOMAP can be computationally expensive, especially for large datasets, due to the computation of the pairwise distances between data points. The motivation behind this study is to improve efficiency by leveraging an approximate method, which is based on random kitchen sinks (RKS). This approach provides a faster way to compute the kernel matrix. Using RKS significantly reduces the computational complexity of ISOMAP while still obtaining a meaningful low-dimensional representation of the data. We compare the performance of the approximate ISOMAP approach using RKS with the traditional t-SNE algorithm. The comparison involves computing the distance matrix using the original high-dimensional data and the low-dimensional data computed from both t-SNE and ISOMAP. The quality of the low-dimensional embeddings is measured using several metrics, including mean squared error (MSE), mean absolute error (MAE), and explained variance score (EVS). Additionally, the runtime of each algorithm is recorded to assess its computational efficiency. The comparison is conducted on a set of protein sequences, used in many bioinformatics tasks. We use three different embedding methods based on k-mers, minimizers, and position weight matrix (PWM) to capture various aspects of the underlying structure and the relationships between the protein sequences. By comparing different embeddings and by evaluating the effectiveness of the approximate ISOMAP approach using RKS and comparing it against t-SNE, we provide insights on the efficacy of our proposed approach. Our goal is to retain the quality of the low-dimensional embeddings while improving the computational performance.

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has generated a renewed interest in the larger family of Coronaviridae, which causes a variety of different respiratory infections in a variety of different hosts. Understanding the mechanisms behind the ability of a family of viruses to spill over into different hosts is an ongoing study. In this work, we studied the relationship between specific amino acid sites and the solvent accessibility of the surface (or spike) protein of different Coronaviridae. Since host specificity hinges on the portion(s) of the protein that interfaces with the host cell membrane, there could be a relationship between information gain in specific amino acid sites and solvent accessibility. We found a connection between sites with high information gain and solvent accessibility within several major subgenera of Coronaviridae. Such a connection could be used to study other lesser-known families of viruses, which is desirable because information gain is much easier to compute when the number of sequences is large, as we show. Finally, we produced a visualization of the sequences within each major subgenus and discussed several regions of interest, as well as focused on some pairs of Coronaviridae hosts of interest.

Abstract The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome—millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses, is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches with different perturbation budgets are more robust (and accurate) than others for specific embedding methods to certain noise simulations on the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.

Human existence is complemented by environmental sounds as by-products of people’s activities as well as intentionally generated sounds that allow human society to function, including transport and traffic sounds and notification sounds. The resulting soundscapes surround and permeate people’s daily existence. Technological, as well as behavioural change causes some of these sounds to become extinct at the local or universal level. While expressions of human communication through spoken words (language) and song are deemed to be heritage and thus formally collected and documented, there is a general lack of consideration of the heritage potential of anthropogenic environmental sounds. Focussing on examples from the state of NSW (Australia), this paper discusses sound loss in the urban heritage environment and advances two variations of a conceptual framework to assist heritage practitioners in decision-making to assess heritage potential in order to safeguard some of these sounds for the future.

Despite church bell ringing being directly influenced by purposive human action, often as a liturgical function, it creates a community soundscape with ascribed heritage values. While general heritage management processes and decisions are informed by heritage professionals with a broader range of experience, we find that church bell ringing is contrary to this process. The COVID-19 pandemic has demonstrated how a stochastic disruptive event can dramatically alter soundscapes on a community-wide scale. Here, the effective power over bell ringing often rested with the individual clergy at the local level and is subject to that individual’s personal preferences. This has serious implications to non-traditional forms of heritage, such as intangible sounds and soundscapes. In realizing the value of sound signals and soundmarks, we highlight the need to formally recognize these sounds of religious settings and consider them in heritage frameworks.

The assessment and documentation of visual, auditory, and olfactory sensory experiences within urban environments is an emerging focus of research that has implications for the understanding of cultural heritage as well as community mental health. The common methodology to identify, describe, and document smells within environmental settings is smell walks, where individuals walk predefined transects, identifying and locating encountered odours and odour attributes (e.g., intensity, hedonic tone). As the locations of smell walks vary (e.g., indoor and outdoor markets, urban parks, etc.), localised environmental parameters such as airflow and temperature affect the dispersion and attenuation of the odours, influencing the results. This paper presents a rapid, systematic review of the factors that influence the attenuation of odours in the urban outdoor environment, in particular, in the context of outdoor markets. Although there is an abundance of literature on wind patterns in urban canyons discussing the influence of microtopography, this can only be applied cum grano salis to outdoor markets settings. Various avenues for future research are outlined.

Annually, there are between 2500 and 3000 Christmas markets in Germany. While purported to be rooted in century-old tradition, the current concept of the markets, shaped in the 1930s, gradually transformed from primarily mercantile operations to experiential events. The experiential dimension is a collection of visual, auditory, and olfactory components that create a compound sensory response: the ‘Christmas atmosphere’. The prevalence of COVID-19 meant that traditional Christmas markets were largely absent from the festive calendar in Germany in 2020, disrupting the usual sensory experiences associated with these events. A review of the online presence showed that augmented markets and virtual reality were subsequently utilized in an attempt to re-create the experience and the ambience of the traditional markets, but had limited interactivity with many of the senses. We explore to what extent these multiple-sensory components may have been lost during the Christmas period of 2020 due to the COVID-19-induced transition from the traditional multisensory live market to a predominantly online experience, and highlight problems which arise through the documentation of such complex intangible heritage.

Biological sequence analysis is an essential step toward building a deeper understanding of the underlying functions, structures, and behaviors of the sequences. It can help in identifying the characteristics of the associated organisms, such as viruses, etc., and building prevention mechanisms to eradicate their spread and impact, as viruses are known to cause epidemics that can become global pandemics. New tools for biological sequence analysis are provided by machine learning (ML) technologies to effectively analyze the functions and structures of the sequences. However, these ML-based methods undergo challenges with data imbalance, generally associated with biological sequence datasets, which hinders their performance. Although various strategies are present to address this issue, such as the SMOTE algorithm, which creates synthetic data, however, they focus on local information rather than the overall class distribution. In this work, we explore a novel approach to handle the data imbalance issue based on generative adversarial networks (GANs), which use the overall data distribution. GANs are utilized to generate synthetic data that closely resembles real data, thus, these generated data can be employed to enhance the ML models’ performance by eradicating the class imbalance problem for biological sequence analysis. We perform four distinct classification tasks by using four different sequence datasets (Influenza A Virus, PALMdb, VDjDB, Host) and our results illustrate that GANs can improve the overall classification performance.

The emergence of third-generation single-molecule sequencing (TGS) technology has revolutionized the generation of long reads, which are essential for genome assembly and have been widely employed in sequencing the SARS-CoV-2 virus during the COVID-19 pandemic. Although long-read sequencing has been crucial in understanding the evolution and transmission of the virus, the high error rate associated with these reads can lead to inadequate genome assembly and downstream biological interpretation. In this study, we evaluate the accuracy and robustness of machine learning (ML) models using six different embedding techniques on SARS-CoV-2 error-incorporated genome sequences. Our analysis includes two types of error-incorporated genome sequences: those generated using simulation tools to emulate error profiles of long-read sequencing platforms and those generated by introducing random errors. We show that the spaced k-mers embedding method achieves high accuracy in classifying error-free SARS-CoV-2 genome sequences, and the spaced k-mers and weighted k-mers embedding methods are highly accurate in predicting error-incorporated sequences. The fixed-length vectors generated by these methods contribute to the high accuracy achieved. Our study provides valuable insights for researchers to effectively evaluate ML models and gain a better understanding of the approach for accurate identification of critical SARS-CoV-2 genome sequences.

Annually, there are between 2500 and 3000 Christmas markets in Germany. While claiming to be rooted in century-old tradition, the current concept of the markets, shaped in the 1930s, gradually transformed from primarily mercantile operations to experiential events. In contemporary times, these markets also have quantifiable social and experiential dimensions. The last of these, the experiential dimension, is a mélange of visual, auditory, and olfactory components that create a compound sensory response—the “Christmas atmosphere”. There are copious intangible elements of these markets, which combined create a sum greater than the addition of each of the individual constituent components. We find the recognition of such collections of entwined intangible heritage is novel, warranting further research and documentation, as standard approaches to the identification and management of intangible cultural heritage are too limiting.

As a social species, humans have developed soundscapes that surround, and to some extent circumscribe, their daily existence. The concept of aural heritage, its conceptualization and its management represent a rapidly expanding area of research, covering aspects of both natural and human heritage. However, there have been no contemporary regional or supra-regional studies that examine the nature of sound making in Christian religious settings, nor the extent to which it is still used. This paper presents the results of a survey into the presence of bells and bell ringing practices among five major Christian denominations in New South Wales, and examines to what extent bell ringing is still practiced and what factors may determine any differentiation. In doing so, it provides an objective basis from which to investigate future changes in bell ringing practices, and provides a solid foundation with reference to aural heritage of sound in a religious setting.

The Washington Arms Limitation Treaty 1922 was arguably one the most significant disarmament treaties of the first half of the 20th century. It can be shown that the heritage items associated with this treaty are still extant. Ship’s bells are one of the few moveable objects that are specific to the operational life of a ship and are therefore highly symbolic in representing a vessel. This paper surveys which bells of the ships scrapped under conditions of the Washington Arms Limitation Treaty are known to exist. A typology of ship’s bells has been developed to understand the nature of bell provisioning to vessels newly commissioned into the U.S. Navy. Each of the countries associated with the Washington Treaty have divergent disposal practices with respect to navy property, and this is reflected in both the prevalence and nature of custodianship of ship’s bells from this period. Such procedures range from the U.S. requirement commanding all surplus Navy property to be deemed government property upon ship deactivation, to the British practice of vending ship’s bells to private parties at public sales. However, ship’s bells, like many obsolete functional items, can be regarded as iconic in terms of heritage and therefore warrant attention for future preservation and presentation in the public domain.

The study of host specificity has important connections to the question about the origin of SARS-CoV-2 in humans which led to the COVID-19 pandemic—an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona)viruses, such as SARS, which was found to be transmitted through civets. The study of the different hosts which can be potential carriers and transmitters of deadly viruses to humans is crucial to understanding, mitigating, and preventing current and future pandemics. In coronaviruses, the surface (S) protein, or spike protein, is important in determining host specificity, since it is the point of contact between the virus and the host cell membrane. In this paper, we classify the hosts of over five thousand coronaviruses from their spike protein sequences, segregating them into clusters of distinct hosts among birds, bats, camels, swine, humans, and weasels, to name a few. We propose a feature embedding based on the well-known position weight matrix (PWM), which we call PWM2Vec, and we use it to generate feature vectors from the spike protein sequences of these coronaviruses. While our embedding is inspired by the success of PWMs in biological applications, such as determining protein function and identifying transcription factor binding sites, we are the first (to the best of our knowledge) to use PWMs from viral sequences to generate fixed-length feature vector representations, and use them in the context of host classification. The results on real world data show that when using PWM2Vec, machine learning classifiers are able to perform comparably to the baseline models in terms of predictive performance and runtime—in some cases, the performance is better. We also measure the importance of different amino acids using information gain to show the amino acids which are important for predicting the host of a given coronavirus. Finally, we perform some statistical analyses on these results to show that our embedding is more compact than the embeddings of the baseline models.

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail, unlike any virus before it. On the one hand, this will help biologists, policymakers, and other authorities to make timely and appropriate decisions to control the spread of the coronavirus. On the other hand, such studies will help to more effectively deal with any possible future pandemic. Since the SARS-CoV-2 virus contains different variants, each of them having different mutations, performing any analysis on such data becomes a difficult task, given the size of the data. It is well known that much of the variation in the SARS-CoV-2 genome happens disproportionately in the spike region of the genome sequence—the relatively short region which codes for the spike protein(s). In this paper, we propose a robust feature-vector representation of biological sequences that, when combined with the appropriate feature selection method, allows different downstream clustering approaches to perform well on a variety of different measures. We use such proposed approach with an array of clustering techniques to cluster spike protein sequences in order to study the behavior of different known variants that are increasing at a very high rate throughout the world. We use a k-mers based approach first to generate a fixed-length feature vector representation of the spike sequences. We then show that we can efficiently and effectively cluster the spike sequences based on the different variants with the appropriate feature selection. Using a publicly available set of SARS-CoV-2 spike sequences, we perform clustering of these sequences using both hard and soft clustering methods and show that, with our feature selection methods, we can achieve higher F1 scores for the clusters and also better clustering quality metrics compared to baselines.

Background: The authors investigated whether acetylcholine-induced contraction in pulmonary venous smooth muscle (PVSM) is associated with the activation of specific protein kinase C (PKC) isoforms.Methods: Isolated canine pulmonary venous rings without endothelium were suspended in modified Krebs-Ringer's buffer for measurement of isometric tension. The effects of nonspecific PKC inhibition (bisindolylmaleimide I; 3 x 10 m) and conventional PKC isoform inhibition (Gö7936 10 m) on the acetylcholine dose-response relation were assessed. The expression of conventional PKC isoforms (alpha, beta, gamma), novel PKC isoforms (delta, epsilon, theta), and atypical PKC isoforms (zeta, iota, mu) was measured in PVSM cells by Western blot analysis. The immunofluorescence technique and confocal microscopy were used to localize the cellular distribution of PKC isoforms before and after the addition of acetylcholine.Results: Acetylcholine caused dose-dependent contraction in E-pulmonary veins. Pretreatment with bisindolylmaleimide I or Gö7936 attenuated acetylcholine contraction. PKC-alpha, -iota, -mu, and -zeta were expressed, whereas PKC-beta, -gamma, -delta, -epsilon;, and -theta were not expressed in PVSM cells. Immunofluorescence staining for PKC isoforms showed that in unstimulated cells, PKC-alpha and PKC-mu were detected only in the cytoplasm. PKC-iota and PKC-zeta also exhibited a cytoplasmic immunofluorescence pattern, which was especially abundant in the perinuclear zone. Activation with acetylcholine induced translocation of PKC-alpha from cytoplasm to membrane, whereas acetylcholine had no effect on the other PKC isoforms. Translocation of PKC-alpha in response to acetylcholine was blocked by the muscarinic receptor antagonist, atropine.Conclusion: Acetylcholine contraction is attenuated by PKC inhibition in PVSM. Acetylcholine induces translocation of PKC-alpha from cytoplasm to membrane in PVSM. These results suggest that PKC-dependent acetylcholine contraction in PVSM may involve activation and translocation of PKC-alpha. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the incidence of whiplash-associated disorder [WAD]. Methods: Emergency admission data for motor vehicle collisions from the Hope Hospital in Manchester, United Kingdom were analyzed from 1982 to 1997. From 1995, whiplash-associated disorders were classed into WAD 1, 2, 3 for their incidence, along with the prevalence of nervousness in these patients. Results: In 1982, seat-belt legislation was introduced, the next year, the prevalence of WAD rose 268%. It subsequently continued to rise at an alarming rate averaging 152% yearly for the next 15 years. The compound percent yearly rise from 1982 to 1990 for all patients involved in road traffic accidents was 7.2% per annum, and for WAD cases 34%. From 1990 to 1997 the road traffic accidents rose compound 12.8%, and for WAD 14%. Among patients classified into WAD grades who were not nervous, WAD 1 and 2 had the best rate of recovery at six months. Among nervous patients, the incidence of recovery for WAD 2 and 3 at six months was reduced from WAD 1. Conclusions: In hospital emergency room admissions, the whiplash incidence has risen at a very high yearly rate, far in excess of general road traffic accident cases. The reasons are probably multiple, and complex. Nervousness among WAD patients appeared to hinder the rate of recovery. [ABSTRACT FROM AUTHOR]

The authors would like to make the following corrections in relation to the published paper (Parker and Spennemann 2020) [...]

For centuries, religious buildings have been using bells to call the faithful to prayer. Bell-ringing activity on church premises does not serve a purely religious function, however, as people in the community may perceive this activity secularly, attributing their own meanings and significances towards these sounds. If bell ringing (or the actual sound) were found to have great significance to a specific community, denomination, or a regionality bracket, this may have future implications in any management of these resources. There is a need to hear the voices of the actual practitioners and their perceptions regarding what they, their congregations, and their host communities feel. This paper represents the first large-scale assessment of the views of practitioners of five major Christian denominations with regards to bell-ringing practice and its role in contemporary society.

Abstract Background Inactivaion of tumor suppressor genes (TSGs) by promoter CpG methylation frequently occurs in tumorigenesis, even in the early stages, contributing to the initiation and progression of human cancers. Deleted in lung and esophageal cancer 1 (DLEC1), located at the 3p22-21.3 TSG cluster, has been identified frequently silenced by promoter CpG methylation in multiple carcinomas, however, no study has been performed for lymphomas yet. Methods We examined the expression of DLEC1 by semi-quantitative reverse transcription (RT)-PCR, and evaluated the promoter methylation of DLEC1 by methylation-specific PCR (MSP) and bisulfite genomic sequencing (BGS) in common lymphoma cell lines and tumors. Results Here we report that DLEC1 is readily expressed in normal lymphoid tissues including lymph nodes and PBMCs, but reduced or silenced in 70% (16/23) of non-Hodgkin and Hodgkin lymphoma cell lines, including 2/6 diffuse large B-cell (DLBCL), 1/2 peripheral T cell lymphomas, 5/5 Burkitt, 6/7 Hodgkin and 2/3 nasal killer (NK)/T-cell lymphoma cell lines. Promoter CpG methylation was frequently detected in 80% (20/25) of lymphoma cell lines and correlated with DLEC1 downregulation/silencing. Pharmacologic demethylation reversed DLEC1 expression in lymphoma cell lines along with concomitant promoter demethylation. DLEC1 methylation was also frequently detected in 32 out of 58 (55%) different types of lymphoma tissues, but not in normal lymph nodes. Furthermore, DLEC1 was specifically methylated in the sera of 3/13 (23%) Hodgkin lymphoma patients. Conclusions Thus, methylation-mediated silencing of DLEC1 plays an important role in multiple lymphomagenesis, and may serve as a non-invasive tumor marker for lymphoma diagnosis.

Abstract Background Invasive ductal and lobular carcinomas (IDC and ILC) are the most common histological types of breast cancer. Clinical follow-up data and metastatic patterns suggest that the development and progression of these tumors are different. The aim of our study was to identify gene expression profiles of IDC and ILC in relation to normal breast epithelial cells. Methods We examined 30 samples (normal ductal and lobular cells from 10 patients, IDC cells from 5 patients, ILC cells from 5 patients) microdissected from cryosections of ten mastectomy specimens from postmenopausal patients. Fifty nanograms of total RNA were amplified and labeled by PCR and in vitro transcription. Samples were analysed upon Affymetrix U133 Plus 2.0 Arrays. The expression of seven differentially expressed genes (CDH1, EMP1, DDR1, DVL1, KRT5, KRT6, KRT17) was verified by immunohistochemistry on tissue microarrays. Expression of ASPN mRNA was validated by in situ hybridization on frozen sections, and CTHRC1, ASPN and COL3A1 were tested by PCR. Results Using GCOS pairwise comparison algorithm and rank products we have identified 84 named genes common to ILC versus normal cell types, 74 named genes common to IDC versus normal cell types, 78 named genes differentially expressed between normal ductal and lobular cells, and 28 named genes between IDC and ILC. Genes distinguishing between IDC and ILC are involved in epithelial-mesenchymal transition, TGF-beta and Wnt signaling. These changes were present in both tumor types but appeared to be more prominent in ILC. Immunohistochemistry for several novel markers (EMP1, DVL1, DDR1) distinguished large sets of IDC from ILC. Conclusion IDC and ILC can be differentiated both at the gene and protein levels. In this study we report two candidate genes, asporin (ASPN) and collagen triple helix repeat containing 1 (CTHRC1) which might be significant in breast carcinogenesis. Besides E-cadherin, the proteins validated on tissue microarrays (EMP1, DVL1, DDR1) may represent novel immunohistochemical markers helpful in distinguishing between IDC and ILC. Further studies with larger sets of patients are needed to verify the gene expression profiles of various histological types of breast cancer in order to determine molecular subclassifications, prognosis and the optimum treatment strategies.

The scientific literature on marine and coastal climate change has proliferated in recent decades. Translating and communicating this evidence in a timely, and accessible manner, is critical to support adaptation, but little is being done to summarise the latest science for decision makers. For Small Island Developing States (SIDS), which are highly vulnerable to marine and coastal climate change impacts, there is an urgent need to make the latest science readily available to inform national policy, leverage climate funding and highlight their vulnerability for international reports and climate negotiations. Climate change report cards are a proven successful way of presenting climate change information in an easily accessible and informative manner. Here we compare the development of marine climate change report cards for Caribbean and Pacific Commonwealth SIDS as a means of translating the latest science for decision makers. Regional engagement, priority issues and lessons learnt in these regions are compared, and future opportunities identified., (Crown Copyright © 2019. Published by Elsevier Ltd. All rights reserved.)

Study Question: Is endometriosis associated with abnormally located endometrial basalis-like (SSEA1+/SOX9+) cells in the secretory phase functionalis and could they contribute to ectopic endometriotic lesion formation?, Summary Answer: Women with endometriosis had an abnormally higher number of basalis-like SSEA1+/SOX9+ epithelial cells present in the stratum functionalis and, since these cells formed 3D structures in vitro with phenotypic similarities to ectopic endometriotic lesions, they may generate ectopic lesions following retrograde menstruation., What Is Known Already: Endometrial basalis cells with progenitor potential are postulated to play a role in the pathogenesis of endometriosis and SSEA1 and nuclear SOX9 (nSOX9) mark basalis epithelial cells that also have some adenogenic properties in vitro. Induction of ectopic endometriotic lesions in a baboon model of endometriosis produces characteristic changes in the eutopic endometrium. Retrograde menstruation of endometrial basalis cells is proposed to play a role in the pathogenesis of endometriosis., Study Design, Size, Duration: This prospective study included endometrial samples from 102 women with and without endometriosis undergoing gynaecological surgery and from six baboons before and after induction of endometriosis, with in vitro assays examining the differentiation potential of human basalis-like cells., Participants/materials, Setting, Methods: The study was conducted at a University Research Institute. SSEA1 and SOX9 expression levels were examined in human endometrial samples from women aged 18-55 years (by immunohistochemistry (IHC) and qPCR) and from baboons (IHC). The differential gene expression and differentiation potential was assessed in freshly isolated SSEA1+ endometrial epithelial cells from women with and without endometriosis (n = 8/group) in vitro. In silico analysis of selected published microarray datasets identified differential regulation of genes of interest for the mid-secretory phase endometrium of women with endometriosis relative to that of healthy women without endometriosis., Main Results and the Role of Chance: Women with endometriosis demonstrated higher number of basalis-like cells (SSEA1+, nSOX9+) in the functionalis layer of the eutopic endometrium compared with the healthy women without endometriosis in the secretory phase of the cycle (P < 0.05). Induction of endometriosis resulted in a similar increase in basalis-like epithelial cells in the eutopic baboon endometrium. The isolated SSEA1+ epithelial cells from the eutopic endometrium of women with endometriosis had higher expression of OCT4, NANOG, FUT4 mRNA (P = 0.05, P = 0.007, P = 0.018, respectively) and they differentiated into ectopic endometriotic gland-like structures in 3D culture, but not into mesodermal lineages (adipose or bone cells)., Large Scale Data: N/A., Limitations, Reasons for Caution: Small sample size. Bioinformatics analysis and results depends on the quality of published microarray datasets and the stringency of patient selection criteria employed. Differentiation of SSEA-1+ cells was only examined for two mesodermal lineages (adipogenic and osteogenic)., Wider Implications of the Findings: Since endometrial epithelial cells with SSEA1+/nSOX9+ basalis-like phenotype generate endometriotic gland-like structures in vitro, they may potentially be a therapeutic target for endometriosis. An in depth analysis of the function of basalis-like eutopic endometrial epithelial cells might provide insights into their potential deregulation in other disorders of the endometrium including heavy menstrual bleeding and endometrial cancer where their function may be aberrant., Study Funding/competing Interest(s): We acknowledge the support by Wellbeing of Women project grant RG1073 (D.K.H., C.E.G.) and R01 HD083273 from the National Institutes of Health (A.T.F.). We also acknowledge the support of Liverpool Women's Hospital Foundation Trust (J.D.), Institute of Translational Medicine (L.D.S., H.A.L., A.J.V., D.K.H.), University of Liverpool, the National Health and Medical Research Council of Australia ID 1042298 (C.E.G.) and the Victorian Government Operational Infrastructure Support Fund. All authors declare no conflict of interest.

Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.

Purpose of Review: There is considerable interest in the idea of generating stem and precursor cells that can differentiate into kidney cells and be used to treat kidney diseases. Within this field, we highlight recent research articles focussing on mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and kidney-derived stem/progenitor cells (KSPCs)., Recent Findings: In preclinical studies, MSCs ameliorate varied acute and chronic kidney diseases. Their efficacy depends on immunomodulatory and paracrine properties but MSCs do not differentiate into functional kidney epithelia. iPSCs can be derived from healthy individuals and from kidney patients by forced expression of precursor genes. Like ESCs, iPSCs are pluripotent and so theoretically they have the potential to form functional kidney epithelia when used therapeutically. KSPCs, existing as cell subsets within adult and developing kidneys, constitute attractive future therapeutic agents., Summary: Results from preclinical studies are encouraging but caution is required regarding potential human therapeutic applications because molecular, morphological and functional characterization of 'kidney cells' generated from ECSs, iPSCs, KSPCs have not been exhaustive. The long-term safety of renal stem and precursor cells needs more study, including potential negative effects on renal growth and their potential for tumor formation.

Most species of invertebrate animals cannot synthesise sterols de novo and many that feed on plants dealkylate phytosterols (mostly C(29) and C(28)) yielding cholesterol (C(27)). The final step of this dealkylation pathway involves desmosterol reductase (DHCR24)-catalysed reduction of desmosterol to cholesterol. We now report the molecular characterisation in the silkworm, Bombyx mori, of such a desmosterol reductase involved in production of cholesterol from phytosterol, rather than in de novo synthesis of cholesterol. Phylogenomic analysis of putative desmosterol reductases revealed the occurrence of various clades that allowed for the identification of a strong reductase candidate gene in Bombyx mori (BGIBMGA 005735). Following PCR-based cloning of the cDNA (1.6 kb) and its heterologous expression in Saccharomyces cerevisae, the recombinant protein catalysed reduction of desmosterol to cholesterol in an NADH- and FAD-dependent reaction.Conceptual translation of the cDNA, that encodes a 58.9 kDa protein, and database searching, revealed that the enzyme belongs to an FAD-dependent oxidoreductase family. Western blotting revealed reductase protein expression exclusively in the microsomal subcellular fraction and primarily in the gut. The protein is peripherally associated with microsomal membranes. 2D-native gel and PAGE analysis revealed that the reductase is part of a large complex with molecular weight approximately 250 kDa. The protein occurs in midgut microsomes at a fairly constant level throughout development in the last two instars, but is drastically reduced during the wandering stage in preparation for metamorphosis. Putative Broad Complex transcription factor-binding sites detectable upstream of the DHCR24 gene may play a role in this down-regulation.

Self-renewal of in vitro cultured mouse embryonic stem (mES) cells is dependent on the presence of leukemia inhibitory factor (LIF). LIF induces overexpression and tyrosine phosphorylation of STAT3 (signal transducer and activator of transcription 3) and its subsequent nuclear translocation. The molecular chaperone heat shock protein 90 (Hsp90) is involved in the activation and maturation of a wide variety of substrate proteins. We investigated the effect of LIF withdrawal on the protein expression levels of STAT3 and Hsp90 and on the interactions between STAT3 and Hsp90. Taken together the data presented here suggest that LIF promotes the interaction of Hsp90 with STAT3 during self-renewal, indicating a potentially pivotal role for Hsp90 in the LIF-based maintenance of self-renewal of mouse embryonic stem cells.

We assessed the roles of the protein kinase C (PKC) and the tyrosine kinase (TK) signaling pathways in regulating capacitative calcium entry (CCE) in human pulmonary artery smooth muscle cells (PASMCs) and investigated the effects of intravenous anesthetics (midazolam, propofol, thiopental, ketamine, etomidate, morphine, and fentanyl) on CCE in human PASMCs. Fura-2-loaded human PASMCs were placed in a dish (37 degrees C) on an inverted fluorescence microscope. Intracellular Ca2+ concentration ([Ca2+]i) was measured as the 340/380 fluorescence ratio in individual PASMCs. Thapsigargin, a sarcoplasmic reticulum Ca2+-adenosine triphosphatase inhibitor, was used to deplete intracellular Ca2+ stores after removing extracellular Ca2+. CCE was then activated by restoring extracellular Ca2+ (2.2 mM). The effects of PKC activation and inhibition, TK inhibition, and the intravenous anesthetics on CCE were assessed. Thapsigargin caused a transient increase in [Ca2+]i. Restoring extracellular Ca2+ caused a rapid peak increase in [Ca2+]i, followed by a sustained increase in [Ca2+]i; i.e., CCE was stimulated in human PASMCs. PKC activation attenuated (P < 0.05), whereas PKC inhibition potentiated (P < 0.05), both peak and sustained CCE. TK inhibition attenuated (P < 0.05) both peak and sustained CCE. Midazolam, propofol, and thiopental each attenuated (P < 0.05) both peak and sustained CCE, whereas ketamine, etomidate, morphine, and fentanyl had no effect on CCE. Our results suggest that CCE in human PASMCs is influenced by both the TK and PKC signaling pathways. Midazolam, propofol, and thiopental each attenuated CCE, whereas ketamine, etomidate, morphine, and fentanyl had no effect on CCE.

Background: Pulmonary venous contraction can increase pulmonary capillary pressure and pulmonary edema. In the present study, we investigated the direct effects of ketamine, etomidate, thiopental, and midazolam on pulmonary venous contraction and myofilament Ca2+ sensitivity in permeabilized pulmonary venous smooth muscle (PVSM)., Methods: The effects of these IV anesthetics on acetylcholine contraction were assessed in isolated canine pulmonary vein rings. Tension and [Ca2+]i were measured simultaneously in fura-2 loaded endothelium-denuded PVSM strips after being permeabilized with alpha-toxin. The effects of the IV anesthetics on tension ([Ca2+]i remains constant) in the absence or the presence of muscarinic receptor activation (acetylcholine) were assessed. The immunofluorescence technique and confocal microscopy were used to localize the cellular distribution of protein kinase C (PKC) isoforms in PVSM cells before and after the addition of ketamine., Results: Ketamine, etomidate, and midazolam each attenuated acetylcholine contraction dose-dependently, whereas thiopental had no effect. None of the IV anesthetics alone had an effect on tension in strips at constant [Ca2+]i (i.e., they had no direct effect on myofilament Ca2+ sensitivity). Acetylcholine increased tension by 56% +/- 7% at constant [Ca2+]i. In acetylcholine-stimulated strips, etomidate, midazolam, and thiopental had no additional effect on tension at constant [Ca2+]i, whereas ketamine decreased tension by 33% +/- 3%. Activation with acetylcholine induced translocation of PKC from cytoplasm to membrane, and this effect was blocked by ketamine., Conclusions: Ketamine, etomidate, and midazolam each attenuated acetylcholine-induced pulmonary venous contraction. Ketamine attenuates acetylcholine contraction by inhibiting the acetylcholine-induced increase in myofilament Ca2+ sensitivity and the acetylcholine-induced translocation of PKCalpha.

Background: The authors' objective was to identify the role of the Na+-Ca2+ exchanger (NCX) in mediating the contractile dysfunction observed in diabetic cardiomyocytes before and after exposure to propofol., Methods: Freshly isolated ventricular myocytes were obtained from normal and diabetic rat hearts. Intracellular concentration of Ca2+ and cell shortening were simultaneously measured in electrically stimulated, ventricular myocytes using fura-2 and video-edge detection, respectively. Postrest potentiation (PRP) and sarcoplasmic reticulum Ca2+ load were used to assess propofol-induced changes in the activity of the NCX., Results: Propofol (10 microM) increased PRP in diabetic cardiomyocytes but had no effect on PRP in normal cardiomyocytes. Removal of sodium enhanced and KB-R7943 (reverse mode NCX inhibitor) blocked PRP in both normal and diabetic cardiomyocytes. In the absence of sodium, propofol enhanced PRP in diabetic cardiomyocytes but had no additional effect in normal cardiomyocytes. KB-R7943 completely blocked propofol-induced potentiation of peak intracellular concentration of Ca2+ and shortening in both cell types. Propofol increased sarcoplasmic reticulum Ca2+ load and prolonged removal of cytosolic Ca2+ in diabetic cardiomyocytes, but not in normal cardiomyocytes. Removal of sodium enhanced propofol-induced increases in sarcoplasmic reticulum Ca2+ load and further prolonged removal of cytosolic Ca2+, whereas KB-R7943 completely blocked propofol-induced increase in sarcoplasmic reticulum Ca2+ load. Protein kinase C inhibition with bisindolylmaleimide I prevented the propofol-induced increase in PRP and prolongation in Ca2+ removal., Conclusions: These data suggest that propofol enhances PRP via activation of reverse mode NCX, but attenuates Ca2+ removal from the cytosol via inhibition of forward mode NCX in diabetic cardiomyocytes. The actions of propofol are mediated via a protein kinase C-dependent pathway.

The physiological adjustment of organisms in response to temperature variation is a crucial part of coping with environmental stress. An important component of the cold response is the increase in membrane lipid unsaturation, and this has been linked to an enhanced resistance to the debilitating or lethal effects of cold. Underpinning the lipid response is the upregulation of fatty acid desaturases (des), particularly those introducing double bonds at the 9-10 position of saturated fatty acids. For plants and microbes there is good genetic evidence that regulation of des genes, and the consequent changes in lipid saturation, are causally linked to generation of a cold-tolerant phenotype. In animals, however, supporting evidence is almost entirely limited to correlations of saturation with cold conditions. We describe our recent attempts to provide a direct test of this relationship by genetic manipulation of the nematode Caenorhabditis elegans. We show that this species displays a strong cold tolerant phenotype induced by prior conditioning to cold, and that this is directly linked to upregulated des activity. However, whilst genetic disruption of des activity and lipid unsaturation significantly reduced cold tolerance, animals retained a substantial component of their stress tolerant phenotype produced by cold conditioning. This indicates that mechanisms other than lipid unsaturation play an important role in cold adaptation.

Pulmonary veins (PV) make a significant contribution to total pulmonary vascular resistance. We investigated the cellular mechanisms by which the intravenous anesthetics propofol and thiopental alter adenosine triphosphate-sensitive potassium (KATP+) channel relaxation in canine PV. The effects of KATP+ channel inhibition (glybenclamide), cyclooxygenase inhibition (indomethacin), nitric oxide synthase inhibition (L-NAME), and L-type voltage-gated Ca2+ channel inhibition (nifedipine) on vasorelaxation responses to levcromakalim (KATP+ channel activator) alone and in combination with the anesthetics were assessed. The maximal relaxation response to levcromakalim was attenuated by removing the endothelium and by L-NAME, but not by indomethacin. Propofol (10(-5), 3x10(-5), and 10(-4) M) and thiopental (10(-4) and 3x10(-4) M) each attenuated levcromakalim relaxation in endothelium-intact (E+) rings, whereas propofol (3x10(-5) and 10(-4) M) and thiopental (3x10(-4) M) attenuated levcromakalim relaxation in endothelium-denuded (E-) rings. In E+ rings, the anesthesia-induced attenuation of levcromakalim relaxation was decreased after pretreatment with L-NAME but not with indomethacin. In E-strips, propofol (10(-4) M) and thiopental (3x10(-4) M) inhibited decreases in tension and intracellular Ca2+ concentration ([Ca2+]i) in response to levcromakalim, and these changes were abolished by nifedipine. These findings indicate that propofol and thiopental attenuate the endothelium-dependent component of KATP+ channel-induced PV vasorelaxation via an inhibitory effect on the nitric oxide pathway. Both anesthetics also attenuate the PV smooth muscle component of KATP+ channel-induced relaxation by reducing the levcromakalim-induced decrease in [Ca2+]i via an inhibitory effect on L-type voltage-gated Ca2+ channels.

Purpose: To replicate an earlier National Cancer Institute of Canada (NCIC) trial that examined the effect on survival of the timing of thoracic radiotherapy (TRT) in patients with limited disease small-cell lung cancer (SCLC)., Patients and Methods: Patients received three cycles of cyclophosphamide, doxorubicin, and vincristine alternating with three cycles of etoposide and cisplatin. Three hundred twenty five chemotherapy- and radiotherapy-naïve patients were randomly assigned to either early TRT administered concurrently in the second cycle or late TRT administered concurrently with the sixth cycle; the dose was 40 Gy in 15 fractions over 3 weeks., Results: TRT was received by 92% and 82% of patients in the early and late arms, respectively (P = .01). Sixty-nine percent of patients in the early arm received all six courses of chemotherapy compared with 80% in the late arm (P = .003). There was no evidence of a survival difference; median overall survival time was 13.7 and 15.1 months in the early and late arms, respectively (P = .23). In a meta-analysis of all eight trials that compared early and late TRT, there were three in which the proportion of patients who completed their planned chemotherapy was similar between the TRT arms (hazard ratio [HR] = 0.73; 95% CI, 0.62 to 0.86) and five in which proportionally fewer patients in the early TRT arm completed their chemotherapy (HR = 1.06; 95% CI, 0.97 to 1.17)., Conclusion: This study failed to show a survival advantage for early TRT with chemotherapy in limited-stage SCLC, unlike the NCIC trial. However, the results of a meta-analysis suggest that it is essential to ensure that the delivery of chemotherapy is optimal when administered with early TRT.

Background: The authors' objective was to assess the role of protein kinase C (PKC) and nitric oxide synthase (NOS) in mediating the effects of propofol on diabetic cardiomyocyte contractility, intracellular free Ca2+ concentration ([Ca2+]i), and myofilament Ca2+ sensitivity., Methods: Freshly isolated ventricular myocytes were obtained from normal and diabetic rat hearts. [Ca2+]i and cell shortening were simultaneously measured in electrically stimulated, ventricular myocytes using fura-2 and video-edge detection, respectively. Actomyosin adenosine triphosphatase activity and troponin I (TnI) phosphorylation were assessed in [32P]orthophosphate-labeled myofibrils. Western blot analysis was used to assess expression of PKC and NOS., Results: Propofol (10 microM) decreased peak shortening by 47 +/- 6% with little effect on peak [Ca2+]i (92 +/- 5% of control) in diabetic myocytes. Maximal actomyosin adenosine triphosphatase activity was reduced by 43 +/- 7% and TnI phosphorylation was greater (32 +/- 6%) in diabetic myofibrils compared with normal. Propofol reduced actomyosin adenosine triphosphatase activity by 17 +/- 7% and increased TnI phosphorylation in diabetic myofibrils. PKC inhibition prevented the propofol-induced increase in TnI phosphorylation and decrease in shortening. Expression of PKC-alpha, PKC-delta, PKC-epsilon, and constitutive NOS were up-regulated and inducible NOS was expressed in diabetic cardiomyocytes. NOS inhibition attenuated the propofol-induced decrease in shortening., Conclusion: Myofilament Ca2+ sensitivity and, to a lesser extent, peak [Ca2+]i are decreased in diabetic cardiomyocytes. Increases in PKC and NOS expression in combination with TnI phosphorylation seem to contribute to the decrease in [Ca2+]i and myofilament Ca2+ sensitivity. Propofol decreases [Ca2+]i and shortening via a PKC-, NOS-dependent pathway.

Purpose: Our objective was to determine whether an L-type Ca2+ channel modulation could alter myocardial depression induced by midazolam or diazepam in adult rat ventricular myocytes., Methods: Freshly isolated rat ventricular myocytes were loaded with fura-2/AM and field-stimulated (0.3 Hz) at 28 degrees C. Amplitude and timing of intracellular Ca2+ concentration ([Ca2+]i) and myocyte shortening were simultaneously monitored in individual cells., Results: Midazolam (3-100 microM) caused a decrease in both peak [Ca2+]i and shortening. Diazepam (30, 100 microM) increased myocyte shortening and peak [Ca2+]i; however, higher concentration of diazepam (300 microM) decreased shortening and peak [Ca2+]i. Bay K 8644 (0.01-10 microM), an L-type Ca2+ channel agonist, caused dose-dependent increases in peak [Ca2+]i and shortening. In contrast, verapamil (0.1-50 microM), an L-type Ca(2+) channel antagonist, caused dose-dependent decreases in peak [Ca2+]i and shortening. Dose-response curves to benzodiazepines on peak [Ca2+]i and shortening were not affected by pretreatment with Bay K 8644 (0.1 microM) or verapamil (1 microM). Diazepam (30, 100 microM), but not midazolam (3-30 microM), increased shortening and [Ca2+]i in the presence or absence of L-type Ca2+ channel modulators. Diazepam (30 microM) and midazolam (10 microM) had no effect on peak [Ca2+]i of a caffeine-induced [Ca2+]i transient, which was used as a measure of SR Ca2+ content., Conclusion: Midazolam and diazepam have differential effects on cardiac E-C coupling. Diazepam, but not midazolam, enhances cardiac E-C coupling independent of L-type Ca2+ channel modulation.

Our objectives were to identify the relative contributions of [Ca2+]i and myofilament Ca2+ sensitivity in the pulmonary venous smooth muscle (PVSM) contractile response to the thromboxane A2 mimetic U-46619 and to assess the roles of PKC, tyrosine kinases (TK), and Rho-kinase (ROK) in that response. We tested the hypothesis that U-46619-induced contraction in PVSM is mediated by both increases in [Ca2+]i and myofilament Ca2+ sensitivity and that the PKC, TK, and ROK signaling pathways are involved. Isometric tension was measured in isolated endothelium-denuded (E-) canine pulmonary venous (PV) rings. In addition, [Ca2+]i and tension were simultaneously measured in fura-2-loaded E- PVSM strips. U-46619 (0.1 nM-1 microM) caused dose-dependent (P < 0.001) contraction in PV rings. U-46619 contraction was attenuated by inhibitors of L-type voltage-operated Ca2+ channels (nifedipine, P < 0.001), inositol 1,4,5-trisphosphate-mediated Ca2+ release (2-aminoethoxydiphenylborate, P < 0.001), PKC (bisindolylmaleimide I, P < 0.001), TK (tyrphostin A-47, P = 0.014), and ROK (Y-27632, P = 0.008). In PV strips, U-46619 contraction was associated with increases in [Ca2+]i and myofilament Ca2+ sensitivity. Both Ca2+ influx and release mediated the early transient increase in [Ca2+]i, whereas the late sustained increase in [Ca2+]i only involved Ca2+ influx. Inhibition of both PKC and ROK (P = 0.006 and P = 0.002, respectively), but not TK, attenuated the U-46619-induced increase in myofilament Ca2+ sensitivity. These results suggest that U-46619 contraction is mediated by Ca2+ influx, Ca2+ release, and increased myofilament Ca2+ sensitivity. The PKC, TK, and ROK signaling pathways are involved in U-46619 contraction.

From modeling studies it has been known for >10 years that purely inhibitory networks can produce synchronous output given appropriate balances of intrinsic and synaptic parameters. Several experimental studies indicate that synchronous activity produced by inhibitory networks is critical to the production of population rhythms associated with various behavioral states. Heterogeneity of inputs to inhibitory networks strongly affect their ability to synchronize. In this paper, we explore how the amount of input heterogeneity to two-cell inhibitory networks affects their dynamics. Using numerical simulations and bifurcation analyses, we find that the ability of inhibitory networks to synchronize in the face of heterogeneity depends nonmonotonically on each of the synaptic time constant, synaptic conductance and external drive parameters. Because of this, an optimal set of parameters for a given cellular model with various biophysical characteristics can be determined. We suggest that this could be a helpful approach to use in determining the importance of different, underlying biophysical details. We further find that two-cell coherence properties are maintained in larger 10-cell networks. As such, we think that a strategy of "embedding" small network dynamics in larger networks is a useful way to understand the contribution of biophysically derived parameters to population dynamics in large networks.