The demonstration of a herpesvirus, related to bovine herpesvirus 1, in reindeer with ulcerative and necrotizing lesions of the upper alimentary tract and nose

In 11 male reindeer, all esposed to transportation stress, signs of conjunctivitis and later on ulcerative and necrotizing lesions of the mucosa of the nostrils and mouth were recorded. Blood and secretions from the nose were sampled. Antibodies to bovine herpesvirus 1 (BHV-1) were detected in 2 animals. No animal had antibodies to bovine viral diarrhoea virus (BVDV). Virus isolation was negative. The sampling was repeated 2 weeks later and complemented with biopsies from the mouth lesions, fixed in formalin. At this occasion 3 animals were seropositive to BHV-1 and in biopsies from 2 of these intranuclear herpesvirus-like particles were found by means of electron microscopy. Four animals, 3 of them seropositive, were treated with cortison during 8 days. The size of the ulcers in the mouth increased in all animals. A herpesvirus was isolated from 3 of them at 10 different occasions. The ultrastructural investigation of the virus suspension demonstrated the presence of typical herpesvirus particles. On day 11 all 4 animals suffered from a severe diarrhoea and anorexia. On day 12 one animal died and on day 13 post challenge with cortison two additional animals died. The remaining animal was slaughtered on day 13. Bacteriological investigation revealed growth of Fusobacterium necrophorum from the spleen and oral wounds of all 4 animals. The animals were obviously subjected to an infection with a herpesvirus colsely related to BHV-1. Virus could be liberated by cortison treatment. It is possible that infections with the found herpesvirus, and the lesions caused by it, may be the background to earlier recorded severe outbreaks of necrobacillosis of the alimentary tract in reindeer herds

SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome

T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy driven by abnormal activity of transcription factors. Here we report an aberrant expression of the developmental transcription factor SIX6 in the TAL1-subtype of T-ALL. Our results demonstrate that the binding of TAL1 and GATA3 transcription factors into an upstream enhancer element directly regulates SIX6 expression. High expression of SIX6 was associated with inferior event-free survival within three independent patient cohorts. At a functional level, CRISPR-Cas9-mediated knockout of the SIX6 gene in TAL1 positive Jurkat cells induced changes in genes associated with the mTOR-, K-RAS-, and TNFα-related molecular signatures but did not impair cell proliferation or viability. There was also no acceleration of T-ALL development within a Myc driven zebrafish tumor model in vivo. Taken together, our results show that SIX6 belongs to the TAL1 regulatory gene network in T-ALL but is alone insufficient to influence the development or maintenance of T-ALL

BRD4 facilitates replication stress-induced DNA damage response.

Previous reports have demonstrated that select cancers depend on BRD4 to regulate oncogenic gene transcriptional programs. Here we describe a novel role for BRD4 in DNA damage response (DDR). BRD4 associates with and regulates the function of pre-replication factor CDC6 and plays an indispensable part in DNA replication checkpoint signaling. Inhibition of BRD4 by JQ1 or AZD5153 resulted in a rapid, time-dependent reduction in CHK1 phosphorylation and aberrant DNA replication re-initiation. Furthermore, BRD4 inhibition sensitized cancer cells to various replication stress-inducing agents, and synergized with ATR inhibitor AZD6738 to induce cell killing across a number of cancer cell lines. The synergistic interaction between AZD5153 and AZD6738 is translatable to in vivo ovarian cell-line and patient-derived xenograft models. Taken together, our study uncovers a new biological function of BRD4 and provides mechanistic rationale for combining BET inhibitors with DDR-targeted agents for cancer therapy

Survival Analysis and Cox Proportional Hazards Model Reporting in Pediatric Leukemia Studies : a Systematic Review

Survival (overall, event free, etc.) is the most-used outcome in clinical oncology studies. This study analyzed methodological reporting of survival analysis in pediatric leukemia studies, focusing on Cox proportional hazards (PH). We performed a systematic review of studies published between 2012 and 2021 in the five highest-ranking oncology and five highest-ranking hematology journals. The included studies had to focus on pediatric leukemia and utilize survival analyses. We extracted data on how the survival analysis methodology was reported and focused on Cox proportional hazards modeling and whether the PH assumption was checked. We screened 561 studies and included 103 in the analysis. The most-used crude survival analysis method was Kaplan–Meier, as 96 (94%) of the 103 studies applied it. Adjusted survival analysis was performed in 80 (78%) of the included studies, and the Cox PH model was used in 77 (96%) of these studies. The PH assumption was mentioned in 18 (23%) of the 77 studies that used the Cox PH model. Only nine studies (12%) stated how the PH assumption was assessed. We noted 10 (13%) studies with possible violations of the PH assumption. Overall, we found a need for improvement in the reporting of survival analysis and especially PH assumption in pediatric leukemia studies. The Cox PH model was the most-used adjusted survival analysis method but checking of the background assumption was not reported in most of the studies.publishedVersionPeer reviewe

Simple integrative preprocessing preserves what is shared in data sources

<p>Abstract</p> <p>Background</p> <p>Bioinformatics data analysis toolbox needs general-purpose, fast and easily interpretable preprocessing tools that perform data integration during exploratory data analysis. Our focus is on vector-valued data sources, each consisting of measurements of the same entity but on different variables, and on tasks where source-specific variation is considered noisy or not interesting. Principal components analysis of all sources combined together is an obvious choice if it is not important to distinguish between data source-specific and shared variation. Canonical Correlation Analysis (CCA) focuses on mutual dependencies and discards source-specific "noise" but it produces a separate set of components for each source.</p> <p>Results</p> <p>It turns out that components given by CCA can be combined easily to produce a linear and hence fast and easily interpretable feature extraction method. The method fuses together several sources, such that the properties they share are preserved. Source-specific variation is discarded as uninteresting. We give the details and implement them in a software tool. The method is demonstrated on gene expression measurements in three case studies: classification of cell cycle regulated genes in yeast, identification of differentially expressed genes in leukemia, and defining stress response in yeast. The software package is available at <url>http://www.cis.hut.fi/projects/mi/software/drCCA/</url>.</p> <p>Conclusion</p> <p>We introduced a method for the task of data fusion for exploratory data analysis, when statistical dependencies between the sources and not within a source are interesting. The method uses canonical correlation analysis in a new way for dimensionality reduction, and inherits its good properties of being simple, fast, and easily interpretable as a linear projection.</p

Discovery of Sexual Dimorphisms in Metabolic and Genetic Biomarkers

Metabolomic profiling and the integration of whole-genome genetic association data has proven to be a powerful tool to comprehensively explore gene regulatory networks and to investigate the effects of genetic variation at the molecular level. Serum metabolite concentrations allow a direct readout of biological processes, and association of specific metabolomic signatures with complex diseases such as Alzheimer's disease and cardiovascular and metabolic disorders has been shown. There are well-known correlations between sex and the incidence, prevalence, age of onset, symptoms, and severity of a disease, as well as the reaction to drugs. However, most of the studies published so far did not consider the role of sexual dimorphism and did not analyse their data stratified by gender. This study investigated sex-specific differences of serum metabolite concentrations and their underlying genetic determination. For discovery and replication we used more than 3,300 independent individuals from KORA F3 and F4 with metabolite measurements of 131 metabolites, including amino acids, phosphatidylcholines, sphingomyelins, acylcarnitines, and C6-sugars. A linear regression approach revealed significant concentration differences between males and females for 102 out of 131 metabolites (p-values<3.8 x 10(-4); Bonferroni-corrected threshold). Sex-specific genome-wide association studies (GWAS) showed genome-wide significant differences in beta-estimates for SNPs in the CPS1 locus (carbamoyl-phosphate synthase 1, significance level: p<3.8 x 10(-10); Bonferroni-corrected threshold) for glycine. We showed that the metabolite profiles of males and females are significantly different and, furthermore, that specific genetic variants in metabolism-related genes depict sexual dimorphism. Our study provides new important insights into sex-specific differences of cell regulatory processes and underscores that studies should consider sex-specific effects in design and interpretation

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

Peer reviewe

Parents' experiences of an abnormal ultrasound examination - vacillating between emotional confusion and sense of reality

<p>Abstract</p> <p>Background</p> <p>An ultrasound examination is an important confirmation of the pregnancy and is accepted without reflection to any prenatal diagnostic aspects. An abnormal finding often comes unexpectedly and is a shock for the parents. The aim was to generate a theoretical understanding of parents' experiences of the situation when their fetus is found to have an abnormality at a routine ultrasound examination.</p> <p>Methods</p> <p>Sixteen parents, mothers and fathers, whose fetus had been diagnosed with an abnormality during an ultrasound scan in the second or third trimester, were interviewed. The study employed a grounded theory approach.</p> <p>Results</p> <p>The core category <it>vacillating between the emotional confusion and sense of reality </it>is related to the main concern <it>assessment of the diagnosis impact on the well-being of the fetus</it>. Two other categories <it>Entering uncertainty </it>and <it>Involved in an ongoing change and adaptation </it>have each five sub-categories.</p> <p>Conclusions</p> <p>Parents are aware of that ultrasound examination is a tool for identifying abnormalities prenatally. The information about the abnormality initially results in broken expectations and anxiety. Parents become involved in ongoing change and adaptation. They need information about the ultrasound findings and the treatment without prolonged delay and in a suitable environment. The examiner who performs the ultrasound examination must be aware of how anxiety can be intensified by environmental factors. All parents should to be offered a professional person to give them <it>s</it>upport as a part of the routine management of this situation.</p

Psychiatric (Axis I) and personality (Axis II) disorders and subjective psychiatric symptoms in chronic tinnitus

Objective: Chronic tinnitus has been associated with several psychiatric disorders. Only few studies have investigated these disorders using validated diagnostic interviews. The aims were to diagnose psychiatric and personality disorders with structured interviews, to assess self-rated psychiatric symptoms and elucidate temporal relations between psychiatric disorders and tinnitus. Design: Current and lifetime DSM-IV diagnoses of axis-I (psychiatric disorders) and axis-II (personality disorders) were assessed using structured clinical interviews (SCID-I and -II). Current subjective psychiatric symptoms were evaluated via self-rating instruments: the Symptom Check List-90 (SCL-90), the Beck Depression Inventory, and the Dissociative Experiences Scale (DES). Study sample: 83 patients (mean age 51.7, 59% men) with chronic, disturbing tinnitus and a median Tinnitus Handicap Inventory score of 32. Results: The rates of lifetime and current major depression were 26.5% and 2.4%. The lifetime rate of obsessive-compulsive personality disorder (type C) was 8.4%. None of the patients had cluster B personality disorder or psychotic symptoms. The SCL-90 subscales did not differ from the general population, and median DES score was low, 2.4. Conclusions: Tinnitus patients are prone to episodes of major depression and often also have obsessive-compulsive personality features. Psychiatric disorders seem to be comorbid or predisposing conditions rather than consequences of tinnitus.Clinical trial reference: ClinicalTrials.gov (ID NCT 01929837).</p