Association of tyrosine hydroxylase 01 (TH01) microsatellite and insulin gene (INS) variable number of tandem repeat (VNTR) with type 2 diabetes and fasting insulin secretion in Mexican population

PURPOSE

A variable number of tandem repeats (VNTR) in the insulin gene (INS) control region may be involved in type 2 diabetes (T2D). The TH01 microsatellite is near INS and may regulate it. We investigated whether the TH01 microsatellite and INS VNTR, assessed via the surrogate marker single nucleotide polymorphism rs689, are associated with T2D and serum insulin levels in a Mexican population.

METHODS

We analyzed a main case-control study (n = 1986) that used univariate and multivariate logistic regression models to calculate the risk conferred by TH01 and rs689 loci for T2D development; rs689 results were replicated in other case-control (n = 1188) and cross-sectional (n = 1914) studies.

RESULTS

TH01 alleles 6, 8, 9, and 9.3 and allele A of rs689 were independently associated with T2D, with differences between sex and age at diagnosis. TH01 alleles with ≥ 8 repeats conferred an increased risk for T2D in males compared with ≤ 7 repeats (odds ratio, ≥ 1.46; 95% confidence interval, 1.1-1.95). In females, larger alleles conferred a 1.5-fold higher risk for T2D when diagnosed ≥ 46 years but conferred protection when diagnosed ≤ 45 years. Similarly, rs689 allele A was associated with T2D in these groups. In males, larger TH01 alleles and the rs689 A allele were associated with a significant decrease in median fasting plasma insulin concentration with age in T2D cases; the reverse occurred in controls.

CONCLUSION

Larger TH01 alleles and rs689 A allele may potentiate insulin synthesis in males without T2D, a process disabled in those with T2D.

Effects of Temperature on Development of Canker-Causing Pathogens in Almond and Prune

Between 2000 and 2020, canker diseases of nut and stone fruit trees have become very widespread and severe in California. This study determined the effects of temperature on the development of canker-causing pathogens of almond and prune. Five pathogen taxa, Botryosphaeria dothidea, Cytospora leucostoma, Diaporthe (Phomopsis) neotheicola, Lasiodiplodia citricola, and Neofusicoccum mediterraneum, were used. Colony growth on medium and canker lesion development on detached shoots were measured at 10, 15, 20, 25, 30, and 35°C. The effects of temperature on colony growth differed among different pathogen taxa, although 25°C was the optimal temperature for most of the pathogens tested. The patterns of lesion growth as response to temperature were different among the different pathogens and tree crops. On almond, the highest growth rates appeared at 30°C for B. dothidea and L. citricola, but at 20°C for N. mediterraneum. The growth rates for C. leucostoma were lower than those of the other three pathogen taxa, with the highest rates recorded at 25°C. However, on prune, C. leucostoma showed greater lesion growth rates at different temperatures than the other pathogen taxa and maximum growth at 30 to 35°C. Similar trends were observed for L. citricola. The growth rates of B. dothidea and N. mediterraneum were comparatively lower than those of C. leucostoma and L. citricola.

The IntAct database: efficient access to fine-grained molecular interaction data

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.

Towards a unified open access dataset of molecular interactions

The International Molecular Exchange (IMEx) Consortium provides scientists with a single body of experimentally verified protein interactions curated in rich contextual detail to an internationally agreed standard. In this update to the work of the IMEx Consortium, we discuss how this initiative has been working in practice, how it has ensured database sustainability, and how it is meeting emerging annotation challenges through the introduction of new interactor types and data formats. Additionally, we provide examples of how IMEx data are being used by biomedical researchers and integrated in other bioinformatic tools and resources.

(-)-Stepholidine blocks expression, but not development, of cocaine conditioned place preference in rats

The purpose of this study was to investigate the effects of (-)-stepholidine (SPD), a compound with dopamine D1 partial agonist and D2/D3 antagonist properties, on the development and expression of cocaine conditioned place preference (CPP). Subjects (N = 65; male Long Evans rats) were tested using a CPP procedure consisting of 3 phases: (1) a 15-min pre-exposure session where animals could explore each compartment freely, (2) eight 30-min conditioning sessions where animals were restricted to one side or the other with cocaine (10 mg/kg) or saline, respectively, on alternating days and (3) a 15-minute preference test session where animals could explore each compartment freely. To test the effects of SPD on expression of cocaine CPP, rats were administered vehicle (distilled water with 20 % DMSO), 10, 15 or 20 mg/kg SPD (intraperitoneally) 30 min prior to the test session. We found that 20 mg/kg of SPD significantly blocked the expression of cocaine CPP. To test the effects of SPD on the development of CPP, 0 (vehicle), 10, 15 or 20mg/kg SPD were administered 30 min prior to each cocaine conditioning session and vehicle before each saline conditioning session; no treatment was given prior to the test session. A preference test showed that each SPD group maintained a CPP similar to the vehicle group. These data indicate that SPD can block the expression of a cocaine CPP but has no effect on its development, suggesting that it inhibits the effects of cocaine cues on cocaine incentive motivated behavior. These results suggest that SPD may be a potential treatment for cue-driven aspects of cocaine use disorder.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Identical and Nonidentical Twins: Risk and Factors Involved in Development of Islet Autoimmunity and Type 1 Diabetes

OBJECTIVE

There are variable reports of risk of concordance for progression to islet autoantibodies and type 1 diabetes in identical twins after one twin is diagnosed. We examined development of positive autoantibodies and type 1 diabetes and the effects of genetic factors and common environment on autoantibody positivity in identical twins, nonidentical twins, and full siblings.

RESEARCH DESIGN AND METHODS

Subjects from the TrialNet Pathway to Prevention Study (N = 48,026) were screened from 2004 to 2015 for islet autoantibodies (GAD antibody [GADA], insulinoma-associated antigen 2 [IA-2A], and autoantibodies against insulin [IAA]). Of these subjects, 17,226 (157 identical twins, 283 nonidentical twins, and 16,786 full siblings) were followed for autoantibody positivity or type 1 diabetes for a median of 2.1 years.

RESULTS

At screening, identical twins were more likely to have positive GADA, IA-2A, and IAA than nonidentical twins or full siblings (all P < 0.0001). Younger age, male sex, and genetic factors were significant factors for expression of IA-2A, IAA, one or more positive autoantibodies, and two or more positive autoantibodies (all P ≤ 0.03). Initially autoantibody-positive identical twins had a 69% risk of diabetes by 3 years compared with 1.5% for initially autoantibody-negative identical twins. In nonidentical twins, type 1 diabetes risk by 3 years was 72% for initially multiple autoantibody-positive, 13% for single autoantibody-positive, and 0% for initially autoantibody-negative nonidentical twins. Full siblings had a 3-year type 1 diabetes risk of 47% for multiple autoantibody-positive, 12% for single autoantibody-positive, and 0.5% for initially autoantibody-negative subjects.

CONCLUSIONS

Risk of type 1 diabetes at 3 years is high for initially multiple and single autoantibody-positive identical twins and multiple autoantibody-positive nonidentical twins. Genetic predisposition, age, and male sex are significant risk factors for development of positive autoantibodies in twins.

Expression Atlas: gene and protein expression across multiple studies and organisms

Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants

Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.

Abstract P1-01-02: Sentinel Node Biopsy Alone for Node Positive Breast Cancer, a Twelve Year Experience at a Single Institution

Background: The decision to perform complete node dissection for a tumor positive sentinel node is becoming more controversial. Five year data from the American College of Surgeon's Z011 trial recently demonstrated no difference in regional control in patients undergoing sentinel node biopsy alone for node positive disease. We report our institution's 12 year experience with sentinel node biopsy alone for tumor positive sentinel node and clinicopathologic factors that are associated with sentinel node biopsy alone.

Patients and Methods: From 1998 to 2009, a retrospective review was performed on 2,139 patients who underwent sentinel node biopsy alone for breast cancer. Of these 2,139 patients, 1,997 were tumor negative, 123 tumor positive and 19 cases were undocumented. Sentinel nodes were staged node positive according to AJCC criteria. Patient and tumor factors associated with sentinel node biopsy alone and locoregional recurrence, distant recurrence and overall survival were examined. Results: One hundred twenty three node positive patients underwent sentinel node biopsy alone with no completion axillary dissection for invasive breast cancer. Eighty two (66.7%) patient's sentinel nodes had macrometastases and 41 (33.3%) had micrometastases. Median follow-up was 8 years (range0.7 to 12yrs). Mean age was 57 years (range 32-92) and stage distribution was as follows: Stage IIA: 76 (62%) patients, Stage IIB: 40 (33%) patients, Stage III: 4 patients (3%), and Stage IV: 1 patient (0.8%). The mean size of the tumors was 1.9cm (range 0.1-9), 79 patients (64%) had grade I/II tumors and 36 (29%) had grade III tumors. Eighty nine (72%) underwent lumpectomy and 34 (28%) underwent mastectomy. When we examined patient and treatment factors that might explain omission of axillary dissection we saw that 95 (77%) patients had no comorbidities, 8 (6.5%) had one comorbidity and 20 (16%) had two or more comorbidities listed. Seventy seven patients (67%) received breast radiation in combination with adjuvant chemotherapy or hormonal therapy. Ninety (73%) patients had three or less sentinel nodes removed and 33 (27%) had four or more sentinel nodes removed. One hundred twenty patients had recurrence data, of which one (0.8%) had an axillary recurrence and 13 (11%) have expired. Of the 13 patients who died, four died of metastatic breast cancer and 9 of other causes. All patients with recurrence had macrometastasis to the lymph nodes. Conclusions: Favorable tumor and patient characteristics and high prevalence of adjuvant therapy may explain why completion axillary dissection was omitted in this group of tumor positive sentinel node patients. This study represents one of the longer follow-up periods in the literature and demonstrates that recurrent regional disease is rare with extended follow-up in patients undergoing sentinel node biopsy alone for node positive disease, even macrometastatic disease.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P1-01-02.

Event recognition using signal spectrograms in long pulse experiments

As discharge duration increases, real-time complex analysis of the signal becomes more important. In this context, data acquisition and processing systems must provide models for designing experiments which use event oriented plasma control. One example of advanced data analysis is signal classification. The off-line statistical analysis of a large number of discharges provides information to develop algorithms for the determination of the plasma parameters from measurements of magnetohydrodinamic waves, for example, to detect density fluctuations induced by the Alfvén cascades using morphological patterns. The need to apply different algorithms to the signals and to address different processing algorithms using the previous results necessitates the use of an event-based experiment. The Intelligent Test and Measurement System platform is an example of architecture designed to implement distributed data acquisition and real-time processing systems. The processing algorithm sequence is modeled using an event-based paradigm. The adaptive capacity of this model is based on the logic defined by the use of state machines in SCXML. The Intelligent Test and Measurement System platform mixes a local multiprocessing model with a distributed deployment of services based on Jini.

Implementation of local area network extension for instrumentation standard trigger capabilities in advanced data acquisition platforms

Synchronization mechanisms are an essential part of the real-time distributed data acquisition systems (DASs) used in fusion experiments. Traditionally, they have been based on the use of digital signals. The approach known as local area network extension for instrumentation (LXI) provides a set of very powerful synchronization and trigger mechanisms. The Intelligent Test Measurement System (ITMS) is a new platform designed to implement distributed data acquisition and fast data processing for fusion experiments. It is based on COMPATPCI technology and its extension to instrumentation (PXI). Hardware and software elements have been developed to include LXI trigger and synchronization mechanisms in this platform in order to obtain a class A LXI instrument. This paper describes the implementation of such a system, involving the following components: commercial hardware running a Linux operating system; a real-time extension to an operating system and network (RTAI and RTNET), which implements a software precision time protocol (PTP) using IEEE1588; an ad hoc PXI module to support hardware implementation of PTP-IEEE 1588; and the multipoint, low-voltage differential signaling hardware LXI trigger bus.

Self-adaptive sampling rate data acquisition in JET's correlation reflectometer

Data acquisition systems with self-adaptive sampling rate capabilities have been proposed as a solution to reduce the shear amount of data collected in every discharge of present fusion devices. This paper discusses the design of such a system for its use in the KG8B correlation reflectometer at JET. The system, which is based on the ITMS platform, continuously adapts the sample rate during the acquisition depending on the signal bandwidth. Data are acquired continuously at the expected maximum sample rate and transferred to a memory buffer in the host processor. Thereafter the rest of the process is based on software. Data are read from the memory buffer in blocks and for each block an intelligent decimation algorithm is applied. The decimation algorithm determines the signal bandwidth for each block in order to choose the optimum sample rate for that block, and from there the decimation factor to be used. Memory buffers are used to adapt the throughput of the three main software modules (data acquisition, processing, and storage) following a typical producer-consumer architecture. The system optimizes the amount of data collected while maintaining the same information. Design issues are discussed and results of performance evaluation are presented.

Genetic mapping of a dominant gene conferring resistance to cassava mosaic disease

Cassava mosaic disease (CMD) is the most-important disease of cassava ( Manihot esculenta) in Africa, and is a potential threat to Latin American (LA) cassava production. Although this viral disease is still unknown in LA, its vector - the whitefly - has recently been found. The disease is best controlled through host-plant resistance, which was first found in third backcross derivatives of an interspecific cross between cassava and Manihot glaziovii, and is thought to be polygenic. Recently, high levels of resistance were also found in several Nigerian cassava landraces. Classical genetic analysis and molecular genetic-mapping of the landraces showed that a major dominant gene confers this resistance. Bulk segregant analysis (BSA) was used to quickly identify a simple sequence repeat (SSR) marker linked to the CMD-resistance gene. The marker, SSRY28, is located on linkage group R of the male-parent-derived molecular genetic map. The gene, designated as CMD2, is flanked by the SSR and RFLP marker GY1 at 9 and 8 cM, respectively. To our knowledge, this is the first report of qualitative virus resistance in cassava, and of molecular markers that tag CMD resistance in cassava. We discuss the use of markers linked to CMD2 for marker-assisted breeding of CMD resistance in Latin America and for increasing the cost-effectiveness of resistance breeding in Africa.

[Failure in the functioning of an implanted automatic defibrillator due to pneumothorax occurring during its implantation ]

A 67-year-old man with chronic bronchitis and coronary artery disease was scheduled to receive an implantable cardioverter defibrillator (ICD) after an episode of sustained monomorphic ventricular tachycardia. During implantation through the left subclavian vein, oxygen saturation decreased to slightly below baseline. Nevertheless, the procedure continued, given that the patient experienced neither breathing difficulties nor pain. When the ICD failed to reverse ventricular fibrillation induced to test the device, an external defibrillator was used. At that point, left-sided pneumothorax was observed by x-ray. Air in the pleural cavity caused an increase in the defibrillation threshold. After insertion of a thoracic drain, the ICD implantation procedure was completed successfully.

Respiratory and analgesic effects of meperidine and tramadol in patients undergoing orthopedic surgery

The respiratory and analgesic effects of i.v. meperidine, tramadol and their correlation with plasma concentrations of meperidine, tramadol and O-demethyltramadol were determined. Forty-eight patients after total hip or knee replacement were randomly distributed into 3 groups (n = 16 each). At the time of analgesia request, they received in a double-blind manner, i.v. single doses of 100 mg meperidine, 100 mg tramadol, or saline. Thirty minutes after treatment, patients who requested additional analgesia were rescued with 75 mg diclofenac and morphine as required. Patients were evaluated at the time of analgesia request and at set intervals during 4 h. Meperidine induced sedation (p < 0.05), respiratory depression (tidal volume, p < 0.047; respiratory rate, p < 0.004; % O2 Sat, p < 0.036), and hypercapnia (PaCO2, p < 0.002). Incidence of nausea and vomiting was higher with tramadol (p < 0.02). For the first 30 min, meperidine produced lower pain intensity scores than tramadol or saline (p < 0.05). At this time, 14/16 patients on saline, 8/16 on meperidine and 11/16 on tramadol were rescued. Onset for meperidine analgesia was 10 min and > 30 min for tramadol. Both opioids produced similar degree of analgesia in patients who were not rescued. A negative correlation (r = -0.99) between analgesia and tramadol concentrations and a poor positive correlation (r = +0.54) with O-demethyltramadol (a metabolite of tramadol) was observed. Pain intensity differences correlated negatively with meperidine plasma concentrations during the first 30 min (r = -0.97) and positively thereafter (r = +0.92). In the present study, meperidine and tramadol produced comparable analgesia, with a different time course profile, but meperidine induced sedation and respiratory depression while tramadol did not.

[Etomidate perfusion in neurosurgery]

In this prospective study, 20 patients undergoing mean duration (2-3 h) neurosurgical operations on fossa cranii posterior, and cervical and dorsolumbar rachis, were induced with 0.3 mg/kg etomidate bolus dose. To maintain anesthesia, etomidate perfusions at 10 micrograms/kg/min (group I) and 20 microg/kg/min (group II) were administered. Fentanyl at fractionated doses was used as analgesic without association to nitrous oxide and relaxation was achieved with pancuronium bromide. Quality of hypnosis, changes in serum concentration of cortisol as well as hemodynamic and electrolyte changes were evaluated. Serum concentrations of cortisol, glucose, sodium and potassium were measured in basal state, and during perioperative and postoperative period. Hemodynamic status was monitored and side effects were recorded. Patients of group I presented signs of deficient hypnosis consisting of marked sympathetic response. When etomidate perfusion ceased, both groups presented serum concentrations of cortisol under the lower normal limit. Six hours after operation, mean serum concentration of cortisol in group 2 patients was significantly lower than in group I patients; in their samples, a dose-dependent recovery was detected. Serum glucose concentration increased during anesthesia and operation and serum electrolyte concentration remained within normal range during perioperative and postoperative periods. Our results demonstrate that a 20 micrograms/kg/min etomidate infusion is adequate to achieve neuroanesthesia when nitrous oxide administration is contraindicated.

Ceftriaxone in the treatment of bacterial meningitis in adults

Twenty-six adults with acute bacterial meningitis were enrolled in an open randomized comparative study. The organisms isolated from CSF were Streptococcus pneumoniae, Staphylococcus epidermidis, Haemophilus influenzae, Escherichia coli and Salmonella typhi. 13 patients (group A) were treated once daily with intravenous ceftriaxone (Rocephin). The 13 patients in group B received ampicillin or ampicillin plus chloramphenicol in 4 doses/day. The mean duration of therapy in groups A and B was 9.9 and 12.3 days, respectively. This difference in the duration of therapy was statistically significant. All patients from group A showed clinical improvement and all were bacteriologically cured. In group B only 12 patients were clinically and bacteriologically cured; 1 patient had to be withdrawn from the therapy because CSF culture remained positive after 48 h of therapy. Ceftriaxone was well tolerated in all patients; ampicillin or ampicillin plus chloramphenicol were associated with diarrhea and skin rash in 6 patients.

Bacillus cereus bacteremia and hemolytic anemia in a patient with hemoglobin SC disease

A patient with hemoglobin SC disease and cholelithiasis was found to have Bacillus cereus bacteremia. Hemolytic anemia developed, for which common causes of hemolysis were excluded, suggesting a relationship with the bacteremia. Following in vitro incubation, type O erythrocytes were hemolyzed by the culture, but not by a bacteria-free filtrate. This case confirms the association between sickle cell disorders and cholelithiasis with B cereus infections. In addition, it provides evidence for in vivo hemolysis with B cereus bacteremia, an organism not previously associated with hemolytic anemia.

Antigenic specificity of chlorpromazine-induced antinuclear antibodies

A few patients have been reported who developed systemic lupus erythematosus (SLE) in the course of prolonged treatment with chlorpromazine. Patients on this drug have also been found to have antinuclear antibodies (ANAs) although they do not develop lupus.

We have studied the antigenic specificity of ANAs in fifty-four patients on longterm chlorpromazine treatment and compared our findings with those on 175 patients on anticonvulsants, 215 patients on isoniazid, 109 SLE patients and fifty-four healthy subjects, sex and age matched to the chlorpromazine patients.

Thirty-nine per cent of patients on chlorpromazine had ANAs which were most frequently directed to single stranded (s)DNA. In contrast, patients on anticonvulsants as well as those on isoniazid had ANA directed to soluble nucleoprotein (sNP) most frequently and none of the patients on isoniazid had ANA to sDNA.

The mechanisms by which chlorpromazine, isoniazid or anticonvulsant intake results in ANAs probably differ. Our findings suggest that development of ANAs in patients on chlorpromazine may be initiated by interaction of the drug with denatured DNA.