Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a

Aberrant de novo methylation of DNA is considered an important mediator of tumorigenesis. To investigate the role of de novo DNA methyltransferase 3a (Dnmt3a) in intestinal tumor development, we analyzed the expression of Dnmt3a in murine colon crypts, murine colon adenomas and human colorectal cancer using RNA fluorescence in situ hybridization (FISH), quantitative PCR and immunostaining. Following conditional deletion of Dnmt3a in the colon of APC((Min/+)) mice, we analyzed tumor numbers, genotype of macroadenomas and laser dissected microadenomas, global and regional DNA methylation and gene expression. Our results showed increased Dnmt3a expression in colon adenomas of APC((Min/+)) mice and human colorectal cancer samples when compared with control tissue. Interestingly, in tumor tissue, RNA FISH analysis showed highest Dnmt3a expression in Lgr5-positive stem/progenitor cells. Deletion of Dnmt3a in APC((Min/+)) mice reduced colon tumor numbers by ~40%. Remaining adenomas and microadenomas almost exclusively contained the non-recombined Dnmt3a allele; no tumors composed of the inactivated Dnmt3a allele were detected. DNA methylation was reduced at the Oct4, Nanog, Tff2 and Cdkn1c promoters and expression of the tumor-suppressor genes Tff2 and Cdkn1c was increased. In conclusion, our results show that Dnmt3a is predominantly expressed in the stem/progenitor cell compartment of tumors and that deletion of Dnmt3a inhibits the earliest stages of intestinal tumor development.

Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature

Tumor endothelial marker 1 (TEM1; also known as endosialin or CD248) is a protein found on tumor vasculature and in tumor stroma. Here, we tested whether TEM1 has potential as a therapeutic target for cancer immunotherapy by immunizing immunocompetent mice with Tem1 cDNA fused to the minimal domain of the C fragment of tetanus toxoid (referred to herein as Tem1-TT vaccine). Tem1-TT vaccination elicited CD8+ and/or CD4+ T cell responses against immunodominant TEM1 protein sequences. Prophylactic immunization of animals with Tem1-TT prevented or delayed tumor formation in several murine tumor models. Therapeutic vaccination of tumor-bearing mice reduced tumor vascularity, increased infiltration of CD3+ T cells into the tumor, and controlled progression of established tumors. Tem1-TT vaccination also elicited CD8+ cytotoxic T cell responses against murine tumor-specific antigens. Effective Tem1-TT vaccination did not affect angiogenesis-dependent physiological processes, including wound healing and reproduction. Based on these data and the widespread expression of TEM1 on the vasculature of different tumor types, we conclude that targeting TEM1 has therapeutic potential in cancer immunotherapy.

Using variability in gene expression as a tool for studying gene regulation

With the advent of quantitative tools for measuring gene expression in single cells, researchers have made the discovery that in many contexts, messenger RNA and protein levels can vary widely from cell to cell, often because of inherently stochastic events associated with gene expression. The study of this cellular individuality has become a field of study in its own right, characterized by a blend of technological development, theoretical analysis, and, more recently, applications to biological phenomena. In this review, we focus on the use of the variability inherent to gene expression as a tool to understand gene regulation. We discuss the use of variability as a natural systems-level perturbation, its use in quantitatively characterizing the biological processes underlying transcription, and its application to the discovery of new gene regulatory interactions. We believe that use of variability can provide new biological insights into different aspects of transcriptional control and can provide a powerful complementary approach to that of existing techniques.

Sexually transmitted infections among HIV-infected heavy drinkers in St Petersburg, Russia

The objective of this study was to estimate the prevalence and identify correlates of four sexually transmitted infections (STIs) among HIV-infected Russians reporting heavy alcohol use and recent unprotected sex, we conducted a cross-sectional analysis of baseline data from the HERMITAGE study. The primary outcome was any current STI, based on urine tests for Neisseria gonorrhoeae, Chlamydia trachomatis and Trichomonas vaginalis and serological testing for infection with Treponema pallidum. Data on potential demographic and behavioural predictors of STI were obtained from surveys administered at study entry. Of 682 participants, 12.8% (95% confidence interval [CI] 10.3, 15.3) tested positive for at least one STI. In a multivariable model adjusted for gender, age and marital status, only sex trade involvement over the last three months was significantly associated with an increased odds of STI (adjusted odds ratio [AOR] 2.00, 95% CI 1.13, 3.55). Given that STIs were common in this HIV-infected cohort, and that few patient characteristics predicted STI, the current practice of screening HIV-infected Russians for syphilis alone merits re-evaluation.

D-Dimer assay as a non invasive test for the diagnosis of left atrial Thrombi in Indian patients with Rheumatic MS

BACKGROUND

Systemic embolism is a serious and sometime fatal complication of rheumatic MS.

OBJECTIVE

We assessed the predictive power of D-Dimer level to predict occurrence of left atrial (LA) thrombi in patients with rheumatic mitral stenosis (MS).

METHODS

D-dimer levels were analyzed for 24 patients with rheumatic MS with LA clot and 22 patients with rheumatic MS with no LA clot undergoing transeosophageal echocardiography. A level more than 4 µg/ml was taken as elevated to predict the presence of LA clot in the study groups.

RESULTS

For a cut-off value of 4 µg/ml, sensitivity was 66.67 % and specificity 100 % for prediction of LA clot and AUC 0.710. A cut-off value of less than 1 µg/ml, sensitivity was 91.67 % and 87. 5 % negative predictive value for ruling out presence of LA clot and AUC 0.721.

CONCLUSION

A higher value of D-dimer can predict the possible presence of a LA clot and very low value can predict absence of clot in patients with rheumatic MS.

Visualizing SNVs to quantify allele-specific expression in single cells

We present a high efficiency fluorescence in situ hybridization method for detecting single nucleotide variants (SNVs) on individual RNA transcripts, both exonic and intronic. We used this method to quantify allelic expression at the population and single cell level, and also to distinguish maternal from paternal chromosomes in single cells.

Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification

Cell differentiation and proliferation are coordinated during animal development, but the link between them remains uncharacterized. To examine this relationship, we combined single-molecule RNA imaging with time-lapse microscopy to generate high-resolution measurements of transcriptional dynamics in Caenorhabditis elegans embryogenesis. We found that globally slowing the overall development rate of the embryo by altering temperature or by mutation resulted in cell proliferation and transcription slowing, but maintaining, their relative timings, suggesting that cell division may directly control transcription. However, using mutants with specific defects in cell cycle pathways that lead to abnormal lineages, we found that the order between cell divisions and expression onset can switch, showing that expression of developmental regulators is not strictly dependent on cell division. Delaying cell divisions resulted in only slight changes in absolute expression time, suggesting that expression and proliferation are independently entrained to a separate clock-like process. These changes in relative timing can change the number of cells expressing a gene at a given time, suggesting that timing may help determine which cells adopt particular transcriptional patterns. Our results place limits on the types of mechanisms that are used during normal development to ensure that division timing and fate specification occur at appropriate times.

Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells

Recently, we developed an oligonucleotide-based probe, ratiometric bimolecular beacon (RBMB), which generates a detectable fluorescent signal in living cells that express the target RNA. Here, we show that RBMBs can also be used to image single RNA transcripts in living cells, when the target RNA is engineered to contain as few as four hybridization sites. Moreover, comparison with single-molecule fluorescence in situ hybridization confirmed that RBMBs could be used to accurately quantify the number of RNA transcripts within individual cells. Measurements of gene expression could be acquired within 30 min and using a wide range of RBMB concentrations. The ability to acquire accurate measurements of RNA copy number in both HT-1080 cells and CHO cells also suggests that RBMBs can be used to image and quantify single RNA transcripts in a wide range of cell lines. Overall, these findings highlight the robustness and versatility of RBMBs as a tool for imaging RNA in live cells. We envision that the unique capabilities of RBMBs will open up new avenues for RNA research.

History of intimate partner violence is associated with sex work but not sexually transmitted infection among HIV-positive female drinkers in Russia

This paper assesses the associations between intimate partner violence (IPV) and sexually transmitted infections (STIs) and sexual risks among HIV-positive female drinkers in St Petersburg, Russia. Survey and STI data were analysed from 285 women in HERMITAGE, a secondary prevention study of HIV-positive heavy drinkers. Logistic and Poisson regression analyses assessed associations of IPV with STI and risky sex. Most women (78%) experienced IPV and 19% were STI positive; 15% sold sex. IPV was not significantly associated with STI, but was with selling sex (adjusted odds ratio = 3.56, 95% confidence interval = 1.02-12.43). In conclusion, IPV is common and associated with sex trade involvement among Russian HIV-positive female drinkers.

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Recently, researchers have uncovered the presence of many long noncoding RNAs (lncRNAs) in embryonic stem cells and believe they are important regulators of the differentiation process. However, there are only a few examples explicitly linking lncRNA activity to transcriptional regulation. Here, we used transcript counting and spatial localization to characterize a lncRNA (dubbed linc-HOXA1) located ∼50 kb from the Hoxa gene cluster in mouse embryonic stem cells. Single-cell transcript counting revealed that linc-HOXA1 and Hoxa1 RNA are highly variable at the single-cell level and that whenever linc-HOXA1 RNA abundance was high, Hoxa1 mRNA abundance was low and vice versa. Knockdown analysis revealed that depletion of linc-HOXA1 RNA at its site of transcription increased transcription of the Hoxa1 gene cis to the chromosome and that exposure of cells to retinoic acid can disrupt this interaction. We further showed that linc-HOXA1 RNA represses Hoxa1 by recruiting the protein PURB as a transcriptional cofactor. Our results highlight the power of transcript visualization to characterize lncRNA function and also suggest that PURB can facilitate lncRNA-mediated transcriptional regulation.

Effects of increased image noise on image quality and quantitative interpretation in brain CT perfusion

BACKGROUND AND PURPOSE

There is a desire within many institutions to reduce the radiation dose in CTP examinations. The purpose of this study was to simulate dose reduction through the addition of noise in brain CT perfusion examinations and to determine the subsequent effects on quality and quantitative interpretation.

MATERIALS AND METHODS

A total of 22 consecutive reference CTP scans were identified from an institutional review board-approved prospective clinical trial, all performed at 80 keV and 190 mAs. Lower-dose scans at 188, 177, 167, 127, and 44 mAs were generated through the addition of spatially correlated noise to the reference scans. A standard software package was used to generate CBF, CBV, and MTT maps. Six blinded radiologists determined quality scores of simulated scans on a Likert scale. Quantitative differences were calculated.

RESULTS

For qualitative analysis, the correlation coefficients for CBF (-0.34; P < .0001), CBV (-0.35; P < .0001), and MTT (-0.44; P < .0001) were statistically significant. Interobserver agreements in quality for the simulated 188-, 177-, 167-, 127-, and 44-mAs scans for CBF were 0.95, 0.98, 0.98, 0.95, and 0.52, respectively. Interobserver agreements in quality for the simulated CBV were 1, 1, 1, 1, and 0.83, respectively. For MTT, the interobserver agreements were 0.83, 0.86, 0.88, 0.74, and 0.05, respectively. For quantitative analysis, only the lowest simulated dose of 44 mAs showed statistically significant differences from the reference scan values for CBF (-1.8; P = .04), CBV (0.07; P < .0001), and MTT (0.46; P < .0001).

CONCLUSIONS

From a reference CTP study performed at 80 keV and 190 mAs, this simulation study demonstrates the potential of a 33% reduction in tube current and dose while maintaining image quality and quantitative interpretations. This work can be used to inform future studies by using true, nonsimulated scans.

Experiences of racial discrimination and relation to sexual risk for HIV among a sample of urban black and African American men

This study aimed to examine racial discrimination and relation to sexual risk for HIV among a sample of urban black and African American men. Participants of this cross-sectional study were black and African American men (N = 703) between the ages of 18 and 65 years, recruited from four urban clinical sites in the northeast. Multivariate logistic regression models were used to analyze the relation of reported racial discrimination to the following: (1) sex trade involvement, (2) recent unprotected sex, and (3) reporting a number of sex partners in the past 12 months greater than the sample average. The majority of the sample (96%) reported racial discrimination. In adjusted analyses, men reporting high levels of discrimination were significantly more likely to report recent sex trade involvement (buying and/or selling) (adjusted odds ratio (AOR) range = 1.7-2.3), having recent unprotected vaginal sex with a female partner (AOR = 1.4, 95% confidence interval (CI), 1.1-2.0), and reporting more than four sex partners in the past year (AOR = 1.4, 95% CI, 1.1-1.9). Findings highlight the link between experiences of racial discrimination and men's sexual risk for HIV.

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Here we report iceFISH, a multiplex imaging method for measuring gene expression and chromosome structure simultaneously on single chromosomes. We demonstrate that chromosomal translocations can alter transcription chromosome-wide, finding substantial differences in transcriptional frequency between genes located on a translocated chromosome in comparison to the normal chromosome in the same cell. Examination of correlations between genes on a single chromosome revealed a cis chromosome-level transcriptional interaction spanning 14.3 megabases.

Differential diagnosis of normal pressure hydrocephalus by MRI mean diffusivity histogram analysis

BACKGROUND AND PURPOSE

Accurate diagnosis of normal pressure hydrocephalus is challenging because the clinical symptoms and radiographic appearance of NPH often overlap those of other conditions, including age-related neurodegenerative disorders such as Alzheimer and Parkinson diseases. We hypothesized that radiologic differences between NPH and AD/PD can be characterized by a robust and objective MR imaging DTI technique that does not require intersubject image registration or operator-defined regions of interest, thus avoiding many pitfalls common in DTI methods.

MATERIALS AND METHODS

We collected 3T DTI data from 15 patients with probable NPH and 25 controls with AD, PD, or dementia with Lewy bodies. We developed a parametric model for the shape of intracranial mean diffusivity histograms that separates brain and ventricular components from a third component composed mostly of partial volume voxels. To accurately fit the shape of the third component, we constructed a parametric function named the generalized Voss-Dyke function. We then examined the use of the fitting parameters for the differential diagnosis of NPH from AD, PD, and DLB.

RESULTS

Using parameters for the MD histogram shape, we distinguished clinically probable NPH from the 3 other disorders with 86% sensitivity and 96% specificity. The technique yielded 86% sensitivity and 88% specificity when differentiating NPH from AD only.

CONCLUSIONS

An adequate parametric model for the shape of intracranial MD histograms can distinguish NPH from AD, PD, or DLB with high sensitivity and specificity.

Hearing loss in rural population : the etiology

Out of the five sensations, hearing is a major one. The gross impairment of hearing especially in the children lead to lack of development of speech and makes the person grossly handicapped. This study consisting of 758 cases from rural area having hearing impairment, was aimed to findout the various aetiological factors resulting in hearing loss. 62.2% of cases belonged to 0-20 years age group. Otitis media (57.25%) was the commonest aetiological factor. Conductive hearing loss was the commonest type of hearing loss in otitis media. 86.17% cases of otitis media were in age group 0-20 years.

Endoscopic transcanal myringoplasty-A study

Aim of this study was to evaluate the role of rigid endoscope in the management of dry central perforation of the tympanic membrane and to compare the results of endoscopic myringoplasty with that of conventional myringoplasty using microscope. In endoscopic group there was 90% graft uptake rate as compared to 85% in microscopic group. The results of endoscopic myringoplasty are comparable to the conventional myringoplasty done under operating microscope and there is no significant difference between the gain in A-B gap in either group.

Global analysis of RNA secondary structure in two metazoans

The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals.

No-scalpel vasectomy by electrocauterization in free range rhesus macaques (Macaca mulatta)

The objective of the study was to standardize a new method of vasectomy in male rhesus macaques (Macaca mulatta). A total of 208 free range male rhesus macaques captured from different locations in Shivalik Hills in a population control programme of the rhesus macaques in India. General anaesthesia was achieved by using a combination of ketamine hydrochloride at 8 mg/kg body weight and xylazine hydrochloride at 2mg/kg body weight intramuscularly in squeeze cage. Surgical procedure of vasectomy was carried out by single-hole no-scalpel technique using a single pre-scrotal skin incision above the median raphae. Spermatic cord was grasped with ringed forceps and was pulled out through the single-hole incision. Vas deferens was separated from the artery-vein complexus and about 3-4 cm portion of vas deferens was resected. Cauterization of both ends of the vas deferens was achieved with electrocautery. The induction time for anaesthesia was 1.40±0.18 min while surgical time for vasectomy was found to be 5.09±0.22 min. Recovery from general anaesthesia was without side-effects after a mean duration of 36.07±1.22 min, whereas the duration of anaesthesia was observed to be 82.27±4.96 min. There were no major complications following the surgery and recovery of animals was smooth. Animals were kept in postoperative care for five days and released at the same capturing site.

P1-11-10: Quality of Breast Cancer Care in a Boston Area Patient Navigator Program

Background: Elimination of disparities is critically important for lessening the burden of cancer. Patient navigator programs (PNPs) assist with all aspects of care, including access, cancer prevention, screening, post-diagnosis care, and survivorship care. Little is known about the effect of PNPs on patient care and outcomes following the diagnosis of breast cancer (BC). We examined quality measures (QMs) of breast cancer care among women participating in the Massachusetts General Hospital Avon Breast Care Patient Navigator Program (MABCP), which provides patient navigation services to disadvantaged minority communities in the greater Boston area.

Methods: Women diagnosed with BC who participated in the MABCP from 2001 to 2011 were followed to determine the proportion whose care was concordant with American Society of Clinical Oncology/National Comprehensive Cancer Network (ASCO/NCCN) QMs. QMs included 1) hormonal therapy (HT) within 1 year of diagnosis for HR+ tumors &gt; 1 cm; 2)chemotherapy within 120 days of diagnosis of HR- &gt;1cm tumors for women &lt;70 years; and 3) post-lumpectomy radiation therapy (XRT). Descriptive statistics were used to report characteristics of MABCP patients.

Results: Of the 186 MABCP patients diagnosed with BC, some treatment data was available on 158 (85%) and race/stage information was available on 149 (80%) [Table 1]. Among the MABCP patients, concordant care was received by 70/74 (95%) for the HT QM, 15/17 (88%) for the chemotherapy QM, and 65/71 (92%) for the XRT QM. In comparison, available benchmark concordance rates of BC patients treated at 8 NCCN centers from 2003–6 are: 340/382 (89%) for the HT QM, 156/179 (87%) for the chemotherapy QM, and 141/148 (95%) for the XRT QM.

Conclusions: Overall, breast cancer care in the MABCP PNP is concordant with published ASCO/NCCN quality measures. At present, the sample is insufficient to compare concordance rates with NCCN patients but preliminarily, it appears that the quality of care is comparable. Future research should include prospective analyses of quality metrics to assess the process and outcomes of patient navigation in diverse settings, compared with control populations.

Elevated levels of IgG3 and IgG4 subclass in paediatric cases of kala azar

Visceral leishmaniasis (VL) or Kala azar (KA) is a systemic disease caused by the parasites of the Leishmania donovani complex. Control measures rely on treatment with antileishmanial agents, however, fraught with problems such as toxicity or drug resistance. The incidence rate is on the rise for children, for reasons yet undefined. Previously we have shown significantly elevated level of IL-10 in children compared to adult KA cases. Here, antileishmanial antibody and C-reactive protein (CRP) levels were investigated in paediatrics and adult patients of KA and post-KA dermal leishmaniasis (PKDL). Level of IgG4 was significantly elevated in PKDL compared to KA, although total IgG and IgG1 were significantly lower. The antileishmania antibody levels of subclass IgG3 and IgG4 were found significantly elevated in paediatrics, however, levels of IgG, IgG1, IgG2 and CRP were comparable in paediatric and adult KA cases. In case of PKDL, levels of IgG and it subclass were similar in the two groups. No significant difference in antileishmanial antibody level was noticed between macular or polymorphic cases of PKDL. The differential antibody intensity in paediatric cases, together with significant level of circulating IL-10, could be considered as a marker of differential disease susceptibility.

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Human cancer cells frequently have regions of their DNA hypermethylated, which results in transcriptional silencing of affected genes and promotion of tumor formation. However, it is still unknown whether cancer-associated aberrant DNA methylation is targeted to specific genomic regions, whether this methylation also occurs in noncancerous cells, and whether these epigenetic events are maintained in the absence of the initiating cause. Here we have addressed some of these issues by demonstrating that transgenic expression of DNA methyltransferase 3b (Dnmt3b) in the mouse colon initiates de novo DNA methylation of genes that are similar to genes that become methylated in human colon cancer. This is consistent with the notion that aberrant methylation in cancer may be attributable to targeting of specific sequences by Dnmt3b rather than to random methylation followed by clonal selection. We also showed that Dnmt3b-induced aberrant DNA methylation was maintained in regenerating tissue, even in the absence of continuous Dnmt3b expression. This supports the concept that transient stressors can cause permanent epigenetic changes in somatic stem cells and that these accumulate over the lifetime of an organism in analogy to DNA mutations.

Pregnancy diagnosis by laparoscopy in free range rhesus macaques (Macaca mulatta)

The present study involved 50 adult female rhesus macaques (Macaca mulatto) of age ranging between 4 to 15 years. Pregnancy diagnosis was done by using laparoscopic method. Anesthesia was achieved by using xylazine (2mg/kg) and ketamine (10mg/kg) intramuscularly. The gravid uterus was located close to the urinary bladder in early pregnancy and in abdominal cavity in the mid and late stage of pregnancy. The procedure was completed within 10 - 12 minutes. There were no complications after the surgery and recovery of animal was smooth and uneventful. The results of this study showed that laparoscopic method is also one of the methods of pregnancy diagnosis in rhesus macaques and it can be a precise and a reliable method of pregnancy diagnosis in rhesus macaques.

Pregnancy diagnosis by laparoscopy in free range rhesus macaques (Macaca mulatta)

The present study involved 50 adult female rhesus macaques (Macaca mulatto) of age ranging between 4 to 15 years. Pregnancy diagnosis was done by using laparoscopic method. Anesthesia was achieved by using xylazine (2mg/kg) and ketamine (10mg/kg) intramuscularly. The gravid uterus was located close to the urinary bladder in early pregnancy and in abdominal cavity in the mid and late stage of pregnancy. The procedure was completed within 10 - 12 minutes. There were no complications after the surgery and recovery of animal was smooth and uneventful. The results of this study showed that laparoscopic method is also one of the methods of pregnancy diagnosis in rhesus macaques and it can be a precise and a reliable method of pregnancy diagnosis in rhesus macaques.

Abused women report greater male partner risk and gender-based risk for HIV: findings from a community-based study with Hispanic women

The purpose of this study was to assess the relationship between intimate partner violence (IPV) and sexual risk in terms of safer sex behaviour and intent, individual and gender-based HIV risk factors, and male partner HIV risk, among a lower-income community-based sample of Hispanic women reporting a current male sexual partner. Baseline survey data on HIV-related behaviours and risk factors gathered from participants (N=170) of an HIV intervention evaluation study for Hispanic women were used for current analyses. Participants were age 18-36 years, predominantly born outside of the continental US (88.8%) and not English fluent (68.2%). Adjusted logistic regression analyses and 95% confidence intervals were conducted to assess the relationships between male-perpetrated IPV in the past three months and sexual risk variables. One-fifth (21.2%) of the sample reported male-perpetrated IPV in the past three months. Abused women were significantly more likely than those not abused in the past three months to report high STD/HIV risk perceptions (OR=3.02, 95% CI=1.33-6.88), gender-based risk including sexual control by male partners (OR=3.09, 95% CI=1.41-6.76) and male partner risk including male infidelity (OR=4.58, 95% CI=1.57-13.32). Results support the need for emphasis on IPV prevention within HIV prevention programmes and demonstrate the need for HIV prevention efforts directed at men with a history of IPV perpetration.

Network-level analysis of cortical thickness of the epileptic brain

Temporal lobe epilepsy (TLE) characterized by an epileptogenic focus in the medial temporal lobe is the most common form of focal epilepsy. However, the seizures are not confined to the temporal lobe but can spread to other, anatomically connected brain regions where they can cause similar structural abnormalities as observed in the focus. The aim of this study was to derive whole-brain networks from volumetric data and obtain network-centric measures, which can capture cortical thinning characteristic of TLE and can be used for classifying a given MRI into TLE or normal, and to obtain additional summary statistics that relate to the extent and spread of the disease. T1-weighted whole-brain images were acquired on a 4-T magnet in 13 patients with TLE with mesial temporal lobe sclerosis (TLE-MTS), 14 patients with TLE with normal MRI (TLE-no), and 30 controls. Mean cortical thickness and curvature measurements were obtained using the FreeSurfer software. These values were used to derive a graph, or network, for each subject. The nodes of the graph are brain regions, and edges represent disease progression paths. We show how to obtain summary statistics like mean, median, and variance defined for these networks and to perform exploratory analyses like correlation and classification. Our results indicate that the proposed network approach can improve accuracy of classifying subjects into two groups (control and TLE) from 78% for non-network classifiers to 93% using the proposed approach. We also obtain network "peakiness" values using statistical measures like entropy and complexity-this appears to be a good characterizer of the disease and may have utility in surgical planning.

Imaging single mRNA molecules in yeast

Yeast cells in an isogenic population do not all display the same phenotypes. To study such variation within a population of cells, we need to perform measurements on each individual cell instead of measurements that average out the behavior of a cell over the entire population. Here, we provide the basic concepts and a step-by-step protocol for a recently developed technique enabling one such measurement: fluorescence in situ hybridization that renders single mRNA molecule visible in individual fixed cells.

Association of white matter hyperintensity measurements on brain MR imaging with cognitive status, medial temporal atrophy, and cardiovascular risk factors

BACKGROUND AND PURPOSE

White matter hyperintensities (WMHs) are frequently characterized as markers of cerebrovascular disease, whereas medial temporal atrophy (MTA) is a recognized marker of Alzheimer disease (AD). Our purpose was to test the reliability of a visual rating system (VRS) in evaluating WMHs and MTA and in distinguishing healthy from cognitively impaired subjects.

MATERIALS AND METHODS

Subjects (n = 192) enrolled in the Florida Alzheimer's Disease Research Center were diagnosed with no cognitive impairment, nonamnestic mild cognitive impairment (na-MCI), amnestic MCI (a-MCI), or probable AD. The severity of WMHs was assessed on T2-weighted fluid-attenuated inversion recovery axial MR images, and the severity of MTA was evaluated on 1.5-mm-thick coronal MR images by using a computer-based visual rating system. Cardiovascular risk factor scores were calculated as the sum of 10 independent cardiovascular risk factors.

RESULTS

WMH and MTA scores were greater in subjects with probable AD, relative to those with no cognitive impairment and na-MCI. MTA scores differentiated subjects with a-MCI from those with no cognitive impairment and na-MCI. The total WMH score was significantly related to MTA (r = 0.39; P < .001) but not to cardiovascular risk factor scores (r = 0.07; P = not significant). The overall correct classification rate of probable AD versus no cognitive impairment by using MTA scores was 81.8%, improving to 86.5% when combined with WMH scores.

CONCLUSIONS

Both MTA and WMH scores distinguished subjects with no cognitive impairment and probable AD. Combining MTA and WMH scores improved the correct classification rate, whereas WMH scores were significantly related to MTA scores, but not to cardiovascular risk factor scores. This finding suggests that among subjects with a-MCI and probable AD, WMHs on MR images are primarily associated with neurodegenerative disease.

Binge drinking and unsafe sex: a study of narcology hospital patients from St. Petersburg, Russia

The purpose of this study was to assess the association between binge alcohol use and unprotected sex in Russian substance users. Participants (N = 181) were narcology hospital patients assessed on demographics, alcohol use, risky sex, and sexually transmitted disease/human immunodeficiency virus (STD/HIV) diagnoses. Adjusted generalized estimating equations (GEEs) logistic regression analysis examined the association between binge drinking and same-day unprotected sex across each of the past 30 days, per participant (N = 5430 observations). Participants were age 18 to 55 years, 75% male, and 64% binge drinking. Sex trade was reported by 27%; history of STDs by 43%; and HIV by 15%. One fourth of daily observations included sex; 88% of these involved unprotected sex. Binge drinking was not associated with same-day unprotected sex (adjusted odds ratio [OR(adj)] = 1.0, 95% confidence interval [CI] = 0.7-1.4, chi(2)(1, N = 5219) = 0.01, ns). Findings document substantial HIV/STD risk and prevalence among Russian narcology patients, but no link between binge drinking and unprotected sex in this population, possibly due to very low rates of condom use generally.

Intimate partner violence perpetration, standard and gendered STI/HIV risk behaviour, and STI/HIV diagnosis among a clinic-based sample of men

Background:

The estimated one in three women worldwide victimised by intimate partner violence (IPV) consistently demonstrate elevated STI/HIV prevalence, with their abusive male partners’ risky sexual behaviours and subsequent infection increasingly implicated. To date, little empirical data exist to characterise the nature of men’s sexual risk as it relates to both their violence perpetration, and STI/HIV infection.

Methods:

Data from a cross-sectional survey of men ages 18–35 recruited from three community-based health clinics in an urban metropolitan area of the northeastern US (n = 1585) were analysed to estimate the prevalence of IPV perpetration and associations of such violent behaviour with both standard (eg, anal sex, injection drug use) and gendered (eg, coercive condom practices, sexual infidelity, transactional sex with a female partner) forms of sexual-risk behaviour, and self-reported STI/HIV diagnosis.

Results:

Approximately one-third of participants (32.7%) reported perpetrating physical or sexual violence against a female intimate partner in their lifetime; one in eight (12.4%) participants self-reported a history of STI/HIV diagnosis. Men’s IPV perpetration was associated with both standard and gendered STI/HIV risk behaviours, and to STI/HIV diagnosis (OR 4.85, 95% CI 3.54 to 6.66). The association of men’s IPV perpetration with STI/HIV diagnosis was partially attenuated (adjusted odds ratio (AOR) 2.55, 95% CI 1.77 to 3.67) in the multivariate model, and a subset of gendered sexual-risk behaviours were found to be independently associated with STI/HIV diagnosis—for example, coercive condom practices (AOR 1.67, 95% CI 1.04 to 2.69), sexual infidelity (AOR 2.46, 95% CI 1.65 to 3.68), and transactional sex with a female partner (AOR 2.03, 95% CI 1.36 to 3.04).

Conclusions:

Men’s perpetration of physical and sexual violence against intimate partners is common among this population. Abusive men are at increased risk for STI/HIV, with gendered forms of sexual-risk behaviour partially responsible for this association. Thus, such men likely pose an elevated infection risk to their female partners. Findings indicate the need for interwoven sexual health promotion and violence prevention efforts targeted to men; critical to such efforts may be reduction in gendered sexual-risk behaviours and modification of norms of masculinity that likely promote both sexual risk and violence

Single-molecule approaches to stochastic gene expression

Both the transcription of mRNAs from genes and their subsequent translation into proteins are inherently stochastic biochemical events, and this randomness can lead to substantial cell-to-cell variability in mRNA and protein numbers in otherwise identical cells. Recently, a number of studies have greatly enhanced our understanding of stochastic processes in gene expression by utilizing new methods capable of counting individual mRNAs and proteins in cells. In this review, we examine the insights that these studies have yielded in the field of stochastic gene expression. In particular, we discuss how these studies have played in understanding the properties of bursts in gene expression. We also compare the array of different methods that have arisen for single mRNA and protein detection, highlighting their relative strengths and weaknesses. In conclusion, we point out further areas where single-molecule techniques applied to gene expression may lead to new discoveries.

Study on the response of diploid, tetraploid and hexaploid species of wheat to the elevated CO2

Study was done to compare the response of Triticum aestivum (hexaploid), Triticum durum (tetraploid) and Triticum monococcum (diploid) wheat species to the elevated CO2 using Free Air CO2 Enrichment (FACE) facility. It was demonstrated that the modern cultivar of wheat Triticum aestivum (hexaploid) was largely sink limited. It appeared to have less photosynthesis per unit leaf area than Triticum monococcum (diploid wheat). While leaf size, grain weight and amylase activity increased with the ploidy level from diploid to hexaploid wheat forms, the photosynthetic rate was reduced significantly. These wheat species responded differentially to the elevated CO2. The larger leaf area and greater seed weight and presence of 38 KDa protein band caused by elevated CO2 had additive effect in improving the productivity of hexaploid wheat by changing the source sink ratio. Whereas, such a source sink balance was not induced by elevated CO2 in diploid wheat. The increasing CO2 may present opportunities to breeders and possibly allow them to select for cultivars responsive to the elevated CO2 with better sink potential.