Identifying high-confidence capture Hi-C interactions using CHiCANE.

The ability to identify regulatory interactions that mediate gene expression changes through distal elements, such as risk loci, is transforming our understanding of how genomes are spatially organized and regulated. Capture Hi-C (CHi-C) is a powerful tool to delineate such regulatory interactions. However, primary analysis and downstream interpretation of CHi-C profiles remains challenging and relies on disparate tools with ad-hoc input/output formats and specific assumptions for statistical modeling. Here we present a data processing and interaction calling toolkit (CHiCANE), specialized for the analysis and meaningful interpretation of CHi-C assays. In this protocol, we demonstrate applications of CHiCANE to region capture Hi-C (rCHi-C) and promoter capture Hi-C (pCHi-C) libraries, followed by quality assessment of interaction peaks, as well as downstream analysis specific to rCHi-C and pCHi-C to aid functional interpretation. For a typical rCHi-C/pCHi-C dataset this protocol takes up to 3 d for users with a moderate understanding of R programming and statistical concepts, although this is dependent on dataset size and compute power available. CHiCANE is freely available at https://cran.r-project.org/web/packages/chicane .

An audit of nurses using standing order directives to administer medications to children at risk of contracting rheumatic fever.

AIM: The following article reports an audit, conducted between July 2014 and July 2017, of adherence to best practice in medication administration and documentation by nurses. METHOD: A sample of 47 registered nurses' (RNs') documentation relating to the administration of 939 medications using standing order directives were examined and scored by seven senior nurses and a medical practitioner against an audit tool. The scores were divided into four quartiles with the top two quartiles demonstrating best practice in adherence to safety standards for the administration of medication. RESULTS: Forty-three RNs (91.5%) scored in the top two quartiles. The remaining four RNs (8.5%), following supervision by a senior nurse, subsequently demonstrated improvement in their documentation to the quartile one range of the audit tool. This audit demonstrates that, following education in diagnosis and treatment of common childhood conditions, the majority of nurses who were audited could diagnose simple conditions of childhood and safely administer medications to them. Moreover, two years after the programme was introduced, the serious sequelae of acute rheumatic fever (ARF) reduced in children aged 5-12 years. CONCLUSION: RNs who took part in the audit used standing order directives to safely administer medications to children. RN prescribing throughout New Zealand should be explored as an effective means to provide timely treatment and improve patient outcomes.

A psycho-linguistic profile of online grooming conversations: A comparative study of prison and police staff considerations.

BACKGROUND: Internet-initiated sexual offences against minors (i.e., online grooming (OG)) is a communicative process of entrapment used by adults to entice minors into sexual activities. Yet, research exploring how the language used by such individuals might reflect their psychological world is scarce. Interestingly, researchers have largely assumed that adults who engage in OG behaviours create a deceptive relationship to reach sexual intent. However, no study to date has investigated the deceptive component of these interactions. OBJECTIVE: To explore the psycholinguistic and deceptive properties of chats where OG is present, from the perspective of front-line specialists. PARTICIPANTS AND SETTING: Prison staff (n = 7) and police officers (n = 9) and sixty-five chat logs from adults convicted of an online sexual offence against a minor. METHODS: A mixed-method approach was employed, whereby qualitative (focus groups) data collection informed subsequent quantitative (the Linguistic Inquiry Word Count (LIWC)) data analyse of adult-child online sexual chats, using the model of OG discourse as the theoretical rationale. RESULTS: Specialist considered that the online abuse/exploitation of minors can occur without deception. Adults who engage in OG behaviour use language that denotes affiliation with a positive emotional tone (p = .003, ηp2 = .59). The communicative focus is the development of an interpersonal relationship, above engagement in sexual talk (p < .001, ηp2 = .96). CONCLUSIONS: Findings challenge the common perception that the relationship is centred on deception and identify the intention of some adults as the development of a perceived genuine interpersonal relationship.

Mana Tu: a whanau ora approach to type 2 diabetes.

In 2017, the National Hauora Coalition, a Maori-led Primary Health Organisation (PHO), was awarded a Long-Term Conditions Partnership Research grant to test the effectiveness of Mana Tu: a whanau ora approach to type 2 diabetes. With moves to replicate aspects of it in programmes around New Zealand, it is timely to describe the rationale for Mana Tu and the key components of its unique model of care. Mana Tu was developed in response to current ethnic and social inequities in type 2 diabetes rates, outcomes and wider determinants. It attempts to address various system, service and patient factors that impact on the whanau's ability to 'mana tu' or 'stand with authority' when living with a long-term condition. Results, including clinical, implementation and cost-effectiveness data, will be collected and analysed over the next two years.

A systematic review of fantasy driven vs. contact driven internet-initiated sexual offences: Discrete or overlapping typologies?

Within the literature individuals who use the internet to facilitate the sexual abuse of a minor are generally classified as being fantasy or contact driven. Classification is based upon the intended location for sexual climax: fantasy driven individuals aim to reach sexual climax online, whereas contact driven individuals target minors to achieve physical sex offline. This review systematically investigates whether there is an empirical basis for the distinction between these two proposed discrete types. Comparison of tactics and behaviour are considered to examine whether the contact vs. fantasy distinction is useful. A two-stage literature selection process, considered against pre-determined inclusion criteria, identified a total of twenty-two studies. As methodological heterogeneity limited the ability to conduct pooled analysis, a narrative synthesis of data employing an interpretive approach was conducted. This showed that the contact and fantasy distinction is ambiguous, given that both groups engage in online behaviours that provide them with online sexual gratification that can also lead to offline contact. Furthermore, no clear pattern of behaviour was found to define contact and fantasy individuals idiosyncratically. The European Online Grooming Project typology is thus proposed as a better representation of this behaviour; intimacy seeking, adaptable and hypersexualized groups. The distinction between these groups focuses primarily on the intensity of the relationship, acknowledging that sexual abuse can occur with or without offline contact. This review also highlights the need for larger, methodologically robust studies that examine the behaviour of online child sexual offenders.

Cognitive Outcomes following Thrombolysis in Acute Ischemic Stroke: A Systematic Review.

BACKGROUND: Patients treated with thrombolytic therapy within 4.5 hours after stroke onset appear to have improved survival and functional outcomes. Poststroke cognitive impairment is associated with reduced quality of life and survival and needs to be reviewed in consideration of the administration of thrombolysis. This review aims to systematically evaluate literature exploring the effect of thrombolysis for ischemic stroke on cognition. METHODS: An electronic search was conducted to identify articles and gray literature applying broad Medical Subject Heading terms. Literature was reviewed with a 2-step process against predetermined inclusion criteria. All relevant studies were included if they investigated global or individual cognitive domains. RESULTS: Three studies satisfied the inclusion criteria but were diverse in outcome measures and duration, their heterogeneity limiting any possible pooled analysis. One study examined long-term treatment effects on global cognition and did not find a positive effect at 6 months. A positive treatment effect was reported in the acute phase in 1 study examining domains of visuoconstructive and perceptive abilities. One study retrospectively analyzed treatment effects on language and found improvement in the acute phase but not in the long term. CONCLUSIONS: The limited existing evidence on the effects of thrombolytic therapy on long- and short-term cognition is varied in both outcome measures and diagnostic classifications, making it difficult to extrapolate results to a global stroke population. This review should be used to inform future research in stroke treatment outcomes and highlights the immediate need for larger, more robust studies in this area.

Antimicrobial stewardship using pharmacy data for the nurse-led school-based clinics in Counties Manukau District Health Board for management of group A streptococcal pharyngitis and skin infection.

AIM: To evaluate antimicrobial usage in the school-based clinics against operating guidelines. METHOD: Antimicrobial prescribing data (2014) from 10/18 participating pharmacies serving 14,153/23,588 primary school children of the programme were accessible. Prescriptions from 5/10 pharmacies were available for identifying type, amount, and indication of the medicine. One pharmacy serving a defined population (n=3,513) with single healthcare provider delivering the school programme was selected for detailed evaluation and identifying individuals receiving multiple treatments. RESULTS: Data from 10 pharmacies (n=7,889 prescriptions) showed 91.2% of prescriptions were for group A streptococcal-positive throat swab, 8.8% for skin infections. More detail from 5/10 pharmacies showed only 2% of group A streptococcal pharyngitis treatments (107/4,672) were not first-line (56 cephalexin and 51 rifampin prescriptions). Fusidic acid (159/452, 35.18%) or cephalexin (169/452, 37.39%) were most commonly used for skin infection. Analysis in the defined population showed <4% (151/4,325) of assessed skin conditions received antimicrobials, and only 6 individuals received more than one course of oral antimicrobial over the year. CONCLUSION: Antimicrobial administration demonstrates high compliance with the protocol. There was very limited use of second-line antimicrobials for recurrent pharyngitis. Most skin infections did not require antimicrobial treatment. Repeated antimicrobials for individuals were rare.

Fractal dimension (df) as a new structural biomarker of clot microstructure in different stages of lung cancer.

Venous thromboembolism (VTE) is common in cancer patients, and is the second commonest cause of death associated with the disease. Patients with chronic inflammation, such as cancer, have been shown to have pathological clot structures with modulated mechanical properties. Fractal dimension (df) is a new technique which has been shown to act as a marker of the microstructure and mechanical properties of blood clots, and can be performed more readily than current methods such as scanning electron microscopy (SEM). We measured df in 87 consecutive patients with newly diagnosed lung cancer prior to treatment and 47 matched-controls. Mean group values were compared for all patients with lung cancer vs controls and for limited disease vs extensive disease. Results were compared with conventional markers of coagulation, fibrinolysis and SEM images. Significantly higher values of df were observed in lung cancer patients compared with controls and patients with extensive disease had higher values than those with limited disease (p< 0.05), whilst conventional markers failed to distinguish between these groups. The relationship between df of the incipient clot and mature clot microstructure was confirmed by SEM and computational modelling: higher df was associated with highly dense clots formed of smaller fibrin fibres in lung cancer patients compared to controls. This study demonstrates that df is a sensitive technique which quantifies the structure and mechanical properties of blood clots in patients with lung cancer. Our data suggests that df has the potential to identify patients with an abnormal clot microstructure and greatest VTE risk.

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.

Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C.

Genome-wide association studies have identified more than 70 common variants that are associated with breast cancer risk. Most of these variants map to non-protein-coding regions and several map to gene deserts, regions of several hundred kilobases lacking protein-coding genes. We hypothesized that gene deserts harbor long-range regulatory elements that can physically interact with target genes to influence their expression. To test this, we developed Capture Hi-C (CHi-C), which, by incorporating a sequence capture step into a Hi-C protocol, allows high-resolution analysis of targeted regions of the genome. We used CHi-C to investigate long-range interactions at three breast cancer gene deserts mapping to 2q35, 8q24.21, and 9q31.2. We identified interaction peaks between putative regulatory elements ("bait fragments") within the captured regions and "targets" that included both protein-coding genes and long noncoding (lnc) RNAs over distances of 6.6 kb to 2.6 Mb. Target protein-coding genes were IGFBP5, KLF4, NSMCE2, and MYC; and target lncRNAs included DIRC3, PVT1, and CCDC26. For one gene desert, we were able to define two SNPs (rs12613955 and rs4442975) that were highly correlated with the published risk variant and that mapped within the bait end of an interaction peak. In vivo ChIP-qPCR data show that one of these, rs4442975, affects the binding of FOXA1 and implicate this SNP as a putative functional variant.

An evaluation of initial vancomycin dosing in infants, children, and adolescents.

Background. The pharmacokinetics of many medications change as we age, thus most would assume dosing strategies would adjust for these changes. The objective of this study is to evaluate the initial vancomycin dosing in three pediatric age groups based on measured serum trough concentrations. Methodology. This retrospective database review included patients aged from 1 month to 18 years old admitted to the Moses H. Cone Memorial Hospital. Patients had to have received vancomycin dosed at 15 mg/kg every 8 hours with an appropriately measured trough concentration. The primary outcome was to determine the percentage of patients in 3 pediatric age groups achieving therapeutic trough concentrations with the initial vancomycin dosing regimen. Results. Twenty-five patients were included in the study. None of the patients had therapeutic trough concentrations after receiving vancomycin 15 mg/kg every 8 hours. Only one patient had a supratherapeutic level, while all of the other patients had levels less than 10 mcg/mL. Conclusions. Vancomycin 15 mg/kg every 8 hours did not provide therapeutic serum trough concentrations for any pediatric age groups. Higher doses and/or more frequent dosing regimens need to be evaluated for each age group to determine the most appropriate strategies for producing therapeutic trough concentrations.

Action of SN 28049, a new DNA binding topoisomerase II-directed antitumour drug: comparison with doxorubicin and etoposide.

AIM: We have examined the cellular action of SN 28049 (N-[2-(dimethylamino)ethyl]-2,6-dimethyl-1-oxo-1,2-dihydrobenzo[b]-1,6-naphthyridine-4-carboxamide), a DNA binding drug with curative activity against the Colon 38 transplantable murine carcinoma, on human tumour cells. Its action has been compared with that of two topoisomerase II-targetted drugs, etoposide and doxorubicin. METHODS: The NZM3 melanoma and HCT116 colon carcinoma cell lines, each expressing wild-type p53, were cultured and responses were compared by flow cytometry, electrophoresis, microscopy, and growth of tumour xenografts. RESULTS: Responses of NZM3 cells to all three drugs, as measured by histone H2AX γ-phosphorylation, induction of the p53 pathway and cell cycle arrest, were comparable and typical of those of topoisomerase II poisons. Xenografts of NZM3 cells responded to SN 28049 with a tumour growth delay of 16 days. In contrast, HCT116 cells had an attenuated DNA damage response to the drugs and SN 28049 had no in vivo activity, consistent with low topoisomerase II activity. However, SN 28049 inhibited HCT116 cell growth in vitro and activated the p53 pathway to induce a state with G(2)/M-phase DNA content, low mitotic index and a high proportion of binucleate cells. Treated cells expressed cyclin E and the senescence marker ß-galactosidase but showed low expression of cyclin B and survivin. In comparison, etoposide caused little p53 expression or cycle arrest, and doxorubicin had an intermediate effect. CONCLUSION: The action of SN 28049 in NZM3 cells is typical of a topoisomerase II poison, but the low topoisomerase IIα activity of HCT116 cells allowed the detection of a second antiproliferative action of SN 28049 in which cells undergo post-mitotic cycle arrest and induction of p53.