Multi-omic profiling of the developing human cerebral cortex at the single-cell level.

The cellular complexity of the human brain is established via dynamic changes in gene expression throughout development that is mediated, in part, by the spatiotemporal activity of cis-regulatory elements (CREs). We simultaneously profiled gene expression and chromatin accessibility in 45,549 cortical nuclei across six broad developmental time points from fetus to adult. We identified cell type-specific domains in which chromatin accessibility is highly correlated with gene expression. Differentiation pseudotime trajectory analysis indicates that chromatin accessibility at CREs precedes transcription and that dynamic changes in chromatin structure play a critical role in neuronal lineage commitment. In addition, we mapped cell type-specific and temporally specific genetic loci implicated in neuropsychiatric traits, including schizophrenia and bipolar disorder. Together, our results describe the complex regulation of cell composition at critical stages in lineage determination and shed light on the impact of spatiotemporal alterations in gene expression on neuropsychiatric disease.

Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease.

Alzheimer's disease (AD) is the most common form of dementia worldwide, with a projection of 151 million cases by 2050. Previous genetic studies have identified three main genes associated with early-onset familial Alzheimer's disease, however this subtype accounts for less than 5% of total cases. Next-generation sequencing has been well established and holds great promise to assist in the development of novel therapeutics as well as biomarkers to prevent or slow the progression of this devastating disease. Here we present a public resource of functional genomic data from the parahippocampal gyrus of 201 postmortem control, mild cognitively impaired (MCI) and AD individuals from the Mount Sinai brain bank, of which whole-genome sequencing (WGS), and bulk RNA sequencing (RNA-seq) were previously published. The genomic data include bulk proteomics and DNA methylation, as well as cell-type-specific RNA-seq and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) data. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource available on the Synapse platform at https://doi.org/10.7303/syn51180043.2 .

Outcomes of Free Flap Reconstruction for Chronic Venous Ulceration in the Lower Limb: A Systematic Review.

BACKGROUND: The mainstay of treatment for venous ulceration is conservative wound management and lifelong compression therapy. For patients with recalcitrant ulcers, free flap reconstruction has been proposed as a treatment option to reconstruct the diseased soft tissues as well as the underlying insufficient venous system. This review systematically evaluates the outcomes of free flap reconstruction for chronic venous ulcers in the lower limb. METHOD: A protocol was developed a priori and registered on the PROSPERO database. A systematic search of literature was performed in MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), clinical trials registries, and OpenGrey from inception to April 2020 according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Studies of patients undergoing free tissue transfer reconstruction for chronic venous ulcers in the lower limb were included. RESULTS: A total of 5 noncomparative cohort studies featuring 56 patients with 62 recalcitrant venous ulcers treated with 64 free flaps who had a mean age of 50 years (range, 17-76 years) were included, and a narrative analysis undertaken. Mean defect size following ulcer debridement was 153.3 cm 2 (range, 24-600 cm 2 ). Defects were reconstructed with muscle (n = 39 [60.9%]), fasciocutaneous (n = 23 [35.9%]), and visceral (n = 2 [3.1%]) free flaps, with latissimus dorsi (n = 16, 25%) and rectus abdominis flaps (n = 16, 25%) being the most frequently used. Mean follow-up ranged from 24 to 125 months. Pooled flap survival rate was 95%. No recurrence within the territory of the flap was reported, but there were 20 instances (35.7%) of new ulcers outside of the flap boundaries. CONCLUSION: There is currently an absence of evidence to support the use of free flap reconstruction for recalcitrant venous ulcers compared with conventional management. Although evidence suggests that it is technically feasible, there is no evidence to suggest it prevents ulceration outside the reconstructed region. Further studies are necessary to evaluate its effectiveness for venous ulcers in the lower limb.

Caffeine enhances activity thermogenesis and energy expenditure in rats.

Caffeine and its derivatives have been used, alone and in combination with other phytochemicals, as weight-loss supplements. Caffeine affects several physiological and behavioural aspects of energy balance, including increasing locomotor activity. This study investigates the potential for caffeine to enhance activity thermogenesis and energy expenditure (EE) even when activity level is held constant. To do this, EE and muscle thermogenesis were measured in rats during treadmill walking regimens, with and without caffeine (25 mg/kg, ip). Activity-related EE was significantly increased throughout the treadmill walking protocol. Muscle heat dissipation, on the other hand, was significantly increased by caffeine only at the end of the 25-minute treadmill test. This study demonstrates that caffeine increases the caloric cost of physical activity, compared to the caloric cost of that same physical activity without caffeine, implicating decreased muscle work efficiency. Combined with the known ability of caffeine to increase locomotor activity, the decreased locomotor efficiency imparted by caffeine may further augment the potential for caffeine to enhance caloric expenditure.

The FACT inhibitor CBL0137 Synergizes with Cisplatin in Small-Cell Lung Cancer by Increasing NOTCH1 Expression and Targeting Tumor-Initiating Cells.

Traditional treatments of small-cell lung cancer (SCLC) with cisplatin, a standard-of-care therapy, spare the tumor-initiating cells (TIC) that mediate drug resistance. Here we report a novel therapeutic strategy that preferentially targets TICs in SCLC, in which cisplatin is combined with CBL0137, an inhibitor of the histone chaperone facilitates chromatin transcription (FACT), which is highly expressed in TICs. Combination of cisplatin and CBL0137 killed patient-derived and murine SCLC cell lines synergistically. In response to CBL0137 alone, TICs were more sensitive than non-TICs, in part, because CBL0137 increased expression of the tumor suppressor NOTCH1 by abrogating the binding of negative regulator SP3 to the NOTCH1 promoter, and in part because treatment decreased the high expression of stem cell transcription factors. The combination of cisplatin and CBL0137 greatly reduced the growth of a patient-derived xenograft in mice and also the growth of a syngeneic mouse SCLC tumor. Thus, CBL0137 can be a highly effective drug against SCLC, especially in combination with cisplatin.Significance: These findings reveal a novel therapeutic regimen for SCLC, combining cisplatin with an inhibitor that preferentially targets tumor-initiating cells. Cancer Res; 78(9); 2396-406. ©2018 AACR.

Radiologically Determined Sarcopenia Predicts Morbidity and Mortality Following Abdominal Surgery: A Systematic Review and Meta-Analysis.

BACKGROUND: Individualised risk prediction is crucial if targeted pre-operative risk reduction strategies are to be deployed effectively. Radiologically determined sarcopenia has been shown to predict outcomes across a range of intra-abdominal pathologies. Access to pre-operative cross-sectional imaging has resulted in a number of studies investigating the predictive value of radiologically assessed sarcopenia over recent years. This systematic review and meta-analysis aimed to determine whether radiologically determined sarcopenia predicts post-operative morbidity and mortality following abdominal surgery. METHOD: CENTRAL, EMBASE and MEDLINE databases were searched using terms to capture the concept of radiologically assessed sarcopenia used to predict post-operative complications in abdominal surgery. Outcomes included 30 day post-operative morbidity and mortality, 1-, 3- and 5-year overall and disease-free survival and length of stay. Data were extracted and meta-analysed using either random or fixed effects model (Revman ® 5.3). RESULTS: A total of 24 studies involving 5267 patients were included in the review. The presence of sarcopenia was associated with a significant increase in major post-operative complications (RR 1.61 95% CI 1.24-4.15 p = <0.00001) and 30-day mortality (RR 2.06 95% CI 1.02-4.17 p = 0.04). In addition, sarcopenia predicted 1-, 3- and 5-year survival (RR 1.61 95% CI 1.36-1.91 p = <0.0001, RR 1.45 95% CI 1.33-1.58 p = <0.0001, RR 1.25 95% CI 1.11-1.42 p = 0.0003, respectively) and 1- and 3-year disease-free survival (RR 1.30 95% CI 1.12-1.52 p = 0.0008). CONCLUSION: Peri-operative cross-sectional imaging may be utilised in order to predict those at risk of complications following abdominal surgery. These findings should be interpreted in the context of retrospectively collected data and no universal sarcopenic threshold. Targeted prehabilitation strategies aiming to reverse sarcopenia may benefit patients undergoing abdominal surgery.

Erratum to: Methods and processes for development of a CONSORT extension for reporting pilot randomized controlled trials.

[This corrects the article DOI: 10.1186/s40814-016-0065-z.].

Methods and processes for development of a CONSORT extension for reporting pilot randomized controlled trials.

BACKGROUND: Feasibility and pilot studies are essential components of planning or preparing for a larger randomized controlled trial (RCT). They are intended to provide useful information about the feasibility of the main RCT-with the goal of reducing uncertainty and thereby increasing the chance of successfully conducting the main RCT. However, research has shown that there are serious inadequacies in the reporting of pilot and feasibility studies. Reasons for this include a lack of explicit publication policies for pilot and feasibility studies in many journals, unclear definitions of what constitutes a pilot or feasibility RCT/study, and a lack of clarity in the objectives and methodological focus. All these suggest that there is an urgent need for new guidelines for reporting pilot and feasibility studies. OBJECTIVES: The aim of this paper is to describe the methods and processes in our development of an extension to the Consolidated Standards of Reporting Trials (CONSORT) Statement for reporting pilot and feasibility RCTs, that are executed in preparation for a future, more definitive RCT. METHODS/DESIGN: There were five overlapping parts to the project: (i) the project launch-which involved establishing a working group and conducting a review of the literature; (ii) stakeholder engagement-which entailed consultation with the CONSORT group, journal editors and publishers, the clinical trials community, and funders; (iii) a Delphi process-used to assess the agreement of experts on initial definitions and to generate a reporting checklist for pilot RCTs, based on the 2010 CONSORT statement extension applicable to reporting pilot studies; (iv) a consensus meeting-to discuss, add, remove, or modify checklist items, with input from experts in the field; and (v) write-up and implementation-which included a guideline document which gives an explanation and elaboration (E&E) and which will provide advice for each item, together with examples of good reporting practice. This final part also included a plan for dissemination and publication of the guideline. CONCLUSIONS: We anticipate that implementation of our guideline will improve the reporting completeness, transparency, and quality of pilot RCTs, and hence benefit several constituencies, including authors of journal manuscripts, funding agencies, educators, researchers, and end-users.

Defining Feasibility and Pilot Studies in Preparation for Randomised Controlled Trials: Development of a Conceptual Framework.

We describe a framework for defining pilot and feasibility studies focusing on studies conducted in preparation for a randomised controlled trial. To develop the framework, we undertook a Delphi survey; ran an open meeting at a trial methodology conference; conducted a review of definitions outside the health research context; consulted experts at an international consensus meeting; and reviewed 27 empirical pilot or feasibility studies. We initially adopted mutually exclusive definitions of pilot and feasibility studies. However, some Delphi survey respondents and the majority of open meeting attendees disagreed with the idea of mutually exclusive definitions. Their viewpoint was supported by definitions outside the health research context, the use of the terms 'pilot' and 'feasibility' in the literature, and participants at the international consensus meeting. In our framework, pilot studies are a subset of feasibility studies, rather than the two being mutually exclusive. A feasibility study asks whether something can be done, should we proceed with it, and if so, how. A pilot study asks the same questions but also has a specific design feature: in a pilot study a future study, or part of a future study, is conducted on a smaller scale. We suggest that to facilitate their identification, these studies should be clearly identified using the terms 'feasibility' or 'pilot' as appropriate. This should include feasibility studies that are largely qualitative; we found these difficult to identify in electronic searches because researchers rarely used the term 'feasibility' in the title or abstract of such studies. Investigators should also report appropriate objectives and methods related to feasibility; and give clear confirmation that their study is in preparation for a future randomised controlled trial designed to assess the effect of an intervention.

Clinical assessment of patients with chest pain; a systematic review of predictive tools.

BACKGROUND: The clinical assessment of patients with chest pain of recent onset remains difficult. This study presents a critical review of clinical predictive tools for the assessment of patients with chest pain. METHODS: Systematic review of observational studies and estimation of probabilities of coronary artery disease (CAD) in patients with chest pain. Searches were conducted in PubMed, Embase, Scopus, and Web of Science to identify studies reporting tools, with at least three variables from clinical history, physical examination or ECG, produced with multivariate analysis, to estimate probabilities of CAD in patients with chest pain of recent onset, published from inception of the database to the 31st July 2015. The references of previous relevant reviews were hand searched. The methodological quality was assessed with standard criteria. Since the incidence of CAD has changed in the past few decades, the date of publication was acknowledged to be relevant in order to use the tool in clinical practice, and more recent papers were considered more relevant. Probabilities of CAD according to the studies of highest quality were estimated and the evidence provided was graded. RESULTS: Twelve papers were included out of the 19126 references initially identified. The methodological quality of all of them was high. The clinical characteristics of the chest pain, age, past medical history of cardiovascular disease, gender, and abnormalities in the ECG were the predictors of CAD most commonly reported across the studies. The most recent papers, with highest methodological quality, and most practical for use in clinical settings, reported prediction or exclusion of CAD with area under the curve 0.90 in Primary Care, 0.91 in Emergency department, and 0.79 in Cardiology. These papers provide evidence of high level (1B) and the recommendation to use their results in the management of patients with chest pain is strong (A). CONCLUSIONS: The risk of CAD can be estimated on clinical grounds in patients with chest pain in different clinical settings with high accuracy. The estimation of probabilities of CAD presented in these studies could be used for a better management of patients with chest pain and also in the development of future predictive tools.

Are missing data adequately handled in cluster randomised trials? A systematic review and guidelines.

BACKGROUND: Missing data are a potential source of bias, and their handling in the statistical analysis can have an important impact on both the likelihood and degree of such bias. Inadequate handling of the missing data may also result in invalid variance estimation. The handling of missing values is more complex in cluster randomised trials, but there are no reviews of practice in this field. OBJECTIVES: A systematic review of published trials was conducted to examine how missing data are reported and handled in cluster randomised trials. METHODS: We systematically identified cluster randomised trials, published in English in 2011, using the National Library of Medicine (MEDLINE) via PubMed. Non-randomised and pilot/feasibility trials were excluded, as were reports of secondary analyses, interim analyses, and economic evaluations and those where no data were at the individual level. We extracted information on missing data and the statistical methods used to deal with them from a random sample of the identified studies. RESULTS: We included 132 trials. There was evidence of missing data in 95 (72%). Only 32 trials reported handling missing data, 22 of them using a variety of single imputation techniques, 8 using multiple imputation without accommodating the clustering and 2 stating that their likelihood-based complete case analysis accounted for missing values because the data were assumed Missing-at-Random. LIMITATIONS: The results presented in this study are based on a large random sample of cluster randomised trials published in 2011, identified in electronic searches and therefore possibly missing some trials, most likely of poorer quality. Also, our results are based on information in the main publication for each trial. These reports may omit some important information on the presence of, and reasons for, missing data and on the statistical methods used to handle them. Our extraction methods, based on published reports, could not distinguish between missing data in outcomes and missing data in covariates. This distinction may be important in determining the assumptions about the missing data mechanism necessary for complete case analyses to be valid. CONCLUSIONS: Missing data are present in the majority of cluster randomised trials. However, they are poorly reported, and most authors give little consideration to the assumptions under which their analysis will be valid. The majority of the methods currently used are valid under very strong assumptions about the missing data, whose plausibility is rarely discussed in the corresponding reports. This may have important consequences for the validity of inferences in some trials. Methods which result in valid inferences under general Missing-at-Random assumptions are available and should be made more accessible.

The cost and cost-effectiveness of opportunistic screening for Chlamydia trachomatis in Ireland.

OBJECTIVE: The objective of this study was to estimate the cost and cost-effectiveness of opportunistic screening for Chlamydia trachomatis in Ireland. METHODS: Prospective cost analysis of an opportunistic screening programme delivered jointly in three types of healthcare facility in Ireland. Incremental cost-effectiveness analysis was performed using an existing dynamic modelling framework to compare screening to a control of no organised screening. A healthcare provider perspective was adopted with respect to costs and included the costs of screening and the costs of complications arising from untreated infection. Two outcome measures were examined: major outcomes averted, comprising cases of pelvic inflammatory disease, ectopic pregnancy and tubal factor infertility in women, neonatal conjunctivitis and pneumonia, and epididymitis in men; and quality-adjusted life-years (QALY) gained. Uncertainty was explored using sensitivity analyses and cost-effectiveness acceptability curves. RESULTS: The average cost per component of screening was estimated at €26 per offer, €66 per negative case, €152 per positive case and €74 per partner notified and treated. The modelled screening scenario was projected to be more effective and more costly than the control strategy. The incremental cost per major outcomes averted was €6093, and the incremental cost per QALY gained was €94,717. For cost-effectiveness threshold values of €45,000 per QALY gained and lower, the probability of the screening being cost effective was estimated at <1%. CONCLUSIONS: An opportunistic chlamydia screening programme, as modelled in this study, would be expensive to implement nationally and is unlikely to be judged cost effective by policy makers in Ireland.

Where do young adults want opportunistic chlamydia screening services to be located?

BACKGROUND: This study measured the acceptability of urine-based chlamydia screening to young adults, where young adults wanted opportunistic chlamydia screening services to be located, and by whom they wanted to be offered screening. METHODS: A cross-sectional survey of 5685 university students and 400 young adult healthcares setting attendees (age: 18-29 years). RESULTS: Ninety-six percent of males and 93% of females said that they would find it acceptable to be offered chlamydia screening. Seventy-six percent of males and 77% of females wanted to be offered screening by a doctor or nurse. Young women would prefer female staff. Most respondents preferred that screening be located in traditional healthcare settings such as General Practices, and offered by either doctors or nurses. More than 90% of respondents did not want screening services to be located in pharmacies and almost all rejected public non-health care screening settings. CONCLUSIONS: Opportunistic chlamydia screening services should be located in traditional healthcare/medical settings, and screening should be offered by doctors and nurses.

6-(4-Fluorophenyl)-8-phenyl-2,3-dihydro-4H-imidazo[5,1-b][1,3]thiazin-4-one: an unusual [6-5] fused-ring system.

The title compound, C(18)H(13)FN(2)OS, is the first structural example of a [6-5] fused ring incorporating the 2,3-dihydro-4H-imidazo[5,1-b][1,3]thiazin-4-one molecular scaffold. The six-membered 2,3-dihydro-1,3-thiazin-4-one ring adopts an envelope conformation, with the S-CH(2) C atom displaced by 0.761 (2) A from the five-atom plane (all within 0.05 A of the mean plane). The imidazole ring is planar. The phenyl ring is twisted from coplanarity with the imidazole ring by 23.84 (5) degrees and the 4-fluorophenyl ring is twisted by 53.36 (6) degrees , due to a close C(aryl)-H...O=C contact with the thiazin-4-one carbonyl O atom. The primary intermolecular interaction involves a CH(2) group with the F atom [C...F = 3.256 (2) A and C-H...F = 137 degrees ].

Sexually acquired infections: do lay experiences of partner notification challenge practice?

AIM: This paper is a report of a study to explore experiences of partner notification for syphilis from the perspectives of gay, bisexual and other men who have sex with men. BACKGROUND: Partner notification is the 'cornerstone' of the prevention and control of sexually acquired infections. As a health strategy, it has been in use for over six decades and is employed across all continents. Its success relies almost entirely on the voluntary response of index patients in disclosing details of their sexual partners and sexual practices and the voluntary response of sexual partners who have been traced. However, internationally, few studies have explicitly explored lay experiences of partner notification. METHOD: A purposive sample of 40 gay, bisexual and other men who have sex with men was recruited from two genitourinary clinics in the Greater Dublin area of Ireland and a variety of gay social venues. Semi-structured interviews were carried out between December 2002 and February 2004. FINDINGS: Men's perspectives on partner notification featured three interweaving stages: on tracing sexual partners, on informing partners and on attending clinics. Participants were in favour of partner notification, but did not find it easy to comply with the demands it made on their relationships. Compliance was difficult not only because of the problem of physically tracing casual and anonymous partners, but also because of the challenge of actually notifying partners. The main incentive for contacts to attend clinics was concern for their own health and that of others. Barriers to attending were fear of being exposed to the stigma of being gay and/or having a sexually acquired infection. CONCLUSION: There is a need to develop evidence-based methods, which are grounded in the lay experience, to support index patients in 'breaking bad news' and for continued efforts to de-stigmatize sexually acquired infections and homosexuality in the view of the general public.

Solution-phase synthesis of a tricyclic pyrrole-2-carboxamide discovery library applying a stetter-Paal-Knorr reaction sequence.

The solution-phase synthesis of a discovery library of 178 tricyclic pyrrole-2-carboxamides was accomplished in nine steps and seven purifications starting with three benzoyl-protected amino acid methyl esters. Further diversity was introduced by two glyoxaldehydes and 41 primary amines. The combination of Pauson-Khand, Stetter, and microwave-assisted Paal-Knorr reactions was applied as a key sequence. The discovery library was designed with the help of QikProp 2.1, and physicochemical data are presented for all pyrroles. Library members were synthesized and purified in parallel and analyzed by LC/MS. Selected compounds were fully characterized.

Microwave-assisted "libraries from libraries" approach toward the synthesis of allyl- and C-cyclopropylalkylamides.

Cascade reactions of internal and terminal alkynes, zirconocene hydrochloride, dimethylzinc, and phosphinoyl imines (prepared in one step from aldehydes and diphenylphosphinoyl amide) lead to allylic phosphinoyl amides after aqueous workup. Microwave acceleration allows the completion of this one-pot reaction sequence in 10 min. These allylic amides can be converted into a variety of derivatives, including carbamates and sulfonamides, or reacted prior to workup with diiodomethane to give novel C-cyclopropylalkylamides. A solution-phase "libraries from libraries" approach was used to generate an intermediate 20-member library which was subsequently expanded to a 100-member library by a series of N-functionalizations. The biological activity was evaluated in an assay for competitive binding to the estrogen receptor (ERalpha), revealing three potent lead compounds of a new structural type.

Indole synthesis by controlled carbolithiation of o-aminostyrenes.

An effective synthesis of the functionalized indole ring system has been developed from substituted o-aminostyrene starting material. Our methodology involves a novel cascade reaction sequence of alkyllithium addition to the styrene double bond and subsequent trapping of the intermediate organolithium with a suitable electrophile, followed by an in situ ring closure and dehydration to generate the indole ring. This new reaction sequence allows for the introduction of molecular diversity at all positions on the indole scaffold. The procedure was shown to be successful with a range of both C and N substituents on the o-aminostyrenes. The reaction sequence was tolerant to the reactivity range of alkyllithiums such as tert-, sec-, and n-butyllithium. The electrophiles used were DMF, which generated indole products with C-2 unsubstituted, and nitriles, which incorporated the nitrile substituent at C-2. The o-aminostyrene starting materials were generated by a Pd-catalyzed cross-coupling reaction of a vinyl boronic acid equivalent with the readily available substituted o-bromoanilines.

tert-Butyl 5-methoxy-3-pentylindole-1-carboxylate.

The molecule of the title compound, C(19)H(27)NO(3), is essentially planar, with all non-H atoms within 0.2 A of the nine-membered indole plane, except for the three tert-butyl C atoms. The C(5) pentyl chain is in an extended conformation, with three torsion angles of 179.95 (13), 179.65 (13) and -178.95 (15) degrees (the latter two angles include the C atoms of the C(5) chain only). Three intramolecular C-H.O=C contacts are present (C.O < 3.05 A and C-H.O > 115 degrees ), and an intermolecular C-H.O=C contact and pi-pi stacking complete the intermolecular interactions.

New organolithium addition methodology to diversely functionalized indoles.

A novel synthetic approach to diversely functionalized indoles is described. Boc-protected ortho-aminostyrenes undergo an alkyllithium addition reaction, thereby generating a lithiated intermediate, which upon reaction with specific electrophiles sets up a cascade reaction process between the reacted electrophile and ortho-amino substituent, facilitating an in situ ring closure, followed by dehydration, to generate an indole ring system. This methodology is demonstrated by the synthesis of a range of 3,5-, 1,3,5-, and 2,3,5-substituted indoles.