Is reproductive development adaptively calibrated to early experience? Evidence from a national sample of females

Many developmental theories have not been sufficiently evaluated using designs that control for unobserved familial confounds. Our long-term goal is to determine the causal structure underlying associations between early environmental conditions and later psychosocial and health outcomes. Our overall objective in this study was to further evaluate predictions derived from applications of life history theory to female reproductive development, key among them that reproductive milestones translate early environmental risk into fertility, health, and behavioral outcomes. To this end, we used female data from the National Longitudinal Survey of Youth 1979 and structural equation modeling to conduct increasingly severe tests, beginning with covariate control and then progressing to sibling control and behavioral genetic designs. After adjusting for confounds varying between sets of siblings, we did not find evidence that age at menarche reflected components of early environment or that any focal outcomes reflected early fragmented family structure (birth to age nine). Although we detected no links between measured environment and individual differences in age at sexual debut, we did find that it reflected both shared and nonshared influences in our behavior genetic models. Interestingly, delayed sexual debut (into young adulthood) reflected identification of parents as the greatest influences and forecasted an array of fertility-related outcomes. Taken together, these findings challenge theories suggesting menarche timing is adaptively calibrated to early environment. They also highlight the need for more research using sibling control and related designs to examine the roles of environments in development. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Treating Chronic, Intractable Pain with a Miniaturized Spinal Cord Stimulation System: 1-Year Outcomes from the AUS-nPower Study During the COVID-19 Pandemic

Purpose

Spinal cord stimulation (SCS) is a highly effective treatment for chronic neuropathic pain. Despite recent advances in technology, treatment gaps remain. A small SCS system with a miniaturized implantable pulse generator (micro-IPG; <1.5 cm3 in volume) and an externally worn power source may be preferred by patients who do not want a large, implanted battery. We report here the long-term outcomes from the first-in-human study evaluating the safety and performance of a new neurostimulation system.

Patients and Methods

This was a prospective, multi-center, open-label, single-arm study to evaluate this SCS system, in the treatment of chronic, intractable leg and low-back pain. Consented subjects who passed screening continued on to the long-term phase of the study. One-year, patient-reported outcomes (PRO's) such as pain (Numeric Rating Scale, NRS), functional disability, quality of life, and mood were captured.

Results

Twenty-six (26) evaluable subjects with permanent implants were included in this analysis. The average leg pain NRS score decreased from 6.8 ± 1.2 at baseline to 1.1 ± 1.2 at the end of the study (p < 0.001), while the average low-back pain NRS score decreased from 6.8 ± 1.2 to 1.5 ± 1.2 (p < 0.001). The responder rate (proportion with ≥50% pain relief) was 91% in the leg(s) and 82% in the low back. There were significant improvements in functional disability (Oswestry Disability Index) and in mood (Beck Depression Inventory), demonstrating a 46% and 62% improvement, respectively (p < 0.001). Eleven-point Likert scales demonstrated the wearable to be very comfortable and very easy to use.

Conclusion

There were considerable challenges conducting a clinical study during the COVID-19 pandemic, such as missed study programming visits. Nevertheless, subjects had significant PRO improvements through 1-year. The small size of the implanted device, along with a proprietary waveform, may allow for improved SCS outcomes and a drop in incidence of IPG-pocket pain.

Global health context for the military in Defence Engagement (Health)

Global health practice is becoming a key enabler within UK Defence and foreign policy. The definition of global health remains debated, though some important themes have been identified including: the multidisciplinary nature of global health, its ethical foundation and the political nature of global health. This paper contributes to the ongoing rational discourse that this important discipline deserves and recommends a framework and principles to apply to military health and care system strengthening in the Defence Engagement (Health) (DE(H)) practitioner role. DE(H) involves complex multiorganisational relationships and processes, and while practitioners should be mindful of the political nature of their role, the broad aims of preventing conflict and building stability mean DE(H) should contribute positively to global health.This paper forms part of a special issue of BMJ Military Health dedicated to Defence Engagement.

Index and biological spectrum of human DNase I hypersensitive sites

DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA^1–5 and contain genetic variations associated with diseases and phenotypic traits^6–8. We created high-resolution maps of DHSs from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA. Here we show that these maps highly resolve the cis-regulatory compartment of the human genome, which encodes unexpectedly diverse cell- and tissue-selective regulatory programs at very high density. These programs can be captured comprehensively by a simple vocabulary that enables the assignment to each DHS of a regulatory barcode that encapsulates its tissue manifestations, and global annotation of protein-coding and non-coding RNA genes in a manner orthogonal to gene expression. Finally, we show that sharply resolved DHSs markedly enhance the genetic association and heritability signals of diseases and traits. Rather than being confined to a small number of distal elements or promoters, we find that genetic signals converge on congruently regulated sets of DHSs that decorate entire gene bodies. Together, our results create a universal, extensible coordinate system and vocabulary for human regulatory DNA marked by DHSs, and provide a new global perspective on the architecture of human gene regulation.

High-resolution maps of DNase I hypersensitive sites from 733 human biosamples are used to identify and index regulatory DNA within the human genome.

Global reference mapping of human transcription factor footprints

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits1, but it remains challenging to distinguish variants that affect regulatory function2. Genomic DNase I footprinting enables the quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin3-6. However, only a small fraction of such sites have been precisely resolved on the human genome sequence6. Here, to enable comprehensive mapping of transcription factor footprints, we produced high-density DNase I cleavage maps from 243 human cell and tissue types and states and integrated these data to delineate about 4.5 million compact genomic elements that encode transcription factor occupancy at nucleotide resolution. We map the fine-scale structure within about 1.6 million DNase I-hypersensitive sites and show that the overwhelming majority are populated by well-spaced sites of single transcription factor-DNA interaction. Cell-context-dependent cis-regulation is chiefly executed by wholesale modulation of accessibility at regulatory DNA rather than by differential transcription factor occupancy within accessible elements. We also show that the enrichment of genetic variants associated with diseases or phenotypic traits in regulatory regions1,7 is almost entirely attributable to variants within footprints, and that functional variants that affect transcription factor occupancy are nearly evenly partitioned between loss- and gain-of-function alleles. Unexpectedly, we find increased density of human genetic variation within transcription factor footprints, revealing an unappreciated driver of cis-regulatory evolution. Our results provide a framework for both global and nucleotide-precision analyses of gene regulatory mechanisms and functional genetic variation.

Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling

The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global impact of chromatin remodelers on regulatory DNA landscapes and how this translates to gene expression. We use precision genome engineering to reawaken homozygously inactivated SMARCA4, a central ATPase of the human SWI/SNF chromatin remodeling complex, in lung adenocarcinoma cells. Here, we combine DNase I hypersensitivity, histone modification, and transcriptional profiling to show that SMARCA4 dramatically increases both the number and magnitude of accessible chromatin sites genome-wide, chiefly by unmasking sites of low regulatory factor occupancy. By contrast, transcriptional changes are concentrated within well-demarcated remodeling domains wherein expression of specific genes is gated by both distal element activation and promoter chromatin configuration. Our results provide a perspective on how global chromatin remodeling activity is translated to gene expression via regulatory DNA.

Neuromodulation of the Dorsal Root Ganglion for Chronic Postsurgical Pain

Objective

The objective of this study is to review the available evidence for dorsal root ganglion (DRG) stimulation for the treatment of complex regional pain syndrome type II (CRPS II; peripheral causalgia) associated with chronic neuropathic postsurgical pain (NPP).

Design

Available literature was identified through a search of the US National Library of Medicine’s Medline database, PubMed.gov. References from published articles also were reviewed for relevant citations.

Results

The data published to date support the use of DRG stimulation to treat chronic NPP of the groin, knee, and foot. NPP following procedures such as thoracotomy, hernia surgery, and knee replacement surgery were identified as some of the conditions for which DRG stimulation is likely to be effective.

Conclusion

DRG stimulation is known to be an effective treatment for focal neuropathic pain. Currently, NPP of the foot, groin, and knee all appear to be the conditions with the most clinical experience, backed by a limited but growing body of evidence. However, prospective studies lag behind real-world clinical experience and are needed to confirm these findings.

A Comprehensive Algorithm for Management of Neuropathic Pain

BACKGROUND

The objective of this review was to merge current treatment guidelines and best practice recommendations for management of neuropathic pain into a comprehensive algorithm for primary physicians. The algorithm covers assessment, multidisciplinary conservative care, nonopioid pharmacological management, interventional therapies, neurostimulation, low-dose opioid treatment, and targeted drug delivery therapy.

METHODS

Available literature was identified through a search of the US National Library of Medicine's Medline database, PubMed.gov. References from identified published articles also were reviewed for relevant citations.

RESULTS

The algorithm provides a comprehensive treatment pathway from assessment to the provision of first- through sixth-line therapies for primary care physicians. Clear indicators for progression of therapy from firstline to sixth-line are provided. Multidisciplinary conservative care and nonopioid medications (tricyclic antidepressants, serotonin norepinephrine reuptake inhibitors, gabapentanoids, topicals, and transdermal substances) are recommended as firstline therapy; combination therapy (firstline medications) and tramadol and tapentadol are recommended as secondline; serotonin-specific reuptake inhibitors/anticonvulsants/NMDA antagonists and interventional therapies as third-line; neurostimulation as a fourth-line treatment; low-dose opioids (no greater than 90 morphine equivalent units) are fifth-line; and finally, targeted drug delivery is the last-line therapy for patients with refractory pain.

CONCLUSIONS

The presented treatment algorithm provides clear-cut tools for the assessment and treatment of neuropathic pain based on international guidelines, published data, and best practice recommendations. It defines the benefits and limitations of the current treatments at our disposal. Additionally, it provides an easy-to-follow visual guide of the recommended steps in the algorithm for primary care and family practitioners to utilize.

Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci

BACKGROUND

Linking genetic risk loci identified by genome-wide association studies (GWAS) to their causal genes remains a major challenge. Disease-associated genetic variants are concentrated in regions containing regulatory DNA elements, such as promoters and enhancers. Although researchers have previously published DNA maps of these regulatory regions for kidney tubule cells and glomerular endothelial cells, maps for podocytes and mesangial cells have not been available.

METHODS

We generated regulatory DNA maps (DNase-seq) and paired gene expression profiles (RNA-seq) from primary outgrowth cultures of human glomeruli that were composed mainly of podocytes and mesangial cells. We generated similar datasets from renal cortex cultures, to compare with those of the glomerular cultures. Because regulatory DNA elements can act on target genes across large genomic distances, we also generated a chromatin conformation map from freshly isolated human glomeruli.

RESULTS

We identified thousands of unique regulatory DNA elements, many located close to transcription factor genes, which the glomerular and cortex samples expressed at different levels. We found that genetic variants associated with kidney diseases (GWAS) and kidney expression quantitative trait loci were enriched in regulatory DNA regions. By combining GWAS, epigenomic, and chromatin conformation data, we functionally annotated 46 kidney disease genes.

CONCLUSIONS

We demonstrate a powerful approach to functionally connect kidney disease-/trait-associated loci to their target genes by leveraging unique regulatory DNA maps and integrated epigenomic and genetic analysis. This process can be applied to other kidney cell types and will enhance our understanding of genome regulation and its effects on gene expression in kidney disease.

Primary blast lung injury simulator: a new computerised model

Mathematical modelling and computational simulation are becoming increasingly important tools in many fields of medicine where in vivo studies are expensive, difficult or impractical. This is particularly the case with primary blast lung injury, and in this paper, we give a brief overview of mathematical models before describing how we generated our blast lung injury simulator and describe some early results of its use.

Neuraxial analgesia is not associated with an increased risk of post-partum relapses in MS

Background:

Obstetrical analgesia remains a matter of controversy because of the fear of neurotoxicity of local anesthetics on demyelinated fibers or their potential relationship with subsequent relapses.

Objective:

To assess the impact of neuraxial analgesia on the risk of relapse during the first 3 months post-partum, with a focus on women who experienced relapses during pregnancy.

Methods:

We analyzed data of women followed-up prospectively during their pregnancies and at least 3 months post-partum, collected in the Pregnancy in Multiple Sclerosis (PRIMS) and Prevention of Post-Partum Relapses with Progestin and Estradiol in Multiple Sclerosis (POPARTMUS) studies between 1992–1995 and 2005–2012, respectively. The association of neuraxial analgesia with the occurrence of a post-partum relapse was estimated by logistic regression analysis.

Results:

A total of 389 women were included, 215 from PRIMS and 174 from POPARTMUS. In total, 156 women (40%) had neuraxial analgesia. Overall, 24% experienced a relapse during pregnancy and 25% in the 3 months post-partum. Women with a pregnancy relapse were more likely to have a post-partum relapse (odds ratio (OR) = 1.83, p = 0.02), independently of the use of neuraxial analgesia. There was no association between neuraxial analgesia and post-partum relapse (OR = 1.08, p = 0.78).

Conclusion:

Neuraxial analgesia was not associated with an increased risk of post-partum relapses, whatever multiple sclerosis (MS) activity during pregnancy.

Abstract P4-02-06: Intratumoral and peritumoral MRI signatures of HER2-enriched subtype also predict pathological response to neoadjuvant chemotherapy in HER2+ breast cancers

Background: Applying the PAM50 classifier to targeted RNA-Sequencing data allows HER2+ tumors to be sub-categorized into intrinsic breast cancer subtypes. HER2+ breast cancers belonging to the HER2-enriched [HER2-E] subtype exhibit the highest rate of response to neoadjuvant therapy with combination of HER2-blockade and chemotherapy, as well as dual-HER2 blockade alone. A non-invasive predictor of PAM50 subtype from clinical dynamic contrast-enhanced MRI [DCE-MRI] could provide valuable clinical guidance in the treatment of HER2+ breast cancer. In this work, we identify a set of computer-extracted heterogeneity features computed within the lesion and its surrounding peritumoral region capable of distinguishing HER2-E from other HER2+ breast cancers [Non-HER2-E]. We then demonstrate that this imaging signature of HER2-E is also predictive of pathological complete response [pCR] in an independent HER2+ testing set, consistent with the HER2-E subtype's elevated response to HER2-targeted therapy.

Methods: The training set consisted of 42 HER2+ patients with both 1.5 or 3 T DCE-MRI and targeted RNA sequencing collected prior to neoadjuvant treatment from a multicenter trial [BrUOG 211B, n=35] and The Cancer Genome Atlas-Breast Cancer project [TCGA-BRCA, n=7]. Intrinsic subtypes were assigned by unsupervised hierarchical clustering of the PAM50 gene set. 19 patients were determined to belong to the HER2-E subtype, while the remaining 23 represented non-HER2-E subtypes [19 HER2-Luminal, 4 HER2-basal]. Lesion boundaries were annotated by an expertly trained radiologist and expanded to 5 annular peritumoral regions in 3 mm increments out to a maximum radius of 15 mm. Computer-extracted heterogeneity features were computed voxelwise within intratumoral and peritumoral regions by first order statistics. A top HER2-E-associated feature from each region was identified by Wilcoxon feature selection and used to train a diagonal linear discriminant analysis [DLDA] classifier to predict HER2-E in a 3-fold cross-validation setting. This classifier was then applied to pCR prediction from DCE-MRI in a testing set of 28 HER2+ patients with available post neoadjuvant chemotherapy surgical specimens at one institution. 16 patients achieved pCR (ypT0/is), while the remainder had partial or no response (non-pCR).

Results: A combination of heterogeneity features within the intratumoral region and annular peritumoral regions out to 12 mm from the tumor yielded optimal results within the training set, with an average HER2-E prediction AUC of .77 +/- .03. When applied to response prediction in an independent testing set, this HER2-E classifier was predictive of pCR (AUC = .72).

Conclusions: Computer-extracted heterogeneity features calculated within the tumor and the surrounding peritumoral environment on DCE-MRI were able to distinguish the HER2-E PAM50 intrinsic subtype from other HER2+ breast cancers. HER2-E was characterized by elevated expression of intratumoral and peritumoral heterogeneity features, indicating a more disordered imaging phenotype within and around the tumor. Additional independent validation of these findings is needed.

Citation Format: Braman N, Prasanna P, Singh S, Beig N, Gilmore H, Etesami M, Bates D, Gallagher K, Bloch BN, Somlo G, Sikov W, Harris L, Plecha D, Varadan V, Madabhushi A. Intratumoral and peritumoral MRI signatures of HER2-enriched subtype also predict pathological response to neoadjuvant chemotherapy in HER2+ breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-02-06.

What Affects Clinicians' Usage of Health Information Exchange?

BACKGROUND: The ability to electronically exchange health information among healthcare providers holds enormous promise to improve care coordination and reduce costs. Provider-to-provider data exchange is an explicit goal of the American Recovery and Reinvestment Act of 2009 and may be essential for the long-term success of the Affordable Care Act of 2010. However, little is known about what factors affect clinicians' usage of health information exchange (HIE) functionality. OBJECTIVE: To identify factors that affect clinicians' HIE usage - in terms of frequency of contributing data to and accessing data from aggregate patient records - and suggest policies for fostering its usage. METHODS: We performed a qualitative study using grounded theory by interviewing clinician-users and HIE staff of one operational HIE which supported aggregate patient record functionality. Fifteen clinicians were interviewed for one hour each about what factors affect their HIE usage. Five HIE staff were asked about technology and training issues to provide context. Interviews were recorded, transcribed and analyzed. Recruitment excluded clinicians with little or no familiarity with the HIE and was restricted to one community and a small number of specialties. RESULTS: Clinicians were motivated to access the HIE by perceived improvements in care quality and time savings, but their motivation was moderated by an extensive list of factors including gaps in data, workflow issues and usability issues. HIE access intensities varied widely by clinician. Data contribution intensities to the HIE also varied widely and were affected by billing concerns and time constraints. CONCLUSIONS: Clinicians, EHR and HIE product vendors and trainers should work toward integrating HIE into clinical workflows. Policies should create incentives for HIE organizations to assist clinicians in using HIE, develop measures of HIE contributions and accesses, and create incentives for clinicians to contribute data to HIEs.

A comparative encyclopedia of DNA elements in the mouse genome

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Conservation of trans-acting circuitry during mammalian regulatory evolution

The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here we show that mouse TF footprints conjointly encode a regulatory lexicon that is ∼95% similar with that derived from human TF footprints. However, only ∼20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Furthermore, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results indicate that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry, enabling and potentiating cis-regulatory plasticity.

Mouse genomic footprinting reveals conservation of transcription factor (TF) recognition repertoires and trans-regulatory circuitry despite massive turnover of DNA elements that contact TFs in vivo.

Having generated genomic DNase I footprinting data of the mouse genome across 25 cell and tissue types, these authors use these data to quantify cis-versus-trans regulatory contributions to mammalian regulatory evolution. They describe more than 600 motifs that collectively are over 95% similar to that recognized in vivo by human transcription factors (TFs). Despite substantial turnover of the cis-regulatory landscape around each TF gene, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Conservation between mouse and human TF regulatory networks is particularly similar at the highest organization level. The work was performed as part of the mouse ENCODE project.

Cell therapy in joint disorders

Context:

Articular cartilage possesses poor natural healing mechanisms, and a variety of non-cell-based and cell-based treatments aim to promote regeneration of hyaline cartilage.

Data Sources:

A review of the literature to December 2013 using PubMed with search criteria including the keywords stem cell, cell therapy, cell transplantation, cartilage, chondral, and chondrogenic.

Study Selection:

Forty-five articles were identified that employed local mesenchymal stem cell (MSC) therapy for joint disorders in humans. Nine comparative studies were identified, consisting of 3 randomized trials, 5 cohort studies, and 1 case-control study.

Study Type:

Clinical review.

Level of Evidence:

Level 4.

Data Extraction:

Studies were assessed for stem cell source, method of implantation, comparison groups, and concurrent surgical techniques.

Results:

Two studies comparing MSC treatment to autologous chondrocyte implantation found similar efficacy. Three studies reported clinical benefits with intra-articular MSC injection over non-MSC controls for cases undergoing debridement with or without marrow stimulation, although a randomized study found no significant clinical difference at 2-year follow-up but reported better 18-month magnetic resonance imaging and histologic scores in the MSC group. No human studies have compared intra-articular MSC therapy to non-MSC techniques for osteoarthritis in the absence of surgery.

Conclusion:

Mesenchymal stem cell–based therapies appear safe and effective for joint disorders in large animal preclinical models. Evidence for use in humans, particularly, comparison with more established treatments such as autologous chondrocyte implantation and microfracture, is limited.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.

The ligamentum teres test: a novel and effective test in diagnosing tears of the ligamentum teres

BACKGROUND

A ligamentum teres (LT) injury is a common finding at the time of hip arthroscopic surgery in patients with chronic groin and hip pain; however, LT tears have been difficult to identify before surgery. There have been no unique features identified on history assessment, physical examination, or imaging that reliably identify injuries of the LT preoperatively.

PURPOSE

To report a new clinical examination to assess the presence of an LT tear: the LT test.

STUDY DESIGN

Cohort study (diagnosis); Level of evidence, 2.

METHODS

The study consisted of 75 patients undergoing hip arthroscopic surgery for multiple lesions. Each patient was evaluated by 2 independent examiners using the LT test, leading to a total of 150 tests being performed. The LT test is conducted with the hip flexed at 70° and 30° short of full abduction; the hip is then internally and externally rotated to its limits of motion. Pain on either internal or external rotation is consistent with a positive LT test result. Hip arthroscopic surgery was then performed and all intra-articular abnormalities noted. Arthroscopic images were taken of each LT and examined by a third independent examiner who determined the presence or absence of a tear. Clinical examination findings were compared with the arthroscopic findings to determine the sensitivity, specificity, and positive and negative predictive values. In addition, the presence of intra-articular pathological lesions was compared with the test results to determine if there was a correlation between the presence of an intra-articular pathological abnormality and a positive LT test result.

RESULTS

Of the 150 examinations performed, the test result was positive 55% of the time (77 examinations). The sensitivity and specificity of the test were 90% and 85%, respectively. The positive predictive value was 84%, and the negative predictive value was 91%. The presence of an LT tear, pincer lesion, and labral tear that required repair was associated with a positive LT test result. The κ coefficient for interobserver reliability was .80.

CONCLUSION

The LT test is an effective way of assessing the presence of LT tears with moderate to high interobserver reliability. In addition to an LT tear, the presence of a pincer lesion or labral tear requiring repair are also associated with a positive LT test result.

A guide to facilitate the early treatment of patients with idiopathic demyelinating disease (multiple sclerosis and neuromyelitis optica)

Definite diagnosis of inflammatory demyelinating disease (multiple sclerosis (MS) and neuromyelitis optica (NMO)) may require time, but early treatment offers the opportunity to maximize patient outcomes. The purpose of this report is to provide guidance to facilitate early treatment decisions for patients with inflammatory demyelinating disease, before definitive diagnosis. Neurology experts reviewed the existing literature and clinical evidence. A treatment decision pathway was developed, defining patients for whom first-line MS disease-modifying therapies (a) are unlikely to be effective, (b) may be effective but require careful monitoring and (c) are likely to provide benefit. This algorithm seeks to ensure that patients, particularly those in Asia, receive appropriate treatment early in inflammatory demyelinating disease.

The accessible chromatin landscape of the human genome

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.

An expansive human regulatory lexicon encoded in transcription factor footprints

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.

Systematic localization of common disease-associated variation in regulatory DNA

Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I) hypersensitive sites (DHSs). Eighty-eight percent of such DHSs are active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes. We identified distant gene targets for hundreds of variant-containing DHSs that may explain phenotype associations. Disease-associated variants systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks. We also demonstrated tissue-selective enrichment of more weakly disease-associated variants within DHSs and the de novo identification of pathogenic cell types for Crohn's disease, multiple sclerosis, and an electrocardiogram trait, without prior knowledge of physiological mechanisms. Our results suggest pervasive involvement of regulatory DNA variation in common human disease and provide pathogenic insights into diverse disorders.

Predicting dysglycaemia in patients under investigation for acute coronary syndrome

AIMS

To examine methods for the identification of previously undetected dysglycaemia [diabetes and impaired glucose tolerance (IGT)] in patients investigated for possible acute coronary syndrome. Specifically, we wished to examine whether the recently advocated use of glycosylated haemoglobin (HbA1c) would enhance detection rates for diabetes in these patients.

METHODS

Patients (n = 200) investigated for possible acute coronary syndrome and not previously known to have diabetes were recruited and anthropometric data collected. Random plasma glucose concentrations followed by oral glucose tolerance tests, HbA1c, fasting lipids, high sensitivity C-reactive protein and homeostatic modular assessment-insulin resistance were obtained during admission. Following discharge, the fasting plasma glucose (FPG) was repeated to determine the importance of sequential fasting levels. The accuracy of individual tests, combinations and sequential testing was assessed using receiver operating characteristic curves. A predictive index (PI) was generated using stepwise logistic regression models.

RESULTS

The prevalence of diabetes and IGT were 21 and 32%, respectively. FPG >6.0 mmol/l and HbA1c ≥ 6.0% had specificities of 94.9% and 93.6% but sensitivities of only 31.7 and 39.0%, respectively. Combination and sequential testing provided little additional benefit. Use of a PI comprising FPG, HbA1c and age provided the best overall performance (75.6% sensitivity, 77.1% specificity, negative predictive value 92.4%).

CONCLUSION

Our data confirm the high prevalence of dysglycaemia in this cohort. The commonly advocated screening tools have significant limitations if used in isolation, combination or sequentially. Our approach using a PI offers improved performance partly as it uses continuous data rather than arbitrary cut-off values.

Angiogenic biomarkers and healing of living cellular constructs

The use of intra-oral soft-tissue-engineered devices has demonstrated potential for oral mucosa regeneration. The aim of this study was to investigate the temporal expression of angiogenic biomarkers during wound healing of soft tissue reconstructive procedures comparing living cellular constructs (LCC) with autogenous free gingival grafts. Forty-four human participants bilaterally lacking sufficient zones of attached keratinized gingiva were randomly assigned to soft tissue surgery plus either LCC or autograft. Wound fluid samples were collected at baseline and weeks 1, 2, 3, and 4 post-operatively and analyzed for a panel of angiogenic biomarkers: angiogenin (ANG), angiostatin (ANT), PDGF-BB, VEGF, FGF-2, IL-8, TIMP-1, TIMP-2, GM-CSF, and IP-10. Results demonstrated a significant increase in expression of ANT, PDGF-BB, VEGF, FGF-2, and IL-8 for the LCC group over the autograft group at the early stages of wound repair. Although angiogenic biomarkers were modestly elevated for the LCC group, no clinical correlation with wound healing was found. This human investigation demonstrates that, during early wound-healing events, expression of angiogenic-related biomarkers is up-regulated in sites treated with LCC compared with autogenous free gingival grafts, which may provide a safe and effective alternative for regenerating intra-oral soft tissues (ClinicalTrials.gov number, NCT01134081).