T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 (Transcript Regulating Endoderm and activated by soX17) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Understanding subterranean variability: the first genus of Bathynellidae (Bathynellacea, Crustacea) from Western Australia described through a morphological and multigene approach

The number of subterranean taxa discovered in the north of Western Australia has substantially increased due to the requirements for environmental surveys related to mining development. Challenges in estimating subterranean biodiversity and distributions are related to lack of knowledge of taxa with convergent morphological characters in a largely unobservable ecosystem setting. An integrated approach is warranted to understand such complexity. Bathynellidae occur in most Australian aquifers, but only one species has been described so far, and the group lacks a reliable taxonomic framework. A new genus and one new species from the Pilbara region of Western Australia, Pilbaranella ethelensis, gen. et sp. nov., is described using both morphological and molecular data. Three additional species of Pilbaranella are defined through mitochondrial and nuclear genes, using Automatic Barcode Gap Discovery and Poisson Tree Processes species delimitation methods. A comparison of morphology and 18S rRNA sequences between Pilbaranella, gen. nov. and known lineages provides the evidentiary basis for the decision to establish a new genus. This study provides a morphological and molecular framework to work with Bathynellidae, especially in Australia where a highly diverse fauna remains still undescribed.

Test Medium for the Growth of Nitrosomonas europaea

A mineral medium for studying the growth of Nitrosomonas europaea was developed and examined. The medium was defined in terms of chemical speciation by using chemical equilibrium computer models. The medium significantly increased the metabolic activity of the organisms compared with previously developed media, yielding a specific growth rate as high as 3.0 day (generation time, 5.5 h). The specific growth rate was enhanced by increasing the inoculum and was linearly correlated with the inoculum-to-total-culture volume ratio on a semilog scale. A reproducible growth rate for N. europaea was obtained with this medium under controlled experimental conditions.

Multisite randomized controlled trials in health services research: scientific challenges and operational issues

Although well-designed randomized controlled trials (RCT) provide the strongest evidence regarding causation, only relatively recently have they been used by health services researchers to study the organization, delivery, quality, and outcomes of care. More recent yet is the extension of multisite RCTs to health services research. Such studies offer numerous methodological advantages over single-site trials: (1) enhanced external validity; (2) greater statistical power when studying conditions with a low incidence or prevalence, small event rate in the outcome (eg, mortality), and/or large variance in the outcome (eg, health care costs); and (3) rapid recruitment to provide health care organizations and policy makers with timely results. This paper begins by outlining the advantages of multisite RCTs over single-site trials. It then discusses both scientific challenges (ie, standardizing eligibility criteria, defining and standardizing the intervention, defining usual care, standardizing the data collection protocol, blinded outcome assessment, data management and analysis, measuring health care costs) and operational issues (ie, site selection, randomization procedures, patient accrual, maintaining enthusiasm, oversight) posed by multisite RCTs in health services research. Recommendations are offered to health services researchers interested in conducting such studies.

Complication after laparoscopic donor nephrectomy: a case report and review

BACKGROUND

Laparoscopic procedures are gaining acceptance in the treatment of benign and some malignant urologic disorders. Recently, laparoscopic techniques have been applied to transplant surgery and touted as a safe alternative to traditional open techniques.

METHODS

We present a patient who developed a complication from laparoscopic donor nephrectomy that required open corrective surgery.

RESULTS

A 25-year-old man underwent laparoscopic donor nephrectomy at a large medical center familiar with the operation. There were no operative or early postoperative complications. Within 6 weeks of the operation, the patient developed signs and symptoms of partial small bowel obstruction. Further evaluation revealed an internal hernia in the retroperitoneum at the site of the nephrectomy. This required a second operation to reduce the hernia and close the defect.

CONCLUSION

Laparoscopic donor nephrectomy remains an evolving technique that has not stood the test of time. Larger series will eventually reveal whether this is the procedure of choice as compared to traditional open donor nephrectomy.

Classifying general medicine readmissions. Are they preventable? Veterans Affairs Cooperative Studies in Health Services Group on Primary Care and Hospital Readmissions

OBJECTIVES

To describe a new quality assessment method used to classify the preventability of hospitalization in terms of patient, clinician, or system factors.

DESIGN

The instrument was developed in two phases. Phase 1 was a prospective comparison of admitting residents' and their attending physicians' classifications of the perceived preventability of consecutive admissions to one Veterans Affairs Medical Center (VAMC) excluding admissions to the intensive care unit (ICU). In phase 2, a panel of 10 physicians rated 811 abstracted records of readmissions from nine VAMCs.

SETTING

Nine VAMCs across the United States with varying degrees of university hospital affiliation.

PATIENTS

Phase 1, 156 patients admitted to the general medicine service at the Durham VAMC. Phase 2, 514 patients accounting for 811 readmissions within 6 months of a general medicine service discharge at nine VAMCs.

MEASUREMENTS AND MAIN RESULTS

Physicians used a checklist to record the reason for hospitalization, the preventability of the hospitalization, and, if preventable, a reason defining preventability, which was classified in terms of system, clinician, and patient factors. In phase 2, two physician panelists assessed preventability for each chart. When two panelists disagreed on the preventability of hospitalization, a third panelist, blind to the original assessments, rated the chart. In phase 1, residents and attending physicians rated 33% and 34% of admissions as preventable (kappa = 0.41), respectively. In phase 2, 277 (34%) of 811 readmissions were deemed preventable. Intraobserver accuracy for the assessment of preventability was 96% (kappa = 0.89). interobserver accuracy was 73% (kappa = 0.43). Hospital system factors accounted for 37% of preventable readmissions, clinician factors for 38%, and patient factors for 21%. The nine hospitals differed markedly in their profile of reasons for preventable readmissions (p = .005).

CONCLUSIONS

Using a new method of determining the preventability of hospitalizations, we identified several factors that might avert hospitalizations. Focusing efforts to identify preventable hospitalizations may yield better methods for managing patients' total health care needs; however, the content of those efforts will vary by institution.

Genital tuberculosis: case report and literature review

A 64-year-old woman complained of abdominal pain and postmenopausal bleeding. A uterine curettage demonstrated acid fast bacilli and non caseating granulomas, indicating Mycobacterium tuberculosis. A chest roentgenogram revealed the presence of bilateral upper lobe calcific granulomas. The epidemiologic, diagnostic, and therapeutic implications of genital tuberculosis are discussed.

Clinical evaluation of intravenous labetalol for the treatment of hypertensive urgency

Antihypertensive medications currently used in the treatment of hypertensive urgencies are limited due to deleterious side effects or requirements for sophisticated monitoring techniques. Labetalol HCl (Trandate) is a unique adrenergic blocking agent that can smoothly lower blood pressure following bolus injection without increasing heart rate or cardiac output. This study evaluates the efficacy and safety of intravenous boluses of labetalol HCl in the treatment of patients presenting to the hospital with a diagnosis of hypertensive urgency (diastolic blood pressure greater than or equal to 110 mm Hg). After baseline blood pressure and heart rate were recorded, 20 consecutive patients were treated with an initial 20-mg bolus of labetalol. Additional boluses of 40, 80, and 160 mg were administered at least 10 minutes apart in a step-wise fashion until control of blood pressure (diastolic blood pressure less than 100 mm Hg) was achieved or a total of 300 mg had been given. Blood pressures and heart rates were recorded at the time of response or following the last dose of labetalol. Mean (+/- SEM) supine systolic blood pressure decreased from 185 +/- 3 to 155 +/- 4 mm Hg (P less than 0.05) following labetalol therapy, and mean supine diastolic pressure decreased from 120 +/- 2 to 98 +/- 2 mm Hg (P less than 0.05). Mean heart rate did not change significantly. Eighteen of the 20 patients exhibited a therapeutic response; nine patients received a total of 20 mg, six required 60 mg, two required 140 mg, one received 300 mg. Of the two patients who did not respond, one received the maximum dose (300 mg).(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of epidermal growth factor on the synthetic activity of human fibroblasts

The influence of epidermal growth factor on DNA and protein synthesis by human gingival fibroblasts was studied. Synchronized cells treated with epidermal growth factor synthesized considerably greater amounts of DNA relative to 10% fetal calf serum and the peak of synthesis ocurred 6 h later than with serum. Epidermal growth factor caused a dose-dependent stimulation of protein synthesis (proline incorporation). Collagen synthesis remained unaffected and, as a result, the proportion of collagen synthesized decreased with increasing epidermal growth factor concentration. Aspirin and indomethacin did not abrogate these effects, indicating that prostaglandins may not be involved.