Challenges and recommendations to improve the installability and archival stability of omics computational tools.

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.

A novel fluorescence-based assay for the rapid detection and quantification of cellular deoxyribonucleoside triphosphates.

Current methods for measuring deoxyribonucleoside triphosphates (dNTPs) employ reagent and labor-intensive assays utilizing radioisotopes in DNA polymerase-based assays and/or chromatography-based approaches. We have developed a rapid and sensitive 96-well fluorescence-based assay to quantify cellular dNTPs utilizing a standard real-time PCR thermocycler. This assay relies on the principle that incorporation of a limiting dNTP is required for primer-extension and Taq polymerase-mediated 5-3' exonuclease hydrolysis of a dual-quenched fluorophore-labeled probe resulting in fluorescence. The concentration of limiting dNTP is directly proportional to the fluorescence generated. The assay demonstrated excellent linearity (R(2) > 0.99) and can be modified to detect between ∼0.5 and 100 pmol of dNTP. The limits of detection (LOD) and quantification (LOQ) for all dNTPs were defined as <0.77 and <1.3 pmol, respectively. The intra-assay and inter-assay variation coefficients were determined to be <4.6% and <10%, respectively with an accuracy of 100 ± 15% for all dNTPs. The assay quantified intracellular dNTPs with similar results obtained from a validated LC-MS/MS approach and successfully measured quantitative differences in dNTP pools in human cancer cells treated with inhibitors of thymidylate metabolism. This assay has important application in research that investigates the influence of pathological conditions or pharmacological agents on dNTP biosynthesis and regulation.

Epidermal Inclusion Cyst Formation: Late Complication of Carpal Tunnel Release.

Background Epidermal inclusion cysts (EIC) are epidermally lined, keratin containing cysts which occur when keratinizing epithelium becomes imbedded in deeper subcutaneous tissue, usually following penetrating trauma, or, rarely, surgery. We describe a case of an EIC presenting as a late complication following open carpal tunnel release (CTR). Case Description A 64-year-old woman with a history of left open CTR 17 years prior presented to our institution with unprovoked left palmar pain, swelling, and fluctuance. Computed tomography imaging confirmed the presence of a multiloculated abscess involving the hypothenar musculature. The abscess developed at the site of a small, pre-existing, asymptomatic mass that the patient recalls developed within months of CTR surgery. She was initially treated with antibiotics and bedside incision and drainage, but required further operative exploration in the setting of persistent erythema and drainage. An inflamed cystic structure consistent with an infected EIC was identified and completely excised. Her wound healed by secondary intention. Her postoperative course was uncomplicated. Pathology confirmed a diagnosis of EIC. Literature Review Only one other case report was found in which the patient presented within 2 years following CTR surgery with what was later confirmed to be an EIC and recurrent median nerve compression symptoms. Clinical Relevance To prevent a delay in definitive surgical care, EIC rupture and subsequent infection should be considered in the differential diagnosis when evaluating patients with a history of prior hand surgery who are presenting with an unprovoked hand abscess, as incision and drainage alone will not adequately treat an EIC.

Rolling with the punches: examining the socialization experiences of kinesiology doctoral students.

PURPOSE: An increasing body of literature examines the socialization experiences of graduate students on a myriad of topics across academic disciplines. However, relatively absent from these discussions are the perspectives of kinesiology doctoral students. Using Weidman, Twale, and Stein's framework for graduate and professional student socialization, this research examined the doctoral education and socialization perspectives of 12 kinesiology students at 3 research institutions. METHOD: A phenomenological case-study approach incorporating interviews, both individual and focus group, and journals served to obtain participants' perspectives. Traditional data analysis, coding, thematic category development, and interpretation techniques were used. RESULTS: Participants provided critical experiences, enlightening perspectives, and specific recommendations regarding their socialization into the kinesiology academic field and profession. Four major thematic categories were derived from the data: (a) transition, when participants highlighted professional, academic, or personal shifts in perspectives occurring during studies; (b) negotiation, when participants pointed out experiences when significant consideration was given to the consequences, risk, and rewards of formal and informal interactions with peers, faculty, and administrators; (c) balance, during which participants described their struggles and successes with meeting academic, professional, and personal obligations; and (d) support, when participants identified emotional, financial, and professional resources that impacted their socialization. CONCLUSIONS: The authenticity and sameness of the participants' experiences call for further scrutiny and discussion of kinesiology doctoral student socialization policies and practices. Suggestions for future research and administrative initiatives are discussed.

Toxicological and toxicokinetic analysis of angiotensin (1-7) in two species.

The objectives of this study were to determine the potential systemic and local toxicity, as well as evaluate the toxicokinetic (TK) profile of angiotensin (1-7) [A(1-7)] when administered daily via subcutaneous injection for 28 days to Sprague-Dawley rats and Beagle dogs. A(1-7) is a member of the renin-angiotensin system and has undergone clinical evaluation for the treatment of chemotherapy-induced myelosuppression. In this present study, A(1-7) was given at 10 mg/(kg day) for 28 days to rats and canines. At day 27, blood was harvested to evaluate the TK parameters. On day 28, systemic toxicology was evaluated. Following A(1-7) administration for 27 days, no plasma A(1-7) accumulation was detected in canines; however, increased A(1-7) plasma concentrations were detected in rats. Despite the accumulation observed in rats, no detectable toxicity was found following A(1-7) administration for 28 days. The TK analysis of A(1-7) revealed a plasma half-life of 20-30 min in both rats and canines. The time to maximum plasma concentration was found to be 15 and 26.25 min in rats and canines, respectively. This study shows that subcutaneous administration of A(1-7) at 10 mg/(kg day) for 28 days did not lead to any detectable toxicities in either rats or canines.

The dual EGFR/HER2 inhibitor lapatinib synergistically enhances the antitumor activity of the histone deacetylase inhibitor panobinostat in colorectal cancer models.

As key molecules that drive progression and chemoresistance in gastrointestinal cancers, epidermal growth factor receptor (EGFR) and HER2 have become efficacious drug targets in this setting. Lapatinib is an EGFR/HER2 kinase inhibitor suppressing signaling through the RAS/RAF/MEK (MAP/ERK kinase)/MAPK (mitogen-activated protein kinase) and PI3K (phosphoinositide 3-kinase)/AKT pathways. Histone deacetylase inhibitors (HDACi) are a novel class of agents that induce cell cycle arrest and apoptosis following the acetylation of histone and nonhistone proteins modulating gene expression and disrupting HSP90 function inducing the degradation of EGFR-pathway client proteins. This study sought to evaluate the therapeutic potential of combining lapatinib with the HDACi panobinostat in colorectal cancer (CRC) cell lines with varying EGFR/HER2 expression and KRAS/BRAF/PIK3CA mutations. Lapatinib and panobinostat exerted concentration-dependent antiproliferative effects in vitro (panobinostat range 7.2-30 nmol/L; lapatinib range 7.6-25.8 µmol/L). Combined lapatinib and panobinostat treatment interacted synergistically to inhibit the proliferation and colony formation in all CRC cell lines tested. Combination treatment resulted in rapid induction of apoptosis that coincided with increased DNA double-strand breaks, caspase-8 activation, and PARP cleavage. This was paralleled by decreased signaling through both the PI3K and MAPK pathways and increased downregulation of transcriptional targets including NF-κB1, IRAK1, and CCND1. Panobinostat treatment induced downregulation of EGFR, HER2, and HER3 mRNA and protein through transcriptional and posttranslational mechanisms. In the LoVo KRAS mutant CRC xenograft model, the combination showed greater antitumor activity than either agent alone, with no apparent increase in toxicity. Our results offer preclinical rationale warranting further clinical investigation combining HDACi with EGFR and HER2-targeted therapies for CRC treatment.

Severe bleeding in a woman heterozygous for the fibrinogen gammaR275C mutation.

The dysfibrinogen gammaR275C can be a clinically silent mutation, with only two out of 17 cases in the literature reporting a hemorrhagic presentation and four cases reporting a thrombotic presentation. We describe here a particularly severe presentation in 54-year-old female patient who required a hysterectomy at 47 years of age due to heavy menstrual bleeding. Coagulation studies revealed a prolonged prothrombin time and thrombin time, a normal fibrinogen antigen level, and a low fibrinogen activity level. Molecular analysis of the patient's DNA revealed a gamma chain gene mutation resulting in an amino acid substitution at residue 275 (gammaR275C). Protein sequencing of the fibrinogen gamma chain confirmed this mutation, which was named Fibrinogen Portland I. This case demonstrates that the gammaR275C mutation can lead to a severe hemorrhagic phenotype.