Detection of chromosomal aneuploidy in ancient genomes.

Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.

Early adaptation to eolian sand dunes by basal amniotes is documented in two Pennsylvanian Grand Canyon trackways.

We report the discovery of two very early, basal-amniote fossil trackways on the same bedding plane in eolian sandstone of the Pennsylvanian Manakacha Formation in Grand Canyon, Arizona. Trackway 1, which is Chelichnus-like, we interpret to be a shallow undertrackway. It displays a distinctive, sideways-drifting, footprint pattern not previously documented in a tetrapod trackway. We interpret this pattern to record the trackmaker employing a lateral-sequence gait while diagonally ascending a slope of about 20°, thereby reducing the steepness of the ascent. Trackway 2 consists only of aligned sets of claw marks. We interpret this trackway to be a deeper undertrackway, made some hours or days later, possibly by an animal that was conspecific with Trackmaker 1, while walking directly up the slope at a speed of approximately 0.1 m/sec. These trackways are the first tetrapod tracks reported from the Manakacha Formation and the oldest in the Grand Canyon region. The narrow width of both trackways indicates that both trackmakers had relatively small femoral abduction angles and correspondingly relatively erect postures. They represent the earliest known occurrence of dunefield-dwelling amniotes-either basal reptiles or basal synapsids-thereby extending the known utilization of the desert biome by amniotes, as well as the presence of the Chelichnus ichnofacies, by at least eight million years, into the Atokan/Moscovian Age of the Pennsylvanian Epoch. The depositional setting was a coastal-plain, eolian dunefield in which tidal or wadi flooding episodically interrupted eolian processes and buried the dunes in mud.

Preservation of latest Cretaceous (Maastrichtian)-Paleocene frogs (Eorubeta nevadensis) of the Sheep Pass Formation of east-central Nevada and implications for paleogeography of the Nevadaplano.

Here we report on exceptional preservation of remains of the frog Eorubeta nevadensis in deposits of the Sheep Pass Formation, ranging from Late Cretaceous to Eocene, in the south Egan Range, Nevada. This formation represents a lacustrine basin within the Sevier retroarc hinterland. The formation is subdivided into six members (A-F); of interest here are members B and C. The base of member B is ?uppermost Cretaceous-Paleocene, while member C is Paleocene. Member B frogs are preserved in three taphonomic modes. Mode 1 frogs are nearly complete and accumulated under attritional processes, with frogs settling on microbial mats, as evidenced by crenulated fabric of entombing limestone. Mode 2 involves accumulation of frogs as a result of attritional processes. These frogs are mostly complete with some showing evidence of invertebrate scavenging. Possible scavengers are gastropods, ostracods, and decapods. Mode 3 is represented by isolated, reworked remains of frogs as a result of storm activity, supported by the association of elements with disarticulated bivalves and mud rip-up clasts. Member C preserves frogs in two taphonomic modes. Mode 4 are nearly complete frogs that accumulated during discrete mass mortality events. Numerous individuals are preserved along bedding planes in identical preservational states. Mode 5 is beds of frog bone hash, which represent increased energy to the depositional system (likely tempestites) and reworking of previously buried frog remains. Taphonomy of the frogs, along with the associated fauna and flora, are consistent with preservation in a cool, temperate lake basin, supporting previous interpretations that the Nevadaplano was an elevated plateau during the late Cretaceous through the Eocene. This is a period of time coincident with a climatic thermal optimum, thus the most parsimonious explanation for a temperate lake at the latitude of east-central Nevada is to invoke high elevation, which is consistent with independent structural and clumped stable isotope studies.

Safety and efficacy of the COMBO bio-engineered stent in an all-comer PCI cohort: 1-Year final clinical outcomes from the MASCOT post-marketing registry.

BACKGROUND: The COMBO stent (OrbusNeich Medical, Ft. Lauderdale, Florida) is a new-generation bio-engineered drug eluting stent, combining an abluminal coating of a bioabsorbable polymer matrix for sustained release of sirolimus and luminal anti-CD34 coating for endothelial progenitor cell capture and rapid endothelialization. METHODS: The Multinational Abluminal Sirolimus Coated BiO-Engineered StenT (MASCOT) registry was a prospective post-marketing study conducted from June 2014-May 2017 across 60 centers globally. Patients were eligible if COMBO stent implantation was attempted, and they received dual antiplatelet therapy (DAPT) per local guidelines. Follow-up was conducted by trained research staff at 1, 6 and 12 months by phone or clinic visit to capture clinical events and DAPT cessation events. The primary endpoint was 1-year target lesion failure (TLF), composite of cardiac death, non-fatal myocardial infarction not clearly attributable to a non-target vessel, or ischemia-driven target lesion revascularization. RESULTS: A total of 2614 patients were enrolled over the study period with 96.7% completion of 1-year follow-up. The mean age of enrolled patients was 62.9 ±â€¯11.2 years and 23.0% were female. Diabetes mellitus was present at baseline in 33.5%. A total of 56.1% patients underwent PCI for acute coronary syndrome (ACS). The 1-year primary endpoint of TLF occurred in 3.4% patients (n = 88). Definite stent thrombosis occurred in 0.5% patients (n = 12). CONCLUSION: The MASCOT post marketing registry provides comprehensive safety and efficacy outcomes following contemporary PCI using the novel COMBO stent in an all-comer population. This platform is associated with low rates of 1-year TLF and ST. CLINICALTRIALS. GOV IDENTIFIER: NCT02183454.

Listening in Naturalistic Scenes: What Can Functional Near-Infrared Spectroscopy and Intersubject Correlation Analysis Tell Us About the Underlying Brain Activity?

Listening to speech in the noisy conditions of everyday life can be effortful, reflecting the increased cognitive workload involved in extracting meaning from a degraded acoustic signal. Studying the underlying neural processes has the potential to provide mechanistic insight into why listening is effortful under certain conditions. In a move toward studying listening effort under ecologically relevant conditions, we used the silent and flexible neuroimaging technique functional near-infrared spectroscopy (fNIRS) to examine brain activity during attentive listening to speech in naturalistic scenes. Thirty normally hearing participants listened to a series of narratives continuously varying in acoustic difficulty while undergoing fNIRS imaging. Participants then listened to another set of closely matched narratives and rated perceived effort and intelligibility for each scene. As expected, self-reported effort generally increased with worsening signal-to-noise ratio. After controlling for better-ear signal-to-noise ratio, perceived effort was greater in scenes that contained competing speech than in those that did not, potentially reflecting an additional cognitive cost of overcoming informational masking. We analyzed the fNIRS data using intersubject correlation, a data-driven approach suitable for analyzing data collected under naturalistic conditions. Significant intersubject correlation was seen in the bilateral auditory cortices and in a range of channels across the prefrontal cortex. The involvement of prefrontal regions is consistent with the notion that higher order cognitive processes are engaged during attentive listening to speech in complex real-world conditions. However, further research is needed to elucidate the relationship between perceived listening effort and activity in these extended cortical networks.

Japan-United States of America Harmonized Assessment by Randomized Multicentre Study of OrbusNEich's Combo StEnt (Japan-USA HARMONEE) study: primary results of the pivotal registration study of combined endothelial progenitor cell capture and drug-eluting stent in patients with ischaemic coronary disease and non-ST-elevation acute coronary syndrome.

Aims: Harmonized Assessment by Randomized Multicentre Study of OrbusNEich's Combo StEnt (HARMONEE) (NCT02073565) was a randomized pivotal registration trial of the Combo stent, which combined sirolimus and an abluminal bioabsorbable polymer with a novel endoluminal anti-CD34+ antibody coating designed to capture endothelial progenitor cells (EPC) and promote percutaneous coronary intervention (PCI) site healing. Methods and results: Clinically stabilized PCI subjects were randomized 1:1 to receive Combo or everolimus-eluting stents (EES). Between February 2014 and June 2016, 572 subjects with 675 coronary lesions underwent 1-year angiography and fractional flow reserve, with optical coherence tomography (OCT) in the first 140 patients. The primary clinical endpoint was non-inferior 1-year target vessel failure (TVF). The primary mechanistic endpoint of EPC capture activity was superior strut coverage by OCT. Target vessel failure occurred in 7.0% Combo (20/287) vs. 4.2% EES (12/285), a 2.8% [95% confidence interval (95% CI) -1.0%, 6.5%] difference, meeting the non-inferiority hypothesis (P = 0.02). There were no cardiac deaths, with one stent thrombosis observed in the EES group. Quantitative coronary angiography late loss with Combo was equivalent to EES. Optical coherence tomography strut coverage at 1 year was superior with Combo vs. EES [91.3% (95% CI 88.7%, 93.8%) vs. 74.8% (95% CI 70.0%, 79.6%), P < 0.001], with homogeneous tissue in 81.2% vs. 68.8%, respectively. Conclusion: Combo stent demonstrated non-inferior 1-year TVF and late loss in a randomized comparison to EES, with superior strut-based tissue coverage by OCT as a surrogate of EPC capture technology activity.

Rationale and design of the Japan-USA harmonized assessment by randomized, multicenter study of OrbusNEich's combo StEnt (Japan-USA HARMONEE): Assessment of a novel DES platform for percutaneous coronary revascularization in patients with ischemic coronary disease and non-ST-elevation acute coronary syndrome.

Tissue trauma associated with stent implantation continues to generate early thrombosis rates of 0.9% to 1.3% for both bare-metal and drug-eluting stent platforms. The Combo sirolimus-eluting stent combines an abluminal, bioabsorbable polymer with a luminal CD34+ antibody designed to capture endothelial progenitor cells. This article describes the design and methods of the HARMONEE trial (NCT02073565), which represents the first randomized controlled trial of the Combo design against a best-in-class contemporary everolimus-eluting stent. Up to 50 sites in Japan and the United States will enroll 286 subjects (271 evaluable) in each of 2 arms, for a total sample size of 572 subjects (542 evaluable). The statistical plan includes both superiority to imputed bare-metal stent control and noninferiority to everolimus-eluting stent on a primary clinical end point of target vessel failure at 1 year. In addition, fractional flow reserve assessment to evaluate the physiology of target vessels in the entire population will augment the end point definition of ischemia-driven target vessel revascularization. Finally, key safety considerations will be evaluated with a subpopulation with optical coherence tomography imaging for strut coverage, late strut malapposition, and plaque volume, as well as serial human antimurine antibody assessments. As the first international prospective randomized coronary intervention study under the "Harmonization by Doing" program, this study represents a unique collaboration between regulators and investigators in Japan and the United States.

Efficiency of statin treatment on EPC recruitment depends on baseline EPC titer and does not improve angiographic outcome in coronary artery disease patients treated with the Genous stent.

The objective of this study was to assess the effect of high-dose atorvastatin treatment on endothelial progenitor cell (EPC) recruitment and angiographic and clinical outcome in coronary artery disease (CAD) patients treated with the Genous EPC-capturing stent. The HEALING IIB study was a multicenter, open-label, prospective trial that enrolled 100 patients. Patients were started on 80 mg atorvastatin qd, at least 2 weeks before the index procedure and continued for at least 4 weeks after the index procedure. Eighty-seven patients were included in this analysis. EPC levels significantly increased as early as 2 weeks after the start of atorvastatin. Remarkably, among this group, 31 patients proved to be nonresponders to atorvastatin treatment (i.e., no increase in EPC levels), while 56 patients were responders (i.e., rise in EPC count between week -2 and 0). Compared to responders, nonresponders had a significantly higher baseline EPC count (76 ± 10 vs. 41 ± 5, p < 0.01) with a lower late luminal loss (LLL) at 6- and 18-month follow-up (FU) (0.61 ± 0.07 vs. 0.88 ± 0.08, p < 0.05, and 0.50 ± 0.08 vs. 0.82 ± 0.08, p < 0.01 respectively). Furthermore, baseline EPC count was inversely correlated with LLL at 6-month FU (R = -0.42, p < 0.001). Patients with a higher EPC count at baseline showed no increase in EPC recruitment in response to statin treatment but had favorable LLL at 6- and 18-month FU, whereas patients with lower EPC count were responsive to statin therapy, but EPCs might be less functional as they had higher LLL at 6- and 18-month FU. These data imply that although statin treatment can enhance EPC titer in patients with low baseline levels, there is no indication for a possible beneficial clinical effect with EPC capture stents.

Final results of the HEALING IIB trial to evaluate a bio-engineered CD34 antibody coated stent (Genous™Stent) designed to promote vascular healing by capture of circulating endothelial progenitor cells in CAD patients.

OBJECTIVE: To assess the safety and efficacy of the Genous™ endothelial progenitor cell (EPC) capturing stent in conjunction with HmG-CoA-reductase inhibitors (statins) to stimulate EPC recruitment, in the treatment of patients with de novo coronary artery lesions. METHODS AND RESULTS: The HEALING IIB study was a multi-center, prospective trial, including 100 patients. The primary efficacy endpoint was late luminal loss by QCA at 6-month follow-up (FU). Although statin therapy increased relative EPC levels by 5.6-fold, the angiographic outcome at 6 month FU was not improved in patients with an overall in-stent late luminal loss of 0.76±0.50 mm. The composite major adverse cardiac events (MACE) rate was 9.4%, whereas 6.3% clinically justified target lesion revascularizations (TLRs) were observed. 2 Patients died within the first 30 days after stent implantation due to angiographically verified in-stent thrombosis. At 12 month FU, MACE and TLR increased to 15.6% and 11.5% respectively and stabilized until 24 month FU. 18 Month angiographic FU showed a significant decrease in late luminal loss (0.67±0.54, 11.8% reduction or 10% by matched serial analysis, P=0.001). CONCLUSION: The HEALING IIB study suggests that statin therapy in combination with the EPC capture stent does not contribute to a reduction of in-stent restenosis formation for the treatment of de novo coronary artery disease. Although concomitant statin therapy was able to stimulate EPC recruitment, it did not improve the angiographic outcome of the bio-engineered EPC capture stent. Remarkably, angiographic late loss was significantly reduced between 6 and 18 months.

Anti-CD34 antibodies immobilized on the surface of sirolimus-eluting stents enhance stent endothelialization.

OBJECTIVES: In this study, we hypothesized that an antihuman-CD34 antibody immobilized on the surface of commercially available sirolimus-eluting stents (SES) could enhance re-endothelialization compared with SES alone. BACKGROUND: Previous experience with antihuman-CD34 antibody surface modified Genous stents (GS) (OrbusNeich Medical, Fort Lauderdale, Florida) has shown enhanced stent endothelialization in vivo. METHODS: In the phase 1 study, stents were deployed in 21 pig coronary arteries for single stenting (9 vessels: 3 GS, 3 SES, and 3 bare-metal stents) and overlapping stenting with various combinations (12 vessels: 4 GS+GS, 4 SES+SES, and 4 GS+SES) and harvested at 14 days for scanning electron and confocal microscopy. In phase 2, immobilized anti-CD34 antibody coating was applied on commercially available SES (SES-anti-CD34, n = 7) and compared with GS (n = 8) and SES (n = 7) and examined at 3 and 14 days by scanning electron/confocal microscopy analysis. RESULTS: In phase 1, single stent implantation showed greatest endothelialization in GS (99%) and in bare-metal stent (99%) compared with SES (55%, p = 0.048). In overlapping stents, endothelialization at the overlapping zone was significantly greater in GS+GS (95 +/- 6%) and GS+SES (79 +/- 5%) compared with the SES+SES (36 +/- 14%) group (p = 0.007). In phase 2, SES-anti-CD34 resulted in increased endothelialization compared with SES alone at 3 days (SES-anti-CD34 36 +/- 26%; SES 7 +/- 3%; and GS 76 +/- 8%; p = 0.01), and 14 days (SES-anti-CD34 82 +/- 8%; SES 53 +/- 20%; and GS 98 +/- 2%; p = 0.009). CONCLUSIONS: Immobilization of anti-CD34 antibody on SES enhances endothelialization and may potentially be an effective therapeutic alternative to improve currently available drug-eluting stents.

OrbusNeich fully absorbable coronary stent platform incorporating dual partitioned coatings.

The field of stent based tissue engineering continues to revolutionise modern medicine by designing novel materials to restore vascular tissue function. Accordingly, the following discussion examines a novel, absorbable, polymeric scaffold engineered in combination with dual therapeutic coating, enabling locally administered temporary scaffolding in the coronary arteries for long term vascular patency and repair. This coronary stent platform consists of an absorbable polymeric material stent structure that incorporates a dual partitioned coating, by means of pro-healing EPC (endothelial progenitor cell) capture technology allowing for rapid endothelial coverage, and an absorbable polymer matrix with sustained elution of sirolimus, a drug controlling neointimal proliferation. This paper provides a brief overview of the various innovations developed by OrbusNeich to create this fully absorbable coronary device platform.

Endothelial progenitor cell capture by stents coated with antibody against CD34: the HEALING-FIM (Healthy Endothelial Accelerated Lining Inhibits Neointimal Growth-First In Man) Registry.

OBJECTIVES: This study was designed to evaluate whether rapid endothelialization of stainless steel stents with a functional endothelium prevents stent thrombosis and reduces the restenotic process. BACKGROUND: A "pro-healing" approach for prevention of post-stenting restenosis is theoretically favored over the use of cytotoxic or cytostatic local pharmacologic therapies. It is believed that the central role of the vascular endothelium is to maintain quiescence of the underlying media and adventitia. METHODS: Sixteen patients with de novo coronary artery disease were successfully treated with implantation of endothelial progenitor cell (EPC) capture stents. RESULTS: Complete procedural and angiographic success was achieved in all 16 patients. The nine-month composite major adverse cardiac and cerebrovascular events (MACCE) rate was 6.3% as a result of a symptom-driven target vessel revascularization in a single patient. There were no other MACCE despite only one month of clopidogrel treatment. At six-month follow-up, mean angiographic late luminal loss was 0.63 +/- 0.52 mm, and percent stent volume obstruction by intravascular ultrasound analysis was 27.2 +/- 20.9%. CONCLUSIONS: This first human clinical investigation of this technology demonstrates that the EPC capture coronary stent is safe and feasible for the treatment of de novo coronary artery disease. Further developments in this technology are warranted to evaluate the efficacy of this device for the treatment of coronary artery disease.