Volatile organic compounds (VOCs) as a rapid means for assessing the source of coprolites.

The odor of rehydrated coprolites can be used as an informal means of fecal identification. To date, the analysis of volatiles emitted by coprolites from different sources has not been attempted, and the possibility of utilizing volatile organic compounds (VOCs) as fecal biomarkers unexplored. VOCs released by coprolites from the Paisley Caves, were analyzed using solid-phase microextraction (SPME), to assess the variance of results from different coprolites (carnivores, herbivores, or humans). Coprolites from carnivores can be clearly distinguished from those produced by herbivores and humans; these latter two are separated to a lesser degree. Eight discriminatory compounds differentiated between the coprolite sources, and their identities were verified using reference standards. Coprolites and their associated sediments could not be differentiated between using this method, suggesting leaching of VOCs into the burial matrix. This work provides an alternative, more rapid way to assess coprolite origin.

Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon.

When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.

Progression of Stargardt Disease as Determined by Fundus Autofluorescence Over a 12-Month Period: ProgStar Report No. 11.

IMPORTANCE: Sensitive outcome measures for disease progression are needed for treatment trials of Stargardt disease. OBJECTIVE: To estimate the progression rate of atrophic lesions in the prospective Natural History of the Progression of Atrophy Secondary to Stargardt Disease (ProgStar) study over a 12-month period. DESIGN, SETTING, AND PARTICIPANTS: This multicenter prospective cohort study was conducted in an international selection of tertiary referral centers from October 21, 2013, to February 15, 2017. Patients who were affected by Stargardt disease, aged 6 years and older at baseline, and harboring disease-causing variants of the ABCA4 gene were enrolled at 9 centers in the United States, United Kingdom, and continental Europe. Data analysis occurred from November 2016 to January 2017. EXPOSURES: Autofluorescence images obtained with a standard protocol were sent to a central reading center, and areas of definitely decreased autofluorescence, questionably decreased autofluorescence, and the total combined area of decreased autofluorescence were outlined and quantified. Progression rates were estimated from linear mixed models with time as the independent variable. MAIN OUTCOMES AND MEASURES: Yearly rate of progression, using the growth of atrophic lesions measured by autofluorescence imaging. RESULTS: A total of 259 study participants (488 eyes; 230 individuals [88.8%] were examined in both eyes) were enrolled (mean [SD] age at first visit, 33.3 [15.1] years; 118 [54.4%] female). Gradable images were available for evaluation for 480 eyes at baseline and 454 eyes after 12 months. At baseline, definitely decreased autofluorescence was present in 306 eyes, and the mean (SD) lesion size was 3.93 (4.37) mm2. The mean total area of decreased autofluorescence at baseline was 4.07 (4.04) mm2. The estimated progression of definitely decreased autofluorescence was 0.76 (95% CI, 0.54-0.97) mm2 per year (P < .001), and the total area of both questionably and definitely decreased autofluorescence was 0.64 (95% CI, 0.50-0.78) mm2 per year (P < .001). Both progression rates depended on initial lesion size. CONCLUSIONS AND RELEVANCE: In Stargardt disease, autofluorescence imaging may serve as a monitoring tool and definitely decreased autofluorescence and total area as outcome measures for interventional clinical trials that aim to slow disease progression. Rates of progression depended mainly on initial lesion size.

Impact of segmentation density on spectral domain optical coherence tomography assessment in Stargardt disease.

PURPOSE: Automated spectral domain optical coherence tomography (SD-OCT) segmentation algorithms currently do not perform well in segmenting individual intraretinal layers in eyes with Stargardt disease (STGD). We compared selective B-scan segmentation strategies for generating mean retinal layer thickness and preserved area data from SD-OCT scans in patients with STGD1. METHODS: Forty-five eyes from 40 Stargardt patients were randomly selected from the ongoing Natural History of the Progression of Atrophy Secondary to Stargardt Disease (ProgStar) study. All eyes underwent SD-OCT using a standard macular volume consisting of 1024 × 49 equally spaced B-scans within a 20 × 20 degree field centered on the fovea. All 49 B-scans were segmented manually to quantify total retina, outer nuclear layer (ONL), photoreceptor inner segments, photoreceptor outer segments (OS), and retinal pigment epithelial layer (RPE). Mean thickness and total area were generated using all 49 B-scans (spaced 122 µm apart), 25 B-scans (every other B-scan, spaced 240 µm apart), 17 B-scans (every third scan, 353 µm apart), and 13 B-scans (every fourth scan, 462 µm apart), as well as by using an "adaptive" method where a subset (minimum 25 B-scans) of B-scans that the grader deemed as significantly different from adjacent B-scans were utilized. Mean absolute and percentage errors were calculated for macular thickness and area of different retinal layers for the different B-scan subset selection strategies relative to using all 49 B-scans, which was considered the reference or ground truth. RESULTS: Mean thickness and area measurements were significantly different for any regularly spaced reduction in B-scan density relative to the ground truth. When an adaptive approach was applied using a minimum of half the scans, the differences relative to ground truth were no longer significantly different. The mean percent differences for the area and thicknesses of the various layers ranged from 0.02 to 33.66 (p < 0.05 for all comparisons) and 0.44 to 7.24 (p > 0.05) respectively. CONCLUSION: Manual segmentation of a subset of B-scans using an adaptive strategy can yield thickness and area measurements of retinal sublayers comparable to the reference ground truth derived from using all B-scans in the volume. These results may have implications for increasing the efficiency of SD-OCT grading strategies in clinical trials for STGD and other related macular degenerative disorders.

Identification and Characterization of Imaging Technique Errors and Artifacts Using Anterior-Segment OCT for Irido-Corneal Angle Evaluations in Glaucoma.

PURPOSE: Anterior-segment OCT (AS-OCT) platforms provide noninvasive and quantifiable evaluations of anterior chamber angle (ACA) anatomy. Although these ACA measurements have been validated with high repeatability and reproducibility, there is a paucity of data previously published regarding the technique errors and artifacts (TEA) that may occur during imaging of the ACA. The purpose of this study was to report on the types and frequency of imaging TEA that are seen in ACA evaluation of a large cohort of patients with open-angle glaucoma. DESIGN: Retrospective, cross-sectional design. PARTICIPANTS: Images were obtained with AS-OCT from 5082 eyes of 2541 patients with glaucoma and were reviewed at the Doheny Image Reading Center (DIRC). METHODS: Images had been captured using AS-OCT devices from 4 different manufacturers (Zeiss Cirrus [Oberkochen, Germany], Heidelberg Spectralis [Heidelberg, Germany], Optovue RTVue [Fremont, CA], or Zeiss Visante). All images were analyzed by 2 independent and certified DIRC image readers for angle opening distance under Schwalbe's line (SL-AOD), and then re-reviewed by a DIRC-certified principal investigator to adjudicate nonconsensus measurements. Images were defined to have TEA when image readers were unable to confidently measure the SL-AOD. MAIN OUTCOME MEASURES: Type and frequency of TEA in the AS-OCT image. RESULTS: Of 5082 eyes reviewed, 208 images (4.09%) were found to have TEA that restricted proper visualization of irido-corneal angle structures and measurements of SL-AOD. The most common TEA was that the image readers were unable to identify Schwalbe's line (74% of TEA images). Other common TEA included poor visualization of the anterior iris surface (15%), misaligned scan location (11%), irregular corneal irregularities (5%), and illumination-related pupillary abnormalities (4%). CONCLUSIONS: This large-scale study presents the types and frequency of TEA found in AS-OCT-derived angle images. More than 95% of the images reviewed were usable for the quantification of irido-corneal angle measurements. Knowing the common types of TEA may help in enhancing the training of both human image readers and in the design of automated algorithms to improve image acquisition and image interpretation parameters. This will become especially useful as AS-OCT becomes more widely used in clinical practice for anterior chamber assessment.

An Early Holocene Record of Cimex (Hemiptera: Cimicidae) From Western North America.

The subfossil remains of 14 cimicids (Hemiptera: Cimicidae) were recovered during archaeological investigations of the Paisley Five Mile Point Cave site (35LK3400), an exceptionally well-dated (n = 229 radiocarbon dates) late Pleistocene-early Holocene rock shelter site in south-central Oregon. Nine of the specimens have been assigned to three modern species of Nearctic Cimicidae-Cimex antennatus Usinger & Ueshima, Cimex latipennis Usinger & Ueshima, and Cimex pilosellus (Horváth)-whereas the remaining five individuals were too fragmentary to positively identify. The chronology of the insect assemblage puts one specimen at circa 5,100 calibrated years before present (cal. yr BP), and the remaining 13 range in age from 9,400 to almost 11,000 cal. yr BP. Although fossil and subfossil cimicid remains have been recovered at other archaeological sites, the fossil record for bed bugs is largely undocumented. The Paisley Caves specimens thus far represent the oldest remains of the genus in probable contact with humans on record.

Identification of anterior chamber angle parameters with a portable SD-OCT device compared to a non-portable SD-OCT.

The aim of this study is to compare a portable spectral domain optical coherence tomography (SD-OCT) device with a non-portable SD-OCT for the identification of anterior chamber angle parameters based on location of Schwalbe's line (SL) and to measure their reproducibility. 99 eyes from 46 normal, healthy participants underwent imaging of the inferior iridocorneal angle with the iVue and Cirrus SD-OCT under well-controlled low-light conditions. SL-angle opening distance (SL-AOD) and SL-trabecular iris space area (SL-TISA) were measured by masked, certified graders at the Doheny Image Reading Center using customized Image J grading software. Inter- and intrainstrument, as well as inter- and intraobserver reproducibility of SL-AOD and SL-TISA measurements were evaluated with intraclass correlation coefficients (ICCs) and Bland-Altman plots with limits of agreement. The mean SL-AOD was 0.814 ± 0.315 mm with the iVue and 0.797 ± 0.294 mm with the Cirrus. The mean SL-TISA was 0.247 ± 0.112 mm2 with iVue and 0.259 ± 0.113 mm2 with Cirrus. Interinstrument correlation coefficients (r) were 0.93 (P < 0.0001), 0.92 (P < 0.0001), and 0.92 (P < 0.0001) for SL_AOD and SL_TISA, respectively. Intraclass correlation coefficient showing the degree of agreement among SL-AOD and SL-TISA was 0.923 (95 % confidence interval 0.885-0.948) and 0.921 (95 % confidence interval 0.883-0.947) for both devices. The agreement for intrainstrument (ICCs > 0.95), intragrader (ICCs > 0.93), and intergrader (ICCs > 0.96) was excellent. Excellent agreement between the two devices was also documented with Bland-Altman analysis. Both instruments provide consistent and reproducible measurements of anterior chamber angle metrics.

Endoscopic Cycloplasty (ECPL) and Lens Extraction in the Treatment of Severe Plateau Iris Syndrome.

PURPOSE: To describe the anatomic and clinical results of the treatment of severe plateau iris syndrome with lens extraction and endoscopic cycloplasty (ECPL). A secondary aim was to describe 4 novel ultrasound biomicroscopy (UBM) measurements for plateau iris syndrome. DESIGN: Prospective case series with UBM evaluation. METHODS: Included were 12 eyes of 6 patients with plateau iris refractory to laser iridotomy and iridoplasty, miotic and other glaucoma medical treatment, with appositional angle closure in at least 3 quadrants. Treatment consisted of lens extraction and ECPL, an endoscopic diode laser treatment of the ciliary processes in the superior, nasal, and inferior quadrants. UBM measurements were taken in all quadrants before and after surgery. The untreated temporal quadrants were used as controls. Measurement parameters included: anterior chamber depth (ACD), angle opening distance (AOD 500), trabecular ciliary process distance (TCPD), iris ciliary process distance (ICPD), iris depth (ID), iridocorneal angle (ICA), and sulcus angle (SA). Four novel measurements included: ciliary process thickness (CPT), ciliary process width (CPW), ciliary process area (CPA), and iris ciliary process contact length (ICPCL). Visual acuity, intraocular pressure, glaucoma medications, and complications were also followed. RESULTS: The ACD, AOD 500, and ICA all increased significantly (P<0.001). ICPD, CPT, CPW, CPA, and ICPL all decreased significantly (P<0.01). Parameters remaining unchanged were: TCPD, ID, and SA. The untreated quadrants showed similar measurements to the preoperative measurements. There were no serious complications noted. DISCUSSION: Treating the ciliary processes with diode laser using an endoscopic approach (ECPL) and lens extraction, results in opening of the anterior chamber angle and shrinkage of the ciliary processes in the treated areas. This effect seems to be primarily a result of the laser treatment in combination rather than the lens extraction alone. This effectively reverses the anatomic cause and angle closure of plateau iris syndrome.

Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves.

The Paisley Caves in Oregon record the oldest directly dated human remains (DNA) in the Western Hemisphere. More than 100 high-precision radiocarbon dates show that deposits containing artifacts and coprolites ranging in age from 12,450 to 2295 (14)C years ago are well stratified. Western Stemmed projectile points were recovered in deposits dated to 11,070 to 11,340 (14)C years ago, a time contemporaneous with or preceding the Clovis technology. There is no evidence of diagnostic Clovis technology at the site. These two distinct technologies were parallel developments, not the product of a unilinear technological evolution. "Blind testing" analysis of coprolites by an independent laboratory confirms the presence of human DNA in specimens of pre-Clovis age. The colonization of the Americas involved multiple technologically divergent, and possibly genetically divergent, founding groups.

Species-specific responses of Late Quaternary megafauna to climate and humans.

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.

DNA from pre-Clovis human coprolites in Oregon, North America.

The timing of the first human migration into the Americas and its relation to the appearance of the Clovis technological complex in North America at about 11,000 to 10,800 radiocarbon years before the present (14C years B.P.) remains contentious. We establish that humans were present at Paisley 5 Mile Point Caves, in south-central Oregon, by 12,300 14C years B.P., through the recovery of human mitochondrial DNA (mtDNA) from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are >1000 14C years earlier than currently accepted dates for the Clovis complex.