Towards Robust Monocular Depth Estimation: Mixing Datasets for Zero-Shot Cross-Dataset Transfer.

The success of monocular depth estimation relies on large and diverse training sets. Due to the challenges associated with acquiring dense ground-truth depth across different environments at scale, a number of datasets with distinct characteristics and biases have emerged. We develop tools that enable mixing multiple datasets during training, even if their annotations are incompatible. In particular, we propose a robust training objective that is invariant to changes in depth range and scale, advocate the use of principled multi-objective learning to combine data from different sources, and highlight the importance of pretraining encoders on auxiliary tasks. Armed with these tools, we experiment with five diverse training datasets, including a new, massive data source: 3D films. To demonstrate the generalization power of our approach we use zero-shot cross-dataset transfer, i.e. we evaluate on datasets that were not seen during training. The experiments confirm that mixing data from complementary sources greatly improves monocular depth estimation. Our approach clearly outperforms competing methods across diverse datasets, setting a new state of the art for monocular depth estimation.

The h-index is no longer an effective correlate of scientific reputation.

The impact of individual scientists is commonly quantified using citation-based measures. The most common such measure is the h-index. A scientist's h-index affects hiring, promotion, and funding decisions, and thus shapes the progress of science. Here we report a large-scale study of scientometric measures, analyzing millions of articles and hundreds of millions of citations across four scientific fields and two data platforms. We find that the correlation of the h-index with awards that indicate recognition by the scientific community has substantially declined. These trends are associated with changing authorship patterns. We show that these declines can be mitigated by fractional allocation of citations among authors, which has been discussed in the literature but not implemented at scale. We find that a fractional analogue of the h-index outperforms other measures as a correlate and predictor of scientific awards. Our results suggest that the use of the h-index in ranking scientists should be reconsidered, and that fractional allocation measures such as h-frac provide more robust alternatives.

Critical carotid artery stenosis involving a persistent primitive hypoglossal artery.

Persistent primitive hypoglossal artery (PPHA) is a rare internal carotid-vertebrobasilar anatomic variant. Awareness of this anomaly and its propensity for atherosclerotic disease is important to avoid misinterpretation of diagnostic studies and to allow appropriate interventional planning. As the predominant vascular supply to the anterior and posterior cerebral circulation, its luminal compromise can lead to devastating ischemic complications. Carotid endarterectomy and carotid stenting have both been performed to treat lesions involving a PPHA. Herein, we report a case of carotid endarterectomy involving a PPHA and discuss the clinical and surgical implications of a carotid lesion in the presence of a PPHA.

Systematic Assessment of Adult Patients' Satisfaction with Various Eosinophilic Esophagitis Therapies.

BACKGROUND AND AIMS: The treatment options for eosinophilic esophagitis (EoE) patients include drugs (proton pump inhibitors [PPIs], swallowed topical corticosteroids [STCs]), elimination diets, and dilation. Given the lack of data, we aimed to assess adult EoE patients' satisfaction with different EoE-specific treatment modalities. PATIENTS AND METHODS: We evaluated therapy satisfaction recalled over a 12-month period using the validated Treatment Satisfaction Questionnaire for Medication that assesses effectiveness, side effects, convenience, and overall satisfaction. The score for each scale ranges from 0 (dissatisfied) to 100 (satisfied). To evaluate satisfaction with nonpharmacologic therapies, the questionnaire was modified and debriefed into three focus groups. The final questionnaire was sent to 147 patients. RESULTS: The patient response rate was 74%. In the last 12 months, 24, 75, 19, and 9% were treated with PPIs, STCs, elimination diet, and dilation, respectively. Patients identified the following considerations as important for therapy choice: effect on symptoms (89%), effect on esophageal inflammation (76%), side effects (69%), and ease of use (58%). Patients found STCs to be effective (83 points), convenient (83 points), and experienced no side effects when using this therapy. When using STCs alone (43%), overall patient satisfaction was high (86 points). Patients judged PPIs to be most convenient (89 points), STCs to be a bit less convenient (83 points), and diet to be most inconvenient (46 points) of the three therapies examined. CONCLUSIONS: Adult EoE patients consider both therapy effect on symptoms and esophageal inflammation as important criteria when choosing EoE therapy and appear to be satisfied with STC use.

Temporal and spatial dynamics of competitive parapatry in chewing lice.

We synthesize observations from 1979 to 2016 of a contact zone involving two subspecies of pocket gophers (Thomomys bottae connectens and T. b. opulentus) and their respective chewing lice (Geomydoecus aurei and G. centralis) along the Río Grande Valley in New Mexico, U.S.A., to test predictions about the dynamics of the zone. Historically, the natural flood cycle of the Rio Grande prevented contact between the two subspecies of pocket gophers. Flood control measures completed in the 1930s permitted contact, thus establishing the hybrid zone between the pocket gophers and the contact zone between their lice (without hybridization). Since that time, the pocket gopher hybrid zone has stabilized, whereas the northern chewing louse species has replaced the southern louse species at a consistent rate of ~150 m/year. The 0.2-0.8 width of the replacement zone has remained constant, reflecting the constant rate of chewing louse species turnover on a single gopher and within a local pocket gopher population. In contrast, the full width of the replacement zone (northernmost G. centralis to southernmost G. aurei) has increased annually. By employing a variety of metrics of the species replacement zone, we are better able to understand the dynamics of interactions between and among the chewing lice and their pocket gopher hosts. This research provides an opportunity to observe active species replacement and resulting distributional shifts in a parasitic organism in its natural setting.

Variation in Endoscopic Activity Assessment and Endoscopy Score Validation in Adults With Eosinophilic Esophagitis.

BACKGROUND & AIMS: Eosinophilic esophagitis (EoE) is assessed endoscopically (endoscopic activity), based on grades of edema, rings, exudates, furrows, and strictures (EREFS). We examined variations in endoscopic assessments of severity, developed and validated 3 EREFS-based scoring systems, and assessed responsiveness of these systems using data from a randomized placebo-controlled trial of patients with EoE. METHODS: For the development set, 5 gastroenterologists reviewed EREFS findings from 266 adults with EoE and provided endoscopist global assessment scores (EndoGA, scale of 0 to 10); variation (ΔEndoGA) was assessed using linear regression. We evaluated simple scores (features given arbitrary values from 0 to 3) and developed 2 scoring systems (adjusted score range, 0-100). We then fitted our linear regression model with mean EndoGA to data from 146 adults recruited in centers in Switzerland and the United States between April 2011 and December 2012. For the validation set, we collected data from 120 separate adults (recruited in centers in Switzerland and the United States between May 2013 and July 2014), assessing regression coefficient-based scores using Bland-Altman method. We assessed the responsiveness of our scoring systems using data from a randomized trial of patients with EoE given fluticasone (n=16) or placebo (n=8). RESULTS: The distribution of EndoGA values differed among endoscopists (mean ΔEndoGA, 2.6±1.8; range 0-6.6). We developed 2 regression-based scoring systems to assess overall and proximal and distal esophageal findings; variation in endoscopic features accounted for more than 90% of the mean EndoGA variation. In the validation group, differences between mean EndoGA and regression-based scores were small (ranging from -4.70 to 2.03), indicating good agreement. In analyses of data from the randomized trial, the baseline to end of study change in patients given fluticasone was a reduction of 24.3 in simple score (reduction of 4.6 in patients given placebo, P=.052); a reduction of 23.5 in regression-based overall score (reduction of 6.56 in patients given placebo, P=.12), and a reduction of 23.8 (reduction of 8.44 in patients given placebo, P=.11). CONCLUSION: Assessments of endoscopic activity in patients with EoE vary among endoscopists. In an analysis of data from a randomized controlled trial, we found that newly developed scoring systems are no better than simple scoring system in detecting changes in endoscopic activity. These results support the use of a simple scoring system in evaluation of endoscopic activity in patients with EoE. clinicaltrials.gov no: NCT00939263 and NCT01386112.

Loss of genetic diversity, recovery and allele surfing in a colonizing parasite, Geomydoecus aurei.

Understanding the genetic consequences of changes in species distributions has wide-ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25-year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post-bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225-generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid-based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.

Adults with eosinophilic oesophagitis identify symptoms and quality of life as the most important outcomes.

BACKGROUND: Well informed patients who are in cohesive partnership with physicians and who have realistic expectations towards therapy are more likely to be adherent, which results in better disease control. AIM: To assess which therapy goals adults with eosinophilic oesophagitis consider relevant. METHODS: Following refinement during three focus groups, a study brochure and questionnaire were sent to 148 patients. Patients ranked the importance (five levels) of short-term (in the next 3 months) and long-term (≥1 year) treatment effect on symptoms, quality of life (QoL), histologically-detected inflammation and fibrosis, endoscopically-detected inflammation, and stricture formation as well as achieving histological remission while asymptomatic. Patients' characteristics associated with treatment goals were identified using logistic regression. RESULTS: Of 109 respondents (mean age 43 years), 85 were men. Over 90% chose symptoms and QoL improvement as important short- and long-term therapy goals. A greater proportion attributed more importance to long-term reduction in endoscopic (90% vs 73%, P < 0.001) and histological (81% vs 62%, P = 0.002) inflammation, and histologically-detected fibrosis (79% vs 64%, P = 0.018) when compared to short-term reduction in these features. Patients (88%) ranked achieving histological remission while being asymptomatic as important. Gender, therapy use, education level, QoL, symptom severity, and history of dilation were associated with patients' choice of treatment goals. CONCLUSIONS: Patients attributed most importance to improvement in symptoms and QoL. Reduction in biological activity was judged less important, but more relevant in the long- compared to the short-term.

Building Castles Made of Pleasure.

To outlive the suicide of one's beloved, an ineffable trauma, entails a complicated grieving process. This paper illustrates the importance of understanding body and self as malleable, invested objects. The treatment of traumatized patients involves redrawing body frontiers, and subsequent reassurance that the body, once delineated and inhabited, won't betray its host. The concepts of objet a and transitional objects help distinguish anxieties related to external loss from anxieties related to the incorporation or reabsorption of an object whose cruel proximity threatens the internal integrity of body experience. The movement toward mourning can be complicated by melancholic incorporation of the deceased, especially in cases of suicide; the volitional nature of such acts retroactively disrupts life narratives, forcing one to create new answers to questions of who and what one was for the other who chose death and to give new connotations to one's prior encounters with death.

Tobacco smoke-induced hypercoagulation in human plasma: role of carbon monoxide.

Virtually every disease state associated with chronic or acute thrombosis has had smoking identified as a risk factor. Further, smoking enhances clot strength as assessed by thrombelastography. Critically, carbon monoxide, a product of cigarette smoking, has been demonstrated to enhance plasmatic coagulation in vitro via modulation of a heme associated with fibrinogen. We hypothesized that plasmatic hypercoagulability and formation of carboxyhemefibrinogen (COHF) detected with thrombelastographic methods would be observed after cigarette smoking. Smoking participants (n = 20, two cigarettes consumed within 90 min, average carboxyhemoglobin concentration of 5%) had plasma collected and normal participant (n = 20) plasma was also obtained. Thrombelastographic analyses revealed that plasma obtained from smokers had an 86% greater velocity of clot growth and 65% larger clot strength than normal participant plasma. Forty-five percent of smokers had plasma clot strength that exceeded the 95th percentile of normal participant plasma values; 45% of smoking participants had detectable COHF; and 20% of smoking participants were both hypercoagulable with COHF present. We conclude that smoking induced a hypercoagulable state and COHF formation in an important portion of participants tested. Future investigations of the effects of smoking, plasmatic hypercoagulation and COHF formation are planned in populations with established atherosclerotic/thrombotic disease.

Can divergent plasmin-antiplasmin-carbon monoxide interactions in young, healthy tobacco smokers explain the 'smoker's paradox'?

In the setting of acute myocardial infarction, decreases in early/late mortality, reocclusion after thrombolysis, and restenosis rate after percutaneous intervention are lower in smokers - this phenomenon has been designated as the 'smoker's paradox'. These benefits of smoking, however, are abrogated by stent placement. We hypothesized that fibrinolytic vulnerability would change in response to smoking, and that inhaled carbon monoxide may play a role. Smoking patients (n = 20, two cigarettes consumed within 90 min, average carboxyhemoglobin concentration of 5%) had plasma collected and normal individual (n = 20) plasma was also obtained. Thrombelastographic analyses conducted with addition of tissue-type plasminogen activator revealed that with the exception of the rate of thrombus generation, there was little difference in fibrinolytic kinetics between normal and smoking individuals. Addition of exogenous carbon monoxide resulted in diminished fibrinolytic response to the same extent in both groups. Subanalyses demonstrated that the smoking cohort had both hyperfibrinolytic and hypofibrinolytic patients as defined by confidence interval (5-95%) values generated from normal individuals. Addition of carbon monoxide reduced hyperfibrinolytic parameter values by 80% in smokers, whereas only a 17% decrease in hypofibrinolytic values changed. Our investigation suggests that 'smoker's paradox' involves a marked change in the character of the plasmin-antiplasmin-carbon monoxide interaction. Further investigation will be required to further define the molecular mechanism responsible for the 'smoker's paradox'.

Freezing does not decrease carbon monoxide-mediated hypercoagulation and hypofibrinolysis in human plasma.

Carbon monoxide (CO) has been demonstrated to enhance coagulation and attenuate fibrinolysis in vitro and in vivo. Hemostasis is affected by CO interactions with key heme-modulated molecules. We wished to determine whether freezing would affect CO-mediated changes in coagulation/fibrinolysis in plasma in anticipation of collecting samples both within our institution and from collaborating centers. Plasma was exposed to CO by addition of 0-100 µmol/l tricarbonyldichlororuthenium (II) dimer, with a portion of plasma immediately frozen at -80 °C. Unfrozen plasma was subjected to thrombelastographic analysis following tissue factor activation, with some samples exposed to tissue type plasminogen activator. Frozen plasma was subsequently thawed and similarly analyzed. Freezing did not significantly change CO-mediated enhancement of coagulation or attenuation of fibrinolysis. Hemostatic changes in plasma exposed to CO are not affected by a freeze-thaw cycle, which will permit local batch processing of samples and transport of samples on dry ice from collaborating centers.

Cophylogeny on a fine scale: Geomydoecus chewing lice and their pocket gopher hosts, Pappogeomys bulleri.

Many species of pocket gophers and their ectoparasitic chewing lice have broadly congruent phylogenies, indicating a history of frequent codivergence. For a variety of reasons, phylogenies of codiverging hosts and parasites are expected to be less congruent for more recently diverged taxa. This study is the first of its scale in the pocket gopher and chewing louse system, with its focus entirely on comparisons among populations within a single species of host and 3 chewing louse species in the Geomydoecus bulleri species complex. We examined mitochondrial DNA from a total of 46 specimens of Geomydoecus lice collected from 11 populations of the pocket gopher host, Pappogeomys bulleri. We also examined nuclear DNA from a subset of these chewing lice. Louse phylogenies were compared with a published pocket gopher phylogeny. Contrary to expectations, we observed a statistically significant degree of parallel cladogenesis in these closely related hosts and their parasites. We also observed a higher rate of evolution in chewing louse lineages than in their corresponding pocket gopher hosts. In addition, we found that 1 louse species (Geomydoecus burti) may not be a valid species, that subspecies within G. bulleri are not reciprocally monophyletic, and that morphological and genetic evidence support recognition of a new species of louse, Geomydoecus pricei.

When cold is better: climate-driven elevation shifts yield complex patterns of diversification and demography in an alpine specialist (American pika, Ochotona princeps).

The genetic consequences of climate-driven range fluctuation during the Pleistocene have been well studied for temperate species, but cold-adapted (e.g., alpine, arctic) species that may have responded uniquely to past climatic events have received less attention. In particular, we have no a priori expectation for long-term evolutionary consequences of elevation shifts into and out of sky islands by species adapted to alpine habitats. Here, we examined the influence of elevation shifts on genetic differentiation and historical demography in an alpine specialist, the American pika (Ochotona princeps). Pika populations are divided into five genetic lineages that evolved in association with separate mountain systems, rather than lineages that reflect individual sky islands. This suggests a role for glacial-period elevation shifts in promoting gene flow among high-elevation populations and maintaining regional cohesion of genetic lineages. We detected a signature of recent demographic decline in all lineages, consistent with the expectation that Holocene climate warming has driven range retraction in southern lineages, but unexpected for northern populations that presumably represent postglacial expansion. An ecological niche model of past and future pika distributions highlights the influence of climate on species range and indicates that the distribution of genetic diversity may change dramatically with continued climate warming.

Systematics and phylogeography of pocket gophers in the genera Cratogeomys and Pappogeomys.

Mitochondrial-DNA sequence data were analyzed from individuals sampled from 38 localities across the complete geographic range of the closely related pocket gopher genera Pappogeomys and Cratogeomys. Results of phylogenetic analysis of 1133 base pairs from the cytochrome b gene are consistent with past hypotheses of relationships among members of the castanops species group within the genus Cratogeomys. However, phylogeographic variation within the gymnurus species group of the genus Cratogeomys differs significantly from relationships reflected by current taxonomy. The data indicate that there are five geographically distinct clades within the gymnurus species group. Members of the two nominal species C. gymnurus and C. tylorhinus are scattered among these clades. The three peripherally isolated species, C. fumosus, C. neglectus, and C. zinseri, do not appear to be genetically distinct from other gymnurus species group taxa. An historical biogeographic hypothesis is proposed that will be tested using nuclear DNA data.

AGE AND MOVEMENT OF A HYBRID ZONE: IMPLICATIONS FOR DISPERSAL DISTANCE IN POCKET GOPHERS AND THEIR CHEWING LICE.

Historical flood records for the Rio Grande Valley of New Mexico suggest that a pocket gopher (Thomomys bottae) hybrid zone previously thought to be 10,000 years old may actually be closer to 50 years old. Measured zone width (defined genetically) is consistent with the hypothesis of recent contact, if we assume a reasonable dispersal distance of approximately 400 m/year for pocket gophers. A five-year study of movement of the contact zone between the two species of chewing lice that parasitize these pocket gophers also is consistent with the hypothesis of recent origin of the zone.

GENETIC DIFFERENTIATION AMONG CHEWING LOUSE POPULATIONS (MALLOPHAGA: TRICHODECTIDAE) IN A POCKET GOPHER CONTACT ZONE (RODENTIA: GEOMYIDAE).

Genetic variation among populations of chewing lice (Geomydoecus actuosi) was examined in relation to chromosomal and electrophoretic variation among populations of their hosts (Thomomys bottae) at a contact zone. Louse demes were characterized by low levels of genetic heterozygosity (H̄ = 0.039) that may result from founder effects during primary infestation of hosts, compounded by seasonal reductions in louse population size. Louse populations sampled from different hosts showed high levels of genetic structuring both within and among host localities. Microgeographic differentiation of louse populations is high (mean FST = 0.092) suggesting that properties of this host-parasite system promote differentiation of louse populations living on different individual hosts. Among-population differentiation in lice (FST = 0.240) was similar to that measured among host populations (FST = 0.236), suggesting a close association between gene flow in pocket gophers and gene flow in their lice.