Showing papers by "Dartmouth College published in 2014"

Learning Spatiotemporal Features with 3D Convolutional Networks

Abstract: We propose a simple, yet effective approach for spatiotemporal feature learning using deep 3-dimensional convolutional networks (3D ConvNets) trained on a large scale supervised video dataset. Our findings are three-fold: 1) 3D ConvNets are more suitable for spatiotemporal feature learning compared to 2D ConvNets; 2) A homogeneous architecture with small 3x3x3 convolution kernels in all layers is among the best performing architectures for 3D ConvNets; and 3) Our learned features, namely C3D (Convolutional 3D), with a simple linear classifier outperform state-of-the-art methods on 4 different benchmarks and are comparable with current best methods on the other 2 benchmarks. In addition, the features are compact: achieving 52.8% accuracy on UCF101 dataset with only 10 dimensions and also very efficient to compute due to the fast inference of ConvNets. Finally, they are conceptually very simple and easy to train and use.

mTOR- and HIF-1α–mediated aerobic glycolysis as metabolic basis for trained immunity

Abstract: Epigenetic reprogramming of myeloid cells, also known as trained immunity, confers nonspecific protection from secondary infections. Using histone modification profiles of human monocytes trained with the Candida albicans cell wall constituent β-glucan, together with a genome-wide transcriptome, we identified the induced expression of genes involved in glucose metabolism. Trained monocytes display high glucose consumption, high lactate production, and a high ratio of nicotinamide adenine dinucleotide (NAD(+)) to its reduced form (NADH), reflecting a shift in metabolism with an increase in glycolysis dependent on the activation of mammalian target of rapamycin (mTOR) through a dectin-1-Akt-HIF-1α (hypoxia-inducible factor-1α) pathway. Inhibition of Akt, mTOR, or HIF-1α blocked monocyte induction of trained immunity, whereas the adenosine monophosphate-activated protein kinase activator metformin inhibited the innate immune response to fungal infection. Mice with a myeloid cell-specific defect in HIF-1α were unable to mount trained immunity against bacterial sepsis. Our results indicate that induction of aerobic glycolysis through an Akt-mTOR-HIF-1α pathway represents the metabolic basis of trained immunity.

Cognitive Reappraisal of Emotion: A Meta-Analysis of Human Neuroimaging Studies

Abstract: In recent years, an explosion of neuroimaging studies has examined cognitive reappraisal, an emotion regulation strategy that involves changing the way one thinks about a stimulus in order to change its affective impact Existing models broadly agree that reappraisal recruits frontal and parietal control regions to modulate emotional responding in the amygdala, but they offer competing visions of how this is accomplished One view holds that control regions engage ventromedial prefrontal cortex (vmPFC), an area associated with fear extinction, that in turn modulates amygdala responses An alternative view is that control regions modulate semantic representations in lateral temporal cortex that indirectly influence emotion-related responses in the amygdala Furthermore, while previous work has emphasized the amygdala, whether reappraisal influences other regions implicated in emotional responding remains unknown To resolve these questions, we performed a meta-analysis of 48 neuroimaging studies of reappraisal, most involving downregulation of negative affect Reappraisal consistently 1) activated cognitive control regions and lateral temporal cortex, but not vmPFC, and 2) modulated the bilateral amygdala, but no other brain regions This suggests that reappraisal involves the use of cognitive control to modulate semantic representations of an emotional stimulus, and these altered representations in turn attenuate activity in the amygdala

Current Thyroid Cancer Trends in the United States

Abstract: Importance We have previously reported on a doubling of thyroid cancer incidence—largely due to the detection of small papillary cancers. Because they are commonly found in people who have died of other causes, and because thyroid cancer mortality had been stable, we argued that the increased incidence represented overdiagnosis. Objective To determine whether thyroid cancer incidence has stabilized. Design Analysis of secular trends in patients diagnosed with thyroid cancer, 1975 to 2009, using the Surveillance, Epidemiology, and End Results (SEER) program and thyroid cancer mortality from the National Vital Statistics System. Setting Nine SEER areas (SEER 9): Atlanta, Georgia; Connecticut; Detroit, Michigan; Hawaii; Iowa; New Mexico; San Francisco–Oakland, California; Seattle–Puget Sound, Washington; and Utah. Participants Men and women older than 18 years diagnosed as having a thyroid cancer between 1975 and 2009 who lived in the SEER 9 areas. Interventions None. Main Outcomes and Measures Thyroid cancer incidence, histologic type, tumor size, and patient mortality. Results Since 1975, the incidence of thyroid cancer has now nearly tripled, from 4.9 to 14.3 per 100 000 individuals (absolute increase, 9.4 per 100 000; relative rate [RR], 2.9; 95% CI, 2.7-3.1). Virtually the entire increase was attributable to papillary thyroid cancer: from 3.4 to 12.5 per 100 000 (absolute increase, 9.1 per 100 000; RR, 3.7; 95% CI, 3.4-4.0). The absolute increase in thyroid cancer in women (from 6.5 to 21.4 = 14.9 per 100 000 women) was almost 4 times greater than that of men (from 3.1 to 6.9 = 3.8 per 100 000 men). The mortality rate from thyroid cancer was stable between 1975 and 2009 (approximately 0.5 deaths per 100 000). Conclusions and Relevance There is an ongoing epidemic of thyroid cancer in the United States. The epidemiology of the increased incidence, however, suggests that it is not an epidemic of disease but rather an epidemic of diagnosis. The problem is particularly acute for women, who have lower autopsy prevalence of thyroid cancer than men but higher cancer detection rates by a 3:1 ratio.

A Critical Review of the Risks to Water Resources from Unconventional Shale Gas Development and Hydraulic Fracturing in the United States

Abstract: The rapid rise of shale gas development through horizontal drilling and high volume hydraulic fracturing has expanded the extraction of hydrocarbon resources in the U.S. The rise of shale gas development has triggered an intense public debate regarding the potential environmental and human health effects from hydraulic fracturing. This paper provides a critical review of the potential risks that shale gas operations pose to water resources, with an emphasis on case studies mostly from the U.S. Four potential risks for water resources are identified: (1) the contamination of shallow aquifers with fugitive hydrocarbon gases (i.e., stray gas contamination), which can also potentially lead to the salinization of shallow groundwater through leaking natural gas wells and subsurface flow; (2) the contamination of surface water and shallow groundwater from spills, leaks, and/or the disposal of inadequately treated shale gas wastewater; (3) the accumulation of toxic and radioactive elements in soil or stream sediments near disposal or spill sites; and (4) the overextraction of water resources for high-volume hydraulic fracturing that could induce water shortages or conflicts with other water users, particularly in water-scarce areas. Analysis of published data (through January 2014) reveals evidence for stray gas contamination, surface water impacts in areas of intensive shale gas development, and the accumulation of radium isotopes in some disposal and spill sites. The direct contamination of shallow groundwater from hydraulic fracturing fluids and deep formation waters by hydraulic fracturing itself, however, remains controversial.

AUV Navigation and Localization: A Review

Abstract: Autonomous underwater vehicle (AUV) navigation and localization in underwater environments is particularly challenging due to the rapid attenuation of Global Positioning System (GPS) and radio-frequency signals. Underwater communications are low bandwidth and unreliable, and there is no access to a global positioning system. Past approaches to solve the AUV localization problem have employed expensive inertial sensors, used installed beacons in the region of interest, or required periodic surfacing of the AUV. While these methods are useful, their performance is fundamentally limited. Advances in underwater communications and the application of simultaneous localization and mapping (SLAM) technology to the underwater realm have yielded new possibilities in the field. This paper presents a review of the state of the art of AUV navigation and localization, as well as a description of some of the more commonly used methods. In addition, we highlight areas of future research potential.

Effective Messages in Vaccine Promotion: A Randomized Trial

Abstract: OBJECTIVES: To test the effectiveness of messages designed to reduce vaccine misperceptions and increase vaccination rates for measles-mumps-rubella (MMR). METHODS: A Web-based nationally representative 2-wave survey experiment was conducted with 1759 parents age 18 years and older residing in the United States who have children in their household age 17 years or younger (conducted June–July 2011). Parents were randomly assigned to receive 1 of 4 interventions: (1) information explaining the lack of evidence that MMR causes autism from the Centers for Disease Control and Prevention; (2) textual information about the dangers of the diseases prevented by MMR from the Vaccine Information Statement; (3) images of children who have diseases prevented by the MMR vaccine; (4) a dramatic narrative about an infant who almost died of measles from a Centers for Disease Control and Prevention fact sheet; or to a control group. RESULTS: None of the interventions increased parental intent to vaccinate a future child. Refuting claims of an MMR/autism link successfully reduced misperceptions that vaccines cause autism but nonetheless decreased intent to vaccinate among parents who had the least favorable vaccine attitudes. In addition, images of sick children increased expressed belief in a vaccine/autism link and a dramatic narrative about an infant in danger increased self-reported belief in serious vaccine side effects. CONCLUSIONS: Current public health communications about vaccines may not be effective. For some parents, they may actually increase misperceptions or reduce vaccination intention. Attempts to increase concerns about communicable diseases or correct false claims about vaccines may be especially likely to be counterproductive. More study of pro-vaccine messaging is needed.

StudentLife: assessing mental health, academic performance and behavioral trends of college students using smartphones

Abstract: Much of the stress and strain of student life remains hidden. The StudentLife continuous sensing app assesses the day-to-day and week-by-week impact of workload on stress, sleep, activity, mood, sociability, mental well-being and academic performance of a single class of 48 students across a 10 week term at Dartmouth College using Android phones. Results from the StudentLife study show a number of significant correlations between the automatic objective sensor data from smartphones and mental health and educational outcomes of the student body. We also identify a Dartmouth term lifecycle in the data that shows students start the term with high positive affect and conversation levels, low stress, and healthy sleep and daily activity patterns. As the term progresses and the workload increases, stress appreciably rises while positive affect, sleep, conversation and activity drops off. The StudentLife dataset is publicly available on the web.

Korea's Thyroid-Cancer “Epidemic” — Screening and Overdiagnosis

Abstract: In 2011, the rate of thyroid-cancer diagnoses in the Republic of Korea was 15 times that observed in 1993, yet thyroid-cancer mortality remains stable — a combination that suggests that the problem is overdiagnosis attributable to widespread thyroid-cancer screening.

Informality and Development

Abstract: In developing countries, informal firms account for up to half of economic activity. They provide livelihood for billions of people. Yet their role in economic development remains controversial. Some, like Hernando De Soto (1989, 2000), see informal firms as an untapped reservoir of entrepreneurial energy, held back by government regulations. In this view, unleashing this energy by reducing entry regulations or improving property rights would fuel growth and development. Others, like Levy (2008), take a more cynical view, stressing the advantages enjoyed by informal firms and workers from avoiding taxes and regulations. A report from the McKinsey Global Institute describes informal firms as parasites competing unfairly with law-abiding formal firms (Farrell 2004). In this view, informality should be suppressed, not unleashed. Still others follow the development tradition of Lewis (1954), Harris and Todaro (1970), and more recently Rauch (1991) and see informality as a byproduct of poverty. From this dual perspective, formal and informal firms are fundamentally different. Productive formal entrepreneurs pay taxes and bear the cost of government regulation to reach new customers, raise capital, and access public goods. These entrepreneurs are often educated and find it more profitable to run bigger formal firms rather than the smaller informal ones. In contrast, informal entrepreneurs are typically uneducated and unproductive, and they run small businesses producing low-quality products for low-income customers using little capital and

Global warming releases microplastic legacy frozen in Arctic Sea ice

Abstract: When sea ice forms it scavenges and concentrates particulates from the water column, which then become trapped until the ice melts. In recent years, melting has led to record lows in Arctic Sea ice extent, the most recent in September 2012. Global climate models, such as that of Gregory et al. (2002), suggest that the decline in Arctic Sea ice volume (3.4% per decade) will actually exceed the decline in sea ice extent, something that Laxon et al. (2013) have shown supported by satellite data. The extent to which melting ice could release anthropogenic particulates back to the open ocean has not yet been examined. Here we show that Arctic Sea ice from remote locations contains concentrations of microplastics are several orders of magnitude greater than those that have been previously reported in highly contaminated surface waters, such as those of the Pacific Gyre. Our findings indicate that microplastics have accumulated far from population centers and that polar sea ice represents a major historic global sink of man-made particulates. The potential for substantial quantities of legacy microplastic contamination to be released to the ocean as the ice melts therefore needs to be evaluated, as do the physical and toxicological effects of plastics on marine life.

Overdiagnosis in Low-Dose Computed Tomography Screening for Lung Cancer

Abstract: Importance Screening for lung cancer has the potential to reduce mortality, but in addition to detecting aggressive tumors, screening will also detect indolent tumors that otherwise may not cause clinical symptoms. These overdiagnosis cases represent an important potential harm of screening because they incur additional cost, anxiety, and morbidity associated with cancer treatment. Objective To estimate overdiagnosis in the National Lung Screening Trial (NLST). Design, Setting, and Participants We used data from the NLST, a randomized trial comparing screening using low-dose computed tomography (LDCT) vs chest radiography (CXR) among 53 452 persons at high risk for lung cancer observed for 6.4 years, to estimate the excess number of lung cancers in the LDCT arm of the NLST compared with the CXR arm. Main Outcomes and Measures We calculated 2 measures of overdiagnosis: the probability that a lung cancer detected by screening with LDCT is an overdiagnosis ( PS ), defined as the excess lung cancers detected by LDCT divided by all lung cancers detected by screening in the LDCT arm; and the number of cases that were considered overdiagnosis relative to the number of persons needed to screen to prevent 1 death from lung cancer. Results During follow-up, 1089 lung cancers were reported in the LDCT arm and 969 in the CXR arm of the NLST. The probability is 18.5% (95% CI, 5.4%-30.6%) that any lung cancer detected by screening with LDCT was an overdiagnosis, 22.5% (95% CI, 9.7%-34.3%) that a non–small cell lung cancer detected by LDCT was an overdiagnosis, and 78.9% (95% CI, 62.2%-93.5%) that a bronchioalveolar lung cancer detected by LDCT was an overdiagnosis. The number of cases of overdiagnosis found among the 320 participants who would need to be screened in the NLST to prevent 1 death from lung cancer was 1.38. Conclusions and Relevance More than 18% of all lung cancers detected by LDCT in the NLST seem to be indolent, and overdiagnosis should be considered when describing the risks of LDCT screening for lung cancer.

Decoding Neural Representational Spaces Using Multivariate Pattern Analysis

Abstract: A major challenge for systems neuroscience is to break the neural code. Computational algorithms for encoding information into neural activity and extracting information from measured activity afford understanding of how percepts, memories, thought, and knowledge are represented in patterns of brain activity. The past decade and a half has seen significant advances in the development of methods for decoding human neural activity, such as multivariate pattern classification, representational similarity analysis, hyperalignment, and stimulus-model-based encoding and decoding. This article reviews these advances and integrates neural decoding methods into a common framework organized around the concept of high-dimensional representational spaces.

The role of microbiome in central nervous system disorders

Abstract: Mammals live in a co-evolutionary association with the plethora of microorganisms that reside at a variety of tissue microenvironments The microbiome represents the collective genomes of these co-existing microorganisms, which is shaped by host factors such as genetics and nutrients but in turn is able to influence host biology in health and disease Niche-specific microbiome, prominently the gut microbiome, has the capacity to effect both local and distal sites within the host The gut microbiome has played a crucial role in the bidirectional gut–brain axis that integrates the gut and central nervous system (CNS) activities, and thus the concept of microbiome–gut–brain axis is emerging Studies are revealing how diverse forms of neuro-immune and neuro-psychiatric disorders are correlated with or modulated by variations of microbiome, microbiota-derived products and exogenous antibiotics and probiotics The microbiome poises the peripheral immune homeostasis and predisposes host susceptibility to CNS autoimmune diseases such as multiple sclerosis Neural, endocrine and metabolic mechanisms are also critical mediators of the microbiome–CNS signaling, which are more involved in neuro-psychiatric disorders such as autism, depression, anxiety, stress Research on the role of microbiome in CNS disorders deepens our academic knowledge about host-microbiome commensalism in central regulation and in practicality, holds conceivable promise for developing novel prognostic and therapeutic avenues for CNS disorders

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

Abstract: Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.

Two‐year seizure reduction in adults with medically intractable partial onset epilepsy treated with responsive neurostimulation: Final results of the RNS System Pivotal trial

Abstract: SummaryObjective To demonstrate the safety and effectiveness of responsive stimulation at the seizure focus as an adjunctive therapy to reduce the frequency of seizures in adults with medically intractable partial onset seizures arising from one or two seizure foci. Methods Randomized multicenter double-blinded controlled trial of responsive focal cortical stimulation (RNS System). Subjects with medically intractable partial onset seizures from one or two foci were implanted, and 1 month postimplant were randomized 1:1 to active or sham stimulation. After the fifth postimplant month, all subjects received responsive stimulation in an open label period (OLP) to complete 2 years of postimplant follow-up. Results All 191 subjects were randomized. The percent change in seizures at the end of the blinded period was −37.9% in the active and −17.3% in the sham stimulation group (p = 0.012, Generalized Estimating Equations). The median percent reduction in seizures in the OLP was 44% at 1 year and 53% at 2 years, which represents a progressive and significant improvement with time (p < 0.0001). The serious adverse event rate was not different between subjects receiving active and sham stimulation. Adverse events were consistent with the known risks of an implanted medical device, seizures, and of other epilepsy treatments. There were no adverse effects on neuropsychological function or mood. Significance Responsive stimulation to the seizure focus reduced the frequency of partial-onset seizures acutely, showed improving seizure reduction over time, was well tolerated, and was acceptably safe. The RNS System provides an additional treatment option for patients with medically intractable partial-onset seizures.

Hydrazone-based switches, metallo-assemblies and sensors

Abstract: The hydrazone functional group has been extensively studied and used in the context of supramolecular chemistry. Its pervasiveness and versatility can be attributed to its ease of synthesis, modularity, and most importantly unique structural properties, which enable its integration in different applications. This review provides an overview of the utilization of hydrazones in three supramolecular chemistry related areas: molecular switches, metallo-assemblies and sensors. These topics were chosen because they highlight the diversity of hydrazones, and emphasize their uniqueness vis-a-vis the imine functional group. Discussion entails (i) chemical and light activated switching of hydrazones, and how this can be used in controlling the properties of self-assembled systems, (ii) the use of hydrazones in the formation of dynamic and stimuli responsive metallogrids, and (iii) the use of hydrazones in detecting metal cations (Zn2+, Cu2+, Hg2+, etc.), anions (F−, CN−, P2O74−, etc.) and neutral molecules (amines, water, Cys, etc.).

Promotional Reviews: An Empirical Investigation of Online Review Manipulation†

Abstract: Firms' incentives to manufacture biased user reviews impede review usefulness. We examine the differences in reviews for a given hotel between two sites: Expedia.com (only a customer can post a review) and TripAdvisor.com (anyone can post). We argue that the net gains from promotional reviewing are highest for independent hotels with single-unit owners and lowest for branded chain hotels with multiunit owners. We demonstrate that the hotel neighbors of hotels with a high incentive to fake have more negative reviews on TripAdvisor relative to Expedia; hotels with a high incentive to fake have more positive reviews on TripAdvisor relative to Expedia. (JEL L15, L83, M31)

Addressing overdiagnosis and overtreatment in cancer: a prescription for change

Abstract: Summary A vast range of disorders—from indolent to fast-growing lesions—are labelled as cancer. Therefore, we believe that several changes should be made to the approach to cancer screening and care, such as use of new terminology for indolent and precancerous disorders. We propose the term indolent lesion of epithelial origin, or IDLE, for those lesions (currently labelled as cancers) and their precursors that are unlikely to cause harm if they are left untreated. Furthermore, precursors of cancer or high-risk disorders should not have the term cancer in them. The rationale for this change in approach is that indolent lesions with low malignant potential are common, and screening brings indolent lesions and their precursors to clinical attention, which leads to overdiagnosis and, if unrecognised, possible overtreatment. To minimise that potential, new strategies should be adopted to better define and manage IDLEs. Screening guidelines should be revised to lower the chance of detection of minimal-risk IDLEs and inconsequential cancers with the same energy traditionally used to increase the sensitivity of screening tests. Changing the terminology for some of the lesions currently referred to as cancer will allow physicians to shift medicolegal notions and perceived risk to reflect the evolving understanding of biology, be more judicious about when a biopsy should be done, and organise studies and registries that offer observation or less invasive approaches for indolent disease. Emphasis on avoidance of harm while assuring benefit will improve screening and treatment of patients and will be equally effective in the prevention of death from cancer.

Integration of Online and Offline Channels in Retail: The Impact of Sharing Reliable Inventory Availability Information

Abstract: Using a proprietary dataset, we analyze the impact of the implementation of a “buy-online, pickup-in-store” (BOPS) project. The implementation of this project is associated with a reduction in online sales and an increase in store sales and traffic. These results can be explained by two simultaneous phenomena: (1) additional store sales from customers who use the BOPS functionality and buy additional products in the stores (cross-selling effect) and (2) the shift of some customers from the online to the brick-and-mortar channel and the conversion of noncustomers into store customers (channel-shift effect). We explain these channel shift patterns as an increase in “research online, purchase offline” (ROPO) behavior enabled by BOPS implementation, and we validate this explanation with evidence from the change of cart abandonment and conversion rates of the brick-and-mortar and online channels. We interpret these results in light of recent operations management literature that analyzes the impact of sharing inventory availability information. Our analysis illustrates the limitations of drawing conclusions about complex interventions using single-channel data.

Reference-free cell mixture adjustments in analysis of DNA methylation data

Abstract: Motivation: Recently there has been increasing interest in the effects of cell mixture on the measurement of DNA methylation, specifically the extent to which small perturbations in cell mixture proportions can register as changes in DNA methylation. A recently published set of statistical methods exploits this association to infer changes in cell mixture proportions, and these methods are presently being applied to adjust for cell mixture effect in the context of epigenome-wide association studies. However, these adjustments require the existence of reference datasets, which may be laborious or expensive to collect. For some tissues such as placenta, saliva, adipose or tumor tissue, the relevant underlying cell types may not be known. Results: We propose a method for conducting epigenome-wide association studies analysis when a reference dataset is unavailable, including a bootstrap method for estimating standard errors. We demonstrate via simulation study and several real data analyses that our proposed method can perform as well as or better than methods that make explicit use of reference datasets. In particular, it may adjust for detailed cell type differences that may be unavailable even in existing reference datasets. Availability and implementation: Software is available in the R package RefFreeEWAS. Data for three of four examples were obtained from Gene Expression Omnibus (GEO), accession numbers GSE37008, GSE42861 and GSE30601, while reference data were obtained from GEO accession number GSE39981. Contact: andres.houseman@oregonstate.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Integration of Online and Offline Channels in Retail: The Impact of Sharing Reliable Inventory Availability Information

Abstract: Using a proprietary data set, we analyze the impact of the implementation of a “buy-online, pick-up-in-store” BOPS project. The implementation of this project is associated with a reduction in online sales and an increase in store sales and traffic. These results can be explained by two simultaneous phenomena: 1 additional store sales from customers who use the BOPS functionality and buy additional products in the stores cross-selling effect and 2 the shift of some customers from the online to the brick-and-mortar channel and the conversion of noncustomers into store customers channel-shift effect. We explain these channel-shift patterns as an increase in “research online, purchase offline” behavior enabled by BOPS implementation, and we validate this explanation with evidence from the change of cart abandonment and conversion rates of the brick-and-mortar and online channels. We interpret these results in light of recent operations management literature that analyzes the impact of sharing inventory availability information. Our analysis illustrates the limitations of drawing conclusions about complex interventions using single-channel data. This paper was accepted by Alok Gupta, special issue on business analytics.

An open science resource for establishing reliability and reproducibility in functional connectomics

Abstract: Efforts to identify meaningful functional imaging-based biomarkers are limited by the ability to reliably characterize inter-individual differences in human brain function. Although a growing number of connectomics-based measures are reported to have moderate to high test-retest reliability, the variability in data acquisition, experimental designs, and analytic methods precludes the ability to generalize results. The Consortium for Reliability and Reproducibility (CoRR) is working to address this challenge and establish test-retest reliability as a minimum standard for methods development in functional connectomics. Specifically, CoRR has aggregated 1,629 typical individuals’ resting state fMRI (rfMRI) data (5,093 rfMRI scans) from 18 international sites, and is openly sharing them via the International Data-sharing Neuroimaging Initiative (INDI). To allow researchers to generate various estimates of reliability and reproducibility, a variety of data acquisition procedures and experimental designs are included. Similarly, to enable users to assess the impact of commonly encountered artifacts (for example, motion) on characterizations of inter-individual variation, datasets of varying quality are included.