Challenges and Opportunities with Causal Discovery Algorithms: Application to Alzheimer's Pathophysiology.


:Causal Structure Discovery (CSD) is the problem of identifying causal relationships from large quantities of data through computational methods. With the limited ability of traditional association-based computational methods to discover causal relationships, CSD methodologies are gaining popularity. The goal of the study was to systematically examine whether (i) CSD methods can discover the known causal relationships from observational clinical data and (ii) to offer guidance to accurately discover known causal relationships. We used Alzheimer's disease (AD), a complex progressive disease, as a model because the well-established evidence provides a "gold-standard" causal graph for evaluation. We evaluated two CSD methods, Fast Causal Inference (FCI) and Fast Greedy Equivalence Search (FGES) in their ability to discover this structure from data collected by the Alzheimer's Disease Neuroimaging Initiative (ADNI). We used structural equation models (which is not designed for CSD) as control. We applied these methods under three scenarios defined by increasing amounts of background knowledge provided to the methods. The methods were evaluated by comparing the resulting causal relationships with the "gold standard" graph that was constructed from literature. Dedicated CSD methods managed to discover graphs that nearly coincided with the gold standard. For best results, CSD algorithms should be used with longitudinal data providing as much prior knowledge as possible.


Sci Rep


Scientific reports


Shen X,Ma S,Vemuri P,Simon G,Alzheimer’s Disease Neuroimaging Initiative.




Has Abstract


2020-02-19 00:00:00












  • Novel Rbfox2 isoforms associated with alternative exon usage in rat cortex and suprachiasmatic nucleus.

    abstract::Transcriptome diversity in adult neurons is partly mediated by RNA binding proteins (RBPs), including the RBFOX factors. RBFOX3/NeuN, a neuronal maturity marker, is strangely depleted in suprachiasmatic nucleus (SCN) neurons, and may be compensated by a change in Rbfox2 expression. In this study, we found no superfici...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Partridge LMM,Carter DA

    更新日期:2017-08-30 00:00:00

  • Canagliflozin, an SGLT2 inhibitor, attenuates the development of hepatocellular carcinoma in a mouse model of human NASH.

    abstract::Sodium glucose cotransporter 2 (SGLT2) inhibitors, an antidiabetic drug, promotes urinary excretion of glucose by blocking its reabsorption in the renal proximal tubules. It is unclear whether SGLT2 inhibition could attenuate nonalcoholic steatohepatitis (NASH) and NASH-associated hepatocellular carcinoma. We examined...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Shiba K,Tsuchiya K,Komiya C,Miyachi Y,Mori K,Shimazu N,Yamaguchi S,Ogasawara N,Katoh M,Itoh M,Suganami T,Ogawa Y

    更新日期:2018-02-05 00:00:00

  • An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations.

    abstract::Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occip...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Stayner C,Poole CA,McGlashan SR,Pilanthananond M,Brauning R,Markie D,Lett B,Slobbe L,Chae A,Johnstone AC,Jensen CG,McEwan JC,Dittmer K,Parker K,Wiles A,Blackburne W,Leichter A,Leask M,Pinnapureddy A,Jennings M,Hor

    更新日期:2017-05-09 00:00:00

  • Low cost, microcontroller based heating device for multi-wavelength differential scanning fluorimetry.

    abstract::Differential scanning fluorimetry is a popular method to estimate the stability of a protein in distinct buffer conditions by determining its 'melting point'. The method requires a temperature controlled fluorescence spectrometer or a RT-PCR machine. Here, we introduce a low-budget version of a microcontroller based h...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Hoeser J,Gnandt E,Friedrich T

    更新日期:2018-01-23 00:00:00

  • A strategy for fabricating porous PdNi@Pt core-shell nanostructures and their enhanced activity and durability for the methanol electrooxidation.

    abstract::Three-dimensionally (3D) porous morphology of nanostructures can effectively improve their electrocatalytic activity and durability for various electrochemical reactions owing to big surface area and interconnected structure. Cyanogel, a jelly-like inorganic polymer, can be used to synthesize various three-dimensional...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Liu X,Xu G,Chen Y,Lu T,Tang Y,Xing W

    更新日期:2015-01-05 00:00:00

  • Impact of nutritional supplements on cognitive development of children in developing countries: A meta-analysis.

    abstract::Nutritional supplements may be important on cognition but the evidence is heterogeneous. This meta-analysis aimed (1) to determine whether nutritional supplements provided to pregnant women or young children could improve cognitive development of children in developing countries, and (2) to explore how supplementation...

    journal_title:Scientific reports

    pub_type: 杂志文章,meta分析


    authors: Ip P,Ho FKW,Rao N,Sun J,Young ME,Chow CB,Tso W,Hon KL

    更新日期:2017-09-06 00:00:00

  • Graded pitch profile for the helicoidal broadband reflector and left-handed circularly polarizing cuticle of the scarab beetle Chrysina chrysargyrea.

    abstract::The cuticle of the beetle Chrysina chrysargyrea reflects left-handed polarized light in the broad spectral range from 340 to 1000 nm. Interference oscillations in the experimental Mueller-matrix spectroscopic ellipsometry data reveal that transparent materials comprise the cuticle. A spectral analysis of the interfere...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Mendoza-Galván A,Del Río LF,Järrendahl K,Arwin H

    更新日期:2018-04-24 00:00:00

  • Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1).

    abstract::Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Broeckx BJ,Coopman F,Verhoeven GE,Bavegems V,De Keulenaer S,De Meester E,Van Niewerburgh F,Deforce D

    更新日期:2014-07-07 00:00:00

  • One-step instant synthesis of protein-conjugated quantum dots at room temperature.

    abstract::We present a new general facile strategy for the preparation of protein-functionalized QDs in a single step at ambient conditions. We demonstrated that highly luminescent red to near-infrared (NIR) protein-functionalized QDs could be synthesized at room temperature in one second through a one-pot reaction that proceed...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: He X,Gao L,Ma N

    更新日期:2013-10-02 00:00:00

  • Regulation of aromatase expression in the anterior amygdala of the developing mouse brain depends on ERβ and sex chromosome complement.

    abstract::During development sex differences in aromatase expression in limbic regions of mouse brain depend on sex chromosome factors. Genes on the sex chromosomes may affect the hormonal regulation of aromatase expression and this study was undertaken to explore that possibility. Male E15 anterior amygdala neuronal cultures e...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Cisternas CD,Cabrera Zapata LE,Arevalo MA,Garcia-Segura LM,Cambiasso MJ

    更新日期:2017-07-13 00:00:00

  • Auranofin, at clinically achievable dose, protects mice and prevents recurrence from Clostridioides difficile infection.

    abstract::Clostridioides difficile is the leading cause of nosocomial infections and a worldwide urgent public health threat. Without doubt, there is an urgent need for new effective anticlostridial agents due to the increasing incidence and severity of C. difficile infection (CDI). The aim of the present study is to investigat...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Abutaleb NS,Seleem MN

    更新日期:2020-05-07 00:00:00

  • Metastability in lipid based particles exhibits temporally deterministic and controllable behavior.

    abstract::The metastable-to-stable phase-transition is commonly observed in many fields of science, as an uncontrolled independent process, highly sensitive to microscopic fluctuations. In particular, self-assembled lipid suspensions exhibit phase-transitions, where the underlying driving mechanisms and dynamics are not well un...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Jacoby G,Cohen K,Barkan K,Talmon Y,Peer D,Beck R

    更新日期:2015-03-30 00:00:00

  • Short-term Effects of Outdoor Air Pollution on Lung Function among Female Non-smokers in China.

    abstract::Short-term exposures to outdoor air pollutants have been associated with lower lung function, but the results are inconsistence. The effects of different pollutant levels on lung function changes are still unclear. We quantified the effects of outdoor air pollution exposure (NO2, PM10, O3, and PM2.5) on lung function ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Zhou Y,Liu Y,Song Y,Xie J,Cui X,Zhang B,Shi T,Yuan J,Chen W

    更新日期:2016-10-13 00:00:00

  • CRISRP/Cas9-mediated knockout of Mct8 reveals a functional involvement of Mct8 in testis and sperm development in a rat.

    abstract::Thyroid hormone (TH) has long been believed to play a minor role in male reproduction. However, evidences from experimental model of thyrotoxicosis or hypothyroidism suggests its role in spermatogenesis. Cellular action of TH requires membrane transport via specific transporters such as monocarboxylate transporter 8 (...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Bae HS,Jin YK,Ham S,Kim HK,Shin H,Cho GB,Lee KJ,Lee H,Kim KM,Koo OJ,Jang G,Lee JM,Lee JY

    更新日期:2020-07-07 00:00:00

  • Soil fungal community development in a high Arctic glacier foreland follows a directional replacement model, with a mid-successional diversity maximum.

    abstract::Directional replacement and directional non-replacement models are two alternative paradigms for community development in primary successional environments. The first model emphasizes turnover in species between early and late successional niches. The second emphasizes accumulation of additional diversity over time. T...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Dong K,Tripathi B,Moroenyane I,Kim W,Li N,Chu H,Adams J

    更新日期:2016-05-31 00:00:00

  • Exactin: A specific inhibitor of Factor X activation by extrinsic tenase complex from the venom of Hemachatus haemachatus.

    abstract::Unwanted clots lead to heart attack and stroke that result in a large number of deaths. Currently available anticoagulants have some drawbacks including their non-specific actions. Therefore novel anticoagulants that target specific steps in the coagulation pathway are being sought. Here we describe the identification...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Girish VM,Kini RM

    更新日期:2016-08-25 00:00:00

  • Myocardin ablation in a cardiac-renal rat model.

    abstract::Cardiorenal syndrome is defined by primary heart failure conditions influencing or leading to renal injury or dysfunction. Dilated cardiomyopathy (DCM) is a major co-existing form of heart failure (HF) with renal diseases. Myocardin (MYOCD), a cardiac-specific co-activator of serum response factor (SRF), is increased ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Mittal A,Rana S,Sharma R,Kumar A,Prasad R,Raut SK,Sarkar S,Saikia UN,Bahl A,Dhandapany PS,Khullar M

    更新日期:2019-04-10 00:00:00

  • Identifying critical recruitment bottlenecks limiting seedling establishment in a degraded seagrass ecosystem.

    abstract::Identifying early life-stage transitions limiting seagrass recruitment could improve our ability to target demographic processes most responsive to management. Here we determine the magnitude of life-stage transitions along gradients in physical disturbance limiting seedling establishment for the marine angiosperm, Po...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Statton J,Montoya LR,Orth RJ,Dixon KW,Kendrick GA

    更新日期:2017-11-01 00:00:00

  • A biphasic nanohydroxyapatite/calcium sulphate carrier containing Rifampicin and Isoniazid for local delivery gives sustained and effective antibiotic release and prevents biofilm formation.

    abstract::Long term multiple systemic antibiotics form the cornerstone in the treatment of bone and joint tuberculosis, often combined with local surgical eradication. Implanted carriers for local drug delivery have recently been introduced to overcome some of the limitations associated with conventional treatment strategies. I...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Qayoom I,Verma R,Murugan PA,Raina DB,Teotia AK,Matheshwaran S,Nair NN,Tägil M,Lidgren L,Kumar A

    更新日期:2020-08-24 00:00:00

  • Cardioprotective medication adherence in Western Australians in the first year after myocardial infarction: restricted cubic spline analysis of adherence-outcome relationships.

    abstract::Adherence to cardioprotective medications following myocardial infarction (MI) is commonly assessed using a binary threshold of 80%. We investigated the relationship between medication adherence as a continuous measure and outcomes in MI survivors using restricted cubic splines (RCS). We identified all patients aged ≥...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Greenland M,Knuiman MW,Hung J,Nedkoff L,Arnet I,Rankin JM,Kilkenny MF,Sanfilippo FM

    更新日期:2020-03-09 00:00:00

  • The effect of chemical erosion on mechanical properties and fracture of sandstone under shear loading: an experimental study.

    abstract::In order to study the effect of water-rock interactions on shear strength characteristics, we performed shearing tests under varying hydrochemical environments. Moreover, a custom meso-shear test equipment for coal rock was used for the tests. Through 3D scanning of the shear fractures and scanning electron microscope...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Chen C,Peng S,Wu S,Xu J

    更新日期:2019-12-27 00:00:00

  • Target contact and exploration strategies in haptic search.

    abstract::In a haptic search task, one has to detect the presence of a target among distractors using the sense of touch. A salient target can be detected faster than a non-salient target. However, little is known about the exploration strategies that are used, especially in 3D search tasks where items are held in the hand. In ...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: van Polanen V,Bergmann Tiest WM,Kappers AM

    更新日期:2014-09-03 00:00:00

  • Alcohol consumption and leukocyte telomere length.

    abstract::The relationship between alcohol consumption and mortality generally exhibits a U-shaped curve. The longevity observed with moderate alcohol consumption may be explained by other confounding factors, and, if such a relationship is present, the mechanism is not well understood. Indeed, the optimal amount of alcohol con...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Dixit S,Whooley MA,Vittinghoff E,Roberts JD,Heckbert SR,Fitzpatrick AL,Lin J,Leung C,Mukamal KJ,Marcus GM

    更新日期:2019-02-05 00:00:00

  • Nematode-free agricultural system of a fungus-growing termite.

    abstract::Fungus-growing termites forage dead plant materials from the field to cultivate symbiotic Termitomyces fungi in the nest. Termite foraging behavior and the entry of symbiotic arthropod inquilines may transfer nematodes into a nest and adversely affect fungus production. To test whether nematodes were transferred to fu...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Kanzaki N,Liang WR,Chiu CI,Yang CT,Hsueh YP,Li HF

    更新日期:2019-06-20 00:00:00

  • Enhancing nanoparticle-based visible detection by controlling the extent of aggregation.

    abstract::Visible indication based on the aggregation of colloidal nanoparticles (NPs) is highly advantageous for rapid on-site detection of biological entities, which even untrained persons can perform without specialized instrumentation. However, since the extent of aggregation should exceed a certain minimum threshold to pro...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Lim S,Koo OK,You YS,Lee YE,Kim MS,Chang PS,Kang DH,Yu JH,Choi YJ,Gunasekaran S

    更新日期:2012-01-01 00:00:00

  • Evidence of Enriched, Hadean Mantle Reservoir from 4.2-4.0 Ga zircon xenocrysts from Paleoarchean TTGs of the Singhbhum Craton, Eastern India.

    abstract::Sensitive High-Resolution Ion Microprobe (SHRIMP) U-Pb analyses of zircons from Paleoarchean (~3.4 Ga) tonalite-gneiss called the Older Metamorphic Tonalitic Gneiss (OMTG) from the Champua area of the Singhbhum Craton, India, reveal 4.24-4.03 Ga xenocrystic zircons, suggesting that the OMTG records the hitherto unknow...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Chaudhuri T,Wan Y,Mazumder R,Ma M,Liu D

    更新日期:2018-05-04 00:00:00

  • A Steep-Slope Transistor Combining Phase-Change and Band-to-Band-Tunneling to Achieve a sub-Unity Body Factor.

    abstract::Steep-slope transistors allow to scale down the supply voltage and the energy per computed bit of information as compared to conventional field-effect transistors (FETs), due to their sub-60 mV/decade subthreshold swing at room temperature. Currently pursued approaches to achieve such a subthermionic subthreshold swin...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Vitale WA,Casu EA,Biswas A,Rosca T,Alper C,Krammer A,Luong GV,Zhao QT,Mantl S,Schüler A,Ionescu AM

    更新日期:2017-03-23 00:00:00

  • Short range magnetic exchange interaction favors ferroelectricity.

    abstract::Multiferroics, where two or more ferroic order parameters coexist, is one of the hottest fields in condensed matter physics and materials science. To search multiferroics, currently most researches are focused on frustrated magnets, which usually have complicated magnetic structure and low magnetic ordering temperatur...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Wan X,Ding HC,Savrasov SY,Duan CG

    更新日期:2016-03-09 00:00:00

  • Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer.

    abstract::Bivalent (poised or paused) chromatin comprises activating and repressing histone modifications at the same location. This combination of epigenetic marks at promoter or enhancer regions keeps genes expressed at low levels but poised for rapid activation. Typically, DNA at bivalent promoters is only lowly methylated i...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Bernhart SH,Kretzmer H,Holdt LM,Jühling F,Ammerpohl O,Bergmann AK,Northoff BH,Doose G,Siebert R,Stadler PF,Hoffmann S

    更新日期:2016-11-23 00:00:00

  • Origin and classification of spontaneous discharges in mouse superficial dorsal horn neurons.

    abstract::Superficial laminae of the spinal cord possess a considerable number of neurons with spontaneous activity as reported in vivo and in vitro preparations of several species. Such neurons may play a role in the development of the nociceptive system and/or in the spinal coding of somatosensory signals. We have used electr...

    journal_title:Scientific reports

    pub_type: 杂志文章


    authors: Lucas-Romero J,Rivera-Arconada I,Roza C,Lopez-Garcia JA

    更新日期:2018-06-27 00:00:00