Immunomodulatory Effects of Anadenanthera colubrina Bark Extract in Experimental Autoimmune Encephalomyelitis.

This study aimed to evaluate the efficacy of the ethanolic extract of Anadenanthera colubrina in modulating the immune response in the Experimental Autoimmune Encephalomyelitis (EAE) model. The ethanolic extract of the dried bark was analyzed by ESI (+) Orbitrap-MS to obtain a metabolite profile, demonstrating a wide variety of polyphenols, such as flavonoids and phenolic acids. Various parameters were evaluated, such as clinical signs, cytokines, cellular profile, and histopathology in the central nervous system (CNS). The ethanolic extract of A. colubrina demonstrated significant positive effects attenuating the clinical signs and pathological processes associated with EAE. The beneficial effects of the extract treatment were evidenced by reduced levels of pro-inflammatory cytokines, such as IL1ß, IL-6, IL-12, TNF, IFN-γ, and a notable decrease in several cell profiles, including CD8+, CD4+, CD4+IFN-γ, CD4+IL-17+, CD11c+MHC-II+, CD11+CD80+, and CD11+CD86+ in the CNS. In addition, histological analysis revealed fewer inflammatory infiltrates and demyelination sites in the spinal cord of mice treated with the extract compared to the control model group. These results showed, for the first time, that the ethanolic extract of A. colubrina exerts a modulatory effect on inflammatory processes, improving clinical signs in EAE, in the acute phase of the disease, which could be further explored as a possible therapeutic alternative.

Antifungal, molecular docking and cytotoxic effect of the essential oil of Cymbopogon citratus (DC) Stapf. and Cymbopogon nardus (L.) Rendle against Candida albicans.

Brazil is renowned for its extensive plant biodiversity, with emphasis on Cymbopogon, C. citratus and C. nardus, with broad antimicrobial potential. Candidemias caused by Candida albicans are highly prevalent in immunosuppressed individuals and are associated with infections by biofilms on medical devices. The aim of this study was to evaluate the antimicrobial potential of essential oils C. citratus and C. nardus against C. albicans in planktonic and biofilm forms. Essential oils were obtained by hydrodistillation and chemical composition evaluated by GC-FID and GC-MS. The minimum inhibitory concentration was determined by the broth microdilution method and the synergy effect of essential oils and amphotericin B were evaluated by the checkerboard test. Biofilm activity was determined by the XTT assay. Cytotoxicity assays performed with VERO cells and molecular docking were performed to predict the effect of oil interaction on the SAP-5 enzyme site. The results showed activity of essential oils against planktonic cells and biofilm of C. albicans. Furthermore, the oils had a synergistic effect, and low cytotoxicity. Molecular docking showed interaction between Cadinene, Caryophyllen oxide, Germacrene D with SAP-5. The results indicate that Cymbopogon spp. studied are anti-Candida, with potential for further application in therapy against infections caused by C. albicans.

The Modulation of Septic Shock: A Proteomic Approach.

Sepsis poses a significant challenge due its lethality, involving multiple organ dysfunction and impaired immune responses. Among several factors affecting sepsis, monocytes play a crucial role; however, their phenotype, proteomic profile, and function in septic shock remain unclear. Our aim was to fully characterize the subpopulations and proteomic profiles of monocytes seen in septic shock cases and discuss their possible impact on the disease. Peripheral blood monocyte subpopulations were phenotype based on CD14/CD16 expression by flow cytometry, and proteins were extracted from the monocytes of individuals with septic shock and healthy controls to identify changes in the global protein expression in these cells. Analysis using 2D-nanoUPLC-UDMSE identified 67 differentially expressed proteins in shock patients compared to controls, in which 44 were upregulated and 23 downregulated. These proteins are involved in monocyte reprogramming, immune dysfunction, severe hypotension, hypo-responsiveness to vasoconstrictors, vasodilation, endothelial dysfunction, vascular injury, and blood clotting, elucidating the disease severity and therapeutic challenges of septic shock. This study identified critical biological targets in monocytes that could serve as potential biomarkers for the diagnosis, prognosis, and treatment of septic shock, providing new insights into the pathophysiology of the disease.

Thurston Geometries in Three-Dimensional New Massive Gravity.

We show that the three-dimensional Thurston geometries are vacuum solutions to the 3D new massive gravity equations of motion. We analyze their Lorentzian counterparts as well.

One-Step Immobilization of Antibodies and DNA on Gold Sensor Surfaces via a Poly-Adenine Oligonucleotide Approach.

Label-free plasmonic biosensors have demonstrated promising capabilities as analytical tools for the detection of virtually any type of biomarker. They are presented as good candidates for precision diagnostics since they offer highly sensitive, cost-effective solutions that can be used in any clinical or laboratory setting without the need for specialized trainees. However, different surface functionalization protocols are required, depending on the nature of the biorecognition element, limiting their capabilities for integrated multi-biomarker detection. Here, we present a simple, yet efficient, one-step immobilization approach that is common for both DNA probes and antibodies. Our immobilization approach relies on the incorporation of poly-adenine (polyA) blocks in both nucleic acid probes and antibodies. PolyA sequences have a remarkable affinity for gold surfaces and can specifically interact with sufficient strength to generate stable, dense, and highly ordered monolayers. We have demonstrated excellent performance of our universal functionalization method, showing limits of detection and quantification in the pM-nM range. Moreover, it was able to reduce up to 50% of the background signal from undiluted serum samples compared to conventional methods, demonstrating the immense potential of this strategy for the direct analysis of human biofluids, essential for rapid point-of-care diagnostics. The polyA-based immobilization approach is a promising alternative for the generation of multiplexed biosensors that can detect both protein and nucleic acid biomarkers for multiparametric diagnostic assays.

Mutational Profiling of Driver Tumor Suppressor and Oncogenic Genes in Brazilian Malignant Pleural Mesotheliomas.

BACKGROUND: Malignant pleural mesothelioma (MPM) is a highly lethal disease comprising a heterogeneous group of tumors with challenging to predict biological behavior. The diagnosis is complex, and the histologic classification includes 2 major subtypes of MPM: epithelioid (∼60% of cases) and sarcomatous (∼20%). Its identification depends upon pathological investigation supported by clinical and radiological evidence and more recently ancillary molecular testing. Treatment options are currently limited, with no known targeted therapies available. OBJECTIVES: To elucidate the mutation profile of driver tumor suppressor and oncogenic genes in a cohort of Brazilian patients. METHODS: We sequenced 16 driver genes in a series of 43 Brazilian malignant mesothelioma (MM) patients from 3 distinct Brazilian centers. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumor tissue blocks, and the TERT promoter region was amplified by PCR followed by direct capillary sequencing. The Illumina TruSight Tumor 15 was used to evaluate 250 amplicons from 15 genes associated with solid tumors (AKT1, GNA11, NRAS, BRAF, GNAQ, PDGFRA, EGFR, KIT, PIK3CA, ERBB2, KRAS, RET, FOXL2, MET,and TP53). Library preparation with the TruSight Tumor 15 was performed before sequencing at the MiSeq platform. Data analysis was performed using Sophia DDM software. RESULTS: Out of 43 MPM patients, 38 (88.4%) were epithelioid subtype and 5 (11.6%) were sarcomatoid histotype. Asbestos exposure was present in 15 (39.5%) patients with epithelioid MPM and 3 (60%) patients with sarcomatoid MPM. We found a TERT promoter mutation in 11.6% of MM, and the c.-146C>T mutation was the most common event. The next-generation sequencing was successful in 33 cases. A total of 18 samples showed at least 1 pathogenic, with a median of 1.8 variants, ranging from 1 to 6. The most mutated genes were TP53 and ERBB2 with 7 variants each, followed by NRAS BRAF, PI3KCA, EGFR and PDGFRA with 2 variants each. KIT, AKT1, and FOXL2 genes exhibited 1 variant each. Interestingly, 2 variants observed in the PDGFRA gene are classic imatinib-sensitive therapy. CONCLUSIONS: We concluded that Brazilian MPM harbor mutation in classic tumor suppressor and oncogenic genes, which might help in the guidance of personalized treatment of MPM.

Site-Specific mRNA Cleavage for Selective and Quantitative Profiling of Alternative Splicing with Label-Free Optical Biosensors.

Alternative splicing of mRNA precursors is a key process in gene regulation, contributing to the diversity of proteomes by the alternative selection of exonic sequences. Alterations in this mechanism are associated with most cancers, enhancing their proliferation and survival, and can be employed as cancer biomarkers. Label-free optical biosensors are ideal tools for the highly sensitive and label-free analysis of nucleic acids. However, their application for alternative splicing analysis has been hampered due to the formation of complex and intricate long-range base-pairing interactions which make the direct detection in mRNA isoforms difficult. To solve this bottleneck, we introduce a methodology for the generation of length-controlled RNA fragments from purified total RNA, which can be easily detected by the biosensor. The methodology seizes RNase H enzyme activity to degrade the upstream and downstream RNA segments flanking the target sequence upon hybridization to specific DNA oligos. It allows the fast and direct monitoring of Fas gene alternative splicing in real time, employing a surface plasmon resonance biosensor. We demonstrate the selective and specific detection of mRNA fragments in the pM-nM concentration range, reducing quantification errors and showing 81% accuracy when compared to RT-qPCR. The site-specific cleavage outperformed random RNA hydrolysis by increasing the detection accuracy by 20%, making this methodology particularly appropriate for label-free quantification of alternative splicing events in complex samples.

An Ultrasensitive Silicon Photonic Ion Sensor Enabled by 2D Plasmonic Molybdenum Oxide.

Silicon photonics has demonstrated great potential in ultrasensitive biochemical sensing. However, it is challenging for such sensors to detect small ions which are also of great importance in many biochemical processes. A silicon photonic ion sensor enabled by an ionic dopant-driven plasmonic material is introduced here. The sensor consists of a microring resonator (MRR) coupled with a 2D restacked layer of near-infrared plasmonic molybdenum oxide. When the 2D plasmonic layer interacts with ions from the environment, a strong change in the refractive index results in a shift in the MRR resonance wavelength and simultaneously the alteration of plasmonic absorption leads to the modulation of MRR transmission power, hence generating dual sensing outputs which is unique to other optical ion sensors. Proof-of-concept via a pH sensing model is demonstrated, showing up to 7 orders improvement in sensitivity per unit area across the range from 1 to 13 compared to those of other optical pH sensors. This platform offers the unique potential for ultrasensitive and robust measurement of changes in ionic environment, generating new modalities for on-chip chemical sensors in the micro/nanoscale.

Optical frequency comb based system for photonic refractive index sensor interrogation.

In this contribution, we demonstrate how an optical frequency comb can be used to enhance the functionality of an integrated photonic biosensor platform. We show that if an optical frequency comb is used to sample the spectral response of a Mach-Zehnder interferometer and if the line spacing is arranged to sample the periodic response at 120° intervals, then it is possible to combine these samples into a single measurement of the interferometer phase. This phase measurement approach is accurate, independent of the bias of the interferometer and robust against intensity fluctuations that are common to each of the comb lines. We demonstrate this approach with a simple silicon photonic interferometric refractive index sensor and show that the benefits of our approach can be obtained without degrading the lower limit of detection of 3.70×10-7 RIU.

Free phenolic compounds extraction from Brazilian halophytes, soybean and rice bran by ultrasound-assisted and orbital shaker methods.

In several countries halophytes are commercially cultivated in low saline or even irrigated with seawater, as well as with saline aquaculture effluent, like a sea asparagus Sarcocornia ambigua, that show a biotechnological potential for bioactive compounds production. However, their recovery from matrix is sometimes inefficient because the lignocellulosic materials difficult the solvent action when drastic conditions are not applied. The ultrasound-assisted extraction (UAE) was optimized by a central composite rotational design for recovery free phenolic compounds (FPC) from the sea asparagus S. ambigua. Optimum conditions were validated and compared with orbital shaker extraction for S. ambigua, other Brazilian halophytes (Apium graveolens, Myrsine parvifolia, Paspalum vaginatum, and Schinus terebinthifolius), soybean and rice bran. Except for P. vaginatum, soybean and rice bran, UAE yielded 18-29% higher FPC than that of the orbital shaker. Besides this analytical performance UAE method optimized is faster than the orbital shaker, providing shorter exposure of the analyst to the extractor solvent and applicable in matrices with different compositions. It was also demonstrated that halophytes species showed to be good natural sources of FPC in a better way as soybean and rice bran. This work was the first to report FPC in M. parvifolia and P. vaginatum.

Anomalocardia brasiliana shellfish shells as a novel and ecofriendly adsorbent of Nylosan Brilliant Blue acid dye.

Malacoculture waste (Anomalocardia brasiliana) shellfish shells (ABSS) were evaluated as adsorbents of Nylosan Brilliant Blue (NBB) acid dye. The ABSS were thermally activated at 1,000 °C for 10 h and then characterized by Fourier-transform infrared spectroscopy, analysis of specific surface area (BET), X-ray diffraction (XRD), and scanning electron microscopy. Point of zero charge (PZC) analysis of ABSS verified pHPZC 13.0. The study of kinetics showed that the pseudo-second-order model fit the experimental data best and the system reached equilibrium within 5 min. Adsorption isotherms followed the Langmuir-Freundlich isotherm and ABSS reached an outstanding maximum adsorption capacity of 405 mg·g-1 under the following optimum conditions: pH 12.4, 303 K, 450 rpm, 2.0 g of adsorbent, and 150 µm average particle size. These conditions were obtained after a previous statistical analysis of the variables. Enthalpy and Gibbs energy obtained in the thermodynamics experiments were -23.79 kJ·mol-1 and -4.07 kJ·mol-1, respectively. These parameters confirm that the process is exothermic, spontaneous, and indicative of the physical nature of the adsorption. The adsorption of NBB onto ABSS tended to be more favorable at a lower temperature. Low value of enthalpy suggested that weak binding forces, such as electrostatic interactions, govern the sorption mechanism. ABSS high availability in the environment, its low toxicity and high efficiency make it a promising ecofriendly adsorbent of textile dyes.

Structural insights from a novel invertebrate triosephosphate isomerase from Litopenaeus vannamei.

Triosephosphate isomerase (TIM; EC 5.3.1.1) is a key enzyme involved in glycolysis and gluconeogenesis. Glycolysis is one of the most regulated metabolic pathways, however little is known about the structural mechanisms for its regulation in non-model organisms, like crustaceans. To understand the structure and function of this enzyme in invertebrates, we obtained the crystal structure of triosephosphate isomerase from the marine Pacific whiteleg shrimp (Litopenaeus vannamei, LvTIM) in complex with its inhibitor 2-phosphogyceric acid (2-PG) at 1.7Å resolution. LvTIM assembles as a homodimer with residues 166-176 covering the active site and residue Glu166 interacting with the inhibitor. We found that LvTIM is the least stable TIM characterized to date, with the lowest range of melting temperatures, and with the lowest activation enthalpy associated with the thermal unfolding process reported. In TIMs dimer stabilization is maintained by an interaction of loop 3 by a set of hydrophobic contacts between subunits. Within these contacts, the side chain of a hydrophobic residue of one subunit fits into a cavity created by a set of hydrophobic residues in the neighboring subunit, via a "ball and socket" interaction. LvTIM presents a Cys47 at the "ball" inter-subunit contact indicating that the character of this residue is responsible for the decrease in dimer stability. Mutational studies show that this residue plays a role in dimer stability but is not a solely determinant for dimer formation.

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome.

Ruminant livestock represent the single largest anthropogenic source of the potent greenhouse gas methane, which is generated by methanogenic archaea residing in ruminant digestive tracts. While differences between individual animals of the same breed in the amount of methane produced have been observed, the basis for this variation remains to be elucidated. To explore the mechanistic basis of this methane production, we measured methane yields from 22 sheep, which revealed that methane yields are a reproducible, quantitative trait. Deep metagenomic and metatranscriptomic sequencing demonstrated a similar abundance of methanogens and methanogenesis pathway genes in high and low methane emitters. However, transcription of methanogenesis pathway genes was substantially increased in sheep with high methane yields. These results identify a discrete set of rumen methanogens whose methanogenesis pathway transcription profiles correlate with methane yields and provide new targets for CH4 mitigation at the levels of microbiota composition and transcriptional regulation.

Does Physician Reimbursement Correlate to Risk in Orthopaedic Trauma?

This study investigated whether current Medicare reimbursements for orthopaedic trauma procedures correlate with complications. A total of 18,510 patients representing 33 orthopaedic trauma procedures from 2005 to 2011 were studied. Adverse events and Medicare payments for each orthopaedic trauma procedure were collected. Linear regressions determined correlations between complications and Medicare payments for orthopaedic trauma procedures. A weak correlation between Medicare payments and complications was found for all procedures (r = .399, p = .021). A 1.0% increase in complications was associated with a payment increase of only $100. There were no correlations between complications and reimbursements for upper extremity (p = .878) and lower extremity (p = .713) procedures. A strong correlation (r = .808, p = .015) existed for hip and pelvic fractures, but a 1.1% increase in hip and pelvic complications correlated with only an increase of $100 in reimbursements. This study is the first to show that Medicare payments are not strongly correlated with complications, therefore demonstrating the potential risks of a bundled payment system for orthopaedic trauma surgeons.

Comparative proteome analysis reveals that blood and sugar meals induce differential protein expression in Aedes aegypti female heads.

Aedes aegypti females ingest sugar or blood to obtain the nutrients needed to maintain cellular homeostasis. During human blood ingestion, female mosquitoes may transmit different viruses such as dengue, yellow fever and, more recently, zika and chikungunya. Here, we report changes in protein expression in the heads of adult female Ae. aegypti mosquitoes in response to the ingestion of blood or sugar. Proteins extracted from the heads of Ae. aegypti fed exclusively on blood (BF) or sugar (SF) were trypsin hydrolyzed (off-gel) and analyzed by the reverse-phase nano-liquid chromatography coupled with hybrid mass spectrometry. A total of 1139 proteins were identified in female heads, representing 7.4% of the predicted proteins in Ae. aegypti genome (total = 15 419 active genes). Gene ontology annotation and categories showed that, in this insect, the head was rich in proteins involved in the metabolic process, proton transport, organelle, macromolecular complex, structural molecule activity, antioxidant activity, and catalytic activity. Our report is the first indicating that many of the annotated genes are translated into functional proteins in heads of adult female Ae. aegypti. Interestingly, we identified 8.7 times more exclusively expressed proteins involved in signal transduction, replication-transcription-translation (5.5 x), and transport (2.9 x) activity in BF than in SF groups. This paper discusses the protein profile of Ae. aegypti female heads and its implications for blood ingestion and carbohydrate intake.

Natural variation in methane emission of sheep fed on a lucerne pellet diet is unrelated to rumen ciliate community type.

Only limited information is available on the roles of different rumen ciliate community types, first described by Eadie in 1962, in enteric methane (CH4) formation by their ruminant hosts. If the different types were differentially associated with CH4 formation, then ciliate community typing could be used to identify naturally high and low CH4-emitting animals. Here we measured the CH4 yields [g CH4 (kg feed dry matter intake, DMI)(-1)] of 118 sheep fed a standard pelleted lucerne diet at two different times, at least 2 weeks apart. There were significant differences (P < 2.2 × 10(-16), Wilcoxon rank sum test) in the CH4 yields (± sd) from sheep selected as high [16.7 ± 1.5 g CH4 (kg DMI)(-1)] and low emitters [13.3 ± 1.5 g CH4 (kg DMI)(-1)]. A rumen sample was collected after each of the two measurements, and ciliate composition was analysed using barcoded 454 Titanium pyrosequencing of 18S rRNA genes. The genera found, in order of mean relative abundance, were Epidinium, Entodinium, Dasytricha, Eudiplodinium, Polyplastron, Isotricha and Anoplodinium-Diplodinium, none of which was significantly correlated with the CH4 emissions ranking associated with the rumen sample. Ciliate communities naturally assembled into four types (A, AB, B and O), characterized by the presence and absence of key genera. There was no difference in CH4 yield between sheep that harboured different ciliate community types, suggesting that these did not underlie the natural variation in CH4 yields. Further research is needed to unravel the nature of interactions between ciliate protozoa and other rumen micro-organisms, which may ultimately lead to contrasting CH4 emission phenotypes.

Sensitive and label-free detection of miRNA-145 by triplex formation.

The development of new strategies for detecting microRNAs (miRNAs) has become a crucial step in the diagnostic field. miRNA profiles depend greatly on the sample and the analytical platform employed, leading sometimes to contradictory results. In this work, we study the use of modified parallel tail-clamps to detect a miRNA sequence involved in tumor suppression by triplex formation. Thermal denaturing curves and circular dichroism (CD) measurements have been performed to confirm that parallel clamps carrying 8-aminoguanine form the most stable triplex structures with their target miRNA. The modified tail-clamps have been tested as bioreceptors in a surface plasmon resonance (SPR) biosensor for the detection of miRNA-145. The detection limit was improved 2.4 times demonstrating that a stable triplex structure is formed between target miRNA and 8-aminoguanine tail-clamp bioreceptor. This new approach is an essential step toward the label-free and reliable detection of miRNA signatures for diagnostic purposes.

Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing.

We explored the detection of genome-wide hypomethylation in plasma using shotgun massively parallel bisulfite sequencing as a marker for cancer. Tumor-associated copy number aberrations (CNAs) could also be observed from the bisulfite DNA sequencing data. Hypomethylation and CNAs were detected in the plasma DNA of patients with hepatocellular carcinoma, breast cancer, lung cancer, nasopharyngeal cancer, smooth muscle sarcoma, and neuroendocrine tumor. For the detection of nonmetastatic cancer cases, plasma hypomethylation gave a sensitivity and specificity of 74% and 94%, respectively, when a mean of 93 million reads per case were obtained. Reducing the sequencing depth to 10 million reads per case was found to have no adverse effect on the sensitivity and specificity for cancer detection, giving respective figures of 68% and 94%. This characteristic thus indicates that analysis of plasma hypomethylation by this sequencing-based method may be a relatively cost-effective approach for cancer detection. We also demonstrated that plasma hypomethylation had utility for monitoring hepatocellular carcinoma patients following tumor resection and for detecting residual disease. Plasma hypomethylation can be combined with plasma CNA analysis for further enhancement of the detection sensitivity or specificity using different diagnostic algorithms. Using the detection of at least one type of aberration to define an abnormality, a sensitivity of 87% could be achieved with a specificity of 88%. These developments have thus expanded the applications of plasma DNA analysis for cancer detection and monitoring.

Quantification of gait parameters in freely walking rodents.

BACKGROUND: Qualitative and quantitative measurements of motor performance are essential for characterizing perturbations of motor systems. Although several methods exist for analyzing specific motor tasks, few behavioral assays are readily available to researchers that provide a complete set of kinematic parameters in rodents. RESULTS: Here we present MouseWalker, an integrated hardware and software system that provides a comprehensive and quantitative description of kinematic features in freely walking rodents. Footprints are visualized with high spatial and temporal resolution by a non-invasive optical touch sensor coupled to high-speed imaging. A freely available and open-source software package tracks footprints and body features to generate a comprehensive description of many locomotion features, including static parameters such as footprint position and stance patterns and dynamic parameters, such as step and swing cycle duration, and inter-leg coordination. Using this method, we describe walking by wild-type mice including several previously undescribed parameters. For example, we demonstrate that footprint touchdown occurs instantaneously by the entire paw with no obvious rostral-caudal or lateral-medial bias. CONCLUSIONS: The readily available MouseWalker system and the large set of readouts it generates greatly increases the currently available toolkit for the analysis of wild type and aberrant locomotion in rodents.

DECODE: an integrated differential co-expression and differential expression analysis of gene expression data.

BACKGROUND: Both differential expression (DE) and differential co-expression (DC) analyses are appreciated as useful tools in understanding gene regulation related to complex diseases. The performance of integrating DE and DC, however, remains unexplored. RESULTS: In this study, we proposed a novel analytical approach called DECODE (Differential Co-expression and Differential Expression) to integrate DC and DE analyses of gene expression data. DECODE allows one to study the combined features of DC and DE of each transcript between two conditions. By incorporating information of the dependency between DC and DE variables, two optimal thresholds for defining substantial change in expression and co-expression are systematically defined for each gene based on chi-square maximization. By using these thresholds, genes can be categorized into four groups with either high or low DC and DE characteristics. In this study, DECODE was applied to a large breast cancer microarray data set consisted of two thousand tumor samples. By identifying genes with high DE and high DC, we demonstrated that DECODE could improve the detection of some functional gene sets such as those related to immune system, metastasis, lipid and glucose metabolism. Further investigation on the identified genes and the associated functional pathways would provide an additional level of understanding of complex disease mechanism. CONCLUSIONS: By complementing the recent DC and the traditional DE analyses, DECODE is a valuable methodology for investigating biological functions of genes exhibiting disease-associated DE and DC combined characteristics, which may not be easily revealed through DC or DE approach alone. DECODE is available at the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/decode/index.html .