Search

Abstract Background The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739–57. https://doi.org/10.1093/plphys/kiab311 .). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties. Results We developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z .) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of $$\:40{0}^{3}$$ on a desktop workstation. Our software and test dataset are freely distributed on Github. Conclusions TopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping.

Abstract Background and aim Liver failure, which is predominantly caused by hepatitis B (HBV) can be improved by an artificial liver support system (ALSS). This study investigated the phenotypic heterogeneity of immunocytes in patients with HBV-related acute-on-chronic liver failure (HBV-ACLF) before and after ALSS therapy. Methods A total of 22 patients with HBV-ACLF who received ALSS therapy were included in the study. Patients with Grade I according to the ACLF Research Consortium score were considered to have improved. Demographic and laboratory data were collected and analyzed during hospitalization. Immunological features of peripheral blood in the patients before and after ALSS were detected by mass cytometry analyses. Results In total, 12 patients improved and 10 patients did not. According to the immunological features data after ALSS, the proportion of circulating monocytes was significantly higher in non-improved patients, but there were fewer γδT cells compared with those in improved patients. Characterization of 37 cell clusters revealed that the frequency of effector CD8+ T (P = 0.003), CD4+ TCM (P = 0.033), CD4+ TEM (P = 0.039), and inhibitory natural killer (NK) cells (P = 0.029) decreased in HBV-ACLF patients after ALSS therapy. Sub group analyses after treatment showed that the improved patients had higher proportions of CD4+ TCM (P = 0.010), CD4+ TEM (P = 0.021), and γδT cells (P = 0.003) and a lower proportion of monocytes (P = 0.012) compared with the non-improved patients. Conclusions Changes in effector CD8+ T cells, effector and memory CD4+ T cells, and inhibitory NK cells are associated with ALSS treatment of HBV-ACLF. Moreover, monocytes and γδT cells exhibited the main differences when patients obtained different prognoses. The phenotypic heterogeneity of lymphocytes and monocytes may contribute to the prognosis of ALSS and future immunotherapy strategies.

In this article, we propose and demonstrate a probe-type multi-core fiber (MCF) sensor for the multi-parameter measurement of seawater. The sensor comprises an MCF and two capillary optical fibers (COFs) with distinct inner diameters, in which a 45° symmetric core reflection (SCR) structure and a step-like inner diameter capillary (SIDC) structure filled with polydimethylsiloxane (PDMS) are fabricated at the fiber end. The sensor is equipped with three channels for different measurements. The surface plasmon resonance (SPR) channel (CHSPR) based on the side-polished MCF is utilized for salinity measurement. The fiber end air cavity, forming the Fabry–Pérot interference (FPI) channel (CHFPI), is utilized for pressure and temperature measurement. Additionally, the fiber Bragg grating (FBG) channel (CHFBG), which is inscribed in the central core, serves as temperature compensation for the measurement results. By combining three sensing principles with space division multiplexing (SDM) technology, the sensor overcomes the common challenges faced by multi-parameter sensors, such as channel crosstalk and signal demodulation difficulties. The experimental results indicate that the sensor has sensitivities of 0.36 nm/‰, −10.62 nm/MPa, and −0.19 nm/°C for salinity, pressure, and temperature, respectively. As a highly integrated and easily demodulated probe-type optical fiber sensor, it can serve as a valuable reference for the development of multi-parameter fiber optic sensors.

Abstract Background Transcriptome-wide association studies (TWASs) have shown great promise in interpreting the findings from genome-wide association studies (GWASs) and exploring the disease mechanisms, by integrating GWAS and eQTL mapping studies. Almost all TWAS methods only focus on one gene at a time, with exception of only two published multiple-gene methods nevertheless failing to account for the inter-dependence as well as the network structure among multiple genes, which may lead to power loss in TWAS analysis as complex disease often owe to multiple genes that interact with each other as a biological network. We therefore developed a Network Regression method in a two-stage TWAS framework (NeRiT) to detect whether a given network is associated with the traits of interest. NeRiT adopts the flexible Bayesian Dirichlet process regression to obtain the gene expression prediction weights in the first stage, uses pointwise mutual information to represent the general between-node correlation in the second stage and can effectively take the network structure among different gene nodes into account. Results Comprehensive and realistic simulations indicated NeRiT had calibrated type I error control for testing both the node effect and edge effect, and yields higher power than the existed methods, especially in testing the edge effect. The results were consistent regardless of the GWAS sample size, the gene expression prediction model in the first step of TWAS, the network structure as well as the correlation pattern among different gene nodes. Real data applications through analyzing systolic blood pressure and diastolic blood pressure from UK Biobank showed that NeRiT can simultaneously identify the trait-related nodes as well as the trait-related edges. Conclusions NeRiT is a powerful and efficient network regression method in TWAS.

BackgroundMinimal change disease (MCD) is one of the most common primary glomerular disorders with high serum IgE levels. This study was aimed to investigate the clinical features of different serum IgE levels in pediatric MCD and evaluate the prognostic significance of serum IgE levels with regard to remission and relapse in pediatric cohort.MethodsThis study enrolled 142 new-onset children diagnosed with biopsy-proven MCD from January 2010 to December 2021 at the Jinling Hospital in Nanjing, China. These cases were divided into three groups according to serum IgE levels. MCD patients’ demographics, clinical parameters, and follow-up data were collected and analyzed. The primary and secondary outcomes were defined as the time to the first complete remission (CR) and the first relapse.ResultsThe results manifested that 85.2% (121/142) of MCD children had high serum IgE levels (IgE > 90.0 IU/ml). A total of 142 patients were divided into the normal-, low-, and high-IgE groups based on the normal reference value level (90.0 IU/ml) and median serum IgE level (597.5 IU/ml). The high-IgE group had a significantly lower cumulative rate of the first CR (log-rank, P = 0.032) and a higher rate of the first relapse (log-rank, P = 0.033) than the normal-IgE and low-IgE groups. Multivariate Cox analysis showed that IgE ≥597.5 IU/ml was independently associated with the delayed first CR [hazard ratio (HR) = 0.566, 95% confidence interval (CI) = 0.330–0.972, P = 0.039] and the early first relapse (HR = 2.767, 95% CI = 1.150–6.660, P = 0.023).ConclusionsSerum IgE levels were an independent correlation factor for pediatric MCD-delayed remissions and early relapses.

IntroductionSome patients with primary focal segmental sclerosis (FSGS) demonstrate complement 3 (C3) deposition in glomerular capillary loops (Cap-C3) and/or mesangial area (Mes-C3). The clinicopathological and prognostic significance of C3 deposition remains incompletely investigated, especially in the pediatric cohort.MethodsWe retrospectively analyzed 264 children of biopsy-proven primary FSGS between January 2003 and December 2020. The correlation between Cap-C3 and renal outcome was evaluated by the Kaplan-Meier method and Cox multivariate regression analysis. Renal end-point event was defined as the development of end-stage renal disease, death for renal disease, or an estimated glomerular filtration rate reduction by at least 50% from baseline.ResultsAmong the 264 patients, 30 (11.4%) had Cap-C3. Kaplan-Meier analysis showed that patients with Cap-C3 had significantly lower renal survival rates than patients without Cap-C3 (60.17% vs. 84.71% at 5 years, 39.49% vs. 65.55% at 10 years, P

BackgroundMinimal change disease (MCD) is the most common pathological subtype of pediatric idiopathic nephrotic syndrome (INS). It has been suggested that IgM deposition might predict kidney function deterioration in the course of MCD. However, the specific role of IgM deposition in the prognosis of MCD is still controversial. This study aims to investigate the clinical significance of IgM deposition on delayed remission and early relapse in a pediatric population.MethodsThis study enrolled 283 children diagnosed with MCD by renal biopsy in a single center from 2010 to 2022. These cases were divided into two groups according to the histopathological deposition of IgM. Patients' demographics, clinical parameters, and follow-up data were collected and analyzed. The primary and secondary outcomes were defined as the time to the first remission and the first relapse.ResultsThe IgM-positive group had a weaker response to steroids (steroid-sensitive: 23.5% vs. 40.8%; steroid-dependent: 74.0% vs. 51.0%; steroid-resistant: 18.4% vs. 8.2%, P = 0.001), and showed more recurrent cases (47.2% vs. 34.4%, P = 0.047) compared with the IgM-negative group. The Kaplan-Meier analysis showed that the IgM-positive group had a lower cumulative rate of the first remission (Log-rank, P

Abstract Background 3D imaging, such as X-ray CT and MRI, has been widely deployed to study plant root structures. Many computational tools exist to extract coarse-grained features from 3D root images, such as total volume, root number and total root length. However, methods that can accurately and efficiently compute fine-grained root traits, such as root number and geometry at each hierarchy level, are still lacking. These traits would allow biologists to gain deeper insights into the root system architecture. Results We present TopoRoot, a high-throughput computational method that computes fine-grained architectural traits from 3D images of maize root crowns or root systems. These traits include the number, length, thickness, angle, tortuosity, and number of children for the roots at each level of the hierarchy. TopoRoot combines state-of-the-art algorithms in computer graphics, such as topological simplification and geometric skeletonization, with customized heuristics for robustly obtaining the branching structure and hierarchical information. TopoRoot is validated on both CT scans of excavated field-grown root crowns and simulated images of root systems, and in both cases, it was shown to improve the accuracy of traits over existing methods. TopoRoot runs within a few minutes on a desktop workstation for images at the resolution range of 400^3, with minimal need for human intervention in the form of setting three intensity thresholds per image. Conclusions TopoRoot improves the state-of-the-art methods in obtaining more accurate and comprehensive fine-grained traits of maize roots from 3D imaging. The automation and efficiency make TopoRoot suitable for batch processing on large numbers of root images. Our method is thus useful for phenomic studies aimed at finding the genetic basis behind root system architecture and the subsequent development of more productive crops.

BackgroundTRIM8 gene mutations have been reported as the genetic basis of autosomal dominant (AD) neuro-renal syndrome in children, which presents with epileptic encephalopathy, focal segmental glomerulosclerosis (FSGS), developmental delay, and mental retardation. In this study, we report the cases of two children with significant proteinuria due to de novo nonsense mutations of the TRIM8 gene.Case PresentationCase 1 was a 7-year-old girl who presented with proteinuria and developmental delay, and her renal biopsy showed FSGS. She developed end-stage renal disease (ESRD) 3 years after onset. Case 2 was another 7-year-old girl who developed proteinuria only at age 3, and renal biopsy showed glomerular segmental mesangial proliferative lesions. The two girls underwent genetic testing but we did not find a positive result in the whole exon. However, cluster analysis revealed two new nonsense mutations of the TRIM8 gene (c.1461C>A, p.Tyr 487* and c.1453C>T, p.Gln485*).ConclusionsWe reported the clinical manifestation of this neuro-renal syndrome for the first time in China. It is necessary to perform genetic testing in children with steroid-resistant significant proteinuria to identify its etiology and avoid the side effects of immunosuppressants.

Catalytic reductive coupling of two electrophiles and one C = C bond is usually performed by two electron transfer metal catalysis. Herein, the authors show a visible light photoredox-catalyzed successive single electron transfer leading to dearomative arylcarboxylation of indoles with CO2 and generating indoline-3-carboxylic acids.

Abstract Background Previous studies of brain structure in methamphetamine users have yielded inconsistent findings, possibly reflecting small sample size and inconsistencies in duration of methamphetamine abstinence as well as sampling and analyses methods. Here we report on a relatively large sample of abstinent methamphetamine users at various stages of long-term abstinence. Methods Chronic methamphetamine users (n = 99), abstinent from the drug ranging from 12 to 621 days, and healthy controls (n = 86) received T1-weighted structural magnetic resonance imaging brain scans. Subcortical and cortical gray-matter volumes and cortical thickness were measured and the effects of group, duration of abstinence, duration of methamphetamine use and onset age of methamphetamine use were investigated using the Freesurfer software package. Results Methamphetamine users did not differ from controls in gray-matter volumes, except for a cluster in the right lateral occipital cortex where gray-matter volume was smaller, and for regions mainly in the bilateral superior frontal gyrui where thickness was greater. Duration of abstinence correlated positively with gray-matter volumes in whole brain, bilateral accumbens nuclei and insulae clusters, and right hippocampus; and with thickness in a right insula cluster. Duration of methamphetamine use correlated negatively with gray-matter volume and cortical thickness of a cluster in the right lingual and pericalcarine cortex. Conclusions Chronic methamphetamine use induces hard-to-recover cortical thickening in bilateral superior frontal gyri and recoverable volumetric reduction in right hippocampus, bilateral accumbens nuclei and bilateral cortical regions around insulae. These alternations might contribute to methamphetamine-induced neurocognitive disfunctions and reflect a regional specific response of the brain to methamphetamine.

It has been reported that the normal adults can suffer from an intracranial aneurysm (IA) that might present the risk of rupture and cause the subarachnoid hemorrhage. Peroxisome proliferator-activated receptor-γ (PPAR-γ) as a nuclear hormone receptor has been identified to involve in the progress of the formation and rupture of IAs. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect PPAR-γmRNA expression in the macrophages of the patients with IAs. The information including fasting blood glucose (FBG), interleukin-6 (IL-6), and systolic blood pressure (SBP) were collected. The aneurysm parameters of all the participants were obtained through the cerebral angiography. Establishing the receiver-operating characteristic curve (ROC curve) evaluated the clinical significances of PPAR-γmRNA for IAs rupture. In this study, we observed that the rupture of IAs was caused by the maximum height of aneurysm ⩾7 mm, the location of aneurysm in posterior communicating artery (PCOM) or anterior communicating artery (ACOM), and the increase of aneurysm size ratio (SR). The levels of SBP and IL-6 in the rupture group were higher than those in the unrupture group, and PPAR-γmRNA expression in the rupture group was also significantly reduced. In addition, heavy drinking was statistically significant between the ruptured and unruptured groups. There was no significant difference in serum FBG level between the two groups. The evidences of this study showed that PPAR-γmRNA was negatively correlated with SBP, SR, and IL-6 levels in rupture group, respectively. The AUC of PPAR-γmRNA in ROC curve was 0.867, indicating that the change of PPAR-γmRNA level had obvious effect on IAs rupture. The aim of this study was to evaluate the potential of PPAR-γ in macrophages to prevent IAs rupture.

BackgroundPatients with progressive thoracic malignancy characterized by large irregular tumors with necrosis and life-threatening symptoms lack effective treatments. We set out to develop a single needle cone puncture method for the Iodine-125 seed (SNCP-125I) brachytherapy, and aim to report the initial results.Methods294 patients with advanced thoracic malignancy were treated with local SNCP-125I brachytherapy between March 2009 and July 2020, followed by thorough evaluation of clinical outcome, overall survival (OS), progression-free survival (PFS) and procedure-related complications after treatment.ResultsThe overall response rate (ORR) among the treated patients was 81.0% (238/294). Life-threatening symptoms due to tumor oppression, hemoptysis and large irregular tumor with necrosis were successfully alleviated after the SNCP-125I treatment with a remission rate at 91% to 94%. The median OS and PFS were 13.6 months and 5.8 months, respectively. Procedure-related side effects including pneumothorax (32/294), blood-stained sputum (8/294), subcutaneous emphysema (10/294), puncture site bleeding (16/294) and chest pain (6/294) were observed. Patients who were able to follow with chemotherapy or immunotherapy experienced extended OS and PFS, as compared with patients who opted to receive hospice care (16.5 months Vs. 11.2 months). Further pathological and immunological analysis showed that SNCP-125I induced tumor lymphocytes infiltration and long-term tumor necrosis.ConclusionSNCP-125I brachytherapy effectively eliminates life-threatening symptoms due to local tumor oppression, hemoptysis and large irregular and necrotic tumors in patients with unresectable chest malignancy and significantly induces local tumor regression. SNCP-125I brachytherapy combines with chemotherapy significantly prolong OS and PFS compare with SNCP-125I brachytherapy alone.

Argonaute protein is loaded with small RNA and scans long stretch of sequences to find complementary target sites. Here, using single-molecule FRET and kinetic modelling, the authors showed that prokaryotic Argonaute protein binds target DNA loosely and slides along the DNA during target search.

Phosphonyl and carboxyl groups are valuable functional groups, however their simultaneous incorporation via catalytic difunctionalization of alkenes has not been realized yet. Here the authors report the phosphonocarboxylation of alkenes with CO2 via visible-light photoredox catalysis.

Abstract We present an algorithm for segmenting a mesh into patches whose boundaries are aligned with prominent ridge and valley lines of the shape. Our key insight is that this problem can be formulated as correlation clustering (CC), a graph partitioning problem originating from the data mining community. The formulation lends two unique advantages to our method over existing segmentation methods. First, since CC is non-parametric, our method has few parameters to tune. Second, as CC is governed by edge weights in the graph, our method offers users direct and local control over the segmentation result. Our technical contributions include the construction of the weighted graph on which CC is defined, a strategy for rapidly computing CC on this graph, and an interactive tool for editing the segmentation. Our experiments show that our method produces qualitatively better segmentations than existing methods on a wide range of inputs.

Despite being the most dominant and widespread small fish species in the lakes along the middle and lower reaches of the Yangtze River basin, Toxabramis swinhonis has been paid little attention by fisheries scientists and little is known about its population characteristics. For this reason, we estimated age, growth, mortality and recruitment of this species based on three shallow lakes, Biandantang Lake, Shengjin Lake and Kuilei Lake (BDT, SJH and KLH, respectively) in this region. A total of 13,585 (8,818 in BDT, 2,207 in SJH and 2,560 in KLH) individuals were collected during monthly sampling from July 2016 to September 2017. The results revealed that the age structures of T. swinhonis consisted of four age groups (0+–3+), with 0+–1+ year old fish comprising more than 98% of the samples. Allometric growth patterns were displayed by fish from all sampling sites and the von Bertalanffy growth functions estimated were Lt = 173.25 (1 – e−1.20 (t + 1.09)): BDT; Lt = 162.75 (1 – e−1.20 (t + 1.08)): SJH and Lt = 215.25 (1 – e−1.20 (t + 1.12)): KLH, respectively. The rates of total mortality (Z), natural mortality (M) and fishing mortality (F) at BDT, SJH and KLH were computed as 5.82, 5.50 and 4.55 year−1; 1.89, 1.87 and 1.75 year−1; 3.93, 3.63 and 2.80 year−1, respectively. Meanwhile, growth performance indices (φ′) were 0.68 (in BDT), 0.66 (in SJH) and 0.62 (in KLH), which indicated that T. swinhonis were overfished slightly in all study areas. Area-specific recruitment patterns were similar to each other, displaying evidence of batch spawning, with major peaks in April and August, accounting for 92.21% (BDT), 88.21% (SJH) and 88.73% (KLH) of total recruitment, respectively. These results showed that brief generation-time, fast growth rate, relatively high natural mortality rate and strong reproductive capacity (r-strategies) are reasons why this species became the most dominant species in many lakes of China.

Objective: To evaluate therapeutic efficacy of different combined antimicrobial treatments against Acinetobacter baumannii ventilator-associated pneumonia (VAP).Methods: Clinical outcomes were retrospectively analyzed to elucidate the efficacy of four combined antimicrobial regimens. The chessboard and micro broth dilution methods determined the minimum inhibitory concentrations (MICs) of four antiseptic drugs singly used and combined two drugs against 36 isolates of multidrug-resistant (MDR) A. baumannii.Results: The incidence of VAP was approximately 6.9% (237/3424) between January 1, 2015 and December 31, and 35.9% (85/237) of the cases were caused by A. baumannii. Among these cases, 60 belonged to AB-VAP, for whom antimicrobial treatment plan was centralized and clinical data was complete. Moreover, all 60 strains of A. baumannii were MDR bacteria from reports microbiological laboratory. Resistance rate was lowest for amikacin (68.3%) and ampicillin sulbactam (71.7%). Resistance rate for imipenem increased from 63.2 to 90.9% during the 3 years. However, in these 60 cases of AB-VAP, the combination between 4 antibiotics was effective in most cases: the effective rate was 75% (18/24) for sulbactam combined with etilmicin, 71.4% (10/14) for sulbactam combined with levofloxacin, 72.7% (8/11) for meropenem combined with etilmicin, and 63.6% (7/11) for meropenem combined with levofloxacin. There was no statistical difference between four regimens (P > 0.05). Sulbactam combined with etilmicin decreased 1/2 of MIC50 and MIC90 of sulbactam while the decreases in etilmicin were more obviously than single drug. When adopting meropenem combined with levofloxacin or etilmicin, the MIC of meropenem reduced to 1/2 of that in applying single drug. As for sulbactam or meropenem combined with levofloxacin, it also lessened the MIC50 of levofloxacin to 1/2 of that for single drug. FIC results suggested that the effects of four combined antimicrobial regimens were additive or unrelated. When sulbactam was combined with etimicin, the additive effect was 63.89%.Conclusion: Drug combination sensitivity test in vitro may be helpful for choosing antimicrobial treatment plans. Sulbactam or meropenem as the basis of treatment regimens can function as the alternatives against AB-VAP. Sulbactam combined with etimicin has been regarded as a recommended regimen in Suizhou, Hubei, China.

Improving computing performance and reducing energy consumption are a major concern in heterogeneous many-core systems. The thread count directly influences the computing performance and energy consumption for a multithread application running on a heterogeneous many-core system. For this work, we studied the interrelation between the thread count and the performance of applications to improve total energy efficiency. A prediction model of the optimum thread count, hereafter the thread count prediction model (TCPM), was designed by using regression analysis based on the program running behaviors and heterogeneous many-core architecture feature. Subsequently, a dynamic predictive thread mapping (DPTM) framework was proposed. DPTM uses the prediction model to estimate the optimum thread count and dynamically adjusts the number of active hardware threads according to the phase changes of the running program in order to achieve the optimal energy efficiency. Experimental results show that DPTM obtains a nearly 49% improvement in performance and a 59% reduction in energy consumption on average. Moreover, DPTM introduces about 2% additional overhead compared with traditional thread mapping for PARSEC (The Princeton Application Repository for Shared-Memory Computers) benchmark programs running on an Intel MIC (Many integrated core) heterogeneous many-core system.

Many-core processors are becoming mainstream computing platforms nowadays. How to map the application threads to specific processing cores and exploit the abundant hardware parallelism of a many-core processor efficiently has become a pressing need. This work proposes a data affinity based threads grouping mapping strategy Data Affinity Grouping based Thread Mapping (DagTM), which categorizes threads into different groups according to their data affinity and the hardware architecture feature of many-core processors. After that, the thread groups are mapped to the specific processing cores to be energy efficiently executed. More specifically, first, the intra-thread data locality is analyzed by computing the data reuse distance, and the inter-thread data affinity is quantified by affinity matrix. Second, the threads are categorized into different groups via affinity subtree spanning algorithm. Finally, the thread groups are assigned to different processing cores through static binding. DagTM is able to reduce conflicts of the shared memory access and additional data transmission, increase utilization of the computing resources, and reduce entire system energy consumption. Experimental results show that DagTM obtains a nearly 14% improvement in computing performance, and a nearly 10% reduction in energy consumption compared with the traditional thread mapping mechanism under the condition of not introducing additional runtime overhead.

Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer IV somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities.