Predicting siRNA potency with random forests and support vector machines

Abstract Background Short interfering RNAs (siRNAs) can be used to knockdown gene expression in functional genomics. For a target gene of interest, many siRNA molecules may be designed, whereas their efficiency of expression inhibition often varies. Results To facilitate gene functional studies, we have developed a new machine learning method to predict siRNA potency based on random forests and support vector machines. Since there were many potential sequence features, random forests were used to select the most relevant features affecting gene expression inhibition. Support vector machine classifiers were then constructed using the selected sequence features for predicting siRNA potency. Interestingly, gene expression inhibition is significantly affected by nucleotide dimer and trimer compositions of siRNA sequence. Conclusions The findings in this study should help design potent siRNAs for functional genomics, and might also provide further insights into the molecular mechanism of RNA interference

Association of APOE ε4/ε4 with fluid biomarkers in patients from the PUMCH dementia cohort

BackgroundApolipoprotein-E (APOE) ε4 is a major genetic risk factor for Alzheimer’s disease (AD). Current studies, which were mainly based on the clinical diagnosis rather than biomarkers, come to inconsistent conclusions regarding the associations of APOE ε4 homozygotes (APOE ε4/ε4) and cerebrospinal fluid (CSF) biomarkers of AD. In addition, few studies have explored the associations of APOE ε4/ε4 with plasma biomarkers. Therefore, we aimed to investigate the associations of APOE ε4/ε4 with fluid biomarkers in dementia and biomarker-diagnosed AD.MethodsA total of 297 patients were enrolled. They were classified into Alzheimer’s continuum, AD, and non-AD, according to CSF biomarkers and/or β amyloid PET results. AD was a subgroup of the AD continuum. Plasma Amyloid β (Aβ) 40, Aβ42, glial fibrillary acidic protein (GFAP), neurofilament light chain (NFL), and phosphorylated tau (P-tau)181 were quantified in 144 of the total population using an ultra-sensitive Simoa technology. We analyzed the associations of APOE ε4/ε4 on CSF and plasma biomarkers in dementia and biomarker diagnosed AD.ResultsBased on the biomarker diagnostic criteria, 169 participants were diagnosed with Alzheimer’s continuum and 128 individuals with non-AD, and among the former, 120 patients with AD. The APOE ε4/ε4 frequencies were 11.8% (20/169), 14.2% (17/120), and 0.8% (1/128) in Alzheimer’s continuum, AD and non-AD, respectively. Only CSF Aβ42 was shown to be decreased in APOE ε4/ε4 carriers than in non-carriers for patients with AD (p = 0.024). Furthermore, we did not find any associations of APOE ε4 with plasma biomarkers of AD and non-AD. Interestingly, we found that in non-AD patients, APOE ε4 carriers had lower CSF Aβ42 (p = 0.018) and higher T-tau/Aβ42 ratios (p < 0.001) and P-tau181/Aβ42 ratios (p = 0.002) than non-carriers.ConclusionOur data confirmed that of the three groups (AD continuum, AD, and non-AD), those with AD had the highest frequency of APOE ɛ4/ɛ4 genotypes. The APOE ɛ4/ɛ4 was associated with CSF levels of Aβ42 but not tau for AD and non-AD, suggesting that APOE ɛ4/ɛ4 affected the Aβ metabolism of both. No associations between APOE ε4/ɛ4 and plasma biomarkers of AD and non-AD were found

Different mechanisms of organic and inorganic phosphorus release from Mollisols induced by low molecular weight organic acids

Enhancement of Pi release by LMWOA increases soil P availability to plant, but the release of Po and the associated kinetics of both Pi and Po release by LMWOA have not been well considered. The aim of this study was to investigate the impacts of citric acid, oxalic acid and malic acid on the kinetic release of Pi and Po in a black clay soil in Northeast China. All kinetic data were well described by Elovich and power functions models (PThe accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

A versatile nodal energy consumption monitoring method for wireless sensor network testbed

Energy efficiency is a critical criterion in wireless sensor networks (WSN). Given the energy consumption of a node, or even the whole network, is precisely measured. Great improvement can be expected in the WSN system optimization. In this paper, we propose a versatile nodal energy consumption monitoring schema, which precisely measures the energy consumption of each node at any moment. In addition, our schema can be integrated with existing testbed technologies to measure the energy consumption of the overall network. Results show that our method can fulfill various challenges in energy consumption measurement in wireless sensor network. We believe the design and implementation of this monitoring schema is an important move towards accurate and flexible energy efficiency analysis. © 2011 IEEE

Energy consumption monitoring for sensor nodes in SNAP

As energy is one of most important aspects for evaluating algorithms' performance, it's crucial to provide a tool to measure the energy consumed. There still was not satisfying solution to monitor energy consumption of every sensor node in large-scale wireless sensor network. In this paper, we propose a new real-time energy monitoring schema as a function component of WSN testbed (sensor network assistant platform, SNAP). Our monitoring schema has the following advantages: real-time accurate energy measurement, the ability to cope with large-scale WSN, side effect free to the monitored nodes, highly adaptive to different kinds of sensor nodes and supporting further energy efficiency analysis on nodes. Noted that all of these advantages are based on SNAP, we introduce the architecture and implementation of our proposed schema together with the counterpart of SNAP. Then we use experimental results to evaluate and demonstrate the performance of this energy consumption monitoring schema

The fate of fertilizer nitrogen in a high nitrate accumulated agricultural soil

Well-acclimatized nitrifiers in high-nitrate agricultural soils can quickly nitrify NH4 + into NO3 - subject to leaching and denitrifying loss. A 120-day incubation experiment was conducted using a greenhouse soil to explore the fates of applied fertilizer N entering into seven soil N pools and to examine if green manure (as ryegrass) co-application can increase immobilization of the applied N into relatively stable N pools and thereby reduce NO3 - accumulation and loss. We found that 87-92% of the applied 15N-labelled NH4 + was rapidly recovered as NO3 - since day 3 and only 2-4% as microbial biomass and soil organic matter (SOM), while ryegrass co-application significantly decreased its recovery as NO3 - but enhanced its recovery as SOM (17%) at the end of incubation. The trade-off relationship between 15N recoveries in microbial biomass and SOM indicated that ryegrass co-application stabilized newly immobilized N via initial microbial uptake and later breakdown. Nevertheless, ryegrass application didn't decrease soil total NO3 - accumulation due to its own decay. Our results suggest that green manure co-application can increase immobilization of applied N into stable organic N via microbial turnover, but the quantity and quality of green manure should be well considered to reduce N release from itself

Effect of chilling rate on heat shock proteins abundance, myofibrils degradation and caspase-3 activity in postmortem muscles

peer reviewedThe objective of this study was to investigate the effect of chilling rate on heat shock proteins (HSP) abundance, myofibrillar proteins degradation and caspase-3 activity of lamb muscle in postmortem. Eighteen longissimus dorsi (LD) muscles from lamb were treated under three different chilling rates—very fast chilling I (VFC-I, 22.2 °C h−1), very fast chilling II (VFC-II, 32.4 °C h−1) and control (1.44 °C h−1)—and stored at −1 °C, −1 °C and 4 °C for 120 h postmortem, respectively. The results showed that myofibril fragmentation index (MFI), the abundance of αβ-crystallin and HSP20, as well as the degradation of HSP27, HSP70, troponin-T and desmin under the VFC-I and VFC-II groups were higher than control. Notably, HSP90 abundance may not be affected by the chilling rate in the late postmortem aging. Additionally, with increasing of chilling rate for postmortem muscle could inhibit caspase-3 activity. Overall, results indicated that chilling rate may affect the process of meat tenderization by changing the abundance levels of heat shock proteins, myofibrillar degradation and apoptotic pathway

Genotypic and phenotypic heterogeneity among Chinese pediatric genetic white matter disorders

Abstract Background The pediatric genetic white matter disorders are characterized by a broad disease spectrum. Genetic testing is valuable in the diagnosis. However, there are few studies on the clinical and genetic spectrum of Chinese pediatric genetic white matter disorders. Methods The participants were enrolled from the cohort of Peking Union Medical College Hospital. They all received history collection, brain MRI and gene sequencing. Their neurologic complaints which were related to white matter disorders occurred before 18. Brain MRI indicated periventricular and/or deep white matter lesions, fazekas grade 2–3. Results Among the 13 subjects, there were 11 males and two females. The average age of onset was 10.0 ± 5.5 years old. The potential genetic variants were found in 84.6% (11/13) subjects. The ABCD1 showed the greatest mutation frequency (30.8%, 4/13). The EIF2B3 A151fs, EIF2B4 c.885 + 2T > G, EIF2B5 R129X and MPV17 Q142X were novel pathogenic/likely pathogenic variants. 100% (4/4) ABCD1 carriers were accompanied by visual impairment, whereas 100% (3/3) EIF2B carriers developed dysuria. 100% (4/4) ABCD1 carriers exhibited diffuse white matter hyperintensities mainly in the posterior cortical regions, while the EIF2B4 and EIF2B5 carriers were accompanied by cystic degeneration. Conclusion There is genotypic and phenotypic heterogeneity among Chinese subjects with pediatric genetic white matter disorders. The knowledge of these clinical and genetic characteristics facilitates an accurate diagnosis of these diseases