Partial least squares (PLS) have gained wide applications especially in chemometrics, metabolomics/metabonomics as well as bioinformatics. Here, we present libPLS, a library that integrates not only ...basic PLS modeling algorithms but also advanced and/or recently developed methods on model assessment, outlier detection, and variable selection. This package is featured in a set of Model Population Analysis (MPA)-type approaches that have not been integrated into a single package yet and thus functionally complement existing toolboxes. libPLS provides an integrated platform for developing PLS regression and/or linear discriminant analysis (PLS-LDA) models. It is written in MATLAB and freely available at www.libpls.net.
•Provide an integrated library for partial least squares regression and discriminant analysis.•Featured in model population analysis approaches.•Contain a series of versatile variable selection methods.
With the advances in innovative instrumentation and various valuable applications, near-infrared (NIR) spectroscopy has become a mature analytical technique in various fields. Variable (wavelength) ...selection is a critical step in multivariate calibration of NIR spectra, which can improve the prediction performance, make the calibration reliable and provide simpler interpretation. During the last several decades, there have been a large number of variable selection methods proposed in NIR spectroscopy. In this paper, we generalize variable selection methods in a simple manner to introduce their classifications, merits and drawbacks, to provide a better understanding of their characteristics, similarities and differences. We also introduce some hybrid and modified methods, highlighting their improvements. Finally, we summarize the limitations of existing variable selection methods, providing our remarks and suggestions on the development of variable selection methods, to promote the development of NIR spectroscopy.
•Generalize variable selection methods in a simple manner to provide a better understanding of their characteristics.•Introduce their modified and hybrid methods and highlighting their improvements.•Summarize the limitations and mention seven aspects of the problem affecting the existing variable selection methods.•Provide our remarks and suggestions on the trends of the development on the variable selection methods in NIR spectra.
Input–output organization of the mouse claustrum Zingg, Brian; Dong, Hong‐Wei; Tao, Huizhong Whit ...
Journal of comparative neurology (1911),
October 15, 2018, Letnik:
526, Številka:
15
Journal Article
Recenzirano
Odprti dostop
Progress in determining the precise organization and function of the claustrum (CLA) has been hindered by the difficulty in reliably targeting these neurons. To overcome this, we used a ...projection‐based targeting strategy to selectively label CLA principal neurons. Combined with adeno‐associated virus (AAV) and monosynaptic rabies tracing techniques, we systematically examined the pre‐synaptic input and axonal output of this structure. We found that CLA neurons projecting to retrosplenial cortex (RSP) collateralize extensively to innervate a variety of higher‐order cortical regions. No subcortical labeling was found, with the exception of sparse terminals in the basolateral amygdala (BLA). This pattern of output was similar to cingulate‐ and visual cortex‐projecting CLA neurons, suggesting a common targeting scheme among these projection‐defined populations. Rabies virus tracing directly demonstrated widespread synaptic inputs to RSP‐projecting CLA neurons from both cortical and subcortical areas. The strongest inputs arose from classically defined limbic regions, including medial prefrontal cortex, anterior cingulate, BLA, ventral hippocampus, and neuromodulatory systems such as the dorsal raphe and cholinergic basal forebrain. These results suggest that the CLA may integrate information related to the emotional salience of stimuli and may globally modulate cortical state by broadcasting its output uniformly across a variety of higher cognitive centers.
Output of mouse claustrum collateralizes broadly to reach a variety of higher‐order frontal and retrohippocampal cortical structures as revealed by AAV tracing in projection‐defined neurons. Claustrum input was demonstrated using monosynaptic rabies tracing and was found to arise predominately from classically defined limbic structures.
A double-exchange interaction (DEI) was demonstrated to boost the oxygen evolution reaction (OER) in spinel oxides. DEI was ignited by synergistic actions of constructing nanoheterojunctions and ...creating oxygen vacancy (VO) in spinel NiCo2O4. DEI between octahedrally coordinated Ni and Co resulted in the generation of superior OER active centers Co(3−δ)+ and Ni3+. The multiple synergistic effects empower the electrocatalyst with exceptional OER activity, with an overpotential of 270 ± 3 mV at 10 mA/cm2 and a Tafel slope of 39 mV/dec, both of which are among the best values for NiCo2O4-based nanostructures, and even better than those for IrO2 and RuO2.
The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL ...gene family members have not yet been performed in wheat.
In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat.
We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Crystalline and porous covalent organic frameworks (COFs) and metal‐organic frameworks (MOFs) materials have attracted enormous attention in the field of photocatalytic H2 evolution due to their ...long‐range order structures, large surface areas, outstanding visible light absorbance, and tunable band gaps. In this work, we successfully integrated two‐dimensional (2D) COF with stable MOF. By covalently anchoring NH2‐UiO‐66 onto the surface of TpPa‐1‐COF, a new type of MOF/COF hybrid materials with high surface area, porous framework, and high crystallinity was synthesized. The resulting hierarchical porous hybrid materials show efficient photocatalytic H2 evolution under visible light irradiation. Especially, NH2‐UiO‐66/TpPa‐1‐COF (4:6) exhibits the maximum photocatalytic H2 evolution rate of 23.41 mmol g−1 h−1 (with the TOF of 402.36 h−1), which is approximately 20 times higher than that of the parent TpPa‐1‐COF and the best performance photocatalyst for H2 evolution among various MOF‐ and COF‐based photocatalysts.
Effective separation: A novel MOF/COF hybrid material assembled by covalent connecting two components, exhibits effective visible‐light‐driven photocatalytic H2 evolution due to the ideal band matching and effectively promoting the separation of the photogenerated charges and holes.
Whole-brain mesoscale mapping in primates has been hindered by large brain sizes and the relatively low throughput of available microscopy methods. Here, we present an approach that combines ...primate-optimized tissue sectioning and clearing with ultrahigh-speed fluorescence microscopy implementing improved volumetric imaging with synchronized on-the-fly-scan and readout technique, and is capable of completing whole-brain imaging of a rhesus monkey at 1 × 1 × 2.5 µm
voxel resolution within 100 h. We also developed a highly efficient method for long-range tracing of sparse axonal fibers in datasets numbering hundreds of terabytes. This pipeline, which we call serial sectioning and clearing, three-dimensional microscopy with semiautomated reconstruction and tracing (SMART), enables effective connectome-scale mapping of large primate brains. With SMART, we were able to construct a cortical projection map of the mediodorsal nucleus of the thalamus and identify distinct turning and routing patterns of individual axons in the cortical folds while approaching their arborization destinations.
Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for ...interrogating transcriptomes because it has been recognized to carry out important biological functions such as gene expression regulation and it has been found to be associated with complex diseases such as cancers. However, methods for detecting IR today are limited. Thus, there is a need to develop novel methods to improve IR detection.
Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events genome-wide from high-throughput RNA-seq data. The command line interface for iREAD is implemented in Python. iREAD takes as input a BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. It then 1) counts all reads that overlap intron regions, 2) detects IR events by analyzing the features of reads such as depth and distribution patterns, and 3) outputs a list of retained introns into a tab-delimited text file. iREAD provides significant added value in detecting IR compared with output from IRFinder with a higher AUC on all datasets tested. Both methods showed low false positive rates and high false negative rates in different regimes, indicating that use together is generally beneficial. The output from iREAD can be directly used for further exploratory analysis such as differential intron expression and functional enrichment. The software is freely available at https://github.com/genemine/iread.
Being complementary to existing tools, iREAD provides a new and generic tool to interrogate poly-A enriched transcriptomic data of intron regions. Intron retention analysis provides a complementary approach for understanding transcriptome.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aberrant expression of microRNAs (miRNAs) plays an important role in gastric cancer (GC) development. miR-93-5p has shown opposing functions in different types of cancers, but the exact expression ...pattern and molecular mechanism of miR-93-5p in GC development remain to be elucidated. Here, we reported that miR-93-5p expression was increased in GC tissues compared with the adjacent normal tissues and that its overexpression was correlated with distant metastasis and poor survival in GC patients. miR-93-5p knockdown inhibited the migration, invasion and proliferation of GC cells in vitro and in vivo, while its overexpression displayed an opposite result. Using an mRNA microarray, we found that miR-93-5p significantly downregulated IFNAR1 expression in GC cells, which was further identified as a direct target of miR-93-5p. IFNAR1 knockdown promoted GC cell migration and invasion, but its restoration could rescue GC cell migration and invasion induced by miR-93-5p overexpression. Moreover, miR-93-5p-IFNAR1 axis increased MMP9 expression via STAT3 pathway in GC cells. Taken together, we reveal that miR-93-5p overexpression is associated with the poor survival of GC patients and miR-93-5p-IFNAR1 axis promotes GC metastasis through activation of STAT3 pathway.
•miR-93-5p overexpression is correlated with the poor survival of GC patients.•INFAR1 is a direct target of miR-93-5p in GC cells.•miR-93-5p/IFNAR1 axis activates the STAT3 signaling pathway in GC metastasis.
Objective： Alzheimer＇s disease and vascular dementia are responsible for more than 80% of dementia cases. These two conditions share common risk factors including hypertension. Cerebral small vessel ...disease （CSVD） is strongly associated with both hypertension and cognitive impairment. In this review, we identify the pathophysiological changes in CSVD that are caused by hypertension and further explore the relationship between CSVD and cognitive impairment. Data Sources： We searched and scanned the PubMed database for recently published literatures up to December 2017. We used the keywords of＂hypertension＂, ＂cerebral small vessel disease＂, ＂＇white matter lesions＂, ＂enlarged perivascular spaces＂, ＂lacunar infarcts＂, ＂cerebral microbleeds＂, and ＂cognitive impairment＂ in the database of PubMed. Study Selection： Articles were obtained and reviewed to analyze the hypertension-induced pathophysiological changes that occur in CSVD and the correlation between CSVD and cognitive impairment. Results： In recent years, studies have demonstrated that hypertension-related changes （e.g., small vascular lesions, inflarnmator3, reactions, hypoperfusion, oxidative stress, damage to autoregulatory processes and the blood-brain barrier, and cerebral amyloid angiopathy） can occur over time in cerebral small vessels, potentially leading to lower cognitive function when blood pressure （BP） control is poor or lacking. Both isolated and co-occurrent CSVD can lead to cognitive deterioration, and this effect may be attributable to a dysfunction in either the cholinergic system or the functionality of cortical and subcortical tracts. Conclusions： We explore the currently available evidence about the hypertensive vasculopathy and inflammatory changes that occur in CSVD. Both are vital prognostic indicators of the development of cognitive impairment. Future studies should be performed to validate the relationship between BP levels and CSVD progression and between the nunabers, volumes, and anatomical locations of CSVD and cognitive impairment.
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