Accumulating experimental studies have indicated that lncRNAs play important roles in various critical biological process and their alterations and dysregulations have been associated with many ...important complex diseases. Developing effective computational models to predict potential disease-lncRNA association could benefit not only the understanding of disease mechanism at lncRNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis and prevention. However, known experimentally confirmed disease-lncRNA associations are still very limited. In this study, a novel model of HyperGeometric distribution for LncRNA-Disease Association inference (HGLDA) was developed to predict lncRNA-disease associations by integrating miRNA-disease associations and lncRNA-miRNA interactions. Although HGLDA didn't rely on any known disease-lncRNA associations, it still obtained an AUC of 0.7621 in the leave-one-out cross validation. Furthermore, 19 predicted associations for breast cancer, lung cancer, and colorectal cancer were verified by biological experimental studies. Furthermore, the model of LncRNA Functional Similarity Calculation based on the information of MiRNA (LFSCM) was developed to calculate lncRNA functional similarity on a large scale by integrating disease semantic similarity, miRNA-disease associations, and miRNA-lncRNA interactions. It is anticipated that HGLDA and LFSCM could be effective biological tools for biomedical research.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
We study the
P
cs
(
4459
)
0
recently observed by LHCb using the method of QCD sum rules. Our results support its interpretation as the
D
¯
∗
Ξ
c
hadronic molecular state of either
J
P
=
1
/
2
-
or
3
.../
2
-
. Within the hadronic molecular picture, the three LHCb experiments observing
P
c
and
P
cs
states (Aaij et al., Phys Rev Lett 115:072001, 2015; Aaij et al., Phys Rev Lett 122:222001, 2019; Aaij et al.,
arXiv:2012.10380
hep-ex, 2012) can be well understood as a whole. This strongly supports the existence of hadronic molecules, whose studies can significantly improve our understanding on the construction of the subatomic world. To verify this picture, we propose to further investigate the
P
cs
(
4459
)
0
to examine whether it can be separated into two states, and to search for the
D
¯
Ξ
c
molecular state of
J
P
=
1
/
2
-
.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Predicting novel microRNA (miRNA)-disease associations is clinically significant due to miRNAs' potential roles of diagnostic biomarkers and therapeutic targets for various human diseases. Previous ...studies have demonstrated the viability of utilizing different types of biological data to computationally infer new disease-related miRNAs. Yet researchers face the challenge of how to effectively integrate diverse datasets and make reliable predictions. In this study, we presented a computational model named Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction (LRSSLMDA), which projected miRNAs/diseases' statistical feature profile and graph theoretical feature profile to a common subspace. It used Laplacian regularization to preserve the local structures of the training data and a L1-norm constraint to select important miRNA/disease features for prediction. The strength of dimensionality reduction enabled the model to be easily extended to much higher dimensional datasets than those exploited in this study. Experimental results showed that LRSSLMDA outperformed ten previous models: the AUC of 0.9178 in global leave-one-out cross validation (LOOCV) and the AUC of 0.8418 in local LOOCV indicated the model's superior prediction accuracy; and the average AUC of 0.9181+/-0.0004 in 5-fold cross validation justified its accuracy and stability. In addition, three types of case studies further demonstrated its predictive power. Potential miRNAs related to Colon Neoplasms, Lymphoma, Kidney Neoplasms, Esophageal Neoplasms and Breast Neoplasms were predicted by LRSSLMDA. Respectively, 98%, 88%, 96%, 98% and 98% out of the top 50 predictions were validated by experimental evidences. Therefore, we conclude that LRSSLMDA would be a valuable computational tool for miRNA-disease association prediction.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The discovery of topological quantum states marks a new chapter in both condensed matter physics and materials sciences. By analogy to spin electronic system, topological concepts have been extended ...into phonons, boosting the birth of topological phononics (TPs). Here, we present a high-throughput screening and data-driven approach to compute and evaluate TPs among over 10,000 real materials. We have discovered 5014 TP materials and grouped them into two main classes of Weyl and nodal-line (ring) TPs. We have clarified the physical mechanism for the occurrence of single Weyl, high degenerate Weyl, individual nodal-line (ring), nodal-link, nodal-chain, and nodal-net TPs in various materials and their mutual correlations. Among the phononic systems, we have predicted the hourglass nodal net TPs in TeO
, as well as the clean and single type-I Weyl TPs between the acoustic and optical branches in half-Heusler LiCaAs. In addition, we found that different types of TPs can coexist in many materials (such as ScZn). Their potential applications and experimental detections have been discussed. This work substantially increases the amount of TP materials, which enables an in-depth investigation of their structure-property relations and opens new avenues for future device design related to TPs.
Metal-organic frameworks (MOFs), a novel class of porous crystalline materials, have drawn enormous attention. Due to the inherent porosity and presence of both metal and organic moieties, MOF-based ...materials are naturally suitable as versatile precursors and sacrificial templates for a wide variety of metal/carbon-based nanostructured materials, such as metal oxides, metal carbides, metal sulfides and their composites. Recent developments in MOF-derived hollow nanostructures with well-defined interior voids and low density have revealed their extensive capabilities and thus give enhanced performance for energy storage and conversion. In this review, we summarize the recent progress in the fabrication of MOF-derived hollow materials and their applications for energy storage, particularly for lithium-ion batteries, sodium-ion batteries, lithium-Se batteries, lithium-sulfur batteries and supercapacitors. The superiorities of MOF-derived hollow materials are highlighted, and major challenges or opportunities for future research on them for electrochemical energy storage are also discussed, with prospective solutions in the light of current progress in MOF-derived hollow nanostructures.
The recent progress and major challenges/opportunities of MOF-derived hollow materials for energy storage are summarized in this review, particularly for lithium-ion batteries, sodium-ion batteries, lithium-Se batteries, lithium-sulfur batteries and supercapacitor applications.
Abstract
The search for new two-dimensional monolayers with diverse electronic properties has attracted growing interest in recent years. Here, we present an approach to construct MA
2
Z
4
monolayers ...with a septuple-atomic-layer structure, that is, intercalating a MoS
2
-type monolayer MZ
2
into an InSe-type monolayer A
2
Z
2
. We illustrate this unique strategy by means of first-principles calculations, which not only reproduce the structures of MoSi
2
N
4
and MnBi
2
Te
4
that were already experimentally synthesized, but also predict 72 compounds that are thermodynamically and dynamically stable. Such an intercalated architecture significantly reconstructs the band structures of the constituents MZ
2
and A
2
Z
2
, leading to diverse electronic properties for MA
2
Z
4
, which can be classified according to the total number of valence electrons. The systems with 32 and 34 valence electrons are mostly semiconductors. Whereas, those with 33 valence electrons can be nonmagnetic metals or ferromagnetic semiconductors. In particular, we find that, among the predicted compounds, (Ca,Sr)Ga
2
Te
4
are topologically nontrivial by both the standard density functional theory and hybrid functional calculations. While VSi
2
P
4
is a ferromagnetic semiconductor and TaSi
2
N
4
is a type-I Ising superconductor. Moreover, WSi
2
P
4
is a direct gap semiconductor with peculiar spin-valley properties, which are robust against interlayer interactions. Our study thus provides an effective way of designing septuple-atomic-layer MA
2
Z
4
with unusual electronic properties to draw immediate experimental interest.
Background
miRNAs and mRNAs have been significantly implicated in tumorigenesis and served as promising prognostic biomarkers for human cancer. Hence, this study was aimed to develop the pivotal ...miRNA biomarkers‐based prognostic signature for salivary adenoid cystic carcinoma.
Methods
The miRNA and mRNA expression data were integrated from the gene expression omnibus database to study their involvement in salivary adenoid cystic carcinoma development and progression. Gene ontology and kyoto encyclopedia of genes and genomes were conducted to analyze the biological pathways. Reverse transcription‑quantitative PCR was used to verify the expression of selected miRNAs in salivary adenoid cystic carcinoma and corresponding normal tissues.
Results
There were 386 differentially expressed genes: 158 upregulated and 228 downregulated genes and 102 differentially expressed miRNAs: 78 upregulated and 24 downregulated miRNAs in the salivary adenoid cystic carcinoma samples. A miRNA‐mRNA network containing 11 miRNAs and 199 genes was subsequently constructed. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis revealed that the genes targeted by the 11 miRNAs were mostly involved in tumor‐related pathways and processes, such as miRNAs in cancer, focal adhesion, neurotrophin signaling pathway, and the PI3K‐Akt signaling pathway. Among them, 4 miRNAs (miR‐375, miR‐494, miR‐34c‐5p, and miR‐331‐3p) were selected to verify by reverse transcription‑quantitative PCR in 36 pairs of collected salivary adenoid cystic carcinoma and adjacent nontumor samples. Overall survival analysis revealed that the higher expression of miR‐331‐3p was significantly associated with a worst overall survival and multivariate Cox regression analysis suggested that hsa‐miR‐331‐3p could be an independent prognostic factor for salivary adenoid cystic carcinoma.
Conclusion
Our results revealed that 4‐miRNAs signature was a powerful prognostic biomarker for salivary adenoid cystic carcinoma, which provide a basis for exploring deeper mechanisms regarding the progression of salivary adenoid cystic carcinoma, and leading to the development of potential therapeutic strategies.
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CMK, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Implantable medical devices have been widely applied in diagnostics, therapeutics, organ restoration, and other biomedical areas, but often suffer from dysfunction and infections due to irreversible ...biofouling. Inspired by the self‐defensive “vine‐thorn” structure of climbing thorny plants, a zwitterion‐conjugated protein is engineered via grafting sulfobetaine methacrylate (SBMA) segments on native bovine serum albumin (BSA) protein molecules for surface coating and antifouling applications in complex biological fluids. Unlike traditional synthetic polymers of which the coating operation requires arduous surface pretreatments, the engineered protein BSA@PSBMA (PolySBMA conjugated BSA) can achieve facile and surface‐independent coating on various substrates through a simple dipping/spraying method. Interfacial molecular force measurements and adsorption tests demonstrate that the substrate‐foulant attraction is significantly suppressed due to strong interfacial hydration and steric repulsion of the bionic structure of BSA@PSBMA, enabling coating surfaces to exhibit superior resistance to biofouling for a broad spectrum of species including proteins, metabolites, cells, and biofluids under various biological conditions. This work provides an innovative paradigm of using native proteins to generate engineered proteins with extraordinary antifouling capability and desired surface properties for bioengineering applications.
A novel engineered BSA@PSBMA protein (bovine serum albumin, BSA and poly(sulfobetaine methacrylate), PSBMA) is developed for surface‐independent coating and to remove the intrinsic limitation of native proteins as antifouling coatings in complex biological environments. High‐efficient resistance to various biofoulants in complex conditions is achieved through using a bionic “vine‐thorn” design to tune the interfacial interactions at the molecular scale.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Super‐hydrophilic cellulose nanocrystals (CNCs) hold great potential in fabricating antifouling surfaces based on their high‐water binding affinity. However, integrating CNCs as a robust surface ...coating on substrate still remains a challenge due to its limited surface adhesion property. Herein, inspired by marine bio‐adhesive strategy, a facile yet universal surface coating method is developed for tightly anchoring CNCs on various substrates with an intermediate adhesive layer composed of tannic acid (TA)/polyethylenimine (PEI)/vanadium(V). Introducing V3+ ions in the assembly process significantly reduces the roughness of the TA/PEI/V bio‐glue layer via coordination chemistry, thus achieving a CNCs coating with a highly‐dense structure and outstandingly low root‐mean‐square roughness (≈2 nm). The super‐hydrophilic CNCs coating exhibits universal and outstanding antifouling properties in inhibiting oil adhesion, protein adsorption or cell attachment, and maintaining its structural integrity and wettability over 100 friction cycles. Additionally, the CNCs‐coated polyvinylidene fluoride (PVDF) membrane shows an ultra‐high water flux over 6000 L m–2 h–1 bar–1 and achieves nearly 100% permeating flux recovery ratio for separation of toluene‐in‐water emulsion containing various foulants. This study demonstrates a universal coating method to settle the long‐standing challenge of robust integration of rigid materials to various substrates for broad engineering and environmental applications.
A universal and scalable cellulose nanocrystals (CNCs) coating strategy is proposed and developed via robustly grafting CNCs onto various substrates by constructing an intermedia adhesive layer. The highly dense CNCs coating exhibits outstanding antifouling and anti‐wear performance for water purification. This study provides a useful method for addressing a long‐standing challenge of the integration of rigid materials as robust surface coatings.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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