DrugE-Rank: Predicting Drug-Target Interactions by Learning to Rank

Identifying drug-target interactions is crucial for the success of drug discovery. Approaches based on machine learning for this problem can be divided into two types: feature-based and similarity-based methods. By utilizing the “Learning to rank” framework, we propose a new method, DrugE-Rank, to combine these two different types of methods for improving the prediction performance of new candidate drugs and targets. DrugE-Rank is available at http://datamining-iip.fudan.edu.cn/service/DrugE-Rank/

Cache attack on MISTY1

Side-channel attacks exploit information from physical implementations of cryptographic systems. Cache attacks have improved at recovering information by combining observations of the victim\u27s cache access and knowledge of the cipher’s structure. Cache attacks have been implemented for most Feistel- and SPN-structured block cipher algorithms, but the security of algorithms for special structures has seen little attention. We perform a Flush+Reload attack on MISTY1, a class of block cipher with a recursive structure. The function is performed before the plaintext input S-box and after the ciphertext output S-box, making it difficult to attack the first and last rounds. However, the key scheduling part of MISTY1 leaks many bits of the key, which, together with the leakage of partial bits of the round key during encryption, is sufficient to recover it. We design an algorithm that can recover the MISTY1 128-bit key after observing encryption one time, and then use leakage during encryption to reduce its complexity. We experiment on 32- and 64-byte cache line environments. An adversary need observe as little as 5 encryptions to recover the 128-bit key in 0.035 second in the first case, and 10 encryptions to recover the key in 2.1 hours in the second case

Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, \u3cem\u3eFrankliniella occidentalis\u3c/em\u3e

Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually

Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, \u3cem\u3eFrankliniella occidentalis\u3c/em\u3e

Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually

In-Plane Anisotropies of Polarized Raman Response and Electrical Conductivity in Layered Tin Selenide

The group IV-VI compound SnSe, with an orthorhombic lattice structure, has recently attracted particular interest due to its unexpectedly low thermal conductivity and high power factor, showing great promise for thermoelectric applications. SnSe displays intriguing anisotropic properties due to the puckered low-symmetry in-plane lattice structure. Low-dimensional materials have potential advantages in improving the efficiency of thermoelectric conversion, due to the increased power factor and decreased thermal conductivity. A complete study of the optical and electrical anisotropies of SnSe nanostructures is a necessary prerequisite in taking advantage of the material properties for high performance devices. Here, we synthesize the single crystal SnSe nanoplates (NPs) by chemical vapor deposition. The angular dependence of the polarized Raman spectra of SnSe NPs shows anomalous anisotropic light-mater interaction. The angle-resolved charge transport of the SnSe NPs expresses a strong anisotropic conductivity behavior. These studies elucidate the anisotropic interactions which will be of use for future ultrathin SnSe in electronic, thermoelectric and optoelectronic devices.Comment: 25 pages, 9 figures, 3 table

Exploring potential genes and mechanisms linking erectile dysfunction and depression

BackgroundThe clinical correlation between erectile dysfunction (ED) and depression has been revealed in cumulative studies. However, the evidence of shared mechanisms between them was insufficient. This study aimed to explore common transcriptomic alterations associated with ED and depression.Materials and methodsThe gene sets associated with ED and depression were collected from the Gene Expression Omnibus (GEO) database. Comparative analysis was conducted to obtain common genes. Using R software and other appropriate tools, we conducted a range of analyses, including function enrichment, interactive network creation, gene cluster analysis, and transcriptional and post-transcriptional signature profiling. Candidate hub crosslinks between ED and depression were selected after external validation and molecular experiments. Furthermore, subpopulation location and disease association of hub genes were explored.ResultsA total of 85 common genes were identified between ED and depression. These genes strongly correlate with cell adhesion, redox homeostasis, reactive oxygen species metabolic process, and neuronal cell body. An interactive network consisting of 80 proteins and 216 interactions was thereby developed. Analysis of the proteomic signature of common genes highlighted eight major shared genes: CLDN5, COL7A1, LDHA, MAP2K2, RETSAT, SEMA3A, TAGLN, and TBC1D1. These genes were involved in blood vessel morphogenesis and muscle cell activity. A subsequent transcription factor (TF)–miRNA network showed 47 TFs and 88 miRNAs relevant to shared genes. Finally, CLDN5 and TBC1D1 were well-validated and identified as the hub crosslinks between ED and depression. These genes had specific subpopulation locations in the corpus cavernosum and brain tissue, respectively.ConclusionOur study is the first to investigate common transcriptomic alterations and the shared biological roles of ED and depression. The findings of this study provide insights into the referential molecular mechanisms underlying the co-existence between depression and ED

Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification

Advances in molecular biological research of Angelica sinensis

Angelica sinensis (Oliv.) Diels belongs to the Apiaceae family. The root of A. sinensis, is used in traditional Chinese medicine for its antioxidant and immune regulation properties. The main active compounds in A. sinensis include organic acids, phthalides and coumarins, and their biosynthetic pathways are the focus of international attention. A. sinensis is prone to early flowering and bolting, which negatively impacts production for several reasons, including germplasm degradation and quality instability in artificial cultivation. The identification of top-geoherbalism of A. sinensis has also become the focus of recent research, as it would allow selection for breeds with excellent medicinal quality and remarkable curative effects. Advances in sequencing technology and bioinformatic methodologies have enabled extensive molecular and genetic studies in A. sinensis. In this review, we summarize the latest molecular research advances related to A. sinensis, including biosynthetic pathways and regulation of active compounds, and molecular underpinnings of early bolting and flowering and top-geoherbalism. We discuss limitations of the current research and propose prospective topics in need of further exploration

Global Standard Stratotype-Section and Point (GSSP) for the conterminous base of the Miaolingian Series and Wuliuan Stage (Cambrian) at Balang, Jianhe, Guizhou, China

The International Commission on Stratigraphy and the IUGS Executive Committee have recently ratified a Global Standard Stratotype-section and Point (GSSP) defining the conterminous base of the third series and the fifth stage of the Cambrian System. The series and the stage are respectively named the Miaolingian Series and Wuliuan Stage, after the Maioling Mountains in southeastern Guizhou and the Wuliu sidehill, Jianhe County, in eastern Guizhou Province, South China, where the GSSP is located. The GSSP is exposed in a natural outcrop near the Balang Village at a position of 26° 44.843′N latitude and 108° 24.830′E longitude. It is defined at the base of a silty mudstone layer 52.8 m above the base of the Kaili Formation in the Wuliu-Zengjiayan section, coinciding with the first appearance of the cosmopolitan oryctocephalid trilobite Oryctocephalus indicus (base of the O. indicus Zone). Secondary global markers at or near the base of the series and stage include the peak of a rather large negative carbon isotopic excursion (ROECE excursion), the simultaneous appearance of many acanthomorphic acritarch forms, a transgressive phase of a major eustatic event, and the last appearance of intercontinental polymerid trilobites, either Bathynotus or Ovatoryctocara. Faunal turnovers close to the base of the Miaolingian Series and Wuliuan Stage have been recognized as being at the base of the Oryctocephalus indicus Zone of Amgan Stage in Siberia, the Delamaran Stage in Laurentia, the Oryctocephalus indicus Zone in the Indian Himalaya and North Greenland, near the base of the Delamaran Stage in Australia, and within the Eccaparadocides sdzuyi Zone in Iberia and the Ornamentaspis frequens Zone in Morocco