msRepDB: a comprehensive repetitive sequence database of over 80 000 species.

Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).

Parallel computing for genome sequence processing.

The rapid increase of genome data brought by gene sequencing technologies poses a massive challenge to data processing. To solve the problems caused by enormous data and complex computing requirements, researchers have proposed many methods and tools which can be divided into three types: big data storage, efficient algorithm design and parallel computing. The purpose of this review is to investigate popular parallel programming technologies for genome sequence processing. Three common parallel computing models are introduced according to their hardware architectures, and each of which is classified into two or three types and is further analyzed with their features. Then, the parallel computing for genome sequence processing is discussed with four common applications: genome sequence alignment, single nucleotide polymorphism calling, genome sequence preprocessing, and pattern detection and searching. For each kind of application, its background is firstly introduced, and then a list of tools or algorithms are summarized in the aspects of principle, hardware platform and computing efficiency. The programming model of each hardware and application provides a reference for researchers to choose high-performance computing tools. Finally, we discuss the limitations and future trends of parallel computing technologies.

Enhancing nasopharyngeal carcinoma cell radiosensitivity by suppressing AKT/mTOR via CENP-N knockdown.

OBJECTIVE: Investigating the impact of centromere protein N (CENP-N) on radiosensitivity of nasopharyngeal carcinoma (NPC) cells. METHODS: Using immunohistochemistry and immunofluorescence to detect CENP-N expression in tissues from 35 patients with radiosensitive or radioresistant NPC. Assessing the effect of combined CENP-N knockdown and radiotherapy on various cellular processes by CCK-8, colony formation, flow cytometry, and Western blotting. Establishing a NPC xenograft model. When the tumor volume reached 100 mm3, a irradiation dose of 6 Gy was given, and the effects of the combined treatment were evaluated in vivo using immunofluorescence and Western blotting techniques. RESULTS: The level of CENP-N was significantly reduced in radiosensitive tissues of NPC (p < 0.05). Knockdown of CENP-N enhanced NPC radiosensitivity, resulting in sensitizing enhancement ratios (SER) of 1.44 (5-8 F) and 1.16 (CNE-2Z). The combined treatment showed significantly higher levels of proliferation suppression, apoptosis, and G2/M phase arrest (p < 0.01) compared to either CENP-N knockdown alone or radiotherapy alone. The combined treatment group showed the highest increase in Bax and γH2AX protein levels, whereas the protein Cyclin D1 exhibited the greatest decrease (p < 0.01). However, the above changes were reversed after treatment with AKT activator SC79. In vivo, the mean volume and weight of tumors in the radiotherapy group were 182 ± 54 mm3 and 0.16 ± 0.03 g. The mean tumor volume and weight in the combined treatment group were 84 ± 42 mm3 and 0.04 ± 0.01 g. CONCLUSION: Knockdown of CENP-N can enhance NPC radiosensitivity by inhibiting AKT/mTOR.

MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish.

MOTIVATION: Compared with the second-generation sequencing technologies, the third-generation sequencing technologies allows us to obtain longer reads (average ∼10 kbps, maximum 900 kbps), but brings a higher error rate (∼15% error rate). Nanopolish is a variant and methylation detection tool based on hidden Markov model, which uses Oxford Nanopore sequencing data for signal-level analysis. Nanopolish can greatly improve the accuracy of assembly, whereas it is limited by long running time since most executive parts of Nanopolish is a serial and computationally expensive process. RESULTS: In this paper, we present an effective polishing tool, Multithreading Nanopolish (MultiNanopolish), which decomposes the whole process of iterative calculation in Nanopolish into small independent calculation tasks, making it possible to run this process in the parallel mode. Experimental results show that MultiNanopolish reduces running time by 50% with read-uncorrected assembler (Miniasm) and 20% with read-corrected assembler (Canu and Flye) based on 40 threads mode compared to the original Nanopolish. AVAILABILITY AND IMPLEMENTATION: MultiNanopolish is available at GitHub: https://github.com/BioinformaticsCSU/MultiNanopolish. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Sterics and Hydrogen Bonding Control Stereochemistry and Self-Sorting in BINOL-Based Assemblies.

Here we demonstrate how the hydrogen-bonding ability of a BINOL-based dialdehyde subcomponent dictated the stereochemical outcome of its subsequent self-assembly into one diastereomeric helicate form when bearing free hydroxy groups, and another in the case of its methylated congener. The presence of methyl groups also altered the self-sorting behavior when mixed with another, short linear dialdehyde subcomponent, switching the outcome of the system from narcissistic to integrative self-sorting. In all cases, the axial chirality of the BINOL building block also dictated helicate metal center handedness during stereospecific self-assembly. A new family of stereochemically pure heteroleptic helicates were thus prepared using the new knowledge gained. We also found that switching from FeII to ZnII, or the incorporation of a longer linear ligand, favored heteroleptic structure formation.

Large Scale Synthesis of Three-dimensional Hierarchical Porous Framework with High Conductivity and its Application in Lithium Sulfur Battery.

Quick capacity loss due to the polysulfide shuttle effects and poor rate performance caused by low conductivity of sulfur have always been obstacles to the commercial application of lithium sulfur batteries. Herein, an in-situ doped hierarchical porous biochar materials with high electron-ion conductivity and adjustable three-dimensional (3D) macro-meso-micropore is prepared successfully. Due to its unique physical structure, the resulting material has a specific surface area of 2124.9 m2 g-1 and a cumulative pore volume of 1.19 cm3 g-1 . The presence of micropores can effectively physically adsorb polysulfides and mesopores ensure the accessibility of lithium ions and active sites and give the porous carbon material a high specific surface area. The large pores provide channels for the storage of electrolyte and the transmission of ions on the surface of the substrate. The combined effect of these three kinds of pores and the N doping formed in-situ can effectively promote the cycle and rate performance of the battery. Therefore, prepared cathode can still reach a reversible discharge capacity of 616 mAh g-1 at a rate of 5 C. After 400 charge-discharge cycles at 1 C, the reversible capacity is maintained at 510.0 mAh g-1 . This new strategy has provided a new approach to the research and industrial-scale production of adjustable hierarchical porous biochar materials.

Homogeneous Reforming of Aqueous Ethylene Glycol to Glycolic Acid and Pure Hydrogen Catalyzed by Pincer-Ruthenium Complexes Capable of Metal-Ligand Cooperation.

Glycolic acid is a useful and important α-hydroxy acid that has broad applications. Herein, the homogeneous ruthenium catalyzed reforming of aqueous ethylene glycol to generate glycolic acid as well as pure hydrogen gas, without concomitant CO2 emission, is reported. This approach provides a clean and sustainable direction to glycolic acid and hydrogen, based on inexpensive, readily available, and renewable ethylene glycol using 0.5 mol % of catalyst. In-depth mechanistic experimental and computational studies highlight key aspects of the PNNH-ligand framework involved in this transformation.

Severe ileum bleeding following adjuvant capecitabine chemotherapy for locally advanced colon cancer: a case report and review of the literature.

BACKGROUND: Capecitabine is a prodrug that is enzymatically converted to its active form, fluorouracil (also called 5-fluorouracil), which is commonly used as adjuvant chemotherapy in colorectal cancer patients. Severe gastrointestinal bleeding induced by capecitabine is rare. Here, we are presenting the first case report of surgery specimen assisted diagnosis of this uncommon condition. CASE PRESENTATION: A 63-year-old Chinese male with a history of colon adenocarcinoma and right hemicolectomy presented with severe lower gastrointestinal bleeding 2 days after finishing capecitabine administration during the first cycle of XELOX adjuvant chemotherapy. Because of the negative findings of active bleeding points by digital subtraction angiography (DSA) or colonoscopy, emergency laparotomy and partial enterectomy were performed. The bloody diarrhea had resolved after surgery and a terminal ileitis was diagnosed after pathological examination of the surgical specimen. CONCLUSIONS: Terminal ileitis induced by capecitabine is likely to be underreported. It should be considered more often as a cause of severe gastrointestinal bleeding during or after treatment with capecitabine agents. Emergency surgery may achieve satisfactory outcomes if endoscopic hemostasis is ineffective. HIGHLIGHTS OF THIS CASE: 1. Gastrointestinal bleeding following capecitabine treatment in colorectal cancer patients might be life-threatening. 2. Terminal ileitis induced by capecitabine should always be considered in the differential diagnosis of severe gastrointestinal bleeding. 3. Awareness of the risk factors such as deficiency of dihydropyrimidine dehydrogenase, advanced age, or right colectomy may aid in reducing capecitabine-related morbidity. 4. When severe bleeding occurs, emergency surgery may achieve satisfactory outcomes if medical and endoscopic interventions are ineffective.

Intussusception after reconstruction following gastrectomy for gastric cancer.

BACKGROUND: Gastric cancer is the most prevalent tumor in Chinese men, and surgery is currently the most important treatment. Billroth II and Roux-en-Y are the anastomosis methods used for reconstruction after gastrectomy. Jejunal intussusception is a rare complication after gastric surgery. MAIN BODY: Intussusception after gastric surgery occurs mostly at the gastrojejunostomy site for Billroth II reconstruction, and the Y-anastomosis site for Roux-en-Y reconstruction. Many studies have reported that postoperative intussusception appears at the anastomosis after bariatric surgery, while a few have reported intussusception at the anastomosis and its distal end after radical gastrectomy. CONCLUSION: A review was carried out to analyze intussusception after radical gastrectomy with roux-en-y anastomosis during the current situation. And the relevant mechanisms, diagnosis, treatment methods, etc. are described, hoping to provide better guidance for clinicians.

The Issue of Recurrently Positive Patients Who Recovered From COVID-19 According to the Current Discharge Criteria: Investigation of Patients from Multiple Medical Institutions in Wuhan, China.

The current discharge criteria for COVID-19 require that patients have 2 consecutive negative results for reverse transcription polymerase chain reaction (RT-PCR) detection. Here, we observed that recurrent positive RT-PCR test results in patients with 3 consecutive negative results (5.4%) were significantly decreased compared with those in patients with 2 consecutive negative results (20.6%); such patients reported positive RT-PCR test results within 1 to 12 days after meeting the discharge criteria. These results confirmed that many recovered patients could show a positive RT-PCR test result, and most of these patients could be identified by an additional RT-PCR test prior to discharge.

Plac8-mediated autophagy regulates nasopharyngeal carcinoma cell function via AKT/mTOR pathway.

To explore the relationship between autophagy and cell function, we investigated how PLAC8-mediated autophagy influences proliferation, apoptosis and epithelial-mesenchymal transition (EMT) in NPC. Colony formation analyses and CCK8 assays were used to assess the proliferative capacity of NPC cells. Transmission electron microscopy (TEM) was used to identify autophagosomes. Autophagic flux was monitored using the tandem monomeric RFP-GFP-tagged LC3 (tfLC3) assay. The rate of apoptosis in NPC cells was analysed by flow cytometry. Western blot analysis was used to evaluate the activation of autophagy and the signalling status of the AKT/mTOR pathway. Our study reveals that knocking out PLAC8 (koPLAC8) induces autophagy and apoptosis, while suppressing NPC cell proliferation and EMT. However, inhibition of autophagy with 3-methyladenine or by knocking down Beclin-1 reverses the cell proliferation, apoptosis and EMT influenced by koPLAC8. We find that koPLAC8 inhibits the phosphorylation of AKT and its downstream target, mTOR. Moreover, immunofluorescence and co-immunoprecipitation reveal complete PLAC8/AKT colocalization and PLAC8/AKT interaction, respectively. Furthermore, knockout of PLAC8 induced autophagy and inactivated AKT/mTOR signalling pathway of NPC xenografts. Overall, our findings demonstrate that koPLAC8 induces autophagy via the AKT/mTOR pathway, thereby inhibiting cell proliferation and EMT, and promoting apoptosis in NPC cells.

Hydrogenative Depolymerization of Nylons.

The widespread crisis of plastic pollution demands discovery of new and sustainable approaches to degrade robust plastics such as nylons. Using a green and sustainable approach based on hydrogenation, in the presence of a ruthenium pincer catalyst at 150 °C and 70 bar H2, we report here the first example of hydrogenative depolymerization of conventional, widely used nylons and polyamides, in general. Under the same catalytic conditions, we also demonstrate the hydrogenation of a polyurethane to produce diol, diamine, and methanol. Additionally, we demonstrate an example where monomers (and oligomers) obtained from the hydrogenation process can be dehydrogenated back to a poly(oligo)amide of approximately similar molecular weight, thus completing a closed loop cycle for recycling of polyamides. Based on the experimental and density functional theory studies, we propose a catalytic cycle for the process that is facilitated by metal-ligand cooperativity. Overall, this unprecedented transformation, albeit at the proof of concept level, offers a new approach toward a cleaner route to recycling nylons.

A Reversible Liquid-to-Liquid Organic Hydrogen Carrier System Based on Ethylene Glycol and Ethanol.

Liquid organic hydrogen carriers (LOHCs) are powerful systems for the efficient unloading and loading molecular hydrogen. Herein, a liquid-to-liquid organic hydrogen carrier system based on reversible dehydrogenative coupling of ethylene glycol (EG) with ethanol catalysed by ruthenium pincer complexes is reported. Noticeable advantages of the current LOHC system is that both reactants (hydrogen-rich components) and the produced esters (hydrogen-lean components) are liquids at room temperature, and the dehydrogenation process can be performed under solvent and base-free conditions. Moreover, the hydrogenation reaction proceeds under low hydrogen pressure (5 bar), and the LOHC system has a relatively high theoretical gravimetric hydrogen storage capacity (HSC>5.0 wt %), presenting an attractive hydrogen storage system.

A Thioxanthone Sensitizer with a Chiral Phosphoric Acid Binding Site: Properties and Applications in Visible Light-Mediated Cycloadditions.

A chiral phosphoric acid with a 2,2'-binaphthol core was prepared that displays two thioxanthone moieties at the 3,3'-position as light-harvesting antennas. Despite its relatively low triplet energy, the phosphoric acid was found to be an efficient catalyst for the enantioselective intermolecular [2+2] photocycloaddition of ß-carboxyl-substituted cyclic enones (e.r. up to 93:7). Binding of the carboxylic acid to the sensitizer is suggested by NMR studies and by DFT calculations to occur by means of two hydrogen bonds. The binding event not only enables an enantioface differentiation but also modulates the triplet energy of the substrates.

Placenta specific 8 gene induces epithelial-mesenchymal transition of nasopharyngeal carcinoma cells via the TGF-ß/Smad pathway.

The present study aimed to investigate the effects and mechanisms of PLAC8 on the epithelial-mesenchymal transition (EMT) of Nasopharyngeal carcinoma (NPC). The expression of PLAC8 in NPC and nasopharyngitis (NPG) tissues from 150 patients was determined using immunohistochemistry. The levels of PLAC8 in five NPC cell lines and nasopharyngeal permanent epithelial cell line were measured using western blotting. We then knocked out or overexpressed PLAC8 in CNE2 cells. Cell proliferation, wound healing, migration, and invasion assays were used to analyze the effects of PLAC8 on the proliferation, migration, and invasion in vivo and vitro. The results showed that the expression of PLAC8 was much higher in NPC tissues than in NPG tissues. The expression of PLAC8 was higher in all the cell lines than in the nasopharyngeal permanent epithelial cells. PLAC8 knockout resulted in significant decreases in cell proliferation, migration, and invasion; associated with lower protein levels of N-cadherin; and increased levels of E-cadherin. Overexpression of PLAC8 had the opposite effect. Furthermore, knockout of PLAC8 inactivated TGF-ß/SMAD signaling pathway and suppressed the growth of NPC xenografts. PLAC8 may promote the carcinogenesis and EMT of NPC via the TGF-ß/Smad pathway, which suggests that PLAC8 may be a potential biomarker for NPC.

Correlating Transcriptional Networks to Acute Rejection in Human Kidney Transplant Biopsies.

Acute rejection (AR) in kidney transplants remains a major cause of allograft failure. This study investigates the association between gene networks and AR in human kidney transplant biopsies with weighted gene co-expression network analysis (WGCNA). The gene expression profiles of 403 (training set) and 702 (validation set) kidney transplant patients' biopsies were analyzed. WGCNA was conducted, and 11 co-regulated gene modules were identified. Each module was investigated with a t-test for AR and survival analysis for graft loss. The association between modules and AR molecular subtypes was also evaluated. Three transcriptional gene modules were associated with AR and graft loss of kidney transplant. One module constitutes unregulated immune response genes in AR and is associated with shorter graft survival (HR = 4.22, p-value = 4.29 × 10-6). This module is more significantly up-regulated in T cell-mediated acute rejection (TCMR) than in non-TCMRs. Hub genes such as HLA-DMA, CORO1A, PYCARD, and CD53 were identified. The expression of the other two modules was down-regulated in AR patients and associated with a good graft prognosis (HR = 0.41 and 0.24, respectively). A systems biology network approach may help uncover gene networks in kidney transplant biopsies associated with AR and contribute to identifying new biomarkers.

Iminium and enamine catalysis in enantioselective photochemical reactions.

Although enantioselective catalysis under thermal conditions has been well established over the last few decades, the enantioselective catalysis of photochemical reactions is still a challenging task resulting from the complex enantiotopic face differentiation in the photoexcited state. Recently, remarkable achievements have been reported by a synergistic combination of organocatalysis and photocatalysis, which have led to the expedient construction of a diverse range of enantioenriched molecules which are generally not easily accessible under thermal conditions. In this tutorial review, we summarize and highlight the most significant advances in iminium and enamine catalysis of enantioselective photochemical reactions, with an emphasis on catalytic modes and reaction types.

Recent Advances in Enantioselective Photochemical Reactions of Stabilized Diazo Compounds.

Diazo compounds have proven to be a useful class of carbenes or metal carbenoids sources under thermal, photochemical, or metal-catalyzed conditions, which can subsequently undergo a wide range of synthetically important transformations. Recently, asymmetric photocatalysis has provoked increasing research interests, and great advances have been made in this discipline towards the synthesis of optically enriched compounds. In this context, the past two decades have been the most productive period in the developments of enantioselective photochemical reactions of diazo compounds due to a better understanding of the reactivities of diazo compounds and the emergence of new catalytic modes, as well as easier access to and treatment of stabilized diazo compounds. This review highlights these impressive achievements according to the reaction type, and the general mechanisms and stereochemical inductions are briefly discussed as well.

Visible-Light-Induced Organic Photochemical Reactions through Energy-Transfer Pathways.

Visible-light photocatalysis is a rapidly developing and powerful strategy to initiate organic transformations, as it closely adheres to the tenants of green and sustainable chemistry. Generally, most visible-light-induced photochemical reactions occur through single-electron transfer (SET) pathways. Recently, visible-light-induced energy-transfer (EnT) reactions have received considerable attentions from the synthetic community as this strategy provides a distinct reaction pathway, and remarkable achievements have been made in this field. In this Review, we highlight the most recent advances in visible-light-induced EnT reactions.

Recent Advances in the Synthesis of Cyclobutanes by Olefin [2 + 2] Photocycloaddition Reactions.

The [2 + 2] photocycloaddition is undisputedly the most important and most frequently used photochemical reaction. In this review, it is attempted to cover all recent aspects of [2 + 2] photocycloaddition chemistry with an emphasis on synthetically relevant, regio-, and stereoselective reactions. The review aims to comprehensively discuss relevant work, which was done in the field in the last 20 years (i.e., from 1995 to 2015). Organization of the data follows a subdivision according to mechanism and substrate classes. Cu(I) and PET (photoinduced electron transfer) catalysis are treated separately in sections 2 and 4 , whereas the vast majority of photocycloaddition reactions which occur by direct excitation or sensitization are divided within section 3 into individual subsections according to the photochemically excited olefin.