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The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use.

Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets.

The source code of GNET2 is available at https//github.com/jianlin-cheng/GNET2.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.The aim of this report was to document a rare case of medication-related osteonecrosis of the jaw (MRONJ) that developed around the already osseointegrated implants in the maxillary right molar region. A 73-year-old woman presented at our university dental hospital in May 2017 with a chief complaint of discomfort near a maxillary implant. During the implant maintenance period, the patient began taking alendronate sodium hydrate (Fosamac ® tablets 35 mg once weekly), an oral bisphosphonate (BP), for treatment of osteoporosis. Eight years after starting implant maintenance, peri-implantitis occurred, for which mechanical cleaning and antimicrobial therapy was performed. Peri-implantitis symptoms disappeared, and the medical condition improved. However, MRONJ developed 4 years after she commenced taking the BP. The patient underwent implant removal and sequestrectomy. There was no postoperative recurrence. The events this patient experienced imply that a local infection around an implant and type 1 diabetes are factors in MRONJ development. It is important to note that implants in patients taking BPs should be more carefully maintained. In addition, we performed literature review and discovered only a few similar cases.The aim was to assess the influence of moderate cigarette-smoking on the clinical (bleeding on probing [BoP] and probing depth [PD]) and radiographic (crestal bone resorption [CBR]) around cement- and screw-retained dental implants at 5 years' follow-up. A questionnaire was used to collect information about age, gender, smoking history, duration of implants in function, jaw location of the implant, and daily toothbrushing and flossing. Peri-implant BoP, PD and CBR were measured in all groups. Group comparisons were performed using one-way analysis of variance and for multiple comparisons, the Bonferroni Post hoc adjustment test was performed. Level of significance was set at P less then 0.05. Forty-eight patients (25 smokers and 23 non-smokers) had cement-retained dental implants; and 48 (24 smokers and 24 non-smokers) had screw-retained dental implants. Among patients with cement and screw-retained dental implants, PD (P less then 0.05) and CBR (P less then 0.05) were significantly higher among smokers than ted to the clinicoradiographic inflammatory parameters around cement- and screw-retained dental implants.Different types of internal implant-abutment connections, namely hexagon and conical, have been used for implant restoration. However, data regarding the benefits of these internal connections in terms of clinical outcomes are scarce. Accordingly, the aim of this study was to compare radiographic marginal bone loss (RMBL) and associated implant complications between implants with internal hexagon (IH) connections and those with internal conical (IC) connections. Forty-nine patients with 98 implants (two per patient) placed in the posterior mandible were recruited. All implants were inserted in pairs in solid D2 bone according to a randomized sequence; the first patient received an IH connection implant on the mesial side while the second patient received an IC connection implant on the mesial side. Each patient received one implant with an IH connection and one with an IC connection, placed side-by-side. Four months after placement, all implants were loaded with single screw-retained ceramic restorations with internal hexagon or conical connections. RMBL and complications, including implant/prosthesis failure, were recorded at the time of implant loading (baseline) and 6, 12, and 36 months after loading. The results revealed no significant between-group differences in RMBL (P = .74), gingival bleeding on probing (P = .29), and complications (P = .32). Thus, the type of internal implant-abutment connection did not affect clinical outcomes, including RMBL and implant/prosthesis failure. Future studies should additionally evaluate long-term prosthesis-related complications such as screw loosening and fracture between the two types of internal connections.

Data mining and data quality evaluation are indispensable constituents of quantitative proteomics, but few integrated tools available.

We introduced obaDIA, a one-step pipeline to generate visualizable and comprehensive results for quantitative proteomics data. obaDIA supports fragment-level, peptide-level and protein-level abundance matrices from DIA technique, as well as protein-level abundance matrices from other quantitative proteomic techniques. The result contains abundance matrix statistics, differential expression analysis, protein functional annotation and enrichment analysis. Additionally, enrichment strategies which use total proteins or expressed proteins as background are optional, and HTML based interactive visualization for differentially expressed proteins in the KEGG pathway is offered, which helps biological significance mining. In short, obaDIA is an automatic tool for bioinformatics analysis for quantitative proteomics.

obaDIA is freely available from https//github.com/yjthu/obaDIA.git.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.The teaching-learning process becomes more attractive when practical classes are used as part of methodological tools. Aiming (i) to stimulate the interest of high school students in the microbiological world and (ii) to provide didactic experience for microbiology graduate students, practical classes were undertaken. These classes were carried out during the years 2016 and 2017, using the infrastructure held at Universidade Federal de Viçosa. Briefly, laboratory classes were prepared and taught by microbiology graduate students and an evaluation questionnaire was answered by the participants after the classes. Approximately 95% of the high school students, from both years, evaluated the experience outside of the school routine as very good and good. A total of 90.09% (2016) and 100% (2017) of graduate students evaluated this experience as very good and good. The relationship between high school and graduate students also increased the curiosity of the former regarding the university environment. Accordingly, the information retention regarding the 'microbiology world' was verified after one year and the students were able to remember important terms related to the microbiology class. In addition, this work allowed graduate students and high school students to build a closer relationship and created an excellent teaching-learning strategy for both.The optimal duration of eculizumab treatment in patients with atypical haemolytic uremic syndrome (aHUS) remains poorly defined. We conducted a prospective national multicentric open-label study in order to assess eculizumab discontinuation in children and adults with aHUS. Fifty-five patients (including 19 children) discontinued eculizumab (mean duration of treatment, 16.5 months). Twenty-eight (51%) patients had complement gene rare variants, mostly in MCP (n= 12, 22%), CFH (n= 6, 11%) and CFI (n=6, 10%) genes. At eculizumab discontinuation, 17 (30%) and 4 (7%) patients had chronic kidney disease stage 3 and 4, respectively. During follow-up, 13 (23%) patients (6 children and 7 adults) experienced aHUS relapse. In multivariable analysis, female gender and the presence of a rare complement gene variant were associated with an increased risk of aHUS relapse, whereas requirement for dialysis during previous episodes of acute aHUS was not. In addition, an increased soluble C5b-9 plasma level at eculizumab discontinuation was associated with a higher risk of aHUS relapse in all patients and in the subset of carriers of complement gene rare variants, in log rank test and in multivariable analysis. Among the 13 relapsing patients, who were all restarted on eculizumab, 11 regained their baseline renal function and two had a worsening of their pre-existing chronic kidney disease, including one patient who progressed to end-stage renal disease. A strategy of eculizumab discontinuation in aHUS patients based on complement genetics is reasonable and safe. It improves the management and quality of life of a sizeable proportion of aHUS patients while reducing the cost of treatment. Trail registration number NCT02574403.Traditional Chinese medicine (TCM), such as Huanglian-Jie-Du-Tang, a heat-clearing and detoxifying decoction is beneficial to alleviation of inflammation-related diseases. The objective of this study is to uncover the effect and mechanism of heat-clearing, detoxifying and blood stasis removing decoction (HDBD) on the treatment of acute soft tissue injury (STI) which is characterized with excessive inflammatory cascade at the onset. Male Sprague-Dawley (SD) rats with hammer beating served as the in vivo models of acute STI. Haematoxylin-eosin (HE) staining was used for histopathology assessment. The levels of inflammatory factors, including prostaglandin E2 (PGE2), tumor necrosis factor-αumTNF-α), interleukin (IL)-1t and IL-6 were measured by enzyme linked immunosorbent assay (ELISA). Human dermal microvascular endothelium cell line HMEC-1 and rat vascular endothelium cell line RAOEC were used to explore the mechanism in vitro. Luciferase gene reporter assay was applied to determine the relationship between miR-26b-5p and COX2. The results showed that HDBD intervention significantly reduced the temperature difference between the healthy side and affected side of rats with hammer beating, together with the decreased levels of COX2, PGE2, TNF-α, IL-6 and IL-1β, and the increased level of miR-26b-5p. In mechanism, miR-26b-5p targeted COX2 and decreased its expression, leading to significant decreases in the levels of PGE2, TNF-α and IL-6 in RAOEC and HMEC-1 cells. In addition, miR-26b-5p inhibition impaired the effects of HDBD on the suppression of PGE2, TNF-α, IL-6 and IL-1β in vitro. In conclusion, this study revealed that HDBD relieved acute STI via modulating miR-26b-5p/COX2 axis to inhibit inflammation.Although both the granular layer of the prefrontal cortex (PFC) and schizophrenia are unique in primates, especially humans, their linkage is unclear. Here, we tested whether schizophrenia is associated with expression profiles of the granule cell (GC)-related genes in the human PFC. We identified 14 candidate GC-related genes with gradually increased expression levels along the gradient of the agranular, dysgranular, light-granular, and granular prefrontal regions based on the densely sampled gene expression data of 6 postmortem human brains, and with more than 10-fold expression in neurons than other cell types based on the single-cell RNA-sequencing data of the human PFC. These GC-related genes were functionally associated with synaptic transmission and cell development and differentiation. selleck screening library The identified 14 GC-related genes were significantly enriched for schizophrenia, but not for depression and bipolar disorder. The expression levels of the 4 stable schizophrenia- and GC-related genes were spatially correlated with gray matter volume differences in the PFC between patients with schizophrenia and healthy controls.