Excellent ratiometric two-photon fluorescent probes for hydrogen sulfide detection based on the fluorescence resonance energy transfer mechanism.

Fluorescence resonance energy transfer (FRET) is an important mechanism to design ratiometric fluorescent probes that are able to detect analytes quantitatively according to the ratio of two well-resolved emission signals. Two-photon (TP) fluorescent probes can realize the detection in living cells and tissues with deeper penetration depth, higher resolution, and lower photodamage in contrast to one-photon fluorescent probes. However, to date, fabricating TP-FRET ratiometric fluorescent probes possessing large two-photon absorption (TPA), high fluorescence quantum yield and perfect FRET efficiency is still challenging. Consequently, to develop excellent TP-FRET ratiometric probes and explore the relationship between their molecular structures and TP fluorescence properties, in this paper, we designed a series of H2S-detecting TP fluorescent probes employing the FRET mechanism based on an experimental probe BCD. Thereafter, we comprehensively evaluated the TP sensing performance of these probes by means of time-dependent density functional theory and quadratic response theory. Furthermore, we determined energy transfer efficiency and fluorescence quantum yield. Significantly, through regulating benzene-fused positions, we successfully improved fluorescence quantum yield and TPA cross-section simultaneously. Large spectral overlap between energy donor emission and acceptor absorption was achieved and near perfect energy transfer efficiency was acquired for all the studied probes. We revealed that these probes exhibit two well-resolved TPA bands, which are contributed by FRET donors and acceptors, respectively. Especially, both the wavelengths and the cross-sections of the two TPA bands agree well with those of energy donors and acceptors, which is the unique TPA spectral profile of FRET probes and has never been previously reported. Moreover, we proposed an excellent TP-FRET probe BCD3 and its product molecule BCD3-H2S, which exhibit large Stokes (141 nm and 88 nm) and emission shifts (5931 cm-1), as well as greatly increased TP action cross-sections (24-fold and 60-fold) in the near-infrared region with respect to BCD and BCD-H2S. Our detailed study can give an insight into the efficient design of novel TP-FRET fluorescent probes.

Association study between drug prescriptions and Alzheimer's disease claims in a commercial insurance database.

In the ongoing effort to discover treatments for Alzheimer's disease (AD), there has been considerable focus on investigating the use of repurposed drug candidates. Mining of electronic health record data has the potential to identify novel correlated effects between commonly used drugs and AD. In this study, claims from members with commercial health insurance coverage were analyzed to determine the correlation between the use of various drugs on AD incidence and claim frequency. We found that, within the insured population, several medications for psychotic and mental illnesses were associated with higher disease incidence and frequency, while, to a lesser extent, antibiotics and anti-inflammatory drugs were associated with lower AD incidence rates. The observations thus provide a general overview of the prescription and claim relationships between various drug types and Alzheimer's disease, with insights into which drugs have possible implications on resulting AD diagnosis.

Serum glial cell line-derived neurotrophic factor (GDNF) a potential biomarker of executive function in Parkinson's disease.

Objective: Evidence shows that the impairment of executive function (EF) is mainly attributed to the degeneration of frontal-striatal dopamine pathway. Glial cell line-derived neurotrophic factor (GDNF), as the strongest protective neurotrophic factor for dopaminergic neurons (DANs), may play a role in EF to some extent. This study mainly explored the correlation between serum GDNF concentration and EF performance in Parkinson's disease (PD). Methods: This study recruited 45 healthy volunteers (health control, HC) and 105 PD patients, including 44 with mild cognitive impairment (PD-MCI), 20 with dementia (PD-D), and 20 with normal cognitive function (PD-N). Neuropsychological tests were performed to evaluate EF (working memory, inhibitory control, and cognitive flexibility), attention, language, memory, and visuospatial function. All subjects were tested for serum GDNF and homovanillic acid (HVA) levels by ELISA and LC-ESI-MS/MS, respectively. Results: PD-MCI patients showed impairments in the trail making test (TMT) A (TMT-A), TMT-B, clock drawing test (CDT) and semantic fluency test (SFT), whereas PD-D patients performed worse in most EF tests. With the deterioration of cognitive function, the concentration of serum GDNF and HVA in PD patients decreased. In the PD group, the serum GDNF and HVA levels were negatively correlated with TMT-A (r GDNF = -0.304, P < 0.01; r HVA = -0.334, P < 0.01) and TMT-B (r GDNF = -0.329, P < 0.01; r HVA = -0.323, P < 0.01) scores. Serum GDNF levels were positively correlated with auditory verbal learning test (AVLT-H) (r = 0.252, P < 0.05) and SFT (r = 0.275, P < 0.05) scores. Serum HVA levels showed a positively correlation with digit span test (DST) (r = 0.277, P < 0.01) scores. Stepwise linear regression analysis suggested that serum GDNF and HVA concentrations and UPDRS-III were the influence factors of TMT-A and TMT-B performances in PD patients. Conclusion: The decrease of serum GDNF concentration in PD patients was associated with impaired inhibitory control, cognitive flexibility, and attention performances. The changes of GDNF and HVA might synergistically participate in the occurrence and development of executive dysfunction in PD patients.

A novel missense mutation in SPAST causes hereditary spastic paraplegia in male members of a family: A case report.

Hereditary spastic paraplegia (HSP) comprises a group of hereditary and neurodegenerative diseases that are characterized by axonal degeneration or demyelination of bilateral corticospinal tracts in the spinal cord; affected patients exhibit progressive spasticity and weakness in the lower limbs. The most common manifestation of HSP is spastic paraplegia type 4 (SPG4), which is caused by mutations in the spastin (SPAST) gene. The present study reports the clinical characteristics of affected individuals and sequencing analysis of a mutation that caused SPG4 in a family. All affected family members exhibited spasticity and weakness of the lower limbs and, notably, only male members of the family were affected. Whole­exome sequencing revealed that all affected individuals had a novel c.1785C>A (p. Ser595Arg) missense mutation in SPAST. Bioinformatics analysis revealed changes in both secondary and tertiary structures of the mutated protein. The novel missense mutation in SPAST supported the diagnosis of SPG4 in this family and expands the spectrum of pathogenic mutations that cause SPG4. Analysis of SPAST sequences revealed that most pathogenic mutations occurred in the AAA domain of the protein, which may have a close relationship with SPG4 pathogenesis.

Design and application of a knowledge network for automatic prioritization of drug mechanisms.

MOTIVATION: Drug repositioning is an attractive alternative to de novo drug discovery due to reduced time and costs to bring drugs to market. Computational repositioning methods, particularly non-black-box methods that can account for and predict a drug's mechanism, may provide great benefit for directing future development. By tuning both data and algorithm to utilize relationships important to drug mechanisms, a computational repositioning algorithm can be trained to both predict and explain mechanistically novel indications. RESULTS: In this work, we examined the 123 curated drug mechanism paths found in the drug mechanism database (DrugMechDB) and after identifying the most important relationships, we integrated 18 data sources to produce a heterogeneous knowledge graph, MechRepoNet, capable of capturing the information in these paths. We applied the Rephetio repurposing algorithm to MechRepoNet using only a subset of relationships known to be mechanistic in nature and found adequate predictive ability on an evaluation set with AUROC value of 0.83. The resulting repurposing model allowed us to prioritize paths in our knowledge graph to produce a predicted treatment mechanism. We found that DrugMechDB paths, when present in the network were rated highly among predicted mechanisms. We then demonstrated MechRepoNet's ability to use mechanistic insight to identify a drug's mechanistic target, with a mean reciprocal rank of 0.525 on a test set of known drug-target interactions. Finally, we walked through repurposing examples of the anti-cancer drug imatinib for use in the treatment of asthma, and metolazone for use in the treatment of osteoporosis, to demonstrate this method's utility in providing mechanistic insight into repurposing predictions it provides. AVAILABILITY AND IMPLEMENTATION: The Python code to reproduce the entirety of this analysis is available at: https://github.com/SuLab/MechRepoNet (archived at https://doi.org/10.5281/zenodo.6456335). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Anatomical elucidation and histological study of pelvic autonomic nerve-plane based female fresh cadaver / 中华妇产科杂志

Objective:To investigate the rationality of nerve-plane sparing radical hysterectomy (NPSRH) for cervical cancer by observing the anatomical and histological characteristics of pelvic autonomic plane based on fresh cadaver.Methods:From October 2015 to September 2020, 14 fresh female cadavers were anatomically and histologically studied in the Laboratory of Anatomy and Embryology Department, Peking Union Medical College, Chinese Academy of Medical Sciences. The median age of the specimens was 79 years (range: 67 to 92 years). Twenty-eight hemi-pelvic specimens were obtained from 14 fresh female cadavers. NPSRH procedures were simulated in 8 hemi-pelvic cavities to prove its feasibility. Detailed dissection was conducted to recognize nerve plane and to observe the distribution of pelvic nerves in 10 hemipelvis. In the other 10 hemipelvis, whole parametrium tissue was taken from the crossing of ureter and the uterine artery to the ureterovesical entrance and be embedded, then continuous section was performed, and was stained by hematoxylin-eosin staining (HE) to observe the relationship of nerves and vessels. Immunohistochemical staining of S100, tyrosine dehydrogenase (TH), and vasoactive intestinal peptide (VIP) were performed to count and distinguish sympathetic and parasympathetic nerves, respectively.Results:(1) The pelvic autonomic nerve-plane was completely preserved in 7 of 8 hemipelvis by simulating NPSRH. (2) After detailed dissection in 10 hemipelvis, it was found that hypogastric nerve, pelvic splanchnic nerve, and their confluence of inferior hypogastric plexus were distributed in a planar statelocating in the ureteral mesentery and its caudal extension. This nerve plane showed a cross relationship with deep uterine vein and its branches. The bladder branches and vesical venous plexus were closely related to the inferior hypogastric plexus. The middle vesical vein and inferior vesical vein were intact in 7 of 10 hemipelvis, and either vesical vein was missing in 3 of them. It was observed that the vesical venous plexus communicated with the deep uterine vein trunk on the medial side of the nerve plane in 6 hemipelvis, while flowed into the deep uterine vein on the lateral side of the nerve plane in 2 hemipelvis, and in the other 2 hemipelvis it directly flowed into the internal iliac vein. (3) It was revealed that autonomic nerves were continuously distributed beneath the ureteral with sagittal plane by HE staining. The average nerve content below the ureteral width was 70.9% of the total in nerve plane by S100 staining. TH and VIP staining showed that the average number of sympathetic fibers was 13.5 and parasympathetic fibers was 8.2, reminding sympathetic predominated.Conclusion:Pelvic autonomic nerves are mainly distributed within the mesangial plane below the ureter, which provides an anatomic justification for NPSRH.

Study on structural characterization, physicochemical properties and digestive properties of euryale ferox resistant starch.

At present, the raw materials for industrialized RS3 products are relatively simple and its purity is low. In addition, the correlation between structure and digestion characteristics of RS3 are rarely studied. In this study, euryale ferox, a kind of annual aquatic herb crop with high content of starch was used as a raw material to prepare RS3 by different methods, including autoclaving, enzymolysis-autoclaving and dual enzymolysis, respectively. The results showed that there were significant differences in the structure and physicochemical properties of the different euryale ferox resistant-enhanced and purified resistant starches (p < 0.05). Purified euryale ferox resistant starches belonged to B + V type crystal and had high thermal stability. After digestion, the structure and thermal properties of euryale ferox resistant-enhanced starches changed a lot. The digestion rate and estimated glycemic index (eGI) of the three kinds of purified euryale ferox RS3 were lower than 20% and 50%, respectively.

Specific determination of hepatitis B e antigen by antibodies targeting precore unique epitope facilitates clinical diagnosis and drug evaluation against hepatitis B virus infection.

Hepatitis B e antigen (HBeAg) is a widely used marker both for chronic hepatitis B (CHB) clinical management and HBV-related basic research. However, due to its high amino acid sequence homology to hepatitis B core antigen (HBcAg), most of available anti-HBe antibodies are cross-reactive with HBcAg resulting in high interference against accurate measurement of the status and level of HBeAg. In the study, we generated several monoclonal antibodies (mAbs) targeting various epitopes on HBeAg and HBcAg. Among these mAbs, a novel mAb 16D9, which recognizes the SKLCLG (aa -10 to -5) motif on the N-terminal residues of HBeAg that is absent on HBcAg, exhibited excellent detection sensitivity and specificity in pairing with another 14A7 mAb targeting the HBeAg C-terminus (STLPETTVVRRRGR, aa141 to 154). Based on these two mAbs, we developed a novel chemiluminescent HBeAg immunoassay (NTR-HBeAg) which could detect HBeAg derived from various HBV genotypes. In contrast to widely used commercial assays, the NTR-HBeAg completely eliminated the cross-reactivity with secreted HBcAg from precore mutant (G1896A) virus in either cell culture or patient sera. The improved specificity of the NTR-HBeAg assay enables its applicability in cccDNA-targeting drug screening in cell culture systems and also provides an accurate tool for clinical HBeAg detection.

Down-Regulated CUEDC2 Increases GDNF Expression by Stabilizing CREB Through Reducing Its Ubiquitination in Glioma.

Abnormally high expression of glial cell line-derived neurotrophic factor (GDNF) derived from glioma cells has essential impacts on gliomagenesis and development, but the molecular basis underlying increased GDNF expression in glioma cells remain unclear. This work aimed to study the molecular mechanisms that may explain the accumulation of GDNF in glioma. Firstly, we observed that cAMP response element-binding protein (CREB), known as an important transcription factor for binding of GDNF promoter region, was highly expressed with an apparent accumulation into the nucleus of glioma cells, which may contribute to the transcription of GDNF. Secondly, CUE domain-containing protein 2 (CUEDC2), a ubiquitin-regulated protein, could increase the amount of binding between the E3 ligase tripartite motif-containing 21 (TRIM21) and CREB and affect the CREB level. Like our previous study, it showed that there was a significantly down-regulation of CUEDC2 in glioma. Finally, our data suggest that GDNF expression is indirectly regulated by transcription factor ubiquitination. Indeed, down-regulation of CUEDC2, decreased the ubiquitination and degradation of CREB, which was associated to high levels of GDNF. Furthermore, abundant CREB involved in the binding to the GDNF promoter region contributes to GDNF high expression in glioma cells. Collectively, it was verified the GDNF expression was affected by CREB ubiquitination regulated by CUEDC2 level.

Structured reviews for data and knowledge-driven research.

Hypothesis generation is a critical step in research and a cornerstone in the rare disease field. Research is most efficient when those hypotheses are based on the entirety of knowledge known to date. Systematic review articles are commonly used in biomedicine to summarize existing knowledge and contextualize experimental data. But the information contained within review articles is typically only expressed as free-text, which is difficult to use computationally. Researchers struggle to navigate, collect and remix prior knowledge as it is scattered in several silos without seamless integration and access. This lack of a structured information framework hinders research by both experimental and computational scientists. To better organize knowledge and data, we built a structured review article that is specifically focused on NGLY1 Deficiency, an ultra-rare genetic disease first reported in 2012. We represented this structured review as a knowledge graph and then stored this knowledge graph in a Neo4j database to simplify dissemination, querying and visualization of the network. Relative to free-text, this structured review better promotes the principles of findability, accessibility, interoperability and reusability (FAIR). In collaboration with domain experts in NGLY1 Deficiency, we demonstrate how this resource can improve the efficiency and comprehensiveness of hypothesis generation. We also developed a read-write interface that allows domain experts to contribute FAIR structured knowledge to this community resource. In contrast to traditional free-text review articles, this structured review exists as a living knowledge graph that is curated by humans and accessible to computational analyses. Finally, we have generalized this workflow into modular and repurposable components that can be applied to other domain areas. This NGLY1 Deficiency-focused network is publicly available at http://ngly1graph.org/. AVAILABILITY AND IMPLEMENTATION: Database URL: http://ngly1graph.org/. Network data files are at: https://github.com/SuLab/ngly1-graph and source code at: https://github.com/SuLab/bioknowledge-reviewer. CONTACT: asu@scripps.edu.

Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network.

BACKGROUND: Computational compound repositioning has the potential for identifying new uses for existing drugs, and new algorithms and data source aggregation strategies provide ever-improving results via in silico metrics. However, even with these advances, the number of compounds successfully repositioned via computational screening remains low. New strategies for algorithm evaluation that more accurately reflect the repositioning potential of a compound could provide a better target for future optimizations. RESULTS: Using a text-mined database, we applied a previously described network-based computational repositioning algorithm, yielding strong results via cross-validation, averaging 0.95 AUROC on test-set indications. However, to better approximate a real-world scenario, we built a time-resolved evaluation framework. At various time points, we built networks corresponding to prior knowledge for use as a training set, and then predicted on a test set comprised of indications that were subsequently described. This framework showed a marked reduction in performance, peaking in performance metrics with the 1985 network at an AUROC of .797. Examining performance reductions due to removal of specific types of relationships highlighted the importance of drug-drug and disease-disease similarity metrics. Using data from future timepoints, we demonstrate that further acquisition of these kinds of data may help improve computational results. CONCLUSIONS: Evaluating a repositioning algorithm using indications unknown to input network better tunes its ability to find emerging drug indications, rather than finding those which have been randomly withheld. Focusing efforts on improving algorithmic performance in a time-resolved paradigm may further improve computational repositioning predictions.

Comparative study of three-dimensional versus two-dimensional laparoscopic C1 radical hysterectomy for cervical cancer / 中华妇产科杂志

Objective To compare the clinical effects and the subjective perception of surgeons with three-dimensional (3D) and two-dimensional (2D) laparoscopic C1 radical hysterectomy surgeries for cervical cancer. Methods The retrospective cohort study was conducted. The clinicopathological data of 101 patients with cervical cancer who received C1 laparoscopic radical hysterectomy (C1-LRH) surgery from June 2015 to August 2017 were collected. Of all patients, 42 cases undergoing 3D laparoscopic surgery and 59 cases undergoing 2D laparoscopic surgery were respectively allocated into the C1-3DLRH group or C1-2DLRH group. The clinical effect and the subjective perception of surgeons were compared between the two groups. Results (1) There was no significant difference between the C1-3DLRH group and C1-2DLRH group in terms of age, body mass index (BMI), International Federation of Gynecology and Obstetrics (FIGO) stage, pathologic type, etc. (all P>0.05). Compared with C1-2DLRH group, the operation time was significantly shortened [(192±54) vs (221±54) minutes, P<0.01], blood loss was significantly less [(102±88) vs (167 ± 117) ml, P<0.01], and the success rate of inferior hypogastric plexus (IHP) bladder branch preservation was significantly increased [86% (36/42) vs 66% (39/59), P<0.05] in C1-3DLRH group. There were no significant difference in the number of lymph nodes, the incidence of operative complications, the infection rate, the time of catheterization and the length of hospitalization between the two groups (all P>0.05). The long-term bladder function was evaluated at the twelfth month after operation, 39 patients in the C1-3DLRH group and 53 patients in the C1-2DLRH group were completed the survey. The results showed that 13% (5/39) of the patients in the C1-3DLRH group had long-term bladder dysfunction, which was lower than that 21% (11/53) of the C1-2DLRH group, but there was no significant difference between the two groups (χ2=0.980, P=0.322). (2) A total of 251 laparoscopic surgeons questionnaires were eligible. The incidence of side effects in the first and second generation of 3D and 2D laparoscopic surgeons was 20.4% (10/49), 6.9% (6/87) and 3.5% (4/115), respectively. The incidence of side effects in the first generation of 3D laparoscopic surgeons was higher than that in the second generation of 3D (χ2=5.463, P=0.019) and 2D laparoscopic surgeons (χ2=12.475, P<0.01). There was no difference between the second generation of 3D and 2D laparoscopic surgeons (χ2=1.208, P=0.272). Conclusions 3D laparoscopy is advantageous to the preservation of autonomic nerve in C1-LRH operation and may improve the quality of operation compared with 2D laparoscopy. The second generation of 3D laparoscopic device might overcome the side effects of the surgeons.

Cross-link regulation of precursor N-cadherin and FGFR1 by GDNF increases U251MG cell viability.

Glial cell line-derived neurotrophic factor (GDNF) is considered to be involved in the development of glioma. However, uncovering the underlying mechanism of the proliferation of glioma cells is a challenging work in progress. We have identified the binding of the precursor of N-cadherin (proN-cadherin) and GDNF on the cell membrane in previous studies. In the present study, we observed increased U251 Malignant glioma (U251MG) cell viability by exogenous GDNF (50 ng/ml). We also confirmed that the high expression of the proN-cadherin was stimulated by exogenous GDNF. Concurrently, we affirmed that lower expression of proN-cadherin correlated with reduced glioma cell viability. Additionally, we observed glioma cell U251MG viability as the phosphorylation level of FGFR1 at Y653 and Y654 was increased after exogenous GDNF treatment, which led to increased interaction between proN-cadherin and FGFR1 (pY653+Y654). Our experiments presented a new mechanism adopted by GDNF supporting glioma development and indicated a possible therapeutic potential via the inhibition of proN-cadherin/FGFR1 interaction.

Decision-making in a bisexual line and a thelytokous Wolbachia-infected line of Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae) regarding behavior toward their hosts.

BACKGROUND: The use of thelytokous Wolbachia-infected Trichogramma (parasitic wasps) has long been considered as a way to enhance the efficacy of biocontrol. However, Wolbachia can affect the host physiology. We compared decision-making between bisexual and thelytokous Wolbachia-infected lines of Trichogramma dendrolimi Matsumura regarding behavior toward fresh and old eggs of Corcyra cephalonica at 25 ± 1 °C and 70 ± 5% relative humidity. RESULTS: The behavioral patterns and sequences of the two lines were basically the same. The durations of various behavioral patterns and values of fitness indicators of the bisexual line on fresh eggs were generally significantly shorter and better, respectively, than on old eggs, whereas the thelytokous line behaved similarly toward the two types of eggs, and differences in most fitness indicators between fresh and old eggs were not significant. On fresh eggs, the durations of various behaviors in the bisexual line were generally significantly shorter than in the thelytokous line and the fitness indicators were generally significantly better. CONCLUSION: Wolbachia affected the fitness of T. dendrolimi negatively. The potential of the thelytokous line as a biocontrol agent would not be as good as that of the bisexual line when decision-making only is considered. Therefore, further evaluations need to be carried out before the thelytokous line can be used in practical biocontrol. © 2018 Society of Chemical Industry.

Expression of NUAK2 in gastric cancer tissue and its effects on the proliferation of gastric cancer cells.

The present study aimed to analyze the expression and effects of NUAK2 in gastric cancer and adjacent normal gastric tissues. The protein expression levels of NUAK2 were detected by western blot analysis. The effects of NUAK2 expression on the proliferation of gastric cancer cells was detected using an MTT and BrdU incorporation assay. Furthermore, the effects of NUAK2 on proliferation and cancer stem cell markers, both protein and microRNA (miRNA), were investigated by western blot analysis and miRNA microarrays, respectively. The results demonstrated that NUAK2 was able to significantly promote the proliferation of SGC-7901 gastric cancer cells. In addition, NUAK2 overexpression decreased the percentage of cells in the G1 phase and increased the percentage of cells in the S phase. Western blot analysis and miRNA microarrays revealed that overexpression of NUAK2 resulted in increased expression levels of proliferation markers, including c-myc, proliferating cell nuclear antigen, cyclin-dependent kinase 2, miRNA 21, and gastric cancer stem cell markers, including aldehyde dehydrogenase 1, CD44 and CD133. In conclusion, NUAK2 expression differed between the tumor and normal gastric tissues. NUAK2 was able to promote the proliferation of gastric cancer cells and regulate their cell cycle. Proliferation and cancer stem cell markers were upregulated by NUAK2 expression. Therefore, the results from the present study suggest that NUAK2 may be a promising target for gastric cancer therapy in the future.

Allicin attenuates macrophage-derived foam cell apoptosis by inhibiting caspase-12 / 中国病理生理杂志

AIM:To investigate the inhibitory effect of allicin on apoptosis and caspase-12 activation of macro-phage-derived foam cells,and to elucidate the underlying molecular mechanisms. METHODS:RAW264.7 macrophages were pretreated with allicin (12.5,25 and 50 mg/L) or 4-phenylbutyric acid(PBA,4 mmol/L) for 1 h and then treated with oxidized low-density lipoprotein(ox-LDL,100 mg/L) or tunicamycin(TM,4 mg/L) for 24 h. The cell viability and apoptosis were examined by MTT assay and flow cytometry with Annexin V-FITC/PI staining,respectively. The activities of caspase-3 in the cells and lactic dehydrogenase (LDH) in the medium were measured. The protein levels of caspase-12 were determined by Western blot. The intracellular lipid accumulation was measured with oil red O staining and the content of intracellular total cholesterol was determined by enzymatic colorimetry. RESULTS:Similar to the endoplasmic reticulum stress (ERS) inhibitor PBA, allicin inhibited ox-LDL-induced injury of RAW264.7 macrophages in a concentration-de-pendent manner,as determined by the increased cell viability and the decreased LDH leakage,apoptosis and caspase-3 ac-tivity. The decrease in cell viability and increases in LDH leakage and apoptosis induced by TM (an ERS inducer) were also suppressed by allicin. Moreover, similar to PBA, allicin remarkably inhibited ox-LDL- or TM-induced activation of caspase-12. Furthermore, allicin remarkably attenuated ox-LDL-induced lipid accumulation in the RAW264.7 cells and foam cells formation in a concentration-dependent manner. CONCLUSION:Allicin may inhibit macrophage-derived foam cell apoptosis induced by ox-LDL,and the mechanism is partially related to suppressing the activation of caspase-12.

Ethanol extract of propolis protects vascular endothelial cells from oxidized low-density lipoprotein-induced apoptosis by inhibiting C/EBP homologous protein expression / 中国病理生理杂志

AIM:To investigate the inhibitory effect of ethanol extract of propolis (EEP) on oxidized low-density lipoprotein (ox-LDL)-induced vascular endothelial cell apoptosis and the underlying molecular mechanisms.METHODS:Human umbilical vein endothelial cells (HUVECs) were pretreated with EEP (7.5,15 and 30 mg/L) or 4-phenylbutyric acid (PBA,4 mmol/L) for 1 h and then treated with ox-LDL (100 mg/L) or tunicamycin (TM,4 mg/L) for 24 h.The cell viability and apoptosis were determined by MTT assay and Annexin V-FITC/PI double staining,respectively.The activities of lactic dehydrogenase (LDH) in the medium and caspase-3 in the HUVECs were measured.The protein and mRNA levels of C/EBP homologous protein (CHOP),a proapoptotic molecule under endoplasmic reticulum stress (ERS),and its downstream Bcl-2 were examined by Western blot and real-time PCR,respectively.RESULTS:Like PBA (an ERS inhibitor),EEP protected HUVECs from ox-LDL-induced injury in a dose-dependent manner,as assessed by the increased cell viability and the decreased LDH release,apoptotic rate and caspase-3 activation.The decrease in cell viability and the increases in LDH release,apoptotic rate and caspase-3 activation induced by TM,an ERS inducer,were also attenuated by EEP.Moreover,EEP suppressed ox-LDL-induced CHOP upregulation and Bcl-2 downregulation,and this effect was similar to that of PBA.Similarly,EEP significantly suppressed TM-induced CHOP upregulation both at the protein and mRNA levels.CONCLUSION:EEP may protect HUVECs from ox-LDL-induced apoptosis,and the mechanism is at least partially involved in suppressing CHOP-mediated ERS-associated apoptotic pathway.

Ethanol extract of propolis protects vascular endothelial cells from oxidized low-density lipoprotein-induced apoptosis by inhibiting C/EBP homologous protein expression / 中国病理生理杂志

AIM:To investigate the inhibitory effect of ethanol extract of propolis (EEP) on oxidized low-density lipoprotein (ox-LDL)-induced vascular endothelial cell apoptosis and the underlying molecular mechanisms.METHODS:Human umbilical vein endothelial cells (HUVECs) were pretreated with EEP (7.5,15 and 30 mg/L) or 4-phenylbutyric acid (PBA,4 mmol/L) for 1 h and then treated with ox-LDL (100 mg/L) or tunicamycin (TM,4 mg/L) for 24 h.The cell viability and apoptosis were determined by MTT assay and Annexin V-FITC/PI double staining,respectively.The activities of lactic dehydrogenase (LDH) in the medium and caspase-3 in the HUVECs were measured.The protein and mRNA levels of C/EBP homologous protein (CHOP),a proapoptotic molecule under endoplasmic reticulum stress (ERS),and its downstream Bcl-2 were examined by Western blot and real-time PCR,respectively.RESULTS:Like PBA (an ERS inhibitor),EEP protected HUVECs from ox-LDL-induced injury in a dose-dependent manner,as assessed by the increased cell viability and the decreased LDH release,apoptotic rate and caspase-3 activation.The decrease in cell viability and the increases in LDH release,apoptotic rate and caspase-3 activation induced by TM,an ERS inducer,were also attenuated by EEP.Moreover,EEP suppressed ox-LDL-induced CHOP upregulation and Bcl-2 downregulation,and this effect was similar to that of PBA.Similarly,EEP significantly suppressed TM-induced CHOP upregulation both at the protein and mRNA levels.CONCLUSION:EEP may protect HUVECs from ox-LDL-induced apoptosis,and the mechanism is at least partially involved in suppressing CHOP-mediated ERS-associated apoptotic pathway.

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

Drug toxicity is a major concern for both regulatory agencies and the pharmaceutical industry. In this context, text-mining methods for the identification of drug side effects from free text are key for the development of up-to-date knowledge sources on drug adverse reactions. We present a new system for identification of drug side effects from the literature that combines three approaches: machine learning, rule- and knowledge-based approaches. This system has been developed to address the Task 3.B of Biocreative V challenge (BC5) dealing with Chemical-induced Disease (CID) relations. The first two approaches focus on identifying relations at the sentence-level, while the knowledge-based approach is applied both at sentence and abstract levels. The machine learning method is based on the BeFree system using two corpora as training data: the annotated data provided by the CID task organizers and a new CID corpus developed by crowdsourcing. Different combinations of results from the three strategies were selected for each run of the challenge. In the final evaluation setting, the system achieved the highest Recall of the challenge (63%). By performing an error analysis, we identified the main causes of misclassifications and areas for improving of our system, and highlighted the need of consistent gold standard data sets for advancing the state of the art in text mining of drug side effects.Database URL: https://zenodo.org/record/29887?ln»en#.VsL3yDLWR_V.

A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available athttps://github.com/SuLab/crowd_cid_relexDatabase URL:https://github.com/SuLab/crowd_cid_relex.