Rapid in-focus corrections on quantitative amplitude and phase imaging using transport of intensity equation method

Transport of intensity equation (TIE) method can acquire sample phase distributions with high speed and accuracy, offering another perspective for cellular observations and measurements. However, caused by incorrect focal plane determination, blurs and halos are induced, decreasing resolution and accuracy in both retrieved amplitude and phase information. In order to obtain high-accurate sample details, we propose TIE based in-focus correction technique for quantitative amplitude and phase imaging, which can locate focal plane and then retrieve both in-focus intensity and phase distributions combining with numerical wavefront extraction and propagation as well as physical image recorder translation. Certified by both numerical simulations and practical measurements, it is believed the proposed method not only captures high-accurate in-focus sample information, but also provides a potential way for fast autofocusing in microscopic system.

Horizontal transfer and functional evaluation of high pathogenicity islands in Avian Escherichia coli

High pathogenicity islands (HPIs) inEscherichia coliencode genes that are primarily involved in iron uptake and regulation, and confer virulence and pathogenicity. The aim of this study was to investigate the transfer ofHPIs in avianE. coliand identify the function ofHPIin the acceptor strain. TheHPItransfer strain was obtained under conditions of low temperature and low iron abundance, and the donor and acceptor strains were confirmed.E. coli HPIs are transferred by horizontal gene transfer events, which are likely mediated primarily by homologous recombination inHPI-adjacent sequences. Assays for biological activity and pathogenicity changes in the acceptor strain indicated thatHPIs might not be involved in pathogenesis in avianE. coli, and thus the main function ofHPIs in this strain of bacteria may be to regulate iron nutrition.

Direct regeneration of cathode materials from spent lithium iron phosphate batteries using a solid phase sintering method

A direct regeneration of cathode materials from spent LiFePO₄ batteries using a solid phase sintering method has been proposed in this article.

Knockdown of tripartite motif 59 (TRIM59) inhibits tumor growth in prostate cancer

OBJECTIVE

Members of the tripartite motif (TRIM) protein family contain a highly conserved N-terminal really interesting new gene (RING) domain that is involved in regulating transcriptional factors and tumor suppressors. In this study, the effects of TRIM59 expression on tumor growth were investigated in prostate cancer.

MATERIALS AND METHODS

The expression of TRIM59 in prostate cancer tissues (n = 15) and prostate cancer cell lines was determined by quantitative reverse transcriptase-PCR (qRT-PCR), Western blotting, and immunohistochemistry. A specific shRNA targeting TRIM59 was employed to knockdown TRIM59 expression in the prostate cancer cell lines PC3 and DU145. The effects of TRIM59 knockdown on cell proliferation were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and colony formation assays. The effects on cell cycle progression were determined by flow cytometry, and a xenograft mouse model of prostate cancer was generated to determine the in vivo effects of TRIM59 knockdown. The effects on cell cycle regulators were determined by Western blotting.

RESULTS

TRIM59 was highly expressed in prostate cancer tissues. Knockdown of TRIM59 significantly inhibited cell proliferation and colony formation, and cell cycle analysis showed that TRIM59-depleted cells accumulated in S-phase. TRIM59 knockdown was shown to inhibit tumorigenesis in mice. In addition, the cell cycle regulators CDC25A, CDC2, and cyclin B1 were decreased by TRIM59 shRNA-mediated knockdown.

CONCLUSIONS

Our study suggests that TRIM59 promotes prostate cancer cell proliferation, possibly through its effects on cell cycle progression.

MicroRNA-203 inhibits tumour growth and metastasis through PDPN

OBJECTIVE

MicroRNAs play an important role in regulating hypopharyngeal cancer development. miR-203 has been previously shown to possess antitumour capabilities in many cancers, but not in hypopharyngeal cancer.

DESIGN

Using human normal and hypopharyngeal cancer specimens, we explored the expression levels of miR-203 in the two groups and further correlated them with different stages of cancer and lymph node metastasis.

SETTING AND PARTICIPANTS

Applying human pharynx FaDu cancer cells and lentiviral transduction technique, we investigated the effects of miR-203 on cancer cell viability, migration and invasion. Moreover, we studied the novel relationship between miR-203 and podoplanin (PDPN) in hypopharyngeal cancer.

RESULTS

The downregulated levels of miR-203 in human hypopharyngeal cancer tissues were associated with advanced cancer stages and lymph node metastasis. High levels of miR-203 inhibited cell viability, migration and invasion of hypopharyngeal cancer cells. Further studies suggested miR-203 directly targeted and inhibited PDPN expression. PDPN silencing suppresses hypopharyngeal cancer cell abilities. In addition, PDPN overexpression was able to reverse miR-203 inhibitory effects on cell viability, migration and invasion.

CONCLUSION

PDPN acts as an oncogene to promote hypopharyngeal cancer cell viability, migration and invasion. miR-203 directly targets PDPN to suppress its expression, thus exerting inhibitory effects on cancer metastasis.

Fluorogenic protein labeling using a genetically encoded unstrained alkene

A new fluorogenic bioorthogonal reaction between styrene (an unstrained alkene) and a tetrazine was developed.

We developed a new fluorogenic bioorthogonal reaction that is based on the inverse electron-demand Diels–Alder reaction between styrene (an unstrained alkene) and a simple tetrazine. The reaction forms a new fluorophore with no literature precedent. We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a styrene-containing amino acid into proteins in response to amber nonsense codon. Fluorogenic labeling of purified proteins and intact proteins in live cells were demonstrated. The fluorogenicity of the styrene–tetrazine reaction can be potentially applied to the study of protein folding and function under physiological conditions with low background fluorescence interference.

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

Pharmacology of a traditional Chinese herb, Shuangren-Anshen capsule, in a hemorrhage mouse model by using an orthogonal array design

Shuangren-Anshen capsule (SAC) is a traditional Chinese herb that was improved in our laboratory. An orthogonal experiment [L9(3)(4)] was used to optimize the extraction conditions. In vivo, a hemorrhage mouse model was established and the hemoglobin contents of normal control, model control, and treated mice were measured. Additionally, the sedative and hypnotic effects of SACs were assessed based on pharmacological parameters such as changes in locomotive activity, forelimb raising, sleep latency, sleep duration, and number of mice that fell asleep. Brain tissue was sectioned and stained to detect changes in cell morphology by microscopy. The optimum extraction was achieved with 3 cycles of decoction for 120 min each with a 10-fold volume of water added. In the model control group, hemoglobin content significantly decreased and pharmacological parameters increased (P < 0.01) relative to that in the normal control group. Compared to the model control group, the group treated with 0.9 g/kg SAC showed significant (P < 0.05) increase or decrease in hemoglobin content and all pharmacological parameters except sleep duration. The groups treated with 1.8 or 3.6 g/kg SAC and the positive control group also showed significant alterations in hemoglobin content and pharmacological parameters (P < 0.05). In addition, SAC exhibited a protective effect on the morphological structures of the damaged nerve cells in the mouse model. Thus, an optimal extraction process was successfully identified. The pharmacological data also suggests that the drug can improve sleep quality. SAC treatment was shown to cause changes in hemoglobin content and cell morphology in a mouse model.

Burden of hospitalization in relapsed acute lymphoblastic leukemia

OBJECTIVE

This study sought to quantify the economic burden of adults with Philadelphia chromosome negative (Ph-) relapsed B-precursor acute lymphoblastic leukemia (ALL) by examining hospitalization events in the US.

RESEARCH DESIGN AND METHODS

The Truven Health MarketScan Commercial Database was used to identify eligible patients hospitalized between April 2009 and July 2014. Eligible patients were continuously enrolled 6 months before (pre-index) their first claim with an eligible relapsed ALL diagnosis (index date) and followed up for a maximum of 18 weeks.

RESULTS

A total of 583 hospitalizations involving 205 adults with Ph(-) relapsed B-precursor ALL were identified. Mean (SD) percentage of follow-up time spent in the hospital was 56.2% (40.0%). Mean (SD) length of stay per hospitalization was 13.1 (15.7) days; mean (SD) reimbursement per hospitalization stay was $89,663 ($195,725). The highest reimbursements were hospitalization for ALL in relapse ($132,137 [$178,742]) and ALL without remission ($120,932 [$134,254]).

CONCLUSIONS

Adults with Ph(-) relapsed B-precursor ALL had repeated and prolonged hospitalizations during chemotherapy treatment associated with extremely high costs. More effective, tolerable treatments are needed.

LIMITATIONS

The key limitation was that the data source included only individuals from the health plans or the mid to large size employers in the MarketScan database. Patients who were not covered under these plans, or were only on Medicaid or only on Medicare, would not appear in our analysis.

Can the referring surgeon enhance accrual of breast cancer patients to medical and radiation oncology trials? The ENHANCE study

INTRODUCTION

The accrual rate to clinical trials in oncology remains low. In this exploratory pilot study, we prospectively assessed the role that engaging a referring surgeon plays in enhancing nonsurgical oncologic clinical trial accrual.

METHODS

Newly diagnosed breast cancer patients were seen by a surgeon who actively introduced specific patient-and physician-centred strategies to increase clinical trial accrual. Patient-centred strategies included providing patients, before their oncology appointment, with information about specific clinical trials for which they might be eligible, as evaluated by the surgeon. The attitudes of the patients about clinical trials and the interventions used to improve accrual were assessed at the end of the study. The primary outcome was the clinical trial accrual rate during the study period.

RESULTS

Overall clinical trial enrolment during the study period among the 34 participating patients was 15% (5 of 34), which is greater than the institution's historical average of 7%. All patients found the information delivered by the surgeon before the oncology appointment to be very helpful. Almost three quarters of the patients (73%) were informed about clinical trials by their oncologist. The top reasons for nonparticipation reported by the patients who did not participate in clinical trials included lack of interest (35%), failure of the oncologist to mention clinical trials (33%), and inconvenience (19%).

CONCLUSIONS

Accrual of patients to clinical trials is a complex multistep process with multiple potential barriers. The findings of this exploratory pilot study demonstrate a potential role for the referring surgeon in enhancing nonsurgical clinical trial accrual.

CpG island evolution in the mammalian DHRS4 gene cluster and its role in the regulation of gene transcription

The dehydrogenase/reductase (SDR family) member 4 (DHRS4) gene is copied during mammalian evolution; therefore, while only one DHRS4 gene is expressed in the mouse genome, the gene cluster consists of two (DHRS4 and DHRS4L1) and three (DHRS4, DHRS4L2, and DHRS4L1) copies in chimpanzees and humans, respectively. In this study, we explored the possible regulatory mechanism of the DHRS4 gene cluster in mammalian evolution by analyzing the promoter sequence, methylation of CpG islands, and RNA expression of the DHRS4 gene cluster in mice, chimpanzees, and humans by bioinformatics prediction, bisulfite sequencing PCR, and real-time reverse transcriptase-PCR. The results indicated that the DHRS4 gene was actively expressed in the three model species. The RNA level of DHRS4L1 was much lower than those of DHRS4 and DHRS4L2, and expressed lower homologous sequence identity to DHRS4 and DHRS4L2. DHRS4L2, the latest evolutionary copy of the DHRS4 gene in mammals, received a high promoter prediction score, and was the only copy of the DHRS4 gene cluster presenting hypermethylated CpG islands in the promoter region. An analysis of the relationship between the promoter characteristics and RNA expression of the DHRS4 gene cluster indicated that the development of CpG islands, in addition to the promoter sequence, during mammalian evolution could modulate the dose compensatory regulation of the copy number-varied DHRS4 gene cluster.

Stereoselectivity of tradinterol's inhibition on proliferation of airway smooth muscle cells induced by acetylcholine through suppressing Ca(2+) signalling

The objective of this study is to investigate whether the inhibition of tradinterol (SPFF) against acetylcholine (ACh)-induced proliferation is mediated by Ca(2+) signaling in airway smooth muscle cells (ASMCs), and whether stereoselectivity of the drug exists. Guinea pig ASMCs were primarily prepared with the method described and treated with ACh combined to SPFF isomers for 24 or 48 hours, respectively. 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay was used to determine the proliferation of the guinea pig ASMCs. Ca(2+) fluorescent intensity in the guinea pig ASMCs, expressed with percentage increase in fluorescence when the intensity was determined with varioskan flash or shown with percentage increase in Geo Mean (GM) measured with flow cytometry, was recorded. Images of the intensity were obtained with fluorescent microscope. 2-APB, an (inositol 1,4,5-trisphosphate receptor) IP3R blocker, and NiCl2, a store-operated channel (SOC) inhibitor, were used to investigate the mechanism of SPFF isomers regulating intracellular Ca(2+) via IP3R on sarcoplasmic reticulum (SR) and/or SOC on plasma membrane. (-)SPFF and (±)SPFF, treated for 48 hours, showed significant inhibition against ACh-induced proliferation. The Ca(2+) elevation induced by ACh was concentration-dependently suppressed by SPFF isomers. (-)SPFF is the most effective but the potency of (±)SPFF is less than that of the former and stronger than that of (+)SPFF based on the half maximal inhibitory concentration (IC50) value. No significant additive effect was observed when (-)SPFF/(±)SPFF was used alone and combined with NiCl2/2-APB. As far as (+)SPFF is concerned, no similar phenomenon was observed. (-)SPFF and (±)SPFF but (+)SPFF showed significant inhibition against the percentage increase in fluorescence induced by CaCl2. It is likely that the influence of IP2RSOC-mediated Ca(2+) signaling in ASMCs helps (-)SPFF and (±)SPFF contribute to the suppression of ASMCs proliferation. Stereoselectivity of SPFF isomers may lead to different levels of suppression of ACh-induced intracellular Ca(2+) and ASMCs proliferation. Moreover, cell cycle analysis with flow cytometry was applied to the evaluation of the action in human ASMCs in order to further confirm the anti-proliferative effect of the drugs. It was found that (-)SPFF, (±)SPFF but (+)SPFF suppressed the elevated rate of cell population in Phase S over all the cells stimulated with ACh, when SPFF and its isomers were individually exposed to the cells for 72 hours. These results that demonstrate the different stereoselective activities of SPFF are in consistent with those obtained from the guinea pig ASMCs.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

The effect of soy or isoflavones on homocysteine levels: a meta-analysis of randomised controlled trials

BACKGROUND

The present study aimed to evaluate the effect of soy or isoflavones on blood homocysteine levels via a systematic review and meta-analysis.

METHODS

Pubmed, Embase, Web of Science and the Cochrane Library (up to 16 December 2015) were used for the literature review. Only randomised controlled trials were included. The primary outcome was the standard mean difference (SMD) of blood homocysteine levels between the experimental and control groups.

RESULTS

Nineteen randomised controlled studies were included for qualitative analysis. Eighteen studies were included in the data synthesis. Soy or isoflavones were found to have no effect on homocysteine levels, with a SMD of -0.21 (95% confidence interval = -0.43 to 0.00, I² =67.7%, random effect model). No publication bias was found among those studies (P = 0.296 for Egger's test, and P = 0.198 for Begg's test).

CONCLUSIONS

Soy or isoflavones were not found to be associated with a reduction in homocysteine levels. Further studies might still be needed in carefully selected populations.

Association analysis of imbalanced interhemispheric functional coordination and early therapeutic efficacy in major depressive disorder: Evidence from resting state fMRI

Introduction

Emerging evidences indicate that the alteration of interhemispheric functional coordination may be involved in the pathogenesis of major depressive disorder (MDD). In present study, we aim to explore the potential marker by using the voxel-mirrored homotopic connectivity (VMHC) approach, which may be contributing to predict the clinical prognosis in MDD.

Methods

Eighty-two MDD patients and 50 normal control (NC) subjects participated in this study. We divided the MDD group into unremitted and remitted group according to the reduction rate of Hamilton Rating Scale for Depression (HAMD) within 2 weeks.

Results

The study detected significantly decreased VMHC in bilateral precuneus (pCu), inferior temporal gyrus (ITG) and increased VMHC in middle frontal gyrus (MFG) and caudate nucleus when compared remitted depression (RD) group to unremitted depression (URD) group. Meanwhile, when compared with NC group, the URD group presented reduced VMHC in bilateral cerebellum anterior lobe, thalamus and postcentral gyrus. Furthermore, the VHMC in media frontal gyrus, postcentral gyrus and precentral gyrus were significantly decreased in RD group. Correlation analysis suggested that reduced VMHC in bilateral pCu was negatively correlated with the baseline HAMD score of URD (r = −0.325, P = 0.041). Receiver operating characteristic (ROC) curve indicated that three regional VMHC changes could identify depressed patient with poorer treatment response: ITG [area under curve (AUC) = 0.699, P = 0.002, 95% CI = 0.586–0.812], MFG (AUC = 0.692, P = 0.003, 95% CI = 0.580–0.805), pCu (AUC = 0.714, P = 0.001, 95% CI = 0.603–0.825).

Conclusion

The current study combined with previous evidence indicates that the subdued intrinsic interhemispheric functional connectivity might represents a novel neural trait involved in the pathophysiology of MDD.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Ferroptosis: process and function

Ferroptosis is a recently recognized form of regulated cell death. It is characterized morphologically by the presence of smaller than normal mitochondria with condensed mitochondrial membrane densities, reduction or vanishing of mitochondria crista, and outer mitochondrial membrane rupture. It can be induced by experimental compounds (e.g., erastin, Ras-selective lethal small molecule 3, and buthionine sulfoximine) or clinical drugs (e.g., sulfasalazine, sorafenib, and artesunate) in cancer cells and certain normal cells (e.g., kidney tubule cells, neurons, fibroblasts, and T cells). Activation of mitochondrial voltage-dependent anion channels and mitogen-activated protein kinases, upregulation of endoplasmic reticulum stress, and inhibition of cystine/glutamate antiporter is involved in the induction of ferroptosis. This process is characterized by the accumulation of lipid peroxidation products and lethal reactive oxygen species (ROS) derived from iron metabolism and can be pharmacologically inhibited by iron chelators (e.g., deferoxamine and desferrioxamine mesylate) and lipid peroxidation inhibitors (e.g., ferrostatin, liproxstatin, and zileuton). Glutathione peroxidase 4, heat shock protein beta-1, and nuclear factor erythroid 2-related factor 2 function as negative regulators of ferroptosis by limiting ROS production and reducing cellular iron uptake, respectively. In contrast, NADPH oxidase and p53 (especially acetylation-defective mutant p53) act as positive regulators of ferroptosis by promotion of ROS production and inhibition of expression of SLC7A11 (a specific light-chain subunit of the cystine/glutamate antiporter), respectively. Misregulated ferroptosis has been implicated in multiple physiological and pathological processes, including cancer cell death, neurotoxicity, neurodegenerative diseases, acute renal failure, drug-induced hepatotoxicity, hepatic and heart ischemia/reperfusion injury, and T-cell immunity. In this review, we summarize the regulation mechanisms and signaling pathways of ferroptosis and discuss the role of ferroptosis in disease.

Pdcd4 deficiency enhances macrophage lipoautophagy and attenuates foam cell formation and atherosclerosis in mice

Macrophage foam cells, a major component of the atherosclerotic lesion, have vital roles in the development of atherosclerosis. Lipoautophagy, a type of autophagy characterized by selective delivery of lipid droplet for lysosomal degradation, may impact atherosclerosis by regulating macrophage foam cell formation. Previously, we reported that programmed cell death 4 (PDCD4), a tumor suppressor, negatively regulated autophagy in tumor cells. However, its roles in macrophage lipoautophagy, foam cell formation and atherosclerosis remain to be established. Here we found that Pdcd4 deficiency clearly improved oxidized low-density lipoproteins-impaired autophagy efflux, promoted autophagy-mediated lipid breakdown in murine macrophages and thus prevented macrophage conversion into foam cells. Importantly, Pdcd4 deficiency in mice significantly upregulated macrophage autophagy in local plaques along with attenuated lipid accumulation and atherosclerotic lesions in high-fat-fed Apolipoprotein E knockout mice. Bone marrow transplantation experiment demonstrated that PDCD4-mediated autophagy in hematopoietic cells contributed to the development of atherosclerosis. These results indicate that endogenous PDCD4 promotes for macrophage foam cell formation and atherosclerosis development via inhibiting autophagy and provides new insights into atherogenesis, suggesting that promoting macrophage autophagy through downregulating PDCD4 expression may be beneficial for treating atherosclerosis.

A photoactivatable Src homology 2 (SH2) domain

A photoactivatable SH2 domain that can be potentially applied as an optogenetic tool to the photocontrol of phosphotyrosine-associated biological processes.

Understanding Risk in the Oldest Old: Frailty and the Metabolic Syndrome in a Chinese Community Sample Aged 90+ Years

OBJECTIVES

To investigate the relationship between frailty and the metabolic syndrome and to evaluate how these contribute to mortality in very old people.

DESIGN

Secondary analysis of data from the Project of Longevity and Aging in Dujiangyan.

SETTING

Community sample from Sichuan Province, China.

PARTICIPANTS

People aged 90+ years (n=767; baseline age=93.7±3.4 years; 68.0% women.

MEASUREMENTS

After a baseline health assessment, participants were followed for four years (54.0% died). A frailty index (FI) was calculated as the sum of deficits present, divided by the 35 health-related deficits considered. Relationships between the FI and the metabolic syndrome were tested; their effect on death was examined.

RESULTS

The mean FI was 0.26 ±0.11. Higher FI scores were associated with a greater risk of death, adjusted for age, sex, education, and metabolic syndrome items. The hazard ratio was 1.03 (95% confidence interval 1.02, 1.04) for each 1% percent increase of the FI. The mortality risk did not change with the metabolic syndrome (odds ratio=0.99; 0.71-1.36).

CONCLUSIONS

In the oldest old, frailty was a significant risk for near-term death, regardless of the metabolic syndrome. Even using age-adjusted models, the epidemiology of late life illness may need to account for frailty routinely.

Association between the AGTR1 A1166C polymorphism and risk of IgA nephropathy: a meta-analysis

Numerous studies have evaluated the association between the A1166C polymorphism in the angiotensin II type 1 receptor (AGTR1) gene and immunoglobulin A nephropathy (IgAN) risk. However, this relationship remains controversial. Our aim was to evaluate the relationship between this polymorphism and IgAN susceptibility by performing a meta-analysis. Articles were identified in the PubMed, Google Scholar, and China National Knowledge Infrastructure databases, and after selection, five eligible studies were included. Statistical analyses were carried out using Stata 12.0, combining data from all the relevant studies. The pooled odds ratios (ORs) regarding the association between the AGTR1 A1166C polymorphism and IgAN risk were not statistically significant [A vs C: OR = 0.64, 95% confidence interval (CI) = 0.24-1.68; AA vs AC+CC: OR = 1.02, 95%CI = 0.74-1.39; CC vs AC+AA: OR = 1.20, 95%CI = 0.48-2.98; AC vs AA+CC: OR = 0.96, 95%CI = 0.70-1.31]. In conclusion, the AGTR1 gene A1166C polymorphism may not be correlated with IgAN susceptibility. However, further studies should be performed to confirm this finding.

Relationship between rs1047763 polymorphism of the C1GALT1 gene and susceptibility to immunoglobulin A nephropathy in Xinjiang Uyghur people

We explored the relationship between rs1047763, a single-nucleotide polymorphism (SNP) of the C1GALT1 gene, and genetic susceptibility to immunoglobulin A nephropathy (IgAN) in Xinjiang Uyghur people. The study comprised 90 patients with IgAN and 90 normal controls recruited from Uyghur people. The distribution of the rs1047763 polymorphism of C1GALT1 in each group was determined by direct sequencing analysis. The gene type, gene frequency, allele type, and allele frequency were calculated by direct counting and the genotype was investigated using the Hardy-Weinberg equilibrium test. The SPSS17.0 software was used for data processing, and genotype and allele frequencies were compared using the χ2 test. In the IgAN group, the AA, AG, and GG genotype frequencies in the rs1047763 polymorphism of the C1GALT1 gene were 21.10, 47.80, and 31.10%, respectively, while AA, AG, and GG genotype frequencies in the control group were 17.8, 40.0, and 42.2%, respectively. There was no statistically significant difference between the two groups (P > 0.05). The rs1047763 SNP of the C1GALT1 gene probably has no correlation with genetic susceptibility to IgAN in Xinjiang Uyghur people.

A randomized, double-blind, phase II, exploratory trial evaluating the palliative benefit of either continuing pamidronate or switching to zoledronic acid in patients with high-risk bone metastases from breast cancer

Previous studies suggest switching from pamidronate to a more potent bone-targeted agent is associated with biomarker and palliative response in breast cancer patients with bone metastases. Until now, this has not been addressed in a double-blind, randomized trial. Breast cancer patients with high-risk bone metastases, despite >3 months of pamidronate, were randomized to either continue pamidronate or switch to zoledronic acid every 4 weeks for 12 weeks. Primary outcome was the proportion of patients achieving a fall in serum C-telopeptide (sCTx) at 12 weeks. Secondary outcomes included difference in mean sCTx, pain scores, quality of life, toxicity, and skeletal-related events (SREs). Seventy-three patients entered the study; median age 61 years (range 37-87). Proportion of patients achieving a fall in sCTx over the 12-week evaluation period was 26/32 (81 %) with zoledronic acid and 18/29 (62 %) with pamidronate (p = 0.095). Mean decrease in sCTx (mean difference between groups = 50 ng/L, 95 % CI 18-84; p = 0.003) was significantly greater in patients who received zoledronic acid. Quality of life, pain scores, toxicity, and frequency of new SREs were comparable between the two arms. While a switch from pamidronate to zoledronic acid resulted in reduction in mean sCTx, there were no significant differences between the arms for proportion of patients achieving a reduction in sCTx, quality of life, pain scores, toxicity or SREs. Given the lack of palliative improvement, the current data do not support a switching strategy.

VCS parameters of neutrophils, monocytes and lymphocytes may indicate local bacterial infection in cancer patients who accepted cytotoxic chemotherapeutics

Bacterial infections increased greatly in cancer patients who accepted cytotoxic chemotherapeutics. VCS parameters of neutrophils were reported to be an indicator for acute bacterial infection accompanied by increased WBC counts. Here we explored the possibility of VCS parameters of neutrophils, monocytes and lymphocytes in indicating the local bacterial infection in cancer patients. A total of 310 cancer patients and 90 healthy controls were retrospectively analyzed, and 190 of them were diagnosed as acute local bacterial infection. The VCS parameters acquired from a Beckman Coulter LH750 haematology analyzer were investigated to determine which VCS parameters could indicate local bacterial infection in cancer patients with leucopenia caused by cytotoxic agents. VCS parameters of cancer patients were significantly affected by infection. For diagnosing bacterial infection of cancer patients, the best single indicator was mean monocyte light scatter (MMS) with a sensitivity of 95.12 % and a specificity of 58.82 % and the area under the curve (AUC) was 0.792. A combination of the following five parameters: mean neutrophil volume (MNV), MMS, mean lymphocyte conductivity (MLC), mean lymphocyte light scatter (MLS) and neutrophil volume distribution width (NDW) could provide a better index in diagnosing bacterial infection than any single parameter (sensitivity 75.8 %, specificity 64.72 %, AUC 0.763). Taking WBC counts into consideration, VCS parameters could better indicate bacterial infection for cancer patients with abnormal WBC level than that with normal WBC level. Aside from neutrophils, the VCS of monocytes and lymphocytes were also ideal indicators for bacterial infection. The combination of VCS parameters could increase the sensitivity, specificity and accuracy of diagnosis of cancer patients.

Downregulation of miR-320a/383-sponge-like long non-coding RNA NLC1-C (narcolepsy candidate-region 1 genes) is associated with male infertility and promotes testicular embryonal carcinoma cell proliferation

Long non-coding RNAs (lncRNAs), which are extensively transcribed from the genome, have been proposed to be key regulators of diverse biological processes. However, little is known about the role of lncRNAs in regulating spermatogenesis in human males. Here, using microarray technology, we show altered expression of lncRNAs in the testes of infertile men with maturation arrest (MA) or hypospermatogenesis (Hypo), with 757 and 2370 differentially down-regulated and 475 and 163 up-regulated lncRNAs in MA and Hypo, respectively. These findings were confirmed by quantitative real-time PCR (qRT-PCR) assays on select lncRNAs, including HOTTIP, imsrna320, imsrna292 and NLC1-C (narcolepsy candidate-region 1 genes). Interestingly, NLC1-C, also known as long intergenic non-protein-coding RNA162 (LINC00162), was down-regulated in the cytoplasm and accumulated in the nucleus of spermatogonia and primary spermatocytes in the testes of infertile men with mixed patterns of MA compared with normal control. The accumulation of NLC1-C in the nucleus repressed miR-320a and miR-383 transcript and promoted testicular embryonal carcinoma cell proliferation by binding to Nucleolin. Here, we define a novel mechanism by which lncRNAs modulate miRNA expression at the transcriptional level by binding to RNA-binding proteins to regulate human spermatogenesis.

Molecular identification of Echinococcus granulosus on the Tibetan Plateau using mitochondrial DNA markers

Cystic echinococcosis (CE) is an important worldwide zoonotic disease that causes large economic losses and human suffering. Echinococcus granulosus, the causative agent of CE, exhibits different genotypes in different locations. In order to identify its genotypes and analyze its genetic structure on the Tibetan Plateau, we collected 72 hydatid cysts from different intermediate hosts and amplified and sequenced their mitochondrial cytochrome c oxidase subunit 2 (cox2) genes. Seventy isolates were identified as the E. granulosus G1 genotype, while two isolates belonged to the G6 genotype. There were 18 haplotypes among the 70 E. granulosus isolates, which exhibited a star-like network pattern and shared a common haplotype (H1). There was little difference between geographical sub-populations. Our results suggest that a recent E. granulosus population expansion occurred on the Tibetan Plateau, suggesting that E. granulosus was introduced into China. This study increases the basic molecular data needed for the molecular diagnosis, epidemiology, prevention, and control of Echinococcus diseases.

MicroRNA-29a promotes apoptosis of monocytes by targeting STAT3 during sepsis

Sepsis is a major cause of morbidity and mortality in critically ill patients. The sepsis syndrome results from a dysregulated inflammatory response to infection that leads to multiple-organ failure, but the underlying mechanisms remain poorly understood. More and more reports show that microRNAs (miRNAs) play an important role in sepsis. In the progression of this syndrome, cells change their behavior in response to cytokines stimulated by sepsis, such as interleukin-10 (IL-10). IL-10 can activate JAK2-STAT3 in the cells to protect them from damage. miR-29a is a potential miRNA directly targeting STAT3. In this study, we investigate the role of miR-29a in targeting STAT3 during sepsis. When cells were treated with IL-10, STAT3 was activated in monocytes, as determined using western blotting. It was verified that STAT3 was a new target gene of miR-29a. miR-29a could inhibit IL-10-induced cytokine release by targeting JAK-STAT3 in monocytes. In conclusion, this study demonstrates for the first time that miR-29a inhibits STAT3 in human monocytes during sepsis.

Foreign Body Emboli following Cerebrovascular Interventions: Clinical, Radiographic, and Histopathologic Features

Foreign material emboli following cerebral, cardiac, and peripheral catheterizations have been reported since the mid-1990s. Catheter coatings have been frequently implicated. The most recent surge of interest in this phenomenon within the neurointerventional community is associated with procedures using flow-diversion devices for the treatment of cerebral aneurysms. Following coil-supported Pipeline embolization in 4 cases and stent-supported coiling in 1, 5 patients developed multiple subcentimeter enhancing lesions, usually with surrounding edema and variable magnetic susceptibility in the vascular territories of the treated aneurysms. Conventional angiography findings were unrevealing. Laboratory work-up showed mild CSF protein elevation with no leukocytosis. Brain biopsy in 2 cases revealed granulomatous angiitis encasing foreign material, identical in stain appearance to a polyvinylpyrrolidone catheter coating. Corticosteroid administration typically produced clinical improvement. A heterogeneous radiographic and clinical course was noted, with rise and fall in the number of enhancing lesions in 2 patients and persistence in others. The etiology may be related to widespread adoption of increasingly sophisticated catheterization techniques.

Magnetic resonance imaging assessment of the ventricular system in the brains of adult and juvenile beagle dogs treated with posaconazole IV Solution

INTRODUCTION

Noxafil® (posaconazole; POS) is a potent, selective triazole antifungal approved for use in adults as an oral suspension, oral tablet and intravenous (IV) Solution. In support of pediatric administration of POS IV Solution to children<two years of age, a nonclinical study in juvenile pre-weaning Beagle dogs was conducted, which showed enlarged lateral ventricles in the brain at the conclusion of a 6 week dosing period.

METHODS

To evaluate the impact of this finding on older age dogs, which would support administration to children>two years of age, two studies were undertaken using magnetic resonance imaging (MRI) to monitor brain ventricle size longitudinally during three months administration of POS IV in adult and juvenile dogs. Necropsy was performed on all animals at the end of the studies. From the baseline MRI images, great variability in ventricle size was noted in both the adult and juvenile dogs; these images were used to distribute differently sized ventricles between treatment and vehicle groups as to not skew group means during the course of the study.

RESULTS

POS IV Solution had no effect on ventricle volume at any timepoint during dosing in either the adult or the juvenile dogs. Further, no gross or histomorphologic differences between groups were observed in either study. Compared to juvenile dogs, MRI analysis showed that adult dogs had larger ventricles, lower variability in all ventricle volumes, and a greater rate of increase in total ventricle volume.

DISCUSSION

Information on growth and development of brains is one of the few areas in which more detailed information is available about humans than about the standard laboratory animals used to model disease and predict toxicities. The use of MRI helped elucidate large natural variabilities in the dog brain, which could have altered the interpretation of this de-risking study, and provided a valuable noninvasive means to monitor the brain ventricles longitudinally.