Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

The mechanism underlying the development of tumors, particularly at early stages, still remains mostly elusive. Here, we report whole-genome long and short read sequencing analysis of 76 lung cancers, focusing on very early-stage lung adenocarcinomas such as adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma. The obtained data is further integrated with bulk and spatial transcriptomic data and epigenomic data. These analyses reveal key events in lung carcinogenesis. Minimal somatic mutations in pivotal driver mutations and essential proliferative factors are the only detectable somatic mutations in the very early-stage of AIS. These initial events are followed by copy number changes and global DNA hypomethylation. Particularly, drastic changes are initiated at the later AIS stage, i.e., in Noguchi type B tumors, wherein cancer cells are exposed to the surrounding microenvironment. This study sheds light on the pathogenesis of lung adenocarcinoma from integrated pathological and molecular viewpoints.

Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins

Atrial fibrillation (AF) is the most frequent persistent arrhythmia. Many genes have been reported as a genetic background for AF. However, most transcriptome analyses of AF are limited to the atrial samples and have not been evaluated by multiple cardiac regions. In this study, we analyzed the expression levels of protein-coding and long noncoding RNAs (lncRNAs) in six cardiac regions by RNA-seq. Samples were donated from six subjects with or without persistent AF for left atria, left atrial appendages, right atria, sinoatrial nodes, left ventricles, right ventricles, and pulmonary veins (PVs), and additional four right atrial appendages samples were collected from patients undergoing mitral valve replacement. In total, 23 AF samples were compared to 23 non-AF samples. Surprisingly, the most influenced heart region in gene expression by AF was the PV, not the atria. The ion channel-related gene set was significantly enriched upon analysis of these significant genes. In addition, some significant genes are cancer-related lncRNAs in PV in AF. A co-expression network analysis could detect the functional gene clusters. In particular, the cancer-related lncRNA, such as SAMMSON and FOXCUT, belong to the gene network with the cancer-related transcription factor FOXC1. Thus, they may also play an aggravating role in the pathogenesis of AF, similar to carcinogenesis. In the least, this study suggests that (1) RNA alteration is most intense in PVs and (2) post-transcriptional gene regulation by lncRNA may contribute to the progression of AF. Through the screening analysis across the six cardiac regions, the possibility that the PV region can play a role other than paroxysmal triggering in the pathogenesis of AF was demonstrated for the first time. Future research with an increase in the number of PV samples will lead to a novel understanding of the pathophysiology of AF.

Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans

The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies.

Phasing analysis of lung cancer genomes using a long read sequencer

Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis of non-small cell lung cancer specimens of 20 Japanese patients. By the combinatory use of short and long read sequencing data, we obtain long phased blocks of 834 kb in N50 length with >99% concordance rate. By analyzing the obtained phasing information, we reveal that several cancer genomes harbor regions in which mutations are unevenly distributed to either of two haplotypes. Large-scale chromosomal rearrangement events, which resemble chromothripsis events but have smaller scales, occur on only one chromosome, and these events account for the observed biased distributions. Interestingly, the events are characteristic of EGFR mutation-positive lung adenocarcinomas. Further integration of long read epigenomic and transcriptomic data reveal that haploid chromosomes are not always at equivalent transcriptomic/epigenomic conditions. Distinct chromosomal backgrounds are responsible for later cancerous aberrations in a haplotype-specific manner.

Cribriform carcinoma in the lymph nodes is associated with distant metastasis, recurrence, and survival among patients with node-positive colorectal cancer

Cribriform lymph node pattern is an independent risk factor for metachronous or synchronous distant metastasis in patients with stage III and IV node-positive colorectal cancer. Multivariable analysis in patients with stage III disease indicated that the cribriform pattern of carcinoma in the lymph nodes was an independent risk factor for recurrence and survival. Kaplan–Meier analysis demonstrated that the group with stage III cribriform-type lymph node carcinoma had shorter recurrence-free and overall survival times than the stage III group with the tubular type (P < 0.001).

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

BACKGROUND

Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified.

RESULTS

Full-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection.

CONCLUSIONS

Our results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells.

Observational Evidence for Stochastic Shock Drift Acceleration of Electrons at the Earth's Bow Shock

The first-order Fermi acceleration of electrons requires an injection of electrons into a mildly relativistic energy range. However, the mechanism of injection has remained a puzzle both in theory and observation. We present direct evidence for a novel stochastic shock drift acceleration theory for the injection obtained with Magnetospheric Multiscale observations at the Earth's bow shock. The theoretical model can explain electron acceleration to mildly relativistic energies at high-speed astrophysical shocks, which may provide a solution to the long-standing issue of electron injection.

Disturbance of the Front Region of Magnetic Reconnection Outflow Jets due to the Lower-Hybrid Drift Instability

A 3D fully kinetic simulation shows that the lower-hybrid drift instability disturbs the front of magnetic reconnection outflow jets and additionally causes energy dissipation. The result is very consistent with a disturbance observed at the dipolarization front (DF) in Earth's magnetotail by the Magnetospheric Multiscale (MMS) mission. A fully kinetic dispersion relation solver, validated by the MMS observations, further predicts that the disturbance of the reconnection jet front could occur over different parameter regimes in space plasmas including Earth's DF and solar flares.

P2725Transthyretin cardiac amyloidosis in heart failure with preserved ejection fraction: Imaging by Tc-99m bone scan

Background

Heart failure with preserved ejection fraction (HFpEF) is a heterogeneous clinical syndrome with multiple underlying causes. Transthyretin amyloidosis (ATTR) is an underdiagnosed cause of HFpEF. Extraosseous uptake, in particular, myocardial uptake, was observed in a number of ATTR patients examined with the bone scan tracers.

Objectives

We sought to determine the prevalence of ATTR as detected by the bone scan among the patients admitted due to HFpEF.

Methods

We screened all consecutive patients ≥60 years old admitted due to HFpEF (left ventricular ejection fraction ≥50%). All eligible patients were offered an echocardiogram and a bone scan (a 99mTc-DPD/MDP/HMDP scintigraphy). Echocardiographic and clinical variables were gathered in all the subjects. The intensity of the myocardial uptake was graded according to a visual scale ranging from 0 to 3 points, in which the absence of uptake was assigned a score of 0 points; uptake less than that of bone (referred to as the adjacent rib), 1 point; uptake similar to that of bone, 2 points; and uptake greater than that of bone, 3 points. The distribution of the uptake in myocardium was defined as focal uptake, diffuse uptake, uptake in a ventricular wall segment, diffuse ventricular uptake, or diffuse biventricular uptake.

Results

The study included 62 HFpEF patients (52% women, 73±9 years). The bone scintigraphic analysis revealed relatively intense myocardial uptake in 7 of 62 patients (11.2%). 7 patients had intense Tc-99m uptake (score of 2–3) in the cardiac region, showing deposition in both right and left ventricles in every case. Patients with amyloid deposition were older (78±6 vs. 70±12 years, p<0.05), had a lower systolic blood pressure (118±23 vs. 148±28 mmHg, p<0.05), and left ventricular ejection fraction (52±11 vs. 58±6%, p<0.05). Both groups had at least moderate left ventricular hypertrophy and abnormal global longitudinal strain with no significant difference between groups. In 6 all the cases, the final diagnosis of amyloidosis was based on the results of abdominal fat aspiration biopsy.

Conclusion

ATTR is an underdiagnosed disease that accounts for a significant number (11.2%) of HFpEF cases. These findings create an opportunity for further investigation in the targeted therapy of patients with HFpEF.

Beam Energy and Centrality Dependence of Direct-Photon Emission from Ultrarelativistic Heavy-Ion Collisions

The PHENIX collaboration presents first measurements of low-momentum (0.4<p_{T}<3  GeV/c) direct-photon yields from Au+Au collisions at sqrt[s_{NN}]=39 and 62.4 GeV. For both beam energies the direct-photon yields are substantially enhanced with respect to expectations from prompt processes, similar to the yields observed in Au+Au collisions at sqrt[s_{NN}]=200. Analyzing the photon yield as a function of the experimental observable dN_{ch}/dη reveals that the low-momentum (>1  GeV/c) direct-photon yield dN_{γ}^{dir}/dη is a smooth function of dN_{ch}/dη and can be well described as proportional to (dN_{ch}/dη)^{α} with α≈1.25. This scaling behavior holds for a wide range of beam energies at the Relativistic Heavy Ion Collider and the Large Hadron Collider, for centrality selected samples, as well as for different A+A collision systems. At a given beam energy, the scaling also holds for high p_{T} (>5  GeV/c), but when results from different collision energies are compared, an additional sqrt[s_{NN}]-dependent multiplicative factor is needed to describe the integrated-direct-photon yield.

Publisher Correction: Electron magnetic reconnection without ion coupling in Earth's turbulent magnetosheath

Change history: In this Letter, the y-axis values in Fig. 3f should go from 4 to -8 (rather than from 4 to -4), the y-axis values in Fig. 3h should appear next to the major tick marks (rather than the minor ticks), and in Fig. 1b, the arrows at the top and bottom of the electron-scale current sheet were going in the wrong direction; these errors have been corrected online.

Loss of the small GTPase Arl8b results in abnormal development of the roof plate in mouse embryos

Lysosomes are acidic organelles responsible for degrading both exogenous and endogenous materials. The small GTPase Arl8 localizes primarily to lysosomes and is involved in lysosomal function. In the present study, using Arl8b gene-trapped mutant (Arl8b^-/- ) mice, we show that Arl8b is required for the development of dorsal structures of the neural tube, including the thalamus and hippocampus. In embryonic day (E) 10.5 Arl8b^-/- embryos, Sox1 (a neuroepithelium marker) was ectopically expressed in the roof plate, whereas the expression of Gdf7 and Msx1 (roof plate markers) was reduced in the dorsal midline of the midbrain. Ectopic expression of Sox1 in Arl8b^-/- embryos was detected also at E9.0 in the neural fold, which gives rise to the roof plate. In addition, the levels of Bmp receptor IA and phosphorylated Smad 1/5/8 (downstream of BMP signaling) were increased in the neural fold of E9.0 Arl8b^-/- embryos. These results suggest that Arl8b is involved in the development of the neural fold and the subsequently formed roof plate, possibly via control of BMP signaling.

The Space Physics Environment Data Analysis System (SPEDAS)

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have "crib-sheets," user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer's Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its "modes of use" with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.

Electron-scale dynamics of the diffusion region during symmetric magnetic reconnection in space

Magnetic reconnection is an energy conversion process that occurs in many astrophysical contexts including Earth's magnetosphere, where the process can be investigated in situ by spacecraft. On 11 July 2017, the four Magnetospheric Multiscale spacecraft encountered a reconnection site in Earth's magnetotail, where reconnection involves symmetric inflow conditions. The electron-scale plasma measurements revealed (i) super-Alfvénic electron jets reaching 15,000 kilometers per second; (ii) electron meandering motion and acceleration by the electric field, producing multiple crescent-shaped structures in the velocity distributions; and (iii) the spatial dimensions of the electron diffusion region with an aspect ratio of 0.1 to 0.2, consistent with fast reconnection. The well-structured multiple layers of electron populations indicate that the dominant electron dynamics are mostly laminar, despite the presence of turbulence near the reconnection site.

Abstract 1883: A novel Axl and Mertk dual inhibitor ONO-7475: A new therapeutic agent for the treatment of FLT3-ITD and -wild-type acute myeloid leukemia (AML) overexpressing

Introduction: The TAM (Tyro3, Axl, and Mertk) receptor tyrosine kinases (RTKs) together with their ligands Gas6 and Pros1 play diverse roles in survival signaling in cancers. Currently, the consensus indicates that therapeutic targeting of TAM RTKs will prove direct antitumor activity and may complement existing immunotherapy regimens to unleash the full power of the anticancer immune response. A number of small-molecule kinase inhibitors targeting TAM RTKs are being developed and tested in preclinical models. ONO-7475 is a highly potent and oral dual inhibitor of Axl and Mertk, currently in a phase 1 clinical study as a therapeutic agent for AML (NCT03176277). Our previous studies demonstrated that ONO-7475 induced complete tumor remission in the FLT3-internal tandem duplication (ITD)-positive AML cell line MV-4-11 mouse xenograft model (Yasuhiro et al., Blood 2014). However, the antitumor activity against FLT3-ITD AML cells was due to Axl inhibition (Ruvolo et al., Haematologica 2017) and the mechanism of Mertk regulation in AML has not been determined. To evaluate this question, we screened 28 AML-derived cell lines for FLT3-wild type (WT) and analyzed the influence of Mertk in proliferation.

Methods: Twenty-eight FLT3-WT AML cell lines were treated with ONO-7475 for 72 hours, and the cell viabilities (IC50 values) were determined. Phospho-Axl (P-Axl), Axl and Mertk were determined by Western blot analysis. P-Mertk was determined by immunoprecipitation. Gene knockdown was achieved in FLT3-WT AML by transfecting with Axl, Mertk, Gas6, Pros1, or scrambled control siRNA.

Results: Six out of 28 FLT3-WT cell lines responded to ONO-7475, and two cell lines, MOLM16 and MKPL1, were highly sensitive (IC50: 4.7nM and 83.5nM). Western blot analysis demonstrated that Axl, Mertk and P-Mertk were overexpressed in these ONO-7475-sensitive cells, and both are classified as megakaryoblastic leukemia (FAB-M7). SiRNA knockdown studies showed that the cell growth in MOLM16 was partially dependent on Mertk (63.5%) but totally dependent on double genes, Axl and Mertk. Furthermore, knockdown of the ligands Gas6 and Pros1 also partially inhibited the cell growth in MOLM16, respectively (46.0%, 49.2%).

Conclusion: Our data suggest that Mertk may play an important role in survival signaling in FLT3-WT AML. Therefore, targeting both Axl and Mertk by ONO-7475 could be a new strategy for the treatment of FLT3-WT patients with AML in addition to FLT3-ITD. Additional work to investigate and clarify for target populations in both FLT3-ITD and -WT AML is currently under way.

Citation Format: Kohei Tanaka, Cuifang Li, Tomomi Hirosaki, Hikaru Kato, Yoshinori Ishikawa, Miho Oka, Hiroshi Egawa, Ryohei Kozaki, Toshio Yoshizawa. A novel Axl and Mertk dual inhibitor ONO-7475: A new therapeutic agent for the treatment of FLT3-ITD and -wild-type acute myeloid leukemia (AML) overexpressing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1883.

Differential Cross Section and Photon-Beam Asymmetry for the γ[over →]p → π^{-}Δ^{++}(1232) Reaction at Forward π^{-} Angles for E_{γ}=1.5-2.95 GeV

Differential cross sections and photon-beam asymmetries for the γ[over →]p→π^{-}Δ^{++}(1232) reaction have been measured for 0.7<cosθ_{π}^{c.m.}<1 and E_{γ}=1.5-2.95  GeV at SPring-8/LEPS. The first-ever high statistics cross-section data are obtained in this kinematical region, and the asymmetry data for 1.5<E_{γ}(GeV)<2.8 are obtained for the first time. This reaction has a unique feature for studying the production mechanisms of a pure uu[over ¯] quark pair in the final state from the proton. Although there is no distinct peak structure in the cross sections, a non-negligible excess over the theoretical predictions is observed at E_{γ}=1.5-1.8  GeV. The asymmetries are found to be negative in most of the present kinematical regions, suggesting the dominance of π exchange in the t channel. The negative asymmetries at forward meson production angles are different from the asymmetries previously measured for the photoproduction reactions producing a dd[over ¯] or an ss[over ¯] quark pair in the final state. Advanced theoretical models introducing nucleon resonances and additional unnatural-parity exchanges are needed to reproduce the present data.

Validating a Markov Model of Treatment for Hepatitis C Virus-related Hepatocellular Carcinoma

Objective: We created and validated a Markov model to simulate the prognosis with treatment for HCV-related hepatocellular carcinoma (HCC) for assessment of cost-effectiveness for alternative treatments of HCC.

Method: Markov state incorporated into the model consisted of the treatment as a surrogate for HCC stage and underlying liver function. Retrospective data of 793 patients from three university hospitals were used to determine Kaplan-Meier survival curves for each treatment and transition probabilities were derived from them.

Results: There was substantial overlap in the 95% CIs of the Markov model predicted and the Kaplan-Meier survival curves for each therapy. The predicted survival curves were also similar with those from the nationwide survey data supporting the external validity of our model.

Conclusions: Our Markov model estimates for prognosis with HCC have both internal and external validity and should be considered applicable for estimating cost-effectiveness related to HCC.

RETRACTED: P444 Shared decision making for switching from oral mesalazine tablets to granules in low adherent inflammatory bowel disease patients

BACKGROUND

Oral mesalazine effectively induces and maintains remission in inflammatory bowel diseases (IBD) patients. However, adherence to the drug regimen is low. Shared decision-making (SDM) is considered effective in promoting treatment adherence in IBD patients. We used SDM to switch non-adherent IBD patients from oral mesalazine tablets to granules and checked the new adherence rates.

METHODS

The IRB of our hospital approved this observational study named 'Evaluation of improvement of adherence by changing oral mesalazine to Pentasa granule in low adherent inflammatory bowel disease patients, IMPACT-PG'. We used the Morisky Medication Adherence Scale (MMAS-8, where an MMAS-8 score of ≥6 indicates good adherence) to assess adherence to oral mesalazine. We met with low adherence patients and explained the benefits and characteristics of mesalazine granules and tablets; we then gave them a choice between continuing with the same pH-dependent mesalazine tablets (with a 20% weight/volume decrease) and switching to oral mesalazine granules (2 g in one stick, 2 g once or twice a day). Primary endpoint was adherence rate in IBD patients with granule or with tablet at 6 months, and secondary endpoint was adherence rate at 12 months. Contributing factors to good adherence to the oral regimen were also examined. The adherence rate was analysed using chi-square test, and contributing factors were determined by multivariate analysis using SPSS ver24.

RESULTS

One hundred and eighty-three patients (126 UC and 57 Crohn's colitis patients) were enrolled and examined adherence by MMAS-8 score. Good adherence ratio was 42.6% (78 of 183). Both higher age and low frequency of medication were significantly more common in adherent patients than in non-adherent patients. Odds ratios of age and the frequency of daily medication were 1.057 (95% CI 1.029-1.086; p < 0.0001) and 0.407 (95% CI 0.218-0.759; p = 0.005), respectively. SDM was performed to the 105 low adherence patients. 67% of the low adherence patients (70 of 105) preferred mesalazine granules. Five patients were dropped out until 6 months, as well as 13 patients were dropped out until 12 months. Remission rates at 0, 6, and 24 months were not significantly different between granule and tablet groups. Adherence rates at 6 [67% (44/66) vs. 32% (11 of 34)] and at 12 [72% (43 of 60) vs. 44% (14 of 32)] months were significantly higher in the granule group than in the tablet group.

CONCLUSIONS

SDM was effective for switching patients from a mesalazine tablet to a granule regimen, and adherence rates were improved in IBD patients.

Re-Examination of Arousing and De-Arousing Effects of Cigarette Smoking

An attempt was made to replicate arousing and de-arousing effects of cigarette smoking originally reported by Golding and Mangan. Changes in electrodermal activity, heart rate, and magnitude in the EEG alpha (7.5—11.5 Hz) and beta (13.5—20 Hz) bands were measured under conditions of both mild sensory isolation as well as stress induced by loud white-noise. Under both conditions, real smoking as well as sham smoking an unlit cigarette increased beta activity and the skin potential response. In contrast, only real smoking produced a significant increase in heart rate, decrease in alpha activity, and increase in skin potential. De-arousing effects reported by Golding and Mangan for white-noise stress were not replicated.

Arl8b is required for lysosomal degradation of maternal proteins in the visceral yolk sac endoderm of mouse embryos

The small GTPase Arl8b localizes primarily to lysosomes and is involved in lysosomal motility and fusion. Here, we show that Arl8b is required for lysosomal degradation of maternal proteins in the visceral yolk sac endoderm (VYSE), an apical cell layer of the visceral yolk sac, of mouse embryos. The VYSE actively takes up maternal materials from uterine fluid and degrades them in lysosomes to provide breakdown products to the embryo as energy sources. Arl8b gene-trap mice (Arl8b−/−) displayed decreased early embryo body size. The Arl8b−/− VYSE exhibited defective endocytic trafficking to the lysosome and accumulation of maternal proteins such as albumin and immunoglobulin G in late endocytic organelles. Furthermore, Transthyretin-Cre;Arl8bflox/flox mice in which Arl8b was ablated specifically in the VYSE also showed decreased embryo body size, defects in trafficking to the lysosome, and reduction of the free amino acid level in the embryos. Taken together, these results suggest that Arl8b mediates lysosomal degradation of maternal proteins in the VYSE, thereby contributing to mouse embryonic development.

Electron-scale measurements of magnetic reconnection in space

Magnetic reconnection is a fundamental physical process in plasmas whereby stored magnetic energy is converted into heat and kinetic energy of charged particles. Reconnection occurs in many astrophysical plasma environments and in laboratory plasmas. Using measurements with very high time resolution, NASA's Magnetospheric Multiscale (MMS) mission has found direct evidence for electron demagnetization and acceleration at sites along the sunward boundary of Earth's magnetosphere where the interplanetary magnetic field reconnects with the terrestrial magnetic field. We have (i) observed the conversion of magnetic energy to particle energy; (ii) measured the electric field and current, which together cause the dissipation of magnetic energy; and (iii) identified the electron population that carries the current as a result of demagnetization and acceleration within the reconnection diffusion/dissipation region.

Centrality-Dependent Modification of Jet-Production Rates in Deuteron-Gold Collisions at √[s(NN)]=200 GeV

Jet production rates are measured in p+p and d+Au collisions at sqrt[s_{NN}]=200  GeV recorded in 2008 with the PHENIX detector at the Relativistic Heavy Ion Collider. Jets are reconstructed using the R=0.3 anti-k_{t} algorithm from energy deposits in the electromagnetic calorimeter and charged tracks in multiwire proportional chambers, and the jet transverse momentum (p_{T}) spectra are corrected for the detector response. Spectra are reported for jets with 12<p_{T}<50  GeV/c, within a pseudorapidity acceptance of |η|<0.3. The nuclear-modification factor (R_{dAu}) values for 0%-100% d+Au events are found to be consistent with unity, constraining the role of initial state effects on jet production. However, the centrality-selected R_{dAu} values and central-to-peripheral ratios (R_{CP}) show large, p_{T}-dependent deviations from unity, challenging the conventional models that relate hard-process rates and soft-particle production in collisions involving nuclei.

A novel HYLS1 homozygous mutation in living siblings with Joubert syndrome

The p.Asp211Gly homozygous HYLS1 mutation is so far known to cause only hydrolethalus syndrome, a lethal malformation syndrome. We report living sibling patients with a homozygous no-stop mutation in exon 4 of HYLS1, NM_145014.2:c.900A>C (p.Ter300TyrextTer11) in the second decade of life. The proband has Joubert syndrome (JS). The younger brother also has JS and an enlarged posterior fossa that was initially diagnosed as Dandy-Walker malformation. The present mutation is unique as it affects the stop codon. The product protein HYLS1 plays an essential role in the formation of the primary cilium. This report provides insight into the spectrum of disorders involving midline brain defects closely related to cilium dysfunction or ciliopathy.

Randomized clinical trial comparing long-term quality of life for Billroth I versus Roux-en-Y reconstruction after distal gastrectomy for gastric cancer

BACKGROUND

Patients' quality of life (QoL) deteriorates remarkably after gastrectomy. Billroth I reconstruction following distal gastrectomy has the physiological advantage of allowing food to pass through the duodenum. It was hypothesized that Billroth I reconstruction would be superior to Roux-en-Y reconstruction in terms of long-term QoL after distal gastrectomy. This study compared two reconstructions in a multicentre prospective randomized clinical trial to identify the optimal reconstruction procedure.

METHODS

Between January 2009 and September 2010, patients who underwent gastrectomy for gastric cancer were randomized during surgery to Billroth I or Roux-en-Y reconstruction. The primary endpoint was assessment of QoL using the Functional Assessment of Cancer Therapy - Gastric (FACT-Ga) questionnaire 36 months after surgery.

RESULTS

A total of 122 patients were enrolled in the study, 60 to Billroth I and 62 to Roux-en-Y reconstruction. There were no differences between the two groups in terms of postoperative complications or mortality, and no significant differences in FACT-Ga total score (P = 0·496). Symptom scales such as epigastric fullness (heaviness), diarrhoea and fatigue were significantly better in the Billroth I group at 36 months after gastrectomy (heaviness, P = 0·040; diarrhoea, P = 0·046; fatigue, P = 0·029). The rate of weight loss in the third year was lower for patients in the Billroth I group (P = 0·046).

CONCLUSION

The choice of anastomotic reconstruction after distal gastrectomy resulted in no difference in long-term QoL in patients with gastric cancer.

REGISTRATION NUMBER

NCT01065688 (http://www.clinicaltrials.gov).

Measurements of Elliptic and Triangular Flow in High-Multiplicity 3He+Au Collisions at √(s(NN))=200 GeV

We present the first measurement of elliptic (v(2)) and triangular (v(3)) flow in high-multiplicity (3)He+Au collisions at √(s(NN))=200  GeV. Two-particle correlations, where the particles have a large separation in pseudorapidity, are compared in (3)He+Au and in p+p collisions and indicate that collective effects dominate the second and third Fourier components for the correlations observed in the (3)He+Au system. The collective behavior is quantified in terms of elliptic v(2) and triangular v(3) anisotropy coefficients measured with respect to their corresponding event planes. The v(2) values are comparable to those previously measured in d+Au collisions at the same nucleon-nucleon center-of-mass energy. Comparisons with various theoretical predictions are made, including to models where the hot spots created by the impact of the three (3)He nucleons on the Au nucleus expand hydrodynamically to generate the triangular flow. The agreement of these models with data may indicate the formation of low-viscosity quark-gluon plasma even in these small collision systems.

Influence of neutralizing antibodies to adalimumab and infliximab on the treatment of psoriasis

BACKGROUND

Current treatment with biologics has produced dramatic therapeutic effects in patients with psoriasis, although these agents occasionally decrease in efficacy. One of the main factors responsible for this attenuation is attributed to the development of antidrug antibodies (ADAs).

OBJECTIVES

To analyse the relationship between serum drug concentrations, the presence of ADAs and treatment efficacy of adalimumab and infliximab, and to determine the optimal use of these biologics.

METHODS

This was a 1-year prospective study in the dermatology departments of Kobe University Hospital and collaborating hospitals. All patients starting a regimen of adalimumab and infliximab for psoriasis were included. We measured the serum concentration of the drugs and titres of antibodies to adalimumab and infliximab, as well as the Psoriasis Area and Severity Index scores at weeks 0, 4, 12, 24 and 48 during the first year of treatment.

RESULTS

We observed a 50% positive rate of ADAs to adalimumab, and a 41% positive rate of ADAs to infliximab. The titres of ADAs showed a wide range from low to high titres. In the high-titre groups, the patients exhibited a decreased clinical response, and demonstrated a negative correlation between titre and clinical response. However, an equivalent therapeutic effect was observed between the low-titre group and the group with no antibodies detected for adalimumab. For infliximab, the patients with ADAs showed decreased clinical response. An apparent negative correlation between antibody production and reduced clinical response was observed.

CONCLUSIONS

Two biologics, adalimumab and infliximab, showed different therapeutic behaviour. The measurement of ADAs and drug concentrations has important implications for treatment with biologics.

Measurement of Long-Range Angular Correlation and Quadrupole Anisotropy of Pions and (Anti)Protons in Central d+Au Collisions at sqrt[s_{NN}]=200 GeV

We present azimuthal angular correlations between charged hadrons and energy deposited in calorimeter towers in central d+Au and minimum bias p+p collisions at sqrt[s_{NN}]=200 GeV. The charged hadron is measured at midrapidity |η|<0.35, and the energy is measured at large rapidity (-3.7<η<-3.1, Au-going direction). An enhanced near-side angular correlation across |Δη|>2.75 is observed in d+Au collisions. Using the event plane method applied to the Au-going energy distribution, we extract the anisotropy strength v_{2} for inclusive charged hadrons at midrapidity up to p_{T}=4.5 GeV/c. We also present the measurement of v_{2} for identified π^{±} and (anti)protons in central d+Au collisions, and observe a mass-ordering pattern similar to that seen in heavy-ion collisions. These results are compared with viscous hydrodynamic calculations and measurements from p+Pb at sqrt[s_{NN}]=5.02 TeV. The magnitude of the mass ordering in d+Au is found to be smaller than that in p+Pb collisions, which may indicate smaller radial flow in lower energy d+Au collisions.

Comparative analysis of developmentally regulated expressions of Gadd45a, Gadd45b, and Gadd45g in the mouse and marmoset cerebral cortex

The cerebral cortex is an indispensable region that is involved in higher cognitive function in the mammalian brain, and is particularly evolved in the primate brain. It has been demonstrated that cortical areas are formed by both innate and activity-dependent mechanisms. However, it remains unknown what molecular changes induce cortical expansion and complexity during primate evolution. Active DNA methylation/demethylation is one of the epigenetic mechanisms that can modify gene expression via the methylation/demethylation of promoter regions. Three growth arrest and DNA damage-inducible small nuclear proteins, Gadd45 alpha, beta, and gamma, have been identified as regulators of methylation status. To understand the involvement of epigenetic factors in primate cortical evolution, we started by analyzing expression of these demethylation genes in the developing common marmoset (Callithrix jacchus) and mouse (Mus musculus) brain. In the marmoset brain, we found that cortical expression levels of Gadd45 alpha and gamma were reduced during development, whereas there was high expression of Gadd45 beta in some areas of the adult brain, including the prefrontal, temporal, posterior parietal and insula cortices, which are particularly expanded in greater primates and humans. Compared to the marmoset brain, there were no clear regional differences and constant or reduced Gadd45 expression was seen between juvenile and adult mouse brain. Double staining with a neuronal marker revealed that most Gadd45-expressing cells were NeuN-positive neurons. Thus, these results suggest the possibility that differential Gadd45 expression affects neurons, contributing cortical evolution and diversity.

DFT-based ab initio MD simulation of the ionic conduction in doped ZrO2 systems under epitaxial strain

Valence distribution and trajectory of oxygen ions in calculated stable structures, which imply oxygen sublattice formation induced by strain and further deformation by oxygen vacancies.

Cold-nuclear-matter effects on heavy-quark production at forward and backward rapidity in d + Au collisions at √sNN = 200 GeV

The PHENIX experiment has measured open heavy-flavor production via semileptonic decay over the transverse momentum range 1 < p(T) < 6  GeV/c at forward and backward rapidity (1.4 < |y| < 2.0) in d+Au and p + p collisions at √sNN = 200  GeV. In central d+Au collisions, relative to the yield in p + p collisions scaled by the number of binary nucleon-nucleon collisions, a suppression is observed at forward rapidity (in the d-going direction) and an enhancement at backward rapidity (in the Au-going direction). Predictions using nuclear-modified-parton-distribution functions, even with additional nuclear-p(T) broadening, cannot simultaneously reproduce the data at both rapidity ranges, which implies that these models are incomplete and suggests the possible importance of final-state interactions in the asymmetric d + Au collision system. These results can be used to probe cold-nuclear-matter effects, which may significantly affect heavy-quark production, in addition to helping constrain the magnitude of charmonia-breakup effects in nuclear matter.

Effect of occlusal rehabilitation on spatial memory and hippocampal neurons after long-term loss of molars in rats

Experimental loss of occlusal support caused by the extraction or grinding of molar teeth has been reported to foment the impairment of learning and memory in laboratory animals. The purpose of this study was to examine the effect of occlusal reconstruction after long-term loss of molars on spatial memory by using 8-arm radial maze and by assessing histopathological changes of neuron density in the hippocampus. Experimental dentures were inserted into the oral cavities of molarless rats to recover the occlusal support. Age-matched groups of control, molarless and denture-wearing rats were trained to perform the maze tasks. The difference of the error incidence in the maze task was evaluated between three groups. The difference of neuron density between three groups was also evaluated at the end of the maze task. Serum corticosterone levels were also measured to estimate the chronic stress, which could be caused by extraction, insertion of the experimental denture or any experimental procedure. The error incidence in the denture-wearing group was significantly higher than that of the control group, but significantly lower than that of the molarless group. Significant differences of neuron density were observed between three groups in each of the hippocampal CA1, CA3 and DG subfields. No significant difference of the serum corticosterone levels between three groups could be observed. From the results of this study, it was suggested that the recovery of occlusal support would bring amelioration of cognitive impairment concomitant with long period loss of molars in rats.

Azimuthal-angle dependence of charged-pion-interferometry measurements with respect to second- and third-order event planes in Au+Au collisions at √[S(NN)]=200 GeV

Charged-pion-interferometry measurements were made with respect to the second- and third-order event plane for Au+Au collisions at sqrt[s_{NN}]=200  GeV. A strong azimuthal-angle dependence of the extracted Gaussian-source radii was observed with respect to both the second- and third-order event planes. The results for the second-order dependence indicate that the initial eccentricity is reduced during the medium evolution, which is consistent with previous results. In contrast, the results for the third-order dependence indicate that the initial triangular shape is significantly reduced and potentially reversed by the end of the medium evolution, and that the third-order oscillations are largely dominated by the dynamical effects from triangular flow.