bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a New Virulent Clade in Enterohemorrhagic Escherichia coli O26:H11/H- Sequence Type 29
Authors: Ishijima Nozomi , Lee Ken-ichi , Kuwahara Tomomi , Nakayama-Imaohji Haruyuki , Yoneda Saori , Iguchi Atsushi , Ogura Yoshitoshi , Hayashi Tetsuya , Ohnishi Makoto , Iyoda Sunao 
Published: February 2017

AbstractEnterohemorrhagic Escherichia coli (EHEC) O26 infections cause severe human diseases such as hemolytic uremic syndrome and encephalopathy, and is the predominant serogroup among non-O157 EHEC in many countries. Shiga toxin (Stx), which consists of two distinct types (Stx1 and Stx2), plays a central role in EHEC pathogenesis. The major stx gene type in EHEC O26 strains is stx1, although isolates with only stx2 have emerged in Japan since 2012 and have been reported in Europe. In this study, we selected 27 EHEC O26 strains isolated in Japan and identified a distinct genetic clade within sequence type (ST) 29, designated ST29C1, that carried only stx2 and had the plasmid gene profile ehxA+/katP−/espP+/etpD−. We showed that ST29C1 strains produced higher Stx2a levels, and greater virulence in Vero cells and in germ-free mice than other lineages. We also showed that ST29C1 was a distinct phylogenetic clade by SNP analysis using whole genome sequences and clearly differed from the major European EHEC O26 virulent clone, which was designated ST29C2 in this study. The combination of toxin production analysis, virulence analysis in Vero cells and germ-free mice, and phylogenetic analysis identified a newly emerging virulent EHEC clade.
Endothelin receptor-specific control of endoplasmic reticulum stress and apoptosis in the kidney
Authors: De Miguel Carmen , Hamrick William C. , Hobbs Janet L. , Pollock David M. , Carmines Pamela K. , Pollock Jennifer S. 
Published: February 2017

AbstractEndothelin-1 (ET-1) promotes renal damage during cardiovascular disease; yet, the molecular mechanisms involved remain unknown. Endoplasmic reticulum (ER) stress, triggered by unfolded protein accumulation in the ER, contributes to apoptosis and organ injury. These studies aimed to determine whether the ET-1 system promotes renal ER stress development in response to tunicamycin. ETB deficient (ETB def) or transgenic control (TG-con) rats were used in the presence or absence of ETA receptor antagonism. Tunicamycin treatment similarly increased cortical ER stress markers in both rat genotypes; however, only ETB def rats showed a 14–24 fold increase from baseline for medullary GRP78, sXBP-1, and CHOP. Pre-treatment of TG-con rats with the ETA blocker ABT-627 for 1 week prior to tunicamycin injection significantly reduced the ER stress response in cortex and medulla, and also inhibited renal apoptosis. Pre-treatment with ABT-627 failed to decrease renal ER stress and apoptosis in ETB def rats. In conclusion, the ET-1 system is important for the development of tunicamycin-induced renal ER stress and apoptosis. ETA receptor activation induces renal ER stress genes and apoptosis, while functional activation of the ETB receptor has protective effects. These results highlight targeting the ETA receptor as a therapeutic approach against ER stress-induced kidney injury.
Robust High-dimensional Bioinformatics Data Streams Mining by ODR-ioVFDT
Authors: Wang Dantong , Fong Simon , Wong Raymond K. , Mohammed Sabah , Fiaidhi Jinan , Wong Kelvin K. L. 
Published: February 2017

AbstractOutlier detection in bioinformatics data streaming mining has received significant attention by research communities in recent years. The problems of how to distinguish noise from an exception and deciding whether to discard it or to devise an extra decision path for accommodating it are causing dilemma. In this paper, we propose a novel algorithm called ODR with incrementally Optimized Very Fast Decision Tree (ODR-ioVFDT) for taking care of outliers in the progress of continuous data learning. By using an adaptive interquartile-range based identification method, a tolerance threshold is set. It is then used to judge if a data of exceptional value should be included for training or otherwise. This is different from the traditional outlier detection/removal approaches which are two separate steps in processing through the data. The proposed algorithm is tested using datasets of five bioinformatics scenarios and comparing the performance of our model and other ones without ODR. The results show that ODR-ioVFDT has better performance in classification accuracy, kappa statistics, and time consumption. The ODR-ioVFDT applied onto bioinformatics streaming data processing for detecting and quantifying the information of life phenomena, states, characters, variables and components of the organism can help to diagnose and treat disease more effectively.
Classification of idiopathic interstitial pneumonias using anti–myxovirus resistance-protein 1 autoantibody
Authors: Hamano Yoshimasa , Kida Hiroshi , Ihara Shoichi , Murakami Akihiro , Yanagawa Masahiro , Ueda Ken , Honda Osamu , Tripathi Lokesh P. , Arai Toru , Hirose Masaki , Hamasaki Toshimitsu , Yano Yukihiro , Kimura Tetsuya , Kato Yasuhiro , Takamatsu Hyota , Otsuka Tomoyuki , Minami Toshiyuki , Hirata Haruhiko , Inoue Koji , Nagatomo Izumi , Takeda Yoshito , Mori Masahide , Nishikawa Hiroyoshi , Mizuguchi Kenji , Kijima Takashi , Kitaichi Masanori , Tomiyama Noriyuki , Inoue Yoshikazu , Kumanogoh Atsushi 
Published: February 2017

AbstractChronic fibrosing idiopathic interstitial pneumonia (IIP) can be divided into two main types: idiopathic pulmonary fibrosis (IPF), a steroid-resistant and progressive disease with a median survival of 2–3 years, and idiopathic non-specific interstitial pneumonia (INSIP), a steroid-sensitive and non-progressive autoimmune disease. Although the clinical courses of these two diseases differ, they may be difficult to distinguish at diagnosis. We performed a comprehensive analysis of serum autoantibodies from patients definitively diagnosed with IPF, INSIP, autoimmune pulmonary alveolar proteinosis, and sarcoidosis. We identified disease-specific autoantibodies and enriched KEGG pathways unique to each disease, and demonstrated that IPF and INSIP are serologically distinct. Furthermore, we discovered a new INSIP-specific autoantibody, anti–myxovirus resistance-1 (MX1) autoantibody. Patients positive for anti-MX1 autoantibody constituted 17.5% of all cases of chronic fibrosing IIPs. Notably, patients rarely simultaneously carried the anti-MX1 autoantibody and the anti–aminoacyl-transfer RNA synthetase autoantibody, which is common in chronic fibrosing IIPs. Because MX1 is one of the most important interferon-inducible anti-viral genes, we have not only identified a new diagnostic autoantibody of INSIP but also obtained new insight into the pathology of INSIP, which may be associated with viral infection and autoimmunity.
Drosophila imaginal disc growth factor 2 is a trophic factor involved in energy balance, detoxification, and innate immunity
Authors: Broz Vaclav , Kucerova Lucie , Rouhova Lenka , Fleischmannova Jana , Strnad Hynek , Bryant Peter J. , Zurovec Michal 
Published: February 2017

AbstractDrosophila imaginal disc growth factor 2 (IDGF2) is a member of chitinase-like protein family (CLPs) able to induce the proliferation of imaginal disc cells in vitro. In this study we characterized physiological concentrations and expression of IDGF2 in vivo as well as its impact on the viability and transcriptional profile of Drosophila cells in vitro. We show that IDGF2 is independent of insulin and protects cells from death caused by serum deprivation, toxicity of xenobiotics or high concentrations of extracellular adenosine (Ado) and deoxyadenosine (dAdo). Transcriptional profiling suggested that such cytoprotection is connected with the induction of genes involved in energy metabolism, detoxification and innate immunity. We also show that IDGF2 is an abundant haemolymph component, which is further induced by injury in larval stages. The highest IDGF2 accumulation was found at garland and pericardial nephrocytes supporting its role in organismal defence and detoxification. Our findings provide evidence that IDGF2 is an important trophic factor promoting cellular and organismal survival.
Crowdsourcing scoring of immunohistochemistry images: Evaluating Performance of the Crowd and an Automated Computational Method
Authors: Irshad Humayun , Oh Eun-Yeong , Schmolze Daniel , Quintana Liza M. , Collins Laura , Tamimi Rulla M. , Beck Andrew H. 
Published: February 2017

AbstractThe assessment of protein expression in immunohistochemistry (IHC) images provides important diagnostic, prognostic and predictive information for guiding cancer diagnosis and therapy. Manual scoring of IHC images represents a logistical challenge, as the process is labor intensive and time consuming. Since the last decade, computational methods have been developed to enable the application of quantitative methods for the analysis and interpretation of protein expression in IHC images. These methods have not yet replaced manual scoring for the assessment of IHC in the majority of diagnostic laboratories and in many large-scale research studies. An alternative approach is crowdsourcing the quantification of IHC images to an undefined crowd. The aim of this study is to quantify IHC images for labeling of ER status with two different crowdsourcing approaches, image-labeling and nuclei-labeling, and compare their performance with automated methods. Crowdsourcing- derived scores obtained greater concordance with the pathologist interpretations for both image-labeling and nuclei-labeling tasks (83% and 87%), as compared to the pathologist concordance achieved by the automated method (81%) on 5,338 TMA images from 1,853 breast cancer patients. This analysis shows that crowdsourcing the scoring of protein expression in IHC images is a promising new approach for large scale cancer molecular pathology studies.
Perceived moral traits of others differentiate the neural activation that underlies inequity-aversion
Authors: Nakatani Hironori , Ogawa Akitoshi , Suzuki Chisato , Asamizuya Takeshi , Ueno Kenichi , Cheng Kang , Okanoya Kazuo 
Published: February 2017

AbstractWe have a social preference to reduce inequity in the outcomes between oneself and others. Such a preference varies according to others. We performed functional magnetic resonance imaging during an economic game to investigate how the perceived moral traits of others modulate the neural activities that underlie inequity-aversion. The participants unilaterally allocated money to three partners (good, neutral, and bad). During presentation of the good and neutral partners, the anterior region of the rostral medial frontal cortex (arMFC) showed increased functional connectivity with the caudate head and the anterior insula, respectively. Following this, participants allocated more money to the good partner, and less to the bad partner, compared with the neutral partner. The caudate head and anterior insula showed greater activation during fair allocation to the good and unfair allocation to the neutral partners, respectively. However, these regions were silent during allocations to the bad partner. Therefore, the arMFC-caudate/insula circuit encompasses distinct neural processes that underlie inequity-aversion in monetary allocations that the different moral traits of others can modulate.
A novel approach to improve poly-γ-glutamic acid production by NADPH Regeneration in Bacillus licheniformis WX-02
Authors: Cai Dongbo , He Penghui , Lu Xingcheng , Zhu Chengjun , Zhu Jiang , Zhan Yangyang , Wang Qin , Wen Zhiyou , Chen Shouwen 
Published: February 2017

AbstractPoly-γ-glutamic acid (γ-PGA) is an important biochemical product with a variety of applications. This work reports a novel approach to improve γ-PGA through over expression of key enzymes in cofactor NADPH generating process for NADPH pool. Six genes encoding the key enzymes in NADPH generation were over-expressed in the γ-PGA producing strain B. licheniformis WX-02. Among various recombinants, the strain over-expressing zwf gene (coding for glucose-6-phosphate dehydrogenase), WX-zwf, produced the highest γ-PGA concentration (9.13 g/L), 35% improvement compared to the control strain WX-pHY300. However, the growth rates and glucose uptake rates of the mutant WX-zwf were decreased. The transcriptional levels of the genes pgsB and pgsC responsible for γ-PGA biosynthesis were increased by 8.21- and 5.26-fold, respectively. The Zwf activity of the zwf over expression strain increased by 9.28-fold, which led to the improvement of the NADPH generation, and decrease of accumulation of by-products acetoin and 2,3-butanediol. Collectively, these results demonstrated that NADPH generation via over-expression of Zwf is as an effective strategy to improve the γ-PGA production in B. licheniformis.
Evaluation of the p16 and Ki-67 Biomarkers as Predictors of the Recurrence of Premalignant Cervical Cancer Lesions after LEEP Conization
Authors: Leite Paulo Macêdo de Oliveira , Tafuri Luciene , Costa Maria Zélia de Oliveira , Lima Maria Inês de Miranda , Simões Renata Toscano 
Published: February 2017

Objective To evaluate the expressions of biomarkers p16 and Ki-67 in low-grade (LG) or high-grade (HG) lesions, and to relate them to risk factors and the recurrence of these lesions.
Methods A retrospective case-control study of 86 patients with LG and HG lesions who underwent a loop electrosurgical excision procedure (LEEP) between 1999 and 2004. The control group was composed of 69 women with no recurrence, and the study group, of 17 patients with recurrence. All patients were followed-up over a two-year period after surgery, and screened every six months, including cytology and colposcopy. Biopsy samples collected from LEEP were submitted to immunohistochemical analysis for p16 and Ki-67. The statistical analysis was performed using the Statistical Package for the Social Sciences software (SPSS, IBM-SPSS, Inc., Chicago, IL, US), with a significant p ​​< 0.05.
Results The biomarkers p16 and Ki-67, separately or combined, showed no relation to recurrence on the total analysis. However, evaluating specifically HG lesions, the positive expression (2+ and 3+) of p16/Ki-67 was associated with recurrence (0.010). In addition, p16 isolated was also more expressive in HG lesions (2+ and 3 + , p = 0.018), but it was unrelated to recurrence.
Conclusion Proteins p16 and Ki-67, both isolated and combined, are not reliable primary markers for the recurrence of cervical lesions in the majority of LG lesions. However, analyzing only the group with prior diagnosis of HG lesions, the expressions of p16 and of p16/Ki-67 were associated with recurrence, and they may be useful in monitoring these cases.
Entropy-driven segregation of polymer-grafted nanoparticles under confinement
Authors: Zhang Ren , Lee Bongjoon , Stafford Christopher M. , Douglas Jack F. , Dobrynin Andrey V. , Bockstaller Michael R. , Karim Alamgir 
Published: February 2017

Significance
Functional polymer nanocomposite thin films demand precise control over the spatial organization of nanoparticles on microscales and nanoscales. We demonstrate that conformational chain entropy can be used as a driving force to direct nanoparticle redistribution in blend systems where the enthalpic interactions are negligible. Tunable segregation of polymer-grafted nanoparticles is achieved within topographically patterned polymeric thin films by varying the relative confinement entropy of chains grafted to nanoparticles versus matrix chains. We identify key factors governing this confinement-induced segregation phenomenon and demonstrate the applicability of this technique to different pattern geometries and nanoparticle systems.
Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties
Authors: Schiemann Sabrina M. , Martín-Durán José M. , Børve Aina , Vellutini Bruno C. , Passamaneck Yale J. , Hejnol Andreas 
Published: February 2017

Significance
Hox genes pattern the anteroposterior axis of all animals that have left and right body sides. In many animals, Hox genes are clustered along the chromosomes and expressed in spatial and temporal order. This coordinated regulation is thought to have preserved the cluster through a developmental constraint. Our study of the genomic organization and the embryonic spatial and temporal expression of Hox genes in sessile marine animals called lampshells (brachiopods) shows that along with having a broken Hox cluster, they lack both temporal and spatial collinearity. Furthermore, we present molecular evidence that the hard tissues (chaetae and shells) of segmented worms, mollusks, and brachiopods share a common origin that dates back to the Early Cambrian.
Irradiation strongly reduces tumorigenesis of human induced pluripotent stem cells
Authors: Inui Shoki , Minami Kazumasa , Ito Emiko , Imaizumi Hiromasa , Mori Seiji , Koizumi Masahiko , Fukushima Satsuki , Miyagawa Shigeru , Sawa Yoshiki , Matsuura Nariaki 
Published: February 2017

AbstractInduced pluripotent stem (iPS) cells have demonstrated they can undergo self-renewal, attain pluripotency, and differentiate into various types of functional cells. In clinical transplantation of iPS cells, however, a major problem is the prevention of tumorigenesis. We speculated that tumor formation could be inhibited by means of irradiation. Since the main purpose of this study was to explore the prevention of tumor formation in human iPS (hiPS) cells, we tested the effects of irradiation on tumor-associated factors such as radiosensitivity, pluripotency and cell death in hiPS cells. The irradiated hiPS cells showed much higher radiosensitivity, because the survival fraction of hiPS cells irradiated with 2 Gy was &lt; 10%, and there was no change of pluripotency. Irradiation with 2 and 4 Gy caused substantial cell death, which was mostly the result of apoptosis. Irradiation with 2 Gy was detrimental enough to cause loss of proliferation capability and trigger substantial cell death in vitro. The hiPS cells irradiated with 2 Gy were injected into NOG mice (NOD/Shi-scid, IL-2 Rγnull) for the analysis of tumor formation. The group of mice into which hiPS cells irradiated with 2 Gy was transplanted showed significant suppression of tumor formation in comparison with that of the group into which non-irradiated hiPS cells were transplanted. It can be presumed that this diminished rate of tumor formation was due to loss of proliferation and cell death caused by irradiation. Our findings suggest that tumor formation following cell therapy or organ transplantation induced by hiPS cells may be prevented by irradiation.
Current Clinical Brain Tumor Imaging
Authors: Villanueva-Meyer Javier E. , Mabray Marc C. , Cha Soonmee 
Published: February 2017

Abstract
Neuroimaging plays an ever evolving role in the diagnosis, treatment planning, and post-therapy assessment of brain tumors. This review provides an overview of current magnetic resonance imaging (MRI) methods routinely employed in the care of the brain tumor patient. Specifically, we focus on advanced techniques including diffusion, perfusion, spectroscopy, tractography, and functional MRI as they pertain to noninvasive characterization of brain tumors and pretreatment evaluation. The utility of both structural and physiological MRI in the post-therapeutic brain evaluation is also reviewed with special attention to the challenges presented by pseudoprogression and pseudoresponse.
Takotsubo Syndrome After Cardiopulmonary Resuscitation During Emergency Cesarean Delivery
Authors: Kraft Katrina , Graf Matthias , Karch Martin , Felberbaum Ricardo 
Published: February 2017

BACKGROUND:
Takotsubo syndrome is a rare, stress-related, and reversible form of acute heart failure primarily affecting postmenopausal women. It is characterized by left ventricular dysfunction with a classic apical and midventricular wall motion abnormality (apical ballooning).

CASE:
A 28-year-old woman, gravida 2 para 1, at 30 4/7 weeks of gestation was admitted with fetal bradycardia, a fully dilated cervix, and breech presentation. During emergency cesarean delivery, the patient had intraoperative cardiac arrest. Resuscitation was successful. Twelve hours postoperatively, after demonstrating symptoms of acute heart failure, she was diagnosed with Takotsubo syndrome.

CONCLUSION:
Peripartum Takotsubo syndrome must be differentiated from peripartum cardiomyopathy. Cesarean delivery and sympathomimetic medications can increase the risk of occurrence. Early recognition and interdisciplinary management are essential in the prevention of serious and potentially fatal complications.
Interpregnancy Interval and Adverse Pregnancy Outcomes
Authors: Hanley Gillian E. , Hutcheon Jennifer A. , Kinniburgh Brooke A. , Lee Lily 
Published: February 2017

OBJECTIVE:
To examine the association between interpregnancy interval and maternal–neonate health when matching women to their successive pregnancies to control for differences in maternal risk factors and compare these results with traditional unmatched designs.

METHODS:
We conducted a retrospective cohort study of 38,178 women with three or more deliveries (two or greater interpregnancy intervals) between 2000 and 2015 in British Columbia, Canada. We examined interpregnancy interval (0–5, 6–11, 12–17, 18–23 [reference], 24–59, and 60 months or greater) in relation to neonatal outcomes (preterm birth [less than 37 weeks of gestation], small-for-gestational-age birth [less than the 10th centile], use of neonatal intensive care, low birth weight [less than 2,500 g]) and maternal outcomes (gestational diabetes, beginning the subsequent pregnancy obese [body mass index 30 or greater], and preeclampsia–eclampsia). We used conditional logistic regression to compare interpregnancy intervals within the same mother and unconditional (unmatched) logistic regression to enable comparison with prior research.

RESULTS:
Analyses using the traditional unmatched design showed significantly increased risks associated with short interpregnancy intervals (eg, there were 232 preterm births [12.8%] in 0–5 months compared with 501 [8.2%] in the 18–23 months reference group; adjusted odds ratio [OR] for preterm birth 1.53, 95% confidence interval [CI] 1.35–1.73). However, these risks were eliminated in within-woman matched analyses (adjusted OR for preterm birth 0.85, 95% CI 0.71–1.02). Matched results indicated that short interpregnancy intervals were significantly associated with increased risk of gestational diabetes (adjusted OR 1.35, 95% CI 1.02–1.80 for 0–5 months) and beginning the subsequent pregnancy obese (adjusted OR 1.61, 95% CI 1.05–2.45 for 0–5 months and adjusted OR 1.43, 95% CI 1.10–1.87 for 6–11 months).

CONCLUSION:
Previously reported associations between short interpregnancy intervals and adverse neonatal outcomes may not be causal. However, short interpregnancy interval is associated with increased risk of gestational diabetes and beginning a subsequent pregnancy obese.