bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft Genome Sequence of Acinetobacter johnsonii C6, an Environmental Isolate Engaging in Interspecific Metabolic Interactions
Authors: Kaas Rolf Sommer , Mordhorst Hanne , Leekitcharoenphon Pimlapas , Dyring Jensen Jacob , Haagensen Janus A. J. , Molin Søren , Pamp Sünje Johanna 
Published: April 2017

ABSTRACT

Acinetobacter johnsonii
C6 originates from creosote-polluted groundwater and performs ecological and evolutionary interactions with
Pseudomonas putida
in biofilms. The draft genome of
A. johnsonii
C6 is 3.7 Mbp and was shaped by mobile genetic elements. It reveals genes facilitating the biodegradation of aromatic hydrocarbons and resistance to antimicrobials and metals.
Complete and Assembled Genome Sequence of Lactobacillus plantarum RI-113 Isolated from Salami
Authors: Inglin Raffael C. , Meile Leo , Klumpp Jochen , Stevens Marc J. A. 
Published: April 2017

ABSTRACT

We present here the complete genome sequence of
Lactobacillus plantarum
RI-113, a strain isolated from salami, which was determined using single-molecule real-time sequencing.
Draft Nuclear Genome Sequence of the Liquid Hydrocarbon–Accumulating Green Microalga
Botryococcus braunii
Race B (Showa)
Authors: Browne Daniel R. , Jenkins Jerry , Schmutz Jeremy , Shu Shengqiang , Barry Kerrie , Grimwood Jane , Chiniquy Jennifer , Sharma Aditi , Niehaus Thomas D. , Weiss Taylor L. , Koppisch Andrew T. , Fox David T. , Dhungana Suraj , Okada Shigeru , Chappell Joe , Devarenne Timothy P. 
Published: April 2017

ABSTRACT

Botryococcus braunii
has long been known as a prodigious producer of liquid hydrocarbon oils that can be converted into combustion engine fuels. This draft genome for the B race of
B. braunii
will allow researchers to unravel important hydrocarbon biosynthetic pathways and identify possible regulatory networks controlling this unusual metabolism.
Complete Genome Sequence of Pseudomonas protegens H78, a Plant Growth–Promoting Rhizobacterium
Authors: Huang Xianqing , Wang Zheng , Liu Yujie , Zhang Xuehong 
Published: April 2017

ABSTRACT

The plant growth–promoting rhizobacterium
Pseudomonas protegens
H78, which was isolated from the rhizosphere of oilseed rape in Shanghai, can produce a large array of antibiotics with a broad spectrum of activities. Here, we report the annotated complete genome sequence of
P. protegens
H78.
Complete Genome Characterization of Chinese Porcine Deltacoronavirus Strain CHN/Tianjin/2016
Authors: Zhao Feng , Sun Ying , Qian Bingxu , Zhang Xiaorong , Wu Yantao 
Published: April 2017

ABSTRACT
As we all know, porcine deltacoronavirus was first detected in Hong Kong, China. Here, we report the complete genome sequence of the Chinese porcine deltacoronavirus strain CHN/Tianjin/2016, which was collected and amplified from clinical fecal samples in March of 2016.
Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria,
Carboxydocella
sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan
Authors: Fukuyama Yuto , Oguro Tatsuki , Omae Kimiho , Yoneda Yasuko , Yoshida Takashi , Sako Yoshihiko 
Published: April 2017

ABSTRACT

Hydrogenogenic carboxydotrophs may provide hydrogen as primary energy for the microbial community via carbon monoxide oxidation. To investigate the genetics of carbon monoxide metabolism, we report here the draft genome sequences of the hydrogenogenic carboxydotrophs
Carboxydocella
sp. strains JDF658 (2.60 Mbp; G+C content, 49.2%) and ULO1 (2.70 Mbp; G+C content, 48.8%).
Genome Sequences of Cluster K Mycobacteriophages DrHayes, Urkel, and SamuelLPlaqson
Authors: Anders Kirk R. , Murphy Alex M. , Ettinger William F. , Kempthorne Douglas , Kittridge Charles , Kures Alex , Lundgren Sarah , Masters Jacob , Noyes Rachel , Winters Christina , Yazzolino Perry , Ziebert Kasandra , Haydock Joseph , Hayes Stephen , Garlena Rebecca A. , Russell Daniel A. , Poxleitner Marianne K. , Ettinger Ann-Scott H. 
Published: April 2017

ABSTRACT

Mycobacteriophages DrHayes, Urkel, and SamuelLPlaqson were isolated from soil samples in Spokane, WA, using
Mycobacterium smegmatis
mc
2
155 grown at room temperature. The three genomes differ by only a few nucleotides, are 60,526 bp long, have 97 predicted protein-coding genes and one tRNA gene, and are members of subcluster K1.
Cell Biology of Hyphal Growth
Authors: Steinberg Gero , Peñalva Miguel A. , Riquelme Meritxell , Wösten Han A. , Harris Steven D. 
Published: April 2017

ABSTRACT
Filamentous fungi are a large and ancient clade of microorganisms that occupy a broad range of ecological niches. The success of filamentous fungi is largely due to their elongate hypha, a chain of cells, separated from each other by septa. Hyphae grow by polarized exocytosis at the apex, which allows the fungus to overcome long distances and invade many substrates, including soils and host tissues. Hyphal tip growth is initiated by establishment of a growth site and the subsequent maintenance of the growth axis, with transport of growth supplies, including membranes and proteins, delivered by motors along the cytoskeleton to the hyphal apex. Among the enzymes delivered are cell wall synthases that are exocytosed for local synthesis of the extracellular cell wall. Exocytosis is opposed by endocytic uptake of soluble and membrane-bound material into the cell. The first intracellular compartment in the endocytic pathway is the early endosomes, which emerge to perform essential additional functions as spatial organizers of the hyphal cell. Individual compartments within septated hyphae can communicate with each other via septal pores, which allow passage of cytoplasm or organelles to help differentiation within the mycelium. This article introduces the reader to more detailed aspects of hyphal growth in fungi.
Mycobacterium avium
Complex Disease
Authors: Daley Charles L. 
Published: April 2017

ABSTRACT

Despite the ubiqitous nature of
Mycobacterium avium
complex (MAC) organisms in the environment, relatively few of those who are infected develop disease. Thus, some degree of susceptibility due to either underlying lung disease or immunosuppression is required. The frequency of pulmonary MAC disease is increasing in many areas, and the exact reasons are unknown. Isolation of MAC from a respiratory specimen does not necessarily mean that treatment is required, as the decision to treatment requires the synthesis of clinical, radiographic, and microbiologic information as well as a weighing of the risks and benefits for the individual patient. Successful treatment requires a multipronged approach that includes antibiotics, aggressive pulmonary hygiene, and sometimes resection of the diseased lung. A combination of azithromycin, rifampin, and ethambutol administered three times weekly is recommend for nodular bronchiectatic disease, whereas the same regimen may be used for cavitary disease but administered daily and often with inclusion of a parenteral aminoglycoside. Disseminated MAC (DMAC) is almost exclusively seen in patients with late-stage AIDS and can be treated with a macrolide in combination with ethambutol, with or without rifabutin: the most important intervention in this setting is to gain HIV control with the use of potent antiretroviral therapy. Treatment outcomes for many patients with MAC disease remain suboptimal, so new drugs and treatment regimens are greatly needed. Given the high rate of reinfection after cure, one of the greatest needs is a better understanding of where infection occurs and how this can be prevented.
Clinical and cost-effectiveness, safety and acceptability ofcommunityintravenousantibioticservice models: CIVAS systematic review
Authors: Mitchell E D , Czoski Murray C , Meads D , Minton J , Wright J , Twiddy M 
Published: April 2017

ObjectiveEvaluate evidence of the efficacy, safety, acceptability and cost-effectiveness of outpatient parenteral antimicrobial therapy (OPAT) models.DesignA systematic review.Data sourcesMEDLINE, EMBASE, CINAHL, Cochrane Library, National Health Service (NHS) Economic Evaluation Database (EED), Research Papers in Economics (RePEc), Tufts Cost-Effectiveness Analysis (CEA) Registry, Health Business Elite, Health Information Management Consortium (HMIC), Web of Science Proceedings, International Pharmaceutical Abstracts, British Society for Antimicrobial Chemotherapy website. Searches were undertaken from 1993 to 2015.Study selectionAll studies, except case reports, considering adult patients or practitioners involved in the delivery of OPAT were included. Studies combining outcomes for adults and children or non-intravenous (IV) and IV antibiotic groups were excluded, as were those focused on process of delivery or clinical effectiveness of 1 antibiotic over another. Titles/abstracts were screened by 1 reviewer (20% verified). 2 authors independently screened studies for inclusion.Results128 studies involving >60 000 OPAT episodes were included. 22 studies (17%) did not indicate the OPAT model used; only 29 involved a comparator (23%). There was little difference in duration of OPAT treatment compared with inpatient therapy, and overall OPAT appeared to produce superior cure/improvement rates. However, when models were considered individually, outpatient delivery appeared to be less effective, and self-administration and specialist nurse delivery more effective. Drug side effects, deaths and hospital readmissions were similar to those for inpatient treatment, but there were more line-related complications. Patient satisfaction was high, with advantages seen in being able to resume daily activities and having greater freedom and control. However, most professionals perceived challenges in providing OPAT.ConclusionsThere were no systematic differences related to the impact of OPAT on treatment duration or adverse events. However, evidence of its clinical benefit compared with traditional inpatient treatment is lacking, primarily due to the dearth of good quality comparative studies. There was high patient satisfaction with OPAT use but the few studies considering practitioner acceptability highlighted organisational and logistic barriers to its delivery.
How are non-numerical prognostic statements interpreted and are they subject to positive bias?
Authors: Moyer Anne , Siess Samantha , Bhinder Sumeet 
Published: April 2017

ObjectivesFrank, clear communication with family members of terminally ill or incapacitated patients has important implications for well-being, satisfaction with care and sound decision-making. However, numerical prognostic statements, particularly more negative ones, have been found to be interpreted in a positively biased manner. Less precise non-numerical statements, preferred by physicians, and particularly statements using threatening terms (dying vs surviving) may be even more subject to such biases.MethodsParticipants (N=200) read non-numerical prognostic statements framed in terms of dying or surviving and indicated their interpretation of likelihood of survival.ResultsEven the most extreme statements were not interpreted to indicate 100% likelihood of surviving or dying, (eg, they will definitely survive, 92.77%). The poorness of prognoses was associated with more optimistically biased interpretations but this was not, however, affected by the wording of the prognoses in terms of dying versus surviving.ConclusionsThe findings illuminate the ways in which commonly used non-numeric language may be understood in numeric terms during prognostic discussions and provide further evidence of recipients' propensity for positive bias.
Proliferation of primary human hepatocytes and prevention of hepatitis B virus reinfection efficiently deplete nuclear cccDNA in vivo
Authors: Allweiss Lena , Volz Tassilo , Giersch Katja , Kah Janine , Raffa Giuseppina , Petersen Joerg , Lohse Ansgar W , Beninati Concetta , Pollicino Teresa , Urban Stephan , Lütgehetmann Marc , Dandri Maura 
Published: April 2017

ObjectiveThe stability of the covalently closed circular DNA (cccDNA) in nuclei of non-dividing hepatocytes represents a key determinant of HBV persistence. Contrarily, studies with animal hepadnaviruses indicated that hepatocyte turnover can reduce cccDNA loads but knowledge on the proliferative capacity of HBV-infected primary human hepatocytes (PHHs) in vivo and the fate of cccDNA in dividing PHHs is still lacking. This study aimed to determine the impact of human hepatocyte division on cccDNA stability in vivo.MethodsPHH proliferation was triggered by serially transplanting hepatocytes from HBV-infected humanised mice into naïve recipients. Cell proliferation and virological changes were assessed by quantitative PCR, immunofluorescence and RNA in situ hybridisation. Viral integrations were analysed by gel separation and deep sequencing.ResultsPHH proliferation strongly reduced all infection markers, including cccDNA (median 2.4 log/PHH). Remarkably, cell division appeared to cause cccDNA dilution among daughter cells and intrahepatic cccDNA loss. Nevertheless, HBV survived in sporadic non-proliferating human hepatocytes, so that virological markers rebounded as hepatocyte expansion relented. This was due to reinfection of quiescent PHHs since treatment with the entry inhibitor myrcludex-B or nucleoside analogues blocked viral spread and intrahepatic cccDNA accumulation. Viral integrations were detected both in donors and recipient mice but did not appear to contribute to antigen production.ConclusionsWe demonstrate that human hepatocyte division even without involvement of cytolytic mechanisms triggers substantial cccDNA loss. This process may be fundamental to resolve self-limiting acute infection and should be considered in future therapeutic interventions along with entry inhibition strategies.
Acute presentation of autoimmune hepatitis: a multicentre study with detailed histological evaluation in a large cohort of patients
Authors: Nguyen Canh Hiep , Harada Kenichi , Ouchi Hirofumi , Sato Yasunori , Tsuneyama Koichi , Kage Masayoshi , Nakano Masayuki , Yoshizawa Kaname , Takahashi Atsushi , Abe Masanori , Kang Jong-Hon , Koike Kazuhiko , Inui Ayano , Fujisawa Tomoo , Takaki Akinobu , Arinaga-Hino Teruko , Torimura Takuji , Suzuki Yoshiyuki , Fujiwara Keiichi , Zeniya Mikio , Ohira Hiromasa , Tanaka Atsushi , Takikawa Hajime 
Published: April 2017

AimsAlthough liver biopsy is crucial to diagnose and guide treatment decisions, a detailed histological analysis of autoimmune hepatitis (AIH) with clinically acute presentations has not yet been performed. This study aimed to characterise the histological features and explore potential histological hallmarks to diagnose the acute presentation of AIH.MethodsWe systematically evaluated liver specimens of 87 adult patients with acute presentation of AIH retrospectively enrolled from Japanese multicentre facilities. Each histological feature was predefined by consensus based on the diagnostic criteria.ResultsKey findings were that acute presentation of AIH revealed histological features of both acute hepatitis and chronic hepatitis accompanying various degrees of fibrosis. The prominent features were lobular necrosis/inflammation (97.7%), plasma cell infiltration (96.4%), emperipolesis (89.3%), pigmented macrophages (84.5%), cobblestone appearance of hepatocytes (82.6%) and perivenular necroinflammatory activity, including centrilobular necrosis (81.4%).ConclusionsThe acute presentation of AIH represents the entire histological spectrum of acute hepatitis and chronic hepatitis with various activity grades and fibrosis stages that clinically correspond to acute-onset AIH and acute exacerbation of classic AIH, respectively. Although there are no pathognomonic features for the pathological diagnosis, the prominent presence of lobular and perivenular necroinflammatory activity, pigmented macrophages and cobblestone appearance of hepatocytes in addition to the classic AIH features, such as plasma cell infiltration and emperipolesis, are useful for the pathological diagnosis of the acute presentation of AIH.
Micellar Delivery of miR-34a Modulator Rubone and Paclitaxel in Resistant Prostate Cancer
Authors: Wen Di , Peng Yang , Lin Feng , Singh Rakesh K. , Mahato Ram I. 
Published: April 2017

Abstract
Treatment of prostate cancer with paclitaxel often fails due to the development of chemoresistance caused by downregulation of the tumor suppressor gene miR-34a. In this study, we demonstrate that codelivery of paclitaxel and 2'-hydroxy-2,4,4',5,6'-pentamethoxychalcone (termed rubone) drives upregulation of miR-34a and chemosensitizes paclitaxel-resistant prostate cancer cells, killing both cancer stem–like cells (CSC) and bulk tumor cells. Rubone upregulated miR-34a and reversed its downstream target genes in DU145-TXR and PC3-TXR cells. Paclitaxel and rubone combination therapy inhibited tumor cell growth, migration, and CSC population growth. We synthesized poly(ethylene glycol)-block-poly(2-methyl-2-carboxyl-propylene carbonate-graft-dodecanol; PEG-PCD) to prepare micelles. The drug-loading capacities were 9.70% ± 0.10% and 5.34% ± 0.02% for paclitaxel and rubone, respectively, controlling a drug release of 60.20% ± 2.67% and 60.62% ± 4.35% release of paclitaxel and rubone at 24 hours. Delivery of miR-34a and rubone decreased PC3-TXR cell viability with increasing paclitaxel concentration. Coincubation with a miR-34a inhibitor diminished the effect of rubone. Paclitaxel IC50 in PC3 and PC3-TXR cells was 55.6 and 2,580 nmol/L, respectively, but decreased to 49.8 and 93.2 nmol/L when treated in combination with rubone, demonstrating a reversal of paclitaxel resistance by rubone. Systemic administration of micelles carrying paclitaxel and rubone inhibited orthotopic prostate tumor growth in nude mice, compared with monotherapy, by reversing the expression of miR-34a, SIRT1, cyclin D1, and E-cadherin. In summary, our results showed how rubone acts as an efficient small-molecule modulator of miR-34a to reverse chemoresistance and further enhance the therapeutic efficacy of paclitaxel in paclitaxel-resistant prostate cancer. Cancer Res; 77(12); 3244–54. ©2017 AACR.
Whither Radioimmunotherapy: To Be or Not To Be?
Authors: Green Damian J. , Press Oliver W. 
Published: April 2017

Abstract
Therapy of cancer with radiolabeled monoclonal antibodies has produced impressive results in preclinical experiments and in clinical trials conducted in radiosensitive malignancies, particularly B-cell lymphomas. Two “first-generation,” directly radiolabeled anti-CD20 antibodies, 131iodine-tositumomab and 90yttrium-ibritumomab tiuxetan, were FDA-approved more than a decade ago but have been little utilized because of a variety of medical, financial, and logistic obstacles. Newer technologies employing multistep “pretargeting” methods, particularly those utilizing bispecific antibodies, have greatly enhanced the therapeutic efficacy of radioimmunotherapy and diminished its toxicities. The dramatically improved therapeutic index of bispecific antibody pretargeting appears to be sufficiently compelling to justify human clinical trials and reinvigorate enthusiasm for radioimmunotherapy in the treatment of malignancies, particularly lymphomas. Cancer Res; 77(9); 2191–6. ©2017 AACR.
Immune Gene Expression Is Associated with Genomic Aberrations in Breast Cancer
Authors: Safonov Anton , Jiang Tingting , Bianchini Giampaolo , Győrffy Balázs , Karn Thomas , Hatzis Christos , Pusztai Lajos 
Published: April 2017

AbstractThe presence of tumor-infiltrating lymphocytes (TIL) is a favorable prognostic factor in breast cancer, but what drives immune infiltration remains unknown. Here we examine if clonal heterogeneity, total mutation load, neoantigen load, copy number variations (CNV), gene- or pathway-level somatic mutations, or germline polymorphisms (SNP) are associated with immune metagene expression in breast cancer subtypes. Thirteen published immune metagenes correlated separately with genomic metrics in the three major breast cancer subtypes. We analyzed RNA-Seq, DNA copy number, mutation and germline SNP data of 627 ER+, 207 HER2+, and 191 triple-negative (TNBC) cancers from The Cancer Genome Atlas. P-values were adjusted for multiple comparisons, and permutation testing was used to assess false discovery rates. Increased immune metagene expression associated significantly with lower clonal heterogeneity estimated by MATH score in all subtypes and with a trend for lower overall mutation, neoantigen, and CNV loads in TNBC and HER2+ cancers. In ER+ cancers, mutation load, neoantigen load, and CNV load weakly but positively associated with immune infiltration, which reached significance for overall mutation load only. No highly recurrent single gene or pathway level mutations associated with immune infiltration. High immune gene expression and lower clonal heterogeneity in TNBC and HER2+ cancers suggest an immune pruning effect and equilibrium between immune surveillance and clonal expansion. Thus, immune checkpoint inhibitors may tip the balance in favor of immune surveillance in these cancers. Cancer Res; 77(12); 3317–24. ©2017 AACR.
In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The ϕ-Index
Authors: Bakas Spyridon , Akbari Hamed , Pisapia Jared , Martinez-Lage Maria , Rozycki Martin , Rathore Saima , Dahmane Nadia , O'Rourke Donald M. , Davatzikos Christos 
Published: April 2017

Abstract
Purpose: The epidermal growth factor receptor variant III (EGFRvIII) mutation has been considered a driver mutation and therapeutic target in glioblastoma, the most common and aggressive brain cancer. Currently, detecting EGFRvIII requires postoperative tissue analyses, which are ex vivo and unable to capture the tumor's spatial heterogeneity. Considering the increasing evidence of in vivo imaging signatures capturing molecular characteristics of cancer, this study aims to detect EGFRvIII in primary glioblastoma noninvasively, using routine clinically acquired imaging.
Experimental Design: We found peritumoral infiltration and vascularization patterns being related to EGFRvIII status. We therefore constructed a quantitative within-patient peritumoral heterogeneity index (PHI/ϕ-index), by contrasting perfusion patterns of immediate and distant peritumoral edema. Application of ϕ-index in preoperative perfusion scans of independent discovery (n = 64) and validation (n = 78) cohorts, revealed the generalizability of this EGFRvIII imaging signature.
Results: Analysis in both cohorts demonstrated that the obtained signature is highly accurate (89.92%), specific (92.35%), and sensitive (83.77%), with significantly distinctive ability (P = 4.0033 × 10−10, AUC = 0.8869). Findings indicated a highly infiltrative-migratory phenotype for EGFRvIII+ tumors, which displayed similar perfusion patterns throughout peritumoral edema. Contrarily, EGFRvIII− tumors displayed perfusion dynamics consistent with peritumorally confined vascularization, suggesting potential benefit from extensive peritumoral resection/radiation.
Conclusions: This EGFRvIII signature is potentially suitable for clinical translation, since obtained from analysis of clinically acquired images. Use of within-patient heterogeneity measures, rather than population-based associations, renders ϕ-index potentially resistant to inter-scanner variations. Overall, our findings enable noninvasive evaluation of EGFRvIII for patient selection for targeted therapy, stratification into clinical trials, personalized treatment planning, and potentially treatment-response evaluation. Clin Cancer Res; 23(16); 4724–34. ©2017 AACR.