bluuebunny/crossref_metadata_2025 huggingface dataset:
Moving metal artifact reduction in cone‐beam CT scans with implanted cylindrical gold markers
Authors: Toftegaard Jakob , Fledelius Walther , Seghers Dieter , Huber Michael , Brehm Marcus , Worm Esben S. , Elstrøm Ulrik V. , Poulsen Per R.
Published: November 2014

Purpose:

Implanted gold markers for image‐guided radiotherapy lead to streaking artifacts in cone‐beam CT (CBCT) scans. Several methods for metal artifact reduction (MAR) have been published, but they all fail in scans with large motion. Here the authors propose and investigate a method for automatic moving metal artifact reduction (MMAR) in CBCT scans with cylindrical gold markers.

Methods:

The MMAR CBCT reconstruction method has six steps. (1) Automatic segmentation of the cylindrical markers in the CBCT projections. (2) Removal of each marker in the projections by replacing the pixels within a masked area with interpolated values. (3) Reconstruction of a marker‐free CBCT volume from the manipulated CBCT projections. (4) Reconstruction of a standard CBCT volume with metal artifacts from the original CBCT projections. (5) Estimation of the three‐dimensional (3D) trajectory during CBCT acquisition for each marker based on the segmentation in Step 1, and identification of the smallest ellipsoidal volume that encompasses 95% of the visited 3D positions. (6) Generation of the final MMAR CBCT reconstruction from the marker‐free CBCT volume of Step 3 by replacing the voxels in the 95% ellipsoid with the corresponding voxels of the standard CBCT volume of Step 4. The MMAR reconstruction was performed retrospectively using a half‐fan CBCT scan for 29 consecutive stereotactic body radiation therapy patients with 2–3 gold markers implanted in the liver. The metal artifacts of the MMAR reconstructions were scored and compared with a standard MAR reconstruction by counting the streaks and by calculating the standard deviation of the Hounsfield units in a region around each marker.

Results:

The markers were found with the same autosegmentation settings in 27 CBCT scans, while two scans needed slightly changed settings to find all markers automatically in Step 1 of the MMAR method. MMAR resulted in 15 scans with no streaking artifacts, 11 scans with 1–4 streaks, and 3 scans with severe streaking artifacts. The corresponding numbers for MAR were 8 (no streaks), 1 (1–4 streaks), and 20 (severe streaking artifacts). The MMAR method was superior to MAR in scans with more than 8 mm 3D marker motion and comparable to MAR for scans with less than 8 mm motion. In addition, the MMAR method was tested on a 4D CBCT reconstruction for which it worked equally well as for the 3D case. The markers in the 4D case had very low motion blur.

Conclusions:

An automatic method for MMAR in CBCT scans was proposed and shown to effectively remove almost all streaking artifacts in a large set of clinical CBCT scans with implanted gold markers in the liver. Residual streaking artifacts observed in three CBCT scans may be removed with better marker segmentation.
Mammalian skin cell biology: At the interface between laboratory and clinic
Authors: Watt Fiona M.
Published: November 2014

Mammalian skin research represents the convergence of three complementary disciplines: cell biology, mouse genetics, and dermatology. The skin provides a paradigm for current research in cell adhesion, inflammation, and tissue stem cells. Here, I discuss recent insights into the cell biology of skin. Single-cell analysis has revealed that human epidermal stem cells are heterogeneous and differentiate in response to multiple extrinsic signals. Live-cell imaging, optogenetics, and cell ablation experiments show skin cells to be remarkably dynamic. High-throughput, genome-wide approaches have yielded unprecedented insights into the circuitry that controls epidermal stem cell fate. Last, integrative biological analysis of human skin disorders has revealed unexpected functions for elements of the skin that were previously considered purely structural.
The melanoma revolution: From UV carcinogenesis to a new era in therapeutics
Authors: Lo Jennifer A. , Fisher David E.
Published: November 2014

Melanoma, the deadliest form of skin cancer, is an aggressive disease that is rising in incidence. Although melanoma is a historically treatment-resistant malignancy, in recent years unprecedented breakthroughs in targeted therapies and immunotherapies have revolutionized the standard of care for patients with advanced disease. Here, we provide an overview of recent developments in our understanding of melanoma risk factors, genomics, and molecular pathogenesis and how these insights have driven advances in melanoma treatment. In addition, we review benefits and limitations of current therapies and look ahead to continued progress in melanoma prevention and therapy. Remarkable achievements in the field have already produced a paradigm shift in melanoma treatment: Metastatic melanoma, once considered incurable, can now be treated with potentially curative rather than palliative intent.
Advances in skin grafting and treatment of cutaneous wounds
Authors: Sun Bryan K. , Siprashvili Zurab , Khavari Paul A.
Published: November 2014

The ability of the skin to repair itself after injury is vital to human survival and is disrupted in a spectrum of disorders. The process of cutaneous wound healing is complex, requiring a coordinated response by immune cells, hematopoietic cells, and resident cells of the skin. We review the classic paradigms of wound healing and evaluate how recent discoveries have enriched our understanding of this process. We evaluate current and experimental approaches to treating cutaneous wounds, with an emphasis on cell-based therapies and skin transplantation.
Rethinking China's new great wall
Authors: Ma Zhijun , Melville David S. , Liu Jianguo , Chen Ying , Yang Hongyan , Ren Wenwei , Zhang Zhengwang , Piersma Theunis , Li Bo
Published: November 2014

Massive seawall construction in coastal wetlands threatens biodiversity
Dialogue between skin microbiota and immunity
Authors: Belkaid Yasmine , Segre Julia A.
Published: November 2014

Human skin, the body’s largest organ, functions as a physical barrier to bar the entry of foreign pathogens, while concomitantly providing a home to myriad commensals. Over a human’s life span, keratinized skin cells, immune cells, and microbes all interact to integrate the processes of maintaining skin’s physical and immune barrier under homeostatic healthy conditions and also under multiple stresses, such as wounding or infection. In this Review, we explore the intricate interactions of microbes and immune cells on the skin surface and within associated appendages to regulate this orchestrated maturation in the context of both host physiological changes and environmental challenges.
How a long-lived fungus keeps mutations in check
Authors: Aanen Duur K.
Published: November 2014

Specific mechanisms of somatic growth protect long-lived fungi and plants from deleterious mutations
New support for ‘gay gene’
Authors: Servick Kelly
Published: November 2014

Replication of 1993 study highlights same region on X chromosome, but some still call evidence inconclusive.
China's peak carbon pledge raises pointed questions
Authors: Malakoff David
Published: November 2014

Modelers move to analyze implications of largest emitter's commitment to stabilize emissions by 2030.
From bench to bedside
Authors: Hurtley Stella , Hines Pamela J. , Mueller Kristen L. , Culotta Elizabeth
Published: November 2014

From bench to bedside
Metformin as adjunct antituberculosis therapy
Authors: Singhal Amit , Jie Liu , Kumar Pavanish , Hong Gan Suay , Leow Melvin Khee-Shing , Paleja Bhairav , Tsenova Liana , Kurepina Natalia , Chen Jinmiao , Zolezzi Francesca , Kreiswirth Barry , Poidinger Michael , Chee Cynthia , Kaplan Gilla , Wang Yee Tang , De Libero Gennaro
Published: November 2014

Metformin can be repurposed as host-directed therapy for tuberculosis.
Science Translational Medicine
Podcast: 19 November 2014
Authors: Verma Inder M. , Nusinovich Yevgeniya
Published: November 2014

Inder M. Verma talks about combining bisphosphonates and rapamycin to treat lung cancer.
Shaping Up with the Gut Microbiota
Authors: Round June L.
Published: November 2014

Host genetics influences the composition of the gut microbiota and reveals a family of bacteria that may prevent weight gain.
DNA Microarray-Based PCR Ribotyping of Clostridium difficile
Authors: Schneeberg Alexander , Ehricht Ralf , Slickers Peter , Baier Vico , Neubauer Heinrich , Zimmermann Stefan , Rabold Denise , Lübke-Becker Antina , Seyboldt Christian
Published: November 2014

This study presents a DNA microarray-based assay for fast and simple PCR ribotyping of
Clostridium difficile
strains. Hybridization probes were designed to query the modularly structured intergenic spacer region (ISR), which is also the template for conventional and PCR ribotyping with subsequent capillary gel electrophoresis (seq-PCR) ribotyping. The probes were derived from sequences available in GenBank as well as from theoretical ISR module combinations. A database of reference hybridization patterns was set up from a collection of 142 well-characterized
C. difficile
isolates representing 48 seq-PCR ribotypes. The reference hybridization patterns calculated by the arithmetic mean were compared using a similarity matrix analysis. The 48 investigated seq-PCR ribotypes revealed 27 array profiles that were clearly distinguishable. The most frequent human-pathogenic ribotypes 001, 014/020, 027, and 078/126 were discriminated by the microarray.
C. difficile
strains related to 078/126 (033, 045/FLI01, 078, 126, 126/FLI01, 413, 413/FLI01, 598, 620, 652, and 660) and 014/020 (014, 020, and 449) showed similar hybridization patterns, confirming their genetic relatedness, which was previously reported. A panel of 50
C. difficile
field isolates was tested by seq-PCR ribotyping and the DNA microarray-based assay in parallel. Taking into account that the current version of the microarray does not discriminate some closely related seq-PCR ribotypes, all isolates were typed correctly. Moreover, seq-PCR ribotypes without reference profiles available in the database (ribotype 009 and 5 new types) were correctly recognized as new ribotypes, confirming the performance and expansion potential of the microarray.
Validation of a Commercial Dry-Form Broth Microdilution Device (Sensititre) for Testing Tedizolid, a New Oxazolidinone
Authors: Jones Ronald N. , Holliday Nicole M. , Rhomberg Paul R.
Published: November 2014

Tedizolid, a novel oxazolidinone antibacterial with potent activity against a wide range of Gram-positive pathogens, was recently approved by regulatory authorities for the treatment of acute bacterial skin and skin structure infections. A commercial broth microdilution device (Sensititre; Thermo Fisher Scientific) was validated using 285 selected Gram-positive isolates, and the device was documented to have 100.0% essential and categorical agreement with reference MIC results and excellent MIC endpoint reproducibility.
Fruits of Virus Discovery: New Pathogens and New Experimental Models
Authors: Wang David
Published: November 2014

The advent of high-throughput sequencing has led to a tremendous increase in the rate of discovery of viral sequences. In some instances, novel pathogens have been identified. What has been less well appreciated is that novel virus discoveries in distinct hosts have led to the establishment of unique experimental systems to define host-virus interactions. These new systems have opened new frontiers in the study of fundamental virology and infectious disease.
Microparticles Provide a Novel Biomarker To Predict Severe Clinical Outcomes of Dengue Virus Infection
Authors: Punyadee Nuntaya , Mairiang Dumrong , Thiemmeca Somchai , Komoltri Chulaluk , Pan-ngum Wirichada , Chomanee Nusara , Charngkaew Komgrid , Tangthawornchaikul Nattaya , Limpitikul Wannee , Vasanawathana Sirijitt , Malasit Prida , Avirutnan Panisadee
Published: November 2014

Shedding of microparticles (MPs) is a consequence of apoptotic cell death and cellular activation. Low levels of circulating MPs in blood help maintain homeostasis, whereas increased MP generation is linked to many pathological conditions. Herein, we investigated the role of MPs in dengue virus (DENV) infection. Infection of various susceptible cells by DENV led to apoptotic death and MP release. These MPs harbored a viral envelope protein and a nonstructural protein 1 (NS1) on their surfaces.Ex vivoanalysis of clinical specimens from patients with infections of different degrees of severity at multiple time points revealed that MPs generated from erythrocytes and platelets are two major MP populations in the circulation of DENV-infected patients. Elevated levels of red blood cell-derived MPs (RMPs) directly correlated with DENV disease severity, whereas a significant decrease in platelet-derived MPs was associated with a bleeding tendency. Removal by mononuclear cells of complement-opsonized NS1–anti-NS1 immune complexes bound to erythrocytes via complement receptor type 1 triggered MP sheddingin vitro, a process that could explain the increased levels of RMPs in severe dengue. These findings point to the multiple roles of MPs in dengue pathogenesis. They offer a potential novel biomarker candidate capable of differentiating dengue fever from the more serious dengue hemorrhagic fever.

IMPORTANCEDengue is the most important mosquito-transmitted viral disease in the world. No vaccines or specific treatments are available. Rapid diagnosis and immediate treatment are the keys to achieve a positive outcome. Dengue virus (DENV) infection, like some other medical conditions, changes the level and composition of microparticles (MPs), tiny bag-like structures which are normally present at low levels in the blood of healthy individuals. This study investigated how MPs in culture and patients' blood are changed in response to DENV infection. Infection of cells led to programmed cell death and MP release. In patients' blood, the majority of MPs originated from red blood cells and platelets. Decreased platelet-derived MPs were associated with a bleeding tendency, while increased levels of red blood cell-derived MPs (RMPs) correlated with more severe disease. Importantly, the level of RMPs during the early acute phase could serve as a biomarker to identify patients with potentially severe disease who require immediate care.
Andes Virus Nucleocapsid Protein Interrupts Protein Kinase R Dimerization To Counteract Host Interference in Viral Protein Synthesis
Authors: Wang Zekun , Mir Mohammad A.
Published: November 2014

Pathogenic hantaviruses delay the type I interferon response during early stages of viral infection. However, the robust interferon response and induction of interferon-stimulated genes observed during later stages of hantavirus infection fail to combat the virus replication in infected cells. Protein kinase R (PKR), a classical interferon-stimulated gene product, phosphorylates the eukaryotic translation initiation factor eIF2α and causes translational shutdown to create roadblocks for the synthesis of viral proteins. The PKR-induced translational shutdown helps host cells to establish an antiviral state to interrupt virus replication. However, hantavirus-infected cells do not undergo translational shutdown and fail to establish an antiviral state during the course of viral infection. In this study, we showed for the first time that Andes virus infection induced PKR overexpression. However, the overexpressed PKR was not active due to a significant inhibition of autophosphorylation. Further studies revealed that Andes virus nucleocapsid protein inhibited PKR dimerization, a critical step required for PKR autophosphorylation to attain activity. The studies reported here establish a hantavirus nucleocapsid protein as a new PKR inhibitor. These studies provide mechanistic insights into hantavirus resistance to the host interferon response and solve the puzzle of the lack of translational shutdown observed in hantavirus-infected cells. The sensitivity of hantavirus replication to PKR has likely imposed a selective evolutionary pressure on hantaviruses to evade the PKR antiviral response for survival. We envision that evasion of the PKR antiviral response by NP has likely helped hantaviruses to exist during evolution and to survive in infected hosts with a multifaceted antiviral defense.

IMPORTANCE
Protein kinase R (PKR), a versatile antiviral host factor, shuts down the translation machinery upon activation in virus-infected cells to create hurdles for the manufacture of viral proteins. The studies reported here reveal that the hantavirus nucleocapsid protein counteracts the PKR antiviral response by inhibiting PKR dimerization, which is required for its activation. We report the discovery of a new PKR inhibitor whose expression in hantavirus-infected cells prevents the PKR-induced host translational shutdown to ensure the continuous synthesis of viral proteins required for efficient virus replication.
p38MAPK and MK2 Pathways Are Important for the Differentiation-Dependent Human Papillomavirus Life Cycle
Authors: Satsuka Ayano , Mehta Kavi , Laimins Laimonis
Published: November 2014

Amplification of human papillomaviruses (HPV) is dependent on the ATM DNA damage pathway. In cells with impaired p53 activity, DNA damage repair requires the activation of p38MAPK along with MAPKAP kinase 2 (MK2). In HPV-positive cells, phosphorylation of p38 and MK2 proteins was induced along with relocalization to the cytoplasm. Treatment with MK2 or p38 inhibitors blocked HPV genome amplification, identifying the p38/MK2 pathway as a key regulator of the HPV life cycle.
Construction and Evaluation of Novel Rhesus Monkey Adenovirus Vaccine Vectors
Authors: Abbink Peter , Maxfield Lori F. , Ng'ang'a David , Borducchi Erica N. , Iampietro M. Justin , Bricault Christine A. , Teigler Jeffrey E. , Blackmore Stephen , Parenteau Lily , Wagh Kshitij , Handley Scott A. , Zhao Guoyan , Virgin Herbert W. , Korber Bette , Barouch Dan H.
Published: November 2014

Adenovirus vectors are widely used as vaccine candidates for a variety of pathogens, including HIV-1. To date, human and chimpanzee adenoviruses have been explored in detail as vaccine vectors. The phylogeny of human and chimpanzee adenoviruses is overlapping, and preexisting humoral and cellular immunity to both are exhibited in human populations worldwide. More distantly related adenoviruses may therefore offer advantages as vaccine vectors. Here we describe the primary isolation and vectorization of three novel adenoviruses from rhesus monkeys. The seroprevalence of these novel rhesus monkey adenovirus vectors was extremely low in sub-Saharan Africa human populations, and these vectors proved to have immunogenicity comparable to that of human and chimpanzee adenovirus vaccine vectors in mice. These rhesus monkey adenoviruses phylogenetically clustered with the poorly described adenovirus species G and robustly stimulated innate immune responses. These novel adenoviruses represent a new class of candidate vaccine vectors.

IMPORTANCE
Although there have been substantial efforts in the development of vaccine vectors from human and chimpanzee adenoviruses, far less is known about rhesus monkey adenoviruses. In this report, we describe the isolation and vectorization of three novel rhesus monkey adenoviruses. These vectors exhibit virologic and immunologic characteristics that make them attractive as potential candidate vaccine vectors for both HIV-1 and other pathogens.
Early Activation of Teleost B Cells in Response to Rhabdovirus Infection
Authors: Abós Beatriz , Castro Rosario , González Granja Aitor , Havixbeck Jeffrey J. , Barreda Daniel R. , Tafalla Carolina
Published: November 2014

To date, the response of teleost B cells to specific pathogens has been only scarcely addressed. In this work, we have demonstrated that viral hemorrhagic septicemia virus (VHSV), a fish rhabdovirus, has the capacity to infect rainbow trout spleen IgM-positive (IgM+) cells, although the infection is not productive. Consequently, we have studied the effects of VHSV on IgM+cell functionality, comparing these effects to those elicited by a Toll-like receptor 3 (TLR3) ligand, poly(I·C). We found that poly(I·C) and VHSV significantly upregulated TLR3 and type I interferon (IFN) transcription in spleen and blood IgM+cells. Further effects included the upregulated transcription of the CK5B chemokine. The significant inhibition of some of these effects in the presence of bafilomycin A1 (BAF), an inhibitor of endosomal acidification, suggests the involvement of an intracellular TLR in these responses. In the case of VHSV, these transcriptional effects were dependent on viral entry into B cells and the initiation of viral transcription. VHSV also provoked the activation of NF-κB and the upregulation of major histocompatibility complex class II (MHC-II) cell surface expression on IgM+cells, which, along with the increased transcription of the costimulatory molecules CD80/86 and CD83, pointed to VHSV-induced IgM+cell activation toward an antigen-presenting profile. Finally, despite the moderate effects of VHSV on IgM+cell proliferation, a consistent effect on IgM+cell survival was detected.

IMPORTANCEInnate immune responses to pathogens established through their recognition by pattern recognition receptors (PRRs) have been traditionally ascribed to innate cells. However, recent evidence in mammals has revealed that innate pathogen recognition by B lymphocytes is a crucial factor in shaping the type of immune response that is mounted. In teleosts, these immediate effects of viral encounter on B lymphocytes have not been addressed to date. In our study, we have demonstrated that VHSV infection provoked immediate transcriptional effects on B cells, at least partially mediated by intracellular PRR signaling. VHSV also activated NF-κB and increased IgM+cell survival. Interestingly, VHSV activated B lymphocytes toward an antigen-presenting profile, suggesting an important role of IgM+cells in VHSV presentation. Our results provide a first description of the effects provoked by fish rhabdoviruses through their early interaction with teleost B cells.
A 9-year-old boy with severe diphtherial infection and cardiac complications
Authors: Washington Charles Henry , Issaranggoon na ayuthaya Satja , Makonkawkeyoon Krit , Oberdorfer Peninnah
Published: November 2014

The incidence of diphtheria has decreased since the introduction of an effective vaccine. However, in countries with low vaccination rates it has now become a re-emerging disease. Complications from diphtheria commonly include upper airway obstruction and cardiac complications. We present a 9-year-old boy who was diagnosed with diphtheria. He presented with fever, tonsilar plaques, respiratory failure and an incomplete vaccination history. He was endotracheal intubated and received diphtheria antitoxin and penicillin on the first day of hospitalisation. He developed progressive arrhythmias and fulminant myocarditis despite early identification and treatment with equine antitoxin and antibiotics. After a temporary transvenous pacemaker insertion due to third-degree atrioventricular block and hypotension for 1 week, he developed myocardial perforation from the pacemaker tip resulting in pericardial effusion. The treatment included emergency pericardiocentesis and pacemaker removal. His electrocardiogram showed a junctional rhythm with occasional premature ventricular complexes. He then developed ventricular tachycardia and cardiac arrest and finally died.
‘STEMI–like’ acute pulmonary embolism, an unusual presentation
Authors: Abdalla Abuelmagd , Kelly Frank
Published: November 2014

We present the case of a 65-year-old man with an atypical presentation of pulmonary embolism (PE) as ST elevation myocardial infarction (STEMI) with high troponin. He presented with acute exertional dyspnoea without chest pain. Since the initial ECG showed ST elevation anteroseptal (V1–V4) with concomitant deep Q waves, a delayed STEMI with probable left ventricular aneurysm was the working diagnosis and was treated accordingly. Nevertheless, his coronary angiography was normal and it was then that PE was suspected. D-dimer was found to be elevated and CT pulmonary angiography confirmed bilateral PE with a large thrombus within the right main pulmonary artery. The patient made good clinical recovery and his ST elevation resolved with anticoagulation. The source was found to be a deep vein thrombosis in his right leg. The treatment was not compromised by the delayed diagnosis as he received timely anticoagulation as part of STEMI management.
Use of intramuscular methadone in managing intravenous drug abuse
Authors: Bezant Edward Michael
Published: November 2014

A 30-year-old woman was referred to the Acute Pain Team for their advice on how to manage her current pain, in light of her unique pre-admission medications. On questioning it was discovered that the patient was receiving 50 mg of intramuscular methadone daily, in the community. She was a former intravenous drug user who had been enrolled into a methadone substitution programme for 10 years and had been receiving her methadone intramuscularly for the past 6 years. It had been discovered that her addiction was not solely to opioids but, moreover, to the process of injecting as well. She was diagnosed with obsessive compulsive disorder, with a needle fixation, and started on the intramuscular methadone regimen on which she has maintained abstinence from heroin for 6 years.
Type-specific HPV prevalence in invasive cervical cancer in the UK prior to national HPV immunisation programme: baseline for monitoring the effects of immunisation
Authors: Mesher David , Cuschieri Kate , Hibbitts Sam , Jamison Jackie , Sargent Alex , Pollock Kevin G , Powell Ned , Wilson Robbie , McCall Fiona , Fiander Alison , Soldan Kate
Published: November 2014

Aims

To establish the human papillomavirus (HPV) type-specific prevalence in cervical cancer and high-grade cervical lesions in the UK prior to the introduction of national HPV vaccination.

Methods

Specimens of cervical cancer (n=1235) and cervical intraepithelial neoplasia (CIN)3 (n=2268) were tested for HPV genotypes in England, Scotland, Wales and Northern Ireland. Data were pooled and weighted estimates presented.

Results

Among cervical cancer cases, 95.8% were positive for at least one high-risk (HR) HPV type. Restricting to those with HR HPV, the proportion positive for HPV16 and/or HPV18 was similar across countries (weighted overall prevalence 83.0%). This proportion decreased with increasing age at diagnosis (p=0.0005). HPV31, HPV33, HPV45, HPV52 and/or HPV58 were detected in 16.1% of HR HPV-positive cervical cancers and there was no significant association with age for these types. For HR HPV-positive CIN3 cases, there was a similar age-specific pattern with the highest positivity of HPV16 and/or HPV18 in the youngest age group (77.2%). The proportion of HR HPV CIN3 cases positive for HPV31, HPV33, HPV45, HPV52 and/or HPV58 was 36.3% in those aged <30 years at diagnosis.

Conclusions

The prevalence of HPV 16 and/or 18 was high in all UK countries and highest in those diagnosed at a younger age. The UK is well placed to monitor the impact of HPV vaccination on type-specific HPV prevalence in cervical disease.
Plasma levels of galectin-3-binding protein reflect type I interferon activity and are increased in patients with systemic lupus erythematosus
Authors: Nielsen Christoffer T , Lood Christian , Østergaard Ole , Iversen Line V , Voss Anne , Bengtsson Anders , Jacobsen Søren , Heegaard Niels H H
Published: November 2014

Objective

Simple measures of type I interferon (IFN) activity constitute highly attractive biomarkers in systemic lupus erythematosus (SLE). We explore galectin-3-binding protein (G3BP) as a novel measure of type I IFN activity and serum/plasma biomarker in large independent cohorts of patients with SLE and controls.

Methods

Serum and plasma G3BP concentrations were quantified using ELISA. Type I IFN activity was assessed by Mx1 reporter gene expression assays and correlated to serum G3BP concentrations (SLE-IFN-α, n=26 and healthy controls (HCs), n=10). Plasma G3BP concentrations in the SLE-Denmark (DK) (n=70) and SLE-Sweden (SE) (n=68) cohorts were compared with the HC-DK (n=47) and HC-SE (n=50) cohorts and patients with systemic sclerosis (n=111). In 15 patients with SLE, serum G3BP in consecutive samples was correlated to disease activity. Correlation analysis between G3BP, clinical parameters including disease activity in the four SLE cohorts was performed.

Results

G3BP concentrations correlated significantly with the IFN-α reporter gene assay (r=0.56, p=0.0005) and with IFN-α gene expression scores (r=0.54, p=0.0002). Plasma concentrations were significantly increased in the SLE-DK and SLE-SE cohorts compared with HCs and patients with systemic sclerosis (p<0.0001 and p=0.0009). G3BP concentrations correlated with disease activity measures in the SLE-DK- and SLE-IFN-α cohorts (p=0.0004 and p=0.05) but not in the SLE-SE cohort (p=0.98). Markedly temporal variation was observed in G3BP levels in the consecutive SLE-samples and was significantly associated with changes in disease activity (r=0.44, p=0.014).

Conclusions

G3BP plasma levels reflect type I IFN activity and are increased in SLE. Associations with disease activity or clinical manifestations are uncertain. This study highlights G3BP as a convenient measure of type I IFN-dependent gene activation.
Comparison of Solitaire thrombectomy and Penumbra suction thrombectomy in patients with acute ischemic stroke caused by basilar artery occlusion
Authors: Son Seungnam , Choi Dae Seob , Oh Min Kyun , Hong Jiho , Kim Soo-Kyoung , Kang Heeyoung , Park Ki-Jong , Choi Nack-Cheon , Kwon Oh-Young , Lim Byeong Hoon
Published: November 2014

Background and purpose

Acute ischemic stroke (AIS) caused by basilar artery occlusion (BAO) is a very severe neurological disease with a high mortality rate and poor clinical outcomes. In this study, we compared our experience of mechanical thrombectomy using the Solitaire stent (Solitaire thrombectomy) and manual aspiration thrombectomy using the Penumbra reperfusion catheter (Penumbra suction thrombectomy) in patients with AIS caused by BAO.

Materials and methods

Between March 2011 and December 2011, 13 patients received Solitaire thrombectomy. In January 2012, the Korean Food and Drug Administration banned the use of the Solitaire stent as a thrombectomy device, and a further 18 patients received Penumbra suction thrombectomy until December 2013. We compared parameters between patients treated with each device.

Results

Successful recanalization rates (Thrombolysis in Cerebral Infarction (TICI) score ≥2b: 84.6% vs 100%, p=0.168) and clinical outcomes (judged by the modified Rankin Scale scores recorded at 3 months: 3.6±2.6 vs 3.2±2.6, p=0.726) were not significantly different between the two groups. However, complete recanalization rates (TICI score of 3: 23.1% vs 72.2%, p=0.015) and total procedure times (101.9±41.4 vs 62.3±34.8 min, p=0.044) were significantly higher, and shorter, respectively, in patients treated by Penumbra suction thrombectomy.

Conclusions

The two thrombectomy devices were associated with similar recanalization rates and clinical outcomes in patients with AIS caused by BAO. However, Penumbra suction thrombectomy seemed to allow more rapid and complete recanalization than Solitaire thrombectomy.
Effect of a prior bout of preconditioning exercise on muscle damage from downhill walking
Authors: Maeo Sumiaki , Ochi Yusuke , Yamamoto Masayoshi , Kanehisa Hiroaki , Nosaka Kazunori
Published: November 2014

This study investigated whether reduced-duration downhill walking (DW) would confer a protective effect against muscle damage induced by a subsequent bout of longer duration DW performed 1 week or 4 weeks later. Healthy young adults were allocated to a control or one of the preconditioning exercise (PRE-1wk or PRE-4wk) groups (10 men and 4 women per group). PRE-1wk and PRE-4wk groups performed 20-min DW (–28% slope, 5 km/h, 10% body mass added to a backpack) 1 week and 4 weeks before 40-min DW, respectively, and the control group performed 40-min DW only. Maximal voluntary contraction (MVC) knee extension torque, plasma creatine kinase (CK) activity, and muscle soreness (100-mm visual analog scale) were measured before, immediately after, and 24, 48, and 72 h after DW, and the changes in these variables were compared among groups. The control group showed symptoms of muscle damage (e.g., prolonged decrease in MVC: –14% ± 10% at 48 h post-DW) after 40-min DW. Changes in all variables after 40-min DW of PRE-1wk and PRE-4wk groups were 54%–61% smaller (P < 0.05) than the control group, without significant differences between PRE-1wk and PRE-4wk groups for MVC and plasma CK activity. Importantly, changes after the preconditioning exercise (20-min DW) were 67%–69% smaller (P < 0.05) than those after the 40-min DW of the control group. These findings suggest that 20-min DW resulting in minor muscle damage conferred a protective effect against subsequent 40-min DW, and its effect could last for more than 4 weeks.
Analysis of pollination neighbourhood size using spatial analysis of pollen and seed production in broadleaf cattail (Typha latifolia)
Authors: Ahee Jordan E. , Van Drunen Wendy E. , Dorken Marcel E.
Published: November 2014

The size of pollination neighbourhoods has important consequences for mating patterns, seed production, gene flow, and patterns of genetic variation across populations. We examined the size of the pollination neighbourhood in a stand of a wind-pollinated clonal plant (Typha latifolia L.; broadleaf cattail) by evaluating spatial patterns of pollen production and seed set by individual shoots. We then simulated spatial patterns of pollen availability to investigate the shape of the pollen dispersal curve. We detected significant positive spatial autocorrelations in seed set over distances up to 5 m. This spatial variation in patterns of seed set appeared to be driven by the local availability of pollen: we found significant cross-correlations between pollen production and seed set over distances of approximately 2 m. The simulations supported this inference; simulated pollen dispersal curves fit observed patterns of seed set when ∼99% of pollen was assumed to disperse over distances less than 2 m. Together, these results indicate that the majority of pollination events occur within very close proximity of pollen sources in T. latifolia. Although within-shoot selfing has long been assumed to be a major pollination mode in T. latifolia, our data indicate that pollination events in the stand were more likely to have involved between-shoot pollination.
Reclamation of boreal forest after oil sands mining: anticipating novel challenges in novel environments
Authors: Audet Patrick , Pinno Bradley D. , Thiffault Evelyne
Published: November 2014

Boreal forests in northern Alberta have a growing anthropogenic footprint due to a rapidly growing oil sands mining industry. Although land reclamation is a necessary aspect of responsible industrial development, these activities nearly always affect higher order landscape components such as the broader landform, and its hydrology and biogeochemistry. Recent anthropogenic impacts are then believed to result in new environmental conditions and obstacles under which the boreal forest is developing, potentially leading to irreversibly different environments that could be characterized as novel ecosystems. Reflecting an emerging trend across the field of restoration ecology, these novel ecosystems are not necessarily undesirable. Instead, they are an unavoidable consequence of pervading anthropogenic effects on natural ecosystems. It is our view that successful reclamation outcomes can still be derived so long as policy and regulatory requirements are afforded the necessary scope and economic flexibility to account for the development of hybrid and novel ecosystems among highly disturbed mine sites. Hence, this analysis seeks to situate current and anticipated challenges affecting the reclamation of boreal forest following oil sands mining by describing (i) how regulatory criteria shape reclamation practices and targeted end goals and (ii) how these approaches embody latest trends and priorities in the area of restoration ecology.
Androgen effects on immune gene expression during parental care in bluegill sunfish (Lepomis macrochirus)
Authors: Partridge Charlyn , Rodgers Chandra M.C. , Knapp Rosemary , Neff Bryan D.
Published: November 2014

Reproductive efforts are energetically costly and often result in significant trade-offs with other metabolic processes. In many animals, androgens influence how this energy is allocated during the breeding period. In this study, androgen levels of parental bluegill sunfish (Lepomis macrochirus Rafinesque, 1819) were manipulated by implanting males with either 11-ketotestosterone (11-KT) or flutamide (an androgen receptor antagonist) shortly after spawning. Parental behaviours were assessed for 3 days after implantation. Differential brain gene expression between the two groups was examined using a 44 000 microarray gene chip. We found that 11-KT-implanted males exhibited lower levels of expression of genes related to immune function compared with flutamide-implanted males, suggesting that high androgen levels negatively affect the male immune system. These data thus indicate that a significant trade-off may exist between maintaining high levels of androgens and decreased immune function in parental male bluegill.
Ecological benefits and risks arising from liming sugar maple dominated forests in northeastern North America
Authors: Moore Jean-David , Ouimet Rock , Long Robert P. , Bukaveckas Paul. A.
Published: November 2014

Liming, the application of carbonate materials (e.g., CaCO3, CaMg(CO3)2) to soils and surface waters, has been used extensively in Europe, and to a lesser extent in Canada and the United States, to mitigate the effects of acid deposition on forest and aquatic ecosystems. This literature review was conducted to assess the effects of liming on ecologically and economically important sugar maple dominated ecosystems of northeastern North America, where it is increasingly used to treat sugar maple dieback. Potential direct and indirect effects were considered to determine whether the use of liming to revitalize these forests could negatively affect other ecological parameters, including those in adjacent aquatic habitats. Based on current scientific literature, it is not anticipated that liming at rates of 1–3 t ha−1would have major detrimental effects on these ecosystems. However, liming could have negative effects on northern hardwood forests with regard to earthworm invasions. The choice of liming as a mitigation tool should be made not only after weighing the potentially negative effects against the benefits of restoring sugar maple dominated stands in poorly buffered soils, but also after considering ecological components that could be lost or never recovered if an acidified forest ecosystem is not limed.
Lê's polyhedron for line singularities
Authors: Menegon Neto Aurélio
Published: November 2014

We study the topology of line singularities, which are complex hypersurface germs with non-isolated singularity given by a smooth curve. We describe the degeneration of its Milnor fiber to the singular hypersurface by means of a vanishing polyhedron in the Milnor fiber. As a milestone, we also study the topology of the degeneration of a complex isolated singularity hypersurface under a nonlocal point of view.
(Pseudo) generalized Kaluza–Klein G-spaces and Einstein equations
Authors: Arcuş Constantin M. , Peyghan Esmaeil
Published: November 2014

Introducing the Lie algebroid generalized tangent bundle of a Kaluza–Klein bundle, we develop the theory of general distinguished linear connections for this space. In particular, using the Lie algebroid generalized tangent bundle of the Kaluza–Klein vector bundle, we present the (g, h)-lift of a curve on the base M and we characterize the horizontal and vertical parallelism of the (g, h)-lift of accelerations with respect to a distinguished linear (ρ, η)-connection. Moreover, we study the torsion, curvature and Ricci tensor field associated to a distinguished linear (ρ, η)-connection and we obtain the identities of Cartan and Bianchi type in the general framework of the Lie algebroid generalized tangent bundle of a Kaluza–Klein bundle. Finally, we introduce the theory of (pseudo) generalized Kaluza–Klein G-spaces and we develop the Einstein equations in this general framework.
Long-Range Dependencies and Statistical Self-Similarity in Computer Memory System
Authors: Strzałka Dominik
Published: November 2014

This paper shows the problem of possible existence of statistical self-similarity and long-range (long-term) dependencies in behavior of computer memory systems. It will be shown, that the hierarchical structure of memory and the dispersion of time constants during accessing successive levels of such a structure, lead to "memory effect" and self-similarity. These effects have not been taken into account so far in computer systems design, management and description. A few methods were used to calculate the Hurst H coefficient, which reflects the statistical self-similarity in time series and the d parameter that represents the problem of long-range dependencies.
AN IMPROVED MARKOV CHAIN APPROXIMATION METHODOLOGY: DERIVATIVES PRICING AND MODEL CALIBRATION
Authors: LO CHIA CHUN , SKINDILIAS KONSTANTINOS
Published: November 2014

This paper presents an improved continuous-time Markov chain approximation (MCA) methodology for pricing derivatives and for calibrating model parameters. We propose a generalized nonequidistant grid model for a general stochastic differential equation, and extend the proposed model to accommodate a jump component. Because the prices of derivatives generated by the MCA models are sensitive to the setting of the chain's state space, we suggest a heuristic determination of the grid spacing such that the Kolmogorov–Smirnov distance between the underlying distribution and the MCA distribution is minimized. The continuous time setting allows us to introduce semi-analytical formulas for pricing European and American style options. The numerical examples demonstrate that the proposed model with a nonequidistant grid setting provides superior results over the equidistant grid setting. Finally, we present the MCA maximum likelihood estimator for a jump-diffusion process. The encouraging results from the simulation and empirical studies provide insight into calibration problems in finance where the density function of a jump-diffusion model is unknown.
Experimental Study on Nonlinear Vibration of Cantilever Cylindrical Shell
Authors: Kumar Ajay , Patel B. P.
Published: November 2014

Nonlinear dynamic behavior of a cantilever cylindrical shell is studied experimentally using non-contact type of electromagnetic shaker, acceleration measurements, and imaging of vibrating shell using two high speed 3D cameras. The response history and frequency spectrum are measured at different locations along the circumference of the free end of the shell for different excitation amplitudes and mode of vibration. The frequency response obtained from acceleration measurements is found to be in good agreement with the simulated response in ANSYS. The response histories from acceleration data and digital image correlation are compared for one case and found to match very well. The traveling wave phenomenon along with participation of higher harmonics and softening nonlinearity are observed. The traveling wave response is observed for certain range of forcing frequency for the shell excited in modes with number of circumferential waves n = 3 and 5. It is shown that the traveling wave response can be detected based on the phase angle difference of response at different circumferential locations.
DFT calculations of tin dioxide crystals containing heavily-doped fluorine
Authors: Marcillo Freddy , Stashans Arvids
Published: November 2014

First-principles calculations based on the density functional theory (DFT) within the generalized gradient approximation have been used in the present research. Fluorine doping in the SnO 2 crystals has been carried out considering a number of different defect concentrations. Dopant influence upon structural, electronic and electrical properties of the tin dioxide has been discussed in detail. The system presents n-type electrical conductivity relating our work directly to a number of empirical studies in this area. An experimental fact that n-type conductivity tends to decrease at rather high fluorine impurity rates has been explained at the theoretical level.
Debt Market Liquidity and Corporate Default Prediction
Authors: Wu Deming , Zhang Suning
Published: November 2014

Recent research on the subprime crisis and rollover risk suggests that debt market liquidity is a major factor affecting the risk of default. This implies that firms that rely heavily on short-term debt, such as commercial paper (CP), are at greater risk of default. Debt market illiquidity could reduce the value of the firm and thus impact the firm's leverage, which is a major factor in predicting default. We estimate the effect of debt market conditions on the probability of default with a discrete-time dynamic hazard model that takes into account measurement error in firm leverage. Our results indicate that rollover risk is a significant factor in causing default, but the risk was higher for nonfinancial firms around 2000–2001 and considerably less entering the subprime crisis.
Mesostructural analysis of S-C fabrics in a shallow shear zone of the Umbria–Marche Apennines (Central Italy)
Authors: Lena G. , Barchi M. R. , Alvarez W. , Felici F. , Minelli G.
Published: November 2014

Several examples of foliated fault zones characterized by penetrative S-C fabric are exposed in the Umbria–Marche region, often associated with major thrusts. These tectonites, dominated by pressure-solution processes, are developed at shallow depths (<3 km) in sedimentary rocks. In this paper, we perform a detailed structural analysis of the Scheggia Thrust Zone (STZ), a significant example of S-C tectonite spectacularly exposed in the Umbria–Marche Apennines. We reconstruct both the architecture and internal structure of the shear zone, focusing on the factors controlling the genesis and development of the tectonic pattern such as: (a) anisotropy; (b) lithological contrast; and (c) distance from the fault core. The STZ shows an intensely cleaved fault core (S-C fabric) and a thick and asymmetric damage zone developed in the footwall rocks. By analysing the spacing of the S-surfaces, we observe that the magnitude of deformation decreases with distance from the fault core. However, far from the fault core the magnitude of deformation is strongly controlled by the lithology of the protolith: almost undeformed calcareous beds alternate with intensely sheared intervals, localized along weak, marly horizons, also characterized by flattened S-planes. Based on these data we have divided the STZ into three subzones where the deformation is mainly driven by: (1) distance from the fault core; and (2) the lithology of the protolith. Marly horizons into these subzones, with respect to the calcareous horizon, show that: (i) S-planes are more closely spaced; and (ii) the angle between C- and S-planes is smaller. Our study confirms that the rhythmic alternation of calcareous and marly rocks can favour the development of foliated fault zones, also producing an increase in pressure-solution cleavage at shallow crustal conditions.