bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retroperitoneal teratoma with somatic malignant transformation: A papillary renal cell carcinoma in a testicular germ cell tumour metastasis following platinum-based chemotherapy
Authors: Zeh Nina , Wild Peter J , Bode Peter K , Kristiansen Glen , Moch Holger , Sulser Tullio , Hermanns Thomas 
Published: February 2013

Abstract

Background
Malignant transformation describes the phenomenon in which a somatic component of a germ cell teratoma undergoes malignant differentiation. A variety of different types of sarcoma and carcinoma, all non-germ cell, have been described as a result of malignant transformation.

Case presentation
A 33-year-old man presented with a left testicular mass and elevated tumour markers. Staging investigations revealed retroperitoneal lymphadenopathy with obstruction of the left ureter and distant metastases. Histopathology from the left radical orchiectomy showed a mixed germ cell tumour (Stage III, poor prognosis). The ureter was stented and four cycles of cisplatin, etoposide and bleomycin chemotherapy administered. After initial remission, the patient recurred four years later with a large retroperitoneal mass involving the renal vessels and the left ureter. Left retroperitoneal lymph node dissection with en-bloc resection of the left kidney was performed.
Histopathology revealed a germ cell tumour metastasis consisting mainly of mature teratoma. Additionally, within the teratoma a papillary renal cell carcinoma was found. The diagnosis was supported by immunohistochemistry showing positivity for AMACR, CD10 and focal expression of RCC and CK7. There was no radiological or histo-pathological evidence of a primary renal cell cancer.

Conclusions
To the best of our knowledge, malignant transformation into a papillary renal cell carcinoma has not been reported in a testicular germ cell tumour metastasis following platinum-based chemotherapy. This histological diagnosis might have implications for potential future therapies. In the case of disease recurrence, renal cell cancer as origin of the recurrent tumour has to be excluded because renal cell carcinoma metastases would not respond well to the classical germ cell tumour chemotherapy regimens.
Si nanopatterning by reactive ion etching through an on-chip self-assembled porous anodic alumina mask
Authors: Gianneta Violetta , Olziersky Antonis , Nassiopoulou Androula G 
Published: February 2013

Abstract
We report on Si nanopatterning through an on-chip self-assembled porous anodic alumina (PAA) masking layer using reactive ion etching based on fluorine chemistry. Three different gases/gas mixtures were investigated: pure SF6, SF6/O2, and SF6/CHF3. For the first time, a systematic investigation of the etch rate and process anisotropy was performed. It was found that in all cases, the etch rate through the PAA mask was 2 to 3 times lower than that on non-masked areas. With SF6, the etching process is, as expected, isotropic. By the addition of O2, the etch rate does not significantly change, while anisotropy is slightly improved. The lowest etch rate and the best anisotropy were obtained with the SF6/CHF3 gas mixture. The pattern of the hexagonally arranged pores of the alumina film is, in this case, perfectly transferred to the Si surface. This is possible both on large areas and on restricted pre-defined areas on the Si wafer.

PACS

78.67.Rb, 81.07.-b, 61.46.-w
Efficiency enhancements in Ag nanoparticles-SiO2-TiO2 sandwiched structure via plasmonic effect-enhanced light capturing
Authors: Xu Jinxia , Xiao Xiangheng , Stepanov Andrey L , Ren Fen , Wu Wei , Cai Guangxu , Zhang Shaofeng , Dai Zhigao , Mei Fei , Jiang Changzhong 
Published: February 2013

Abstract
TiO2-SiO2-Ag composites are fabricated by depositing TiO2 films on silica substrates embedded with Ag nanoparticles. Enhancement of light absorption of the nanostructural composites is observed. The light absorption enhancement of the synthesized structure in comparison to TiO2 originated from the near-field enhancement caused by the plasmonic effect of Ag nanoparticles, which can be demonstrated by the optical absorption spectra, Raman scattering investigation, and the increase of the photocatalytic activity. The embedded Ag nanoparticles are formed by ion implantation, which effectively prevents Ag to be oxidized through direct contact with TiO2. The suggested incorporation of plasmonic nanostructures shows a great potential application in a highly efficient photocatalyst and ultra-thin solar cell.
The expression of interleukin-32 is activated by human cytomegalovirus infection and down regulated by hcmv-miR-UL112-1
Authors: Huang Yujing , Qi Ying , Ma Yanping , He Rong , Ji Yaohua , Sun Zhengrong , Ruan Qiang 
Published: February 2013

AbstractBackgroundInterleukin-32 (IL-32) is an important factor in innate and adaptive immune responses, which activates the p38MAPK, NF-kappa B and AP-1 signaling pathways. Recent reports have highlighted that IL-32 is regulated during viral infection in humans.MethodsEnzyme-linked immunosorbent assays (ELISA) were carried out to detect IL-32 levels in serum samples. Detailed kinetics of the transcription of IL-32 mRNA and expression of IL-32 protein during human cytomegalovirus (HCMV) infection were determined by semi-quantitative RT-PCR and western blot, respectively. The expression levels of hcmv-miR-UL112-1 were detected using TaqMan® miRNA assays during a time course of 96 hours. The effects of hcmv-miR-UL112-1 on IL-32 expression were demonstrated by luciferase assay and western blot, respectively.ResultsSerum levels of IL-32 in HCMV-IgM positive patients (indicating an active HCMV infection) were significantly higher than those in HCMV-IgM negative controls. HCMV infection activated cellular IL-32 transcription mainly in the immediately early (IE) phase and elevated IL-32 protein levels between 6 and 72 hours post infection (hpi) in the human embryonic lung fibroblast cell line, MRC-5. The expression of hcmv-miR-UL112-1 was detected at 24 hpi and increased gradually as the HCMV-infection process was prolonged. In addition, it was demonstrated that hcmv-miR-UL112-1 targets a sequence in the IL-32 3′-UTR. The protein level of IL-32 in HEK293 cells could be functionally down-regulated by transfected hcmv-miR-UL112-1.ConclusionsIL-32 expression was induced by active HCMV infection and could be functionally down-regulated by ectopically expressed hcmv-miR-UL112-1. Our data may indicate a new strategy of immune evasion by HCMV through post-transcriptional regulation.
An attenuated Lassa vaccine in SIV-infected rhesus macaques does not persist or cause arenavirus disease but does elicit Lassa virus-specific immunity
Authors: Zapata Juan C , Poonia Bhawna , Bryant Joseph , Davis Harry , Ateh Eugene , George Lanea , Crasta Oswald , Zhang Yan , Slezak Tom , Jaing Crystal , Pauza C David , Goicochea Marco , Moshkoff Dmitry , Lukashevich Igor S , Salvato Maria S 
Published: February 2013

Abstract

Background
Lassa hemorrhagic fever (LHF) is a rodent-borne viral disease that can be fatal for human beings. In this study, an attenuated Lassa vaccine candidate, ML29, was tested in SIV-infected rhesus macaques for its ability to elicit immune responses without instigating signs pathognomonic for arenavirus disease. ML29 is a reassortant between Lassa and Mopeia viruses that causes a transient infection in non-human primates and confers sterilizing protection from lethal Lassa viral challenge. However, since the LHF endemic area of West Africa also has high HIV seroprevalence, it is important to determine whether vaccination could be safe in the context of HIV infection.

Results
SIV-infected and uninfected rhesus macaques were vaccinated with the ML29 virus and monitored for specific humoral and cellular immune responses, as well as for classical and non-classical signs of arenavirus disease. Classical disease signs included viremia, rash, respiratory distress, malaise, high liver enzyme levels, and virus invasion of the central nervous system. Non-classical signs, derived from profiling the blood transcriptome of virulent and non-virulent arenavirus infections, included increased expression of interferon-stimulated genes (ISG) and decreased expression of COX2, IL-1β, coagulation intermediates and nuclear receptors needed for stress signaling. All vaccinated monkeys showed ML29-specific antibody responses and ML29-specific cell-mediated immunity.

Conclusion
SIV-infected and uninfected rhesus macaques responded similarly to ML29 vaccination, and none developed chronic arenavirus infection. Importantly, none of the macaques developed signs, classical or non-classical, of arenavirus disease.
Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples
Authors: Zhang Eileen Z , Bartels Doug J , Frantz JDan , Seepersaud Sheila , Lippke Judith A , Shames Benjamin , Zhou Yi , Lin Chao , Kwong Ann , Kieffer Tara L 
Published: February 2013

AbstractBackgroundDirect-acting antiviral (DAAs) agents for hepatitis C virus (HCV) span a variety of targets, including proteins encoded by the NS3/4A, NS4B, NS5A, and NS5B genes. Treatment with DAAs has been shown to select variants with sequence changes in the HCV genome encoding amino acids that may confer resistance to the treatment. In order to assess these effects in patients, a Reverse Transcription Polymerase Chain Reaction (RT-PCR) method was developed to sequence these regions of HCV from patient plasma.MethodsA method was developed to amplify and sequence genotype 1 HCV RNA from patient plasma. Optimization of HCV RNA isolation, cDNA synthesis, and nested PCR steps were performed. The optimization of HCV RNA isolation, design of RT-PCR primers, optimization of RT-PCR amplification conditions and reagents, and the evaluation of the RT-PCR method performance is described.ResultsThe optimized method is able to successfully, accurately, and reproducibly amplify near full-length genotype 1 HCV RNA containing a wide range of concentrations (103to 108IU/mL) with a success rate of 97%. The lower limit of detection was determined to be 1000 IU/mL HCV RNA.ConclusionsThis assay allows viral sequencing of all regions targeted by the most common DAAs currently in development, as well as the possibility to determine linkage between variants conferring resistance to multiple DAAs used in combination therapy.
Hevea brasiliensis cell suspension peroxidase: purification, characterization and application for dye decolorization
Authors: Chanwun Thitikorn , Muhamad Nisaporn , Chirapongsatonkul Nion , Churngchow Nunta 
Published: February 2013

Abstract
Peroxidases are oxidoreductase enzymes produced by most organisms. In this study, a peroxidase was purified from Hevea brasiliensis cell suspension by using anion exchange chromatography (DEAE-Sepharose), affinity chromatography (Con A-agarose) and preparative SDS-PAGE. The obtained enzyme appeared as a single band on SDS-PAGE with molecular mass of 70 kDa. Surprisingly, this purified peroxidase also had polyphenol oxidase activity. However, the biochemical characteristics were only studied in term of peroxidase because similar experiments in term of polyphenol oxidase have been reported in our pervious publication. The optimal pH of the purified peroxidase was 5.0 and its activity was retained at pH values between 5.0–10.0. The enzyme was heat stable over a wide range of temperatures (0–60°C), and less than 50% of its activity was lost at 70°C after incubation for 30 min. The enzyme was completely inhibited by β-mercaptoethanol and strongly inhibited by NaN3; in addition, its properties indicated that it was a heme containing glycoprotein. This peroxidase could decolorize many dyes; aniline blue, bromocresol purple, brilliant green, crystal violet, fuchsin, malachite green, methyl green, methyl violet and water blue. The stability against high temperature and extreme pH supported that the enzyme could be a potential peroxidase source for special industrial applications.
Additive value of blood neutrophil gelatinase-associated lipocalin to clinical judgement in acute kidney injury diagnosis and mortality prediction in patients hospitalized from the emergency department
Authors: Di Somma Salvatore , Magrini Laura , De Berardinis Benedetta , Marino Rossella , Ferri Enrico , Moscatelli Paolo , Ballarino Paola , Carpinteri Giuseppe , Noto Paola , Gliozzo Biancamaria , Paladino Lorenzo , Di Stasio Enrico 
Published: February 2013

Abstract
Introduction
Acute kidney injury (AKI) is a common complication among hospitalized patients. The aim of this study was to evaluate the utility of blood neutrophil gelatinase-associated lipocalin (NGAL) assessment as an aid in the early risk evaluation for AKI development in admitted patients.

Methods
This is a multicenter Italian prospective emergency department (ED) cohort study in which we enrolled 665 patients admitted to hospital from the ED.

Results
Blood NGAL and serum creatinine (sCr) were determined at ED presentation (T0), and at: 6 (T6), 12 (T12), 24 (T24) and 72 (T72) hours after hospitalization. A preliminary assessment of AKI by the treating ED physician occurred in 218 out of 665 patients (33%), while RIFLE AKI by expert nephrologists was confirmed in 49 out of 665 patients (7%). The ED physician's initial judgement lacked sensitivity and specificity, overpredicting the diagnosis of AKI in 27% of the cohort, while missing 20% of those with AKI as a final diagnosis.
The area under the receiver operating characteristic curve (AUC), obtained at T0, for blood NGAL alone in the AKI group was 0.80. When NGAL at T0 was added to the ED physician's initial clinical judgment the AUC was increased to 0.90, significantly greater when compared to the AUC of the T0 estimated glomerular filtration rate (eGFR) obtained either by modification of diet in renal disease (MDRD) equation (0.78) or Cockroft-Gault formula (0.78) (P = 0.022 and P = 0.020 respectively). The model obtained by combining NGAL with the ED physician's initial clinical judgement compared to the model combining sCr with the ED physician's initial clinical judgement, resulted in a net reclassification index of 32.4 percentage points. Serial assessment of T0 and T6 hours NGAL provided a high negative predictive value (NPV) (98%) in ruling out the diagnosis of AKI within 6 hours of patients' ED arrival. NGAL (T0) showed the strongest predictive value for in-hospital patient's mortality at a cutoff of 400 ng/ml.

Conclusions
Our study demonstrated that assessment of a patient's initial blood NGAL when admitted to hospital from the ED improved the initial clinical diagnosis of AKI and predicted in-hospital mortality. Blood NGAL assessment coupled with the ED physician's clinical judgment may prove useful in deciding the appropriate strategies for patients at risk for the development of AKI.
See related commentary by Legrand et al.,http://ccforum.com/content/17/2/132
Translational control of human neutrophil responses by MNK1
Authors: Fortin Carl F , Mayer Thomas Z , Cloutier Alexandre , McDonald Patrick P 
Published: February 2013

ABSTRACTA growing number of inflammatory and immune processes in vivo have been shown to be influenced by neutrophil-derived cytokines. Whereas the underlying transcriptional mechanisms are increasingly well understood, the translational regulation of this neutrophil response remains largely unexplored. Here, we show that the MNK1, which participates in translational control in several cell types, is activated in response to physiological neutrophil agonists (LPS, TNF-α) in the cytoplasmic and nuclear compartments. With the use of various pharmacological inhibitors, we found that MNK1 activation takes place downstream of the TAK1-p38 MAPK axis in neutrophils, whereas the MEK/ERK, JNK, PI3K, and PKC pathways are not involved. Pharmacological blockade of MNK1, as well as overexpression experiments, established that cytokine protein synthesis (but not gene expression) is under the control of MNK1 in neutrophils. Likewise, MNK1 inhibition reversed the antiapoptotic effect of LPS and TNF-α in neutrophils, and this was accompanied by a decreased expression of the antiapoptotic protein Mcl-1. Thus, MNK1 appears to be an important regulator of neutrophil responses. Although MNK1 inhibition did not affect protein recruitment to mRNA caps, it decreased the phosphorylation of molecules implicated in translation initiation control, such as S6K, S6, and hyperphosphorylated 4E-BP1. These molecular targets of MNK1 are shared with those of PI3K in neutrophils, and accordingly, MNK1 inhibition partially impaired the belated PI3K/Akt activation elicited by LPS or TNF in these cells. Given the importance of neutrophils and their products in numerous chronic inflammatory disorders, MNK1 could represent an attractive therapeutic target.
Preterm neonates display altered plasmacytoid dendritic cell function and morphology
Authors: Schüller S S , Sadeghi K , Wisgrill Lukas , Dangl A , Diesner S C , Prusa A R , Klebermasz-Schrehof K , Greber-Platzer S , Neumüller J , Helmer H , Husslein P , Pollak A , Spittler A , Förster-Waldl E 
Published: February 2013

Abstract
Functionality and morphology of pDCs of preterm newborns, with emphasis on TLR9 triggered IFN-α production.
Bacterial and viral infections cause high rates of morbidity and mortality in premature newborns. In the setting of viral infection, pDCs play a key role as strong producers of IFN-α upon TLR9 activation. We analyzed pDC frequency, phenotype, morphology, and function in CB of preterm and term newborns in comparison with adults. Whereas all age groups show similar pDC numbers, BDCA-2, CD123, and TLR9 levels, the expression of BDCA-4 and capacity to produce IFN-α upon TLR9 challenge were decreased significantly in preterm neonates. Furthermore, we show by means of electron microscopy that pDCs from preterm newborns exhibit a distinct, “immature” morphology. Taken together, these findings suggest decreased functionality of pDCs in the premature newborn. The reduced capacity to produce IFN-α is likely to render such infants more susceptible to viral infections.
The Ntcheu derotation splint for lower limb traction
Authors: Doorgakant Ashtin , Parmar Rishee , Ngulube Christopher 
Published: February 2013

Summary The Ntcheu derotation splint is recommended as a tool to improve the care of patients in lower limb traction. It avoids the various problems associated with the traditional plaster boot that is routinely used (stiffness, pressure sores, cost and time). It is easy to make, is relatively low cost and uses widely available materials.
Clinical profile of children with moderate-to-severe eosinophilia presenting to a tertiary hospital in Nepal
Authors: Shrestha Shrijana , Timila Dipsal , Karki Utkarsh , Shrestha Ashis , Bhandary Shital 
Published: February 2013

Summary Fifty children (mean age 8 years) with an absolute eosinophil count ranging from 1956 to 28,500 were studied in a tertiary hospital in Nepal. Most had multisystem involvement: 47 had constitutional symptoms; 38 had gastrointestinal symptoms; and 37 had respiratory symptoms. Abdominal pain, fever, cough and weight loss were the most common presentations while pleural effusion, ascites, pericardial effusion, abdominal nodes and high erythrocyte sedimentation rates were the common investigational findings.
The value of health partnerships: a practical approach to evidence
Authors: Ritman Dan , Zegeye Hana 
Published: February 2013

Summary Your April editorial 1 points out that there is little strong evidence of the effectiveness and impact of health links – or health partnerships, as they are often known – in terms of the processes and particularly the outcomes of health care. We believe this reflects the inherent complexity of the health systems and the consequent challenges for robust measurement. However, health partnerships use a range of evaluation methods that provide valuable, qualitative and descriptive information about change and performance management, which can help demonstrate the effectiveness of health partnerships.
Structure of caa
3 cytochrome c oxidase – a nature-made enzyme-substrate complex
Authors: Noor Mohamed Radzi , Soulimane Tewfik 
Published: February 2013

Abstract
Aerobic respiration, the energetically most favorable metabolic reaction, depends on the action of terminal oxidases that include cytochrome c oxidases. The latter forms a part of the heme-copper oxidase superfamily and consists of three different families (A, B, and C types). The crystal structures of all families have now been determined, allowing a detailed structural comparison from evolutionary and functional perspectives. The A2-type oxidase, exemplified by the Thermus thermophilus caa
3 oxidase, contains the substrate cytochrome c covalently bound to the enzyme complex. In this article, we highlight the various features of caa
3 enzyme and provide a discussion of their importance, including the variations in the proton and electron transfer pathways.
Allele Identification for Transcriptome-Based Population Genomics in the Invasive PlantCentaurea solstitialis
Authors: Dlugosch Katrina M , Lai Zhao , Bonin Aurélie , Hierro José , Rieseberg Loren H 
Published: February 2013

AbstractTranscriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.