bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of BRAF molecular analysis in the management of papillary thyroid carcinoma: analysis of cytological and histological samples
Authors: Capelli L. , Marfisi C. , Puccetti M. , Saragoni L. , De Paola F. , Zaccaroni A. , Chiadini E. , Gagliardi L. , Ferretti G. , Zoli W. , Ulivi P. 
Published: August 2014

BackgroundAlthough fine needle aspiration (FNA) is the standard diagnostic test for the characterization of a suspicious thyroid nodule, in some cases cytological evaluation is inconclusive. The aim of this study was to determine the role of BRAF mutation in aiding diagnosis and to verify whether archival cytological samples could be suitable for molecular analysis.MethodsEighty‐five patients with suspicious (Thy4) or follicular (Thy3) lesions on cytology were resubmitted to a second FNA for BRAF mutation analysis. Of these, 56 subsequently underwent surgery. The usefulness of archival samples for molecular analysis was also studied in a second cohort of 42 patients with a confirmed diagnosis of papillary thyroid carcinoma for whom both archived paraffin‐embedded histological samples and cytological smears were available. A further 15 patients with paired fresh FNA and archived cytological and histological samples were recruited.ResultsBRAF mutation was found in the fresh FNA samples from 10 of 56 patients who had surgery with previous inconclusive cytology (4/45, 9%, Thy3 and 6/11, 55%, Thy4). The BRAF test showed a specificity and positive predictive value of 100% (26/26 and 10/10, respectively), sensitivity of 33% (10/30) and negative predictive value of 57% (26/46). There was absolute concordance between the BRAF results obtained with 42 histological and cytological archived samples. BRAF analysis on 15 archived cytological samples showed absolute concordance with histology, whereas there was one false negative on the matched fresh FNA.ConclusionBRAF analysis is a highly specific test that can facilitate cytological diagnosis in some cases and can also be performed on archived cytological samples.
Competing uses for China's straw: the economic and carbon abatement potential of biochar
Authors: Clare Abbie , Shackley Simon , Joseph Stephen , Hammond James , Pan Genxing , Bloom Anthony 
Published: August 2014

AbstractChina is under pressure to improve its agricultural productivity to keep up with the demands of a growing population with increasingly resource‐intensive diets. This productivity improvement must occur against a backdrop of carbon intensity reduction targets, and a highly fragmented, nutrient‐inefficient farming system. Moreover, the Chinese government increasingly recognizes the need to rationalize the management of the 800 million tonnes of agricultural crop straw that China produces each year, up to 40% of which is burned in‐field as a waste. Biochar produced from these residues and applied to land could contribute to China's agricultural productivity, resource use efficiency and carbon reduction goals. However competing uses for China's straw residues are rapidly emerging, particularly from bioenergy generation. Therefore it is important to understand the relative economic viability and carbon abatement potential of directing agricultural residues to biochar rather than bioenergy. Using cost‐benefit analysis (CBA) and life‐cycle analysis (LCA), this paper therefore compares the economic viability and carbon abatement potential of biochar production via pyrolysis, with that of bioenergy production via briquetting and gasification. Straw reincorporation and in‐field straw burning are used as baseline scenarios. We find that briquetting straw for heat energy is the most cost‐effective carbon abatement technology, requiring a subsidy of $7 MgCO2e−1 abated. However China's current bioelectricity subsidy scheme makes gasification (NPV $12.6 million) more financially attractive for investors than both briquetting (NPV $7.34 million), and pyrolysis ($−1.84 million). The direct carbon abatement potential of pyrolysis (1.06 MgCO2e per odt straw) is also lower than that of briquetting (1.35 MgCO2e per odt straw) and gasification (1.16 MgCO2e per odt straw). However indirect carbon abatement processes arising from biochar application could significantly improve the carbon abatement potential of the pyrolysis scenario. Likewise, increasing the agronomic value of biochar is essential for the pyrolysis scenario to compete as an economically viable, cost‐effective mitigation technology.
Immunohistochemical panel for the diagnosis of Hirschsprung's disease using antibodies to MAP2, calretinin, GLUT1 and S100
Authors: Bachmann Leonhard , Besendörfer Manuel , Carbon Roman , Lux Philipp , Agaimy Abbas , Hartmann Arndt , Rau Tilman T 
Published: August 2014

AimsThe diagnosis of Hirschsprung's disease is currently based on the identification of aganglionosis and the presence of an increase in acetylcholinesterase‐positive hypertrophic nerve fibres in the large bowel submucosa. However, acetylcholinesterase staining is laborious and requires a skilled technician. The aim of this study was to identify a method for diagnosing Hirschsprung's disease reliably using an immunohistochemical panel of recently proposed markers.Methods and resultsSixty‐nine specimens from 37 patients were evaluated. MAP2 and calretinin antibodies were shown to stain ganglia reliably in the submucosal and myenteric plexuses of normal tissue. By contrast, reduced staining of ganglia was observed in patients with Hirschsprung's disease. Staining for GLUT1 and S100 was used to evaluate the number and thickness of nerve fibres. Gain of GLUT1 and S100 expression was in contrast to the loss of calretinin and MAP2. Hypertrophic submucosal nerve fibres in Hirschsprung's disease develop a perineurium with a ring‐like GLUT1 staining pattern similar in size and intensity to that observed in deeper subserosal tissue.ConclusionsThe diagnosis of Hirschsprung's disease using immunohistochemical panels could be as accurate as with conventional frozen section techniques. In particular, the use of a combination of markers for ganglia and hypertrophic nerve fibres highlighting a prominent perineurium in Hirschsprung's disease could be an alternative method.
Primary cutaneous anaplastic large cell lymphomas with 6p25.3 rearrangement exhibit particular histological features
Authors: Onaindia Arantza , Montes‐Moreno Santiago , Rodríguez‐Pinilla Socorro M , Batlle Ana , González de Villambrosía Sonia , Rodríguez Antonio M , Alegre Víctor , Bermúdez Glenda M , González‐Vela Carmen , Piris Miguel A 
Published: August 2014

AimsCD30‐positive primary cutaneous lymphoproliferative disorders include several entities with differing clinical presentation but overlapping histological features, including lymphomatoid papulosis and primary cutaneous anaplastic large cell lymphoma (C‐ALCL). DUSP22–IRF4 locus translocation is present in 20–57% of C‐ALCLs, and has also been described in a series of 11 lymphomatoid papulosis patients, where it was associated with a particular biphasic histological pattern, including pagetoid reticulosis‐type epidermal infiltration. We aimed to study whether the presence of this translocation may define distinctive histological features in C‐ALCL.Methods and resultsWe collected three cases of C‐ALCL with histological features similar to those described in the new variant of lymphomatoid papulosis with 6p25.3 rearrangement. We studied their histological features and immunophenotype, using a panel of antibodies against CD30, TCR‐βF1, TCR‐γ, CD4, CD8, CD20, Ki‐67 and ALK. FISH analyses were performed using an IRF4–DUSP22 break‐apart probe for the study of the 6p25.3 rearrangement. FISH results were positive in the three cases, which all showed distinctive histological and immunohistochemical features: a diffuse dermal infiltrate of atypical medium‐to‐large cells, and marked epidermotrophism with small, atypical intra‐epidermal lymphocytes.ConclusionsOur findings suggest that the presence of 6p25.3 rearrangement might be related to this particular biphasic pattern.
Transcription activator‐like effector nuclease (TALEN)‐mediated female‐specific sterility in the silkworm, Bombyx mori
Authors: Xu J. , Wang Y. , Li Z. , Ling L. , Zeng B. , James A. A. , Tan A. , Huang Y. 
Published: August 2014

AbstractEngineering sex‐specific sterility is critical for developing transgene‐based sterile insect technology. Targeted genome engineering achieved by customized zinc‐finger nuclease, transcription activator‐like effector nuclease (TALEN) or clustered, regularly interspaced, short palindromic repeats/Cas9 systems has been exploited extensively in a variety of model organisms; however, screening mutated individuals without a detectable phenotype is still challenging. In addition, genetically recessive mutations only detectable in homozygotes make the experiments time‐consuming. In the present study, we model a novel genetic system in the silkworm, Bombyx mori, that results in female‐specific sterility by combining transgenesis with TALEN technologies. This system induces sex‐specific sterility at a high efficiency by targeting the female‐specific exon of the B. mori doublesex (Bmdsx) gene, which has sex‐specific splicing isoforms regulating somatic sexual development. Transgenic animals co‐expressing TALEN left and right arms targeting the female‐specific Bmdsx exon resulted in somatic mutations and female mutants lost fecundity because of lack of egg storage and abnormal external genitalia. The wild‐type sexual dimorphism of abdominal segment was not evident in mutant females. In contrast, there were no deleterious effects in mutant male moths. The current somatic TALEN technologies provide a promising approach for future insect functional genetics, thus providing the basis for the development of attractive genetic alternatives for insect population management.
Innate immune regulation by STAT‐mediated transcriptional mechanisms
Authors: Li Haiyan S. , Watowich Stephanie S. 
Published: August 2014

SummaryThe term innate immunity typically refers to a quick but non‐specific host defense response against invading pathogens. The innate immune system comprises particular immune cell populations, epithelial barriers, and numerous secretory mediators including cytokines, chemokines, and defense peptides. Innate immune cells are also now recognized to play important contributing roles in cancer and pathological inflammatory conditions. Innate immunity relies on rapid signal transduction elicited upon pathogen recognition via pattern recognition receptors (PRRs) and cell:cell communication conducted by soluble mediators, including cytokines. A majority of cytokines involved in innate immune signaling use a molecular cascade encompassing receptor‐associated Jak protein tyrosine kinases and STAT (signal transducer and activator of transcription) transcriptional regulators. Here, we focus on roles for STAT proteins in three major innate immune subsets: neutrophils, macrophages, and dendritic cells (DCs). While knowledge in this area is only now emerging, understanding the molecular regulation of these cell types is necessary for developing new approaches to treat human disorders such as inflammatory conditions, autoimmunity, and cancer.
Complex interactions of transcription factors in mediating cytokine biology in T cells
Authors: Li Peng , Spolski Rosanne , Liao Wei , Leonard Warren J. 
Published: August 2014

SummaryT‐helper (Th) cells play critical roles within the mammalian immune system, and the differentiation of naive CD4+ T cells into distinct T‐helper subsets is critical for normal immunoregulation and host defense. These carefully regulated differentiation processes are controlled by networks of cytokines, transcription factors, and epigenetic modifications, resulting in the generation of multiple CD4+ T‐cell subsets, including Th1, Th2, Th9, Th17, Treg, and Tfh cells. In this review, we discuss the roles of transcription factors in determining the specific type of differentiation and in particular the role of interleukin‐2 (IL‐2) in promoting or inhibiting Th differentiation. In addition to discussing master regulators and subset‐specific transcription factors for distinct T‐helper cell populations, we focus on signal transducer and activator of transcription (STAT) proteins and on the cooperative action of interferon regulatory factor 4 (IRF4) with activator protein 1 (AP‐1) family proteins and STAT3 in the assembly of complexes that broadly influence T‐cell differentiation.
Orchestration of plasma cell differentiation by Bach2 and its gene regulatory network
Authors: Igarashi Kazuhiko , Ochiai Kyoko , Itoh‐Nakadai Ari , Muto Akihiko 
Published: August 2014

SummaryBach2 is a basic region‐leucine zipper (bZip) transcription factor that forms heterodimers with small Maf oncoproteins and binds to target genes, thus repressing their expression. Bach2 is required for class switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes in activated B cells. Bach2 represses the expression of Prdm1 encoding Blimp‐1 repressor and thereby inhibits terminal differentiation of B cells to plasma cells. This causes a delay in the induction of Prdm1, thereby securing a time window for the expression of Aicda encoding activation‐induced cytidine deaminase (AID) required for both CSR and SHM. Based on the characteristics of a gene regulatory network (GRN) involving Bach2 and Prdm1 and its dynamics, a ‘delay‐driven diversity’ model was introduced to explain the responses of activated B cells. Bach2 is also required for the proper differentiation and function of peripheral T cells. In the absence of Bach2, CD4+ T cells show increased differentiation to effector cells producing higher levels of Th2‐related cytokines, such as IL‐4 and IL‐10, and a reduction in the generation of regulatory T cells. Bach2 represses many genes in T cells, including Prdm1, suggesting that the Bach2‐Prdm1 pathway is also important in maintaining the homeostasis of T cells. Furthermore, Bach2 is essential for the function of alveolar macrophages. Therefore, Bach2 orchestrates both acquired and innate immunity at multiple points. Its connection with disease is also reviewed in this report.
Staying innate: transcription factor maintenance of innate lymphoid cell identity
Authors: Di Santo James P. 
Published: August 2014

SummaryInnate and adaptive lymphocytes are characterized by phenotypic and functional characteristics that result from genomic rearrangements (in the case of antigen‐specific B and T cells) coupled with selective gene expression patterns that are generated in a context‐dependent fashion. Cell‐intrinsic expression of transcription factors (TFs) play a critical role in the regulation of gene expression that establish the distinct lymphoid subsets but also have been proposed to play an ongoing role in the maintenance of lineage‐associated transcriptional signatures that comprise lymphocyte identity. This is the case for CD19+ B cells that require Pax5 expression throughout their lifespan, as well as for diverse T‐helper subsets that have specialized immune functions. Innate lymphoid cells (ILCs) comprise diverse effectors cells that differentiate under TF control and have critical roles in the early stages of immune responses. In this review, ILC development is reviewed and the requirement for persistent TF expression in the maintenance of transcriptional signatures that define ILC identity is explored.
ID'ing innate and innate‐like lymphoid cells
Authors: Verykokakis Mihalis , Zook Erin C. , Kee Barbara L. 
Published: August 2014

SummaryThe immune system can be divided into innate and adaptive components that differ in their rate and mode of cellular activation, with innate immune cells being the first responders to invading pathogens. Recent advances in the identification and characterization of innate lymphoid cells have revealed reiterative developmental programs that result in cells with effector fates that parallel those of adaptive lymphoid cells and are tailored to effectively eliminate a broad spectrum of pathogenic challenges. However, activation of these cells can also be associated with pathologies such as autoimmune disease. One major distinction between innate and adaptive immune system cells is the constitutive expression of ID proteins in the former and inducible expression in the latter. ID proteins function as antagonists of the E protein transcription factors that play critical roles in lymphoid specification as well as B‐ and T‐lymphocyte development. In this review, we examine the transcriptional mechanisms controlling the development of innate lymphocytes, including natural killer cells and the recently identified innate lymphoid cells (ILC1, ILC2, and ILC3), and innate‐like lymphocytes, including natural killer T cells, with an emphasis on the known requirements for the ID proteins.
Deciphering the epigenetic code of T lymphocytes
Authors: Allan Rhys S. , Nutt Stephen L. 
Published: August 2014

SummaryThe multiple lineages and differentiation states that constitute the T‐cell compartment all derive from a common thymic precursor. These distinct transcriptional states are maintained both in time and after multiple rounds of cell division by the concerted actions of a small set of lineage‐defining transcription factors that act in conjunction with a suite of chromatin‐modifying enzymes to activate, repress, and fine‐tune gene expression. These chromatin modifications collectively provide an epigenetic code that allows the stable and heritable maintenance of the T‐cell phenotype. Recently, it has become apparent that the epigenetic code represents a therapeutic target for a variety of immune cell disorders, including lymphoma and acute and chronic inflammatory diseases. Here, we review the recent advances in epigenetic regulation of gene expression, particularly as it relates to the T‐cell differentiation and function.
Mi‐2/NuRD chromatin remodeling complexes regulate B and T‐lymphocyte development and function
Authors: Dege Carissa , Hagman James 
Published: August 2014

SummaryMi‐2/nucleosomal remodeling and deacetylase (NuRD) complexes are important epigenetic regulators of chromatin structure and gene expression. Mi‐2/NuRD complexes are an assemblage of proteins that combine key epigenetic regulators necessary for (i) histone deacetylation and demethylation, (ii) binding to methylated DNA, (iii) mobilization of nucleosomes, and (iv) recruitment of additional regulatory proteins. Depending on their context in chromatin, Mi‐2/NuRD complexes either activate or repress gene transcription. In this regard, they are important regulators of hematopoiesis and lymphopoiesis. Mi‐2/NuRD complexes maintain pools of hematopoietic stem cells. Specifically, components of these complexes control multiple stages of B‐cell development by regulating B‐cell specific transcription. With one set of components, they inhibit terminal differentiation of germinal center B cells into plasma B cells. They also mediate gene repression together with Blimp‐1 during plasma cell differentiation. In cooperation with Ikaros, Mi‐2/NuRD complexes also play important roles in T‐cell development, including CD4 versus CD8 fate decisions and peripheral T‐cell responses. Dysregulation of NuRD during lymphopoiesis promotes leukemogenesis. Here, we review general properties of Mi‐2/NuRD complexes and focus on their functions in gene regulation and development of lymphocytes.
Incisional negative pressure wound therapy after hemiarthroplasty for femoral neck fractures – reduction of wound complications
Authors: Pauser Johannes , Nordmeyer Matthias , Biber Roland , Jantsch Jonathan , Kopschina Carsten , Bail Hermann J , Brem Matthias H 
Published: August 2014

AbstractThe aim of the study was to evaluate the use of incisional negative pressure wound therapy (iNPWT) in wound healing after femoral neck fracture (FNF) treated with hip hemiarthroplasty (HA) and its influence on postoperative seromas, wound secretion, as well as time and material consumption for dressing changes. The study is a prospective randomised evaluation of iNPWT in patients with large surgical wounds after FNF. Patients were randomised either to be treated by iNPWT (group A) or a standard wound dressing (group B). Follow‐up included ultrasound measurements of seroma volumes on postoperative days 5 and 10, duration of wound secretion, and time and material spent for wound dressing changes. For comparison of the means, we used the t‐test for independent samples, P > 0·05 was considered significant. There were 21 patients randomised in this study. Group A (11 patients, 81·6 ± 5·2 years of age) developed a seroma of 0·257 ± 0·75 cm3 after 5 days and had a secretion of 0·9 ± 1·0 days, and the total time for dressing changes was 14·8 ± 3·9 minutes, whereas group B (ten patients, 82·6 ± 8·6 years of age) developed a seroma of 3·995 ± 5·01 cm3 after 5 days and had a secretion of 4·3 ± 2·45 days, and the total time for dressing changes was 42·9 ± 11·0 minutes. All mentioned differences were significant. iNPWT has been used on many different types of traumatic and non‐traumatic wounds. This prospective, randomised study has demonstrated decreased development of postoperative seromas, reduction of total wound secretion days and reduction of needed time for dressing changes.
Large Strain Response and Fatigue‐Resistant Behavior in Ternary Bi0.5Na0.5TiO3–BaTiO3–Bi(Zn0.5Ti0.5)O3 Solid Solutions
Authors: Li Yan , Wang Feifei , Ye Xiang , Xie Yiqun , Tang Yanxue , Sun Dazhi , Shi Wangzhou , Zhao Xiangyong , Luo Haosu 
Published: August 2014

A ternary solid solution (1 − x)(0.88Bi0.5Na0.5TiO3–0.12BaTiO3)‐xBi(Zn0.5Ti0.5)O3 (BNBZT, BNBZTx) was designed and fabricated using the traditional solid‐state reaction method. The temperature and composition dependence of dielectric, ferroelectric, piezoelectric, and fatigue properties were systematically investigated and a schematic phase diagram was proposed. The substitution with Bi(Zn0.5Ti0.5)O3 was found to shift the phase transition (ferroelectric tetragonal to relaxor pseudocubic phase) to lower temperatures. At a critical composition x of 0.05, large electric‐field‐induced strain response with normalized strain Smax/Emax as high as 526 pm/V was obtained under a moderate field of 4 kV/mm around room temperature. The strain exhibited good temperature stability within the temperature range of 25°C–120°C. In addition, excellent fatigue‐resistant behavior was observed in the proposed BNBZT solid solution after 106 bipolar cycles. These give the BNBZT system great potential as environmental friendly solid‐state actuator.