Miracle-dz/UniFAR-FTUs huggingface dataset:
CDK5 Regulates Paclitaxel Sensitivity in Ovarian Cancer Cells by Modulating AKT Activation, p21Cip1- and p27Kip1-Mediated G1 Cell Cycle Arrest and Apoptosis

Cyclin-dependent kinase 5 (CDK5) is a cytoplasmic serine/ threonine kinase. Knockdown of CDK5 enhances paclitaxel sensitivity in human ovarian cancer cells. This study explores the mechanisms by which CDK5 regulates paclitaxel sensitivity in human ovarian cancers. Multiple ovarian cancer cell lines and xenografts were treated with CDK5 small interfering RNA (siRNA) with or without paclitaxel to examine the effect on cancer cell viability, cell cycle arrest and tumor growth. CDK5 protein was measured by immunohistochemical staining of an ovarian cancer tissue microarray to correlate CDK5 expression with overall patient survival. Knockdown of CDK5 with siRNAs inhibits activation of AKT which significantly correlates with decreased cell growth and enhanced paclitaxel sensitivity in ovarian cancer cell lines. In addition, CDK5 knockdown alone and in combination with paclitaxel induced G1 cell cycle arrest and caspase 3 dependent apoptotic cell death associated with post-translational upregulation and nuclear translocation of TP53 and p27Kip1 as well as TP53-dependent transcriptional induction of p21Cip1 in wild type TP53 cancer cells. Treatment of HEYA8 and A2780 wild type TP53 xenografts in nu/nu mice with CDK5 siRNA and paclitaxel produced significantly greater growth inhibition than either treatment alone. Increased expression of CDK5 in human ovarian cancers correlates inversely with overall survival. CDK5 modulates paclitaxel sensitivity by regulating AKT activation, the cell cycle and caspase-dependent apoptosis. CDK5 inhibition can potentiate paclitaxel activity in human ovarian cancer cells.
PARP‐1 deficiency blocks IL‐5 expression through calpain‐dependent degradation of STAT‐6 in a murine asthma model

To cite this article: Datta R, Naura AS, Zerfaoui M, Errami Y, Oumouna M, Kim H, Ju J, Ronchi VP, Haas AL, Boulares AH. PARP‐1 deficiency blocks IL‐5 expression through calpain‐dependent degradation of STAT‐6 in a murine asthma model. Allergy 2011; 66: 853–861.
Natural killer lines and clones with apparent antigen specificity

Fresh CD3-, CD16+ lymphocytes that adhered to selected allogeneic lymphoblastoid cell lines (LCL) were cultured with LCL in the presence of IL-2-containing medium. The resulting lines as well as clones derived from these lines expressed CD16 and/or CD56, but lacked detectable CD3 or TCR-alpha/beta or TCR-gamma/delta complexes on the cell surface. Northern blot analysis failed to detect CD3 epsilon or TCR-beta transcripts, but revealed the presence of a TCR-gamma chain transcript in one of these lines. In addition to displaying potent cytolytic activity against K562 erythroleukemia cells (a classical NK target), the vast majority of these lines and clones lysed their specific stimulator LCL to a significantly greater extent than irrelevant LCL. This selective killing was inhibited by the addition of cold stimulator LCL or K562 cells, or anti-LFA 1 mAbs, but not by irrelevant LCL or mAbs to CD3, class I or class II MHC antigens. These results indicate that some CD3- lymphocytes, phenotypically indistinguishable from NK cells, can recognize and lyse allogeneic targets in a specific manner.
Crystallisation behaviour during tensile loading of laser treated Fe–Si–B metallic glass

Effect of tensile loading on crystallisation behaviour of as-cast and laser thermal treated Fe–Si–B metallic glass foils was investigated. Tensile loading lacked any marked influence on the crystallisation behaviour of as-cast and structurally relaxed laser-treated metallic glass foils. Furthermore, the average crystallite/grain size in partially crystallised laser-treated metallic glass foil was nearly equal to the average crystallite/grain size in the region away from the fracture of the same partially crystallised laser-treated metallic glass foil after tensile loading. However, a significant crystallite/grain growth/coarsening of the order of two and half times was observed in the fractured region compared to the region around it for the laser-treated partially crystallised metallic glass foils. The simultaneous effects of stress generation and temperature rise during tensile loading were considered to play a key role in crystallite/grain growth/coarsening.
Characteristics of Hospital-Acquired and Community-Onset Blood Stream Infections, South-East Austria

Purpose The objective of this study was to compare epidemiology, causative pathogens, outcome, and levels of laboratory markers of inflammation of community-onset (i.e. community-acquired and healthcare-associated) and hospital-acquired bloodstream infection (BSI) in South-East Austria. Methods In this prospective cohort study, 672 patients fulfilling criteria of systemic inflammatory response syndrome with positive peripheral blood cultures (277 community-onset [192 community-acquired, 85 healthcare-associated BSI], 395 hospital-acquired) were enrolled at the Medical University of Graz, Austria from 2011 throughout 2012. Clinical, microbiological, demographic as well as outcome and laboratory data was collected. Results Escherichia coli followed by Staphylococcus aureus were the most frequently isolated pathogens. While Streptococcus spp. and Escherichia coli were isolated more frequently in patients with community-onset BSI, Enterococcus spp. , Candida spp. , Pseudomonas spp. , Enterobacter spp. , and coagulase-negative staphylococci were isolated more frequently among those with hospital-acquired BSI. With regard to the outcome, 30-day (82/395 vs. 31/277; p = 0.001) and 90-day mortality (106/395 vs. 35/277; p<0.001) was significantly higher among patients with hospital-acquired BSI even though these patients were significantly younger. Also, hospital-acquired BSI remained a significant predictor of mortality in multivariable analysis. At the time the blood cultures were drawn, patients with community-onset BSI had significantly higher leukocyte counts, neutrophil-leucocyte ratios as well as C-reactive protein, procalcitonin, interleukin-6 and serum creatinine levels when compared to those with hospital-acquired BSI. Patients with healthcare-associated BSI presented with significantly higher PCT and creatinine levels than those with community-acquired BSI. Conclusions Hospital-acquired BSI was associated with significantly higher 30- and 90-day mortality rates. Hospital-acquired BSI therefore poses an important target for the most aggressive strategies for prevention and infection control.
Biochemical Characterization of Bacteriophage T4 Mre11-Rad50 Complex*

The Mre11-Rad50 complex (MR) from bacteriophage T4 (gp46/47) is involved in the processing of DNA double-strand breaks. Here, we describe the activities of the T4 MR complex and its modulation by proteins involved in homologous recombination. T4 Mre11 is a Rad50- and Mn2+-dependent dsDNA exonuclease and ssDNA endonuclease. ATP hydrolysis is required for the removal of multiple nucleotides via dsDNA exonuclease activity but not for the removal of the first nucleotide or for ssDNA endonuclease activity, indicating ATP hydrolysis is only required for repetitive nucleotide removal. By itself, Rad50 is a relatively inefficient ATPase, but the presence of Mre11 and dsDNA increases ATP hydrolysis by 20-fold. The ATP hydrolysis reaction exhibits positive cooperativity with Hill coefficients ranging from 1.4 for Rad50 alone to 2.4 for the Rad50-Mre11-DNA complex. Kinetic assays suggest that approximately four nucleotides are removed per ATP hydrolyzed. Directionality assays indicate that the prevailing activity is a 3′ to 5′ dsDNA exonuclease, which is incompatible with the proposed role of MR in the production of 3′ ssDNA ends. Interestingly, we found that in the presence of a recombination mediator protein (UvsY) and ssDNA-binding protein (gp32), Mre11 is capable of using Mg2+ as a cofactor for its nuclease activity. Additionally, the Mg2+-dependent nuclease activity, activated by UvsY and gp32, results in the formation of endonuclease reaction products. These results suggest that gp32 and UvsY may alter divalent cation preference and facilitate the formation of a 3′ ssDNA overhang, which is a necessary intermediate for recombination-mediated double-strand break repair.
Mixed glioblastoma multiforme and sarcoma. A clinicopathologic study of 26 radiation therapy oncology group cases

Twenty‐six cases are reported of gliosarcoma (GS) retrieved from a series of 1479 glioblastomas (GBM) that were part of five consecutive, randomized Phase II or III malignant glioma protocols initiated by the Radiation Therapy Oncology Group between 1974 and 1983. The clinicopathologic features of these 26 cases, including actuarial survival times, were compared with the remaining 1453 GBM. The minimal qualitative and quantitative histologic criteria required to diagnose GS are presented. In most cases the sarcomatous component was a malignant fibrous histiocytoma; a minority were fibrosarcoma. No significant differences between GS and GBM were found with regard to age, sex, pretreatment Karnofsky performance status, tumor location, size, median survival (8.3 and 9.6 months, respectively), and actuarial survival. None of the treatment regimens, which included various combinations of radiation therapy and chemotherapy, improved the survival of GS over GBM. Selective involvement of the temporal lobe by GS was not found, and the frequency of GS was determined to be only 1.8% of all GBM.
The structure and function of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Haemophilus influenzae.

The gene encoding the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase of Haemophilus influenzae has been cloned and expressed in Escherichia coli. A complex of the purified protein with a substrate analog has been crystallized and its structure solved by multiple anomalous dispersion using phase information obtained from a single crystal of selenomethione-labeled protein. The enzyme folds into a four-stranded antiparallel beta-sheet flanked on one side by two alpha-helices and on the other by three consecutive alpha-helices, giving a novel beta1alpha1beta2beta3alpha2beta4alpha3alpha4alpha5 polypeptide topology. The three-dimensional structure of a binary complex has been refined at 2.1 A resolution. The location of the substrate analog and a sulfate ion gives important insight into the molecular mechanism of the enzyme.
Flow Cytometry Study of Blood Cell Subtypes Reflects Autoimmune and Inflammatory Processes in Autoimmune Polyendocrine Syndrome Type I

Autoimmune polyendocrine syndrome type I (APS I) is a recessive disorder caused by mutations in the autoimmune regulator (AIRE) gene. AIRE is expressed in medullary epithelial cells where it activates transcription of organ‐specific proteins in thymus, thereby regulating autoimmunity. Patients with APS I have, in addition to autoimmune manifestations in endocrine organs, also often ectodermal dystrophies and chronic mucocutaneous candidiasis. The aim of this study was to characterize immune cell subpopulations in patients with APS I and their close relatives. Extensive blood mononuclear cell immunophenotyping was carried out on 19 patients with APS I, 18 first grade relatives and corresponding sex‐ and age‐matched healthy controls using flow cytometry. We found a significant relative reduction in T helper cells coexpressing CCR6 and CXCR3 in patients with APS I compared to controls (mean = 4.10% versus 5.94% respectively, P = 0.035). The pools of CD16+ monocytes and regulatory T cells (Tregs) were also lower in patients compared with healthy individuals (mean = 15.75% versus 26.78%, P = 0.028 and mean = 4.12% versus 6.73%, P = 0.029, respectively). This is the first report describing reduced numbers of CCR6+CXCR3+ T helper cells and CD16+ monocytes in patients with APS I We further confirm previous findings of reduced numbers of Tregs in these patients.
Events surrounding the early development of Euglena chloroplasts: experiments with streptomycin in non-dividing cells.

SUMMARY: The concentration of streptomycin (Sm) which selectively inhibits light-induced chloroplast development in non-dividing Euglena is the same as that which induces the loss of green-colony forming ability in dividing organisms. This concentration of Sm has no effect on division or viability. Chlorophyll synthesis is insensitive to streptomycin for the first 12 h of development but is strongly inhibited after this time. Between 72 and 96 h after the beginning of chloroplast development, Sm-treated organisms contain 10 % of the chlorophyll and 24 % of the carotenoids of algae developing in the absence of the antibiotic. The chlorophyll-to-carotenoid ratio in treated organisms at 72 to 96 h is 0.9, the same as is found at 12 h for organisms developing in the absence of Sm. In the presence of streptomycin, Euglena never develops the ability to fix CO2 photosynthetically, although CO2 fixation after 12 h of development in the absence of the antibiotic can be readily detected. At 12 h of chloroplast development the following parameters are at comparable levels in Sm-treated and untreated organisms: the bound forms of chlorophyll, centration of cytochrome 552, the activities of ribulose diphosphate carboxylase, NADP-triose phosphate dehydrogenase, the enzymes converting ribose-5-phosphate to ribulose diphosphate, and photosystem II activity measured as dye reduction.
Reconstruction and Finite Element Mesh Generation of Abdominal Aortic Aneurysms From Computerized Tomography Angiography Data With Minimal User Interactions

Evaluating rupture risk of abdominal aortic aneurysms is critically important in reducing related mortality without unnecessarily increasing the rate of elective repair. According to the current clinical practice aneurysm rupture risk is (mainly) estimated from its maximum diameter and/or expansion rate; an approach motivated from statistics but known to fail often in individuals. In contrast, recent research demonstrated that patient specific biomechanical simulations can provide more reliable diagnostic parameters, however current structural model development is cumbersome and time consuming. This paper used 2D and 3D deformable models to reconstruct aneurysms from computerized tomography angiography data with minimal user interactions. In particular, formulations of frames and shells, as known from structural mechanics, were used to define deformable modes, which in turn allowed a direct mechanical interpretation of the applied set of reconstruction parameters. Likewise, a parallel finite element implementation of the models allows the segmentation of clinical cases on standard personal computers within a few minutes. The particular topology of the applied 3D deformable models supports a fast and simple hexahedral-dominated meshing of the arising generally polyhedral domain. The variability of the derived segmentations (luminal: 0.50(SD 0.19) mm; exterior 0.89(SD 0.45) mm) with respect to large variations in elastic properties of the deformable models was in the range of the differences between manual segmentations as performed by experts (luminal: 0.57(SD 0.24) mm; exterior: 0.77(SD 0.58) mm), and was particularly independent from the algorithm's initialization. The proposed interaction of deformable models and mesh generation defines finite element meshes suitable to perform accurate and efficient structural analysis of the aneurysm using mixed finite element formulations.
Selective Activation of hTRPV1 by N-Geranyl Cyclopropylcarboxamide, an Amiloride-Insensitive Salt Taste Enhancer

TRPV1t, a variant of the transient receptor potential vanilloid-1 (TRPV1) has been proposed as a constitutively active, non-selective cation channel as a putative amiloride-insensitive salt taste receptor and shares many properties with TRPV1. Based on our previous chorda tympani taste nerve recordings in rodents and human sensory evaluations, we proposed that N-geranylcyclopropylcarboxamide (NGCC), a novel synthetic compound, acts as a salt taste enhancer by modulating the amiloride/benzamil-insensitive Na+ entry pathways. As an extension of this work, we investigated NGCC-induced human TRPV1 (hTRPV1) activation using a Ca2+-flux signaling assay in cultured cells. NGCC enhanced Ca2+ influx in hTRPV1-expressing cells in a dose-dependent manner (EC50 = 115 µM). NGCC-induced Ca2+ influx was significantly attenuated by ruthenium red (RR; 30 µM), a non-specific blocker of TRP channels and capsazepine (CZP; 5 µM), a specific antagonist of TRPV1, implying that NGCC directly activates hTRPV1. TRPA1 is often co-expressed with TRPV1 in sensory neurons. Therefore, we also investigated the effects of NGCC on hTRPA1-expressing cells. Similar to hTRPV1, NGCC enhanced Ca2+ influx in hTRPA1-expressing cells (EC50 = 83.65 µM). The NGCC-induced Ca2+ influx in hTRPA1-expressing cells was blocked by RR (30 µM) and HC-030031 (100 µM), a specific antagonist of TRPA1. These results suggested that NGCC selectively activates TRPV1 and TRPA1 in cultured cells. These data may provide additional support for our previous hypothesis that NGCC interacts with TRPV1 variant cation channel, a putative amiloride/benzamil-insensitive salt taste pathway in the anterior taste receptive field.
Clinical, radiographic and HLA associations as markers for different patterns of psoriatic arthritis.

OBJECTIVE The aim of this study was to examine whether the five clinical forms of psoriatic arthritis (PsA) identified by Moll and Wright (Semin Arthritis Rheum 1973;3:55-78) could be clearly distinguished, especially as the disease evolved over time, to analyse whether radiographic features or HLA associations could define subsets with greater precision and to identify predictors of disease outcome. METHODS Seventy-three patients (37 males and 36 females) were followed for a median time of 8 yr (range 1-16 yr). A standard clinical protocol was used to assess patients at each visit and two clinical scores. based on the joint areas involved, were defined to evaluate the mode of onset and the evolution of arthritis. X-ray films of the hands, feet and sacroiliac joints were taken and the patients were divided into two categories according to the presence or absence of erosions and an X-ray erosion score was also used. Three classification methods were used to define the different clinical subsets. HLA-A, B and DR antigens were tested by standard microlymphocytotoxicity assays. A multiple linear regression model was used in the statistical analysis. RESULTS The five classical clinical subsets defined by Moll and Wright did not remain since distinct peripheral arthritis patterns tended to evolve over time. Only two discrete groups were identified, axial disease (AD) (sacroilitis with or without peripheral arthritis) in 29% of cases and peripheral disease (PD) without sacroilitis in 71%. AD was positively associated with the duration of arthritis (P < 0.04), presence of mutilation (P < 0.02) and the joint area score over disease evolution (JASE) (P < 0.02). There were erosions in 71% of the patients. Erosions correlated with the presence of mutilation (P < 0.007) and with the JASE (P < 0.0005). HLA-B27 was found in 43% of patients with AD, but only in 11% of PD patients (P < 0.01). No other clear HLA correlations were found. CONCLUSIONS Despite the relatively small number of patients, this longitudinal study suggests that only two clinical subsets can be clearly defined in PsA, AD and PD; these are primarily determined on clinical grounds although HLA-B27 is strongly associated with AD. The evolution of PD pattern with time means that narrower peripheral arthritis subsets are of little clinical use.
Pure type systems with explicit substitutions

Abstract We introduce a new formulation of pure type systems (PTSs) with explicit substitution and de Bruijn indices and formally prove some of its meta-theory. Using techniques based on Normalisation by Evaluation, we prove that untyped conversion can be typed for predicative PTSs. Although this equivalence was settled by Siles and Herbelin for the conventional presentation of PTSs, we strongly conjecture that our proof method can also be applied to PTSs with η.
Numb deficiency in cerebellar Purkinje cells impairs synaptic expression of metabotropic glutamate receptor and motor coordination

Significance Protein Numb controls cell fate by interacting with a number of signaling molecules, critical for maintaining neural stem cells and neuronal development in the central nervous system. However, the function of Numb has not been studied in mature neurons. Here, we found that deletion of Numb in cerebellar Purkinje cells causes deficits in motor learning, which can be ascribed to a reduced level of synaptic metabotropic glutamate 1 receptor (mGlu1). Although Numb deficiency does not alter the expression of mGlu1-associated proteins and activity-dependent plasticity of mGlu1, it inhibits intracellular trafficking of mGlu1. To our knowledge, our work is the first to demonstrate an important function of Numb in mature neurons. Protein Numb, first identified as a cell-fate determinant in Drosophila, has been shown to promote the development of neurites in mammals and to be cotransported with endocytic receptors in clathrin-coated vesicles in vitro. Nevertheless, its function in mature neurons has not yet been elucidated. Here we show that cerebellar Purkinje cells (PCs) express high levels of Numb during adulthood and that conditional deletion of Numb in PCs is sufficient to impair motor coordination despite maintenance of a normal cerebellar cyto-architecture. Numb proved to be critical for internalization and recycling of metabotropic glutamate 1 receptor (mGlu1) in PCs. A significant decrease of mGlu1 and an inhibition of long-term depression at the parallel fiber–PC synapse were observed in conditional Numb knockout mice. Indeed, the trafficking of mGlu1 induced by agonists was inhibited significantly in these mutants, but the expression of ionotropic glutamate receptor subunits and of mGlu1-associated proteins was not affected by the loss of Numb. Moreover, transient and persistent forms of mGlu1 plasticity were robustly induced in mutant PCs, suggesting that they do not require mGlu1 trafficking. Together, our data demonstrate that Numb is a regulator for constitutive expression and dynamic transport of mGlu1.
Nuclear morphometric findings in undetermined cytology: A possible clue for prediction of BRAF mutation in papillary thyroid carcinomas

ABSTRACT Purpose: To investigate the possible relationship between the nuclear morphometric characteristics (nuclear perimeter, roundness, nuclear area, and nuclear shape) and BRAF mutation status in papillary thyroid carcinoma cases with a prior diagnosis of undetermined cytology. Materials and methods: Total thyroidectomy specimens obtained from 48 patients with papillary thyroid carcinoma with a prior diagnosis of undetermined cytology were included. Morphometric analysis under light microscopy included measurements of the perimeter, shape factor, nuclear area, and roundness of thyrocyte nuclei from the cytological smear preparations. Mutational analysis, including immunohistochemistry and polymerase chain reaction, was performed in formalin fixed paraffin embedded tissue blocks. Results: BRAF V600E mutation was detected in 7 of 48 cases (14.5%). The nuclear perimeter and nuclear area in mutated cases were significantly higher than the wild type (p = 0.005). Shape factor (p = 0.681) and roundness (p = 0.752) values did not significantly differ between the wild-type and mutant groups. No significant relationship was evident between BRAF expression and BRAF point mutation. Conclusion: In cases with positivity for BRAF mutation, the nuclear perimeter and nuclear area were significantly increased. These findings suggest that morphometric variables are predictive markers for papillary thyroid carcinoma cases with positivity for BRAF mutation. However, further trials on larger series are warranted to understand the significance and predictive value of nuclear morphometric analysis in these circumstances.