Miracle-dz/UniFAR-FTUs huggingface dataset:
Atomistic and Molecular Effects on the Surface Morphology and Film Conformation of Perfluoropolyether Lubricant Layer

In this paper, we analyzed atomistic and molecular architectural effects on the film microstructure and morphological properties for the monolayer perfluoropolyether (PFPE) lubricant film by investigating PFPEs with different molecular structures and functionalities (Zdol, Ztetraol, Ztetraol multidentate, and TA-30) via large-scale coarse-grained bead-spring molecular dynamics originating from the atomistic theory. Film surface morphology was examined by average height and root mean square roughness, and the internal clusters of functional groups on the surface were characterized by the radial distribution function of functional groups, followed by the quantitative estimation of adhesion ratio and coordination number. We also illustrate the effects of molecular structure on the film conformation, which is useful to molecular design criteria for the head-disk interface.
PKC alpha protein but not kinase activity is critical for glioma cell proliferation and survival

Protein kinase C alpha (PKCα) has been implicated in tumor development with high levels of PKCα expression being associated with various malignancies including glioblastomas and tumors of the breast and prostate. To account for its upregulation in these cancers, studies have suggested that PKCα plays a role in promoting cell survival. Here we show by siRNA depletion in U87MG glioma cells that a critical threshold level of PKCα protein expression is essential for their growth in the presence of serum and for their survival following serum deprivation. Derivation of PKCα wt and KO mouse embryo fibroblast cell lines confirms a role for PKCα in protecting cells from apoptosis induced by serum deprivation. Notably, PKCα was found to mediate chemo‐protection in these fibroblastic cell lines. In U87MG cells PKCα does not confer chemoprotection though this likely reflects growth arrest associated with its depletion. To determine the requirements for catalytic function, comparison was made between distinct classes of PKC inhibitors. In contrast to loss of PKCα protein, inhibition of PKC kinase activity in glioma cell lines does not significantly inhibit growth or survival. Conversely, inhibition with calphostin C, which targets the regulatory domain of PKC, potently inhibits proliferation and induces apoptosis. Evidence is presented that it is the fully phosphorylated, folded form of PKCα that confers this activity‐independent behaviour. These results indicate an essential pro‐proliferative and pro‐survival role for PKCα in glioma but question the use of ATP competitive inhibitors as therapeutics, either alone, or in combination with chemotoxic agents. © 2008 Wiley‐Liss, Inc.
Gene profiling techniques and their application in angiogenesis and vascular development

The analysis of gene expression in specific tissues and physiological processes has evolved over the last 20 years from the painstaking identification of selected genes to the relatively efficient and open‐ended surveying of potentially all genes expressed in a tissue. Current art for gene discovery includes the use of large‐scale arrays of cDNA sequences or oligonucleotides, and molecular ‘tagging’ techniques such as GeneCalling and SAGE. Common to each of these techniques is a reliance on the increasingly comprehensive databases of human and mouse EST and full‐length gene sequences. Early efforts to characterize candidate genes were limited by their narrow scope, while current efforts are confounded by the enormous volume of data returned. Sophisticated software tools are an integral part of the analysis, helping to organize information into coherent groups with temporal or functional similarity. These techniques, in conjunction with the continued analysis of human genetic syndromes, transgenic, and knockout mice, have driven genetic analysis of angiogenesis and vascular development from describing which individual genes are involved to defining the outlines of regulatory networks. Copyright © 2001 John Wiley & Sons, Ltd.
Chromatin-Associated Genes Protect the Yeast Genome From Ty1 Insertional Mutagenesis

Chromosomal genes modulate Ty retrotransposon movement in the genome of Saccharomyces cerevisiae. We have screened a collection of 4739 deletion mutants to identify those that increase Ty1 mobility (Ty1 restriction genes). Among the 91 identified mutants, 80% encode products involved in nuclear processes such as chromatin structure and function, DNA repair and recombination, and transcription. However, bioinformatic analyses encompassing additional Ty1 and Ty3 screens indicate that 264 unique genes involved in a variety of biological processes affect Ty mobility in yeast. Further characterization of 33 of the mutants identified here show that Ty1 RNA levels increase in 5 mutants and the rest affect mobility post-transcriptionally. RNA and cDNA levels remain unchanged in mutants defective in transcription elongation, including ckb2Δ and elf1Δ, suggesting that Ty1 integration may be more efficient in these strains. Insertion-site preference at the CAN1 locus requires Ty1 restriction genes involved in histone H2B ubiquitination by Paf complex subunit genes, as well as BRE1 and RAD6, histone H3 acetylation by RTT109 and ASF1, and transcription elongation by SPT5. Our results indicate that multiple pathways restrict Ty1 mobility and histone modifications may protect coding regions from insertional mutagenesis.
Whole Body Bone, Fat, and Lean Mass in Black and White Men

This research describes the effects of age, ethnicity, and body size and composition on whole body bone mass and bone density in healthy black and white men. We measured 79 male subjects, 42 white and 37 black, ranging in age from 33 to 64 years. Whole body bone mineral content (WBBMC) and bone mineral density (WBBMD), as well as fat and lean mass, were evaluated with a Hologic 1000W bone densitometer. We explore the utility of different methods of controlling for variations in body size in the two ethnic groups. There are statistically significant ethnic differences only in the bone mass variables. The black men had a 15% higher WBBMC (3111 vs. 2712 g, p < 0.0001) and a 8% higher WBBMD (1.25 vs. 1.16 g/cm2, p = 0.001) than the white men. Dividing WBBMD by height reduced the black/white difference to 6%. WBBMC, WBBMC/height, and WBBMD are strongly and significantly correlated with weight, body mass index (BMI), and body composition; correlations tended to be lower for WBBMD/height. Age is not significantly correlated with any of the variables in either ethnic group (p ≥ 0.10). In multivariate linear regression models for predicting WBBMC or WBBMD, the two best models contained height, weight, and an interaction of ethnicity and weight (model r2 = 0.72 for WBBMC and r2 = 0.47 for WBBMD); and height, lean mass, and an ethnicity–fat interaction (model r2 = 0.69 for WBBMC and r2 = 0.46 for WBBMD). Using analysis of covariance, we found that controlling for lean mass and height reduced the black/white difference in bone mass from 14.7 to 9.8%.
Red blood cell deformability and aggregation in chronic venous disease patients with varicose veins.

INTRODUCTION Red blood cells' (RBC) rheological properties are disturbed in chronic venous disease (CVD). The aim of the study was to compare deformability and aggregation of erythrocytes taken from the varicose vein and the antecubital vein of patients with chronic venous disease. MATERIALS AND METHODS Blood samples were taken from twelve CVD patients presenting clinical, aetiological, anatomical and pathological elements (CEAP) stages II and III. Blood was sampled from varicose veins and antecubital veins of patients (as control). Deformability and aggregation of RBC were analysed with a Laser-assisted Optical Rotational Cell Analyser (LORCA). RESULTS A significant increase in deformability was found in varicose vein RBC for shear stress values 4.24, 8.23 and 15.96 Pa as compared to RBC from the antecubital vein. The aggregation index was significantly lower and aggregation halftime was significantly increased for RBC taken from antecubital veins than for RBC from varicose veins. DISCUSSION In conclusion, RBC taken from varicose and antecubital veins of CVD patients are not entirely rheologically comparable and show different deformability and aggregation. Varicose vein RBC are more deformable and show a higher tendency for aggregation than antecubital vein RBC. Perhaps the deformability of varicose vein RBC has been increased as a compensation mechanism in subjects with CVD, due to increased resistance in their microcirculation.
The role of dynamic contrast-enhanced MRI in differentiation of local recurrence and residual soft-tissue tumor versus post-treatment changes.

OBJECTIVES To evaluate the reliability of dynamic contrast-enhanced MRI in the diagnosis of local recurrence of malignant soft-tissue tumors after receiving treatment. METHODS From March 2002 till December 2009 we performed dynamic contrast enhanced MRI in 95 patients with soft-tissue tumor after receiving treatment (surgery, radiotherapy, chemotherapy). Patients were classified according to five types of TIC. RESULTS The recurrent disease was suspected in 47 patients and the biopsy was recommended. In 8 cases (TIC II), the biopsy was performed due to long-term post-treatment changes. Histological results proved STT recurrence in 45 patients; in 10 patients (8 with TIC II), biopsy revealed hypervascular granulation tissue, florid inflammation and reactive changes. The sensitivity for dynamic contrast-enhanced MR examination was 100 %, specificity 80 %, positive predictive value (PPV) 95.7 % and negative predictive value (NPV) 100 %. CONCLUSION Our results indicate that TICs III, IV and V raise high suspicion of local tumor recurrence and require percutaneous imaging-guided biopsy. TIC of type II usually represents a pseudomass and the biopsy should be performed only in selected cases with increased risk of recurrent disease based on multidisciplinary approach. On the basis of literature review as well as our experiences we created a reliable algorithm proposed for diagnosing the residual or recurrent soft-tissue tumors (Tab. 2, Fig. 6, Ref. 20).
Endoreplication: A Molecular Trick during Animal Neuron Evolution

The occurrence of endoreplication has been repeatedly reported in many organisms, including protists, plants, worms, arthropods, molluscs, fishes, and mammals. As a general rule, cells possessing endoreplicated genomes are largesized and highly metabolically active. Endoreplication has not been frequently reported in neuronal cells that are typically considered to be fully differentiated and nondividing, and which normally contain a diploid genome. Despite this general statement, various papers indicate that giant neurons in molluscs, as well as supramedullary and hypothalamic magnocellular neurons in fishes, contain DNA amounts larger than 2C. In order to study this issue in greater detail here, we review the available data about endoreplication in invertebrate and vertebrate neurons, and discuss its possible functional significance. As a whole, endoreplication seems to be a sort of molecular trick used by neurons in response to the high functional demands that they experience during evolution.
A novel 2L-Y DC-DC converter topologies for high conversion ratio renewable application

The projected 2L-Y DC-DC Converter topologies are new members of the XY converter family. The 2L-Y converter is a combination of two single stage converters consisting, one is 2L converter and another is Y converter. Based on the configuration of Y converter four new topologies called a 2L-LVD converter, 2L-2LVD converter, 2L-2LCVD converter and 2L-2LCmVD converter are derived, discussed and analyzed in this paper. Due to higher conversion ratio capability of the proposed 2L-Y converter, it provides a workable solution for photovoltaic and electrical drive applications. The striking features of 2L-Y converter topologies are only one controlled device, negative output, Transformer-less topology, compact structure and having a minimum internal resistance. The proposed 2L-Y converters are simulated into MATLAB and simulation results are confirmed the theoretical analysis.
Predictors of future falls in Parkinson disease

Background: Falls are a major health and injury problem for people with Parkinson disease (PD). Despite the severe consequences of falls, a major unresolved issue is the identification of factors that predict the risk of falls in individual patients with PD. The primary aim of this study was to prospectively determine an optimal combination of functional and disease-specific tests to predict falls in individuals with PD. Methods: A total of 101 people with early-stage PD undertook a battery of neurologic and functional tests in their optimally medicated state. The tests included Tinetti, Berg, Timed Up and Go, Functional Reach, and the Physiological Profile Assessment of Falls Risk; the latter assessment includes physiologic tests of visual function, proprioception, strength, cutaneous sensitivity, reaction time, and postural sway. Falls were recorded prospectively over 6 months. Results: Forty-eight percent of participants reported a fall and 24% more than 1 fall. In the multivariate model, a combination of the Unified Parkinson's Disease Rating Scale (UPDRS) total score, total freezing of gait score, occurrence of symptomatic postural orthostasis, Tinetti total score, and extent of postural sway in the anterior-posterior direction produced the best sensitivity (78%) and specificity (84%) for predicting falls. From the UPDRS items, only the rapid alternating task category was an independent predictor of falls. Reduced peripheral sensation and knee extension strength in fallers contributed to increased postural instability. Conclusions: Falls are a significant problem in optimally medicated early-stage PD. A combination of both disease-specific and balance- and mobility-related measures can accurately predict falls in individuals with PD.
Analysis and clinical findings of cases positive for the novel synthetic cannabinoid receptor agonist MDMB-CHMICA

Abstract Context: MDMB-CHMICA is a synthetic cannabinoid receptor agonist which has caused concern due to its presence in cases of adverse reaction and death. Method: 43 cases of suspected synthetic cannabinoid ingestion were identified from patients presenting at an Emergency Department and from post-mortem casework. These were subjected to liquid-liquid extraction using tertiary-butyl methyl ether and quantitatively analysed by Electrospray Ionisation Liquid Chromatography–tandem Mass Spectrometry. For positive samples, case and clinical details were sought and interrogated. Results: 11 samples were found positive for MDMB-CHMICA. Concentrations found ranged from <1 to 22 ng/mL (mean: 6 ng/mL, median: 3 ng/mL). The age range was 15–44 years (mean: 26 years, median: 21 years), with the majority (82%) of positive results found in males. Clinical presentations included hypothermia, hypoglycaemia, syncope, recurrent vomiting, altered mental state and serotonin toxicity, with corresponding concentrations of MDMB-CHMICA as low as <1 ng/mL. Duration of hospitalisation ranged from 3 to 24 h (mean: 12 h, median: 8 h). Discussion: The concentration range presented in this case series is indicative of MDMB-CHMICA having a high potency, as is known to be the case for other synthetic cannabinoid receptor agonists. The age range and gender representation were consistent with that reported for users of other drugs of this type. The clinical presentations observed were typical of synthetic cannabinoid receptor agonists and show the difficulties in identifying reactions potentially associated with drugs of this type. Conclusion: The range of MDMB-CHMICA concentrations in Emergency Department presentations (n = 9) and post-mortem cases (n = 2) was reported. No correlation between the concentration of this drug and clinical presentation or cause of death was reported in this sample. However, the potential for harm associated with low concentrations of MDMB-CHMICA and the symptoms of toxicity being non-specific were highlighted.
Information retrieval from large number of Web sites

Many Web information retrieval methods are related to special Web sites, for example, the method based on extracting rules and the one based on training page samples. These methods can do well in a Web site but fail in the others without adding new rules or inputting new training pages manually. Furthermore, if the template of the Web site is changed, it has to redesign the extracting rules or re-inputting the training pages. It is hard to be maintained and used to extract information from large number of different Web sites. In the paper, there is a new method that is based on the keywords of a certain topic, instead of rules and training pages. Experimental evaluation on a large of Web pages from different Web sites indicates that this method correctly and automatically extracts the information ignoring which Web sites the pages come from. This method has been applied to the system of intelligent searching and mining of electronic business successfully.
The tumorigenicity of diploid and aneuploid human pluripotent stem cells

Human embryonic stem cells (HESCs) and induced pluripotent stem cells (HiPSCs) offer an immense potential as a source of cells for regenerative medicine. However, the ability of undifferentiated HESCs to produce tumors in vivo presents a major obstacle for the translation of this potential into clinical reality. Therefore, characterizing the nature of HESC-derived tumors, especially their malignant potential, is extremely important in order to evaluate the risk involved in their clinical use. Here we review recent observations on the tumorigenicity of human pluripotent stem cells. We argue that diploid, early passage, HESCs produce benign teratomas without undergoing genetic modifications. Conversely, HESCs that acquired genetic or epigenetic changes upon adaptation to in vitro culture can produce malignant teratocarcinomas. We discuss the molecular mechanisms of HESC tumorigenicity and suggest approaches to prevent tumor formation from these cells. We also discuss the differences in the tumorigenicity between mouse embryonic stem cells (MESCs) and HESCs, and suggest methodologies that may help to identify cellular markers for culture adapted HESCs.
A platform for electrical capacitance tomography large-scale benchmark dataset generating and image reconstruction

A platform for electrical capacitance tomography benchmark dataset generating and image reconstruction is presented. The platform is established on MATLAB with a GUI, and works with 2-dimensional models built on the Unite element analysis software COMSOL Multiphysics. The generated dataset currently consists of 37850 data samples, in which sample contains a capacitance vector and its corresponding permittivity distribution. Data pattern and PCA analysis are also preliminarily carried out on the current dataset.
Recommendation strategy using expanded neighbor collaborative filtering

The evaluation of recommender system is often biased towards accuracy, which is hard to balance all participants' interests. In this paper, a novel recommendation strategy using expanded neighbor collaborative filtering (ECF) is presented. Different from the standard collaborative filtering (CF), this recommendation strategy takes into account the second-order neighbors, which are expected to contribute to the coverage and diversity of recommendation. A transferring similarity is proposed to link the given user with second-order neighbors via nearest neighbors. Based on MovieLens dataset, the strategy was test on several typical similarity indexes. The numerical results confirmed the improvements on coverage and diversity compared to the benchmark CF, without affecting accuracy obviously.
Let them fly or light them up: matrix‐assisted laser desorption/ionization time of flight (MALDI‐TOF) mass spectrometry and fluorescence in situ hybridization (FISH)

This review focuses on clinical bacteriology and by and large does not cover the detection of fungi, viruses or parasites. It discusses two completely different but complementary approaches that may either supplement or replace classic culture‐based bacteriology. The latter view may appear provocative in the light of the actual market penetration of molecular genetic testing in clinical bacteriology. Despite its elegance, high specificity and sensitivity, molecular genetic diagnostics has not yet reached the majority of clinical laboratories. The reasons for this are manifold: Many microbiologists and medical technologists are more familiar with classical microbiological methods than with molecular biology techniques. Culture‐based methods still represent the work horse of everyday routine. The number of available FDA‐approved molecular genetic tests is limited and external quality control is still under development. Finally, it appears difficult to incorporate genetic testing in the routine laboratory setting due to the limited number of samples received or the lack of appropriate resources. However, financial and time constraints, particularly in hospitals as a consequence of budget cuts and reduced length of stay, lead to a demand for significantly shorter turnaround times that cannot be met by culture‐dependent diagnosis. As a consequence, smaller laboratories that do not have the technical and personal equipment required for molecular genetic amplification techniques may adopt alternative methods such as fluorescence in situ hybridization (FISH) that combines easy‐to‐perform molecular hybridization with microscopy, a technique familiar to every microbiologist. FISH is hence one of the technologies presented here. For large hospital or reference laboratories with a high sample volume requiring massive parallel high‐throughput testing we discuss matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF) of nucleic acids, a technology that has evolved from the post‐genome sequencing era, for high‐throughput sequence variation analysis (1, 2).
Arabidopsis μ-adaptin subunit AP1M of adaptor protein complex 1 mediates late secretory and vacuolar traffic and is required for growth

Adaptor protein (AP) complexes are the predominant coat proteins of membrane vesicles in post-Golgi trafficking of mammalian cells. Each AP complex contains a specific medium subunit, μ-adaptin, that selects cargo proteins bearing sequence-specific sorting motifs. Much less is known about the AP complexes and their μ subunits in plants. Because of uncertain homology, the μ-adaptins of Arabidopsis have been designated muA through muD [Happel et al. (2004) Plant J 37(5):678–693]. Furthermore, only muD has been assigned to a specific AP complex, AP-3, involved in Golgi-vacuolar trafficking [Niihama et al. (2009) Plant Cell Physiol 50(12):2057–2068, Zwiewka et al. (2011) Cell Res 21(12):1711–1722, and Wolfenstetter et al. (2012) Plant Cell 24(1):215–232]. In contrast, the μ subunit of neither the post-Golgi trafficking AP-1 complex nor the endocytic AP-2 complex has been identified. Here, we report the functional analysis of redundant AP-1 μ-adaptins AP1M1 (also known as muB1) and AP1M2 (also known as muB2). Coimmunoprecipitation revealed that both AP1M2 and its less strongly expressed isoform AP1M1 are complexed with the large subunit γ-adaptin of AP-1. In addition, AP1M2 was localized at or near the trans-Golgi network. Knockout mutations of AP1M2 impaired pollen function and arrested plant growth whereas the ap1m1 ap1m2 double mutant was nearly pollen-lethal. At the cellular level, the absence of AP1M2 entailed inhibition of multiple trafficking pathways from the trans-Golgi network to the vacuole and to the plasma membrane in interphase and to the plane of cell division in cytokinesis. Thus, AP-1 is crucial in post-Golgi trafficking in plant cells and required for cell division and plant growth.