Miracle-dz/UniFAR-FTUs huggingface dataset:
Establishment of a PF2D‐MS/MS platform for rapid profiling and semiquantitative analysis of membrane protein biomarkers

Current proteome profiling techniques have identified relatively few mammalian membrane proteins despite their numerous important functions. To establish a standard throughput‐potential profiling platform for membrane proteins, Triton X‐100‐solubilized rat liver microsomal proteins were separated on a 2‐D separation system (2‐D liquid phase fractionation (PF2D)) in two different pH ranges (4.0–8.5 and 7.0–10.5). This system produced 182 proteins with more than two transmembrane domain (TMD), including 16 TMDs with high confidence. Comparative 2‐D liquid maps with high resolution and reproducibility have been constructed for liver microsome from the phenobarbital (PB) treated rats. PF2D was also found to be useful for the semiquantification of some representative cytochrome P450 family proteins (e.g., cytochrome P450 2B2) that were induced by PB treatment compared with untreated controls. Thus, the combination of both high‐detection capacity and rapid preliminary semiquantification in a PF2D platform could become a standard system for the routine analysis of membrane proteins.
Enhancing Performance of GIS on Cloud Computing

Cloud computing provides a way of determining dynamically scalable and virtualized resources as a service over the Internet. GIS is a technology, which could use Cloud Computing for distributed parallel processing of a large set of data, store and share the results with users around the world. GIS is beneficial and works well when it be available to everyone, everywhere, anytime and with downcast fee of minimal sized in terms of technology and outlay. Cloud Computing used to portray and help users to use GIS applications in an easy way. This paper will study some example of a data structure like a K-d tree and Quad trees of GIS application and compare between them when storing these data structures on Cloud computing, the paper also portrays the results of the study of data structure on cloud computing platforms to retrieve data from cloud computing. The paper provides an application for “finding neighborhood from existing data stored.
Integration of Fibaro system to intruder and hold-up alarm systems

The Fibaro is a system for automation of smart households, which ensures not only the functions of comfort and power saving, but it also offers the security functions. These security functions were checked and examined in this paper from several perspectives. The evaluation of two submitted model realizations of Intruder and Hold-Up Alarm Systems (I&HAS) with using of the Fibaro system was presented: the Proprietary model, which works with manufacturers’ detectors, and the Integration model including the standard loop I&HAS to the Fibaro system. These comfort functions were examined in this paper from the point of view of the functional safety and fulfillment of the normative requirements for the I&HAS. The examination of functional reliability consisted of verification of the ability of the control unit to correctly respond to changes in detection conditions inducted through the relevant sensor. The functional tests were conducted in several steps. Thanks to the functional tests the unreliability of the control unit Fibaro HC Lite to register a larger number of detection messages had to be confirmed. The result of this work was the demonstration of inappropriateness of utilisation of installations according to the Proprietary model. Simultaneously the Integration model was evaluated from a point of view of valid norms with assigning of the first security level, however, the conditions unaffected the I&HAS.
Maturation‐Dependent Thiol Loss Increases Chondrocyte Susceptibility to Apoptosis

The major aim of the current investigation was to evaluate the role of thiols during chondrocyte maturation and apoptosis. Using a thiol‐sensitive fluorescent probe, we found that in chick growth plate chondrocytes, hypertrophy is accompanied by a decrease in the glutathione content. In this study, we show that the maturation‐dependent loss of thiol, although not causing death of maturing chondrocytes, drastically increases susceptibility to apoptosis by oxidative and nitrosoactive stress. To investigate how the loss of thiol content in cultured chondrocytes affects the expression of the hypertrophic phenotype, we chemically manipulated intracellular thiol levels and analyzed the expression of important maturation markers. We found that thiol depletion causes a decrease in the expression of osteopontin, type X and type II collagen and a significant loss of alkaline phosphatase activity, suggesting that the expression of the hypertrophic phenotype is tightly regulated by redox levels in chondrocytes. Furthermore, severe thiol depletion profoundly affected cell survival under oxidative and nitrosoactive stress. It was concluded that the loss of thiol reserve is not only linked to the expression of the hypertrophic phenotype but also influenced chondrocyte survival, linking chondrocyte maturation and the activation of the apoptotic pathway.
Ephrin b2 receptor and microsatellite status in lymph node-positive colon cancer survival.

BACKGROUND Ephrin B2 receptor (EphB2) is a target of the canonical wnt pathway implicated in colorectal carcinogenesis, and its down-regulation may be associated with adverse prognosis. We evaluated its prognostic value in resected colon cancer stratified by microsatellite status and other clinicopathologic characteristics. METHODS We identified all cases of resected stage III colon cancer from 1995 to 2009 managed in the Capital Health district of Nova Scotia. Tissue microarrays were constructed and immunohistochemistry (IHC) for tumor EphB2 staining assigned into quartiles. Microsatellite status was evaluated by IHC for MutL homolog 1 (MLH1) and MutS homolog 2 (MSH2). Microsatellite stable tumors were defined as both MLH1/MSH2 (+/+); tumors staining otherwise were classified with microsatellite instability (MSI-H). Primary and secondary outcomes were disease-free survival (DFS) and overall survival (OS), respectively. RESULTS We identified 159 cases with sufficient tissue for microarray analysis having a median follow-up of 3.47 years (range, 0.14-14). Median age was 61, 52% were male, 40% had an event, and 29% died. MSI-H was present in 18 (13%). Univariate analysis of EphB2 expression on DFS and OS showed a hazard ratio (HR) of 2.00 (P = .01) and 2.14 (P = .03), respectively. Multivariate analysis of EphB2 expression on DFS and OS showed an HR of 2.24 and 2.23, respectively, with tumor IHC ≤ 50%. CONCLUSIONS In this cohort, decreased EphB2 expression was an independent prognostic factor for recurrence and death and may have prognostic relevance in tumors with MSI-H. However, this would require prospective validation in a larger study.
THE REPUTATIONAL IMPACT OF CORPORATE GOVERNANCE: THE CASE OF POISON PILLS

This paper examines the reputational consequences of corporate governance arrangements and, in so doing, attempts to establish stronger linkages between the literatures on governance and corporate reputation. We first examine whether governance arrangements matter for overall firm reputation and then begin to address the question of how and why they might matter by exploring a number of different contingencies. We investigate these issues by considering how poison pills impacted the overall reputation of large corporations from 1985–1989, the time period when this practice gained prominence. Our results show that poison pills did indeed negatively affect the overall reputation of firms even after controlling for various measures of financial performance. In addition, we find that assessments of firm reputation differed somewhat depending on the characteristics of the firm (i.e., its relative visibility) and upon the reputation granting audience (executives vs. analysts). We also find evidence of temporal .
[German Acupuncture Trials (gerac) address problems of methodology associated with acupuncture studies].

OBJECTIVE Conflicting or ambivalent findings on the effectiveness of body acupuncture in pain treatment are often attributed to flaws in study methodology. The paper describes the methodology used for the German Acupuncture Trials (gerac), which demonstrates that it is possible to design acupuncture studies in accordance with the standards of good clinical practice. METHOD Approximately 1000 chronic pain sufferers per indication (migraine, tension-type headache, low back pain (cLBP), or gonarthrosis) are randomly allocated to one of three treatment groups (verum acupuncture, sham acupuncture, or established conservative therapy). Patients are blind to the type of acupuncture. All patients receive ten sessions of treatment (two per week) with an option of adding five more treatments in cases of slight but insufficient improvement (number of headache days or von Korff pain score). Participating physicians are in private practice, representing a variety of specialties. All have completed at least a 140-hour training course in acupuncture. Mandatory and optional verum and sham points are predefined. The point selection is individualized according to the criteria of traditional Chinese medicine (TCM). Primary outcome measures are number of headache days per month, von Korff Graded Chronic Pain Scale or Hannover Functional Ability Questionnaire (cLBP), or WOMAC scores (gonarthrosis). Data are assessed by trained telephone interviewers not involved in treatment and blind to types of acupuncture. PRESENT STATUS Over 500 participating physicians in ten urban areas of Germany. Patient recruitment for cLBP and gonarthrosis was completed in November 2003 and March 2004 respectively. Recruitment for chronic headaches will be completed in autumn 2004. CONCLUSIONS The gerac trials prove that it is possible to design and carry out acupuncture studies in accordance to stringent standards of methodology and clinical practice. The results will form a basis for the assessment of acupuncture effectiveness in Germany and abroad.
Frequency of Human Leukocyte Antigen-A 24 Alleles in Patients With Melanoma Determined by Human Leukocyte Antigen-A Sequence-Based Typing

The analysis of immune responses of patients with melanoma has led to the identification of melanoma-associated antigens targeted by T cells. Cytotoxic T lymphocytes recognize peptides from melanoma-associated antigens presented on the cancer cell surface in the context of HLA class I molecules. Immunodominant melanoma-associated antigen epitopes are being evaluated for their ability to immunize patients with advanced melanoma. However, these vaccination efforts are limited by the extensive polymorphism of the HLA class I heavy chain, which occurs in functional domains of the molecule. Patients with melanoma with the HLA-A-24 phenotype were recruited for vaccination with the peptide AFLPWHRLF from the melanoma-associated antigen tyrosinase. This peptide is recognized in association with HLA-A*2402. The HLA-A24 family includes at least 15 alleles whose frequency and ability to present the same peptide are unknown. The distribution of HLA-A24 alleles was studied in a melanoma population for the practical purpose of identifying patients suitable for vaccination with HLA-A*2402 epitopes. An HLA-A locus-specific polymerase chain reaction method followed by sequencing was developed to determine the HLA-A alleles in genomic DNA. HLA-A 24 was also typed in healthy persons of various ethnic backgrounds to further explore the HLA-A24 family. In white persons, the HLA-A*2402 allele was most common (in 85% of white persons and in 97% of the patients with melanoma). Fewer persons carried the HLA-A*2403 allele (13% in all samples, 3% in melanoma patients). Finally, two new alleles, HLA-A*2422 and HLA-A*24 null, were identified. These results suggest that vaccination with HLA-A*2402–associated epitopes has the potential for broad use in this patient population.
A specific secretion system mediates PPE41 transport in pathogenic mycobacteria

Mycobacterial genomes contain two unique gene families, the so‐called PE and PPE gene families, which are highly expanded in the pathogenic members of this genus. Here we report that one of the PPE proteins, i.e. PPE41, is secreted by pathogenic mycobacteria, both in culture and in infected macrophages. As PPE41 lacks a signal sequence a dedicated secretion system must be involved. A single gene was identified in Mycobacterium marinum that showed strongly reduced PPE41 secretion. This gene was located in a gene cluster whose predicted proteins encode components of an ESAT‐6‐like secretion system. This cluster, designated ESX‐5, is conserved in various pathogenic mycobacteria, but not in the saprophytic species Mycobacterium smegmatis. Therefore, different regions of this cluster were introduced in M. smegmatis. Only introduction of the complete ESX‐5 locus resulted in efficient secretion of heterologously expressed PPE41. This PPE secretion system is also involved in the virulence of pathogenic mycobacteria, as the ESX‐5 mutant of M. marinum was affected in spreading to uninfected macrophages.
How much ozone bactericidal activity is compromised by plasma components?

Aims: Evaluation of bactericidal effect of different concentrations of ozone when used (a) as a gas, or (b) dissolved in saline. The addition of hydrogen peroxide or 4‐hydroxynonenal dissolved in saline was also tested, as well as the effect of human plasma.
Study on the Influence Path of Brand Virtual Community Interaction on Customer Loyalty

Virtual brand community is developed based on network technology and has become the theoretical and academic research focus. Interaction in the virtual brand community has a major impact on customer loyalty. This paper studied the impact mechanism on the impacts of the network interaction in virtual community on customer loyalty. The results revealed that the different dimensions, including the two-way communication, customer participation and cooperation of interaction in virtual brand community, have a significant positive relationship with customer perceived value. Then, customer perceived value positively affected trust and customer loyalty and trust had a significant positive impact on customer loyalty.
Conditional Bursting Enhances Resonant Firing in Neocortical Layer 2–3 Pyramidal Neurons

The frequency response properties of neurons are critical for signal transmission and control of network oscillations. At subthreshold membrane potential, some neurons show resonance caused by voltage-gated channels. During action potential firing, resonance of the spike output may arise from subthreshold mechanisms and/or spike-dependent currents that cause afterhyperpolarizations (AHPs) and afterdepolarizations (ADPs). Layer 2–3 pyramidal neurons (L2–3 PNs) have a fast ADP that can trigger bursts. The present study investigated what stimuli elicit bursting in these cells and whether bursts transmit specific frequency components of the synaptic input, leading to resonance at particular frequencies. We found that two-spike bursts are triggered by step onsets, sine waves in two frequency bands, and noise. Using noise adjusted to elicit firing at ∼10 Hz, we measured the gain for modulation of the time-varying firing rate as a function of stimulus frequency, finding a primary peak (7–16 Hz) and a high-frequency resonance (250–450 Hz). Gain was also measured separately for single and burst spikes. For a given spike rate, bursts provided higher gain at the primary peak and lower gain at intermediate frequencies, sharpening the high-frequency resonance. Suppression of bursting using automated current feedback weakened the primary and high-frequency resonances. The primary resonance was also influenced by the SK channel-mediated medium AHP (mAHP), because the SK blocker apamin reduced the sharpness of the primary peak. Our results suggest that resonance in L2–3 PNs depends on burst firing and the mAHP. Bursting enhances resonance in two distinct frequency bands.
Requirement of the Nitrogen Starvation-Induced Protein Sll0783 for Polyhydroxybutyrate Accumulation in Synechocystis sp. Strain PCC 6803

ABSTRACT Nitrogen is often a limiting nutrient in natural habitats. Therefore, cyanobacteria have developed multiple responses, which are controlled by transcription factor NtcA and the PII-signaling protein, to adapt to nitrogen deficiency. Transcriptional analyses of Synechocystis sp. strain PCC 6803 under nitrogen-deficient conditions revealed a highly induced gene (sll0783) which is annotated as encoding a conserved protein with an unknown function. This gene is part of a cluster of seven genes and has potential NtcA-binding sites in the upstream region. Homologues of this cluster occur in some unicellular, nondiazotrophic cyanobacteria and in several Alpha, Beta-, and Gammaproteobacteria, as well as in some Gram-positive bacteria. Most of the heterotrophic bacteria harboring this gene cluster are able to fix nitrogen and to produce polyhydroxybutyrate (PHB), whereas of the cyanobacteria, only Synechocystis sp. strain PCC 6803 can accumulate PHB. In this work, a Synechocystis sp. strain PCC 6803 sll0783 gene knockout mutant is characterized. This mutant is unable to accumulate PHB, a carbon and energy storage compound. In contrast, the levels of the carbon storage compound glycogen and the PHB precursor acetyl coenzyme A were similar to those of the wild type, indicating that the PHB-deficient phenotype does not likely result from a global deficiency in carbon metabolism. A specific deficiency in PHB synthesis was implied by the fact that the mutant exhibits impaired PHB synthase activity during prolonged nitrogen starvation. However, the expression of PHB synthase-encoding genes was not strongly affected in the mutant, suggesting that the impaired PHB synthase activity observed depends on a posttranscriptional process in which the product of sll0783 is involved.
A Method of Profiling Microbial Communities Based on a Most-Probable-Number Assay That Uses BIOLOG Plates and Multiple Sole Carbon Sources

ABSTRACT A new approach to the community-level BIOLOG assay was proposed. This assay, which we call the BIOLOG-MPN assay, is a most-probable-number (MPN) assay that uses BIOLOG plates and multiple sole carbon sources, and the profiles obtained by this assay consist of MPNs estimated for the substrates in the BIOLOG plates. In order to demonstrate the performance of the BIOLOG-MPN assay, it was applied to pure cultures, model bacterial communities that contain two strains in different ratios, and microbial community samples. MPN estimation using BIOLOG plates worked well for the substrates on which utilizers can grow at a sufficiently high rate for color development under the conditions of the assay procedure. Furthermore, the results obtained using model communities showed that the MPNs obtained reflected the mixing ratios of pure cultures in the model communities. The profiles obtained using model communities and community samples were differentiated properly by statistical analyses. The results suggest that the BIOLOG-MPN assay is a promising procedure for obtaining a quantitative picture of the community structure.
Crystalline phase and orientation control of manganese nitride grown on MgO(001) by molecular beam epitaxy

The phase and orientation of manganese nitride grown on MgO(001) using molecular beam epitaxy are shown to be controllable by the manganese/nitrogen flux ratio as well as the substrate temperature. The most N-rich phase, θ phase (MnN), is obtained at very low Mn/N flux ratio. At increased Mn/N flux ratio, the next most N-rich phase, the η phase (Mn3N2), is obtained having its c axis normal to the surface plane. Further increasing the Mn/N flux ratio, the η phase (Mn3N2) having its c axis in the surface plane is obtained. Finally, the e phase (Mn4N) is obtained at yet higher Mn/N flux ratio. The structural phase variation with Mn/N flux ratio is due to the kinetic control of the surface chemical composition, which determines the energetically most favorable phase. For a given Mn/N flux ratio, the phase is also found to be a function of the substrate temperature, with the less N-rich phase occurring at the higher substrate temperature. The change of phase with temperature is attributed to the change in the .
Human round spermatids from azoospermic men exhibit oocyte-activation and Ca2+ oscillation-inducing activities

Summary During mammalian fertilization, intracellular Ca2+ oscillations are important for both oocyte activation and embryonic development. As the ability of round spermatids (ROS) to induce Ca2+ oscillations and oocyte activation is different between species, we examined Ca2+ oscillation- and oocyte activation-inducing abilities of human ROS originating from patients with non-obstructive azoospermia. Human ROS from 11 non-obstructive azoospermic patients were collected during their TESE–ICSI cycles. Following injection into mature unfertilized mouse oocytes, we examined the oocyte-activating and Ca2+ oscillation-inducing activities of ROS by using Ca2+ imaging and confocal laser scanning microscopy (mouse test). In these 11 cases, clinical TESE–ICSI using mature testicular spermatozoa was successful, with the exception of one case in which only one sperm-injected oocyte was not fertilized. The mean fertilization rate was 70.1% (40–100%); the mean cleavage rate was 97.9% (46/47). Two pregnancies were established from 10 transfer cycles (PR; 20%). When the ROS from these patients were injected into mouse oocytes, the ROS from all patients induced at least some intracellular Ca2+ oscillations (25–100%). In all patients, 40 out of 82 oocytes injected with ROS exhibited normal oscillation patterns of [Ca2+]i. Human spermatogenetic cells acquired oocyte-activating and Ca2+ oscillation-inducing abilities at the round spermatid stage, an earlier stage than found for rodent cells. These data indicate that human ROS might be useful for clinical treatments of non-obstructive azoospermic patients exhibiting mature spermatozoa in biopsied specimens.
Lactic acidosis not hyperlactatemia as a predictor of inhospital mortality in septic emergency patients

Objective: To compare the prognostic abilities of lactic acidosis and hyperlactatemia and determine the influence of metabolic acidosis when attempting to predict the outcome of septic patients using serum lactate levels. Method: 126 patients with severe sepsis or septic shock were prospectively included in this study at an emergency department. Haemodynamic variables, simplified acute physiology score (SAPS) II, arterial blood gas studies and serum lactate levels were obtained at the time of presentation (0 h) and 4 h after presentation. The probability of mortality was calculated using SAPS II scores and compared with actual inhospital mortality at different serum lactate levels and arterial pH. Survival curves for lactic acidosis and severe hyperlactatemia were analysed using the Kaplan–Meier method. Results: The calculated probability of mortality decreased from 35.7% (95% CI 30.2 to 41.2) at presentation to 29.3% (95% CI 24.2 to 34.4) at 4 h post-presentation. 27.0% of patients (34) died in hospital. Arterial pH and SAPS II scores were independent factors for predicting mortality of septic patients, at 0 h and 4 h. Serum lactate levels were closely related to severity of illness and metabolic acidosis in septic patients. Patients with lactic acidosis had significantly higher inhospital mortality than patients with normal pH and normal lactate levels by Kaplan–Meier survival analysis as determined based on measurements made at 0 h and 4 h (p<0.001, p<0.001 by the log-rank test, respectively). No significant difference in survival was found between patients with hyperlactatemia and those with normal pH and serum lactate levels. Conclusion: Lactic acidosis not hyperlactatemia was found to predict inhospital mortality more exactly in severe sepsis and septic shock patients. The acid-base state should be considered when attempting to predict the outcome of septic patients using serum lactate levels.