Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathophysiology of Endometriosis: Role of High Mobility Group Box-1 and Toll-Like Receptor 4 Developing Inflammation in Endometrium

Oxidative stress has been proposed as a potential factor associated with the establishment and progression of endometriosis. Although a few studies have shown possible mechanisms which may play roles in development, progression of endometriosis, few are known in regards of initiation of the disease, especially in the relationship with endometrium. The aim of our study was to investigate whether normal endometrium may be changed by Damage-associated molecular patterns (DAMPs), which may contribute developing pathologic endometrium to induce endometriosis. Endometrial tissues were obtained from 10 patients with fibroids undergoing hysterectomy at a university hospital. High mobility group box-1 (HMGB-1), which is a representative DAMP, has been chosen that may induce alteration in endometrium. In preceding immunohistochemistry experiments using paraffin-block sections from endometriosis (N = 33) and control (N = 27) group, retrospectively, HMGB-1 expression was shown in both epithelial and stromal cell. HMGB-1 expression was significantly increased in secretory phase of endometriosis group, comparing to the controls. To examine the alteration of endometrial stromal cell (HESC) by oxidative stress in terms of HMGB-1, cell proliferation and expression of its receptor, TLR4 was measured according to recombinant HMGB-1 use. Cell proliferation was assessed by CCK-8 assay; real-time PCR and western blotting were used to quantify Toll like receptor 4 (TLR4) mRNA and protein expression respectively. A TLR4 antagonist (LPS-RS) and an inhibitor of the NF-κB pathway (TPCA-1, an IKK-2 inhibitor) were used to confirm the relationships between HMGB-1, TLR4, and the NF-κB pathway. Passive release of HMGB-1 was significantly proportional to the increase in cell death (P<0.05). HESCs showed significant proliferation following treatment with rHMGB-1 (P<0.05), and increased TLR4 expression was observed following rHMGB-1 treatment (P<0.05) in a concentration-dependent manner. Treatment with a TLR4 antagonist and an NF-κB inhibitor resulted in suppression of rHMGB-1-induced HESC proliferation (P<0.05). Levels of IL-6 were significantly decreased following treatment with an NF-κB inhibitor (P<0.05). Our results support the development of altered, pathological endometrium resulted from oxidative stress in normal endometrium. These findings may provide important insights into the changes in endometrium linking the development and progression of endometriosis.
Participation of the molecular chaperone DnaK in intracellular growth of Brucella suis within U937‐derived phagocytes

In the intracellular bacterium Brucella suis, the molecular chaperone DnaK was induced under heat‐shock conditions and at low pH. Insertional inactivation of dnaK and dnaJ within the dnaK/J locus led to the conclusion that DnaK, but not DnaJ, was required for growth at 37°C in vitro. Viability of the dnaK null mutant was also greatly affected at low pH. Under conditions allowing intracellular multiplication, the infection of U937‐derived phagocytes resulted in long‐lasting DnaK induction in the wild‐type bacteria. In infection experiments performed with both mutants at the reduced temperature of 30°C, the dnaK mutant of B. suis survived but failed to multiply within U937 cells, whereas the wild‐type strain and the dnaJ mutant multiplied normally. Complementation of the dnaK mutant with the cloned dnaK gene restored growth at 37°C, increased resistance to acid pH, and increased intracellular multiplication. This is the first report of the effects of dnaK inactivation in a pathogenic species, and of the temperature‐independent contribution of DnaK to intracellular multiplication of the pathogen B. suis.
Cost of hospitalization for and risk factors associated with vancomycin-resistant Enterococcus faecium infection and colonization.

The increase in costs of hospitalization for patients with drug-resistant infection may be associated with drug resistance itself or with the severity of the underlying illness that predisposes patients to acquire the drug-resistant infection. To address this issue, risk factors and cost of hospitalization were compared for patients infected or colonized with vancomycin-susceptible Enterococcus faecium (VSEF) or vancomycin-resistant E. faecium (VREF) in a large tertiary-care hospital in New York City. From January 1995 through December 1996, 157 patients with VSEF and 262 patients with VREF were identified. CMI (case-mix index) was assigned to each patient as a measure of severity of illness, with a CMI of 1 considered to represent illness of average severity. For all patients who were assigned a CMI of <3, the cost per day of hospitalization for patients with VREF was significantly greater than that for patients with VSEF. However, for patients with a CMI of >3, there was no difference between cost of hospitalization for patients with VREF and that for patients with VSEF. These observations indicate that, although vancomycin resistance is associated with an increased cost of hospitalization for less severely ill patients with VREF, patients with severe underlying illness, regardless of vancomycin resistance, incur similar hospitalization costs.
Manufacturing plant location selection in logistics network using Analytic Hierarchy Process

Purpose: In recent years, numerous companies have moved their manufacturing plants to China to capitalize on lower cost and tax. Plant location has such an impact on cost, stocks, and logistics network but location selection in the company is usually based on subjective preference of high ranking managers. Such a decision-making process might result in selecting a location with a lower fixed cost but a higher operational cost. Therefore, this research adapts real data from an electronics company to develop a framework that incorporates both quantitative and qualitative factors for selecting new plant locations. Design/methodology/approach: In-depth interviews were conducted with 12 high rank managers (7 of them are department manager, 2 of them are vice-president, 1 of them is senior engineer, and 2 of them are plant manager) in the departments of construction, finance, planning, production, and warehouse to determine the important factors. A questionnaire survey is then conducted for comparing factors which are analyzed using the Analytic Hierarchy Process (AHP). Findings: Results show that the best location chosen by the developed framework coincides well with the company’s primal production base. The results have been presented to the company’s high ranking managers for realizing the accuracy of the framework. Positive responses of the managers indicate usefulness of implementing the proposed model into reality, which adds to the value of this research. Practical implications: The proposed framework can save numerous time-consuming meetings called to compromise opinions and conflictions from different departments in location selection. Originality/value: This paper adapts the Analytic Hierarchy Process (AHP) to incorporate quantitative and qualitative factors which are obtained through in-depth interviews with high rank managers in a company into the location decision.
Approximate inference techniques with expectation constraints

This paper discusses inference problems in probabilistic graphical models that often occur in a machine learning setting. In particular it presents a unified view of several recently proposed approximation schemes. Expectation consistent approximations and expectation propagation are both shown to be related to Bethe free energies with weak consistency constraints, i.e. free energies where local approximations are only required to agree on certain statistics instead of full marginals.
Blood flow determination using recursive processing: a digital radiographic method.

Temporal filtration of fluoroscopic video sequences is being used as an alternative to pulsed digital subtraction angiography. Using the same image processing architecture and a slight modification in processing logic a parametric image can be synthesized from such a temporally filtered image sequence in virtual real time, i.e., an image sequence that spans T seconds takes exactly T seconds to process. Off-line computer processing is not required. Initial phantom studies imply that the time to maximum opacification (tmax) can be used to determine absolute and relative blood flow with a high confidence level (r greater than .989). Phantom and animal examples are presented.
Availability constraints for avionic data buses

The three traditional objectives of computer security are confidentiality, integrity and availability. Availability can be defined as the prevention of denial of service. Confidentiality and integrity have been addressed in several theoretical works whereas the concept of availability has not been much investigated by the scientific community. This paper is an attempt to define through a case study the concept of availability. We first define a set of availability constraints that avionic data bus protocols should enforce. Then, we consider the ARINC 629 basic protocol (BP) which was implemented on the Boeing 777, and we check whether that ARINC 629 BP respects our availability constraints or not.
Mechanisms of Base Substitution Mutagenesis in Cancer Genomes

Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.
Detection of antibodies to a pathogenic mycoplasma in desert tortoises (Gopherus agassizii) with upper respiratory tract disease

Mycoplasma agassizii (proposed species novum) is the etiologic agent of an upper respiratory tract disease in the desert tortoise (Gopherus agassizii), which is threatened in most of its range. An enzyme-linked immunosorbent assay (ELISA) for the detection of M. agassizii-specific antibodies in desert tortoises was developed with a monoclonal antibody with specificity for desert tortoise immunoglobulin light chain. Plasma samples from one group of tortoises were tested immediately before and 1 month after challenge either with nasal exudate containing M. agassizii or with a purified preparation of M. agassizii. Plasma samples from a second group of known healthy and sick tortoises were also tested. In the first group, the ELISA detected seroconversion in individual tortoises following challenge with M. agassizii. In the second group, ELISA results were positively correlated with the health status of the tortoises, as determined by clinical and pathologic findings. In addition, the ELISA revealed that tortoise antimycoplasma antibodies were specific for M. agassizii when samples were assayed against M. agassizii, M. pulmonis, M. testudinis, and M. gallisepticum antigens. The observed direct correlation between the presence of nasal mucosal lesions and M. agassizii-specific antibodies proved that the ELISA reliably diagnosed M. agassizii infection in desert tortoises and advocates its use for monitoring M. agassizii-induced upper respiratory tract disease in free-ranging desert tortoises.
Characterization of surface roughness effects on pressure drop in single-phase flow in minichannels

Roughness features on the walls of a channel wall affect the pressure drop of a fluid flowing through that channel. This roughness effect can be described by (i) flow area constriction and (ii) increase in the wall shear stress. Replotting the Moody’s friction factor chart with the constricted flow diameter results in a simplified plot and yields a single asymptotic value of friction factor for relative roughness values of e∕D>0.03 in the fully developed turbulent region. After reviewing the literature, three new roughness parameters are proposed (maximum profile peak height Rp, mean spacing of profile irregularities RSm, and floor distance to mean line Fp). Three additional parameters are presented to consider the localized hydraulic diameter variation (maximum, minimum, and average) in future work. The roughness e is then defined as Rp+Fp. This definition yields the same value of roughness as obtained from the sand-grain roughness [H. Darcy, Recherches Experimentales Relatives au Mouvement de L’Eau dans.
Bidirectional regulation of Aβ levels by Presenilin 1

Significance Alzheimer’s disease is the most common neurodegenerative disorder, affecting more than 5 million people in the United States. Multiple lines of evidence suggest that the accumulation of toxic oligomers and aggregates of β-amyloid (Aβ) peptide are the primary causes of neurodegeneration. Aβ originates from sequential cleavage of the amyloid precursor protein (APP). The APP first cleavage is by β-secretase and yields β-C-terminal fragment (βCTF). In turn, βCTF is cleaved by Presenilin 1 (PS1) to produce Aβ. In this work, we show that PS1, in addition to generating Aβ, can also decrease Aβ levels by directing βCTF degradation through autophagy. This previously unrecognized mechanism of regulation of Aβ by Presenilin 1 could provide an attractive target for potential Alzheimer’s disease therapies. Alzheimer’s disease (AD) is characterized by accumulation of the β-amyloid peptide (Aβ), which is generated through sequential proteolysis of the amyloid precursor protein (APP), first by the action of β-secretase, generating the β-C-terminal fragment (βCTF), and then by the Presenilin 1 (PS1) enzyme in the γ-secretase complex, generating Aβ. γ-Secretase is an intramembranous protein complex composed of Aph1, Pen2, Nicastrin, and Presenilin 1. Although it has a central role in the pathogenesis of AD, knowledge of the mechanisms that regulate PS1 function is limited. Here, we show that phosphorylation of PS1 at Ser367 does not affect γ-secretase activity, but has a dramatic effect on Aβ levels in vivo. We identified CK1γ2 as the endogenous kinase responsible for the phosphorylation of PS1 at Ser367. Inhibition of CK1γ leads to a decrease in PS1 Ser367 phosphorylation and an increase in Aβ levels in cultured cells. Transgenic mice in which Ser367 of PS1 was mutated to Ala, show dramatic increases in Aβ peptide and in βCTF levels in vivo. Finally, we show that this mutation impairs the autophagic degradation of βCTF, resulting in its accumulation and increased levels of Aβ peptide and plaque load in the brain. Our results demonstrate that PS1 regulates Aβ levels by a unique bifunctional mechanism. In addition to its known role as the catalytic subunit of the γ-secretase complex, selective phosphorylation of PS1 on Ser367 also decreases Aβ levels by increasing βCTF degradation through autophagy. Elucidation of the mechanism by which PS1 regulates βCTF degradation may aid in the development of potential therapies for Alzheimer’s disease.
Maximally permissive deadlock prevention policy for FMS based on elementary siphons

Behavior permissiveness is the most important criterion in evaluating the performance of a supervisor. For a special class of Petri nets, S3PR, this paper present a deadlock policy which can give a maximally permissive supervisor. By using iterative method, Siphons in a net system are distinguished by elementary and dependent ones, only elementary siphons are required to create a set of generalized mutual exclusion constraints (GMEC) expressed by the marking vector. Monitors based on the GMEC are added to the plant model such that the siphons in the resultant net are all invariant-controlled and no emptiable siphon is generated due to the addition of the monitors. This novel deadlock prevention policy can usually lead to a maximally permissive supervisor by adding a smaller number of monitors and arcs, the proposed policy can work excellently in appropriate size petri net system. Finally the manufacturing example is utilized to illustrate the proposed policy.
ORGANISATIONAL CONTEXT AND INSTITUTIONAL FORCES : KNOWLEDGE SHARING IN IKEA AND SCA

2 INTRODUCTION In tandem with the increasing interest in knowledge management and organisational learning, knowledge sharing has received strong attention among companies and academics over the last years. Sharing knowledge internally in organisations is often a key concern, and a central means to reap benefits of knowledge and learning. The rationale behind internal knowledge sharing in comparison to e.g. education or other forms of acquisition of knowledge, is cost efficiency, a higher degree of trust (e.g. Inkpen & Tsang, 2005), and the possibility to generate knowledge that is idiosyncratic to a specific organisation, hence providing uniqueness which can lead to sustained competitive advantage (e.g. Barney, 1991). However, knowledge sharing is complicated because it depends on a range of matters relating to knowledge itself, organisational structure and relations, and on the will of people to partake in knowledge sharing. Considering theory on success and failure factors, however, empirical work strongly emphasises cognitive issues (such as tacitness, absorptive capacity, causal ambiguity, cognitive variety and more) as explanatory factors. Other groups of factors, such as organisational context or institutional forces (e.g. individual and group motivation, and norms and values) are addressed more scarcely. With this paper we want to balance the picture, and discuss not just cognitive factors but also the impact of organisational and institutional factors. The purpose of the paper is to increase the understanding of how organisational context and institutional forces, in parallel with cognitive issues, impact firm-internal knowledge sharing in multinational corporations (MNC). The following section discusses factors that MNC will have to manage and deal with in their endeavours to distribute and share knowledge internally in their organisations. The empirical case studies are then presented, based on the relevant constructs identified in the theoretical part. The paper centres upon two qualitative case studies, furniture giant IKEA, and European paper packaging leader SCA Packaging, and their efforts to share knowledge across hundreds of local units worldwide. In the case of IKEA, the key concern is to make sure new stores across the world adhere to core IKEA principles, work methods and 3 standard offerings while still adapting to local market preferences. In the SCA case, the challenge lies in distributing experiences and hardcore production knowledge across 250 relatively autonomous profit centre packaging plants in Europe. Finally, lessons learned from the two cases are compared with theory and key observations are highlighted in order to discuss and extend current theory. …
Behavior of technetium in alkaline solution : Identification of non-pertechnetate species in high-level nuclear waste tanks at the hanford reservation

Technetium is a long-lived ( 99 Tc: 213,000 year half-life) fission product found in nuclear waste and is one of the important isotopes of environmental concern. The known chemistry of technetium suggests that it should be found as pertechnetate, TcO 4 , in the extremely basic environment of the nuclear waste tanks at the Hanford site. However, other chemical forms of technetium are present in significant amounts in certain tanks, and these non-pertechnetate species complicate the treatment of the waste. The only spectroscopic characterization of these non-pertechnetate species is a series of X-ray absorption near edge structure (XANES) spectra of actual tank waste. To better understand the behavior of technetium under these conditions, we have investigated the reduction of pertechnetate in highly alkaline solution in the presence of compounds found in high-level waste. These results and the X-ray absorption fine structure (XAFS) spectra of these species are compared to the chemical behavior and XANES spectra of the actual non-pertechnetate species. The identity of the non-pertechnetate species is surprising.
Changes in circulating mesenchymal stem cells, stem cell homing factor, and vascular growth factors in patients with acute ST elevation myocardial infarction treated with primary percutaneous coronary intervention

Objective: To investigate the spontaneous occurrence of circulating mesenchymal stem cells (MSC) and angiogenic factors in patients with ST elevation acute myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (PCI). Design: In 20 patients with STEMI, blood samples were obtained on days 1, 3, 7, 14, 21, and 28 after the acute PCI. Fifteen patients with a normal coronary angiography formed a control group. MSC (CD45−/CD34−), plasma stromal derived factor 1 (SDF-1), vascular endothelial growth factor A (VEGF-A), and fibroblast growth factor 2 (FGF-2) were measured by multiparametric flow cytometry and enzyme linked immunosorbent assay (ELISA). Results: Circulating CD45−/CD34− cells were significantly decreased on day 7 compared with day 3. Cell counts normalised one month after the acute onset of STEMI. The changes were mainly seen in patients with a large infarction. Plasma SDF-1 increased significantly from day 3 to day 28, and VEGF-A and FGF-2 increased significantly from day 7 to day 28. Conclusions: Spontaneous sequential fluctuations in MSC and the increase in vascular growth factor concentrations after STEMI suggest that the optimal time for additional stem cell therapy is three weeks after a myocardial infarction to obtain the maximum effects by stimulating endogenous growth factors on the delivered stem cells.