Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiplex PCR Targeting tpi (Triose Phosphate Isomerase), tcdA (Toxin A), and tcdB (Toxin B) Genes for Toxigenic Culture of Clostridium difficile

ABSTRACT A multiplex PCR toxigenic culture approach was designed for simultaneous identification and toxigenic type characterization of Clostridium difficile isolates. Three pairs of primers were designed for the amplification of (i) a species-specific internal fragment of the tpi (triose phosphate isomerase) gene, (ii) an internal fragment of the tcdB (toxin B) gene, and (iii) an internal fragment of the tcdA (toxin A) gene allowing distinction between toxin A-positive, toxin B-positive (A+B+) strains and toxin A-negative, toxin B-positive (A−B+) variant strains. The reliability of the multiplex PCR was established by using a panel of 72 C. difficile strains including A+B+, A−B−, and A−B+ toxigenic types and 11 other Clostridium species type strains. The multiplex PCR assay was then included in a toxigenic culture approach for the detection, identification, and toxigenic type characterization of C. difficile in 1,343 consecutive human and animal stool samples. Overall, 111 (15.4%) of 721 human samples were positive for C. difficile; 67 (60.4%) of these samples contained A+B+ toxigenic isolates, and none of them contained A−B+ variant strains. Fifty (8%) of 622 animal samples contained C. difficile strains, which were toxigenic in 27 (54%) cases, including 1 A−B+ variant isolate. Eighty of the 721 human stool samples (37 positive and 43 negative for C. difficile culture) were comparatively tested by Premier Toxins A&B (Meridian Bioscience) and Triage C. difficile Panel (Biosite) immunoassays, the results of which were found concordant with toxigenic culture for 82.5 and 92.5% of the samples, respectively. The multiplex PCR toxigenic culture scheme described here allows combined diagnosis and toxigenic type characterization for human and animal C. difficile intestinal infections.
Electronic Data Interchange: Research Review and Future Directions

For nearly two decades, electronic data interchange (EDI) has been widely viewed as a technology pivotal to supply chain management that has also provided benefits to firms on multiple levels. Despite a substantial body of literature, there are a number of conflicting and inconclusive research results in this field. In this study, we synthesize the diverse body of research in EDI by organizing the literature into an initial theoretical framework. Based on a meta-analysis of results from the empirical literature, we seek to clarify conflicting results from the literature in order to develop a more unified theoretical framework of contextual variables associated with EDI adoption factors and outcomes. From a managerial standpoint, our literature-based framework offers a set of guidelines for making successful EDI adoption and implementation decisions.
Androgen receptor in Sertoli cells regulates DNA double-strand break repair and chromosomal synapsis of spermatocytes partially through intercellular EGF-EGFR signaling

Spermatogenesis does not progress beyond the pachytene stages of meiosis in Sertoli cell-specific AR knockout (SCARKO) mice. However, further evidence of meiotic arrest and underlying paracrine signals in SCARKO testes is still lacking. We utilized co-immunostaining of meiotic surface spreads to examine the key events during meiotic prophase I. SCARKO spermatocytes exhibited a failure in chromosomal synapsis observed by SCP1/SCP3 double-staining and CREST foci quantification. In addition, DNA double-strand breaks (DSBs) were formed but were not repaired in the mutant spermatocytes, as revealed by γ-H2AX staining and DNA-dependent protein kinase (DNA-PK) activity examination. The later stages of DSB repair, such as the accumulation of the RAD51 strand exchange protein and the localization of mismatch repair protein MLH1, were correspondingly altered in SCARKO spermatocytes. Notably, the expression of factors that guide RAD51 loading onto sites of DSBs, including TEX15, BRCA1/2 and PALB2, was severely impaired when either AR was down-regulated or EGF was up-regulated. We observed that some ligands in the epidermal growth factor (EGF) family were over-expressed in SCARKO Sertoli cells and that some receptors in the EGF receptor (EGFR) family were ectopically activated in the mutant spermatocytes. When EGF-EGFR signaling was repressed to approximately normal by the specific inhibitor AG1478 in the cultured SCARKO testis tissues, the arrested meiosis was partially rescued, and functional haploid cells were generated. Based on these data, we propose that AR in Sertoli cells regulates DSB repair and chromosomal synapsis of spermatocytes partially through proper intercellular EGF-EGFR signaling.
Importance of Data Quality in Virtual Metrology

The purpose of VM is to enable the manufacturers to conjecture the wafer quality and deduce the causes of defects without performing physical metrology. VM requires a large amount of sensor data retrieved from production tools. However, inappropriateness and instability of the data collection system, which leads to incorrectness, fragment and asynchrony of data collected, may lead to inaccurate conjecture results. Hence, not only precision of the VM conjecture module but also quality of the collected data are essential to ensure accurate and stable VM results for improving production yield. In this work, the importance of data quality to VM is investigated. The data quality mechanism is proposed for data characteristic analysis, data anomaly detection, data cleaning, data normalization, and data reduction. Besides, the equipment of semiconductor chemical vapor deposition (CVD) is adopted as a practical example to illustrate the significance of data quality mechanism, and further verify feasibility and effectiveness of VM
Medial artery calcification in ESRD patients is associated with deposition of bone matrix proteins.

BACKGROUND In non-ESRD patients, recent studies have demonstrated that the process of vascular calcification resembles developmental osteogenesis. Patients with ESRD are known to have excessive vascular calcification, but this has previously been attributed to the non-cell-mediated process of metastatic calcification. METHODS To determine if the calcification observed in patients with ESRD is related to a cell-mediated process, we removed a piece of inferior epigastric artery at the time of renal transplant. Calcium content of the entire vessel was quantified with spiral computed tomography (CT). The vessel was then examined histologically for calcification and the presence of bone matrix proteins by immunohistochemistry, and medial and intimal thickness quantified by histomorphometry. These findings were correlated with demographic, clinical and laboratory values. RESULTS The proximal inferior epigastric artery was obtained from 41 patients undergoing renal transplantation, but two were inadequate for histologic examination. Twenty-seven of the remaining vessels had no evidence of calcification by MacNeal's or Alizarin red pH 4.2 staining, five vessels had mild/moderate calcification, and seven had severe calcification, all in the medial layer. Calcification assessed histologically was closely correlated with calcification score as assessed by spiral CT, normalized for vessel weight (P=0.027). Positive immunostaining for the bone matrix proteins osteopontin, type I collagen, bone sialoprotein, and alkaline phosphatase was strongly correlated with calcification (all P < or = 0.001), as was a history of coronary artery disease (P < 0.001), and diabetes (P=0.034). The calcification score by spiral CT correlated with these same factors and the serum phosphorus and calcium x phosphorus product (P=0.032 and 0.037). The location of immunostaining for the bone proteins was strongly associated with the presence of calcification. However, positive immunostaining also was observed in association with disorganization of the vascular smooth muscle cells in the medial layer due to deposition of a matrix-like substance, prior to overt calcification. CONCLUSIONS In patients with ESRD undergoing renal transplantation, vascular calcification of the medial layer of the inferior epigastric artery is common (44%), can be detected by spiral CT, and is associated with deposition of bone matrix proteins. This implies an active cell-mediated process, raising hope that directed intervention can arrest this process.
Donor Insemination — A Substitute for the Infertile Male

Summary: Investigation, assessment, and the results of treatment of 114 couples requesting donor insemination (A.I.D.) are reported. Where the male factor for infertility was the only recognisable one, 66% of patients became pregnant in an average of 3 months of treatment; where there was an additional female infertility factor, 32% of patients became pregnant in an average of 9 treatment months.
Urban damage evaluation using polarimetric SAR data

This paper focuses on earthquake/tsunami damage investigation over urban areas by exploring the multitemporal spaceborne ALOS/PALSAR PolSAR data. The polarimetric scattering mechanism changes before- and after-tsunami, at the city block scale, have been examined using model-based decomposition and PO angle techniques. These analyzes are used to establish the relationships between the polarimetric scattering mechanism changes and damage levels. The basic scattering structures such as ground-wall dihedral structures from the built-up areas were found to be stable even over a long temporal baseline. Two polarimetric indexes have been proposed for damage level indication. Experimental results validate the efficiency of these two indicators, since the built-up areas with different damage levels can be well discriminated. These results demonstrate the importance and efficiency of full polarimetric information for natural disaster assessment.
The antigenic differentiation of seven strains of Mycoplasma hyorhinis by growth-inhibition, metabolism-inhibition, latex-agglutination, and polyacrylamide-gel-electrophoresis tests.

SUMMARY Seven strains of Mycoplasma hyorhinis obtained from different geographic areas were compared by growth-inhibition, metabolism-inhibition and latex-agglutination tests. Although serologically interrelated, the strains showed differences ranging from slight to profound, and therefore division into subtypes was suggested. Statistical analysis by the coefficient of concordance and by the rank correlation coefficient supported the finding that all three sero-logical methods are probably equally suitable for serological differentiation. Polyacrylamide gel electrophoresis revealed no appreciable differences among the strains.
Human α-enolase from endothelial cells as a target antigen of anti–endothelial cell antibody in Behçet's disease

Objective To identify and recombine a protein of the human dermal microvascular endothelial cell (HDMEC) that specifically reacts with anti–endothelial cell antibody (AECA) in the serum of patients with Behcet's disease (BD), and to evaluate the usefulness of this protein in BD. Methods The proteomics technique, with 2-dimensional gel electrophoresis and matrix-assisted laser desorption ionization−time-of-flight (MALDI-TOF) mass spectrometry, was used to identify and recombine HDMEC antigen. Western blotting and enzyme-linked immunosorbent assay (ELISA) of recombinant protein isolated by gene cloning were performed on serum from healthy controls, patients with BD, and patients with other rheumatic diseases (rheumatoid arthritis, systemic lupus erythematosus, and Wegener's granulomatosis). Results Eighteen of 40 BD patients had serum IgM antibody to HDMEC antigen. The purified protein that reacted with AECA in BD patient sera was found to be α-enolase by 2-dimensional gel electrophoresis followed by immunoblotting and MALDI-TOF mass spectrometry. Recombinant α-enolase protein was isolated and refined by gene cloning. On Western blots, AECA-positive IgM from the sera of patients with active BD reacted strongly with recombinant human α-enolase. BD patient sera positive for anti–α-enolase did not react with human γ-enolase. On dot-blotting, reactivity to human α-enolase was detected only in the IgM-positive group. Fifteen of the 18 AECA-positive sera that were positive for the HDMEC antigen showed reactivity to recombinant α-enolase IgM antibody by ELISA. Conclusion The α-enolase protein is the target protein of serum AECA in BD patients. This is the first report of the presence of IgM antibodies to α-enolase in endothelial cells from the serum of BD patients. Although further studies relating this protein to the pathogenesis of BD will be necessary, α-enolase and its antibody may prove useful in the development of new diagnostic and treatment modalities in BD.
Feasibility of Eye-tracking based Glasses-free 3D Autostereoscopic Display Systems for Medical 3D Images

Medical image diagnosis processes with stereoscopic depth by 3D display have not been developed widely yet and remain understudied Many stereoscopic displays require glasses that are inappropriate for use in clinical diagnosis/explanation/operating processes in hospitals. An eye-tracking based glasses-free three-dimensional autostereoscopic display monitor system has been developed, and its feasibility for medical 3D images was investigated, as a cardiac CT 3D navigator. Our autostereoscopic system uses slit-barrier with BLU, and it is combined with our vision-based eye tracking system to display 3D images. Dynamic light field rendering technique is applied with the 3D coordinates calculated by the eye-tracker, in order to provide a single viewer the best 3D images with less x-talk. To investigate the feasibility of our autostereoscopic system, 3D volume was rendered from 3D coronary CTA images (512 by 512 by 400). One expert reader identified the three main artery structures (LAD, LCX and RCA) in shorter time than existing 2D display. The reader did not report any eye fatigue or discomfort. In conclusion, we proposed a 3D cardiac CT navigator system with a new glasses-free 3D autostereoscopy, which may improve diagnosis accuracy and fasten diagnosis process.
In vitro and in vivo behaviour of NDF‐expanded monkey Schwann cells

Schwann cells, the myelin‐forming cells of the peripheral nervous system may play a major role in the regeneration and remyelination not only of the peripheral but also of the central nervous system. The discovery of the mitogenicity of human recombinant forms of neuregulins (glial growth factors) on primate Schwann cells allows us to envisage a considerable expansion of these cells in culture with a view to autologous transplantation in the central nervous system. To assay this possibility, we used human recombinant neu‐differentiation factor beta (NDFβ) to expand monkey Schwann cells derived from perinatal and adult nerve biopsies. We report that NDFβ containing the epidermal growth factor (EGF)‐like domain (residues 177–228) is a potent mitogen for monkey Schwann cells but is more effective on perinatal than adult Schwann cells. Moreover, continuous treatment with NDFβ, does not seem to prevent Schwann cells differentiation into myelin‐forming cells after their transplantation into the demyelinated mouse spinal cord. These observations, in addition to the close similarities of in vitro behaviour which exist between human and monkey Schwann cells, indicate that monkey Schwann cells could be an ideal tool to study the potential and limits of autologous transplantation in a non‐human primate model of central nervous system demyelination.
Research methodology: endocrinologic measurements in exercise science and sports medicine.

OBJECTIVE To provide background information on methodologic factors that influence and add variance to endocrine outcome measurements. Our intent is to aid and improve the quality of exercise science and sports medicine research endeavors of investigators inexperienced in endocrinology. BACKGROUND Numerous methodologic factors influence human endocrine (hormonal) measurements and, consequently, can dramatically compromise the accuracy and validity of exercise and sports medicine research. These factors can be categorized into those that are biologic and those that are procedural-analytic in nature. RECOMMENDATIONS Researchers should design their studies to monitor, control, and adjust for the biologic and procedural-analytic factors discussed within this paper. By doing so, they will find less variance in their hormonal outcomes and thereby will increase the validity of their physiologic data. These actions can assist the researcher in the interpretation and understanding of endocrine data and, in turn, make their research more scientifically sound.
Determination of drug‐induced changes in functional MRI signal using a pharmacokinetic model

As the applications of functional magnetic resonance imaging (fMRI) expand, there is a need for the development of new strategies for data extraction and analysis that do not require the presentation of stimuli in a repeated on/off pattern. A description and evaluation of a method and computer algorithm for the detection and analysis of brain activation patterns following acute drug administration using fMRI are presented. A waveform analysis protocol (WAP) input function has been developed that is based upon the single‐dose pharmacokinetics of a drug of interest. As a result of this analysis, regional brain activation can be characterized by its localization and intensity of activation, onset of action, time to peak effect, and duration of action. A global statistical test for significant drug effects based upon the probability of a voxel being activated by a saline vehicle injection is applied to grouped data on a voxel by voxel basis. Representative data are presented using nicotine as a prototypical agent. Using this method, statistically significant drug‐induced brain activation has been identified in several key cortical and subcortical brain regions. Hum Brain Mapping 8:235–244, 1999. © 1999 Wiley‐Liss, Inc.
Epistemicism and modality

Abstract What kind of semantics should someone who accepts the epistemicist theory of vagueness defended in Timothy Williamson’s Vagueness (1994) give a definiteness operator? To impose some interesting constraints on acceptable answers to this question, I will assume that the object language also contains a metaphysical necessity operator and a metaphysical actuality operator. I will suggest that the answer is to be found by working within a three-dimensional model theory. I will provide sketches of two ways of extracting an epistemicist semantics from that model theory, one of which I will find to be more plausible than the other.
DNA-mediated transfer of multiple drug resistance and plasma membrane glycoprotein expression

Colchicine-resistant Chinese hamster ovary (CHO) cell mutants whose resistance results from reduced drug permeability have been isolated previously in our laboratories. This reduced permeability affects a wide range of unrelated drugs, resulting in the mutants displaying a multiple drug resistance phenotype. A 170,000-dalton cell surface glycoprotein (P-glycoprotein) was identified, and its expression appears to correlate with the degree of resistance. In this study we were able to confer the multiple drug resistance phenotype on sensitive mouse L cells by DNA-mediated gene transfer of DNA obtained from the colchicine-resistant mutants. P-glycoprotein was detected in plasma membranes of these DNA transformants by staining with an antiserum raised against membranes of mutant CHO cells. These results are consistent with a causal relationship between P-glycoprotein expression and the multiple drug resistance phenotype.
Improving asthma management: one health plan's experience.

OBJECTIVE To demonstrate that including the patient's perspective of disease control (patient-reported symptoms) in asthma treatment and management decisions improves patient outcomes and reduces healthcare resource utilization. STUDY DESIGN Two study phases gathered patients' assessments of disease control. Phase 1 used a retrospective physician questionnaire. Phase 2 used a patient questionnaire at each office visit. Physicians and patients were members of the Independent Health Association, a health insurer in upstate New York. METHODS Phase 1 gathered patients' assessment of asthma control retrospectively using a physician questionnaire. Physicians received a list of pediatric patients in their practice who had intermittent and persistent asthma as their primary diagnosis. They reviewed a sample of these actively managed patients and answered 10 questions about them. Phase 2 was designed to include the patient's perspective. The Asthma Control Test was sent to every patient with asthma to complete and to bring to each physician visit. RESULTS In phase 1, emergency department visits and hospitalizations for asthma decreased during the program. Emergency department visits decreased from 3.71 to 2.92 per year (P < .01), and hospitalizations decreased from 0.83 to 0.81 per year (not statistically significant). Results for phase 2 are not yet available. CONCLUSIONS Although not a controlled program, for the participating practices the Independent Health Association health plan seems to have improved patient outcomes when they included retrospective, documented, patient-reported symptoms in their asthma management decisions. Emergency department visits and hospitalizations decreased. Managed care organizations should consider adding the patient's perspective of disease control to their asthma management decisions.
Precision Obtained Using an Artificial Neural Network for Predicting the Material Removal Rate in Ultrasonic Machining

The present study proposes a back propagation artificial neural network (BPANN) to provide improved precision for predicting the material removal rate (MRR) in ultrasonic machining. The BPANN benefits from the advantage of artificial neural networks (ANNs) in dealing with complex input-output relationships without explicit mathematical functions. In our previous study, a conventional linear regression model and improved nonlinear regression model were established for modelling the MRR in ultrasonic machining to reflect the influence of machining parameters on process response. In the present work, we quantitatively compare the prediction precision obtained by the previously proposed regression models and the presently proposed BPANN model. The results of detailed analyses indicate that the BPANN model provided the highest prediction precision of the three models considered. The present work makes a positive contribution to expanding the applications of ANNs and can be considered as a guide for modelling complex problems of general machining.