Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of gyrA and grlA mutations in stepwise-selected ciprofloxacin-resistant mutants of Staphylococcus aureus

Fluoroquinolone-resistant mutants were obtained in vitro from Staphylococcus aureus RN4220 by stepwise selection on increasing concentrations of ciprofloxacin. Results from sequence analysis of the quinolone resistance-determining region of GyrA and of the corresponding region of GrlA, the DNA topoisomerase IV subunit, showed an alteration of Ser-80 to Tyr (corresponding to Ser-83 of Escherichia coli GyrA) or Glu-84 to Lys in GrlA of both low- and high-level quinolone-resistant mutants. Second-step mutants were found to have, in addition to a mutation in grlA, reduced accumulation of norfloxacin or an alteration in GyrA at Ser-84 to Leu or Glu-88 to Lys. Third-step mutants derived from second-step mutants with reduced accumulation were found to have a mutation in gyrA. The results from this study demonstrated that mutations in gyrA or mutations leading to reduced drug accumulation occur after alteration of GrlA, supporting the previous findings (L. Ferrero, B. Cameron, B. Manse, D. Lagneaux, J. Crouzet, A. Famechon, and F. Blanche, Mol. Microbiol. 13:641-653, 1994) that DNA topoisomerase IV is a primary target of fluoroquinolones in S. aureus.
Generalized data transformations for enhancing cache behavior

The performance gap between processors and off-chip memories has widened in the last years and is expected to widen even more. Today, it is widely accepted that caches improve significantly the performance of programs, since most of the programs exhibit temporal and/or spatial locality in their memory reference patterns. However conflict misses can be a major obstacle preventing an application from utilizing the data cache effectively. While array padding can reduce conflict misses it can also increase the data space requirements significantly. In this paper, we present a compiler-based data transformation strategy, called the "generalized data transformations," for reducing inter-array conflict misses in embedded applications. We present the theory behind the generalized data transformations and discuss how they can be integrated with compiler-based loop transformations. Our experimental results demonstrate that the generalized data transformations are very effective in improving data cache behavior of embedded applications.
Systems that prevent unwanted represcription of drugs withdrawn because of adverse drug events: a systematic review

Represcription of medication that was withdrawn after the occurrence of an adverse drug event (including allergy), is a recognized medication safety issue on a patient level. We performed a systematic review to identify systems (electronic and nonelectronic) that can prevent the represcription of drugs withdrawn because of an adverse drug event and the effects of these systems. The review was performed using PRISMA and Cochrane guidelines. PubMed and Embase were searched for articles describing systems that can prevent represcription of drugs that had been withdrawn for causing an adverse drug event. Information on the characteristics of the studies, systems, and if present results achieved with such systems, was extracted. The results showed that of 6793 articles screened, 137 full-text articles were assessed for eligibility. A total of 45 studies describing 33 systems (28 electronic) were included. The five nonelectronic systems used allergy bracelets or allergy labels on hospital medical records or on drug orders. Systems differed in the way adverse drug events were documented and how users were alerted to drug represcription. Most systems functioned within a specific healthcare setting. Of 12 studies that compared pre- and post-intervention periods or wards with and without intervention, 7 showed a reduction in represcription after adverse drug event. In conclusion, several systems have been developed that can prevent the represcription of drugs that elicited an adverse drug event, but the evidence that these systems are effective is limited.
2-aroylindoles, a novel class of potent, orally active small molecule tubulin inhibitors.

2-Aroylindoles with 5-methoxy-1H-2-indolyl-phenylmethanone (D-64131) as the lead structure were discovered as a new class of synthetic, small molecule tubulin inhibitors. By competitively binding with [(3)H]colchicine to alphabeta-tubulin and inhibiting microtubule formation, cycling cells were arrested in the G(2)-M phase of the cell division cycle. The proliferation of tumor cells from 12 of 14 different organs and tissues was inhibited with mean IC(50)s of 62 nM and 24 nM by D-64131 and D-68144, respectively, comparable with the potency of paclitaxel with mean IC(50) of 10 nM. By measuring the cytotoxicity in a human colon carcinoma cell model with ectopic ecdysone-inducible expression of the cyclin-dependent kinase inhibitor p21(WAF1), specificity toward cycling cells was demonstrated. In contrast to microtubule inhibitors from natural sources, 2-aroylindoles did not alter the polymerization-dependent GTPase activity of beta-tubulin and are not substrates of the multidrug resistance/multidrug resistance protein efflux pump. No cross-resistance toward cell lines with multidrug resistance/multidrug resistance protein independent resistance phenotypes became evident. In animal studies, no signs of systemic toxicity were observed after p.o. dosages of up to 400 mg/kg of D-64131. In xenograft experiments with the human amelanoic melanoma MEXF 989, D-64131 was highly active with treatment resulting in a growth delay of 23.4 days at 400 mg/kg. Therefore, D-64131 and analogues have the potential to be developed for cancer therapy, replacing or supplementing standard therapy regimens with tubulin-targeting drugs from natural sources.
Manufacturing or Repairing Composite Parts and Components Using Laser Scanning Technology

Many aerospace and automotive parts are made from advanced composite materials for increased performance and weight savings. Composite tooling is used to manufacture composite parts when they are manufactured by the original equipment manufacturer, but this tooling is typically not available in an aircraft repair station or automotive repair shop. The authors have developed a method using laser-scanning technology to design composite tooling that could be used to manufacture replacement parts or repair damage to a structure. The scanning system is portable and could be used to scan components while they are on the aircraft or vehicle or when they are removed. The laser scanner will produce a solid model and CAD/CAM software will be used to develop the tool geometry and program tool paths for CNC machining.
Researching Ethics and Morality in Information Systems: Some Guiding Questions

Research on ethical and moral issues in information systems is increasingly recognized as legitimate and important. It raises a number of problems, however, that are often difficult for IS scholars to recognize and address. This paper therefore aims to provide guidance for IS scholars interested in undertaking or evaluating ethics-related research. The guidance is given in the form of questions that should be considered in order to avoid unnecessary mistakes and duplication of efforts. The questions presented cover the concept of ethics, the level of normative engagement, the relationship to prior work within IS and adjacent disciplines, the consistency of different aspects of ethics and the justification of normative conclusions. For each question the central issues under debate are elaborated and then the relevance of the question for IS research is discussed. The set of questions provides a guiding framework that will contribute to the improvement of the quality of ethics-related research in IS.
Severe Cytomegalovirus Meningitis in an Immunocompetent Patient ; A Case Report

Cytomegalovirus (CMV) is a DNA virus and is a member of the Herpesviridae family. There are few reports of CMV meningitis in immunocompetent adults. We reported an immunocompetent patient presenting with CMV meningitis and discussed the important relevant management issues. A 37-year-old male patient with fever, headache, confusion, nuchal rigidity and vomiting was presented to the emergency department. Chest radiography, brain CT and MRI were normal. Subsequently, he underwent a lumbar puncture and examination of the cerebrospinal fluid revealed lymphocytic pleocytosis. Polymerase chain reaction (PCR) of CSF was positive for cytomegalovirus DNA (Viral load=1000copies/ml) and therefore, treated with intravenous ganciclovir. In immunocompetent patients with acute meningitis with predominance of lymphocytes, CMV meningitis has to be included in the differential diagnosis and has to be ruled out with PCR testing of the cerebrospinal fluid.
HLA Class I Antigen Processing Machinery Component Expression and Intratumoral T-Cell Infiltrate as Independent Prognostic Markers in Ovarian Carcinoma

Purpose: Defects in the antigen processing machinery (APM) may provide tumor cells with a mechanism to escape immune recognition. The purpose of this study is to determine the clinical significance of APM component down-regulation and tumor-infiltrating T cells in ovarian carcinoma. Experimental Design: After institutional review board approval, tumor samples from 150 patients with invasive epithelial ovarian cancers were examined for TAP1, TAP2, tapasin, HLA class I heavy chain (HLA-HC), β2 microglobulin, and T-cell (CD3+ and CD8+) tumor infiltration using immunohistochemistry. Results: The majority of tumors had either heterogeneous or positive expression of TAP1, TAP2, HLA-HC, and β2 microglobulin (66.7%, 73.3%, 70.7%, and 63.3%, respectively), except tapasin for which 58% of the tumors lacked expression. Furthermore, 67% and 88% of the lesions possessed intratumoral and peritumoral CD3+ or CD8+ cells, respectively. The majority of APM component expression examined was significantly associated with both intratumoral and peritumoral T-cell infiltration (P < 0.05). The expression of APM components and the presence of intratumoral T-cell infiltrates were significantly associated with improved survival (all P ≤ 0.01); however, peritumoral T-cell infiltrates did not significantly affect survival (P = 0.33). APM component down-regulation (P < 0.001), lack of intratumoral T-cell infiltrates (P = 0.03), and suboptimal cytoreduction (P < 0.001) were independent prognostic markers for death from ovarian carcinoma. Conclusion: The negative effect of APM component down-regulation by itself and in combination with absent intratumoral T-cell infiltration on the survival of patients with ovarian carcinoma implies a role for immune escape in addition to immunosurveillance in the clinical course of disease.
Enrichment of the amino acid l-isovaline by aqueous alteration on CI and CM meteorite parent bodies

The distribution and enantiomeric composition of the 5-carbon (C5) amino acids found in CI-, CM-, and CR-type carbonaceous meteorites were investigated by using liquid chromatography fluorescence detection/TOF-MS coupled with o-phthaldialdehyde/N-acetyl-l-cysteine derivatization. A large l-enantiomeric excess (ee) of the α-methyl amino acid isovaline was found in the CM meteorite Murchison (lee = 18.5 ± 2.6%) and the CI meteorite Orgueil (lee = 15.2 ± 4.0%). The measured value for Murchison is the largest enantiomeric excess in any meteorite reported to date, and the Orgueil measurement of an isovaline excess has not been reported previously for this or any CI meteorite. The l-isovaline enrichments in these two carbonaceous meteorites cannot be the result of interference from other C5 amino acid isomers present in the samples, analytical biases, or terrestrial amino acid contamination. We observed no l-isovaline enrichment for the most primitive unaltered Antarctic CR meteorites EET 92042 and QUE 99177. These results are inconsistent with UV circularly polarized light as the primary mechanism for l-isovaline enrichment and indicate that amplification of a small initial isovaline asymmetry in Murchison and Orgueil occurred during an extended aqueous alteration phase on the meteorite parent bodies. The large asymmetry in isovaline and other α-dialkyl amino acids found in altered CI and CM meteorites suggests that amino acids delivered by asteroids, comets, and their fragments would have biased the Earth's prebiotic organic inventory with left-handed molecules before the origin of life.
Science and practice of core stability and strength testing

This study deals with a gap between science and practice in the testing of core stability and strength and presents our approach to solving this issue. Typical core stability tests require the subject to maintain a neutral spinal posture while under load in a quadrupedal or supine position and assess the endurance of global core muscles. However, most of these non-dynamometric tests have been developed for use in clinical and research settings. A suitable alternative represents torsional tests performed under stable or unstable conditions and instrumented tests in the form of trunk repositioning and load release tasks. Core strength is measured in terms of how much weight can be lifted, how many repetitions can be performed, or how long a neutral stable position can be maintained. In the laboratory, isometric and isokinetic dynamometers are frequently used. Isometric strength measurements are usually recommended as a standard for lifting tasks. However, such measurements underestimate the loads on the spine during dynamic movement. A deadlift to high pull exercise that involves working major muscle groups in the upper and lower body may best simulate the demands of jobs comprising of lifting tasks. Furthermore, isokinetic loading does not occur in daily human activities and is not specific to the requirements of sports. Given that rotational power is a better predictor of athlete performance, the test adapted from the wood chop exercise on a weight stack machine may provide conditions imposed by sports. One can also use a system that allows evaluation of muscle power during seated or standing trunk rotations with a barbell placed on the shoulders. These tests utilizing portable diagnostic systems may be implemented in functional diagnostics for athletes and sedentary or manual workers whose activities involve lifting tasks or trunk rotations under unloading or loading conditions; so complementing existing testing methods.
SVM-based Obstacles Recognition for Road Vehicle Applications

This paper describes an obstacle Recognition System based on SVM and vision. The basic components of the detected objects are first located in the image and then combined with a SVM-based classifier. A distributed learning approach is proposed in order to better deal with objects variability, illumination conditions, partial occlusions and rotations. A large database containing thousands of object examples extracted from real road images has been created for learning purposes. We present and discuss the results achieved up to date.
Multifunctional Polymer Nanocomposites with Core-Shell Structure for Magnetoresistance and Electromagnetic Shielding

Magnetoresistance (MR) behaviors of polyaniline (PANI) nanocomposites were adjusted with the assistance of the 0, 1 and 2 dimensional carbon nanofillers (carbon black, carbon fiber, carbon nanotube and graphene). The PANI nanocomposites were synthesized by a facial surface initiated polymerization method. The enhanced thermal stability were noticed in these carbon based PANI nanocomposites. Meanwhile, the enhanced dielectric constant was observed in the PANI nanocomposites compared to pure PANI, indicating these materials have potential for electromagnetic interference shielding and energy storage. A quasi 3-d electron conduction mechanism was observed in all PANI nanocomposites through the Mott variable range hopping (VRH) model. The responses of the localization length, density of state at fermi level, average hopping length and hopping energy of the PANI nanocomposites with different morphological carbon nanofillers to the magnetic field were studied by a wave-function shrinkage model.
Molecular genetics of the LDL receptor gene in familial hypercholesterolemia

The low density lipoprotein (LDL) receptor is a cell surface transmembrane protein that mediates the uptake and lysosomal degradation of plasma LDL, thereby providing cholesterol to cells. Mutations disrupting the function of this receptor produce autosomal dominant familial hypercholesterolemia (FH). Affected individuals have elevated plasma levels of LDL, which causes premature coronary atherosclerosis. To date, 71 mutations in the LDL receptor gene have been characterized at a molecular level. In this report, we describe 79 additional mutations and review the insights that all 150 mutations have provided into the structure/function relationship of the receptor protein and the clinical manifestations of FH. © 1992 Wiley‐Liss, Inc.
Measuring Physical Activity with Sensors: A Qualitative Study

Long term wearing of motion and heart rate sensors are essential aspects for longitudinal studies on physical activity measurement studies. We conducted a qualitative study with seven subjects in a total of 13 test sessions to identify usability and handling problems associated with Stayhealth RT3, Actigraph GT1M and Polar RS800 sensors. We found that battery life limitation is the most recurrent technical problem and long term wear of heart rate sensors produces discomfort and skin irritation.
Pombe's thirteen – control of fission yeast cell division by the septation initiation network

The septation initiation network (SIN) regulates aspects of cell growth and division in Schizosaccharomyces pombe and is essential for cytokinesis. Insufficient signalling results in improper assembly of the contractile ring and failure of cytokinesis, generating multinucleated cells, whereas too much SIN signalling uncouples cytokinesis from the rest of the cell cycle. SIN signalling is therefore tightly controlled to coordinate cytokinesis with chromosome segregation. Signalling originates from the cytoplasmic face of the spindle pole body (SPB), and asymmetric localisation of some SIN proteins to one of the two SPBs during mitosis is important for regulation of the SIN. Recent studies have identified in vivo substrates of the SIN, which include components involved in mitotic control, those of the contractile ring and elements of the signalling pathway regulating polarised growth. The SIN is also required for spore formation following meiosis. This has provided insights into how the SIN performs its diverse functions in the cell cycle and shed new light on its regulation.
Pipelined Bursts in Real-Time Scheduling

We consider the problem of performance guarantees for a hard real-time le system. We adopt an idea called constant-throughput resource management to manage the disk subsystem in a predictable way. This type of management leads us to the idea of static-priority periodic scheduling of bursty requests; a bursty request increases the task period, execution time, and deadline by a common multiplier of one or more. We derive critical instant tests and utilization formulae for this new type of scheduling workload. To achieve better performance, we pipeline the requests and generalize important earlier work on pipelined scheduling. We show that at least 50% of a burst-managed resource may be used for real-time requests, by setting the pipeline factor equal to the maximumburst factor. For the le system we conclude that at least 50% of the disk's time may be dedicated to data transfer, with modest buuering and start-up latencies. The other 50% of the disk's time could be dedicated to seeking. Our design allows the system administrator to choose this split (50-50, 90-10, or whatever) at disk format time, and trades fragmentation for improved performance. We also discuss other applications of bursty scheduling, i.e. managing jitter in real-time networks, performing MPEG transfer, sizing real-time caches, and managing transient overloads through explicit scheduling.
A new path delay test scheme based on path delay inertia

This paper proposes a new path delay test scheme based on path delay inertia. The scheme only applies pulses of specified widths, which are proportional to path delays, to paths-under-test. It is simple, eliminating the conventional two-pattern test for delay faults. Issues, such as sensitivity of applied pulse widths w.r. t. path delay, related with the scheme were studied and an experimental chip was implemented to demonstrate the scheme.
Cardiomyopathy Syndrome of Atlantic Salmon (Salmo salar L.) Is Caused by a Double-Stranded RNA Virus of the Totiviridae Family

ABSTRACT Cardiomyopathy syndrome (CMS) of farmed and wild Atlantic salmon (Salmo salar L.) is a disease of yet unknown etiology characterized by a necrotizing myocarditis involving the atrium and the spongious part of the heart ventricle. Here, we report the identification of a double-stranded RNA virus likely belonging to the family Totiviridae as the causative agent of the disease. The proposed name of the virus is piscine myocarditis virus (PMCV). On the basis of the RNA-dependent RNA polymerase (RdRp) sequence, PMCV grouped with Giardia lamblia virus and infectious myonecrosis virus of penaeid shrimp. The genome size of PMCV is 6,688 bp, with three open reading frames (ORFs). ORF1 likely encodes the major capsid protein, while ORF2 encodes the RdRp, possibly expressed as a fusion protein with the ORF1 product. ORF3 seems to be translated as a separate protein not described for any previous members of the family Totiviridae. Following experimental challenge with cell culture-grown virus, histopathological changes are observed in heart tissue by 6 weeks postchallenge (p.c.), with peak severity by 9 weeks p.c. Viral genome levels detected by real-time reverse transcription (RT)-PCR peak earlier at 6 to 7 weeks p.c. The virus genome is detected by in situ hybridization in degenerate cardiomyocytes from clinical cases of CMS. Virus genome levels in the hearts from clinical field cases correlate well with the severity of histopathological changes in heart tissue. The identification of the causative agent for CMS is important for improved disease surveillance and disease control and will serve as a basis for vaccine development against the disease.
A Hierarchical Aspect-Sentiment Model for Online Reviews

To help users quickly understand the major opinions from massive online reviews, it is important to automatically reveal the latent structure of the aspects, sentiment polarities, and the association between them. However, there is little work available to do this effectively. In this paper, we propose a hierarchical aspect sentiment model (HASM) to discover a hierarchical structure of aspect-based sentiments from unlabeled online reviews. In HASM, the whole structure is a tree. Each node itself is a two-level tree, whose root represents an aspect and the children represent the sentiment polarities associated with it. Each aspect or sentiment polarity is modeled as a distribution of words. To automatically extract both the structure and parameters of the tree, we use a Bayesian nonparametric model, recursive Chinese Restaurant Process (rCRP), as the prior and jointly infer the aspect-sentiment tree from the review texts. Experiments on two real datasets show that our model is comparable to two other hierarchical topic models in terms of quantitative measures of topic trees. It is also shown that our model achieves better sentence-level classification accuracy than previously proposed aspect-sentiment joint models.