Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of children with Chlamydophila (Chlamydia) pneumoniae and Mycoplasma pneumoniae respiratoryinfections by real‐time PCR assay and serological tests  

We examined 73 children with respiratory infections for Chlamydophila (Chlamydia) pneumoniae and Mycoplasma pneumoniae using real‐time PCR assay and serological tests. C. pneumoniae and M. pneumoniae infections were found in 11 (15.1%) and 6 (8.2%) cases, respectively. The sensitivities and specificities of real‐time PCR versus definite diagnosis of acute infection were 63.6% and 100% for C. pneumoniae, and 100% and 100% for M. pneumoniae, respectively. C. pneumoniae PCR‐negative results appeared to be due to poor growth of the organism. The sensitivity and specificity of ImmunoCard tests were 33.3% and 82.1%, respectively, indicating that the efficacy of rapid diagnosis was disputable. The present results suggest that real‐time PCR is suitable for rapid diagnosis as a first screening test to determine first‐line antibacterial agents to be used against these infectious diseases.
Leprosy of the larynx

Abstract The result of a study conducted on 30 patients of lepromatous leprosy regarding laryngeal involvement is presented. The incidence of leprous laryngitis is 36.6 per cent in this part of India in lepromatous leprosy patients. Leprosy is long standing disease so laryngeal lesions developed gradually and may be asymptomatic in some cases while others have been found to have variety of clinical manifestation in form of congestion, infiltration, nodulation, thickening and fibrosis. Anti-leprosy chemotherapy is equally effective on these lesions. A screening survey of laryngeal pathology in such cases should be done periodically.
Comparison of methods to detect enteroviral genome in frozen and fixed myocardium by polymerase chain reaction.

BACKGROUND Understanding the pathogenesis of viral myocarditis is linked to the availability of sensitive assays to detect viral genome in clinical material. Recent advances in molecular techniques permit detection of viral-specific RNA in tissue samples. We describe here a comparison of different methods for RNA extraction, reverse transcription, and gene amplification of Coxsackievirus B3 virus in fixed and frozen mouse myocardium. EXPERIMENTAL DESIGN Homogenized Coxsackie B3 virus-infected myocardium was assayed for virus titer and formalin fixed, paraffin-embedded sections from the same heart were subjected to RNA extraction by 3 different methods. Optimal conditions were determined for a one-step assay combining reverse transcription and the polymerase chain reaction to detect enteroviral genome in RNA extracted by these different methods. The presence of amplifiable cDNA was confirmed by amplification of porphobilinogen deaminase mRNA as a positive control. RESULTS Extraction of RNA from paraffin-embedded myocardium after overnight digestion with proteinase K (200 micrograms/ml) and 0.5% sodium dodecyl sulfate was the most efficient of the three methods compared. With our optimized polymerase chain reaction assay, in which the cDNA synthesis and amplification steps are combined, we detected as little as 10 TCID50 of virus from frozen viral stocks and tissue homogenates and 1.0 TCID50 of virus from fixed tissue. CONCLUSIONS This sensitive polymerase chain reaction assay will facilitate examination of archival clinical samples to establish a retrospective diagnosis of enterovirus infection.
INHIBITION OF PRECURSOR INCORPORATION INTO NUCLEIC ACIDS OF MAMMALIAN TISSUES BY ANTIMALARIAL AMINOQUINOLINES

1 Chloroquine, primaquine and ethidium inhibited thymidine incorporation into deoxyribonucleic acid of rat tissues when administered concurrently with the labelled precursor. 2 Chloroquine and primaquine inhibited the incorporation of uridine and adenine, but not orotate, into various ribonucleic acid fractions of liver of rats and mice. These drugs had no effect on leucine incorporation into hepatic protein in rats or mice. 3 Although chloroquine and primaquine are active against different stages in the life cycle of the malarial parasites, the two aminoquinolines exert similar effects in rodent tissues.
Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions

In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.
Population genetic structure of the African elephant in Uganda based on variation at mitochondrial and nuclear loci: evidence for male‐biased gene flow

A drastic decline has occurred in the size of the Uganda elephant population in the last 40 years, exacerbated by two main factors; an increase in the size of the human population and poaching for ivory. One of the attendant consequences of such a decline is a reduction in the amount of genetic diversity in the surviving populations due to increased effects of random genetic drift. Information about the amount of genetic variation within and between the remaining populations is vital for their future conservation and management. The genetic structure of the African elephant in Uganda was examined using nucleotide variation of mitochondrial control region sequences and four nuclear microsatellite loci in 72 individuals from three localities. Eleven mitochondrial DNA (mtDNA) haplotypes were observed, nine of which were geographically localized. We found significant genetic differentiation between the three populations at the mitochondrial locus while three out of the four microsatellite loci differentiated KV and QE, one locus differentiated KV and MF and no loci differentiated MF and QE. Expected heterozygosity at the four loci varied between 0.51 and 0.84 while nucleotide diversity at the mitochondrial locus was 1.4%. Incongruent patterns of genetic variation within and between populations were revealed by the two genetic systems, and we have explained these in terms of the differences in the effective population sizes of the two genomes and male‐biased gene flow between populations.
A collaborative control framework for driver assistance systems

This paper proposes a driver assistance system with a collaborative control framework between the human driver and a Collision Avoidance System (CAS) for vehicles on the road while considering the driver drowsiness status. Driver drowsiness detection is performed with two inputs: driver's facial data from a camera mounted in front of the driver and steering wheel data from the car controller system. We use the driver's drowsiness state as an input to the collaborative control framework in which the CAS algorithm runs in parallel with the human control and only intervenes under certain situations to assist the human driver. Experiments were performed on a simulated vehicle driving testbed to evaluate our drowsiness detection system and demonstrate the effectiveness of the proposed collaborative control framework.
The Effects of Gap Junctions on Propagation in Myocardium: A Modified Cable Theory a

In recent years it has become apparent that continuous cable theory gives an inadequate explanation of propagation and its failure in myocardial tissue. There is a growing body of experimental evidence demonstrating that the discreteness of myocardial cells and the gap junctions that couple them, cannot be ignored. To illustrate, we cite three experiments. In the first, Spach and his collaborator^'-^ showed the results of early stimulus a t a single point of canine crista terminalis. More recently, Jalife and collaborator^^^^ and Balke et a1.6 reported the results of stimulating sheep and dog (respectively) epicardium that was perfused with heptanol, an agent that is presumed to impair the function of gap junctions. The results of these experiments are in distinct disagreement with classic cable theory, but more disconcerting, the experiments of Spach et al. appear to disagree with those of Jalife's group and Balke et al. Spach et al. found that a t certain premature stimulus values longitudinal propagation (i.e., in the direction of the cell's long axis) failed while transverse propagation was successful. Jalife and collaborators found just the opposite. As the concentration of heptanol in the cells increased, transverse propagation was the first to fail, while longitudinal propagation was successful. Balke et al. did not add enough heptanol to cells to induce block, but observed, similar to Jalife and company, that the propagation velocity in the transverse direction slowed more rapidly as a function of heptanol concentration than did the longitudinal propagation. Cable theory does not predict the failure of propagation, let alone that failure should occur preferentially in one of the two directions, or in which of the two directions propagation will first fail. The observations of Spach have been a major cause for concern, and in response there have been a number of numerical investigations of the effects of discreteness and anisotropy on propagation in These investigations suggest that some of the experimental observations can be explained by taking into account the discreteness of gap junctions. Because they are based on large-scale numerical computations, however, they are very much dependent on the specific details of the model that is used and difficult to adapt from one experimental setup to another. Furthermore, being numerical rather than analytical in nature, they do not lend themselves to easy
Four novel mutations in APOB causing heterozygous and homozygous familial hypobetalipoproteinemia

Familial hypobetalipoproteinemia (FHBL) is a rare codominant disorder of lipoprotein metabolism characterized by low levels of low‐density lipoprotein (LDL) cholesterol and apolipoprotein (apo) B. Heterozygotes for FHBL have less‐than‐half normal LDL‐cholesterol and apoB concentrations, whereas homozygotes have extremely low or undetectable LDL‐cholesterol and apoB levels. These reductions in LDL‐cholesterol and apoB have been suggested to provide FHBL subjects with resistance to atherosclerosis. FHBL can be caused by mutations in the APOB gene on chromosome 2. We present four novel mutations and one previously described mutation in APOB causing FHBL in five families. Immunoblotting and DNA sequencing were used to characterize the novel mutation apoB‐40.3 (c.5564underscore;5565insC) and the previously reported mutation apoB‐80.5 (c.11040T>G). The apoB‐6.9 (c.1018underscore;1025del) and apoB‐25.8 (c.3600T>A) mutations were identified by DNA sequence analysis, as variants shorter than apoB‐31 are not detectable in plasma. A fifth mutation, the splice variant c.82+1G>A, was identified by sequencing and was found in a homozygous subject. In ∼50% of the FHBL subjects, plasma alanine aminotransferase concentrations were mildly increased, suggestive of fatty liver. All affected FHBL subjects had low to low‐normal serum vitamin E concentrations, highlighting the important and recognized relationship between lipid and vitamin E concentrations. © 2003 Wiley‐Liss, Inc.
Chronic hepatitis C: Interferon retreatment of relapsers. A meta‐analysis of individual patient data

Relapse after interferon (IFN) therapy for chronic hepatitis C virus (HCV) infection occurs in 50% of patients after the initial response. The benefit of retreatment with IFN alone has not been assessed in large controlled studies. To assess the effectiveness and the tolerability of IFN retreatment and to identify the optimal second course regimen, we performed a meta‐analysis of individual patient's data on a set of 549 patients (mean age 43.8 years; 12.2 SD, men: 65%) who had an end‐of‐treatment biochemical response to a first IFN course and then relapsed. Retreatment was started within 24 months after the end of the first course. Biochemical end‐of‐treatment responses (ETR) and sustained responses (SR) were observed in 405 of 549 (73.8%; 95% confidence interval [CI] 70.1‐77.5) and in 124 of 549 (22.6%; CI 19.1‐26.1) patients, respectively. One hundred seventy‐five of 404 patients (43.3%; CI 38.6‐48.2) developed an end‐of‐treatment, biochemical, and virological response when retreated. A biochemical and virological SR to retreatment occurred in 73 of 494 (14.8%; CI 11.7‐18) patients. Thirty‐two patients (5.8%; CI 3.5‐7.8) stopped retreatment for adverse effects. Biochemical and virological SR was predicted independently by logistic regression analysis using a negative HCV RNA at the end of the first cycle of IFN (P= .01) and by retreatment with a high IFN dose (P= .03). Age, cirrhosis, genotype, and γ‐glutamyl transferase levels before retreatment were not significant by multivariate analysis. The excellent tolerability of IFN monotherapy retreatment makes it an option for patients who transiently cleared HCV‐RNA during their first IFN course. Patients should be retreated with a high IFN dose regardless of the strength of the dose received during the previous course of treatment.
Improved Tracking by Mitigating the Influence of the Human Body

This paper presents a location tracking system that improves its performance by mitigating the influence caused by the human body of the user being tracked. The presence of such a user will influence the signal path between a body-worn mobile device and a receiving node. This influence will vary with the user's location and orientation and, as a result, the performance will deteriorate. By making use of the user's orientation towards the fixed infrastructure nodes, the influence of the body can be explicitly compensated, hereby improving the tracking accuracy. The overall system performance is extensively verified with experiments on a building-wide testbed. Compensating for this human body shadowing results in a relative improvement of 23.6%.
Increased alpha‐B‐crystallin expression in mammary metaplastic carcinomas

Chan S‐K, Lui P C W, Tan P‐H, Yamaguchi R, Moriya T, Yu A M C, Shao M‐M, Hliang T, Wong S‐I & Tse G M (2011) Histopathology59, 247–255
Inorganic Nitrogen Assimilation in Yeasts: Alteration in Enzyme Activities Associated with Changes in Cultural Conditions and Growth Phase

Ammonia assimilation has been investigated in four strains of Saccharomyces cerevisiae by measuring, at intervals throughout the growth cycle, the activities of several enzymes concerned with inorganic ammonia assimilation. Enzyme activities in extracts of cells were compared after growth in complete and defined media. The effect of shift from growth in a complete to growth in a defined medium (and the reverse) was also determined. The absence of aspartase (EC 4.3.1.1, l-aspartate-ammonia lyase) activity, the low specific activities of alanine dehydrogenase, glutamine synthetase [EC 6.3. 1.2, l-glutamate-ammonia ligase (ADP)], and the marked increase in activity of the nicotinamide adenine dinucleotide phosphate-linked glutamate dehydrogenase (NADP-GDH) [EC 1.4. 1.4, l-glutamate:NADP-oxidoreductase (deaminating)] during the early stages of growth support the conclusion that yeasts assimilate ammonia primarily via glutamate. The NADP-GDH showed a rapid increase in activity just before the initiation of exponential growth, reached a maximum at the mid-exponential stage, and then gradually declined in activity in the stationary phase. The NADP-GDH reached a higher level of activity when the yeasts were grown on the defined medium as compared with complete medium. The nicotinamide adenine dinucleotide-linked glutamate dehydrogenase (NAD-GDH) [EC 1.4. 1.2, l-glutamate:NAD-oxidoreductase (deaminating)] showed only slight increases in activity during the exponential phase of growth. There was an inverse relationship in that the NADP-GDH increased in activity as the NAD-GDH decreased. The NAD-GDH activity was higher after growth on the complete medium. The glutamate-oxaloacetate transaminase (EC 2.6.1.1. l-aspartate:2-oxoglutarate aminotransferase) activity rose and fell in parallel with the NADP-GDH, although its specific activity was somewhat lower. Although other ammonia-assimilatory enzymes were demonstrable, it seems unlikely that their combined activities could account for the remainder of the ammonia-assimilatory capacity not accounted for by the NADP-GDH. The ability of aspartate to serve as effectively as glutamate as the sole source of nitrogen for the growth of yeast apparently resides in their ability to utilize aspartate for amino acid biosynthesis via transamination.
Use of machine learning methods for prediction of acute toxicity in organs at risk following prostate radiotherapy.

PURPOSE The goal of this study is to investigate the advantages of large scale optimization methods vs conventional classification techniques in predicting acute toxicity for urinary bladder and rectum due to prostate irradiation. METHODS Clinical and dosimetric data of 321 patients undergoing prostate conformal radiotherapy were recorded. Gastro-intestinal and genito-urinary acute toxicities were scored according to the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer (RTOG/EORTC) scale. Patients were classified in two categories to separate mild (Grade < 2) from severe toxicity levels (Grade > 2). Machine learning methods at different complexity were implemented to predict toxicity as a function of multiple variables. The first approach consisted of a large scale optimization method, based on genetic algorithms (GAs) and artificial neural networks (ANN). The second approach was a binary classifier based on support vector machines (SVM). RESULTS The ANN and SVM-based solutions showed comparable prediction accuracy, exhibiting an area under the receiver operating characteristic (ROC) curve of 0.7. Different sensitivity and specificity features were measured for the two approaches. The ANN algorithm showed enhanced sensitivity if combined with appropriate classification criteria. CONCLUSIONS The results demonstrate that high sensitivity in toxicity prediction can be achieved with optimized ANNs, that are put forward to represent a valuable support in medical decisions. Future studies will be focused on enlarging the available patient database to increase the reliability of toxicity prediction algorithms and to define optimal classification criteria.
The relationship between low back magnetic resonance imaging, surgery, and spending: impact of physician self-referral status.

OBJECTIVE To examine the relationship between use of magnetic resonance imaging (MRI) and receipt of surgery for patients with low back pain. DATA SOURCES Medicare claims for a 20 percent sample of beneficiaries from 1998 to 2005. STUDY DESIGN We identify nonradiologist physicians who appear to begin self-referral arrangements for MRI between 1999 and 2005, as well as their patients who have a new episode of low back pain care during this time. We focus on regression models that identify the relationship between receipt of MRI and subsequent use of back surgery and health care spending. Receipt of MRI may be endogenous, so we use physician acquisition of MRI as an instrument for receipt of MRI. The models adjust for demographic and socioeconomic covariates as well as month, year, and physician fixed effects. DATA COLLECTION/EXTRACTION METHODS We include traditional, fee-for-service Medicare beneficiaries with a visit to an orthopedist or primary care physician for nonspecific low back pain, and no claims for low back pain in the year prior. PRINCIPAL FINDINGS In the first stage, acquisition of MRI equipment is a strongly correlated with patients receiving MRI scans. Among patients of orthopedists, receipt of an MRI scan increases the probability of having surgery by 34 percentage points. Among patients of primary care physicians, receiving a low back MRI is not statistically significantly associated with subsequent surgery receipt. CONCLUSIONS Orthopedists and primary care physicians who begin billing for the performance of MRI procedures, rather than referring patients outside of their practice for MRI, appear to change their practice patterns such that they use more MRI for their patients with low back pain. These increases in MRI use appear to lead to increases in low back surgery receipt and health care spending among patients of orthopedic surgeons, but not of primary care physicians.
Retinoids and Cancer: Antitumoral Effects of ATRA, 9-cis RA and the New Retinoid IIF on the HL-60 Leukemic Cell Line

Objective: To compare the antitumoral effects of all-trans retinoic acid (ATRA) and 9-cis retinoic acid (9-cis RA) with those of 5-OH,11-O-hydrophenanthrene (IIF), a new derivative of retinoic acid. Materials and Methods: The effect of retinoids was tested on cell line HL-60. Cell differentiation and apoptosis were evaluated by morphological and biochemical analysis as bcl-2 protein and by DNA fragmentation assay. The ability to activate retinoic acid receptors (RAR) and/or retinoid X receptors (RXR) and to modulate gene expression was determined by transactivation assay. Results: With cell line HL-60, the antiproliferative effect of IIF was stronger than that of ATRA and 9-cis RA. Following retinoid treatment, cells appeared to differentiate and apoptotic cells were observed. The appearance of DNA laddering and a decrease in the amount of bcl-2 protein confirmed apoptosis. IIF transcriptionally activated RXR-γ more than RAR-α. Conclusion: The findings indicate that IIF transcriptionally activates RXR-γ preferentially, induces apoptosis and has a more antiproliferative activity than ATRA and 9-cis RA on cell line HL-60.