Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.

The statistical properties of sample estimation and bootstrap estimation of phylogenetic variability from a sample of nucleotide sequences are studied by using model trees of three taxa with an outgroup and by assuming a constant rate of nucleotide substitution. The maximum-parsimony method of tree reconstruction is used. An analytic formula is derived for estimating the sequence length that is required if P, the probability of obtaining the true tree from the sampled sequences, is to be equal to or higher than a given value. Bootstrap estimation is formulated as a two-step sampling procedure: (1) sampling of sequences from the evolutionary process and (2) resampling of the original sequence sample. The probability that a bootstrap resampling of an original sequence sample will support the true tree is found to depend on the model tree, the sequence length, and the probability that a randomly chosen nucleotide site is an informative site. When a trifurcating tree is used as the model tree, the probability that one of the three bifurcating trees will appear in > or = 95% of the bootstrap replicates is < 5%, even if the number of bootstrap replicates is only 50; therefore, the probability of accepting an erroneous tree as the true tree is < 5% if that tree appears in > or = 95% of the bootstrap replicates and if more than 50 bootstrap replications are conducted. However, if a particular bifurcating tree is observed in, say, < 75% of the bootstrap replicates, then it cannot be claimed to be better than the trifurcating tree even if > or = 1,000 bootstrap replications are conducted. When a bifurcating tree is used as the model tree, the bootstrap approach tends to overestimate P when the sequences are very short, but it tends to underestimate that probability when the sequences are long. Moreover, simulation results show that, if a tree is accepted as the true tree only if it has appeared in > or = 95% of the bootstrap replicates, then the probability of failing to accept any bifurcating tree can be as large as 58% even when P = 95%, i.e., even when 95% of the samples from the evolutionary process will support the true tree. Thus, if the rate-constancy assumption holds, bootstrapping is a conservative approach for estimating the reliability of an inferred phylogeny for four taxa.
Early Analgesia for Children With Acute Abdominal Pain

Objectives. The objectives of this study were to determine whether the administration of morphine to children with acute abdominal pain would impede the diagnosis of appendicitis and to determine the efficacy of morphine in relieving the pain. Methods. This was a double-blind, randomized, placebo-controlled trial involving 5- to 16-year-old children who presented to the emergency department of a children’s hospital with a chief complaint of acute abdominal pain that was thought by the pediatric emergency attending physician to require a surgical consultation. Subjects were randomized to receive intravenously administered morphine or normal saline solution. Clinical data and the emergency physician’s confidence in his or her clinical diagnosis (0–100%) were recorded systematically with a standardized form. This was repeated 15 minutes after administration of the study medication. The surgeon assessed the child within 1 hour and completed a similar data collection sheet. Pain was assessed, with a color analog scale, before and after study medication administration. Each subject was monitored for 2 weeks after enrollment. Results. One hundred eight children were enrolled; 52 received morphine and 56 received a placebo saline solution. There were no differences between groups in demographic variables or the degree of pain. There were no differences between groups in the diagnoses of appendicitis or perforated appendicitis or the number of children who were observed and then underwent laparotomy. The reduction in the mean pain score was significantly greater in the morphine group (2.2 vs 1.2 cm). The emergency physicians’ and surgeons’ confidence in their diagnoses was not affected by the administration of morphine. Conclusions. Our data show that morphine effectively reduces the intensity of pain among children with acute abdominal pain and morphine does not seem to impede the diagnosis of appendicitis.
IMMUNOREACTIONS INVOLVING PLATELETS. V. POST-TRANSFUSION PURPURA DUE TO A COMPLEMENT-FIXING ANTIBODY AGAINST A GENETICALLY CONTROLLED PLATELET ANTIGEN. A PROPOSED MECHANISM FOR THROMBOCYTOPENIA AND ITS RELEVANCE IN "AUTOIMMUNITY".

thrombocytopenic state developing in the underlying disorder an of bone the of thrombocytopenic purpura antibody remaining in the supernatant serum using the average results of 3 different dilutions. Individual points for each amount of platelets used were obtained with platelets from a different donor. The C'-fixing activity of the platelets (@ high-activity, 0 low-activity) was determined as described
HIV incidence determination in the United States: a multiassay approach.

BACKGROUND Accurate testing algorithms are needed for estimating human immunodeficiency virus (HIV) incidence from cross-sectional surveys. METHODS We developed a multiassay algorithm (MAA) for HIV incidence that includes the BED capture enzyme immunoassay (BED-CEIA), an antibody avidity assay, HIV load, and CD4(+) T-cell count. We analyzed 1782 samples from 709 individuals in the United States who had a known duration of HIV infection (range, 0 to >8 years). Logistic regression with cubic splines was used to compare the performance of the MAA to the BED-CEIA and to determine the window period of the MAA. We compared the annual incidence estimated with the MAA to the annual incidence based on HIV seroconversion in a longitudinal cohort. RESULTS The MAA had a window period of 141 days (95% confidence interval [CI], 94-150) and a very low false-recent misclassification rate (only 0.4% of 1474 samples from subjects infected for >1 year were misclassified as indicative of recent infection). In a cohort study, annual incidence based on HIV seroconversion was 1.04% (95% CI, .70%-1.55%). The incidence estimate obtained using the MAA was essentially identical: 0.97% (95% CI, .51%-1.71%). CONCLUSIONS The MAA is as sensitive for detecting recent HIV infection as the BED-CEIA and has a very low rate of false-recent misclassification. It provides a powerful tool for cross-sectional HIV incidence determination.
IMAGING AFTER DISCRETE SCATTERING EVENTS 3 . 1 Looking Around Corners

Ultrafast imaging has been a key enabler to many novel imaging modalities, including looking behind corners and imaging behind scattering layers. With picosecond time resolution and unconventional sensing geometries, ultrafast imaging can fundamentally impact sensing capabilities in industrial and biomedical applications. This paper reviews the fundamentals, recent advances, and the future prospects of ultrafast imaging-based modalities.
Door-to-Needle Time in Acute Stroke Treatment and the “July Effect”

Intravenous thrombolysis improves outcomes in acute ischemic stroke in a time-dependent fashion. As in teaching hospitals, clinical outcomes may worsen due to the arrival of new inexperienced house staff early in the academic year (July effect, JE), we evaluated the impact of the “JE” on the door-to-needle time for intravenous thrombolysis and other stroke outcomes. In this retrospective cohort study, we assessed all acute ischemic strokes treated with intravenous thrombolysis between July 2003 and June 2016. Among 101 patients, there was no detrimental July effect on the door-to-needle time, rate of thrombolysis within 60 minutes of arrival, thrombolysis of stroke mimics, post-thrombolysis intracranial hemorrhages, National Institutes of Health Stroke Scale, and modified Rankin Scale outcomes.
Reflections on the rise in asthma morbidity and mortality.

Morbidity and mortality for asthma appear to be on the increase in the United States and many other Western countries.1-7The prevalence of this common condition may also be increasing.8,9These trends are worrisome, because they come at a time when morbidity and mortality from many chronic diseases are decreasing, when we think we have a fairly sound understanding of the pathophysiology of asthma, and when we believe we have more effective drugs for its management. Asthma mortality rates declined in the United States and Canada from 1965 through 1978 and then started to rise again. From 1980 to 1987, total deaths from asthma in the United States increased from 2891 to 4360.3 This represents a 31% increase in the death rate, from 1.3/100 000 population to 1.7/100 000. The rate for females increased more rapidly than the rate for males, and death rates were generally higher for
Instant Camera Translation and Voicing for Signs

Optical Character Recognition (OCR) is a class of problems that converts images or handwritten texts to machine-encoded text. In this project, we focus on one aspect of the general OCR problems and apply image processing techniques to sign image recognition for people who are not familiar with English. We incorporate four different kinds of algorithms that either handle the input image at text level or image level, and build a neat and useful Android application to facilitate instant English-to-Chinese translation and voicing. Such application has the advantage of in-phone computation, and thus saves the trouble of the communication with the servers. In addition, we perform detailed analysis on the algorithms and compare them under different cases. The statistical aspects concerning the accuracy, robustness and speed of each algorithm are presented.
A Workshop Series Using Peer-grading to Build Drug Information, Writing, Critical-thinking, and Constructive Feedback Skills

Objective. To utilize a skills-based workshop series to develop pharmacy students’ drug information, writing, critical-thinking, and evaluation skills during the final didactic year of training. Design. A workshop series was implemented to focus on written (researched) responses to drug information questions. These workshops used blinded peer-grading to facilitate timely feedback and strengthen assessment skills. Each workshop was aligned to the didactic coursework content to complement and extend learning, while bridging and advancing research, writing, and critical thinking skills. Assessment. Attainment of knowledge and skills was assessed by rubric-facilitated peer grades, faculty member grading, peer critique, and faculty member-guided discussion of drug information responses. Annual instructor and course evaluations consistently revealed favorable student feedback regarding workshop value. Conclusion. A drug information workshop series using peer-grading as the primary assessment tool was successfully implemented and was well received by pharmacy students.
On the Design Process of a 6-kVA Quasi-Z-inverter Employing SiC Power Devices

This paper presents the design process of a 6-kVA quasi-Z-source inverter built with SiC power devices, in particular, employing SiC MOSFETs and SiC Schottky diodes. The main design target is to find the optimal parameters and a good agreement between the efficiency and power density of the converter. The performance of the system may be influenced not only by the switching frequency but also from the specific pulsewidth modulated (PWM) method or type of SiC MOSFET, and, therefore, various design cases are analyzed. At a final step, the 6 kVA/3 × 400 VAC inverter employing the 80 mΩ SiC MOSFETs and operating at 100 kHz with the minimum switching number method is chosen for investigation and a laboratory prototype is built. From experiments, the high performance of the designed system is confirmed. More specifically, it is shown that an efficiency above 95.6% (at 400 VDC, B = 1.9) and a power density higher than 2 kW/dm3 have been reached. Last but not least, the obtained results, which can be recognized as leading in the area of impedance source converters, show the great benefits gained by employing the new power semiconductor devices.
Fungi in lake ecosystems

This review highlights the presence and ecological roles of fungi in lakes, and aims to stim- ulate research in aquatic mycology. In the study of lentic systems, this field is an almost completely neglected topic and, if considered at all, has often been restricted to specific groups of fungi, such as yeasts, filamentous fungi (e.g. aquatic hyphomycetes), or phycomycetes (an obsolete taxonomic category that included various fungal and fungal-like organisms). We document that aquatic fungi are common in various lentic habitats. They play potentially crucial roles in nutrient and carbon cycling and interact with other organisms, thereby influencing food web dynamics. The development and application of molecular methods have greatly increased the potential for unraveling the biodiversity and ecological roles of fungi in lake ecosystems. We searched the literature for reports on all fungi occurring in lake ecosystems. The present study summarizes information on the highly diverse mycoflora in lake micro- habitats and highlights the main processes they influence. We also point out ecological niches of fungi in lakes that have been examined only superficially or ignored completely. We demonstrate that we now have the methodology to perform systematic studies to finally fill in some of the large gaps in this field.
Selective Suppression of JV-Acetylglucosaminyltransferase III Activity in a Human Hepatoblastoma Cell Line Transfected with Hepatitis B Virus1

UUP-<V-acetylglucosamine:ÃŸ-u-mannoside ÃŸ-l,4WV-acetylglucosaminyl-transferase III (GnT-III) is a key enzyme in the branching of asparagine-linkcd oligosaccharides, which are present in surface membrane proteins of various tissues and in secretory glycoproteins. The activity of GnT-III was assayed in 2 human hepatoblastoma cell lines, lluhd. which was the parental cell line, and 11lÃ¬diI, which was established by transfection of 3 tandem copies of the hepatitis B virus genome into Huh6. A significant difference in GnT-III activity was found between Iluhh and HB611 (136 Â± 18.3 pmol/h/mg versus 6.7 Â±2.4 pmol/h/mg; mean Â±SD, P < 0.001), whereas levels of the glycosyltransferases a-3-o-mannoside /! -l,4-\-acetylglucosaminyltransferase IV, a-6-ii-mannoside ÃŸ-l,6-/V-acetylglu- cosaminyltransferase-V, ÃŸ-l,4-galactosyltransferase were almost the same in both cell lines. Northern blot analysis indicated that the decreased activity of GnT-III in HB611 was due to the decreased transcript. When 11lÃ¬di1 was treated with interferon-a, expression of hepatitis B virus-related mRNA decreased, and the activity of GnT-III increased from 8.5 Â±3.8 to 22.0 Â±7.2 pmol/h/mg (mean Â±SU, /' < 0.05). This increase was not found in Iluhd. Binding capacity with erythrocyte phytohemagglutinin in these cells using fluorescence-activated cell sorter analysis was different, suggesting that the structure of sugar chain on the cell surface might be altered by suppression of GnT-III activity. This is the first report that hepatitis B virus selectively suppressed the GnT-III activity in hepatoblas toma cells.
Removal of Low Frequency Noise from ECG signal using Genetic Algorithm

- The Electrocardiogram is commonly used technique for non-invasive analysis of the electrical activity of the heart in real-time. Electrocardiographic signals can be degraded by different types of noises like power-line interference, electrode contact, motion artifacts, muscle contraction, baseline drift, instrumental noise and electrosurgical noise. Baseline noise is low frequency signal caused by the loose connection of electrode and skin. Genetic algorithm is applied to remove this type of noise to get better diagnosis of the signal and observe the results in term of mean square error of the error signal for baseline wander noise. In this paper, the comparison of the results obtained from genetic algorithm and the results obtained from the digital FIR filters are done. To validate this method, the recording of signals from MIT-BIH is used. The examining of the purposed algorithm was conducted in MATLAB environment
A Novel Busbar Protection Based on Fault Component Integrated Impedance

This paper describes a novel principle for protecting busbars. The principle uses the ratio between the fault component voltage and the fault component differential current of the busbar to detect faults, which is defined as the fault component integrated impedance in this paper. The fault component integrated impedance of an external fault reflects the capacitance impedance of the busbar whereas that of an internal fault reflects the parallel connection result of the impedances of all the feeders connected to the busbar. As a result, the magnitudes of the integrated impedances are quite different between an external fault and an internal fault. According to such a characteristic, the criterion of fault detection is put forward, which has the inherent immunity to the impact of current flowing out when a fault occurs in the protection zone of the breaker-and-a-half busbar and is insensitive to fault resistance. The impact of the current transformer (CT) saturation on the proposed principle is discussed in this paper. Following the changes on the argument of the fault component integrated impedance, a feasible CT saturation detection algorithm is presented. EMTP simulation results verify the sensitivity and reliability of the proposed principle.
Identification of novel RP2 mutations in a subset of X‐linked retinitis pigmentosa families and prediction of new domains

X‐linked Retinitis Pigmentosa (XLRP) shows a huge genetic heterogeneity with almost five distinct loci on the X chromosome. So far, only two XLRP genes have been identified, RPGR (or RP3) and RP2, being mutated in approximately 70% and 10% of the XLRP patients. Clinically there is no clearly significative difference between RP3 and RP2 phenotypes. In the attempt to assess the degree of involvement of the RP2 gene, we performed a complete mutation analysis in a cohort of patients and we identified five novel mutations in five different XLRP families. These mutations include three missense mutations, a splice site mutation, and a single base insertion, which, because of frameshift, anticipates a stop codon. Four mutations fall in RP2 exon 2 and one in exon 3. Evidence that such mutations are different from the 21 RP2 mutations described thus far suggests that a high mutation rate occurs at the RP2 locus, and that most mutations arise independently, without a founder effect. Our mutation analysis confirms the percentage of RP2 mutations detected so far in populations of different ethnic origin. In addition to novel mutations, we report here that a deeper sequence analysis of the RP2 product predicts, in addition to cofactor C homology domain, further putative functional domains, and that some novel mutations identify RP2 amino acid residues which are evolutionary conserved, hence possibly crucial to the RP2 function. Hum Mutat 18:109–119, 2001. © 2001 Wiley‐Liss, Inc.
Multishot for High Spatial Resolution

Conventional Cartesian non-diffusion pulse sequences acquire k-space in multiple excitations (a.k.a. shots). As the phase errors originating from motion during the diffusion preparation time are random in nature and large compared to the phase used to spatially encode the image, the use of multi-shot sequences with diffusion gradients is not straightforward, and in most cases severe image ghosting will result.
Plasmid-Encoded Multidrug Resistance of Salmonella typhi and some Enteric Bacteria in and around Kolkata, India: A Preliminary Study

The present study investigates the occurrence of R-plasmid in Salmonella typhi isolates from enteric fever cases in and around Kolkata (1991-2001), India following in vitro conjugation experiments, isolation of plasmid DNAs and agarose gel electrophoretic analysis. The multidrug resistant (MDR) S. typhi strains contained a transferable plasmid conferring resistance to ampicillin, chloramphenicol, cotrimoxazole and tetracycline. The plasmid encoding ACCoT-resistance of Escherichia coli, Klebsiella pneumoniae and Proteus vulgaris were conjugative and co-migrated with the plasmid of MDR S. typhi isolates. The antibiotic sensitive S. typhi isolates did not contain any plasmid. Thus the findings of the present study confirmed the instability of the R-plasmid in S. typhi, and that the antibiotic sensitive S. typhi strains acquired the R-plasmid from other enteric bacteria such as E. coli, K. pneumoniae and P.vulgaris to undergo a suitable adaptation for survival in the changing antibiotic environment.
Boundary Constrained Control of Delayed Nonlinear Schrödinger Equation

This paper studies regional boundary stabilization of nonlinear Schrödinger equation with state delay and bounded internal disturbance. The boundary constrained control law is designed by using the backstepping method. Regional input-to-state stability of the perturbed system with time-delay is established by a Lyapunov function and a generalized Halanay's inequality. Estimates on the set of initial conditions are found starting from which the solutions are exponentially attracted to a bounded set. A numerical example demonstrates the efficiency of the results.
Air Trapping: A Cause of Heterogeneous Attenuation

Purpose: To investigate important factors affecting the frequency of air trapping through observation of normal lung attenuation, and propose a cause of heterogeneous attenuation. Materials and Methods: In this ethical committee-approved study, a total of 109 patients (30 males, 79 females; mean age, 58.2 years; range, 27 - 81 years) were included. All patients had undergone inspiratory and expiratory chest thin-section computed tomography (CT) examinations and pulmonary function tests. Air trapping on CT images was graded subjectively. Hounsfield units (HU) lung attenuation value and lung volume were measured on CT images. All variables (age, sex, indices of pulmonary function test results, air trapping score, HU value, and rate of change in lung volume) were compared by diagnoses and air trap- ping findings cohorts. The correlation between lung function test results and expiratory HU attenuation were analyzed. Results: Interstitial pneumonia showed higher and bronchiolitis obliterans showed lower HU attenuation at normal and air trapping regions. The variables affecting air trapping findings were age, a ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1.0/FVC), maximal expiratory flow at 50% of forced vital capacity (MEF50), HU attenuation at normal regions, and rate of change in lung volume. Compared with expiratory HU attenuation, significant positive correlation was shown to FEV1.0/FVC and negative correlation to single-breath diffusion capacity for carbon monoxide, which was confirmed by a simple regression analysis. Conclusion: It can be suggested that lung attenuation can increase when fibrosis is advanced, and this is exaggerated when lungs are compressed.