Miracle-dz/UniFAR-FTUs huggingface dataset:
The Pursuit of Clinical Truth: Role of Epidemiology/Observation Studies

The need for evidence‐based medicine as a foundation for optimal patient care requires application of the best scientific methods. Various methods used in the search for clinical truth are discussed. The most powerful method to test a clinical hypothesis is the randomized, controlled clinical trial. By contrast, epidemiology/observation studies (EOS) have inherent weaknesses that can lead to erroneous conclusions. Five such examples, two older and three very recent, are discussed to provide historical perspective and demonstrate potential problems with EOS. Each incident has produced widespread consternation or confusion among physicians. Types of bias leading to errors in EOS are discussed, and the need is emphasized for more rigorous evaluation of EOS by investigators, as well as editors, to avoid repetition of past mistakes and to ensure publication of correct medical information.
Investigation of Entropy and Complexity Measures for Detection of Seizures in the Neonate

The performance of three Entropy/complexity measures in detecting EEG seizures in the neonate were investigated in this study. A dataset containing EEG recordings from 11 neonates, with documented electrographic seizures, was employed in this study. Based on patient independent tests Shannon Entropy was found to provide the best in discrimination between seizure and non-seizure EEG in the neonate. Lempel-Ziv complexity and Multi-scale Entropy were second and third respectively, while Sample Entropy did not prove a useful feature for discriminating seizure patterns from non-seizure patterns.
Auctioning the Airwaves: The Contest for Broadband PCS Spectrum

The House and Senate of the United States Congress recently passed legislation that directs the FCC to establish a system for using auctions to allocate the use of radio spectrum for personal communications services. There is a unique and unprecedented set of issues that arise in this context, which are of interest to economists, industry analysts, regulators, and policymakers. We discuss these issues and evaluate their likely impact on the outcome of the spectrum auctions. In addition, we argue that there may be pitfalls in the auction procedure adopted by the FCC, and we discuss possible alternative procedures. Coauthors are William W. Sharkey, Yossef Spiegel, and Simon Wilkie. Copyright 1995 by MIT Press.
Heat shock protein expression and temperature distribution in prostate tumours treated with laser irradiation and nanoshells

Purpose: Sub-lethal temperature elevations in the tumour incurred during laser cancer therapy can induce heat shock protein (HSP) expression leading to enhanced tumour survival and recurrence. Nanoshells utilised in combination with laser therapy can potentially enable selective heat deposition, greater thermal injury, and diminished HSP expression in the tumour. The study objective was to measure the distribution of temperature and HSP expression in prostate tumours in response to laser therapy alone or with nanoshells to determine if these combinatorial therapies can minimise HSP expression. Methods: PC3 cells were inoculated in the backs of CB17-Prkd c SCID/J mice and treated with external laser irradiation (wavelength of 810 nm, irradiance of 5 W/cm2, spot size of 5 mm, and heating duration of 3 min) alone or in combination with gold nanoshells (diameter of 55 nm and outer gold shell thickness of 10 nm) introduced into the tumour 24 h prior to laser treatment. Magnetic resonance temperature imaging was used to measure the distribution of temperature elevation in the tumours during laser treatment. Tumours were sectioned 16 h following laser treatment, stained for Hsp27 and Hsp70, imaged with a confocal microscope, and HSP expression levels were quantified as a function of depth in the tumours. Results: Maximum temperature elevations at the tumour surface were 28°C for laser treatment only and 50°C for laser heating in combination with gold nanoshells. Laser therapy alone caused significant induction of HSP expression in the first few millimeters of the tumour depth, whereas decreasing HSP expression occurred with greater tumour depth. Tumours treated with laser and nanoshells experienced substantial temperatures (73–78°C) at the tumour surface and temperatures greater than 53°C in the first few millimeters which eliminated HSP expression. Conclusion: Inclusion of nanoshells in laser therapy can provide a mechanism for enhancing heat deposition capable of eliminating HSP expression within a larger tumour region compared to laser heating alone.
Major Depression Before and After Myocardial Infarction: Its Nature and Consequences

The prevalence and prognostic impact of previous depression, depression in the hospital, and depression after discharge were studied in 222 patients admitted for acute myocardial infarction (MI). Patients were interviewed 1 week, 6 months, and 12 months after the index MI using a modified version of the Diagnostic Interview Schedule (DIS); patients also completed the Beck Depression Inventory (BDI). Patients or family members were recontacted at 18 months to determine survival. Some 27.5% of patients had at least one episode of major depression before their MI, but only 7.7% were depressed at some point during the year preceding the infarct. Overall, 31.5% of patients experienced depression in the hospital or during the year postdischarge. Some 35 patients were depressed in the hospital, 30 became depressed between discharge and 6 months, and five more between 6 and 12 months after the MI. History of depression increased the risk of depression in the hospital and after discharge. Depression in the hospital was associated with an increased risk of mortality over 18 months. Patients who experienced a recurrent depression in the hospital were at particularly high risk. Although patients who became depressed after discharge differed from those who remained depression-free in terms of age, history of depression, BDI scores, and the number of depression symptoms on the DIS in the hospital, a model including these variables identified only 14.7% of the patients who became depressed after returning home. Post-MI depression is common and largely unrelated to medical and psychosocial factors.
A Formal Verification Framework for Static Analysis ? As well as its instantiation to the resource analyzer costa and formal verification tool KeY

Static analysis tools, such as resource analyzers, give useful information on software systems, especially in real-time and safety-critical applications. Therefore, the question of the reliability of the obtained results is highly important. static analyzers typically combine a range of complex techniques, make use of external tools, and evolve quickly. To formally verify such systems is not a realistic option. In this work we a different approach whereby, instead of the tools, we formally verify the results of the tools. The central idea of such a formal verification framework for static analysis is the method-wise translation of the information about a program gathered during its static analysis into specification contracts that contain enough information for them to be verified automatically. We instantiate this framework with costa, a state-of-the-art static analysis system for sequential Java programs, for producing resource guarantees and KeY, a state-of-the-art verification tool, for formally verifying the correctness of such resource guarantees. Resource guarantees allow to be certain that programs will run within the indicated amount of resources, which may refer to memory consumption, number of instructions executed, etc. Our results show that the proposed tool cooperation can be used for automatically producing verified resource guarantees.
Human cytomegalovirus IE2 86-kilodalton protein binds p53 but does not abrogate G1 checkpoint function

Physical interactions between human cytomegalovirus (HCMV) immediate-early (IE) proteins and key cell cycle regulatory proteins have been suggested as a mechanism whereby this herpesvirus modifies cellular control of proliferation. Observed similarities to interactions of other DNA virus proteins (human papillomavirus type 16 E6 and E7, simian virus 40 large T antigen, and adenovirus type 5 E1A and E1B) with cell cycle modulatory proteins such as p53 and Rb have suggested that HCMV IE proteins may likewise alter the G1-to-S phase transition. The IE2 region gene product IE86 has been shown to specifically bind p53, potentially modifying p53 G1 checkpoint function. To examine this possibility, p53-mediated G1 arrest in the presence of IE86 was assessed. Retroviral constructs were created to facilitate the stable expression of IE86 and IE72, another IE protein implicated in HCMV-mediated alteration of cell cycle progression. Western analysis and immunoprecipitation confirmed IE protein expression and binding of IE86 to p53, respectively. Chloramphenicol acetyltransferase assays examining the ability of IE86 to repress activity from the HCMV major IE promoter or activate the HCMV early promoter for the 2.2-kb class of RNAs demonstrated the functional integrity of the IE86 protein. Induction of DNA damage in normal, uninfected fibroblasts (FB) or FB expressing IE86 by actinomycin D (Act D) resulted in increased p53 levels, a predominance of the hypophosphorylated form of Rb, and increased expression of both p21(CIP1/WAF1) and mdm-2. Fluorescence-activated cell sorting revealed that both uninfected and IE86-expressing FB experienced dramatic G1 arrest following exposure to Act D. The clear demonstration of these p53-dependent responses in the presence of IE86 indicates that binding to this viral protein does not compromise the ability of p53 to elicit growth arrest following DNA damage.
Adhesion property of carbon nanotube micelles for high-quality printed transistors

Ink property for high-quality printed carbon nanotube (CNT) transistor was investigated and it was found that adhesion property of the semiconducting (s-) CNT micelles was a key issue. Anionic surfactants would prevent the s-CNT micelles from being adsorbed to the surface which was functionalized by amino groups and deteriorate the device characteristics. High-quality and high-uniform CNT transistors were obtained by using anionic surfactant free s-CNT ink, and a pressure sensor sheet was successfully demonstrated. The CNT transistors were fabricated by mask-less printing and potentialities of on-demand and on-line fabrication of large-area electronics utilizing printed CNT transistors were shown.
Mapping nucleotides in the 126-kDa protein gene that control the differential symptoms induced by two strains of tobacco mosaic virus.

The differential symptom determinants of the Holmes' masked (M) and U1 strains of tobacco mosaic virus previously were mapped to the 5'-coterminal open reading frame (ORF) encoding the 126-kDa protein and the N-terminal two-thirds of the 183-kDa protein. Both proteins influence viral RNA accumulation, but the function of, and impact on, symptom formation by large domains within the 126-kDa gene, which are not conserved with sequences in analogous ORFs from other related viruses, are unknown. In the current study, cDNA clones representing each strain (i.e., MIC-TMV and U1-TMV) were mutated in these nonconserved domains to further define the nucleotides responsible for mosaic symptom induction on Nicotiana tabacum. Progeny virus of a mutant containing only eight nucleotide substitutions from the MIC-TMV sequence to the U1-TMV sequence within the 126-kDa protein ORF of MIC-TMV induced U1-TMV-like symptoms. Single or multiple substitutions among these eight nucleotides further defined residues critical for symptom modulation. Complementary substitutions in the MIC-TMV and U1-TMV sequences did not always yield progeny virus that induced complementary visual symptoms. Progeny of some mutants contained second-site spontaneous mutations at specific positions shown to influence symptom phenotype. For a subset of the stable site-directed mutants, there was no correlation between severity of systemic symptoms and chlorotic lesion size or virus accumulation in these chlorotic lesions on inoculated leaves.
Computer programs for estimating substrate flux into steady‐state biofilms from pseudoanalytical solutions

Fixed‐film processes employing microorganisms attached to an inert surface (biofilms) are widely used for biological treatment of municipal and industrial wastewater. For optimal design and analysis of these processes, mathematical models are necessary that describe the dynamics of contaminant transport within these biofilms and the associated contaminant utilization by the microorganisms. However, these governing equations that typically involve Fickian diffusion for contaminant transport and Monod kinetics for contaminant utilization are inherently nonlinear and have no closed form solutions except under special conditions. This can restrict their use in the classroom as cumbersome numerical techniques must be used for their solution. This problem is well documented in the literature and several authors have presented pseudoanalytical solutions that replace numerical solutions with algebraic equations. In the present study, we present pseudoanalytical solution‐based computer programs for estimating substrate flux and biofilm thickness for a steady‐state biofilm. Depending upon the intended end use, these programs can either partially or totally automate the solution process. In the partial automation mode, they can serve to enhance student understanding of important concepts related to steady‐state biofilms, while complete automation can help bring more challenging and realistic problems associated with steady‐state biofilms into the classroom. The programs have been tested on MATLAB version 5.0 and are available as freeware for educational purposes. © 2002 Wiley Periodicals, Inc. Comput Appl Eng Educ 10: 26–32, 2002; Published online in Wiley InterScience (www.interscience.wiley.com.); DOI 10.1002/cae.10017
Low-Complexity Character Extraction in Low-Contrast Scene Images

There is wide application for the extraction of textual information from low-contrast, complex natural images. We are particularly interested in segmentation and thresholding algorithms for use in a portable text-to-speech system for the vision impaired. Reading low-contrast LCD displays is the target application. We present a low-complexity method for automatically extracting text of any size, font, and format from images acquired by a video camera that may be poorly focused and aimed, under conditions of inadequate and uneven illumination. The new method consists of fast thresholding that combines a local variance measure with a logical stroke-width method, and with a low-complexity statistical and contextual noise segmentation. The performance of this method compares favorably with more complex methods for the extraction of characters from scene images. Initial results are encouraging for application in a robust portable reader.
Algebraic formulations for the solution of the nullspace‐free eigenvalue problem using the inexact Shift‐and‐Invert Lanczos method

Given the generalized symmetric eigenvalue problem Ax=λMx, with A semidefinite and M definite, we analyse some algebraic formulations for the approximation of the smallest non‐zero eigenpairs, assuming that a sparse basis for the null space is available. In particular, we consider the inexact version of the Shift‐and‐Invert Lanczos method, and we show that apparently different algebraic formulations provide the same approximation iterates, under some natural hypotheses. Our results suggest that alternative strategies need to be explored to really take advantage of the special problem setting, other than reformulating the algebraic problem. Experiments on a real application problem corroborate our theoretical findings. Copyright © 2002 John Wiley & Sons, Ltd.
Isolation of poliovirus 2C mutants defective in viral RNA synthesis

Two poliovirus mutants were isolated that contain an oligonucleotide linker insertion in the 2C-coding region of the viral genome. One, 2C-31, has a strongly temperature-sensitive phenotype and the other, 2C-32, forms small plaques on HeLa cell monolayers at all temperatures. Both mutants have a severe temperature-sensitive defect in viral RNA synthesis but little effect on the types of viral protein that are made. Temperature shift experiments showed that the 2C function is continuously required for viral RNA synthesis to proceed. The 2C mutants could be complemented in trans by mutants with mutations in other viral proteins. Protein 2C is also the locus of the guanidine resistance and dependence mutants, a drug whose action also affects viral RNA synthesis. Thus, protein 2C is one that is needed continually for viral RNA synthesis and, at least with these temperature-sensitive alleles, can be provided in trans.
MLH1 constitutional and somatic methylation in patients with MLH1 negative tumors fulfilling the revised Bethesda criteria

Lynch syndrome (LS) is a tumor predisposing condition caused by constitutional defects in genes coding for components of the mismatch repair (MMR) apparatus. While hypermethylation of the promoter of the MMR gene MLH1 occurs in about 15% of colorectal cancer samples, it has also been observed as a constitutional alteration, in the absence of DNA sequence mutations, in a small number of LS patients. In order to obtain further insights on the phenotypic characteristics of MLH1 epimutation carriers, we investigated the somatic and constitutional MLH1 methylation status of 14 unrelated subjects with a suspicion of LS who were negative for MMR gene constitutional mutations and whose tumors did not express the MLH1 protein. A novel case of constitutional MLH1 epimutation was identified. This patient was affected with multiple primary tumors, including breast cancer, diagnosed starting from the age of 55 y. Investigation of her offspring by allele specific expression revealed that the epimutation was not stable across generations. We also found MLH1 hypermethylation in cancer samples from 4 additional patients who did not have evidence of constitutional defects. These patients had some characteristics of LS, namely early age at onset and/or positive family history, raising the possibility of genetic influences in the establishment of somatic MLH1 methylation.
The Canine Factor VIII cDNA and 5’ Flanking Sequence

Summary Factor VIII is a trace plasma glycoprotein involved as a cofactor in the activation of factor X by factor IXa. Inherited deficiency of factor VIII results in the X-linked bleeding disorder hemophilia A which has been documented in humans, horses, sheep and dogs. In this report, the putative proximal promoter, 5’ untranslated region, complete coding sequence and 3’ untranslated region of the canine factor VIII gene have been characterized. When compared to the human gene, the 5’ flanking region shows conservation of transcription factor binding sites in the 5’ untranslated region. Alignment of the amino acid sequence with that of the previously reported human, mouse and pig proteins demonstrates sequence identity of between 77 and 92% for the A1, A2, A3, C1 and C2 domains but an identity of only between 44 and 62% for the central B domain. The three thrombin cleavage sites are conserved in the canine sequence as are the protein C cleavage sites and the von Wille-brand factor binding region. In addition, all six tyrosine residues that are known to undergo sulfation in the human protein are conserved in the dog. The 3’ untranslated region of the canine gene extends 1.5 kilo-bases. The initial 700 basepairs of this sequence are highly GC rich and the sequence terminates with 2 alternative potential polyadenylation sites. The knowledge of this sequence, in combination with a well described canine model of hemophilia A, provides the necessary starting point for studies addressing the long-term evaluation of factor VIII gene therapy using a homologous transgene.
Enhancing techniques for efficient topic hierarchy integration

Here, we study the problem of integrating documents from different sources into a comprehensive topic hierarchy. Our objective is to develop efficient techniques that improve the accuracy of traditional categorization methods by incorporating categorization information provided by data sources into categorization process. Notice that in the World-Wide Web, categorization information is often available from information sources. We present several enhancing techniques that use categorization information to enhance traditional methods such as naive Bayes and support vector machines. Experiment on collections from Openfind and Yam, and Google and Yahoo! , well-known popular Web sites in Taiwan and USA, respectively, shows that our techniques significantly improve the classification accuracy from, for example, 55% to 66% for Naive Bayes, and from 57% to 67% for SVM for the data set collected from Yam and Openfind.
Flow-injection post chemiluminescence determination of phenol

A post-chemiluminescence (PCL) phenomenon was observed when phenol solution was injected into the reaction mixture after the finish of chemiluminescence (CL) reaction of alkaline potassium ferricyanide and calcein. The optimum conditions for this chemiluminescent reaction are in detail studied using a flow injection system. Based on the PCL reaction, a rapid and sensitive method for the determination of phenol was established. The linear response range of this method was from 1.0×10-6 to 1.0×10-4 g/mL with a linear correlation coefficient of 0.9986. The relative standard deviation for 5.0×10-5 g/mL phenol was 1.8 % (n = 11). The detection limit was 3×10-7 g/mL. This method has been successfully applied to the determination of phenol in waste water, and the results are satisfactory.
Body composition analysis of small pigs by dual-energy x-ray absorptiometry.

We evaluated the use of dual-energy x-ray absorptiometry (DXA) for measuring the gross body composition of small subjects in 97 pigs that ranged from 5 to 27 kg live body weight. Scans were performed using a Lunar DPXL densitometer in the pediatric mode (Version 3.8e). The DXA scans of the live pigs provided measurements of total fat, lean, and bone mineral content. After scanning, the pigs were killed, the entire body was ground, and samples were analyzed chemically (CHEM) for fat, protein, ash, and water content. We found that DXA significantly underestimated the percentage of fat in the body (DXA, 6.9+/-.33% vs CHEM, 10.9+/-.31%, P < .001). The correlation (r) between DXA and chemical measures of percentage fat was . 86 and for grams of fat it was . 96. Lean tissue mass measured by DXA was highly correlated with CHEM measurements of total grams of body water (r = .99), total grams of body protein (r = .94), and lean body mass (r = .99). The average DXA bone mineral content was within 2% of the amount estimated from total body ash and the correlation between the two values was . 94. The relationships between DXA and CHEM measurements for percentages of body composition of pigs that weighed between 5 and 27 kg are described by the following regression equations: %fatCHEM = 5.22 + [. 817.fatDXA], (r = .86, standard error of the estimate, SEE = 1.56); %proteinCHEM = -7.8 + [. 256%leanDXA], (r = .35, SEE = 2.3); %waterCHEM = -5.2 + [. 808-%leanDXA], (r = .59, SEE = 3.67). These results are consistent with previously reported results and suggest that even though direct use of DXA readings may not be sufficiently accurate, the high degree of correlation indicates that with proper calibration the DXA values can be used to predict body composition.