Miracle-dz/UniFAR-FTUs huggingface dataset:
Achievable performance bound for ITSE optimal controller design

This paper proposes a methodology to compute achievable performance bounds in the control of linear, stable discrete-time SISO plants. The performance is measured using a time-weighted cost function (ITSE) that quantifies the control error for a step reference or a step output disturbance. The proposed methodology relies on the use of a function space product that, for stable systems, can be defined in both frequency and time domain. The solution technique requires the expansion of stable functions in orthogonal series. An analytical expression is found for the computation of the optimal coefficients of the expansion. Numerical examples are given to illustrate the results.
Expression of HSP70 in response to heat-shock and its cDNA cloning from Mediterranean blue mussel

Expression of HSP70 in response to heat-shock was investigated at the protein and mRNA levels in Mediterranean blue mussel. Western and Northern blot analyses revealed that HSP70 was expressed following heat-shock in the mantle at both protein and mRNA levels, suggesting that gene expression of HSP70 is implicated in the cellular response to heat-shock stress in mussel. It was then attempted to clone HSP70 cDNA in order to determine the primary structure of mussel HSP70. As a result, two full-length cDNA encoding HSP70 were isolated from a cDNA library prepared from the heat-shocked mantle. The isolated cDNA consist of single open reading frames of 2067 bp and 1911 bp which encode proteins of 689 amino acids and 637 amino acids, respectively. Both HSP70 cDNA encode an ATPase do main, and a substrate-binding do main in addition to a Glu-Glu-Val-Asp (EEVD) peptide motif that is specific for cytosolic HSP70. These findings suggest that the cDNA clones obtained in the present study encode cytosolic HSP70.
A plea for intra-laboratory reference limits. Part 2. A bimodal retrospective concept for determining reference limits from intra-laboratory databases demonstrated by catalytic activity concentrations of enzymes

Abstract Background: The current recommendations for establishing intra-laboratory reference limits (RLs) cannot be fulfilled by most laboratories because of the expense involved. In the current study, a bimodal method was developed to derive RLs from data stored in a laboratory information system without any assumption concerning the distribution of the diseased subgroup. Methods: A smoothed kernel density function (Dmix) was estimated for the distribution of combined data for non-diseased and diseased adult subjects. It was assumed that the “central” part of the distribution represents the non-diseased population, which was defined and used to estimate a Gaussian distribution of either the original values or Box-Cox transformed data. This normal distribution was now considered the distribution of the non-diseased subgroup (Dnd). Percentiles were calculated to obtain retrospective RLs. The density function of the diseased subgroup (Dd) was calculated by subtracting the non-diseased density function from Dmix (Dd=Dmix–Dnd). The intersection point of the Dnd and Dd curves identified the RL with the highest diagnostic efficiency. Results: The model was applied to catalytic activity concentrations of several enzymes with data from different laboratories. The RLs obtained were similar to recently published consensus values. Differences between laboratories were small but significant. Gender stratification was necessary for alanine aminotransferase (ALT), aspartate aminotransferase (AST), and γ-glutymaltransferse (γ-GT), not significant for lipase and amylase and inconsistent among the laboratories for alkaline phosphatase (AP) and lactate dehydrogenase (LDH). Age stratification was only tested for two groups (18–49 and ≥50 years) and was significant for AST (females only), γ-GT and lipase, not significant for amylase and inconsistent for AP, LDH and ALT. For γ-GT, further stratification for age in decades was necessary for males. Creatine kinase MB (CK-MB) values were not stratified owing to the low number of data available. Conclusions: Retrospective RLs derived from intra-laboratory data pools for the catalytic activity concentration of enzymes using a modified procedure plausibly agreed with published consensus values. However, most RLs varied significantly among laboratories, thus supporting the “old” plea for intra-laboratory RLs. Clin Chem Lab Med 2007;45:1043–57.
Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing

N6-methyladenosine (m6A) residues are present as internal base modifications in most higher eucaryotic mRNAs; however, the biological function of this modification is not known. We describe a method for localizing and quantitating m6A within a large RNA molecule, the genomic RNA of Rous sarcoma virus. Specific fragments of 32P-labeled Rous sarcoma virus RNA were isolated by hybridization with complementary DNA restriction fragments spanning nucleotides 6185 to 8050. RNA was digested with RNase and finger-printed, and individual oligonucleotides were analyzed for the presence of m6A by paper electrophoresis and thin-layer chromatography. With this technique, seven sites of methylation in this region of the Rous sarcoma virus genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m6A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m6A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. Previous studies have determined that methylation occurs only in the sequences Gm6AC and Am6AC. We observed a high frequency of methylation at PuGm6ACU sequences. The possible involvement of m6A in RNA splicing events is discussed.
Open cascades as simple solutions to providing ultrasensitivity and adaptation in cellular signaling

Cell signaling is achieved predominantly by reversible phosphorylation–dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative-feedback loop with a buffering node, or incoherent feed-forward loop with a proportioner node. In this paper—using Goldbeter and Koshland-type expressions—we propose a differential equation model to describe a generic, open signaling cascade that elicits an adaptation response. This is accomplished by coupling N phosphorylation–dephosphorylation cycles unidirectionally, without any explicit feedback loops. Using this model, we show that as the length of the cascade grows, the steady states of the downstream cycles reach a limiting value. In other words, our model indicates that there are a minimum number of cycles required to achieve a maximum in sensitivity and amplitude in the response of a signaling cascade. We also describe for the first time that the phenomenon of ultrasensitivity can be further subdivided into three sub-regimes, separated by sharp stimulus threshold values: OFF, OFF-ON-OFF, and ON. In the OFF-ON-OFF regime, an interesting property emerges. In the presence of a basal amount of activity, the temporal evolution of early cycles yields damped peak responses. On the other hand, the downstream cycles switch rapidly to a higher activity state for an extended period of time, prior to settling to an OFF state (OFF-ON-OFF). This response arises from the changing dynamics between a feed-forward activation module and dephosphorylation reactions. In conclusion, our model gives the new perspective that open signaling cascades embedded in complex biochemical circuits may possess the ability to show a switch-like adaptation response, without the need for any explicit feedback circuitry.
Phase II trial of bevacizumab plus gemcitabine in patients with advanced pancreatic cancer.

PURPOSE Vascular endothelial growth factor (VEGF) plays a key role in the biology and prognosis of pancreatic cancer. Inhibitors of VEGF suppress the growth of pancreatic cancer in preclinical models. The objectives of this phase II study were to assess the response rate and overall survival of pancreatic cancer patients who received gemcitabine with the recombinant humanized anti-VEGF monoclonal antibody bevacizumab. PATIENTS AND METHODS Patients with previously untreated advanced pancreatic cancer received gemcitabine 1,000 mg/m(2) intravenously over 30 minutes on days 1, 8, and 15 every 28 days. Bevacizumab, 10 mg/kg, was administered after gemcitabine on days 1 and 15. Tumor measurements were assessed every two cycles. Plasma VEGF levels were obtained pretreatment. RESULTS Fifty-two patients were enrolled at seven centers between November 2001 and March 2004. All patients had metastatic disease, and 83% had liver metastases. Eleven patients (21%) had confirmed partial responses, and 24 (46%) had stable disease. The 6-month survival rate was 77%. Median survival was 8.8 months; median progression-free survival was 5.4 months. Pretreatment plasma VEGF levels did not correlate with outcome. Grade 3 and 4 toxicities included hypertension in 19% of the patients, thrombosis in 13%, visceral perforation in 8%, and bleeding in 2%. CONCLUSION The combination of bevacizumab plus gemcitabine is active in advanced pancreatic cancer patients. Additional study is warranted. A randomized phase III trial of gemcitabine plus bevacizumab versus gemcitabine plus placebo is ongoing in the Cancer and Leukemia Group B.
A Privacy-Enhancing Radio Frequency Identification Tag: Implementation of the Clipped Tag

The use of RFID tags for the tagging of individual consumer items is a distinct possibility The "clipped tag" has been suggested for individual items in order to enhance consumer privacy. The clipped tag allows the consumer to tear off a portion of the tag in order to transform a tag that may be read at a range of 10 meters to one than can only be read at a few cm. The use of these tags puts privacy protection in the hands of the consumer, provides a visual indication that the tag has been modified, but makes it possible for the tag to be used later for returns, recalls, or recycling. This paper describes an implementation of the clipped tag as a garment hang tag
Establishment and characterization of a new embryonic cell line from the silkworm, Bombyx mori

Insect cell lines are widely used for basic and applied research in the fields of insect pathology, genetics, and molecular biology. In the present study, a new continuous cell line designated BmE-SWU3 was established from blastokinesis-stage embryos of the silkworm Bombyx mori (Furong strain). The primary culture was initially performed using Grace’s medium supplemented with 20 % foetal bovine serum (FBS) at a constant temperature of 27 °C. The dominant cell type was round and spindle-shaped. Thus far, this cell line has been cultured continuously for 60 passages. The cell doubling time was approximately 3.0 days. The SSR profile of BmE-SWU3 differs from those of the silkworm BmE and BmN-SWU1 cell lines and from those of the Spodoptera frugiperda cell line Sf9 and the Drosophila cell line S2. However, the SSR profiles among the various passages of BmE-SWU3 were stable and identical. This new cell line was highly susceptible to Bombyx mori nucleopolyhedrovirus (BmNPV). Semi-quantitative RT-PCR indicated that the tissue-specific gene expression patterns were completely distinct from those of BmE and BmN-SWU1.
An Overview and Analysis of Voice Authentication Methods

Current solutions for passwords and authentication are insecure and have been hacked very regularly. As more and more information is on the Internet, the need for secure authentication has become ever more necessary. Biometric based authentication provides a promising solution because voice biometrics, like fingerprints, create unique identifiers for individuals. We present an analysis of current voice biometric software, propose a security policy for a voice authentication system, and provide two different implementations of potential voice authentication systems that aim to fix some of the deficits of the available open source solutions. In addition, we provide an evaluation of the advantages and disadvantages of our own implementations. Our code is available in a public repository at https://github.mit. edu/jodiec/6857 and https://github.mit. edu/ashoup/dejavuDemo.
Techniques towards understanding shear dependent thrombus formation

Several novel techniques are presented to provide both a qualitative and quantitative method of analysing shear dependent thrombus growth in real-time. Thrombus geometries are grown (in vitro) and imaged through four-dimensional (4D) confocal microscopy. Techniques to reconstruct a time corrected stack of confocal images into a three-dimensional (3D) surface are presented. The flow of blood (in silico) over the thrombus geometry is modelled by attaining a solution to the incompressible and steady state Navier-Stokes equations through the OpenFOAM package. Previous work ‎[5] has shown thrombus growth and platelet activation is highly sensitive to shear. As such the methods presented allow for the shear forces which platelets undergo prior to adhesion to be correlated with a range of parameters, including growth. The combination of these techniques allow for highly temporally and spatially resolved comparisons to be made as to the underlying mechanisms of platelet adhesion and aggregation.
Health-related quality of life and its growing importance in clinical practice.

With improving socioeconomic conditions and quality of medical care, patients around the world are becoming more concerned about the impact of disease on their daily life and social interactions. It is particularly important for chronic diseases like diabetes and hypertension that the impact of disease should not only be judged by its mortality but also by its social impact and disability. Unfortunately physicians are often being too concerned about the disease and treatment tend to overlook patients’ perception about their illness and their threshold for tolerance of discomfort.
Glycosylphosphatidylinositol-anchored Glucanosyltransferases Play an Active Role in the Biosynthesis of the Fungal Cell Wall*

A novel 1,3-β-glucanosyltransferase isolated from the cell wall of Aspergillus fumigatus was recently characterized. This enzyme splits internally a 1,3-β-glucan molecule and transfers the newly generated reducing end to the non-reducing end of another 1,3-β-glucan molecule forming a 1,3-β linkage, resulting in the elongation of 1,3-β-glucan chains. The GEL1 gene encoding this enzyme was cloned and sequenced. The predicted amino acid sequence of Gel1p was homologous to several yeast protein families encoded by GAS of Saccharomyces cerevisiae,PHR of Candida albicans, and EPD ofCandida maltosa. Although the expression of these genes is required for correct morphogenesis in yeast, the biochemical function of the encoded proteins was unknown. The biochemical assays performed on purified recombinant Gas1p, Phr1p, and Phr2p showed that these proteins have a 1,3-β-glucanosyltransferase activity similar to that of Gel1p. Biochemical data and sequence analysis have shown that Gel1p is attached to the membrane through a glycosylphosphatidylinositol in a similar manner as the yeast homologous proteins. The activity has been also detected in membrane preparations, showing that this 1,3-β-glucanosyltransferase is indeed active in vivo. Our results show that transglycosidases anchored to the plasma membrane via glycosylphosphatidylinositols can play an active role in fungal cell wall synthesis.
Leveraging model representations for system level design tools

New sophisticated EDA tools and methodologies are needed to make products viable in the marketplace by simplifying and reducing the different design stages. They are based on representations that have to be clean, complete and easy to manipulate. The needed key features are standardization, metadata programming, reflectivity and introspection. This work proposes a methodology based on . Net framework presenting all these features and allowing simpler specification, synthesis, validation and the creation of tools that cost less and take less time to build/customize. We present the simulator of ESys.Net as a case study. ESys.Net is an existing . Net based platform for system design.
Neurochemical and Psychoanalytical Approaches to Mania

There have been two main theoretical approaches towards understanding the pathogenesis of mania, the neurochemical and the psychoanalytical. Although the psychoanalytical approach is perhaps more concerned with the content and meaning of the illness for each individual than is the neurochemical, there are certain similarities between the ways in which both theories account for the observed clinical phenomena. This paper reviews the current neurochemical and psychoanalytic theories in the context of the relevant clinical findings and attempts to draw parallels between the two approaches.
Taguchi method based model predictive control design for laser scanner

In this paper, a Taguchi method based digital control scheme for the galvanometer laser scanner system is developed to overcome the system's inherent shortcomings. First and foremost, a second-order model of the galvanometer is derived using the step response approach. Subsequently, due to the capability of online calculation and good control performance, the Model Predictive Control (MPC) approach is employed to deal with the position control problems of the system. In the proposed approach, the optimal parameters of the MPC are determined using the Taguchi method. Furthermore, performance comparison among the proposed Taguchi method-based MPC, the GA-based PID controller and the Pseudo Derivative Feedback (PDF) with Feedforward controller modified in this paper is also performed. Finally, several experiments are conducted to verify the feasibility of the proposed approach. Experimental results demonstrate that the proposed approach can effectively reduce the settling time, maximum overshoot, and steady-state error of the galvanometer system under different amplitudes of step input commands.
Generation of Yersinia pestis Attenuated Strains by Signature-Tagged Mutagenesis in Search of Novel Vaccine Candidates

ABSTRACT In a search for novel attenuated vaccine candidates for use against Yersinia pestis, the causative agent of plague, a signature-tagged mutagenesis strategy was used and optimized for a subcutaneously infected mouse model. A library of tagged mutants of the virulent Y. pestis Kimberley53 strain was generated. Screening of 300 mutants through two consecutive cycles resulted in selection of 16 mutant strains that were undetectable in spleens 48 h postinfection. Each of these mutants was evaluated in vivo by assays for competition against the wild-type strain and for virulence following inoculation of 100 CFU (equivalent to 100 50% lethal doses [LD50] of the wild type). A wide spectrum of attenuation was obtained, ranging from avirulent mutants exhibiting competition indices of 10−5 to 10−7 to virulent mutants exhibiting a delay in the mean time to death or mutants indistinguishable from the wild type in the two assays. Characterization of the phenotypes and genotypes of the selected mutants led to identification of virulence-associated genes coding for factors involved in global bacterial physiology (e.g., purH, purK, dnaE, and greA) or for hypothetical polypeptides, as well as for the virulence regulator gene lcrF. One of the avirulent mutant strains (LD50, >107 CFU) was found to be disrupted in the pcm locus, which is presumably involved in the bacterial response to environmental stress. This Kimberley53pcm mutant was superior to the EV76 live vaccine strain because it induced 10- to 100-fold-higher antibody titers to the protective V and F1 antigens and because it conferred efficacious protective immunity.
Erratum zu: Böden in Permafrostgebieten der Arktis als Kohlenstoffsenke und Kohlenstoffquelle. Polarforschung, 81(1): 33-46, 2011

Tab. 1: Tab. 1: Eine Übersicht von Kohlenstoff-Studien in unterschiedlichen Permafrostregionen. Dargestellt sind Teilergebnisse der genannten Studien zu Permafrost beeinflussten Böden. Diese Liste zeigt nur einige Beispiele und erhebt keinen Anspruch auf Vollständigkeit. SOC = Boden eigener organischer Kohlenstoff. Tab. 1: Overview of carbon studies from different permafrost regions. Only results related to the permafrost-affected soils are presented. This list shows only some examples and is not intended to be exhaustive. SOC = soil organic carbon. Umbruch 81-2 12.10. 2012 12:30 Uhr Seite 156
The association between cognitive factors, pain and disability in patients with idiopathic chronic neck pain

Purpose. The aim of this study was to establish the relationship between known cognitive factors and levels of pain and disability in patients with idiopathic chronic neck pain. Method. Ninety-four patients referred for physiotherapy because of chronic neck pain completed measures of pain, disability, catastrophising, pain-related fear, pain vigilance and awareness and self-efficacy beliefs. Hierarchical multiple regression analyses were then performed to establish whether the cognitive factors were significant determinants of levels of pain and disability. Results. The cognitive measures were significantly related to levels of pain and disability, explaining 23% of the variance in pain intensity and 30% of the variance in disability. Specifically, greater catastrophising (β = 0.37, p < 0.05) and lower pain vigilance and awareness (β = − 0.32, p < 0.05) were associated with greater pain intensity. Moreover, greater catastrophising (β = 0.26, p < 0.05) and lower functional self-efficacy beliefs (β = − 0.34, p < 0.001) were significantly associated with greater levels of disability. Conclusions. Cognitive factors were strongly related to levels of pain and disability in patients with chronic neck pain. In view of this, targeting the modification of these cognitive factors should be an integral part of therapy when treating patients with idiopathic chronic neck pain.