Miracle-dz/UniFAR-FTUs huggingface dataset:
Lecture 5 Geometric Approaches

We look at some geometric approaches to nonrobustness. An intriguing idea here is the notion of " fixed precision geometry ". After all, if nonrobustness is a geometric phenomenon, it makes sense to modify the geometry to reflect the fixed precision we find in numbers. There are many ways to create such ersatz geometries, which in various ways try to recover the basic properties of standard Euclidean geometry. We illustrate several such geometries through a discussion of " fixed precision lines ". §1. What is a Finite Precision Line? Since qualitative errors is geometric in nature, we may attempt to modify the underlying geometry to be achieve robust behavior. E.g., with finite precision arithmetic, it seems reasonable to replace standard Euclidean geometry by some finite precision geometry. We have already met such a geometry in Chapter 1: we interpreted the standard epsilon-tweaking trick as manipulating new kinds of " points " and " lines " , namely, fat points and fat lines. There are many potential candidates for finite-precision geometries, even for the simple concept of lines. We give some common answers [26]. to the question " what is a finite precision line? " Each answer can be viewed as representative of a general approach to finite precision geometry. (a) fat line (b) polyline (c) rounded parameter lines (d) digital line
Glycosaminoglycan-binding microbial proteins in tissue adhesion and invasion: key events in microbial pathogenicity.

Glycosaminoglycans such as heparin, heparan sulphate and dermatan sulphate, are distributed widely in the human body. Several glycosaminoglycans form part of the extracellular matrix and heparan sulphate is expressed on all eukaryotic surfaces. The identification of specific binding to different glycosaminoglycan molecules by bacteria (e.g., Helicobacter pylori, Bordetella pertussis and Chlamydia trachomatis), viruses (e.g., herpes simplex and dengue virus), and protozoa (e.g., Plasmodium and Leishmania), is therefore of great interest. Expression of glycosaminoglycan-binding proteins depends on growth and culture conditions in bacteria, and differs in various phases of parasite development. Glycosaminoglycan-binding microbial proteins may mediate adhesion of microbes to eukaryotic cells, which may be a primary mechanism in mucosal infections, and are also involved in secondary effects such as adhesion to cerebral endothelia in cerebral malaria or to synovial membranes in arthritis caused by Borrelia burgdorferi. It has been suggested that they may enhance intracellular survival in macrophages. Microbial binding of heparin may interfere with heparin-dependent growth factors. Whether or not glycosaminoglycan-binding proteins mediate invasion of epithelial cells is a matter of controversy. Heparin and other glycosaminoglycans may have potential uses as therapeutic agents in microbial infections and could form part of future vaccines against such infections.
Localization of an accessory helicase at the replisome is critical in sustaining efficient genome duplication

Genome duplication requires accessory helicases to displace proteins ahead of advancing replication forks. Escherichia coli contains three helicases, Rep, UvrD and DinG, that might promote replication of protein-bound DNA. One of these helicases, Rep, also interacts with the replicative helicase DnaB. We demonstrate that Rep is the only putative accessory helicase whose absence results in an increased chromosome duplication time. We show also that the interaction between Rep and DnaB is required for Rep to maintain rapid genome duplication. Furthermore, this Rep–DnaB interaction is critical in minimizing the need for both recombinational processing of blocked replication forks and replisome reassembly, indicating that colocalization of Rep and DnaB minimizes stalling and subsequent inactivation of replication forks. These data indicate that E. coli contains only one helicase that acts as an accessory motor at the fork in wild-type cells, that such an activity is critical for the maintenance of rapid genome duplication and that colocalization with the replisome is crucial for this function. Given that the only other characterized accessory motor, Saccharomyces cerevisiae Rrm3p, associates physically with the replisome, our demonstration of the functional importance of such an association indicates that colocalization may be a conserved feature of accessory replicative motors.
ACHINE L EARNING FOR G ENE B EHAVIOUR C LASSIFICATION Karan Mangla

An interesting problem in biology is to determine the activation phase of genes. The human body contains nearly 20,000 genes. Many of these genes play a wide variety of roles in the cell cycle. Identifying the phase of activation of the gene can help determine its function in the gene. Experimentally determining the phase of all these genes can be expensive. Our tool attempts to use machine learning to determine the activation phase of a gene based on its expression profile. We first normalize the genes to be able to capture activation and deactivation. Next we apply SVM on this dataset using a small number of preclassified genes as our training set. Since genes can be active in multiple phases, we created a separate classifier for each activation phase.
Villous trophoblasts cultured on semi-permeable membranes form an effective barrier to the passage of high and low molecular weight particles.

An effective in vitro model of the placental villous syncytium cultured on semi-permeable substrata is essential for studies of infectious pathogen transmission from mother to fetus. Current models using amniotic membranes or thinner artificial membranes show significant leakage, suggesting disruption of tight junctions or the presence of gaps between syncytial units. Such disruption and discontinuity of trophoblast cultures are probably the result of high stromal cell contamination, poor viability and lack of proliferation in culture. We have successfully cultured confluent layers of tight-junctioned syncytium on semi-permeable insert membranes using highly viable purified cytotrophoblasts and an alternating multiple seeding and differentiation technique. Using criteria including transepithelial diffusion of high and low molecular weight substances, electrical resistance and directional secretion of the matrix metalloproteinase, MMP-9, we demonstrate that these cultures form effective and functional physical barriers that can be maintained for up to 1 month.
A comparison of two network-based file servers

This paper compares two working file servers in terms of their design goals, implementation issues, performance, and service experience. One server, the Xerox Distributed File System (XDFS) [10], was built at the Xerox Palo Alto Research Center; the other, the Cambridge File Server (CFS) [2, 3, 4], was built at the Cambridge University Computer Laboratory. Both file servers support concurrent random access to files over a network, and each offers an atomic transaction mechanism covering modifications to files.
Inference of a structured data model in migrating a legacy system to Java

Central to any legacy migration project is the translation of the data model. Decisions made here will have strong implications to the rest of the translation. Some legacy languages lack a structured data model, relying instead on explicit programmer control of the overlay of variables. In this paper we present our experience inferring a structured data model in such a language as part of a migration of eight million lines of code to Java. We discuss the common idioms of coding that were observed and give an overview of our solution to this problem.
Data Reduction Techniques for Instance-Based Learning from Human/Computer Interface Data

We describe the task of user-oriented anomaly detection for computer security. In this domain the goal is to develop a model of a computer user’s normal behavioral patterns and to detect anomalous conditions as deviations from expected behaviors. We present an instance-based learning (IBL) system for profiling users and examine some domain constraints with respect to our approach. In particular, we explore the data reduction problem; this domain is subject to unbounded data and concept drift but is constrained by limited resources so we must limit the size of the learned model. We empirically examine the data reduction performance of two clustering methods – an EM procedure, K-centers, and a greedy clustering method developed to address domain characteristics. We evaluate the relative strengths of the two methods along three performance axes: accuracy, mean time to generation of an alarm (TTA), and data compression.
Finding Domain Specific Polar Words for Sentiment Classification

This paper presents a method of using conditional random fields (CRF) for extracting polar words and determining the overall sentiment of text. We frame sentiment classification as a feature selection problem and conduct three sets of experiments by using: prior polarity lexicons, bag-of-words classifiers and CRF sequence models. The results show the potential of utilizing CRFs in discovering high quality context-dependent polar features.
Mechanisms for object caching in distributed applications using Java RMI

Remote Method Invocation (RMI), a mechanism to access remote objects in Java‐based distributed applications, uses network communication for each method invocation. Consequently, using RMI in a wide‐area environment can cause poor application performance. One solution to improve performance is to cache the objects such that network communication is not necessary for each method invocation. In this paper, we present mechanisms to transparently add object caching to RMI. These mechanisms are compatible with existing RMI applications and use an event‐based model to support different consistency policies. The mechanisms also include the ability to adaptively select the consistency policy for an object based on its usage pattern. A novel feature of our mechanisms is the use of a ‘reduced object’, which is a partial representation of the RMI object. We experimentally evaluate and demonstrate the benefits of our mechanisms. Copyright © 2006 John Wiley & Sons, Ltd.
Reducing Artifacts in JPEG Decompression Via a Learned Dictionary

The JPEG compression method is among the most successful compression schemes since it readily provides good compressed results at a rather high compression ratio. However, the decompressed result of the standard JPEG decompression scheme usually contains some visible artifacts, such as blocking artifacts and Gibbs artifacts (ringing), especially when the compression ratio is rather high. In this paper, a novel artifact reducing approach for the JPEG decompression is proposed via sparse and redundant representations over a learned dictionary. Indeed, an effective two-step algorithm is developed. The first step involves dictionary learning and the second step involves the total variation regularization for decompressed images. Numerical experiments are performed to demonstrate that the proposed method outperforms the total variation and weighted total variation decompression methods in the measure of peak of signal to noise ratio, and structural similarity.
Do parents reinforce somatic complaints in their children?

OBJECTIVE To examine the influence of parental solicitousness on self-reported somatic complaints in school-age children. DESIGN AND MAIN OUTCOME MEASURES Participants were 564 children (mean age 10 years) and their parents. Children completed self-report measures of somatic complaints, parental solicitousness, depressiveness, fear, and sense of coherence. Somatic complaints were assessed again 6 months later. Parents also completed a questionnaire about solicitousness. RESULTS Parental solicitousness as reported by children or parents was unrelated to the frequency of self-reported somatic complaints. Symptoms of depression, fear, and lower sense of coherence were associated with more somatic complaints, but did not interact with parental solicitousness. CONCLUSION Parental solicitousness seems unrelated to more frequent somatic complaints in schoolchildren.
Floorplanning with constraint extraction based on interconnecting information analysis

After the phase of high level synthesis, a lot of design information is hidden for the floorplanning process. As a result, the floorplanning process which is only aiming at decreasing area and wirelength may cause design failure for the circuits, because of ignoring some hidden constraints. In this paper, we propose a method to extract some geometric constraints based on interconnecting information analysis. And a new floorplanning algorithm with CBL representation which can handle these constraints is also proposed. And the final experimental results prove the effectiveness of our method.
Development of an Integrated Design and Simulation Environment for Concurrent Base-Arm Motion Control of Space Manipulators

To develop and verify the mot ion control of space manipulators experimentally, a manipulator system with a freely-moving base is needed. In addition, an integrated design and simulation environment is required for the system to study the operation under various conditions and in different scenarios before implementing the control scheme on the experimental hardware setup. Lastly, certain experiments need to be designed to validate and compare the performance of various control schemes quantitatively. This paper discusses the development of a new free-base manipulator system with its integrated design and simulation environment, as well as the design of a set of experiments that can statistically evaluate the performance of concurrent base-arm motion control schemes.
Short-Term Regulation of FcγR-Mediated Phagocytosis by TLRs in Macrophages: Participation of 5-Lipoxygenase Products

TLRs recognize a broad spectrum of microorganism molecules, triggering a variety of cellular responses. Among them, phagocytosis is a critical process for host defense. Leukotrienes (LTs), lipid mediators produced from 5-lipoxygenase (5-LO) enzyme, increase FcγR-mediated phagocytosis. Here, we evaluated the participation of TLR2, TLR3, TLR4, and TLR9 in FcγR-mediated phagocytosis and whether this process is modulated by LTs. Rat alveolar macrophages (AMs), murine bone marrow-derived macrophages (BMDMs), and peritoneal macrophages (PMs) treated with TLR2, TLR3, and TLR4 agonists, but not TLR9, enhanced IgG-opsonized sheep red blood cell (IgG-sRBC) phagocytosis. Pretreatment of AMs or BMDMs with drugs that block LT synthesis impaired the phagocytosis promoted by TLR ligands, and TLR potentiation was also abrogated in PMs and BMDMs from 5-LO−/− mice. LTB4 production induced by IgG engagement was amplified by TLR ligands, while cys-LTs were amplified by activation of TLR2 and TLR4, but not by TLR3. We also noted higher ERK1/2 phosphorylation in IgG-RBC-challenged cells when preincubated with TLR agonists. Furthermore, ERK1/2 inhibition by PD98059 reduced the phagocytic activity evoked by TLR agonists. Together, these data indicate that TLR2, TLR3, and TLR4 ligands, but not TLR9, amplify IgG-mediated phagocytosis by a mechanism which requires LT production and ERK-1/2 pathway activation.
Pitfalls and Possibilities in the Analysis of Biomass Allocation Patterns in Plants

Plants can differentially allocate biomass to leaves, stems, roots, and reproduction, and follow ontogenetic trajectories that interact with the prevailing climate. Various methodological tools exist to analyze the resulting allocation patterns, based either on the calculation of biomass ratios or fractions of different organs at a given point in time, or on a so-called allometric analysis of biomass data sampled across species or over an experimental growth period. We discuss the weak and strong points of each of these methods. Although both approaches have useful features, we suggest that often a plot of biomass fractions against total plant size, either across species or in the comparison of treatment effects, combines the best of both worlds.
Capacity of Orthogonal STBC in Spatially Correlated Nakagami-m Fading Channels with Partial Channel Side Information at the Transmitter

We analyze the capacity of multiple-input multiple-output (MIMO) systems employing orthogonal space-time block codes (STBC) in spatially correlated Nakagami-m fading channels under different power and rate adaptation policies. In this regard, we assume that partial channel state information (CSI) in form of the instantaneous post-processing signal-to-noise ratio (SNR) at the receiver-side is available to the transmitter, which might be efficiently fed back using a low-rate feedback channel. Numerical results illustrate the impact of fading correlation and the fading severity on the capacity and outline the performance differences between the distinctive adaptation policies
ESTIMATING VELOCITIES AND ACCELERATIONS OF ANIMAL LOCOMOTION: A SIMULATION EXPERIMENT COMPARING NUMERICAL DIFFERENTIATION ALGORITHMS

Functional biologists employ numerical differentiation for many purposes, including (1) estimation of maximum velocities and accelerations as measures of behavioral performance, (2) estimation of velocity and acceleration histories for biomechanical modeling, and (3) estimation of curvature, either of a structure during movement or of the path of movement itself. I used a computer simulation experiment to explore the efficacy of ten numerical differentiation algorithms to reconstruct velocities and accelerations accurately from displacement data. These algorithms include the quadratic moving regression (MR), two variants of an automated Butterworth filter (BF1-2), four variants of a method based on the signal9s power spectrum (PSA1-4), an approximation to the Wiener filter due to Kosarev and Pantos (KPF), and both a generalized cross-validatory (GCV) and predicted mean square error (MSE) quintic spline. The displacement data simulated the highly aperiodic escape responses of a rainbow trout Oncorhynchus mykiss and a Northern pike Esox lucius (published previously). I simulated the effects of video speed (60, 125, 250, 500 Hz) and magnification (0.25, 0.5, 1 and 2 screen widths per body length) on algorithmic performance. Four performance measures were compared: the per cent error of the estimated maximum velocity (Vmax) and acceleration (Amax) and the per cent root mean square error over the middle 80 % of the velocity (VRMSE) and acceleration (ARMSE) profiles. The results present a much more optimistic role for numerical differentiation than suggested previously. Overall, the two quintic spline algorithms performed best, although the rank order of the methods varied with video speed and magnification. The MSE quintic spline was extremely stable across the entire parameter space and can be generally recommended. When the MSE spline was outperformed by another algorithm, both the difference between the estimates and the errors from true values were very small. At high video speeds and low video magnification, the GCV quintic spline proved unstable. KPF and PSA2-4 performed well only at high video speeds. MR and BF1-2 methods, popular in animal locomotion studies, performed well when estimating velocities but poorly when estimating accelerations. Finally, the high variance of the estimates for some methods should be considered when choosing an algorithm.
Transmission Risk Factors and Treatment of Pediatric Shigellosis During a Large Daycare Center-Associated Outbreak of Multidrug Resistant Shigella sonnei: Implications for the Management of Shigellosis Outbreaks Among Children

Background: Shigellosis outbreaks in daycare centers result in substantial disease and economic burdens in the United States. The emergence of multidrug resistant Shigella strains raises questions regarding control of transmission within daycare centers and treatment for children. From May to October 2005, 639 Shigella sonnei cases were reported in northwest Missouri, mostly among persons exposed to daycare centers. Methods: We conducted a case-control investigation among licensed daycare centers (LDCs) in northwest Missouri to determine transmission risk factors, tested isolates for antimicrobial resistance, and described treatment practices. Case LDCs had secondary attack rates of shigellosis ≥2% (range, 2%–25%) and control LDCs ≤2% (range, 0%–1.3%). We interviewed LDC staff and performed on-site inspections. Thirty-one outbreak isolates were tested for antimicrobial resistance. We interviewed physicians and reviewed health department outbreak-related treatment data. Results: We enrolled 18 case and 21 control LDCs. LDCs with ≥1 sink in every room (odds ratio [OR]: 0.1; 95% confidence interval [CI]: 0.02–0.5) or a diapering station in every room (OR: 0.1; 95% CI: 0.01–0.6) were less likely to be case-LDCs. Resistance to ampicillin and trimethoprim-sulfamethoxazole was found in 90% of the outbreak strains. Among 210 children treated with antimicrobial agents, azithromycin was used in 92 (44%) while a fluoroquinolone was used in 11 (5%) children. Conclusions: During a large daycare center-associated shigellosis outbreak, strains were highly resistant to ampicillin and trimethoprim-sulfamethoxazole. Children were frequently treated with azithromycin and occasionally fluoroquinolones. Appropriate handwashing and diapering infrastructure are necessary to minimize spread of shigellosis within daycare centers, and could reduce use of antimicrobial agents.
Evaluation of a new efficient procedure for single-nucleotide polymorphism genotyping: tetra-primer amplification refractory mutation system-polymerase chain reaction

Abstract Tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) is a new efficient method for single-nucleotide polymorphism (SNP) genotyping. To determine the optimal conditions for ARMS-PCR we attempted to genotype ten SNPs. DNA was extracted from the peripheral blood of 168 unrelated healthy Japanese volunteers. Two problems inhibited uniform efficiency of the amplification of three bands. The first problem was the lower amplification efficiency of the shorter and allele-specific products compared with the largest product. This phenomenon was overcome by increasing the relative concentration of the inner primers. The second problem was non-specific amplification of the shorter products. To reduce the amplification of these nonspecific bands, adjusting any one of the following PCR conditions was effective: i) reducing the ratio of the inner primer concentration relative to that of the outer primers; ii) increasing the annealing temperature for the initial 5–10 cycles; iii) hot start PCR. With these procedures all ten of the SNPs were successfully genotyped. Our present data may be useful in the further application of tetra-primer ARMS-PCR to SNP genotyping.