Miracle-dz/UniFAR-FTUs huggingface dataset:
Subnetwork hierarchies of biochemical pathways

MOTIVATION The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied. RESULTS We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks. AVAILABILITY An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp. umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION Supplementary material is available at http://www.tp. umu.se/forskning/networks/meta/
Self-Rapport: A Note on Psychology and Instruction

It is argued in this note that we can take instruction and give it because we instruct ourselves, with a self-rapport as the basic movement of our cognitive activity or thinking. Psychology does not, it is argued, have to explain human curiosity or human understanding; but it can talk about how to and how we deal with these things — that is, their conditions of operation — if it pays attention to the instructional facts. When attention is given to the interactive and social context of cognition, some educationists' criticisms of instructional psychology may be countered, and the psychology of cognition and its development will benefit from being more reality oriented. It is concluded that the empiricism of psychology is not a cold recording of behaviour, but rather a study of instructive plans for action, with both better plans and better action as the goal.
Pearl: a CMOS timing analyzer

Pearl is a timing analyzer that has been used to verify both full-custom VLSI and gate array designs. Rather than verify that a design meets a given clock timing, Pearl automatically determines the minimum error-free clock period and duty cycles. The author describes the mechanism used to determine the timing relationship each node in the circuit has with respect to the clock edges. He then shows how these dependencies, together with the setup and hold time requirements of latches and registers in the circuit, are used to formulate timing constraints between the clock edges. These timing requirements are solved using a linear programming algorithm to determine the minimum time of each clock edge. The algorithm is first described for the case of a circuit composed of functional models and then applied to MOS switch circuits. The author also describes transistor signal-flow direction rules for CMOS circuits used to eliminate false paths. <<ETX>>
EFFECTS OF UNILATERAL AND BILATERAL LABYRINTHECTOMY AND INTRACRANIAL SECTION OF EIGHTH NERVE: EXPERIMENTS ON MONKEYS

Despite the importance of the vestibular system for the maintenance of posture and equilibrium, as may be inferred from the numerous secondary connections of the central nuclei, relatively few observations have been made concerning the behavior of higher mammals, such as the monkey, after carefully controlled experimental lesions of the vestibular system have been produced. A great number of observations have been made on lower forms, such as the rabbit, cat and dog. A complete bibliography of all the experiments preceding those of the last few years may be found in the writings of Camis, 1 Griffith, 2 Maxwell 3 and Magnus. 4 So far as we can determine reference has been made in only two contributions to the effects on behavior of lesions of endorgans in the monkey. Beyer and Lewandowsky 5 mentioned briefly the effects of the removal of an inner ear in one monkey, and in addition
The use of thermal imaging to evaluate body temperature changes of athletes during training and a study on the impact of physiological and morphological factors on skin temperature

Purpose. The aim of this study was to assess the temperature changes of selected body surfaces (the arm and forearm) as a res­ ponse to 90­minute physical exercise as well as to analyze the impact of physiological and morphological factors on the dynamics of temperature change. Methods. A study group that consisted of 12 professional volleyball players was subjected to endurance training which lasted 90 minutes. Numerous physiological and morphological factors were measured, with mean temperatures registered from the body surface of the upper extremities before, immediately after, and ten min after physical effort by a thermal camera (SC500 ThermaCAM camera) at room temperature. Results. After physical exercise, a fall in skin temperature result­ ing from prolonged sweating during the dynamic exercise tests was observed. The temperature changes in volleyball players, recorded in a series of tests, were found to be larger on the front surfaces of their upper extremities when compared to the rear. In addition, statistically significant positive correlation between maximum oxygen uptake (VO 2max ) and %Hr max , calculated with the decrease in skin temperatures, was found. Conclusions. The strong and statistically significant influence of maximum oxygen uptake on the drop in surface temperature of the upper extremities (arm and forearm) immediately after the exercise indicates that thermography can be used as an additional, non­invasive method that provides information on a player’s fitness level in comparison to other athletes.
Texas Lifestyle Limits Transmission of Dengue Virus

Urban dengue is common in most countries of the Americas, but has been rare in the United States for more than half a century. In 1999 we investigated an outbreak of the disease that affected Nuevo Laredo, Tamaulipas, Mexico, and Laredo, Texas, United States, contiguous cities that straddle the international border. The incidence of recent cases, indicated by immunoglobulin M antibody serosurvey, was higher in Nuevo Laredo, although the vector, Aedes aegypti, was more abundant in Laredo. Environmental factors that affect contact with mosquitoes, such as air-conditioning and human behavior, appear to account for this paradox. We conclude that the low prevalence of dengue in the United States is primarily due to economic, rather than climatic, factors.
The 'Reality' of Rhetoric and the Learning organization in the UK

The concept of the learning organization has been prominent in management thinking in theory and practice for the past decade, with many books and articles being written in both North America and Europe and many employers in both the private and public sectors embracing it in their employment strategies. Becoming one is seen as a key to combating - and indeed thriving in - uncertain and adverse operating conditions. The last few decades of management theory have seen an explosion in constructs which carry significant amounts of persuasive language and the learning organization is no different. This paper attempts to problematize the learning organization in terms of the rhetoric inherent its theory. First, it charts where the rhetoric has come from and, second, identifies and analyses certain leitmotifs that are discernible in much of the prominent literature: turbulence and change, unitarism, empowerment, and personal development. Ultimately, this paper attempts to map conceptually the implications of the rhetoric for the employee in the learning organization.
Quantitative approaches to the study of bistability in the lac operon of Escherichia coli

In this paper, the history and importance of the lac operon in the development of molecular and systems biology are briefly reviewed. We start by presenting a description of the regulatory mechanisms in this operon, taking into account the most recent discoveries. Then we offer a survey of the history of the lac operon, including the discovery of its main elements and the subsequent influence on the development of molecular and systems biology. Next the bistable behaviour of the operon is discussed, both with respect to its discovery and its molecular origin. A review of the literature in which this bistable phenomenon has been studied from a mathematical modelling viewpoint is then given. We conclude with some brief remarks.
Crosstalk noise reduction in synthesized digital logic circuits

As CMOS technology scales into the deep submicrometer regime, digital noise is becoming a metric of importance comparable to area, timing, and power, for analysis and design of CMOS VLSI systems. Noise has two detrimental effects in digital circuits: First, it can destroy logical information carried by a circuit net. Second, it causes delay uncertainty: Non critical paths might become critical because of noise. As a result, circuit speed becomes limited by noise, primarily because of capacitive coupling between wires. Most design approaches address the crosstalk noise problem at the layout generation stage, or via postlayout corrections. With continued scaling, too many circuit nets require corrections for noise, causing a design convergence problem. This work suggests to consider noise at the gate-level netlist generation stage. The paper presents a simplified analysis of on-chip crosstalk models, and demonstrates the significance of crosstalk between local wires within synthesized circuit blocks. A design flow is proposed for automatically synthesizing CMOS circuits that have improved robustness to noise effects, using standard tools, by limiting the range of gate strengths available in the cell library. The synthesized circuits incur a penalty in area/power, which can be partially recovered in a single postlayout corrective iteration. Results of design experiments indicate that delay uncertainty is the most important noise-related concern in synthesized static CMOS logic. Using a standard synthesis methodology, critical path delay differences up to 18% of the clock cycle time have been observed in functional blocks of microprocessor circuits. By using the proposed design flow, timing uncertainty was reduced to below 3%, with area and power penalties below 20%.
Workspaces of a walking machine and their graphical representation. Part I: kinematic workspaces

Summary This paper addresses the kinematic workspaces of a walking machine and their graphical representation. The workspaces for walking machines are denned and the methods for investigating various workspaces are presented; the kinematic workspace constraints are established; the displacement is analysed; an algorithm for investigation of kinematic workspaces is presented; and the position and orientation kinematic workspaces are analysed and graphically represented for an example walking machine design.
Reference Group Influence on Product and Brand Purchase Decisions

Consumer perceptions of reference group influence on product and brand decisions were examined using 645 members of a consumer panel and 151 respondents in a followup study. Differences for 16 products in informational, value expressive, and utilitarian influence were investigated in a nested repeated measures design. The results support hypothesized differences in reference group influence between publicly and privately consumed products and luxuries and necessities.
A Parallel Algorithm for Bayesian Network Parameter Learning Based on Factor Graph

Bayesian Network parameter learning is one of the core issues of Bayesian Network research. The parameter estimation of Bayesian Network from large incomplete dataset can be very compute-intensive. A factor graph based Bayesian Network parameter learning algorithm using MapReduce is presented in this paper, which decomposes one Bayesian Network into factors and gets the Bayesian Network parameter through computing the conditional probability tables of each factor independently using Expectation Maximization (EM) algorithm within MapReduce framework. Experimental results show that when the number of training samples is 107, the speed of this parallel algorithm can get 2~6 times the speed of Sequential Expectation Maximization. The algorithm can reduce the training time significantly with increasing the number of Hadoop nodes. Compared with the existing parallel EM method using MapReduce, this algorithm has also a higher speed and can avoid the problem of load imbalance at the same time.
Expanding the Activity of Tissue Inhibitors of Metalloproteinase (TIMP)-1 against Surface-Anchored Metalloproteinases by the Replacement of Its C-Terminal Domain: Implications for Anti-Cancer Effects

Tissue inhibitors of metalloproteinases (TIMPs) are the endogenous inhibitors of the matrix metalloproteinases (MMPs) and a disintegrin and metalloproteinases (ADAMs). TIMP molecules are made up of two domains: an N-terminal domain that associates with the catalytic cleft of the metalloproteinases (MP) and a smaller C-terminal domain whose role in MP association is still poorly understood. This work is aimed at investigating the role of the C-terminal domain in MP selectivity. In this study, we replaced the C-terminal domain of TIMP-1 with those of TIMP-2, -3 and -4 to create a series of “T1:TX” chimeras. The affinity of the chimeras against ADAM10, ADAM17, MMP14 and MMP19 was investigated. We can show that replacement of the C-terminal domain by those of other TIMPs dramatically increased the affinity of TIMP-1 for some MPs. Furthermore, the chimeras were able to suppress TNF-α and HB-EGF shedding in cell-based setting. Unlike TIMP-1, T1:TX chimeras had no growth-promoting activity. Instead, the chimeras were able to inhibit cell migration and development in several cancer cell lines. Our findings have broadened the prospect of TIMPs as cancer therapeutics. The approach could form the basis of a new strategy for future TIMP engineering.
Comparative Transcriptional and Translational Analysis of Leptospiral Outer Membrane Protein Expression in Response to Temperature

Background Leptospirosis is a global zoonosis affecting millions of people annually. Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry. Past studies found that various leptospiral outer membrane proteins are differentially expressed at different temperatures. However, our microarray studies highlighted a divergence between protein abundance and transcript levels for some proteins. Given the abundance of post-transcriptional expression control mechanisms, this finding highlighted the importance of global protein analysis systems. Methodology/Principal Findings To complement our previous transcription study, we evaluated differences in the proteins of the leptospiral outer membrane fraction in response to temperature upshift. Outer membrane protein-enriched fractions from Leptospira interrogans grown at 30°C or overnight upshift to 37°C were isolated and the relative abundance of each protein was determined by iTRAQ analysis coupled with two-dimensional liquid chromatography and tandem mass spectrometry (2-DLC/MS-MS). We identified 1026 proteins with 99% confidence; 27 and 66 were present at elevated and reduced abundance respectively. Protein abundance changes were compared with transcriptional differences determined from the microarray studies. While there was some correlation between the microarray and iTRAQ data, a subset of genes that showed no differential expression by microarray was found to encode temperature-regulated proteins. This set of genes is of particular interest as it is likely that regulation of their expression occurs post-transcriptionally, providing an opportunity to develop hypotheses about the molecular dynamics of the outer membrane of Leptospira in response to changing environments. Conclusions/Significance This is the first study to compare transcriptional and translational responses to temperature shift in L. interrogans. The results thus provide an insight into the mechanisms used by L. interrogans to adapt to conditions encountered in the host and to cause disease. Our results suggest down-regulation of protein expression in response to temperature, and decreased expression of outer membrane proteins may facilitate minimal interaction with host immune mechanisms.
Antibacterial Activity of Protocatechuic Acid Ethyl Ester on Staphylococcus aureus Clinical Strains Alone and in Combination with Antistaphylococcal Drugs

The aim of the presented study was to examine in vitro the antibacterial activity of protocatechuic acid ethyl ester (ethyl 3,4-dihydroxybenzoate, EDHB) against Staphylococcus aureus clinical isolates alone and in the combination with four selected antibiotics. The EDHB antimicrobial activity was tested against twenty S. aureus strains isolated from the clinical samples, and three reference strains. The phenotypes and genotypes of resistance to methicillin for the tested strains were defined as well as the phenotypic resistance to macrolides, lincosamides and streptogramin B (MLSB). EDHB displayed diverse activity against examined S. aureus strains with the minimal inhibitory concentration (MIC) within the range from 64 to 1024 µg/mL. Addition of ¼ MIC of EDHB into the Mueller-Hinton Agar (MHA) resulted in augmented antibacterial effect in the presence of clindamycin. In the case of cefoxitin no synergistic effect with EDHB was noted. For erythromycin and vancomycin the decrease of mean MICs in the presence of EDHB was observed but did not reach statistical significance. The results of the present study showed that in vitro EDHB possesses antibacterial activity against S. aureus clinical strains and triggers a synergistic antimicrobial effect with clindamycin and to the lesser extent with erythromycin and vancomycin.
Finding Speedup in Parallel Processors

While recently the focus of architects and programmers has been on multi core, the alternative of processor node plus array oriented accelerator has some significant advantages especially in compute intensive static applications. We propose an acceleration methodology based on FPGA arrays (but, in principle it could be GPU or Cell based). The methodology uses a comprehensive application analysis supported by high performance FPGA hardware. The analysis provides a dataflow graph of the application which is replicated in SIMD for multiple data strips until limited by the pin bandwidth, then pipelined (MISD) until circuit limited. An oil exploration application shows the possibility of speedup of over 300x over an Intel Xeon.
Gonadotropin Ovulation Induction (OI) and Intrauterine Insemination IUI): An Outdated Therapy

Traditionally, ovulation induction (OI) with intrauterine insemination (IUI) has been a strategy used to maximize pregnancy outcomes in patients attempting pregnancy. A common pattern of performing OI/IUI historically has been to begin OI using oral medications, such as Clomiphene Citrate or Letrozole, and then escalating medical management to include injectable Gonadotropins such as follicle stimulating hormone (FSH). However, current medical literature shows Gonadotropin IUI to be associated inferior to other available fertility therapies in terms of both medical risks and cost effectiveness. Therefore, Gonadotropin IUI is now thought to be a suboptimal intervention for many patients. Based on current medical literature, the role of Gonadotropin IUI is likely to continually decline in the future. This trend will benefit patients by decreasing medical risks and increasing the cost effectiveness of fertility treatments.
Simultaneous two-view epipolar geometry estimation and motion segmentation by 4D tensor voting

We address the problem of simultaneous two-view epipolar geometry estimation and motion segmentation from nonstatic scenes. Given a set of noisy image pairs containing matches of n objects, we propose an unconventional, efficient, and robust method, 4D tensor voting, for estimating the unknown n epipolar geometries, and segmenting the static and motion matching pairs into n, independent motions. By considering the 4D isotropic and orthogonal joint image space, only two tensor voting passes are needed, and a very high noise to signal ratio (up to five) can be tolerated. Epipolar geometries corresponding to multiple, rigid motions are extracted in succession. Only two uncalibrated frames are needed, and no simplifying assumption (such as affine camera model or homographic model between images) other than the pin-hole camera model is made. Our novel approach consists of propagating a local geometric smoothness constraint in the 4D joint image space, followed by global consistency enforcement for extracting the fundamental matrices corresponding to independent motions. We have performed extensive experiments to compare our method with some representative algorithms to show that better performance on nonstatic scenes are achieved. Results on challenging data sets are presented.
Lipoprotein Receptors Redundantly Participate in Entry of Hepatitis C Virus

Scavenger receptor class B type 1 (SR-B1) and low-density lipoprotein receptor (LDLR) are known to be involved in entry of hepatitis C virus (HCV), but their precise roles and their interplay are not fully understood. In this study, deficiency of both SR-B1 and LDLR in Huh7 cells was shown to impair the entry of HCV more strongly than deficiency of either SR-B1 or LDLR alone. In addition, exogenous expression of not only SR-B1 and LDLR but also very low-density lipoprotein receptor (VLDLR) rescued HCV entry in the SR-B1 and LDLR double-knockout cells, suggesting that VLDLR has similar roles in HCV entry. VLDLR is a lipoprotein receptor, but the level of its hepatic expression was lower than those of SR-B1 and LDLR. Moreover, expression of mutant lipoprotein receptors incapable of binding to or uptake of lipid resulted in no or slight enhancement of HCV entry in the double-knockout cells, suggesting that binding and/or uptake activities of lipid by lipoprotein receptors are essential for HCV entry. In addition, rescue of infectivity in the double-knockout cells by the expression of the lipoprotein receptors was not observed following infection with pseudotype particles bearing HCV envelope proteins produced in non-hepatic cells, suggesting that lipoproteins associated with HCV particles participate in the entry through their interaction with lipoprotein receptors. Buoyant density gradient analysis revealed that HCV utilizes these lipoprotein receptors in a manner dependent on the lipoproteins associated with HCV particles. Collectively, these results suggest that lipoprotein receptors redundantly participate in the entry of HCV.
Brain size and ‘intelligence’

This review was prompted by recent claims—made in the search for a biological basis to ‘intelligence’—of a relationship between the latter and brain size. Attention is drawn to the methodological deficiencies of the early studies which found such a relationship, and the carelessness and bias which have marked some of the earlier reviews. A recent—and by far the most satisfactory—study found no correlation between brain size and IQ. It is naive to extrapolate from infrahuman to the human species since the evolved capabilities of all are ecologically conditioned and incomparable; and Homo sapiens has apparently shown no increase in brain size since its emergence as a species. Apart from its interest for present controversies over ‘intelligence’, the history of work on brain size and its review are a lesson in the devices of bias. They also point to the need to refer to original sources rather than rely on possibly biased middlepersons.