Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovering Interesting Association Rules in Medical Data

We are presently exploring the idea of discovering association rules in medical data. There are several technical aspects which make this problem challenging. In our case medical data sets are small, but have high dimensionality. Information content is rich: there exist numerical, categorical, time and even image attributes. Data records are generally noisy. We explain how to map medical data to a transaction format suitable for mining rules. The combinatorial nature of association rules matches our needs, but current algorithms are unsuitable for our purpose. We thereby introduce an improved algorithm to discover association rules in medical data which incorporates several important constraints. Some interesting results obtained by our program are discussed and we explain how the program parameters were set. We believe many of the problems we come across are likely to appear in other domains.
Synthesis and Characterization of Bioactive Sol – Gel Glass: A Preliminary Study

Bioactive glasses based on SiO2-CaO-P2O5 system have been synthesized by sol – gel process. The powder glass obtained has been characterized by X-ray diffraction, X-ray fluorescence spectroscopy (XRF), and Fourier transform-infrared spectroscopy (FTIR). In vitro study reveals formation of apatite layer at surface of powder glass, after 3 days of soaking in simulated body fluid.
Less afterload sensitivity in short-term hibernating than in acutely ischemic and stunned myocardium.

Short-term hibernating myocardium is characterized by reduced contractile function during persistent moderate ischemia, the recovery of metabolic parameters, and the absence of necrosis. To study the afterload dependence of regional wall excursion in short-term hibernating myocardium, in 11 enflurane-anesthetized swine the left anterior descending coronary artery was cannulated and hypoperfused for 90 min to reduce anterior systolic wall thickening (WT, sonomicrometry) by 60%. Under control conditions, at 5 and 90 min ischemia the descending thoracic aorta was acutely constricted to increase left ventricular (LV) pressure by 30 mmHg. Under control conditions, increased LV pressure resulted in decreased WT [i.e., a negative slope of the relationship between WT and LV end-systolic pressure: -11.2 +/- 4.2 (SD) microm/mmHg]. This slope was further significantly decreased at 5 min ischemia (-26.5 +/- 8.8 microm/mmHg) but returned toward control values in short-term hibernating myocardium at 90 min ischemia (-17.2 +/- 6.6 microm/mmHg). At 30 min reperfusion, the slope was once more significantly decreased (-27.8 +/- 8.1 microm/mmHg). In conclusion, WT in short-term hibernating myocardium is less afterload dependent than in acutely ischemic and reperfused myocardium.
Multiscale morphology of the galaxy distribution

Many statistical methods have been proposed in the last years for analysing the spatial distribution of galaxies. Very few of them, however, can handle properly the border effects of complex observational sample volumes. In this paper, we first show how to calculate the Minkowski Functionals (MFs) taking into account these border effects. We then present a multiscale extension of the MF which gives us more information about how the galaxies are spatially distributed. A range of examples using Gaussian random fields illustrate the results. Finally, we have applied the Multiscale Minkowski Functionals (MMFs) to the 2dF Galaxy Redshift Survey data. The MMF clearly indicates an evolution of morphology with scale. We also compare the 2dF real catalogue with mock catalogues and found that A cold dark matter simulations roughly fit the data, except at the finest scale.
Increased oxygen radical‐dependent inactivation of metabolic enzymes by liver microsomes after chronic ethanol consumption

Enzymatic and nonenzymatic mixed‐function oxidase systems have been shown to generate an oxidant that catalyzes the inactivation of glutamine synthetase and other metabolic enzymes. Recent studies have shown that microsomes isolated from rats chronically fed ethanol generate reactive oxygen intermediates at elevated rates compared with controls. Microsomes from rats fed ethanol were found to be more effective than control microsomes in catalyzing the inactivation of enzymes added to the incubation system. The enzymes studied were alcohol dehydrogenase, lactic dehydrogenase, and pyruvate kinase. The inactivation process by both types of microsomal preparations was sensitive to catalase and glutathione plus glutathione peroxidase, but was not affected by superoxide dismutase or hydroxyl radical scavengers. Iron was required for the inactivation of the added enzymes; microsomes from the rats fed ethanol remained more effective than control microsomes in catalyzing the inactivation of enzymes in the absence or presence of several ferric complexes. The inactivation of enzymes was enhanced by the addition of menadione or paraquat to the microsomes, and rates of inactivation were higher with the microsomes from the ethanol‐fed rats. The enhanced generation of reactive oxygen intermediates and increased inactivation of enzymes by microsomes may contribute toward the hepatotoxic effects associated with ethanol consumption. —Dicker, E. ; Cederbaum, A. I. Increased oxygen radical‐dependent inactivation of metabolic enzymes by liver microsomes after chronic ethanol consumption. FASEB J. 2: 2901‐2906; 1988.
A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes

By accumulation of somatic mutations, cancer genomes evolve, diverging away from the genome of the host. It remains unclear to what extent somatic evolutionary divergence is comparable across different regions of the cancer genome versus concentrated in specific genomic elements. We present a novel computational framework, SASE-mapper, to identify genomic regions that show signatures of accelerated somatic evolution (SASE) in a subset of samples in a cohort, marked by accumulation of an excess of somatic mutations compared to that expected based on local, context-aware background mutation rates in the cancer genomes. Analyzing tumor whole genome sequencing data for 365 samples from 5 cohorts we detect recurrent SASE at a genome-wide scale. The SASEs were enriched for genomic elements associated with active chromatin, and regulatory regions of several known cancer genes had SASE in multiple cohorts. Regions with SASE carried specific mutagenic signatures and often co-localized within the 3D nuclear space suggesting their common basis. A subset of SASEs was frequently associated with regulatory changes in key cancer pathways and also poor clinical outcome. While the SASE-associated mutations were not necessarily recurrent at base-pair resolution, the SASEs recurrently targeted same functional regions, with similar consequences. It is likely that regulatory redundancy and plasticity promote prevalence of SASE-like patterns in the cancer genomes.
A Genetic Screen Targeting the Tumor Necrosis Factor/Eiger Signaling Pathway: Identification of Drosophila TAB2 as a Functionally Conserved Component

Signaling by tumor necrosis factors (TNFs) plays a prominent role in mammalian development and disease. To fully understand this complex signaling pathway it is important to identify all regulators and transduction components. A single TNF family member, Eiger, is encoded in the Drosophila genome, offering the possibility of applying genetic approaches for pursuing this goal. Here we present a screen for the isolation of novel genes involved in the TNF/Eiger pathway. On the basis of Eiger's ability to potently activate Jun-N-terminal kinase (JNK) and trigger apoptosis, we used the Drosophila eye to establish an assay for dominant suppressors of this activity. In a large-scale screen the Drosophila homolog of TAB2/3 (dTAB2) was identified as an essential component of the Eiger-JNK pathway. Genetic epistasis and biochemical protein-protein interaction assays assign an adaptor role to dTAB2, linking dTRAF1 to the JNKKK dTAK1, demonstrating a conserved mechanism of TNF signal transduction in mammals and Drosophila. Thus, in contrast to morphogenetic processes, such as dorsal closure of the embryo, in which the JNK pathway is activated by the JNKKK Slipper, Eiger uses the dTAB2-dTAK1 module to induce JNK signaling activity.
Vascular load reduction control based on operator's skill for catheter insertion

This paper proposes a method for vascular load reduction control that operates in regard to the load on contact points of catheter and blood vessels in catheter insertion. We make an extracorporeal estimation of the load on the contact points, and perform control with a robot arm to reduce the estimated load. We aim to reduce the vascular load through extracting and vibrating action as actually applied by operators. In order to confirm the effectiveness of the proposed method, we conduct an evaluation experiment where a wire is inserted in a tube that simulates a blood vessel. As a result of the experiment we were able to estimate the force on the contact points with an accuracy of an estimation error of 9.1%. Moreover, through vibration control we were able to reduce the load to below 0.1[N] for places where there was an overload of more than 0.5[N]. For vibration control, the experiment also enabled us to derive an effective parameter adjustment method to remove obstructions.
Spotlight on EPDM Elastomers

Abstract Etylene-propylene diene monomer (EPDM) rubbers have become widely recognized as an important class of elastomers in an enormous variety of consumer-type products. Typical examples where this material is used include seals around automotive doors, trunks, and windows; hosing materials used in automotive radiator applications, ply-roofing material in construction; specialty sealing gaskets and O-rings for various consumer products; electrical sheathing; plastic blends such as automotive bumpers; oil modifiers; and many others. EPDM is a unique material, having almost exceptional environmental resistance properties and capable of bcing extended to high levels of filler loading, while maintaining good physical as well as elasticlike properties. Additionally, unlike many other polymers, it can be synthesized over a wide range of molecular weights, and molecular and compositional distributions. This enables EPDM to be produced as a material tailored to the end-use application.
XMulator: A Listener-Based Integrated Simulation Platform for Interconnection Networks

Simulation is perhaps the most cost-effective tool to evaluate the operation of a system under design. A flexible, easy to extend, fully object-oriented, and multilayered simulator for interconnection networks can be a very useful tool for multicomputer designers and researchers. It is so desirable to attach newly designed components to the existing models and to exploit detailed results. This paper presents XMulator, an object-oriented listener-based simulation environment for evaluating multicomputer interconnection networks. The simulator involves a toolbox of various network topologies, routing algorithms, switching techniques, and flexible router models. This work introduces a simulator, using listener-based integration methodology, which has a great impact on extensibility of the system. Mixed-mode event processing improves the performance of the simulator. By decoupling individual parts of the code, XMulator enables independent code development and creates a flexible and extensible environment for different aspects of network design. This simulator uses XML format to define network topologies, input parameters, and outputs reports providing a high level of flexibility. To the best of the authors' knowledge, it is the first simulator enabled to simulate any arbitrary interconnection topology under different working conditions including in the presence of faults
The vapor compression refrigeration cycle

This article is a review of the basic principles of a cycle widely used to create the refrigeration effect that provides both human comfort and process cooling. While a semantic differentiation often is made for cooling and dehumidifying air for human comfort (air conditioning) and cooling for products and processes (refrigeration), all mechanical cooling applications depend on the previously mentioned refrigeration effect.
Role of brain glycogen in the response to hypoxia and in susceptibility to epilepsy

Although glycogen is the only carbohydrate reserve of the brain, its overall contribution to brain functions remains unclear. It has been proposed that glycogen participates in the preservation of such functions during hypoxia. Several reports also describe a relationship between brain glycogen and susceptibility to epilepsy. To address these issues, we used our brain-specific Glycogen Synthase knockout (GYS1Nestin-KO) mouse to study the functional consequences of glycogen depletion in the brain under hypoxic conditions and susceptibility to epilepsy. GYS1Nestin-KO mice presented significantly different power spectra of hippocampal local field potentials (LFPs) than controls under hypoxic conditions. In addition, they showed greater excitability than controls for paired-pulse facilitation evoked at the hippocampal CA3–CA1 synapse during experimentally induced hypoxia, thereby suggesting a compensatory switch to presynaptic mechanisms. Furthermore, GYS1Nestin-KO mice showed greater susceptibility to hippocampal seizures and myoclonus following the administration of kainate and/or a brief train stimulation of Schaffer collaterals. We conclude that brain glycogen could play a protective role both in hypoxic situations and in the prevention of brain seizures.
Spk1, a new kinase from Saccharomyces cerevisiae, phosphorylates proteins on serine, threonine, and tyrosine

A Saccharomyces cerevisiae lambda gt11 library was screened with antiphosphotyrosine antibodies in an attempt to identify a gene encoding a tyrosine kinase. A subclone derived from one positive phage was sequenced and found to contain an 821-amino-acid open reading frame that encodes a protein with homology to protein kinases. We tested the activity of the putative kinase by constructing a vector encoding a glutathione-S-transferase fusion protein containing most of the predicted polypeptide. The fusion protein phosphorylated endogenous substrates and enolase primarily on serine and threonine. The gene was designated SPK1 for serine-protein kinase. Expression of the Spk1 fusion protein in bacteria stimulated serine, threonine, and tyrosine phosphorylation of bacterial proteins. These results, combined with the antiphosphotyrosine immunoreactivity induced by the kinase, indicate that Spk1 is capable of phosphorylating tyrosine as well as phosphorylating serine and threonine. In in vitro assays, the fusion protein kinase phosphorylated the synthetic substrate poly(Glu/Tyr) on tyrosine, but the activity was weak compared with serine and threonine phosphorylation of other substrates. To determine if other serine/threonine kinases would phosphorylate poly(Glu/Tyr), we tested calcium/calmodulin-dependent protein kinase II and the catalytic subunit of cyclic AMP-dependent protein kinase. The two kinases had similar tyrosine-phosphorylating activities. These results establish that the functional difference between serine/threonine- and tyrosine-protein kinases is not absolute and suggest that there may be physiological circumstances in which tyrosine phosphorylation is mediated by serine/threonine kinases.
Prediction of the aggregation propensity of proteins from the primary sequence: Aggregation properties of proteomes

In the cell, protein folding into stable globular conformations is in competition with aggregation into non‐functional and usually toxic structures, since the biophysical properties that promote folding also tend to favor intermolecular contacts, leading to the formation of β‐sheet‐enriched insoluble assemblies. The formation of protein deposits is linked to at least 20 different human disorders, ranging from dementia to diabetes. Furthermore, protein deposition inside cells represents a major obstacle for the biotechnological production of polypeptides. Importantly, the aggregation behavior of polypeptides appears to be strongly influenced by the intrinsic properties encoded in their sequences and specifically by the presence of selective short regions with high aggregation propensity. This allows computational methods to be used to analyze the aggregation properties of proteins without the previous requirement for structural information. Applications range from the identification of individual amyloidogenic regions in disease‐linked polypeptides to the analysis of the aggregation properties of complete proteomes. Herein, we review these theoretical approaches and illustrate how they have become important and useful tools in understanding the molecular mechanisms underlying protein aggregation.
A large scale Linux-Kernel based benchmark for feature location research

Many software maintenance tasks require locating code units that implement a certain feature (termed as feature location). Feature location has been an active research area for more than two decades. However, there is lack of publicly available, large scale benchmarks for e valuating and comparing feature location approaches. In this paper, we present a LinuxKernel based benchmark for feature location research. This benchmark is large scale and extensible. By providing rich feature and program information and accurate ground-truth links between features and code units, it supports the e valuation of a wide range of feature location approaches. It allows researchers to gain deeper insights into existing approaches and how they can be improved. It also enables communication and collaboration among different researchers. (video: http://www.youtube.com/watch? v=3D_HihwRNeK3I).
Unsupervised Category Discovery via Looped Deep Pseudo-Task Optimization Using a Large Scale Radiology Image Database

Obtaining semantic labels on a large scale radiology image database (215,786 key images from 61,845 unique patients) is a prerequisite yet bottleneck to train highly effective deep convolutional neural network (CNN) models for image recognition. Nevertheless, conventional methods for collecting image labels (e.g., Google search followed by crowd-sourcing) are not applicable due to the formidable difficulties of medical annotation tasks for those who are not clinically trained. This type of image labeling task remains non-trivial even for radiologists due to uncertainty and possible drastic inter-observer variation or inconsistency. In this paper, we present a looped deep pseudo-task optimization procedure for automatic category discovery of visually coherent and clinically semantic (concept) clusters. Our system can be initialized by domain-specific (CNN trained on radiology images and text report derived labels) or generic (ImageNet based) CNN models. Afterwards, a sequence of pseudo-tasks are exploited by the looped deep image feature clustering (to refine image labels) and deep CNN training/classification using new labels (to obtain more task representative deep features). Our method is conceptually simple and based on the hypothesized "convergence" of better labels leading to better trained CNN models which in turn feed more effective deep image features to facilitate more meaningful clustering/labels. We have empirically validated the convergence and demonstrated promising quantitative and qualitative results. Category labels of significantly higher quality than those in previous work are discovered. This allows for further investigation of the hierarchical semantic nature of the given large-scale radiology image database.
Maskless lithography with the solid immersion lens nanoprobes

The International Technology Roadmap for Semiconductors (ITRS) shows that 45 nm and lower feature sizes are required in lithographic production before the year 2007. Both immersion lithography and EUV lithography can play major roles in realizing this goal. However, a maskless lithography system capable of producing 45 nm features is an attractive option for small-volume semiconductor fabrication, such as with ASIC manufactures. Compared with a conventional lithography system, the maskless feature of the system allows the chip designer to be free of the very expensive process of mask fabrication and to shortcut development time. In this paper, we discuss a new maskless lithography concept employing an array of solid immersion lens (SIL) nano-probes. The nano-probes are efficient near-field transducers. Each transducer is the combination a SIL, a dielectric probe tip and an antenna structure. The nano-probes are fabricated in arrays that dramatically improve throughput. By combining these technologies, it should be possible to fabricate an efficient array of near-field transducers with optical spot dimensions of around 20 nm when illuminated by a 405 nm laser diode source. This paper plans to address, for the first time, the efficient generation of an array of light spots with dimensions of λ/20 or less that couple efficiently into dielectric films, like photoresist.
Self-Repairing Codes for distributed storage — A projective geometric construction

Self-Repairing Codes (SRC) are codes designed to suit the need of coding for distributed networked storage: they not only allow stored data to be recovered even in the presence of node failures, they also provide a repair mechanism where as little as two live nodes can be contacted to regenerate the data of a failed node. In this paper, we propose a new instance of self-repairing codes, based on constructions of spreads coming from projective geometry. We study some of their properties to demonstrate the suitability of these codes for distributed networked storage.
Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp. Strain PCC 68031[W]

The amount of inorganic carbon represents one of the main environmental factors determining productivity of photoautotrophic organisms. Using the model cyanobacterium Synechocystis sp. PCC 6803, we performed a first metabolome study with cyanobacterial cells shifted from high CO2 (5% in air) into conditions of low CO2 (LC; ambient air with 0.035% CO2). Using gas chromatography-mass spectrometry, 74 metabolites were reproducibly identified under different growth conditions. Shifting wild-type cells into LC conditions resulted in a global metabolic reprogramming and involved increases of, for example, 2-oxoglutarate (2OG) and phosphoenolpyruvate, and reductions of, for example, sucrose and fructose-1,6-bisphosphate. A decrease in Calvin-Benson cycle activity and increased usage of associated carbon cycling routes, including photorespiratory metabolism, was indicated by synergistic accumulation of the fumarate, malate, and 2-phosphoglycolate pools and a transient increase of 3-phosphoglycerate. The unexpected accumulation of 2OG with a concomitant decrease of glutamine pointed toward reduced nitrogen availability when cells are confronted with LC. Despite the increase in 2OG and low amino acid pools, we found a complete dephosphorylation of the PII regulatory protein at LC characteristic for nitrogen-replete conditions. Moreover, mutants with defined blocks in the photorespiratory metabolism leading to the accumulation of glycolate and glycine, respectively, exhibited features of LC-treated wild-type cells such as the changed 2OG to glutamine ratio and PII phosphorylation state already under high CO2 conditions. Thus, metabolome profiling demonstrated that acclimation to LC involves coordinated changes of carbon and interacting nitrogen metabolism. We hypothesize that Synechocystis has a temporal lag of acclimating carbon versus nitrogen metabolism with carbon leading.