Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased renal retention of 99mTc-methylene diphosphonate after nephron-sparing surgery.

UNLABELLED Nephron-sparing surgery has become established as an effective treatment for localized renal cell carcinoma when preservation of renal function is necessary. The surgery usually requires temporary renal artery occlusion and may induce ischemic renal damage. In this study, we retrospectively evaluated renal activity on bone scintigraphy after nephron-sparing surgery. METHODS Eleven patients who underwent nephron-sparing surgery for renal cell carcinoma and had a normal contralateral kidney were studied. A total of 12 bone scintigraphy images with 99mTc-labeled methylene diphosphonate were obtained within 1 y after surgery in these patients to assess skeletal metastasis. Activity in the spared renal parenchyma was compared visually with that in the contralateral normal kidney. RESULTS The tumor was successfully resected in every patient, and no clinically significant complications occurred. Activity in the spared renal parenchyma was elevated in six of seven examinations performed within 21 d after surgery. In three examinations, the increase in renal activity was heterogeneous, being relatively prominent near the surgical margin. Increased renal activity was not observed on five examinations performed 3 mo or more after surgery. CONCLUSION Renal retention of bone-seeking agents is elevated in the early period after nephron-sparing surgery, probably as a result of ischemic insult during the surgical procedure. Bone scintigraphy may aid in evaluating the presence and degree of ischemic damage of the spared renal parenchyma.
Consultant-2: pre- and post-processing of Machine Learning applications

Abstract The knowledge acquisition bottleneck in the development of large knowledge-based applications has not yet been resolved. One approach which has been advocated is the systematic use of Machine Learning (ML) techniques. However, ML technology poses difficulties to domain experts and knowledge engineers who are not familiar with it. This paper discusses Consultant-2, a system which makes a first step towards providing system support for a " pre- and post-processing " methodology where a cyclic process of experiments with an ML tool, its data, data description language and parameters attempts to optimize learning performance. Consultant-2 has been developed to support the use of Machine Learning Toolbox (MLT), an integrated architecture of 10 ML tools, and has evolved from a series of earlier systems. Consultant-0 and Consultant-1 had knowledge only about how to choose an ML algorithm based on the nature of the domain data. Consultant-2 is the most sophisticated. It, additionally, has knowledge about how ML experts and domain experts pre-process domain data before a run with the ML algorithm, and how they further manipulate the data and reset parameters after a run of the selected ML algorithm, to achieve a more acceptable result. How these several KBs were acquired and encoded is described. In fact, this knowledge has been acquired by interacting both with the ML algorithm developers and with domain experts who had been using the MLT toolbox on real-world tasks. A major aim of the MLT project was to enable a domain expert to use the toolbox directly; i.e. without necessarily having to involve either a ML specialist or a knowledge engineer. Consultant's principal goal was to provide specific advice to ease this process.
Molecular Marker Identification for Relapse Prediction in 5-FU-Based Adjuvant Chemotherapy in Gastric and Colorectal Cancers

To confirm the clinical significance of NF-κB and JNK protein expression from experimentally identified candidates for predicting prognosis for patients with 5-FU treatment, we evaluated the protein expression of surgically removed specimens. A total of 79 specimens were obtained from 30 gastric and 49 colorectal cancer patients who underwent R0 resection followed by postoperative 5-FU based adjuvant chemotherapy. Immunohistochemical examinations of NF-κB and JNK on tissue microarrays (TMAs) revealed that significantly shorter time-to-relapse (TTR) in both NF-κB(+) and JNK(−) subgroups in both gastric (NF-κB(+), p = 0.0002, HR11.7. 95%CI3 3.2–43.4; JNK(−), p = 0.0302, HR4.4, 95%CI 1.2–16.6) and colon (NF-κB(+), p = 0.0038, HR36.9, 95%CI 3.2–426.0; JNK(−), p = 0.0098, HR3.2, 95%CI 1.3–7.7) cancers. These protein expression patterns also show strong discriminately power in gastric cancer patients for overall survival rate, suggesting a potential utility as prognostic or chemosensitivity markers. Baseline expression of these proteins using gastric cancer cell lines demonstrated the reciprocal patterns between NF-κB and JNK, while 5-FU exposure of these cell lines only induced NF-κB, suggesting that NF-κB plays a dominant role in the response to 5-FU. Subsequent siRNA experiments confirmed that gene knockdown of NF-κB increased 5-FU-specific sensitivity, whereas that of JNK did not affect the chemosensitivity. These results suggest that the expression of these proteins may aid in the decisions involved with adjuvant chemotherapy for gastrointestinal tract cancers.
Remote Sensing Image Scene Classification Using Multi-Scale Completed Local Binary Patterns and Fisher Vectors

An effective remote sensing image scene classification approach using patch-based multi-scale completed local binary pattern (MS-CLBP) features and a Fisher vector (FV) is proposed. The approach extracts a set of local patch descriptors by partitioning an image and its multi-scale versions into dense patches and using the CLBP descriptor to characterize local rotation invariant texture information. Then, Fisher vector encoding is used to encode the local patch descriptors (i.e., patch-based CLBP features) into a discriminative representation. To improve the discriminative power of feature representation, multiple sets of parameters are used for CLBP to generate multiple FVs that are concatenated as the final representation for an image. A kernel-based extreme learning machine (KELM) is then employed for classification. The proposed method is extensively evaluated on two public benchmark remote sensing image datasets (i.e., the 21-class land-use dataset and the 19-class satellite scene dataset) and leads to superior classification performance (93.00% for the 21-class dataset with an improvement of approximately 3% when compared with the state-of-the-art MS-CLBP and 94.32% for the 19-class dataset with an improvement of approximately 1%).
Transcriptome of the Alternative Ethanol Production Strain Dekkera bruxellensis CBS 11270 in Sugar Limited, Low Oxygen Cultivation

Dekkera bruxellensis can outcompete Saccharomyces cerevisiae in environments with low sugar concentrations. It is usually regarded as a spoilage yeast but has lately been identified as an alternative ethanol production organism. In this study, global gene expression in the industrial isolate D. bruxellensis CBS 11270 under oxygen and glucose limitation was investigated by whole transcriptome sequencing using the AB SOLiD technology. Among other observations, we noted expression of respiratory complex I NADH-ubiquinone reductase although D. bruxellensis is a Crabtree positive yeast. The observed higher expression of NADH-generating enzymes compared to NAD+-generating enzymes might be the reason for the previously observed NADH imbalance and resulting Custer effect in D. bruxellensis. Low expression of genes involved in glycerol production is probably the molecular basis for high efficiency of D. bruxellensis metabolism under nutrient limitation. No D. bruxellensis homologs to the genes involved in the final reactions of glycerol biosynthesis were detected. A high number of expressed sugar transporter genes is consistent with the hypothesis that the competitiveness of D. bruxellensis is due to a higher affinity for the limiting substrate.
Advanced volume painting with game controllers

Volume painting is an interactive segmentation technique for volumetric datasets. While volume painting facilitates quickly creating segmentations, e.g., for illustration purposes, segmenting features precisely is often problematic. The volume painting system we present addresses two common problems. First, we introduce several data-dependent painting mechanisms to make precisely segmenting features of interest easy. Second, we use game controllers such as a joystick and a gamepad to create a simple user interface to our system while still providing full control over the large amount of parameters of the painting mechanism. We demonstrate our work giving several examples and compare the effectiveness of the various brushes. We prove that our system is intuitive to use with preliminary user testing. The results indicate that our volume painting framework is an effective, interactive segmentation tool.
Induction of malignant transformation of cocultivated hematopoietic stem cells by X-irradiation of murine bone marrow stromal cells in vitro.

X-irradiation of purified primary cultures of mouse bone marrow stroma or permanent cloned marrow stromal cell lines in plateau phase decreases production of macrophage progenitor cell-specific colony-stimulating factor to a plateau minimum of 40% of control levels after doses of 50 to 500 Gy delivered at 2 Gy/min. After 50 Gy there is increased bioavailability of another growth factor(s) that is distinct from macrophage progenitor cell-specific colony-stimulating factor, granulocyte-macrophage progenitor cell colony-stimulating factor, or colony-stimulating factor for multipotential hematopoietic stem cells (interleukin 3). Liquid-phase cocultivation of irradiated stromal cells with either nonadherent cells from continuous marrow cultures or cloned dual granulocyte-macrophage progenitor cell colony-stimulating factor/interleukin 3-dependent hematopoietic progenitor cell lines induces evolution over 5 weeks of factor-independent colony-forming cells. Subcultured factor-independent colonies generated clonal malignant cell lines with multiple distinct karyotypic alterations. Inoculation of 10(6) cells s.c. from factor-independent clones into syngeneic mice produces local granulocytic monomyeloid tumors with spread to spleen, lymph nodes, and bone marrow. These data provide the first demonstration in vitro of indirect X-irradiation leukemogenesis through cells of the marrow stroma.
Magnetic eigenmaps for community detection in directed networks

Communities in directed networks have often been characterized as regions with a high density of links, or as sets of nodes with certain patterns of connection. Our approach for community detection combines the optimization of a quality function and a spectral clustering of a deformation of the combinatorial Laplacian, the so-called magnetic Laplacian. The eigenfunctions of the magnetic Laplacian, which we call magnetic eigenmaps, incorporate structural information. Hence, using the magnetic eigenmaps, dense communities including directed cycles can be revealed as well as "role" communities in networks with a running flow, usually discovered thanks to mixture models. Furthermore, in the spirit of the Markov stability method, an approach for studying communities at different energy levels in the network is put forward, based on a quantum mechanical system at finite temperature.
Improved Kalman gain computation for multichannel frequency-domain adaptive filtering and application to acoustic echo cancellation

For multichannel adaptive filtering applications like acoustic echo cancellation, sophisticated, but efficient algorithms are necessary that take both auto- and cross-correlations of the excitation signals into account. Based on a recently published frequency-domain framework, we examine in this contribution the computation of the so-called frequency-domain Kalman gain, which is crucial in the multichannel case to meet the above requirements for correlated input signals. We present an extended scheme with increased computational efficiency for a higher number of input channels. Robust convergence behaviour during perturbation of the desired signal is ensured by a new dynamical regularization. Application of the new algorithm to multichannel acoustic echo cancellation with real-world signals achieves improved performance.
Codon72 polymorphism in the p53 tumor suppressor gene in oral lichen planus lesions in a Thai population.

BACKGROUND Oral lichen planus (OLP) is a T-cell mediated autoimmune disease in which autocytotoxic CD8+ T cells (CTLs) trigger apoptosis of oral epithelial cells. Activated CTLs can produce Fas ligand and by binding to Fas lead to apoptosis. This Fas pathway and the action of p53 tumour suppressor gene are important in producing apoptosis. Current data demonstrate a link between these two factors at the transcriptional level. OBJECTIVE The purpose of this study was to investigate the p53 polymorphism at codon 72 which results in encoding of either proline or arginine. METHODS Our study used 97 OLP cases and 94 control blood samples from non-OLP individuals and performed PCR-RFLP. RESULTS Compared to control individuals, we found a significant increase in occurrence in OLP patients of the proline encoding cytosine allele (adjusted odd ratio (95% CI)=2.29 (1.42-3.70) and p=0.001). In addition, in individuals with the non-erosive type of OLP, the same situation was evident (OR=2.29, 95% CI (1.38-3.78), p=0.001). Furthermore, we noted a significantly higher prevalence of homozygosity [OR=3.17, 95% CI(1.58-7.25), p=0.001) for the p53 pro allele in the OLP group, which indicates a recessive mode of inheritance. CONCLUSION Our data suggest a strong association between the pro/pro genotype and OLP, and that the process of apoptosis, in which p53 plays a role, is a factor in OLP pathogenesis.
A 3D metaphor for software production visualization

Software development is difficult because software is complex, the software production process is complex and understanding of software systems is a challenge. We propose a 3D visual approach to depict software production cost related program information to support software maintenance. The information helps us to reduce software maintenance costs, to plan the use of personnel wisely, to appoint experts efficiently and to detect system problems early.
Retrieval and on-the-fly alignment of sequence fragments from the HIV database

MOTIVATION The amount of HIV-1 sequence data generated (presently around 42000 sequences, of which more than 22000 are from the V3 region of the viral envelope) presents a challenge for anyone working on the analysis of these data. A major problem is obtaining the region of interest from the stored sequences, which often contain but are not limited to that region. In addition, multiple alignment programs generally cannot deal with the large numbers of sequences that are available for many HIV-1 regions. We set out to provide our users with a tool that will retrieve and create an initial alignment of the HIV sequences that are available for a given genomic region. RESULTS The MPAlign (Multiple Pairwise Alignment) web interface is a collection of Perl scripts that retrieves sequences from the Los Alamos HIV sequence database based on a number of search parameters. All sequences were pairwise-aligned to a model sequence using the Hidden Markov Model-based program HMMER. The HMMER model is general enough to accommodate virtually all HIV-1 sequences stored in the database. To create a multiple sequence alignment, gaps were inserted into the sequences during retrieval, so that they are aligned to one another. Retrieving and aligning the almost 560 gp120 sequences (approximately>1500 nt) stored in the database is at least 1500 times faster than a similar Clustal alignment.
Joint scaling laws in functional and evolutionary categories in prokaryotic genomes

We propose and study a class-expansion/innovation/loss model of genome evolution taking into account biological roles of genes and their constituent domains. In our model, numbers of genes in different functional categories are coupled to each other. For example, an increase in the number of metabolic enzymes in a genome is usually accompanied by addition of new transcription factors regulating these enzymes. Such coupling can be thought of as a proportional ‘recipe’ for genome composition of the type ‘a spoonful of sugar for each egg yolk’. The model jointly reproduces two known empirical laws: the distribution of family sizes and the non-linear scaling of the number of genes in certain functional categories (e.g. transcription factors) with genome size. In addition, it allows us to derive a novel relation between the exponents characterizing these two scaling laws, establishing a direct quantitative connection between evolutionary and functional categories. It predicts that functional categories that grow faster-than-linearly with genome size to be characterized by flatter-than-average family size distributions. This relation is confirmed by our bioinformatics analysis of prokaryotic genomes. This proves that the joint quantitative trends of functional and evolutionary classes can be understood in terms of evolutionary growth with proportional recipes.
Algorithms and data structures for flash memories

Flash memory is a type of electrically-erasable programmable read-only memory (EEPROM). Because flash memories are nonvolatile and relatively dense, they are now used to store files and other persistent objects in handheld computers, mobile phones, digital cameras, portable music players, and many other computer systems in which magnetic disks are inappropriate. Flash, like earlier EEPROM devices, suffers from two limitations. First, bits can only be cleared by erasing a large block of memory. Second, each block can only sustain a limited number of erasures, after which it can no longer reliably store data. Due to these limitations, sophisticated data structures and algorithms are required to effectively use flash memories. These algorithms and data structures support efficient not-in-place updates of data, reduce the number of erasures, and level the wear of the blocks in the device. This survey presents these algorithms and data structures, many of which have only been described in patents until now.
Title A Matched Filter Approximation for SC / MMSE Iterative Equalizers

This letter proposes a new iterative ISI equalization algorithm that offers low computational complexity: order 2 with channel memory length . The proposed algorithm is an extension of Reynolds and Wang’s SC/MMSE (Soft Canceler followed by MMSE filter) equalizer: approximations are used properly to reduce the computational complexity. It is shown that the approximations used in the proposed algorithm do not cause any serious performance degradations from the trellis-based iterative equalization algorithms.
Efflux-mediated response of Staphylococcus aureus exposed to ethidium bromide.

OBJECTIVES By adapting an antibiotic-susceptible Staphylococcus aureus strain to increasing concentrations of ethidium bromide, a known substrate of efflux pumps (EPs), and by phenotypically and genotypically analysing the resulting progeny, we characterized the molecular mechanisms of S. aureus adaptation to ethidium bromide. METHODS S. aureus ATCC 25923 was grown in increasing concentrations of ethidium bromide. The MICs of representatives of eight classes of antibiotics, eight biocides and two dyes against ATCC 25923 and its ethidium bromide-resistant progeny ATCC 25923(EtBr) were determined with or without six efflux pump inhibitors (EPIs). Efflux activity in the presence/absence of EPIs was evaluated by real-time fluorometry. The presence and expression of eight EP genes were assayed by PCR and quantitative RT-PCR (qRT-PCR), respectively. Mutations in grlA, gyrA and norA promoter regions were screened by DNA sequencing. RESULTS Compared with its parental strain, ATCC 25923(EtBr) was 32-fold more resistant to ethidium bromide and also more resistant to biocides and hydrophilic fluoroquinolones. Resistance to these could be reduced by the EPIs chlorpromazine, thioridazine and reserpine. Increased efflux of ethidium bromide by ATCC 25923(EtBr) could be inhibited by the same EPIs. qRT-PCR showed that norA was 35-fold over-expressed in ATCC 25923(EtBr), whereas the remaining EP genes showed no significant increase in their expression. Sequencing of the norA promoter region revealed a 70 bp deletion in ATCC 25923(EtBr). CONCLUSIONS Exposure of S. aureus to quaternary compounds such as ethidium bromide results in decreased susceptibility of the organism to a wide variety of compounds, including quinolones and biocides through an efflux-mediated response, which for strain ATCC 25923 is mainly NorA-mediated. This altered expression may result from alterations in the norA promoter region.
A randomized controlled trial of the effects of a combination of static and dynamic magnetic fields on carpal tunnel syndrome.

OBJECTIVE To determine if a physics-based combination of simultaneous static and time-varying dynamic magnetic field stimulation to the wrist 4 hours/day for 2 months can reduce subjective neuropathic pain and influence objective electrophysiologic parameters of patients with carpal tunnel syndrome (CTS). METHODS Randomized, double-blinded, placebo-controlled trial of 36 symptomatic hands. Primary endpoints were visual analog scale (VAS) and neuropathic pain scale (NPS) scores at baseline and 2 months and a Patient's Global Impression of Change (PGIC) questionnaire at the end of 2 months. Secondary endpoints were neurologic examination, median nerve distal latencies (compound muscle action potential [CMAP]/sensory nerve action potential [SNAP]), dynamometry, pinch gauge readings, and current perception threshold (CPT) scores. An "active" device was provided gratis at the end of the study, with 15 subjects voluntarily remaining within the open protocol an additional 2-10 months and using the preselected primary and secondary parameters. RESULTS (two months). Of the 31 hands, 25 (13 magnet, 12 sham) had moderate to severe pain (VAS > 4). The VAS and PGIC revealed a nonsignificant pain reduction. NPS analyses (anova) demonstrated a statistically significant reduction of "deep" pain (35% downward arrow vs 12% upward arrow, P = 0.018), NPS Total Composite (decreases of 42% vs 24%, P = 0.042), NPS Total Descriptor Score (NPS 8; 43% vs 24%), and NPS 4 (42% vs 11%). Motor strength, CMAP/SNAP, and CPT scores were not significantly changed. Of the 15 hands with up to 10 months of active PEMF (pulsed electromagnetic fields) exposure, there was objective improvement in nerve conduction (CMAP = 53%, SNAP = 40%, >1 SD), and subjective improvement on examination (40%), pain scores (50%), and PGIC (70%). No detectable changes in motor strength and CPT. CONCLUSIONS PEMF exposure in refractory CTS provides statistically significant short- and longterm pain reduction and mild improvement in objective neuronal functions. Neuromodulation appears to influence nociceptive-C and large A-fiber functions, probably through ion/ligand binding.
PILGRIM: A location broker and mobility-aware recommendation system

Mobile computing adds a mostly unexplored dimension to data mining: user's position is a relevant piece of information, and recommendation systems, selecting and ranking links of interest to the user, have the opportunity to take location into account. In this paper a mobility-aware recommendation system that considers the location of the user to filter recommended links is proposed. To avoid the potential problems and costs of insertion by hand, a new middleware layer, the location broker, maintains a historic database of locations and corresponding links used in the past and develops models relating resources to their spatial usage pattern. These models are used to calculate a preference metric when the current user is asking for resources of interest. Mobility scenarios are described and analyzed in terms of possible user requirements. The features of the PILGRIM mobile recommendation system are outlined together with a preliminary experimental evaluation of different metrics.