Miracle-dz/UniFAR-FTUs huggingface dataset:
ASA: Agent-based secure ARP cache management

Address resolution protocol (ARP) is widely used to maintain mapping between data link (e.g. MAC) and network (e.g. IP) layer addresses. Although most hosts rely on automated and dynamic management of ARP cache entries, current implementation is well-known to be vulnerable to spoofing or denial of service (DoS) attacks. There are many tools that exploit vulnerabilities of ARP protocols, and past proposals to address the weaknesses of the `original` ARP design have been unsatisfactory. Suggestions that ARP protocol definition be modified would cause serious and unacceptable compatibility problems. Other proposals require customised hardware be installed to monitor malicious ARP traffic, and many organisations cannot afford such cost. This study demonstrates that one can effectively eliminate most threats caused by the ARP vulnerabilities by installing anti-ARP spoofing agent (ASA), which intercepts unauthenticated exchange of ARP packets and blocks potentially insecure communications. The proposed approach requires neither modification of kernel ARP software nor installation of traffic monitors. Agent uses user datagram protocol (UDP) packets to enable networking among hosts in a transparent and secure manner. The authors implemented agent software on Windows XP and conducted an experiment. The results showed that ARP hacking tools could not penetrate hosts protected by ASA.
Prevention of diet‐induced type 2 diabetes in the C57BL/6J mouse model by an antidiabetic herbal formula

Significant positive effects of an antidiabetes herbal formula (ADHF) on the prevention of progressive diet‐induced type 2 diabetes (NIDDM) in the well recognized C57BL/6J mouse model were demonstrated. The results of the present studies confirm that C57BL/6J mice, through a genetic predisposition, developed NIDDM‐like symptoms on a regular schedule when fed solely on a diabetes induction diet containing high fat, high simple carbohydrate and low fibre. Blood glucose levels consistent with type 2 diabetes were detected after 8 weeks on this induction diet. In contrast, no members of the prevention study groups of C57BL/6J mice, which had ADHF mixed into their diabetes induction diet, developed progressive evidence of NIDDM‐like symptoms. Specific parameters observed to be significantly reduced in mice in the prevention diet groups fed ADHF mixed into the diabetes induction diet compared with the diabetes positive control groups fed diabetes induction diet only were clinical signs, blood glucose and serum insulin levels, insulin resistance and histopathological changes in major organs. This is the first report to our knowledge to show in vivo evidence for the successful prevention of progressive NIDDM‐like symptoms by the addition of an anti‐diabetes herbal formula to a effective diabetes induction diet. Copyright © 2003 John Wiley & Sons, Ltd.
Lung Cancer Susceptibility Model Based on Age, Family History and Genetic Variants

Background Epidemiological and pedigree studies suggest that lung cancer results from the combined effects of age, smoking, impaired lung function and genetic factors. In a case control association study of healthy smokers and lung cancer cases, we identified genetic markers associated with either susceptibility or protection to lung cancer. Methodology/Principal Findings We screened 157 candidate single nucleotide polymorphisms (SNP) in a discovery cohort of 439 subjects (200 controls and 239 lung cancer cases) and identified 30 SNPs associated with either the healthy smokers (protective) or lung cancer (susceptibility) phenotype. After genotyping this 30 SNP panel in a validation cohort of 491 subjects (248 controls and 207 lung cancers) and, using the same protective and susceptibility genotypes from our discovery cohort, a 20 SNP panel was selected based on replication of SNP associations in the validation cohort. Following multivariate logistic regression analyses, including the selected SNPs from runs 1 and 2, we found age and family history of lung cancer to be significantly and independently associated with lung cancer. Numeric scores were assigned to both the SNP and demographic data, and combined to form a simple algorithm of risk. Conclusions/Significance Significant differences in the distribution of the lung cancer susceptibility score was found between normal controls and lung cancer cases, which remained after accounting for differences in lung function. Validation in other case-control and prospective cohorts are underway to further define the potential clinical utility of this model.
Combined Evidence Annotation of Transposable Elements in Genome Sequences

Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated “TE models” in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila.
COCO-Text: Dataset and Benchmark for Text Detection and Recognition in Natural Images

This paper describes the COCO-Text dataset. In recent years large-scale datasets like SUN and Imagenet drove the advancement of scene understanding and object recognition. The goal of COCO-Text is to advance state-of-the-art in text detection and recognition in natural images. The dataset is based on the MS COCO dataset, which contains images of complex everyday scenes. The images were not collected with text in mind and thus contain a broad variety of text instances. To reflect the diversity of text in natural scenes, we annotate text with (a) location in terms of a bounding box, (b) fine-grained classification into machine printed text and handwritten text, (c) classification into legible and illegible text, (d) script of the text and (e) transcriptions of legible text. The dataset contains over 173k text annotations in over 63k images. We provide a statistical analysis of the accuracy of our annotations. In addition, we present an analysis of three leading state-of-the-art photo Optical Character Recognition (OCR) approaches on our dataset. While scene text detection and recognition enjoys strong advances in recent years, we identify significant shortcomings motivating future work.
Prognostic classification of relapsing favorable histology Wilms tumor using cDNA microarray expression profiling and support vector machines

Treatment of Wilms tumor has a high success rate, with some 85% of patients achieving long‐term survival. However, late effects of treatment and management of relapse remain significant clinical problems. If accurate prognostic methods were available, effective risk‐adapted therapies could be tailored to individual patients at diagnosis. Few molecular prognostic markers for Wilms tumor are currently defined, though previous studies have linked allele loss on 1p or 16q, genomic gain of 1q, and overexpression from 1q with an increased risk of relapse. To identify specific patterns of gene expression that are predictive of relapse, we used high‐density (30 k) cDNA microarrays to analyze RNA samples from 27 favorable histology Wilms tumors taken from primary nephrectomies at the time of initial diagnosis. Thirteen of these tumors relapsed within 2 years. Genes differentially expressed between the relapsing and nonrelapsing tumor classes were identified by statistical scoring (t test). These genes encode proteins with diverse molecular functions, including transcription factors, developmental regulators, apoptotic factors, and signaling molecules. Use of a support vector machine classifier, feature selection, and test evaluation using cross‐validation led to identification of a generalizable expression signature, a small subset of genes whose expression potentially can be used to predict tumor outcome in new samples. Similar methods were used to identify genes that are differentially expressed between tumors with and without genomic 1q gain. This set of discriminators was highly enriched in genes on 1q, indicating close agreement between data obtained from expression profiling with data from genomic copy number analyses. © 2004 Wiley‐Liss, Inc.
Laser ablation as a processing technique for metallic and polymer layered structures

A study of the laser ablation process for application in processing metallic and polymer layered structures is presented. The central result of this study is that, by operating with laser pulses of different fluences, it is possible to selectively remove polymer overlayers on metallic films and metallic films from polymer layers, provided the metallic films are sufficiently thin. Careful choice of the fluence allowed both of these processes to be carried out with minimal damage to the underlying material. The damage produced has been characterized by laser processing through visual inspection, profilometry, and electron microscopy. In the case of polymer layers, the effect of exposure to laser irradiation through spectroscopic studies in the infrared, visible, and ultraviolet portion of the spectrum has also been studied. For the metallic layers, we have correlated the visible damage observed with changes in the electrical resistivity of the films. >
The Topological Theory of Belief

Stalnaker introduced a combined epistemic-doxastic logic that can formally express a strong concept of belief, a concept which captures the ‘epistemic possibility of knowledge’. In this paper we first provide the most general extensional semantics for this concept of ‘strong belief’, which validates the principles of Stalnaker’s epistemic-doxastic logic. We show that this general extensional semantics is a topological semantics, based on so-called extremally disconnected topological spaces. It extends the standard topological interpretation of knowledge (as the interior operator) with a new topological semantics for belief. Formally, our belief modality is interpreted as the ‘closure of the interior’. We further prove that in this semantics the logic KD45 is sound and complete with respect to the class of extremally disconnected spaces and we compare our approach to a different topological setting in which belief is interpreted in terms of the derived set operator. In the second part of the paper we study (static) belief revision as well as belief dynamics by providing a topological semantics for conditional belief and belief update modalities, respectively. Our investigation of dynamic belief change, is based on hereditarily extremally disconnected spaces. The logic of belief KD45 is sound and complete with respect to the class of hereditarily extremally disconnected spaces (under our proposed semantics), while the logic of knowledge is required to be S4.3. Finally, we provide a complete axiomatization of the logic of conditional belief and knowledge, as well as a complete axiomatization of the corresponding dynamic logic.
Flux corrections to anomaly cancellation in M-theory on a manifold with boundary

We show how the coupling of gravitinos and gauginos to fluxes modifies anomaly cancellation in M-theory on a manifold with boundary. Anomaly cancellation continues to hold, after a shift of the definition of the gauge currents by a local gauge invariant expression in the curvatures and E8 fieldstrengths. We compute the first nontrivial correction of this kind. Warning: Ian Moss has called into question several of the numerical coefficients in the extended Dirac operators in this paper. We have not confirmed this but the reader is warned not to trust the precise coefficients in the formulae for the Dirac operators and heat kernel expansions. We believe these possible errors do not change our qualitative conclusions. One of us intends to return to the issue and recheck the formulae. We thank Ian Moss for pointing out these problems.
Face Recognition from Unconstrained Images: Progress with Prototypes

Artificial face recognition systems typically do not attempt to handle very variable images. By comparison, human perceivers can recognize familiar faces over much more varied conditions. We describe a prototype face representation based on simple image-averaging. We have argued that this forms a good candidate for understanding human face perception. Here we examine the stability of these representations by asking (i) how quickly they converge; and (U) how resistant they are to contamination due to previous misidentifications. We conclude that face averages provide promising representations for use in artificial recognition
Mutant Prevention Concentration as a Measure of Fluoroquinolone Potency against Mycobacteria

ABSTRACT Mutant prevention concentration (MPC) has been proposed as a new measure of antibiotic potency by which the ability to restrict selection of resistant mutants is evaluated. To determine whether MPC provides potency information unavailable from the more customary measurement of the MIC, 18 fluoroquinolones were examined for their ability to block the growth of Mycobacterium smegmatis and to select resistant mutants from wild-type populations. Both MPC and MIC were affected by changes in the moiety at the fluoroquinolone C-8 position and in alkyl groups attached to the C-7 piperazinyl ring. When eight resistant mutants, altered in the gyrase A protein, were tested with fluoroquinolones having either a methoxy or a hydrogen at the C-8 position, the MIC for the most resistant mutant correlated better with the MPC than did the MIC for wild-type cells. For C-8-fluorine derivatives, which were generally less active than the C-8-methoxy compounds but which were more active than C-8-hydrogen derivatives, the MICs for both the mutant and the wild type correlated well with the MPCs. Thus, measurement of the MICs for wild-type cells can reflect the ability of a quinolone to restrict the selection of resistance, but often it does not. With the present series of compounds, the most potent contained a C-8-methoxy and a small group attached to the C-7 ring.
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

Whether codon usage fine-tunes mRNA translation in mammals remains controversial, with recent papers suggesting that production of proteins in specific Gene Ontological (GO) pathways can be regulated by actively modifying the codon and anticodon pools in different cellular conditions. In this work, we compared the sequence content of genes in specific GO categories with the exonic genome background. Although a substantial fraction of variability in codon usage could be explained by random sampling, almost half of GO sets showed more variability in codon usage than expected by chance. Nevertheless, by quantifying translational efficiency in healthy and cancerous tissues in human and mouse, we demonstrated that a given tRNA pool can equally well translate many different sets of mRNAs, irrespective of their cell-type specificity. This disconnect between variations in codon usage and the stability of translational efficiency is best explained by differences in GC content between gene sets. GC variation across the mammalian genome is most likely a result of the interplay between genome repair and gene duplication mechanisms, rather than selective pressures caused by codon-driven translational rates. Consequently, codon usage differences in mammalian transcriptomes are most easily explained by well-understood mutational biases acting on the underlying genome.
Efficacy and Safety of Automatic Remote Monitoring for Implantable Cardioverter-Defibrillator Follow-Up: The Lumos-T Safely Reduces Routine Office Device Follow-Up (TRUST) Trial

Background— Monitoring implantable cardiac device function and patient condition is important. The Lumos-T Safely Reduces Routine Office Device Follow-Up (TRUST) trial tested the hypothesis that remote home monitoring with automatic daily surveillance (HM) is safe and effective for implantable cardioverter-defibrillator follow-up for 1 year and enables rapid physician evaluation of significant events. Methods and Results— In total, 1339 patients were randomized 2:1 to HM or conventional follow-up. Follow-up checks occurred at 3, 6, 9, 12, and 15 months after implantation. HM was used before office visits at 3 and 15 months in the HM group. At 6, 9, and 12 months, HM only was used but was followed by office visits if necessary. Conventional patients were evaluated with office visits only. Scheduled office visits and unscheduled evaluations, incidence of morbidity, and time elapsed from first event occurrence in each patient to physician evaluation were tracked for each group. HM and conventional patients were similar (age, 63.3±12.8 versus 64.0±12.1 years; gender, 72.0% versus 73.1% male; New York Heart Association class II, 55.9% versus 60.4%; pathology: left ventricular ejection fraction, 29.0±10.7% versus 28.5±9.8%; coronary artery disease, 64.8% versus 71.7%; primary prevention indication, 72.2% versus 73.8%; and dual-chamber implants, 57.8% versus 56.6%). HM reduced total in-hospital device evaluations by 45% without affecting morbidity. In the HM group, 85.8% of all 6-, 9-, and 12-month follow-ups were performed remotely only, indicating that HM provided sufficient assessment in the majority. Median time to evaluation was <2 days in the HM group compared with 36 days in the conventional group (P<0.001) for all arrhythmic events. Conclusions— HM is safe and allows more rapid detection of actionable events compared with conventional monitoring in patients with implantable electronic cardiac devices. Clinical Trials Registration— URL: http:/www.clinicaltrials. gov. Unique identifier: NCT00336284.
Information architecture: blueprints for the Web

<b>Information Architecture: Blueprints for the Web</b><br><b><i>Christina Wodtke</i></b><br><i>New Riders, Indianapolis, 2003</i><br><i>ISBN 0-7357-1250-6 $29.99</i>
Prostaglandin-E2 Mediated Increase in Calcium and Phosphate Excretion in a Mouse Model of Distal Nephron Salt Wasting

Contribution of salt wasting and volume depletion to the pathogenesis of hypercalciuria and hyperphosphaturia is poorly understood. Pendrin/NCC double KO (pendrin/NCC-dKO) mice display severe salt wasting under basal conditions and develop profound volume depletion, prerenal renal failure, and metabolic alkalosis and are growth retarded. Microscopic examination of the kidneys of pendrin/NCC-dKO mice revealed the presence of calcium phosphate deposits in the medullary collecting ducts, along with increased urinary calcium and phosphate excretion. Confirmatory studies revealed decreases in the expression levels of sodium phosphate transporter-2 isoforms a and c, increases in the expression of cytochrome p450 family 4a isotypes 12 a and b, as well as prostaglandin E synthase 1, and cyclooxygenases 1 and 2. Pendrin/NCC-dKO animals also had a significant increase in urinary prostaglandin E2 (PGE-2) and renal content of 20-hydroxyeicosatetraenoic acid (20-HETE) levels. Pendrin/NCC-dKO animals exhibit reduced expression levels of the sodium/potassium/2chloride co-transporter 2 (NKCC2) in their medullary thick ascending limb. Further assessment of the renal expression of NKCC2 isoforms by quantitative real time PCR (qRT-PCR) reveled that compared to WT mice, the expression of NKCC2 isotype F was significantly reduced in pendrin/NCC-dKO mice. Provision of a high salt diet to rectify volume depletion or inhibition of PGE-2 synthesis by indomethacin, but not inhibition of 20-HETE generation by HET0016, significantly improved hypercalciuria and salt wasting in pendrin/NCC dKO mice. Both high salt diet and indomethacin treatment also corrected the alterations in NKCC2 isotype expression in pendrin/NCC-dKO mice. We propose that severe salt wasting and volume depletion, irrespective of the primary originating nephron segment, can secondarily impair the reabsorption of salt and calcium in the thick ascending limb of Henle and/or proximal tubule, and reabsorption of sodium and phosphate in the proximal tubule via processes that are mediated by PGE-2.
Neural Control of Renin Secretion in Anesthetized Dogs: Interaction of Cardiopulmonary and Carotid Baroreceptors

Vagal cold block increased arterial blood pressure but not the secretion of renin (radioimmunoassay) in 17 of 20 anesthetized mechanically ventilated dogs with aortic nerves cut and carotid sinuses intact. Vagal block caused an increase in renin secretion in four dogs with aortic nerves cut when the carotid sinuses were vascularly isolated; this was abolished or greatly attenuated when the carotid baroreflex was allowed to function normally. In five dogs with aortic nerves cut, vagal cold block caused an increase in arterial blood pressure and in inhibitory nerve traffic from the carotid baroreceptors. In 7 of 10 dogs, a nonhypotensive hemorrhage (4 ml/kg) increased renin secretion before but not after vagotomy. Nine of 11 dogs released renin during hemorrhage before and after sham vagotomy. Inhibitory traffic from carotid sinus baroreceptors was not decreased by nonhypotensive hemorrhage. The experiments show that (1) cardiopulmonary receptors with vagal afferents exert a tonic inhibition of renin secretion in the presence of normally functioning carotid baroreceptors; (2) cardiopulmonary receptors can respond to a decrease in blood volume to which arterial baroreceptors are insensitive; and (3) when free to exert their normal buffering influence, carotid baroreceptors can markedly or totally inhibit the release of renin which results from complete interruption of afferent vagal traffic from cardiopulmonary receptors. The study shows that the reflex change in renin secretion may vary, depending on whether only one receptor system is involved or whether two or more systems interact in response to the disturbance.