Miracle-dz/UniFAR-FTUs huggingface dataset:
Coverage in wireless ad-hoc sensor networks

Sensor networks pose a number of challenging conceptual and optimization problems such as location, deployment, and tracking. One of the fundamental problems in sensor networks is the calculation of the coverage. In Meguerdichian et al. (2001), it is assumed that the sensor has uniform sensing ability. In this paper, we give efficient distributed algorithms to optimally solve the best-coverage problem raised in Meguerdichian. Here, we consider the sensing model: the sensing ability diminishes as the distance increases. As energy conservation is a major concern in wireless (or sensor) networks, we also consider how to find an optimum best-coverage-path with the least energy consumption. We also consider how to find an optimum best-coverage-path that travels a small distance. In addition, we justify the correctness of the method proposed in Meguerdichian, that uses the Delaunay triangulation to solve the best coverage problem. Moreover, we show that the search space of the best coverage problem can be confined to the relative neighborhood graph, which can be constructed locally.
Audio Surveillance

Despite surveillance systems becoming increasingly ubiquitous in our living environment, automated surveillance, currently based on video sensory modality and machine intelligence, lacks most of the time the robustness and reliability required in several real applications. To tackle this issue, audio sensory devices have been incorporated, both alone or in combination with video, giving birth in the past decade, to a considerable amount of research. In this article, audio-based automated surveillance methods are organized into a comprehensive survey: A general taxonomy, inspired by the more widespread video surveillance field, is proposed to systematically describe the methods covering background subtraction, event classification, object tracking, and situation analysis. For each of these tasks, all the significant works are reviewed, detailing their pros and cons and the context for which they have been proposed. Moreover, a specific section is devoted to audio features, discussing their expressiveness and their employment in the above-described tasks. Differing from other surveys on audio processing and analysis, the present one is specifically targeted to automated surveillance, highlighting the target applications of each described method and providing the reader with a systematic and schematic view useful for retrieving the most suited algorithms for each specific requirement.
Evaluating HPV‐negative CIN2+ in the ATHENA trial

A post hoc analysis of the ATHENA study was performed to determine whether true HPV‐negative cervical lesions occur and whether they have clinical relevance. The ATHENA database was searched for all CIN2 or worse (CIN2+) cases with cobas HPV‐negative results and comparison was made with Linear Array (LA) and Amplicor to detect true false‐negative HPV results. Immunostaining with p16 was performed on these cases to identify false‐positive histology results. H&E slides were re‐reviewed by the study pathologists with knowledge of patient age, HPV test results and p16 immunostaining. Those with positive p16 immunostaining and/or a positive histopathology review underwent whole tissue section HPV PCR by the SPF10/LiPA/RHA system. Among 46,887 eligible women, 497 cases of CIN2+ were detected, 55 of which tested negative by the cobas® HPV Test (32 CIN2, 23 CIN3/ACIS). By LA and/or Amplicor, 32 CIN2+ (20 CIN2, 12 CIN3/ACIS) were HPV positive and categorized as false‐negatives by cobas HPV; nine of 12 false‐negative CIN3/ACIS cases were p16+. There were 23 cases (12 CIN2, 11 CIN3/ACIS) negative by all HPV tests; seven of 11 CIN3/ACIS cases were p16+. H&E slides were available for six cases for re‐review and all were confirmed as CIN3/ACIS. Tissue PCR was performed on the six confirmed CIN3/ACIS cases (and one without confirmation): four were positive for HPV types not considered oncogenic, two were positive for oncogenic genotypes and one was indeterminate. In summary, subanalysis of a large cervical cancer screening study did not identify any true CIN3/ACIS not attributable to HPV.
Common cortical and subcortical targets of the dorsolateral prefrontal and posterior parietal cortices in the rhesus monkey: evidence for a distributed neural network subserving spatially guided behavior

Common efferent projections of the dorsolateral prefrontal cortex and posterior parietal cortex were examined in 3 rhesus monkeys by placing injections of tritiated amino acids and HRP in frontal and parietal cortices, respectively, of the same hemisphere. Terminal labeling originating from both frontal and parietal injection sites was found to be in apposition in 15 ipsilateral cortical areas: the supplementary motor cortex, the dorsal premotor cortex, the ventral premotor cortex, the anterior arcuate cortex (including the frontal eye fields), the orbitofrontal cortex, the anterior and posterior cingulate cortices, the frontoparietal operculum, the insular cortex, the medial parietal cortex, the superior temporal cortex, the parahippocampal gyrus, the presubiculum, the caudomedial lobule, and the medial prestriate cortex. Convergent terminal labeling was observed in the contralateral hemisphere as well, most prominently in the principal sulcal cortex, the superior arcuate cortex, and the superior temporal cortex. In certain common target areas, as for example the cingulate cortices, frontal and parietal efferents terminate in an array of interdigitating columns, an arrangement much like that observed for callosal and associational projections to the principal sulcus (Goldman-Rakic and Schwartz, 1982). In other areas, frontal and parietal terminals exhibit a laminar complementarity: in the depths of the superior temporal sulcus, prefrontal terminals are densely distributed within laminae I, III, and V, whereas parietal terminals occupy mainly laminae IV and VI directly below the prefrontal bands. Subcortical structures also receive apposing or overlapping projections from both prefrontal and parietal cortices. The dorsolateral prefrontal and posterior parietal cortices project to adjacent, longitudinal domains of the neostriatum, as has been described previously (Selemon and Goldman-Rakic, 1985); these projections are also found in close apposition in the claustrum, the amygdala, the caudomedial lobule, and throughout the anterior medial, medial dorsal, lateral dorsal, and medial pulvinar nuclei of the thalamus. In the brain stem, both areas of association cortex project to the intermediate layers of the superior colliculus and to the midline reticular formation of the pons. (ABSTRACT TRUNCATED AT 400 WORDS)
Expression of MAGE‐antigens in normal tissues and cancer

The human MAGE gene family encodes products that can be recognized by autologous cytotoxic T cells. Because MAGE genes are silent in most normal tissues except testis but are activated in a variety of neoplastic lesions, MAGE antigens represent ideal targets for immunotherapy. Current knowledge of MAGE gene expression is based primarily on mRNA typing and relatively little is known about MAGE protein expression. Monoclonal antibody (MAb) 57B, originally thought to be specific for MAGE‐3, but now known to be reactive with other MAGE components, was used in the present study to analyze MAGE expression in a panel of normal and malignant tissues. In tests with a wide range of normal tissues, only spermatogenic cells of testis were reactive with 57B. In tumor tissues, significant immunoreactivity was observed in malignant melanomas and carcinomas of the lung, head and neck as well as urinary bladder. No 57B reactivity was seen with colorectal, prostatic or renal cell carcinomas. Lipo‐ and myosarcomas, as well as malignant fibrous histiocytoma (MFH), were negative, but synovial sarcomas showed intense immunoreactivity. A subset of seminomas was also strongly reactive with 57B. Tumor specimens showed great variability in the number of tumor cells showing 57B reactivity, with some tumors showing only small isolated clusters of positive cells to other tumors with uniform staining throughout the tumor. Int. J. Cancer 85:460–465, 2000. © 2000 Wiley‐Liss, Inc.
Reducing Type I Errors in Tn-Seq Experiments by Correcting the Skew in Read Count Distributions

Sequencing of transposon-mutant libraries using next-generation sequencing (Tn-Seq) has become a popular method for determining which genes and non-coding regions are essential for growth under various conditions in bacteria. For methods that rely on comparison of read-counts at transposon insertion sites, proper normalization of Tn-Seq datasets is vitally important. Real Tn-Seq datasets often exhibit a significant skew and can be dominated by high counts at a small number of sites (often for nonbiological reasons). If two datasets that are not appropriately normalized are compared, it might cause the artifactual appearance of conditionally essential genes in a statistical test, constituting type I errors (false positives). In this paper, we propose a novel method for normalization of Tn-Seq datasets that corrects for the skew in read count distributions by fitting them to a Beta-Geometric distribution. We show that this read-count correction procedure reduces the number of false positives when comparing replicate datasets grown under the same conditions (for which no genuine differences in essentiality are expected).
The listener as a source of sound change

This paper is an update with some revisions on the paper “The listener as a source of sound change” published in 1981 as well as related papers published subsequently. First, arguments will be presented to reinforce the claim that sound change is free of teleology, i.e., purposeful change – neither on the part of the speaker nor the listener. Related to this is that the product of sound change does not yield a better or optimal means of vocal communication. Second, I will revisit and revise my claims about the features eligible for dissimilation vs. those not eligible. I will revisit and re-emphasize my claims that sound change can be regarded as ‘nature’s speech perception experiment’. Finally, I will update my claim that the mechanisms of sound change can be studied empirically, i.e., in the laboratory – as foreseen by von Raumer, Brucke, Rosapelly, Rousselot, and others more than a century ago.
Pgs28 belongs to a family of epidermal growth factor-like antigens that are targets of malaria transmission-blocking antibodies

Although Pgs28, a 28-kD surface protein of Plasmodium gallinaceum ookinetes, was previously thought not to be a target of transmission- blocking antibodies, we found that polyclonal antisera to Pgs28 completely blocked parasite infectivity to Aedes aegypti mosquitoes. Antisera raised against reduced Pgs28 were less effective in blocking transmission than were antisera to nonreduced Pgs28; thus, the target epitope(s) of transmission-blocking antibodies appears to be conformation dependent. In stage-specific assays, polyclonal antisera impaired the in vitro transformation of zygotes to mature ookinetes, as well as the in vivo development of mature ookinetes to oocysts. Using microsequence of immunoaffinity-purified Pgs28, we cloned the 666-bp open reading frame of the Pgs28 gene. The deduced amino acid sequence of Pgs28 is strikingly similar to that of a P. gallinaceum zygote surface protein, Pgs25, and its P. falciparum analogue, Pfs25. Pgs28, like Pgs25 and Pfs25, has a presumptive secretory signal sequence, followed by four epidermal growth factor-like domains, and a terminal hydrophobic region.
Maternal Metformin Treatment Improves Developmental and Metabolic Traits of IUGR Fetuses

Metformin is an anti-hyperglycemic drug widely used for the treatment of insulin resistance and glucose intolerance and is currently considered for preventing large-for-gestational-age (LGA) offspring in pregnant women affected by obesity or diabetes. Our hypothesis was the opposite—metformin may be used for improving the development of offspring affected by intrauterine growth restriction (IUGR) and preventing the appearance of small-for-gestational-age (SGA) neonates in non-obese and non-diabetic but malnourished pregnancies. The current study, performed in a swine preclinical model of IUGR by undernutrition, showed that fetuses in the treated group showed no significant increases in body-weight, but showed a significantly higher weight of the brain, the total thoracic and abdominal viscera, the liver, the kidneys, the spleen, and the adrenal glands. Maternal metformin treatment was also related to significant increases in the fetal plasma concentration of parameters indicative of glycemic (glucose and fructosamine) and lipid profiles (triglycerides). Overall, these results suggest a protective effect of the treatment on the developmental competence of the fetuses. These findings may be of high value for human medicine in case of maternal malnutrition, since metformin is a cheap drug easily available, but also in case of placental deficiency, since metformin seems to improve placental development and function.
New converter circuitry for high v applications using Switched Inductor Multilevel Converter

This paper presents an analysis and design of a a high voltage gain DC-DC converter. This converter is a single stage DC-DC multilevel boost converter topology with very large voltage gain conversion ratio. It is called a Switched Inductor Multilevel Boost Converter (SIMLBC). It converts a low voltage level to high voltage level to be used in any application that requires high voltages. The capacitors in the output circuit provide a different output dc levels suitable for multilevel inverter applications. The main problem of any multilevel converter is the efficiency because there are a lot of components that consume power. So this work investigates practical circuit analysis. The non-ideal voltage gain of the new topology and their efficiency of the system are derived. The equivalent series resistance (ESR) of the capacitors, dc winding resistance (DCR) of the two inductors, the forward voltage of the diodes, and the drain-source resistance of the switch have been taken into consideration. The calculated efficiency of the system is compared to the simulation one to validate the analyses. Mathcad software is used to compare the simulation with the calculation and experimental results. Results provide the guidelines for an accurate and efficient design.
Adalimumab in the therapy of uveitis in childhood

Purpose: Chronic anterior uveitis in children often takes a serious course. Despite various immunosuppressive drugs some children do not respond sufficiently and there is a high risk of them becoming seriously disabled. Anti-TNF alpha therapy has been shown by our group and others to be mostly ineffective (Etanercept) or partly effective (Infliximab) with the risk of anaphylactic reactions. Here we report on 18 young patients treated with Adalimumab (Humira®), a complete humanised anti-TNF alpha antibody. Methods: We retrospectively analysed 18 patients, who were treated with Adalimumab (20–40 mg, every 2 weeks, when ineffective every week); 17 had juvenile idiopathic arthritis, one was without detectable underlying disease. The age at onset of arthritis varied from 0.5–15 years and for uveitis from 2–19 years. Patients were included when the previous anti-inflammatory therapy had been ineffective. It consisted of systemic steroids (n = 18), Cyclosporin A (n = 18), Methotrexate (n = 18), Azathioprine (n = 12), Mycophenolate mofetil (n = 4), Cyclophosphamide (n = 2), Leflunomide (n = 3), Etanercept (n = 8) and Infliximab (n = 5). The grading for uveitis was: (a) effective: no relapse or more than two relapses less than before treatment, (b) mild: one relapse less than before treatment, (c) no response: no change in relapse rate and (d) worsening: more relapses under treatment than before. The grading for arthritis (depending on the clinical findings), using three out of six parameters of the ACR PED Criteria, was: effective, mild, no response, worsening. Results: For arthritis (n = 16) the response to Adalimumab was effective in 10 of 16 patients, mild in three patients, three did not respond. For uveitis (n = 18) Adalimumab was effective in 16, mild in one child, and one patient did not show any effect. After a very good response initially a shorter application time had to be used to maintain the good anti-inflammatory effect in one child. Additional immunosuppressive treatment was used in seven of the effectively treated children. Due to elevation of liver enzymes in one patient, who also took MTX, Adalimumab had to be discontinued. No anaphylactic reactions or increased frequency of infections since start of Adalimumab treatment was reported. Conclusions: For our group of children with long lasting disease our results show that Adalimumab was effective or mildly effective against the arthritis in 81%, but in uveitis in 88%. While these results regarding arthritis are comparable with other TNF-alpha blocking drugs (Etanercept), Adalimumab seems to be much more effective against uveitis than Etanercept. Anaphylactic reactions, found in a previous study from our group after Infliximab treatment, were not seen with Adalimumab. The necessary dosage and the treatment period, which probably have to be defined individually for each patient, remain unclear.
A Penalized Linear and Nonlinear Combined Conjugate Gradient Method for the Reconstruction of Fluorescence Molecular Tomography

Conjugate gradient method is verified to be efficient for nonlinear optimization problems of large-dimension data. In this paper, a penalized linear and nonlinear combined conjugate gradient method for the reconstruction of fluorescence molecular tomography (FMT) is presented. The algorithm combines the linear conjugate gradient method and the nonlinear conjugate gradient method together based on a restart strategy, in order to take advantage of the two kinds of conjugate gradient methods and compensate for the disadvantages. A quadratic penalty method is adopted to gain a nonnegative constraint and reduce the illposedness of the problem. Simulation studies show that the presented algorithm is accurate, stable, and fast. It has a better performance than the conventional conjugate gradient-based reconstruction algorithms. It offers an effective approach to reconstruct fluorochrome information for FMT.
Cognitive media types for multimedia information access

Multimedia repositories, libraries, and databases o er the potential for providing students with access to a wide variety of interconnected information resources. However, in order to realize this potential, multimedia systems should provide access to information and activities that support e ective knowledge construction and learning by students. This article proposes a theoretical framework for organizing information and activities in educational hypermedia systems. We show that such systems should not be characterized primarily in terms of the kinds of physical media types that can be accessed; instead, the important aspect is the content that can be represented within a physical media, rather than the physical media itself. We propose a theory of \cognitive media types" based on the inferential and learning processes of human users. The theory highlights speci c media characteristics that facilitate speci c problem solving actions, which in turn are enabled by speci c kinds of physical media. We present an implemented computer system, called AlgoNet, that supports hypermedia information access and constructive learning activities for self-paced learning in computer and engineering disciplines. Extensive empirical evaluations with undergraduate students suggest that self-paced interactive learning environments, coupled with multimedia information access and constructive activities organized into cognitive media types, can support and help students develop deep intuitions about important concepts in a given domain. Article to appear in Journal of Educational Multimedia and Hypermedia. Please address correspondence to: Dr. Mimi Recker, UTDC, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand. Phone: 64-4-471-5306. Fax: 64-4-495-5284. Email: mimi.recker@vuw.ac. nz.
Prevalence of tick-borne pathogens at various workplaces in forest exploitation environment.

BACKGROUND The objective of the study was the evaluation of the infection of ticks with pathogenic microorganisms at various workplaces (timber acquisition, forest growing, forest cultivation, forest protection). MATERIAL AND METHODS Eight hundred sixty one Ixodes ricinus ticks collected from 4 workplaces were examined for the presence of Borrelia burgdorferi, Anaplasma phagocytophilum and Babesia microti by polymerase chain reaction (PCR). Then, a comparative analysis of the relative density and infection of ticks at individual workplaces was done. In the statistical analysis, Chi2 test, and Pearson's test for correlation were applied. RESULTS The differences in infection (15.9-50%) of ticks with B: burgdorferi between the examined workplaces were highly significant, with the highest percentage observed at forest growing. The percentages of infection of ticks with A. phagocytophilum at individual workplaces ranged from 1.1-3.7%, and differences were statistically insignificant. The percentages of infections of ticks with Babesia microti at individual workplaces fluctuated from 3.6-4.4% and differences were also insignificant. Co-infections of ticks with 2 or 3 pathogens were rare. CONCLUSIONS Co-infections with B. burgdorferi and B. microti showed a significant relationship with the workplaces, while those with B. burgdorferi and A. phagocytophilum did not show such a dependence. No significant positive correlation was found between the relative density of ticks and the frequencies of infections with B. burgdorferi, A. phagocytophilum and B. microti.
Exploring Extensions to Machine-learning based Gene Normalisation

One of the foundational text-mining tasks in the biomedical domain is the identification of genes and protein names in journal papers. However, the ambiguous nature of gene names means that the performance of information management tasks such as query-based retrieval will suffer if gene name mentions are not explicitly mapped back to a unique identifier in order to resolve issues relating to synonymy (i.e. many different lexical forms representing the same gene) and ambiguity (i.e. many distinct genes sharing the same lexical form). This task is called gene name normalisation, and was recently investigated at the BioCreative Challenge (Hirschman et al., 2004b), a text-mining evaluation forum focusing on core biomedical text processing tasks. In this work, we present a machine learning approach to gene normalisation based on work by Crim et al. (2005). We compare this system with a number of simple dictionary lookup-based methods. We also investigate a number of novel features not used by Crim et al. (2005). Our results show that it is difficult to improve upon the original set of features used by Crim et al. We also show that for some organisims gene name normalisation can be successfully performed using simple dictionary lookup techniques.