Miracle-dz/UniFAR-FTUs huggingface dataset:
Phantoms for diffuse optical imaging based on totally absorbing objects, part 1: basic concepts

Abstract. The design of inhomogeneous phantoms for diffuse optical imaging purposes using totally absorbing objects embedded in a diffusive medium is proposed and validated. From time-resolved and continuous-wave Monte Carlo simulations, it is shown that a given or desired perturbation strength caused by a realistic absorbing inhomogeneity of a certain absorption and volume can be approximately mimicked by a small totally absorbing object of a so-called equivalent black volume (equivalence relation). This concept can be useful in two ways. First, it can be exploited to design realistic inhomogeneous phantoms with different perturbation strengths simply using a set of black objects with different volumes. Further, it permits one to grade physiological or pathological changes on a reproducible scale of perturbation strengths given as equivalent black volumes, thus facilitating the performance assessment of clinical instruments. A set of plots and interpolating functions to derive the equivalent black volume corresponding to a given absorption change is provided. The application of the equivalent black volume concept for grading different optical perturbations is demonstrated for some examples.
CLN3, the protein associated with batten disease: Structure, function and localization

Batten disease, an inherited neurodegenerative storage disease affecting children, results from the autosomal recessive inheritance of mutations in Cln3. The function of the CLN3 protein remains unknown. A key to understanding the pathology of this devastating disease will be to elucidate the function of CLN3 at the cellular level. CLN3 has proven difficult to study as it is predicted to be a membrane protein expressed at relatively low levels. This article is a critical review of various approaches used in examining the structure, trafficking, and localization of CLN3. We conclude that CLN3 is likely resident in the lysosomal/endosomal membrane. Different groups have postulated conflicting orientations for CLN3 within this membrane. In addition, CLN3 undergoes several posttranslational modifications and is trafficked through the endoplasmic reticulum and Golgi. Recent evidence also suggests that CLN3 traffics via the plasma membrane. Although the function of this protein remains elusive, it is apparent that genetic alterations in Cln3 may have a direct affect on lysosomal function. © 2005 Wiley‐Liss, Inc.
Multi-Channel Opportunistic Routing in Multi-Hop Wireless Networks

We propose and investigate Multi-Channel Extremely Opportunistic Routing (MCExOR) which is a protocol that extends Extremely Opportunistic Routing by utilizing multiple RF channels in multi-hop wireless networks. Large numbers of transmissions per end-to-end delivery combined with interference are the main reasons for the low capacity of wireless multi-hop networks. MCExOR reduces the overall number of transmissions in wireless multi-hop networks by opportunistically skipping nodes in a packet’s forwarding path. The use of multiple non overlapping RF channels contributes to the reduction of overall interference. In contrast to other approaches MCExOR only needs one RF transceiver per device. We present algorithms for route discovery and packet forwarding. A significant benefit of MCExOR is that the selection of RF channels is independent of the routing function. Finally, with the help of simulations we show that MCExOR outperforms traditional protocols like ad-hoc on-demand distance vector routing through the simultaneous use of multiple RF channels. In combination with realistic radio propagation models an increase in the throughput is observed due to the opportunistic feature of MCExOR. With the increasing number of RF channels the overall throughput increases superproportionally. Unlike other multi channel approaches even a single packet flow can benefit from the existence of multiple channels.
Design, implementation and performance validation of UOMPro artificial hand: Towards affordable hand prostheses

In this paper, an anthropometric, active artificial prosthetic hand named UOMPro (University of Moratuwa Prosthetic) is proposed. The UOMPro hand is realized during research on developing affordable hand prostheses for use by people mainly in developing countries where purchasing high cost state-of-the-art commercial hand prostheses may be beyond their capacity. The proposed hand is developed with an affordable cost (< 850 USD) and it consists of 6 Degrees of Freedom (DOF) including flexion/extension motions of five fingers and abduction/adduction motion of the thumb finger. Under actuated fingers are fabricated using a combination of 3D printed parts and CNC machined aluminum which addresses drawbacks in fully 3D printed hands. All components of the electronic control circuit which are responsible for low-level controlling of the hand are placed inside the hand where a simple serial communication interface is provided to link with high-level control methods. The implemented low-level controller can communicate with either a high-level controller that sends individual fingers position commands or a high-level controller which sends hand grip pattern commands. A set of experiments are conducted to validate the performance of the overall system and results are presented with potential future directions.
Low Folate and Selenium in the Mouse Maternal Diet Alters Liver Gene Expression Patterns in the Offspring after Weaning

During pregnancy, selenium (Se) and folate requirements increase, with deficiencies linked to neural tube defects (folate) and DNA oxidation (Se). This study investigated the effect of a high-fat diet either supplemented with (diet H), or marginally deficient in (diet L), Se and folate. Pregnant female mice and their male offspring were assigned to one of four treatments: diet H during gestation, lactation and post-weaning; diet L during gestation, lactation and post-weaning; diet H during gestation and lactation but diet L fed to offspring post-weaning; or diet L during gestation and lactation followed by diet H fed to offspring post-weaning. Microarray and pathway analyses were performed using RNA from colon and liver of 12-week-old male offspring. Gene set enrichment analysis of liver gene expression showed that diet L affected several pathways including regulation of translation (protein biosynthesis), methyl group metabolism, and fatty acid metabolism; this effect was stronger when the diet was fed to mothers, rather than to offspring. No significant differences in individual gene expression were observed in colon but there were significant differences in cell cycle control pathways. In conclusion, a maternal low Se/folate diet during gestation and lactation has more effects on gene expression in offspring than the same diet fed to offspring post-weaning; low Se and folate in utero and during lactation thus has persistent metabolic effects in the offspring.
The design and architecture of reticularspaces: an activity-based computing framework for distributed and collaborative smartspaces

Interactive workspaces are increasingly physically distributed, highlighting the challenge of building interfaces that support group interaction with digital documents through multiple locations and devices. This paper presents the technical implementation and user interface of ReticularSpaces. Based on the concepts and principles of Activity-Based Computing (ABC), ReticularSpaces implements a novel approach to smart space user interfaces, and supports task-based information management, mobility, and collaboration.
Oligoamine analogues in combination with 2-difluoromethylornithine synergistically induce re-expression of aberrantly silenced tumour-suppressor genes

Epigenetic gene silencing is an important mechanism in the initiation and progression of cancer. Abnormal DNA CpG island hypermethylation and histone modifications are involved in aberrant silencing of tumour-suppressor genes. LSD1 (lysine-specific demethylase 1) was the first enzyme identified to specifically demethylate H3K4 (Lys4 of histone H3). Methylated H3K4 is an important mark associated with transcriptional activation. The flavin adenine dinucleotide-binding amine oxidase domain of LSD1 is homologous with two polyamine oxidases, SMO (spermine oxidase) and APAO (N1-acetylpolyamine oxidase). We have demonstrated previously that long-chain polyamine analogues, the oligoamines, are inhibitors of LSD1. In the present paper we report the synergistic effects of specific oligoamines in combination with DFMO (2-difluoromethylornithine), an inhibitor of ornithine decarboxylase, in human colorectal cancer cells. DFMO treatment depletes natural polyamines and increases the uptake of exogenous polyamines. The combination of oligoamines and DFMO results in a synergistic re-expression of aberrantly silenced tumour-suppressor genes, including SFRP2 (secreted frizzled-related protein 2), which encodes a Wnt signalling pathway antagonist and plays an anti-tumorigenic role in colorectal cancer. The treatment-induced re-expression of SFRP2 is associated with increased H3K4me2 (di-methyl H3K4) in the gene promoter. The combination of LSD1-inhibiting oligoamines and DFMO represents a novel approach to epigenetic therapy of cancer.
The classification of staphylococci from colonized ventriculo-atrial shunts

Micrococcaceae isolated from the shunt, ventricles, and bloodstream of children with colonized ventriculo-venous shunts were classified within the scheme of Baird-Parker (1963). With one exception, all belonged to subgroup II of the genus Staphylococcus; tests were therefore devised for division within this subgroup, and results are reported in 30 cases from this and other hospitals. Skin and nasal staphylococci isolated from many of these patients were compared with those recovered from their shunts and blood. Evidence is offered for the occasional coexistence of more than one strain of staphylococcus in colonized shunts and in the bloodstream. Successive recolonization of replaced shunts was apparently not necessarily caused by the same type of staphylococcus. Nasal and skin micrococcaceae from many other babies, both in hospital and in parental care, from hospital staff and from adults selected at random from non-hospital sources, were similarly classified. The validity and significance of the findings are discussed.
Motor unit recruitment patterns 2: the influence of myoelectric intensity and muscle fascicle strain rate

SUMMARY To effectively meet the force requirements of a given movement an appropriate number and combination of motor units must be recruited between and within muscles. Orderly recruitment of motor units has been shown to occur in a wide range of skeletal muscles, however, alternative strategies do occur. Faster motor units are better suited to developing force rapidly, and produce higher mechanical power with greater efficiency at faster shortening strain rates than slower motor units. As the frequency content of the myoelectric signal is related to the fibre type of the active motor units, we hypothesised that, in addition to an association between myoelectric frequency and intensity, there would be a significant association between muscle fascicle shortening strain rate and myoelectric frequency content. Myoelectric and sonomicrometric data were collected from the three ankle extensor muscles of the rat hind limb during walking and running. Myoelectric signals were analysed using wavelet transformation and principal component analysis to give a measure of the signal frequency content. Sonomicrometric signals were analysed to give measures of muscle fascicle strain and strain rate. The relationship between myoelectric frequency and both intensity and muscle fascicle strain rate was found to change across the time course of a stride, with differences also occurring in the strength of the associations between and within muscles. In addition to the orderly recruitment of motor units, a mechanical strategy of motor unit recruitment was therefore identified. Motor unit recruitment is therefore a multifactorial phenomenon, which is more complex than typically thought.
White matter abnormalities in long-term heroin users: a preliminary neuroimaging meta-analysis

Abstract Background: Diffusion tensor imaging has been used to explore white matter changes in heroin-dependent patients; however, results have been inconsistent. Objectives: The current study meta-analytically examines the neuroimaging findings of all studies published before 2014 using the novel technique of Effect Size Signed Differential Mapping (ES-SDM). Methods: Two independent investigators searched three databases for whole-brain voxel-based fractional anisotropy morphometric studies involving heroin use without comorbid polysubstance abuse. Of 59 initial primary studies, four met stringent inclusion criteria. Results: Results from this preliminary analysis indicate that heroin abusers may have significant reductions in fractional anisotropy in the bilateral frontal sub-gyral regions extending from the limbic structures to the prefrontal association cortices, implicating damage to the cingulum and superior longitudinal fasciculus. Exploratory moderator analyses indicate that the potential damage in the left cingulate gyrus may increase with longer use and decrease after long-term abstinence. Conclusion: These preliminary findings suggest that heroin abuse is significantly associated with damage to white matter integrity. These results are considered preliminary and analyses should be revisited with more primary studies focusing on either long- or short-term abuse as well as abstinence.
Who Is in There? Exploration of Endophytic Bacteria within the Siphonous Green Seaweed Bryopsis (Bryopsidales, Chlorophyta)

Associations between marine seaweeds and bacteria are widespread, with endobiotic bacterial-algal interactions being described for over 40 years. Also within the siphonous marine green alga Bryopsis, intracellular bacteria have been visualized by electron microscopy in the early ‘70s, but were up to now never molecularly analyzed. To study this partnership, we examined the presence and phylogenetic diversity of microbial communities within the cytoplasm of two Bryopsis species by combining fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Sequencing results revealed the presence of Arcobacter, Bacteroidetes, Flavobacteriaceae, Mycoplasma, Labrenzia, Phyllobacteriaceae and Xanthomonadaceae species. Although the total diversity of the endobiotic communities was unique to each Bryopsis culture, Bacteroidetes, Mycoplasma, Phyllobacteriaceae, and in particular Flavobacteriaceae bacteria, were detected in several Bryopsis samples collected hundreds of kilometres apart. This suggests that Bryopsis closely associates with well-defined endophytic bacterial communities of which some members possibly maintain an endosymbiotic relationship with the algal host.
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum

The MIPS Fusarium graminearum Genome Database (FGDB) was established as a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat, barley and maize. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The results of gene prediction tools were integrated with the help of comparative data on related species to result in a set of 13.718 annotated protein coding genes. This rigorous approach involved adding or modifying gene models and represents a coding sequence gold standard for the genus Fusarium. The gene loci improvements results in 2461 genes which either are new or have different structures compared to the Broad Institute assembly 3 gene set. Moreover the database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets. The resource is accessible on http://mips.gsf. de/genre/proj/FGDB/.
Simultaneous Heterotrophic Nitrification and Aerobic Denitrification by Chryseobacterium sp. R31 Isolated from Abattoir Wastewater

A heterotrophic carbon utilizing microbe (R31) capable of simultaneous nitrification and denitrification (SND) was isolated from wastewater of an Indian slaughterhouse. From an initial COD value of 583.0 mg/L, 95.54% was removed whilst, from a starting NH4 +-N concentration of 55.7 mg/L, 95.87% was removed after 48 h contact. The concentrations of the intermediates hydroxylamine, nitrite, and nitrate were low, thus ensuring nitrogen removal. Aerobic denitrification occurring during ammonium removal by R31 was confirmed by utilization of both nitrate and nitrite as nitrogen substrates. Glucose and succinate were superior while acetate and citrate were poor substrates for nitrogen removal. Molecular phylogenetic identification, supported by chemotaxonomic and physiological properties, assigned R31 as a close relative of Chryseobacterium haifense. The NH4 +-N utilization rate and growth of strain R31 were found to be higher at C/N = 10 in comparison to those achieved with C/N ratios of 5 and 20. Monod kinetic coefficients, half saturation concentration (K s), maximum rate of substrate utilization (k), yield coefficient, (Y) and endogenous decay coefficient (K d) indicated potential application of R31 in large-scale SND process. This is the first report on concomitant carbon oxidation, nitrification, and denitrification in the genus Chryseobacterium and the associated kinetic coefficients.
Excess mortality related to alcohol and smoking among hospital-treated patients with psoriasis.

BACKGROUND Psoriasis is seen as a disease that does not kill. However, it is associated with alcohol intake and smoking. Thus, there could be excess mortality due to causes related to alcohol intake and smoking among patients with psoriasis. DESIGN A cohort was identified from the nationwide Hospital Discharge Register from January 1, 1973, through December 31, 1984, and mortality was followed up for 22 years by linkage with the Cause-of-Death Register, from January 1, 1973, through December 31, 1995. PATIENTS A cohort of 3132 men and 2555 women admitted to inpatient treatment with psoriasis as the principal diagnosis. MAIN OUTCOME MEASURES Date and underlying cause of death. RESULTS We observed 1918 deaths in contrast to the 1211 deaths expected on the basis of the national mortality rates. The all-cause standardized mortality ratio (SMR) for men was 1.62 (95% confidence interval [CI], 1.52-1.71); for women, 1.54 (95% CI, 1.43-1.64). Among men, the highest SMRs were found for alcohol psychosis (8.91 [95% CI, 2.89-20.70]) and liver disease, ie, cirrhosis, fatty liver, and hepatitis (6.98 [95% CI, 5.34-8.96]). Among women, the highest SMR was found for liver disease (5.06 [95% CI, 2.70-8.65]). Excess mortality was high for all causes of death directly related to alcohol; the SMR for men was 4.46 (95% CI, 3.60-5.45); for women, 5.60 (95% CI, 2.98-8.65). CONCLUSIONS Patients with moderate to severe psoriasis are at increased risk for death. Alcohol is a major cause for this excess mortality.
Role of Heat Shock Proteins in Skeletal Muscle

The ability of the human organism to respond with rapid and appropriate modification during physiological challenges is an essential feature for its own survival. These modifications are inseparable from a satisfactory adjustment of the physiological processes of the whole body, where physiological systems tend to maintain relatively constant composition of the internal environment (milieu interieur), despite the constant challenges that the body is submitted daily to, which is known as homeostatic control [1, 2].
Natural language interaction with the web of data by mining its textual side

The Semantic Web is an extension of the classical web. The data and schemas it adds coexist with the documents that were already linked and available. This not only allows interoperability, reusability and potentially unforeseen applications of opened data, but it also creates a unique situation of availability on the web of huge collections of the same pieces of information available at the same time as text and as structured data. An interesting example is the couple Wikipedia-DBpedia: exploiting these interlinked structured and unstructured data sources in parallel can offer a great potential for both Natural Language Processing and Semantic Web applications. Starting from these observations, this paper addresses the problem of enhancing interactions between non-expert users and data available on the Web. In particular, we present QAKiS, a system for open domain Question Answering over linked data, that addresses the problem of question interpretation as a relation-based match, where fragments of the question are matched to binary relations of the triple store, using relational textual patterns automatically collected. In the current version, the relational patterns are automatically extracted from Wikipedia, while DBpedia is the data set to be queried using a natural language interface.
Comparison of Antimicrobial Efficacy of IKI and NaOCl Irrigants in Infected Root Canals: An In Vivo Study

INTRODUCTION Effective debridement of the root canal system with chemical irrigants prior to obturation is the key to long-term success of endodontic therapy. The purpose of this study is to compare the antibacterial activity of 2.5% sodium hypochlorite (NaOCl) and 2% iodine potassium iodide (IKI) solutions as intracanal disinfectant in infected root canals during one-visit endodontic treatment procedure. MATERIALS AND METHODS Thirty single-rooted teeth with necrotic pulps in 27 patients were selected according to specific inclusion/exclusion criteria and divided into two random groups. In group I, canals were irrigated with 2.5% NaOCl during instrumentation and in group II canals were initially irrigated with sterile saline during biomechanical preparation and then exposed to a 5-minute final irrigation with 2% IKI. Bacterial samples were taken before treatment (S1), and at the end of treatment (S2). Mann-Whitney U test was used for analysis. RESULTS Bacteria were present in all initial samples. NaOCl was able to significantly reduce the number of colony forming units (CFU) from S1 to S2 in approximately 90% of canals. Only 15% reductions in CFUs occurred after irrigation/instrumentation in group II; this degree of disinfection was not statistically significant. CONCLUSION According to this study, although root canal irrigation with 2.5% NaOCl could not eradicate all bacteria within the canals; it was significantly superior in comparison with 2% IKI use.