Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Antifungal Susceptibility Testing of Non-Aspergillus Molds

Non-Aspergillus molds including Mucorales, Fusarium, and Scedosporium, etc. are emerging pathogens leading to higher mortality in immunocompromised patients. Fifty-two isolates of genetically confirmed non-Aspergillus molds representing 16 species from 8 genera were collected to evaluate the performance of the Bruker matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) in identification of non-Aspergillus molds. Antifungal susceptibilities were determined through the Clinical & Laboratory Standards Institute (CLSI) M38-A2 broth microdilution method and the Sensititre YeastOne colorimetric method. Bruker MALDI-TOF MS identified 57.7% (30/52) of isolates cultured in broth and 15.4% (8/52) of isolates cultured on solid agar media to the species level, respectively, according to standard interpretation criteria. Lowering the species level cut-off value (COV) from ≥2.0 to ≥1.7 could improve the MALDI-TOF MS species-level identification rate to 67.3% (38/52) for isolates cultured on solid media, with a slight increase of false identification rate of 2.6% (1/38). Amphotericin B was the most in vitro fungistatic-active agent for 98.1% (51/52) of the tested non-Aspergillus molds, with minimum inhibitory concentrations (MICs) of ≤2 μg/mL. The susceptibilities to triazoles varied, with MICs of 0.12 to >16 μg/mL among different species of non-Aspergillus molds. The correlation between the CLSI method and Sensititre YeastOne on antifungal susceptibility testing of non-Aspergillus molds was good, with essential agreement (EA) rates of >90% for triazoles and echinocandins except amphotericin B, which had a lower EA rate of 84.6%. In conclusion, a favorable performance of the Bruker MALDI-TOF MS in identification of clinical non-Aspergillus isolates directly inoculated on solid agar media could be achieved with the adoption of alternative interpretation criteria. Antifungal susceptibility testing is important for non-Aspergillus molds, especially when information on triazole susceptibility is required, and the Sensititre YeastOne is a practical and reliable method to determine antifungal susceptibilities of non-Aspergillus molds.
Biochemical and Structural Characterization of the Interaction between the Siderocalin NGAL/LCN2 (Neutrophil Gelatinase-associated Lipocalin/Lipocalin 2) and the N-terminal Domain of Its Endocytic Receptor SLC22A17*

The neutrophil gelatinase-associated lipocalin (NGAL, also known as LCN2) and its cellular receptor (LCN2-R, SLC22A17) are involved in many physiological and pathological processes such as cell differentiation, apoptosis, and inflammation. These pleiotropic functions mainly rely on NGAL's siderophore-mediated iron transport properties. However, the molecular determinants underlying the interaction between NGAL and its cellular receptor remain largely unknown. Here, using solution-state biomolecular NMR in conjunction with other biophysical methods, we show that the N-terminal domain of LCN2-R is a soluble extracellular domain that is intrinsically disordered and interacts with NGAL preferentially in its apo state to form a fuzzy complex. The relatively weak affinity (≈10 μm) between human LCN2-R-NTD and apoNGAL suggests that the N terminus on its own cannot account for the internalization of NGAL by LCN2-R. However, human LCN2-R-NTD could be involved in the fine-tuning of the interaction between NGAL and its cellular receptor or in a biochemical mechanism allowing the receptor to discriminate between apo- and holo-NGAL.
A mode-based pattern for feature requirements, and a generic feature interface

In this paper, we propose a pattern for decomposing and structuring the model of a feature's behavioural requirements, based on modes of operation (e.g., Active, Inactive, Failed) that are common to features in multiple domains. Interestingly, the highest-level modes of the pattern can serve as a generic behavioural interface for all features that adhere to the pattern. We have applied the pattern in modelling the behavioural requirements of 19 automotive features that were specified in 5 production-grade requirements documents. We found that the pattern was applicable to all 19 features, and that our proposed generic feature interface was applicable to 50 out of 57 inter-feature references.
Microbiome Changes in Healthy Volunteers Treated with GSK1322322, a Novel Antibiotic Targeting Bacterial Peptide Deformylase

ABSTRACT GSK1322322 is a novel antibacterial agent under development, and it has known antibacterial activities against multidrug-resistant respiratory and skin pathogens through its inhibition of the bacterial peptide deformylase. Here, we used next-generation sequencing (NGS) of the bacterial 16S rRNA genes from stool samples collected from 61 healthy volunteers at the predosing and end-of-study time points to determine the effects of GSK1322322 on the gastrointestinal (GI) microbiota in a phase I, randomized, double-blind, and placebo-controlled study. GSK1322322 was administered either intravenously (i.v.) only or in an oral-i.v. combination in single- and repeat-dose-escalation infusions. Analysis of the 16S rRNA sequence data found no significant changes in the relative abundances of GI operational taxonomic units (OTUs) between the prestudy and end-of-study samples for either the placebo- or i.v. -only-treated subjects. However, oral-i.v. treatment resulted in significant decreases in some bacterial taxa, the Firmicutes and Bacteroidales, and increases in others, the Betaproteobacteria, Gammaproteobacteria, and Bifidobacteriaceae. Microbiome diversity plots clearly differentiated the end-of-study oral-i.v. -dosed samples from all others collected. The changes in genome function as inferred from species composition suggest an increase in bacterial transporter and xenobiotic metabolism pathways in these samples. A phylogenetic analysis of the peptide deformylase protein sequences collected from the published genomes of clinical isolates previously tested for GSK1322322 in vitro susceptibility and GI bacterial reference genomes suggests that antibiotic target homology is one of several factors that influences the response of GI microbiota to this antibiotic. Our study shows that dosing regimen and target class are important factors when considering the impact of antibiotic usage on GI microbiota. (This clinical trial was registered at the GlaxoSmithKline Clinical Study Register under study identifier PDF 113376.)
Modeling Dynamics in Time-SeriesCross-Section Political Economy Data

Ethylene-acrylic acid type interpolymer compositions and films having increased slip and reduced block. A compositionally uniform interpolymer is compounded with at least one amide additive of the formula R1-CO-NH-R2 in which R1 is selected from saturated alkyl groups having from 13 to 25 carbon atoms and mono-olefinically unsaturated alkyl groups having from 17 to 23 carbon atoms and in which R2 is selected from saturated alkyl groups having 14 to 26 carbon atoms and mono-olefinically unsaturated alkyl groups having from 18 to 24 carbon atoms; and optionally, finely divided inorganic. In another embodiment, a compositionally uniform or a compositionally non-uniform interpolymer is compounded with: (i) about 0.025-1 weight percent of saturated secondary fatty acid amide; (ii) about 0.025-1 weight percent of unsaturated or mixed unsaturated secondary fatty acid amide; and optionally (iii) about 0.025-1.5 weight percent of finely divided inorganic.
Collagen Type Distribution in the Healthy Human Tympanic Membrane

Background: A weakening of the collagen fibers of the lamina propria of the tympanic membrane is a prerequisite for the formation of a retraction pocket. The various collagen types differ in tensile strength. The distribution of the different collagen types in the lamina propria of the healthy human tympanic membrane has not been reported before. Methods: Immunohistochemical staining for collagen Types I, II, III, and IV in healthy human tympanic membranes harvested during translabyrinthine surgery for acoustic neuroma. The staining was semiquantified using light microscopy. Results: Collagen Type II was the most abundant collagen of the lamina propria. When subdividing the staining between the 2 fiber layers of the lamina propria, it was observed that the inner layer was enriched with Type III relative to Type II, as reflected in staining patterns. In the outer radial fiber layer of the lamina propria, staining for collagen Type II was predominant. The fibrous annulus could be subdivided into an inner and an outer portion by immunohistochemistry. The inner portion stained strongest for collagen Type II and to a lesser extent for Type I. The outer portion stained strongest for collagen Type III and Type I. Conclusion: The differences in distribution of collagen types in the different fiber layers of the lamina propria suggest that the lattice of connective tissue supporting the tympanic membrane is not uniform. Understanding the differences in collagen type distribution and in the physical properties of the individual collagen types themselves may contribute to a comprehensive model of retraction pocket pathogenesis.
The strengths and weaknesses of Gordonia: A review of an emerging genus with increasing biotechnological potential

This review about the genus Gordonia provides a current overview of recent research on a young genus that was introduced in the year 1997 (). This emerging genus has attracted increasing environmental, industrial, biotechnological and medical interest during the last few years, in particular due to the capabilities of its members to degrade, transform, and synthesize organic compounds as well as to the pathogenic effects that have been described in many case studies. The number of publications about Gordonia has increased significantly after the year 2004 (the year of the first Gordonia review published by Arenskötter et al.) describing 13 new validly published species (type strains), many newly described physiological and metabolic capabilities, new patent applications and many new case reports of bacterial infections. Members of the genus Gordonia are widely distributed in nature and it is therefore important to unravel the species richness and metabolic potential of gordoniae in future studies to demonstrate their environmental impact especially on the degradation of persistent organic compounds and their ecological participation in the carbon cycle of organic material in soil and water. This review summarizes mainly the current state of importance and potential of the members of this genus for the environmental and biotechnological industry (“the strengthsâ) and briefly its pathogenic impact to humans (“the weaknessesâ).
DIY Smart Home: The Development of an Exemplary Internet of Things Infrastructure for Computer Science Education

The generic term smart home describes among other things the increase of quality of life, security and reduction of energy consumption in our homes and workplaces through automated processes. These processes enable educators to work up realistic and tangible aspects of computing science using everyday examples. Programming, networks, communication protocols, web design and development, electrical engineering, data science, CAD and even project management can be combined with smart home in terms of content. For this reason, we have used open source tools to develop a cost-effective infrastructure that combines the above-mentioned aspects in a single kit. This kit is based on various in-house developed sensors and actuators based on the ESP8266, a Raspberry Pi as the central unit and Node-RED as the framework for linking the hardware. This hardware can be connected without writing code or previous knowledge, enables a quick experience of success while offering much potential for internal differentiation in teaching.
Polarization Engineering in Nanoscale Waveguides Using Lossless Media

A device that achieves controllable rotation of the state of polarization by rotating the orientation of the eigenmodes of a waveguide by 45° is introduced and analyzed. The device can be implemented using lossless materials on the nanoscale and helps circumvent the inherent polarization dependence of photonic devices realized within the silicon-on-insulator platform. We propose and evaluate two novel polarization rotator-based schemes to achieve polarization engineering functions: 1) A multipurpose device, with dimensions on the order of a few wavelengths which can function as a polarization splitter or an arbitrary linear polarization state generator. 2) An energy efficient optical modulator that utilizes eigenmode rotation and epsilon near zero effects to achieve high extinction ratio, polarization insensitive amplitude modulation without the need to sweep the device geometry to match the TE and TM mode attributes. By using indium tin oxide as an example for a tunable material, the proposed modulator provides polarization insensitive operation and can be realized with a modulation bandwidth of 112 GHz, a length of 1800 nm, an energy per bit of 7.5 f.J and an optical bandwidth of 210 nm.
Reliability and Discriminant Validity of the Children's Drug-Use Survey

The Children's Drug Use Survey assesses involvement with alcohol, marijuana, inhalants, and “pills” and includes experimental psycho-social items. It is short, easy to read, and is constructed so that it does not encourage drug use. Data are presented showing that the drug-use items have high reliability and discriminant validity. The scales should be useful for studying drug involvement in both minority and nonminority youth and possess adequate reliability for use as low as the fourth grade.
Multiple Local and Recent Founder Effects of TGM1 in Spanish Families

Background Mutations in the TGM1 gene encoding transglutaminase 1 are a major cause of autosomal recessive congenital ichthyosis. In the Galician (NW Spain) population, three mutations, c.2278C>T, c. 1223_1227delACAC and c.984+1G>A, were observed at high frequency, representing ∼46%, ∼21% and ∼13% of all TGM1 gene mutations, respectively. Moreover, these mutations were reported only once outside of Galicia, pointing to the existence of historical episodes of local severe genetic drift in this region. Methodology/Principal Findings In order to determine whether these mutations were inherited from a common ancestor in the Galician population, and to estimate the number of generations since their initial appearance, we carried out a haplotype-based analysis by way of genotyping 21 SNPs within and flanking the TGM1 gene and 10 flanking polymorphic microsatellite markers spanning a region of 12 Mb. Two linkage disequilibrium based methods were used to estimate the time to the most recent common ancestor (TMRCA), while a Bayesian-based procedure was used to estimate the age of the two mutations. Haplotype reconstruction from unphased genotypes of all members of the affected pedigrees indicated that all carriers for each of the two mutations harbored the same haplotypes, indicating common ancestry. Conclusions/Significance In good agreement with the documentation record and the census, both mutations arose between 2,800–2,900 years ago (y.a.), but their TMRCA was in the range 600–1,290 y.a. , pointing to the existence of historical bottlenecks in the region followed by population growth. This demographic scenario finds further support on a Bayesian Coalescent Analysis based on TGM1 haplotypes that allowed estimating the occurrence of a dramatic reduction of effective population size around 900–4,500 y.a. (95% highest posterior density) followed by exponential growth.
Interference Assessment for the Spectrum Sharing between IMT-2020 and Inter-Satellite Service

This paper analyzes interference coexistence of IMT-2020 (International Mobile Telecommunications-2020) and inter-satellite service where both systems operate in the same spectrum band of 25.25–27.5 GHz. This work can be regarded as a good reference to the research community, industry and regulators which are currently investigating spectrum requirements and technology options for 5G system. Considering the interference scenario between the return inter-orbit link of data relay satellite system and downlink of IMT-2020, we adopt realistic system parameters and radiation pattern, combined with very recent channel from the literature. Simulation results indicate that the interference from IMT-2020 downlink to Data Relay Satellite (DRS) is above the interference level while the LEO spacecraft cause acceptable interference to IMT-2020 downlink.
Heterogeneity of Pneumocystis Sterol Profiles of Samples from Different Sites in the Same Pair of Lungs Suggests Coinfection by Distinct Organism Populations

ABSTRACT Sterol profiles of samples taken from different sites of aPneumocystis-infected human lung showed large variations in pneumocysterol similar to those that occur among samples from different patients. Thus, the influence of diet or drugs on pneumocysterol accumulation was ruled out, suggesting distinct phenotypic populations as the basis for the heterogeneity.
Analysis of mixed C-means clustering approach for brain tumour gene expression data

Data mining has become an important topic in effective analysis of gene expression data due to its wide application in the biomedical industry. A gene cluster is a set of two or more genes that serve to encode for the same or similar products. Gene clustering is the process of grouping related genes in the same cluster as at the foundation of different genomic studies that aim at analysing the function of genes. Several advanced techniques have been proposed for data clustering and many of them have been applied to gene expression data, with partial success. The goal of gene clustering is to identify important genes and perform cluster discovery on samples. This paper reviews three of the most representative off-line clustering techniques: fuzzy C-means clustering, hierarchical clustering, and mixed C-means clustering. These techniques are implemented and tested against a brain tumour gene expression dataset. The performance of the three techniques is compared based on 'goodness of clustering' evaluation measures and mixed C-means show best performance than the other two clustering techniques for the brain tumour gene expression data.
Neural Mechanisms of Choice Diversification

When asked to select several options at once, people tend to choose a greater diversity of items than when they are asked to make these selections one at a time. Using functional magnetic resonance imaging (fMRI), we provide novel insight into the neural mechanisms underlying diversification in portfolio choices. We found that, as participants made multiple selections from a menu of different options, the current state of their choice portfolio (i.e., the previously selected options) dynamically modulates activity in the neural valuation system in response to the options under evaluation. More specifically, we found that activity in the ventral striatum (VS) decreases when the option has already been selected (“satiation”), while activity in the ventromedial prefrontal cortex increases when other options have previously been selected (“novelty-seeking”). Our findings reveal two processes that drive diversification in portfolio choices, and suggest that the context of previous selections strongly impacts how the brain evaluates current choice options.
Impaired secretion of parathyroid hormone, but not refractoriness of osteoblast, is a major mechanism of low bone turnover in hemodialyzed patients with diabetes mellitus.

Diabetic bone disease is characterized by low bone turnover resulting from either impaired secretion of parathyroid hormone (PTH) or refractoriness of osteoblasts to PTH. The present study was performed to elucidate which factor contributes more to the reduction in bone turnover by comparison between 64 hemodialyzed patients with diabetes mellitus and 106 hemodialyzed patients without diabetes mellitus. Only men were enrolled to avoid the influence of the menstrual cycle on bone metabolism. Serum intact PTH (iPTH) levels were significantly lower in hemodialyzed patients with diabetes than those without diabetes, although no significant difference existed in age, duration of hemodialysis therapy, or serum calcium or phosphate levels. Of the biochemical markers measured, serum intact osteocalcin (iOC) and deoxypyridinoline levels were significantly lower in patients with diabetes, although serum bone-specific alkaline phosphatase (BAP) and pyridinoline levels did not differ significantly between the two groups of patients. When patients were restricted to those with serum iPTH levels greater than 180 pg/mL, this parameter correlated significantly in a positive manner with both serum iOC and BAP levels and negatively with bone mineral density at distal radius 1/3. Regression slopes between iPTH levels and these parameters were not significantly different between the two groups of patients, indicating the absence of refractoriness of bone to PTH in patients with diabetes. In conclusion, our findings suggest that impaired PTH secretion, but not refractoriness of osteoblasts to PTH, may be responsible for the low bone turnover in hemodialyzed patients with diabetes.
Teaching physics with 670-nm diode lasers—experiments with Fabry–Perot cavities

In a previous paper we described details of the construction of stabilized 670‐nm diode lasers for use in undergraduate physics laboratories. We report here a series of experiments that can be performed using the 670‐nm diode laser, a homemade scanning Fabry–Perot cavity, a helium–neon laser, a simple photodiode, and a few pieces of electronics hardware. The experiments include: (1) an introduction to the scanning confocal Fabry–Perot cavity, and to its use as an optical spectrum analyzer; (2) laser frequency modulation and observation of FM sidebands using the optical spectrum analyzer; and (3) the Pound–Drever method for servo‐locking a Fabry–Perot cavity to a laser. These experiments are relatively easy to set up and perform, yet they demonstrate a number of useful optical principles and experimental techniques.
Combining parallel coordinates with multi-objective evolutionary algorithms in a real-world optimisation problem

Optimisation problems based upon real-world instances often contain many objectives. Many existing Multi-Objective Evolutionary Algorithm techniques return a set of solutions from which the user must make a final selection; typically such a set of solutions may take the form of a non-dominated set. The size of such fronts, especially for larger numbers of objectives, can make it difficult for the user to make a selection of the final solution. This paper outlines an initial investigation into combining elements of Parallel Coordinate plots with multi-objective evolutionary algorithms to allow the user to specify solution areas of interest prior to executing the algorithm. The algorithm encourages the evolution of solutions in these areas through selection pressure. The user is presented with one solution from each area on a Parallel Coordinates plot allowing a simple, informed decision as to the solution to be chosen. This paper uses a Workforce Scheduling and Routing Problem (WSRP) to demonstrate the approach. The WSRP formulation used was previously cited in literature as a multi-objective problem, we formulate it as a 5 objective problem. Our initial results suggest that this approach has potential and is worth investigating further.