Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and Biochemical Characterization of 4-Carboxy-2-Hydroxymuconate-6-Semialdehyde Dehydrogenase and Its Role in the Protocatechuate 4,5-Cleavage Pathway inSphingomonas paucimobilis SYK-6

ABSTRACT Protocatechuate (PCA) is the key intermediate metabolite in the lignin degradation pathway of Sphingomonas paucimobilisSYK-6 and is metabolized to pyruvate and oxaloacetate via the PCA 4,5-cleavage pathway. We characterized the 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase gene (ligC). CHMS is the 4,5-cleavage product of PCA and is converted into 2-pyrone-4,6-dicarboxylate (PDC) by LigC. We found thatligC was located 295 bp downstream of ligB, which encodes the large subunit of the PCA 4,5-dioxygenase. TheligC gene consists of a 945-bp open reading frame encoding a polypeptide with a molecular mass of 34,590 Da. The deduced amino acid sequence of ligC showed 19 to 20% identity with 3-chlorobenzoate cis-dihydrodiol dehydrogenase ofAlcaligenes sp. strain BR60 and phthalatecis-dihydrodiol dehydrogenases of Pseudomonas putida NMH102-2 and Burkholderia cepacia DBO1, which are unrelated to group I, II, and III microbial alcohol dehydrogenases (M. F. Reid and C. A. Fewson, Crit. Rev. Microbiol. 20:13–56, 1994). The ligC gene was expressed inEscherichia coli and LigC was purified to near homogeneity. Production of PDC from CHMS catalyzed by LigC was confirmed in the presence of NADP+ by electrospray ionization-mass spectrometry and gas chromatography-mass spectrometry. LigC is a homodimer. The isoelectric point, optimum pH, and optimum temperature were estimated to be 5.3, 8.0, and 25°C, respectively. TheKm for NADP+ was estimated to be 24.6 ± 1.5 μM, which was approximately 10 times lower than that for NAD+ (252 ± 3.9 μM). TheKms for CHMS in the presence of NADP+ and NAD+ are 26.0 ± 0.5 and 20.6 ± 1.0 μM, respectively. Disruption of ligC inS. paucimobilis SYK-6 prevented growth with vanillate. Only PCA was accumulated during the incubation of vanillate with the whole cells of the ligC insertion mutant (DLC), indicating a lack of PCA 4,5-dioxygenase activity in DLC. However, the introduction ofligC into DLC restored its ability to grow on vanillate. PDC was suggested to be an inducer for ligAB gene expression.
Brain Extraction Methods for Neonates

Brain extraction is a very important preprocessing step for neuroimage analysis. Many automatic brain extraction tools have been developed during the past decade, however, most of them have been designed for adult brains. Since the morphology and shape are quite different between brains of adults and neonates, this makes them less suitable for neonatal brain extraction. In this paper, we introduce three methods which are specifically tailored for newborns and compare them against three state-of-the-art skullstripping tools. The results show that our methods yield more accurate outcomes than these tools.
Field-induced aggregates in a bilayer ferrofluid characterized by ultrasound spectroscopy

This paper presents dynamic changes in ferrofluid properties during a magnetic field sweep. The study reported was performed on a ferrofluid with a double layer of surfactant used to prevent aggregation of particles. The ferrofluid parameters (the radius and volume of the cluster, the elastic force constant) were studied by the ultrasound wave absorption method as a function of the dynamically changing magnetic field. During the application of the magnetic field from 0 to 100 kA m−1 the structure in the ferrofluid evolves and become anisotropic. The magnetic field was found to stimulate formation of micrometre clusters and exponential increase in the elastic force constant.
Spatial Distribution of Stem Cell-Like Keratinocytes in Dissected Compound Hair Follicles of the Dog

Hair cycle disturbances are common in dogs and comparable to some alopecic disorders in humans. A normal hair cycle is maintained by follicular stem cells which are predominately found in an area known as the bulge. Due to similar morphological characteristics of the bulge area in humans and dogs, the shared particularity of compound hair follicles as well as similarities in follicular biomarker expression, the dog is a promising model to study human hair cycle and stem cell disorders. To gain insight into the spatial distribution of follicular keratinocytes with stem cell potential in canine compound follicles, we microdissected hair follicles in anagen and telogen from skin samples of freshly euthanized dogs. The keratinocytes isolated from different locations were investigated for their colony forming efficiency, growth and differentiation potential as well as clonal growth. Our results indicate that i) compound and single hair follicles exhibit a comparable spatial distribution pattern with respect to cells with high growth potential and stem cell-like characteristics, ii) the lower isthmus (comprising the bulge) harbors most cells with high growth potential in both, the anagen and the telogen hair cycle stage, iii) unlike in other species, colonies with highest growth potential are rather small with an irregular perimeter and iv) the keratinocytes derived from the bulbar region exhibit characteristics of actively dividing transit amplifying cells. Our results now provide the basis to conduct comparative studies of normal dogs and those with hair cycle disorders with the possibility to extend relevant findings to human patients.
Design and Performance Analysis of a Fairness-Based License-Assisted Access and Resource Scheduling Scheme

In face of the explosive surge of mobile data services, spectrum aggregation or carrier aggregation technology has been proposed to improve system throughput and spectrum efficiency (SE) by aggregating licensed and unlicensed spectrum bands. However, the system performances would be severely deteriorated by the channel access collision if the channel access and resource scheduling approaches are not coordinated among different networks in the same spectrum band. Therefore, in order to improve the system throughput and the SE, a fairness-based license-assisted access and resource scheduling scheme are designed for the coexisting systems, incorporating long term evolution-advanced and WiFi systems in the unlicensed band. The optimal sizes of the contention window in the proposed fairness-based channel access approach are obtained in terms of various density ratios between these two systems. Furthermore, a novel resource scheduling approach employing linear programming is proposed to maximize the utility function with the goal of improving the service experience of users and the SE with various spectrum qualities. The theoretical proofs and simulation results verify the enhanced performances of the proposed approaches in terms of key metrics, such as throughput, SE, delay, and packet loss ratio.
Standardized Assessment of Concussion (SAC): On-Site Mental Status Evaluation of the Athlete

Objective: This study investigated the clinical utility of the Standardized Assessment of Concussion (SAC) in detecting concussion in athletes. Method: Athletic trainers administered the SAC to 568 nonconcussed high school and college football players prior to the 1995 and 1996 football seasons. Thirty-three of these players experienced concussion and were tested immediately following injury; 28 of the 33 underwent additional follow-up testing 48 hours after the injury. Results: Concussed players scored significantly below nonconcussed controls on all SAC measures and significantly below their own pre-injury baseline performance. Follow-up testing documented return to preinjury baseline. Conclusion: These findings support the SAC's effectiveness in detecting concussion and tracking recovery in order to determine a player's fitness to return to play.
Lack of compliance by UK andrology laboratories with World Health Organization recommendations for sperm morphology assessment.

BACKGROUND Sperm morphology is known to correlate with the probability of conception both in vitro and in vivo, but the assessment of sperm morphology in the laboratory remains problematic. The 4th edition (1999) of the World Health Organization (WHO) Laboratory Manual has attempted to improve matters by giving rigorous recommendations regarding sperm morphology assessment. However, it is unknown how well these recommendations have been implemented in practice. METHODS A survey of the methods used to undertake the assessment of sperm morphology during semen analysis was undertaken in 37 laboratories in the UK. RESULTS In total, only two laboratories (5%) were compliant with all current WHO guidelines regarding morphology assessment, including methods of staining and observation, classifying and sampling methods, and the participation in internal and external quality control programmes. CONCLUSION These results illustrate an urgent need for education and training initiatives to encourage laboratories to become compliant with current WHO guidelines for sperm morphology assessment.
Characterization and Partial Purification of Aldose-6-phosphate Reductase (Alditol-6-Phosphate:NADP 1-Oxidoreductase) from Apple Leaves.

Aldose-6-phosphate reductase (alditol 6-phosphate:NADP 1-oxidoreductase) was isolated and characterized from mature apple leaves (Malus domestica cv. Starkrimson). The enzyme was purified 79-fold. The enzyme catalyzed the following reversible reaction: d-glucose 6-phosphate + NADPH + H(+) right arrow over left arrow d-sorbitol 6-phosphate + NADP(+). No activity was detected when NAD(+) was substituted for NADP(+) or when NADH was substituted for NADPH. The enzyme reduced d-galactose 6-phosphate at a higher rate than d-glucose 6-phosphate. d-Mannose 6-phosphate and 2-deoxy-d-glucose 6-phosphate were reduced at low rates. d-Glucose 1-phosphate, d-fructose 6-phosphate, d-ribose 5-phosphate, d-glucose, and sorbitol did not serve as substrates. The pH optimum for both d-sorbitol 6-phosphate oxidation and d-glucose 6-phosphate reduction was 9.5. The K(m) values for d-sorbitol 6-phosphate oxidation and d-glucose 6-phosphate reduction were 3.9 and 20 millimolar, respectively. AgNO(3) (0.1 millimolar) and p-chloromercuribenzoate (1.0 millimolar) completely inhibited the enzyme.Aldose-6-phosphate reductase activity was also detected in mature leaves from Golden Delicious and Antonovka apples (Malus domestica), Conference and Bartlett pears (Pyrus communis), Redhaven peach (Prunus persica), and Perfection apricot (Prunus armeniaca). This suggests that the enzyme has a wide distribution and plays an important role in sorbitol synthesis.
O-GlcNAc cycling shows neuroprotective potential in C. elegans models of neurodegenerative disease

C. elegans has proven to be an excellent organism in which to model human neurodegenerative disease.1–7 The worm’s simple nervous system, lineage, and neural maps, easily scored movement phenotypes, and robust forward and reverse genetics make it optimal for studying age-dependent processes on a reasonable time scale. A popular approach has been the introduction of transgenes expressing GFP-tagged proteotoxic human proteins into neurons leading to visible aggregation or movement phenotypes.2,4,6,8–13 In addition, the maintenance of proteostasis networks has been extensively studied using the power of worm genetics.8–13 These networks include genes involved in insulin-like signaling, the heat shock response, the response to hypoxia, and mTOR and AMPK pathways linked to aging.14 Another pathway with suggestive links to neurodegeneration is the O-GlcNAc cycling pathway, a nutrient-dependent post-translational modification known to be altered in brains from patients with Alzheimer disease.15–19 In this commentary, we summarize our recent findings showing that viable mutants of O-GlcNAc cycling in C. elegans dramatically alter the neurotoxicity of four distinct C. elegans models of neurodegenerative disease.7 Mutants in O-GlcNAc cycling alter the toxicity of mutant tau, polyglutamine expansion reporters, and amyloid β-peptide. The findings further suggest that O-GlcNAc cycling acts at many steps in the lifecycle of aggregation-prone targets. The C. elegans system is likely to continue to provide insights into this complex problem. The involvement of O-GlcNAc cycling in the maintenance of proteostasis raises the possibility of targeting the enzymes catalyzing this critical post-translational modification for therapeutic intervention.
Recolonization of the subgingival microflora after scaling and root planing in human periodontitis.

The purpose of this study was to evaluate the recolonization patterns of the subgingival microflora of adult periodontitis patients after a single session of scaling and root planing. In each of eight patients, three clinically diseased sites were investigated microbiologically by darkfield microscopy and cultural analysis. After initial clinical and microbiological parameters were determined, each subject received a single session of scaling and root planing but no oral hygiene instructions. Clinical indices were measured and microbial parameters were reassessed 7, 21, and 60 days after treatment in a manner such that each of the test sites was sampled only once after treatment. Recolonization was evaluated by matching any single site with its own preoperative site. A significant improvement in probing depth was noted for up to 60 days after treatment, while the gingival index did not change markedly during the course of the study. The microbial composition of treated sites 7 days after scaling and root planing, as determined by both cultural and darkfield data, was similar to that of periodontally healthy sites. Differences between cultural and darkfield data became apparent at the 21 day sampling point. The darkfield data showed that the sites consisted of cocci with few spirochetes. Cultural data demonstrated that the majority of the cocci were anaerobic, namely Streptococcus intermedius, Veillonella parvula, and Peptostreptococcus micros. At 60 days, there was no significant variation in any of the parameters from pretreatment levels. The most prevalent anaerobic rods prior to and 60 days after therapy were Fusobacterium nucleatum, Bacteroides gingivalis, and B. intermedius. (ABSTRACT TRUNCATED AT 250 WORDS)
The Radiation Hardness Assurance Facility at INFN-LNS Catania for the Irradiation of Electronic Components in Air

This paper describes the beam flux monitoring system that has been developed at the Superconducting Cyclotron at INFN-LNS (Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Catania, Italy) in order to monitor the beam parameters such as energy, flux, beam profile, for SEE (Single Event Effects) cross-sections determination and DD (Displacement Damage) studies. In order to have an accurate and continuous monitoring of beam parameters we have developed fully automatic dosimetry setup to be used during SEE (with heavy ions) and DD (with protons up to 60 MeV) tests of electronic devices and systems. The final goal of our activity is to demonstrate that the operation of such a system in air is not detrimental to the accuracy on controlling the beam profile, energy and fluence delivered onto the DUT (Device Under Test) surface, even with non relativistic heavy ions. We have tested our beam monitoring system with the “Reference SEU monitor” developed by ESA/ESTEC, the results are discussed here.
Primary Intrathoracic Dermatofibrosarcoma Protuberans

Dermatofibrosarcoma protuberans (DFSP) is defined as a low-grade sarcoma derived from an uncertain cell of origin in the reticular dermis. We report a fibrosarcomatous variant of DFSP (FS-DFSP) that arose primarily in the deep thoracic soft tissue. The patient was a 9-year-old girl who presented with dyspnea and low-grade fevers without a clinically detectable mass or a history of skin lesion. Imaging studies revealed a 10-cm mass entirely confined within the thoracic cavity. Three years after a marginal excision with adjuvant chemotherapy and radiotherapy, the tumor recurred in the paraspinal region. Histologically, the primary and recurrent tumors comprised a high-grade spindle cell sarcoma, with a small component of storiform, low-grade, CD34-positive spindle cells, classic for an ordinary DFSP. The diagnosis of FS-DFSP was confirmed molecularly by the demonstration of a COL1A1-PDGFB fusion by fluorescence in situ hybridization and reverse transcription-polymerase chain reaction analyses. To our knowledge, this is the first documented case of a genetically confirmed deep-seated DFSP without an associated superficial soft tissue or dermal component. The implication of this case on expanding the clinical spectrum of DFSP will have to be elucidated in future studies by applying molecular pathologic tools in deep-seated sarcomas in the proper morphologic context.
A fast RBM-hidden-nodes based extreme learning machine

In this paper, we propose an Extreme Learning Machine (ELM) approach for solving large and complex data problems. In contrast to existing approaches, we embed hidden nodes that are designed using Restricted Boltzmann machine (RBM) into the classical ELM, exhibiting excellent generalization performances. To overcome the high computational complexity involved especially on large datasets, hidden nodes are derived from RBM trained in turn by multiple random subsets of data sampled from the original datasets instead of the entire dataset in one time. The resultant algorithm proposed is labeled here as FRBM-H-ELM in short. Comprehensive experiments and comparisons are conducted to assess the FRBM-H-ELM against the traditional Extreme Learning Machine. The results obtained demonstrated the superior generalization performance and efficiency of FRBM-H-ELM.
Planning of UWB indoor positioning network using binary integer linear programming

The ultra wide band (UWB) is a promising indoor positioning sensor. Its precise range measurement and wall penetration capability are well suited for indoor navigation. UWB anchor locations must also be carefully determined to achieve the optimal performance of a UWB positioning. However, previous approaches on the UWB anchor placement resulted in poor positioning accuracy around corners of an indoor environment and ignored UWB wall penetration effects. To overcome those shortcomings, this paper introduces an advanced method of an UWB anchor network design that provides high positioning accuracy in all user space and minimises uncertainty due to UWB signal wall penetrations with a binary integer linear programming. It is expected that the presented method would provide a reliable positioning performance that is needed for the navigation of autonomous systems.
Vaccination, seizures and ‘vaccine damage’

Purpose of reviewConcerns about the safety of vaccination have plagued the community, with reduction in vaccine uptake resulting in increased risk of epidemics. Vaccination has been implicated in the cause of febrile seizures, ‘vaccine encephalopathy’ and autistic spectrum disorders. Evaluation of alleged associations is complicated by evolution in the vaccination field. This review focuses on the risk of seizures following vaccination and the alleged associations of vaccination with vaccine encephalopathy and also with autism spectrum disorders. Recent findingsOver the last decade the introduction of new vaccines such as the acellular pertussis vaccine has produced a reduction in seizures following vaccination, the outcome of which was benign even with older vaccines. New evidence emerged in 2006 showing that cases of alleged ‘vaccine encephalopathy’ are due to mutations within a sodium channel gene. The weight of epidemiological evidence does not support a relationship between vaccination and childhood epileptic encephalopathies or autism spectrum disorders. SummaryVaccines are safer than ever before, but the challenge remains to convey this message to society in such a way that produces change in attitudes to vaccination and subsequent increase in vaccine coverage.
Cloning and characterization of two immunophilin-like genes, ilpA and fkpA, on a single 3.9-kilobase fragment of Aeromonas hydrophila genomic DNA

Antiserum to Aeromonas hydrophila A6 cell envelopes was shown in a previous study (C. Y. F. Wong, G. Mayrhofer, M. W. Heuzenroeder, H. M. Atkinson, D. M. Quinn, and R. L. P. Flower, FEMS Immunol. Med. Microbiol. 15:233-241, 1996) to protect mice against lethal infection by this organism. In this study, colony blot analysis of an A. hydrophila genomic library using antiserum to A. hydrophila A6 cell envelopes revealed a cosmid clone expressing a 30-kDa protein which has not been described previously in aeromonads. The nucleotide sequence of a 3.9-kb fragment derived from this cosmid which expressed the 30-kDa protein revealed two potential open reading frames (ORFs) with homology to known immunophilin proteins. ORF1 encoded a 212-amino-acid protein (molecular mass, 22.4 kDa) with 56% identity to the immunophilin SlyD protein of Escherichia coli. ORF1 was subsequently designated ilpA (immunophilin-like protein). ORF3 encoded a potential gene product of 268 amino acids with a typical signal sequence and a predicted molecular size of 28.7 kDa. The inferred amino acid sequence showed 46% identity with the sequence of the FkpA protein of E. coli and 40% identity with the sequence of the macrophage infectivity potentiator (Mip) protein of Legionella pneumophila. ORF3 was designated fkpA (FK506 binding protein) by analogy with the E. coli FkpA protein. Expression of the FkpA protein was confirmed by Western blot (immunoblot) analysis, which detected a 30-kDa protein, with antiserum to the Mip protein of Legionella longbeachae and a specific antiserum to anA. hydrophila 30-kDa membrane protein. PCR and Southern analysis showed that a DNA sequence encoding FkpA was found in all 178 aeromonads of diverse origins tested. A nonpolar insertion mutation in the fkpA gene did not attenuate virulence in a suckling mouse model nor did it affect the expression of hemolysins or DNase. This suggests that either the fkpA gene is not essential in the virulence of A. hydrophila under these conditions or there are other genes in A. hydrophila coding for proteins with similar functions.
60-GHz dual-polarized two-dimensional switch-beam wideband antenna array of magneto-electric dipoles

Dual-polarized substrate-integrated aperture-coupled magneto-electric (ME) dipole antenna is proposed. By employing the radiating element and the substrate integrated waveguide (SIW) beam-forming networks, a 60-GHz 2 × 2 two-dimensional switch-beam antenna array, which can generate four tilted beams with dual polarizations, is designed, fabricated, and measured. Wide bandwidth and good radiation performance are obtained.
ROLE OF GLUTAMATE DEHYDROGENASE AND GLUTAMINE SYNTHETASE IN CHLORELLA VULGARIS DURING ASSIMILATION OF AMMONIUM WHEN JOINTLY IMMOBILIZED WITH THE MICROALGAE‐GROWTH‐PROMOTING BACTERIUM AZOSPIRILLUM BRASILENSE 1

Enzymatic activities of glutamate dehydrogenase (GDH) and glutamine synthetase (GS) participating in the nitrogen metabolism and related ammonium absorption were assayed after the microalga Chlorella vulgaris Beij. was jointly immobilized with the microalgae‐growth‐promoting bacterium Azospirillum brasilense. At initial concentrations of 3, 6, and 10 mg · L−1 NH4+, joint immobilization enhances growth of C. vulgaris but does not affect ammonium absorption capacity of the microalga. However, at 8 mg · L−1 NH4+, joint immobilization enhanced ammonium absorption by the microalga without affecting the growth of the microalgal population. Correlations between absorption of ammonium per cell and per culture showed direct (negative and positive) linear correlations between these parameters and microalga populations at 3, 6, and 10 mg · L−1 NH4+, but not at 8 mg · L−1 NH4+, where the highest absorption of ammonium occurred. In all cultures, immobilized and jointly immobilized, having the four initial ammonium concentrations, enzymatic activities of Chlorella are affected by A. brasilense. Regardless of the initial concentration of ammonium, GS activity in C. vulgaris was always higher when jointly immobilized and determined on a per‐cell basis. When jointly immobilized, only at an initial concentration of 8 mg · L−1 NH4+ was GDH activity per cell higher.