Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of psl, a Locus Encoding a Potential Exopolysaccharide That Is Essential for Pseudomonas aeruginosa PAO1 Biofilm Formation

ABSTRACT Bacteria inhabiting biofilms usually produce one or more polysaccharides that provide a hydrated scaffolding to stabilize and reinforce the structure of the biofilm, mediate cell-cell and cell-surface interactions, and provide protection from biocides and antimicrobial agents. Historically, alginate has been considered the major exopolysaccharide of the Pseudomonas aeruginosa biofilm matrix, with minimal regard to the different functions polysaccharides execute. Recent chemical and genetic studies have demonstrated that alginate is not involved in the initiation of biofilm formation in P. aeruginosa strains PAO1 and PA14. We hypothesized that there is at least one other polysaccharide gene cluster involved in biofilm development. Two separate clusters of genes with homology to exopolysaccharide biosynthetic functions were identified from the annotated PAO1 genome. Reverse genetics was employed to generate mutations in genes from these clusters. We discovered that one group of genes, designated psl, are important for biofilm initiation. A PAO1 strain with a disruption of the first two genes of the psl cluster (PA2231 and PA2232) was severely compromised in biofilm initiation, as confirmed by static microtiter and continuous culture flow cell and tubing biofilm assays. This impaired biofilm phenotype could be complemented with the wild-type psl sequences and was not due to defects in motility or lipopolysaccharide biosynthesis. These results implicate an as yet unknown exopolysaccharide as being required for the formation of the biofilm matrix. Understanding psl-encoded exopolysaccharide expression and protection in biofilms will provide insight into the pathogenesis of P. aeruginosa in cystic fibrosis and other infections involving biofilms.
Reconfigurable LC-reflectarray setup and characterisation

This paper presents the realisation and characterisation of an electronically reconfigurable reflectarray based on liquid crystals at 35 GHz, which is able to electronically steer the main beam continuously in between ±35°. To extract the characteristics of each single tunable unit cell directly on the reflectarray, a specific near field measurement setup is used to enable spatial resolution of the reflected magnitudes and phases.
Imaging Tumor Angiogenesis With Contrast Ultrasound and Microbubbles Targeted to &agr;v&bgr;3

Background Angiogenesis is a critical determinant of tumor growth and metastasis. We hypothesized that contrastenhanced ultrasound (CEU) with microbubbles targeted to &agr;v‐integrins expressed on the neovascular endothelium could be used to image angiogenesis. Methods and Results Malignant gliomas were produced in 14 athymic rats by intracerebral implantation of U87MG human glioma cells. On day 14 or day 28 after implantation, CEU was performed with microbubbles targeted to &agr;v&bgr;33 by surface conjugation of echistatin. CEU perfusion imaging with nontargeted microbubbles was used to derive tumor microvascular blood volume and blood velocity. Vascular &agr;v‐integrin expression was assessed by immunohistochemistry, and microbubble adhesion was characterized by confocal microscopy. Mean tumor size increased markedly from 14 to 28 days (2±1 versus 35±14 mm2, P<0.001). Tumor blood volume increased by ≈35% from day 14 to day 28, whereas microvascular blood velocity decreased, especially at the central portions of the tumors. On confocal microscopy, &agr;v&bgr;3‐targeted but not control microbubbles were retained preferentially within the tumor microcirculation. CEU signal from &agr;v&bgr;3‐targeted microbubbles in tumors increased significantly from 14 to 28 days (1.7±0.4 versus 3.3±1.0 relative units, P<0.05). CEU signal from &agr;v&bgr;3‐targeted microbubbles was greatest at the periphery of tumors, where &agr;v‐integrin expression was most prominent, and correlated well with tumor microvascular blood volume (r=0.86). Conclusions CEU with microbubbles targeted to &agr;v&bgr;3 can noninvasively detect early tumor angiogenesis. This technique, when coupled with changes in blood volume and velocity, may provide insights into the biology of tumor angiogenesis and be used for diagnostic applications. (Circulation. 2003;108:336‐341.)
Single primer pair for amplifying segments of distinct Shiga-like-toxin genes by polymerase chain reaction

By using a single synthetic oligonucleotide primer pair in the polymerase chain reaction, we amplified specific Shiga-like-toxin (SLT) gene segments from DNAs of 20 clinical Escherichia coli isolates, irrespective of whether they produce SLT-I, SLT-II, or heretofore uncategorized SLTs. These segments were not detectable in any of 20 nontoxigenic E. coli strains. The primers deduced from a conserved region among SLT genes are so-called degenerate-sequence primers; i.e., they contain intentionally introduced sequence ambiguities to overcome minor sequence variations within different SLT genes. In direct gel hybridization with genomic DNA, both primers recognized SLT-I and SLT-II DNA sequences. Amplified sequences of target DNA obtained by polymerase chain reaction were visualized after gel electrophoresis by ethidium bromide staining, and definitive identification of the amplification product as an SLT gene segment was achieved by hybridization to SLT-I- and SLT-II-specific 20-base oligonucleotide probes complementary to a portion of the amplified sequences but not to the primers. The detecting oligonucleotide probes shared only 30% base homology and were shown to recognize specifically SLT-I or SLT-II sequences within genomic DNA. Moreover, they were used to distinguish whether the amplified sequence originated from SLT-I or SLT-II genes. The PCR system with the primers described here is a powerful technique to amplify SLT sequences in E. coli strains that produce serologically distinct SLTs and will facilitate identification of these pathogens, particularly among a multitude of nonpathogenic E. coli strains.
Tetrakis(3-cyanopyridine-κN 1)bis(thiocyanato-κN)cobalt(II) 1,4-dioxane disolvate

In the crystal structure of the title compound, {[Co(NCS)2(C6H4N2)4]·2C4H8O2}, the CoII cations are octahedrally coordinated by two terminal N-bonded thiocyanate anions and four N-bonded 3-cyanopyridine ligands. The asymmetric unit consists of one CoII cation, which is located on a special position with site symmetry 2/m, one thiocyanate anion and one dioxane molecule, located on a crystallographic mirror plane, as well as one 3-cyanopyridine ligand in a general position. The crystal structure consists of discrete complexes of [Co(NCS)2(3-cyanopyridine)4], as well as two non-coordinating 1,4-dioxane solvent molecules which are disordered due to symmetry.
Immunochemical quantification of crossline as a fluorescent advanced glycation endproduct in erythrocyte membrane proteins from diabetic patients with or without retinopathy

Crossline is a novel advanced glycation endproduct (AGE) which has both a crosslink and fluorescence similar to AGE‐protein in vivo. To assess the association of AGEs to the development of diabetic retinopathy we developed a sensitive and specific enzyme‐linked immunosorbent assay (ELISA) for crossline in blood samples and investigated the association of the development of retinopathy and erythrocyte membrane protein (EMP)‐crossline concentrations in patients with Type 2 diabetes mellitus (Type 2 DM). Crossline formation in EMP exceeded that in haemoglobin and was detectable in normal EMP samples without pretreatment by this ELISA system. Mean (±SE) EMP crossline levels were elevated 1.6‐fold in diabetic patients without retinopathy (7.6 ± 0.5 pmol mg−1, p < 0.005), 2.2‐fold in diabetic patients with non‐proliferative retinopathy (10.5 ± 0.6 pmol mg−1, p < 0.001) and 2.6‐fold in diabetic patients with proliferative retinopathy (12.0 ± 0.6 pmol mg−1, p < 0.001) compared with healthy control subjects (4.7 ± 0.5 pmol mg−1). Type 2 DM patients with retinopathy had significantly higher EMP‐crossline levels than those without retinopathy (p < 0.005). Our data suggest that elevated EMP‐crossline concentrations are associated with the presence of retinopathy in patients with Type 2 DM and EMP‐crossline measured by our ELISA may provide a useful marker for assessing the role of glycation in the development of diabetic retinopathy. © 1998 John Wiley & Sons, Ltd.
Pathologic Potential of Variant Clones of the Oshima Strain of Far-Eastern Subtype Tick-Borne Encephalitis Virus

Tick-borne encephalitis virus (TBEV) is a zoonotic agent that causes acute central nervous system (CNS) disease in humans. We previously suggested that immune response in addition to CNS infection contribute to mouse mortality following TBEV infection. However, we did not examine the influence of virus variants in the previous study. Therefore, in this study, we investigated the biological and pathologic potentials of the variant clones in the TBEV Oshima strain. We isolated eight variant clones from the stock virus of the Oshima 5-10. These variants exhibited different plaque morphologies in BHK cells and pathogenic potentials in mice. Full sequences of viral genomes revealed that each of the variant clones except one had specific combinations of nucleotide and amino acid changes at certain positions different from the parent strain. We also showed that an amino acid substitution of Glu122→Gly in the E protein could have affected virus infection and replication in vivo, as well as the attenuated pathogenicity in mice. These data confirm the presence of virus variants or quasispecies from the parent strain. Further elucidation of the effect of each variant clone on immune responses such as the T-cell response is an important priority in the development of an effective vaccine and treatment strategies for tick-borne encephalitis.
Nuclear envelope expansion is crucial for proper chromosomal segregation during a closed mitosis

ABSTRACT Here, we screened a 10,371 library of diverse molecules using a drug-sensitive fission yeast strain to identify compounds which cause defects in chromosome segregation during mitosis. We identified a phosphorium-ylide-based compound Cutin-1 which inhibits nuclear envelope expansion and nuclear elongation during the closed mitosis of fission yeast, and showed that its target is the β-subunit of fatty acid synthase. A point mutation in the dehydratase domain of Fas1 conferred in vivo and in vitro resistance to Cutin-1. Time-lapse photomicrography showed that the bulk of the chromosomes were only transiently separated during mitosis, and nucleoli separation was defective. Subsequently sister chromatids re-associated leading to chromosomal mis-segregation. These segregation defects were reduced when the nuclear volume was increased and were increased when the nuclear volume was reduced. We propose that there needs to be sufficient nuclear volume to allow the nuclear elongation necessary during a closed mitosis to take place for proper chromosome segregation, and that inhibition of fatty acid synthase compromises nuclear elongation and leads to defects in chromosomal segregation. Summary: Identification of a new fatty acid synthase inhibitor for nuclear division by a chemical genetic screen revealed a link between nuclear envelope expansion and faithful chromosome segregation in a closed mitosis.
Health-related Quality of Life in People With Hereditary Multiple Exostoses

Background: Hereditary multiple exostoses (HME) is a rare genetic disorder, which can be associated with severe complications that may significantly affect the health-related quality of life (HRQL). Our primary objective was to describe the baseline HRQL in HME individuals at the British Columbia’s Children’s Hospital HME clinic and the Multiple Hereditary Exostoses Coalition compared with relevant Canadian and US population norms. This is the first study to explore the HRQL among adults and children with HME. Methods: Previously validated instruments Short Form-36 version 2, Short form-6D, and Child Health Questionnaire Parent Form 50 were used to assess the HRQL of individuals with HME. The scores from these instruments were compared with the relevant population norms. The British Columbia’s Children’s Hospital and Multiple Hereditary Exostoses coalition populations were also compared with each other. Results: The study sample consisted of 100 participants including 57 adults and 43 children. The mean age for Short Form 36 version 2 survey was 40.10±13.01 years and for Child Health Questionnaire Parent Form 50 was 9.93±3.48 years. Adult HME population had lower scores than both the US and Canadian general population in all domains except for emotional role limitations. Short Form -6D utility scores (0.65) indicates the quality of life for some individuals is near death and for others it is comparable or better than individuals with rheumatoid arthritis. Children with HME scored less than the US general population; particularly lower scores were seen in bodily pain (51.2 vs. 81.7) and emotional self-esteem (52.0 vs. 79.8). Conclusions: HME population has lower HRQL than the general population. These data provide a benchmark for individuals with HME. From such data, future research on HME disease progression and effectiveness of treatments/interventions can be tracked over time. Level of Evidence: Level II, This is a prognostic, prospective study with participants enrolled at different points in their disease.
SIGNAL SCAN 3.0: new database and program features

SIGNAL SCAN is a program that utilizes a transcription factor database to find potential transcription factor binding sites in DNA sequences. The program is now in its third version. The SIGNAL SCAN transcription factor database format has changed and the program output format has been improved. New features allow the user to update the SIGNAL SCAN database automatically, to retrieve original journal citations and to develop user signal databases. The program now uses an indexing algorithm, improving scanning speed by a factor of 3. SIGNAL SCAN is now network compatible and is available for IBM-compatible PC, Unix and VMS platforms.
Air-bearing sliders and plane-plane-concave tips for atomic force microscope cantilevers

This paper explores strategies for fabricating and maintaining a sharp atomic force microscope (AFM) tip suitable for AFM data storage applications. To this end, AFM cantilevers have been incorporated into micromachined sled carriers and air-bearing sliders. These supports act to limit the maximum loading force on the AFM tip and allow for improved vibration immunity for the AFM cantilever in comparison to macroscopic loading schemes. Readback from a patterned rotating disk has been demonstrated using these devices. Silicon-carbide AFM cantilevers with diamond tips have been fabricated in a process compatible with that of the sleds and sliders. Molded silicon-nitride tips defined by the intersection of three surfaces have also been fabricated for AFM cantilevers. The molds for plane-plane-concave tips are defined by two silicon {111} planes and a silicon-dioxide curved surface. By geometry, the three surfaces necessarily have a unique intersection point, which may improve the consistency in sharpness of these tips relative to conventional pyramidal tips.
Participation in dementia research: rates and correlates of capacity to give informed consent

Background: Many people participating in dementia research may lack capacity to give informed consent and the relationship between cognitive function and capacity remains unclear. Recent changes in the law reinforce the need for robust and reproducible methods of assessing capacity when recruiting people for research. Aims: To identify numbers of capacitous participants in a pragmatic randomised trial of dementia treatment; to assess characteristics associated with capacity; to describe a legally acceptable consent process for research. Methods: As part of a pragmatic randomised controlled trial of Ginkgo biloba for mild-moderate dementia, we used a consenting algorithm that met the requirements of existing case law and the exigencies of the new Mental Capacity Act. We decided who had capacity to give informed consent for participation in the trial using this algorithm and sought predictors of capacity. Results: Most participants (76%) with mild-moderate dementia in this trial were unable to give informed consent according to the legal criteria. When adjusted for confounding, the Mini Mental State examination did not predict the presence of capacity. Conclusion: Cognitive testing alone is insufficient to assess the presence of capacity. Researchers and clinicians need to be aware of the challenging processes regarding capacity assessment. We outline a procedure which we believe meets the ethical and legal requirements.
EVALUATION OF MAIZE HALF SIB FAMILIES FOR MATURITY AND GRAIN YIELD ATTRIBUTES

This study was undertaken at the Research Farm of KP Agricultural University, Peshawar during 2008 to evaluate half-sib maize families for maturity, yield and yield related traits. One hundred and forty four halfsib families derived from maize variety Pahari were used in the study. The experiment was laid out in 12X12 partial balance lattice design with two replications. Results indicated that the half-sib families were significantly different from one another for all the traits studied. Among the 144 families, maximum anthesissilking interval (3.5) was recorded for HS-74. On the other hand minimum anthesis silking interval (2) was recorded for HS-53. Maximum plant height (192.5cm) was observed for HS-67 while minimum (140 cm) was recorded for HS- 101. Minimum ear height (48 cm) was observed for HS-98 while maximum (97.5 cm) was recorded for HS-78. HS-2 exhibited the maximum ear length (18.5) whereas HS-77, HS-20 and HS-32 showed the minimum ear length (12 cm). Highest kernel rows ear -1 (16) was observed for HS-12 and HS-113 wherea s minimum (11) was recorded for HS-9, HS-72, HS-102 and HS-138. Maxim um 100 grains weight (33.6 g) was exhibited by HS-93 while minimum (20 g) was exhibited by HS-84. Highest (6987 kg) grain yield was recorded for HS-51 while minimum (2269 kg) was showed by HS-102. Maximum heritability estimate (0.88) was observed for days to mid silking, while minimum (0.46) was observed for kernel rows cob -1 . Maximum correlation of yield was recorded with plant height and ear length. These results suggest that these half-sib families could be used as source of improved maize germplasm for developing maize genotypes with superior attributes.
Physiopathologie de l’infarctus cérébral du sujet jeune : rôle de la résine de cannabis dans l’atteinte vasculaire et l’altération mitochondriale cérébrales

Nous avons montre : a) qu’il existe un lien entre la consommation de cannabis et la presence de stenoses arterielles intracrâniennes multifocales chez le jeune adulte victime d’infarctus cerebral, b) que la prevalence des stenoses arterielles intracrâniennes atteint un tiers des cas dans une cohorte de 159 infarctus cerebraux du jeune adulte, c) que 13% des infarctus cerebraux dans cette serie repondent aux criteres angiographiques du syndrome de vasoconstriction cerebrale reversible declenche majoritairement par la consommation de cannabis, d) que le tetrahydrocannabinol (THC, le principal produit actif du cannabis) inhibe in vitro la chaine respiratoire mitochondriale de cerveau de rat, et induit une generation significative de peroxyde d’hydrogene. La generation de radicaux libres pourrait etre un des mecanismes possibles de toxicite cerebrale du THC en jeu lors d’un infarctus cerebral.
Adaptive superpixel segmentation aggregating local contour and texture features

Superpixel segmentation targets at grouping pixels in an image into atomic regions that align well with the natural object boundaries. In this paper, we propose a novel superpixel segmentation method based on an iterative and adaptive clustering algorithm that embraces color, contour, texture, and spatial features together. The algorithm adjusts the weights of different features automatically in a content-aware way, so as to fit the requirements of various image instances. More specifically, in each iteration, the weights in the aggregation function are adjusted according to the discriminabilities of features in the current working scenario. This way, the algorithm not only possesses improved robustness but also relieves the burden of setting the parameters manually. Experimental verification shows that the algorithm outperforms existing peer algorithms in terms of commonly used evaluation metrics, while using a low computational cost.
[Nicotine dependence and psychiatric comorbidity among university students].

OBJECTIVE The relationship between psychiatric disorders and nicotine use has been studied in recent years. In this study, the comorbidity between psychiatric disorders and nicotine dependence (ND) and nicotine abstinence (NA) was evaluated in a randomly selected group of university students. METHOD We used the 12-month version of CIDI 2.1 (Composite International Diagnostic Interview) for the interviews of a total of 323 students (M/F: 168/155), who were randomly selected among and represented all students in Selçuk University. The mean age of students was 20.9 (SD: 5.4, range: 16-34). ND, NA and other psychiatric disorders were diagnosed according to DSM-IV criteria. RESULTS One-year prevalence of ND and NA was 17% (n=55) and 4% (n=13), respectively among the 323 students interviewed. The prevalence of any psychiatric disorders other than ND and NA was 26.3% (n=85). Students who had psychiatric disorders had a higher relative risk than those who did not have psychiatric disorders (30.6% versus 12.2%, odds ratio: 3.2, 95% CI 1.7-5.8; p<0.001). ND was also observed more commonly in students who were diagnosed with any of these disorders than in those free of these disorders: alcohol dependence or abuse (72.7% versus 15.1%), any mood disorder (36.0% versus 15.4%) and any anxiety disorder (29.3% versus 13.9%). CONCLUSION This study suggests that ND in young adults is associated with a higher rate of psychiatric disorders.
A Novel Frequency Reuse Scheme for OFDMA Based Relay Enhanced Cellular Networks

We address the problem of frequency reuse schemes in the downlink of the fixed two-hop orthogonal frequency division multiple access (OFDMA) cellular relaying networks. There has been little work on specific frequency reuse schemes for this system in the literatures, although this is the key element for realizing the potential capacity and coverage increase offered by the relay. Therefore, we propose a novel frequency reuse scheme for spectrum efficiency enhancement. Based on this scheme, inter-cell interference (ICI) and SINR received by one- hop and two-hop users are analyzed. System-level simulation results show that our presented frequency reuse scheme can achieve significant improvement on spectrum efficiency compared to modified soft frequency reuse (MSFR) scheme.