Miracle-dz/UniFAR-FTUs huggingface dataset:
A functional polymorphism in the matrix metalloproteinase‐1 gene promoter is associated with susceptibility and aggressiveness of head and neck cancer

Matrix metalloproteinases (MMPs) play an important role in several steps of cancer development. A single guanine insertion polymorphism (2G) in the MMP1 promoter sequence at −1,607 creates an Ets binding site and thus results in enhancing transcriptional activity. This study aimed to evaluate the contribution of this 2G polymorphism on susceptibility and aggressiveness of HNSCC. A panel of HNSCC cell lines and peritumoral fibroblasts were examined for the MMP1 genotypes and expression levels. Genomic DNA was extracted from peripheral blood of 300 patients with newly diagnosed HNSCC and from 300 age‐ and gender‐matched cancer‐free controls. Genotyping was carried out using a PCR‐RFLP assay. The levels of MMP1 mRNA expression were evaluated by the quantitative RT‐PCR and a correlation with different genotype was determined. Odds ratio (OR) for cancer risk were calculated using multivariate logistic regression. In addition, a correlation between the 2G/2G genotype and clinicopathological parameters was examined. Eleven out of 18 HNSCC cell lines showed the 2G/2G genotype (61%) and only 1 cell line had the 1G/1G genotype (5.6%). Cell lines with the 2G/2G genotype expressed significantly higher mean MMP1 mRNA level than those with other genotypes. In clinical model, subjects carrying the homozygous 2G/2G genotype had a higher risk of head and neck cancer compared with subjects with other genotypes (adjusted OR: 2.28; 95% CI: 1.58–3.27), controlling for major confounders. A correlation between promoter polymorphisms and the levels of MMP1 expression in cancer tissues was found, and this 2G/2G genotype was correlated with the adverse clinicopathological parameters. Finally, the highest level of MMP1 enhancement was demonstrated in the coculture of tumor cells and peritumoral fibroblasts of 2G homozygotes. These findings suggest that the presence of 2G polymorphism at the MMP1 promoter is associated with the development and progression of HNSCC. © 2005 Wiley‐Liss, Inc.
Predicting survival of grass shrimp (Palaemonetes pugio) exposed to naphthalene, fluorene, and dibenzothiophene

The composition and persistence of dissolved polycyclic aromatic hydrocarbons (PAHs) released to the water column during oil spills are altered by weathering, tidal transport, and addition of dispersants. Conventional toxicity effect metrics, such as the median lethal concentration (LC50), are inaccurate predictors of mortality from all toxicant exposure duration/concentration combinations likely to occur during spills. In contrast, survival models can predict the proportions of animals dying as a consequence of exposures differing in duration and intensity. Extending previous work with ethylnaphthalene, dimethylnaphthalene, and phen‐anthrene, survival time models were developed that include exposure duration and concentration to predict time to death for grass shrimp (Palaemonetes pugio). Two additional PAHs (naphthalene and fluorene) and a heterocyclic aromatic hydrocarbon (dibenzothiophene) were evaluated for the present study. Preliminary explorations of these models confirmed that quantitative structure‐activity regression models were possible for predicting survival model parameters from compound characteristics. Conventional 48‐h LC50s also were calculated for the compounds and combined with published LC50s to predict relative PAH toxicity to P. pugio based on octanol‐water partitioning.
Hemichannels Are Required for Amyloid β-Peptide-Induced Degranulation and Are Activated in Brain Mast Cells of APPswe/PS1dE9 Mice

Mast cells (MCs) store an array of proinflammatory mediators in secretory granules that are rapidly released upon activation by diverse conditions including amyloid beta (Aβ) peptides. In the present work, we found a rapid degranulation of cultured MCs through a pannexin1 hemichannel (Panx1 HC)-dependent mechanism induced by Aβ25–35 peptide. Accordingly, Aβ25–35 peptide also increased membrane current and permeability, as well as intracellular Ca2+ signal, mainly via Panx1 HCs because all of these responses were drastically inhibited by Panx1 HC blockers and absent in the MCs of Panx1−/− mice. Moreover, in acute coronal brain slices of control mice, Aβ25–35 peptide promoted both connexin 43 (Cx43)- and Panx1 HC-dependent MC dye uptake and histamine release, responses that were only Cx43 HC dependent in Panx1−/− mice. Because MCs have been found close to amyloid plaques of patients with Alzheimer's disease (AD), their distribution in brain slices of APPswe/PS1dE9 mice, a murine model of AD, was also investigated. The number of MCs in hippocampal and cortical areas increased drastically even before amyloid plaque deposits became evident. Therefore, MCs might act as early sensors of amyloid peptide and recruit other cells to the neuroinflammatory response, thus playing a critical role in the onset and progression of AD.
The effectiveness of monetary policy in small Open-Economy: An SVAR study for Pakistan

This paper examines the effectiveness of monetary policy and its transmission channels in Pakistan. Unlike previous studies, this paper considers external variables, including world commodity prices and tradeweighted variables of output and interest rate. This study has employed the structural vector autoregressive (SVAR) model with block-exogeneity and non-recursive identification scheme in modeling monetary policy shocks in Pakistan. The results have revealed that the effectiveness of monetary policy in Pakistan is limited in stabilizing key domestic variables. The shutdown methodology in SVAR has been used to examine the strength of monetary policy transmission channels i.e. interest rate, credit, exchange rate and asset price channels. The interest rate channel of monetary policy is only effective in the short run while credit channel in both short run and long run. This finding assures the State Bank of Pakistan (SBP) to rely on interest rate channel to control inflation and utilize the credit channel to enhance the output in the long run. JEL Classification: C32, E52, E58, F41
Inherited susceptibility to acute pyelonephritis: a family study of urinary tract infection.

BACKGROUND Urinary tract infections (UTIs) are important causes of morbidity and death. The present study investigated whether genetic factors influence susceptibility to acute pyelonephritis (APN). CXCR1 expression was investigated as a factor predisposing to APN, because low CXCR1 expression has been associated with disease susceptibility in mice and disease-prone children. METHODS The families of APN-prone children (n=130) and of age-matched control subjects without UTI (n=101) were studied. Three-generation pedigrees of UTI-associated morbidity were established by means of structured interviews of the families. CXCR1 expression was quantified by flow cytometric analysis of peripheral blood neutrophils obtained from family members and control subjects. RESULTS APN was significantly more common in the family members of the APN-prone children (20 [15%] of 130 family members) than in the relatives of the control subjects (3 [3%] of 101 family members) (P<.002). Acute cystitis, in contrast, occurred with equal frequency in both groups (19%; P=1.0). Some families included many affected individuals, consistent with a dominant pattern of inheritance, whereas other families showed a recessive pattern of disease susceptibility. CXCR1 expression was significantly lower in the APN-prone children and in their relatives than in pediatric and adult control subjects (P<.0001). CONCLUSIONS Our results suggest that susceptibility to APN is inherited and that low CXCR1 expression might predispose to disease.
Longitudinal course and predictors of suicidal ideation in a rural community sample

Objective: Suicide rates in rural Australia are higher than in urban areas. No existing research has explored the long-term patterns and predictors of change in suicidal ideation within rural areas. This report uses longitudinal data and multiple time points to determine predictors of the trajectory of suicidal ideation in rural Australia. Method: Participants in the Australian Rural Mental Health Study (ARMHS) completed self-report surveys at baseline, 12 and 36 months, reporting their psychological and social well-being, and suicidal ideation. Generalised linear mixed models explored these factors as correlates and predictors of suicidal ideation across 3 years using multiple data points. Results: A total of 2135 participants completed at least one wave of ARMHS, and hence were included in the current analysis. Overall, 8.1% reported suicidal ideation during at least one study wave, 76% of whom reported suicidal ideation intermittently rather than consistently across waves. Across the three time points, suicidal ideation was significantly associated with higher psychological distress (OR 1.30, 95% CI 1.23 to 1.37), neuroticism (OR 1.15, 95% CI 1.04 to 1.27), and availability of support (OR 0.80, 95% CI 0.69 to 0.92), with a non-significant association with unemployment (OR 1.73, 95% CI 0.93 to 3.24) even after controlling for the effects of perceived financial hardship. Future suicidal ideation was significantly predicted by distress (OR 1.16, 95% CI 1.09 to 1.23) and neuroticism (OR 1.17, 95% CI 1.03 to 1.32), with a non-significant association with unemployment (OR 2.11, 95% CI 0.41 to 2.27). Predictive effects for marital status, social networks, sense of community and availability of support did not remain significant in the full multivariate analysis. Conclusions: Fluctuations in suicidal ideation are common, and may be associated with changes in psychological and social well-being. Public health strategies, focusing on encouraging help-seeking among those with higher psychological distress, lower social support, and unstable or absent employment opportunities, may be a useful long-term initiative to reduce the prevalence of suicidal ideation in the general rural community.
Fate of Escherichia coli O157:H7 in Manure-Amended Soil

ABSTRACT Escherichia coli O157:H7 cells survived for up to 77, >226, and 231 days in manure-amended autoclaved soil held at 5, 15, and 21°C, respectively. Pathogen populations declined more rapidly in manure-amended unautoclaved soil under the same conditions, likely due to antagonistic interactions with indigenous soil microorganisms. E. coli O157:H7 cells were inactivated more rapidly in both autoclaved and unautoclaved soils amended with manure at a ratio of 1 part manure to 10 parts soil at 15 and 21°C than in soil samples containing dilute amounts of manure. The manure-to-soil ratio, soil temperature, and indigenous microorganisms of the soil appear to be contributory factors to the pathogen's survival in manure-amended soil.
Cortical abnormalities in Alzheimer's disease

Regional cerebral glucose metabolism, an index of neuronal activity, was compared in 20 patients with Alzheimer's disease and 8 age‐matched normal volunteers by positron emission tomography following {18F}2‐fluoro‐2‐deoxy‐D‐glucose administration. Overall cortical glucose utilization in the Alzheimer's group was 10 to 49% below that of control individuals. The posterior parietal cortex and contiguous portions of posterior temporal and anterior occipital lobes were most severely affected; frontal cortex was relatively spared. This pattern of cortical involvement is consistent with the major clinical features of Alzheimer's disease. Comparison of patients with early and more advanced dementia suggested that a substantial decline in glucose metabolism occurs before cognitive impairment becomes evident; once the patient is symptomatic, however, small additional metabolic decrements are associated with a marked deterioration in intellectual function.
Online Professional Skills Workshops: Perspectives from Distance Education Graduate Students.

While many online graduate students are gaining academic and scholarly knowledge, the opportunities for students to develop and hone professional skills essential for the workplace are lacking. Given the virtual environment of distance learning, graduate students are often expected to glean professional skills such as analytical thinking, self-awareness, flexibility, team-building, and problem-solving inherently through informal means (Cleveland-Innes & Ally, 2012). The goal of this study was to evaluate the experiences of online graduate students participating in synchronous online professional skills workshops. Students attended the sessions from the various graduate programs at an online Canadian university. The discussions from the focus group held at the end of the project were used to achieve the research goals. This paper used a phenomenological lens to accomplish its research goals. The participants reported that they experienced a “sense of community” and learned skills that were not included in their academic programs.
Determination of the quality parameters of pike perch Sander lucioperca caught by gillnet, longline and harpoon in Turkey

The effects of the different catching methods (gillnet, longline, harpoon) on sensory, chemical (pH, total volatile base nitrogen, K-value) and microbiological (total viable count [TVC]) changes in pike perch Sander lucioperca stored in ice were investigated. The same soaking time was used for both gillnet and longline fishing. The catching method had considerable influence on the freshness quality of pike perch. The acceptable shelf life was 15 days for pike perch caught by gillnet, and 22 days for longline and harpoon. The initial concentrations of inosine monophosphate (2.4 μmol/g) in pike perch caught by gillnet were significantly lower (P<0.05) than longline (4.1 μmol/g). and especially by harpoon (16.7 μmol/g). However, the initial K-values for fish caught by harpoon were significantly (P<0.05) lower (24.36%) than fish caught by longline and gillnet (57.69%, 64.41%, respectively). The average K, Ki, G and H-values at rejection day in terms of sensory assessment were approximately 90, 98, 156 and 40%, respectively, for all catching methods during ice storage. However, TVC reached 7.0 log cfu/g after approximately 11 days of storage for fish caught by gillnet, 19 days for fish caught by longline and 8 days for fish caught by harpoon. The result of this study suggests that the best catching method for preserving the freshness of pike perch is longline, based on the data obtained from the sensory and microbiological analysis.
Structural and metabolic relationship between the molybdenum cofactor and urothione.

The molybdenum cofactor isolated from sulfite oxidase (sulfite: ferricytochrome c oxidoreductase, EC 1.8.2.1) and xanthine dehydrogenase (xanthine:NAD+ oxidoreductase, EC 1.2.1.37) in the presence of iodine and KI (form A) has been shown to contain a pterin nucleus with an unidentified substituent in the 6 position [Johnson, J. L. , Hainline, B. E. & Rajagopalan, K. V. (1980) J. Biol. Chem. 255, 1783-1786]. A second inactive form of the cofactor was isolated aerobically but in the absence of iodine and KI. The latter cofactor derivative (form B) is highly fluorescent, has a visible absorption band at 395 nm and, like form A, contains a phosphate group. Cleavage of the phosphate ester bond with alkaline phosphatase exposes a glycol function that is sensitive to periodate. Oxidation of form B with alkaline permanganate yields a highly polar compound with properties of a sulfonic acid, suggesting that the active molybdenum cofactor might contain sulfur. The sulfur-containing pterin urothione characterized by Goto et al. [Goto, M. , Sakurai, A. , Ohta, K. & Yamakami, H. (1969) J. Biochem. 65, 611-620] had been isolated from human urine. The permanganate oxidation product of urothione, characterized by Goto et al. as pterin-6-carboxylic-7-sulfonic acid, is identical to that obtained from form B. Because urothione also contains a periodate-sensitive glycol substituent, a structural relationship is suggested. The finding that urine samples from patients deficient in the molybdenum cofactor are devoid of urothione demonstrates a metabolic link between the two molecules.
Position Dependence of Coupling Efficiency of Grating Coupler in Waveguide Cavity

A grating coupler (GC) in a thin film waveguide is an integrated-optic component for coupling a guided wave to/from a free-space wave via the waveguide surface. A GC in a waveguide cavity resonator can provide high-efficiency vertical coupling with small aperture. The coupling efficiency was discussed with a dependence on a position of the GC in the cavity resonator by using an analytical model based on the coupled mode theory. The maximum efficiency can be obtained by centering the GC in the cavity. The efficiency can be eliminated by shifting the position of the GC from the center by a quarter of the grating period of the GC. GCs with and without the quarter-period shift were designed and fabricated in a Si-N waveguide on a SiO2 substrate for operating at 1.55 µm wavelength. The cavity resonator consisted of a pair of distributed Bragg reflectors and was integrated with the GC by the same process simultaneously. The output coupling and its elimination were demonstrated experimentally.
Evaluation of HF band NFC/RFID antennas for smart shelf applications

A mass number of tagged items are predicted to be in use in future applications of HF RFID/NFC systems. One such application, where items such as books or other items contained on a shelf or in a cupboard, can use RFID technology to ascertain the position and logging of such items in addition to identifying their existence on the shelf hence defined as a smart shelf. In the first instance, a new theoretical approach is presented to increase bandwidth of RFID reader antennas operating at HF band to improve the reception of the backscattered RFID response. A prototype antenna is designed and evaluated by measurement for its capability in being used for smart shelf applications. The more bandwidth will support subcarrier frequencies for the all the existing HF RFID standards (ISO/IEC 15693 and ISO/IEC14443) to be detected more easily and thus leads to increased range of identification. Also, it is shown that in the presence of books, the HF RFID technology is capable of identifying the distance of a tag antenna based on the received H-field, which could be used in a smart shelf management system.
An in vitro, short‐term culture method for mammalian haploid round spermatids amenable for molecular manipulation

Extensive chromatin remodeling is a characteristic feature of mammalian spermiogenesis. To date, methods for the molecular manipulation of haploid spermatids are not available as there is a lack of a well‐established culture system. Biochemical experiments and knockout studies reveal only the final outcome; studying the incremental details of the intricate mechanisms involved is still a challenge. We have established an in vitro culture system for pure haploid round spermatids isolated from rat testes that can be maintained with good viability for up to 72 hr. Changes in cell morphology and flagellar growth were also studied in the cultured spermatids. Further, we have demonstrated that upon treatment of cells with specific histone deacetylase inhibitors, sodium butyrate and trichostatin A, there is an increase in the hyperacetylation status of histone H4, mimicking an important event characteristic of histone replacement process that occurs during later stages of spermiogenesis. We have also tried various methods for introducing DNA and protein into these round spermatids in culture, and report that while DNA transfection is still a challenging task, protein transfection could be achieved using Chariot™ peptide as a transfection reagent. Thus, the method described here sets a stage to study the molecular roles of spermatid‐specific proteins and chromatin remodelers in the cellular context. Mol. Reprod. Dev. 79:19–30, 2012. © 2011 Wiley Periodicals, Inc.
Estimating Equations for Parameters in Stochastic Growth Models from Tag–Recapture Data

Summary. James (1991, Biometrics47, 1519–1530) constructed unbiased estimating functions for estimating the two parameters in the von Bertalanffy growth curve from tag‐recapture data. This paper provides unbiased estimating functions for a class of growth models that incorporate stochastic components and explanatory variables. A simulation study using seasonal growth models indicates that the proposed method works well while the least‐squares methods that are commonly used in the literature may produce substantially biased estimates. The proposed model and method are also applied to real data from tagged rock lobsters to assess the possible seasonal effect on growth.
Editing Fluid Sequences Using Space Warping Technique

In this paper, we introduce a novel algorithm for editing fluid sequences using space warping technique. This technique allows us obtain user-specified flow sequence based on original sequence. Our algorithm analyzes the motion of input fluid sequence, computes the geometry transformation between the flow lines of input sequence and the user-specified flow lines, and then synthesizes the edited sequences. By this way, we can solve the computational cost of simulating fluid sequences. And we can obtain different forms of fluid sequences by editing available continuous flow patterns. We use this technique to edit sequences of smoke sequences for experiment in this paper.
Impact of nose-only exposure system on pulmonary gene expression

Nose-only exposure is used to study the distribution and toxicity of airborne contaminants. Restraint of animals in nose-only tubes causes stress, but the impact on pulmonary mRNA levels is unknown. Since stress and xenobiotics activate common pathways, we assessed whether nose-only exposure would alter expression of toxicologically relevant genes in the lungs. To identify candidate genes for further analysis, we first interrogated microarray data to examine time-dependent changes in gene expression in air-control animals from a nose-only inhalation study involving male wild-type C57BL/6 mice and transgenic tumor necrosis factor (TNF)-α over-expressing littermates. Comparison of transcript levels immediately and 24 h after a single 4-h nose-only exposure to air revealed differential expression of 280 genes (false discovery rate-adjusted, p < .05). Functional analysis revealed enrichment of immune response, apoptosis, and signalling terms, consistent with effects of restraint stress. We then selected a subset of target genes for comparison of naive animals and air-exposed animals from the inhalation study by real-time polymerase chain reaction (PCR). Expression of genes involved in stress (BNIP, sestrin-1, CDKN1A [p21], GADD45γ), glucocorticoid-response (GILZ, Sgk), and signal transduction (MAP3K6, C/EBP-δ) was increased as a result of nose-only exposure (p < .05). In contrast, proinflammatory factors (lymphotoxin-β, chemokine receptor CXCR5) were decreased (p < .05). Immune gene responses observed in wild-type animals were reduced in animals with lung inflammation, indicating that pathological states can modify the response to nose-only exposure. Observed responses may warrant consideration in the evaluation of materials delivered by nose-only inhalation, and suggest that incorporation of naive animals into nose-only studies should be considered as a best practice.
Multiview image rectification algorithm for parallel camera arrays

Abstract. An algorithm for multiview images captured by a parallel multicamera array is presented. An ergodic method is proposed for tracing the ideal rotation matrix and the preferred locations of the optical centers. Moreover, the camera’s intrinsic parameters are optimized in order to obtain the ideal projection matrix from which the image rectifying transform matrix (IRTM) is further derived. Then, the multiview image is rectified based on the IRTM. Experimental results show that this proposed algorithm dramatically improves accuracy. Moreover, the robustness of this algorithm is superior to the robustness of the previous method.