Miracle-dz/UniFAR-FTUs huggingface dataset:
Kaempferol inhibited VEGF and PGF expression and in vitro angiogenesis of HRECs under diabetic-like environment

Diabetic retinopathy (DR) is one of the common and specific microvascular complications of diabetes. This study aimed to investigate the anti-angiogenic effect of kaempferol and explore its underlying molecular mechanisms. The mRNA expression level of vascular endothelial growth factor (VEGF) and placenta growth factor (PGF) and the concentrations of secreted VEGF and PGF were measured by qTR-PCR and ELISA assay, respectively. Human retinal endothelial cells (HRECs) proliferation, migration, and sprouting were measured by CCK-8 and transwell, scratching wound, and tube formation assays, respectively. Protein levels were determined by western blot. High glucose (25 mM) increased the mRNA expression levels of VEGF and PGF as well as the concentrations of secreted VEGF and PGF in HRECs, which can be antagonized by kaempferol (25 µM). Kaempferol (5-25 µM) significantly suppressed cell proliferation, migration, migration distance and sprouting of HRECs under high glucose condition. The anti-angiogenic effect of kaempferol was mediated via downregulating the expression of PI3K and inhibiting the activation of Erk1/2, Src, and Akt1. This study indicates that kaempferol suppressed angiogenesis of HRECs via targeting VEGF and PGF to inhibit the activation of Src-Akt1-Erk1/2 signaling pathway. The results suggest that kaempferol may be a potential drug for better management of DR.
Dendritic Cells from Oral Cavity Induce Foxp3+ Regulatory T Cells upon Antigen Stimulation

Evidence is accumulating that dendritic cells (DCs) from the intestines have the capacity to induce Foxp3+CD4+ regulatory T cells (T-regs) and regulate immunity versus tolerance in the intestines. However, the contribution of DCs to controlling immunity versus tolerance in the oral cavity has not been addressed. Here, we report that DCs from the oral cavity induce Foxp3+ T-regs as well as DCs from intestine. We found that oral-cavity-draining cervical lymph nodes contained higher frequencies of Foxp3+ T-regs and ROR-γt+ CD4+T cells than other lymph nodes. The high frequency of Foxp3+ T-regs in the oral-cavity-draining cervical lymph nodes was not dependent on the Toll like receptor (TLR) adaptor molecules, Myd88 and TICAM-1 (TRIF). In contrast, the high frequency of ROR-γt+ CD4+T cells relies on Myd88 and TICAM-1. In vitro data showed that CD11c+ DCs from oral-cavity-draining cervical lymph nodes have the capacity to induce Foxp3+ T-regs in the presence of antigen. These data suggest that, as well as in the intestinal environment, antigen-presenting DCs may play a vital role in maintaining tolerance by inducing Foxp3+ T-regs in the oral cavity.
Discovery of the Corallivorous Polyclad Flatworm, Amakusaplana acroporae, on the Great Barrier Reef, Australia – the First Report from the Wild

The role of corallivory is becoming increasingly recognised as an important factor in coral health at a time when coral reefs around the world face a number of other stressors. The polyclad flatworm, Amakusaplana acroporae, is a voracious predator of Indo-Pacific acroporid corals in captivity, and its inadvertent introduction into aquaria has lead to the death of entire coral colonies. While this flatworm has been a pest to the coral aquaculture community for over a decade, it has only been found in aquaria and has never been described from the wild. Understanding its biology and ecology in its natural environment is crucial for identifying viable biological controls for more successful rearing of Acropora colonies in aquaria, and for our understanding of what biotic interactions are important to coral growth and fitness on reefs. Using morphological, histological and molecular techniques we determine that a polyclad found on Acropora valida from Lizard Island, Australia is A. acroporae. The presence of extracellular Symbiodinium in the gut and parenchyma and spirocysts in the gut indicates that it is a corallivore in the wild. The examination of a size-range of individuals shows maturation of the sexual apparatus and increases in the number of eyes with increased body length. Conservative estimates of abundance show that A. acroporae occurred on 7 of the 10 coral colonies collected, with an average of 2.6±0.65 (mean ±SE) animals per colony. This represents the first report of A. acroporae in the wild, and sets the stage for future studies of A. acroporae ecology and life history in its natural habitat.
Pathogenesis of non-familial colorectal carcinomas with high microsatellite instability

Aims—Microsatellite instability (MSI) was first observed in hereditary non-polyposis colorectal carcinoma (HNPCC) and was subsequently seen in non-familial colorectal carcinoma. The relation between MSI and cancer associated genes in non-familial colorectal carcinomas has yet to be evaluated. To clarify this matter, changes in cancer associated genes were examined in non-familial colorectal carcinomas. Methods—Alterations in the adenomatous polyposis coli (APC), p53, and Ki-ras genes were analysed in 24 MSI high (alterations in four to seven of seven loci), nine MSI low (alterations in one to three of seven loci), and 31 MSI negative non-familial carcinomas. The hMSH2 and hMLH1 genes were also analysed in 24 MSI high carcinomas. Results—Both the frequencies and types of alterations in the APC and p53 genes in MSI high carcinomas were the same as those in MSI low and MSI negative carcinomas; however, they were different from those seen in HNPCC. The frequency of Ki-ras mutation was significantly lower in the MSI high cases (two of 24; 8%) than in the others (15 of 38; 39%). Somatic mutation of hMSH2 or hMLH1 was detected in six of 24 (25%) of the MSI high cases. Conclusions—These results suggest that APC and p53 alterations occur irrespective of microsatellite instability status in non-familial colorectal carcinomas, and that Ki-ras mutation is not involved in MSI high non-familial colorectal carcinoma. The pathogenesis of these carcinomas may differ from both the usual adenoma–carcinoma sequence and HNPCC carcinogenesis.
A branch & cut algorithm for the windy general routing problem and special cases

In this paper, we present an exact algorithm for the Windy General Routing Problem. This problem generalizes many important Arc Routing Problems and also has some interesting real‐life applications. The Branch & Cut method presented here is based on a cutting‐plane algorithm that identifies violated inequalities of several classes of facet‐inducing inequalities for the corresponding polyhedron. The whole procedure has been tested over different sets of instances and is capable of solving to optimality large‐size instances of several routing problems defined on undirected, mixed, and windy graphs. © 2007 Wiley Periodicals, Inc. NETWORKS, Vol. 49(4), 245–257 2007
Wigner functions with boundaries

We consider the general Wigner function for a particle confined to a finite interval and subject to Dirichlet boundary conditions. We derive the boundary corrections to the “stargenvalue” equation and to the time evolution equation. These corrections can be cast in the form of a boundary potential contributing to the total Hamiltonian which together with a subsidiary boundary condition is responsible for the discretization of the energy levels. We show that a completely analogous formulation (in terms of boundary potentials) is also possible in standard operator quantum mechanics and that the Wigner and the operator formulations are also in one-to-one correspondence in the confined case. In particular, we extend Baker’s converse construction to bounded systems. Finally, we elaborate on the applications of the formalism to the subject of Wigner trajectories, namely in the context of collision processes and quantum systems displaying chaotic behavior in the classical limit.
Count Them In: A Quantitative Investigation into the Relationship and Differences Between Minority Youth Leadership Capacity and School Factors

This quantitative study investigated the leadership capacity of minority youth. The research used a sample population of 322 ninth and tenth grade urban school students, in a medium sized secondary school in the lower Hudson Valley of New York. The participants completed the Youth Leadership Questionnaire, an 18 item self-report instrument that measured leadership capacity in relation to Self-concept, Self-efficacy, and Emotional Intelligence. After totaling each of the composite scores of the Youth Leadership Questionnaire, Independent t-tests and a Spearman correlation were run to determine relationships and differences between minority youth leadership capacity (based on the YLQ) and gender, achievement, attendance, grade, extracurricular activities, and socioeconomic status. The study revealed that no relationship existed between the YLQ scores of ninth and tenth grade minority urban school students and school dependent variables, which were achievement, gender, extracurricular activities, attendance, grade, and socioeconomic status. Furthermore, the study revealed there were no differences between ninth and tenth grade minority urban school students YLQ scores as related to the variables of gender, achievement level, school attendance, grade level, participation in extracurricular activities, and socioeconomic status as measured by the three variables in the YLQ. The findings indicated that all youth have leadership capacity as determined by the Youth Leadership Questionnaire three domains: self-concept, emotional intelligence, and selfefficacy. The lowest score, scored on the YLQ in this study was 60 and the highest scored was 124. Degree Type Dissertation Degree Name Doctor of Education (EdD) Department Executive Leadership First Supervisor Ronald Valenti Second Supervisor Winsome Gregory Subject Categories Education This dissertation is available at Fisher Digital Publications: http://fisherpub.sjfc. edu/education_etd/146 Count Them In: A Quantitative Investigation into the Relationship and Differences Between Minority Youth Leadership Capacity and School Factors
Current View on Phytoplasma Genomes and Encoded Metabolism

Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘Candidatus Phytoplasma' genomes that include those of ‘Ca. P. asteris' strains OY-M and AY-WB, ‘Ca. P. australiense,' and ‘Ca. P. mali'. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca. P. mali' is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.
Na/K pump current in aggregates of cultured chick cardiac myocytes

Spontaneously beating aggregates of cultured embryonic chick cardiac myocytes, maintained at 37 degrees C, were voltage clamped using a single microelectrode switching clamp to measure the current generated by the Na/K pump (Ip). In resting, steady-state preparations an ouabain- sensitive current of 0.46 +/- 0.03 microA/cm2 (n = 22) was identified. This current was not affected by 1 mM Ba, which was used to reduce inward rectifier current (IK1) and linearize the current-voltage relationship. When K-free solution was used to block Ip, subsequent addition of Ko reactivated the Na/K pump, generating an outward reactivation current that was also ouabain sensitive. The reactivation current magnitude was a saturating function of Ko with a Hill coefficient of 1.7 and K0.5 of 1.9 mM in the presence of 144 mM Nao. The reactivation current was increased in magnitude when Nai was increased by lengthening the period of time that the preparation was exposed to K-free solution prior to reactivation. When Nai was raised by 3 microM monensin, steady-state Ip was increased more than threefold above the resting value to 1.74 +/- 0.09 microA/cm2 (n = 11). From these measurements and other published data we calculate that in a resting myocyte: (a) the steady-state Ip should hyperpolarize the membrane by 6.5 mV, (b) the turnover rate of the Na/K pump is 29 s-1, and (c) the Na influx is 14.3 pmol/cm2.s. We conclude that in cultured embryonic chick cardiac myocytes, the Na/K pump generates a measurable current which, under certain conditions, can be isolated from other membrane currents and has properties similar to those reported for adult cardiac cells.
MICHAC: Defect Prediction via Feature Selection Based on Maximal Information Coefficient with Hierarchical Agglomerative Clustering

Defect prediction aims to estimate software reliability via learning from historical defect data. A defect prediction method identifies whether a software module is defect-prone or not according to metrics that are mined from software projects. These metric values, also known as features, may involve irrelevance and redundancy, which will hurt the performance of defect prediction methods. Existing work employs feature selection to preprocess defect data to filter out useless features. In this paper, we propose a novel feature selection framework, MICHAC, short for defect prediction via Maximal Information Coefficient with Hierarchical Agglomerative Clustering. MICHAC consists of two major stages. First, MICHAC employs maximal information coefficient to rank candidate features to filter out irrelevant ones, second, MICHAC groups features with hierarchical agglomerative clustering and selects one feature from each resulted group to remove redundant features. We evaluate our proposed method on 11 widelystudied NASA projects and four open-source AEEEM projects using three different classifiers with four performance metrics (precision, recall, F-measure, and AUC). Comparison with five existing methods demonstrates that MICHAC is effective in selecting features in defect prediction.
Revenue optimization in the generalized second-price auction

We consider the optimization of revenue in advertising auctions based on the generalized second-price (GSP) paradigm, which has become a de facto standard. We examine several different GSP variants (including squashing and different types of reserve prices), and consider how to set their parameters optimally. One intriguing finding is that charging each advertiser the same per-click reserve price ("unweighted reserve prices") yields dramatically more revenue than the quality-weighted reserve prices that have become common practice. This result is robust, arising both from theoretical analysis and from two different kinds of computational experiments. We also identify a new GSP variant that is revenue optimal in restricted settings. Finally, we study how squashing and reserve prices interact, and how equilibrium selection affects the revenue of GSP when features such as reserves or squashing are applied.
APPROXIMATION BY LOG-CONCAVE DISTRIBUTIONS, WITH APPLICATIONS TO REGRESSION

We study the approximation of arbitrary distributions P on d-dimensional space by distributions with log-concave density. Approximation means minimizing a Kullback―Leibler-type functional. We show that such an approximation exists if and only if P has finite first moments and is not supported by some hyperplane. Furthermore we show that this approximation depends continuously on P with respect to Mallows distance D 1 (·, ·). This result implies consistency of the maximum likelihood estimator of a log-concave density under fairly general conditions. It also allows us to prove existence and consistency of estimators in regression models with a response Y = μ(X) + e, where X and e are independent, μ(·) belongs to a certain class of regression functions while e is a random error with log-concave density and mean zero.
Quality of Life in Bipolar Type I Disorder in a One-Year Followup

Objectives. The aims of this study were (i) to compare Quality of Life (QOL) of patients with bipolar disorder (BD) type I to those with schizophrenia during a one-year period after hospitalization and (ii) to assess the association of different domains of QOL with severity of clinical symptoms and level of functioning in bipolar patients group. Method. A hundred and two participants were consecutively recruited before discharge from an acute hospitalization. To measure QOL as the main outcome variable, the Farsi (Persian) version of the World Health Organization's QOL Instrument Short Version (WHOQOL BREF) was used. Affective symptoms, overall functioning, and severity of mental illness were assessed as well. The assessment procedure was repeated four, eight, and 12 months after discharge. Results. No significant differences were found between patients with BD and schizophrenia on four domains of WHOQOL BREF at the baseline and the four, eight, and 12 month assessments. Within the subjects with bipolar I disorder, the most stable finding was negative association of depression severity with WHOQOL-BREF on the all four domains during repeated assessments. Conclusion. The findings suggest that persistent depressive symptoms might be the primary determinant of impaired QOL in patients with bipolar I disorder.
How Children of LGBQ Parents Negotiate Courtesy Stigma over the Life Course

Drawing on in-depth interviews with 28 U.S. adults who have at least one lesbian, gay, bisexual, or queer (LGBQ) parent, we examine how this group negotiates the courtesy stigma of a parent’s sexual identity over the life course. Respondents reported less control over revealing courtesy stigma during childhood, when they were closely linked to their parents, but increased ability to conceal parents’ sexual orientation as they aged. During childhood and adolescence, parents’ gender presentation and choice of partner(s) impacted the visibility and degree of courtesy stigma, as did their peer networks and social environments. As adults, respondents continued to face issues of visibility; those who identified as heterosexual struggled to gain acceptance within LGBQ communities, while those who identified as LGBQ negotiated fears about how their own sexual orientation reflected upon their families of origin. Recognizing that people with one or more LGBQ parents face courtesy—rather than direct—stigma sheds light on past research, while providing a sociological framework with which to analyze future work on this population.
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood–brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness.
Digital force-feedback for protein unfolding experiments using atomic force microscopy

Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand–receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.
Characterization of Antisera Specific to NK1, NK2, and NK3 Neurokinin Receptors and their Utilization to Localize Receptors in the Rat Gastrointestinal Tract

Understanding the physiological role of tachykinins requires precise cellular and subcellular localization of their receptors. We raised antisera by immunizing rabbits with peptides corresponding to portions of the intracellular tails of the rat neurokinin 1, 2, and 3 receptors (NK1-R, NK2-R, NK3-R). Receptors were localized by immunofluorescence and confocal microscopy. NK1-R, NK2-R, and NK3-R were detected at the plasma membrane of transfected cells with minimal intracellular stores. Staining was abolished by preabsorption of the antisera with the peptides used for immunization. Nontransfected cells were unstained. Each antiserum only stained cells transfected with the appropriate receptor and did not stain cells transfected with the other receptors. Therefore, the antisera are specific and do not cross-react with other neurokinin receptors. We examined the distribution of the neurokinin receptors in the gastrointestinal tract of the rat. NK1-R was detected in myenteric and submucosal neurons and in interstitial cells of Cajal. NK2-R was localized to circular and longitudinal muscle cells and to nerve endings in the plexuses. NK3-R was detected in numerous myenteric and submucosal neurons. Some neurons expressed both NK1-R and NK3-R. Receptors were detected at the plasma membrane and in endosomes. Cells expressing the receptors were closely associated with tachykinin-containing nerve fibers. Thus, NK1-R and NK3-R mediate neurotransmission by tachykinins within enteric nerve plexuses, and NK1-R and NK2-R mediate the effects of tachykinins on interstitial and smooth muscle cells, respectively.