Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistent Organic Pollutants and Inflammatory Markers in a Cross-Sectional Study of Elderly Swedish People: The PIVUS Cohort

Background: Persistent organic pollutants (POPs) are compounds that are generated through various industrial activities and released in the surrounding environment. Different animal studies have shown effects of different POPs on various inflammatory markers. Objective: Because very few studies have been conducted in humans, we assessed the associations between different POPs and inflammatory markers in a large population-based sample of elderly men and women (all 70 years of age) from Sweden. Methods: This cross-sectional study investigated the concentrations of several polychlorinated biphenyls (PCBs), organochlorine pesticides, polychlorinated dibenzo-p-dioxin, and brominated diphenyl ether congeners and their association with a number of inflammatory markers [vascular cell adhesion molecule 1 (VCAM-1), intercellular adhesion molecule 1 (ICAM-1), E-selectin, C-reactive protein (CRP), total leucocyte count, tumor necrosis factor α (TNF-α), monocyte chemotactic protein 1 (MCP-1), and interleukin 6 (IL-6)] in 992 individuals. These individuals were recruited from the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) cohort. We used a total toxic equivalency (TEQ) value that measures toxicological effects with the relative potencies of various POPs. Results: Following adjustment for potential confounders, the TEQ value (driven mainly by PCB-126) was significantly associated with levels of ICAM-1 (p < 10–5). A similar trend was also observed between sum of PCBs and VCAM-1 (p < 0.001). No significant associations were observed between levels of POPs and other inflammatory markers. Conclusions: TEQ values were associated with levels of ICAM-1, to a lesser degree also with VCAM-1, but not with CRP and several other inflammatory markers. These findings suggest an activation of vascular adhesion molecules by POPs, and particularly by PCB-126. Citation: Kumar J, Lind PM, Salihovic S, van Bavel B, Ingelsson E, Lind L. 2014. Persistent organic pollutants and inflammatory markers in a cross-sectional study of elderly Swedish people: The PIVUS cohort. Environ Health Perspect 122:977–983; http://dx.doi. org/10.1289/ehp.1307613
Democratization and the Rule of Law ∗

This paper provides a theory of the interactions between democratization and the emergence of rule of law. Heterogeneous individuals can make costly investments in protection against expropriation by others and the state. The public enforcement of property rights, whose cost depends on these investments, is chosen by the politically enfranchised population. We characterize the dynamic evolution of the economy in which both the political regime and property rights are endogenously determined. There are multiple politico-economic equilibria in terms of public and private property rights protection, which interact with different democratization scenarios whose determinants and consequences are studied. Democratic transitions under conflict may lead to failed democracies with worse property rights protection than oligarchies. Democratic transitions supported by a large consensus, however, serve as coordination device and lead to better protection of property and more stable polities. JEL-classification: H10, O10, N10
Semiclassical states, effective dynamics, and classical emergence in loop quantum cosmology

We construct physical semiclassical states annihilated by the Hamiltonian constraint operator in the framework of loop quantum cosmology as a method of systematically determining the regime and validity of the semiclassical limit of the quantum theory. Our results indicate that the evolution can be effectively described using continuous classical equations of motion with nonperturbative corrections down to near the Planck scale below which the Universe can only be described by the discrete quantum constraint. These results, for the first time, provide concrete evidence of the emergence of classicality in loop quantum cosmology and also clearly demarcate the domain of validity of different effective theories. We prove the validity of modified Friedmann dynamics incorporating discrete quantum geometry effects which can lead to various new phenomenological applications. Furthermore the understanding of semiclassical states allows for a framework for interpreting the quantum wave functions and understanding questions of a semiclassical nature within the quantum theory of loop quantum cosmology.
Estimation of Mean Annual Runoff Across Southeast Australia by Incorporating Vegetation Types into Budyko Framework

Abstract This paper uses the Budyko and Fu models to estimate mean annual runoff in 0.05° grid cells across southeast Australia, and assesses the estimates against observations in 323 catchments. The results show that the Budyko model can provide reasonable estimates of runoff and is suitable for data limited regions. In regions where there are some streamflow data available, the calibration of a single parameter in the Fu model gives better runoff estimates than the Budyko model and similar to regionalised rainfall-runoff models. In drier regions, the consideration of different vegetation types in the Fu model can improve the modelling results.
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions. Current evaluations indicate, however, that very different error models apply to the novel high-throughput sequencing methods. While the most frequent error-type in Illumina reads are mismatches, reads produced by 454's GS FLX predominantly contain insertions and deletions (indels). Even though 454 sequencers are able to produce longer reads, the method is frequently applied to small RNA (miRNA and siRNA) sequencing. Fast and accurate matching in particular of short reads with diverse errors is therefore a pressing practical problem. We introduce a matching model for short reads that can, besides mismatches, also cope with indels. It addresses different error models. For example, it can handle the problem of leading and trailing contaminations caused by primers and poly-A tails in transcriptomics or the length-dependent increase of error rates. In these contexts, it thus simplifies the tedious and error-prone trimming step. For efficient searches, our method utilizes index structures in the form of enhanced suffix arrays. In a comparison with current methods for short read mapping, the presented approach shows significantly increased performance not only for 454 reads, but also for Illumina reads. Our approach is implemented in the software segemehl available at http://www.bioinf. uni-leipzig.de/Software/segemehl/.
Ultra-Wideband Bandpass Filter With a Notch-Band Using Stub-Loaded Ring Resonator

A quadruple-mode ultra-wideband (UWB) bandpass filter with a notch-band and wide upper stopband is presented in this letter. The UWB filter is realized using a ring resonator which is loaded with two sets of stubs, i.e., one is loaded in the center and two little stubs at the symmetrical side locations. The loaded stubs are used to create transmission zeros in upper stopband thus high modes are suppressed greatly. Moreover, two identical via-loaded ring resonators are inserted within the stub-loaded ring resonator, to create a notch-band around 5-6 GHz to avoid WLAN signals. Two reflection poles appear in the notch-band, resulting in a switchable bandwidth of the notch-band. Finally, a UWB filter with a notch-band is simulated and fabricated, and measured results provide an experimental validation of predicted performance of the filter.
Effects of adenylate cyclase toxin from Bordetella pertussis on human neutrophil interactions with Coccidioides immitis and Staphylococcus aureus

Bordetella pertussis extract that contained adenylate cyclase toxin produced large increases in human neutrophil cyclic AMP levels and inhibited their oxidative burst, as reflected by luminol-enhanced chemiluminescence and superoxide release. The adenylate cyclase toxin-containing extract blocked neutrophil-mediated inhibition of N-acetylglucosamine incorporation by arthroconidia of Coccidioides immitis in a dose-dependent fashion but had no effect on neutrophil phagocytosis of Candida glabrata and only a slight inhibitory effect on arthroconidial attachment. Neither purified pertussis toxin nor extracts from Bordetella mutants lacking the adenylate cyclase toxin affected neutrophil-mediated inhibition of arthroconidial N-acetylglucosamine incorporation. These studies indicate that adenylate cyclase toxin, alone or in concert with other B. pertussis-elaborated toxins, blocks neutrophil inhibition of arthroconidia, primarily by affecting neutrophil responses other than attachment or phagocytosis.
Priming tissue-specific cellular immunity in a phase I trial of autologous dendritic cells for prostate cancer.

We attempted to induce therapeutic immunity against prostate-derived tissues in patients suffering from progressive hormone-refractory metastatic prostate carcinoma. Thirteen patients were treated with two infusions, 1 month apart, of autologous dendritic cells (APC8015) preexposed ex vivo to PA2024, a fusion protein consisting of human granulocyte/macrophage-colony stimulating factor (GM-CSF) and human prostatic acid phosphatase (PAP). The infusions were followed by three s.c. monthly doses of PA2024 without cells. Three groups of patients each received PA2024 at 0.3, 0.6, or 1.0 mg/injection. All Ps were two-sided. Treatment was well tolerated. After infusions of APC8015, patients experienced only mild (grade 1-2) short-lived fever and/or chills, myalgia, pain, and fatigue. One patient developed grade 3 fatigue. Four patients developed mild local reactions to s.c. PA2024. Twelve patients were evaluable for response to treatment. Circulating prostate-specific antigen levels dropped in three patients. T cells, drawn from patients after infusions of APC8015, but not before, could be stimulated in vitro by GM-CSF (P = 0.0004) and PAP (P = 0.0001), demonstrating broken immune tolerance against these two normal proteins. Injections of PA2024 did not influence the reactivity of T cells against PAP and GM-CSF. However, antibodies to GM-CSF and, to a much lesser extent, to PAP reached maximum titers only after two or even three injections of PA2024, showing that directly injected PA2024 was involved in stimulation of humoral immunity. Dendritic cells exposed to antigen ex vivo can induce antigen-specific cellular immunity in prostate cancer patients, warranting further studies of this mode of immunotherapy.
Microelectrophoresis of cholinergic and aminergic drugs on paraventricular neurons.

Moss, ROBERT L. , I. URBAN, AND B. A. CROSS. Microelectrophoresis OJ cholinergic and aminergic drugs on paraventricular neurons. Am. J. Physiol. 223(Z) : 3 10-3 18. 1972. -Acetylcholine, monoamines, amino acids, and antagonistic agents were applied microelectrophoretically to cells in the paraventricular (PV) nucleus of the rabbit hypothalamus. Successful drug applications and extracellular recordings were made on 37 1 cells of which 255 were identified as neurosecretory cells by antidromic stimulation of the neurohypophysis. The remaining 116 cells, though located in the paraventricular nucleus, were not antidromically invaded, and were considered to be nonneurosecretory. Acetylcholine excited 91 y0 of the neurosecretory PV cells. When tested with noradrenaline 8391, of these cells displayed a pronounced inhibition. Opposite effects were observed for the nonneurosecretory PV cells, i. e. , 767 o were inhibited by acetylcholine, and 81 7. excited by noradrenaline. In some cells, but not others, acetylcholine excitations were blocked by atropine or dihydro-p-erythroidine. Glutamate had a powerful excitant action, and in all PV cells tested y-aminobutyric acid was uniformly inhibitory. Dopamine and 5-HT had variable effects. The results are compatible with a functional role for both noradrenaline and acetylcholine in the synaptic regulation of cell activity in the PV nucleus of the hypothalamus.
RUTICO: Recommending Successful Learning Paths Under Time Constraints

Nowadays using E-learning platforms such as Intelligent Tutoring Systems (ITS) that support users to learn subjects are quite common. Despite the availability and the advantages of these systems, they ignore the learners' time limitation for learning a subject. In this paper we propose RUTICO, that recommends successful learning paths with respect to a learner's knowledge background and under a time constraint. RUTICO, which is an example of Long Term goal Recommender Systems (LTRS), after locating a learner in the course graph, it utilizes a Depth-first search (DFS) algorithm to find all possible paths for a learner given a time restriction. RUTICO also estimates learning time and score for the paths and finally, it recommends a path with the maximum score that satisfies the learner time restriction. In order to evaluate the ability of RUTICO in estimating time and score for paths, we used the Mean Absolute Error and Error. Our results show that we are able to generate a learning path that maximizes a learner's score under a time restriction.
Comparison of prognosis and specific features according to tumor size in small-sized breast cancer with extensive lymph node involvement.

81 Background: As known, larger tumor size and more extensive lymph node (LN) involvement have been considered an independent factor for poor prognosis of breast cancer. We evaluated if very small tumor size may be a factor of worse prognosis compared to larger tumor in small sized breast cancer with LN involvement. METHODS A retrospective analysis was made in a single center of all 1400 patients with small (below 2cm, T1) sized and LN involved (N1~N3) breast cancer without metastasis diagnosed between 2004 and 2014. Their ages ranged from 23 to 88 years (mean age 49.1 ± 9.9 years) and mean follow-up was 31 months. All patients were performed with surgery including axillary LN dissection without neo-adjuvant chemotherapy. We subdivided their tumor size to 4 group (T1m, T1a, T1b and T1c) grading by 7th AJCC cancer staging. The number of patients in each group is as follows: T1m = 17, T1a = 63, T1b = 214, T1c = 1106. The specific features related to mortality were analyzed according to the minor groups and they were compared with one another by Chi-square test and Kaplan-Meier analysis. RESULTS Total expired patients were 39 (2.8%) and the number (the rate in each group) of the minor groups is as follows: T1m = 1 (5.9%), T1a = 1 (1.6%), T1b = 7 (3.3%), T1c = 22 (2.0%). Overall survival of smaller sized tumor groups ( ≤ 1cm, T1m+T1a+T1b) are significantly decreased than the other larger sized group T1c in T1N1 staged patients (p = 0.004). There are significant differences in estrogen receptor, progesterone receptor, nuclear grade, recurrence among the 4 minor groups in whole patients group. In the analysis of nuclear grade, the results show higher grade in T1m than T1a, T1m than T1b, T1b than T1c. Especially, recurrence of T1m is significantly more frequent than T1a (17.6% vs 3.2%, P = 0.03) or T1b (17.6% vs 4.2%, p = 0.016). CONCLUSIONS In conclusion, this study indicates smaller sized tumor with LN involvement can progress worse compared to larger tumor. This result supports very small size can be another predictive factor for prognosis in small sized breast cancer with LN involvement.
Two calcium currents in Neanthes arenaceodentatus egg cell membranes.

Two distinct types of Ca currents, Ca(I) and Ca(II), were found in the eggs of the marine polychaete Neanthes arenaceodentatus and studied under voltage‐clamp conditions. Ca(I) and Ca(II) channels differ in their selectivity sequences, show different sensitivities to blocking by Cd, and have different activation thresholds. These facts indicate that the channels responsible for Ca(I) and Ca(II) currents are unique and different. Both Ca(I) and Ca(II) currents decrease with time under a maintained depolarization. This relaxation exhibits different kinetics, with those for Ca(II) being an order of magnitude slower than for Ca(I). The Ca(I) current relaxation has been shown previously to be due to a voltage‐dependent inactivation. The magnitude of relaxation of the Ca(II) current elicited by a test‐voltage step immediately following a conditioning‐voltage step paralleled the magnitude of the peak of the Ca(II) current flowing during the conditioning pulse. The kinetics of the current relaxation depended upon bath Ca concentration, the kinetics slowing down as the bath Ca was increased. These observations are consistent with an external depletion being the cause of the current relaxation for the Ca(II) channel.
A Corticosteroid-Responsive Transcription Factor, Promyelocytic Leukemia Zinc Finger Protein, Mediates Protection of the Cochlea from Acoustic Trauma

Animals can be induced to resist cochlear damage associated with acoustic trauma by exposure to a variety of “conditioning” stimuli, including restraint stress, moderate level sound, heat stress, hypoxia, and corticosteroids. Here we identify in mice a corticosteroid-responsive transcription factor, PLZF (promyelocytic leukemia zinc finger protein), which mediates conditioned protection of the cochlea from acoustic trauma. PLZF mRNA levels in the cochlea are increased following conditioning stimuli, including restraint stress, dexamethasone administration, and moderate-to-high level acoustic stimulation. Heterozygous mutant (luxoid.Zbtb16LU/J) mice deficient in PLZF have hearing and responses to acoustic trauma similar to their wild type littermates but are unable to generate conditioning-induced protection from acoustic trauma. PLZF immunoreactivity is present in the spiral ganglion, lateral wall of the cochlea, and organ of Corti, all targets for acoustic trauma. PLZF is also present in the brain and PLZF mRNA in brain is elevated following conditioning stimuli. The identification of a transcription factor that mediates conditioned protection from trauma provides a tool for understanding the protective action of corticosteroids, which are widely used in treating acute hearing loss, and has relevance to understanding the role of corticosteroids in trauma protection.
An evaluation of the latest in vitro tools for drug metabolism studies

Introduction: Drugs are indispensable for human welfare nevertheless there is a lack of safe drugs. Obtaining pharmacokinetics information, especially metabolism, is a requirement during preclinical and clinical drug development so that in vitro tools represent a simple path where it is possible to assess drug toxicity and predict drug safety in humans. Areas covered: This review covers the latest in vitro tools developed for assessing drug toxicity in different organs. A special focus is given to hepatic models, as it is the main organ responsible for drug metabolism and consequently bioactivation and detoxification reactions. Three-dimensional culture models have been widely developed, resembling in vivo-like conditions, and are also discussed in this review. Expert opinion: Several in vitro tools to assess hepatic drug metabolism have been developed, however, novel in vitro methods to investigate extra-hepatic drug metabolism still need to be improved. These methods are able to reduce the number of animal used in preclinical experiments, but in vivo tests are mandatory for drug approval and commercialization.
On the Number of Linear Regions of Deep Neural Networks

We study the complexity of functions computable by deep feedforward neural networks with piecewise linear activations in terms of the symmetries and the number of linear regions that they have. Deep networks are able to sequentially map portions of each layer's input-space to the same output. In this way, deep models compute functions that react equally to complicated patterns of different inputs. The compositional structure of these functions enables them to re-use pieces of computation exponentially often in terms of the network's depth. This paper investigates the complexity of such compositional maps and contributes new theoretical results regarding the advantage of depth for neural networks with piecewise linear activation functions. In particular, our analysis is not specific to a single family of models, and as an example, we employ it for rectifier and maxout networks. We improve complexity bounds from pre-existing work and investigate the behavior of units in higher layers.
The functions of social support as protective factors for suicidal ideation in a sample of air force personnel.

This study examined various functions of social support (i.e., tangible, esteem, belonging, and appraisal) were examined as protective factors for suicidal ideation in a sample of 273 active duty Air Force Security Forces personnel. Generalized linear regression analyses were conducted to determine if various social support functions were differentially associated with the presence and severity of suicidal ideation, both as main effects and as moderators of emotional distress. None of the four social support functions differentiated suicidal from nonsuicidal Airmen, but esteem support (i.e., feeling respected, encouraged, and valued by others) was associated with significantly less severe suicidal ideation (B = -.074, SE = .025, p = .003). A significant interaction of tangible support (i.e., access to material resources) with emotional distress indicated that emotional distress was associated with more severe suicidal ideation only among Airmen reporting low levels of tangible support (B = .006, SE = .003, p = .018). When considered concurrently, both tangible and self-esteem functions of social support are differentially associated with decreased suicidal ideation among Airmen, but belonging (i.e., having someone to do things with) and appraisal (i.e., having someone to talk to about problems) functions were not. Findings suggest that different aspects of social support affect suicidal ideation in different ways.
A static model for predicting disrupted network behavior

This paper compares actual and perceived travel times and presents a model for predicting traffic flows when there is a network disruption. The goal of this research is to demonstrate the necessity of accounting for possible differences in travel time perception and actual travel times, and also to show trends in how the route choices change based on the transformation of the perceived travel times. The model is separated into three phases: equilibrium assignment, link travel time transform, and logit assignment. The transform of the link travel times is best represented by an inverse cumulative Normal distribution, and the corresponding values provide quantifiable measure of the severity of a traffic network disruption. This methodology is then tested on a network to evaluate the resulting route choice patterns.