Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Healthcare Environment and Associations with Clinical Outcomes of People Living with HIV/AIDS

Abstract Despite three decades of dramatic treatment breakthroughs in antiretroviral regimens, clinical outcomes for people living with HIV vary greatly. The HIV treatment cascade models the stages of care that people living with HIV go through toward the goal of viral suppression and demonstrates that <30% of those living with HIV/AIDS in the United States have met this goal. Although some research has focused on the ways that patient characteristics and patient‐provider relationships contribute to clinical adherence and treatment success, few studies to date have examined the ways that contextual factors of care and the healthcare environment contribute to patient outcomes. Here, we present qualitative findings from a mixed‐methods study to describe contextual and healthcare environment factors in a Ryan White Part C clinic that are associated with patients' abilities to achieve viral suppression. We propose a modification of Andersen's Behavioral Model of Health Services Utilization, and its more recent adaptation developed by Ulett et al., to describe the ways that clinic, system, and provider factors merge to create a system of care in which more than 86% of the patient population is virally suppressed.
A Study on the Semantic Relatedness of Query and Document Terms in Information Retrieval

The use of lexical semantic knowledge in information retrieval has been a field of active study for a long time. Collaborative knowledge bases like Wikipedia and Wiktionary, which have been applied in computational methods only recently, offer new possibilities to enhance information retrieval. In order to find the most beneficial way to employ these resources, we analyze the lexical semantic relations that hold among query and document terms and compare how these relations are represented by a measure for semantic relatedness. We explore the potential of different indicators of document relevance that are based on semantic relatedness and compare the characteristics and performance of the knowledge bases Wikipedia, Wiktionary and WordNet.
Eosinophils Increase Neuron Branching in Human and Murine Skin and In Vitro

Cutaneous nerves are increased in atopic dermatitis, and itch is a prominent symptom. We studied the functional interactions between eosinophils and nerves in human and mouse skin and in culture. We demonstrated that human atopic dermatitis skin has eosinophil granule proteins present in the same region as increased nerves. Transgenic mice in which interleukin-5 (IL-5) expression is driven by a keratin-14 (K14) promoter had many eosinophils in the epidermis, and the number of nerves was also significantly increased in the epidermis. In co-cultures, eosinophils dramatically increased branching of sensory neurons isolated from the dorsal root ganglia (DRG) of mice. This effect did not occur in DRG neurons co-cultured with mast cells or with dead eosinophils. Physical contact of the eosinophils with the neurons was not required, and the effect was not blocked by an antibody to nerve growth factor. DRG neurons express eotaxin-1, ICAM-1 and VCAM-1, which may be important in the recruitment, binding, and activation of eosinophils in the region of cutaneous nerves. These data indicate a pathophysiological role for eosinophils in cutaneous nerve growth in atopic dermatitis, and suggest they may present a therapeutic target in atopic dermatitis and other eosinophilic skin conditions with neuronal symptoms such as itch.
Modulation of calcium channels in arterial smooth muscle cells by dihydropyridine enantiomers

The actions of the optical enantiomers of BAY K 8644 and Sandoz 202,791 were studied on barium inward currents recorded using the whole-cell configuration of the patch clamp technique from enzymatically isolated smooth muscle cells from the rabbit ear artery. The enantiomers were applied by bath perfusion or rapidly by a concentration jump technique, which enabled the study of drug action under equilibrium and nonequilibrium conditions. A larger effect of agonists was seen on peak inward current in 110 mM Ba when small rather than large depolarizations were applied. The midpoint voltage of the steady-state inactivation curve of IBa was -12.8 +/- 1.9 mV (n = 4) in the absence of drug, -16.4 +/- 2.5 mV (n = 4) in 1 microM (+)202,791, and -31.4 +/- 0.4 mV (n = 4) in 1 microM (-)202,791. The rate of onset of action of the agonist and antagonist enantiomers of BAY K 8644 and Sandoz 202,791 was studied by rapid application during 20-ms depolarizing steps from different holding potentials to +30 mV at 1 or 0.2 Hz. The drugs were applied as concentration jumps between two single pulses of a pulse train. The rates of onset of drug action on peak IBa during a 1-Hz pulse train were concentration dependent over the range of 100 nM-3 microM for both (+) and (-)202,791. The rate of onset of inhibition of peak current by antagonist enantiomers was not significantly influenced by the test pulse frequency. At a holding potential of -60 mV, the onset rate of the increase in peak IBa on application of 1 microM of agonist enantiomers (+)202,791 or (-)BAY K 8644 during a train of pulses occurred with mean time constants of 2.1 +/- 0.7 s (n = 7) and 2.3 +/- 0.2 s (n = 4), respectively. The onset of current increase on application of 1 microM (+)202,791 during a single voltage clamp step to 20 mV was faster, with a mean time constant of 380 +/- 80 ms (n = 3).
Carotenoid trade-off between parasitic resistance and sexual display: an experimental study in the blackbird (Turdus merula)

Many parasites depress the expression of the carotenoid-based colour displays of their hosts, and it has been hypothesized that animals face a trade-off in carotenoid allocation between immune functions and ‘degree of ornamentation’. While numerous correlative studies suggest that parasite infection decreases the intensity of carotenoid-based colour displays, the existence of this trade-off has never been demonstrated experimentally in a host–parasite model. In this study, we used the blackbird (Turdus merula) and Isospora (an intestinal parasite) to assess whether this trade-off does indeed exist. Blackbirds were supplemented with carotenoids while simultaneously being exposed to parasites. Supplemented males circulated more carotenoids in the blood and developed more brightly coloured bills than unsupplemented males. In addition, supplementation slowed down the replication rate of parasites. Supplementation with carotenoids enabled infected birds to maintain their bill coloration, whereas birds that were infected but not supplemented showed reduced bill coloration. At the same time, infection slowed carotenoid assimilation in the blood. Overall, we demonstrated that bill colour reflects a bird's health, and that only males with a carotenoid-rich diet are capable of coping with costs associated with parasitic infection. Carotenoids are thus traded off between host physiological response to parasites and secondary sexual traits. Further investigations are required to determine the physiological mechanisms that govern this trade-off.
Unbiased Recursive Partitioning: A Conditional Inference Framework

Recursive binary partitioning is a popular tool for regression analysis. Two fundamental problems of exhaustive search procedures usually applied to fit such models have been known for a long time: overfitting and a selection bias towards covariates with many possible splits or missing values. While pruning procedures are able to solve the overfitting problem, the variable selection bias still seriously affects the interpretability of tree-structured regression models. For some special cases unbiased procedures have been suggested, however lacking a common theoretical foundation. We propose a unified framework for recursive partitioning which embeds tree-structured regression models into a well defined theory of conditional inference procedures. Stopping criteria based on multiple test procedures are implemented and it is shown that the predictive performance of the resulting trees is as good as the performance of established exhaustive search procedures. It turns out that the partitions and therefore the models induced by both approaches are structurally different, confirming the need for an unbiased variable selection. Moreover, it is shown that the prediction accuracy of trees with early stopping is equivalent to the prediction accuracy of pruned trees with unbiased variable selection. The methodology presented here is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Data from studies on glaucoma classification, node positive breast cancer survival and mammography experience are re-analyzed.
Evaluating Inflation Targeting Using a Macroeconometric Model

Abstract This paper uses a structurally estimated macroeconometric model, denoted the MC model, to evaluate inflation targeting in the United States. Various interest rate rules are tried with differing weights on inflation and output, and various optimal control problems are solved using differing weights on inflation and output targets. Price-level targeting is also considered. The results show that 1) there are output costs to inflation targeting, especially for price shocks, 2) price-level targeting is dominated by inflation targeting, 3) the estimated interest rate rule of the Fed (in Table 4) is consistent with the Fed placing equal weights on inflation and unemployment in a loss function, 4) the estimated interest rate rule does a fairly good job at lowering variability, and 5) considerable economic variability is left after the Fed has done its best. Overall, the results suggest that the Fed should continue to behave as it has in the past.
On-line decision support for emergency trauma management.

The overall goal of the TraumAID project is to improve the delivery of quality trauma care during the initial definitive phase of patient management. To this end, we are applying artificial intelligence techniques such as rule-based reasoning, planning, and plan inference. The current system, TraumAID 2.0, consists of (1) an electronic version of the standard trauma flow sheet implemented in HyperCard, that allows information to be entered by a dedicated member of the trauma team called a "scribe nurse" during trauma resuscitation; (2) a rule-based reasoner able to draw diagnostic conclusions from patient findings and test results, and identify what management goals they imply; (3) a planner that takes the set of currently relevant goals and identifies what (partially-ordered) sequence of actions is most appropriate under the circumstances; and (4) two complementary modes ofinformation presentation a graphic display of TraumAID's recommended management plan that can be shown on a monitor positioned in the trauma bay, and a critiquing interface (TraumaTIQ) that uses the goals and plans computed by TraumAID 2.0 to interpret physician orders and comment on them when appropriate. Because both interfaces can present information at a time and place where it could make a difference to the quality and/or cost of patient care, both implement the ideal of realtime quality assurance. Papers describing TraumAID have previously appeared in the literature [1, 2, 3, 4, 5, 7]. TraumAID 2.0 has been validated retrospectively, and its management plans found significantly preferable to actual care [1]. The system is about to be field-tested in the Emergency Center at the Medical College of Pennsylvania (MCP). The system to be field-tested links our HyperCard interface asynchronously to the core system executing in Macintosh Common Lisp on a Quadra 700. The development version, implemented in Lucid Common Lisp within X-Windows on a SPARCserver 690MP, interacts with the developer through a simple Tk/Tcl interface. With respect to our proposed demonstration, we will use segments from videotapes of trauma resuscitations to convey the environment and activities of a trauma team in an Emergency Center, and demonstrate TraumAID's support for data entry during patient management, its capabilities for reasoning and multiple-goal plan formation, and both its graphic and critiquing approaches to real-time information delivery. Such videotapes have been used for educational purposes at the MCP Emergency Center for several years [6].
Multiple-antenna channel hardening and its implications for rate feedback and scheduling

Wireless data traffic is expected to grow over the next few years and the technologies that will provide data services are still being debated. One possibility is to use multiple antennas at base stations and terminals to get very high spectral efficiencies in rich scattering environments. Such multiple-input/multiple-output (MIMO) channels can then be used in conjunction with scheduling and rate-feedback algorithms to further increase channel throughput. This paper provides an analysis of the expected gains due to scheduling and bits needed for rate feedback. Our analysis requires an accurate approximation of the distribution of the MIMO channel mutual information. Because the exact distribution of the mutual information in a Rayleigh-fading environment is difficult to analyze, we prove a central limit theorem for MIMO channels with a large number of antennas. While the growth in average mutual information (capacity) of a MIMO channel with the number of antennas is well understood, it turns out that the variance of the mutual information can grow very slowly or even shrink as the number of antennas grows. We discuss implications of this "channel-hardening" result for data and voice services, scheduling, and rate feedback. We also briefly discuss the implications when shadow fading effects are included.
Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies

Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids.
ADVISOR: Personalized Video Soundtrack Recommendation by Late Fusion with Heuristic Rankings

Capturing videos anytime and anywhere, and then instantly sharing them online, has become a very popular activity. However, many outdoor user-generated videos (UGVs) lack a certain appeal because their soundtracks consist mostly of ambient background noise. Aimed at making UGVs more attractive, we introduce ADVISOR, a personalized video soundtrack recommendation system. We propose a fast and effective heuristic ranking approach based on heterogeneous late fusion by jointly considering three aspects: venue categories, visual scene, and user listening history. Specifically, we combine confidence scores, produced by SVMhmm models constructed from geographic, visual, and audio features, to obtain different types of video characteristics. Our contributions are threefold. First, we predict scene moods from a real-world video dataset that was collected from users' daily outdoor activities. Second, we perform heuristic rankings to fuse the predicted confidence scores of multiple models, and third we customize the video soundtrack recommendation functionality to make it compatible with mobile devices. A series of extensive experiments confirm that our approach performs well and recommends appealing soundtracks for UGVs to enhance the viewing experience.
Zoledronate and Molecular Iodine Cause Synergistic Cell Death in Triple Negative Breast Cancer through Endoplasmic Reticulum Stress

ABSTRACT Women consuming molecular iodine (I2) through seaweeds suffer the least from breast cancers. Zoledronate (Zol) is in clinical use for alleviation of bone pain in cancer patients. Triple negative breast cancers exhibit high mortality due to lack of neoadjuvant chemotherapy. I2 and Zol independently cause weak antiproliferative and apoptotic effect. So far, their combined effects have not been tested. We analyzed the effect of combination of I2 with Zol as a potent adjuvant therapeutic agent for triple negative breast cancer cells (MDA-MBA-231) and in the mice model of breast cancer. Cell viability, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, Western blotting, real-time PCR, flow cytometry, and other assays were performed for assessing cell death, calcium levels, and migration potential, respectively, in treated cells. The increased caspase 8, increased [Ca2+]c levels, and endoplasmic reticulum (ER) stress resulted in apoptosis. Real time and fluorescence-based analysis demonstrated that the combination treatment targets ER Ca2+ homeostasis chaperons leading to apoptosis. Combination therapy reduces metalloproteinases 2 and 9, inhibits invasion/migration of cells, and prevents growth of tumor in mice. I2 + Zol combination treatment induces synergistic increase in ER-mediated apoptosis, reduces invasion/migration potential of MDA-MB-231 cells, and exhibits antiproliferative property in vivo demonstrating its potential as combination therapy.
Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA

Chlamydia abortus, an obligate intracellular bacterium, is the most common infectious cause of abortion in small ruminants worldwide and has zoonotic potential. We applied multilocus sequence typing (MLST) together with multiple-locus variable-number tandem repeat analysis (MLVA) to genotype 94 ruminant C. abortus strains, field isolates and samples collected from 1950 to 2011 in diverse geographic locations, with the aim of delineating C. abortus lineages and clones. MLST revealed the previously identified sequence types (STs) ST19, ST25, ST29 and ST30, plus ST86, a recently-assigned type on the Chlamydiales MLST website and ST87, a novel type harbouring the hemN_21 allele, whereas MLVA recognized seven types (MT1 to MT7). Minimum-spanning-tree analysis suggested that all STs but one (ST30) belonged to a single clonal complex, possibly reflecting the short evolutionary timescale over which the predicted ancestor (ST19) has diversified into three single-locus variants (ST86, ST87 and ST29) and further, through ST86 diversification, into one double-locus variant (ST25). ST descendants have probably arisen through a point mutation evolution mode. Interestingly, MLVA showed that in the ST19 population there was a greater genetic diversity than in other STs, most of which exhibited the same MT over time and geographical distribution. However, the evolutionary pathways of C. abortus STs seem to be diverse across geographic distances with individual STs restricted to particular geographic locations. The ST30 singleton clone displaying geographic specificity and represented by the Greek strains LLG and POS was effectively distinguished from the clonal complex lineage, supporting the notion that possibly two separate host adaptations and hence independent bottlenecks of C. abortus have occurred through time. The combination of MLST and MLVA assays provides an additional level of C. abortus discrimination and may prove useful for the investigation and surveillance of emergent C. abortus clonal populations.
Semantify.it, a Platform for Creation, Publication and Distribution of Semantic Annotations

The application of semantic technologies to content on the web is, in many regards, important and urgent. Search engines, chatbots, intelligent personal assistants and other technologies increasingly rely on content published as semantic structured data. Yet, the process of creating this kind of data is still complicated and widely unknown. The this http URL platform implements an approach to solve three of the most challenging question regarding the publication of structured semantic data, namely: a) what vocabulary to use, b) how to create annotation files and c) how to publish or integrate annotations within a website without programming. This paper presents the idea and the development of the this http URL platform. It demonstrates that the creation process of semantically annotated data does not have to be hard, shows use cases and pilot users of the created software and presents where the development of this platform or alike projects lead to in the future.
Neuronal correlates of anticipation related to turn-taking in conversations

Speakers and listeners switch their roles with small or even no time lag during conversations. Such accurate timing requires the next speaker of a conversation to anticipate the moment when the current turn is going to end, because the production system is quite slow and the response must be underway before the other speaker has stopped speaking. How people are able to anticipate the end of a turn is topic of current research. In earlier work it was shown that anticipation of a turn-end relies more on the semantic and syntactic information of a turn than on the prosody (De Ruiter et al., 2006). However, it is yet unclear how lexico-syntactic information helps in predicting the moment when a turn ends. We hypothesize that people can predict the time of turn-ends by predicting the upcoming word forms that finish the turn. We have shown that turns which end-point can be more accurately predicted have also more predictable last words (Magyari, De Ruiter, 2008). Evidence for anticipatory processes that pre-activate words during sentence processing has been around for some time (DeLong et al., 2005), but turn-taking provides evidence that language comprehension should help also in estimating the duration of the upcoming linguistic information. Such forward-looking processing is crucial for response preparation.