Miracle-dz/UniFAR-FTUs huggingface dataset:
Is there an energetic-based trade-off between thermoregulation and the acute phase response in zebra finches?

SUMMARY There has been recent interest in understanding trade-offs between immune function and other fitness-related traits. At proximate levels, such trade-offs are presumed to result from the differential allocation of limited energy resources. Whether the costs of immunity are sufficient to necessitate such energy reallocation remains unclear. We tested the metabolic and behavioural response of male zebra finches (Taeniopygia guttata) to the combined effects of thermoregulation and generation of an acute phase response (APR). The APR is the first line of defence against pathogens, and is considered energetically costly. We predicted that at cold temperatures zebra finches would exhibit an attenuated APR when compared with individuals at thermoneutrality. We challenged individuals with bacterial lipopolysaccharide (LPS), an immunogenic compound that stimulates an APR. Following LPS injection, we measured changes in food intake, body mass, activity, and resting and total energy expenditure. When challenged with LPS under ad libitum food, individuals at both temperatures decreased food intake and activity, resulting in similar mass loss. In contrast to predicted energetic trade-offs, cold-exposed individuals injected with LPS increased their nocturnal resting energy expenditure more than did individuals held at thermoneutrality, yet paradoxically lost less mass overnight. Although responding to LPS was energetically costly, resulting in a 10% increase in resting expenditure and 16% increase in total expenditure, there were few obvious energetic trade-offs. Our data support recent suggestions that the energetic cost of an immune response may not be the primary mechanism driving trade-offs between immune system function and other fitness-related traits.
Regression to the mean in multiple sclerosis

In order to ensure sufficient disease activity, patients with relapsing remitting (RR) multiple sclerosis (MS) are often included in randomized placebo-controlled trials, only if they have a high baseline activity. These patients, whose evolution is unusual in the pre-study period, will tend to show a more usual behavior when followed up over a period of time. This phenomenon is known as regression to the mean. Regression to the mean should be taken into account in correctly interpreting long-term studies of cohorts treated without a placebo control group, which use the baseline period as control. The aim of this study was to evaluate the relevance of this phenomenon in a non-treated cohort of RRMS patients, selected with similar criteria to those used in randomized placebo-controlled clinical trials. Forty-four patients with definite RRMS, with two or more relapses in the previous two years, and a baseline EDSS ≤ 5.5 were prospectively followed. The mean number of relapses spontaneously decreased from 1.72 (SD: 1.4) in the year prior to enrolment, to 1.0 (SD: 1.3) during the first year of follow-up (PB < 0.05). Regression to the mean may explain as much as 40% of the reduction in the relapse rate from the baseline period to the period on-study.
HiCS: High Contrast Subspaces for Density-Based Outlier Ranking

Outlier mining is a major task in data analysis. Outliers are objects that highly deviate from regular objects in their local neighborhood. Density-based outlier ranking methods score each object based on its degree of deviation. In many applications, these ranking methods degenerate to random listings due to low contrast between outliers and regular objects. Outliers do not show up in the scattered full space, they are hidden in multiple high contrast subspace projections of the data. Measuring the contrast of such subspaces for outlier rankings is an open research challenge. In this work, we propose a novel subspace search method that selects high contrast subspaces for density-based outlier ranking. It is designed as pre-processing step to outlier ranking algorithms. It searches for high contrast subspaces with a significant amount of conditional dependence among the subspace dimensions. With our approach, we propose a first measure for the contrast of subspaces. Thus, we enhance the quality of traditional outlier rankings by computing outlier scores in high contrast projections only. The evaluation on real and synthetic data shows that our approach outperforms traditional dimensionality reduction techniques, naive random projections as well as state-of-the-art subspace search techniques and provides enhanced quality for outlier ranking.
Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients

Objectives The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens. Design Site specific subgingival plaque samples (n = 54), pooled subgingival plaque samples (n = 18) and stimulated saliva samples (n = 18) were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing) and microbial community profiles were compared using Spearman rank correlation coefficient. Results Pronounced intraindividual differences were recorded in site-specific microbial profiles, and site-specific information was in general not reflected by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94), compared to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94) in pooled subgingival samples. Conclusions Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate for pooled subgingival samples when screening for presence of periopathogens. Future large-scale studies are needed to confirm findings from this study.
Robust Pseudo Random Fields for Light-Field Stereo Matching

Markov Random Fields are widely used to model lightfield stereo matching problems. However, most previous approaches used fixed parameters and did not adapt to lightfield statistics. Instead, they explored explicit vision cues to provide local adaptability and thus enhanced depth quality. But such additional assumptions could end up confining their applicability, e.g. algorithms designed for dense light fields are not suitable for sparse ones. ,,In this paper, we develop an empirical Bayesian framework—Robust Pseudo Random Field—to explore intrinsic statistical cues for broad applicability. Based on pseudo-likelihood, it applies soft expectation-maximization (EM) for good model fitting and hard EM for robust depth estimation. We introduce novel pixel difference models to enable such adaptability and robustness simultaneously. We also devise an algorithm to employ this framework on dense, sparse, and even denoised light fields. Experimental results show that it estimates scene-dependent parameters robustly and converges quickly. In terms of depth accuracy and computation speed, it also outperforms state-of-the-art algorithms constantly.
Increased expression of multifunctional serine protease, HTRA1, in retinal pigment epithelium induces polypoidal choroidal vasculopathy in mice

Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in the elderly. Wet AMD includes typical choroidal neovascularization (CNV) and polypoidal choroidal vasculopathy (PCV). The etiology and pathogenesis of CNV and PCV are not well understood. Genome-wide association studies have linked a multifunctional serine protease, HTRA1, to AMD. However, the precise role of HTRA1 in AMD remains elusive. By transgenically expressing human HTRA1 in mouse retinal pigment epithelium, we showed that increased HTRA1 induced cardinal features of PCV, including branching networks of choroidal vessels, polypoidal lesions, severe degeneration of the elastic laminae, and tunica media of choroidal vessels. In addition, HTRA1 mice displayed retinal pigment epithelium atrophy and photoreceptor degeneration. Senescent HTRA1 mice developed occult CNV, which likely resulted from the degradation of the elastic lamina of Bruch's membrane and up-regulation of VEGF. Our results indicate that increased HTRA1 is sufficient to cause PCV and is a significant risk factor for CNV.
International Journal of Behavioral Nutrition and Physical Activity Seasonal Variation in Objectively Assessed Physical Activity among Children and Adolescents in Norway: a Cross-sectional Study

Background: The literature on seasonality in children and youth's physical activity participation is inconsistent. The aims of this study were to: 1) compare physical activity across seasons and describe activity patterns within seasons, and 2) to determine compliance with current physical activity recommendations across seasons among 9-and 15-year-olds living in a climatically diverse country.
Plasma Estrogen Levels Are Associated With Severity of Injury and Outcomes After Aneurysmal Subarachnoid Hemorrhage

Background: Biochemical mediators alter cerebral perfusion and have been implicated in delayed cerebral ischemia (DCI) and poor outcomes after aneurysmal subarachnoid hemorrhage (aSAH). Estrogens (estrone [E1] and estradiol [E2]) are mediators with neuroprotective properties that could play a role in DCI. This study explored associations between plasma estrogen levels and outcomes following aSAH. Methods: Plasma samples from 1–4, 4–6, and 7–10 days after hemorrhage from 99 adult aSAH patients were analyzed for estrogen levels using liquid chromatography tandem mass spectrometry. DCI was operationalized as radiographic/ultrasonic evidence of impaired cerebral blood flow accompanied by neurological deterioration. Outcomes were assessed using the Modified Rankin Scale at 3 and 12 months after hemorrhage. Statistical analysis included correlation, regression, and group-based trajectory. Results: Higher E1 and E2 levels were associated with higher Hunt and Hess grade (E1, p = .01; E2, p = .03), the presence of DCI (E1, p = .02; E2, p = .02), and poor 3-month outcomes (E1, p = .002; E2, p = .002). Trajectory analysis identified distinct populations over time for E1 (61% E1 high) and E2 (68% E2 high). Patients in higher trajectory groups had higher Fisher grades (E1, p = .008; E2, p = .01), more frequent DCI (E1, p = .04; E2, p = .08), and worse 3-month outcomes (E1, p = .01; E2, p = .004) than low groups. Conclusions: These results provide the first clinical evidence that plasma E1 and E2 concentrations are associated with severity of injury and outcomes after aSAH.
RHEOLOGY OF HUMAN BLOOD. STUDIES ON THE FLOW OF FRESH VENOUS BLOOD AND OF CITRATED BLOOD THROUGH TUBING OF DIAMETERS BETWEEN 0.09 AND 0.20 CM.

Numerous studies have demonstrated that the rheological properties of blood are anomalous, in particular, that rate of flow through cylindrical tubing is not related linearly to the imposed gradient in pressure and that the viscosity of blood increases at low rates of flow (1-10). These data, and similar data obtained by means of other viscometric methods (11-13), are characteristic of non-Newtonian flow (14) and necessitate that any study of the rheological properties of blood must examine the dependence of viscosity upon applied shearing stress.
Human-competitive tagging using automatic keyphrase extraction

This paper connects two research areas: automatic tagging on the web and statistical keyphrase extraction. First, we analyze the quality of tags in a collaboratively created folksonomy using traditional evaluation techniques. Next, we demonstrate how documents can be tagged automatically with a state-of-the-art keyphrase extraction algorithm, and further improve performance in this new domain using a new algorithm, "Maui", that utilizes semantic information extracted from Wikipedia. Maui outperforms existing approaches and extracts tags that are competitive with those assigned by the best performing human taggers.
Preparing for what the reporting checklists will not tell you: the PREPARE Trial guide for planning clinical research to avoid research waste

For the early career researcher or PhD student about to have a leading role in a clinical trial, it would be a tremendous help to have a ‘How to’ guide, consisting of advice and key literature to help the researcher move successfully along the initial trial pathway from research question to protocol completion. While the ideal trial team should include experienced trialists, who participate in the preparatory research meetings, this support is not always available. The PREPARE Trial guide is intended to assist the early career researcher in this situation, but not replace an experienced trial team and regular research meetings. The guide may also serve as preparation for research meetings, or part of curricula for courses on research methodology, to be used by experienced PhD supervisor, trialist or lecturer. Evidence from randomised controlled trials (RCTs) is often wasted1 2 (for a collection of papers relating to this issue, please see http://researchwaste.net/). Many trials are not published, and hence the results are not reported, which is indeed a waste. There are many reasons for this waste, but we believe that at least some trials are discontinued because of poor trial planning. Similarly, many completed and published trials suffer from fundamental flaws or poor conduct due to lack of preparation and careful planning. Some flaws in the conception or planning phase prior to the finalised trial protocol and registration are difficult to rectify once the trial starts. For example, patients may decline participation if the study involves delaying or withholding treatment, or if the experimental condition is deemed unfeasible by patients. This can be avoided, for example, by involving patients in the planning of the trial or by conducting pilot or feasibility studies prior to the full-scale trial. In many cases, the planning of a trial is as least as important as …
Semi-Supervised Adaptation of RNNLMs by Fine-Tuning with Domain-Specific Auxiliary Features

Recurrent neural network language models (RNNLMs) can be augmented with auxiliary features, which can provide an extra modality on top of the words. It has been found that RNNLMs perform best when trained on a large corpus of generic text and then fine-tuned on text corresponding to the sub-domain for which it is to be applied. However, in many cases the auxiliary features are available for the sub-domain text but not for the generic text. In such cases, semi-supervised techniques can be used to infer such features for the generic text data such that the RNNLM can be trained and then fine-tuned on the available in-domain data with corresponding auxiliary features. In this paper, several novel approaches are investigated for dealing with the semi-supervised adaptation of RNNLMs with auxiliary features as input. These approaches include: using zero features during training to mask the weights of the feature sub-network; adding the feature sub-network only at the time of fine-tuning; deriving the features using a parametric model and; back-propagating to infer the features on the generic text. These approaches are investigated and results are reported both in terms of PPL and WER on a multi-genre broadcast ASR task.
Determination of the transient stability boundary

This work presents an efficient method to determine the transient stability boundary. In terms of the power system variables, the required boundary is nonlinear. The method adopted in This work is to transform the original power system variables into a higher dimensional feature space using a nonlinear transformation. It has been shown that well established linear estimation methods can be used in the feature space to determine a linear boundary. This linear boundary is equivalent to a nonlinear boundary in the original power system variable space.
Numerical Characterization of DNA Sequence Based on Dinucleotides

Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of β–globin for 11 species, and the utility of this new method is demonstrated.
Interleukin 1 potentiates the lethal effect of tumor necrosis factor alpha/cachectin in mice

Human rIL-1 alpha and human rIL-1 beta were examined for their ability to potentiate the lethal and hypothermic effects of mouse rTNF-alpha in mice. The LD50 of rTNF-alpha was 1.5 micrograms/mouse, whereas the LD50 of rTNF-alpha was reduced to 0.4 micrograms/mouse and 0.5 micrograms/mouse when rTNF-alpha was administered in combination with a nonlethal dose of rIL-1 alpha or rIL-1 beta, respectively. A similar rTNF-alpha enhancing effect of the rIL-1 was observed on the temperature response. The results show that the rIL-1 markedly potentiate the effects of rTNF-alpha on lethality and temperature in mice, and support our suggestion that TNF-alpha and IL-1 may have synergistic lethal effect in human septic shock.
Validation of parallelizing transformations of sequential programs

Transformations for high‐performance superscalar, vector, and parallel processors maximize parallelism and memory locality. Often parallelizing compilers apply transformations, such as loop parallelization and loop vectorization, to convert a sequential array‐handling program into a parallel program. Validation of such transformations is extremely useful in the prevalent high‐performance computing environment. This paper proposes a novel algorithm for construction of the dependence graph of the generated parallel programs. These transformations are validated by checking equivalence of the dependence graphs of the original sequential program and the transformed parallel program using a standard algorithm reported in the literature. The above equivalence checker works even when the above parallelizing transformations are preceded by various enabling transformations except for loop collapsing transformation that changes the dimensions of the arrays. In the present paper, the scope of the equivalence checker has been expanded to handle this special case by informing it of the correspondence between the index spaces of the corresponding of input and output arrays in the sequential and the parallel programs. The proposed methods are implemented and tested against a set of available benchmark programs that are parallelized by the polyhedral auto‐parallelizer LooPo and the auto‐vectorizer Scout.
Hypertension Caused by Angiotensin II Infusion Involves Increased Superoxide Production in the Central Nervous System

Hypertension caused by angiotensin II (Ang II) infusion is associated with oxidative stress in the peripheral vasculature and kidney. The role of redox mechanisms in the central nervous system (CNS), a tissue known to be pivotal in Ang II–dependent hypertension, has not been investigated. We recently identified superoxide (O2·−) in the brain as a key signaling intermediate in the transient pressor response elicited by acute injection of Ang II directly into the CNS. Here we tested the hypothesis that hypertension caused by chronic systemic infusion of Ang II is mediated by a central neurogenic mechanism involving O2·−. Infusion of Ang II (600 ng · kg−1 · min−1) over a 2-week period in mice caused a gradually developing hypertension that was correlated with marked elevations in O2·− production specifically in the subfornical organ (SFO), a brain region lying outside the blood–brain barrier and known to be a primary sensor for blood-borne Ang II. Adenoviral-mediated delivery of cytoplasmically targeted superoxide dismutase (SOD) selectively to this site prevented the hypertension and the increased O2·− production, whereas gene transfer of SOD targeted to the extracellular matrix had no effect. These data suggest that increased intracellular O2·− production in the SFO is critical in the development of Ang II–induced hypertension.
Association of Ficolin-2 Serum Levels and FCN2 Genetic Variants with Indian Visceral Leishmaniasis

Background Visceral leishmaniasis (VL), one of the neglected tropical diseases, is endemic in the Indian subcontinent. Ficolins are circulating serum proteins of the lectin complement system and involved in innate immunity. Methods We have estimated ficolin-2 serum levels and analyzed the functional variants of the encoding gene FCN2 in 218 cases of VL and in 225 controls from an endemic region of India. Results Elevated levels of serum ficolin-2 were observed in VL cases compared to the controls (adjusted P<0.0001). The genetic analysis revealed that the FCN2 structural variant +6359 C>T (p.T236M) was associated with VL (OR=2.2, 95% CI=1.23-7.25, P=0.008) and with high ficolin-2 serum levels. We also found that the FCN2*AAAC haplotype occurred more frequently among healthy controls when compared to cases (OR=0.59, 95%CI=0.37-0.94, P=0.023). Conclusions Our findings indicate that the FCN2 variant +6359C>T is associated with the occurrence of VL and that ficolin-2 serum levels are elevated in Leishmania infections.
MemInsight: platform-independent memory debugging for JavaScript

JavaScript programs often suffer from memory issues that can either hurt performance or eventually cause memory exhaustion. While existing snapshot-based profiling tools can be helpful, the information provided is limited to the coarse granularity at which snapshots can be taken. We present MemInsight, a tool that provides detailed, time-varying analysis of the memory behavior of JavaScript applications, including web applications. MemInsight is platform independent and runs on unmodified JavaScript engines. It employs tuned source-code instrumentation to generate a trace of memory allocations and accesses, and it leverages modern browser features to track precise information for DOM (document object model) objects. It also computes exact object lifetimes without any garbage collector assistance, and exposes this information in an easily-consumable manner for further analysis. We describe several client analyses built into MemInsight, including detection of possible memory leaks and opportunities for stack allocation and object inlining. An experimental evaluation showed that with no modifications to the runtime, MemInsight was able to expose memory issues in several real-world applications.