Miracle-dz/UniFAR-FTUs huggingface dataset:
Interpreting meta-analysis according to the adequacy of sample size. An example using isoniazid chemoprophylaxis for tuberculosis in purified protein derivative negative HIV-infected individuals

Objective: To illustrate the utility of statistical monitoring boundaries in meta-analysis, and provide a framework in which meta-analysis can be interpreted according to the adequacy of sample size. To propose a simple method for determining how many patients need to be randomized in a future trial before a meta-analysis can be deemed conclusive. Study design and setting: Prospective meta-analysis of randomized clinical trials (RCTs) that evaluated the effectiveness of isoniazid chemoprophylaxis versus placebo for preventing the incidence of tuberculosis disease among human immunodeficiency virus (HIV)-positive individuals testing purified protein derivative negative. Assessment of meta-analysis precision using trial sequential analysis (TSA) with LanDeMets monitoring boundaries. Sample size determination for a future trials to make the meta-analysis conclusive according to the thresholds set by the monitoring boundaries. Results: The meta-analysis included nine trials comprising 2,911 trial participants and yielded a relative risk of 0.74 (95% CI, 0.53–1.04, P = 0.082, I2 = 0%). To deem the meta-analysis conclusive according to the thresholds set by the monitoring boundaries, a future RCT would need to randomize 3,800 participants. Conclusion: Statistical monitoring boundaries provide a framework for interpreting meta-analysis according to the adequacy of sample size and project the required sample size for a future RCT to make a meta-analysis conclusive.
Hearing Screening and Diagnostic Evaluation of Children With Unilateral and Mild Bilateral Hearing Loss

More than 90% of newborns in the United States are now being screened for hearing loss. A large fraction of cases of unilateral hearing loss and mild bilateral hearing loss are not currently identified through newborn hearing screening. This is of concern because a preponderance of research has demonstrated that unilateral hearing loss and mild bilateral hearing loss can lead to developmental delays and educational problems for some children. To help address this probable underidentification of unilateral hearing loss and mild bilateral hearing loss among infants and children, the Centers for Disease Control and Prevention Early Hearing Detection and Intervention program and the Marion Downs Hearing Center convened a workshop in Breckenridge, Colorado, in July 2005. During this workshop, several issues related to screening and diagnosing unilateral hearing loss and mild bilateral hearing loss were identified, as well as recommendations for future research in this area. Issues identified included the lack of standardized definitions for permanent unilateral hearing loss and mild bilateral hearing loss; the use of screening protocols that are primarily designed to identify bilateral and unilateral hearing losses of a moderate degree or greater (eg, above 40 dB); calibration of screening equipment; availability of facilities that can provide the full range of audiologic, diagnostic, and management services to this pediatric population; and an overall lack of awareness by many professionals and families about the potential effect of unilateral hearing loss and mild bilateral hearing loss. Suggestions for future research, such as identifying ways to improve the identification of cases of unilateral hearing loss and mild bilateral hearing loss, were also discussed.
Descriptive analysis of and overall survival after surgical treatment of lung metastases*

OBJECTIVE: To describe demographic characteristics, surgical results, postoperative complications, and overall survival rates in surgically treated patients with lung metastases. METHODS: This was a retrospective analysis of 119 patients who underwent a total of 154 lung metastasis resections between 1997 and 2011. RESULTS: Among the 119 patients, 68 (57.1%) were male and 108 (90.8%) were White. The median age was 52 years (range, 15-75 years). In this sample, 63 patients (52.9%) presented with comorbidities, the most common being systemic arterial hypertension (69.8%) and diabetes (19.0%). Primary colorectal tumors (47.9%) and musculoskeletal tumors (21.8%) were the main sites of origin of the metastases. Approximately 24% of the patients underwent more than one resection of the lesions, and 71% had adjuvant treatment prior to metastasectomy. The rate of lung metastasis recurrence was 19.3%, and the median disease-free interval was 23 months. The main surgical access used was thoracotomy (78%), and the most common approach was wedge resection with segmentectomy (51%). The rate of postoperative complications was 22%, and perioperative mortality was 1.9%. The overall survival rates at 12, 36, 60, and 120 months were 96%, 77%, 56%, and 39%, respectively. A Cox analysis confirmed that complications within the first 30 postoperative days were associated with poor prognosis (hazard ratio = 1.81; 95% CI: 1.09-3.06; p = 0.02). CONCLUSIONS: Surgical treatment of lung metastases is safe and effective, with good overall survival, especially in patients with fewer metastases.
Inhibition of Inward Rectifier K+ Currents by Angiotensin II in Rat Atrial Myocytes: Lack of Effects in Cells from Spontaneously Hypertensive Rats

We examined the effects of angiotensin II (Ang II) on inward rectifier K+ currents (IK1) in rat atrial myocytes. [125I]Ang II–binding assays revealed the presence of both Ang II type 1 (AT1) and type 2 (AT2) receptors in atrial membrane preparations. Ang II inhibited IK1 in isolated atrial myocytes with an IC50 of 46 nmol/l. This inhibition was abolished by the AT1 antagonist RNH6270 but not at all by the AT2 antagonist PD123319. Treatment of cells with pertussis toxin or a synthetic decapeptide corresponding to the carboxyl-terminus of Giα-3 abolished the inhibition by Ang II, indicating the role of a Gi-dependent signaling pathway. Accordingly, Ang II failed to inhibit IK1 in the presence of forskolin, dibutyryl-cAMP or protein kinase A catalytic subunits. In spite of the increased binding capacities for [125I]Ang II, Ang II failed to affect IK1 in cells from spontaneously hypertensive rats (SHR). AT1 immunoprecipitation from atrial extracts revealed decreased amounts of Giα-2 and Giα-3 proteins associated with this receptor in SHR as compared with controls. The reduced coupling of AT1 with Giα proteins may underlie the unresponsiveness of atrial IK1 to Ang II in SHR cells.
Architecture and implementation of multimodal plug and play

This paper describes the handling of multimodality in the Embassi system. Here, multimodality is treated in two modules. Firstly, a modality fusion component merges speech, video traced pointing gestures, and input from a graphical user interface. Secondly, a presentation planning component decides upon the modality to be used for the output, i.e., speech, an animated life-like character (ALC) and/or the graphical user interface, and ensures that the presentation is coherent and cohesive. We describe how these two components work and emphasize one particular feature of our system architecture: All modality analysis components generate output in a common semantic description format and all render components process input in a common output language. This makes it particularly easy to add or remove modality analyzers or renderer components, even dynamically while the system is running. This plug and play of modalities can be used to adjust the system's capabilities to different demands of users and their situative context. In this paper we give details about the implementations of the models, protocols and modules that are necessary to realize those features.
Observer Design for a Core Circadian Rhythm Network

The paper investigates the observer design for a core circadian rhythm network in Drosophila and Neurospora. Based on the constructed highly nonlinear differential equation model and the recently proposed graphical approach, we design a rather simple observer for the circadian rhythm oscillator, which can well track the state of the original system for various input signals. Numerical simulations show the effectiveness of the designed observer. Potential applications of the related investigations include the real-world control and experimental design of the related biological networks.
Fitness and evolutionary stability in game theoretic models of finite populations

We investigate two methods of measuring fitness in evolutionary games played among members of a finite population. Classical notions of stability account for the action of selection only, and use immediate reproductive gains as a measure of fitness. This classical interpretation of fitness is what we call reproductive fitness (RF), and is found in the early studies of evolutionary stability in finite populations. More recent work has incorporated the influence of random genetic drift by applying fixation probability (FP) as a measure of fitness. When defined in this way, fitness represents a measure of ultimate evolutionary success. Our main result describes an equivalence between candidate evolutionarily stable strategies under both the RF and FP interpretations of fitness. We apply this result to matrix games in which the use of mixed strategies is permitted, and find here an equivalence between the RF and FP conditions for evolutionary stability.
Cecropia peltata Accumulates Starch or Soluble Glycogen by Differentially Regulating Starch Biosynthetic Genes[W][OA]

Cecropia peltata is a tropical tree that, like other plants, makes insoluble starch in its leaves. However, C. peltata also makes soluble glycogen in small food bodies specially produced for mutualistic ants. We provide evidence that this ability to make either polymer is brought about by differential regulation of the same set biosynthetic genes. The branched glucans glycogen and starch are the most widespread storage carbohydrates in living organisms. The production of semicrystalline starch granules in plants is more complex than that of small, soluble glycogen particles in microbes and animals. However, the factors determining whether glycogen or starch is formed are not fully understood. The tropical tree Cecropia peltata is a rare example of an organism able to make either polymer type. Electron micrographs and quantitative measurements show that glycogen accumulates to very high levels in specialized myrmecophytic structures (Müllerian bodies), whereas starch accumulates in leaves. Compared with polymers comprising leaf starch, glycogen is more highly branched and has shorter branches—factors that prevent crystallization and explain its solubility. RNA sequencing and quantitative shotgun proteomics reveal that isoforms of all three classes of glucan biosynthetic enzyme (starch/glycogen synthases, branching enzymes, and debranching enzymes) are differentially expressed in Müllerian bodies and leaves, providing a system-wide view of the quantitative programming of storage carbohydrate metabolism. This work will prompt targeted analysis in model organisms and cross-species comparisons. Finally, as starch is the major carbohydrate used for food and industrial applications worldwide, these data provide a basis for manipulating starch biosynthesis in crops to synthesize tailor-made polyglucans.
‘Nedoceratops’: An Example of a Transitional Morphology

Background The holotype and only specimen of the chasmosaurine ceratopsid dinosaur ‘Nedoceratops hatcheri’ has been the source of considerable taxonomic debate since its initial description. At times it has been referred to its own genus while at others it has been considered synonymous with the contemporaneous chasmosaurine Triceratops. Most recently, the debate has focused on whether the specimen represents an intermediate ontogenetic stage between typical young adult Triceratops and the proposed mature morphology, which was previously considered to represent a distinct genus, ‘Torosaurus’. Methodology/Principal Findings The only specimen of ‘Nedoceratops hatcheri’ was examined and the proposed diagnostic features of this taxon were compared with other chasmosaurine ceratopsids. Every suggested autapomorphy of ‘Nedoceratops’ is found in specimens of Triceratops. In this study, Triceratops includes the adult ‘Torosaurus’ morphology. The small parietal fenestra and elongate squamosals of Nedoceratops are consistent with a transition from a short, solid parietal-squamosal frill to an expanded, fenestrated condition. Objections to this hypothesis regarding the number of epiossifications of the frill and alternations of bone surface texture were explored through a combination of comparative osteology and osteohistology. The synonymy of the three taxa was further supported by these investigations. Conclusions/Significance The Triceratops, ‘Torosaurus’, and ‘Nedoceratops’ morphologies represent ontogenetic variation within a single genus of chasmosaurine: Triceratops. This study highlights how interpretations of dinosaur paleobiology, biodiversity, and systematics may be affected by ascribing ontogenetic and other intraspecific variation a taxonomic significance.
Ring shaped 6.7 GHz methanol maser emission around a young high-mass star

We report on EVN imaging of the 6.7 GHz methanol maser emission from the candidate high-mass protostar G23.657-0.127. The masers originate in a nearly circular ring of 127 mas radius and 12 mas width. The ring structure points at a central exciting object which characteristics are typical for a young massive star; its bolometric luminosity is estimated to be ≤ $3.2\times10^4~{L}_{\odot}$ and ≤ $1.2\times 10^5~{L}_{\odot}$ for near (5.1 kpc) and far (10.5 kpc) kinematic distances, respectively. However, the spatial geometry of the underlying maser region remains ambiguous. We consider scenarios in which the methanol masers originate in a spherical bubble or in a rotating disc seen nearly face-on.
Analysis of LMS algorithm with delayed coefficient adaptation for sinusoidal reference

In this paper, we analyse the stability of LMS algorithms with delayed coefficient adaptation, such as FxLMS and DLMS algorithms, when sinusoidal references are used. We demonstrate that in two common situations, that are two in-phase and quadrature sinusoidal components and a tapped delay line with a large number of weights, the adaptive system turns to be linear and time-invariant. Without the need of any independence assumption, stability is then analysed in those two situations and an upper bound for the adaptation step size is derived.
Motion-Based Autonomous Grounding: Inferring External World Properties from Encoded Internal Sensory States Alone

How can we build artificial agents that can autonomously explore and understand their environments? An immediate requirement for such an agent is to learn how its own sensory state corresponds to the external world properties: It needs to learn the semantics of its internal state (i.e., grounding). In principle, we as programmers can provide the agents with the required semantics, but this will compromise the autonomy of the agent. To overcome this problem, we may fall back on natural agents and see how they acquire meaning of their own sensory states, their neural firing patterns. We can learn a lot about what certain neural spikes mean by carefully controlling the input stimulus while observing how the neurons fire. However, neurons embedded in the brain do not have direct access to the outside stimuli, so such a stimulus-to-spike association may not be learnable at all. How then can the brain solve this problem? (We know it does.) We propose that motor interaction with the environment is necessary to overcome this conundrum. Further, we provide a simple yet powerful criterion, sensory invariance, for learning the meaning of sensory states. The basic idea is that a particular form of action sequence that maintains invariance of a sensory state will express the key property of the environmental stimulus that gave rise to the sensory state. Our experiments with a sensorimotor agent trained on natural images show that sensory invariance can indeed serve as a powerful objective for semantic grounding.
An Abnormal Mitochondrial–Hypoxia Inducible Factor-1&agr;–Kv Channel Pathway Disrupts Oxygen Sensing and Triggers Pulmonary Arterial Hypertension in Fawn Hooded Rats: Similarities to Human Pulmonary Arterial Hypertension

Background— The cause of pulmonary arterial hypertension (PAH) was investigated in humans and fawn hooded rats (FHR), a spontaneously pulmonary hypertensive strain. Methods and Results— Serial Doppler echocardiograms and cardiac catheterizations were performed in FHR and FHR/BN1, a consomic control that is genetically identical except for introgression of chromosome 1. PAH began after 20 weeks of age, causing death by ≈60 weeks. FHR/BN1 did not develop PAH. FHR pulmonary arterial smooth muscle cells (PASMCs) had a rarified reticulum of hyperpolarized mitochondria with reduced expression of electron transport chain components and superoxide dismutase-2. These mitochondrial abnormalities preceded PAH and persisted in culture. Depressed mitochondrial reactive oxygen species (ROS) production caused normoxic activation of hypoxia inducible factor (HIF-1&agr;), which then inhibited expression of oxygen-sensitive, voltage-gated K+ channels (eg, Kv1.5). Disruption of this mitochondrial-HIF-Kv pathway impaired oxygen sensing (reducing hypoxic pulmonary vasoconstriction, causing polycythemia), analogous to the pathophysiology of chronically hypoxic Sprague-Dawley rats. Restoring ROS (exogenous H2O2) or blocking HIF-1&agr; activation (dominant-negative HIF-1&agr;) restored Kv1.5 expression/function. Dichloroacetate, a mitochondrial pyruvate dehydrogenase kinase inhibitor, corrected the mitochondrial-HIF-Kv pathway in FHR-PAH and human PAH PASMCs. Oral dichloroacetate regressed FHR-PAH and polycythemia, increasing survival. Chromosome 1 genes that were dysregulated in FHRs and relevant to the mitochondria-HIF-Kv pathway included HIF-3&agr; (an HIF-1&agr; repressor), mitochondrial cytochrome c oxidase, and superoxide dismutase-2. Like FHRs, human PAH-PASMCs had dysmorphic, hyperpolarized mitochondria; normoxic HIF-1&agr; activation; and reduced expression/activity of HIF-3&agr;, cytochrome c oxidase, and superoxide dismutase-2. Conclusions— FHRs have a chromosome 1 abnormality that disrupts a mitochondria-ROS-HIF-Kv pathway, leading to PAH. Similar abnormalities occur in idiopathic human PAH. This study reveals an intersection between oxygen-sensing mechanisms and PAH. The mitochondria-ROS-HIF-Kv pathway offers new targets for PAH therapy.
Chip multithreading systems need a new operating system scheduler

The unpredictable nature of modern workloads, characterized by frequent branches and control transfers, can result in processor pipeline utilization as low as 19%. Chip multithreading (CMT), a processor architecture combining chip multiprocessing and hardware multithreading, is designed to address this issue. Hardware vendors plan to ship CMT systems within the next two years; understanding how such systems will perform is crucial if we are to use them to full advantage.Our simulation experiments show that a CMT-savvy operating system scheduler could improve application performance by a factor of two. In this paper we describe our initial analysis of application performance on CMT systems and propose a design for a scheduler tailored for the needs of a CMT system.
A Generative Approach to Traversal-based Generic Programming

The development of complex software requires the implementation of functions over a variety of recursively defined data structures. Much of the corresponding code is not necessarily difficult, but more tedious and/or repetitive and sometimes easy to get wrong. Data structure traversals fall into this category, particularly in object-oriented languages where traversal code is spread throughout many cooperating modules. In this paper we present a new form of generic programming using traversals that lends itself to a flexible, safe, and efficient generative implementation. We describe the approach, its relation to generic and generative programming, and our implementation and resulting performance.
Computing of applied digital ecosystems

A primary motivation for our research in digital ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the computing technologies that contribute to these properties have not been made explicit in digital ecosystems research. Here, we discuss how different computing technologies can contribute to providing the necessary self-organising features, including Multi-Agent Systems (MASs), Service-Oriented Architectures (SOAs), and distributed evolutionary computing (DEC). The potential for exploiting these properties in digital ecosystems is considered, suggesting how several key features of biological ecosystems can be exploited in Digital Ecosystems, and discussing how mimicking these features may assist in developing robust, scalable self-organising architectures. An example architecture, the Digital Ecosystem, is considered in detail. The Digital Ecosystem is then measured experimentally through simulations, considering the self-organised diversity of its evolving agent populations relative to the user request behaviour.
Agreement between two methods for measuring urine pH in cats and dogs.

OBJECTIVE To compare urine pH of cats and dogs determined by use of a dipstrip and a pH meter. DESIGN Prospective study. SAMPLE POPULATION 109 urine samples from 88 cats that were clinically normal or had signs of irritative urination, 52 samples from 13 clinically normal dogs, and 3 samples from 3 dogs with urinary tract infections. PROCEDURE Measurements of urine pH were obtained by use of a dipstrip and pH meter, and degree of agreement between measurements was evaluated. RESULTS Mean difference (+/- 2 SD) between the 2 methods was 0.1 +/- 0.9 pH units. Only 65 of 164 (40%) samples measured by use of a dipstrip were within 0.25 pH units of results obtained by use of the pH meter. CLINICAL IMPLICATIONS When an accurate measurement of urine pH is critical for clinical decision making, the measurement should be made by use of a pH meter. Dipstrips typically are not accurate enough to be clinically useful.
Change Blindness Images

Change blindness refers to human inability to recognize large visual changes between images. In this paper, we present the first computational model of change blindness to quantify the degree of blindness between an image pair. It comprises a novel context-dependent saliency model and a measure of change, the former dependent on the site of the change, and the latter describing the amount of change. This saliency model in particular addresses the influence of background complexity, which plays an important role in the phenomenon of change blindness. Using the proposed computational model, we are able to synthesize changed images with desired degrees of blindness. User studies and comparisons to state-of-the-art saliency models demonstrate the effectiveness of our model.