Miracle-dz/UniFAR-FTUs huggingface dataset:
Androgen deprivation therapy for prostate cancer.

CONTEXT Prostate cancer is the most common nonskin cancer and second most common cause of cancer mortality in US men. Androgen deprivation therapy (ADT), specifically surgical or medical castration, is the first line of treatment against advanced prostate cancer and is also used as an adjuvant to local treatment of high-risk disease. OBJECTIVE To review systematically the evidence on the risks and benefits of ADT for prostate cancer as well as clinical management of its adverse effects. EVIDENCE ACQUISITION We performed MEDLINE searches of English-language literature (1966 to March 2005) using the terms androgen deprivation therapy, hormone treatment, and prostate cancer. We reviewed bibliographies of literature to extract other relevant articles. Studies were selected based on clinical pertinence, with an emphasis on controlled study design. EVIDENCE SYNTHESIS Androgen deprivation therapy is effective for palliation in many patients with advanced prostate cancer and improves outcomes for high-risk patients treated with radiation therapy for localized disease. Although patients with increasing prostate-specific antigen levels after local treatment without metastatic disease frequently undergo ADT, the benefits of this strategy are not clear. Adverse effects of ADT include decreased libido, impotence, hot flashes, osteopenia with increased fracture risk, metabolic alterations, and changes in cognition and mood. CONCLUSIONS Androgen deprivation therapy has clear roles in the management of advanced prostate cancer and high-risk localized disease. The benefits of ADT in other settings need to be weighed carefully against substantial risks and adverse effects on quality of life.
Imperative Programming with Dependent Types (Extended Abstract)

In this paper, we enrich imperative programming with a form of dependent types. We start with explaining some motivations for this enrichment and mentioning some major obstacles that need to be overcome. We then present the design of a source level dependently typed imperative programming languageXanadu, forming both static and dynamic semantics and then establishing the type soundness theorem. We also present realistic examples, which have all been verified in a prototype implementation, in support of the practicality of Xanadu. We claim that the language design of Xanadu is novel and it serves as an informative example that demonstrates a means to combine imperative programming with dependent types.
Inferring Function Using Patterns of Native Disorder in Proteins

Natively unstructured regions are a common feature of eukaryotic proteomes. Between 30% and 60% of proteins are predicted to contain long stretches of disordered residues, and not only have many of these regions been confirmed experimentally, but they have also been found to be essential for protein function. In this study, we directly address the potential contribution of protein disorder in predicting protein function using standard Gene Ontology (GO) categories. Initially we analyse the occurrence of protein disorder in the human proteome and report ontology categories that are enriched in disordered proteins. Pattern analysis of the distributions of disordered regions in human sequences demonstrated that the functions of intrinsically disordered proteins are both length- and position-dependent. These dependencies were then encoded in feature vectors to quantify the contribution of disorder in human protein function prediction using Support Vector Machine classifiers. The prediction accuracies of 26 GO categories relating to signalling and molecular recognition are improved using the disorder features. The most significant improvements were observed for kinase, phosphorylation, growth factor, and helicase categories. Furthermore, we provide predicted GO term assignments using these classifiers for a set of unannotated and orphan human proteins. In this study, the importance of capturing protein disorder information and its value in function prediction is demonstrated. The GO category classifiers generated can be used to provide more reliable predictions and further insights into the behaviour of orphan and unannotated proteins.
Improved Neural Networks with Random Weights for Short-Term Load Forecasting

An effective forecasting model for short-term load plays a significant role in promoting the management efficiency of an electric power system. This paper proposes a new forecasting model based on the improved neural networks with random weights (INNRW). The key is to introduce a weighting technique to the inputs of the model and use a novel neural network to forecast the daily maximum load. Eight factors are selected as the inputs. A mutual information weighting algorithm is then used to allocate different weights to the inputs. The neural networks with random weights and kernels (KNNRW) is applied to approximate the nonlinear function between the selected inputs and the daily maximum load due to the fast learning speed and good generalization performance. In the application of the daily load in Dalian, the result of the proposed INNRW is compared with several previously developed forecasting models. The simulation experiment shows that the proposed model performs the best overall in short-term load forecasting.
The “source-simplification” aspect of signaling

In decentralized control, a control agent often has the possibility of ‘signaling,’ i.e. the ability to affect the observations of other agents, enabling the agents to ‘talk. ’ Signaling has been noted to make many decentralized control problems, in particular the celebrated Witsenhausen counterexample, hard. In this paper, in order to refine the understanding of signaling, we identify two separate notions of signaling that relate to Witsenhausen's counterexample: source-simplification and the presence of an implicit communication channel. We isolate the two aspects aspect of signaling by constructing two variations on the counterexample. Studying these variations, we conclude that the source-simplification aspect plays the more significant role in the counterexample. As a demonstration of the utility of this refinement, we formulate and address finite-time-horizon versions of the counterexample and of our second variation on the counterexample. For these problems, we use the understanding developed for Witsenhausen's counterexample to obtain asymptotically-approximately- optimal strategies in some cases. Finally, we suggest a thermodynamic analogy to signaling in the counterexample paralleling a similar analogy for Kalman filtering proposed by Mitter and Newton.
Absolute Bounds on the Mean of Sum, Product, etc.: A Probabilistic Extension of Interval Arithmetic

We extend the main formulas of interval arithmetic for different arithmetic operations x1 ⊕ x2 to the case when, for each input xi, in addition to the interval xi = [xi, xi] of possible values, we also know its mean Ei (or an interval Ei of possible values of the mean), and we want to find the corresponding bounds for x1 ⊕ x2 and its mean. Error estimation for indirect measurements: an important practical problem. A practically important class of statistical problems is related to data processing (indirect measurements). Some physical quantities y – such as the distance to a star or the amount of oil in a given well – are impossible or difficult to measure directly. To estimate these quantities, we use indirect measurements, i.e., we measure some easier-to-measure quantities x1, . , xn which are related to y by a known relation y = f(x1, . . . , xn), and then use the measurement results xi (1 ≤ i ≤ n) to compute an estimate ỹ for y as ỹ = f(x1, . . . , xn). For example, to find the resistance R, we measure current I and voltage V , and then use the known relation R = V/I to estimate resistance as R = V / I. Measurement are never 100% accurate, so in reality, the actual value xi of i-th measured quantity can differ from the measurement result xi. In probabilistic terms, xi is a random variable; its probability distribution describes the probabilities of different possible value of measurement error ∆xi def = xi− xi. It is desirable to describe the error ỹ − y of the result of data processing. Often, we know (or assume) that the measurement error ∆xi of each direct measurement is normally distributed with a known standard deviation σi, and that measurement errors corresponding to different measurements are independent. These assumptions – justified by the central limit theorem, according to which sums of independent identically distributed random variables with finite
How Wide Are European Borders? On the Integration Effects of Monetary Unions †

We use consumer price data for 81 European cities (in Germany, Austria, Finland, Italy, Spain, Portugal and Switzerland) to study the impact of the introduction of the euro on goods market integration. Employing both aggregated and disaggregated consumer price index (CPI) data we confirm previous results which showed that the distance between European cities explains a significant amount of the variation in the prices of similar goods in different locations. We also find that the variation of relative prices is much higher for two cities located in different countries than for two equidistant cities in the same country. Under the EMU, the elimination of nominal exchange rate volatility has largely reduced these border effects, but distance and border still matter for intra-European relative price volatility.
Optimization of NIR Spectral Data Management for Quality Control of Grape Bunches during On-Vine Ripening

NIR spectroscopy was used as a non-destructive technique for the assessment of chemical changes in the main internal quality properties of wine grapes (Vitis vinifera L.) during on-vine ripening and at harvest. A total of 363 samples from 25 white and red grape varieties were used to construct quality-prediction models based on reference data and on NIR spectral data obtained using a commercially-available diode-array spectrophotometer (380–1,700 nm). The feasibility of testing bunches of intact grapes was investigated and compared with the more traditional must-based method. Two regression approaches (MPLS and LOCAL algorithms) were tested for the quantification of changes in soluble solid content (SSC), reducing sugar content, pH-value, titratable acidity, tartaric acid, malic acid and potassium content. Cross-validation results indicated that NIRS technology provided excellent precision for sugar-related parameters (r2 = 0.94 for SSC and reducing sugar content) and good precision for acidity-related parameters (r2 ranging between 0.73 and 0.87) for the bunch-analysis mode assayed using MPLS regression. At validation level, comparison of LOCAL and MPLS algorithms showed that the non-linear strategy improved the predictive capacity of the models for all study parameters, with particularly good results for acidity-related parameters and potassium content.
Testing interconnects in a system chip

Testing of interconnects on a printed circuit board has been studied and the procedure has been standardized in the IEEE 1149.1 (JTAG) standard. The system-on-chip (SOC) technology allows us to integrate on the same chip, most of the electronics on a PCB. However, since an SOC operates at a much higher speed and has a very large packaging density, testing its interconnects is different. For example, one must address the crosstalk faults with chip-level interconnects. Not much literature exists on the topic of testing interconnects in core-based systems. We propose a graph-theoretic framework for the problem and a genetic algorithm for testing core interconnects. Our algorithm addresses the issues of test application time, test area overhead, fault-coverage and test power.
Linking Cranial Kinematics, Buccal Pressure, and Suction Feeding Performance in Largemouth Bass

The rate and magnitude of buccal expansion are thought to determine the pattern of water flow and the change in buccal pressure during suction feeding. Feeding events that generate higher flow rates should induce stronger suction pressure and allow predators to draw prey from further away. We tested these expectations by measuring the effects of prey capture kinematics on suction pressure and the effects of the latter on the distance from which prey were drawn—termed suction distance. We simultaneously, but not synchronously, recorded 500‐Hz video and buccal pressure from 199 sequences of four largemouth bass, Micropterus salmoides, feeding on goldfish. From the video, we quantified several kinematic variables associated with the head and jaws of the feeding bass that were hypothesized to affect pressure. In a multiple regression, kinematic data accounted for 79.7% of the variation among strikes in minimum pressure. Faster mouth opening and hyoid depression were correlated with lower pressures, a larger area under the pressure curve, and a faster rate of pressure reduction. In contrast, buccal pressure variables explained only 16.5% of the variation in suction distance, and no single pressure variable had a significant relationship with suction distance. Thus, although expected relationships between head kinematics and buccal pressure were confirmed, suction distance was only weakly related to buccal pressure. Three explanations are considered. First, bass may not attempt to maximize the distance from which prey are drawn. Second, the response of prey items to suction‐induced flow depends on prey behavior and orientation and is, therefore, subject to considerable variation. Third, previous theoretical work indicates that water velocity decays exponentially with distance from the predator’s mouth, indicating that variation among strikes in flow at the mouth opening is compressed away from the mouth. These findings are consistent with other recent data and suggest that suction distance is a poor metric of suction feeding performance.
Dynamic surface matching by geodesic mapping for 3D animation transfer

This paper presents a novel approach that achieves complete matching of 3D dynamic surfaces. Surfaces are captured from multi-view video data and represented by sequences of 3D manifold meshes in motion (3D videos). We propose to perform dense surface matching between 3D video frames using geodesic diffeomorphisms. Our algorithm uses a coarse-to-fine strategy to derive a robust correspondence map, then a probabilistic formulation is coupled with a voting scheme in order to obtain local unicity of matching candidates and a smooth mapping. The significant advantage of the proposed technique compared to existing approaches is that it does not rely on a color-based feature extraction process. Hence, our method does not lose accuracy in poorly textured regions and is not bounded to be used on video sequences of a unique subject. Therefore our complete surface mapping can be applied to: (1) texture transfer between surface models extracted from different sequences, (2) dense motion flow estimation in 3D video, and (3) motion transfer from a 3D video to an unanimated 3D model. Experiments are performed on challenging publicly available real-world datasets and show compelling results.
Two distinct rhythmic motor patterns are driven by common premotor and motor neurons in a simple vertebrate spinal cord

Xenopus embryos show two distinct rhythmic motor patterns: swimming and struggling. Both can be generated by spinal cord circuitry and evoked by stimulation of a single skin sensory pathway (Soffe, 1991b). This presents a valuable opportunity to explore mechanisms for vertebrate motor pattern switching. Swimming and struggling have been compared using intracellular recording from spinal neurons in immobilized embryos. Underlying synaptic drive was similar; motoneurons and premotor interneurons were excited in phase with ipsilateral motor root discharge and inhibited in phase with contralateral motor root discharge. Excitation was stronger during struggling and associated with short bursts of impulses, contrasting with single spikes per cycle during swimming. Excitation was reduced in both patterns by local application of 1 mM kynurenic acid, indicating excitatory amino acid mediation. Inhibition was antagonized by 1 microM strychnine, indicating glycine mediation. Many motoneurons (76%) and premotor interneurons (68%) fired during both swimming and struggling, including examples of all three spinal premotor interneuron classes. Most of the remaining motoneurons (20%) and premotor interneurons (24%) fired only during struggling, providing roughly 30% more active neurons than during swimming. To investigate whether new neuronal classes become active during struggling, recordings were made from sensory neurons and sensory interneurons. Rohon-Beard sensory neurons did not fire during either swimming or struggling. Dorsolateral commissural sensory interneurons received rhythmic, strychnine-sensitive inhibition during both swimming and struggling and also did not fire. Neither of these neuronal classes is therefore recruited to the circuitry for struggling. Although behaviorally distinct, Xenopus embryo swimming and struggling motor patterns appear to employ similar synaptic drive. I propose that this reflects the common nature of much of the premotor circuitry that drives them. Extra neurons are recruited to this circuitry during struggling, but only from within classes that also participate in swimming.
Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain

Neuropathic pain, caused by a lesion in the somatosensory system, is a severely impairing mostly chronic disease. While its underlying molecular mechanisms are not thoroughly understood, neuroimmune interactions as well as changes in the pain pathway such as sensitization of nociceptors have been implicated. It has been shown that not only are different cell types involved in generation and maintenance of neuropathic pain, like neurons, immune and glial cells, but, also, intact adjacent neurons are relevant to the process. Here, we describe an experimental approach to discriminate damaged from intact adjacent neurons in the same dorsal root ganglion (DRG) using differential fluorescent neuronal labelling and fluorescence-activated cell sorting (FACS). Two fluorescent tracers, Fluoroemerald (FE) and 1-dioctadecyl-3,3,3,3-tetramethylindocarbocyanine perchlorate (DiI), were used, whose properties allow us to distinguish between damaged and intact neurons. Subsequent sorting permitted transcriptional analysis of both groups. Results and qPCR validation show a strong regulation in damaged neurons versus contralateral controls as well as a moderate regulation in adjacent neurons. Data for damaged neurons reveal an mRNA expression pattern consistent with established upregulated genes like galanin, which supports our approach. Moreover, novel genes were found strongly regulated such as corticotropin-releasing hormone (CRH), providing novel targets for further research. Differential fluorescent neuronal labelling and sorting allows for a clear distinction between primarily damaged neuropathic neurons and “bystanders,” thereby facilitating a more detailed understanding of their respective roles in neuropathic processes in the DRG.
Cytokine and Chemokine Production by Human Pancreatic Islets Upon Enterovirus Infection

Enteroviruses of the human enterovirus B species (HEV-Bs) (e.g., coxsackie B viruses [CVBs] and echoviruses) have been implicated as environmental factors that trigger/accelerate type 1 diabetes, but the underlying mechanism remains elusive. The aim of this study was to gain insight into the cytokines and chemokines that are produced by human pancreatic islets upon infection with CVBs. To this end, we studied the response of human islets of Langerhans upon mock or CVB3 infection. Using quantitative PCR, we showed that upon CVB3 infection, transcription of interferon (IFN), IFN-stimulated genes, and inflammatory genes was induced. Analysis of secreted cytokines and chemokines by Luminex technology confirmed production and secretion of proinflammatory cytokines (e.g., interleukin [IL]-6 and tumor necrosis factor-α) as well as various chemotactic proteins, such as IFN-γ–induced protein 10, macrophage inflammatory protein (MIP)-1α, MIP-1β, and IL-8. Infection with other HEV-Bs induced similar responses, yet their extent depended on replication efficiency. Ultra violet–inactivated CVB3 did not induce any response, suggesting that virus replication is a prerequisite for antiviral responses. Our data represent the first comprehensive overview of inflammatory mediators that are secreted by human islets of Langerhans upon CVB infection and may shed light on the role of enteroviruses in type 1 diabetes pathogenesis.
Additional File 1 of Avoiding Transcription Factor Competition at Promoter Level Increases the Chances of Obtaining Oscillations

Stripping gene expression down to bare bones, one can say that two phases are common to all organisms: the gene is transcribed into messenger RNA (mRNA) and this mRNA is then translated into protein. Ever since the pioneering works of F. Jacob and J. Monod in the 1950s, the study of transcriptional regulation in prokaryotes and eukaryotes has revealed many other crucial actors in this elaborated play [1]. We shall consider here a simplified version of the process [2, 3] that allows us a direct relation to the Hill function, the one generally employed in mathematical modeling of genetic circuits. The Hill function accounts for the cooperative nature (positive or negative) of various binding sites in the promoter region. It provides a simple way of introducing this cooperative effect, even though it may not be an accurate representation of the underlying dynamics. But let us consider a simple case of transcriptional regulation by a protein that acts as regulator in the dimer form. Let X, X 2 , D denote the protein, the associated dimer and a (free) DNA promoter site, respectively. We may write the equilibrium reactions (2) with D b denoting the promoter state occupied with the dimer and K i , the equilibrium constants. Defining concentrations as x = [X], x 2 = [X 2 ], d f = [D], d b = [D b ], one has: x 2 = K d x 2 , d b = K b d f x 2 = K b K d d f x 2 , and we define K ≡ K b K d. Moreover, the total concentration of the promoter, d T , is constant: d f + d b = d T , leading to the expressions for the free DNA promoter d f = d T 1 1+Kx 2 and occupied or bound promoter d b = d T Kx 2 1+Kx 2. The rate of transcription, r, that is the rate of mRNA production will depend on whether the transcription occurs predominantly from d f or from d b : r = α f d f + α b d b = d T α f + α b Kx 2 1 + Kx 2 (3) = b + d T α b Kx n 1+Kx n if x n is an activator (α b α f) b + d T α f …