Miracle-dz/UniFAR-FTUs huggingface dataset:
A Simpler Method for Predicting Weight Loss in the First Year after Roux-en-Y Gastric Bypass

Factors postulated to predict weight loss after gastric bypass surgery, include race, age, gender, technique, height, and initial weight. This paper contained 1551 gastric bypass patients (85.9% female). Operations were performed by one surgeon (MLO) at community hospitals in Southern California from 1989 to 2008 with 314 being laparoscopic and 1237 open. We created the following equation: In[percent weight] = At2 − Bt, where t was the time after operation (days) and A and B are constants. Analysis was completed on R-software. The model fits with R2 value 0.93 and gives patients a realistic mean target weight with a confidence interval of 95% for the first year. Conclusion. We created a curve predicting weight loss after surgery as a percentage of initial weight. Initial weight was the single most important predictor of weight loss after surgery. Other recorded variables accounted for less than 1% of variability. Unknown factors account for the remaining 6-7%.
High-Resolution Aerial Image Labeling With Convolutional Neural Networks

The problem of dense semantic labeling consists in assigning semantic labels to every pixel in an image. In the context of aerial image analysis, it is particularly important to yield high-resolution outputs. In order to use convolutional neural networks (CNNs) for this task, it is required to design new specific architectures to provide fine-grained classification maps. Many dense semantic labeling CNNs have been recently proposed. Our first contribution is an in-depth analysis of these architectures. We establish the desired properties of an ideal semantic labeling CNN, and assess how those methods stand with regard to these properties. We observe that even though they provide competitive results, these CNNs often underexploit properties of semantic labeling that could lead to more effective and efficient architectures. Out of these observations, we then derive a CNN framework specifically adapted to the semantic labeling problem. In addition to learning features at different resolutions, it learns how to combine these features. By integrating local and global information in an efficient and flexible manner, it outperforms previous techniques. We evaluate the proposed framework and compare it with state-of-the-art architectures on public benchmarks of high-resolution aerial image labeling.
Integrated Analysis of Long Non-coding RNAs (LncRNAs) and mRNA Expression Profiles Reveals the Potential Role of LncRNAs in Skeletal Muscle Development of the Chicken

Long non-coding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation. However, little is currently known about the mechanisms by which they regulate skeletal muscle development in the chicken. In this study, we used RNA sequencing to profile the leg muscle transcriptome (lncRNA and mRNA) at three stages of skeletal muscle development in the chicken: embryonic day 11 (E11), embryonic day 16 (E16), and 1 day after hatching (D1). In total, 129, 132, and 45 differentially expressed lncRNAs, and 1798, 3072, and 1211 differentially expressed mRNAs were identified in comparisons of E11 vs. E16, E11 vs. D1, and E16 vs. D1, respectively. Moreover, we identified the cis- and trans-regulatory target genes of differentially expressed lncRNAs, and constructed lncRNA-gene interaction networks. In total, 126 and 200 cis-targets, and two and three trans-targets were involved in lncRNA-gene interaction networks that were constructed based on the E11 vs. E16, and E11 vs. D1 comparisons, respectively. The comparison of the E16 vs. D1 lncRNA-gene network comprised 25 cis-targets. We determined that lncRNA target genes are potentially involved in cellular development, and cellular growth and proliferation using Ingenuity Pathway Analysis. The gene networks identified for the E11 vs. D1 comparison were involved in embryonic development, organismal development and tissue development. The present study provides an RNA sequencing based evaluation of lncRNA function during skeletal muscle development in the chicken. Comprehensive analysis facilitated the identification of lncRNAs and target genes that might contribute to the regulation of different stages of skeletal muscle development.
Comparative Distal Limb Anatomy Reveals a Primitive Trait in 2 Breeds of Equus caballus

The 55-million-year history of equine phylogeny has been well documented from the skeletal record, however not the soft tissue structures that are now vestigial in modern horse. A recent study reported 2 ligamentous structures resembling functional 3rd and 4th interosseous muscles were evident in Dutch Konik horses. The current study investigates this finding and compares it to members of the genus Equus to identify either a breed anomaly or functional primitive trait. Distal limbs (n=571) were dissected from 4 species of Equus; E. caballus, E. asinus, E. przewalskii and E. burchelli beohmi. Breed representatives of E.caballus (n=18) included the primitive Dutch Konik. The 2nd and or 4th interosseous muscle was evident in all 4 species, but only 2 breeds of E.caballus expressed this trait - the Dutch Konik and Bosnian Mountain Horse. These 2 breeds were the only close descendants of the extinct Tarpan (Equus ferus ferus) represented in this study. In conclusion, the 2nd and 4th interosseous muscles originated from the distal nodule of respective splint bones and inserted into the corresponding branches of the 3rd interosseous muscle proximal to the sesamoids. Suggesting a functional role in medial and lateral joint stability and a primitive trait in modern equids.
Probabilistic neural networks for classification, mapping, or associative memory

It can be shown that by replacing the sigmoid activation function often used in neural networks with an exponential function, a neural network can be formed which computes nonlinear decision boundaries. This technique yields decision surfaces which approach the Bayes optimal under certain conditions. There is a continuous control of the linearity of the decision boundaries, from linear for small training sets to any degree of nonlinearity justified by larger training sets. A four-layer neural network of the type proposed can map any input pattern to any number of classifications. The input variables can be either continuous or binary. Modification of the decision boundaries based on new data can be accomplished in real time simply by defining a set of weights equal to the new training vector. The decision boundaries can be implemented using analog 'neurons', which operate entirely in parallel. The organization proposed takes into account the projected pin limitations of neural-net chips of the near future. By a change in architecture, these same components could be used as associative memories, to compute nonlinear multivariate regression surfaces, or to compute a posteriori probabilities of an event. <<ETX>>
Phase separation in solutions of monoclonal antibodies and the effect of human serum albumin

We report the observation of liquid-liquid phase separation in a solution of human monoclonal antibody, IgG2, and the effects of human serum albumin, a major blood protein, on this phase separation. We find a significant reduction of phase separation temperature in the presence of albumin, and a preferential partitioning of the albumin into the antibody-rich phase. We provide a general thermodynamic analysis of the antibody-albumin mixture phase diagram and relate its features to the magnitude of the effective interprotein interactions. Our analysis suggests that additives (HSA in this report), which have moderate attraction with antibody molecules, may be used to forestall undesirable proetin condensation in antibody solutions. Our findings are relevant to understanding the stability of pharmaceutical solutions of antibodies and the mechanisms of cryoglobulinemia.
Safety in purkinje to ventricular conduction and reentrant activity under simulated 1B ischemia

During the subacute phase of ischemia, electrophysiological alterations and cellular uncoupling set the stage for reentry. In the present work, we have developed a computational model of a fiber and a ring composed by Purkinje cells coupled to a ventricular fiber, which includes a 1B ischemic zone, a border zone and a normal zone. Simulations have been conducted to analyze the effects of cellular uncoupling and hyperkalemia on AP propagation. The results have shown that propagation block (safety factor SF < 1) occurred for low and high ventricular coupling (Rendo 5 Omegamiddotcm2 and 40 Omegamiddotcm2 respectively) as long as hyperkalemia was severe. Additionally, intermediate cellular coupling favored propagation. In the ring model, reentry was obtained for low values of Rendo. In conclusion, cellular uncoupling during 1B ischemia and hyperkalemia are crucial factors in the generation of propagation block, and reentry.
Exemplar-based prediction of global object shape from local shape similarity

We propose a novel method that enables a robot to identify a graspable object part of an unknown object given only noisy and partial information that is obtained from an RGB-D camera. Our method combines the benefits of local with the advantages of global methods. It learns a classifier that takes a local shape representation as input and outputs the probability that a grasp applied at this location will be successful. Given a query data point that is classified in this way, we can retrieve all the locally similar training data points and use them to predict latent global object shape. This information may help to further prune positively labeled grasp hypotheses based on, e.g. relation to the predicted average global shape or suitability for a specific task. This prediction can also guide scene exploration to prune object shape hypotheses. To learn the function that maps local shape to grasp stability we use a Random Forest Classifier. We show that our method reaches the same classification performance as the current state-of-the-art on this dataset which uses a Convolutional Neural Network. Additionally, we exploit the natural ability of the Random Forest to cluster similar data. For a positively predicted query data point, we retrieve all the locally similar training data points that are associated with the same leaf nodes of the Random Forest. The main insight from this work is that local object shape that affords a grasp is also a good predictor of global object shape. We empirically support this claim with quantitative experiments. Additionally, we demonstrate the predictive capability of the method on some real data examples.
DO HETEROGENEOUS EXPECTATIONS CONSTITUTE A CHALLENGE FOR POLICY INTERACTION?

Yes, indeed; at least for macroeconomic policy interaction. We examine a Neo-Classical economy and provide the conditions for policy arrangements to successfully stabilize the economy when agents have either rational or adaptive expectations. For a contemporaneous-data monetary policy rule, the monetarist solution is unique and stationary under a passive fiscal/active monetary policy regime if monetary policy appropriately incorporates expectational heterogeneity. In contrast, the active fiscal/passive monetary policy regime's fiscalist solution is prone to explosiveness due to empirically plausible expectational heterogeneity. Nevertheless, this can be a well-defined, rather orthodox equilibrium. For operational monetary policy rules, only the results for the fiscalist solution prevail. Moreover, our results are plausible from an adaptive learning viewpoint.
Herpes Simplex Virus gE/gI and US9 Proteins Promote Transport of both Capsids and Virion Glycoproteins in Neuronal Axons

ABSTRACT Following reactivation from latency, alphaherpesviruses replicate in sensory neurons and assemble capsids that are transported in the anterograde direction toward axon termini for spread to epithelial tissues. Two models currently describe this transport. The Separate model suggests that capsids are transported in axons independently from viral envelope glycoproteins. The Married model holds that fully assembled enveloped virions are transported in axons. The herpes simplex virus (HSV) membrane glycoprotein heterodimer gE/gI and the US9 protein are important for virus anterograde spread in the nervous systems of animal models. It was not clear whether gE/gI and US9 contribute to the axonal transport of HSV capsids, the transport of membrane proteins, or both. Here, we report that the efficient axonal transport of HSV requires both gE/gI and US9. The transport of both capsids and glycoproteins was dramatically reduced, especially in more distal regions of axons, with gE−, gI−, and US9-null mutants. An HSV mutant lacking just the gE cytoplasmic (CT) domain displayed an intermediate reduction in capsid and glycoprotein transport. We concluded that HSV gE/gI and US9 promote the separate transport of both capsids and glycoproteins. gE/gI was transported in association with other HSV glycoproteins, gB and gD, but not with capsids. In contrast, US9 colocalized with capsids and not with membrane glycoproteins. Our observations suggest that gE/gI and US9 function in the neuron cell body to promote the loading of capsids and glycoprotein-containing vesicles onto microtubule motors that ferry HSV structural components toward axon tips.
Exocytotic Insertion of Calcium Channels Constrains Compensatory Endocytosis to Sites of Exocytosis

Proteins inserted into the cell surface by exocytosis are thought to be retrieved by compensatory endocytosis, suggesting that retrieval requires granule proteins. In sea urchin eggs, calcium influx through P-type calcium channels is required for retrieval, and the large size of sea urchin secretory granules permits the direct observation of retrieval. Here we demonstrate that retrieval is limited to sites of prior exocytosis. We tested whether channel distribution can account for the localization of retrieval at exocytotic sites. We find that P-channels reside on secretory granules before fertilization, and are translocated to the egg surface by exocytosis. Our study provides strong evidence that the transitory insertion of P-type calcium channels in the surface membrane plays an obligatory role in the mechanism coupling exocytosis and compensatory endocytosis.
The Japanese FrameNet Project: An Introduction

This paper presents an overview of the Japanese FrameNet (JFN) research project, which began in July 2002. The goal of JFN is to create a corpus-based lexicon of Japanese described in terms of frame semantics. An important question being asked by JFN is whether Japanese words can be described in FrameNet style, i.e., along the same lines as English words. This point is illustrated in this paper with an example of preliminary analysis of Japanese motion verbs. The Japanese FrameNet can be described as a lexicographic project with an eye to finding out similarities and differences between Japanese and English pertaining to their lexical and grammatical
Estimation of the Distribution of Tabebuia guayacan (Bignoniaceae) Using High-Resolution Remote Sensing Imagery

Species identification and characterization in tropical environments is an emerging field in tropical remote sensing. Significant efforts are currently aimed at the detection of tree species, of levels of forest successional stages, and the extent of liana occurrence at the top of canopies. In this paper we describe our use of high resolution imagery from the Quickbird Satellite to estimate the flowering population of Tabebuia guayacan trees at Barro Colorado Island (BCI), in Panama. The imagery was acquired on 29 April 2002 and 21 March 2004. Spectral Angle Mapping via a One-Class Support Vector machine was used to detect the presence of 422 and 557 flowering tress in the April 2002 and March 2004 imagery. Of these, 273 flowering trees are common to both dates. This study presents a new perspective on the effectiveness of high resolution remote sensing for monitoring a phenological response and its use as a tool for potential conservation and management of natural resources in tropical environments.
Small-size low losses GSM and DCS harmonic filters integrated in a low cost 130 nm high resistivity SOI CMOS technology

RF front end modules (FEMs) are currently realized using a variety of technologies. However, since integration drives wireless business in order to achieve the appropriate cost and form factor, we see significant research concerning FEM integration on silicon [1]. In this quest, SOI technology has already addressed two key blocks, the antenna switch and the power amplifier. In this paper, we will focus our investigation on high performance passives functions in order to demonstrate the capability of SOI CMOS technology to integrate the whole FEM. To do so, GSM and DCS harmonic filters have been achieved in a 130 nm SOI CMOS technology. Measured performances (insertion losses ∼1dB and harmonic rejection greater than 30 dB) are clearly competitive with most commercially available Integrated Device Passive (IPD) solutions.
The Performance of A Diversity-based MC-CDMA in the Presence of Frequency Offset and Inter-Carrier Interferences

The performance of multi-carrier code division multiple access (MC-CDMA) systems that employ random spreading sequence in downlink frequency selective fading channels is analyzed. An expression of the probability density function (pdf) of multiple access interference (MAI), inter-carrier-interference (ICI) and noise is derived for MC-CDMA systems in terms of the number of users, the spreading factor, the number of sub-carriers, mobile station's velocity, and frequency offset. The results show that the effects of frequency offset become crucial as system loading increases. The precise error-rate analysis is extended to a system using multichannel reception with maximal ratio combining (MRC). It is demonstrated, through both analysis and numerical evaluation, that the error-rate performance over a frequency selective channel deteriorates by increasing frequency offset. In addition, it is clear from the results that using multichannel reception enhances system performance.
Primary charge separation in mutant reaction centers of Rhodobacter capsulatus

Excited-state decays of the special pair of Rhodobacter capsulatus and 10 mutants as a function of temperature are presented. The mutations are at the symmetry-related sites L181 and M208. All the decays are nonexponential, although the degree of nonexponentially depends strongly on the mutant and the temperature. We correlated the changes in decay time with mutation-induced changes in the redox potential of the ground state of the special pair. The qualitative form of the decays led us to explore a model based on a small Gaussian distribution of free energy gaps for the electron-transfer process. The model is used to estimate the reorganization energy arising from low-frequency protein and intramolecular modes coupled to the electron transfer. Our fitting procedure gives values of [le]250 and 500 cm[sup [minus]1] at 292 and 22 K, respectively. A consideration of possible errors leads us to conclude that the room temperature value could be no larger than twice the fitted value (i.e., [le]500 cm[sup [minus]1]). The implications of our results for the mechanism of primary charge separation are discussed. 89 refs., 9 figs., 2 tabs.
Birational Geometry and Localisation of Categories

We explore connections between places of function fields over a base field F and birational morphisms between smooth F- varieties. This is done by considering various categories of fractions involving function fields or varieties as objects, and constructing func- tors between these categories. The main result is that in the localised category S −1 b Sm(F), where Sm(F) denotes the usual category of smooth varieties over F and Sb is the set of birational morphisms, the set of morphisms between two objects X and Y , with Y proper, is the set of R-equivalence classes Y (F(X))/R.
Progressive Bayesian estimation with deterministic particles

This paper introduces an enhanced method for progressive Bayesian estimation based on a set of deterministic samples. The information of a given measurement is gradually introduced in order to avoid particle degeneration, which is usually encountered in standard particle filters. The main contribution of this paper is to derive a new method for exploiting smoothness assumptions about the unknown underlying density function of the state.
A Natural Model of Leishmania major Infection Reveals a Prolonged “Silent” Phase of Parasite Amplification in the Skin Before the Onset of Lesion Formation and Immunity

A model of Leishmania major infection in C57BL/6 mice has been established that combines two main features of natural transmission: low dose (100 metacyclic promastigotes) and inoculation into a dermal site (the ear dermis). The evolution of the dermal lesion could be dissociated into two distinct phases. The initial “silent” phase, lasting 4–5 wk, favored establishment of the peak load of parasites in the dermis in the absence of lesion formation or any overt histopathologic changes in the site. The second phase corresponds to the development of a lesion associated with an acute infiltration of neutrophils, macrophages, and eosinophils into the dermis and was coincident with the killing of parasites in the site. The onset of immunity/pathology was correlated with the appearance of cells staining for IL-12p40 and IFN-γ in the epidermal compartment, and an expansion of T cells capable of producing IFN-γ in the draining lymph node. Parasite growth was not enhanced over the first 4.5 wk in anti-CD4-treated mice, SCID mice, or C57BL/6 mice deficient in IL-12p40, IFN-γ, CD40 ligand, or inducible NO synthase. These mice all failed to ultimately control infection in the site, but in some cases (anti-CD4 treated, IL-12p40−/−, CD40 ligand−/−, and SCID) high dermal parasite loads were associated with little or no pathology. These results extend to a natural infection model a role for Th1 cells in both acquired resistance and lesion formation, and document the remarkable avoidance of this response during a prolonged phase of parasite amplification in the skin.