Miracle-dz/UniFAR-FTUs huggingface dataset:
SOFM-MLP: a hybrid neural network for atmospheric temperature prediction

Here, first we study the effectiveness of multilayer perceptron networks (MLPs) for prediction of the maximum and the minimum temperatures based on past observations on various atmospheric parameters. To capture the seasonality of atmospheric data, with a view to improving the prediction accuracy, we then propose a novel neural architecture that combines a self-organizing feature map (SOFM) and MLPs to realize a hybrid network named SOFM-MLP with better performance. We also demonstrate that the use of appropriate features such as temperature gradient can not only reduce the number of features drastically, but also can improve the prediction accuracy. These observations inspired us to use a feature selection MLP (FSMLP) instead of MLP, which can select good features online while learning the prediction task. FSMLP is used as a preprocessor to select good features. The combined use of FSMLP and SOFM-MLP results in a network system that uses only very few inputs but can produce good prediction.
CD4+ T Cell and NK Cell Interplay Key to Regression of MHC Class Ilow Tumors upon TLR7/8 Agonist Therapy

Current immunotherapy targets CD8+ T cells. For tumors that have escaped the immune system, activating NK cells with TLR7/8 agonists generated tumor-specific CD4+ T cells that successfully eliminated tumors in a mouse model, providing additional therapeutic opportunities. One of the next challenges in cancer immunotherapy is the resistance of tumors to T-cell–based treatments through loss of MHC class I. Here, we show that under these circumstances, the Toll-like receptor (TLR)-7/8 ligand imiquimod, but not the TLR3 ligand poly I:C or TLR9 ligand CpG, mediated an effective antitumor response. The rejection of these immune-escaped cancers was mediated by NK cells and CD4+ T cells, whereas activated CD8+ T cells were dispensable. Application of the innate immune stimulator at a distant site activated NK cells and thereby elicited tumor-specific T-cell responses in tumor-bearing mice. Mechanistically, imiquimod activated NK cells to kill tumor cells, resulting in release of tumor antigens and induction of tumor-specific CD4+ T cells. These T helper cells provoked a strong induction of CXCL9 and CXCL10 in the tumor environment. Simultaneously, imiquimod induced the expression of the cognate chemokine receptor CXCR3 on peripheral lymphocytes. This ignited intratumoral CD4+ T-cell infiltration and accumulation, which was critical for tumor rejection; CXCR3 blocking antibodies mitigated the clinical response. In the effector phase, NK cell recruitment to tumors and their activation depended on CD4+ T cells. Together, we have uncovered a potent immune axis of tumor-specific CD4+ T cells and NK cells that eliminates escaped MHC-Ilow tumors. Cancer Immunol Res; 5(8); 642–53. ©2017 AACR.
Hearing Aid-controlled Beamformer for Binaural Speech Enhancement Using a Model-based Approach

The understanding of speech from a particular speaker in the presence of other interfering speakers can be severely degraded for a hearing impaired person. Beamforming techniques have been proven to be effective to improve the speech understanding in such scenarios. However, the number of microphones in a hearing aid (HA) is limited due to the space and power constraints present in the HA. In this paper, we propose to use an external device e.g., a microphone array, that can communicate with the HA to overcome this limitation. We propose a method to control this external device based on the look direction of the HA user. We show, by means of simulations, the robustness of the proposed method at very low SNRs in a reverberant scenario. Moreover, we have also conducted experiments that show the benefit of using this framework for binaural and monaural enhancement.
Identifying and Categorizing Disaster-Related Tweets

This paper presents a system for classifying disaster-related tweets. The focus is on Twitter data generated before, during, and after Hurricane Sandy, which impacted New York in the fall of 2012. We propose an annotation schema for identifying relevant tweets as well as the more ﬁne-grained categories they represent, and develop feature-rich classiﬁers for relevance and ﬁne-grained categorization
MC‐3 receptor and the inflammatory mechanisms activated in acute myocardial infarct

Investigation of the mechanisms activated by endogenous inhibitory pathways can lead to identification of novel targets for cardiovascular inflammatory pathologies. Here we exploited the potential protective role that melanocortin receptor type 3 (MC3‐R) activation might play in a myocardial ischemia‐reperfusion injury model. In resting conditions, mouse and rat heart extracts expressed MC3‐R mRNA and protein, without changes following ischemia‐reperfusion. At the cellular level heart macrophages, but not fibroblasts or cardiomyocytes, expressed this receptor, as demonstrated by immunogold labeling. In vivo, administration of the melanocortin agonist MTII (10 μg per mouse equivalent to 9.3 nmol) 30 min prior to ischemia (25 min) attenuated mouse heart 2 h reperfusion injury by ∼40%, an effect prevented by the mixed MC3/4‐R antagonist SHU9119 but not by the selective MC4‐R antagonist HS204. Similar results were obtained when the compound was given at the beginning of the reperfusion period. Importantly, delayed myocardial damage as measured 24 h post‐reperfusion was equally protected by administration of 10 μg MTII. The focus on MC3‐R was also substantiated by analysis of the recessive yellow (e/e) mouse, bearing a mutated (inactive) MC1‐R, in which MTII was fully protective. Myocardial protection was associated with reduced markers of systemic and local inflammation, including cytokine contents (interleukin‐1 and KC) and myeloperoxidase activity. In conclusion, this study has highlighted a previously unrecognized protective role for MC3‐R activation on acute and delayed heart reperfusion injury. These data may open new avenues for therapeutic intervention against heart and possibly other organ ischemia‐reperfusion injury.
Oleasides; novel cardenolides with an unusual framework in Nerium (Nerium 10).

During the course of re-investigation of the cardiac glycosides of Nerium, new cardenolides with a novel aglycone moiety were isolated and named oleasides A-F. The structure of the aglycone, oleagenin, was established as 3β-hydroxy-15 (14→8) abeo-5β-(8R)-14-oxo-card-20 (22)-enolide, and the sugar moieties were identified as D-diginose (oleaside A), D-digitalose (-B), β-D-glucosyl-D-diginose (-C), 4-O-β-D-glucosyl-D-digitalose (-D), β-gentiobiosyl-D-diginose (-E) and 4-O-β-gentiobiosyl-D-digitalose (-F).
On the probabilistic properties of the solutions of some high-dimensional optimization problems arising in Statistics

We study the probabilistic properties of the solutions of certain high-dimensional optimization problems arising in statistics. More specifically, if for 1 ≤ i ≤ n, Xi ∈ R and i ∈ R, we study the properties of β̂ = argminβ∈Rp 1 n n ∑ i=1 ρ( i −X ′ iβ) + τ 2 ‖β‖ , in the high-dimensional setting where p/n tends to a finite non-zero limit. While most the work is done for τ > 0, we show that under some extra assumptions on ρ, it is possible to recover the case τ = 0 as a limiting case when p/n < 1. This implies that we can derive results for the unpenalized (i.e τ = 0) standard “regression M-estimate” problem where i is replaced by Yi = X ′ iβ0 + i, with β0 an arbitrary deterministic vector in R, characterizing in this case the behavior of β̂ − β0. Our assumptions on Xi’s are very general and cover for instance cases where Xi’s are i.i. d with independent entries. Importantly, our proof handles the case where these entries are not Gaussian. While our main focus is on the case of i.i. d i’s, our proof technique can also handle the case of i’s with different distributions and we give some details on this problem at the end of the paper.
Tangible Immersion for Ecological Design

We introduce tangible immersion—virtual reality coupled with tangible interaction—to foster interdisciplinary collaboration in a critical yet creative design process. Integrating tangible, embodied interaction with geospatial modeling and immersive virtual environments (IVE) can make 3D modeling fast and natural, while enhancing it with realistic graphics and quantitative analytics. We have developed Tangible Landscape, a technology that links a physical model with a geographic information system and 3D-modeling platform through a real-time cycle of interaction, 3D scanning, geospatial computation, and 3D rendering. With this technology, landscape architects, other professionals, and the public can collaboratively explore design alternatives through an iterative process of intuitive ideation, geocomputational analysis, realistic rendering, and critical analysis. This is demonstrated with a test case for interdisciplinary problem-solving, in which a landscape architect and geoscientist use Tangible Landscape to collaboratively design landforms, hydrologic systems, planting, and a trail network for a brownfield site. Using this tangible immersive environment they rapidly explored alternative scenarios. We discuss how the participants used real-time analytics to collaboratively assess trade-offs between environmental and experiential factors, balancing landscape complexity, biodiversity, remediation capacity, and aesthetics. Together they explored how the relationship between landforms and natural processes affected the performance of the designed landscape. Technologies that couple tangible geospatial modeling with IVEs have the potential to transform the design process by breaking down disciplinary boundaries, but may also offer new ways to imagine space and democratize design.
API Usage in Descriptions of Source Code Functionality

In this paper, we present a study exploring the use of API keywords within method summaries. We conducted a web-based study where we asked participants to rank Java method summaries based on five levels of detail, from low level to high level. We found that programmers widely use API in both high and low level summaries. Specifically, we found that 76.78% of higher level summaries contain Java API keywords. Additionally, we found that 93.75% of lower level summaries also contain them. This also shows that, in general, as the detail level decreases, the number of API keywords within the summary increases. It is our hope that this line of research will spark a discussion about API usage outside of source code. It is possible that method summaries are not the only form of documentation that API usage plays an important role. We believe these may be important results that could lead to an improvement for API usability design.
Molecular phylogeny of advanced snakes (Serpentes, Caenophidia) with an emphasis on South American Xenodontines: a revised classification and descriptions of new taxa

Este trabalho apresenta uma analise filogenetica molecular das serpentes avancadas (Caenophidia), realizada com base na analise de sequencias de dois genes mitocondriais (rRNA 12S e 16S) e de um gene nuclear (c-mos; 1681 pares de bases no total) e com 131 taxons terminais, amostrados a partir das principais linhagens de Caenophidia, com enfase nos xenodontineos neotropicais. A analise de parcimonia dos dados mediante otimizacao direta resultou em uma arvore filogenetica bem resolvida que, por um lado, corrobora alguns dos clados identificados em analises anteriores e por outro, estabelece novas hipoteses sobre a composicao de outros grupos e do relacionamento entre eles. Os principais resultados obtidos salientam: (1) a alocacao de Achrochordus, xenodermatideos e pareatideos como grupos externos sucessivos de todos os demais cenofidios (incluindo viperideos, elapideos, atractaspidideos e todos os grupos de "colubrideos"); (2) que, em relacao ao ultimo grupo, viperideos e homalopsideos podem ser considerados como clados irmaos dos demais; (3) a existencia, dentro do grande grupo dos cenofidia, dos seguintes sub-grupos: psamophiideos afro-asiaticos (incluindo o genero Mimophis, de Madagascar), Elapidae (incluindo os hidrophiineos, mas excluindo Homoroselaps, associado aos atractaspidideos), Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae e Xenodontinae. A analise sugere algumas alteracoes de cunho taxonomico dentro dos xenodontineos, incluindo realocacoes genericas para Alsophis elegans, Liophis amarali e modificacoes substanciais em relacao a Xenodontini e a radiacao dos xenodontineos das Antilhas. Tambem e a aqui apresentada uma revisao da classificacao de Caenophidia, baseada inicialmente nas analises moleculares, mas provendo diagnoses morfologicas para muitos dos clados incluidos, realcando os grupos que ainda merecem atencao especial no futuro. Sao aqui nomeados originalmente dois grandes clados dentro de Caenophidia, uma nova subfamilia dentro de Dipsadidae e, dentro de Xenodontinae, cinco novas tribos e seis novos generos, sendo ainda dois generos revalidados. Os generos Xenoxybelis e Pseudablabes sao considerados sinonimos de Philodryas; Erythrolamprus, sinonimo de Liophis; Lystrophis e Waglerophis, sinonimos de Xenodon.
Maximum likelihood scale parameter estimation: An application to gain estimation for QAM constellations

In this paper we address the problem of scale parameter estimation, introducing a reduced complexity Maximum Likelihood (ML) estimation procedure. The estimator stems from the observation that, when the estimandum acts as a shift parameter on a multinomially distributed statistic, direct maximization of the likelihood function can be conducted by an efficient DFT based procedure. A suitable exponential warping of the observation's domain is known to transform a scale parameter problem into a shift estimation problem, thus allowing the afore mentioned reduced complexity ML estimation for shift parameter to be applied also in scale parameter estimation problems. As a case study, we analyze a gain estimator for general QAM constellations. Simulation results and theoretical performance analysis show that the herein presented estimator outperforms selected state of the art high order moments estimator, approaching the Cramér-Rao Lower Bound (CRLB) for a wide range of SNR.
Widespread signatures of negative selection in the genetic architecture of human complex traits

Estimation of the joint distribution of effect size and minor allele frequency (MAF) for genetic variants is important for understanding the genetic basis of complex trait variation and can be used to detect signature of natural selection. We develop a Bayesian mixed linear model that simultaneously estimates SNP-based heritability, polygenicity (i.e. the proportion of SNPs with nonzero effects) and the relationship between effect size and MAF for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752), and show that on average across 28 traits, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (p < 0.05/28 =1.8×10−3) signatures of natural selection for 23 out of 28 traits including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. We further apply the method to 27,869 gene expression traits (N = 1,748), and identify 30 genes that show significant (p < 2.3×10−6) evidence of natural selection. All the significant estimates of the relationship between effect size and MAF in either complex traits or gene expression traits are consistent with a model of negative selection, as confirmed by forward simulation. We conclude that natural selection acts pervasively on human complex traits shaping genetic variation in the form of negative selection.
EasyClone‐MarkerFree: A vector toolkit for marker‐less integration of genes into Saccharomyces cerevisiae via CRISPR‐Cas9

Abstract Saccharomyces cerevisiae is an established industrial host for production of recombinant proteins, fuels and chemicals. To enable stable integration of multiple marker‐free overexpression cassettes in the genome of S. cerevisiae, we have developed a vector toolkit EasyClone‐MarkerFree. The integration of linearized expression cassettes into defined genomic loci is facilitated by CRISPR/Cas9. Cas9 is recruited to the chromosomal location by specific guide RNAs (gRNAs) expressed from a set of gRNA helper vectors. Using our genome engineering vector suite, single and triple insertions are obtained with 90–100% and 60–70% targeting efficiency, respectively. We demonstrate application of the vector toolkit by constructing a haploid laboratory strain (CEN.PK113‐7D) and a diploid industrial strain (Ethanol Red) for production of 3‐hydroxypropionic acid, where we tested three different acetyl‐CoA supply strategies, requiring overexpression of three to six genes each. Among the tested strategies was a bacterial cytosolic pyruvate dehydrogenase complex, which was integrated into the genome in a single transformation. The publicly available EasyClone‐MarkerFree vector suite allows for facile and highly standardized genome engineering, and should be of particular interest to researchers working on yeast chassis with limited markers available.
Women miss out on coronary care

Objective: To determine whether the process of reverse left ventricular remodelling in response to carvedilol is dependent on baseline heart rate (BHR), heart rhythm, or heart rate reduction (HRR) in response to carvedilol. Design: Retrospective analysis of serial echocardiograms in 257 patients with chronic systolic heart failure at baseline and at 12–18 months after starting carvedilol. Reverse left ventricular remodelling was determined by changes in left ventricular end diastolic dimension (LVEDD), end systolic dimension (LVESD), and fractional shortening (LVFS). Setting: Heart failure clinic within a university teaching hospital. Main outcome measures: Changes in LVEDD, LVESD, and LVFS. Results: LVEDD and LVESD decreased by 2.6 (0.4) mm and 4.9 (0.5) mm, respectively (mean (SEM)), and LVFS increased by 4.3 (0.5)% (all p < 0.0001 v baseline). Simple regression revealed no significant relation between BHR or HRR and the changes in LVEDD, LVESD, or LVFS. Stratification of patients into high and low BHR groups (above and below the mean) or according to the baseline heart rhythm (sinus rhythm v atrial fibrillation) showed no differences between groups in the extent of reverse left ventricular remodelling. Improvements in left ventricular function and dimensions were associated with significant improvements in New York Heart Association functional class. Conclusions: The benefits of carvedilol in terms of reverse left ventricular remodelling and symptomatic improvement in patients with chronic heart failure are independent of BHR, heart rhythm, and the HRR that occurs in response to carvedilol.
Novel Endothelial Cell-Specific AQP1 Knockout Mice Confirm the Crucial Role of Endothelial AQP1 in Ultrafiltration during Peritoneal Dialysis

The water channel aquaporin-1 (AQP1) mediates about 50% ultrafiltration during a 2-hour hypertonic dwell in global AQP1 knockout (AQP1-/-) mice. Although AQP1 is widely expressed in various cell types including mesothelial cells, the ultrafiltration has been assumed to be mediated via endothelial AQP1 of the peritoneum. The partial embryonic lethality and reduced body weight in AQP1-/- mice may reflect potential confounding phenotypic effects evoked by ubiquitous AQP1 deletion, which may interfere with functional analysis of endothelial AQP1. Using a Cre/loxP approach, we generated and characterised endothelial cell- and time-specific AQP1 knockout (AQP1fl/fl; Cdh5-Cre+) mice. Compared to controls, AQP1fl/fl; Cdh5-Cre+ mice showed no difference in an initial clinical and biological analysis at baseline, including body weight and survival. During a 1-hour 3.86% mini-peritoneal equilibration test (mini-PET), AQP1fl/fl; Cdh5-Cre+ mice exhibited strongly decreased indices for AQP1-related transcellular water transport (43.0% in net ultrafiltration, 93.0% in sodium sieving and 57.9% in free water transport) compared to controls. The transport rates for small solutes of urea and glucose were not significantly altered. Our data provide the first direct experimental evidence for the functional relevance of endothelial AQP1 to the fluid transport in peritoneal dialysis and thereby further validate essential predictions of the three-pore model of peritoneal transport.
Strategy and structure in interaction: What determines the boundaries of the firm?

This paper analyzes empirically the boundaries of the firm based on Williamson's perspective on what determines firm size. It uses firm performance (risk-adjusted profitability and growth) as dependent variable; and firm organization, diseconomies of scale (atmospheric consequences, bureaucratic insularity, incentive limits, and communication distortion), economies of scale, and asset specificity as independent variables in a structural equation model. Data were collected from the 784 largest US manufacturing firms in 1998. The results confirm Williamson's framework and show that strategy and structure interact concurrently to determine the boundary of the firm.
Modeling and control technics for autonomous electric and hybrid vehicles path following

Autonomous electric vehicle path following area has known wide improvement during the last previous years especially with the appearance of new sophisticated control algorithms. The main focus of these control algorithms is to guarantee high performance in term of stability and path tracking with small distance error. In this research, an overview about the most common technics used in autonomous electric vehicle motion is presented. First, a description of geometric path tracking which depends on the relation between vehicle dimension and its position with respect to the trajectory is introduced. Then, in order to investigate the vehicle responses with respect to its velocity and acceleration a kinematic path tracking is considered. Neglecting the applied forces on the vehicle may impose some robustness problems. Therefore, considering a dynamic path tracking with advanced control technics is needed. At the end a comparison between the considered technics is done.
Very short echo time proton MR spectroscopy of human brain with a standard transmit/receive surface coil

A method for localized proton spectroscopy of the human brain is proposed which can be used with a standard transmit/receive planar surface coil producing an inhomogeneous RF field. Water suppression is accomplished by a train of full passage adiabatic pulses with optimized frequencies and delays, which account for variation in the water resonance frequency and the spin‐lattice relaxation time. The robust method requires minimal pulse calibration and provides high‐quality spectra even at very short echo times and in the absence of outer volume saturation and, therefore, is well suited for clinical in vivo spectroscopy. Performance of the method is demonstrated on a test object and on MR spectra from the human brain at 3 T. Magn Reson Med 44:964–967, 2000. © 2000 Wiley‐Liss, Inc.