nils-herrmann/clean_scirepeval huggingface dataset:
Formyl peptide receptor modulators: a patent review and potential applications for inflammatory diseases (2012 2015)
Venue: Expert opinion on therapeutic patents

The activation of leukocytes and the subsequent immune cascade play an essential role in sterile and infectious inflammation. Dysregulation of these immune responses or excess leukocyte activation can induce tissue damage, organ dysfunction and mortality. Formyl peptide receptors (FPRs) are functionally diverse pattern recognition receptors responsible for recognizing different endogenous damage associated molecular patterns or exogenous pathogen associated molecular patterns. FPRs mediate leukocyte activation during inflammation. FPR1 antagonists and FPR2 agonists have demonstrated significant anti inflammatory effects based on in vitro and in vivo studies. An increasing number of synthesized compounds targeting FPRs, especially potential FPR1 antagonists and FPR2 agonists, have been disclosed in patents.  This article summarizes the current pharmacology patents related to FPR family modulators and their therapeutic indications based on a review of patent applications disclosed between 2012 and 2015.  In this review, FPR1 modulators comprise b 1,3 glucan synthase inhibitors containing an FPR ligand moiety, template fixed peptidomimetics, cyclosporin H, and dipeptide derivatives. FPR2 modulators include phenylurea, bridged spiro[2.4]heptane ester, naphthalene, aminotriazole, polycyclic pyrrolidine 2,5 dione, imidazolidine 2,4 dione, (2 ureidoacetamido)alkyl, amide, oxazolyl methylether, oxazole, thiazole, and crystalline potassium salt derivatives. These compounds have potential applications for human conditions such as inflammatory lung diseases, ischemia reperfusion injury, sepsis, inflammatory bowel disease, and wound healing. FPRs are emerging as important targets for treating leukocyte dominant inflammation.
Correlation of B type natriuretic peptide levels and echocardiographic parameters in preterm infants with patent ductus arteriosus
Venue: Korean journal of pediatrics

This study aimed to evaluate the correlation, according to postnatal age, between plasma B type natriuretic peptide (BNP) levels and echocardiographic parameters for the assessment of patent ductus arteriosus (PDA) in preterm infants with respiratory distress.  We enrolled 42 preterm infants with respiratory distress who underwent serial echocardiographic evaluation with simultaneous plasma BNP measurements until ductal closure. The correlations between BNP levels and the following 4 representative echocardiographic parameters were studied: diameter of the ductus arteriosus (DA) ratio of the left atrial diameter to the aortic diameter (LA/Ao) ratio of the PDA diameter to the infant's left pulmonary artery diameter (PDA/LPA) and the antegrade diastolic flow of LPA (DFLPA) Results BNP levels were significantly correlated to the magnitude of the ductal shunt, comprising the DA diameter, PDA/LPA ratio, LA/Ao ratio, and antegrade DFLPA for the overall study period. The earliest significant correlation, starting from postnatal day 2, was observed between the LA/Ao ratio and BNP levels. The PDA/LPA ratio and the antegrade DFLPA showed significant correlations with BNP levels postnatal day 3 onward, and with the DA diameter, postnatal day 5 onward.  BNP levels and echocardiographic parameters showed a positive correlation, but the significance of the correlations differed according to the postnatal age, especially during the first few days of life.
B type natriuretic peptide levels normalise in preterm infants without a patent ductus arteriosus by the fifth postnatal day
Venue: Acta paediatrica

Few published reports have established B type natriuretic peptide (BNP) levels in preterm infants without a patent ductus arteriosus (PDA) This study addressed that gap in our knowledge by establishing a reference range for BNP levels during the first two weeks of life in preterm infants without a PDA.
Pre symptomatic prediction of morbitidies in preterm infants with patent ductus arteriosus by targeted neonatal echocardiography and brain type natriuretic peptide

Our objective was to compare patent ductus arteriosus (PDA) diameter, PDA score and brain type natriuretic peptide (BNP) measurements at 48 72 hours of life, for prediction of neonatal morbidities. We hypothesized that use of a PDA score with BNP, may improve pre symptomatic prediction of PDAs associated with adverse outcomes.  Infants 31 weeks GA were prospectively studied by targeted neonatal echocardiogram (TNE) at 48 72 hours age, composite PDA score and serum BNP assay; the clinical team remained blinded. PDA was independently diagnosed by echocardiography at time of clinical suspicion (6 2 days) and treated at discretion of the clinical team. Primary outcome was survival with one or more of adverse outcomes (intraventricular hemorrhage [IVH] bronchopulmonary dysplasia [BPD] retinopathy of prematurity [ROP] necrotizing enterocolitis [NEC]  A PDA was present in 56 of 70 infants studied at 48 72 hours; 30 were eventually diagnosed with PDA but never required treatment, 19 required medical treatment, 7 surgical ligation. After adjustment for gestation, PDA diameter did not predict any adverse outcome, PDA score was associated with increased risk of any adverse outcome and high BNP was associated with IVH, BPD, or survival with any adverse outcome.  Comprehensive PDA evaluation at 48 72 hours of age may predict the subsequent occurrence of adverse outcomes and may be useful to define the PDA treatment threshold.
Two dimensional quantum percolation with binary nonzero hopping integrals.
Venue: Physical review. E

In a previous work [Dillon and Nakanishi,  (2014)EPJBFY1434 602810.1140/epjb/e2014 50397 4] we numerically calculated the transmission coefficient of the two dimensional quantum percolation problem and mapped out in detail the three regimes of localization, i.e. exponentially localized, power law localized, and delocalized, which had been proposed earlier [Islam and Nakanishi,  (2008)PLEEE81539 375510.1103/PhysRevE.77.061109] We now consider a variation on quantum percolation in which the hopping integral (w) associated with bonds that connect to at least one diluted site is not zero, but rather a fraction of the hopping integral (V=1) between nondiluted sites. We study the latter model by calculating quantities such as the transmission coefficient and the inverse participation ratio and find the original quantum percolation results to be stable for w>0 over a wide range of energy. In particular, except in the immediate neighborhood of the band center (where increasing w to just 0.02Vappears to eliminate localization effects) increasing w only shifts the boundaries between the three regimes but does not eliminate them until w reaches 10% 40% of V.
Comparison of selected startup ecosystems in Germany and in the USA Explorative analysis of the startup environments

The startup ecosystems in Germany and in the US are different in several dimensions and they have a huge impact on the success of startups. In this study the factors that affects the startup ecosystems are compared. It is analyzed what startups consider as critical to their success and how this varies based on the location of the startups. Using the developed scoring mechanism, the study compares the relative scores of various success factors between the German and American startups to identify areas for improvement. The findings suggest that Germany is successful in implementing co working spaces and incubators but it lacks on accelerator programs. Further, it needs to develop a better support system for their startups while the German startups themselves need to focus on building a stronger internal team in order to boost the startup ecosystem.
Conspiracies between Learning Algorithms, Circuit Lower Bounds and Pseudorandomness
Venue: Computational Complexity Conference

We prove several results giving new and stronger connections between learning, circuit lower bounds and pseudorandomness. Among other results, we show a generic learning speedup lemma, equivalences between various learning models in the exponential time and subexponential time regimes, a dichotomy between learning and pseudorandomness, consequences of non trivial learning for circuit lower bounds, Karp Lipton theorems for probabilistic exponential time, and NC$^1$ hardness for the Minimum Circuit Size Problem.
Advanced hybrid welding and manufacturing technologies

In this study, a detailed analysis of hybrid weld manufacturing technologies that can significantly contribute to the joining of materials has been carried out. Past, present and future projection, advantages, dis advantages, technological barriers and drawbacks of the processes are given. Detailed explanations of the recent developments of hybrid weld manufacturing technologies and main components are given. Potential industrial applications are assessed and evaluated using economic and technological results. The developments in hybrid welding manufacturing technologies generally improved metallurgical and mechanical properties of weld joints. Hybrid processes usually combine the benefits of each individual process. Due to low heat input, hybrid welds create fine grain structures, minimize base material dilution and achieve high toughness and mechanical properties. These processes are especially appropriate for high performance alloys and dissimilar metal joining. The results of this study conclude that reasonable costs and improved properties of the processed materials will lead to massive use of hybrid welding manufacturing technologies.
Representation, equality, and inclusion in deliberative systems: desiderata for a good account

What has become known as 'the systemic turn' in the recent literature on deliberative democracy looks like a promising development. However, while much theorizing has been devoted to the question of what a deliberative system may look like, very little has been offered in terms of criteria for what is required for a system to be deliberative democratic. This paper aims to contribute to the systemic approach by setting out a number of desiderata that a satisfactory account of deliberative systems should consider when developing such criteria. This is done by analyzing the main properties of a deliberative system in relation to three essential aspects of democracy: representation, equality, and inclusion. Among other things, it is argued that when theorizing criteria for what a deliberative system requires, a systemic account should carefully distinguish between political and epistemic representation, between political and epistemic equality, and between political and epistemic inclusion.
Empowerment as Surrender: How Women Lost the Battle for Emancipation as They Won Equality and Inclusion

This analysis addresses the way second wave feminism, through its incontestable achievements in terms of both political mobilization and intellectual critique, failed to address the larger structural sources of the injustice the movement fought, thereby falling short of the lasting emancipation it aspired to achieve. This is a story of "failure by success." I also chart a path for recasting the feminist agenda from the point of view of a broader critique of contemporary capitalism, in which instances of gender injustice are symptomatic of broader forms of domination to which men and women are equally subjected.
Emergent structures and dynamics of cell colonies by contact inhibition of locomotion
Venue: Proceedings of the National Academy of Sciences

The regular distribution of mesenchymal cells, the formation of epithelial monolayers, or their collapse into spheroidal tumors illustrates the broad range of possible organizations of cells in tissues. Unveiling a physical picture of their emergence and dynamics is of critical importance to understand tissue morphogenesis or cancer progression. Although the role of cell substrate and cell cell adhesion in the organization of cell colonies has been widely studied, the impact of the cell type specific contact inhibition of locomotion (CIL) remains unclear. Here, we include this interaction in simulations of active particles and find a number of structures and collective dynamics that recapitulate existing tissue phenotypes. We give analytical predictions for the epithelial mesenchymal transition and the formation of 3D aggregates as a function of cell cell adhesion and CIL strengths. Thus, our findings shed light on the physical mechanisms underlying multicellular organization. Cells in tissues can organize into a broad spectrum of structures according to their function. Drastic changes of organization, such as epithelial mesenchymal transitions or the formation of spheroidal aggregates, are often associated either to tissue morphogenesis or to cancer progression. Here, we study the organization of cell colonies by means of simulations of self propelled particles with generic cell like interactions. The interplay between cell softness, cell cell adhesion, and contact inhibition of locomotion (CIL) yields structures and collective dynamics observed in several existing tissue phenotypes. These include regular distributions of cells, dynamic cell clusters, gel like networks, collectively migrating monolayers, and 3D aggregates. We give analytical predictions for transitions between noncohesive, cohesive, and 3D cell arrangements. We explicitly show how CIL yields an effective repulsion that promotes cell dispersal, thereby hindering the formation of cohesive tissues. Yet, in continuous monolayers, CIL leads to collective cell motion, ensures tensile intercellular stresses, and opposes cell extrusion. Thus, our work highlights the prominent role of CIL in determining the emergent structures and dynamics of cell colonies.
Phase Segregation of Passive Advective Particles in an Active Medium.
Venue: Physical review letters

Localized contractile configurations or asters spontaneously appear and disappear as emergent structures in the collective stochastic dynamics of active polar actomyosin filaments. Passive particles which (un)bind to the active filaments get advected into the asters, forming transient clusters. We study the phase segregation of such passive advective scalars in a medium of dynamic asters, as a function of the aster density and the ratio of the rates of aster remodeling to particle diffusion. The dynamics of coarsening shows a violation of Porod behavior; the growing domains have diffuse interfaces and low interfacial tension. The phase segregated steady state shows strong macroscopic fluctuations characterized by multiscaling and intermittency, signifying rapid reorganization of macroscopic structures. We expect these unique nonequilibrium features to manifest in the actin dependent molecular clustering at the cell surface.
High resolution LIDAR based depth mapping using bilateral filter
Venue: 2016 IEEE 19th International Conference on Intelligent Transportation Systems (ITSC)

High resolution depth maps, obtained by upsampling sparse range data from a 3D LIDAR, find applications in many fields ranging from sensory perception to semantic segmentation and object detection. Upsampling is often based on combining data from a monocular camera to compensate the low resolution of a LIDAR. This paper, on the other hand, introduces a novel framework to obtain dense depth map solely from a single LIDAR point cloud; which is a research direction that has been barely explored. The formulation behind the proposed depth mapping process relies on local spatial interpolation, using sliding window (mask) technique, and on the Bilateral Filter (BF) where the variable of interest, the distance from the sensor, is considered in the interpolation problem. In particular, the BF is conveniently modified to perform depth map upsampling such that the edges (foreground background discontinuities) are better preserved by means of a proposed method which influences the range based weighting term. Other methods for spatial upsampling are discussed, evaluated and compared in terms of different error measures. This paper also researches the role of the mask's size in the performance of the implemented methods. Quantitative and qualitative results from experiments on the KITTI Database, using LIDAR point clouds only, show very satisfactory performance of the approach introduced in this work.
Sketch to Text Generation: Toward Contextual, Creative, and Coherent Composition
Venue: INLG

The need for natural language generation (NLG) arises in diverse, multimodal contexts: ranging from describing stories captured in a photograph, to instructing how to prepare a dish using a given set of ingredients, and to composing a sonnet for a given topic phrase. One common challenge among these types of NLG tasks is that the generation model often needs to work with relatively loose semantic correspondence between the input prompt and the desired output text. For example, an image caption that appeals to readers may require pragmatic interpretation of the scene beyond the literal content of the image. Similarly, composing a new recipe requires working out detailed how to instructions that are not directly specified by the given set of ingredient names. In this talk, I will discuss our recent approaches to generating contextual, creative, and coherent text given a relatively lean and noisy input prompt with respect to three NLG tasks: (1) creative image captioning, (2) recipe composition, and (3) sonnet composition. A recurring theme is that our models learn most of the end to end mappings between the input and the output directly from data without requiring manual annotations for intermediate meaning representations. I will conclude the talk by discussing the strengths and the limitations of these types of data driven approaches and point to avenues for future research.
Distribution of waiting time for dynamic pickup and delivery problems
Venue: Ann. Oper. Res.

Pickup and delivery problems have numerous applications in practice such as parcel delivery and passenger transportation. In the dynamic variant of the problem, not all information is available in advance but is revealed during the planning process. Thus, it is crucial to anticipate future events in order to generate high quality solutions. Previous work has shown that the use of waiting strategies has the potential to save costs and maximize service quality. We adapt various waiting heuristics to the pickup and delivery problem with time windows. Previous research has shown, that specialized waiting heuristics utilizing anticipatory knowledge potentially outperform general heuristics. Direct policy search based on evolutionary computation and a simulation model is proposed as a methodology to automatically specialize waiting strategies to different problem characteristics. Based on the strengths of the previously introduced waiting strategies, we propose a novel waiting heuristic that can utilize historical request information based on an intensity measure which does not require an additional data preprocessing step. The performance of the waiting heuristics is evaluated on a single set of benchmark instances containing various instance classes that differ in terms of spatial and temporal properties. The diverse set of benchmark instances is used to analyze the influence of spatial and temporal instance properties as well as the degree of dynamism to the potential savings that can be achieved by anticipatory waiting and the incorporation of knowledge about future requests.
EN ES CS: An English Spanish Code Switching Twitter Corpus for Multilingual Sentiment Analysis
Venue: LREC

Code switching texts are those that contain terms in two or more different languages, and they appear increasingly often in social media. The aim of this paper is to provide a resource to the research community to evaluate the performance of sentiment classification techniques on this complex multilingual environment, proposing an English Spanish corpus of tweets with code switching (EN ES CS CORPUS) The tweets are labeled according to two well known criteria used for this purpose: SentiStrength and a trinary scale (positive, neutral and negative categories) Preliminary work on the resource is already done, providing a set of baselines for the research community.
Inhibition of heme oxygenase activity using a microparticle formulation of zinc protoporphyrin in an acute hemolytic newborn mouse model
Venue: Pediatric Research

Increased bilirubin production due to hemolysis can lead to neonatal hyperbilirubinemia. Inhibition of heme oxygenase (HO) the rate limiting enzyme in heme catabolism, by metalloporphyrins (Mps) may be an ideal preventive strategy for neonatal hemolytic disease. Zinc protoporphyrin (ZnPP) is a naturally occurring Mp, potent, not phototoxic, with minimal HO 1 upregulation, but is not orally absorbed. Recently, we designed a lipid based ZnPP formulation (ZnPP Lipid) which is orally absorbed by newborn mice. Here, we evaluated the efficacy of ZnPP Lipid in heme loaded newborn mice, a model analogous to hemolytic infants.After 24 h of heme administration (30 umol/kg s.c. 4 d old mice were given 30 umol ZnPP Lipid/kg via intragastric injections. After 3 h, liver and brain HO activity were measured. HO 1 upregulation was assessed by determinations of HO 1 protein, promoter activity, and mRNA by Western blot, in vivo bioluminescence imaging, and RT PCR, respectively.After heme loading, liver HO activity significantly increased ~1.6 fold, which was inhibited in a dose dependent manner by ZnPP Lipid. A dose of 30 umol/kg returned activity to control levels. Brain HO activity was not inhibited. No significant increases in liver and brain HO 1 protein, promoter activity, and mRNA were observed.ZnPP Lipid is effective and thus has potential for treating neonatal hyperbilirubinemia due to hemolysis.
Hemolytic Disease of the Fetus and Newborn: Modern Practice and Future Investigations.
Venue: Transfusion medicine reviews

Red blood cell (RBC) sensitization occurs in some women in response to exposure to paternally derived RBC antigens during pregnancy or to nonself antigens on transfused RBCs during their lifetime. Once sensitized, future pregnancies may be at risk for hemolytic disease of the fetus and newborn. Although great strides have been made over the past few decades in terms of identifying blood group antigens and in predicting fetal anemia through the use of noninvasive monitoring, many questions remain in terms of understanding RBC alloimmunization risk factors, preventative therapies, and treatment strategies. At the present time, there is room for improvement in these areas in both developed and developing countries. Evidence based, universal guidelines describing recommended RBC antigen matching transfusion strategies for girls or women, before pregnancy or during intrauterine transfusions, would be welcomed. A better understanding of the mechanism(s) of action of Rh immunoglobulin, first introduced more than half of a century ago and one of the most successful immunoprophylaxis therapies in existence today, would also be a large step forward. For example, answers to questions of the role(s) that fetal RBC clearance, antigen masking, antigen modulation, and immune suppression play in the effectiveness of Rh immunoglobulin may help to guide the development of novel preventative therapies during pregnancy for immunization to RhD and non RhD antigens. Furthermore, a better understanding of the importance of anti RhD or other alloantibody glycosylation patterns may be beneficial not only in developing such novel immunoprophylaxis therapies but also in predicting the clinical significance of existing maternal alloantibodies. One other area of need includes the development of therapies beyond intrauterine transfusions to mitigate the dangers of maternal alloantibodies to developing fetuses. We challenge physicians, scientists, and funding agencies to prioritize studies of RBC alloimmunization and hemolytic disease of the fetus and newborn and to invest in the children of our future.