nils-herrmann/clean_scirepeval huggingface dataset:
Electrospun biodegradable nanofibers scaffolds for bone tissue engineering

Many polymeric materials have been developed and introduced for bone regeneration. Especially, their nanofibrous forms are mostly applied for artificial extracellular matrices. Polymeric materials in their nanofibrous form show some potent properties such as high surface to volume ratio, tunable porosity, and ease of surface functionalization. Benefiting from the properties of their main polymer and additives, they can provide new opportunities for cell seeding, proliferation, and new 3D tissue formation. This article focuses on most cited polymeric nanofibrous scaffolds fabricated by electrospinning and recent achievements. They were divided into two main categories: natural (collagen, silk, keratin, gelatin, chitosan, and alginate) and synthetic (e.g. polycaprolactone, polylactic acid, and polyglycolic acid) polymers. The role of several additives like hydroxyapatite, bone morphogenetic proteins (BMPs) tricalcium phosphate, and collagen type I in improving the adhesion, differentiation, and tissue formation of stem cells were discussed. Finally, the osteogenic capacity and ability of nanofibrous scaffolds to support the growth of clinically relevant bone tissue were briefly studied.
Learning control of population transfer between subspaces of quantum systems using an adaptive target scheme
Venue: 2016 International Joint Conference on Neural Networks (IJCNN)

An adaptive target scheme is implemented for learning control of population transfer between subspaces of quantum systems. In this control scheme, the target state is updated according to the renormalized yield in the desired subspace throughout the learning iterations, to obtain the desired laser control field. In the numerical experiments, we perform learning control simulations based on a V type three subspace quantum system. The field obtained by learning control can transfer the population to the target subspace with high probability. In comparison with a fixed target state, this adaptive target scheme proves to be more efficient for the quantum control problem under consideration.
Probing Extreme density Matter with Gravitational wave Observations of Binary Neutron Star Merger Remnants

We present a proof of concept study, based on numerical relativity simulations, of how gravitational waves (GWs) from neutron star merger remnants can probe the nature of matter at extreme densities. Phase transitions and extra degrees of freedom can emerge at densities beyond those reached during the inspiral, and typically result in a softening of the equation of state (EOS) We show that such physical effects change the qualitative dynamics of the remnant evolution, but they are not identifiable as a signature in the GW frequency, with the exception of possible black hole formation effects. The EOS softening is, instead, encoded in the GW luminosity and phase and is in principle detectable up to distances of the order of several megaparsecs with advanced detectors and up to hundreds of megaparsecs with third generation detectors. Probing extreme density matter will require going beyond the current paradigm and developing a more holistic strategy for modeling and analyzing postmerger GW signals.
Metabolic engineering of CHO cells to alter lactate metabolism during fed batch cultures.
Venue: Journal of biotechnology

Recombinant yeast pyruvate carboxylase (PYC2) expression was previously shown to be an effective metabolic engineering strategy for reducing lactate formation in a number of relevant mammalian cell lines, but, in the case of CHO cells, did not consistently lead to significant improvement in terms of cell growth, product titer and energy metabolism efficiency. In the present study, we report on the establishment of a PYC2 expressing CHO cell line producing a monoclonal antibody and displaying a significantly altered lactate metabolism compared to its parental line. All clones exhibiting strong PYC2 expression were shown to experience a significant and systematic metabolic shift toward lactate consumption, as well as a prolonged exponential growth phase leading to an increased maximum cell concentration and volumetric product titer. Of salient interest, PYC2 expressing CHO cells were shown to maintain a highly efficient metabolism in fed batch cultures, even when exposed to high glucose levels, thereby alleviating the need of controlling nutrient at low levels and the potential negative impact of such strategy on product glycosylation. In bioreactor operated in fed batch mode, the higher maximum cell density achieved with the PYC2 clone led to a net gain (20% in final volumetric productivity.
Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time
Venue: Biotechnology and bioengineering

The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution of genomic and epigenetic modifications towards phenotype evolution, comprehensive genome and epigenome data are presented for six related CHO cell lines, both in response to perturbations (different culture conditions and media as well as selection of a specific phenotype with increased transient productivity) and in steady state (prolonged time in culture under constant conditions) Clear transitions were observed in DNA methylation patterns upon each perturbation, while few changes occurred over time under constant conditions. Only minor DNA methylation changes were observed between exponential and stationary growth phase; however, throughout a batch culture the histone modification pattern underwent continuous adaptation. Variation in genome sequence between the six cell lines on the level of SNPs, InDels, and structural variants is high, both upon perturbation and under constant conditions over time. The here presented comprehensive resource may open the door to improved control and manipulation of gene expression during industrial bioprocesses based on epigenetic mechanisms. Biotechnol. Bioeng.  2241 2253.
Selection of chemically defined media for CHO cell fed batch culture processes
Venue: Cytotechnology

Two CHO cell clones derived from the same parental CHOBC(r) cell line and producing the same monoclonal antibody (BC G, a low producing clone; BC P, a high producing clone) were tested in four basal media in all possible combinations with three feeds =12 conditions) in fed batch cultures. Higher amino acid feeding did not always lead to higher mAb production. The two clones showed differences in cell physiology, metabolism and optimal medium feed combinations. During the phase transitions of all cultures, cell metabolism showed a shift represented by lower specific consumption and production rates, except for the specific glucose consumption rate in cultures fed by Actifeed A/B. The BC P clone fed by Actifeed A/B showed a threefold cell volume increase and an increase of the specific consumption rate of glucose in the stationary phase. Since feeding was based on glucose this resulted in accumulation of amino acids for this feed, while this did not occur for the poorer feed (EFA/B) The same feed also led to an increase of cell size for the BC G clone, but to a lesser extent.
The Evolution of LTE Physical Layer Control Channels
Venue: IEEE Communications Surveys Tutorials

Physical layer control signals in cellular communications serve the purpose of delivering physical layer control messages in a timely fashion to support cell radio resource management and data transmissions between the network and the mobile users. This article describes the evolution of 3GPP LTE in control channel design. The legacy LTE control channels (Release 8) have proven to be well designed robust channels for signaling physical layer messages. However, emerging wireless communication transmission technologies continue to challenge the traditional design of LTE control channels. We have reached a point where a totally new design of the control channels has to be provided in order for the new transmission features to be introduced into LTE. In this article we first give an overview of the legacy LTE control channel, and present the new challenges. We then describe in depth the new solutions provided by LTE (Release 11) Finally, we address the limitations of the new design, which are recently identified in certain newly emerging applications, in particular, the machine type communications. A new round of evolution is hence imperative. New solutions provided by next release of LTE (Release 13) are presented.
Modeling of Radio Channels With Leaky Coaxial Cable for LTE M Based CBTC Systems
Venue: IEEE Communications Letters

Due to some disadvantages of wireless local area networks (WLANs) in communication based train control (CBTC) systems, long term evolution for metro (LTE M) has been proposed to be the main communication method for future urban rail transit systems. In this letter, we model the channel of LTE M with leaky coaxial cable for CBTC systems. Specifically, the proposed model is based on real field CBTC channel measurement results. Both path loss and small scale fading are studied. The Akaike information criterion (AIC) is applied to determine the model of small scale fading. We show that lognormal distribution is suitable for small scale fading, and the corresponding parameters of lognormal distribution are also determined from the measurement results.
Online Source Rate Control for Adaptive Video Streaming Over HSPA and LTE Style Variable Bit Rate Downlink Channels
Venue: IEEE Transactions on Vehicular Technology

Online source rate control (RC) is designed for video streaming over high speed packet access (HSPA) and Long Term Evolution (LTE) style variable bit rate (VBR) downlink channels. The problem is formulated as the adaptive adjustment of the operational mode of a video encoder based on the buffer overflow probability (BOP) feedback received from the radio link control (RLC) layer at the base station (BS) This allows us to maximize the attainable visual quality while keeping the transmitter BOP below a desired threshold and maintaining a video delay as low as possible. We derive an online measurement based BOP estimation model for the RLC buffer, which is capable of operating with no prior knowledge of the channel variations and of the video characteristics. Based on this estimation model, an online adaptive RC algorithm is proposed to seamlessly adapt the bit stream to the characteristics of VBR channels. Our experiments are conducted in multiuser scenarios using VBR video encoding combined with adaptive modulation and coding (AMC) in the transceiver. The results demonstrate that the proposed source RC regime supports near instantaneous yet smooth bit stream adaptability, which makes it useful for HSPA and LTE style systems for the sake of accommodating unknown video traffic characteristics and dynamically fluctuating propagation conditions.
Validation of the Moral Foundations Questionnaire in Turkey and its relation to cultural schemas of individualism and collectivism

Theory (MFT) is claimed to be universally applicable, the data brought to bear in its support come from a self selected population with mostly English speaking participants. To the best of our knowledge, the theory has not been hitherto tested in a predominantly Muslim country with non western moral and religious sensibilities. In Study 1 we replicated previous findings using Turkish participants by showing through confirmatory factor analyses that the 5 factor structure of MFT provided a better fit than alternative models. In Study 2 the participants' cultural schemas of individualism and collectivism were experimentally manipulated to see the distinctness and separate manipulability of the five individual foundations. The individualism prime led to an increased concern with the harm dimension whereas the collectivism manipulation led to an increased concern with the loyalty dimension. Taken together, the findings suggest that the 5 factor model of morality is the best fitting model in Turkey as well and that it is useful in predicting the results of cultural prime manipulations.
A joint economic lot size model with financial collaboration and uncertain investment opportunity

Establishing long term relationships among the members of a supply chain has become necessary to enhance the supply chain's competitiveness in a globalized environment. Besides coordinating operational decisions, such as how much and when to produce or to order, the members of a supply chain may also share financial resources or act jointly on the capital market. This is important especially when companies have unequal access to capital, for example because they are located in countries with different economic conditions and banking policies and/or they have different credit ratings. The joint financing of investments across the supply chain may thus ensure the stability of production and of the flow of products to the customers. In addition, it strengthens the established relationships among the supply chain members. The paper at hand takes up these issues and presents a joint economic lot size model that allows investments financed cooperatively by the members of the supply chain. In particular, it considers a two stage single vendor single buyer supply chain and assumes that the vendor has the option to invest in increasing its production rate. The outcome of these attempts to improve production capabilities, however, is uncertain and subject to an investment success probability. Due to different access to capital, the vendor and the buyer may also share the investment and the outcome uncertainty, which can be beneficial to both parties.
Variation and design criterion of heat load ratio of generator for air cooled lithium bromide water double effect absorption chiller

The heat load ratio of generator (HLRG) is a special system parameter because it is not fixed at the design value but changes with the working condition. For the air cooled chiller, the deviation from the design working condition occurs easily due to the variation of the surrounding temperature. The system is likely to suffer from crystallization when the working condition is different from the designed one if the HLRG is designed improperly. Consequently, the design criterion of HLRG based on a broad range of working condition is essential and urgent to the development of air cooled lithium bromide water double effect absorption chiller. This paper mainly deals with the variation of HLRG with the working condition as well as corresponding design criterion. Four types of double effect chillers named series, pre parallel, rear parallel and reverse parallel flow system were considered. The parametric model was developed by the introduction of a new thermodynamic relationship of generator. The change of HLRG for different types of chillers with the working condition was analyzed and compared. The corresponding design criterion of HLRG was presented. This paper is helpful for further improvement of the performance and reliability of air cooled lithium bromide water double effect absorption chiller.
Effects of a Urinary Food Supplemented with Milk Protein Hydrolysate and L tryptophan on Feline Idiopathic Cystitis Results of a Case Series in 10 Cats

The effects of a urinary food supplemented with milk protein hydrolysate and L tryptophan fed for eight weeks in eighteen household cats with feline idiopathic cystitis (FIC) are described. Cat emotional, quality of life (QOL) and taste perception scores were recorded every fortnight, as were feline lower urinary tract disease (FLUTD) signs. Eight cats did not complete the study due to various reasons (six of which were due to non food related factors) In the ten cats that completed the study, FLUTD signs, cat emotional and QOL scores improved significantly during the study period. Taste perception of the food was rated excellent throughout the study. Relevance and novel information. FIC is frequently seen in veterinary practice and is difficult to manage. Stress is a known risk factor in the development of FIC. At present, no studies of urinary foods with ingredients known to control anxiety in cats with FIC have been reported. This case series provides provisional evidence that such food improves both FLUTD signs and anxietyrelated behaviours in cats with FIC.
Effects of free amino acids on cytokine secretion and proliferative activity of feline T cells in an in vitro study using the cell line MYA 1
Venue: Cytotechnology

In vitro studies might be an interesting screening method for targeted in vivo studies in the field of immunonutrition and help to reduce and refine animal studies. As the role of amino acids for immune function of cats has not been evaluated in detail so far, the present study aimed at investigating the effects of eight different amino acids (arginine, leucine, isoleucine, valine, glutamine, lysine, threonine and tryptophan) in six concentrations each (0, 0.25, 0.5, 1, 2 and 8x the cat blood level) on cytokine secretion and proliferative activity of feline T cells (MYA 1) in vitro. The results demonstrated that high doses of arginine increased IL 4, IL 10 and TNF a secretion of T cells, while increasing concentrations of lysine increased IL 10 secretion and proliferative activity of the T cells. High doses of leucine enhanced GM CSF and IL 10 secretion, while concentrations of threonine in the cell culture media greater than blood concentration also increased GM CSF and additionally TNF a secretion of the cells. The effects of glutamine and isoleucine on T cell function were only small. In conclusion, the present in vitro study could evaluate the immunomodulating potential of specific amino acids for feline T cell function. High doses of arginine, lysine, leucine and threonine had a significant impact on cytokine secretion and proliferative activity of the T cells. Targeted in vivo studies should investigate the clinical relevance of dietary supplementation of those amino acids in healthy and diseased cats as a next step.
A Social Contract Theory Of Organizations

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Wideband printed dipole antenna fed using modified planar marchand balun
Venue: 2016 International Electronics Symposium (IES)

In this paper, the development of wideband printed dipole antenna which is fed using modified planar Marchand balanced unbalanced (balun) circuit is presented. The antenna is intended to operate at frequency of 3.3GHz with wideband response for wireless application. A modified planar Marchand balun is chosen to transform an unbalanced circuit of coaxial input to a balanced circuit of printed dipole antenna. The choice of Marchand balun type is due to its characteristics such as low loss, wide bandwidth response, and easy for planar structure implementation. The proposed antenna is implemented on a 1.6mm thick Arlon Diclad 527 dielectric substrate. The experimental characterization shows that the realized antenna has the bandwidth response of 600MHz for voltage standing wave ratio (VSWR) =2 ranges from the frequency of 3GHz 3.6GHz with the gain achievement of 5.69dBi 5.85dBi for the frequency range of 3.3GHz 3.4GHz.
A Translation Based Knowledge Graph Embedding Preserving Logical Property of Relations
Venue: NAACL

This paper proposes a novel translation based knowledge graph embedding that preserves the logical properties of relations such as transitivity and symmetricity. The embedding space generated by existing translation based embeddings do not represent transitive and symmetric relations precisely, because they ignore the role of entities in triples. Thus, we introduce a role specific projection which maps an entity to distinct vectors according to its role in a triple. That is, a head entity is projected onto an embedding space by a head projection operator, and a tail entity is projected by a tail projection operator. This idea is applied to TransE,  and TransD to produce lppTransE, lppTransR, and lppTransD, respectively. According to the experimental results on link prediction and triple classification, the proposed logical property preserving embeddings show the state of the art performance at both tasks. These results prove that it is critical to preserve logical properties of relations while embedding knowledge graphs, and the proposed method does it effectively.
Qualitative Data Cleaning
Venue: Proc. VLDB Endow.

Data quality is one of the most important problems in data management, since dirty data often leads to inaccurate data analytics results and wrong business decisions. Data cleaning exercise often consist of two phases: error detection and error repairing. Error detection techniques can either be quantitative or qualitative; and error repairing is performed by applying data transformation scripts or by involving human experts, and sometimes both. In this tutorial, we discuss the main facets and directions in designing qualitative data cleaning techniques. We present a taxonomy of current qualitative error detection techniques, as well as a taxonomy of current data repairing techniques. We will also discuss proposals for tackling the challenges for cleaning "big data" in terms of scale and distribution.
Effective Data Cleaning with Continuous Evaluation
Venue: IEEE Data Eng. Bull.

Enterprises have been acquiring large amounts of data from a variety of sources to build their own "Data Lakes" with the goal of enriching their data asset and enabling richer and more informed analytics. The pace of the acquisition and the variety of the data sources make it impossible to clean this data as it arrives. This new reality has made data cleaning a continuous process and a part of day to day data processing activities. The large body of data cleaning algorithms and techniques is strong evidence of how complex the problem is, yet, it has had little success in being adopted in real world data cleaning applications. In this article we examine how the community has been evaluating the effectiveness of data cleaning algorithms, and if current data cleaning proposals are solving the right problems to enable the development of deployable and effective solutions.
Ontology Based Rewriting Data Cleaning Operations
Venue: C3S2E

Dealing with increasing amounts of data creates the need to deal with redundant, inconsistent and/or complementary repositories which may be different in their data models and/or in their schema. Current data cleaning techniques developed to tackle data quality problems are just suitable for scenarios were all repositories share the same model and schema. Recently, an ontology based methodology was proposed to overcome this limitation. In this paper, this methodology is briefly described and applied to a real scenario in the health domain with data quality problems.