Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Methods for the Identification of differentially expressed Genes in two group Microarray Experiments

This paper proposes a novel algorithm for the identification of differentially expressed genes in two group microarray experiments. The algorithm, called PUL, is compared to other popular algorithms using published implementations. The comparison is based on established measurements in information retrieval (Recall and Precision). Surprisingly a clear ordering in performance of the algorithms was observed. PUL outperformed other algorithms by a factor of two. PUL was applied successfully in different practical applications. For these experiments the importance of the genes proposed by PUL were independently verified. Contact: ultsch@informatik.uni-marburg.de
Developing Human Social Cultural and Behavioral ( HSCB ) Ontologies to Support Simulations

Most constructive simulation developers have historically focused primarily on military platforms that are structured into well defined organizations. The organizations or individual platforms have been modeled as entities that move, shoot, and communicate. However, the realities of recent conflicts have produced new demands for simulations that represent counterinsurgency operations. These applications’ requirements create new challenges for the simulation community. It is difficult to develop consensus perspectives on the Human Social Cultural and Behavioral (HSCB) domain in order to develop conceptual models for the simulations. Ontologies can be used to formally specify controlled vocabularies and to unambiguously describe semantic relationships. Ontologies are being developed by the U.S. Army to represent and characterize portions of the HSCB domain. These ontologies are potentially useful for simulation development activities including conceptual modeling, data interchange, and interoperability. The Web Ontology Language – OWL provides an open non-proprietary method for describing these ontologies.
Double Umbilical Cord Blood Transplantation after Novel Myeloablative Conditioning Using a Regimen of Fludarabine , Busulfan , and Total Lymphoid Irradiation

INTRODUCTION Umbilical cord blood (UCB) has become an increasingly utilized alternative cell source for hematopoietic stem cell transplantation. Less stringent criteria for HLA matching allows for greater access to suitable units, and a suitable UCB unit can be made available in days [1,2]. In adults and larger children, single-unit UCB transplantation has been linked to slower neutrophil recovery and higher likelihood of graft failure because of low cell dose [3-6]. To overcome singleUCB cell dose limitations, a double-unit umbilical cord blood transplantation (dCBT) strategy was introduced and successfully validated in several adult studies [7-9]. At this time, the optimal myeloablative conditioning regimen before dCBT in regards to engraftment, treatmentrelated mortality (TRM), or prevention of relapse remains unknown. Most successful trials to date have utilized total body irradiation (TBI)ebased myeloablative conditioning regimens in combination with cyclophosphamide and/or fludarabine [10-12]. Although these regimens may exert a potent antitumor effect and sufficient immunosuppression to facilitate mismatched unrelated cord blood engraftment, the toxicity with this approach may be contributing to the overall increased TRM seen with dCBT. Fludarabine and busulfan 3.2 mg/kg i.v 4 (FluBu4) is a widely used myeloablative regimen for bone marrow and peripheral hematopoietic stem cell transplantation, with favorable tolerability and lower TRM, compared with other myeloablative regimens [13-15]. Experience with FluBu4 in the setting of UCB transplantation is limited. In a previous study (Duke, MD Anderson Cancer Center) where FluBu4 was utilized, engraftment was low [15,16]. To augment immunosuppressionwithout significantly adding toxicity, we conducted a pilot study to assess the safety and efficacy of performing dCBT using FluBu4 followed by low-dose total lymphoid irradiation (TLI) at 400 cGy (FluBu4/ TLI) as our preparative regimen. PATIENTS AND METHODS
European Conference on Information Systems ( ECIS ) Summer 10-6-2011 ANTECEDENTS AND CONSEQUENCES OF TRUST IN SUPPLY CHAIN : THE ROLE OF INFORMATION TECHNOLOGY

Trust has been a central construct in studies of inter-firm relationships. Many operational, organizational, social, and cultural factors have been identified to have significant impact on inter-firm trust. In this study, we investigate the role of information technology in generating inter-firm trust and the consequences of this trust in the context of supply networks. Using structural equation modeling techniques, our data show that the level of information systems integration among the partner firms in a supply network significantly impacts the trust among the firms which, together with the integrated information systems, explains more than half of the variances in information sharing and business process coupling in the network. Given the substantial evidence in the literature on the impact of information sharing and process coupling on supply chain performance, we conclude that information systems integration among the partners is critical to supply network performance. We also confirm that information systems flexibility and use of standards in information systems significantly contribute to the level of systems integration among the partners in supply networks as suggested in prior studies. Our findings extend the current literature on inter-firm trust by considering the role of information technology in addition to other important factors already identified.
Collection Saliency Map Mesh Saliency Word Assignment Reconstruction Word Frequency Parameterization Result Word Cloud Generation

Word art has characteristics of both text and an image by combining words into a collage that depicts an associated shape or object. This type of artwork has the unique perceptual property that when seen as a whole, it is perceived similar to an image, but when viewing a part, it can be read word by word. Thus word art can serve a dual purpose, efficiently communicating a theme using shape, and accurately communicating meaning using text.
AN ANALYSIS OF THE CONTRIBUTION OF BENCHMARKING TO THE PERFORMANCE OF COMMUNITY BASED ORGANIZATIONS IN KISUMU CITY , KENYA

There is concurrence in organizations’ development conversation that benchmarking is important in community development. In the face of economic, climate, health and food crises, benchmarking an organization with other organizations to design and implement strategies that minimize the impact of events remain relevant for sustaining progress. The study was set to analyze the contribution of benchmarking to the performance of Community Based Organizations in Kisumu City, Kenya. The study made use of correlation design and targeted 1202 respondents from 16 active Community Based Organizations in Kisumu City. The sample size obtained through Fisher’s model was 291 respondents. Stratified sampling method was used to reach out to the respondents. Structured questionnaire tested for validity and reliability was made use of in data collection. The results revealed a statistically significant strong positive correlation coefficient (R = .657; p<.05) between benchmarking and performance. Benchmarking had a statistically significant contribution to the performance of Community Based Organizations (F (1,289) = 219.343; p< . 05) attributing 43.1% variance. For every one standard deviation increase in benchmarking performance increased by . 657 units. In conclusion, benchmarking made a statistically significant contribution to the performance of Community Based Organizations. The study recommends: intensified practice of benchmarking in organizations with a view to enhancing performance; and identifying other benchmarking operational strategies that can be used in organizations with a view to improving performance.
Improving Stack LSTMs by Combining Syllables and Morphemes for Korean Dependency Parsing

Stack LSTM기반 의존 파싱은 전이 기반 파싱에서 스택과 버퍼의 내용을 Stack LSTM으로 인코딩하여 이들을 조합하여 파서 상태 벡터(parser state representation)를 유도해 낸후 다음 전이 액션을 결정하는 방식이다. Stack LSTM기반 의존 파싱에서는 버퍼 초기화를 위해 단어 표상 (word representation) 방식 이 중요한데, 한국어와 같이 형태적으로 복잡한 언어 (morphologically rich language)의 경우에는 무수히 많은 단어가 파생될 수 있어 이들 언어에 대해 단어 임베딩 벡터를 직접적으로 얻는 방식에는 한계가 있 다. 본 논문에서는 Stack LSTM 을 한국어 의존 파싱에 적용하기 위해 음절-태그과 형태소의 표상들을 결 합 (hybrid)하여 단어 표상을 얻어내는 합성 방법을 제안한다. Sejong 테스트셋에서 실험 결과, 제안 단어 표상 방법은 음절-태그 및 형태소를 이용한 방법을 더욱 개선시켜 UAS 93.65% (Rigid평가셋에서는 90.44%)의 우수한 성능을 보여주었다.
MODEL ADAPTATION FOR STATISTICAL MACHINE TRANSLATION

Statistical machine translation (SMT) systems use statistical learning methods to learn how to translate from large amounts of parallel training data. Unfortunately, SMT systems are tuned to the domain of the training data and need to be adapted before they can be used to translate data in a different domain. First, we consider a semi-supervised technique to perform model adaptation. We explore new feature extraction techniques, feature combinations and their effects on performance. In addition, we introduce an unsupervised variant of Minimum Error Rate Training (MERT), which can be used to tune the SMT model parameters. We do this by using another SMT model that translates in the reverse direction. We apply this variant of MERT to the model adaptation task. Both of the techniques we explore in this thesis produce promising results in exhaustive experiments we performed for translation from French to English in different domains.
Datalog Engine Input Program Intensional Database ( Analysis ) Extensional Database ( Relations ) Extractor Query Result Datalog Interpreter Parser Semantic Checker Intensional Database Extensional Database Semi-Naive Evaluation Query Result C + + Executable Datalog Compiler Parser Semantic Checker 

SOUFFLÉ is an open source programming framework that performs static program analysis expressed in Datalog on very large code bases, including points-to analysis on OpenJDK7 (1.4M program variables, 350K objects, 160K methods) in under a minute. SOUFFLÉ is being successfully used for Java security analyses at Oracle Labs due to (1) its high-performance, (2) support for rapid program analysis development, and (3) customizability. SOUFFLÉ incorporates the highly flexible Datalog-based program analysis paradigm while exhibiting performance results that are on-par with manually developed state-of-the-art tools. In this tool paper, we introduce the SOUFFLÉ architecture, usage and demonstrate its applicability for large-scale code analysis on the OpenJDK7 library as a use case.
Malignant Chondroid Syringoma of Axilla : A rare entity at a rare site

The Chondroid Syringoma (CS) are rare mixed tumours of the skin, benign or malignant, arising from the eccrine sweat glands due to the differentiation of the pleuripotent stem cells of the epithelial and mesenchymal tissues. [1,2] The incidence of CS is very rare accounting to just <0.098% amongst the primary cutaneous tumors. We present a case of recurrent malignant CS arising from the sweat glands of left axilla. This rare case stands as a testimony to the importance of immunohistochemistry in establishing the diagnosis of such rare entities. We have tried to explore the role of clinicians is identifying such rare cases as well as various treatment modalities being used to provide the patient with disease free survival along with good quality of life.
Effects of elevated temperature and fluorine pollution on relations between the pedunculate oak ( Quercus robur ) and oak powdery mildew

Effects of elevated temperature and soil pollution with fluorine on host-pathogen relations were studied in seedlings of the pedunculate oak (Quercus robur L.) inoculated with oak powdery mildew (Microsphaera alphitoides Griff. et Maubl.) and control seedlings. The plants were grown for 1 month in elevated temperature (on average by 1.6°C) and soil pollution with sodium fluoride (330 ppm F). The above factors did not have any significant effect on nitrogen content of leaves or on concentrations of metabolites favourable to growth and development of the fungal pathogen (total non-structural carbohydrates, including soluble carbohydrates and starch) and those unfavourable to fungi (soluble phenols, condensed tannins and lignins). The elevated temperature and fluorine pollution did not affect the leaf infection rate. However, a significant temperature × pollution interaction was observed in inoculated seedlings. At the elevated temperature, fluorine caused a less severe infection by powdery mildew. This could be due to a direct toxic effect of fluorine on the pathogen or by an indirect influence, resulting from changes in levels of other metabolites, which were not analysed in this study. The inoculation of oak seedlings with powdery mildew caused a decline in the carbohydrate content of leaves but did not have any significant effect on levels of other analysed metabolites. However, it significantly affected the distribution of phenols and lignins in oak leaves. Those compounds accumulated within necrotic lesions and in adjacent cells. Our results do not enable drawing definite conclusions on effects of a slight rise in temperature and a relatively low level of fluorine pollution of the soil on relations between the pedunculate oak and oak powdery mildew. Lower values of the leaf infection rate in seedlings growing in elevated temperature and fluorine pollution suggest that in warmer years a lower level of infection by M. alphitoides may be expected in areas affected by fluorine pollution. Additional key words: environmental pollution, phenols, tannins, lignins, carbohydrates, starch, nitrogen. Addresses: 1University of Warmia and Mazury, Faculty of Biology, Department of Genetics, Pl. Łódzki 3, PL 10-727 Olsztyn, jgrzebyta@gazeta.pl 2Institute of Dendrology, Parkowa 5, PL 62-035 Kórnik, pkarolew@man.poznan. pl 2005, vol. 53, 27–33 28 Jacek Grzebyta et al.
Exploring optical switching in subwavelength hole arrays

Fabrication of an ultrafast all-optical switch is one of the challenges in modern optics. In order not to limit the speed of data transfer with an electronic switching element, it is necessary to eliminate conversion of an optical signal to an electrical signal. Optically nonlinear materials, materials that have a strongly intensity-dependent refractive index, are the most likely candidates to make an all-optical switch. A change in refractive index alone is not enough to make a good all-optical switch. It must be possible to block and unblock the signal with this change in refractive index. To do so, we here present an experiment in which a nonlinear material is used as a substrate for a metallic subwavelength hole array. The transmission spectra through such an array shows sharp, wavelength-dependent features. Furthermore, the transmission is much higher than expected based on the open fraction of the array, for certain wavelengths. The combination of the strong resonances of the array and the enhanced fields on the interface between the array and the nonlinear material should yield strong switching behaviour. The location and shape of the features in the transmission spectrum of a metallic subwavelength hole array depend on the refractive index of the dielectric materials the array is in contact with. By exploiting the spectral features and the effects of a change in refractive index of the nonlinear substrate, we attempt to demonstrate the suitability of this system for building an all-optical switch.
Sector-Level Frictions and Aggregate Productivity

This paper examines the extent to which sector-level frictions affect aggregate productivity. I show that a broad range of sector-level frictions can be summarized as an implication of sector-level taxes on factor inputs. I introduce and analyze a simple multisector model with sector-specific taxes on factor inputs; based on this model, I define allocational efficiency indexes, which measure how the distribution of frictions affects aggregate productivity. I construct these indexes using sector-level data and find that the productivity gap caused by the sector-level frictions is large and explains a sizable amount of the differences in aggregate productivity across developed countries. JEL Codes: E23, O11, O41, O47 ∗Graduate School of Economics, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. Email: shuhei aoki@mail.goo. ne.jp, tel: +81-3-3812-5658. The old version of this paper is titled “A Simple Accounting Framework for Frictions on Sectoral Resource Allocation,” and was presented at the 2006 Fall JEA meeting. I thank Toni Braun and Fumio Hayashi for their guidance, and Minoru Kitahara, Julen Esteban-Pretel, Katsuya Takii, and Kyoji Fukao for their helpful comments and suggestions. All remaining errors are mine.
CHAPTER 2 Korteweg – de Vries equation : solitons and undular bores

The Korteweg–de Vries (KdV) equation is a fundamental mathematical model for the description of weakly nonlinear long wave propagation in dispersive media. It is known to possess a number of families of exact analytic solutions. Two of them – solitons and nonlinear periodic travelling waves – are of particular interest from the viewpoint of fluid dynamics applications as they occur as typical asymptotic outcomes in a broad class of initial/boundary-value problems. Two different major approaches have been developed in the last four decades to deal with the problems involving solitons and nonlinear periodic waves: inverse scattering transform and the Whitham method of slow modulations. We review these methods and show the relations between them. Emphasis is made on solving the KdV equation with largescale initial data. In this case, the longtime evolution leads to the formation of an expanding undular bore, a modulated travelling wave connecting two different nonoscillating flows. Another problem considered is the propagation of a solitary wave through a variable environment in the framework of the variable-coefficient KdV equation. If the background environment varies slowly, the solitary wave deforms adiabatically and an extended small-amplitude trailing shelf is generated ensuring the conservation of mass. On a long time scale, the trailing shelf evolves, via an intermediate stage of an undular bore, into a secondary soliton train.
NEIGHBOUR SIMILARITY TRUST AGAINST SYBIL TACKS IN P 2 P E-COMMERCE

Open-access distributed systems such as peer-to-peer systems are particularly vulnerable to sybil attacks, where a malicious user creates multiple fake identities (called sybil nodes). Without a trusted central authority that can tie identities to real human beings, defending against sybil attacks is quite challenging. Among the small number of decentralized approaches, our recent SybilGuard protocol leverages a key insight on social networks to bound the number of sybil nodes accepted. Despite its promising direction, SybilGuard can allow a large number of sybil nodes to be accepted. Furthermore, SybilGuard assumes that social networks are fast-mixing, which has never been confirmed in the real world. This paper presents the novel SybilLimit protocol that leverages the same insight as SybilGuard, but offers dramatically improved and near-optimal guarantees. The number of sybil nodes in our experiments for a million-node system. We further prove that SybilLimit’s guarantee is a most a factor away from optimal when considering approaches based on fast-mixing social networks. Finally, based on three large-scale real-world social networks, we provide the first evidence that real-world social networks are indeed fast-mixing. This validates the fundamental assumption behind SybilLimit’s and SybilGuard’s approach.
Chapter 2 Modeling and Analysis of Gene Regulatory Networks

In many ways, a living cell can be compared to a complex factory animated by molecular nanomachines, mainly proteins complexes. Hence it is easy to conceive that the expression of proteins, which are cellular effectors, cannot be constant. On the contrary, it is highly dependent on the general context; environmental conditions (pH, temperature, oxygenation, nutrient availability), developmental stage of an organism (fetal spectrum of proteins differ from adult proteins in mammals), response to a stress (UV irradiation, presence of a chemical toxic, osmotic pressure alteration) and even diseases (cancer, attack of a pathogen) are examples of contextual changes in the level of protein expression. In order to understand this cellular state plasticity, a simplified view of this machinery, following general transfers of information according to the central dogma of molecular biology, is the sequence of events: (1) stimulation via a signaling pathway (e.g. presence of an environmental stimulation, followed by internal transduction of the signal), (2) effective stimulation of a transcription factor, (3) activation of the transcription of a particular gene, (4) production of messenger RNA (mRNA) (see Fig. 2.1), (5) translation of mRNA, i.e. production of a functional
Depth recovery from a single defocused image based on depth locally consistency

Demand to depth estimation from a single image is emerging in more and more multimedia applications, such as human-computer interaction, 3D video generation and representation. In this paper, we manage to solve this challenging problem by using the defocused cues contained in the image. Our algorithm is based on depth local consistency assumption that the scene in input image can be modeled as multiple planar surfaces, and each over-segmented patch corresponds to a small p lanar surface in the 3D scene. As a result, a graph-based algorithm is firstly applied to obtain an over-segmentation result of the input image. Based on the sharp edge prior, the blur amounts on the boundaries of segmentations are calculated according to the edge width at the corresponding locations. Then, the blur amounts of the unknown regions are interpolated from the boundary regions using a plane fitting method. In the next, an image guided filtering method is applied to refine the obtained blur map. To eliminate the affect of the tiny textures, an L0 gradient minimization algorithm is applied to the input image to preserving the prominent boundaries, and the resulting image is served as the guided image. At last, based on a simple geometry prior of photograph, a binary graph cut algorithm is adopted to eliminate the ambiguity in the depth map over the focal plane. The performance of our algorithm is evaluated by various test images. The results demonstrate our algorithm produces high quality depth maps, outperforming state of the art.
Ozone pollution during stratosphere-troposphere exchange events over equatorial Africa

Both natural factors such as thunderstorm events and anthropogenic activities contribute to very high ozone production. On the flight route from Johannesburg to Vienna enhanced ozone and relative humidity spikes were observed by MOZAIC (Measurements of Ozone by Airbus In service airCraft). MOZAIC recorded high resolution in-situ ozone and relative humidity at a flying altitude of 250-200 hPa at equatorial Africa. This area is one of the lightning hot spot regions of the world. We report introduction of enhanced ozone of stratospheric origin into the troposphere during two events and the resulting pollution. Vertical cross-section of potential vorticity over the region of interest showed high PV intrusion below the tropopause level. Both OLR (Outgoing longwave radiation) and vertical wind have indicated presence of strong convection. Cloud water content transport and high latent heat have confirmed the existence of thunderstorm activity coupled to PV intrusion. The two distinct events are characterized by very low ozone within the thunderstorm cloud and very high ozone of stratospheric origin outside the thunderstorm cloud. The events have produced ambient air pollution