Miracle-dz/UniFAR-FTUs huggingface dataset:
Resolution reelle des systemes polynomiaux en dimension positive

Cette these traite de l'etude des solutions reelles des systemes polynomiaux en dimension positive. Plus precisement, il s'agit de determiner au moins un point par composante connexe sur une variete algebrique reelle, dans le cadre des methodes de points critiques. La premiere partie est consacree a des rappels concernant les outils algorithmiques utilises dans le document et l'etat de l'art en ce qui concerne la resolution reelle des systemes polynomiaux de dimension positive. Dans la deuxieme partie, un premier algorithme de resolution reelle est donne dans le cas des hypersurface. Cet algorithme n'effectue qu'une seule deformation infinitesimale dans le cas des hypersurfaces singulieres. Plusieurs outils de calculs efficaces pour les systemes zero-dimensionnels a coefficients infinitesimaux sont presentes. Dans le deuxieme chapitre, un algorithme sans deformation infinitesimale est donne pour trouver au moins un point par composante connexe sur une variete algebrique reelle definie par plusieurs equations polynomiales. Cet algorithme s'avere plus efficace que ses conccurents. Dans un troisieme temps, nous montrons comment en prenant en compte des informations sur la projection de la variete et en integrant l'etude d'ensembles constructibles dans le processus de resolution, les algorithmes precedents peuvent etre optimises. Enfin, nous montrons comment l'usage de ces algorithmes a permis de resoudre de maniere automatisee un cas du probleme d'interpolation de birkhoff qui restait ouvert.
Prediction of -association in hereditary non- breast carcinomas with array-CGH

Background While new defects in BRCA1 are still being found, it is unclear whether current breast cancer diagnostics misses many BRCA1-associated cases. A reliable test that is able to indicate the involvement of BRCA1 deficiency in cancer genesis could support decision making in genetic counselling and clinical management. To find BRCA1-specific markers and explore the effectiveness of the current diagnostic strategy, we designed a classification method, validated it and examined whether we could find BRCA1-like breast tumours in a group of patients initially diagnosed as non-BRCA1/2 mutation carriers. Methods A classifier was built based on array-CGH profiles of 18 BRCA1-related and 32 control breast tumours, and validated on independent sets of 16 BRCA1-related and 16 control breast carcinomas. Subsequently, we applied the classifier to 48 breast tumours of patients from Hereditary Breast and Ovarian Cancer (HBOC) families in whom no germ line BRCA1/BRCA2 mutations were identified. Results The classifier showed an accuracy of 91% when applied to the validation sets. In 48 non-BRCA1/2 patients, only two breast tumours presented a BRCA1-like CGH profile. Additional evidence for BRCA1 dysfunction was found in one of these tumours. Conclusion We here S. A. Joosse and E. H. van Beers are shared first authors. Johannes L. Peterse—deceased. Electronic supplementary material The online version of this article (doi:10.1007/s10549-008-0117-z) contains supplementary material, which is available to authorized users. S. A. Joosse E. H. van Beers H. Horlings Division of Experimental Therapy, The Netherlands Cancer Institute NKI/AvL, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands e-mail: s.joosse@nki.nl S. A. Joosse e-mail: s.joosse@nki.nl Present Address: E. H. van Beers Skyline-Diagnostics B.V, Rotterdam, The Netherlands I. H. G. Tielen J. L. Peterse F. B. L. Hogervorst P. M. Nederlof Department of Pathology, The Netherlands Cancer Institute NKI/AvL, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands N. Hoogerbrugge M. J. Ligtenberg Department of Human Genetics, Radboud University Nijmegen Medical Centre, P. O. Box 9101, 6500HB Nijmegen, The Netherlands M. J. Ligtenberg Department of Pathology, Radboud University Nijmegen Medical Centre, P. O. Box 9101, 6500HB Nijmegen, The Netherlands L. F. A. Wessels Department of Molecular Biology, The Netherlands Cancer Institute NKI/AvL, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands P. Axwijk S. Verhoef Family Cancer Clinic, The Netherlands Cancer Institute NKI/ AvL, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands P. M. Nederlof (&) Postbus 90203, 1006BE Amsterdam, The Netherlands e-mail: p.nederlof@nki.nl 123 Breast Cancer Res Treat (2009) 116:479–489 DOI 10.1007/s10549-008-0117-z
Oxidized low-density lipoprotein and 15-deoxy-Δ12,14-PGJ2 increase mitochondrial complex I activity in endothelial cells

Ceaser, Erin K. , Anup Ramachandran, Anna-Liisa Levonen, and Victor M. Darley-Usmar. Oxidized lowdensity lipoprotein and 15-deoxy-PGJ2 increase mitochondrial complex I activity in endothelial cells. Am J Physiol Heart Circ Physiol 285: H2298–H2308, 2003. First published July 24, 2003; 10.1152/ajpheart.00508. 2003. —Oxidized lipids are capable of initiating diverse cellular responses through both receptor-mediated mechanisms and direct posttranslational modification of proteins. Typically, exposure of cells to low concentrations of oxidized lipids induces cytoprotective pathways, whereas high concentrations result in apoptosis. Interestingly, mitochondria can contribute to processes that result in either cytoprotection or cell death. The role of antioxidant defenses such as glutathione in adaptation to stress has been established, but the potential interaction with mitochondrial function is unknown and is examined in this article. Human umbilical vein endothelial cells (HUVEC) were exposed to oxidized LDL (oxLDL) or the electrophilic cyclopentenone 15-deoxy-PGJ2 (15d-PGJ2). We demonstrate that complex I activity, but not citrate synthase or cytochrome-c oxidase, is significantly induced by oxLDL and 15d-PGJ2. The mechanism is not clear at present but is independent of the induction of GSH, peroxisome proliferator-activated receptor (PPAR), and PPAR. This response is dependent on the induction of oxidative stress in the cells because it can be prevented by nitric oxide, probucol, and the SOD mimetic manganese(III) tetrakis(4-benzoic acid) porphyrin chloride. This increased complex I activity appears to contribute to protection against apoptosis induced by 4-hydroxynonenal.
GROWING UP IN PORTUGAL : CAPE VERDEAN ANCESTRY CHILDREN EXHIBIT LOW OVERWEIGHT AND OBESITY COMPARED TO PORTUGUESE IN URBAN

Ana Andre (AA) and Ines Varela Silva (IVS) agreed on the conception and design of the study and AA prepared the first manuscript. AA collected data referent to 2013 database. AA produced all statistical analysis and interpretation of the data. IVS, Paula Griffiths, Cristina Padez and Vítor Rosado Marques contributed to all sections of the manuscript, checked procedures and all authors read and approved final manuscript.
The Role of Requirements in Open Source IT Innovation

The requirements process is a collection of activities in software engineering which purpose it is to define the functionality and properties of a future system-to-be, taking into account the environment and the problem domain. However simple as it may sound, it is a difficult undertaking, and it would seem that OS requirements are handled in a particular manner. Further, requirements can be seen as being intimately linked to IT innovation as representing attempts to create a certain vision of a future IT system. If open source organisations are as different to traditional ones as it is often claimed, then it is likely that requirements are handled differently and thus play a different role in influencing IT innovation. This essay thus proposes the study of the role of requirements in open source IT innovation.
clustering techniques to of

Microbialites are a product of trapping and binding of sediment by microbial communities, and are considered to be some of the most ancient records of life on Earth. It is a commonly held belief that microbialites are limited to extreme, hypersaline settings. However, more recent studies report their occurrence in a wider range of environments. 5 The goal of this study is to explore whether microbialite-bearing sites share common geochemical properties. We apply statistical techniques to distinguish any common traits in these environments. These techniques ultimately could be used to address questions of microbialite distribution: are microbialites restricted to environments with speciﬁc characteristics; or are they more broadly distributed? A dataset containing 10 hydrographic characteristics of several microbialite sites with data on pH, conductivity, alkalinity, and concentrations of several major anions and cations was constructed from previously published studies. In order to group the water samples by their natural similarities and di ﬀ erences, a clustering approach was chosen for analysis. k means clustering with partial distances was applied to the dataset with missing values, and 15 separated the data into two clusters. One of the clusters is formed by samples from atoll Kiritimati (central Paciﬁc Ocean), and the second cluster contains all other observations. Using these two clusters, the missing values were imputed by k nearest neighbor method, producing a complete dataset that can be used for further multivariate analysis. Salinity is not found to be an important variable deﬁning clustering, and 20 although pH deﬁnes clustering in this dataset, it is not an important variable for microbialite formation. Clustering and imputation procedures outlined here can be applied to an expanded dataset on microbialite characteristics in order to determine properties associated with microbialite-containing environments. eral outline of methods that could be applied to an expanded multivariate dataset with missing values. Also, di ﬀ erent imputation techniques could be applied and compared against the one presented here. These results indicate that, contrary to commonly held beliefs about microbialite formation, salinity and high pH are not important variables. It is clear that as long as the 5 conditions for carbonate precipitation are met, microbialites can form at a range of pH. Moving forward, the methods outlined in this study can be used to construct a larger dataset which compares these results to those from other microbialite-forming environments, and non-microbialite forming environments.
ELKS1 localizes the synaptic vesicle priming protein bMunc13-2 to a specific subset of active zones

hippocampal neurons, two different Munc13s—Munc13-1 and bMunc13-2—medi-ate opposite forms of presynaptic short-term plasticity and thus differentially affect neuronal network characteristics. We found that most presynapses of cortical and hippocampal neurons contain only Munc13-1, whereas ∼ 10% contain both Munc13-1 and bMunc13-2. Whereas the presynaptic recruitment and activation of Munc13-1 depends on Rab3-inter-acting proteins (RIMs), we demonstrate here that bMunc13-2 is recruited to synapses by the AZ protein ELKS1, but not ELKS2, and that this recruitment determines basal SV priming and short-term plasticity. Thus, synapse-specific interactions of different Munc13 isoforms with ELKS1 or RIMs are key determinants of the molecular and functional heterogeneity of presynaptic AZs.
Denoising of Images using Deep Convolutional Neural Networks (DCNN)

- We present an approach to low-level vision that combines two main ideas: the use of convolutional networks as an image processing architecture and an unsupervised learning procedure that synthesizes training samples from specific noise models. We demonstrate this approach on the challenging problem of natural image denoising. Using a test set with a hundred natural images, we find that convolutional networks provide comparable and in some cases superior performance to state of the art wavelet and Markov random field (MRF) methods. Moreover, we find that a convolutional network offers similar performance in the blind denoising setting as compared to other techniques in the non-blind setting. We also show how convolutional networks are mathematically related to MRF approaches by presenting a mean field theory for an MRF specially designed for image denoising. Although these approaches are related, convolutional networks avoid computational difficulties in MRF approaches that arise from probabilistic learning and inference. This makes it possible to learn image processing architectures that have a high degree of representational power, but whose computational expense is significantly less than that associated with inference in MRF approaches with even hundreds of parameters
A CHARACTERIZATION OF THE FINITE PROJECTIVE SYMPLECTIC GROUPS PSp4 (q)

In this paper we present a characterization of the projective symplectic groups PSp4 (q) in dimension 4 over finite fields of odd characteristic, in terms of the structure of the centralizer of an involution. The group PSp4 (q) is simple, of order \q\q2 + l)(q2 — I)2, with a Sylow 2-subgroup whose center has order 2, so that involutions which lie in the centers of Sylow 2-subgroups form a single conjugacy class (see §1). We shall prove the following result.
Ultrastructural and immunohistochemical characterization of the physiological and pathological inactivity of the equine endometrium

In mares, the winter anestrus extends in the northern hemisphere from the last ovulation in September/October until the first ovulation of the subsequent ovulatory season (March/April) (Ginther 1992). In general, during winter anestrus, the ovarian follicles are smaller than 20 mm in diameter, serum LH, estradiol and progesterone values are basal, whereas the FSH level is unchanged compared to the breeding season and the melatonin concentration is high (Ginther 1992). Numerous factors controlling the equine anestrus, as melatonin (Fitzgerald and Smith 1995), length of day light (Palmer and Guillaume 1992), opioids (Aurich et al. 1994) and others have been identified, though the mechanisms were not completely understood until now. One important fact is the wide range of indiviual variations regarding the clinical behaviour and the ovarian activity (Fitzgerald and Smith 1995). However, estrus activity occurs even during the anovulatory season in pregnant and in ovariectomized mares, possibly due to androgen synthesis by the adrenal glands (Ginther 1992). During the breeding season, anestrus behaviour may be the result of pregnancy, bad body condition, chromosomal abnormalities, persistent corpora lutea, or ovarian tumors (Allen 1977, Hughes and Stabenfeld 1977). Furthermore, endometrial inactivity at this time may be caused by ovarian H. Aupperle et al.
Complexity analysis and optimal algorithms for decentralized decision making

Coordination of distributed entities is required for problems arising in many areas, including multi-robot systems, networking applications, e-commerce applications, and the control of autonomous space vehicles. Because decisions must often be made without a global view of the system, coordination can be difficult. This dissertation focuses on the development of principled tools for solving problems of distributed decision making. As a formal framework for such problems, we use the decentralized partially observable Markov decision process (DEC-POMDP). This framework is very general, incorporating stochastic action effects, uncertainty about the system state, and limited communication. It has been adopted for use in the fields of control theory, operations research, and artificial intelligence. Despite this fact, a number of fundamental questions about the computational aspects of the model have gone unanswered. One contribution of this thesis is an analysis of the worst-case complexity of solving DEC-POMDPs. It was previously established that for a single agent, the finite-horizon version of the problem is PSPACE-complete. We show that the general problem is NEXP-complete, even if there are only two agents whose observations together determine the system state. This complexity result illustrates a fundamental difference between single agent and multiagent decision-making problems. In contrast to the single agent problem, the multiagent problem provably does not admit a polynomial-time algorithm. Furthermore, assuming that EXP and NEXP are distinct, the problem requires super-exponential time to solve in the worst case. A second contribution is an optimal policy iteration algorithm for solving DEC-POMDPs. Stochastic finite-state controllers are used to represent policies. A controller can include a correlation device, which allows agents to correlate their actions without communicating during execution. The algorithm alternates between expanding the controller and performing value-preserving transformations, which modify a controller without sacrificing value. We present two efficient value-preserving transformations, one which can reduce the size of the controller and another which can improve its value while keeping the size fixed. Our policy iteration algorithm serves as the first nontrivial exact algorithm for DEC-POMDPs.
Molecular and Functional Characterization of PEBP Genes in Barley Reveal the Diversification of Their Roles in Flowering

Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305–8602, Japan (R.K., H.K., H.H.); Institute of the Society for Techno-innovation of Agriculture, Forestry, and Fisheries, Tsukuba 305–0854, Japan (T.A.); Barley Research Subteam, National Institute of Crop Science, Tsukuba 305–8518, Japan (T.T.); and Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305–8572, Japan (H.H.)
Multiple pathways to avoid IFN-β sensitivity of HIV-1 by mutations in capsid

Multiple pathways to avoid IFN-β sensitivity of HIV-1 by mutations in capsid 1 2 3 Tahmina Sultana*, João I. Mamede, Akatsuki Saito, Hirotaka Ode, Kyotaro Nohata, 4 Romy Cohen*, Emi E. Nakayama, Yasumasa Iwatani , Masahiro Yamashita, Thomas J. 5 Hope‡, Tatsuo Shioda‡ 6 7 8 Research Institute for Microbial Diseases, Osaka University, Osaka, Japan 9 Department of Cell and Developmental Biology, Northwestern University, Chicago, Illinois, 10 USA 11 Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, 12 Japan 13 Aaron Diamond AIDS Research Center, New York, New York, USA 14 Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, 15 Japan 16 17 18 Tahmina Sultana, João I. Mamede, and Akatsuki Saito contributed equally to this work. 19 20 21 ‡Address correspondence to Thomas J. Hope (thope@northwestern.edu) or Tatsuo Shioda 22 (shioda@biken.osaka-u.ac.jp). 23 24 25 *Present address: Tahmina Sultana, Department of Cell and Developmental Biology, 26 Northwestern University, Chicago, Illinois, USA; Romy Cohen, VECT-HORUS SAS, Faculté 27 de Médecine, Marseille, France. 28 29 30 Running title: Multiple pathways to avoid IFN sensitivity of HIV-1 31 JVI Accepted Manuscript Posted Online 11 September 2019 J. Virol. doi:10.1128/JVI.00986-19 Copyright © 2019 Sultana et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Electroencephalogram Based Biomarkers for Detection of Alzheimer’s Disease

Alzheimer’s disease (AD) is an age-related progressive and neurodegenerative disorder, which is characterized by loss of memory and cognitive decline. It is the main cause of disability among older people. The rapid increase in the number of people living with AD and other forms of dementia due to the aging population rep-resents a major challenge to health and social care systems worldwide. Degeneration of brain cells due to AD starts many years before the clinical manifestations become clear. Early diagnosis of AD will contribute to the development of effective treatments that could slow, stop, or prevent significant cognitive decline. Consequently, early diagnosis of AD may also be valuable in detecting patients with dementia who have not obtained a formal early diagnosis, and this may provide them with a chance to access suitable healthcare facilities. An early diagnosis biomarker capable of measuring brain cell degeneration due to AD would be valuable. Potentially, electroencephalogram (EEG) can play a valuable role in the early diagnosis of AD. EEG is noninvasive and low cost, and provides valuable information about brain dynamics in AD. Thus, EEG-based biomarkers may be used as a first-line decision-support tool in AD diagnosis and could complement other AD biomarkers.
‐ Mining Applications for Analyzing Contractor ’ s Risk in

Contractors responsible for the whole execution of engineering, procurement, and con‐ struction (EPC) projects are exposed to multiple risks due to various unbalanced contracting meth‐ ods such as lump‐sum turn‐key and low‐bid selection. Although systematic risk management ap‐ proaches are required to prevent unexpected damage to the EPC contractors in practice, there were no comprehensive digital toolboxes for identifying and managing risk provisions for ITB and con‐ tract documents. This study describes two core modules, Critical Risk Check (CRC) and Term Fre‐ quency Analysis (TFA), developed as a digital EPC contract risk analysis tool for contractors, using artificial intelligence and text‐mining techniques. The CRC module automatically extracts risk‐in‐ volved clauses in the EPC ITB and contracts by the phrase‐matcher technique. A machine learning model was built in the TFA module for contractual risk extraction by using the named‐entity recog‐ nition (NER) method. The risk‐involved clauses collected for model development were converted into a database in JavaScript Object Notation (JSON) format, and the final results were saved in pickle format through the digital modules. In addition, optimization and reliability validation of these modules were performed through Proof of Concept (PoC) as a case study, and the modules were further developed to a cloud‐service platform for application. The pilot test results showed that risk clause extraction accuracy rates with the CRC module and the TFA module were about 92% and 88%, respectively, whereas the risk clause extraction accuracy rates manually by the engi‐ neers were about 70% and 86%, respectively. The time required for ITB analysis was significantly shorter with the digital modules than by the engineers.
Valorisation of wet residues of brewing processes using hydrothermal carbonization

1 Division of Bioprocess and Biomedical Engineering; Faculty of Chemistry; Wroclaw University of Science and Technology; Norwida 4/6, Wrocław 50-373, Poland 2 Department of Boilers, Combustion and Energy Systems; Faculty of Mechanical and Power Engineering; Wroclaw University of Science and Technology; Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland * corresponding author: mateusz.jackowski@pwr.edu. pl ; lukasz.niedzwiecki@pwr.edu. pl
Comparison of frontal alpha asymmetry among schizophrenia patients , 1 major depressive disorder patients , and healthy controls 2 3 4

Cognitive Science Research Group, Korea Brain Research Institute, Daegu, South Korea 6 Department of Psychiatry, College of Medicine, The Catholic University of Korea, Seoul, South 7 Korea 8 9 10 11 *Correspondence: 12 Jeong-Ho Chae, MD. Ph.D 13 Department of Psychiatry, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, 14 Seocho-gu, Seoul 137-701, South Korea 15 TEL: 82-2-2258-6083 16 FAX: 82-2-594-3870 17