Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Characterization of the Extracellular Polysaccharide from Vibrio cholerae O1 El-Tor

The ability to form biofilms is important for environmental survival, transmission, and infectivity of Vibrio cholerae, the causative agent of cholera in humans. To form biofilms, V. cholerae produces an extracellular matrix composed of proteins, nucleic acids and a glycoconjugate, termed Vibrio exopolysaccharide (VPS). Here, we present the data on isolation and characterization of the polysaccharide part of the VPS (VPS-PS), which has the following structure: where α-D-Glc is partially (∼20%) replaced with α-D-GlcNAc. α-GulNAcAGly is an amide between 2-acetamido-2-deoxy-α-guluronic acid and glycine. Apparently, the polysaccharide is bound to a yet unidentified component, which gives it high viscosity and completely suppresses any NMR signals belonging to the sugar chains of the VPS. The only reliable method to remove this component at present is a treatment of the whole glycoconjugate with concentrated hydrochloric acid.
Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data

Repurposing FDA-approved drugs with the aid of gene signatures of disease can accelerate the development of new therapeutics. A major challenge to developing reliable drug predictions is heterogeneity. Different gene signatures of the same disease or drug treatment often show poor overlap across studies, as a consequence of both biological and technical variability, and this can affect the quality and reproducibility of computational drug predictions. Existing algorithms for signature-based drug repurposing use only individual signatures as input. But for many diseases, there are dozens of signatures in the public domain. Methods that exploit all available transcriptional knowledge on a disease should produce improved drug predictions. Here, we adapt an established meta-analysis framework to address the problem of drug repurposing using an ensemble of disease signatures. Our computational pipeline takes as input a collection of disease signatures, and outputs a list of drugs predicted to consistently reverse pathological gene changes. We apply our method to conduct the largest and most systematic repurposing study on lung cancer transcriptomes, using 21 signatures. We show that scaling up transcriptional knowledge significantly increases the reproducibility of top drug hits, from 44% to 78%. We extensively characterize drug hits in silico, demonstrating that they slow growth significantly in nine lung cancer cell lines from the NCI-60 collection, and identify CALM1 and PLA2G4A as promising drug targets for lung cancer. Our meta-analysis pipeline is general, and applicable to any disease context; it can be applied to improve the results of signature-based drug repurposing by leveraging the large number of disease signatures in the public domain.
Throughput of Cellular Systems with Conferencing Mobiles and Cooperative Base Stations

This paper considers an enhancement to multicell processing for the uplink of a cellular system, whereby the mobile stations are allowed to exchange messages on orthogonal channels of fixed capacity (conferencing). Both conferencing among mobile stations in different cells and in the same cell (inter- and intracell conferencing, resp.) are studied. For both cases, it is shown that a rate-splitting transmission strategy, where part of the message is exchanged on the conferencing channels and then transmitted cooperatively to the base stations, is capacity achieving for sufficiently large conferencing capacity. In case of intercell conferencing, this strategy performs convolutional pre-equalization of the signal encoding the common messages in the spatial domain, where the number of taps of the finite-impulse response equalizer depends on the number of conferencing rounds. Analysis in the low signal-to-noise ratio regime and numerical results validate the advantages of conferencing as a complementary technology to multicell processing.
Abnormal sterols in cholesterol-deficiency diseases cause secretory granule malformation and decreased membrane curvature

Cholesterol is an abundant lipid in eukaryotic membranes, implicated in numerous structural and functional capacities. Here, we have investigated the mechanism by which cholesterol affects secretory granule biogenesis in vivo using Dhcr7-/- and Sc5d-/- mouse models of the human diseases, Smith-Lemli-Opitz syndrome (SLOS) and lathosterolosis. These homozygous-recessive multiple-malformation disorders are characterized by the functional absence of one of the last two enzymes in the cholesterol biosynthetic pathway, resulting in the accumulation of precursors. Cholesterol-deficient mice exhibit a significant decrease in the numbers of secretory granules in the pancreas, pituitary and adrenal glands. Moreover, there was an increase in morphologically aberrant granules in the exocrine pancreas of Dhcr7-/- acinar cells. Regulated secretory pathway function was also severely diminished in these cells, but could be restored with exogenous cholesterol. Sterol precursors incorporated in artificial membranes resulted in decreased bending rigidity and intrinsic curvature compared with cholesterol, thus providing a cholesterol-mediated mechanism for normal granule budding, and an explanation for granule malformation in SLOS and lathosterolosis.
A Message-Passing Paradigm for Resource Allocation

We propose a message-passing paradigm for resource allocation problems. This is a framework for decentralized management that generalizes price-based systems by allowing incentives to vary across activities and consumption levels. Message-based incentives are defined through a new equilibrium concept. We demonstrate that message-based incentives lead to systemoptimal behavior for convex resource allocation problems, yet yield allocations superior to those from price-based incentives for non-convex resource allocation problems. We describe a distributed and asynchronous algorithm for computing equilibrium messages and allocations, and demonstrate this in the context of a network resource allocation problem.
DbDHunter: An ensemble-based anomaly detection approach to detect drive-by download attacks

Drive-by download attacks, typically implemented in JavaScript, are among the most common attack vectors in recent years. To confront these attacks, several anomaly detection techniques have been proposed. The techniques are able to detect previously unseen drive-by download attacks, but they often produce many false alarms that make them difficult to use in practice. In this paper, we address this problem by presenting DbDHunter, a novel ensemble-based anomaly detection approach to detect drive-by download attacks. It is motivated by the observation that the detection performance of an ensemble that is composed of multiple base classifiers tends to be better than any of them. DbDHunter constructs an initial ensemble of one-class classifiers and applies a binary particle swarm optimization algorithm, called SwarmSnips, on the ensemble to find a near-optimal sub-ensemble for classifying web pages as benign or malicious. To combine the outputs of one-class classifiers in the sub-ensemble, DbDHunter uses a specific ordered weighted averaging operator, called the SIOWA operator. The results of our experiments performed on a dataset of benign and malicious web pages show that DbDHunter can achieve about 96.3% detection rate, 1.8% false alarm rate, and 97% accuracy.
Mining quad closure patterns in Instagram

Quad Closure is a group of four people who are connected with each other. In this paper, we propose a new group recognition method for Instagram which are based on triadic closure method to determine groups on dynamic social networks (e.g likes and comments) between users as named Quad Closure. Social networks are not easily classified because of their complexity. We study how an open quad closure becomes close quad and the possibility of finding this process. There are a wide variety of factors having effects on this process. These factors include users' background information like active using time piece, photos tag frequency and sentimental analyze on comments. We try to create a unique model to predict formation of quad closure with all these factors and we share our experimental results on data taken from Instagram and show the success of our method on quad closure patterns.
Automatic generation of SPL structurally valid products: An approach based on progressive composition of partial configurations

Software product line is a recent discipline in software engineering. It mainly intends to rationalize the process of developing highly similar systems by a strategic and planned software reuse beforehand. One major contribution of this paradigm is the introduction of feature diagram allowing the management of the variability. It provides a framework for modeling reusable components and ensures their appropriate incorporation. This is a graphical tree-like notation that shows the hierarchical organization of features and specify theirs dependencies. With a large number of features, the generation of all valid products is extremely difficult. In fact, the wide variability defined leads to combinatorial explosion of the number of possible combinations. So, exhaustive testing is rarely feasible in practice. To remedy this problem, we propose in this paper an automatic tool allowing the avoidance of the search space exploration. It proceeds by a progressive construction of partial configurations. From the elementary features, the idea is to gradually build larger combinations until obtaining the desired products. This treatment is based principally on an ascending exploration of the feature diagram. The proposed techniques are set up based on the graph transformations approach and the developed grammars are implemented using AToM3 environment. An illustrative example is presented.
Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association

The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
Lambda-renormalized Einstein-Schrodinger theory with spin-0 and spin-1/2 sources

The Einstein-Schrodinger theory is extended to include spin-0 and spin-1/2 sources, and the theory is derived from a Lagrangian density which allows other fields to be easily added. The original theory is also modified by including a cosmological constant caused by zero-point fluctuations. This cosmological constant which multiplies the symmetric metric is assumed to be nearly cancelled by Schrodinger's ``bare'' cosmological constant which multiplies the nonsymmetric fundamental tensor, such that the total ``physical'' cosmological matches measurement. We show that the resulting Lambda-renormalized Einstein-Schrodinger theory closely approximates ordinary Einstein-Maxwell theory and one-particle quantum mechanics. In particular, the field equations match the ordinary Einstein and Maxwell equations except for additional terms which are $<10^{-16}$ of the usual terms for worst-case field strengths and rates-of-change accessible to measurement. We also show that the theory predicts the exact Lorentz force equation and the exact Klein-Gordon and Dirac equations. And the theory becomes exactly Einstein-Maxwell theory and one-particle quantum mechanics in the limit as the cosmological constant from zero-point fluctuations goes to infinity. Lastly, we discuss the merits of our Lagrangian density compared to the Einstein-Maxwell Lagrangian density.
When are two heads better than one? Visual perception and information transfer affect vigilance coordination in foraging groups

Animals frequently raise their heads to check for danger. In a group, individuals generally raise their heads independently. Earlier models suggest that all group members could gain by coordinating their vigilance, i.e., each member raising its head when others are not. We re-examine these suggestions, considering groups of different sizes, in light of empirical findings that: (1) animals can sometimes detect a predator without raising their heads, and (2) when one member of a group detects a predator, the information does not always spread to other members of the group. Including these effects in models generally decreases the value of coordinated vigilance. Coordinated vigilance is highly favored only when animals have a low probability of detecting predators without lifting their heads but a high probability of being warned when another member of the group detects a predator. For other combinations, coordinated vigilance has little value and may have a negative value. Group size has contrasting effects depending on how social information is obtained. Coordination is favored in smaller groups when one or more detecting individuals provide a constant amount of information to individuals unaware of the predator. On the other hand, coordination is favored in larger groups if each detecting individual provides unaware individuals with an independent source of information (i.e., if the amount of information increases as the number of detecting individuals increases). These results depend on the balance of an escape due to social information and dilution of risk in groups with imperfect information spread. This framework could be tested by examining species with different visual fields and in different environments. Copyright 2004.
Race/skin color differentials in potential years of life lost due to external causes.

OBJECTIVE Deaths by external causes represent one of the most important challenges for public health and are the second cause of death in Brazil. The aim of this study was to analyze differentials in mortality by external causes according to race/skin color. METHODS A descriptive study was carried out in Salvador, Northeastern Brazil, using 9,626 cases of deaths by external causes between 1998 and 2003. Data were obtained from the Forensic Medicine Institute and from Instituto Brasileiro de Geografia e Estatística (Brazilian Institute of Geography and Statistics). The indicator 'potential years of life lost' was utilized to identify the existence of differences among age groups, sex groups and race/skin color groups. RESULTS Deaths by external causes provoked the loss of 339,220 potential years of life, of which 210,000 were due to homicides. Nonwhite individuals died at earlier ages and lost 12.2 times as much potential years of life due to deaths by homicidies than white individuals. Although the nonwhite (black and mixed) population was three times larger than the white population, its number of potential years of life lost was 30 times higher. The population of blacks was 11.4 % smaller than the white population, but its loss of potential years of life was almost three times higher. Even after the adjustment for age, the differences observed in the indicator potential years of life lost/100,000 inhabitants and in the ratios between strata according to race/skin color were maintained. CONCLUSIONS The results showed differentials in mortality by external causes according to race/skin color in Salvador. The nonwhite population had greater loss of potential years of life, higher average number of years not lived and, on average, they died at an earlier age due to homicides, traffic accidents an all other external causes.
PENGARUH RELIGIUSITAS DAN ETHICAL CLIMATE TERHADAP ETHICAL BEHAVIOR

Tujuan dari penelitian ini adalah untuk mengukur pengaruh religiusitas dan ethical climate terhadap ethical behavior. Metode penelitian ini adalah kuantitatif. Populasi penelitian adalah mahasiswa internasional Master dan Ph.D pada Graduate School of Business Othman Yeop Abdullah Universiti Utara Malaysia. Teknik pengambilan sampel menggunakan non-probability sampling dengan teknik pemilihan sampel adalah accidental sampling . Ada 31 responden yang mengisi kuesioner. Hasil penelitian menunjukkan secara sendiri-sendiri ( parsial ) bahwa religiusitas memiliki pengaruh yang positif tidak signifikan terhadap perilaku etis. Ethical climate memiliki pengaruh yang positif dan signifikan terhadap perilaku etis. Sementara secara bersama-sama ( simultan ) religiusitas dan ethical climate memiliki pengaruh yang positif dan signifikan terhadap perilaku etis.
Size and Weight of Shortest Path Trees with Exponential Link Weights

We derive the distribution of the number of links and the average weight for the shortest path tree (SPT) rooted at an arbitrary node to $m$ uniformly chosen nodes in the complete graph of size $N$ with i.i. d. exponential link weights. We rely on the fact that the full shortest path tree to all destinations (ie, $m=N-1$) is a uniform recursive tree to derive a recursion for the generating function of the number of links of the SPT, and solve this recursion exactly. The explicit form of the generating function allows us to compute the expectation and variance of the size of the subtree for all $m$. We also obtain exact expressions for the average weight of the subtree.
TGFβ Signaling in Myeloid Cells Regulates Mammary Carcinoma Cell Invasion through Fibroblast Interactions

Metastasis is the most devastating aspect of cancer, however we know very little about the mechanisms of local invasion, the earliest step of metastasis. During tumor growth CD11b+Gr1+ cells, known also as MDSCs, have been shown to promote tumor progression by a wide spectrum of effects that suppress the anti-tumor immune response. In addition to immunosuppression, CD11b+Gr1+ cells promote metastasis by mechanisms that are currently unknown. CD11b+Gr1+ cells localize near fibroblasts, which remodel the ECM and leave tracks for collective cell migration of carcinoma cells. In this study we discovered that CD11b+Gr1+ cells promote invasion of mammary carcinoma cells by increasing fibroblast migration. This effect was directed by secreted factors derived from CD11b+Gr1+ cells. We have identified several CD11b+Gr1+ cell secreted proteins that activate fibroblast migration, including CXCL11, CXCL15, FGF2, IGF-I, IL1Ra, Resistin, and Shh. The combination of CXCL11 and FGF2 had the strongest effect on fibroblast migration that is associated with Akt1 and ERK1/2 phosphorylation. Analysis of subsets of CD11b+Gr1+ cells identified that CD11b+Ly6ChighLy6Glow cells increase fibroblast migration more than other myeloid cell populations. Additionally, tumor-derived CD11b+Gr1+ cells promote fibroblast migration more than splenic CD11b+Gr1+ cells of tumor-bearing mice. While TGFβ signaling in fibroblasts does not regulate their migration toward CD11b+Gr1+ cells, however deletion of TGFβ receptor II on CD11b+Gr1+ cells downregulates CXCL11, Shh, IGF1 and FGF2 resulting in reduced fibroblast migration. These studies show that TGFβ signaling in CD11b+Gr1+ cells promotes fibroblast directed carcinoma invasion and suggests that perivascular CD11b+Ly6ChighLy6Glow cells may be the stimulus for localized invasion leading to metastasis.
Multiresolution Sinusoidal Speech Model Using Elliptic Band Pass Filter

The sinusoidal speech model represents a speech signal as a linear combination of sinusoids with time-varying parameters {amplitudes, frequencies, and phases}. However, one drawback of this model is that the analysis window width is generally fixed in analyzing the signal. Since each sinusoidal parameter has different frequencies, an analysis window with fixed width can’t guarantee an optimum spectral resolution to each sinusoidal parameter. In this paper, we propose and implement a multiresolution sinusoidal speech model using elliptic band pass filter to overcome this drawback and to estimate the sinusoidal parameters more precisely. Experimental results have shown that the proposed model can achieve better performance than that of the classical sinusoidal model.
Nitrogen transformations in boreal forest soils in response to extreme manipulation treatments

providing me these excellent working facilities and the support of Metla. I want to thank my supervisor Docent Aino Smolander for her endless support and encouragement. As for the past few years I was engaged with an another project, I think I could not have completed this work without having such a good supervisor! I also value the fun field trips we shared. To the "extended soil group" I am grateful for the friendly atmosphere and for all the help. Doctors Taina and Outi – my idols in the process of becoming one myself-I consider myself extremely lucky for having friends like you. you for the great moments we have shared both in and out of work. Special thanks to Tuula for constructive comments on my texts and Hannu for organizing those fun boat trips. Veikko, I really appreciate your skills in analytical chemistry, without you there would be no terpenes in this work. Thank you to Pirkko and Hillevi for taking care of the paperwork, Anne, Leena and Sari for drawing excellent figures (and for not getting annoyed with me continuously changing them), Marja for help in statistics and Maarit M. for help in the laboratory. I also appreciate very much the help from the people in Keskuslaboratorio, especially the numerous FIA measurements done by Marja-Leena and Pirkko H. Aino for the very fruitful cooperation. My special thanks to Heljä-Sisko for skillfully coordinating this project and for the nice field trips, to Antti-Jussi for constant help with problems related to deposition and leaching and to Joonas for revising the language of this thesis. Warm thanks to Heikki Heino and Leo Aspholm from the Hämeenlinna Waterworks and Risto Reijonen from the Finnish Groundwater Techniques for the possibility to conduct research on Ahvenisto esker infiltration site and for the pleasant cooperation. I also appreciate very much the help in the fieldwork by the personnel of the Hämeenlinna Waterworks. The "ViVa"-project was funded by the Waterworks of the cities of Hämeenlinna, Jyväskylä, Mikkeli, the Tampere-Valkeakoski area, the Turku area and the Tuusula area, which are all acknowledged. and Tuula for the helpful atmosphere and for the coffee breaks full of laughter. My special thanks to my new supervisor Jarkko Hantula – you must be one of the most understanding person on earth. I also have very fond memories of the adventure in Scotland with Eeva, Jarkko and Michael. I want to thank …