Miracle-dz/UniFAR-FTUs huggingface dataset:
Kernel functions based on triplet similarity comparisons

We propose two ways of defining a kernel function on a data set when the only available information about the data set are similarity triplets of the form "Object A is more similar to object B than to object C". Studying machine learning and data mining problems based on such restricted information has become very popular in recent years since it can easily be provided by humans via crowd sourcing. While previous approaches try to construct a low-dimensional Euclidean embedding of the data set that reflects the given similarity triplets, we aim at defining meaningful kernel functions on the data set that correspond to high-dimensional embeddings. These kernel functions can subsequently be used to apply all the standard kernel methods to solve tasks such as clustering, classification or principal component analysis on the data set.
Function of JARID2 in bovines during early embryonic development

Histone lysine modifications are important epigenetic modifications in early embryonic development. JARID2, which is a member of the jumonji demethylase protein family, is a regulator of early embryonic development and can regulate mouse development and embryonic stem cell (ESC) differentiation by modifying histone lysines. JARID2 can affect early embryonic development by regulating the methylation level of H3K27me3, which is closely related to normal early embryonic development. To investigate the expression pattern of JARID2 and the effect of JARID2-induced H3K27 methylation in bovine oocytes and early embryonic stages, JARID2 mRNA expression and localization were detected in bovine oocytes and early embryos via qRT-PCR and immunofluorescence in the present study. The results showed that JARID2 is highly expressed in the germinal vesicle (GV), MII, 2-cell, 4-cell, 8-cell, 16-cell and blastocyst stages, but the relative expression level of JARID2 in bovine GV oocytes is significantly lower than that at other oocyte/embryonic stages (p < 0.05), and JARID2 is expressed primarily in the nucleus. We next detected the mRNA expression levels of embryonic development-related genes (OCT4, SOX2 and c-myc) after JARID2 knockdown through JARID2-2830-siRNA microinjection to investigate the molecularpathwayunderlying the regulation of H3K27me3 by JARID2 during early embryonic development. The results showed that the relative expression levels of these genes in 2-cell embryos weresignificantly higher than those in the blastocyst stage, and expression levels were significantly increased after JARID2 knockdown. In summary, the present study identified the expression pattern of JARID2 in bovine oocytes and at each early embryonic stage, and the results suggest that JARID2 plays a key role in early embryonic development by regulating the expression of OCT4, SOX2 and c-myc via modification of H3K27me3 expression. This work provides new data for improvements in the efficiency of in vitro embryo culture as well as a theoretical basis for further studying the regulatory mechanisms involved in early embryonic development.
Opportunities for computer abuse : assessing a crime specific approach in the case of Barings Bank

Within the field of IS security little has been written on the subject of criminal opportunity. More precisely, little has been written on what exactly constitutes an opportunity, and the relationship between employees, who may might act as potential offenders, and the IS context in which such opportunities may be afforded. The purpose of this study is to assess the feasibility of a model known as the 'crime specific opportunity structure', which, as the name suggests maps out those elements which are thought to form an opportunity. Drawing on a number of criminological theories, the model considers the role of potential offenders in a work place setting by viewing them as rational decision-makers, who assess their environment, and possible opportunities, in cost-benefit terms. Furthermore, the model takes a crime-specific approach as each type of crime is made up of a unique mix of elements. Ignoring the idiosyncratic nature of specific crimes severely reduces an understanding of each type of crime, and further hinders effective prevention programmes. An ethnographic account of the collapse of a financial institution is used to assess the feasibility of the model.
Adiposity in relation to vitamin D status and parathyroid hormone levels: a population-based study in older men and women.

OBJECTIVE In small case-control studies, obesity was associated with worse vitamin D status. Our aim was to assess the association of adiposity (anthropometric measures as well as dual energy x-ray absorptiometry) with serum 25-hydroxyvitamin D (25-OH-D) and serum PTH levels in a large population-based study including older men and women. METHODS Subjects were participants of the Longitudinal Aging Study Amsterdam and were aged 65 yr and older. In 453 participants, serum 25-OH-D and PTH were determined, and body mass index, waist circumference, waist to hip ratio, sum of skin folds, and total body fat percentage by dual energy x-ray absorptiometry were measured. RESULTS After adjustment for potential confounders, higher body mass index, waist circumference, and sum of skin folds were statistically significantly associated with lower 25-OH-D (standardized beta values were -0.136, -0.137, and -0.140, respectively; all P < 0.05) and with higher PTH (0.166, 0.113, and 0.114, respectively; all P < 0.05). Total body fat percentage was more strongly associated with 25-OH-D and PTH (-0.261 and 0.287, respectively; both P < 0.001) compared with anthropometric measures. Total body fat percentage remained associated with 25-OH-D after adjustment for PTH, and with PTH after adjustment for 25-OH-D. CONCLUSION Precisely measured total body fat is inversely associated with 25-OH-D levels and is positively associated with PTH levels. The associations were weaker if anthropometric measures were used, indicating a specific role of adipose tissue. Regardless of the possible underlying mechanisms, it may be relevant to take adiposity into account when assessing vitamin D requirements.
Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project

Abstract The advent of next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome data. However, these new approaches may present some errors and bias due to alignment, genotype calling, and imputation methods. Despite these flaws, data obtained by next-generation sequencing can be valuable for population and evolutionary studies of specific genes, such as genes related to how pigmentation evolved among populations, one of the main topics in human evolutionary biology. Melanocortin-1 receptor (MC1R) is one of the most studied genes involved in pigmentation variation. As MC1R has already been suggested to affect melanogenesis and increase risk of developing melanoma, it constitutes one of the best models to understand how natural selection acts on pigmentation. Here we employed a locally developed pipeline to obtain genotype and haplotype data for MC1R from the raw sequencing data provided by the 1000 Genomes FTP site. We also compared such genotype data to Phase 3 VCF to evaluate its quality and discover any polymorphic sites that may have been overlooked. In conclusion, either the VCF file or one of the presently described pipelines could be used to obtain reliable and accurate genotype calling from the 1000 Genomes Phase 3 data.
Using checklists to review static analysis warnings

Static analysis tools find silly mistakes, confusing code, bad practices and property violations. But software developers and organizations may or may not care about all these warnings, depending on how they impact code behavior and other factors. In the past, we have tried to identify important warnings by asking users to rate them as severe, low impact or not a bug. In this paper, we observe that the user's rating may be more complicated depending on whether the warning is feasible, changes code behavior, occurs in deployed code and other factors. To better model this, we ask users to review warnings using a checklist which enables more detailed reviews. We find that reviews are consistent across users and across checklist questions, though some users may disagree about whether to fix or filter out certain bug classes.
Motion Sickness Adaptation: A Neural Mismatch Model 1

Introduction In almost all susceptible individuals, continued exposure to a provocative motion stimulus leads to the diminution and eventual disappearance of established motion sickness reactions (see Reason & Brand 1975). This reduction in symptomatology takes place without any change in the nauseogenic stimulus; indeed, it is the absence of such variation that promotes its occurrence. These observations are clearly of considerable importance for elucidating the factors involved in the aetiology of motion sickness, as they demonstrate the existence of processes within the individual that are capable of counteracting the disturbing properties of the imposed motion without recourse to any external agency. It follows, therefore, that a better appreciation of how this vis medicatrix naturae operates must bring us closer to understanding how these curious and inappropriate reactions become established in the first place, since adaptation and provocation appear to be two sides of the same coin. The theoretical arguments presented here are directed toward answering two basic questions concerning the aetiology of motion sickness. First, what is the essential nature of the provocative stimulus? How do we explain the occurrence of motion sickness over such a wide range of apparently diverse circumstances? What, for example, do the conditions that elicit space sickness have in common with those that induce seasickness, airsickness, car sickness, camel sickness, swing sickness, simulator sickness, and so on? This question is dealt with briefly as a necessary prelude to the main concern of this paper, namely: what are the mechanisms underlying the acquisition of protective adaptation, and ofits sequel mal de debarquement ? The principal research findings relating to the efTects and after-effects of protective adaptation are summarized, and a neural mismatch model is described which attempts to account for these data.
Growth, fatty acid profile in major lipid classes and lipid fluidity of Aurantiochytrium mangroveiSK-02 As a function of growth temperature

Aurantiochytrium mangrovei Sk-02 was grown in a medium containing glucose (40 g/l), yeast extract (10 g/L) and sea salts (15 g/L) at temperatures ranging from 12 to 35°C. The fastest growth (µmax= 0.15 h-1) and highest fatty acid content of 415 mg/g-dry cell weight were found in the cells grown at 30°C. However, the cells grown at 12°C showed the highest percentage of polyunsaturated fatty acid (PUFA) (48.6% of total fatty acid). The percentage of docosahexaenoic acid (DHA) and pentadecanoic acid (C15:0) decreased with an increase in the growth temperature, whereas, palmitic acid (C16:0), stearic acid (C18:0) and DPA (C22:5n6) increased with an increase in the growth temperature. The composition of the major lipid class (%w/w) was slightly affected by the growth temperature. The fluidity of the organelle membrane or intracellular lipid (by DPH measurement) decreased with an increase in the growth temperatures, while the plasma membrane fluidity (by TMA-DPH measurement) could still maintain its fluidity in a wide range of temperatures (15 - 37°C). Furthermore, the distribution of DHA was found to be higher (36 – 54%) in phospholipid (PL) as compared to neutral lipid (NL) (20 - 41%).
Let the market drive deployment: a strategy for transitioning to BGP security

With a cryptographic root-of-trust for Internet routing(RPKI [17]) on the horizon, we can finally start planning the deployment of one of the secure interdomain routing protocols proposed over a decade ago (Secure BGP [22], secure origin BGP [37]). However, if experience with IPv6 is any indicator, this will be no easy task. Security concerns alone seem unlikely to provide sufficient local incentive to drive the deployment process forward. Worse yet, the security benefits provided by the S*BGP protocols do not even kick in until a large number of ASes have deployed them. Instead, we appeal to ISPs' interest in increasing revenue-generating traffic. We propose a strategy that governments and industry groups can use to harness ISPs' local business objectives and drive global S*BGP deployment. We evaluate our deployment strategy using theoretical analysis and large-scale simulations on empirical data. Our results give evidence that the market dynamics created by our proposal can transition the majority of the Internet to S*BGP.
Graph Connectivities, Network Coding, and Expander Graphs

We present a new algebraic formulation to compute edge connectivities in a directed graph, using the ideas developed in network coding. This reduces the problem of computing edge connectivities to solving systems of linear equations, thus allowing us to use tools in linear algebra to design new algorithms. Using the algebraic formulation we obtain faster algorithms for computing single source edge connectivities and all pairs edge connectivities, in some settings the amortized time to compute the edge connectivity for one pair is sub linear. Through this connection, we have also found an interesting use of expanders and super concentrators to design fast algorithms for some graph connectivity problems.
Pulmonary hypertension in cystic fibrosis with advanced lung disease.

RATIONALE The impact of pulmonary hypertension (PH) on survival in cystic fibrosis (CF) remains unclear. OBJECTIVES To determine the influence of PH on survival in the CF population. METHODS The United Network for Organ Sharing database was queried from 1987 to 2013 to identify first-time lung transplant candidates who were tracked from wait list entry date until death or censoring to determine influence of PH. Using right heart catheterization measurements, mild PH was defined as mean pulmonary artery pressure greater than or equal to 25 mm Hg and severe greater than or equal to 35 mm Hg. MEASUREMENTS AND MAIN RESULTS Of 2,781 CF patients, 2,100 were used for univariate analysis, 764 for Kaplan-Meier survival function, 687 for multivariate Cox models, and 576 and 132 for matching on the propensity of mild PH and severe PH, respectively. Univariate Cox analysis found significant differences in survival for mild PH (hazard ratio [HR], 1.747; 95% confidence interval [CI], 1.387-2.201; P < 0.001) and severe PH (HR, 2.299; 95% CI, 1.639-3.225; P < 0.001). Further assessment by multivariate Cox models identified significant risk for death associated with mild PH (HR, 1.757; 95% CI, 1.367-2.258; P < 0.001) and severe PH (HR, 2.284; 95% CI, 1.596-3.268; P < 0.001). Cox regression stratified on matched pairs of PH cases and control subjects confirmed the risk for death for mild PH (HR, 1.919; 95% CI, 1.290-2.85; P = 0.001) and severe PH (HR, 4.167; 95% CI, 1.709-10.157; P = 0.002). CONCLUSIONS The manifestation of PH is associated with significantly increased risk for death in CF patients with advanced lung disease.
Predicting the occurrence of acute hypotensive episodes: The PhysioNet Challenge

The PhysioNet Challenge 2009 addresses the prediction of acute hypotensive episodes (AHEs), which are serious clinical events since they could result in multiple organ failure and eventually in death. This objective is pursued with two different events: a) event 1: the separation of records with critical AHE (subgroup H1) in the forecast window (FW), the one-hour period immediately following a specified time T0, from records from patients with no documented AHEs at any time during their hospital stay (subgroup C1) and b) event 2: the separation of records with an AHE in the FW (group H) from records without any AHE in the FW (group C). Both events have been approached, using a subset of information common to the whole dataset, through the extraction of significant features from the last hours before T0 of the ABP and HR time series, linearly interpolated in the empty intervals and processed with a median filter for suppressing most artifacts. Decision tree classifiers based on these features have been designed for event 1 and 2, having better performances than classifiers based on support vector machine. The H1/C1 classifier (event 1) correctly classified all cases of the learning set (15 H1, 15 C1) producing also a perfect score on test set A. The H/C classifier (event 2) correctly classified 91.67% of the cases in the training set (30 H, 30 C) and obtained a score of 75% on test set B.
Design strategy of on-chip inductors for highly integrated RF systems

This paper describes a physical model for spiral inductors on silicon which is suitable for circuit simulation and layout optimization. Key issues related to inductor modeling such as skin effect and silicon substrate loss are discussed. An effective ground shield is devised to reduce substrate loss and noise coupling. A practical design methodology based on the trade-off between the series resistance and oxide capacitance of an inductor is presented. This method is applied to optimize inductors in state-of-the-art processes with multilevel interconnects. The impact of interconnect scaling, copper metallization and low-K dielectric on the achievable inductor quality factor is studied.
Identifying Patients with Poststroke Mild Cognitive Impairment by Pattern Recognition of Working Memory Load-Related ERP

The early detection of subjects with probable cognitive deficits is crucial for effective appliance of treatment strategies. This paper explored a methodology used to discriminate between evoked related potential signals of stroke patients and their matched control subjects in a visual working memory paradigm. The proposed algorithm, which combined independent component analysis and orthogonal empirical mode decomposition, was applied to extract independent sources. Four types of target stimulus features including P300 peak latency, P300 peak amplitude, root mean square, and theta frequency band power were chosen. Evolutionary multiple kernel support vector machine (EMK-SVM) based on genetic programming was investigated to classify stroke patients and healthy controls. Based on 5-fold cross-validation runs, EMK-SVM provided better classification performance compared with other state-of-the-art algorithms. Comparing stroke patients with healthy controls using the proposed algorithm, we achieved the maximum classification accuracies of 91.76% and 82.23% for 0-back and 1-back tasks, respectively. Overall, the experimental results showed that the proposed method was effective. The approach in this study may eventually lead to a reliable tool for identifying suitable brain impairment candidates and assessing cognitive function.
Exploring the Usage of Topic Modeling for Android Malware Static Analysis

The rapid growth in smartphone and tablet usage over the last years has led to the inevitable rise in targeting of these devices by cyber-criminals. The exponential growth of Android devices, and the buoyant and largely unregulated Android app market, produced a sharp rise in malware targeting that platform. Furthermore, malware writers have been developing detection-evasion techniques which rapidly make anti-malware technologies ineffective. It is hence advisable that security expert are provided with tools which can aid them in the analysis of existing and new Android malware. In this paper, we explore the use of topic modeling as a technique which can assist experts to analyse malware applications in order to discover their characteristic. We apply Latend Dirichlet Allocation (LDA) to mobile applications represented as opcode sequences, hence considering a topic as a discrete distribution of opcode. Our experiments on a dataset of 900 malware applications of different families show that the information provided by topic modeling may help in better understanding malware characteristics and similarities.
Interactive Occlusion and Automatic Object Placement for Augmented Reality

We present several techniques for producing two visual and modeling effects in augmented reality. The first effect involves interactively calculating the occlusions between real and virtual objects. The second effect utilizes a collision detection algorithm to automatically move dynamic virtual objects until they come in contact with static real objects in augmented reality. All of the techniques utilize calibrated data derived from images of a real‐world environment.
Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships

Abstract A new scleractinian coral species, Pachyseris inattesa sp. n. , is described from the Red Sea. Despite a superficial resemblance with some species in the agariciid genus Leptoseris with which it has been previously confused, P. inattesa sp. n. has micro-morphological characters typical of the genus Pachyseris. This genus, once part of the Agariciidae, is comprised of five extant species and is widely distributed throughout the tropical Indo-Pacific. It is currently incertae sedis as a result of recent molecular analysis and appears to be closely related to the Euphylliidae. A molecular phylogenetic reconstruction including P. inattesa sp. n. , the genus type species P. rugosa, and P. speciosa, all present in the Red Sea, was performed using the mitochondrial intergenic spacer between COI and 16S-rRNA. The results confirm that P. inattesa sp. n. is a monophyletic lineage closely related to the other Pachyseris species examined.
Changes in Brain Adenosine during Bicuculline‐Induced Seizures in Rats: Effects of Hypoxia and Altered Systemic Blood Pressure

We analyzed brain tissue in 139 rats for adenosine and its metabolites, inosine and hypoxanthine, during the initial 120 seconds of seizures induced by bicuculline. We also measured ATP, ADP, AMP, phosphocreatine (PCr), and lactate. We divided the rats into four groups by adjustment of their preictal arterial oxygen tension: group I, PaO2> 200 mm Hg), adenosine increased within ten seconds of the onset seizures and remained elevated even after 120 seconds. Elevations in inosine and hypoxanthine were delayed compared to the increases in adenosine. A reduction PaO2(50 mm Hg) or systemic blood pressure during seizures caused a further augmentation in the increase brain adenosine levels. During the seizure period, transient changes in adenine nucleotides and energy charge were observed, but PCr remained de-pressed and lactate continued to rise. The rapid sustained increase in cerebral adenosine levels, temporally paralleling the changes in cerebral blood flow, supports role for adenosine the regulation of cerebral blood flow. CircRes 47: 568-577, 1980
Learning of generalized manipulation strategies in the context of Programming by Demonstration

In Programming by Demonstration, abstract manipulation knowledge has to be learned, that can be used by an autonomous robot system in different environments with arbitrary obstacles. In this work, manipulation strategies are learned by observation of a human teacher and represented as a flexible, constraint-based representation of the search space for motion planning. The learned manipulation strategy contains a large set of automatically generated features, which are generalized using additional demonstrations of the teacher. The generalized manipulation strategy is executed on a real bimanual anthropomorphic robot system in different environments with arbitrary obstacles using constrained motion planning.