Miracle-dz/UniFAR-FTUs huggingface dataset:
Happy Birthday! A trend analysis on past MSR papers

On the occasion of the 10th anniversary of the MSR conference, it is a worthwhile exercise to meditate on the past, present and future of our research discipline. Indeed, since the MSR community has experienced a big influx of researchers bringing in new ideas, state-of-the art technology and contemporary research methods it is unclear what the future might bring. In this paper, we report on a text mining exercise applied on the complete corpus of MSR papers to reflect on where we come from; where we are now; and where we should be going. We address issues like the trendy (and outdated) research topics; the frequently (and less frequently) cited cases; the popular (and emerging) mining infrastructure; and finally the proclaimed actionable information which we are deemed to uncover.
Adaptive and self-configurable honeypots

Honeypot evangelists propagate the message that honeypots are particularly useful for learning from attackers. However, by looking at current honeypots, most of them are statically configured and managed, which requires a priori knowledge about attackers. In this paper we propose a high-interaction honeypot capable of learning from attackers and capable of dynamically changing its behavior using a variant of reinforcement learning. It can strategically block the execution of programs, lure the attacker by substituting programs and insult attackers with the intent of revealing the attacker's nature and ethnic background. We also investigated the fact that attackers could learn to defeat the honeypot and discovered that attacker and honeypot interests sometimes diverge.
Densification arising from sampling fixed graphs

During the past decade, a number of different studies have identified several peculiar properties of networks that arise from a diverse universe, ranging from social to computer networks. A recently observed feature is known as network densification, which occurs when the number of edges grows much faster than the number of nodes, as the network evolves over time. This surprising phenomenon has been empirically validated in a variety of networks that emerge in the real world and mathematical models have been recently proposed to explain it. Leveraging on how real data is usually gathered and used, we propose a new model called Edge Sampling to explain how densification can arise. Our model is innovative, as we consider a fixed underlying graph and a process that discovers this graph by probabilistically sampling its edges. We show that this model possesses several interesting features, in particular, that edges and nodes discovered can exhibit densification. Moreover, when the node degree of the fixed underlying graph follows a heavy-tailed distribution, we show that the Edge Sampling model can yield power law densification, establishing an approximate relationship between the degree exponent and the densification exponent. The theoretical findings are supported by numerical evaluations of the model. Finally, we apply our model to real network data to evaluate its performance on capturing the previously observed densification. Our results indicate that edge sampling is indeed a plausible alternative explanation for the densification phenomenon that has been recently observed.
ENVIRONMENTAL CONCERN: CONCEPTUAL DEFINITIONS, MEASUREMENT METHODS, AND RESEARCH FINDINGS

A serious threat to human beings and their environment is the continuous and accelerating overuse and destruction of natural resources. Bearing this in mind, it is unfortunate that efforts to permanently change people's environmentally destructive behaviour through interventions has typically not been met with success. A necessary condition may be an increase in environmental concern and knowledge about the effects and consequences of the ongoing environmental deterioration for future generations. Studies are reviewed that have attempted to show (1) correlations between determinants, such as socio-demographic and/or psychological factors, and environmental concern, and (2) an impact of environmental concern on environmentally responsible behaviour. In general, correlations with background factors are weak. Factors affecting behaviour appear to be knowledge, internal locus of control (positive control beliefs), personal responsibility, and perceived threats to personal health. The need for further research that attempts to specify the process leading to environmentally responsible behaviour is highlighted. A new framework is presented which integrates some of the previous research.
Hypothermia augments NF-kappaB activity and the production of IL-12 and IFN-gamma.

BACKGROUND The differentiation of Th1 and Th2 is strictly regulated by humoral and cellular factors. The imbalance between Th1 and Th2 is considered to be the pathogenesis of allergic and autoimmune disorders. It is important to elucidate the effect of environmental factors, such as temperature, on the expression of cytokines of Th1 and Th2. METHODS We investigated the expression of IFN-gamma, IL-4, IL-5, IL-10 and IL-12 from LPS- or PHA-stimulated PBMCs at 30 degrees C or 37 degrees C using ELISA and Real-time PCR. We measured the change of NF-kappaB activity at 30 degrees C or 37 degrees C with LPS stimulation using the reporter gene assay. RESULTS IFN-gamma production from LPS-stimulated PBMCs at 30 degrees C was up-regulated compared with 37 degrees C. IL-5 and IL-10 production from PHA-stimulated PBMCs at 30 degrees C were down-regulated compared with 37 degrees C. This augmented IFN-gamma production was caused by the up-regulation of IL-12 production from CD14+ blood monocytes. Both IL-12 mRNA and IL12 protein at 30 degrees C were up-regulated compared with 37 degrees C. NF-kappaB, the key molecule for the expression of IL-12, was also augmented at 30 degrees C compared with 37 degrees C. CONCLUSIONS Hypothermia up-regulated the expression of IL-12 and IFN-gamma due to the augmented NF-kappaB activity. It is suggested that hypothermia modifies the pattern of cytokine gene expression.
Access Selection with Anticipatory Vertical Handover for Multi-Access Networks

This paper presents the study of the access selection (AS) problem in a multi-access wireless network. The contributions of this paper could be classified in two groups. Firstly, we extend previous investigations in terms of performance results, regarding a system-level dynamic evaluation. Performance indicators like coverage, SNR, rate and offered traffic load are included as algorithm criteria. An AS algorithm based on theoretical throughput estimation is also evaluated. Secondly, we propose a sub-optimum access selection solution, in which the arriving user as well as a few ongoing users are (re)assigned according to the new systems' conditions, following the specific optimization criterion. This solution selects candidate users to a vertical handover and anticipates the user context transfer. The approaches presented here assume a generic system modeling and user throughput characteristics as performance indicator. Our simulation campaigns could demonstrate that the access selection with anticipatory vertical handover provides gains about 300% in the 10th percentile of the user session throughput
IsocraticSeparationof ATP and Its DegradationProductsfrom BiologicalFluidsby Automated LiquidChromatography KimK

Two groups of metabolites (a) IMP, AMP, ADP, ATP, and CAMP in extracts of fibroblastsand erythrocytes and (b) hypoxanthine,xanthine, adenosine, and Inosine in plasma and wine have been separated by ion-pairing reversedphase chromatographyon a Bondapak C18 column, with use of the following reagents: 60 mmol/L KH2PO4, 0.45 mmol/Ltetrabutylammoniumphosphate,and 1.26 mol/Lacetonitrile,pH 3.2 (at 23 #{176}C) (groupa) and 20 mmol/LKH2P04, 0.45 mmol/Ltetrabutylammoniumphosphate,and 0.35 mol/L acetonitrile,pH 2.70 (at 24 #{176}C) (groupb). Under bothsets of conditions,the compoundsare completelyseparatedin <15 mm. The separation is isocratic, so the method is easily adaptable to automation.
Cerebello-Cortical Differences in Effective Connectivity of the Dominant and Non-dominant Hand during a Visuomotor Paradigm of Grip Force Control

Structural and functional differences are known to exist within the cortical sensorimotor networks with respect to the dominant vs. non-dominant hand. Similarly, the cerebellum, a key structure in the sensorimotor network with its cerebello-cortical connections, has been reported to respond differently when using the dominant vs. non-dominant hand. Several groups have already investigated causal interactions during diverse motor paradigms using effective connectivity but few have studied the larger visuomotor network, including key structures such as the parietal cortex and the cerebellum, with both hands. Moreover, the effect of force level on such interactions is still unclear. We therefore sought to determine the hemispheric asymmetries in the cerebello-cortical sensorimotor network in right-handers at two force levels (5% and 10% maximum voluntary contraction) for both hands. Cerebello-cortical modulations were investigated in 28 healthy, right-handed volunteers by determining the effective connectivity during a visuomotor task at two force levels under fMRI. A network was built consisting of the left and right primary motor (M1), ventral premotor (PMv) and posterior parietal cortices (PPC), in addition to the supplementary motor area (SMA), and the ipsilateral cerebellum (Cer) to the hand performing the motor task. Task performance (precision of isometric grip force tracking) did not differ between hands, nor did task-related activations in the sensorimotor areas apart from the contralateral primary motor cortex. However, during visuomotor control of the non-dominant hand, connectivity analysis revealed causal modulations between (i) the ipsilateral cerebellum and SMA, and (ii) the ipsilatearl cerebellum and contralateral PPC, which was not the case when using the dominant hand. These cerebello-cortical modulations for the non-dominant hand were more present at the higher of the two force levels. We conclude that precision force generation executed with the non-dominant hand, compared to the dominant hand, may require enhanced cerebello-cortical interaction to ensure equivalent left-right task performance.
The SALAMI protein structure search server

Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh. uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page lists the related proteins, details of the sequence and structure similarity and implied sequence alignments. Via a simple structure viewer, one can view superpositions of query and library structures and finally download superimposed coordinates. The alignment method is very tolerant of large gaps and insertions, and tends to produce slightly longer alignments than other similar programs.
Enhanced T-Cell Expression of RANK Ligand in Acute Coronary Syndrome: Possible Role in Plaque Destabilization

Objective—Based on its role in inflammation and matrix degradation, we hypothesized a role for osteoprotegerin (OPG), RANK, and RANK ligand (RANKL) in coronary artery disease. Methods and Results—We examined the expression of various members of the OPG/RANKL/RANK axis in patients with stable and unstable angina and in the atherosclerotic lesions of apolipoprotein E–deficient (apoE−/−) mice. Our findings were: (1) Serum levels of OPG were raised in patients with unstable angina (n=40), but not in those with stable angina (n=40), comparing controls (n=20); (2) mRNA levels of RANKL were increased in T-cells in unstable angina patients accompanied by increased expression of RANK in monocytes; (3) strong immunostaining of OPG/RANKL/RANK was seen within thrombus material obtained at the site of plaque rupture during acute myocardial infarction; (4) OPG/RANKL/RANK was expressed in the atherosclerotic plaques of apoE−/− mice, with RANKL located specifically to the plaques; and (5) RANKL enhanced the release of monocyte chemoattractant peptide-1 in mononuclear cells from unstable angina patients, and promoted matrix metalloproteinase (MMP) activity in vascular smooth muscle cells. Conclusions—We show enhanced expression of the OPG/RANKL/RANK system both in clinical and experimental atherosclerosis, with enhanced T-cell expression of RANKL as an important feature of unstable disease.
A gender- and sexual orientation-dependent spatial attentional effect of invisible images

Human observers are constantly bombarded with a vast amount of information. Selective attention helps us to quickly process what is important while ignoring the irrelevant. In this study, we demonstrate that information that has not entered observers' consciousness, such as interocularly suppressed (invisible) erotic pictures, can direct the distribution of spatial attention. Furthermore, invisible erotic information can either attract or repel observers' spatial attention depending on their gender and sexual orientation. While unaware of the suppressed pictures, heterosexual males' attention was attracted to invisible female nudes, heterosexual females' attention was attracted to invisible male nudes, gay males behaved similarly to heterosexual females, and gay/bisexual females performed in-between heterosexual males and females.
Quinolinic acid modulates the activity of src family kinases in rat striatum: in vivo and in vitro studies

Quinolinic acid (QA) has been shown to evoke neurotoxic events via NMDA receptor (NMDAR) overactivation and oxidative stress. NMDARs are particularly vulnerable to free radicals, which can modulate protein tyrosine kinase (PTK) and phosphotyrosine phosphatase (PTP) activities. The src family of tyrosine kinases are associated with the NMDAR complex and regulate NMDA channel function. Because QA is an NMDAR agonist as well as a pro‐oxidant agent, we investigated whether it may affect the activity of PTKs and PTPs in vivo and in vitro. In synaptosomes prepared from striata dissected 15 min, 30 min or 15 days after bilateral injection of QA we observed modulation of the phosphotyrosine pattern; a significant decrease in PTP activity; and a sustained increase in c‐src and lyn activity at 15 and 30 min after treatment with QA, followed by a decrease 2 weeks later. Striatal synaptosomes treated in vitro with QA showed time‐ and dose‐dependent modulation of c‐src and lyn kinase activities. Moreover, the nitric oxide synthase inhibitor NG‐nitro‐l‐arginine‐methyl ester, the NMDAR antagonist d‐2‐amino‐5‐phosphonovaleric acid and pyruvate suppressed the QA‐induced modulation of c‐src activity. These findings suggest a novel feature of QA in regulating src kinase activity through the formation of reactive radical species and/or NMDAR overactivation.
A comprehensive survey of mutations in the OPA1 gene in patients with autosomal dominant optic atrophy.

PURPOSE To characterize the spectrum of mutations in the OPA1 gene in a large international panel of patients with autosomal dominant optic atrophy (adOA), to improve understanding of the range of functional deficits attributable to sequence variants in this gene, and to assess any genotype-phenotype correlations. METHODS All 28 coding exons of OPA1, intron-exon splice sites, 273 bp 5' to exon 1, and two intronic regions with putative function were screened in 94 apparently unrelated white patients of European origin with adOA by single-strand conformational polymorphism (SSCP)-heteroduplex analysis and direct sequencing. Clinical data were collated, and putative mutations were tested for segregation in the respective families by SSCP analysis or direct sequencing and in 100 control chromosomes. Further characterization of selected splice site mutations was performed by RT-PCR of patient leukocyte RNA. Staining of mitochondria in leukocytes of patients and control subjects was undertaken to assess gross differences in morphology and cellular distribution. RESULTS Twenty different mutations were detected, of which 14 were novel disease mutations (missense, nonsense, deletion-frameshift, and splice site alterations) and six were known mutations. Mutations were found in 44 (47%) of the 94 families included in the study. Ten new polymorphisms in the OPA1 gene were also identified. Mutations occur throughout the gene, with three clusters emerging: in the mitochondrial leader, in the highly conserved guanosine triphosphate (GTP)-binding domain, and in the -COOH terminus. Examination of leukocyte mitochondria from two unrelated patients with splice site mutations in OPA1 revealed no abnormalities of morphology or cellular distribution when compared with control individuals. CONCLUSIONS This study describes 14 novel mutations in the OPA1 gene in patients with adOA, bringing the total number so far reported to 54. It is likely that many cases of adOA are due to mutations outside the coding region of OPA1 or to large-scale rearrangements. Evaluation of the mutation spectrum indicates more than one pathophysiological mechanism for adOA. Preliminary data suggests that phenotype-genotype correlation is complex, implying a role for other genetic modifying or environmental factors. No evidence was found of pathologic changes in leukocyte mitochondria of patients with adOA.
Decision forest for multivariate time series analysis

Nowadays with time series accounting for an increasingly large fraction of world's supply of data, there has been an explosion of interest in mining time series data. This paper proposes a multivariate time series classification model which is both effective in classifier's accuracy and comprehensibility. It is composed of two stages: a supervised clustering for pattern extraction and soft discretization decision forest. In supervised clustering, some real time series instances from the training dataset will be selected as class dedicated patterns. While in decision forest, the rule induction helps to improve the knowledge acquisition of the classifier. In addition, soft discretization would further improve the accuracy and comprehensibility of the classifier.
Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

Background Transmitted HIV-1 drug resistance can compromise initial antiretroviral therapy (ART); therefore, its detection is important for patient management. The absence of drug-associated selection pressure in treatment-naïve persons can cause drug-resistant viruses to decline to levels undetectable by conventional bulk sequencing (minority drug-resistant variants). We used sensitive and simple tests to investigate evidence of transmitted drug resistance in antiretroviral drug-naïve persons and assess the clinical implications of minority drug-resistant variants. Methods and Findings We performed a cross-sectional analysis of transmitted HIV-1 drug resistance and a case-control study of the impact of minority drug resistance on treatment response. For the cross-sectional analysis, we examined viral RNA from newly diagnosed ART-naïve persons in the US and Canada who had no detectable (wild type, n = 205) or one or more resistance-related mutations (n = 303) by conventional sequencing. Eight validated real-time PCR-based assays were used to test for minority drug resistance mutations (protease L90M and reverse transcriptase M41L, K70R, K103N, Y181C, M184V, and T215F/Y) above naturally occurring frequencies. The sensitive real-time PCR testing identified one to three minority drug resistance mutation(s) in 34/205 (17%) newly diagnosed persons who had wild-type virus by conventional genotyping; four (2%) individuals had mutations associated with resistance to two drug classes. Among 30/303 (10%) samples with bulk genotype resistance mutations we found at least one minority variant with a different drug resistance mutation. For the case-control study, we assessed the impact of three treatment-relevant drug resistance mutations at baseline from a separate group of 316 previously ART-naïve persons with no evidence of drug resistance on bulk genotype testing who were placed on efavirenz-based regimens. We found that 7/95 (7%) persons who experienced virologic failure had minority drug resistance mutations at baseline; however, minority resistance was found in only 2/221 (0.9%) treatment successes (Fisher exact test, p = 0.0038). Conclusions These data suggest that a considerable proportion of transmitted HIV-1 drug resistance is undetected by conventional genotyping and that minority mutations can have clinical consequences. With no treatment history to help guide therapies for drug-naïve persons, the findings suggest an important role for sensitive baseline drug resistance testing.
A Methodological Approach to Eliciting Affective Educational Recommendations

The emotional situation of the learner can influence the learning process. For this reason, we are researching how educational recommender systems can take advantage of affective computing to improve the recommendation support in educational scenarios. The paper reports works carried out involving 18 educators and 77 learners to elicit and design emotional feedback to be provided for learners in terms of personalized recommendations. To this end, user centered design methods and data mining techniques are used.
A Fast and Lightweight System for Multilingual Dependency Parsing

We present a multilingual dependency parser with a bidirectional-LSTM (BiLSTM) feature extractor and a multi-layer perceptron (MLP) classifier. We trained our transition-based projective parser in UD version 2.0 datasets without any additional data. The parser is fast, lightweight and effective on big treebanks. In the CoNLL 2017 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies, the official results show that the macro-averaged LAS F1 score of our system Mengest is 61.33%.
Adaptive Beamforming Based Inband Fronthaul for Cost-Effective Virtual Small Cell in 5G Networks

In order to exploit the potential capacity of 5G, the deployment of ultra-dense small cells is an approach that can dramatically increase the radio resource reuse factor and network capacity. However, network densification with a large number of small cells brings challenges due to increased network complexity, deployment cost and inter-cell interference. In this paper, a new 5G architecture with virtual small cells (VSCs), which are dynamically formed by grouping a number of user devices in close proximity and adapted according to traffic condition, is proposed to improve the cost and energy efficiency compared with the traditional fixed deployment of small cells. In each virtual small cell, one mobile device is selected as a cell head (CH) to aggregate intra- cell traffic using unlicensed band transmissions and then communicates with its macro-cell base station in a licensed band through beamformed transmission, which reduces the inter-cell interference and improves spectrum efficiency. In this paper, a highly directional beamforming technique is employed to enable a dedicated inband fronthaul link for VSC. Our work focuses on how to design adaptive beamforming to minimize the transmit power under throughput requirements and power constraints. Both the mathematical analysis and simulation results demonstrate that VSCs can increase power efficiency dramatically while providing flexibility and reduced cellular load, when compared with macrocell only deployment and traditional fixed small cells scenario.