Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectroscopic analysis of myoglobin and cytochrome c dynamics in isolated cardiomyocytes during hypoxia and reoxygenation

Raman microspectroscopy was applied to monitor the intracellular redox state of myoglobin and cytochrome c from isolated adult rat cardiomyocytes during hypoxia and reoxygenation. The nitrite reductase activity of myoglobin leads to the production of nitric oxide in cells under hypoxic conditions, which is linked to the inhibition of mitochondrial respiration. In this work, the subsequent reoxygenation of cells after hypoxia is shown to lead to increased levels of oxygen-bound myoglobin relative to the initial levels observed under normoxic conditions. Increased levels of reduced cytochrome c in ex vivo cells are also observed during hypoxia and reoxygenation by Raman microspectroscopy. The cellular response to reoxygenation differed dramatically depending on the method used in the preceding step to create hypoxic conditions in the cell suspension, where a chemical agent, sodium dithionite, leads to reduction of cytochromes in addition to removal of dissolved oxygen, and bubbling-N2 gas leads to displacement of dissolved oxygen only. These results have an impact on the assessment of experimental simulations of hypoxia in cells. The spectroscopic technique employed in this work will be used in the future as an analytical method to monitor the effects of varying levels of oxygen and nutrients supplied to cardiomyocytes during either the preconditioning of cells or the reperfusion of ischaemic tissue.
The shared epitope is a marker of severity associated with selection for, but not with response to, infliximab in a large rheumatoid arthritis population

Objective: To determine whether joint destruction, indication for, and response to infliximab in rheumatoid arthritis are associated with the shared epitope (SE) or selected cytokine gene polymorphisms (interleukin (IL) 1B, IL1-RN, and tumour necrosis α). Methods: In a large rheumatoid arthritis population of 930 patients from the same area (Rhône-Alpes, France), patients with (n = 198) or without infliximab treatment (n = 732) were compared according to their genetic status. Clinical, biological, and radiological data were collected. Typing for SE status and cytokine polymorphisms was carried out using enzyme linked oligosorbent assay. Statistical analysis was by χ2 testing and calculation of odds ratios (OR). Results: A dose relation was observed between the number of SE copies and joint damage in the whole rheumatoid population (OR, 1 v 0 SE copy = 2.38 (95% confidence interval, 1.77 to 3.19), p<0.001; OR 2 v 0 SE copy = 3.92 (2.65 to 5.80), p<0.001. The SE effect increased with disease duration but was not significant before two years. Selection for infliximab treatment (n = 198) was associated with increased disease activity, joint damage, and the presence of the SE with a dose effect. In all, 66.2% patients achieved an ACR20 improvement. No clinical or genetic factors were able to predict the clinical response to infliximab. Conclusions: This post-marketing study in a large cohort of rheumatoid arthritis patients indicates a linkage between rheumatoid arthritis severity, selection for treatment with infliximab, and the presence and dose of the SE.
Identification of essential residues for binding and activation in the human 5-HT7(a) serotonin receptor by molecular modeling and site-directed mutagenesis

The human 5-HT7 receptor is expressed in both the central nervous system and peripheral tissues and is a potential drug target in behavioral and psychiatric disorders. We examined molecular determinants of ligand binding and G protein activation by the human 5-HT7(a) receptor. The role of several key residues in the 7th transmembrane domain (TMD) and helix 8 were elucidated combining in silico and experimental mutagenesis. Several single and two double point mutations of the 5-HT7(a) wild type receptor were made (W7.33V, E7.35T, E7.35R, E7.35D, E7.35A, R7.36V, Y7.43A, Y7.43F, Y7.43T, R8.52D, D8.53K; E7.35T-R7.36V, R8.52D-D8.53K), and their effects upon ligand binding were assessed by radioligand binding using a potent agonist (5-CT) and a potent antagonist (SB269970). In addition, the ability of the mutated 5-HT7(a) receptors to activate G protein after 5-HT-stimulation was determined through activation of adenylyl cyclase. In silico investigation on mutated receptors substantiated the predicted importance of TM7 and showed critical roles of residues E7.35, W7.33, R7.36 and Y7.43 in agonist and antagonist binding and conformational changes of receptor structure affecting adenylyl cyclase activation. Experimental data showed that mutants E7.35T and E7.35R were incapable of ligand binding and adenylyl cyclase activation, consistent with a requirement for a negatively charged residue at this position. The mutant R8.52D was unable to activate adenylyl cyclase, despite unaffected ligand binding, consistent with the R8.52 residue playing an important role in the receptor-G protein interface. The mutants Y7.43A and Y7.43T displayed reduced agonist binding and AC agonist potency, not seen in Y7.43F, consistent with a requirement for an aromatic residue at this position. Knowledge of the molecular interactions important in h5-HT7 receptor ligand binding and G protein activation will aid the design of selective h5-HT7 receptor ligands for potential pharmacological use.
Malicious URL Detection using Machine Learning: A Survey

Malicious URL, a.k. a. malicious website, is a common and serious threat to cybersecurity. Malicious URLs host unsolicited content (spam, phishing, drive-by exploits, etc.) and lure unsuspecting users to become victims of scams (monetary loss, theft of private information, and malware installation), and cause losses of billions of dollars every year. It is imperative to detect and act on such threats in a timely manner. Traditionally, this detection is done mostly through the usage of blacklists. However, blacklists cannot be exhaustive, and lack the ability to detect newly generated malicious URLs. To improve the generality of malicious URL detectors, machine learning techniques have been explored with increasing attention in recent years. This article aims to provide a comprehensive survey and a structural understanding of Malicious URL Detection techniques using machine learning. We present the formal formulation of Malicious URL Detection as a machine learning task, and categorize and review the contributions of literature studies that addresses different dimensions of this problem (feature representation, algorithm design, etc.). Further, this article provides a timely and comprehensive survey for a range of different audiences, not only for machine learning researchers and engineers in academia, but also for professionals and practitioners in cybersecurity industry, to help them understand the state of the art and facilitate their own research and practical applications. We also discuss practical issues in system design, open research challenges, and point out some important directions for future research.
Circadian Abnormalities in Motor Activity in a BAC Transgenic Mouse Model of Huntington’s Disease

Huntington’s disease (HD) is a progressive neurodegenerative disease marked by psychiatric and motor problems. Recently, these findings have been extended to deficits in sleep and circadian function that can be observed in HD patients and in HD mouse models, with abnormal sleep patterns correlating with symptom severity in patients. Here, we studied the behavior of the BAC HD mouse model using an 24/7 automated system; the results indicate significant lengthening of the circadian period in the mutant mice. These results reinforce previous findings in HD models and symptomatic HD patients, indicating that circadian dysfunction is a core feature of HD.
Microscopic and macroscopic manipulation of gold nanorod and its hybrid nanostructures [Invited]

Gold nanorods (GNRs) have potential applications ranging from biomedical sciences and emerging nanophotonics. In this paper, we will review some of our recent studies on both microscopic and macroscopic manipulation of GNRs. Unique properties of GNR nanoparticles, such as efficient surface plasmon amplifications effects, are introduced. The stable trapping, transferring, positioning and patterning of GNRs with nonintrusive optical tweezers will be shown. Vector beams are further employed to improve the trapping performance. On the other hand, alignment of GNRs and their hybrid nanostructures will be described by using a film stretch method, which induces the anisotropic and enhanced absorptive nonlinearities from aligned GNRs. Realization and engineering of polarized emission from aligned hybrid GNRs will be further demonstrated, with relative excitation–emission efficiency significantly enhanced. Our works presented in this review show that optical tweezers possess great potential in microscopic manipulation of metal nanoparticles and macroscopic alignment of anisotropic nanoparticles could help the macroscopic samples to flexibly represent the plasmonic properties of single nanoparticles for fast, cheap, and high-yield applications.
CORAL - online monitoring in distributed applications: issues and solutions

In this paper we describe and evaluate issues that come up in the development of online monitoring systems which connect software tools to a running distributed application. Our primary intension was to elaborate how to deal with complex middleware mechanisms that cater for the middleware functionality in a way transparent to the users and tools. Our current implementation, called Coral, manages DSM mechanisms that provide an abstraction of shared memory on loosely coupled hardware, and allows multiple tools to perform consistent yet efficient operations on the entities being monitored. Since our primary design choice with Coral was portability we will port Coral to distributed environments based on the SOA technology.
Effect of Latent Semantic Indexing for Clustering Clinical Documents

The measurement of similarity between documents is usually influenced by sparseness of term-document matrix. Latent semantic indexing (LSI) is an alternative method to solve the problem, and the dimension reduction by LSI improves the performance of the measurement of the similarity. In this study, LSI is examined as a method to cluster clinical documents containing the same clinical problems or disorders. The similarity of clinical documents was measured effectively with LSI. LSI performed better on clinical documents which can be characterized with medical terms, various expressions for the same concepts, abbreviations and typos, than editorials. Our result showed that LSI is useful for the measurement of the similarity of the clinical documents examined in this study. And the correlation between co-occurrence of terms and similarity is also analyzed as an important aspect of LSI. Not only the co-occurring terms but unshared terms between documents were found as factors influencing the similarity.
Binding capacity and cis-acting efficiency of DNA regulatory sequences can be distinguished in an in vivo competition assay.

Initiation of gene transcription in eukaryotes involves two consecutive steps at least. In a first phase, transcription factors bind to cis-regulatory elements, generally located upstream of the core promoter region of the target gene. In a second phase, the resulting protein-DNA complex interacts with the general transcription machinery to achieve successful initiation (1). Changes in DNA structure, such as those linked to DNA methylation, might impede either step or both, thus preventing the onset of transcription (2). We have tested this hypothesis in an attempt to elucidate the mechanisms by which DNA methylation represses the rat prolactin (rPRL) gene expression (3). To this aim, we have developed an in vivo DNA competition assay that enables us to discriminate between binding capacities and cis-acting efficiencies of methylated and unmethylated DNA sequences. This assay relies on a previous observation showing that in vitro methylation of an expression vector, bearing chloramphenicol acetyltransferase (CAT) gene under the control of the proximal promoter of the rPRL gene, totally abolished CAT activity in transfected GH3 rat pituitary cells (Figure In the assay described here, similarly to conventional competition assay, a fixed amount of expression vector is cotransfected with an excess of competitor DNA. The original ofthe is to use, as a competitor DNA, a vector virtually identical to the expression i.e., constituting a full target for transcription factors, but totally devoid of reporter gene activity. a should allow to selectively monitor the binding capacities of the DNA sequence. By providing a simple way to analyze in the binding characteristics of transcription
Determine the User Country of a Tweet

In the widely used message platform Twitter, about 2% of the tweets contains the geographical location through exact GPS coordinates (latitude and longitude). Knowing the location of a tweet is useful for many data analytics questions. This research is looking at the determination of a location for tweets that do not contain GPS coordinates. An accuracy of 82% was achieved using a Naive Bayes model trained on features such as the users' timezone, the user's language, and the parsed user location. The classifier performs well on active Twitter countries such as the Netherlands and United Kingdom. An analysis of errors made by the classifier shows that mistakes were made due to limited information and shared properties between countries such as shared timezone. A feature analysis was performed in order to see the effect of different features. The features timezone and parsed user location were the most informative features.
Plasmids Carrying blaCMY -2/4 in Escherichia coli from Poultry, Poultry Meat, and Humans Belong to a Novel IncK Subgroup Designated IncK2

The blaCMY -2/4-carrying IncB/O/K-like plasmids of seven Escherichia coli strains from poultry, poultry meat and human urine samples were examined using comparative analysis of whole plasmid sequences. The incompatibility group was determined by analysis of the incRNAI region and conjugation assays with strains containing the IncK and IncB/O reference plasmids. Strains were additionally characterized using MLST and MIC determination. The complete DNA sequences of all plasmids showed an average nucleotide identity of 91.3%. Plasmids were detected in E. coli sequence type (ST) 131, ST38, ST420, ST1431, ST1564 and belonged to a new plasmid variant (IncK2) within the IncK and IncB/O groups. Notably, one E. coli from poultry meat and one from human contained the same plasmid. The presence of a common recently recognized IncK2 plasmid in diverse E. coli from human urine isolates and poultry meat production suggests that the IncK2 plasmids originated from a common progenitor and have the capability to spread to genetically diverse E. coli in different reservoirs. This discovery is alarming and stresses the need of rapidly introducing strict hygiene measures throughout the food chain, limiting the spread of such plasmids in the human settings.
Improving Networking Server Performance with Programmable Network Interfaces

Networking servers, such as web servers, have been widely deployed in recent years. While developments in the operating system and applications continue to improve server performance, programmable network interfaces with local memory provide new opportunities to improve server performance through extended network services on the network interface. However, due to their embedded nature, programmable processors on the network interface may suffer from inadequate processing power when compared to non-programmable application-specific network interfaces. This thesis first shows that exploiting a multiprocessor architecture and task-level concurrency in network interface processing enables programmable network interfaces to overcome the performance disadvantages over application-specific network interfaces that result from programmability. Then, the thesis presents a network service on a programmable network interface that exploits the storage capacity of the interfaces to alleviate the local I/O interconnect bottleneck, thereby improving server performance. Thus, these two results show that programmable network interfaces can offset the performance disadvantages due to programmability and improve networking server performance through extended network services that exploit their computation power and storage capacity.
Tuomas Aura Title : Commitment-based device pairing with synchronized drawing Year : 2014 Version : Post print

Secure device pairing is a widely studied problem. Local wireless connections such as Bluetooth and WiFi typically rely on user-entered secret keys or manually verified authentication codes. Several recent proposals replace these with contextual or location-dependent sensor inputs, which are assumed to be secret from anyone not present at the location where the pairing takes place. These protocols have to cope with a fuzzy secret, i.e. noisy secret input that differs between the devices. In this paper, we overview such protocols and propose a new variation using time-based opening of commitments. Our protocol has the advantage of treating the fuzzy secret as one piece of data rather than requiring it to be partitioned into time intervals, and being more robust against variations in input entropy than those based on error correction codes. The protocol development is motivated by the discovery of a novel human source for the fuzzy secret: synchronized drawing with two fingers of the same hand on two touch screens or surfaces. Metrics for measuring the distance between the drawings are described and evaluated. We implement a prototype of this surprisingly simple and natural pairing mechanism and show that it accurately differentiates between true positives and man-in-the-middle attackers.
Negative frequency-dependent preferences and variation in male facial hair

Negative frequency-dependent sexual selection maintains striking polymorphisms in secondary sexual traits in several animal species. Here, we test whether frequency of beardedness modulates perceived attractiveness of men's facial hair, a secondary sexual trait subject to considerable cultural variation. We first showed participants a suite of faces, within which we manipulated the frequency of beard thicknesses and then measured preferences for four standard levels of beardedness. Women and men judged heavy stubble and full beards more attractive when presented in treatments where beards were rare than when they were common, with intermediate preferences when intermediate frequencies of beardedness were presented. Likewise, clean-shaven faces were least attractive when clean-shaven faces were most common and more attractive when rare. This pattern in preferences is consistent with negative frequency-dependent selection.
Combination of Intra-Articular and Intraosseous Injections of Platelet Rich Plasma for Severe Knee Osteoarthritis: A Pilot Study

The aim of this study was to assess a novel approach to treating severe knee osteoarthritis by targeting synovial membrane, superficial articular cartilage, synovial fluid, and subchondral bone by combining intra-articular injections and intraosseous infiltrations of platelet rich plasma. We explored a new strategy consisting of intraosseous infiltrations of platelet rich plasma into the subchondral bone in combination with the conventional intra-articular injection in order to tackle several knee joint tissues simultaneously. We assessed the clinical outcomes through osteoarthritis outcome score (KOOS) and the inflammatory response by quantifying mesenchymal stem cells in synovial fluid. There was a significant pain reduction in the KOOS from baseline (61.55 ± 14.11) to week 24 (74.60 ± 19.19), after treatment (p = 0.008), in the secondary outcomes (symptoms, p = 0.004; ADL, p = 0.022; sport/rec., p = 0.017; QOL, p = 0.012), as well as VAS score (p < 0.001) and Lequesne Index (p = 0.008). The presence of mesenchymal stem cells in synovial fluid and colony-forming cells one week after treatment decreased substantially from 7.98 ± 8.21 MSC/μL to 4.04 ± 5.36 MSC/μL (p = 0.019) and from 601.75 ± 312.30 to 139.19 ± 123.61 (p = 0.012), respectively. Intra-articular injections combined with intraosseous infiltrations of platelet rich plasma reduce pain and mesenchymal stem cells in synovial fluid, besides significantly improving knee joint function in patients with severe knee osteoarthritis. This trial is registered on EudraCT with the number 2013-003982-32.
Emotion Regulation Feeding Practices Link Parents' Emotional Eating to Children's Emotional Eating: A Moderated Mediation Study.

UNLABELLED Past research suggests an association between parents' and children's emotional eating, but research has yet to examine mechanisms underlying this association. OBJECTIVE The current study examined whether feeding for emotion regulation mediates the association between parents' and children's emotional eating, and whether this association is moderated by children's self-regulation in eating. METHOD 95 parents reported on their own and their children's emotional eating, their children's self-regulation in eating, as well as their feeding practices. RESULTS Findings revealed that feeding for emotion regulation mediated the association between parents' and children's emotional eating when children's self-regulation in eating was low, but not when self-regulation in eating was high. CONCLUSION The current findings demonstrate the complexity of the link between parents' and children's emotional eating, suggesting practitioners should consider both feeding practices and children's self-regulation in eating when designing intervention programs.
An improvement iterative approach for wideband digital predistortion using under-sampling

The performance of the traditional approach of wideband digital pre-distortion (DPD) of radio frequency (RF) power amplifier (PA) is subject to the analog to digital converter (ADC) sampling rate of transmitter. In this paper, an improvement DPD iterative approach is proposed. Firstly, DPD input signal and PA output signal are under-sampled by Zhu's generalized sampling theorem (ZGST). Secondly, an optimized iterative model is employed to obtain DPD model. The parameters of it can be extracted by DPD input signal and PA output signal. This improvement DPD iterative approach not only reduces hardware requirement of ADC sampling rate but also gives almost same linear performance with that by full sampling rate. The performance is validated by measurement result.