Miracle-dz/UniFAR-FTUs huggingface dataset:
The Phosphatase MKP1 Is a Transcriptional Target of p53 Involved in Cell Cycle Regulation*

The tumor suppressor p53 protein suppresses cell growth by inducing cell cycle arrest or apoptosis. Despite the fact that p53-dependent p21-mediated G1 arrest induced by DNA damage is well defined, the role of p53 in the cell cycle in response to the MAKP signaling remains to be determined. Here we show that MKP1, a member of the dual specificity protein phosphatase family capable of inactivating MAPKs, is a transcriptional target of p53. MKP1 mRNA and protein levels were increased upon p53 activation in several well defined p53-regulated cell systems. p53 bound to a consensus p53 binding site located in the second intron of the MKP1 gene and transactivated MKP1 in reporter gene assays. Inhibition of phosphatase activity impaired p53-mediated G1 arrest in arrested human glioblastoma GM cells in response to growth factor stimuli. Importantly conditional expression of MKP1 prevented arrested human cancer cells from entering into the cell cycle. Thus, these results provide a novel mechanism by which p53 controls the cell cycle in response to the MAPK signaling in the absence of DNA damage and suggest that p53 may negatively control the MAKP pathway via MKP1.
Computational Decision Support: Regret-based Models for Optimization and Preference Elicitation

Decision making is a fundamental human, organizational, and societal activity, involving several key (and sometimes implicit) steps: the formulation of a set of options or decisions; information gathering to help assess the outcomes of these decisions and their likelihood; some assessment of the relative utility or desirability of the possible outcomes; and an assessment of the tradeoffs involved to determine an appropriate course of action. Advances in information and communication technology have changed the nature of the decisions that face individuals, professionals, and organizations. Sophisticated devices, ubiquitous sensors, and the increasing use of online mechanisms to mediate personal, professional, and business communications and transactions has resulted in an explosion in the data available to support decision making. Apart from data proliferation, the range and complexity of the options facing decision makers has also increased: networked communication has drastically reduced search costs, and sophisticated computational models have greatly expanded the capacity for reasoning about complex decision structures (e.g., policies, configurations of decision variables, etc.). Computer-aided decision support is vital for several reasons. First, computational methods are critical in helping decision makers wade through of huge volumes of data to extract relevant information. Tremendous strides in information retrieval and machine learning have offered ever-more sophisticated algorithms for data mining and relevance detection. Second, while computers have long been used for decision support, the new richness of data sources and complexity of decision spaces bring with them demands for more sophisticated forms of algorithmic optimization to help decision makers determine suitable courses of action. However, even with sophisticated algorithms at their disposal, decision support tools require considerable information about the decision maker’s preferences to function effectively. This is especially true when we consider putting decision support in the hands of the “masses,” that is, people who make decisions without having (or needing) a rich understanding of the underlying domain or its dynamics. Many ingredients of a decision scenario can be fixed—options, likelihood of outcomes, relevance of information sources, etc., may be the same for each user of a decision support tool. What varies are the preferences of the users, each of whom has different goals or objectives in mind. Hence, this information cannot be coded into the system in advance. Unfortunately, no decision support system can recommend decisions without some idea of what these preferences are, giving rise to the preference bottleneck: how do we get the preferences of the user (or organization) “into” the decision support system? The preference bottleneck is one of the greatest impediments to the wide-scale deployment of
An Indexing Scheme for Typed Feature Structures

This paper describes an indexing substrate for typed feature structures (ISTFS), which is an efficient retrieval engine for typed feature structures. Given a set of typed feature structures, the ISTFS efficiently retrieves its subset whose elements are unifiable or in a subsumption relation with a query feature structure. The efficiency of the ISTFS is achieved by calculating a unifiability checking table prior to retrieval and finding the best index paths dynamically.
PEACE: A Novel Privacy-Enhanced Yet Accountable Security Framework for Metropolitan Wireless Mesh Networks

Recently, multihop wireless mesh networks (WMNs) have attracted increasing attention and deployment as a low-cost approach to provide broadband Internet access at metropolitan scale. Security and privacy issues are of most concern in pushing the success of WMNs for their wide deployment and for supporting service-oriented applications. Despite the necessity, limited security research has been conducted toward privacy preservation in WMNs. This motivates us to develop PEACE, a novel Privacy-Enhanced yet Accountable seCurity framEwork, tailored for WMNs. On one hand, PEACE enforces strict user access control to cope with both free riders and malicious users. On the other hand, PEACE offers sophisticated user privacy protection against both adversaries and various other network entities. PEACE is presented as a suite of authentication and key agreement protocols built upon our proposed short group signature variation. Our analysis shows that PEACE is resilient to a number of security and privacy related attacks. Additional techniques were also discussed to further enhance scheme efficiency.
Revival of Continuous Suture Technique in Aortic Valve Replacement in Patient with Aortic Valve Stenosis a Novel Modified Technique

Objective The continuous suture technique has numerous advantages as simple, quick, and effective for aortic valve replacement; however, it is technically difficult. We have modified the continuous suture technique and evaluated our new technique in patients with aortic stenosis. Methods Between July 2007 and May 2010, 86 patients with aortic valve stenosis underwent aortic valve replacement alone or with other concomitant cardiac procedures including mitral valve surgery in our hospital. The patients were randomly divided into two groups: group A (n = 43) in which the continuous suture technique with some modifications was used and group B (n = 43) in which the conventional interrupted suture technique was used. There were no statistical differences between two groups in age, sex, body surface area, concomitant cardiac procedures, blood loss, and postoperative extubation time. Results The aortic cross-clamp time, cardiopulmonary bypass time, operation time, and hospital stay were significantly shorter in group A than that in group B, and the valve size was significantly larger in group A. No perivalvular leak was detected in postoperative echocardiograms. All patients recovered satisfactorily without complications associated with suture technique or prosthesis. During follow-up of 4 to 38 months, there were no clinically significant complications in group A, while one patient in group B developed perivalvular leakage requiring reoperation 3 months after surgery. Conclusions Our modified continuous suture method is useful for aortic valve replacement in patients with aortic stenosis and beneficial for the patients because the procedure is less invasive and a larger valve can be implanted.
Glucansucrases produced by fructophilic lactic acid bacteria Lactobacillus kunkeei H3 and H25 isolated from honeybees

Twenty fructophilic isolates from the stomachs of honeybee Apis mellifera ligustica from the region of Plovdiv, Bulgaria were obtained. Fructophilic isolates H3 and H25 showed formation of mucous colonies during cultivation on medium with sucrose, suggesting exopolysaccharide synthesis. The sequencing analysis of 16S rRNA identified isolates H3 and H25 as fructophilic lactic acid bacteria Lactobacillus kunkeei. The in situ analysis and periodic acid‐Schiff's staining, showed that Lb. kunkeei H3 and H25 produce extracellular glucansucrases with molecular weight of about 300 kDa. In the cell‐associated fractions, additional glucansucrase is detected with molecular weight of about 180 kDa. The content of α‐(1 → 6) linkages in the glucans synthesized with extracellular glucansucrases from H3 and H25 after dextranase hydrolysis was significantly lower than this one of the classical dextran – about 35 and 62%, respectively. These results suggest a more branched structure of the studied polymers.
Dynamic GOP structure selection to support QoS in vertical handoff

This paper proposes a dynamic GOP structure selection method to provide seamless video streaming for vertical handoff in the heterogeneous wireless network. The proposed method dynamically changes the interval of I-pictures by using the received signal strength indication (RSSI) and the pilot strength (Ec/Io) in order to reduce error propagation due to packet losses. Thus, with the proposed method, the client can always receive the I-picture right after vertical handoff. Experimental results show that the proposed method can significantly reduce the video quality degradation caused by vertical handoff in the real-time video encoding applications.
Intra-Abdominal Infections: Prevalence and Risk Factors of ESBLs Infections.

BACKGROUND Extended-Spectrum Beta-Lactamases (ESBLs)-producing bacteria are increasing challenge in the treatment of both community acquired and nosocomial intra-abdominal infections (IAIs). Investigating the characteristics ofpatients with the IAIs caused by ESBL-producing bacteria and assessing the risk factors of ESBLs infection will lead to appropriate therapeutic management. OBJECTIVE To determine prevalence of ESBL-producing bacteria in IAIs in Phramongkutklao Hospital and identify risk factor of the ESBL-infections. MATERIAL AND METHOD We performed a retrospective cross sectional study ofpatients admitted in Phramongkutklao Hospital between January 1 and December 30, 2012 to determine the prevalence and risk factors acquiring ESBL-producing bacteria in IAIs and the outcomes of these infections. RESULTS Sixty-one patients were studied, of whom 45 (73.8%) had community-acquired and 16 (26.2%) had nosocomial IAIs. ESBL-producing bacteria were positive in 18 patients, 7 (15.6%) in community acquired and 11 (68.8%) nosocomial infection. The common gram negative bacilli were Escherichia coli, Klebsiella pneumoniae. Univariate analysis showed three factors including nosocomial infection, prior admission within one month, and prior use of antibiotics, in particular, cephalosporin, and beta-lactam/beta-lactamase inhibitor (BLBI), to be associated with ESBL-producing bacterial infections. In the multivariate analysis, nosocomial infection (odds ratio [OR], 5.26; 95% confidence interval [CI], (1.07-25.88); p = 0.041) was independent factor that related to the ESBL-infection in IAIs. CONCLUSION Nosocomial infection was found as an independent factor significantly associated with ESBL-infection in IAIs. Other critical issues remain debatable and more controversial are due to the limited number of the study's patients.
Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome

The short QT syndrome (SQTS) is a genetically heterogeneous condition characterized by abbreviated QT intervals and an increased susceptibility to arrhythmia and sudden death. This simulation study identifies arrhythmogenic mechanisms in the rapid-delayed rectifier K+ current (IKr)-linked SQT1 variant of the SQTS. Markov chain (MC) models were found to be superior to Hodgkin-Huxley (HH) models in reproducing experimental data regarding effects of the N588K mutation on KCNH2-encoded hERG. These ionic channel models were then incorporated into human ventricular action potential (AP) models and into 1D and 2D idealised and realistic transmural ventricular tissue simulations and into a 3D anatomical model. In single cell models, the N588K mutation abbreviated ventricular cell AP duration at 90% repolarization (APD90) and decreased the maximal transmural voltage heterogeneity (δV) during APs. This resulted in decreased transmural heterogeneity of APD90 and of the effective refractory period (ERP): effects that are anticipated to be anti-arrhythmic rather than pro-arrhythmic. However, with consideration of transmural heterogeneity of IKr density in the intact tissue model based on the ten Tusscher-Noble-Noble-Panfilov ventricular model, not only did the N588K mutation lead to QT-shortening and increases in T-wave amplitude, but δV was found to be augmented in some local regions of ventricle tissue, resulting in increased tissue vulnerability for uni-directional conduction block and predisposing to formation of re-entrant excitation waves. In 2D and 3D tissue models, the N588K mutation facilitated and maintained re-entrant excitation waves due to the reduced substrate size necessary for sustaining re-entry. Thus, in SQT1 the N588K-hERG mutation facilitates initiation and maintenance of ventricular re-entry, increasing the lifespan of re-entrant spiral waves and the stability of scroll waves in 3D tissue.
Static analysis for detecting taint-style vulnerabilities in web applications

The number and the importance of web applications have increased rapidly over the last years. At the same time, the quantity and impact of security vulnerabilities in such applications have grown as well. Since manual code reviews are time-consuming, error-prone and costly, the need for automated solutions has become evident. In this paper, we address the problem of vulnerable web applications by means of static source code analysis. More precisely, we use flow-sensitive, interprocedural and context-sensitive data flow analysis to discover vulnerable points in a program. In addition to the taint analysis at the core of our engine, we employ a precise alias analysis targeted at the unique reference semantics commonly found in scripting languages. Moreover, we enhance the quality and quantity of the generated vulnerability reports by employing an iterative two-phase algorithm for fast and precise resolution of file inclusions. The presented concepts are targeted at the general class of taint-style vulnerabilities and can be easily applied to the detection of vulnerability types such as SQL injection, cross-site scripting (XSS), and command injection. We implemented the presented concepts in Pixy, a high-precision static analysis tool aimed at detecting cross-site scripting and SQL injection vulnerabilities in PHP programs. To demonstrate the effectiveness of our techniques, we analyzed a number of popular, open-source web applications and discovered hundreds of previously unknown vulnerabilities. Both the high analysis speed as well as the low number of generated false positives show that our techniques can be used for conducting effective security audits.
Applicability of Process Viewing Patterns in Business Process Management

Process views are an emerging concept for coping with the increasing complexity of process models. We understand a process view as the result of specific transformations applied to a process model. In this paper we discuss concrete scenarios of process view transformations for providing assistance in business process management. We show how elementary patterns of view transformations can be combined to support the design, deployment, monitoring and analysis of business processes. The process views proposed in this paper are technology independent and can be applied to any process language which can be represented by a process graph, such as the Business Process Modeling Notation (BPMN) and Event-driven Process Chains (EPC).
Real-time pedestrian tracking in indoor environments

Tracking pedestrians in indoor environments has increasingly become a needed topic to optimize human activities in case of emergency interventions, guidance, entertainment, healthcare, advertisement, etc. Additionally, portable and wearable devices are overtaking traditional computers. Their ubiquitous/pervasive features added to their increasing technical specifications and sensing capabilities have made them an attractive option for indoor pedestrian tracking based on dead-reckoning (DR). This paper presents a solution for real-time tracking of pedestrians in indoor environments using sensing raw data from low cost sensors (such as accelerometer or gyroscope) embedded in modern smartphones. The proposed application combines a simplified DR approach, based on the identification of human gait for step detection and distance estimation, along with the detection of identifiable indoor signatures such as corners. The application was implemented and tested on Android-based mobile phones obtaining an accuracy of 89.93% in common indoor human motion displacements.
Towards understanding upstream Web traffic

While downstream Web traffic has been studied in detail, upstream Web traffic has not received much attention yet. We argue that upstream traffic deserves the same or even higher attention since data flows towards Web servers generally entail privacy-relevant user information. Our aim is to understand where to and how much data users send to Web services. To this end, we examine HTTP(S) requests of two 24 hour traces recorded at a gateway of a campus network. As HTTP is highly repetitive, we introduce a scalable approach to remove redundant parts from upstream Web traffic, yielding an approximation of actual information flow. We identify thirteen classes of Web services covering up to 95% of all outgoing HTTP information. Our methodology further allows to quantify and compare the share of information different Web service classes receive. We find that advertisement and analytics services receive two times more information during Web browsing than all first party Web services together.
Optical quantification of molecular interaction strength in protein condensates

Biomolecular condensates have recently been identified as a ubiquitous means of intracellular organization. Investigating the molecular interactions determining the formation, and physical properties of biomolecular condensates provides key insights for understanding their biological function, and dysfunction. Here, we applied Brillouin microscopy and quantitative phase imaging to quantify average molecular interaction strength, dry mass density, and protein volume fraction in protein condensates in vitro. We monitored the physical changes in FUS condensates in response to altering temperature and ion concentration. Conditions favoring phase separation increased Brillouin shift, linewidth, and dry mass density. In contrast to solidification by chemical crosslinking, physical aging of condensates had only a small impact on the Brillouin shift. Physical aging was suppressed at a high ion concentration. Finally, we characterized sequence variations of the low-complexity domain of hnRNPA1 that change the driving force for phase separation and found that they also alter the physical properties of the condensates. Our results provide a new experimental perspective on the physical properties of protein condensates and their sensitivity to solution conditions, sequence, and as a function of time.
Constant companions: Wild zebra finch pairs display extreme spatial cohesion

Many animals maintain long-term monogamous partnerships, but the extent to which partners interact varies substantially and has implications for the scope of cooperation between pair members. Zebra finches are monogamously paired for life, raising questions as to if and how they maintain pair cohesion in the absence of having territories and in the absence of long-range signals. While zebra finches are the best studied songbird in captivity, their social and spatial behaviour in the wild is poorly understood. Determining pair cohesion in songbirds to date has almost exclusively been studied only at specific locations, such as nesting or feeding sites where bird presence can be logged incidentally, without quantifying broader movements. Here, we used automated tracking to continuously monitor the movements of radio-tagged zebra finch pairs during a period with breeding activity. We reveal extremely high pair cohesion with pairs using nearly identical home ranges and maintaining close spatial proximity throughout the day. This characterisation of extremely high spatio-temporal coordination of zebra finch pairs provides novel and important insights into the operation and benefits of monogamous relationships in highly mobile taxa, such as birds.
Delving into human α1,4-galactosyltransferase acceptor specificity: the role of enzyme dimerization

Glycosyltransferases (GTs) exhibit precise donor and acceptor specificities, governed by intricate mechanisms, including protein assembly. Human α1,4-galactosyltransferase (A4galt), a Golgi apparatus-resident GT, catalyzes the synthesis of Gb3 glycosphingolipid (GSL) and P1 glycotope on glycoproteins (GPs), receptors for Shiga toxin type 1 (Stx1) and 2 (Stx2). These toxins are produced by enterohemorrhagic Escherichia coli and can lead to severe outcomes, such as hemolytic-uremic syndrome (HUS). To elucidate the molecular basis of A4galt specificity towards GSLs and GPs, we explored its interaction with GP-specific β1,4-galactosyltransferase 1 (B4galt1) and GSL-specific β1,4-galactosyltransferase isoenzymes 5 and 6 (B4galt5 and B4galt6). Using a novel NanoBiT assay, we demonstrated that A4galt could form homodimers and heterodimers with B4galt1 and B4galt5. Furthermore, by employing AlphaFold for state-of-the-art structural prediction, we analyzed the interactions and structures of these enzyme complexes. Our analysis highlighted that the A4galt-B4galt5 heterodimer exhibited the highest prediction confidence, indicating a significant role of A4galt heterodimers in determining enzyme specificity toward GSLs and GPs. These insights not only increase our knowledge about glycosylation processes but also open avenues for developing new therapeutic approaches to Shiga toxin-related diseases.