Miracle-dz/UniFAR-FTUs huggingface dataset:
Methionine Biosynthesis in Staphylococcus aureus Is Tightly Controlled by a Hierarchical Network Involving an Initiator tRNA-Specific T-box Riboswitch

In line with the key role of methionine in protein biosynthesis initiation and many cellular processes most microorganisms have evolved mechanisms to synthesize methionine de novo. Here we demonstrate that, in the bacterial pathogen Staphylococcus aureus, a rare combination of stringent response-controlled CodY activity, T-box riboswitch and mRNA decay mechanisms regulate the synthesis and stability of methionine biosynthesis metICFE-mdh mRNA. In contrast to other Bacillales which employ S-box riboswitches to control methionine biosynthesis, the S. aureus metICFE-mdh mRNA is preceded by a 5′-untranslated met leader RNA harboring a T-box riboswitch. Interestingly, this T-box riboswitch is revealed to specifically interact with uncharged initiator formylmethionyl-tRNA (tRNAi fMet) while binding of elongator tRNAMet proved to be weak, suggesting a putative additional function of the system in translation initiation control. met leader RNA/metICFE-mdh operon expression is under the control of the repressor CodY which binds upstream of the met leader RNA promoter. As part of the metabolic emergency circuit of the stringent response, methionine depletion activates RelA-dependent (p)ppGpp alarmone synthesis, releasing CodY from its binding site and thereby activating the met leader promoter. Our data further suggest that subsequent steps in metICFE-mdh transcription are tightly controlled by the 5′ met leader-associated T-box riboswitch which mediates premature transcription termination when methionine is present. If methionine supply is limited, and hence tRNAi fMet becomes uncharged, full-length met leader/metICFE-mdh mRNA is transcribed which is rapidly degraded by nucleases involving RNase J2. Together, the data demonstrate that staphylococci have evolved special mechanisms to prevent the accumulation of excess methionine. We hypothesize that this strict control might reflect the limited metabolic capacities of staphylococci to reuse methionine as, other than Bacillus, staphylococci lack both the methionine salvage and polyamine synthesis pathways. Thus, methionine metabolism might represent a metabolic Achilles' heel making the pathway an interesting target for future anti-staphylococcal drug development.
Elevated Pentraxin 3 in bone metastatic breast cancer is correlated with osteolytic function

Pentraxin 3 (PTX3), a modulator of tumor-associated inflammation, is known to be positively correlated with tumor grade and severity of malignancies, but its exact role remains unclear. This study found that PTX3 expression was up-regulated in distant bone metastases of breast cancer compared to lung, liver, and brain metastases in 64 human breast cancer patients. Elevated expression of PTX3 was correlated with poor survival in patients with breast cancer. PTX3 expression was also up-regulated in a bone metastatic breast cancer cell line and further enhanced by pro-inflammatory cytokine TNFα. Administration of PTX3 promoted the migratory potential of breast cancer cells and the mobilization of macrophages, a precursor of osteoclasts (OCs), toward breast cancer cells. In addition, elevated expression of PTX3 by TNFα led to enhanced OC formation, implying the distinct role of PTX3 in osteolytic bone metastasis of breast cancer cells. Furthermore, PTX3 silencing using siRNA-specific siRNA prevented breast cancer cell migration, macrophage Chemotaxis, and subsequent OC formation. These findings provide an important insight into the key role of PTX3 in inflammation-associated osteolytic complications of breast cancer.
The Conceptual Calculus For Automatic Program Understanding

The CAN system for automatic understanding of LISP programs is presented. When applied on a LISP program, CAN needs no assertion about what the program is intended to do. CAN's general task is to associate e meaning to a program, from which it is able to diagnose semantic properties (unused portions of code, undefinitions, underused programs, classes Of data for which evaluation of an expression never terminates), and to exhibit deep semantic properties. CAN's underlying theory is the conceptual calculus, based on the clausal form of predicate logic. It involves two main ideas : - an Induction principle specially adapted to program understanding (as opposed to program verification). - An extension of unificetion to equation solving.
Locating and checking of a BGA pin's position using gray level

A machine vision system for SMT-mounting machine applications is usually a two-stage algorithm. It first measures the centroid and rotation angle of the SMD, and then checks each pin's area, position error, and grid coordinate location. In this paper, a set of complete procedures is proposed to locate and check the BGA image. During the locating procedures, we first calculate a threshold of the frame using an iterative threshold algorithm. If an object is found under this threshold, then the pin's area is calculated by the local threshold by using a momentum algorithm. After that, whether this object is a pin or not is decided by its neighbors' relative positions, the approximate rotation angle for finding the outer pins is calculated, and the centroid as well as the rotation angle of a BGA component is calculated by the rectangular least squares algorithm. The checking procedure also measures each pin's area using the momentum algorithm, then it calculates the radius of the moving sum using each pin's area, and finally measures the position error using a moving sum algorithm and judges each pin's type by gray level. The new method uses the gray level statistic information to solve the empty pad's problem and utilizes the symmetrical property of a circle to deal with the shape problem. Lastly, the CRC algorithm is used to check the correspondence between each pin and its pin type. This new method has a high accuracy and a low execution time. It can meet the crucial timing requirement of a high-speed SMT machine through experimental verification.
Interpreting network communicability with stochastic models and data

The recently introduced concept of dynamic communicability is a valuable tool for ranking the importance of nodes in a temporal network. Two metrics, broadcast score and receive score, were introduced to measure the centrality of a node with respect to a model of contagion based on time-respecting walks. This article examines the temporal and structural factors influencing these metrics by considering a versatile stochastic temporal network model. We analytically derive formulae to accurately predict the expectation of the broadcast and receive scores when one or more columns in a temporal edge-list are shuffled. These methods are then applied to two publicly available data-sets and we quantify how much the centrality of each individual depends on structural or temporal influences. From our analysis we highlight two practical contributions: a way to control for temporal variation when computing dynamic communicability, and the conclusion that the broadcast and receive scores can, under a range of circumstances, be replaced by the row and column sums of the matrix exponential of a weighted adjacency matrix given by the data.
Extending Rectangular Range Reporting with Query Sensitive Analysis

In this paper, we consider the problem of reporting the new points incorporated by on-line sequences of nested rectangular range queries where all queries in a sequence have the same orientation, but the orientation of each sequence may differ. Worst case lower bound results show that time and space efficient solutions to this problem are unlikely. Here we present a linear space solution that performs partially ordered searches of a box-decomposition subdivision. It uses information obtained from the results of processing previous queries to assist in processing each new query in a sequence. A query sensitive analysis shows the algorithm is most effective for “targeted” queries — queries that target space containing a high density of data relative to the space immediately surrounding the query. Such queries are typical of those made by region growing surface reconstruction techniques, the primary application considered here. To substantiate this intuition, we have implemented a version of the algorithm and run it on real range data and sequences of queries representative of those made by region growing surface reconstruction techniques. The empirical results provide strong support for this in-
Non-contrast-enhanced MR portography and hepatic venography with time-spatial labeling inversion pulses: comparison at 1.5 Tesla and 3 Tesla

Background A 3 Tesla (3 T) magnetic resonance (MR) scanner is a promising tool for upper abdominal MR angiography. However, there is no report focused on the image quality of non-contrast-enhanced MR portography and hepatic venography at 3 T. Purpose To compare and evaluate images of non-contrast-enhanced MR portography and hepatic venography with time-spatial labeling inversion pulses (Time-SLIP) at 1.5 Tesla (1.5 T) and 3 T. Material and Methods Twenty-five healthy volunteers were examined using respiratory-triggered three-dimensional balanced steady-state free-precession (bSSFP) with Time-SLIP. For portography, we used one tagging pulse (selective inversion recovery) and one non-selective inversion recovery pulse; for venography, two tagging pulses were used. The relative signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were quantified, and the quality of visualization was evaluated. Results The CNRs of the main portal vein, right portal vein, and left portal vein at 3 T were better than at 1.5 T. The image quality scores for the portal branches of segment 4, 5, and 8 were significantly higher at 3 T than at 1.5 T. The CNR of the right hepatic vein (RHV) at 3 T was significantly lower than at 1.5 T. The image quality scores of RHV and the middle hepatic vein were higher at 1.5 T than at 3 T. For RHV visualization, the difference was statistically significant. Conclusion Non-contrast-enhanced MR portography with Time-SLIP at 3 T significantly improved visualization of the peripheral branch in healthy volunteers compared with1.5 T. Non-contrast-enhanced MR hepatic venography at 1.5 T was better than at 3 T.
Oefening baart kunst: Crowdingtraining verbetert visuele functies van slechtziende kinderen

Crowding is a visual perceptual phenomenon that refers to impaired ability to recognize a suprathreshold object when it is presented in the vicinity of other objects. Crowding therefore poses a limit on object recognition. The phenomenon is regarded to be one of the reasons why young children need large textbook letters. Several studies have provided evidence that crowding imposes a bottleneck on reading speed, and reading long words. Thus, crowding influences visual perception and object recognition in young children. Recent studies show that crowding is stronger in children with visual impairment than in children with normal vision. But which factors are responsible for these strong crowding effects? And how can we reduce crowding in children with visual impairment for whom low visual acuity in itself already poses a bottleneck on object recognition? This review article tries to answer these questions. This knowledge is useful for educational psychologists, because crowding can interfere with the acquisition of academic skills and reading. Keywords: crowding, learning, visual impairment, visual acuity, visual attention.
Surgical Treatment of Pediatric Epileptic Encephalopathies

Pediatric epileptiform encephalopathies are a group of neurologically devastating disorders related to uncontrolled ictal and interictal epileptic activity, with a poor prognosis. Despite the number of pharmacological options for treatment of epilepsy, many of these patients are drug resistant. For these patients with uncontrolled epilepsy, motor and/or neuropsychological deterioration is common. To prevent these secondary consequences, surgery is often considered as either a curative or a palliative option. Magnetic resonance imaging to look for epileptic lesions that may be surgically treated is an essential part of the workup for these patients. Many surgical procedures for the treatment of epileptiform encephalopathies have been reported in the literature. In this paper the evidence for these procedures for the treatment of pediatric epileptiform encephalopathies is reviewed.
Smart SecureGov: mobile government security framework

In order to support secure information sharing and interoperability of e-government systems, Public Information Sharing Center (PISC) in Korea adopted SecureGov framework that consists of multiple security mechanisms: access control scheme called Enterprise Digital Right Management (E-DRM) to prevent illegal use and leakage, a forgery prevention technology using a 2-D barcode to prevent illegal modification of the data, and PKI scheme to ensure the authenticity of the user and delivered data. These security mechanisms had been sufficient to ensure secure exchange of information between two organizations, preventing illegal modification, edits, or transfers of sensitive data to a third parties for unintended purposes in the age of wired PC based computing environment. However, with a wide spread use of mobile devices and micro devices, including smart phones and wearable devices, additional security mechanisms are required to prevent the insider attacks, such as a leakage of highly sensitive and confidential documents or conversations by taking secretive photos or illegal recordings. In this paper, we present the Smart SecureGov framework that focuses on the tracking technologies in case of smart device-based leakage occurs. The security mechanisms, such as a text watermarking technology, image or audio watermarking technologies, are proposed to detect the authenticity of the leaked document or media and to trace back to the origin of leaks. The Smart SecureGov framework is an evolution to counter against the new risks and threats posed by mobile and smart digital media technologies.
RFID Anti-Collision Algorithm Based on Occurrence Position

Aiming at the data redundancy problem in process of anti-collision in RFID, an OP(occurrence position) algorithm is proposed in this study, OP algorithm is based on the theory of direct georeference and BS (binary search) algorithm, improve traditional binary search mechanism by changing data transformed by anti-collision commands, data transformed by anti-collision commands in OP algorithm contains the same information as those data in BS algorithm, but contains less data bits than that in BS algorithm. Analysis is made for binary search algorithm used in process of anti-collision and shortcomings are given, analysis for ALOHA algorithm is also given, then principles of OP algorithm which is proposed to improve those shortcomings existing in BS algorithm and ALOHA algorithm are elaborated, analysis is also made for OP algorithm. Finally a module for OP algorithm is established on transmission delay and data redundancy, results of simulations show that OP algorithm has even higher capability than other Binary Search algorithm and has better suitability on occasion of much more tags.
Testosterone for the aging male; current evidence and recommended practice

An international consensus document was recently published and provides guidance on the diagnosis, treatment and monitoring of late-onset hypogonadism (LOH) in men. The diagnosis of LOH requires biochemical and clinical components. Controversy in defining the clinical syndrome continues due to the high prevalence of hypogonadal symptoms in the aging male population and the non-specific nature of these symptoms. Further controversy surrounds setting a lower limit of normal testosterone, the limitations of the commonly available total testosterone result in assessing some patients and the unavailability of reliable measures of bioavailable or free testosterone for general clinical use. As with any clinical intervention testosterone treatment should be judged on a balance of risk versus benefit. The traditional benefits of testosterone on sexual function, mood, strength and quality of life remain the primary goals of treatment but possible beneficial effects on other parameters such as bone density, obesity, insulin resistance and angina are emerging and will be reviewed. Potential concerns regarding the effects of testosterone on prostate disease, aggression and polycythaemia will also be addressed. The options available for treatment have increased in recent years with the availability of a number of testosterone preparations which can reliably produce physiological serum concentrations.
The complexity of circuit value and network stability

A method for nontrivially restricting fanout in a circuit is developed. The complexity of the circuit value problem and a new problem, network stability, is studied when fanout is limited. This leads to new classes or problems within P. It is conjectured that the new classes are different from P and incomparable to NC. One of these classes, CC, contains several natural complete problems, including circuit value for comparator circuits, lex-first maximal matching, and problems related to stable marriage and stable roommates. A parallel algorithm for circuit value that runs in time about the square root of the number of gates, a linear-time sequential algorithm for network stability, and logspace reductions between circuit value and network stability are obtained. <<ETX>>
Optimisation of IEEE 1500 Wrappers and User Defined TAMs

With the adoption of the IEEE 1500 [1] Standard, the opportunity exists for System on Chip (SoC) designers to specify test systems in a generic way. As the IEEE 1500 Standard does not address the specification and design of the on-chip Test Access Mechanism (TAM), considerable effort may still be required if test engineers are to optimise testing SoCs with IEEE 1500 Wrapped Cores. This paper describes novel research activity based on the design of TAMs that are compatible with IEEE 1500 wrapped cores. Taking into account previous work on Test Resource Partitioning (TRP), functional testing using the system bus and TAM architectures, a novel approach is introduced that allows some elements of the system bus to be used as part of the TAM while retaining compatibility with the IEEE 1500 wrapped cores. A small microcontroller SoC design based on the AMBA APB bus is used to investigate this approach. A crucial element of this approach involves interfacing the combined TAM to the mandatory Wrapper Serial Port (WSP) and the optional Wrapper Parallel Port (WPP) of the IEEE 1500 wrapped cores in the chip. Test Application Time (TAT) results are presented that establish the viability of the ideas described, as well as comparative analysis of TAT results derived from a number of test structures based on these techniques.
Packet capturing on parallel architectures

Nowadays commodity hardware is offering an ever increasing degree of parallelism: CPUs are equipped with more and more cores and a new generation of NICs can dispatch packets across multiple queues. Software based network monitoring can leverage the opportunity offered by this new trend in order to target a level of performance which was unattainable with single core technologies. In this paper, which is the result of a thorough measurement campaign, we explore the potential of parallelism when coupled with existing packet capturing technologies and show how, by accurately tuning configurations, a huge performance gain can be obtained. We also show how minimal configuration changes can dramatically affect the overall throughput.
Inhibition of TIR Domain Signaling by TcpC: MyD88-Dependent and Independent Effects on Escherichia coli Virulence

Toll-like receptor signaling requires functional Toll/interleukin-1 (IL-1) receptor (TIR) domains to activate innate immunity. By producing TIR homologous proteins, microbes inhibit host response induction and improve their own survival. The TIR homologous protein TcpC was recently identified as a virulence factor in uropathogenic Escherichia coli (E. coli), suppressing innate immunity by binding to MyD88. This study examined how the host MyD88 genotype modifies the in vivo effects of TcpC and whether additional, TIR-domain containing proteins might be targeted by TcpC. In wild type mice (wt), TcpC enhanced bacterial virulence, increased acute mortality, bacterial persistence and tissue damage after infection with E. coli CFT073 (TcpC+), compared to a ΔTcpC deletion mutant. These effects were attenuated in Myd88−/− and Tlr4−/− mice. Transcriptomic analysis confirmed that TcpC inhibits MYD88 dependent gene expression in CFT073 infected human uroepithelial cells but in addition the inhibitory effect included targets in the TRIF and IL-6/IL-1 signaling pathways, where MYD88 dependent and independent signaling may converge. The effects of TcpC on bacterial persistence were attenuated in Trif −/− or Il-1β −/− mice and innate immune responses to ΔTcpC were increased, confirming that Trif and Il-1β dependent targets might be involved in vivo, in addition to Myd88. Furthermore, soluble TcpC inhibited Myd88 and Trif dependent TLR signaling in murine macrophages. Our results suggest that TcpC may promote UTI-associated pathology broadly, through inhibition of TIR domain signaling and downstream pathways. Dysregulation of the host response by microbial TcpC thus appears to impair the protective effects of innate immunity, while promoting inflammation and tissue damage.
Bayesian Learning in Reproducing Kernel Hilbert Spaces

Support Vector Machines nd the hypothesis that corresponds to the centre of the largest hypersphere that can be placed inside version space, i.e. the space of all consistent hypotheses given a training set. The boundaries of version space touched by this hypersphere deene the support vectors. An even more promising approach is to construct the hypothesis using the whole of version space. This is achieved by the Bayes point: the midpoint of the region of intersection of all hy-perplanes bisecting version space into two volumes of equal magnitude. It is known that the centre of mass of version space approximates the Bayes point 30]. The centre of mass is estimated by averaging over the trajectory of a billiard in version space. We derive bounds on the generalisation error of Bayesian classiiers in terms of the volume ratio of version space and parameter space. This ratio serves as an eeective VC dimension and greatly innuences generalisation. We present experimental results indicating that Bayes Point Machines consistently outperform Support Vector Machines. Moreover, we show theoretically and experimentally how Bayes Point Machines can easily be extended to admit training errors.