Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Processing of Propeptide Inhibitors of Rap Phosphatases in Bacillus subtilis

ABSTRACT In the phosphorelay signal transduction system for sporulation initiation in Bacillus subtilis, the opposing activities of histidine kinases and aspartyl phosphate phosphatases determine the cell's decision whether to continue with vegetative growth or to initiate the differentiation process. Regulated dephosphorylation of the Spo0A and Spo0F response regulators allows a variety of negative signals from physiological processes that are antithetical to sporulation to impact on the activation level of the phosphorelay. Spo0F∼P is the known target of two related phosphatases, RapA and RapB. In addition to RapA and RapB, a third member of the Rap family of phosphatases, RapE, specifically dephosphorylated the Spo0F∼P intermediate in response to competence development. RapE phosphatase activity was found to be controlled by a pentapeptide (SRNVT) generated from within the carboxy-terminal domain of the phrE gene product. A synthetic PhrE pentapeptide could (i) complement the sporulation deficiency caused by deregulated RapE activity of aphrE mutant and (ii) inhibit RapE-dependent dephosphorylation of Spo0F∼P in in vitro experiments. The PhrE pentapeptide did not inhibit the phosphatase activity of RapA and RapB. These results confirm previous conclusions that the specificity for recognition of the target phosphatase is contained within the amino acid sequence of the pentapeptide inhibitor.
comparison of the Serum Levels of Trace Elements in Areas with High or Low Rate of Esophageal Cancer

BACKGROUND There is a critical role for trace elements in cancer prevention. Since northeast Iran is known as a high risk area for esophageal cancer, this study was designed to compare the serum levels of some trace elements in high and low rate areas of Golestan province. METHODS We used 240 fasting serum samples obtained in 2011 from eastern and western parts of Golestan province during the non-communicable diseases’ screening program. To carry out laboratory examinations, the samples were firstly deproteinated and then the concentrations of the intended elements were measured by an atomic absorption spectrometer. A total of 227 samples were used in the present study and the remaining 13 samples were excluded due to inappropriate conditions. RESULTS The mean serum level of zinc in the high-risk region was significantly lower than that in the low-risk region. But no significant difference was detected in serum levels of copper, magnesium, and manganese in the low-risk and high-risk regions. CONCLUSION As this study was an ecological study with no comparison between patients with cancer and healthy population, its results cannot be used for the general population. Therefore, complementary studies including case-control studies are suggested for further evaluation of the relationship between these elements and the incidence of esophageal cancer.
Service-oriented autonomous decentralized community communication technique for a complex adaptive information system

In rapidly changing large-scale information system, users' requirements are changing constantly. To address the extreme dynamism in the large-scale information system, we have proposed the autonomous community information system (ACIS). It is a decentralized bilateral-hierarchy architecture that forms a community of individual end-users (community members) having the same interests and demands in somewhere, at specified time. ACIS allows the community members to mutually cooperate and share information without loading up any single node excessively. We propose an autonomous decentralized community communication technique to assure a flexible, scalable and multilateral communication among the community members. The main ideas behind this communication technique are: content-code communication (community service-based) for flexible information service provision/utilization and multilateral benefits communication for scalable and productive cooperation among members. All members communicate productively for the satisfaction of all the community members. The scalability of the system's response time regardless of the number of the community members has been shown by simulation. Thus, the autonomous decentralized community communication technique reveals significant results of the response time with continuous increasing in the total number of members.
Shear Strength of Large Beams

This paper considers the problem of the effect of absolute size on the shear strength of reinforced concrete beams. The results of previous tests are compared and a brief description is given of the way in which beams carry shear force, which is consistent with recent data. Tests on a series of 15 beams in which true scale models were used, with a depth range of 150-1000 mm (6-40 in.) are described. The test results indicate that, when beams are modeled correctly, the effect of absolute size is small. In practice it may not always be possible to design beams of the type in which the size effect is insignificant. For these cases, design advice is given.
Medical treatment of dystonia

Medications such as anticholinergic drugs, dopamine modulators, baclofen, muscle relaxants, and other pharmacologic agents have been used for a long time to treat dystonia, but the introduction of botulinum toxin and deep brain stimulation clearly revolutionized the symptomatic treatment of this neurological movement disorder. Therapy of dystonia can be divided into the following categories: (1) physical, supportive, and ancillary therapy; (2) pharmacologic treatment; (3) chemodenervation with botulinum toxin; and (4) peripheral and central surgery (deep brain stimulation). Except in some cases of secondary dystonia, pathogenesis‐targeted or disease‐modifying therapy is currently not available. This review focuses on evidence‐based medical treatment of dystonia, highlighting recent advances, with emphasis on individualized approach. © 2013 Movement Disorder Society
Practical Extensions of a Randomized Testing Tool

Many efficient random testing algorithms for object-oriented software have been proposed due to their simplicity and reasonable code coverage; however, even the state-of-the-art random test algorithms yield very low code coverage (around 22%) on large-scale software. We propose four testing techniques to improve test coverage. The proposed techniques are pluggable to any existing random testing techniques for object-oriented software. We incorporated our techniques to a state-of-the-art random testing tool and tested large-scale software, including Java Collections, Apache Ant, and ASM. Our experimental study shows that the proposed techniques increase at most 21% of branch coverage - a significant improvement.
From boring to scoring – a collaborative serious game for learning and practicing mathematical logic for computer science education

In this study, we address the problem of low retention and high dropout rates of computer science university students in early semesters of the studies. Complex and high abstract mathematical learning materials have been identified as one reason for the dropout rate. In order to support the understanding and practicing of core mathematical concepts, we developed a game-based multitouch learning environment in which the need for a suitable learning environment for mathematical logic was combined with the ability to train cooperation and collaboration in a learning scenario. As application domain, the field of mathematical logic had been chosen. The development process was accomplished along three steps: First, ethnographic interviews were run with 12 students of computer science revealing typical problems with mathematical logic. Second, a multitouch learning environment was developed. The game consists of multiple learning and playing modes in which teams of students can collaborate or compete against each other. Finally, a twofold evaluation of the environment was carried out (user study and cognitive walk-through). Overall, the evaluation showed that the game environment was easy to use and rated as helpful: The chosen approach of a multiplayer game supporting competition, collaboration, and cooperation is perceived as motivating and “fun. ”
Shock waves and cosmological matrix models

We find the shock wave solutions in a class of cosmological backgrounds with a null singularity, each of these backgrounds admits a matrix description. A shock wave solution breaks all supersymmetry meanwhile indicates that the interaction between two static D0-branes cancel, thus provides basic evidence for the matrix description. The probe action of a D0-brane in the background of another suggests that the usual perturbative expansion of matrix model breaks down.
Formation Process of Super‐Water‐Repellent Al2O3 Coating Films with High Transparency by the Sol–Gel Method

Alumina thin films with a roughness of 20 to 50 nm were formed by immersing porous alumina gel films prepared by the sol-gel method in boiling water. When hydrolyzed fluoroalkyltrimethoxysilane was coated on the alumina films, the contact angle for water was increased with an increase of immersion time, and immersion for 30 s was long enough to give super-water-repellency and high transparency; the contact angle for water of the film was 165° and the transmittance for the visible light was higher than 92%. It was found that the surface of the alumina gel films immersed in boiling water consisted of boehmite crystals. It was shown that the existence of air in the hydrophobic pores on the surface caused the super-water-repellency.
Structural and Spectroscopic Characterization of P450 BM3 Mutants with Unprecedented P450 Heme Iron Ligand Sets

Two novel P450 heme iron ligand sets were generated by directed mutagenesis of the flavocytochrome P450 BM3 heme domain. The A264H and A264K variants produce Cys-Fe-His and Cys-Fe-Lys axial ligand sets, which were validated structurally and characterized by spectroscopic analysis. EPR and magnetic circular dichroism (MCD) provided fingerprints defining these P450 ligand sets. Near IR MCD spectra identified ferric low spin charge-transfer bands diagnostic of the novel ligands. For the A264K mutant, this is the first report of a Cys-Fe-Lys near-IR MCD band. Crystal structure determination showed that substrate-free A264H and A264K proteins crystallize in distinct conformations, as observed previously in substrate-free and fatty acid-bound wild-type P450 forms, respectively. This, in turn, likely reflects the positioning of the I α helix section of the protein that is required for optimal configuration of the ligands to the heme iron. One of the monomers in the asymmetric unit of the A264H crystals was in a novel conformation with a more open substrate access route to the active site. The same species was isolated for the wildtype heme domain and represents a novel conformational state of BM3 (termed SF2). The “locking” of these distinct conformations is evident from the fact that the endogenous ligands cannot be displaced by substrate or exogenous ligands. The consequent reduction of heme domain conformational heterogeneity will be important in attempts to determine atomic structure of the full-length, multidomain flavocytochrome, and thus to understand in atomic detail interactions between its heme and reductase domains.
Rising Methicillin-Resistant Staphylococcus aureus Infections in Ear, Nose, and Throat Diseases

The increasing incidence of methicillin-resistant Staphylococcus aureus infections (MRSA) in ENT diseases is becoming a big clinical concern. Here two patients are described who developed MRSA infections presented with unusual post-FESS epistaxis and postmastoidectomy perichondrial abscess and failed treatment with broad spectrum intravenous antibiotics. Following treatment with oral linezolid combined with local mupirocin dressing both patients fully recovered.
Pulse: A Dynamic Deadlock Detection Mechanism Using Speculative Execution

Deadlock can occur wherever multiple processes interact. Most existing static and dynamic deadlock detection tools focus on simple types of deadlock, such as those caused by incorrect ordering of lock acquisitions. In this paper, we propose Pulse, a novel operating system mechanism that dynamically detects various types of deadlock in application programs. Pulse runs as a system daemon. Periodically, it scans the system for processes that have been blocked for a long time (e.g., waiting on I/O events). To determine if these processes are deadlocked, Pulse speculatively executes them ahead to discover their dependences. Based on this information, it constructs a general resource graph and detects deadlock by checking if the graph contains cycles. The ability to look into the future allows Pulse to detect deadlocks involving consumable resources, such as synchronization semaphores and pipes, which no existing tools can detect. We evaluate Pulse by showing that it can detect deadlocks in the classical dining-philosophers and smokers problems. Furthermore, we show that Pulse can detect a well-known deadlock scenario, which is widely referred to as a denial-of-service vulnerability, in the Apache web server. Our results show that Pulse can detect all these deadlocks within three seconds, and it introduces little performance overhead to normal applications that do not deadlock.
Robust principle component analysis based four-dimensional computed tomography

The purpose of this article for four-dimensional (4D) computed tomography (CT) is three-fold. (1) A new spatiotemporal model is presented from matrix perspective with the row dimension in space and the column dimension in time, namely, Robust PCA based 4DCT model (Robust Principle Component Analysis based 4D CT). That is, instead of viewing the 4D object as a temporal collection of three-dimensional (3D) images and looking for local coherence in time or space independently, we perceive it as a mixture of low-rank matrix and sparse matrix to explore the maximum temporal coherence of spatial structure among phases. Here the low-rank matrix corresponds to the “background” or reference state, which is stationary over time or similar in structure; the sparse matrix stands for the “motion” or time-varying component, e.g., heart motion in cardiac imaging, which is often either approximately sparse itself or can be sparsified in the proper basis. Besides 4D CT, this Robust PCA based 4DCT model should be applicable in other imaging problems for motion reduction or/and change detection with the least amount of data, such as multi-energy CT, cardiac MRI, and hyperspectral imaging. (2) A dynamic strategy for data acquisition, i.e., a temporally spiral scheme, is proposed that can potentially maintain the similar reconstruction accuracy with much fewer projections of the data. The key point of this dynamic scheme is to reduce the total number of measurements and hence the radiation dose, by acquiring complementary data in different phases while reducing redundant measurements of the common background structure. (3) An accurate, efficient, yet simple-to-implement algorithm based on split Bregman method is developed for solving the model problem with the sparse representation in tight frames
Pseudorandom number generation by p-adic ergodic transformations: an addendum

The paper study counter-dependent pseudorandom number gen- erators based on m-variate (m > 1) ergodic mappings of the space of 2-adic integers Z2. The sequence of internal states of these generators is defined by the recurrence law xi+1 = H B i (xi) mod 2 n , whereas their output sequence is zi = F B i (xi) mod 2 n; here xj, zj are m-dimensional vectors over Z2. It is shown how the results obtained for a univariate case could be extended to a multivariate case.
Parallel skeletons for structured composition

In this paper, we propose a straightforward solution to the problems of compositional parallel programming by using skeletons as the uniform mechanism for structured composition. In our approach parallel programs are constructed by composing procedures in a conventional base language using a set of high-level, pre-defined, functional, parallel computational forms known as skeletons. The ability to compose skeletons provides us with the essential tools for building further and more complex application-oriented skeletons specifying important aspects of parallel computation. Compared with the process network based composition approach, such as PCN, the skeleton approach abstracts away the fine details of connecting communication ports to the higher level mechanism of making data distributions conform, thus avoiding the complexity of using lower level ports as the means of interaction. Thus, the framework provides a natural integration of the compositional programming approach with the data parallel programming paradigm.
Estimation of electrode location in a rat motor cortex by laminar analysis of electrophysiology and intracortical electrical stimulation

While the development of microelectrode arrays has enabled access to disparate regions of a cortex for neurorehabilitation, neuroprosthetic and basic neuroscience research, accurate interpretation of the signals and manipulation of the cortical neurons depend upon the anatomical placement of the electrode arrays in a layered cortex. Toward this end, this report compares two in vivo methods for identifying the placement of electrodes in a linear array spaced 100 µm apart based on in situ laminar analysis of (1) ketamine–xylazine-induced field potential oscillations in a rat motor cortex and (2) an intracortical electrical stimulation-induced movement threshold. The first method is based on finding the polarity reversal in laminar oscillations which is reported to appear at the transition between layers IV and V in laminar ‘high voltage spindles’ of the rat cortical column. Analysis of histological images in our dataset indicates that polarity reversal is detected 150.1 ± 104.2 µm below the start of layer V. The second method compares the intracortical microstimulation currents that elicit a physical movement for anodic versus cathodic stimulation. It is based on the hypothesis that neural elements perpendicular to the electrode surface are preferentially excited by anodic stimulation while cathodic stimulation excites those with a direction component parallel to its surface. With this method, we expect to see a change in the stimulation currents that elicits a movement at the beginning of layer V when comparing anodic versus cathodic stimulation as the upper cortical layers contain neuronal structures that are primarily parallel to the cortical surface and lower layers contain structures that are primarily perpendicular. Using this method, there was a 78.7 ± 68 µm offset in the estimate of the depth of the start of layer V. The polarity reversal method estimates the beginning of layer V within ±90 µm with 95% confidence and the intracortical stimulation method estimates it within ±69.3 µm. We propose that these methods can be used to estimate the in situ location of laminar electrodes implanted in the rat motor cortex.
Singing Mice, Songbirds, and More: Models for FOXP2 Function and Dysfunction in Human Speech and Language

In 2001, a point mutation in the forkhead box P2 (FOXP2) coding sequence was identified as the basis of an inherited speech and language disorder suffered by members of the family known as “KE. ” This mini-symposium review focuses on recent findings and research-in-progress, primarily from five laboratories. Each aims at capitalizing on the FOXP2 discovery to build a neurobiological bridge between molecule and phenotype. Below, we describe genetic through behavioral techniques used currently to investigate FoxP2 in birds, rodents, and humans for discovery of the neural bases of vocal learning and language.
Transfer of the MSH2·MSH6 Complex from Proliferating Cell Nuclear Antigen to Mispaired Bases in DNA*

Proliferating cell nuclear antigen (PCNA) is thought to play a role in DNA mismatch repair at the DNA synthesis step as well as in an earlier step. Studies showing that PCNA interacts with mispair-binding protein complexes, MSH2·MSH3 and MSH2·MSH6, and that PCNA enhances MSH2·MSH6 mispair binding specificity suggest PCNA may be involved in mispair recognition. Here we show that PCNA and MSH2·MSH6 form a stable ternary complex with a homoduplex (G/C) DNA, but MSH2·MSH6 binding to a heteroduplex (G/T) DNA disrupts MSH2·MSH6 binding to PCNA. We also found that the addition of ATP or adenosine 5′-O-(thiotriphosphate) restores MSH2·MSH6 binding to PCNA, presumably by disrupting MSH2·MSH6 binding to the heteroduplex (G/T) DNA. These results support a model in which MSH2·MSH6 binds to PCNA loaded on newly replicated DNA and is transferred from PCNA to mispaired bases in DNA.
Automated detection of diabetic retinopathy: barriers to translation into clinical practice

Automated identification of diabetic retinopathy (DR), the primary cause of blindness and visual loss for those aged 18–65 years, from color images of the retina has enormous potential to increase the quality, cost–effectiveness and accessibility of preventative care for people with diabetes. Through advanced image analysis techniques, retinal images are analyzed for abnormalities that define and correlate with the severity of DR. Translating automated DR detection into clinical practice will require surmounting scientific and nonscientific barriers. Scientific concerns, such as DR detection limits compared with human experts, can be studied and measured. Ethical, legal and political issues can be addressed, but are difficult or impossible to measure. The primary objective of this review is to survey the methods, potential benefits and limitations of automated detection in order to better manage translation into clinical practice, based on extensive experience with the systems we have developed.
Feedback Regulation of Glucose Transporter Gene Transcription in Kluyveromyces lactis by Glucose Uptake

ABSTRACT In the respirofermentative yeast Kluyveromyces lactis, only a single genetic locus encodes glucose transporters that can support fermentative growth. This locus is polymorphic in wild-type isolates carrying either KHT1and KHT2, two tandemly arranged HXT-like genes, or RAG1, a low-affinity transporter gene that arose by recombination between KHT1 andKHT2. Here we show that KHT1 is a glucose-induced gene encoding a low-affinity transporter very similar to Rag1p. Kht2p has a lower Km (3.7 mM) and a more complex regulation. Transcription is high in the absence of glucose, further induced by low glucose concentrations, and repressed at higher glucose concentrations. The response ofKHT1 and KHT2 gene regulation to high but not to low concentrations of glucose depends on glucose transport. The function of either Kht1p or Kht2p is sufficient to mediate the characteristic response to high glucose, which is impaired in akht1 kht2 deletion mutant. Thus, the KHTgenes are subject to mutual feedback regulation. Moreover, glucose repression of the endogenous β-galactosidase (LAC4) promoter and glucose induction of pyruvate decarboxylase were abolished in the kht1 kht2 mutant. These phenotypes could be partially restored by HXT gene family members fromSaccharomyces cerevisiae. The results indicate that the specific responses to high but not to low glucose concentrations require a high rate of glucose uptake.