Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of catalase, peroxidase, and superoxide dismutase within the genus Legionella

We examined 40 strains of Legionella for reduced-oxygen scavenging enzymes. Using a simple reaction chamber with a Swinney filter for the Beers and Sizer assay, we determined the catalase activity of live cells grown on buffered charcoal-yeast extract agar. For 29 strains of Legionella pneumophila, the apparent first-order rate constants for catalase ranged from 0.000 to 0.005. Similarly, low values ranging from 0.001 to 0.005 were observed for Legionella wadsworthii, Legionella oakridgensis, and Legionella gormanii. High catalase activities were found for Legionella jordanis, Legionella longbeachae, Legionella micdadei, and Legionella bozemanii, with first-order rate constant values of 0.010 to 0.035. Cell-free extracts were analyzed for catalase, peroxidase, and superoxide dismutase. Cell-free extracts of all strains had superoxide dismutase levels ranging from 8.2 to 30.5 U per mg of protein. The species could be characterized by their catalase and peroxidase since L. pneumophila and L. gormanii had only peroxidase (relative molecular weight [Mr], 150,000); L. dumoffii had a peroxidase (Mr, 150,000) plus a catalase (Mr, 174,000); and all remaining species had catalase only (Mr, 300,000, 220,000, or 150,000).
Association between Genetic Polymorphisms of Inflammatory Response Genes and Acute Pancreatitis

ABSTRACT Inflammation plays a central role in the pathophysiology of acute pancreatitis (AP). We hypothesized that changes in the function of key components of the inflammatory cascade, caused by genetic polymorphisms, could determine the development and/or severity of AP. We studied the following polymorphisms in 269 patients: IL23R rs11209026, TNF rs1800629, RIPK2 rs42490, NOD2 rs9302752, MCP1 rs1024611 and NFKB1 rs28362491. The rs11209026 A allele was related to the presence of AP (p = 0.007261; OR = 1 .523). Epistasis analysis revealed that AP susceptibility was increased by interaction between IL23R rs11209026 and TNF rs1800629 (p = 1.205 × 10−5; ORinteraction = 4.031). The rs42490-G allele was associated with an increased risk of severe pancreatitis (p = 0.01583; OR = 2.736), severe or moderately severe pancreatitis (p = 0.04206; OR = 1.609), and death (p = 0.03226; OR = 3.010). In conclusion, these results point to a plausible role for genetic polymorphisms in IL23R and RIPK2 in the development and severity of AP.
Fitting a Single Active Appearance Model Simultaneously to Multiple Images

Active Appearance Models (AAMs) are a well studied 2D deformable model. One recently proposed extension of AAMs to multiple images is the CoupledView AAM. Coupled-View AAMs model the 2D shape and appearance of a face in two or more views simultaneously. The major limitation of CoupledView AAMs, however, is that they are specific to a particular set of cameras, both in geometry and the photometric responses. In this paper, we describe how a single AAM can be fit to multiple images, captured simultaneously by cameras with arbitrary geometry and response functions. Our algorithm retains the major benefits of Coupled-View AAMs: the integration of information from multiple images into a single model, and improved fitting robustness.
NBTI-aware DVFS: A new approach to saving energy and increasing processor lifetime

Scaling process technology necessitates the introduction of wide design-time guard bands that ensure lifetime reliability as circuits wear out over time. In this paper, we show how to utilize this knowledge of the guard band and a predictive model to absolutely improve processor power consumption and lifetime without impacting the processor performance against Negative Bias Temperature Instability (NBTI) degradation. For the first time, we evaluate the long-term potential and impact of NBTI-aware job-to-core mapping quantitatively and account for process variations in the system. Our approach saves up to 16% of the dynamic energy consumed and improve lifetime by two years.
CHAPTER 1 Antibody Engineering : Optimizing the Delivery Vehicle

The progression of monoclonal antibodies (MAbs) for radioimmunotherapy (RIT) has beendrivenby theneed to solvea series of problems.Asvariants of antibodies have beendevelopedandevaluated inpreclinical studies, opportunities and limitationshave become evident. Recent advances in DNA technology have led to the ability to tailor and manipulate the immunoglobulin (Ig) molecule for specific functions and in vivo properties. This chapter discusses the use of monoclonal antibodies for radiotherapy with an emphasis on the problems that have been encountered and the subsequent solutions. The exploration of monoclonal antibodies as vehicles for the delivery of radionuclides for therapy has been ongoing for almost 50 years (1). In 1948, Pressman and Keighley reported the first in vivo use of a radiolabeled antibody for imaging (2). Ten years later, the first report of radiolabeled tumor-specific antibodies was utilized for radioimmunodiagnosis, and in 1960, radiolabeled antibodies were used to selectively deliver a therapeutic dose of radiation to tumor tissue (1, 3). Even at these early stages, investigators were quick to realize the obstacles associated with utilizing antibodies for radioimmunotherapy. Radiation doses delivered to tumors in patients were too low to have significant effects on tumor growth, and the prolonged retention of the radiolabeled antibodies in the blood led to toxicity complications (4). The inherent heterogeneity in specificity and affinity of polyclonal antibodies resulted in in vivo variability. The advent of hybridoma technology and the ability to generate monospecific, monoclonal antibodies produced a resurgence in the use of antibodies as “magicbullets” (5, 6). In the1980s, the literature explodedwith reports of radiolabeled MAbs being evaluated in the clinical setting, initially in radioimmunodiagnostic applications, confirming that MAbs against tumor-associated antigens could target
Relevant use of Klotho in FGF19 subfamily signaling system in vivo

α-Klotho (α-Kl) and its homolog, β-Klotho (β-Kl) are key regulators of mineral homeostasis and bile acid/cholesterol metabolism, respectively. FGF15/ humanFGF19, FGF21, and FGF23, members of the FGF19 subfamily, are believed to act as circulating metabolic regulators. Analyses of functional interactions between α- and β-Kl and FGF19 factors in wild-type, α-kl −/−, and β-kl −/− mice revealed a comprehensive regulatory scheme of mineral homeostasis involving the mutually regulated positive/negative feedback actions of α-Kl, FGF23, and 1,25(OH)2D and an analogous regulatory network composed of β-Kl, FGF15/humanFGF19, and bile acids that regulate bile acid/cholesterol metabolism. Contrary to in vitro data, β-Kl is not essential for FGF21 signaling in adipose tissues in vivo, because (i) FGF21 signals are transduced in the absence of β-Kl, (ii) FGF21 could not be precipitated by β-Kl, and (iii) essential phenotypes in Fgf21 −/− mice (decreased expressions of Hsl and Atgl in WAT) were not replicated in β-kl −/− mice. These findings suggest the existence of Klotho-independent FGF21 signaling pathway(s) where undefined cofactors are involved. One-to-one functional interactions such as α-Klotho/FGF23, β-Klotho/FGF15 (humanFGF19), and undefined cofactor/FGF21 would result in tissue-specific signal transduction of the FGF19 subfamily.
The Effects of Imitation Dynamics on Vaccination Behaviours in SIR-Network Model

We present a series of SIR-network models, extended with a game-theoretic treatment of imitation dynamics which result from regular population mobility across residential and work areas and the ensuing interactions. Each considered SIR-network model captures a class of vaccination behaviours influenced by epidemic characteristics, interaction topology, and imitation dynamics. Our focus is the resultant vaccination coverage, produced under voluntary vaccination schemes, in response to these varying factors. Using the next generation matrix method, we analytically derive and compare expressions for the basic reproduction number R0 for the proposed SIR-network models. Furthermore, we simulate the epidemic dynamics over time for the considered models, and show that if individuals are sufficiently responsive towards the changes in the disease prevalence, then the more expansive travelling patterns encourage convergence to the endemic, mixed equilibria. On the contrary, if individuals are insensitive to changes in the disease prevalence, we find that they tend to remain unvaccinated. Our results concur with earlier studies in showing that residents from highly connected residential areas are more likely to get vaccinated. We also show that the existence of the individuals committed to receiving vaccination reduces R0 and delays the disease prevalence, and thus is essential to containing epidemics.
On the Input Acceptance of Transactional Memory

We present the Input Acceptance of Transactional Memory (TM). Despite the large interest for performance of TMs, no existing research work has investigated the impact of solving a conflict that does not need to be solved. Traditional solutions for a TM to be correct is to delay or abort a transaction as soon as it presents a risk to violate consistency. Both alternatives are costly and should be avoided if consistency is actually preserved. To address this problem, we introduce the input acceptance of a TM as its ability to commit transactions, we upper-bound the input acceptance of existing TMs and propose a new TM with higher input acceptance.
Speciation, Divergence, and the Origin of Gryllus rubens: Behavior, Morphology, and Molecules

The last 25 years or so has seen a huge resurgence of interest in speciation research. This has coincided with the development and widespread use of new tools in molecular genetics, especially DNA sequencing, to inform ecological and evolutionary questions. Here I review about a decade of work on the sister species of field crickets Gryllus texensis and G. rubens. This work has included analysis of morphology, behavior, and the mitochondrial DNA molecule. The molecular work in particular has dramatically re-shaped my interpretation of the speciational history of these taxa, suggesting that rather than ‘sister’ species we should consider these taxa as ‘mother-daughter’ species with G. rubens derived from within a subset of ancestral G. texensis.
Effect of Reaction Temperature and Sonication Pretreatment in the Hydrothermal Process on the Morphology of Titanate NanoStructure

Nawin VIRIYA-EMPIKUL1,2, Tawatchai CHARINPANITKUL2, Noriaki SANO3, Apinan SOOTTITANTAWAT2, Takeyuki KIKUCHI4, Kajornsak FAUNGNAWAKIJ1 and Wiwut TANTHAPANICHAKOON1 1National Nanotechnology Center, National Science and Technology Development Agency (NSTDA), Klong Luang, Phathumthani 12120, Thailand 2Center of Excellence in Particle Technology (CEPT), Department of Chemical Engineering, Chulalongkorn University, Patumwan, Bangkok 10330, Thailand 3Department of Chemical Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto-shi, Kyoto 615-8510, Japan 4Department of Engineering Science, University of Hyogo, 2167, Shosha, Himeji-shi, Hyogo 671-2201, Japan
One Class per Named Entity: Exploiting Unlabeled Text for Named Entity Recognition

In this paper, we present a simple yet novel method of exploiting unlabeled text to further improve the accuracy of a high-performance state-of-the art named entity recognition (NER) system. The method utilizes the empirical property that many named entities occur in one name class only. Using only unlabeled text as the additional resource, our improved NER system achieves an F1 score of 87.13%, an improvement of 1.17% in F1 score and a 8.3% error reduction on the CoNLL 2003 English NER official test set. This accuracy places our NER system among the top 3 systems in the CoNLL 2003 English shared task.
LOW POWER TEST PATTERN GENERATION USING TEST-PER-SCAN TECHNIQUE FOR BIST IMPLEMENTATION

This paper introduces the function of test cases with minimal power for Built-In-Self-Test (BIST) implementation. This method intends Test-Per-Scan (TPS) based test cases using Multiple Single Input Change (MSIC) architecture. Multiple SIC patterns are developed by using EX-OR operation of twisted ring counter and test design algorithms like Linear Feedback Shift Register (LFSR),Bit-Swapping LFSR (BSLFSR), and Cellular Automata (CA). These patterns are used to a diminish number of transitions in the test patterns that are generated. The preferred method uses Test-Per-Scan technique for generating Multiple SIC test patterns. TPS diminished the power consumption during test mode. The seed generator used in TPS is modified LFSR ’ s i.e., BS-LFSR, Cellular Automata (CA). BS-LFSR is composed of with an LFSR with a multiplexer. In CA, it also presents a variation on a BIST technique, which is from a one-dimensional cellular automaton; the pseudo random bit generator is generated. The proposed Hybrid Cellular Automata (HCA) using the rules 90 and 150 to generate the pseudo random designs. Moreover, the CA implementations illustrates properties of data compression like LFSRs and that they exhibit locally and with topological consistency significant attributes for a VLSI design. In this proposed method, LFSR is replaced with BS-LFSR, and HCA. Simulation and synthesis outcome with ISCAS c432 benchmark determine that Multiple SIC can reduce the power consumption
Extensible Provisioning Protocol (EPP) Contact Mapping

This document describes an Extensible Provisioning Protocol (EPP) mapping for the provisioning and management of individual or organizational social information identifiers (known as "contacts") stored in a shared central repository. Specified in Extensible Markup Language (XML), the mapping defines EPP command syntax and semantics as applied to contacts.
Simultaneous Magnetic Resonance Angiography and Multiparametric Mapping in the Transient-state

Quantitative Transient-state Imaging (QTI) is a non-random, dictionary-less MR Fingerprinting alternative. Through iterative reconstructions, QTI recovers a series of contrast-weighted images from transientstate acquisitions and subsequently estimates the parameters that best describe the resulting dynamic signal evolutions. Here, we extend the QTI framework by incorporating a simple velocity model that accounts for blood flowing into and out of the imaging slice. The model, however wrong, can be very useful: it predicts signal hyperintensities in the presence of flow, allowing for the simultaneous reconstruction of MR Angiography images, hundreds of dynamic contrast-weighted images, and their corresponding parametric maps.
Network system design affects distributed parallel computing

Computational Grid is essential for scientific advance, and advanced technology research and development because single system computing power is restricted by processor clock speed advancing. Increment of processor clock speed starts decreasing due to the minimum size of silicon dies v.s the distance that electrons can travel in one clock cycle driven by the light speed. The maximum processor clock speed affects not only computation power, but also communication capability because current network subsystem relies on the system resources, such as CPU, to move data from/to network. To provide a high performance and scalable network subsystem for distributed computation systems, intuitively, making network subsystem to use less or not to depend on these system resources is the key. This paper will analyze system resources consumed in each network subsystem layer/module, and address what design decision in network subsystem advance, such as Jumbo Frame, Network on Chip (NoC) --- to remove system resource consumptions for network operations --- will be able to increase the computation power on distributed computational systems.
Cortical reorganization in recent-onset tinnitus patients by the Heidelberg Model of Music Therapy

Pathophysiology and treatment of tinnitus still are fields of intensive research. The neuroscientifically motivated Heidelberg Model of Music Therapy, previously developed by the German Center for Music Therapy Research, Heidelberg, Germany, was applied to explore its effects on individual distress and on brain structures. This therapy is a compact and fast application of nine consecutive 50-min sessions of individualized therapy implemented over 1 week. Clinical improvement and long-term effects over several years have previously been published. However, the underlying neural basis of the therapy's success has not yet been explored. In the current study, the therapy was applied to acute tinnitus patients (TG) and healthy active controls (AC). Non-treated patients were also included as passive controls (PTC). As predicted, the therapeutic intervention led to a significant decrease of tinnitus-related distress in TG compared to PTC. Before and after the study week, high-resolution MRT scans were obtained for each subject. Assessment by repeated measures design for several groups (Two-Way ANOVA) revealed structural gray matter (GM) increase in TG compared to PTC, comprising clusters in precuneus, medial superior frontal areas, and in the auditory cortex. This pattern was further applied as mask for general GM changes as induced by the therapy week. The therapy-like procedure in AC also elicited similar GM increases in precuneus and frontal regions. Comparison between structural effects in TG vs. AC was calculated within the mask for general GM changes to obtain specific effects in tinnitus patients, yielding GM increase in right Heschl's gyrus, right Rolandic operculum, and medial superior frontal regions. In line with recent findings on the crucial role of the auditory cortex in maintaining tinnitus-related distress, a causative relation between the therapy-related GM alterations in auditory areas and the long-lasting therapy effects can be assumed.
Association between N-terminal proB-type Natriuretic Peptide and Depressive Symptoms in Patients with Acute Myocardial Infarction

Background: While depression and certain cardiac biomarkers are associated with acute myocardial infarction (AMI), the relationship between them remains largely unexplored. We examined the association between depressive symptoms and biomarkers in patients with AMI. Methods: We performed a cross-sectional study using data from 103 patients with AMI between March 2013 and September 2014. The levels of depression, N-terminal proB-type natriuretic peptide (NT-proBNP), and troponin I (TnI) were measured at baseline. The patients were divided into two groups: those with depressive symptoms and those without depressive symptoms according to Zung Self-rating Depression Scale (SDS) score. Baseline comparisons between two groups were made using Student's t-test for continuous variables, Chi-square or Fisher's exact test for categorical variables, and Wilcoxon test for variables in skewed distribution. Binomial logistic regression and multivariate linear regression were performed to assess the association between depressive symptoms and biomarkers while adjusting for demographic and clinical variables. Results: Patients with depressive symptoms had significantly higher NT-proBNP levels as compared to patients without depressive symptoms (1135.0 [131.5, 2474.0] vs. 384.0 [133.0, 990.0], Z = −2.470, P = 0.013). Depressive symptoms were associated with higher NT-proBNP levels (odds ratio [OR] = 2.348, 95% CI: 1.344 to 4.103, P = 0.003) and higher body mass index (OR = 1.169, 95% confidence interval [CI]: 1.016 to 1.345, P = 0.029). The total SDS score was associated with the NT-proBNP level (&bgr; = 0.327, 95% CI: 1.674 to 6.119, P = 0.001) after multivariable adjustment. In particular, NT-proBNP was associated with three of the depressive dimensions, including core depression (&bgr; = 0.299, 95% CI: 0.551 to 2.428, P = 0.002), cognitive depression (&bgr; = 0.320, 95% CI: 0.476 to 1.811, P = 0.001), and somatic depression (&bgr; = 0.333, 95% CI: 0.240 to 0.847, P = 0.001). Neither the overall depressive symptomatology nor the individual depressive dimensions were associated with TnI levels. Conclusions: Depressive symptoms, especially core depression, cognitive depression, and somatic depression, were related to high NT-proBNP levels in patients with AMI.
FASTer FTL for Enterprise-Class Flash Memory SSDs

For the past decade, numerous methods have been proposed for the design of a flash translation layer (FTL), which is the core engine of flash memory drives that critically determines the performance of the drives. In this paper, we revisit one of the popular FTL schemes called FAST, and augment it with new optimization techniques aiming particularly at online transaction processing (OLTP) workloads. As flash memory solid state drives (SSDs) are increasingly adopted for large-scale enterprise-class storage systems, it is important to develop an FTL that can deal with OLTP workloads in a scalable manner, which are characterized by a large number of small, random and skewed IO operations. With the proposed optimization methods such as giving a second chance to valid pages and isolating cold ones, the enhanced FTL, called FASTer, outperforms FAST considerably. In our experiments, FASTer reduced average elapsed time by more than 30 percent, and minimized the fluctuation of response time drastically. Overall, the performance of FASTer was comparable to a page mapping FTL, which tends to consume much more DRAM space to store a large mapping table. This will make the FASTer FTL one of the most cost effective and scalable FTL schemes for OLTP workloads.
Migraine Aura and Related Phenomena: Beyond Scotomata and Scintillations

Migraine affects the cortical physiology and may induce dysfunction both ictally and interictally Although visual symptoms predominate during aura, other contiguous cortical areas related to less impressive symptoms are also impaired in migraine. Answers from 72.2% migraine with aura and 48.6% of migraine without aura patients on human faces and objects recognition, colour perception, proper names recalling and memory in general showed dysfunctions suggestive of prosopagnosia, dyschromatopsia, ideational apraxia, alien hand syndrome, proper name anomia or aphasia, varying in duration and severity. Symptoms frequently occurred in a successively building-up pattern fitting with the geographical distribution of the various cortical functions. When specifically inquired, migraineurs reveal less evident symptoms that are not usually considered during routine examination. Spreading depression most likely underlies the aura symptoms progression. Interictal involvement indicates that MWA and MWoA are not completely silent outside attacks, and that both subforms of migraine may share common mechanisms.
Query From Examples: An Iterative, Data-Driven Approach to Query Construction

In this paper, we propose a new approach, called Query from Examples (QFE), to help non-expert database users construct SQL queries. Our approach, which is designed for users who might be unfamiliar with SQL, only requires that the user is able to determine whether a given output table is the result of his or her intended query on a given input database. To kick-start the construction of a target query Q, the user first provides a pair of inputs: a sample database D and an output table R which is the result of Q on D. As there will be many candidate queries that transform D to R, QFE winnows this collection by presenting the user with new database-result pairs that distinguish these candidates. Unlike previous approaches that use synthetic data for such pairs, QFE strives to make these distinguishing pairs as close to the original (D,R) pair as possible. By doing so, it seeks to minimize the effort needed by a user to determine if a new database-result pair is consistent with his or her desired query. We demonstrate the effectiveness and efficiency of our approach using real datasets from SQLShare, a cloud-based platform designed to help scientists utilize RDBMS technology for data analysis.