Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathway Confirmation and Flux Analysis of Central Metabolic Pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

ABSTRACT Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (GC-MS) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) indicate the lack of an oxidatively functional tricarboxylic acid (TCA) cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80% of the lactate was converted to acetate and that the reactions involved are the primary route of energy production [NAD(P)H and ATP production]. Independently of the TCA cycle, direct cleavage of acetyl coenzyme A to CO and 5,10-methyl tetrahydrofuran also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or the reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.
Mental Images of Text : Learning Document Similarity using Web Photos

Modern search engines rely solely on text to analyze the content of Web documents. However, it is well known that humans often incorporate ”mental visualization” in the form of mental images in order to interpret text. Psychological studies have demonstrated that humans are able to create these visual perceptions even in absence of external visual stimuli. Such a physiological behavior in the human brain suggests that incorporating visual information to text analysis in the machines could be beneficial as well. In this paper, we present a method that incorporates the idea of mental images to learn a document similarity metric exploiting both text and visual data. The key idea behind our method is to associate a visual representation to the most salient portions of the original text. We do so by leveraging text-based image search engines: the photos retrieved using these textual queries can be viewed as akin to the mental images used by humans. We then combine these images with the original text representation in order to perform a joint analysis of text and visual data. In this paper we demonstrate this approach on the task of semantically clustering Web search results for a given query. Our experiments indicate that incorporating images leads to increased accuracy rates relative to systems relying on text only. In addition, our method learns a universal document similarity metric which can be successfully generalized to any queries and arbitrary documents, a property that provides an efficient framework to perform predictions at search time. Finally, we show that the concept of mental images can be successfully applied to different text domains, which suggests that our method can be generalized to many different tasks.
Transcription from the Thyroid Hormone-dependent Promoter of the Xenopus laevis Thyroid Hormone Receptor βA Gene Requires a Novel Upstream Element and the Initiator, but Not a TATA Box*

The thyroid hormone receptor (TR) β genes in Xenopus laevis are regulated by thyroid hormone in all organs of an animal during metamorphosis. This autoregulation appears to be critical for systematic transformations of different organs as a tadpole is transformed into a frog. To understand this autoregulation, we have previously identified a thyroid hormone response element in the hormone-dependent promoter of the X. laevisTRβA gene. We report here the detailed characterization of the promoter. We have now mapped the transcription start site and demonstrated the existence of an initiator element at the start site critical for promoter function. More important, our deletion and mutational experiments revealed a novel upstream DNA element that is located 125 base pairs upstream of the start site and that is essential for active transcription from the promoter. Promoter reconstitution experiments showed that this novel element does not function as an enhancer, but acts as a core promoter element, which, together with the initiator, directs accurate transcription from the promoter. Finally, we provide evidence for the existence of a protein(s) that specifically recognizes this element. Our studies thus demonstrate that the TRβA promoter has a unique organization consisting of an initiator and a novel upstream promoter element. Such an organization may be important for the ubiquitous but tissue-dependent temporal regulation of the gene by thyroid hormone during amphibian metamorphosis.
Effect of Moderate Aerobic Training on Bone Metabolism Indices among Adult Humans

Objective: This study assessed the osteogenic effect (T-Score) and changes in bone markers in healthy subjects by 12-weeks of aerobic training. Methods: Total 65 healthy subjects (36 males, 29 females), their age ranged between 30 and 60 years with normal body mass index, were recruited to participate in this study and they were selected among healthy subjects who do not have any metabolic disorders and were not receiving any medication that could affect the bone turnover. Standardized physical examination and collection of serum samples were performed at base line and after 12 weeks of moderate aerobic training to measure bone formation markers (osteocalcin (OC) and bone specific alkaline Phosphatase (BAP) and bone resorption marker Deoxypyridinoline (DPD), and serum calcium. Each subject participated in exercise training program for 12 weeks, three times per week. Results: The results showed that the 12 weeks of moderate aerobic training produced a significant improvement in all bone metabolism indices including Serum bone-specific alkaline phosphatase, serum osteocalcin, serum free Calcium and bone mineral density among all subjects. Conclusion : Moderate intensity of aerobic training exerts significant positive effects on bone formation marker and bone density associated with a significant decrease in the rate of bone resorption that could assist in preventing or decelerating osteoporosis.
Time -frequency wavelet transform coherence of cardio-respiratory signals during exercise

Wavelet transform coherence (WTC) is a method originally introduced to discover transient linear correlations in random processes. We adjusted and modified the WTC to establish it as a tool for the evaluation of the autonomic nervous system (ANS) activity by applying a bivariate analysis of the cardiorespiratory signals. The WTC provides insight into the transient linear order of the system through the computation of time-frequency maps. Quantitative methods for specific time or frequency bands are also introduced. The WTC was implemented on data from an experimental protocol which included graded exercise stress testing (GXT) with 8 normal subjects. The WTC time-frequency map exhibited a novel presentation of the dynamical changes in RSA phenomena. Furthermore, an integration over the respiratory frequency band revealed a significant (p < 0.001) drop of HR-Respiration coherence around 75% of the maximum effort.
New Security Models and Provably-Secure Schemes for Basic Query Support in Outsourced Databases

In this paper, we take a closer look at the security of outsourced databases (aka Database-as-the-Service or DAS), a topic of emerging importance. DAS allows users to store sensitive data on a remote, untrusted server and retrieve desired parts of it on request. At ﬁrst we focus on basic, exact-match query functionality, and then extend our treatment to preﬁx-matching and, to a more limited extent, range queries as well. We propose several searchable encryption schemes that are not only practical enough for use in DAS in terms of query-processing efﬁciency but also provably-provide privacy and authenticity of data under new deﬁnitions of security that we introduce. The schemes are easy to implement and are based on standard cryptographic primitives such as block ciphers, symmetric encryption schemes, and message authentication codes. As we are some of the ﬁrst to apply the provable-security framework of modern cryptography to this context, we believe our work will help to properly analyze future schemes and facilitate further research on the subject in general.
Feynman graphs and generalized eikonal approach to high energy knock-out processes

The cross section of hard semiexclusive A(e,e{sup {prime}}N)(A{minus}1) reactions for fixed missing energy and momentum is calculated within the eikonal approximation. Relativistic dynamics and kinematics of high energy processes are unambiguously accounted for by using the analysis of appropriate Feynman diagrams. A significant dependence of the final state interactions on the missing energy is found, which is important for interpretation of forthcoming color transparency experiments. A new, more stringent kinematic restriction on the region where the contribution of short-range nucleon correlations is enhanced in semiexclusive knock-out processes is derived. It is also demonstrated that the use of light-cone variables leads to a considerable simplification of the description of high energy knock-out reactions. {copyright} {ital 1997} {ital The American Physical Society}
Modified multiple-measurement vector model for SAR imaging

The multiple measurement vectors (MMV) model can be used to effectively represent the jointly sparse signals. However, this model cannot be directly used in the scenario of synthetic aperture radar (SAR) imaging. The reason is that, the MMV model requires that the multiple sparse vectors have the common sparse pattern, while the SAR range profiles at different pulses have different sparse structures due to the range migration effect. In this paper, a modified MMV model is proposed for SAR imaging. The range migration effect is embedded into the proposed model, and a modified orthogonal matching pursuit (OMP) algorithm is developed to obtain the high-resolution range profile. Then the cross-range focusing is performed by traditional matched filtering operation. Simulations and experimental results are presented to demonstrate the effectiveness of the proposed model and algorithm.
Short- and long-term outcomes after laparoscopic and open hepatic resection: systematic review and meta-analysis.

BACKGROUND Laparoscopic liver resection (LLR) is now considered a feasible alternative to open liver resection (OLR) in selected patients. Nevertheless studies comparing LLR and OLR are few and concerns remain about long-term oncological equivalence. The present study compares outcomes with LLR vs. OLR using meta-analytical methods. METHODS Electronic literature searches were conducted to identify studies comparing LLR and OLR. Short-term outcomes evaluated included operating time, blood loss, length of hospital stay, peri-operative morbidity and resection margin status. Longer-term outcomes included local and distant recurrence, and overall (OS) and disease-free survival (DFS). Meta-analyses were performed using the Mantel-Haenszel method and Cohen's d method, with results expressed as odds ratio (OR) or standardized mean difference (SMD), respectively, with 95% confidence intervals (CI). RESULTS Twenty-six studies met the inclusion criteria with a population of 1678 patients. LLR resulted in longer operating time, but reduced blood loss, portal clamp time, overall and liver-specific complications, ileus and length of stay. No difference was found between LLR and OLR for oncological outcomes. DISCUSSION LLR has short-term advantages and seemingly equivalent long-term outcomes and can be considered a feasible alternative to open surgery in experienced hands.
Tempo variation based multilayer filters for query by humming

In this paper we propose a methodology of multilayer filters based on tempo variation for realizing a query by humming (QBH) system. Firstly the original query clip is used to search for the candidate songs. If the results are unreliable, the clip is linearly scaled twice for more candidates. If the results are still unreliable, the clip is scaled more times for retrieval. To sort all the candidates, a new matching algorithm called key transposition recursive alignment (KTRA) is presented, which improves the retrieval accuracy. Experimental results on the 2010 MIREX QBH query corpus show that the proposed method can achieve a relative improvement of 20.9% as well as an acceleration factor of 2.09 simultaneously compared to a state-of-the-art method.
The gender schema: how contrasts and multiple characteristics affect metaphorical gender in adults

Schemata are an aspect of cognition consisting of hypothetical constructs that are then used in a person’s perception of the world around them. Various cognitive processes manipulate a person’s schemata – one of these is gender. Gender is often defined as a social category system that is built around the distinction of male and female; however, it has also been suggested that objects and features of a person’s world can be metaphorically associated with the concept. In the following study seventy‐one participants undertook a survey that aimed to investigate how the metaphorical gender of an item changed when compared to other items or was paired up with another characteristic. The results supported previous research in the area that suggested that an item’s metaphorical gender can change depending on the context.
Simulation and design of micro pressure sensors applied to measure the intracranial pressure

This paper reports a micrometer level pressure sensor to measure the intracranial pressure (ICP). The sensor is based on the piezoresistive effect. The piezoresistive pressure sensor is simulated and designed by using nonlinear programming Optimizing and Finite Element Analysis (FEA) tools. The sensor is fabricated by MEMS process. From tests, the sensor samples performances match up the design. KeywordsICP;sensor;MEMS;simulation;design
The social construction of risk in child trafficking discourses : a study of melodramatic tactics in child trafficking narratives

Child trafficking is a term used to define situations where children are forced, coerced or tricked to migrate for the purpose of their future exploitation. The issue of child trafficking is a well established UK policy concern initially emerging in the seventeenth century. The issue re-appeared in the late nineteenth century influenced by the social purity movement. This generated an infamous media expose which led to parliamentary debates and legislative changes. Child trafficking resurfaced as a UK policy concern periodically in the twentieth century as children were once again forced to migrate. At the start of the twenty-first century child trafficking is back on the UK national policy agenda following pressure exerted by international anti-trafficking networks and Non Government Organisations. This study examines the social construction of risk in current and historical child trafficking UK policy discourses. Interviews with key informants in the ports safeguarding sector are discussed, together with an analysis of policy documents and primary historical sources. The construction of risk in these child trafficking discourses appear in a specific format which is explained by drawing on the conceptual lens of melodramatic tactics. This analysis reveals how narratives of child trafficking tend to have a stereotypical tragic child victim, who is forcibly separated from their family, and in need of protection from dangerous criminals who aim to deceive and exploit them. The employment of these melodramatic tactics is a central feature of current UK child trafficking policy discourses. Research studies which situate migrant children as competent social actors illuminate accounts of triumph, and these contrast with the outrage-driven protest drama which has current and enduring appeal in UK child trafficking policy discourses. The implications of these findings are discussed in the context of current UK child trafficking policy and recommendations about future research with children on the move are also proposed.
Predictive chemical kinetics : enabling automatic mechanism generation and evaluation

The use of petroleum-based fuels for transportation accounted for more than 25% of the total energy consumed in 2012, both in the United States and throughout the world. The finite nature of world oil reserves and the effects of burning petroleumbased fuels on the world’s climate have motivated efforts to develop alternative, renewable fuels. A major category of alternative fuels is biofuels, which potentially include a wide variety of hydrocarbons, alcohols, aldehydes, ketones, ethers, esters, etc. To select the best species for use as fuel, we need to know if it burns cleanly, controllably, and efficiently. This is especially important when considering novel engine technologies, which are often very sensitive to fuel chemistry. The large number of candidate fuels and the high expense of experimental engine tests motivates the use of predictive theoretical methods to help quickly identify the most promising candidates. This thesis presents several contributions in the areas of predictive chemical kinetics and automatic mechanism generation, particularly in the area of reaction kinetics. First, the accuracy of several methods of automatic, high-throughput estimation of reaction rates are evaluated by comparison to a test set obtained from the NIST Chemical Kinetics Database. The methods considered, including the classic Evans-Polanyi correlation, the “rate rules” method currently used in the RMG software, and a new method based on group contribution theory, are shown to not yet obtain the order-ofmagnitude accuracy desired for automatic mechanism generation. Second, a method of very accurate computation of bimolecular reaction rates using ring polymer molecular dynamics (RPMD) is presented. RPMD rate theory enables the incorporation of quantum effects (zero-point energy and tunneling) in reaction kinetics using classical molecular dynamics trajectories in an extended phase space. A general-purpose software package named RPMDrate was developed for conducting such calculations, and the accuracy of this method was demonstrated by investigating the kinetics and kinetic isotope effect of the reaction OH + CH4 −→ CH3 + H2O. Third, a general framework for incorporating pressure dependence in thermal unimolecular reactions, which require an inert third body to provide or remove the energy needed for reaction via bimolecular collisions, was developed. Within this framework, several methods of reducing the full, master equation-based model to a set of phenomenological rate coefficients k(T, P ) are compared using the chemically-activated reaction of acetyl radical with oxygen as a case study, and recommendations are made as to when each method should be used. This also resulted in a general-purpose code for calculating pressure-dependent kinetics, which was applied to developing an ab initio model of the reaction of the Criegee biradical CH2OO with small carbonyls that reproduces recent experimental results.
Efficient text localization in born-digital images by local contrast-based segmentation

Text localization in born-digital images is usually performed using methods designed for scene text images. Based on the observation that text strokes in born-digital images mostly have complete contours and the pixels on the contours have high contrast compared with the adjacent non-text pixels, we propose a method to extract candidate text components using local contrast. First, the image is segmented into smooth and non-smooth regions. After removing non-text smooth regions, the remaining smooth regions are merged with non-smooth regions to form a candidate text image, which is binarized into high-value and low-value connected components (CCs). The CCs undergo CC filtering, line grouping and line classification to give the text localization result. Experimental results on the born-digital dataset of ICDAR2013 robust reading competition demonstrate the efficiency and superiority of the proposed method.
β1 Integrin‐dependent binding of Jurkat cells to fibronectin is regulated by a serine‐threonine phosphatase

We investigated the effects of signaling molecule inhibitors on the expression and function of β1 integrins in Jurkat cells. Jurkat cells expressed α4β1 and α5β1, with significant levels of constitutively activated β1 integrins as assessed by labeling with mAb 15/7 that distinguishes between activation states. Adhesion to fibronectin (Fn) was mediated equally through α4 and α5 subunits, and was potentiated by the β1 integrin activating mAb 8A2. Fn adhesion was decreased by okadaic acid through effects on both α4β1 and α5β1. Tyrphostin A23 also decreased adhesion but was less potent. Neither inhibitor had any effect on the surface expression of total or activated β1 integrins. The effect of tyrphostin was completely reversed by 8A2; the effect of okadaic acid was only partially reversed. Using Calyculin A, we determined that Jurkat adhesion to Fn was regulated via protein phosphatase 1, independent of the levels of integrins or integrin activation epitopes. Activation of Jurkat cells with a CD3‐stimulating mAb enhanced adhesion to Fn and was partially blocked by okadaic acid. These data demonstrate different regulatory pathways for constitutive versus activation‐dependent adhesion via β1 integrins, and implicate both tyrosine kinases and serine‐threonine phosphatases in integrin function. J. Leukoc. Biol. 64: 753–758; 1998.
Human Power Output and Muscle Fatigue

In human locomotion the ability to generate and sustain power output is of fundamental importance. This review examines the implications for power output of having variability in the metabolic and contractile properties within the population of muscle fibres which comprise the major locomotory muscles. Reference is made to studies using an isokinetic cycle ergometer by which the global power/velocity relationship for the leg extensor muscles can be determined. The data from these studies are examined in the light of the force velocity characteristics of human type I and type II muscle fibres. The 'plasticity' of fibre properties is discussed with reference to the 'acute' changes elicited by exercise induced fatigue and changes in muscle temperature and 'chronic' changes occurring following intensive training and ageing.