Miracle-dz/UniFAR-FTUs huggingface dataset:
Coexpression of the B subunit of Shiga toxin 1 and EaeA from enterohemorrhagic Escherichia coli in Vibrio cholerae vaccine strains

A promoterless gene for the Shiga toxin 1 B subunit (stxB1) has been placed under transcriptional control of the Vibrio cholerae heat shock gene htpG. A chromosomal enterohemorrhagic Escherichia coli fragment containing eaeA and 400 bp of upstream DNA was added to the construct, downstream of stxB1; no transcription terminators were located between the two genes. The plasmid construct was confirmed by DNA sequencing; in vitro transcription-translation studies demonstrated expression of EaeA from the plasmid. The htpGp-->stxB1, eaeA construct was inserted into lacZ on the chromosome of Peru2, an El Tor V. cholerae strain with both attRS1 sequences and the entire cholera toxin genetic element deleted, and into lacZ in JRB10, a Peru2 derivative that has a second copy of htpGp-->stxB1 also inserted in the V. cholerae virulence gene irgA. Two plasmid constructs, one containing stxB1 under the control of the tac promoter and another containing htpGp-->stxB1,eaeA, were transformed into Peru2. Expression of StxB1 by these constructs was quantified by enzyme-linked immunosorbent assay and was highest in the plasmid construct with stxB1 under the control of the tac promoter. Localization of EaeA to the outer membrane of the vector strains was demonstrated both by Western blotting and by immunofluorescence with an anti-EaeA antibody. A rabbit model for colonization by V. cholerae was used to compare the immune responses to the two heterologous antigens, StxB1 and EaeA, expressed by these strains. Rabbits immunized with Peru2 transformed with a plasmid carrying tac-->stxB1 developed neutralizing serum anti-StxB1 immunoglobulin G antibody responses. One of two rabbits immunized with a strain carrying a chromosomal copy of eaeA developed a marked immune response against EaeA. The plasmid construct containing htpGp-->stxB1,eaeA was unstable, producing low levels of StxB1 in vitro and not evoking anti-EaeA antibody responses in vivo following oral immunization. Chromosomal insertion of eaeA may be preferred for future expression of this antigen in V. cholerae vaccine constructs.
Nonlinear features of neonatal heart rate dynamics

The aim of this study was to investigate the short-term heart rate variability (HRV) as an index of the cardiac autonomic control development in healthy full-term neonates using various new complexity and irreversibility measures. HRV in 20 healthy full-term neonates was compared to HRV recorded in healthy young adults. Besides traditional time and frequency domain measures, we assessed HRV complexity measures including normalized complexity index (NCf), normalized unpredictability index (NUPf), pattern classification (OV%, 1 V%, 2LV%, 2UV%) and multiscale irreversibility indices (P%, G%, E). HRV magnitude was significantly decreased in the neonatal group compared to the adults. HR V complexity measures, i.e. indices NCf, NUPf and pattern indices 1 V%, 2LV%, were also significantly reduced. Pattern classification parameter OV% and Porta's irreversibility index P% showed significant increase in newborns compared to adults suggesting the shift in the sympathovagal balance of neonates towards sympathetic predominance. Moreover, surrogate data analysis of irreversibility indices revealed asymmetrical nature of the HRV series present already in the neonatal age suggesting the nonlinear nature of HR V dynamic even very shortly after birth.
Fractional-order smoothed pseudo wigner-ville distribution and its applications in machinery fault diagnosis

Lower time-frequency resolution is caused by Smoothed pseudo Wigner-Ville distribution (SPWVD) in suppressing cross-terms interference, which limits its application in the processing of the non-stationary vibration signals. This paper proposes a novel fractional-order smoothed pseudo Wigner-Ville distribution (FrSPWVD) to solve the above problem. The details about step of the calculation are as follows: the appropriate fractional order of original signals are determined firstly; then fractional order Fourier transform transforms the original signals in the most appropriate fractional domain, and transformed signals are analyzed by SPWVD; lastly, parameters of original signals are accurately extracted according to the corresponding appropriate fractional order and fractional frequency of signals. By analyzing the signals in the most appropriate fractional domain, the proposed time-frequency distribution can obtain the time-frequency representation with much higher resolution compared to the classical SPWVD. Simulation results and fault diagnosis cases show the efficiency of the proposed method.
Distinct patterns of brain activity in young carriers of the APOE e4 allele

The APOE ε4 allele is a risk factor for late-life pathological changes that is also associated with anatomical and functional brain changes in middle-aged and elderly healthy subjects. We investigated structural and functional effects of the APOE polymorphism in 18 young healthy APOE ε4-carriers and 18 matched noncarriers (age range: 20–35 years). Brain activity was studied both at rest and during an encoding memory paradigm using blood oxygen level-dependent fMRI. Resting fMRI revealed increased “default mode network” (involving retrosplenial, medial temporal, and medial-prefrontal cortical areas) coactivation in ε4-carriers relative to noncarriers. The encoding task produced greater hippocampal activation in ε4-carriers relative to noncarriers. Neither result could be explained by differences in memory performance, brain morphology, or resting cerebral blood flow. The APOE ε4 allele modulates brain function decades before any clinical or neurophysiological expression of neurodegenerative processes.
Structure of NKp65 bound to its keratinocyte ligand reveals basis for genetically linked recognition in natural killer gene complex

The natural killer (NK) gene complex (NKC) encodes numerous C-type lectin-like receptors that govern the activity of NK cells. Although some of these receptors (Ly49s, NKG2D, CD94/NKG2A) recognize MHC or MHC-like molecules, others (Nkrp1, NKRP1A, NKp80, NKp65) instead bind C-type lectin-like ligands to which they are genetically linked in the NKC. To understand the basis for this recognition, we determined the structure of human NKp65, an activating receptor implicated in the immunosurveillance of skin, bound to its NKC-encoded ligand keratinocyte-associated C-type lectin (KACL). Whereas KACL forms a homodimer resembling other C-type lectin-like dimers, NKp65 is monomeric. The binding mode in the NKp65–KACL complex, in which a monomeric receptor engages a dimeric ligand, is completely distinct from those used by Ly49s, NKG2D, or CD94/NKG2A. The structure explains the exceptionally high affinity of the NKp65–KACL interaction compared with other cell–cell interaction pairs (KD = 6.7 × 10−10 M), which may compensate for the monomeric nature of NKp65 to achieve cell activation. This previously unreported structure of an NKC-encoded receptor–ligand complex, coupled with mutational analysis of the interface, establishes a docking template that is directly applicable to other genetically linked pairs in the NKC, including Nkrp1–Clr, NKRP1A–LLT1, and NKp80–AICL.
A Framework for Invertible, Real-Time Constant-Q Transforms

Audio signal processing frequently requires time-frequency representations and in many applications, a non-linear spacing of frequency bands is preferable. This paper introduces a framework for efficient implementation of invertible signal transforms allowing for non-uniform frequency resolution. Non-uniformity in frequency is realized by applying nonstationary Gabor frames with adaptivity in the frequency domain. The realization of a perfectly invertible constant-Q transform is described in detail. To achieve real-time processing, independent of signal length, slice-wise processing of the full input signal is proposed and referred to as sliCQ transform. By applying frame theory and FFT-based processing, the presented approach overcomes computational inefficiency and lack of invertibility of classical constant-Q transform implementations. Numerical simulations evaluate the efficiency of the proposed algorithm and the method's applicability is illustrated by experiments on real-life audio signals .
Resolving uncertainties during trace analysis

Software models provide independent perspectives onto software systems. Ideally, all models should use the same model element to describe the same part of a system. Practically, models elements are not shared because of syntactic and semantic differences among modeling notations. Trace dependencies explicitly maintain the commonalities among the distinct model elements. Generating and maintaining trace dependencies is difficult, costly, and highly error-prone. Automated trace analysis techniques are scarce. This paper extends an existing, testing-based technique for generating and maintaining trace dependencies. It is based on the commonality principle: if two model elements of different perspectives are the same then they must have the same source code. The existing approach associates test scenarios with model elements, tests them, and observes what lines of code are being executed. Model elements are considered the same/similar if their testing uses the same/overlapping lines of code. This paper extends the existing approach (and tool) by giving the user a richer, more powerful, yet precise language on how to relate model elements, test scenarios, and source code (the input). This allows some forms of uncertainties to exist in input data without sacrificing reliability. The extended approach also identifies "shared code. " Shared code works against the commonality principle in that model elements do not relate if they overlap solely on their use of generic source code (e.g., queue). As a pre-requisite, our approach requires an executable and observable software system and test scenarios.
Terminalia chebula Extract Protects OGD-R Induced PC12 Cell Death and Inhibits LPS Induced Microglia Activation

Terminalia chebula, native to Southeast Asia, is a popular medicinal plant in Ayurveda. It has been previously reported to have strong antioxidant and anti-inflammatory efficacy. In this study, we aimed to investigate if fruit extract from T. chebula might protect neuronal cells against ischemia and related diseases by reduction of oxidative damage and inflammation in rat pheochromocytoma cells (PC12) using in vitro oxygen-glucose deprivation followed by reoxygenation (OGD-R) ischemia and hydrogen peroxide (H2O2) induced cell death. Cell survival was evaluated by a 2-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Free radical scavenging, lipid peroxidation and nitric oxide inhibition were measured by diphenyl-1-picrylhydrazyl (DPPH), thiobarbituric acid (TBA) and Griess reagent, respectively. We found that T. chebula extract: (1) increases the survival of cells subjected to OGD-R by 68%, and H2O2 by 91.4%; (2) scavenges the DPPH free radical by 96% and decreases malondialdehyde (MDA) levels from 237.0 ± 15.2% to 93.7 ± 2.2%; (3) reduces NO production and death rate of microglia cells stimulated by lipopolysaccharide (LPS). These results suggest that T. chebula extract has the potential as a natural herbal medicine, to protect the cells from ischemic damage and the possible mechanism might be the inhibition of oxidative and inflammatory processes.
Lead exposure and intelligence in 7-year-old children: the Yugoslavia Prospective Study.

For a prospective study of lead exposure and early development, we recruited pregnant women from a lead smelter town and from an unexposed town in Yugoslavia and followed their children through 7 years of age. In this paper we consider associations between lifetime lead exposure, estimated by the area under the blood lead (BPb) versus time curve (AUC7), and intelligence, with particular concern for identifying lead's behavioral signature. The Wechsler Intelligence Scales for Children-Version III (WISC-III) was administered to 309 7-year-old children, 261 of whom had complete data on intelligence, blood lead, and relevant sociodemographic covariates (i.e., Home Observation for the Measurement of the Environment (HOME), birth weight, gender, sibship size, and maternal age, ethnicity, intelligence, and education). These showed anticipated associations with 7-year intelligence, explaining 41-4% of the variance in Full Scale, Performance, and Verbal IQ. Before covariate adjustment, AUC7 was unrelated to intelligence; after adjustment, AUC7 explained a significant 2.8%-4.2% of the variance in IQ. After adjustment, a change in lifetime BPb from 10 to 30 micro/dl related to an estimated decrease of 4.3 Full Scale IQ points; estimated decreases for Verbal and Performance IQ were 3.4 and 4.5 points, respectively. AUC7 was significantly and negatively related to three WISC-III factor scores: Freedom from Distractibility, Perceptual Organization, and Verbal Comprehension; the association with Perceptual Organization was the strongest. Consistent with previous studies, the IQ/lead association is small relative to more powerful social factors. Findings offer support for lead's behavioral signature; perceptual-motor skills are significantly more sensitive to lead exposure than are the language-related aspects of intelligence. ImagesFigure 1. AFigure 1. BFigure 1. CFigure 1. DFigure 2.
Towards high performance virtual routers on commodity hardware

Modern commodity hardware architectures, with their multiple multi-core CPUs and high-speed system interconnects, exhibit tremendous power. In this paper, we study performance limitations when building both software routers and software virtual routers on such systems. We show that the fundamental performance bottleneck is currently the memory system, and that through careful mapping of tasks to CPU cores, we can achieve forwarding rates of 7 million minimum-sized packets per second on mid-range server-class systems, thus demonstrating the viability of software routers. We also find that current virtualisation systems, when used to provide forwarding engine virtualisation, yield aggregate performance equivalent to that of a single software router, a tenfold improvement on current virtual router platform performance. Finally, we identify principles for the construction of high-performance software router systems on commodity hardware, including full router virtualisation support.
HashGAN: Attention-aware Deep Adversarial Hashing for Cross Modal Retrieval

As the rapid growth of multi-modal data, hashing methods for cross-modal retrieval have received considerable attention. Deep-networks-based cross-modal hashing methods are appealing as they can integrate feature learning and hash coding into end-to-end trainable frameworks. However, it is still challenging to find content similarities between different modalities of data due to the heterogeneity gap. To further address this problem, we propose an adversarial hashing network with attention mechanism to enhance the measurement of content similarities by selectively focusing on informative parts of multi-modal data. The proposed new adversarial network, HashGAN, consists of three building blocks: 1) the feature learning module to obtain feature representations, 2) the generative attention module to generate an attention mask, which is used to obtain the attended (foreground) and the unattended (background) feature representations, 3) the discriminative hash coding module to learn hash functions that preserve the similarities between different modalities. In our framework, the generative module and the discriminative module are trained in an adversarial way: the generator is learned to make the discriminator cannot preserve the similarities of multi-modal data w.r. t. the background feature representations, while the discriminator aims to preserve the similarities of multi-modal data w.r. t. both the foreground and the background feature representations. Extensive evaluations on several benchmark datasets demonstrate that the proposed HashGAN brings substantial improvements over other state-of-the-art cross-modal hashing methods.
A Game-Based Mechanism of Relay Selection for Wireless Network Security

In the wireless Ad-hoc networks, the Relays which transmit message are selfish, they need to consume their energy and compute resources to transmit message. For the problems of the message transmission interrupted by Relay selfishness and the decrease of secrecy rates, we have proposed a Relay-selection method to ensure the security of the Ad-hoc network using game theory incentive mechanism. The method introduces virtual currency, which encourages and regulates the cooperation between different nodes, and proposes the incentives mechanism of twice quotation competition based on virtual currency measurement. According to the secrecy rate and quotation, source nodes will select one Relay which makes the maximum secrecy rate utility. Simulations show that the proposed method improves the average secrecy rate per user up by 20%~32% compared with the conventional Relay selection method.
A Minimal Solution to the Generalized Pose-and-Scale Problem

We propose a novel solution to the generalized camera pose problem which includes the internal scale of the generalized camera as an unknown parameter. This further generalization of the well-known absolute camera pose problem has applications in multi-frame loop closure. While a well-calibrated camera rig has a fixed and known scale, camera trajectories produced by monocular motion estimation necessarily lack a scale estimate. Thus, when performing loop closure in monocular visual odometry, or registering separate structure-from-motion reconstructions, we must estimate a seven degree-of-freedom similarity transform from corresponding observations. Existing approaches solve this problem, in specialized configurations, by aligning 3D triangulated points or individual camera pose estimates. Our approach handles general configurations of rays and points and directly estimates the full similarity transformation from the 2D-3D correspondences. Four correspondences are needed in the minimal case, which has eight possible solutions. The minimal solver can be used in a hypothesize-and-test architecture for robust transformation estimation. Our solver also produces a least-squares estimate in the overdetermined case. The approach is evaluated experimentally on synthetic and real datasets, and is shown to produce higher accuracy solutions to multi-frame loop closure than existing approaches.
Stability and Accuracy in Incremental Speech Recognition

Conventional speech recognition approaches usually wait until the user has finished talking before returning a recognition hypothesis. This results in spoken dialogue systems that are unable to react while the user is still speaking. Incremental Speech Recognition (ISR), where partial phrase results are returned during user speech, has been used to create more reactive systems. However, ISR output is unstable and so prone to revision as more speech is decoded. This paper tackles the problem of stability in ISR. We first present a method that increases the stability and accuracy of ISR output, without adding delay. Given that some revisions are unavoidable, we next present a pair of methods for predicting the stability and accuracy of ISR results. Taken together, we believe these approaches give ISR more utility for real spoken dialogue systems.
Introduction to Volume Graphics

This paper is a surv ey of volume graphics.It includes an introduction to v olumetric data and to v olume modeling techniques, such as v oxelization, texture mapping, amorphous phenomena, block operations, constructi ve solid modeling, and v olume sculpting.A comparison between surf ace graphics and v olume graphics is gi ven, along with a consideration of v olume graphics adv antages and weaknesses. The paper concludes with a discussion on special-purpose v olume rendering hardw are.
Photostimulable Near-Infrared Persistent Luminescent Nanoprobes for Ultrasensitive and Longitudinal Deep-Tissue Bio-Imaging

In vivo fluorescence imaging suffers from suboptimal signal-to-noise ratio and shallow detection depth, which is caused by the strong tissue autofluorescence under constant external excitation and the scattering and absorption of short-wavelength light in tissues. Here we address these limitations by using a novel type of optical nanoprobes, photostimulable LiGa5O8:Cr3+ near-infrared (NIR) persistent luminescence nanoparticles, which, with very-long-lasting NIR persistent luminescence and unique photo-stimulated persistent luminescence (PSPL) capability, allow optical imaging to be performed in an excitation-free and hence, autofluorescence-free manner. LiGa5O8:Cr3+ nanoparticles pre-charged by ultraviolet light can be repeatedly (>20 times) stimulated in vivo, even in deep tissues, by short-illumination (~15 seconds) with a white light-emitting-diode flashlight, giving rise to multiple NIR PSPL that expands the tracking window from several hours to more than 10 days. Our studies reveal promising potential of these nanoprobes in cell tracking and tumor targeting, exhibiting exceptional sensitivity and penetration that far exceed those afforded by conventional fluorescence imaging.
Psychiatry in the Scientific Image

In Psychiatry in the Scientific Image, Dominic Murphy looks at psychiatry from the viewpoint of analytic philosophy of science, considering three issues: how we should conceive of, classify, and explain mental illness. If someone is said to have a mental illness, what about it is mental? What makes it an illness? How might we explain and classify it? A system of psychiatric classification settles these questions by distinguishing the mental illnesses and showing how they stand in relation to one another. This book explores the philosophical issues raised by the project of explaining and classifying mental illness. Murphy argues that the current literature on mental illness -- exemplified by the Diagnostic and Statistical Manual of Mental Disorders -- is an impediment to research; it lacks a coherent concept of the mental and a satisfactory account of disorder, and yields too much authority to commonsense thought about the mind. He argues that the explanation of mental illness should meet the standards of good explanatory practice in the cognitive neurosciences, and that the classification of mental disorders should group symptoms into conditions based on the causal structure of the normal mind.
Job Auctions

This paper proposes job auctions as a theory of wage determination in models of labor markets with search frictions. Workers apply for jobs by bidding in auctions, and firms reward the job to the applicant who offers it the most profit. In equilibrium, more productive applicants always outbid less productive ones, but the threat of competition holds down the former’s wage demand. The equilibrium of the job auction model is always efficient, in contrast to standard search models. The model produces a distinctive and empirically testable relationship between the wage-productivity schedule, the unemployment-productivity schedule, and the underlying labor productivity distribution. The model also predicts that the minimum wage will have a ripple effect on workers for whom it is not binding, by reducing the competition from less productive workers. ∗This paper is a substantial revision of the second chapter of my MIT Ph.D. dissertation, “Do Good Guys Come in First? How Wage Determination Affects The Ranking of Job Applicants”. I am grateful to numerous individuals and seminar participants for their helpful comments and discussions. Thanks in particular to my thesis advisors Daron Acemoglu and Olivier Blanchard. I also thank the Alfred P. Sloan Foundation and National Science Foundation grant SBR-9709881 for financial support. Job Auctions Robert Shimer