Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbon Monoxide Inhibits Porcine Reproductive and Respiratory Syndrome Virus Replication by the Cyclic GMP/Protein Kinase G and NF-κB Signaling Pathway

ABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses to the pork industry worldwide each year. Our previous research demonstrated that heme oxygenase-1 (HO-1) can suppress PRRSV replication via an unknown molecular mechanism. In this study, inhibition of PRRSV replication was demonstrated to be mediated by carbon monoxide (CO), a downstream metabolite of HO-1. Using several approaches, we demonstrate that CO significantly inhibited PRRSV replication in both a PRRSV permissive cell line, MARC-145, and the predominant cell type targeted during in vivo PRRSV infection, porcine alveolar macrophages (PAMs). Our results showed that CO inhibited intercellular spread of PRRSV; however, it did not affect PRRSV entry into host cells. Furthermore, CO was found to suppress PRRSV replication via the activation of the cyclic GMP/protein kinase G (cGMP/PKG) signaling pathway. CO significantly inhibits PRRSV-induced NF-κB activation, a required step for PRRSV replication. Moreover, CO significantly reduced PRRSV-induced proinflammatory cytokine mRNA levels. In conclusion, the present study demonstrates that CO exerts its anti-PRRSV effect by activating the cellular cGMP/PKG signaling pathway and by negatively regulating cellular NF-κB signaling. These findings not only provide new insights into the molecular mechanism of HO-1 inhibition of PRRSV replication but also suggest potential new control measures for future PRRSV outbreaks. IMPORTANCE PRRSV causes great economic losses each year to the swine industry worldwide. Carbon monoxide (CO), a metabolite of HO-1, has been shown to have antimicrobial and antiviral activities in infected cells. Our previous research demonstrated that HO-1 can suppress PRRSV replication. Here we show that endogenous CO produced through HO-1 catalysis mediates the antiviral effect of HO-1. CO inhibits PRRSV replication by activating the cellular cGMP/PKG signaling pathway and by negatively regulating cellular NF-κB signaling. These findings not only provide new insights into the molecular mechanism of HO-1 inhibition of PRRSV replication but also suggest potential new control measures for future PRRSV outbreaks.
A memory-efficient adaptive Huffman coding algorithm for very large sets of symbols

Summary form only given. The problem of computing the minimum redundancy codes as we observe symbols one by one has received a lot of attention. However, existing algorithms implicitly assumes that either we have a small alphabet or that we have an arbitrary amount of memory at our disposal for the creation of a coding tree. In real life applications one may need to encode symbols coming from a much larger alphabet, for e.g. coding integers. We introduce a new algorithm for adaptive Huffman coding, called algorithm M, that uses space proportional to the number of frequency classes. The algorithm uses a tree with leaves that represent sets of symbols with the same frequency, rather than individual symbols. The code for each symbol is therefore composed of a prefix (specifying the set, or the leaf of the tree) and a suffix (specifying the symbol within the set of same-frequency symbols). The algorithm uses only two operations to remain as close as possible to the optimal: set migration and rebalancing. We analyze the computational complexity of algorithm M, and point to its advantages in terms of low memory complexity and fast decoding. Comparative experiments were performed with algorithm M on the Calgary corpus, with static Huffman coding as well as with another adaptive Huffman coding algorithms, algorithm /spl Lambda/ of Vitter. Experiments show that M performs comparably or better than the other algorithms but requires much less memory. Finally, we present an improved algorithm, M/sup +/, for non-stationary data, which models the distribution of the data in a fixed-size window in the data sequence.
Robust Beamforming via Worst-Case SINR Maximization

Minimum variance beamforming, which uses a weight vector that maximizes the signal-to-interference-plus-noise ratio (SINR), is often sensitive to estimation error and uncertainty in the parameters, steering vector and covariance matrix. Robust beamforming attempts to systematically alleviate this sensitivity by explicitly incorporating a data uncertainty model in the optimization problem. In this paper, we consider robust beamforming via worst-case SINR maximization, that is, the problem of finding a weight vector that maximizes the worst-case SINR over the uncertainty model. We show that with a general convex uncertainty model, the worst-case SINR maximization problem can be solved by using convex optimization. In particular, when the uncertainty model can be represented by linear matrix inequalities, the worst-case SINR maximization problem can be solved via semidefinite programming. The convex formulation result allows us to handle more general uncertainty models than prior work using a special form of uncertainty model. We illustrate the method with a numerical example.
Addressing the Sparsity of Location Information on Twitter

Micro-blogging services such as Twitter have gained enormous popularity over the last few years leading to massive volumes of user generated content. In combination with the proliferation of smart-phones, this information is generated live from a multitude of content contributors. Interestingly, the content and timestamp of tweets is not the only information that can produce useful knowledge. The location information of users is of great significance since it can be utilized in a variety of applications such as emergency identification, tracking the spread of a disease and advertising. Unfortunately, information regarding location is very rare since many users do not accurately specify their location, and fewer posts have geographic coordinates. In this work, we aim to confront this data sparsity issue. Utilizing Twitter’s social graph and content, we are able to obtain users from a specific location. We optimize our method to work with minimum amount of queries considering the large volume of data in such settings. We also provide a mechanism for geo-locating a tweet within a city and present the qualitative enrichment in our data, achieved by our method.
Is the Universe Closed by Baryons? Nucleosynthesis with a Late-decaying Massive Particle

A late decaying (7 > 105sec), massive (M 2 10 GeV) particle initiates a new phase of nucleosynthesis in the keV era. Light element production takes place when the hadronic decay products interact with the amb ient protons and ’ 4 He causing hadronic showers and 4 He hadrodestruction. The primordial abundances of D, 3He, 6Li and ‘Li-are given by the fixed points of the corresponding rate equations in which hadroproduct ion balances photodestruction. Since fixed points erase all previous memory, the primordial abundances of these elements are completely independent of the physics before the keV era, whose only important role is to provide at least the observed abundance of 4He. Any overabundance of 4He is subsequently hadrodissociated. The primordial element abundances are inagreement with observations; furthermore they are independent of RBhz . for a very broad range of ClBhz which includes the previously forbidden range 0.03 -5 flBhz 5 1.1. An ideal candidate for the late decaying particle may be the gravitino. --
Pressure-adaptive differences in proteolytic inactivation of M4-lactate dehydrogenase homologues from marine fishes.

The inactivation by hydrostatic pressure of muscle-type lactate dehydrogenase (M4-LDH, EC 1.1.1.27; L-lactate: NAD+ oxidoreductase) homologues from five shallow-living and six deep-living marine teleost fishes was compared. The pressures which inactivate these enzymes are much higher than the pressures experienced by any of the species. To determine whether hydrostatic pressure effects on protein aggregation state and conformation might influence proteolysis, the inactivation of LDH by the proteases, trypsin (EC 3.4.21.4) and subtilisin (EC 3.4.4.16) was determined at atmospheric pressure and 1,000 atm pressure. At 10 degrees C and atmospheric pressure, the enzymes of the shallow-living fishes are inactivated four times faster by trypsin and three times faster by subtilisin than are the homologues of the deep-living species. At 1,000 atm pressure, the homologues of shallow-occurring fishes were inactivated 28 to 64% more than predicted from the summed effects of denaturation by 1,000 atm pressure and tryptic inactivation at atmospheric pressure. In contrast, the homologues of the deep-sea species were inactivated by trypsin 0 to 21% more than expected. At 1,000 atm, inactivation by subtilisin increased to a similar degree for enzymes from both deep- and shallow-living species. However, at 1,000 atm, the M4-LDH homologues of the deep-sea species lost less activity (55.3%) than did the homologues of the shallow species (86.4%). In comparisons made at 200 atm, a pressure typical of the habitat of the deep-occurring species, tryptic inactivation of the LDH of the shallow-living Sebastes melanops was increased 14%. No pressure inactivation of the enzyme is evident at 200 atm. (ABSTRACT TRUNCATED AT 250 WORDS)
A shape feature based bovw method for image classification using N-gram and spatial pyramid coding scheme

Image classification is a general visual analysis task based on the image content coded by its representation. In this research, we proposed an image representation method that is based on the perceptual shape features and their spatial distributions. A natural language processing concept, N-gram, is adopted to generate a set of perceptual shape visual words for encoding image features. By combining hierarchical visual words and spatial pyramid, Spatio-Shape Pyramid representation is constructed to reduce the semantic gaps. Experimental results show that the proposed method outperforms other state-of-the-art methods.
AuraMirror: artistically visualizing attention

We present AuraMirror, a system that visualizes virtual windows of attention: the commodity of visual attention people exchange during interactions in small groups. AuraMirror acts as a dynamic 'painting' that passively gathers and displays attentional data by superimposing auras over each viewer's head in a real time video mirror. This permits users to see how they distribute their attention in group interactions, and the effect of interruption on this process. Finally, we describe how AuraMirror can be extended to model attention among both participants and ubiquitous devices.
Long-term functional outcome of trigger finger

Abstract Purpose: The purpose of this study was to explore the long-term functional outcomes of trigger finger (TF) as perceived by the patient. Methods: Three study groups were included in the study: prolonged follow up TF group (at least 1-year post-treatment) (PF-TF), patients with acute TF and a control group. The first group was recruited retrospectively and included all patients who were diagnosed with TF in one orthopedic clinic and were contacted by phone, 109 agreed to participate. The acute TF and healthy controls participated in a previous controlled study. The Quick Disabilities of the Arm Shoulder and Hand (QuickDASH) and numeric pain scale (NPS) were the main outcome measures. Results: Both TF groups reported significantly higher levels of disability, particularly in activities requiring strength and more severe pain in comparison with the control group. The acute TF group reported significantly higher levels of disability and pain than the PF-TF group. Seventy-two percent of acute TF group reported moderate to severe pain, in comparison with 37% of the PF-TF group. Conclusion: According to these data, substantial long-term disability and pain persist in both the acute and chronic settings. Implications for rehabilitation Recovery from TF may be a prolonged process and a long term follow up should be considered in clinical practice. The present study found that TF leads to significant disability, therefore, activity and participation should be addressed in practice. Assessment of TF interventions should include outcomes that address the client's perspective using standardized measures of disability, such as the QuickDASH.
Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa

Background The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with Salmonella enterica serovar Typhi (S. Typhi) as an important cause of bacteremia in children. Methods A total of 128 S. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance. Results Several distinct S. Typhi genotypes were identified in Nigeria that were related to other clusters of S. Typhi isolates from north, west and central regions of Africa. The rapidly expanding S. Typhi clade 4.3. 1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with S. Typhi. Conclusions These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid.
Effect of Age on the Response to in vitro Ischemia and Reperfusion of the Rabbit Bladder

Background/Aims: Urinary bladder dysfunction secondary to outlet obstruction is a common condition, seen in both children and adults. Using in vitro models of ischemia/reperfusion (I/R), we compared the contractile and biochemical responses of bladders isolated from young and old rabbits. Materials and Methods: Fourteen male New Zealand White rabbits were separated into two groups of 7. Group 1 (young) included rabbits 6–7 weeks old and group 2 (old) consisted of rabbits 2 years old. Isolated bladder body strips were subjected to in vitro I/R, and the effects on contractility were determined. The strips were then frozen and stored for quantitative malondialdehyde (MDA) analysis. Results: Contractile responses of young and old rabbit bladders to all forms of stimulation – field stimulation (FS), carbachol and potassium chloride (KCl) – were equal. The rate of tension to 32 Hz FS was significantly higher for group 1 in comparison with group 2. The old and young rabbits were equally sensitive to I/R in regard to FS, but the old rabbits were more sensitive to I/R in regard to carbachol and KCl stimulation. Basal MDA concentration of both young and aged bladder strips were similar. Ischemia mediated a significant increase in MDA in bladder strips from both young and old rabbits, but the MDA level was significantly greater for the young than for the old. Conclusion: Although the level of oxidative damage was greater in the young rabbit bladders, functionally, the old rabbit bladders were more sensitive to I/R damage.
Constrained principal component analysis reveals functionally connected load‐dependent networks involved in multiple stages of working memory

Constrained principal component analysis (CPCA) with a finite impulse response (FIR) basis set was used to reveal functionally connected networks and their temporal progression over a multistage verbal working memory trial in which memory load was varied. Four components were extracted, and all showed statistically significant sensitivity to the memory load manipulation. Additionally, two of the four components sustained this peak activity, both for approximately 3 s (Components 1 and 4). The functional networks that showed sustained activity were characterized by increased activations in the dorsal anterior cingulate cortex, right dorsolateral prefrontal cortex, and left supramarginal gyrus, and decreased activations in the primary auditory cortex and “default network” regions. The functional networks that did not show sustained activity were instead dominated by increased activation in occipital cortex, dorsal anterior cingulate cortex, sensori‐motor cortical regions, and superior parietal cortex. The response shapes suggest that although all four components appear to be invoked at encoding, the two sustained‐peak components are likely to be additionally involved in the delay period. Our investigation provides a unique view of the contributions made by a network of brain regions over the course of a multiple‐stage working memory trial. Hum Brain Mapp, 2011. © 2010 Wiley‐Liss, Inc.
Risk Factors for Transient Urinary Incontinence after Holmium Laser Enucleation of the Prostate

Purpose To investigate the factors associated with the occurrence of and recovery from transient urinary incontinence (TUI) after holmium laser enucleation of the prostate (HoLEP). Materials and Methods From March 2009 to December 2012, 391 consecutive patients treated with HoLEP for benign prostatic hyperplasia were enrolled. Information regarding age, prostate volume, International Prostate Symptom Score, Overactive Bladder Symptom Score, peak urinary flow rate, postvoid residual urine, and operation time was collected. TUI was defined as a patient complaint of urine leakage, regardless of type. Logistic regression was used to investigate the factors associated with the occurrence of TUI, and the Kaplan-Meier test was used to analyze the TUI recovery period. Results TUI after HoLEP occurred in 65 patients (16.6%), 52 patients of whom (80.0%) showed recovery within three months. Stress and urge urinary incontinence and postvoid dribbling occurred in 16 patients (4.1%), 29 patients (7.4%), and 33 patients (8.4%), respectively. Age (odds ratio [OR]=3.494; 95% confidence interval [CI]=1.565~7.803; p=0.002) and total operation time (OR=3.849; 95% CI=1.613~9.185; p=0.002) were factors that significantly affected the occurrence of TUI. Conclusions TUI, defined as any type of urine leakage, occurred after HoLEP in some patients, most of whom recovered within three months. Stress urinary incontinence occurred in only 4% of patients after HoLEP. Age and total operation time were associated with the occurrence of postoperative TUI.
Examining the validity and reliability of the Activities-Specific Balance Confidence Scale-6 (ABC-6) in a diverse group of older adults

Losing confidence in the ability to maintain balance can be more debilitating than a fall. Therefore, considering the importance of measuring balance confidence, the purpose of this study was to examine the validity and reliability of the ABC-6, a shortened version of the ABC16, among diverse older adults. Participants were 251 diverse (72.1% African Americans, 62.5% low-income, 61% low-education) older adults (M age = 71.2 years, SD = 8.9). Participants volunteered for a falls risk screening which assessed multiple falls risk factors and balance confidence. The ABC-6 had excellent internal consistency reliability, substantial intraclass correlations, significant moderate to large correlations with physical activity, mobility, balance, and total falls risk, the ability to discriminate between fallers and nonfallers, and it was the only significant predictor of total falls risk. The ABC-6 was a valid and reliable measure of balance confidence and is a suitable measure for use among diverse older adults. INDEX WORDS: Balance confidence, ABC-16, ABC-6, Falls EXAMINING THE VALIDITY AND RELIABILTIY OF THE ACTIVITIES-SPECIFIC BALANCE CONFIDENCE SCALE-6 (ABC-6) IN A DIVERSE GROUP OF OLDER ADULTS
Contemplating the evolution of attachment and cognition in a collaborative learning environment

This study investigates the evolution of attachment and cognition by considering them to be products of the ontogenetic and evolutionary pressures acting on the developing individual. It is argued that the unique cognitive capabilities of humans evolved through the attachment system because of the strong selection for plasticity that has shaped our evolutionary history. The possibility that the attachment system represents the substrate for the development of our unique cognitive capabilities is investigated by looking at the relative performance of secure versus insecure preschoolers in solving cognitively engaging tasks within a theoretically- informed collaborative learning environment. Security of attachment to the mother and cognitive performance were evaluated for a sample of 38 children (mean age, 49 months). Results indicated that attachment security was associated with overall performance (accuracy), critical thinking skills, and short-term memory. Moreover, mother- child attachment security was related to maternal sensitivity and children's empathy. Finally, a negative association between security and variability in cognitive performance was detected. Security-related differences in cognitive performance, sensitivity, and empathy are interpreted in light of ultimate and proximate perspectives. It is argued that while attachment research traditionally favors ultimate-level explanations, it can no longer disregard the important role that proximate factors and biology play on the developing individual. Attachment is viewed as a continuum of adaptive patterns that are all maintained by evolution because of selection for plasticity. The possibility that attachment is continuously (versus categorically) distributed is investigated by looking at the variability in cognitive performance between secure and insecure children. Critiques are advanced to the use of the Strange Situation Procedure as attachment assessment tool both on its typological classification of attachment types, as well as on its methodology. Lastly, this work explores ontogenetic and phylogenetic arguments about the rise of theory of mind in our species. Opposing views on the ontogenetic appearance of theory of mind like capabilities and on the phylogenetic implications of their emergence are combined as a way to better comprehend the reasons behind the evolution of human's unique cognition
High resolution observations and mass modelling of the CLASS gravitational lens B 1152 + 199

We present a series of high resolution radio and optical observations of the CLASS gravitational lens system B1152+199 obtained with the Multi-Element Radio-Linked Interferometer Network (MERLIN), Very Long Baseline Array (VLBA) and Hubble Space Telescope (HST). Based on the milliarcsecond-scale substructure of the lensed radio components and precise optical astrometry for the lensing galaxy, we construct models for the system and place constraints on the galaxy mass profile. For a single galaxy model with surface mass density Σ(r) ∝ r , we find that 0.95 ≤ β ≤ 1.21 at 2σ confidence. Including a second deflector to represent a possible satellite galaxy of the primary lens leads to slightly steeper mass profiles.