Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary rescue and the limits of adaptation

Populations subject to severe stress may be rescued by natural selection, but its operation is restricted by ecological and genetic constraints. The cost of natural selection expresses the limited capacity of a population to sustain the load of mortality or sterility required for effective selection. Genostasis expresses the lack of variation that prevents many populations from adapting to stress. While the role of relative fitness in adaptation is well understood, evolutionary rescue emphasizes the need to recognize explicitly the importance of absolute fitness. Permanent adaptation requires a range of genetic variation in absolute fitness that is broad enough to provide a few extreme types capable of sustained growth under a stress that would cause extinction if they were not present. This principle implies that population size is an important determinant of rescue. The overall number of individuals exposed to selection will be greater when the population declines gradually under a constant stress, or is progressively challenged by gradually increasing stress. In gradually deteriorating environments, survival at lethal stress may be procured by prior adaptation to sublethal stress through genetic correlation. Neither the standing genetic variation of small populations nor the mutation supply of large populations, however, may be sufficient to provide evolutionary rescue for most populations.
Guidelines for Bowel Preparation before Video Capsule Endoscopy

The preparation for video capsule endoscopy (VCE) of the bowel suggested by manufacturers of capsule endoscopy systems consists only of a clear liquid diet and an 8-hour fast. While there is evidence for a benefit from bowel preparation for VCE, so far there is no domestic consensus on the preparation regimen in Korea. Therefore, we performed this study to recommend guidelines for bowel preparation before VCE. The guidelines on VCE were developed by the Korean Gut Image Study Group, part of the Korean Society of Gastrointestinal Endoscopy. Four key questions were selected. According to our guidelines, bowel preparation with polyethylene glycol (PEG) solution enhances small bowel visualization quality (SBVQ) and diagnostic yield (DY), but it has no effect on cecal completion rate (CR). Bowel preparation with 2 L of PEG solution is similar to that with 4 L of PEG in terms of the SBVQ, DY, and CR of VCE. Bowel preparation with fasting or PEG solution combined with simethicone enhances the SBVQ, but it does not affect the CR of VCE. Bowel preparation with prokinetics does not enhance the SBVQ, DY, or CR of VCE.
Panic stations: surveillance in the UK

IN GEORGE ORWELL’S novel 1984, surveillance and censorship, along with propaganda, were the prime means by which power was exercised. So it’s alarming that today, in the real world, surveillance itself has become a means of censorship – not least because it encourages that most insidious form, self-censorship. After all, if you think that your online activity is subject to state surveillance, and that what you’re doing may be illegal, then you may just decide not to click that mouse. On the other hand, you may think that illegal activity online is the province only of paedophiles and terrorists. In which case you might be in for a nasty shock. Once, censorship operated largely by banning the production, distribution and exhibition of material deemed taboo. The information age has, of course, made those tasks far more difficult. So politicians have changed tack and, increasingly, have introduced laws that make it illegal to possess certain kinds of material – in UK law, the act of merely downloading that material can count as possession. Though the internet has made it difficult to censor material, new media have greatly facilitated the tracking down of individuals suspected of producing or disseminating this material, since all online activity leaves a trail; as Gus Hosein and Eric King point out (‘Age of Insecurity’, Index on Censorship, Volume 40, 2/2011), ‘in the 21st century, law enforcement is just a few clicks of the mouse away. ’ When the UK home secretary Theresa May was first challenged over the Draft Communications Data Bill, which contains so many possibilities for increased electronic surveillance that it has been called the ‘Snoopers’ Charter’, she declared in the tabloid newspaper the Sun on 3 April 2012 that ‘only suspected terrorists, paedophiles or serious criminals will be investigated’. In other words, the same old refrain: if you’ve got nothing to hide, you’ve got nothing to fear. In December 2012 it was announced that the bill would be redrafted after considerable disagreement within the coalition government. However, once one begins to examine the relevant legislation and, crucially, how it has been interpreted by police and prosecutors in specific cases, it becomes clear that those other than terrorists or paedophiles may indeed have a great deal to fear.
A modified constrained constant modulus approach to blind adaptive multiuser detection

An alternative blind adaptive multiuser detection is investigated based on modified constrained constant modulus (CM) criterion. It is shown that the performance of a CM-based receiver is limited by the received power of the desired user. In this paper, we show that the limitation can be avoided using the noncanonical constraint CM criterion and that in the presence of channel noise the modified CM criterion function is strictly convex by properly selecting some constant. With analyzing the extrema of the cost function, we point out how to select the constant. Moreover, a simple stochastic gradient algorithm for implementing our scheme is presented, and the convergence properties of the algorithm are analyzed. Simulation examples are given to demonstrate the performance of the proposed scheme.
( Under the Direction of

The AGDISP aerial spray simulation model is used to predict the deposition of spray material released from an aircraft. Determining the optimal input values to AGDISP in order to produce a desired spray material deposition is extremely difficult (NP hard). SAGA, an intelligent optimization method based on the simple genetic algorithm, was developed to solve this problem. Our project is the subsequent work of SAGA. We apply several nature inspired heuristics, mainly based on genetic algorithms, to this problem. The first method still uses the genetic algorithm, but changes genetic algorithm type, selection method, crossover and mutation operators. The second method applies a neural network to improve the initial population, crossover and mutation. The third method uses GADO, a general-purpose approach to solving the parametric design problem. The fourth method uses simulated annealing. Finally, we compare their performance in the aerial spray deposition problem.
Born-infeld cosmologies

We present a model for an inhomogeneous and anisotropic early universe filled with a nonlinear electromagnetic field of Born–Infeld (BI) type. The effects of the BI field are compared with the linear case (Maxwell). Since the curvature invariants are well behaved then we conjecture that our model does not present an initial big bang singularity. The existence of the BI field modifies the curvature invariants at t=0 as well as sets bounds on the amplitude of the conformal metric function.
Enhanced Chord-Based Routing Protocol Using Neighbors' Neighbors Links

A fundamental problem that confronts peer-to- peer applications is the efficient location of the node that stores desired data items. Chord protocol adopts finger tables to achieve O(logN) mean lookup path length for an N node system. To many time-sensitive applications, the requirement of optimal lookup path length is more critical. Our focus in this paper is to study how to shorten the lookup path length through optimizing routing protocol based on Chord. The contribution of this paper is a more efficient Chord-based routing protocol using neighbors' neighbors links for lookup in a dynamic peer-to-peer system with frequent node arrivals and departures. Results from theoretical analysis and simulations show that both logical path length and physical end-to-end path latency of our protocol are shorter than Chord with the assist of neighbors' neighbors links per node.
P2DHMM: A Novel Web Object Information Extraction Model

Due to the difference between web page and plain text document, the concept of web object is introduced in this paper. Besides, the supposed state transition and the emission symbol conditions are improved based on Pseudo two dimension hidden Markov model (P2D-HMM), and a novel web objects information extraction method is proposed. Finally, through an example, it shows that the proposed method has a very high precision for web objects information extraction
Properties of Hemolysin and Protease Produced by Aeromonas trota

We examined the properties of exotoxins produced by Aeromonas trota (A. enteropelogenes), one of the diarrheagenic species of Aeromonadaceae. Nine of 19 A. trota isolates that grew on solid media containing erythrocytes showed hemolytic activity. However, the hemolytic activities of the culture supernatants of these hemolytic strains of A. trota were markedly lower than those of A. sobria when cultured in liquid medium, and the amount of hemolysin detected by immunoblotting using antiserum against the hemolysin produced by A. sobria was also low. A mouse intestine loop assay using living bacterial cells showed that A. trota 701 caused the significant accumulation of fluid, and antiserum against the hemolysin produced suppressed the enterotoxic action of A. trota 701. These results indicated that A. trota 701 was diarrheagenic and the hemolysin produced was the causative agent of the enterotoxic activity of A. trota. The hemolysin in A. sobria was previously shown to be secreted in a preform (inactive form) and be activated when the carboxy-terminal domain was cleaved off by proteases in the culture supernatant. Since mature hemolysin was detected in the culture supernatants of A. trota, we analyzed the extracellular protease produced by A. trota. Fifteen of 19 A. trota isolates that grew on solid media containing skim milk showed proteolytic activity. We subsequently found that most A. trota isolates possessed the serine protease gene, but not the metalloprotease gene. Therefore, we determined the nucleotide sequence of the serine protease gene and its chaperone A. trota gene. The results obtained revealed that the deduced amino acid sequences of serine protease and the chaperone were homologous to those of A. sobria with identities of 83.0% and 75.8%, respectively.
Orbitrap Mass Analyzer – Overview and Applications in Proteomics

The orbitrap mass analyzer is proving itself as a useful addition to a proteomics tool box. The key attributes of this analyzer are accurate mass and high resolution similar to those achievable with FT ICR instrumentation. The basic principles underlying these capabilities, and how they translate into benefits in real‐life proteomics experiments are discussed. The focus is on reviewing examples of protein identification with bottom‐up and top‐down approaches, and detection of post‐translational modifications.
Performance Evaluation of an Embedded  $d$–  $q$ WPT-Based Digital Protection for IPMSM Drives

This paper presents the implementation and performance evaluation of an embedded digital protection for three-phase (3φ) interior permanent-magnet synchronous motor (IPMSM) drives. The presented digital protection is established through extracting the high-frequency subband present in the d-q-axis components of the currents drawn by the protected IPMSM. The desired high-frequency subband is extracted using the wavelet packet transform (WPT) from the d-q-axis current components, which are obtained from the controller of the IPMSM drive. The extracted high-frequency subband contains signature information that allows detecting and classifying transient disturbances into fault and nonfault events. The presented method is insensitive to the variations in the drive parameters, loading levels, nature of electrical faults (open circuit or short circuit), and operation of the drive controller. These features of the d-q WPT-based digital protection simplify its implementation and facilitate its embedding within the controller of the IPMSM drive. The performance of the d-q WPT-based digital protection is experimentally evaluated on a laboratory 5-hp IPMSM drive for various fault and nonfault events. Test results demonstrate fast, accurate, and reliable detection, classification, and response to fault and nonfault events.
Hyaluronic Acid Based Hydrogels for Regenerative Medicine Applications

Hyaluronic acid (HA) hydrogels, obtained by cross-linking HA molecules with divinyl sulfone (DVS) based on a simple, reproducible, and safe process that does not employ any organic solvents, were developed. Owing to an innovative preparation method the resulting homogeneous hydrogels do not contain any detectable residual cross-linking agent and are easier to inject through a fine needle. HA hydrogels were characterized in terms of degradation and biological properties, viscoelasticity, injectability, and network structural parameters. They exhibit a rheological behaviour typical of strong gels and show improved viscoelastic properties by increasing HA concentration and decreasing HA/DVS weight ratio. Furthermore, it was demonstrated that processes such as sterilization and extrusion through clinical needles do not imply significant alteration of viscoelastic properties. Both SANS and rheological tests indicated that the cross-links appear to compact the network, resulting in a reduction of the mesh size by increasing the cross-linker amount. In vitro degradation tests of the HA hydrogels demonstrated that these new hydrogels show a good stability against enzymatic degradation, which increases by increasing HA concentration and decreasing HA/DVS weight ratio. Finally, the hydrogels show a good biocompatibility confirmed by in vitro tests.
Determination of optimal frequency ranges using common spatial pattern images

In this paper we present brain maps constructed for Visualization of Arrow Movement (VAM) mental tasks with EEG signals recorded from 20 locations on the scalp. Method of Common Spatial Patterns (CSP) is employed to generate the spatial maps after filtering raw EEG signals into nine different frequency bands. Separate CSPs were obtained for six subjects who participated in this study. These brain maps show distinct spatial patterns that can be used for distinguishing two mental tasks in VAM. For every subject, optimal frequency range which is useful in distinguishing mental tasks in VAM was obtained.
Amnion Epithelial Cells Promote Lung Repair via Lipoxin A4.

: Human amnion epithelial cells (hAECs) have been shown to possess potent immunomodulatory properties across a number of disease models. Recently, we reported that hAECs influence macrophage polarization and activity, and that this step was dependent on regulatory T cells. In this study, we aimed to assess the effects of hAEC-derived proresolution lipoxin-A4 (LXA4) on T-cell, macrophage, and neutrophil phenotype and function during the acute phase of bleomycin-induced lung injury. Using C57Bl6 mice, we administered 4 million hAECs intraperitoneally 24 hours after bleomycin challenge. Outcomes were measured at days 3, 5, and 7. hAEC administration resulted in significant changes to T-cell, macrophage, dendritic cell, and monocyte/macrophage infiltration and phenotypes. Endogenous levels of lipoxygenases, LXA4, and the lipoxin receptor FPR2 were elevated in hAEC-treated animals. Furthermore, we showed that the effects of hAECs on macrophage phagocytic activity and T-cell suppression are LXA4 dependent, whereas the inhibition of neutrophil-derived myleoperoxidase by hAECs is independent of LXA4. This study provides the first evidence that lipid-based mediators contribute to the immunomodulatory effects of hAECs and further supports the growing body of evidence that LXA4 is proresolutionary in lung injury. This discovery of LXA4-dependent communication between hAECs, macrophages, T cells, and neutrophils is important to the understanding of hAEC biodynamics and would be expected to inform future clinical applications. SIGNIFICANCE In this study, stem-like cells derived from the human placenta, called human amnion epithelial cells (hAECs), were shown to prevent lung injury by producing a lipid-based molecule called lipoxin A4. This molecule works by encouraging interactions between a variety of immune cells in the lungs to effect repair. Following hAEC administration, fewer proinflammatory immune cells were attracted to the lungs and their activity was suppressed to achieve resolution of lung injury. The findings from this study will help inform the design of safe and efficacious hAEC therapy for lung disease.
Pulmonary , gastrointestinal and urogenital pharmacology Lipid-lowering agents inhibit hepatic steatosis in a non-alcoholic steatohepatitis-derived hepatocellular carcinoma mouse model

Non-alcoholic fatty liver disease (NAFLD) is associated with various metabolic disorders, and the therapeutic strategies for treating NAFLD and non-alcoholic steatohepatitis (NASH) have not been fully established. In the present study, we examined whether lipid-lowering agents inhibited the progression of NAFLD and tumorigenesis in a non-alcoholic steatohepatitis-derived hepatocellular carcinoma model mouse (STAM mice) generated by streptozotocin injection and a high-fat diet. Seven-week-old STAM mice were divided into groups fed a high-fat diet (Ctl) or a high-fat diet supplemented with ezetimibe (Ez), fenofibrate (Ff), rosuvastatin (Rs), ezetimibe plus fenofibrate (EF), or ezetimibe plus rosuvastatin (ER) for 4 weeks. At the end of the experiments, an oral glucose tolerance test, an insulin tolerance test, biochemical analyses using serum and liver, and a histological analysis of liver were performed in 11-week-old STAM mice. The lipid-lowering agents did not affect the body weight or the casual blood glucose levels in any of the groups. The serum triglyceride level was significantly decreased by Ff, Rs, and EF. Glucose tolerance was improved by Ez and Ff, but none of these agents improved insulin sensitivity. A histochemical analysis revealed that the lipid-lowering agents, with the exception of Rs, significantly inhibited the progression of hepatic steatosis. Nonetheless, no significant changes in the incidence of hepatic tumors were observed in any of the groups. Lipid-lowering agents inhibited the progression of hepatic steatosis without suppressing tumorigenesis in STAM mice. Our data has implications for the mechanism underlying steatosis-independent hepatic tumorigenesis in mice. & 2015 Elsevier B.V. All rights reserved.
[The negative regulatory effect of IFN-gamma on cognitive function of human natural killer cells].

OBJECTIVE To investigate the regulatory effect of IFN-gamma on recognition of target cells by human natural killer (NK) cells. METHODS The cytotoxic activity of human NK cell lines (NK92, NKL) was detected by MTT method. Expression of NK cell receptors (NKG2D, NKG2A/B, KIR2DL1 and KIR2DS1) and MICA on target cells (the ligand of NKG2D) was measured by RT-PCR. RESULTS Both NK92 and NKL cells exerted higher cytotoxicity to tumor cells with MICA expression, while tumors without MICA expression could resist NK cell lysis. IFN-gamma (> 1000 U/ml) inhibited NK lysis of tumor cells with MICA expression through down-regulating the expression of NKG2D, but up-regulating the expression of NKG2A/B and KIR2DL1. CONCLUSION IFN-gamma has a negative effect on activation and cytotoxicity of human NK cells by altering the balance between the expression of activating and inhibitory receptors on NK cells in favor of inhibition. This may serve to limit NK cell over-activation in vivo.
Temporally coherent stereo matching using kinematic constraints

This paper explores a simple yet effective way to generate temporally coherent disparity maps from binocular video sequences based on kinematic constraints. Given the disparity map at a certain frame, the proposed approach computes the set of possible disparity values for each pixel in the subsequent frame, assuming a maximum displacement constraint (in world coordinates) allowed for each object. These disparity sets are then used to guide the stereo matching procedure in the subsequent frame, generating a temporally coherent disparity map. Experimental results indicate that the proposed approach produces temporally coherent disparity maps comparable to or better than competitive methods.
Femoral Strength and Posture in Terrestrial Birds and Non‐Avian Theropods

Osteological and experimental evidence suggest a change in femoral posture between non‐avian dinosaurs (in which the femur presumably was carried in a subvertical position) and birds (in which the femur is held nearly horizontal during most phases of terrestrial locomotion). In this study, we used a broad comparative sample to test the hypothesis that cross‐sectional properties of the femur records evidence of this presumed change in posture. Imax and Imin (second moment of area, related to resistance to bending) and cross‐sectional area (indicating resistance to compression) were measured from computed tomography scans of the femora of 30 species of flightless or primarily terrestrial birds, one probable non‐dinosaur dinosauromorph, and at least four species of non‐avian theropods. It was predicted that birds should have more eccentrically shaped femoral midshafts as measured by Imax/Imin (reflecting greater bending) and comparatively smaller cross‐sectional areas than non‐avians. Results show that no significant differences occur between non‐avian dinosaurs and birds for any parameter, and the samples overlapped broadly in many cases. Thus, cross‐sectional properties cannot be used to infer differences in femoral posture between the two groups. This surprising finding might be explained by the fact that femoral postures were not drastically different or that a gradation of postures occurred in each sample. It is also possible that bone loading during life was not closely correlated with cross‐sectional morphology. We conclude that cross‐sectional properties should be used with caution in determining the posture and behaviors of extinct animals, and only in conjunction with other morphological information. Anat Rec, 292:1406–1411, 2009. © 2009 Wiley‐Liss, Inc.