Miracle-dz/UniFAR-FTUs huggingface dataset:
Electron Microscopic Examination of Factors Influencing the Expression of Filamentous Surface Structures on Clinical and Environmental Isolates of Aeromonas veronii biotype sobria

Strains of Aeromonas veronii biotype sobria isolated from clinical and environmental sources were examined for their expression of surface structures under a variety of culture conditions. When grown on solid media at 37 C, more than 95% of bacteria from the majority of strains isolated from human diarrheal feces and chicken carcasses were non‐piliated or expressed only a few pili of long, flexible morphology per cell. Strains isolated from water or other foods were much more likely to express pili. Heavily piliated strains (all sources) possessed pili of several morphological types, including long, flexible pili of varying widths and rigid pili of varying lengths. Expression of pili was favored by growth at temperatures ca. 20 C and below and growth in liquid medium. Most fecal strains expressed some pili under these conditions. In addition, other surface structures (fibrillar aggregates, fibrillar networks, bundle‐forming pili) were seen on some strains from most sources. These were also seen most frequently when bacteria were grown in liquid media at temperatures ca. 20 C and below. Pili expression was not dramatically influenced by growth under anaerobic conditions, or in iron‐depleted media, or by combinations of the above conditions. The role of the above surface structures in Aeromonas pathogenicity remains to be elucidated.
Epigenetic Potentiation of NY-ESO-1 Vaccine Therapy in Human Ovarian Cancer

Odunsi and colleagues show that the DNA methyltransferase inhibitor decitabine augmented the efficacy of the NY-ESO-1 vaccine and doxorubicin treatment of patients with refractory epithelial ovarian cancer, demonstrating the potential of the combined chemo-immunotherapy regimen. The cancer–testis/cancer germline antigen, NY-ESO-1, is a vaccine target in epithelial ovarian cancer (EOC), but its limited expression is a barrier to vaccine efficacy. As NY-ESO-1 is regulated by DNA methylation, we hypothesized that DNA methyltransferase inhibitors may augment NY-ESO-1 vaccine therapy. In agreement, global DNA hypomethylation in EOC was associated with the presence of circulating antibodies to NY-ESO-1. Preclinical studies using EOC cell lines showed that decitabine treatment enhanced both NY-ESO-1 expression and NY-ESO-1–specific CTL-mediated responses. On the basis of these observations, we performed a phase I dose-escalation trial of decitabine, as an addition to NY-ESO-1 vaccine and doxorubicin liposome chemotherapy, in 12 patients with relapsed EOC. The regimen was safe, with limited and clinically manageable toxicities. Both global and promoter-specific DNA hypomethylation occurred in blood and circulating DNAs, the latter of which may reflect tumor cell responses. Increased NY-ESO-1 serum antibodies and T-cell responses were observed in the majority of patients, and antibody spreading to additional tumor antigens was also observed. Finally, disease stabilization or partial clinical response occurred in six of ten evaluable patients. On the basis of these encouraging results, evaluation of similar combinatorial chemo-immunotherapy regimens in EOC and other tumor types is warranted. Cancer Immunol Res; 2(1); 37–49. ©2014 AACR.
Exploiting Attitude Sensing in Vision-Based Navigation for an Airship

An Attitude Heading Reference System (AHRS) is used to compensate for rotational motion, facilitating vision-based navigation above smooth terrain by generating virtual images to simulate pure translation movement. The AHRS combines inertial and earth field magnetic sensors to provide absolute orientation measurements, and our recently developed calibration routine determines the rotation between the frames of reference of the AHRS and the monocular camera. In this way, the rotation is compensated, and the remaining translational motion is recovered by directly finding a rigid transformation to register corresponding scene coordinates. With a horizontal ground plane, the pure translation model performs more accurately than image-only approaches, and this is evidenced by recovering the trajectory of our airship UAV and comparing with GPS data. Visual odometry is also fused with the GPS, and ground plane maps are generated from the estimated vehicle poses and used to evaluate the results. Finally, loop closure is detected by looking for a previous image of the same area, and an open source SLAM package based in 3D graph optimization is employed to correct the visual odometry drift. The accuracy of the height estimation is also evaluated against ground truth in a controlled environment.
University ’ s repository of research publications and other research outputs On the interpretation of gravity variations in the presence of active hydrothermal systems : Insights from the Nisyros Caldera , Greece Journal Article

We report on short-term (over tens of minutes) residual gravity changes recorded at the restless Nisyros caldera in Greece via a series of discrete measurements at benchmarks within or in proximity to a hydrothermal area located along the caldera floor. The obtained time series reveal sinusoidal gravity variations with amplitudes of up to 25 μGal and wavelengths of 40-50 min. Degassing of a magmatic source coupling into (shallow) hydrothermal systems including the ascent of steam pockets and transient pressure variations during steam/liquid interface propagation appear to be the most likely causative process for the observed short-term variations. We assess standard protocols of micro-gravity surveys for hazard assessment in volcanic areas in the light of these findings and propose additional techniques, such as continuous gravimetry, for the discrimination of hydrothermal signals from deeper-seated, i.e. magmatic, signals during gravity monitoring of restless volcanoes hosting active hydrothermal systems. D R A F T September 11, 2005, 2:00pm D R A F T GOTTSMANN ET AL.: GRAVITY CHANGES AT NISYROS CALDERA 3
No evidence for serosubtype-restricted protection among teenagers vaccinated with the Norwegian group B outer membrane vesicle vaccine.

To the Editor—We read with great interest the article by Jones et al. [1] describing the dynamics of carriage of Neisseria meningitidis among military recruits. Of particular interest was their finding of serosubtype-specific bactericidal responses to the acquired meningococcal strains, a finding that supported previous results from various laboratories on the role of PorA antigens in eliciting bactericidal antibodies. However, we disagree with their statement when discussing the protection of the Norwegian B:15:P1.7,16 outer membrane vesicle (OMV) vaccine. Referring to a study that involved only a small number of vaccinees who became ill with meningococcal disease [2], Jones et al. claimed that meningococcal infections in recipients of this vaccine were caused by heterologous strains only, indicating serosubtype-specific protection. We have analyzed all strains from participants who contracted meningococcal disease during the protection trial done among teenagers in Norway [3]. In the blinded part of the trial, 6 of 12 vaccinees and 10 of 24 placebo controls became ill with strains expressing PorA with P1.7 or P1.16 (or both) subtypes [4]. When the results for the first year of the following open trial were included, 10 of 20 vaccinees and 16 of 35 controls were infected with corresponding strains [5]. These data show no significant differences in the distribution of strains with vaccine-like subtypes causing disease among vaccinees and controls (x test with Yates’s correction, ). P 1 . 90 Guttormsen et al. [2] reported that 4 of 7 vaccinees and 3 of 18 nonvaccinees were infected with B:15:P1.12 strains. Such strains were later found to be localized mainly to the western part of Norway [6]. This is the region where most of the patients studied by Guttormsen et al. [2] live, which might explain the authors’ assumption of some subtype-specific protection. However, from their data, we find no significant difference in the distribution of the P1.12 subtype between the 2 patient groups (Fisher’s exact test, ). Three of the vaccinees infected P 5 . 066 with B:15:P1.12 strains had been immunized 3 years prior to disease [2], and the protection of the OMV vaccine has been shown to wane following a two-dose regimen [7]. The possibility that vaccination might select for infectious strains with mutations in the P1.7,16 PorA has also been analyzed previously [8], but no indication for the emergence of such strains was demonstrated. Thus, the data available give no evidence to conclude that infection of teenagers vaccinated with the Norwegian OMV vaccine was only caused by heterologous strains.
A promising new wavelength region for three-photon fluorescence microscopy of live cells

We report three‐photon laser scanning microscopy (3PLSM) using a bi‐directional pumped optical parametric oscillator (OPO) with signal wavelength output at λ= 1500 nm. This novel laser was used to overcome the high optical loss in the infrared spectral region observed in laser scanning microscopes and objective lenses that renders them otherwise difficult to use for imaging. To test our system, we performed 3PLSM auto‐fluorescence imaging of live plant cells at λ= 1500 nm, specifically Spirogyra, and compared performance with two‐photon excitation (2PLSM) imaging using a femtosecond pulsed Ti:Sapphire laser at λ= 780 nm. Analysis of cell viability based on cytoplasmic organelle streaming and structural changes of cells revealed that at similar peak powers, 2PLSM caused gross cell damage after 5 min but 3PLSM showed little or no interference with cell function after 15 min. The λ= 1500 nm OPO is thus shown to be a practical laser source for live cell imaging.
Effect of tributyltin (TBT) in the metabolic activity of TBT‐resistant and sensitive estuarine bacteria

The effect of tributyltin (TBT) on growth and metabolic activity of three estuarine bacteria with different TBT resistance profiles was investigated in an organic‐rich culture medium (TSB) and in phosphate buffered saline (PBS) buffer. Exposure to TBT was assessed by determining its effect on growth (OD600 nm measurement), bacterial productivity (leucine incorporation), viability (CFU counts), aggregation and cell size (from Live/Dead analysis), ATP and NADH concentrations. TBT exposure resulted in decrease of bacterial density, cell size, and metabolic activity. In addition, cell aggregates were observed in the TBT‐treated cultures. TBT strongly affected bacterial cell metabolism and seemed to exert an effect on its equilibrium, interfering with cell activity. Also, TBT toxicity was lower when cells were grown in TSB than in PBS, suggesting that a nutrient‐rich growth medium can protect cells from TBT toxicity. This study contributes to our understanding of the TBT‐resistant cell behavior reflected in its physiology and metabolic activity. This information is of utmost importance for further studies of TBT bioremediation. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012.
Room equalization based on iterative simple complex smoothing of acoustic impulse responses

This paper presents a room equalization method based on iterative simple complex smoothing of measured acoustic impulse responses. This is useful in cases of long duration impulse responses. Corresponding time reduced impulse responses are derived which conform to perceptual principles. The smoothed impulse responses are then used to design equalization filters. Results from an audio-conferencing reverberant room using objective and subjective tests show that we can improve the measured and perceived quality of audio reproduction.
Characterization of Growth-Differentiation Factor 15, a Transforming Growth Factor β Superfamily Member Induced following Liver Injury

ABSTRACT We have identified a new murine transforming growth factor β superfamily member, growth-differentiation factor 15 (Gdf15), that is expressed at highest levels in adult liver. As determined by Northern analysis, the expression ofGdf15 in liver was rapidly and dramatically up-regulated following various surgical and chemical treatments that cause acute liver injury and regeneration. In situ hybridization analysis revealed distinct patterns of Gdf15 mRNA localization that appeared to reflect the known patterns of hepatocyte injury in each experimental treatment. In addition, treatment of two hepatocyte-like cell lines with either carbon tetrachloride or heat shock inducedGdf15 mRNA expression, indicating that direct cellular injury can induce Gdf15 expression in the absence of other cell types, such as inflammatory cells. In order to investigate the potential functions of Gdf15, we created Gdf15 null mice by gene targeting. Homozygous null mice were viable and fertile. Despite the dramatic regulation of Gdf15 expression observed in the partial-hepatectomy and carbon tetrachloride injury models, we found no differences in the injury responses between homozygous null mutants and wild-type mice. Our findings suggest either that Gdf15 does not have a regulatory role in liver injury and regeneration or that Gdf15 function within the liver is redundant with that of other signaling molecules.
Bioequivalence evaluation of two flutamide preparations in healthy female subjects.

In the present study two different preparations containing 250 mg flutamide (3'-trifluoromethyl-4'-nitro-2-methyl-propionylanilide, CAS 13311-84-7) were compared in 20 female subjects. The trial was performed in a randomized two-way cross-over design. Each subject received one tablet with 250 mg flutamide in each period. The two treatment periods were separated by a wash-out phase of 7 days. Blood samples were obtained just before dosing and 18 times during the subsequent 36 h. The plasma concentrations of flutamide, 2-hydroxyflutamide and trifluoromethylnitroaniline were determined by HPLC with UV-detection. Due to the low plasma levels of the parent drug flutamide, the data of the pharmacologically active metabolite 2-hydroxyflutamide (CAS 52806-53-8) were used for bioequivalence assessment. The following mean values were obtained after administration of the test and reference preparation respectively: Flutamide: AUC0-36 = 95.82 ng.h/ml vs 93.33 ng.h/ml, Cmax = 44.78 ng/ml vs 38.73 ng/ml, tmax = 1.71 h vs 1.66 h, 2-hydroxyflutamide: AUC0-infinity = 6090.73 ng.h/ml vs 6068.83 ng. h/ml, Cmax = 772.74 ng/ml vs 779.84 ng/ml, tmax = 2.21 h vs 2.17 h, t1/2 = 8.21 h vs 8.32 h, trifluoromethylnitroaniline: AUC0-infinity = 1771.87 ng.h/ml vs 1701.44 ng.h/ml, Cmax = 173.36 ng/ml vs 171.32 ng/ml, tmax = 2.74 h vs 2.63 h, t1/2 = 10.75 h vs 9.83 h. The two preparations proved to be bioequivalent.
Bit Error Rate Estimate of Finite Length Turbo Codes

A novel method of estimating the BER performance of finite length turbo codes in a binary AWGN channel is proposed. We consider the asymptotes of BER performance at low and high E b N0 resulted from the small and large extrinsic values, respectively. The BER performance curve transitions between two asymptotes in the waterfall region, where the transition probability is approximately obtained by using the SNR transfer characteristic band of extrinsic values in the turbo decoding algorithm. Then, the BER estimate of finite length turbo codes is obtained by using two asymptotes at low and high E b N0 and the transition probability b N0 including the waterfall region, either. Thus, there exists the need for a new methodology to estimate the BER performance of the finite length turbo codes which is meaningful over all E b N0 . In this paper, we propose a novel method to estimate the BER performance of the finite length turbo codes over all E b N0 . The BER performance curve has asymptotes at low E b N0 as well as at high E b N0 . The BER performance curve experiences a transition from the BER asymptote at low E b N0 to that at high Eb
Predicting Drug Side Effects Using Data Analytics and the Integration of Multiple Data Sources

The development of automated approaches employing computational methods using data from publicly available drugs datasets for the prediction of drug side effects has been proposed. This paper presents the use of a hybrid machine learning approach to construct side effect classifiers using an appropriate set of data features. The presented approach utilizes the perspective of data analytics to investigate the effect of drug distribution in the feature space, categorize side effects into several intervals, adopt suitable strategies for each interval, and construct data models accordingly. To verify the applicability of the presented method in side effect prediction, a series of experiments were conducted. The results showed that this approach was able to take into account the characteristics of different types of side effects, thereby achieve better predictive performance. Moreover, different feature selection schemes were coupled with the modeling methods to examine the corresponding effects. In addition, analyses were performed to investigate the task difficulty in terms of data distance and similarity. Examples of visualized networks of associations between drugs and side effects are also discussed to further evaluate the results.
Tight bounds for strategyproof classification

Strategyproof (SP) classification considers situations in which a decision-maker must classify a set of input points with binary labels, minimizing expected error. Labels of input points are reported by self-interested agents, who may lie so as to obtain a classifier more closely matching their own labels. These lies would create a bias in the data, and thus motivate the design of truthful mechanisms that discourage false reporting. We here answer questions left open by previous research on strategyproof classification [12, 13, 14], in particular regarding the best approximation ratio (in terms of social welfare) that an SP mechanism can guarantee for n agents. Our primary result is a lower bound of 3--2/n on the approximation ratio of SP mechanisms under the shared inputs assumption; this shows that the previously known upper bound (for uniform weights) is tight. The proof relies on a result from Social Choice theory, showing that any SP mechanism must select a dictator at random, according to some fixed distribution. We then show how different randomizations can improve the best known mechanism when agents are weighted, matching the lower bound with a tight upper bound. These results contribute both to a better understanding of the limits of SP classification, as well as to the development of similar tools in other, related domains such as SP facility location.
Internally Randomized Control Trial of Radiation Exposure Using Ultra-low Radiation Imaging Versus Traditional C-arm Fluoroscopy for Patients Undergoing Single-level Minimally Invasive Transforaminal Lumbar Interbody Fusion

Study Design. Randomized controlled trial. Objective. To compare radiation exposure between ultra-low radiation imaging (ULRI) with image enhancement and standard-dose fluoroscopy for patients undergoing minimally invasive transforaminal lumbar interbody fusion (MIS TLIF). Summary of Background Data. Although the benefits of MIS are lauded by many, there is a significant amount of radiation exposure to surgeon and operating room personnel. Our goal with this work was to see if by using ultra-low dose radiation settings coupled with image enhancement, this exposure could be minimized. Methods. An institutional review board approved, prospective, internally randomized controlled trial was performed comparing ultra-low dose settings coupled with image enhancement software to conventional fluoroscopic imaging. In this study, each patient served as their own control, randomly assigning one side of MIS-TLIF for cannulation and K-wire placement using each imaging modality. Further, the case was also randomly divided into screw placement and cage placement/final images to allow further comparisons amongst patients. Radiation production from the C-arm fluoroscope and radiation exposure to all operating room personnel were recorded. Results. Twenty-four patients were randomly assigned to undergo a single level MIS-TLIF. In no case was low radiation imaging abandoned, and no patient had a neurologic decline or required hardware repositioning. Everyone in the operating room—the physician, scrub nurse, circulator, and anesthesiologist—all benefited with 61.6% to 83.5% reduction in radiation exposure during cannulation and K-wire placement to screw insertion aided by ULRI. In every case but the anesthesiologist dose, this was statistically significant (P < 0.05). This benefit required no additional time (P = 0.78 for K-wire placement). Conclusion. ULRI, when aided by image enhancement software, affords the ability for all parties in the operating room to substantially decrease their radiation exposure compared with standard-dose C-arm fluoroscopy without adding additional time or an increased complication rate. Level of Evidence: 2
Accurate Estimation of Low Fundamental Frequencies From Real-Valued Measurements

In this paper, the difficult problem of estimating low fundamental frequencies from real-valued measurements is addressed. The methods commonly employed do not take the phenomena encountered in this scenario into account and thus fail to deliver accurate estimates. The reason for this is that they employ asymptotic approximations that are violated when the harmonics are not well-separated in frequency, something that happens when the observed signal is real-valued and the fundamental frequency is low. To mitigate this, we analyze the problem and present some exact fundamental frequency estimators that are aimed at solving this problem. These estimators are based on the principles of nonlinear least-squares, harmonic fitting, optimal filtering, subspace orthogonality, and shift-invariance, and they all reduce to already published methods for a high number of observations. In experiments, the methods are compared and the increased accuracy obtained by avoiding asymptotic approximations is demonstrated.
Follow up: Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer

In 2012, we reported 30 compound data sets and/or programs developed in our laboratory in a data article and made them freely available to the scientific community to support chemoinformatics and computational medicinal chemistry applications. These data sets and computational tools were provided for download from our website. Since publication of this data article, we have generated 13 new data sets with which we further extend our collection of publicly available data and tools. Due to changes in web servers and website architectures, data accessibility has recently been limited at times. Therefore, we have also transferred our data sets and tools to a public repository to ensure full and stable accessibility. To aid in data selection, we have classified the data sets according to scientific subject areas. Herein, we describe new data sets, introduce the data organization scheme, summarize the database content and provide detailed access information in ZENODO (doi: 10.5281/zenodo.8451 and doi:10.5281/zenodo.8455).