Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Signature of Acute Liver Failure: From Discovery and Verification in a Pig Model to Confirmation in Humans*

Acute liver failure (ALF) is a fatal condition hallmarked by rapid development. The present study aimed to describe the dynamic alterations of serum proteins associated with ALF development, and to seek for novel biomarkers of ALF. Miniature pigs (n = 38) were employed to establish ALF models by infusing d-galactosamine (GALN, 1.3 g/kg). A total of 1310 serum proteins were compared in pooled serum samples (n = 10) before and 36 h after GALN administration through label-free quantitation (LFQ) based shotgun proteomics. Functional analysis suggested a significant enrichment of ALF-related proteins involved in energy metabolism. Temporal changes of 20 energy metabolism related proteins were investigated in individual pigs (n = 8) via parallel reaction monitoring (PRM) based targeted proteomics. In addition, mitochondrion degeneration and gene expression alteration of aerobic metabolism genes were confirmed in GALN-insulted pig liver. In clinical validation study enrolled 34 ALF patients and 40 healthy controls, fructose-1,6-bisphosphatase 1 (FBP1) showed a prognostic value for short-term survival (30 days) equal to that of the Model of End-stage Liver Disease score (ROC-AUC = 0.778). Survival analysis suggested significantly higher death-related hazard in ALF patients with higher FBP1 levels (>16.89 μg/dL) than in those with lower FBP1 levels (p = 0.002). Additionally, serum retinol binding protein 4 (RBP4) level was found decreased prior to ALT elevation in GALN-insulted pig model. We also confirmed that serum level of RBP4 is significantly lower in ALF patients (p < 0.001) as compared with healthy controls. In summary, this translational study, displayed by multistaged proteomics techniques, unveiled underlying functional changes related to the development of ALF and facilitated the discovery of novel ALF markers.
Fast as a shadow, expressive as a tree: hybrid memory monitoring for C

One classical approach to ensuring memory safety of C programs is based on storing block metadata in a tree-like datastructure. However it becomes relatively slow when the number of memory locations in the tree becomes high. Another solution, based on shadow memory, allows very fast constant-time access to metadata and led to development of several highly optimized tools for detection of memory safety errors. However, this solution appears to be insufficient for evaluation of complex memory-related properties of an expressive specification language. In this work, we address memory monitoring in the context of runtime assertion checking of C programs annotated in E-ACSL, an expressive specification language offered by the FRAMA-C framework for analysis of C code. We present an original combination of a tree-based and a shadow-memory-based techniques that reconciles both the efficiency of shadow memory with the higher expressiveness of annotations whose runtime evaluation can be ensured by a tree of metadata. Shadow memory with its instant access to stored metadata is used whenever small shadow metadata suffices to evaluate required annotations, while richer metadata stored in a compact prefix tree (Patricia trie) is used for evaluation of more complex memory annotations supported by E-ACSL. This combined monitoring technique has been implemented in the runtime assertion checking tool for E-ACSL. Our initial experiments confirm that the proposed hybrid approach leads to a significant speedup with respect to an earlier implementation based on a Patricia trie alone without any loss of precision.
Supervised classification of etoposide-treated in vitro adherent cells based on noninvasive imaging morphology

Abstract. Single-cell studies using noninvasive imaging is a challenging, yet appealing way to study cellular characteristics over extended periods of time, for instance to follow cell interactions and the behavior of different cell types within the same sample. In some cases, e.g., transplantation culturing, real-time cellular monitoring, stem cell studies, in vivo studies, and embryo growth studies, it is also crucial to keep the sample intact and invasive imaging using fluorophores or dyes is not an option. Computerized methods are needed to improve throughput of image-based analysis and for use with noninvasive microscopy such methods are poorly developed. By combining a set of well-documented image analysis and classification tools with noninvasive microscopy, we demonstrate the ability for long-term image-based analysis of morphological changes in single cells as induced by a toxin, and show how these changes can be used to indicate changes in biological function. In this study, adherent cell cultures of DU-145 treated with low-concentration (LC) etoposide were imaged during 3 days. Single cells were identified by image segmentation and subsequently classified on image features, extracted for each cell. In parallel with image analysis, an MTS assay was performed to allow comparison between metabolic activity and morphological changes after long-term low-level drug response. Results show a decrease in proliferation rate for LC etoposide, accompanied by changes in cell morphology, primarily leading to an increase in cell area and textural changes. It is shown that changes detected by image analysis are already visible on day 1 for 0.25-μM etoposide, whereas effects on MTS and viability are detected only on day 3 for 5-μM etoposide concentration, leading to the conclusion that the morphological changes observed occur before and at lower concentrations than a reduction in cell metabolic activity or viability. Three classifiers are compared and we report a best case sensitivity of 88% and specificity of 94% for classification of cells as treated/untreated.
Imatinib and spironolactone suppress hepcidin expression

Disorders of iron metabolism are largely attributed to an excessive or insufficient expression of hepcidin, the master regulator of systemic iron homeostasis. Here, we investigated whether drugs targeting genetic regulators of hepcidin can affect iron homeostasis. We focused our efforts on drugs approved for clinical use to enable repositioning strategies and/or to reveal iron-related side effects of widely prescribed therapeutics. To identify hepcidin-modulating therapeutics, we re-evaluated data generated by a genome-wide RNAi screen for hepcidin regulators. We identified ‘druggable’ screening hits and validated those by applying RNAi of potential drug targets and small-molecule testing in a hepatocytic cell line, in primary murine and human hepatocytes and in mice. We initially identified spironolactone, diclofenac, imatinib and Suberoylanilide hydroxamic acid (SAHA) as hepcidin modulating drugs in cellular assays. Among these, imatinib and spironolactone further suppressed liver hepcidin expression in mice. Our results demonstrate that a commonly used anti-hypertensive drug, spironolactone, which is prescribed for the treatment of heart failure, acne and female hirsutism, as well as imatinib, a first-line, lifelong therapeutic option for some frequent cancer types suppress hepcidin expression in cultured cells and in mice. We expect these results to be of relevance for patient management, which needs to be addressed in prospective clinical studies.
Detection of TeV photons from the active galaxy Markarian 421

PHOTONS of TeV energy have been observed from a few sources in our Galaxy, notably the Crab Nebula1. We report here the detection of such photons from an extragalactic source, the giant elliptical galaxy Markarian 421. Mk 421 has a nucleus of the BL Lacertae type2,3, and emission from it has been observed at radio4–6, optical3,6 and X-ray6–8 frequencies, and most recently in the MeV-GeV bands, by the EGRET detector aboard the Compton observatory9. In March–June 1992, we observed Mk 421 with the Whipple Observatory γ-ray telescope10, a ground-based detector that images Cerenkov light from air showers, and found a signal with statistical significance of 6er above background. The flux above 0.5 TeV is 0.3 of that from the Crab Nebula. The source location agrees with the position of Mk 421 within the angular uncertainty (6 arc minutes) of the Whipple instrument. The fact that we have observed this relatively nearby source (redshift z = 0.031), whereas active galaxies and quasars that are brighter at EGRET energies but more distant have not been detected in the TeV energy range, may be consistent with suggestions11,12 that TeV photons are strongly attenuated by interaction with extragalactic starlight.
Time‐varying effects of aromatic oil constituents on the survival of aquatic species: Deviations between model estimates and observations

There is a need to study the time course of toxic chemical effects on organisms because there might be a time lag between the onset of chemical exposure and the corresponding adverse effects. For aquatic organisms, crude oil and oil constituents originating from either natural seeps or human activities can be relevant case studies. In the present study the authors tested a generic toxicokinetic model to quantify the time‐varying effects of various oil constituents on the survival of aquatic organisms. The model is based on key parameters applicable to an array of species and compounds with baseline toxicity reflected by a generic, internal toxicity threshold or critical body burden (CBB). They compared model estimates with experimental data on the effects of 8 aromatic oil constituents on the survival of aquatic species including crustaceans and fish. The average model uncertainty, expressed as the root mean square error, was 0.25 (minimum–maximum, 0.04–0.67) on a scale between 0 and 1. The estimated survival was generally lower than the measured survival right after the onset of oil constituent exposure. In contrast, the model underestimated the maximum mortality for crustaceans and fish observed in the laboratory. Thus, the model based on the CBB concept failed to adequately predict the lethal effects of the oil constituents on crustaceans and fish. Possible explanations for the deviations between model estimates and observations may include incorrect assumptions regarding a constant lethal body burden, the absence of biotransformation products, and the steady state of aromatic hydrocarbon concentrations in organisms. Clearly, a more complex model approach than the generic model used in the present study is needed to predict toxicity dynamics of narcotic chemicals. Environ Toxicol Chem 2017;36:128–136. © 2016 SETAC
Performance of armor materials for the ITER divertor

Neutronic analyses using MCNP4A were performed on the TAC-4 design of the International Thermonuclear Experimental Reactor (ITER) divertor. The purpose of this study was to compare the performance of three candidate materials, graphite, beryllium and tungsten, in the divertor environment. The focus of the study was the effect of neutron damage on the mechanical properties, using the displacements per atom (dpa) as the method of determination. From this calculation of dpa, an extrapolation to published data under a fast fission fluence was done. In general, the graphite divertor showed a severe decrease in its thermal conductivity. The effects of this decrease in thermal conductivity on the heat transfer properties of a graphite armor were calculated. The maximum allowable thickness of a graphite armor given this degradation in the thermal conductivity was determined and the evolution of the surface temperature over a full power year was calculated. The code DKR-PULSAR was then used with input flux from MCNP to determine the activation and the afterheat for the materials. The pulsing scheme modeled was 1000 pulses of 1000 seconds in duration with a 2200 second turnaround time. Results show that tungsten is the most highly activated. In general, the tungsten has an activity two orders of magnitude higher than the beryllium which in turn has an activity approximately two orders of magnitude higher than the graphite. The important materials issues for each of the candidate materials have been determined and recommendations as to materials selection for the ITER divertor have been made. Due to its extreme levels of activation, the use of tungsten as an armor must be minimized. Thesis Supervisors: Professor Mujid Kazimi Professor John Meyer Titles: Professor of Nuclear Engineering Professor of Nuclear Engineering
Peroneal perforator pedicle propeller flap for lower leg soft tissue defect reconstruction: Clinical applications and treatment of venous congestion

Objective To describe the characteristics of the perforator vessel in the peroneal artery of the lower leg and to explore the use of perforator pedicle propeller flaps to repair soft tissue defects in the lower leg, heel and foot. Methods This retrospective study enrolled patients with soft tissue defects of the distal lower leg, heel and foot who underwent surgery using peroneal perforator-based propeller flaps. The peroneal artery perforators were identified preoperatively by colour duplex Doppler ultrasound. The flap was designed based on the preoperatively-identified perforator location, with the posterior border of the fibula employed as an axis, and the perforator vessel as the pivot point of rotation. Patients were followed-up to determine the outcomes. Results The study analysed 36 patients (mean age, 39.7 years). The majority of the soft tissue defects were on the heel (20; 55.6%). The donor-site of the flap was closed in 11 patients by direct suturing and skin grafting was undertaken in 25 patients. Postoperative complications included venous congestion (nine patients), which was managed with delayed wound coverage and bleeding therapy. All wounds were eventually cured and the flaps were cosmetically acceptable. Conclusions The peroneal perforator pedicle propeller flap is an appropriate choice to repair soft tissue defects of the distal limbs.
HnRNP L represses cryptic exons

The fidelity of RNA splicing is regulated by a network of splicing enhancers and repressors, although the rules that govern this process are not yet fully understood. One mechanism that contributes to splicing fidelity is the repression of nonconserved cryptic exons by splicing factors that recognize dinucleotide repeats. We previously identified that TDP-43 and PTBP1/PTBP2 are capable of repressing cryptic exons utilizing UG and CU repeats, respectively. Here we demonstrate that hnRNP L (HNRNPL) also represses cryptic exons by utilizing exonic CA repeats, particularly near the 5′SS. We hypothesize that hnRNP L regulates CA repeat repression for both cryptic exon repression and developmental processes such as T cell differentiation.
Real-time dynamic gesture recognition system based on depth perception for robot navigation

Natural human robot interaction based on the dynamic hand gesture is becoming a popular research topic in the past few years. The traditional dynamic gesture recognition methods are usually restricted by the factors of illumination condition, varying color and cluttered background. The recognition performance can be improved by using the hand-wearing devices but this is not a natural and barrier-free interaction. To overcome these shortcomings, the depth perception algorithm based on the Kinect depth sensor is introduced to carry out 3D hand tracking. We propose a novel start/end point detection method for segmenting the 3D hand gesture from the hand motion trajectory. Then Hidden Markov Models (HMMs) are implemented to model and classify the hand gesture sequences and the recognized gestures are converted to control commands for the interaction with the robot. Seven different hand gestures performed by two hands can sufficiently navigate the robot. Experiments show that the proposed dynamic hand gesture interaction system can work effectively in the complex environment and in real-time with an average recognition rate of 98.4%. And further experiments for the robot navigation also verify the robustness of our system.
Research on magnetorheological fluid and application in optical machining

The mechanism and application of magnetrheolgical(MR) fluid is introduced. High shear stress can be attained of MR fluid applying magnetic field. The hardened MR fluid can be used to controllable polish optical workpiece by mixing certain amount of polishing abrasive. Rochester University had gone the first step in magnetorheological finishing of optical glass. MR fluid can get nano scale surface quality.
Inhibitors of protein synthesis and RNA synthesis prevent neuronal death caused by nerve growth factor deprivation

We have developed an experimental paradigm to study the mechanism by which nerve growth factor (NGF) allows the survival of sympathetic neurons. Dissociated sympathetic neurons from embryonic day-21 rats were grown in vitro for 7 d in the presence of NGF. Neurons were then deprived of trophic support by adding anti-NGF antiserum, causing them to die between 24 and 48 h later. Ultrastructural changes included disruption of neurites, followed by cell body changes characterized by an accumulation of lipid droplets, changes in the nuclear membrane, and dilation of the rough endoplasmic reticulum. No primary alterations of mitochondria or lysosomes were observed. The death of NGF-deprived neurons was characterized biochemically by assessing [35S]methionine incorporation into TCA precipitable protein and by measuring the release of the cytosolic enzyme adenylate kinase into the culture medium. Methionine incorporation began to decrease approximately 18 h post-deprivation and was maximally depressed by 36 h. Adenylate kinase began to appear in the culture medium approximately 30 h after deprivation, reaching a maximum by 54 h. The death of NGF-deprived neurons was entirely prevented by inhibiting protein or RNA synthesis. Cycloheximide, puromycin, anisomycin, actinomycin-D, and dichlorobenzimidazole riboside all prevented neuronal death subsequent to NGF deprivation as assessed by the above morphologic and biochemical criteria. The fact that sympathetic neurons must synthesize protein and RNA to die when deprived of NGF indicates that NGF, and presumably other neurotrophic factors, maintains neuronal survival by suppressing an endogenous, active death program.
Automatic multi-camera remix from single video

In this paper we present a first of its kind automatic multi-camera video remix creation system from a single video, referred to as SmartView. We present a novel method which uses the fusion of multimodal content analysis and cinematic rules, for creating a multi-camera experience. Further, a playback metadata based model, which consists of playback instructions for metadata-aware media player, allows for providing a remix experience without editing the original video content. This approach produces a low footprint, which is suitable for on-device processing in resource constrained mobile devices. The research prototype demonstrates the feasibility of such a system with current off-the-shelf mobile devices. The SmartView creation process was seen to take less time than the video duration. 5 out of 9 test users found the fully automatic SmartView remix experience to be better than the conventional playback. The user customized SmartView remix was preferred over conventional playback.
Style Tokens: Unsupervised Style Modeling, Control and Transfer in End-to-End Speech Synthesis

In this work, we propose "global style tokens" (GSTs), a bank of embeddings that are jointly trained within Tacotron, a state-of-the-art end-to-end speech synthesis system. The embeddings are trained with no explicit labels, yet learn to model a large range of acoustic expressiveness. GSTs lead to a rich set of significant results. The soft interpretable "labels" they generate can be used to control synthesis in novel ways, such as varying speed and speaking style - independently of the text content. They can also be used for style transfer, replicating the speaking style of a single audio clip across an entire long-form text corpus. When trained on noisy, unlabeled found data, GSTs learn to factorize noise and speaker identity, providing a path towards highly scalable but robust speech synthesis.
Comparison between Lead-Acid and Li-Ion Accumulators in Stand-Alone Photovoltaic System Using the Gross Energy Requirement Criteria

The high economic (and energetic) cost of storage accumulator system is still limiting the proliferation of SAPV system. Presently, due to its technical maturity and its low economical investment cost, the storage system universally used in SAPV market, is the lead-acid technology. Nevertheless, the advantages offered by the Lithium-ion (Li-ion) technology in terms of better charging/discharging efficiencies and ageing make Li-ion accumulators more and more envisioned in such applications. In this paper, sizing optimisations of SAPV systems have been lead for each accumulator technology considered. The photovoltaic system has been simulated hour by hour on the whole cycle life duration. Experimental outcomes, lead in order to establish a complete energetic model for Li-ion accumulators, are presented in this paper. Results have been compared using the Gross Energy Requirement (GER) criterion of the whole SAPV system. Results show that Li-ion technology allows us to reduce the energy cost of SAPV systems notably when considering a simulation duration corresponding to the expected life time of PV panels.
Rate of convergence for data augmentation and inverse Bayes formula method in the genetic linkage model

Many statistical problems can be formulated as the missing data problems. The data augmentation algorithm and the inverse Bayes formula are important tools for constructing iterative optimization or samplings via the introduction of unobserved data or latent variables. As a Markov Chain Monte Carlo method, the data augmentation algorithm has its autocorrelation. Nevertheless, the convergence rate of the data augmentation algorithm is not known in the Genetic Linkage Model, and the same is true for the inverse Bayes formula method. In this article, we analyze the convergence rates of the data augmentation algorithm and the inverse Bayes formula method in the genetic linkage model, and through simulation results we get their convergence rates.
Combining object modeling and recognition for active scene exploration

Active scene exploration incorporates object recognition methods for analyzing a scene of partially known objects and exploration approaches for autonomous modeling of unknown parts. In this work, recognition, exploration, and planning methods are extended and combined in a single scene exploration system, enabling advanced techniques such as multi-view recognition from planned view positions and iterative recognition by integration of new objects from a scene. Here, a geometry based approach is used for recognition, i.e. matching objects from a database. Unknown objects are autonomously modeled and added to the recognition database. Next-Best-View planning is performed both for recognition and modeling. Moreover, 3D measurements are merged in a Probabilistic Voxel Space, which is utilized for planning collision free paths, minimal occlusion views, and verifying the poses of the recognized objects against all previous information. Experiments on an industrial robot with attached 3D sensors are shown for scenes with household and industrial objects.