Miracle-dz/UniFAR-FTUs huggingface dataset:
Sample preparation and storage can change arsenic speciation in human urine.

BACKGROUND Stability of chemical speciation during sample handling and storage is a prerequisite to obtaining reliable results of trace element speciation analysis. There is no comprehensive information on the stability of common arsenic species, such as inorganic arsenite [As(III)], arsenate [As(V)], monomethylarsonic acid, dimethylarsinic acid, and arsenobetaine, in human urine. METHODS We compared the effects of the following storage conditions on the stability of these arsenic species: temperature (25, 4, and -20 degrees C), storage time (1, 2, 4, and 8 months), and the use of additives (HCl, sodium azide, benzoic acid, benzyltrimethylammonium chloride, and cetylpyridinium chloride). HPLC with both inductively coupled plasma mass spectrometry and hydride generation atomic fluorescence detection techniques were used for the speciation of arsenic. RESULTS We found that all five of the arsenic species were stable for up to 2 months when urine samples were stored at 4 and -20 degrees C without any additives. For longer period of storage (4 and 8 months), the stability of arsenic species was dependent on urine matrices. Whereas the arsenic speciation in some urine samples was stable for the entire 8 months at both 4 and -20 degrees C, other urine samples stored under identical conditions showed substantial changes in the concentration of As(III), As(V), monomethylarsonic acid, and dimethylarsinic acid. The use of additives did not improve the stability of arsenic speciation in urine. The addition of 0.1 mol/L HCl (final concentration) to urine samples produced relative changes in inorganic As(III) and As(V) concentrations. CONCLUSIONS Low temperature (4 and -20 degrees C) conditions are suitable for the storage of urine samples for up to 2 months. Untreated samples maintain their concentration of arsenic species, and additives have no particular benefit. Strong acidification is not appropriate for speciation analysis.
Local delivery of HMGB1 in gelatin sponge scaffolds combined with mesenchymal stem cell sheets to accelerate fracture healing

Fracture nonunion and delayed union continue to pose challenges for orthopedic surgeons. In the present study, we combined HMGB1 gelatin sponges with MSC sheets to promote bone healing after surgical treatment of rat tibial fractures. The HMGB1 gelatin sponge scaffolds supported the expansion of mesenchymal stem cells (MSCs) and promoted the osteogenic differentiation of MSCs and MSC sheets. Lentiviral vectors were then used to overexpress HMGB1 in MSCs. The results indicated that HMGB1 promotes the osteogenic differentiation of MSCs through the STAT3 pathway. Both siRNA and a STAT3 inhibitor downregulated STAT3, further confirming that HMGB1 induces the osteogenic differentiation of MSCs partly via the STAT3 signal pathway. In a rat tibial osteotomy model, we demonstrated the ability of HMGB1 gelatin sponge scaffolds to increase bone formation. The addition of MSC sheets further enhanced fracture healing. These findings support the use of HMGB1-loaded gelatin sponge scaffolds combined with MSC sheets to enhance fracture healing after surgical intervention.
A Model-Based Control Approach for Locomotion Control of Legged Robots Semester project Master Program : Robotics and Autonomous Systems Micro-Technique

In this project, a new method is proposed for controlling legged robots. This method takes dynamics of the robot into account to have better nominal tracking of desired trajectories and more compliant environmental interactions at the same time. We have incorporated also natural dynamics of the robot into the system by using off-line calculated gaits extracted from optimizations on energy. So the main control loop in this method consists of a feed-forward block that generates actuator torques given desired trajectories and also a feedback block designed and tuned specifically for the structure of the robot. A trajectory planner uses known optimal trajectories together with some control laws that modify these trajectories to have better robustness in different situations. We successfully tested this method on two robots. The first one was a monopod robot with two actuators and five degrees of freedom. On this robot, we integrated a high level controller that made the robot capable of performing locomotion on sloped terrains up to ±20◦ and rough terrains up to variance of 0.03 in terrain surface. On second robot which was a 2D quadruped robot using bounding gait, we ended up with stabilization of feed-forward, feedback and trajectory planner. This robot showed more robustness to the roughness of the terrain. The proposed control method could be a good candidate for control problems concerning compliance environmental interactions and energy optimality.
NF-kappaB-induced oxidative stress contributes to mitochondrial and cardiac dysfunction in type II diabetes.

AIMS Inflammatory molecules and their transcription factor, nuclear factor kappa-B (NF-kappaB), are thought to play important roles in diabetes-induced cardiac dysfunction. Here, we investigated the effects of pyrrolidine dithiocarbamate (PDTC), a NF-kappaB inhibitor, in diabetic mice. METHODS AND RESULTS Obese db/db mice and heterozygous lean mice (n = 8) were allowed free access to drinking water (control) or water containing PDTC (100 mg/kg) for 20 weeks. Left ventricular (LV) function was measured using echocardiography at baseline and at study end. Mice were sacrificed and LV removed for gene expression, biochemical, immunofluorescence, and mitochondrial assays. LV and mitochondrial reactive oxygen species (ROS), superoxide and peroxynitrite were measured using electron spin resonance spectroscopy. Enhanced NF-kappaB activity in db/db mice was associated with increased oxidative stress as demonstrated by increased ROS, superoxide, and peroxynitrite production, and increased NF-kappaB, gp91phox, and Nox1 expression; PDTC ameliorated these effects. Mitochondrial free radical production and structural damage were higher in the db/db group than in the control, db/db PDTC, and PDTC-treated heterozygous animal groups. CONCLUSION This study demonstrates that NF-kappaB blockade with PDTC mitigates oxidative stress and improves mitochondrial structural integrity directly, through down-regulation of increased oxygen-free radicals, thereby increasing ATP synthesis and thus restoring cardiac function in type II diabetes.
By-pass Laminar-Turbulent Transition of the Wind-Driven Free Surface Flow

The laminar-turbulent transition of wind-induced spatially developing surface boundary layer in water at the entrance of a water tank is investigated experimentally. Observations of the velocity field were made both by flow visualisation techniques using dye injection and laser Doppler velocimeter measurements. Two stages in the development of the perturbations have been clearly identified. First, a slow growth of streamwise longitudinal vortices embedded into the laminar flow is followed by a rapid development of secondary instabilities till to breakdown. The picture is similar to the by-pass transition to turbulence of a rigid plate boundary layer. At the second stage, peculiar to this flow, an explosive deepening of the boundary layer and fast development of inflexional instabilities occur. The critical fetch, where the shear boundary layer collapses and the first turbulent spots appear, is not linked to any critical Reynolds number but was found to be inversely proportional to the friction velocity squared.
Cysteine-scanning Mutagenesis and Disulfide Mapping Studies of the Conserved Domain of the Twin-arginine Translocase TatB Component*

The cytoplasmic membrane protein TatB is an essential component of the Escherichia coli twin-arginine (Tat) protein translocation pathway. Together with the TatC component it forms a complex that functions as a membrane receptor for substrate proteins. Structural predictions suggest that TatB is anchored to the membrane via an N-terminal transmembrane α-helix that precedes an amphipathic α-helical section of the protein. From truncation analysis it is known that both these regions of the protein are essential for function. Here we construct 31 unique cysteine substitutions in the first 42 residues of TatB. Each of the substitutions results in a TatB protein that is competent to support Tat-dependent protein translocation. Oxidant-induced disulfide cross-linking shows that both the N-terminal and amphipathic helices form contacts with at least one other TatB protomer. For the transmembrane helix these contacts are localized to one face of the helix. Molecular modeling and molecular dynamics simulations provide insight into the possible structural basis of the transmembrane helix interactions. Using variants with double cysteine substitutions in the transmembrane helix, we were able to detect cross-links between up to five TatB molecules. Protein purification showed that species containing at least four cross-linked TatB molecules are found in correctly assembled TatBC complexes. Our results suggest that the transmembrane helices of TatB protomers are in the center rather than the periphery of the TatBC complex.
The Prefrontal Cortex Modulates Category Selectivity in Human Extrastriate Cortex

Different categories of visual objects evoke distinct stimulus-evoked sensory responses in extrastriate visual cortex. Although numerous lines of evidence support a distinct representational neural architecture, the mechanisms underlying the modulation of the category selectivity by top–down influences remains uncertain. In this study, we investigate the causal role of the PFC in the modulation of evoked activity to face and scene stimuli in the extrastriate cortex. We used two experimental approaches to disrupt prefrontal cortical function—repetitive TMS to PFC in healthy participants (Experiment 1) and focal PFC lesions in stroke patients (Experiment 2). After these perturbations to normal PFC function (pre- vs. post-TMS and lesion vs. intact hemisphere), stimulus-evoked activity in extrastriate cortex exhibited less distinct category selectivity to faces and scenes. These two experiments provide convergent evidence highlighting a direct role of PFC in the top–down modulation of bottom–up visual signals.
Making Compression Algorithms for Unicode Text

The majority of online content is written in languages other than English, and is most commonly encoded in UTF-8, the world's dominant Unicode character encoding. Traditional compression algorithms typically operate on individual bytes. While this approach works well for the single-byte ASCII encoding, it works poorly for UTF-8, where characters often span multiple bytes. Previous research has focused on developing Unicode compressors from scratch, which often failed to outperform established algorithms such as bzip2. We develop a technique to modify byte-based compressors to operate directly on Unicode characters, and implement variants of LZW and PPM that apply this technique. We find that our method substantially improves compression effectiveness on a UTF-8 corpus. On ASCII and binary files, our variants perform similarly to the original unmodified compressors.
Analysis of various potential prognostic markers and survival data in clear cell renal cell carcinoma

ABSTRACT Purpose Clear cell renal cell cancers frequently harbor Von Hippel-Lindau gene mutations, leading to stabilization of the hypoxia-inducible factors (HIFs) and their target genes. In this study, we investigated the relationship between vascular endothelial growth factor (VEGF), HIF-1α, HIF-2α, p53 positivity, microvessel density, and Ki-67 rates with prognostic histopathologic factors (Fuhrman nuclear grade, stage, and sarcomatoid differentiation) and survival in clear cell renal cell carcinomas. Material and Methods Seventy-two nephrectomy specimens diagnosed as clear cell renal cell carcinoma between 2000 and 2012 were reevaluated. Immunohistochemically VEGF, HIF-1α, HIF-2α, p53, CD34 (for microvessel density evaluation), and Ki-67 antibodies were applied to the tumor areas. The relationships of these antibodies with prognostic factors and survival rates were evaluated with statistical analyses. Results Mean survival time was 105.6 months in patients with ccRCC. Patients with high expression of VEGF, HIF-1α and HIF-2α positivity, a high Ki-67 proliferation index, and a high microvessel density evaluation score had a shorter survival time (p<0.05). Conclusions Our findings supported that with the use of these immunohistochemical markers, prognosis of renal cell carcinoma may be predicted at the first step of patient management. New treatment modalities targeted to HIF-1α and HIF-2α might be planned as well as VEGF-targeted therapies in the management of clear cell renal cell carcinomas.
Conditional Prediction Intervals of Wind Power Generation

A generic method for the providing of prediction intervals of wind power generation is described. Prediction intervals complement the more common wind power point forecasts, by giving a range of potential outcomes for a given probability, their so-called nominal coverage rate. Ideally they inform of the situation-specific uncertainty of point forecasts. In order to avoid a restrictive assumption on the shape of forecast error distributions, focus is given to an empirical and nonparametric approach named adapted resampling. This approach employs a fuzzy inference model that permits to integrate expertise on the characteristics of prediction errors for providing conditional interval forecasts. By simultaneously generating prediction intervals with various nominal coverage rates, one obtains full predictive distributions of wind generation. Adapted resampling is applied here to the case of an onshore Danish wind farm, for which three point forecasting methods are considered as input. The probabilistic forecasts generated are evaluated based on their reliability and sharpness, while compared to forecasts based on quantile regression and the climatology benchmark. The operational application of adapted resampling to the case of a large number of wind farms in Europe and Australia among others is finally discussed.
Complement-mediated serum sensitivity among spirochetes that cause Lyme disease

Borrelia burgdorferi-related isolates were tested for their sensitivity to normal human serum (NHS) and their ability to activate complement. By dark-field microscopy, electron microscopy, and subsurface plating, it was shown that exposure of a Borrelia garinii isolate to 10% or more NHS resulted in immobilization, blebbing, and killing of the spirochetes. These effects were mediated by complement, since they were not seen after heat treatment of NHS, in the presence of EDTA, or in an agammaglobulinemic serum. All seven B. garinii type 5 or 6 and all four VS116/M19 strains were serum sensitive, whereas all eight Borrelia afzelii, five of eight B. garinii type 4, and three of seven B. burgdorferi sensu stricto isolates were serum resistant. The other isolates were partially serum sensitive. Four serum-sensitive B. garinii isolates had been isolated from human cerebrospinal fluid. Most likely, activation of both the alternative pathway and the classical pathway of complement was involved, since bactericidal activity was diminished in properdin-deficient sera as well as in a C1q-depleted serum and in a C4-deficient serum. Bactericidal activity could be restored when a serum lacking C1q or C4 was mixed with a properdin-deficient serum. Isolates with various genetic backgrounds were equally able to activate C3 as measured by enzyme-linked immunosorbent assay. In the presence of Mg-EGTA, C3 was activated by all isolates after exposure to > or = 10% NHS. This study shows that B. burgdorferi-related spirochetes can be either serum sensitive or serum resistant in vitro and that this characteristic is associated with their genetic background.
VIDSEEK: Dynamic Multi-dimensional Browsing of Video Archives

We describe a dynamic Web-based digital video library browsing system (VIDSEEK) that allows users to preview the contents of the VISION digital video library via automatically selected and organized keyframes. Our system supports dynamic clustering-on-demand, which allows users organize the digital video library clips into clusters based on multiple user-specified video features. The system also supports category-based browsing, which allows users to interactively and dynamically filter the VISION digital video library clips based on a given set of constraints, such as video source, keywords, and date of capture. We use efficient techniques to create the video abstractions, and dynamic organization, i.e., categorization or clustering, of the video abstractions to provide a sophisticated tool for video archive exploration.
Type VII Collagen Gene Mutations (c.8569G>T and c.4879G>A) Result in the Moderately Severe Phenotype of Recessive Dystrophic Epidermolysis Bullosa in a Korean Patient

Dystrophic epidermolysis bullosa (DEB) are caused by mutations in the COL7A1 gene, which encodes type VII collagen. Even though more than 500 different COL7A1 mutations have been identified in DEB, it still remains to be under-investigated. To investigate the mutation of COL7A1 in moderately severe phenotype of recessive DEB (RDEB) in a Korean patient, the mutation detection strategy was consisted of polymerase chain reaction (PCR) amplification of genomic DNA, followed by heteroduplex analysis, nucleotide sequencing of the PCR products demonstrating altered mobility. In this study, we found that one mutation (c.8569G>T) was detected within exon 116. The mutation of c.8569G>T in exon 116 changed the GAG (Glu) to TAG, eventually resulted in premature termination of type VII collagen polypeptide. Furthermore the mother did not have the mutation c.8569G>T in exon 116. The other novel mutation (c.4879G>A) was detected within exon 51 of both patient and mother, thereby resulting in changing valine (Val) to isoleucine (Ile) in type VII collagen polypeptide. Taken together, in this study we identified compound heterozygosity for COL7A1 mutations (c.8569G>T and c.4879G>A) in moderately severe RDEB in a Korean patient. We hope that this data contribute to the expanding database on COL7A1 mutations in DEB.
Visual Compression of Workflow Visualizations with Automated Detection of Macro Motifs

This paper is concerned with the creation of 'macros' in workflow visualization as a support tool to increase the efficiency of data curation tasks. We propose computation of candidate macros based on their usage in large collections of workflows in data repositories. We describe an efficient algorithm for extracting macro motifs from workflow graphs. We discovered that the state transition information, used to identify macro candidates, characterizes the structural pattern of the macro and can be harnessed as part of the visual design of the corresponding macro glyph. This facilitates partial automation and consistency in glyph design applicable to a large set of macro glyphs. We tested this approach against a repository of biological data holding some 9,670 workflows and found that the algorithmically generated candidate macros are in keeping with domain expert expectations.
A numerical model for submarine telegraph communication

Transmission Line Matrix (TLM) is a modern numerical method which is particularly suited to treating electromagnetic problems This paper describes the application of TLM to the propagation of telegraph signals in ocean cables. It is shown that the non-ideal properties of the cable, the transmitter and the receiver were significant factors in the ability to receive signals at a time when people had no concept of the importance of impedance matching. The paper concludes with a demonstration of the benefits of a cable whose electrical parameters comply with the Heaviside distortionless condition.
The potential of nestin-expressing hair follicle stem cells in regenerative medicine

The hair follicle bulge area is an abundant, easily accessible source of actively growing pluripotent adult stem cells. Nestin, a protein marker for neural stem cells, is also expressed in follicle stem cells and their immediate, differentiated progeny. Green fluorescent protein (GFP), whose expression is driven by the nestin regulatory element in transgenic mice, serves to mark hair follicle stem cells. The pluripotent nestin-driven GFP stem cells are positive for the stem cell marker CD34, but negative for keratinocyte marker keratin 15, suggesting their relatively undifferentiated state. These cells can differentiate into neurons, glia, keratinocytes, smooth muscle cells and melanocytes in vitro. In vivo studies show that nestin-driven GFP hair follicle stem cells can differentiate into blood vessels and neural tissue after transplantation to the subcutis of nude mice. Hair follicle stem cells implanted into the gap region of a severed sciatic or tibial nerve greatly enhance the rate of nerve regeneration and the restoration of nerve function. The follicle cells transdifferentiate largely into Schwann cells, which are known to support neuron regrowth. The transplanted mice regain the ability to walk normally. Thus, hair follicle stem cells provide an effective, accessible, autologous source of stem cells for treatment of peripheral nerve injury.
Active Video Summarization: Customized Summaries via On-line Interaction with the User

To facilitate the browsing of long videos, automatic video summarization provides an excerpt that represents its content. In the case of egocentric and consumer videos, due to their personal nature, adapting the summary to specific user's preferences is desirable. Current approaches to customizable video summarization obtain the user's preferences prior to the summarization process. As a result, the user needs to manually modify the summary to further meet the preferences. In this paper, we introduce Active Video Summarization (AVS), an interactive approach to gather the user's preferences while creating the summary. AVS asks questions about the summary to update it on-line until the user is satisfied. To minimize the interaction, the best segment to inquire next is inferred from the previous feedback. We evaluate AVS in the commonly used UTEgo dataset. We also introduce a new dataset for customized video summarization (CSumm) recorded with a Google Glass. The results show that AVS achieves an excellent compromise between usability and quality. In 41% of the videos, AVS is considered the best over all tested baselines, including summaries manually generated. Also, when looking for specific events in the video, AVS provides an average level of satisfaction higher than those of all other baselines after only six questions to the user.