Miracle-dz/UniFAR-FTUs huggingface dataset:
Intravenous magnetic nanoparticle cancer hyperthermia

Magnetic nanoparticles heated by an alternating magnetic field could be used to treat cancers, either alone or in combination with radiotherapy or chemotherapy. However, direct intratumoral injections suffer from tumor incongruence and invasiveness, typically leaving undertreated regions, which lead to cancer regrowth. Intravenous injection more faithfully loads tumors, but, so far, it has been difficult achieving the necessary concentration in tumors before systemic toxicity occurs. Here, we describe use of a magnetic nanoparticle that, with a well-tolerated intravenous dose, achieved a tumor concentration of 1.9 mg Fe/g tumor in a subcutaneous squamous cell carcinoma mouse model, with a tumor to non-tumor ratio > 16. With an applied field of 38 kA/m at 980 kHz, tumors could be heated to 60°C in 2 minutes, durably ablating them with millimeter (mm) precision, leaving surrounding tissue intact.
A Cluster Framework for Data Mining Models - An Application to Intensive Medicine

Clustering is a technique widely applied in Data Mining problems due to the granularity, accuracy and adjustment of the models induced. Although the referred results, this approach generates a considerable large set of models, which difficult the comprehension, the visualization and the application to new cases. This paper presents a framework to deal with the enounced problem supported by a three-dimensional matrix structure. The usability and benefits of this instrument are demonstrated trough a case study in the area of intensive medicine.
Progressive Prioritized Multiview Stereo

This work proposes a progressive patch based multiview stereo algorithm able to deliver a dense point cloud at any time. This enables an immediate feedback on the reconstruction process in a user centric scenario. With increasing processing time, the model is improved in terms of resolution and accuracy. The algorithm explicitly handles input images with varying effective scale and creates visually pleasing point clouds. A priority scheme assures that the limited computational power is invested in scene parts, where the user is most interested in or the overall error can be reduced the most. The architecture of the proposed pipeline allows fast processing times in large scenes using a pure open-source CPU implementation. We show the performance of our algorithm on challenging standard datasets as well as on real-world scenes and compare it to the baseline.
Interactive comment on “ Improved rain-rate and drop-size retrievals from airborne and spaceborne Doppler radar

A common thread across the reviews was a request for more justification of the retrieval of a height-invariant Nw, and for evaluation of the retrievals through the vertical profile. In response we have added Figs. 5, 9 & 12 evaluating the averaged vertical profile of retrieved and forward-modelled variables in key precipitation regimes: moderate stratiform rain (case 1), light stratiform rain with strong evaporation (case 2), and moderate warm rain (case 3).
Identification of Toposome, A Novel Multisubunit Complex Containing Topoisomerase II-alpha

Topoisomerase ? -alpha plays essential roles in chromosome segregation. However, it is not well understood how topoisomerase II? exerts its function during mitosis. In this report, we find that topoisomerase ? forms a multisubunit complex, named toposome, containing two ATPase/helicase proteins (RNA helicase A and RHII/Gu), one serine/threonine protein kinase (SRPK1), one HMG protein (SSRP1), and two pre-mRNA splicing factors (PRP8 and hnRNP C). Toposome separates entangled circular chromatin DNA about fourfold more efficiently than topoisomerase ? -alpha. Interestingly, this decatenation reaction yields knotted circles, which are not seen in reactions provided with monomeric circular DNA. Our results also show that interaction among toposome-associated proteins is highest in G2/M phase but drastically diminishes in G1/S phase. These results suggest that toposome is a dynamic complex whose assembly or activation is subject to cell cycle regulation.
Ability of optical coherence tomography to visualize the entry port of spontaneous coronary artery dissection.

51-year-old man was admitted to a local hospital with sudden onset of severe back pain diagnosed as acute type A aortic dissection on contrast computed tomography (CT). The patient was transferred to Kobe University Hospital and underwent total arch replacement. He had no cardiac risk factors except for obesity, and no connective tissue disorders or clinical features of Marfan syndrome. From the intraoperative findings, the entry of the aortic dissection was confirmed to be in the aortic arch without coronary artery ostium involvement. On the fourth day after the
Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification

Significance FIC-domain enzymes are found in all kingdoms of life and catalyze posttranslational modifications of various target proteins to modulate their function. Because the vast majority of Fic proteins are expressed in an inhibited form, their physiological importance has escaped attention for a long time. This article reveals an autonomous mechanism of inhibition relief for class III Fic proteins, which hinges on autoadenylylation of an inhibitory helix. Because the process occurs in cis, the Fic enzyme constitutes a molecular timer that operates independent of enzyme concentration. Furthermore, we show that Fic-mediated adenylylation of DNA gyrase leads to bacterial growth arrest. Thus, the time-dependent inactivation of DNA gyrase may serve as a switch to bacterial dormancy under starvation or other stress conditions. Filamentation induced by cyclic AMP (FIC)-domain enzymes catalyze adenylylation or other posttranslational modifications of target proteins to control their function. Recently, we have shown that Fic enzymes are autoinhibited by an α-helix (αinh) that partly obstructs the active site. For the single-domain class III Fic proteins, the αinh is located at the C terminus and its deletion relieves autoinhibition. However, it has remained unclear how activation occurs naturally. Here, we show by structural, biophysical, and enzymatic analyses combined with in vivo data that the class III Fic protein NmFic from Neisseria meningitidis gets autoadenylylated in cis, thereby autonomously relieving autoinhibition and thus allowing subsequent adenylylation of its target, the DNA gyrase subunit GyrB. Furthermore, we show that NmFic activation is antagonized by tetramerization. The combination of autoadenylylation and tetramerization results in nonmonotonic concentration dependence of NmFic activity and a pronounced lag phase in the progress of target adenylylation. Bioinformatic analyses indicate that this elaborate dual-control mechanism is conserved throughout class III Fic proteins.
Large data visualization on distributed memory multi-GPU clusters

Data sets of immense size are regularly generated on large scale computing resources. Even among more traditional methods for acquisition of volume data, such as MRI and CT scanners, data which is too large to be effectively visualized on standard workstations is now commonplace. One solution to this problem is to employ a 'visualization cluster,' a small to medium scale cluster dedicated to performing visualization and analysis of massive data sets generated on larger scale supercomputers. These clusters are designed to fit a different need than traditional supercomputers, and therefore their design mandates different hardware choices, such as increased memory, and more recently, graphics processing units (GPUs). While there has been much previous work on distributed memory visualization as well as GPU visualization, there is a relative dearth of algorithms which effectively use GPUs at a large scale in a distributed memory environment. In this work, we study a common visualization technique in a GPU-accelerated, distributed memory setting, and present performance characteristics when scaling to extremely large data sets.
Egg consumption, serum total cholesterol concentrations and coronary heart disease incidence: Japan Public Health Center-based prospective study

Limited egg consumption is often recommended to reduce serum cholesterol concentration for the prevention of CHD. We examined the association of egg consumption and total cholesterol concentration with the risk of CHD. A total of 90 735 subjects (19 856 men and 21 408 women, aged 40–59 years in cohort I; 23 463 men and 26 008 women, aged 40–69 years in cohort II) were followed from 1990–4 to the end of 2001 under the Japan Public Health Center-based prospective study. Total cholesterol was obtained in 36 % of the subjects. Men and women were combined for the analyses. The subjects were categorised into four groups according to egg consumption. Subjects with total cholesterol ≥2200 mg/l were less frequent in frequent egg consumption groups in both cohorts (trend P<0·0001). Subjects with <1 d/week of egg consumption were more likely to avoid a cholesterol-rich diet. Egg consumption was not associated with the risk of CHD, although total cholesterol was significantly related to the risk of CHD. The multivariate hazard ratio of CHD in subjects with total cholesterol ≥2400 v. <1800 mg/l was 2·17 (95 % CI 1·22, 3·85; trend P=0·0018). In conclusion, eating eggs more frequently, up to almost daily, was not associated with an increase in CHD incidence for middle-aged Japanese men and women. Subjects with hypercholesterolaemia were less frequently in frequent egg consumption groups, probably because they avoided eating eggs.
A new method for weight updating in fuzzy cognitive maps using system feedback

Abstarct: Fuzzy Cognitive Maps (FCMs) have found many applications in social -fnancial -political problems. In this paper we propose a method of FCM operation, which can be used to represent and control any real system, including traditional electro-mechanical systems. In the proposed approach the FCM reaches its equilibrium point using direct feedback from the node values of the real system and the limitations imposed by the control objectives for the node values of the system. The experts’ knowledge, which is represented in the weights of the nodes’ interconnections, undergoes a continuous on-line adaptation based on feedback from the real system. An algorithm for weight updating is proposed, which is based on system feedback and which includes specially designed matrices that lead the FCM and consequently the real system associated with it in a balanced equilibrium state. The proposed methodology is tested by simulating the operation of a hydroelectric plant.
Where Is the Road for Issue Reports Classification Based on Text Mining?

Currently, open source projects receive various kinds of issues daily, because of the extreme openness of Issue Tracking System (ITS) in GitHub. ITS is a labor-intensive and time-consuming task of issue categorization for project managers. However, a contributor is only required a short textual abstract to report an issue in GitHub. Thus, most traditional classification approaches based on detailed and structured data (e.g., priority, severity, software version and so on) are difficult to adopt. In this paper, issue classification approaches on a large-scale dataset, including 80 popular projects and over 252,000 issue reports collected from GitHub, were investigated. First, four traditional text-based classification methods and their performances were discussed. Semantic perplexity (i.e., an issues description confuses bug-related sentences with nonbug-related sentences) is a crucial factor that affects the classification performances based on quantitative and qualitative study. Finally, A two-stage classifier framework based on the novel metrics of semantic perplexity of issue reports was designed. Results show that our two-stage classification can significantly improve issue classification performances.
Alveolar–capillary reserve during exercise in patients with chronic obstructive pulmonary disease

Background Factors limiting exercise in patients with COPD are complex. With evidence for accelerated pulmonary vascular aging, destruction of alveolar–capillary bed, and hypoxic pulmonary vasoconstriction, the ability to functionally expand surface area during exercise may become a primary limitation. Purpose To quantify measures of alveolar–capillary recruitment during exercise and the relationship to exercise capacity in a cohort of COPD patients. Methods Thirty-two subjects gave consent (53% male, with mean ± standard deviation age 66±9 years, smoking 35±29 pack-years, and Global Initiative for Chronic Obstructive Lung Disease (GOLD) classification of 0–4: 2.3±0.8), filled out the St George’s Respiratory Questionnaire (SGRQ) to measure quality of life, had a complete blood count drawn, and underwent spirometry. The intrabreath (IB) technique for lung diffusing capacity for carbon monoxide (IBDLCO) and pulmonary blood flow (IBQc, at rest) was also performed. Subsequently, they completed a cycle ergometry test to exhaustion with measures of oxygen saturation and expired gases. Results Baseline average measures were 44±21 for SGRQ score and 58±11 for FEV1/FVC. Peak oxygen consumption (VO2) was 11.4±3.1 mL/kg/min (49% predicted). The mean resting IBDLCO was 9.7±5.4 mL/min/mmHg and IBQc was 4.7±0.9 L/min. At the first workload, heart rate (HR) increased to 92±11 bpm, VO2 was 8.3±1.4 mL/kg/min, and IBDLCO and IBQc increased by 46% and 43%, respectively, compared to resting values (p,0.01). The IBDLCO/Qc ratio averaged 2.0±1.1 at rest and remained constant during exercise with marked variation across subjects (range: 0.8–4.8). Ventilatory efficiency plateaued at 37±5 during exercise, partial pressure of mix expired CO2/partial pressure of end tidal CO2 ratio ranged from 0.63 to 0.67, while a noninvasive index of pulmonary capacitance, O2 pulse × PetCO2 (GxCap) rose to 138%. The exercise IBDLCO/Qc ratio was related to O2 pulse (VO2/HR, r=0.58, p<0.01), and subjects with the highest exercise IBDLCO/Qc ratio or the greatest rise from rest had the highest peak VO2 values (r=0.65 and 0.51, respectively, p<0.05). Of the noninvasive gas exchange measures of pulmonary vascular function, GxCap was most closely associated with DLCO, DLCO/Qc, and VO2 peak. Conclusion COPD patients who can expand gas exchange surface area as assessed with DLCO during exercise relative to pulmonary blood flow have a more preserved exercise capacity.
Quantifying the vitamin D3 synthesizing potential of UVB lamps at specific distances over time.

The purpose of this study was to quantify the ultraviolet B (UVB) output and in vitro previtamin D(3) synthesis over time from various artificial light sources. Three incandescent lamps, T-Rex Active UVHeat 160 watt spot, T-Rex Active UVHeat 160 watt flood, and ZooMed PowerSun 160 watt flood, and two 1.2 m fluorescent lamps, Sylvania Blacklight 350 BL and ZooMed Reptisun 5.0, were studied. Total UVB irradiance and concentration of previtamin D synthesized using an in vitro ampoule model were quantified initially and at monthly intervals for 1 year. Incandescent lamps were measured at distances of 0.9 and 1.5 m while fluorescent lamps were measured at distances of 30.5 and 45.7 cm at the lamp's center, using both the radiometer and ampoules. Fluorescent lamp irradiance was also measured at the lamp's ends. Data were analyzed as a repeated measures split-plot in time using SAS with all mean differences determined using Least Squares Means. Incandescent lamp irradiance differences were seen at various distances. The UVHeat lamps had consistently higher previtamin D(3) production and irradiance readings compared with the PowerSun lamp. Reptisun 5.0 was consistently higher in UVB irradiance over Sylvania BL 350 at both 30.5 and 45.7 cm. However, there were no differences when comparing conversion of 7-dehydrocholesterol to previtamin D(3). Irradiance differences were detected between the centers and ends of the fluorescent lamps. Until UVB requirements for vitamin D(3) synthesis in animals are determined, it is impossible to state that one light is superior to another.
Magnetic Levitation Haptic Augmentation for Virtual Tissue Stiffness Perception

Haptic-based tissue stiffness perception is essential for palpation training system, which can provide the surgeon haptic cues for improving the diagnostic abilities. However, current haptic devices, such as Geomagic Touch, fail to provide immersive and natural haptic interaction in virtual surgery due to the inherent mechanical friction, inertia, limited workspace and flawed haptic feedback. To tackle this issue, we design a novel magnetic levitation haptic device based on electromagnetic principles to augment the tissue stiffness perception in virtual environment. Users can naturally interact with the virtual tissue by tracking the motion of magnetic stylus using stereoscopic vision so that they can accurately sense the stiffness by the magnetic stylus, which moves in the magnetic field generated by our device. We propose the idea that the effective magnetic field (EMF) is closely related to the coil attitude for the first time. To fully harness the magnetic field and flexibly generate the specific magnetic field for obtaining required haptic perception, we adopt probability clouds to describe the requirement of interactive applications and put forward an algorithm to calculate the best coil attitude. Moreover, we design a control interface circuit and present a self-adaptive fuzzy proportion integration differentiation (PID) algorithm to precisely control the coil current. We evaluate our haptic device via a series of quantitative experiments which show the high consistency of the experimental and simulated magnetic flux density, the high accuracy (0.28 mm) of real-time 3D positioning and tracking of the magnetic stylus, the low power consumption of the adjustable coil configuration, and the tissue stiffness perception accuracy improvement by 2.38 percent with the self-adaptive fuzzy PID algorithm. We conduct a user study with 22 participants, and the results suggest most of the users can clearly and immersively perceive different tissue stiffness and easily detect the tissue abnormality. Experimental results demonstrate that our magnetic levitation haptic device can provide accurate tissue stiffness perception augmentation with natural and immersive haptic interaction.
MeDNN: A distributed mobile system with enhanced partition and deployment for large-scale DNNs

Deep Neural Networks (DNNs) are pervasively used in a significant number of applications and platforms. To enhance the execution efficiency of large-scale DNNs, previous attempts focus mainly on client-server paradigms, relying on powerful external infrastructure, or model compression, with complicated pre-processing phases. Though effective, these methods overlook the optimization of DNNs on distributed mobile devices. In this work, we design and implement MeDNN, a local distributed mobile computing system with enhanced partitioning and deployment tailored for large-scale DNNs. In MeDNN, we first propose Greedy Two Dimensional Partition (GTDP), which can adaptively partition DNN models onto several mobile devices w.r. t. individual resource constraints. We also propose Structured Model Compact Deployment (SMCD), a mobile-friendly compression scheme which utilizes a structured sparsity pruning technique to further accelerate DNN execution. Experimental results show that, GTDP can accelerate the original DNN execution time by 1.86–2.44x with 2–4 worker nodes. By utilizing SMCD, 26.5% of additional computing time and 14.2% of extra communication time are saved, on average, with negligible effect on the model accuracy.
Sequence Quality Control Sequence Quality Control

Some HIV researchers are convinced that careful lab work is enough to prevent contamination. After seeing many examples of contamination pass by, we disagree. Contamination happens frequently, even in the best laboratories. It is not a thing of the past; cases of contamination can still be found in new publications. Screening for contamination should be done before the analysis of the sequences, and periodically during the course of large sequencing studies, so problems can be detected and corrected early. To show what contamination looks like in practice, we have collected some illustrative examples of (mostly published) datasets where contamination is a problem, and included some references that discuss instances and consequences of contamination. Following the steps below will help to check your sequences. They are no substitute for common sense and precautions, but they may help reveal contamination in your sequences. We have created interactive Web pages
Visualizing Ontologies with VOWL 1

Visualizations can be very useful when working with ontologies. The Visual Notation for OWL Ontologies (VOWL) is a comprehensive and well-specified visual language for the user-oriented representation of ontologies. It defines graphical depictions for most elements of the OWL Web Ontology Language that are combined to a force-directed graph layout visualizing the ontology. In contrast to related work, VOWL aims for an intuitive representation that is also understandable to users less familiar with ontologies. This article presents VOWL in detail and describes its implementation in two different tools: ProtégéVOWL and WebVOWL. The first is a plugin for the ontology editor Protégé, the second a standalone application entirely based on open web standards. Both tools demonstrate the applicability of VOWL by means of various ontologies. In addition, the results of three user studies conducted to evaluate the comprehensibility and usability of VOWL are summarized. They are complemented by latest insights gained from an expert interview and from testing the visual scope and completeness of VOWL with a benchmark ontology. The evaluations helped to improve VOWL and confirm that it creates comparatively intuitive and usable ontology visualizations.
Preliminary investigation of hydroxyapatite microstructures prepared by flash sintering

Flash sintering is a novel and emerging route for sintering ceramics within a few seconds, even under pressure-less conditions. In the current study, hydroxyapatite (HA) was fully densified by flash sintering at a furnace temperature of 1020°C. Flash sintering with constant electric fields of 750 and 1000 V cm−1 reduced the grain growth rate significantly compared to that sintered in the absence of an electric field at 1400°C. The microstructure of HA consolidated by flash sintering was compared with that of the without electric field sintered samples. The flash-sintered samples showed smaller grains (160 ∼ 320 nm) than the without electric field sintered samples (∼15 µm). The samples with a higher applied electric field showed slightly better densification than those with the lower field by flash sintering. Overall, the electric flash reduces the sintering temperature effectively and decreases the holding time to densify highly insulating ceramics, such as HA.
Clustering Interestingness Measures with Positive Correaltion

Selecting interestingness measures has been an important problem in knowledge discovery in database. A lot of measures have been proposed to extract the knowledge from large databases and many authors have introduced the interestingness properties for selecting a suitable measure for a given application. Some measures are adequate for some applications but the others are not, and it is difficult to capture what the best measures for a given data set are. In this paper, we present a new approach implemented in a tool to select the groups or clusters of objective interestingness measures that are highly correlated in an application. The final goal relies on helping the user to select the subset of measures that is the best adapted to discover the best rules according to his/her preferences.