Miracle-dz/UniFAR-FTUs huggingface dataset:
Visualizing graphs in three dimensions

It has been known for some time that larger graphs can be interpreted if laid out in 3D and displayed with stereo and/or motion depth cues to support spatial perception. However, prior studies were carried out using displays that provided a level of detail far short of what the human visual system is capable of resolving. Therefore, we undertook a graph comprehension study using a very high resolution stereoscopic display. In our first experiment, we examined the effect of stereoscopic display, kinetic depth, and using 3D tubes versus lines to display the links. The results showed a much greater benefit for 3D viewing than previous studies. For example, with both motion and stereoscopic depth cues, unskilled observers could see paths between nodes in 333 node graphs with less than a 10% error rate. Skilled observers could see up to a 1000-node graph with less than a 10% error rate. This represented an order of magnitude increase over 2D display. In our second experiment, we varied both nodes and links to understand the constraints on the number of links and the size of graph that can be reliably traced. We found the difference between number of links and number of nodes to best account for error rates and suggest that this is evidence for a “perceptual phase transition. ” These findings are discussed in terms of their implications for information display.
A central role for TRPS1 in the control of cell cycle and cancer development

The eukaryotic cell cycle is controlled by a complex regulatory network, which is still poorly understood. Here we demonstrate that TRPS1, an atypical GATA factor, modulates cell proliferation and controls cell cycle progression. Silencing TRPS1 had a differential effect on the expression of nine key cell cycle-related genes. Eight of these genes are known to be involved in the regulation of the G2 phase and the G2/M transition of the cell cycle. Using cell synchronization studies, we confirmed that TRPS1 plays an important role in the control of cells in these phases of the cell cycle. We also show that silencing TRPS1 controls the expression of 53BP1, but not TP53. TRPS1 silencing also decreases the expression of two histone deacetylases, HDAC2 and HDAC4, as well as the overall HDAC activity in the cells, and leads to the subsequent increase in the acetylation of histone4 K16 but not of histone3 K9 or K18. Finally, we demonstrate that TRPS1 expression is elevated in luminal breast cancer cells and luminal breast cancer tissues as compared with other breast cancer subtypes. Overall, our study proposes that TRPS1 acts as a central hub in the control of cell cycle and proliferation during cancer development.
Resistance Development of Cystic Fibrosis Respiratory Pathogens When Exposed to Fosfomycin and Tobramycin Alone and in Combination under Aerobic and Anaerobic Conditions

Although antibiotics from different classes are frequently prescribed in combination to prevent the development of resistance amongst Cystic Fibrosis (CF) respiratory pathogens, there is a lack of data as to the efficacy of this approach. We have previously shown that a 4∶1 (w/w) combination of fosfomycin and tobramycin (F∶T) has excellent activity against CF pathogens with increased activity under physiologically relevant anaerobic conditions. Therefore, the aim of this study was to determine whether F∶T could delay or prevent the onset of resistance compared to either fosfomycin or tobramycin alone under aerobic and anaerobic conditions. The frequency of spontaneous mutants arising following exposure to fosfomycin, tobramycin and F∶T was determined for clinical Pseudomonas aeruginosa and MRSA isolates under aerobic and anaerobic conditions. The effect of sub-inhibitory concentrations of fosfomycin, tobramycin and F∶T on the induction of resistance was also investigated, with the stability of resistance and fitness cost associated with resistance assessed if it developed. P. aeruginosa and MRSA isolates had a lower frequency of spontaneous mutants to F∶T compared to fosfomycin and tobramycin under both aerobic and anaerobic conditions. There was a maximum two-fold increase in F∶T MICs when P. aeruginosa and MRSA isolates were passaged in sub-inhibitory F∶T for 12 days. In contrast, sequential resistance to fosfomycin and tobramycin developed quickly (n = 3 days for both) after passage in sub-inhibitory concentrations. Once developed, both fosfomycin and tobramycin resistance was stable and not associated with a biological fitness cost to either P. aeruginosa or MRSA isolates. The results of this study suggest that F∶T may prevent the development of resistance compared to fosfomycin or tobramycin alone under aerobic and physiologically relevant anaerobic conditions. F∶T may be a potential treatment option in CF patients chronically colonised by MRSA and/or P. aeruginosa.
Intrinsic plasmids influence MicF-mediated translational repression of ompF in Yersinia pestis

Yersinia pestis, which is the causative agent of plague, has acquired exceptional pathogenicity potential during its evolution from Y. pseudotuberculosis. Two laterally acquired plasmids, namely, pMT1 and pPCP1, are specific to Y. pestis and are critical for pathogenesis and flea transmission. Small regulatory RNAs (sRNAs) commonly function as regulators of gene expression in bacteria. MicF, is a paradigmatic sRNA that acts as a post-transcriptional repressor through imperfect base pairing with the 5′-UTR of its target mRNA, ompF, in Escherichia coli. The high sequence conservation and minor variation in the RNA duplex of MicF-ompF has been reported in Yersinia. In this study, we utilized super-folder GFP reporter gene fusion to validate the post-transcriptional MicF-mediated regulation of target mRNA ompF in Y. pestis. Unexpectedly, upon MicF overexpression, the slightly upregulated expression of OmpF were found in the wild-type strain, which contradicted the previously established model. Interestingly, the translational repression of ompF target fusions was restored in the intrinsic plasmids-cured Y. pestis strain, suggesting intrinsic plasmids influence the MicF-mediated translational repression of ompF in Y. pestis. Further examination showed that plasmid pPCP1 is likely the main contributor to the abolishment of MicF-mediated translational repression of endogenous or plasmid-borne ompF. It represents that the possible roles of intrinsic plasmids should be considered upon investigating sRNA-mediated gene regulation, at least in Y. pestis, even if the exact mechanism is not fully understood.
Resistin is linked to inflammation, and leptin to metabolic syndrome, in women with inflammatory arthritis

Objective: To investigate how inflammation and metabolic syndrome (MetS) are associated with adipokine levels in patients with inflammatory arthritis. Methods: Fifty-four female patients with arthritis were enrolled in the study. Twenty (37%) of these patients had MetS, which was diagnosed according to the definition of the International Diabetes Federation (IDF). Interleukin (IL)-6 and four adipokines (resistin, leptin, adiponectin, and adipsin) were determined by immunoassay. Healthy women with body mass index (BMI) between 22 and 25 kg/m2 served as controls. Results: The patients with arthritis had higher levels of resistin than the healthy controls. This difference was clear in patients without MetS (17.4 in patients vs. 10.8 ng/mL in controls, p < 0.001), and even higher resistin levels were found in the patients with MetS (20.7 ng/mL; p < 0.001 vs. healthy controls; and p = 0.095 vs. patients without MetS). In the patients with arthritis and MetS, resistin correlated positively with IL-6 (Pearson’s r = 0.5, p = 0.03). Leptin levels were increased in arthritis patients with MetS as compared to healthy controls, but not in patients without MetS. The statistically significant difference between patients with MetS and controls remained when leptin was adjusted with BMI. Accordingly, adiponectin levels were lower in patients with MetS than in healthy controls (p < 0.05). Leptin, adiponectin, and adipsin did not correlate with the inflammatory cytokine IL-6 or with C-reactive protein (CRP). Conclusions: The results show that high resistin levels are associated with arthritis independently of MetS, whereas leptin is increased only in arthritis patients with MetS.
Influence of Altitude Exposure on Coronary Flow Reserve

Background—Although no data exist on the effect of altitude exposure on coronary flow reserve (CFR), patients with coronary artery disease (CAD) are advised not to exceed moderate altitudes of ≈2500 m above sea level. We studied the influence of altitude on myocardial blood flow (MBF) in controls and CAD patients. Methods and Results—In 10 healthy controls and 8 patients with CAD, MBF was measured by positron emission tomography and 15O-labeled water at rest, during adenosine stress, and after supine bicycle exercise. This protocol was repeated during inhalation of a hypoxic gas mixture corresponding to an altitude of 4500 m (controls) and 2500 m (CAD). Workload was targeted to comparable heart rate–blood pressure products at normoxia and hypoxia. Resting MBF increased significantly in controls at 4500 m (+24%, P <0.01) and in CAD patients at 2500 m (+24%, P <0.05). Altitude had no influence on adenosine-induced hyperemia and CFR. Exercise-induced hyperemia increased significantly in controls (+38%, P <0.01) at 4500 m (despite a reduction in workload, −28%, P <0.0001) but not in CAD patients at 2500 m (moderate decrease in workload, −11%, P <0.05). Exercise-induced reserve was preserved in controls (+10%, P =NS) but decreased in CAD patients (−18%, P <0.005). Conclusions—At 2500 m altitude, there is a significant decrease in exercise-induced reserve in CAD patients, indicating that compensatory mechanisms might be exhausted even at moderate altitudes, whereas healthy controls have preserved reserve up to 4500 m. Thus, patients with CAD and impaired CFR should be cautious when performing physical exercise even at moderate altitude.
Analyzing the Creative Problem-Solving Process: Inventing a Product from a Given Recyclable Item

Detailed documentations of creative invention are scarce in the professional literature, but could be useful to those engaging in or studying the problem solving process. This investigation describes the creative process of graduate students (7 female, 4 male) in a problem-solving theory and practice course grappling with the task of creating products from four identical recyclable items that were circular, star-impressed bottoms of plastic juice bottles. Several popular models of the problem-solving process are compared to the participants’ steps in this invention problem. Participants first provided emotional reactions to the given ill-defined problem of making a product from the specified items. They used several techniques to generate ideas and to restrict or define the problem, choosing an optimal product that fits their require-ments. An analysis of participants’ reflections concerning their creative process showed that although participants first found the problem challenging and could not conceptualize effective products, the idea-generating activities assisted them in making a wide variety of useful products. Participants’ knowledge and skill areas were highlighted by their choices of products. After completing and presenting a first product, participants engaged in additional activities to generate ideas for a second product. The second product was either an improvement of the first product, a new but related product, or a product inspired by the work of others in the class. Products of this loosely defined problem included: maracas, dish, spin top, candy suckers, closet organizers, party decorations, yoyo, ladybug, wall decor, flowers, catch game, party hat, candle holders, moth life cycle, catapult game, toy clock, goblets, castanets, accessory organizer, and spice shaker.
Comparing the Calcium Binding Abilities of Two Soybean Calmodulins: Towards Understanding the Divergent Nature of Plant Calmodulins[W]

The expression of calmodulin isoforms with unique Ca2+ binding affinities could confer on plant cells an additional ability to translate the distinct Ca2+ signals that accompany various stimuli. Using isoforms of conserved and divergent calmodulin sequences, this study finds that differences in affinity and the effect of competing Mg2+ tunes the responsiveness of the isoforms to the appropriate Ca2+ signature. The discovery that plants contain multiple calmodulin (CaM) isoforms of variable sequence identity to animal CaM suggested an additional level of sophistication in the intracellular role of calcium regulation in plants. Past research has focused on the ability of conserved or divergent plant CaM isoforms to activate both mammalian and plant protein targets. At present, however, not much is known about how these isoforms respond to the signal of an increased cytosolic calcium concentration. Here, using isothermal titration calorimetry and NMR spectroscopy, we investigated the calcium binding properties of a conserved (CaM1) and a divergent (CaM4) CaM isoform from soybean (Glycine max). Both isoforms bind calcium with a semisequential pathway that favors the calcium binding EF-hands of the C-terminal lobe over those of the N-terminal lobe. From the measured dissociation constants, CaM4 binds calcium with a threefold greater affinity than CaM1 (Kd,Ca,mean of 5.0 versus 14.9 μM) but has a significantly reduced selectivity against the chemically similar magnesium cation that binds preferentially to EF-hand I of both isoforms. The implications of a potential magnesium/calcium competition on the activation of CaM1 and CaM4 are discussed in context with their ability to respond to stimulus-specific calcium signatures and their known physiological roles.
Albumin replacement in severe sepsis or septic shock.

To the Editor: The Albumin Italian Outcome Sepsis study conducted by Caironi et al. (April 10 issue)1 is the third large-scale, randomized trial to compare albumin with crystalloids in adult patients with severe sepsis. The first such trial was the Saline versus Albumin Fluid Evaluation study.2 In addition, the Early Albumin Resuscitation during Septic Shock study has been completed and its mortality results published.3 In all three trials, mortality was lower among patients receiving albumin, and the respective relative risks coincided closely, ranging from 0.87 to 0.94 (Fig. 1). Although the effect did not attain statistical significance in any of the individual trials, the pooled relative risk in all three trials is 0.92 (95% confidence interval [CI], 0.84 to 1.00; P = 0.046), indicating a significant reduction in mortality associated with albumin use among adults with severe sepsis. This result supports the conclusion of a previous metaanalysis involving predominantly small trials with different control fluids and patient populations.4 The result is also consistent with the observed reduction in mortality associated with albumin use among patients with spontaneous bacterial peritonitis, a disease that shares important pathophysiological features with severe sepsis.5
Consensus with robustness to outliers via distributed optimization

Over the past few years, a number of distributed algorithms have been developed for integrating the measurements acquired by a wireless sensor network. Among them, average consensus algorithms have drawn significant attention due to a number of practical advantages, such as robustness to noise in the measurements, robustness to changes in the network topology and guaranteed convergence to the centralized solution. However, one of the main drawbacks of existing consensus algorithms is their inability to handle outliers in the measurements. This is because they are based on minimizing a Euclidean (L2) loss function, which is known to be sensitive to outliers. In this paper, we propose a distributed optimization framework that can handle outliers in the measurements. The proposed framework generalizes consensus algorithms to robust loss functions that are strictly convex or convex, such as the Huber loss or the L1-loss. This generalization is achieved by posing the robust consensus problem as a constrained optimization problem, which is solved using distributed versions of classical primal-dual and augmented Lagrangian optimization methods. The resulting algorithms include the classical average consensus as a particular case. Synthetic experiments evaluate our robust consensus framework for several robust cost functions and show their advantages over the classical average consensus algorithm.
Scaling network verification using symmetry and surgery

On the surface, large data centers with about 100,000 stations and nearly a million routing rules are complex and hard to verify. However, these networks are highly regular by design; for example they employ fat tree topologies with backup routers interconnected by redundant patterns. To exploit these regularities, we introduce network transformations: given a reachability formula and a network, we transform the network into a simpler to verify network and a corresponding transformed formula, such that the original formula is valid in the network if and only if the transformed formula is valid in the transformed network. Our network transformations exploit network surgery (in which irrelevant or redundant sets of nodes, headers, ports, or rules are ``sliced'' away) and network symmetry (say between backup routers). The validity of these transformations is established using a formal theory of networks. In particular, using Van Benthem-Hennessy-Milner style bisimulation, we show that one can generally associate bisimulations to transformations connecting networks and formulas with their transforms. Our work is a development in an area of current wide interest: applying programming language techniques (in our case bisimulation and modal logic) to problems in switching networks. We provide experimental evidence that our network transformations can speed up by 65x the task of verifying the communication between all pairs of Virtual Machines in a large datacenter network with about 100,000 VMs. An all-pair reachability calculation, which formerly took 5.5 days, can be done in 2 hours, and can be easily parallelized to complete in
Video as a new teaching tool to increase student motivation

The main objective of this research is to explore the results of the use of videos as an educational tool which helps increasing students' motivation in any discipline. The study is based on several streaming videos created as a support material for learning and used by 12 lecturers with 487 students in three different degrees of engineering (Mechanical, Industrial and Management, and Aeronautical) at the School of Industrial and Aeronautical Engineering of Terrassa (ETSEIAT). The paper describes the different areas and ways in which this innovative learning tool has been used and emphasizes the skills developed in each application. Finally, it presents the results of the impact of the use of videos upon students' motivation.
Asymptomatic shedding of herpes simplex virus 1 and 2: implications for prevention of transmission.

It is counterintuitive that sexual transmission of herpes simplex virus (HSV) more commonly results from contact during a short episode of asymptomatic shedding than from contact with lesions. After all, virus titers are much higher and the average duration of shedding is much longer when lesions are present [1, 2], and the risk of transmission following a single contact with lesions is undoubtedly much higher than a single contact with asymptomatic shedding. More than 2 decades ago, the role of asymptomatic shedding in transmission of HSV was suggested by evaluation of recent sex partners implicated in transmission of genital herpes and by evaluation of mothers who transmitted HSV to neonates yet lacked a history of genital herpes [3-6]. In a study published in 1985, recent sex partners of persons with first-episode genital herpes were interviewed and eval-
Transmission Mechanism of Wearable Devices Using the Human Body as a Transmission Channel

In recent years, the development of the information and communication devices, such as cellular phones, personal digital assistants (PDAs), digital video cameras, pocket video games, and so forth, has been progressing rapidly. This evolution gives increased convenience to our daily lives. In the near future, these appliances will begin to be attached to our body, in the form of wearable computers that can be connected to internal and external network systems [1]. However, [2] notes that there is currently no method for these personal devices to directly exchange data. We would like to exchange the data in the wearable devices without any physical constraints, such as external wire connections that may be easily tangled. The solution for networking these personal devices has been proposed as PANs that use the human body as a transmission channel [2, 3]. One of the merits of this system is that data can be exchanged by our natural actions, such as simply touching the receiver, and the user can be clearly aware of connection. Figure 4.1 shows the future applications. We can use these transmission systems for security, electronic money, amusement, and so forth. Although many studies have been made on the development of wearable devices using the human body as a transmission channel, little is known about the transmission mechanism of such devices in the physical layer, from the viewpoint of the interaction between the electromagnetic wave and the human body [2–14]. Electromagnetic communication trials using the human body as a transmission medium have been carried out for more than a decade. However, most of the research has been conducted by researchers who just want to utilize the results, and until recently the physical mechanisms have not been studied. This chapter investigates the transmission mechanisms of the wearable devices using the human body as a transmission medium [15–23]. Figure 4.2 shows the communication system [9] of the PAN using a 10-MHz carrier frequency [24]. When a user wearing the transmitter touches the electrode of the receiver, a trans-
Serotonin Increases Phosphorylation of Synaptic 4EBP through TOR, but Eukaryotic Initiation Factor 4E Levels Do Not Limit Somatic Cap-Dependent Translation in Aplysia Neurons

ABSTRACT The target of rapamycin (TOR) plays an important role in memory formation in Aplysia californica. Here, we characterize one of the downstream targets of TOR, the eukaryotic initiation factor 4E (eIF4E) binding protein (4EBP) from Aplysia. Aplysia 4EBP contains the four critical phosphorylation sites regulated by TOR as well as an N-terminal RAIP motif and a C-terminal TOS site. Aplysia 4EBP was hypophosphorylated in synaptosomes, and serotonin addition caused a rapamycin-sensitive increase in 4EBP phosphorylation both in synaptosomes and in isolated neurites. Aplysia 4EBP was regulated in a fashion similar to that of mammalian 4EBPs, binding to eIF4E when dephosphorylated and releasing eIF4E after phosphorylation. Overexpression of 4EBP in the soma of Aplysia neurons caused a specific decrease in cap-dependent translation that was rescued by concomitant overexpression of eIF4E. However, eIF4E overexpression by itself did not increase cap-dependent translation, suggesting that increasing levels of free eIF4E by phosphorylating 4EBP is not important in regulating cap-dependent translation in the cell soma. Total levels of eIF4E were also regulated by 4EBP, suggesting that 4EBP can also act as an eIF4E chaperone. These studies demonstrate the conserved nature of 4EBP regulation and its role in cap-dependent translation and suggest differential roles of 4EBP phosphorylation in the soma and synapse.