Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking declarative approximate selection predicates

Declarative data quality has been an active research topic. The fundamental principle behind a declarative approach to data quality is the use of declarative statements to realize data quality primitives on top of any relational data source. A primary advantage of such an approach is the ease of use and integration with existing applications. Over the last few years several similarity predicates have been proposed for common quality primitives (approximate selections, joins, etc) and have been fully expressed using declarative SQL statements. In this paper we propose new similarity predicates along with their declarative realization, based on notions of probabilistic information retrieval. In particular we show how language models and hidden Markov models can be utilized as similarity predicates for data quality and present their full declarative instantiation. We also show how other scoring methods from information retrieval, can be utilized in a similar setting. We then present full declarative specifications of previously proposed similarity predicates in the literature, grouping them into classes according to their primary characteristics. Finally, we present a thorough performance and accuracy study comparing a large number of similarity predicates for data cleaning operations. We quantify both their runtime performance as well as their accuracy for several types of common quality problems encountered in operational databases.
A Riemannian Framework for Matching Point Clouds Represented by the Schrödinger Distance Transform

In this paper, we cast the problem of point cloud matching as a shape matching problem by transforming each of the given point clouds into a shape representation called the Schrödinger distance transform (SDT) representation. This is achieved by solving a static Schrödinger equation instead of the corresponding static Hamilton-Jacobi equation in this setting. The SDT representation is an analytic expression and following the theoretical physics literature, can be normalized to have unit 2 norm - making it a square-root density, which is identified with a point on a unit Hilbert sphere, whose intrinsic geometry is fully known. The Fisher-Rao metric, a natural metric for the space of densities leads to analytic expressions for the geodesic distance between points on this sphere. In this paper, we use the well known Riemannian framework never before used for point cloud matching, and present a novel matching algorithm. We pose point set matching under rigid and non-rigid transformations in this framework and solve for the transformations using standard nonlinear optimization techniques. Finally, to evaluate the performance of our algorithm - dubbed SDTM - we present several synthetic and real data examples along with extensive comparisons to state-of-the-art techniques. The experiments show that our algorithm outperforms state-of the-art point set registration algorithms on many quantitative metrics.
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Genome‐scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between and within metabolic pathways. The developed method and model are expected to increase the use of model‐based design in metabolic engineering.
Optically Controlled Manipulation of Single Nano-Objects by Thermal Fields

This dissertation presents and explores a technique to confine and manipulate single and multiple nano-objects in solution by exploiting the thermophoretic interactions with local temperature gradients. The method named thermophoretic trap uses an all-optically controlled heating via plasmonic absorption by a gold nano-structure designed for this purpose. The dissipation of absorbed laser light to thermal energy generates a localized temperature field. The spatial localization of the heat source thereby leads to strong temperature gradients that are used to drive a particle or molecule into a desired direction. The behavior of nano-objects confined by thermal inhomogeneities is explored experimentally as well as theoretically. The monograph treats three major experimental stages of development, which essentially differ in the way the heating laser beam is shaped and controlled. In a first generation, a static heating of an appropriate gold structure is used to induce a steady temperature profile that exhibits a local minimum in which particles can be confined. This simple realization illustrates the working principle best. In a second step, the static heating is replaced. A focused laser beam is used to heat a smaller spatial region. In order to confine a particle, the beam is steered in circles along a circular gold structure. The trapping dynamics are studied in detail and reveal similarities to the well-established Paul trap. The largest part of the thesis is dedicated to the third generation of the trap. While the hardware is identical to the second generation, using the realtime information on the position of the trapped object to heat only particular sites of the gold structure strongly increases the efficiency of the trap compared to the earlier versions. Beyond that, the optical feedback control allows for an active shaping of the effective virtual trapping potential by applying modified feedback rules, including e.g. a double-well or a box-like potential. This transforms the formerly pure trapping device to a versatile technique for micro and nano-fluidic manipulation. The physical and technical contributions to the limits of the method are explored. Finally, the feasibility of trapping single macro-molecules is demonstrated by the confinement of λ-DNA for extended time periods over which the molecules center-of-mass motion as well as its conformational dynamics can be studied. This work has been funded by the European Union and the Free State of Saxony.
Interactive procedural simulation of paper tearing with sound

We present a phenomenological model for the real-time simulation of paper tearing and sound. The model uses as input rotations of the hand along with the index and thumb of left and right hands to drive the position and orientation of two regions of a sheet of paper. The motion of the hands produces a cone shaped deformation of the paper and guides the formation and growth of the tear. We create a model for the direction of the tear based on empirical observation, and add detail to the tear with a directed noise model. Furthermore, we present a procedural sound synthesis method to produce tearing sounds during interaction. We show a variety of paper tearing examples and discuss applications and limitations.
GD3 ganglioside directly targets mitochondria in a bcl‐2‐controlled fashion

Lipid and glycolipid diffusible mediators are involved in the intracellular progression and amplification of apoptotic signals. GD3 ganglioside is rapidly synthesized from accumulated ceramide after the clustering of death‐inducing receptors and triggers apoptosis. Here we show that GD3 induces dissipation of ΔΨm and swelling of isolated mitochondria, which results in the mitochondrial release of cytochrome c, apoptosis inducing factor, and caspase 9. Soluble factors released from GD3‐treated mitochondria are sufficient to trigger DNA fragmentation in isolated nuclei. All these effects can be blocked by cyclosporin A, suggesting that GD3 is acting at the level of the permeability transition pore complex. We found that endogenous GD3 accumulates within mitochondria of cells undergoing apoptosis after ceramide exposure. Accordingly, suppression of GD3 synthase (ST8) expression in intact cells substantially prevents ceramide‐induced ΔΨm dissipation, indicating that endogenously synthesized GD3 induces mitochondrial changes in vivo. Finally, enforced expression of bcl‐2 significantly prevents GD3‐induced mitochondrial changes, caspase 9 activation, and apoptosis. These results show that mitochondria are a key destination for apoptogenic GD3 ganglioside along the lipid pathway to programmed cell death and indicate that relevant GD3 targets are under bcl‐2 control. —Rippo, M. R. , Malisan, F. , Ravagnan, L. , Tomassini, B. , Condo, I. , Costantini, P., Susin, S. A. , Rufini, A. , Todaro, M. , Kroemer, G. , Testi, R. GD3 ganglioside directly targets mitochondria in a bcl‐2‐controlled fashion. FASEB J. 14, 2047–2054 (2000)
Evaluating Wireless LAN Access Methods in Presence of Transmission Errors

Several modifications of the IEEE 802.11 DCF access method have been proposed recently to improve the performance of wireless LANs. Up to now, such proposals have only been compared under ideal channel conditions. In this paper, we evaluate the impact of transmission errors on their performance in terms of aggregate throughput and fairness.
Impact of Full Duplex Scheduling on End-to-End Throughput in Multi-Hop Wireless Networks

There have been some rapid advances on the design of full duplex (FD) transceivers in recent years. Although the benefits of FD have been studied for single-hop wireless communications, its potential on throughput performance in a multi-hop wireless network remains unclear. As for multi-hop networks, a fundamental problem is to compute the achievable end-to-end throughput for one or multiple communication sessions. The goal of this paper is to offer some fundamental understanding on end-to-end throughput performance limits of FD in a multi-hop wireless network. We show that through a rigorous mathematical formulation, we can cast the multi-hop throughput performance problem into a formal optimization problem. Through numerical results, we show that in many cases, the end-to-end session throughput in a FD network can exceed 2x of that in a half duplex (HD) network. Our finding can be explained by the much larger design space for scheduling that is offered by removing HD constraints in throughput maximization problem. The results in this paper offer some new understandings on the potential benefits of FD for end-to-end session throughput in a multi-hop wireless network.
AGING IN HOSTILE ENVIRONMENT MODELED BY CELLULAR AUTOMATA WITH GENETIC DYNAMICS

We model the evolution of a population on a 2D cellular automata (CA) lattice. Every individual holds a binary "genetic code". The code length and the number of "1"s in the chain correspond to the maximal and actual life-time of individual, respectively. The "genetic code" code is divided onto three life-episodes: "youth", "maturity" and "old age". Only "mature" individuals can procreate. We investigate the duration of the life-episodes and their role in protecting the population from extinction in hostile environments. We observe that in the stable environment, which does not influence the life-time of individuals, the "youth" and the "maturity" periods extend extremely long during evolution, while the "old age" remains short. The situation is different for hostile plaque-like conditions. Under these circumstances, the "youth" period vanishes, while the longer "old age" period stabilizes the population growth, increases its average age and thereby increases its chance of survival. We can conclude that the idle life-episodes set up the control mechanisms, which allow for self-adaptation of the population to varying environmental conditions.
The Annexin A2/p11 complex is required for efficient invasion of Salmonella Typhimurium in epithelial cells

The facultative intracellular pathogen, Salmonella enterica, triggers its own uptake into non‐phagocytic epithelial cells. Invasion is dependent on a type 3 secretion system (T3SS), which delivers a cohort of effector proteins across the plasma membrane where they induce dynamic actin‐driven ruffling of the membrane and ultimately, internalization of the bacteria into a modified phagosome. In eukaryotic cells, the calcium‐ and phospholipid‐binding protein Annexin A2 (AnxA2) functions as a platform for actin remodelling in the vicinity of dynamic cellular membranes. AnxA2 is mostly found in a stable heterotetramer, with p11, which can interact with other proteins such as the giant phosphoprotein AHNAK. We show here that AnxA2, p11 and AHNAK are required for T3SS‐mediated Salmonella invasion of cultured epithelial cells and that the T3SS effector SopB is required for recruitment of AnxA2 and AHNAK to Salmonella invasion sites. Altogether this work shows that, in addition to targeting Rho‐family GTPases, Salmonella can intersect the host cell actin pathway via AnxA2.
The niche graphs of doubly partial orders

The competition graph of a doubly partial order is known to be an interval graph. The competition-common enemy graph of a doubly partial order is also known to be an interval graph unless it contains a cycle of length 4 as an induced subgraph. In this paper, we show that the niche graph of a doubly partial order is not necessarily an interval graph. In fact, we prove that, for each n � 4, there exists a doubly partial order whose niche graph contains an induced subgraph isomorphic to a cycle of length n. We also show that if the niche graph of a doubly partial order is triangle-free, then it is an interval graph.
Cut-off rate and signal design for the Rayleigh fading space-time channel

We consider the single-user computational cut-off-rate for the complex Rayleigh flat fading spatio-temporal channel under a peak power constraint. Determination of the cut-off rate requires maximization of an average error exponent over all possible space-time codeword probability distributions. This error exponent is monotone decreasing in a measure of dissimilarity between pairs of codeword matrices. For low SNR the dissimilarity function reduces to a trace norm of differences between outer products of pairs of codewords. We characterize the cut-off rate and the rate achieving constellation under different operating regimes depending on the number of transmit and receive antennas, the number of codewords in the constellation, and the received SNR.
Damping inter-area modes of oscillation using an adaptive fuzzy power system stabilizer

This paper introduces an indirect variable-structure adaptive fuzzy controller as a power system stabilizer (IDVSFPSS) used to damp inter-area modes of oscillation following disturbances in power systems. In contrast to IEEE standard multi-band power system stabilizer (MB-PSS) , indirect adaptive fuzzy-based stabilizer are more efficient because they cope with oscillations at different operating points. A nominal model of the power system is identified on-line using a variable structure identifier. A feedback linearization-based control law is implemented using the identified model. The gains of the controller are tuned via a particle swarm optimization routine to ensure system stability and minimum sum of the squares of the speed deviations. A benchmark problem of a 4-machine 2-area power system is used to demonstrate the performance of the proposed controller and to show its superiority over other conventional stabilizers used in the literature.
Preparation of 0.05% FK506 suspension eyedrops and its pharmacokinetics after topical ocular administration.

PURPOSE To investigate the stability of FK506 eye suspension and its pharmacokinetics in rabbit aqueous humor, as well as its distribution in eye tissues. METHODS Sedimentation rate, flocculation value, redispersion time, rheological study, and accelerated experiment were determined for evaluating the stability of FK506 suspension. In a single-dose pharmacokinetic study, six rabbits were instilled a 25-microL drop of 0.05% FK506 suspension and aqueous humor samples were collected at different intervals after administration. In a multiple-dose pharmacokinetic study, a 25-microL drop of FK506 suspension was instilled into the right eye of six rabbits four times a day for 7 days. On the eighth day, aqueous humor samples were collected before the administration of the first, second, third dose, and at different checkpoints after the third dose. For tissue distribution study, six eyes per time points (18 rabbits in total) were treated with single dose of FK506 suspension, and the eyes were enucleated at 60, 100, and 240 min after treatment, then eye tissues were collected. The concentrations of FK506 in all samples were determined by LC-MS/MS. RESULTS The preliminary results indicated that the stability of FK506 suspension was in accord with the standards of Chinese pharmacopoeia. The maximum concentrations of aqueous humor after single dose and multiple dose administrations were 31.40 +/- 9.32 ng/mL and 37.73 +/- 11.25 ng/mL, respectively. The concentration of FK506 in cornea at 60, 100, and 240 min after a single dose were 402.0 +/- 96.8 ng/g, 363.8 +/- 84.5 ng/g, and 220 +/- 62.3 ng/g, respectively. Determination of pharmacokinetic parameters of single-dose and multiple-dose administration, as well as the FK506 concentrations in eye tissues, showed that the FK506 formulation and the dosing regimen ensured the therapeutic concentration of FK506 for treating corneal allograft rejection. CONCLUSIONS Based on the stability, single-dose and multiple-dose pharmacokinetics, and tissue distribution, FK506 suspension eyedrops may be a suitable candidate for clinical application in ophthalmology.
Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells

MOTIVATION Tumor necrosis factor-alpha (TNF-α), a major inflammatory cytokine, is closely related to several cardiovascular pathological processes. However, its effects on the cell cycle of vascular endothelial cells (VECs) have been the subject of some controversy. To investigate the molecular mechanism underlying this process, we constructed time-course protein-protein interaction (PPI) networks of TNF-α induced regulation of cell cycle in VECs using microarray datasets and genome-wide PPI datasets. Then, we analyzed the topological properties of the responsive PPI networks and calculated the node degree and node betweenness centralization of each gene in the networks. We found that p21, p27 and cyclinD1, key genes of the G1/S checkpoint, are in the center of responsive PPI networks and their roles in PPI networks are significantly altered with induction of TNF-α. According to the following biological experiments, we proved that TNF-α can promote G(1)/S transition of cell cycle in VECs and facilitate the cell cycle activation induced by vascular endothelial growth factor. CONTACT shaoli@mail.tsinghua. edu.cn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
A Methodology for Constructing Marginal Abatement Cost Curves for Climate Action in Cities

As drivers of climate action, cities are taking measures to reduce greenhouse gas (GHG) emissions, which if left unabated pose a challenge to meeting long-term climate targets. The economics of climate action needs to be at the forefront of climate dialogue to prioritize investments among competing mitigation measures. A marginal abatement cost (MAC) curve is an effective visualization of climate action that initiates a technical and economic discussion of the cost-effectiveness and abatement potential of such actions among local leaders, policy makers, and climate experts. More commonly demonstrated for countries, MAC curves need to be developed for cities because of their heterogeneity, which vary in their urban activities, energy supply, infrastructure stock, and commuting patterns. The methodology for constructing bottom-up MAC curves for cities is presented for technologies that offer fuel switching and/or energy efficiencies, while considering technology lifetimes, city-specific electricity and fuel prices, and emission intensities. Resulting MAC curves are unique to every city, and chart the pathway towards low-carbon growth by prioritizing measures based on cost-effectiveness. A case study of Toronto’s climate targets demonstrates the prioritization of select technologies. Leveraging MAC curves to support climate programs enables cities to strategically invest in financing climate action and designing incentives.
Effect of Repetitive Transcranial Magnetic Stimulation on Hand Function of Spastic Cerebral Palsy Children

Repetitive Transcranial magnetic stimulation (rTMS) is emerging as a new investigation as well as treatment tool for various neurological and psychiatric diseases. Recent studies showed its application as treatment tool in movement disorders, where rTMS stimulation on primary motor cortex alters physiological patterns of motor threshold; motor evoked potential and cortical plasticity which induces motor activity. Recent studies on rTMS combined with rehabilitation therapy demonstrated functional improvement in motor activities of spastic cerebral palsy (sCP) children. Thus, this study was designed to evaluate the effect of rTMS on hand function of sCP patients. Forty-five children diagnosed as sCP participated in this study after written consent from their parents or guardians. They were divided into three groups- control (CG) and interventional group (IG-A and IG-B). Participants in CG were provided only physical therapy (PT) of 30 minutes duration daily for 20 days and those in IG were administered rTMS frequency of 5Hz (IG-A) and 10Hz (IG-B) for 15 minutes consisting of 1500 pulses daily for 20 days; followed by PT as given to CG. Quality of upper extremity skill test (QUEST) scoring was used for evaluating the improvement in hand function of sCP patients. The pre (before starting any therapy) versus post (after completion of 20 sessions) mean QUEST score between different groups were statistically significant (p<0.01) and the mean change was 0.61, 2.46 and 2.87 in CG, IG-A and IG-B respectively. However, encouraging functional improvement in hand function was observed in diplegic patients in the age group of 2-6 years employing 5Hz frequency and higher frequency (10Hz) induced better activity in hemiplegic and quadriplegic patient of older age groups (7-16 years).