Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Characterization of a Second Porin Isoform in Drosophila melanogaster

Mitochondrial porins or voltage-dependent anion-selective channels are channel-forming proteins mainly found in the mitochondrial outer membrane. Genome sequencing of the fruit fly Drosophila melanogaster revealed the presence of three additional porin-like genes. No functional information was available for the different gene products. In this work we have studied the function of the gene product closest to the known Porin gene (CG17137 coding for DmPorin2). Its coding sequence was expressed in Escherichia coli. The recombinant DmPorin2 protein is able to form channels similar to those formed by DmPorin1 reconstituted in artificial membranes. Furthermore, DmPorin2 is clearly voltage-independent and cation-selective, whereas its counterpart isoform 1 is voltage-dependent and anion-selective. Sequence comparison of the two porin isoforms indicates the exchange of four lysines in DmPorin1 for four glutamic acids in DmPorin2. We have mutated two of them (Glu-66 and Glu-163) to lysines to investigate their role in the functional features of the pore. The mutants E163K and E66K/E163K are endowed with an almost full inversion of the ion selectivity. Both single mutations partially restore the voltage dependence of the pore. We found that an additional effect with the double mutant E66K/E163K was the restoration of voltage dependence. Protein structure predictions highlight a 16 β-strand pattern, typical for porins. In a three-dimensional model of DmPorin2, Glu-66 and Glu-163 are close to the rim of the channel, on two opposite sides. DmPorin2 is expressed in all the fly tissues and in all the developmental stages tested. Our main conclusions are as follows. 1) The CG17137 gene may express a porin with a functional role in D. melanogaster. 2) We have identified two amino acids of major relevance for the voltage dependence of the porin pore.
Synthesis and Anti‐inflammatory Effect of Chalcones

The process of degranulation of mast cells and neutrophils contributes to inflammatory disorders. Activation of microglial cells and macrophages is believed to be involved in inflammatory, infectious and degenerative diseases of the CNS. Combining the potent inhibition of chemical mediators released by the degranulation of mast cells or neutrophils and from the activated microglial cells or macrophages, would lead to a promising antiinflammatory agent for the treatment of peripheral and central inflammation. A series of chalcone derivatives have been reported to have potent anti‐inflammatory activity. In an effort to continually develop potent anti‐inflammatory agents, novel series of chalcones, 2′‐hydroxy‐ and 2′,5′‐dihydroxychalcones were synthesized and their inhibitory effects on the activation of mast cells, neutrophils, microglial cells and macrophages were evaluated in‐vitro. The chalcones were prepared by Claisen‐Schmidt condensation of appropriate acetophenones with an appropriate aromatic aldehyde. The alkoxychalcones were prepared with appropriate hydroxychalcones and alkyl iodide and the dihydroxychalcones were prepared by hydrogenation of an appropriate chalcone with Pd/C.
Effect of a Pholiota adiposa Extract on Fat Mass in Hyperlipidemic Mice

The purpose of this study was to investigate the effect of a Pholiota adiposa extract on fat mass in hyperlipidemic mice fed on a high-fat diet. The water extracts from P. adiposa (ASI 24018) were not affected in the total triglyceride contents and epididymal fat mass in mice fed on a high-fat diet, but the retroperitoneal fat mass decreased significantly. This result suggests that the P. adiposa extract may be a potential candidate for use as a functional food that can act as a prophylactic against hyperlipidemia. However, the P. adiposa extract showed no effect in the total triglyceride contents and epididymal fat mass.
SINGLE-MOLECULE PCR IN A PICOWELL ARRAY SIMULTANIOUSLY IMMOBILIZING PCR PRODUCTS TO A PDMS COVERSLIDE

For the first time, we amplified single DNA-molecules (“Digital PCR”) randomly distributed in a picowell array and simultaneously immobilized the generated PCR-products to the surface of a PDMS coverslide (“solid-phase PCR”) which was used as sealing of the picowells during PCR. First, by this unprecedented technique PCR-products can be recovered for both, further reactions/analysis and counting the number of initial DNA-molecules from digital signals with a good signal to noise ratio of 10. Second, our experiments demonstrate the currently smallest low-volume on-chip PCR in an array of 18.5 pL wells. This may enable single-cell PCR experiments by filling PCR microreactors with truly single-cells due to geometrical constriction.
Evaluation of Traffic Safety and Passenger Comfort of KTX considering Vertical Deformation of Steel-Composite Arch Bridge due to Temperature Change

교량 상 열차의 주행안전성 및 승차감 확보는 철도교량 고유의 특징이다. 이에 대한 대부분의 연구는 2차 변형이 없는 상태에서의 신규 교량에서 수행되었으나, 장경간화 되고 있는 교량설계의 추세와 기후변화 폭이 점점 커지는 상황에 따라 온도 변형 시의 교량의 변형을 고려한 주행안전성 및 승차감 확보에 대한 검토가 필요하다. 본 연구에서는 일반적인 철도교량에 비해 온도변화에 따른 교량의 변형이 상대적으로 클 것으로 예상되는 장경간 강합성 아치교에 대해 하절기와 동절기에서의 주행안전성 및 승차감에 대해 실 열차 주행시험에 의한 열차에서의 응답과 교량에서의 응답을 동시에 측정하여 분석하였다. 또한 극한 온도를 가정하여 3차원 교량-열차 상호작용 해석을 수행해 교량의 온도변형을 고려한 주행안전성 및 승차감을 검토하였다.
Multiple Kernel Two-Step Tracking

In tracking tasks, representing a target region as a weighted histogram has opened possibilities which led to excellent results, as mean shift or camshift algorithms. This representation is extracted from the image by giving weights with kernels and it depends on the properties of the kernels. By a first order Taylor approximation of the histograms it is possible to perform a tracking using several kernels, interpreted as different sources of information. This representation improves the possibilities and gives more flexibility when facing problems of tracking, as occlusions, model variance or projective deformations of the image. In this paper we use this multi-kernel model representation to perform a simultaneous tracking of the entire object and also of each different part individually. This is performed in a new two-step process. In the first step we perform the multikernel estimation and in a second step we update the model representation taking into account single kernel estimations, representing the local movement of each part. From a probabilistic view of the Matusita metric we analyze the usefulness of this method against partial occlusions and some projective transformations like zooms or 3D rotations and articulated movements.
Survival analysis and prognostic nomogram for patients undergoing resection of extrahepatic cholangiocarcinoma.

BACKGROUND Tumor location of extrahepatic cholangiocarcinoma (CCA) might influence survival after resection. METHODS A consecutive series of 175 patients who had undergone a potentially curative resection of extrahepatic CCA was analyzed. We calculated concordance indices of different constructed prognostic models for survival including TNM (tumour-node-metastasis) staging and developed a nomogram of the most sensitive model. RESULTS Overall cancer-specific survival rates were 83%, 58%, and 26% at 1, 2, and 5 years, respectively. Cancer-specific survival according to location was 42% for proximal, 23% for mid, and 19% for distal CCA after 5 years. Tumor location was not an independent significant predictor (P = 0.06). A prognostic model using all potential prognostic variables predicted survival better compared with TNM staging (concordance index 0.65 versus 0.63). A reduced model containing only lymph node status, microscopically residual tumor status, and tumor differentiation grade, also outperformed TNM staging (concordance index 0.66). CONCLUSIONS Tumor location of extrahepatic CCA does not independently predict cancer-specific survival after resection. We developed a nomogram, based on a prognostic model with lymph node status, microscopically residual tumor status of resection margins, and tumor differentiation grade, that predicted survival better than TNM staging.
FIST: A fast, lightweight, FPGA-friendly packet latency estimator for NoC modeling in full-system simulations

FIST (Fast Interconnect Simulation Techniques) is a fast and simple packet latency estimator to replace time-consuming detailed Network-on-Chip (NoC) models in full-system performance simulators. FIST combines ideas from analytical network modeling and execution-driven simulation models. The main idea is to abstractly model each router as a load-delay curve and sum load-dependent delay at each visited router to obtain a packet's latency by tracking each router's load at runtime. The resulting latency estimator can accurately capture subtle load-dependent behaviors of a NoC but is much simpler than a full-blown execution-driven model. We study two variations of FIST in the context of a software-based, cycle-level simulation of a tiled chip-multiprocessor (CMP). We evaluate FIST's accuracy and performance relative to the CMP simulator's original execution-driven 2D-mesh NoC model. A static FIST approach (trained offine using uniform random synthetic traffic) achieves less than 6% average error in packet latency and up to 43× average speedup for a 16×16 mesh. A dynamic FIST approach that adds periodic online training reduces the average packet latency error to less than 2% and still maintains an average speedup of up to 18× for a 16×16 mesh. Moreover, an FPGA-based realization of FIST can simulate 2D-mesh networks up to 24×24 nodes, at 3 to 4 orders of magnitude speedup over software-based simulators.
An Efficient Pilot Design Scheme for Sparse Channel Estimation in OFDM Systems

This paper investigates the pilot placement problem for sparse channel estimation in orthogonal frequency division multiplexing (OFDM) systems. Prompted by the success of the compressed sensing technique in recovering sparse signals from undersampled measurements, compressed sensing has been successfully applied for pilot-aided sparse channel estimation in OFDM systems to reduce the transmitted overhead. However, the selection of pilot tones significantly affects channel estimation performance. Seeking optimal pilot placement for sparse channel estimation, in the sense of minimum mean-square error of the channel estimation, through an exhaustive search of all possible pilot placements is extremely computationally intensive. To reduce the computational complexity and simultaneously maximize the accuracy of sparse channel estimation, cross-entropy optimization is introduced to determine the optimal pilot placement. Computer simulation results demonstrate that the pilot index sequences obtained using the proposed method performed better compared with those obtained using the conventional equispaced scheme and the random search method.
Evaluation of Optic Nerve Head Using a Newly Developed Stereo Retinal Imaging Technique by Glaucoma Specialist and Non–Expert-Certified Orthoptist

Purpose:To evaluate the reproducibility and interexaminer consistency in analyzing the optic disc parameters using a newly fundus stereoscopic camera, and their correlation with parameters of the Heidelberg Retina Tomograph II (HRT II) was also examined. Methods:This study examined 53 eyes of 53 healthy volunteers (mean age, 21.8 y). Fifty-five eyes of 55 glaucoma patients (mean age, 59.3 y) were also involved. A Nonmyd WX retinal camera was used for stereoscopic fundus imaging. The diagnostic parameters for the optic nerve head analyses were examined under the following conditions: (1) the intraexaminer reproducibility was determined by a certified orthoptist (CO) with 1 year’s experience, with the appropriate coefficient of variation in 8 healthy eyes; and (2) the interexaminer consistency of the diagnostic parameters by both glaucoma specialist and CO was examined in 45 healthy eyes and 55 glaucomatous eyes. By subgroup analysis, the healthy eyes were classified into 2 groups based on the degree of myopia, the optic disc of glaucomatous eye was classified into 4 types: focal ischemic, generalized enlargement, myopic, and senile sclerotic, and also classified into 3 stages (early, moderate, and severe) by Hodapp-Anderson-Parrish scale. (3) The correlation of parameters common to Nonmyd WX and HRT II was examined in 18 eyes of randomly selected patients. Results:The results were as follows: (1) Mean coefficient of variation of 2.6% to 17.6%, with volume parameters considerably lower than the other parameters. (2) In both groups, a high or moderate degree of consistency was obtained (r=0.40 to 0.99; P=0.032 to <0.0001), except only the upper rim width in healthy subjects (r=0.28; P=0.137). In particular, good consistency was obtained in healthy eye with >−3 D of myopia, in glaucoma patients with the generalized type of optic disc and severe glaucomatous stage. (3) A strong correlation with HRT II was obtained only in the cup area and the disc area by both specialist and CO (r=0.75 to 0.90; P=0.0003 to <0.0001). Conclusions:Our studies indicated that most of the parameters were highly reproducible and consistent, and less difference was found between the results obtained by an experienced glaucoma specialist and a non–expert CO in patients with deep cupping and severe eye, but the examiner needs a clear understanding of the criteria for the rim and the cup.
An operational semantics of cache coherent multicore architectures

This paper presents a formal semantics of multicore architectures with private cache, shared memory, and instantaneous inter-core communications. The purpose of the semantics is to provide an operational understanding of how low-level read and write operations interact with caches and main memory. The semantics is based on an abstract model of cache coherence and allows formal reasoning over parallel programs that execute on any given number of cores. We prove correctness properties expressed as invariants for the preservation of program order, data-race free execution of low-level operations, and no access to stale data.
Geometric Evolutionary Dynamics of Protein Interaction Networks

Understanding the evolution and structure of protein-protein interaction (PPI) networks is a central problem of systems biology. Since most processes in the cell are carried out by groups of proteins acting together, a theoretical model of how PPI networks develop based on duplications and mutations is an essential ingredient for understanding the complex wiring of the cell. Many different network models have been proposed, from those that follow power-law degree distributions and those that model complementarity of protein binding domains, to those that have geometric properties. Here, we introduce a new model for PPI network (and thus gene) evolution that produces well-fitting network models for currently available PPI networks. The model integrates geometric network properties with evolutionary dynamics of PPI network evolution.
Combining the multi-agent flood algorithm with frontier-based exploration in search & rescue applications

The Multi-Agent Flood algorithm is an algorithm to control multiple autonomous agents to explore unknown terrain and to find p oints of interest in t he newly uncovered territory. It does so by using a mix of indirect and direct communication. The direct communication via radio signals allows for a faster exchange of data between the agents. This layered communication model allows for a robust data transfer that is needed in SAR scenarios, as the algorithm can still use the indirect part of the model if the direct part is not available anymore. Currently the exploration done by the agents is decided randomly without any intelligent input based on the gathered data. The agents will simply try to move along a line until they will hit an obstacle or a point of interest is found. This work introduces ways to steer the autonomous agents based on the collected data, additionally this data will be used to decide which part of the map should be explored next. Another optimization of the performance is also the increased cooperation between the agents, as the agents will also exchange these destination points, thus reducing the number of agents which will explore the same part of the area, leading to a greater spread of the agents through the terrain.
Influence of Heliobond on Immediate Nanoleakge and Microtensile at Resin-Dentin Interface (An In Vitro Study)

Purpose: The purpose of the present study is to evaluate nanoleakage and microtensile bond strength of different resin composite materials bonded to dentin. Material and methods: Teeth will be divided into three main equal groups according to filling material. Each main equal group will be subdivided into two equal subgroups according to application mode (self-etch vs. Etch and rinse mode) (n=20). Then each subgroup will be further divided in to smaller Subgroups. Subgroup 1: using filtek TM Z250 with G-bond plus (G-aenial) (self-etching mode), then application of hydrophopic resin coating (Heliobond). Subgroup 2: using filtek TM Z250 with G-bond plus (G-aenial) (self-etching mode), without application of hydrophobic resin coating (Helio bond). Subgroup 3: using filtek TM Z250 with G-bond plus (G-aenial) (etch and rinse mode), then application of hydrophobic resin coating (Heliobond). Subgroup 4: using filtek TM Z250 with G-bond plus (G-aenial) (etch and rinse mode), without application of hydrophobic resin coating (Heliobond). Conclusion: An extra hydrophobic layer coating improved the immediate in vitro performance (µTBS and NL) of the universal adhesive systems that studied in SE mode. However, NL pattern is material-dependent and aging stability seems not to be related with the adhesive strategy.
Passivation of Interfaces in Thin Film Solar Cells: Understanding the Effects of a Nanostructured Rear Point Contact Layer

Thin film solar cells based in Cu(In,Ga)Se2 (CIGS) are among the most efficient polycrystalline solar cells, surpassing CdTe and even polycrystalline silicon solar cells. For further developments, the CIGS technology has to start incorporating different solar cell architectures and strategies that allow for very low interface recombination. In this work, ultrathin 350 nm CIGS solar cells with a rear interface passivation strategy are studied and characterized. The rear passivation is achieved using an Al2O3 nanopatterned point structure. Using the cell results, photoluminescence measurements, and detailed optical simulations based on the experimental results, it is shown that by including the nanopatterned point contact structure, the interface defect concentration lowers, which ultimately leads to an increase of solar cell electrical performance mostly by increase of the open circuit voltage. Gains to the short circuit current are distributed between an increased rear optical reflection and also due to electrical effects. The approach of mixing several techniques allows us to make a discussion considering the different passivation gains, which has not been done in detail in previous works. A solar cell with a nanopatterned rear contact and a 350 nm thick CIGS absorber provides an average power conversion efficiency close to 10%.
A novel text classification based on Mahalanobis distance

In text mining field, The KNN (K Nearest Neighbors) is one of the oldest and simplest methods of text classification. But it is known to be sensitive to the distance (or similarity) function used in classifying a test instance, this disadvantage can cause low classification accuracy and limit the KNN classifier's utilization in text classification in text mining. In this paper, we introduce Mahalanobis distance in text classification area, and proposed an algorithm (MDKNN) base on this theory. Experiment show that our method has comparable or better performance than KNN Classifier and Naïve Bayes classifier in text classification.
An Architecture for Multimedia Connection Management

Abstract : What ingredients are needed to enable widespread personal teleconferencing over the Internet and NREN? The major focus of our work in the Multimedia Conferencing Project at ISI is on the design and implementation of protocols at a number of levels in the protocol stack; at the lower levels, real-time data communication services for the Internet in general; and at higher levels, a connection management architecture to facilitate connections among heterogeneous systems. In this paper, we confine our discussion to higher level issues: an overall connection architecture, a connection control protocol, and configuration management. Multimedia, Teleconferencing, Connection architecture, Connection management, Configuration management, Connection control protocol.
The Role of Frontal Lobe White Matter Integrity and Executive Functioning in Predicting Adaptive Functioning in Alzheimer's Disease

Alzheimer’s disease (AD) is the most common form of dementia and is characterized by a gradual deterioration of the patients’ ability to independently perform day to day activities. Researchers have discovered significant changes in neuroanatomy, cognition and behavior that are related to the disease process of AD and researchers continue to uncover new variables, such as the presence of vascular risk factors, which may further increase our ability to understand and characterize the disease. The purpose of this study is to identify the neuroanatomical, cognitive and behavioral variables that best predict impairment of instrumental activities of daily living in individuals with probable AD. Reduced white matter integrity in the dorsolateral prefrontal cortex as well as the presence of vascular risk factors significantly predicted impairments in activities of daily living (ADLs). Executive functioning skills, typically described as frontal lobe system behaviors, were positively associated with ADLs. Further, executive functions fully mediated the relationship between frontal lobe white matter integrity and ADLs. A better understanding of the variables responsible for diminished ADLs in AD will allow researchers and clinicians to better target prevention and intervention strategies and ultimately help individuals with AD to maintain their independence for a longer duration. INDEX WORDS: Executive functions, Neuroanatomy, Neuroimaging, Adaptive functioning, Vascular risk factors THE ROLE OF FRONTAL LOBE WHITE MATTER INTEGRITY AND EXECUTIVE FUNCTIONING IN PREDICTING ADAPTIVE FUNCTIONING IN ALZHEIMER’S DISEASE
Embedding graceful deception system in visual navigation for elderly health care

In the past sensors and surveillance systems were installed in the home environment to capture user activities. However, blind spots exist in areas out of reach of sensors. Obstacles and furniture are some barriers that cause fall down of elderly in the home environment. A motion sensor is mounted on Arduino platform to design a visual navigation system in service robot. Colors and depth of images are used to predict the walking route of elderly and to navigate the service robot. The service robot is functioned to use strategy inferred from fuzzy output to make the elderly detour from any possible collision with barriers. A graceful deception model and fuzzy inference system are proposed in this paper. In case an incident is predicted to happen in the current walking route, the proposed system will calculate the dangerous degree to avoid colliding with obstacles. Experiment results are given to verify the effectiveness of the presented work.