Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting the colloidal nanocrystal library to construct electronic devices

Assembling nanocrystal devices A wide range of materials can be grown as high-quality colloidal nanocrystals, with properties spanning from conductors to semiconductors and insulators. Although these materials have been included in electronic devices, they usually only form a single component within the device. Choi et al. took a variety of solution-processable colloidal nanocrystals to form all of the device components. Through the development of the right materials, interfaces, and processing steps, they constructed an all-colloid field effect transistor. Science, this issue p. 205 Semiconductor devices are constructed solely from a range of colloidal nanocrystals. Synthetic methods produce libraries of colloidal nanocrystals with tunable physical properties by tailoring the nanocrystal size, shape, and composition. Here, we exploit colloidal nanocrystal diversity and design the materials, interfaces, and processes to construct all-nanocrystal electronic devices using solution-based processes. Metallic silver and semiconducting cadmium selenide nanocrystals are deposited to form high-conductivity and high-mobility thin-film electrodes and channel layers of field-effect transistors. Insulating aluminum oxide nanocrystals are assembled layer by layer with polyelectrolytes to form high–dielectric constant gate insulator layers for low-voltage device operation. Metallic indium nanocrystals are codispersed with silver nanocrystals to integrate an indium supply in the deposited electrodes that serves to passivate and dope the cadmium selenide nanocrystal channel layer. We fabricate all-nanocrystal field-effect transistors on flexible plastics with electron mobilities of 21.7 square centimeters per volt-second.
Measurement of information processing load and visual load on a dynamic information processing task

A dynamic visual information processing task was designed to investigate time-based and intensity-based factors on an operator's information processing load as measured by reaction time, pupil diameter, and eye movement parameters. The time-based factor was manipulated by the target rate and scanning rate while the intensity-based factor was manipulated by the difference between a simple reaction task and a physical matching (choice reaction) task. Nine participants tracked the scanning line at two different scanning rates and were required to respond to two designated targets presented singly at two different temporal frequencies. The results indicated that task difficulty (the intensity-based factor) had a significant effect on the reaction time. Target rate and scanning rate were integrated as one time-based factor in terms of three sweeping angles. The time-based factor was found to have a significant effect on the fixation time, saccade amplitude, fixation frequency, eye movement speed, reaction time and hit rate. No interaction effect was found between time-based and intensity-based factors. The time pressure (defined by the time required divided by the time available) based on a model human processor was positively related to scanning rate, target rate and task difficulty. It was found to be the most objective and reliable if time required can be reliably predicted based on a predictive model approach.
Motion correction in optical coherence tomography volumes on a per A-scan basis using orthogonal scan patterns

High speed Optical Coherence Tomography (OCT) has made it possible to rapidly capture densely sampled 3D volume data. One key application is the acquisition of high quality in vivo volumetric data sets of the human retina. Since the volume is acquired in a few seconds, eye movement during the scan process leads to distortion, which limits the accuracy of quantitative measurements using 3D OCT data. In this paper, we present a novel software based method to correct motion artifacts in OCT raster scans. Motion compensation is performed retrospectively using image registration algorithms on the OCT data sets themselves. Multiple, successively acquired volume scans with orthogonal fast scan directions are registered retrospectively in order to estimate and correct eye motion. Registration is performed by optimizing a large scale numerical problem as given by a global objective function using one dense displacement field for each input volume and special regularization based on the time structure of the acquisition process. After optimization, each volume is undistorted and a single merged volume is constructed that has superior signal quality compared to the input volumes. Experiments were performed using 3D OCT data from the macula and optic nerve head acquired with a high-speed ultra-high resolution 850 nm spectral OCT as well as wide field data acquired with a 1050 nm swept source OCT instrument. Evaluation of registration performance and result stability as well as visual inspection shows that the algorithm can correct for motion in all three dimensions and on a per A-scan basis. Corrected volumes do not show visible motion artifacts. In addition, merging multiple motion corrected and registered volumes leads to improved signal quality. These results demonstrate that motion correction and merging improves image quality and should also improve morphometric measurement accuracy from volumetric OCT data.
Pulmonary Microvascular Albumin Leak Is Associated with Endothelial Cell Death in Murine Sepsis-Induced Lung Injury In Vivo

Sepsis is a systemic inflammatory response that targets multiple components of the cardiovascular system including the microvasculature. Microvascular endothelial cells (MVEC) are central to normal microvascular function, including maintenance of the microvascular permeability barrier. Microvascular/MVEC dysfunction during sepsis is associated with barrier dysfunction, resulting in the leak of protein-rich edema fluid into organs, especially the lung. The specific role of MVEC apoptosis in septic microvascular/MVEC dysfunction in vivo remains to be determined. To examine pulmonary MVEC death in vivo under septic conditions, we used a murine cecal ligation/perforation (CLP) model of sepsis and identified non-viable pulmonary cells with propidium iodide (PI) by intravital videomicroscopy (IVVM), and confirmed this by histology. Septic pulmonary microvascular Evans blue (EB)-labeled albumin leak was associated with an increased number of PI-positive cells, which were confirmed to be predominantly MVEC based on specific labeling with three markers, anti-CD31 (PECAM), anti-CD34, and lectin binding. Furthermore, this septic death of pulmonary MVEC was markedly attenuated by cyclophosphamide-mediated depletion of neutrophils (PMN) or use of an anti-CD18 antibody developed for immunohistochemistry but shown to block CD18-dependent signaling. Additionally, septic pulmonary MVEC death was iNOS-dependent as mice lacking iNOS had markedly fewer PI-positive MVEC. Septic PI-positive pulmonary cell death was confirmed to be due to apoptosis by three independent markers: caspase activation by FLIVO, translocation of phosphatidylserine to the cell surface by Annexin V binding, and DNA fragmentation by TUNEL. Collectively, these findings indicate that septic pulmonary MVEC death, putatively apoptosis, is a result of leukocyte activation and iNOS-dependent signaling, and in turn, may contribute to pulmonary microvascular barrier dysfunction and albumin hyper-permeability during sepsis.
Expression and Cellular Localization of Inducible Nitric Oxide Synthase in Lipopolysaccharide-treated Rat Kidneys

Although inducible nitric oxide synthase (iNOS) is known to play significant roles in the kidney, its renal localization has long been controversial. To resolve this issue, the authors identified iNOS-positive cell types in rat kidneys using double immunohistochemistry and confirmed iNOS positivity using enzyme histochemistry with NADPH-diaphorase (NADPH-d) and in situ RT-PCR. Adult male Sprague-Dawley rats were injected intraperitoneally with lipopolysaccharide (LPS) or saline as a control and sacrificed at various time intervals after injection. Quantitative real-time reverse transcriptase polymerase chain reaction showed that iNOS was not expressed in control kidneys but was induced in LPS-treated kidneys. iNOS immunostaining was strongest 6 to 18 hr after injection and decreased gradually to control levels by day 7. Double immunohistochemistry and NADPH-d revealed that iNOS expression was induced in the interstitial cells, glomerular parietal epithelial cells, the proximal part of the short-looped descending thin limb, the upper and middle papillary parts of the long-looped descending thin limb, some inner medullary collecting duct cells, and almost all calyceal and papillary epithelial cells. The present study determines the precise localization of iNOS in LPS-treated rat kidneys and provides an important morphological basis for examining the roles of iNOS in sepsis-induced acute kidney injury.
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures

According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. We present a public database of 2405 refined NMR solution structures [statistical torsion angle potentials (STAP) refinement of the NMR database, http://psb.kobic. re.kr/STAP/refinement] from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analysed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, χ1-χ2 rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research.
A new lithologic classification method for tight sandstone reservoirs based on rock components and logging response characteristics

The original lithology classification method for tight sandstone reservoirs has a low prediction accuracy and it does not accurately reflect reservoir characteristics. We propose a new method that uses thin sections, logging curves, and core physical data to classify the lithology of the Ordos Basin, China. First, the relationship between the rock components and physical properties in the study area was analyzed and we found that quartz and rock debris played an active role in the properties of the reservoir, while feldspar minerals in the reservoir had a negative effect on it. Second, we synthesized the logging response characteristics of various rock components and divided the lithology into (1) high feldspar content, low quartz content, low rock debris content, and (2) low feldspar content, high quartz content, high rock debris content, using ((quartz + rock debris)/feldspar) as an index for lithologic classification. The lithology identification model was established using a support vector machine approach with a regression accuracy of 84.62%. Applying the model to the well in the study area to distinguish the lithology, results were in good agreement with thin section data, the physical properties of the reservoir, and the production capacity. Lithology can effectively reflect reservoir characteristics and play an important guiding role in the identification of reservoirs and the evaluation of productivity.
Memory Intensive Branch-and-Bound Search for Graphical Models

AND/OR search spaces have recently been introduced as a unifying paradigm for advanced algorithmic schemes for graphical models. The main virtue of this representation is its sensitivity to the structure of the model, which can translate into exponential time savings for search algorithms. AND/OR Branch-and-Bound (AOBB) is a new algorithm that explores the AND/OR search tree for solving optimization tasks in graphical models. In this paper we extend the algorithm to explore an AND/OR search graph by equipping it with a context-based adaptive caching scheme similar to good and no-good recording. The efficiency of the new graph search algorithm is demonstrated empirically on various benchmarks, including the very challenging ones that arise in genetic linkage analysis.
A Review on Cocktail Approach for Travel Package Recommendation

One of the important applications in modern computing is to provide better travel services for tourists. This paper provides a study of utilizing online travel information for the personalized travel package recommendation. Many recommender systems lack an organized framework to dynamically incorporate multiple types of additional context information existing in the tourism domain, such as the travel area, season, and price of the travel packages. First we analyze the properties of the previous travel packages and develop a TAST (tourist-area-season-topic) model. This TAST model helps to represent different travel packages and different topic distributions of tourist, taking out of topic is specified on both the tourists and the natural characteristics of the landscapes. According to the topic model representation, a cocktail approach is incepted so that to form lists for personalized travel package recommendation. The TAST model is expanded to the tourist-relation-area-season topic (TRAST) model for collecting the relationships among the tourists for all travel groups. Then analyze both the TAST and TRAST models, and cocktail recommendation approach on the current travel package information TAST model works better than the old recommendation system by adding tourist's relationships as TAST model can effectively catches the unique properties of travel data and cocktail approach, an effective estimation for travel group formation can be done using TRAST model.
A Sensitive Sequence Comparison Method

Biologists highly rely on good algorithms to find the homologous regions in bimolecular sequences. One advanced homology search program, Pat-ternHunter, has been developed in 2002. Unlike the well-known program Blast using a consecutive model, it benefited from gapped (nonconsecu-tive) model to work better. By observing and analyzing some significant properties of gapped-models, we propose a new program, which extends from using single gapped-model to multiple gapped models.
A Scalable XML Access Control System

This paper presents the design of a scalable XML access control system. The system has the following features. First, it can regulate access control at a ne graularity (e.g., at the tag level). Second, it stores XML documents as tables in relational databases. Third, it is eAEcient compared to existing systems as it only examines the relevant data. Fourth, it is scalable as it can handle very large XML documents that may not t into the main memory. Finally, it provides very fast initial response time.
Harvest of Ephemeral Runoff for Artificial Groundwater Recharge in Arid Basin Water Management

Harvest of springtime flow to a playa in Lemmon Valley, north of Reno, was evaluated as a means of increasing local groundwater supplies through artificial recharge. Surface water and groundwater studies in the donor area estimated the long-term harvestable volumes. Hydrogeologic and geochemical models of the receiving area were used to determine the effects of artificial recharge. Costs for the harvest/recharge program were estimated to compare favorably with alternative water supply solutions.
On the impact of packet sampling on Skype traffic classification

Nowadays, traffic classification technology addresses the exciting challenge of dealing with ever-increasing network speeds, which implies more computational load especially when on-line classification is required, but avoiding to reduce classification accuracy. However, while the research community has proposed mechanisms to reduce load, such as packet sampling, the impact of these mechanisms on traffic classification has been only marginally studied. This paper addresses such study focusing on Skype application given its tremendous popularity and continuous expansion. Skype, unfortunately, is based on a proprietary design, and typically uses encryption mechanisms, making the study of statistical traffic characteristics and the use of Machine Learning techniques the only possible solution. Consequently, we have studied Skypeness, an open-source system that allows detecting Skype at multi-10Gb/s rates applying such statistical principles. We have assessed its performance applying different packet sampling rates and policies concluding that classification accuracy is significantly degraded when packet sampling is applied. Nevertheless, we propose a simple modification in Skypeness that lessens such degradation. This consists in scaling the measured packet interarrivals used to classify according to the sampling rate, which has resulted in a significant gain.
Clustered Elias-Fano Indexes

State-of-the-art encoders for inverted indexes compress each posting list individually. Encoding clusters of posting lists offers the possibility of reducing the redundancy of the lists while maintaining a noticeable query processing speed. In this article, we propose a new index representation based on clustering the collection of posting lists and, for each created cluster, building an ad hoc reference list with respect to which all lists in the cluster are encoded with Elias-Fano. We describe a posting lists clustering algorithm tailored for our encoder and two methods for building the reference list for a cluster. Both approaches are heuristic and differ in the way postings are added to the reference list: according to their frequency in the cluster or according to the number of bits necessary for their representation. The extensive experimental analysis indicates that significant space reductions are indeed possible, beating the best state-of-the-art encoders.
A Split-Luciferase Reporter Recognizing GFP and mCherry Tags to Facilitate Studies of Protein–Protein Interactions

The use of fluorescently-tagged proteins in microscopy has become routine, and anti-GFP (Green fluorescent protein) affinity matrices are increasingly used in proteomics protocols. However, some protein–protein interactions assays, such as protein complementation assays (PCA), require recloning of each protein as a fusion with the different parts of the complementation system. Here we describe a generic system where the complementation is separated from the proteins and can be directly used with fluorescently-tagged proteins. By using nanobodies and performing tests in cell-free expression systems, we accelerated the development of multiple reporters, detecting heterodimers and homodimers or oligomers tagged with GFP or mCherry. We demonstrate that the system can detect interactions at a broad range of concentrations, from low nanomolar up to micromolar.
Calculation of the Deviatoric Stress Field in New Zealand

I model the vertically averaged deviatoric stress field for New Zealand using velocity and crustal density data. I use a thin sheet model of a viscously deforming lithosphere, averaging over a depth of 100 km and solve the stress balance equation. Two methods of solving the stress balance equation are compared: one method solves first for deviatoric stresses due to gravitational potential energy per unit volume before accounting for deviatoric stresses due to boundary conditions; the other method assumes an isotropic viscosity to relate deviatoric stress to strain rate, solving for the viscosity field. Under synthetic testing, the two step method is able to cope with high levels of noise but contains edge effects. The method solving for viscosity is accurate at low noise levels, however, it is unreliable at high noise levels. I apply the two step method to New Zealand using a Quaternary and a GPS-derived velocity model. Vertically averaged deviatoric stress magnitudes are found to be 10-30 MPa, similar to magnitudes found for other plate-boundary zones. Gravitational and boundary stresses each account for approximately half of the full deviatoric stress. Effective viscosities are found to be 1-10×10²¹ Pa s in the regions of most active deformation, which can be interpreted in terms of the long term strength of the lithosphere controlled by temperature and/or lithology.
A probabilistic model for stuck-on faults in combinational logic gates

Reliability in advanced CMOS devices is a critical issue that can supersede the benefits of technology shrinking process. The Probabilistic Transfer Matrix (PTM) is the basis of more common reliability evaluation models. This work presents a probabilistic model for stuck-on faults in combinational logic gates, considering the individual fault probability of each logic function input vector. It shows that considering the same fault probability for all input vectors underestimates the input influence on the gate reliability. These probabilities can be used as inputs in PTM models to provide results that are more accurate and increase the circuit reliability.
Two functional psbD genes in the cyanobacterium Synechococcus sp. strain PCC 7942

The cyanobacterium Synechococcus sp. strain PCC 7942 has two copies of the psbD gene which encodes the D2 polypeptide of the photosystem II (PSII) reaction center. One of the genes, psbDI, overlaps the open reading frame of another photosystem II gene, psbC; the psbDII gene is monocistronic. Gene inactivation experiments had previously shown that psbDII is dispensable under normal laboratory growth conditions. However, similar experiments with psbDI never produced viable psbDI-inactivated mutants, presumably because psbC expression depends on transcription through psbDI. The experiments described here were designed to assess the need for psbDI independent of the need for expression of psbC. A strain, AMC027, was engineered in which a second copy of psbC was expressed from the psbDII locus. Northern (RNA) blot analysis confirmed that both psbDI and psbDII gave rise to dicistronic messages containing psbC sequences in AMC027. In this genetic background, it was possible to inactivate psbDI, creating strain AMC050 and indicating that the psbDII gene is functional. Western immunoblot analysis showed that the products of psbD and psbC, the PSII proteins D2 and CP43, respectively, were present in thylakoids of AMC050, but at reduced levels relative to the wild type, the mutant AMC027, and two psbDII-inactivated mutants. AMC050 consistently formed small colonies on plates and competed poorly in mixed-culture experiments. This suggested that, although not essential for viability, expression from the psbDI locus is required to produce sufficient D2 and CP43 for optimal growth.