Miracle-dz/UniFAR-FTUs huggingface dataset:
Wildland Fire and Chaparral Succession Along the California-Baja California Boundary

Theunited States-Mexico international bound- ary from El Paso, Texas to the Pacific Coast shows clear differences in plant communities that were homogeneous prior to being split by a continuous fence at the turn of the century. This study evaluates how disparate fire regimes in California (fire suppression) and northern Baja Cali- fornia (little or no fire control) have influenced succes- sion in the chamise (Adenostoma fasciculatum) chaparral communities spanning the international boundary be- tween the border towns of JacumC and Tecate. Fire history was reconstructed using U.S. Forest Service fire maps and repeat aerial photography. Once plotted onto topographic maps and dated, the bums were divided into age-classes and sampled using 50 m point-quarter transects to develop successional chronosequences. Although fires are more frequent and smaller on the Mexican side of the border, our repeat photographs of the boundary monument markers together with field samples show that chaparral succession is similar across the international boundary in species composition, stem densities, and average mass shrub height. Chamisechaparral appears to be stable under disparate fire regimes because sprouting habits and latent seed pools permit efficient stand estab- lishment under either short or long fire intervals. Chap- arral recovery during the period examined here is unre- lated to fire size because recolonization of bums by long- range seed dispersal is not a trait of the majority of the local shrub species and the shrubs either resprout or germinate from soil seed reservoirs.
Structural Characterization of Interaction between Human Ubiquitin-specific Protease 7 and Immediate-Early Protein ICP0 of Herpes Simplex Virus-1*

Background: Herpesvirus infection is dependent upon the viral E3 ligase ICP0 and its interaction with the human deubiquitinating enzyme USP7. Results: The interaction between USP7 and ICP0 was structurally characterized using solution NMR. Conclusion: ICP0 is recognized by ubiquitin-like domains 1 and 2 (UBL12) of the USP7. Significance: Details of the USP7/ICP0 interaction provide new insights into function of the USP7 ubiquitin-like domains. Human ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that prevents protein degradation by removing polyubiquitin chains from its substrates. It regulates the stability of a number of human transcription factors and tumor suppressors and plays a critical role in the development of several types of cancer, including prostate and small cell lung cancer. In addition, human USP7 is targeted by several viruses of the Herpesviridae family and is required for effective herpesvirus infection. The USP7 C-terminal region (C-USP7) contains five ubiquitin-like domains (UBL1–5) that interact with several USP7 substrates. Although structures of the USP7 C terminus bound to its substrates could provide vital information for understanding USP7 substrate specificity, no such data has been available to date. In this work we have demonstrated that the USP7 ubiquitin-like domains can be studied in isolation by solution NMR spectroscopy, and we have determined the structure of the UBL1 domain. Furthermore, we have employed NMR and viral plaque assays to probe the interaction between the C-USP7 and HSV-1 immediate-early protein ICP0 (infected cell protein 0), which is essential for efficient lytic infection and virus reactivation from latency. We have shown that depletion of the USP7 in HFF-1 cells negatively affects the efficiency of HSV-1 lytic infection. We have also found that USP7 directly binds ICP0 via its C-terminal UBL1–2 domains and mapped the USP7-binding site for ICP0. Therefore, this study represents a first step toward understanding the molecular mechanism of C-USP7 specificity toward its substrates and may provide the basis for future development of novel antiviral and anticancer therapies.
Optimal Design of New Cascaded Switch-Ladder Multilevel Inverter Structure

In this paper, a new cascade switch-ladder multilevel inverter topology is presented which can generate a large number of output voltage levels. First, a fundamental switch-ladder multilevel inverter structure is described. Then, the structure of recommended cascade topology based on series connection of fundamental switch-ladder topologies is presented. To generate maximum number of levels with minimum number of switching elements, dc sources, and voltage on switches, the proposed cascade topology is optimized. Comparison results prove that the presented cascade topology requires fewer numbers of components. Also, the value of voltage rating on switches is less than other structures. Experimental results for two topologies are analyzed to verify the performance of the proposed topology.
Randomized trial showing efficacy and safety of twice‐daily remogliflozin etabonate for the treatment of type 2 diabetes

We compared the efficacy of twice‐daily doses of remogliflozin etabonate (RE) and once‐daily pioglitazone with placebo for reduction in glycated haemoglobin (HbA1c) concentration. In this 12‐week, double‐blind, randomized, active‐ and placebo‐controlled trial, 336 treatment‐naïve subjects with type 2 diabetes and an HbA1c of 7.0–9.5% (53–80 mmol/mol) were randomized to RE (50, 100, 250, 500 or 1000 mg twice daily), matching placebo or 30 mg pioglitazone once daily. The primary endpoint was change in HbA1c from baseline. Other endpoints included changes in body weight, lipid levels, safety and tolerability. RE produced a decreasing dose response in HbA1c at week 12 (p < 0.001), with reductions in HbA1c versus placebo ranging from 0.64 to 1.07% (p < 0.001). Statistically significant reductions in body weight for RE compared with placebo were also observed. Twice‐daily RE resulted in a dose‐ordered improvement in glycaemic control and was generally well tolerated.
Pattern Recognition of Genomic Features with Microarrays: Site Typing of Mycobacterium Tuberculosis Strains

Mycobacterium tuberculosis (M. tb.) strains differ in the number and locations of a transposon-like insertion sequence known as IS6110. Accurate detection of this sequence can be used as a fingerprint for individual strains, but can be difficult because of noisy data. In this paper, we propose a non-parametric discriminant analysis method for predicting the locations of the IS6110 sequence from microarray data. Polymerase chain reaction extension products generated from primers specific for the insertion sequence are hybridized to a microarray containing targets corresponding to each open reading frame in M. tb. To test for insertion sites, we use microarray intensity values extracted from small windows of contiguous open reading frames. Rank-transformation of spot intensities and first-order differences in local windows provide enough information to reliably determine the presence of an insertion sequence. The nonparametric approach outperforms all other methods tested in this study.
Shadow correction in high dynamic range images for generating orthophotos

High dynamic range imagery is widely used in remote sensing. With the widespread use of aerial digital cameras such as the DMC, ADS40, RMK-D, and UltraCamD, high dynamic range imaging is generally expected for generating minuteness orthophotos in digital aerial photogrammetry. However, high dynamic range images (12-bit, 4,096 gray levels) are generally compressed into an 8-bit depth digital image (256 gray levels) owing to huge amount of data and interface with peripherals such as monitors and printers. This means that a great deal of image data is eliminated from the original image, and this introduces a new shadow problem. In particular, the influence of shadows in urban areas causes serious problems when generating minuteness orthophotos and performing house detection. Therefore, shadow problems can be solved by addressing the image compression problems. There is a large body of literature on image compression techniques such as logarithmic compression and tone mapping algorithms. However, logarithmic compression tends to cause loss of details in dark and/or light areas. Furthermore, the logarithmic method intends to operate on the full scene. This means that high-resolution luminance information can not be obtained. Even though tone mapping algorithms have the ability to operate over both full scene and local scene, background knowledge is required. To resolve the shadow problem in digital aerial photogrammetry, shadow areas should be recognized and corrected automatically without the loss of luminance information. To this end, a practical shadow correction method using 12-bit real data acquired by DMC is investigated in this paper.
EFFECTS OF STATSGO AND SSURGO AS INPUTS ON SWAT MODEL'S SNOWMELT SIMULATION 1

ABSTRACT: Soil data comprise a basic input of SWAT (Soil and Water Assessment Tool) for a watershed application. For watersheds where site specific soil data are unavailable, the two U.S. Department of Agriculture (USDA) soil databases, the State Soil Geographic (STATSGO) and Soil Survey Geographic (SSURGO) databases, may be the best alternatives. Although it has been noted that SWAT models using the STATSGO and SSURGO data may give different simulation results for water, sediment, and agricultural chemical yields, information is scarce on the effects of using these two databases in predicting streamflows that are predominantly generated from melting snow in spring. The objective of this study was to assess the effects of using STATSGO versus SSURGO as an input for the SWAT model's simulation of the streamflows in the upper 45 percent of the Elm River watershed in eastern North Dakota. Designating the model as SWAT‐STATSGO when the STATSGO data were used and SWAT‐SSURGO when the SSURGO data were used, SWAT‐STATSGO and SWAT‐SSURGO were separately calibrated and validated using the observed daily streamflows. The results indicated that SWAT‐SSURGO provided an overall better prediction of the discharges than SWAT‐STATSGO, although both did a good and comparable job of predicting the high streamflows. However, SWAT‐STATSGO predicted the low streamflows more accurately and had a slightly better performance during the validation period. In addition, the discrepancies between the discharges predicted by these two SWAT models tended to be larger at upstream locations than at those farther downstream within the study area.
The Fault Location of Optical Cable for Communications Based on GIS

GIS (Geographical Information System) is an information system to acquire, store, manage, describe and analyze the concerned spatial and geographical data of the global surface. GIS is introduced to the optical cable for communications fields such as maintenance, resources management and construction. For communications cable fault location is difficult to assign, the efficiency of maintenance is low and other issues, we design a fault location algorithm based on GIS, which can point the fault of optical cable rapidly and accurately. In this paper, according to basic working principle of OTDR, specific characteristics and requirements of cable optical communications for maintenance, we establish a GIS system of a fiber optic cable, in order to realize informationization of fiber optical cable maintenance and improve the maintenance efficiency of fiber optic cable.
Image processing techniques for wafer defect cluster identification

Electrical testing determines whether each die on a wafer functions as originally designed. But these tests don't detect all the defective dies in clustered defects on the wafer, such as scratches, stains, or localized failed patterns. Although manual checking prevents many defective dies from continuing on to assembly, it does not detect localized failure patterns-caused by the fabrication process-because they are invisible to the naked eye. To solve these problems, we propose an automatic, wafer-scale, defect cluster identifier. This software tool uses a median filter and a clustering approach to detect the defect clusters and to mark all defective dies. Our experimental results verify that the proposed algorithm effectively detects defect clusters, although it introduces an additional 1% yield loss of electrically good dies. More importantly, it makes automated wafer testing feasible for application in the wafer-probing stage.
Finding Place in Making Connections Communities: Applying GIS to Residents’ Perceptions of Their Neighborhoods

The growing recognition that place matters has led to numerous foundation- and government-sponsored initiatives that address the needs of disadvantaged neighborhoods and families in tandem. Fundamental to these people-based and place-based strategies is the assumption that residents are both the beneficiaries and the cocreators of improvements in their neighborhoods and the systems that serve them. However, despite the centrality of place in these community initiatives, defining neighborhoods as they are experienced by residents has proven challenging. This paper demonstrates how a household survey can be used to ascertain residents’ views of the place they refer to as their neighborhood. The study uses data from the Making Connections (MC) target areas in 10 cities. A representative sample of households were asked the name of their neighborhoods and instructed on how to draw maps of their neighborhoods as they viewed them. GIS tools were used to uncover spaces within the MC target areas that residents included in their definitions of neighborhood as well as spaces that seemed to fall outside their collective definitions. The study revealed several overlapping areas that constituted resident-defined neighborhoods within most Making Connections target areas. The paper discusses the implications of this diversity of resident neighborhood perceptions for community change initiatives.
Numerical condition of feedforward networks with opposite transfer functions

Numerical condition affects the learning speed and accuracy of most artificial neural network learning algorithms. In this paper, we examine the influence of opposite transfer functions on the conditioning of feedforward neural network architectures. The goal is not to discuss a new training algorithm nor error surface geometry, but rather to present characteristics of opposite transfer functions which can be useful for improving existing or to develop new algorithms. Our investigation examines two situations: (1) network initialization, and (2) early stages of the learning process. We provide theoretical motivation for the consideration of opposite transfer functions as a means to improve conditioning during these situations. These theoretical results are validated by experiments on a subset of common benchmark problems. Our results also reveal the potential for opposite transfer functions in other areas of, and related to neural networks.
Scalable Anonymous Communication with Provable Security

A key problem in Tor's architecture is that it requires users to maintain a global view of the system, which will become costly as the size of the network increases. Several peer-to-peer approaches have been proposed in order to alleviate the scalability concerns of the Tor network, but they are only able to provide heuristic security; in fact, the security community has been quite successful at breaking the state of the art systems using both passive and active attacks. In this paper, we explore new primitives for scalable anonymous communication, with a focus on providing provable security guarantees. First, we propose a new approach for secure peer-to-peer anonymous communication based on a reciprocal neighbor policy. Secondly, we propose PIR-Tor, a client-server scalable architecture for anonymous communications based on Private Information Retrieval.
An Effective Question Expanding Method for Question Classification in cQA services

This paper introduces a new question expanding method for question classification in cQA services. Input questions are mostly generated by a small size of text in the cQA services, and test inputs consist of only a question whereas training data do a pair of question and answer. Thus, the input questions cannot provide enough information for good classification in many cases. To solve this problem, we propose the question expanding method by pseudo relevant feedback and automatic answer generation. For pseudo relevant feedback, we first find relevant question-answer pairs related to an input question using the Indri search engine, and then top relevant words are chosen as expanded words. The automatic answer generation tries to create pseudo answers by adding question-related words using translation probabilities from questions to answers by Giza++. As a result, we obtain the significant improved performances when two approaches are effectively combined.
A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants

The Golden Gate (GG) modular assembly approach offers a standardized, inexpensive and reliable way to ligate multiple DNA fragments in a pre-defined order in a single-tube reaction. We developed a GG based toolkit for the flexible construction of binary plasmids for transgene expression in plants. Starting from a common set of modules, such as promoters, protein tags and transcribed regions of interest, synthetic genes are assembled, which can be further combined to multigene constructs. As an example, we created T-DNA constructs encoding multiple fluorescent proteins targeted to distinct cellular compartments (nucleus, cytosol, plastids) and demonstrated simultaneous expression of all genes in Nicotiana benthamiana, Lotus japonicus and Arabidopsis thaliana. We assembled an RNA interference (RNAi) module for the construction of intron-spliced hairpin RNA constructs and demonstrated silencing of GFP in N. benthamiana. By combination of the silencing construct together with a codon adapted rescue construct into one vector, our system facilitates genetic complementation and thus confirmation of the causative gene responsible for a given RNAi phenotype. As proof of principle, we silenced a destabilized GFP gene (dGFP) and restored GFP fluorescence by expression of a recoded version of dGFP, which was not targeted by the silencing construct.
Parallel Code for One-sided Jacobi-Method

One sided block Jacobi algorithm for the singular value decomposition (SVD) of matrix can be a method of choice to compute SVD efficiently and accurately in parallel. A given matrix is logically partitioned into block columns and is subjected to an iteration process. In each iteration step, for given two block columns, their Gram matrix is generated, its symmetric eigenvalue decomposition (EVD) is computed and the update of block columns by matrix-matrix multiplication is performed. Another possibility is to omit the generation of Gram matrix and the update, so that there is no matrix-matrix multiplication at all. A local matrix is formed by the two block columns. We can compute its QR decomposition first to reduce the dimension and decrease the off-diagonal norm, and the one-sided serial Jacobi SVD is called (either for a local matrix or its R-factor). Since the matrix coming out from the one-sided Jacobi SVD algorithm is the same as the original matrix after update, we are done. Crucial for this new approach is an efficient implementation of the QR decomposition for tall and skinny matrices as well as a fast and accurate (serial) one-sided Jacobi SVD algorithm. Another improvement of the algorithm would be to replace the static (fixed) local stopping criterion in the inner EVD or SVD computations by the dynamic (flexible) one to reduce the work done by these routines in one parallel iteration step. Since the orthogonality of columns is crucial at the end of the algorithm, one could progressively set the local stopping criterion as the computation proceeds. We tried to implement the proposed approaches and compare the achieved results with the standard algorithm.
KiF: a stateful SIP fuzzer

With the recent evolution in the VoIP market, where more and more devices and services are being pushed on a very promising market, assuring their security becomes crucial. Among the most dangerous threats to VoIP, failures and bugs in the software implementation will still rank high on the list of vulnerabilities. In this paper we address the issue of detecting such vulnerabilities using a stateful fuzzer. We describe an automated attack approach capable to self-improve and to track the state context of a target device. We implemented our approach and were able to discover vulnerabilities in market leading and well known equipments and software.
Semi‐distributed flood runoff model at the subcontinental scale for southwestern Iran

Rainfall–runoff modelling, as a surface hydrological process, on large‐scale data‐poor basins is currently a major topic of investigation that requires the model parameters be identified by using basin physical characteristics rather than calibration. This paper describes the application of the TOPMODEL framework accompanied by a kinematic wave model to the Karun River sub‐basins in southwestern Iran with just one conceptual parameter for calibration. ISLSCP1, HYDRO1K and Reynolds data sets are presented in a geographical information system and used as data sources for meteorological information, hydrological features and soil characteristics of the study area respectively. The results show that although the model developed can adequately predict flood runoff in the catchment with only one calibrated parameter, it is suggested that the effect of surface reservoirs be considered in the proposed model. Copyright © 2007 John Wiley & Sons, Ltd.
Adaptive LDPC codes for MIMO transceiver with adaptive spectral efficiency

By using a multi-rate low density parity check (LDPC) code, we propose an LDPC coded multiple-input multiple-output (MIMO) transceiver with adaptive spectral efficiency which allows data transmission in wireless networks at rates near the channel capacity with arbitrarily low probability of error. Equipped with multiple transmit and multiple receiver antennae, the proposed LDPC coded MIMO transceiver can maximize either coding gain with space-time diversity technique or channel capacity with space-time multiplexing technique. Since the proposed multi-rate LDPC code is constructed based on a single master parity check matrix using a row-removing approach, a single universal encoder (decoder) suffices to handle all rates. Thus, the proposed approach makes the proposed scheme feasible in a subscriber station, such as a cellular phone, to maximize the total channel capacity with a guaranteed quality-of-service. The simulation results indicate that an LDPC coded MIMO transceiver with a spectral efficiency of 1, 2, 3, 4, and 5 bits/symbol/Hz can achieve extremely reliable transmission in a Rayleigh fading channel at the signal-to-noise ratio (SNR) per bit of -2.5, 0.25, 2, 4.75, and 6.5 dB, respectively, when two transmit and two receiver antennae are used for space-time diversity.
Performance comparison of turbo codes with LDPC codes and with BCH codes for forward error correcting codes

In the field of communication, one of the most thriving and prevalent subject is the channel coding. Channel coding generally deals with the bandwidth which is the bit-rate or information storage capacity. It is a technical field which relies heavily on cost. In fact, it is undeniable that cost is the most crucial element in every system. Nowadays, together with the latency or time element which is also an equally significant factor, especially in mobile communication. The objective of this paper is to analyse and compare distinctively the three types of codes namely, turbo codes, LDBC codes and BCH codes, all simulated respectively in MATLAB environment. According to the conducted studies, it is evident that the BCH codes are excellent in performance compared to other codes. The turbo code, despite requiring maximum processing to decode the message has fairly good performance as well. Regardless of the level of processing, all the codes possess good & reliable performances compared to other codes.