Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification scheme for genes expressed during formation and progression of the avian primitive streak

We have systematically examined the expression patterns of thirteen genes by in situ hybridization during the formation and progression of the avian primitive streak. Based on common patterns of expression, we classify these genes into three distinct groups. Group 1 genes, subdivided into group 1A (Wnt8c, Slug, Vg1, and Nodal) and group 1B (Fgf8, Brachyury, and Cripto), were expressed first in the epiblast and then, throughout most of the length of the primitive streak. Group 2 genes, namely, cNot1, Sonic hedgehog (Shh), Hnf3β and Chordin, were confined to the rostral end of the primitive streak, and then, to Hensen's node. In contrast, Group 3 genes, comprising Goosecoid (GSC) and Crescent, were expressed in the hypoblast. This classification scheme provides a rational basis for categorizing genes expressed during avian gastrulation, and such systematization is likely to provide insight into the relationships among different genes and their potential roles in key events of gastrulation. Anat Rec 262:221–226, 2001. © 2001 Wiley‐Liss, Inc.
Market reaction to bad news: The case of bankruptcy filings

Although there is an extensive literature on the market's anticipation of, and short-term reaction to, the bankruptcy event, the longer-term reaction to Chapter 11 filing has not been properly examined to date. We investigate the subsequent performance of the 351 non-financial, non-utility firms entering into bankruptcy protection between 1979 and 2005, and which continue trading on a major exchange. Consistent with previous research, we find negative abnormal and raw returns both before, and at the Chapter 11 date. However, more importantly, we find a strong, negative and statistically significant post-bankruptcy abnormal return of at least -28% over the 12-month period after the event date. Such market underreaction is consistent with research in other domains suggesting that the market has difficulty in dealing appropriately with extreme bad news events. We also find that the post-Chapter 11 drift is distinct from other reported market anomalies. Potential explanations for our anomalous results are presented.
Classification between normal and adventitious lung sounds using deep neural network

In this paper, a new classification method is proposed to distinguish between normal and adventitious lung sounds. Firstly, using a dual channel electronical stethoscope, the active noise control (ANC) approach is employed to enhance the lung sounds which are subject to noise contamination in practical environment. Secondly, hidden Markov model (HMM) is utilized to characterize normal or adventitious lung sounds, which adopts maximum likelihood approach to calculate the acoustic likelihood for each respiratory phase. Thirdly, a deep neutral network (DNN) estimates the posterior probability of HMM for each observation, instead of the traditional Gaussian mixture model (GMM). And the acoustic input features of DNN consist of Mel frequency cepstral coefficients (MFCCs) extracted from each frame of lung sound samples. To evaluate the proposed DNN-HMM framework for lung sound classification, the recognition rate is compared between proposed method and traditional GMM-HMM approach. The results indicate that the proposed classification method can significantly improve the classification performance.
Novel Circularly Polarized Substrate Integrated Waveguide Slot Antenna By Using A Polarizer Technique

circularly-polarized antenna is built based on new SIW(substrate integrated waveguide) structure which contains cavity-backed resonator and a conventional polarized ring with two square slits in inner and outer ring that differ 90° at position and is proposed for right-handed circular polarization (RHCP) and fabricated in two separate layers. A broadband impedance bandwidth of 13.9% and a RHCP axial ratio of 0.5GHz have been obtained under the condition of less than VSWR ≤2 and axial ratio≤ 3 dB, respectively.
Polymerase chain reaction in the early diagnosis of HIV-1 infection in high risk subjects.

We investigated the presence of the HIV-1 infection using the polymerase chain reaction (PCR) test in seronegative sexual partners of HIV-infected subjects and in children born to seropositive mothers. By using PCR assay, no HIV-1 DNA was detected in 32 female partners of HIV positive patients including three pregnant women who were also studied during pregnancy and after delivery. HIV-1 DNA was found in 12 out of 38 children born to seropositive mothers; five of them also had detectable serum HIV-1 p24 Ag levels. On the whole, our data stress the importance of using a very sensitive technique, i.e. PCR, for the early diagnosis of HIV-1 infection.
Prospects of optimization of energy production by LIDAR assisted control of wind turbines

In the presented work two approaches to increase the energy production of wind turbines are studied assuming the usage of a wind speed measurement provided by a nacelle based LIDAR system: The first approach uses the knowledge of the incoming wind speed to assist variable speed control. The second approach uses the wind direction information measured by a LIDAR system for yaw control. From this first analysis only marginal benefit can be gained by the LIDAR assisted speed control, but an increase of energy production by a couple of percent can be expected by LIDAR assisted yaw control.
A commensal symbiotic factor derived from Bacteroides fragilis promotes human CD39+Foxp3+ T cells and Treg function

Polysaccharide A (PSA) derived from the human commensal Bacteroides fragilis is a symbiosis factor that stimulates immunologic development within mammalian hosts. PSA rebalances skewed systemic T helper responses and promotes T regulatory cells (Tregs). However, PSA-mediated induction of Foxp3 in humans has not been reported. In mice, PSA-generated Foxp3+ Tregs dampen Th17 activity thereby facilitating bacterial intestinal colonization while the increased presence and function of these regulatory cells may guard against pathological organ-specific inflammation in hosts. We herein demonstrate that PSA induces expression of Foxp3 along with CD39 among naïve CD4 T cells in vitro while promoting IL-10 secretion. PSA-activated dendritic cells are essential for the mediation of this regulatory response. When cultured with isolated Foxp3+ Tregs, PSA enriched Foxp3 expression, enhanced the frequency of CD39+HLA-DR+ cells, and increased suppressive function as measured by decreased TNFα expression by LPS-stimulated monocytes. Our findings are the first to demonstrate in vitro induction of human CD4+Foxp3+ T cells and enhanced suppressive function of circulating Foxp3+ Tregs by a human commensal bacterial symbiotic factor. Use of PSA for the treatment of human autoimmune diseases, in particular multiple sclerosis and inflammatory bowel disease, may represent a new paradigm in the approach to treating autoimmune disease.
SWAT Ungauged: Hydrological Budget and Crop Yield Predictions in the Upper Mississippi River Basin

Physically based, distributed hydrologic models are increasingly used in assessments of water resources, best management practices, and climate and land use changes. Model performance evaluation in ungauged basins is an important research topic. In this study, we propose a framework for developing Soil and Water Assessment Tool (SWAT) input data, including hydrography, terrain, land use, soil, tile, weather, and management practices, for the Upper Mississippi River basin (UMRB). We also present a performance evaluation of SWAT hydrologic budget and crop yield simulations in the UMRB without calibration. The uncalibrated SWAT model ably predicts annual streamflow at 11 USGS gauges and crop yield at a four-digit hydrologic unit code (HUC) scale. For monthly streamflow simulation, the performance of SWAT is marginally poor compared with that of annual flow, which may be due to incomplete information about reservoirs and dams within the UMRB. Further validation shows that SWAT can predict base flow contribution ratio reasonably well. Compared with three calibrated SWAT models developed in previous studies of the entire UMRB, the uncalibrated SWAT model presented here can provide similar results. Overall, the SWAT model can provide satisfactory predictions on hydrologic budget and crop yield in the UMRB without calibration. The results emphasize the importance and prospects of using accurate spatial input data for the physically based SWAT model. This study also examines biofuel-biomass production by simulating all agricultural lands with switchgrass, producing satisfactory results in estimating biomass availability for biofuel production.
Anisotropic Diffusion in the Hypercube

Denoising of hyperspectral images in the domain of imaging spectroscopy by vectorial anisotropic diffusion is addressed. Anisotropic diffusion has shown to be a powerful denoising technique with many applications in several fields of image processing, and in the recent years, some significant advances have been published. However, these had not yet been specifically adapted to hyperspectral imagery. This paper reviews recent advances in anisotropic diffusion for multivalued images, analyzes their application to hyperspectral images, and proposes a new diffusion method which takes advantage of the recent improvements and conforms to the specificities of hyperspectral remote sensing. Some examples are provided using both a noisy image and a clean image with added noise
eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data

ABSTRACT The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain23F-1 clonal complex of Streptococcus pneumoniae, “population snapshots” of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.
Analysis of the Optimal Cooperation Scope of Bandwidth Sharing in vehicular networks

This paper investigates the Optimal Cooperation Scope (OCS) for Cooperative Bandwidth Sharing (CBS) in vehicular networks. Three relay schemes based on optimal single path relay and opportunistic relay for multihop CBS are proposed and studied. The OCS is solved as the maximum physical distance or hops between the bandwidth requester and bandwidth helper in the optimal solution to maximize the CBS benefit. OCSs for different environments and with different relay schemes are given in the paper. The results indicate that the OCS is sensitive to the cost weight and may also be larger when using a proper opportunistic relay based scheme than using the optimal single path based one.
F0 peak timing, height, and shape as independent features

A considerable amount of evidence from several intonation languages (e.g., German, English, Italian) supports the idea that F0 peak timing, height, and shape variables form a feature bundle, which is used to encode two-fold intonational (e.g., sentence-level) pitch accent distinctions such as L+H* vs. L*+H. The three types of features in the bundle can be weighted differently but the outcome seems to be functionally equivalent. In this sense, they are ‘substitute phonetic features’. This paper presents data from two distinct prosodic dialect types of Swedish, a pitch-accent language, suggesting that these F0 variables can also be used independently of each other in order to encode two different contrasts (i.e., a three-fold contrast), each of which phonetically and functionally related to the L+H* vs. L*+H distinction in an intonation language. For Central Swedish, we observe two peak raising strategies which go along with differently shaped rises: ‘extending’ (= faster rise) and ‘shifting’ (= slower rise), which tend to be used to signal ‘speaker-related’ emphasis (e.g., ‘surprise’) or ‘messagerelated’ emphasis (e.g., ‘correction’), respectively. For Southern Swedish, we observe an ‘extended’ peak and an ‘extended and delayed’ peak.
Primary Market Design in the Presence of When-Issued Markets

We analyse the pricing and allocation of unseasoned securities by means of mechanisms such as auctions or bookbuilding. Our analysis allows the pricing and allocation rules to be based not only on investors’ bids, but also on information revealed through pre-issue trading of the securities in a when-issued or betting market. The results explain why mechanisms for pricing equity securities typically allow information from pre-issue markets to affect the issue price, while those for pricing Treasuries do not.
Quantifying software test process and product reliability simultaneously

Software reliability models (SRMs) are used to assess software reliability and to control quantitatively software testing. In this paper we consider metrics-based SRMs and tackle a statistical estimation of both software test process and product reliability simultaneously. The basic idea is to apply the Markov-dependent Poisson regression to describe the random testing environment by a discrete-time Markov chain. We formulate four Markov-dependent Poisson regression-based SRMs and develop the EM (expectation-maximization) algorithms to estimate the maximum likelihood estimates of model parameters. Numerical examples with real software project data show that our approach is useful to quantify both of software test process and software product reliability, and can answer the question why the stability of test process can lead to the improvement of software product reliability.
Unsupervised learning of dynamical and molecular similarity using variance minimization

In this report, we present an unsupervised machine learning method for determining groups of molecular systems according to similarity in their dynamics or structures using Ward's minimum variance objective function. We first apply the minimum variance clustering to a set of simulated tripeptides using the information theoretic Jensen-Shannon divergence between Markovian transition matrices in order to gain insight into how point mutations affect protein dynamics. Then, we extend the method to partition two chemoinformatic datasets according to structural similarity to motivate a train/validation/test split for supervised learning that avoids overfitting.
Corn monitoring and crop yield using optical and RADARSAT-2 images

In agriculture, soil and crop conditions change from day to day and throughout the growing season. Agricultural targets also vary spatially with differences observed from field to field, as well as within individual fields. The heterogeneity of corn-growing conditions in Mexico makes accurate data for crop type, crop condition and crop yield prediction difficult to obtain. Yield predictions are needed by the federal government to estimate, ahead of harvest time, the amount of corn required to be imported in order to meet the expected domestic shortfall. In this project a methodology for the estimation of corn yield ahead of harvest time is developed which uses radar and optical remote sensing and which specifically considers the corn-growing situation in Central Mexico. Radar based crop type classification requires data sets with multiple polarizations. Recent research to assess relative classification accuracies of multi-polarized combinations for target crops using airborne data has been reported. In addition to identifying crop type and variety, identifying crop growth stage is valuable. Crop condition, loosely defined as the vigor or health of a crop in a particular growth stage, is related to crop productivity and yield; however, the relationship is complex. Main crop condition indicators include biomass, height, leaf area and contents of plant water, chlorophyll and nitrogen. Crop-type and crop-condition mapping are among the applications that are expected to benefit the most from the technical enhancements embodied by RADARSAT-2. The potential of RADARSAT-1 data for these applications has been rated as "limited", whereas for RADARSAT-2 data this potential is anticipated to be "strong". The Science and Operational Applications Research for RADARSAT-2 Program (SOAR) is promoting the evaluation of Synthetic Aperture Radar (SAR) capabilities by providing images to selected research projects which include the present one.objectives of this project are: a) use RADARSAT-2 data and optical data to determine cultivated areas and monitor crop condition for obtaining better estimations of crop yield; b) obtain polarization signatures from RADARSAT-2 data for corn and relate these to Leaf Area Index and photosynthetic active radiation (PAR) crop parameters and vegetation indexes, to establish indicators of crop condition and produce estimates for crop yield; c) use field data collected for three key corn crop growth stages over 300 pilot plots during 2001-2006, and increase the number of plots to build a database to support accuracy studies using RADARSAT-2 data.The expected benefits of this project are: to obtain knowledge about crop type, crop condition and crop yield with better accuracy than with current methodologies; to support national corn farmers associations; to design agriculture related activities within State agriculture plans; to support the corn product industry and aid government decision making. Relevant results and economical impact will imply operational usage of RADARSAT- 2 data in the agricultural sector in Mexico.
A novel method and system for stereotactic surgical procedures

A novel three-dimension (3-D) augmented reality system using autostereoscopic images was developed for surgical navigation. The 3D images are created by computer reconstruction and the polarized stereo projection system, which provides geometrically accurate 3-D spatial images and reproduces motion parallax with polarized eyeglasses. The spatially projected 3-D images are superimposed onto the surgical area and viewed via two semitransparent mirrors. A set of accurate spatial image registration methods based on the coordinate transformation relationship of the world coordinate system, the CT image coordinate system, the view plane coordinate system of VtkCamera and the image plane coordinate system of projectors were developed for registration of 3D virtual images and corresponding lesion areas. Preliminary phantom experiments showed that the average errors of 4 selected reference points are 1.6548mm, 1.8956mm, 2.5630mm, 2.3560mm (observer' heigh 1650mm) and 1.8648mm, 3.1614mm, 2.3904mm, 2.6416mm (observer' height: 1750mm) which meet the clinical requirement. Trapezium distortion of the projectors is 0.6 pixel distance. The differences of observers' height, interpupillary distance and motion have little effect on the accuracy of registration. Part of the human eye may have automatic focusing function thus increasing the actual registration accuracy.
Dampak Set Peluang Investasi Terhadap Nilai Perusahaan Publik di Bursa Efek Jakarta

The objective of this research is to get an understanding on the effect of investment deciÂ¬sions on value of a company using Structural Equation Model (SEM). It is expected that this model will give more comprehensive analysis on the effect of the investment decisions on value of the fir. This analysis was based on target population of 259 public companies at Jakarta Stock Exchange, with following finding. The investment decision effect on the value of the companies, respectively 12,25%. The theoretical finding on this research can be developed to make an investment decision at stock exÂ¬change. In other words, the investment decision made by companies will have some means of effect on companyâ€™s value compare with other factors. Keywords:Â Â Â structural equation mode, investÂ¬ment opportuÂ¬nity set, return saham, market value
CORBA Security: An Introduction to Safe Computing with Objects

1. Objects and Security. What Are Objects? How Do Objects Send Messages? What Is Security? Protection. Authorization. Accountability. Availability. Assurance. 2. Object Security. Special Object Security Requirements. Naming. Scale. Encapsulation. An Overview of the CORBA Security Model. 3. Policy. Protection and Policy. Subjects. Objects. Actions. Access Control Policy. Message Protection Policy. Audit Policy. Non-Repudiation Policy. 4. Identification, Authentication, and Privilege. Subjects. Authentication and Credentials. Contexts. 5. Access Control. Managing Access Control Policy. The Problem of Scale. Controlling Access Control Policy Scale. Privilege Attributes Are Groups of Subjects. Domains Are Groups of Objects. Required Rights Are Groups of Actions. Enforcing Access Control Policy. The accessDecision Procedure. Combining Policies to Make Access Decisions. 6. Message Protection. Managing Message Protection Policy. Quality of Protection. Defining Message Protection Policy. Enforcing Message Protection Policy. 7. Delegation. The Secure Proxy Problem. Managing Delegation Policy. Enforcing Delegation Policy. 8. Security Auditing. Managing Audit Policy. Event Generation Policy. Enforcing Audit Policy. Audit Decisions. Audit Channels. 9. Non-Repudiation. Disputes, Evidence, and the Burden of Proof. Disputes. Non-Repudiation Evidence. Non-Repudiation Policies. Managing Non-Repudiation Policy. Enforcing Non-Repudiation Policy. Non-Repudiation Credentials. Generating Non-Repudiation Evidence. Arbitrating Disputes Using Non-Repudiation Evidence. Examples of Disputes. Non-Repudiation Service Structures. 10. Questions to Ask Your Secure Object System Vendor. Suggested Reading. Glossary. Index. 0201325659T04062001
Marketing System and Market Integration of Different Egg Markets in Bangladesh

The objectives of the study were to estimate costs and margins, seasonal price variation and to test market integration of egg. Primary and secondary data were used for this study. The higher marketing cost was incurred by aratdars and the lowest by retailer. On the other hand, retailers earned the highest net marketing margins. Analysis of market integration shows that egg market in Bangladesh was well integrated. The study identified some problems related to economic, technical, marketing, social and natural calamities aspects and suggested some measures for solving these problems. Key word s: Engle Granger co-integration, Marketing cost & Margin, Market integration, Egg.