Miracle-dz/UniFAR-FTUs huggingface dataset:
Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.
A Bayesian Approach to Diffusion Models of Decision-Making and Response Time

We present a computational Bayesian approach for Wiener diffusion models, which are prominent accounts of response time distributions in decision-making. We first develop a general closed-form analytic approximation to the response time distributions for one-dimensional diffusion processes, and derive the required Wiener diffusion as a special case. We use this result to undertake Bayesian modeling of benchmark data, using posterior sampling to draw inferences about the interesting psychological parameters. With the aid of the benchmark data, we show the Bayesian account has several advantages, including dealing naturally with the parameter variation needed to account for some key features of the data, and providing quantitative measures to guide decisions about model construction.
Alteration of Cellular and Humoral Immunity by Mutant p53 Protein and Processed Mutant Peptide in Head and Neck Cancer

Purpose: To determine if serologic recognition of p53 mutations at the protein level depends upon the ability of mutant p53 to express new peptide epitopes that bind to human leukocyte antigen (HLA) class II molecules, we used anti-p53 antibody production as a marker for HLA class II–restricted T-cell involvement in head and neck cancer. Experimental Design: An anti-p53 antibody response was correlated with specific p53 mutations and the patients' HLA class II alleles and haplotypes. HLA binding studies and in vitro stimulation (IVS) of peripheral blood mononuclear cells were done using a mutant versus wild-type HLA-DQ7-binding p53 peptide. Results: Certain HLA-DQ and HLA-DR alleles were frequently present in p53 seropositive patients who produced serum anti-p53 antibodies. Selected mutated p53 peptides fit published allele-specific HLA class II binding motifs for the HLA-DQ7 or HLA-DR1 molecules. Moreover, a mutant p53 peptide bound with a 10-fold greater affinity than the wild-type p53 peptide to HLA-DQ7 molecules. IVS of CD4+ T cells from seven healthy HLA-DQ7+ donors using this mutant p53 peptide (p53220C) was associated with a partial T helper type 2 phenotype compared with IVS using the wild-type p53210-223 peptide. Conclusions: Our results support the hypothesis that mutated p53 neoantigens can bind to specific HLA class II molecules, leading to a break in tolerance. This may lead to skewing of the CD4+ T lymphocyte response toward a tumor-permissive T helper type 2 profile in head and neck cancer patients, as manifested by seropositivity for p53.
A High-Density SNP Map for Accurate Mapping of Seed Fibre QTL in Brassica napus L

A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape) was constructed in a late-generation recombinant inbred line (RIL) population, using genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL), cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.
Design, Fabrication, and Testing of an Electrohydrodynamic Ion-drag Micropump

—This paper presents the design, fabrication, and testing of a novel electrohydrodynamic (EHD) ion-drag mi-cropump. In order to maximize the electrical field gradients that are responsible for EHD pumping, we incorporated three-dimensional (3-D) triangular bumps of solder as part of the EHD electrodes. To form these bumps, Niobium was sputter-deposited onto a ceramic substrate, coated with photoresist, optically exposed and etched using a reactive ion etcher to define the electrode pattern. The substrate was then " dipped " into a molten solder pool. Since the solder adheres only to the metallic film, bumps of solder form on the electrodes, giving the electrodes a significant 3-D character. The overall dimensions of the micropump are 19 mm 32 mm 1.05 mm. Four different designs were fabricated and tested. Static pressure tests were performed with a 3M Thermal Fluid (HFE-7100) as the working fluid and the optimum design was identified. The results with the thermal fluid were highly promising and indicated a pumping head of up to 700 Pa at an applied voltage of 300 V. The experimental results for the four different designs show that the presence of the 3-D bump structures significantly improves the pumping performance. Also, a much better pumping performance was obtained with the micropump in which the emitter had a saw-tooth shape. [816]
Effect of dowel length on the retention of 2 different prefabricated posts.

OBJECTIVE To compare in vitro the retentive values of stainless steel, parallel-sided posts to quartz-fiber, tapered posts for 2 different dowel lengths (5 and 10 mm). METHOD AND MATERIALS Both post systems were cemented with a dual-cure adhesive resin cement. Single-rooted extracted human teeth (n = 40) were decoronated and randomly divided into 4 groups of 10 samples each. Posts of 5 and 10 mm in length were luted with the resin cement. Each sample was placed on a universal testing machine, and using a push-out method, a vertical load was applied at a crosshead speed of 2 mm/min. The amount of force required to dislodge the post was recorded. The effect of post type and length was evaluated using a 2-way analysis of variance. RESULTS A statistically significant main effect was found for post length (P <.001), with the 10-mm posts of both post systems requiring greater force to dislodge than the 5-mm posts. There was no interaction between post length and post type (P >.05). CONCLUSION It is concluded from this study that there is no statistical difference in retention between quartz-fiber, tapered posts and stainless steel, parallel-sided posts when they are cemented with the same resin cement (P >.05). The study also concludes that adequate retentive values are achieved with both post systems at the shorter, 5-mm post length.
Favorite Folders: A Configurable, Scalable File Browser

Microsoft Windows Explorer, the most widely used file browser in Microsoft Windows, shows almost all directories in the file system. However, most users usually access only a subset of the directories in their machine. If the file browser shows only the directories users are interested in, they can select the directory they want more easily and quickly. This paper introduces a configurable, scalable file system explorer that reduces selection time by showing only the directories users want to see. We give users an easy way to hide directories behind a special ellipsis node. In addition, those hidden directories are one click away. We present a preliminary field study conducted to validate the concept of Favorite Folders and a theoretical model to predict the performance times.
Doubly-Attentive Decoder for Multi-modal Neural Machine Translation

We introduce a Multi-modal Neural Machine Translation model in which a doubly-attentive decoder naturally incorporates spatial visual features obtained using pre-trained convolutional neural networks, bridging the gap between image description and translation. Our decoder learns to attend to source-language words and parts of an image independently by means of two separate attention mechanisms as it generates words in the target language. We find that our model can efficiently exploit not just back-translated in-domain multi-modal data but also large general-domain text-only MT corpora. We also report state-of-the-art results on the Multi30k data set.
Children and Video Games: Addiction, Engagement, and Scholastic Achievement

The aim of this study is to assess the relationship between video gaming habits and elementary school students' academic performance. More specifically, we seek to examine the usefulness of a distinction between addiction and high engagement and assess the predictive validity of these concepts in the context of scholastic achievement. Three hundred thirty-three children ages 8 to 12 years from two primary schools in Singapore were selected to participate in this study. A survey utilizing Danforth's Engagement-Addiction (II) scale and questions from DSM-IV was used to collect information from the schoolchildren, while their grades were obtained directly from their teachers. The findings indicate that addiction tendencies are consistently negatively related to scholastic performance, while no such relationship is found for either time spent playing games or for video game engagement. The implications of these findings are discussed.
Relaxation of Adaptive Evolution during the HIV-1 Infection Owing to Reduction of CD4+ T Cell Counts

Background The first stages of HIV-1 infection are essential to establish the diversity of virus population within host. It has been suggested that adaptation to host cells and antibody evasion are the leading forces driving HIV evolution at the initial stages of AIDS infection. In order to gain more insights on adaptive HIV-1 evolution, the genetic diversity was evaluated during the infection time in individuals contaminated by the same viral source in an epidemic cluster. Multiple sequences of V3 loop region of the HIV-1 were serially sampled from four individuals: comprising a single blood donor, two blood recipients, and another sexually infected by one of the blood recipients. The diversity of the viral population within each host was analyzed independently in distinct time points during HIV-1 infection. Results Phylogenetic analysis identified multiple HIV-1 variants transmitted through blood transfusion but the establishing of new infections was initiated by a limited number of viruses. Positive selection (dN/dS>1) was detected in the viruses within each host in all time points. In the intra-host viruses of the blood donor and of one blood recipient, X4 variants appeared respectively in 1993 and 1989. In both patients X4 variants never reached high frequencies during infection time. The recipient, who X4 variants appeared, developed AIDS but kept narrow and constant immune response against HIV-1 during the infection time. Conclusion Slowing rates of adaptive evolution and increasing diversity in HIV-1 are consequences of the CD4+ T cells depletion. The dynamic of R5 to X4 shift is not associated with the initial amplitude of humoral immune response or intensity of positive selection.
The plasma vitamin B12 binding substance. I. Its detection in the seromucoid fraction of plasma from normal subjects and patien with chronic myelocytic leukemia.

In vivo labeling. After overnight fasts, patients were given 0.57 ,ug. of Co"B,, by mouth and fed one hour later. Blood samples were withdrawn into heparinized syringes at three hour intervals up to 12 hours, then at 24 and 36 hours. After assaying the radioactivity in 4 ml. of whole plasma from each sample, 10 to 20 ml. of plasma from the sample having the highest cpm was fractionated according to the previously described methods. The cpm in each fraction were expressed as the per cent of cpm present in whole plasma.
Regulation of cytokine production by soluble CD23: costimulation of interferon gamma secretion and triggering of tumor necrosis factor alpha release

Soluble CD23 (sCD23) has multiple IgE-independent biological activities. In the present study, we examined the regulatory effect of sCD23 on cytokine production by human peripheral blood mononuclear cells (PBMC). We show that sCD23 enhances by about 80-fold the interleukin 2 (IL-2)-induced interferon gamma (IFN-gamma) production and by about 10-fold the response to IL-12. This potentiating activity is time and dose dependent and is not associated with a significant effect on DNA synthesis. The sCD23 costimulatory activity for IFN-gamma synthesis is drastically reduced in monocyte-depleted PBMC, suggesting that monocytes may be the target for sCD23. This hypothesis was supported by the following observations. First, sCD23 alone is a potent inducer of tumor necrosis factor alpha (TNF-alpha) production by PBMC and this effect disappears after monocyte depletion. The triggering of TNF-alpha release is specifically inhibited by neutralizing anti-CD23 monoclonal antibody (mAb). In addition, IL-2 and IL-12 synergize with sCD23 to induce TNF-alpha production. Second, sCD23 triggers the release of other inflammatory mediators such as IL-1 alpha, IL-1 beta, and IL-6. Finally, TNF-alpha production in response to IL-2 and sCD23 precedes IFN-gamma and IFN-gamma secretion is significantly inhibited by anti-TNF-alpha mAb, indicating that the sCD23 costimulatory signal for IFN-gamma production may be partially mediated by TNF-alpha release. It is proposed that sCD23 is a proinflammatory cytokine that, in addition, may play an important role in the control of the immune response via the enhancement of IFN-gamma production.
Neurotoxicity of Acrylamide in Exposed Workers

Acrylamide (ACR) is a water-soluble chemical used in different industrial and laboratory processes. ACR monomer is neurotoxic in humans and laboratory animals. Subchronic exposure to this chemical causes neuropathies, hands and feet numbness, gait abnormalities, muscle weakness, ataxia, skin and in some cases, cerebellar alterations. ACR neurotoxicity involves mostly the peripheral but also the central nervous system, because of damage to the nerve terminal through membrane fusion mechanisms and tubulovescicular alterations. Nevertheless, the exact action mechanism is not completely elucidated. In this paper we have reviewed the current literature on its neurotoxicity connected to work-related ACR exposure. We have analyzed not only the different pathogenetic hypotheses focusing on possible neuropathological targets, but also the critical behavior of ACR poisoning. In addition we have evaluated the ACR-exposed workers case studies. Despite all the amount of work which have being carried out on this topic more studies are necessary to fully understand the pathogenetic mechanisms, in order to propose suitable therapies.
Assessment of DMFT and enamel hypoplasia among junior high school children in Iran.

AIM The main purpose of this study was to assess the prevalence and distribution of decayed, missing, and filled teeth (DMFT) and enamel hypoplasia in 12-year old students in junior high school in Iran. MATERIALS AND METHODS This descriptive study was carried out in 2001 on 1,223 12-year old students, which were randomly selected in Yazd and Hadi-Shahr, Iran. A questionnaire was designed to record the status of the teeth along with the occupational and educational levels of parents. Data was analyzed using SPSS software, the Chi-square test, and analysis of variance (ANOVA). RESULTS The mean DMFT score was 1.8 +/- 1.75 and 28.6% of the students were caries-free. There was no significant relationship between DMFT and the rate of dental caries with parents' education and occupation. The percentage of enamel hypoplasia was 32.7%. No statistically significant relationships were found between hypoplasia and DMFT with regard to gender. The relationship between enamel hypoplasia with DMFT score and dental caries was statistically significant. CONCLUSION In the present study findings for DMFT scores in 12-year old junior high school children are higher than global standards according to the World Health Organization (WHO) references for the year 2000. There was a strong association between enamel hypoplasia and dental caries, and this subject suggests early diagnosis of enamel defects, health education programs, and suitable treatments should be emphasized in junior high school-aged children.
Exploiting statistical information for implementation of instruction scratchpad memory in embedded system

A method to both reduce energy and improve performance in a processor-based embedded system is described in this paper. Comprising of a scratchpad memory instead of an instruction cache, the target system dynamically (at runtime) copies into the scratchpad code segments that are determined to be beneficial (in terms of energy efficiency and/or speed) to execute from the scratchpad. We develop a heuristic algorithm to select such code segments based on a metric, called concomitance. Concomitance is derived from the temporal relationships of instructions. A hardware controller is designed and implemented for managing the scratchpad memory. Strategically placed custom instructions in the program inform the hardware controller when to copy instructions from the main memory to the scratchpad. A novel heuristic algorithm is implemented for determining locations within the program where to insert these custom instructions. For a set of realistic benchmarks, experimental results indicate the method uses 41.9% lower energy (on average) and improves performance by 40.0% (on average) when compared to a traditional cache system which is identical in size
What is Hidden among Translation Rules

Most of the machine translation systems rely on a large set of translation rules. These rules are treated as discrete and independent events. In this short paper, we propose a novel method to model rules as observed generation output of a compact hidden model, which leads to better generalization capability. We present a preliminary generative model to test this idea. Experimental results show about one point improvement on TER-BLEU over a strong baseline in Chinese-to-English translation.
Analyzing the cost and benefit of pair programming

We use a combination of metrics to understand, model, and evaluate the impact of pair programming on software development. Pair programming is a core technique in the hot process paradigm of extreme programming. At the expense of increased personnel cost, pair programming aims at increasing both the team productivity and the code quality as compared to conventional development. In order to evaluate pair programming, we use metrics from three different categories: process metrics such as the pair speed advantage of pair programming; product metrics such as the module breakdown structure of the software; and project context metrics such as the market pressure. The pair speed advantage is a metric tailored to pair programming and measures how much faster a pair of programmers completes programming tasks as compared to a single developer. We integrate the various metrics using an economic model for the business value of a development project. The model is based on the standard concept of net present value. If the market pressure is strong, the faster time to market of pair programming can balance the increased personnel cost. For a realistic sample project, we analyze the complex interplay between the various metrics integrated in our model. We study for which combinations of the market pressure and pair speed advantage the value of the pair programming project exceeds the value of the corresponding conventional project. When time to market is the decisive factor and programmer pairs are much faster than single developers, pair programming can increase the value of a project, but there also are realistic scenarios where the opposite is true. Such results clearly show that we must consider metrics from different categories in combination to assess the cost-benefit relation of pair programming.
Safe and effective determinant evaluation

The problem of evaluating the sign of the determinant of a small matrix aries in many geometric algorithms. Given an n*n matrix A with integer entries, whose columns are all smaller than M in Euclidean norm, the algorithm given evaluates the sign of the determinant det A exactly. The algorithm requires an arithmetic precision of less than 1.5n+2lgM bits. The number of arithmetic operations needed is O(n/sup 3/)+O(n/sup 2/) log OD(A)/ beta , where OD(A) mod det A mod is the product of the lengths of the columns of A, and beta is the number of 'extra' bits of precision, min(lg(1/u)-1.1n-2lgn-2,lgN-lgM-1.5n-1), where u is the roundoff error in approximate arithmetic, and N is the largest representable integer. Since OD(A)<or=M/sup n/, the algorithm requires O(n/sup 3/lgM) time, and O(n/sup 3/) time when beta = Omega (logM). <<ETX>>