Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vivo Electroporation Enhances the Immunogenicity of an HIV-1 DNA Vaccine Candidate in Healthy Volunteers

Background DNA-based vaccines have been safe but weakly immunogenic in humans to date. Methods and Findings We sought to determine the safety, tolerability, and immunogenicity of ADVAX, a multigenic HIV-1 DNA vaccine candidate, injected intramuscularly by in vivo electroporation (EP) in a Phase-1, double-blind, randomized placebo-controlled trial in healthy volunteers. Eight volunteers each received 0.2 mg, 1 mg, or 4 mg ADVAX or saline placebo via EP, or 4 mg ADVAX via standard intramuscular injection at weeks 0 and 8. A third vaccination was administered to eleven volunteers at week 36. EP was safe, well-tolerated and considered acceptable for a prophylactic vaccine. EP delivery of ADVAX increased the magnitude of HIV-1-specific cell mediated immunity by up to 70-fold over IM injection, as measured by gamma interferon ELISpot. The number of antigens to which the response was detected improved with EP and increasing dosage. Intracellular cytokine staining analysis of ELISpot responders revealed both CD4+ and CD8+ T cell responses, with co-secretion of multiple cytokines. Conclusions This is the first demonstration in healthy volunteers that EP is safe, tolerable, and effective in improving the magnitude, breadth and durability of cellular immune responses to a DNA vaccine candidate. Trial Registration ClinicalTrials.gov NCT00545987
PCR-based Method for Screening Libraries

One of the fundamental techniques of molecular biology is the isolation of a rare clone from a complex mixture of DNA sequences contained within a library. The isolation of cDNA and genomic clones from highly complex libraries is often an early step in studies aimed at understanding basic biological processes as well as in applied biological research. In a typical genomic library with an average insert size of 20,000 bp from an organism with a haploid genome size of 2 x 10 bp, the occurrence of a single-copy gene will be approximately 1/10. Likewise, for cDNA clones within a highly complex library derived from a tissue or cell line that expresses many different genes, a particular clone may occur with a similarly low frequency. Screening of libraries of high complexity by techniques such as filter hybridization (Benton and Davis 1977) or expression cloning (Wong et al. 1985) is therefore a labor-intensive and time-consuming process because of the large number of clones that must be screened to obtain the clone of interest. PCR results in the amplification of a given nucleic acid sequence by many orders of magnitude (Saiki et al. 1985). When applied to the screening of highly complex DNA libraries contained within either bacteriophage or plasmid vectors, PCR offers the opportunity to identify rare DNA sequences in complex mixtures of molecular clones by increasing the abundance of a particular sequence, thereby allowing the easy identification of a particular clone in a portion of the library. This is accomplished by subdividing the original library into pools of decreased complexity and screening each pool or groups of pools for a given DNA sequence (Fig 1). A pool that contains the desired clone is subsequently subdivided into smaller pools, each of which is screened using the same PCR protocol that was used for the primary screen. After several cycles of subdividing and screening, the initially rare clone is greatly enriched and can be easily obtained as a pure clone (Israel 1993). A method for screening highly complex DNA libraries using PCR is described in this chapter. This method allows a library of high complexity to be screened in a short time and provides an alternative to more traditional and time-consuming screening methods that entail plaque or colony hybridization, or methods that require the expression of a functional gene product. The main advantages of this screening technique are its speed, sensitivity, and ease. Some providers of molecular biology reagents, such as MRC geneservice, have PCR-ready library pools available for screening. In addition, the method as described below requires more than one oligonucleotide to anneal correctly to the template DNA and/or PCR product, thereby providing a high degree of stringency for a true positive signal. 24
Motion Planning and Coordination for Robot Systems Based on Representation Space

This paper proposes a general motion planning and coordination strategy for robot systems. The representation space (RS) of a robot system is constructed to describe the distributions of system attributes. The reachable area in the RS, denoting the attribute set that the system can be of, indicates the system's ability to accomplish tasks. Moreover, it also describes the influences of the internal and external constraints on the system's capability. Task realization is transformed to finding a trajectory in the RS for the system attributes to transit along under constraints. Meanwhile, the realizable conditions of a prescribed task by the robot system of specific configurations are discussed. If the task is realizable, the optimal strategy for task execution could further be figured out. Otherwise, it could be transformed to be realizable via task reassignment or system reconfigurations so that a connected path could be found for the transition of the system attributes from the starting point to the goal in the RS. The proposed scheme contributes to designing, planning, and coordination of the robotic tasks. Experiments on path planning of a robot manipulator and formation movement of a multirobot system, as well as coordination of a mobile manipulator system, are conducted to show the validity and generalization of the proposed method.
“Less is More:” Information Systems Planning in an Uncertain Environment

An unpredictable environment, having complex markets, rapid change, and threatening competitors, can impede IS planning. A survey of 131 Chief Information Officers and 103 senior non-IS managers of U.S. manufacturing firms found that more situation analysis, less strategy conception, and less strategy implementation planning predicted greater IS contribution to the organization. These findings suggest that planners consider conducting situational analysis with greater meticulousness, and strategy conception and strategy implementation planning with greater agility than they currently do.
Indexing XML Data with UB-trees

Using the terminology usual in databases, it is possible to view XML as a language for data modelling. To retrieve XML data from XML databases, several query languages have been proposed. The common feature of these languages is the use of regular path expressions. Users are allowed to navigate through arbitrary long paths in the data by regular path expressions. Several index structures for XML data have been developed in recent years in order to address this problem. This paper is going to show how the UB-trees can index and retrieve XML documents efficiently. UB-trees were introduced by R. Bayer as a structure for indexing n-dimensional space. The basic idea of UB-tree index is that the indexing is performed at the lowest level of the given XML data.
Predicting Disease Transmission from Geo-Tagged Micro-Blog Data

Researchers have begun to mine social network data in order to predict a variety of social, economic, and health related phenomena. While previous work has focused on predicting aggregate properties, such as the prevalence of seasonal influenza in a given country, we consider the task of fine-grained prediction of the health of specific people from noisy and incomplete data. We construct a probabilistic model that can predict if and when an individual will fall ill with high precision and good recall on the basis of his social ties and co-locations with other people, as revealed by their Twitter posts. Our model is highly scalable and can be used to predict general dynamic properties of individuals in large real-world social networks. These results provide a foundation for research on fundamental questions of public health, including the identification of non-cooperative disease carriers ("Typhoid Marys"), adaptive vaccination policies, and our understanding of the emergence of global epidemics from day-to-day interpersonal interactions.
Relationships among vitamin D, disease activity, pain and disability in rheumatoid arthritis.

BACKGROUND AND OBJECTIVES Vitamin D is a steroid hormone with important skeletal and non-skeletal biologic functions. Vitamin D deficiency is common and manifests with musculoskeletal symptoms. In rheumatoid arthritis (RA), vitamin D deficiency may be associated with increased disease activity and disability. We aimed to estimate the relationship between Vitamin D level and disease activity, pain, and disability in RA. METHODS Data were drawn from 62 RA patients seen in an academic arthritis clinic. 25(OH)D levels were evaluated along with markers of RA disease activity, physician and patient global assessments, pain (VAS) and HAQ. DAS-28 was calculated. Vitamin D deficiency was defined as 25(OH)D levels<30ng/ml. RESULTS Sixty-one percent of RA patients were classified as vitamin D deficient. In patients with active RA (DAS 28 score≥2.6), 25(OH)D was moderately and inversely associated with DAS 28 (-0.38), pain (-0.49) and HAQ (-0.54) (p<0.01). However, no significant associations were found between 25(OH)D and these variables in patients in remission (DAS 28<2.6). Vitamin D deficient patients with active RA had six times the odds (OR=6.0, 95% CI 1.2-31.2) of being moderately or severely disabled (HAQ≥1.25). CONCLUSIONS Vitamin D deficiency was common in this RA group. In patients with moderate to high disease activity, vitamin D deficiency was associated with higher DAS scores, pain and disability. Clinicians in northern climates may wish to monitor vitamin D status in their RA patients.
Prospects of Modification in Belt Conveyors-A Review

Now a day’s Belt conveyor system not only used in mining industries but also applied in cement industries, power plant, food industries, production industries etc. So it is essential equipment for in house material transportation today. The paper presents the review of belt conveyor design modification and latest technologies or methodologies used in different applications to reduce failures, maintenance cost and equipment related fatal accidents occurs during operation. The focus is on methodologies as Design modification, Drum and pulley failures, Belt design and its failure, energy & efficiency, friction, inspection, operation & maintenance and fire & safety. The analysis shows, different design parameters required for different applications such as coal mines, cement and food industries. Some of the common design parameters required in each application and the importance of each parameter which impacts on different application. Keywords— Belt Conveyor, Design Modification, Failures, Maintenance, pulley.
Noise, Stability, and Linewidth Performance of 10-GHz Optical Frequency Combs Generated from the Nested Cavity Architecture

iii ACKNOWLEDGMENTS . v TABLE OF CONTENTS . vi LIST OF FIGURES . viii LIST OF TABLES . xiv LIST OF ACRONYMS/ABBREVIATIONS . xv CHAPTER 1: MOTIVATION . 1 CHAPTER 2: BACKGROUND AND ARCHITECTURE . 5 2.1 Semiconductor gain with external fiber cavity . 6 2.2 Supermode suppression . 10 2.3 Length stabilization . 11 2.4 Dispersion compensation . 14 2.5 Summary of the Nested Cavity Architecture . 15 2.6 Previous Work . 16 CHAPTER 3: OPTICAL AND RF PERFORMANCE ASSOCIATED WITH CAVITY LENGTH AND INTRACAVITY POWER. 17 3.1 Optical performance . 17 3.1. 1 Linewidth . 17 3.1. 2 Optical combline stability . 20 3.2 RF performance: residual phase noise . 22 3.3 Proposed systems . 25 vii CHAPTER 4: TRADE-OFFS ASSOCIATED WITH LENGTH, GAIN SATURATION, AND FPE FINESSE . 30 4.1 Cavity length and operating bandwidth . 30 4.2 Gain and saturation power. 31 4.3 Length and free-running stability . 32 CHAPTER 5: NOTABLE RESULTS . 34 5.1 System Performance . 34 5.1. 1 System 1: SOA, short cavity, 10000 finesse FPE . 34 5.1. 2 System 2: SOA, long cavity, 10000 finesse FPE . 37 5.1. 3 System 3: SCOWA, short cavity, 10000 finesse FPE . 39 5.1. 4 System 4: SCOWA, long cavity, 10000 finesse FPE . 43 5.1. 5 System 5: SCOWA, short cavity, 1000 finesse FPE . 45 5.2 Discussion . 47 5.2.1 Phase Noise of Photodetected Output . 47 5.2.2 Long term Optical Frequency Stability. 48 5.2.3 Optical Mode Linewidth . 49 CHAPTER 6: SUMMARY AND OUTLOOK. 55 REFERENCES . 57
Toxicological and biochemical analysis of the susceptibility of sylvatic Triatoma infestans from the Andean Valley of Bolivia to organophosphate insecticide

To increase our knowledge of the natural susceptibility of Triatoma infestans to an organophosphate insecticide, we performed toxicological and biochemical studies on three sylvatic populations from Bolivia and two populations from domestic dwellings from Bolivia and Argentina. Fifty-per-cent lethal doses (LD50) were determined based on the topical application of fenitrothion on first instar nymphs and mortality was assessed at 24 h. Both type of populations exhibited LD50ratios significantly higher than 1 with a range of the values (1.42-2.47); the maximum value were found in a sylvatic (-S) population, Veinte de Octubre-S. Samples were biochemically analysed using a glutathione S-transferase activity assay. The highest significant activity was obtained for Veinte de Octubre-S and the lowest activity was obtained for the reference population (102.69 and 54.23 pmol per minute per mg of protein respectively). Two out of the three sylvatic populations (Veinte de Octubre-S and Kirus Mayu-S) exhibited significantly higher glutathione S-transferase activity than that of the reference population. Based on this analysis of the natural susceptibility of this organism to organophosphate insecticides, continental and focal surveys of organophosphate susceptibility should be conducted to evaluate the evolution and distribution of this phenomenon.
Low frequency noise characteristics of bow-tie THz detectors based on InGaAs

Experimental investigation of low frequency noise characteristics of the In0.53Ga0. 47As/InP bow-tie terahertz detectors with a near monolayer of InAs has been carried out in (77-300) K temperature range. Spectral density of voltage fluctuations of investigated diodes at room temperature is proportional to 1/f, while below 200 K Lorentzian-type spectra dominate. Characteristic times of the observed charge carrier capture and release processes are distributed between ten microseconds and millisecond; activation energy of the processes is in the range from 0,04 eV to 0,36 eV.
Geoinformation mapping of transport in the Baikal region

Transportation of the Baikal region is one of the components of a united transport complex of our country and Mongolia. We developed a semantic classification of cartographic symbols of transport systems with a view to streamlining the structure of thematic layers and the system of cartographic sign mapping of transport. Using this classification, geoinformation mapping of the transport of the Baikal region was carried out. To represent the transport of this territory, several semantic parameters were chosen that characterize both the transport complex and its possible impact on the environment (main transport types, infrastructure facilities, density of highways). The existing and projected constructions of railway tracks, highways, as well as pipelines are shown as linear objects. Point features show major airports, ports and piers. The background is the density of motor roads in the administrative regions of the Baikal region and aimaks of Mongolia. Therefore, the transport of the Baikal region was analyzed with an integrative approach on the basis of the created map, and also using other literary sources and statistical data. The main types of transport in the region, their spatial location, as well as infrastructure of transport facilities are considered. Prospects for the development of regional transport are presented.
Bichromatic Line Segment Intersection Counting in O(n sqrt(log n)) Time

We give an algorithm for bichromatic line segment intersection counting that runs in O ( n √ log n ) time under the word RAM model via a reduction to dynamic prede-cessor search, oﬄine point location, and oﬄine dynamic ranking. This algorithm is the ﬁrst to solve bichromatic line segment intersection counting in o ( n log n ) time.
Factors Influencing Sustainable Cocoa Production in Northern Haiti

Given the environmental concerns on the one hand, especially soil erosion and deforestation, and the hope that the global cocoa market offers on the other hand, cocoa production is a potential candidate to simultaneously guarantee a competitive return to investment for farmers in northern Haiti and mitigate the negative environmental impact of farming practices. It becomes crucial for policy makers and investors to know and understand the key elements of the decision to produce cocoa. Though there has been substantial effort to improve the cocoa sector in Haiti, cocoa production systems in Haiti lag behind in the area of sustainability. To address the lack of information on key criteria farmers rely upon to produce cocoa sustainably, this study identifies factors influencing the sustainable cocoa production adoption decision. The act of adopting sustainable cocoa production in this study is defined by the rehabilitation of old cocoa farms and the establishment of new cocoa plantings that fit into agroforestry management systems. This study also is a first attempt at describing the current state of sustainable cocoa production in Haiti. A qualitative method was used to conduct this research. The approach used was focus groups. Fourteen focus groups and seven individual interviews provided data used to answer the research question. Additionally, a SWOT analysis was conducted on the cocoa sector. Results of the investigation indicate that farm gate price, farm size, property ownership, land configuration and rural infrastructures, networking, and animal feeding practices were key determinants of sustainable cocoa production in northern Haiti. In addition to these factors influencing sustainable cocoa production in northern Haiti, the SWOT analysis identified key elements that constrained or might help with expansion and growth of the cocoa sector. Weaknesses include lack of maintenance and rehabilitation of farms. One of the best
EphA2 signaling is impacted by carcinoembryonic antigen cell adhesion molecule 1-L expression in colorectal cancer liver metastasis in a cell context-dependent manner

We have shown that carcinoembryonic antigen cell adhesion molecule 1 long isoform (CEACAM1-L) expression in MC38 metastatic colorectal cancer (CRC) cells results in liver metastasis inhibition via CCL2 and STAT3 signaling. But other molecular mechanisms orchestrating CEACAM1-L-mediated metastasis inhibition remain to be defined. We screened a panel of mouse and human CRC cells and evaluated their metastatic outcome after CEACAM1 overexpression or downregulation. An unbiased transcript profiling and a phospho-receptor tyrosine kinase screen comparing MC38 CEACAM1-L-expressing and non-expressing (CT) CRC cells revealed reduced ephrin type-A receptor 2 (EPHA2) expression and activity. An EPHA2-specific inhibitor reduced EPHA2 downstream signaling in CT cells similar to that in CEACAM1-L cells with decreased proliferation and migration. Human CRC patients exhibiting high CEACAM1 in combination with low EPHA2 expression benefited from longer time to first recurrence/metastasis compared to those with high EPHA2 expression. With the added interaction of CEACAM6, we denoted that CEACAM1 high- and EPHA2 low-expressing patient samples with lower CEACAM6 expression also exhibited a longer time to first recurrence/metastasis. In HT29 human CRC cells, down-regulation of CEACAM1 along with CEA and CEACAM6 up-regulation led to higher metastatic burden. Overall, CEACAM1-L expression in poorly differentiated CRC can inhibit liver metastasis through cell context-dependent EPHA2-mediated signaling. However, CEACAM1’s role should be considered in the presence of other CEACAM family members.
Joint estimation of age, gender and ethnicity: CCA vs. PLS

Human age, gender and ethnicity are valuable demographic information about a population. These measures are also considered important soft biometric traits for human recognition or search. Usually the three traits are studied separately. A recent study [9] shows that the three traits can be estimated simultaneously based on a multi-label regression formulation. The linear and kernel partial least squares (PLS) models are adopted to solve the multi-label regression problem in [9]. In this study, we investigate the canonical correlation analysis (CCA) based methods, including linear CCA, regularized CCA (rCCA), and kernel CCA (KCCA), and compare to the PLS models in solving the joint estimation problem. Interestingly, we found a consistent ranking of the five methods in estimating age, gender, and ethnicity. More importantly, we found that the CCA based methods can derive an extremely low dimensionality in estimating age, gender and ethnicity, which has not been shown in previous research, to the best of our knowledge. The experiments are conducted on a very large database of more than 55,000 face images.
Contrast-Invariant Orientation Tuning in Cat Visual Cortex: Thalamocortical Input Tuning and Correlation-Based Intracortical Connectivity

The origin of orientation selectivity in visual cortical responses is a central problem for understanding cerebral cortical circuitry. In cats, many experiments suggest that orientation selectivity arises from the arrangement of lateral geniculate nucleus (LGN) afferents to layer 4 simple cells. However, this explanation is not sufficient to account for the contrast invariance of orientation tuning. To understand contrast invariance, we first characterize the input to cat simple cells generated by the oriented arrangement of LGN afferents. We demonstrate that it has two components: a spatial-phase-specific component (i.e., one that depends on receptive field spatial phase), which is tuned for orientation, and a phase-nonspecific component, which is untuned. Both components grow with contrast. Second, we show that a correlation-based intracortical circuit, in which connectivity between cell pairs is determined by the correlation of their LGN inputs, is sufficient to achieve well tuned, contrast-invariant orientation tuning. This circuit generates both spatially opponent, “antiphase” inhibition (“push–pull”), and spatially matched, “same-phase” excitation. The inhibition, if sufficiently strong, suppresses the untuned input component and sharpens responses to the tuned component at all contrasts. The excitation amplifies tuned responses. This circuit agrees with experimental evidence showing spatial opponency between, and similar orientation tuning of, the excitatory and inhibitory inputs received by a simple cell. Orientation tuning is primarily input driven, accounting for the observed invariance of tuning width after removal of intracortical synaptic input, as well as for the dependence of orientation tuning on stimulus spatial frequency. The model differs from previous push–pull models in requiring dominant rather than balanced inhibition and in predicting that a population of layer 4 inhibitory neurons should respond in a contrast-dependent manner to stimuli of all orientations, although their tuning width may be similar to that of excitatory neurons. The model demonstrates that fundamental response properties of cortical layer 4 can be explained by circuitry expected to develop under correlation-based rules of synaptic plasticity, and shows how such circuitry allows the cortex to distinguish stimulus intensity from stimulus form.