Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient object detection via structured learning and local classifiers

Object detection has made great strides recently. However, it is still facing two big challenges: detection accuracy and computational efficiency. In this thesis, we present an automatic efficient object detection framework to detect object instances in images using bounding boxes, which can be trained and tested easily on current personal computers. Our framework is a sliding-window based approach, and consists of two major components: (1) efficient object proposal generation, predicting possible object bounding boxes, and (2) efficient object proposal verification, classifying each bounding box in a multiclass manner. For object proposal generation, we formulate this problem as a structured learning problem and investigate structural support vector machines (SSVMs) with our proposed scale/aspect-ratio quantization scheme and ranking constraints. A general ranking-order decomposition algorithm is developed for solving the formulation efficiently, and applied to generate proposals using a two-stage cascade. Using image gradients as features, our object proposal generation method achieves state-of-the-art results in terms of object recall at a low cost in computation. For object proposal verification, we propose two locally linear and one locally nonlinear classifiers to approximate the nonlinear decision boundaries in the feature space efficiently. Inspired by the kernel trick, these classifiers map the original features into another feature space explicitly where linear classifiers are employed for classification, and thus have linear computational complexity in both training and testing, similar to that of linear classifiers. Therefore, in general, our classifiers can achieve comparable accuracy to kernel based classifiers at the cost of lower computational time. To demonstrate its efficiency and generality, our framework is applied to four different object detection tasks: VOC detection challenges, traffic sign detection, pedestrian detection, and face detection. In each task, it can perform reasonably well with acceptable detection accuracy and good computational efficiency. For instance, on VOC datasets with 20 object classes, our method achieved about 0.1 mean average precision (AP) within 2 hours of training and 0.05 second of testing a 500× 300 pixel image using a mixture of MATLAB and C++ code on a current personal computer.
Detection of Anaplasma marginale and A. phagocytophilum in Bovine Peripheral Blood Samples by Duplex Real-Time Reverse Transcriptase PCR Assay

ABSTRACT Insufficient diagnostic sensitivity and specificity coupled with the potential for cross-reactivity among closely related Anaplasma species has made the accurate determination of infection status problematic. A method for the development of simplex and duplex real-time quantitative reverse transcriptase PCR (qRT-PCR) assays for the detection of A. marginale and A. phagocytophilum 16S rRNA in plasma-free bovine peripheral blood samples is described. The duplex assay was able to detect as few as 100 copies of 16S rRNA of both A. marginale and A. phagocytophilum in the same reaction. The ratio of 16S rRNA to 16S DNA copies for A. marginale was determined to be 117.9:1 (95% confidence interval [95% CI], 100.7:1, 135.2:1). Therefore, the detection limit is the minimum infective unit of one A. marginale bacterium. The duplex assay detected nonequivalent molar ratios as high as 100-fold. Additionally, the duplex assay and a competitive enzyme-linked immunosorbent assay (cELISA) were used to screen 237 samples collected from herds in which anaplasmosis was endemic. When the cELISA was evaluated by the results of the qRT-PCR, its sensitivity and specificity for the detection of A. marginale infection were found to be 65.2% (95% CI, 55.3%, 75.1%) and 97.3% (95% CI, 94.7%, 99.9%), respectively. A. phagocytophilum infection was not detected in the samples analyzed. One- and two-way receiver operator characteristic curves were constructed in order to recommend the optimum negative cutoff value for the cELISA. Percentages of inhibition of 20 and 15.3% were recommended for the one- and two-way curves, respectively. In conclusion, the duplex real-time qRT-PCR assay is a highly sensitive and specific diagnostic tool for the accurate and precise detection of A. marginale and A. phagocytophilum infections in cattle.
Reversing hypomethylation of TIAM 1 promoter inhibits TIAM 1 gene expression and cell proliferation and migration in colorectal cancer

Objective: To investigate the reversing effect of hypomethylation status of T lymphoma invasion and metastasis 1 (TIAM1) gene promoter on TIAM1 expression and evaluate the biological behavior of colorectal cancer cells in vivo and in vitro. Methods: DNA methyltransferase was used to hypermethylate the predicted TIAM1 promotor. Then the luciferase activity of the unmethylated TIAM1 promoter (UP-T) and hypermethylated TIAM1 promoter (MP-T) was examined by Dual Luciferase Reporter assay. We constructed plasmids with the PGL3.0-Basic-hypermethylated-promoter-TIAM1-cDNA vector and PGL3.0-Basic-unmethylated-promoter-TIAM1-cDNA vector and then transfected them into cell lines HT29, LS174T and SW480. Expression of TIAM1 protein were examined by Western blot. Subsequently, the biological behavior of the transfected cells were assessed by MTT, plate colony formation and in-vitro invasion analysis. SW480 cells labeled with green fluorescent protein (SW480/GFP) were treated with S-adenosylmethionine (SAM, methyl donor), S-adenosylhomocysteine (SAH, non-methyl donor), respectively. A visualized orthotopic animal model was built by injecting the above three group cells into nude mice subcutaneously and intravenously. Then the effects of aberrant DNA methylation on the biological behavior of colorectal cancer cells were detected in vivo. Results: The hypermethylated TIAM1 promoter showed lower luciferase activity than that of the unmethylated promoter. Expression of TIAM1 protein was statistically decreased in MP-T transfectant. Furthermore, a significant suppressed proliferation, migration and invasion ability were observed in MP-T transfectant cells as compared with those in the UP-T transfectant cells (P<0.05). Hypermethylation of SW480/GFP cells resulted in decreased proliferation, migration and invasion abilities in vivo. Conclusion: Aberrant methylation of TIAM1 promoter was closely related to aberrant TIAM1 expression in colorectal cancer. Reversing hypomethylation status of TIAM1 promoter can lead to inhibition of cell growth, migration and decreased invasion capacity of colorectal cancer in vivo and in vitro, which implied a potential therapy pathway for colorectal cancer clinically.
Transport‐mediated angiogenesis in 3D epithelial coculture

Increasing interest has focused on capturing the complexity of tissues and organs in vitro as models of human pathophysiological processes. In particular, a need exists for a model that can investigate the interactions in three dimensions (3D) between epithelial tissues and a microvascular network since vascularization is vital for reconstructing functional tissues in vitro. Here, we implement a microfluidic platform to analyze angiogenesis in 3D cultures of rat primary hepatocytes and rat/human microvascular endothelial cells (rMVECs/hMVECs). Liver and vascular cells were cultured on each sidewall of a collagen gel scaffold between two microfluidic channels under static or flow conditions. Morphogenesis of 3D hepatocyte cultures was found to depend on diffusion and convection across the nascent tissue. Furthermore, rMVECs formed 3D capillary‐like structures that extended across an intervening gel to the hepatocyte tissues in hepatocyterMVEC coculture while they formed 2D sheet‐like structures in rMVEC monoculture. In addition, diffusion of fluorescent dextran across the gel scaffold was analyzed, demonstrating that secreted proteins from the hepatocytes and MVECs can be exchanged across the gel scaffold by diffusional transport. The experimental approach described here is useful more generally for investigating microvascular networks within 3D engineered tissues with multiple cell types in vitro. —Sudo, R. ,Chung, S. , Zervantonakis, I. K. , Vickerman, V. , Toshimitsu, Y. , Griffith, L. G. , Kamm, R. D. Transportmediated angiogenesis in 3D epithelial coculture. FASEBJ. 23, 2155–2164 (2009)
Methods for isolating Campylobacter jejuni from low-turbidity water

Membrane filtration methods were developed and evaluated for the quantitative recovery of Campylobacter jejuni from environmental waters of low turbidity. The best procedure studied involved passaging the test water through a filter (pore size, 0.45 micron) and plating it facedown on Campylobacter-selective agar. The filter was removed after overnight incubation, and the plate was streaked for isolation and then reincubated. This method, with or without prefiltration through 5.0- and 0.6-micron-pore-size membranes consistently resulted in the recovery of 30 C. jejuni CFU/250 ml of seeded natural waters. The other methods, plating the final filter face-up or preincubation of the filter in an enrichment medium, were not as sensitive. The technique described above could be useful in the routine monitoring of finished waters for C. jejuni or during investigations of suspected waterborne outbreaks for water of low turbidity.
Dissolved Organic Matter Influences N2 Fixation in the New Caledonian Lagoon (Western Tropical South Pacific)

Specialized prokaryotes performing biological dinitrogen (N2) fixation ('diazotrophs') provide an important source of fixed nitrogen in oligotrophic marine ecosystems such as tropical and subtropical oceans. In these waters, cyanobacterial photosynthetic diazotrophs are well known to be abundant and active, yet the role and contribution of non-cyanobacterial diazotrophs are currently unclear. The latter are not photosynthetic (here called 'heterotrophic') and hence require external sources of organic matter to sustain N2 fixation. Here we added the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) to estimate the N2 fixation potential of heterotrophic diazotrophs as compared to autotrophic ones. Additionally, we explored the influence of dissolved organic matter (DOM) on these diazotrophs along a coast to open ocean gradient in the surface waters of a subtropical coral lagoon (New Caledonia). Total N2 fixation (samples not amended with DCMU) ranged from 0.66 to 1.32 nmol N L-1 d-1. The addition of DCMU reduced N2 fixation by >90%, suggesting that the contribution of heterotrophic diazotrophs to overall N2 fixation activity was minor in this environment. Higher contribution of heterotrophic diazotrophs occurred in stations closer to the shore and coincided with the decreasing lability of DOM, as shown by various colored DOM and fluorescent DOM (CDOM and FDOM) indices. This suggests that heterotrophic N2 fixation is favored when labile DOM compounds are available. We tested the response of diazotrophs (in terms of nifH gene expression and bulk N2 fixation rates) upon the addition of a mix of carbohydrates ('DOC' treatment), amino acids ('DON' treatment), and phosphonates and phosphomonesters ('DOP' treatment). While nifH expression increased significantly in Trichodesmium exposed to the DOC treatment, bulk N2 fixation rates increased significantly only in the DOP treatment. The lack of nifH expression by gammaproteobacteria, in any of the DOM addition treatments applied, questions the contribution of non-cyanobacterial diazotrophs to fixed nitrogen inputs in the New Caledonian lagoon. While the metabolism and ecology of heterotrophic diazotrophs is currently elusive, a deeper understanding of their ecology and relationship with DOM is needed in the light of increased DOM inputs in coastal zones due to anthropogenic pressure.
Identification of ZBP-89 as a Novel GATA-1-Associated Transcription Factor Involved in Megakaryocytic and Erythroid Development

ABSTRACT A complete understanding of the transcriptional regulation of developmental lineages requires that all relevant factors be identified. Here, we have taken a proteomic approach to identify novel proteins associated with GATA-1, a lineage-restricted zinc finger transcription factor required for terminal erythroid and megakaryocytic maturation. We identify the Krüppel-type zinc finger transcription factor ZBP-89 as being a component of multiprotein complexes involving GATA-1 and its essential cofactor Friend of GATA-1 (FOG-1). Using chromatin immunoprecipitation assays, we show that GATA-1 and ZBP-89 cooccupy cis-regulatory elements of certain erythroid and megakaryocyte-specific genes, including an enhancer of the GATA-1 gene itself. Loss-of-function studies in zebrafish and mice demonstrate an in vivo requirement for ZBP-89 in megakaryopoiesis and definitive erythropoiesis but not primitive erythropoiesis, phenocopying aspects of FOG-1- and GATA-1-deficient animals. These findings identify ZBP-89 as being a novel transcription factor involved in erythroid and megakaryocytic development and suggest that it serves a cooperative function with GATA-1 and/or FOG-1 in a developmental stage-specific manner.
Motifs in Reconstructed RST Discourse Trees

Abstract In line with the compositionality criterion and hierarchy principle of Rhetorical Structure Theory (RST), this study converts each tree in the RST Discourse Treebank into three trees with mere ultimate nodes being clauses, sentences and paragraphs, respectively. It examines the motifs of rhetorical relations along three taxonomies at the three granularity levels and also lengths of these motifs, and finds they observe the negative binomial distribution and positive negative binomial distribution respectively. The study demonstrates the applicability of RST relational analysis between same-level terminal units, which works with various granularities.
A Systematic Review and Meta-Analysis of the Riskof Increasing Adiposity on Barrett's Esophagus

OBJECTIVES:Esophageal adenocarcinoma and its precursor lesion, Barrett's esophagus, are increasing in incidence in western populations. Gastroesophageal reflux disease (GERD) and high body mass index (BMI) are known risk factors, but it is unclear whether BMI mediates its risk on Barrett's esophagus independently. This systematic review and meta-analysis investigated whether increasing BMI is associated with Barrett's esophagus as compared to general population and GERD controls.METHODS:Search strategies were conducted in MEDLINE (U.S. National Library of Medicine, Bethesda, MD) (1966–2005) and EMBASE (Reed Elsevier PLC, Amsterdam, The Netherlands) (1980–2005). Studies to be included were required to present “current” BMI data for consecutively recruited Barrett's esophagus patients and appropriate comparison arms with a minimum number of 30 subjects in each.RESULTS:The literature search produced 5,501 hits from which 295 papers were extracted. Only 10 studies met the criteria for inclusion. The Statistics/Data Analysis (STATA) program was used to conduct random effects meta-analyses. Nine studies comparing the BMI of the Barrett's esophagus and GERD groups produced a pooled odds ratio (OR) of 0.99 per kg/m2 (95% confidence interval [CI] 0.97–1.01, I2 = 52%), while the pooled estimate of three studies comparing Barrett's esophagus with general population controls was 1.02 per kg/m2 (95% CI 1.01–1.04, I2 = 0%). CONCLUSIONS:Increasing adiposity is only an indirect risk factor of Barrett's esophagus through the precursor lesion of GERD. Hence, BMI status has no predictive value with respect to GERD patients and their risk of progression to Barrett's esophagus.
Influence of canopy density on snow distribution in a temperate mountain range

We analyse spatial variability and different evolution patterns of snowpack in a mixed beech–fir stand in the central Pyrenees. Snow depth and density were surveyed weekly along six transects of contrasting forest cover during a complete accumulation and melting season; we also surveyed a sector unaffected by canopy cover. Forest density was measured using the sky view factor (SVF) obtained from digital hemispherical photographs. During periods of snow accumulation and melting, noticeable differences in snow depth and density were found between the open site and those areas covered by forest canopy. Principal component analysis provided valuable information in explaining these observations. The results indicate a high variability in snow accumulation within forest areas related to differences in canopy density. Maximum snow water equivalent (SWE) was reduced by more than 50% beneath dense canopies compared with clearings, and this difference increased during the melting period. We also found significant temporal variations: when melting began in sectors with low SVF, most of the snow had already thawed in areas with high SVF. However, specific conditions occasionally produced a different response of SWE to forest cover, with lower melting rates observed beneath dense canopies. The high values of correlation coefficients for SWE and SVF (r > 0·9) indicate the reliability of predicting the spatial distribution of SWE in forests when only a moderate number of observations are available. Digital hemispherical photographs provide an appropriate tool for this type of analysis, especially for zenith angles in the range 35–55 . Copyright © 2007 John Wiley & Sons, Ltd.
Imprinting of Hatchery-Reared Salmon to Targeted Spawning Locations: A New Embryonic Imprinting Paradigm for Hatchery Programs

Straying by hatchery-reared salmon is a major concern for conservation and recovery of many salmon populations. Fisheries managers have attempted to minimize negative ecological and genetic interactions between hatchery and wild fish by using parr-smolt acclimation facilities to ensure successful olfactory imprinting and homing fidelity. However, the effectiveness of offsite acclimation for returning adults to targeted locations has been mixed. Since laboratory and field studies indicate that the period of hatching and emergence from the natal gravel is a sensitive period for olfactory imprinting, we propose an alternative imprinting approach wherein salmon are exposed as embryos to targeted waters transferred to their rearing hatchery. To test the feasibility of this approach, we conducted a series of electrophysiological and behavioral experiments to determine whether water can be successfully transferred, stored, and treated for pathogens without jeopardizing its chemical integrity. Stream water could .
First report of anthracnose (Colletotrichum trifolii) on Cullen australasicum (syn. Psoralea australasica)

We report the incidence of anthracnose caused by Colletotrichum trifolii on Cullen australasicum, a native Australian legume. Natural infection was observed on plants grown in a genetic resources characterisation experiment at Waite Research Precinct, Adelaide. The affected plants showed wilting of the branches and light brown lesions on the leaves. The characteristic symptom was a bluish black discolouration on the infected leaves and stems. In some plants, the infection spread from the leaves and stems across the entire plant leading to the death of the plant.
Peptides Which Bind to E-selectin and Block Neutrophil Adhesion (*)

E-selectin is an inducible cell adhesion molecule which mediates rolling of neutrophils on the endothelium, an early event in the development of an inflammatory response. Inhibition of selectin-mediated rolling is a possible means for controlling inflammation-induced diseases, and several classes of compounds have been tested for this use. We describe here the use of recombinant peptide library screening for identification and optimization of novel ligands which bind to E-selectin. Several of these peptides bind with K values in the low nanomolar range and block E-selectin-mediated adhesion of neutrophils in static and flow-cell assays. Administration of the peptide to mice undergoing an acute inflammatory response reduced the extent of neutrophil transmigration to the site of inflammation, demonstrating the utility of this compound as a potential therapeutic. The identification of a peptide ligand for E-selectin suggests that the complete natural ligand for this adhesion molecule may include protein as well as carbohydrate moieties.
PREDICTING FECAL COLIFORM BACTERIA LEVELS IN THE CHARLES RIVER, MASSACHUSETTS, USA 1

In Massachusetts, the Charles River Watershed Association conducts a regular water quality monitoring and public notification program in the Charles River Basin during the recreational season to inform users of the river's health. This program has relied on laboratory analyses of river samples for fecal coliform bacteria levels, however, results are not available until at least 24 hours after sampling. To avoid the need for laboratory analyses, ordinary least squares (OLS) and logistic regression models were developed to predict fecal coliform bacteria concentrations and the probabilities of exceeding the Massachusetts secondary contact recreation standard for bacteria based on meteorological conditions and streamflow. The OLS models resulted in adjusted R2s ranging from 50 to 60 percent. An uncertainty analysis reveals that of the total variability of fecal coliform bacteria concentrations, 45 percent is explained by the OLS regression model, 15 percent is explained by both measurement and space sampling error, and 40 percent is explained by time sampling error. Higher accuracy in future bacteria forecasting models would likely result from reductions in laboratory measurement errors and improved sampling designs.
Atmospheric circulation patterns associated with extreme precipitation amounts in Greece

Abstract. The main synoptic conditions associated with extreme precipitation amounts in Greece are examined by using a multivariate statistical methodology comprising S-mode Factor Analysis and k-means Cluster Analysis. The following data were used : i) daily precipitation amounts (measured at 06:00 UTC) for the meteorological stations of Hellenikon (Athens), Thessaloniki (northern Greece) and Ioannina (western Greece) and ii) daily (18:00 UTC) 2.5×2.5 grid point values of 500 hPa geopotential height, mean sea-level pressure and 1000–500 hPa thickness at 273 grid points over Europe (10 W to 40 E and 30 N to 60 N), for the period 1970–2002. The dates corresponding to the upper 5% of the frequency distribution of precipitation are selected for each one of the three stations. In total, 369 dates are used, some of them being common among the three stations. The corresponding 369×273 data matrices of 500 hPa geopotential height, mean sea-level pressure and 1000–500 hPa thickness are constructed. The rows refer to the 369 extreme precipitation cases and the columns refer to the 273 grid points. The three matrices are unified into one 369×819 matrix. In order to reduce the dimensionality of the data set, S-mode Factor Analysis is applied to the unified matrix, revealing 7 factors accounting for 85% of the total variance. Finally, k-means Cluster Analysis is applied to the factor scores matrix, classifying the 369 cases into 9 clusters. For each one of the 9 clusters, the mean 18:00 UTC patterns of the above parameters are constructed and presented. These patterns correspond to the main distinct atmospheric circulation structures favoring extreme precipitation amounts in Greece. Most of the patterns are characterized by enhanced cyclonic activity over or near the Greek area. The differences among the 9 circulation structures refer mainly to the position and the intensity of the surface and the upper air synoptic systems involved. Some of the 9 synoptic conditions favor extreme precipitation amounts mainly at one or two of the three stations while some others equally affect the three stations.