Miracle-dz/UniFAR-FTUs huggingface dataset:
A Stochastic Approach for Selective Search Algorithms

This thesis introduces a new algorithm that generates candidate proposals for an object detection pipeline. We introduce Stochastic Selective Search (SSS), a segmentation based selective search method, which differs from previous work in two ways. First and most importantly, SSS is much faster than current state-of-the-art algorithms while maintaining comparable accuracy. This is a result of our efficient stochastic segment merging process. Other work requires the computation of features to determine the order in which segments are merged. We show that currently used features from other work does not improve the results of SSS significantly and are therefore omitted. This makes our algorithm nearly twice as fast as the fastest prior selective search algorithms. Secondly, due to the stochastic merging process of SSS, it is not critically affected when two wrong segments are merged during the merging process, which leads to object proposals of higher quality. We show that SSS outperforms existing deterministic selective search methods while generating the same amount of proposals in less time. Additionally, we demonstrate the performance of our SSS algorithm in a state-of-the-art object detection pipeline based on convolutional networks.
Striatal-Enriched Protein Tyrosine Phosphatase Expression and Activity in Huntington's Disease: A STEP in the Resistance to Excitotoxicity

Striatal-enriched protein tyrosine phosphatase (STEP) is highly expressed in striatal projection neurons, the neuronal population most affected in Huntington's disease. Here, we examined STEP expression and phosphorylation, which regulates its activity, in N-terminal exon-1 and full-length mutant huntingtin mouse models. R6/1 mice displayed reduced STEP protein levels in the striatum and cortex, whereas its phosphorylation was increased in the striatum, cortex, and hippocampus. The early increase in striatal STEP phosphorylation levels correlated with a deregulation of the protein kinase A pathway, and decreased calcineurin activity at later stages further contributes to an enhancement of STEP phosphorylation and inactivation. Accordingly, we detected an accumulation of phosphorylated ERK2 and p38, two targets of STEP, in R6/1 mice striatum at advanced stages of the disease. Activation of STEP participates in excitotoxic-induced cell death. Because Huntington's disease mouse models develop resistance to excitotoxicity, we analyzed whether decreased STEP activity was involved in this process. After intrastriatal quinolinic acid (QUIN) injection, we detected higher phosphorylated STEP levels in R6/1 than in wild-type mice, suggesting that STEP inactivation could mediate neuroprotection in R6/1 striatum. In agreement, intrastriatal injection of TAT–STEP increased QUIN-induced cell death. R6/2, Tet/HD94, and HdhQ7/Q111 mice striatum also displayed decreased STEP protein and increased phosphorylation levels. In Tet/HD94 mice striatum, mutant huntingtin transgene shutdown reestablished STEP expression. In conclusion, the STEP pathway is severely downregulated in the presence of mutant huntingtin and may participate in compensatory mechanisms activated by striatal neurons that lead to resistance to excitotoxicity.
Cytokine Expression Pattern in Benign Prostatic Hyperplasia Infiltrating T Cells and Impact of Lymphocytic Infiltration on Cytokine mRNA Profile in Prostatic Tissue

The aim of the study is to characterize the type of immune response in benign prostatic hyperplasia (BPH) tissue. BPH tissue–derived T cells (n = 10) were isolated, activated (PMA + ionomycin), and analyzed for intracellular reactivity with anti–IFN-γ and IL-2, -4, -5, -6, -10, and -13, as well as TNF-α and -β by four-color flow cytometry. Lymphokine release was tested using Th1/Th2 cytokine bead arrays. The amount of IFN-γ and IL-2, -4, -13, and TGF-β mRNA expressed in normal prostate (n = 5) was compared with that in BPH tissue separated into segments with normal histology (n = 5), BPH histology with (n = 10) and without (n = 10) lymphocytic infiltration, and BPH nodules (n = 10). Expression of lymphokine receptors was analyzed by immunohistology, flow cytometry, and RT-PCR. We found that 28 ± 18% of BPH T helper cells were IFN-γ+/IL-4− Th1 cells, 10 ± 2% were IFN-γ−/IL-4+ Th2, and 12 ± 6% were IFN-γ+/IL-4+ Th0 cells. In relation, cytotoxic and double-negative BPH T lymphocytes showed a slight decrease in Th1 and Th0 in favor of Th2. In double-positive BPH T lymphocytes, the trend toward Th2 (35 ± 15%) was significant (Th1: 12 ± 7%; Th0: 5 ± 4%). Lymphokine release upon stimulation was found in the case of IL-2, IL-5, IFN-γ, and TNF-α > 4 μg; of IL-4 > 2 μg; and of IL-10 > 1 μg/ml. Expression of lymphokine mRNA in tissue was increased (2- to 10-fold) in infiltrated BPH specimens with and without BPH histology. The infiltrated BPH specimens with normal histology differed from those with BPH histology, most evident by the significant decrease in IFN-γ and the increase in TGF-β mRNA expression. Infiltrated BPH specimens with BPH histology expressed significantly more IFN-γ (5-fold), IL-2 (10-fold), and IL-13 (2.8-fold) when compared with noninfiltrated BPH specimens. BPH nodules, however, showed the highest level of expression of IL-4 and IL-13, with only intermediate levels of IFN-γ and very low levels of IL-2 mRNA. Immune response in histologically less transformed BPH specimens is primarily of type 1, whereas in chronically infiltrated nodular BPH and especially within BPH nodules, it is predominantly of type 0 or type 2.
Management and Outcomes of Intracranial Tuberculomas Developing During Antituberculous Therapy: Case Report and Review

Intracranial tuberculomas account for a large proportion of intracranial space-occupying lesions in the developing world.1 They usually resolve with standard antituberculous therapy,2 but a “paradoxical” emergence or enlargement has been observed during antituberculous therapy in some patients. We report the manifestation of intracranial tuberculomas in a 17-year-old man receiving treatment for pulmonary tuberculosis and review the published English language literature describing the clinical characteristics, treatment, and outcome of intracranial tuberculomas arising during antituberculous therapy. Patient Report
Automatic discovery of technology trends from patent text

Patent text is a rich source to discover technological progresses, useful to understand the trend and forecast upcoming advances. For the importance in mind, several researchers have attempted textual-data mining from patent documents. However, previous mining methods are limited in terms of readability, domain-expertise, and adaptability. In this paper, we first formulate the task of technological trend discovery and propose a method for discovering such a trend. We complement a probabilistic approach by adopting linguistic clues and propose an unsupervised procedure to discover technological trends. Based on the experiment, our method is promising not only in its accuracy, 77% in R-precision, but also in its functionality and novelty of discovering meaningful technological trends.
Platelet Activating Factor Contributes to Vascular Leak in Acute Dengue Infection

Background Although plasma leakage is the hallmark of severe dengue infections, the factors that cause increased vascular permeability have not been identified. As platelet activating factor (PAF) is associated with an increase in vascular permeability in other diseases, we set out to investigate its role in acute dengue infection. Materials and Methods PAF levels were initially assessed in 25 patients with acute dengue infection to determine if they were increased in acute dengue. For investigation of the kinetics of PAF, serial PAF values were assessed in 36 patients. The effect of dengue serum on tight junction protein ZO-1 was determined by using human endothelial cell lines (HUVECs). The effect of dengue serum on and trans-endothelial resistance (TEER) was also measured on HUVECs. Results PAF levels were significantly higher in patients with acute dengue (n = 25; p = 0.001) when compared to healthy individuals (n = 12). In further investigation of the kinetics of PAF in serial blood samples of patients (n = 36), PAF levels rose just before the onset of the critical phase. PAF levels were significantly higher in patients with evidence of vascular leak throughout the course of the illness when compared to those with milder disease. Serum from patients with dengue significantly down-regulated expression of tight junction protein, ZO-1 (p = 0.004), HUVECs. This was significantly inhibited (p = 0.004) by use of a PAF receptor (PAFR) blocker. Serum from dengue patients also significantly reduced TEER and this reduction was also significantly (p = 0.02) inhibited by prior incubation with the PAFR blocker. Conclusion Our results suggest the PAF is likely to be playing a significant role in inducing vascular leak in acute dengue infection which offers a potential target for therapeutic intervention.
Effects of peer review and editing on the readability of articles published in Annals of Internal Medicine.

OBJECTIVE To measure the effect of the peer review and editorial processes on the readability of original articles. DESIGN Comparison of manuscripts before and after the peer review and editorial processes. SETTING Annals of Internal Medicine between March 1 and November 30, 1992. MANUSCRIPTS: One hundred one consecutive manuscripts reporting original research. MEASUREMENTS Assessment of readability by means of two previously validated indexes: the Gunning fog index (units of readability in the fog index roughly correlate to years of education) and the Flesch reading ease score. Each manuscript was analyzed for readability and length on receipt and after it had passed through the peer review and editorial processes. Text and abstracts were analyzed similarly but separately. Mean readability scores were compared by two-tailed t tests for paired observations. RESULTS Mean (+/- SD) initial readability scores of manuscripts and abstracts by the Gunning fog index were 17.16 +/- 1.55 and 16.65 +/- 2.80, respectively. At publication, scores were 16.85 +/- 1.42 and 15.64 +/- 2.42 (P = .0005 and P < .0001 for before-after differences, respectively). By comparison, studies of other print media showed scores of about 11 for the New York Times editorial page and about 18 for a typical legal contract. Similar changes were found for the Flesch scores. The median length of the manuscripts increased by 2.6% and that of the abstracts by 4.2% during the processes. CONCLUSIONS The peer review and editorial processes slightly improved the readability of original articles and their abstracts, but both remained difficult to read at publication. Better readability scores may improve readership.
Long-term Water Balance of an Inland River Basin in an Arid Area, North-Western China

China, like many other countries in the region suffers from the water scarcity and problems of desertification and land degradation. One of the most useful approaches to deal with such a problem in the region is water balance study and analysis of different components involved to get an overview of the water supply and demand of the region so that engineers and policy makers can use that in their decision. Different hydrologic models have been developed for different conditions e.g. catchment size and data availability. Hydrologic Modeling System (HEC-HMS) among them is capable to simulate different catchment sizes with well detailed information as well as limited data availability. Geographic Information System (GIS) is also used as a useful tool to delineate sub-basins and extract terrain and physical characteristics of the region and associate them to the hydrologic model. Long term water balance for years between 1963 and 2001 was studied at Shiyang River basin, an inland catchment in Gansu province in western part of China. Calibration for the model could not be applied because of immense data limitation, though the model computes a fairly good estimation of water volume of the region which was applied in water balance equation. The hydrologic components e.g. water supply and demand of the region was determined and the trend of changes of the components were also presented for the study period. The study shows a good cooperation between GIS and HEC-HMS to apply for water balance study and gives a good estimation of component values despite limited data.
Hadoop-GIS: A High Performance Spatial Data Warehousing System over MapReduce

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present Hadoop-GIS - a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive.
Emergent Gravity, Matrix Models and UV/IR Mixing

We verify explicitly that UV/IR mixing for noncommutative gauge theory can be understood in terms of an induced gravity action, as predicted by the identification [1] of gravity within matrix models of NC gauge theory. More precisely, we obtain the Einstein-Hilbert action by integrating out a scalar field in the adjoint. It arises from the well-known UV/IR mixing of NC gauge theory, which is carefully re-analyzed and interpreted in terms of gravity. The matrix model therefore contains gravity as an IR effect, due to UV/IR mixing.
Combination Treatment of Prostate Cancer Cell Lines with Bioactive Soy Isoflavones and Perifosine Causes Increased Growth Arrest and/or Apoptosis

Purpose: To determine whether targeting the androgen receptor (AR) and Akt pathways using a combination of genistein combined polysaccharide (GCP) and perifosine is more effective at inducing growth arrest/apoptosis in prostate cancer cells compared with treatment with GCP or perifosine as single agents. Experimental Design: The effect of GCP and perifosine treatment was assessed in five prostate cancer cell lines: LNCaP (androgen sensitive), LNCaP-R273H, C4-2, Cds1, and PC3 (androgen insensitive). A clonogenic assay assessed the long-term effects on cell growth and survival. Flow cytometry and Western blot analysis of poly(ADP)ribose polymerase cleavage were used to assess short-term effects. Preliminary studies to investigate mechanism of action included Western blot for P-Akt, Akt, P-p70S6K, p70S6K, p53, and p21; prostate-specific antigen analysis; and the use of myristoylated Akt and AR-specific small interfering RNA. Results: Combination treatment with GCP and perifosine caused a decrease in clonogenic potential in all cell lines. In short-term assays, growth arrest was observed in the majority of cell lines, as well as increased inhibition of Akt activity and induction of p21 expression. Increased apoptosis was only observed in LNCaP. Knockdown of AR caused a further increase in apoptosis. Conclusion: Combination treatment with GCP and perifosine targets the Akt pathway in the majority of the prostate cancer cell lines and causes increased inhibition of cell growth and clonogenicity. In LNCaP, combination treatment targets both the Akt and AR pathways and causes increased apoptosis. These data warrant clinical validation in prostate cancer patients.
Evaluation of Anti-Quorum-Sensing Activity of Edible Plants and Fruits through Inhibition of the N-Acyl-Homoserine Lactone System in Chromobacterium violaceum and Pseudomonas aeruginosa

Background: To find out an alternative strategy to antibiotic usage against bacterial infection. Materials and Methods: The purpose of this study is to describe the quorum-sensing (QS) inhibitory activity of edible plants and fruits against N-acyl-homoserine lactone (AHL)-mediated violacein production in Chromobacterium violaceum and virulence factor expression in Pseudomonas aeruginosa PAO1. Results: Aqueous extracts of Ananas comosus (Bromeliaceae), Musa paradiciaca (Musaceae), Manilkara zapota (Sapotaceae) and Ocimum sanctum (Lamiaceae) were prepared and anti-QS activity of each extract was tested against AHL-mediated phenotypic expressions of C. violaceum and PAO1. Most of these extracts showed significant reduction in AHL-mediated violacein production in C. violaceum as well as pyocyanin pigment, staphylolytic protease, elastase production and biofilm formation in PAO1. However, these extracts were not inhibitory to bacterial growth, revealing that the QS inhibition by the extracts is not related to static or killing effects on the bacteria. Conclusions: The present study identified the anti-QS activity of A. comosus, M. paradiciaca, M. zapota and O. sanctum. An AHL-inactivating compound from these plant sources can be used as an alternative to antibiotic compounds to prevent AHL-mediated bacterial infection in higher organisms.
The balance between positive and negative interactions in a savanna

Facilitation (the positive effects of one species on another), in theory, can lead to positive spatial associations between species. Competition (the negative effects of one species on another) can lead to negative spatial associations. Therefore the magnitude and the direction of the spatial association between Quercus fusiformis and Juniperus ashei were measured in multiple savanna sites on the Edwards Plateau in central Texas. Stratified random sampling was used to determine the number of Juniperus ashei individuals in each of three size classes found in each of three types of habitat (under Quercus fusiformis canopy, under Juniperus ashei canopy, and in open grassy areas). This observed spatial distribution was compared with the distribution generated by a null model that assumed no interaction between J. ashei individuals and habitat type. J. ashei individuals were found in significantly higher than expected frequencies under woody canopies and in significantly lower than expected frequencies in the open grassland. The positive association with Quercus fusiformis and Juniperus ashei canopies was significant for all size classes of target J. ashei individuals, but the strength of the pattern decreased with size. Mechanisms other than facilitation could explain the spatial distribution of J. ashei on the Edwards Plateau (e.g. seed dispersal). This study suggests that if facilitation exists in this system, it probably occurs between woody canopy and J. ashei during the early stages of its life history.
Blind Saccades: An Asynchrony between Seeing and Looking

Saccades may not always wait for the completion of the perceptual analysis. By taking advantage of a motion-induced illusion of position and of the spontaneous scatter of saccade latency, we showed that in normal observers, regular saccades (latency, ∼200 ms) were accurately directed to the target, whereas at higher latencies, saccades were increasingly biased by visual motion until they reflected the perceptual illusion. We reconstructed the time course of saccadic direction coding and identified an early phase in which saccades are mostly predictive (latencies less than ∼100 ms), followed by a phase in which saccades are guided by the target position signal (latencies ∼100–250 ms), and a later phase associated with the buildup of mislocalization (∼250–450 ms). This transient dissociation between action and perception indicates that seeing and looking are based on asynchronous processes, possibly because of independent thresholds for saccades and perceptual localization. The metrics of a saccade would then reflect the evolution of cortical visual signals from a predictive state to a perceptual state, passing through an intermediate visuomotor state. If saccades occur during the visuomotor state, they escape the tricks of perception.
Is epsilon-aminocaproic acid as effective as aprotinin in reducing bleeding with cardiac surgery?: a meta-analysis.

BACKGROUND Although aprotinin is known to be effective in reducing postoperative hemorrhage after cardiac surgery, epsilon-aminocaproic acid, an alternative antifibrinolytic, is considerably less expensive. Because the results of 3 small randomized clinical trials comparing these 2 agents directly were inconclusive, we performed a meta-analysis to compare the relative effectiveness and adverse-effect profile of these 2 agents against placebo. METHODS AND RESULTS Data from 52 randomized clinical trials published between 1985 and 1998 involving the use of epsilon-aminocaproic acid (n=9) or aprotinin (n=46) in patients undergoing cardiac surgery were abstracted. Our primary outcomes were total blood loss, red blood cell transfusion rates and amounts, reexploration, stroke, myocardial infarction, and mortality. The meta-analysis revealed substantial reductions in total blood loss with epsilon-aminocaproic acid and low-dose aprotinin (each with a 35% reduction versus placebo, P<0.001) and high-dose aprotinin (53% reduction, P<0.001). There were identical reductions in total postoperative transfusions with epsilon-aminocaproic acid (61% reduction versus placebo, P<0. 010) and high-dose aprotinin (62% reduction, P<0.001). The proportion of patients transfused was similarly reduced with epsilon-aminocaproic acid (OR, 0.32; 95% CI, 0.15 to 0.69) and high-dose aprotinin (OR, 0.28; 0.22 to 0.37). Although both drugs reduced rates of reexploration to similar degrees, this effect was statistically significant only with high-dose aprotinin (OR, 0.39; 0. 24 to 0.61). epsilon-Aminocaproic acid and aprotinin had no effect on risks of postoperative myocardial infarction or overall mortality. CONCLUSIONS Because the 2 antifibrinolytic agents appear to have similar efficacies, the considerably less-expensive epsilon-aminocaproic acid may be preferred over aprotinin for reducing hemorrhage with cardiac surgery.