gebhart/patrepeval huggingface dataset:
Point Cloud Attribute Compression Using 3-D Intra Prediction and Shape-Adaptive Transforms (2016)

With the increased proliferation of applications using 3-D capture technologies for applications such as virtual reality, mobile mapping, scanning of historical artifacts, and 3-D printing, representing these kinds of data as 3-Dpoint clouds has become a popular method for storing and conveying the data independently of how it was captured. A point cloud consists of a set of coordinates indicating the location of each point, along with one or more attributes such as color associated with each point. Because the size of point cloud data can be quite large, compression is needed to efficiently store or transmit this data. This paper, motivated by techniques currently being used for image and video coding, proposes methods using 3-D block-based prediction and transform coding to compress point cloud attributes. Experimental results using a modified shape-adaptive DCT tailored for use in 3-D point clouds and a benchmark using 3-D graph transforms are shown.
Discriminative Feature Learning for Real-Time SAR Automatic Target Recognition With the Nonlinear Analysis Cosparse Model (2018)

This letter presents an efficient application of the nonlinear analysis cosparse model (NACM) to the task of real-time synthetic aperture radar automatic target recognition (ATR). In contrast to the conventional synthesis sparse representation model, NACM enables efficient sparse feature extraction and selection using a feed-forward mechanism. Furthermore, NACM does not require a sparsity-inducing regularizer. This model uses a task-driven learning framework, in which a naive Bayes or a discriminative classifier is adaptively learned along with the regularized features. Experimental results with the moving and stationary target acquisition and recognition benchmark demonstrate the effectiveness and efficiency of our proposed approach. Compared with traditional classification algorithms using sparse representation, our approach not only achieves higher or comparable recognition accuracy but also dramatically reduces the execution time for real-time ATR.
Insulin-Like Growth Factor I Synergizes with Interleukin 4 for Hematopoietic Cell Proliferation Independent of Insulin Receptor Substrate Expression (1999)

In the present study, we investigated the potential role of insulin-like growth factor I (IGF-I) receptor (IGF-IR) in cell proliferation by overexpressing it in 32D myeloid progenitor cells. The overexpression of IGF-IR caused the transfectants to proliferate in response to IGF-I in the absence of insulin receptor substrate (IRS) expression. The activation of overexpressed wild-type IGF-IR, but not that of an ATP-binding mutant of IGF-IR, resulted in the increased tyrosine phosphorylation of several intracellular proteins, including SHC, Src homology 2-containing inositol-5-phosphatase, protein kinase C-delta, and Erk2. Grb2 association with SHC and mitogen-activated protein kinase (MAPK) activity was also enhanced in response to IGF-I stimulation. Interestingly, the stimulation of the IGF-IR transfectants with interleukin 4 (IL-4) also resulted in strong mitogenesis independent of IRS expression. Moreover, IGF-I and/or IL-4 induced long-term cell growth of the IGF-IR transfectants. IL-4 was able to synergize with IGF-I for DNA synthesis, even in the parental 32D cells and a pro-B-cell line, Baf3, indicating the physiological importance of the two growth factors in hematopoietic cell proliferation. IL-4 stimulation of the IGF-IR transfectants resulted in enhanced tyrosine phosphorylation of SHC, Erk2, and signal transducer and activator of transcription 6 (STAT6) proteins. Both IL-4 and IGF-I were able to induce c-myc early response gene expression, and this expression was maximal in the presence of both factors. Finally, we demonstrated that a MAPK kinase inhibitor was able to suppress mitogenesis of the IGF-IR transfectants in response to IGF-I and/or IL-4. Together, our results suggest that IL-4 synergizes with IGF-I for hematopoietic cell proliferation, likely through cross talk between SHC/Grb2/MAPK and STAT6 pathways and through c-myc gene up-regulation.
Palladium (0) catalyzed Suzuki cross-coupling reactions of 2,4-dibromothiophene: selectivity, characterization and biological applications (2015)

A series of novel 2-aryl1-4-bromothiophenes (2a–f), biarylthiophenes with non-identical aryl groups (3a–e) and biarylthiophenes with identical aryl groups (4a–f) were synthesized in moderate to excellent yields by using different arylboronic acids in a Suzuki–Miyaura cross-coupling reaction. The experimental results showed that the use of K2CO3 as base resulted in moderate yields compared with that of good yields obtained upon using K3PO4. The highest yield obtained using K3PO4 was 82% for 2, 4-bis (4-chlorophenyl) thiophene (4d). The synthesized compounds in the present study were examined for their biofilm inhibition and hemolysis assay. Among all compounds 2, 4-bis (4-methoxyphenyl) thiophene (4b) was found to strongly inhibit the formation of bacterial biofilm against E. coli. The compound 4b exhibited higher inhibition (80.92%) compared with the standard Rifampicin with 97.43% inhibition. The compound 2, 4-bis (4-chlorophenyl) thiophene (4d) displayed strong anti-biofilm activity with its ability to prevent the formation of Pasteurell amultocida biofilm at the percent inhibition of 74.53%. In addition, 2f showed the highest percentage hemolysis 16.0% compared with that of the standard Triton-X-100. 3
In vitro cultivation of Treponema pallidum: independent confirmation (1982)

In vitro cultivation of the virulent Nichols strain of Treponema pallidum was achieved in a tissue culture system as described by A. H. Fieldsteel, D. L. Cox, and R. A. Moeckli (Infect. Immun. 32:908-915, 1981). In 7 of 8 experiments, 8.9- to 26.2-fold increases in the number of T. pallidum were observed over a 12- to 12-day period of incubation.
Identification of a Continuously Stable and Commercially Available Cell Line for the Identification of Infectious African Swine Fever Virus in Clinical Samples (2020)

African swine fever virus (ASFV) is causing outbreaks both in domestic pigs and wild boar in Europe and Asia. In 2018, the largest pig producing country, China, reported its first outbreak of African swine fever (ASF). Since then, the disease has quickly spread to all provinces in China and to other countries in southeast Asia, and most recently to India. Outbreaks of the disease occur in Europe as far west as Poland, and one isolated outbreak has been reported in Belgium. The current outbreak strain is highly contagious and can cause a high degree of lethality in domestic pigs, leading to widespread and costly losses to the industry. Currently, detection of infectious ASFV in field clinical samples requires accessibility to primary swine macrophage cultures, which are infrequently available in most regional veterinary diagnostic laboratories. Here, we report the identification of a commercially available cell line, MA-104, as a suitable substrate for virus isolation of African swine fever virus.
Wnt7b stimulates embryonic lung growth by coordinately increasing the replication of epithelium and mesenchyme (2008)

The effects of Wnt7b on lung development were examined using a conditional Wnt7b-null mouse. Wnt7b-null lungs are markedly hypoplastic, yet display largely normal patterning and cell differentiation. In contrast to findings in prior hypomorphic Wnt7b models, we find decreased replication of both developing epithelium and mesenchyme, without abnormalities of vascular smooth muscle development. We further demonstrate that Wnt7b signals to neighboring cells to activate both autocrine and paracrine canonical Wnt signaling cascades. In contrast to results from hypomorphic models, we show that Wnt7b modulates several important signaling pathways in the lung. Together, these cascades result in the coordinated proliferation of adjacent epithelial and mesenchymal cells to stimulate organ growth with few alterations in differentiation and patterning.
Irestatin, a potent inhibitor of IRE1α and the unfolded protein response, is a hypoxia-selective cytotoxin and impairs tumor growth (2007)

3514 Background: The unfolded protein response (UPR) is an adaptive response to the toxic accumulation of misfolded proteins in the endoplasmic reticulum (ER), and is activated in solid tumors. IRE1a is a core component of the UPR and responds to ER stress through activation of its dual kinase and endonuclease domains. The IRE1a endonuclease splices the mRNA for XBP-1, generateing a potent transcription factor that is required for tumor growth. Methods: We developed a fibrosarcoma cell line expressing a fusion of unprocessed XBP-1 inserted upstream of firefly luciferase. Under ER stress, IRE1a catalyzes the removal of a 26-nt intronic sequence from the XBP-1 mRNA, introducing a shift in reading frame that permits translation of luciferase. We screened a chemical library of 66,000 small molecules for inhibitors of XBP-luciferase activity and identified 12 molecules, termed irestatins, which consistently inhibited the IRE1a signaling module without affecting the activity of a control CMV-luciferase reporter. We pursued several of the most potent irestatins, including irestatin 9389, which inhibited XBP-luciferase activity with an IC50 of ∼25 nM. Results: Irestatin-mediated inhibition of the IRE1a endonuclease impairs the growth of malignant myeloma cells and inhibits the survival of oxygen-starved tumor cells in vitro. Exposure to irestatin 9389 (2.5 μM) had a negligible effect on the survival of HT1080 cells cultured under normal oxygen conditions. However, in cells cultured under hypoxia for 48 hours, irestatin 9389 inhibited colony formation by nearly 80-fold (48% vs. 0.62%). A two-week course of treatment with single-agent irestatin 9389 (50 mg/kg) administered every other day by i.p. bolus injection was well tolerated and strongly inhibited the growth of subcutaneous HT1080 tumor xenografts (1790 ± 380 mm 3 vs. 480 ± 210 mm 3 ; P<0.01). Conclusion: Irestatins define a novel class of hypoxia- and ER stress-selective agents targeted to the underlying physiological response to the tumor microenvironment. Intratumoral inhibition of the UPR can potentiate cell death and impair tumor growth. Molecular intervention against central components of the UPR may represent an effective therapeutic strategy in cancer treatment. No significant financial relationships to disclose.
A Study of the Structural Similarity Image Quality Measure with Applications to Image Processing (2012)

Since its introduction in 2004, the Structural Similarity (SSIM) index has gained widespread popularity as an image quality assessment measure. SSIM is currently recognized to be one of the most powerful methods of assessing the visual closeness of images. That being said, the Mean Squared Error (MSE), which performs very poorly from a perceptual point of view, still remains the most common optimization criterion in image processing applications because of its relative simplicity along with a number of other properties that are deemed important. In this thesis, some necessary tools to assist in the design of SSIM-optimal algorithms are developed. This work combines theoretical developments with experimental research and practical algorithms.\n\nThe description of the mathematical properties of the SSIM index represents the principal theoretical achievement in this thesis. Indeed, it is demonstrated how the SSIM index can be transformed into a distance metric. Local convexity, quasi-convexity, symmetries and invariance properties are also proved. The study of the SSIM index is also generalized to a family of metrics called normalized (or M-relative) metrics.\n\nVarious analytical techniques for different kinds of SSIM-based optimization are then devised. For example, the best approximation according to the SSIM is described for orthogonal and redundant basis sets. SSIM-geodesic paths with arclength parameterization are also traced between images. Finally, formulas for SSIM-optimal point estimators are obtained.\n\nOn the experimental side of the research, the structural self-similarity of images is studied. This leads to the confirmation of the hypothesis that the main source of self-similarity of images lies in their regions of low variance.\n\nOn the practical side, an implementation of local statistical tests on the image residual is proposed for the assessment of denoised images. Also, heuristic estimations of the SSIM index and the MSE are developed. \n\nThe research performed in this thesis should lead to the development of state-of-the-art image denoising algorithms. A better comprehension of the mathematical properties of the SSIM index represents another step toward the replacement of the MSE with SSIM in image processing applications.
Music Playlist Recommendation Based on User Heartbeat and Music Preference (2009)

In this paper, we present a new user heartbeat and preference aware music recommendation system. The system can not only recommend a music playlist based on the user's music preference but also the music playlist is generated based on the user's heartbeat. If the user's heartbeat is higher than the normal heartbeat which is 60-100 beats per minutes (age 18 and over) or 70-100 beats per minutes (age 6-18), the system generates a user preferred music playlist using Markov decision process to transfer the user's heartbeat back to the normal range with the minimum time cost; if the user's heartbeat is normal, the system generates a user preferred music playlist to keep the user's heartbeat within the normal range; If the user's heartbeat is lower than the normal heartbeat, the system generates a user preferred music playlist using Markov decision process to uplift the user's heartbeat back to the normal range with the minimum time cost.
Study of Mycoprotein Production Using Fusarium oxysporum PTCC 5115 and Reduction of its RNA Content (2008)

In this research, production of mycoprotein by Fusarium oxysporum (PTCC 5115) was investigated. In order to achieve the highest production yield, cultivation parameters including temperature, agitation speed, carbon and nitrogen sources were optimized by applying the Taguchi design. The optimum conditions obtained for mycoprotein production were: 25°C, 150 rpm, 5 g of glucose per liter and 3.4 g of ammonium dihydrogen phosphate per liter which resulted in the product containing 42% (w/w) crude protein. RNA content was reduced to an acceptable level through heat treatment of fungal biomass at 65°C for 15 min. This heat shock procedure reduced RNA level to less than 1%, which is recognized as an acceptable level for human food grade products.
A cocaine insensitive chimeric insect serotonin transporter reveals domains critical for cocaine interaction (2002)

Serotonin transporters are key target sites for clinical drugs and psychostimulants, such as fluoxetine and cocaine. Molecular cloning of a serotonin transporter from the central nervous system of the insect Manduca sexta enabled us to define domains that affect antagonist action, particularly cocaine. This insect serotonin transporter transiently expressed in CV-1 monkey kidney cells exhibits saturable, high affinity Na+ and Cl- dependent serotonin uptake, with estimated Km and Vmax values of 436 +/- 19 nm and 3.8 +/- 0.6 x 10-18 mol.cell.min-1, respectively. The Manduca high affinity Na+/Cl- dependent transporter shares 53% and 74% amino acid identity with the human and fruit fly serotonin transporters, respectively. However, in contrast to serotonin transporters from these two latter species, the Manduca transporter is inhibited poorly by fluoxetine (IC50 = 1.23 micro m) and cocaine (IC50 = 12.89 micro m). To delineate domains and residues that could play a role in cocaine interaction, the human serotonin transporter was mutated to incorporate unique amino acid substitutions, detected in the Manduca homologue. We identified a domain in extracellular loop 2 (amino acids 148-152), which, when inserted into the human transporter, results in decreased cocaine sensitivity of the latter (IC50 = 1.54 micro m). We also constructed a number of chimeras between the human and Manduca serotonin transporters (hSERT and MasSERT, respectively). The chimera, hSERT1-146/MasSERT106-587, which involved N-terminal swaps including transmembrane domains (TMDs) 1 and 2, was remarkably insensitive to cocaine (IC50 = 180 micro m) compared to the human (IC50 = 0.431 micro m) and Manduca serotonin transporters. The chimera MasSERT1-67/hSERT109-630, which involved only the TMD1 swap, showed greater sensitivity to cocaine (IC50 = 0.225 micro m) than the human transporter. Both chimeras showed twofold higher serotonin transport affinity compared to human and Manduca serotonin transporters. Our results show TMD1 and TMD2 affect the apparent substrate transport and antagonist sensitivity by possibly providing unique conformations to the transporter. The availability of these chimeras facilitates elucidation of specific amino acids involved in interactions with cocaine.
Dynamic Voltage and Frequency Scaling in Multimedia Servers (2013)

In this paper, we experimentally investigate the scope and usefulness of Dynamic Voltage and Frequency Scaling (DVFS) in multimedia servers. For our experiment, we considered four scaling policies, two heterogeneous servers, and two different application scenarios. In the first scenario, we used an IO-Intensive multimedia downloading application while in the second scenario we used a predominately CPU-Intensive application, namely, a video transcoder. We will show that while the advantage of DVFS for IO-Intensive applications is apparent, it is not so for CPU-Intensive applications. The advantage in IO-Intensive applications depends on the selection of frequencies in the machine and the way the CPU speed scales. We observed that the choice of a particular DFVS technique became more consequential when the machine had a wide selection of operation frequencies while a gradual change in the operation frequency was more energy efficient. For CPU-Intensive applications, the use of DVFS was counter productive and the overhead of scaling was not negligible.
Cyclical Annealing Schedule: A Simple Approach to Mitigating KL Vanishing (2019)

Variational autoencoders (VAEs) with an auto-regressive decoder have been applied for many natural language processing (NLP) tasks. The VAE objective consists of two terms, (i) reconstruction and (ii) KL regularization, balanced by a weighting hyper-parameter β. One notorious training difficulty is that the KL term tends to vanish. In this paper we study scheduling schemes for β, and show that KL vanishing is caused by the lack of good latent codes in training the decoder at the beginning of optimization. To remedy this, we propose a cyclical annealing schedule, which repeats the process of increasing βmultiple times. This new procedure allows the progressive learning of more meaningful latent codes, by leveraging the informative representations of previous cycles as warm re-starts. The effectiveness of cyclical annealing is validated on a broad range of NLP tasks, including language modeling, dialog response generation and unsupervised language pre-training.
Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning (2018)

Many interesting problems in machine learning are being revisited with new deep learning tools. For graph-based semisupervised learning, a recent important development is graph convolutional networks (GCNs), which nicely integrate local vertex features and graph topology in the convolutional layers. Although the GCN model compares favorably with other state-of-the-art methods, its mechanisms are not clear and it still requires a considerable amount of labeled data for validation and model selection. In this paper, we develop deeper insights into the GCN model and address its fundamental limits. First, we show that the graph convolution of the GCN model is actually a special form of Laplacian smoothing, which is the key reason why GCNs work, but it also brings potential concerns of over-smoothing with many convolutional layers. Second, to overcome the limits of the GCN model with shallow architectures, we propose both co-training and self-training approaches to train GCNs. Our approaches significantly improve GCNs in learning with very few labels, and exempt them from requiring additional labels for validation. Extensive experiments on benchmarks have verified our theory and proposals.
Manganese superoxide dismutase expression inhibits soft agar growth in JB6 clone41 mouse epidermal cells (1997)

Manganese superoxide dismutase (MnSOD) has been found to be depleted in a variety of tumor cells as well as in in vitro transformed cell lines, suggesting that MnSOD may function as an anticarcinogen by protecting the cell from oxidant-induced carcinogenesis. The relationship between MnSOD expression and tumor promotion was studied by transfection of a human MnSOD cDNA into the promotable mouse epidermal cell line JB6 clone41. The effect of MnSOD overexpression on the promotion-sensitive phenotype of JB6 cells was assessed by measuring growth characteristics such as growth rate and the ability to form colonies in soft agar. Compared with the parental and vector-transfected (gpt) control cells, MnSOD-overexpressing cells had a slower growth rate and their ability to form colonies in soft agar was significantly decreased in response to 12-O-tetradecanoylphorbol-13-acetate (TPA) treatment. Since the transformation-sensitive phenotype of JB6 clone41 cells is associated with increased expression of the transcription factor AP-1, we compared c-jun and c-fos mRNA expression in MnSOD-transfected and control JB6 cells. Overexpression of MnSOD led to a significant decrease in c-jun and c-fos expression in response to treatment with TPA or the oxidant promoter superoxide. These findings indicate that the promotion-sensitive phenotype of JB6 clone41 cells can be reverted by increasing MnSOD intracellularly. A possible mechanism is that elevated MnSOD expression might change the intracellular redox state by altering the balance of reactive oxygen species. This could lead to a modulation of TPA and oxidant-induced signal transduction pathways controlling cell growth and differentiation.
The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic (2016)

In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.