gebhart/patrepeval huggingface dataset:
Intracellular Association of Glycine Receptor with Gephyrin Increases Its Plasma Membrane Accumulation Rate (2004)

Gephyrin, a tubulin-binding protein, is the core of inhibitory postsynaptic scaffolds stabilizing glycine receptors (GlyRs) and/or GABA(A) receptors. Previous ultrastructural studies in vivo and in vitro have reported a localization of gephyrin to intracellular cisternas during development or after glycinergic denervation (Seitanidou et al., 1992; Colin et al., 1996, 1998). These data were compatible with a traffic of this cytoplasmic, but membrane-associated, protein together with membrane proteins such as GlyR after exocytosis and/or endocytosis pathways. We have now investigated the consequences of a GlyR-gephyrin interaction on the localization and the dynamics of these two molecules in African green monkey kidney cells (COS-7) cells and in neurons transfected with green fluorescent protein-tagged-gephyrin and myc-tagged GlyR alpha1 subunits. In these experiments, myc-tagged GlyR alpha1 contained, or did not contain, the gephyrin-binding sequence (betagb) of the GlyR beta subunit. We report here that GlyR-gephyrin interaction localizes gephyrin to GlyR-containing organelles. Videomicroscopy and nocodazole treatment indicate that the movements of these vesicles are microtubule dependent. Expressing GlyR alpha1 with a thrombin cleavage site between the myc-tag and the N terminal of the GlyR alpha1 subunit (Rosenberg et al., 2001) allowed monitoring of newly inserted receptors in the cell surface. Using temperature changes to block GlyR in, and then release it from, the trans-Golgi network, we show that gephyrin accelerates the accumulation of GlyR at the cell surface. Therefore, our data strongly suggest that some GlyR clusters are associated with gephyrin on their way to the cell surface and that this association increases the accumulation of GlyR at the plasma membrane.
Can Spatiotemporal 3D CNNs Retrace the History of 2D CNNs and ImageNet? (2017)

The purpose of this study is to determine whether current video datasets have sufficient data for training very deep convolutional neural networks (CNNs) with spatio-temporal three-dimensional (3D) kernels. Recently, the performance levels of 3D CNNs in the field of action recognition have improved significantly. However, to date, conventional research has only explored relatively shallow 3D architectures. We examine the architectures of various 3D CNNs from relatively shallow to very deep ones on current video datasets. Based on the results of those experiments, the following conclusions could be obtained: (i) ResNet-18 training resulted in significant overfitting for UCF-101, HMDB-51, and ActivityNet but not for Kinetics. (ii) The Kinetics dataset has sufficient data for training of deep 3D CNNs, and enables training of up to 152 ResNets layers, interestingly similar to 2D ResNets on ImageNet. ResNeXt-101 achieved 78.4% average accuracy on the Kinetics test set. (iii) Kinetics pretrained simple 3D architectures outperforms complex 2D architectures, and the pretrained ResNeXt-101 achieved 94.5% and 70.2% on UCF-101 and HMDB-51, respectively. The use of 2D CNNs trained on ImageNet has produced significant progress in various tasks in image. We believe that using deep 3D CNNs together with Kinetics will retrace the successful history of 2D CNNs and ImageNet, and stimulate advances in computer vision for videos. The codes and pretrained models used in this study are publicly available. https://github.com/kenshohara/3D-ResNets-PyTorch
DNA Topoisomerases: Structure, Function, and Mechanism (2001)

DNA topoisomerases solve the topological problems associated with DNA replication, transcription, recombination, and chromatin remodeling by introducing temporary single- or double-strand breaks in the DNA. In addition, these enzymes fine-tune the steady-state level of DNA supercoiling both to facilitate protein interactions with the DNA and to prevent excessive supercoiling that is deleterious. In recent years, the crystal structures of a number of topoisomerase fragments, representing nearly all the known classes of enzymes, have been solved. These structures provide remarkable insights into the mechanisms of these enzymes and complement previous conclusions based on biochemical analyses. Surprisingly, despite little or no sequence homology, both type IA and type IIA topoisomerases from prokaryotes and the type IIA enzymes from eukaryotes share structural folds that appear to reflect functional motifs within critical regions of the enzymes. The type IB enzymes are structurally distinct from all other known topoisomerases but are similar to a class of enzymes referred to as tyrosine recombinases. The structural themes common to all topoisomerases include hinged clamps that open and close to bind DNA, the presence of DNA binding cavities for temporary storage of DNA segments, and the coupling of protein conformational changes to DNA rotation or DNA movement. For the type II topoisomerases, the binding and hydrolysis of ATP further modulate conformational changes in the enzymes to effect changes in DNA topology.
Facile Synthesis of 4-Hydroxycinnamyl p-Coumarates (1998)

Coniferyl p-coumarate (4-hydroxy-3-methoxycinnamyl 4-hydroxycinnamate) and sinapyl p-coumarate (3,5-dimethoxy-4-hydroxycinnamyl 4-hydroxycinnamate) were synthesized in high overall yield. In this improved method acetate was used as the phenol protecting group instead of 2,4-dinitrophenyl ether; selective deacetylation, without cinnamate ester hydrolysis, was accomplished with neat pyrrolidine. Keywords: Coniferyl p-coumarate; sinapyl p-coumarate; lignin; acylation; grasses; radical coupling; deacetylation
Apoptosis of hepatoma cells SMMC-7721 induced byGinkgo bilobaseed polysaccharide (2002)

GBSP could potentially induce the apoptosis of SMMC-7721 cells.
The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes (2003)

Expression of amino acid biosynthesis genes in bacteria is often repressed when abundant supplies of the cognate amino acid are available. Repression of the Bacillus subtilis lysC gene by lysine was previously shown to occur at the level of premature termination of transcription. In this study we show that lysine directly promotes transcription termination during in vitro transcription with B. subtilis RNA polymerase and causes a structural shift in the lysC leader RNA. We find that B. subtilis lysC is a member of a large family of bacterial lysine biosynthesis genes that contain similar leader RNA elements. By analogy with related regulatory systems, we designate this leader RNA pattern the "L box." Genes in the L box family from Gram-negative bacteria appear to be regulated at the level of translation initiation rather than transcription termination. Mutations of B. subtilis lysC that disrupt conserved leader features result in loss of lysine repression in vivo and loss of lysine-dependent transcription termination in vitro. The identification of the L box pattern also provides an explanation for previously described mutations in both B. subtilis and Escherichia coli lysC that result in lysC overexpression and resistance to the lysine analog aminoethylcysteine. The L box regulatory system represents an example of gene regulation using an RNA element that directly senses the intracellular concentration of a small molecule.
Gene therapy for hemophilia (2006)

Gene therapy has been successful in a patient with hemophilia B, but expression was unstable due to an immune response. Abrogating immune responses is the next major hurdle for achieving long-lasting gene therapy.
Conclusion (1994)

R. S. Thomas’s Experimenting with an Amen carries the argument of this book virtually into the nineties — especially if a realistic reader-reception period is allowed.1 However, all but one of the poets considered above belong/ed to a now ageing generation. It was that generation, I have implied throughout, which negotiated the emergence of postmodernity and evaluated its implication in the remnants of both modernity and modernism. Yet we are clearly now in a newer situation — if only because of the widespread assimilation of the postmodern thesis itself — and there are many fresh voices which have sought to define our current situation. Whilst working on this book I have read, for instance, The New British Poetry: 1968–882 and Contemporary Poetry Meets Modern Theory,3 both of which are mainly concerned with the work of younger poets. I should have liked myself to have considered the contributions of Roy Fisher, Lee Harwood and Tom Raworth, in particular, not to mention some more recent American poets. However, I am not sure my sense of the “Poetry of Postmodernity” would have been much modified, though it would have been enriched. But any book has to end somewhere. Since the Second World War there has been a dialogical relationship between English and American poets (most dramatically symbolised in the now almost mythical marriage of Sylvia Plath and Ted Hughes) which has created a privileged, even rarified, space for the representation of quasi-global postmodernity. That has been the focus of the book.
Spectral beam combining of YB-doped fiber lasers in an external cavity (1999)

The outputs of two fiber lasers have been combined in an external cavity. This proof-of-concept demonstration shows the feasibility of beam combining many (tens to hundreds) fiber gain elements.
Receptor-like Genes in the Major Resistance Locus of Lettuce Are Subject to Divergent Selection (1998)

Disease resistance genes in plants are often found in complex multigene families. The largest known cluster of disease resistance specificities in lettuce contains the RGC2 family of genes. We compared the sequences of nine full-length genomic copies of RGC2 representing the diversity in the cluster to determine the structure of genes within this family and to examine the evolution of its members. The transcribed regions range from at least 7.0 to 13.1 kb, and the cDNAs contain deduced open reading frames of approximately 5. 5 kb. The predicted RGC2 proteins contain a nucleotide binding site and irregular leucine-rich repeats (LRRs) that are characteristic of resistance genes cloned from other species. Unique features of the RGC2 gene products include a bipartite LRR region with >40 repeats. At least eight members of this family are transcribed. The level of sequence diversity between family members varied in different regions of the gene. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions was lowest in the region encoding the nucleotide binding site, which is the presumed effector domain of the protein. The LRR-encoding region showed an alternating pattern of conservation and hypervariability. This alternating pattern of variation was also found in all comparisons within families of resistance genes cloned from other species. The Ka /Ks ratios indicate that diversifying selection has resulted in increased variation at these codons. The patterns of variation support the predicted structure of LRR regions with solvent-exposed hypervariable residues that are potentially involved in binding pathogen-derived ligands.
OmniTouch (2011)

OmniTouch is a wearable depth-sensing and projection system that enables interactive multitouch applications on everyday surfaces. Beyond the shoulder-worn system, there is no instrumentation of the user or environment. Foremost, the system allows the wearer to use their hands, arms and legs as graphical, interactive surfaces. Users can also transiently appropriate surfaces from the environment to expand the interactive area (e.g., books, walls, tables). On such surfaces - without any calibration - OmniTouch provides capabilities similar to that of a mouse or touchscreen: X and Y location in 2D interfaces and whether fingers are "clicked" or hovering, enabling a wide variety of interactions. Reliable operation on the hands, for example, requires buttons to be 2.3cm in diameter. Thus, it is now conceivable that anything one can do on today's mobile devices, they could do in the palm of their hand.
Characterization of an Extracellular Keratinase from Microsporum canis. (2000)

Extracellular keratinase (Ekase) 48-, 34- and 31.5-kDa polypeptides, which were isolated from Microsporum canis and examined by immunoblotting reacted with a monoclonal antibody against Ekase of M. canis. We analyzed the amino acid and determined the first 17 amino acid NH2-terminal sequences of the 48-, 34- and 31.5-kDa polypeptides. These polypeptides had a high aspartic acid, glycine and alanine content, respectively. The first 17 amino acid residues of the 34-kDa polypeptide were homologous to those of thermomycolin. This indicated that the 34-kDa polypeptide of Ekase is homologous to the thermomycolin produced by Malbranchea pulchella. Furthermore, Ekase was very heat-stable in the presence of 50 mM CaCl2 at 55 degrees C, since 50% of the initial activity remained. In contrast, no activity was detected after heating in the absence of CaCl2. These results indicate a close relationship between dermatophytes and M. pulchella.
CXCR4 inhibitor AMD3100 disrupts the interaction of multiple myeloma cells with the bone marrow microenvironment and enhances their sensitivity to therapy (2009)

The interaction of multiple myeloma (MM) cells with their microenvironment in the bone marrow (BM) provides a protective environment and resistance to therapeutic agents. We hypothesized that disruption of the interaction of MM cells with their BM milieu would lead to their sensitization to therapeutic agents such as bortezomib, melphalan, doxorubicin, and dexamethasone. We report that the CXCR4 inhibitor AMD3100 induces disruption of the interaction of MM cells with the BM reflected by mobilization of MM cells into the circulation in vivo, with kinetics that differed from that of hematopoietic stem cells. AMD3100 enhanced sensitivity of MM cell to multiple therapeutic agents in vitro by disrupting adhesion of MM cells to bone marrow stromal cells (BMSCs). Moreover, AMD3100 increased mobilization of MM cells to the circulation in vivo, increased the ratio of apoptotic circulating MM cells, and enhanced the tumor reduction induced by bortezomib. Mechanistically, AMD3100 significantly inhibited Akt phosphorylation and enhanced poly(ADP-ribose) polymerase (PARP) cleavage as a result of bortezomib, in the presence of BMSCs in coculture. These experiments provide a proof of concept for the use of agents that disrupt interaction with the microenvironment for enhancement of efficacy of cytotoxic agents in cancer therapy.
High-power, 8W CW, single-quantum-well laser diode array (1988)

Single-quantum-well laser diode arrays are reported to operate up to 6W CW and 8W CW for 100 μm and 200μm aperture sources, respectively, prior to overheating of the active region.
Review article: Is obesity an inflammatory illness? Role of low‐grade inflammation and macrophage infiltration in human white adipose tissue (2006)

There are at least two scientific evidences of human obesity as a chronic inflammatory illness: first, the well-described moderate increase of inflammatory factors in the circulation in obese subjects, and second, the recent identification of macrophage cells infiltrating the white adipose tissue (WAT). These observations led to a revision of the physiopathology of obesity and its co-morbidities. It has been suggested that the 'low-grade' inflammatory state associates with metabolic and cardiovascular complications of obesity. Weight loss is able to improve this inflammatory state by both significantly decreasing circulating inflammatory molecules and macrophage cell infiltration in WAT depots. However, the mechanisms of WAT macrophage recruitment into the adipose tissue and their role in obesity complications have not been defined. This review aims to point out the knowledge on inflammatory cytokines associated with obesity and focuses on macrophage infiltration in human WAT, discussing their recruitment and role. The interactions of macrophages with adipocytes will certainly be the subject of intense investigations in the future.
Optimization of Illumination Frequency and Preclinical Validation of a Wide-field Structured Illumination Microscope Designed for Imaging in situ Tumor Margins (2013)

We present a widefield structured illumination microscope for imaging surgical tumor margins in situ. The impact of frequency and turbidity on optical section thickness and SNR was characterized to determine the optimal imaging frequency.
Identification and characterization of the endophytic plant growth prompter Bacillus Cereus strain mq23 isolated from Sophora Alopecuroides root nodules (2011)

Endophytes MQ23 and MQ23R isolated from Sophora alopecuroides root nodules were characterized by observing their ability to promote plant growth and employing molecular analysis techniques. Results showed that MQ23 and MQ23R are potential N2-fixing endophytes and belong to the same species as Bacillus cereus. MQ23 was shown to be able to produce siderophores, IAA, and demonstrate certain antifungal activity to plant pathogenic fungi. Co-inoculation with MQ23+MQ23II showed a more significant effect than inoculation alone in vitro for most of positive actions suggesting they have a cooperative interaction. Results of plant inoculation with endophytes indicated that the growth indexes of co-inoculated MQ23+MQ23II were higher than those of inoculated alone (p<0.05) (the exception being for root fresh weight) when compared to negative control. There have been little of any studies of nonrhizobial putative endophytes with growth-promotion attributes in S. alopecuroides root nodules. This could be exploited as potential bio-inoculants and biocontrol agents in agriculture.
HPV status‐independent association of alcohol and tobacco exposure or prior radiation therapy with promoter methylation of FUSSEL18, EBF3, IRX1, and SEPT9, but not SLC5A8, in head and neck squamous cell carcinomas (2009)

Abstract Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with more than half a million people being diagnosed with the disease annually. Within the last 2 decades, the human papillomavirus (HPV) has been found to be associated with this malignancy. More recently, HPV‐infected HNSCC has been found to exhibit higher levels of global DNA methylation. In a recent study, we identified five tumor suppressive genes ( IRX1 , EBF3 , SLC5A8 , SEPT9 , and FUSSEL18 ) as frequently methylated in HNSCC biopsies using a global methylation analysis via restriction landmark genomic scanning. In this study, we verify these genes as valid methylation markers in two separate sets of HNSCC specimens. By using the available clinical information linked to the patient specimens, we found a strong association between promoter methylation of FUSSEL18 , IRX1 , and EBF3 and prior radiation therapy ( P &lt; 0.0001) irrespective of HPV status. Also, promoter methylation of FUSSEL18 and SEPTIN9 was found to correlate significantly with exposure to alcohol and tobacco ( P = 0.021). Importantly, in this study, we preliminarily show a trend between HPV16 positivity and specific target gene hypermethylation of IRX1 , EBF3 , SLC5A8 , and SEPT9 . If replicated in a larger study, the HPV status may be a patient selection biomarker when determining the most efficacious treatment modality for these different subsets of patients (e.g., inclusion or exclusion of epigenetic therapies). Equally notable and independent of HPV status, hypermethylation of the promoters of a subset of these genes in recurrences especially in the setting of prior radiation or in the setting of alcohol and tobacco use might help guide adjunctive inclusion or exclusion or epigenetic therapy. © 2009 Wiley‐Liss, Inc.
Sustained Exposure to Nicotine Leads to Extramedullary Hematopoiesis in the Spleen (2006)

The effect of sustained exposure to nicotine, a major constituent of cigarette smoke, on hematopoiesis in the bone marrow (BM) and spleen was evaluated in a murine model. BALB/c mice were exposed to nicotine subcutaneously using 21-day slow-release pellets. Exposure to nicotine had no effect on the proliferation of long-term BM cultures or on their ability to form colonies. However, there was a significant decrease in the generation of lineage-specific progenitor cells, specifically eosinophil (colony-forming unit [CFU]-Eos) progenitors, in the BM of nicotine-exposed mice compared with control mice. Surprisingly, sustained exposure of mice to nicotine was found to induce significant hematopoiesis in the spleen. There was a significant increase in total colony formation as well as eosinophil-, granulocyte-macrophage-, and B-lymphocyte-specific progenitors (CFU-Eos, CFU-GM, and CFU-B, respectively) in nicotine-exposed mice but not in control mice. Sustained exposure to nicotine was associated with significant inhibition of rolling and migration of enriched hematopoietic stem/progenitor cells (HSPCs) across BM endothelial cells (BMECs) in vitro as well as decreased expression of beta2 integrin on the surface of these cells. Although sustained exposure to nicotine has only a modest effect on BM hematopoiesis, our studies indicate that it significantly induces extramedullary hematopoiesis in the spleen. Decreased interaction of nicotine-exposed HSPCs with BMECs (i.e., rolling and migration) may result in altered BM homing of these cells, leading to their seeding and proliferation at extramedullary sites such as the spleen.
A Worldwide Study of the Huntington's Disease Mutation: The Sensitivity and Specificity of Measuring CAG Repeats (1994)

CAG trinucleotide expansion is the molecular basis of Huntington's disease worldwide and is a highly sensitive and specific marker for inheritance of the disease mutation.
Sutureless Closed Hemorrhoidectomy: A New Technique (2001)

The "tissue-welding" properties of this device and the shape of the electrode handpiece may be successfully applied to the performance of an operation most appropriately described as a "modified sutureless closed hemorrhoidectomy." This pilot study shows that this new technique is simple and safe, significantly shortens the operation, and is followed by a significantly easier and shorter recovery.
Tetrahydrocannabivarin exhibits anticonvulsant effects in a piriform cortical brain slice model of epileptiform activity (2006)

Cannabis has been historically used as an anticonvulsant by epilepsy sufferers as long ago as the 1840s (O'Shaughnessy, 1842), although more recent research has highlighted both pro(Kalant, 2004) and anti-convulsant (Alger, 2004) effects of cannabinoids, suggesting that pro-/anti-seizure activity may be dependent upon the relative phytocannabinoid content within herbal cannabis preparations (Whalley et al., 2004).