gebhart/patrepeval huggingface dataset:
Movie genome: alleviating new item cold start in movie recommendation (2019)

As of today, most movie recommendation services base their recommendations on collaborative filtering (CF) and/or content-based filtering (CBF) models that use metadata (e.g., genre or cast). In most video-on-demand and streaming services, however, new movies and TV series are continuously added. CF models are unable to make predictions in such a scenario, since the newly added videos lack interactions—a problem technically known as new item cold start (CS). Currently, the most common approach to this problem is to switch to a purely CBF method, usually by exploiting textual metadata. This approach is known to have lower accuracy than CF because it ignores useful collaborative information and relies on human-generated textual metadata, which are expensive to collect and often prone to errors. User-generated content, such as tags, can also be rare or absent in CS situations. In this paper, we introduce a new movie recommender system that addresses the new item problem in the movie domain by (i) integrating state-of-the-art audio and visual descriptors, which can be automatically extracted from video content and constitute what we call the movie genome; (ii) exploiting an effective data fusion method named canonical correlation analysis, which was successfully tested in our previous works Deldjoo et al. (in: International Conference on Electronic Commerce and Web Technologies. Springer, Berlin, pp 34–45, 2016b; Proceedings of the Twelfth ACM Conference on Recommender Systems. ACM, 2018b), to better exploit complementary information between different modalities; (iii) proposing a two-step hybrid approach which trains a CF model on warm items (items with interactions) and leverages the learned model on the movie genome to recommend cold items (items without interactions). Experimental validation is carried out using a system-centric study on a large-scale, real-world movie recommendation dataset both in an absolute cold start and in a cold to warm transition; and a user-centric online experiment measuring different subjective aspects, such as satisfaction and diversity. Results show the benefits of this approach compared to existing approaches.
On the Separation of Signals from Neighboring Cells in Tetrode Recordings (1997)

Abstract We discuss a solution to the problem of separating waveforms produced by multiple cells in an extracellular neural recording. We take an explicitly probabilistic approach, using latent-variable models of varying sophistication to describe the distribution of waveforms produced by a single cell. The models range from a single Gaussian distribution of waveforms for each cell to a mixture of hidden Markov models. We stress the overall statistical structure of the approach, allowing the details of the generative model chosen to depend on the specific neural preparation.
Down-regulation of the receptor for advanced glycation end-products (RAGE) supports non-small cell lung carcinoma (2004)

The receptor for advanced glycation end-products (RAGE) is a transmembrane receptor of the immunoglobulin superfamily. Several ligands binding to RAGE have been identified, including amphoterin. Experimental studies have given rise to the discussion that RAGE and its interaction with amphoterin contribute to tumour growth and metastasis. However, none of the studies considered a differential transcription profile in cancer that might change the interpretation of the study results when comparing RAGE in tumours with histologically normal tissues. Here we show that RAGE is strongly reduced at the mRNA and even more so at the protein level in non-small cell lung carcinomas compared with normal lung tissues. Down-regulation of RAGE correlates with higher tumour (TNM) stages but does not depend on the histological subtypes, squamous cell lung carcinoma and adenocarcinoma. Subsequent overexpression of full-length human RAGE in lung cancer cells (NCI-H358) showed diminished tumour growth under some conditions. While proliferation of RAGE-expressing cells was less than that of cells expressing the cytoplasmic domain deletion mutant DeltacytoRAGE or mock-transfected NCI-H358 in monolayer cultures, RAGE cells also formed smaller tumours in spheroid cultures and in vivo in athymic mice compared with DeltacytoRAGE cells. Moreover, we observed a more epithelial growth of RAGE-expressing, but also of DeltacytoRAGE-expressing, cells on collagen layers, whereas mock NCI-H358 cells kept their tumour morphology. This observation was supported by immunofluorescence analyses demonstrating that RAGE preferentially localizes at intercellular contact sites, independent of expression of the cytoplasmic domain. Thus, down-regulation of RAGE may be considered as a critical step in tissue reorganization and the formation of lung tumours.
Learning to extract symbolic knowledge from the World Wide Web (1998)

The goal of the Web-KB project is to develop automatic methods for constructing and maintaining large knowledge bases whose contents mirror those of the World Wide Web. We argue for the feasibility of a system which, given a manually constructed ontology and a seed knowledge base comprising a set of labeled Web pages, learns to instantiate knowledge-base objects and relations from the Web. Such a system could construct a knowledge base supporting concept-oriented queries to the Web, or serve as a resource for Web-based problem solvers and search agents. At the heart of this task are two general sub-problems: identifying instances of the classes, and identifying instances of the relations that are defined in the ontology. The first sub-problem includes the task of recognizing cases in which individual Web pages correspond to the classes of interest, and the second sub-problem includes the task of identifying cases in which pairs of pages instantiate the ontology&amp;apos;s relations. We present the results of initial experiments into the use of text classification and relational learning for these tasks, and sketch problems for future research.
The Membrane-Proximal Region of Vesicular Stomatitis Virus Glycoprotein G Ectodomain Is Critical for Fusion and Virus Infectivity (2003)

The glycoprotein (G) of vesicular stomatitis virus (VSV) is responsible for binding of virus to cells and for mediating virus entry following endocytosis by inducing fusion of the viral envelope with the endosomal membrane. The fusion peptide of G is internal (residues 116 to 137) and exhibits characteristics similar to those of other internal fusion peptides, but recent studies have implicated the region adjacent to the transmembrane domain as also being important for G-mediated membrane fusion. Sequence alignment of the membrane-proximal region of G from several different vesiculoviruses revealed that this domain is highly conserved, suggesting that it is important for G function. Mutational analysis was used to show that this region is not essential for G protein oligomerization, transport to the cell surface, or incorporation into virus particles but that it is essential for acid-induced membrane fusion activity and for virus infectivity. Deletion of the 13 membrane-proximal amino acids (N449 to W461) dramatically reduced cell-cell fusion activity and reduced virus infectivity approximately 100-fold, but mutation of conserved aromatic residues (W457, F458, and W461) either singly or together had only modest effects on cell-cell fusion activity; recombinant virus encoding these mutants replicated as efficiently as wild-type (WT) VSV. Insertion of heterologous sequences in the juxtamembrane region completely abolished membrane fusion activity and virus infectivity, as did deletion of residues F440 to N449. The insertion mutants showed some changes in pH-dependent conformational changes and in virus binding, which could partially explain the defects in membrane fusion activity, but all the other mutants were similar to WT G with respect to conformational changes and virus binding. These data support the hypothesis that the membrane-proximal domain contributes to G-mediated membrane fusion activity, yet the conserved aromatic residues are not essential for membrane fusion or virus infectivity.
Chiroptical properties of poly{2, 5‐bis[(S)‐2‐methylbutoxy]‐1, 4‐phenylene vinylene} (1997)

The photoluminescent and electroluminescent properties of conjugated polymers are, in part, controlled by interchain interactions in solid films. A study of the (chir)optical properties of optically active BMB‐PPV (see Figure) shows that circular dichroism spectroscopy is very powerful in detecting association of the polymer. Two different forms of BMB‐PPV are reported to be present in solution, depending on the solvent. magnified image
ALTERNATE PROCESSES FOR USE IN SOY PROTEIN ISOLATION BY INDUSTRIAL ULTRAFILTRATION MEMBRANES (1979)

ABSTRACT Two alternative procedures have been developed for use in soy protein isolation with industrial membrane systems. These are (1) membrane processing soy extract at a higher pH (pH 11) and temperature (74°C) than previously done to produce a hydrolyzed product, (2) extracting soy protein with Ca(OH) 2 (instead of NaOH) and membrane processing at pH 7. Hydrolyzed products were found to possess different physical and functional properties than previous products. Extracting soy protein with Ca(OH) 2 produced a high‐calcium, low‐sodium product having unusually high nitrogen solubility over a wide pH range.
Structural requirements for neuropeptide Y18-36-evoked hypotension: a systematic study (1992)

It has been shown that NPY and select C-terminal fragments of NPY that evoke a hypotensive response upon intraarterial administration in the rat also cause mast cell degranulation and histamine release in vitro. Additionally, elevation of plasma histamine levels has been observed concomitant with the hypotensive effect of NPY and various C-terminal fragments. In order to investigate whether the hypotensive response to NPY18-36 is correlated to this observed elevation of histamine in vivo, we sought to characterize the structural requirements for each activity. We conducted a systematic replacement of each amino acid in NPY18-36 by its D-isomer. Additionally, various modifications were made to the N- or C-terminii of NPY18-36. The following rank order of potency was obtained for the hypotensive action of these analogues of NPY18-36 relative to NPY18-36. Only one analogue ([D-Tyr21]NPY18-36) exhibited significantly enhanced potency. Eleven analogues of NPY18-36, ([D-Thr32]-, [D-Arg35]-, [D-Ile31]-, [D-Leu30]-, [D-Tyr27]-, [D-Ser22]-, [D-Tyr36]-, [D-Gln34]-, [D-Asn29]-, [D-Ala23]-, and [D-Arg33]NPY18-36) were equipotent with NPY18-36. Four analogues ([D-His26]-, [D-Ile28]-, and [D-Ala18]NPY18-36 and -NPY18-27) had reduced potency (10-80%) while eight analogues ([D-Arg19]-, [D-Tyr20], [D-Leu24]-, [D-Arg25]-, [Ac-Ala18]-, [Me-Ala18]-, [desamino-Ala18]NPY18-36 and NPY18-36 free acid) failed to produce a significant hypotensive response (less than 10%) at the doses tested. The sensitivity of NPY18-36 to chiral inversion of single residues or other modifications at the N-terminus suggested the presence of a conformationally well defined N-terminal pharmacophore. Additionally, five NPY18-36 analogues were tested for elevation of plasma histamine levels. The rank order of potency ([D-Thr32]NPY18-36 = [D-Tyr21]NPY18-36 much greater than NPY18-36 greater than [D-Ala18]NPY18-36 greater than [Ac-Ala18]NPY18-36) was correlated with each analogue's potency at evoking a hypotensive response. In contrast, NPY1-36 failed to evoke an elevation in plasma histamine levels despite its hypotensive effects. Hence, we conclude that the magnitude of the hypotensive response evoked by an NPY18-36 analogue is primarily a function of its ability to elevate plasma histamine levels. However, the mechanism underlying NPY1-36-evoked hypotension appears to be different.
GCG: The Wisconsin Package of Sequence Analysis Programs (2003)

The GCG programs, also called the “Wisconsin Package,” comprise a powerful suite of tools for manipulating, analyzing, and comparing nucleotide and protein sequences (). The initials GCG stand for Genetics Computer Group, which is a subsidiary of Oxford Molecular Group (Campbell, CA). The Wisconsin Package includes more than 130 programs, each of which functions as a tool for performing a specific task, such as translating a nucleotide coding sequence or determining restriction enzyme cutting sites. Most GCG programs use one file as input and write the results to another file. The output files from many GCG programs are suitable as input to other GCG (or other) programs. In many cases, complex problems can be solved by using several GCG programs in succession.
Cholesterol-Dependent Cytolysins, a Family of Versatile Pore-Forming Toxins (2005)

The cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins that are produced by more than 20 species from the genera Clostridium , Streptococcus , Listeria , Bacillus , and Arcanobacterium . The pore-forming mechanism of these toxins exhibits two hallmark characteristics:
OX40 Agonists and Combination Immunotherapy: Putting the Pedal to the Metal (2015)

Recent studies have highlighted the therapeutic efficacy of immunotherapy, a class of cancer treatments that utilize the patient's own immune system to destroy cancerous cells. Within a tumor the presence of a family of negative regulatory molecules, collectively known as "checkpoint inhibitors," can inhibit T cell function to suppress anti-tumor immunity. Checkpoint inhibitors, such as CTLA-4 and PD-1, attenuate T cell proliferation and cytokine production. Targeted blockade of CTLA-4 or PD-1 with antagonist monoclonal antibodies (mAbs) releases the "brakes" on T cells to boost anti-tumor immunity. Generating optimal "killer" CD8 T cell responses also requires T cell receptor activation plus co-stimulation, which can be provided through ligation of tumor necrosis factor receptor family members, including OX40 (CD134) and 4-1BB (CD137). OX40 is of particular interest as treatment with an activating (agonist) anti-OX40 mAb augments T cell differentiation and cytolytic function leading to enhanced anti-tumor immunity against a variety of tumors. When used as single agents, these drugs can induce potent clinical and immunologic responses in patients with metastatic disease. However, each of these agents only benefits a subset of patients, highlighting the critical need for more effective combinatorial therapeutic strategies. In this review, we will discuss our current understanding of the cellular and molecular mechanisms by which OX40 agonists synergize with checkpoint inhibitor blockade to augment T cell-mediated anti-tumor immunity and the potential opportunities for clinical translation of combinatorial immunotherapeutic strategies.
Protein fabrication automation (2007)

Facile "writing" of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid-handling robotics, a liquid-handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full-length synthetic ORFs. The process is robust and scalable.
Prolonged enhancement of the micturition reflex in the cat by repetitive stimulation of bladder afferents (1999)

1. Prolonged modulation of the parasympathetic micturition reflex was studied in cats anaesthetized by alpha-chloralose. Reflex discharges were recorded from a thin pelvic nerve filament to the bladder and evoked by stimulation of the remaining ipsilateral bladder pelvic nerves or urethral branches of the pudendal nerve. 2. Stimulation of bladder or urethral afferents at Adelta intensity evoked micturition reflexes with a latency of 90-120 ms. Such reflexes were much enhanced following repetitive conditioning stimulation of the same afferents at 20 Hz for 5 min. 3. The reflex enhancement lasted more than 1 h after the conditioning stimulation. The effect was not prevented by a preceding complete transection of the sympathetic supply to the bladder. A prolonged suppression of the reflex was obtained after conditioning stimulation of afferents in the dorsal clitoris nerves. 4. It is proposed that the prolonged modulations of the micturition reflex represent physiological adaptive processes, which preserve a flawless function of the bladder during life. The observations provide a theoretical explanation for the beneficial effect of electric nerve stimulation in patients with voiding disorders.
Contact Point Localization for Articulated Manipulators with Proprioceptive Sensors and Machine Learning (2018)

A model-based Machine Learning (ML) approach is presented to detect and localize external contacts on a 6 degree of freedom (DoF) serial manipulator. This approach only requires the use of proprioceptive sensors (joint positions, velocities and one-dimensional (ID) joint torques already available in the robot arm). Good results are obtained with Random Forests (RFs) and Multi-Layer-Perceptrons (MLPs) leading to a precise localization of the contact link and its orientation. Apart from the link in contact and the orientation of the force, RFs and MLPs are also able to differentiate between contact points on the same link and orientation but with different distances to the joint axis. We experimentally verify this approach on simulated and real data obtained from the Kinova Jaco 2 manipulator and compare it to an optimization based approach.
Recording of Ion Channel Activity in Planar Lipid Bilayer Experiments (2013)

Planar lipid bilayer is an electrophysiological technique that enables study of functional activities of ion channels, porins, and other pore-forming molecular complexes. The main purpose of this method is to monitor ion channels' behavior at the single molecule level in the artificial membranes. Here, I describe the details of this technique that will underline formation of the lipid bilayers and incorporation and activation of the ion channel protein.
Ethernet ring protection for carrier ethernet networks (2008)

Ethernet technologies are rapidly gaining importance as a prevailing solution for carrier networks. Ethernet ring protection switching, defined in ITU-T Recommendation G.8032, provides a means of achieving carrier network requirements for ring network topologies. This article outlines the novel concepts in this Ethernet ring protection switching mechanism and discusses the fundamental operating principles by which the automatic protection switching (APS) protocol works. In addition, several feature enhancements in protection behavior and solutions being considered for the next phase of standardization are discussed.
Human antibodies accelerate the rate of remyelination following lysolecithin‐induced demyelination in mice (2002)

Immunoglobulin-based therapies are becoming increasingly common for the treatment of neurologic and autoimmune diseases in humans. In this study, we demonstrate that systemic administration of either polyclonal human immunoglobulins or specific human monoclonal antibodies can accelerate the rate of CNS remyelination following toxin-induced demyelination. Injection of lysolecithin directly into the spinal cord results in focal demyelinated lesions. In contrast to other murine models of demyelinating disease, the mechanism of demyelination following lysolecithin injection is independent of immune system activation, and chronic inflammation at the site of the lesion is minimal. Administration of polyclonal human IgM (pHIgM) or a serum-derived human monoclonal antibody (sHIgM22) resulted in approximately a twofold increase in remyelinating axons when compared to animals treated with saline or with antibodies that do not promote repair. Both pHIgM and sHIgM22 show strong binding to CNS white matter and oligodendrocytes, while antibodies that did not accelerate remyelination do not. This differential staining pattern suggests that enhanced remyelination may result from direct stimulation of oligodendrocyte remyelination by binding to surface receptors on oligodendrocytes or glial progenitor cells. We propose the use of human polyclonal IgM or specific human monoclonal IgM antibodies as potential therapies to enhance myelin repair following CNS injury and disease.
Prolonged and preferential production of polymeric immunoglobulin A in response to Streptococcus pneumoniae capsular polysaccharides (1996)

Streptococcus pneumoniae is an invasive mucosal pathogen for which host defense is dependent on capsular polysaccharide-specific antibody. Capsule-specific immunoglobulin G (IgG), IgM, and IgA are produced following pneumococcal vaccination and infection. Serum IgA has two molecular forms, polymeric and monomeric. These forms may modulate the avidity of antigen binding and evolve over time as the immune response matures. Therefore, we sequentially characterized the molecular forms of serum IgA to three serotypes of pneumococcal capsular polysaccharides (types 8, 12F, and 14) after pneumococcal vaccination and after natural infection with type 14 S. pneumoniae. Although typically the form of IgA in antigen-specific systemic responses to protein antigens is predominantly polymeric in sera of patients shortly after exposure and shifts to the monomeric form in sera obtained several weeks later, the form of IgA in response to each pneumococcal capsular polysaccharide remained predominantly polymeric 1 month after natural infection and up to I year following vaccination. In contrast, IgA to pneumococcal cell wall polysaccharide was both polymeric and monomeric. Moreover, the form of IgA in response to polyribosyl-ribitol-phosphate (PRP), the capsular polysaccharide of Haemophilus influenzae type b, was predominantly monomeric in the sera of 8 of 10 subjects tested 1 to 3 months after vaccination with either PRP alone or the diphtheria toxoid conjugate of PRP. We conclude that systemic responses to pneumococcal capsular polysaccharides are distinct in the production of predominantly polymeric IgA over time. The persistence of polymeric IgA may facilitate binding and clearance of pneumococci from the systemic circulation or reflect limited maturation of the immune response to pneumococcal capsular polysaccharides.