gebhart/patrepeval huggingface dataset:
Metabolic Substrates Exhibit Differential Effects on Functional Parameters of Mouse Sperm Capacitation1 (2012)

Although substantial evidence exists that sperm ATP production via glycolysis is required for mammalian sperm function and male fertility, conflicting reports involving multiple species have appeared regarding the ability of individual glycolytic or mitochondrial substrates to support the physiological changes that occur during capacitation. Several mouse models with defects in the signaling pathways required for capacitation exhibit reductions in sperm ATP levels, suggesting regulatory interactions between sperm metabolism and signal transduction cascades. To better understand these interactions, we conducted quantitative studies of mouse sperm throughout a 2-h in vitro capacitation period and compared the effects of single substrates assayed under identical conditions. Multiple glycolytic and nonglycolytic substrates maintained sperm ATP levels and comparable percentages of motility, but only glucose and mannose supported hyperactivation. These monosaccharides and fructose supported the full pattern of tyrosine phosphorylation, whereas nonglycolytic substrates supported at least partial tyrosine phosphorylation. Inhibition of glycolysis impaired motility in the presence of glucose, fructose, or pyruvate but not in the presence of hydroxybutyrate. Addition of an uncoupler of oxidative phosphorylation reduced motility with pyruvate or hydroxybutyrate as substrates but unexpectedly stimulated hyperactivation with fructose. Investigating differences between glucose and fructose in more detail, we demonstrated that hyperactivation results from the active metabolism of glucose. Differences between glucose and fructose appeared to be downstream of changes in intracellular pH, which rose to comparable levels during incubation with either substrate. Sperm redox pathways were differentially affected, with higher levels of associated metabolites and reactive oxygen species generated during incubations with fructose than during incubations with glucose.
Mapping allosteric connections from the receptor to the nucleotide-binding pocket of heterotrimeric G proteins (2007)

Heterotrimeric G proteins function as molecular relays that mediate signal transduction from heptahelical receptors in the cell membrane to intracellular effector proteins. Crystallographic studies have demonstrated that guanine nucleotide exchange on the Galpha subunit causes specific conformational changes in three key "switch" regions of the protein, which regulate binding to Gbetagamma subunits, receptors, and effector proteins. In the present study, nitroxide side chains were introduced at sites within the switch I region of Galphai to explore the structure and dynamics of this region throughout the G protein cycle. EPR spectra obtained for each of the Galpha(GDP), Galpha(GDP)betagamma heterotrimer and Galpha(GTPgammaS) conformations are consistent with the local environment observed in the corresponding crystal structures. Binding of the heterotrimer to activated rhodopsin to form the nucleotide-free (empty) complex, for which there is no crystal structure, causes prominent changes relative to the heterotrimer in the structure of switch I and contiguous sequences. The data identify a putative pathway of allosteric changes triggered by receptor binding and, together with previously published data, suggest elements of a mechanism for receptor-catalyzed nucleotide exchange.
Development and Progression of Psoriasif orm Dermatitis and Systemic Lesions in the Flaky Skin (<i>fsn</i>) Mouse Mutant (1997)

Flaky skin (fsn) mutant mice were originally described as a mouse model for psoriasis accompanied by hematological abnormalities. However, homozygous (fsn/fsn) mice develop a number of other pathological changes. Systematic evaluation of over 300 fsn/fsn and normal littermate control (+/+ or +/fsn) mice was carried out to characterize these changes. Psoriasiform skin lesions were first evident as focal epidermal hyperplasia and inflammation at 2 weeks of age. These lesions became confluent and diffuse by 3-4 weeks of age and were associated with marked dermal infiltration of lymphocytes and small numbers of neutrophils and macrophages. Mast cell numbers increased significantly in the dermis from 2 weeks of age onward. Diffuse dermal neovascularization accompanied these cutaneous changes. Systemic lesions included progressive and massive papillomatosis of the stratified squamous epithelium of the forestomach, hyperplasia and dysplasia of the glandular stomach, increased apoptosis of cecal enterocytes, renal glomerulopathy associated with immune complex and complement deposition, testicular degeneration, mixed inflammatory cell infiltrates and fibrosis around portal triads in the liver, splenomegaly due to massive erythropoiesis, and granulomatous lymphadenitis. This spontaneous mouse mutation provides a useful model for modulating neovascularization and keratinocyte hyperproliferation, especially since the cutaneous changes resemble some forms of psoriasis in humans.
Room-temperature ionic liquids: a novel versatile lubricant. (2001)

Alkylimidazolium tetrafluoroborates are promising versatile lubricants for the contact of steel/steel, steel/aluminium, steel/copper, steel/SiO2, Si3N4/SiO2, steel/Si(100), steel/sialon ceramics and Si3N4/sialon ceramics; they show excellent friction reduction, antiwear performance and high load-carrying capacity.
R-form lipopolysaccharides (LPS) of Gram-negative bacteria as possible vaccine antigens (1997)

The antigenic and immunogenic properties of R-form lipopolysaccharides (LPS) of Pseudomonas aeruginosa, Salmonella spp., Escherichia coli and Shigella spp. were studied. The results showed the presence of antigenic relationships among P. aeruginosa R mutants with different structures of the LPS core lipid A region and also among E. coli, Shigella and P. aeruginosa R-LPS, but not with S. minnesota Re-LPS. Vaccines prepared with R-LPS proved to be effective preparations for the active immunization of mice against P. aeruginosa infection. The vaccine stimulated 40-100% protection in mice depending upon the scheme of immunization.
An essential role for macrophage migration inhibitory factor in the tuberculin delayed-type hypersensitivity reaction. (1996)

30 years ago, investigations into the molecular basis of the delayed-type hypersensitivity reaction (DTH) provided evidence for the first lymphokine activity: a lymphocyte-derived mediator called macrophage migration inhibitory factor (MIF), which inhibited the random migration of peritoneal macrophages. Despite the long-standing association of MIF with the DTH reaction and the cloning of a human protein with macrophage migration inhibitory activity, the precise role of MIF in this classic cell-mediated immune response has remained undefined. This situation has been further complicated by the fact that two other cytokines, interferon gamma and IL-4, similarly inhibit macrophage migration and by the identification of mitogenic contaminants in some preparations of cloned human MIF. Using recently developed molecular probes for mouse MIF, we have examined the role of this protein in a classical model of DTH, the tuberculin reaction in mice. Both MIF messenger RNA and protein were expressed prominently in DTH lesions, as assessed by reverse transcription polymerase chain reaction, in situ hybridization, and immunostaining with anti-MIF antibody. The predominant cellular origin of MIF appeared to be the monocyte/macrophage, a cell type identified recently to be a major source of MIF release in vivo. The administration of neutralizing anti-MIF antibodies to mice inhibited significantly the development of DTH, thus affirming the central role of MIF in this classic immunological response.
Reversal of Aging-Related Neuronal Ca2+ Dysregulation and Cognitive Impairment by Delivery of a Transgene Encoding FK506-Binding Protein 12.6/1b to the Hippocampus (2015)

This paper reports critical tests of a novel hypothesis that proposes a molecular mechanism of unhealthy brain aging and possibly, Alzheimer's disease. For more than 30 years, evidence has been accumulating that brain aging is associated with dysregulation of calcium in neurons. Recently, we found that FK506-binding protein 12.6/1b (FKBP1b), a small protein that regulates calcium, declines with aging in the hippocampus, a brain region important for memory. Here we used gene therapy approaches and found that raising FKBP1b reversed calcium dysregulation and memory impairment in aging rats, allowing them to perform a memory task as well as young rats. These studies identify a potential molecular mechanism of brain aging and may also have implications for treatment of Alzheimer's disease.
Consistent recovery of stimuli encoded with a neural ensemble (2009)

We consider the problem of reconstructing finite energy stimuli from a finite number of contiguous spikes. The reconstructed signal satisfies a consistency condition: when passed through the same neuron, it triggers the same spike train as the original stimulus. The recovered stimulus has to also minimize a quadratic smoothness criterion. We show that under these conditions, the problem of recovery has a unique solution and provide an explicit reconstruction algorithm for stimuli encoded with a population of integrate-and-fire neurons. We demonstrate that the quality of reconstruction improves as the size of the population increases. Finally, we demonstrate the efficiency of our recovery method for an encoding circuit based on threshold spiking that arises in neuromorphic engineering.
A p16 INK4a -Insensitive CDK4 Mutant Targeted by Cytolytic T Lymphocytes in a Human Melanoma (1995)

A mutated cyclin-dependent kinase 4 (CDK4) was identified as a tumor-specific antigen recognized by HLA-A2. 1-restricted autologous cytolytic T lymphocytes (CTLs) in a human melanoma. The mutated CDK4 allele was present in autologous cultured melanoma cells and metastasis tissue, but not in the patient's lymphocytes. The mutation, an arginine-to-cysteine exchange at residue 24, was part of the CDK4 peptide recognized by CTLs and prevented binding of the CDK4 inhibitor p16INK4a, but not of p21 or of p27KIP1. The same mutation was found in one additional melanoma among 28 melanomas analyzed. These results suggest that mutation of CDK4 can create a tumor-specific antigen and can disrupt the cell-cycle regulation exerted by the tumor suppressor p16INK4a.
X-Linked Alport Syndrome (2003)

Alport syndrome (AS) is a type IV collagen hereditary disease characterized by progressive hematuric nephritis, hearing loss, and ocular changes. Mutations in the COL4A5 collagen gene are responsible for the more common X-linked dominant form of the disease characterized by much less severe disease in girls and women. A "European Community Alport Syndrome Concerted Action" (ECASCA) group was established to delineate the Alport syndrome phenotype in each gender and to determine genotype-phenotype correlations in a large number of families. Data concerning 329 families, 250 of them with an X-linked transmission, were collected. Characteristics of heterozygous girls and women belonging to the 195 families with proven COL4A5 mutation are compared with those of hemizygous boys and men. Hematuria was observed in 95% of carriers and consistently absent in the others. Proteinuria, hearing loss, and ocular defects developed in 75%, 28%, and 15%, respectively. The probability of developing end-stage renal disease or deafness before the age of 40 yr was 12% and 10%, respectively, in girls and women versus 90 and 80%, respectively, in boys and men. The risk of progression to end-stage renal disease appears to increase after the age of 60 yr in women. Because of the absence of genotype-phenotype correlation and the large intrafamilial phenotypic heterogeneity, early prognosis of the disease in X-linked Alport syndrome carriers remains moot. Risk factors for developing renal failure have been identified: the occurrence and progressive increase in proteinuria, and the development of a hearing defect.
A Semidwarf Phenotype of Barley uzu Results from a Nucleotide Substitution in the Gene Encoding a Putative Brassinosteroid Receptor (2003)

Brassinosteroids (BRs) play important roles throughout plant growth and development. Despite the importance of clarifying the mechanism of BR-related growth regulation in cereal crops, BR-related cereal mutants have been identified only in rice (Oryza sativa). We previously found that semidwarf barley (Hordeum vulgare) accessions carrying the "uzu" gene, called "uzu" barley in Japan, are non-responding for brassinolide (BL). We then performed chemical and molecular analyses to clarify the mechanisms of uzu dwarfism using isogenic line pairs of uzu gene. The response of the uzu line to BL was significantly lower than that of its corresponding normal line. Measurement of BRs showed that the uzu line accumulates BRs, similar to known BR-insensitive mutants. The marker synteny of rice and barley chromosomes suggests that the uzu gene may be homologous to rice D61, a rice homolog of Arabidopsis BR-insensitive 1 (BRI1), encoding a BR-receptor protein. A barley homolog of BRI1, HvBRI1, was isolated by using degenerate primers. A comparison of HvBRI1 sequences in uzu and normal barley varieties showed that the uzu phenotype is correlated with a single nucleotide substitution. This substitution results in an amino acid change at a highly conserved residue in the kinase domain of the BR-receptor protein. These results may indicate that uzu dwarfism is caused by the missense mutation in HvBRI1. The uzu gene is being introduced into all hull-less barley cultivars in Japan as an effective dwarf gene for practical use, and this is the first report about an agronomically important mutation related to BRs.
Discovery and validation of cell cycle arrest biomarkers in human acute kidney injury (2013)

ClinicalTrials.gov number NCT01209169.
Inhibition of Mouse Tumor Metastasis with Nojirimycin-related Compounds. (1996)

The antimetastatic activity of ten compounds structurally related to nojirimycin A was examined using a pulmonary metastatic model of mouse B16 melanoma. Nojirimycin B, deoxynojirimycin, D-gluco-delta-lactam, CP3068 and CP3069 are structural analogues of nojirimycin A, and showed potent or moderate antimetastatic activities. Nojirimycin A, nojirimycin B, deoxynojirimycin and D-gluco-delta-lactam showed potent or moderate inhibitory activities against alpha-glucosidase, beta-glucosidase and beta-mannosidase, but CP3068 and CP3069 in which the structures were related to D-gluco-delta-lactam showed no inhibitory activities. CP3041, CP3042, CP3043, CP3045 and CP3048 are analogues of sodium D-glucaro-delta-lactam (ND2001), a carboxy derivative of nojirimycin A, and showed potent or moderate antimetastatic activities. But no analogue was superior to ND2001 concerning with antimetastatic and anti-beta-glucuronidase activities. CP3041 and CP3042 showed potent and moderate inhibitory activities against beta-glucuronidase, respectively, but CP3043, CP3045 and CP3048 showed little or no activities.
Effective Combination of Innate and Adaptive Immunotherapeutic Approaches in a Mouse Melanoma Model (2017)

Most cancer immunotherapies include activation of either innate or adaptive immune responses. We hypothesized that the combined activation of both innate and adaptive immunity will result in better antitumor efficacy. We have previously shown the synergy of an agonistic anti-CD40 mAb (anti-CD40) and CpG-oligodeoxynucleotides in activating macrophages to induce tumor cell killing in mice. Separately, we have shown that a direct intratumoral injection of immunocytokine (IC), an anti-GD2 Ab linked to IL-2, can activate T and NK cells resulting in antitumor effects. We hypothesized that activation of macrophages with anti-CD40/CpG, and NK cells with IC, would cause innate tumor destruction, leading to increased presentation of tumor Ags and adaptive T cell activation; the latter could be further augmented by anti-CTLA-4 Ab to achieve tumor eradication and immunological memory. Using the mouse GD2<sup>+</sup> B78 melanoma model, we show that anti-CD40/CpG treatment led to upregulation of T cell activation markers in draining lymph nodes. Anti-CD40/CpG + IC/anti-CTLA-4 synergistically induced regression of advanced s.c. tumors, resulting in cure of some mice and development of immunological memory against B78 and wild type B16 tumors. Although the antitumor effect of anti-CD40/CpG did not require T cells, the antitumor effect of IC/anti-CTLA-4 was dependent on T cells. The combined treatment with anti-CD40/CpG + IC/anti-CTLA-4 reduced T regulatory cells in the tumors and was effective against distant solid tumors and lung metastases. We suggest that a combination of anti-CD40/CpG and IC/anti-CTLA-4 should be developed for clinical testing as a potentially effective novel immunotherapy strategy.
Biometric Gait Authentication Using Accelerometer Sensor (2006)

This paper presents a biometric user authentication based on a person’s gait. Unlike most previous gait recognition approaches, which are based on machine vision techniques, in our approach gait patterns are extracted from a physical device attached to the lower leg. From the output of the device accelerations in three directions: vertical, forward-backward, and sideways motion of the lower leg are obtained. A combination of these accelerations is used for authentication. Applying two different methods, histogram similarity and cycle length, equal error rates (EER) of 5% and 9% were achieved, respectively.
Semantic Indexing of Multimedia Content Using Visual, Audio, and Text Cues (2003)

We present a learning-based approach to the semantic indexing of multimedia content using cues derived from audio, visual, and text features. We approach the problem by developing a set of statistical models for a predefined lexicon. Novel concepts are then mapped in terms of the concepts in the lexicon. To achieve robust detection of concepts, we exploit features from multiple modalities, namely, audio, video, and text. Concept representations are modeled using Gaussian mixture models (GMM), hidden Markov models (HMM), and support vector machines (SVM). Models such as Bayesian networks and SVMs are used in a late-fusion approach to model concepts that are not explicitly modeled in terms of features. Our experiments indicate promise in the proposed classification and fusion methodologies: our proposed fusion scheme achieves more than 10% relative improvement over the best unimodal concept detector.
Fitness consequences of a regulatory polymorphism in a seasonal environment (2003)

Gene regulation is commonly assumed to have evolved in response to environmental variability. Although tightly regulated in Escherichia coli strain K12, transcriptional control of arginine biosynthesis is deregulated in strain B. Caused by a single amino acid replacement in the arginine repressor, these contrasting regulatory strategies result in a fitness tradeoff. The K12 repressor is selectively favored in the presence of arginine and disfavored in its absence. In environments that cycle between high and low arginine, short seasons favor the K12 allele, whereas long seasons favor the B allele. Unexpectedly then, deregulated expression is adaptive in some seasonal habitats.
Batch Policy Gradient Methods for Improving Neural Conversation Models (2017)

We study reinforcement learning of chatbots with recurrent neural network architectures when the rewards are noisy and expensive to obtain. For instance, a chatbot used in automated customer service support can be scored by quality assurance agents, but this process can be expensive, time consuming and noisy. Previous reinforcement learning work for natural language processing uses on-policy updates and/or is designed for on-line learning settings. We demonstrate empirically that such strategies are not appropriate for this setting and develop an off-policy batch policy gradient method (BPG). We demonstrate the efficacy of our method via a series of synthetic experiments and an Amazon Mechanical Turk experiment on a restaurant recommendations dataset.
The role of cytokines in the generation of inflammation and tissue damage in experimental gram-positive meningitis. (1990)

Cytokines mediate many host responses to bacterial infections. We determined the inflammatory activities of five cytokines in the central nervous system: TNF-alpha, IL-1 alpha, IL-1 beta, macrophage inflammatory protein 1 (MIP-1), and macrophage inflammatory protein 2 (MIP-2). Using a rabbit model of meningeal inflammation, each cytokine (except IL-1 beta) induced enhanced blood brain barrier permeability, leukocytosis in cerebrospinal fluid, and brain edema. Homologous antibodies to each mediator inhibited leukocytosis and brain edema, and moderately decreased blood brain barrier permeability. In rabbits treated with anti-CD-18 antibody to render neutrophils dysfunctional for adhesion, each cytokine studied lost the ability to cause leukocytosis and brain edema. After intracisternal challenge with pneumococci, antibodies to TNF or IL-1 prevented inflammation, while anti-MIP-1 or anti-MIP-2 caused only a 2-h delay in the onset of inflammation. We suggest these cytokines have multiple inflammatory activities in the central nervous system and contribute to tissue damage during pneumococcal meningitis.
Selective Functionalization of a Genetically Encoded Alkene-Containing Protein via “Photoclick Chemistry” in Bacterial Cells (2008)

We report a tetrazole-based, photoclick chemistry that can be employed to selectively functionalize an alkene genetically encoded in a protein inside E. coli cells. The reaction involved the treatment of E. coli cells with cell-permeable tetrazoles followed by a brief photo irradiation at 302 nm (4 min) and an overnight incubation at 4 degrees C. This in vivo alkene functionalization procedure was simple, straightforward, and nontoxic to E. coli cells. Additionally, fluorescent adducts were formed, facilitating the monitoring of the reaction in vivo. This reaction should offer a new tool for the study of alkene-containing proteins in living systems.
An Efficient Synthesis of 2-Substituted 6-Methylpurine Bases and Nucleosides by Fe- or Pd-Catalyzed Cross-Coupling Reactions of 2,6-Dichloropurines (2003)

Fe-catalyzed cross-coupling reactions of 9-substituted or protected 2,6-dichloropurines with 1 equiv of methylmagnesium chloride gave regioselectively 2-chloro-6-methylpurines in good yields. The same reactions with 3 equiv of methylmagnesium chloride or Pd-catalyzed reactions with trimethylaluminum afforded 2,6-dimethylpurines. The 2-chloro-6-methylpurines underwent another coupling with phenylboronic acid to give 6-methyl-2-phenylpurines. All reactions were perfomed for Bn- and THP-protected purine bases as well as for acyl-protected ribosides and 2-deoxyribosides. After deprotection, free purine bases and nucleosides were obtained.
A Workflow for Patient-Individualized Virtual Angiogram Generation Based on CFD Simulation (2012)

Increasing interest is drawn on hemodynamic parameters for classifying the risk of rupture as well as treatment planning of cerebral aneurysms. A proposed method to obtain quantities such as wall shear stress, pressure, and blood flow velocity is to numerically simulate the blood flow using computational fluid dynamics (CFD) methods. For the validation of those calculated quantities, virtually generated angiograms, based on the CFD results, are increasingly used for a subsequent comparison with real, acquired angiograms. For the generation of virtual angiograms, several patient-specific parameters have to be incorporated to obtain virtual angiograms which match the acquired angiograms as best as possible. For this purpose, a workflow is presented and demonstrated involving multiple phantom and patient cases.