gebhart/patrepeval huggingface dataset:
Structural Models for the Metal Centers in the Nitrogenase Molybdenum-Iron Protein (1992)

Structural models for the nitrogenase FeMo-cofactor and P-clusters are proposed based on crystallographic analysis of the nitrogenase molybdenum-iron (MoFe)-protein from Azotobacter vinelandii at 2.7 angstrom resolution. Each center consists of two bridged clusters; the FeMo-cofactor has 4Fe:3S and 1Mo:3Fe:3S clusters bridged by three non-protein ligands, and the P-clusters contain two 4Fe:4S clusters bridged by two cysteine thiol ligands. Six of the seven Fe sites in the FeMo-cofactor appear to have trigonal coordination geometry, including one ligand provided by a bridging group. The remaining Fe site has tetrahedral geometry and is liganded to the side chain of Cys alpha 275. The Mo site exhibits approximate octahedral coordination geometry and is liganded by three sulfurs in the cofactor, two oxygens from homocitrate, and the imidazole side chain of His alpha 442. The P-clusters are liganded by six cysteine thiol groups, two which bridge the two clusters, alpha 88 and beta 95, and four which singly coordinate the remaining Fe sites, alpha 62, alpha 154, beta 70, and beta 153. The side chain of Ser beta 188 may also coordinate one iron. The polypeptide folds of the homologous alpha and beta subunits surrounding the P-clusters are approximately related by a twofold rotation that may be utilized in the binding interactions between the MoFe-protein and the nitrogenase Fe-protein. Neither the FeMo-cofactor nor the P-clusters are exposed to the surface, suggesting that substrate entry, electron transfer, and product release must involve a carefully regulated sequence of interactions between the MoFe-protein and Fe-protein of nitrogenase.
Real time car driver's condition monitoring system (2010)

Driver's drowsiness and fatigue have been major causes of the serious traffic accidents, which make this an area of great socioeconomic concern. This paper describes the design of ECG (Electrocardiogram) sensor with conductive fabric electrodes and PPG (Photoplethysmogram) sensor to obtain physiological signals for car driver's health condition monitoring. ECG and PPG signals are transmitted to base station connected to the server PC via personal area network for practical test. Intelligent health condition monitoring system is designed at the server to analyze the PPG and ECG signals. Our purpose for intelligent health condition monitoring system is managed to process HRV signals analysis derived from the physiological signals in time and frequency domain and to evaluate the driver's drowsiness status.
The two membrane proximal domains of CD4 interact with the T cell receptor. (1996)

During T cell activation, CD4 is intimately involved in colocalizing the T cell receptor (TCR) with its specific peptide ligand bound to class II molecules of the major histocompatibility complex (MHC). Previously, the COOH-terminal residues, Trp62/63, which flank the immunodominant epitope of hen egg lysozyme (HEL 52-61), were shown to have a profound effect on TCR recognition. CD4 maintains the fidelity of this interaction when short peptides are used. To determine which portion of CD4 was responsible for this effect, a series of CD4 mutants were made and transfected into CD4 loss variants of two HEL 52-61-specific T cell hybridomas. Surprisingly, some CD4 mutants that failed to interact with MHC class II molecules (D2 domain mutant) or with p56kk (cytoplasmic-tailless mutant) restored responsiveness. Nevertheless, a significant reduction in association between cytoplasmic-tailless CD4 and the TCR, as determined by fluorescence resonance energy transfer, was observed. Thus, neither colocalization of CD4 and the TCR nor signal transduction via CD4 was solely responsible for the functional restoration of these T cell hybridomas by wild-type CD4. However, substitution of the two membrane proximal domains of murine CD4 (D3 and D4) with domains from human CD4 or intercellular adhesion molecule 1 not only abrogated its ability to restore function, but also substantially reduced its ability to associate with the TCR. Furthermore, the mouse/human CD4 chimera had a potent dominant negative effect on T cell function in the presence of equimolar concentrations of wild-type CD4. These data suggest that the D3/D4 domains of CD4 may interact directly or indirectly with the TCR-CD3 complex and influence the signal transduction processes. Given the striking structural differences between CD4 and CD8 in this region, these data define a novel and unique function for CD4.
The Intestinal Life Cycle of Bacillus subtilis and Close Relatives (2006)

Bacillus subtilis is considered a soil organism for which endospore formation provides a means to ensure long-term survival in the environment. We have addressed here the question of what happens to a spore when ingested. Spores displaying on their surface a heterologous antigen, tetanus toxin fragment C (TTFC), were shown to generate anti-TTFC responses not to the antigen contained in the primary oral inoculum but to those displayed on spores that had germinated and then resporulated. We then used reverse transcription-PCR to determine expression of vegetative genes and sporulation-specific genes in the mouse gut following oral dosing with spores. Significant levels of germination and sporulation were documented. Using natural isolates of B. subtilis that could form biofilms, we showed that these strains could persist in the mouse gut for significantly longer than the laboratory strain. Moreover, these isolates could grow and sporulate anaerobically and exhibited a novel phenomenon of being able to form spores in almost half the time required for the laboratory isolate. This suggests that spores are not transient passengers of the gastrointestinal tract but have adapted to carry out their entire life cycle within this environment. This is the first report showing an intestinal life cycle of B. subtilis and suggests that other Bacillus species could also be members of the gut microflora.
Bispecific Antibodies in Cancer Therapy, from the Laboratory to the Clinic (1999)

Bispecific monoclonal antibodies (BiMAb) have been shown to be able to contribute to an immunological approach in cancer therapy. In this review, essential aspects regarding the production of BiMAb and modes to apply them in immunotherapy for cancer are discussed. The pros and cons of BiMAb are considered, and the development from application in animal models to clinical studies is reviewed. The most important clinical trials are summarized, and the different problems encountered are discussed. Provided some crucial problems can be overcome, BiMAb will have a place in the treatment of cancer, especially in the setting of minimal residual disease.
From orbital hybridization to chemotherapeutics neutralization (2009)

To the editor:

Recently in Blood , Schonthal and colleagues reported in an elegant study that green tea polyphenols interact directly with bortezomib and other boronic acid–based proteasome inhibitors and block their anticancer effects.[1][1] This subject has significant practice implications. By
Peristalsis evoked by 5‐HT and renzapride: evidence for putative 5‐HT4receptor activation (1991)

The effect of 5-hydroxytryptamine and renzapride was studied on the peristaltic reflex elicited in vitro in the guinea-pig ileum. Both agents evoked the reflex at subthreshold intraluminal pressures (50% of threshold) and were blocked by ICS 205-930 (3 microM), but not ondansetron (5 microM). This novel finding suggests strongly that the prokinetic action of renzapride and gut motility stimulating action of 5-hydroxytryptamine are mediated via agonism at the putative 5-HT4 receptor.
Alopecia areata (2007)

Alopecia areata (AA) is a nonscarring, autoimmune, inflammatory, hair loss on the scalp, and/or body. Etiology and pathogenesis are still unknown. The most common site affected is the scalp. Histopathology is characterized by an increased number of the catagen and telogen follicles, the presence of inflammatory lymphocytic infiltrate in the peribulbar region ("swarm of bees"). Corticosteroids are the most popular drugs for the treatment of this disease. Etiologic and pathogenic mechanisms, as well as other current treatments available will be discussed in this article.
Porcine Lung Surfactant Protein D: Complementary DNA Cloning, Chromosomal Localization, and Tissue Distribution, (2000)

Porcine organs and lung surfactant have medically important applications in both xenotransplantation and therapy. We have started to characterize porcine lung surfactant by cloning the cDNA of porcine surfactant protein D (SP-D). SP-D and SP-A are important mediators in innate immune defense for the lung and possibly other mucosal surfaces. Porcine SP-D will also be an important reagent for use in existing porcine animal models for human lung infections. The complete cDNA sequence of porcine SP-D, including the 5' and 3' untranslated regions, was determined from two overlapping bacteriophage clones and by PCR cloning. Three unique features were revealed from the porcine sequence in comparison to SP-D from other previously characterized species, making porcine SP-D an intriguing species addition to the SP-D/collectin family. The collagen region contains an extra cysteine residue, which may have important structural consequences. The other two differences, a potential glycosylation site and an insertion of three amino acids, lie in the loop regions of the carbohydrate recognition domain, close to the carbohydrate binding region and thus may have functional implications. These variations were ruled out as polymorphisms or mutations by confirming the sequence at the genomic level in four different pig breeds. Porcine SP-D was shown to localize primarily to the lung and with less abundance to the duodenum, jejunum, and ileum. The genes for SP-D and SP-A were also shown to colocalize to a region of porcine chromosome 14 that is syntenic with the human and murine collectin loci.
Biology of Oligodendrocyte and Myelin in the Mammalian Central Nervous System (2001)

Oligodendrocytes, the myelin-forming cells of the central nervous system (CNS), and astrocytes constitute macroglia. This review deals with the recent progress related to the origin and differentiation of the oligodendrocytes, their relationships to other neural cells, and functional neuroglial interactions under physiological conditions and in demyelinating diseases. One of the problems in studies of the CNS is to find components, i.e., markers, for the identification of the different cells, in intact tissues or cultures. In recent years, specific biochemical, immunological, and molecular markers have been identified. Many components specific to differentiating oligodendrocytes and to myelin are now available to aid their study. Transgenic mice and spontaneous mutants have led to a better understanding of the targets of specific dys- or demyelinating diseases. The best examples are the studies concerning the effects of the mutations affecting the most abundant protein in the central nervous myelin, the proteolipid protein, which lead to dysmyelinating diseases in animals and human (jimpy mutation and Pelizaeus-Merzbacher disease or spastic paraplegia, respectively). Oligodendrocytes, as astrocytes, are able to respond to changes in the cellular and extracellular environment, possibly in relation to a glial network. There is also a remarkable plasticity of the oligodendrocyte lineage, even in the adult with a certain potentiality for myelin repair after experimental demyelination or human diseases.
A scalable comparison-shopping agent for the World-Wide Web (1997)

Article A scalable comparison-shopping agent for the World-Wide Web Share on Authors: Robert B. Doorenbos Department of Computer Science and Engineering, University of Washington, Seattle, WA Department of Computer Science and Engineering, University of Washington, Seattle, WAView Profile , Oren Etzioni Department of Computer Science and Engineering, University of Washington, Seattle, WA Department of Computer Science and Engineering, University of Washington, Seattle, WAView Profile , Daniel S. Weld Department of Computer Science and Engineering, University of Washington, Seattle, WA Department of Computer Science and Engineering, University of Washington, Seattle, WAView Profile Authors Info & Claims AGENTS '97: Proceedings of the first international conference on Autonomous agentsFebruary 1997 Pages 39–48https://doi.org/10.1145/267658.267666Online:08 February 1997Publication History 278citation1,139DownloadsMetricsTotal Citations278Total Downloads1,139Last 12 Months36Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Pathological inclusion bodies in tauopathies contain distinct complements of tau with three or four microtubule‐binding repeat domains as demonstrated by new specific monoclonal antibodies (2003)

Pathological inclusions containing fibrillar aggregates of hyperphosphorylated tau protein are a characteristic feature in the tauopathies, which include Alzheimer's disease, frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17), progressive supranuclear palsy, corticobasal degeneration and Pick's disease. Tau isoform composition and cellular and regional distribution as well as morphology of these inclusions vary in each disorder. Recently, several pathological missense and exon 10 splice-donor site mutations of the tau gene were identified in FTDP-17. Exon 10 codes for the second of four microtubule-binding repeat domains. The splice-site mutations result in increased inclusion of exon 10 which causes a relative increase in tau isoforms containing four microtubule-binding repeat domains over those containing three repeat domains. This could be a central aetiological mechanism in FTDP-17 and, perhaps, other related tauopathies. We have investigated changes in the ratio and distribution of three-repeat and four-repeat tau in the different tauopathies as a basis of the phenotypic range of these disorders and the selective vulnerability of different subsets of neurones. In this study, we have developed two monoclonal antibodies, RD3 and RD4 that effectively distinguish these closely related tau isoforms. These new isoform-specific antibodies are useful tools for analysing tau isoform expression and distribution as well as pathological changes in the human brain.
Maxillofacial Surgery and Obstructive Sleep Apnea: A Review of 80 Patients (1989)

To determine the effectiveness of the surgical treatment of obstructive sleep apnea, we retrospectively evaluated 80 patients. One group consisted of 55 patients who had undergone a limited osteotomy of the anterior mandible: inferior sagittal osteotomy with hyoid myotomy and suspension. Important criteria for the selection of these patients were normal pulmonary function, normal mandibular skeletal development, and the absence of morbid obesity. Polysomnography revealed that 37 patients (67%) had responded to the surgical treatment and 18 patients (33%) had not. The second group of 25 patients, selected for morbid obesity, severe mandibular deficiency, and failure of other surgical procedures, had undergone maxillomandibular osteotomy with hyoid advancement. All patients in the second group showed good results, as determined by polysomnography.
Antimetastatic Effects of Blocking PD-1 and the Adenosine A2A Receptor (2014)

Adenosine targeting is an attractive new approach to cancer treatment, but no clinical study has yet examined adenosine inhibition in oncology despite the safe clinical profile of adenosine A2A receptor inhibitors (A2ARi) in Parkinson disease. Metastasis is the main cause of cancer-related deaths worldwide, and therefore we have studied experimental and spontaneous mouse models of melanoma and breast cancer metastasis to demonstrate the efficacy and mechanism of a combination of A2ARi in combination with anti-PD-1 monoclonal antibody (mAb). This combination significantly reduces metastatic burden and prolongs the life of mice compared with either monotherapy alone. Importantly, the combination was only effective when the tumor expressed high levels of CD73, suggesting a tumor biomarker that at a minimum could be used to stratify patients that might receive this combination. The mechanism of the combination therapy was critically dependent on NK cells and IFNγ, and to a lesser extent, CD8(+) T cells and the effector molecule, perforin. Overall, these results provide a strong rationale to use A2ARi with anti-PD-1 mAb for the treatment of minimal residual and metastatic disease.
Overexpression of aldo‐keto reductase 1C2 is associated with disease progression in patients with prostatic cancer (2010)

Overexpression of AKR1C2 is associated with disease progression in prostatic cancer.
Molecular Cloning and Characterization of the Noncatalytic Subunit of the Rab3 Subfamily-specific GTPase-activating Protein (1998)

We recently purified and characterized from rat brain a GTPase-activating protein (GAP) specific for the Rab3 small G protein subfamily implicated in Ca2+-dependent exocytosis. Rab3 GAP showed two bands with Mr of about 130,000 (p130) and 150,000 (p150) on SDS-polyacrylamide gel electrophoresis. p130, but not p150, showed the catalytic activity. Because p150 was likely the subunit of Rab3 GAP, here we cloned the cDNA of p150, determined its primary structure, and characterized it. The tissue and subcellular distribution patterns of p150 and p130 were similar, and both the proteins were enriched in the synaptic soluble fraction. p150 was co-immunoprecipitated with p130 from this fraction. Recombinant p150 formed a heterodimer with recombinant p130 as estimated by sucrose density gradient ultracentrifugation. Recombinant p150 neither showed the Rab3A GAP activity nor affected the activity of recombinant p130. When p150 and p130 were co-expressed in the cells, the subcellular localization of each protein did not change. These results indicate that p150 is the noncatalytic subunit of Rab3 GAP.
Deformability-based red blood cell separation in deterministic lateral displacement devices—A simulation study (2014)

We show, via three-dimensional immersed-boundary-finite-element-lattice-Boltzmann simulations, that deformability-based red blood cell (RBC) separation in deterministic lateral displacement (DLD) devices is possible. This is due to the deformability-dependent lateral extension of RBCs and enables us to predict a priori which RBCs will be displaced in a given DLD geometry. Several diseases affect the deformability of human cells. Malaria-infected RBCs, for example, tend to become stiffer than their healthy counterparts. It is therefore desirable to design microfluidic devices which can detect diseases based on the cells' deformability fingerprint, rather than preparing samples using expensive and time-consuming biochemical preparation steps. Our findings should be helpful in the development of new methods for sorting cells and particles by deformability.
Monitoring of Intracellular Ca2+ Elevation in a Single Neural Cell Using a Fluorescence Microscope/Video-Camera System (1986)

For monitoring the changes in intracellular free Ca2+ concentration ([Ca2+]i), we developed a simple system combining a fluorescence microscope, an image intensifier, a video-camera, a cathode ray tube display and a photodiode, employing quin2 as a Ca2+ indicator. We recorded increases of the fluorescence intensity due to [Ca2+]i rises, when high K+ medium, neurotransmitter and Ca2+ ionophore were applied to the single cells of nervous system origin in culture. The present system is capable of simultaneous detection of the [Ca2+]i changes from multiple separate cells.
<title>Biomechanism of low-energy laser irradiation is similar to a general adaptive reaction</title> (1994)

After more than 30 years of applications of low-energy laser, many hypotheses remain about the mechanisms underlying its biologic and therapeutic effects. The majority of hypotheses are based on bioeffects as a function of the photoinduction of biochemical processes. This approach is problematic, however, because it is difficult to single out biochemical processes that could not be altered by laser action. An alternative view to understanding the bioactivity of laser exposure is that such activity, either by cells, tissue, organ systems, or the whole organism, is an adaptive response to stress. This paper summarizes briefly three experiments conducted in our clinic utilizing low-level laser, and describes in some detail an experiment comparing the action of laser with a known nonspecific, chemical adaptogen.
Varied Transcriptional Efficiencies of Multiple Arabidopsis U6 Small Nuclear RNA Genes (2007)

Abstract Arabidopsis U6 small nuclear RNA (snRNA) promoters are those transcribed by RNA polymerase III, but all the core elements for transcriptional initiation are located in the 5’promoter region. Previously, three Arabidopsis U6 snRNA genes ( U6‐1, U6‐26 , and U6‐29 ) were identified. Herein, we have further identified three new U6 loci ( U6‐4, U6‐5 , and U6‐6 ) in the Arabidopsis genome. Alignment of these revealed that the upstream sequence element and TATA elements were contained in six U6 promoters. In addition, a unique, highly conserved element named the “CAT” element was observed in the promoter region. To understand the expression patterns of these U6 genes in Arabidopsis , we fused these promoters to the DNA segment of β‐ glucuronidase and then transferred these six constructs into Arabidopsis. Real‐time reverse transcription‐polymerase chain reaction analysis of these fused transcripts indicated that the newly identified U6 genes are active in Arabidopsis and that the U6‐26 promoter seems to have higher transcriptional activity in leaf, stem, flower and silique. These results help to understand the function of these U6 snRNAs in Arabidopsis.
Learning probabilistic models of link structure (2003)

Most real-world data is heterogeneous and richly interconnected. Examples include the Web, hypertext, bibliometric data and social networks. In contrast, most statistical learning methods work with &amp;quot;flat&amp;quot; data representations, forcing us to convert our data into a form that loses much of the link structure. The recently introduced framework of probabilistic relational models (PRMs) embraces the object-relational nature of structured data by capturing probabilistic interactions between attributes of related entities. In this paper, we extend this framework by modeling interactions between the attributes and the link structure itself. An advantage of our approach is a unified generarive model for both content and relational structure. We propose two mechanisms for representing a probabilistic distribution over link structures: reference uncertainty and existence uncertainty. We describe the appropriate conditions for using each model and present learning algorithms for each. We present experimental results showing that the learned models can be used to predict link structure and, moreover, the observed link structure can be used to provide better predictions for the attributes in the model.