gebhart/patrepeval huggingface dataset:
Favin versus concanavalin A: Circularly permuted amino acid sequences (1979)

We have determined the tentative amino acid sequence of the beta chain (M(r) 20,000) of the lectin favin. In previous studies, we have shown that the alpha chain (M(r) 5600) of this lectin is homologous to a region in the middle of the concanavalin A (Con A) sequence (residues 70-119). Now we present evidence that the beta chain is homologous to two discrete segments of Con A. The homology begins at residue 120 of Con A, extends to the COOH terminus (residue 237) and continues without interruption through the NH(2)-terminal 69 residues of Con A. Together, the alpha and beta chains of favin account for a polypeptide chain equivalent in size to that of Con A. The comparison of the two proteins thus reveals a circular permutation of extensive homologous sequences. The favin molecule contains residues identical to many of the residues postulated to be involved in sugar binding by Con A, and contains all of the direct metal ligands as well as residues homologous to most of the residues that form the beta-pleated sheets of Con A. These homologies suggest that the three-dimensional structures of the two lectins are likely to be very similar. Moreover, favin appears to be even more closely related in primary structure and sugar specificity to the lectins from pea and lentil, raising the possibility that all of these lectins may have structures that resemble Con A. Some of these similarities may also extend to the lectins from soybean, peanut, and red kidney bean, which have different sugar specificities but share sequence homologies with the favin beta chain.
Recent advances in hereditary spastic paraplegia (2001)

The hereditary spastic paraplegias are a group of rare disorders that are characterized by great clinical and genetic heterogeneity. There has been an exponential increase in the number of HSP loci mapped in recent years, with nine out of the 17 loci reported during the past 2 years. Eight loci have now been identified for the autosomal-dominant form, and seven of these are associated with pure HSP. Spastic paraplegia-4 remains the most frequent locus, and is usually associated with a pure phenotype. Although the corresponding spastin gene was only recently identified, over 50 mutations have been described to date, which renders molecular diagnosis difficult. Five loci are known for autosomal-recessive HSP, and four of these are associated with complex forms, all with different phenotypes. Two genes have been identified: paraplegin and sacsin. Finally, three loci have been identified in X-linked HSP, two of which are complex forms. The genes that encode L1 and PLP were the first to be identified in HSP disorders. Surprisingly, the five genes encode proteins of different families, making understanding and diagnosis of HSP even more difficult. The discovery of new genes should hopefully help to clarify the pathophysiology of these disorders.
Direct sequence spreading UWB systems: frequency domain processing for enhanced performance and throughput (2004)

In this work, we propose an innovative high performance, high throughput direct sequence spreading (DSS) ultra wideband (UWB) system. Our proposed system employs a novel multi-carrier pulse waveform at the UWB transmit side: At the receiver side, the received DSS UWB pulse is decomposed into its subcarriers and recombined to (1) exploit diversity in the frequency domain and (2) provide resistance to inter symbol interference (ISI) and/or multi-access interference (MAI). As a direct result, the proposed frequency-based UWB DSS system is shown to significantly outperform time-based DSS UWB systems, offering significant gain in throughput (up to 32 fold) without performance degradation, or, alternatively, avoiding error floors due to MAI that limit the performance of time-based systems.
In-Situ Scanning Tunneling Microscopy Imaging of the Reductive Desorption Process of Alkanethiols on Au(111) (1998)

The reductive desorption process of self-assembled monolayers of 1-hexadecanethiol, 1-propanethiol, and 3-mercaptopropionic acid on Au(111) has been studied in 0.5 M KOH solution by in-situ scanning tunneling microscopy (STM) and cyclic voltammetry. In-situ STM images of the monolayers at the potentials between −0.2 V and the reduction potentials of each thiols show the pits that are commonly seen in STM images of thiol self-assembled monolayers. A drastic morphological change takes place in the STM image around the peak potential in a cyclic voltammogram for the reductive desorption of adsorbed thiols. The images indicate that 3-mercaptopropionic acid molecules diffuse away from the surface after the reduction because of its higher solubility, while 1-propanethiol and 1-hexadecanethiol molecules stay in the vicinity of the surface forming aggregates. The partial recovery of the 1-hexadecanethiol monolayer after the anodic scan, suggested by cyclic voltammograms, is confirmed by STM, whereas 1-propanethiol aggregates remain at the surface without being reoxidized. The difference in the reoxidation behavior reflects the different amphiphilic properties of the desorbed molecules and the resultant molecular organizations formed on the surface.
Effect of Soluble Complement Receptor-1 on Neutrophil Accumulation after Traumatic Brain Injury in Rats (1995)

As part of the acute inflammatory response, neutrophils accumulate in the central nervous system after injury. Recently, a soluble human recombinant complement receptor (sCR1; BRL 55730; T Cell Sciences, Inc., Cambridge, MA, U.S.A.) has been developed that inhibits the activation of both the classical and the alternative pathways of complement. sCR1 attenuates the effects of the acute inflammatory response in several models of injury outside the central nervous system. The role of complement in traumatic brain injury, however, remains undefined. We hypothesized that treatment with sCR1 would attenuate neutrophil accumulation in the brain after cerebral trauma. Using a randomized, blinded protocol, 18 anesthetized Sprague-Dawley rats were pre-treated with sCR1 or saline (control) at both 2 h and 2 min before trauma (weight drop) to the exposed right parietal cortex. A third dose of sCR1 (or saline) was given 6 h after trauma. Coronal brain sections centered on the site of trauma were obtained at 24 h after trauma and analyzed for myeloperoxidase (MPO) activity as a marker of neutrophil accumulation. Complete blood counts with differential were obtained before treatment with sCR1 and at 24 h after trauma. At 24 h after trauma, brain MPO activity was reduced by 41% in sCR1-treated rats compared with control rats [0.1599 +/- 0.102 versus 0.2712 +/- 0.178 U/g (mean +/- SD); p = 0.02]. The neutrophil count in peripheral blood increased approximately twofold in both groups. Neutrophil accumulation occurring in the brain after trauma is inhibited by sCR1 treatment. This suggests that complement activation is involved in the local inflammatory response to traumatic brain injury and plays an important role in neutrophil accumulation in the injured brain.
Emerging Disease Issues and Fungal Pathogens Associated with HIV Infection (1996)

Fungal diseases are increasing among patients infected with human immunodeficiency virus (HIV) type 1. Infections due to Candida and Cryptococcus are the most common. Although mucocutaneous candidiasis can be treated with oral antifungal agents, increasing evidence suggests that prolonged use of these drugs results in both clinical and microbiologic resistance. The optimal therapy for cryptococcal meningitis remains unresolved, although initial treatment with amphotericin B, followed by life-long maintenance therapy with fluconazole, appears promising. Most cases of histoplasmosis, coccidioidomycosis, and blastomycosis occur in regions where their causative organisms are endemic, and increasing data suggest that a significant proportion of disease is due to recent infection. Aspergillosis is increasing dramatically as an opportunistic infection in HIV-infected patients, in part because of the increased incidence of neutropenia and corticosteroid use in these patients. Infection due to Penicillium marneffei is a rapidly growing problem among HIV-infected patients living in Southeast Asia. Although the advent of oral azole antifungal drugs has made primary prophylaxis against fungal diseases in HIV-infected patients feasible, many questions remain to be answered before the preventive use of antifungal drugs can be advocated.
On the Relation of Slow Feature Analysis and Laplacian Eigenmaps (2011)

The past decade has seen a rise of interest in Laplacian eigenmaps (LEMs) for nonlinear dimensionality reduction. LEMs have been used in spectral clustering, in semisupervised learning, and for providing efficient state representations for reinforcement learning. Here, we show that LEMs are closely related to slow feature analysis (SFA), a biologically inspired, unsupervised learning algorithm originally designed for learning invariant visual representations. We show that SFA can be interpreted as a function approximation of LEMs, where the topological neighborhoods required for LEMs are implicitly defined by the temporal structure of the data. Based on this relation, we propose a generalization of SFA to arbitrary neighborhood relations and demonstrate its applicability for spectral clustering. Finally, we review previous work with the goal of providing a unifying view on SFA and LEMs.
3-D computer graphics based on integral photography (2001)

Integral photography (IP), which is one of the ideal 3-D photographic technologies, can be regarded as a method of capturing and displaying light rays passing through a plane. The NHK Science and Technical Research Laboratories have developed a real-time IP system using an HDTV camera and an optical fiber array. In this paper, the authors propose a method of synthesizing arbitrary views from IP images captured by the HDTV camera. This is a kind of image-based rendering system, founded on the 4-D data space Representation of light rays. Experimental results show the potential to improve the quality of images rendered by computer graphics techniques.
Production of cytokines by mouse peritoneal cells treated with Tołpa Torf Preparation (TTP): dependence on age and strain of mice. (1993)

Production of two cytokines: Interferon beta (IFN-beta) and tumor necrosis factor alpha (TNF-alpha) by freshly isolated resident mouse peritoneal cells (RPC) treated with immunostimulating drug Tołpa* Torf Preparation (TTP) was investigated. Nontoxic concentrations of TTP (10 and 100 micrograms/ml) potentiated the cytokine production by RPC of BALB/c mice. The observed effects were dose-dependent. The optimal cytokine-inducing concentration of TTP was 100 micrograms/ml. The effect of TTP depended on the age of mice. The high potentiation (16-fold) of IFN-beta and TNF-alpha production by TTP was observed when 5 and 8 week-old mice were used. However, in RPC isolated from one year old mice, only two (fold) potentiation of IFN and TNF was observed. The activities of the same commercial preparations of TTP were compared in the RPC cultures isolated from mice of the three different strains: BALB/c, C3H/HeJ and NZB. The significant stimulation (16-32-fold) of TNF and IFN was observed in the cells isolated from BALB/c mice. In contrast, only slight stimulation of IFN and TNF (1-3-fold) was observed in cells of NZB mice. Peritoneal cells of C3H mice did not respond to stimulation with TTP.
Tolerance induction by megadose hematopoietic progenitor cells: expansion of veto cells by short-term culture of purified human CD34+ cells (2002)

Stem cell-dose escalation is one way to overcome immune rejection of incompatible stem cells. However, the number of hematopoietic precursors required for overcoming the immune barrier in recipients pretreated with sublethal regimens cannot be attained with the state-of-the-art technology for stem cell mobilization. This issue was addressed by the observation that cells within the human CD34(+) population are endowed with veto activity. In the current study, we demonstrated that it is possible to harvest about 28- to 80-fold more veto cells on culturing of purified CD34(+) cells for 7 to 12 days with an early-acting cytokine mixture including Flt3-ligand, stem cell factor, and thrombopoietin. Analysis of the expanded cells with fluorescence-activated cell-sorter scanning revealed that the predominant phenotype of CD34(+)CD33(-) cells used at the initiation of the culture was replaced at the end of the culture by cells expressing early myeloid phenotypes such as CD34(+)CD33(+) and CD34(-)CD33(+). These maturation events were associated with a significant gain in veto activity as exemplified by the minimal ratio of veto to effector cells at which significant veto activity was detected. Thus, whereas purified unexpanded CD34(+) cells exhibited veto activity at a veto-to-effector cell ratio of 0.5, the expanded cells attained an equivalent activity at a ratio of 0.125. The availability of novel sources of veto cells such as those in this study might contribute to the realization of immunologic tolerance in "minitransplants," without any risk of graft-versus-host disease.
Tension Band Wiring-Bone Grafting for Spondylolysis and Spondylolisthesis (1989)

Patients with spondylolysis or spondylolisthesis with persistent symptoms often require surgical treatment. The purpose of this article is to present a new surgical technique and clinical results of 13 patients with symptomatic spondylolysis/spondylolisthesis who were treated with tension band wiring (intra- or intersegmental) and bone grafting techniques. This article also presents the results of biomechanical effects of these tension band wiring methods on canine lumbar spines with experimental spondylolytic defects. Thirteen adult patients, three with spondylolysis, and ten with spondylolytic spondylolisthesis, were treated with intrasegmental or intersegmental wiring with bone grafting technique, and the clinical results were evaluated at the mean follow-up period of 20 months. Patients with spondylolysis were treated with intrasegmental wiring (transverse processes to the spinous process of the same segment) with bone grafting at the lytic defect. Patients with spondylolytic spondylolisthesis were treated with intersegmental wiring (transverse process of the segment with defect to the spinous process of the same segment and to the spinous process of the segment below) with bone grafting to the defect and one-level fusion. All 13 patients had a solid spinal fusion and/or healing of the defect at the follow-up evaluation. Eleven had excellent clinical results; one a good, and one a fair result. The results of the biomechanical study showed that the experimental spondylolytic defect produced a significant decrease in bending stiffness (flexion-extension), and the wiring techniques (both the intra- and intersegment) increased the bending stiffness to that of the normal intact spinal segment.
Ultrafiltration for proteomic sample preparation (2004)

Proteome analysis represents significant challenges to the existing sample preparation techniques. Traditional methods, such as two-dimensional electrophoresis, typically separate high-molecular-weight proteins while discarding low-molecular-weight species. This approach is well justified considering the complexity of any proteome. However, it is desirable to extract the maximum amount of information from each sample to investigate the entire range of biomolecules. We have demonstrated that ultrafiltration not only improves two-dimensional electrophoresis (2-DE) resolution of the protein fraction but also yields the low-molecular-weight fraction amenable for further analysis by high-resolution mass spectrometry. This approach was successfully adapted to the variety of biological samples including cell and tissue lysates and serum. Therefore, ultrafiltration offers an alternative sample preparation technique that enables more thorough analysis of a proteome.
Evolution and organization of the fibrinogen locus on chromosome 4: gene duplication accompanied by transposition and inversion. (1985)

Human fibrinogen cDNA probes for the alpha-, beta-, and gamma-polypeptide chains have been used to isolate the corresponding genes from human genomic libraries. There is a single copy of each gene. Restriction endonuclease analysis of isolated genomic clones and human genomic DNA indicates that the human alpha-, beta-, and gamma-fibrinogen genes are closely linked in a 50-kilobase region of a single human chromosome: the alpha-gene in the middle flanked by the beta-gene on one side and the gamma-gene on the other. The alpha- and gamma-chain genes are oriented in tandem and transcribed toward the beta-chain gene. The beta-chain gene is transcribed from the opposite DNA strand toward the gamma- and alpha-chain genes. The three genes have been localized to the distal third of the long arm of chromosome 4, bands q23-q32, by in situ hybridization with fibrinogen cDNAs and by examination of DNA from multiple rodent-human somatic cell hybrids. Alternative explanations for the present arrangement of the three fibrinogen genes involve either a three-step mechanism with inversion of the alpha/gamma-region or a two-step mechanism involving remote transposition and inversion. The second more simple mechanism has a precedent in the origin of repeated regions of the fibrinogen and immunoglobulin genes.
The proto-oncogene of v-eyk (v-ryk) is a novel receptor-type protein tyrosine kinase with extracellular Ig/GN-III domains. (1994)

v-ryk is the oncogene in the avian acute oncogenic retrovirus RPL30, its cellular counterpart, c-ryk, is described in this report. To avoid the confusion caused by another gene with the same name, we renamed v-ryk to be v-eyk, thereby changing the proto-oncogene's name to c-eyk. c-eyk is expressed highly in chicken spleen and moderately in many other tissues including embryonic tissues. Its cDNA is 3061 base pairs encoding a receptor-type protein tyrosine kinase (PTK) of 974 amino acids. Compared to c-Eyk, v-Eyk is a truncated PTK lacking the extracellular and transmembrane regions of c-Eyk in addition to two amino acid changes. c-Eyk has two C2-type Ig domains and two FN-III domains in its extracellular region, forming a new subfamily of receptor-type PTK together with UFO/Axl/Ark. As suggested by Ig/Fn-III domains in many cell adhesion molecules, this subfamily of PTK may mediate cell-cell interaction.
Guidelines for the management of atrial fibrillation: The Task Force for the Management of Atrial Fibrillation of the European Society of Cardiology (ESC) (2010)

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, occurring in 1–2% of the general population. Over 6 million Europeans suffer from this arrhythmia, and its prevalence is estimated to at least double in the next 50 years as the population ages. It is now 4 years since the last AF guideline was published, and a new version is now needed. AF confers a 5-fold risk of stroke, and one in five of all strokes is attributed to this arrhythmia. Ischaemic strokes in association with AF are often fatal, and those patients who survive are left more disabled by their stroke and more likely to suffer a recurrence than patients with other causes of stroke. In consequence, the risk of death from AF-related stroke is doubled and the cost of care is increased 1.5-fold. There has been much research into stroke prevention, which has influenced this guideline. In the majority of patients there appears to be an inexorable progression of AF to persistent or permanent forms, associated with further development of the disease that may underlie the arrhythmia. Some advance has been made in the understanding of the dynamic development of AF from its preclinical state as an ‘arrhythmia-in-waiting’ to its final expression as an irreversible and end-stage cardiac arrhythmia associated with serious adverse cardiovascular events. Much recent therapeutic effort with ‘upstream therapies’ has been expended to slow or halt the progression of AF due to underlying cardiovascular disease and to AF itself. Limited success has been achieved and is recognized in this guideline.
Monoclonal antibody screening of a phage-displayed random peptide library reveals mimotopes of chemokine receptor CCR5: implications for the tertiary structure of the receptor and for an N-terminal binding site for HIV-1 gp120 (2000)

The chemokine receptor CCR5 contains seven transmembrane-spanning domains. It binds chemokines and acts as co-receptor for macrophage (m)-tropic (or R5) strains of HIV-1. Monoclonal antibodies (mAb) to CCR5, 3A9 and 5C7, were used for biopanning a nonapeptide cysteine (C)-constrained phage-displayed random peptide library to ascertain contact residues and define tertiary structures of possible epitopes on CCR5. Reactivity of antibodies with phagotopes was established by enzyme-linked immunosorbent assay (ELISA). mAb 3A9 identified a phagotope C-HASIYDFGS-C (3A9 / 1), and 5C7 most frequently identified C-PHWLRDLRV-C (5C7 / 1). Corresponding peptides were synthesized. Phagotopes and synthetic peptides reacted in ELISA with corresponding antibodies and synthetic peptides inhibited antibody binding to the phagotopes. Reactivity by immunofluorescence of 3A9 with CCR5 was strongly inhibited by the corresponding peptide. Both mAb 3A9 and 5C7 reacted similarly with phagotopes and the corresponding peptide selected by the alternative mAb. The sequences of peptide inserts of phagotopes could be aligned as mimotopes of the sequence of CCR5. For phage 3A9 / 1, the motif SIYD aligned to residues at the N terminus and FG to residues on the first extracellular loop; for 5C7 / 1, residues at the N terminus, first extracellular loop, and possibly the third extracellular loop could be aligned and so would contribute to the mimotope. The synthetic peptides corresponding to the isolated phagotopes showed a CD4-dependent reactivity with gp120 of a primary, m-tropic HIV-1 isolate. Thus reactivity of antibodies raised to CCR5 against phage-displayed peptides defined mimotopes that reflect binding sites for these antibodies and reveal a part of the gp120 binding sites on CCR5.
A new interactive method for coronary arteries segmentation based on tubular anisotropy (2009)

In this paper we present a new interactive method for tubular structure extraction. The main application and motivation for this work is vessel tracking in 3D medical images. The basic tools are minimal paths solved using the fast marching algorithm. This leads to interactive tools for the physician by clicking on a small number of points in order to obtain a minimal path between two points or a set of paths in the case of a tree structure. Our method is based on a variant of the minimal path method that models the vessel as a centerline and surface by adding one dimension for the local radius around the centerline. The crucial step of our method is the definition of the local metrics to minimize (based on the local orientation using a Riemannian Metric). This approach is made available for the physician using an Object Oriented Language (OOL) interface. We show results on two CT cardiac images for coronary arteries segmentation.
Mechanochemical assembly of hydrogen bonded organic-organometallic solid compounds (2002)

Solvent-free reactions with molecular systems have been exploited to prepare hybrid organic-organometallic solids: grinding of the complex [Fe(eta 5-C5H4COOH)2] with solid bases B generates quantitatively the corresponding hydrogen bonded salts [Fe(eta 5-C5H4COOH)(eta 5-C5H4COO)][HB] (B = 1,4-diazabicyclo[2.2.2]octane, 1,4-phenylenediamine); gas-solid reactions are also possible with volatile bases.
The Maine Womenʼs Health Study (1994)

Hysterectomy is highly effective for relief of symptoms associated with common nonmalignant gynecologic conditions. Symptom relief following hysterectomy is associated with a marked improvement in quality of life. New problems are reported after hysterectomy by a limited number of women.