gebhart/patrepeval huggingface dataset:
Structure of the streptococcal endopeptidase IdeS, a cysteine proteinase with strict specificity for IgG (2004)

Pathogenic bacteria have developed complex and diverse virulence mechanisms that weaken or disable the host immune defense system. IdeS (IgG-degrading enzyme of Streptococcus pyogenes) is a secreted cysteine endopeptidase from the human pathogen S. pyogenes with an extraordinarily high degree of substrate specificity, catalyzing a single proteolytic cleavage at the lower hinge of human IgG. This proteolytic degradation promotes inhibition of opsonophagocytosis and interferes with the killing of group A Streptococcus. We have determined the crystal structure of the catalytically inactive mutant IdeS-C94S by x-ray crystallography at 1.9-A resolution. Despite negligible sequence homology to known proteinases, the core of the structure resembles the canonical papain fold although with major insertions and a distinct substrate-binding site. Therefore IdeS belongs to a unique family within the CA clan of cysteine proteinases. Based on analogy with inhibitor complexes of papain-like proteinases, we propose a model for substrate binding by IdeS.
Measurement of the shape of the surface of the back in patients with scoliosis. The standing and forward-bending positions. (1987)

In order to determine if the configuration of the trunk is altered when a patient changes from an upright to a forward-bending position, the shape of the surface of the back of fifty-six patients who had adolescent idiopathic scoliosis was recorded, by means of Raster stereophotography, with each patient in three postures: standing erect, bending forward with the hands between the knees (forward bend 1), and bending forward with the hands touching the toes (forward bend 2). The effect of placing one foot on a block to produce a limb-length difference was also studied in the standing position (thirty patients) and in the forward-bending position (eighteen patients). The degree of rotation of the surface of the back and of kyphosis and lordosis of the surface of the trunk was measured from sections in the sagittal plane that were plotted from the computerized measurements of the surface of the back. Qualitatively similar rotation of the surface of the back was found in both the standing position and the forward-bending position. When the patient was in the forward-bending position, the degree of rotation of the surface of the back was minimally changed in the thoracic region but increased in the lumbar region. The amount of rotation of the surface of the back was similar in both forward bending with the hands to the knees and forward bending with the hands to the toes.(ABSTRACT TRUNCATED AT 250 WORDS)
Continuous Particle Separation Through Deterministic Lateral Displacement (2004)

We report on a microfluidic particle-separation device that makes use of the asymmetric bifurcation of laminar flow around obstacles. A particle chooses its path deterministically on the basis of its size. All particles of a given size follow equivalent migration paths, leading to high resolution. The microspheres of 0.8, 0.9, and 1.0 micrometers that were used to characterize the device were sorted in 40 seconds with a resolution of approximately 10 nanometers, which was better than the time and resolution of conventional flow techniques. Bacterial artificial chromosomes could be separated in 10 minutes with a resolution of approximately 12%.
Adaptive RBF classifier for object recognition in image sequences (2000)

This paper presents an adaptive NN-RBF classifier developed for object recognition under continuously time-varying perceptual conditions. The classifier is a hybrid of a neural net and a control environment. Adaptability of the classifier involves processes of image analysis, reinforcement generation, and classifier modification. An NN-RBF classifier is applied to a single image of a sequence. A feedback reinforcement generation mechanism evaluates the classification results when compared to the previous images and activates classifier modification, if needed. Classifier modification selects a strategy and employs four behaviors in adapting the classifier's structure and parameters. The developed approach is tested on indoor and outdoor image sequences.
Quantitative comparison between the transplantability of human and murine tumors into the brain of NCr/Sed-nu/nu nude and severe combined immunodeficient mice. (1993)

In previous reports, nude mice have demonstrated residual immunoreactivity against xenografts. Severe combined immunodeficient (SCID) mice lack functional T- and B-cells. These animals are expected to be better hosts in which to perform preclinical studies on human tumors. The purpose of this study is to quantitate the advantage of SCID mice over nude mice in terms of transplantability of human and murine tumors and the importance of residual immunity in SCID mice. The transplantation assays are described by an assay based on the number of tumor cells required to transplant tumor into 50% of recipients (TD50). Seven human tumors of different histology and four murine tumor cell lines were used. Serial 2-10-fold dilutions of cells were injected (0.1 ml) into the flanks of normal and whole-body irradiated WBI nude and SCID mice. The results showed that in 6 of 6 human tumor cell lines studied, TD50S for SCID mice were 2.4 to 200 times lower than that of nude mice (significant in 5 cell lines). In contrast, in 2 of 3 murine tumors, TD50S in WBI SCID mice were significantly higher than that found in nude mice. When SCID and nude mice received WBI, TD50S were lower than those of nonirradiated animals in 5 of 5 xenografts (significant in 2 cell lines for nude mice and in 5 cell lines for SCID mice). We concluded that WBI SCID mice are significantly better recipients of human tumor xenografts than nude mice. There is a factor of 10-1625 gain in TD50S in favor of the WBI SCID mice when compared to nonirradiated nude mice. WBI has, however, an important effect on SCID mice which may suggest a detectable residual immunoreactivity, perhaps due to natural killer cells. These data demonstrate that WBI SCID mice are better models for human tumor transplantation that nude mice and, although WBI at 6 Gy suppressed significantly the immune system of nude mice, a certain level of immunoreactivity against xenografts is still maintained.
Blood–CSF barrier function in the rat embryo (2006)

Abstract Blood–cerebrospinal fluid (CSF) barrier function and expansion of the ventricular system were investigated in embryonic rats (E12–18). Permeability markers (sucrose and inulin) were injected intraperitoneally and concentrations measured in plasma and CSF at two sites (lateral and 4th ventricles) after 1 h. Total protein concentrations were also measured. CSF/plasma concentration ratios for endogenous protein were stable at ∼ 20% at E14–18 and subsequently declined. In contrast, ratios for sucrose (100%) and inulin (40%) were highest at the earliest ages studied (E13–14) and then decreased substantially. Between E13 and E16 the volume of the lateral ventricles increased over three‐fold. Decreasing CSF/plasma concentration ratios for small, passively diffusing molecules during embryonic development may not reflect changes in permeability. Instead, increasing volume of distribution appears to be important in this decline. The intracellular presence of a small marker (3000 Da biotin–dextranamine) in plexus epithelial cells following intraperitoneal injection indicates a transcellular route of transfer. Ultrastructural evidence confirmed that choroid plexus tight junctions are impermeable to small molecules at least as early as E15, indicating the blood–CSF barrier is morphologically and functionally mature early in embryonic development. Comparison of two albumins (human and bovine) showed that transfer of human albumin (surrogate for endogenous protein) was 4–5 times greater than bovine, indicating selective blood‐to‐CSF transfer. The number of plexus epithelial cells immunopositive for endogenous plasma protein increased in parallel with increases in total protein content of the expanding ventricular system. Results suggest that different transcellular mechanisms for protein and small molecule transfer are operating across the embryonic blood–CSF interface.
The Endometrium as a Source of Mesenchymal Stem Cells for Regenerative Medicine1 (2015)

Stem cell therapies have opened new frontiers in medicine with the possibility of regenerating lost or damaged cells. Embryonic stem cells, induced pluripotent stem cells, hematopoietic stem cells, and mesenchymal stem cells have been used to derive mature cell types for tissue regeneration and repair. However, the endometrium has emerged as an attractive, novel source of adult stem cells that are easily accessed and demonstrate remarkable differentiation capacity. In this review, we summarize our current understanding of endometrial stem cells and their therapeutic potential in regenerative medicine.
Antibody-based tumor vascular theranostics targeting endosialin/TEM1 in a new mouse tumor vascular model (2014)

The development of a new robust endothelial graft model expressing human tumor vascular proteins will help accelerate the development of novel theranostics targeting the tumor vasculature, which exhibit affinity specifically to human targets but not their murine counterparts. Our results also demonstrate the theranostic potential of MORAb-004 as PET imaging tracer and naked antibody therapy for TEM1-positive tumor.
Directivity of singers (2005)

Studies of acoustical balance between singers within a choir by means of room acoustical measurements have shown that the directional sound propagation of the source is important. For this reason the directivity of female and male singers for different vowels has been measured in this investigation. Measurements of a pilot study and some first measurements in 1998 have been supplemented with new measurements and an enhanced setup. A special measurement setup with reference and recording microphones was used to collect the directivity data. A resolution of 10 deg for azimuth and elevation angle was obtained. The results will be shown in 3D spherical plots with frequency adjustments in semitones from 80 to 8000 Hz. The measurements are compared to an artificial singer’s directivity, and the influence of a sheet music binder in front of a singer will be shown. The results give information on the directivity of singers and are relevant for the prediction of self-to-other-ratios that result from placement and formation aspects within a choir.
Characterization of a defensin in bark and fruit tissues of peach and antimicrobial activity of a recombinant defensin in the yeast, Pichia pastoris (2003)

Herein the cloning and characterization of a defensin gene ( PpDfn1 ) from a cDNA library made from peach ( Prunus persica [L.] Batsch) winter bark tissues is described. A partial clone obtained from the library was extended to full length by 5′ Rapid Amplification of cDNA Ends (RACE). The open reading frame of 237 bp codes for a 79 amino acid peptide related to the defensin family of proteins. Sequence comparison of the encoded protein using blast analysis revealed significant homology to defensins from other plant species. RNA gel blot analysis indicated that the gene is seasonally expressed in bark tissues of 1‐year‐old shoots, and is also expressed in early fruit development. Results of quantitative RT‐PCR and protein blot analysis were similar to those of RNA gel blot analyses for the bark tissues. A recombinant version, rDFN1 was expressed in the yeast, Pichia pastoris . It was found that rDFN1 inhibited germination of the fungal pathogens Penicillium expansum and Botrytis cinerea , but not the Gram‐negative bacterium Erwinia amylovora . The potential physiological role of PpDFN1 and its antimicrobial properties are discussed.
Seed‐Mediated Growth of Bimetallic Prisms (2005)

Bimetallic Ag/Au prisms (Figure, top) and corrugated core-shell nanoparticles (Figure, bottom) are synthesized using seed-mediated growth. The sizes and shapes of these core–shell nanoparticles are tailored by varying the stoichiometric Au3+/Ag+ ratio. Decreasing Au3+/Ag+ ratio results in nanoparticles with thicker gold shells and roughened surfaces, and surface plasmon bands that are red-shifted to the near-IR region of the electromagnetic spectrum.
Relationship between Packing Structure and Headgroups of Self-Assembled Monolayers on Au(111):  Bridging Experimental Observations through Computer Simulations (1998)

Computational studies including geometry optimizations and molecular dynamics (MD) simulations are carried out for self-assembled monolayers of n-alkanethiols (RSH, R = C16H33, C17H35) and 4‘-alkoxybiphenyl-4-thiols (ROC12H8SH, R = C16H33, C17H35) on the (111) surface of gold with a full atomic representation force field. In this work, we combine the information derived from scanning tunneling microscopy (STM), surface reflection infrared spectra (IR), and computational studies to uncover the origins of different odd−even effects observed by IR for long chain n-alkanethiols and 4‘-alkoxybiphenyl-4-thiols and then to establish a relationship between chemical structures of the headgroups and packing structures of thiols on Au(111). Computationally, the odd−even effect is monitored by the relative magnitude of z-components (the direction normal to the Au surface) of the methyl group. Although both n-alkanethiols and 4‘-alkoxybiphenyl-4-thiols occupy the same spacing on Au(111), according to our simulation results, their favored packing structures are different. Because the headgroup of 4‘-alkoxybiphenyl-4-thiol (−SC12H8O−) is more rigid than that of n-alkanethiol (−S−), 4‘-alkoxybiphenyl-4-thiol prefers more structured packing arrangements and thus its odd−even effect is stronger than that of n-alkanethiol. In other words, the flexibility of the headgroup greatly influences the variety of possible packing structures. Finally, with this new relationship, we are able to rationalize the strong odd−even effect of a new SAM molecule, n-alkyldithioic acid, on Au(111).
The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1 (2004)

We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of capsule carbohydrate and flagella surface structures were identified. Bacillus cereus ATCC 10987 contains a single large plasmid (pBc10987), of approximately 208 kb, that is similar in gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk.
Trans-splicing in protozoa and helminths. (1992)

Trans-splicing is defined as the process whereby exons derived from two separately transcribed RNAs are joined together. In one type of trans-splicing, nuclear pre-mRNAs acquire their 5' terminal exon (the spliced leader) from a small spliced leader RNA (SL RNA) via an RNA processing reaction that is directly analagous to the removal of intervening sequences (cis-splicing). Such leader-addition by trans-splicing has been extensively studied in trypanosomatid protozoans and in nematodes. This review summarizes recent advances in research on trans-splicing in these two systems. Progress in elucidating functionally significant sequence elements within SL RNAs and progress in understanding the mechanism and biological role of trans-splicing is discussed.
Molecular cloning, DNA sequence, and gene expression of the oxalyl-coenzyme A decarboxylase gene, oxc, from the bacterium Oxalobacter formigenes (1994)

Oxalic acid, a highly toxic by-product of metabolism, is catabolized by a limited number of bacterial species by an activation-decarboxylation reaction which yields formate and CO2. oxc, the gene encoding the oxalic acid-degrading enzyme oxalyl-coenzyme A decarboxylase, was cloned from the bacterium Oxalobacter formigenes. The DNA sequence revealed a single open reading frame of 1,704 bp capable of encoding a 568-amino-acid protein with a molecular weight of 60,691. The identification of a presumed promoter region and a rho-independent termination sequence indicates that this gene is not part of a polycistronic operon. A PCR fragment encoding the open reading frame, when overexpressed in Escherichia coli, produced a product which cross-reacted antigenically with native enzyme on Western blots (immunoblots), appeared to form homodimers spontaneously, and exhibited enzymatic activity similar to that of the purified native enzyme.
Deterioration of spermatozoal plasma membrane is associated with an increase of sperm lyso-phosphatidylcholines (2002)

Spermatozoa with plasma membranes that lost their asymmetry or permeability for larger molecules can be identified by binding of annexin V to membrane phosphatidylserine (PS). Paramagnetic annexin-V-conjugated microbeads (AN-MB) can be used to eliminate these spermatozoa by magnetic activated cell sorting (MACS). Semen samples of six healthy volunteers with normal spermiogram parameters were divided into two sperm fractions by MACS as a function of bound AN-MB, and their individual lipid compositions were examined by matrix-assisted laser desorption and ionisation time-of-flight mass spectrometry (MALDI-TOF MS). As a model system, liposomes composed of phosphatidylcholines (PC) from egg yolk were digested by phospholipase A2 (PLA2). The MALDI-TOF mass spectra of organic extracts of both sperm subpopulations differed significantly. The ratio between lyso-phosphatidylcholine LPC 16 : 0 and PC 16 : 0/22 : 6 was approximately 2.5-4.7-fold higher (median 2.9) in the sperm group binding AN-MB than in spermatozoa with intact membrane unable to bind AN-MB. The ratio between LPC 22 : 6 and PC 16 : 0/22 : 6 was also enhanced in the spermatozoa with impaired membrane structure (factor in the range: 1.9-3.9; median 2.6). These alterations corresponded to the effects of PLA2 on artificial phospholipids. It is concluded that spermatozoa with deteriorated membrane and exposed PS are characterized by an increased lyso-phosphatidylcholine content that is likely generated by phospholipases.
Living free radical polymerization with reversible addition - fragmentation chain transfer (the life of RAFT) (2000)

Free radical polymerization with reversible addition–fragmentation chain transfer (RAFT polymerization) is discussed with a view to answering the following questions: (a) How living is RAFT polymerization? (b) What controls the activity of thiocarbonylthio compounds in RAFT polymerization? (c) How do rates of polymerization differ from those of conventional radical polymerization? (d) Can RAFT agents be used in emulsion polymerization? Retardation, observed when high concentrations of certain RAFT agents are used and in the early stages of emulsion polymerization, and how to overcome it by appropriate choice of reaction conditions, are considered in detail. Examples of the use of thiocarbonylthio RAFT agents in emulsion and miniemulsion polymerization are provided. © 2000 Society of Chemical Industry
Comparison of Bilateral-Subtraction and Single-Image Processing Techniques in the Computerized Detection of Mammographic Masses (1993)

The incorporation of asymmetric information appears to be useful for computerized identification of possible masses on mammograms.
Molecular Variation at the In(2L)t Proximal Breakpoint Site in Natural Populations of Drosophila melanogaster and D. simulans (2000)

Abstract A previous study of nucleotide polymorphism in a Costa Rican population of Drosophila melanogaster found evidence for a nonneutral deficiency in the number of haplotypes near the proximal breakpoint of In(2L)t, a common inversion polymorphism in this species. Another striking feature of the data was a window of unusually high nucleotide diversity spanning the breakpoint site. To distinguish between selective and neutral demographic explanations for the observed patterns in the data, we sample alleles from three additional populations of D. melanogaster and one population of D. simulans. We find that the strength of associations among sites found at the breakpoint varies between populations of D. melanogaster. In D. simulans, analysis of the homologous region reveals unusually elevated levels of nucleotide polymorphism spanning the breakpoint site. As with American populations of D. melanogaster, our D. simulans sample shows a marked reduction in the number of haplotypes but not in nucleotide diversity. Haplotype tests reveal a significant deficiency in the number of haplotypes relative to the neutral expectation in the D. simulans sample and some populations of D. melanogaster. At the breakpoint site, the level of divergence between haplotype classes is comparable to interspecific divergence. The observation of interspecific polymorphisms that differentiate major haplotype classes in both species suggests that haplotype classes at this locus are considerably old. When considered in the context of other studies on patterns of variation within and between populations of D. melanogaster and D. simulans, our data appear more consistent with the operation of selection than with simple demographic explanations.
Reduced Choroidal Neovascular Membrane Formation in Matrix Metalloproteinase-2–Deficient Mice (2003)

The present study demonstrated that MMP-2 mRNA and protein are upregulated during experimental CNV in the mouse. The marked difference in thickness of the CNV membrane between wild-type and MMP-2-deficient mice shows that MMP-2 is involved in the formation of experimental CNV in the mouse. These results suggest that pharmacologic targeting of MMPs, including MMP-2, may reduce formation of CNV in conditions such as age-related macular degeneration.
The many hats of protein kinase Cδ: one enzyme with many functions (2014)

A large number of protein substrates are phosphorylated by each protein kinase under physiological and pathological conditions. However, it remains a challenge to determine which of these phosphorylated substrates of a given kinase is critical for each cellular response. Genetics enabled the generation of separation-of-function mutations that selectively cause a loss of one molecular event without affecting others, thus providing some tools to assess the importance of that one event for the measured physiological response. However, the genetic approach is laborious and not adaptable to all systems. Furthermore, pharmacological tools of the catalytic site are not optimal due to their non-selective nature. In the present brief review, we discuss some of the challenges in drug development that will regulate the multifunctional protein kinase Cδ (PKCδ).
Management of orbital lymphangioma using intralesional injection of OK-432 (2000)

An intralesional injection of OK-432 shrunk the lymphangioma without functional disturbance and scar in the facial skin. OK-432 may be useful for orbital lymphangioma, but further studies are still warranted to determine efficacy, complications, and the optimal dose for safe treatment.
In Vitro and In Vivo Activities of DA-7867, a New Oxazolidinone, against Aerobic Gram-Positive Bacteria (2005)

In vitro and in vivo activities of DA-7867 were assessed against methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, and penicillin-resistant Streptococcus pneumoniae. All isolates were inhibited by DA-7867 at <or=0.78 microg/ml, a four-times-lower concentration than that of inhibition by linezolid. For murine infection models, DA-7867 also exhibited greater efficacy than linezolid against all isolates tested.