gebhart/patrepeval huggingface dataset:
The role of mucus in antibody-mediated rapid expulsion of Trichinella spiralis in suckling rats. (1990)

Rat pups suckling dams parasitized by Trichinella spiralis express rapid expulsion, a protective response that is associated with the entrapment of infectious muscle larvae in intestinal mucus. Immunofluorescent studies revealed that antibodies were bound to the surfaces of the entrapped larvae. Mucus binding and rapid expulsion occurred in normal pups dosed with larvae coated with antibodies prepared from infected rat serum. Subsequent experiments revealed that entrapped larvae escaped from mucus after 2 hr in vitro incubation in saline. Escape correlated with the loss of the surface-bound antibodies, suggesting that mucus entrapment was reversible and dependent on antibody coating. Finally, when protective antibodies were injected 1, 2 or 6 hr after larvae were administered to pups, the parasites were forced to leave their epithelial niche and became enveloped in mucus. The above findings suggest that mucus trapping of T. spiralis larvae is dependent upon the coating of larvae by antibody, but that trapping is reversible, and is not in itself the pivotal event in rapid expulsion. The primary mechanism of rapid expulsion appears to be antibody-mediated inhibition of processes required for the parasite to maintain itself in the epithelium.
Serum levels of chitotriosidase as a marker of disease activity and clinical stage in sarcoidosis (2004)

Although the data need to be validated by further investigation, the observations made in this study seem to indicate that serum chitotriosidase concentrations may be a useful marker for monitoring sarcoidosis disease activity and prognosis.
Glycosylphosphatidylinositol Anchor Modification Machinery Deficiency Is Responsible for the Formation of Pro-Prion Protein (PrP) in BxPC-3 Protein and Increases Cancer Cell Motility (2015)

The normal cellular prion protein (PrP) is a glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein. However, in pancreatic ductal adenocarcinoma cell lines, such as BxPC-3, PrP exists as a pro-PrP retaining its glycosylphosphatidylinositol (GPI) peptide signaling sequence. Here, we report the identification of another pancreatic ductal adenocarcinoma cell line, AsPC-1, which expresses a mature GPI-anchored PrP. Comparison of the 24 genes involved in the GPI anchor modification pathway between AsPC-1 and BxPC-3 revealed 15 of the 24 genes, including PGAP1 and PIG-F, were down-regulated in the latter cells. We also identified six missense mutations in DPM2, PIG-C, PIG-N, and PIG-P alongside eight silent mutations. When BxPC-3 cells were fused with Chinese hamster ovary (CHO) cells, which lack endogenous PrP, pro-PrP was successfully converted into mature GPI-anchored PrP. Expression of the individual gene, such as PGAP1, PIG-F, or PIG-C, into BxPC-3 cells does not result in phosphoinositide-specific phospholipase C sensitivity of PrP. However, when PIG-F but not PIG-P is expressed in PGAP1-expressing BxPC-3 cells, PrP on the surface of the cells becomes phosphoinositide-specific phospholipase C-sensitive. Thus, low expression of PIG-F and PGAP1 is the major factor contributing to the accumulation of pro-PrP. More importantly, BxPC-3 cells expressing GPI-anchored PrP migrate much slower than BxPC-3 cells bearing pro-PrP. In addition, GPI-anchored PrP-bearing AsPC-1 cells also migrate slower than pro-PrP bearing BxPC-3 cells, although both cells express filamin A. “Knocking out” PRNP in BxPC-3 cell drastically reduces its migration. Collectively, these results show that multiple gene irregularity in BxPC-3 cells is responsible for the formation of pro-PrP, and binding of pro-PrP to filamin A contributes to enhanced tumor cell motility.
Clinical and electroencephalographic features of simple partial seizures (1988)

The clinical and electroencephalographic features of 87 simple partial seizures in 14 patients were studied with video-EEG telemetry. The patients were able to respond to verbal stimuli during all seizures and, later, could clearly recall ictal events. To determine whether the EEG changes in simple partial seizures could be reliably observed, a reader blindly reviewed four EEGs of equal duration for each seizure. These EEGs consisted of one ictal and three nonictal recordings obtained at predetermined times before the seizure. There were 27 motor seizures (mean duration, 86 seconds; range, 2 to 250 seconds), all involving clonic movements of the head and/or upper extremities; 8 (30%) of these had a sensory component (pain in 6, paresthesia in 2). An EEG change, usually localized spikes or sharp waves over the contralateral or both rolandic regions, was identifiable in nine (33%) of the motor seizures. The 60 nonmotor seizures (mean duration, 63 seconds; range, 8 to 375 seconds) involved a variety of symptoms, including somatosensory/special sensory (3 seizures), autonomic (26 seizures), cognitive (1 seizure), affective (14 seizures), and mixed, or more than one category of nonmotor symptoms (16 seizures). In only nine (15%) of the nonmotor seizures was there an ictal EEG change, usually localized spikes or paroxysmal theta activity over the temporal region. Overall, among the 87 simple partial seizures, only 18 (21%) revealed ictal EEG changes. Thus, a normal EEG is common during simple partial seizures and does not exclude the diagnosis.
Allorecognition by T Lymphocytes and Allograft Rejection (2016)

Recognition of donor antigens by recipient T cells in secondary lymphoid organs initiates the adaptive inflammatory immune response leading to the rejection of allogeneic transplants. Allospecific T cells become activated through interaction of their T cell receptors with intact allogeneic major histocompatibility complex (MHC) molecules on donor cells (direct pathway) and/or donor peptides presented by self-MHC molecules on recipient antigen-presenting cells (APCs) (indirect pathway). In addition, recent studies show that alloreactive T cells can also be stimulated through recognition of allogeneic MHC molecules displayed on recipient APCs (MHC cross-dressing) after their transfer <i>via</i> cell-cell contact or through extracellular vesicles (semi-direct pathway). The specific allorecognition pathway used by T cells is dictated by intrinsic and extrinsic factors to the allograft and can influence the nature and magnitude of the alloresponse and rejection process. Consequently, various organs and tissues such as skin, cornea, and solid organ transplants are recognized differently by pro-inflammatory T cells through these distinct pathways, which may explain why these grafts are rejected in a different fashion. On the other hand, the mechanisms by which anti-inflammatory regulatory T cells (Tregs) recognize alloantigen and promote transplantation tolerance are still unclear. It is likely that thymic Tregs are activated through indirect allorecognition, while peripheral Tregs recognize alloantigens in a direct fashion. As we gain insights into the mechanisms underlying allorecognition by pro-inflammatory and Treg cells, novel strategies are being designed to prevent allograft rejection in the absence of ongoing immunosuppressive drug treatment in patients.
α-thalassaemia (2010)

Alpha-thalassaemia is inherited as an autosomal recessive disorder characterised by a microcytic hypochromic anaemia, and a clinical phenotype varying from almost asymptomatic to a lethal haemolytic anaemia.It is probably the most common monogenic gene disorder in the world and is especially frequent in Mediterranean countries, South-East Asia, Africa, the Middle East and in the Indian subcontinent. During the last few decades the incidence of alpha thalassaemia in North-European countries and Northern America has increased because of demographic changes. Compound heterozygotes and some homozygotes have a moderate to severe form of alpha thalassaemia called HbH disease. Hb Bart's hydrops foetalis is a lethal form in which no alpha-globin is synthesized. Alpha thalassaemia most frequently results from deletion of one or both alpha genes from the chromosome and can be classified according to its genotype/phenotype correlation. The normal complement of four functional alpha-globin genes may be decreased by 1, 2, 3 or all 4 copies of the genes, explaining the clinical variation and increasing severity of the disease. All affected individuals have a variable degree of anaemia (low Hb), reduced mean corpuscular haemoglobin (MCH/pg), reduced mean corpuscular volume (MCV/fl) and a normal/slightly reduced level of HbA2. Molecular analysis is usually required to confirm the haematological observations (especially in silent alpha-thalassaemia and alpha-thalassaemia trait). The predominant features in HbH disease are anaemia with variable amounts of HbH (0.8-40%). The type of mutation influences the clinical severity of HbH disease. The distinguishing features of the haemoglobin Bart's hydrops foetalis syndrome are the presence of Hb Bart's and the total absence of HbF. The mode of transmission of alpha thalassaemia is autosomal recessive. Genetic counselling is offered to couples at risk for HbH disease or haemoglobin Bart's Hydrops Foetalis Syndrome. Carriers of alpha+- or alpha0-thalassaemia alleles generally do not need treatment. HbH patients may require intermittent transfusion therapy especially during intercurrent illness. Most pregnancies in which the foetus is known to have the haemoglobin Bart's hydrops foetalis syndrome are terminated due to the increased risk of both maternal and foetal morbidity.
Blackbody Infrared Radiative Dissociation of Bradykinin and Its Analogues:  Energetics, Dynamics, and Evidence for Salt-Bridge Structures in the Gas Phase (1996)

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.
Optimization-Based Control (2010)

ly, this is a constrained optimization problem where we seek a feasible trajectory (x(t), u(t)) that minimizes the cost function
Multifunctional Cytotoxic Stealth Nanoparticles. A Model Approach with Potential for Cancer Therapy (2009)

Here we report on a highly versatile nanoparticle-based core/shell drug delivery system consisting of cytotoxic stealth carrier particles. Their multifunctional shells, mandatory for addressing different diagnostic/treatment requirements, are constructed using a single assembly process in which various different functionalities are incorporated in a modular fashion. More specifically, we discuss a robust electrostatic and covalent layer-by-layer (LBL) assembly strategy as engineering approach toward nanoparticles with multilayer shells that combine all of the following properties: (i) a small size distribution of the nanoparticle carrier, (ii) a high stability in physiological media, (iii) attachment of a pro-drug in covalent form and thus a low toxicity of the carrier system, (iv) the triggered release and activation of the drug only after endocytosis and enzymatic cleavage, and (v) "stealthiness" and thus protection against uptake by macrophages. The fact that we employ small nanoparticles as carriers is predicted to enhance the accumulation of active drug in the tumor tissue (i.e., enhanced permeability and retention of tumor tissues, EPR). To establish this system as a proof of concept, we use the smallest nanoparticles within the interesting size range of about 25-100 nm for EPR targeting since these are the most difficult to functionalize and because they possess the highest surface area. On the basis of gold nanoparticle cores, our system allows for precise control of particle size and size distribution and also for easy monitoring of the dispersion stability by the naked eye.
Membrane Binding of Peptides Containing Both Basic and Aromatic Residues. Experimental Studies with Peptides Corresponding to the Scaffolding Region of Caveolin and the Effector Region of MARCKS (2000)

We have studied the binding of peptides containing both basic and aromatic residues to phospholipid vesicles. The peptides caveolin(92-101) and MARCKS(151-175) both contain five aromatic residues, but have 3 and 13 positive charges, respectively. Our results show the aromatic residues insert into the bilayer and anchor the peptides weakly to vesicles formed from the zwitterionic lipid phosphatidylcholine (PC). Incorporation of a monovalent acidic lipid (e.g., phosphatidylserine, PS) into the vesicles enhances the binding of both peptides via nonspecific electrostatic interactions. As predicted from application of the Poisson-Boltzmann equation to atomic models of the peptide and membranes, the enhancement is larger (e.g., 10(4)- vs 10-fold for 17% PS) for the more basic MARCKS(151-175). Replacing the five Phe with five Ala residues in MARCKS(151-175) decreases the binding to 10:1 PC/PS vesicles only slightly (6-fold). This result is also consistent with the predictions of our theoretical model: the loss of the attractive hydrophobic energy is partially compensated by a decrease in the repulsive Born/desolvation energy as the peptide moves away from the membrane surface. Incorporating multivalent phosphatidylinositol 4, 5-bisphosphate (PIP(2)) into PC vesicles produces dramatically different effects on the membrane binding of the two peptides: 1% PIP(2) enhances caveolin(92-101) binding only 3-fold, but increases MARCKS(151-175) binding 10(4)-fold. The strong interaction between the effector region of MARCKS and PIP(2) has interesting implications for the cellular function of MARCKS.
Identification of a Class of Chromatin Boundary Elements (1998)

Boundary elements are thought to define the ends of functionally independent domains of genetic activity. An assay for boundary activity based on this concept measures the ability to insulate a bracketed, chromosomally integrated reporter gene from position effects. Despite their presumed importance, the few examples identified to date apparently do not share sequence motifs or DNA binding proteins. The Drosophila protein BEAF binds the scs' boundary element of the 87A7 hsp70 locus and roughly half of polytene chromosome interband loci. To see if these sites represent a class of boundary elements that have BEAF in common, we have isolated and studied several genomic BEAF binding sites as candidate boundary elements (cBEs). BEAF binds with high affinity to clustered, variably arranged CGATA motifs present in these cBEs. No other sequence homologies were found. Two cBEs were tested and found to confer position-independent expression on a mini-white reporter gene in transgenic flies. Furthermore, point mutations in CGATA motifs that eliminate binding by BEAF also eliminate the ability to confer position-independent expression. Taken together, these findings suggest that clustered CGATA motifs are a hallmark of a BEAF-utilizing class of boundary elements found at many loci. This is the first example of a class of boundary elements that share a sequence motif and a binding protein.
Cryo-electron Microscopy Structures of Chimeric Hemagglutinin Displayed on a Universal Influenza Vaccine Candidate (2016)

Chimeric hemagglutinin proteins are set to undergo human clinical trials as a universal influenza vaccine candidate, yet no structural information for these proteins is available. Using cryo-electron tomography, we report the first three-dimensional (3D) visualization of chimeric hemagglutinin proteins displayed on the surface of the influenza virus. We show that, unexpectedly, the chimeric hemagglutinin structure differs from those of naturally occurring hemagglutinins by displaying a more open head domain and a dramatically twisted head/stalk arrangement. Despite this unusual spatial relationship between head and stalk regions, virus preparations expressing the chimeric hemagglutinin are fully infectious and display a high glycoprotein density, which likely helps induction of a broadly protective immune response.
Three separate epitopes on human IFN-alpha variants defined by monoclonal antibodies and their role in the binding to receptors. (1992)

Two monoclonal antibodies (mAbs) designed 9-1-1 and 2-2-1, produced by murine hybridoma clones, raised to recombinant IFN-alpha 2c and one mAb, designed 3A3-2, raised to recombinant IFN-alpha 88, have been characterized with respect to neutralization of IFN antiviral and antiproliferative activities. The regions of IFN molecule which these antibodies are directed against have been defined by analyzing cross- reactivity with four IFN-alpha subtypes (IFN-alpha 88, IFN-alpha 2a, IFN-alpha 2b, IFN-alpha 2c) and two fragments of IFN-alpha 88. An analysis of cross-reactivity patterns with IFN-alpha 88 and IFN-alpha 2c indicated that 3A3-2 mAb was directed to an epitope on IFN-alpha 88 not overlapping with epitopes of other mAbs, however its localization was not exactly defined. The epitope recognized by 9-1-1 mAb was present on IFN-alpha 88 and IFN-alpha 2c, and also was not overlapping the epitopes of other mAbs. Using another variant IFN-alpha 2a, containing Lys instead of Arg at position 23, for competitive binding study it was shown that Arg 23 was implicated in the epitope recognized by 9-1-1 mAb. The competition study with IFN-alpha 88 fragments allowed to locate the epitope recognized by 2-2-1 mAb between amino acid residues 51 and 166. The epitope blocking test indicated that 2-2-1 mAb was directed to an epitope overlapping that of previously reported for mAb NK-2, located around Glu at position 113.(ABSTRACT TRUNCATED AT 250 WORDS)
A Parallel VLSI Architecture for Layered Decoding for Array LDPC Codes (2007)

The VLSI implementation complexity of a low density parity check (LDPC) decoder is largely influenced by interconnect and the storage requirements. Here, the proposed layout-aware layered decoder architecture utilizes the data-reuse properties of min-sum, layered decoding and structured properties of array LDPC codes. This results in a significant reduction of logic and interconnects requirements of the decoder when compared to the state-of-the-art LDPC decoders. The ASIC implementation of the proposed fully parallel architecture achieves throughput of 4.6 Gbps (for a maximum of 15 iterations). The chip size is 2.3 mm times 2.3 mm in 0.13 micron technology
Stabilization of ballooning modes with sheared toroidal rotation (1995)

Stabilization of magnetohydrodynamic ballooning modes by sheared toroidal rotation is demonstrated using a shifted circle equilibrium model. A generalized ballooning mode representation is used to eliminate the fast Alfvén wave, and an initial value code solves the resulting equations. The s−α diagram (magnetic shear versus pressure gradient) of ballooning mode theory is extended to include rotational shear. In the ballooning representation, the modes shift periodically along the field line to the next point of unfavorable curvature. The shift frequency (dΩ/dq, where Ω is the angular toroidal velocity and q is the safety factor) is proportional to the rotation shear and inversely proportional to the magnetic shear. Stability improves with increasing shift frequency and direct stable access to the second stability regime occurs when this frequency is approximately one-quarter to one-half the Alfvén frequency, ωA=VA/qR.
Interstitial photoradiation therapy for primary solid tumors in pet cats and dogs. (1981)

Photoradiation therapy, a new method for treatment of solid malignant tumors, depends upon the tumor localization and retention of hematoporphyrin derivative, which is activated in vivo by light in the red region of the spectrum. As currently applied to cutaneous and s.c. lesions, the light dose is limited by both normal tissue reactions and the effective penetration of the light through the tissues. In this report, primary solid malignant lesions in pet cats and dogs have been treated by interstitial photoradiation therapy by applying the activating light from a laser [635 +/- 5 (S. D.) nm] directly into the tumor masses thrugh a 200-micrometer quartz fiber optic. Twelve of 14 lesions (four osteosarcomas, two squamous cell carcinomas, two malignant melanomas, one mast cell sarcoma, one fibrosarcoma, one sebaceous gland sarcoma, and a metastatic prostatic carcinoma) responded to treatment, and three are currently considered permanently controlled at 1 year or more following treatment. This method has not only allowed photoradiation therapy to be applied to some remote lesions but has also nearly eliminated normal tissue effects, thus greatly extending the applicability of this treatment to a wide range of human tumors.
Increasing maximum tumor dose to manage range uncertainties in IMPT treatment planning (2013)

The accuracy of intensity modulated proton therapy (IMPT) is sensitive to range uncertainties. Geometric margins, as dosimetric surrogates, are ineffective and robust optimization strategies are needed. These, however, lead to increased normal tissue dose. We explore here how this dose increase can be reduced by increasing the maximum tumor dose instead. We focus on range uncertainties, modeled by scaling the stopping powers 5% up (undershoot) or down (overshoot) compared to the nominal scenario. Robust optimization optimizes for target dose conformity in the most likely scenario, not the worst, while constraining target coverage for the worst-case scenario. Non-robust plans are also generated. Different maximum target doses are applied (105% versus 120% versus 140%) to investigate the effect on normal tissue dose reduction. The method is tested on a homogeneous and a lung phantom and on a liver patient. Target D99 of the robust plans equals the prescription dose of 60 GyE for all scenarios, but decreases to 36 GyE for the non-robust plans. The mean normal tissue dose in a 2 cm ring around the target is 11% to 31% higher for the robust plans. This increase can be reduced to -8% and 3% (compared to the non-robust plan) by allowing a maximum tumor dose of 120% instead of 105%. Thus robustness leads to more normal tissue dose, but it can be compensated by allowing a higher maximum tumor dose.