gebhart/patrepeval huggingface dataset:
Identifying Diagnostic Peptides for Lyme Disease through Epitope Discovery (2001)

Serum antibodies from patients with Lyme disease (LD) were used to affinity select peptide epitopes from 12 large random peptide libraries in phage display format. The selected peptides were surveyed for reactivity with a panel of positive sera (from LD patients) and negative sera (from subjects without LD), thus identifying 17 peptides with a diagnostically useful binding pattern: reactivity with at least three positive sera and no reactivity with any of the negative sera. The peptides define eight sequence motifs, none of which can be matched convincingly with segments of proteins from Borrelia burgdorferi, the LD pathogen; evidently, then, they are "mimotopes," mimicking natural pathogen epitopes without matching contiguous amino acids of pathogen proteins. Peptides like these could be the basis of a new diagnostic enzyme-linked immunosorbent assay for LD, with sufficient specificity and sensitivity to replace expensive immunoblotting tests that are currently required for definitive serological diagnosis. Moreover, the method used to discover these peptides did not require any knowledge of the pathogen and involved generic procedures that are applicable to almost any infectious disease, including emerging diseases for which no pathogen has yet been identified.
Ovarian cancer mouse models: a summary of current models and their limitations (2009)

Development of mouse models representing human spontaneous ovarian cancer has been hampered by the lack of understanding of the etiology of this very complex disease. Mouse models representing the different types of ovarian cancer are needed to understand how epithelial ovarian cancer differs from granulosa cell tumors. Many different methods have been used to generate a viable genetic model with limited success. This review focuses on the methods of various investigators and the limitations of each model in establishing a reproducible and inheritable line to study this disease.
Structural evaluation of human and sheep bone and comparison with synthetic hydroxyapatite by FT‐Raman spectroscopy (1995)

The composition of whole human and sheep cortical bone tissue, and of a synthetic hydroxyapatite (P120), were compared using Fourier transform Raman (FT-Raman) spectroscopy. Deproteination procedures to remove the bulk of the collagen present in bone tissue allowed isolation of the mineral phase. A comparison of the spectra obtained from both whole and deproteinated bone with those of synthetic hydroxyapatite showed direct correlation only in the region of 952 cm-1 (symmetric P-O mode). In contrast, human and sheep bone were very closely matched in both, the organic and inorganic structures. The results demonstrate that deproteination of bone is not a necessary precursor to obtain spectral information.
Introduction (1993)

The present study builds on an earlier work (Baxter, 1988) which examined how psychological and sociological concepts contributed to a better understanding of economic behaviour, in particular in the fields of consumer behaviour and labour market behaviour. An interesting feature of the earlier analysis was the manner in which the common behavioural foundations helped to cement links between the different fields of study. In economics, the common links are provided by the basic assumption of ‘rational’ behaviour, as exemplified by utility maximisation and profit maximisation. It is increasingly being recognised, however, that these basic axioms have to be supplemented if economics is to extend its analysis into new fields. But the question arises that, if we are continually having to supplement the basic axioms, would it not be preferable to take the matter to its logical conclusion and adopt much broader behavioural foundations? Such an alternative approach becomes increasingly attractive if it can be demonstrated that these broader foundations would still permit the development of meaningful hypotheses for empirical testing, and even offer scope for the rigorous mathematical analysis which is now such a feature of economics.
Parameters of the human genome. (1991)

Chromosome arm lengths are the critical parameters of the human genome. The physical length is required to scale radiation hybrid and other maps to megabases. The genetic lengths in males and females are required for probabilities of exclusion and synteny, choice of well-spaced loci for linkage tests, and comparison with centromeric maps based on nondisjunction. Interpolation of new data into a map is possible only when the length is known, including the distances from centromere and telomeres to the nearest markers. Current evidence on physical parameters including the reliable measurements of relative lengths from flow cytometry but only a crude estimate of genome size (3200 megabases). Evidence on genetic parameters includes chiasma counts and linkage maps corrected for failure to sample telomeres, giving an autosomal size of 2809 centimorgans in males and 4782 centimorgans in females. Estimates of the physical and sex-specific genetic lengths are presented for each chromosome arm. Any linkage analysis that yields substantially larger estimates raises a suspicion of an inappropriate mapping function or typing errors.
Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria (1998)

The diversity of the predominant bacteria in the human gastrointestinal tract was studied by using 16S rRNA-based approaches. PCR amplicons of the V6 to V8 regions of fecal 16S rRNA and ribosomal DNA (rDNA) were analyzed by temperature gradient gel electrophoresis (TGGE). TGGE of fecal 16S rDNA amplicons from 16 individuals showed different profiles, with some bands in common. Fecal samples from two individuals were monitored over time and showed remarkably stable profiles over a period of at least 6 months. TGGE profiles derived from 16S rRNA and rDNA amplicons showed similar banding patterns. However, the intensities of bands with similar mobilities differed in some cases, indicating a different contribution to the total active fraction of the prominent fecal bacteria. Most 16S rRNA amplicons in the TGGE pattern of one subject were identified by cloning and sequence analysis. Forty-five of the 78 clones matched 15 bands, and 33 clones did not match any visible band in the TGGE pattern. Nested PCR of amplified 16S rDNA indicated preferential amplification of a sequence corresponding to 12 of the 33 nonmatching clones with similar mobilities in TGGE. The sequences matching 15 bands in the TGGE pattern showed 91.5 to 98.7% homology to sequences derived from different Clostridium clusters. Most of these were related to strains derived from the human intestine. The results indicate that the combination of cloning and TGGE analysis of 16S rDNA amplicons is a reliable approach to monitoring different microbial communities in feces.
A technique for detecting antifungal activity of proteins separated by polyacrylamide gel electrophoresis (1991)

A technique was developed for the detection of antifungal activity of proteins after discontinuous polyacrylamide gel electrophoresis under native conditions. The antifungal activity is detected as growth inhibition zones in a homogeneous fungal lawn, grown in an agar layer spread on top of the polyacrylamide gel. The position of proteins with antifungal activity can be determined on a diffusion blot prepared from the same gel. The technique is illustrated for three antifungal plant proteins, i.e. alpha-purothionin, Urtica dioica agglutinin, and tobacco chitinase.
Femtosecond differential transmission measurements on low temperature GaAs metal–semiconductor–metal structures (1997)

We report on differential transmission measurements on low temperature grown (LT)-GaAs with and without applied electrical fields at different wavelengths. Electrical fields up to 100 kV/cm can be applied via an interdigitated contact structure to our LT GaAs samples which have been removed from the substrate by epitaxial lift off. In the presence of an electric field, both, the absorption bleaching due to phase space filling and field induced absorption changes due to the Franz–Keldysh effect contribute to the transmission changes. We observe an extended carrier lifetime with applied field. The response time of a biased metal–semiconductor–metal detector, therefore, exceeds the carrier life time of the substrate material.
Putative structure and functions of a poly-beta-hydroxybutyrate/calcium polyphosphate channel in bacterial plasma membranes. (1988)

A poly-beta-hydroxybutyrate complex extracted from the plasma membranes of genetically competent Escherichia coli contained polyhydroxybutyrate:polyphosphate:calcium in molar ratios approximating 1:1:0.5. The chain length of the polyhydroxybutyrate was estimated as 120-200 subunits, and that of the polyphosphate was estimated as 130-170 subunits. The extracted complex, when incorporated into liposomes, exhibited a lipid phase transition in the same temperature range as that of the membrane complex in whole cells as well as the same properties of irreversibility, lability, and sensitivity to chelating buffers. Space-filling molecular models and molecular energy minimization methods (Charmm) were used to develop and evaluate a plausible structure for the complex. It is proposed that the polyhydroxybutyrate forms an exolipophilic-endopolarophilic helix around an inner framework helix of calcium polyphosphate. The calcium ions link the two polymers by forming ionic bonds with phosphoryl oxygens of the polyphosphate and ion-dipole bonds with the ester carbonyl oxygens of the polyhydroxybutyrate. This symmetrical structure forms a channel through the membrane and may play a role in the transport of calcium, phosphate, and DNA.
Lycopene Supplementation Prevents the Development of Spontaneous Smooth Muscle Tumors of the Oviduct in Japanese Quail (2004)

Leiomyomas (fibroids) are benign tumors of the uterus affecting millions of women. Spontaneous leiomyomas of the oviduct are common tumors of the Japanese quail (Coturnix coturnix japonica), which makes it a good animal model for screening potential agents for testing in the prevention and treatment of human myoma uteri. Because dietary intake of lycopene has been associated with a reduced risk of a variety of human cancers, we investigated the effects of lycopene supplementation on the development of leiomyomas in the oviduct of Japanese quail. We also measured serum levels of oxidative stress markers [malondialdehyde (MDA) and homocysteine], lycopene, vitamins C, E, and A, and tissue biomarkers Bcl-2 and Bax expression. One hundred twenty quails (6 mo old) were assigned to 3 treatment groups consisting of 4 replicates of 10 birds in each group. Birds were fed either a basal diet (group C) or the basal diet supplemented with 100 mg (group L1) or 200 mg (group L2) of lycopene per kilogram of diet. The animals were sacrificed after 285 days and the tumors were identified. Lycopene supplementation decreased the number of leiomyomas compared with control subjects (P=0.056). The tumors in lycopene-fed birds were smaller than those found in control birds (P=0.01). There were no significant differences in the expression of tissue Bcl-2 and Bax among the study groups. Serum vitamins C, E, and A increased (P=0.01), whereas MDA and homocysteine concentrations decreased (P=0.01) with lycopene supplementation. No measurable lycopene could be detected in the serum of control birds, whereas a dose-dependent increase was observed in the serum of lycopene-supplemented birds. The results indicate that dietary supplementation with lycopene reduces the incidence and size of spontaneously occurring leiomyoma of the oviduct in the Japanese quail. Clinical trials should be conducted to investigate the efficacy of lycopene supplementation in the prevention and treatment of uterine leiomyoma in humans.
Induction of non-apoptotic cell death by sodium 5,6-benzylidene-L-ascorbate in a human salivary gland tumor cell line. (2000)

We investigated whether sodium 5,6-benzylidene-L-ascorbate (SBA) induces apoptotic cell death in a human salivary gland tumor cell line HSG, using two different cytochemical methods. Millimolar concentrations of SBA dose-dependently reduced the viable cell number of HSG cells, accompanied by the detachment of dying cells from the culture plates. The nuclei of the dying cells were not stained with TUNEL reagent, indicating the lack of DNA nicks or fragments. On the other hand, the nuclei of epigallocatechin gallate (EGCG)-treated cells (positive control) were TUNEL-positive, demonstrating the production of DNA nicks or fragments. Furthermore, the cytoplasms of SBA-treated cells were not stained with M30 monoclonal antibody, which reacts with the degradation products of cytokeratin 18 by the activated caspases, in contrast to those of EGCG-treated cells. These results suggest that SBA induces non-apoptotic cell death, possibly necrosis, in HSG cells.
Allele-Specific Suppression of Mutant Huntingtin Using Antisense Oligonucleotides: Providing a Therapeutic Option for All Huntington Disease Patients (2014)

Huntington disease (HD) is an inherited, fatal neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. The mutant protein causes neuronal dysfunction and degeneration resulting in motor dysfunction, cognitive decline, and psychiatric disturbances. Currently, there is no disease altering treatment, and symptomatic therapy has limited benefit. The pathogenesis of HD is complicated and multiple pathways are compromised. Addressing the problem at its genetic root by suppressing mutant huntingtin expression is a promising therapeutic strategy for HD. We have developed and evaluated antisense oligonucleotides (ASOs) targeting single nucleotide polymorphisms that are significantly enriched on HD alleles (HD-SNPs). We describe our structure-activity relationship studies for ASO design and find that adjusting the SNP position within the gap, chemical modifications of the wings, and shortening the unmodified gap are critical for potent, specific, and well tolerated silencing of mutant huntingtin. Finally, we show that using two distinct ASO drugs targeting the two allelic variants of an HD-SNP could provide a therapeutic option for all persons with HD; allele-specifically for roughly half, and non-specifically for the remainder.
Self‐Discharge of LiMn2 O 4/C Li‐Ion Cells in Their Discharged State: Understanding by Means of Three‐Electrode Measurements (1998)

The potential distribution through plastic Li‐ion cells during electrochemical testing was monitored by means of three‐ or four‐electrode measurements in order to determine the origin of the poor electrochemical performance (namely, premature cell failure, poor storage performance in the discharged state) of /C Li‐ion cells encountered at 55°C. Several approaches to insert reliably one or two reference electrodes that can be either metallic lithium or an insertion compound such as into plastic Li‐ion batteries are reported. Using a reference electrode, information regarding the evolution of (i) the state of charge of each electrode within a Li‐ion cell, (ii) their polarization, and (iii) their rate capability can be obtained. From these three‐electrode electrochemical measurements, coupled with chemical analyses, X‐ray diffraction, and microscopy studies, one unambiguously concludes that the poor 55°C performance is mainly due to the instability of the phase toward Mn dissolution in ‐type electrolytes. A mechanism, based on Mn dissolution, is proposed to account for the poor storage performance of /C Li‐ion cells.
Optimized Structural Designs for Stretchable Silicon Integrated Circuits (2009)

Materials and design strategies for stretchable silicon integrated circuits that use non-coplanar mesh layouts and elastomeric substrates are presented. Detailed experimental and theoretical studies reveal many of the key underlying aspects of these systems. The results shpw, as an example, optimized mechanics and materials for circuits that exhibit maximum principal strains less than 0.2% even for applied strains of up to approximately 90%. Simple circuits, including complementary metal-oxide-semiconductor inverters and n-type metal-oxide-semiconductor differential amplifiers, validate these designs. The results suggest practical routes to high-performance electronics with linear elastic responses to large strain deformations, suitable for diverse applications that are not readily addressed with conventional wafer-based technologies.
Advances in the management of epithelial ovarian cancer. (2001)

More than 23,400 new cases of ovarian cancer and 13,900 deaths are expected in the United States this year. Epithelial ovarian cancer is the most common histologic type of ovarian malignancy. Although there have been advances in the chemotherapeutic treatment of ovarian cancer, the five year survival of women with advanced-stage disease is 25-30%. Because the disease is typically asymptomatic until the disease has metastasized and because effective screening strategies are not unavailable, 70-75% of women present with advanced-stage disease. Of ovarian cancer cases, 90-95% are sporadic and 5-10% associated with germ-line mutations, including BRCA1 and BRCA2. Known risk factors for ovarian cancer include nulliparity and a strong family history of ovarian cancer. The use of oral contraceptives is known to decrease the risk of ovarian cancer: five years of use will decrease the risk by 50%. The staging of ovarian cancer (according to the International Federation of Obstetrics and Gynecology) requires surgical exploration. Determining the extent of disease is essential to appropriate management. Survival in patients with metastatic disease is improved in those who undergo optimal primary cytoreductive surgery. Adjuvant chemotherapy is recommended in patients with high-risk, early-stage disease and all patients with advanced-stage disease. Standard chemotherapy is a combination of paclitaxel and carboplatin. Selected patients with recurrent disease can undergo secondary cytoreductive surgery. Second-line chemotherapy for patients who initially respond to paclitaxel and carboplatin and who have a prolonged disease progression-free intervals (longer than 12 months) can be re-treated with either drug or both. Those whose responses to initial therapy were less successful can be treated with other chemotherapeutic agents--e.g., liposomal doxorubicin, topotecan, etoposide, gemcitabine or taxotere.
Green tea polyphenols reduce autoimmune symptoms in a murine model for human Sjogren's syndrome and protect human salivary acinar cells from TNF-α-induced cytotoxicity (2007)

Sjogren's syndrome (SS) is a relatively common autoimmune disorder. A key feature of SS is lymphocytic infiltration of the salivary and lacrimal glands, associated with the destruction of secretory functions of these glands. Current treatment of SS targets the symptoms but is unable to reduce or prevent the damage to the glands. We reported previously that the major green tea polyphenol (GTP) epigallocatechin-3-gallate (EGCG) inhibits autoantigen expression in normal human keratinocytes and immortalized normal human salivary acinar cells (Hsu et al. 2005). However, it is not known whether GTPs have this effect in vivo, if they can reduce lymphocytic infiltration, or protect salivary acinar cells from tumor necrosis factor-alpha (TNF-alpha)-induced cytotoxicity. Here, we demonstrate that in the NOD mouse, a model for human SS, oral administration of green tea extract reduced the serum total autoantibody levels and the autoimmune-induced lymphocytic infiltration of the submandibular glands. Further, we show that EGCG protected normal human salivary acinar cells from TNF-alpha-induced cytotoxicity. This protection was associated with specific phosphorylation of p38 MAPK, and inhibitors of the p38 MAPK pathway blocked the protective effect. In conclusion, GTPs may provide a degree of protection against autoimmune-induced tissue damage in SS, mediated in part through activation of MAPK elements.
Structural Basis for the Biological Activities of Bovine Seminal Ribonuclease (1995)

Bovine seminal ribonuclease (BS-RNase) is a homolog of RNase A with special biological properties that include specific antitumor, aspermatogenic, and immuno-suppressive activities. Unlike RNase A, BS-RNase is a dimer cross-linked by disulfide bonds between Cys31 of one subunit and Cys32 of the other. At equilibrium, this dimer is a mixture of two distinct quaternary forms, M = M and M x M. The conversion of M = M to M x M entails the exchange of NH2-terminal alpha-helices between subunits. Here, the cytotoxic activities of purified M x M were shown to be greater than those of purified M = M, despite extensive equilibration of M = M and M x M during the time course of the assays. Replacing Cys31 or Cys32 with a serine residue did not compromise the enzymatic activity of dimeric BS-RNase, but reduced both the fraction of M x M at equilibrium and the cytotoxicity. We conclude that the M x M form is responsible for the special biological properties of BS-RNase. Since cytosolic ribonuclease inhibitor binds tightly to monomeric but not dimeric BS-RNase and only the M x M form can remain dimeric in the reducing environment of the cytosol, we propose that BS-RNase has evolved its M x M form to retain its lethal enzymatic activity in vivo.
Current ebola vaccines (2012)

The most pressing remaining challenge is now to move these vaccine candidates forward into human trials and toward licensure. In order to achieve this, it will be necessary to establish the mechanisms and correlates of protection for these vaccines, and to continue to demonstrate their safety, particularly in potentially immunocompromised populations. However, already now there is sufficient evidence that, from a scientific perspective, a vaccine protective against ebolaviruses is possible.
Polycomb group proteins and heritable silencing of Drosophila Hox genes (2001)

Early in Drosophila embryogenesis, transcriptional repressors encoded by Gap genes prevent the expression of particular combinations of Hox genes in each segment. During subsequent development, those Hox genes that were initially repressed in each segment remain off in all the descendent cells, even though the Gap repressors are no longer present. This phenomenon of heritable silencing depends on proteins of the Polycomb Group (PcG) and on cis-acting Polycomb response elements (PREs) in the Hox gene loci. We have removed individual PcG proteins from proliferating cells and then resupplied these proteins after a few or several cell generations. We show that most PcG proteins are required throughout development: when these proteins are removed, Hox genes become derepressed. However, we find that resupply of at least some PcG proteins can cause re-repression of Hox genes, provided that it occurs within a few cell generations of the loss of repression. These results suggest a functional distinction between transcriptional repression and heritable silencing: in at least some contexts, Hox genes can retain the capacity to be heritably silenced, despite being transcribed and replicated. We propose that silenced Hox genes bear a heritable, molecular mark that targets them for transcriptional repression. Some PcG proteins may be required to define and propagate this mark; others may function to repress the transcription of Hox genes that bear the mark.