gebhart/patrepeval huggingface dataset:
Ultrastructure of Human Spermatozoa with Complete Subcellular Derangement (1982)

The ultrastructure of highly abnormal spermatozoa from an infertile man is described. Nearly all cellular elements were completely deranged, and only occasionally a near-normal spermatozoon was found. The defects might be the result of a defective function of the “manchette” and the “spindle shaped body” that occur during spermiogenesis, but disappear during late maturation of the spermatozoon.
Therapeutic ultrasound phased arrays: practical consideration and design strategies (2002)

Focused high-intensity ultrasound is used for a wide range of therapeutic applications including hyperthermia cancer therapy, myocardial ablation, drug delivery/drug activation, and ultrasound surgery. Although many different applicators are capable of generating acceptable power levels for ultrasound therapy, multiple element arrays offer the most flexible option for ultrasound power delivery. The various engineering and economic trade-offs, which optimize the phased array aperture with respect to the channel count, usually result in element sizes which are far from ideal. These array elements excite lateral modes, which reduce the electric to acoustic efficiency significantly (down to 10-20%). This problem can be solved with piezo-composite technology. Piezo-composite transducers resonate cleanly in the thickness mode with 55-65% efficiency, producing sufficient power for thermal therapy.
NGF gene expression in actively growing brain glia (1991)

Previous work suggested that brain NGF acts locally on cells adjacent to sites of synthesis, in addition to any putative actions on distant, projecting perikarya. To define the basis of local action, we used a sensitive nuclease protection assay to identify cells expressing the NGF gene in vivo and in vitro. In addition to neurons, glia from a variety of developing brain areas synthesized NGF mRNA, suggesting that CNS glia exhibit a generalized capacity to express the gene. Expression was associated with active glial growth. Stimulation of growth with serum increased NGF message 2-fold in culture. Moreover, rapidly growing, low-density glial cultures exhibited 8-fold higher levels of NGF mRNA than quiescent, confluent cultures. The optic nerve, which contains all 3 major types of glia, expressed the message in vivo during neonatal development. In contrast, expression was barely detectable in the adult optic nerve. Transection, which induces glial proliferation, elicited de novo appearance of NGF mRNA in the adult nerve. Our observations suggest that active glial growth is associated with expression of the NGF gene and raise the possibility that actively growing glia in the developing or injured brain regulate neuronal growth through the elaboration of NGF.
Autoantibodies to Igf-1 Binding Sites in Thyroid Associated Ophthalmopathy (1993)

Graves' disease is an autoimmune disorder but the nature of the association between hyperthyroidism and ophthalmopathy is not yet understood. Serum autoantibodies to orbital tissues have previously been identified and the cross-reactivity with orbital and thyroid antigens has been implicated in the development of thyroid-associated ophthalmopathy (TAO). The ophthalmopathy of Graves' disease is remarkable for the hypertrophy of extraocular muscles and proliferation of fibroblasts within the orbit; features which suggest a possible involvement of growth factors. The present study was therefore undertaken to investigate the interaction of IgGs extracted from the sera of patients with Graves' disease, with or without overt ophthalmopathy, with respect to IGF-1 receptor binding sites on fibroblasts from human orbital tissue. IGF-1 binding sites were demonstrated on human orbital fibroblast monolayers grown from eye muscle explants. These cells exhibited a population of high affinity IGF-1 binding sites (Kd, 0.5nM SEM +/- 0.05). IgG prepared from sera taken from patients with Graves' disease (n = 23) significantly inhibited [125I]IGF-1 binding to orbital fibroblasts when compared to IgGs prepared from normal volunteers (n = 13, p < 0.002). It was found that 12 of 23 (52%) patients' IgG samples gave rise to significant levels of inhibition of [125I]IGF-1 binding to orbital fibroblasts. The IgG preparations did not bind directly to IGF-1. This study demonstrates that IgG prepared from patients with Graves' disease with or without overt ophthalmopathy interact with IGF-1 binding sites on orbital fibroblasts whereas IgG from normal subjects had no significant effect.(ABSTRACT TRUNCATED AT 250 WORDS)
Design of a Highly Efficient 2–4-GHz Octave Bandwidth GaN-HEMT Power Amplifier (2010)

In this paper, the design, implementation, and experimental results of a high-efficiency wideband GaN-HEMT power amplifier are presented. A method based on source-pull/load-pull simulation has been used to find optimum source and load impedances across the bandwidth and then used with a systematic approach to design wideband matching networks. Large-signal measurement results show that, across 1.9-4.3 GHz, 9-11-dB power gain and 57%-72% drain efficiency are obtained while the corresponding power-added efficiency (PAE) is 50%-62%. Moreover, an output power higher than 10 W is maintained over the band. Linearized modulated measurements using a 20-MHz long-term evolution signal with 11.2-dB peak-to-average ratio show an average PAE of 27% and 25%, an adjacent channel leakage ratio of -44 and -42 dBc at 2.5 and 3.5 GHz, respectively.
Molecular Specificity of Haustorial Induction in Agalinis purpurea (L.) Raf. (Scrophulariaceae)* (1982)

An exogenous signal normally contained in host root exudate is required for initiation of the haustorium by the root parasite Agalinis purpurea (L.) Raf. (Scrophulariaceae). Two flavonoids that induce haustoria have been isolated from gum tragacanth and a number of structural analogues have been synthesized. The results show that a high degree of molecular specificity is required for haustorial induction. Both isolated flavonoids contain substituted 3-methoxyphenol functionality, and synthetic analogues have shown that 4-substituted 3-methoxyphenol functionality is critical for high levels of haustorial induction. These data provide a model for understanding host recognition at the level of haustorial induction in parasitic angiosperms.
Molecular Biotechnology: Therapeutic Applications and Strategies (1996)

Genome--Based Medicine. Human Gene Therapy. Drug Discovery by Combinatorial Chemistry and Molecular Diversity. Protein Engineering and Computer--Assisted Drug Design. Re--Engineering the Immune Response. Appendix. Glossary. Index.
QUALITATIVE AND QUANTITATIVE DETERMINATION OF GENETICALLY MODIFIED BT-RICE (2009)

Fluorescent qualitative and quantitative method were firstly developed for the detection of Genetically Modified BT-rice. Based on endogenous control gene (sps) and construct-specific gene (BT) sequence,we designed target-specific primers and fluorescent probes for the identification of Genetically Modified BT-rice. DNA was extracted and diluted which as standard DNA to gain standard curve. PCR was performed on genomic DNAs extracted from BT-rice,and other GM events. As reference DNAs,100 % DNA samples was serial diluted (10-fold). Limit of detection of the method was 0.5 %. At the 0.5 % level,the bias (mean vs true value) for BT-rice was 20.0 %.
Genomic Disorders: Molecular Mechanisms for Rearrangements and Conveyed Phenotypes (2005)

Rearrangements of our genome can be responsible for inherited as well as sporadic traits. The analyses of chromosome breakpoints in the proximal short arm of Chromosome 17 (17p) reveal nonallelic homologous recombination (NAHR) as a major mechanism for recurrent rearrangements whereas nonhomologous end-joining (NHEJ) can be responsible for many of the nonrecurrent rearrangements. Genome architectural features consisting of low-copy repeats (LCRs), or segmental duplications, can stimulate and mediate NAHR, and there are hotspots for the crossovers within the LCRs. Rearrangements introduce variation into our genome for selection to act upon and as such serve an evolutionary function analogous to base pair changes. Genomic rearrangements may cause Mendelian diseases, produce complex traits such as behaviors, or represent benign polymorphic changes. The mechanisms by which rearrangements convey phenotypes are diverse and include gene dosage, gene interruption, generation of a fusion gene, position effects, unmasking of recessive coding region mutations (single nucleotide polymorphisms, SNPs, in coding DNA) or other functional SNPs, and perhaps by effects on transvection.
Thrombelastography/thromboelastometry (2005)

The term thrombelastograph (TEG) was used to describe the trace produced from the measurement of the viscoelastic changes associated with fibrin polymerization. Recently the term rotational thromboelastometry has been applied to the output of the ROTEM instrument. Since its first description in 1948, the TEG/ROTEM has been successfully used in the near patient assessment of haemostasis. The greatest use has been the application of TEG-guided transfusion of blood components in hepatic and more widely in cardiac surgery. Recent years have seen a renewed interest in the technology with applications for both pharmaceutical monitoring and patient screening being described. The present review gives a broad overview of the developments and applications related to thrombelastography/thromboelastometry.
Design and construction of the KSTAR tokamak (2001)

The extensive design effort for KSTAR has been focused on two major aspects of the KSTAR project mission - steady-state-operation capability and advanced tokamak physics. The steady state aspect of the mission is reflected in the choice of superconducting magnets, provision of actively cooled in-vessel components, and long pulse current drive and heating systems. The advanced tokamak aspect of the mission is incorporated in the design features associated with flexible plasma shaping, double null divertor and passive stabilizers, internal control coils and a comprehensive set of diagnostics. Substantial progress in engineering has been made on superconducting magnets, the vacuum vessel, plasma facing components and power supplies. The new KSTAR experimental facility with cryogenic system and deionized water cooling and main power systems has been designed, and the construction work is under way for completion in 2004.
Altered Adipose and Plasma Sphingolipid Metabolism in Obesity (2006)

The adipose tissue has become a central focus in the pathogenesis of obesity-mediated cardiovascular and metabolic disease. Here we demonstrate that adipose sphingolipid metabolism is altered in genetically obese (ob/ob) mice. Expression of enzymes involved in ceramide generation (neutral sphingomyelinase [NSMase], acid sphingomyelinase [ASMase], and serine-palmitoyl-transferase [SPT]) and ceramide hydrolysis (ceramidase) are elevated in obese adipose tissues. Our data also suggest that hyperinsulinemia and elevated tumor necrosis factor (TNF)-alpha associated with obesity may contribute to the observed increase in adipose NSMase, ASMase, and SPT mRNA in this murine model of obesity. Liquid chromatography/mass spectroscopy revealed a decrease in total adipose sphingomyelin and ceramide levels but an increase in sphingosine in ob/ob mice compared with lean mice. In contrast to the adipose tissue, plasma levels of total sphingomyelin, ceramide, sphingosine, and sphingosine 1-phosphate (S1P) were elevated in ob/ob mice. In cultured adipocytes, ceramide, sphingosine, and S1P induced gene expression of plasminogen activator inhibitor-1, TNF-alpha, monocyte chemoattractant protein-1, interleukin-6, and keratinocyte-derived chemokine. Collectively, our results identify a novel role for sphingolipids in contributing to the prothrombotic and proinflammatory phenotype of the obese adipose tissue currently believed to play a major role in the pathogenesis of obesity-mediated cardiovascular and metabolic disease.
The molecular mechanisms of alkylating agent-related acute myeloid leukaemia (2009)

Alkylating chemotherapy agents are used with considerable success to treat numerous human malignancies, including lung cancer, breast cancer, Hodgkin lymphoma and multiple myeloma. Alkylating agents encompass a broad range of structurally diverse agents that includes nitrogen mustards, methylating agents, platinating agents and nitrosoureas.
A potential role of heat shock proteins and nicotinamide N‐methyl transferase in predicting response to radiation in bladder cancer (2002)

The use of definitive radiotherapy for treatment of invasive bladder cancer has the advantage of preserving bladder function, but tumour regression is only achieved in approximately 40-50% of patients. Knowledge of the molecular basis of sensitivity to ionizing radiation and identification of potential molecular predictors will provide useful information regarding patient response and thus help clinicians to individualize treatment. The recent application of cDNA expression array technology provides a useful tool to investigate hundreds or even thousands of genes in a single experiment. In our study, we have used the Atlas human stress cDNA array trade mark to investigate the expression profile of stress-related and DNA repair genes in a radioresistant bladder carcinoma cell line (MGH-U1) and its radiosensitive subclone (S40b). This provides an ideal situation to study genes related to radiation because the genotypes of both cell lines are basically similar and differential changes detected are likely to be related to the different radiosensitivity phenotype. Of 234 genes blotted on the array, 3 genes (Heat shock protein 90, Heat shock protein 27 and Nicotinamide N-methyl transferase) showed consistent downregulation in the radiosensitive clone in 2 independent experiments. These results were further confirmed for HSP27 and NNMT using Sybr Green I-based real-time QRT-PCR. The role of heat shock proteins (HSPs) in response to radiation remains to be determined; however, the results of our present work suggest a possible role of HSP27 in determining radiosensitivity. Our study also opens avenues for the investigation of genes, such as NNMT, which has not previously been linked to response to radiation.
Mass spectrometry for the characterization of unsulfated chondroitin oligosaccharides from 2‐mers to 16‐mers. Comparison with hyaluronic acid oligomers (2008)

This study reports for the first time the complete liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) and tandem mass spectrometry (MS/MS) analyses performed in negative ion mode of saturated unsulfated chondroitin oligosaccharides up to 16-mers and comparison with hyaluronic acid (HA) oligomers differing only in the nature of the hexosamine residue. MS/MS of the chondroitin disaccharide on the singly charged precursor at m/z 396.1 afforded a glycosidic cleavage C1 product ion at m/z 192.9. In the tetrasaccharide, C2 (m/z 396.0) and C3 (m/z 572.0) product anions were generated by glycosidic cleavage. A C5 [M-2H]2- product ion at m/z 475.1 was generated by the glycosidic cleavage of the hexasaccharide, and a C7 ion (m/z 664.6, charge state of -2) was produced from the octasaccharide. The same fragmentation pattern of deprotonated oligomers was observed for the largest oligosaccharides, from 10- to 16-mers. There has been no previous report of MS/MS spectra for unsulfated chondroitin oligomers of these sizes. Unsulfated saturated chondroitin oligosaccharides with x-mer units and larger than a tetrasaccharide dissociate to almost exclusively form CX-1-type ions. Saturated HA oligomers also afforded the same fragmentation pattern as deprotonated oligomers by ESI-MS and MS/MS analyses. Thus, under the experimental conditions used in the current study, we were unable to distinguish between unsulfated chondroitin and HA.
Members of the syndecan family of heparan sulfate proteoglycans are expressed in distinct cell-, tissue-, and development-specific patterns. (1994)

The syndecans are a gene family of four transmembrane heparan sulfate proteoglycans that bind, via their HS chains, diverse components of the cellular microenvironment. To evaluate the expression of the individual syndecans, we prepared cDNA probes to compare mRNA levels in various adult mouse tissues and cultured mouse cells representing various epithelial, fibroblastic, endothelial, and neural cell types and B cells at various stages of differentiation. We also prepared antibody probes to assess whether the extracellular domains of the individual syndecans are shed into the conditioned media of cultured cells. Our results show that all cells and tissues studied, except B-stem cells, express at least one syndecan family member; most cells and tissues express multiple syndecans. However, each syndecan family member is expressed selectively in cell-, tissue-, and development-specific patterns. The extracellular domain of all syndecan family members is shed as an intact proteoglycan. Thus, most, if not all, cells acquire a distinctive repertoire of the four syndecan family members as they differentiate, resulting in selective patterns of expression that likely reflect distinct functions.
Antibodies Capable of Releasing Diphtheria Toxin in Response to the Low pH Found in Endosomes (1997)

Diphtheria toxin (DT) undergoes a rapid conformational change in response to the acidity encountered within endosomes. That transition is integral to the passage of its catalytic domain into the cytosol and thus its lethal action. The importance of this translocation mechanism led us to develop several monoclonal antibodies that bind DT at neutral pH but spontaneously release the toxin when critical epitopes denature or unfold upon lowering the pH to 4.5-5.5. Hybridomas were selected using a microtiter plate assay that measured the pH-dependent detachment of antibody from immobilized toxin. The acid-sensitive epitopes involved were on the catalytic, transmembrane, and receptor binding domains of DT. This pH-induced disruption of the binding of toxin to these monoclonal antibodies was analyzed by sedimentation velocity ultracentrifugation. Antibody combining sites were fully occupied at pH 5.5, partially bound at pH 5.0, and totally empty at pH 4.5. It was estimated that the Ka for antibody-toxin binding was approximately 1000-fold lower at pH 5.0 than at neutral pH. This novel acid-triggered release mechanism provides a basis for delivery of antibody-bound toxin into cells accompanied by its immediate dissociation as the complex enters acidic vesicles.
Genetics of the malignant progression of astrocytoma (1991)

The tendency of human cancers to progress towards a more malignant state over time is a well described biological phenomenon. Recent investigations elucidating the genetic nature of malignancy and the possible mechanisms responsible for this evolution have suggested that a sequential pathway may exist whereby a cell population accumulates a nested set of genetic aberrations which endow it with the ability to overwhelm other populations and dominate the tumor. Human astrocytomas are a dramatic case in point, where specific genetic events of amplification and deletion are seemingly related to the stages of malignancy. The identification of these aberrations represents the first stage in the dissection of the temporal process of this cancer. Its augmentation with functional analyses will likely allow a fuller genetic description of in vivo transformation.
Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments (2019)

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.
Pathogenesis and Consequences of HIV-Associated Wasting (2004)

Weight loss is a negative prognostic indicator in patients infected with HIV. Mortality rates rise measurably with as little as 3-5% weight loss over 6 months. The sensitivity of this measure is at least partly due to the correlation between weight loss and a metabolic cachexia that has been observed with other infections, trauma, and some cancers. However, the cachexia in patients with HIV, commonly termed wasting, may also be due to, or exacerbated by, reduced caloric intake, gastrointestinal dysfunction, or metabolic abnormalities independent of abnormal energy expenditure. In patients with HIV wasting, therapies should be directed both at reversing the underlying source of protein energy malnutrition and at other factors that may be contributing to weight loss.
Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: a HAP2-HAP3-responsive site. (1988)

We analyzed upstream activation sequence 2 (UAS2), one of two independent UAS elements in the CYC1 gene of Saccharomyces cerevisiae. Deletions and linker scanning mutations across the 87 base pairs previously defined as UAS2 showed two separate functional elements required for full activity. Region 1, from -230 to -200, contains the principal activation site and responds to the trans-acting regulatory loci HAP2 and HAP3. A portion of region 1 is homologous to two other HAP2-HAP3-responsive UASs and includes the G----A transition mutation UP1, which increases UAS2 activity. This consensus sequence TNATTGGT bears striking similarity to several CAAT box sequences of higher cells. Region 2, from -192 to -178, substantially enhances the activity of region 1, yet has little activity by itself. These regions bind distinct proteins found in crudely fractionated yeast extracts.