gebhart/patrepeval huggingface dataset:
Roles of poly-3-hydroxybutyrate (PHB) and glycogen in symbiosis of Sinorhizobium meliloti with Medicago sp. (2007)

Poly-3-hydroxybutyrate (PHB) and glycogen are major carbon storage compounds in Sinorhizobium meliloti. The roles of PHB and glycogen in rhizobia-legume symbiosis are not fully understood. Glycogen synthase mutations were constructed by in-frame deletion (glgA1) or insertion (glgA2). These mutations were combined with a phbC mutation to make all combinations of double and triple mutants. PHB was not detectable in any of the mutants containing the phbC mutation; glycogen was not detectable in any of the mutants containing the glgA1 mutation. PHB levels were significantly lower in the glgA1 mutant, while glycogen levels were increased in the phbC mutant. Exopolysaccharide (EPS) was not detected in any of the phbC mutants, while the glgA1 and glgA2 mutants produced levels of EPS similar to the wild-type. Symbiotic properties of these strains were investigated on Medicago truncatula and Medicago sativa. The results indicated that the strains unable to synthesize PHB, or glycogen, were still able to form nodules and fix nitrogen. However, phbC mutations caused greater nodule formation delay on M. truncatula than on M. sativa. Time-course studies showed that (1) the ability to synthesize PHB is important for N(2) fixation in M. truncatula nodules and younger M. sativa nodules, and (2) the blocking of glycogen synthesis resulted in lower levels of N(2) fixation on M. truncatula and older nodules on M. sativa. These data have important implications for understanding how PHB and glycogen function in the interactions of S. meliloti with Medicago spp.
The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain (1997)

Degeneration is the process whereby Clostridium acetobutylicum ATCC 824 loses the capacity to produce acetone and butanol after repeated vegetative transfers or in continuous culture. Two degenerate mutants (M5 and DG1) of C. acetobutylicum ATCC 824 do not contain the four genes (ctfA, ctfB, adc, and aad) for acetone and butanol formation. Strain ATCC 824 contains a 210-kb plasmid (pSOL1) which is absent in M5 and DG1. pSOL1 carries the four acetone and butanol formation genes. A restriction map of pSOL1 was constructed by using ApaI, SmaI, SstII, and NarI digestions. M5 and DG1 could be complemented for acetone and butanol formation by expressing the corresponding genes (ctfA, ctfB, and adc for acetone; aad for butanol) on the plasmid. Degeneration of this strain thus appears to be the result of pSOL1 loss.
Decreased reliance on lactate during exercise after acclimatization to 4,300 m (1991)

We hypothesized that the increased exercise arterial lactate concentration on arrival at high altitude and the subsequent decrease with acclimatization were caused by changes in blood lactate flux. Seven healthy men [age 23 +/- 2 (SE) yr, wt 72.2 +/- 1.6 kg] on a controlled diet were studied in the postabsorptive condition at sea level, on acute exposure to 4,300 m, and after 3 wk of acclimatization to 4,300 m. Subjects received a primed-continuous infusion of [6,6-2D]glucose (Brooks et al. J. Appl. Physiol. 70:919-927, 1991) and [3-13C]lactate and rested for a minimum of 90 min followed immediately by 45 min of exercise at 101 +/- 3 W, which elicited 51.1 +/- 1% of the sea level peak O2 consumption (VO2peak; 65 +/- 2% of both acute altitude and acclimatization). During rest at sea level, lactate appearance rate (Ra) was 0.52 +/- 0.03 mg.kg-1.min-1; this increased sixfold during exercise to 3.24 +/- 0.19 mg.kg-1.min-1. On acute exposure, resting lactate Ra rose from sea level values to 2.2 +/- 0.2 mg.kg-1.min-1. During exercise on acute exposure, lactate Ra rose to 18.6 +/- 2.9 mg.kg-1.min-1. Resting lactate Ra after acclimatization (1.77 +/- 0.25 mg.kg-1.min-1) was intermediate between sea level and acute exposure values. During exercise after acclimatization, lactate Ra (9.2 +/- 0.7 mg.kg-1.min-1) rose from resting values but was intermediate between sea level and acute exposure values. The increased exercise arterial lactate concentration response on arrival at high altitude and subsequent decrease with acclimatization are due to changes in blood lactate appearance.(ABSTRACT TRUNCATED AT 250 WORDS)
Electroluminescent Conjugated Polymers—Seeing Polymers in a New Light (1998)

A new exciting interdisciplinary research field has evolved following the discovery that conjugated polymers can emit light when put into light-emitting diodes. A myriad of light-emitting polymers (examples of which are shown below) shining in various colors have been developed through chemical intuition and structural design.
A Survey of Glove-Based Systems and Their Applications (2008)

Hand movement data acquisition is used in many engineering applications ranging from the analysis of gestures to the biomedical sciences. Glove-based systems represent one of the most important efforts aimed at acquiring hand movement data. While they have been around for over three decades, they keep attracting the interest of researchers from increasingly diverse fields. This paper surveys such glove systems and their applications. It also analyzes the characteristics of the devices, provides a road map of the evolution of the technology, and discusses limitations of current technology and trends at the frontiers of research. A foremost goal of this paper is to provide readers who are new to the area with a basis for understanding glove systems technology and how it can be applied, while offering specialists an updated picture of the breadth of applications in several engineering and biomedical sciences areas.
Respiratory system mechanics in mice measured by end-inflation occlusion (1995)

Characterization of pulmonary function parameters in mice will facilitate the dissection of genetic mechanisms underlying airway hyperresponsiveness. We evaluated acetylcholine (ACh)-induced respiratory system resistance (Rrs) and elastance (Ers) in A/J and C3H/HeJ mice and compared these results with the previously used airway pressure-time index (APTI). A low-dead-space ventilatory system was designed to ventilate anesthetized mice with constant inspiratory flow. The end-inflation occlusion method was used to measure Rrs and Ers at baseline and after intravenous ACh (12.5-75.0 micrograms/kg) challenge. ACh induced a dose-dependent rise in Rrs and Ers in A/J mice, whereas minimal changes were observed in C3H/HeJ mice. A/J mice had a higher baseline Rrs, yet the response to ACh was independent of baseline Rrs. Additionally, sequential ACh challenges led to augmented responses. Rrs, Ers, and APTI were strongly correlated, and each was useful to detect differences in interstrain cholinergic-induced airway responsiveness. The Rrs detected the smallest differences between the strains of mice studied.
Automatic Filtering and Monitoring of Real-Time Reservoir and Production Data (2005)

Abstract This paper addresses data filtering and compression of reservoir and production data. Up to now such filtering has been done either manually by the engineers or through filtering techniques - such as wavelets - by expert users. In both cases the data filtering and compression is quite a time consuming exercise for the engineers. It has been demonstrated that filtering and compression of data quite successfully can be done using wavelet techniques. However, automatic filtering and compression is needed in order for the wavelet techniques to be applicable for real-time reservoir and production management. The "automated wavelet" has not been available due to manual determination of filter settings and the large computational effort associated by running wavelet transform rapidly in a real-time environment. This paper presents and demonstrates a methodology for solving all these problems, allowing wavelet-based de-noising and compression of large amount of data with a minimum of non-expert engineering effort and a minimum of computational effort. The methodology has been successfully tested on several real-time reservoir and production data sources. The filtered data can be used for real-time monitoring, and we demonstrate how transients, underlying trends, noise level and slugging (oscillations) can be monitored using the real-time wavelet transform. A slug number is introduced for slug detection, while a pattern recognition approach is applied for transient detections.
Direct Interrogation of DNA Content Distribution in Nanoparticles by a Novel Microfluidics-Based Single-Particle Analysis (2014)

Nonviral gene delivery holds great promise not just as a safer alternative to viral vectors in traditional gene therapy applications, but also for regenerative medicine, induction of pluripotency in somatic cells, and RNA interference for gene silencing. Although it continues to be an active area of research, there remain many challenges to the rational design of vectors. Among these, the inability to characterize the composition of nanoparticles and its distribution has made it difficult to probe the mechanism of gene transfection process, since differences in the nanoparticle-mediated transfection exist even when the same vector is used. There is a lack of sensitive methods that allow for full characterization of DNA content in single nanoparticles and its distribution among particles in the same preparation. Here we report a novel spectroscopic approach that is capable of interrogating nanoparticles on a particle-by-particle basis. Using PEI/DNA and PEI-g-PEG/DNA nanoparticles as examples, we have shown that the distribution of DNA content among these nanoparticles was relatively narrow, with the average numbers of DNA of 4.8 and 6.7 per particle, respectively, in PEI/DNA and PEI-g-PEG/DNA nanoparticles. This analysis enables a more accurate description of DNA content in polycation/DNA nanoparticles. It paves the way toward comparative assessments of various types of gene carriers and provides insights into bridging the efficiency gap between viral and nonviral vehicles.
TLR1/TLR2 Agonist Induces Tumor Regression by Reciprocal Modulation of Effector and Regulatory T Cells (2011)

Using TLR agonists in cancer treatment can have either beneficial or detrimental effects. Therefore, it is important to determine their effect on the tumor growth and understand the underlying mechanisms in animal tumor models. In this study, we report a general immunotherapeutic activity of a synthetic bacterial lipoprotein (BLP), a TLR1/TLR2 agonist, on established lung carcinoma, leukemia, and melanoma in mice. Systemic treatment of 3LL tumor-bearing mice with BLP, but not LPS, led to a dose-dependent tumor regression and a long-lasting protective response against tumor rechallenge. The BLP-mediated tumor remission was neither mediated by a direct tumoricidal activity nor by innate immune cells, because it lacked therapeutic effect in immunodeficient SCID mice. Instead, BLP treatment reduced the suppressive function of Foxp3(+) regulatory T cells (Tregs) and enhanced the cytotoxicity of tumor-specific CTL in vitro and in vivo. Furthermore, adoptive cotransfer of BLP-pretreated but not untreated CTL and Tregs from wild-type but not from TLR2(-/-) mice was sufficient to restore antitumor immunity in SCID mice by reciprocally modulating Treg and CTL function. These results demonstrate that the TLR1/TLR2 agonist BLP may have a general tumor therapeutic property involving reciprocal downregulation of Treg and upregulation of CTL function. This property may play an important role in the development of novel antitumor strategies.
Real-Time Intravital Imaging Establishes Tumor-Associated Macrophages as the Extraskeletal Target of Bisphosphonate Action in Cancer (2014)

Bisphosphonates are assumed to act solely in bone. However, mouse models and clinical trials show that they have surprising antitumor effects outside bone. We provide unequivocal evidence that bisphosphonates target TAMs, but not tumor cells, to exert their extraskeletal effects, offering a rationale for use in patients with early disease.
Immunoprecipitation of cell surface structures of cloned cytotoxic T lymphocytes by clone-specific antisera. (1984)

Clones of cytotoxic T lymphocytes (CTL) differ in their specific reactivity with diverse target cell antigens. To learn about the uniqueness of individual CTL clones we injected rats and mice with cloned CTL in an effort to prepare clone-specific antisera and to analyze the CTL surface molecules that were immunoprecipitated by these antisera. Three clones were studied. They were all derived from BALB.B mice and were specific for antigens encoded by the major histocompatibility complex of the H-2d haplotype. Antisera raised in rats against individual clones contained antibodies to lymphocyte function-associated antigen type 1 (LFA-1) and inhibited the cytotoxic activity of all of the clones. In contrast, BALB/c and BALB.K mice injected with individual clones consistently yielded alloantisera that were clone specific in their ability to inhibit CTL-mediated lysis of target cells (P815). In addition, these alloantisera immunoprecipitated from extracts of 125I-radiolabeled CTL a disulfide-bonded dimer consisting of approximately equal to 45-kilodalton subunits. This dimer resembles the putative T-cell antigen-recognition receptor recently identified in several laboratories. The alloantisera also immunoprecipitated CTL surface molecules that were associated with beta 2-microglobulin and that differed in apparent molecular mass (37-38 kilodaltons) in different clones.
Breast cancer in young women: effect of chemotherapy on ovarian function, fertility, and birth defects. (1994)

A comprehensive review of the literature was done to assess the effect of adjuvant chemotherapy for operable breast cancer on ovarian function, fertility, and birth defects. Data were limited. Cyclophosphamide, an alkylating agent, is the major cause of amenorrhea, which is due to primary ovarian failure. Ovarian dysfunction is related to age, dose, and duration of treatment. In women less than 35, pregnancy following adjuvant chemotherapy is possible. However, data are limited regarding the impact of subsequent pregnancy on the results of breast cancer. There appears to be no increased risk of teratogenesis in offspring exposed to chemotherapy after the first trimester of pregnancy. Prospective data on women who have subsequent pregnancies and on their offspring are very limited. Formation of a registry for long-term follow-up of young women detailing reproductive potential and follow-up of offspring is needed.
Atrial fibrillation: a major contributor to stroke in the elderly. The Framingham Study. (1987)

Chronic atrial fibrillation without valvular disease has been associated with increased stroke incidence. The impact of atrial fibrillation on the risk of stroke with increasing age was examined in 5184 men and women in the Framingham Heart Study. After 30 years of follow-up, chronic atrial fibrillation appeared in 303 persons. Age-specific incidence rates steadily increased from 0.2 per 1000 for ages 30 to 39 years to 39.0 per 1000 for ages 80 to 89 years. The proportion of strokes associated with this arrhythmia was 14.7%, 68 of the total 462 initial strokes, increasing steadily with age from 6.7% for ages 50 to 59 years to 36.2% for ages 80 to 89 years. In contrast to the impact of cardiac failure, coronary heart disease, and hypertension, which declined with age, atrial fibrillation was a significant contributor to stroke at all ages.
Identification of gastrin as a growth peptide in human pancreatic cancer (1995)

The present study reports the first evidence that the gastrointestinal peptide gastrin stimulates the growth of several human pancreatic cancer cells in culture and in tumors transplanted to nude mice. Gastrin promoted growth of all cell lines tested at a dose comparable to the binding affinity, providing evidence for a physiologically relevant receptor. The stimulatory effects of gastrin were blocked by the CCK-B/gastrin receptor antagonist L-365,260 and not by the CCK-A receptor antagonist L-364,718. Growth of PANC-1 cells in culture were inhibited by L-365,260, suggesting that gastrin is tonically produced by PANC-1 cells for regulation of growth. Athymic nude mice bearing PANC-1 xenografts were treated for 24 days subcutaneously with either 1% bovine serum albumin (diluent), pentagastrin (1 mg/kg), or L-365,260 (1 mg/kg) twice daily. Tumors from the pentagastrin-treated mice were found to weigh more and have greater protein and DNA content than controls, whereas these values were all decreased in tumors of L-365,260-treated mice. Receptor binding capacity changed in tumors of animals treated with the peptide or antagonist, suggesting a regulatory process. Gastrin immunoreactivity was detected in a transplanted PANC-1 human tumor. These results identify gastrin as a potent trophic peptide that actively stimulates growth of human pancreatic cancer and does so through a CCK-B/gastrin-like receptor.
Cardiovascular responses to insulin in the absence of hypoglycemia (1962)

Cardiovascular responses to intravenous administration of insulin were studied in lightly anesthetized dogs treated with a neuromuscular blocking agent. An early transient pressor response was observed. This abrupt increase in arterial pressure appeared 2–9 min after insulin was given. It was accompanied by increases in cardiac output and right atrial pressure. It occurred in the presence of hyperglycemia and in the absence of hypoglycemia. It was not altered by glucagon but it could be antagonized by ganglionic and adrenergic blocking drugs and by pentobarbital. The response could be produced when insulin was given in the carotid artery in doses that caused no effect when injected in a systemic vein. The experiments suggest that insulin may have a direct action on the brain.
Catalase gene of the yeast Candida tropicalis (1987)

A clone harbouring the genomic DNA sequence for the peroxisomal catalase of an n-alkane-utilizable yeast, Candida tropicalis, has been isolated by the hybrid-selection method and confirmed with a probe of catalase partial cDNA. Nucleotide sequence analysis of the cloned DNA disclosed that the gene fragment coding for catalase had a length of 1455 base pairs (corresponding to 485 amino acids; m = 54937 Da), and that the size of this enzyme was the smallest among all catalases reported hitherto. No intervening sequence was found in this coding region and some portions coincided with the amino acid sequences obtained from the analysis of the purified catalase. The comparison with three peroxisomal catalases from rat liver, bovine liver and human kidney, and one cytosolic catalase from Saccharomyces cerevisiae has revealed that catalase from C. tropicalis was more homologous to the peroxisomal enzymes than to the cytosolic one. C. tropicalis used the codons of the high-expression type. Amino acid residues were all conserved at the active and heme-binding sites. In the N and C-terminal regions there was no characteristic signal sequence or consensus sequence. However, a noticeable region, which can be discriminated between peroxisomal and cytosolic catalases, was proposed.
Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. (1995)

We have shown previously that the majority of RNA polymerase II complexes initiated at the c-myc gene are paused in the promoter-proximal region, similar to observations in the Drosophila hsp70 gene. Our analyses define the TATA box or initiator sequences in the c-myc gene as necessary components for the establishment of paused RNA polymerase II. Deletion of upstream sequences or even the TATA box does not influence significantly the degree of transcriptional initiation or pausing. Deletion of both the TATA box and sequences at the transcription initiation site, however, abolishes transcriptional pausing of transcription complexes but still allows synthesis of full-length RNA. Further analyses with synthetic promoter constructs reveal that the simple combination of upstream activator with TATA consensus sequences or initiator sequences act synergistically to recruit high levels of RNA polymerase II complexes. Only a minor fraction of these complexes escapes into regions further downstream. Several different trans-activation domains fused to GAL4-DNA-binding domains, including strong activators such as VP16, do not eliminate promoter-proximal pausing of RNA polymerase. Thus, we conclude that pausing of RNA polymerase II is a common phenomenon in eukaryotic transcription and does not require complex promoter structures. Further analyses reveal that enhancers have a modest influence on transcription initiation and on release of transcription complexes out of the pause site but may function primarily to increase the elongation competence of transcription complexes.
Molecular-beam epitaxy of the half-Heusler alloy NiMnSb on (In,Ga)As/InP (001) (2003)

We report the growth of the half-Heusler alloy NiMnSb on InP (001) by molecular-beam epitaxy using a lattice-matched (In,Ga)As buffer. High-resolution x-ray diffraction confirms a high crystalline quality. Spot-profile analysis low-energy electron diffraction measurements show well-defined surface reconstructions. The samples show the expected high Curie temperature and an uniaxial anisotropy.
Enhancement of Cancer Radiation Therapy by Use of Adenovirus-Mediated Secretable Glucose-Regulated Protein 94/gp96 Expression (2005)

Tumor-derived glucose-regulated protein 94 (GRP94/gp96) has shown great promise as a tumor vaccine. However, current protein-based approaches require the availability of large quantities of tumor tissue, which are often not possible. In addition, the efficacy of immunotherapy is often not ideal when used alone. In this study, we explored the therapeutic efficacy of a combined GRP94/gp96-based genetic immunotherapy and radiation therapy strategy in the weakly immunogenic and highly metastatic 4T1 murine mammary cancer model. An adenovirus encoding a modified, secretable form of GRP94 gene (AdsGRP94) was constructed and evaluated in various antitumor experiments. Lethally irradiated, virus-infected cells were used as vaccines. Adenoviral vectors were also injected directly into tumors in conjunction with tumor irradiation. Vaccination with lethally irradiated, AdsGRP94-infected 4T1 cells completely prevented subsequent tumor growth from challenge inoculations of as many as 10(7) cells per mouse. In established tumor models, vaccinations alone had minimal effect on local and metastatic tumor growth. However, when vaccination was combined with radiation therapy and i.t. AdsGRP94 injections, local tumor growth and pulmonary metastasis were markedly inhibited. In some cases, complete tumor regression was observed. In these cases, the mice were resistant to subsequent tumor challenge and remain tumor free up to 10 months after initial therapy. Our results indicate that combined AdsGRP94-based immunotherapy and radiation therapy may be a potentially effective strategy for cancer treatment.