gebhart/patrepeval huggingface dataset:
Subunit interactions of class I histocompatibility antigens (1985)

The kinetics of dissociation of iodinated beta 2-microglobulin (beta 2m) from the papain-solubilized class I histocompatibility antigen HLA-B7 have been investigated. In the presence of unlabeled beta 2m, most of the HLA dissociates according to a single rate constant, whereas in the absence of unlabeled beta 2m, the system approaches an equilibrium dependent upon the initial HLA concentration. When iodinated beta 2m is incubated with unlabeled HLA-B7, the rate of incorporation of beta 2m into the complex is much less dependent on the concentration than is expected for a simple association/dissociation system; instead, the system behaves as if the "activity" (in a thermodynamic sense) of the HLA heavy-chain intermediate cannot surpass a critical concentration. The dissociation rate for each class I specificity is a function of temperature, ionic strength, pH, and the status of the heavy chain (papain solubilized vs. detergent solubilized). High temperature, high ionic strength, and extremes of pH promote dissociation. The intact molecule dissociates about 10 times more slowly than the papain-solubilized molecule. In contrast, the rate of dissociation of all papain-solubilized class I antigens tested falls within the range of about a factor of 2. The presence of the carbohydrate has no effect on the rate of dissociation. The possibility that HLA class I antigen dissociation may occur in vivo within acidic internal vesicles is discussed.
Clinical significance of immunohistochemical expression of cancer/testis tumor-associated antigens (MAGE-A1, MAGE-A3/4, NY-ESO-1) in patients with non-small cell lung cancer. (2014)

This study demonstrated that the expression of MAGE-A3/4 antigen might be a valuable prognostic factor regarding survival in patients with NSCLC.
T-cell receptor V alpha and C alpha alleles associated with multiple and myasthenia gravis. (1989)

Polymorphic markers in genes encoding that alpha chain of the human T-cell receptor (TcR) have been detected by Southern blot analysis in Pss I digests. Polymorphic bands were observed at 6.3 and 2.0 kilobases (kb) with frequencies of 0.30 and 0.44, respectively, in the general population. Using the polymerase chain reaction (PCR) method, we amplified selected sequences derived from the full-length TcR alpha cDNA probe. These PCR products were used as specific probes to demonstrate that the 6.3-kb polymorphic fragment hybridizes to the variable (V)-region probe and the 2.0-kb fragment hybridizes to the constant (C)-region probe. Segregation of the polymorphic bands was analyzed in family studies. To look for associations between these markers and autoimmune diseases, we have studied the restriction fragment length polymorphism distribution of the Pss I markers in patients with multiple sclerosis, myasthenia gravis, and Graves disease. Significant differences in the frequency of the polymorphic V alpha and C alpha markers were identified between patients and healthy individuals.
Genomic profiling of circulating tumor DNA (ctDNA) from patients (pts) with advanced non-small cell lung cancer (NSCLC). (2017)

9025 Background: Tissue biopsy is the gold standard for detection of genomic alterations (GA) and selection of matched targeted therapies in NSCLC, but ctDNA assay provides a possible complementary approach for some pts. Methods: Hybrid-capture based genomic profiling of 62 genes using a ctDNA assay (FoundationACT™) was performed on blood samples from 1,019 consecutive NSCLC pts. The fraction of ctDNA in the blood was estimated using the maximum somatic allele frequency (MSAF) for each sample. Results: Pt characteristics: Median age 69 years (range 8-94); 54% were female. Histologies included adenocarcinoma (n = 720), NSCLC not otherwise specified (NSCLC NOS; n = 179), squamous cell (n = 57), LC NOS (n = 51), large cell (n = 6), and sarcomatoid (n = 6). ≥1 reportable GA was detected in 71% of all cases and in 83% of cases with evidence of ctDNA in the blood (MSAF &gt; 0). For 22 pts with paired blood and tissue samples collected within 30 days and MSAF &gt; 0, 33/64 (52%) GA detected in tissue were also detected in ctDNA. In 55 pts for whom tissue was insufficient for analysis, ≥1 GA was detected in ctDNA in 43 (78%) cases. For 856 cases with MSAF &gt; 0, an average of 1.8 GA/sample were reported. GA were most frequently detected in TP53 (57%), EGFR (23%) and KRAS (17%). Comparative analysis with the tissue-based FoundationCORE™ database (n = 19,264) showed similar frequencies of GA per gene, although KRAS mutation was more frequent in tissue than ctDNA (27% vs 17%, P &lt; 0.0001), and EGFR T790M was more frequent in ctDNA than tissue (7% vs 2%, P &lt; 0.0001), likely reflecting use of liquid versus tissue biopsy after relapse on targeted therapy .Kinase fusions ( ALK, ROS1, RET, FGFR3, PDGFRA) were identified in 5% (39/856) of cases. Diverse and novel mechanisms of acquired resistance (AR) were detected in ctDNA including MET Y1230C and EGFR amplification post-crizotinib, FGFR3-TACC3 fusion post-EGFR inhibitor, and multiple EGFRAR mutations post-osimertinib. Conclusions: In this series, use of a rigorously validated capture-based assay revealed evidence of ctDNA in the blood in 84% of cases. Our results provide clinical support for use of this assay as a complementary technology to tissue-based genomic testing in a subset of pts with NSCLC.
High-performance heterogeneous catalysis with surface-exposed stable metal nanoparticles (2014)

Protection of metal nanoparticles from agglomeration is critical for their functions and applications. The conventional method for enhancing their stability is to cover them with passivation layers to prevent direct contact. However, the presence of a protective shell blocks exposure of the metal species to reactants, thereby significantly impeding the nanoparticles' utility as catalysts. Here, we report that metal nanoparticles can be prepared and used in a surface-exposed state that renders them inherently catalytically active. This strategy is realised by spatial confinement and electronic stabilisation with a dual-module mesoporous and microporous three-dimensional π-network in which surface-exposed nanoparticles are crystallised upon in situ reduction. The uncovered palladium nanoparticles serve as heterogeneous catalysts that are exceptionally active in water, catalyse unreactive aryl chlorides for straightforward carbon-carbon bond formation and are stable for repeated use in various types of cross couplings. Therefore, our results open new perspectives in developing practical heterogeneous catalysts.
[Severe aplastic anemia remarkably improved by a treatment with antilymphocyte globulin, high-dose methylprednisolone and danazol]. (1989)

Sixteen-years-old female with severe aplastic anemia received a therapy combined with antilymphocyte globulin (ALG), high-dose methylprednisolone (m-PSL) and danazol. At the hospitalization, hematological examination demonstrated as follows; reticulocyte 21,000/microliters, granulocyte 350/microliters, platelet 10,000/microliters and hypocellular bone marrow. Treatment schedule were 1) m-PSL 1,000 mg (day 1-4), 500 mg (5-8)--then tapered. 2) ALG lg/day (day 4-8) 3) danazol 600 mg/day. During ALG administration, leukocytopenia and thrombocytopenia appeared but thereafter hematological recovery was obtained and the patient was free from supportive care. She developed mild diabetes mellitus and moderate liver dysfunction, nevertheless, both of which were controlled. At 3 months after the beginning of the treatment, hematological examination demonstrated as follows; reticulocyte 236,000/microliters, granulocyte 1,900/microliters, platelet 56,000/microliters and normocellular bone marrow. Although this immunosuppressive therapy was remarkably effective to this patient, immunological relation to the onset of aplastic anemia was not demonstrated in in vitro examination. This combined therapy seems to be effective one for patients with severe aplastic anemia.
Anti-invasive effect of contortrostatin, a snake venom disintegrin, and TNF-alpha on malignant glioma cells. (2001)

The combined use of contortrostatin and CG-TNF-alpha may have potential for malignant glioma therapy by effectively inhibiting glioma cell invasion.
Measuring populations to improve vaccination coverage (2016)

In low-income settings, vaccination campaigns supplement routine immunization but often fail to achieve coverage goals due to uncertainty about target population size and distribution. Accurate, updated estimates of target populations are rare but critical; short-term fluctuations can greatly impact population size and susceptibility. We use satellite imagery to quantify population fluctuations and the coverage achieved by a measles outbreak response vaccination campaign in urban Niger and compare campaign estimates to measurements from a post-campaign survey. Vaccine coverage was overestimated because the campaign underestimated resident numbers and seasonal migration further increased the target population. We combine satellite-derived measurements of fluctuations in population distribution with high-resolution measles case reports to develop a dynamic model that illustrates the potential improvement in vaccination campaign coverage if planners account for predictable population fluctuations. Satellite imagery can improve retrospective estimates of vaccination campaign impact and future campaign planning by synchronizing interventions with predictable population fluxes.
RARE imaging: A fast imaging method for clinical MR (1986)

Based on the principles of echo imaging, we present a method to acquire sufficient data for a 256 X 256 image in from 2 to 40 s. The image contrast is dominated by the transverse relaxation time T2. Sampling all projections for 2D FT image reconstruction in one (or a few) echo trains leads to image artifacts due to the different T2 weighting of the echo. These artifacts cannot be described by a simple smearing out of the image in the phase direction. Proper distribution of the phase-encoding steps on the echoes can be used to minimize artifacts and even lead to resolution enhancement. In spite of the short data acquisition times, the signal amplitudes of structures with long T2 are nearly the same as those in a conventional 2D FT experiment. Our method, therefore, is an ideal screening technique for lesions with long T2.
Cardiomyocyte differentiation by GATA-4-deficient embryonic stem cells (1997)

In situ hybridization studies, promoter analyses and antisense RNA experiments have implicated transcription factor GATA-4 in the regulation of cardiomyocyte differentiation. In this study, we utilized Gata4-/- embryonic stem (ES) cells to determine whether this transcription factor is essential for cardiomyocyte lineage commitment. First, we assessed the ability of Gata4-/- ES cells form cardiomyocytes during in vitro differentiation of embryoid bodies. Contracting cardiomyocytes were seen in both wild-type and Gata4-/- embryoid bodies, although cardiomyocytes were observed more often in wild type than in mutant embryoid bodies. Electron microscopy of cardiomyocytes in the Gata4-/- embryoid bodies revealed the presence of sarcomeres and junctional complexes, while immunofluorescence confirmed the presence of cardiac myosin. To assess the capacity of Gata4-/- ES cells to differentiate into cardiomyocytes in vivo, we prepared and analyzed chimeric mice. Gata4-/- ES cells were injected into 8-cell-stage embryos derived from ROSA26 mice, a transgenic line that expresses beta-galactosidase in all cell types. Chimeric embryos were stained with X-gal to discriminate ES cell- and host-derived tissue. Gata4-/- ES cells contributed to endocardium, myocardium and epicardium. In situ hybridization showed that myocardium derived from Gata4-/- ES cells expressed several cardiac-specific transcripts, including cardiac alpha-myosin heavy chain, troponin C, myosin light chain-2v, Nkx-2.5/Csx, dHAND, eHAND and GATA-6. Taken together these results indicate that GATA-4 is not essential for terminal differentiation of cardiomyocytes and suggest that additional GATA-binding proteins known to be in cardiac tissue, such as GATA-5 or GATA-6, may compensate for a lack of GATA-4.
Highly hydrophilic and stable polypeptide/single-wall carbon nanotube conjugates (2008)

A polymeric dispersing agent for single-wall carbon nanotubes (SWCNTs) in water was synthesized by 4-(pyren-1-yl)butanoylation of the amine groups of poly-L-lysine. The pyrene content of 4-(pyren-1-yl)butanoylated polylysine (PBPL) was optimized so that a maximal dispersion effect of the SWCNTs was obtained. High molecular weight PBPL (>300000 g mol−1) exceeds the widely used surfactant sodium dodecylsulfate (SDS) as a dispersing agent yielding a 27% higher SWCNT concentration in dispersion. The high stability of the PBPL/SWCNT conjugates is demonstrated by removing the conjugates from dispersion through filtration, washing, and redispersion in only water. The resulting redispersions do not contain free PBPL and the importance of having SWCNT dispersions in the absence of free dispersing agent is discussed. For SDS dispersions, poor redispersion properties have been observed. The binding of PBPL onto the SWCNTs was studied by atomic force microscopy, optical absorbance spectroscopy, and fluorescence spectroscopy.
Spherulitic brushite stones in the dental pulp of a cow (1998)

Pulp stones of human teeth usually contain biological apatite. In the dental pulp of a cow, aged 12 years, we observed spherulitic pulp stones, up to approximately 200 microns in diameter, consisting of radially arranged crystals with several kinds of light microscopy and scanning electron microscopy including the secondary electron and the backscattered electron signals. The crystals extending fan-like towards the periphery showed a rectangular shape, and they had subunits of elongated crystallites and fine slits of NaOCl-dissolved substances, probably including organic matter and amorphous mineral. By using energy-dispersive X-ray microanalysis, large amounts of Ca and P, and trace elements of Na, Mg, Cl, and Fe were detected from the stones. The calcium phosphate crystals were identified as biological brushite by shape, Ca/ P molar ratio, and electron diffraction pattern. Core regions of the stones containing granular structures, probably erythrocytes, were always present in blood vessels, and rectangular crystals frequently penetrated the vessel walls. Under the decalcified sections, the nidi were completely or incompletely dissolved, but the peripheries showed a radial arrangement of erythrocytes. Thus, the nidi may be thrombus or necrotic blood cells including erythrocytes. Such calcospherulites in the dental pulp of a cow were similar to the spherulitic pulp stones in human deciduous teeth reported previously, however, their nidi were present in different regions.
Parkin-deficient mice are not a robust model of parkinsonism (2005)

Mutations in the human parkin gene cause autosomal recessive juvenile parkinsonism, a heritable form of Parkinson's disease (PD). To determine whether mutations in the mouse parkin gene (Park2) also result in a parkinsonian phenotype, we generated mice with a targeted deletion of parkin exon 2. Using an extensive behavioral screen, we evaluated neurological function, motor ability, emotionality, learning, and memory in aged Parkin-deficient mice. The behavioral profile of Parkin-deficient mice on a B6;129S4 genetic background was strikingly similar to that of control mice, and most differences were not reproducible by using coisogenic mice on a 129S4 genetic background. Moreover, catecholamine levels in the striatum, olfactory bulb, and spinal cord of Parkin-deficient mice were normal. In contrast to previous studies using independently generated Parkin-deficient mice, we found no evidence for nigrostriatal, cognitive, or noradrenergic dysfunction. Understanding why Parkin-deficient mice do not exhibit robust signs of parkinsonism could advance knowledge and treatment of PD.
Sentinels at the wall: cell wall receptors and sensors (2007)

The emerging view of the plant cell wall is of a dynamic and responsive structure that exists as part of a continuum with the plasma membrane and cytoskeleton. This continuum must be responsive and adaptable to normal processes of growth as well as to stresses such as wounding, attack from pathogens and mechanical stimuli. Cell expansion involving wall loosening, deposition of new materials, and subsequent rigidification must be tightly regulated to allow the maintenance of cell wall integrity and co-ordination of development. Similarly, sensing and feedback are necessary for the plant to respond to mechanical stress or pathogen attack. Currently, understanding of the sensing and feedback mechanisms utilized by plants to regulate these processes is limited, although we can learn from yeast, where the signalling pathways have been more clearly defined. Plant cell walls possess a unique and complicated structure, but it is the protein components of the wall that are likely to play a crucial role at the forefront of perception, and these are likely to include a variety of sensor and receptor systems. Recent plant research has yielded a number of interesting candidates for cell wall sensors and receptors, and we are beginning to understand the role that they may play in this crucial aspect of plant biology.
Abstract 17285: A Selective Transforming Growth Factor-β and Growth Differentiation Factor-15 Ligand Trap Attenuates Pulmonary Hypertension (2014)

Introduction: Excessive Transforming Growth Factor-β (TGF-β) signaling has been implicated in pulmonary arterial hypertension (PAH), based on activation of TGF-β effectors and transcriptional targets in affected lungs and the ability of TGF-β type I receptor (ALK5) inhibitors to improve experimental PAH. However, clinical use of ALK5 inhibitors has been limited by cardiovascular toxicity. Hypothesis: We tested whether or not selective blockade of TGF-β and Growth Differentiation Factor (GDF) ligands using a recombinant TGFβ type II receptor extracellular domain Fc fusion protein (TGFBRII-Fc) could impact experimental PAH. Methods: Male SD rats were injected with monocrotaline (MCT) and received vehicle or TGFBRII-Fc (15 mg/kg, twice per week, i.p.). C57BL/6 mice were treated with SU-5416 and hypoxia (SUGEN-HX) and received vehicle or TGFBRII-Fc. RNA-Seq was used to profile transcriptional changes in lungs of MCT rats. Circulating levels of GDF-15 were measured in 241 PAH patients and 41 healthy controls. Human pulmonary artery smooth muscle cells were used to examine signaling in vitro . Results: TGFBRII-Fc is a selective ligand trap, inhibiting the ability of GDF-15, TGF-β1, TGF-β3, but not TGF-β2 to activate SMAD2/3 in vitro . In MCT rats, prophylactic treatment with TGFBRII-Fc normalized expression of TGF-β transcriptional target PAI-1, attenuated PAH and vascular remodeling. Delayed administration of TGFBRII-Fc in rats with established PAH at 2.5 weeks led to improved survival, decreased PAH and remodeling at 5 weeks. Similar findings were observed in SUGEN-HX mice. No valvular abnormalities were found with TGFBRII-Fc treatment. RNA-Seq revealed GDF-15 to be the most highly upregulated TGF-β ligand in the lungs of MCT rats, with only modest increases in TGF-β1 and no change in TGF-β2/3 observed, suggesting a dominant role of GDF-15 in the pathophysiology of this model. Plasma levels of GDF-15 were significantly increased in patients with diverse etiologies of WHO Group I PAH. Conclusions: These findings demonstrate that a selective TGF-β/GDF-15 trap attenuates experimental PAH, remodeling and mortality, without causing valvulopathy. These data highlight the potential role of GDF-15 as a pathogenic molecule and therapeutic target in PAH.
PAPR Reduction Scheme with SOCP for MIMO-OFDM Systems (2008)

Combination of multiple-input multiple-output (MIMO) with orthogonal frequency division multiplexing (OFDM) has become a promising candidate for high performance wireless communications. However one major disadvantage of MIMO-OFDM systems lies in a prohibitively large peak-to-average power ratio (PAPR) of the transmitted signal on each antenna. In this paper we extend from SISO to MIMO systems a method based on allocating dedicated subcarriers for PAPR mitigation. These subcarriers are located on unused subcarriers of OFDM spectrum under the assumption they all fall under the power mask. This is originally implemented with a SOCP optimization algorithm applied before space time coding scheme. This jointly mitigates PAPR on each MIMO branch scheme. This approach does not degrade the bit-error-rate (BER) and the data bit rate and no side information (SI) transmission is required. Simulation results are presented in the IEEE 802.16 WiMAX standard contexts: an Alamouti space time code with two transmitted antennas and 256 OFDM subcarriers are considered where 56 of which are unused and allocated for PAPR reduction. PAPR gains up to 7dB are obtained depending on mean power increase limitation. Moreover, with a spectrum mask constraint, this method is standard compliant.
Role of Polyadenylation in Nucleocytoplasmic Transport of mRNA (1996)

To examine the role of polyadenylation in the nuclear export of mRNA, we have replaced the poly(A) signal in a Rev-responsive human immunodeficiency virus type 1-based reporter gene with a cis-acting hammerhead ribozyme. Transcripts from this gene thus acquire a 3' terminus by cis-ribozyme cleavage rather than by polyadenylation. The nuclear and cytoplasmic distribution of transcripts was investigated using transient gene expression and quantitative RNase protection assays. In the absence of Rev, a basal level of polyadenylated unspliced mRNA transcribed from a poly(A) signal-containing control reporter gene was detected in the cytoplasm of transfected COS7 cells. However, cytoplasmic ribozyme-cleaved unspliced RNA was only barely detectable. The nuclear/cytoplasmic (n/c) ratio of polyadenylated RNAs was 3.8, while the n/c ratio for ribozyme cis-cleaved RNAs was 33. The cytoplasmic localization of the polyadenylated unspliced mRNA was enhanced about 10-fold in the presence of Rev and the Rev-responsive element. In marked contrast to this, ribozyme cleaved RNA accumulated almost exclusively (n/c ratio of 28) in the nucleus in the presence of Rev. Actinomycin D time course analysis suggested that the low levels of the cytoplasmic ribozyme-cleaved RNAs in both the presence and absence of Rev were due to serve export deficiency of ribozyme-cleaved RNA. Finally, by inserting a 90-nucleotide poly(A) stretch directly upstream of the ribozyme cassette, we have demonstrated that a long stretch of poly(A) near the 3' end of a ribozyme-cleaved transcript is not sufficient for directing mRNA export. Taken together, these results suggest that polyadenylation is required for the nucleocytoplasmic transport of mRNA and that Rev interaction with the Rev-responsive element cannot bypass this requirement.
InAsSb and InPSb materials for mid infrared photodetectors (2010)

III-V semiconductor materials are under active investigation for use as optical detectors in the mid infrared wavelength region from 3 to 12 μm. In this paper we summarize recent progress on the development of III-V materials for this application based on the material InAsSb. We first present the results of investigations in the use of strained balanced type II superlattices of InAsSb/InAs to extend the absorption wavelength of this material system beyond the limits of the maximum InAsSb bulk value. We present results on the growth of InPSb heterojunction structures with the aim of reducing thermal diffusion current and surface leakage. Finally we present some preliminary device results indicating the promise of this material system.