gebhart/patrepeval huggingface dataset:
Molecular cloning, purification, and serological characterization of MPT63, a novel antigen secreted by Mycobacterium tuberculosis (1997)

Proteins that are actively secreted by Mycobacterium tuberculosis generate immune responses in the infected host. This has prompted the characterization of protein components of mycobacterial culture filtrates to develop subunit vaccines and immunodiagnostic reagents. Fractionation of filtrates of M. tuberculosis cultures has yielded an abundant protein called MPT63, which has an apparent molecular mass of 18 kDa. We report the molecular cloning and nucleotide sequence of the mpt63 gene, purification of recombinant MPT63 antigen from Escherichia coli cells, and serological characterization of MPT63. Nucleotide sequence analysis of mpt63 identified an open reading frame encoding a protein of 159 amino acids (aa) consisting of a 29-aa secretion signal peptide and a 130-aa mature MPT63 protein. Recombinant MPT63 protein, purified from E. coli cells, and native MPT63, purified from M. tuberculosis culture filtrates, were indistinguishable in serological assays. Thus, the recombinant protein constitutes a valuable reagent for immunological studies. MPT63 evoked humoral immune responses in guinea pigs infected with virulent M. tuberculosis by the aerosol route. The mpt63 gene is found only in species of the M. tuberculosis complex, as shown by DNA hybridization experiments. Moreover, polyclonal antibody against MPT63 does not cross-react with proteins of a common environmental mycobacterial species, Mycobacterium avium. The absence of cross-reactive epitopes makes MPT63 an attractive candidate as an M. tuberculosis complex-specific diagnostic reagent. In particular, evaluation of MPT63 as an M. tuberculosis complex-specific reagent for diagnostic skin testing is under way.
Safety and immunogenicity of 15-valent pneumococcal conjugate vaccine (PCV-15) compared to PCV-13 in healthy older adults (2019)

In healthy adults ≥ 50 years of age, both new formulations of PCV15 displayed acceptable safety profiles and induced serotype-specific immune responses comparable to PCV13.
Adhesion between Semihard Polymer Materials Containing Cyclodextrin and Adamantane Based on Host–Guest Interactions (2015)

The adhesion between hard materials without any glue is difficult but challenging topic because hard materials inhibit molecular mobility and have a large gap on the adhesive interface. Here we show that host–guest interactions realize a strong adhesive strength between semihard materials based on polyacrylamide xerogel by using a minimal amount of water. The adhesive strength between βCD xerogel(x) and Ad xerogel(y), where βCD and Ad denote β-cyclodextrin and adamantane, respectively, increases as the molar ratio (mol %) of host (x) or guest (y) molecules increases, which indicates that adhesion between βCD xerogel(x) and Ad xerogel(y) is due to complexation between the βCD and the Ad units. Adhesion between βCD xerogel(10) and Ad xerogel(5) displays a robust adhesive strength (5.1 MPa). Competitive experiments using small molecules confirmed the importance of host–guest interactions in adhesion. Optical microscopic observations of the adhesion interfaces reveal that both sides of βCD xerogel(x) and Ad xerogel(y) pull together, reflecting the specific adhesive nature between the two materials. Furthermore, a self-healable semihard material, βCD-Ad xerogel(0.3, 0.4) modified with both 0.3 mol % of βCD and 0.4 mol % of Ad, shows an 88% stress recovery ratio. These results indicate that βCD and Ad moieties function as glue on the molecular level in the solid state.
Calibration of YSZ Sensors for the Measurement of Oxygen Concentration in Liquid Pb-Bi Eutectic (2003)

Although liquid lead-bismuth eutectic (LBE) is a good candidate for coolant in the subcritical transmutation blanket, it is known to be corrosive to stainless steel, the material of the carrying tubes and containers. Such long-term corrosion problem can be prevented by producing and maintaining a protective oxide layer on the exposed surface of stainless steel. For this purpose, it is required to accurately control the concentration of oxygen dissolved in LBE. Currently, YSZ (Yttria Stabilized Zirconia) oxygen sensors, based on an existing automotive oxygen sensor, with molten bismuth saturated with oxygen as the reference, have been selected for oxygen-concentration measurement. The oxygen concentration difference across the solid electrolyte and the resultant oxygen ion conduction inside the electrolyte establishes an electromagnetic force that is used to measure the ppb level concentration of oxygen dissolved in liquid LBE. A set of calibration curves of voltage vs. temperature ranging from 300 0C to 500 0C under various oxygen concentrations in liquid LBE for the YSZ oxygen sensor has been obtained and is presented in this paper. Although the current calibration strategy using the direct injection of hydrogen and oxygen is still inadequate to determine the oxygen concentration in the system, we have found a good candidate for our purpose, which is varying hydrogen to water steam ratio in the system. 1.
Protein Profiling of Microdissected Pancreas Carcinoma and Identification of HSP27 as a Potential Serum Marker (2007)

The detection of DJ-1 and HSP27 in pure defined tissue and the retrieval of HSP27 in serum by antibody-based methods identifies a potential marker for pancreatic cancer.
In vitro activation of CPP32 and Mch3 by Mch4, a novel human apoptotic cysteine protease containing two FADD-like domains. (1996)

Emerging evidence suggests that an amplifiable protease cascade consisting of multiple aspartate specific cysteine proteases (ASCPs) is responsible for the apoptotic changes observed in mammalian cells undergoing programmed cell death. Here we describe the cloning of two novel ASCPs from human Jurkat T-lymphocytes. Like other ASCPs, the new proteases, named Mch4 and Mch5, are derived from single chain proenzymes. However, their putative active sites contain a QACQG pentapeptide instead of the QACRG present in ail known ASCPs. Also, their N termini contain FADD-like death effector domains, suggesting possible interaction with FADD. Expression of Mch4 in Escherichia coli produced an active protease that, like other ASCPs, was potently inhibited (Kj = 14 nM) by the tetrapeptide aldehyde DEVD-CHO. Interestingly, both Mch4 and the serine protease granzyme B cleave recombinant proCPP32 and proMch3 at a conserved IXXD-S sequence to produce the large and small subunits of the active proteases. Granzyme B also cleaves proMch4 at a homologous IXXD-A processing sequence to produce mature Mch4. These observations suggest that CPP32 and Mch3 are targets of mature Mch4 protease in apoptotic cells. The presence of the FADD-like domains in Mch4 and Mch5 suggests a role for these proteases in the Fas-apoptotic pathway. In addition, these proteases could participate in the granzyme B apoptotic pathways.
802.11a transmitter: a case study in microarchitectural exploration (2006)

Hand-held devices have rigid constraints regarding power dissipation and energy consumption. Whether a new functionality can be supported often depends upon its power requirements. Concerns about the area (or cost) are generally addressed after a design can meet the performance and power requirements. Different micro-architectures have very different area, timing and power characteristics, and these need RTL-level models to be evaluated. In this paper we discuss the microarchitectural exploration of an 802.11a transmitter via synthesizable and highly-parameterized descriptions written in Bluespec SystemVerilog (BSV). We also briefly discuss why such architectural exploration would be practically infeasible without appropriate linguistic facilities. No knowledge of 802.11a or BSV is needed to read this paper
Targeting of multiple signalling pathways by heat shock protein 90 molecular chaperone inhibitors (2006)

The last decade has seen the molecular chaperone heat shock protein 90 (HSP90) emerge as an exciting target for cancer therapy. This is because HSP90 is involved in maintaining the conformation, stability, activity and cellular localisation of several key oncogenic client proteins. These include, amongst others, ERBB2, C-RAF, CDK4, AKT/PKB, steroid hormone receptors, mutant p53, HIF-1alpha , survivin and telomerase hTERT. Therefore, modulation of this single drug target offers the prospect of simultaneously inhibiting all the multiple signalling pathways and biological processes that have been implicated in the development of the malignant phenotype. The chaperone function of HSP90 requires the formation of a multichaperone complex, which is dependent on the hydrolysis of ATP and ADP/ATP exchange. Most current inhibitors of HSP90 act as nucleotide mimetics, which block the intrinsic ATPase activity of this molecular chaperone. The first-in-class inhibitor to enter and complete phase I clinical trials was the geldanamycin analogue, 17-allylamino-17-demethoxygeldanamycin. The results of these trials have demonstrated that HSP90 is a valid drug target. Evidence of clinical activity has been seen in patients with melanoma, breast and prostate cancer. This article provides a personal perspective of the present efforts to increase our understanding of the molecular and cellular consequences of HSP90 inhibition, with examples from work in our own laboratory. We also review the discovery and development of novel small-molecule inhibitors and discuss alternative approaches to inhibit HSP90 activity, both of which offer exciting prospects for the future.
Molecular physiology of cardiac delayed rectifier K+ channels. (1997)

Delayed rectifier K+ current in cardiac myocytes is the sum of two distinct currents, IKr and IKs. The molecular basis of these channels has recently been defined. HERG subunits coassemble to form IKr channels. KvLQT1 and minK subunits coassemble to form IKs channels. Mutations in HERG or KVLQT1 genes predispose affected individuals to ventricular arrhythmias and sudden death.
A two-phased approach for natural language parsing into formal logic (2017)

Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2017.
Adipose Tissue Engineering by Human Adipose-Derived Stromal Cells (2006)

Tissue engineering has emerged as a promising alternative approach to current clinical treatments for restoration of soft tissue defects. The purpose of this study was to investigate adipose tissue formation in vitro and in vivo by using human adipose-derived stromal cells (ADSCs) utilizing a gelatin sponge (Gelform) as a scaffold. Adipogenic potentials of human ADSCs were demonstrated by Oil-O-red staining and cellular morphology. After seeding human ADSCs in a density of 3 x 10(6) cells/ml on three-dimensional gelatin sponges, tissue-engineered constructs were exposed to adipogenic differentiation medium for in vitro studies and implanted in the backs of severe combined immunodeficient (SCID) mice for in vivo adipose regeneration. Adipogenesis of ADSC-seeded gelatin sponges was confirmed by Oil-O-red staining after 4 weeks of in vitro incubation. The optical density of the elution from Oil-O-red staining of adipogenic constructs is significantly higher than that of the control group (p < 0.05, n = 4). With short-term in vitro differentiation, adipogenic constructs turned into fat tissue 4 weeks after in vivo implantation, confirmed by biochemical and immunohistochemical examination. No adipogenic-morphological change or fat formation was observed in in vitro or in vivo studies when ADSCs were exposed to a control medium without adipogenic stimulation. These results indicate that engineered adipose tissue can be achieved using human ADSCs and biocompatible and degradable gelatin sponges.
Antibody-dependent enhancement of human immunodeficiency virus type 1 (HIV-1) infection in vitro by serum from HIV-1-infected and passively immunized chimpanzees. (1989)

Based on recent reports of antibody-dependent enhancement of human immunodeficiency virus type 1 (HIV-1) infection in vitro by serum from HIV-1-infected humans, sera from HIV-1 antibody-positive chimpanzees (Pan troglodytes) was evaluated for enhancing activity in an in vitro infection assay that uses MT-2 cells (a human lymphoblastoid cell line). Although fresh chimpanzee serum was found to have pronounced infection-enhancing properties in the absence of antibody to HIV-1, this effect was abolished by heat inactivation (57 degrees C, 1 hr) or treatment with cobra venom anticomplementary protein. Heat-inactivated, HIV-1 antibody-positive chimpanzee serum could enhance HIV-1 infection of MT-2 cells in vitro when combined with fresh, normal human serum. By serial serum samples from three HIV-1-infected chimpanzees, HIV-1 antibody-positive chimpanzees are shown to develop enhancing antibodies early in infection (2 mo postchallenge), whereas neutralizing antibodies develop later. Over the course of HIV-1 infection, this enhancing activity decreases while neutralizing activity increases, suggesting a possible role for enhancing and neutralizing activities in HIV-1 pathogenesis. The enhancing activity of an IgG fraction used to passively immunize chimpanzees against HIV-1 infection is shown to be present at dilutions as high as 1:65,000, offering an interesting possible reason for the failure of passive immunization to protect chimpanzees from HIV infection. These results suggest that serum from HIV-1-immunized chimpanzees might be tested to determine whether current HIV-1 candidate vaccines induce production of antibodies that mediate antibody-dependent enhancement of HIV-1 infection in this in vitro assay.
Artificial Genetic Systems:  Exploiting the “Aromaticity” Formalism To Improve the Tautomeric Ratio for Isoguanosine Derivatives (2004)

The tautomerism of 2'-deoxy-7-deaza-isoguanosine (2) was studied and compared to that of 2'-deoxyisoguanosine (1). The fixed (1)N-methyl (8) and O-methyl (4) derivatives were synthesized to represent the pure extremes of each tautomer. The replacement of the imidazole ring in 1 with a pyrrole ring in 2 makes the keto form in the latter more favored by 2 orders of magnitude (K(TAUT) for 2 approximately 10(3), as opposed to K(TAUT) for 1 approximately 10).
In situ H2 production and utilization by natural populations of N2-fixing blue-green algae (1982)

Contemporaneous in situ acetylene-reduction, 15 N 2 -fixation, and 3 H 2 -exchange assays reveal parallel patterns of N 2 fixation and H 2 utilization in natural populations of the blue-green algae Anabaena and Aphanizomenon. As spring and summer blooms progress, increasing ratios of acetylene reduction versus 15 N 2 fixation closely follow elevated rates of cellular H 2 utilization. Both acetylene-reduction and H 2 -utilization rates were largely attributable to blue-green algae as opposed to associated bacteria and other phytoplankton. It is concluded that elevated H 2 utilization reflects increased H 2 production via nitrogenase. This can be substantiated by monitoring rising acetylene-reduction versus 15 N 2 -fixation ratios during bloom development. Simultaneous deployment of the above techniques provides evidence for (a) in situ H 2 production and (b) seasonal trends in rates of H 2 production among natural blue-green algal populations.
Engineering an efficient secretion of leech carboxypeptidase inhibitor in Escherichia coli (2009)

These results support the hypothesis that heterologous secreted proteins require proper coupling between translation and translocation for optimal high-level production in E. coli.
High-Dose Recombinant Human Erythropoietin Stimulates Reticulocyte Production in Patients with Multiple Organ Dysfunction Syndrome (1998)

Despite increased cytokine levels, pharmacologic EPO blood levels were associated with increased reticulocyte counts in patients with multiple organ dysfunction syndrome.
Ruthenium-Catalyzed Azide−Alkyne Cycloaddition: Scope and Mechanism (2008)

The catalytic activity of a series of ruthenium(II) complexes in azide-alkyne cycloadditions has been evaluated. The [Cp*RuCl] complexes, such as Cp*RuCl(PPh 3) 2, Cp*RuCl(COD), and Cp*RuCl(NBD), were among the most effective catalysts. In the presence of catalytic Cp*RuCl(PPh 3) 2 or Cp*RuCl(COD), primary and secondary azides react with a broad range of terminal alkynes containing a range of functionalities selectively producing 1,5-disubstituted 1,2,3-triazoles; tertiary azides were significantly less reactive. Both complexes also promote the cycloaddition reactions of organic azides with internal alkynes, providing access to fully-substituted 1,2,3-triazoles. The ruthenium-catalyzed azide-alkyne cycloaddition (RuAAC) appears to proceed via oxidative coupling of the azide and alkyne reactants to give a six-membered ruthenacycle intermediate, in which the first new carbon-nitrogen bond is formed between the more electronegative carbon of the alkyne and the terminal, electrophilic nitrogen of the azide. This step is followed by reductive elimination, which forms the triazole product. DFT calculations support this mechanistic proposal and indicate that the reductive elimination step is rate-determining.
Surface Treatment and Doping Dependence of In2O3 Nanowires as Ammonia Sensors (2003)

Devices based on single-crystalline In2O3 nanowires were used to detect ammonia gas via electrical measurements at room temperature. Interesting phenomena have been observed, as the direction of the conductance modulation upon NH3 exposure depends on both the initial state of the nanowire surface and the nanowire doping concentration. For nanowires with surfaces cleaned via UV illumination in a vacuum, the conductance has been found to increase for lightly doped nanowires and decrease for heavily doped nanowires upon exposure. In contrast, for nanowires residing in ambient atmosphere, i.e., under practical conditions, the conductance has been consistently observed to increase upon NH3 exposure, regardless of the doping concentration. This is explained by considering electron transfer between In2O3 nanowires and NH3. Our work clearly demonstrates the potential of using In2O3 nanowires as NH3 sensors under practical conditions.
Herpes simplex virus DNA replication: the UL9 gene encodes an origin-binding protein. (1988)

Herpes simplex virus 1 contains seven genes that are necessary and sufficient for origin-dependent DNA synthesis in cultured cells. We have expressed the product of one of these genes, UL9, in insect cells by using a baculovirus expression vector. The apparent size of the UL9 protein, both in insect cells and in herpes simplex virus-infected Vero cells, is 82,000 Da. By using an immunoassay for protein-DNA interaction, we have shown that UL9 protein binds specifically to the herpes simplex virus origins of DNA replication, oriS and oriL. DNase I "footprint" analysis has shown that the UL9 protein interacts with two related sites on oriS, located on each arm of a nearly perfect palindrome. Our data strongly suggest that the origin-binding activity described previously by Elias et al. [Elias, P., O'Donnell, M. E., Mocarski, E. S. & Lehman, I. R. (1986) Proc. Natl. Acad. Sci. USA 83, 6322-6326] is the product of the UL9 gene.
Concatenations of polar codes with outer BCH codes and convolutional codes (2014)

We analyze concatenation schemes of polar codes with outer binary BCH codes and convolutional codes. We show that both BCH-polar and Convolutional-polar (Conv-polar) codes can have frame error rate that decays exponentially with the frame length, which is a substantial improvement over standalone polar codes. With the increase in the cutoff rate of the channel after polarization, long constraint-length convolutional codes with sequential decoding suffice to achieve a frame error rate that decays exponentially with the frame length, whereas the average decoding complexity is low. Numerical results show that both BCH-polar codes and Conv-polar codes can outperform stand-alone polar codes for some lengths and choice of decoding algorithms used to decode the outer codes. For the additive white Gaussian noise channel, Conv-polar codes substantially outperform concatenated Reed Solomon-polar codes with a careful choice of the lengths of inner and outer codes.
On comparing heterogeneity across biomarkers (2014)

Microscopy reveals complex patterns of cellular heterogeneity that can be biologically informative. However, a limitation of microscopy is that only a small number of biomarkers can typically be monitored simultaneously. Thus, a natural question is whether additional biomarkers provide a deeper characterization of the distribution of cellular states in a population. How much information about a cell's phenotypic state in one biomarker is gained by knowing its state in another biomarker? Here, we describe a framework for comparing phenotypic states across biomarkers. Our approach overcomes the current limitation of microscopy by not requiring costaining biomarkers on the same cells; instead, we require staining of biomarkers (possibly separately) on a common collection of phenotypically diverse cell lines. We evaluate our approach on two image datasets: 33 oncogenically diverse lung cancer cell lines stained with 7 biomarkers, and 49 less diverse subclones of one lung cancer cell line stained with 12 biomarkers. We first validate our method by comparing it to the "gold standard" of costaining. We then apply our approach to all pairs of biomarkers and use it to identify biomarkers that yield similar patterns of heterogeneity. The results presented in this work suggest that many biomarkers provide redundant information about heterogeneity. Thus, our approach provides a practical guide for selecting independently informative biomarkers and, more generally, will yield insights into both the connectivity of biological networks and the complexity of the state space of biological systems.
ATP-dependent translocation of ricin across the membrane of purified endosomes. (1993)

Ricin translocation was demonstrated (using both fluorescence- and radiolabel-based assays) across the membrane of endosomes purified from mouse lymphocytes. Selectivity of the process was shown by the absence of translocation activity of transferrin and horseradish peroxidase used as membrane-bound and fluid-phase endosome labels, respectively. Endocytosed 125I-ricin translocation was found to be strictly ATP- (Km approximately 4 mM) and temperature-dependent, with up to 30% endosomal 125I-ricin appearing in the external medium after 2 h at 37 degrees C. No treatments neutralizing the acidic endosome pH (ammonium chloride, nigericin, chloroquine) significantly impaired ricin translocation, and the pH gradient across the endosome membrane is not required for this process. Chase experiments showed that the ability of 125I-ricin to translocate increases with its depth in the endocytic system (i.e. plasma membrane << early endosomes < late endosomes). Both A and B ricin chains displayed translocation ability as demonstrated by the results of our assay on ricin, ricin B, transferrin-ricin A, and transferrin-ricin B conjugates. Biological activity of both ricin chains is preserved after translocation as shown by the inhibitory effect of the A chain on cell-free protein synthesis and the binding of the B chain to lactose-agarose.