gebhart/patrepeval huggingface dataset:
Temporal, spatial, and morphologic features of hair cell regeneration in the avian basilar papilla (2000)

Hair cell-selective antibodies were used in combination with the nucleotide bromode-oxyuridine (BrdU) to examine the temporal, spatial, and morphologic progression of auditory hair cell regeneration in chicks after a single gentamicin injection. New hair cells are first identifiable with an antibody to class III beta (beta) tubulin (TuJ1) by 14 hours after BrdU incorporation, but progenitor cells in S phase and M phase are TuJ1-negative. TuJ1 labeling reveals that new hair cells are first detected at 3 days after gentamicin, in the base, and the emergence and maturation of regenerating hair cells spreads apically over time. Differentiation of regenerating hair cells consists of a progressive series of morphologic changes. During early differentiation (14 hours to 1 day after BrdU), regenerating hair cells are round or fusiform and remain near the lumen, where they are generated. During intermediate differentiation (2-4 days after BrdU), regenerating hair cells resemble support cells; their somata are elongated, their nuclei are in the support cell layer, and they appear to contact both the lumenal surface and the basal lamina. The 275-kDa hair cell antigen is first expressed in regenerating hair cells during this period. During late differentiation (7 days after BrdU and later), TuJ1-positive cells acquire the globose shape of mature hair cells. Labeling with antibodies to hair cell antigen, calmodulin, and ribosomal RNA confirms this morphologic progression. Examination of sister cells born at 3 days post-gentamicin reveals that there is equal likelihood that they will assume the hair cell or support cell fate (i.e., both asymmetric and symmetric differentiation occur).
GROWTH CONTROL OF DIFFERENTIATED FETAL RAT HEPATOCYTES IN PRIMARY MONOLAYER CULTURE (1974)

Dialyzed fetal bovine serum contains two distinct growth-controlling macromolecular fractions: one stimulates and the other inhibits proliferation of primary cultured differentiated fetal rat hepatocytes. Both fractions are precipitated by ammonium sulfate (50% saturation, pH 7.4, 4 degrees C). Serum fraction I (SFI, mol wt >/= 120,000 daltons estimated by gel filtration with Bio-gel P200) appears to contain at least two factors which function, respectively, to initiate DNA synthesis (activity pH 4-10 stable) and to increase the rate at which initiated cells traverse the cell cycle (activity pH 4 and pH 10 labile). Intraperitoneal injections of SFI into adult rats have produced detectable stimulation of hepatic but not renal DNA synthesis. Serum fraction II (SFII, mol wt 40,000-80,000 daltons) suppresses in vitro incorporation of CH(3)-[(3)H]thymidine into DNA under conditions which diminish neither cell viability nor cell attachment. Mixing experiments indicate that SFI and SFII mutually antagonize each other with respect to DNA synthesis and cell multiplication. Thus, both the relative and absolute serum levels of multiple factors control in vitro fetal hepatocyte proliferation.
A path towards quantum supremacy with superconducting qubits (2017)

A key milestone on the path towards building a quantum computer will be the demonstration of an algorithm which exceeds the capabilities of any classical computer - achieving so called quantum supremacy. The challenge in developing such an algorithm lies in balancing computational complexity with experimental feasibility, particularly in the presence of errors. In this thesis, we design superconducting qubits and algorithms with the goal of finding such a balance. We implement a wide variety of control protocols, including parametric drive, adiabatic control, floquet evolution and time-domain spectroscopy. These tools are used to the study topological invariants, quantum chaos, quantum statistical mechanics, chiral symmetry breaking and many-body localization. We present experimental techniques for characterizing the complexity and fidelity of these algorithms and show that quantum supremacy is achievable using existing technology.
Determination of Ideal Broth Formulations Needed to Prepare Hydrous Cerium Oxide Microspheres via the Internal Gelation Process (2009)

A simple test tube methodology was used to determine optimum process parameters for preparing hydrous cerium oxide microspheres via the internal gelation process.1 Broth formulations of cerium ammonium nitrate [(NH4)2Ce(NO3)6], hexamethylenetetramine, and urea were found that can be used to prepare hydrous cerium oxide gel spheres in the temperature range of 60 to 90 C. A few gel-forming runs were made in which microspheres were prepared with some of these formulations to be able to equate the test-tube gelation times to actual gelation times. These preparations confirmed that the test-tube methodology is reliable for determining the ideal broth formulations.
Identification of an antigenic epitope and receptor binding domain of human C5a. (1987)

Nine different murine anti-human C5a monoclonal antibodies have been produced and characterized. They exhibit Kas for the 125I-labeled ligand that range from 0.4 to 48 X 10(8) M-1, and they display limited cross-reactivity with C5a from other species. Each of these antibodies has been found to compete with the granulocyte C5a receptor for binding site(s) on the C5a polypeptide. Exploration of the antigenic topography of C5a revealed that the immunodominant portion of this glycopolypeptide resides between residues Lys20 and Arg37, with the area surrounding Cys27 being particularly important. In addition, a specific C5a derived tryptic peptide containing these amino acid residues competes with 125I-C5a for binding to the receptor. These observations are consistent with previously published data and suggest that this area of the C5a molecule is an important part of the receptor "recognition domain", and thus plays a critical role in the C5a receptor interaction.
Using wormhole switching for networks on chip : feasibility analysis and microarchitecture adaptation (2005)

Network-on-Chip (NoC) is proposed as a systematic approach to address future System-on-Chip (SoC) design difficulties. Due to its good performance and small buffering requirement, wormhole switching is being considered as a main network flow control mechanism for on-chip networks. Wormhole switching for NoCs is challenging from NoC application design and switch complexity reduction. In a NoC design flow, mapping an application onto the network should conduct a feasibility analysis in order to determine whether the messages’ timing constraints can be satisfied, and whether the network can be efficiently utilized. This is necessary because network contentions lead to nondeterministic behavior in message delivery. For wormhole-switched networks, we have formulated a contention tree model to accurately capture network contentions and reflect the concurrent use of links. Based on this model, the timing bounds of real-time messages can be derived. Furthermore, we have developed an algorithm to test the feasibility of real-time messages in the networks. From the wormhole switch micro-architecture level, switch complexity should be minimized to reduce cost but with reasonable performance penalty. We have investigated the flit admission and flit ejection problems that concern how the flits of packets are admitted into and ejected from the network, respectively. For flit admission, we propose a novel coupling scheme which binds a flit-admission queue with an output physical channel. Our results show that this scheme achieves a reduction of up to 8% in switch area and up to 35% in switch power over other comparable solutions. For flit ejection, we propose a p-sink model which differs from a typical ideal ejection model in that it uses only p flit sinks to eject flits instead of p • v flit sinks as required by the ideal model, where p is the number of physical channels of a switch and v is the number of virtual channels per physical channel. With this model, the buffering cost of flit sinks only depends on p, i.e., is irrespective of v. We have evaluated the coupled flit-admission technique and p-sink model in a 2D 4 x 4 mesh network. In our experiments, they exhibit only limited performance penalties in some cases. We believe that these cost-effective models are promising candidates to be used in wormhole-switched on-chip networks.
Highly efficient, long lived AlGaAs lasers fabricated by silicon impurity induced disordering (1986)

The process of silicon impurity induced disordering has been used to fabricate very efficient buried heterostructure AlGaAs lasers with lifetimes in the thousands of hours at 50 °C. These devices operate in a single transverse mode up to 25 mW, and in a single longitudinal mode with adjacent mode suppression of 23 dB.
Proteomic method identifies proteins nitrated in vivo during inflammatory challenge (2001)

Inflammation in asthma, sepsis, transplant rejection, and many neurodegenerative diseases associates an up-regulation of NO synthesis with increased protein nitration at tyrosine. Nitration can cause protein dysfunction and is implicated in pathogenesis, but few proteins that appear nitrated in vivo have been identified. To understand how this modification impacts physiology and disease, we used a proteomic approach toward targets of protein nitration in both in vivo and cell culture inflammatory disease models. This approach identified more than 40 nitrotyrosine-immunopositive proteins, including 30 not previously identified, that became modified as a consequence of the inflammatory response. These targets include proteins involved in oxidative stress, apoptosis, ATP production, and other metabolic functions. Our approach provides a means toward obtaining a comprehensive view of the nitroproteome and promises to broaden understanding of how NO regulates cellular processes.
Biodegradation of Polyethers (Polyethylene Glycol, Polypropylene Glycol, Polytetramethylene glycol, and Others) (2001)

Abstract Introduction Historical Outline Chemical Structures Biodegradation of PEG Aerobic Biodegradation of PEG Anaerobic Biodegradation and Metabolism of PEG Extracellular One‐electron Oxidation of PEG Biodegradation of PPG Biodegradation of PTMG Biodegradation of Miscellaneous Polyethers Physiology Production Outlook and Perspectives Patents Acknowledgments
Analog-to-Information Study Phase (2007)

Many communications and Radar receivers must process data over a very wide band, which requires either high-rate analog-to-digital converters (ADCs) or multichannel receivers. The information content of that wideband data, however, is often sparse in some basis. Analog-to-Information (A2I) receivers exploit this sparseness in both the digital and analog domains by non-adaptively spreading the signal energy (analog) and using digital signal processing to recover the signal from an ADC sampling at a sub-Nyquist rate. A subsampled ADC implies the use of fewer receiver channels or less expensive, lower- rate devices. This report documents the signal processing techniques for such receivers developed by the MIT Lincoln Laboratory/GMR Research and Technology team in the study phase of the A2I program. We have developed two new A2I signal processing methods, both significantly outperforming compressed sensing (CS) techniques currently in the literature, which typically fail when signals occupy more than 15-20% of the downsampled band. One of our methods, Nonlinear Affine processing (NoLaff), uses a nonlinear front-end to spread signal energy before the sub-Nyquist ADC, and uses hypothesis testing to reconstruct the signal. In simulations, this technique has shown that it can reconstruct wideband signals occupying up to 72% of the downsampled basis, It is also much less sensitive to the difficulties CS has detecting signals with large magnitude variation in the compressible basis. Our other method, called Variable Projection and Unfolding (VPU), spreads the signal energy using random linear projections similar to those used in compressed sensing, but is able to reconstruct signals occupying nearly 100% of the downsampled basis. VPU achieves this using a technique similar to matching pursuit; the key difference being that VPU searches over blocks of consecutive columns rather than one column at a time.
Mouse cellular retinoic acid binding protein: cloning, complementary DNA sequence, and messenger RNA expression during the retinoic acid-induced differentiation of F9 wild type and RA-3-10 mutant teratocarcinoma cells. (1989)

Retinoic acid, a natural derivative of vitamin A (retinol), induces mouse F9 teratocarcinoma stem cells to differentiate into nontumorigenic parietal endoderm cells. The mouse cellular retinoic acid binding protein (CRABP) has been implicated in the mechanism of action of retinoic acid (RA), since a mutant F9 cell line, RA-3-10, which possesses less than 5% of the wild type level of [3H]RA:CRABP binding activity, fails to differentiate in response to RA. In order to study the CRABP in this RA-induced differentiation process, we have cloned and sequenced the full-length mouse CRABP complementary DNA and have characterized its expression in wild type F9 and mutant cells. The mouse CRABP mRNA is a single, low abundant mRNA approximately 800 bases in length. The steady state level of the CRABP mRNA was measured in untreated stem cells and after the addition of RA alone, dibutyryl cyclic AMP plus theophylline (CT), or retinoic acid, dibutyryl cyclic AMP and theophylline (RACT) to F9 wild type and the mutant RA-3-10 cells. The CRABP mRNA was present in wild type F9 stem cells, and the level of its expression was changed by RA. When RA was added to F9 wild type cells, the steady state level of CRABP mRNA decreased 2- to 3-fold. When RACT was added to wild type cells, the level of CRABP mRNA increased and then decreased, resulting in a peak of CRABP mRNA expression between 24 and 48 h. In contrast, untreated mutant RA-3-10 cells had a lower level of CRABP mRNA than wild type stem cells, and the mutant cells responded quite differently to the addition of RA and RACT. The addition of RA caused an impressive 60-fold increase in the steady state level of CRABP mRNA in RA-3-10 cells by 120 h. One interpretation of this result is that there is negative regulation of CRABP mRNA expression, mediated directly or indirectly by the wild type functional CRABP protein, and that this regulation is aberrant in the RA-3-10 cells.
Novel Docosatrienes and 17S-Resolvins Generated from Docosahexaenoic Acid in Murine Brain, Human Blood, and Glial Cells (2003)

Docosahexaenoic acid (DHA, C22:6) is highly enriched in brain, synapses, and retina and is a major omega-3 fatty acid. Deficiencies in this essential fatty acid are reportedly associated with neuronal function, cancer, and inflammation. Here, using new lipidomic analyses employing high performance liquid chromatography coupled with a photodiode-array detector and a tandem mass spectrometer, a novel series of endogenous mediators was identified in blood, leukocytes, brain, and glial cells as 17S-hydroxy-containing docosanoids denoted as docosatrienes (the main bioactive member of the series was 10,17S-docosatriene) and 17S series resolvins. These novel mediators were biosynthesized via epoxide-containing intermediates and proved potent (pico- to nanomolar range) regulators of both leukocytes reducing infiltration in vivo and glial cells blocking their cytokine production. These results indicate that DHA is the precursor to potent protective mediators generated via enzymatic oxygenations to novel docosatrienes and 17S series resolvins that each regulate events of interest in inflammation and resolution.
A Microcarrier‐Based Cultivation System for Expansion of Primary Mesenchymal Stem Cells (2006)

Microcarrier cultures have been shown to allow extensive cell expansion of tissue engineering relevant cells, such as chondrocytes, while maintaining their phenotype. Our aim was to investigate the in vitro three-dimensional expansion of porcine bone-marrow-derived primary mesenchymal stem cells (MSC) using commercially available Cytodex type 1, type 2, and type 3 microcarriers. In comparison, the Cytodex type 1 microcarriers showed the best results for adherence with over 80% adherent cells after 3 h of incubation, analyzed by the Poisson distribution. Different start cell densities ranging from 1 to 3 x 106 cells per 100 cm2 had only a minor influence on adhesion. The proliferation was examined on Cytodex type 1 microcarriers over a cultivation time of 28 days, which could reveal cell growth and proof of cells recolonizing freshly added microcarriers. Scanning electron microscopy displayed appropriate cell morphology and confirmed cell proliferation. After enzymatic harvest from microcarriers, the osteogenic and chondrogenic differentiation of these cells was induced and shown by relevant histochemistry, such as von Kossa and Alcian blue staining. Totaling the results, we have shown that the three-dimensional expansion of MSC on microcarriers represents a beneficial alternative to the conventional two-dimensional monolayer cultivation method.
The β subunit of CKII negatively regulates Xenopus oocyte maturation (1997)

CKII (formerly known as casein kinase II) is a ubiquitously expressed enzyme that plays an important role in regulating cell growth and differentiation. The beta subunit of CKII (CKIIbeta) is not catalytic but forms heterotetramers with the catalytic subunit alpha to generate an alpha2beta2 holoenzyme. In Xenopus oocytes, CKIIbeta also associates with another serine/threonine kinase, Mos. As a key regulator of meiosis, Mos is necessary and sufficient to initiate oocyte maturation. We have previously shown that the binding of CKIIbeta to Mos represses Mos-mediated mitogen-activated protein kinase (MAPK) activation and that the ectopic expression of CKIIbeta inhibits progesterone-induced Xenopus oocyte maturation. We have now used an antisense oligonucleotide technique to reduce the endogenous CKIIbeta protein level in Xenopus oocytes, and we find that oocytes with a reduced content of CKIIbeta are more sensitive to low doses of progesterone and show accelerated MAPK activation and germinal vesicle breakdown. Furthermore, ectopic expression of a Mos-binding fragment of CKIIbeta suppressed the effect of antisense oligonucleotide. These results suggest that the endogenous CKIIbeta normally sets a threshold level for Mos protein, which must be exceeded for Mos to activate the MAPK signaling pathway and induce oocyte maturation.
Retinal pigment epithelial lipofuscin and melanin and choroidal melanin in human eyes. (1986)

Optical measurements of the pigments of the retinal pigment epithelium (RPE) and choroid were made on 38 human autopsy eyes of both blacks and whites, varying in age between 2 wk and 90 yr old. Lipofuscin in melanin-bleached RPE was measured as fluorescence at 470 mm following excitation at 365 nm and was found to be proportional to fluorescence measured at 560 nm in unbleached tissue. Transmission measurements of RPE and choroidal melanin were converted and expressed as optical density units. The choroidal melanin content increased from the periphery to the posterior pole. RPE melanin concentration decreased from the periphery to the posterior pole with an increase in the macula. Conversely, the amount of RPE lipofuscin increased from the periphery to the posterior pole with a consistent dip at the fovea. There was an inverse relationship between RPE lipofuscin concentration and RPE melanin concentration. The RPE melanin content was similar between whites and blacks. Lipofuscin concentration was significantly greater (P = 0.002) in the RPE of whites compared to blacks; whereas blacks had a significantly greater (P = 0.005) choroidal melanin content than whites. The amounts of both choroidal and RPE melanin showed a trend of decreasing content with aging, whereas the amount RPE lipofuscin tended to increase (whites greater than blacks). Per fundus area, the amount of choroidal melanin was always greater than that in the RPE. There was a statistically significant (P = 0.001) increase in RPE height with age, most marked in eyes of whites after age 50 and correlated with the increase in lipofuscin concentration.
Photon radiotherapy for the treatment of high-grade gliomas (2007)

High-grade gliomas are diseases characterized by poor overall survival despite aggressive multimodality therapy. Radiation therapy has been unequivocally established as the mainstay of therapy after surgical intervention, regardless of the extent of surgical resection. Despite theoretical and technological advances in the planning and delivery of radiation therapy, overall survival remains grim. In this review, we outline the evolution of radiation therapy, report the pivotal trials that have shaped this therapy and speculate on the future direction of this field.
The emerging JBIG2 standard (1998)

The Joint Bi-Level Image Experts Group (JBIG), an international study group affiliated with ISO/IEC and ITU-T, is in the process of drafting a new standard for lossy and lossless compression of bilevel images. The new standard, informally referred to as JBIG2, will support model-based coding for text and halftones to permit compression ratios up to three times those of existing standards for lossless compression. JBIG2 will also permit lossy preprocessing without specifying how it is to be done, In this case, compression ratios up to eight times those of existing standards may be obtained with imperceptible loss of quality. It is expected that JBIG2 will become an international standard by 2000.
The SCFCOI1 Ubiquitin-Ligase Complexes Are Required for Jasmonate Response in Arabidopsis (2002)

Xie and colleagues previously isolated the Arabidopsis COI1 gene that is required for response to jasmonates (JAs), which regulate root growth, pollen fertility, wound healing, and defense against insects and pathogens. In this study, we demonstrate that COI1 associates physically with AtCUL1, AtRbx1, and either of the Arabidopsis Skp1-like proteins ASK1 or ASK2 to assemble ubiquitin-ligase complexes, which we have designated SCF(COI1). COI1(E22A), a single amino acid substitution in the F-box motif of COI1, abolishes the formation of the SCF(COI1) complexes and results in loss of the JA response. AtRbx1 double-stranded RNA-mediated genetic interference reduces AtRbx1 expression and affects JA-inducible gene expression. Furthermore, we show that the AtCUL1 component of SCF(COI1) complexes is modified in planta, where mutations in AXR1 decrease the abundance of the modified AtCUL1 of SCF(COI1) and lead to a reduction in JA response. Finally, we demonstrate that the axr1 and coi1 mutations display a synergistic genetic interaction in the double mutant. These results suggest that the COI1-mediated JA response is dependent on the SCF(COI1) complexes in Arabidopsis and that the AXR1-dependent modification of the AtCUL1 subunit of SCF(COI1) complexes is important for JA signaling.