gebhart/patrepeval huggingface dataset:
Production of Donor T Cells Is Critical for Induction of Donor-Specific Tolerance and Maintenance of Chimerism (2004)

Nonmyeloablative conditioning has significantly reduced the morbidity associated with bone marrow transplantation. The donor hemopoietic cell lineage(s) responsible for the induction and maintenance of tolerance in nonmyeloablatively conditioned recipients is not defined. In the present studies we evaluated which hemopoietic stem cell-derived components are critical to the induction of tolerance in a total body irradiation-based model. Recipient B10 mice were pretreated with mAbs and transplanted with allogeneic B10.BR bone marrow after conditioning with 100-300 cGy total body irradiation. The proportion of recipients engrafting increased in a dose-dependent fashion. All chimeric recipients exhibited multilineage donor cell production. However, induction of tolerance correlated strictly with early production of donor T cells. The chimeras without donor T cells rejected donor skin grafts and demonstrated strong antidonor reactivity in vitro, while possessing high levels of donor chimerism. These animals lost chimerism within 8 mo. Differentiation into T cells was aborted at a prethymic stage in recipients that did not produce donor T cells. Moreover, donor Ag-driven clonal deletion of recipient T cells occurred only in chimeras with donor T cells. These results demonstrate that donor T cell production is critical in the induction of transplantation tolerance and the maintenance of durable chimerism. In addition, donor T cell production directly correlates with the deletion of potentially alloreactive cells.
Emerging roles of the bone morphogenetic protein pathway in cancer: potential therapeutic target for kinase inhibition (2016)

Bone morphogenetic proteins (BMPs) belong to the transforming growth factor-β (TGF-β) family signalling pathway. Similar to TGF-β, the complex roles of BMPs in development and disease are demonstrated by their dichotomous roles in various cancers and cancer stages. Although early studies implicated BMP signalling in tumour suppressive phenotypes, the results of more recent experiments recognize BMPs as potent tumour promoters. Many of these complexities are becoming illuminated by understanding the role of BMPs in their contextual role in unique cell types of cancer and the impact of their surrounding tumour microenvironment. Here we review the emerging roles of BMP signalling in cancer, with a focus on the molecular underpinnings of BMP signalling in individual cancers as a valid therapeutic target for cancer prevention and treatment.
Random Phasing of High-Power Lasers for Uniform Target Acceleration and Plasma-Instability Suppression (1984)

By converting a coherent wave to a random-phased wave, the intensity profile on a target becomes easily controllable. Planar as well as spherical targets were irradiated for the first time by the random-phased wave. The targets were uniformly accelerated without being affected by the small-scale intensity nonuniformities. The $\frac{3}{2}$-harmonic emission shows that the plasma waves at $\frac{{n}_{c}}{4}$ are only weakly excited in a spherical plasma. Irradiation with short-wavelength, random-phased beams will be suitable for compression.
ESTIMACIÓN DE LA CAPACIDAD DE CARGA TURÍSTICA DE LA RESERVA NATURAL VOLCÁN MOMBACHO, GRANADA, NICARAGUA (2007)

Este estudio identifica los principales factores que inciden en la determinación de la CCT de los senderos El Cráter, El Puma y El Cafetal de la Reserva Natural Volcán Mombacho. La Capacidad de carga turística se consideró tal y como propone Cifuentes en su metodología, en tres niveles: Capacidad de Carga Física (CCF), Capacidad de Carga Real (CCR) y Capacidad de Carga Efectiva (CCE) (Cifuentes, M. 1999). Se estimó la Capacidad de Manejo (CM) de la RNVM, en 74.24%, obteniendo en el sendero El Cráter una CCE de 442 visitas/día, en el sendero El Puma de 93 visitas/día, y en el sendero El Cafetal de 753 visitas/día. Si se lograse un incremento de la CM en un 80%; el sendero El Cráter incrementaría su CCE a 476 visitas/día; el sendero El Puma a 101visitas/día; y el sendero El Cafetal a 811 visitas/día. Este escenario está calculado para visitantes con propósitos eco turísticos. Debido a que las visitas de estudiantes de colegio, muestran un comportamiento diferente, se realizó el cálculo considerando dichos elementos en los factores de corrección para los Sendero El Cráter y El Cafetal (El Puma no es frecuentado por estudiantes de colegio). La CCE para estudiantes en el sendero El Cráter fue de 236 visitas/día, con una CM del 74.24%, y para un escenario del 80% de CM se calcula en 255 visitas/día; para el sendero El Cafetal se calculó en 403 visitas/día a un 74.24% de CM y 434 visitas/día a una CM del80%. Las visitas máximas reportadas para el año 2003 fueron en los meses de Enero y Junio, con 298 y 305 visitas/día; en el año 2002 se reportan los meses de Marzo y Mayo con 366 y 298 visitas/día; la visitación al Sendero El Cráter no excede aún la CCE calculada, no así si los visitantes fueran estudianregistes de colegio. Si la tendencia de la visitación continua incrementándose con los años, se requerirá que la administración de la RNVM restringa el número de visitas en los períodos picos de las mismas.
Reactive Oxygen Species–Mediated Mitochondria-to-Nucleus Signaling: A Key to Aging and Radical-Caused Diseases (2006)

Mitochondria-generated reactive oxygen species have been implicated as a common feature that connects aging of organisms and age-related diseases. Efficient elimination of these radicals by antioxidants correlates with increased life span. Understanding how the mitochondrion signals to the nucleus to regulate antioxidant proteins might be a key to aging processes and treatment of human diseases.
Data storage based on proximal probe techniques (invited) (abstract) (1996)

Recently, there has been considerable interest in examining the feasibility of using proximal probe techniques as the basis for a data storage device. These techniques, derived from the scanning tunneling microscope (STM) and atomic force microscope (AFM), provide a potential pathway to reaching the ultrahigh densities needed in the decades ahead. While these techniques offer high areal density, a number of formidable technical challenges must be met, however, in order to produce a device with realistic data rate, error rate, and overall reliability. In this talk we will review some of the approaches that have been taken, including those based on the STM, the AFM, and near-field optics. We will focus on the efforts in our laboratory to demonstrate realistic data rates at reasonably high densities using thermomechanical writing with an AFM tip, and near-field recording with a solid immersion lens. The prospects for parallel tip arrays and issues of overall implementation will also be addressed.
Bioethics and knowledge. (1990)

The acquisition of knowledge must be regarded as the first duty, as affirmed by Claude Bernard and Jacques Monod. It occupies a place in the forefront of other duties--respect for the individual and his liberty and dignity--to which the duty of knowledge must be subordinated. An attempt must be made to reconcile these diverse obligations. These three situations are described by stressing the importance of the principles that govern these studies: respect for the individual; respect for science; restriction of human experiments to what is strictly necessary; scrupulous assessment of the balance of risks and advantages; the human body is not an object of commerce; free and informed consent; solidarity between men.
Eukaryotic Oligosaccharyltransferase Generates Free Oligosaccharides during N-Glycosylation (2013)

Asparagine (N)-linked glycosylation regulates numerous cellular activities, such as glycoprotein quality control, intracellular trafficking, and cell-cell communications. In eukaryotes, the glycosylation reaction is catalyzed by oligosaccharyltransferase (OST), a multimembrane protein complex that is localized in the endoplasmic reticulum (ER). During N-glycosylation in the ER, the protein-unbound form of oligosaccharides (free oligosaccharides; fOSs), which is structurally related to N-glycan, is released into the ER lumen. However, the enzyme responsible for this process remains unidentified. Here, we demonstrate that eukaryotic OST generates fOSs. Biochemical and genetic analyses using mutant strains of Saccharomyces cerevisiae revealed that the generation of fOSs is tightly correlated with the N-glycosylation activity of OST. Furthermore, we present evidence that the purified OST complex can generate fOSs by hydrolyzing dolichol-linked oligosaccharide, the glycan donor substrate for N-glycosylation. The heterologous expression of a single subunit of OST from the protozoan Leishmania major in S. cerevisiae demonstrated that this enzyme functions both in N-glycosylation and generation of fOSs. This study provides insight into the mechanism of PNGase-independent formation of fOSs. Background: The enzyme generating free oligosaccharides (fOSs) in the lumen of the endoplasmic reticulum (ER) has been unidentified. Results: Oligosaccharyltransferase (OST), the N-glycosylating enzyme, hydrolyzes dolichol-linked oligosaccharides to release the fOSs. Conclusion: OST is responsible for the generation of fOSs in the ER lumen. Significance: This study provides a mechanistic insight into the formation of luminal fOSs in yeast.
The thickness of the epidermis (1973)

Epidermal thickness has been accurately measured on 214 samples of skin from 188 volunteers. Variations with the individual, body site, sex and age are described and discussed. An original technique of measurement has been developed which has several advantages over conventional methods. In particular, quick straight‐forward measurements are possible on volunteer skin rather than post mortem material, and the method eliminates errors arising from the skin's elasticity. These improvements in accuracy have confirmed that much information in the literature on epidermal thickness, is misleading as the results are based on inaccurate techniques of measurement.
Patterns of molecular evolution in dioecious and non‐dioecious <i>Silene</i> (2012)

Dioecy (i.e. having separate sexes) is a rather rare breeding system in flowering plants. Such rareness may result from a high probability of extinction in dioecious species because of less efficient dispersal and the costs of sexual selection, which are expected to harm dioecious species' survival on the long term. These handicaps should decrease the effective population size (Ne) of dioecious species, which in turn should reduce the efficacy of selection. Moreover, sexual selection in dioecious species is expected to specifically affect some genes, which will evolve under positive selection. The relative contribution of these effects is currently unknown and we tried to disentangle them by comparing sequence evolution between dioecious and non-dioecious species in the Silene genus (Caryophyllaceae), where dioecy has evolved at least twice. For the dioecious species in the section Melandrium, where dioecy is the oldest, we found a global reduction of purifying selection, while on some, male-biased genes, positive selection was found. For section Otites, where dioecy evolved more recently, we found no significant differences between dioecious and non-dioecious species. Our results are consistent with the view that dioecy is an evolutionary dead end in flowering plants, although other scenarios for explaining reduced Ne cannot be ruled out. Our results also show that contrasting forces act on the genomes of dioecious plants, and suggest that some time is required before the genome of such plants bears the footprints of dioecy.
PROMOTION OF MALIGNANT ASTROCYTOMA CELL MIGRATION BY OSTEOPONTIN EXPRESSED IN THE NORMAL BRAIN: DIFFERENCES IN INTEGRIN SIGNALING DURING CELL ADHESION TO OSTEOPONTIN VS. VITRONECTIN (2002)

The extracellular matrix of the normal adult brain lacks expression of most of the adhesive glycoproteins that are known to promote cell attachment, and it has been thought that the malignant invasion of astrocytoma tumor is mediated primarily by remodeling of the matrix by the tumor cells. It has been reported, however, that normal brain neuropil does contain a protein(s) that promotes cell attachment. Therefore, we explored the possibility that the cell attachment protein, osteopontin, is expressed in the normal human brain. Here, we report that osteopontin is expressed in the cortical gray and white matter of normal adult brain, with the levels of osteopontin expression being equivalent to those in malignant astrocytic tumor biopsies as assessed by Western blot analysis. Immunoblotting identified osteopontin polypeptides with relative molecular weights of 60- and 65-kDa in normal brain white matter and in astrocytic tumors, with an additional 70-kDa polypeptide being identified in normal cortical gray matter and in some astrocytic tumors. Recombinant osteopontin was found to promote attachment of U-251MG human malignant astrocytoma cells in a process that was inhibited by anti-integrin monoclonal antibodies anti-alphavbeta3 (75%), anti-alphavbeta5 (80%), and anti-alpha5 (40%). On attachment, integrins alphavbeta5 and alphavbeta3 localized to focal adhesions, and there was an alteration in cell morphology with the formation of lamellae-like processes. The attachment was associated with activation of Rac in a slow and prolonged fashion and rapid activation of Rho. Similarly, integrins alphavbeta5 and alphavbeta3 localized to focal adhesions on attachment of the U-251MG cells to vitronectin, but on this substrate, the cells assumed a spread and flat morphology, and there was rapid activation of both Rac and Rho. Extracts of normal brain white matter were capable of promoting haptotactic migration, and this response was inhibitable by monoclonal antibodies anti-alphavbeta3 and anti-alpha5. Depletion of the osteopontin in these extracts abrogated the haptotactic response significantly (50%). These data indicate that the cell attachment protein, osteopontin, is expressed in the normal adult brain and that it has the potential to promote malignant astrocytoma cell invasion.
Barley smuts (Revised 1973) (1973)

Barley smuts, caused by fungi, have been a disease prob lem in the barley crop since it was first grown.At one time smut was just smut, but we now recognize three distinct species on barley.Being able to distinguish among these species is important when deciding which control measures to use.
Expression, regulation, and function of P2X<sub>4</sub>purinergic receptor in human cervical epithelial cells (2002)

Micromolar concentrations of ATP stimulate biphasic change in transepithelial conductance across CaSki cultures on filters, an acute transient increase (phase I response; triggered by P2Y(2) receptor and mediated by calcium mobilization-dependent cell volume decrease) followed by a slower decrease in permeability (phase II response). Phase II response is mediated by augmented calcium influx and protein kinase C-dependent increase in tight junctional resistance. The objective of the study was to determine the role of P2X(4) receptor as a mediator of phase II response. Human cervical epithelial cells express P2X(4) receptor mRNA (1.4-, 2.2-, and 4.4-kb isoforms by Northern blot analysis) and P2X(4) protein. Depletion of vitamin A reversibly downregulated P2X(4) receptor mRNA and protein and ATP-induced calcium influx. Depletion of vitamin A abrogated phase II response, and the effect could be partially reversed only with retinoic acid receptor (RAR)-selective retinoids but not retinoid X receptor (RXR) agonists. Depletion of vitamin A also abrogated protein kinase C increase in tight junctional resistance, and the effect could not be reversed with retinoids. Depletion of vitamin A also abrogated phase I increase in permeability and reversibly downregulated P2Y(2) receptor mRNA and ATP-induced calcium mobilization. However, in contrast to phase II response, both RAR and RXR agonists could fully reverse those effects. These results suggest that phase II response is mediated by a P2X(4) receptor mechanism.
Isolation and characterization of bacteriophages of the<i>Burkholderia cepacia</i>complex (2005)

The Burkholderia cepacia complex consists of nine phenotypically similar but genotypically distinct beta-proteobacteria that are metabolically diverse and highly antibiotic resistant. Because of this exceptional intrinsic antibiotic resistance, infections with B. cepacia complex members are difficult to treat clinically and new alternative therapies are required. One strategy that holds some promise is the use of naturally occurring antibacterial bacteriophages that could potentially bind to and lyse B. cepacia complex cells in vivo. Towards that end, we used enrichment techniques to isolate lytic and lysogenic bacteriophages specific to the B. cepacia complex. The newly isolated bacteriophages were characterized by host range analysis, electron microscopy, genome restriction analysis, and partial DNA sequencing. These isolates include a bacteriophage with one of the broadest host ranges yet identified for any bacteriophage specific to the B. cepacia complex, and the first description of bacteriophages capable of lysing B. ambifaria.
Tn <i>5406</i> , a New Staphylococcal Transposon Conferring Resistance to Streptogramin A and Related Compounds Including Dalfopristin (2002)

ABSTRACT We characterized a new transposon, Tn 5406 (5,467 bp), in a clinical isolate of Staphylococcus aureus (BM3327). It carries a variant of vgaA , which encodes a putative ABC protein conferring resistance to streptogramin A but not to mixtures of streptogramins A and B. It also carries three putative genes, the products of which exhibit significant similarities (61 to 73% amino acid identity) to the three transposases of the staphylococcal transposon Tn 554 . Like Tn 554 , Tn 5406 failed to generate target repeats. In BM3327, the single copy of Tn 5406 was inserted into the chromosomal att554 site, which is the preferential insertion site of Tn 554 . In three other independent S. aureus clinical isolates, Tn 5406 was either present as a single plasmid copy (BM3318), as two chromosomal copies (BM3252), or both in the chromosome and on a plasmid (BM3385). The Tn 5406 -carrying plasmids also contain two other genes, vgaB and vatB . The insertion sites of Tn 5406 in BM3252 were studied: one copy was in att554 , and one copy was in the additional SCCmec element. Amplification experiments revealed circular forms of Tn 5406 , indicating that this transposon might be active. To our knowledge, a transposon conferring resistance to streptogramin A and related compounds has not been previously described.
The Amino-terminal Domain of the Vacuolar Proton-translocating ATPase a Subunit Controls Targeting and in Vivo Dissociation, and the Carboxyl-terminal Domain Affects Coupling of Proton Transport and ATP Hydrolysis (2001)

The 100-kDa "a" subunit of the vacuolar proton-translocating ATPase (V-ATPase) is encoded by two genes in yeast, VPH1 and STV1. The Vph1p-containing complex localizes to the vacuole, whereas the Stv1p-containing complex resides in some other intracellular compartment, suggesting that the a subunit contains information necessary for the correct targeting of the V-ATPase. We show that Stv1p localizes to a late Golgi compartment at steady state and cycles continuously via a prevacuolar endosome back to the Golgi. V-ATPase complexes containing Vph1p and Stv1p also differ in their assembly properties, coupling of proton transport to ATP hydrolysis, and dissociation in response to glucose depletion. To identify the regions of the a subunit that specify these different properties, chimeras were constructed containing the cytosolic amino-terminal domain of one isoform and the integral membrane, carboxyl-terminal domain from the other isoform. Like the Stv1p-containing complex, the V-ATPase complex containing the chimera with the amino-terminal domain of Stv1p localized to the Golgi and the complex did not dissociate in response to glucose depletion. Like the Vph1p-containing complex, the V-ATPase complex containing the chimera with the amino-terminal domain of Vph1p localized to the vacuole and the complex exhibited normal dissociation upon glucose withdrawal. Interestingly, the V-ATPase complex containing the chimera with the carboxyl-terminal domain of Vph1p exhibited a higher coupling of proton transport to ATP hydrolysis than the chimera containing the carboxyl-terminal domain of Stv1p. Our results suggest that whereas targeting and in vivo dissociation are controlled by sequences located in the amino-terminal domains of the subunit a isoforms, coupling efficiency is controlled by the carboxyl-terminal region.
A modified Gerchberg-Saxton algorithm for one-dimensional motion artifact correction in MRI (1991)

A novel method for the suppression of one-dimensional translational motion artifacts in two-dimensional Fourier transform magnetic resonance images is presented. It is shown that the motion causes an additional phase factor in the detected signal and that this phase error can be removed using a modified Gerchberg-Saxton (1972) algorithm. The major differences between this algorithm and other phase retrieval algorithms are: (1) the phase information is not totally unavailable, but in a corrupted form; and (2) the algorithm does not try to recover the entire phase information from the magnitude of the detected signal, but rather to correct the distorted phase using the average phase error. The method has been successfully tested using computer simulations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Transversality and lattice surgery: Exploring realistic routes toward coupled logical qubits with trapped-ion quantum processors (2019)

Active quantum error correction has been identified as a crucial ingredient of future quantum computers, motivating the recent experimental efforts to encode logical quantum bits using small topological codes. In addition to the demonstration of the beneficial role of the encoding, a break-even point in the progress towards large-scale quantum computers will be the implementation of a universal set of gates. This midterm challenge will soon be faced by various quantum technologies, which urges the need of realistic assessments of their prospects. In this work, we pursue this goal by assessing the capability of current trapped-ion architectures in facing one of the most demanding parts of this quest: the implementation of an entangling controlled-NOT (CNOT) gate between encoded logical qubits. We present a detailed comparative study of two alternative strategies for trapped-ion topological color codes, either a transversal or a lattice-surgery approach, characterized by a detailed microscopic modeling of both current technological capabilities and experimental sources of noise afflicting the different operations. Our careful fault-tolerant design, together with a low-resource optimization, allows us to determine via exhaustive numerical simulations the experimental regimes where each of the approaches becomes favorable. We hope that our study thereby contributes to guiding the future development of trapped-ion quantum computers.