gebhart/patrepeval huggingface dataset:
An Investigation of Adolescent Health in Vietnam (1997)

Despite the fact that adolescents share health risks attendant upon rapid social change Viet Nam has not yet created a division of adolescent health. This paper summarizes results on sex behavior and attitudes of adolescents obtained as part of a larger survey undertaken in 1997 to identify adolescent risk behaviors and attitudes in order to create appropriate interventions. Data were gathered from 1110 students (47.7% male 43.8% female 8.5% unknown) at eight randomly selected schools in Ho Chi Minh City via a pretested self-administered closed-format questionnaire. It was found that 4.7% of males and 0.8% of females reported having had sexual intercourse (but 6.4% preferred not to this question and 3.6% did not respond). However 34.8% of males and 9.6% of females approved of premarital sex. Nearly equal proportions indicated a need to use contraception when engaging in sexual intercourse (48.3%) or had no opinion (45.8%). However 72% said that condoms are necessary to prevent HIV infection and sexually transmitted diseases (26% had no opinion on this subject). These findings reflect both the conservative and the changing values of Viet Nam. The usefulness of the data is compromised because so many respondents chose not to answer specific questions and because the survey involved only in-school youth. It is of interest that only a slight majority of respondents were totally opposed to premarital sex. Traditional values seem more tenacious among female respondents.
Three-Dimensional Structures Self-Assembled from DNA Bricks (2012)

We describe a simple and robust method to construct complex three-dimensional (3D) structures by using short synthetic DNA strands that we call "DNA bricks." In one-step annealing reactions, bricks with hundreds of distinct sequences self-assemble into prescribed 3D shapes. Each 32-nucleotide brick is a modular component; it binds to four local neighbors and can be removed or added independently. Each 8-base pair interaction between bricks defines a voxel with dimensions of 2.5 by 2.5 by 2.7 nanometers, and a master brick collection defines a "molecular canvas" with dimensions of 10 by 10 by 10 voxels. By selecting subsets of bricks from this canvas, we constructed a panel of 102 distinct shapes exhibiting sophisticated surface features, as well as intricate interior cavities and tunnels.
A large-scale insertional mutagenesis screen in zebrafish (1999)

It is estimated that approximately 2500 genes are essential for the normal development of a zebrafish embryo. A mutation in any one of these genes can result in a visible developmental defect, usually followed by the death of the embryo or larva by days 5-7 of age. We are performing a large-scale insertional mutagenesis screen in the zebrafish with the goal of isolating approximately 1000 embryonic mutations. We plan to clone a significant fraction of the mutated genes, as these are the genes important for normal embryogenesis of a vertebrate. To achieve this goal, we prepared approximately 36, 000 founder fish by injecting blastula-stage embryos with one of two pseudotyped retroviruses. We estimate that together these fish harbor between 500,000-1,000,000 proviral insertions in their germ lines. The protocol we have devised and the size of our facility allow us to breed approximately 80,000-150,000 of these insertions to homozygosity within 2 years. Because a pilot screen conducted earlier in our laboratory revealed that the frequency of mutations obtained with this type of insertional mutagen is 1 embryonic lethal mutation per 70-100 proviral insertions, screening 100,000 insertions should yield at least 1000 mutants. Here we describe the protocol for the screen and initial results with the first of the two retroviral vectors used, a virus designated F(5). We screened an estimated 760 insertions among F(3) progeny from 92 F(2) families and obtained 9 recessive embryonic lethal mutations. Thus, the efficiency of mutagenesis with this viral vector is approximately one-ninth that observed with the chemical mutagen ENU in zebrafish. We have also obtained two dominant mutations, one of which is described here. As expected, mutated genes can be readily identified. So far, genes mutated in four of the nine recessive mutants and one of the two dominant mutants have been cloned. Further improvements to this technology could make large-scale insertional mutagenesis screening and rapid gene cloning accessible to relatively small zebrafish laboratories.
Neutrophil Transmigration Mediated by the Neutrophil-Specific Antigen CD177 Is Influenced by the Endothelial S536N Dimorphism of Platelet Endothelial Cell Adhesion Molecule-1 (2010)

The human neutrophil-specific adhesion molecule CD177 (also known as the NB1 alloantigen) becomes upregulated on the cell surface in a number of inflammatory settings. We recently showed that CD177 functions as a novel heterophilic counterreceptor for the endothelial junctional protein PECAM-1 (CD31), an interaction that is mediated by membrane-proximal PECAM-1 IgD 6, which is known to harbor an S(536)N single nucleotide polymorphism of two major isoforms V(98)N(536)G(643) and L(98)S(536)R(643) and a yet-to-be-determined region on CD177. In vitro transendothelial migration experiments revealed that CD177(+) neutrophils migrated significantly faster through HUVECs expressing the LSR, compared with the VNG, allelic variant of PECAM-1 and that this correlated with the decreased ability of anti-PECAM-1 Ab of ITIM tyrosine phosphorylation in HUVECs expressing the LSR allelic variant relative to the VNG allelic variant. Moreover, engagement of PECAM-1 with rCD177-Fc (to mimic heterophilic CD177 binding) suppressed Ab-induced tyrosine phosphorylation to a greater extent in cells expressing the LSR isoform compared with the VNG isoform, with a corresponding increased higher level of beta-catenin phosphorylation. These data suggest that heterophilic PECAM-1/CD177 interactions affect the phosphorylation state of PECAM-1 and endothelial cell junctional integrity in such a way as to facilitate neutrophil transmigration in a previously unrecognized allele-specific manner.
Jesús M. Silva Sánchez (2000)

El profesor Jesus Silva comenta algunas cuestiones de interes en el ambito del Derecho Penal, la Politica Criminal y la Criminologia. Asimismo, explica cual ha sido su trayectoria investigadora y academica y se pronuncia sobre el estado actual de la ciencia penal y acerca de cual puede ser su previsible futuro. En particular, cabe destacar sus reflexiones sobre el pensamiento de Jakobs, el libre arbitrio como fundamento del Derecho y la convivencia, la fundamentacion del injusto, y un etcetera que el lector de este resumen puede facilmente completar leyendo directamente las palabras del doctor Silva en el texto de la conversacion.
Antibiotic prescribing for self limiting respiratory tract infections in primary care: summary of NICE guidance (2008)

Antibiotics probably provide little benefit for a large proportion of respiratory tract infections that present in primary care. Respiratory tract infections are largely self limiting, and complications are likely to be rare if antibiotics are withheld. However, respiratory tract infections account for 60% of all antibiotic prescribing in primary care,1 and the prescribing patterns for antibiotics vary widely among general practices, without evidence of significant benefit among higher prescribers. Three different management strategies for antibiotics can be used for patients with respiratory tract infection who present in primary care: no antibiotic prescribing; delayed (or deferred) prescribing, in which a prescription is written for use at a later date if symptoms worsen or do not start to settle in the expected timescale; and immediate prescribing. This article summarises the most recent recommendations from the National Institute for Health and Clinical Excellence (NICE) on antibiotic prescribing for self limiting respiratory tract infections in primary care.2 NICE recommendations are based on systematic reviews of best available evidence. When minimal evidence is available, recommendations are based on the Guideline Development Group’s opinion of what constitutes good practice. Evidence levels for the recommendations are given in italic in square brackets. ### Management strategies for antibiotics #### Adults and children (3 months or older) with acute otitis media; acute sore throat, acute pharyngitis, or acute tonsillitis; common cold; acute rhinosinusitis; acute cough or acute bronchitis
Evolutionary Architecture Search For Deep Multitask Networks (2018)

Multitask learning, i.e. learning several tasks at once with the same neural network, can improve performance in each of the tasks. Designing deep neural network architectures for multitask learning is a challenge: There are many ways to tie the tasks together, and the design choices matter. The size and complexity of this problem exceeds human design ability, making it a compelling domain for evolutionary optimization. Using the existing state of the art soft ordering architecture as the starting point, methods for evolving the modules of this architecture and for evolving the overall topology or routing between modules are evaluated in this paper. A synergetic approach of evolving custom routings with evolved, shared modules for each task is found to be very powerful, significantly improving the state of the art in the Omniglot multitask, multialphabet character recognition domain. This result demonstrates how evolution can be instrumental in advancing deep neural network and complex system design in general.
Mitogenesis in Response to PDGF and Bombesin Abolished by Microinjection of Antibody to PIP 2 (1988)

The turnover of phosphatidylinositol 4,5-bisphosphate (PIP2) is believed to constitute a crucial step in the signaling pathways for stimulation of cells by a variety of bioactive substances, including mitogens, but decisive evidence for the idea has not been obtained. In the present study, a monoclonal antibody to PIP2 was microinjected into the cytoplasm of NIH 3T3 cells before or after exposure to mitogens. The antibody completely abolished nuclear labeling with [3H]thymidine induced by platelet-derived growth factor and bombesin, but not by fibroblast growth factor, epidermal growth factor, insulin, or serum. The findings strongly suggest that PIP2 breakdown is crucial in the elicitation and sustaining of cell proliferation induced by some types of mitogens such as platelet-derived growth factor and bombesin.
Genes for Plasmodium falciparum surface antigens cloned by expression in COS cells. (1990)

Two genes encoding membrane antigens of Plasmodium falciparum were isolated by transient expression in mammalian cells and selection with human immune sera from African adults exposed to P. falciparum malaria. COS-7 cells were transfected with a plasmid expression library constructed from P. falciparum genomic DNA, and cells expressing reactive malaria antigens on their surface were enriched by adherence to antibody-coated dishes. One of the genes isolated is distinctive in that it does not contain repeat sequences typical of many malarial genes cloned by immunoscreening of bacterial expression libraries. The second gene apparently encodes a polymorphic version of the P. falciparum merozoite surface antigen Ag513, since the two sequences are identical in the 5' and 3' coding regions but diverge completely in the center. The COS-7 expression system provides an alternate means for cloning genes encoding malarial membrane antigens by using those antibodies in complex immune sera that bind membrane-associated, nondenatured molecules.
Nanoscale internally referenced oxygen sensors produced from self-assembled nanofilms on fluorescent nanoparticles (2005)

A novel sensor fabrication concept using indicators trapped in nanoengineered ultrathin films deposited on fluorescent nanoparticles is demonstrated for oxygen sensing. The nanoscale systems are based on the quenching of tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) immobilized within polyelectrolyte multilayers deposited on the surface of nanoparticle templates. The ionically bound nanofilms create a porous scaffold into which controlled precipitation of the chromophore is achieved using a combination of electrostatic attraction and dye insolubility in water. The fluorescent nanoparticles act as physical scaffolds and also provide a complementary spectral signature for use as an internal intensity reference. Oxygen sensors created on 100-nm yellow-green fluorescent particles exhibit a linear Stern-Volmer behavior with a quenching constant of 1.06 mM and sensitivity of 60%, which demonstrates that the dye is still partially accessible to oxygen following immobilization. To demonstrate the feasibility of intracellular metabolic monitoring with such nanoprobes, the oxygen sensors were chemically delivered into human dermal fibroblasts with no apparent loss in cell viability. The results prove that the approach to sensor production is facile and leads to sensitive systems that can be further optimized for improved response, and these findings support the further development of similar self-referenced probes toward quantitative intracellular analysis.
Increased G2 chromosomal radiosensitivity in cancer patients: the role of cdk1/cyclin-B activity level in the mechanisms involved (2000)

The cdk1/cyclin-B activity levels during the G2 to M transition impair DNA repair processes and play a major role in the yield of chromatid breaks induced after G2-irradiation. Regulation of cdk1/cyclinB complex activity rather than deficient repair enzymes of DNA damage may underlie the mechanisms of G2 radiosensitivity.
Simultaneous phase control of Li2 wave packets in two electronic states (2002)

State-selective phase control of rotational Li2 wave packets, prepared simultaneously in the E(1∑g+) electronic state by one photon absorption and the A(1∑u+) electronic state by resonant impulsive stimulated Raman scattering, is demonstrated. Following the initial population of a rovibrational launch state on the A electronic potential energy curve with a cw laser, a single sub-picosecond wave packet preparation pulse centered near 800 nm simultaneously creates a two-state rotational wave packet in the E state (νE=18, JE=23 and 25) and a three-state rotational wave packet in the A state (νA=15, JA=22, 24, and 26). A temporally delayed 800 nm probe pulse subsequently ionizes both electronic components of the wave packet to allow measurement of the time-dependent coherence in these two electronic states. Via phase manipulation of resonant transition frequencies contained within the preparation pulse, the phases of the E(18,25) and A(15,26) quantum states are either varied concurrently or individually controlled, whereas the phases of the other rovibronic states of the wave packet are in all cases held essentially constant. This phase manipulation is shown to be more complex than a simple additive effect involving the phases applied to the resonant frequencies. These experimental results are compared with the predictions of second order time-dependent perturbation theory. Although systematic discrepancies exist, most likely due to an additional phase introduced during the two-photon probe process, once these differences are accounted for, good agreement is found between experiment and perturbation theory.
Inhibitor-induced enzyme activation in organic solvents. (1988)

The enzymatic activity of the protease subtilisin in anhydrous organic solvents can be dramatically increased by pretreating the enzyme before it is placed in the nonaqueous medium. For instance, lyophilization of subtilisin from aqueous solution containing competitive inhibitors (followed by their removal) created an enzyme which was up to 100 times more active than the enzyme lyophilized in the absence of such ligands. This phenomenon of ligand-induced "enzyme memory" also extends to the stability, affinity, and substrate specificity of subtilisin in organic solvents.
An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones (2002)

We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing initiative, the method has been used and refined in our laboratory since September 2000. Amenable to large scale projects, we have used the method to generate >7 Mb of accurate sequence from 3695 candidate full-length cDNAs. Sequencing is accomplished through the insertion of Mu transposon into cDNAs, followed by sequencing reactions primed with Mu-specific sequencing primers. Transposon insertion reactions are not performed with individual cDNAs but rather on pools of up to 96 clones. This pooling strategy reduces the number of transposon insertion sequencing libraries that would otherwise be required, reducing the costs and enhancing the efficiency of the transposon library construction procedure. Sequences generated using transposon-specific sequencing primers are assembled to yield the full-length cDNA sequence, with sequence editing and other sequence finishing activities performed as required to resolve sequence ambiguities. Although analysis of the many thousands (22 785) of sequenced Mu transposon insertion events revealed a weak sequence preference for Mu insertion, we observed insertion of the Mu transposon into 1015 of the possible 1024 5mer candidate insertion sites.
TBA225, a fusion toxoid vaccine for protection and broad neutralization of staphylococcal superantigens (2019)

Superantigens (SAgs) play a major role in the pathogenesis of Staphylococcus aureus and are associated with several diseases, including food poisoning, bacterial arthritis, and toxic shock syndrome. Monoclonal antibodies to these SAgs, primarily TSST-1, SEB and SEA have been shown to provide protection in animal studies and to reduce clinical severity in bacteremic patients. Here we quantify the pre-existing antibodies against SAgs in many human plasma and IVIG samples and demonstrate that in a major portion of the population these antibody titers are suboptimal and IVIG therapy only incrementally elevates the anti-SAg titers. Our in vitro neutralization studies show that a combination of antibodies against SEA, SEB,and TSST-1 can provide broad neutralization of staphylococcal SAgs. We report a single fusion protein (TBA<sub>225</sub>) consisting of the toxoid versions of TSST-1, SEB and SEA and demonstrate its immunogenicity and protective efficacy in a mouse model of toxic shock. Antibodies raised against this fusion vaccine provide broad neutralization of purified SAgs and culture supernatants of multiple clinically relevant S. aureus strains. Our data strongly supports the use of this fusion protein as a component of an anti-virulence based multivalent toxoid vaccine against S. aureus disease.
Gene Expression Profiling of RNA Extracted from FFPE Tissues: NuGEN Technologies’ Whole-Transcriptome Amplification System (2011)

Gene expression profiling of RNA isolated from formalin fixed, paraffin-embedded (FFPE) tissue samples has been historically challenging. Yet FFPE samples are sought-after because of the in-depth retrospective records typically associated with them rendering these samples a valuable resource for translational medicine studies. Extensive degradation, chemical modifications, and cross-linking have made it difficult to isolate RNA of sufficient quality required for large-scale gene expression profiling studies. NuGEN Technologies’ WT-Ovation™ FFPE System linearly amplifies RNA from FFPE samples through a robust and simple whole-transcriptome approach using as little as 50 ng total RNA isolated from FFPE samples. The amplified material may be labeled with validated kits and/or protocols from NuGEN for analysis on any of the major gene expression microarray platforms, including: Affymetrix, Agilent, and Illumina gene expression arrays. Results compare well with those obtained using RNA from fresh-frozen samples. RNA quality from FFPE samples varies significantly and neither sample age nor sample size analysis via gel electrophoresis or the Agilent Bioanalyzer system accurately predict materials suitable for amplification. Therefore, NuGEN has validated a correlative qPCR-based analytical method for the RNA derived from FFPE samples which effectively predicts array results. The NuGEN approach enables fast and successful analysis of samples previously thought to be too degraded for gene expression analysis.
AACR Centennial Series: The Biology of Cancer Metastasis: Historical Perspective (2010)

Metastasis resistant to therapy is the major cause of death from cancer. Despite almost 200 years of study, the process of tumor metastasis remains controversial. Stephen Paget initially identified the role of host-tumor interactions on the basis of a review of autopsy records. His "seed and soil" hypothesis was substantiated a century later with experimental studies, and numerous reports have confirmed these seminal observations. An improved understanding of the metastatic process and the attributes of the cells selected by this process is critical for the treatment of patients with systemic disease. In many patients, metastasis has occurred by the time of diagnosis, so metastasis prevention may not be relevant. Treating systemic disease and identifying patients with early disease should be our goal. Revitalized research in the past three decades has focused on new discoveries in the biology of metastasis. Even though our understanding of molecular events that regulate metastasis has improved, the contributions and timing of molecular lesion(s) involved in metastasis pathogenesis remain unclear. Review of the history of pioneering observations and discussion of current controversies should increase understanding of the complex and multifactorial interactions between the host and selected tumor cells that contribute to fatal metastasis and should lead to the design of successful therapy.
Sorting by diffusion: An asymmetric obstacle course for continuous molecular separation (1999)

A separation technique employing a microfabricated sieve has been demonstrated by observing the motion of DNA molecules of different size. The sieve consists of a two-dimensional lattice of obstacles whose asymmetric disposition rectifies the Brownian motion of molecules driven through the device, causing them to follow paths that depend on their diffusion coefficient. A nominal 6% resolution by length of DNA molecules in the size range 15-30 kbp may be achieved in a 4-inch (10-cm) silicon wafer. The advantage of this method is that samples can be loaded and sorted continuously, in contrast to the batch mode commonly used in gel electrophoresis.
Low-temperature silicon homoepitaxy by ultrahigh vacuum electron cyclotron resonance chemical vapor deposition (1994)

High quality silicon homoepitaxial layers are successfully grown at 560 °C by ultrahigh vacuum electron cyclotron resonance chemical vapor deposition (UHV-ECRCVD) using a SiH4/H2 plasma. The effects of substrate dc bias on the in situ hydrogen plasma clean and the subsequent silicon epitaxial growth are examined by the reflection high-energy electron diffraction (RHEED), secondary ion mass spectroscopy (SIMS), and cross-section transmission electron microscopy (XTEM). It is observed that the substrate dc bias plays a significant role in obtaining a damage-free, clean Si substrate prior to epitaxial growth. Severe damage in the Si surface is observed by XTEM, though RHEED shows a streaky pattern, when the substrate is electrically floating, but the damage can be suppressed with +10 V dc bias to the substrate. Substrate dc bias during plasma deposition drastically changes the crystal structure from polycrystalline at −50 V to high quality epitaxial silicon at substrate biases greater than +50 V. Precise control of the ion energy during in situ cleaning and plasma deposition is very important in low-temperature Si epitaxy by UHV-ECRCVD and it is possible by proper control of the substrate dc bias.