gebhart/patrepeval huggingface dataset:
The Sequence of the Human Genome (2001)

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
Efficacy and safety of the dipeptidyl peptidase‐4 inhibitor, sitagliptin, compared with the sulfonylurea, glipizide, in patients with type 2 diabetes inadequately controlled on metformin alone: a randomized, double‐blind, non‐inferiority trial (2007)

In this study, the addition of sitagliptin compared with glipizide provided similar HbA(1c)-lowering efficacy over 52 weeks in patients on ongoing metformin therapy. Sitagliptin was generally well tolerated, with a lower risk of hypoglycaemia relative to glipizide and with weight loss compared with weight gain with glipizide.
Noiseless Quantum Codes (1997)

In this paper we study a model quantum register $R$ made of $N$ replicas (cells) of a given finite-dimensional quantum system S. Assuming that all cells are coupled with a common environment with equal strength we show that, for $N$ large enough, in the Hilbert space of $R$ there exists a linear subspace ${C}_{N}$ which is dynamically decoupled from the environment. The states in ${C}_{N}$ evolve unitarily and are therefore decoherence-dissipation free. The space ${C}_{N}$ realizes a noiseless quantum code in which information can be stored, in principle, for an arbitrarily long time without being affected by errors.
Immunoaffinity Extraction for Liquid Chromatographic Determination of Equilin and its Metabolites in Plasma (1996)

Immunoaffinity extraction for the high-performance liquid chromatographic determination of equilin and its metabolites in plasma has been achieved. The antibody raised against an equilin 3-O-carboxymethyl ether-bovine serum albumin conjugate was characterized as having a high affinity for equilin and equilenin. One mL of the immunoaffinity adsorbent prepared by immobilization of an antibody was capable of retaining up to 1 microgram of equilin and equilenin, to 100 ng of other metabolites including 2-methoxylated and 17 beta-reduced compounds, and to 0.3 micrograms of glucuronic acid conjugates at C-3. The adsorbates were recovered qualitatively by elution with 90% aqueous (v/v) methanol without any interfering peaks on the chromatogram.
The Rate of Folding Dictates Substrate Secretion by the Escherichia coli Hemolysin Type 1 Secretion System (2010)

Secretion of the Escherichia coli toxin hemolysin A (HlyA) is catalyzed by the membrane protein complex HlyB-HlyD-TolC and requires a secretion sequence located within the last 60 amino acids of HlyA. The Hly translocator complex exports a variety of passenger proteins when fused N-terminal to this secretion sequence. However, not all fusions are secreted efficiently. Here, we demonstrate that the maltose binding protein (MalE) lacking its natural export signal and fused to the HlyA secretion signal is poorly secreted by the Hly system. We anticipated that folding kinetics might be limiting secretion, and we therefore introduced the "folding" mutation Y283D. Indeed this mutant fusion protein was secreted at a much higher level. This level was further enhanced by the introduction of a second MalE folding mutation (V8G or A276G). Secretion did not require the molecular chaperone SecB. Folding analysis revealed that all mutations reduced the refolding rate of the substrate, whereas the unfolding rate was unaffected. Thus, the efficiency of secretion by the Hly system is dictated by the folding rate of the substrate. Moreover, we demonstrate that fusion proteins defective in export can be engineered for secretion while still retaining function.
Characterization of translational frame exception patients in Duchenne/Becker muscular dystrophy (1993)

The clinical progression of Duchenne muscular dystrophy (DMD) patients with deletions can be predicted in 93% of cases by whether the deletion maintains or disrupts the translational reading frame (frameshift hypothesis). We have identified and studied a number of patients who have deletions that do not conform to the translational frame hypothesis. The most common exception to the frameshift hypothesis is the deletion of exons 3 to 7 which disrupts the translational reading frame. We identified a Becker muscular dystrophy (BMD) patient, an intermediate, and a DMD patient with this deletion. In all three cases, dystrophin was detected and localized to the membrane. One DMD patient with an inframe deletion of exons 4-18 produced no dystrophin. One patient with a mild intermediate phenotype and a deletion of exon 45, which shifts the reading frame, produced no dystrophin. Two patients with large inframe deletions had discordant phenotypes (exons 3-41, DMD; exons 13-48, BMD), but both produced dystrophin that localized to the sarcolemma. The DMD patient, 113, indicates that dystrophin with an intact carboxy terminus can be produced in Duchenne patients at levels equivalent to some Beckers. The dystrophin analysis from these patients, together with patients reported in the literature, indicate that more than one domain can localize dystrophin to the sarcolemma. Lastly, the data shows that although most patients show correlation of clinical severity to molecular data, there are rare patients which do not conform.
Target-free approach for vision-based structural system identification using consumer-grade cameras (2016)

Recent reports on America's infrastructure have emphasized the importance of structural health monitoring of civil infrastructures. System identification is a key component of many structural health monitoring strategies. Current system identification methods estimate models of a structure by measuring displacements, accelerations, and strains with wired or wireless sensors. However, these methods typically involve installation of a limited number of sensors at discrete locations and require additional data acquisition devices. To overcome these limitations, computer vision-based techniques have been introduced recently that employ high-speed and high-resolution cameras. Such cameras can be quite costly and require tedious installation of targets. This paper investigates the potential of using consumer-grade cameras for structural system identification without the need to install targets. The underlying methods for target-free displacement measurements are introduced, including region of interest selection, feature detection, point tracking, and outlier removal. A set of experiments are conducted to assess the efficacy of the proposed approach by comparing the accuracy of the identified model with one obtained using a conventional wired system. Careful comparison of the results demonstrates the significant potential of the proposed approach. Copyright © 2016 John Wiley & Sons, Ltd.
Two-handed virtual manipulation (1998)

We discuss a two-handed user interface designed to support three-dimesional neurosurgical visualization. By itself, this system is a “point design,” an example of an advanced user interface technique. In this work, we argue that in order to understand why interaction techniques do or do not work, and to suggest possibilities for new techniques, it is important to move beyond point design and to introduce careful scientific measurement of human behavioral principles. In particular, we argue that the common-sense viewpoint that “two hands save time by working in parallel” may not always be an effective way to think about two-handed interface design because the hands do not necessarily work in parallel (there is a structure to two-handed manipulation) and because two hands do more than just save time over one hand (two hands provide the user with more information and can structure how the user thinks about a task). To support these claims, we present an interface design developed in collaboration with neurosurgeons which has undergone extensive informal usability testing, as well as a pair of formal experimental studies which investigate behavioral aspects of two-handed virtual object manipulation. Our hope is that this discussion will help others to apply the lessons in our neurosurgery application to future two-handed user interface designs.
Hybrid metal–polymer composites from functional block copolymers (2005)

Abstract The combination of metals and polymers in hybrid materials is a research area of great current interest. A number of methods for controlling the positioning of metallic species within polymer matrices on the nanometer scale have been developed. This highlight focuses on the use of functional block copolymers for the localization of metal species, especially nanoparticles, on the nanometer scale through block copolymer phase segregation. Research from the author's group on the use of alkyne‐functional block copolymers for the preparation of cobalt‐containing materials is discussed in this context. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4323–4336, 2005
Insulin-like Growth Factor (IGF)-binding Protein 5 Forms an Alternative Ternary Complex with IGFs and the Acid-labile Subunit (1998)

Up to 90% of circulating insulin-like growth factors (IGF-I and IGF-II) are carried in heterotrimeric complexes with a binding protein (IGFBP) and a liver-derived glycoprotein known as the acid-labile subunit. IGFBP-3 is considered unique among the six well characterized IGFBPs in its ability to complex with the acid-labile subunit. However, a basic carboxyl-terminal domain of IGFBP-3, known to be involved in its interaction with the acid-labile subunit, is shared by IGFBP-5, suggesting the possibility of ternary complexes containing IGFBP-5. We now demonstrate using three independent methods that human IGFBP-5, when occupied by IGF-I or IGF-II, forms ternary complexes of approximately 130 kDa with the acid-labile subunit. IGFBP-3 competes with approximately twice the potency of IGFBP-5 for the formation of such complexes. No other IGFBP complexes with the acid-labile subunit itself or competes with IGFBP-5 for complex formation. As observed for IGFBP-3, ternary complexes containing IGFBP-5 form preferentially in the presence of IGF-I, even though IGFBP-5 has a preferential affinity for IGF-II over IGF-I. By size fractionation chromatography, serum IGFBP-5 co-elutes predominantly with ternary complexes. The demonstration of IGFBP-5-containing ternary complexes indicates an unrecognized form of IGF transport in the circulation and an additional mechanism for regulating IGF bioavailability.
Protein kinase D1 (PKD1) activation mediates a compensatory protective response during early stages of oxidative stress-induced neuronal degeneration (2011)

Collectively, our results demonstrate that PKCδ-dependent activation of PKD1 represents a novel intrinsic protective response in counteracting early stage oxidative damage in neuronal cells. Our results suggest that positive modulation of the PKD1-mediated compensatory protective mechanism against oxidative damage in dopaminergic neurons may provide novel neuroprotective strategies for treatment of PD.
Formation of Tobacco-Specific Nitrosamines (TSNA) During Air-Curing: Conditions and Control (2005)

Abstract The present review deals with studies performed during several consecutive years on the effect of air-curing on tobacco-specific nitrosamine (TSNA) formation and quality of tobacco. Temperature, relative humidity, water content and water activity data were collected during curing of dark tobacco in traditional air-curing barns and bulk-curing barns of different sizes, and chemical analysis of the cured tobacco were performed.
Alloy Formation of Gold−Silver Nanoparticles and the Dependence of the Plasmon Absorption on Their Composition (1999)

Gold−silver alloy nanoparticles with varying mole fractions are prepared in aqueous solution by the co-reduction of chlorauric acid HAuCl4 and silver nitrate AgNO3 with sodium citrate. As the optical absorption spectra of their solutions show only one plasmon absorption it is concluded that mixing of gold and silver leads to a homogeneous formation of alloy nanoparticles. The maximum of the plasmon band blue-shifts linearly with increasing silver content. This fact cannot be explained by a simple linear combination of the dielectric constants of gold and silver within the Mie theory. On the other hand, the extinction coefficient is found to decrease exponentially rather than linearly with increasing gold mole fraction xAu. Furthermore, the size distribution of the alloy nanoparticles is examined using transmission electron microscopy (TEM). High-resolution TEM (HRTEM) also confirms the formation of homogeneous gold−silver alloy nanocrystals.
Adsorption calculations and modeling (1994)

'Adsorption Calculations and Modelling' provides readers with practical, useful information about how to make adsorption calculations and formulate models describing adsorption processes. Unlike most books on this subject, this book treats both gas phase adsorption and liquid phase adsorption with equal emphasis, and supplies a rigorous treatment of multi-component adsorption. It also covers adsorption applications in environmental applications including the use of impregnated adsorbents for protection against toxic gases and carbon adsorption in water and wastewater treatment
Administration of dendritic cells transduced with antisense oligodeoxyribonucleotides targeting CD80 or CD86 prolongs allograft survival (2003)

Transduction with antisense ODN targeting CD80 or CD86mRNA is a feasible and effective approach to modify DCs that renders them tolerogenic by inducing T-cell hyporesponsiveness and apoptosis. This may lead to the development of new therapeutic strategies in transplantation.
A low-cost transparent electric field sensor for 3d interaction on mobile devices (2014)

We contribute a thin, transparent, and low-cost design for electric field sensing, allowing for 3D finger and hand tracking and gestures on mobile devices. Our approach requires no direct instrumentation of the hand or body, and is non-optical, allowing for a compact form-factor that is resilient to ambient illumination. Our simple driver electronics are based on an off-the-shelf chip that removes the need for building custom analog electronics. We describe the design of our transparent electrode array, and present a machine learning algorithm for mapping from signal measurements at the receivers to 3D positions. We demonstrate non-contact motion gestures, and precise 3D hand and finger localization. We conclude by discussing limitations and future work.
Host defenses againstStaphylococcus aureusinfection require recognition of bacterial lipoproteins (2006)

Toll-like receptors and other immune-signaling pathways play important roles as sensors of bacterial pattern molecules, such as peptidoglycan, lipoprotein, or teichoic acid, triggering innate host immune responses that prevent infection. Immune recognition of multiple bacterial products has been viewed as a safeguard against stealth infections; however, this hypothesis has never been tested for Staphylococcus aureus, a frequent human pathogen. By generating mutations that block the diacylglycerol modification of lipoprotein precursors, we show here that S. aureus variants lacking lipoproteins escape immune recognition and cause lethal infections with disseminated abscess formation, failing to elicit an adequate host response. Thus, lipoproteins appear to play distinct, nonredundant roles in pathogen recognition and host innate defense mechanisms against S. aureus infections.
Image simulation and surface reconstruction of undercut features in atomic force microscopy (2007)

CD-AFMs (critical dimension atomic force microscopes) are instruments with servo-control of the tip in more than one direction. With appropriately "boot-shaped" or flared tips, such instruments can image vertical or even undercut features. As with any AFM, the image is a dilation of the sample shape with the tip shape. Accurate extraction of the CD requires a correction for the tip effect. Analytical methods to correct images for the tip shape have been available for some time for the traditional (vertical feedback only) AFMs, but were until recently unavailable for instruments with multi-dimensional feedback. Dahlen et al. [J. Vac. Sci. Technol. B23, pp. 2297-2303, (2005)] recently introduced a swept-volume approach, implemented for 2-dimensional (2D) feedback. It permits image simulation and sample reconstruction, techniques previously developed for the traditional instruments, to be extended for the newer tools. We have introduced [X. Qian and J. S. Villarrubia, <i>Ultramicroscopy</i>, in press] an alternative dexel-based method, that does the same in either 2D or 3D. This paper describes the application of this method to sample shapes of interest in semiconductor manufacturing. When the tip shape is known (e.g., by prior measurement using a tip characterizer) a 3D sample surface may be reconstructed from its 3D image. Basing the CD measurement upon such a reconstruction is shown here to remove some measurement artifacts that are not removed (or are incompletely removed) by the existing measurement procedures.
FUNCTIONAL IMPLICATIONS OF THE GROWTH-SUPPRESSOR ONCOPROTEIN P53 (1992)

The nuclear phosphoprotein p53, named according to its apparent molecular weight on SDS-polyacrylamide gels is expressed, albeit at low levels, in a variety of cell types. In normal cells, it seems to be required for cell proliferation whereas in transformed cells it is frequently a target for mutations. Wild-type p53 has a growth-suppressor function which is completely abolished in mutant p53. However, there is ample evidence that mutant p53 has not only lost the suppressor activity but contributes as a dominant oncogene to tumorigenesis. In line with these observations wild-type p53 has a growth inhibitory function even when introduced in rapidly proliferating tumor cells whereas mutant p53 has a growth promoting function. Wild-type p53 and mutant p53 exhibit different DNA binding activities which may be implicated in transcriptional regulation and in DNA replication. Furthermore, both wild-type and mutant p53 play a role in controlling the transition of cells through at least two different restriction points of the cell cycle. Besides these functions in growth control p53 also plays an active role during embryonic development. Expression of p53 is high in cells predetermined to differentiate and decreases upon differentiation. Since embryonic cells express wild-type p53, a progressive role during differentiation has to be attributed to wild-type p53. Thus, this review will try to highlight some of the significant advances in the most rapidly evolving field of the functional implications of p53 in cell biology and tumorigenesis.
The Free Radical Theory of Aging Matures (1998)

The free radical theory of aging, conceived in 1956, has turned 40 and is rapidly attracting the interest of the mainstream of biological research. From its origins in radiation biology, through a decade or so of dormancy and two decades of steady phenomenological research, it has attracted an increasing number of scientists from an expanding circle of fields. During the past decade, several lines of evidence have convinced a number of scientists that oxidants play an important role in aging. (For the sake of simplicity, we use the term oxidant to refer to all "reactive oxygen species," including O2-., H2O2, and .OH, even though the former often acts as a reductant and produces oxidants indirectly.) The pace and scope of research in the last few years have been particularly impressive and diverse. The only disadvantage of the current intellectual ferment is the difficulty in digesting the literature. Therefore, we have systematically reviewed the status of the free radical theory, by categorizing the literature in terms of the various types of experiments that have been performed. These include phenomenological measurements of age-associated oxidative stress, interspecies comparisons, dietary restriction, the manipulation of metabolic activity and oxygen tension, treatment with dietary and pharmacological antioxidants, in vitro senescence, classical and population genetics, molecular genetics, transgenic organisms, the study of human diseases of aging, epidemiological studies, and the ongoing elucidation of the role of active oxygen in biology.
Catalytic Unfolding and Proteolysis of Cytochrome c Induced by Synthetic Binding Agents (2004)

A class of polyanionic copper porphyrin dimers is shown to selectively increase the susceptibility of cytochrome c to proteolysis through binding-induced disruption of tertiary and secondary structure. The free energy of the protein conformation leading to proteolytic attack is stabilized by about 2.4 kcal/mol in the bound state. The proteolytic acceleration is catalytic in nature, requiring only a fraction of an equivalent of metalloporphyrin to effect complete, rapid digestion in the presence of a protease.