gebhart/patrepeval huggingface dataset:
In vivocharacterization of activatable cell penetrating peptides for targeting protease activity in cancer (2009)

Activatable cell penetrating peptides (ACPPs) are novel in vivo targeting agents comprised of a polycationic cell penetrating peptide (CPP) connected via a cleavable linker to a neutralizing polyanion (). Adsorption and uptake into cells are inhibited until the linker is proteolyzed. An ACPP cleavable by matrix metalloproteinase-2 (MMP-2) in vitro was the first one demonstrated to work in a tumor model in vivo, but only HT-1080 xenografts and resected human squamous cell carcinomas were tested. Generality to other cancer types, in vivo selectivity of ACPPs for MMPs, and spatial resolution require further characterization. We now show that ACPPs can target many xenograft tumor models from different cancer sites, as well as a thoroughly studied transgenic model of spontaneous breast cancer (mouse mammary tumor virus promoter driving polyoma middle T antigen, MMTV-PyMT). Pharmacological inhibitors and genetic knockouts indicate that current ACPPs are selective for MMP-2 and MMP-9 in the above in vivo models. In accord with the known local distribution of MMP activity, accumulation is strongest at the tumor-stromal interface in primary tumors and associated metastases, indicating better spatial resolution (<50 mum) than other currently available MMP-cleavable probes. We also find that background uptake of ACPPs into normal tissues such as cartilage can be decreased by appending inert macromolecules of 30-50 KDa to the polyanionic inhibitory domain. Our results validate an approach that should generally deliver imaging agents and chemotherapeutics to sites of invasion, tumor-promoting inflammation, and metastasis.
Cutaneous lymphoma incidence patterns in the United States: a population-based study of 3884 cases (2009)

There have been no prior large population-based studies focusing on cutaneous lymphomas (CL) in the United States. Using the Surveillance, Epidemiology and End Results (SEER) program data, we analyzed age-adjusted CL incidence rates (IRs) and survival rates by sex and race/ethnicity. There were 3884 CLs diagnosed during 2001-2005. Cutaneous T-cell lymphomas (CTCLs) accounted for 71% (age-adjusted incidence rate [IR] = 7.7/1 000 000 person-years), whereas cutaneous B-cell lymphomas(CBCLs) accounted for 29% (IR = 3.1/1 000 000 person-years). Males had a statistically significant higher IR of CL than females (14.0 vs 8.2/1 000 000 person-years, respectively; male-female IR ratio [M/F IRR] = 1.72; P < .001). CL IRs were highest among blacks and non-Hispanic whites (both 11.5/1 000 000 person-years), followed by Hispanic whites (7.9) and Asian/Pacific Islanders (7.1). The CTCL IR was highest among blacks (10.0/1 000 000 person-years), whereas the CBCL IR was highest among non-Hispanic whites (3.5). Over the past 25 years, the CL IR increased from 5.0/1 000 000 person-years during 1980-1982 to 14.3 during 2001-2003. During 2004-2005, the CL IR was 12.7. This recent apparent change could be incomplete case ascertainment or potential leveling off of IRs. CLs rates vary markedly by race and sex, supporting the notion that they represent distinct disease entities.
Dimensioning of self-healing rings and their interconnections (2002)

A new hierarchical self-healing ring (H-SHR) architecture for survivability is proposed and dimensioned. First, the dimensioning of single SHRs (unidirectional and bidirectional) is considered. Closed form expressions of required capacity are presented for single SHRs under three uniform demand patterns. For general demand, a new routing algorithm which complements the shortest path routing algorithm in attempt to reduce the capacity requirement is proposed. Then it is shown that the dimensioning of H-SHRs can be converted into the dimensioning of each single rings inside it by performing translation of original demand. Thus the new routing algorithm can be used in dimensioning of H-SHR networks. Closed form expressions for uniform H-SHRs using shortest path routing are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
On the benefits of acquiring peptide fragment ions at high measured mass accuracy (2008)

The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages.
Molecular structure, polymorphism, and toxicity of lantadene a, the pentacyclic triterpenoid from the hepatotoxic plant Lantana camara (1991)

Lantadene A (22 beta-angeloyloxy-3-oxo-olean-12-en-28-oic acid), a pentacyclic triterpenoid compound from lantana (Lantana camara) leaves has been obtained in two polymorphic forms I and II. Form I had white, fluffy, and rod-shaped uniform crystals. Form II particles were irregular, shining, and polyhedral. The two forms differed in melting behavior. The powder x-ray diffraction of form I showed sharp peaks whereas from II did not contain distinct peaks. From single-crystal three-dimensional x-ray structure determination, the molecular structure of form I has been established. A/B and B/C rings of the molecule are trans fused while D/E rings are cis fused. The packing of the molecule is stabilized by hydrogen bonding. Form I of lantadene A was non-toxic to guinea pigs on oral administration. Form II induced ictericity and toxicity associated with decrease in feed intake and fecal output, hepatomegaly, increase in plasma bilirubin, and acid phosphatase activity.
Silicon nanoparticle synthesis by short-period thermal anneals at atmospheric pressure in argon (2011)

Silicon nanoparticles have been studied for a wide variety of applications including nanoelectronic, photovoltaic, and optoelectronic devices. In this work, silicon nanoparticles were synthesized by short-period annealing of silicon-on-insulator substrates to temperatures ranging between 600 and 900 °C in argon gas at atmospheric pressure. Two different top silicon layers were deposited by ion-beam sputtering onto oxidized substrates. The thinner 6 nm top layer samples were annealed to temperatures for 30 s periods while thicker 15 nm top layer samples were annealed for 60 s periods. For both sets of samples, nanoparticles were observed to form at all the anneal temperatures through imaging by AFM. One long-period UHV anneal study, with 30-min anneal times, observed nanoparticle formation at temperatures similar to the current work while another similar long-period UHV anneal reported nanoparticle formation only above well-defined formation temperatures that depended upon the starting top layer thickness. In the current work, the average nanoparticle radius was found to increase both with the final anneal temperature and anneal period. For the highest anneal temperatures of the 6 nm top layer samples, a changing surface topography indicated that the thinner Si source layer was becoming depleted and the nanoparticle formation process was nearing completion. No such changes were observed for the thicker 15 nm samples at the same temperatures.
Heparin-Induced Thrombocytopenia (HIT): An Overview of 230 Patients Treated with Orgaran (Org 10172) (1993)

Heparin-induced thrombocytopenia (HIT) with thrombosis occurs in about 1 in 2,000 heparin-treated patients. The arterial or venous thromboses may threaten life and limb hence alternative anticoagulation is needed. Some alternative treatments are possible i.e. LMWH, Ancrod, prostacyclin analogues, Dextran, aspirin and oral anticoagulants, but each has its drawbacks. This report reviews treatment of HIT patients with Orgaran (Org 10172), a low molecular weight heparinoid. Because of its proven antithrombotic activity Orgaran was used to treat 230 HIT patients. One hundred and fifty, nine patients presented with at least one thrombotic problem, which in 88 was due to the heparin use. 92.8% of the patients were considered to have adequately responded to Orgaran during the treatment period. Fifty-nine deaths (25.7%) occurred of which 7 (3.0%) were attributed to Orgaran use. The remaining 52 deaths, 27 of which occurred after Orgaran treatment was successfully terminated, were due to the severe underlying disorders in these patients. These results and the lower cross-reactivity rate (approximately 10%) with the heparin-induced antibody compared with that of the LMWH (> 90%) suggest that although problems remain, Orgaran can be a valuable alternative treatment for patients who suffer from HIT and who require anticoagulation.
Tissue engineering of cardiac valves: re-seeding of acellular porcine aortic valve matrices with human mesenchymal progenitor cells. (2005)

This study has shown, for the first time, that human MPC have the capacity to infiltrate an acellular porcine valve matrix under static conditions in vitro. Future studies will comprise culture under pulsatile flow in a physiological heart valve bioreactor to maintain the desired cell phenotype and increase cell density.
Serum amyloid A‐derived peptides, present in human rheumatic synovial fluids, induce the secretion of interferon‐γ by human CD4+ T‐lymphocytes (2000)

Serum amyloid A (SAA) is a major acute-phase protein whose biochemical functions remain largely obscure. Human rheumatic synovial fluids were screened by high performance liquid chromatography mass spectrometry for SAA-derived peptides, specifically the sequence AGLPEKY (SAA(98-104)) which was previously shown to modulate various leukocyte functions. Two such fluids were found to contain a truncated version of SAA(98-104). Synthetic SAA(98-104) and several of its analogs were shown capable of binding isolated human CD(4)(+) T-lymphocytes and stimulating them to produce interferon-gamma. Given the high acute-phase serum level of SAA and its massive proteolysis by inflammatory related enzymes, SAA-derived peptides may be involved in host defense mechanisms.
Identification of the structural mutation responsible for the dibucaine-resistant (atypical) variant form of human serum cholinesterase. (1989)

A point mutation in the gene for human serum cholinesterase was identified that changes Asp-70 to Gly in the atypical form of serum cholinesterase. The mutation in nucleotide 209, which changes codon 70 from GAT to GGT, was found by sequencing a genomic clone and sequencing selected regions of DNA amplified by the polymerase chain reaction. The entire coding sequences for usual and atypical cholinesterases were compared, and no other consistent base differences were found. A polymorphic site near the C terminus of the coded region was detected, but neither allele at this locus segregated consistently with the atypical trait. The nucleotide-209 mutation was detected in all five atypical cholinesterase families examined. There was complete concordance between this mutation and serum cholinesterase phenotypes for all 14 heterozygous and 6 homozygous atypical subjects tested. The mutation causes the loss of a Sau3A1 restriction site; the resulting DNA fragment length polymorphism was verified by electrophoresis of 32P-labeled DNA restriction fragments from usual and atypical subjects. Dot-blot hybridization analysis with a 19-mer allele-specific probe to the DNA amplified by the polymerase chain reaction distinguished between the usual and atypical genotypes. We conclude that the Asp-70----Gly mutation (acidic to neutral amino acid substitution) accounts for reduced affinity of atypical cholinesterase for choline esters and that Asp-70 must be an important component of the anionic site. Heterogeneity in atypical alleles may exist, but the Asp-70 point mutation may represent an appreciable portion of the atypical gene pool.
Effect of reducing disulfide-containing proteins on electrospray ionization mass spectra (1990)

Electrospray ionization produces multiply charged molecular ions for biomolecules with molecular weights in excess of 100,000. This allows mass spectrometers with limited mass-to-charge range to extend their molecular weight range by a factor equal to the number of charges. The maximum number of observed charges for peptides and smaller proteins correlates well with the number of basic amino acid residues (Arg, Lys, His), except for disulfide-containing molecules, such as lysozyme and bovine albumin. However, reduction of disulfide linkages with 1,4-dithiothreitol (Cleland's reagent) may allow the protein to be in an extended conformation and make "buried" basic residues available for protonation to yield higher charged molecular ions by the electrospray ionization process. For larger proteins reduction of disulfide bridges greatly increases the maximum charge state, but charging of basic amino acid residues remains less efficient than for smaller proteins.
Human Tribbles 3 Protects Nuclear DNA from Cytidine Deamination by APOBEC3A (2012)

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Functional Genomics: Expression Analysis of Escherichia coli Growing on Minimal and Rich Media (1999)

DNA arrays of the entire set of Escherichia coli genes were used to measure the genomic expression patterns of cells growing in late logarithmic phase on minimal glucose medium and on Luria broth containing glucose. Ratios of the transcript levels for all 4,290 E. coli protein-encoding genes (cds) were obtained, and analysis of the expression ratio data indicated that the physiological state of the cells under the two growth conditions could be ascertained. The cells in the rich medium grew faster, and expression of the majority of the translation apparatus genes was significantly elevated under this growth condition, consistent with known patterns of growth rate-dependent regulation and increased rate of protein synthesis in rapidly growing cells. The cells grown on minimal medium showed significantly elevated expression of many genes involved in biosynthesis of building blocks, most notably the amino acid biosynthetic pathways. Nearly half of the known RpoS-dependent genes were expressed at significantly higher levels in minimal medium than in rich medium, and rpoS expression was similarly elevated. The role of RpoS regulation in these logarithmic phase cells was suggested by the functions of the RpoS dependent genes that were induced. The hallmark features of E. coli cells growing on glucose minimal medium appeared to be the formation and excretion of acetate, metabolism of the acetate, and protection of the cells from acid stress. A hypothesis invoking RpoS and UspA (universal stress protein, also significantly elevated in minimal glucose medium) as playing a role in coordinating these various aspects and consequences of glucose and acetate metabolism was generated. This experiment demonstrates that genomic expression assays can be applied in a meaningful way to the study of whole-bacterial-cell physiology for the generation of hypotheses and as a guide for more detailed studies of particular genes of interest.
Clinical Trials of Transplant Tolerance: Slow But Steady Progress (2003)

The search for tolerance therapies that would thwart the alloimmune response following organ transplantation while preserving a patient's protective immune response has been a formidable goal for clinical immunologists. Over the past few decades, a more detailed understanding of the molecular events associated with T-cell recognition and activation has demonstrated the feasibility of various tolerance approaches, such as costimulation blockade, in numerous animal models of both autoimmunity and transplantation. Yet, only a few promising new therapies have reached the early stages of human clinical development. In contrast, the use of T-cell depleting induction therapy has become widespread, and new trials have been designed with immunosuppressive drug withdrawal in mind. Furthermore, nonmyeloablative mixed chimeric approaches have allowed complete immunosuppressive withdrawal in some limited cases. In the course of these investigations, however, what has become increasingly clear is that the distinctions between immunosuppression and tolerance have been blurred as the success and durability of the therapies rely as much on the state of the organ and organism as they do the mechanism of action of the drug. In this review, we provide a summary of the progress and lessons in promoting clinical transplant tolerance and an overview of promising agents.
Gemcitabine Transport in Xenopus Oocytes Expressing Recombinant Plasma Membrane Mammalian Nucleoside Transporters (1999)

Mammalian nucleoside transporters vary widely in their affinity and capacity to transport gemcitabine. Variation in the tumor and tissue distribution of plasma membrane nucleoside transporter proteins may contribute to the solid tumor activities and schedule-dependent toxic effects of gemcitabine.
A Bipedal Walking Robot with Efficient and Human-Like Gait (2006)

Here we present the design of a passive-dynamics based, fully autonomous, 3-D, bipedal walking robot that uses simple control, consumes little energy, and has human-like morphology and gait. Design aspects covered here include the freely rotating hip joint with angle bisecting mechanism; freely rotating knee joints with latches; direct actuation of the ankles with a spring, release mechanism, and reset motor; wide feet that are shaped to aid lateral stability; and the simple control algorithm. The biomechanics context of this robot is discussed in more detail in [1], and movies of the robot walking are available at Science Online and http://www.tam.cornell.edu/~ruina/powerwalk.html. This robot adds evidence to the idea that passive-dynamic approaches might help design walking robots that are simpler, more efficient and easier to control.
The Anti-Cloak (2008)

A kind of transformation media, which we shall call the "anti-cloak", is proposed to partially defeat the cloaking effect of the invisibility cloak. An object with an outer shell of "anti-cloak" is visible to the outside if it is coated with the invisible cloak. Fourier-Bessel analysis confirms this finding by showing that external electromagnetic wave can penetrate into the interior of the invisibility cloak with the help of the anti-cloak.
Plant Mitochondrial Recombination Surveillance Requires Unusual RecA and MutS Homologs (2007)

For >20 years, the enigmatic behavior of plant mitochondrial genomes has been well described but not well understood. Chimeric genes appear, and occasionally are differentially replicated or expressed, with significant effects on plant phenotype, most notably on male fertility, yet the mechanisms of DNA replication, chimera formation, and recombination have remained elusive. Using mutations in two important genes of mitochondrial DNA metabolism, we have observed reproducible asymmetric recombination events occurring at specific locations in the mitochondrial genome. Based on these experiments and existing models of double-strand break repair, we propose a model for plant mitochondrial DNA replication, chimeric gene formation, and the illegitimate recombination events that lead to stoichiometric changes. We also address the physiological and developmental effects of aberrant events in mitochondrial genome maintenance, showing that mitochondrial genome rearrangements, when controlled, influence plant reproduction, but when uncontrolled, lead to aberrant growth phenotypes and dramatic reduction of the cell cycle.
All change at Holliday junction (1997)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Structure‐based optimization of designed Armadillo‐repeat proteins (2012)

The armadillo domain is a right-handed super-helix of repeating units composed of three α-helices each. Armadillo repeat proteins (ArmRPs) are frequently involved in protein-protein interactions, and because of their modular recognition of extended peptide regions they can serve as templates for the design of artificial peptide binding scaffolds. On the basis of sequential and structural analyses, different consensus-designed ArmRPs were synthesized and show high thermodynamic stabilities, compared to naturally occurring ArmRPs. We determined the crystal structures of four full-consensus ArmRPs with three or four identical internal repeats and two different designs for the N- and C-caps. The crystal structures were refined at resolutions ranging from 1.80 to 2.50 Å for the above mentioned designs. A redesign of our initial caps was required to obtain well diffracting crystals. However, the structures with the redesigned caps caused domain swapping events between the N-caps. To prevent this domain swap, 9 and 6 point mutations were introduced in the N- and C-caps, respectively. Structural and biophysical analysis showed that this subsequent redesign of the N-cap prevented domain swapping and improved the thermodynamic stability of the proteins. We systematically investigated the best cap combinations. We conclude that designed ArmRPs with optimized caps are intrinsically stable and well-expressed monomeric proteins and that the high-resolution structures provide excellent structural templates for the continuation of the design of sequence-specific modular peptide recognition units based on armadillo repeats.
Characterization of common salivary protein 1, a product of rat submandibular, sublingual, and parotid glands. (1993)

We have isolated and characterized cDNA clones derived from a developmentally regulated neonatal rat submandibular gland salivary protein gene called "common salivary protein 1" (CSP1). Identical clones were also identified in cDNA libraries from adult male parotid, submandibular, and sublingual glands. CSP1 transcripts are at least 10-fold more abundant in the sublingual gland than in the submandibular or parotid glands. In situ hybridization and immunocytochemical localization demonstrated the presence of CSP1 transcripts and proteins in sublingual gland serous demilune cells, parotid and submandibular gland intercalated duct cells, and in the type III (proacinar) cells of the neonatal submandibular gland. This cell-type distribution is similar to that described by Ball and colleagues (Ball, W. D., Hand, A. R., and Johnson, A. O. (1988) Dev. Biol. 125, 265-279) for the developmentally regulated submandibular gland B1-immunoreactive proteins. Immunoblotting of salivary secretion identified proteins of M(r) 20,000 in sublingual, 16,000 in submandibular and 22,000 and 16,000 in parotid gland. The M(r) 20,000 sublingual and 22,000 parotid proteins represent N-glycosylated forms of a M(r) 16,000 apoprotein, suggesting that these salivary proteins arise by post-translational modification of a common precursor.