gebhart/patrepeval huggingface dataset:
On the construction and decoding of concatenated polar codes (2013)

A scheme for concatenating the recently invented polar codes with interleaved block codes is considered. By concatenating binary polar codes with interleaved Reed-Solomon codes, we prove that the proposed concatenation scheme captures the capacity-achieving property of polar codes, while having a significantly better error-decay rate. We show that for any ε > 0, and total frame length N, the parameters of the scheme can be set such that the frame error probability is less than 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-N 1-ε</sup> , while the scheme is still capacity achieving. This improves upon 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-N 0.5-ε</sup> , the frame error probability of Arikan's polar codes. We also propose decoding algorithms for concatenated polar codes, which significantly improve the error-rate performance at finite block lengths while preserving the low decoding complexity.
Comprehensive Detection and Serotyping of Human Adenoviruses by PCR and Sequencing (2004)

Human adenoviruses are common pathogens associated with many diseases, including respiratory, gastrointestinal, and ocular infections. Because they are now being increasingly recognized as agents of life-threatening disseminated infection in immunocompromised patients, robust and sensitive laboratory detection methods are needed for their rapid diagnosis. We describe here a PCR assay using a single primer pair, targeting a region of the hexon gene containing hypervariable region 7, that can detect all known human adenovirus serotypes and allows for serotype determination through the analysis of the nucleotide sequence. This comprehensive assay has proven effective for diagnosing adenoviruses at the serotype level in a broad range of patient specimens, including conjunctival, nasopharyngeal, stool, blood, and urine specimens.
Aneuploid sperm formation in rainbow trout exposed to the environmental estrogen 17α-ethynylestradiol (2008)

Environmental contaminants that mimic native estrogens (i.e., environmental estrogens) are known to significantly impact a wide range of vertebrate species and have been implicated as a source for increasing human male reproductive deficiencies and diseases. Despite the widespread occurrence of environmental estrogens and recognized detrimental effects on male vertebrate reproduction, no specific mechanism has been determined indicating how reduced fertility and/or fecundity is achieved. Previous studies show that male rainbow trout, Oncorhynchus mykiss, exposed to the environmental estrogen 17alpha-ethynylestradiol (EE2) before gamete formation and fertilization produce progeny with significantly reduced embryonic survival. To determine whether this observed decrease results from sperm chromosome alterations during spermatogenesis, male rainbow trout were exposed to 10 ng of EE2/l for 50 days. After exposure, semen was collected and sperm aneuploidy levels analyzed with two chromosome markers by fluorescent in situ hybridization. In vitro fertilizations were also conducted by using control and exposed sperm crossed to eggs from an unexposed female for offspring analysis. Evaluations for nucleolar organizer region number and karyotype were performed on developing embryos to determine whether sperm aneuploidy translated into embryonic aneuploidy. Results conclusively show increased aneuploid sperm formation due to EE2 exposure. Additionally, embryonic cells from propagated progeny of individuals possessing elevated sperm aneuploidy display high levels of embryonic aneuploidy. This study concludes that EE2 exposure in sexually developing male rainbow trout increases levels of aneuploid sperm, providing a mechanism for decreased embryonic survival and ultimately diminished reproductive success in EE2 exposed males.
Renal Artery Embolization Using a New Liquid Embolic Material Obtained by Partial Hydrolysis of Polyvinyl Acetate (Embol): Initial Experience in Six Patients (2000)

Embol is easy to use, its radiopacity is adequate and it is a safe and effective embolic material which provides immediate and total occlusion of renal vascular lesions.
CAMEO: a program for the logical prediction of the products of organic reactions (1990)

Abstract
In situ fluorescence microscopy visualization and characterization of nanometer-scale carbon nanotubes labeled with 1-pyrenebutanoic acid, succinimidyl ester (2006)

In order to characterize hybrid bio/abio technology utilizing carbon nanotubes (CNTs), in situ, real-time, yet noninvasive methods of accurate and reliable imaging are needed for observing CNTs’ interactions with biological materials, i.e., DNA, in biologically relevant aqueous environments. Optical visualization and characterization of individual CNTs in aqueous solutions were explored in this study using 1-pyrenebutanoic acid, succinimidyl ester (PSE) and a conventional fluorescence microscope. The results demonstrate the potential of fluorescence microscopy based on PSE-based staining methodology monitoring with nanometer resolution of individual CNTs and their manipulation with biological materials in bio/abio hybrid systems.
The promoters of the genes for colicin production, release and immunity in the ColA plasmid: effects of convergent transcription and Lex A protein (1986)

The initiation sites of transcription in vivo for the three genes caa, cai and cal encoding respectively colicin A (Caa), the immunity protein (Cai) and the pColA lysis protein (Cal) have been analysed by nuclease S1 mapping. This analysis demonstrates that caa and cal form an operon. cai is located between these two genes and transcribed in the opposite direction from its own promoter. The start sites for caa and cai have also been determined in vitro. For caa, the same start site was found in vivo and in vitro. In contrast, for cai the most efficient start site in vitro was not used in vivo. LexA protein strongly repressed the in vivo and in vitro transcription of the caa-cal operon. As determined by DNase 1 protection experiments, LexA protein binds with a high affinity to an approximately 40 bp long sequence just downstream of the Pribnow box. The sequence of the binding site is composed of two overlapped "SOS boxes". Two transcripts of the caa-cal operon were detected by blot hybridization. The longer mRNA can direct the synthesis of both Caa and Cal while the shorter one is terminated at the end of caa. When the transcription of the caa-cal operon is induced, there is a strong interference with cai transcription.
Regulation of Human Placental Development by Oxygen Tension (1997)

Cytotrophoblasts, specialized placental cells, proliferate early in pregnancy and then differentiate into tumor-like cells that establish blood flow to the placenta by invading the uterus and its vasculature. In this study, cytotrophoblasts cultured under hypoxic conditions (2 percent oxygen), mimicking the environment near the uterine surface before 10 weeks of gestation, continued proliferating and differentiated poorly. When cultured in 20 percent oxygen, mimicking the environment near uterine arterioles, the cells stopped proliferating and differentiated normally. Thus, oxygen tension determines whether cytotrophoblasts proliferate or invade, thereby regulating placental growth and cellular architecture.
The Green Book (2021)

Depth Psychology and Climate Change: The Green Book is a clarion call to all humanity to wake up and work together toward both imagining and actualizing a viable ecological transformation before it’s too late. Dale Mathers, editor of this thought-provoking volume, has recruited a talented team of Jungian analysts to help us understand the complexity of climate change denial as well as to offer suggestions as to what might be done to remedy this urgent ecological crisis. Each author of the fourteen chapters brings a unique depth psychology perspective to addressing these pressing ecosystem concerns.
Ganglioside antibodies and neuropathies (2008)

The wealth of scientific data is now driving the design of novel, targeted therapies. This preclinical research is outlined and suggestions made as to how this might be translated into clinical practice.
Continuous Production of Carbon‐Supported Cubic and Octahedral Platinum‐Based Catalysts Using Conveyor Transport System (2016)

A conveyor transport system is developed for the continuous production of carbon-supported uniform Pt nanocubes, and Pt<sub>3</sub> Ni nanocubes and octahedra in a single-reaction system under hot carbon monoxide environment. Oleylamine is critical for the high loading and even the dispersion of Pt nanocubes on a carbon support. The metal catalyst shows high performance in electrocatalytic oxidation of methanol.
PLGA Nanoparticle−Peptide Conjugate Effectively Targets Intercellular Cell-Adhesion Molecule-1 (2007)

Targeted delivery of therapeutics possesses the potential to localize therapeutic agents to a specific tissue as a mechanism to enhance treatment efficacy and abrogate side effects. Antibodies have been used clinically as therapeutic agents and are currently being explored for targeting drug-loaded nanoparticles. Peptides such as RGD peptides are also being developed as an inexpensive and stable alternative to antibodies. In this study, cyclo(1,12)PenITDGEATDSGC (cLABL) peptide was used to target nanoparticles to human umbilical cord vascular endothelial cell (HUVEC) monolayers that have upregulated intercellular cell-adhesion molecule-1 (ICAM-1) expression. The cLABL peptide has been previously demonstrated to possess high avidity for ICAM-1 receptors on the cell surface. Poly( dl-lactic-coglycolic acid) nanoparticles conjugated with polyethylene glycol and cLABL demonstrated rapid binding to HUVEC with upregulated ICAM-1, which was induced by treating cells with the proinflammatory cytokine, interferon-gamma. Binding of the nanoparticles could be efficiently blocked by preincubating cells with free peptide suggesting that the binding of the nanoparticles is specifically mediated by surface peptide binding to ICAM-1 on HUVEC. The targeted nanoparticles were rapidly endocytosed and trafficked to lysosomes to a greater extent than the untargeted PLGA-PEG nanoparticles. Verification of peptide-mediated nanoparticle targeting to ICAM-1 may ultimately lead to targeting therapeutic agents to inflammatory sites expressing upregulated ICAM-1.
Conjugation of N-acylated amino sugars to protein by reductive alkylation using sodium cyanoborohydride: application to an azo derivative of α-amanitin (1991)

Reductive alkylation mediated by cyanoborohydride is an attractive approach to the conjugation of small molecules, such as drugs, to proteins. This reaction is specific for protein amino groups and can be conducted under mild conditions with little risk of protein polymerization. However, the lability of the aldehyde function that is needed in such reactions presents a difficulty. We have investigated the use of derivatives of D-galactosamine and D-glucosamine in reductive alkylation, since these sugars contain aldehyde groups that are inherently protected and that may be readily linked to other molecules through their amino groups. The amino groups of these sugars were acylated with N-4-nitro-benzoylglycylglycine. Studies of the reductive coupling of the resultant adducts to bovine serum albumin revealed that conjugation to albumin is strongly dependent on cyanoborohydride, is much faster in the presence of borate, and shows a marked increase in rate between pH 7.0 and 9.0. In the presence of borate, the glucosamine derivative coupled much more rapidly than did the galactosamine derivative. The aryl nitro group of the glucosamine adduct was selectively reduced to an amine, diazotized, and reacted with alpha-amanitin to form an azo compound. This azo derivative was reductively coupled to form conjugates that inhibit calf thymus RNA polymerase II.
Axial Flow Catheter Pump for Circulatory Support (2002)

A percutaneously insertable catheter pump is technically feasible. Hydrodynamic efficacy allows sufficient cardiac support under simulated shock condition.
Tat- and Rev-directed antisense RNA expression inhibits and abolishes replication of human immunodeficiency virus type 1: a temporal analysis (1992)

Replication of human immunodeficiency virus type 1 (HIV-1) was inhibited by stable intracellular expression of antisense RNA in the human T-lymphoid cell line Jurkat. When the viral subregion encoding the HIV-1 activator proteins was targeted, the extent of antisense RNA-mediated inhibition was greater than 97% during the first 2 weeks postinfection. Later in the time course, productive HIV-1 infection broke through at high initial infective doses. However, at initial multiplicities of infection equal to or smaller than 0.1, HIV-1 production was not detectable during the 5 weeks of observation. The results underline the effectiveness of stable intracellular antisense RNA expression in inhibiting HIV-1 replication.
Efficacy and safety of rituximab in type II mixed cryoglobulinemia (2003)

The best treatment of type II mixed cryoglobulinemia (MC) has still to be defined. Antiviral treatment for the frequent underlying infectious trigger hepatitis C virus (HCV) may be ineffective, contraindicated, or not tolerated in a fraction of cases, whereas current immunosuppressive treatments may lead to relevant complications. Selective B-cell blockade with rituximab was used in this study, based on favorable results in preliminary experience. Fifteen consecutive patients with type II MC (HCV-related in 12 of 15) were treated with rituximab, 375 mg/m(2) intravenously weekly for 4 weeks. Only medium- to low-dose steroids were allowed, if already administered at the time of recruitment. All patients had active disease, poorly controlled or difficult to manage with previous treatments, including corticosteroids in all. Efficacy and safety of rituximab therapy were evaluated in the following 6 months. The overall follow-up after rituximab treatment ranged from 9 to 31 months. Rituximab proved effective on skin vasculitis manifestations (ulcers, purpura, or urticaria), subjective symptoms of peripheral neuropathy, low-grade B-cell lymphoma, arthralgias, and fever. Nephritis of recent onset went into remission in one case. Laboratory features, that is, significantly decreased serum rheumatoid factor and cryoglobulins and increased C4, were consistent with the clinical efficacy. Treatment was well tolerated, with no infectious complications. Thrombosis of retinal artery or self-limiting panniculitis occurred in one patient each. Rituximab may represent a safe and effective alternative to standard immunosuppression in type II MC. Controlled studies are needed to better define drug indications and the cost-efficacy profile in the different systemic manifestations.
In vitro and in vivo studies of neutral cyclometallated complexes against murine leukæmias (2005)

Cyclometallated µ-halogeno dimers derived from nitrogen donor ligands (1-phenylpyrazoles, 2-phenylpyridine, and 1-(2′-pyridyl)indole) were treated with unidentate nitrogen and phosphorus donor ligands to give a series of neutral monomeric palladium(II) and platinum(II) complexes. An initial prescreen of the complexes against the mouse lymphoid leukæmia cell line L1210 indicated that the complexes exhibited growth inhibitory activity over a relatively wide concentration range. Two factors that gave rise to increased activity were steric hindrance about the metal centre resulting from hindered ligands such as 2,6-dimethylpyridine, or the presence of a phosphorus donor ligand. Little correlation between palladium and platinum complexes was noted. Four complexes were selected for further in vivo study and, while none of the palladium complexes showed more than marginal activity against P388 leukæmia at doses below toxic levels, one platinum complex with a hindered metal centre did display significant antitumour activity against this model.Key words: cyclometallation, palladium, platinum, cytotoxicity, anticancer.
Plasmonic Properties of Supported Pt and Pd Nanostructures (2006)

The plasmonic properties of nanodisk arrays of Pt, Pd, and, for comparison, Ag are studied over a large size and spectral range and analyzed theoretically by an electrostatic model. Pt and Pd nanodisks exhibit broad localized surface plasmons with a higher sensitivity of the plasmon to the disk aspect ratio compared to Ag. Extinction cross-sections are generally about 50% smaller for Pt and Pd. The spectral plasmon positions, line-widths, and extinction cross-sections are well reproduced by the model.
Alternative splicing and genomic structure of the Wilms tumor gene WT1. (1991)

The chromosome 11p13 Wilms tumor susceptibility gene WT1 appears to play a crucial role in regulating the proliferation and differentiation of nephroblasts and gonadal tissue. The WT1 gene consists of 10 exons, encoding a complex pattern of mRNA species: four distinct transcripts are expressed, reflecting the presence or absence of two alternative splices. Splice I consists of a separate exon, encoding 17 amino acids, which is inserted between the proline-rich amino terminus and the zinc finger domains. Splice II arises from the use of an alternative 5' splice junction and results in the insertion of 3 amino acids between zinc fingers 3 and 4. RNase protection analysis demonstrates that the most prevalent splice variant in both human and mouse is that which contains both alternative splices, whereas the least common is the transcript missing both splices. The relative distribution of splice variants is highly conserved between normal fetal kidney tissue and Wilms tumors that have intact WT1 transcripts. The ratio of these different WT1 mRNA species is also maintained as a function of development in the mouse kidney and in various mouse tissues expressing WT1. The conservation in structure and relative levels of each of the four WT1 mRNA species suggests that each encoded polypeptide makes a significant contribution to normal gene function. The control of cellular proliferation and differentiation exerted by the WT1 gene products may involve interactions between four polypeptides with distinct targets and functions.
Platelet‐Derived Growth Factor‐Modulated Guided Tissue Regenerative Therapy (1995)

The goal of this study was to develop an effective regenerative therapy capable of achieving periodontal regeneration of Class III furcation defects. We attempted to achieve this goal by combining three therapeutic approaches. First, the lesion was protected by an expanded polytetrafluoroethylene barrier membrane that prevents migration of gingival fibroblasts as well as osteogenic cells from the mucoperiosteal flaps. Second, platelet-derived growth factor-BB (PDGF-BB), which has potent chemotactic and mitogenic effects on periodontal ligament fibroblasts (PDL), was used to promote migration of fibroblasts and their proliferation on the root surface. Third, the root surface, demineralized by citric acid conditioning, was chosen as the primary site for PDGF-BB application. The demineralized root surface appeared to have the capability of providing a sustained release of the applied growth factor. This seemed to facilitate rapid repopulation of PDL fibroblasts on the root surface and new PDL formation in the early stages of repair, which contributed to complete periodontal regeneration without root resorption and ankylosis in later stages. Combining these approaches, we developed a therapy referred to as "PDGF-modulated guided tissue regenerative therapy." Unlike guided tissue regenerative therapy alone (without PDGF-BB), this therapy effectively promoted periodontal regeneration of Class III furcation defects in the beagle dog without significant ankylosis or root resorption.
X-ray Structures of Torpedo californica Acetylcholinesterase Complexed with (+)-Huperzine A and (−)-Huperzine B:  Structural Evidence for an Active Site Rearrangement, (2002)

Kinetic and structural data are presented on the interaction with Torpedo californica acetylcholinesterase (TcAChE) of (+)-huperzine A, a synthetic enantiomer of the anti-Alzheimer drug, (-)-huperzine A, and of its natural homologue (-)-huperzine B. (+)-Huperzine A and (-)-huperzine B bind to the enzyme with dissociation constants of 4.30 and 0.33 microM, respectively, compared to 0.18 microM for (-)-huperzine A. The X-ray structures of the complexes of (+)-huperzine A and (-)-huperzine B with TcAChE were determined to 2.1 and 2.35 A resolution, respectively, and compared to the previously determined structure of the (-)-huperzine A complex. All three interact with the "anionic" subsite of the active site, primarily through pi-pi stacking and through van der Waals or C-H.pi interactions with Trp84 and Phe330. Since their alpha-pyridone moieties are responsible for their key interactions with the active site via hydrogen bonding, and possibly via C-H.pi interactions, all three maintain similar positions and orientations with respect to it. The carbonyl oxygens of all three appear to repel the carbonyl oxygen of Gly117, thus causing the peptide bond between Gly117 and Gly118 to undergo a peptide flip. As a consequence, the position of the main chain nitrogen of Gly118 in the "oxyanion" hole in the native enzyme becomes occupied by the carbonyl of Gly117. Furthermore, the flipped conformation is stabilized by hydrogen bonding of Gly117O to Gly119N and Ala201N, the other two functional elements of the three-pronged "oxyanion hole" characteristic of cholinesterases. All three inhibitors thus would be expected to abolish hydrolysis of all ester substrates, whether charged or neutral.
Epitope spreading in systemic lupus erythematosus: Identification of triggering peptide sequences (2002)

International audience
Videofluoroscopic Studies of Swallowing Dysfunction and the Relative Risk of Pneumonia (2003)

Our findings indicate that the likelihood of developing pneumonia is directly related to the degree of swallowing dysfunction seen on videofluoroscopic studies. Patients with no laryngeal penetration-regardless of whether they had normal or abnormal swallowing-have the lowest risk of developing pneumonia. Patients with laryngeal penetration, tracheobronchial aspiration, or silent tracheobronchial aspiration are, in increasing order of magnitude, significantly more likely to develop pneumonia than patients with normal swallowing.
Primary structure of the variable regions of two canine immunoglobulin heavy chains (1977)

The complete amino acid sequences of the variable regions of two canine immunoglobulin heavy chains have been determined by automated Edman degradation and found to be strongly homologous to the human VHIII subgroup. The canine sequences were identical with each other at 76 of 113 residue positions. Twenty-three of the 37 differences are located within the four hypervariable regions previously defined by the sequences of several human VHIII proteins. Forty-five of 77 framework residue positions are invariant in the seven human and two canine VHIII proteins which have been completely sequences. The canine proteins are 78% homologous to the framework of the human prototype. Phylogenetically associated residues before the first hypervariable region were confirmed and several potential phylogenetically associated residues were identified between the first and third hypervariable regions. This study represents the first complete amino acid sequences of VH regions of spontaneously occurring, nonhuman homogeneous immunoglobulins. The date demonstrate a high degree of preservation of VHIII structure in another species.