gebhart/patrepeval huggingface dataset:
Electrochemical Gate-Controlled Conductance of Single Oligo(phenylene ethynylene)s (2005)

We have studied electron transport properties of unsubstituted oligo(phenylene ethynylene) (OPE) (1) and nitro-substituted OPE (2) covalently bound to two gold electrodes. The conductance values of single 1 and 2 are approximately 13 and approximately 6 nS, respectively. In addition to a decrease in the conductance, the presence of the nitro moiety leads to asymmetric I-V characteristics and a negative differential resistance-like (NDR-like) behavior. We have altered the nitro-substituted OPE by electrochemically reducing the nitro group and by varying the pH of the electrolyte. The conductance decreases linearly with the electron-withdrawing capability (i.e., Hammett substituent values) of the corresponding reduced species. In contrast, the conductance of 1 is independent of the pH and the electrode potential.
Effects of Drug Loading on the Antitumor Activity of a Monoclonal Antibody Drug Conjugate (2004)

By decreasing drug loading per antibody, the therapeutic index was increased demonstrating that drug loading is a key design parameter for antibody-drug conjugates.
Developmental regulation of myosin gene expression in mouse cardiac muscle. (1990)

Expression of the two isoforms of cardiac myosin heavy chain (MHC), MHC alpha and MHC beta, in mammals is regulated postnatally by a variety of stimuli, including serum hormone levels. Less is known about the factors that regulate myosin gene expression in rapidly growing cardiac muscle in embryos. Using isoform-specific 35S-labeled cRNA probes corresponding to the two MHC genes and the two myosin alkali light chain (MLC) genes expressed in cardiac muscle, we have investigated the temporal and spatial pattern of expression of these different genes in the developing mouse heart by in situ hybridization. Between 7.5 and 8 d post coitum (p.c.), the newly formed cardiac tube begins to express MHC alpha, MHC beta, MLC1 atrial (MLC1A), and MLC1 ventricular (MLC1V) gene transcripts at high levels throughout the myocardium. As a distinct ventricular chamber forms between 8 and 9 d p.c., MHC beta mRNAs begin to be restricted to ventricular myocytes. This process is complete by 10.5 d p.c. During this time, MHC alpha mRNA levels decrease in ventricular muscle cells but continue to be expressed at high levels in atrial muscle cells. MHC alpha transcripts continue to decrease in ventricular myocytes until 16 d p.c., when they are detectable at low levels, but then increase, and finally replace MHC beta mRNAs in ventricular muscle by 7 d after birth. Like MHC beta, MLC1V transcripts become restricted to ventricular myocytes, but at a slower rate. MLC1V mRNAs continue to be detected at low levels in atrial cells until 15.5 d p.c. MLC1A mRNA levels gradually decrease but are still detectable in ventricular cells until a few days after birth. This dynamic pattern of changes in the myosin phenotype in the prenatal mouse heart suggests that there are different regulatory mechanisms for cell-specific expression of myosin isoforms during cardiac development.
A Systematic Review of Secretin for Children With Autism Spectrum Disorders (2011)

Secretin has been studied extensively in multiple randomized controlled trials, and there is clear evidence that it lacks benefit. The studies of secretin included in this review uniformly point to a lack of significant impact of secretin in the treatment of ASD symptoms. Given the high strength of evidence for a lack of effectiveness, secretin as a treatment approach for ASDs warrants no further study.
Synthesis and Alignment of Silver Nanorods and Nanowires and the Formation of Pt, Pd, and Core/Shell Structures by Galvanic Exchange Directly on Surfaces (2007)

Here we describe the synthesis of Ag nanorods (NRs) (aspect ratio <20) and nanowires (NWs) (aspect ratio > or =20) directly on surfaces by seed-mediated growth. The procedure involves attaching gold seed nanoparticles (Au NPs) to 3-mercaptopropyltrimethoxysilane (MPTMS)-functionalized silicon or glass surfaces and growing them into NRs/NWs by placing the substrates into a solution containing cetyltrimethylammonium bromide (CTAB), silver nitrate, and ascorbic acid with the pH ranging from 7 to 12. Under our conditions, Ag NRs/NWs grow optimally at pH 10.6 with a 3% yield, where spherical, triangular, and hexagonal nanostructures represent the other byproducts. The length of Ag NRs/NWs ranges from 50 nm to more than 10 microm, the aspect ratio (AR) ranges from 1.4 to >300, and the average diameter is approximately 35 nm. Approximately 40% of the 1D structures are NRs, and 60% are NWs as defined by their ARs. We also report the alignment of Ag NRs/NWs directly on surfaces by growing the structures on amine-functionalized Si(100) surfaces after an amidation reaction with acetic acid and a method to improve the percentage of Ag NRs/NWs on the surface by removing structures of other shapes with adhesive tape. Surface-grown Ag NRs/NWs also react with salts of palladium, platinum, and gold via galvanic exchange reactions to form high-surface-area 1D structures of the corresponding metal. The combination of the seed-mediated growth of Ag on Au NRs followed by the galvanic exchange of Ag with Pd leads to interesting core/shell NRs grown directly on surfaces. We used scanning electron microscopy, UV-vis spectroscopy, and X-ray photoelectron spectroscopy to characterize the surface-grown nanostructures.
Bioactive sol‐gel foams for tissue repair (2001)

Bioactive glasses are known to have the ability to regenerate bone, but their use has been restricted mainly to powder, granules, or small monoliths. This work reports on the development of sol-gel foams with potential applications as bone graft implants or as templates for the in vitro synthesis of bone tissue for transplantation. These bioactive foams exhibit a hierarchical structure with interconnected macropores (10-500 microm) and a mesoporous framework typical of gel-glasses (pores of 2-50 nm). The macroporous matrixes were produced through a novel route that comprises foaming of sol-gel systems. Three glass systems were tested to verify the applicability of this manufacturing route, namely SiO(2), SiO(2)-CaO, and SiO(2)-CaO-P(2)O(5). This new class of material combines large pores to support vascularization and 3-D tissue growth with the ability that bioactive materials have to provide bone-bonding and controlled release of ionic biologic stimuli to promote bone cell proliferation by gene activation.
Oct4 distribution and level in mouse clones: consequences for pluripotency (2002)

Somatic cell clones often fail at a developmental stage coincident with commencement of differentiation. The transcription factor Oct4 is expressed during cleavage stages and is essential for the differentiation of the blastocyst. Oct4 expression becomes restricted to the inner cell mass and epiblast. After gastrulation Oct4 is active only in germ cells and is silent in somatic cells. Here, Oct4 and an Oct4-GFP transgene were used as markers for which gene reprogramming could be directly related to the developmental potential of somatic cell clones. Cumulus cell clones initiated Oct4 expression at the correct stage but showed an incorrect spatial expression in the majority of blastocysts. The ability of clones to form outgrowths was reduced, and the outgrowths had low or even undetectable levels of Oct4 RNA or GFP. The quality of GFP signals in blastocysts correlated with the ability to generate outgrowths that maintain GFP expression and the frequency of embryonic stem (ES) cell derivation. Abnormal Oct4 expression in clones is either directly or indirectly caused by reprogramming errors and is indicative of a general failure to reset the genetic program. The abnormal Oct4 expression may be associated with aberrant expression of other crucial developmental genes, leading to abnormalities at various embryonic stages. Regardless of other genes, the variations observed in Oct4 levels alone account for the majority of failures currently observed for somatic cell cloning.
Suprasternal direct aortic approach transcatheter aortic valve replacement avoids sternotomy and thoracotomy: first-in-man experience (2015)

The SuprAA System provides direct aortic/innominate access without sternal or thoracotomy incision. Patient recovery to normal activity is maximized, sheath size limitations are eliminated and valve deployment is precise. This innovative system creates a new and exciting minimally invasive approach for high-risk patients with aortic stenosis.
Function and Regulation of the β3 Integrins in Hemostasis and Vascular Biology (1995)

The beta 3 integrins, alpha IIb beta 3 and alpha V beta 3, are prominently expressed on the surfaces of platelets and endothelial cells, respectively. This vascular localization places them in a strategic position to perform adhesive functions necessary for hemostasis, wound healing and angiogenesis. In addition, these integrins are now known to serve a signaling function, whereby environmental cues on either side of the plasma membrane can be transmitted across the membrane to the other side. Indeed, preliminary studies indicate that these dual function receptors are wired to other signaling pathways within platelets and endothelial cells, thus helping to explain how integrin-mediated cell anchorage can affect cytoskeletal organization and cell motility as well as endothelial cell growth, differentiation and apoptosis.
Antigenic differentiation of avian pneumovirus isolates using polyclonal antisera and mouse monoclonal antibodies (1993)

Avian pneumovirus (AVP) isolates F83, CC220 and 1260 from Great Britain and 1556, 657/4, 2119 and 872/S from France, Hungary, Italy and Spain, respectively, were compared in ELISA and virus neutralization (VN) tests for reactions with chicken polyclonal sera against each of the viruses and monoclonal antibodies (MAbs) against two British isolates. ELISA test results using the polyclonal antisera indicated that all seven viruses were antigenically related, but some variation between strains could be detected, especially when antigens were prepared from infected cells using Nonidet P40 (NP40) rather than freezing and thawing. In VN tests results also showed that all viruses tested were related but there was evidence that the three British isolates showed closer relationships with each other than with the viruses from Italy, Hungary and Spain. In ELISA tests, isolates F83 and 1556 bound all 11 MAbs and 1260 reacted with 10/11 MAbs. Isolate CC220 showed reaction with all the MAbs but for 8/11 MAbs the optical density differences were low. Isolates 2119 and 872/S both reacted only with MAb 4 and none of the MAbs reacted with 657/4.
Suppression of growth and protein secretion defects in Escherichia coli secA mutants by decreasing protein synthesis (1986)

We devised a new selection for conditionally lethal suppressors of secA mutants. This selection allows the isolation of both temperature-sensitive and cold-sensitive suppressor mutations, whereas previous studies were limited to nonlethal or cold-sensitive suppressor mutations. Two temperature-sensitive suppressor mutations lie in genes required for protein synthesis: asnS, the gene for the asparaginyl-tRNA synthetase, and divE, which encodes the tRNASer1. A previously characterized mutation in alaS, the gene for the alanyl-tRNA synthetase, suppresses the growth and secretion defects of a secA mutant. Although the primary effects of these suppressor mutations are different, it is likely that they cause suppression of secA mutations by altering the rate of protein synthesis, since the protein synthesis inhibitors, chloramphenicol and tetracycline, also suppress secA mutations. Chloramphenicol also suppresses the growth defect of certain other sec mutants. We postulate that the impaired secretory capacity of sec mutants can be offset by decreasing the rate of elongation of secreted proteins or by decreasing the total amount of secreted proteins per cell. The results indicate that our initial goal to identify cellular secretory components as suppressors of secA mutations might be difficult to achieve because of a high frequency of nonspecific suppressors that alter protein synthesis. Unexpectedly, the suppressor approach provides a direct genetic selection for mutants in protein synthesis.
A Novel Human Gene Closely Related to the abl Proto-Oncogene (1986)

A DNA sequence related to the abl proto-oncogene was identified in human placenta. Molecular cloning and nucleotide sequence analysis revealed two putative exons whose predicted amino acid sequence was most homologous to the corresponding sequences of c-abl and v-abl but was related to other tyrosine kinase genes as well. The new sequence was localized by in situ hybridization and somatic cell genetic analysis to human chromosome 1q24-25, which differs from the location of any previously identified tyrosine kinase gene. The detection of a novel 12-kb transcript by this gene in human normal and tumor cells establishes it as a new member of the tyrosine kinase family that is closely related to but distinct from c-abl.
Interleukin-6 and soluble interleukin-2-receptor in psoriatic arthritis: correlations with clinical and laboratory parameters. (1997)

Our study shows that IL-6 and sIL-2R may play a role in the pathogenetic mechanism of psoriatic arthritis.
Human genetics of the abdominal aortic aneurysm. (1984)

The results of recent studies suggest that genetic factors may be important in the pathogenesis of abdominal aortic aneurysms. In the present report, the apparent mechanisms of inheritance in 16 families with a total of 41 affected individuals are summarized. The results suggest that there may be both X-linked and autosomal dominant forms of the disease, with the X-linked variant as the more common type. A multifactorial mechanism cannot be ruled out from the results of the present data.
Lasers and Light Therapy for Acne Vulgaris (2005)

Acne vulgaris remains an emotionally and debilitating dermatologic disease, and is conventionally treated with a variety of oral and topical therapies with a number of significant side effects. An evolving understanding of laser-tissue interactions involving Propionibacterium acnes-produced porphyrins, and the development of infrared nonablative lasers to target sebaceous glands, has lead to the development of an escalating number of laser, light and radiofrequency devices for acne. Used as monotherapy or in combination, these devices are showing promise as a method to clear acne in a convenient, non-invasive manner, though there remains a clear need for long-term data and randomized, blinded studies.
New Methods for the Synthesis of Glycosides and Oligosaccharides—Are There Alternatives to the Koenigs‐Knorr Method? [New Synthetic Methods (56)] (1986)

Abstract Glycoproteins, glycolipids, and glycophospholipids (glycoconjugates) are components of membranes. The oligosaccharide residue is responsible for intercellular recognition and interaction; it acts as a receptor for proteins, hormones, and viruses and governs immune reactions. These significant activities have stimulated interest in oligosaccharides and glycoconjugates. With their help it should be possible to clarify the molecular basis of these phenomena and to derive new principles of physiological activity. Major advances in the synthesis of oligosaccharides have been made by the use of the Koenigs‐Knorr method, in which glycosyl halides in the presence of heavy‐metal salts are employed to transfer the glycosyl group to nucleophiles. The disadvantages of this procedure have led to an intensive search for new methods. Such methods will be discussed in this article. Emphasis is placed on glycoside and saccharide formation by 1‐ O ‐alkylation, on the trichloroacetimidate method, and on activation through the formation of glycosylsulfonium salts and glycosyl fluorides.
Purification and characterization of a new DNA-dependent ATPase with helicase activity from Escherichia coli. (1987)

A previously unreported single-stranded DNA-dependent nucleoside 5'-triphosphatase with DNA unwinding activity has been purified from extracts of Escherichia coli lacking the F factor. Fractions of the purified enzyme contain a major polypeptide of Mr = 75,000 which contains the active site(s) for both ATP hydrolysis and helicase activity. This is consistent with the results of gel filtration chromatography which indicate a native molecular mass of 75 kDa. The 75-kDa helicase has a preference for ATP (dATP) as a substrate in the hydrolysis reaction and requires the presence of a single-stranded DNA cofactor. The helicase reaction catalyzed by the enzyme has been characterized using an in vitro strand displacement assay. The 75-kDa helicase displaces a 71-nucleotide DNA fragment in an enzyme concentration-dependent and time-dependent reaction. The helicase reaction depends on the presence of a hydrolyzable nucleoside 5'-triphosphate (NTP) suggesting that NTP hydrolysis is required for the unwinding activity. In addition, the enzyme can displace a 343-nucleotide DNA fragment albeit less efficiently. The direction of the unwinding reaction is 3' to 5' with respect to the strand of DNA on which the enzyme is bound. The molecular size of this helicase and the direction of the unwinding reaction are similar to both helicase II and Rep protein. However, the 75-kDa helicase has been shown to be distinct from both helicase II and Rep protein using immunological, physical, and genetic criteria. The discovery of a new helicase brings the total number of helicases found in E. coli cell extracts (lacking F factor) to five.
Ovarian hyperstimulation syndrome and development of pulmonary embolism in pregnancy: case report (2010)

Ovarian hyperstimulation syndrome caused by assisted reproductive technology can lead to pulmonary embolism, a rare but serious side effect.
Inhibition of Fe-S cluster biosynthesis decreases mitochondrial iron export: Evidence that Yfh1p affects Fe-S cluster synthesis (2002)

Decreased expression of Yfh1p in the budding yeast, Saccharomyces cerevisiae, and the orthologous human gene frataxin results in respiratory deficiency and mitochondrial iron accumulation. The absence of Yfh1p decreases mitochondrial iron export. We demonstrate that decreased expression of Nfs1p, the yeast cysteine desulfurase that plays a central role in Fe-S cluster synthesis, also results in mitochondrial iron accumulation due to decreased export of mitochondrial iron. In the absence of Yfh1p, activity of Fe-S-containing enzymes (aconitase, succinate dehydrogenase) is decreased, whereas the activity of a non-Fe-S-containing enzyme (malate dehydrogenase) is unaffected. Aconitase protein was abundant even though the activity of aconitase was decreased in both aerobic and anaerobic conditions. These results demonstrate a direct role of Yfh1p in the formation of Fe-S clusters and indicate that mitochondrial iron export requires Fe-S cluster biosynthesis.
Safety and Immunogenicity of Haemophilus Influenzae Type B Polysaccharide or Conjugate Vaccines in an Elderly Adult Population (2004)

Elderly adults develop protective anticapsular antibody responses to unconjugated and conjugated PRP vaccine. The higher anticapsular antibody responses to the D conjugate but not to the OMP conjugate in the elderly, which is the reverse of that observed in immunized infants, implies fundamental differences in the immunological mechanisms by which the two age groups respond to PRP and by which the OMP and D conjugates elicit anticapsular antibody responses.
Mapping of cystic fibrosis transmembrane conductance regulator membrane topology by glycosylation site insertion (1994)

Technical difficulties in obtaining three-dimensional structures of intrinsic membrane proteins continues to limit understanding of their function. However, considerable insight can be gained from their two-dimensional topological arrangement in the lipid bilayer. Efficient molecular genetic approaches are available to discern the topology of prokaryotic but not of eukaryotic membrane proteins. The absolute asymmetry of the sidedness of their N-glycosylation was employed here to develop such a method using the cystic fibrosis transmembrane conductance regulator (CFTR). Insertion by in vitro mutagenesis of N-glycosylation consensus sequences (NXS/T) in predicted cytoplasmic and extracytoplasmic loops between hydrophobic sequences capable of traversing the membrane established the membrane topology of CFTR. This provides the first experimental evaluation of the original topological model of CFTR based solely on hydropathy algorithms and a method which may be generally applicable for the in vivo evaluation of the topology of other mammalian membrane proteins.
The Kabat Database and a Bioinformatics Example (2004)

In 1969, Elvin A. Kabat of Columbia University College of Physicians and Surgeons and Tai Te Wu of Cornell University Medical College began to collect and align amino acid sequences of human and mouse Bence Jones proteins and immunoglobulin (Ig) light chains. This was the beginning of the Kabat Database. They used a simple mathematical formula to calculate the various amino acid substitutions at each position and predict the precise locations of segments of the light-chain variable region that would form the antibody-combining site from a variability plot (1). The Kabat Database is one of the oldest biological sequence databases, and for many years was the only sequence database with alignment information.
Site-Directed Mutagenesis by Inverse PCR (2003)

Site-directed mutagenesis has revolutionized the study of protein structure and function by enabling the controlled and systematic production of mutant proteins. Early methods of site-directed mutagenesis involved the use of a mutated oligonucleotide primer to prime synthesis of a target single-stranded DNA template. These approaches were very inefficient, yielding success rates of 1–5% (). A dramatic improvement in the efficiency of generating mutations resulted from the use of single-stranded, uracil-containing DNA molecules isolated from ung − dut− Escherichia coli strains (see Chapter 3). Again, the mutation is introduced in a mutated oligonucleotide primer. Selection against the wild-type sequence parent DNA occurs on transformation into wild-type E. coli. Mutagenesis by this method was relatively efficient, with rates of 15–35%, but required a number of subcloning steps involving single-stranded M13 phage clones (). It was only following the development of the polymerase chain reaction (PCR) that the two concepts were combined, dramatically improving the efficiency of the whole procedure.
The adenovirus capsid: major progress in minor proteins (2005)

Human adenoviruses have been the subject of intensive investigation since their discovery in the early 1950s: they have served as model pathogens, as probes for studying cellular processes and, more recently, as efficient gene-delivery vehicles for experimental gene therapy. As a result, a detailed insight into many aspects of adenovirus biology is now available. The capsid proteins and in particular the hexon, penton-base and fibre proteins (the so-called major capsid proteins) have been studied extensively and their structure and function in the virus capsid are now well-defined. On the other hand, the minor proteins in the viral capsid, i.e. proteins IIIa, VI, VIII and IX, have received much less attention. Only the last few years have witnessed a sharp increase in the number of studies on their structure and function. Here, a review of the minor capsid proteins is provided, with a focus on new insights into their position and role in the capsid and the opportunities that they provide for improving human adenovirus-derived gene-delivery vectors.