gebhart/patrepeval huggingface dataset:
Lamellar Keratoplasty Treatment of Fungal Corneal Ulcers With Acellular Porcine Corneal Stroma (2015)

The fundamental problem of corneal transplantation is a severe shortage of donor tissues worldwide, resulting in approximately 1.5 million new cases of blindness annually. To explore an alternative to donor corneas, we conducted a clinical study in which implanted acellular porcine corneal stromas (APCSs) replaced the pathologic anterior corneas in 47 patients who had experienced fungal corneal infections. Subsequently, we demonstrated the safety and efficacy of APCSs in human keratoplasty for a minimum follow-up period of 6 months, during which time no recurrence of infection was observed. All corneal ulcers healed with the return of neovascularization. In addition, our results indicated that epithelialization occurred in all APCS grafts except four grafts; for these four, the grafts dissolved to varying degrees. Furthermore, most porcine grafts (n = 41) gradually became transparent without rejection, and an improvement of more than two lines in best corrected visual acuity (BCVA) was achieved in 34 eyes (∼72%). Finally, no patients showed any severe adverse reaction or any significant change in postoperative systemic safety indicators. Thus, we concluded that APCS grafts are safe and efficacious during lamellar keratoplasty in treating corneal fungal ulcers and potentially for other clinical diseases.
Nitric acid pretreatment for the passivation of boron emitters for n-type base silicon solar cells (2008)

We have developed a simple method to passivate industrially produced boron-doped emitters for n-type base silicon solar cells using an ultrathin (∼1.5nm) silicon dioxide layer between the silicon emitter and the silicon nitride antireflection coating film. This ultrathin oxide is grown at room temperature by soaking the silicon wafers in a solution of nitric acid prior to the deposition of the silicon nitride antireflection coating film. The n-type solar cells processed in such a way demonstrate a conversion efficiency enhancement of more than 2% absolute over the solar cells passivated without the silicon dioxide layer.
Chloroplast transit peptides the perfect random coil? (1991)

Structural analysis of chloroplast transit peptides (cTPs), including secondary structure prediction and analysis of 'cTP-like' peptides of known 3D structure, suggests that cTPs are essentially flexible peptides devoid of regular secondary or tertiary structure. It is proposed that cTPs may be designed to interact with a succession of different chaperones on the chloroplast protein-import pathway.
In vitro and in vivo characterization of iris pigment epithelial cells cultured on amniotic membranes. (2006)

The more advanced degree of differentiation of IPE cells grown on AMs indicates that AMs are a better substrate to culture IPE cells than plastic plates. This was supported by the greater protection of photoreceptors of RCS rats when IPE cell sheets cultured on AMs were transplanted in the subretinal space.
MicroencapsulatedBifidobacterium longumsubsp.infantisATCC 15697 Favorably Modulates Gut Microbiota and Reduces Circulating Endotoxins in F344 Rats (2014)

The gut microbiota is a bacterial bioreactor whose composition is an asset for human health. However, circulating gut microbiota derived endotoxins cause metabolic endotoxemia, promoting metabolic and liver diseases. This study investigates the potential of orally delivered microencapsulated Bifidobacterium infantis ATCC 15697 to modulate the gut microbiota and reduce endotoxemia in F344 rats. The rats were gavaged daily with saline or microencapsulated B. infantis ATCC 15697. Following 38 days of supplementation, the treated rats showed a significant (P < 0.05) increase in fecal Bifidobacteria (4.34 ± 0.46 versus 2.45 ± 0.25% of total) and B. infantis (0.28 ± 0.21 versus 0.52 ± 0.12 % of total) and a significant (P < 0.05) decrease in fecal Enterobacteriaceae (0.80 ± 0.45 versus 2.83 ± 0.63% of total) compared to the saline control. In addition, supplementation with the probiotic formulation reduced fecal (10.52 ± 0.18 versus 11.29 ± 0.16 EU/mg; P = 0.01) and serum (0.33 ± 0.015 versus 0.30 ± 0.015 EU/mL; P = 0.25) endotoxins. Thus, microencapsulated B. infantis ATCC 15697 modulates the gut microbiota and reduces colonic and serum endotoxins. Future preclinical studies should investigate the potential of the novel probiotic formulation in metabolic and liver diseases.
Construction of Murine Phage Antibody Library and Selection of Ricin‐Specific Single‐Chain Antibodies (1999)

A murine phage antibody library containing 1.7 x 10(8) independent clones was constructed and then screened by affinity panning of anti-ricin antibody fragments. First, mRNA was purified from the total RNA extracted from fresh spleens of nonimmunized mice of Kunming, and then the total antibody variable region cDNA was amplified via reverse transcription-polymerase chain reaction. Gene fragments encoding VH and VL were amplified and assembled into a single gene by using a DNA linker encoding a pentadecapeptide (Gly4Ser)3 through primary PCR. Finally the recombinant DNA fragments were cloned into the phagemid pCANTAB 5E vector and electroporated into Escherichia coli TG1. The recombinant phage particles displaying functional single-chain fragment variable regions (scFvs) were rescued by reinfection of helper phage M13KO7, thus constructing a murine antibody library. Two ricin-specific scFvs strains were selected from the phage antibody library by using affinity panning. The target antigen, ricin, was biotinylated with photobiotin and the biotin-labeled ricin interacted with the phage antibody library. Subsequent addition of streptavidincoated paramagnetic beads isolated the biotinylated ricin-binding phage particle complex. Washing, elution, and reinfection of the isolated complex then proceeded sequentially. After six rounds of panning, 2 strains of the 34 clones were verified to show greater specific affinity to ricin.
Recombinant human tumor necrosis factor increases mRNA levels and surface expression of HLA-A,B antigens in vascular endothelial cells and dermal fibroblasts in vitro. (1986)

Recombinant human tumor necrosis factor (TNF), purified to greater than 99% homogeneity, increases surface expression of class I major histocompatibility complex (MHC) antigens to a maximum of 9-fold on cultured human endothelial cells (HEC) and human dermal fibroblasts (HDF). The increase is concentration dependent (peak 20-100 units/ml) and time dependent (nearly maximal by 4 days); expression remains elevated in the continued presence of TNF and requires greater than 7 days to return to basal levels upon TNF withdrawal. The increase in surface expression appears to result from increases in steady-state mRNA levels for the class I antigens, although the increase in mRNA is proportionately greater than for surface expression. No surface expression of or mRNA for class II MHC antigens is detectable in either control or TNF-treated HEC or HDF. These effects are similar to those produced by leukocyte or fibroblast (type I) interferons (IFNs). The protein synthesis inhibitor cycloheximide (CHX), when added coincidentally with type I IFNs, leads to superinduction of mRNA for class I MHC antigens and, unexpectedly, leads to the appearance of mRNA for class II MHC antigens. CHX has no effect by itself upon mRNA levels for class I or class II MHC antigens, nor does it modulate the increases in mRNA produced by immune (type II) IFN. Most interesting, CHX blocks the increase in mRNA for class I MHC antigens induced by TNF. Thus TNF appears to act on MHC gene expression through a newly synthesized protein intermediate. Our results provide direct evidence that TNF can modulate gene expression in normal (untransformed) cell types and contribute to understanding the complex nature of MHC gene regulation. Finally, they suggest that TNF may act in vivo as an immunoregulatory molecule.
Apoptosis: A Review of Programmed Cell Death (2007)

The process of programmed cell death, or apoptosis, is generally characterized by distinct morphological characteristics and energy-dependent biochemical mechanisms. Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell death. Inappropriate apoptosis (either too little or too much) is a factor in many human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. The ability to modulate the life or death of a cell is recognized for its immense therapeutic potential. Therefore, research continues to focus on the elucidation and analysis of the cell cycle machinery and signaling pathways that control cell cycle arrest and apoptosis. To that end, the field of apoptosis research has been moving forward at an alarmingly rapid rate. Although many of the key apoptotic proteins have been identified, the molecular mechanisms of action or inaction of these proteins remain to be elucidated. The goal of this review is to provide a general overview of current knowledge on the process of apoptosis including morphology, biochemistry, the role of apoptosis in health and disease, detection methods, as well as a discussion of potential alternative forms of apoptosis.
Recognition and cleavage of hairpin structures in nucleic acids by oligodeoxynucleotides (1994)

The possibility of designing antisense oligodeoxynucleotides complementary to non-adjacent single-stranded sequences containing hairpin structures was studied using a DNA model system. The structure and stability of complexes formed by a 17mer oligonucleotide with DNA fragments containing hairpin structures was investigated by spectroscopic measurements (melting curves) and chemical reactions (osmium tetroxide reaction, copper-phenanthroline cleavage). A three-way junction was formed when the oligonucleotide was bound to both sides of the hairpin structure. When the complementary sequences of the two parts of the oligonucleotide were separated by a sequence which could not form a hairpin, the oligonucleotide exhibited a slightly weaker binding than to the hairpin-containing target. An oligodeoxynucleotide-phenanthroline conjugate was designed to form Watson-Crick base pairs with two single-stranded regions flanking a hairpin structure in a DNA fragment. In the presence of Cu2+ ions and a reducing agent, two main cleavage sites were observed at the end of the duplex structure formed by the oligonucleotide-phenanthroline conjugate with its target sequence. Competition experiments showed that both parts of the oligonucleotide must be bound in order to observe sequence-specific cleavage. Cleavage was still observed with target sequences which could not form a hairpin, provided the reaction was carried out at lower temperatures. These results show that sequence-specific recognition and modification (cleavage) can be achieved with antisense oligonucleotides which bind to non-adjacent sequences in a single-stranded nucleic acid.
Nanoscale Protein Pores Modified with PAMAM Dendrimers (2007)

We describe nanoscale protein pores modified with a single hyperbranched dendrimer molecule inside the channel lumen. Sulfhydryl-reactive polyamido amine (PAMAM) dendrimers of generations 2, 3 and 5 were synthesized, chemically characterized, and reacted with engineered cysteine residues in the transmembrane pore alpha-hemolysin. Successful coupling was monitored using an electrophoretic mobility shift assay. The results indicate that G2 and G3 but not G5 dendrimers permeated through the 2.9 nm cis entrance to couple inside the pore. The defined molecular weight cutoff for the passage of hyperbranched PAMAM polymers is in contrast to the less restricted accessibility of flexible linear poly(ethylene glycol) polymers of comparable hydrodynamic volume. Their higher compactness makes sulfhydryl-reactive PAMAM dendrimers promising research reagents to probe the structure of porous membrane proteins with wide internal diameters. The conductance properties of PAMAM-modified proteins pores were characterized with single-channel current recordings. A G3 dendrimer molecule in the channel lumen reduced the ionic current by 45%, indicating that the hyperbranched and positively charged polymer blocked the passage of ions through the pore. In line with expectations, a smaller and less dense G2 dendrimer led to a less pronounced current reduction of 25%. Comparisons to recordings of PEG-modified pores revealed striking dissimilarities, suggesting that differences in the structural dynamics of flexible linear polymers vs compact dendrimers can be observed at the single-molecule level. Current recordings also revealed that dendrimers functioned as ion-selectivity filters and molecular sieves for the controlled passage of molecules. The alteration of pore properties with charged and hyperbranched dendrimers is a new approach and might be extended to inorganic nanopores with applications in sensing and separation technology.
FAQ: a framework for fast Approximate Query processing on Temporal data (2014)

Temporal queries on time evolving data are at the heart of a broad range of business and network intelligence applications ranging from consumer behavior analysis, trend analysis, temporal pattern mining, sentiment analysis on social media, cyber security, and network monitoring. In this work, we present an innovative data structure called Fast Approximate Query-able(FAQ), which provides a unified framework for temporal query processing on Big Data. FAQ uses a novel composition of data sketching, wavelet-style differencing for temporal compression, and quantization, and handles diverse kinds of queries including distinct counts, set membership, frequency estimation, top-K, p-norms, empirical entropy, and distance queries such as Histogram lp-norm distance (including Euclidean and Manhattan distance), cosine similarity, Jaccard coefficient, and rank correlation. Experiments on a real-life multi dimensional network monitoring data sets demonstrate speedups of 92x achieved by FAQ over a flat representation of data for a mixed temporal query workload.
Evolutionary relationships among pyridoxal‐5′‐phosphate‐dependent enzymes (1994)

Pyridoxal-5'-phosphate-dependent enzymes catalyze manifold reactions in the metabolism of amino acids. A comprehensive comparison of amino acid sequences has shown that most of these enzymes can be assigned to one of three different families of homologous proteins. The sequences of the enzymes of each family were aligned and their homology confirmed by profile analysis. Scrutiny of the reactions catalyzed by the enzymes showed that their affiliation with one of the three structurally defined families correlates in most cases with their regio-specificity. In the largest family, the covalency changes of the substrate occur at the same carbon atom that carries the amino group forming the imine linkage with the coenzyme. This family was thus named alpha family. It comprises glycine hydroxymethyltransferase, glycine C-acetyltransferase, 5-aminolevulinate synthase, 8-amino-7-oxononanoate synthase, all aminotransferases (with the possible exception of subgroup III), a number of other enzymes relatively closely related with the aminotransferases and very likely a certain group of amino acid decarboxylases as well as tryptophanase and tyrosine phenol-lyase which, however, catalyze beta-elimination reactions. The beta family includes L- and D-serine dehydratase, threonine dehydratase, the beta subunit of tryptophan synthase, threonine synthase and cysteine synthase. These enzymes catalyze beta-replacement or beta-elimination reactions. The gamma family incorporates O-succinylhomoserine (thiol-lyase, O-acetylhomoserine (thiol)-lyase, and cystathionine gamma-lyase, which catalyze gamma-replacement or gamma-elimination reactions, as well as cystathionine beta-lyase. The alpha and gamma family might be distantly related with one another, but are clearly not homologous with the beta family. Apparently, the primordial pyridoxal-5'-phosphate-dependent enzymes were regio-specific catalysts, which first specialized for reaction specificity and then for substrate specificity. The following pyridoxal-5'-phosphate-dependent enzymes seem to be unrelated with the alpha, beta or gamma family by the criterion of profile analysis:alanine racemase, selenocysteine synthase, and many amino acid decarboxylases. These enzymes may represent yet other families of B6 enzymes.
The local information content of the protein structural database (1993)

A simple study of the information available within proteins of known structure reveals both the limits of structure prediction based on overall statistical correlations between sequence and structure, and the areas where there is still a possibility for further structural database exploitation.
Isolation of duplicated human c-src genes located on chromosomes 1 and 20. (1985)

The oncogene (v-src) of Rous sarcoma virus apparently arose by transduction of the chicken gene known as c-src(chicken). We isolated DNA fragments representative of two src-related loci from recombinant DNA bacteriophage libraries of the human genome. One of these loci, c-src1(human), appeared to direct the synthesis of a 5-kilobase polyadenylated RNA that presumably encodes pp60c-src(human). Probes specific for the other locus, c-src2(human), did not hybridize to polyadenylated RNA prepared from a variety of human cell lines. Partial nucleotide sequence determinations of the loci demonstrated that c-src1(human) is highly related to chicken c-src and that c-src2(human) is slightly more divergent. The sequences imply that the final two coding exons of each human locus are identical in length to those of chicken c-src and that the location of an amber stop codon is unchanged in all three loci. c-src1(human) has been mapped to chromosome 20, and the second locus is located on chromosome 1. We conclude that c-src1(human) is the analog of c-src(chicken) and that the duplicated locus, c-src2(human), may also be expressed.
Reversibility of the insulin-stimulated phosphorylation of ATP citrate lyase and a cytoplasmic protein of subunit Mr 22000 in adipose tissue (1982)

Exposure of rat epididymal adipose tissue to insulin leads to a 2-fold increase in incorporation of [32P]phosphate into ATP citrate lyase and a cytoplasmic protein of Mr 22000. A smaller increase and decrease in incorporation into cytoplasmic proteins of Mr 63000 and 20000 respectively were also observed. Subsequent addition of anti-insulin serum largely reversed these changes within 15 min, indicating that the alterations in 32P incorporation represented changes in net phosphate content of the proteins.
The kinetics of hematopoiesis in the light horse II. The hematological response to hemorrhagic anemia. (1975)

Hemorrhagic anemia was experimentally produced in three Standardbred horses by removing approximately 63% of the red cell mass and the accompanying plasma during a three day interval. Red cell parameters were examined daily for 45 days and then weekly until termination of the experiment 250 days after production of the anemia. Leukocytes, platelets and bone marrow aspirates were examined at regular intervals for 25 days after the final phlebotomy. At 24 hours after the last bleeding, 75-selenomethionine was injected intravenously to measure the lifespan of the newly produced erythrocytes. The erythrocyte lifespan was found to be 139 days as compared to the 155 day erythrocyte lifespan for three normal standardbred horses measured previously by similar techniques. The maximum decrease in erythrocyte numbers occurred four, two and two days following the last phlebotomy to 43, 39 and 44% of the original values. The prebleeding erythrocyte levels were regained at approximately 63, 91 and 98 days respectively. During the initial 45 days post phlebotomy the maximum increase in mean cell colume was 2, 4 and 7 mj-3 respectively. During the recovery period there was erythrocyte production of 6.84, 6.99, and 6.12 x 10-9 cells/kg/day. At the same time the absolute production of hemoglobin was 44.6, 50.0, and 51.0/gm/day or on a relative basis 0.096, 0.114 and 0.113 gm/kg/day.
Analogs of (A2'p)nA. Correlation of structure of analogs of ppp(A2'p)2A and (A2'p)2A with stability and biological activity. (1982)

Analogs of (A2'p)2A core and ppp(A2'p)2A were chemically synthesized and their susceptibility to phosphodiesterase degradation and ability to either activate an endonuclease or to inhibit cell growth were determined. The absence of the internal 3'-OH groups ((3'dA2'p)2A) resulted in a 5-fold increase in stability, but also in a 10-fold decrease in activity, as measured by (a) activation of an endonuclease in cell-free extracts and inhibition of protein synthesis in intact cells by the 5'-triphosphate species and (b) inhibition of DNA synthesis in synchronized cells by the core analogs. An uncharged derivative of this analog containing two methylphosphotriesters, although significantly more stable, was even less active. Additional deletion of the terminal 3'-OH ((3'd A2'p)23'dA) resulted in a further 6-fold increase in stability (30-fold overall increase in stability), as well as approximately a 2-fold increase in ability to inhibit cell growth, as compared to the natural 2'5' A core. The analog lacking a terminal 2'-OH as well as lacking the internal 3'-OH group ((3'dA2'p)22'dA) showed an overall 15-fold increased stability, yet showed very little activity in inhibiting cell growth. The most stable (120-fold increased overall stability) as well as most active analog was a xyloadenosine analog of 2'5' A core, (xyloA2'p)2xyloA. These results show that modification of the 3'-terminal OH appears to be most important in increasing 2'-5' A core stability as well as biological activity. However, the mechanism of cell growth inhibition by these 2'-5' A core analogs may involve pathways different from those utilized by the 2'-5' A-dependent endonuclease.
Laser programmed vias for restructurable VLSI (1980)

A technique has been developed which uses a laser to form selectively connecting vias between two levels of aluminum wiring on a silicon wafer. The same laser can remove metal thus providing a capability of either adding or deleting connections in fully fabricated devices. Experiments have been performed with a commercial IC mask trimmer using a 100 nsec pulse width neodymium YAG laser. Single pulses provide low resistivity connections with no thermal annealing required. The inter-metal insulating layer is formed by sputtering 2600 Å of amorphous silicon. Chains containing forty 6.3 µm × 6.3µm vias between first and second level metal were successfully connected with low resistances and high current capability. At a thickness of 4400 Å of thermal oxide breakthrough to the substrate limits the operating margins on laser power to only 10% above the power for 100% via contacts; at one micron breakthrough is eliminated entirely.
Deadly Exposure (2008)

In the Northern Hemisphere, winter is coming; so too are the seasonal episodes of cold and flu. With such a wide range of viruses causing a multitude of human and animal diseases, there remains a lucrative market for drugs that can target multiple classes of viruses and hence boost the current armory of antiviral therapies. The challenge is to develop therapies that are specific, yet avoid stimulating drug resistance.