gebhart/patrepeval huggingface dataset:
Mechanical properties of a self-assembling oligopeptide matrix (1998)

We have begun studies of a novel type of biomaterial derived from a recently-discovered class of ionic self-complementary oligopeptides. These short peptides (typically 8, 16, 24, or 32 amino acid residues with internally-repeating sequences) self-assemble in aqueous salt solution into three-dimensional matrices capable of favorable interactions with cells, and offer promise for useful bioengineering design based on rational changes in sequence. In this paper we present preliminary results on mechanical properties, combining experimental and theoretical approaches, of one particular example of these peptide materials, EFK8. The static elastic modulus was measured using an apparatus designed to allow sample fabrication and mechanical testing in the same system with the sample in aqueous solution. The material microstructure was examined by SEM and the measurements interpreted with the aid of a model for cellular solids. Values for the elastic modulus increased from 1.59 +/- 0.06 to 14.7 +/- 1.0 kPa for peptide concentrations increasing from 2.7 to 10 mg ml-1. SEM photographs showed the microstructure to consist of a relatively homogeneous lattice with fiber thickness of 10-30 nm independent of peptide concentration, but with fiber density increasing with peptide concentration. This behavior is consistent with scaling predictions from the cellular solids model and yields an estimate for the individual fiber elastic modulus in the range of 1-20 MPa. We therefore have provided some initial physical principles for guiding improvement of the mechanical properties of these new materials.
Simplified-antiresonant reflecting optical waveguide (S-ARROW)-type VCSELs (2003)

A two-step MOCVD growth process is used to fabricate antiguided VCSELs incorporating a simplified-antiresonant reflecting optical waveguide (S-ARROW) design. Preliminary results show lasing in both the guided modes of the reflecting ring as well as the leaky modes of the S-ARROW. Optimization for high-single-mode powers is discussed.
Two-Dimensional Mapping of Copper and Zinc in Liver Sections by Laser Ablation–Inductively Coupled Plasma Mass Spectrometry (2003)

Elemental mapping of trace elements generated by LA-ICP-MS can be very precise so that small changes in the elemental concentration in the tissue can be detected and nonuniform spatial distribution of the elements in tissues can be established.
A repetitive antigen of Plasmodium falciparum that is homologous to heat shock protein 70 of Drosophila melanogaster. (1986)

We describe an antigen of Plasmodium falciparum, defined by a cDNA clone designated Ag63. The antigen is an abundant, soluble cytoplasmic polypeptide of Mr 75,000 present in all stages of asexual development in the blood and in gametocytes, but not in sporozoites. The sequence of the cDNA clone revealed that, like many other antigens of P. falciparum, it contains tandemly repeated amino acid sequences, in this case Gly-Gly-Met-Pro. However, the rest of the sequence is 70% homologous at the amino acid level to the heat shock protein hsp70 of Drosophila melanogaster.
Exceptionally Potent and Broadly Cross-Reactive, Bispecific Multivalent HIV-1 Inhibitors Based on Single Human CD4 and Antibody Domains (2013)

Soluble forms of the human immunodeficiency virus type 1 (HIV-1) primary receptor CD4 (soluble CD4 [sCD4]) have been extensively characterized for a quarter of a century as promising HIV-1 inhibitors, but they have not been clinically successful. By combining a protein cavity-filling strategy and the power of library technology, we identified an engineered cavity-altered single-domain sCD4 (mD1.22) with a unique combination of excellent properties, including broad and potent neutralizing activity, high specificity, stability, solubility, and affinity for the HIV-1 envelope glycoprotein gp120, and small molecular size. To further improve its neutralizing potency and breadth, we generated bispecific multivalent fusion proteins of mD1.22 with another potent HIV-1 inhibitor, an antibody domain (m36.4) that targets the coreceptor-binding site on gp120. The fusion proteins neutralized all HIV-1 isolates tested, with potencies about 10-, 50-, and 200-fold higher than those of the broadly neutralizing antibody VRC01, the U.S. FDA-approved peptide inhibitor T20, and the clinically tested sCD4-Fc fusion protein CD4-Ig, respectively. In addition, they exhibited higher stability and specificity and a lower aggregation propensity than CD4-Ig. Therefore, mD1.22 and related fusion proteins could be useful for HIV-1 prevention and therapy, including eradication of the virus.
Animal models of ischemic stroke: balancing experimental aims and animal care. (2004)

Animal models of ischemic stroke are examples of an induced model that can present challenges from the perspectives of protocol review and animal management. The review presented here will include a brief summary of the current state of knowledge about clinical stroke; a general synopsis of important unanswered research questions that justify use of animal stroke models; an overview of various animal models of ischemic stroke, including strengths and limitations; and a discussion of animal care issues relative to ischemic stroke models. Good communication and interactive education among primary investigators, laboratory animal veterinarians and caretakers, and institutional animal care and use committee members are critical in achieving a balance between research objectives and animal care issues when using animal stroke models.
Building symbolic information for 3D human body modeling from range data (2003)

The work is concerned with the signal-to-symbol problem of building skinned, segmented, landmarked and labeled 3D models of the whole human body from range data. A fully automated model based process is presented that takes raw range data, cleans and skins it, and then locates "interesting" features, to enrich the surface with symbolic information for specific applications. The method is validated via volumetrics in medicine and surface anthropometry.
A high‐throughput screen of cell‐death‐inducing factors in Nicotiana benthamiana identifies a novel MAPKK that mediates INF1‐induced cell death signaling and non‐host resistance to Pseudomonas cichorii (2007)

A high-throughput overexpression screen of Nicotiana benthamiana cDNAs identified a gene for a mitogen-activated protein kinase kinase (MAPKK) as a potent inducer of the hypersensitive response (HR)-like cell death. NbMKK1 protein is localized to the nucleus, and the N-terminal putative MAPK docking site of NbMKK1 is required for its function as a cell-death inducer. NbMKK1-mediated leaf-cell death was compromised in leaves where NbSIPK expression was silenced by virus-induced gene silencing. A yeast two-hybrid assay showed that NbMKK1 and NbSIPK physically interact, suggesting that NbSIPK is one of the downstream targets of NbMKK1. Phytophthora infestans INF1 elicitor-mediated HR was delayed in NbMKK1-silenced plants, indicating that NbMKK1 is involved in this HR pathway. Furthermore, the resistance of N. benthamiana to a non-host pathogen Pseudomonas cichorii was compromised in NbMKK1-silenced plants. These results demonstrate that MAPK cascades involving NbMKK1 control non-host resistance including HR cell death.
Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening (1997)

An efficient beta-fucosidase was evolved by DNA shuffling from the Escherichia coli lacZ beta-galactosidase. Seven rounds of DNA shuffling and colony screening on chromogenic fucose substrates were performed, using 10,000 colonies per round. Compared with native beta-galactosidase, the evolved enzyme purified from cells from the final round showed a 1,000-fold increased substrate specificity for o-nitrophenyl fucopyranoside versus o-nitrophenyl galactopyranoside and a 300-fold increased substrate specificity for p-nitrophenyl fucopyranoside versus p-nitrophenyl galactopyranoside. The evolved cell line showed a 66-fold increase in p-nitrophenyl fucosidase specific activity. The evolved fucosidase has a 10- to 20-fold increased kcat/Km for the fucose substrates compared with the native enzyme. The DNA sequence of the evolved fucosidase gene showed 13 base changes, resulting in six amino acid changes from the native enzyme. This effort shows that the library size that is required to obtain significant enhancements in specificity and activity by reiterative DNA shuffling and screening, even for an enzyme of 109 kDa, is within range of existing high-throughput technology. Reiterative generation of libraries and stepwise accumulation of improvements based on addition of beneficial mutations appears to be a promising alternative to rational design.
BAMLET Activates a Lysosomal Cell Death Program in Cancer Cells (2010)

A complex of human alpha-lactalbumin and oleic acid (HAMLET) was originally isolated from human milk as a potent anticancer agent. It kills a wide range of transformed cells of various origins while leaving nontransformed healthy cells largely unaffected both in vitro and in vivo. Importantly, purified alpha-lactalbumins from other mammals form complexes with oleic acid that show biological activities similar to that of HAMLET. The mechanism by which these protein-lipid complexes kill tumor cells is, however, largely unknown. Here, we show that complex of bovine alpha-lactalbumin and oleic acid (BAMLET), the bovine counterpart of HAMLET, kills tumor cells via a mechanism involving lysosomal membrane permeabilization. BAMLET shows potent cytotoxic activity against eight cancer cell lines tested, whereas nontransformed NIH-3T3 murine embryonic fibroblasts are relatively resistant. BAMLET accumulates rapidly and specifically in the endolysosomal compartment of tumor cells and induces an early leakage of lysosomal cathepsins into the cytosol followed by the activation of the proapoptotic protein Bax. Ectopic expression of three proteins known to stabilize the lysosomal compartment, i.e. heat shock protein 70 (Hsp70), Hsp70-2, and lens epithelium-derived growth factor, confer significant protection against BAMLET-induced cell death, whereas the antiapoptotic protein Bcl-2, caspase inhibition, and autophagy inhibition fail to do so. These data indicate that BAMLET triggers lysosomal cell death pathway in cancer cells, thereby clarifying the ability of alpha-lactalbumin:oleate complexes to kill highly apoptosis-resistant tumor cells.
Tunable Fresnel lens using nanoscale polymer-dispersed liquid crystals (2003)

An electrically tunable Fresnel zone plate lens is demonstrated using nanoscale polymer-dispersed liquid crystal droplets. In the voltage-off state, the zone plate behaves like a positive lens. The measured diffraction efficiency is close to the theoretical limit and is controllable by voltage. The major advantages of such a Fresnel lens are simple fabrication, large aperture size, polarization independent, and fast switching speed, although the required operating voltage is relatively high.
Orientation within the Exosporium and Structural Stability of the Collagen-Like Glycoprotein BclA of Bacillus anthracis (2005)

Bacillus anthracis spores, which cause anthrax, are enclosed by an exosporium consisting of a basal layer and an external hair-like nap. The filaments of the nap are composed of BclA, a glycoprotein containing distinct N-terminal (NTD) and C-terminal (CTD) domains separated by an extended collagen-like central region. In this study, we used immunogold electron microscopy to show that the CTD of BclA forms the distal end of each filament of the hair-like nap, indicating that the NTD is attached to the basal layer. Ten randomly chosen anti-BclA monoclonal antibodies, raised against spores or exosporium, reacted with the CTD, consistent with its exterior location. We showed that recombinant BclA (rBclA), encoded by the B. anthracis Sterne strain and synthesized in Escherichia coli, forms a collagen-like triple helix as judged by collagenase sensitivity and circular dichroism spectroscopy. In contrast, native BclA in spores was resistant to collagenase digestion. Thermal denaturation studies showed that the collagen-like region of rBclA exhibited a melting temperature (T(m)) of 37 degrees C, like mammalian collagen. However, rBclA trimers exhibited T(m) values of 84 degrees C and 95 degrees C in buffer with and without sodium dodecyl sulfate, respectively. CTD trimers exhibited the same T(m) values, indicating that the high temperature and detergent resistances of rBclA were due to strong CTD interactions. We observed that CTD trimers are resistant to many proteases and readily form large crystalline sheets. Structural data indicate that the CTD is composed of multiple beta strands. Taken together, our results suggest that BclA and particularly its CTD form a rugged shield around the spore.
[The roots of Cha and Gambir]. (2005)

This article attempts to trace the origin of tea. The author believes the ancient Chinese tea, "chia", is either Jicha (water extract from the pith of Acacia catechu that grows naturally in the mountainous border between the Yunnan province of China and southern Asian countries) or Jicha-Kagikazura (water extract from the young branches and leaves of Uncaris gambir, originally found in India/Sri Lanka). Both were pulverized after being kiln-dried and then mixed with water to produce a thick suspension, or tea. Although the drink is bitter and has an astringent property, it has a particular flavor with a refreshing after-taste. Its components with medicinal properties include tannin, catechin, and various flavonoids, making us believe it was worthwhile for the people at the time to consume the drink regularly. Generally speaking, tea cultivation in China flourished south of the Yangzi Jiang River including the present Zhejiang and Anhui provinces. Depending on the regions, there were words for tea in various languages, including the names of places where particular teas were grown. In addition to the names that appear in the famous Chajing book, it is interesting to note Da Fang pronounced tea as "TAH". Because the area south of the Yangzi Jiang has traditionally been active in foreign trade since the ancient and middle ages. People in this region consumed various foreign originated teas as well. This included Gambir, which was introduced to southern Asia (including present Malaysia and Indonesia) and was consumed as an herbal tea under names such as Guo Luo or Ju Luo teas. Paan, from India, also uses Gambir paste and was a popular chewing refreshment to prevent diseases caused by miasma as well as to keep one's mouth clean. The name A-sen-yaku used in Japan was taken from the plant name Acasia, and Gambir was used to dye Buddhist monks' Ke-Ra bags to a blackish yellow color. The Daikanwa dictionary states the Ra in the name, which means thin silk, was later replaced with "A". The official name for Ji-cha [Er Cha] in modern China is "Gaiji-cha", [Hal-Er Cha], which comes from the name of a variety of tea made by the Ai-Ni tribal subgroup of the ethnic Ha-Ni in Yunnan province. The [see character in text] character is pronounced "ni", which is a homophony of [character in text]. Based on these facts, "Ai-Ni" should be considered the same as "Hai-Ni". Because the ethnic groups in Yunnan province used primitive and tough tea leaves, which were eaten instead of being infused in water, the leaves were first fermented by being buried in the ground. Even today, people of these ethnic groups prefer fungus-fermented black tea with a particular flavor. In contrast, the ethnic Hans used and still use improved and softer young shoots of tea leaves to prepare mainly green tea. It has recently been discovered that Acapsia, as well as Gambir, has anti-oxidant properties, and that consumption over time is effective against many lifestyle-related adult diseases. It may be well worthwhile to cast fresh light upon ancient tea drinking customs.
On‐line measurement of gas‐exchange conditions in fermentation processes (1975)

Abstract Gas‐exchange conditions of C. ulilis cultures were analyzed by an on‐line, real‐time operating digital computer interfaced with a 250 liter, highly instrumented fermentor. Information obtained from the computer was correlated with wet chemical analytical data related to nucleic acid, protein, and ethyl alcohol production rates. Once the correlation was established, the computed gas‐exchange data, especially the RQ which functions as an indicator of the cells physiological condition, could be used as a real‐time process status indicator which follows or forecasts events during the fermentation. It was also found that electrical noises generted on the sensor‐instrument level may handicap the interpretation of the meaning of computed process status indicators. Since “clear” data is considered as a prerequisite to follow the physiological conditions and perform control of environmental variables, a special computer program is necessary to filter the electric noises at the sensor‐instrument level prior to the on‐line, real‐time data analysis for process status identification.
Modeling, Analysis, and Design of Graphene Nano-Ribbon Interconnects (2009)

Graphene nanoribbons (GNRs) are considered as a prospective interconnect material. A comprehensive conductance and delay analysis of GNR interconnects is presented in this paper. Using a simple tight-binding model and the linear response Landauer formula, the conductance model of GNR is derived. Several GNR structures are examined, and the conductance among them and other interconnect materials [e.g., copper (Cu), tungsten (W), and carbon nanotubes (CNTs)] is compared. The impact of different model parameters (i.e., bandgap, mean free path, Fermi level, and edge specularity) on the conductance is discussed. Both global and local GNR interconnect delays are analyzed using an RLC equivalent circuit model. Intercalation doping for multilayer GNRs is proposed, and it is shown that in order to match (or better) the performance of Cu or CNT bundles at either the global or local level, multiple zigzag-edged GNR layers along with proper intercalation doping must be used and near-specular nanoribbon edge should be achieved. However, intercalation-doped multilayer zigzag GNRs can have better performance than that of W, implying possible application as local interconnects in some cases. Thus, this paper identifies the on-chip interconnect domains where GNRs can be employed and provides valuable insights into the process technology development for GNR interconnects.
PGC-1α regulates the neuromuscular junction program and ameliorates Duchenne muscular dystrophy (2007)

The coactivator PGC-1alpha mediates key responses of skeletal muscle to motor nerve activity. We show here that neuregulin-stimulated phosphorylation of PGC-1alpha and GA-binding protein (GABP) allows recruitment of PGC-1alpha to the GABP complex and enhances transcription of a broad neuromuscular junction gene program. Since a subset of genes controlled by PGC-1alpha and GABP is dysregulated in Duchenne muscular dystrophy (DMD), we examined the effects of transgenic PGC-1alpha in muscle of mdx mice. These animals show improvement in parameters characteristic of DMD, including muscle histology, running performance, and plasma creatine kinase levels. Thus, control of PGC-1alpha levels in skeletal muscle could represent a novel avenue to prevent or treat DMD.
Two different genes encode fibronectin binding proteins in Staphylococcus aureus (1991)

A gene encoding a fibronectin binding protein (FnBP) has recently been isolated and sequenced from Staphylococcus aureus strain 8325-4. In the same bacterial strain, 682 bp downstream to the stop codon of this gene (fnbA), a second gene termed fnbB has not been discovered, encoding another FnBP (FnBPB). The two genes show in large parts striking sequence homologies. The complete amino acid sequence encoded by fnbB has been deduced and compared to that deduced from fnbA. In FnBPB a stretch of 66 amino acids downstream to the signal peptide has 75% identity with the corresponding region in FnBPA. At the C-terminal site another 394 amino acid stretch is almost identical in both gene products. This stretch contains the 38 amino acid long D repeats, the wall spanning Wr repeats and the hydrophobic membrane spanning domain. In FnBPA each of the three D repeats has been identified as a fibronectin binding structure. These structures are highly conserved in FnBPB and most likely represent the major Fn-binding domain of this protein. However, a subclone of gene fnbB lacking the coding region for the D repeats also clearly expresses fibronectin binding activity. This additional binding site is so far unique for FnBPB and interacts like the D domains with the N-terminal 24-31-kDa fragment of fibronectin. The purified recombinant FnBP fragment (not containing the D repeats) completely inhibits the binding of fibronectin to whole cells of S. aureus.
Factor IX Padua: them that have, give (2012)

In this issue of Blood, Finn et al have taken a factor IX variant with increased specific activity associated with thrombophilia and used it to improve gene therapy of hemophilia B in dogs, and Cantore et al have shown similar results in mice.
Comparison of the bovine herpesvirus 1 gI gene and the herpes simplex virus type 1 gB gene (1988)

In a previous report, we localized the gene for a 130-kilodalton envelope glycoprotein (gI) of bovine herpesvirus 1 (BHV-1) to a 3.6-kilobase HpaI-KpnI restriction endonuclease fragment from the long unique region of the BHV-1 genome (map position 0.405 to 0.432) and showed that a herpes simplex virus 1 (HSV-1) glycoprotein B (gB) probe uniquely hybridized to this BHV-1 restriction fragment. Here we present the complete nucleotide sequence of the BHV-1 gI gene and the predicted 932-amino-acid sequence of the gI primary translation product. Comparison with the published nucleotide sequence of the HSV-1 (KOS) gB gene (D. J. Bzik, B. A. Fox, N. A. DeLuca, and S. Person, Virology 133:301-314, 1984) reveals a similarity of 56.3% at the nucleotide level and 45.9% at the amino acid level. Upstream of the proposed gI coding region are potential mRNA transcriptional promoter elements including a TATA box and multiple Sp1 binding sites (GC boxes). Downstream of the gI coding region are two sequence elements associated with mRNA cleavage and polyadenylation (AATAAA and a GT-rich region roughly 30 nucleotides further downstream). Like HSV-1 gB, the predicted gI amino acid sequence exhibits two broad hydrophobic regions likely to represent a transient amino-terminal signal sequence and a transmembrane anchor domain (near the carboxyl terminus). Additional features shared with gB include 6 potential N-linked glycosylation sites and 10 highly conserved cysteine residues in the gI extracellular domain. Two regions of nonsimilarity between gI and gB are a centrally located 22-amino-acid region of gI for which there is essentially no gB counterpart and the transient amino-terminal leaders which differ in both size and sequence. The hydrophobic signal sequence of the gI leader, unlike that of gB, is preceded by an unusually large region of predominantly hydrophilic amino acids. The unusual length of the gI leader may result from an overlap between that portion of the gI coding region and a potential upstream coding region.