gebhart/patrepeval huggingface dataset:
Synthesis and Characterization of Chimeric Proteins Based on Cellulase and Xylanase from an Insect Gut Bacterium (2011)

Insects living on wood and plants harbor a large variety of bacterial flora in their guts for degrading biomass. We isolated a Paenibacillus strain, designated ICGEB2008, from the gut of a cotton bollworm on the basis of its ability to secrete a variety of plant-hydrolyzing enzymes. In this study, we cloned, expressed, and characterized two enzymes, β-1,4-endoglucanase (Endo5A) and β-1,4-endoxylanase (Xyl11D), from the ICGEB2008 strain and synthesized recombinant bifunctional enzymes based on Endo5A and Xyl11D. The gene encoding Endo5A was obtained from the genome of the ICGEB2008 strain by shotgun cloning. The gene encoding Xyl11D was obtained using primers for conserved xylanase sequences, which were identified by aligning xylanase sequences in other species of Paenibacillus. Endo5A and Xyl11D were overexpressed in Escherichia coli, and their optimal activities were characterized. Both Endo5A and Xyl11D exhibited maximum specific activity at 50°C and pH 6 to 7. To take advantage of this feature, we constructed four bifunctional chimeric models of Endo5A and Xyl11D by fusing the encoding genes either end to end or through a glycine-serine (GS) linker. We predicted three-dimensional structures of the four models using the I-TASSER server and analyzed their secondary structures using circular dichroism (CD) spectroscopy. The chimeric model Endo5A-GS-Xyl11D, in which a linker separated the two enzymes, yielded the highest C-score on the I-TASSER server, exhibited secondary structure properties closest to the native enzymes, and demonstrated 1.6-fold and 2.3-fold higher enzyme activity than Endo5A and Xyl11D, respectively. This bifunctional enzyme could be effective for hydrolyzing plant biomass owing to its broad substrate range.
Synthese und strukturchemische Untersuchungen von Münzmetall(I)-Quecksilber(II)-sulfidhalogeniden sowie Charakterisierung von Titandioxid-Photokatalysatoren - Einfluss von Synthesemethode und Dotierung (2004)

Diese Dissertation gliedert sich in zwei unterschiedliche Themenbereiche: Im ersten Teil der Arbeit wird über die Fortschritte im Bereich der Synthese und Charakterisierung der Münzmetall(I)-Quecksilber(II)-sulfidhalogenide sowie verwandter Verbindungen berichtet. Hier gelang die Synthese und strukturchemische Beschreibung der Verbindungen CuHgSI, CuHg2S2I, a-AgHgSI, b-AgHgSI und Ag2HgSI2. Zur Kristallstrukturbestimmung wurde hauptsächlich die Röntgenstrukturanalyse an Einkristallen eingesetzt. Die Charakterisierung der Verbindungen wurde durch differenzthermoanalytische Messungen, Schwingungsspektroskopie und Berechnungen der Elektronenlokalisierungsfunktionen ergänzt. Mit Hilfe dieser Untersuchungen gelang die Entwicklung eines Ordnungsprinzips für alle bisher strukturell beschriebenen Münzmetall(I)-Quecksilber(II)-sulfidhalogenide. Der zweite Teil dieser Dissertation behandelt die im Bereich der Titandioxid-Photokatalysatoren durchgeführten Experimente zum Einfluss von Dotierungen und Synthesevariationen auf die Eigenschaften der Katalysatormaterialien. Hierbei wurden erstmals bidotierte (gleichzeitige n- und p-Dotierung) Titandioxidpulver charakterisiert. Die katalytische Wirksamkeit der Materialien wurde mittels Abbauexperimenten an Modellsubstanzen untersucht.
Influence of oxygen adsorption from atmosphere on surface tension of liquid silicon (2021)

Influences of temperature and oxygen adsorption on the surface tension of liquid silicon were investigated by the oscillating droplet method using the electromagnetic levitation technique. Oxygen partial pressure in the vicinity of the liquid surface was controlled by the theoretically derived Ratto, Ricci, and Arato model and the effectiveness of which was experimentally confirmed from the in situ observation of oxidation and reduction behaviors of the droplet surface in this study. The surface tension of liquid silicon was decreased with increasing oxygen partial pressure in the vicinity of the liquid surface due to oxygen adsorption at low temperature, whereas the surface tension converged to a pure state value at high temperature regardless of the oxygen partial pressure due to a decrease in the equilibrium constant of oxygen adsorption reaction. As a result, “boomerang shape” temperature dependence of surface tension was observed; the gradient of the temperature dependence of surface tension was gradually increased with elevating temperature and then became a constant value at high temperature. The influences of oxygen adsorption and temperature on surface tension were successfully derived from the measurement result by using the Szyszkowski equation. Furthermore, the changes in enthalpy and entropy for oxygen adsorption on liquid silicon were also estimated.
Serological homologies between H1 degrees and H5 include the carboxyl-terminal domain. (1985)

We have reported previously that antibodies to chicken H5 and antibodies to H1 both cross-react with mammalian H1 degree (Mura, C. V., and Stollar, B. D. (1981) J. Biol. Chem. 256, 9767-9769). The antigenic sites in H1 degree recognized by these antibodies were analyzed using immunoblotting. Peptides of H1 degree were prepared by partial digestion with acetic acid and tested for reactivity with: 1) antibodies induced by H5 alone, which reacted primarily with the central globular region of H5; 2) antibodies induced by H5 X RNA complexes, which reacted with this domain as well as the basic COOH-terminal domain; and 3) antiserum to calf thymus H1. Anti-H5 antibodies (anti-globular region) cross-reacted with H1 degree peptides that co-migrated with peptides of H5 that contain the globular region, but did not cross-react with H1. Anti-H5/RNA antibodies (anti-globular + anti-COOH-terminal) cross-reacted with these peptides and, in addition, with a lysine-rich H1 degree peptide that co-migrated with the basic COOH-terminal H5 peptide. This H1 degree peptide, but not the putative globular H1 degree peptides, was also recognized by an antiserum to calf H1 which was primarily reactive with the large, COOH-terminal N-bromosuccinimide fragment of calf H1. A weaker cross-reaction between this antiserum and the carboxyl-terminal domain of H5 could be visualized when large quantities of H5 were used in immunoblots. The results indicate that structural homologies between H5 and H1 degree extend beyond the globular region and into the lysine-rich carboxyl-terminal domain. Antigenic homologies between H1 degree and H1 are also at least partially localized in this domain. H1 degree is serologically intermediate between H5 and H1.
Application of Directly Coupled High-performance Liquid Chromatography–Nuclear Magnetic Resonance–Mass Spectrometry to the Detection and Characterisation of the Metabolites of 2-Bromo-4-trifluoromethylaniline in Rat Urine (1997)

Directly coupled HPLC–NMR–MS was used to identify the major urinary metabolite of 2-bromo-4-trifluoromethylaniline in the rat as the sulfate conjugate of 2-bromo-4-trifluoromethyl-6-hydroxyaniline. This metabolite could not have been fully characterised using HPLC–NMR or HPLC–MS alone as the sulfate group is ‘NMR silent’ and MS would not have enabled the position of substitution on the aromatic ring to have been assigned. The need to carefully select HPLC solvents for directly coupled HPLC–NMR–MS so that NMR and MS data can both be obtained is also shown.
Terahertz repetition rates from harmonic modelocked monolithic compound-cavity laser diodes (2002)

Novel compound-cavity laser diodes are modelocked at a harmonic of the fundamental round-trip frequency to achieve repetition rates of up to 2.1 THz. The devices are fabricated from GaAs-AlGaAs material at a wavelength of 860 nm and incorporate two gain sections with an etched slot reflector between them, and a saturable absorber section. Autocorrelation studies are used to investigate device behaviour for different reflector types and reflectivity. These lasers may find applications in terahertz imaging, medicine, ultrafast optical links, and atmospheric sensing.
Dimensions in program synthesis (2010)

Program Synthesis, which is the task of discovering programs that realize user intent, can be useful in several scenarios: enabling people with no programming background to develop utility programs, helping regular programmers automatically discover tricky/mundane details, program understanding, discovery of new algorithms, and even teaching.
Bis-Lactam as Acceptor (2017)

Key words bis-lactam acceptor - donor–acceptor polymers - organic solar cell
Biomarkers in Systemic Sclerosis (2010)

Systemic sclerosis is an autoimmune inflammatory disorder of unknown etiologycharacterized b y pronounced fibroproliferative alterations in the microvasculature, and frequent cellular and humoral immunity abnormalities, culminating in a severe and often progressive fibrotic process. Numerous biomarkers reflecting the three main pathogenetic mechanisms in systemic sclerosis have been described; however, aside from several disease-specific autoantibodies, other biomarkers have not been thoroughly validated and require further study. Thus, there is an unmet need for validated biomarkers for diagnosis, disease classification, and evaluation of organ involvement and therapeutic response in systemic sclerosis.
Ultrafast Heme−Residue Bond Formation in Six-Coordinate Heme Proteins: Implications for Functional Ligand Exchange (2008)

A survey is presented of picosecond kinetics of heme-residue bond formation after photolysis of histidine, methionine, or cysteine, in a broad range of ferrous six-coordinate heme proteins. These include human neuroglobin, a bacterial heme-binding superoxide dismutase (SOD), plant cytochrome b 559, the insect nuclear receptor E75, horse heart cytochrome c and the heme domain of the bacterial sensor protein Dos. We demonstrate that the fastest and dominant phase of binding of amino acid residues to domed heme invariably takes place with a time constant in the narrow range of 5-7 ps. Remarkably, this is also the case in the heme-binding SOD, where the heme is solvent-exposed. We reason that this fast phase corresponds to barrierless formation of the heme-residue bond from a configuration close to the bound state. Only in proteins where functional ligand exchange occurs, additional slower rebinding takes place on the time scale of tens of picoseconds after residue dissociation. We propose that the presence of these slower phases reflects flexibility in the heme environment that allows external ligands (O2, CO, NO, . . .) to functionally replace the internal residue after thermal dissociation of the heme-residue bond.
The emergence of molecular gynecology: homeobox and Wnt genes in the female reproductive tract (2000)

Reproductive tissues respond to steroid hormones and thus are particularly vulnerable to the effects of exogenous steroid ‘mimic’ compounds (endocrine disrupters). One such endocrine disrupter, diethylstilbestrol (DES), is linked to gynecological cancers and changes in uterine structure that reduce or completely abrogate reproductive competence. Until recently, little was known about the identity of target genes and signaling pathways involved in pathologies linked to endocrine disrupters such as DES. We outline genetic, cellular and molecular roles for patterning genes, with emphasis on homeobox and Wnt genes. There is evidence that changes in the expression of Wnt and homeogenes underlie many of the defects induced by DES. Data obtained from murine systems will likely apply to a broad spectrum of gynecological pathologies involving abnormal cell behaviors ranging from fibroids to malignant tumors. Knowledge garnered from modern molecular genetics should lead to progress in the emerging field of molecular gynecology. BioEssays 22:902–910, 2000. © 2000 John Wiley & Sons, Inc.
Polypropylene-Process selection criteria (1984)

Production based on traditional catalysts involved, after the polymerization reaction, catalyst residues removal (deashing) and separation of isotactic polypropylene (desired product) from atactic polypropylene (low-value product). The deashing reaction poisoned the unreacted monomers and any solvents, requiring purification of these before recycle to the reaction. An effluent treatment section was also needed. The new catalysts developed by Montedison* in cooperation with Mitsui Petrochemicals in the last few years allow the polymer structure, yield, selectivity and morphology to be controlled in the reaction stage. The production processes have therefore been drastically simplified. In addition, the complete control over catalysis has resulted in remarkable quality improvements and in an expanded product range.
Scaffold-free Three-dimensional Graft From Autologous Adipose-derived Stem Cells for Large Bone Defect Reconstruction (2015)

Long bone nonunion in the context of congenital pseudarthrosis or carcinologic resection (with intercalary bone allograft implantation) is one of the most challenging pathologies in pediatric orthopedics. Autologous cancellous bone remains the gold standard in this context of long bone nonunion reconstruction, but with several clinical limitations. We then assessed the feasibility and safety of human autologous scaffold-free osteogenic 3-dimensional (3D) graft (derived from autologous adipose-derived stem cells [ASCs]) to cure a bone nonunion in extreme clinical and pathophysiological conditions. Human ASCs (obtained from subcutaneous adipose tissue of 6 patients and expanded up to passage 4) were incubated in osteogenic media and supplemented with demineralized bone matrix to obtain the scaffold-free 3D osteogenic structure as confirmed in vitro by histomorphometry for osteogenesis and mineralization. The 3D "bone-like" structure was finally transplanted for 3 patients with bone tumor and 3 patients with bone pseudarthrosis (2 congenital, 1 acquired) to assess the clinical feasibility, safety, and efficacy. Although minor clones with structural aberrations (aneuploidies, such as tri or tetraploidies or clonal trisomy 7 in 6%-20% of cells) were detected in the undifferentiated ASCs at passage 4, the osteogenic differentiation significantly reduced these clonal anomalies. The final osteogenic product was stable, did not rupture with forceps manipulation, did not induce donor site morbidity, and was easily implanted directly into the bone defect. No acute (<3 mo) side effects, such as impaired wound healing, pain, inflammatory reaction, and infection, or long-term side effects, such as tumor development, were associated with the graft up to 4 years after transplantation. We report for the first time that autologous ASC can be fully differentiated into a 3D osteogenic-like implant without any scaffold. We demonstrated that this engineered tissue can safely promote osteogenesis in extreme conditions of bone nonunions with minor donor site morbidity and no oncological side effects.
Fixation of the Cemented Stem: Clinical Relevance of the Porosity and Thickness of the Cement Mantle (2009)

The aim of this review paper is to define the fixation of the cemented stem. Polymethyl methacrylate, otherwise known as "bone cement", has been used in the fixation of hip implants since the early 1960s. Sir John Charnley, the pioneer of modern hip replacement, incorporated the use of cement in the development of low frictional torque hip arthroplasty. In this paper, the concepts of femoral stem design and fixation, clinical results, and advances in understanding of the optimal use of cement are reviewed. The purpose of this paper is to help understanding and discussions on the thickness and the porosity of the cement mantle in total hip arthroplasty. Cement does not act as an adhesive, as sometimes thought, but relies on an interlocking fit to provide mechanical stability at the cement-bone interface, while at the prosthesis- cement interface it achieves stability by optimizing the fit of the implant in the cement mantle, such as in a tapered femoral stem.
Nanoscale Defects and Surface Preparation in Nanomanufacturing (2017)

The field of particle removal and surface cleaning in general extends far beyond the electronics industry. An era of the most challenging cleaning applications in nanomanufacturing is upon us. Surfaces prepared for nanoscale applications, such as deposition of mono-layers or self-assembly of nanoelements, need to be completely free of any particulate contamination on the order of a nanometer or less. Nanoscale contamination removal from nanostructures has been studied both experimentally and theoretically using numerical modeling. One promising approach is the use of high-frequency pulsating flow to enhance transport from small cavities by enhanced convective mixing. The double layer force, which can be attractive or repulsive, also plays a role in the removal of particles. A computational fluid dynamic model has been developed to get a better understanding of the detachment mechanism and the particle removal and transport during megasonic cleaning and the effect of time and frequency on cleaning.
Whole-animal Imaging and Flow Cytometric Techniques for Analysis of Antigen-specific CD8+ T Cell Responses after Nanoparticle Vaccination (2015)

Traditional vaccine adjuvants, such as alum, elicit suboptimal CD8+ T cell responses. To address this major challenge in vaccine development, various nanoparticle systems have been engineered to mimic features of pathogens to improve antigen delivery to draining lymph nodes and increase antigen uptake by antigen-presenting cells, leading to new vaccine formulations optimized for induction of antigen-specific CD8+ T cell responses. In this article, we describe the synthesis of a “pathogen-mimicking” nanoparticle system, termed interbilayer-crosslinked multilamellar vesicles (ICMVs) that can serve as an effective vaccine carrier for co-delivery of subunit antigens and immunostimulatory agents and elicitation of potent cytotoxic CD8+ T lymphocyte (CTL) responses. We describe methods for characterizing hydrodynamic size and surface charge of vaccine nanoparticles with dynamic light scattering and zeta potential analyzer and present a confocal microscopy-based procedure to analyze nanoparticle-mediated antigen delivery to draining lymph nodes. Furthermore, we show a new bioluminescence whole-animal imaging technique utilizing adoptive transfer of luciferase-expressing, antigen-specific CD8+ T cells into recipient mice, followed by nanoparticle vaccination, which permits non-invasive interrogation of expansion and trafficking patterns of CTLs in real time. We also describe tetramer staining and flow cytometric analysis of peripheral blood mononuclear cells for longitudinal quantification of endogenous T cell responses in mice vaccinated with nanoparticles.
The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design (2016)

The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein folding and improve structure prediction efforts, especially with respect to difficult to characterize states, such as disordered or unfolded states. Host-guest peptide series are a useful tool in examining the propensities of the amino acids free from the surrounding protein structure. Here, we compare the distributions of the backbone dihedral angles (φ/ψ) of the 20 proteogenic amino acids in two different sequence contexts using the AAXAA and GGXGG host-guest pentapeptide series. We further examine their intrinsic behaviors across three environmental contexts: water at 298 K, water at 498 K, and 8 M urea at 298 K. The GGXGG systems provide the intrinsic amino acid propensities devoid of any conformational context. The alanine residues in the AAXAA series enforce backbone chirality, thereby providing a model of the intrinsic behavior of amino acids in a protein chain. Our results show modest differences in φ/ψ distributions due to the steric constraints of the Ala side chains, the magnitudes of which are dependent on the denaturing conditions. One of the strongest factors modulating φ/ψ distributions was the protonation of titratable side chains, and the largest differences observed were in the amino acid propensities for the rarely sampled αL region.
Clinical relevance of breast and gastric cancer-associated polymorphisms as potential susceptibility markers for oral clefts in the Brazilian population (2017)

The results suggest that polymorphic variants in AXIN2 and CDH1 may be associated with NSCL ± P susceptibility, and reinforce the putative link between cancer and oral clefts.
Buffered Bloom Filters on Solid State Storage. (2010)

Bloom Filters are widely used in many applications including database management systems. With a certain allowable error rate, this data structure provides an efficient solution for membership queries. The error rate is inversely proportional to the size of the Bloom filter. Currently, Bloom filters are stored in main memory because the low locality of operations makes them impractical on secondary storage. In multi-user database management systems, where there is a high contention for the shared memory heap, the limited memory available for allocating a Bloom filter may cause a high rate of false positives. In this paper we are proposing a technique to reduce the memory requirement for Bloom filters with the help of solid state storage devices (SSD). By using a limited memory space for buffering the read/write requests, we can afford a larger SSD space for the actual Bloom filter bit vector. In our experiments we show that with significantly less memory requirement and fewer hash functions the proposed technique reduces the false positive rate effectively. In addition, the proposed data structure runs faster than the traditional Bloom filters by grouping the inserted records with respect to their locality on the filter. 1.
The Total Synthesis of Proposed Immunoactive Glycolipids from S. Pneumoniae and a Re-evaluation of Their Immunological Activity (2021)

Invariant natural killer T cells (iNKT) are responsible for the production of pro-inflammatory cytokines which induce a systemic immune response. They are distinctive in possessing an invariant T-cell receptor that recognizes glycolipid antigens presented by the class I major histocompatibility complex-related protein CD1d, conserved across multiple mammalian species in a class of proteins well-renowned for their high degree of polymorphism. This receptor’s first identified antigen is the potent α-galactose ceramide, KRN7000, a glycosphingolipid isolated from bacteria that were found on a Japanese marine sponge. The corresponding terrestrial antigen remained unidentified until quite recently, when diacylglycerol-containing glycolipids, reported to activate iNKT cells, were isolated from Streptococcus pneumoniae. We report the total synthesis and immunological re-evaluation of these two glycolipids. The compounds are unable to meaningfully activate iNKT cells. Computational modelling shows that these ligands, while being capable of interacting with the CD1d receptor, create a different surface for the binary complex that makes formation of the ternary complex with the iNKT T-cell receptor difficult. Together these results suggest that the reported activity might have been due to an impurity in the original isolated sample and highlights the importance of taking care when reporting biological activity from isolated natural products.