gebhart/patrepeval huggingface dataset:
Rapid Evolution of β-Glucuronidase Specificity by Saturation Mutagenesis of an Active Site Loop (2004)

Protein engineers have widely adopted directed evolution as a design algorithm, but practitioners have not come to a consensus about the best method to evolve protein molecular recognition. We previously used DNA shuffling to direct the evolution of Escherichia coli beta-glucuronidase (GUS) variants with increased beta-galactosidase activity. Epistatic (synergistic) mutations in amino acids 557, 566, and 568, which are part of an active site loop, were identified in that experiment (Matsumura, I., and Ellington, A. D. (2001) J. Mol. Biol. 305, 331-339). Here we show that site saturation mutagenesis of these residues, overexpression of the resulting library in E. coli, and high throughput screening led to the rapid evolution of clones exhibiting increased activity in reactions with p-nitrophenyl-beta-d-xylopyranoside (pNP-xyl). The xylosidase activities of the 14 fittest clones were 30-fold higher on average than that of the wild-type GUS. The 14 corresponding plasmids were pooled, amplified by long PCR, self-ligated with T4 DNA ligase, and transformed into E. coli. Thirteen clones exhibiting an average of 80-fold improvement in xylosidase activity were isolated in a second round of screening. One of the evolved proteins exhibited a approximately 200-fold improvement over the wild type in reactivity (k(cat)/K(m)) with pNP-xyl, with a 290,000-fold inversion of specificity. Sequence analysis of the 13 round 2 isolates suggested that all were products of intermolecular recombination events that occurred during whole plasmid PCR. Further rounds of evolution using DNA shuffling and staggered extension process (StEP) resulted in modest improvement. These results underscore the importance of epistatic interactions and demonstrate that they can be optimized through variations of the facile whole plasmid PCR technique.
Countercurrent purification of the tetrahydro iso‐α acids derived from Humulus lupulus L. (2010)

A comprehensive two-dimensional liquid chromatography system was developed to precisely describe the molecular heterogeneity of fatty alcohol ethoxylates. The end-group functionality was analyzed by gradient HPLC while ethylene oxide oligomer distributions were characterized by liquid adsorption chromatography. A baseline separation of all functionality fractions irrespective of the ethylene oxide oligomer chain length was achieved on nonpolar X-Terra(®) C(18) with a methanol-water gradient, whereas an isocratic flow of isopropanol-water on a polar Chromolith(®) Si column gave a separation according to the oligomer chain length without interference of the end-group distribution. The combination of these two methods to conduct online two-dimensional liquid chromatography experiments resulted in a comprehensive two-dimensional picture on the molecular heterogeneity of the sample.
Tailoring Many-Body Interactions to Solve Hard Combinatorial Problems (1997)

A quantum machine consisting of interacting linear clusters of atoms is proposed for the 3SAT problem. Each cluster with two relevant states of collective motion can be used to register a Boolean variable. Given any 3SAT Boolean formula the interactions among the clusters can be so tailored that the ground state(s) (possibly degenerate) of the whole system encodes the satisfying truth assignment(s) for it. This relates the 3SAT problem to the dynamics of the properly designed glass system.
Physical mechanisms of transient enhanced dopant diffusion in ion-implanted silicon (1997)

Implanted B and P dopants in Si exhibit transient enhanced diffusion (TED) during annealing which arises from the excess interstitials generated by the implant. In order to study the mechanisms of TED, transmission electron microscopy measurements of implantation damage were combined with B diffusion experiments using doping marker structures grown by molecular-beam epitaxy (MBE). Damage from nonamorphizing Si implants at doses ranging from 5×1012 to 1×1014/cm2 evolves into a distribution of {311} interstitial agglomerates during the initial annealing stages at 670–815 °C. The excess interstitial concentration contained in these defects roughly equals the implanted ion dose, an observation that is corroborated by atomistic Monte Carlo simulations of implantation and annealing processes. The injection of interstitials from the damage region involves the dissolution of {311} defects during Ostwald ripening with an activation energy of 3.8±0.2 eV. The excess interstitials drive substitutional B into electrically inactive, metastable clusters of presumably two or three B atoms at concentrations below the solid solubility, thus explaining the generally observed immobile B peak during TED of ion-implanted B. Injected interstitials undergo retarded diffusion in the MBE-grown Si with an effective migration energy of ∼3.5 eV, which arises from trapping at substitutional C. The concept of trap-limited diffusion provides a stepping stone for understanding the enormous disparity among published values for the interstitial diffusivity in Si. The population of excess interstitials is strongly reduced by incorporating substitutional C in Si to levels of ∼1019/cm3 prior to ion implantation. This provides a promising method for suppressing TED, thus enabling shallow junction formation in future Si devices through dopant implantation. The present insights have been implemented into a process simulator, allowing for a significant improvement of the predictive modeling of TED.
Ventricular fibrillation in myopathic human hearts: mechanistic insights from in vivo global endocardial and epicardial mapping (2007)

Ventricular fibrillation (VF) is an important cause of sudden cardiac death and cardiovascular mortality in patients with cardiomyopathy. Although it was generally believed that chaotic reentrant wavefronts underlie VF in humans, there is emerging evidence of spatiotemporal organization during early VF. The mechanism of this organization of electrical activity in early VF is unknown in myopathic hearts. We studied early VF in vivo, intraoperatively in five cardiomyopathic patients. Simultaneous electrograms were obtained from the epicardium and endocardium in left ventricular cardiomyopathy and from the endocardium in right ventricular myopathy. The Hilbert transform was used to derive the phase of the electrograms. Rotors were identified by isolating phase singularity points. Rotors were present in all of the myopathic hearts studied during VF and cumulatively lasted a mean of 3.2 +/- 2.0 s of the 7.0 +/- 4.0 s of the VF segments analyzed. For each surface mapped, 3.6 +/- 2.9 rotors were identified for the duration mapped. The average number of cycles completed by these rotors was 4.9 +/- 4.9. The longest rotor lasted 10.2 +/- 6.2 rotations and lasted 2.0 +/- 1.2 s. The rotors on the endocardium had a cycle length of 192 +/- 33 ms compared with 220 +/- 15 ms on the epicardium (P=0.08). There is centrifugal activation of electrical activity from these rotors, and they give rise to domains that activate at faster rates with evidence of conduction block at the border with slower domains. These rotors frequently localized to border regions of myocardium with bipolar electrogram amplitude of <0.5 mV. The organization of electrical activity during early VF in myopathic human hearts is characterized by wavefronts emanating from a few rotors.
Angiogenesis: a new diagnostic aspect of obstetric and gynecologic echography (1993)

An ultrasounds triplex system (pulsed Doppler, Color mode, B mode) has been employed to study ovarian and uterine circulatory changes in fertile, infertile and postmenopausal patients. PI and mean percentage variation of PI mean values have been used. No difference has been detected in uterine haemodynamics between fertile women and those infertile patients getting pregnant by IVF-ET procedure. Patients who did not obtain the pregnancy showed different uterine and endometrial Color Doppler patterns. Furthermore, a typical endometrial blood flow has been detected both in fertile patients and infertile patients who get pregnant. Color Doppler seems to be an useful tool in the monitoring of fibroids blood supply and the uterine blood supply, especially for the clinical monitoring of GnRH analogues therapies. The technique has been also employed for the study of ectopic pregnancy. The evaluation of both uterine and throphoblast haemodynamics has resulted in a good indicator of the pregnancy progression. Concerning the ovarian pathology the color Doppler evaluation has been useful to differentiate ovarian malignant cysts from inflammatory or disfunctional masses. Nevertheless, the most interesting results have been obtained from the study of endometrial and ovarian tumors. Indeed, in the most cases, a mass supply blood flow has been detected, although in some cases no angiogenetic color flow has been found. No difference has been found in uterine artery velocimetry between malign or benign pathologies. Furthermore, histological data supporting our findings are presented.
Identification of potential conserved RNA secondary structure throughout influenza A coding regions (2011)

Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for conserved secondary structure. The predictions are based on identifying regions of unusual thermodynamic stabilities and are correlated with studies of suppression of synonymous codon usage (SSCU). The results indicate that secondary structure is favored in the (+) sense influenza RNA. Twenty regions with putative conserved RNA structure have been identified, including two previously described structured regions. Of these predictions, eight have high thermodynamic stability and SSCU, with five of these corresponding to current annotations (e.g., splice sites), while the remaining 12 are predicted by the thermodynamics alone. Secondary structures with high conservation of base-pairing are proposed within the five regions having known function. A combination of thermodynamics, amino acid and nucleotide sequence comparisons along with SSCU was essential for revealing potential secondary structures.
T Regulatory and Primed Uncommitted CD4 T Cells Express CD73, Which Suppresses Effector CD4 T Cells by Converting 5′-Adenosine Monophosphate to Adenosine (2006)

CD73 (5'-ectonucleotidase) is expressed by two distinct mouse CD4 T cell populations: CD25+ (FoxP3+) T regulatory (Treg) cells that suppress T cell proliferation but do not secrete IL-2, and CD25- uncommitted primed precursor Th (Thpp) cells that secrete IL-2 but do not suppress in standard Treg suppressor assays. CD73 on both Treg and Thpp cells converted extracellular 5'-AMP to adenosine. Adenosine suppressed proliferation and cytokine secretion of Th1 and Th2 effector cells, even when target cells were activated by anti-CD3 and anti-CD28. This represents an additional suppressive mechanism of Treg cells and a previously unrecognized suppressive activity of Thpp cells. Infiltration of either Treg or Thpp cells at inflammatory sites could potentially convert 5'-AMP generated by neutrophils or dying cells into the anti-inflammatory mediator adenosine, thus dampening excessive immune reactions.
Fatty acids as natural uncouplers preventing generation of O⋅−2 and H2O2 by mitochondria in the resting state (1998)

Both natural (laurate) and artificial (m-chlorocarbonylcyanide phenylhydrazone; CCCP) uncouplers strongly inhibit O2.- and H2O2 formation by rat heart mitochondria oxidizing succinate. Carboxyatractylate, an ATP/ADP antiporter inhibitor, abolishes the laurate inhibition, the CCCP inhibition being unaffected. Atractylate partially releases the inhibition by laurate and decelerates the releasing effect of carboxyatractylate. GDP is much less effective than carboxyatractylate in releasing the laurate inhibition of reactive oxygen species (ROS) formation. Micromolar laurate concentrations arresting the ROS formation cause strong inhibition of reverse electron transfer from succinate to NAD+, whereas State 4 respiration and the transmembrane electric potential difference (delta psi) level are affected only slightly. It is suggested that (i) free fatty acids operate as natural 'mild uncouplers' preventing the transmembrane electrochemical H+ potential difference (delta muH+) from being above a threshold critical for ROS formation by complex I and, to a lesser degree, by complex III of the respiratory chain, and (ii) it is the ATP/ADP-antiporter, rather than uncoupling protein 2, that is mainly involved in this antioxidant mechanism of heart muscle mitochondria.
DNA polymerase insertion fidelity. Gel assay for site-specific kinetics. (1987)

A quantitative assay based on gel electrophoresis is described to measure nucleotide insertion kinetics at an arbitrary DNA template site. The assay is used to investigate kinetic mechanisms governing the fidelity of DNA synthesis using highly purified Drosophila DNA polymerase alpha holoenzyme complex and M13 primer-template DNA. Km and Vmax values are reported for correct insertion of A and misinsertion of G, C, and T opposite a single template T site. The misinsertion frequencies are 2 X 10(-4) for G-T and 5 X 10(-5) for both C-T and T-T relative to normal A-T base pairs. The dissociation constant of the polymerase-DNA-dNTP complex, as measured by Km, plays a dominant role in determining the rates of forming right and wrong base pairs. Compared with Km for insertion of A opposite T (3.7 +/- 0.7 microM), the Km value is 1100-fold greater for misinsertion of G opposite T (4.2 +/- 0.4 mM), and 2600-fold greater for misinsertion of either C or T opposite T (9.8 +/- 4.2 mM). These Km differences indicate that in the enzyme binding site the stability of A-T base pairs is 4.3 kcal/mol greater than G-T pairs and 4.9 kcal/mol greater than C-T or T-T pairs. In contrast to the large differences in Km, differences in Vmax are relatively small. There is only a 4-fold reduction in Vmax for insertion of G opposite T and an 8-fold reduction for C or T opposite T, compared with the correct insertion of A. For the specific template T site investigated, the nucleotide insertion fidelity for Drosophila polymerase alpha seems to be governed primarily by a Km discrimination mechanism.
Cerebrovascular accident after percutaneous rf thermocoagulation of the trigeminal ganglion (1976)

A case of cerebrovascular accident associated with percutaneous radiofrequency thermocoagulation of the trigeminal ganglion is presented in the hope of alerting other surgeons to this possible complication.
Serine proteases: new players in diarrhoea-predominant irritable bowel syndrome (2008)

Comment on: "Increased faecal serine protease activity in diarrhoeic&#13;\nIBS patients: a colonic lumenal factor impairing&#13;\ncolonic permeability and sensitivity". Gecse K, Róka R,&#13;\nFerrier L, Leveque M, Eutamene H, Cartier C, Ait-&#13;\nBelgnaoui A, Rosztóczy A, Izbéki F, Fioramonti J, et al.&#13;\nGut 2008; 57:591-9.
In vivo Microscopic Photoacoustic Spectroscopy for Non-Invasive Glucose Monitoring Invulnerable to Skin Secretion Products (2018)

Photoacoustic spectroscopy has been shown to be a promising tool for non-invasive blood glucose monitoring. However, the repeatability of such a method is susceptible to changes in skin condition, which is dependent on hand washing and drying due to the high absorption of infrared excitation light to the skin secretion products or water. In this paper, we present a method to meet the challenges of mid-infrared photoacoustic spectroscopy for non-invasive glucose monitoring. By obtaining the microscopic spatial information of skin during the spectroscopy measurement, the skin region where the infrared spectra is insensitive to skin condition can be locally selected, which enables reliable prediction of the blood glucose level from the photoacoustic spectroscopy signals. Our raster-scan imaging showed that the skin condition for in vivo spectroscopic glucose monitoring had significant inhomogeneities and large variability in the probing area where the signal was acquired. However, the selective localization of the probing led to a reduction in the effects of variability due to the skin secretion product. Looking forward, this technology has broader applications not only in continuous glucose monitoring for diabetic patient care, but in forensic science, the diagnosis of malfunctioning sweat pores, and the discrimination of tumors extracted via biopsy.
Human natural anti-Gal IgG regulates alternative complement pathway activation on bacterial surfaces. (1992)

One percent of circulating IgG in humans recognizes galactose alpha 1,3 galactose residues (anti-Gal) and is synthesized in response to stimulation by enteric bacteria. In this study, we found that the prevalence of binding of anti-Gal to blood isolates is significantly higher than its binding to normal stool isolates. When anti-Gal bound onto the lipopolysaccharide of a representative blood isolate, Serratia marcescens #21, it blocked its alternative complement pathway (ACP) lysis and made the organism serum resistant. In contrast, when anti-Gal bound to the capsular polysaccharide of a serum sensitive Serratia, #7, it increased ACP killing of this strain. The mechanism of blockade of ACP lysis by anti-Gal did not involve a decrease in the number of C3 molecules deposited onto Serratia #21 or an inhibition of the binding of C3b to its LPS, nor did it change the iC3b and C3d degradation products of bound C3b or prevent membrane attack complex formation on this organism. Our findings suggest that the effect of anti-Gal on immune lysis is dependent on the bacterial outer membrane structure to which it binds. We postulate that anti-Gal may play a role in the survival of selected Enterobacteriacae in Gram-negative sepsis by blocking ACP-mediated lysis of such bacteria by the nonimmune host, and that this effect depends on where anti-Gal finds its epitope on the bacterial outer membrane.
The formalin test in mice: effect of formalin concentration (1990)

The effect of different formalin concentrations on the nociceptive response in the formalin test was examined in mice. Subcutaneous formalin injection induces 2 distinct periods of high licking activity: an early phase lasting the first 5 min, and a late phase lasting 20-30 min after the injection. Formalin concentrations of 0.02-0.2% induced only the early phase, while concentrations of 1% or more induced both the early phase and the late phase. The ability of the test to show the antinociceptive effect of morphine and acetylsalicylic acid was similar for high and low formalin concentrations. For both these analgesics, a lower dose was needed to induce antinociception in the late phase than in the early phase using the same formalin concentration. Indomethacin had no effect in the early phase. In the late phase indomethacin induced antinociception when 1% formalin was used, while no significant effect was observed using 5% formalin. Clear histological changes in the paw were demonstrated after formalin concentrations that induced both phases. Lower formalin concentrations induced only very small changes. Using a low formalin concentration (0.2%), repeated testing using the same paw could be performed at intervals of 1 week without any significant change in the response. It was concluded that the formalin concentration should be kept as low as possible to minimize the suffering of the animal. Formalin concentrations of 0.05-0.2% are recommended for studying the early phase. Formalin concentrations of 1% or higher have to be used when studying the nociceptive response in the late phase.
Polymeric gastrointestinal MR contrast agents (1991)

Combining either paramagnetic (gadolinium chelates) or superparamagnetic (ferrite) contrast agents with polymers such as polyethylene glycol or cellulose, or with simple sugars such as dextrose, results in mixtures that exhibit improved T1 and/or T2 relaxivity compared with that of the contrast agent alone. It is suggested that the addition of such inexpensive and nontoxic polymers or saccharides may improve the effectiveness and decrease the cost of enteric contrast agents.
Preparation and Characterization of Titania-Coated Polystyrene Spheres and Hollow Titania Shells (2001)

A procedure has been developed to coat colloidal polystyrene spheres with a smooth and well-defined layer of amorphous titanium dioxide. The thickness of the coating can be easily varied from a few nanometers upward and can be increased further by seeded growth. The resulting composite particles are very monodisperse. The core−shell particles can be turned into spherical hollow titania shells by dissolution of the polystyrene cores in suspension or by calcination of the dried particles in a furnace. Calcination also crystallizes the titania into its anatase form. The coated particles were characterized with electrophoresis, thermogravimetric analysis, X-ray diffraction, electron microscopy, and light scattering. We find that the coating strongly densifies when the particles are dried but that it is not dense and about twice as thick when the particles are still in suspension. Calcination results in spherical shells composed of a dense arrangement of TiO2 (anatase) nanocrystals. This way, we obtained colloidal crystals consisting of hollow shells.
Antisense mediated exon skipping therapy for duchenne muscular dystrophy (DMD) (2011)

Duchenne Muscular Dystrophy (DMD) is a lethal disease caused by mutations in the dystrophin gene (DMD) that result in the absence of essential muscle protein dystrophin. Among many different approaches for DMD treatment, exon skipping, mediated by antisense oligonucleotides, is one of the most promising methods for restoration of dystrophin expression. This approach has been tested extensively targeting different exons in numerous models both in vitro and in vivo. During the past 10 years, there has been a considerable progress by using DMD animal models involving three types of antisense oligonucleotides (2'-O-methyl phosphorothioate (2OME-PS), phosphorodiamidate morpholino oligomer (PMO)) and peptide nucleic acid (PNA).
Role of the Vascular Endothelial Growth Factor Pathway in Tumor Growth and Angiogenesis (2004)

New blood vessel formation (angiogenesis) is a fundamental event in the process of tumor growth and metastatic dissemination. Hence, the molecular basis of tumor angiogenesis has been of keen interest in the field of cancer research. The vascular endothelial growth factor (VEGF) pathway is well established as one of the key regulators of this process. The VEGF/VEGF-receptor axis is composed of multiple ligands and receptors with overlapping and distinct ligand-receptor binding specificities, cell-type expression, and function. Activation of the VEGF-receptor pathway triggers a network of signaling processes that promote endothelial cell growth, migration, and survival from pre-existing vasculature. In addition, VEGF mediates vessel permeability, and has been associated with malignant effusions. More recently, an important role for VEGF has emerged in mobilization of endothelial progenitor cells from the bone marrow to distant sites of neovascularization. The well-established role of VEGF in promoting tumor angiogenesis and the pathogenesis of human cancers has led to the rational design and development of agents that selectively target this pathway. Studies with various anti-VEGF/VEGF-receptor therapies have shown that these agents can potently inhibit angiogenesis and tumor growth in preclinical models. Recently, an anti-VEGF antibody (bevacizumab), when used in combination with chemotherapy, was shown to significantly improve survival and response rates in patients with metastatic colorectal cancer and thus, validate VEGF pathway inhibitors as an important new treatment modality in cancer therapy.