gebhart/patrepeval huggingface dataset:
Faculty Opinions recommendation of A site-selective dual anchoring strategy for artificial metalloprotein design. (2005)

Introducing nonnative metal ions or metal-containing prosthetic groups into a protein can dramatically expand the repertoire of its functionalities and thus its range of applications. Particularly challenging is the control of substrate-binding and thus reaction selectivity such as enantioselectivity. To meet this challenge, both non-covalent and single-point attachments of metal complexes have been demonstrated previously. Since the protein template did not evolve to bind artificial metal complexes tightly in a single conformation, efforts to restrict conformational freedom by modifying the metal complexes and/or the protein are required to achieve high enantioselectivity using the above two strategies. Here we report a novel site-selective dual anchoring (two-point covalent attachment) strategy to introduce an achiral manganese salen complex (Mn(salen)), into apo sperm whale myoglobin (Mb) with bioconjugation yield close to 100%. The enantioselective excess increases from 0.3% for non-covalent, to 12.3% for single point, and to 51.3% for dual anchoring attachments. The dual anchoring method has the advantage of restricting the conformational freedom of the metal complex in the protein and can be generally applied to protein incorporation of other metal complexes with minimal structural modification to either the metal complex or the protein. PMID: 15339144
Rheumatoid Factors in Health and Disease: Structure, Function, Induction and Regulation (2002)

o v i t c h , G .M .13 A b r a s s , C .K .3 1 7 , 3 3 7 D a r n e ll, A . 3 7 5 A b u -H a m d a n .D .K . 2 4 8 D a u g ir d a s .J .T .173 A g u s , Z .S .6 9 D a v id s o n , S .M .19 A h m a d .M .8 6 D a v id s o n , W .D . 1 9 ,3 1 7 A la u p o v ic , P .9 2 D e M a r c h i, S. 2 8 0 A l p e n .M .A .86 D e P a o li, P . 2 8 0 A n d e r s o n .C . 3 6 9 D c s a i, S .G . 2 4 8 A n d r a s s y , K .193 D o b y a n , D . 3 1 5 , 3 2 8 , 3 6 7 A tk in s , R .C .177 D o m in g u e z .J .H .152 A t t m a n .P .-O .9 2 D o n a d o n , W . 2 8 0 B a n k s .R .A .114 D o r h o u t M e e s , E .J . 2 2 7 D o u k a s , M .3 2 9 B a n s a l .V .K .3 1 2 B a sile , A . 2 8 0 E n d o h , M .184 B a u m a l.R . 2 4 4 E p s te in , M .137 B c lu f f i.G . 2 5 6 B e n z o n a n a , G . 2 1 5 F a v r e .H . 2 1 5 B e rg s tro m , L .B .188 F e in s te in , D .I .4 3 B i a v a .C .G . 2 0 8 F e in s te in , E .I. 4 3 , 5 8 , 7 7 , 2 6 2 B la u , R .5 8 F e r r e r , O . 3 7 5 B o e r.P . 2 2 7 F ik rig , S .3 2 B o lto n .C .F .3 6 9 F in c k , E. 2 6 2 B o m m e r , J .193 F is h e r , P .B .3 8 B o s io , M . 2 5 6 F o x , L. 135 B o te y , A . 3 7 5 F r a n c is , R .B .. J r .4 3 B o w e r, J .D .7 F u jim i, S .3 5 5 B rig g s.W .A . 2
Organic chemistry at anodes and photoanodes (2018)

Organic oxidation reactions can replace the anodic oxygen evolution of water splitting for clean hydrogen generation paired with high-value product.
Effects of iron on the degradation of triphenyltin by pyoverdins isolated from <i>Pseudomonas chlororaphis</i> (2002)

Abstract The yellow compound pyoverdin was isolated from the bacteria Pseudomonas chlororaphis , isolated from mud in Japan. A study of the effects of iron, phosphorus, manganese and zinc on degradation of triphenyltin (TPT) by pyoverdin (20 mg) was carried out in distilled water (30 ml) containing 6 µg l −1 concentration of TPT at 20 °C for 48 or 96 h. The organotins in water were analyzed by gas chromatograph–mass spectrometry in the selected ion mode. The degradation of TPT by pyoverdin decreased with increase of phosphorus at 0–35 mg l −1 and Fe‐EDTA at 0–2 mg l −1 concentrations. Also, degradation of diphenyltin by pyoverdin decreased with increase of Mn‐EDTA at 0–1 mg l −1 and Zn‐EDTA at 0–1 mg l −1 . On the other hand, degradation of TPT by pyoverdin was found to be unaffected by manganese and zinc in water. Copyright © 2002 John Wiley & Sons, Ltd.
Continuous Static Gait with Twisting Trunk of a Metamorphic Quadruped Robot (2018)

Abstract. The natural quadrupeds, such as geckos and lizards, often twist their trunks when moving. Conventional quadruped robots cannot perform the same motion due to equipping with a trunk which is a rigid body or at most consists of two blocks connected by passive joints. This paper proposes a metamorphic quadruped robot with a reconfigurable trunk which can implement active trunk motions, called MetaRobot I. The robot can imitate the natural quadrupeds to execute motion of trunk twisting. Benefiting from the twisting trunk, the stride length of this quadruped is increased comparing to that of conventional quadruped robots. In this paper a continuous static gait benefited from the twisting trunk performing the increased stride length is introduced. After that, the increased stride length relative to the trunk twisting will be analysed mathematically. Other points impacting the implementation of the increased stride length in the gait are investigated such as the upper limit of the stride length and the kinematic margin. The increased stride length in the gait will lead the increase of locomotion speed comparing with conventional quadruped robots, giving the extent that natural quadrupeds twisting their trunks when moving. The simulation and an experiment on the prototype are then carried out to illustrate the benefits on the stride length and locomotion speed brought by the twisting trunk to the quadruped robot.
SPECIFIC AND NONSPECIFIC RESISTANCE TO LOCAL GRAFT-VERSUS-HOST REACTION IN F1 HYBRIDS PRETREATED INTRAVENOUSLY WITH PARENT-STRAIN SPLEEN CELLS (1987)

B6D2F1 hybrid mice pretreated i.v. with 5 X 10(7) spleen cells from B6 donors seven days earlier (B6-pretreated B6D2F1 hybrids) develop resistance to local GVHR induced by the subcutaneous injection of spleen cells of either B6 (GVHR-B6) or D2 (GVHR-D2) origin. This resistance has specific and a nonspecific components that concern the GVHR-B6 and the GVHR-D2, respectively. The two types of resistance to GVHR are neither induced under the same conditions nor mediated by the same mechanism. Specific resistance to GVHR is observed in B6D2F1 hybrids pretreated with unseparated, anti-Lyt-1.2+C' treated or 1000 rads-irradiated B6 cells, but not in B6D2F1 hybrids pretreated with anti-Thy-1.2+C' or anti Lyt-2.2+C'-treated B6 cells. In contrast, nonspecific resistance to GVHR is induced only by pretreatment with unseparated B6 cells. Treatment of B6 cells with anti-Thy-1.2, anti-Lyt-1.2, or anti-Lyt-2.2 moAb plus C', or their irradiation at 1000 rads completely abolishes their capacity to induce the nonspecific resistance to GVHR. Moreover, specific resistance to GVHR can be transferred to normal B6D2F1 mice by injection of nylon-adherent, anti-Thy-1.2+C'-treated or 2000-rads-irradiated, but not unseparated or nylon-nonadherent, B6-pretreated B6D2F1 spleen cells. Treatment of nylon-adherent B6-pretreated B6D2F1 cells with anti H-2d antiserum plus C' does not affect their capacity to transfer specific resistance to GVHR. Nonspecific resistance to GVHR can be transferred by unseparated, anti-Lyt-1.1+C' or anti Lyt-2.1+C'-treated, but not by anti-Thy-1.2+C' anti-Lyt-1.2+C', anti-Lyt-2.2+C'-treated or 2000-rads-irradiated B6-pretreated B6D2F1 spleen cells. Both types of resistance are observed in B6D2F1 hybrids pretreated with more than 2.5 X 10(7) B6 spleen cells.
Viral hijacking of the nucleolar DNA-damage response machinery: a novel mechanism to regulate host cell biology (2019)

Recent landmark studies indicate that the nucleolus plays key roles in stress responses including the DNA-damage response (DDR). The latter involves interactions of components of the DDR machinery including NBS1 with the sub-nucleolar protein Treacle, a key mediator of ribosomal RNA (rRNA) transcription and processing, implicated in Treacher-Collins syndrome. Using comparative proteomics, confocal and single molecule super-resolution imaging, and infection under BSL-4 containment, we have shown for the first time that the nucleolar DDR pathway is targeted by infectious pathogens [1]. We found that the matrix (M) proteins of Hendra virus and Nipah virus, highly lethal viruses of the Henipavirus genus (order Mononegavirales), target Treacle to inhibit its function, thereby silencing rRNA biogenesis, consistent with mimicking NBS1-Treacle interaction during a DDR. Furthermore, inhibition of Treacle expression/function enhanced henipavirus production. These data identify a novel mechanism for viral subversion of host cell biology by appropriating the nucleolar DDR and represent, to our knowledge, the first direct intra-nucleolar function for proteins of any mononegavirus [1, 2]. For the presentation I will discuss our new data, which is advancing our understanding both of the mechanisms impacted by the Henipavirus-Treacle interaction, and potential roles of such interactions in infection by other viruses, including highly lethal lyssaviruses [3]. [1] Rawlinson et al. Nature Communications 2018.9 : 3057 (2018) [2] Rawlinson et al. Cellular Microbiology 2015. 17(8):1108–20 [3] Oksayan et al. Journal of Virology 2015.89(3):1939–43
Practical Analysis of Composite Laminates J. N. Reddy and A. Miravete (1998)

Abstract
Monitoring a Hypothetical Channelopathy in Chronic Fatigue Syndrome (2003)

This study was aimed at monitoring of a previously suggested channelopathy in Chronic Fatigue Syndrome, and at searching for possible explanations by means of immune system characteristics. Twenty-seven CFS patients and 20 age and sex matched healthy volunteers were recruited. RNase L-ratio, percent of the norm of whole body potassium content, serum electrolytes (sodium, calcium and potassium), immune cells, blood cell count and erythrocyte sedimentation rate were determined. More than fifty percent of our patients presented with abnormal whole body potassium content. Eight patients had increased, while six had depleted potassium content. Discriminant function analysis revealed that the CFS patients and control subjects could be differentiated on immunophenotyping with the predominant cell differences being the increase in CD19+ CD5+ (mature B-) cells and the decrease in CD3-CD16+ CD56+ (NK) cells in both the percentage and count distributions. The fall in NK-cells was very strongly associated with increases in the RNase L-ratio and falls in serum calcium levels. In addition, four patients with low serum calcium levels showed lower whole body potassium levels. In conclusion, these observations suggest a channelopathy in a subset of CFS patients, probably induced by the deregulated 2-5A RNase L antiviral pathway.
Effect of poly(ADP ribose) synthetase inhibition on burn and smoke inhalation injury in sheep (2003)

We investigated the role of the nuclear enzyme poly (ADP ribose) synthetase (PARS) in the pathogenesis of combined burn and smoke inhalation (burn/smoke) injury in an ovine model. Eighteen sheep were operatively prepared for chronic study. PARS inhibition was achieved by treatment with a novel and selective PARS inhibitor INO-1001. The PARS inhibitor attenuated 1) lung edema formation, 2) deterioration of gas exchange, 3) changes in airway blood flow, 4) changes in airway pressure, 5) lung histological injury, and 6) systemic vascular leakage. Lipid oxidation and plasma nitrite/nitrate (stable breakdown products of nitric oxide) levels were suppressed with the use of INO-1001. We conclude that PARS inhibition attenuates various aspects of the pathophysiological response in a clinically relevant experimental model of burn/smoke inhalation injury.
The Star-type Color Pattern in Petunia hybrida ‘Red Star’ Flowers is Induced by Sequence-Specific Degradation of Chalcone Synthase RNA (2005)

Petunia hybrida 'Red Star' is a variety whose flowers exhibit a star-type red and white bicolor pattern. We analyzed the mRNA levels of six genes involved in anthocyanin biosynthesis. Only the level of chalcone synthase (CHS) mRNA was depressed in the unpigmented flower sectors. Both transcriptional activity and the accumulation of short interfering RNA of CHS in the unpigmented sectors were detected. Viral infection blocked the generation of CHS-silenced sectors. These results indicate that sequence-specific degradation of CHS RNA is the primary cause of the formation of white sectors in 'Red Star' flowers.
A new spectral index for assessing depth of anesthesia based on the cumulative power spectrum of the EEG (2006)

Jospin, M.; Jensen, E. W.; Caminal, P.; Kaplan, D. T.; Vereecke, H.; Struys, M. M.R.F. Author Information
Bioactive Constituents from Chinese Natural Medicines. XXIX. Monoterpene and Monoterpene Glycosides from the Roots of Rhodiola sachalinensis (2008)

A new monoterpene, sachalol, and three new monoterpene glycosides, sachalosides VI, VII, VIII, were isolated from Rhodiolae Radix, the roots of Rhodiola sachalinensis. The absolute stereostructures of new monoterpenes were elucidated on the basis of chemical and physicochemical evidence including the application of the modified Mosher's method.
QUANTUM CHEMICAL INTERPRETATION OF THE REACTION BETWEEN L-ASCORBIC ACID AND FORMALDEHYDE AND ITS BIOLOGICAL SIGNIFICANCE (1991)

We have recognized a new nucleophilic addition reaction between L-ascorbic acid and 
formaldehyde in biological circumstances (pH 7.4, T = 300 K). UV spectroscopic investi-
gation showed that the C2=C3 double bond of ascorbic acid rapidly disappears during 
the reaction, verifying that the addition breaks the double bond. On the other hand, 13C 
NMR studies have proved that on atom C2 an additional C-C single bond is formed. Ex-
act interpretation of the reaction mechanism is possible only by using quantum chemical 
argumentations. Ab initio calculations show that in ionized (anionic) form of L-ascorbic 
acid in water solution the Mulliken excess atomic charge is strongly negative on atom C2 
while C1 and C3 exhibit significant positive net charges. Coulombic attraction arranges 
formaldehyde's C=O double bond over the C2=C3 double bond of ascorbic acid and the 
interaction of the two loose π-electron systems causes forming of a new σ C-C bond. The 
described reaction plays a protective role in biological systems, since in this way the toxic 
carcinogenic formaldehyde can be eliminated.
Dynamic Stark Effect in Strongly Coupled Microcavity Exciton Polaritons (2012)

We present experimental observations of a nonresonant dynamic Stark shift in strongly coupled microcavity quantum well exciton polaritons--a system which provides a rich variety of solid-state collective phenomena. The Stark effect is demonstrated in a GaAs/AlGaAs system at 10 K by femtosecond pump-probe measurements, with the blueshift approaching the meV scale for a pump fluence of 2 mJ cm(-2) and 50 meV red detuning, in good agreement with theory. The energy level structure of the strongly coupled polariton Rabi doublet remains unaffected by the blueshift. The demonstrated effect should allow generation of ultrafast density-independent potentials and imprinting well-defined phase profiles on polariton condensates, providing a powerful tool for manipulation of these condensates, similar to dipole potentials in cold-atom systems.
Quaternary Reed-Muller Expansions of Mixed Radix Arguments in Cryptographic Circuits (2009)

Circuits built using multi-valued fixed polarity Reed-Muller expansions based on Galois field arithmetic, in particular quaternary expansions over GF(4), normally display high efficiency in terms of power consumption, area, etc. However, security application specific gate level mapping shows inefficient results for uniform radix expansions. The idea of the research here is to consolidate binary and quaternary Galois field arithmetic within a single circuit in such a way that the mathematical representations can benefit down to the gate level model. A direct method to compute quaternary fixed polarity Reed-Muller expansions of mixed radix arguments is proposed and implemented in a synthesis tool. The results for the various types of power-balanced signal encoding catered for the security application are compared and analysed.
<i>N</i>-Formyl Cocaine: A Study of Cocaine Comparison Parameters (1991)

Abstract N-formyl cocaine has been found to be a processing impurity (via potassium permanganate oxidation) in clandestine cocaine processing. Chemical isolation and spectroscopic data are presented. Its occurrence in illicit cocaine samples is examined for its value in sample comparisons. A general discussion of clandestine cocaine processing and permanganate oxidation is included.
Posterior brain in fetuses with open spina bifida at 11 to 13 weeks (2010)

At 11 to 13 weeks the majority of fetuses with OSB have measurable abnormalities in the posterior brain.
Fast high resolution 3D laser scanning by real-time object tracking and segmentation (2012)

This paper presents a real-time contour tracking and object segmentation algorithm for 3D range images. The algorithm is used to control a novel micro-mirror based imaging laser scanner, which provides a dynamic trade-off between resolution and frame rate. The micro-mirrors are controllable, enabling us to speed up acquisition significantly by only sampling on the object that is tracked and of interest. As the hardware is under development, we benchmark our algorithms on data from a SICK LMS100-10000 laser scanner mounted on a tilting platform. We find that objects are tracked and segmented well on pixel-level; that frame rate/resolution can be increased 3-4 times through our approach compared to scanners having static scan trajectories, and that the algorithm runs in 30 ms/image on a Intel Core i7 CPU using a single core.
Deep Multi-scale Convolutional Neural Network for Dynamic Scene Deblurring (2017)

Non-uniform blind deblurring for general dynamic scenes is a challenging computer vision problem as blurs arise not only from multiple object motions but also from camera shake, scene depth variation. To remove these complicated motion blurs, conventional energy optimization based methods rely on simple assumptions such that blur kernel is partially uniform or locally linear. Moreover, recent machine learning based methods also depend on synthetic blur datasets generated under these assumptions. This makes conventional deblurring methods fail to remove blurs where blur kernel is difficult to approximate or parameterize (e.g. object motion boundaries). In this work, we propose a multi-scale convolutional neural network that restores sharp images in an end-to-end manner where blur is caused by various sources. Together, we present multi-scale loss function that mimics conventional coarse-to-fine approaches. Furthermore, we propose a new large-scale dataset that provides pairs of realistic blurry image and the corresponding ground truth sharp image that are obtained by a high-speed camera. With the proposed model trained on this dataset, we demonstrate empirically that our method achieves the state-of-the-art performance in dynamic scene deblurring not only qualitatively, but also quantitatively.
Gonadotrophic hormone in<i>Eulalia viridis</i>(Polychaeta, Annelida): Stimulation of vitellogenesis (1995)

Summary Incorporation of 3H-leucine into TCA extracted, water soluble oocyte proteins is significantly enhanced in in vivo cultures of Eulalia viridis which have intact supra-oesophageal ganglia and those which have undergone replacement therapy when compared to decerebrate treatments. This response is gonad specific, with no differences in the rate of uptake of 3H-leucine into gut proteins between treatments. There was no significant difference in the rate of protein synthesis between oocytes cultured in vitro in the presence or absence of supra-oesophageal ganglion homogenate on culture medium containing 3H-leucine. However, oocytes cultured in the presence of supra-oesophageal ganglion homogenate do show a significant increase in the rate of uptake of radiolabel when compared to oocytes cultured in the absence of prostomial homogenate when cultured on medium containing 3H-labelled oocyte protein. These results indicate the presence of a gonadotrophic hormone in the supra-oesophageal ganglion of Eulalia viridis which promotes the uptake of external egg protein into developing oocytes. It is suggested that this is, at least in part, a heterosynthetic process with 3H-leucine being incorporated into an external protein before incorporation into the developing oocytes.
The role of RhoC in growth and metastatic capacity of melanoma (2009)

These results further support a role for RhoC in growth and metastasis of melanoma.
Low-Complexity Optical FFT Scheme Enabling Tbit/s All-Optical OFDM Communication (2010)

A practical scheme to perform the fast Fourier transform in the optical domain is introduced. Optical real-time FFT signal processing is done at speeds far beyond the limits of electronic digital processing, and at a negligible energy expenditure. To illustrate the power of the method we demonstrate an optical 400 Gbit/s OFDM receiver. It performs an optical real-time FFT on the consolidated OFDM data stream, thereby demultiplexing the signal into lower bit rate subcarrier tributaries, which can then be processed electronically.
Thermal Stabilization of an Endoglucanase by Cyclization (2012)

An intein-driven protein splicing approach allowed for the covalent linkage between the N- and C-termini of a polypeptide chain to create circular variants of the endo-β-1,3-1,4-glucanase, LicA, from Bacillus licheniformis. Two circular variants, LicA-C1 and LicA-C2, which have connecting loops of 20 and 14 amino acids, respectively, showed catalytic activities that are approximately two and three times higher, respectively, compared to that of the linear LicA (LicA-L1). The thermal stability of the circular variants was significantly increased compared to the linear form. Whereas the linear glucanase lost half of its activity after 3 min at 65 °C, the two circular variants have 6-fold (LicA-C1) and 16-fold (LicA-C2) increased half-life time of inactivation. In agreement with this, fluorescence spectroscopy and differential scanning calorimetry studies revealed that circular enzymes undergo structural changes at higher temperatures compared to that of the linear form. The effect of calcium on the conformational stability and function of the circular LicAs was also investigated, and we observed that the presence of calcium ions results in increased thermal stability. The impact of the length of the designed loops on thermal stability of the circular proteins is discussed, and it is suggested that cyclization may be an efficient strategy for the increased stability of proteins.
3D Finite Element Analysis for the High Speed Machining of Hardened Steel (2002)

The objective of this research is to illustrate the importance of modeling the right/similar chip formation with experimental results. When machining ‘difficult to cut’ materials at high cutting speeds, segmented chips are usually formed. When modeling the cutting process, it is important to consider the type of chip formed, as this affects the stress field generated in the workpiece. The modeled chips have to be the same type as those obtained during experimental work. However very few published models were capable of modeling the 3D oblique cutting with segmented chip formation. This paper presents a finite element model that includes a user customized catastrophic slip criterion and crack propagation module to model segmented chip formation in orthogonal & oblique machining of hardened AISI 4340 steel (52±2 HRC). Predicted cutting forces and chip thickness for segmented chips were in close agreement with experimental data. The modeled plastic strain and temperature distribution/magnitude were very different for continuous and segmented chip formation.