gebhart/patrepeval huggingface dataset:
Stabilization of the autoproteolysis of TNF-alpha converting enzyme (TACE) results in a novel crystal form suitable for structure-based drug design studies (2006)

The crystallization of TNF-alpha converting enzyme (TACE) has been useful in understanding the structure-activity relationships of new chemical entities. However, the propensity of TACE to undergo autoproteolysis has made enzyme handling difficult and impeded the identification of inhibitor soakable crystal forms. The autoproteolysis of TACE was found to be specific (Y352-V353) and occurred within a flexible loop that is in close proximity to the P-side of the active site. The rate of autoproteolysis was found to be proportional to the concentration of TACE, suggesting a bimolecular reaction mechanism. A limited specificity study of the S(1)' subsite was conducted using surrogate peptides and suggested substitutions that would stabilize the proteolysis of the loop at positions Y352-V353. Two mutant proteases (V353G and V353S) were generated and proved to be highly resistant to autoproteolysis. The kinetics of the more resistant mutant (V353G) and wild-type TACE were compared and demonstrated virtually identical IC(50) values for a panel of competitive inhibitors. However, the k(cat)/K(m) of the mutant for a larger substrate (P6 - P(6)') was approximately 5-fold lower than that for the wild-type enzyme. Comparison of the complexed wild-type and mutant structures indicated a subtle shift in a peripheral P-side loop (comprising the mutation site) that may be involved in substrate binding/turnover and might explain the mild kinetic difference. The characterization of this stabilized form of TACE has yielded an enzyme with similar native kinetic properties and identified a novel crystal form that is suitable for inhibitor soaking and structure determination.
The Serrated Trailing Edge Influence on Flapping-wing Acoustics (2020)

The acoustics emitted from a rigid hovering low-aspect-ratio rectangular wing is investigated numerically in this study. The wing undergoes the stroke and pitching motion at a Reynolds number of 176 and a Mach number of 0.176. A hybrid method coupling a 3D incompressible N-S equation solver based on the immersed boundary (IB) method with the FW-H acoustic analogy is utilised to study the far-field acoustics. The effects of the serrated trailing edge on aerodynamics and aeroacoustics are discussed by considering the wavenumber k and amplitude 2h. It is found that the square wave trailing edge with the high wavenumber and amplitude can reduce the acoustics and enhance the lift force.
Foveated video compression with optimal rate control (2001)

Previously, fovcated video compression algorithms have been proposed which, in certain applications, deliver high-quality video at reduced bit rates by seeking to match the nonuniform sampling of the human retina. We describe such a framework here where foveated video is created by a nonuniform filtering scheme that increases the compressibility of the video stream. We maximize a new foveal visual quality metric. the foveal signal-to-noise ratio (FSNR) to determine the best compression and rate control parameters for a given target bit rate. Specifically, we establish a new optimal rate control algorithm for maximizing the FSNR using a Lagrange multiplier method defined on a curvilinear coordinate system. For optimal rate control, we also develop a piecewise R-D (rate-distortion)/R-Q (rate-quantization) model. A fast algorithm for searching for an optimal Lagrange multiplier lambda* is subsequently presented. For the new models, we show how the reconstructed video quality is affected, where the FSNR is maximized, and demonstrate the coding performance for H.263,+,++/MPEG-4 video coding. For H.263/MPEG video coding, a suboptimal rate control algorithm is developed for fast, high-performance applications. In the simulations, we compare the reconstructed pictures obtained using optimal rate control methods for foveated and normal video. We show that foveated video coding using the suboptimal rate control algorithm delivers excellent performance under 64 kb/s.
Use of environmental DNA in assessment of fish functional and phylogenetic diversity (2021)

Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
Amplified On-Chip Fluorescence Detection of DNA Hybridization by Surface-Initiated Enzymatic Polymerization (2011)

We describe the incorporation of multiple fluorophores into a single stranded DNA (ssDNA) chain using terminal deoxynucleotidyl transferase (TdT), a template-independent DNA polymerase that catalyzes the sequential addition of deoxynucleotides (dNTPs) at the 3′–OH group of an oligonucleotide primer; we term this methodology surface initiated enzymatic polymerization (SIEP) of DNA. We found that long (>1 Kb) ssDNA homopolymer can be grown by SIEP, and that the length of the ssDNA product is determined by the monomer to oligonucleotide initiator ratio. We observed efficient initiation (≥50%) and narrow polydispersity of the extended product when fluorescently labeled nucleotides are incorporated. TdT’s ability to incorporate fluorescent dNTPs into a ssDNA chain was characterized by examining the effect of the molar ratios of fluorescent dNTP to natural dNTP on the degree of fluorophore incorporation and the length of the polymerized DNA strand. These experiments allowed us to optimize the polymerization conditions to incorporate up to ∼50 fluorescent Cy3-labeled dNTPs per kilobase into a ssDNA chain. With the goal of using TdT as an on-chip labeling method, we also quantified TdT mediated signal amplification on the surface by immobilizing ssDNA oligonucleotide initiators on a glass surface followed by SIEP of DNA. The incorporation of multiple fluorophores into the extended DNA chain by SIEP translated to a ∼45 fold signal amplification compared to the incorporation of a single fluorophore. SIEP was then employed to detect hybridization of DNA, by the posthybridization, on-chip polymerization of fluorescently labeled ssDNA that was grown from the 3′–OH of target strands that hybridized to DNA probes that were printed on a surface. A dose–response curve for detection of DNA hybridization by SIEP was generated, with a ∼1 pM limit of detection and a linear dynamic range of 2 logs.
Silyl Migrations in d-Xylose Derivatives: Total Synthesis of a Marine Quinoline Alkaloid (2013)

A versatile method for the synthesis of orthogonally protected D-xylose 1-thioethers is described using unusual silyl group migrations which were pivotal in the synthesis of 4,8-dimethyl-6-O-(2',4'-di-O-methyl-β-D-xylopyranosyl)hydroxyquinoline confirming the structure and absolute configuration of the natural product.
Temporal light field reconstruction for rendering distribution effects (2011)

Traditionally, effects that require evaluating multidimensional integrals for each pixel, such as motion blur, depth of field, and soft shadows, suffer from noise due to the variance of the high-dimensional integrand. In this paper, we describe a general reconstruction technique that exploits the anisotropy in the temporal light field and permits efficient reuse of samples between pixels, multiplying the effective sampling rate by a large factor. We show that our technique can be applied in situations that are challenging or impossible for previous anisotropic reconstruction methods, and that it can yield good results with very sparse inputs. We demonstrate our method for simultaneous motion blur, depth of field, and soft shadows.
Revision of Failed Cerclage Is Associated With Higher Risk of Premature Birth Compared to Primary Cerclage [24N] (2016)

INTRODUCTION: Little is known about the outcome of revising failed cerclage, previously placed for sonographically short mid-trimester cervix. Our previous data reported higher risk of premature delivery in patients (pts) with revision compared to single cerclage. We aim to find if addition of 23 pts to previously reported 54 changes the results. METHODS: This is a cohort of 77 pts with ultrasound cervical length (CL) of <25 mm at 16–24 6/7 weeks (wks) who underwent high MacDonald cerclage. Nine pts required revision to correct a failed cerclage (performed by other operators). Failed cerclage was defined as presence of prolapsed membrane beyond cerclage or CL distal to cerclage of <1 cm. All surgeries were performed or supervised by one operator (FB). Gestational age (GA) at delivery, and other obstetrical outcomes, were compared between 2 groups. RESULTS: 68/77 pts had primary cerclages, 9/77 pts had revision cerclages. 4 pregnancy losses noted (2 in primary, 2 in revision). Pts with revision had shorter delivery GA; mean of 27 3/7 (±6.7) vs 36 2/7 (±4.1) wks (P=.003). Birth weight was lower in revision group; mean 1345 (±1056) vs 2830 grams (±816) (P=.005). More babies in revision group had NICU admissions 5/7 (71.4%) vs 14/64 (22%) pts (P=.008). CONCLUSION: Patients with revision cerclages have higher premature delivery compared to successful primary cerclages. Revised cerclages were associated with a high take-home baby (7/9 or 78%) but also with high preterm delivery rate (8/9 or 89%), which should be considered when counseling pts with failed cerclages and candidates for revision cerclage.
Micro-machined heat pipes in silicon MCM substrates (2002)

Multichip modules (MCMs) containing power components need a substrate with excellent heat spreading capability both to avoid hot spots and to move dissipated heat toward the system heat sinks. Polycrystalline diamond is an excellent MCM heat spreading substrate but remains several orders of magnitude too expensive and somewhat more difficult to process than conventional mother-board materials. Today's power MCMs concentrate on moderately priced silicon wafers and aluminum nitride ceramic with their improved thermal conductivity and good thermal expansion match to power semiconductor components in comparison to traditional alumina and printed wiring board materials. However even silicon and AIN substrates are challenged by designers' thermal needs. We report on the fabrication of micro-heat pipes embedded in silicon MCM substrates (5/spl times/5 cm) by the use of micromachined capillary wick structures and hermetic micro-cavities. This passive microstructure results in more than a 5 times improvement in heat spreading capability of the silicon MCM substrate over a large range of power densities and operating temperatures. Thus diamond-like cooling is possible at silicon prices.
Theoretical and Experimental Analyses of Energy Efficient Air Dehumidification Systems for Tropical Climates Using Membrane Technology (2011)

This paper presents the analytical and experimental analysis of a membrane based air-dehumidification system for handling the latent loads efficiently. This is important for tropical countries like Singapore where the humidity content of ambient air is high and therefore, air conditioning systems need to handle large latent load. A detailed COMSOL simulation model was set-up in order to simulate the water diffusion through the membrane. Experimental results from a real size membrane dehumidification unit are used to validate the mathematical model. Our investigations show that the moisture content of ambient air may be reduced by more than 5 g per kg of air if the dehumidification process is driven by the gradient between the water content of ambient air and the water content of exhaust air form air-conditioned spaces. With the exception of low electricity requirement for air transport, there is no electric energy consumption in the system. Therefore, the membrane system discussed in this paper is an efficient and alternative way of air dehumidification for air conditioning applications, potentially reducing the electricity consumption of air conditioning system in tropics.
Maltodextrin-binding protein hybrids carrying epitopes from the preS2 region of hepatitis B virus: expression, antibody-binding and preliminary crystallographic studies (1997)

Five hybrid constructions of maltodextrin-binding protein (MBP), each containing an inserted epitope(s) from the preS2 region of the envelope proteins of hepatitis B virus (HBV), have been expressed. The anti-preS2 monoclonal antibody S2.3 was shown to cross-react with the MBP hybrid constructions, demonstrating that the epitopes presented by these recombinant proteins mimic the antigenic behaviour of the native viral antigen. In addition, all five hybrid proteins have been crystallized. Preliminary structural solutions obtained by molecular replacement indicate that the native conformation of MBP is preserved in the hybrid constructions despite the significant length of the epitope insertions.
Long PCR Facilitates Concise Cloning and Sequencing with a Minimal Tiling Set of Templates (1997)

We demonstrate a rapid cloning and sequencing strategy for kilobase-size DNA segments using DNase I and long PCR. In a single-tube protocol, deletions were formed in a plasmid insert by two enzymatic cuts, one at a fixed site and one at random. The doubly cut molecules were recircularized to generate a library of plasmids carrying deletions of various sizes and transformed into E. coli. The plasmid inserts were directly amplified from transformant colonies by long PCR and sized on a high-resolution agarose gel. A minimal tiling set, selected from the amplified material, was used directly as templates for long-read sequencing. The system is useful for inserts up to about 3.5 kb for de novo sequencing (both strands) or 6 kb for confirmatory sequencing (one strand).
Secondary aerosol formation from stress-induced biogenic emissions and possible climate feedbacks (2013)

Abstract. Atmospheric aerosols impact climate by scattering and absorbing solar radiation and by acting as ice and cloud condensation nuclei. Secondary organic aerosols (SOA) comprise an important component of atmospheric aerosols. Biogenic volatile organic compounds (BVOC) emitted by vegetation are a major source of SOA. Pathogens and insect attacks, heat waves and droughts can induce stress to plants that may impact their BVOC emissions, and hence the yield and type of formed SOA, and possibly their climatic effects. This raises questions whether stress-induced changes in SOA formation may attenuate or amplify effects of climate change. In this study we assess the potential impact of stress-induced BVOC emissions on SOA formation for tree species typical for mixed deciduous and Boreal Eurasian forests. We studied the photochemical SOA formation for infested plants in a laboratory setup under well-controlled conditions and applied in addition heat and drought stress. The results indicate that stress conditions substantially modify SOA formation. While sesquiterpenes, methyl salicylate, and C17-BVOC increase SOA yield, green leaf volatiles suppress SOA formation. By classifying emission types, stressors and SOA formation potential, we propose possible climatic feedbacks regarding aerosol effects. We conclude that stress situations for plants due to climate change should be considered in climate-vegetation feedback mechanisms.
Wide en bloc extra-articular excision of the elbow for sarcoma with complex reconstruction (2007)

We describe a consecutive series of five patients with bone or soft-tissue sarcomas of the elbow and intra-articular extension treated by complex soft tissue, allograft bone and prosthetic joint replacement after wide extra-articular en bloc excision. All had a pedicled myocutaneous latissimus dorsi rotation flap for soft-tissue cover and reconstruction of the triceps. Wide negative surgical margins were obtained in all five patients. No local wound complications or infections were seen. There were no local recurrences at a mean follow-up of 60 months (20 to 105). The functional results were excellent in four patients and good in one. Longer term follow-up is necessary to confirm the durability of the elbow reconstruction.
Superenhanced Removal of Fungal Biofilms by Protease‐Functionalized Amphotericin B Nanocarriers (2020)

A strong enhancement in the antifungal activity of amphotericin B (AmpB) encapsulated into shellac nanoparticles (NPs) surface functionalized with protease is reported. These AmpB‐loaded shellac NPs are fabricated by pH‐induced nucleation of aqueous solutions of shellac and AmpB in the presence of Poloxamer 407 (P407) as a steric stabilizer. The AmpB‐loaded shellac NPs are surface coated with the cationic protease Alcalase 2.4L FG. The performance of the AmpB‐encapsulated NPs against Candida albicans is evaluated. The AmpB‐loaded shellac NPs show a remarkable boost of their antifungal action compared to free AmpB when applied to C. albicans in both planktonic and biofilm forms. The surface functionalization with a cationic protease allows the NPs to adhere to the fungal cell walls, delivering AmpB directly to their membranes. Additionally, the hydrolyzing activity of the protease coating degrades the biofilm matrix, thus increasing the effectiveness of the encapsulated AmpB compared to free AmpB at the same concentration. The protease‐coated AmpB‐loaded shellac NPs show no greater toxicity to human adult keratinocyte cells (HaCaT) compared to the free AmpB. These AmpB nanocarriers demonstrat increased efficacy against C. albicans and can be potentially used to treat fungal biofilm infection in the clinic, for example, in recalcitrant chronic wounds.
Literary Feature Reviews (1988)

Negritude and after: changing perspectives in French‐language African fiction The Black Cloth: A Collection of African Folktales. Bernard Binlin Dadie. Translated from the French by Karen C Hatch. Amherst, Massachusetts: The University of Massachusetts Press. 1987. 140pp.np . hb Black Docker. Sembene Ousmane. Translated from the French by Ros Schwartz. London: Heinemann Educational Books. 1987. 120pp. £3.95pb Tribaliks: Contemporary Congolese Stories. Henri Lopes. Translated from the French by Andrea Leskes. London: Heinemann Educational Books. 1987. 86pp. £3.95pb The Laughing Cry: An African Cock and BuU Story. Henri Lopes. Translated from the French by Gerald Moore. London: Readers International. 1987. 260pp. £4.95pb Chinese literature in renaissance Mulberry and Peach: Two Women of China. Hualing Nieh. London: Women's Press. 1986. 197 pp. £3.95pb One Half of the Sky: Selection from Contemporary Women Writers of China. Edited and translated from the Chinese by R A Roberts and Angela Knox London: William Heinemann. 1987. 143 pp. £11.95hb Leaden Wings. Zhang Jie. Translated from the Chinese by Gladys Yang London: Virago Press. 1987. 180 pp. £3.95pb Waves. Bei Dao. Edited by Bonnie S McDougall. Translated from the Chinese by Bonnie S McDougall and Susette Ternent Cooke. London: William Heinemann. 1987. 234 pp. £11.95hb
Oil organogel system for magnetorheological fluid (2016)

A new approach to dispersing magnetic particles <italic>via</italic> an oil organogel formed by a low molecular weight gelator to prepare MRF.
Escherichia coliNissle 1917-derived factors reduce cell death and late apoptosis and increase transepithelial electrical resistance in a model of 5-fluorouracil-induced intestinal epithelial cell damage (2014)

We evaluated the capacity for supernatants (SNs) derived from Escherichia coli Nissle 1917 (EcN), cultured under different growth conditions, to prevent 5-fluorouracil (5-FU)-induced intestinal epithelial cell damage. EcN was cultured in: Luria Bertani (LB) broth, tryptone soya broth (TSB), de Man Rogosa Sharpe (MRS) broth, and M17 broth supplemented with 10% (v/v) lactose solution (M17). Intestinal epithelial cells (IEC-6) were treated with the following EcN SNs: LB(+), TSB(+), MRS(+), and M17(+) in the presence and absence of 5-FU (1.5 or 5 μM). Cell viability, apoptotic activity and cell monolayer permeability were measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, and transepithelial electrical resistance (TER) assays, respectively. 5-FU significantly reduced cell viability (P<0.05) at both 24 and 48 h. However, only EcN SN produced from LB and M17 growth media significantly decreased cell death induced by 5-FU (by approximately 10% after 24 and 48 h; and 10% after 24 h, respectively [P<0.05]). When measured by flow cytometry all EcN SNs in the presence of 5-FU increased the proportion of viable cells (by 3-5% for 24 h, 3-7% for 48 h, P<0.05) and reduced late-apoptotic cells after 24 and 48 h, compared with 5-FU control. Moreover, all EcN SNs significantly reduced the disruption of IEC-6 cell barrier function induced by 5-FU by 7-10% (P<0.05), compared with DMEM control. We conclude that EcN derived factors could potentially reduce the severity of intestinal mucositis.
Direct evidence for a β1-adrenergic receptor–directed autoimmune attack as a cause of idiopathic dilated cardiomyopathy (2004)

Today, dilated cardiomyopathy (DCM) represents the main cause of severe heart failure and disability in younger adults and thus is a challenge for public health. About 30% of DCM cases are genetic in origin; however, the large majority of cases are sporadic, and a viral or immune pathogenesis is suspected. Following the established postulates for pathogenesis of autoimmune diseases, here we provide direct evidence that an autoimmune attack directed against the cardiac beta(1)-adrenergic receptor may play a causal role in DCM. First, we immunized inbred rats against the second extracellular beta(1)-receptor loop (beta(1)-EC(II); 100% sequence identity between human and rat) every month. All these rats developed first, receptor-stimulating anti-beta(1)-EC(II) Ab's and then, after 9 months, progressive severe left ventricular dilatation and dysfunction. Second, we transferred sera from anti-beta(1)-EC(II)-positive and Ab-negative animals every month to healthy rats of the same strain. Strikingly, all anti-beta(1)-EC(II)-transferred rats also developed a similar cardiomyopathic phenotype within a similar time frame, underlining the pathogenic potential of these receptor Ab's. As a consequence, beta(1)-adrenergic receptor-targeted autoimmune DCM should now be categorized with other known receptor Ab-mediated autoimmune diseases, such as Graves disease or myasthenia gravis. Although carried out in an experimental animal model, our findings should further encourage the development of therapeutic strategies that combat harmful anti-beta(1)-EC(II) in receptor Ab-positive DCM patients.