gebhart/patrepeval huggingface dataset:
Production of lysine by pyruvate kinase mutants of Brevibacterium flavum. (1983)

A mutant, No. 1-231, resistant to S-P-aminoethyty-L-cysteine (AEC) plus threonine which was previously derived from a low citrate synthase mutant (No. 1 5-8) of Brevibacterium flavum, produced 41 g/liter of lysine (as HC1 salt, 41 %yield) and showed pyruvate kinase and homoserine dehydrogenase activities of about 1/10 and 1/20 as much as those of No. 15-8, respectively, but its aspartokinase was still normally sensitive to the feedback inhibition by lysine plus threonine. Another AEC-resistant mutant, No. 2-190, from No. 15-8 showed aspartokinase insensitive to the feedback inhibition without any change in pyruvate kinase and homoserine dehydrogenase activities. In addition, both the two AEC-resistant mutants and parent No. 1 5-8 showedpartial desensitization of phosphoenolpyruvate carboxylase to the feedback inhibition by L-aspartic acid. β-Fluoropyruvic acid-sensitive mutants No. 22 and No. 2-1 1 were derived from No. 1-231.These sensitive strains produced 51 g/liter of lysine (51 %yield) and were found to be completely defective in homoserine dehydrogenase activity. It was concluded from the results that depression of pyruvate kinase activity leads to an increase in lysine production.
Chemical Modification and Site-directed Mutagenesis of Conserved HXXH and PP-loop Motif Arginines and Histidines in the Murine Bifunctional ATP Sulfurylase/Adenosine 5′-Phosphosulfate Kinase (1999)

The sulfurylase domain of the mouse bifunctional enzyme ATP sulfurylase/adenosine 5'-phosphosulfate (APS) kinase contains HXXH and PP-loop motifs. To elucidate the functional importance of these motifs and of conserved arginines and histidines, chemical modification and site-directed mutagenesis studies were performed. Chemical modification of arginines and histidines with phenylglyoxal and diethyl pyrocarbonate, respectively, renders the enzyme inactive in sulfurylase, kinase, and overall assays. Data base searches and sequence comparison of bifunctional ATP sulfurylase/APS kinase and monofunctional ATP sulfurylases shows a limited number of highly conserved arginines and histidines within the sulfurylase domain. Of these conserved residues, His-425, His-428, and Arg-421 are present within or near the HXXH motif whereas His-506, Arg-510, and Arg-522 residues are present in and around the PP-loop. The functional role of these conserved residues was further studied by site-directed mutagenesis. In the HXXH motif, none of the alanine mutants (H425A, H428A, and R421A) had sulfurylase or overall activity, whereas they all exhibited normal kinase activity. A slight improvement in reverse sulfurylase activity (<10% residual activity) and complete restoration of forward sulfurylase was observed with R421K. Mutants designed to probe the PP-loop requirements included H506A, R510A, R522A, R522K, and D523A. Of these, R510A exhibited normal sulfurylase and kinase activity, R522A and R522K showed no sulfurylase activity, and H506A had normal sulfurylase activity but produced an effect on kinase activity (<10% residual activity). The single aspartate, D523A, which is part of the highly conserved GRD sequence of the PP-loop, affected both sulfurylase and kinase activity. This mutational analysis indicates that the HXXH motif plays a role only in the sulfurylase activity, whereas the PP-loop is involved in both sulfurylase and kinase activities. Residues specific for sulfurylase activity have also been distinguished from those involved in kinase activity.
Spectroscopic and Protein Chemical Analyses Demonstrate the Presence of C-Mannosylated Tryptophan in Intact Human RNase 2 and Its Isoforms (1996)

Recently, the C-mannosylation of a specific tryptophan residue in RNase 2 from human urine has been reported [Hofsteenge, J., et al. (1994) Biochemistry 33, 13524-13530; de Beer, T., et al. (1995) Biochemistry 34, 11785-11789]. In those studies, identification of this unusual modification was accomplished by mass spectrometric and NMR spectroscopic analysis of peptide fragments. The evidence for the occurrence of C2-alpha-mannosyltryptophan [(C2-Man-)Trp] in the intact protein relied exclusively on the detection of the same phenylthiohydantoin derivatives during Edman degradation. In this paper, we have (1) excluded the possibility that (C2-Man-)Trp arose artificially under the acidic conditions previously employed for protein and peptide isolation and analysis, by maintaining the pH > 5 throughout these procedures, (2) demonstrated the occurrence of (C2-Man-)Trp in the intact protein, by NMR spectroscopy, (3) showed that (C2-Man-)Trp is not unique for RNase 2 from urine but that it is also present in the enzyme isolated from erythrocytes, and (4) found also that high-molecular mass isoforms of urinary RNase 2 are C-mannosylated. These observations firmly establish C-mannosylation as a novel way of post-translationally attaching carbohydrate to protein, in addition to the well-known N- and O-glycosylations. Furthermore, the NMR data, in combination with molecular dynamics calculations, indicate that in the native protein the mannopyranosyl residue is in a different conformation than in the glycopeptide or denatured protein, due to protein-carbohydrate interactions.
A noise-robust frequency domain technique for estimating planar roto-translations (2000)

This work presents a new method for estimating planar roto-translations that operates in the frequency domain and as such, is not based on features. Since the proposed technique uses all the image information, it is very robust against noise, it can be very accurate; estimation errors on the rotational angle varies from a few hundredths to a few tenths of a degree, depending on the noise level. Experimental evidence of this performance is presented, and the mathematical reasons behind these characteristics are explained in depth. Another remarkable feature of the algorithm consists in that it works in Cartesian coordinates, bypassing the need to transform from the Cartesian to the polar domain, which, typically, is a numerically delicate and computationally onerous task. The proposed technique can become an effective tool for unsupervised estimation of roto-translations by means of implementations based on FFT algorithms.
Auxin Response Factors Mediate <i>Arabidopsis</i> Organ Asymmetry via Modulation of KANADI Activity (2005)

Members of the KANADI gene family in Arabidopsis thaliana regulate abaxial identity and laminar growth of lateral organs. Promoter APETALA3-mediated ectopic expression of KANADI restricts petal expansion and was used in a genetic screen for factors involved in KANADI-mediated signaling. Through this screen, mutations in ETTIN (ETT; also known as Auxin Response Factor3 [ARF3]) were isolated as second site suppressors and found to ameliorate ectopic KANADI activity throughout the plant as well. Mutant phenotypes of ett are restricted to flowers; however, double mutants with a closely related gene ARF4 exhibit transformation of abaxial tissues into adaxial ones in all aerial parts, resembling mutations in KANADI. Accordingly, the common RNA expression domain of both ARFs was found to be on the abaxial side of all lateral organs. Truncated, negatively acting gene products of strong ett alleles map to an ARF-specific, N-terminal domain of ETT. Such gene products strongly enhance abaxial tissue loss only when ARF activities are compromised. As KANADI is not required for either ETT or ARF4 transcription, and their overexpression cannot rescue kanadi mutants, cooperative activity is implied. ARF proteins are pivotal in mediating auxin responses; thus, we present a model linking transient local auxin gradients and gradual partitioning of lateral organs along the abaxial/adaxial axis.
Lecithin fatty acid composition in bile and plasma of man, dogs, rats, and oxen (1965)

The lecithins of bile and plasma from nine patients, three dogs, four rats, and two steers (oxen) were extracted and their fatty acid patterns were determined. In all four species the lecithin of bile had a higher concentration of palmitic acid than did that of plasma. The concentration of stearic and arachidonic acids was higher in plasma lecithin. These differences were statistically significant.The work of others shows that biliary and plasma lecithins are both derived from the liver. Plasma lecithin fatty acid composition was not noticeably changed on passage through the tissues. We conclude, therefore, that the different patterns indicate either the presence of two functionally distinct pools of lecithin in the liver, or selection from a single heterogeneous pool.
Phase Ib trial of atezolizumab in combination with nab-paclitaxel in patients with metastatic triple-negative breast cancer (mTNBC). (2016)

1009 Background: Atezolizumab (atezo; MPDL3280A) is a humanized MAb that inhibits binding of PD-L1 to PD-1 and B7.1, thus restoring tumor-specific T-cell immunity. Atezo has single-agent activity in mTNBC. Combining atezo with chemotherapy is hypothesized to enhance tumor-specific T-cell immunity by exposing the immune system to high levels of tumor antigens and modulating T-cell and NK cell functions. This arm of a Phase Ib study evaluated atezo + nab-paclitaxel (pac) in patients (pts) with mTNBC treated with ≤ 3 prior lines of therapy. Methods: Primary endpoints were safety and tolerability; secondary endpoints included clinical activity. Pts received atezo 800 mg q2w (d1,15) and nab-pac 125 mg/m2 q1w (d1,8,15) q3 of 4 wks. After nab-pac discontinuation, maintenance atezo was allowed until loss of clinical benefit. ORR was assessed by RECIST v1.1. PD-L1 staining on tumor cells and tumor-infiltrating immune cells was scored using the SP142 IHC assay. Results: 32 pts were safety evaluable (median follow-up 5.21 mo [range 0.6-12.6]). All pts were female, with a median age of 56 y (range 32-84); 81% were ECOG PS 1, and 87% had prior taxanes. The most common treatment-related AE was decreased neutrophil count (53% all grade; 41% Gr 3-4). No DLTs or related deaths occurred. 24 pts (dosed by June 1, 2015) were efficacy evaluable (Table). 3 pts developed new lesions with PR in target lesions that were scored as RECIST PD, but remained on treatment with prolonged biologic response. Responses occurred in pts whose tumors expressed PD-L1 and in those with little to no PD-L1 expression. Nab-pac did not affect atezo-induced proliferation of circulating activated CD8+ T cells. Conclusions: These results are the first to demonstrate that atezo + nab-pac is tolerable with promising activity in mTNBC. Updated results and tissue correlates will be presented. An ongoing Phase III trial is evaluating this regimen in previously untreated mTNBC pts. Clinical trial information: NCT01633970.Best Response, % 1L n = 9 2L n = 8 3L+ n = 7 All pts N = 24 Confirmed ORR (95% CI) 67 (30, 93) 25 (3, 65) 29 (4, 71) 42 (22, 63) ORRa (95% CI) 89 (52, 100) 75 (35, 97) 43 (10, 82) 71 (49, 87) CR 11 0 0 4 PR 78 75 43 67 SD 11 25 29 21 a Including investigator-assessed unconfirmed responses.
Evaluation of local MCP‐1 and IL‐12 nanocoatings for infection prevention in open fractures (2009)

The increasing incidence of bacterial infection and the appearance of Staphylococcus aureus (S. aureus) strains that are resistant to commonly used antibiotics has made it important to develop non-antibiotic approaches for infection prevention. The aim of this study was to develop local monocyte chemoattractant protein-1 (MCP-1) and interleukin-12 p70 (IL-12 p70) therapies to prevent S. aureus infection by enhancing the recruitment and activation of macrophages, which are believed to play an important role in infection prevention as the first line of defense against invading pathogens. Nanocoating systems for MCP-1 and IL-12 p70 deliveries were prepared, and their release characteristics desirable for infection prevention in open fractures were explored. Local MCP-1 therapy reduced S. aureus infection and influenced white blood cell populations, and local IL-12 p70 treatment had a more profound effect on preventing S. aureus infection. No synergistic relationship in decreasing S. aureus infection was observed when MCP-1 and IL-12 p70 treatments were combined. This reported new approach may reduce antibiotic use and antibiotic resistance.
Nanoparticle assemblies: dimensional transformation of nanomaterials and scalability (2013)

Integration of nanoparticles (NPs) and other nanomaterials with existing technologies must take place in order to substantially widen the spectrum of their applications. This task can be simplified by taking advantage of NP assemblies provided that they retain the unique properties of nanomaterials in organized systems of larger dimensions. There is a large variety of methods of assembling NPs into superstructures containing 10-10(10) particles that include field-, bio-, and interface-directed techniques as well as self-organization. Some of them can traverse the scales from typical lengths of 10(-9) m (nano) to 10(-5) m (micro) and 10(1) m (macro) conducive to other technologies. Such dimensional transformation of nanomaterials makes possible utilization of well-established processing techniques, and hardware tools operating at these scales. Therefore, answering the question "What types of the assembly techniques are suitable for such a task?" is vital for the future application of nanoscale materials in any field of use. These techniques must result in organized structures of at least 5 × 10(-7) m in size, offer relative simplicity and fault tolerance. This review focuses on the recent development of NP assembly techniques that have the possibility of satisfying these requirements. The expected applications and future developments are also discussed.
What a difference a hole makes : The commercial value of the innas hydraulic transformer (1999)

Secondary controlled systems with a common pressure rail (CPR) are an alternative to current load sensing systems. These CPR-systems offer a combination of flexibility and efficiency that can never be attained with flow controlled systems. In other fields of technology, well-known examples of common rail systems are the electricity grid and the recently developed common rail injection systems for diesel engines. Nevertheless, despite the promising principle and the many advantages of secondary control, these systems have not become a success in the hydraulic field. Without doubt, the lack of hydraulic transformers on the market which have an acceptable performance and characteristics at an acceptable price level, has been a major obstacle. In order to find a better solution, a hydraulic transformer has been developed which could be acceptable in terms of costs, controllability and efficiency. This paper discusses the state-of-the-art of the development of this so-called Innas Hydraulic Transformer (IHT), its commercial value and its applications. A direct comparison with current flow control components is not possible since the IHT is meant for CPR-systems. For this reason the evaluation will be performed on a system level, comparing current flow controlled systems with the new IHT based CPR-systems.
Charge Transfer Dissociation (CTD) Mass Spectrometry of Peptide Cations Using Kiloelectronvolt Helium Cations (2014)

A kiloelectronvolt beam of helium ions is used to ionize and fragment precursor peptide ions starting in the 1+ charge state. The electron affinity of helium cations (24.6 eV) exceeds the ionization potential of protonated peptides and can therefore be used to abstract an electron from--or charge exchange with--the isolated precursor ions. Kiloelectronvolt energies are used, (1) to overcome the Coulombic repulsion barrier between the cationic reactants, (2) to overcome ion-defocussing effects in the ion trap, and (3) to provide additional activation energy. Charge transfer dissociation (CTD) of the [M+H](+) precursor of Substance P gives product ions such as [M+H](2+•) and a dominant series of a ions in both the 1+ and 2+ charge states. These observations, along with the less-abundant a + 1 ions, are consistent with ultraviolet photodissociation (UVPD) results of others and indicate that C-C(α) cleavages are possible through charge exchange with helium ions. Although the efficiencies and timescale of CTD are not yet suitable for on-line chromatography, this new approach to ion activation provides an additional potential tool for the interrogation of gas phase ions.
Detection and feature extraction of bridges in airborne and spaceborne SAR image data (2007)

Operational SAR satellite systems such as ENVISAT-ASAR and RADARSAT-1 deliver image data of a rather coarse resolution, which allows the recognition or feature extraction only for large man-made objects. State of the art airborne SAR sensors on the other hand provide spatial resolution in the order well below a half meter. In such data many features of urban objects can be identified and used for recognition. Core elements of man-made infrastructure are bridges. In case of bridges over water, the oblique side looking imaging geometry of SAR sensors may lead to special signature in a SAR image depending on the aspect. In this paper, the appearance of bridges over water in SAR data is discussed. Geometric constraints concerning the changing of this signature are investigated using simulation techniques based on an adapted ray tracing. Furthermore, an approach is presented to detect bridges over water and to derive object features from spaceborne and airborne SAR images in the context of disaster management. RADARSAT-1 data with a spatial resolution of about 9 m as well as high-resolution airborne SAR data of geometric sampling distance better than 40 cm are investigated.
Customer satisfaction for financial services : the role of products, services and information technology (1999)

http://deepblue.lib.umich.edu/bitstream/2027.42/35807/2/b1963533.0001.001.pdf
Rheotaxis facilitates upstream navigation of mammalian sperm cells (2014)

A major puzzle in biology is how mammalian sperm maintain the correct swimming direction during various phases of the sexual reproduction process. Whilst chemotaxis may dominate near the ovum, it is unclear which cues guide spermatozoa on their long journey towards the egg. Hypothesized mechanisms range from peristaltic pumping to temperature sensing and response to fluid flow variations (rheotaxis), but little is known quantitatively about them. We report the first quantitative study of mammalian sperm rheotaxis, using microfluidic devices to investigate systematically swimming of human and bull sperm over a range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions, and chirality of the flagellar beat leads to stable upstream spiralling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. A minimal mathematical model is presented that accounts quantitatively for the experimental observations.DOI: http://dx.doi.org/10.7554/eLife.02403.001.
Direct hydroxylation of fats and derivatives with a hydrogen peroxide tungstic acid system (1967)

Abstract The direct preparation of threo ‐1,2‐glycols without isolation of intermediates from oleic acid, methyl oleate, and oleyl alcohol by oxidation with a hydrogen peroxide (70%)‐tungstic acid system at pH 0‐1 and 45‐55C without solvent has now been shown to be an efficient, high‐yield reaction. The threo ‐isomers are formed from intermediate epoxides by in situ hydration with accompanying inversion. Preincorporation of about 2% of the glycol reaction product into oleic acid or methyl oleate speeds up the oxidation reactions markedly and adds to their control and reproducibility. With oleyl alcohol, addition of reaction product is not necessary. Castor and olive oils are also readily oxidized to almost complete elimination of unsaturation, but the products are only 50‐60% 1,2‐glycols, owing to intra‐ and intermolecular polyether information. Addition of reaction product is unnecessary with castor oil, but with olive oil the reaction rate is greatly accelerated by incorporation of 2% of reaction product. Preconditioning (5 hr) of the hydrogen peroxide with the tungstic acid permits slightly faster oxidation rates. Emulsions are also rapidly oxidized under appropriate conditions, but these systems are more complicated to prepare and work up than oxidation of the substrates directly. Tentative reaction mechanisms are proposed in which an inorganic polyperoxytungstic acid is the effective oxidizing agent and hydroxyl‐containing species are important interfacial or complexing agents between the substrate and oxidant system.
Large Scale Synthesis and Gas-Sensing Properties of Anatase TiO<sub>2</sub> Three-Dimensional Hierarchical Nanostructures (2010)

Three-dimensional (3D) crystalline anatase titanium dioxide (TiO(2)) hierarchical nanostructures were synthesized through a facile and controlled hydrothermal and after-annealing process. The formation mechanism for the anatase TiO(2) 3D hierarchical nanostructures was investigated in detail. The 3D hierarchical nanostructures morphologies are formed by self-organization of several tens of radially distributed thin petals with a thickness of several nanometers with a larger surface area. The surface area of TiO(2) hierarchical nanostructures determined by the Brunauer-Emmett-Teller (BET) adsorption isotherms was measured to be 64.8 m(2) g(-1). Gas sensing properties based on the hierarchical nanostructures were investigated. A systematic study on sensitivity as a function of temperatures and gas concentrations was carried out. It reveals an improved ethanol gas sensing response property with a sensitivity of about 6.4 at 350 degrees C upon exposure to 100 ppm ethanol vapor for the TiO(2) hierarchical nanostructures. A gas sensing mechanism based on the adsorption-desorption of oxygen on the surface of TiO(2) is discussed and analyzed. This novel gas sensor can be multifunctional and promising for practical applications. Furthermore, the hierarchical nanostructures with high surface area can find variety of potential applications such as solar cells, biosensors, catalysts, etc.
Coordinated network scheduling: a framework for end-to-end services (2002)

In multi-hop networks, packet schedulers at downstream nodes have an opportunity to make up for excessive latencies due to congestion at upstream nodes. Similarly when packets incur low delays at upstream nodes, downs stream nodes can reduce priority and schedule other packets first. The goal of this paper is to define a framework for design and analysis of coordinated network scheduling (CNS) which exploit such inter-node coordination. The first provide a general CNS definition which enables us to classify a number of schedulers from the literature including, FIFO+, CEDF and work-conserving CJVC as examples of CNS schedulers. We then develop a distributed theory of traffic envelopes which enables us to derive end-to-end statistical admission control conditions for CNS schedulers. We show that CNS schedulers are able to limit traffic distortion to within a narrow range resulting in improved end-to-end performance and more efficient resource utilization.