gebhart/patrepeval huggingface dataset:
Computed<sup>13</sup>C NMR Chemical Shifts via Empirically Scaled GIAO Shieldings and Molecular Mechanics Geometries. Conformation and Configuration from<sup>13</sup>C Shifts (1997)

Accurate (rms error ∼3 ppm) predictions of 13C chemical shifts are achieved for many of the common structural types of organic molecules through empirical scaling of shieldings calculated from gauge including atomic orbitals (GIAO) theory with a small basis set and with geometries obtained from computationally inexpensive molecular mechanics methods. Earlier GIAO calculations are shown to be much better at predicting relative chemical shifts when density functional theory with the B3LYP hybrid functional is used to account for electron correlation, in comparison with Hartree−Fock calculations. The GIAO isotropic shieldings need to be empirically scaled to achieve good numerical agreement with experimental δC. GIAO calculations with different small basis sets are compared for a set of 38 model compounds containing C, H, O, and N with MMX and MM3 force fields and B3LYP/6-31G* optimizations providing the geometries. The best MM3-based results are obtained with B3LYP/3-21G(X,6-31+G*)//MM3 calculations in which the 3-21G basis set is augmented for heteroatoms with polarization and diffuse functions. The examples of the (E)- and (Z)-2-butenes, axial and equatorial methylcyclohexanes, exo- and endo-2-norbornanols, vulgarin and epivulgarin, and chair and twist-boat forms of 3α-hydroxy-2β-(4-morpholinyl)-5αH-androstan-17-one are examined to establish whether δpred values could determine the structure if only one of each pair of structures were available to provide experimental δC values. The δpred from B3LYP/3-21G(X,6-31+G*)//MM3 calculations are adequate for addressing questions of conformation and relative stereochemistry.
Network topologies: inference, modeling, and generation (2008)

Accurate measurement, inference and modeling techniques are fundamental to Internet topology research. Spatial analysis of the Internet is needed to develop network planning, optimal routing algorithms, and failure detection measures. A first step toward achieving such goals is the availability of network topologies at different levels of granularity, facilitating realistic simulations of new Internet systems. The main objective of this survey is to familiarize the reader with research on network topology over the past decade. We study techniques for inference, modeling, and generation of the Internet topology at both the router and administrative levels. We also compare the mathematical models assigned to various topologies and the generation tools based on them. We conclude with a look at emerging areas of research and potential future research directions.
Chemical Composition of Parenchyma and Sclerenchyma Cell Walls Isolated from Orchardgrass and Switchgrass (1991)

The isolation and analysis of cell‐wall types (CWT) such as parenchyma and sclerenchyma provide a means of understanding the complex chemistry of forage fiber. Our objective was to compare the composition of purenchyma and sclerenchyma cell walls of field grown orchard grass ( Dactylis glomerata L.) and switch grass ( Panicum virgatum L.) harvested at four stages of plant maturity. Leaf blades, leaf sheaths, and stems were analyzed for fiber constituents. Parenchyma and sclerenchyma cell walls were mechanically isolated from plant parts and analyzed for neutral sugars, alkali‐labile phenolic acids, and lignin. Neutral‐detergent fiber (NDF), hemicellulose, cellulose, and lignin concentrations differed ( P < 0.05) between plant parts. Parenchyma cell walls differed widely in composition, with urabinose ranging from 25 to 81 g kg −1 ; xylose, 92 to 282 g kg −1 ; glucose, 410 to 634 g kg −1 ; p‐coumaric acid, 1 to 19 g kg −1 ; ferulic acid, 2 to 10 g kg −1 ; and lignin, 38 to 104 g kg −1 . Sclerenchyma cell walls were more uniform in composition, with arabinose ranging from 10 to 30 g kg −1 ; xylose, 204 to 330 g kg −1 ; glucose, 411 to 533 g kg −l ; p ‐conmaric acid, 5 to 16 g kg −1 ; ferulic acid, 3 to 9 g kg −1 ; and lignin, 51 to 99 g kg −1 . In most cases, the ratios of xylose to urabinose and p‐coumaric acid to ferulic acid were lower (P < 0.05) in purenchyma compared with sclerenchyma, and in leaf blade or leaf sheath CWT compared with those of the stem. These results suggest that the chemistry of CWT is complex and that studies of heterogenous preparations such as NDF are confounded by the chemical diversity of CWT contained in forages.
Generation of Cell-Permeable Artificial Zinc Finger Protein Variants (2010)

Designed or artificial zinc finger proteins (ZFPs) are one of the most promising DNA-binding proteins that target genomic sequences of interest in vitro and in vivo. Conjugation of other functional domains such as transcriptional regulatory domains and endonucleases to ZFPs provided powerful molecular tools to modulate endogenous gene expression and genetic information. These ZFP variants have been introduced into cells as DNA-encoding ZFP variants by using plasmids or viral vectors. As an alternative delivery method of ZFP variants, we developed cell-permeable ZFP variants by fusing cell-penetrating peptides to ZFP variants. We will describe how to generate cell-permeable artificial ZFP variants and how to examine the cell permeabilities by immunofluorescent staining.
Arginine and antioxidant supplement on performance in elderly male cyclists: a randomized controlled trial (2010)

An arginine and antioxidant-containing supplement increased the anaerobic threshold at both week one and week three in elderly cyclists. No effect on VO2 max was observed. This study indicated a potential role of L-arginine and antioxidant supplementation in improving exercise performance in elderly.
Speed Estimation From a Tri-axial Accelerometer Using Neural Networks (2007)

We propose a speed estimation method with human body accelerations measured on the chest by a tri-axial accelerometer. To estimate the speed we segmented the acceleration signal into strides measuring stride time, and applied two neural networks into the patterns parameterized from each stride calculating stride length. The first neural network determines whether the subject walks or runs, and the second neural network with different node interactions according to the subject's status estimates stride length. Walking or running speed is calculated with the estimated stride length divided by the measured stride time. The neural networks were trained by patterns obtained from 15 subjects and then validated by 2 untrained subjects' patterns. The result shows good agreement between actual and estimated speeds presenting the linear correlation coefficient r=0.9874. We also applied the method to the real field and track data.
Pertussis toxin treatment of whole blood. A novel approach to assess G protein function in congestive heart failure. (1990)

This study was designed to assess G protein function in mononuclear leukocytes (MNL) of patients with congestive heart failure (CHF). MNL membranes were ADP-ribosylated in vitro in the presence of pertussis or cholera toxin. The amount of pertussis toxin substrates did not differ significantly between CHF patients (6,100 +/- 224 fmol/mg, n = 23) and age-matched healthy control subjects (5,812 +/- 972 fmol/mg protein, n = 19). Among the CHF patients, no differences were observed between those with idiopathic and ischemic CHF. The amount of cholera toxin substrates also did not differ significantly between CHF patients (7,522 +/- 1,405 fmol/mg protein, n = 11) and control subjects (5,654 +/- 707 fmol/mg protein, n = 14). Moreover, basal and isoproterenol- and prostaglandin E1-stimulated cyclic AMP (cAMP) accumulation in MNL was similar in control subjects and patients. To detect more subtle alterations of the cAMP-generating system, we incubated anticoagulated blood with 250-400 ng/ml pertussis toxin for 4 hours at 37 degrees C. This treatment completely ADP-ribosylated the MNL pertussis toxin substrates. Incubation with pertussis toxin did not change basal or prostaglandin E1-stimulated cAMP generation in MNL of control subjects, but it significantly enhanced stimulated generation (443 +/- 44 vs. 643 +/- 93 pmol/10(7) cells, p less than 0.025) in MNL of CHF patients. This enhancement was most pronounced in the most severely ill patients (New York Heart Association class IV) and correlated with plasma norepinephrine levels, another marker of CHF severity (r = 0.798, n = 11, p less than 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)
A soft robotic exosuit improves walking in patients after stroke (2017)

Stroke-induced hemiparetic gait is characteristically slow and metabolically expensive. Passive assistive devices such as ankle-foot orthoses are often prescribed to increase function and independence after stroke; however, walking remains highly impaired despite-and perhaps because of-their use. We sought to determine whether a soft wearable robot (exosuit) designed to supplement the paretic limb's residual ability to generate both forward propulsion and ground clearance could facilitate more normal walking after stroke. Exosuits transmit mechanical power generated by actuators to a wearer through the interaction of garment-like, functional textile anchors and cable-based transmissions. We evaluated the immediate effects of an exosuit actively assisting the paretic limb of individuals in the chronic phase of stroke recovery during treadmill and overground walking. Using controlled, treadmill-based biomechanical investigation, we demonstrate that exosuits can function in synchrony with a wearer's paretic limb to facilitate an immediate 5.33 ± 0.91° increase in the paretic ankle's swing phase dorsiflexion and 11 ± 3% increase in the paretic limb's generation of forward propulsion (<i>P</i> < 0.05). These improvements in paretic limb function contributed to a 20 ± 4% reduction in forward propulsion interlimb asymmetry and a 10 ± 3% reduction in the energy cost of walking, which is equivalent to a 32 ± 9% reduction in the metabolic burden associated with poststroke walking. Relatively low assistance (~12% of biological torques) delivered with a lightweight and nonrestrictive exosuit was sufficient to facilitate more normal walking in ambulatory individuals after stroke. Future work will focus on understanding how exosuit-induced improvements in walking performance may be leveraged to improve mobility after stroke.
Facile Strategy to Well-Defined Water-Soluble Boronic Acid (Co)polymers (2007)

A facile route to well-defined boronic acid (co)polymers from stable and easily manipulated boronic ester monomers is presented. The polymerization of 4-pinacolatoborylstyrene by reversible addition−fragmentation chain transfer (RAFT) yielded polymeric boronic acid precursors. Selection of stoichiometry allowed tuning of polymerization kinetics and targeting specific molecular weights in the range of Mn = 17000−32000 g/mol. The resulting low polydispersity poly(4-pinacolatoborylstyrene) homopolymers were employed as macro-chain transfer agents for block copolymerization with N,N-dimethylacrylamide to yield amphiphilic block copolymers that formed micelles in aqueous media. The pinacol ester derivatized (co)polymers were easily deprotected by a mild and convenient strategy to yield free boronic acid polymers
Severity of Obstructive Sleep Apnea is Associated with Cardiac Troponin I Concentrations in a Community-based Sample: Data from the Akershus Sleep Apnea Project (2014)

Increased obstructive sleep apnea (OSA) severity is independently associated with higher concentrations of hs-TnI, suggesting that frequent apneas or hypoxemia in OSA may cause low-grade myocardial injury.
Value added Web: integrating WWW with a TINA service management platform (1999)

One of the most spectacular developments of this decade is the enormous growth of the Internet. One of the most popular services of the Internet is the World Wide Web (WWW). It may be expected that the Web will be used to provide more sophisticated services, e.g., video on demand. Customers will be prepared to pay for such services, because of the exclusive content and the quality of the (broadband) transport network needed to transfer the information. Consequently, we need a way to manage these services, without violating the ease of use provided by current WWW. In this paper we present a solution based on TINA's business model. We introduce the value added Web (VAW), which is an integration of the WWW with TINA service management. This combination adds the benefits of the TINA business model to the WWW. A VAW session appears as a normal WWW session, except that it allows charging for specific content and the setup of connections with an agreed quality of service. The VAW business model assumes that users only have a direct relation with a retailer and that the retailer is responsible for charging. This paper describes the rationale behind VAW and the design and implementation of a prototype of VAW.
MicroRNAs in C. elegans Aging: Molecular Insurance for Robustness? (2009)

The last decade has witnessed a revolution in our appreciation of the extensive regulatory gene expression networks modulated by small untranslated RNAs. microRNAs (miRNAs), ~22 nt RNAs that bind imperfectly to partially homologous sites on target mRNAs to regulate transcript expression, are now known to influence a broad range of biological processes germane to development, homeostatic regulation and disease. It has been proposed that miRNAs ensure biological robustness, and aging has been described as a progressive loss of system and cellular robustness, but relatively little work to date has addressed roles of miRNAs in longevity and healthspan (the period of youthful vigor and disease resistance that precedes debilitating decline in basic functions). The C. elegans model is highly suitable for testing hypotheses regarding miRNA impact on aging biology: the lifespan of the animal is approximately three weeks, there exist a wealth of genetic mutations that alter lifespan through characterized pathways, biomarkers that report strong healthspan have been defined, and many miRNA genes have been identified, expression-profiled, and knocked out. 50/114 C. elegans miRNAs change in abundance during adult life, suggesting significant potential to modulate healthspan and lifespan. Indeed, miRNA lin-4 has been elegantly shown to influence lifespan and healthspan via its lin-14 mRNA target and the insulin signaling pathway. 27 of the C. elegans age-regulated miRNAs have sequence similarity with both fly and human miRNAs. We review current understanding of a field poised to reveal major insights into potentially conserved miRNA-regulated networks that modulate aging.
Programmable impulse neural circuits (1991)

A description is given of CMOS electronic circuits which emulate natural neurons at a more detailed level than that typically used by artificial neural network models. A pulse-firing circuit which realizes general short-term neuron dynamics is discussed. Both fixed and programmable synapse circuits for realizing long-term dynamics are also described. Together, these establish the basic structures required for the implementation of programmable impulse neural networks.
A collector of distinction: Sir William Holburne (1793-1874) (2003)

Diabetic kidney disease (DKD) is one of the main complications of diabetic microangiopathy. The pathogenesis of DKD is very complex, including autophagy, inflammation, oxidative stress. Although a series of treatment intervention have achieved certain results in the treatment of diabetic nephropathy, still cannot reverse the kidney injury of diabetic nephropathy. The kidney is one of the most important organs of energy metabolism. Renal function is highly dependent on phagocytosis of mitochondria, and aberrant or defective autophagic mechanisms are central to the pathology of many renal diseases. Under high glucose conditions, mitochondrial fragments accumulate in the kidney, suggesting that mitochondrial clearance mechanisms may be attenuated with changes in mitochondrial transformation mechanisms. However, the exact mechanism of mitophagy regulation in DKD has not been elucidated. Recent advances in autophagy have renewed interest in these signaling pathways and molecules in the pathogenesis of DKD. Investigating autophagy and its associated signaling molecules may provide potential unique targets for therapeutic intervention in DKD.
Effect of Capacitation on Bull Sperm Binding to Homologous Oviductal Epithelium1 (1996)

Sperm binding to oviductal epithelium is thought to be an important mechanism regulating sperm reservoir formation in the oviduct. On the basis of evidence in the hamster, we hypothesized that capacitation affects release of bovine sperm, allowing them to fertilize. Oviducts were obtained from the ovulatory side of estrous Holstein heifers. The isthmic and ampullar epithelia were milked out and reduced to fragments, which formed everted vesicles (explants). Explants were placed in tissue culture wells in TALP medium and incubated at 39 degrees C in 5% CO2. Frozen-thawed sperm were prepared by swim-up in TALP and capacitated by incubation for 4 h in TALP with 20 micrograms/ml heparin (without glucose). Uncapacitated sperm were used immediately after dilution into capacitation medium. Within 2 h of surgery, sperm were added to the explants and incubated with them for 15 min. Sperm and explants were videotaped, and the tapes were analyzed to determine the numbers of sperm bound per surface area. ANOVA did not show a difference between the number of sperm bound/0.1 mm2 in the isthmus and ampulla (p > 0.05); however, an effect of capacitation was detected (p = 0.0015). Also, the percentage of capacitated sperm, determined by chlortetracycline labeling, was greater in sperm that remained free-swimming in the presence of explants than in the absence of explants (p = 0.001). In conclusion, capacitation appears to be involved in the release of bovine sperm from oviductal epithelium and therefore could enable sperm to leave the reservoir and fertilize oocytes.
Multicast performance of large-scale antenna systems (2013)

A multicast large-scale antenna system (LSAS) provides distinct programs simultaneously to different groups of users. We analyze the performance of using a common reverselink pilot sequence for the estimation of user channels receiving the same program, and derive an optimal reverse/forward-link combined power control scheme that equalizes the throughput among all users. Equal throughput to all users is effected through a combination of proper forward-link power allocation among user groups and power control on the reverse-link pilots of each individual user. The power control scheme is optimal in the sense that the equalized per-user throughput is maximized. Compared with an LSAS that uses a distinct pilot sequence for each user, our approach provides the following advantages: simultaneously support of many more users; substantially higher throughput per-user; lower user terminal power consumption.
A regulatory role of activated T‐lymphocytes on human megakaryocytopoiesis <i>in vitro</i> (1985)

Cellular interactions responsible for regulating in vitro megakaryocytopoiesis were studied using a microagar culture system which permits the simultaneous proliferation of human megakaryocytic progenitor cells (CFU-M) and T-lymphocytic colonies (CFU-TL). The proliferation of these colony types depends mainly on two factors: phytohaemagglutinin (PHA) and erythropoietin (EP). The direct addition of increasing PHA concentrations to the liquid overlayer resulted in a parallel increase of CFU-M and CFU-TL. If the T-lymphocytes were removed by an E-rosetting technique a marked diminution of CFU-M and CFU-TL numbers was observed. However, monocyte depletion resulted in a marked augmentation of CFU-M proliferation compared to unfractionated mononuclear cells. In order to confirm that the reduction of CFU-M proliferation observed after T-depletion was primarily mediated by the absence of T-lymphocytes, we have co-cultured different concentrations of previously removed autologous T-lymphocytes with a constant number of T-depleted bone marrow cells. A parallel increase of CFU-TL and CFU-M was found if 0.75 - 7.5 X 10(4) T-lymphocytes were added to the culture. In conclusion, our results indicate that activated T-lymphocytes augment proliferation of human bone marrow CFU-M and that monocytes are less important for the growth of megakaryocytic colonies.
Using an information retrieval system to retrieve source code samples (2006)

Software developers often face steep learning curves in using a new framework, library, or new versions of frameworks for developing their piece of software. In large organizations, developers learn and explore use of frameworks, rarely realizing, several peers may have already explored the same. A tool that helps locate samples of code, demonstrating use of frameworks or libraries would provide benefits of reuse, improved code quality and faster development. This paper describes an approach for locating common samples of source code from a repository by providing extensions to an information retrieval system. The approach improves the existing approaches in two ways. First, it provides the scalability of an information retrieval system, supporting search over thousands of source code files of an organization. Second, it provides more specific search on source code by preprocessing source code files and understanding elements of the code as opposed to considering code as plain text.
Development of an integrated optic oxygen sensor using a novel, generic platform (2004)

This paper describes the development of a generic platform for enhanced, integrated optic sensors based on fluorescence detection. The platform employs a novel optical configuration in order to achieve enhanced performance and has inherent multianalyte detection capability. The sensor element comprises a multimode ridge waveguide that has been patterned with an analyte-sensitive fluorescent spot, which is excited directly using a LED. The platform was applied to the detection of gaseous oxygen as a proof of principle. The sol-gel-derived sensor spots were doped with an oxygen-sensitive fluorescent dichlororuthenium dye complex and intensity-based calibration data were generated from the oxygen-dependent waveguide output. The sensor achieved a LOD of 0.62% and a resolution of less than 0.96% gaseous oxygen, which compares favourably with a similar, recently reported system. This device highlights the combination of inexpensive rapid prototyping techniques and a dedicated sensor enhancement strategy that together facilitate the production of an effective prototype sensor platform.
Sensory defects in Necdin deficient mice result from a loss of sensory neurons correlated within an increase of developmental programmed cell death (2006)

Overall, our data show clearly that, in early development of the nervous system, Necdin is an anti-apoptotic or survival factor.
Direct Analysis of Intact Proteins from <i>Escherichia coli</i> Colonies by Liquid Extraction Surface Analysis Mass Spectrometry (2014)

Top-down identification of proteins by liquid extraction surface analysis (LESA) mass spectrometry has previously been reported for tissue sections and dried blood spot samples. Here, we present a modified "contact" LESA method for top-down analysis of proteins directly from living bacterial colonies grown in Petri dishes, without any sample pretreatment. It was possible to identify a number of proteins by use of collision-induced dissociation tandem mass spectrometry followed by searches of the data against an E. coli protein database. The proteins identified suggest that the method may provide insight into the bacterial response to environmental conditions. Moreover, the results show that the "contact" LESA approach results in a smaller sampling area than typical LESA, which may have implications for spatial profiling.