gebhart/patrepeval huggingface dataset:
A genetic locus involved in iron utilization unique to some Campylobacter strains (1997)

Two genes involved in iron utilization in Campylobacter coli VC167 T1 have been characterized. The cfrA gene encodes a protein with a predicted Mr of 77,653 which, after processing of the leader sequence, has a predicted Mr of 75,635. This protein has significant sequence identity to siderophore receptors of several bacteria, and site-specific mutants defective in cfrA do not synthesize one of two major iron-repressible outer membrane proteins. An adjacent gene encodes a TonB-like protein; a mutant in this gene lost the ability to utilize hemin, ferrichrome, and enterochelin as iron sources. The cfrA and tonB genes of VC167 T1 hybridized to all strains of C. coli and most strains of C. jejuni examined but did not hybridize to several other strains of C. jejuni, suggesting that the thermophilic campylobacters can be separated into two categories based on the presence of these two iron utilization genes.
Regulation of p53 Localization and Activity by Ubc13 (2006)

The abundance and activity of p53 are regulated largely by ubiquitin ligases. Here we demonstrate a previously undisclosed regulation of p53 localization and activity by Ubc13, an E2 ubiquitin-conjugating enzyme. While increasing p53 stability, Ubc13 decreases p53 transcriptional activity and increases its localization to the cytoplasm, changes that require its ubiquitin-conjugating activity. Ubc13 elicits K63-dependent ubiquitination of p53, which attenuates Hdm2-induced polyubiquitination of p53. Ubc13 association with p53 requires an intact C-terminal domain of p53 and is markedly stronger with a p53 mutant that cannot tetramerize. Expression of Ubc13 in vivo increases the pool of monomeric p53, indicating that Ubc13 affects tetramerization of p53. Significantly, wild-type but not mutant Ubc13 is associated with polysomes and enriches p53 within this fraction. In response to DNA damage, Ubc13 is no longer capable of facilitating p53 monomerization, in part due to a decrease in its own levels which is p53 dependent. Our findings point to a newly discerned mechanism important in the regulation of p53 organization, localization, and activity by Ubc13.
Dietary Protein Restriction Lowers Plasma Insulin-Like Growth Factor I (IGF-I), Impairs Cortical Bone Formation, and Induces Osteoblastic Resistance to IGF-I in Adult Female Rats<sup>1</sup> (2000)

Dietary protein deficiency, common in elderly, is associated with decreased areal bone mineral density and plasma insulin-like growth factor I (IGF-I). To investigate the early adaptation of bone cells to protein restriction, 6-month-old female rats were pair-fed with isocaloric 15% (control) or 2.5% casein diets for 14 days. Animals were then treated daily with rhIGF-I/IGFBP-3 (1:4, 2.5 mg IGF-I/kg BW) or with vehicle for 10 days. After double-labeling, proximal metaphysis and mid-diaphysis of the tibia were analyzed histomorphometrically. Plasma osteocalcin, IGF-I, and urinary deoxypyridinoline were quantified. After 14 days of protein restriction, significant drops in plasma osteocalcin (13%) and IGF-I (37%), in periosteal formation (83%) and mineral apposition (49%) rates are observed, indicating a decreased osteoblast recruitment and activity. In cancellous bone, a significant decrease in active eroded surfaces (27%) and osteoclast number (24%) indicates a transient depression of resorption. In rats fed the 15% casein diet, rhIGF-I/IGFBP-3 increases cancellous (42%) and periosteal (600%) formation rates, indicating an increased osteoblast recruitment. In protein-restricted rats, rhIGF-I/IGFBP-3 fails to increase cancellous or periosteal bone formation and plasma osteocalcin is significantly lower than in 15% casein+rhIGF-I/ IGFBP-3 rats. Protein restriction induces osteoblast resistance to rhIGF-I/IGFBP-3 in both bone envelopes. Low plasma IGF-I and osteoblast resistance to IGF-I, may contribute to the impaired periosteal formation.
On the applicability of Kramers–Krönig relations for ultrasonic attenuation obeying a frequency power law (2000)

In the recent literature concern has been raised regarding the validity of Kramers-Kronig relations for media with ultrasonic attenuation obeying a frequency power law. It is demonstrated, however, that the Kramers-Kronig dispersion relations for application to these types of media are available. The developed dispersion relations are compared with measurements on several liquids, and agreement is found to better than 1 m/s over the experimentally available bandwidth. A discussion regarding the validity of these dispersion relations, in particular how the dispersion relations relate to the so-called Paley-Wiener conditions, forms the conclusion.
Studies of a magnetically compressed electron beam (1969)

An experimental investigation of the problem of magnetically compressing a perveance <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.54 \times 10^{-6}</tex> A/V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3/2</sup> beam is reported. The feasibility of magnetic compression is demonstrated by passing this beam, compressed in area by a factor of 1000, through a drift tube 0.014 inch in diameter and 1 inch long with 95 percent transmission. The success of the magnetic-compression technique rests on the hitherto unsuspected ability of the beam to damp out undulations and to lose its thermal structure within a relatively short distance. A semiempirical theory from which the field required to maintain the compressed beam can be calculated is also presented.
Far different levels of gene expression provided by an oriented cloning system in<i>Bacillus subtilis</i>and<i>Escherichia coli</i> (2003)

A gene expression system for both Bacillus subtilis and Escherichia coli was developed. The expression vector, pHASH102, produces any combination of promoter and open reading frame to be expressed based on the T-extended cloning method. Because the pHASH series vectors are designed to shuttle between the genome and a high copy plasmid in B. subtilis, the expression profiles of copy number dependence can be examined systematically. We demonstrated that vectors with Pr, Pspac, and PS10 promoters are suitable for the overexpression of GFPuv. Moreover, aadK encoding aminoglycoside 6-adenylyltransferase (a streptomycin-resistance gene) of B. subtilis was successfully overexpressed in both B. subtilis and E. coli. These highly expressed GFPuv and aadK genes can be used as a genetic marker for both organisms.
Mechanisms Involved in Placebo and Nocebo Responses and Implications for Drug Trials (2011)

Drug trials often compare active drugs with inert placebos under double-blind conditions. This standard design is increasingly being questioned in light of recent progress in understanding the mechanisms behind the placebo response.1,2 The growing knowledge of the neurobiology of placebo is forcing us to reconsider the significance of the placebo in clinical practice, with consequent profound implications for the design of clinical trials. Clinical Pharmacology & Therapeutics (2011); 90 5, 722–726. doi:10.1038/clpt.2011.204
ChemInform Abstract: Solvent‐Free Synthesis of Monastrol Derivatives Catalyzed by NaHSO<sub>4</sub>. (2010)

Abstract An environmentally friendly three‐ component Biginelli cyclocondensation is used for the synthesis of monastrol derivatives which are an interesting class of compounds in cancer research.Depending on the combination of the three components products of type (IV) or (VII) are obtained.
Zwitterionic amphiphile coated magnetofluorescent nanoparticles – synthesis, characterization and tumor cell targeting (2015)

Magnetofluorescent nanoparticles (MFNPs) have recently attracted significant research interests due to their potential applications in biological manipulation and imaging. In this work, through a simple and fast self-assembling process, we first report the preparation of zwitterionic MFNPs (ZW-MFNPs) in the form of micelles using our newly synthesized zwitterionic amphiphiles, CuInS<sub>2</sub>/ZnS quantum dots, and MnFe<sub>2</sub>O<sub>4</sub> magnetic nanoparticles. ZW-MFNPs integrate both MnFe<sub>2</sub>O<sub>4</sub> magnetic nanoparticles and CuInS<sub>2</sub>/ZnS quantum dots in their hydrophobic cores and zwitterionic groups such as carboxybetaine and sulfobetaine on their hydrophilic shells. ZW-MFNPs possess dual imaging properties, high (Mn + Fe) recovery, excellent stability in aqueous solutions with a wide pH/ionic-strength range and physiological media, minimal cytotoxicity, and specific targeting to brain tumor cells after bioconjugation with chlorotoxin. The unique characteristics of ZW-MFNPs may open an avenue for these particles to be employed in broad biomedical applications.
Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure−Selectivity Relationships (2005)

Quantitative Structure-Selectivity Relationships (QSSR) are developed for a library of 40 phase-transfer asymmetric catalysts, based around quaternary ammonium salts, using Comparative Molecular Field Analysis (CoMFA) and closely related variants. Due to the flexibility of these catalysts, we use molecular dynamics (MD) with an implicit Generalized Born solvent model to explore their conformational space. Comparison with crystal data indicates that relevant conformations are obtained and that, furthermore, the correct biphenyl twist conformation is predicted, as illustrated by the superiority of the resulting model (leave-one-out q(2) = 0.78) compared to a random choice of low-energy conformations for each catalyst (average q(2) = 0.22). We extend this model by incorporating the MD trajectory directly into a 4D QSSR and by Boltzmann-weighting the contribution of selected minimized conformations, which we refer to as '3.5D' QSSR. The latter method improves on the predictive ability of the 3D QSSR (leave-one-out q(2) = 0.83), as confirmed by repeated training/test splits.
Development of a chronically implanted microelectrode array for intraneural electrical stimulation for prosthetic sensory feedback (1999)

Thesis (S.M.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 1999.
Nonlinear dynamics and ferroelectric materials (2002)

The aim of the presented paper is to show that the application of analysis methods of dissipative chaotic systems is a useful tool for the study of structural phase transitions and the large signal behaviour of ferroelectric materials. The series resonance circuit with a ferroelectric capacitor is a practical realization of a nonlinear dynamical system which exhibits period-doubling behaviour and chaos if the amplitude and the frequency of the driving voltage have suitable values. The response function of the nonlinear dynamical system is used for the determination of the nonlinear coefficients of the sample.
Degradation of 17β-Estradiol by a Gram-Negative Bacterium Isolated from Activated Sludge in a Sewage Treatment Plant in Tokyo, Japan (2002)

A 17beta-estradiol (E2)-degrading bacterium was isolated from activated sludge in a sewage treatment plant in Tokyo, Japan. The isolate was suggested to be a new Novosphingobium species. Gas chromatography-mass spectrometry and (1)H nuclear magnetic resonance analyses of the metabolites of E2 degradation suggested that no toxic products accumulated in the culture medium.
Quantum-switched heterojunction bistable bipolar transistor by chemical beam epitaxy (1990)

We proposed and demonstrated a novel bistable transistor−the quantum-switched heterojunction bistable bipolar transistor. The transistor has two current states. With increasing base-emitter voltage, the collector current is switched from high to low, while the base current is switched from low to high. Bistability is observed for a certain range of base voltage. This device has potential applications in implementing high-speed single bipolar transistor memories, gain quenching in light-emitting devices, and optoelectronic switching.
Upgrading of heavy oil from the San Joaquin Valley of California by aqueous pyrolysis (1995)

Midway Sunset crude oil and well-head oil were treated at elevated temperatures in a closed system with the presence of water. Mild to moderate upgrading, as measured by increase in API gravity, was observed at 400{degrees}C or above. Reduced pressure operation exhibited upgrading activity comparable to upgrading under normal aqueous pyrolysis conditions. Reduced pressure operation was obtained by the use of specific blending methods, a surfactant, and the proper amount of water. The use of additives provided additional upgrading. The best of the minimum set tested was Co(II) 2-ethylhexanoate. Fe(III) 2-ethylhexanoate also showed some activity under certain conditions.
An analysis of mode-locked arrays of automatic level control oscillators (1994)

The locking region for beat frequency entrained, or mode-locked arrays of discrete microwave oscillators, is exceedingly small, which presents great difficulty in array design. This paper shows that introducing a time-delayed gain control loop can enhance the entrainment region and that this region is maximized for a coupling phase of 90 degrees. For this value of coupling phase the location, size, shape, and orientation of the stable mode locking region is derived for arrays of arbitrary size. A study of the dependence of the stable mode locking region on the number of array elements shows that the region becomes highly eccentric as the number increases, thus making array tuning difficult and causing high sensitivity to particular oscillator tuning errors. The analysis is confirmed with a low frequency realization of a three-element array.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Nonsynclronous Time Division with Holding and with Random Sampling (1952)

There is a general type of system in which an indefinitely large number of transmitters can have access to any of an indefinitely large number of receivers over a medium of limited bandwidth. In these systems, signal-to-noise ratio goes down as more transmitters are used simultaneously. This paper describes a particular system which sends samples by means of coded pulse groups sent at random times. The signal-to-noise ratio is good in the absence of interference and the effect of interference is minimized by holding the previous sample if a sample is lost. An experimental system worked satisfactorily and gave close to the predicted signal-to-noise ratio. Such a system might be used to provide communication and automatic switching in rural telephony, or for other applications.
In vivo tracking of hematopoietic cells in the retina of chimeric mice with a scanning laser ophthalmoscope (2012)

We examine the effect of bone marrow transplantation (BMT) on retinal cell turnover by performing simultaneous cell tracking of native microglia and engrafting donor bone marrow-derived cell (BMDC) populations in the retinae of live mice using a custom-built multi-color confocal scanning laser ophthalmoscope (SLO) specifically developed for murine retinal imaging. CX3CR1GFP/+ mice whose retinal microglia express the green fluorescent protein (GFP) were exposed to a lethal dose of gamma radiation and subsequently rescued with bone marrow cells from universal DsRed donor mice. Over a time course of four months after the irradiation and BMT, progressive loss of GFP+ microglia was accompanied by delayed engraftment of DsRed+ BMDC. Morphologic examination revealed that the remaining GFP+ microglia were ramified, while engrafting DsRed+ cells exhibited both ramification and dendriform shape. Leukocyte endothelial interaction, normally absent in healthy retinal vasculature, was observed even after three months, indicating sustained inflammation long after the radiation exposure. Fluorescein angiography demonstrated that the blood-retina barrier is compromised early after irradiation. In vivo imaging provides a powerful means to study dynamic cellular processes over a broad range of timescales from seconds to months that have previously not been accessible by ex vivo analysis.
Modelling for semiconductor spintronics (2005)

The authors summarise semiclassical modelling methods, including drift-diffusion, kinetic transport equation and Monte Carlo simulation approaches, utilised in studies of spin dynamics and transport in semiconductor structures. As a review of the work by the authors' group, several examples of applications of these modelling techniques are presented.
Requirement of the N-Terminal Region of Orthobunyavirus Nonstructural Protein NSm for Virus Assembly and Morphogenesis (2006)

The nonstructural protein NSm of Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family, is encoded by the M segment in a polyprotein precursor, along with the virion glycoproteins, in the order Gn-NSm-Gc. As little is known of its function, we examined the intracellular localization, membrane integrality, and topology of NSm and its role in virus replication. We confirmed that NSm is an integral membrane protein and that it localizes in the Golgi complex, together with Gn and Gc. Coimmunoprecipitation assays and yeast two-hybrid analysis demonstrated that NSm was able to interact with other viral proteins. NSm is predicted to contain three hydrophobic (I, III, and V) and two nonhydrophobic (II and IV) domains. The N-terminal nonhydrophobic domain II was found in the lumen of an intracellular compartment. A novel BUNV assembly assay was developed to monitor the formation of infectious virus-like-particles (VLPs). Using this assay, we showed that deletions of either the complete NSm coding region or domains I, II, and V individually seriously compromised VLP production. Consistently, we were unable to rescue viable viruses by reverse genetics from cDNA constructs that contained the same deletions. However, we could generate mutant BUNV with deletions in NSm domains III and IV and also a recombinant virus with the green fluorescent protein open reading frame inserted into NSm domain IV. The mutant viruses displayed differences in their growth properties. Overall, our data showed that the N-terminal region of NSm, which includes domain I and part of domain II, is required for virus assembly and that the C-terminal hydrophobic domain V may function as an internal signal sequence for the Gc glycoprotein.
Efficacy and Safety of Calcipotriene Plus Betamethasone Dipropionate Aerosol Foam in Patients With Psoriasis Vulgaris--a Randomized Phase III Study (PSO-FAST). (2015)

Cal/BD foam was efficacious, achieved rapid itch relief and was well tolerated in patients with body psoriasis. This innovative aerosol foam formulation is expected to become a valuable treatment option.
Buffer intensity of seawater1 (1975)

The buffer intensities of a NaCI solution and of seawater were measured to determine the effect of ion‐pairing on the dissociation reactions of carbonic acid and, through these reactions, on the buffering of oceanic waters.
Genetic and Immunochemical Characterization of Thiocyanate-Degrading Bacteria in Lake Water (2002)

Natural aquatic and soil samples were screened for the presence of thiocyanate-degrading bacteria. Using thiocyanate supplementation, we established an enrichment culture containing such bacteria from lake water. The dominant bacteria had the scnC-LS5 gene encoding thiocyanate hydrolase, which was closely related to the enzyme found previously in Thiobacillus thioparus THI115 isolated from activated sludge.
Estimating statistical aggregates on probabilistic data streams (2007)

The probabilistic-stream model was introduced by Jayram et al. [20].It is a generalization of the data stream model that issuited to handling "probabilistic" data, where each item of the stream represents a probability distribution over a set of possible events. Therefore, a probabilistic stream determines a distribution over apotentially exponential number of classical "deterministic" streams where each item is deterministically one of the domain values.
Language Transfer (1989)

The author shows how similarities and differences between languages can influence grammar, vocabulary, and pronunciation acquisition. Terence Odlin reconsiders a question that many language teachers and educational researchers have addressed: How much influence can a learner's native language have in making the acquisition of a new language easy or difficult? Odlin analyzes and interprets research showing many ways in which similarities and differences between languages can influence the acquisition of grammar, vocabulary, and pronunciation. In addition, he provides a detailed look at work on other areas important for the study of transfer, including discourse, individual variation, and sociolinguistic factors. Language teachers, applied linguists, and educational researchers will find this volume extremely valuable to their work.
Cellular Protection with Proanthocyanidins Derived from Grape Seeds (2002)

Grape seed proanthocyanidins have been reported to possess a broad spectrum of pharmacological and medicinal properties against oxidative stress. We have demonstrated that IH636 proanthocyanidin extract (GSPE) provides excellent protection against free radicals in both in vitro and in vivo models. GSPE had significantly better free radical scavenging ability than vitamins C, E and beta-carotene and demonstrated significant cytotoxicity towards human breast, lung and gastric adenocarcinoma cells, while enhancing the growth and viability of normal cells. GSPE protected against tobacco-induced apoptotic cell death in human oral keratinocytes and provided protection against cancer chemotherapeutic drug-induced cytotoxicity in human liver cells by modulating cell cycle/apoptosis regulatory genes such as bcl2, p53 and c-myc. Recently, the bioavailability and mechanistic pathways of cytoprotection by GSPE were examined on acetaminophen-induced hepatotoxicity and nephrotoxicity, amiodarone-induced pulmonary toxicity, doxorubicin-induced cardiotoxicity, DMN-induced immunotoxicity and MOCAP-induced neurotoxicity in mice. Serum chemistry changes, integrity of genomic DNA and histopathology were assessed. GSPE pre-exposure provided near complete protection in terms of serum chemistry changes and DNA damage, as well as abolished apoptotic and necrotic cell death in all tissues. Histopathological examination reconfirmed these findings. GSPE demonstrated concentration-/dose-dependent inhibitory effects on the drug metabolizing enzyme cytochrome P450 2E1, and this may be a major pathway for the anti-toxic potential exerted by GSPE. Furthermore, GSPE treatment significantly decreased TNFalpha-induced adherence of T-cells to HUVEC by inhibiting VCAM-1 expression. These results demonstrate that GSPE is highly bioavailable and may serve as a potential therapeutic tool in protecting multiple target organs from structurally diverse drug- and chemical-induced toxicity.