gebhart/patrepeval huggingface dataset:
Bacterial Origin for the Isoprenoid Biosynthesis Enzyme HMG-CoA Reductase of the Archaeal Orders Thermoplasmatales and Archaeoglobales (2001)

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase or HMGR) fulfills an essential role in archaea, as it is required for the synthesis of isoprenoid ethers, the main component of archaeal cell membranes. There are two clearly homologous but structurally different classes of the enzyme, one found mainly in eukaryotes and archaea (class 1), and the other found in bacteria (class 2). This feature facilitated the identification of several cases of interdomain lateral gene transfer (LGT), in particular, the bacterial origin for the HMGR gene from the archaeon Archaeoglobus fulgidus. In order to investigate if this LGT event was recent and limited in its scope or had a broad and long-term impact on the recipient and its related lineages, the HMGR gene was amplified and sequenced from a variety of archaea. The survey covered close relatives of A. fulgidus, the only archaeon known prior to this study to possess a bacterial-like HMGR; representatives of each main euryarchaeal group were also inspected. All culturable members of the archaeal group Archaeoglobales were found to display an HMGR very similar to the enzyme of the bacterium Pseudomonas mevalonii. Surprisingly, two species of the genus Thermoplasma also harbor an HMGR of bacterial origin highly similar to the enzymes found in the Archaeoglobales. Phylogenetic analyses of the HMGR gene and comparisons to reference phylogenies from other genes confirm a common bacterial origin for the HMGRs of Thermoplasmatales and Archaeoglobales. The most likely explanation of these results includes an initial bacteria-to-archaea transfer, followed by a another event between archaea. Their presence in two divergent archaeal lineages suggests an important adaptive role for these laterally transferred genes.
The treatment of the mallet finger by the Oakley splint (1974)

Abstract The Oakley splint for mallet finger deformity is described. A method of manufacture is shown and the results which follow its use are recorded.
White Matter Alteration in Idiopathic Normal Pressure Hydrocephalus: Tract-Based Spatial Statistics Study (2011)

Our results suggest that patients with iNPH have various patterns of white matter damage and that TBSS analysis is a promising tool for performing accurate voxelwise statistical analysis of the iNPH brain, with the exception of misregistered areas.
A combined finite element, boundary integral and spherical harmonic method for close-packed sonar arrays (2002)

Acoustic interactions within a sonar array are known to affect the array performance as well as the life expectancy of the transducers themselves. The ability to predict array performance is required for large close-packed arrays of acoustic transducers. In these cases, traditional full finite element or coupled finite element-boundary element methods prove costly. The general approach is to combine a single transducer finite element model with an analytic description of the surrounding fluid and neighboring transducers in the array. The finite element model produces the dynamic system matrix. The boundary integral equation relates surface pressure and velocity. Boundary elements are partitioned for the case of the surface of an arbitrary body circumscribed by a spherical surface to provide an implicit transfer of surface pressures to spherical fluid pressures and particle velocities. These quantities are then transformed in terms of spherical harmonics. The resulting series is combined with a spherical harmonic representation of the fluid using the addition theorem for multiple scatterers. This technique has been exercised to evaluate an array of electrically driven piezoelectric shell transducers. Results are compared to a coupled finite element-boundary element method.
Estradiol-Induced Regression in T47D:A18/PKCα Tumors Requires the Estrogen Receptor and Interaction with the Extracellular Matrix (2009)

Several breast cancer tumor models respond to estradiol (E(2)) by undergoing apoptosis, a phenomenon known to occur in clinical breast cancer. Before the application of tamoxifen as an endocrine therapy, high-dose E(2) or diethystilbesterol treatment was successfully used, albeit with unfavorable side effects. It is now recognized that such an approach may be a potential endocrine therapy option. We have explored the mechanism of E(2)-induced tumor regression in our T47D:A18/PKCalpha tumor model that exhibits autonomous growth, tamoxifen resistance, and E(2)-induced tumor regression. Fulvestrant, a selective estrogen receptor (ER) down-regulator, prevents T47D:A18/PKCalpha E(2)-induced tumor growth inhibition and regression when given before or after tumor establishment, respectively. Interestingly, E(2)-induced growth inhibition is only observed in vivo or when cells are grown in Matrigel but not in two-dimensional tissue culture, suggesting the requirement of the extracellular matrix. Tumor regression is accompanied by increased expression of the proapoptotic FasL/FasL ligand proteins and down-regulation of the prosurvival Akt pathway. Inhibition of colony formation in Matrigel by E(2) is accompanied by increased expression of FasL and short hairpin RNA knockdown partially reverses colony formation inhibition. Classic estrogen-responsive element-regulated transcription of pS2, PR, transforming growth factor-alpha, C3, and cathepsin D is independent of the inhibitory effects of E(2). A membrane-impermeable E(2)-BSA conjugate is capable of mediating growth inhibition, suggesting the involvement of a plasma membrane ER. We conclude that E(2)-induced T47D:A18/PKCalpha tumor regression requires participation of ER-alpha, the extracellular matrix, FasL/FasL ligand, and Akt pathways, allowing the opportunity to explore new predictive markers and therapeutic targets.
Ipsilateral Medial and Lateral Discoid Meniscus with Medial Meniscus Tear (2016)

We report a rare case of ipsilateral medial and lateral discoid meniscus with medial meniscus tear. The medial discoid meniscus with tear was treated with partial meniscectomy, whereas the lateral discoid meniscus without tear was only followed up.
Structure elucidation and biosynthetic gene cluster analysis of caniferolides A–D, new bioactive 36-membered macrolides from the marine-derived <i>Streptomyces caniferus</i> CA-271066 (2019)

Bioassay-guided isolation based on the antifungal activity of a culture broth of the marine-derived actinomycete Streptomyces caniferus CA-271066 led to the discovery of new 36-membered polyol macrolides, caniferolides A-D (1-4). Their connectivity was determined by spectroscopic methods including ESITOF-MS and 1D/2D NMR. The relative stereochemistry of each stereocluster in these compounds was established using NOE analysis, the universal database method and J-based configuration analysis, further assisted by comparisons with NMR data of structurally related macrolides. Genome sequencing followed by detailed bioinformatics analysis led to the identification of the corresponding biosynthetic gene cluster and allowed the prediction of the stereochemical outcome of their biosynthesis, confirming the relative stereochemistry of each stereocluster already determined by NMR and establishing their stereochemical relationship, ultimately rendering the absolute configuration of all chiral centers. Furthermore, based on our results and already published data, it has been possible to derive the complete absolute configuration of the related macrolides PM100117 and PM100118, astolides A and B, and deplelides A and B. Caniferolides A-D have shown pronounced antifungal activity against Candida albicans and Aspergillus fumigatus alongside antiproliferative activity against five human tumoral cell lines.
Optical properties of In<sub>x</sub>Al<sub>1−x</sub>N film and nanocolumns (2009)

We analyzed photoluminescence (PL) spectra of In-rich InxAl1−xN nanocolumns (NCs; x = 0.80) and film (x = 0.82) using the free-electron recombination to bound (FERB) model. The FERB model fits well to the PL spectra of the In-rich InxAl1−xN film and NCs, which implies that light-emitting properties of In-rich InxAl1−xN are similar to those of InN. We obtained bandgap energies and electron carrier densities from the results of fitting the PL spectra.
New developments in experimental models of inflammatory bowel disease (2004)

These data are providing fundamental insights into the pathogenesis of IBD and thus are forming the basis of new therapeutic approaches, many of which will be translated to the clinic in the near future.
Studies of Immunization With Living Rubella Virus (1965)

A SEVERE epidemic of rubella appeared throughout a large part of the United States early in 1964, resulting in infection of many pregnant women.<sup>1,2</sup>During the last months of 1964 and early in 1965 numerous infants were born with congenital abnormalities, including cataracts, congenital heart disease, thrombocytopenia, hepatosplenomegaly, bone lesions, and central nervous system damage.<sup>3,4</sup>A causal relationship between maternal rubella and congenital abnormalities had been established over the past 20 years by clinical and epidemiologic observation.<sup>5-9</sup>More recently, the relationship has been substantiated by serological studies of newborn infants with abnormalities<sup>10-12</sup>as well as by the frequent recovery of rubella virus from these same infants.<sup>3,4,13,14</sup>The incidence of congenital abnormalities due to the 1964 rubella epidemic is as yet incompletely assessed, but early estimates have ranged between 0.3% to 4.0% of infants in utero during the epidemic.<sup>4,15,16</sup> This current experience, in addition to
Rapid fabrication of poly(dimethylsiloxane)-based microchip capillary electrophoresis devices using CO2 laser ablation (2005)

The use of CO(2) laser ablation for the patterning of capillary electrophoresis (CE) microchannels in poly(dimethylsiloxane)(PDMS) is described. Low-cost polymer devices were produced using a relatively inexpensive CO(2) laser system that facilitated rapid patterning and ablation of microchannels. Device designs were created using a commercially available software package. The effects of PDMS thickness, laser focusing, power, and speed on the resulting channel dimensions were investigated. Using optimized settings, the smallest channels that could be produced averaged 33 microm in depth (11.1% RSD, N= 6) and 110 microm in width (5.7% RSD, N= 6). The use of a PDMS substrate allowed reversible sealing of microchip components at room temperature without the need for cleanroom facilities. Using a layer of pre-cured polymer, devices were designed, ablated, and assembled within minutes. The final devices were used for microchip CE separation and detection of the fluorescently labeled neurotransmitters aspartate and glutamate.
Sound Transmission in a Lung Phantom Model (2013)

Alterations in the structure and function of the pulmonary system that occur in disease or injury often give rise to measurable changes in lung sound production and transmission. A better understanding of sound transmission and how it is altered by injury and disease might improve interpretation of lung sound measurements, including new lung imaging modalities that are based on an array measurement of the acoustic field on the torso surface via contact sensors or are based on a 3-dimensional measurement of the acoustic field throughout the lungs and torso using magnetic resonance elastography. It is beneficial to develop a computational acoustic model that would accurately simulate generation, transmission and noninvasive measurement of sound and vibration within the pulmonary system and torso caused by both internal and external sources. In the present study, sound transmission in the airway tree and coupling to and transmission through the surrounding lung parenchymal tissue were investigated on a mechanical lung phantom with a built-in bifurcating airway tree through airway insonification. Sound transmission in the airway tree was studied by applying the Horsfield self-consistent model of asymmetric dichotomy for the bronchial tree. The acoustics of the bifurcating airway segments and lung phantom surface motion were measured by microphones and scanning laser Doppler vibrometty respectively. Finite element simulations of sound transmission in the lung phantom were performed. Good agreement was achieved between experiments and finite element simulations. This study validates the computational approach for sound transmission and provides insights for simulations on real lungs.
Desbutylhalofantrine: Evaluation of QT Prolongation and Other Cardiovascular Effects after Intravenous Administration In Vivo (2003)

Desbutylhalofantrine (Hfm) is an active and equipotent metabolite of halofantrine (Hf). Both compounds are effective in the treatment of sensitive and multidrug-resistant and In vitro data and interpretation of some clinical studies of Hf have suggested that, unlike Hf, Hfm may be devoid of adverse cardiac effects. The aim of these investigations was to provide the first in vivo examination of the intrinsic capacity of Hfm to affect repolarization in the heart, using an anesthetized rabbit model. Using a dose-rising regimen, Hfm was administered IV at doses of 1, 1, 2, 4, and 8 mg/kg and the baseline rate-corrected QT interval (QTc) value of 377 +/- 13 ms rose to 394 +/- 16, 396 +/- 12, 429 +/- 18, 433 +/- 16, and 489 +/- 15 ms, respectively. There were no significant changes in blood pressure, heart rate, or PR or QRS intervals. The Hfm plasma concentrations were quantitated after high-performance liquid chromatographic analysis, the results indicating a significant correlation between Hfm plasma concentration and QT(c) prolongation. The study also identified a concentration-dependent hemolysis of erythrocytes after administration of Hfm. The conclusions from this study are that IV administration of Hfm does cause a significant prolongation of the QT(c) interval in a rabbit model.
Local Drug Delivery for the Treatment of Neurotology Disorders (2019)

Neurotology disorders such as vertigo, tinnitus, and hearing loss affect a significant proportion of the population (estimated 39 million in the United States with moderate to severe symptoms). Yet no pharmacological treatments have been developed, in part due to limitations in effective drug delivery to the anatomically protected inner ear compartment. Intratympanic delivery, a minimally invasive injection performed in the office setting, offers a potential direct route of administration. Currently, off-label use of therapeutics approved to treat disorders via systemic administration are being injected intratympanically, mostly in the form of aqueous solutions, but provide variable levels of drug exposure for a limited time requiring repeated injections. Hence, current drug delivery approaches for neurotology disorders are sub-optimal. This review, following a description of pharmacokinetic considerations of the inner ear, explores the merits of novel delivery approaches toward the treatment of neurotology disorders. Methodologies employing local delivery to the inner ear are described, including direct intracochlear delivery as well as intratympanic methods of infusion and injection. Intratympanic injection delivery formulation strategies including hydrogels, polymers and nanoparticulate systems are explored. These approaches represent progress toward more effective delivery options for the clinical treatment of a variety of neurotology disorders.
Low frequency acoustic emissions from large horizontal axis wind turbines (1989)

Available test data and theoretical predictions of LF noise from large wind turbines of the type to be used for energy generation are briefly summarized. The main LF noise sources are identified as tower-wake/blade interactions and rotor-plane inflow gradients. Sound-pressure time histories, measured and calculated narrow-band and rotational noise spectra, and noise radiation patterns for the WTS-4 and WWG-0600 wind turbines are presented graphically.
A new ultrasound tissue-equivalent material. (1980)

Two limitations on the animal-hide gelatin and graphite powder tissue equivalent (TE) materials are that they cannot be produced consistently with speeds of sound less than 1,570 m/s at room temperature (22 degrees C) and that irreparable damage can result if the materials are raised to temperatures above 32.5 degrees C. An acceptable substitute polysaccharide gel (agar) has a high melting point (78 degrees C) and can be made to exhibit speeds of sound over the range 1,498 m/s to over 1,600 m/s at 22 degrees C. Thus TE material made with agar is environmentally stable and can be manufactured to exhibit the important speed of sound, 1,540 m/s.
Variability and Vulnerability at the Ecological Level: Implications for Understanding the Social Determinants of Health (2002)

Objectives. We examined variability in disease rates to gain understanding of the complex interactions between contextual socioeconomic factors and health. Methods. We compared mortality rates between New York and California counties in the lowest and highest quartiles of socioeconomic status (SES), assessed rate variability between counties for various outcomes, and examined correlations between outcomes’ sensitivity to SES and their variability. Results. Outcomes with mortality rates that differed most by county SES were among those whose variability across counties was high (e.g., AIDS, homicide, cirrhosis). Lower- SES counties manifested greater variability among outcome measures. Conclusions. Differences in health outcome variability reflect differences in SES impact on health. Health variability at the ecological level might reflect the impact of stressors on vulnerable populations.
Large structures in diblock copolymer micellar solution (2004)

The association properties in water solution of poly(dimethylsiloxane)-b-poly(ethyleneoxide) diblock copolymer was investigated by static and dynamic light scattering in a wide range of concentrations and temperatures. The presence of a long hydrophilic poly(ethyleneoxide) (PEO) chain causes a weak tendency to microphase separation of the system which is responsible for some relevant effects. First of all we observe a late micellization process which is characterized by an unusually high value of the critical micellar concentration (c(cmc) =0.007 g/cm3) and by an unusually small aggregation number (approximately 6) of the generated micelles. Moreover, the composition of the highly hydrated micelles has been found to change sensitively with temperature. On increasing temperature dehydration of micelles has been observed together with a contemporaneous increase in the aggregation number, whereas the hydrodynamic radius remains constant in the whole range investigated. The long hydrophilic chains also stimulate an efficient entanglement process between micelles. The interpenetrating PEO chains belonging to different micelles causes the depletion of the solvent in the outer layer of micelles. The result is the formation, just after the micellization process takes place, of thermodynamically stable clusters of entangled micelles. These large structures, which are present in the system in small concentrations, maintain their structural properties unchanged in a wide range of concentrations and temperatures, and provide indirect evidence of a weak attractive component to the intermicellar interaction potential.
Mono‐ and Dicoordinate Germanium(0) as a Four‐Electron Donor (2018)

We report the synthesis and isolation of molecular iron germanide motifs in the stoichiometry of Fe<sub>3</sub> Ge and Fe<sub>2</sub> Ge, which are stabilized by the coordination of N-heterocyclic carbene (NHC) and carbon monoxide (CO) ligands. NHCiPr2Me2 ⋅Ge[Fe(CO)<sub>4</sub> ][Fe<sub>2</sub> (CO)<sub>8</sub> ] (NHCiPr2Me2 =1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene), a germanium(0) ligand with just one NHC as an auxiliary ligand, assumes a bridging coordination mode between a mononuclear [Fe(CO)<sub>4</sub> ] and a dinuclear [(CO)<sub>4</sub> FeFe(CO)<sub>4</sub> ] unit with rapid exchange between the two binding modes in solution. The electronic structure of this species is analysed by NBO and ELF calculations with DFT methods, as well as the mechanistic details of its fluxional coordination behaviour. Treatment of NHCiPr2Me2 ⋅Ge[Fe(CO)<sub>4</sub> ] [Fe<sub>2</sub> (CO)<sub>8</sub> ] with the sterically less demanding NHCMe4 (NHCMe4 =1,3,4,5-tetramethylimidazol-2-ylidene) leads to a dinuclear iron complex (NHCMe4 )<sub>2</sub> Ge[Fe(CO)<sub>4</sub> ]<sub>2</sub> that contains a bridging germylone ligand with two stabilizing NHC equivalents.
The Active Site of a Lon Protease from Methanococcus jannaschii Distinctly Differs from the Canonical Catalytic Dyad of Lon Proteases (2004)

ATP-dependent Lon proteases catalyze the degradation of various regulatory proteins and abnormal proteins within cells. Methanococcus jannaschii Lon (Mj-Lon) is a homologue of Escherichia coli Lon (Ec-Lon) but has two transmembrane helices within its N-terminal ATPase domain. We solved the crystal structure of the proteolytic domain of Mj-Lon using multiwavelength anomalous dispersion, refining it to 1.9-angstroms resolution. The structure displays an overall fold conserved in the proteolytic domain of Ec-Lon; however, the active site shows uniquely configured catalytic Ser-Lys-Asp residues that are not seen in Ec-Lon, which contains a catalytic dyad. In Mj-Lon, the C-terminal half of the beta4-alpha2 segment is an alpha-helix, whereas it is a beta-strand in Ec-Lon. Consequently, the configurations of the active sites differ due to the formation of a salt bridge between Asp-547 and Lys-593 in Mj-Lon. Moreover, unlike Ec-Lon, Mj-Lon has a buried cavity in the region of the active site containing three water molecules, one of which is hydrogen-bonded to catalytic Ser-550. The geometry and environment of the active site residues in Mj-Lon suggest that the charged Lys-593 assists in lowering the pK(a) of the Ser-550 hydroxyl group via its electrostatic potential, and the water in the cavity acts as a proton acceptor during catalysis. Extensive sequence alignment and comparison of the structures of the proteolytic domains clearly indicate that Lon proteases can be classified into two groups depending on active site configuration and the presence of DGPSA or (D/E)GDSA consensus sequences, as represented by Ec-Lon and Mj-Lon.
A Metroplex Capacity Enhancement Strategy through Coordinated Use of Runway Dependencies (2011)

An airport metroplex consists of two or more airports in close proximity whose arrival and departure operations are highly interdependent. Consequently, dependencies arise from interacting traffic streams in the shared airspace. These dependencies complicate the task of managing metroplex resources, resulting in reduced capacity and congestion. A generic metroplex runway dependency metric is developed in this paper to compactly measure how runway features affect traffic. Metroplex capacity diagrams were generated to measure capacity envelopes and also to study the most frequently used and the highest capacity runway configurations at the New York/New Jersey metroplex (NYNJ). Ideas from a new operational concept called the ‘flexible operations concept’ were used to identify options to enhance capacity at NYNJ. Under this concept, arrival flights can land at any of the constituent airports of a metroplex instead of a fixed airport. An optimization technique that combines the runway dependency metric, capacity diagrams and the flexible operations concept is developed so that operations can be spread optimally across metroplex runways. Example problems are presented to demonstrate the optimization scheme. Results from the proof-of-concept studies indicate that flexible arrivals are a viable option to enhance metroplex capacity during low departure periods.