gebhart/patrepeval huggingface dataset:
Liver Graft Volume Estimation in 100 Living Donors: Measure Twice, Cut Once (2005)

Estimation of graft volume (GV) is critical in living donor liver transplantation. This study examines the accuracy of formula-derived GV estimates and compares them to both radiogically-derived estimates and actual measurements. We first compared formula-derived estimates of GV and compared them to actual volumes to provide estimates for both right lobe (RL) and left lateral segment (LLS) GV. We then applied these formulae to a validation cohort. Finally, we evaluated both formula-derived and radiologically-derived estimates by comparing them to actual GV measurements. There is a marginal concordance between formula-derived calculation and GV for RL donors, but the error ratio was lower than for radiologic estimates. In contrast, MRI measurements for LLS grafts demonstrated a lower error ratio than formula-derived estimation. Formula-derived estimates of GV should be routinely used in the initial screening of potential living donors as long as their limitations are appreciated.
Blast furnace campaign prolongation philosophies in Germany (2007)

To maximize furnace campaigns and to minimize production downtimes through short lining times, the entire integral blast furnace area, including the auxiliary units, has to be theoretically partitioned. The evolution of measures for extending furnace life is in conjunction with the investigation and understanding of the in some respects very complicated wear mechanisms and their causes. Of most importance are the constructional, material and process engineering measures to reduce wear and the measuring instrumentation for early detection and progress monitoring of wear.
Defining the Syrian hamster as a highly susceptible preclinical model for SARS-CoV-2 infection (2020)

Following emergence in late 2019, SARS-CoV-2 rapidly became pandemic and is presently responsible for millions of infections and hundreds of thousands of deaths worldwide. There is currently no approved vaccine to halt the spread of SARS-CoV-2 and only very few treatment options are available to manage COVID-19 patients. For development of preclinical countermeasures, reliable and well-characterized small animal disease models will be of paramount importance. Here we show that intranasal inoculation of SARS-CoV-2 into Syrian hamsters consistently caused moderate broncho-interstitial pneumonia, with high viral lung loads and extensive virus shedding, but animals only displayed transient mild disease. We determined the infectious dose 50 to be only five infectious particles, making the Syrian hamster a highly susceptible model for SARS-CoV-2 infection. Neither hamster age nor sex had any impact on the severity of disease or course of infection. Finally, prolonged viral persistence in interleukin 2 receptor gamma chain knockout hamsters revealed susceptibility of SARS-CoV-2 to adaptive immune control. In conclusion, the Syrian hamster is highly susceptible to SARS-CoV-2 making it a very suitable infection model for COVID-19 countermeasure development.
Data from The Interaction of SWI/SNF with the Ribosome Regulates Translation and Confers Sensitivity to Translation Pathway Inhibitors in Cancers with Complex Perturbations (2023)

&lt;div&gt;Abstract&lt;p&gt;Subunits from the chromatin remodelers mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) are mutated, deleted, or amplified in more than 40% of cancers. Understanding their functions in normal cells and the consequences of cancerous alterations will provide insight into developing new targeted therapies. Here we examined whether mSWI/SNF mutations increase cellular sensitivity to specific drugs. Taking advantage of the DepMap studies, we demonstrate that cancer cells harboring mutations of specific mSWI/SNF subunits exhibit a genetic dependency on translation factors and are sensitive to translation pathway inhibitors. Furthermore, mSWI/SNF subunits were present in the cytoplasm and interacted with the translation initiation machinery, and short-term inhibition and depletion of specific subunits decreased global translation, implicating a direct role for these factors in translation. Depletion of specific mSWI/SNF subunits also increased sensitivity to mTOR-PI3K inhibitors. In patient-derived breast cancer samples, mSWI/SNF subunits expression in both the nucleus and the cytoplasm was substantially altered. In conclusion, an unexpected cytoplasmic role for mSWI/SNF complexes in translation suggests potential new therapeutic opportunities for patients afflicted by cancers demonstrating alterations in their subunits.&lt;/p&gt;Significance:&lt;p&gt;This work establishes direct functions for mSWI/SNF in translation and demonstrates that alterations in mSWI/SNF confer a therapeutic vulnerability to translation pathway inhibitors in cancer cells.&lt;/p&gt;&lt;/div&gt;
An Apparatus for Studying Wear Damage in UHMWPE: Description and Initial Test Results (1998)

Abstract Wear of ultra high molecular weight polyethylene (UHMWPE) in total joint arthroplasties causes release of particulate debris that contributes to long term complications such as osteolysis and implant loosening (Wright and Goodman, 1996). Despite the magnitude of this clinical problem, little is known about wear mechanisms in UHMWPE implant components and the factors that control them. Total knee replacement designs, for example, require non-conforming metallic on UHMWPE joint surfaces to assure appropriate kinematics and function. Finite element analysis (FEA) has shown that contact between such surfaces leads to high surface and subsurface stresses (Bartel, et al., 1986). Dynamic FEA has also that shown that femoral rollback on the tibia results in considerable residual stresses in the polyethylene (Estupiñán, et al., 1996). In an effort to complement our analytical studies of stresses associated with wear damage, we have developed a wear apparatus. Our objective is to independently control factors including geometry of the joint surfaces, contact load, the presence (sliding) or absence (rolling) of surface velocity, and the polyethylene material properties, so as to experimentally examine their effects on the creation of damage similar to that observed on retrieved joint implants.
Spectroscopic Detection of Pathogens (2000)

The goal of this LDRD Research project was to provide a preliminary examination of the use of infrared spectroscopy as a tool to detect the changes in cell cultures upon activation by an infectious agent. Due to a late arrival of funding, only 5 months were available to transfer and setup equipment at UTTM,develop cell culture lines, test methods of in-situ activation and collect kinetic data from activated cells. Using attenuated total reflectance (ATR) as a sampling method, live cell cultures were examined prior to and after activation. Spectroscopic data were collected from cells immediately after activation in situ and, in many cases for five successive hours. Additional data were collected from cells activated within a test tube (pre-activated), in both transmission mode as well as in ATR mode. Changes in the infrared data were apparent in the transmission data collected from the pre-activated cells as well in some of the pre-activated ATR data. Changes in the in-situ activated spectral data were only occasionally present due to (1) the limited time cells were studied and (2) incomplete activation. Comparison of preliminary data to infrared bands reported in the literature suggests the primary changes seen are due an increase in ribonucleic acid (RNA) production. This work will be continued as part of a 3 year DARPA grant.
Predictor-Based Compensation for Electromechanical Delay During Neuromuscular Electrical Stimulation (2011)

Electromechanical delay (EMD) is a biological artifact that arises due to a time lag between electrical excitation and tension development in a muscle. EMD is known to cause degraded performance and instability during neuromuscular electrical stimulation (NMES). Compensating for such input delay is complicated by the unknown nonlinear muscle force-length and muscle force-velocity relationships. This paper provides control development and a mathematical stability analysis of a NMES controller with a predictive term that actively accounts for EMD. The results are obtained through the development of a novel predictor-type method to address the delay in the voltage input to the muscle. Lyapunov-Krasovskii functionals are used within a Lyapunov-based stability analysis to prove semi-global uniformly ultimately bounded tracking. Experiments on able-bodied volunteers illustrate the performance and robustness of the developed controller during a leg extension trajectory following task.
Soliton Microcomb Generation in a III-V Photonic Crystal Cavity (2023)

Photonic crystals, material structures in which the dielectric function varies periodically in one, two, or three dimensions, can provide exquisite control over the propagation and confinement of light. By tailoring their band structure, exceptional optical effects can be achieved, such as slow light propagation or, through the creation of photonic bandgaps, optical cavities with both a high quality factor and a small mode volume. Photonic crystal cavities have been used to realize compact nano-lasers and achieve strong coupling to quantum emitters, such as semiconductor quantum dots, color centers, or cold atoms. A useful attribute of photonic crystals is the ability to create chirped mirrors. Chirping has underpinned advances in ultra-fast lasers based on bulk mirrors, but has yet to be fully exploited in integrated photonics, where it could provide a means to engineer otherwise unattainable dispersion profiles for a range of nonlinear optical applications, including soliton frequency comb generation. The vast majority of integrated resonators for frequency combs make use of microring geometries, where only waveguide width and height are varied to engineer dispersion. Generation of frequency combs has been demonstrated with one-dimensional photonic crystal cavities made of silicon nitride, but the low index contrast prevents formation of broad soliton combs. We overcome these challenges by using a photonic-crystal Fabry-Pérot resonator made of gallium phosphide, a material with a high refractive index and a Kerr nonlinearity 200 times larger than that of silicon nitride. We employ chirped photonic crystal mirrors to provide anomalous dispersion. With subharmonic pulsed pumping at an average power of 23.6 mW, we are able to access stable dissipative Kerr frequency combs. We demonstrate soliton formation with a 3-dB bandwidth of 3.0 THz, corresponding to a pulse duration of 60 fs.
Coherently Controlled Ballistic Charge Currents Injected in Single-Walled Carbon Nanotubes and Graphite (2008)

Ballistic electrical currents are optically injected into aligned single-walled carbon nanotubes and bulk graphite at 300 K via quantum interference between single and two photon absorption of phase-related 700 and 1400 nm, 150 fs pulses. The transient currents are detected via the emitted terahertz radiation. Optical phase and power dependence are consistent with the quantum interference optical process. Under similar excitation conditions, the peak current for a forest of nanotubes, with a diameter distribution of approximately 2.5 +/- 1.5 nm, is 9 +/- 1 times larger than that in graphite. At peak focused intensities of 10 GW cm(-2) (1400 nm) and 0.15 GW cm(-2) (700 nm), the peak current is approximately 1 nA per nanotube. The peak current for pump light polarized along the tubes is approximately 3.5 times higher than that for light polarized perpendicular to the tubes.
Assessment of time from cytoreductive nephrectomy (CN) to initiation of targeted therapy (TT) in patients with metastatic renal cell carcinoma (mRCC). (2014)

e15614 Background: For patients (pts) with de novo mRCC, the initiation of TT typically occurs at a window of 4-6 weeks following CN. Although this practice is thought to mitigate impaired wound healing, bleeding and other complications (cx) in the perioperative period potentially related to antiangiogenic TT, there is limited data to support this practice. Methods: An institutional database including over 670 pts with RCC was interrogated. Pts with de novo mRCC who had received CN and subsequent TT were identified. When available, demographic data, Charlson comorbidity index (CCI), body mass-index (BMI) and surgical data (estimated blood loss [EBL], intraoperative cx, etc.) were recorded. ICD-9 codes recorded up to 90 days following CN were evaluated; newly applied diagnoses with possible relationship to surgery were considered to be potential postoperative cx. For continuous variables, the Spearman correlation test was used to determine associations with time to TT. For categorical variables, Kaplan-Meier analyses were conducted to determine if time to TT varied across subgroups. Results: Of 270 pts with mRCC, 79 pts received CN. Of these, 34 pts received TT as an initial treatment strategy (others received IL-2, IFN or chemotherapy). The final analysis included the 28 pts with a documented date of TT initiation. Median time to TT was 45.5 days (range, 28-93). Median overall survival for the overall cohort was 17.2 months. No association was found between age, BMI, CCI, and time to TT; however, a correlation was found between number of sites of metastasis and time to TT (r=0.4922, P=0.0078). Time to TT did not vary by race (Caucasian vs. other) or class of TT (VEGF-directed therapy vs. mTOR inhibitor). Furthermore, EBL and the frequency of intraoperative cx did not vary by time to TT. The most frequently encountered postoperative cx included pleural effusion, pain, fatigue and nausea. Conclusions: With the caveat of our small sample size, the lack of an association between operative cx and time to TT suggests that an abbreviated timeframe between CN and TT may be entertained. These findings warrant exploration in larger series and/or prospective validation.
Coexistence in the chemostat with secondary metabolites (2005)

The study considers two species competing for one limiting nutrient in an open system like the chemostat. One species produces a secondary metabolite, which has a growth-inhibiting effect on the species, but can also be exploited as a secondary resource. A basic model is introduced which consists of four nonlinear ordinary differential equations and incorporates metabolite production and \tconsumption. As a first variant of this basic model we include interspecific competition. A second variant considers the introduction of a lethal inhibitor, that cannot be eliminated by one of the species and is selective for the stronger competitor. \nWe find that our basic model either supports the competitive exclusion principle or creates stable coexistence. The eventual outcome depends on the choice of \tparameter values. The dynamic of the system changes in a fundamental way, if interspecific competition is included; a supercritical as well as a subcritical Hopf \tbifurcation occur for appropriate parameter values. We discuss our results in relation to data from an experimental model system, which serves as basis for our \tmathematical assumptions and is motivated by pathogens related to the genetic disease Cystic Fibrosis.
Phenotypic Characterization of a<i>copA</i>Mutant of Neisseria gonorrhoeae Identifies a Link between Copper and Nitrosative Stress (2011)

NGO0579 is annotated copA in the Neisseria gonorrhoeae chromosome, suggesting that it encodes a cation-transporting ATPase specific for copper ions. Compared to wild-type cells, a copA mutant was more sensitive to killing by copper ions but not to other transition metals. The mutant also accumulated a greater amount of copper, consistent with the predicted role of CopA as a copper efflux pump. The copA mutant showed a reduced ability to invade and survive within human cervical epithelial cells, although its ability to form a biofilm on the surface of these cells was not significantly different from that of the wild type. In the presence of copper, the copA mutant exhibited increased sensitivity to killing by nitrite or nitric oxide. Therefore, we concluded that copper ion efflux catalyzed by CopA is linked to the nitrosative stress defense system of Neisseria gonorrhoeae. These observations suggest that copper may exert its effects as an antibacterial agent in the innate immune system via an interaction with reactive nitrogen species.
Hemodynamics of atherosclerotic mice (2002)

Apolipoprotein-E knockout mice are often used as models of human atherosclerosis, but little is known of the hemodynamic consequences. Using noninvasive Doppler methods, it was found that heart rate and blood pressure were normal but that aortic pulse wave velocity, mean aortic and mitral blood velocities, and peripheral wave reflections were increased. It was also demonstrated that heart weight/body weight ratio was increased, and that hematocrit was decreased. The changes are consistent with decreased peripheral vascular resistance and compliance and with volume overload cardiac hypertrophy.
Self-Assembly of Cyclic Peptides into Nanotubes and Then into Highly Anisotropic Crystalline Materials (2001)

C3-symmetric lactams in a tube: Specially designed rigid disc-shaped macrolactams self-assemble as endless tubes by means of backbone–backbone hydrogen bonds and van der Waals contacts (see scheme). All the tubes with very strong dipoles further aggregate in a parallel fashion and all the dipoles are still oriented in the same direction.
Quantifying headphone listening experience in virtual sound environments using distraction (2022)

Abstract Headphones are commonly used in various environments including at home, outside and on public transport. However, the perception and modelling of the interaction of headphone audio and noisy environments is relatively unresearched. This work investigates the headphone listening experience in noisy environments using the perceptual attributes of distraction and quality of listening experience. A virtual sound environment was created to simulate real-world headphone listening, with variations in foreground sounds, background contexts and busyness, headphone media content and simulated active noise control. Listening tests were performed, where 15 listeners rated both distraction and quality of listening experience across 144 stimuli using a multiple-stimulus presentation. Listener scores were analysed and compared to a computational model of listener distraction. The distraction model was found to be a good predictor of the perceptual distraction rating, with a correlation of 0.888 and an RMSE of 13.4%, despite being developed to predict distraction in the context of audio-on-audio interference in sound zones. In addition, perceived distraction and quality of listening experience had a strong negative correlation of − 0.953. Furthermore, the busyness and type of the environment, headphone media, loudness of the foreground sound and active noise control on/off were significant factors in determining the distraction and quality of listening experience scores.
Cartilage Oligomeric Matrix Protein Inhibits Vascular Smooth Muscle Calcification by Interacting With Bone Morphogenetic Protein-2 (2011)

Our data strongly suggest that COMP is a novel inhibitor of vascular calcification. The imbalance between the effects of COMP and BMP-2 may provide new insights into the pathophysiology of vascular calcification.
Extended parametric gain range in photonic crystal fibers with strongly frequency-dependent field distributions (2014)

The parametric gain range of a degenerate four-wave mixing process is determined in the undepleted pump regime. The gain range is considered with and without taking the mode field distributions of the four-wave mixing components into account. It is found that the mode field distributions have to be included to evaluate the parametric gain correctly in dispersion-tailored speciality fibers and that mode profile engineering can provide a way to increase the parametric gain range.
Treating Fibrous Insulation to Reduce Thermal Conductivity (2009)

A chemical treatment reduces the convective and radiative contributions to the effective thermal conductivity of porous fibrous thermal-insulation tile. The net effect of the treatment is to coat the surfaces of fibers with a mixture of transition-metal oxides (TMOs) without filling the pores. The TMO coats reduce the cross-sectional areas available for convection while absorbing and scattering thermal radiation in the pores, thereby rendering the tile largely opaque to thermal radiation. The treatment involves a sol-gel process: A solution containing a mixture of transition-metal-oxide-precursor salts plus a gelling agent (e.g., tetraethylorthosilicate) is partially cured, then, before it visibly gels, is used to impregnate the tile. The solution in the tile is gelled, then dried, and then the tile is fired to convert the precursor salts to the desired mixed TMO phases. The amounts of the various TMOs ultimately incorporated into the tile can be tailored via the concentrations of salts in the solution, and the impregnation depth can be tailored via the viscosity of the solution and/or the volume of the solution relative to that of the tile. The amounts of the TMOs determine the absorption and scattering spectra.
Identification and characterization of a phenyl-thiazolyl-benzoic acid derivative as a novel RAR/RXR agonist (2019)

In this study, a phenyl-thiazolyl-benzoic acid derivative (PTB) was identified as a potent agonist of RXRα and RARα. PTB was characterized in nuclear receptor binding, reporter gene, cell differentiation and cell growth assays. PTB bound directly to RXRα and RARα, but not to PPARα, δ(β) or γ. PTB fully activated reporter genes with enhancer elements for RXRα/RXRα, and partially activated reporter genes with enhancer elements for RARα/RXRα, PPARδ(β) and PPARγ. Furthermore, PTB induced differentiation and inhibited the growth of human APL cells. Thus, PTB is a novel dual agonist of RXRα and RARα and works as both a differentiation inducer and a proliferation inhibitor to leukemic cells.
Characterization of translational initiation sites in<i>E. coli</i> (1982)

We characterize the Shine and Dalgarno sequence of 124 known gene beginnings. This information is used to make "rules" which help distinguish gene beginning from other sites in a library of over 78,000 bases of mRNA. Gene beginnings are found to have information besides the initiation codon and Shine and Dalgarno sequence which can be used to make better "rules".