gebhart/patrepeval huggingface dataset:
Reliability of the Spinal Instability Neoplastic Score (SINS) among radiation oncologists: an assessment of instability secondary to spinal metastases (2014)

Among radiation oncologists SINS is a highly reliable, reproducible, and valid assessment tool to address a key question in tumor related spinal disease: Is the spine 'stable' or is there 'current or possible instability' that warrants surgical assessment?
Femtosecond to Millisecond Dynamics of Light Induced Allostery in the Avena sativa LOV Domain (2017)

The rational engineering of photosensor proteins underpins the field of optogenetics, in which light is used for spatiotemporal control of cell signaling. Optogenetic elements function by converting electronic excitation of an embedded chromophore into structural changes on the microseconds to seconds time scale, which then modulate the activity of output domains responsible for biological signaling. Using time-resolved vibrational spectroscopy coupled with isotope labeling, we have mapped the structural evolution of the LOV2 domain of the flavin binding phototropin Avena sativa (AsLOV2) over 10 decades of time, reporting structural dynamics between 100 fs and 1 ms after optical excitation. The transient vibrational spectra contain contributions from both the flavin chromophore and the surrounding protein matrix. These contributions are resolved and assigned through the study of four different isotopically labeled samples. High signal-to-noise data permit the detailed analysis of kinetics associated with the light activated structural evolution. A pathway for the photocycle consistent with the data is proposed. The earliest events occur in the flavin binding pocket, where a subpicosecond perturbation of the protein matrix occurs. In this perturbed environment, the previously characterized reaction between triplet state isoalloxazine and an adjacent cysteine leads to formation of the adduct state; this step is shown to exhibit dispersive kinetics. This reaction promotes coupling of the optical excitation to successive time-dependent structural changes, initially in the β-sheet and then α-helix regions of the AsLOV2 domain, which ultimately gives rise to Jα-helix unfolding, yielding the signaling state. This model is tested through point mutagenesis, elucidating in particular the key mediating role played by Q513.
[The clinical profiles of primary biliary cirrhosis with a suboptimal biochemical response to ursodeoxycholic acid]. (2011)

To observe the characteristics of primary biliary cirrhosis (PBC) with a suboptimal biochemical response to ursodeoxycholic acid. A total of 38 Chinse PBC patients (5 male patients, 33 female patients, average age 55 years old) with treatment of ursodeoxycholic acid in our hospital from January 1999 to January 2009 were erolled and studied retrospectively. 17 suboptimal biochemical responders mainly presented with liver diseases related symptoms including jaundice (41.1%), fatigue, anorexia (23.5%), edema and abdominal distension (11.7%). 21 good biochemical responders mainly presented with abnormal liver function tests without symptoms. The suboptimal biochemical responders had significantly higher baseline levels of total serum bilirubin, alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, immunoglobulin G and globulin as compared to the good biochemical responsers. There were no differences in gender, age and the dose of UDCA. PBC patients with liver diseases related symptoms, marked abnormal liver tests and characteristics of autoimmune hepatitis may have a suboptimal biochemical response to ursodeoxycholic acid treatment.
Comparison between different MEMS Laterally Vibrating Resonator Technologies for Passive Voltage Amplification in an RF Front-End System (2018)

This paper describes the challenges associated with attainingpassive voltage gain by means of piezoelectric MEMS Laterally VibratingResonators (LVRs) in an RF frontend (RFFE) system. LVR technologies based ondifferent piezoelectric films – Aluminum Nitride (AlN), Scandium-dopedAluminum Nitride (Sc x Al 1–x N), and Y-cut and X-cut Lithium Niobate(LN) – are compared in regards to their impact on the sensitivity of anultra-low power wake-up resonant micromechanical receiver (RMR) [1]. Due tothe outstanding performance in terms of quality factor at resonance $(Q_{s})$ and electromechanical coupling $(k_{t}^{2})$, X-cut LithiumNiobate resonators are identified as the optimal approach for this radioarchitecture. Design, fabrication, and testing of an array of X-cut LNresonators is finally presented to demonstrate the capabilities of thistechnology.
High-Abundance Polypeptides of the Human Plasma Proteome Comprising the Top 4 Logs of Polypeptide Abundance (2008)

Abstract Background: Plasma contains thousands of proteins, but a small number of these proteins comprise the majority of protein molecules and mass. Content: We surveyed proteomic studies to identify candidates for high-abundance polypeptide chains. We searched the literature for information on the plasma concentrations of the most abundant components in healthy adults and for the molecular mass of the mature polypeptide chains in plasma. Because proteomic studies usually dissociate proteins into polypeptide chains or detect short peptide segments of proteins, we summarized data on individual peptide chains for proteins containing multiple subunits or polypeptides. We collected data on about 150 of the most abundant polypeptides in plasma. The abundant polypeptides span approximately the top 4 logs of concentration in plasma, from 650 to 0.06 μmol/L on a molar basis or from about 50 000 to 1 mg/L mass abundance. Conclusions: Data on the concentrations of the high-abundance peptide chains in plasma assist in understanding the composition of plasma and potential approaches for clinical laboratory or proteomic analysis of plasma proteins. Development of more extensive databases regarding the plasma concentrations of proteins in health and diseases would promote diagnostic and proteomic advances.
Hydrophilins from distant organisms can protect enzymatic activities from water limitation effectsin vitro (2005)

ABSTRACT Hydrophilins are a wide group of proteins whose defining characteristics are high hydrophilicity index (&gt; 1.0) and high glycine content (&gt; 6%). The transcripts of most hydrophilins accumulate in response to water deficit in organisms such as plants, fungi and bacteria. In plants, most of the known Late Embryogenesis Abundant (LEA) proteins belong to this group (Garay‐Arroyo et al ., Journal of Biological Chemistry 275, 5668–5674, 2000). To gain insight into the function of hydrophilins, an in vitro assay was developed in which the enzymes malate dehydrogenase (MDH) or lactate dehydrogenase (LDH) are subjected to controlled partial water removal. Subtle changes in conformation during partial water removal were detected using 1‐anilinonaphtalene‐8‐sulphonate (ANS), a fluorescent probe, whose emission at 460 nm increases when bound to hydrophobic groups. The results show that water limitation conditions imposed in this in vitro assay induce changes in MDH or LDH protein structures, which correlate with enzyme inactivation. It is also shown that plant, fungal and bacterial hydrophilins are able to protect enzymatic activities from water‐loss effects in this in vitro system, in a wide range of water potentials. In addition, the data in this work indicate that the presence of hydrophilins also avoids the MDH and LDH conformational modifications caused during the assay. These results show that hydrophilins are able to protect enzymatic activities from inactivation due to in vitro partial water limitation and thus suggest a function for these proteins in vivo .
Experimental Study of the Influence of Valve Timing on Hydraulic Motor Efficiency (2015)

The timing of the valves of a hydraulic motor plays an important role in determining the throttling energy. To reduce this dominating energy loss, the timing of the valves must allow the fluid in the chamber to be precompressed and decompressed such that there is minimal pressure differential across the transitioning valve. The optimal valve timing to achieve precompression and decompression is a function of the motor displacement, angular velocity, pressure, and air content of the fluid, thus to achieve high efficiency at all conditions, active valve timing is required. The valves in most hydraulic motor architectures are mechanically timed to the piston displacement, rendering it impossible to change the valve timing as a function of operating conditions. This paper presents one novel valve architecture that allows for such processes: a rotary valve that is controlled independently of the piston displacement, enabling active timing control. To validate the concept and test the motor valve at fixed timing and fixed displacement conditions, a prototype valve was installed on a single cylinder 3.5 cc/rev slider-crank piston motor. The nominal timing of the valve was optimized for operation for a pressure of 7 MPa, 2% entrained air by volume, and an angular velocity between 10 and 30 Hz. A model, including the pressure dynamics, leakage, compressibility, check valve dynamics, and geometry dependent parameters is developed, simulated, and compared to the experiment. The experimental system includes instrumentation for measuring the inlet and outlet flow rates, piston position, and pressure in the inlet, outlet, and cylinder. A comparison between the model and experimental data shows good agreement and demonstrate the large impact of valve timing on efficiency.
A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a (2019)

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independently of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably reaches a lower limit of detection (LOD) of ≈ 6.8 nM fluorescein, which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs with an LOD of 3.7 nM using a Cas13a-based fluorescence assay. Cas13a is an RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device may be used in educational settings, through providing low cost instrumentation for quantitative assays or as a platform to integrate hardware, software and biochemistry concepts in the future.
Virtual screening for high affinity guests for synthetic supramolecular receptors (2015)

The protein/ligand docking software GOLD, which was originally developed for drug discovery, has been used in a virtual screen to identify small molecules that bind with extremely high affinities (<i>K</i> ≈ 10<sup>7</sup> M<sup>-1</sup>) in the cavity of a cubic coordination cage in water. A scoring function was developed using known guests as a training set and modified by introducing an additional term to take account of loss of guest flexibility on binding. This scoring function was then used in GOLD to successfully identify 15 new guests and accurately predict the binding constants. This approach provides a powerful predictive tool for virtual screening of large compound libraries to identify new guests for synthetic hosts, thereby greatly simplifying and accelerating the process of identifying guests by removing the reliance on experimental trial-and-error.
Curatr: a web application for creating, curating and sharing a mass spectral library (2017)

Supplementary data are available at Bioinformatics online.
Rapid synthesis of new 2-methyl-7-nitro-5-substituted-2,3-dihydroimidazo[5,1-b]oxazole as potential antibacterial drugs through one-pot cyclization and Suzuki–Miyaura coupling (2018)

Original 2-methyl-7-nitro-5-substituted-2,3-dihydroimidazo[5,1-b]oxazoles were prepared by reacting 1-(2,5-dibromo-4-nitro-1H-imidazol-1-yl)propan-2-ol and various arylboronic acids through “one-pot” cyclization and Suzuki–Miyaura reactions under microwave irradiation.
Keratoprosthesis. Personal experience (2014)

Abstract Purpose Comment the Barcelona experience with different types of keratoprostheses Methods Six cases of different keratoprostheses implanted at the Barraquer Eye Center in Barcelona from 1955 to 2014 are discussed. Results The first keratoprosthesis implanted in Spain was a Dorzee acrylic keratoprosthesis in a case of bilateral chemical burn in 1955 with good functional and anatomic result for five years, when extrusion ocurred with simultaneous superior retinal detachment. The second case refers implantation of a Dorzee‐Barraquer‐Cardona acrylic keratoprosthesis in 1958 in a patient with terminal glaucoma. There was good anatomical retention until the patient’s death in 1970. In the third case a Cardona keratoprosthesis was implanted in 1960 after severe failure of two corneal transplants. Acute endophthalmitis ocurred after a satisfactory anatomical and functional result for 8 years. The fourth case shows extrusion of a Teflon‐supported keratoprosthesis (Girard). The fifth case discusses implantation of an osteo‐odonto‐keratoprosthesis (Strampelli)after blast injury with good anatomical and functional result for 10 years. The last case refers to the experience with the Boston keratoprosthesis in our Center since 2006. Conclusion Clinical experience for more than 50 years at the Barraquer Eye Center confirms evolution of the original Dorzee‐Keratoprosthesis to the nowadays widely used Boston keratoprosthesis. In spite of progress in surgical technique, design and postoperative treatment, anatomical and functional results continue being a challenge for KPro surgeons due to the relatively high frequency of unresolvable serious sight‐destructive complications.
Reduction of diagnostic fail data volume and tester time using a dynamic N-cover algorithm (2016)

This paper presents an algorithm for reducing the test data volume collected by a tester for defect diagnosis of an IC and the tester time. The tester executes the tests and transfers the failing test responses one by one from the tester capture memory to the tester data-logs. While the tester is transferring the fail data, the proposed algorithm analyzes the failing outputs for every test and determines if the test is a potential contributor to the identification of defects. If not, then the test is eliminated from the tester data-logs. Otherwise, the test may replace an existing test or be added as a new test. The addition and replacement of tests continue until the algorithm determines that the fail data transferred to the tester data-logs is sufficient for accurate defect diagnosis. The early termination of the fail data transfer reduces the overall tester time. The effectiveness of the method was verified using real defects in industry fabricated dies. The algorithm was also implemented in a test program library and integrated into a production fail flow for sort data-log optimization. The overhead of the algorithm was minimal, and yielded a 5x reduction in the test data trasfer time.
An on-off Temporal Filter Circuit for Computing Motion Energy (2006)

Motion energy units are important components of biologically inspired algorithms for image motion analysis. We describe an analog VLSI temporal filter circuit that can be cascaded with a spatial filter to implement the spatio-temporal filters required to compute motion energy. This circuit adopts an on-off differential representation used by a previously developed chip for spatial filtering. It has two main advantages over previous continuous-time temporal filtering circuits used to compute motion energy. First, its outputs are in exact quadrature phase, rather than an approximation. Second, it halves the total temporal filter order required to compute motion energy. We describe the filter architecture, analyze its dynamics theoretically, and provide measurement results from a prototype fabricated in a 1.5-mum CMOS n-well process
ChemInform Abstract: THERMISCHE UMLAGERUNG VON 5,5‐DIDEUTERO‐BICYCLO(2,1,0)PENTAN (1973)

Abstract Benzylquecksilberjodid (I) und deuteriertes Diazomethan (II) geben das Benzyl mercurijodmethan (III), das mit Cyclobuten (IV) zum deuterierten Bicyclopen tan (V) reagiert.
Polycyclic aromatic hydrocarbon (PAH)–DNA adducts and breast cancer: modification by gene promoter methylation in a population-based study (2020)

Polycyclic aromatic hydrocarbons (PAH)-DNA adducts have been associated with breast cancer incidence. Aberrant changes in DNA methylation may be an early event in carcinogenesis. However, possible relations between PAH-DNA adducts, methylation and breast cancer are unknown. The objectives of this study were to (1) assess associations between PAH-DNA adducts and breast cancer, stratified by DNA methylation markers; and, (2) to examine interactions between adducts and DNA methylation in association with breast cancer and tumor subtype.
Believable Social and Emotional Agents. (1996)

One of the key steps in creating quality interactive drama is the ability to create quality interactive characters (or believable agents). Two important aspects of such characters will be that they appear emotional and that they can engage in social interactions. My basic approach to these problems has been to use a broad agent architecture and minimal amounts of modeling of other agent in the environment. This approach is based on an understanding of the artistic nature of the problem. To enable agent-builders (artists) to create emotional agents, I provide a general framework for building emotional agents, default emotion-processing rules, and discussion about how to create quality, emotional characters. My framework gets a lot of its power from being part of a broad agent architecture. The concept is simple: the agent will be emotionally richer if there are more things to have emotions about and more ways to express them. This reliance on breadth has also meant that I have been able...
Photochemistry and Luminescence of Cyclometallated Complexes (1992)

This chapter contains sections titled: Introduction Ground state properties Luminescence Photochemistry Conclusion
New challenges for WHO FCTC compliance in Russia and Eurasian Economic Union (2019)

Introduction\nIntroduction\nAccording to GATS 2009 vs 2016, prevalence of current smoking among adults in Russia declined from 39.4% to 30.9%; number of deaths from tobacco use in 2015 was about 300,000. New challenges for WHO FCTC compliance emerged.\n\nMethods\nReview of official documents and industry sources.\n\nResults\nTobacco smoking and sales of cigarettes in Russia are declining, opposite for novel products: vapes, e-cigarettes and heated tobacco. Legal provisions on smoking cessation for about 30 mln smokers did not materialize yet. National tobacco control strategy outlining legal regulations for 2010-5 expired; drafting for 2016/7/8/9 continues. Tobacco industry promotes novel products as harm reduction; provides massive foreign direct investment, enjoys concessions/privileges from State and support from business, education, research and health organizations, NGOs; PMI is leading. Russia in eyes of industry belongs to region of Eastern Europe, Middle East and Africa. \nRegulation of novel tobacco products is absent. Taxation of tobacco products is inadequate, favors industry interests and novel products. Russia is turning into global center for production and dissemination, including illegal, of novel tobacco products. Pro-tobacco policy is increasingly formulated by supranational Eurasian economic union (EAEU), which is not party to WHO FCTC, and has no relations with WHO; EAEU regulations on tobacco excise might not correspond to WHO FCTC compliance by EAEU Member States; EAEU FTA favor tobacco.\n\nConclusions\nTobacco use prevention and control based on WHO FCTC compliance is of primary importance for Russia and EAEU; EAEU should join Convention and Protocol to eliminate illicit trade in tobacco products.
The smooth Colonel meets the Reverend (2009)

Kernel smoothing techniques have attracted much attention and some notoriety in recent years. The attention is well deserved as kernel methods free researchers from having to impose rigid parametric structure on their data. The notoriety arises from the fact that the amount of smoothing (i.e., local averaging) that is appropriate for the problem at hand is under the control of the researcher. In this study we provide a deeper understanding of kernel smoothing methods for discrete data by leveraging the unexplored links between hierarchical Bayes models and kernel methods for discrete processes. Several potentially useful results are thereby obtained, including bounds on when kernel smoothing can be expected to dominate non-smooth (e.g., parametric) approaches in mean squared error and suggestions for thinking about the appropriate amount of smoothing.
ChemInform Abstract: Formation of γ‐Oxoacids and 1H‐Pyrrol‐2(5H)‐ones from α,β‐Unsaturated Ketones and Ethyl Nitroacetate. (2011)

Abstract Addition of the nitroacetate (II) to enones followed by treatment with H 2 O 2 / K 2 CO 3 is found to afford γ‐oxoacids like (III).
Light absorption processes and optimization of ZnO/CdTe core–shell nanowire arrays for nanostructured solar cells (2015)

The absorption processes of extremely thin absorber solar cells based on ZnO/CdTe core-shell nanowire (NW) arrays with square, hexagonal or triangular arrangements are investigated through systematic computations of the ideal short-circuit current density using three-dimensional rigorous coupled wave analysis. The geometrical dimensions are optimized for optically designing these solar cells: the optimal NW diameter, height and array period are of 200 ± 10 nm, 1-3 μm and 350-400 nm for the square arrangement with CdTe shell thickness of 40-60 nm. The effects of the CdTe shell thickness on the absorption of ZnO/CdTe NW arrays are revealed through the study of two optical key modes: the first one is confining the light into individual NWs, the second one is strongly interacting with the NW arrangement. It is also shown that the reflectivity of the substrate can improve Fabry-Perot resonances within the NWs: the ideal short-circuit current density is increased by 10% for the ZnO/fluorine-doped tin oxide (FTO)/ideal reflector as compared to the ZnO/FTO/glass substrate. Furthermore, the optimized square arrangement absorbs light more efficiently than both optimized hexagonal and triangular arrangements. Eventually, the enhancement factor of the ideal short-circuit current density is calculated as high as 1.72 with respect to planar layers, showing the high optical potentiality of ZnO/CdTe core-shell NW arrays.