gebhart/patrepeval huggingface dataset:
A semantic analysis of the annotations of the human genome (2005)

The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene-function assignments. A subsequent literature search found that 138 of these gene-functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene-function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database.
#3648 INDIVIDUALIZED ANEMIA THERAPY IMPROVES HEMOGLOBIN OUTCOMES AND DECREASES EPOETIN BETA DRUG EXPOSURE IN HEMODIALYSIS PATIENTS (2023)

Abstract Background and Aims Anemia is a common complication in hemodialysis (HD) patients. Its treatment with erythropoiesis-stimulating agents (ESAs) is challenging due to a nonlinear dose-response relationship and time delays between ESA administration and hemoglobin (Hgb) response. Anemia treatment protocols are frequently used in clinical settings. However, high variability of patient-specific disease characteristics complicate attainment and maintenance of desired Hgb levels. We developed a novel fully personalized ESA dose recommendation tool and present clinical results of a multi-center, randomized controlled trial (RCT) using this software. Method We conducted an RCT in adult HD patients in six dialysis facilities in the US. Patients were randomized 1:1 and treated with our personalized ESA dose recommendation tool for twenty-six weeks (intervention group) or continued to be treated using an anemia protocol that was used as part of standard of care in those clinics (control group). The recommendation tool utilized a physiology-based model of anemia to estimate patient-specific physiological key characteristics, such as red blood cell lifespan, to create a patient-individual model from recent routine clinical data (gender, height, weight, Hgb measurements, and ESA treatment). These key characteristics and model-based outcome predictions were used to generate patient-specific ESA dose recommendations to stabilize Hgb levels in a target window of 10–11 g/dL. Dose recommendations were disseminated to the anemia managers of patients enrolled in the study for evaluation and further decision-making (Figure 1). This procedure was repeated biweekly with updated clinical data. Results Ninety-six patients were enrolled in the RCT. Patients were included in the statistical analysis when they remained in the clinical study for at least 30 days (n = 45 control group, n = 46 intervention group). We evaluated outcome measures showing efficacy and efficiency of the treatment in achieving target Hgb levels. Hgb-related outcomes were significantly different between the two study groups, with an improved Hgb control in the intervention arm, manifesting in a reduction of the Hgb distance to target by more than 30%. Epoetin-beta utilization in the intervention group was decreased by over 20%, while iron-related parameters showed no difference between the two arms (Table 1). Acceptance rate of dose recommendations was high; roughly 95% of the recommendations were accepted and implemented by the clinical staff. Conclusion A therapy software for personalized anemia management was developed for use with epoetin beta. The model-based ESA dose recommendation tool was evaluated in a clinical RCT in HD patients. Hgb control improved significantly in the group using the novel software tool, while ESA usage decreased, thus providing more efficient anemia management for the individual patient while reducing epoetin-beta drug exposure.
Electrostatically Controlled Quantum Dot Monofunctionalization for Interrogating the Dynamics of Protein Complexes in Living Cells (2012)

Quantum dots (QD) are powerful labels for probing diffusion and interaction dynamics of proteins on the single molecule level in living cells. Protein cross-linking due to multifunctional QD strongly affects these properties. This becomes particularly critical when labeling interaction partners with QDs for interrogating the dynamics of complexes. We have here implemented a generic method for QD monofunctionalization based on electrostatic repulsion of a highly negatively charged peptide carrier. On the basis of this method, monobiotinylated QDs were prepared with high yield as confirmed by single molecule assays. These QDs were successfully employed for probing the assembly and diffusion dynamics of binary and ternary cytokine-receptor complexes on the surface of living cells by dual color single QD tracking. Thus, sequential and dynamic recruitment of the type I interferon receptor subunits by the ligand could be observed.
Electrochemical fabrication of n-Si/Au Schottky junctions (1998)

We report on the electrochemical deposition of gold films onto n-type silicon. Gold deposition occurs through progressive nucleation and diffusion limited growth. A high density of gold nuclei was obtained by using a short potential pulse to −1.6 V(Ag/AgCl), and subsequent growth was performed at about −1.1 V(Ag/AgCl) where the growth rate is kinetically limited. Transmission electron microscopy showed that high quality, continuous gold films were formed with an average grain size on the order of 50–70 nm. The electrical properties of the electrochemically deposited Si/Au Schottky junctions are comparable to junctions prepared by evaporation or sputtering techniques.
Quantitative analysis of the working area and angle of attack for the retrosigmoid, combined petrosal, and transcochlear approaches to the petroclival region (2006)

The CP approach offers a more extensive working area than the RS for lesions involving the anterolateral surface of the brainstem, but not for petroclival lesions. The TC approach provides the widest corridor, improving the working area and angle of attack to both areas, but hearing must be sacrificed and the facial nerve is at risk.
A 3.1 mW 8b 1.2 GS/s Single-Channel Asynchronous SAR ADC With Alternate Comparators for Enhanced Speed in 32 nm Digital SOI CMOS (2013)

An 8b 1.2 GS/s single-channel Successive Approximation Register (SAR) ADC is implemented in 32 nm CMOS, achieving 39.3 dB SNDR and a Figure-of-Merit (FoM) of 34 fJ per conversion step. High-speed operation is achieved by converting each sample with two alternate comparators clocked asynchronously and a redundant capacitive DAC with constant common mode to improve the accuracy of the comparator. A low-power, clocked capacitive reference buffer is used, and fractional reference voltages are provided to reduce the number of unit capacitors in the capacitive DAC (CDAC). The ADC stacks the CDAC with the reference capacitor to reduce the area and enhance the settling speed. Background calibration of comparator offset is implemented. The ADC consumes 3.1 mW from a 1 V supply and occupies 0.0015 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Intratumor Administration of the Photosensitizer Pc 4 Affords Photodynamic Therapy Efficacy and Selectivity at Short Drug-Light Intervals (2010)

We evaluated intratumor (IT) versus intravenous (IV) administration of the photosensitizer Pc 4 with respect to tumor photosensitizer concentration, specificity, and responses to irradiation. BALB/c mice bearing intradermal EMT6 tumors were given 0.3 mg/kg Pc 4 injected IT or IV through the tail vein. Photosensitizer concentration was evaluated by chloroform extraction and localization assessed by fluorescence imaging and spectroscopy in vivo. Tumors were irradiated at 667 nm, 50 mW/cm(2), and 100 J/cm(2). Cures were defined as no palpable tumor 90 days after irradiation. Tumor Pc 4 concentrations 1 hour after IT administration were 35,000-fold higher than measured 24 hours after IV administration (0.112 vs 0.317 x 10(-5)microg Pc 4/mg tumor). Exquisite tumor selectivity was observed 1 hour after IT injection. Fluorescence imaging of freshly sectioned tumors revealed no regions devoid of sensitizer at this time point, with pixel intensities in a midline section within a factor of 3 of the peak intensity. For identical photosensitizer doses, IT administration significantly improved tumor responses to irradiation, with more than 70% of tumors cured with IT-Pc 4-PDT. In this model, IT-Pc 4 administration provides improved tumor control, greater selectivity, and opportunity for a short drug-light interval.
Spatio-temporal error concealment in video by denoised temporal extrapolation refinement (2013)

In video communication, the concealment of distortions caused by transmission errors is important for allowing for a pleasant visual quality and for reducing error propagation. In this article, Denoised Temporal Extrapolation Refinement is introduced as a novel spatiotemporal error concealment algorithm. The algorithm operates in two steps. First, temporal error concealment is used for obtaining an initial estimate. Afterwards, a spatial denoising algorithm is used for reducing the imperfectness of the temporal extrapolation. For this, Non-Local Means denoising is used which is extended by a spiral scan processing order and is improved by an adaptation step for taking the preliminary temporal extrapolation into account. In doing so, a spatio-temporal error concealment results. By making use of the refinement, a visually noticeable average gain of 1 dB over pure temporal error concealment is possible. With this, the algorithm also is able to clearly outperform other spatio-temporal error concealment algorithms.
ChemInform Abstract: Domino Syntheses of Five‐, Six‐ and Seven‐Membered O‐, N‐ and S‐ Heterocycles from α‐, β‐ and γ‐Substituted Carboxylic Esters. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Temperature dependence of conventional and effective pyroelectric coefficients for compositionally graded BaxSr1−xTiO3 films (1998)

Ferroelectric thin films (∼1.2 μm) of BaxSr1−xTiO3 with gradients in composition normal to the growth surface were formed on platinum substrates by metalorganic decomposition. Effective (pseudo) pyroelectric coefficients as large as 0.06 μC/cm2 K have been obtained from these active ferroelectric devices under the application of an ac field (charge pumping). In contrast, a value of only −0.003 μC/cm2 K has been measured for the conventional pyroelectric coefficient.
Temperature-dependent photoluminescence of GaInP/AlGaInP multiple quantum well laser structure grown by metalorganic chemical vapor deposition with tertiarybutylarsine and tertiarybutylphosphine (2003)

A GaInP/AlGaInP multiple quantum well laser structure was grown by low-pressure metalorganic chemical vapor deposition with tertiarybutylarsine and tertiarybutylphosphine. Laser diodes fabricated from this structure lased at room temperature. Photoluminescence (PL) measurements were performed from 10 to 230 K. The PL energy increased with temperature from 10 to 70 K and decreased above 70 K. The former was attributed to thermal activation of trapped carriers due to localization in the quantum wells, while the latter was attributed to temperature-induced band-gap shrinkage. The PL intensity as a function of temperature was fitted by employing two nonradiative recombination mechanisms with good agreement, resulting in two activation energies that correspond to losses of photogenerated carriers to nonradiative centers.
MOLECULAR DYNAMICS SIMULATIONS OF LIQUID CRYSTAL MOLECULES AT AN AIR-WATER INTERFACE (2004)

Abstract Molecular dynamics simulations were done for terminally alkyl and alkoxy substituted azobenzene liquid crystal (LC) molecules at an air-water interface using realistic (LC and water) molecular models. The simulation result were compared with those of a corresponding amphiphilic modification, i.e. terminal ω-carboxyalkoxy substituted azobenzene. Comparison with a LC with a different mesogen core, phenylpyrimidine, was also made. The interaction energetics were found to be more or less similar both in the alkyl and alkoxy terminated azobenzene and its amphiphilic modification, i.e. cohesive energy dominated over adhesive energy. In contrast, a large difference was found between alkyl and alkoxy terminated azobenzene and phenylpyrimidine LCs; cohesive and adhesive energy contributions were competitive in the latter molecule. Keywords: amphiphileLangmuir monolayermolecular simulation
Cell surface antigens of human malignant melanoma. III. Recognition of autoantibodies with unusual characteristics. (1977)

The sera of three patients with malignant melanoma showing reactivity with surface antigens of cultured autologous melanoma cells were analyzed by mixed hemadsorption and immune adherence assays in conjunction with absorption tests. In contrast to the melanoma-specific antigens demonstrated previously, the surface antigens detected by these sera occurred on a broad range of nucleated cells, both normal and malignant, from human, monkey, mouse, and chicken sources. Each serum had a characteristic pattern of reactivity in absorption tests, indicating the detection of distinct antigenic systems. Two sera showed auto-, allo-, and xenoreactivity, as well as the capacity to distinguish different cell populations in the same individual. The other serum reacted with an antigen apparently universally present on nucleated cells from a variety of species, but absent on erythrocytes. As these patients had been treated with chemotherapy, this may have played a role in the emergence of these broadly reactive autoantibodies.
Semi-blind Nonlinear Equalization in Coherent Multi-Span Transmission System with Inhomogeneous Span Parameters (2010)

Semi-blind sequence is proposed for optimizing the nonlinear equalization parameters from limited prior knowledge of link. Its performance is demonstrated in an extreme case where the fiber type of a span is incorrectly informed.
Fabrication of microchannel using planar photolithography (2005)

We have developed a new method for fabrication of microchannels and microcavities using only planar lithography processes. In this approach, microchannels are formed by spin-coating resist, exposure and development. Since only photoresist is used as the material and only standard lithography processes are employed in fabrication, this method is completely compatible with electronics that may have been fabricated on the same substrate. For single level microchannels, the resist is first exposed with the sidewall patterns of the channels. This is followed by another exposure with enhanced absorption to seal the channel. Enhanced absorption is achieved by mismatching the resist and the exposure wavelength. The latent channel structure is finally revealed by development. This approach can be further extended to fabricate complex multi-level microchannel system by repeating the basic approach. In this work, we fabricated single level channel up to 1.2mm long with 4&#956;m by 2&#956;m cross-section and demonstrated its utility by flowing water through it. We also fabricated multi-level microchannel system with unique 3D structure using the extended approach.
Iron(III) Corroles and Porphyrins as Superior Catalysts for the Reactions of Diazoacetates with Nitrogen‐ or Sulfur‐Containing Nucleophilic Substrates: Synthetic Uses and Mechanistic Insights (2008)

A thorough mechanistic investigation has been performed on the reactions of primary and secondary amines with diazoacetates, which proceed uniquely quickly and efficiently when catalyzed by iron(III) corroles and porphyrins. Two major differences in relation to other metal-based catalysts are that the iron complexes are not poisoned by excess amine and that metal-carbene intermediates are apparently not involved in the reaction pathway. The results instead point towards nitrogen ylide intermediates formed by nucleophilic attack of the amines on diazoacetate-coordinated iron complexes. Nitrogen ylides are also formed when allyl- and propargyl-substituted tertiary amines react with diazoacetates, a scenario that smoothly leads to 2,3-rearrangement reaction products with catalytic amounts of the iron(III) complexes. Similar findings regarding the superiority of the iron(III) complexes (in terms of catalyst loading, chemical yields, and reaction conditions) were obtained with thiols (S--H insertion) and sulfides (2,3-rearrangement reactions), which suggest similar mechanisms operate in these cases.
Design Features, Developmental Status, and Experimental Results With the Heartmate III Centrifugal Left Ventricular Assist System With a Magnetically Levitated Rotor (2007)

A long-term left ventricular assist system for permanent use in advanced heart failure is being developed on the basis of a compact centrifugal pump with a magnetically levitated rotor and single-fault-tolerant electronics. Key features include its "bearingless" (magnetic levitation) design, textured surfaces similar to the HeartMate XVE left ventricular assist device (LVAD) to reduce anticoagulation requirements and thromboembolism, a sensorless flow estimator, and an induced pulse mode for achieving an increased level of pulsatility with continuous flow assistance. In vitro design verification testing is underway. Preclinical testing has been performed in calves demonstrating good in vivo performance at an average flow rate of 6 L/min (maximum: >11 L/min) and normal end-organ function and host response. Induced pulse mode demonstrated the ability to produce a physiological pulse pressure in vivo. Thirteen LVADs have achieved between 16 to 40 months of long-term in vitro reliability testing and will be continued until failure. Both percutaneous and fully implanted systems are in development, with a modular connection for upgrading without replacing the LVAD.
Thermotropic liquid-crystalline properties of some novel hexuronic acid derivatives bearing a single or two alkyl chains (1997)

We have recently developed a new method forO-glycosidation of totally O-unprotected aldoses and uronic acids. Either pyranosides or the corresponding furanosidic isomers are thus obtained in one step from natural carbohydrates. This paper is concerned with the thermotropic liquid-crystalline phases of alkyl β-d-galacto-(or gluco)-furanosiduronic acids bearing a saturated alkyl chain at the anomeric position and of some dialkylated derivatives. Phase identifications and measurements of phase transition data were carried out by differential scanning calorimetry (DSC), polarizing optical microscopy and small angle X-ray diffraction studies. Uronic derivatives have quite crystalline structures; upon heating, these compounds exhibit a smectic A* transformation.
Evidence of a mate-finding cue in the hermaphrodite nematode Caenorhabditis elegans (2002)

When males of the roundworm Caenorhabditis elegans come into association with their hermaphroditic counterparts they cease foraging behavior and begin to mate. Here we detail several assays used to demonstrate that a diffusible cue is correlated with this process. This cue is sexually dimorphic, given off only by the hermaphrodite and eliciting a response only in the male. Males are attracted to, reverse direction of movement frequently, and remain in regions of agar conditioned with hermaphrodites. From our studies we suggest a form of kinesis that works by attracting males to their mating partners from a distance and functions, once males arrive, in holding attracted males in close proximity. The hermaphrodite vulva is not required for the cue. Males from general sensory mutants osm-5 and osm-6 fail to respond to the cue, whereas male-specific mutants lov-1 and pkd-2 respond. Finally, that males from multiple isolates of C. elegans also respond similarly to this cue indicates that this cue is robust and has been maintained during recent evolution.
A modified bilayer resist approach for 45 nm flash lithography (2008)

Advancing technology nodes in semiconductor manufacturing require more demanding lithographic performance for patterning. The advent of 45 nm development necessitated dual damascene lithography moving from a KrF-based bilayer approach to one that includes an ArF photoresist for higher resolution. There are multiple methods for an ArF dual damascene (via first, trench last) system, including bilayer, trilayer and hard mask approaches. Flash manufacturing demands are sensitive to process cost of ownership, so more complex approaches such as trilayer and hard mask film stacks were not as attractive. One method examined as an ArF dual damascene solution was a so-called "modified bilayer" approach, which is a combination of both KrF and ArF resist materials; in particular, this film stack allows for the use of ArF silicon-containing resists along with a variety of anti-reflective and gap fill underlayer materials. The modified bilayer approach afforded many advantages, including chemical compatibility, etch performance and process robustness. The modified bilayer approach represents a culmination of learning that has enabled 45 nm back end of the line (BEOL) dual damascene processing with ArF silicon-containing photoresists.
Al2O3 e-Beam Evaporated onto Silicon (100)/SiO2, by XPS (2013)

We report the XPS characterization of a thin film of Al2O3 (35 nm) deposited via e-beam evaporation onto silicon (100). The film was characterized with monochromatic Al Kα radiation. An XPS survey scan, an Al 2p narrow scan, an O 1s narrow scan, and the valence band spectrum were collected. The Al2O3 thin film is used as a diffusion barrier layer for templated carbon nanotube (CNT) growth in the preparation of microfabricated thin layer chromatography plates.
Synthesis of 2,6-Hexa-Tert-Butylterphenyl Derivatives, 2,6-(2,4,6-t-Bu₃C₆H₂)₂C₆H₃X, Where X = I, Li, OH, SH, N₃, or NH₂ (2017)

A “double benzyne” reaction between 1,3-dichloro-2-iodobenzene and 2,4,6-t-Bu₃C₆H₂MgBr followed by the addition of iodine led to 2,6-(2,4,6-t-Bu₃C₆H₂)₂C₆H₃I (HTBTI) in 65% yield. Lithiation of HTBTI with Li-t-Bu gave Li(Et₂O)₂HTBT from which HTBTSH, HTBTN₃, HTBTNH₂, and HTBTOH were prepared. An X-ray structure of W(OHTBT)₂Cl₄ shows that the two HTBTO ligands are trans to one another with the t-Bu₃C6H₂ groups on one HTBTO interdigitated with the t-Bu₃C6H₂ groups on the other HTBTO.