gebhart/patrepeval huggingface dataset:
Newborn screening for Morquio disease and other lysosomal storage diseases: results from the 8-plex assay for 70,000 newborns (2020)

Routine newborn screening of MPS 4A and other LSDs were made possible by the 8-plex LSD screening assay. However, detailed phenotype prediction and the time to start treatment will need further elucidation.
Adjuvant-carrying synthetic vaccine particles augment the immune response to encapsulated antigen and exhibit strong local immune activation without inducing systemic cytokine release (2014)

Augmentation of immunogenicity can be achieved by particulate delivery of an antigen and by its co-administration with an adjuvant. However, many adjuvants initiate strong systemic inflammatory reactions in vivo, leading to potential adverse events and safety concerns. We have developed a synthetic vaccine particle (SVP) technology that enables co-encapsulation of antigen with potent adjuvants. We demonstrate that co-delivery of an antigen with a TLR7/8 or TLR9 agonist in synthetic polymer nanoparticles results in a strong augmentation of humoral and cellular immune responses with minimal systemic production of inflammatory cytokines. In contrast, antigen encapsulated into nanoparticles and admixed with free TLR7/8 agonist leads to lower immunogenicity and rapid induction of high levels of inflammatory cytokines in the serum (e.g., TNF-a and IL-6 levels are 50- to 200-fold higher upon injection of free resiquimod (R848) than of nanoparticle-encapsulated R848). Conversely, local immune stimulation as evidenced by cellular infiltration of draining lymph nodes and by intranodal cytokine production was more pronounced and persisted longer when SVP-encapsulated TLR agonists were used. The strong local immune activation achieved using a modular self-assembling nanoparticle platform markedly enhanced immunogenicity and was equally effective whether antigen and adjuvant were co-encapsulated in a single nanoparticle formulation or co-delivered in two separate nanoparticles. Moreover, particle encapsulation enabled the utilization of CpG oligonucleotides with the natural phosphodiester backbone, which are otherwise rapidly hydrolyzed by nucleases in vivo. The use of SVP may enable clinical use of potent TLR agonists as vaccine adjuvants for indications where cellular immunity or robust humoral responses are required.
Silicon films for heterojunction solar cells by hot-wire CVD (2019)

Using hot-wire chemical vapor deposition (HWCVD), an attractive alternative to the established plasma-enhanced chemical vapor deposition (PECVD), we aim to deposit silicon films for silicon heterojunction (SHJ) solar cell applications. Because of the absence of energetic particles in HWCVD, the layers grow softly and free of damage, hence promising excellent surface passivation and therefore highly efficient solar cells. We report the investigation of intrinsic silicon films, acting as passivation layers, by adjustment of the deposition parameters, with a focus on the substrate temperature as the most important factor. Passivation layers, prepared with differing deposition parameters, were characterized by measurement of the minority-carrier lifetimes using the photoconductance method. At 6 nm a-Si:H thickness, average minority-carrier lifetimes of 1.2 ms were obtained on textured substrates. By combining the optimized HWCVD passivation films and doped silicon films deposited by PECVD, cell efficiencies of 19.7% were achieved. By also depositing the n- und p-doped a-Si:H films by HWCVD cell efficiencies above 18.2% were obtained on a 145 x 145 mm2 cell area.
RELIABILTY OF ELECTROMAGNETIC TRACKING IN DESCRIBING PITCHING MECHANICS (2011)

The purpose of this study was to establish the reliability of an electromagnetic tracking device (ETD) in analyzing young baseball pitchers. Two data collection sessions in which throwing kinematics were recorded were conducted across a five day span. Joint kinematics were calculated using the International Shoulder Group recommendations. Correlation analyses examining inter-day reliability of the ETD showed that the system was within acceptable limits (r > 0.73). Throughout the selected instances of the pitch cycle, the ETD used in the current study was shown to be reliable across multiple data collection session with ICCs ranging from r = 0.73 to 0.86. It appears so long as the setup, sensor attachment, and digitization protocols remain consistent across data collection sessions, ETD’s are a reliable tool in analyzing throwing movements in younger subjects.
Fig S1 from Tumor Intrinsic Efficacy by SHP2 and RTK Inhibitors in KRAS-Mutant Cancers (2023)

&lt;p&gt;(A) Effects of SHP099 and erlotinib on proliferation of EGFR-dependent and RAS/RAF wildtype Detroit-562 and KYSE520 cells grown in 2D monolayer or 3D spheroids (with 20% matrigel) for 6 days. The colored dotted lines at the bottom of graphs are the percentage of Day 0 reading of DMSO-treated cells normalized to that of Day 6 in 2D and 3D, respectively. The black hyphenated lines visualize IC50 values. Error bars denote standard error of the mean. (B-C) Immunoblot of indicated proteins in T3M-4 cells treated with DMSO, SHP099 (10 µM), or trametinib (10 nM) for 2 hours in 2D and 3D culture, respectively. Tubulin serves as a protein loading control. (D) Heatmap depicts Log2 fold change of genes differentially regulated in 2D and 3D following 19 hours after treatment with SHP099. Duplicate samples were analyzed and are depicted. GO ontology was performed using DAVID (42,43) derived from genes with 2-fold change relative to DMSO control.&lt;/p&gt;
Gene sequences of chicken BDNF and NT-3 (1992)

The respective amino acid sequences of mature brain-derived neurotrophic factor (BDNF) and of mature neurotrophin-3 (NT-3) are identical among mammals, making these among the structurally conserved factors known. Here we show that only a single conservative amino acid substitution distinguishes the chicken mature NT-3 protein from its mammalian counterpart. Chicken mature BDNF shows slightly more variation, differing from mammalian BDNF at several positions. We also note the presence of amino acid sequence motifs in the precursor protein sequences of chicken BDNF and NT-3 that are universally conserved among all known mammalian neurotrophin precursors and have been demonstrated to play a crucial role in promoting correct processing of the pro-proteins.
Reinforcement Learning Enabled Autonomous Manufacturing Using Transfer Learning and Probabilistic Reward Modeling (2022)

Here we propose a reinforcement learning enabled physical autonomous manufacturing system (AMS) that is capable of learning the manufacturing process parameters to autonomously fabricate a complex-geometry artifact with desired performance characteristics. The poor sample efficiency of traditional RL algorithms challenges real-world manufacturing decision making due to a high variable cost from raw material, machine utilization, and labor costs. To make decision making sample efficient, we propose to leverage a first-principles based source task for training, transfer effective representations from trained knowledge, and then use these representations to interact with the physical system to learn a probabilistic model of the target reward function. We deploy this idea to a novel dataset obtained from a custom physical AMS machine that can autonomously manufacture phononic crystals, a complex geometry artifact with spectral response as performance characteristic. We demonstrate that our method uses as low as 25 artifacts to model the interesting part of the target reward function and find an artifact with high reward. This task typically requires manual design of phononic crystals and extensive empirical iterations on the order of hundreds.
Cover Picture: Ternary Ag/MgO‐SiO2 Catalysts for the Conversion of Ethanol into Butadiene (ChemSusChem 6/2015) (2015)

The cover picture shows the cradle-to-cradle value chain from biomass, in this case corn starch, which is fermented to bio-ethanol and converted by our process to butadiene. The butadiene then serves as a building block for renewable rubber tires. The latter can be recycled or incinerated and serve again as feedstock. More details on the process of direct formation of butadiene from ethanol using a silver-loaded MgO-SiO2 catalyst can be found in the Full Paper by W. Janssens et al. on page 994 (DOI: 10.1002/cssc.201402894).
To help aging populations, classify organismal senescence (2019)

Comprehensive disease classification and staging is required to address unmet needs of aging populations
CRAWDAD workshop 2007 (2008)

Wireless network researchers are hungry for data about how real users, applications, and devices use real networks under real network conditions. CRAWDAD , the Community Resource for Archiving Wireless Data at Dartmouth, is an NSF-funded project that is building a wireless network data archive for the research community. We host wireless data, and provide tools and documents to make it easy to collect and use wireless network data. We hope that this resource will help researchers to identify and evaluate real and interesting problems in mobile and pervasive computing. This report outlines the CRAWDAD project and summarizes the third CRAWDAD workshop, held at MobiCom 2007.
Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study (2020)

Exercise modulates metabolism and the gut microbiome. Brief exposure to low mT-range pulsing electromagnetic fields (PEMFs) was previously shown to accentuate in vitro myogenesis and mitochondriogenesis by activating a calcium-mitochondrial axis upstream of PGC-1α transcriptional upregulation, recapitulating a genetic response implicated in exercise-induced metabolic adaptations. We compared the effects of analogous PEMF exposure (1.5 mT, 10 min/week), with and without exercise, on systemic metabolism and gut microbiome in four groups of mice: (a) no intervention; (b) PEMF treatment; (c) exercise; (d) exercise and PEMF treatment. The combination of PEMFs and exercise for 6 weeks enhanced running performance and upregulated muscular and adipose Pgc-1α transcript levels, whereas exercise alone was incapable of elevating Pgc-1α levels. The gut microbiome Firmicutes/Bacteroidetes ratio decreased with exercise and PEMF exposure, alone or in combination, which has been associated in published studies with an increase in lean body mass. After 2 months, brief PEMF treatment alone increased Pgc-1α and mitohormetic gene expression and after >4 months PEMF treatment alone enhanced oxidative muscle expression, fatty acid oxidation, and reduced insulin levels. Hence, short-term PEMF treatment was sufficient to instigate PGC-1α-associated transcriptional cascades governing systemic mitohormetic adaptations, whereas longer-term PEMF treatment was capable of inducing related metabolic adaptations independently of exercise.
INVESTIGATION OF LIGHT‐INDUCED CONFORMATION CHANGES IN SPIROPYRAN‐MODIFIED SUCCINYLATED POLY(l‐LYSINE) (1995)

To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(L-lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide alpha-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- vs dark-adapted solutions (6.38 +/- 0.03 M-1 vs 6.56 +/- 0.03 M-1), but not for the nucleation parameter sigma (1.2 +/- 0.4 10(-3) vs 1.3 +/- 0.3 x 10(-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure-based design, synthesis and biological evaluation of a novel series of isoquinolone and pyrazolo[4,3-c]pyridine inhibitors of fascin 1 as potential anti-metastatic agents (2019)

Fascin is an actin binding and bundling protein that is not expressed in normal epithelial tissues but overexpressed in a variety of invasive epithelial tumors. It has a critical role in cancer cell metastasis by promoting cell migration and invasion. Here we report the crystal structures of fascin in complex with a series of novel and potent inhibitors. Structure-based elaboration of these compounds enabled the development of a series with nanomolar affinities for fascin, good physicochemical properties and the ability to inhibit fascin-mediated bundling of filamentous actin. These compounds provide promising starting points for fascin-targeted antimetastatic therapies.
Experimental Study on the Basic Phenomena of Flame Stabilization Mechanism in a Porous Burner for Premixed Combustion Application (2012)

One solution to intensify heat recirculation in a premixed burner and, thus, to enhance the flame stability is to employ porous inert material. Through the highly stable premixed flames low temperature combustion can be achieved employing high excess air ratios which beneficially results in a reduction of the NOx formation by the thermal pathway. Additionally, minimization of temperature and flow inhomogeneities, insensitivity to the fuel supply fluctuation, and damping of flow pulsations are beneficial properties of a porous burner leading to high power dynamic range. Heat transport properties of the solid porous inert media and the strongly tortuous flow path through this structure play a key role for the internal heat recirculation and for flame stabilization as its macroscopic manifestation. These properties strongly depend on the structure geometry and/or physical properties of the material. With an aim to quantify the contribution of the basic physical processes in a porous burner and to optimize its performance the present work reveals a comprehensive experimental study on the flame stability and emissions of such a burner containing different reticulate ceramic sponge structures. It was shown that in order to quantify the contribution of each heat transport mechanism of the global heat recirculation phenomenon and to estimate its relative importance experiments along a three-dimensional matrix (geometry, material, thermodynamic conditions) are required. The quantification of each relevant heat transport mechanism contribution was achieved using one-dimensional volume averaged analysis and comparison with experiments. Furthermore, such comprehensive experimental data with defined boundary conditions provide a necessary prerequisite for numerical validation cases.
Maintenance prioritization to achieve cost savings (2004)

Traditional maintenance prioritization is focused on identifying equipment that requires the most immediate attention. The remaining group of equipment is grouped into the general category of "satisfactory". While the identification of unsatisfactory equipment remains a critical function of maintenance, an improvement in equipment prioritization can identify substantial potential cost savings without sacrificing reliability. An integrated approach of analysis and prioritization is required, but the benefits of any such new approach must be quantified in the expected dollar savings.
Quantitative introduction of a given macromolecule into cells by fusion with erythrocyte ghosts using a fluorescence activated cell sorter. (1978)

FITC-conjugated bovine serum albumin (FITC-BSA) molecules were quantitatively introduced into human erythrocyte ghosts by gradual hemolysis. When the ghosts and L cells were fused with UV-inactivated HVJ (Sendai virus), FITC-BSA was introduced into the cytoplasm of the L cells and fluorescence could be observed inthe cells with a fluorescence microscope. A mixture of L cells and ghosts was introduced into a fluorescence activated cell sorter (FACS), which could separate the mononuclear cells on the basis of their light-scattering profile. Four distinct populations of mononuclear cells were found by fluorescence analysis. These populations were separated from the cell mixture and found to correspond to cells fused with one, two and three ghosts and unfused cells. After separation, the cells from each population could form colonies in culture. As a given macromolecule can be quantitatively introduced into erythrocyte ghosts with the FITC-BSA, after fusion of these ghosts with cells, this sorting method is useful for separating cells containing a definite number of macromolecules.
Parasitic Absorption and Internal Quantum Efficiency Measurements of Solid‐State Dye Sensitized Solar Cells (2013)

Abstract The internal quantum efficiency (IQE) of solid‐state dye sensitized solar cells (ssDSCs) is measured using a hybrid optical modeling plus absorptance measurement approach which takes into account the parasitic absorption of the hole transport material (HTM). Across device thicknesses of 1 to 4 microns, ssDSCs sensitized with Z907 and TT1 dyes display relatively constant IQEs of approximately 88% and 36%, respectively, suggesting excellent charge collection efficiencies for both dyes but poor carrier injection for TT1 devices. The addition of more coadsorbent is shown to increase the IQE of TT1 up to approximately 58%, but significantly lowers dye loading. Finally, optical losses due to absorption by the HTM are quantified and found to be a significant contribution to photocurrent losses for ssDSCs sensitized with poor absorbers such as Z907, as the weak absorption of the dye gives the HTM opportunity for significant parasitic absorption within the active layer.
Generalizing multi-touch direct manipulation (2009)

The appeal of direct manipulation with multi-touch interfaces stems from the experience it offers. As the user slides their fingers along a touch surface, objects react by rotating, translating, and scaling themselves so that the same point on an object always remains underneath the same fingertip. Since objects move in a predictable and realistic fashion, users are given the impression of "gripping" real objects. Direct manipulation essentially provides an intuitive and controllable mapping between points in local space and points in screen space, without the need for any explicit gesture processing.
Tracking properties and steady-state performance of RLS adaptive filter algorithms (1986)

Adaptive signal processing algorithms derived from LS (least squares) cost functions are known to converge extremely fast and have excellent capabilities to "track" an unknown parameter vector. This paper treats analytically and experimentally the steady-state operation of RLS (recursive least squares) adaptive filters with exponential windows for stationary and nonstationary inputs. A new formula for the "estimation-noise" has been derived involving second- and fourth-order statistics of the filter input as well as the exponential windowing factor and filter length. Furthermore, it is shown that the adaptation process associated with "lag effects" depends solely on the exponential weighting parameter λ. In addition, the calculation of the excess mean square error due to the lag for an assumed Markov channel provides the necessary information about tradeoffs between speed of adaptation and steady-state error. It is also the basis for comparison to the simple LMS algorithm, in a simple case of channel identification, it is shown that the LMS and RLS adaptive filters have the same tracking behavior. Finally, in the last part, we present new RLS restart procedures applied to transversal structures for mitigating the disastrous results of the third source of noise, namely, finite precision arithmetic.
Synthesis and fungicidal activity of tubulin polymerisation promoters. Part 1: pyrido[2,3‐ b ]pyrazines (2009)

8-Amino-7-aryl-6-halogen-substituted pyrido[2,3-b]pyrazines have been prepared as 6,6-biheterocyclic analogues of similarly substituted triazolopyrimidine fungicides. A concise four-step synthesis route has been worked out to prepare these novel compounds from commercially available starting materials. [(R)-(1,2-Dimethylpropyl)]-[6-fluoro-7-(2,4,6-trifluorophenyl)pyrido[2,3-b]pyrazin-8-yl]amine showed excellent activity against three economically important phytopathogens.
Sample Preparation for Textile Nanofiber Composites (2005)

Abstract The increased emphasis on nano-structured materials is placing an ever increasing demand on sample preparation techniques to unveil such fine structure. Nano-structured fibers are even more difficult because of the ease with which these materials can smear even when prepared under liquid nitrogen (LN2) as shown (Figure 1). This is especially true for the islandin- the-sea structures where it is rather hard to reveal the island structures due to smearing. In the search for a possible solution, a sample preparation technique that has shown great results in other composite structures of different polymer blends was applied to these structures.
Spinning magnetic trap for automated microfluidic assay systems (2012)

While sophisticated analyses have been performed using lab-on-chip devices, in most cases the sample preparation is still performed off chip. The global need for easy-to-use, disposable testing devices necessitates that sample processing is automated and that transport complexity between the processing and analytical components is minimal. We describe a complete sample manipulation unit for performing automated target capture, efficient mixing with reagents, and controlled target release in a microfluidic channel, using an array of spinning magnets. The "MagTrap" device consists of 6 pairs of magnets in a rotating wheel, situated immediately beneath the microchannel. Rotation of the wheel in the direction opposite to the continuous flow entraps and concentrates the bead-target complexes and separates them from the original sample matrix. As the wheel rotates and the active pair of magnets moves away from the microchannel, the beads are released and briefly flow downstream before being trapped and pulled upstream by the next pair of magnets. This dynamic and continuous movement of the beads ensures that the full surface area of each bead is exposed to reagents and prevents aggregation. The release of the target-bead complexes for further analysis is facilitated by reversing the rotational direction of the wheel to sweep the beads downstream. Sample processing with the MagTrap was demonstrated for the detection of E. coli in a range of concentrations (1 × 10(3), 1 × 10(4) and 1 × 10(6) cells ml(-1)). Results show that sample processing with the MagTrap outperformed the standard manual protocols, improving the detection capability while simultaneously reducing the processing time.