gebhart/patrepeval huggingface dataset:
Xylaramide, a New Antifungal Compound, and Other Secondary Metabolites from Xylaria longipes (1996)

Xylaramide (1), possessing potent antifungal activity towards Nematospora coryli and Saccharomyces cerevisiae, was isolated from the culture fluids of the wood-inhabiting ascomycete Xylaria longipes together with tyrosol (2), 2,5-bis(hydroxymethyl)furan (3) and 2-hexyli-dene-3-methylsuccinic acid (4). The latter has been known as a Xylaria metabolite for many years. Compounds 2 and 3 have been previously reported from other fungi, whereas 1 is a new natural N-(2-phenylethenyl)-2-hydroxypropanamide. The isolation, structure determination and biological properties of xylaramide are described. The biological activities of the other compounds are included.
Using Machine Learning to Guide Simulations Over Unique Samples from Trip Profiles (2018)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Electric vehicles are highly sensitive to variations in environmental factors (like temperature, drive style, grade, etc.). The distribution of real-world range of electric vehicles due to these environmental factors is an important consideration in target setting. This distribution can be obtained by running several simulations of an electric vehicle for a number of high-frequency velocity, grade, and temperature real-world trip profiles. However, in order to speed up simulation time, a unique set of drive profiles that represent the entire real-world data set needs to be developed.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;In this study, we consider 40,000 unique velocity and grade profiles from various real-world applications in EU. We generate metadata that describes these profiles using trip descriptor variables. Due to the large number of descriptor variables when considering second order effects, we normalize each descriptor and use principal component analysis to reduce the dimensions of our dataset to six components. This is based on achieving a high explained variance ratio. Clustering is then performed on this dataset using the k-means algorithm implemented in Scikit-learn. We select sample representative trips by optimizing between the inertia obtained from the k-means algorithm and the explained variance ratio of principal component analysis. The number of representative trips selected is also driven by the performance of simulations for real-world range calculations. Range simulations can now be performed on these select representative trips to obtain a distribution of expected real-world range.&lt;/div&gt;&lt;/div&gt;
Eukaryotic operon-like transcription of functionally related genes in Drosophila (2006)

Complex biological processes require coordinated function of many genes. One evolutionary solution to the problem of coordinately expressing functionally related genes in bacteria and nematodes is organization of genes in operons. Surprisingly, eukaryotic operons are considered rare outside the nematode lineage. In Drosophila melanogaster, we found lounge lizard (llz), which encodes a degenerin/ENaC cation channel, cotranscribed with CheB42a, a nonhomologous gene of unknown function residing <100 bp upstream. These two genes were transcribed from a single promoter as one primary transcript and were processed posttranscriptionally to generate individual mRNAs. The mechanism did not involve alternative splicing, and it differed from the trans splicing used in nematode operons. Both genes were expressed in the same tissues, and previous work suggested that both may be involved in courtship behavior. A bioinformatic approach identified numerous additional loci as potential Drosophila operons. These data reveal eukaryotic operon-like transcription of functionally related genes in Drosophila. The results also suggest that operon-based transcription may be more common in eukaryotes than previously appreciated.
Production of PDGF‐like growth factor by breast cancer cell lines (1985)

The breast cancer cell line T47D produces factors which show mitogenic activity for 3T3 cells. Here we describe the partial purification of one of these factors and show that it has properties similar to platelet-derived growth factor (PDGF). The T47D factor is a heat-stable hydrophobic protein with a molecular weight of around 30,000, which inhibits the binding of 125I-EGF in a temperature-dependent manner. This 30 kd protein does not act synergistically with PDGF or fibroblast-derived growth factor (FDGF; also PDGF-like) in stimulating DNA synthesis; moreover, like these two factors, its mitogenic activity can be inhibited by an antiserum raised against human PDGF. A PDGF-like growth factor was also found in the serum-free medium of the breast cancer cell line MDA-MB-157. Since PDGF acts on mesenchymal cells, the production of PDGF-like growth factors by breast cancer cells suggests a basis for the intense stromal reaction seen in human breast cancers.
Improving Flow Distribution in a Suction Channel for a Highly Efficient Centrifugal Compressor (2012)

Design parameters for suction channels of process centrifugal compressors were investigated, and an optimization method to enhance stage efficiency by using the new design parameters was proposed. From results of computational fluid dynamics, the passage sectional area ratios <TEX>$A_c/A_e$</TEX>, <TEX>$A_e/A_s$</TEX> and <TEX>$A_c/A_s$</TEX> were found to be the dominant parameters for the pressure loss and circumferential flow distortion, where <TEX>$A_c$</TEX>, <TEX>$A_e$</TEX> and <TEX>$A_s$</TEX> are passage sectional areas for the casing upstream side, casing entrance and impeller eye, respectively. The Base suction channel was optimized using the new design parameters, and the Base and Optimized types were tested. Test results showed that the Optimized suction channel achieved 3.8% higher stage efficiency than the Base suction channel while maintaining the same operating range.
Corrigendum: Growth Inhibitory Effects of Adhatoda vasica and Its Potential at Reducing Listeria monocytogenes in Chicken Meat (2017)

[This corrects the article on p. 1260 in vol. 8, PMID: 28769879.].
Recovery of Motor Function after Mixed and Motor Nerve Repair with Processed Nerve Allograft (2019)

PNAs were safe and provided functional motor recovery in mixed and motor nerve repairs. Outcomes compare favorably to historical controls for nerve autograft and exceed those for hollow tube conduit. PNA may be considered as an option when reconstructing major peripheral nerve injuries.
Deletions of the elastin gene at 7q11.23 occur in approximately 90% of patients with Williams syndrome. (1995)

To investigate the frequency of deletions of the elastin gene in patients with Williams syndrome (WS), we screened 44 patients by both FISH and PCR amplification of a dinucleotide repeat polymorphism. FISH was performed using cosmids containing either the 5' or the 3' end of the elastin gene. PCR analysis was performed on the patients and their parents with a (CA)n repeat polymorphism found in intron 17 of the elastin locus. Of the 44 patients screened, 91% were shown to be deleted by FISH. Using the DNA polymorphism, both maternally (39%) and paternally (61%) derived deletions were found. Four patients were not deleted for elastin but have clinical features of WS. Since deletions of elastin cannot account for several features found in WS, these patients will be valuable in further delineation of the critical region responsible for the WS phenotype. Although PCR can be useful for determining the parental origin of the deletion, our results demonstrate that FISH analysis of the elastin locus provides a more rapid and informative test to confirm a clinical diagnosis of WS. The presence of two copies of the elastin locus in a patient does not, however, rule out WS as a diagnosis.
A weighted mean shift, normalized cuts initialized color gradient based geodesic active contour model: applications to histopathology image segmentation (2010)

While geodesic active contours (GAC) have become very popular tools for image segmentation, they are sensitive to model initialization. In order to get an accurate segmentation, the model typically needs to be initialized very close to the true object boundary. Apart from accuracy, automated initialization of the objects of interest is an important pre-requisite to being able to run the active contour model on very large images (such as those found in digitized histopathology). A second limitation of GAC model is that the edge detector function is based on gray scale gradients; color images typically being converted to gray scale prior to computing the gradient. For color images, however, the gray scale gradient results in broken edges and weak boundaries, since the other channels are not exploited for the gradient determination. In this paper we present a new geodesic active contour model that is driven by an accurate and rapid object initialization scheme-weighted mean shift normalized cuts (WNCut). WNCut draws its strength from the integration of two powerful segmentation strategies-mean shift clustering and normalized cuts. WNCut involves first defining a color swatch (typically a few pixels) from the object of interest. A multi-scale mean shift coupled normalized cuts algorithm then rapidly yields an initial accurate detection of all objects in the scene corresponding to the colors in the swatch. This detection result provides the initial boundary for GAC model. The edge-detector function of the GAC model employs a local structure tensor based color gradient, obtained by calculating the local min/max variations contributed from each color channel (e.g. R,G,B or H,S,V). Our color gradient based edge-detector function results in more prominent boundaries compared to classical gray scale gradient based function. We evaluate segmentation results of our new WNCut initialized color gradient based GAC (WNCut-CGAC) model against a popular region-based model (Chan & Vese) on a total of 60 digitized histopathology images. Across a total of 60 images, the WNCut-CGAC model yielded an average overlap, sensitivity, specificity, and positive predictive value of 73%, 83%, 97%, 84%, compared to the Chan & Vese model which had corresponding values of 64%, 75%, 95%, 72%. The rapid and accurate object initialization scheme (WNCut) and the color gradient make the WNCut-CGAC scheme, an ideal segmentation tool for very large, color imagery.
Self-Calibration-Based Robust Near-Field Adaptive Beamforming for Microphone Arrays (2007)

Near-field beamforming using a microphone array has found many applications, such as sound acquisition in small rooms. However, robust near-field adaptive beamforming (NABF) against focal point errors has not been studied much in the literature until recently. In this brief, a robust near-field adaptive beamformer is proposed. The proposed method is developed by combining a new formulation of the point-constrained NABF and a self-calibration technique, in the presence of focal point uncertainties. The proposed method suffers from no loss in the degrees of freedom for interference rejection. Compared with conventional calibration-based adaptive beamformers, the proposed method has the advantage of not needing a noise-free calibration signal. Simulation results demonstrate that the performance of the proposed method is superior to that of the existing methods
Generation and Characterization of a Cell Type-Specific, Inducible Cre-Driver Line to Study Olfactory Processing (2021)

In sensory systems of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioral repertoires. These often correspond to different cell types at various stages in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral cells (MCs) and tufted cells (TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, Cre-driver lines that distinguish them do not yet exist. Here, we sought to identify genes that are differentially expressed between MCs and TCs of the mouse, with an ultimate goal to generate a cell type-specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018). Many genes were differentially expressed, but only a few showed consistent expressions in MCs and at the specificity required. After further validating these putative markers using ISH, two genes (i.e., <i>Pkib</i> and <i>Lbdh2</i>) remained as promising candidates. Using CRISPR/Cas9-mediated gene editing, we generated Cre-driver lines and analyzed the resulting recombination patterns. This indicated that our new inducible Cre-driver line, <i>Lbhd2-CreERT2</i>, can be used to genetically label MCs in a tamoxifen dose-dependent manner, both in male and female mice, as assessed by soma locations, projection patterns, and sensory-evoked responses <i>in vivo</i> Hence, this is a promising tool for investigating cell type-specific contributions to olfactory processing and demonstrates the power of publicly accessible data in accelerating science.<b>SIGNIFICANCE STATEMENT</b> In the brain, distinct cell types play unique roles. It is therefore important to have tools for studying unique cell types specifically. For the sense of smell in mammals, information is processed first by circuits of the olfactory bulb, where two types of cells, mitral cells and tufted cells, output different information. We generated a transgenic mouse line that enables mitral cells to be specifically labeled or manipulated. This was achieved by looking for genes that are specific to mitral cells using a large and public gene expression dataset, and creating a transgenic mouse using the gene editing technique, CRISPR/Cas9. This will allow scientists to better investigate parallel information processing underlying the sense of smell.
Two-Year Serum Metal Ion Levels in MITCH Resurfacing (2013)

The purpose of this study was to prospectively measure serum cobalt and chromium ion levels in patients who had MITCH Resurfacing (Stryker) and to correlate these with acetabular component orientation (anteversion and inclination). Twenty-seven patients were enrolled in the study. Serum ion levels were measured pre-operatively, six weeks, six months, twelve months and twenty-four months post-operatively. Axial CT scans of the pelvis were used to measure cup anteversion and plain radiographs used to measure cup inclination. The median serum cobalt and chromium levels at one year were 14.5 nmol/l (range, 6 nmol/l to 59 nmol/l) and 36 nmol/l (range, 17nmol/l to 63 nmol/l) respectively. The median serum cobalt and chromium levels at two years were 16.5 nmol/l (range, 6 nmol/l to 75 nmol/l) and 37.5 nmol/l (range, 13 nmol/l to 109 nmol/l) respectively. The mean cup inclination was 43° (range, 30° to 60°). The mean cup anteversion was 19° (range, 1° to 47°). There was no clear correlation with cup position and serum ion levels. There was one outlier with slightly elevated chromium (109 nmol/l) in a female with a small head size. All patients at all time points showed serum cobalt and chromium levels below the level indicating a high-risk implant (7 parts per billion or chromium >134 nmol/l and cobalt > 119 nmol/l). Our results show no clear relationship between cup position and serum metal ions in this group of patients with relatively well-positioned components
Farnesyltransferase inhibition overcomes the adaptive resistance to osimertinib in EGFR -mutant NSCLC (2022)

ABSTRACT Drug-tolerant “dormant” cells (DTC) have emerged as one of the major non-genetic mechanisms driving resistance to targeted therapy in lung cancer, although the sequence of events leading to entry and exit from dormancy remain poorly described. Here, we performed real-time monitoring of the cell cycle dynamics during the adaptive response to Epidermal Growth Factor Receptor tyrosine kinase inhibitors (EGFR-TKi) in a panel of EGFR-mutated lung cancer cell lines. We identified a rare population of S/G2 cycling cells (referred to as early escapers) that emerged in the first hours of treatment amongst stably arrested and progressively dying G1 cells. We determined that early escapers evolved from a non-proliferative differentiated alveolar type 1 (AT1) phenotype which was invariably associated with cytoskeletal remodeling through Rho/ROCK pathway activation. Using a panel of Rho-pathway inhibitors, we found that the farnesyltransferase inhibitor tipifarnib induced a complete clearance of EGFR-TKi-induced DTC thus fully preventing relapse in vitro . Using a xenograft model and a PDX model of EGFR L858R/T790M lung cancer, co-treatment with tipifarnib prevented relapse to osimertinib for up to 6 months with no evidence of toxicity. Among the farnesylated proteins regulated during osimertinib treatment, concomitant inhibition of RHOE and LaminB1 was sufficient to recapitulated FTIs’ effect. Osimertinib and tipifarnib co-treatment completely suppressed the emergence of AT1 phenotype, prevented mitosis of S/G2-treated cells and increased the apoptotic response through activation of ATF4-CHOP-dependent Integrated Stress Response (ISR) pathway. Our data strongly support the use of tipifarnib in combination with osimertinib in patients to effectively and durably prevent relapse.
Focused-ion-beam-based rapid prototyping of nanoscale magnetic devices (2003)

In this tutorial, focused-ion-beam (FIB)-based fabrication is considered from a very unconventional angle. FIB is considered not as a fabrication tool that can be used for mass production of electronic devices, similar to optical and E-beam—based lithography, but rather as a powerful tool to rapidly fabricate individual nanoscale magnetic devices for prototyping future electronic applications. Among the effects of FIB-based fabrication of magnetic devices, the influence of Ga+-ion implantation on magnetic properties is presented. With help of magnetic force microscopy (MFM), it is shown that there is a critical doze of ions that a magnetic material can be exposed to without experiencing a change in the magnetic properties. Exploiting FIB from such an unconventional perspective is especially favourable today when the future of so many novel technologies depends on the ability to rapidly fabricate prototype nanoscale magnetic devices. As one of the most illustrative examples, the multi-billion-dollar data storage industry is analysed as the technology field that strongly benefited from implementing FIB in the above-described role. The essential role of FIB in the most recent trend of the industry towards perpendicular magnetic recording is presented. Moreover, other emerging and fast-growing technologies are considered as examples of nanoscale technologies whose future could strongly depend on the implementation of FIB in the role of a nanoscale fabrication tool for rapid prototyping. Among the other described technologies are 'ballistic' magnetoresistance, patterned magnetic media, magnetoresistive RAM (MRAM), and magnetic force microscopy.
Integration Concepts for the Fabrication of LTCC Structures (2005)

At the Keck Smart Materials Integration Laboratory at Penn State University, low‐temperature co‐fired ceramic (LTCC) material systems have been used to fabricate a number of devices for a variety of applications. This article presents an overview of the integration of the concepts and materials that we have used to achieve miniaturization and unique device function. Examples of microwave filters, metamaterial antennas, and a dielectrophoretic cell sorter will be presented, with emphasis on device modeling and design, prototype construction methods, and test results.
Spin–Orbit versus Hyperfine Coupling-Mediated Intersystem Crossing in a Radical Pair (2023)

While spin-orbit coupling (SOC) is typically the dominant interaction that couples singlet and triplet states within individual chromophores, hyperfine coupling (HFC) becomes important in multichromophoric systems, particularly in relation to the radical pair mechanism. Here, we use TD-DFT to calculate the spin-orbit coupling and hyperfine coupling between the first singlet and triplet charge transfer states of the radical pair <sup>2</sup>Pyrene<sup>-</sup> and <sup>2</sup><i>N</i>,<i>N</i>-dimethylaniline<sup>+</sup>. We show that, as the intermolecular donor-acceptor distance grows, SOC decays to zero (as one would expect) because singlet and triplet states are characterized by identical orbitals in space, while the HFC remains comparatively constant. The switching region occurs around 4 Å, beyond which HFC dominates over SOC as far as defining the rate of intersystem crossing (ISC).
The soluble CD83 protein prevents bone destruction by inhibiting the formation of osteoclasts and inducing resolution of inflammation in arthritis (2022)

Here we show that soluble CD83 induces the resolution of inflammation in an antigen-induced arthritis (AIA) model. Joint swelling and the arthritis-related expression levels of IL-1β, IL-6, RANKL, MMP9, and OC-Stamp were strongly reduced, while Foxp3 was induced. In addition, we observed a significant inhibition of TRAP<sup>+</sup> osteoclast formation, correlating with the reduced arthritic disease score. In contrast, cell-specific deletion of CD83 in human and murine precursor cells resulted in an enhanced formation of mature osteoclasts. RNA sequencing analyses, comparing sCD83- with mock treated cells, revealed a strong downregulation of osteoclastogenic factors, such as Oc-Stamp, Mmp9 and Nfatc1, Ctsk, and Trap. Concomitantly, transcripts typical for pro-resolving macrophages, <i>e</i>.<i>g</i>., Mrc1/2, Marco, Klf4, and Mertk, were upregulated. Interestingly, members of the metallothionein (MT) family, which have been associated with a reduced arthritic disease severity, were also highly induced by sCD83 in samples derived from RA patients. Finally, we elucidated the sCD83-induced signaling cascade downstream to its binding to the Toll-like receptor 4/(TLR4/MD2) receptor complex using CRISPR/Cas9-induced knockdowns of TLR4/MyD88/TRIF and MTs, revealing that sCD83 acts <i>via</i> the TRIF-signaling cascade. In conclusion, sCD83 represents a promising therapeutic approach to induce the resolution of inflammation and to prevent bone erosion in autoimmune arthritis.