gebhart/patrepeval huggingface dataset:
Intrinsically Disordered Synthetic Polymers in Biomedical Applications (2023)

In biology and medicine, intrinsically disordered synthetic polymers bio-mimicking intrinsically disordered proteins, which lack stable three-dimensional structures, possess high structural/conformational flexibility. They are prone to self-organization and can be extremely useful in various biomedical applications. Among such applications, intrinsically disordered synthetic polymers can have potential usage in drug delivery, organ transplantation, artificial organ design, and immune compatibility. The designing of new syntheses and characterization mechanisms is currently required to provide the lacking intrinsically disordered synthetic polymers for biomedical applications bio-mimicked using intrinsically disordered proteins. Here, we present our strategies for designing intrinsically disordered synthetic polymers for biomedical applications based on bio-mimicking intrinsically disordered proteins.
Ripple wavelength, amplitude, and configuration in lyotropic liquid crystals as a function of effective headgroup size (1987)

We present differential scanning calorimetry (DSC) and freeze-fracture electron micrographs of the Pβ' phase of dimyristoylphosphatidylcholine (DMPC) multilamellar liposomes in excess water with varying fractions of N-methyl substituted dimyristoylphosphatidylethanolamine (DMPE * ). DMPE * was chosen as a dopant to eliminate the mismatch between the areas of the polar headgroup and the hydrocarbon chains of DMPC. DSC results show that the Pβ' phase disappears at a DMPE * mole fraction of about 0.15. Two distinct ripple configurations are observed at all DMPE * fractions that exhibited a Pβ' phase ; an asymmetric ripple of wavelength 12.0 nm and amplitude less than 6 nm and a symmetric ripple of incommensurate wavelength 22.0 nm and an amplitude of at least 9 nm. Defects, such as disclinations and grain boundaries are stabilized by DMPE *, but the ripple shapes, wavelength and amplitudes are unaffected. DMPE* also seems to prevent the annihilation of the ripples below the pretransition. The results are discussed in relation to continuum descriptions of the Pβ' phase.
Intercalation binding of 6‐substituted naphthothiopheneamides to DNA: Enthalpy and entropy components (1991)

N-(3-dimethylaminopropyl)naphtho[2,1-b]thiophene-4-carboxamide and the 6-substituted methoxy, methyl, fluoro, chloro, bromo, trifluoromethyl, and cyano derivatives have been shown to bind to DNA via intercalation with binding constants in the 35-900 X 10(3) range at 25 degrees C, pH 7, and [Na+] = 0.019M. Both electron-donating and -withdrawing substituents enhance intercalation binding, but the binding affinity is most enhanced by the cyano substituent. Calorimetric titrations for calf thymus DNA differ dramatically from those reported for ethidium [Hopkins et al. (1990) Biopolymers Vol. 29, pp. 449-459]. Apparent enthalpy parameters (delta HB) for intercalation are constant only at low coverage of sites and become much more positive as saturation is approached. In the plateau region, delta HB values for the parent and the cyano-, fluoro-, chloro-, and bromo-substituted compounds are nearly the same (approximately -5.9 kcal/mol). For the methyl- (-6.8 kcal/mol) and methoxy- (-7.5 kcal/mol) substituted compounds, the delta HB values are more exothermic than that for the unsubstituted compound, whereas delta HB for the trifluoromethyl compound is approximately 1 kcal/mol less exothermic. The corresponding delta SB values, corrected for mixing effects, are in the 7-15-cal/deg/mol range and are approximately linearly related to delta HB if the cyano derivative is excluded.
Collagen Signaling Enhances Tumor Progression after Anti-VEGF Therapy in a Murine Model of Pancreatic Ductal Adenocarcinoma (2013)

There is growing evidence that antiangiogenic therapy stimulates cancer cell invasion and metastasis. However, the underlying molecular mechanisms responsible for these changes have not been fully defined. Here, we report that anti-VEGF therapy promotes local invasion and metastasis by inducing collagen signaling in cancer cells. We show that chronic VEGF inhibition in a genetically engineered mouse model of pancreatic ductal adenocarcinoma (PDA) induces hypoxia, a less differentiated mesenchymal-like tumor cell phenotype, TGF-β expression, and collagen deposition and signaling. In addition, we show that collagen signaling is critical for protumorigenic activity of TGF-β in vitro. To further model the impact of collagen signaling in tumors, we evaluated PDA in mice lacking Sparc, a protein that reduces collagen binding to cell surface receptors. Importantly, we show that loss of Sparc increases collagen signaling and tumor progression. Together, these findings suggest that collagen actively promotes PDA spread and that enhanced disease progression associated with anti-VEGF therapy can arise from elevated extracellular matrix-mediated signaling.
A Shape Generation Method for 3D Printed Antennas With Unintuitive Geometries (2022)

Additive manufacturing used in combination with versatile shape generation methods can enable designers to realize unintuitive antenna designs with bespoke electromagnetic behaviors that would normally be extremely difficult or even impossible to manufacture using conventional techniques. In this paper, we present a new custom algorithm that produces arbitrary three-dimensional (3D) meander line antennas. This algorithm is used in conjunction with multi-objective optimization to create two quadrifilar helix antennas (QHAs) and one monopole antenna, all with unique electromagnetic performances. One QHA has a wide bandwidth, high broadside gain, and compact size, while the other has a dual-band nature with different radiation patterns in each band. Similarly, the monopole example is a dual-wideband design which targets Wi-Fi applications. These structures possess a meander radius that varies with height as well as conductor thickness that varies along the meander path which allows for improved antenna performance over conventional meander line antennas. An example design was fabricated and tested in order to validate the performance of the optimized virtual antenna model.
Saliency-Based Multiple Region of Interest Detection From a Single 360° Image (2022)

360&#x00B0; images are informative &#x2013; it contains omnidirectional visual information around the camera. However, the areas that cover a 360&#x00B0; image is much larger than the human&#x2019;s field of view, therefore important information in different view directions is easily overlooked. To tackle this issue, we propose a method for predicting the optimal set of Region of Interest (RoI) from a single 360&#x00B0; image using the visual saliency as a clue. To deal with the scarce, strongly biased training data of existing single 360&#x00B0; image saliency prediction dataset, we also propose a data augmentation method based on the spherical random data rotation. From the predicted saliency map and redundant candidate regions, we obtain the optimal set of RoIs considering both the saliency within a region and the Interaction-Over-Union (IoU) between regions. We conduct the subjective evaluation to show that the proposed method can select regions that properly summarize the input 360&#x00B0; image.
Abstract 19614: Formation of 3D Cardiac Tissues From Human Pluripotent Stem Cells Using a Highly Reproducible, One-Step Encapsulation Approach (2014)

Human induced pluripotent stem cells (hiPSCs) provide great potential for improving drug testing, facilitating myocardial repair, and investigating heart development. Currently, SC derived cardiomyocytes (CMs) are pre-differentiated from hiPSCs, dissociated, and combined with a biomaterial to form 3D cardiac tissues. This demands additional cell-handling, results in a high level of cell loss, and disrupts pre-existing cell-cell junctions. Here we describe a one-step approach to directly encapsulate and differentiate hiPSCs into 3D cardiac tissues. HiPSCs were combined with poly(ethylene glycol)-fibrinogen and photocrosslinked to form 200 μm thick tissues. Encapsulated hiPSCs (day -3) were cultured in their pluripotent state for three days where they proliferated. On day 0, cardiac differentiation was initiated. Tissues showed areas of contractions starting on day 7, resulting in synchronously contracting tissues which retained their function over three months. Sarcomeric α-actinin and gap junction protein connexin 43 (Cx43) were expressed by day 10; aligned sarcomeres (day 30) and mature gap junctions (Fig. 1a) developed over time. CM maturation increased significantly from day 10 to day 30, as quantified by the ratio of β over α myosin heavy chain gene expression; Cx43 expression increased from 0.5±0.3 (day 20) to 1.0±0.1 (day 30). Additionally, day 15 CMs showed 1:1 correspondence to electrical stimuli of up to 2 Hz. Finally, TEM of day 130 tissues showed structural features of mature CMs, including Z-bands, T-tubules, and intercalated discs (Fig. 1b). In summary, this one-step encapsulation approach successfully produces highly reproducible 3D cardiac tissues with mature and functional features. Furthermore, these physiologically relevant CMs can be used to produce printed microislands, macrotissues, spheroids, or single CMs, based on the desired downstream application.

Fig. 1. 3D encapsulation of hiPSCs produce functional cardiac tissues.

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The pmrCAB Operon Mediates Polymyxin Resistance in Acinetobacter baumannii ATCC 17978 and Clinical Isolates through Phosphoethanolamine Modification of Lipid A (2011)

The emergence of multidrug resistance among Acinetobacter baumannii is leading to an increasing dependence on the use of polymyxins as last-hope antibiotics. Here, we utilized genetic and biochemical methods to define the involvement of the pmrCAB operon in polymyxin resistance in this organism. Sequence analysis of 16 polymyxin B-resistant strains, including 6 spontaneous mutants derived from strain ATCC 17978 and 10 clinical isolates from diverse sources, revealed that they had independent mutations in the pmrB gene, encoding a sensor kinase, or in the response regulator PmrA. Knockout of the pmrB gene in two mutants and two clinical isolates led to a decrease in the polymyxin B susceptibility of these strains, which could be restored with the cloned pmrAB genes from the mutants but not from the wild type. Reverse transcription-quantitative PCR (RT-qPCR) analysis also showed a correlation between the expression of pmrC and polymyxin B resistance. Characterization of lipid A species from the mutant strains, by thin-layer chromatography and mass spectrometry, indicated that the addition of phosphoethanolamine to lipid A correlated with resistance. This addition is performed in Salmonella enterica serovar Typhimurium by the product of the pmrC gene, which is a homolog of the pmrC gene from Acinetobacter. Knockout of this gene in the mutant R2 [pmrB(T235I)] reversed resistance as well as phosphoethanolamine modification of lipid A. These results demonstrate that specific alterations in the sequence of the pmrCAB operon are responsible for resistance to polymyxins in A. baumannii.
Numerical Computation of Turbulent Flow Fields in a Fan-stirred Combustion Bomb (2019)

This work presents a numerical study of the initial turbulent flow characteristics prior to ignition in a fan-stirred combustion vessel. The moving mesh methodology has been applied to account for the rotational movement of eight fans mounted within the vessel. The transient, highly-resolved numerical simulations resolve the 3D turbulent flow field in the whole vessel and complement 2D measurements of the flow field. The calculated turbulence intensities yield reasonably good agreement with measured data, showing a nearly linear increase with the rotation speed of the fans ω. The same applies for the spectra of the turbulent kinetic energy. The rms of velocity fluctuations is almost constant and the same in each direction in the core region with a diameter of approx. 2 cm, confirming the homogeneity and isotropy of the generated turbulent flow field in the fan-stirred bomb, as observed in previous experiments. The calculated integral length scale agrees well with the measured value, which increases with ω or the turbulent Reynolds number Ret, respectively. The calculated rates of decay of the Kolmogorov and Taylor lengths with Ret have shown a quantitatively good agreement with the hypothesis proposed by Kolmogorov for isotropic turbulence, which justifies the validity and reliability of the numerical simulations. The present study serves as a reference for assessing the uncertainties given by common 2D measurement techniques, which allows a more accurate analysis of the turbulence characteristics and the turbulence-flame interactions in a fan-stirred combustion vessel.
Image To Tree with Recursive Prompting (2023)

Extracting complex structures from grid-based data is a common key step in automated medical image analysis. The conventional solution to recovering tree-structured geometries typically involves computing the minimal cost path through intermediate representations derived from segmentation masks. However, this methodology has significant limitations in the context of projective imaging of tree-structured 3D anatomical data such as coronary arteries, since there are often overlapping branches in the 2D projection. In this work, we propose a novel approach to predicting tree connectivity structure which reformulates the task as an optimization problem over individual steps of a recursive process. We design and train a two-stage model which leverages the UNet and Transformer architectures and introduces an image-based prompting technique. Our proposed method achieves compelling results on a pair of synthetic datasets, and outperforms a shortest-path baseline.
Single-cell analysis of Schistosoma mansoni identifies a conserved genetic program controlling germline stem cell fate (2021)

Schistosomes are parasitic flatworms causing one of the most prevalent infectious diseases from which millions of people are currently suffering. These parasites have high fecundity and their eggs are both the transmissible agents and the cause of the infection-associated pathology. Given its biomedical significance, the schistosome germline has been a research focus for more than a century. Nonetheless, molecular mechanisms that regulate its development are only now being understood. In particular, it is unknown what balances the fate of germline stem cells (GSCs) in producing daughter stem cells through mitotic divisions versus gametes through meiosis. Here, we perform single-cell RNA sequencing on juvenile schistosomes and capture GSCs during de novo gonadal development. We identify a genetic program that controls the proliferation and differentiation of GSCs. This program centers around onecut, a homeobox transcription factor, and boule, an mRNA binding protein. Their expressions are mutually dependent in the schistosome male germline, and knocking down either of them causes over-proliferation of GSCs and blocks germ cell differentiation. We further show that this germline-specific regulatory program is conserved in the planarian, schistosome's free-living evolutionary cousin, but the function of onecut has changed during evolution to support GSC maintenance.
Iron Stores Modulate Hepatic Hepcidin Expression by an <i>HFE</i>-Independent Pathway (2005)

The central pathogenetic step in HFE-related hemochromatosis is an impaired basal expression of HAMP rather than a lack of HAMP upregulation in response to iron stores. An HFE-independent pathway that seems to involve TFR2 and HJV can regulate HAMP expression under conditions of iron overload.
Optimizing Information Credibility in Social Swarming Applications (2010)

With the advent of smartphone technology, it has become possible to conceive of entirely new classes of applications. Social swarming, in which users armed with smartphones are directed by a central director to report on events in the physical world, has several real-world applications: search and rescue, coordinated fire-fighting, and the DARPA balloon hunt challenge. In this paper, we focus on the following problem: how does the director optimize the selection of reporters to deliver credible corroborating information about an event. We first propose a model, based on common intuitions of believability, about the credibility of information. We then cast the problem posed above as a discrete optimization problem, and introduce optimal centralized solutions and an approximate solution amenable to decentralized implementation whose performance is about 20% off on average from the optimal (on real-world datasets derived from Google News) while being 3 orders of magnitude more computationally efficient. More interesting, a time-averaged version of the problem is amenable to a novel stochastic utility optimization formulation, and can be solved optimally, while in some cases yielding decentralized solutions. To our knowledge, we are the first to propose and explore the problem of extracting credible information from a network of smartphones.
Coordination Power Adjustment of Surface‐Regulating Polymers for Shaping Gold Polyhedral Nanocrystals (2011)

PVP (poly(vinyl pyrrolidone)) is a common polymer that behaves as a surface-regulating agent that shapes metal nanocrystals in the polyol process. We have used different polymers containing tertiary amide groups, namely PVCL (poly(vinyl caprolactam)) and PDMAm (poly(N,N-dimethyl acrylamide)), for the synthesis of gold polyhedrons, including octahedrons, cuboctahedrons, cubes, and higher polygons, under the present polyol reaction conditions. The basicity and surface coordination power of the polymers are in the order of PVCL, PVP, and PDMAm. A correlation is observed between the coordination power of the polymers and the resulting gold nanocrystal size. Strong coordination and electron donation from the polymer functional groups to the gold surface restrict particle growth rates, which leads to small nanocrystals. The use of PVCL can yield gold polyhedral structures with small sizes, which cannot be achieved in the reactions with PVP. Simultaneous hydrolysis of the amide group in PDMAm leads to carboxylate functionality, which is very useful for generating chemical and bioconjugates through the formation of ester and amide bonds.
Abstract B43: Germline and somatic mutations, immune signatures, and epigenetic alterations linked to neighborhood determinants of health differ in Black and non-Latino White head and neck cancer patients (2018)

Abstract Somatic mutations play an important role in cancer prognosis and can pave the way for precision medicine to overcome cancer disparities. Current models hold that solid tumors evolve from microscopic clonal cellular proliferations driven through progressive histologic stages by the acquisition of somatic alterations. The accumulation of somatic mutations is associated to varying rates of stem cell divisions, leading to replicative errors that arise in response to hereditary burden, environmental stressors, or random error. Environmental, lifestyle, and neighborhood factors track closely with the acquisition of DNA methylation alterations and may partly explain the differential accumulation of genetic alterations in cancer patients. However, the combined roles of germline and somatic mutation burden, promoter methylation, and neighborhood characteristics in cancer disparities are unknown, in large part because most of the genomic studies have been performed on genomes of European descendants. Here we show that neighborhood characteristics linked to genetic, epigenetic, and tumor-associated immune signatures differ in Black and non-Latino White (NLW) head and neck squamous cell carcinoma (HNSCC) patients. Promoter methylation in PAX genes is associated to neighborhood characteristics at the zip code level (p&amp;lt;0.05). We also show that the number of tumor-infiltrating lymphocytes (TILs), the frequency of TP53 mutations, and a C -&amp;gt; A germline mutation in JAK3, chr19:17954215 (protein P132T), differ in Black when compared to NLW HNSCC patients (p&amp;lt;0.05). Our results demonstrate that genetic, epigenetic, and immuno-oncology alterations differ in racially diverse HNSCC patients. TILs and JAK3 germline mutations also vary across sex and anatomic tumor site. Finally, we show that molecular alterations are linked to known neighborhood stressors at the zip code level. Together, these data suggest that paired molecular and social determinants of health at the neighborhood level can inform the delivery of precision oncology services to racial and ethnically diverse populations. Citation Format: Rafael Guerrero-Preston, Fahcina Lawson, Laura Manuel, Blanca Valle, Tal Hadar, Bianca Rivera, Oluwasina Folawiyo, Adriana Baez Bermejo, Luigi Marchionni, Wayne Koch, William Westra, David Sidransky. Germline and somatic mutations, immune signatures, and epigenetic alterations linked to neighborhood determinants of health differ in Black and non-Latino White head and neck cancer patients [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr B43.
Evaluation Of Lithographic Performance Of X-Ray Stepper XS-1 (1998)

X-ray Lithography is widely considered to be the most promising technology for the fabrication of next-generation ICs. To evaluate its practicality, a newly designed X-ray stepper (XS-1) has been build and installed at the NTT SR facility.1) This paper reports the results of an evaluation of lithographic performance, including critical dimension (CD) control and overlay accuracy.
The single particle tracking system (2010)

In an optical tweezers system, the force measurement with a resolution less than pico-Newton can be achieved by precise measurement and analysis of the trapped particle trajectory. Typically, this single particle tracking technique is realized by a quadrant position sensor which detects the scattering lights of the trapping laser beam from the trapped particle. However, as the radius of the trapped particle is larger than the wavelength of the trapped laser, the scattering pattern becomes complicated, and it limits the tracking region and the signal sensitivity on the trapped particle. To solve this issue, an extra probing laser with optimized focal offset according to the trapping laser is applied to improve the flexibility and performance of our particle tracking system for each particle size. A rule of thumb between the optimized focal offsets and particle size is also concluded from the experimental results and theoretical simulations.