gebhart/patrepeval huggingface dataset:
Inkjet Printing of Growth Factor Concentration Gradients and Combinatorial Arrays Immobilized on Biologically-Relevant Substrates (2009)

Current methods for engineering immobilized, 'solid-phase' growth factor patterns have not addressed the need for presentation of the growth factors in a biologically-relevant context. We developed an inkjet printing methodology for creating solid-phase patterns of unmodified growth factors on native biological material substrates. We demonstrate this approach by printing gradients of fluorescently labeled bone morphogenetic protein-2 (BMP-2) and insulin-like growth factor-II (IGF-II) bio-inks on fibrin-coated surfaces. Concentration gradients were created by overprinting individual substrate locations using a dilute bio-ink to modulate the surface concentration of deposited growth factor. Persistence studies using fluorescently-labeled BMP-2 verified that the gradients retained their shape for up to 7 days. Desorption experiments performed with (125)I-BMP-2 and (125)I-IGF-II were used to quantify the surface concentration of growth factor retained on the substrate for up to 10 days in serum containing media after rinsing of the unbound growth factor. The inkjet method is programmable so the gradient shape can be easily modified as demonstrated by printed linear gradients with varying slopes and exponential gradients. In addition, the versatility of this method enabled combinatorial arrays of multiple growth factors to be created by printing overlapping patterns. The overlapping printing method was used to create a combinatorial square pattern array consisting of various surface concentrations of BMP-2 and fibroblast growth factor-2 (FGF-2). C2C12 myogenic precursor cells were seeded on the arrays and alkaline phosphatase staining was performed to determine the effect of FGF-2 and BMP-2 surface concentration on guiding C2C12 cells towards an osteogenic lineage. These results demonstrate the utility of inkjet printing for creating orthogonal growth factor gradients to investigate how combinations of immobilized growth factors influence cell fate.
Improved antifouling properties of polymer membranes using a ‘layer-by-layer’ mediated method (2013)

Polymeric reverse osmosis membranes were modified with antifouling polymer brushes through a 'layer by layer' (LBL) mediated method. Based on pure physical electrostatic interaction, the attachment of LBL films did not alter separation performance of the membranes. In addition, the incorporation of an LBL film also helped to amplify the number of potential reaction sites on the membrane surfaces for attachment of antifouling polymer brushes, which were then attached to the surface. Attachment of the brushes included two different approaches, grafting to and grafting from. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and water contact angle measurements showed successful growth of the LBL films and subsequently the polymer brushes. Using this method to modify reverse osmosis membranes, preliminary performance testing showed the antifouling properties of the as-modified membranes were much better than the virgin membrane with no significant loss in water flux and salt rejection.
Integrated Biosensor for Rapid and Point-of-Care Sepsis Diagnosis (2018)

Sepsis is an often fatal condition that arises when the immune response to an infection causes widespread systemic organ injury. A critical unmet need in combating sepsis is the lack of accurate early biomarkers that produce actionable results in busy clinical settings. Here, we report the development of a point-of-care platform for rapid sepsis detection. Termed IBS (integrated biosensor for sepsis), our approach leverages (i) the pathophysiological role of cytokine interleukin-3 (IL-3) in early sepsis and (ii) a hybrid magneto-electrochemical sensor for IL-3 detection. The developed platform produces test results within 1 h from native blood samples and detects IL-3 at a sensitivity of <10 pg/mL; this performance is >5-times faster and >10-times more sensitive than conventional enzyme-linked immunoadsorbent assays, the current gold standard. Using clinical samples, we show that elevated plasma IL-3 levels are associated with high organ failure rate and thus greater risk of mortality, confirming the potential of IL-3 as a sepsis diagnostic biomarker. With further system development ( e. g., full automation, data security measures) and rigorous validation studies, the compact and fast IBS could be a practical clinical tool for timely diagnosis and proactive treatment of sepsis.
MR Parameters for Imaging Titanium Spinal Instrumentation (1997)

The presence of stainless steel implants along a spinal column causes extreme distortion of data collected by magnetic resonance (MR) imaging. The recent availability of titanium alloy spinal instrumentation systems suggests that MR imaging evaluation of the instrumented spine may now be feasible. The objective of this study was to perform MR imaging examinations on spines implanted with titanium alloy instrumentation and to determine the parameters that yield the highest quality images with the least amount of artifact. A titanium pedicle screw construct was implanted into the lumbar spine of two fresh human cadaveric specimens. Sequential spin echo MR scans were performed using various TE and TR ratios on each intact specimen. The resultant images were quantitatively graded for clarity of adjacent soft tissue and osseous structures. Excellent T1- and T2-weighted images with well-defined neural structures were obtained with minimal artifact. The optimal T1-weighted image was obtained with TE = 16 and TR = 500-600, whereas the optimal T2-weighted image was obtained with TE = 60 and TR = 1,300-1,600. By using appropriate settings, high-quality MR scans in both the T1- and T2-weighted modes can be obtained with minimal metal artifact.
DNA Polymerase V Allows Bypass of Toxic Guanine Oxidation Products in Vivo (2007)

Reactive oxygen and nitrogen radicals produced during metabolic processes, such as respiration and inflammation, combine with DNA to form many lesions primarily at guanine sites. Understanding the roles of the polymerases responsible for the processing of these products to mutations could illuminate molecular mechanisms that correlate oxidative stress with cancer. Using M13 viral genomes engineered to contain single DNA lesions and Escherichia coli strains with specific polymerase (pol) knockouts, we show that pol V is required for efficient bypass of structurally diverse, highly mutagenic guanine oxidation products in vivo. We also find that pol IV participates in the bypass of two spiroiminodihydantoin lesions. Furthermore, we report that one lesion, 5-guanidino-4-nitroimidazole, is a substrate for multiple SOS polymerases, whereby pol II is necessary for error-free replication and pol V for error-prone replication past this lesion. The results spotlight a major role for pol V and minor roles for pol II and pol IV in the mechanism of guanine oxidation mutagenesis.
Privacy preserving trusted social feedback (2014)

With the growth of social networks, recommender systems have taken advantage of the social network graph structures to provide better recommendation. In this paper, we propose a privacy preserving trusted social feedback (TSF) system, in which users obtain feedback on questions or items from their friends. It is different from and independent of a typical recommender system because the responses from friends are not automated but tailored to specific questions. TSF can be used to complement the results from a recommender system. Our experimental prototype runs on the Google App Engine and utilises the Facebook social network graph. In our experimental evaluation, we have looked at users' perceptions of privacy and their trust in the prototype as well as the performances on the client side and the cloud side.
Bolstering : The last mile with multipath TCP (2017)

The rapid uptake of bandwidth-consuming services such as video on demand and linear tv has many service providers struggling to keep pace with ever increasing bandwidth demands. The problem is part ...
Eye-Gaze Activity in Crowds: Impact of Virtual Reality and Density (2020)

When we are walking in crowds, we mainly use visual information to avoid collisions with other pedestrians. Thus, gaze activity should be considered to better understand interactions between people in a crowd. In this work, we use Virtual Reality (VR) to facilitate motion and gaze tracking, as well as to accurately control experimental conditions, in order to study the effect of crowd density on eye-gaze behavior. Our motivation is to better understand how interaction neighborhood (i.e., the subset of people actually influencing one’s locomotion trajectory) changes with density. To this end, we designed two experiments. The first one evaluates the biases introduced by the use of VR on the visual activity when walking among people, by comparing eye-gaze activity while walking in a real and virtual street. We then designed a second experiment where participants walked in a virtual street with different levels of pedestrian density. We demonstrate that gaze fixations are performed at the same frequency despite increases in pedestrian density, while the eyes scan a narrower portion of the street. These results suggest that in such situations walkers focus more on people in front and closer to them. These results provide valuable insights regarding eye-gaze activity during interactions between people in a crowd, and suggest new recommendations in designing more realistic crowd simulations.
Cell Injury-Induced Release of Fibroblast Growth Factor 2: Relevance to Intracerebral Mesenchymal Stromal Cell Transplantations (2015)

Beneficial effects of intracerebral transplantation of mesenchymal stromal cells (MSC) and their derivatives are believed to be mediated mostly by factors produced by engrafted cells. However, the mesenchymal cell engraftment rate is low, and the majority of grafted cells disappear within a short post-transplantation period. Here, we hypothesize that dying transplanted cells can affect surrounding tissues by releasing their active intracellular components. To elucidate the type, amounts, and potency of these putative intracellular factors, freeze/thaw extracts of MSC or their derivatives were tested in enzyme-linked immunosorbent assays and bioassays. We found that fibroblast growth factor (FGF)2 and FGF1, but not vascular endothelial growth factor and monocyte chemoattractant protein 1 levels were high in extracts despite being low in conditioned media. Extracts induced concentration-dependent proliferation of rat cortical neural progenitor cells and human umbilical vein endothelial cells; these proliferative responses were specifically blocked by FGF2-neutralizing antibody. In the neuropoiesis assay with rat cortical cells, both MSC extracts and killed cells induced expression of nestin, but not astrocyte differentiation. However, suspensions of killed cells strongly potentiated the astrogenic effects of live MSC. In transplantation-relevant MSC injury models (peripheral blood cell-mediated cytotoxicity and high cell density plating), MSC death coincided with the release of intracellular FGF2. The data showed that MSC contain a major depot of active FGF2 that is released upon cell injury and is capable of acutely stimulating neuropoiesis and angiogenesis. We therefore propose that both dying and surviving grafted MSC contribute to tissue regeneration.
Supplementary Figure S1 from Targeted Imaging of Colonic Tumors in Smad3<sup>−/−</sup> Mice Discriminates Cancer and Inflammation (2023)

Supplementary Figure S1 from Targeted Imaging of Colonic Tumors in Smad3&lt;sup&gt;−/−&lt;/sup&gt; Mice Discriminates Cancer and Inflammation
Antimicrobial prophylaxis for endocarditis: emotion or science? (2006)

Yet another guideline on the prevention of infective endocarditis has been published, this time limiting prophylaxis to high-risk patients.
A DNN based Normalized Time-frequency Weighted Criterion for Robust Wideband DoA Estimation (2023)

Deep neural networks (DNNs) have greatly benefited direction of arrival (DoA) estimation methods for speech source localization in noisy environments. However, their localization accuracy is still far from satisfactory due to the vulnerability to nonspeech interference. To improve the robustness against interference, we propose a DNN based normalized time-frequency (T-F) weighted criterion which minimizes the distance between the candidate steering vectors and the filtered snapshots in the T-F domain. Our method requires no eigendecomposition and uses a simple normalization to prevent the optimization objective from being misled by noisy filtered snapshots. We also study different designs of T-F weights guided by a DNN. We find that duplicating the Hadamard product of speech ratio masks is highly effective and better than other techniques such as direct masking and taking the mean in the proposed approach. However, the best-performing design of T-F weights is criterion-dependent in general. Experiments show that the proposed method outperforms popular DNN based DoA estimation methods including widely used subspace methods in noisy and reverberant environments.
Cross-Language Information Propagation for Arabic Mention Detection (2009)

In the last two decades, significant effort has been put into annotating linguistic resources in several languages. Despite this valiant effort, there are still many languages left that have only small amounts of such resources. The goal of this article is to present and investigate a method of propagating information (specifically mention detection) from a resource-rich language into a relatively resource-poor language such as Arabic. Part of the investigation is to quantify the contribution of propagating information in different conditions based on the availability of resources in the target language. Experiments on the language pair Arabic-English show that one can achieve relatively decent performance by propagating information from a language with richer resources such as English into Arabic alone (no resources or models in the source language Arabic). Furthermore, results show that propagated features from English do help improve the Arabic system performance even when used in conjunction with all feature types built from the source language. Experiments also show that using propagated features in conjunction with lexically derived features only (as can be obtained directly from a mention annotated corpus) brings the system performance at the one obtained in the target language by using feature derived from many linguistic resources, therefore improving the system when such resources are not available. In addition to Arabic-English language pair, we investigate the effectiveness of our approach on other language pairs such as Chinese-English and Spanish-English.
On the Compressibility of NP Instances and Cryptographic Applications (2006)

We initiate the study of compression that preserves the solution to an instance of a problem rather than preserving the instance itself. Our focus is on the compressibility of NP decision problems. We consider NP problems that have long instances but relatively short witnesses. The question is, can one efficiently compress an instance and store a shorter representation that maintains the information of whether the original input is in the language or not. We want the length of the compressed instance to be polynomial in the length of the witness rather than the length of original input. Such compression enables to succinctly store instances until a future setting will allow solving them, either via a technological or algorithmic breakthrough or simply until enough time has elapsed. We give a new classification of NP with respect to compression. This classification forms a stratification of NP that we call the VC hierarchy. The hierarchy is based on a new type of reduction called W-reduction and there are compression-complete problems for each class. Our motivation for studying this issue stems from the vast cryptographic implications compressibility has. For example, we say that SAT is compressible if there exists a polynomial p(middot, middot) so that given a formula consisting of m clauses over n variables it is possible to come up with an equivalent (w.r.t satisfiability) formula of size at most p(n, log m). Then given a compression algorithm for SAT we provide a construction of collision resistant hash functions from any one-way function. This task was shown to be impossible via black-box reductions (D. Simon, 1998), and indeed the construction presented is inherently non-black-box. Another application of SAT compressibility is a cryptanalytic result concerning the limitation of everlasting security in the bounded storage model when mixed with (time) complexity based cryptography. In addition, we study an approach to constructing an oblivious transfer protocol from any one-way function. This approach is based on compression for SAT that also has a property that we call witness retrievability. However, we mange to prove severe limitations on the ability to achieve witness retrievable compression of SAT
Abstract 3136: Discovery of low abundance colorectal cancer related biomarkers by the ADAPT Biotargeting System (2019)

Abstract Disease biomarkers play an essential role in disease-diagnostics and in monitoring their responses to therapies. Identification of low to medium abundance biomarkers is one of the biggest challenges in the field. We have developed Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT), a method in which libraries of single-stranded oligodeoxynucleotides (ssODNs) are enriched for sequences that bind to targets existing in samples in various amounts. Pull-downs with enriched libraries followed by LC-MS/MS allows for the enrichment and identification of low abundance biomarkers that cannot be identified by conventional proteomics. A highly diverse library of 1011 ssODNs was subjected to multiple rounds of positive selection against formalin-fixed paraffin-embedded (FFPE) colorectal cancer tissue with negative selection against adjacent non-cancer tissue of the same specimen. An enriched library of ~3x106 ssODNs that bound preferentially to cancer tissue was obtained and used in combination with LC-MS/MS to identify biomarkers related to colorectal cancer. Using this approach, a total of 14 proteins were identified in cancer but not in non-cancer tissue lysates. Their identification was only possible due to their enrichment by binding of the immobilized ssODN library to the cancer sample since the same proteins were undetectable by conventional proteomics. Immunohistochemical staining (IHC) of multiple colorectal cancer cases verified that several of the identified target proteins, including nucleophosmin (NPM1) and synaptotagmin-like protein 2 (SYTL2), showed higher expression in cancer tissue compared to adjacent non-cancer tissue. Our data indicate the potential of the ADAPT platform to profile small differences between cancer affected and unaffected tissue and provide a novel approach for cancer biomarker discovery. Citation Format: Tassilo Hornung, Jelena Zarkovic, Michelle Kassner, Matthew Rosenow, Mark R. Miglarese, Günter Mayer, Michael Famulok, David B. Spetzler. Discovery of low abundance colorectal cancer related biomarkers by the ADAPT Biotargeting System [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3136.
Severe Hemolysis and Pulmonary Hypertension in a Neonate With Upshaw–Schulman Syndrome (2016)

Pulmonary involvement is extremely rare in thrombotic thrombocytopenic purpura. In this report, we present a girl patient with congenital thrombotic thrombocytopenic purpura, known as Upshaw-Schulman syndrome (USS), complicated with severe hemolysis and pulmonary hypertension (PH). The assay results of a disintegrin-like and metalloprotease with thrombospondin type 1 motifs 13 (ADAMTS13) activity measured by FRETS-VWF73 and ADAMTS13-act-ELISA were different. Hyperbilirubinemia (total bilirubin, 25.3 mg/dL) interfered strongly with the FRETS-VWF73 assay. Plasma levels of ADAMTS13 activity by act-ELISA were <0.5% of normal. The diagnosis of USS was confirmed by ADAMTS13 gene analysis, which showed compound heterozygous mutations of p.G139Vfs*17 and p.I673F. The p.G139Vfs*17 mutation was previously unreported, and its effect in splicing was confirmed by reverse transcription polymerase chain reaction. The patient received oxygen therapy for PH and exchange blood transfusion for severe hemolysis. The PH resolved without specific treatment. Based on these findings, the PH may have been caused by free hemoglobin that scavenged nitrogen oxide or platelet thrombi in the lungs caused by ADAMTS13 deficiency. Thus, severe PH can occur in neonatal patients with USS, and severe hemolysis might result in overestimation of ADAMTS 13 activity. Both possibilities are important for the diagnosis and management of USS.
Rose Oxides: A Facile Chemo and Chemo‐Enzymatic Approach (2005)

Abstract Nonracemic rose oxides were synthesized from racemic or nonracemic monoterpene alcohol citronellol by a novel chemo and chemo‐enzymatic route. After the key step of bromomethoxylation of citronellol, the intermediate was dehydrobrominated by a base, followed by an acid catalyzed demethoxylation along with cyclization to furnish rose oxides in high yield. The racemic dehydrobrominated precursor was also kinetically resolved using various lipases to produce nonracemic rose oxides.
Learning-Based Depth and Pose Estimation for Monocular Endoscope with Loss Generalization (2021)

Gastroendoscopy has been a clinical standard for diagnosing and treating conditions that affect a part of a patient's digestive system, such as the stomach. Despite the fact that gastroendoscopy has a lot of advantages for patients, there exist some challenges for practitioners, such as the lack of 3D perception, including the depth and the endoscope pose information. Such challenges make navigating the endoscope and localizing any found lesion in a digestive tract difficult. To tackle these problems, deep learning-based approaches have been proposed to provide monocular gastroendoscopy with additional yet important depth and pose information. In this paper, we propose a novel supervised approach to train depth and pose estimation networks using consecutive endoscopy images to assist the endoscope navigation in the stomach. We firstly generate real depth and pose training data using our previously proposed whole stomach 3D reconstruction pipeline to avoid poor generalization ability between computer-generated (CG) models and real data for the stomach. In addition, we propose a novel generalized photometric loss function to avoid the complicated process of finding proper weights for balancing the depth and the pose loss terms, which is required for existing direct depth and pose supervision approaches. We then experimentally show that our proposed generalized loss performs better than existing direct supervision losses.