gebhart/patrepeval huggingface dataset:
Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy (2022)

Allergic diseases affect many individuals world-wide and are dependent on the interaction between allergens and antibodies of the IgE isotype. Allergen-specific immunotherapy (AIT) can alter the development of the disease, e.g., through induction of allergen-specific IgG that block allergen-IgE interactions. The knowledge of epitopes recognized by allergy-causing and protective antibodies are limited. Therefore, we developed an allergome-wide peptide microarray, aiming to track linear epitope binding patterns in allergic diseases and during AIT. Here, we focused on immune responses to grass pollen allergens and found that such epitopes were commonly recognized before initiation of AIT and that AIT commonly resulted in increased antibody production against additional epitopes already after 1 year of treatment. The linear epitope binding patterns were highly individual, both for subjects subjected to and for individuals not subjected to AIT. Still, antibodies against some linear epitopes were commonly developed during AIT. For example, the two rigid domains found in grass pollen group 5 allergens have previously been associated to a diversity of discontinuous epitopes. Here, we present evidence that also the flexible linker, connecting these domains, contains regions of linear epitopes against which antibodies are developed during AIT. We also describe some commonly recognized linear epitopes on Phl p 2 and suggest how antibodies against these epitopes may contribute to or prevent allergy in relation to a well-defined stereotyped/public IgE response against the same allergen. Finally, we identify epitopes that induce cross-reactive antibodies, but also antibodies that exclusively bind one of two highly similar variants of a linear epitope. Our findings highlight the complexity of antibody recognition of linear epitopes, with respect to both the studied individuals and the examined allergens. We expect that many of the findings in this study can be generalized also to discontinuous epitopes and that allergen peptide microarrays provide an important tool for enhancing the understanding of allergen-specific antibodies in allergic disease and during AIT.
Cover Image, Volume 69, Issue 9 (2021)

Cover Illustration: Suppressing disease-induced upregulation of Gfap or Vimentin prevents Müller Glial hypertrophy. (See Hippert C, Graca AB, et al, https://doi.org/10.1002/glia.24034.)
Otolaryngology Residency Interviewing Dates and Practices: What Should an Applicant Expect? (2018)

NA Laryngoscope, 129:2280-2285, 2019.
Platelet-Rich Plasma in Anterior Cruciate Ligament Quadriceps Tendon Bone Reconstruction—Impact of PRP Administration on Pain, Range of Motion Restoration, Knee Stability, Tibial Tunnel Widening and Functional Results (2021)

Background: Using Platetet-Rich Plasma (PRP) in anterior cruciate ligament reconstruction (ACLR) has been suggested to improve patient outcomes. The aim of this study was to assess the impact of PRP administration on pain, range of motion (ROM) restoration and the functional results of ACLR performed with quadriceps tendon bone (QTB) autografts. Methods: A total of 106 patients were included in this multicenter study. Fifty-two patients underwent single-bundle QTB ACLR and 54 patients underwent the same procedure with additional PRP administration. Results: Mean time of need for on-demand analgesia was 8 days in the PRP group and 11 days in no-PRP group. Symmetric full extension was restored in a mean of 40 days in the PRP group and 53 days in the no-PRP group. Ninety degrees of flexion was restored at a mean of 21 days in the PRP group and 25 days in the no-PRP group. At 18 months postoperatively, the mean side-to-side difference in anterior tibial translation with the use of an arthrometer (Rolimeter, Aircast Europa) was 1.3 mm in the PRP group vs. 2.7 mm in the no-PRP group. Mean tibial tunnel widening was 1.4 mm in the PRP group vs. 2.1 mm in the no-PRP group. The mean score in the pain section of the KOOS scale was 93 in the PRP group vs. 89 in the no-PRP group. For the IKDC scale, 53 patients in the PRP group graded A or B and 1 patient graded C. In the no-PRP group, 48 patients graded A or B and 4 patients graded C or D. Conclusions: The use of PRP in QTB ACLR may decrease the need for on-demand analgesia and accelerate ROM restoration as well as improve knee stability, lessen the extent of tibial tunnel widening and potentially diminish pain at 18 months postoperatively. Further studies will be needed to confirm all authors’ conclusions.
Profiling the Surfaceome Identifies Therapeutic Targets for Cells with Hyperactive mTORC1 Signaling (2019)

Aberrantly high mTORC1 signaling is a known driver of many cancers and human disorders, yet pharmacological inhibition of mTORC1 rarely confers durable clinical responses. To explore alternative therapeutic strategies, herein we conducted a proteomics survey to identify cell surface proteins upregulated by mTORC1. A comparison of the surfaceome from <i>Tsc1</i><sup>-/-</sup><i>versus Tsc1</i><sup>+/+</sup> mouse embryonic fibroblasts revealed 59 proteins predicted to be significantly overexpressed in <i>Tsc1</i><sup>-/-</sup> cells. Further validation of the data in multiple mouse and human cell lines showed that mTORC1 signaling most dramatically induced the expression of the proteases neprilysin (NEP/CD10) and aminopeptidase N (APN/CD13). Functional studies showed that constitutive mTORC1 signaling sensitized cells to genetic ablation of NEP and APN, as well as the biochemical inhibition of APN. In summary, these data show that mTORC1 signaling plays a significant role in the constitution of the surfaceome, which in turn may present novel therapeutic strategies.
Ultrafast near-field imaging of exciton-polariton dynamics in WSe_2 waveguides at room temperature (2017)

Van der Waals (vdW) materials, weakly bound layered compounds, have received enormous interest as they offer a malleable playground for a wide range of physical properties in thermal, electronic and optical devices. In particular, owing to their inherent deep subwavelength light confinement, they support a variety of light-matter interactions phenomena such as plasmons, excitons and phonons conveyed as polaritonic modes. Specifically, semiconductor vdW materials such as WSe_2 are particularly attractive for photonic and quantum integrated technologies since they sustain VIS-NIR exciton-polariton modes at room temperature. In the quest to unravel the underlying physics of these intriguing phenomena, advanced subdiffraction imaging techniques such as SNOM has provided valuable insights on the nature of the EP coupling mechanism to the waveguide modes sustained in vdW materials. While most of these works focused on the steady state of the EP, the spatio-temporal dynamics of EP formation, happening in the sub-picosecond regime, remains largely unexplored. Hence, a direct imaging at the femtosecond-nanoscale of the EP evolution is critical to the understanding of these coupled light-matter states. Here we report for the first time the ultrafast and deep-subwavelength imaging of EP formation and propagation in WSe2 waveguides. Our method, based on a novel ultrafast pump-probe near-field imaging, allows to directly visualize the EP time evolution at room temperature. More specifically, and in agreement with our time dependent model, we directly observe a significantly slow EP wave packet group velocity of v_g~0.017c which is attributed to the bandgap renormalization originating in the light coupling near the exciton transition. These findings suggest that vdW materials could be used for slow light with applications in light storage for memory, enhanced optical nonlinearity, sensing and more.
Columnar nanostructured polymer films containing ionic liquids in supramolecular one‐dimensional nanochannels (2014)

ABSTRACT Ionic liquids have attracted a considerable attention as the next generation electrolytes for energy devices. We have developed new free‐standing and nanostructured polymer films in which ionic liquids are confined into one‐dimensionally ordered nanochannels. These polymer films have been obtained by photopolymerization of hydrogen‐bonded supramolecular columnar liquid‐crystalline self‐assemblies of an imidazolium‐based ionic liquid and a wedge‐shaped diol compound containing polymerizable groups. The macroscopically parallel alignment of the columnar structures on a glass substrate has been achieved by the application of mechanical shearing, and subsequently fixed into polymer films by UV irradiation. This ionic liquid‐containing polymer film exhibits higher ionic conductivity than that of the previously reported one‐dimensional polymer film obtained by in situ photopolymerization of a covalent‐type columnar liquid‐crystalline imidazolium salt. The noncovalent supramolecular approach to one‐dimensionally ion‐conductive polymer films has led to improvement on conductive properties. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53 , 366–371
Influence of annealing under reducing ambient on properties of ZnO thin films prepared by mist CVD (2011)

Abstract The resistivity of ZnO thin films grown at 300 °C with mist CVD method can be decreased about 3 orders of magnitude, from 6.2 Ωcm as deposited to 2.2×10 ‐2 Ωcm for the film after post annealing at 350 °C under reducing ambient of 5% H 2 in N 2 (forming gas: FG) with increasing mobility and without changing carrier density. It is thought that the electrical properties of the ZnO thin films with a large amount of impurities due to the low temperature growth are changed without changing surface morphology, crystal structure and impurity content after annealed in the reducing ambient. This can be explained by the decrease of disorder in the band gap in the grain and lowering of the Schottky barrier height in the grain boundaries due to the H 2 interaction with oxygen. The model is supported by the quick decrease of resistivity under FG annealing. (© 2012 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Using 3D scanning to support conservation treatments for paintings (2020)

Abstract Various imaging techniques are used to visualise issues regarding a painting’s appearance before, during and after conservation treatments, i.e. visible light photography (VIS) raking light photography (RAK), ultraviolet fluorescence photography (UVF) and reflectance transformation imaging (RTI). However, these techniques cannot always visualise and/or quantify conservation issues. This paper presents a new approach: colour, gloss, topography imaging (CGT). CGT’s applicability as a non-invasive tool for evaluating and documenting conservation treatments in comparison to VIS, UVF, RAK and RTI is discussed. Applying this to case studies with different conservation dilemmas illustrates the technique’s potential and drawbacks. CGT can visualise issues such as gloss variations, resulting from (previous) cleaning tests, (partial) varnish removal, and possibly dirt and material degradation. Furthermore, CGT can elucidate topographical issues such as bulging, and losses, and also visualise high-frequency surface variations (e.g. canvas weave and crack pattern). This results in an improvement of documenting a painting’s condition, and the evaluation of treatments and their effects on the visual appearance may be quantified. In conclusion, this research shows that CGT is able to better visualise texture, gloss and colour information than existing techniques like technical photography, facilitating a more precise documentation and localisation of previous and current conservation treatments.
Triggerable tough hydrogels for gastric resident dosage forms (2017)

Abstract Systems capable of residing for prolonged periods of time in the gastric cavity have transformed our ability to diagnose and treat patients. Gastric resident systems for drug delivery, ideally need to be: ingestible, be able to change shape or swell to ensure prolonged gastric residence, have the mechanical integrity to withstand the forces associated with gastrointestinal motility, be triggerable to address any side effects, and be drug loadable and release drug over a prolonged period of time. Materials that have been primarily utilized for these applications have been largely restricted to thermoplastics and thermosets. Here we describe a novel set of materials, triggerable tough hydrogels, meeting all these requirement, supported by evaluation in a large animal model and ultimately demonstrate the potential of triggerable tough hydrogels to serve as prolonged gastric resident drug depots. Triggerable tough hydrogels may be applied in myriad of applications, including bariatric interventions, drug delivery, and tissue engineering.
A Unique Expression of Keratin 14 in a Subset of Trophoblast Cells (2015)

The placenta, a transient organ in human, is essential for pregnancy maintenance and for fetal growth and development. Trophoblast and stromal cells are the main cell types present in human placenta. Trophoblast cells are present in different subtypes depending on their differentiation state and their temporal and spatial location during pregnancy. The stromal cells are of extraembryonic mesenchymal origin and are important for villous formation and maintenance. Interestingly, many pregnancy-related diseases are associated with defect in trophoblast differentiation and villous integrity. Therefore, it's crucial to specifically identify each type of placental cells using specific markers. Keratins (CK) are widely used as marker of epithelial cells, cancer origin identification and in some cases as marker of stem/progenitor cells. Vimentin is widely used as marker of mesenchymal cells. The aim of this study is to characterize the presence of different keratins in human trophoblast cells and vimentin in stromal cells. Using immunohistochemistry on term placental sections, our results show that vimentin is solely expressed in stromal-mesenchymal cells while keratins 5, 7, 8, 14 and 19 are expressed in trophoblast cells. Interestingly, all keratins tested, except for keratin 14, were evenly expressed in all trophoblast cells. Keratin 14 was expressed in a subset of CK7 positive cells. Moreover, the same results were obtained when using freshly isolated cytotrophoblast cells or BeWo cells. In conclusion, this study is a crucial step in the advancement of our knowledge in placental cell type identification and characterization.
Supplementary Tables 1-11 from HDAC Inhibition Enhances the &lt;i&gt;In Vivo&lt;/i&gt; Efficacy of MEK Inhibitor Therapy in Uveal Melanoma (2023)

&lt;p&gt;Supplementary Table S1- Antibodies used for protein expression in western blotting experiments Supplementary Table S2 - Assays used for gene expression in RT-qPCR experiments Supplementary Table S3 - Antibodies used for protein expression in immunofluorescence experiments Supplementary Table S4 - Inhibitory concentration 50% (IC50) of MEKi after 72h in uveal melanoma cell lines (nM) Supplementary Table S5 - Members of the GSEA GO_REGULATION_OF_PHOSPHATIDYLINOSITOL_3_KINASE_SIGNALING family Supplementary Table S6 - Members of the GSEA GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_KINASE_ACTIVITY family Supplementary Table S7 - Members of the GSEA GO_TRANSMEMBRANE_RECEPTOR_PROTEIN_TYROSINE_KINASE_ACTIVITY family Supplementary Table S8 - Members of the GSEA HIPPO_TARGETS family Supplementary Table S9 - Members of the GSEA REACTOME_GPCR_LIGAND_BINDING Family Supplementary Table S10 - Compounds used in the drug screening Supplementary Table S11 - Members of the GSEA HALLMARK_PI3K_AKT_MTOR_SIGNALING&lt;/p&gt;
Developmental stage-dependent metabolic regulation during meiotic differentiation in budding yeast (2014)

Our systems-level analysis shows that reprogramming of the central metabolism during the meiotic differentiation is controlled at different hierarchical levels to meet the metabolic and energetic needs at successive developmental stages.
Supplementary Figure 5 from Combination of Anti-HER3 Antibody MM-121/SAR256212 and Cetuximab Inhibits Tumor Growth in Preclinical Models of Head and Neck Squamous Cell Carcinoma (2023)

&lt;p&gt;PDF file - 74KB, The body weight changes in mice during treatment.&lt;/p&gt;
Data from A First-Time-in-Human Study of GSK2636771, a Phosphoinositide 3 Kinase Beta-Selective Inhibitor, in Patients with Advanced Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; The PI3K/protein kinase B (AKT) pathway is commonly activated in several tumor types. Selective targeting of p110β could result in successful pathway inhibition while avoiding the on- and off-target effects of pan-PI3K inhibitors. GSK2636771 is a potent, orally bioavailable, adenosine triphosphate-competitive, selective inhibitor of PI3Kβ.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We evaluated the safety, pharmacokinetics, pharmacodynamics and antitumor activity of GSK2636771 to define the recommended phase II dose (RP2D). During the dose-selection and dose-escalation stages (parts 1 and 2), patients with &lt;i&gt;PTEN&lt;/i&gt;-deficient advanced solid tumors received escalating doses of GSK2636771 (25–500 mg once daily) using a modified 3+3 design to determine the RP2D; tumor type-specific expansion cohorts (part 3) were implemented to further assess tumor responses at the RP2D.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; A total of 65 patients were enrolled; dose-limiting toxicities were hypophosphatemia and hypocalcemia. Adverse events included diarrhea (48%), nausea (40%), and vomiting (31%). Single- and repeat-dose exposure increased generally dose proportionally. GSK2636771 400 mg once daily was the RP2D. Phospho/total AKT ratio decreased with GSK2636771 in tumor and surrogate tissue. A castrate-resistant prostate cancer (CRPC) patient harboring &lt;i&gt;PIK3CB&lt;/i&gt; amplification had a partial response for over a year; an additional 10 patients derived durable (≥24 weeks) clinical benefit, including two other patients with CRPC with &lt;i&gt;PIK3CB&lt;/i&gt; alterations (≥34 weeks). GSK2636771 400 mg once daily orally induced sufficient exposure and target inhibition with a manageable safety profile.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Genomic aberrations of &lt;i&gt;PIK3CB&lt;/i&gt; may be associated with clinical benefit from GSK2636771. &lt;i&gt;Clin Cancer Res; 23(19); 5981–92. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Resolution acuity across the visual field for mesopic and scotopic illumination (2020)

We investigated the classical question of why visual acuity decreases with decreasing retinal illuminance by holding retinal eccentricity fixed while illumination varied. Our results indicate that acuity is largely independent of illuminance at any given retinal location, which suggests that under classical free-viewing conditions acuity improves as illumination increases from rod threshold to rod saturation because the retinal location of the stimulus is permitted to migrate from a peripheral location of maximum sensitivity but poor acuity to the foveal location of maximum acuity but poor sensitivity. Comparison with anatomical sampling density of retinal neurons suggests that mesopic acuity at all eccentricities and scotopic acuity for eccentricities beyond about 20° is limited by the spacing of midget ganglion cells. In central retina, however, scotopic acuity is further limited by spatial filtering due to spatial summation within the large, overlapping receptive fields of the A-II class of amacrine cells interposed in the rod pathway between rod bipolars and midget ganglion cells. Our results offer a mechanistic interpretation of the clinical metrics for low-luminance visual dysfunction used to monitor progression of retinal disease.
CyTOF-Lec: Single-cell Glycomics Analysis Reveals Glycan Features Defining Cells Differentially Susceptible to HIV (2022)

ABSTRACT High-parameter single-cell phenotyping has enabled in-depth classification and interrogation of immune cells, but to date has not allowed for glycan characterization. Here, we develop CyTOF-Lec as an approach to simultaneously characterize many protein and glycan features of human immune cells at the single-cell level. We implemented CyTOF-Lec to compare glycan features between different immune subsets from blood and multiple tissue compartments, and to characterize HIV-infected cell cultures. Using bioinformatics approaches to distinguish preferential infection of cellular subsets from viral-induced remodeling, we demonstrate that HIV upregulates the levels of cell surface fucose and sialic acid in a cell- intrinsic manner, and that memory CD4+ T cells co-expressing high levels of fucose and sialic acid are highly susceptible to HIV infection. Sialic acid levels were found to distinguish memory CD4+ T cell subsets expressing different amounts of viral entry receptors, pro-survival factors, homing receptors, and activation markers, and to play a direct role in memory CD4+ T cells’ susceptibility to HIV infection. The ability of sialic acid to distinguish memory CD4+ T cells with different susceptibilities to HIV infection was experimentally validated through sorting experiments. Together, these results suggest that HIV remodels not only cellular proteins but also glycans, and that glycan expression can differentiate memory CD4+ T cells with vastly different susceptibility to HIV infection.
Investigation on Hydrogenation of Metal–Organic Frameworks HKUST-1, MIL-53, and ZIF-8 by Hydrogen Spillover (2013)

The stabilities of three moisture-stable MOFs containing different metal clusters, i.e., HKUST-1 (Cu), MIL-53(Al), and ZIF-8 (Zn), were investigated in dihydrogen and dissociated hydrogen (caused by doped Pt nanoparticles) environments. X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and X-ray-excited Auger electron spectroscopy (XAES) results showed that all three MOFs were stable in dihydrogen environment. However, the structure of Pt-doped HKUST-1 collapsed in the presence of dissociated hydrogen due to the higher reduction potential of Cu compared with H, and the degree of reduction that occurred to the divalent copper in HKUST-1 increased with temperature. Unlike HKUST-1, MIL-53 and ZIF-8 maintained their structures in both dihydrogen and dissociated hydrogen environments at temperatures up to 150 °C. Moreover, comparison of Pt-doped HKUST-1 samples synthesized by chemical vapor deposition (CVD) and incipient wetness impregnation showed that the contact between the doped Pt particles (dissociation source) and MOFs (receptor) significantly affected hydrogen spillover.
Black Phosphorus: Ambient Protection of Few‐Layer Black Phosphorus via Sequestration of Reactive Oxygen Species (Adv. Mater. 27/2017) (2017)

Few-layer black phosphorous (BP) has emerged as a promising candidate for next-generation nanophotonic and nanoelectronic devices. However, rapid ambient degradation of mechanically-exfoliated BP poses challenges in its practical use in devices. In article number 1700152, Sumeet Walia, Vipul Bansal, and co-workers describe an approach that allows the material to remain stable without requiring its isolation from the ambient environment, opening opportunities to implement BP and other environmentally-sensitive two-dimensional (2D) materials for electronic applications.