gebhart/patrepeval huggingface dataset:
Response to Letter to the Editor re: Comparison of Stand-alone Lateral Lumbar Interbody Fusion Versus Open Laminectomy and Posterolateral Instrumented Fusion in the Treatment of Adjacent Segment Disease Following Previous Lumbar Fusion Surgery (2020)

We would like to thank the authors of the Letter to the Editor for their assessment and feedback regarding our study. We appreciate the comments and would like to address them in this forum. Overall, we would like to reiterate that the main purpose of this study is that adjacent segment degeneration (ASD) can be safely and effectively treated by either a posterior or stand-alone lateral approach with good radiographic and clinical outcomes. In the current nonrandomized study, lateral (LLIF) surgery was associated with reduced perioperative morbidity and improved postoperative radiographic sagittal parameters compared to posterolateral fusion. The authors correctly point out that we did not measure subsidence in the cohort that received interbody fusions. This was not the primary intent of the study. The study focused on clinical and radiographic alignment outcomes and reoperations. This study suggested that clinical outcomes and restoration of lordosis achieved with interbody cages were maintained for the duration of follow-up, suggesting any subsidence did not appear to have a profound effect on clinically relevant outcomes. As the authors of this letter point out, we used previously described radiographic measures to assess for fusion.1–3 We agree that CT measurements allow for a more detailed assessment of osseous fusion. However, as discussed in the limitations portion of our manuscript, this is a retrospective study, and routine CT scans on patients that are asymptomatic following surgery are not part of our standard of care, nor practical in the setting of providing value-based postoperative care in a health-care landscape that is increasingly constrained. Again, our additional focus was on the clinical outcomes following this procedure, and no patients presented with a symptomatic pseudarthrosis. The authors feel that either PLF or LLIF can be successfully performed with a thoughtful understanding of the pathology to be addressed and the surgical goals. Thank you again for your review and comments regarding this study. We hope that the methods and findings related to this study will formulate additional research to address the complication of adjacent segment degeneration in the lumbar spine.
System-wide vitreous proteome dissection reveals impaired sheddase activity in diabetic retinopathy (2022)

<b>Rationale:</b> Diabetic retinopathy (DR) is a major complication of diabetes mellitus causing significant vision loss. DR is a multifactorial disease involving changes in retinal microvasculature and neuronal layers, and aberrations in vascular endothelial growth factors (VEGF) and inflammatory pathways. Despite the success of anti-VEGF therapy, many DR patients do not respond well to the treatment, emphasizing the involvement of other molecular players in neuronal and vascular aberrations in DR. <b>Methods:</b> We employed advanced mass spectrometry-based proteome profiling to obtain a global snapshot of altered protein abundances in vitreous humor from patients with proliferative DR (PDR) in comparison to individuals with epiretinal membrane without active DR or other retinal vascular complications. Global proteome correlation map and protein-protein interaction networks were used to probe into the functional inclination of proteins and aberrated molecular networks in PDR vitreous. In addition, peptide-centric analysis of the proteome data was carried out to identify proteolytic processing, primarily ectodomain shedding events in PDR vitreous. Functional validation experiments were performed using preclinical models of ocular angiogenesis. <b>Results:</b> The vitreous proteome landscape revealed distinct dysregulations in several metabolic, signaling, and immune networks in PDR. Systematic analysis of altered proteins uncovered specific impairment in ectodomain shedding of several transmembrane proteins playing critical roles in neurodegeneration and angiogenesis, pointing to defects in their regulating sheddases, particularly ADAM10, which emerged as the predominant sheddase. We confirmed that ADAM10 protease activity was reduced in animal models of ocular angiogenesis and established that activation of ADAM10 can suppress endothelial cell activation and angiogenesis. Furthermore, we identified the impaired ADAM10-AXL axis as a driver of retinal angiogenesis. <b>Conclusion:</b> We demonstrate restoration of aberrant ectodomain shedding as an effective strategy for treating PDR and propose ADAM10 as an attractive therapeutic target. In all, our study uncovered impaired ectodomain shedding as a prominent feature of PDR, opening new possibilities for advancement in the DR therapeutic space.
Ultraviolet detector based on graphene/SiC heterojunction (2015)

There has been significant research on graphene as a sensor owing to the inherent high sensitivity and surface area associated with two-dimensional (2D) materials. Often, the ability of graphene to form heterojunctions with wide-bandgap semiconductors is overlooked. In this study, we present a detector based on an epitaxial graphene/SiC heterojunction, exploiting the 2D nature of graphene to minimize absorption losses for high-efficiency sensing while simultaneously taking advantage of the epitaxial p–n junction to achieve low reverse leakage. We measured a quantum efficiency above 80% at 4 eV using a graphene/SiC p–n heterojunction with a dark current <1 nA/cm2.
Subcutaneous Bupivacaine Infiltration and Postoperative Pain Perception After Percutaneous Nephrolithotomy (2007)

In this preliminary pilot study no significant differences in patient reported pain scores were observed. However, a trend toward decreased postoperative narcotic use was seen in patients receiving subcutaneous Marcaine administration around the nephrostomy tube tract. Further studies are warranted to define additional measures to reduce discomfort in those requiring nephrostomy tube drainage following percutaneous nephrolithotomy.
Review of in vivo optical molecular imaging and sensing from x-ray excitation (2021)

Discovery of x-ray-excited reporters combined with optimized x-ray scan sequences can improve imaging resolution and sensitivity.
Retinal microvasculature: population epidemiology and concordance in Australian children aged 11–12 years and their parents (2019)

Arteriolar and venular calibre were similar to previously documented measures in midlife adult and late childhood populations. Population parent-child concordance values align with moderate polygenic heritability reported in smaller studies.
Al-2.128 Stamp (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress (2022)

Poaceae plants can locally accumulate iron to suppress pathogen infection. It remains unknown how pathogens overcome host-derived iron stress during their successful infections. Here, we report that Fusarium graminearum (Fg), a destructive fungal pathogen of cereal crops, is challenged by host-derived high-iron stress. Fg infection induces host alkalinization, and the pH-dependent transcription factor FgPacC undergoes a proteolytic cleavage into the functional isoform named FgPacC30 under alkaline host environment. Subsequently FgPacC30 binds to a GCCAR(R = A/G)G element at the promoters of the genes involved in iron uptake and inhibits their expression, leading to adaption of Fg to high-iron stress. Mechanistically, FgPacC30 binds to FgGcn5 protein, a catalytic subunit of Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, leading to deregulation of histone acetylation at H3K18 and H2BK11, and repression of iron uptake genes. Moreover, we identified a protein kinase FgHal4, which is highly induced by extracellular high-iron stress and protects FgPacC30 against 26S proteasome-dependent degradation by promoting FgPacC30 phosphorylation at Ser2. Collectively, this study uncovers a novel inhibitory mechanism of the SAGA complex by a transcription factor that enables a fungal pathogen to adapt to dynamic microenvironments during infection.
Diffuse Optical Imaging in Scattering Media with Highly Contrasted Absorption Coefficients: Application to Small Animal Imaging (2006)

Fluorescence tomography of highly contrasted media requires to built and to take into account a precise description of the attenuation coefficients map. Using this attenuation map provides new opportunities to handle complex acquisition geometries.
Graph‐based optimization of epitope coverage for vaccine antigen design (2017)

Epigraph is a recently developed algorithm that enables the computationally efficient design of single or multi-antigen vaccines to maximize the potential epitope coverage for a diverse pathogen population. Potential epitopes are defined as short contiguous stretches of proteins, comparable in length to T-cell epitopes. This optimal coverage problem can be formulated in terms of a directed graph, with candidate antigens represented as paths that traverse this graph. Epigraph protein sequences can also be used as the basis for designing peptides for experimental evaluation of immune responses in natural infections to highly variable proteins. The epigraph tool suite also enables rapid characterization of populations of diverse sequences from an immunological perspective. Fundamental distance measures are based on immunologically relevant shared potential epitope frequencies, rather than simple Hamming or phylogenetic distances. Here, we provide a mathematical description of the epigraph algorithm, include a comparison of different heuristics that can be used when graphs are not acyclic, and we describe an additional tool we have added to the web-based epigraph tool suite that provides frequency summaries of all distinct potential epitopes in a population. We also show examples of the graphical output and summary tables that can be generated using the epigraph tool suite and explain their content and applications. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Statistics in Medicine published by John Wiley & Sons Ltd.
Effects of Multiple Electron Acceptors on Microbial Interactions in a Hydrogen-Based Biofilm (2013)

To investigate interactions among multiple electron acceptors in a H2-fed biofilm, we operated a membrane biofilm reactor with H2-delivery capacity sufficient to reduce all acceptors. ClO4– and O2 were input electron acceptors in all stages at surface loadings of 0.08 ± 0.006 g/m2-d (1.0 ± 0.7 e– meq/m2-d) for ClO4– and 0.51 g/m2-d (76 e– meq/m2-d) for O2. SO42– was added in Stage 2 at 3.77 ± 0.39 g/m2-d (331 ± 34 e– meq/m2-d), and NO3– was further added in Stage 3 at 0.72 ± 0.03 g N/m2-d (312 ± 13 e– meq/m2-d). At steady state for each stage, ClO4–, O2, and NO3– (when present in the influent) were completely reduced; measured SO42– reduction decreased from 78 ± 4% in Stage 2 to 59 ± 4% in Stage 3, when NO3– was present. While perchlorate-reducing bacteria (PRB), assayed by qPCR targeting the pcrA gene, remained stable throughout, sulfate-reducing bacteria (SRB), assayed by the dsrA gene, increased almost 3 orders of magnitude when significant SO42– reduction occurred in stage 2. The abundance of denitrifying bacteria (DB), assayed by the nirK and nirS genes, increased in Stage 3, while SRB remained at high numbers, but did not increase. Based on pyrosequencing analyses, β-Proteobacteria dominated in Stage 1, but ε-Proteobacteria became more important in Stages 2 and 3, when the input of multiple electron acceptors favored genera with broader electron-accepting capabilities. Sulfuricurvum (a sulfur oxidizer and NO3– reducer) and Desulfovibrio (a SO42– reducer) become dominant in Stage 3, suggesting redox cycling of sulfur in the biofilm.
Mixed-Timescale Deep-Unfolding for Joint Channel Estimation and Hybrid Beamforming (2022)

In massive multiple-input multiple-output (MIMO) systems, hybrid analog-digital beamforming is an essential technique for exploiting the potential array gain without using a dedicated radio frequency chain for each antenna. However, due to the large number of antennas, the conventional channel estimation and hybrid beamforming algorithms generally require high computational complexity and signaling overhead. In this work, we propose an end-to-end deep-unfolding neural network (NN) joint channel estimation and hybrid beamforming (JCEHB) algorithm to maximize the system sum rate in time-division duplex (TDD) massive MIMO. Specifically, the recursive least-squares (RLS) algorithm and stochastic successive convex approximation (SSCA) algorithm are unfolded for channel estimation and hybrid beamforming, respectively. In order to reduce the signaling overhead, we consider a mixed-timescale hybrid beamforming scheme, where the analog beamforming matrices are optimized based on the channel state information (CSI) statistics offline, while the digital beamforming matrices are designed at each time slot based on the estimated low-dimensional equivalent CSI matrices. We jointly train the analog beamformers together with the trainable parameters of the RLS and SSCA induced deep-unfolding NNs based on the CSI statistics offline. During data transmission, we estimate the low-dimensional equivalent CSI by the RLS induced deep-unfolding NN and update the digital beamformers. In addition, we propose a mixed-timescale deep-unfolding NN where the analog beamformers are optimized online, and extend the framework to frequency-division duplex (FDD) systems where channel feedback is considered. Simulation results show that the proposed algorithm can significantly outperform conventional algorithms with reduced computational complexity and signaling overhead.
Understanding the mechanisms of photodecarbonylation of the photoprecursors of higher poly(acene)s (2007)

Polyacenes, linear poly(benzenoid) hydrocarbons, are significant compounds for various electronic applications. Smaller lower molecular weight members of the series (anthracene, tetracene, and pentacene) have been extensively investigated for their use as semiconductors, as active layers in organic field-effect transistors (OFETs) and in organic light-emitting diodes (OLEDs). Smaller HOMO-LUMO gaps might be achieved by synthesizing even higher poly(acene)s such as hexacene and heptacene. Nevertheless, an increased instability and insolubility associated with the increasing number of fused rings has become a synthetic challenge for chemists. We have recently developed a photochemical route that allows one to easily synthesize heptacene in rigid media from an &#945;-diketone photoprecursor, thus opening a pathway to utilize these compounds in the construction of suitable devices. Photodecarbonylations of &#945;-diketones are unusual reactions. In most instances, dione excited states become electron transfer acceptors. The decarbonylation is driven by the stability of the resulting aromatic hydrocarbon. We have studied the nature of the excited states involved in photodecarbonylation of the &#945;-diketones and the structure of the carbon monoxide fragment(s). Results obtained on the mechanism of photodecarbonylation investigated using nanosecond flash photolysis and ultra-fast pump-probe techniques are discussed.
Letter to the Editor and Reply: Toxicity of Copper in Drinking Water (2010)

To the Editor: This journal recently published a collection of five articles (Stern, 2010; Krewski et al., 2010a; Krewski et al., 2010b; Deveau, 2010; Meek et al., 2010) on the safety and toxicity ...
Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28 (2021)

Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/).
Iterative Approach to Oligo(arylenevinylene)s Containing Tetrasubstituted Vinylene Units (2010)

Monodispersed oligo(arylenevinylene)s containing tetrasubstituted vinylene units were stereoselectively synthesized in an efficient manner by iteration of two different kinds of palladium-catalyzed reactions.
Single-piece polycrystalline silicon accumulation/depletion/inversion model with implicit/explicit surface-potential solutions (2005)

A single-piece analytical equation for the surface potential at the polycrystalline-silicon (poly-Si) gate of a metal-oxide-semiconductor field-effect transistor is presented, which accounts for the poly-accumulation, poly-depletion, and poly-inversion effects. It is shown that the model accurately describes the physical behavior of the surface potentials, gate charge, and capacitance, with smooth transitions, which has been verified with iterative, explicit, and numerical solutions. The proposed model can be used in implicit or explicit surface-potential-based formulations.
Correction: Conformationally restricted benzothienoazepine respiratory syncytial virus inhibitors: their synthesis, structural analysis and biological activities (2018)

Correction for ‘Conformationally restricted benzothienoazepine respiratory syncytial virus inhibitors: their synthesis, structural analysis and biological activities’ by Euan A. F. Fordyce <italic>et al.</italic>, <italic>Med. Chem. Commun.</italic>, 2018, DOI: 10.1039/c8md00033f.
Reference values for and interpretation of the Singapore Caregiver Quality of Life Scale: a quantile regression approach (2020)

Percentiles and effect size estimates are provided to facilitate interpretation of the SCQOLS.
Deletion of CD1d in Adipocytes Aggravates Adipose Tissue Inflammation and Insulin Resistance in Obesity (2017)

Adipose tissue inflammation is an important factor in obesity that promotes insulin resistance. Among various cell types in adipose tissue, immune cells actively regulate inflammatory responses and affect whole-body energy metabolism. In particular, invariant natural killer T (iNKT) cells contribute to mitigating dysregulation of systemic energy homeostasis by counteracting obesity-induced inflammation in adipose tissue. However, the molecular mechanisms by which adipose iNKT cells become activated and mediate anti-inflammatory roles in obese adipose tissue have not been thoroughly understood yet. In the current study, we demonstrate that adipocyte CD1d plays a key role in the stimulation of adipose iNKT cells, leading to anti-inflammatory responses in high-fat diet (HFD)-fed mice. Accordingly, adipocyte-specific CD1d-knockout (CD1d<sup>ADKO</sup>) mice showed reduced numbers of iNKT cells in adipose tissues and decreased responses to α-galactosylceramide-induced iNKT cell activation. Additionally, HFD-fed CD1d<sup>ADKO</sup> mice revealed reduced interleukin-4 expression in adipose iNKT cells and aggravated adipose tissue inflammation and insulin resistance. Collectively, these data suggest that adipocytes could selectively stimulate adipose iNKT cells to mediate anti-inflammatory responses and attenuate excess proinflammatory responses in obese adipose tissue.
Onychomycosis due to <i>Trichophyton soudanense</i> in Switzerland (1998)

We report 2 cases of onychomycosis of the finger- and toenails due to Trichophyton soudanense with a typical clinical picture different from the hyperkeratosis of T. rubrum subungual onychomycosis.
Generalized scale: Theory, algorithms, and applications in image analysis (2004)

Magnetic Resonance (MR) Imaging (MRI), a non-invasive method for imaging the human body, has revolutionized medical imaging. MR image processing, particularly segmentation, and analysis are used extensively in medical and clinical research for advancing our understanding of the various diseases of the human body, for their diagnosis, and for developing strategies to treat them. These efforts face two major difficulties—the first due to image intensity inhomogeneity present as a background variation component, and the second due to the non-standardness of the MR image intensities. Scale is a fundamental concept useful in almost all image processing and analysis tasks. Broadly speaking, scale related work can be divided into multi-scale representations (global models) and local scale models. In this thesis, we present a new morphometric scale model that we refer to as generalized scale which combines the properties of local scale models with the global spirit of multi-scale representations. We contend that this semi-locally adaptive nature of generalized scale confers it certain distinct advantages over other scale formulations, making it readily applicable to solving a range of general image processing tasks. In the context of this thesis, however, we limit ourselves to addressing two issues that are relevant to MR image processing, namely, (1) correcting for image intensity inhomogeneity (referred to as inhomogeneity correction), and (2) correcting for the non-standardness of the MR image intensities (referred to as intensity standardization). While the importance of intensity standardization and inhomogeneity correction in MR image analysis is well established, their behavior has been studied only in isolation, and their influence on each other has thus far not been addressed. Part of this thesis work is centered on studying the possible effects of one method on the other, in order to find the sequence of inhomogeneity correction and intensity standardization operations that will produce the best overall image quality. The results of extensive quantitative and qualitative evaluation of our methods on nearly 6000 3D clinical and phantom MR data sets are also presented.