gebhart/patrepeval huggingface dataset:
FANCM c.5101C>T mutation associates with breast cancer survival and treatment outcome (2016)

Breast cancer (BC) is a heterogeneous disease, and different tumor characteristics and genetic variation may affect the clinical outcome. The FANCM c.5101C > T nonsense mutation in the Finnish population associates with increased risk of breast cancer, especially for triple-negative breast cancer patients. To investigate the association of the mutation with disease prognosis, we studied tumor phenotype, treatment outcome, and patient survival in 3,933 invasive breast cancer patients, including 101 FANCM c.5101C > T mutation carriers and 3,832 non-carriers. We also examined association of the mutation with nuclear immunohistochemical staining of DNA repair markers in 1,240 breast tumors. The FANCM c.5101C > T mutation associated with poor 10-year breast cancer-specific survival (hazard ratio (HR)=1.66, 95% confidence interval (CI) 1.09-2.52, p = 0.018), with a more pronounced survival effect among familial cases (HR = 2.93, 95% CI 1.5-5.76, p = 1.80 × 10<sup>-3</sup> ). Poor disease outcome of the carriers was also found among the estrogen receptor (ER) positive subgroup of patients (HR = 1.8, 95% CI 1.09-2.98, p = 0.021). Reduced survival was seen especially among patients who had not received radiotherapy (HR = 3.43, 95% CI 1.6-7.34, p = 1.50 × 10<sup>-3</sup> ) but not among radiotherapy treated patients (HR = 1.35, 95% CI 0.82-2.23, p = 0.237). Significant interaction was found between the mutation and radiotherapy (p = 0.040). Immunohistochemical analyses show that c.5101C > T carriers have reduced PAR-activity. Our results suggest that FANCM c.5101C > T nonsense mutation carriers have a reduced breast cancer survival but postoperative radiotherapy may diminish this survival disadvantage.
Memory technology for the post CMOS era (2005)

One of the tasks of the International Technology Roadmap for Semiconductors (ITRS) Emerging Research Devices (ERD) Technology Working Group (TWG) is to seek out memory technologies presented in the research literature and weigh whether they have the potential to serve in 22-nm and smaller IC generations. The motive for this effort is to develop data that can help guide research investment decisions. In 2004, the ERD TWG summarized some quantitative attributes of four alternative memory approaches, and developed a potential/risk score for each. While this effort falls far short of identifying a specific technology, it is at least a beginning. This article describes the nature of the challenge and reports initial study results.
Heidegger's politics (2011)

Heidegger's politics, and the debate as to whether his philosophy lends itself readily to Nazi ideology, is normally considered central to reading and interpreting his thought. Some thinkers, however, rejecting any suggestion of the “ad hominem argument” linking the life and work, suggest that Heidegger's personal political views and behaviour be regarded as philosophically insignificant, because a philosophy and moral character exist independently: “Being an original philosopher … is the result of some neural kink that occurs independently of other kinks … Philosophical talent and moral character swing free of each other” (Rorty 1998: 32–3). This standpoint tries to evaluate Heidegger's thinking on its merits while rejecting one of Heidegger's fundamental convictions – that thinking and meaning derive from one's concrete experience of being-in-the-world – which implies that “authentic” philosophizing arises from authentic existence (although this does not necessarily mean that others will view an “authentic existence” as morally acceptable).
Creation of a Bioengineered Skin Flap Scaffold with a Perfusable Vascular Pedicle (2017)

Full-thickness skin loss is a challenging problem due to limited reconstructive options, demanding 75 million surgical procedures annually in the United States. Autologous skin grafting is the gold standard treatment, but results in donor-site morbidity and poor aesthetics. Numerous skin substitutes are available on the market to date, however, none truly functions as full-thickness skin due to lack of a vascular network. The creation of an autologous full-thickness skin analogue with a vascular pedicle would result in a paradigm shift in the management of wounds and in reconstruction of full-thickness skin defects. To create a clinically relevant foundation, we generated an acellular skin flap scaffold (SFS) with a perfusable vascular pedicle of clinically relevant size by perfusion decellularization of porcine fasciocutaneous flaps. We then analyzed the yielded SFS for mechanical properties, biocompatibility, and regenerative potential in vitro and in vivo. Furthermore, we assessed the immunological response using an in vivo model. Finally, we recellularized the vascular compartment of an SFS and reconnected it to a recipient's blood supply to test for perfusability. Perfusion decellularization removed all cellular components with preservation of native extracellular matrix composition and architecture. Biaxial testing revealed preserved mechanical properties. Immunologic response and biocompatibility assessed via implantation and compared with native xenogenic skin and commercially available dermal substitutes revealed rapid neovascularization and complete tissue integration. Composition of infiltrating immune cells showed no evidence of allorejection and resembled the inflammatory phase of wound healing. Implantation into full-thickness skin defects demonstrated good tissue integration and skin regeneration without cicatrization. We have developed a protocol for the generation of an SFS of clinically relevant size, containing a vascular pedicle, which can be utilized for perfusion decellularization and, ultimately, anastomosis to the recipient vascular system after precellularization. The observed favorable immunological response and good tissue integration indicate the substantial regenerative potential of this platform.
HIV-1 Tat-Induced Microgliosis and Synaptic Damage via Interactions between Peripheral and Central Myeloid Cells (2011)

Despite the ability of combination antiretroviral treatment (cART) to reduce viral burden to nearly undetectable levels in cerebrospinal fluid and serum, HIV-1 associated neurocognitive disorders (HAND) continue to persist in as many as half the patients living with this disease. There is growing consensus that the actual substrate for HAND is destruction of normal synaptic architecture but the sequence of cellular events that leads to this outcome has never been resolved. To address whether central vs. peripheral myeloid lineage cells contribute to synaptic damage during acute neuroinflammation we injected a single dose of the HIV-1 transactivator of transcription protein (Tat) or control vehicle into hippocampus of wild-type or chimeric C57Bl/6 mice genetically marked to distinguish infiltrating and resident immune cells. Between 8-24 hr after injection of Tat, invading CD11b(+) and/or myeloperoxidase-positive leukocytes with granulocyte characteristics were found to engulf both microglia and synaptic structures, and microglia reciprocally engulfed invading leukocytes. By 24 hr, microglial processes were also seen ensheathing dendrites, followed by inclusion of synaptic elements in microglia 7 d after Tat injection, with a durable microgliosis lasting at least 28 d. Thus, central nervous system (CNS) exposure to Tat induces early activation of peripheral myeloid lineage cells with phagocytosis of synaptic elements and reciprocal microglial engulfment of peripheral leukocytes, and enduring microgliosis. Our data suggest that a single exposure to a foreign antigen such as HIV-1 Tat can lead to long-lasting disruption of normal neuroimmune homeostasis with deleterious consequences for synaptic architecture, and further suggest a possible mechanism for enduring neuroinflammation in the absence of productive viral replication in the CNS.
High frame rate synthetic aperture duplex imaging (2013)

Conventional color flow images are limited in velocity range and can either show the high velocities in systole or be optimized for the lower diastolic velocities. The full dynamics of the flow is, thus, hard to visualize. The dynamic range can be significantly increased by employing synthetic aperture flow imaging as demonstrated in this paper. Synthetic aperture, directional beamforming, and cross-correlation are used to produce B-mode and vector velocity images at high frame rates. The frame rate equals the effective pulse repetition frequency of each imaging mode. Emissions for making the B-mode images and velocity maps are interleaved in a 1-to-1 ratio. This provides continuous data allowing a wide range of velocities to be estimated. Two cases are considered in the flow estimation: In the first case, the angle of the flow is determined from the B-mode image. In the other case, the angle is determined by estimating the flow velocity in all directions and choosing the one with the strongest correlation. The method works for all angles, including fully axial and fully transverse flows. Field II simulations with a 192 element, 7 MHz linear array are made of laminar, transverse flow profiles. For a simulated peak velocity of 0.5 m/s, the relative bias is -6.8% and the relative standard deviation is 6.1%. The bias on the angle is 0.98 degrees with a standard deviation of 2.39 degrees when using the flow estimator to determine the angle. For a peak velocity of 0.05 m/s, the relative bias of the velocity estimation is -1.8% and the relative standard deviation 5.4%. The approach can thus estimate both high and low velocities with equal accuracy and thereby makes it possible to present vector flow images with a high dynamic range. Measurements are made using the SARUS research scanner, a linear array transducer similar to the simulated one, and a recirculating flow rig with a blood mimicking fluid and a parabolic flow profile with a peak velocity of approximately 0.3 m/s. The relative bias of the velocity estimation is 0.19% and the mean relative standard deviation 4.9%. For the direction estimation, the bias is 3.2 degrees with a standard deviation of 1.6 degrees.
Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus (2020)

Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5' gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type-specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.
National Trends in Post-Acute Care Costs Following Total Hip Arthroplasty from 2010 through 2018 (2021)

Over the last decade, the rate of home discharge after THA increased while rehospitalization and ED visit rates declined, resulting in a substantial decrease in total and post-acute care costs. Post-acute care costs declined most rapidly after the introduction of the new Medicare bundled payment programs in 2013 and 2016.
Effects of Graphene in Dye-Sensitized Solar Cells Based on Nitrogen-Doped TiO2 Composite (2015)

Graphene (GR) exhibits impressive photoelectric properties, including a large specific surface area, high charge-carrier mobility, high conductance, and fast electron transfer. In this study, the effect of GR on the performance of dye-sensitized solar cells (DSSCs) was investigated by mixing GR into N-doped TiO2 photoelectrodes. GR/N-doped TiO2 (GNT) nanoparticles were prepared using the sol–gel method. After preparation, the presence of GR in the photoelectrodes was confirmed using transmission electron microscopy (TEM), X-ray diffraction (XRD), and Raman spectroscopy analyses. After the addition of GR, the photoelectrodes displayed enhanced dye adsorption properties with lower internal resistances and faster transport times. Accordingly, DSSCs with these photoelectrodes generated high current density with a low electron-recombination rate. The maximum power conversion efficiency of DSSCs with GR/N-doped photoelectrodes was 9.32% with optimized DSSC parameters; this represents an enhancement of approximately 22% over that of DSSCs with N-doped photoelectrodes. The addition of excess GR weakened the crystallization of particles on the surface of photoelectrodes, which resulted in low dye adsorption and decreased efficiency of the DSSCs. In summary, the addition of GR promoted increased dye loading and enhanced DSSC efficiency. The optimal amount of GR for high-efficiency DSSCs was successfully determined in this study.
Improving the quality of 2D solid-state NMR spectra of microcrystalline proteins by covariance analysis (2009)

Gaining time, resolution and sensitivity at the same time: covariance processing of two-dimensional NMR spectra of microcrystalline proteins improves spectral quality over conventional Fourier transformation despite a significant reduction of the experimental time.
Dorsal Raphe Dopamine Neurons Represent the Experience of Social Isolation (2016)

The motivation to seek social contact may arise from either positive or negative emotional states, as social interaction can be rewarding and social isolation can be aversive. While ventral tegmental area (VTA) dopamine (DA) neurons may mediate social reward, a cellular substrate for the negative affective state of loneliness has remained elusive. Here, we identify a functional role for DA neurons in the dorsal raphe nucleus (DRN), in which we observe synaptic changes following acute social isolation. DRN DA neurons show increased activity upon social contact following isolation, revealed by in vivo calcium imaging. Optogenetic activation of DRN DA neurons increases social preference but causes place avoidance. Furthermore, these neurons are necessary for promoting rebound sociability following an acute period of isolation. Finally, the degree to which these neurons modulate behavior is predicted by social rank, together supporting a role for DRN dopamine neurons in mediating a loneliness-like state. PAPERCLIP.
Antifibrotic role of vascular endothelial growth factor in pulmonary fibrosis (2017)

The chronic progressive decline in lung function observed in idiopathic pulmonary fibrosis (IPF) appears to result from persistent nonresolving injury to the epithelium, impaired restitution of the epithelial barrier in the lung, and enhanced fibroblast activation. Thus, understanding these key mechanisms and pathways modulating both is essential to greater understanding of IPF pathogenesis. We examined the association of VEGF with the IPF disease state and preclinical models in vivo and in vitro. Tissue and circulating levels of VEGF were significantly reduced in patients with IPF, particularly in those with a rapidly progressive phenotype, compared with healthy controls. Lung-specific overexpression of VEGF significantly protected mice following intratracheal bleomycin challenge, with a decrease in fibrosis and bleomycin-induced cell death observed in the VEGF transgenic mice. In vitro, apoptotic endothelial cell-derived mediators enhanced epithelial cell injury and reduced epithelial wound closure. This process was rescued by VEGF pretreatment of the endothelial cells via a mechanism involving thrombospondin-1 (TSP1). Taken together, these data indicate beneficial roles for VEGF during lung fibrosis via modulating epithelial homeostasis through a previously unrecognized mechanism involving the endothelium.
Photonics-based millimeter-wave radar system for handheld applications (2017)

A frequency-modulated continuous-wave (FM-CW) radar system at 94 GHz with a bandwidth of 2 GHz is configured by an optical millimeter-wave synthesizer for short-range application in handheld operation. Combination of an inertial measurement unit and a fiber-remoted radar system help realizing simple radar head configuration.
Event-Based, Timescale Invariant Unsupervised Online Deep Learning With STDP (2018)

Learning of hierarchical features with spiking neurons has mostly been investigated in the database framework of standard deep learning systems. However, the properties of neuromorphic systems could be particularly interesting for learning from continuous sensor data in real-world settings. In this work, we introduce a deep spiking convolutional neural network of integrate-and-fire (IF) neurons which performs unsupervised online deep learning with spike-timing dependent plasticity (STDP) from a stream of asynchronous and continuous event-based data. In contrast to previous approaches to unsupervised deep learning with spikes, where layers were trained successively, we introduce a mechanism to train all layers of the network simultaneously. This allows approximate online inference already during the learning process and makes our architecture suitable for online learning and inference. We show that it is possible to train the network without providing implicit information about the database, such as the number of classes and the duration of stimuli presentation. By designing an STDP learning rule which depends only on relative spike timings, we make our network fully event-driven and able to operate without defining an absolute timescale of its dynamics. Our architecture requires only a small number of generic mechanisms and therefore enforces few constraints on a possible neuromorphic hardware implementation. These characteristics make our network one of the few neuromorphic architecture which could directly learn features and perform inference from an event-based vision sensor.
Development of Highly Fluorogenic Styrene Probes for Visualizing RNA in Live Cells (2023)

Styrene dyes are useful imaging probes and fluorescent sensors due to their strong fluorogenic responses to environmental changes or binding macromolecules. Previously, indole-containing styrene dyes have been reported to selectively bind RNA in the nucleolus and cytoplasm. However, the application of these indole-based dyes in cell imaging is limited by their moderate fluorescence enhancement and quantum yields, as well as relatively high background associated with these green-emitting dyes. In this work, we have investigated the positional and electronic effects of the electron donor by generating regioisomeric and isosteric analogues of the indole ring. Select probes exhibited large Stokes shifts, enhanced molar extinction coefficients, and bathochromic shifts in their absorption and fluorescence wavelengths. In particular, the indolizine analogues displayed high membrane permeability, strong fluorogenic responses upon binding RNA, compatibility with fluorescence lifetime imaging microscopy (FLIM), low cytotoxicity, and excellent photostability. These indolizine dyes not only give rise to rapid, sensitive, and intense staining of nucleoli in live cells but can also resolve subnucleolar structures enabling highly detailed studies of nucleolar morphology. Furthermore, our dyes can partition into RNA coacervates and resolve the formation of multiphase complex coacervate droplets. These indolizine-containing styrene probes offer the highest fluorescence enhancement among the RNA-selective dyes reported in the literature; thus, these new dyes are excellent alternatives to the commercially available RNA dye, SYTO RNASelect, for visualizing RNA in live cells and <i>in vitro</i>.
Recommended Personal Protective Equipment for Cochlear Implant and Other Mastoid Surgery During the COVID‐19 Era (2020)

4 Laryngoscope, 130:2693-2699, 2020.
Optical Disc Drives: A Study of Variation (2011)

Optical disc drives vary significantly in their performance. Here we report a principal components analysis performed on data from new drives, which separates out the better performing drives and finds correlations among drive test variables.
Kalman filtering for compressed sensing (2010)

Compressed sensing is a new emerging field dealing with the reconstruction of a sparse or, more precisely, a compressed representation of a signal from a relatively small number of observations, typically less than the signal dimension. In our previous work we have shown how the Kalman filter can be naturally applied for obtaining an approximate Bayesian solution for the compressed sensing problem. The resulting algorithm, which was termed CSKF, relies on a pseudo-measurement technique for enforcing the sparseness constraint. Our approach raises two concerns which are addressed in this paper. The first one refers to the validity of our approximation technique. In this regard, we provide a rigorous treatment of the CSKF algorithm which is concluded with an upper bound on the discrepancy between the exact (in the Bayesian sense) and the approximate solutions. The second concern refers to the computational overhead associated with the CSKF in large scale settings. This problem is alleviated here using an efficient measurement update scheme based on Krylov subspace method.
Vitamin D–dependent induction of cathelicidin in human macrophages results in cytotoxicity against high-grade B cell lymphoma (2015)

Infiltration by macrophages represents a characteristic morphological hallmark in high-grade lymphatic malignancies such as Burkitt's lymphoma (BL). Although macrophages can, in principle, target neoplastic cells and mediate antibody-dependent cellular cytotoxicity (ADCC), tumor-associated macrophages (TAMs) regularly fail to exert direct cytotoxic functions. The underlying mechanisms responsible for this observation remain unclear. We demonstrate that inflammatory M1 macrophages kill proliferating high-grade B cell lymphoma cells by releasing the antimicrobial peptide cathelicidin in a vitamin D-dependent fashion. We show that cathelicidin directly induces cell death by targeting mitochondria of BL cells. In contrast, anti-inflammatory M2 macrophages and M2-like TAMs in BL exhibit an altered vitamin D metabolism, resulting in a reduced production of cathelicidin and consequently in inability to lyse BL cells. However, treatment of M2 macrophages with the bioactive form of vitamin D, 1,25D3, or a vitamin D receptor agonist effectively induces cathelicidin production and triggers tumoricidal activity against BL cells. Furthermore, rituximab-mediated cytotoxicity of vitamin D-treated M2 macrophages is cathelicidin-dependent. Finally, vitamin D treatment of 25-hydroxyvitamin D (25D)-deficient volunteers in vivo or primary TAMs in vitro improves rituximab-mediated ADCC against B cell lymphoma cells. These data indicate that activation of the vitamin D signaling pathway activates antitumor activity of TAMs and improves the efficacy of ADCC.