gebhart/patrepeval huggingface dataset:
Experimental and <i>Ab Initio</i> Ultrafast Carrier Dynamics in Plasmonic Nanoparticles (2017)

Ultrafast pump-probe measurements of plasmonic nanostructures probe the nonequilibrium behavior of excited carriers, which involves several competing effects obscured in typical empirical analyses. Here we present pump-probe measurements of plasmonic nanoparticles along with a complete theoretical description based on first-principles calculations of carrier dynamics and optical response, free of any fitting parameters. We account for detailed electronic-structure effects in the density of states, excited carrier distributions, electron-phonon coupling, and dielectric functions that allow us to avoid effective electron temperature approximations. Using this calculation method, we obtain excellent quantitative agreement with spectral and temporal features in transient-absorption measurements. In both our experiments and calculations, we identify the two major contributions of the initial response with distinct signatures: short-lived highly nonthermal excited carriers and longer-lived thermalizing carriers.
Data from Polymeric Nanoparticle-Encapsulated Hedgehog Pathway Inhibitor HPI-1 (NanoHHI) Inhibits Systemic Metastases in an Orthotopic Model of Human Hepatocellular Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To illustrate the prognostic significance of hedgehog (Hh) signaling in patients with hepatocellular carcinoma (HCC) and to evaluate the efficacy of a novel nanoparticle-encapsulated inhibitor of the Hh transcription factor, &lt;i&gt;Gli1&lt;/i&gt; (NanoHHI) using &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; models of human HCCs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patched1 (&lt;i&gt;Ptch1&lt;/i&gt;) expression was detected in tumor tissue microarrays of 396 patients with HCC who underwent curative surgical resection during February 2000 to December 2002. Prognostic significance was assessed using Kaplan–Meier survival estimates and log-rank tests. The effects of NanoHHI alone and in combination with sorafenib were investigated on HCC cell lines. Primary HCC tumor growth and metastasis were examined &lt;i&gt;in vivo&lt;/i&gt; using subcutaneous and orthotopic HCC xenografts in nude mice.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Elevated expression of &lt;i&gt;Ptch1&lt;/i&gt; in HCC tissues was significantly related to disease recurrence, as well as a shorter time to recurrence in patients with HCC. &lt;i&gt;In vitro&lt;/i&gt;, NanoHHI significantly inhibited the proliferation and invasion of HCC cell lines. NanoHHI potently suppressed &lt;i&gt;in vivo&lt;/i&gt; tumor growth of HCC xenografts in both subcutaneous and orthotopic milieus, and in contrast to sorafenib, resulted in significant attenuation of systemic metastases in the orthotopic setting. Furthermore, NanoHHI significantly decreased the population of CD133-expressing HCC cells, which have been implicated in tumor initiation and metastases.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Downstream Hh signaling has prognostic significance in patients with HCC as it predicts early recurrence. Gli inhibition through NanoHHI has profound tumor growth inhibition and antimetastatic effects in HCC models, which may provide a new strategy in the treatment of patients with HCC and prevention post-operative recurrence. &lt;i&gt;Clin Cancer Res; 18(5); 1291–302. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Chronic recurrent multifocal osteomyelitis in children with hypophosphatasia explained by anti-inflammatory nucleotidase activity of tissue nonspecific alkaline phosphatase in mesenchymal and hematopoietic cells (2019)

International audience
BFD in Demand Mode over Point-to-Point MPLS LSP (2019)

This document describes procedures for using Bidirectional Forwarding
Detection (BFD) in Demand mode to detect data plane failures in
Multiprotocol Label Switching (MPLS) point-to-point Label Switched
Paths.
MSA/MAS Hyper-Dimensional Spectral File Format - A Straw-Man Proposal (2011)

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.
Agricultural adaptation to climate change: observations from the Mid-Hills of Nepal (2013)

Abstract This paper provides empirical evidence of agricultural adaptation strategies being adopted in the Mid-Hills regions of Nepal in response to climate change. Farmers were interviewed across four districts and climate change observations were reported, most notably those of increased temperatures and unpredictable precipitation. Agricultural adaptation strategies adopted in response to climate change were varied, with agroforestry and organic farming being the most popular practices. Most adaptation strategies were thought to be development-facing actions to reduce vulnerability, rather than specifically addressing climate change. From this research it is evident that indigenous knowledge, financial support and increased accessibility all play a pivotal role for successful climate change adaptation in the Mid-Hills. This case study provides valuable evidence-based research of autonomous adaptation techniques in a highly climate-vulnerable location of Nepal. Recommendations are made for donors to learn from best-practice and adopt local knowledge when investing in climate change adaptation strategies to most effectively reduce the vulnerability of some of the world's poorest communities. Keywords: Nepalagricultureclimate changeadaptationvulnerabilityadaptive capacityclimate risk
On the use of numerical modelling for near-field pollutant dispersion in urban environments − A review (2015)

This article deals with the state-of-the-art of experimental and numerical studies carried out regarding air pollutant dispersion in urban environments. Since the simulation of the dispersion field around buildings depends strongly on the correct simulation of the wind-flow structure, the studies performed during the past years on the wind-flow field around buildings are reviewed. This work also identifies errors that can produce poor results when numerically modelling wind flow and dispersion fields around buildings in urban environments. Finally, particular attention is paid to the practical guidelines developed by researchers to establish a common methodology for verification and validation of numerical simulations and/or to assist and support the users for a better implementation of the computational fluid dynamics (CFD) approach.
Novel design concept and technology for the switching mode circuit based on the electromagnetic wave theory and the nonlinear undulation theory (2010)

This paper presents the novel concept of the generation mechanism of the solitary electromagnetic wave (SEMW) by the switching device. SEMW concept is formed by fusing the electromagnetic wave (EMW) theory and the nonlinear undulation theory. The examples of the application for the signal line (SL) and the power line (PL) on the VLSI and the low impedance lossy line (LILL) technologies derived from the SEMW concept are also presented. SEMW concept and these technologies will contribute to the progress of the switching mode circuit.
Detecting mental states of alertness with genetic algorithm variable selection (2013)

The objective of the present work is to develop a method able to automatically determine mental states of vigilance; i.e., a person's state of alertness. Such a task is relevant to diverse domains, where a person is expected or required to be in a particular state. For instance, pilots or medical staffs are expected to be in a highly alert state, and this method could help to detect possible problems. In this paper, an approach is developed to predict the state of alertness (“normal” or “relaxed”) from the study of electroencephalographic signals (EEG) collected with a limited number of electrodes. The EEG of 58 participants in the two alertness states (116 records) were collected via a cap with 58 electrodes. After a data validation step, 19 subjects were retained for further analysis. A genetic algorithm was used to select an optimal subset of electrodes. Common spatial pattern (CSP) coupled to linear discriminant analysis (LDA) was used to build a decision rule and thus predict the alertness of the participants. Different subset sizes were investigated and the best result was obtained by considering 9 electrodes (correct classification rate of 73.68%).
Data from The Oncoprotein SF2/ASF Promotes Non–Small Cell Lung Cancer Survival by Enhancing Survivin Expression (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; SF2/ASF is a splicing factor recently described as an oncoprotein. In the present work, we examined the role of SF2/ASF in human non–small cell lung cancer (NSCLC) and analyzed the molecular mechanisms involved in SF2/ASF-related carcinogenesis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; SF2/ASF protein levels were analyzed in 81 NSCLC patients by immunohistochemistry. SF2/ASF downregulation cellular models were generated using small interfering RNAs, and the effects on proliferation and apoptosis were evaluated. Survivin and SF2/ASF expression in lung tumors was analyzed by Western blot and immunohistochemistry. Survival curves and log-rank test were used to identify the association between the expression of the proteins and time to progression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Overexpression of SF2/ASF was found in most human primary NSCLC tumors. &lt;i&gt;In vitro&lt;/i&gt; downregulation of SF2/ASF induced apoptosis in NSCLC cell lines. This effect was associated with a reduction in the expression of survivin, an antiapoptotic protein widely upregulated in cancer. In fact, SF2/ASF specifically bound survivin mRNA and enhanced its translation, via a mammalian target of rapamycin complex 1 (mTORC1) pathway-dependent mechanism, through the phosphorylation and inactivation of the translational repressor 4E-BP1. Moreover, SF2/ASF promoted the stability of survivin mRNA. A strong correlation was observed between the expression of SF2/ASF and survivin in tumor biopsies from NSCLC patients, supporting the concept that survivin expression levels are controlled by SF2/ASF. Furthermore, combined expression of these proteins was associated with prognosis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; This study provides novel data on the mTORC1- and survivin-dependent mechanisms of SF2/ASF-related carcinogenic potential, and shows that SF2/ASF and survivin expression is involved in NSCLC progression. Clin Cancer Res; 16(16); 4113–25. ©2010 AACR.&lt;/p&gt;&lt;/div&gt;
Tacrolimus-resistant SARS-CoV-2-specific T cell products to prevent and treat severe COVID-19 in immunosuppressed patients (2022)

Solid organ transplant (SOT) recipients receive therapeutic immunosuppression that compromises their immune response to infections and vaccines. For this reason, SOT patients have a high risk of developing severe coronavirus disease 2019 (COVID-19) and an increased risk of death from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Moreover, the efficiency of immunotherapies and vaccines is reduced due to the constant immunosuppression in this patient group. Here, we propose adoptive transfer of SARS-CoV-2-specific T cells made resistant to a common immunosuppressant, tacrolimus, for optimized performance in the immunosuppressed patient. Using a ribonucleoprotein approach of CRISPR-Cas9 technology, we have generated tacrolimus-resistant SARS-CoV-2-specific T cell products from convalescent donors and demonstrate their specificity and function through characterizations at the single-cell level, including flow cytometry, single-cell RNA (scRNA) Cellular Indexing of Transcriptomes and Epitopes (CITE), and T cell receptor (TCR) sequencing analyses. Based on the promising results, we aim for clinical validation of this approach in transplant recipients. Additionally, we propose a combinatory approach with tacrolimus, to prevent an overshooting immune response manifested as bystander T cell activation in the setting of severe COVID-19 immunopathology, and tacrolimus-resistant SARS-CoV-2-specific T cell products, allowing for efficient clearance of viral infection. Our strategy has the potential to prevent severe COVID-19 courses in SOT or autoimmunity settings and to prevent immunopathology while providing viral clearance in severe non-transplant COVID-19 cases.
Oculo‐visual abnormalities in Parkinson's disease: Possible value as biomarkers (2018)

Parkinson's disease (PD) is one of the most common neurodegenerative disorders and the second leading cause of dementia worldwide. With an aging population, the prevalence of the disease has dramatically increased. Clinical management has advanced through recent developments in dopaminergic imaging and genetic risk profiling. However, early and accurate diagnosis of the disorder remains a challenge, largely because of the lack of noninvasive and inexpensive reliable diagnostic tests. Besides the well-studied cerebral neurodegeneration that underlies the cardinal symptoms of PD (ie, bradykinesia, tremor, rigidity, and postural instability), ocular changes have also been described in PD, including visual dysfunction, pupil abnormality, lens opacity, and retinal neuronal loss and dysfunction. These ocular pathological processes are related to α-synuclein deposition, and dopamine deficiency in the retina-mirroring the defining pathological features of PD in the brain. Together, these observations support the notion that the eye can serve as a window to the brain, providing clinicians with noninvasive methods to visualize disease. This review focuses on recent advances in the characterization of ocular changes in PD and their promising use as biomarkers in the eye, which can be potentially used for aiding in early diagnosis, tracking disease progression, and valuating novel therapeutic strategies. © 2018 International Parkinson and Movement Disorder Society.
Acetabular Component Positioning in Primary THA via an Anterior, Posterolateral, or Posterolateral-navigated Surgical Technique (2013)

The purpose of this study was to compare the acetabular component alignment in patients undergoing primary total hip arthroplasty (THA) via 3 surgical techniques: direct anterior using intraoperative fluoroscopy, posterolateral using an external alignment guide (posterolateral conventional), and posterolateral using computer navigation (posterolateral navigated). Two surgeons performed the direct, anterior THAs; 2 surgeons performed the posterolateral-conventional THAs; and 1 surgeon performed the posterolateral-navigated THAs. The most recent 110 THAs performed using each approach were reviewed, and Einsel-Bild-Roentgen analysis software was used to measure the acetabular component abduction and anteversion. One-way analysis of variance showed the anterior cohort to have a more horizontal alignment of the acetabular component (P,.001); 90.9% of the acetabular components in the posterolateral- navigated cohort were within 40°610° and 15°610° for both acetabular abduction and anteversion, respectively, vs 70% in the posterolateral-conventional (P,.001), and 68.2% in the anterior cohort (P,.001). The anterior technique using intraoperative fluoroscopy does not improve acetabular positioning compared with the conventional, posterolateral technique.
Composing Ensembles of Pre-trained Models via Iterative Consensus (2022)

Large pre-trained models exhibit distinct and complementary capabilities dependent on the data they are trained on. Language models such as GPT-3 are capable of textual reasoning but cannot understand visual information, while vision models such as DALL-E can generate photorealistic photos but fail to understand complex language descriptions. In this work, we propose a unified framework for composing ensembles of different pre-trained models -- combining the strengths of each individual model to solve various multimodal problems in a zero-shot manner. We use pre-trained models as "generators" or "scorers" and compose them via closed-loop iterative consensus optimization. The generator constructs proposals and the scorers iteratively provide feedback to refine the generated result. Such closed-loop communication enables models to correct errors caused by other models, significantly boosting performance on downstream tasks, e.g. improving accuracy on grade school math problems by 7.5%, without requiring any model finetuning. We demonstrate that consensus achieved by an ensemble of scorers outperforms the feedback of a single scorer, by leveraging the strengths of each expert model. Results show that the proposed method can be used as a general purpose framework for a wide range of zero-shot multimodal tasks, such as image generation, video question answering, mathematical reasoning, and robotic manipulation. Project page: https://energy-based-model.github.io/composing-pretrained-models.
New basic science initiatives for improved understanding of radiation-induced multi-organ dysfunction syndrome (MODS) (2005)

Multi-organ dysfunction syndrome (MODS), which may lead to multi-organ failure (MOF), is a major clinical problem in patients following accidental exposure to ionising radiation (IR). Although inflammatory “one hit” and “two hit” models have recently been proposed to account for the development of MOF, we are only just beginning to understand the complex pathophysiology of IR-induced MODS and MOF. This paper summarises the main findings of a recent panel discussion at “The Advanced Research Workshop on Radiation-induced Multi-organ Involvement and Failure: a challenge for pathogenetic, diagnostic and therapeutic approaches and research”, which was held on 14 November 2003 at the Science Conference Center at Schloss Reisensburg of the University of Ulm. This panel discussion focused on future molecular and clinical research priorities to improve our knowledge regarding possible initiation events following IR exposure that may lead to MODS. Additionally, specific recommendations for improving our understanding of the events that initiate and control MODS were summarised.
Serum deprivation of vascular smooth muscle cells enhances collagen gene expression. (1988)

Vascular smooth muscle cells produce the bulk of connective tissue protein in major arteries. Previously, we demonstrated that collagen synthesis by cultured bovine aortic smooth muscle cells in exponential growth is low and increases as cells approach confluence and growth slows. To evaluate more directly the effects of the proliferative state, subconfluent cultures of smooth muscle cells were incubated in medium supplemented with 0.5% fetal calf serum; under these conditions of growth factor deprivation, cells become quiescent within 72 h. The mRNA levels for type I and III collagens increased markedly within 12 h; at 48 h, they were between 2- and 15-fold higher than in cells growing exponentially. Upon addition of serum to quiescent cultures, cells re-entered the cycle, and collagen mRNA levels decreased. Expression of alpha 1(I), alpha 2(I), and alpha 1(III) mRNAs differed significantly, indicating differential gene regulation. In nuclear run-off assays, changes detected in collagen transcription were insufficient to account for changes in mRNA levels, suggesting additional post-transcriptional sites of control. The inverse response of collagen expression to the proliferative state suggests that exposure of smooth muscle cells in vivo to factors which influence their growth state could have profound effects on the structure of the arterial wall.
Simvastatin and environmental enrichment effect on recognition and temporal order memory after mild-to-moderate traumatic brain injury (2014)

Persistent SO and TO memory deficits follow TBI in animals; Simv and EE seem to be promising therapies of TBI memory deficits.
Expression of structurally diverse Qa-2-encoded molecules on the surface of cloned cytotoxic T lymphocytes. (1984)

Extracts of 125I-labeled cloned murine cytotoxic T lymphocytes (CTL) were immunoprecipitated with alloantisera to the cloned CTL and rabbit antisera to beta-2 microglobulin. Polyacrylamide gel electrophoresis (PAGE) of the specific precipitates revealed, as expected, 125I-labeled components that corresponded to products of class I genes of the major histocompatibility complex (MHC). However, additional class I gene products of relatively low apparent molecular weight (Mr) were also observed. Similar analyses of spleen cells from a variety of MHC-congenic mouse strains suggested that the class I molecules of relatively low Mr are encoded in the Qa-2 region of the MHC, and this was confirmed by immunoprecipitation with a monoclonal antibody to Qa-2. Surprisingly, however, the cell surface Qa-2 molecules of different CTL clones differed in Mr, in isoelectric focusing (IEF) pattern, and in the number of distinguishable molecules expressed per clone: some clones seemed to express only a single Qa-2-encoded molecule while others expressed two distinct ones. Treatment of the immunoprecipitated Qa-2 with endoglycosidase F (Endo F) resulted in a decrease in Mr of approximately 5,000-6,000, corresponding to the expected loss of N-linked oligosaccharides, but the decrease did not eliminate structural variability among the clones. Structural diversity of the Qa-2-encoded molecules expressed on CTL could arise because CTL clones differ (a) in the particular Qa-2 genes they express, (b) in the way they splice Qa-2 gene transcripts or, perhaps, (c) in Endo F-resistant oligosaccharides on their Qa-2 molecules.
Impact of rectal balloon‐filling materials on the dosimetry of prostate and organs at risk in photon beam therapy (2013)

The use of rectal balloon in radiotherapy of prostate cancer is shown to be effective in reducing prostate motion and minimizing rectal volume, thus reducing rectal toxicity. Air-filled rectal balloon has been used most commonly, but creates dose perturbation at the air-tissue interface. In this study, we evaluate the effects of rectal balloon-filling materials on the dose distribution to the target and organs at risk. The dosimetric impact of rectal balloon filling was studied in detail for a typical prostate patient, and the general effect of the balloon filling was investigated from a study of ten prostate patients covering a wide range of anterior-posterior and left-right separations, as well as rectal and bladder volumes. Hounsfield units (HU) of the rectal balloon filling was changed from -1000 HU to 1000 HU at an interval of 250 HU, and the corresponding changes in the relative electron density (RED) was calculated. For each of the HU of the rectal balloon filling, a seven-field IMRT plan was generated with 6 MV and 15 MV photon beams, respectively. Dosimetric evaluation was performed with the AAA algorithm for inhomogeneity corrections. A detailed study of the rectal balloon filling shows that the GTV, PTV, rectal, and bladder mean dose decreased with increasing values of RED in the rectal balloon. There is significant underdosage in the target volume at the rectum-prostate interface with an air-filled balloon as compared to that with a water-filled balloon for both 6 MV and 15 MV beams. While the dosimetric effect of the rectal balloon filling is reduced when averaged over ten patients, generally an air-filled balloon results in lower minimum dose and lower mean dose in the overlap region (and possibly the PTV) compared to those produced by water-filled or contrast-filled balloons. Dose inhomogeneity in the target volume is increased with an air-filled rectal balloon. Thus a water-filled or contrast-filled rectal balloon is preferred to an air-filled rectal balloon in EBRT of prostate treatment.