gebhart/patrepeval huggingface dataset:
Key actors in cancer therapy: epigenetic modifiers (2019)

Epigenetic reprogramming plays a crucial role in the tumorigenicity and maintenance of tumor-specific gene expression that especially occurs through DNA methylation and/or histone modifications. It has well-defined mechanisms. It is known that alterations in the DNA methylation pattern and/or the loss of specific histone acetylation/methylation markers are related to several hallmarks of cancer, such as drug resistance, stemness, epithelial-mesenchymal transition, and metastasis. It has also recently been highlighted that epigenetic alterations are critical for the regulation of the stemlike properties of cancer cells (tumor-initiating cells; cancer stem cells). Cancer stem cells are thought to be responsible for the recurrence of cancer which makes the patient return to the clinic with metastatic tumor tissue. Hence, the dysregulation of epigenetic machinery represents potential new therapeutic targets. Therefore, compounds with epigenetic activities have become crucial for developing new therapy regimens (e.g., antimetastatic agents) in the fight against cancer. Here, we review the epigenetic modifiers that have already been used in the clinic and/or in clinical trials, related preclinical studies in cancer therapy, and the smart combination strategies that target cancer stem cells along with the other cancer cells. The emerging role of epitranscriptome (RNA epigenetic) in cancer therapy has also been included in this review as a new avenue and potential target for the better management of cancer-beneficial epigenetic machinery.
Social Media and Web Sensing on Interior and Urban Design (2022)

Social media and web sites provide an access to pub-lic opinions on certain aspects and therefore play an important role in getting insights on targeted audiences. Designers have been investigating how to use them for grasping social feelings and needs associated with the arrangement of spaces that surround people in everyday life to find inspiration and come up with ideas for adaptive designs. Following this, we propose a novel design-oriented tool-set that retrieves and analyses online public information from Twitter and focused content from relevant web sites. We present the data collection pipeline and multilingual analysis algorithms like concept extraction and sentiment analysis on interior and urban design. Finally, we showcase an application of the proposed tool-set within two case studies.
Local immune responses to tuberculin skin challenge in Mycobacterium bovis BCG-vaccinated baboons: a pilot study of younger and older animals (2021)

Individuals over the age of 65 are highly susceptible to infectious diseases, which account for one-third of deaths in this age group. Vaccines are a primary tool to combat infection, yet they are less effective in the elderly population. While many groups have aimed to address this problem by studying vaccine-induced peripheral blood responses in the elderly, work from our lab and others demonstrate that immune responses to vaccination and infectious challenge may differ between tissue sites and the periphery. In this pilot study, we established an in vivo delayed-type hypersensitivity model of Mycobacterium bovis BCG vaccination and tuberculin skin test in two adult and two aged baboons. Vaccination generates BCG-specific immune cells that are recruited to the skin upon tuberculin challenge. We tested short term recall responses (8 weeks post-vaccination) and long term recall responses (25 weeks post-vaccination) by performing skin punch biopsies around the site of tuberculin injection. In short term recall responses, we found increased oxidation and decreased production of immune proteins in aged baboon skin at the site of TST challenge, in comparison to adult skin. Differences between adult and aged animals normalized in the long term response to tuberculin. In vitro, aged peripheral blood mononuclear cells had increased migration and functional responses to antigen-specific stimulation, suggesting that age-related changes in the tissue in vivo impairs aged immune recall responses to antigenic challenge. These findings highlight the impact of age-associated changes in the local tissue environment in memory recall responses, which may be more broadly applied to the study of other tissues. Moreover, these findings should be considered in future studies aimed at understanding and improving aging immune responses to vaccination and tissue challenge.
Acrylamide Production in Autoclaved Rodent Feed (2018)

Sterilization of rodent feed by steam autoclaving is a common practice in many research institutions. Often we only consider the beneficial effects of this process-the reduction of microbial contamination-and forget that the high temperatures and pressures can have negative effects on diet quality. The purpose of our study was to assess both the physical and chemical changes to a standard rodent feed autoclaved at multiple sterilization temperatures and the effects of the treated diets on mice. Pelleted NIH31 rodent feed was autoclaved at 4 sterilization temperatures (230, 250, 260, and 270 °F). Feed pellet hardness and the acrylamide concentrations of the diets were tested and compared with irradiated NIH31 feed. Study diets were fed to mice for 28 d, after which tissue samples were collected for analysis of acrylamide, glycidamide (the active metabolite of acrylamide), and genotoxicity. Both feed pellet hardness and acrylamide concentration increased with increasing sterilization temperatures; however, neither affected feed intake or body weight gain. Plasma acrylamide and glycidamide were significantly elevated only in mice fed NIH31 diet autoclaved at 270 °F compared with the irradiated feed, whereas urine acrylamide and glycidamide metabolites were significantly elevated in most autoclaved diets. Liver DNA adducts, which correlate with genotoxicity, were significantly elevated in all autoclaved diets compared with the irradiated diet. Institutions that autoclave their animal diets should carefully consider the temperatures necessary to achieve feed sterilization and the type of studies in which these autoclaved diets are used.
Deficiency of the Copper Chaperone for Superoxide Dismutase Increases Amyloid-β Production (2010)

The copper chaperone for superoxide dismutase (CCS) binds to both the β-site AβPP cleaving enzyme (BACE1) and to the neuronal adaptor protein X11α. BACE1 initiates AβPP processing to produce the amyloid-β (Aβ) peptide deposited in the brains of Alzheimer's disease patients. X11α also interacts directly with AβPP to inhibit Aβ production. However, whether CCS affects AβPP processing and Aβ production is not known. Here we show that loss of CCS increases Aβ production in both CCS knockout neurons and CCS siRNA-treated SHSY5Y cells and that this involves increased AβPP processing at the BACE1 site.
The value of intraoperative optical coherence tomography imaging in vitreoretinal surgery (2014)

The role of iOCT in vitreoretinal surgery continues to be defined by active research and enhancements to integrative technologies. Further research is needed to better define the specific applications of iOCT that impact patient outcomes and surgical decision-making. Future advancements in integrative systems, OCT-friendly instrumentation, and software algorithms will further expand the horizon of iOCT in the vitreoretinal surgical theater. As OCT transformed the clinical management of the vitreoretinal conditions, iOCT has the potential to be a paradigm-shifting technology in the operating room.
CT Colonography for the Detection of Nonpolypoid Adenomas: Sensitivity Assessed With Restricted National CT Colonography Trial Criteria (2014)

In this large screening population, nonpolypoid adenomas had a very low prevalence (<1%), and advanced pathologic features were uncommon in polyps<10 mm in diameter. Most nonpolypoid adenomas are technically visible at CTC. The prospective sensitivity is similar to that for polypoid adenomas when the interpretation combines both 2D and 3D review.
State-of-the-Art Strategies for the Vascularization of Three-Dimensional Engineered Organs (2019)

Engineering three-dimensional (3D) implantable tissue constructs is a promising strategy for replacing damaged or diseased tissues and organs with functional replacements. However, the efficient vascularization of new 3D organs is a major scientific and technical challenge since large tissue constructs or organs require a constant blood supply to survive in vivo. Current approaches to solving this problem generally fall into the following three major categories: (a) cell-based, (b) angiogenic factor-based, and (c) scaffold-based. In this review, we summarize state-of-the-art technologies that are used to develop complex, stable, and functional vasculature for engineered 3D tissue constructs and organs; additionally, we have suggested directions for future research.
DR-BiLSTM: Dependent Reading Bidirectional LSTM for Natural Language\n Inference (2018)

We present a novel deep learning architecture to address the natural language\ninference (NLI) task. Existing approaches mostly rely on simple reading\nmechanisms for independent encoding of the premise and hypothesis. Instead, we\npropose a novel dependent reading bidirectional LSTM network (DR-BiLSTM) to\nefficiently model the relationship between a premise and a hypothesis during\nencoding and inference. We also introduce a sophisticated ensemble strategy to\ncombine our proposed models, which noticeably improves final predictions.\nFinally, we demonstrate how the results can be improved further with an\nadditional preprocessing step. Our evaluation shows that DR-BiLSTM obtains the\nbest single model and ensemble model results achieving the new state-of-the-art\nscores on the Stanford NLI dataset.\n
Abstract IA09: Comprehensive genomic characterization of head and neck squamous cell carcinomas (2017)

Abstract Large and comprehensive genomic analyses of head and neck squamous cell carcinomas (HNSCC) are greatly increasing our understanding of the heterogeneity of this disease and identifying the key genomic changes that drive these tumors. HNSCC tumors associated with HPV are distinct from HNSCC disease linked to tobacco exposure (HPV-positive versus HPV-negative). HPV- tumors are characterized by: 1) amplification of receptor tyrosine kinases (RTK); 2) genomic loss of TP53 and loss of CKDN2A/RB1 by a variety of mechanisms including truncating mutation, deletion, and/or alternative splicing; 3) amplification of CCND1/CDK4/CDK6; 4) activation of NFE2L2/KEAP1/CUL3; and 5) loss of NOTCH1/FAT1/AJUBA. In contrast, HPV-positive HNSCCs harbor: 1) RTK amplification; 2) FGFR2/3 mutations and/or FGFR3-TACC3 fusions; 3) CDKN2A loss; and 4) E2F1 amplification. Interestingly, activating mutations in the PIK3CA oncogene are found in approximately one third of HPV-negative HNSCC and in over fifty percent of HPV-positive tumors. Mutually exclusive mutations in RAS family genes, specifically RHOA, KRAS, and HRAS, are present but infrequently found in HNSCC (6% of TCGA cases). Amplification of chromosome 3q, a region containing the TP63, SOX2, and PIK3CA genes, is seen in the majority of both HPV-negative and HPV-positive HNSCC. HPV-negative HNSCCs demonstrate clear evidence of molecular heterogeneity, as demonstrated by expression profiling studies indicating diverse biologic subclasses within HPV-negative disease, including a class of tumors without EGFR amplification and/or overexpression, previously termed “atypical” HNSCCs, which consist of approximately 20% of HPV-negative cases and the majority of HPV-positive HNSCCs. An intriguing mutational pattern identified by TCGA was a subset of HPV-negative HNSCC originating in the oral cavity with few to no copy-number alterations statistically enriched for HRAS, CASP8, and PIK3CA mutations and lack of TP53 mutation. With increasing genetic profiling of HNSCC cell lines and patient-derived xenografts, there is increasing opportunity to rationally select preclinical models to test specific precision medicine hypotheses. Citation Format: Jennifer R. Grandis. Comprehensive genomic characterization of head and neck squamous cell carcinomas [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr IA09.
Monkeypox Virus Infection in Humans across 16 Countries — April–June 2022 (2022)

In this case series, monkeypox manifested with a variety of dermatologic and systemic clinical findings. The simultaneous identification of cases outside areas where monkeypox has traditionally been endemic highlights the need for rapid identification and diagnosis of cases to contain further community spread.
Reduced N-Acetylaspartate to Creatine Ratio in the Posterior Cingulate Correlates with Cognition in Alzheimer's Disease following Four Months of Rivastigmine Treatment (2014)

This positive correlation between changes in NAA/Cr and changes in cognitive performance suggests that the NAA/Cr ratio could be an objective indicator of a response to rivastigmine treatment.
Site‐Selective Iron(III) Chloride‐Catalyzed Arylation of 4‐Aryl‐4‐methoxy‐2,5‐cyclohexadienones for the Synthesis of Polyarylated Phenols (2016)

Abstract The iron(III) chloride‐catalyzed Friedel–Crafts arylation of 4‐aryl‐4‐methoxy‐2,5‐cyclohexadienones, which were easily prepared by the phenyliodine(III) diacetate (PIDA)‐mediated oxidation of 4‐arylphenols in methanol, proceeded site‐selectively to form meta ‐terphenyl (2,4‐diarylphenol) derivatives in good yields. The subsequent PIDA‐mediated oxidation and iron(III) chloride‐catalyzed Friedel–Crafts arylation of the resulting products gave the corresponding 2,4,6‐triarylphenol derivatives. The present method provides useful highly substituted polyarylated compounds. magnified image
Vascular compliance in hypertension (1988)

Pulse contour analysis was used to determine systemic arterial vascular compliance in hypertensive (HT) and normotensive (NT) subjects. In seven hypertensives aged 43-58 yrs (mean age 52.1+or-5.5 yrs) and seven normotensives aged 33-59 yrs (mean age 43.7+or-9.9 yrs) both large artery (C1) and distal arterial (C2) compliance were determined from a peripheral arterial pressure waveform and cardiac output. Age differences were not statistically significant. Mean arterial pressure was 29% higher in HT (p<0.001). Cardiac output was 12% higher and heart rate was 6% lower in HT, but these differences were not significant. Systemic vascular resistance was 17% higher in HT (NS), while proximal and distal arterial compliance were 15% and 70% lower, respectively, in HT compared to NT. Only the difference in C2 was significant (p<0.02). Thus, distal vascular compliance may be a clinically useful parameter for evaluating hypertensive subjects before and during therapeutic intervention.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Recherche du couplage fort lumière-matière dans les microcavités à base de GaN (2003)

International audience
Sex and Tamoxifen confound murine experimental studies in cardiovascular tissue engineering (2021)

Tissue engineered vascular grafts hold promise for the creation of functional blood vessels from biodegradable scaffolds. Because the precise mechanisms regulating this process are still under investigation, inducible genetic mouse models are an important and widely used research tool. However, here we describe the importance of challenging the baseline assumption that tamoxifen is inert when used as a small molecule inducer in the context of cardiovascular tissue engineering. Employing a standard inferior vena cava vascular interposition graft model in C57BL/6 mice, we discovered differences in the immunologic response between control and tamoxifen-treated animals, including occlusion rate, macrophage infiltration and phenotype, the extent of foreign body giant cell development, and collagen deposition. Further, differences were noted between untreated males and females. Our findings demonstrate that the host-response to materials commonly used in cardiovascular tissue engineering is sex-specific and critically impacted by exposure to tamoxifen, necessitating careful model selection and interpretation of results.
Revisiting localized deformation in sand with complex systems (2013)

Complex systems techniques are used to analyse X-ray micro-CT measurements of grain kinematics in Hostun sand under triaxial compression. Network nodes with the least mean shortest path length to all other nodes, or highest relative closeness centrality, reside in the region where the persistent shear band ultimately develops. This trend, whereby a group of grains distinguishes themselves from the rest in the sample, remarkably manifests from the onset of loading. The shear band's boundaries and thickness, evident from the network communities' borders and essentially constant mean size, provide corroborating evidence of early detection of strain localization. Our findings raise the possibility that the formation and the location of the persistent shear band may be decided in the nascent stages of loading, well before peak shear stress. Grain-scale digital image correlation strain measurements and statistical tests confirm the results are robust. Moreover, the trends are unambiguously reproduced in a discrete element simulation of plane strain compression.
Method of using infrared radiation for assembling a first component with a second component (2023)

A method of assembling a first component for assembly with a second component involves a heating device which includes an enclosure having a cavity for inserting a first component. An array of infrared energy generators is disposed within the enclosure. At least a portion of the first component is inserted into the cavity, exposed to infrared energy and thereby heated to a temperature wherein the portion of the first component is sufficiently softened and/or expanded for assembly with a second component.
Use of GSO for inelastic gamma-ray spectroscopy measurements in the borehole (2002)

A novel inelastic gamma-ray spectroscopy tool using GSO (gadolinium oxyorthosilicate) detectors has been optimized for oil saturation measurements in the borehole. The use of GSO detectors has made it possible to perform gamma-ray spectroscopy in a small diameter tool at elevated temperatures. The design was optimized by taking into account the properties of the GSO scintillator in addition to other physical processes that affect the statistics of the measurement. The ability to compensate the oil saturation measurement for varying borehole fluid has also been demonstrated. The large neutron cross section of the gadolinium in the scintillation crystal, its second decay constant, and the desired precision of the coil saturation measurement were found to have important consequences in the tool design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Liquid Crystal based Tunable Photonic Devices for Emission or Detection around 1.55 μm (2021)

International audience
Customizable 3D-printed architecture with ZnO-based hierarchical structures for enhanced photocatalytic performance (2018)

ZnO-based hierarchical structures including nanoparticles (NPs), nanorods (NRs) and nanoflowers (NFs) on a 3D-printed backbone were effectively fabricated via the combination of the fused deposition modelling (FDM) 3D-printing technique and hydrothermal reaction. The photocatalytic performance of the ZnO-based hierarchical structures on the 3D-backbone was verified via the degradation of the organic pollutant methylene blue, which was monitored by UV-vis spectroscopy. The new photocatalytic architectures used in this investigation give an effective approach and wide applicability to overcome the limitation of photocatalysts such as secondary removal photocatalyst processes.
PD-L1/L2 tumor profile and long-term survival in mRCC patients after intratumoral administration of a cell-based allogeneic immune enhancer. (2016)

e14531 Background: Initial data from a Phase I/II study in patients (pts) with recently diagnosed metastatic renal cell carcinoma (mRCC) demonstrated that intratumoral administration of a cell-based immune enhancer (proinflammatory allogeneic DCs aimed to recruit and activate endogenous ”bystander” DCs) before nephrectomy was associated with a prominent intratumoral infiltration of CD8+ T cells in a majority of pts. Methods: Long-term survival as well as data on PD-L1/L2 tumor profile and tumor response after subsequent sunitinib treatment has been studied. Results: All evaluated clear-cell tumor samples (n = 8) exhibited a positive and usually general expression of PD-L2 that correlated positively in intensity with degree of CD8+ T cell infiltration while PD-L1 expression was absent in all tumor samples. Two out of 3 pts who to date have received subsequent treatment with sunitinib have experienced an objective tumor response. One patient exhibited a sarcomatoid tumor histology and another patient with 4 brain metastases responded with a complete disappearance of all 4 brain lesions and is still free from CNS-lesions 28 months after initiation of Sunitinib. Median OS for MSKCC intermediate risk (n = 5) or high risk pts (n = 6) is still not reached but is currently (01FEB2016) 37.5 and 28.2 months, respectively. Conclusions: The current mOS has by far surpassed reported mOS of 15.2 and 9.0 months in comparable intermediate and high-risk pts with recently diagnosed mRCC receiving upfront mono-therapy with sunitinib. The objective tumor responses seen in two pts after addition of sunitinib is surprising since historical data indicate that brain metastases as well as sarcomatoid transformation are higly resistant to sunitinib treatment. Taken together, our findings indicate that intratumoral administration of an off-the-shelf immune enhancer consisting of proinflammatory allogeneic DCs induces a CTL-mediated anti-tumor response that may prolong survival in mRCC-patients. Data on patients who have received additional treatment with sunitinib (known to downregulate myeloid-derived suppresor cell number and function) indicate a synergistic anti-tumoral effect. Clinical trial information: NCT01525017.
Analysis and comparison of variations in double edge triggered flip-flops (2014)

In this paper, the impact of variations on the most representative double-edge triggered flip-flop (FF) topologies is comparatively evaluated in 65-nm CMOS. The analysis explicitly considers fundamental sources of variations such as process, voltage and temperature (PVT) variations. For each FF topology, the variations of the performance, the energy per cycle and the leakage power are statistically evaluated through Monte Carlo simulations. The analysis explicitly includes the important impact of layout parasitics in different respects. First, they are accounted for in the circuit optimization loop, rather than being considered an afterthought. In addition, interconnect variations are explicitly considered in the statistical characterization of the flip-flops. Results for the different FF topologies are compared to identify the potential advantages and drawbacks of each topology. To gain an insight into the impact of transistor sizing and load, each FF topology is analyzed under a wide range of design targets and loads. The conclusions of the analysis are a useful tool to assist the designer in the preliminary variation budgeting before detailed circuit design, as well as in selecting the most appropriate topology for a targeted application.