gebhart/patrepeval huggingface dataset:
Histone Modification Profiling in Normal and Transformed Human Embryonic Stem Cells Using Micro Chromatin Immunoprecipitation, Scalable to Genome-Wide Microarray Analyses (2013)

Comparing normal human embryonic stem cells (hESCs) to those that have acquired cellular properties of neoplasm provides a unique opportunity to study the distinguishing molecular features of human cellular transformation. As global alterations in the epigenetic landscape are a common feature of cancer, we sought to investigate the loci-specific and global differences between normal and transformed hESCs using ChIP-PCR and ChIP-microarray (also known as ChIP-chip). Here, specific emphasis was placed on optimizing ChIP for low cell numbers (termed micro-ChIP; μChIP) towards applications where the target population is rare, such as the case for somatic human tumors containing a low frequency of cancer stem cell populations and for single-colony analysis of embryonic and induced pluripotent stem cells emerging from initial derivation. Using these methods, we suggest that μChIP-PCR and microarray analysis is thus a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer, and regenerative medicine where target populations regulating the biological process can only be isolated in small numbers.
Compass orientation of sockeye salmon fry from a complex river system (1981)

Sockeye salmon (Oncorhynchus nerka) fry from the Weaver Creek – Harrison Lake population were tested to determine whether they exhibited directional orientation in the absence of water flow. The fry oriented in a generally north-northeast direction. The presence of the moon greatly enhanced the strength of the northward orientation response, and the moon may have provided the fry with guidance information. Tests with newly emerged fry indicated little or no response to a directionally altered magnetic field. Both the passage of time and exposure to Harrison River – Harrison Lake water enhanced the compass orientation response, implying that an inherited response is triggered by environmental and temporal cues.
Fabrication of Y2O3:Bi3+,Eu3+ Fluorescent Nanosheet Films By Electrophoretic Deposition (2016)

Spectral down-shifters convert near-UV light, to which silicon solar cells typically have low sensitivity, to visible light that solar cells can convert to electric power. They can therefore improve the photoelectric conversion efficiency of the solar cells. Y 2 O 3 :Bi 3+ ,Eu 3+ nanosheets absorb near-UV light and emit red light. The nanosheets possess high photostability under the continuous near-UV excitation. In this study, we make efforts to fabricate Y 2 O 3 :Bi 3+ ,Eu 3+ fluorescent nanosheet films on ITO-coated glass substrates by electrophoretic deposition. Bi(NO 3 ) 3 ･5H 2 O (0.004 mmol) was dissolved in ethylene glycol (2.6 mL). Y(NO 3 ) 3 ･6H 2 O (0.956 mmol) and Eu(NO 3 ) 3 ･6H 2 O (0.040 mmol) were dissolved in ultrapure water (30 mL). The aqueous solution was added to the ethylene glycol solution, and then the mixed solution was mixed with triethylamine (3 mL). The total volume of the suspension was adjusted to 40 mL by adding ultrapure water, and the resulting suspension was heated in an autoclave at 160 °C . After centrifugation and freeze-drying, the powdered product was heated to 600 °C and kept at that temperature for 2 h to obtain calcined sample. The calcined sample was mixed with an aqueous solution of trisodium citrate, and stirred for 2 h. Citrate-modified nanosheets were re-dispersed to an NaOH aqueous solution (pH=11). An aqueous emulsion of silicone-modified acrylic resin was added to the nanosheet suspension as a binder. A nanosheet film was fabricated on an ITO-coated glass substrate at the anode side by application of a constant voltage in the prepared suspension. The absolute values of zeta potentials of Y 2 O 3 : Bi 3+ ,Eu 3+ nanosheets dispersed in ultrapure water increased after modification with citrate ions. The increase in zeta potentials verifies that citrate ions act as a stabilizing agent to prevent aggregation of the nanosheets. The deposited film exhibited red luminescence under UV light. According to SEM observation, the film was composed of Y 2 O 3 : Bi 3+ ,Eu 3+ nanosheets and nanoparticles of silicone-modified acrylic resin.
Does where you Gaze on an Image Affect your Perception of Quality? Applying Visual Attention to Image Quality Metric (2007)

The aim of an objective image quality assessment is to find an automatic algorithm that evaluates the quality of pictures or video as a human observer would do. To reach this goal, researchers try to simulate the Human Visual System (HVS). Visual attention is a main feature of the HVS, but few studies have been done on using it in image quality assessment. In this work, we investigate the use of the visual attention information in their final pooling step. The rationale of this choice is that an artefact is likely more annoying in a salient region than in other areas. To shed light on this point, a quality assessment campaign has been conducted during which eye movements have been recorded. The results show that applying the visual attention to image quality assessment is not trivial, even with the ground truth.
Frequency response as a surrogate eigenvalue problem in topology optimization (2017)

Summary This article discusses the use of frequency response surrogates for eigenvalue optimization problems in topology optimization that may be used to avoid solving the eigenvalue problem. The motivation is to avoid complications that arise from multiple eigenvalues and the computational complexity associated with computation of eigenvalues in very large problems. Copyright © 2017 John Wiley &amp; Sons, Ltd.
Transfer loss in acoustic charge transport devices due to electron traps induced by proton bombardment (1989)

An experiment is described in which electron traps are introduced into an acoustic charge transport (ACT) channel in a controlled manner by proton bombardment. The characteristics of the electron traps, including activation energies, capture cross sections, and concentration profiles, are measured using deep-level transient spectroscopy. The transfer performance of the ACT device is evaluated through measurements of the periodic pulse degradation and the frequency response characteristics of the device. Comparisons are made with the theoretically predicted dependence of transfer loss on trap parameters. The use of traps induced by proton bombardment allows the effects of trapping loss to be isolated from the other response characteristics of the ACT device and therefore provides a detailed picture of the behavior of trap-related transfer loss. The results of this study illustrate the dependence of trapping loss on trap concentration and provide a means for correlating ACT device response characteristics to specific trapping levels.
Incentive-Based Mechanism for Truthful Occupant Comfort Feedback in Human-in-the-Loop Building Thermal Management (2017)

Energy inefficiency and underlying occupant discomfort associated with building thermal management systems have led to the development of a human-in-the-loop control system. Minimizing total energy use and maximizing comfort of all the occupants present is the major objective of such system based on human comfort feedback. However, the approaches proposed so far lack a built-in mechanism to elicit truthful comfort feedback from the occupants. In this paper, we utilize an incentive-based mechanism design framework to elicit true thermal comfort feedback (function) from the occupants present. This requires the building occupants to “purchase” or spend credits to achieve their personalized comfort levels within their zone of occupancy. The comfort pricing policy has been derived as an extension of the Vickrey-Clarke-Groves pricing. It ensures incentive compatibility of the mechanism, which implies that an occupant acting in self-interest cannot stand to benefit by declaring their comfort function untruthfully. This would hold irrespective of the thermal comfort choices made by the other occupants present in the building. We further propose as to how this mechanism could be implemented in practice with limited comfort feedback complexity, where the building operator would iteratively learn and refine the occupants comfort function based on simple 2-D comfort feedback (preferred temperature setting, and willingness-to-pay value) by the occupant. Simulations using parameters based on our Watervliet experimental facility demonstrates the effectiveness of the proposed mechanism.
Model of Unidirectional Transluminal Gene Transfer (2004)

Gene transfer assays in vitro are poor indicators of transduction efficacy observed in vivo. We designed and optimized an intermediate model for assessing and quantifying unidirectional transduction ex vivo. The model enables simultaneous transmucosal evaluation of up to 96 different variables under the same tissue conditions. We show that the model is versatile and suitable for use with different vectors (adenovirus and AAV), different reporter genes (beta-galactosidase and green fluorescent protein), and viscera with various tissue features such as peritoneum and urothelium. Ex vivo transduction assays may correlate better with in vivo gene transfer results. Because the experimental model described here can be performed in small samples, it may enable translational applications in tissues of human origin.
Modeles de sequences de longueurs variables : application au traitement du langage ecrit et de la parole (1996)

L'efficacite des algorithmes utilises pour le traitement automatique de la parole et du langage naturel depend de la bonne definition des formes supposees structurer le materiau linguistique. En regle generale, cette structure sous-jacente n'est pas connue, de sorte qu'elle doit etre definie a priori, ou alors inferee a partir de grosses bases de donnees. Le modele multi gramme releve de cette derniere approche : il constitue un outil statistique permettant de detecter des motifs recurrents dans des suites d'observations. Il est particulierement bien approprie pour la description des phenomenes linguistiques, ou les processus de redondance mis en œuvre se traduisent par l'utilisation de sequences de tailles variables, aussi bien au niveau acoustique, phonetique que syntaxique. La bonne detection de ces sequences devrait pouvoir servir avantageusement certaines applications relevant du traitement automatique du langage et de la parole. Les travaux presentes dans cette these permettent d'explorer les possibilites offertes par l'approche multi gramme pour la modelisation statistique du langage, pour la recherche d'un jeu minimal d'unites formelles de synthese, pour la transcription orthographique-phonetique, et pour la definition d'unites acoustiques utilisables en reconnaissance de la parole continue.
Co/Ni(111) superlattices studied by microscopy, x-ray absorption, andab initiocalculations (2012)

We explore the origins of perpendicular magnetic anisotropy in epitaxial and textured Co/Ni(111) superlattices using a combination of thin-film growth, structural characterization, x-ray magnetic circular dichroism (XMCD), and ab initio calculations. Transmission electron microscopy and x-ray diffraction experiments allow us to show that the ``bulk'' magnetoelastic contribution to the total magnetic energy is small compared to the interface anisotropy. The magnetic properties are studied by using XMCD at the Co and Ni ${L}_{2,3}$ edges. Hysteresis loops performed at the Co ${L}_{3}$ edge confirm the perpendicular magnetization for Co thicknesses up to four monolayers. The spin and orbital moments were deduced using the XMCD sum rules. The results are explained by considering two kinds of magnetic moments for Co, distinguishing the interfaces from the rest of the layers. Both effective spin and orbital moments of Co atoms are found to be enhanced at the Co-Ni interfaces, whereas the magnetic moment of Co surrounded by Co is similar to the bulk value. Ab initio calculations allow us to show a strong enhancement of the dipole operator contribution on Co atoms at the interface that is partly responsible for this high effective spin moment at the interface. Such a moment enhancement is not observed for Ni, with the dipole operator contribution being close to zero. Finally, we observed a very surprising proportionality between the effective spin and orbital moments, independent of the absorption edge or deposition technique used. We assign this peculiar behavior to the fact that the magnetic dipole operator involved in the sum rules is closely linked to the increase of the Co orbital moment at the interface. Based on XMCD results obtained on both molecular beam epitaxy and sputter-deposited samples, this link allows us to show the extreme sensitivity of the perpendicular anisotropy with the chemical ordering at the interface.
Low-temperature GaN growth on silicon substrates by single gas-source epitaxy and photo-excitation (2005)

We report a unique low-temperature growth method for epitaxial GaN on Si(111) substrates via a ZrB2(0001) buffer layer. The method utilizes the decomposition of a single gas-source precursor (D2GaN3)3 on the substrate surface to form GaN. The film growth process is further promoted by irradiation of ultraviolet light to enhance the growth rate and ordering of the film. The best epitaxial film quality is achieved at a growth temperature of 550°C with a growth rate of 3nm∕min. The films exhibit intense photoluminescence emission at 10K with a single peak at 3.48eV, indicative of band-edge emission for a single-phase hexagonal GaN film. The growth process achieved in this study is compatible with low Si processing temperatures and also enables direct epitaxy of GaN on ZrB2 in contrast to conventional metalorganic chemical vapor deposition based approaches.
Get with the guidelines: management of chronic obstructive pulmonary disease in emergency departments in Europe and Australasia is sub-optimal (2021)

Background Exacerbations of chronic obstructive pulmonary disease (COPD) are common in emergency departments (ED). Guidelines recommend administration of inhaled bronchodilators, systemic corticosteroids and antibiotics along with non-invasive ventilation (NIV) for patients with respiratory acidosis. Aim To determine compliance with guideline recommendations for patients treated for COPD in ED in Europe (EUR) and South East Asia/Australasia (SEA) and to compare management and outcomes. Methods In each region, an observational prospective cohort study was performed that included patients presenting to ED with the main complaint of dyspnoea during three 72-h periods. This planned sub-study included those with an ED primary discharge diagnosis of COPD. Data were collected on demographics, clinical features, treatment, disposition and in-hospital mortality. We determined overall compliance with guideline recommendations and compared treatments and outcome between regions. Results A total of 801 patients was included from 122 ED (66 EUR and 46 SEA). Inhaled bronchodilators were administered to 80.3% of patients, systemic corticosteroids to 59.5%, antibiotics to 44 and 60.6% of patients with pH Conclusion Compliance with guideline recommended treatments, in particular administration of corticosteroids and NIV, was sub-optimal in both regions. Improved compliance has the potential to improve patient outcome.
Data from T-cell Landscape in a Primary Melanoma Predicts the Survival of Patients with Metastatic Disease after Their Treatment with Dendritic Cell Vaccines (2023)

&lt;div&gt;Abstract&lt;p&gt;Tumor-infiltrating lymphocytes appear to be a predictor of survival in many cancers, including cutaneous melanoma. We applied automated multispectral imaging to determine whether density and distribution of T cells within primary cutaneous melanoma tissue correlate with survival of metastatic melanoma patients after dendritic cell (DC) vaccination. CD3&lt;sup&gt;+&lt;/sup&gt; T cell infiltration in primary tumors from 77 metastatic melanoma patients was quantified using the ratio of intratumoral versus peritumoral T-cell densities (I/P ratio). Patients with longer survival after DC vaccination had stronger T-cell infiltration than patients with shorter survival in a discovery cohort of 19 patients (&lt;i&gt;P&lt;/i&gt; = 0.000026) and a validation cohort of 39 patients (&lt;i&gt;P&lt;/i&gt; = 0.000016). I/P ratio was the strongest predictor of survival in a multivariate analysis including M substage and serum lactate dehydrogenase level. To evaluate I/P ratio as a predictive biomarker, we analyzed 19 chemotherapy-treated patients. Longer survival times of DC-vaccinated compared with chemotherapy-treated patients was observed for high (&lt;i&gt;P&lt;/i&gt; = 0.000566), but not low (&lt;i&gt;P&lt;/i&gt; = 0.154) I/P ratios. In conclusion, T-cell infiltration into primary melanoma is a strong predictor of survival after DC vaccination in metastatic melanoma patients who, on average, started this therapy several years after primary tumor resection. The infiltration remains predictive even after adjustment for late-stage prognostic markers. Our findings suggest that the I/P ratio is a potential predictive biomarker for treatment selection. &lt;i&gt;Cancer Res; 76(12); 3496–506. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
TL1A, a TNF-like molecule, regulates the differentiation of human TH17 cells (133.21) (2009)

Abstract TL1A is a member of the TNF superfamily that mediates a strong co-stimulation of TH1 cells by enhancing IFN-γ production by CD4+ T cells. The expression of TL1A is increased in inflamed mucosa of Crohn's Disease patients and in murine models of ileitis. We have shown that TL1A is induced in human antigen-presenting cells (APCs) by Fc γ Receptor but not TLR signaling. Furthermore, neutralizing TL1A antibodies attenuate colitis by attenuating TH1 and TH17 responses in a chronic model of colitis. However, it remains to be elucidated if TL1A enhances de novo differentiation of TH17 cells. Here we demonstrate that FcγR signaling in APCs leads to the concomitant induction of TL1A, IL-6, TGF-β, and IL-23. TL1A, in combination with TGF-β and IL-6, promotes the differentiation of human TH17 cells from naive CD4+ T cells and leads to a unique cell population of IL-17/IFN-γ producing TH17 cells. Furthermore, TL1A enhances the IL-17 production by committed CD45RO+CCR6+ TH17 cells. TL1A also enhances the induction of RORA mRNA but not RORC mRNA. However, the enhanced RORA mRNA levels corresponded to an increase in IL-17 mRNA under the same conditions suggesting that enhancement of RORA mRNA by TL1A is sufficient to enhance production of IL-17. Our findings establish an important role of TL1A in promoting human TH17 cell differentiation and function and may provide a potential target for therapeutic intervention in TH17 driven diseases.
Human Telomerase RNA Expression and MIB-1 (Ki-67) Proliferation Index Distinguish Hemangioblastomas from Metastatic Renal Cell Carcinomas (1997)

Hemangioblastomas are low-grade, capillary rich neoplasms of the cerebellum and spinal cord that can occur sporadically or in the setting of Von Hippel-Lindau syndrome. The present study analyzed the utility of proliferation potential in differentiating hemangioblastoma from RCC metastatic to the central nervous system using a MIB-1 (Ki-67) labeling index and assessment of expression of the RNA component of telomerase. Immunohistochemical analysis for epithelial membrane antigen (EMA) and MIB-1 was performed on paraffin-embedded sections of 27 hemangioblastomas and 5 RCC metastatic to the central nervous system. All but one hemangioblastoma demonstrated low or negative MIB-1 immunoreactivity, while 4 of 5 RCC metastases had moderate or high labeling indices. Telomerase RNA expression was assessed in 10 hemangioblastomas and in all 5 metastatic RCC by in Situ hybridization. All 10 hemangioblastomas demonstrated a lack of expression of telomerase RNA, while all 5 metastatic RCCs showed moderate to strong expression. Our results suggest that the MIB-1 labeling index is useful in differentiating hemangioblastoma from metastatic RCC and assessment of telomerase expression can also provide novel information on the difference in growth potential of these tumors.
Mobile Music Touch: The effect of primary tasks on passively learning piano sequences (2010)

The Mobile Music Touch (MMT) system allows users to learn to reproduce piano note sequences while performing other tasks. The system consists of a mobile Bluetooth-enabled computing device and a fingerless glove with embedded vibrators corresponding to each finger and thumb. Melodies to be learned are played over the user's headphones repeatedly. As each note is played, the finger corresponding to the appropriate piano key is stimulated. Past experiments have shown that users could learn simple note sequences even though they were performing a reading comprehension test. Here, we investigate different primary tasks to determine which, if any, interfere with the Passive Haptic Learning (PHL) effect. In a 12 participant within-subject user study, no overall difference was observed in the number of passive sessions required to learn a random note sequence when users viewed a film, played a memory game, or followed a walking path as their primary task. However, individual differences in scores suggest that the type of primary task may have a greater or lesser effect for a given user.
A Novel 2-D Synthetic Aperture Focusing Technique for Acoustic-Resolution Photoacoustic Microscopy (2018)

Acoustic-resolution photoacoustic microscopy (AR-PAM) is a promising technology for vascular or tumor-targeted molecular imaging. Unique advantages of AR-PM are its non-invasive, non-ionizing real-time, and deeper imaging depth. AR-PAM typically uses an ultrasound transducer with a high acoustic numerical aperture (NA) to enable deeper imaging depth. While high NA achieves good lateral resolution in the focal plane but significantly degrades the lateral resolution in the out-of-focus region. Synthetic aperture focusing technique (SAFT) has been introduced to overcome this out-of-focus degradation by synthesizing the correlated signals. Several 2-D SAFTs have been also reported to improve degraded resolution in all directions. However, the resolution enhancement of the previously reported 2-D SAFTs are suboptimal and are not equivalent to the 1-D SAFT performance under an ideal condition with the sample orientation perpendicular to the synthetic aperture direction. In this paper, we present a new 2-D SAFT called 2-D directional SAFT that improves the lateral resolution significantly and we compare our results against 1-D SAFT under ideal condition. We applied this algorithm to phantom and in vivo images to show the improvement in image quality. We also implement this algorithm in a graphical processing unit to achieve high performance to show the practicality of implementing this new algorithm in a system.
Graphene-Based PhotoFET for Optical and Radiation Detection. (2020)

Abstract not provided.