gebhart/patrepeval huggingface dataset:
Spatial and Single-Cell Transcriptional Profiling Identifies Functionally Distinct Human Dermal Fibroblast Subpopulations (2018)

Previous studies have shown that mouse dermis is composed of functionally distinct fibroblast lineages. To explore the extent of fibroblast heterogeneity in human skin, we used a combination of comparative spatial transcriptional profiling of human and mouse dermis and single-cell transcriptional profiling of human dermal fibroblasts. We show that there are at least four distinct fibroblast populations in adult human skin, not all of which are spatially segregated. We define markers permitting their isolation and show that although marker expression is lost in culture, different fibroblast subpopulations retain distinct functionality in terms of Wnt signaling, responsiveness to IFN-γ, and ability to support human epidermal reconstitution when introduced into decellularized dermis. These findings suggest that ex vivo expansion or in vivo ablation of specific fibroblast subpopulations may have therapeutic applications in wound healing and diseases characterized by excessive fibrosis.
Use of Hepatocytes in Adhesion and Suspension Cultures for Liver Support Bioreactors (1989)

Hepatocyte cultivation in bioreactors for hybrid liver support systems is possible under two conditions: attached to a substrate like membranes or microcarriers or in suspension culture. To compare the ammonia metabolism of hepatocytes cultivated under these two conditions, cultures of primary seeded rat hepatocytes were cultivated either attached to collagen coated tissue culture plastic or as a suspension culture. During the time course of culture, the ability of hepatocytes to reduce the ammonia content of the medium decreased in both adhesion and suspension cultures, though to different extents. In suspension cultures, ammonia content was reduced from 350 microM to about 100 microM (day 4) and to about 180 microM (day 6). No significant reduction was seen on day 8 of culture. In contrast, hepatocytes attached to collagen coated dishes remained viable and functional for at least 8 days after plating, reducing ammonia content from 350 microM to 70 microM (day 4), 90 microM (day 6) and 180 microM (day 8). The period of useful metabolism of hepatocytes in bioreactors for hybrid liver support systems appears to depend on the culture conditions.
COMPARATIVE STUDY OF ET-BASED AND SOIL MOISTURE-BASED IRRIGATION FOR AL BATINAH REGION IN OMAN (2014)

ISHS International Conference on Agricultural Engineering: New Technologies for Sustainable Agricultural Production and Food Security COMPARATIVE STUDY OF ET-BASED AND SOIL MOISTURE-BASED IRRIGATION FOR AL BATINAH REGION IN OMAN
Delayed signatures of underground nuclear explosions (2016)

Radionuclide signals from underground nuclear explosions (UNEs) are strongly influenced by the surrounding hydrogeologic regime. One effect of containment is delay of detonation-produced radioxenon reaching the surface as well as lengthening of its period of detectability compared to uncontained explosions. Using a field-scale tracer experiment, we evaluate important transport properties of a former UNE site. We observe the character of signals at the surface due to the migration of gases from the post-detonation chimney under realistic transport conditions. Background radon signals are found to be highly responsive to cavity pressurization suggesting that large local radon anomalies may be an indicator of a clandestine UNE. Computer simulations, using transport properties obtained from the experiment, track radioxenon isotopes in the chimney and their migration to the surface. They show that the chimney surrounded by a fractured containment regime behaves as a leaky chemical reactor regarding its effect on isotopic evolution introducing a dependence on nuclear yield not previously considered. This evolutionary model for radioxenon isotopes is validated by atmospheric observations of radioxenon from a 2013 UNE in the Democratic People's Republic of Korea (DPRK). Our model produces results similar to isotopic observations with nuclear yields being comparable to seismic estimates.
Excitation of Whispering Gallery Modes in Fibres by Fibres (1998)

We have recently reported the use of a narrow single-mode fibre taper to excite whispering gallery modes (WGMs) in fused silica microspheres[1]. Here we demonstrate the similar excitation of WGMs in dielectric cylinders. The dielectric cylinder is itself a tapered fibre, made by stretching the fibre in a flame to give a filament of predictable diameter. The two tapers are positioned at right angles and in contact. The transmission spectrum of the "sensor" taper (measured using a tunable diode laser) has dips at wavelengths where light is coupled from its guided mode to a WGM in the "target" taper.
An SEM on a Chip (1997)

Abstract A silicon microfabrication technique has been applied toward the development of a Miniature Scanning Electron Microscope (MSEM). The fabrication technology is not only precise but is inexpensive compared to conventional methods of electron microscope construction and is easily extended to the construction of arrays of MSEMs for applications in high throughput e-beam lithography and wafer inspection. An electrostatic electron lens consists of a series of planar electrodes with central apertures that are precisely aligned to and electrically isolated from one another. This structure is fabricated using silicon as the electrode material and Pyrex optical fibers as the insulators. The electrodes are fabricated on four inch (100) orientation silicon wafers that are patterned on both sides and anisotropically etched to form four orthogonal v-grooves and an open diaphragm with a circular aperture in the center. The apertures are formed by reactive ion etching. The wafers are then diced to create approximately 100 7 mm by 9 mm electrodes.
Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins (2009)

Type 2C protein phosphatases (PP2Cs) are vitally involved in abscisic acid (ABA) signaling. Here, we show that a synthetic growth inhibitor called pyrabactin functions as a selective ABA agonist. Pyrabactin acts through PYRABACTIN RESISTANCE 1 (PYR1), the founding member of a family of START proteins called PYR/PYLs, which are necessary for both pyrabactin and ABA signaling in vivo. We show that ABA binds to PYR1, which in turn binds to and inhibits PP2Cs. We conclude that PYR/PYLs are ABA receptors functioning at the apex of a negative regulatory pathway that controls ABA signaling by inhibiting PP2Cs. Our results illustrate the power of the chemical genetic approach for sidestepping genetic redundancy.
Reciprocity and power balance for piecewise continuous media with imperfect interfaces (2004)

The interaction of elastodynamic waves with imperfect interfaces is usually described by the so‐called linear slip model. In this model it is assumed that the particle displacement of an elastic wave at an interface jumps by a finite amount, linearly proportional to the stress at the interface. In this paper we postulate general boundary conditions at arbitrarily shaped imperfect interfaces for acoustic waves in fluids, elastodynamic waves in solids, electromagnetic waves in matter, poroelastic waves in porous solids, and seismoelectric waves in porous solids in such a way that they cover the linear slip model and other existing models for imperfect interfaces. These boundary conditions are expressed by a single matrix‐vector equation in the space‐frequency domain. Using this equation, we extend two unified reciprocity theorems (one of the convolution type and one of the correlation type) for the various wave phenomena, with an extra integral over the imperfect interfaces. By considering two special cases of these reciprocity theorems, we observe that (1) source‐receiver reciprocity remains valid when the source and receiver are separated by imperfect interfaces and that (2) the extra integral in the correlation‐type reciprocity theorem quantifies the power dissipated by the imperfect interfaces.
Adenovirus Armed With TNFa and IL2 Added to aPD-1 Regimen Mediates Antitumor Efficacy in Tumors Refractory to aPD-1 (2021)

Immune checkpoint inhibitors such as anti-PD-1 have revolutionized the field of oncology over the past decade. Nevertheless, the majority of patients do not benefit from them. Virotherapy is a flexible tool that can be used to stimulate and/or recruit different immune populations. T-cell enabling virotherapy could enhance the efficacy of immune checkpoint inhibitors, even in tumors resistant to these inhibitors. The T-cell potentiating virotherapy used here consisted of adenoviruses engineered to express tumor necrosis factor alpha and interleukin-2 in the tumor microenvironment. To study virus efficacy in checkpoint-inhibitor resistant tumors, we developed an anti-PD-1 resistant melanoma model <i>in vivo</i>. In resistant tumors, adding virotherapy to an anti-PD-1 regimen resulted in increased survival (p=0.0009), when compared to anti-PD-1 monotherapy. Some of the animals receiving virotherapy displayed complete responses, which did not occur in the immune checkpoint-inhibitor monotherapy group. When adenoviruses were delivered into resistant tumors, there were signs of increased CD8 T-cell infiltration and activation, which - together with a reduced presence of M2 macrophages and myeloid-derived suppressor cells - could explain those results. T-cell enabling virotherapy appeared as a valuable tool to counter resistance to immune checkpoint inhibitors. The clinical translation of this approach could increase the number of cancer patients benefiting from immunotherapies.
Midlife Metabolic Profile and the Risk of Late-Life Cognitive Decline (2017)

Among metabolic syndrome components, the effects of higher plasma glucose levels on cognitive decline (CD) have been considered in few studies. We evaluated the associations among midlife glycemia, total cholesterol, high-density lipoprotein cholesterol, triglycerides, midlife insulin resistance [homeostasis model assessment for insulin resistance (HOMA-index)], and CD in the older subjects of the population-based MICOL Study (Castellana Grotte, Italy) at baseline (M1) and at follow-ups seven (M2) and twenty years later (M3). At M1, a dementia risk score and a composite cardiovascular risk score for dementia were calculated. For 797 subjects out of 833, we obtained a Mini-Mental State Examination (MMSE) score at M3, subdividing these subjects in three cognitive functioning subgroups: normal cognition, mild CD, and moderate-severe CD. Mean fasting glycemia at baseline was significantly higher in moderate-severe CD subgroup (114.6±71.4 mg/dl) than in the normal cognition subgroup (101.2±20.6). Adjusting for gender, age, and other metabolic components, higher fasting glycemia values both at M1 [odds ratio (OR) = 1.31; 95% confidence interval (CI): 1.08-1.59] and M2 (OR = 1.26; 95% CI: 1.01-1.57) were associated with an increased risk of moderate-severe CD. Mean HOMA index value was significantly higher in the moderate-severe CD subgroup (5.7±9.4) compared to the normal cognition subgroup (2.9±1.4) at M1. The dementia risk probability (MMSE < 24) increased moving through higher categories of the dementia risk score and decreased as long as the cardiovascular score increased. The present findings highlighted the indication to control blood glucose levels, regardless of a diagnosis of diabetes mellitus, as early as midlife for prevention of late-life dementia.
Control of Solid Waste Using Low Temperature Oxidation (2006)

&lt;div class="htmlview paragraph"&gt;A safe, effective means to control solid waste is a critical need on long-term space missions. With current waste models, 1300 kg of waste occupying a volume 20 m&lt;sup&gt;3&lt;/sup&gt; will be generated in a 180-day mission to Mars. Unprocessed waste poses a biological hazard to crew health and morale. The waste processing methods currently under consideration include incineration, microbial oxidation, pyrolysis and compaction. Although each has advantages, no single method has yet been developed that is safe, recovers valuable resources including oxygen and water, and has low energy and space requirements. Thus, the objective of this project was to develop a low temperature oxidation process to convert waste cleanly and rapidly to carbon dioxide and water.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;In this Small Business Innovative Research (SBIR) Phase I project, TDA Research Inc. (TDA) conducted tests to measure the rates of oxidation using ozone with five model waste components. We used wheat straw to represent food scraps, cellulose to represent waste paper, methionine to represent feces, urea for other biological waste, and high density polyethylene (HDPE) for plastic and plastic wrapping. We measured the oxidation rates of individual waste components and also a mixture of all five. At temperatures less than or equal to 200°C, we obtained a maximum waste oxidation rate of 68 grams per hour per liter of reactor volume with high selectivity for carbon dioxide and water. In addition we obtained very low concentrations of NO&lt;sub&gt;X&lt;/sub&gt;. In all cases, we found that less than 1% of the nitrogen in the waste compounds was converted to NO&lt;sub&gt;X&lt;/sub&gt;. Finally, we found that the highest oxidation rates obtained in this project approach those rates needed to design a reasonably sized system for use onboard spacecraft and the estimated equivalent system mass (ESM) for this method of waste control is similar to values estimated for other, less efficient methods.&lt;/div&gt;
The (2018)

This paper describes our system (SLT-Interactions) for the CoNLL 2018 shared task: Multilingual Parsing from Raw Text to Universal Dependencies. Our system performs three main tasks: word segmentation (only for few treebanks), POS tagging and parsing. While segmentation is learned separately, we use neural stacking for joint learning of POS tagging and parsing tasks. For all the tasks, we employ simple neural network architectures that rely on long short-term memory (LSTM) networks for learning task-dependent features. At the basis of our parser, we use an arc-standard algorithm with Swap action for general non-projective parsing. Additionally, we use neural stacking as a knowledge transfer mechanism for cross-domain parsing of low resource domains. Our system shows substantial gains against the UDPipe baseline, with an average improvement of 4.18% in LAS across all languages. Overall, we are placed at the 12 th position on the official test sets.
Synthesis of N‐Aryl Pyridin‐2‐ones via Ligand Coupling Reactions Using Pentavalent Organobismuth Reagents. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Ankle Localization of a Primary Bone Large B-Cell Lymphoma (2021)

Plain X-Ray of a primary bone large B-cell lymphoma in an 84-year-old patient (Figure 1 and 2). She consulted for a swelling of the right ankle with functional impotence, in a context of altered general condition for many months. The radiographic appearance was typical, showing a shaft and metaphyseal “moth-eaten” osteolytic lesion, with periosteal reaction and thickening of the opposite soft tissues. The diagnosis of B-cell lymphoma was confirmed with histological examination of tissue samples from percutaneous computed tomography-guided biopsy of the lesion. Primary bone lymphoma is rare, accounting for 5% of malignant bone tumors, and mostly large B-cell lymphomas. Moreover, localization usually predominating at the roots of the axial skeleton, explained by the persistence of red bone marrow. Even if it presents in an unusual site, this case highlights the importance of considering typical imaging characteristics of a lesion.
Outflanking and securely using the PIN/TAN-System (2004)

The PIN/TAN-system is an authentication and authorization scheme used in e-business. Like other similar schemes it is successfully attacked by criminals. After shortly classifying the various kinds of attacks we accomplish malicious code attacks on real World Wide Web transaction systems. In doing so we find that it is really easy to outflank these systems. This is even supported by the users' behavior. We give a few simple behavior rules to improve this situation. But their impact is limited. Also the providers support the attacks by having implementation flaws in their installations. Finally we show that the PIN/TAN-system is not suitable for usage in highly secure applications.
Targeted Protein Degradation through E2 Recruitment (2022)

Abstract Targeted protein degradation (TPD) with Proteolysis Targeting Chimeras (PROTACs), heterobifunctional compounds consisting of protein targeting ligands linked to recruiters of E3 ubiquitin ligases, has arisen as a powerful therapeutic modality to induce the proximity of target proteins with E3 ligases to ubiquitinate and degrade specific proteins in cells. Thus far, PROTACs have primarily exploited the recruitment of E3 ubiquitin ligases or their substrate adapter proteins but have not exploited the recruitment of more core components of the ubiquitin-proteasome system (UPS). In this study, we used covalent chemoproteomic approaches to discover a covalent recruiter against the E2 ubiquitin conjugating enzyme UBE2D—EN67—that targets an allosteric cysteine, C111, without affecting the enzymatic activity of the protein. We demonstrated that this UBE2D recruiter could be used in heterobifunctional degraders to degrade neo-substrate targets in a UBE2D-dependent manner, including BRD4 and the androgen receptor. Overall, our data highlight the potential for the recruitment of core components of the UPS machinery, such as E2 ubiquitin conjugating enzymes, for TPD, and underscore the utility of covalent chemoproteomic strategies for identifying novel recruiters for additional components of the UPS.
Efficient eco-friendly inverted quantum dot sensitized solar cells (2015)

Recent progress in quantum dot (QD) sensitized solar cells has demonstrated the possibility of low-cost and efficient photovoltaics. However, the standard device structure based on n-type materials often suffers from slow hole injection rate, which may lead to unbalanced charge transport. We have fabricated efficient p-type (inverted) QD sensitized cells, which combine the advantages of conventional QD cells with p-type dye sensitized configurations. Moreover, p-type QD sensitized cells can be used in highly promising tandem configurations with n-type ones. QDs without toxic Cd and Pb elements and with improved absorption and stability were successfully deposited onto mesoporous NiO electrode showing good coverage and penetration according to morphological analysis. Detailed photophysical charge transfer studies showed that high hole injection rates (10<sup>8</sup> s<sup>-1</sup>) observed in such systems are comparable with electron injection in conventional n-type QD assemblies. Inverted solar cells fabricated with various QDs demonstrate excellent power conversion efficiencies of up to 1.25%, which is 4 times higher than the best values for previous inverted QD sensitized cells. Attempts to passivate the surface of the QDs show that traditional methods of reduction of recombination in the QD sensitized cells are not applicable to the inverted architectures.
Data associated with the publication: Cerebellar patients have intact feedback control that can be leveraged to improve reaching (2020)

Cerebellar patients have intact feedback control that can be leveraged to improve reaching. Contains data and code written in MATLAB. All of the data was collected from the Kinarm (BKIN Technologies Ltd.). Please download the README document from the Files list for details on content and for viewing and reprocessing the data.
Peptide Mimetic of the Third Cytoplasmic Loop of the PTH/PTHrP Receptor (1996)

The third cytoplasmic loop of seven transmembrane helix receptors is important both for the coupling to and activation of the heterotrimeric G-protein. Here, the structural characterization of two peptides containing the sequence of the putative third cytoplasmic loop of the parathyroid hormone/parathyroid hormone related peptide receptor in aqueous solution and in the presence of micelles is presented. The 27-amino acid peptide has been examined both in a linear form and cyclized with a linker of 8 methylenes designed to maintain a distance of 12 Å between the N- and C-termini, modeling the distance observed between transmembrane α-helices in bacteriorhodopsin. In aqueous solution both peptides are relatively unstructured. In contrast, in the presence of sodium dodecylsulfate micelles the linear peptide adopts a well-defined extended conformation with approximately 30% α-helix. The cyclic peptide possesses an N-terminal, ten amino acid α-helical domain followed by seven amino acids which protrude out in a well-defined loop. These results indicate the importance of the membrane environment and the role of the structural constraint achieved by cyclization; the octamethylene linker restricts the peptide to conformations possible while attached to transmembrane helices V and VI thus mimicking the conformation of the loop in the native receptor.
Animating the Link Between Operational Semantics and Algebraic Semantics for a Probabilistic Timed Shared-Variable Language (2009)

Complex software systems typically involve features like time, concurrency and probability, where probabilistic computations play an increasing role. It is challenging to formalize languages comprising all these features. We have integrated probability, time and concurrency in one single model (called PTSC), where the concurrency feature is modelled using shared-variable based communication. Meanwhile, we have also explored the link between the operational semantics and algebraic semantics, where our approach was started from algebraic laws via head normal form. This paper considers the animation of the link between operational semantics and algebraic semantics for PTSC. Our approach is by using Prolog as the development language. Firstly we explore the animation of the operational semantics for PTSC. The link of the two semantics is proceeded via the concept of head normal form. Secondly the generation of head normal form is explored, especially the animation of parallel expansion laws. Finally we consider the animation of deriving operational semantics by a provided derivation strategy via head normal form. The results animated from the first and the third exploration indicate that our operational semantics is sound and complete with respect to head normal form (or algebraic laws in general).