gebhart/patrepeval huggingface dataset:
Supplementary Figures S1 - S7 from Discovery of Biomarkers Predictive of GSI Response in Triple-Negative Breast Cancer and Adenoid Cystic Carcinoma (2023)

&lt;p&gt;S1: NOTCH gene rearrangement in breast cancer cell lines and human breast tumors. S2: NOTCH gene rearrangement and sensitivity to MRK-003. S3: HES4 expression is associated with NOTCH gene-rearrangement or activating mutation in NOTCH. S4: HES4 expression is a poor prognostic marker in TNBC. S5: Proliferation inhibition by combination therapy with MRK-003 and ERK inhibitor (SCH772984). S6: Effect of MRK-003 treatment on CD44+/CD24 high stem-like cell population. S7: N1ICD level correlates with mutation status and is predictive of MRK-003 response in xenograft models.&lt;/p&gt;
Amorphous silicon 5 bit flash analog to digital converter (2012)

A 5-bit fully flash A/D converter (ADC) is built using only n-channel amorphous silicon hydride (a-Si:H) thin film transistors (TFT), metal resistors and capacitors. The circuit is built on silicon using a low temperature process, compatible with flexible plastic substrates. The circuit consumes a power of 13.6 mW running at a speed of 2 k samples/sec. The measurements show reasonably good characteristics, achieving a DNL of less than ±1 LSB and INL of less than ±1.8 LSB without calibration.
Reperfusion of chronic tissue ischemia: nitrite and dipyridamole regulation of innate immune responses (2010)

Chronic and intermittent ischemic vascular disorders represent a burgeoning clinical challenge. Previous studies have focused on the idea that therapeutic angiogenesis strategies could alleviate tissue ischemia; however, it is now appreciated that vascular disease is not simply limited to vascular wall cells but also influenced by simultaneously occurring inflammatory responses. Our laboratory has discovered that pharmacological treatment of permanent tissue ischemia with dipyridamole significantly augments ischemic tissue reperfusion, angiogenesis, and arteriogenesis over time. We have found that the beneficial effects of dipyridamole therapy are due to its ability to increase tissue nitric oxide bioavailability that corrects tissue redox imbalance. Importantly, we have also discovered that dipyridamole treatment invoking nitric oxide (NO) production significantly downregulates various innate immune response genes during chronic ischemic tissue injury. These findings demonstrate that dipyridamole-induced production of nitrite/NO significantly decreases inflammatory responses while increasing vascular growth in ischemic tissues.
Optimization of a mouse locomotor rating system to evaluate compression-induced spinal cord injury: correlation of locomotor and morphological injury indices (2006)

Weight placement at T-12 in the mouse causes reproducible SCI. A new mBBB scoring system is useful for accurately assessing locomotor dysfunction following SCI in mice and is well correlated with histological assessment of spinal cord white matter.
A versatile, multi-laser twin-microscope system for light-sheet imaging (2020)

Light-sheet microscopy offers faster imaging and reduced phototoxicity in comparison to conventional point-scanning microscopy, making it a preferred technique for imaging biological dynamics for durations of hours or days. Such extended imaging sessions pose a challenge, as it reduces the number of specimens that can be imaged in a given day. Here, we present a versatile light-sheet imaging instrument that combines two independently controlled microscope-twins, built so that they can share an ultrafast near-infrared laser and a bank of continuous-wave visible lasers, increasing the throughput and decreasing the cost. To permit a wide variety of specimens to be imaged, each microscope-twin provides flexible imaging parameters, including (i) operation in one-photon and/or two-photon excitation modes, (ii) delivery of one to three light-sheets via a trio of orthogonal excitation arms, (iii) sub-micron to micron imaging resolution, (iv) multicolor compatibility, and (v) upright (with provision for inverted) detection geometry. We offer a detailed description of the twin-microscope design to aid instrument builders who wish to construct and use similar systems. We demonstrate the instrument's versatility for biological investigation by performing fast imaging of the beating heart in an intact zebrafish embryo, deep imaging of thick patient-derived tumor organoids, and gentle whole-brain imaging of neural activity in behaving larval zebrafish.
Tunable transformer for qubits based on flux states (2003)

Flux states of an RF SQUID are promising candidates for the implementation of quantum bits (qubits) for quantum computing. Accurate measurements of the flux states, especially in the time domain, require a controllable coupling between a qubit and a readout circuit (e.g., a dc SQUID magnetometer). Since the readout circuit can also be a source of decoherence, such a controllable coupling also allows one to control (minimize) the back action of the magnetometer. For this purpose we suggest a balanced, tunable transformer. This has a gradiometer configuration such that each arm is broken by a small loop containing two Josephson junctions. As a result the inductance of each arm can be adjusted by an applied bias flux. In the symmetrical case there is no coupling between the qubit and the magnetometer while a desired coupling can be achieved by changing the asymmetry of the arms. Similar transformers may be be useful for achieving controllable, lossless coupling that is required between qubits. Theoretical analysis of the noise back action of the transformer as well as preliminary experimental results are presented.
In-Cylinder Pressure Modelling with Artificial Neural Networks (2011)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;More and more stringent emission regulations require advanced control technologies for combustion engines. This goes along with increased monitoring requirements of engine behaviour. In case of emissions behaviour and fuel consumption the actual combustion efficiency is of highest interest. A key parameter of combustion conditions is the in-cylinder pressure during engine cycle. The measurement and detection is difficult and cost intensive. Hence, modelling of in-cylinder conditions is a promising approach for finding optimum control behaviour. However, on-line controller design requires real-time scenarios which are difficult to model and current modelling approaches are either time consuming or inaccurate.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This paper presents a new approach of in-cylinder condition prediction. Rather than reconstructing in-cylinder pressure signals from vibration transferred signals through cylinder heads or rods this approach predicts the conditions. It is described what possible impacting parameters are used in order to virtually sense and simulate the in-cylinder conditions during an upcoming cycle. The modelling methods that are used in this context are artificial neural networks. The key parameters for modelling of in-cylinder pressure are identified as inputs and a network structure is trained with data generated from an engine model that is validated against data from a real medium-duty diesel engine. The resulting network can be used either for controller design or in case of available measurements for input as on-board monitoring and diagnostic tool. The resulting model structure shows some sufficient and promising correlation results.&lt;/div&gt;&lt;/div&gt;
The circulating metabolome in idiopathic pulmonary fibrosis (IPF) (2019)

<b>Introduction:</b> The circulating metabolome, reflecting underlying cellular processes and biology, has not been characterised in patients with IPF. <b>Aim:</b> To determine differential metabolite expression in patients with IPF vs controls. <b>Methods:</b> Patients with IPF that was diagnosed or confirmed at the enrolling center in the past 6 months (n=300) were drawn from the multicenter IPF-PRO Registry. Controls (n=100) without known lung disease were of similar age and sex distribution. Metabolites (408 in 11 major groups) were quantified using the Absolute IDQ p400HR kit. Of 398 metabolites detected, 303 were carried forward to analysis. Data were log2 transformed and linear regression used to compare metabolite expression in IPF vs control groups. <b>Results:</b> Patients with IPF were predominantly male (74.3%), former smokers (67.3%), with a median age of 70. Median (Q1, Q3) % predicted FVC and DL<sub>CO</sub> were 69.7 (61.0, 80.2) and 40.6 (31.7, 49.4), respectively. 229 metabolites were differentially expressed in the IPF vs. control group based on p-values corrected to control the false discovery rate at 5%, with 79 having a |log<sub>2</sub>FC|≥0.585 and 40 having a |log<sub>2</sub>FC|≥1. The top 40 metabolites that were differentially expressed came from 5 major groups (Figure). <b>Conclusions:</b> IPF associates with a distinct circulating metabolome. Further analysis of the IPF metabolome might aid the development of diagnostic biomarkers or the definition of novel disease endotypes.
Activation of the Nrf2/HO-1 signaling pathway contributes to the protective effects of coptisine against oxidative stress-induced DNA damage and apoptosis in HaCaT keratinocytes (2019)

In this study, the protective effect of coptisine on the oxidative damage-mediated apoptosis was evaluated in cultured human HaCaT keratinocytes. The results demonstrate that preincubation of cells with coptisine prior to H2O2 stimulation resulted in significant inhibition of cytotoxicity and DNA damage associated with the inhibition of reactive oxygen species (ROS) accumulation. Coptisine also restored H2O2-induced mitochondrial dysfunction and decrease of ATP production, and prevented apoptosis by inhibiting Bax/Bcl-2 ratio, caspase-3 activity, and poly(ADP-ribose) polymerase degradation. Interestingly, the expressions of nuclear factor-erythroid-2-related factor 2 (Nrf2) and its active form, phosphorylated Nrf2, were strikingly promoted by coptisine in the presence of H2O2, which was associated with a marked increase in the expression of heme oxygenase-1 (HO-1). However, coptisine-induced HO-1 expression was completely abrogated by Nrf2-specific small interfering RNA (Nrf2-siRNA), which suggests that the increased expression of HO-1 by coptisine is Nrf2-dependent. In addition, Nrf2-siRNA transfection significantly eliminated the protective effect of coptisine on H2O2-induced cytotoxicity, and this effect was similar to that by zinc protoporphyrin IX (ZnPP), an HO-1 specific inhibitor. Furthermore, the protective effects of coptisine against H2O2-induced cytotoxicity were abolished by ZnPP, indicating that coptisine protects keratinocytes against oxidative stress-induced injury through activation of the Nrf2/HO-1 signaling pathway.
Adaptive neighborhood selection for real-time surface normal estimation from organized point cloud data using integral images (2012)

In this paper we present two real-time methods for estimating surface normals from organized point cloud data. The proposed algorithms use integral images to perform highly efficient border- and depth-dependent smoothing and covariance estimation. We show that this approach makes it possible to obtain robust surface normals from large point clouds at high frame rates and therefore, can be used in real-time computer vision algorithms that make use of Kinect-like data.
Messung von Tropfengrößenverteilungen in Regen — ein Vergleich zweier Meßmethoden (1996)

First results of raindrop size measurements obtained by two instruments whose operation principles are basically different are presented and the necessary procedure of comparison is described. The two devices are (i) a disdrometer which converts the mechanical momentum transferred by hydrometeors to a sensible surface into an electrical signal which allows a quantitative size classification and (ii) a Malvern Particle Sizer evaluating the particles' sizes in a specific volume by laser diffraction. The results differ in the range of small drop sizes, for large drops the agreement is quite good. Possible reasons for the differences are discussed.
Impact of carrier mobility and lifetime on the potential performance of a plasmonic detector (2021)

This work studies the performance of a Ge-based plasmonic detector with carrier mobility and lifetime variation. The performance is evaluated in terms of the detector's dark current, photocurrent, and detection bandwidth.
Viscoelasticity of the trachea and its effects on flow limitation (2005)

To test the hypothesis that peak expiratory flow is determined by the wave-speed-limiting mechanism, we studied the time dependency of the trachea and its effects on flow limitation. For this purpose, we assessed the relationship between transmural pressure and cross-sectional area [the tube law (TL)] of six excised human tracheae under controlled conditions of static (no flow) and forced expiratory flow. We found that TLs of isolated human tracheae followed quite well the mathematical representation proposed by Shapiro (Shapiro AH. J Biomech Eng 99: 126-147, 1977) for elastic tubes. Furthermore, we found that the TL measured at the onset of forced expiratory flow was significantly stiffer than the static TL. As a result, the stiffer TL measured at the onset of forced expiratory flow predicted theoretical maximal expiratory flows far greater than those predicted by the more compliant static TL, which in all cases studied failed to explain peak expiratory flows measured at the onset of forced expiration. We conclude that the observed viscoelasticity of the tracheal walls can account for the measured differences between maximal and "supramaximal" expiratory flows seen at the onset of forced expiration.
Unsupervised learning of correlated quantum dynamics on disordered lattices (2021)

Quantum particles co-propagating on disordered lattices develop complex non-classical correlations due to an interplay between quantum statistics, inter-particle interactions, and disorder. Here we present a deep learning algorithm based on Generative Adversarial Networks, capable of learning these correlations and identifying the physical control parameters in a completely unsupervised manner. After one-time training on a data set of unlabeled examples, the algorithm can generate, without further calculations, a much larger number of unseen yet physically correct new examples. Furthermore, the knowledge distilled in the algorithm's latent space identifies disorder as the relevant control parameter. This allows post-training tuning of the level of disorder in the generated samples to values the algorithm was not explicitly trained on. Finally, we show that a trained network can accelerate the learning of new, more complex problems. These results demonstrate the ability of neural networks to learn the rules of correlated quantum dynamics in an unsupervised manner and offer a route to their use in quantum simulations and computation.
Silicon Analogues of the Nonpeptidic GnRH Antagonist AG‐045572: Syntheses, Crystal Structure Analyses, and Pharmacological Characterization (2011)

AG-045572 (CMPD1, 1 a) is a nonpeptidic gonadotropin-releasing hormone (GnRH) antagonist that has been investigated for the treatment of sex hormone-related diseases. In the context of systematic studies on sila-substituted drugs, the silicon analogue disila-AG-045572 (1 b) and its derivative 2 were prepared in multi-step syntheses and characterized by elemental analyses (C, H, N), NMR spectroscopic studies (1H, 13C, 29Si), and single-crystal X-ray diffraction. The pharmacological properties of compounds 1 a, 1 b, and 2 were compared in terms of their in vitro potency at cloned human and rat GnRH receptors. Compounds 1 a and 2 were also examined in regard to their pharmacokinetics and in vivo efficacy in both castrated rat (luteinizing hormone (LH) suppression) and intact rat (testosterone suppression) models. The efficacy and pharmacokinetic profiles of 1 a and its silicon-containing analogue 2 appear similar, indicating that replacement of the 5,6,7,8-tetrahydronaphthalene ring system by the 1,3-disilaindane skeleton led to retention of efficacy. Therefore, the silicon compound 2 represents a novel drug prototype for the design of potent, orally available GnRH antagonists suitable for once-daily dosing.
Use of non-Gaussian time-of-flight kernels for image reconstruction of Monte Carlo simulated data of ultra-fast PET scanners (2020)

Results for the idealised scanner showed that the CTR kernel was in excellent agreement with the simulated time differences. In terms of K-L distance outperformed the a fitted normal distribution for all tested crystal sizes. In the case of the ultra-fast configurations, a convolution kernel between the CTR and a Gaussian showed the best agreement with the simulated data below 40 ps timing resolution. In terms of CRC, the CTR kernel demonstrated improvements, with values that ranged up to 3.8% better CRC for the thickest crystal. In terms of spatial resolution, evaluated at the 60th iteration, the use of CTR kernel showed a modest improvement of the peek-to-valley ratios up to 1% for the 10-mm crystal, while for larger crystals, a clear trend was not observed. In addition, we showed that edge artefacts can appear in the reconstructed images when the timing kernel used for the reconstruction is not carefully optimised. Further iterations, can help improve the edge artefacts.
Al-2.106 Positive-Tone Development (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Luminescent europium complex-laden coatings as exceptional downshifters for organic dye-sensitized solar cells (2014)

As a feasible option for photovoltaic technology to meet the growing energy demand, dye-sensitized solar cells (DSSCs) have attracted much attention due to their low cost, ease of fabrication and good performance. In particular, metal-free organic dyes are currently under investigation because of their low cost and high molar extinction coefficient; thus, they are ideal sensitizer for large-scale applications. However, their absorption range is often narrow, so that an important portion of the solar spectrum is not absorbed. In this context, we think that luminescent materials, which are capable of converting a broad spectrum of light into photons of a particular wavelength, can be used to improve the light harvesting efficiency of the solar-cell-based energy conversion process. In this work, for the first time ever new crosslinked fluoropolymeric systems are employed as luminescent downshifters for organic-dye-sensitized solar cells. The effect of these parameters on the photovoltaic cells and the study of devices aging will be presented
Anticoagulants in Thrombosis and Cancer: The Missing Link (2002)

Many cancer patients reportedly have a hypercoagulable state, with recurrent thrombosis due to the impact of cancer cells and chemotherapy on the coagulation cascade. Studies have demonstrated that unfractionated heparin (UFH) or low-molecular-weight heparin (LMWH) interferes with various processes involved in tumor growth and metastasis. These processes might include fibrin formation, binding of heparin to angiogenic growth factors such as basic fibroblast growth factor and vascular endothelial growth factor, modulation of tissue factor, and other mechanisms. Clinical trials have indicated a clinically relevant effect of LMWH as compared with UFH on the survival of cancer patients with deep vein thrombosis. Similarly, the impact of warfarin on the survival of cancer patients with thromboembolic disorders was demonstrated. Recent studies from our laboratory defined the role of an LMWH (tinzaparin), warfarin, anti-factor VIIa, and recombinant tissue factor pathway inhibitor in the modulation of angiogenesis, tumor growth, and tumor metastasis.
Tissue-specific modifier alleles determine Mertk loss-of-function traits (2022)

Knockout (KO) mouse models play critical roles in elucidating biological processes behind disease-associated or disease-resistant traits. As a presumed consequence of gene KO, mice display certain phenotypes. Based on insight into the molecular role of said gene in a biological process, it is inferred that the particular biological process causally underlies the trait. This approach has been crucial towards understanding the basis of pathological and/or advantageous traits associated with <i>Mertk</i> KO mice. <i>Mertk</i> KO mice suffer from severe, early-onset retinal degeneration. MERTK, expressed in retinal pigment epithelia, is a receptor tyrosine kinase with a critical role in phagocytosis of apoptotic cells or cellular debris. Therefore, early-onset, severe retinal degeneration was described to be a direct consequence of failed MERTK-mediated phagocytosis of photoreceptor outer segments by retinal pigment epithelia. Here, we report that the loss of <i>Mertk</i> alone is not sufficient for retinal degeneration. The widely used <i>Mertk</i> KO mouse carries multiple coincidental changes in its genome that affect the expression of a number of genes, including the <i>Mertk</i> paralog <i>Tyro3</i>. Retinal degeneration manifests only when the function of <i>Tyro3</i> is concomitantly lost. Furthermore, <i>Mertk</i> KO mice display improved anti-tumor immunity. MERTK is expressed in macrophages. Therefore, enhanced anti-tumor immunity was inferred to result from the failure of macrophages to dispose of cancer cell corpses, resulting in a pro-inflammatory tumor microenvironment. The resistance against two syngeneic mouse tumor models observed in <i>Mertk</i> KO mice is not, however, phenocopied by the loss of <i>Mertk</i> alone. Neither <i>Tyro3</i> nor macrophage phagocytosis by alternate genetic redundancy accounts for the absence of anti-tumor immunity. Collectively, our results indicate that context-dependent epistasis of independent modifier alleles determines <i>Mertk</i> KO traits.