gebhart/patrepeval huggingface dataset:
A highly manufacturable trench isolation process for deep submicron DRAMs (2002)

A simple Shallow Trench Isolation (STI) process is proposed for deep sub-micron DRAM applications. The features of this STI flow are tapered trench sidewalls, a slight trench reoxidation, a vertical B field implant, a CMP-only planarization, and disposable oxide spacers to smooth the trench corners. The scalability of this process makes it suitable for 256 Mb to 4 Gb DRAM generations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Maximizing gain in high-throughput screening using conformal prediction (2018)

Iterative screening has emerged as a promising approach to increase the efficiency of screening campaigns compared to traditional high throughput approaches. By learning from a subset of the compound library, inferences on what compounds to screen next can be made by predictive models, resulting in more efficient screening. One way to evaluate screening is to consider the cost of screening compared to the gain associated with finding an active compound. In this work, we introduce a conformal predictor coupled with a gain-cost function with the aim to maximise gain in iterative screening. Using this setup we were able to show that by evaluating the predictions on the training data, very accurate predictions on what settings will produce the highest gain on the test data can be made. We evaluate the approach on 12 bioactivity datasets from PubChem training the models using 20% of the data. Depending on the settings of the gain-cost function, the settings generating the maximum gain were accurately identified in 8-10 out of the 12 datasets. Broadly, our approach can predict what strategy generates the highest gain based on the results of the cost-gain evaluation: to screen the compounds predicted to be active, to screen all the remaining data, or not to screen any additional compounds. When the algorithm indicates that the predicted active compounds should be screened, our approach also indicates what confidence level to apply in order to maximize gain. Hence, our approach facilitates decision-making and allocation of the resources where they deliver the most value by indicating in advance the likely outcome of a screening campaign.
Building an Information Literate Population Through Problem Based Learning Experiences (2013)

University students navigate the Internet with exceptional ease, comfort, and confidence. Although they are facile with technology in the sense of finding information, they are not always proficient at recognizing misleading, flawed, or incorrect information. These are skills that an information literate person possesses. Today's technologically savvy youth are the next generation's leaders. . .
NONAUTONOMOUS SADDLE-NODE BIFURCATIONS IN THE QUASIPERIODICALLY FORCED LOGISTIC MAP (2011)

We provide a local saddle-node bifurcation result for quasiperiodically forced interval maps. As an application, we give a rigorous description of saddle-node bifurcations of 3-periodic graphs in the quasiperiodically forced logistic map with small forcing amplitude.
Gene Pool Similarities of Potato Cyst Nematode Populations Assessed by AFLP Analysis (1996)

AFLP was used to characterize 24 potato cyst nematode populations. This novel DNA fingerprinting technique enabled the identification of 987 marker loci by screening only 12 primer combinations. Data on presence or absence polymorphisms and data on the intensities of corresponding DNA fragments were collected. Separate analysis of both data sets revealed similar dendrograms for the nine G. rostochiensis populations included in this study. Both dendrograms consisted of two groups containing three and five related populations, respectively. One population differed from either of these groups. Each group represented a different pathotype as defined by Kort et al. (J. Kort, H. Ross, H. J. Rumpenhorst, and A. R. Stone, Nematologica 23:333-339, 1977). Previously, a similar arrangement was found after analysis of the genetic variation using random amplified polymorphic DNA (RAPD) (R. T. Folkertsma, J. N. A. M. Rouppe van der Voort, M. P. E. van Gent-Pelzer, K. E. de Groot, W. J. van den Bos, A. Schots, J. Bakker, and F. J. Gommers, Phytopathology 84:807-811, 1994). For the 15 G. pallida populations analyzed, complex AFLP patterns were obtained and therefore only qualitative AFLP data were used. Incongruities were observed between clustering on the basis of AFLP data and classical pathotyping. This strongly confirms earlier findings obtained with RAPDs, because the AFLP markers used in this study outnumbered the population characteristics revealed by RAPDs by a factor of five. To arrive at a reliable pathotype designation of potato cyst nematode populations molecular data and virulence characteristics should be integrated. Possible causes for the difference in distribution of polymorphisms among g. rostochiensis and G. pallida populations are discussed.
Distinct Gene Mutations Are Associated With Clinicopathologic Features in Urachal Carcinoma (2022)

Urachal carcinoma demonstrates frequent gene mutations that are associated with distinct clinicopathologic features. Gene mutation may underlie the development and progression of this aggressive disease.
Nuclear protein 1 (Nupr1/com1/p8) transcriptionally regulates p21 in breast cancer cells (2007)

2102 Nuclear protein 1 (Nupr1), also known as p8 or candidate of metastasis-1, is often up-regulated in both primary tumors and metastases, including breast and pancreatic cancer as well as thyroid neoplasms. Nupr1 is upregulated in response to stress, including serum-deprivation, oxidative stress, staurosporine and doxorubicin. This study investigates the potential role of Nupr1 in cell-cycle control in breast cancer via transcriptional regulation of a cell cycle arrest gene, p21CIP1. Luciferase assays using the p21 promoter showed that Nupr1 is capable of stimulating expression of p21, and that this stimulation is largely abrogated in the presence of a p53 dominant-negative mutant as well as the oncogenic p300-binding protein, E1A. p300 and p53 interact and bind to the promoter of p21 to activate transcription. p300 has been identified as an interactor of Nupr1, and hence we checked if Nupr1 is also able to interact with p53. Our immunoprecipitation experiments indicate an interaction between p53 and Nupr1 in a breast tumor cell line as well as in human embryonic kidney cells. Nupr1 is capable of binding DNA, but appears to require a partner to convey specificity; therefore, it is logical to speculate that Nupr1 associates with p53 and p300, and that this complex binds the p21 promoter to stimulate transcription. The results thus disclose a putative important new role for Nupr1 in the regulation of gene transcription.
Core modal spatial-structuring in inhibited-coupling hollow-core fibers (2019)

A profound knowledge of the cladding mode properties and their interaction with the core modes is decisive for successfully designing inhibited-coupling (IC) guiding hollow-core photonic-crystal fibers (HC-PCFs). In IC fibers, the core and cladding modes coupling is robustly minimized due to a strong mismatch between their transverse phases and a small overlap between their fields. In the latest years, great attention has been given to IC fibers, especially since the introduction of the hypocycloid core contour concept [3], which entailed a dramatic loss reduction and preceded the development of single-ring tubular-lattice (SR-TL) HC-PCFs [4]. The interest on SR-TL HC-PCFs is due to their noteworthy properties such as geometric simplicity and the absence of connecting nodes in the fiber cladding, which favors IC guidance. Efforts on SR-TL HC-PCFs development entailed the accomplishment of ultra-low loss and broad transmission bandwidth [5]. Here, we show that the alteration of the lattice-tubes azimuthal position in SR-TL HC-PCFs causes modifications in the mode loss hierarchy and can be used to select the propagation of specific higher order modes (HOMs). It can be done by conveniently enlarging the spacing between the cladding tubes and by providing additional leakage to the fundamental mode while keeping low impact in the confinement loss (CL) of specific HOMs. It allows obtaining uncommon intensity profiles and polarization properties at the fiber output allowing it to act as a mode shaper.
Signal representation and system response (1999)

Perhaps the most familiar example of a signal is a musical sound. Plucking a string on a guitar causes that string to vibrate up and down as illustrated in Figure 1.1(a). Plotting the vertical position of one point on the string as a function, x(), of time, t, reveals the periodic motion of the string (Figure 1.1(b)). The motion of the string alters the pressure in the air around the string and the pressure of the air will oscillate in sympathy with the movement of the string. The pressure wave radiates from the guitar towards the microphone which converts the fluctuations in pressure to an electrical voltage oscillation (Figure 1.2(a)). All of these oscillations are examples of signals. All of them carry information. Listening to a recording of the electrical signal, most people would be able to identify the instrument being played, i.e. would be able to distinguish between a guitar and a piano. Some people might be able to identify the pitch and hence the note being played.
A fluorescence based GEF exchange assay in a high throughput screen format (2005)

5912 The Ras superfamily of small GTPases serves as binary switches cycling between GDP-bound inactive and GTP-bound active state, which process is regulated by guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs) and guanine nucleotide dissociation inhibitors (GDIs). GEFs catalyze the exchange of GDP for GTP to generate the active state of small GTPases in response to extracellular signals. The GEF family is composed of more than 70 members in human, constituting the largest family that regulates small GTPases. Many GEF proteins have been identified as oncogenes and more and more GEFs have been found involved in human disease such as cancer, thus attracting more attentions for potential therapies in cancer treatment. Recently developed fluorescence analogs of guanine nucleotides have greatly improved the technical ability to define the real time exchange reaction of GEFs, including kinetic and thermodynamic properties, eliminating the need for traditional radioactive labeling method. This fluorescence based assay takes advantage of the spectroscopic difference between bound and unbound fluorescent analogs to guanine nucleotides and thus is able to monitor the states of small GTPases. One of most widely used fluorescent analogs is mant (N-methylanthraniloyl) fluorophores. Once bound to GTPases, this fluorophore emission intensity increases dramatically. Therefore, the enhancement of fluorescent intensity will reflect the activities of known or unknown GEF proteins. Since conventional fluorescence based assays are mostly performed in a cuvette (2 ml volume) and not suitable for high throughput screen, we developed a mant fluorophore based GEF assay suitable for both 96-well and 384-well format. For example, human Dbs protein exhibited exchange activity towards Cdc42, RhoA in both 96-well and 384-well format, with similar kinetic parameters as 2 ml volume reaction. This assay can be applied to multiple research purposes such as characterizing the known or unknown GEFs and discovering GEF inhibitors in a high throughput screen format.
Bridging the Gap Between Clean Data Training and Real-World Inference for Spoken Language Understanding (2021)

Spoken language understanding (SLU) system usually consists of various pipeline components, where each component heavily relies on the results of its upstream ones. For example, Intent detection (ID), and slot filling (SF) require its upstream automatic speech recognition (ASR) to transform the voice into text. In this case, the upstream perturbations, e.g. ASR errors, environmental noise and careless user speaking, will propagate to the ID and SF models, thus deteriorating the system performance. Therefore, the well-performing SF and ID models are expected to be noise resistant to some extent. However, existing models are trained on clean data, which causes a \textit{gap between clean data training and real-world inference.} To bridge the gap, we propose a method from the perspective of domain adaptation, by which both high- and low-quality samples are embedding into similar vector space. Meanwhile, we design a denoising generation model to reduce the impact of the low-quality samples. Experiments on the widely-used dataset, i.e. Snips, and large scale in-house dataset (10 million training examples) demonstrate that this method not only outperforms the baseline models on real-world (noisy) corpus but also enhances the robustness, that is, it produces high-quality results under a noisy environment. The source code will be released.
Gaussian curvature–driven direction of cell fate toward osteogenesis with triply periodic minimal surface scaffolds (2022)

Leaf photosynthesis, coral mineralization, and trabecular bone growth depend on triply periodic minimal surfaces (TPMSs) with hyperboloidal structure on every surface point with varying Gaussian curvatures. However, translation of this structure into tissue-engineered bone grafts is challenging. This article reports the design and fabrication of high-resolution three-dimensional TPMS scaffolds embodying biomimicking hyperboloidal topography with different Gaussian curvatures, composed of body inherent β-tricalcium phosphate, by stereolithography-based three-dimensional printing and sintering. The TPMS bone scaffolds show high porosity and interconnectivity. Notably, compared with conventional scaffolds, they can reduce stress concentration, leading to increased mechanical strength. They are also found to support the attachment, proliferation, osteogenic differentiation, and angiogenic paracrine function of human mesenchymal stem cells (hMSCs). Through transcriptomic analysis, we theorize that the hyperboloid structure induces cytoskeleton reorganization of hMSCs, expressing elongated morphology on the convex direction and strengthening the cytoskeletal contraction. The clinical therapeutic efficacy of the TPMS scaffolds assessed by rabbit femur defect and mouse subcutaneous implantation models demonstrate that the TPMS scaffolds augment new bone formation and neovascularization. In comparison with conventional scaffolds, our TPMS scaffolds successfully guide the cell fate toward osteogenesis through cell-level directional curvatures and demonstrate drastic yet quantifiable improvements in bone regeneration.
Effect of Patient-Specific Preanalytic Variables on CSF Aβ1–42 Concentrations Measured on an Automated Chemiluminescent Platform (2020)

The preanalytical variables examined here do not have significant effects on Aβ1-42 concentrations if fresh samples are processed within 2 h. However, a gradient effect can be observed on Aβ1-42 concentrations after the first 5 mL of collection and blood contamination has a significant impact on Aβ1-42 concentrations once specimens have been frozen.
Effect of compromised liver function and acute kidney injury on the pharmacokinetics of thymoquinone in a rat model (2020)

The current research explored the effect of hepatic and renal dysfunctions on the pharmacokinetics of thymoquinone (TQ) in a rat model.An acute kidney injury was induced using gentamicin and a liver damage was elicited using a single dose of d-galactosamine. For the pharmacokinetic studies, TQ was administered as IV injection or and PO route to rats.The concentrations of TQ and pharmacokinetic parameters were calculated using a non-compartmental analysis. The systemic clearance (Cl) of TQ after IV dosing was slightly reduced in the liver dysfunction group compared to healthy controls (<i>p</i> = 0.0013). Similarly, the estimated volume of distribution at steady state (Vss) was marginally decreased (<i>p</i> = 0.001). However, in rats with acute kidney injury exhibited a larger Vss as opposed to normal renal function (511.28 ± 21.03 ml/kg <i>vs</i>. 442.25 ± 31.43 ml/kg; <i>p</i> = 0.0001). Whereas oral Cl and terminal volume of distribution (Vz) of TQ were reduced by ∼50% in the liver dysfunction group (<i>p</i> = 0.0001). These changes were associated with more systemic exposure as measured by AUC<sub>0-∞</sub> in rats with compromised liver functions. The estimated plasma protein binding TQ was 99.84 ± 0.03% in healthy controls, 97.05 ± 0.57% with kidney injury rats, and 95.75 ± 0.64% in liver dysfunctionThe findings of the present study suggest that liver dysfunction could potentially modify the disposition of TQ administered orally, and therefore, a smaller maintenance dose is probably required to avoid accumulation.
Bulge testing of single- and dual-layer thin films (2001)

The bulge testing technique determines the mechanical properties of solid thin films by measuring the deformation that forms in response to the application of a controlled differential pressure to a thin film window. By comparing the pressure-displacement relation with a mechanical model, the elastic modulus and residual stress in the film can be measured. While the bulge testing technique can be quite effective, the technique is not routinely used because of difficulties that often arise with using this technique. The difficulties include specimen preparation and mounting, automated bulge height measurement and the correlation of bulge deformation with the mechanical properties of the thin film. This paper describes developments in the bulge testing technique that alleviate many of these difficulties, as well as presenting results from the testing of single and dual layer thin films. Single film tests were conducted on samples of B-doped-Si, SiC, and diamond-like carbon. A total of 135 windows with three different window aspect ratios and two different thicknesses were investigated. In a preliminary study to determine the feasibility of extending the technique to the testing of multilayer films, the mechanics of a dual layer system were measured. The dual layer system was an Al layer on top of B-doped-Si. The results from the single film test were that the elastic moduli of the B-doped-Si were close to nominal bulk values and the diamond-like carbon was about half that of diamond. The SiC elastic moduli measurements were inconclusive because of the large prestress. Elastic moduli measurements from nanoindentation were about 50% higher. It should be noted that neither the variation of the aspect ratio nor the variation of the film thickness led to different results. The measured prestresses agreed quite well with wafer curvature measurement. The dual-layer measurements yielded values for the elastic modulus of thin film Al that were within 5% of the nominal bulk values.
Visible and IR Data Fusion Technique Using the Contourlet Transform (2009)

In the last few years image fusion has gained considerable attention, where it can provide remarkable outputs for many image applications (i.e., detection of hidden objects). Images with different specifications (resolution, spectral, and spatial) can be fused to produce an output image that combines the best features of all input images. The quality of the output image varies based on the application. In this paper, a new region-based image fusion technique using the Contourlet Transform (CT) is proposed. The presented fusion approach combines the visual information from a visual colored image, and some information about the hidden objects from an IR image. The fused output image is better for human and machine interpretation, where it preserves the original chromaticity of the visual input image. The input images are segmented into small regions more suitable for the proposed algorithm. The segmentation process is performed in the frequency domain. The presented region-based fusion approach is more robust than the traditional pixel-based techniques, where it reduces: the blurring effects, sensitivity to the misregistration problem, and noise effects in the input images. Experimental results demonstrate the capability of the presented fusion technique in detecting hidden weapons and objects. Moreover, the algorithm preserves very high percentage of the input image's spectral components.
Differential usage of NF‐κB activating signals by IL‐1β and TNF‐α in pancreatic beta cells (2012)

The cytokines interleukin (IL)-1β and tumor necrosis factor (TNF)-α induce β-cell death in type 1 diabetes via NF-κB activation. IL-1β induces a more marked NF-κB activation than TNF-α, with higher expression of genes involved in β-cell dysfunction and death. We show here a differential usage of the IKK complex by IL-1β and TNF-α in β-cells. While TNF-α uses IKK complexes containing both IKKα and IKKβ, IL-1β induces complexes with IKKα only; this effect is achieved by induction of IKKβ degradation via the proteasome. Both IKKγ and activation of the TRAF6-TAK1-JNK pathway are involved in IL-1β-induced IKKβ degradation.
Automatic computer aided diagnosis tool using component-based SVM (2008)

Alzheimer type dementia (ATD) is a progressive neurodegenerative disorder first affecting memory functions and then gradually affecting all cognitive functions with behavioral impairments and eventually causing death. Functional brain imaging including single-photon emission computed tomography (SPECT) is commonly used to guide the clinician’s diagnosis. However, conventional evaluation of these scans often relies on manual reorientation, visual reading and semiquantitative analysis of certain regions of the brain. These steps are time consuming, subjective and prone to error. This paper shows a fully automatic computer-aided diagnosis (CAD) system for improving the accuracy in the early diagnosis of the Alzheimer’s disease. The proposed approach is based on a first automatic feature selection, and secondly a combination of component-based support vector machine (SVM) classification and a pasting votes technique of ensemble SVM classifiers.
Combined use of tofacitinib (pan-JAK inhibitor) and ruxolitinib (a JAK1/2 inhibitor) for refractory T-cell prolymphocytic leukemia (T-PLL) with a JAK3 mutation (2019)

A 62-year-old male presented with lymphocytosis and splenomegaly. A diagnosis of T-PLL was made based on bone marrow examination. The patient was initially observed but after a year developed progr...
Early Tissue Reaction to Textured Breast Implant Surfaces (1992)

Capsular contracture around breast implants with smooth surfaces continues to be an unpredictable complication. Some surgeons believe that silicone implants covered with porous polyurethane foam have a lowered potential to contract. These textured implants are not as biocompatible as silicone. Recently, silicone implants with textured surfaces have been introduced with the hope that the incidence of unacceptable implant contracture will be reduced. Using a rat implant model, the tissue reaction to textured implant surfaces was assessed. The implant surfaces evaluated were Silastic II, Siltex, MISTI, Biocell, Silastic MSI, and Même. Disks of each implant material were implanted under the dorsal skin of rats for a period of 28 days. Each implant with its surrounding tissue was excised, processed for histological analysis, and assessed for the tissue's response to the implant with particular emphasis on the formation of a continuous collagen capsule. The results indicated that the magnitude of surface texturing influenced the development of a complete capsule. Implant surfaces with a texture of less than 150 microns in height or depth (Silastic II, Siltex, and MISTI) resulted in the formation of complete capsules. An implant (Biocell) with irregular texturing (200-350 microns) produced an organized capsule over most of its surface with localized interruptions of the capsule at the sites of its deepest cavities. Implant surfaces with texturing that exceeded 350 microns in height or depth (Silastic MSI and Même) resulted in inhibition of the formation of a continuous capsule during this 28-day study.