gebhart/patrepeval huggingface dataset:
Pre-training Recommender Systems via Reinforced Attentive Multi-relational Graph Neural Network (2021)

Recently, Graph Neural Networks (GNNs) have proven their effectiveness for recommender systems. Existing studies have applied GNNs to capture collaborative relations in the data. However, in real-world scenarios, the relations in a recommendation graph can be of various kinds. For example, two movies may be associated either by the same genre or by the same director/actor. If we use a single graph to elaborate all these relations, the graph can be too complex to process. To address this issue, we bring the idea of pre-training to process the complex graph step by step. Based on the idea of divide-and-conquer, we separate the large graph into three sub-graphs: user graph, item graph, and user-item interaction graph. Then the user and item embeddings are pre-trained from user and item graphs, respectively. To conduct pre-training, we construct the multi-relational user graph and item graph, respectively, based on their attributes.In this paper, we propose a novel Reinforced Attentive Multi-relational Graph Neural Network (RAM-GNN) to pre-train user and item embeddings on the user and item graph prior to the recommendation step. Specifically, we design a relation-level attention layer to learn the importance of different relations. Next, a Reinforced Neighbor Sampler (RNS) is applied to search the optimal filtering threshold for sampling top-k similar neighbors in the graph, which avoids the over-smoothing issue. We initialize the recommendation model with the pre-trained user/item embeddings. Finally, an aggregation-based GNN model is utilized to learn from the collaborative relations in the user-item interaction graph and provide recommendations. Our experiments demonstrate that RAM-GNN outperforms other state-of-the-art graph-based recommendation models and multi-relational graph neural networks.
Near‐Infrared Ternary Tandem Solar Cells (2018)

The paucity of near-infrared (NIR) organic materials with high absorption at long wavelengths, combined with large diffusion lengths and charge mobilities, is an impediment to progress in achieving high-efficiency organic tandem solar cells. Here a subcell is employed within a series tandem stack that comprises a solution-processed ternary blend of two NIR-absorbing nonfullerene acceptors and a polymer donor combined with a small-molecular-weight, short-wavelength fullerene-based subcell grown by vacuum thermal evaporation. The ternary cell achieves a power conversion efficiency of 12.6 ± 0.3% with a short-circuit current of 25.5 ± 0.3 mA cm<sup>-2</sup> , an open-circuit voltage of 0.69 ± 0.01 V, and a fill factor of 0.71 ± 0.01 under 1 sun, AM 1.5G spectral illumination. The success of this device is a result of the nearly identical offset energies between the lowest unoccupied molecular orbitals (LUMOs) of the donors with the highest occupied molecular orbital (HOMO) of the acceptor, resulting in a high open-circuit voltage. A tandem structure with an antireflection coating combining these subcells demonstrates a power conversion efficiency of 15.4 ± 0.3%.
Neural-net computing for interpretation of semiconductor film optical ellipsometry parameters (1996)

Optical ellipsometry has been found to be a promising technique for monitoring process parameters, such as film composition and film thickness, of semiconductor wafers grown with molecular beam epitaxy. Whereas it is a straightforward task to calculate ellipsometry angles given the thickness of the film and the refractive indexes of the film and substrate, it is a difficult task to invert that mathematical relationship. However, the process must be inverted if the measured parameters are to be interpreted meaningfully in terms of film composition and film thickness. This paper reports on the use of neural-net computing for the inverse mapping of measured ellipsometry parameters. We used a functional-link net which is very efficient in function approximation. The advantage of using the net, however, is not only its speed, but also because some other net architecture characteristics allow us to perform the task in a holistic manner.
Differential Utilization of Calcitonin Gene Regulatory DNA Sequences in Cultured Lines of Medullary Thyroid Carcinoma and Small-Cell Lung Carcinoma (1990)

Regulation of expression of the human calcitonin gene was found to differ between two tumor lines of different tissue origin, medullary thyroid carcinoma (TT line) and small-cell lung carcinoma (DMS53 line). Distal 5' DNA elements between -750 and -2000 exhibited a stronger basal activity in DMS53 than in TT cells, whereas proximal DNA sequences between -132 and -252 mediated a dramatic cyclic AMP response in TT but not DMS53 cells.
62‐6: Invited Paper: Narrow‐Band Phosphors for Next Generation MiniLED and MicroLED Displays (2021)

Both phosphors and quantum dots are currently used in liquid crystal displays (LCDs), with GE's KSF narrow red phosphor demonstrating the best possible red color point, reliability, and efficiency. Next generation miniLED and microLED based displays require excellent color quality (gamut) and high brightness which will require color conversion materials with high EQE and narrow emission peaks. Here we describe recent advancements in narrow‐band phosphors which are being implemented in next‐generation miniLED displays, and being considered for enabling full‐color microLED displays of the future due to their excellent optical performance and robust nature.
Functional Doppler Imaging: A Feasibility Study (2007)

Abstract—We have developed a new method, called 2D flow index mapping (2D-FIM), for quantitative imaging of functional hemodynamic indices, such as resistive index (RI), by retrospective analysis of power Doppler flow waveforms from one complete cardiac cycle. To evaluate this method, a feasibility study was performed in renal transplant patients undergoing routine duplex examination and normal volunteers. Baseband quadrature-demodulated ultrasound echoes were acquired from the parenchyma of the transplant kidneys (n=9) and from normal native kidneys (n=4). The RI values computed from arterial Doppler signals were measured using 2D-FIM. These indices showed a high correlation (Pearson’s r =0.8, P&amp;lt;0.0004) with the values measured using spectral Doppler waveforms. Our preliminary results demonstrate the feasibility of 2D-FIM in renal transplant patients. Further refinement of these methods could lead to visualizing the functional hemodynamics in various complex vascular beds as well as for a more complete functional hemodynamic assessment in renal transplant patients. Keywords-Resistive Index; 2D flow index mapping; renal transplant; power Doppler; functional color Doppler
Efficacy of the therapeutic HPV vaccine in patients with cervical intraepithelial neoplasia 3: phase 2 clinical trial (2019)

Objective: Cervical intraepithelial neoplasia (CIN) 3 is a pre-malignant lesion that may progress to cervical cancer. This phase 2 clinical trial was designed to determine the efficacy of the therapeutic DNA vaccine GX-188E for inducing regression of HPV type 16/18-associated CIN3.
Methods: We conducted a prospective, randomized, multicenter, open-label, phase 2 clinical trial of GX-188E in CIN3 patients positive for HPV type 16/18. The therapeutic vaccine was administered as an intramuscular injection by electroporation. Patients were randomly assigned to receive either 1-mg or 4-mg doses of GX-188E. The primary endpoint was to determine the histopathological regression to ＜CIN1 at visit 7 (V7; 20 weeks after the first GX-188E injection), and an extension study was pursued until visit 8 (V8; 36 weeks after the first GX-188E injection). HPV sequencing analysis and an ex vivo IFN-γ ELISPOT assay were performed using the collected cervical biopsy and blood samples from patients, respectively.
Results: In total, 72 patients were enrolled and underwent randomization. Among them, 52% (33/64) at V7 and 67% (35/52) of patients at V8 presented histopathological regression after receiving the GX-188E injection. We found that 73% (24/33) of the patients at V7 and 77% (27/35) of the patients at V8 showed histopathological regression with HPV clearance. HPV clearance and histopathological regression were significantly associated at V7 (odds ratio=13.867, 95% CI: 4.070-47.249, p＜0.001) and at V8 (odds ratio=25.313, 95% CI: 4.750- 14.883, p＜0.001). Compared to the measurements at V1 (baseline), the patients at V8 with HPV clearance showed significantly higher fold-changes in their IFN-γ ELISPOT responses compared to those without HPV clearance (t-test, p=0.002). The HPV sequence analysis revealed that the HPV type 16 E6/E7 variants D25E (T178G), V83L (G350T), and N29S (A647G) were associated with histopathological regression at V8.
Conclusions: GX-188E is the first therapeutic vaccine to show greater than 50% efficacy against a cohort containing only CIN3 patients with HPV type 16/18 in a phase 2 clinical trial. Thus, this vaccine may be a clinically feasible, non-surgical therapy for treating cervical pre-malignancy in the near future.
Targeting endosialin/CD248 through antibody-mediated internalization results in impaired pericyte maturation and dysfunctional tumor microvasculature (2015)

Over-expression of endosialin/CD248 (herein referred to as CD248) has been associated with increased tumor microvasculature in various tissue origins which makes it an attractive anti-angiogenic target. In an effort to target CD248, we have generated a human CD248 knock-in mouse line and MORAb-004, the humanized version of the mouse anti-human CD248 antibody Fb5. Here, we report that MORAb-004 treatment significantly impacted syngeneic tumor growth and tumor metastasis in the human CD248 knock-in mice. In comparison with untreated tumors, MORAb-004 treated tumors displayed overall shortened and distorted blood vessels. Immunofluorescent staining of tumor sections revealed drastically more small and dysfunctional vessels in the treated tumors. The CD248 levels on cell surfaces of neovasculature pericytes were significantly reduced due to its internalization. This reduction of CD248 was also accompanied by reduced α-SMA expression, depolarization of pericytes and endothelium, and ultimately dysfunctional microvessels. These results suggest that MORAb-004 reduced CD248 on pericytes, impaired tumor microvasculature maturation and ultimately suppressed tumor development.
ASIC Hardware Implementation of the IDEA NXT Encryption Algorithm (2006)

Symmetric-key block ciphers are often used to provide data confidentiality with low complexity, especially in the case of dedicated hardware implementations. IDEA NXT is a novel block cipher family, which has many interesting features and is targeted to multimedia streaming encryption. Different values can be assigned to the hardware architecture parameters in order to scale the security and the performance of the cipher. In this paper, we implement the IDEA NXT algorithm in custom silicon, using a commercial technology library; different optimizations are applied in order to satisfy different constraints in terms of latency and area occupation, maintaining a high level of security. After giving an overview of the IDEA NXT design, a discussion of the implementation choices and trade offs is given, highlighting the similarities and the main differences with regards to other block ciphers. To the authors' knowledge this is the first paper describing such work
New insights into the noise reduction Wiener filter (2006)

The problem of noise reduction has attracted a considerable amount of research attention over the past several decades. Among the numerous techniques that were developed, the optimal Wiener filter can be considered as one of the most fundamental noise reduction approaches, which has been delineated in different forms and adopted in various applications. Although it is not a secret that the Wiener filter may cause some detrimental effects to the speech signal (appreciable or even significant degradation in quality or intelligibility), few efforts have been reported to show the inherent relationship between noise reduction and speech distortion. By defining a speech-distortion index to measure the degree to which the speech signal is deformed and two noise-reduction factors to quantify the amount of noise being attenuated, this paper studies the quantitative performance behavior of the Wiener filter in the context of noise reduction. We show that in the single-channel case the a posteriori signal-to-noise ratio (SNR) (defined after the Wiener filter) is greater than or equal to the a priori SNR (defined before the Wiener filter), indicating that the Wiener filter is always able to achieve noise reduction. However, the amount of noise reduction is in general proportional to the amount of speech degradation. This may seem discouraging as we always expect an algorithm to have maximal noise reduction without much speech distortion. Fortunately, we show that speech distortion can be better managed in three different ways. If we have some a priori knowledge (such as the linear prediction coefficients) of the clean speech signal, this a priori knowledge can be exploited to achieve noise reduction while maintaining a low level of speech distortion. When no a priori knowledge is available, we can still achieve a better control of noise reduction and speech distortion by properly manipulating the Wiener filter, resulting in a suboptimal Wiener filter. In case that we have multiple microphone sensors, the multiple observations of the speech signal can be used to reduce noise with less or even no speech distortion.
Legends for supplemental figures and table from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (2023)

&lt;p&gt;Legends for supplemental figures S1-S15 and tables S1-S11&lt;/p&gt;
Memory-efficient low-compute segmentation algorithms for edge ultrasound devices: continuous bladder monitoring (2023)

Abstract Post-operative urinary retention is a medical condition where patients cannot urinate despite having a full bladder. Ultrasound imaging of the bladder is intermittently used to estimate urine volume for early diagnosis and management of urine retention. Moreover, the use of bladder ultrasound can reduce the need for an indwelling urinary catheter and the risk of catheter-associated urinary tract infection. Wearable ultrasound devices combined with machine-learning based bladder volume estimation algorithms reduce the burdens of nurses in hospital settings and improve outpatient care. However, existing algorithms are memory and computation intensive, thereby demanding the use of expensive GPUs. In this paper, we develop and validate a low-compute memory-efficient deep learning model for accurate bladder region segmentation and urine volume calculation. B-mode ultrasound bladder images of 360 patients were divided into training and validation sets; another 74 patients were used as the test dataset. Our 1-bit quantized models with 4-bits and 6-bits skip connections achieved an accuracy within 3.8% and 2.6%, respectively, of a full precision state-of-the-art neural network (NN) without any floating-point operations and with an 11.5× and 9.0× reduction in memory requirements to fit under 150 kB. The means and standard deviations of the volume estimation errors, relative to estimates from ground-truth clinician annotations, were 5.0±33 ml and 6.8±29 ml, respectively. This lightweight NN can be easily integrated on the wearable ultrasound device for automated and continuous monitoring of urine volume. Our approach can potentially be extended to other clinical applications such as monitoring blood pressure and fetal heart rate.
SKI-606, a novel Src kinase inhibitor, blocks migration and invasion of human breast cancer cells (2007)

AACR Annual Meeting-- Apr 14-18, 2007; Los Angeles, CA

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Src family kinase (SFK) activity is elevated in human breast cancer and is often associated with aggressive disease. Numerous studies point to the central roles of SFKs, notably c-Src, in regulating multiple signaling pathways involved in proliferation, adhesion, motility, and survival of human tumors, thus implicating c-Src as a potential target for cancer therapy. We examined the effects of SKI-606, a novel, orally bioavailable, highly-selective Src family kinase inhibitor, on human breast cancer cells in order to assess its potential for breast cancer treatment. Importantly, our results show that SKI-606 caused a dramatic decrease in cell motility and invasion of human breast cancer cell lines with an IC50 of ~250 nM. These changes were accompanied by an increase in cell-to-cell adhesion, membrane localization of beta-catenin, and a decrease in matrix metalloproteinase-9 activity. Contrary to expectations, inhibition of Src activity did not coincide with inhibition of cell proliferation and survival. Studies of Src/Yes/Fyn knockout cells with restored c-Src provide genetic evidence that the mechanism of action of SKI-606 depends on targeting c-Src. Analysis of downstream effectors of c-Src revealed that SKI-606 inhibits the phosphorylation of focal adhesion kinase (FAK), proline-rich tyrosine kinase 2 (Pyk2) and Crk-associated substrate (p130CAS). Our findings indicate that SKI-606 inhibits signaling pathways involved in controlling tumor cell motility and invasion, suggesting that SKI-606 is a promising new therapeutic agent.
Clinical Use of the Self-Assembling Peptide RADA16: A Review of Current and Future Trends in Biomedicine (2021)

RADA16 is a synthetic peptide that exists as a viscous solution in an acidic formulation. In an acidic aqueous environment, the peptides spontaneously self-assemble into β-sheet nanofibers. Upon exposure and buffering of RADA16 solution to the physiological pH of biological fluids such as blood, interstitial fluid and lymph, the nanofibers begin physically crosslinking within seconds into a stable interwoven transparent hydrogel 3-D matrix. The RADA16 nanofiber hydrogel structure closely resembles the 3-dimensional architecture of native extracellular matrices. These properties make RADA16 formulations ideal topical hemostatic agents for controlling bleeding during surgery and to prevent post-operative rebleeding. A commercial RADA16 formulation is currently used for hemostasis in cardiovascular, gastrointestinal, and otorhinolaryngological surgical procedures, and studies are underway to investigate its use in wound healing and adhesion reduction. Straightforward application of viscous RADA16 into areas that are not easily accessible circumvents technical challenges in difficult-to-reach bleeding sites. The transparent hydrogel allows clear visualization of the surgical field and facilitates suture line assessment and revision. The shear-thinning and thixotropic properties of RADA16 allow its easy application through a narrow nozzle such as an endoscopic catheter. RADA16 hydrogels can fill tissue voids and do not swell so can be safely used in close proximity to pressure-sensitive tissues and in enclosed non-expandable regions. By definition, the synthetic peptide avoids potential microbiological contamination and immune responses that may occur with animal-, plant-, or mineral-derived topical hemostats. <i>In vitro</i> experiments, animal studies, and recent clinical experiences suggest that RADA16 nanofibrous hydrogels can act as surrogate extracellular matrices that support cellular behavior and interactions essential for wound healing and for tissue regenerative applications. In the future, the unique nature of RADA16 may also allow us to use it as a depot for precisely regulated drug and biopharmaceutical delivery.
Allosteric Regulation of Supramolecular Oligomerization and Catalytic Activity via Coordination-Based Control of Competitive Hydrogen-Bonding Events (2014)

Herein, we demonstrate that the activity of a hydrogen-bond-donating (HBD) catalyst embedded within a coordination framework can be allosterically regulated in situ by controlling oligomerization via simple changes in coordination chemistry at distal Pt(II) nodes. Using the halide-induced ligand rearrangement reaction (HILR), a heteroligated Pt(II) triple-decker complex, which contains a catalytically active diphenylene squaramide moiety and two hydrogen-bond-accepting (HBA) ester moieties, was synthesized. The HBD and HBA moieties were functionalized with hemilabile ligands of differing chelating strengths, allowing one to assemble them around Pt(II) nodes in a heteroligated fashion. Due to the hemilabile nature of the ligands, the resulting complex can be interconverted between a flexible, semiopen state and a rigid, fully closed state in situ and reversibly. FT-IR spectroscopy, (1)H DOSY, and (1)H NMR spectroscopy titration studies were used to demonstrate that, in the semiopen state, intermolecular hydrogen-bonding between the HBD and HBA moieties drives oligomerization of the complex and prevents substrate recognition by the catalyst. In the rigid, fully closed state, these interactions are prevented by steric and geometric constraints. Thus, the diphenylene squaramide moiety is able to catalyze a Friedel-Crafts reaction in the fully closed state, while the semiopen state shows no reactivity. This work demonstrates that controlling catalytic activity by regulating aggregation through supramolecular conformational changes, a common approach in Nature, can be applied to man-made catalytic frameworks that are relevant to materials synthesis, as well as the detection and amplification of small molecules.
A new method based on SOA for ACCS software integration (2010)

The aim of ACCS (Army Command and Control System) software integration is to facilitate information sharing among military command and control system and other information systems. This paper provides a service-oriented architecture (SOA) method of software integration based on the actuality of the ACCS, which includes developing an ESB-based integration model, using pattern integration and data duplication methods, and establishing databases. Authors developed several command and control systems with the method which proved it is efficient and can be used in military software development.
A Robust Servo-Electronic Controller for Brake Force Distribution (1990)

In this paper a control system which achieves ideal brake force distribution between the front and the rear wheels of a vehicle during normal braking is studied. Ideal brake proportioning is achieved by dynamically controlling the rear-wheel speed to track the front-wheel speed. Electro-hydraulic brake actuators, which are installed at the rear brakes of the vehicle, are used to modulate the brake-line pressure. A simple linear model of the actuators was developed. This model is derived from experimental response data. Based on this model, a robust servomechanism controller, which achieves ideal brake proportioning by rear-wheel speed control, is designed, implemented, and tested. Test results indicate that the robust servo-mechanism controller achieves a very good wheel speed tracking performance.
Active shape models exploiting slice-to-slice correlation in segmentation of 3D CTA AAA images (2001)

An automated method for the segmentation of thrombus in abdominal aortic aneurysms (AAA) from CTA data is presented. Three segmentation schemes, inspired by Active Shape Model (ASM) segmentation, were investigated. (1) The original ASM scheme as proposed by Cootes and Taylor [1], applied to sequential slices, using the contour obtained in one slice as the initial contour in the adjacent slice. (2) A similar approach, steered by profile greyvalue correlation with adjacent slices rather than by correlation with profiles from the training data and (3) as in (2), with additional attraction to nearby edges.