gebhart/patrepeval huggingface dataset:
Adaptive Self-training for Few-shot Neural Sequence Labeling (2020)

Sequence labeling is an important technique employed for many Natural Language Processing (NLP) tasks, such as Named Entity Recognition (NER), slot tagging for dialog systems and semantic parsing. Large-scale pre-trained language models obtain very good performance on these tasks when fine-tuned on large amounts of task-specific labeled data. However, such large-scale labeled datasets are difficult to obtain for several tasks and domains due to the high cost of human annotation as well as privacy and data access constraints for sensitive user applications. This is exacerbated for sequence labeling tasks requiring such annotations at token-level. In this work, we develop techniques to address the label scarcity challenge for neural sequence labeling models. Specifically, we develop self-training and meta-learning techniques for training neural sequence taggers with few labels. While self-training serves as an effective mechanism to learn from large amounts of unlabeled data -- meta-learning helps in adaptive sample re-weighting to mitigate error propagation from noisy pseudo-labels. Extensive experiments on six benchmark datasets including two for massive multilingual NER and four slot tagging datasets for task-oriented dialog systems demonstrate the effectiveness of our method. With only 10 labeled examples for each class for each task, our method obtains 10% improvement over state-of-the-art systems demonstrating its effectiveness for the low-resource setting.
Comparison of surface PSDs calculated from both AFM profiles and scatter data (1998)

The paper reviews the process for comparing PSD's generated by profile measurements and scatter measurements. Rayleigh scatter as a noise source is reviewed and a new polarization based measurement is presented for discrimination between roughness scatter and particulate scatter. AFM results are compared for both a molybdenum mirror and a silicon wafer. The mirror compares well but 2D detrending technique used impacts the results for the wafer.
An Alkynylboronic Ester Annulation: Development of Synthetic Methods for Application to Diversity‐Oriented Organic Synthesis. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Uncooled 43-Gb/s InGaAlAs Light Source for 10-km Transmission (2011)

A 1.3-μm-range uncooled electroabsorption/distributed-feedback (EA/DFB) laser was demonstrated. Incorporating an InGaAlAs multiple quantum well (MQW) modulator, a low-capacitance structure, and butt-joint integration, this laser successfully demonstrated 43-Gb/s 10-km transmission for the first time. The developed laser achieved clearly opened eye diagrams with dynamic extinction ratio of over 7 dB over a wide temperature range (25 °C to 85 °C).
Structure and properties of new liquid crystalline cubane‐1,4‐dicarboxylic acid derivatives (2005)

New symmetrical esters of cubane‐1,4‐dicarboxylic acid have been prepared. These compounds have the bulky cubane moiety as the central building block. Five classes of derivative have been synthesized: (a) bis[(4‐alkyl)phenyl]cubane‐1,4‐dicarboxylates; (b) bis[(4‐alkoxy)phenyl]cubane‐1,4‐dicarboxylates; (c) the two chiral derivatives bis(cholestenyl)cubane‐1,4‐dicarboxylate, and (S)‐bis[4‐(2‐methylbutyloxycarbonyl)phenyl]cubane‐1,4‐dicarboxylate; (d) three members of the bis [4‐(2,2‐alkoxycarbonylvinyl)phenyl]cubane‐1,4‐dicarboxylates; and (e) bis[(4′‐ethoxycarbonyl)‐1,1′‐biphenyl‐4‐yl]cubane‐1,4‐dicarboxylate. The shorter homologues of the alkoxyphenyl ester series exhibited a nematic (N) phase. No mesophase was observed for the pentyl derivative, while the higher homologues showed a smectic A (SmA) phase according to X‐ray investigations. The 4‐alkylphenyl and chiral derivatives showed only a melting point. The double swallow tailed bis[4‐(2,2‐alkoxycarbonylvinyl)phenyl)]cubane‐1,4‐dicarboxylates also exhibited no mesophase behaviour. On increasing the number of aromatic rings on both sides of the central cubane moiety, N and SmA phases appeared at higher temperatures. In binary mixtures of homologues of alkoxyphenylcubane esters, the temperature range of the SmA phase of the individual compounds became wider and enantiotropic in nature.
Abstract 5357: Inhibition of collagen receptor discoidin domain receptor-1 (DDR1) tyrosine kinase enhances cytotoxicity of anti-mesothelin immunotoxin for cancer therapy (2015)

Abstract Discoidin domain receptor 1 (DDR1) is an emerging anti-cancer target that belongs to the family of tyrosine kinases that are activated by collagen, the most abundant component of extracellular matrix (ECM). Collagen mediated induction of DDR1 facilitates cell adhesion, migration, proliferation and matrix remodeling. The collagen/DDR1 axis is also thought to modulate tumor-stromal interaction and potentially can affect tumor response to therapy. Mesothelin is a cell-surface tumor-associated antigen over-expressed in several human cancers including mesothelioma, ovarian, lung, breast, and pancreatic cancers with limited expression on normal cells. RG7787 is a clinically optimized recombinant immunotoxin (RIT) being developed in collaboration with Roche that should enter clinical trials late this year. It consists of a humanized anti-mesothelin Fab fused to domain III of Pseudomonas exotoxin A in which immunogenic B cell epitopes are silenced. Activation of tyrosine kinase mediated signaling in tumor cells has been shown to modulate the activity of RITs. Therefore, we hypothesized that DDR1 regulates RIT activity and its inhibition might enhance the activity of RG7787. Knockdown of DDR1 by siRNA or its inhibition with a novel and specific inhibitor, ‘7rh’, synergistically enhanced the cytotoxic activity of RG7787 in several cancer cell lines. Investigation into the mechanism of action showed the knockdown of DDR1 increased mesothelin expression, internalization of RG7787, and enhanced inhibition of protein synthesis. Furthermore, stimulation of DDR1 activity by collagen treatment protected cancer cells from killing by RG7787. However, this collagen mediated resistance of cancer cells to RIT therapy can be overcome by addition of 7rh. Combination of 7rh with RG7787 synergistically inhibited growth of A431/H9 tumors in nude mice. In conclusion, we report that collagen protects cells from killing by RITs through DDR1 and that lowering DDR1 protein or inhibiting DDR1 kinase activity enhances the cytotoxic activity of RITs. Our data suggest that the combination of ‘7rh’ and RG7787 represents a novel therapeutic strategy to target mesothelin-expressing cancers. These data also provide insight into how tumor stroma might be protecting cancer cells from therapy. Citation Format: Fatima G. Ali-Rahmani, David Fitzgerald, Scott Martin, Paresma Patel, Craig Thomas, Ira Pastan. Inhibition of collagen receptor discoidin domain receptor-1 (DDR1) tyrosine kinase enhances cytotoxicity of anti-mesothelin immunotoxin for cancer therapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5357. doi:10.1158/1538-7445.AM2015-5357
Evaluation of Metastatic Meningioma With 2-Deoxy-2-[18F]Fluoro-D-Glucose PET/CT (2005)

Although meningioma is typically a benign tumor, in rare instances, it metastasizes. The current case example exhibits moderately increased metabolism despite findings of high-grade malignancy on biopsy.
Moir&#x00E9; artifact prediction in a variable data printing environment (2008)

With the introduction of the digital press in recent years, the cost of short-run printing jobs has decreased. The “print-on-the-fly” capability of these digital presses makes it possible to compose documents based on the contents extracted from various databases. The traditional proofing method in print shops focuses on human visual inspection of one hard copy among thousands of print-outs. However, in variable data printing (VDP), each instance of the same template could use different texts, fonts, and images obtained through various capturing devices. Visual inspection of every copy is not cost efficient in the VDP environment. In this paper, we present a scheme to automatically predict the presence of moiré artifacts in the print-out before the actual printing take place. Only the images that may induce moiré artifact with respect to the targeted press will be identified and adaptive image processing can be applied to eliminate the potential artifact.
765 A Phase I Study of an IL-4-HSV-tk Gene-modified Autologous Glioma Vaccine: Technical Challenges and Promising Initial Results (2001)

INTRODUCTION: Patients with recurrent malignant gliomas have a poor prognosis with a median progression-free survival of less than 3 months. The use of novel, immunotherapeutically based strategies represents an appealing approach for such patients, provided issues of safety and efficacy can be confirmed. METHODS: Our ongoing IL4-HSV-TK autologous glioma vaccine protocol represents a translation of promising in vitro results into a clinically relevant strategy. The numerous regulatory hurdles posed daunting challenges. After approval of the study by the PRC, IRB, IBC, RAC, FDA, and NCI, patient enrollment was permitted. Important entry criteria were the presence of a recurrent malignant glioma that could be resected sufficiently to render the patient steroid-independent, and the demonstration of intact cell-mediated immunity. Patients were to be treated with 2 courses of vaccination with IL4-transduced fibroblasts admixed with irradiated autologous tumor cells followed by ganciclovir administration. The development and clinical application of this protocol represented a...
An ARID family protein binds to the African swine fever virus encoded ubiquitin conjugating enzyme, UBCv1 (2000)

The NH(2)-terminal end of a protein, named SMCp, which contains an ARID (A/T rich interaction domain) DNA binding domain and is similar to the mammalian SMCY/SMCX proteins and retinoblastoma binding protein 2, was shown to bind the African swine fever virus encoded ubiquitin conjugating enzyme (UBCv1) using the yeast two hybrid system and in in vitro binding assays. Antisera raised against the SMCp protein were used to show that the protein is present in the cell nucleus. Immunofluorescence showed that although UBCv1 is present in the nucleus in most cells, in some cells it is in the cytoplasm, suggesting that it shuttles between the nucleus and cytoplasm. The interaction and co-localisation of UBCv1 with SMCp suggest that SMCp may be a substrate in vivo for the enzyme.
Control of the Association State of Tetrameric Glucose-Fructose Oxidoreductase from Zymomonas mobilis as the Rationale for Stabilization of the Enzyme in Biochemical Reactors (1998)

Tetrameric, NADP-containing glucose-fructose oxidoreductase (GFOR) from Zymomonas mobilis catalyzes the oxidation of glucose into glucono-delta-lactone coupled to the reduction of fructose to sorbitol. GFOR is inactivated during substrate turnover in vitro, the long-term stability of the enzyme during conversions in biochemical reactors thereby being drastically reduced. The process of inactivation is triggered by structural transitions that are induced by the lactone product and involves aggregation as the ultimate cause of irreversible inactivation. Guanidinium hydrochloride-induced changes in the conformation of GFOR seem to be similar to those observed in the presence of lactone, and are manifested by incubation time-dependent increases in protein fluorescence and the solvent-exposed hydrophobic surface. The formation of high-order protein associates in solution in the presence of this denaturant proceeds from the native tetramer to a reversibly inactivated octamer and then to a dodecameric form that cannot be reactivated through spontaneous or assisted refolding. Therefore, stabilization of GFOR during turnover requires that the marked tendency of the enzyme to form aggregates is prevented efficiently. This goal has been accomplished in the presence of low urea concentrations (1.0 M), which led to a 10-fold increase in the half-life of GFOR under operational conditions.
Sequential Generation of Linear Cluster States from a Single Photon Emitter (2020)

We present an all-fiber compact scheme to scalably generate arbitrary number polarization entangled photons. A single solid-state quantum dot was utilized as a high-brightness single photon source. We demonstrate entanglement of up to four photons.
Learning to Reconstruct Texture-less Deformable Surfaces from a Single\n View (2018)

Recent years have seen the development of mature solutions for reconstructing\ndeformable surfaces from a single image, provided that they are relatively\nwell-textured. By contrast, recovering the 3D shape of texture-less surfaces\nremains an open problem, and essentially relates to Shape-from-Shading. In this\npaper, we introduce a data-driven approach to this problem. We introduce a\ngeneral framework that can predict diverse 3D representations, such as meshes,\nnormals, and depth maps. Our experiments show that meshes are ill-suited to\nhandle texture-less 3D reconstruction in our context. Furthermore, we\ndemonstrate that our approach generalizes well to unseen objects, and that it\nyields higher-quality reconstructions than a state-of-the-art SfS technique,\nparticularly in terms of normal estimates. Our reconstructions accurately model\nthe fine details of the surfaces, such as the creases of a T-Shirt worn by a\nperson.\n
Supplementary Figures and Tables 3, 5 and 6 from Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy (2023)

&lt;p&gt;Supplementary Figures 1-3 and Tables 1, 3, 4 and 6&lt;/p&gt;
Supplemental Figure S3 from A Novel Bispecific Antibody Targeting EGFR and cMet Is Effective against EGFR Inhibitor–Resistant Lung Tumors (2023)

&lt;p&gt;Effect of Crizotinib on H1975 and H1975-HGF Xenograft Tumors&lt;/p&gt;
A comparison between the effect of step-down heating in a tumour and a normal tissue invivo (1991)

A comparison between the effect of step-down heating (SDH) obtained in a C3H mammary carcinoma grown in the feet of CDF1 mice and the skin of normal CDF1 feet is presented. Water-bath heating was used, and SDH was obtained by giving a 44.7 degrees C/10 min treatment followed by heating at 42.2 degrees C for variable times. Single heating at 42.2 degrees C and step-up heating (SUH), i.e. 42.2 degrees C followed by 44.7 degrees C/10 min, were used as controls. The endpoint was the heating time at 42.2 degrees C to obtain either a definite tumour growth time (TGT50) or a specific skin score level (RD50) in 50% of the animals. The effect of SDH and SUH was quantified by the step-down ratio (SDR), calculated as the ratio of the heating times at 42.2 degrees C to obtain the specific endpoint. In both assays the effect of SDH was seen as a significant left shift of the SDH dose-response curve compared to the curve for single heating and SUH. For the comparison of the tumour and the normal tissue response, damage levels with comparable heating times for single heating were used. The therapeutic effect was then investigated by calculating the therapeutic gain factor (TGF), where TGF = SDR(tumour)/SDR(normal tissue). Neither SUH nor SDH gave a TGF significantly different from 1. The results suggest that SDH may be used clinically to shorten the heating time without decreasing the therapeutic effect.
ChemInform Abstract: A Convenient Synthetic Route to Spiro[indole‐3,4′‐piperidin]‐2‐ones. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An evaluation of segment duration effects in HTTP adaptive streaming over mobile networks (2015)

In HTTP adaptive streaming, the length of each video segment is not strictly specified; choosing segment duration is an implementation-specific decision. In this paper, we evaluate the effects of segment duration to video streaming performance in various network conditions. By carrying out experiments we realize that the choice of segment duration has a profound impact on several aspects including end-user's experience as well as the effects on the server and network side. Our experimental results provide preliminary suggestions on the choice of segment duration in certain streaming situations.
Worst- and Best-Case Coverage in Sensor Networks (2005)

Abstract—Wireless ad hoc sensor networks have recently emerged as a premier research topic. They have great long-term economic potential, ability to transform our lives, and pose many new system-building challenges. Sensor networks also pose a number of new conceptual and optimization problems. Here, we address one of the fundamental problems, namely, coverage. Sensor coverage, in general, answers the questions about the quality of service (surveillance) that can be provided by a particular sensor network. We briefly discuss the definition of the coverage problem from several points of view and formally define the worst and best-case coverage in a sensor network. By combining computational geometry and graph theoretic techniques, specifically the Voronoi diagram and graph search algorithms, we establish the main highlight of the paper—an optimal polynomial time worst and average case algorithm for coverage calculation for homogeneous isotropic sensors. We also present several experimental results and analyze potential applications, such as using best and worst-case coverage information as heuristics to deploy sensors to improve coverage. Index Terms—Sensor networks, coverage, maximal breach, maximal support, best-case coverage, worst-case coverage. 1
Abstract 1215: Targeting TIP1 with a novel radiosensitizing antibody-drug conjugate (ADC) enhances the therapeutic efficacy of radiation for non-small cell lung carcinoma treatment (2021)

Abstract Tax-interacting protein 1 (TIP1) is a multifunctional protein involved in cellular motility, cellular adhesion, migration, cancer cell protection from ionizing radiation, and metastasis. We found that TIP1 is a radiation inducible antigen that is translocated to the cancer cell surface. Antibody-drug-conjugates (ADCs) are emerging as promising anti-cancer immunoconjugates. ADCs carry antitumor payloads and allow site-specific targeting of cancer with increased cytotoxicity and decreased side effect profiles as compared to conventional chemotherapy. Monomethyl auristatin E (MMAE) is a potent radiosensitizing microtubule inhibitor with enhanced cancer cytotoxicity in combination with radiotherapy. We developed ADCs against radiation-inducible TIP1 for lung cancer treatment in combination with radiation. Out of the various anti-TIP1 antibodies, we prioritized the lead antibody that shows high affinity to TIP1 protein on the cancer cell surface and in vivo irradiated lung cancers. Our lead antibody, 7H5 undergoes endocytosis in cancer cells in vitro. We conjugated 7H5 to VcMMAE. Hydrophobic interaction chromatography (HIC) was performed to determine drug-to-antibody ratio (DAR). We obtained an average DAR of 3.7. Cytotoxic potential of 7H5-VcMMAE was evaluated in A549 and H1299 NSCLC cells. Cells were exposed to 7H5-VcMMAE or 7H5-antibody alone at various doses. At 10nM concentration, ~70% reduction in viable cells was observed following 7H5-VcMMAE treatment compared to 7H5 alone in both A549 (p=0.0032) and H1299 cells (p=0.0010). 7H5-VcMMAE sensitized A549 and H1299 cells to radiation as observed by significantly decreased (p&amp;lt;0.001) surviving fraction compared to 7H5 alone. In vivo therapeutic efficacy of the 7H5-VcMMAE was determined using mice bearing hind-limb human NSCLC tumors. The ADC showed a prolonged delay in tumor growth and improved tumor control was achieved with IR + 7H5-VcMMAE in A549 and H1299 hind-limb tumor models. Furthermore, mice in all groups displayed no toxicity associated with treatment. Our study suggests that targeting radiation-inducible TIP1 with a radiosensitizing ADC is a promising strategy to enhance therapeutic efficacy in lung cancer. This novel approach of targeting cancer using ADCs to radiation-inducible antigens will lead to clinical trials in lung cancer patients treated with radiotherapy. Citation Format: Calvin Lewis, Abhay K. Singh, Dinesh Thotala, Dennis E. Hallahan, Vaishali Kapoor. Targeting TIP1 with a novel radiosensitizing antibody-drug conjugate (ADC) enhances the therapeutic efficacy of radiation for non-small cell lung carcinoma treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1215.
A Novel Class of Cysteine Protease Inhibitors:  Solution Structure of Staphostatin A from Staphylococcus aureus (2003)

A series of secreted proteases are included among the virulence factors documented for Staphylococcus aureus. In light of increasing antibiotic resistance of this dangerous human pathogen, these proteases are considered as suitable targets for the development of novel therapeutic strategies. The recent discovery of staphostatins, endogenous, highly specific, staphylococcal cysteine protease inhibitors, opened a possibility for structure-based design of low molecular weight analogues. Moreover, the crystal structure of staphostatin B revealed a distinct folding pattern and an unexpected, substrate-like binding mode. The solution structure of staphostatin A reported here confirms that staphostatins constitute a novel, distinct class of cysteine protease inhibitors. In addition, the structure knowledge-based mutagenesis studies shed light on individual structural features of staphostatin A, the inhibition mechanism, and the determinants of distinct specificity of staphostatins toward their target proteases.
Notice of Removal: Evaluation of a new non-invasive ultrasonic device for venous recanalization: Assessment of feasibility and safety of thrombotripsy at 2.25 MHz in an in vitro model of recent venous thrombosis (2017)

Removed.
Fundamental Mode Approach to Forward Problem Solutions in EMI Scattering ---- Inferring fundamental solutions from training data (2004)

Electromagnetic induction is the leading technology for discrimination of subsurface metallic targets such as unexploded ordnance (UXO). The cleanup problem requires solution of remote sensing inverse problem inevitably based on some very fast forward algorithms for calculating EMI. The forward model must determine responses of arbitrarily complicated metallic objects. Here a very fast and complete forward solution system is presented, based on fundamental mode excitations. For a given target (or a set of targets), the EMI responses to fundamental modes are obtained from training data and saved. Any realistic excitation field is then decomposed into a limited number of constituent fundamental modes and the scatterer's EMI response is obtained by superposition of the fundamental mode solutions. In this paper we define the fundamental excitations explicitly and consider their rationale; show how to construct any particular solutions from solutions to the fundamental excitations; and focus particularly on how to obtain, retain, express responses to the fundamental solutions in the face of inherent ill-conditioning.