gebhart/patrepeval huggingface dataset:
Part-of-Speech Tagging by Latent Analogy (2010)

Part-of-speech tagging is often a critical first step in various speech and language processing tasks. High-accuracy taggers (e.g., based on conditional random fields) rely on well chosen feature functions to ensure that important characteristics of the empirical training distribution are reflected in the trained model. This makes them vulnerable to any discrepancy between training and tagging corpora, and, in particular, accuracy is adversely affected by the presence of out-of-vocabulary words. This paper explores an alternative tagging strategy based on the principle of latent analogy, which was originally introduced in the context of a speech synthesis application. In this approach, locally optimal tag subsequences emerge automatically from an appropriate representation of global sentence-level information. This solution eliminates the need for feature engineering, while exploiting a broader context more conducive to word sense disambiguation. Empirical evidence suggests that, in practice, tagging by latent analogy is essentially competitive with conventional Markovian techniques, while benefiting from substantially less onerous training costs. This opens up the possibility that integration with such techniques may lead to further improvements in tagging accuracy.
ChemInform Abstract: The Synthesis of 9‐Oxo‐9,10‐dihydroacridine‐4‐carboxylic Acids via the Jourdan‐Ullmann Reaction of Anthranilic Acids and Methyl 2‐Iodobenzoates. (1988)

Abstract The anthranilic acids (I) are coupled with the o‐iodobenzoates (II), using the Jourdan‐Ullmann method to produce the N‐arylanthranilic acids (III).
Abstract 3249: Circulating cytokine associations with clinical outcomes in melanoma patients treated with checkpoint inhibitors (2023)

Abstract Background: aCTLA-4/aPD-1 combination therapy has significantly improved clinical outcomes in patients with metastatic melanoma, with 50%-60% of patients responding to treatment, but predictors of response are poorly characterized. In this study, we set out to evaluate the hypothesis that circulating cytokines and peripheral white blood cell composition may predict response to therapy. Methods: We quantified cytokines and complete blood counts from 89 patients with advanced melanoma treated with combination therapy from three points in time: pre-treatment, one month and approximately three months after starting therapy. We evaluated the association between peripheral blood circulating features, cytokines and clinical labs values, and clinical outcome using predictive modeling, and investigated the prognostic values of these features using survival analysis. Results: Pre-treatment, patients with durable clinical benefit (DCB) had higher IL23, lower CXCL6, and lower IL10 levels. The ratio of neutrophils to lymphocytes (NLR) pre-treatment was not associated with response, but higher NLR one month after starting therapy predicted poorer progression free survival (PFS) and overall survival (OS), primarily driven by an increase in absolute lymphocytes. A multivariate model demonstrated that baseline CXCL6, IL10, IL23 were independent predictors of therapy response, and the combined model has reached an area under the curve (AUC) of 0.8 in prediction of response to combination therapy. Low IL10 and CXCL6 identified an excellent prognosis group, while high CXCL6 and low IL23 characterized a very poor prognosis group of patients. Conclusions: Baseline measurement of cytokines IL23, CXCL6, and IL10 can predict metastatic melanoma patients’ response to ipi/nivo combination treatment. Higher neutrophils-to-lymphocytes ratio approximately one month after therapy started associates with worse survival outcome. Our study presented circulating features from a relatively accessible and less costly avenue, peripheral blood, to be predictive of response to combination immune checkpoint blockade. Citation Format: Jiajia Chen, Giuseppe Tarantino, Mariano Severgnini, Joanna Baginska, Anita Giobbie-Hurder, Michael Manos, Janice D. Russell, Jason L. Weirather, Kathleen Pfaff, Amy Y. Huang, Scott J. Rodig, Srinika Ranashinge, David Liu, F.Stephen Hodi. Circulating cytokine associations with clinical outcomes in melanoma patients treated with checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3249.
Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking (2021)

We have performed dynamic docking between a prototypic G-protein-coupled receptor (GPCR) system, the β<sub>2</sub>-adrenergic receptor, and its antagonist, alprenolol, using one of the enhanced conformation sampling methods, multicanonical molecular dynamics (McMD), which does not rely on any prior knowledge for the definition of the reaction coordinate. Although we have previously applied our McMD-based dynamic docking protocol to various globular protein systems, its application to GPCR systems would be difficult because of their complicated design, which include a lipid bilayer, and because of the difficulty in sampling the configurational space of a binding site that exists deep inside the GPCR. Our simulations sampled a wide array of ligand-bound and ligand-unbound structures, and we measured 427 binding events during our 48 μs production run. Analysis of the ensemble revealed several stable and meta-stable structures, where the most stable structure at the global free energy minimum matches the experimental one. Additional canonical MD simulations were used for refinement and validation of the structures, revealing that most of the intermediates are sufficiently stable to trap the ligand in these intermediary states and furthermore validated our prediction results. Given the difficulty in reaching the orthosteric binding site, chemical optimization of the compound for the second ranking configuration, which binds near the pocket's entrance, might lead to a high-affinity allosteric inhibitor. Accordingly, we show that the application of our methodology can be used to provide crucial insights for the rational design of drugs that target GPCRs.
In ovo time-lapse analysis of chick hindbrain neural crest cell migration shows cell interactions during migration to the branchial arches (2000)

Hindbrain neural crest cells were labeled with DiI and followed in ovo using a new approach for long-term time-lapse confocal microscopy. In ovo imaging allowed us to visualize neural crest cell migration 2-3 times longer than in whole embryo explant cultures, providing a more complete picture of the dynamics of cell migration from emergence at the dorsal midline to entry into the branchial arches. There were aspects of the in ovo neural crest cell migration patterning which were new and different. Surprisingly, there was contact between neural crest cell migration streams bound for different branchial arches. This cell-cell contact occurred in the region lateral to the otic vesicle, where neural crest cells within the distinct streams diverted from their migration pathways into the branchial arches and instead migrated around the otic vesicle to establish a contact between streams. Some individual neural crest cells did appear to cross between the streams, but there was no widespread mixing. Analysis of individual cell trajectories showed that neural crest cells emerge from all rhombomeres (r) and sort into distinct exiting streams adjacent to the even-numbered rhombomeres. Neural crest cell migration behaviors resembled the wide diversity seen in whole embryo chick explants, including chain-like cell arrangements; however, average in ovo cell speeds are as much as 70% faster. To test to what extent neural crest cells from adjoining rhombomeres mix along migration routes and within the branchial arches, separate groups of premigratory neural crest cells were labeled with DiI or DiD. Results showed that r6 and r7 neural crest cells migrated to the same spatial location within the fourth branchial arch. The diversity of migration behaviors suggests that no single mechanism guides in ovo hindbrain neural crest cell migration into the branchial arches. The cell-cell contact between migration streams and the co-localization of neural crest cells from adjoining rhombomeres within a single branchial arch support the notion that the pattern of hindbrain neural crest cell migration emerges dynamically with cell-cell communication playing an important guidance role.
Utilisation of artificial intelligence for the development of an EUS-convolutional neural network model trained to enhance the diagnosis of autoimmune pancreatitis (2020)

The developed EUS-CNN model accurately differentiated AIP from PDAC and benign pancreatic conditions, thereby offering the capability of earlier and more accurate diagnosis. Use of this model offers the potential for more timely and appropriate patient care and improved outcome.
Graphene-type sheets of Nb1−xWxS2: synthesis and in situ functionalization (2013)

Enlightened by the discovery of graphenes, a variety of inorganic analogues have been synthesized and characterized in recent years. Solvated Nb1-xWxS2 analogues of graphene-type sheets were prepared by lithiation and exfoliation of multistacked Nb1-xWxS2 coin roll nanowires (CRNWs), followed by in situ functionalization with gold nanoparticles to synthesize gold-loaded Nb1-xWxS2/Au nanocomposites. The Nb1-xWxS2 nanosheets and the corresponding Nb1-xWxS2/Au nanocomposites were characterized by high resolution electron microscopy (HRTEM), energy-dispersive X-ray spectroscopy (EDX), scanning transmission electron microscopy (STEM), dynamic light scattering (DLS) and scanning force microscopy (AFM). The graphene-type sheets are stable in water and other solvents and can be functionalized similarly as chalcogen-terminated surfaces (e.g. with Au nanoparticles).
Monocyte Chemotactic Protein-Induced Protein 1 (MCPIP-1): A Key Player of Host Defense and Immune Regulation (2021)

Inflammatory response is a host-protective mechanism against tissue injury or infections, but also has the potential to cause extensive immunopathology and tissue damage, as seen in many diseases, such as cardiovascular diseases, neurodegenerative diseases, metabolic syndrome and many other infectious diseases with public health concerns, such as Coronavirus Disease 2019 (COVID-19), if failure to resolve in a timely manner. Recent studies have uncovered a superfamily of endogenous chemical molecules that tend to resolve inflammatory responses and re-establish homeostasis without causing excessive damage to healthy cells and tissues. Among these, the monocyte chemoattractant protein-induced protein (MCPIP) family consisting of four members (MCPIP-1, -2, -3, and -4) has emerged as a group of evolutionarily conserved molecules participating in the resolution of inflammation. The focus of this review highlights the biological functions of MCPIP-1 (also known as Regnase-1), the best-studied member of this family, in the resolution of inflammatory response. As outlined in this review, MCPIP-1 acts on specific signaling pathways, in particular NFκB, to blunt production of inflammatory mediators, while also acts as an endonuclease controlling the stability of mRNA and microRNA (miRNA), leading to the resolution of inflammation, clearance of virus and dead cells, and promotion of tissue regeneration <i>via</i> its pleiotropic effects. Evidence from transgenic and knock-out mouse models revealed an involvement of MCPIP-1 expression in immune functions and in the physiology of the cardiovascular system, indicating that MCPIP-1 is a key endogenous molecule that governs normal resolution of acute inflammation and infection. In this review, we also discuss the current evidence underlying the roles of other members of the MCPIP family in the regulation of inflammatory processes. Further understanding of the proteins from this family will provide new insights into the identification of novel targets for both host effectors and microbial factors and will lead to new therapeutic treatments for infections and other inflammatory diseases.
Liposomes in Immunodiagnostics (2019)

Liposomes can be made out of thousands of natural or synthetic lipids that are commercially available. Depending on the lipids chosen, they can be cationic, anionic, or neutral and can have headgroups containing reactive moieties such as amines, carboxyls, sugars, or sulfhydryls. An overwhelming number of research articles exist on various applications of liposomes. The chapter reviews applications of liposomes for immunodiagnostic assays. Liposomes have exhibited a potential for signal enhancement and higher sensitivities when used in immunodiagnostic applications. In Lytic assay, liposomes carry a ligand on the surface and marker molecules inside. The liposome lyses when exposed to sample-containing analyte molecules which bind specifically to the ligand. Lysis of the liposomes results in the release of the marker molecules that can then be detected analytically. Cytolysin-based assays require fewer steps and are faster and considerably more versatile than the complement-dependent approaches.
Structured discriminative models for noise robust continuous speech recognition (2011)

Recently there has been interest in structured discriminative models for speech recognition. In these models sentence posteriors are directly modelled, given a set of features extracted from the observation sequence, and hypothesised word sequence. In previous work these discriminative models have been combined with features derived from generative models for noise-robust speech recognition for continuous digits. This paper extends this work to medium to large vocabulary tasks. The form of the score-space extracted using the generative models, and parameter tying of the discriminative model, are both discussed. Update formulae for both conditional maximum likelihood and minimum Bayes' risk training are described. Experimental results are presented on small and medium to large vocabulary noise-corrupted speech recognition tasks: AURORA 2 and 4.
In Search of Spectroscopic Signatures of Periodontitis: A SERS-Based Magnetomicrofluidic Sensor for Detection of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans (2021)

Recently, <i>Porphyromonas gingivalis</i>, the keystone pathogen implicated in the development of gum disease (periodontitis), was detected in the brains of Alzheimer's disease patients, opening up a fascinating possibility that it is also involved in the pathobiology of this neurodegenerative illness. To verify this hypothesis, an unbiased, specific, and sensitive method to detect this pathogen in biological specimens is needed. To this end, our interdisciplinary studies demonstrate that <i>P. gingivalis</i> can be easily identified by surface-enhanced Raman scattering (SERS). Moreover, based on SERS measurements, <i>P. gingivalis</i> can be distinguished from another common periodontal pathogen, <i>Aggregatibacter actinomycetemcomitans</i>, and also from ubiquitous oral <i>Streptococcus</i> spp. The results were confirmed by principal component analysis (PCA). Furthermore, we have shown that different <i>P. gingivalis</i> and <i>A. actinomycetemcomitans</i> strains can easily adsorb to silver-coated magnetic nanoparticles (Fe<sub>2</sub>O<sub>3</sub>@AgNPs). Thus, it is possible to magnetically separate investigated bacteria from other components of a specimen using the microfluidic chip. To obtain additional enhancement of the Raman signal, the NPs adsorbed to bacterial cells were magnetically attracted to the Si/Ag SERS platform. Afterward, the SERS spectra could be recorded. Such a time-saving procedure can be very helpful in rapid medical diagnostics and thus in starting the appropriate pharmacological therapy to prevent the development of periodontitis and associated comorbidities, e.g., Alzheimer's disease.
Kappa Opioid Receptors Drive a Tonic Aversive Component of Chronic Pain (2019)

Pain is a multidimensional experience and negative affect, or how much the pain is "bothersome", significantly impacts the sufferers' quality of life. It is well established that the κ opioid system contributes to depressive and dysphoric states, but whether this system contributes to the negative affect precipitated by the occurrence of chronic pain remains tenuous. Using a model of persistent pain, we show by quantitative real-time-PCR, florescence <i>in situ</i> hybridization, Western blotting and GTPgS autoradiography an upregulation of expression and the function of κ opioid receptors (KORs) and its endogenous ligand dynorphin in the mesolimbic circuitry in animals with chronic pain compared with surgical controls. Using <i>in vivo</i> microdialysis and microinjection of drugs into the mesolimbic dopamine system, we demonstrate that inhibiting KORs reinstates evoked dopamine release and reward-related behaviors in chronic pain animals. Chronic pain enhanced KOR agonist-induced place aversion in a sex-dependent manner. Using various place preference paradigms, we show that activation of KORs drives pain aversive states in male but not female mice. However, KOR antagonist treatment was effective in alleviating anxiogenic and depressive affective-like behaviors in both sexes. Finally, ablation of KORs from dopamine neurons using AAV-TH-cre in KOR<sup>loxP</sup> mice prevented pain-induced aversive states as measured by place aversion assays. Our results strongly support the use of KOR antagonists as therapeutic adjuvants to alleviate the emotional, tonic-aversive component of chronic pain, which is argued to be the most significant component of the pain experience that impacts patients' quality of life.<b>SIGNIFICANCE STATEMENT</b> We show that KORs are sufficient to drive the tonic-aversive component of chronic pain; the emotional component of pain that is argued to significantly impact a patient's quality of life. The impact of our study is broadly relevant to affective disorders associated with disruption of reward circuitry and thus likely contributes to many of the devastating sequelae of chronic pain, including the poor response to treatment of many patients, debilitating affective disorders (other disorders including anxiety and depression that demonstrate high comorbidity with chronic pain) and substance abuse. Indeed, coexisting psychopathology increases pain intensity, pain-related disability and effectiveness of treatments (Jamison and Edwards, 2013).
Cytogenetic and molecular predictors of response in patients with myeloid malignancies without del[5q] treated with lenalidomide (2012)

Normal karyotype and gain of chromosome 8 material was predictive of response to LEN in non-del[5q] patients with myeloid malignancies.
Reviews (1994)

Power and the Praise Poem: Southern African Voices in History. Leroy Vail and Landeg White, (University Press ofVirginia/James Currey, 1991, pb £11.95). Mating. Norman Rush, (Jonathan Cape, 1992, hb. £15.99, Vintage, 1993, ph.£5.99). The Natal Papers of ‘John Ross‘. Charles Rawden Maclean, (Ed.) Stephen Gray, (University of Natal Press: Pietermaritzburg, 1992, pb (SA) R57–57). Cetshwayo's Dutchman. Cornelius Vijn, (Ed. and trans.) J W Colenso, Bishop of Natal, 1880. (Greenhill Books: London, 1988, hb). Dambudzo Marechera: A Source Book on his Life and Work. Flora Veit‐Wild, (HdnsZell Publishers, 1992, hb). Cemetery of Mind. Dambudzo Marechera, (Baobab Books, Harare, 1992, pb. £6.50). Pawns. Charles Samupindi, (Baobab Books, Harare, 1992, pb. £6.50). Fruits and Other Poems. Titus Moetsabi, (Zimbabwe Publishing House, Harare, 1992, pb.£5.00). Third World Express. Mongane Wally Serote, (David Philip, Cape Town & Johannesburg, 1992, pb. R24.95). Guava Juice. Sandile Dikeni, (Mayibuye Booh, Bellville [Cape], 1992, pb.) Emergency Poems. Keith Gottschalk, (Mayibuye Books, Bellville [Cape], 1992, pb.) Gardens of Struggle. Barry Feinbu'rg, (Mayibuye Books, Bellville [Cape], 1992, pb.) The Coffee Shop Poems. Karen Press, (Snailpress, Plumstead [Cape], 1993, pb.) Avalon Court. Gladys Thomas, (Skotaville Publishers, Braamfontein, 1992, pb. £5). The View from the Stockade. Landeg White, (Dangaroo Press, 1991, pb.) Bounty. Landeg White, (Dangaroo Press, 1993, pb.) The First Life of Adamastor. André Brink, (Seeker & Warburg, 1993, pb. £7.99). Stedman and Joanna ‐ a Love in Bondage. Beryl Gilroy, (Vantage Press USA, 1991, hb). Nehanda. Yvonne Vera (Baobab Books, 1993, pb. £6.25). War Child. Stephen Gray (Serif, 1993, pb. £9.99). Cultural Struggle & Development in Southern Africa. (ed.) Preben Kaarsholm (London: James Currey, and Harare: Baobab, and Portsmouth, New Hampshire, Heinemann, 1991, hb. £30, pb. £11.95). The Chattering Wagtails of Mikuyu Prison. Jack Mapanje, (Heinemann, 1993, pb. £5.99). One Dark Body. Charlotte Watson Sherman, (Women's Press, 1993, pb. £6.99).
Molecular cloning of peroxidase cDNAs from dehydration-treated fibrous roots of sweetpotato and their differential expression in response to stress (2008)

Three peroxidase (POD) cDNAs were isolated from dehydration-treated fibrous roots of sweetpotato (Ipomoea batatas) plant via the screening of a cDNA library, and their expressions were assessed to characterize functions of each POD in relation to environmental stress. Three PODs were divided into two groups, designated the basic PODs (swpb4, swpb5) and the anionic PODs (swpa7), on the basis of the pI values of mature proteins. Fluorescence microscope analysis indicated that three PODs are secreted into the extracellular space. RTPCR analysis revealed that POD genes have diverse expression patterns in a variety of plant tissues. Swpb4 was abundantly expressed in stem tissues, whereas the expression levels of swpb5 and swpa7 transcripts were high in fibrous and thick pigmented roots. Swpb4 and swpa7 showed abundant expression levels in suspension cultured cells. Three POD genes responded differently in the leaf and fibrous roots in response to a variety of stresses including dehydration, temperature stress, stress-associated chemicals, and pathogenic bacteria.
Intravesical NGF Antisense Therapy using Lipid Nanoparticle for Interstitial Cystitis (2013)

Abstract : Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating disorder characterized by persistent pelvic pain associated with bladder symptoms including urinary frequency and urgency. Previous studies have indicated that overexpression of nerve growth factor (NGF) is a important factor in the symptom development of IC/BPS. This project evaluates the feasibility of an anti-NGF bladder drug delivery system as a potential investigational drug product. The project aims include exploration, manufacture, characterization, and nonclinical animal testing of a liposome NGF-antisense formulation targeting IC/BPS. During the project period investigators conducted nonclinical experiments and analyzed results from an animal efficacy experiment conducted during the previous period. The project is ongoing.
Enhancing the frequency stability of a NEMS oscillator with electrostatic and mechanical nonlinearities (2009)

We show how to achieve large-amplitude oscillation and good frequency stability in a nonlinear NEMS oscillator by using a softening nonlinearity to locally balance the hardening behaviour of the Duffing nonlinearity for a given motion amplitude. The case when the softening behaviour is obtained via electrostatic biasing is theoretically investigated, under parallel-plate assumptions, for a fully-capacitive pulse-actuated resonant structure. This is validated by simulated data, in the case of a resonant clamped-clamped beam.