gebhart/patrepeval huggingface dataset:
Direct identification of major histocompatibility complex class I-bound tumor-associated peptide antigens of a renal carcinoma cell line by a novel mass spectrometric method. (1998)

Melanoma and renal cell carcinoma (RCC) are thought to be the most immunogenic human tumors. Presently a series of tumor-specific peptides of melanoma is being tested in clinical trials with different immunotherapy protocols. In contrast, only one decameric peptide (SPSSNRIRNT) derived from one (ORF2) of three possible open reading frames (ORFs) of a gene named RAGE (Renal tumor AntiGEn) was shown to be the target for tumor-specific CTLs on renal carcinoma cells. One reason for the lack of identification of tumor antigens on RCC compared with melanoma may be the difficulty in generating tumor-specific CTLs as screening instruments. Therefore, our approach was directly to isolate and identify peptides bound to HLA class I molecules of the HLA-A2 and -B8 homozygous RCC line A-498. High performance liquid chromatography-fractionated peptides eluted with acid from immunoaffinity-purified HLA class I-peptide complexes were sequenced and identified for the first time by the novel and highly sensitive mass spectrometric method matrix-assisted laser desorption ionization-post source decay (MALDI-PSD) from minute amounts of 100 fmol to 1.5 pmol of the fractionated peptide samples. Fourteen peptide sequences first deduced from interpretations of the mass spectra were also shown to fulfill other reliability criteria such as matching the mass spectra of the respective synthetic peptides. Some peptides were identified to be derived from genes preferentially activated in malignant tissues or resulted from a possibly mutated gene. The most promising candidate for a CTL epitope is a decameric peptide (PASKKTDPQK) derived from another possible ORF (ORF5) of the RAGE gene and probably presented in association with HLA-B8. This peptide was synthesized and used for the in vitro induction of CTLs that lysed the A-498 cells and another HLA-B8-positive RCC line significantly more strongly than either other RAGE-positive but HLA-B8-negative RCC lines or K562 cells. Sensitive sequencing by MALDI-PSD thus may provide a powerful method of identifying potentially tumor-specific and HLA-restricted antigens, even on native malignant cells and tissues.
Automatic Synthesis of Regular Expressions from Examples (2014)

A system that can produce regular expressions from user-provided examples performed with high precision and recall in 12 text-extraction tasks from real-world datasets, demonstrating the effectiveness of text extraction based on genetic programming.
Synthesis of Clay Minerals at Low Temperatures (1955)

Abstract Numerous attempts have shown that it seems to be impossible to crystallize co-precipitates of silica and hydroxides; we therefore attempted to prepare clay minerals starting from solutions of their constituents. By allowing these dilute solutions (tenths of milligrams per liter) to pass slowly into a flask containing distilled water, it has been possible to prepare substances similar to clay minerals. These have been identified by x-rays, chemical analysis, dehydration curves, and electron micrographs. Using as cations Mg, Fe 2+ , Fe 3+ , and Ni, minerals of the montmorillonite type have been prepared for various pH values (generally greater than 7). Below this, value, depending on the cations; oxides, hydroxides, or amorphous materials are obtained. Under certain conditions in the absence of silica the glass vessel was attacked, and anti-gorites of Mg and Ni were then obtained. Always when the supply of silica was small, and with the cation introduced in the form of a very dilute solution, the process gave rise to montmorillonite. In the presence of K, illites were sometimes formed. The method seems to be of very general application. Only the purely aluminum minerals offer difficulties of preparation. The significance of these results is discussed.
Local Spectral Clustering for Overlapping Community Detection (2018)

Large graphs arise in a number of contexts and understanding their structure and extracting information from them is an important research area. Early algorithms for mining communities have focused on global graph structure, and often run in time proportional to the size of the entire graph. As we explore networks with millions of vertices and find communities of size in the hundreds, it becomes important to shift our attention from macroscopic structure to microscopic structure in large networks. A growing body of work has been adopting local expansion methods in order to identify communities from a few exemplary seed members. In this article, we propose a novel approach for finding overlapping communities called L emon ( L ocal E xpansion via M inimum O ne N orm). Provided with a few known seeds , the algorithm finds the community by performing a local spectral diffusion. The core idea of L emon is to use short random walks to approximate an invariant subspace near a seed set, which we refer to as local spectra . Local spectra can be viewed as the low-dimensional embedding that captures the nodes’ closeness in the local network structure. We show that L emon ’s performance in detecting communities is competitive with state-of-the-art methods. Moreover, the running time scales with the size of the community rather than that of the entire graph. The algorithm is easy to implement and is highly parallelizable. We further provide theoretical analysis of the local spectral properties, bounding the measure of tightness of extracted community using the eigenvalues of graph Laplacian. We thoroughly evaluate our approach using both synthetic and real-world datasets across different domains, and analyze the empirical variations when applying our method to inherently different networks in practice. In addition, the heuristics on how the seed set quality and quantity would affect the performance are provided.
Sprained ankles as they relate to the basketball player. (1993)

Concepts based on newer medical information concerning ankle injuries have changed in recent years. With these changing concepts, the method of treatment has also changed. It is the purpose of this article to review some of the commonly known information concerning ankle sprains, to emphasize the association of subtalar injury with the ankle sprain complex, to outline new information concerning the static stabilizers on the lateral aspect of the ankle, and finally, to utilize this information in producing a rationale for a new type of surgical treatment for chronic instability of the ankle.
Synchronous, Focally Modulated β-Band Oscillations Characterize Local Field Potential Activity in the Striatum of Awake Behaving Monkeys (2003)

Synchronous oscillatory activity has been observed in a range of neural networks from invertebrate nervous systems to the human frontal cortex. In humans and other primates, sensorimotor regions of the neocortex exhibit synchronous oscillations in the β-frequency band (∼15-30 Hz), and these are also prominent in the cerebellum, a brainstem sensorimotor region. However, recordings in the basal ganglia have suggested that such β-band oscillations are not normally a primary feature of these structures. Instead, they become a dominant feature of neural activity in the basal ganglia in Parkinson9s disease and in parkinsonian states induced by dopamine depletion in experimental animals. Here we demonstrate that when multiple electrodes are used to record local field potentials, 10-25 Hz oscillations can be readily detected in the striatum of normal macaque monkeys. These normally occurring oscillations are highly synchronous across large regions of the striatum. Furthermore, they are subject to dynamic modulation when monkeys perform a simple motor task to earn rewards. In the striatal region representing oculomotor activity, we found that small focal zones could pop in and out of synchrony as the monkeys made saccadic eye movements, suggesting that the broadly synchronous oscillatory activity interfaces with modular spatiotemporal patterns of task-related activity. We suggest that the background β-band oscillations in the striatum could help to focus action-selection network functions of cortico-basal ganglia circuits.
Radicals derived from heteroaromatic systems. II. Thiazolyl radicals (1970)

2-Thiazolylhydrazine and all three thiazole carbonyl peroxides have been synthesized and examined as radical precursors in solution in benzene, bromobenzene, and cumene. Silver oxide oxidation of the hydrazine or thermal decomposition of the 2-peroxide gives good yields of 2-arylthiazoles but negligible amounts of esters; in cumene a trace of bicumyl is formed. The isomer ratios in bromobenzene and cumene fully support the involvement of 2-thiazolyl radicals (1).The 4-carbonyl peroxide gives fair yields of 4-arylthiazoles but the phenyl ester is also a major product in benzene, indicative of reactions of both 4-thiazolyl radicals (2) and thiazole-4-carbonyloxy radicals. The 5-peroxide gives no products clearly diagnostic of 5-thiazolyl radicals (3) or thiazole-5-carbonyloxy radicals. Bicumyl is a major product of the reactions of the 4- and the 5-peroxides in cumene.
Photochemical Preparation of Highly Water‐Soluble Pendant [60]Fullerene‐Aminopolymers (1997)

Abstract— In order to introduce fullerene cages into an aqueous environment, pendant [60]fullerene‐poly(propionylethyle‐neimine‐co‐ethyleneimine) was prepared photochemical‐ly. The pendant polymer is highly water soluble, with equivalent aqueous solubilities of the polymer‐bound [60]fullerene much higher than the solubility of [60]ful‐lerene in toluene. The photochemical reaction between [60]fullerene and secondary amine moieties in the ami‐nopolymers likely follows a photoinduced electron transfer‐proton transfer mechanism. The pendant polymer structures, which are represented by dehydrogenated di‐and tetra‐aminofullerene linkages, were characterized by use of proton and 13C NMR, Fourier transform‐infrared spectroscopy, gel‐permeation chromatography and optical spectroscopic methods.
Amphiphilic propane-l,2-diol derivatives incorporating calamitic structural units (1991)

Abstract Novel amphiphilic propane-1,2-diol derivatives incorporating a wide variety of calamitic structural units, like biphenyl, dicyclohexyl. phenylbemzoate, phenyl pyrimidine and phenylthiadiazole, were synthesized and their mesomorphic behaviour studied. Most of these compounds exhibit broad smectic A and C mesophases in the water-free state. These mesophases could be stabilized further by addition of water. The transition temperatures depend mainly on the hydrophilic properties of the rigid core and on the length of the spacer by which the core is connected to the diol unit.
Rate control of VBR H.261 video on frame relay networks (2002)

The H.261 video compression standard provides an efficient scheme for the transmission of low bit-rate video traffic over high-speed networks. We introduce a modified H.261 codec that produces variable bit-rate (VBR) output for transmission over an integrated services frame relay (FR) network. We show that the quality of service requirements of VBR video can be met in the presence of inter-LAN data traffic by making use of the backward explicit congestion notification (BECN) facility, in conjunction with a modified H.261 video codec whose rate is controlled by the congestion notifications. We also show that the performance of the control mechanism is significantly influenced by a subset of network threshold and codec control parameters which is identified using 2/sup k/ factorial analysis techniques. We obtain optimal ranges of values for these parameters using mean field annealing optimization methods. Finally, we show that variable quantization rate control is more effective for this purpose than variable frame rate control and that the improvement in performance over that of an uncontrolled network is significant.
Electricity from biogas (1994)

Biogas is a medium-Btu methane and carbon dioxide mix produced by bacterial decomposition of organic matter. Its sources include landfills, waste water sludges, and animal wastes. It can fuel energy applications, of which electricity generation is a frequently-preferred option. The greatest current U.S. biogas recovery and energy use is at landfills, where biogas at about 80 landfill sites fuels a total of approximately 300 MWe. Wastewater treatment plants and confined animal waste management systems support additional electric power production. Generation of electricity from biogas can present difficulties due to the generally small scale of the generating facility, variable energy content of the gas, fluctuating availability, contaminant problems, and often-demanding control needs. However, such difficulties are being successfully addressed and economics for electricity generation are often favorable as biogas can be essentially {open_quotes}free{close_quotes} fuel. Biogas recovery and use has the additional advantage of mitigating a potent greenhouse gas. Biogas from U.S. landfills alone could fuel about 1% of U.S. electrical generation while giving climate change benefit equivalent to reducing CO{sub 2} emissions in the electricity sector by more than 10%. Growth in landfill gas use will be facilitated by recent regulations, advances in equipment, and improved management techniques such as {open_quotes}controlledmore » landfilling{close_quotes}. The potential for biogas recovery and electricity production from sewage sludges, animal wastes and other organic resources such as agricultural residues is uncertain but probably exceeds the estimate for landfills.« less
Alutacenoic Acids A and B, Rare Naturally Occurring Cyclopropenone Derivatives Isolated from Fungi:  Potent Non-Peptide Factor XIIIa Inhibitors (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAlutacenoic Acids A and B, Rare Naturally Occurring Cyclopropenone Derivatives Isolated from Fungi: Potent Non-Peptide Factor XIIIa InhibitorsHiroshi Kogen, Toshihiro Kiho, Keiko Tago, Shuichi Miyamoto, Tomoyuki Fujioka, Noriko Otsuka, Keiko Suzuki-Konagai, and Takeshi OgitaView Author Information Exploratory Chemistry Research Laboratories Pharmacological and Molecular Biological Research Laboratories, and Biomedical Research Laboratories Sankyo Co., Ltd., 2-58, Hiromachi 1-chome Shinagawa-ku Tokyo, 140-8710 Japan Cite this: J. Am. Chem. Soc. 2000, 122, 8, 1842–1843Publication Date (Web):February 10, 2000Publication History Received7 July 1999Published online10 February 2000Published inissue 1 March 2000https://pubs.acs.org/doi/10.1021/ja992355shttps://doi.org/10.1021/ja992355srapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1059Altmetric-Citations41LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Amides,Inhibition,Inhibitors,Peptides and proteins,Reaction products Get e-Alerts
Basics of JavaScript for Animation (2011)

If the first chapter is a somewhat philosophical overview of animation, this one is a technical overview of what it takes to create an HTML5 document and how to animate using a canvas element and JavaScript. This chapter covers the essentials of document structure, animation loops, JavaScript objects, and user interaction. The techniques you learn here are used throughout the rest of the book.KeywordsConstructor FunctionEvent HandlerHTML5 DocumentMouse CursorCallback FunctionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Epigenetics of prostate cancer: beyond DNA methylation (2006)

Epigenetic mechanisms permit the stable inheritance of cellular properties without changes in DNA sequence or amount. In prostate carcinoma, epigenetic mechanisms are essential for development and progression, complementing, amplifying and diversifying genetic alterations. DNA hypermethylation affects at least 30 individual genes, while repetitive sequences including retrotransposons and selected genes become hypomethylated. Hypermethylation of several genes occurs in a coordinate manner early in carcinogenesis and can be exploited for cancer detection, whereas hypomethylation and further hypermethylation events are associated with progression. DNA methylation alterations interact with changes in chromatin proteins. Prominent alterations at this level include altered patterns of histone modification, increased expression of the EZH2 polycomb histone methyltransferase, and changes in transcriptional corepressors and coactivators. These changes may make prostate carcinoma particularly susceptible to drugs targeting chromatin and DNA modifications. They relate to crucial alterations in a network of transcription factors comprising ETS family proteins, the androgen receptor, NKX3.1, KLF, and HOXB13 homeobox proteins. This network controls differentiation and proliferation of prostate epithelial cells integrating signals from hormones, growth factors and cell adhesion proteins that are likewise distorted in prostate cancer. As a consequence, prostate carcinoma cells appear to be locked into an aberrant state, characterized by continued proliferation of largely differentiated cells. Accordingly, stem cell characteristics of prostate cancer cells appear to be secondarily acquired. The aberrant differentiation state of prostate carcinoma cells also results in distorted mutual interactions between epithelial and stromal cells in the tumor that promote tumor growth, invasion, and metastasis.
Nocturnal frontal lobe epilepsy: A clinical and polygraphic overview of 100 consecutive cases (1999)

Nocturnal frontal lobe epilepsy (NFLE) has been delineated as a distinct syndrome in the heterogeneous group of paroxysmal sleep-related disturbances. The variable duration and intensity of the seizures distinguish three non-rapid eye movement-related subtypes: paroxysmal arousals, characterized by brief and sudden recurrent motor paroxysmal behaviour; nocturnal paroxysmal dystonia, motor attacks with complex dystonic-dyskinetic features; and episodic nocturnal wanderings, stereotyped, agitated somnambulism. We review the clinical and polysomnographic data related to 100 consecutive cases of NFLE in order to define the clinical and neurophysiological characteristics of the different seizure types that constitute NFLE. NFLE seizures predominate in males (7:3). Age at onset of the nocturnal seizures varies, but centres during infancy and adolescence. A familial recurrence of the epileptic attacks is found in 25% of the cases, while 39% of the patients present a family history of nocturnal paroxysmal episodes that fit the diagnostic criteria for parasomnias. A minority of cases (13%) have personal antecedents (such as birth anoxia, febrile convulsions) or brain CT or MRI abnormalities (14%). In many patients, ictal (44%) and interictal (51%) EEGs are uninformative. Marked autonomic activation is a common finding during the seizures. NFLE does not show a tendency to spontaneous remission. Carbamazepine completely abolishes the seizures in approximately 20% of the cases and gives remarkable relief (reduction of the seizures by at least 50%) in another 48%. VideoEEG recordings confirm that NFLE comprises a spectrum of distinct phenomena, different in intensity but representing a continuum of the same epileptic condition. We believe that the detailed clinical and videoEEG characterization of patients with NFLE represents the first step towards a better understanding of the pathogenic mechanisms and different clinical outcomes of the various seizure types that constitute the syndrome.
CARACTERÍSTICAS ENDOSCÓPICAS , HISTOLÓGICAS E INMUNOLÓGICAS DE LA MUCOSA DIGESTIVA EN NIÑOS AUTISTAS CON SÍNTOMAS GASTROINTESTINALES. Segundo Premio Trabajo Cientifico. LI Congreso Nacional de Pediatría 2005 (2006)

"Introducción: El autismo es un desorden del neurodesarrollo cuya etiología es desconocida. Se evalúa la función y estructura de la mucosa digestiva buscando asociación entre cambios histológicos y etiopatogenia. objetivos: Describir los hallazgos endoscópicos, histológicos e inmunológicos de la mucosa digestiva de niños autistas y controles con similares síntomas gastrointestinales. Métodos: 45 niños autistas, 1,98 años +/- 1,37, 32 varones, 13 hembras; 57 controles, 3,28 años +/- 2,57, 30 varones, 27 hembras. Histor ia clínica, laboratorio, estudios endoscópicos, análisis histológico e inmunohistoquímica. Resultados: Histológicos: inflamación crónica del esófago, estómago, duodeno y colon en autistas; duodeno: incremento linfocitos intraepiteliales p<0.001, colon mayor infiltrado linfoplasmocitario p= 0.001. Autistas más esofagitis por reflujo (88,88%), Gas tritis Crónica Activa, hiperplasia nodular linfoide (HNL) e infección por H. pylori (55,56%) diferencia significativa entre grupos p<0.001, p=0.01. Duodenitis Crónica Activa con HNL38/45; 23/45 infección por Giardia intestinalis , 26/45 alteración en vellosidades intestinales, un celíaco. Asociación entre la presencia de HNL e infección por H. pylori en estómago, en duodeno por Giardia intestinalis p=0.002. Ileitis Crónica Activa con HNL sin infección en 6, Colitis Crónica Activa con HNL 33/45. Conclusiones: Los niños autistas presentan alta incidencia de enfermedad gastrointestinal con alteraciones endoscópicas, histológicas e inmunológicas. Observamos alteraciones inmunológicas e inmunohistoquímicas en biopsias digestivas compatibles con la respuesta inmune encontrada en pacientes con alergia alimentaria. Hallazgos: HNL, infiltrado eosinofílico, prevalencia de CD4> CD8 habla a favor de reacción alérgica tipoTh2, menor proporción CD8>CD4 sugiere reacción alérgica tipo Th1. La reacción alérgica presentada por este grupo de pacientes autistas es de tipo mixto. Arch Venez Pueric Pediatr 69 (1): 19-25"
Hedgehog/GLI Signaling Activates Suppressor of Cytokine Signaling 1 (SOCS1) in Epidermal and Neural Tumor Cells (2013)

Sustained hedgehog (Hh) signaling mediated by the GLI transcription factors is implicated in many types of cancer. Identification of Hh/GLI target genes modulating the activity of other pathways involved in tumor development promise to open new ways for better understanding of tumor development and maintenance. Here we show that SOCS1 is a direct target of Hh/GLI signaling in human keratinocytes and medulloblastoma cells. SOCS1 is a potent inhibitor of interferon gamma (IFN-y)/STAT1 signaling. IFN-у/STAT1 signaling can induce cell cycle arrest, apoptosis and anti-tumor immunity. The transcription factors GLI1 and GLI2 activate the SOCS1 promoter, which contains five putative GLI binding sites, and GLI2 binding to the promoter was shown by chromatin immunoprecipitation. Consistent with a role of GLI in SOCS1 regulation, STAT1 phosphorylation is reduced in cells with active Hh/GLI signaling and IFN-у/STAT1 target gene activation is decreased. Furthermore, IFN-у signaling is restored by shRNA mediated knock down of SOCS1. Here, we identify SOCS1 as a novel Hh/GLI target gene, indicating a negative role of Hh/GLI pathway in IFN-y/STAT1 signaling.