gebhart/patrepeval huggingface dataset:
B‐cell epitope mapping of theNeisseria meningitidisP64k protein using overlapping peptides (2000)

A common meningococcal antigen designated P64k has been identified, cloned and expressed in Escherichia coli. The recombinant antigen is highly immunogenic in several animal species and its immunogenicity in healthy human volunteers is under investigation. Recently, P64k has been used as an immunological carrier for weak immunogens. To characterize the B-cell epitopes on P64k, recognized by immune sera obtained from mice, rabbits and monkeys, multiple overlapping peptides were synthesized and screened for antibody binding. Peptides covering the complete sequence of the P64k protein, 59 in all, of 20 amino acids each (overlapped by 10 residues), were synthesized. A number of continuous epitopes were detected with all sera, when immune and pre-immune bleeds were compared. For mouse and monkey sera, a few major antigenic peptides were identified, while the recognition of the rabbit serum was much more heterogeneous. Despite variation in the exact location of continuous epitopes defined by different anti-P64k sera, we found an immunogenic core region within the molecule, composed of amino acids Asp(524)-Gly(533). Consistently, in this protein segment there was an amino acid stretch located in a beta-hairpin loop, which is exposed to the solvent in the previously determined three-dimensional structure of the protein. This region is protruding and accessible to a sphere with a radius of 9 A.
Marrow-Infiltrating Lymphocytes – Role in Biology and Cancer Therapy (2016)

The past several years have witnessed the acceptance of immunotherapy into the mainstream of therapies for patients with cancer. This has been driven by the clinical successes of antibodies to the checkpoint inhibitors, CTLA-4 and PD-1, capable of imparting long-term remissions in several solid tumors as well as Hodgkin's lymphoma (1) and the therapeutic successes of adoptive T-cell transfer with chimeric antigen receptors (2) or modified T-cell receptors (3) that have mostly utilized peripheral T-cells. One emerging area of therapeutic T cell intervention has been the utilization of marrow-infiltrating lymphocytes (MILs) - a novel form of adoptive T-cell therapy. This approach was initially developed to increase the likelihood of a precursor T-cell population with an enhanced tumor specificity in bone marrow (BM)-derived malignancies. However, the unique attributes of BM T-cells and their interaction with their microenvironment provide significant rationale to utilize these cells therapeutically in diseases that extend beyond hematologic malignancies.
Neuronal Nitric Oxide Synthase mRNA Upregulation in Rat Sensory Neurons after Spinal Nerve Ligation: Lack of a Role in Allodynia Development (1999)

Pharmacological evidence suggests a functional role for spinal nitric oxide (NO) in the modulation of thermal and/or inflammatory hyperalgesia. To assess the role of NO in nerve injury-induced tactile allodynia, we examined neuronal NO synthase (nNOS) expression in the spinal cord and dorsal root ganglia (DRG) of rats with tactile allodynia because of either tight ligation of the left fifth and sixth lumbar spinal nerves or streptozotocin-induced diabetic neuropathy. RNase protection assays indicated that nNOS mRNA (1) was upregulated in DRG, but not spinal cord, neurons on the injury side beginning 1 d after nerve ligation, (2) peaked (approximately 10-fold increase) at 2 d, and (3) remained elevated for at least 13 weeks. A corresponding increase in DRG nNOS protein was also observed and localized principally to small and occasionally medium-size sensory neurons. In rats with diabetic neuropathy, there was no significant change in DRG nNOS mRNA. However, similar increases in DRG nNOS mRNA were observed in rats that did not develop allodynia after nerve ligation and in rats fully recovered from allodynia 3 months after the nerve ligation. Systemic treatment with a specific pharmacological inhibitor of nNOS failed to prevent or reverse allodynia in nerve-injured rats. Thus, regulation of nNOS may contribute to the development of neuronal plasticity after specific types of peripheral nerve injury. However, upregulation of nNOS is not responsible for the development and/or maintenance of allodynia after nerve injury.
An Amplitude Stabilization Technique for Nonlinear Optoelectronic Filtering (2020)

The nonlinear optoelectronic (NLOE) filter represents a novel class of filters whose filtering operation is based a signal reaching a specific amplitude rather than falling within a specific range of frequencies. This amplitude filtering aspect carries with it a stringent amplitude stability requirement where the input signal must be precisely maintained at a specific level for the signal to be rejected. In many real-world settings, the signal amplitudes are not precisely known or held constant over long periods of time, which greatly inhibits the application of this filter outside the laboratory. We report here a novel amplitude-stabilization scheme that locks the signal amplitude (<; 0.004 dB) to the precise level required for filter operation. Using this stabilization technique, we demonstrate a record NLOE filter suppression of 71 dB for a 3.1 GHz interferer signal relative to a second RF signal located at an 8-kHz offset. We also show the ability to maintain a >50 dB level of suppression over a period of one hour or more.
Revealing the role of phospholipase Cβ3 in the regulation of VEGF-induced vascular permeability (2012)

VEGF induces vascular permeability (VP) in ischemic diseases and cancer, leading to many pathophysiological consequences. The molecular mechanisms by which VEGF acts to induce hyperpermeability are poorly understood and in vivo models that easily facilitate real-time, genetic studies of VP do not exist. In the present study, we report a heat-inducible VEGF transgenic zebrafish (Danio rerio) model through which VP can be monitored in real time. Using this approach with morpholino-mediated gene knock-down and knockout mice, we describe a novel role of phospholipase Cβ3 as a negative regulator of VEGF-mediated VP by regulating intracellular Ca2+ release. Our results suggest an important effect of PLCβ3 on VP and provide a new model with which to identify genetic regulators of VP crucial to several disease processes.
Topological interface states in the natural heterostructure (PbSe)5(Bi2Se3)6 with BiPb defects (2018)

We study theoretically the electronic band structure of (${\mathrm{PbSe})}_{5}$(${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$)${}_{6}$, which consists of an ordinary insulator PbSe and a topological insulator ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$. The first-principles calculations show that this material has a gapped Dirac-cone energy dispersion inside the bulk, which originates from the topological states of ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ layers encapsulated by PbSe layers. Furthermore, we calculate the band structures of (${\mathrm{Bi}}_{x}{\mathrm{Pb}}_{1\ensuremath{-}x}\mathrm{Se}$)${}_{5}$(${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$)${}_{6}$ with ${\mathrm{Bi}}_{\mathrm{Pb}}$ antisite defects included in the PbSe layers. The result shows that a high density of ${\mathrm{Bi}}_{\mathrm{Pb}}$ defects can exist in real materials, consistent with the experimentally estimated $x$ of more than 30%. The ${\mathrm{Bi}}_{\mathrm{Pb}}$ defects strongly modify the band alignment between ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ and PbSe layers, while the topological interface states of ${\mathrm{Bi}}_{2}{\mathrm{Se}}_{3}$ are kept as a gapped Dirac-cone-like dispersion.
Teaching Technology Fellowship Report on “Demonstration/Measurement System for Wireless Networks” (2007)

This paper is the final report for a Teaching Technology Fellowship project conducted between July 2005 and May 2007. This project involved integrating a wireless network measurement experiment into the curriculum of CS4514, Computer Networks, during the WPI B06 undergraduate term. After presenting goals and objectives, the chronology of preparation and execution of the project plan are discussed. The paper assesses the results of the B06 wireless measurement experience against a B05 offering of Computer Networks that included a wireless design assignment. A discussion of observations about the positive and negative aspects of this experimental pedagogical effort is provided as a summary.
One‐dimensional self‐weight consolidation with continuous drainage boundary conditions: Solution and application to clay‐drain reclamation (2019)

Summary Traditional consolidation theories cannot provide good predictions of consolidation settlement in land reclamation because of their assumptions that the influence of soil's self‐weight is often neglected, and the drainage boundary is considered as fully pervious/impervious. In view of these limitations, an analytical solution is derived for one‐dimensional self‐weight consolidation problems with a continuous drainage boundary using the finite Fourier sine transform method. Following the classical Terzaghi's small strain theory, the soil's self‐weight is considered to produce consolidation settlement in dredged materials with a constant coefficient of consolidation. The continuous drainage boundary can essentially describe the time‐dependent variation of drainage capacity at the interface between two adjacent soil layers. By reducing the interface parameters, the effectiveness of the calculation is demonstrated against the Terzaghi's solution. The influence of interface parameters and soil's self‐weight stress coefficient on self‐weight consolidation is discussed. As expected, the rate of consolidation considering the self‐weight stress is faster, although the dependency of consolidation rate on the material property of void ratio is neglected. Moreover, the plane of maximum excess pore‐water pressure is estimated as a function of time factor, based on which a design chart is developed to optimize the layout of horizontal drains in land reclamation.
Aportaciones al conocimiento de la flora briológica española. Nótula XIII: hepáticas y musgos de Mallorca (Islas Baleares) (2001)

Resumen: Durante los trabajos de campo llevados a cabo en Mallorca durante la XVII Reunion de Briologia organizada por la Sociedad Espanola de Briologia se recogieron 126 briofitos (110 musgos y 11 hepaticas). Nueve de ellos constituyen novedades para las islas Baleares: Aschisma carniolicum, Bryum gemmilucens, Crossidium laevipilum, Didymodon sicculus, Gongylanthus ericetorum, Gymnostomum lanceolatum, Orthotrichum cupulatum var. riparium, Pterygoneurum sampaianum y Weissia condensa var. armata. Ademas, se amplia la distribucion geografica en la isla de algunas especies raras o escasamente recolectadas.
Mining Xylose Isomerase Producing Microbes (2020)

An aerobic, rod shaped, mesophilic, gram positive xylitol producing bacterial isolates were made from different enriched substrates. Xylose isomerase is an enzyme that catalyzes the interconversion of D-xylose and D-xylulose. The microbes producing xylulose from xylose via xylose isomerase enzyme were screened for the xylose isomerase activity based on 2, 3, 5-Triphenyl tetrazolium dye retention capacity. Among the fourteen isolates screened, only six isolates showed the positive results by retaining the dye of which XLY3 was the best. Phylogenetic and sequence analysis of 16SrRNA gene showed 98 % homology to Bacillus endophyticus
Discovery and Evolution of Base-Free Neutral Phase-Transfer Reaction System (2014)

Although quaternary onium salts-catalyzed phase-transfer reactions are generally believed to require base additives, we discovered even without any base additives conjugate additions of 3-substituted oxindoles to nitroolefins proceeded smoothly in the presence of lipophilic quaternary ammonium bromide under water-organic biphasic conditions. The mechanism of this novel base-free neutral phase-transfer reaction system was investigated, and the assumed catalytic cycle was presented together with interesting effects of water and lipophilicity of the phase-transfer catalyst. The base-free neutral phase-transfer reaction system could be applied to highly enantioselective conjugate addition and aldol reactions under the influence of chiral bifunctional ammonium bromides as key catalysts. The efficient approach for the design of chiral quaternary phosphonium bromides as chiral phase-transfer catalysts was also introduced. A catalyst library with various structures has readily been constructed by the use of commercially available chiral phosphines as catalyst precursors. The optimized catalyst has successfully been applied to highly enantioselective conjugate additions and sulfenylation under base-free neutral phase-transfer conditions with low catalyst loading.
Influence of temperature and spawning effort on Haliotis tuberculata mortalities caused by Vibrio harveyi: an example of emerging vibriosis linked to global warming (2009)

Abstract Since 1998, Haliotis tuberculata mass mortalities have been occurring regularly in wild abalone populations in France during their reproductive period and in conjunction with seawater summer temperature maxima and Vibrio harveyi presence. To confirm the importance of bacterial exposure, temperature and reproductive status on abalone susceptibility, experimental infections via bath exposure were performed using abalone ranging from immature to reproductively mature. Ripe abalone were more susceptible to the bacterium than immature specimens ( P &lt;0.001), and a difference of only 1 °C in temperature had a highly significant impact on the mortalities ( P &lt;0.001). The natural mortalities that were surveyed during summer 2007 confirmed that recent epidemic losses of European abalone appeared in conjunction with host reproductive stress, elevated temperatures and presence of the pathogen V. harveyi . In view of the elevation of the mean summer temperatures observed in Brittany and Normandy over the last 25 years, this temperature‐dependent vibriosis represents a new case of emerging disease associated with global warming.
Quantitative Imaging in Medicine and Surgery: progress & perspective. (2013)

Modern imaging techniques can be employed to collect both quantitative anatomic information and in vivo metabolic or functional information. Quantitative imaging methods that have been proven to correlate with clinical outcomes can play an important role in clinical decisions (1,2). Presently, a gap exists between the physics-based development of new techniques and the applications used in the study of disease. There is a need for targeted investigations that might establish the usefulness of more quantitative imaging measures for the assessment of disease state. In order to further advance and promote quantitative imaging and imaging biomarkers to be included in future radiologic practices, there is also a critical need to develop and validate algorithms that can process imaging data to provide clinical information for decision-making, and ideally automatically (3).
Reddish-Orange Long-Lasting Phosphorescence of Ca[sub 2]Si[sub 5]N[sub 8]:Eu[sup 2+],Tm[sup 3+] Phosphor (2010)

Reddish-orange long-lasting phosphorescence materials, various amounts of - and -co-doped phosphors , were prepared by the conventional high temperature solid-state reaction method, and their luminescence properties were systematically investigated by photoluminescence spectra, afterglow spectra, afterglow decay curves, and thermoluminescence spectra. The materials exhibited strong reddish-orange emission bands in a wavelength range of 500–750 nm with peak positions at about 600 nm due to the transition of the ion. Furthermore, these phosphors emitted strong reddish-orange long-lasting phosphorescence with an afterglow time of more than 1 h after turning off the activating lamp in the light perception of the dark-adapted human eye . Such afterglow of phosphors was attributed to the recombination of holes and electrons that were trapped within the lattice defect centers. The results of the thermoluminescence spectra indicated that the increase in the predominating band at 350 K, which was associated with the charge-trapping centers, was responsible for the enhancement of the afterglow properties of .
Spin parity studies of the eta pi decay of the A2 meson and investigation of the A2 production mechanism in the reaction pi-minus proton goes to A2-minus proton (1971)

The results of a spin parity analysis of the ηπ<sup>-</sup> decay mode of the A<sub>2</sub><sup>-</sup> meson produced in the reaction π-p → A<sub>2</sub><sup>-</sup>p are presented.
The AmphiHex: A novel amphibious robot with transformable leg-flipper composite propulsion mechanism (2012)

The amphibious robot is so attractive and challenging for its broad application and its complex working environment. It should walk on rough ground, maneuver underwater and pass through transitional terrain such as sand and mud, simultaneously. To tackle with such a complex task, a novel amphibious robot (AmphiHex-I) with transformable leg-flipper composite propulsion is proposed and developed. This paper presents the detailed structure design of the transformable leg-flipper propulsion mechanism and its drive module, which enables the amphibious robot passing through the terrain, water and transitional zone between them. A preliminary theoretical analysis is conducted to study the interaction between the elliptic leg and transitional environment such as granular medium. An orthogonal experiment is designed to study the leg locomotion in the sandy and muddy terrain with different water content. Finally, basic propulsion experiments of AmphiHex-I are launched, which verified the locomotion capability on land and underwater is achieved by the transformable leg-flipper mechanism.
Design of the automatic ontology building system about the specific domain knowledge (2006)

Nowadays, ontology is being studied on the various parts. Especially, as the study on the semantic Web has actively progressed, the applicable range of the ontology is getting wide. At the result, many ontologies are existed in the web. Based on this theory, several problems happened on the ontology side. Among these problems, the significant issue is how to address the heterogeneity and consistency between the ontologies that were made about the same domain. In this paper, we give the possibility for building the ontology automatically based on the existing knowledge data. And we could expect to address the problem of the ontology reliability. In this paper, we suggest the new methodology for building the ontology automatically based on the WordNet and we design and implement the automatic ontology building system. Thus, we could expect that the users are able to build the ontology more consistently and easily.
Abstract 5057: The insulin-like growth factor receptor I promotes motility and invasion of bladder cancer cells through Akt- and MAPK-dependent activation of paxillin (2010)

Abstract The insulin-like growth factor receptor I (IGF-IR) plays an essential role in transformation by promoting cell growth and protecting cancer cells from apoptosis. Aberrant IGF-IR signaling is implicated in several types of tumors, including carcinomas of the lung, breast, prostate, pancreas, liver and colon. However, whether the IGF-IR contributes to the transforming phenotype of urothelial cells has not been clearly established but recent data suggest that the IGF-IR is over-expressed in bladder cancer. In this study we demonstrated by immunohistochemical analysis that the IGF-IR is over-expressed in invasive bladder cancer (T3/T4) tissues compared to non-malignant controls. We have also characterized the mechanism of action of the IGF-IR in cancer urothelial cells using urothelial carcinoma-derived 5637 and T24 cells. Although activation of the IGF-IR did not appreciably affect their growth, it did promote migration and stimulate in vitro wound closure and invasion through extracellular matrix. These effects required the activation of the Akt and MAPK pathways and IGF-I induced Akt- and MAPK-dependent phosphorylation of paxillin, which relocated at dynamic focal adhesions at the protruding edge of migrating urothelial cancer cells. Using siRNA strategies we also demonstrated that paxillin was necessary for promoting IGF-I-mediated motility and invasion in bladder cancer cells. In conclusion, our results provide the first evidence for a role of the IGF-IR in motility and invasion of bladder cancer cells, and support the hypothesis that the IGF-IR may play a critical role in the establishment of the invasive phenotype in urothelial neoplasia. The IGF-IR could represent a novel molecular target in bladder cancer and could also serve as a novel tumor biomarker for diagnosis and possibly prognosis of bladder tumors. This work has been supported by the Benjamin Perkins Bladder Cancer Fund, the Martin Greitzer Fund and National Institutes of Health Grants RO1 DK068419 (A.M.) and RO1 CA39481 and RO1 CA047282 (R.V.I.). §Present address: Medimmune, One Medimmune Way, Gaithersburg, MD 20878 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5057.
Schrödinger's Tree -- On Syntax and Neural Language Models (2021)

In the last half-decade, the field of natural language processing (NLP) has undergone two major transitions: the switch to neural networks as the primary modeling paradigm and the homogenization of the training regime (pre-train, then fine-tune). Amidst this process, language models have emerged as NLP's workhorse, displaying increasingly fluent generation capabilities and proving to be an indispensable means of knowledge transfer downstream. Due to the otherwise opaque, black-box nature of such models, researchers have employed aspects of linguistic theory in order to characterize their behavior. Questions central to syntax -- the study of the hierarchical structure of language -- have factored heavily into such work, shedding invaluable insights about models' inherent biases and their ability to make human-like generalizations. In this paper, we attempt to take stock of this growing body of literature. In doing so, we observe a lack of clarity across numerous dimensions, which influences the hypotheses that researchers form, as well as the conclusions they draw from their findings. To remedy this, we urge researchers make careful considerations when investigating coding properties, selecting representations, and evaluating via downstream tasks. Furthermore, we outline the implications of the different types of research questions exhibited in studies on syntax, as well as the inherent pitfalls of aggregate metrics. Ultimately, we hope that our discussion adds nuance to the prospect of studying language models and paves the way for a less monolithic perspective on syntax in this context.
A case of primary mediastinal rhabdomyosarcoma. (1999)

症例は24歳, 男性.1996年5月から咳嗽ならびに呼吸困難が持続するため近医受診, 胸部異常陰影指摘され精査目的で入院となる.胸部CTでは前縦隔から右胸腔内に大きく突出する腫瘤陰影と右胸水を認め, 針生検より縦隔横紋筋肉腫と診断した.手術により腫瘍の完全切除を行い得たが, 早期に広範な局所再発を来たし術後6ヵ月で死亡した.縦隔原発横紋筋肉腫は極めて稀な悪性度の高い腫瘍であり, 治療にあたっては従来の外科切除だけでなく化学療法も含めた集学的治療が重要であると考える.
DW-LOCOS: a convenient VLSI isolation technique (1995)

An alternative process scheme for dry local oxidation is presented. It has several advantages when compared with the conventional wet process. For example, dry local oxidation of silicon reduces the bird`s beak length as well as retarding the appearance of field oxide thinning in submicrometre mask openings. Furthermore, it avoids detrimental gate oxide thinning and reduces the complexity of the process, because it can be performed at the same time as the well drive-in (DW-LOCOS). Preliminary results demonstrate that there is no degradation in the electrical characteristics of diodes and MOS capacitor test structures, thus permitting DW-LOCOS to be advantageously incorporated into CMOS-VLSI processing sequences.