gebhart/patrepeval huggingface dataset:
Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells (2009)

The enormous diversity of the naive T cell repertoire is instrumental in generating an immune response to virtually any foreign antigen that can be processed into peptides that bind to MHC molecules. The low frequency of antigen-specific naive T cells, their high activation threshold, and the constrains of antigen-processing and presentation have hampered analysis of naive repertoires to complex protein antigens. In this study, libraries of polyclonally expanded naive T cells were used to determine frequency and antigen dose-response of human naive CD4(+) T cells specific for a variety of antigens and to isolate antigen-specific T cell clones. In the naive repertoire, T cells specific for primary antigens, such as KLH and Bacillus anthracis protective antigen, and for recall antigens, such as tetanus toxoid, cytomegalovirus, and Mycobacterium tuberculosis purified protein derivative, were detected at frequencies ranging from 5 to 170 cells per 10(6) naive T cells. Antigen concentrations required for half-maximal response (EC50) varied over several orders of magnitude for different naive T cells. In contrast, in the memory repertoire, T cells specific for primary antigens were not detected, whereas T cells specific for recall antigens were detected at high frequencies and displayed EC50 values in the low range of antigen concentrations. The method described may find applications for evaluation of vaccine candidates, for testing antigenicity of therapeutic proteins, drugs, and chemicals, and for generation of antigen-specific T cell clones for adoptive cellular immunotherapy.
Multilayered Laminated Structures (2019)

This chapter describes a system for the controlled release of chemicals through multilayered laminated structures and shows how this knowledge is being utilized to improve pest management and other practices. The Hercon® controlled release system of dispensing active ingredients consists of several layers of laminated polymeric material. The nonporous, homogeneous polymeric films, usually referred to as solution-diffusion membranes, are used in Hercon® dispensing systems. The reservoir/membrane distribution coefficient can be estimated from the solubility parameter of the diffusant, which can be calculated using Hildebrand’s solubility theory. Hercon Insectape® insecticidal strip is a cockroach control product designed for use in residences and in commercial, institutional, and industrial establishments. The Hercon® technology has also been used to dispense insect attractants or pheromones, a technique useful in pest management. Mass trapping with a new, inexpensive, and highly efficient trap baited with a Luretape™ showed potential for direct control of the gypsy moth in light infestations.
Data-driven development of Virtual Sign Language Communication Agents (2018)

Engaging deaf and hearing people in common discussions requires interfaces to help them understand each other, such as robot agents that translate spoken language into Sign Language (SL) expressions and vice-versa. However, the recognition and generation of signed sentences is a complex task of high dimensionality that cannot be solved in sufficient quality yet. Thus, it is necessary to develop new technologies of improved performances. The sequence to sequence neural network model, traditionally used for machine translation, is adapted to the above two tasks by treating a SL sequence as a multi-dimensional sentence. We defined an encoding of the SL annotations and conducted experiments on the network structure to define a most accurate translation model. This study proves the network trainable and possibly applicable in real-life with an extended dataset, which shall be tested for deployment in virtual translation assistants in the following.
A Multidisciplinary survey on controversies in the use of EUS-guided FNA: assessing perspectives of surgeons, oncologists and gastroenterologists (2011)

Controversies as to ideal application of EUS-FNA persist. Optimal guidelines should reflect the needs and concerns of the multidisciplinary team who treat patients who need EUS-FNA. Multi-specialty meetings assembled to manage patients with these disorders may be enlightening and may help develop consensus.
Synthesis and Relaxometric Characterization of a New Mn(II)‐EDTA‐Deoxycholic Acid Conjugate Complex as a Potential MRI Blood Pool Agent (2016)

Abstract Gd(III)‐complexes have been employed for more than twentyfive years as MRI contrast agents. In the last decade, considerations about potential toxicity of residual gadolinium in patients suffering from severe kidney diseases have moved researchers to evaluate alternative solutions, among them Mn(II)‐complexes, to shorten T 1 and achieve good image contrast. In this article we report on the synthesis of a new Mn(II)‐chelate, endowed with a deoxycholic acid residue designed to interact reversibly with serum albumin and to boost the usually low relaxivity associated with Mn(II)‐complexes. Its detailed relaxometric characterization and the analysis of albumin binding behaviour showed remarkable properties, suggesting its potential use as MRI blood pool agent.
Ultrafast carrier dynamics in InGaN MQW laser diode (2003)

The ultrafast carrier dynamics in InGaN multiple quantum well (MQW) laser diodes were investigated using a time-resolved bias-lead monitoring techniques. Both pump and probe beams were from the second harmonic generation (SHG) of a tunable 100-fs Ti:Sapphire modelocked laser. From the optical selection rules of TE and TM polarized lights, one can selectively excite and probe different valance subbands to conduction band transitions in the MQW structure with different polarized pump and probe light. Using this technique, ultrafast inter-subband hole relaxation processes were found to dominate the observed carrier dynamics.
Redesigning regulatory components of quorum-sensing system for diverse metabolic control (2022)

Quorum sensing (QS) is a ubiquitous cell-cell communication mechanism that can be employed to autonomously and dynamically control metabolic fluxes. However, since the functions of genetic components in the circuits are not fully understood, the developed QS circuits are still less sophisticated for regulating multiple sets of genes or operons in metabolic engineering applications. Here, we discover the regulatory roles of a CRP-binding site and the lux box to -10 region within luxR-luxI intergenic sequence in controlling the lux-type QS promoters. By varying the numbers of the CRP-binding site and redesigning the lux box to -10 site sequence, we create a library of QS variants that possess both high dynamic ranges and low leakiness. These circuits are successfully applied to achieve diverse metabolic control in salicylic acid and 4-hydroxycoumarin biosynthetic pathways in Escherichia coli. This work expands the toolbox for dynamic control of multiple metabolic fluxes under complex metabolic background and presents paradigms to engineer metabolic pathways for high-level synthesis of target products.
Tissue Inhibitor of Metalloproteinase-3 Deficiency Inhibits Blood Pressure Elevation and Myocardial Microvascular Remodeling Induced by Chronic Administration of N.OMEGA.-Nitro-L-Arginine Methyl Ester in Mice (2007)

Hypertension is a major risk factor for cardiovascular disease. Thus, prevention of hypertension and consequent organ damage is important for reducing its incidence. In the present study, we examined the involvement of tissue inhibitor of metalloproteinase-3 (Timp-3) in N(omega)-nitro-L-arginine methyl ester (L-NAME)-induced hypertension and accompanying vascular remodeling in mice. L-NAME was orally administered to wild-type (WT) and Timp-3 knockout (KO) mice for 6 weeks, blood pressure was monitored, and histological changes in myocardial arteries were examined. After L-NAME administration, blood pressure was lower in Timp-3 KO mice than in WT mice. The coronary arteries of WT and Timp-3 KO mice were similar after L-NAME treatment and showed no differences compared to untreated control mice. However, cardiac microvessels differed histologically between WT and Timp-3 KO mice. Vascular walls were less thickened in Timp-3 KO than in WT mice, and fibrotic changes were significantly reduced in Timp-3 KO mice. Moreover, the L-NAME-induced production of reactive oxygen species in cardiac microvessels was lower in Timp-3 KO than in WT mice. These results indicate that Timp-3 plays an important role in L-NAME-induced hypertension and myocardial vascular remodeling. Our findings suggest that Timp-3 may be a novel therapeutic target for the treatment of hypertension and consequent organ damage.
Ambient Electrosynthesis of Ammonia: Electrode Porosity and Composition Engineering (2018)

Ammonia, a key precursor for fertilizer production, convenient hydrogen carrier, and emerging clean fuel, plays a pivotal role in sustaining life on Earth. Currently, the main route for NH<sub>3</sub> synthesis is by the heterogeneous catalytic Haber-Bosch process (N<sub>2</sub> +3 H<sub>2</sub> →2 NH<sub>3</sub> ), which proceeds under extreme conditions of temperature and pressure with a very large carbon footprint. Herein we report that a pristine nitrogen-doped nanoporous graphitic carbon membrane (NCM) can electrochemically convert N<sub>2</sub> into NH<sub>3</sub> in an acidic aqueous solution under ambient conditions. The Faradaic efficiency and rate of production of NH<sub>3</sub> on the NCM electrode reach 5.2 % and 0.08 g m<sup>-2</sup> h<sup>-1</sup> , respectively. Functionalization of the NCM with Au nanoparticles dramatically enhances these performance metrics to 22 % and 0.36 g m<sup>-2</sup> h<sup>-1</sup> , respectively. As this system offers the potential to be scaled to industrial levels it is highly likely that it might displace the century-old Haber-Bosch process.
Multiomic profiling of the acute stress response in the mouse hippocampus (2022)

The acute stress response mobilizes energy to meet situational demands and re-establish homeostasis. However, the underlying molecular cascades are unclear. Here, we use a brief swim exposure to trigger an acute stress response in mice, which transiently increases anxiety, without leading to lasting maladaptive changes. Using multiomic profiling, such as proteomics, phospho-proteomics, bulk mRNA-, single-nuclei mRNA-, small RNA-, and TRAP-sequencing, we characterize the acute stress-induced molecular events in the mouse hippocampus over time. Our results show the complexity and specificity of the response to acute stress, highlighting both the widespread changes in protein phosphorylation and gene transcription, and tightly regulated protein translation. The observed molecular events resolve efficiently within four hours after initiation of stress. We include an interactive app to explore the data, providing a molecular resource that can help us understand how acute stress impacts brain function in response to stress.
Real-Time Phase Trimming of Mach-Zehnder Interferometers by Femtosecond Laser Annealing of Germanium Implanted Waveguides (2018)

We demonstrate a real-time trimming technique, enabling accurate and permanent correction of typical fabrication based phase errors of integrated Mach-Zehnder Interferometers (MZIs). The output signal can be monitored during entire annealing process.
Will the Making of Plasmacytoid Dendritic Cells in Vitro Help Unravel Their Mysteries? (2000)

In this issue, two papers describe the in vitro generation of an intriguing subset of human dendritic cells (DCs), the plasmacytoid DCs (pDCs [([1][1]), ([2][2])]). For nearly 20 years after their discovery ([3][3]), DCs had to be painstakingly isolated from tissues ([4][4]). Progress was rather
Silicon in synthesis: an exceptionally short synthesis of dl-11.alpha.-hydroxyestrone methyl ether (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSilicon in synthesis: an exceptionally short synthesis of dl-11.alpha.-hydroxyestrone methyl etherStevan Djuric, Tarun Sarkar, and Philip MagnusCite this: J. Am. Chem. Soc. 1980, 102, 22, 6885–6886Publication Date (Print):October 15, 1980Publication History Published online1 May 2002Published inissue 15 October 1980https://pubs.acs.org/doi/10.1021/ja00542a055https://doi.org/10.1021/ja00542a055research-articleACS PublicationsRequest reuse permissionsArticle Views295Altmetric-Citations74LEARN 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-Alertsclose Get e-Alerts
Single‐Crystal Polythiophene Microwires Grown by Self‐Assembly (2006)

Single-crystal polythiophene microwires with unprecedented electrical characteristics such as low resistance (0.5 MΩ), a channel current as high as 25 μA, and well-resolved gate modulation (see figure) have been obtained by specific control over the supramolecular organization of individual polymer chains, which show preferential well-ordered interchain stacking along the wire axis. This approach offers a promising protocol for new flexible electronics.
Modulation of Chemoselectivity by Protein Additives. Remarkable Effects in the Oxidation of Hyperforin (2004)

Protein additives have a dramatic effect on the H(2)O(2) oxidation of hyperforin, either protecting the enolized phloroglucinol core from oxidation (human albumin) or promoting (HRP and ovalbumin) reaction pathways derived from the intermediacy of the enollactone 4, a minor component of the oxidation mixture in the absence of protein additives. To rationalize the exquisite specificity of several steps and their mechanistic oddity, an organocatalytic effect is postulated. The use of protein additives allows a straightforward and multigram preparation of the enollactone 6, an interesting multifunctionalized scaffold for bioactivity induction and/or modulation.
Molecular characterization of three erbB transducing viruses generated during avian leukosis virus-induced erythroleukemia: extensive internal deletion near the kinase domain activates the fibrosarcoma- and hemangioma-inducing potentials of erbB (1988)

Three new erbB transducing viruses generated during avian leukosis virus-induced erythroblastosis have been cloned and sequenced, and their transforming abilities have been analyzed. Provirus 9134 E1 expresses an amino-terminally truncated erbB product that is analogous to the proviral insertionally activated c-erbB gag-erbB fusion product. This virus efficiently induces erythroblastosis, but does not transform fibroblasts in vitro or induce sarcomas in vivo. In contrast, virus 9134 S3 expresses an erbB product identical to the erbB product of 9134 E1, with the exception of a large internal deletion located between the kinase domain and the putative autophosphorylation site, P1. Interestingly, this virus is no longer capable of inducing erythroblastosis, but can induce both fibrosarcomas and hemangiomas in vivo. Provirus 9134 F3 has sustained an approximately 23-amino-acid carboxy-terminal truncation and is capable of inducing both erythroblastosis and sarcomagenesis. This virus expresses an erbB product with the shortest carboxy-terminal truncation sufficient to reveal the sarcomagenic potential of this protein. The distinct transforming properties of these viruses indicate that different structural domains of the erbB product confer distinct disease specificities.
An inferior alveolar intraneural cyst: a case example and an anatomical explanation to support the articular theory within cranial nerves (2015)

The authors describe the case of an intraneural ganglion cyst involving a cranial nerve (V3), which was found to have a joint connection in support of an articular origin within the cranial nerves. An inferior alveolar intraneural cyst was incidentally discovered on a plain radiograph prior to edentulation. It was resected from within the mandibular canal with no joint connection perceived at surgery. Histologically, the cyst was confirmed to be an intraneural ganglion cyst. Reinterpretation of the preoperative CT scan showed the cyst arising from the temporomandibular joint. This case is consistent with the articular (synovial) theory of intraneural ganglion cysts. An anatomical explanation and potential joint connection are provided for this case as well as several other cases of intraneural cysts in the literature, and thus unifying cranial nerve involvement with accepted concepts of intraneural ganglion cyst formation and propagation.
Efficient Representation for Natural Language Processing via Kernelized Hashcodes. (2017)

Kernel methods have produced state-of-the-art results for a number of NLP tasks such as relation extraction, but suffer from poor scalability due to the high cost of computing kernel similarities between natural language structures. A recently proposed technique, kernelized locality-sensitive hashing (KLSH), can significantly reduce the computational cost, but is only applicable to classifiers operating on kNN graphs. Here we propose to use random subspaces of KLSH codes for efficiently constructing an explicit representation of NLP structures suitable for general classification methods. Further, we propose an approach for optimizing the KLSH model for classification problems by maximizing an approximation of mutual information between the KLSH codes (feature vectors) and the class labels. We evaluate the proposed approach on biomedical relation extraction datasets, and observe significant and robust improvements in accuracy w.r.t. state-of-the-art classifiers, along with drastic (orders-of-magnitude) speedup compared to conventional kernel methods.
Cancer patients’ preferences for return of somatic and germline whole-exome sequencing results: Data from the CANSEQ study. (2014)

1535 Background: The introduction of whole-exome sequencing (WES) into routine cancer care presents novel challenges for patient education and informed consent. In light of the recent American College of Medical Genetics and Genomics recommendations for the return of actionable germline incidental findings, it is imperative to understand patients’ preferences for the return of WES findings. Methods: Advanced lung and colorectal cancer patients were offered WES. Preferences for the return of somatic and germline findings were obtained at consent. Attitudes about genetic testing and genetic knowledge were elicited through a baseline survey. Results: We approached 97 patients for participation, of whom 92 (95%) enrolled. Eighty-six patients completed the survey (completion rate 93%); 49% lung, 58% female, mean age 65 (standard deviation (sd) 11.4), 79% white, 21% ≤ high school education, 22% ≥ advanced degree. The vast majority of patients wanted to learn about somatic and germline WES findings. Preferences for return of results were highest for somatic findings that can be used to select a clinical trial (97%) and for positive prognostic findings (99%). Most patients also wanted return of germline pharmacogenetic (cancer-related 99%; non-cancer related 94%), cancer risk (96%), and treatable non-cancer risk (96%) results. Preferences for the return of somatic results with negative prognostic implications (86%), results indicating germline risk for non-treatable, non-cancer conditions (85%), and carrier status (88%) were slightly lower. Patients had highly positive attitudes about genetic testing but relatively low genetic knowledge, answering a mean of 54% of items correctly on a 7-item scale (sd 24.7). Conclusions: Patients with advanced lung and colorectal cancer express strong preferences for the return of somatic and germline WES findings. Despite patients’ positive attitudes about genetic testing, relatively low levels of genetic knowledge may present challenges to adequate informed consent and highlight the need for high-quality sequencing-related patient education.
Galanin modulates the neural niche to favour perineural invasion in head and neck cancer (2015)

Perineural invasion (PNI) is an indicator of poor survival in multiple cancers. Unfortunately, there is no targeted treatment for PNI since the molecular mechanisms are largely unknown. PNI is an active process, suggesting that cancer cells communicate with nerves. However, nerve-tumour crosstalk is understudied due to the lack of in vivo models to investigate the mechanisms. Here we developed an in vivo model of PNI to characterize this interaction. We show that the neuropeptide galanin (GAL) initiates nerve-tumour crosstalk via activation of its G protein-coupled receptor, GALR2. Our data reveal a novel mechanism by which GAL from nerves stimulates GALR2 on cancer cells to induce NFATC2-mediated transcription of cyclooxygenase-2 and GAL. Prostaglandin E2 promotes cancer invasion, and in a feedback mechanism, GAL released by cancer induces neuritogenesis, facilitating PNI. This study describes a novel in vivo model for PNI and reveals the dynamic interaction between nerve and cancer.
Using a Reference Point for Local Configuration of SIFT-like Features for Object Recognition with Serious Background Clutter (2011)

Object recognition can be performed on local or global features. While local features are more robust against occlusions, global features are more powerful to distinguish among many objects. In this paper we propose a novel approach in construction of a shape model from local features aimed at achieving high discriminative power as global features have, while keeping the robustness of local features. We utilize a common reference point expressing the relative position of local features like in a star graph representation. This model is dynamically calculated during recognition which makes it flexible. With our approach we achieve an improved recognition performance of 2% compared to other shape models and even 6% compared to approaches that do not utilize shape information.