gebhart/patrepeval huggingface dataset:
Cellular uptake of an α-AApeptide (2011)

Some short and cationic peptides such as the Tat peptide can cross the cell membrane and function as vectors for intracellular delivery. Here we show that an α-AApeptide is able to penetrate the membranes of living cells from an extracellular environment and enter the endosome and cytoplasm of cells. The efficiency of the cellular uptake is comparable to a Tat peptide (48-57) of the same length and is unexpectedly superior to an α-peptide with identical functional groups. The mechanism of uptake is similar to that of the Tat peptide and is through endocytosis by an energy-dependent pathway. Due to the easy synthesis of the α-AApeptides, their resistance to proteolytic hydrolysis, and their low cytotoxicity, α-AApeptides represent a new class of transporters for the delivery of drugs.
Densifying Forest Biomass into Large Round Bales (1984)

ABSTRACT A large round-bale hay baler was modified to examine the concept of baling forest biomass in large round bales. Material baled, feed orientation, and baler belt tension were varied to observe their effects on the baling process and bale density. Torque and power required to drive the baler were measured
Loop and Backbone Modifications of Peptide Nucleic Acid Improve G-Quadruplex Binding Selectivity (2009)

Targeting guanine (G) quadruplex structures is an exciting new strategy with potential for controlling gene expression and designing anticancer agents. Guanine-rich peptide nucleic acid (PNA) oligomers bind to homologous DNA and RNA to form hetero-G-quadruplexes but can also bind to complementary cytosine-rich sequences to form heteroduplexes. In this study, we incorporated backbone modifications into G-rich PNAs to improve the selectivity for quadruplex versus duplex formation. Incorporation of abasic sites as well as chiral modifications to the backbone were found to be effective strategies for improving selectivity as shown by UV-melting and surface plasmon resonance measurements. The enhanced selectivity is due primarily to decreased affinity for complementary sequences, since binding to the homologous DNA to form PNA-DNA heteroquadruplexes retains high affinity. The improved selectivity of these PNAs is an important step toward using PNAs for regulating gene expression by G-quadruplex formation.
Searching Annotated Broadcast Content on Mobile and Stationary Devices (2004)

This paper describes, within the framework of the European IST SAVANT project, the development of a search engine that supports transparent access to annotated broadcast content from different types of user devices. For this purpose, the search engine makes use of emerging standards such as MPEG-7, TV-Anytime and MPEG-21.
RFI suppression in SAR based on approximated spectral decomposition algorithm (2012)

In this reported work, radio frequency interferences (RFI) in synthetic aperture radar (SAR) are suppressed using novel tools. Introduced first are the random sampling techniques that are commonly used in large-scale machine learning areas to obtain the RFI subspace via the approximated spectral decomposition. Thus, one can reconstruct the RFI signals efficiently and then remove them from the original received SAR pulses one by one. The performance of the algorithm was tested on a P-band real dataset.
Spin–Orbit Coupling Analyses of the Geometrical Effects on Phosphorescence in Ir(ppy)3 and Its Derivatives (2013)

Theoretical investigations were performed for typical iridium complexes, Ir(C∧N)3, Ir(C∧N)2(C’∧N’), Ir(C∧N)2(N ∧O) and Ir(C∧N)2(O∧O), at the MCSCF+SOCI+SOC//B3LYP/SBKJC+p level of theory. For Ir(dfppy)2(pic) (so-called FIrpic) and its related complexes, the introduction of a fluoride into ppy ligands provides a blue shift of about 20 nm for emission spectra, while the replacement of a pic ligand by an acac ligand does not seriously affect the emission spectra of these complexes. It is proposed that the homo-cis,hetero-O-cis isomer (HC-5f, see text) of FIrpic should be used as a brighter blue-color material instead of the homo-N-trans isomer (HNT-5f). The energy difference between these isomers is less than 1 kcal/mol, and the energy barrier of the isomerization between these isomers is calculated to be larger than 30 kcal/mol. It was also found that the use of two ancillary ligands, such as Ir(C∧N)(N ∧O)2 and Ir(C∧N)(O∧O)2, is unfortunately inappropriate to energetically lift the π* orbital.
Percutaneous Techniques for Endoluminal Carotid Interventions (1996)

While the RCF route is more familiar to the majority of interventionists and provides adequate access in most situations, traversing the arch and negotiating acute angles at the ostia of the great vessels may render this method infeasible. The direct puncture technique is a useful alternative; however, it requires more expertise to prevent potentially disastrous access-site complications. One further caveat must be stated: regardless of the access approach selected, the opportunity for serious, debilitating-and lethal-complications is always present in cerebrovascular interventions. At this earliest phase in our experience with carotid stenting, cautious investigative methodologies must prevail.
Clinical Activity of the Immunoconjugate CMC-544 in B-Cell Malignancies: Preliminary Report of the Expanded Maximum Tolerated Dose (MTD) Cohort of a Phase 1 Study. (2006)

Abstract Introduction: CMC-544 is an antibody-targeted chemotherapy agent composed of a humanized antibody that specifically targets the CD22 antigen, conjugated to calicheamicin, a potent cytotoxic antitumor agent. Malignant cells of mature B-lymphocyte lineage express CD22, suggesting that CMC-544 may be useful for treating lymphomas of B-cell origin. A phase 1 dose-escalation trial of CMC-544 was performed at 14 European and US sites with 36 patients in the dose escalation portion and 48 in the expanded MTD portion. The MTD dose was 1.8 mg/m2 every 4 weeks. In the dose escalation phase the main toxicities observed were thrombocytopenia, asthenia, nausea, neutropenia, elevated liver function tests (LFTs) and anorexia. Grade 3–4 levels were only seen for thrombocytopenia, asthenia, neutropenia and LFTs (incidence of 40%, 13%, 9% and 9% respectively). Responses were seen in 8/22 (36%) patients (Advani A, et. al. Blood, abstract# 230, 2005:106). We now report the results of the expanded cohort at the MTD. Patients and Methods: Relapsed/refractory lymphoma patients were treated at the 1.8 mg/m2 dose level every 4 weeks. In addition to safety data, preliminary efficacy data (assessed using the International Workshop to Standardize Response Criteria for NHL) were collected. Results: As of July 2006, 48 patients were treated: median age 57 years (range 26–75); 51% females; 61% with ≥ 4 prior lines of therapy; 22 (46%) follicular lymphomas (FL) and 26 (54%) diffuse large B-cell lymphomas (DLBCL). Data were available on 48 patients evaluable for safety and 34 patients (19 FL and 15 DLBCL) evaluable for response. The overall safety profile was manageable; the most common drug-related adverse events (all grades) included thrombocytopenia (90%; the only bleeding noted was grade 1–2 epistaxis [12%]), asthenia (57%), nausea (39%), neutropenia (37%) and elevated levels of AST/SGOT (41%), ALT/SGPT (18%), alkaline phosphatase (27%) and bilirubin (18%). Grade 3–4 AEs that occurred with a frequency ≥ 10% included thrombocytopenia (57%) and neutropenia (29%). Responses in evaluable patients are shown in Table 1. The objective response rate was 69% and 33% for patients with FL and DLBCL, respectively. Conclusions: CMC-544 exhibits effficacy against recurrent/refractory B-cell lymphomas, with the main toxicity being clinically manageable, self limited thrombocytopenia. These encouraging data support the continuing development of CMC-544. Number (%) of Responses in Evaluable Patients: Response Follicular Lymphoma (n=19) DLBCL (n=15) ORR = Overall Remission Rate, (CR/CRu+PR) CR/CRu 6 (31.7) 2 (13.3) PR 7 (36.8) 3 (20.0) ORR 13 (68.5) 5 (33.3)
Fusions of anthrax toxin lethal factor to the ADP-ribosylation domain of Pseudomonas exotoxin A are potent cytotoxins which are translocated to the cytosol of mammalian cells. (1992)

The lethal factor (LF) and edema factor (EF) components of anthrax toxin are toxic to animal cells only if internalized by interaction with the protective antigen (PA) component. PA binds to a cell surface receptor and is proteolytically cleaved to expose a binding site for LF and EF. To study how LF and EF are internalized and trafficked within cells, LF was fused to the translocation and ADP-ribosylation domains (domains II and III, respectively) of Pseudomonas exotoxin A. LF fusion proteins containing Pseudomonas exotoxin A domains II and III were less toxic than those containing only domain III. Fusion proteins with a functional endoplasmic reticulum retention sequence, REDLK, at the carboxyl terminus of domain III were less toxic than those with a nonfunctional sequence, LDER. The most potent fusion protein, FP33, had an EC50 = 2 pM on Chinese hamster ovary cells, exceeding that of native Pseudomonas exotoxin A (EC50 = 420 pM). Toxicity of all the fusion proteins required the presence of PA and was blocked by monensin. These data suggest that LF and LF fusion proteins are efficiently translocated from acidified endosomes directly to the cytosol without trafficking through other organelles, as is required for Pseudomonas exotoxin A. This system provides a potential vehicle for importing diverse proteins into the cytosol of mammalian cells.
Scavenger Receptors and Their Potential as Therapeutic Targets in the Treatment of Cardiovascular Disease (2010)

Scavenger receptors act as membrane-bound and soluble proteins that bind to macromolecular complexes and pathogens. This diverse supergroup of proteins mediates binding to modified lipoprotein particles which regulate the initiation and progression of atherosclerotic plaques. In vascular tissues, scavenger receptors are implicated in regulating intracellular signaling, lipid accumulation, foam cell development, and cellular apoptosis or necrosis linked to the pathophysiology of atherosclerosis. One approach is using gene therapy to modulate scavenger receptor function in atherosclerosis. Ectopic expression of membrane-bound scavenger receptors using viral vectors can modify lipid profiles and reduce the incidence of atherosclerosis. Alternatively, expression of soluble scavenger receptors can also block plaque initiation and progression. Inhibition of scavenger receptor expression using a combined gene therapy and RNA interference strategy also holds promise for long-term therapy. Here we review our current understanding of the gene delivery by viral vectors to cells and tissues in gene therapy strategies and its application to the modulation of scavenger receptor function in atherosclerosis.
High-dimensional optical quantum logic in large operational spaces (2019)

Abstract The probabilistic nature of single-photon sources and photon–photon interactions encourages encoding as much quantum information as possible in every photon for the purpose of photonic quantum information processing. Here, by encoding high-dimensional units of information (qudits) in time and frequency degrees of freedom using on-chip sources, we report deterministic two-qudit gates in a single photon with fidelities exceeding 0.90 in the computational basis. Constructing a two-qudit modulo SUM gate, we generate and measure a single-photon state with nonseparability between time and frequency qudits. We then employ this SUM operation on two frequency-bin entangled photons—each carrying two 32-dimensional qudits—to realize a four-party high-dimensional Greenberger–Horne–Zeilinger state, occupying a Hilbert space equivalent to that of 20 qubits. Although high-dimensional coding alone is ultimately not scalable for universal quantum computing, our design shows the potential of deterministic optical quantum operations in large encoding spaces for practical and compact quantum information processing protocols.
Towards Secure Collaboration on the Semantic Web (2003)

Web technologies enable collaborative work to be done more efficiently and effectively. A user can share resources with others on the Web and perform his or her job based on a pre-defined policy for collaboration. During the collaboration, the user may need to create new resources, merge, split, exchange, or update resources created by other users. To support these services on the Web, we need machine-understandable as well as machine-readable metadata about the resources. The concept of a Semantic Web has been introduced to satisfy this requirement. Although the Semantic Web will provide more accurate and efficient services on the Web, it also introduces new problems that were not considered before, especially, in regards to security, interoperability, and transparency to users and organizations. In this paper, we discuss the requirements to support secure collaboration on the Semantic Web. We mainly focus on identification and analysis of the security problems associated with the Semantic Web, while suggesting possible solutions to each problem.
Total synthesis of amphotericin B (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of amphotericin BK. C. Nicolaou, R. A. Daines, T. K. Chakraborty, and Y. OgawaCite this: J. Am. Chem. Soc. 1987, 109, 9, 2821–2822Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://pubs.acs.org/doi/10.1021/ja00243a043https://doi.org/10.1021/ja00243a043research-articleACS PublicationsRequest reuse permissionsArticle Views2669Altmetric-Citations58LEARN 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 Get e-Alerts
DNA vaccines : methods and protocols (2014)

DNA Vaccines: Methods and Protocols, Third Edition explores innovative approaches and technologies used to design, deliver, and enhance the efficacy of DNA vaccines. Featuring applications which should be of great value in moving vaccines from research to clinic, this detailed volume includes sections on DNA vaccine design and enhancement, delivery systems, production, purification, and quality, as well as chapters on new vaccine applications. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, DNA Vaccines: Methods and Protocols, Third Edition serves the important role of further documenting the potential of the DNA vaccination as a platform technology for treatment and prevention of human disease
Induction of Inflammatory Bowel Disease in Immunodeficient Mice by Depletion of Regulatory T Cells (1999)

The severe combined immunodeficiency (SCID) model of colitis shares many features of idiopathic inflammatory bowel disease (IBD) in humans. The SCID model is highly reproducible and easily manipulated, and as such provides a useful tool for studying mucosal immune regulation as it relates to the pathogenesis and treatment of IBD in humans. This unit describes a cell transfer system in which SCID mice are reconstituted with CD4(+) CD45RB(high) cells to induce IBD. The CD4(+) cells are isolated by immunomagnetic negative selection using monoclonal antibodies, and are then separated by fluorescent cell sorting into CD45RB(high) and CD45RB(low) cells. The former population reproducibly induces disease in recipients. A support protocol describes methods to monitor disease progression, which is characterized by weight loss, loose stools, and histologically assessed lesions in the colon.
Effects of iron deficiency anemia and its treatment on fibroblast growth factor 23 and phosphate homeostasis in women (2013)

Fibroblast growth factor 23 (FGF23) is an osteocyte-derived hormone that regulates phosphate and vitamin D homeostasis. Through unknown mechanisms, certain intravenous iron preparations induce acute, reversible increases in circulating FGF23 levels that lower serum phosphate in association with inappropriately low levels of calcitriol, similar to genetic diseases of primary FGF23 excess. In contrast, studies in wild-type mice suggest that iron deficiency stimulates fgf23 transcription but does not result in hypophosphatemia because FGF23 is cleaved within osteocytes by an unknown catabolic system. We tested the association of iron deficiency anemia with C-terminal FGF23 (cFGF23) and intact FGF23 (iFGF23) levels in 55 women with a history of heavy uterine bleeding, and assessed the longitudinal biochemical response over 35 days to equivalent doses of randomly-assigned, intravenous elemental iron in the form of ferric carboxymaltose (FCM) or iron dextran. Iron deficiency was associated with markedly elevated cFGF23 (807.8 ± 123.9 relative units [RU]/mL) but normal iFGF23 (28.5 ± 1.1 pg/mL) levels at baseline. Within 24 hours of iron administration, cFGF23 levels fell by approximately 80% in both groups. In contrast, iFGF23 transiently increased in the FCM group alone, and was followed by a transient, asymptomatic reduction in serum phosphate <2.0 mg/dL in 10 women in the FCM group compared to none in the iron dextran group. Reduced serum phosphate was accompanied by increased urinary fractional excretion of phosphate, decreased calcitriol levels, and increased parathyroid hormone levels. These findings suggest that iron deficiency increases cFGF23 levels, and that certain iron preparations temporarily increase iFGF23 levels. We propose that intravenous iron lowers cFGF23 in humans by reducing fgf23 transcription as it does in mice, whereas carbohydrate moieties in certain iron preparations may simultaneously inhibit FGF23 degradation in osteocytes leading to transient increases in iFGF23 and reduced serum phosphate.
Robust L∞ homography estimation using reduced image feature covariances from an RGB image (2012)

Image features are regularly used in computer and machine vision applications to solve problems pertaining to image geometry. The effectiveness of techniques used rely on how accurately corresponding features are located in two (or more) images. Current techniques define a feature as a variation in intensity within a pixel neighborhood. The greater the change, the more pronounced a feature becomes, and is thus more accurately located. The remaining uncertainty is characterized via a covariance matrix, which is used to weight the influence of each feature on model estimation. As our first contribution, we propose a novel technique to decrease feature location uncertainty. Considering uncertainty information from all three channels of an RGB image, we employ covariance intersection (CI) to reduce measurement errors leading to a decrease in homography (H) estimation error. Our second contribution is to use an L∞ filter capable of dealing with system uncertainties to estimate H. By feeding the feature location uncertainty information into our filter, we observe significantly improved estimates of the homography. Our filtering approach outperforms covariance weighted optimization techniques proposed in literature shown through a number of examples.
Engineered Fusokine GIFT4 Licenses the Ability of B Cells to Trigger a Tumoricidal T-cell Response (2014)

Engineered chimeric cytokines can generate gain-of-function activity in immune cells. Here, we report potent antitumor activity for a novel fusion cytokine generated by N-terminal coupling of GM-CSF to IL4, generating a fusokine termed GIFT4. B cells treated with GIFT4 clustered GM-CSF and IL4 receptors on the cell surface and displayed a pan-STAT hyperphosphorylation associated with acquisition of a distinct phenotype and function described to date. In C57BL/6J mice, administration of GIFT4 expanded endogenous B cells and suppressed the growth of B16F0 melanoma cells. Furthermore, B16F0 melanoma cells engineered to secrete GIFT4 were rejected immunologically in a B-cell-dependent manner. This effect was abolished when GIFT4-expressing B16F0 cells were implanted in B-cell-deficient mice, confirming a B-cell-dependent antitumor effect. Human GIFT4-licensed B cells primed cytotoxic T cells and specifically killed melanoma cells in vitro and in vivo. Taken together, our results demonstrated that GIFT4 could mediate expansion of B cells with potent antigen-specific effector function. GIFT4 may offer a novel immunotherapeutic tool and define a previously unrecognized potential for B cells in melanoma immunotherapy.
Phenotypic and functional characterization of lymphocytes derived from normal and HIV-1-infected human lymph nodes (1999)

Lymph nodes are the major site of cell-to-cell transmission and replication of HIV-1. Trafficking of CD4+ T lymphocytes into lymph nodes provides a continual supply of susceptible target lymphocytes, and conversely, recruitment of CD8+ T lymphocytes may be critical for the host response that attempts to control HIV-1 replication. The present study was undertaken as no detailed assessment of lymphocyte subpopulations in HIV-1-infected lymph nodes has previously been reported. Peripheral blood and single-cell suspensions prepared from lymph nodes of patients with HIV-1 and control subjects were analysed using three-colour flow cytometry. Approximately 80% of the lymphocytes in control lymph nodes were CD3+ T lymphocytes, of which over 65% were CD4+. The majority of the CD4+ and CD8+ T lymphocytes obtained from both lymph nodes and blood of control subjects were immunologically naive (CD45RA+). By contrast, in HIV-1-infected patients there was a significant reduction in the proportion of CD4+ T lymphocytes and an expansion of the CD8+ T lymphocyte subset in both lymph nodes and peripheral blood. Furthermore, a high proportion of these T lymphocytes displayed a marker for immunological memory (CD45RO+). T lymphocytes derived from HIV-1-infected lymph nodes also showed altered expression of the adhesion molecules, L-selectin and very late antigen-4 (VLA-4), but not leucocyte function-associated antigen-1 (LFA-1). In an in vitro adhesion assay, lymphocytes from HIV-1-infected nodes were significantly more adhesive than control lymphocytes on fibronectin, as well as recombinant human intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) substrates. This combination of altered lymphocyte subpopulations in the HIV-1-infected lymph nodes, as well as enhanced adhesion phenotype and function, suggests that T lymphocyte traffic to lymph nodes in HIV disease may be an important determinant of pathogenesis.