gebhart/patrepeval huggingface dataset:
Development, characterization, and biological properties of meningococcal immunotype L3,7,(8),9-specific monoclonal antibodies (1994)

In this study, we characterize the properties of nine monoclonal antibodies (MAbs) that recognize meningococcal lipopolysaccharides (LPS). The following three specific MAbs that had not been described previously were elicited in BALB/c mice by using an immunotype L3,7,9 oligosaccharide-tetanus toxoid conjugate in combination with Quil A: 4D1-B3, 3A12-E1, and 4A8-B2. These MAbs reacted with L3,7,9 LPS on immunoblots and in the LPS enzyme-linked immunosorbent assay (ELISA) and recognised strains containing L3, L3,7, L8 (except 3A12-E1), or L9 LPS in the whole-cell ELISA. The six other MAbs have been described in previous studies (K. Saukkonen, M. Leinonen, H. Abdillahi, and J.T. Poolman, Vaccine 7:325-328, 1989; R.J.P.M. Scholten, B. Kuipers, H.A. Valkenburg, J. Danjert, W.D. Zollinger, and J.T. Poolman, J. Med. Microbiol., in press) and were obtained after immunization with outer membrane protein complexes containing LPS: MN15A11, MN15A8-1, MN15A17-1, MN11A11G, MN14F20-11, and MN14F21-11. MN15A11 was specific for L3,7,9 LPS and displayed properties similar to those of 3A12-E1. MN15A17-1, MN14F20-1, and MN11A11G were cross-reactive, and MN14F21-11 was specific for the L1,8 immunotype. Epitope specificities of MAbs reacting with L3,7,(8),9 strains were analyzed. MAbs 4D1-B3, 3A12-E1, and 4A8-B2 recognized phosphoethanolamine group-containing oligosaccharide-specific epitopes. MN15A11 and MN15A17-1 were probably directed against a conformational epitope, although for MN5A11 recognition of an unknown L3,7,9-specific epitope in the 2-keto-3-deoxyoctulosonic acid (KDO)-lipid A region cannot be excluded. MN15A8-1, a strongly cross-reactive MAb, recognized a determinant which included the KDO-lipid A region and the more terminal saccharides.(ABSTRACT TRUNCATED AT 250 WORDS)
Activation of an estrogen/estrogen receptor signaling by BIG3 through its inhibitory effect on nuclear transport of PHB2/REA in breast cancer (2009)

Breast cancer is known to be a hormone-dependent disease, and estrogens through an interaction with estrogen receptor (ER) enhance the proliferative and metastatic activity of breast tumor cells. Here we show a critical role of transactivation of BIG3, brefeldin A-inhibited guanine nucleotide-exchange protein 3, in activation of the estrogen/ER signaling in breast cancer cells. Knocking-down of BIG3 expression with small-interfering RNA (siRNA) drastically suppressed the growth of breast cancer cells. Subsequent coimmunoprecipitation and immunoblotting assays revealed an interaction of BIG3 with prohibitin 2/repressor of estrogen receptor activity (PHB2/REA). When BIG3 was absent, stimulation of estradiol caused the translocation of PHB2/REA to the nucleus, enhanced the interaction of PHB2/REA and ERalpha, and resulted in suppression of the ERalpha transcriptional activity. On the other hand, when BIG3 was present, BIG3 trapped PHB2/REA in the cytoplasm and inhibited its nuclear translocation, and caused enhancement of ERalpha transcriptional activity. Our results imply that BIG3 overexpression is one of the important mechanisms causing the activation of the estrogen/ERalpha signaling pathway in the hormone-related growth of breast cancer cells.
Intratracheal Recombinant Surfactant Protein D Prevents Endotoxin Shock in the Newborn Preterm Lamb (2006)

Intratracheal recombinant human SP-D prevented shock caused by endotoxin released from the lung during ventilation in the premature newborn.
Bayesian Network Approach to Cell Signaling Pathway Modeling (2002)

The modeling of cellular signaling pathways is an emerging field. Sachs et al. illustrate the application of Bayesian networks to an example cellular pathway involving the activation of focal adhesion kinase (FAK) and extracellular signal-regulated kinase (ERK) in response to fibronectin binding to an integrin. They describe how to use the analysis to select from among proposed models, formulate hypotheses regarding component interactions, and uncover potential dynamic changes in the interactions between these components. Although the data sets currently available for this example problem are too small to definitively point to a particular model, the approach and results provide a glimpse into the power that these methods will achieve once the technology for obtaining the necessary data becomes readily available.
Development of intercellular junctions in the pulmonary epithelium of the foetal lamb (1978)

The integrity of epithelial tight junctions in foetal mammalian lungs is essential to maintain the unique ionic composition of lung liquid, and to prevent leakage of serum proteins into peripheral air spaces. In the present study the development of intercellular junctions of the lining epithelium of foetal lamb lungs during gestation was examined by light and electron microscopy. Both thin sections and freeze-fracture replicas were examined by electron microscopy. By 39 days of gestation, epithelial tight junctions consist of a minimum of 3.1 +/- 1.6 (s.D.) and a maximum of 5.8 +/- 2.0 discontinuous rows of particles and short segments of strands on P face ridges and in complementary E face grooves, while from 58 to 76 days they are composed of a network of 4.3 +/- 1.6 to 7.7 +/- 1.9 focally interrupted P face strands. Complementary replicas show that many of the discontinuities on the P face are due to separation of junctional particles on to the E face during fracturing, and not to an absence of junctional particles. From 76 days to term, epithelial tight junctions (exclusive of upper airway epithelium which was not examined) resemble those of adult lungs, and consist of a continuous network of 4.5 +/- 2.0 to 7.5 +/- 2.5 P face strands and complementary particle-free grooves. Permeability measurements, published elsewhere, indicate that the epithelium is functionally 'tight' from 69 days onwards. Tight junctions in peripheral air-space epithelium, therefore, are structurally continuous and functionally 'tight' early in foetal lung development, and form seals at one end of long, narrow intercellular spaces; these features may be important for coupled ion and water transport. When the bounding epithelial cells become flattened, these narrow intercellular spaces remain intact as a result of complex interdigitations of adjacent cell membranes. Desmosomes were present throughout gestation near the abluminal side of the tight junctions and occasionally near the base of the intercellular space. These junctions may serve to connect cells to each other at a time when tight junctions may be mechanically weak. In addition, gap junctions are associated with tight junctions from the glandular through the canalicular stages of lung development. They disappear by 120 days when the epithelial cells are differentiated.
Solving stubborn-wound problem could save millions, team says. (1999)

Why do some wounds refuse to heal? A team in London, Ont., is attempting to determine the cellular and molecular clues that could lead to better treatment of recalcitrant wounds.
Crystal Structure of Glucose Dehydrogenase from Bacillus megaterium IWG3 at 1.7 Resolution (2001)

The crystal structure of glucose dehydrogenase (GlcDH) from Bacillus megaterium IWG3 has been determined to an R-factor of 17.9% at 1.7 A resolution. The enzyme consists of four identical subunits, which are similar to those of other short-chain reductases/dehydrogenases (SDRs) in their overall folding and subunit architecture, although cofactor binding sites and subunit interactions differ. Whereas a pair of basic residues is well conserved among NADP(+)-preferring SDRs, only Arg39 was found around the adenine ribose moiety of GlcDH. This suggests that one basic amino acid is enough to determine the coenzyme specificity. The four subunits are interrelated by three mutually perpendicular diad axes (P, Q, and R). While subunit interactions through the P-axis for GlcDH are not so different from those of the other SDRs, those through the Q-axis differ significantly. GlcDH was found to have weaker hydrophobic interactions in the Q-interface. Moreover, GlcDH lacks the salt bridge that stabilizes the subunit interaction in the Q-interface in the other SDRs. Hydrogen bonds between Q-axis related subunits are also less common than in the other SDRs. The GlcDH tetramer dissociates into inactive monomers at pH 9.0, which can be attributed mainly to the weakness of the Q-axis interface.
Characterization of mouse interleukin-12 p40 homodimer binding to the interleukin-12 receptor subunits (1999)

Interleukin-12 (IL-12) is a heterodimeric cytokine composed of two disulfide-bonded subunits, p35 and p40, which has important regulatory effects on T cells and natural killer (NK) cells. In contrast to heterodimeric IL-12, a homodimer of the p40 subunit, designated (p40)2, has been shown to be a potent IL-12 antagonist. To study the interaction between (p40)2 and the known IL-12 receptor (IL-12R) subunits, IL-12Rbeta1 and IL-12Rbeta2, we directly measured the binding activity of mouse (p40)2 to ConA-activated lymphoblasts and purified B cells from splenocytes of C57BL/6J mice. These results demonstrated the presence of both high (Kd about 5 pM) and low affinity (Kd about 15 nM) binding sites for mouse 125I-labeled (p40)2. To elucidate which of the IL-12R subunits binds mouse (p40)2, binding studies of mouse 125I-labeled (p40)2 to Ba/F3 cells expressing recombinant mouse IL-12Rbeta1 and/or mouse IL-12Rbeta2 were carried out. Mouse IL-12Rbeta1 bound mouse 125I-labeled (p40)2 with high and low affinities, comparable to that observed on Con A blasts and B cells. In contrast, mouse IL-12Rbeta2 bound mouse 125I-labeled (p40)2 very poorly. These data demonstrate that similar to IL-12, mouse (p40)2 binds with both high and low affinity to Con A blasts and B cells, and that IL-12Rbeta1 is responsible for mediating the specific binding of mouse (p40)2.
The Fourth Helical Secondary Structure of β‐Peptides: The (P)‐28‐Helix of a β‐Hexapeptide Consisting of (2R,3S)‐3‐Amino‐2‐hydroxy Acid Residues (2003)

Small change with great effect! An oligomer of α-hydroxy-β-amino acids folds into a right-handed helical structure (see picture) in MeOH; in contrast, the methyl analogue has a pleated sheet structure. Including this new helix, four different helical secondary structures of β-peptides have been discovered—a structural diversity that should allow the generation of elaborate proteomimetics. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z50290_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Inhibitors of Amyloid Toxicity Based on β-sheet Packing of Aβ40 and Aβ42 (2006)

Amyloid fibrils associated with Alzheimer's disease and a wide range of other neurodegenerative diseases have a cross beta-sheet structure, where main chain hydrogen bonding occurs between beta-strands in the direction of the fibril axis. The surface of the beta-sheet has pronounced ridges and grooves when the individual beta-strands have a parallel orientation and the amino acids are in-register with one another. Here we show that in Abeta amyloid fibrils, Met35 packs against Gly33 in the C-terminus of Abeta40 and against Gly37 in the C-terminus of Abeta42. These packing interactions suggest that the protofilament subunits are displaced relative to one another in the Abeta40 and Abeta42 fibril structures. We take advantage of this corrugated structure to design a new class of inhibitors that prevent fibril formation by placing alternating glycine and aromatic residues on one face of a beta-strand. We show that peptide inhibitors based on a GxFxGxF framework disrupt sheet-to-sheet packing and inhibit the formation of mature Abeta fibrils as assayed by thioflavin T fluorescence, electron microscopy, and solid-state NMR spectroscopy. The alternating large and small amino acids in the GxFxGxF sequence are complementary to the corresponding amino acids in the IxGxMxG motif found in the C-terminal sequence of Abeta40 and Abeta42. Importantly, the designed peptide inhibitors significantly reduce the toxicity induced by Abeta42 on cultured rat cortical neurons.
ESTIMATING SURFACE NORMALS IN NOISY POINT CLOUD DATA (2004)

In this paper we describe and analyze a method based on local least square fitting for estimating the normals at all sample points of a point cloud data (PCD) set, in the presence of noise. We study the effects of neighborhood size, curvature, sampling density, and noise on the normal estimation when the PCD is sampled from a smooth curve in ℝ 2 or a smooth surface in ℝ 3 , and noise is added. The analysis allows us to find the optimal neighborhood size using other local information from the PCD. Experimental results are also provided.
Modulation of Hematopoietic Chemokine Effects In Vitro and In Vivo by DPP-4/CD26 (2016)

Dipeptidyl peptidase 4 (DPP4)/CD26 truncates certain proteins, and this posttranslational modification can influence their activity. Truncated (T) colony-stimulating factors (CSFs) are decreased in potency for stimulating proliferation of hematopoietic progenitor cells (HPCs). T-CXCL12, a modified chemokine, is inactive as an HPC chemotactic, survival, and enhancing factor for replating or ex-vivo expansion of HPCs. Moreover, T-CSFs and T-CXCL12 specifically downmodulates the positively acting effects of their own full-length molecule. Other chemokines have DPP4 truncation sites. In the present study, we evaluated effects of DPP4 inhibition (by Diprotin A) or gene deletion of HPC on chemokine inhibition of multicytokine-stimulated HPC, and on chemokine-enhancing effects on single CSF-stimulated HPC proliferation, as well as effects of DPP4 treatment of a number of chemokines. Myelosuppressive effects of chemokines with, but not without, a DPP4 truncation site were greatly enhanced in inhibitory potency by pretreating target bone marrow (BM) cells with Diprotin A, or by assaying their activity on dpp4/cd26(-/-) BM cells. DPP4 treatment of myelosuppressive chemokines containing a DPP4 truncation site produced a nonmyelosuppressive molecule, but one which had the capacity to block suppression by that unmodified chemokine both in vitro and in vivo. Additionally, DPP4 treatment ablated the single cytokine-stimulated HPC-enhancing activity of CCL3/MIP-1α and CCL4/MIP-1β, and blocked the enhancing activity of each unmodified molecule, in vitro and in vivo. These results highlight the functional posttranslational modulating effects of DPP4 on chemokine activities, and information offering additional biological insight into chemokine regulation of hematopoiesis.
Learning to look up: Realtime monocular gaze correction using machine learning (2015)

We revisit the well-known problem of gaze correction and present a solution based on supervised machine learning. At training time, our system observes pairs of images, where each pair contains the face of the same person with a fixed angular difference in gaze direction. It then learns to synthesize the second image of a pair from the first one. After learning, the system gets the ability to redirect the gaze of a previously unseen person by the same angular difference as in the training set. Unlike many previous solutions to gaze problem in videoconferencing, ours is purely monocular, i.e. it does not require any hardware apart from an in-built web-camera of a laptop. Being based on efficient machine learning predictors such as decision forests, the system is fast (runs in real-time on a single core of a modern laptop). In the paper, we demonstrate results on a variety of videoconferencing frames and evaluate the method quantitatively on the hold-out set of registered images. The supplementary video shows example sessions of our system at work.
Advances in the treatment of anorexia nervosa: a review of established and emerging interventions (2017)

Evidence generation on the treatment of AN has dramatically accelerated, with our understanding of the role of family-based approaches for adolescents more nuanced and a range of psychological approaches available for the treatment of adults. Evidence on emerging treatments and from forthcoming trials suggests that there is a shift towards more targeted brain-based interventions. Future studies need to focus on elucidating mechanisms of action of treatments and what works best for whom.
Design and Construction of a Testing Platform and Estimating Attenuation Painting Reflectivity to Laser Beam (2011)

The project has been described the design and construction of a reliable optical testing platform used for evaluate the reflectivity of metal surfaces treated with special paintings required for laser beam attenuation. The platform comprises an Nd-YAG laser system which has been designed and fabricated with specifications to be compatible with their corresponding in laser range finder transmitters used for various applications. The reflectivity of various attenuating paintings, at different detection angles, has been observed. Moreover, the variation of the reflected energy with painting type and metal type to be painted has been studied experimentally. Results illustrated the existence of a definite angle, at which the reflectivity was maximum (specular reflection). On the other hand, samples with attenuation paintings have constant very low diffusive reflectivity and are independent of the detection angle.
High-performance enhancement-mode InAlAs/InGaAs HEMTs using non-alloyed ohmic contact and Pt-based buried-gate (2002)

In this paper, we demonstrate greatly improved R/sub S/ in an E-HEMT structure using non-alloyed ohmic contact and Pt-based buried gate approaches. First, the non-alloyed ohmic contact technique was used to produce very low contact resistance and to provide sharply defined ohmic edges. Second, in the fabrication of our E-HEMT's, we first intentionally fabricated depletion-mode HEMTs (D-HEMTs). Subsequently, by annealing the sample at 250/spl deg/C, these D-HEMTs were changed to E-HEMTs as a result of the Pt-InAlAs reaction taking place under the gate electrode, while the channel region between source and gate remained undepleted. This allowed a small R/sub S/ to be maintained An excellent transconductance (g/sub m/) of 1170 mS/mm was achieved for an E-HEMT with a 0.5-/spl mu/m-gate.
Phase 1 Trial of AMA1-C1/Alhydrogel plus CPG 7909: An Asexual Blood-Stage Vaccine for Plasmodium falciparum Malaria (2008)

ClinicalTrials.gov NCT00344539.
Tyrosinase as a marker for transgenic mice (1991)

Note: Institute of Cell and Tumor Biology, German Cancer Research Center, Heidelberg. Reference GR-BEERMANN-ARTICLE-1991-001doi:10.1093/nar/19.4.958 Record created on 2008-01-22, modified on 2017-05-12
Almost-linear time decoding algorithm for topological codes (2021)

In order to build a large scale quantum computer, one must be able to correct errors extremely fast. We design a fast decoding algorithm for topological codes to correct for Pauli errors and erasure and combination of both errors and erasure. Our algorithm has a worst case complexity of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>O</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:mi>n</mml:mi><mml:mi>α</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy="false">)</mml:mo><mml:mo stretchy="false">)</mml:mo></mml:math>, where <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>n</mml:mi></mml:math> is the number of physical qubits and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>α</mml:mi></mml:math> is the inverse of Ackermann's function, which is very slowly growing. For all practical purposes, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>α</mml:mi><mml:mo stretchy="false">(</mml:mo><mml:mi>n</mml:mi><mml:mo stretchy="false">)</mml:mo><mml:mo>≤</mml:mo><mml:mn>3</mml:mn></mml:math>. We prove that our algorithm performs optimally for errors of weight up to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo stretchy="false">(</mml:mo><mml:mi>d</mml:mi><mml:mo>−</mml:mo><mml:mn>1</mml:mn><mml:mo stretchy="false">)</mml:mo><mml:mrow class="MJX-TeXAtom-ORD"><mml:mo>/</mml:mo></mml:mrow><mml:mn>2</mml:mn></mml:math> and for loss of up to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>d</mml:mi><mml:mo>−</mml:mo><mml:mn>1</mml:mn></mml:math> qubits, where <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>d</mml:mi></mml:math> is the minimum distance of the code. Numerically, we obtain a threshold of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>9.9</mml:mn><mml:mi mathvariant="normal">%</mml:mi></mml:math> for the 2d-toric code with perfect syndrome measurements and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mn>2.6</mml:mn><mml:mi mathvariant="normal">%</mml:mi></mml:math> with faulty measurements.
Real-time in vivo imaging of human gastrointestinal ultrastructure by use of endoscopic optical coherence tomography with a novel efficient interferometer design (1999)

We report on the design and initial clinical experience with a real-time endoscopic optical coherence tomography (EOCT) imaging system. The EOCT unit includes a high-speed optical coherence tomography interferometer, endoscope-compatible catheter probes, and real-time data capture and display hardware and software. Several technological innovations are introduced that improve EOCT efficiency and performance. In initial clinical studies using the EOCT system, the esophagus, stomach, duodenum, ileum, colon, and rectum of patients with normal endoscopic findings were examined. In these initial investigations, EOCT imaging clearly delineated the substructure of the mucosa and submucosa in several gastrointestinal organs; microscopic structures such as glands, blood vessels, pits, villi, and crypts were also observed.
Peptide neuroprotection through specific interaction with brain tubulin (2006)

This study aimed to identify the neuronal target for the potent neuroprotective peptide NAP. When added to pheochromocytoma cells (neuronal model), NAP was found in the intracellular milieu and was co-localized with microtubules. NAP induced neurite outgrowth and protected primary neurons against microtubule-associated ZnCl2 toxicity. Rapid microtubule reorganization into distinct microtubules ensued after NAP addition to both pheochromocytoma cells and primary cerebral cortical neurons, but not to fibrobalsts. While binding neuronal tubulin and protecting pheochromocytoma cells against oxidative stress, NAP did not bind tubulin extracted from fibroblasts, nor did it protect those cells against oxidative stress. Affinity chromatography identified the brain-specific betaIII-tubulin as a major NAP binding protein. Paclitaxel (a microtubule aggregating agent that interacts with beta-tubulin) reduced NAP tubulin binding. Thus, the underlying mechanism for the neuroprotection offered by NAP is targeting neuronal microtubules that are essential for neuronal survival and function.
The Metabolic Syndrome and Total and Cardiovascular Disease Mortality in Middle-aged Men (2002)

Cardiovascular disease and all-cause mortality are increased in men with the metabolic syndrome, even in the absence of baseline CVD and diabetes. Early identification, treatment, and prevention of the metabolic syndrome present a major challenge for health care professionals facing an epidemic of overweight and sedentary lifestyle.