gebhart/patrepeval huggingface dataset:
Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT) (2017)

Optical methods capable of manipulating neural activity with cellular resolution and millisecond precision in three dimensions will accelerate the pace of neuroscience research. Existing approaches for targeting individual neurons, however, fall short of these requirements. Here we present a new multiphoton photo-excitation method, termed three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT), which allows precise, simultaneous photo-activation of arbitrary sets of neurons anywhere within the addressable volume of a microscope. This technique uses point-cloud holography to place multiple copies of a temporally focused disc matching the dimensions of a neuron's cell body. Experiments in cultured cells, brain slices, and in living mice demonstrate single-neuron spatial resolution even when optically targeting randomly distributed groups of neurons in 3D. This approach opens new avenues for mapping and manipulating neural circuits, allowing a real-time, cellular resolution interface to the brain.
Structural and functional characterization of the trifunctional antibody catumaxomab (2010)

The Triomab family of trifunctional, bispecific antibodies that maintain an IgG-like shape are novel tumor targeting agents. These chimeras consist of two half antibodies, each with one light and one heavy chain, that originate from parental mouse IgG2a and rat IgG2b isotypes. This combination allows cost-effective biopharmaceutical manufacturing at an industrial scale since this specific mouse/rat isotype combination favors matching of corresponding antibody halves during production by means of quadroma technology. Whereas every Triomab family member is composed of an anti-CD3 rat IgG2b half antibody for T cell recognition, the antigen binding site presented by the mouse IgG2a isotype is exchangeable. Several Triomab antibodies have been generated that bind to tumor-associated antigens, e.g., EpCAM (catumaxomab), HER2/neu (ertumaxomab), CD20 (FBTA05), gangliosides GD2/GD3 (Ektomun), on appropriate tumor target cells associated with carcinomas, lymphomas or melanomas. Catumaxomab (Removab) was launched in Europe for treatment of malignant ascites in April 2009. Here, we report the structural and functional characterization of this product. Mass spectrometry revealed an intact mass of 150511 Dalton (Da) and 23717 Da, 24716 Da, 51957 Da and 52019 Da of the reduced and alkylated rat light chain, mouse light chain, rat heavy chain, mouse heavy chain chains, respectively. The observed masses were in agreement with the expected masses based on the amino acid sequence obtained from cDNA sequencing. The glycosylation profile was similar to other human IgG consisting of biantennary oligosaccharides with different numbers of terminal galactose. CD spectroscopy showed mainly beta-sheets secondary structure that is typical for IgG antibodies. Binding measurement revealed the unique trifunctional features of catumaxomab. Other analytical tools were used to evaluate characteristics of catumaxomab preparations, including the presence of isoforms and aggregates.
Native Electrophoresis-Coupled Activity Assays Reveal Catalytically-Active Protein Aggregates of Escherichia coli β-Glucuronidase (2015)

-glucuronidase is found as a functional homotetramer in a variety of organisms, including humans and other animals, as well as a number of bacteria. This enzyme is important in these organisms, catalyzing the hydrolytic removal of a glucuronide moiety from substrate molecules. This process serves to break down sugar conjugates in animals and provide sugars for metabolism in bacteria. While -glucuronidase is primarily found as a homotetramer, previous studies have indicated that the human form of the protein is also catalytically active as a dimer. Here we present evidence for not only an active dimer of the E. coli form of the protein, but also for several larger active complexes, including an octomer and a 16mer. Additionally, we propose a model for the structures of these large complexes, based on computationally-derived molecular modeling studies. These structures may have application in the study of human disease, as several diseases have been associated with the aggregation of proteins.
Bronchiolitis Obliterans after Human Lung Transplantation (2002)

SCOPUS: re.j
Imiquimod and resiquimod as novel immunomodulators (2001)

Augmenting the host's natural immune response to viruses by the administration of exogenous cytokines such as interferon-alpha (IFN-alpha) is a strategy increasingly employed in antiviral therapeutics. Enhancing the release of endogenous cytokines is, however, an alternative approach. The imidazoquinolinamines imiquimod and resiquimod have demonstrated potency as inducers of IFN-alpha and other cytokines both in vitro and in vivo. Cytokine gene activation is mediated via the signal transducer and activator of transcription 1 (STAT-1) and involves the transcription factors NFkappaB and alpha4F1. Antiviral activity has been demonstrated against a variety of viruses, and clinical efficacy has been demonstrated against genital warts, herpes genitalis and molluscum contagiosum. Imiquimod is administered as a 5% cream (Aldara) and has been licensed for the treatment of anogenital warts in immunocompetent patients. Complete clearance of warts has been observed in up to half of treated patients with only local side effects reported. Resiquimod can be administered topically but also exists as an oral formulation. The range of potential infections for which these agents may have clinical utility includes chronic hepatitis C virus infection and Kaposi's sarcoma. In addition, the imidazoquinolinamines may find roles in the therapy of cancers and as vaccine adjuvants.
Improvements on non-equilibrium and transport Green function techniques: The next-generation transiesta (2016)

We present novel methods implemented within the non-equilibrium Green function code (NEGF) TRANSIESTA based on density functional theory (DFT). Our flexible, next-generation DFT–NEGF code handles devices with one or multiple electrodes (N≥1) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable matrix inversion, performance-critical pivoting, and hybrid parallelization. Additionally, a generic NEGF “post-processing” code (TBTRANS/PHTRANS) for electron and phonon transport is presented with several novelties such as Hamiltonian interpolations, N≥1 electrode capability, bond-currents, generalized interface for user-defined tight-binding transport, transmission projection using eigenstates of a projected Hamiltonian, and fast inversion algorithms for large-scale simulations easily exceeding 10 atoms on workstation computers. The new features of both codes are demonstrated and bench-marked for relevant test systems.
Tocilizumab (2009)

Roche is co-developing tocilizumab (Actemra, RoActemra), a humanized anti-interleukin-6 receptor (IL-6R) monoclonal antibody, with Chugai Pharmaceutical. Tocilizumab is marketed in Japan for Castleman disease and several types of arthritis. The product is approved in the European Union for treatment of moderate-to-severe rheumatoid arthritis, and is currently undergoing review by the US Food and Drug Administration for this condition. Tocilizumab has also been studied for potential use in the treatment of other IL-6 related disorders including Crohn disease.
DMAP mediated one-pot domino thienannulation: a versatile, regioselective and green mechanochemical route to naphtho[2,3-b]thiophenes (2013)

Solvent-free mechanochemical route to naphtho[2,3-b]thiophenes via [3 + 2] oxidative heteroannulation of α-enolicdithioesters and β-oxothioamides with 1,4-naphthoquinone has been achieved at room temperature.
Advanced electronic and optoelectronic materials by Atomic Layer Deposition: An overview with special emphasis on recent progress in processing of high-k dielectrics and other oxide materials (2004)

The principle and practice of Atomic Layer Deposition (ALD) are described with special emphasis on the advantages of the method for processing of thin films for advanced applications in electronics, catalysis and sensor technology. The examples of ALD-processed materials include ZrO2 and other high-k dielectrics especially the rare earth oxides, SnO2 for gas sensors and ZnO for optoelectronics. The various precursor chemistries leading to these materials are discussed. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Diltiazem Improves Cardiac Function and Exercise Capacity in Patients With Idiopathic Dilated Cardiomyopathy (1996)

Background Evidence is arising that calcium antagonists in idiopathic dilated cardiomyopathy (IDC) may have beneficial effects on virus-induced cardiopathology, alcohol toxicity, microcirculatory disorders, and impaired calcium cycling, all possibly involved in the pathogenesis of the disease. Thus, the effect of adjunct diltiazem (60 to 90 mg TID) on standard treatment was investigated. Methods and Results The Diltiazem in Dilated Cardiomyopathy (DiDi) trial was a randomized, double-blind, placebo-controlled, multicenter trial of 186 patients (92 receiving diltiazem, 94 receiving placebo) with IDC diagnosed by coronary angiography, catheterization of the left side of the heart, and a left ventricular ejection fraction of &lt;0.50 (mean, 0.34±0.11). The effect of adjunct diltiazem treatment on transplant listing–free survival, hemodynamics, exercise capacity, and subjective status was investigated. During the 24-month study period, 33 patients dropped out of the study; 153 patients finished the study protocol. Twenty-seven patients died or had a listing for heart transplantation: 16 in the placebo group and 11 in the diltiazem group. The transplant listing–free survival rate was 85% for diltiazem and 80% for placebo recipients ( P =.444). After 24 months, only diltiazem significantly increased cardiac index at rest ( P =.01) and under a workload ( P =.02), systolic and diastolic pressures ( P =.003 and P =.004), stroke volume index ( P =.003), and stroke work index ( P =.000) and decreased both pulmonary artery pressure under workload ( P =.007) and heart rate ( P =.001). Diltiazem also increased exercise capacity ( P =.002) and subjective well-being ( P =.01). Adverse reactions were minor and evenly distributed in both groups, except for an increase in the PQ interval in the diltiazem group. Conclusions In patients with IDC, the adjunct therapy of diltiazem improves cardiac function, exercise capacity, and subjective status without deleterious effects on transplant listing–free survival.
Robust focus measure for unsupervised auto-focusing based on optimum discrete cosine transform coefficients (2011)

In this paper we present a robust focus measure for unsupervised auto-focusing based on optimum discrete cosine transform (DCT) coefficients. DCT has a low computational complexity due to real-valued coefficients, and a small number of coefficients have to be calculated to achieve a good spectral representation of an image. The focusing region of an input image is divided into nonoverlapping 8 × 8 sub-images, and spectra of sub-images are obtained by 8 × 8 DCT. The focusing measure is computed from the middle frequency components. By appropriately chosen DCT coefficients, the proposed focusing measure is robust to Gaussian and impulsive noises. Experimental results show that the proposed method is more effective than the traditional methods based on the comparison with well-known autofocusing uncertainty measure (AUM).
Basic Fibroblast Growth Factor Increases Collateral Blood Flow in Rats With Femoral Arterial Ligation (1996)

The potential for exogenous infusion of basic fibroblast growth factor (bFGF) to increase collateral blood flow to dependent tissue was quantified in adult male rats with peripheral arterial insufficiency. Occlusion of the femoral artery at a proximal site did not infringe on resting blood flow to the distal hindlimb muscle, but did remove the blood flow reserve. Blood flow to the hindlimb muscles was measured with radiolabeled microspheres using an isolated hindlimb preparation perfused in the descending aorta (Krebs-Henseleit bicarbonate, 5% albumin medium containing red blood cells [40% hematocrit]) at 100 mm Hg. Calf muscle blood flow changed modestly (approximately equal to 50%) with infusion of only the carrier (heparin/saline), increased markedly over the first 2 weeks of bFGF infusion (1 microgram/d into the femoral artery), but did not change further with infusion for 4 weeks. Waiting 2 weeks after 1 week of bFGF infusion did not further increase the intermediate improvement in blood flow. The improved collateral blood flow and increased muscle capillary density likely contributed to the enhanced muscle performance observed during nerve stimulation in situ. X-ray films of arterial casts identified an expansion of upper thigh vessels that likely served as collaterals. In animals with peripheral arterial insufficiency, short-term exogenous infusion of bFGF is effective at inducing vascular expansion that is sufficient to improve the flow reserve of dependent distal tissue and enhance muscle function. This raises the expectation that a similar response in patients with peripheral arterial insufficiency would significantly improve morbidity, including the symptoms of intermittent claudication.
The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins (2002)

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis . The Ciona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona , suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.
An Efficient Synthesis of 3-Aminocyclopent-2-en-1-one (1991)

A two step, efficient synthesis of the key intermediate 3-aminocyclopent-2-en-1-one starting from 1,3-cyclopentanedione is described. This involves the reaction of ammonia gas with 3-ethoxycyclopent-2-en-1-one.
Molecular Control of Mammalian Myoblast Fusion (2008)

The fusion of postmitotic mononucleated myoblasts to form syncytial myofibers is a critical step in the formation of skeletal muscle. Myoblast fusion occurs both during development and throughout adulthood, as skeletal muscle growth and regeneration require the accumulation of additional nuclei within myofibers. Myoblasts must undergo a complex series of molecular and morphological changes prior to fusing with one another. Although many molecules regulating myoblast fusion have been identified, the precise mechanism by which these molecules act in concert to control fusion remains to be elucidated. A comprehensive understanding of how myo-blast fusion is controlled may contribute to the treatment of various disorders associated with loss of muscle mass. In this chapter, we examine progress made toward elucidating the cellular and molecular pathways involved in mammalian myoblast fusion. Special emphasis is placed on the molecules that regulate myofiber formation without discernibly affecting biochemical differentiation.
DNA sequence encoding the NH2-terminal peptide involved in transport of lambda receptor, an Escherichia coli secretory protein. (1980)

lamB encodes the lambda receptor of Escherichia coli, an outer membrane protein. We have identified the beginning of the lamB gene by correlating DNA nucleotide sequence with a partial sequence of the primary translation product of lamB. We show that lambda receptor is synthesized as a precursor containing an extra 25 amino acids at its NH2 terminus. These amino acids are predominately hydrophobic and probably comprise a structure required for initiation of transport of lambda receptor from the cytoplasm to the outer membrane.
Progressive squamous epithelial neoplasia in K14-human papillomavirus type 16 transgenic mice (1994)

To model human papillomavirus-induced neoplastic progression, expression of the early region of human papillomavirus type 16 (HPV16) was targeted to the basal cells of the squamous epithelium in transgenic mice, using a human keratin 14 (K14) enhancer/promoter. Twenty-one transgenic founder mice were produced, and eight lines carrying either wild-type or mutant HPV16 early regions that did not express the E1 or E2 genes were established. As is characteristic of human cancers, the E6 and E7 genes remained intact in these mutants. The absence of E1 or E2 function did not influence the severity of the phenotype that eventually developed in the transgenic mice. Hyperplasia, papillomatosis, and dysplasia appeared at multiple epidermal and squamous mucosal sites, including ear and truncal skin, face, snout and eyelids, and anus. The ears were the most consistently affected site, with pathology being present in all lines with 100% penetrance. This phenotype also progressed through discernible stages. An initial mild hyperplasia was followed by hyperplasia, which further progressed to dysplasia and papillomatosis. During histopathological progression, there was an incremental increase in cellular DNA synthesis, determined by 5-bromo-2'-deoxyuridine incorporation, and a profound perturbation in keratinocyte terminal differentiation, as revealed by immunohistochemistry to K5, K14, and K10 and filaggrin. These K14-HPV16 transgenic mice present an opportunity to study the role of the HPV16 oncogenes in the neoplastic progression of squamous epithelium and provide a model with which to identify genetic and epigenetic factors necessary for carcinogenesis.
Electrical conductivities of aqueous solutions of KCl, KOH and HCl, and the ionization of water at high shock pressures (1969)

Measurements have been made of the electrical conductivities of aqueous solutions of KCl, KOH and HCl at shock wave pressures in the range 70–133 kbar. The molar conductivity of KCl was not measurably different from its normal value, and this finding is interpreted as meaning that although the temperature jump in the shock front tends to increase the mobilities of K+ and Cl– ions, the simultaneous jump in density has an opposite and cancelling effect. On the other hand, the conductivities of HCl and KOH increased several fold, indicating that the excess mobilities of hydrogen ions and hydroxyl ions increase by a factor of 3-6 under the shock conditions. By combining the measured ionic conductivities with earlier measurements of the conductivity of pure water it has been estimated that the ionization product Kw of water increases to about 0.09 mol2 kg–2 at a shock pressure af 133 kbar. It is suggested that the ionization of water into H3O+ and OH– ions becomes nearly complete at 200 kbar and that this transformation may be responsible for the difference in the pressure-volume behaviour of shocked water below and above the 150–200 kbar region.
Tuning the SP to FM transition of cobalt nanoparticles in view of biomedical applications (2002)

No abstract prepared.
Dairy consumption and 6-y changes in body weight and waist circumference in middle-aged French adults (2008)

The relation of dairy products and calcium intake with changes in weight and WC may differ according to sex, initial body-weight status, and type of dairy products. The negative association between dairy products and anthropometric changes observed in overweight men was not explained by dairy calcium intakes, which suggests that other components of dairy products or specific dietary patterns associated with dairy consumption may help to explain the observed associations.
MICROGNATHIA AND ASSOCIATED CLEFT PALATE (PIERRE ROBIN SYNDROME) (1960)

WOOLF, ROBERT M. M.D.; GEORGIADE, NICHOLAS M.D.; PICKRELL, KENNETH L. M.D. Author Information
Web-based design and analysis tools for CRISPR base editing (2018)

We develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.
Bench-to-bedside review: sepsis is a disease of the microcirculation. (2004)

Microcirculatory perfusion is disturbed in sepsis. Recent research has shown that maintaining systemic blood pressure is associated with inadequate perfusion of the microcirculation in sepsis. Microcirculatory perfusion is regulated by an intricate interplay of many neuroendocrine and paracrine pathways, which makes blood flow though this microvascular network a heterogeneous process. Owing to an increased microcirculatory resistance, a maldistribution of blood flow occurs with a decreased systemic vascular resistance due to shunting phenomena. Therapy in shock is aimed at the optimization of cardiac function, arterial hemoglobin saturation and tissue perfusion. This will mean the correction of hypovolemia and the restoration of an evenly distributed microcirculatory flow and adequate oxygen transport. A practical clinical score for the definition of shock is proposed and a novel technique for bedside visualization of the capillary network is discussed, including its possible implications for the treatment of septic shock patients with vasodilators to open the microcirculation.
Laminin α5 guides tissue patterning and organogenesis (2013)

Laminins (LM) are extracellular matrix molecules that contribute to and are required for the formation of basement membranes. They participate in the modulation of epithelial/mesenchymal interactions and are implicated in organogenesis and maintenance of organ homeostasis. Among the LM molecules, the LM α5 chain (LMα5) is one of the most widely distributed LM in the developing and mature organism. Its presence in some basement membranes during embryogenesis is absolutely required for maintenance of basement membrane integrity and thus for proper organogenesis. LMα5 also regulates the expression of genes important for major biological processes, in part by repressing or activating signaling pathways, depending upon the physiological context.
Identity and Cultural Change (1993)

In psychology, the study of tradition-directed societies (Riesman, 1950) has usually served to “confirm” existing theories as being of universal validity. The same holds true of psychoanalysis: in 1929, Geza Roheim travelled to Normanby Island in Melanesia to prove the universality of the Oedipus complex. He did so in reaction to Bronislaw Malinowski, whose research with the Trobriand Islanders had led him to question that idea. Similarly, C. G. Jung thought he recognized specific archetypal manifestations of the collective unconscious in the tribal traditions of primitive populations. The primary concern of the psychoanalysts was to identify and understand certain regularities in the aliens and to draw parallels between alien and western psychological processes. They were aware of the different psychological structure of members of tradition-directed societies, but their evaluation was biased by their feeling of mental and moral superiority. This bias often resulted in an overly obvious reproduction of the earlier colonialist power structures. Ultimately, the alienness of those populations was as frightening as their similarity; they reminded us of the alien within ourselves, of our own unconscious which Freud called the foreign, or alien, interior.