gebhart/patrepeval huggingface dataset:
Early restriction of peripheral and proximal cell lineages during formation of the lung (2002)

To establish the timing of lineage restriction among endodermal derivatives, we developed a method to label permanently subsets of lung precursor cells at defined times during development by using Cre recombinase to activate floxed alkaline phosphatase or green fluorescent protein genes under control of doxycycline-dependent surfactant protein C promoter. Extensive or complete labeling of peripheral lung, thyroid, and thymic epithelia, but not trachea, bronchi, or gastrointestinal tract occurred when mice were exposed to doxycycline from embryonic day (E) 4.5 to E6.5. Nonoverlapping cell lineages of conducting airways (trachea and bronchi), as distinct from those of peripheral airways (bronchioles, acini, and alveoli), were established well before formation of the definitive lung buds at E9-9.5. At E11.5, the labeled precursors of peripheral lung were restricted to relatively few cells along the bronchial tubes and clusters in bronchial tips and lateral buds. Thereafter, these cells underwent marked expansion to form the entire gas-exchange region in the lung. This study demonstrates early restriction of endodermal progenitor cells forming peripheral as compared with proximal airways, identifies distinct cell lineages in conducting airways, and distinguishes neuroepithelial and tracheal-bronchial gland cell lineages from those lining peripheral regions of the lung. This system for conditional gene addition or deletion is useful for the study of lung morphogenesis and gene function in vivo, and identifies progenitor cells that may serve as useful targets for cell or gene replacement for pulmonary disorders.
Syncytium-inducing mutations localize to two discrete regions within the cytoplasmic domain of herpes simplex virus type 1 glycoprotein B (1993)

Herpes simplex virus type 1 glycoprotein B (gB) is essential for virus entry, an event involving fusion of the virus envelope with the cell surface membrane, and virus-induced cell-cell fusion, resulting in polykaryocyte, or syncytium, formation. The experiments described in this report employed a random mutagenesis strategy to develop a more complete genetic map of mutations resulting in the syn mutant phenotype. The results indicate that syn mutations occur within two essential and highly conserved hydrophilic, alpha-helical regions of the gB cytoplasmic domain. Region I is immediately proximal to the transmembrane domain and includes residues R796 to E816/817. Region II is localized centrally in the cytoplasmic domain and includes residues A855 and R858. Positively charged residues were particularly affected in both regions, suggesting that charge interactions may be required to suppress the syn mutant phenotype. No syn mutations were identified within the transmembrane domain. A virus containing a rate of entry (roe) mutation at residue A851, either within or immediately proximal to syn region II, was isolated. Since roe mutations have also been discovered in the external domain of gB, it appears likely that the external and cytoplasmic domains cooperate in virus penetration. Moreover, the observation that both roe and syn mutations occur in the cytoplasmic domain further suggests that gB functions in an analogous manner in both membrane fusion events. It might be predicted from these observations that membrane fusion involves transduction of a fusion signal along the gB molecule through the transmembrane domain. Communication between the external and cytoplasmic domain may thus be required for gB-mediated membrane fusion events.
Characterization of two receptors for TRAIL1 (1997)

Two receptors for TRAIL, designated TRAIL-R2 and TRAIL-R3, have been identified. Both are members of the tumor necrosis factor receptor family. TRAIL-R2 is structurally similar to the death-domain-containing receptor TRAIL-R1 (DR-4), and is capable of inducing apoptosis. In contrast, TRAIL-R3 does not promote cell death. TRAIL-R3 is highly glycosylated and is membrane bound via a putative phosphatidylinositol anchor. The extended structure of TRAIL-R3 is due to the presence of multiple threonine-, alanine-, proline- and glutamine-rich repeats (TAPE repeats). TRAIL-R2 shows a broad tissue distribution, whereas the expression of TRAIL-R3 is restricted to peripheral blood lymphocytes (PBLs) and skeletal muscle. All three TRAIL receptors bind TRAIL with similar affinity, suggesting a complex regulation of TRAIL-mediated signals.
Laser Printing of Stem Cells for Biofabrication of Scaffold-Free Autologous Grafts (2010)

Stem cells are of widespread interest in regenerative medicine due to their capability of self-renewal and differentiation, which is regulated by their three-dimensional microenvironment. In this study, a computer-aided biofabrication technique based on laser-induced forward transfer (LIFT) is used to generate grafts consisting of mesenchymal stem cells (MSCs). We demonstrate that (i) laser printing does not cause any cell damage; (ii) laser-printed MSC grafts can be differentiated toward bone and cartilage; (iii) LIFT allows printing of cell densities high enough for the promotion of chondrogenesis; (iv) with LIFT three-dimensional scaffold-free autologous tissue grafts can be fabricated keeping their predefined structure, and (v) predifferentiated MSCs survived the complete printing procedure and kept their functionality. We believe that our results will find important applications in stem cell biology and tissue engineering.
Vector Systems for Prenatal Gene Therapy: Principles of Adeno-Associated Virus Vector Design and Production (2012)

Vectors based on adeno-associated virus (AAV) show great promise for safe, efficacious therapeutic gene transfer in extensive pre-clinical data and, recently, in clinical trials. Careful vector design and choice from a range of natural or synthetic pseudotypes allow targeted, efficient, and sustained expression of therapeutic genes. The efficiency of gene delivery can be further enhanced through the use of drug pre-treatment or co-infection with a suitable helper virus. This chapter describes current best practice for AAV production, including complete methods for: (1) efficient generation of vector without the use of helper viruses, simplifying the transition to GMP-grade production for clinical applications; (2) efficient and easily scalable purification of the virus by affinity chromatography, allowing rapid production of highly concentrated, high titre stocks; (3) reliable quantification and assaying of viral stocks, along with short- and long-term storage considerations.
The xylan-degrading enzyme systems of Penicillium capsulation and Talaromyces emersonii (1991)

Conference Article| February 01 1991 The xylan-degrading enzyme systems of Penicillium capsulation and Talaromyces emersonii EDIVALDO X.F. FILHO; EDIVALDO X.F. FILHO 1Department of Biochemistry, University College, Galway, Ireland Search for other works by this author on: This Site PubMed Google Scholar MARIA G. TUOHY; MARIA G. TUOHY 1Department of Biochemistry, University College, Galway, Ireland Search for other works by this author on: This Site PubMed Google Scholar JÜRGEN PULS; JÜRGEN PULS *BFH, Institut für Holzchemie, Leuschnerstraße 91, D-2080 Hamburg 80, FRG Search for other works by this author on: This Site PubMed Google Scholar MICHAEL P. COUGHLAN MICHAEL P. COUGHLAN 1Department of Biochemistry, University College, Galway, Ireland Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1991) 19 (1): 25S. https://doi.org/10.1042/bst019025s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation EDIVALDO X.F. FILHO, MARIA G. TUOHY, JÜRGEN PULS, MICHAEL P. COUGHLAN; The xylan-degrading enzyme systems of Penicillium capsulation and Talaromyces emersonii. Biochem Soc Trans 1 February 1991; 19 (1): 25S. doi: https://doi.org/10.1042/bst019025s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1991 Biochemical Society1991 Article PDF first page preview Close Modal You do not currently have access to this content.
Case Study Method of Learning – Its Effectiveness (2014)

Educationists across the globe have been using different pedagogies to make the learning a better experience. One such tried and tested method which has witnessed considerable success and acceptance is the case study method. Case studies are a representation of activities/situations based on topics that demonstrate theoretical concepts in an applied setting. The aim of this paper is to have an overview of the existing case study method of teaching and try to evolve certain extensions to make this method more effective. This thought process has led to the introduction of a concept termed as “My Case”.

Key words: Pedagogy, Case study, My Case.
Ureaplasma urealyticum intrauterine infection: role in prematurity and disease in newborns. (1993)

Ureaplasma urealyticum, a common commensal of the urogenital tract of sexually mature humans, is gaining recognition as an important opportunistic pathogen during pregnancy. While its etiologic significance in many aspects of adverse pregnancy remains controversial, recent evidence indicates that U. urealyticum in the absence of other organisms is a cause of chorioamnionitis. Furthermore, ureaplasmal infection of the chorioamnion is significantly associated with premature spontaneous labor and delivery. In at least some cases, it appears to be causal. Present evidence indicates that U. urealyticum is a cause of septicemia, meningitis, and pneumonia in newborn infants, particularly those born prematurely. There is strong but not definitive evidence that ureaplasmal infection of the lower respiratory tract can lead to development of chronic lung disease in very low-birth-weight infants. Although risk factors for colonization of the lower genitourinary tract have been identified, little information is available concerning risk factors for intrauterine infection and host immune responses to invasive infection. Recent establishment of animal models of respiratory and central nervous system diseases should provide an opportunity to evaluate risk factors, pathogenic mechanisms, and operative immune mechanisms. However, the most critical need is additional information concerning indications for diagnosis and treatment as well as efficacy of treatment.
Method to quantify accuracy of position feedback signals of a three-dimensional two-photon laser-scanning microscope (2015)

Two-photon laser-scanning microscopy enables to record neuronal network activity in three-dimensional space while maintaining single-cellular resolution. One of the proposed approaches combines galvanometric x-y scanning with piezo-driven objective movements and employs hardware feedback signals for position monitoring. However, readily applicable methods to quantify the accuracy of those feedback signals are currently lacking. Here we provide techniques based on contact-free laser reflection and laser triangulation for the quantification of positioning accuracy of each spatial axis. We found that the lateral feedback signals are sufficiently accurate (defined as <2.5 µm) for a wide range of scan trajectories and frequencies. We further show that axial positioning accuracy does not only depend on objective acceleration and mass but also its geometry. We conclude that the introduced methods allow a reliable quantification of position feedback signals in a cost-efficient, easy-to-install manner and should be applicable for a wide range of two-photon laser scanning microscopes.
Stochastic Neighbor Embedding (2002)

We describe a probabilistic approach to the task of embedding highdimensional objects into a low-dimensional space in a way that preserves neighbor identities. A Gaussian is centered on each object in the highdimensional space and the densities under this Gaussian are used to define a probability distribution over all the potential neighbors of the object.
Disturbances of magnesium concentrations in various brain areas in Alzheimer's disease. (2000)

Our first project aimed at the determination of the average values of Mg in normal human brain (20 individuals, mean age 70 years). Ten brain parts were selected from both hemispheres. Determinations were carried out by inductively coupled plasma atomic emission spectrometry, inductively coupled plasma mass spectrometry and instrumental neutron activation analysis methods. In order to investigate the precision and the accuracy of the methods five biological standard reference materials were analyzed. The present results show a non-homogeneous distribution of Mg in normal human brain. Regions corresponding to each other in both hemispheres show almost identical concentration. The second goal was to study the possible Mg concentration changes in Alzheimer's disease (nine patients, ten brain parts). Mg values are found to be significantly decreased in brain regions of diseased patients compared to the controls.
A novel high-gain image sensor cell based on Si p-n APD in charge storage mode operation (1990)

A high-gain image sensor cell based on Si-avalanche p-n photodiodes in the charge-storage mode from below to above the breakdown voltage region without avalanche discharge during the readout time period is described. Photoelectron conversion characteristics of a proposed dual-gate avalanche photodiode (APD) image sensor cell in below-breakdown voltage operation were analyzed on the assumption that multiplication gain during storage time, which depends on APD bias, followed an empirical formula involving multiplication gain and reverse bias in DC bias condition. The above-breakdown voltage operation is also considered. Experimental results agree with results from analytical models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
<title>New advancements in charge-coupled device technology: subelectron noise and 4096 x 4096 pixel CCDs</title> (1990)

This paper reports on two new advancements in CCD technology. The first area of development has produced a special purpose CCD designed for ultra low-signal level imaging and spectroscopy applications that require sub-electron read noise floors. A nondestructive output circuit operating near its 1/f noise regime is clocked in a special manner to read a single pixel multiple times. Off-chip electronics average the multiple values, reducing the random noise by the square-root of the number of samples taken. Noise floors below 0.5 electrons rms are reported. The second development involves the design and performance of a high resolution imager of 4096 x 4096 pixels, the largest CCD manufactured in terms of pixel count. The device utilizes a 7.5-micron pixel fabricated with three-level poly-silicon to achieve high yield.
DUB-1, a deubiquitinating enzyme with growth-suppressing activity. (1996)

Cytokines regulate cell growth by inducing the expression of specific target genes. Using the differential display method, we have cloned a cytokine-inducible immediate early gene, DUB-1 (for deubiquitinating enzyme). DUB-1 is related to members of the UBP superfamily of deubiquitinating enzymes, which includes the oncoprotein Tre-2. A glutathione S-transferase-DUB-1 fusion protein cleaved ubiquitin from a ubiquitin-beta-galactosidase protein. When a conserved cysteine residue of DUB-1, required for ubiquitin-specific thiol protease activity, was mutated to serine (C60S), deubiquitinating activity was abolished. Continuous expression of DUB-1 from a steroid-inducible promoter induced growth arrest in the G1 phase of the cell cycle. Cells arrested by DUB-1 expression remained viable and resumed proliferation upon steroid withdrawal. Our results suggest that DUB-1 regulates cellular growth by modulating either the ubiquitin-dependent proteolysis or the ubiquitination state of an unknown growth regulatory factor(s).
Human insulin from a precursor overexpressed in the methylotrophic yeastPichia pastoris and a simple procedure for purifying the expression product (2001)

The methylotrophic yeast Pichia pastoris, which proved successful in producing many heterologous proteins, was used to express an insulin precursor. A transformant with a high copy number of the gene integrated into the chromosome was obtained by the dot-blotting method. In high-density fermentation using a simple culture medium composed mainly of salt and methanol, the expression level reached 1.5 g/L. A simple two-step method was established to purify the expression product from the culture medium with an overall recovery of about 80%. After tryptic transpeptidation, human insulin with full receptor binding capacity and biological activity was obtained. In the presence of zinc, the recombinant human insulin could be crystallized in the rhombohedral form.
A Novel Method to Construct Taxonomy Electrical Appliances Based on Load Signaturesof (2007)

A load signature is an electrical expression that a load device or appliance distinctly possesses. Load signatures can be applied to produce many useful services and products, such as, determining the energy usage of individual appliances, monitoring the health of critical equipment, monitoring power quality, and developing facility management tools. Load signatures of typical yet extensive loads are needed to be collected before applying them to different services and products. As there are an enormous number of electrical appliances, it is beneficial to classify the appliances for building a well-organized load signature database. The objective of this study is to develop an effective method to classify the loads. A 2-dimensional form of load signatures, voltage-current (V-l) trajectory, is suggested for characterizing the typical household appliances.Hierarchical clustering method was employed to classify the appliances and construct the taxonomy of the appliances. The taxonomy based on V-l trajectory was compared to the taxonomies based on traditional power metrics and eigenvectors in the previous studies. It was found that the groups of appliances in the taxonomy based on V-I trajectory were well-separated and had engineering meanings .
Microfabricated coupled inductors for DC-DC converters for microprocessor power delivery (2004)

High-current, low-voltage power converters with fast transient response are needed for powering digital systems such as microprocessors. Microfabricated coupled inductors for such power converters are discussed. A four-phase microfabricated magnetic structure with 14 nH of inductance per phase has been fabricated for a 5 MHz, 5 V-to-1 V, 10 A dc-dc converter. The first prototype devices have been built with nickel-iron (NiFe) cores and copper conductors on a silicon substrate. Small-signal measurements on the inductors have been performed and predictions have been confirmed. A model for analyzing the performance of coupled inductors is presented. The devices have been implemented in a prototype converter and the measured performance is compared with the predicted results.
Nitrate as a redox co-catalyst for the aerobic Pd-catalyzed oxidation of unactivated sp3-C–H bonds (2012)

This paper describes a new method for the catalytic aerobic oxygenation of unactivated sp(3)-C-H bonds. This transformation utilizes Pd(OAc)(2) as a catalyst in conjunction with NaNO(3) as a redox co-catalyst. Both oxime ether and pyridine derivatives are effective directing groups for these reactions. The oxygen incorporated into the product derives from the solvent (acetic acid). Preliminary results show that the addition of simple NaCl to the reaction mixture results in aerobic chlorination under analogous conditions.
Cerebrospinal Fluid Levels ofβ-Amyloid 1-42, but Not of Tau, Are Fully Changed Already 5 to 10 Years Before the Onset of Alzheimer Dementia (2012)

<h3>Context</h3>Early detection of prodromal Alzheimer disease (AD) is important because new disease-modifying therapies are most likely to be effective when initiated during the early stages of disease.<h3>Objectives</h3>To assess the ability of the cerebrospinal fluid (CSF) biomarkers total tau (T-tau), phosphorylated tau (P-tau), andβ-amyloid 1-42 (Aβ42) to predict future development of AD dementia within 9.2 years in patients with mild cognitive impairment (MCI) and to compare CSF biomarkers between early and late converters to AD.<h3>Design</h3>A clinical study with a median follow-up of 9.2 years (range, 4.1-11.8 years).<h3>Setting</h3>Memory disorder clinic.<h3>Patients</h3>A total of 137 patients with MCI who underwent lumbar puncture at baseline.<h3>Main Outcome Measure</h3>Conversion to AD dementia.<h3>Results</h3>During follow-up, 72 patients (53.7%) developed AD and 21 (15.7%) progressed to other forms of dementia. At baseline, CSF Aβ42 levels were reduced and T-tau and P-tau levels were elevated in patients who converted to AD during follow-up compared with nonconverters (P &lt; .001). Baseline CSF Aβ42 levels were equally reduced in patients with MCI who converted to AD within 0 to 5 years (early converters) compared with those who converted between 5 and 10 years (late converters). However, CSF T-tau and P-tau levels were significantly higher in early converters vs late converters. A baseline Aβ42:P-tau ratio predicted the development of AD within 9.2 years with a sensitivity of 88%, specificity of 90%, positive predictive value of 91%, and negative predictive value of 86%.<h3>Conclusions</h3>Approximately 90% of patients with MCI and pathologic CSF biomarker levels at baseline develop AD within 9 to 10 years. Levels of Aβ42 are already fully decreased at least 5 to 10 years before conversion to AD dementia, whereas T-tau and P-tau seem to be later markers. These results provide direct support in humans for the hypothesis that altered Aβ metabolism precedes tau-related pathology and neuronal degeneration.
RACK1, a Protein Kinase C Anchoring Protein, Coordinates the Binding of Activated Protein Kinase C and Select Pleckstrin Homology Domains in Vitro (1999)

The pleckstrin homology (PH) domain, identified in numerous signaling proteins including the beta-adrenergic receptor kinase (betaARK), was found to bind to various phospholipids as well as the beta subunit of heterotrimeric G proteins (Gbeta) [Touhara, K., et al. (1994) J. Biol. Chem. 269, 10217-10220]. Several PH domain-containing proteins are also substrates of protein kinase C (PKC). Because RACK1, an anchoring protein for activated PKC, is homologous to Gbeta (both contain seven repeats of the WD-40 motif), we determined (i) whether a direct interaction between various PH domains and RACK1 occurs and (ii) the effect of PKC on this interaction. We found that recombinant PH domains of several proteins exhibited differential binding to RACK1. Activated PKC and the PH domain of beta-spectrin or dynamin-1 concomitantly bound to RACK1. Although PH domains bind acidic phospholipids, the interaction between various PH domains and RACK1 was not dependent on the phospholipid activators of PKC, phosphatidylserine and 1, 2-diacylglycerol. Binding of these PH domains to RACK1 was also not affected by either inositol 1,4,5-triphosphate (IP(3)) or phosphatidylinositol 4,5-bisphosphate (PIP(2)). Our in vitro data suggest that RACK1 binds selective PH domains, and that PKC regulates this interaction. We propose that, in vivo, RACK1 may colocalize the kinase with its PH domain-containing substrates.