gebhart/patrepeval huggingface dataset:
IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances (2014)

Antibody class switch recombination (CSR) in B lymphocytes joins two DNA double-strand breaks (DSBs) lying 100-200 kb apart within switch (S) regions in the immunoglobulin heavy-chain locus (IgH). CSR-activated B lymphocytes generate multiple S-region DSBs in the donor Sμ and in a downstream acceptor S region, with a DSB in Sμ being joined to a DSB in the acceptor S region at sufficient frequency to drive CSR in a large fraction of activated B cells. Such frequent joining of widely separated CSR DSBs could be promoted by IgH-specific or B-cell-specific processes or by general aspects of chromosome architecture and DSB repair. Previously, we found that B cells with two yeast I-SceI endonuclease targets in place of Sγ1 undergo I-SceI-dependent class switching from IgM to IgG1 at 5-10% of normal levels. Now, we report that B cells in which Sγ1 is replaced with a 28 I-SceI target array, designed to increase I-SceI DSB frequency, undergo I-SceI-dependent class switching at almost normal levels. High-throughput genome-wide translocation sequencing revealed that I-SceI-generated DSBs introduced in cis at Sμ and Sγ1 sites are joined together in T cells at levels similar to those of B cells. Such high joining levels also occurred between I-SceI-generated DSBs within c-myc and I-SceI- or CRISPR/Cas9-generated DSBs 100 kb downstream within Pvt1 in B cells or fibroblasts, respectively. We suggest that CSR exploits a general propensity of intrachromosomal DSBs separated by several hundred kilobases to be frequently joined together and discuss the relevance of this finding for recurrent interstitial deletions in cancer.
The roles of FGFs in the early development of vertebrate limbs (1998)

‘‘Fibroblast growth factor’’ (FGF) was first identified 25 years ago as a mitogenic activity in pituitary extracts (Armelin 1973; Gospodarowicz 1974). This modest observation subsequently led to the identification of a large family of proteins that affect cell proliferation, differentiation, survival, and motility (for review, see Basilico and Moscatelli 1992; Baird 1994). Recently, evidence has been accumulating that specific members of the FGF family function as key intercellular signaling molecules in embryogenesis (for review, see Goldfarb 1996). Indeed, it may be no exaggeration to say that, in conjunction with the members of a small number of other signaling molecule families [including WNT (Parr and McMahon 1994), Hedgehog (HH) (Hammerschmidt et al. 1997), and bone morphogenetic protein (BMP) (Hogan 1996)], FGFs are responsible for inducing and/or regulating the subsequent development of most organs in the vertebrate body. The purpose of this review is to discuss the functions performed by members of the FGF family in one of the best-studied vertebrate developmental systems—limb formation. It focuses initially on what is known about FGF function in the established limb bud and then discusses the mechanisms by which the signaling centers that control outgrowth and patterning of the established limb bud are formed, emphasizing possible roles played by FGFs in these processes. Finally, it discusses the potential role of FGFs in the induction of limb development. The insights into the requirement for FGF signaling in bone development that have been gained from analyses of mutations in human and mouse FGF receptor (FGFR) genes will not be discussed, as those studies have been the subject of several recent reviews (Wilkie et al. 1995; Yamaguchi and Rossant 1995; De Moerlooze and Dickson 1997; Webster and Donoghue 1997).
Low-complexity video coding for receiver-driven layered multicast (1997)

The "Internet Multicast Backbone," or MBone, has risen from a small, research curiosity to a large-scale and widely used communications infrastructure. A driving force behind this growth was the development of multipoint audio, video, and shared whiteboard conferencing applications. Because these real-time media are transmitted at a uniform rate to all of the receivers in the network, a source must either run at the bottleneck rate or overload portions of its multicast distribution tree. We overcome this limitation by moving the burden of rate adaptation from the source to the receivers with a scheme we call receiver-driven layered multicast, or RLM. In RLM, a source distributes a hierarchical signal by striping the different layers across multiple multicast groups, and receivers adjust their reception rate by simply joining and leaving multicast groups. We describe a layered video compression algorithm which, when combined with RLM, provides a comprehensive solution for scalable multicast video transmission in heterogeneous networks. In addition to a layered representation, our coder has low complexity (admitting an efficient software implementation) and high loss resilience (admitting robust operation in loosely controlled environments like the Internet). Even with these constraints, our hybrid DCT/wavelet-based coder exhibits good compression performance. It outperforms all publicly available Internet video codecs while maintaining comparable run-time performance. We have implemented our coder in a "real" application-the UCB/LBL videoconferencing tool vic. Unlike previous work on layered video compression and transmission, we have built a fully operational system that is currently being deployed on a very large scale over the MBone.
The Helix-Hinge-Helix Structural Motif in Human Apolipoprotein A-I Determined by NMR Spectroscopy, (1997)

The conformation of a synthetic peptide of 46 residues from apoA-I was investigated by fluorescence, CD, and 2D NMR spectroscopies in lipid-mimetic environments. ApoA-I(142-187) is mainly unstructured in water but helical in SDS or dodecylphosphocholine (DPC), although the peptide only associates with DPC at approximately the critical micellar concentration. Solution structures of apoA-I(142-187) were determined by distance geometry calculations based on 450 (in DPC-d38) or 397 (in SDS-d25) NOE-derived distance restraints, respectively. Backbone RMSDs for superimposing the two helical regions 146-162 and 168-182 are 0.98 +/- 0.22 (2.38 +/- 0.20) and 1.99 +/- 0.42 (2.02 +/- 0.21) A in DPC (SDS), respectively. No interhelical NOE was found, suggesting that helix-helix interactions between the two helical domains in apoA-I(142-187) are unlikely. Similar average, curved helix-hinge-helix structures were found in both SDS and DPC micelles with the hydrophobic residues occupying the concave face, indicating that hydrophobic interactions dominate. Intermolecular NOESY experiments, performed in the presence of 50% protonated SDS, confirm that the two amphipathic helices and Y166 in the hinge all interact with the micelle. The involvement of Y166 in lipid binding is supported by fluorescence spectroscopy as well. On the basis of all the data above, we propose a model for the peptide-lipid complexes wherein the curved amphipathic helix-hinge-helix structural motif straddles the micelle. The peptide-aided signal assignment achieved for apoA-I(122-187) (66mer) and apoA-I suggests that such a structural motif is retained in the longer peptide and most likely in the intact protein.
Repellency of Skin-Surface Lipids of Humans to Mosquitoes (1965)

Skin lipids obtained from the washings, in acetone or diethyl ether, of the foreheads or arms of humans are very repellent to female Aedes aegypti when evaluated in a dual-port olfactometer. By means of thin-layer chromatography, the repellent substances can be separated from nonrepellent material also present in skin lipids.
The proteome of neural stem cells from adult rat hippocampus (2003)

BACKGROUND: Hippocampal neural stem cells (HNSC) play an important role in cerebral plasticity in the adult brain and may contribute to tissue repair in neurological disease. To describe their biological potential with regard to plasticity, proliferation, or differentiation, it is important to know the cellular composition of their proteins, subsumed by the term proteome. RESULTS: Here, we present for the first time a proteomic database for HNSC isolated from the brains of adult rats and cultured for 10 weeks. Cytosolic proteins were extracted and subjected to two-dimensional gel electrophoresis followed by protein identification through mass spectrometry, database search, and gel matching. We could map about 1141 PlusMinus; 209 (N = 5) protein spots for each gel, of which 266 could be identified. We could group the identified proteins into several functional categories including metabolism, protein folding, energy metabolism and cellular respiration, as well as cytoskeleton, Ca2+ signaling pathways, cell cycle regulation, proteasome and protein degradation. We also found proteins belonging to detoxification, neurotransmitter metabolism, intracellular signaling pathways, and regulation of DNA transcription and RNA processing. CONCLUSIONS: The HNSC proteome database is a useful inventory which will allow to specify changes in the cellular protein expression pattern due to specific activated or suppressed pathways during differentiation or proliferation of neural stem cells. Several proteins could be identified in the HNSC proteome which are related to differentiation and plasticity, indicating activated functional pathways. Moreover, we found a protein for which no expression has been described in brain cells before.
A single monoclonal antibody identifies T-cell lineage of childhood lymphoid malignancies (1983)

Immunophenotyping studies with monoclonal antibodies have revealed the heterogeneity of childhood acute lymphoblastic leukemia (ALL) and non- Hodgkin's lymphoma (NHL). The lymphoid malignancies of T-cell lineage are particularly heterogeneous and, until now, no single monoclonal antibody has been found to identify all cases of T-ALL and T-NHL. A monoclonal antibody, 4H9, recognizes an antigen of 40,000 molecular weight on normal and malignant T cells. Thirty-six cases of childhood T- ALL and T-NHL were tested, and in all cases, the malignant blast cells were reactive with 4H9, whereas malignant cells from 61 cases of non-T ALL and NHL were not reactive with 4H9. Monoclonal antibody 4H9 is a sensitive and specific reagent for the identification of childhood T- cell ALL and NHL and should be extremely useful in immunophenotyping studies of lymphoid malignancies.
Chemical Mediators of Migraine: Preclinical and Clinical Observations (2011)

Migraine is a neurovascular disorder, and although the pathophysiology of migraine has not been fully delineated, much has been learned in the past 50 years. This knowledge has been accompanied by significant advancements in the way migraine is viewed as a disease process and in the development therapeutic options. In this review, we will focus on 4 mediators (nitric oxide, histamine, serotonin, and calcitonin gene-related peptide) which have significantly advanced our understanding of migraine as a disease entity. For each mediator we begin by reviewing the preclinical data linking it to migraine pathophysiology, first focusing on the vascular mechanisms, then the neuronal mechanisms. The preclinical data are then followed by a review of the clinical data which support each mediator's role in migraine and highlights the pharmacological agents which target these mediators for migraine therapy.
Non‐small cell lung carcinomas with neuroendocrine features. A light microscopic, immunohistochemical and ultrastructural study of 11 cases (1988)

Eleven resected primary lung carcinomas classified as large cell carcinomas or squamous cell carcinomas, but showing some microscopic resemblances to bronchial carcinoid and small cell carcinoma, were studied. All cases were neurone-specific enolase and protein gene product 9.5 positive, indicating neuroendocrine differentiation. Staining for bombesin, C-terminal peptide of human pro-bombesin and chromogranin was positive in some cases. Electron microscopy showed dense-core granules in six of seven cases investigated, the remaining case showing small granules of uncertain nature. All but one patient died within 15 months after operation. These data indicate that neuroendocrine differentiation in non-small cell carcinomas of the lung may in some cases be suspected on routine histology. The follow-up data suggest that the identification of these cases might have implications for prognosis and therapy, and consequently for diagnostic lung tumour classification.
Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052 (2013)

Production of butanol by solventogenic clostridia is controlled through metabolic regulation of the carbon flow and limited by its toxic effects. To overcome cell sensitivity to solvents, stress-directed evolution methodology was used three decades ago on Clostridium beijerinckii NCIMB 8052 that spawned the SA-1 strain. Here, we evaluated SA-1 solventogenic capabilities when growing on a previously validated medium containing, as carbon- and energy-limiting substrates, sucrose and the products of its hydrolysis d-glucose and d-fructose and only d-fructose. Comparative small-scale batch fermentations with controlled pH (pH 6.5) showed that SA-1 is a solvent hyper-producing strain capable of generating up to 16.1 g l(-1) of butanol and 26.3 g l(-1) of total solvents, 62.3 % and 63 % more than NCIMB 8052, respectively. This corresponds to butanol and solvent yields of 0.3 and 0.49 g g(-1), respectively (63 % and 65 % increase compared with NCIMB 8052). SA-1 showed a deficiency in d-fructose transport as suggested by its 7 h generation time compared with 1 h for NCIMB 8052. To potentially correlate physiological behaviour with genetic mutations, the whole genome of SA-1 was sequenced using the Illumina GA IIx platform. PCR and Sanger sequencing were performed to analyse the putative variations. As a result, four errors were confirmed and validated in the reference genome of NCIMB 8052 and a total of 10 genetic polymorphisms in SA-1. The genetic polymorphisms included eight single nucleotide variants, one small deletion and one large insertion that it is an additional copy of the insertion sequence ISCb1. Two of the genetic polymorphisms, the serine threonine phosphatase cbs_4400 and the solute binding protein cbs_0769, may possibly explain some of the observed physiological behaviour, such as rerouting of the metabolic carbon flow, deregulation of the d-fructose phosphotransferase transport system and delayed sporulation.
Graphical Tactile Displays for Visually-Impaired People (2007)

This paper presents an up-to-date survey of graphical tactile displays. These devices provide information through the sense of touch. At best, they should display both text and graphics (text may be considered a type of graphic). Graphs made with shapeable sheets result in bulky items awkward to store and transport; their production is expensive and time-consuming and they deteriorate quickly. Research is ongoing for a refreshable tactile display that acts as an output device for a computer or other information source and can present the information in text and graphics. The work in this field has branched into diverse areas, from physiological studies to technological aspects and challenges. Moreover, interest in these devices is now being shown by other fields such as virtual reality, minimally invasive surgery and teleoperation. It is attracting more and more people, research and money. Many proposals have been put forward, several of them succeeding in the task of presenting tactile information. However, most are research prototypes and very expensive to produce commercially. Thus the goal of an efficient low-cost tactile display for visually-impaired people has not yet been reached.
Composition, antimicrobial, antioxidant, and antiproliferative activity ofOriganum dictamnus(dittany) essential oil (2015)

The results revealed that O. dictamnus essential oil is a noteworthy growth inhibitor against the microbes studied. It also possesses significant antioxidant activity and demonstrated excellent cytotoxicity against HepG2 cells. Taken together, O. dictamnus essential oil may represent an effective and inexpensive source of potent natural antimicrobial agents with health-promoting properties, which may be incorporated in food systems.
ARTERIOVENOUS FISTULA FOLLOWING TRANSFEMORAL ANGIOGRAPHY (1990)

A case of femoral arteriovenous fistula due to transfemoral angiography, diagnosed accidentally 6 years later, is presented.
Enhanced polyglutamylation of aminopterin relative to methotrexate in the Ehrlich ascites tumor cell in vitro. (1985)

The polyglutamylation of aminopterin and methotrexate (N10-methylaminopterin) was compared in the Ehrlich ascites tumor in vitro. Three poly-gamma-glutamyl conjugates of methotrexate and aminopterin were detected, although at an equal (1 microM) extracellular drug concentration, the net accumulation of aminopterin polyglutamates exceeded that for the methotrexate polyglutamyl derivatives by a factor of 9. When compensation was made for transport differences between these compounds by adjusting the extracellular drug concentrations to achieve equivalent intracellular monoglutamyl substrate levels, the polyglutamylation of aminopterin was still 2.8-fold greater than that for methotrexate, suggesting that aminopterin is a better substrate for the folylpolyglutamate synthetase as well as the transport carrier. An additional metabolite of aminopterin was detected within seconds following drug exposure. This derivative did not bind tightly to dihydrofolate reductase, yet it was rapidly converted to a polyglutamate. The formation of both aminopterin polyglutamates and these novel derivatives was enhanced by increases in the free intracellular level of aminopterin. Aminopterin polyglutamates were bound tightly to dihydrofolate reductase and were retained intracellularly relative to unaltered aminopterin when Ehrlich cells containing these forms were suspended in drug-free medium. These findings support a role for the polyglutamylation of aminopterin as a critical element in drug action and as a factor in addition to membrane transport in the disparate antifolate potencies of aminopterin and methotrexate.
New Highly Diastereoselective Synthesis of Phosphoramidates. A Route to Chiral Methylp-Nitrophenyl Alkylphosphonates (1998)

International audience
Comparison of the Adsorption of Linear Alkanesulfonate and Linear Alkylbenzenesulfonate Surfactants at Liquid Interfaces (2000)

Linear alkanesulfonates and linear alkylbenzenesulfonates constitute a large fraction of the surfactants used in commercial detergents and cleansers. Despite the industrial significance and the possible environmental impact of these compounds, very little is known regarding the molecular properties of these compounds and how they relate to macroscopic properties desired in applications. This study employs vibrational sum frequency spectroscopy (VSFS) to examine and compare the molecular structure of surfactants in these two classes as they adsorb at organic/water and air/water interfaces. The linear alkane- and alkylbenzenesulfonates studied are, respectively, dodecanesulfonate and dodecylbenzenesulfonate. By measurement and comparison of the vibrational spectra of these adsorbed surfactants, changes in the orientation of the aromatic ring and the conformation of the alkyl chains are examined as a function of the number density of surfactant molecules at the interface. The change in aromatic ring orientation as a function of surface concentration is quite different for the dodecylbenzenesulfonate at the air/water interface relative to that at the organic/water interface (CCl4/water). The alkyl chains of the dodecylbenzenesulfonate are highly disordered at both interfaces as a function of interfacial concentration, in stark contrast to what is observed for the dodecanesulfonate. These results are discussed in terms of the disruptive nature of the benzene ring and the higher degree of hydrophobicity of the alkyl chain relative to the benzene ring near the ionic sulfonate group.
Training a Molecular Gun on Killer E. coli (1998)

Researchers at the National Institutes of Health are closing in on the development of the first vaccine against
 Escherichia coli
 O157:H7, a pathogenic version of the common gut bacterium. Tests of an experimental vaccine showed promise in adults earlier this year, and the researchers are about to apply for approval to test it in young children. If the trial gets the go-ahead and the preparation passes further tests, experts say, a vaccine for people and one for livestock could be available early next century.
Summary and Recommendations of the Academy's State of the Science Conference on Upper Limb Prosthetic Outcome Measures (2009)

The Academy's Ninth State of the Science Conference included a group of engineers, prosthetists, and therapists brought together to discuss upper limb prosthetic outcome measures. After a presentation of the evidence based review and discussions on the history of the field and the various perspectives from the various professions, the panel reviewed those outcome measures found to be recommended and those thought to be worth consideration by the Evidence Based Review and the Upper Limb Prosthetics Outcome Measures Group. Outcome measures with the potential to address certain research questions are identified. Throughout the various discussions of the SSC group, a list was kept of commonly identified issues, questions, and missing links. From this list, the panel identified seven key research priority questions. These priority questions and items included in the discussions are presented.
Genetics of Aux/IAA and ARF action in plant growth and development. (2002)

Dramatic advances in our understanding of auxin signal-response pathways have been made in recent years. Much of this new knowledge has come through the study of mutants in Arabidopsis thaliana. Mutations have been identified in a wide variety of auxin-response components, including auxin transporters, protein kinases and phosphatases, components of a ubiquitin-proteosome pathway, and transcriptional regulators. This review focuses on mutations that affect auxin-modulated transcription factors, in particular those in the Aux/IAA and AUXIN RESPONSE FACTOR (ARF) genes. Mutants in members of these related gene families exhibit phenotypes that indicate both unique localized functions, as well as overlapping redundant functions, throughout plant development - from embryogenesis to flowering. Effects of specific mutations on Aux/IAA and ARF protein functions at the biochemical and physiological levels will be discussed. We will also discuss potential mechanisms for interactions between auxin and light response pathways that are suggested by these mutants.
Engineering des genetischen Codes: Molekularbiologie und Organische Chemie kombiniert (2003)

Stell dir vor …︁ der natürliche Biosyntheseapparat verarbeitet ortsspezifisch jede nichtproteinogene Aminosäure! Spektakuläre Fortschritte bei der Manipulation des genetischen Codes vergrößern die Auswahl der zur Protein-Biosynthese verfügbaren Aminosäuren. Jüngste Beispiele für die posttranslationale chemische Modifikation von Proteinen, die nichtnatürliche Aminosäuren enthalten, werden vorgestellt (siehe Schema).