gebhart/patrepeval huggingface dataset:
Altruistic self‐removal of health‐compromised honey bee workers from their hive (2010)

Social insect colonies represent distinct units of selection. Most individuals evolve by kin selection and forgo individual reproduction. Instead, they display altruistic food sharing, nest maintenance and self-sacrificial colony defence. Recently, altruistic self-removal of diseased worker ants from their colony was described as another important kin-selected behaviour. Here, we report corroborating experimental evidence from honey bee foragers and theoretical analyses. We challenged honey bee foragers with prolonged CO(2) narcosis or by feeding with the cytostatic drug hydroxyurea. Both treatments resulted in increased mortality but also caused the surviving foragers to abandon their social function and remove themselves from their colony, resulting in altruistic suicide. A simple model suggests that altruistic self-removal by sick social insect workers to prevent disease transmission is expected under most biologically plausible conditions. The combined theoretical and empirical support for altruistic self-removal suggests that it may be another important kin-selected behaviour and a potentially widespread mechanism of social immunity.
Using the physical layer for wireless authentication in time-variant channels (2008)

The wireless medium contains domain-specific information that can be used to complement and enhance traditional security mechanisms. In this paper we propose ways to exploit the spatial variability of the radio channel response in a rich scattering environment, as is typical of indoor environments. Specifically, we describe a physical-layer authentication algorithm that utilizes channel probing and hypothesis testing to determine whether current and prior communication attempts are made by the same transmit terminal. In this way, legitimate users can be reliably authenticated and false users can be reliably detected. We analyze the ability of a receiver to discriminate between transmitters (users) according to their channel frequency responses. This work is based on a generalized channel response with both spatial and temporal variability, and considers correlations among the time, frequency and spatial domains. Simulation results, using the ray-tracing tool WiSE to generate the time-averaged response, verify the efficacy of the approach under realistic channel conditions, as well as its capability to work under unknown channel variations.
Characterization of the Zymomonas mobilis glucose facilitator gene product (glf) in recombinant Escherichia coli: examination of transport mechanism, kinetics and the role of glucokinase in glucose transport (1995)

Zymomonas mobilis is known to transport glucose by a facilitated diffusion process. A putative glucose facilitator gene (glf), closely related to a large family of glucose transporters, is located in a cluster of genes that code for enzymes of glucose metabolism. The Z. mobilis glf gene is able to complement glucose transport in an Escherichia coli strain that is defective in native glucose transport and glucokinase. In this study, the recombinant E. coli was shown to be capable of influx counterflow when preloaded with glucose and had an apparent Km for glucose of approximately 1.1-2.9 mM, consistent with the function of Glf as a low-affinity glucose facilitator. The ability of glucokinase mutants expressing glf to transport glucose made it clear that glucokinase activity was not required for Glf-dependent glucose transport. The possibility that glucokinase can interact with Glf to improve the affinity for glucose was not supported since expression of the Z. mobilis glucokinase gene, in addition to glf, did not affect the Km of Glf for glucose in recombinant E. coli. The inability of various sugars to compete with glucose during glucose transport by recombinant E. coli expressing glf indicated that Glf is specific for glucose. While the results of fructose transport assays did not completely rule out the possibility of very low affinity for fructose, the apparent specificity of Glf for glucose makes it possible that Z. mobilis utilizes a different transporter(s) for fructose.
Current and residual functional disability associated with psychopathology: findings from the Netherlands Mental Health Survey and Incidence Study (NEMESIS) (2000)

Mental health care providers should be aware that the extent and the type of disability may vary with the different types of disorders and among different groups within the population. Since recovery from functional limitations may not be complete or may take more time than the remission of the psychiatric symptomatology, non-psychiatric follow-up care is needed. The high number of lost work days is relevant from an economic perspective. There is a need for illness-specific disability assessment instruments.
Fine-tuning the degree of organic functionalization of mesoporous silica nanosphere materials via an interfacially designed co-condensation method (2004)

A synthetic method that can fine tune the amount of chemically accessible organic functional groups on the pore surface of MCM-41 type mesoporous silica nanosphere (MSN) materials has been developed by electrostatically matching various anionic organoalkoxysilanes with the cationic cetyltrimethylammonium bromide micelles in a base-catalyzed condensation reaction of tetraethoxysilane.
Protoplast transformation in coryneform bacteria and introduction of an alpha-amylase gene from Bacillus amyloliquefaciens into Brevibacterium lactofermentum (1986)

The goal of this study was to investigate the likelihood of developing useful transformation systems for coryneform bacteria. Two species of coryneform bacteria, Brevibacterium lactofermentum and Corynebacterium lilium, were transformed with chimeras constructed from pUB110 and a cryptic coryneform plasmid (pGX1901). C. lilium protoplasts were also efficiently transfected with phage CS1 DNA. High transformation and transfection frequencies were obtained after only 2 min of lysozyme treatment of lysozyme-sensitive mutants. A series of experiments was also conducted to determine whether DNA from other species of important industrial microbes from the genus Bacillus could be expressed in coryneform bacteria. Evidence of restriction of Bacillus subtilis DNA by B. lactofermentum was observed but could be overcome. A Bacillus amyloliquefaciens alpha-amylase gene (amyEBamP) was subcloned onto a plasmid able to replicate in B. lactofermentum. B. lactofermentum transformants for this plasmid expressed amylase activity and produced material cross-reactive to amylase antibody.
High-Level Multiplex DNA Amplification (2001)

We present data on efficient amplification of large number of DNA targets using a single-tube polymerase chain reaction (PCR). This is a further enhancement of our approach to multiplexed PCR based on PCR suppression, which allows multiple DNA amplification using only one sequence-specific primer per amplicon while the second primer is common for all targets (Broude, N.E., et al., Proc. Natl. Acad. Sci. USA 98, 206-211, 2001). The reaction conditions have been optimized for simultaneous synthesis of 30 DNA targets, mostly consisting of fragments containing single nucleotide polymorphisms (SNP). The size of the amplified fragments, derived from many different human chromosomes, varies from 100 to 600 bp. We conclude that this method has potential for highly multiplexed DNA amplification useful for SNP analyses, DNA diagnostics, and forensics.
Structure Evolution in Segmented Poly(ester urethane) in Shape-Memory Process (2010)

A segmented poly(ester urethane) shape-memory polymer with poly(ε-caprolactone) (PCL) soft segment and urethane hard segment was studied by FTIR to investigate the structural evolution in the shape-memory cycle. It was revealed that in the cold drawing programming process, first the amorphous PCL chains start to orient along the drawing direction, and then, the hard segment and the crystalline PCL chains orient upon further extension, accompanied by the weakening of the hydrogen bonds along the drawing direction between the hard segments and stress-induced disaggregation and recrystallization of the crystalline PCL. In the recovery process, the hard segments restore first with the parallel hydrogen bonds strengthening and then the amorphous PCL chains restore the original random orientation, and finally the crystalline PCL chains lose their alignment to a less-oriented state.
Functional coupling and differential regulation of the Phospholipase A2-cyclooxygenase pathways in inflammation (1999)

Prostaglandins generated by the phospholipase A2 (PLA2)/cyclooxygenase (COX) pathway are well known to mediate diverse intracellular and extracellular effects that regulate mammalian development, vascular function, renal physiology, parturition, and immune responses to infection or wounding. In immune-mediated diseases and in certain cancers, this pathway is aberrantly up-regulated and excessive prostaglandin production contributes to the pathology. It is now known that there are two isoforms of COX and multiple secreted and intracellular PLA2 enzymes. The use of isoform-specific inhibitors, coupled with antisense and in vivo gene deletion experiments, has identified independent pathways of arachidonic acid metabolism, which are differentially regulated at the levels of gene expression, protein phosphorylation, and cellular localization. There is cross-talk between the pathways at the level of PLA2 and substrate supply to the two isoforms of COX is apparently compartmentalized. Knockout studies have shown that the two COX isoforms play independent roles in immediate and delayed agonist-induced prostaglandin synthesis. Cytosolic PLA2-alpha is essential for both responses. Inducible secreted forms of PLA2 are, as yet, not essential for either response with the exception of the in vitro murine mast cell immediate response and instances of murine macrophage prostaglandin synthesis. These enzymes amplify the delayed response and are likely to modulate the severity of immune-mediated diseases.
Catalytic Hydrolysis of p-Nitrophenyl Esters in the Presence of Representative Ammonium Aggregates. Specific Activation of a Cholesteryl Nucleophile Bound to a Dialkylammonium Bilayer Membrane (1979)

Abstract Catalytic hydrolysis of p-nitrophenyl esters (acetate and nonanoate) by hydroxamate and imidazole nucleophiles was studied at 30 °C in the presence of aqueous aggregates of single-chain (hexadecyl), double-chain (didodecyl and dioctadecyl) and triple-chain (trioctyl) ammonium amphiphiles. These three types of ammonium salts give rise to very different aggregate morphologies. The rate constant of ester cleavage by the nucleophiles was enhanced several hundred folds in the presence of these hydrophobic aggregates. Simple long-chain nucleophiles possessed esterolytic reactivities which reflect the hydrophobic microenvironment of the respective aggregates: single-chain&amp;lt;double-chain&amp;lt;triple-chain. On the other hand, the cholesteryl ester of imidazolecarboxylic acid showed an especially high reactivity when bound to the didodecylammonium bilayer. Cholic acid-derived nucleophiles showed normal reactivity patterns. Apparently, specific binding of the cholesterol derivative to the bilayer is responsible for the unusual catalytic behavior.
Über die Reaktion von 2‐Diazo‐1,3‐diketonen mit 1,3‐ambident‐nucleophilen Phosphor‐Yliden: Eine neue Synthese von Monoheteroatom‐Fünf‐ und ‐Sechsringen (1991)

Reaction of 2‐Diazo‐1,3‐diketones with 1,3‐Ambident‐Nucleophilic Phosphorus Ylides: A New Synthesis of Monoheteroatomic Five‐ and Six‐Membered Rings The thermolysis of 2‐diazo‐1,3‐diketones 1 with 1,3‐ambidentnucleophilic 3‐imino‐ 3 , 3‐thioxo‐ 10 or 3‐oxophosphoanes 11 proceeds either by Wittig reaction, leading to the formation of the pyrrole 7 or thiophene nucleus 12 , or competitively via a mechanism which involves both Wolff rearrangement and Wittig reaction by the acylcarbonyl, whereby 2‐pyridones 8 , 2‐pyrones 14 or the indenyl acetophenone 15 , respectively, are formed. The rates of these processes are strongly determined by substituent effects. As an exception to the general pattern of behavior, the cyclic acyl ketene derived from diazodimedone undergoes Wittig reaction with 3 through the ketene carbonyl, giving the quinoline derivative 9 . The structure of 9 was confirmed by X‐ray diffraction analysis.
P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations (2009)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTP450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM CalculationsSason Shaik*†, Shimrit Cohen†, Yong Wang†, Hui Chen†, Devesh Kumar‡§, and Walter Thiel*‡View Author Information Institute of Chemistry and the Lise-Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel, and Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany* E-mail: S.S., [email protected]; W.T., [email protected]. Further contact information for S.S.: phone, +972-2-6585909; fax, +972-2-6584680/6585345.†The Hebrew University of Jerusalem.‡Max-Planck-Institut für Kohlenforschung.§Current address: Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad 500 607, India.Cite this: Chem. Rev. 2010, 110, 2, 949–1017Publication Date (Web):October 8, 2009Publication History Received30 March 2009Published online8 October 2009Published inissue 10 February 2010https://pubs.acs.org/doi/10.1021/cr900121shttps://doi.org/10.1021/cr900121sreview-articleACS PublicationsCopyright © 2009 American Chemical SocietyRequest reuse permissionsArticle Views15210Altmetric-Citations891LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Chemical calculations,Organic reactions,Peptides and proteins,Quantum mechanics,Reaction mechanisms Get e-Alerts
Highly scalable NAND flash memory with robust immunity to program disturbance using symmetric inversion-type source and drain structure (2008)

The symmetric inversion-type S/D structure has been employed for achieving available program disturbance for scaled NAND flash memory beyond sub-40 nm node. The inversion S/D structure enables the channel doping to be reduced due to non-existence of n-lateral diffusion and it suppresses charge sharing between program-inhibit channels, resulting in superior program disturbance. Moreover, the cells show better current drivability in the technology node less than 50 nm by more successful working of gate fringing field with smaller word-line gap, compared to those with the n-diffused S/D junction.
Multimodal Nanoprobes Evaluating Physiological Pore Size of Brain Vasculatures in Ischemic Stroke Models (2014)

Ischemic stroke accounts for 80% strokes and originates from a reduction of cerebral blood flow (CBF) after vascular occlusion. For treatment, the first action is to restore CBF by thrombolytic agent recombinant tissue‐type plasminogen activator (rt‐PA). Although rt‐PA benefits clinical outcome, its application is limited by short therapeutic time window and risk of brain hemorrhage. Different to thrombolytic agents, neuroprotectants reduce neurological injuries by blocking ischemic cascade events such as excitotoxicity and oxidative stress. Nano‐neuroprotectants demonstrate higher therapeutic effect than small molecular analogues due to their prolonged circulation lifetime and disrupted blood–brain barrier (BBB) in ischemic region. Even enhanced BBB permeability in ischemic territories is verified, the pore size of ischemic vasculatures determining how large and how efficient the therapeutics can pass is barely studied. In this work, nanoprobes (NPs) with different diameters are developed. In vivo multimodal imaging indicates that NP uptakes in ischemic region depended on their diameters and the pore size upper limit of ischemic vasculatures is determined as 10–11 nm. Additionally, penumbra defined as salvageable ischemic tissues performed a higher BBB permeability than infarct core. This work provides a guideline for developing nano‐neuroprotectants by taking advantage of the locally enhanced BBB permeability in ischemic brain tissues.
Microfluidic DNA fragmentation for on-chip genomic analysis (2011)

We report a high-throughput clog-free microfluidic deoxyribonucleic acid (DNA) fragmentation chip that is based on hydrodynamic shearing. Salmon sperm DNA has been reproducibly fragmented down to ∼ 5k bp fragment lengths by applying low hydraulic pressures (≤1 bar) across micromachined constrictions positioned in larger microfluidic channels that create point-sink flow with large velocity gradients near the constriction entrance. Long constrictions (100 µm) produce shorter fragment lengths compared to shorter constrictions (10 µm), while increasing the hydrodynamic pressure requirement. Sample recirculation (10 ×) in short constrictions reduces the mean fragment length and fragment length variation, and improves yield compared to single-pass experiments without increasing the hydrodynamic pressure.
Transduction of NO-bioactivity by the red blood cell in sepsis: novel mechanisms of vasodilation during acute inflammatory disease (2004)

Sepsis is an acute inflammatory disease characterized by dysfunctional blood flow and hypotension. Nitric oxide (NO) is elevated during sepsis and plays an integral role in the associated vascular pathology. However, precise mechanisms and functions of NO in sepsis remain unclear. In this study, we show that red blood cells (RBCs) are foci for nitrosative reactions during acute inflammation, resulting in the formation of cells that can promote systemic vascular relaxation in an uncontrolled manner. Specifically, using experimental models of endotoxemia and surgical sepsis, NO adducts were found in the RBCs, including S-nitrosohemoglobin (SNOHb). These RBCs, referred to as septic RBCs, spontaneously stimulated vasodilation in a manner consistent with elevated SNOHb concentrations. Moreover, relaxation was cyclic guanosine monophosphate (cGMP) dependent and was inhibited by RBC lysis and glutathione but not by the NO scavenger 2-(4-carboxyphenyl)-4,4,5,5 tetramethylimidazoline 1-oxyl 3-oxide (C-PTIO). The potential mechanism of septic RBC-mediated vasorelaxation is discussed and may involve the intermediate, nitroxyl (HNO). Coupled with data showing that NO adducts in septic RBCs were dependent on the inducible nitric oxide synthase and correlated with plasma nitrite, these findings provide a novel framework to understand mechanisms underlying dysfunctional blood flow responses during sepsis. Specifically, the concept that RBCs directly mediate systemic hypotension through NO-dependent mechanisms is discussed.
The design of a practical and reliable fall detector for community and institutional telecare (2000)

Falls are one of the greatest obstacles to independent living for frail and elderly people. Their early detection is an important step in providing people with the reassurance and confidence necessary to maintain an active lifestyle. We have investigated a worn fall detector linked to a community alarm system. A worn device is the only one which is satisfactory, provided that it generates few false alarms. The fall detector we have developed is the size of a small radio pager. It uses a two-stage detection process which senses shock and the orientation of the wearer. A fall is detected within 20 s and triggers a radio signal to a community alarm system. Tests were devised using a jointed mannequin to simulate five modes of falling to understand the effects of impact at different parts of the body. This allowed us to select the appropriate trigger threshold and wearing positions for the sensor. Prototypes were evaluated with 20 people to observe false alarms. The final design allowed reliable detection in 180 different falling scenarios.
Elevated leukocyte count in cerebrospinal fluid of patients with chronic inflammatory demyelinating polyneuropathy (2018)

Cerebrospinal fluid (CSF) examination is often part of the diagnostic work-up of a patient suspected of having chronic inflammatory demyelinating polyneuropathy (CIDP). According to the European Federation of Neurological Societies and the Peripheral Nerve Society (EFNS/PNS) criteria, an elevated protein level without pleocytosis (leukocytes <10 cells/µl) is supportive of the diagnosis CIDP. It is unclear how many CSF leukocytes are compatible with the diagnosis CIDP and how extensive the diagnostic work-up should be in patients with a demyelinating neuropathy and pleocytosis. We performed a retrospective study at two tertiary neuromuscular referral clinics and identified 14 out of 273 (6%) patients with CIDP with elevated CSF leukocytes (≥10 cells/µl). All these patients met the EFNS/PNS criteria for definite or probable CIDP. Eight patients (57%) presented with a subacute onset and four patients with an antecedent infection. Most patients responded well to therapy, and eight patients are currently in remission. In four patients, lumbar puncture was repeated. A spontaneous decrease in leukocytes before start of treatment was found in three patients. Our data indicate that a mild to moderate pleocytosis in CSF does not exclude the diagnosis of CIDP, especially in patients with a subacute onset of disease.
Molecular Orientational Structures in Ferroelectric, Ferrielectric and Antiferroelectric Smectic Liquid Crystal Phases as Studied by Conoscope Observation (1990)

Molecular orientational structures in MHPOBC were studied by means of conoscope observation. Contrary to a ferroelectric response of the conoscope to an electric field in the smectic C * phase, the conoscopic figure in the antiferroelectric smectic C A * phase does not shift its center and is biaxial with its optic plane perpendicular to the field direction. This conoscope change is only due to a dielectric contribution, indicating the existence of the inherent threshold in the electric field induced transition to the ferroelectric phase. In between the ferroelectric and antiferroelectric phases, a kind of ferrielectric phase was clearly distinguished in the field response of the conoscopic figure; the shift of the conoscope center perpendicular to the applied field and the biaxial optic plane parallel to the field suggest a novel molecular orientational structure.
Applications of cell sorting in biotechnology (2006)

Due to its unique capability to analyze a large number of single cells for several parameters simultaneously, flow cytometry has changed our understanding of the behavior of cells in culture and of the population dynamics even of clonal populations. The potential of this method for biotechnological research, which is based on populations of living cells, was soon appreciated. Sorting applications, however, are still less frequent than one would expect with regard to their potential. This review highlights important contributions where flow cytometric cell sorting was used for physiological research, protein engineering, cell engineering, specifically emphasizing selection of overproducing cell lines. Finally conclusions are drawn concerning the impact of cell sorting on inverse metabolic engineering and systems biology.