gebhart/patrepeval huggingface dataset:
BqsR/BqsS Constitute a Two-Component System That Senses Extracellular Fe(II) in Pseudomonas aeruginosa (2011)

Pseudomonas aeruginosa is a ubiquitous gram-negative bacterium best known as the predominant opportunistic pathogen infecting the lungs of cystic fibrosis patients. In this context, it is thought to form biofilms, within which locally reducing and acidic conditions can develop that favor the stability of ferrous iron [Fe(II)]. Because iron is a signal that stimulates biofilm formation, we performed a microarray study to determine whether P. aeruginosa strain PA14 exhibits a specific transcriptional response to extracellular Fe(II). Among the genes that were most upregulated in response to Fe(II) were those encoding the two-component system BqsR/BqsS, previously identified for its role in P. aeruginosa strain PAO1 biofilm decay (13); here, we demonstrate its role in extracellular Fe(II) sensing. bqsS and bqsR form an operon together with two small upstream genes, bqsP and bqsQ, and one downstream gene, bqsT. BqsR/BqsS sense extracellular Fe(II) at physiologically relevant concentrations (>10 μM) and elicit a specific transcriptional response, including its autoregulation. The sensor distinguishes between Fe(II), Fe(III), and other dipositive cations [Ca(II), Cu(II), Mg(II), Mn(II), Zn(II)] under aerobic or anaerobic conditions. The gene that is most upregulated by BqsR/BqsS, as measured by quantitative reverse transcription-PCR (qRT-PCR), is PA14_04180, which is predicted to encode a periplasmic oligonucleotide/oligosaccharide-binding domain (OB-fold) protein. Coincident with phenazine production during batch culture growth, Fe(II) becomes the majority of the total iron pool and bqsS is upregulated. The existence of a two-component system that senses Fe(II) indicates that extracellular Fe(II) is an important environmental signal for P. aeruginosa.
A walk through the web&#x2019;s video clips (2008)

Approximately 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> video clips are posted every day on the Web. The popularity of Web-based video databases poses a number of challenges to machine vision scientists: how do we organize, index and search such large wealth of data? Content-based video search and classification have been proposed in the literature and applied successfully to analyzing movies, TV broadcasts and lab-made videos. We explore the performance of some of these algorithms on a large data-set of approximately 3000 videos. We collected our data-set directly from the Web minimizing bias for content or quality, way so as to have a faithful representation of the statistics of this medium. We find that the algorithms that we have come to trust do not work well on video clips, because their quality is lower and their subject is more varied. We will make the data publicly available to encourage further research.
A robotic needle-positioning and guidance system for CT-guided puncture:Ex vivoresults (2014)

Purpose: To test the feasibility of a robotic needle-guidance platform during CT-guided puncture ex vivo. Material and methods: Thin copper wires inserted into a torso phantom served as targets. The phantom was placed on a carbon plate and the robot-positioning unit (RPU) of the guidance platform (iSYS Medizintechnik GmbH, Kitzbuehel, Austria) was attached. Following CT imaging and automatic registration a double oblique trajectory was planned and the RPU was remotely moved into appropriate position and angulation. A 17G-puncture needle was then manually inserted until the preplanned depth, permanently guided by the RPU. The CT scan was repeated and the distance between the actual needle tip and the target was evaluated. Results: Automatic registration was successful in ten experiments and the median duration of an experiment was 9.6 (6.4–46.0) minutes. The angulation of the needle path in x-y and z-axis was within 15.6° to 32.6°, and -32.8° to 3.2°, respectively and the needle insertion depth was 92.8 ± 14.4 mm. The Euclidean distance between the actual needle tip and the target was 2.3 ± 0.8 (range, 0.9–3.7) mm. Conclusion: Automatic registration and accurate needle placement close to small targets was demonstrated. Study settings and torso phantom were very close to the clinical reality.
Grazing limitation and nutrient limitation in marine ecosystems: Steady state solutions of an ecosystem model with multiple food chains (1994)

Here I develop a model with multiple phytoplankton-zooplankton food chains where each food chain is based on a different size class of algae. Model parameters were chosen to allow food chains based on smaller algal size classes to dominate under oligotrophic conditions, with larger size classes being added sequentially with increased nutrient loading. The model makes use of allometric relations among size classes to minimize the number of free parameters, facilitating numerical exploration of its steady state behavior. The model is simple, yet it is complex enough to allow simultaneous predator limitation of algal size classes (or species) and nutrient limitation of total phytoplankton biomass. This perspective, not obtainable from models with single phytoplankton and zooplankton size classes, is applied to the particular case of elevated nitrate levels in the equatorial Pacific. The model shows clearly that it is possible for each phytoplankton size class to be limited by its herbivores, while at the same time micronutrient (notably iron) deficiency may limit the number of size classes that can exist in the community and hence the total phytoplankton biomass that can be supported.
Mechanotransduction – a field pulling together? (2008)

Mechanical stresses are ever present in the cellular environment, whether through external forces that are applied to tissues or endogenous forces that are generated within the active cytoskeleton. Despite the wide array of studies demonstrating that such forces affect cellular signaling and function, it remains unclear whether mechanotransduction in different contexts shares common mechanisms. Here, I discuss possible mechanisms by which applied forces, cell-generated forces and changes in substrate mechanics could exert changes in cell function through common mechanotransduction machinery. I draw from examples that are primarily focused on the role of adhesions in transducing mechanical forces. Based on this discussion, emerging themes arise that connect these different areas of inquiry and suggest multiple avenues for future studies.
Three-dimensional imaging system based on a light-emitting diode array (2007)

A two-dimensional light-emitting diode array is used to replace the viewing-zone-forming optics in-multiview full-parallax three-dimensional image display systems. Since the array is not working merely as the viewing-zone-forming optics but also as the backlight panel for the liquid-crystal display (LCD) panel, it allows constructing three-dimensional imaging systems having the same structure as the current LCD display. The designed system displays images with good depth sense.
Tregitopes switch on Tregs (2008)

In this issue of Blood, De Groot and colleagues report the identification and functional characterization of Tregitopes, which are Treg-activating regions in the Fc portion of the IgG molecule. This important finding has the potential to bring understanding about a number of phenomena related to Ig, including tolerance to Ab variable regions, the tolerogenic properties of immunoglobulin-Ag conjugates, the weak immunogenicity of Fc fusion proteins, and the therapeutic and regulatory effects of clinical preparations of IVIg on autoimmune and inflammatory diseases.
Techniques for Assessment of Intravascular Volume in Critically Ill Patients (2009)

Fluid replacement is considered the cornerstone of resuscitation in the ICU.However, only about 50% of critically ill hemodynamically unstable patients are fluid responsive; furthermore, both under-resuscitation and overzealous fluid administration adversely affect outcome Consequently, the resuscitation of critically ill patients requires an accurate assessment of the patients' intravascular volume status and their volume responsiveness. This paper reviews the evolution and accuracy of methods for assessing fluid responsiveness in critically ill patients.
Human c-Myc Isoforms Differentially Regulate Cell Growth and Apoptosis in Drosophila melanogaster (2005)

The human c-myc proto-oncogene, implicated in the control of many cellular processes including cell growth and apoptosis, encodes three isoforms which differ in their N-terminal region. The functions of these isoforms have never been addressed in vivo. Here, we used Drosophila melanogaster to examine their functions in a fully integrated system. First, we established that the human c-Myc protein can rescue lethal mutations of the Drosophila myc ortholog, dmyc, demonstrating the biological relevance of this model. Then, we characterized a new lethal dmyc insertion allele, which permits expression of human c-Myc in place of dMyc and used it to compare physiological activities of these isoforms in whole-organism rescue, transcription, cell growth, and apoptosis. These isoforms differ both quantitatively and qualitatively. Most remarkably, while the small c-MycS form truncated for much of its N-terminal trans-activation domain efficiently rescued viability and cell growth, it did not induce detectable programmed cell death. Our data indicate that the main functional difference between c-Myc isoforms resides in their apoptotic properties and that the N-terminal region, containing the conserved MbI motif, is decisive in governing the choice between growth and death.
Deconvolution of Combinatorial Libraries for Drug Discovery: A Model System (1995)

Iterative synthesis and screening strategies have recently been used to identify unique active molecules from complex synthetic combinatorial libraries. These techniques have many advantages over traditional screening methods, including the potential to screen large numbers of compounds to identify an active molecule while avoiding analytical separations and structural determination of unknown compounds. It is not clear, however, whether these techniques identify the most active molecular species in the mixtures and, if so, how often. Two key factors which may affect success of the selection process are the presence of many active compounds in the library with a range of activities and the chosen order of unrandomization. The importance of these factors has not been previously studied. Moreover, the impact of experimental errors in determination of subset activities or in randomization during library synthesis is not known. We describe here a model system based on oligonucleotide hybridization that addresses these questions using computer simulations. The results suggested that, within achievable experimental and library synthesis error, iterative deconvolution methods generally find either the best molecule or one with activity very close to the best. The presence of many active compounds in a library influenced the profile of subset activities, but did not preclude selection of a molecule with near optimal activity.
Identification of Three Tyrosine Residues of Glycoprotein Ibα with Distinct Roles in von Willebrand Factor and α-Thrombin Binding (1995)

The interaction between von Willebrand factor (vWF) and the platelet membrane glycoprotein (GP) Ib-IX-V complex is essential for platelet adhesion at sites of vascular injury under high shear stress flow conditions. Moreover, GP Ib-IX-V may contribute to the mechanisms of platelet activation through its high affinity binding of alpha-thrombin. There are two distinct but partially overlapping regions of GP Ib alpha thought to be involved in interacting with vWF (residues 251-279) and alpha-thrombin (residues 271-284); they share three tyrosine residues (positions 276, 278, and 279) that have recently been shown to be sulfated (Dong, J., Li, C. Q., and Lopez, J.A. (1994) Biochemistry 33, 13946-13953). To define the functional role of these three residues, we have introduced selected mutations in a soluble recombinant GP Ib alpha fragment (corresponding to the sequence 1-302 of the mature protein) that binds vWF and alpha-thrombin with the same attributes as intact GP Ib-IX-V complex. Fragments containing a single Tyr-->Phe substitution either at position 276 or 278 or 279 exhibited normal interaction with vWF but markedly reduced or absent binding of alpha-thrombin. GP Ib alpha fragment with normal sequence but synthesized under sulfate-free conditions also failed to bind alpha-thrombin and, in addition, had markedly reduced interaction with vWF. The simultaneous substitution of three neighboring Asp residues with Asn at positions 272, 274, and 277, a multiple mutation that may impair Tyr sulfation, also resulted in loss of binding of both ligands. These results define distinct structural features of GP Ib alpha selectively involved in supporting the interaction with vWF or alpha-thrombin.
Prediction of MHC-Peptide Binding: A Systematic and Comprehensive Overview (2009)

T cell immune responses are driven by the recognition of peptide antigens (T cell epitopes) that are bound to major histocompatibility complex (MHC) molecules. T cell epitope immunogenicity is thus contingent on several events, including appropriate and effective processing of the peptide from its protein source, stable peptide binding to the MHC molecule, and recognition of the MHC-bound peptide by the T cell receptor. Of these three hallmarks, MHC-peptide binding is the most selective event that determines T cell epitopes. Therefore, prediction of MHC-peptide binding constitutes the principal basis for anticipating potential T cell epitopes. The tremendous relevance of epitope identification in vaccine design and in the monitoring of T cell responses has spurred the development of many computational methods for predicting MHC-peptide binding that improve the efficiency and economics of T cell epitope identification. In this report, we will systematically examine the available methods for predicting MHC-peptide binding and discuss their most relevant advantages and drawbacks.
A wide-field time-domain fluorescence lifetime imaging microscope with optical sectioning (2002)

This article describes a wide-field time-domain fluorescence lifetime imaging (FLIM) microscope with optical sectioning. The FLIM system utilizes a wide-field time-gated optical image intensifier, with a minimum gate width of 85 ps, to achieve high temporal resolution of fluorescence decays induced by ultrashort laser pulses. Different configurations, using excitation pulses of picojoule energy at 80 MHz repetition rate and of nanojoule energy at 10 kHz, are compared. The instrument has a temporal dynamic range spanning from 100 ps to tens of μs and is shown to have a temporal discrimination better than 10 ps. When applied to laser dye samples, it has produced FLIM maps demonstrating sensitivity to variations in both chemical species and local environment, e.g., viscosity. Wide-field optical sectioning is achieved using the technique of structured illumination, which is applied to remove out-of-focus light that can result in lifetime artifacts. The sectioning strength, which may be adjusted by choosing an appropriate spatial modulation frequency, is characterized and shown to be comparable to that of a confocal microscope. Practical considerations concerned with improving the quality of sectioned fluorescence lifetime maps, including using a large bit depth camera, are discussed.
INHIBITION OF INSULIN DEGRADATION BY INSULIN-LIKE GROWTH FACTORS (1983)

The effect of insulin-like growth factors (IGF 1 and IGF 2) on insulin degradation was studied with the use of a preparation of insulin protease from rat skeletal muscle. Insulin, IGF 1 and IGF 2 inhibited 125I-insulin degradation by this enzyme. IGF 2 was the most potent inhibitor and IGF 1 was the least potent. These results are similar to what has been reported previously for the insulin-degrading activity in the serum of a diabetic patient who was resistant to sc and im insulin. Insulin protease also degraded 125I-iodo IGF 1 and 125I-iodo IGF 2. 125I-iodo IGF 2 was degraded more rapidly than was 125I-iodo IGF 1. 125I-iodoinsulin was degraded more rapidly than 125I-iodo IGF 2. With all three peptides, immunoprecipitation was a more sensitive measure of degradation than was trichloroacetic acid precipitation. The results suggest that insulin protease may be responsible for the degradation of insulin-like growth factors as well as of insulin.
The isomeric transformation of urea into ammonium cyanate in aqueous solutions (1948)

Walker & Hambly (1895) showed that the isomeric transformation of ammonium cyanate into urea (Wohler, 1828) was spontaneously reversible in aqueous solutions. At equilibrium at 1000, a 0-lM- solution of urea was said to contain approximately 95 % urea and 5% ammonium cyanate. Werner
Scaling of atomic layer etching of SiO2 in fluorocarbon plasmas: Transient etching and surface roughness (2021)

Fabricating sub-10 nm microelectronics places plasma processing precision at atomic dimensions. Atomic layer etching (ALE) is a cyclic plasma process used in semiconductor fabrication that has the potential to remove a single layer of atoms during each cycle. In self-limiting ideal ALE, a single monolayer of a material is consistently removed in each cycle, typically expressed as EPC (etch per cycle). In plasma ALE of dielectrics, such as SiO2 and Si3N4, using fluorocarbon gas mixtures, etching proceeds through deposition of a thin polymer layer and the process is not strictly self-terminating. As a result, EPC is highly process dependent and particularly sensitive to the thickness of the polymer layer. In this paper, results are discussed from a computational investigation of the ALE of SiO2 on flat surfaces and in short trenches using capacitively coupled plasmas consisting of a deposition step (fluorocarbon plasma) and an etch step (argon plasma). We found that ALE performance is a delicate balance between deposition of polymer during the first half cycle and etching (with polymer removal) during the second half cycle. In the absence of complete removal of the overlying polymer in each cycle, ALE may be transient as the polymer thickness grows with each cycle with a reduction in EPC until the thickness is too large to enable further etching. Small and statistical amounts of polymer left from a previous cycle can produce statistical variation in polymer thickness on the next cycle, which in turn can lead to a spatially dependent EPC and ALE roughness. Based on synergy between Ti (sputtering time) and Tp (passivation time), dielectric ALE can be described as having three modes: deposition, roughening surface (transitioning to etch-stop), and smooth surface with steady-state EPC.
Prediction of hypotension in hemodialysis patients (2014)

Intradialytic hypotension (IDH) is the most common adverse complication during hemodialysis. Its early prediction and prevention will dramatically improve the quality of life for patients with an end stage renal disease. In a recent study, changes in the normalized envelope of the test statistic of the photoplethysmograpic (PPG) signal were found to predict acute symptomatic IDH. In the present study, the PPG-based predictor is generalized to include a patient-dependent threshold which incorporates on-line information on heart rate variability and heart rate turbulence. From datasets with patients prone and resistant to IDH, the results show that symptomatic IDH could be correctly predicted in 9 out of 14 cases, while 5 out of 24 were falsely predicted. In a subset of the data containing only patients prone to IDH, acute symptomatic IDH could be correctly predicted in 5 out of 5 cases, with one false prediction out of 14. When testing the robustness of the predictor, no significant changes were observed in the test statistic when controlled changes occurred in dialysis fluid temperature, ultrafiltration rate and body position.
Characterization of a Helical Protein Designed from First Principles (1988)

The question of how the primary amino acid sequence of a protein determines its three-dimensional structure is still unanswered. One approach to this problem involves the de novo design of model peptides and proteins that should adopt desired three-dimensional structures. A systematic approach was aimed at the design of a four-helix bundle protein. The gene encoding the designed protein was synthesized and the protein was expressed in Escherichia coli and purified to homogeneity. The protein was shown to be monomeric, highly helical, and very stable to denaturation by guanidine hydrochloride (GuHCl). Thus a globular protein has been designed that is capable of adopting a stable, folded structure in aqueous solution.
Facilitated Regeneration in the Rat Peripheral Nervous System Using Applied Electric Fields (1988)

The efficacy of applied electric fields in promoting regeneration of the transected and frozen rat sciatic nerve was studied. Three groups were studied at 6, 12, and 18 days post-lesion; nerves treated with 1.5 microA of direct current where the cathode was oriented distal to the lesion, nerves treated with the anode distal to the lesion, or no current delivered to the nerve. Regeneration in this severely damaged mammalian peripheral nerve model was quantitated by counting fluorescent antibody profiles to neurofilament protein distal to the lesion site. The results indicated that only cathodal current, applied distal to the lesion, significantly increased the rate of regeneration compared to controls. Such results help to elucidate mechanisms by which electric fields can facilitate regeneration in the mammalian nervous system.
A Practical Guide to Basal and Prandial Insulin Therapy (1985)

Separating basal and meal-related insulin requirements allows a systematic approach to subcutaneous insulin therapy. Simple guidelines for both the doctor and patient can cater for the spectrum of severity of diabetes. A non-insulin-dependent diabetic who, despite dieting, continues to have moderate fasting hyperglycaemia (6-10 mmol/l) may need only a basal insulin supplement, whereas a totally insulin-dependent diabetic usually needs similar amounts of basal and meal-related insulin. The likely insulin requirements of individual diabetics can be predicted, including the increased amounts required by obese patients. The algorithms have been developed using ultralente to provide the basal insulin requirement, but the principles and doses probably apply to other similarly long-acting insulins or an insulin pump. The insulin doses can be easily altered for varying lifestyles, including night work, religious fasts or long distance aeroplane travel, and for temporary disturbances such as operations or intercurrent infections.
Unsupervised Bayesian Detection of Independent Motion in Crowds (2006)

While crowds of various subjects may offer applicationspecific cues to detect individuals, we demonstrate that for the general case, motion itself contains more information than previously exploited. This paper describes an unsupervised data driven Bayesian clustering algorithm which has detection of individual entities as its primary goal. We track simple image features and probabilistically group them into clusters representing independently moving entities. The numbers of clusters and the grouping of constituent features are determined without supervised learning or any subject-specific model. The new approach is instead, that space-time proximity and trajectory coherence through image space are used as the only probabilistic criteria for clustering. An important contribution of this work is how these criteria are used to perform a one-shot data association without iterating through combinatorial hypotheses of cluster assignments. Our proposed general detection algorithm can be augmented with subject-specific filtering, but is shown to already be effective at detecting individual entities in crowds of people, insects, and animals. This paper and the associated video examine the implementation and experiments of our motion clustering framework.