gebhart/patrepeval huggingface dataset:
Time-Dependent Single-Molecule Raman Scattering as a Probe of Surface Dynamics (2001)

Large spectral fluctuations, on a time scale of many seconds, are demonstrated in the surface-enhanced Raman scattering of single rhodamine 6G molecules adsorbed on silver nanocrystals and excited at 532 nm. These fluctuations are especially evident in the case of the vibrational bands at 614 and 774 cm-1. A definite connection between spectral fluctuations and changes in the shape of the diffuse background emitted with the SERS spectrum is seen, pointing to the possible origin of both in a molecule-surface charge transfer phenomenon. The rate of spectral fluctuations is shown to depend linearly on laser intensity through a nonthermal mechanism. The rate of fluctuations can also be modified by changing the anion concentration in the solution on top of the silver colloids. Analysis of the results suggests that the fluctuations are due to motion of the adsorbed molecule on the surface, triggered by photodesorption events that are mediated by electron tunneling between the molecule and surface. Our results show that single-molecule Raman scattering can serve as a sensitive local probe for the dynamics of adsorbed molecules under ambient conditions.
Recognizing Textual Entailment with Deep-Shallow Semantic Analysis and Logical Inference (2010)

Abstract—In this paper, the architecture and evaluation of a new system for recognizing textual entailment (RTE) is presented. It is conceived as an adaptable and modular environ-ment allowing for a high-coverage syntactic and semantic text analysis combined with logical inference. For the syntactic and semantic analysis it combines an HPSG-based deep semantic analysis with a shallow one supported by statistical models in order to increase the quality and accuracy of results. For recognizing textual entailment we use logical inference of first-order employing model-theoretic techniques and automated reasoning tools. The inference is supported with problem-relevant background knowledge extracted automatically and on demand from external sources like, e.g., WordNet, YAGO, and OpenCyc, or other, experimental sources with, e.g., manually defined presupposition resolutions, or with general and com-mon sense knowledge. The system comes with a graphical user interface for control and presentation purposes. The evaluation shows that the success rate of the presented RTE system is comparable with that of the best logic-based approaches. Keywords-recognizing textual entailment; semantic analysis; logical inference; knowledge integration; semantic reasoning. I.
The Alkyl<i>tert</i>-Butyl Ether Intermediate 2-Hydroxyisobutyrate Is Degraded via a Novel Cobalamin-Dependent Mutase Pathway (2006)

Fuel oxygenates such as methyl and ethyl tert-butyl ether (MTBE and ETBE, respectively) are degraded only by a limited number of bacterial strains. The aerobic pathway is generally thought to run via tert-butyl alcohol (TBA) and 2-hydroxyisobutyrate (2-HIBA), whereas further steps are unclear. We have now demonstrated for the newly isolated beta-proteobacterial strains L108 and L10, as well as for the closely related strain CIP I-2052, that 2-HIBA was degraded by a cobalamin-dependent enzymatic step. In these strains, growth on substrates containing the tert-butyl moiety, such as MTBE, TBA, and 2-HIBA, was strictly dependent on cobalt, which could be replaced by cobalamin. Tandem mass spectrometry identified a 2-HIBA-induced protein with high similarity to a peptide whose gene sequence was found in the finished genome of the MTBE-degrading strain Methylibium petroleiphilum PM1. Alignment analysis identified it as the small subunit of isobutyryl-coenzyme A (CoA) mutase (ICM; EC 5.4.99.13), which is a cobalamin-containing carbon skeleton-rearranging enzyme, originally described only in Streptomyces spp. Sequencing of the genes of both ICM subunits from strain L108 revealed nearly 100% identity with the corresponding peptide sequences from M. petroleiphilum PM1, suggesting a horizontal gene transfer event to have occurred between these strains. Enzyme activity was demonstrated in crude extracts of induced cells of strains L108 and L10, transforming 2-HIBA into 3-hydroxybutyrate in the presence of CoA and ATP. The physiological and evolutionary aspects of this novel pathway involved in MTBE and ETBE metabolism are discussed.
Comparison of Oxycodone in Vitreous Humor and Blood Using EMIT(R) Screening and Gas Chromatographic-Mass Spectrometric Quantitation (2009)

Vitreous humor may serve as a useful alternative specimen for oxycodone analysis in death investigations where blood samples are not available or are of poor quality or limited quantity. The purpose of this study was to investigate the relationship between immunoassay results and gas chromatography-mass spectrometry (GC-MS) quantitation of oxycodone in postmortem vitreous humor and blood. When used with vitreous humor calibrators, the Microgenics DRI Oxycodone (EMIT) Assay was found to be linear from 25 to 500 ng/mL with an limit of detection of 25 ng/mL. Vitreous humor and postmortem blood precipitate immunoassay responses in 57 oxycodone-positive cases were found to be correlated (r(2) = 0.69, p < 0.01). Confirmation and quantitation of oxycodone in vitreous humor by GC-MS was linear from 50 to 1000 ng/mL with a limit of detection of 10 ng/mL and a limit of quantitation of 50 ng/mL. In 30 cases, oxycodone vitreous humor concentrations ranged from less than 50 to 945 ng/mL, and blood concentrations ranged from 103 to 768 ng/mL. The average vitreous humor/blood ratio was 1.16 and ranged from 0.12 to 3.26. Disparities between vitreous fluid and blood oxycodone concentrations were seen in a few cases.
Preadipocyte differentiation in vitro: Identification of a highly active adipogenic agent (1988)

A highly active adipogenic agent was identified in an in vitro adipose conversion system. This agent, ADD 4743 (or ADD), was synthesized by Takeda Chemical Industries (Osaka) as a 3-hydroxy derivative of an oral antidiabetic agent, ciglitazone, and has been presumed to be an active metabolite of the latter substance. When ST 13 mouse preadipose cells were treated with micromolar concentrations of ADD they rapidly and uniformly converted into lipid-accumulating adipocytelike cells within 8-11 days after cell seeding. The degree of adipose conversion and lipid accumulation induced by ADD far exceeded those of the previously known inducing agents such as indomethacin plus insulin. The highly potent adipogenic activity of ADD was confirmed with two other preadipose cell lines (3T3 L1 and RMT rat preadipose cells). In addition to adipogenic activity, ADD inhibited cell proliferation of preadipose cells specifically. Activity of ADD induced lipid accumulation and growth inhibition of ST 13 cells, exhibiting very similar dose-response relationships. Cell proliferation or triacylglycerol content of nonadipocytic mesenchymal cells or epithelial cells were not affected by ADD. These observations strongly suggest that ADD-induced growth inhibition is not due to the nonspecific toxicity of the drug but is tightly associated with the adipocytic character of the treated cells. The present observation provides evidence that ADD would be a powerful agent in studies that involve preadipocyte differentiation.
What Can the Spinal Cord Teach Us about Learning and Memory? (2010)

The work of recent decades has shown that the nervous system changes continually throughout life. Activity-dependent central nervous system (CNS) plasticity has many different mechanisms and involves essentially every region, from the cortex to the spinal cord. This new knowledge radically changes the challenge of explaining learning and memory and greatly increases the relevance of the spinal cord. The challenge is now to explain how continual and ubiquitous plasticity accounts for the initial acquisition and subsequent stability of many different learned behaviors. The spinal cord has a key role because it is the final common pathway for all behavior and is a site of substantial plasticity. Furthermore, because it is simple, accessible, distant from the rest of the CNS, and directly connected to behavior, the spinal cord is uniquely suited for identifying sites and mechanisms of plasticity and for determining how they account for behavioral change. Experimental models based on spinal cord reflexes facilitate study of the gradual plasticity that makes possible most rapid learning phenomena. These models reveal principles and generate concepts that are likely to apply to learning and memory throughout the CNS. In addition, they offer new approaches to guiding activity-dependent plasticity so as to restore functions lost to injury or disease.
A slotted waveguide setup as scaled instrument-landing-system for measuring scattering of an A380 and large objects (2010)

At an airport the instrument-landing-system (ILS) provides aircraft on landing approach with both the lateral and vertical guidance to the runway. It is known that the lateral landing course information (localizer) can be disturbed due to reflections on large aircraft taxiing near the runway. Investigating such disturbance scenarios in a scaled setup requires an accurate and flexible modelling of a scaled ILS. This paper presents an antenna setup consisting of two slotted waveguides as scaled localizer of the instrument landing system. The design itself allows individual pattern forming to be applicable to various ILS at different airports. Measured antenna patterns correspond well to simulations demonstrating the feasibility of this approach. Additionally, measurements of ILS disturbance scenarios with large objects, such as an A380, a B747 and a sphere are presented for landing approaches. This paper compares the scattering behaviour of the mentioned aircraft and focuses on how to specify the influence of individual scatterers, e. g. the fuselage or the tail fin.
Differential but Competitive Binding of Nogo Protein and Class I Major Histocompatibility Complex (MHCI) to the PIR-B Ectodomain Provides an Inhibition of Cells (2011)

Binding of class I MHC molecules (MHCI) to an inhibitory receptor, PIR-B, expressed on B cells and myeloid cells provides constitutive cellular inhibition, thus ensuring peripheral tolerance. Recent unexpected findings pointed to a novel inhibitory role of PIR-B in neurite regeneration through binding to three axonal outgrowth inhibitors of myelin, including Nogo. Thus, it becomes interesting to determine whether the actions of the inhibitory myelin proteins and MHCI could coexist independently or be mutually exclusive as to the PIR-B-mediated immune and neural cell inhibition. Here, we present data supporting the competition of Nogo- and MHCI-mediated inhibition where they coexist. Kinetic analyses of Nogo and MHCI binding to the whole or a part of the recombinant PIR-B ectodomain revealed that PIR-B binds with higher affinity to Nogo than MHCI and that the MHCI binding only occurred with the N-terminal domains of PIR-B, whereas Nogo binding occurred with either the N- or C-terminal ectodomains. Importantly, kinetic tests indicated that the binding to PIR-B of Nogo and MHCI was competitive. Both endogenous and exogenous Nogo intensified the PIR-B-mediated suppression of interleukin-6 release from lipopolysaccharide-stimulated wild-type, but not PIR-B-deficient, cultured mast cells, indicating that PIR-B mediates Nogo-induced inhibition. Thus, we propose a novel mechanism by which PIR-B-mediated regulation is achieved differentially but competitively via MHCI and Nogo in cells of the immune system.
Ligand-dependent changes in intrinsic fluorescence of S-adenosylhomocysteine hydrolase: Implications for the mechanism of inhibitor-induced inhibition (1993)

Different forms of S-adenosylhomocysteine (AdoHcy) hydrolase (NAD+, apo, and NADH forms) were prepared, and the effects of ligand binding on the intrinsic tryptophan fluorescence were investigated. Binding of AdoHcy hydrolase (NAD+ form) with its mechanism-based inhibitors [e.g., (1'R,2'S,3'R)-9-(2',3'-dihydroxycyclopentan-1'-yl)adenine] caused significant quenching (35%) of the intrinsic tryptophan fluorescence of the enzyme. A ligand-induced conformational change in the tertiary structure of the enzyme accounted for an initial 10% quenching of the fluorescence, with further fluorescence quenching occurring in a time-dependent manner. This time-dependent quenching of fluorescence was consistent with the time-dependent inactivation of the enzyme and the time-dependent reduction of the enzyme-bound NAD+ to NADH. The time-dependent quenching of the intrinsic tryptophan fluorescence is largely the result of resonance energy transfer from tryptophan(s) in the enzyme to the enzyme-bound NADH. This interpretation is supported by the observations that the formation of enzyme-bound NADH quenched the intensity of the intrinsic tryptophan fluorescence and that the enzyme-bound NADH fluorescence was excited by light at wavelengths consistent with the absorption spectrum of tryptophan. Additional support for the involvement of NADH in the time-dependent tryptophan fluorescence quenching came from the observation that this quenching could only be observed when binding caused simultaneous reduction of the enzyme-bound NAD+ to NADH.(ABSTRACT TRUNCATED AT 250 WORDS)
Picosecond optical sampling using four-wave mixing in fibre (1991)

An all-optical sampling system with 20 ps resolution realised by employing four-wave mixing in a fibre is demonstrated. Using only semiconductor laser sources, picosecond pulses are displayed on a microsecond time scale with a low speed receiver.
A gentle introduction to deep learning in medical image processing (2019)

This paper tries to give a gentle introduction to deep learning in medical image processing, proceeding from theoretical foundations to applications. We first discuss general reasons for the popularity of deep learning, including several major breakthroughs in computer science. Next, we start reviewing the fundamental basics of the perceptron and neural networks, along with some fundamental theory that is often omitted. Doing so allows us to understand the reasons for the rise of deep learning in many application domains. Obviously medical image processing is one of these areas which has been largely affected by this rapid progress, in particular in image detection and recognition, image segmentation, image registration, and computer-aided diagnosis. There are also recent trends in physical simulation, modeling, and reconstruction that have led to astonishing results. Yet, some of these approaches neglect prior knowledge and hence bear the risk of producing implausible results. These apparent weaknesses highlight current limitations of deep ()learning. However, we also briefly discuss promising approaches that might be able to resolve these problems in the future.
Effect of Charge and Molecular Weight on the Functionality of Gelatin Carriers for Corneal Endothelial Cell Therapy (2006)

Cell transplantation strategies usually involve the use of supporting carrier materials because of the soft and fragile nature of these grafts. In this work, a cell-adhesive gelatin hydrogel carrier was fabricated to deliver cultivated human corneal endothelial cell (HCEC) sheets, which were harvested from thermo-responsive poly(N-isopropylacrylamide) (PNIPAAm)-grafted culture surfaces. The carrier disks, consisting of gelatins with a different isoelectric point (IEP = 5.0 and 9.0) and a molecular weight (MW) ranging from 3 to 100 kDa, were subjected to 16.6 kGy gamma irradiation for sterilization. The effect of IEP and MW of the raw gelatins (i.e., before irradiation) on the functionality of sterilized disks was studied by determinations of mechanical property, water content, dissolution degree, and cytocompatibility. Irrespective of the IEP of raw gelatin, hydrogel disks prepared with high MW (100 kDa) exhibited a greater tensile strength, lower water content, and slower dissolution rate than those made of low MW gelatin (8 and 3 kDa). From the investigation of cellular responses to the disks, the negatively charged gelatin (IEP = 5.0) groups were more cytocompatible when compared with their positively charged counterparts (IEP = 9.0) at the same MW (100 kDa). Additionally, in the negatively charged gelatin groups, only a slight increase in pro-inflammatory cytokine expression was observed with increasing MW of gelatin from 3 to 100 kDa. It is concluded that the gamma-sterilized hydrogel disks made from raw gelatins (IEP = 5.0, MW = 100 kDa) with appropriate dissolution degree and acceptable cytocompatibility are capable of providing stable mechanical support, making these carriers promising candidates for intraocular delivery of cultivated HCEC sheets.
Local Resiniferatoxin Induces Long-Lasting Analgesia in a Rat Model of Full Thickness Thermal Injury (2016)

These results indicate that local RTX induces long-lasting analgesia in a rat model of pain associated with burn. While opioids are undesirable in trauma patients due to side effects, RTX may provide valuable long-term, nonopioid analgesia for burn patients.
Surprise-Based Learning for Developmental Robotics (2008)

This paper presents a learning algorithm called surprise-based learning (SBL) capable of providing a physical robot the ability to autonomously learn and plan in an unknown environment without any prior knowledge of its actions or their impact on the environment. This is achieved by creating a model of the environment using prediction rules. A prediction rule describes the observations of the environment prior to the execution of an action and the forecasted or predicted observation of the environment after the action. The algorithm learns by investigating "surprises", which are inconsistencies between the predictions and observed outcome. SBL has been successfully demonstrated on a modular robot learning and navigating in a small static environment.
INFLUENCE OF GRANULE SIZE ON VISCOSITY OF CORNSTARCH SUSPENSION (1995)

ABSTRACT The influence of granule size and size distribution in gelatinized suspensions of 2.6% cornstarch heated at fixed temperatures between 70–90C on the power law viscosity was measured by laser diffraction. In the early stages of gelatinization, where the granule size standard deviation was less than 12 μm, dilatant behavior was observed over the shear rate range 200–1100 S −1 . At constant starch concentration and without granule rupture, suspension consistency, K, increased exponentially with granule mean diameter while the flow behavior index, n, decreased linearly with increase in the extent of gelatinization and the standard deviation of the granule size. The variation of K with granule size and that of n with standard deviation were found to be independent of temperature over 70–90C. In the later stages of gelatinization, where the granules lose their integrity, suspension viscosity progressively decreased as granule rupture continued.
Presentation of allergen in different food preparations affects the nature of the allergic reaction – a case series (2003)

The fat content of a challenge vehicle has a profound effect on the reaction experienced after allergen ingestion. This is another factor to be considered in assessing the risk of certain foods to food-allergic consumers and adds another dimension to clinical, research and regulatory practice.
Eliciting clinical empathy via transmission of patient-specific symptoms of Parkinson’s disease (2018)

Clinical empathy can have numerous benefits for patients, clinicians, and health-care providers. Traditional empathy training techniques (e.g. storytelling, videos, or disease simulators) are centered on the health condition rather than the individual. This condition-centric approach perpetuates the belief that the disease, rather than the patient, is at the core of the experience. This process can be ineffective in generating the ability to understand and accurately acknowledge the feelings of another. A more effective means of eliciting empathy can be through technology-mediated symptom transference for transmitting an individual patient’s actual experience, rather than a simulation, to the user—a process termed “tele-empathy.” We developed an investigational digital tele-empathy device for use toward patients with Parkinson’s disease (PD), known as SymPulse™. The device plays back muscle tremors using an armband, giving the wearer a replication of the involuntary muscle activity that a patient with PD feels. The purpose of the current study was to determine whether the SymPulse™ device could enhance feelings of empathy in test participants (wearing the device) versus control participants (not wearing the device). A sample of 45 participants (22 test; 23 control) reported their level of empathy via self-report questionnaires. Results revealed significantly higher empathy scale scores for test compared to control participants, demonstrating the effectiveness of the SymPulse™ for use in tele-empathy. The use of such technology for eliciting tele-empathy may have practical and clinical implications for providing effective training to health-care providers.
Tissue Culture of Maize I. Callus Induction and Growth (1975)

Abstract Callus induction and subculture was successful with mature embryos and stem sections of seedlings of Zea mays L. on Linsmaier and Skoog's medium modified to contain 4 mg/I of 2,4‐D and 1 g/I of casamino acids. — 2,4‐D was superior to NAA and IAA for both callus induction and growth. Callus subcultured on NAA formed abundant roots on agar‐solidified media and numerous root‐like primordia in liquid cultures. — Kinetin had no effect on callus induction in the presence of 2,4‐D and neither kinetin nor gibberellic acid stimulated callus growth during subculture. — Callus grew equally well on the medium of Linsmaier and Skoog, that of Schenk and Hildebrandt, and the B‐5 medium of Gamborg and Eveleigh containing 2% sucrose, 4 mg/I of 2,4‐D and 1 g/I of casamino acids. — The callus grew more rapidly at 25°C than at 30°C or 35°C. Little difference was noted at any temperature in callus growth in alternating light (16 h) and dark (8 h) or continuous dark. — Sucrose was superior to glucose and maltose in both liquid and agar‐solidified cultures. Lactose and galactose failed to support callus growth.