gebhart/patrepeval huggingface dataset:
Application of proteomic technologies for prostate cancer detection, prognosis, and tailored therapy (2010)

Prostate cancer affects 3 in 10 men over the age of 50 years, and, unfortunately, the clinical course of the disease is poorly predicted. At present, there is no means that can distinguish indolent from aggressive/metastatic tumors. Thus, a personalized clinical approach could be helpful in diagnosing clinically relevant disease and guiding appropriate patient therapy. Individualized medicine requires a deep knowledge of the molecular mechanisms underpinning prostate cancer carcinogenesis. Proteomics may be the most powerful way to uncover biomarkers of detection, prognosis, and prediction, as proteins do the work of the cell and represent the majority of the diagnostic markers and drug targets today. Proteomic technologies are rapidly advancing beyond the two-dimensional gel separation techniques of the past to new types of mass spectrometry and protein microarray analyses. Biological fluids and tissue-cell proteomes from men with prostate cancer are being explored to identify diagnostic and prognostic biomarkers and therapeutic targets using these new proteomic approaches. Traditional and novel proteomic technology and their application to prostate cancer studies in translational research will be presented and discussed in this review. Proteomics coupled with powerful nanotechnology-based biomarker discovery approaches may provide a new and exciting opportunity for body fluid-borne biomarker discovery and characterization. While innovative mass spectrometry technology and nanotrap could be applied to improve the discovery and measurement of biomarkers for the early detection of prostate cancer, the use of tissue proteomic tools such as the reverse-phase protein microarray may provide new approaches for personalization of therapies tailored to each tumor's unique pathway activation network.
Response to “Comment on ‘The origins of pressure-induced phase transitions during the surface texturing of silicon using femtosecond laser irradiation’” [J. Appl. Phys. 113, 126102 (2013)] (2013)

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The chemistry of low dosage clathrate hydrate inhibitors (2013)

This review aims to introduce the chemistry of low dosage inhibitors of clathrate hydrate formation within the context of their role in the oil and gas industry. The review covers both kinetic hydrate inhibitors and anti-agglomerants from the point of view of structure-function relationships, focussing on recent refinements in mechanistic understanding and chemical design, and the consequently evolving and increasingly fine-tuned properties of these fascinating compounds.
Electrospun polystyrene fibers for HIV entrapment (2014)

The high versatility and ease of electrospinning of polymer solutions have recently resulted in electrospun fibers, which are of interest for a wide variety of chemical and biomedical applications. This is partially due to the high surface area of the fibers, which is attractive for the detection and capture of (bio)chemicals. In the present work, polystyrene (PS) fibers were electrospun and coated with cationic poly(allylamine hydrochloride) (PAH) or anionic dextran sulfate sodium (DSS). The fibers were physicochemically characterized. Upon incubation in a dispersion of inactivated HIV-1, avid binding of HIV to all types of fibers occurred. By atomic force microscopy and spatial selective photobleaching, the binding of the inactivated HIV-1 particles to the fibers could be confirmed. Interestingly, all fibers, especially the DSS-coated and PAH-coated ones, resulted in a significant reduction of infection of CD4+ TZMbl cells by replication-competent HIV-1. On top, DSS-coated PS fibers were not toxic for vaginal epithelial cells, which may make these fibers of potential interest to inhibit HIV infection in the context of topical prevention. Copyright © 2014 John Wiley & Sons, Ltd.
Rate of acoustic formant transition change on categorical perception (1980)

A comparison was made of the effect of rate of acoustic formant transition change on the categorical perception functions for stop-consonant-vowel (CV) syllables with 40- and 80-ms formant transitions. Two place of articulation continua representing the phonemic categories /ba/ and /da/ containing transitions of 40 and 80 ms were presented to subjects in both identification and discrimination tasks. In the 80-ms signals, the entire formant transition spectrum was extended. Individual identification functions were fit using probit analysis. Extending the duration of formant transitions while keeping the manner of articulation constant significantly effected the identification function. Discrimination for within-category stimulus comparison was enhanced for the extended formant transitions.
An investigation of the effects of ultrasound on degradable polyanhydride matrices (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn investigation of the effects of ultrasound on degradable polyanhydride matricesAntony D'Emanuele, Joseph Kost, Jennifer L. Hill, and Robert LangerCite this: Macromolecules 1992, 25, 2, 511–515Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/ma00028a002https://doi.org/10.1021/ma00028a002research-articleACS PublicationsRequest reuse permissionsArticle Views257Altmetric-Citations32LEARN 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 Get e-Alerts
A National Field Study of Quality Assessment of CoaguChek Point-of-Care Testing Prothrombin Time Monitors (2006)

A system for quality assessment (QA) of the CoaguChek (Roche Diagnostics, Mannheim, Germany) point-of-care testing prothrombin time monitor has been developed by the European Concerted Action on Anticoagulation. Hitherto there has not been an adequate rapid method for CoaguChek QA. Sets of 5 certified international normalized ratio (INR) plasma samples were tested on 539 CoaguChek monitors by experienced staff at 9 Netherlands Thrombosis Centers and results compared with certified INR. A 15% or more deviation has been classified as significant deviation. Overall mean and certified INR values were similar, but 20.3% of participants showed a 15% or more deviation from the certified INR on at least 1 of the 5 QA plasma samples. Statistically significant differences in results with different lots of CoaguChek test strips were found. There is need for large scale QA of CoaguChek monitors. The importance of the 5 CoaguChek certified INR QA plasma samples being tested on a single occasion is demonstrated.
The T‐type calcium channel blocker Z944 reduces conditioned fear in Genetic Absence Epilepsy Rats from Strasbourg and the non‐epileptic control strain (2019)

Genetic Absence Epilepsy Rats from Strasbourg (GAERS) are a rodent model of childhood absence epilepsy (CAE) that display a gain-of-function mutation in the gene encoding the Cav3.2 T-type calcium channel. GAERS demonstrate heightened learning and delayed extinction of fear conditioning. Our objective in the present study was to examine the effects of the pan-T-type calcium channel blocker Z944 on the acquisition, consolidation and extinction of conditioned fear in GAERS and the non-epileptic control (NEC) strain. Z944 (10 mg/kg; ip) was administered 15 min prior to either acquisition, extinction day 1 (24 hr later), acquisition and extinction day 1, or during the consolidation (post-acquisition) of tone-cued fear conditioning. Extinction was examined 24 and 48 hr after conditioning. In drug naïve GAERS, increased freezing during the acquisition and extinction phases of fear conditioning was found. Short-term effects of Z944 on performance were observed as Z944 increased freezing during testing on the day it was administered. Z944 administered prior to the acquisition phase had a long-term effect on extinction. Specifically, both GAERS and NECs showed a decrease in freezing during extinction relative to drug naïve GAERS and NEC rats respectively. Regardless of strain or treatment, female rats showed reduced extinction of fear relative to male rats. These results demonstrate that T-type calcium channels contribute to the neural systems that mediate the learning and memory of conditioned fear. Overall, these findings suggest that T-type calcium channel blockers show promise in the treatment of learning impairments observed in disorders such as CAE.
IL-8 Dictates Glycosaminoglycan Binding and Stability of IL-18 in Cystic Fibrosis (2009)

Dysregulation of airway inflammation contributes to lung disease in cystic fibrosis (CF). Inflammation is mediated by inflammatory cytokines, including IL-8, which illustrates an increase in biological half-life and proinflammatory activity when bound to glycosaminoglycans (GAGs). The aim of this project was to compare IL-8 and IL-18 for their relative stability, activity, and interaction with GAGs, including chondroitin sulfate, hyaluronic acid, and heparan sulfate, present in high quantities in the lungs of patients with CF. Bronchoalveolar lavage fluid was collected from patients with CF (n = 28), non-CF controls (n = 14), and patients with chronic obstructive pulmonary disease (n = 12). Increased levels of IL-8 and reduced concentrations of IL-18 were detected in bronchial samples obtained from CF individuals. The low level of IL-18 was not a defect in IL-18 production, as the pro- and mature forms of the molecule were expressed and produced by CF epithelial cells and monocytes. There was, however, a marked competition between IL-8 and IL-18 for binding to GAGs. A pronounced loss of IL-18 binding capacity occurred in the presence of IL-8, which displaced IL-18 from these anionic-matrices, rendering the cytokine susceptible to proteolytic degradation by neutrophil elastase. As a biological consequence of IL-18 degradation, reduced levels of IL-2 were secreted by Jurkat T lymphocytes. In conclusion, a novel mechanism has been identified highlighting the potential of IL-8 to determine the fate of other inflammatory molecules, such as IL-18, within the inflammatory milieu of the CF lung.
Physicochemical studies on the copper(ii) binding by glycated collagen telopeptides (2015)

Emerging evidence indicates that levels of advanced glycation end-products (AGEs) correlate with age- and diabetes-related organ damage and may play a causative role in such damage. Increased chelation of Cu(II) ions appears to play an important role in this process, however, the precise relationship between formation of AGEs and accumulation of Cu(II) is yet to be determined. The interaction between AGEs and Cu(II) has been investigated using a collagenous peptide that has been site-specifically modified by a key AGE. Potentiometric titration showed that introduction of this AGE increased the capacity of the host-peptide to bind Cu(II). This result was confirmed by mass spectrometric characterisation of the AGE-modified peptide-Cu(II) system.
SENDD: Sparse Efficient Neural Depth and Deformation for Tissue Tracking (2023)

Deformable tracking and real-time estimation of 3D tissue motion is essential to enable automation and image guidance applications in robotically assisted surgery. Our model, Sparse Efficient Neural Depth and Deformation (SENDD), extends prior 2D tracking work to estimate flow in 3D space. SENDD introduces novel contributions of learned detection, and sparse per-point depth and 3D flow estimation, all with less than half a million parameters. SENDD does this by using graph neural networks of sparse keypoint matches to estimate both depth and 3D flow anywhere. We quantify and benchmark SENDD on a comprehensively labelled tissue dataset, and compare it to an equivalent 2D flow model. SENDD performs comparably while enabling applications that 2D flow cannot. SENDD can track points and estimate depth at 10fps on an NVIDIA RTX 4000 for 1280 tracked (query) points and its cost scales linearly with an increasing/decreasing number of points. SENDD enables multiple downstream applications that require estimation of 3D motion in stereo endoscopy.
The Reaction in the Formation of Polyionic Polymer Complexes (1972)

イオン席が主鎖にある積層型ポリカチオン重合体とポリスチレンスルホン酸ナトリウムからポリイオン錯合体(PIC)を生成する反応を検討し,ペンダント型ポリカチオンからなるPICと比較考察した。水溶液中のPIC生成反応は化学量論的にきわめてすみやかに進行し,PICは系中に沈殿する。反応生成物の赤外吸収スペクトルがアニナンとカチオンを等モルに混合したものに-致することと,溶解性が成分のポリイオン重合体といちじるしく異なることから,イオン橋かけした網状構造が示唆される。ポリカチオンとして積層型ポリカチオン重合体を用いた場合,生成PICに過剰のポリアニオンを添加すると再溶解現象が観察される。これは疎水部で保護されていない錯体の結合部に過剰のポリアニオンが静電的に相互作用して,塩型結合を弱めるからと考えられる。錯体の溶解挙動は成分とするポリカチオンの構造によって相違し,三成分溶媒系(水-有機溶媒-中性塩)に対する溶解曲線は,ペンダント型ポリカチオンを成分とする錯体にくらべ積層型ではかなり溶解領域が小さい。
Volumetric bond-selective imaging and spectroscopic analysis of cellular Tau fibrils through a fluorescence-guided computational chemical microscope (Conference Presentation) (2023)

To uncover the pathological mechanism of neurodegenerative diseases, simple and cost-effective analytical methods are highly desirable to obtain biochemistry and morphology information on Tau protein aggregation. Here, we demonstrate the fluorescence-guided computational mid-infrared photothermal microscope, termed Fluorescence-guided Bond-selective Intensity Diffraction Tomography (FBS-IDT). FBS-IDT enables hyperspectral 3D bond-selective refractive index map recovery on Tau fibrils in cells. Depth-resolved mid-infrared fingerprint spectra extraction and related secondary protein structure analysis are demonstrated. 3D reconstruction of β sheet in Tau fibril is realized mainly based on the mid-infrared photothermal effects.
ChemInform Abstract: Effect of Additives on Catalytic Activity of 12‐Molybdophosphoric Acid for Methacrolein Oxidation. (1990)

Abstract It is found that the addition of As 5+ to H 3 PMo 12 O 40 improves the selectivity to methacrylic acid (MAA) but lowers the conversion efficiency of the catalyst, whereas addition of Cu 2+ improves the catalytic activity but lowers the MAA selectivity.
Hemolytic Effect of Therapeutic Drugs (1962)

FOR MANY YEARS hemolytic reactions have been recognized as hazards which accompany the administration of certain classes of therapeutic agents including sulfonamides, sulfones, benzene, and quinoline derivatives. Although some episodes of drug-induced hemolysis can be attributed to hypersensitivity, most reactions cannot be explained by an immune mechanism. In 1941 Emerson, Ham, and Castle suggested that some hemolytic drugs and chemical compounds, or their degradation products, functioned as oxidants in reversible oxidation-reduction systems in the erythrocytes and, thereby, caused methemoglobin formation, increased osmotic fragility, and hemolysis. Recently Jandl et al., showed, in vitro, that oxidant drugs capable of acting as redox intermediates oxidize hemoglobin, first reversibly to methemoglobin and eventually irreversibly to oxidation products resembling Heinz bodies; they postulated that administration of these drugs enhanced the oxidation of hemoglobin and other vital cellular components in vivo and, thus, interfered with cellular integrity. In 1926 Cordes reported the occurrence of hemolytic anemia in
ChemInform Abstract: Electronic Excitation and n‐Electron Interaction in Borazine. (1986)

Abstract The extent of n‐electron interaction in ‐borazine, B 3 N 3 H 6 , has been investigated by comparing its spectral properties (valence‐shell and inner‐shell electron energy loss spectra, MCD, photoelectron and electron transmission spectra) with those of benzene and cyclohexane.
Time resolved measurement of dynamic micro-magnetic field by stroboscopic electron beam tomography (1992)

Dynamic behavior of magnetic recording head fields has a significant influence on the writing/reading speed of magnetic recording systems. We previously introduced stroboscopic electron beam tomography, which could measure the three-dimensional dynamic magnetic field distribution close to the head surface. At this time, we introduce an improved version of the electron beam tomography system. With the new system, the timing relationship between the driving current of recording heads and the generated magnetic fields can be measured with l ns timing resolution.
Translabyrinthine vestibular schwannoma resection with simultaneous cochlear implantation (2017)

Single-stage cochlear implantation and translabyrinthine tumor resection is a feasible and safe option to consider for auditory rehabilitation in rare situations.
Precore-mediated inhibition of hepatitis B virus progeny DNA synthesis (1993)

The capacities to induce the synthesis of hepatitis B virus (HBV) unit-length DNA were compared for two HBV DNAs with an overall sequence diversity of about 10%. They had been cloned from serum (DNA2) and from a hepatocellular carcinoma (DNA4), respectively. As a major difference, DNA4 carries a translational stop signal preventing the synthesis of precore protein. Progeny DNA yields obtained after transfection with respective pregenome transcription units allocated DNA2 to a low-replicator and DNA4 to a high-replicator phenotype. Cotransfection of DNA2 interfered with progeny DNA synthesis induced by DNA4. By mutual exchange of restriction fragments, the region on the viral genome responsible for the differing replicator phenotypes was confined to a sequence comprising the 3'-terminal part of the X gene, core promoter, encapsidation signal epsilon, precore/core gene, and 5'-terminal part of the pol gene. Point mutations in DNA2 abolishing proper expression of the precore gene strongly enhanced the yield of progeny DNA, whereas cotransfection of a precore expression plasmid with DNA4 or with the mutated DNA2 substantially lowered the amount of progeny DNA. Hence, precore expression acts as an inhibitory principle for HBV replication. The same stop mutation as in DNA4 has been found to arise frequently in virus carriers. Loss of precore expression and concomitant conversion to a more severe hepatitis, as observed in the course of a chronic infection, thus can be explained by a relaxation of replication-level control.
Surface recombination in ZnO nanorods grown by chemical bath deposition (2008)

Vertically well-aligned ZnO nanorods on Si substrates were prepared by a two-step chemical bath deposition (CBD) method. The optical properties of the grown ZnO nanorods were investigated by time resolved photoluminescence spectroscopy. It was found that the effective decay time of the near bandgap recombination in the CBD grown ZnO nanorods strongly depends on the diameter of the ZnO nanorods. Typically, the decay curves obtained from these ZnO nanorods show a combination of two exponential decays. The experimental results show that the fast exponential decay is related to the surface recombination and the slow decay is related to the “bulk” decay. The measured decay time of the effective surface recombination decreases with decreasing diameter, while the bulk decay time remains unchanged. The results also show that an annealing treatment around 500 °C significantly reduces the surface recombination rate. A simple carrier and exciton diffusion equation is also used to determine the surface recombination velocity, which results in a value between 1.5 and 4.5 nm/ps.
Design, Surface Treatment, Cellular Plating, and Culturing of Modular Neuronal Networks Composed of Functionally Inter-connected Circuits (2015)

The brain operates through the coordinated activation and the dynamic communication of neuronal assemblies. A major open question is how a vast repertoire of dynamical motifs, which underlie most diverse brain functions, can emerge out of a fixed topological and modular organization of brain circuits. Compared to in vivo studies of neuronal circuits which present intrinsic experimental difficulties, in vitro preparations offer a much larger possibility to manipulate and probe the structural, dynamical and chemical properties of experimental neuronal systems. This work describes an in vitro experimental methodology which allows growing of modular networks composed by spatially distinct, functionally interconnected neuronal assemblies. The protocol allows controlling the two-dimensional (2D) architecture of the neuronal network at different levels of topological complexity. A desired network patterning can be achieved both on regular cover slips and substrate embedded micro electrode arrays. Micromachined structures are embossed on a silicon wafer and used to create biocompatible polymeric stencils, which incorporate the negative features of the desired network architecture. The stencils are placed on the culturing substrates during the surface coating procedure with a molecular layer for promoting cellular adhesion. After removal of the stencils, neurons are plated and they spontaneously redirected to the coated areas. By decreasing the inter-compartment distance, it is possible to obtain either isolated or interconnected neuronal circuits. To promote cell survival, cells are co-cultured with a supporting neuronal network which is located at the periphery of the culture dish. Electrophysiological and optical recordings of the activity of modular networks obtained respectively by using substrate embedded micro electrode arrays and calcium imaging are presented. While each module shows spontaneous global synchronizations, the occurrence of inter-module synchronization is regulated by the density of connection among the circuits.
Time-reversal mirrors and rough surfaces: Experiment (1999)

A novel acoustic time-reversal technique has been tested for determining the surface-height autocorrelation function and rms height of rough surfaces. A time-reversal mirror (TRM) was used to insonify periodically and “randomly” rough surfaces of otherwise flat samples immersed in water. The standard use of the TRM is as follows: transmit an initial planar pulse, record the signals at each array element, digitally time reverse each signal, and then retransmit the time-reversed signal. As expected from time-reversal symmetry, one approximately recovers the incident planar pulse after the reflection of the retransmitted wave. The new technique is a simple modification of this procedure. Namely, as before, we record and time reverse the initial reflection. However, we next translate the transducer a fixed distance parallel to the surface before retransmitting. For very small displacements, little change is observed in the TRM’s signal. For larger and larger translations, the TRM’s signal decorrelates, i.e., it less and less resembles the incident pulse. The signal’s decorrelation as a function of displacement is directly related to the autocorrelation function of the rough surface—within the limits set by the system’s point response function. The TRM was used both in reflection mode and in transmission mode. Samples consisted of “randomly” rough surfaces of metal and plastic plates, as well as metal plates machined to have periodically rough surfaces. Evidence is provided that the time-reversal mirror is sensitive to the surface-height autocorrelation and, in favorable cases, determines the autocorrelation function and rms height.