gebhart/patrepeval huggingface dataset:
Differentiation of linear and branched hydrocarbons by a fluorinated polyimide film (1995)

This paper described the use of a polyimide film on a surface acoustic wave device for chemical sensing of hydrocarbons. Infrared studies of the polymer film during analyte dosing indicated preferential adsorption of linear hydrocarbons into the film. This work was supported by the United States Department of Energy.
Hemifistularin 3: a degraded peptide or biogenetic precursor? Isolation from a sponge of the order verongida from the coral sea or generation from base treatment of 11-oxofistularin 3 (1993)

Hemifistularin 3 10, contained in a new species of sponge of the family Aplysinellidae, order Verongida, from the Coral Sea, corresponds to the right half of 11-oxofistularin 3 6, also contained in this sponge, and from which it can be obtained in a peculiar base-catalysed degradation. This raises the question of whether or not hemifistularin 3 is the first example of a biogenetically degraded peptide, or rather an elaborated biogenetic precursor, in sponges of the order Verongida. The new compounds 19-deoxyfistularin 3 8 and 19-deoxy-11-oxofistularin 3 9 have also been isolated from the same sponge.
Change of Intrapulmonary Shunt after Liver Transplantation in Irreversible Acute or Chronic Liver Diseases (2003)

Background and Objectives:The intrapulmonary shunt, after a liver transplantation, is expected to improve, but the frequency, and predictors, of improvement are not well known. We studied the frequency of the improvement in the intrapulmonary shunt, and the relation between this improvement and the clinical parameters, using contrast echocardiography in liver transplant candidates. Subjects and Methods:Preoperative and postoperative contrast echocardiography, with intravenous agitated saline, was performed in 25 liver transplant candidates (M:F=19: 6, mean age=46±10). The extent of the intrapulmonary shunt was semi-quantitatively assessed on a grade scale from 0 to 4+, according to the degree of appearance of the contrast in the left heart chambers. The etiology of the underlying chronic liver disease, Child-Pugh classification scores, pulmonary function tests and arterial blood gas analyses were all evaluated. The change in the shunt grade after the liver transplantation, and the association of these changes, with clinical parameters, were also evaluated. Results:Twenty-four (96%) of the 25 patients showed positive results for the intrapulmonary shunt on preoperative contrast echocardiography. At follow up, the shunt was visible in only 5 (21%) patients. All 24 patients whose preoperative echocardiography revealed a positive intrapulmonary shunt showed an improvement in the intrapulmonary shunt after the liver transplantation. There was a significant correlation between the improvements in the shunt and the Child-Pugh classification scores (r=0.59, p=0.02). Conclusion:Contrast echocardiography is a feasible, noninvasive, method for the detection of changes in the intrapulmonary shunt before and after a liver transplantation, and the intrapulmonary shunt is improved after a liver transplantation in most patients. (Korean Circulation J 2003;33 (3):212-217)
Computer-aided design of clustered-dot color screens based on a human visual system model (2002)

We address the problem of optimal periodic clustered-dot color-screen design. In traditional clustered-dot color screening, the screen for each colorant is rotated to a different angle relative to the others. If the angles are not carefully chosen, visible moire and rosette artifacts may appear These artifacts primarily result from the interaction of the periodic structures associated with the halftone screens of different colorants. Registration errors can also introduce unwanted artifacts in the screened images. Using lattice theory and a model for the perceived rendered halftone, we present a systematic method for designing moire- and rosette-free clustered-dot color screens for discrete-raster color systems. We also investigate strategies for choosing the periodicities so that the resulting screen is robust to registration errors.
Baseline Corticosteroid Use and Corticosteroid-Free Clinical Remission in Crohn’s Disease Patients Treated With Certolizumab Pegol in the PRECiSE 2 Trial (2012)

The efficacy of certolizumab pegol as a corticosteroid-sparing agent has not been thoroughly evaluated. A post hoc analysis evaluated this question in a 26-week randomized, double-blind, placebo-controlled trial performed in adults with moderate to severe Crohn’s disease who were stratified by corticosteroid use at baseline (PRECiSE 2 trial, NCT00152425).1 Adult patients (N = 668) with active Crohn’s disease (Crohn’s Disease Activity Index [CDAI] 220-450) were enrolled and received open-label induction therapy with certolizumab pegol (400 mg administered subcutaneously at Weeks 0, 2, and 4). Patients who responded at Week 6 to certolizumab pegol induction therapy (the intent-to-treat [ITT] population) were randomized to continuous therapy with 400 mg certolizumab pegol or placebo every 4 weeks through Week 24, with follow-up at Week 26. While corticosteroid tapering was not mandatory, the number of patients eligible to taper corticosteroids was evaluated, along with the number of patients that initiated corticosteroid tapering between Weeks 8 and 12. Patients who, in the investigator’s opinion, showed a clinical response 8-12 weeks from their first injection of certolizumab pegol were eligible to taper corticosteroids. The decision to initiate corticosteroid tapering was at the discretion of the investigator. Corticosteroid-free clinical remission (defined as a CDAI score of ≤150 and discontinuation of all oral steroids) was evaluated in the certolizumab pegol arm at Week 26 using a last observation carried forward imputation. Among 215 patients with a response to certolizumab pegol induction therapy at Week 6 (the ITT population in the certolizumab pegol arm), 34% (74/215) were treated with corticosteroids at baseline. 70% (52/74) of the patients in the certolizumab pegol arm on corticosteroids at baseline were eligible to taper corticosteroid treatment. Of these eligible patients, 87% (45/52) initiated a taper of their corticosteroid treatment. 31% (14/45) of the population on corticosteroids at baseline that initiated a taper were in a corticosteroid-free clinical remission at Week 26. Additionally, 38% (82/215) of the ITT population and 49% (68/140) of the population not on corticosteroids at baseline were in corticosteroidfree clinical remission at Week 26. Approximately one third of patients on corticosteroids at baseline were able to achieve clinical remission and successfully taper corticosteroids with certolizumab pegol in the PRECiSE 2 trial. Further investigation is warranted regarding the significant proportion of patients who were able to taper off of corticosteroids while on maintenance therapy with certolizumab pegol, as well as the reasons that some patients did not initiate a corticosteroid taper when they were eligible.
A light‐activated method for repair of corneal surface defects (2011)

PTB is a superior method for securing AM over OSD with improved wound healing compared to sutures.
The Effect of Frequency Doubled Double Pulse Nd:YAG Laser Fiber Proximity to the Target Stone on Transient Cavitation and Acoustic Emission (2007)

While bubble size was noted to increase with a larger stone-to-fiber distance using the holmium laser, to consistently generate cavitation bubbles and shock waves using the FREDDY laser the laser fiber should be operated within 3.0 mm of the target stone. These findings have significant implications during clinical laser stone fragmentation.
Semantic segmentation with a sparse convolutional neural network for event reconstruction in MicroBooNE (2021)

We present the performance of a semantic segmentation network, sparsessnet, that provides pixel-level classification of MicroBooNE data. The MicroBooNE experiment employs a liquid argon time projection chamber for the study of neutrino properties and interactions. sparsessnet is a submanifold sparse convolutional neural network, which provides the initial machine learning based algorithm utilized in one of MicroBooNEs ${\ensuremath{\nu}}_{e}$-appearance oscillation analyses. The network is trained to categorize pixels into five classes, which are reclassified into two classes more relevant to the current analysis. The output of sparsessnet is a key input in further analysis steps. This technique, used for the first time in liquid argon time projection chambers data and is an improvement compared to a previously used convolutional neural network, both in accuracy and computing resource utilization. The accuracy achieved on the test sample is $\ensuremath{\ge}99%$. For full neutrino interaction simulations, the time for processing one image is $\ensuremath{\approx}0.5\text{ }\text{ }\mathrm{sec}$, the memory usage is at 1 GB level, which allows utilization of most typical CPU worker machine.
Intelligible Language Modeling with Input Switched Affine Networks (2016)

The computational mechanisms by which nonlinear recurrent neural networks (RNNs) achieve their goals remains an open question. There exist many problem domains where intelligibility of the network model is crucial for deployment. Here we introduce a recurrent architecture composed of input-switched affine transformations, in other words an RNN without any nonlinearity and with one set of weights per input. We show that this architecture achieves near identical performance to traditional architectures on language modeling of Wikipedia text, for the same number of model parameters. It can obtain this performance with the potential for computational speedup compared to existing methods, by precomputing the composed affine transformations corresponding to longer input sequences. As our architecture is affine, we are able to understand the mechanisms by which it functions using linear methods. For example, we show how the network linearly combines contributions from the past to make predictions at the current time step. We show how representations for words can be combined in order to understand how context is transferred across word boundaries. Finally, we demonstrate how the system can be executed and analyzed in arbitrary bases to aid understanding.
COLLINARUS: collection of image-derived non-linear attributes for registration using splines (2009)

ABSTRACT We present a new method for fully automatic non-rigid registration of multimodal imagery, including structuraland functional data, that utilizes multiple texutral feature images to drive an automated spline based non-linearimage registration procedure. Multimodal image registration is signicantly more complicated than registrationof images from the same modality or protocol on account of diculty in quantifying similarity between dierentstructural and functional information, and also due to possible physical deformations resulting from the dataacquisition process. The COFEMI technique for feature ensemble selection and combination has been previouslydemonstrated to improve rigid registration performance over intensity-based MI for images of dissimilar modali-ties with visible intensity artifacts. Hence, we present here the natural extension of feature ensembles for drivingautomated non-rigid image registration in our new technique termed Collection of Image-derived Non-linearAttributes for Registration Using Splines (COLLINARUS). Qualitative and quantitative evaluation of the COL-LINARUS scheme is performed on several sets of real multimodal prostate images and synthetic multiprotocolbrain images. Multimodal (histology and MRI) prostate image registration is performed for 6 clinical data setscomprising a total of 21 groups of in vivo structural (T2-w) MRI, functional dynamic contrast enhanced (DCE)MRI, and ex vivo WMH images with cancer present. Our method determines a non-linear transformation toalign WMH with the high resolution in vivo T2-w MRI, followed by mapping of the histopathologic cancer extentonto the T2-w MRI. The cancer extent is then mapped from T2-w MRI onto DCE-MRI using the combinednon-rigid and ane transformations determined by the registration. Evaluation of prostate registration is per-formed by comparison with the 3 time point (3TP) representation of functional DCE data, which provides anindependent estimate of cancer extent. The set of synthetic multiprotocol images, acquired from the BrainWebSimulated Brain Database, comprises 11 pairs of T1-w and proton density (PD) MRI of the brain. Following theapplication of a known warping to misalign the images, non-rigid registration was then performed to recover theoriginal, correct alignment of each image pair. Quantitative evaluation of brain registration was performed bydirect comparison of (1) the recovered deformation eld to the applied eld and (2) the original undeformed andrecovered PD MRI. For each of the data sets, COLLINARUS is compared with the MI-driven counterpart of theB-spline technique. In each of the quantitative experiments, registration accuracy was found to be signicantly(p< 0.05) for COLLINARUS compared with MI-driven B-spline registration. Over 11 slices, the mean absoluteerror in the deformation eld recovered by COLLINARUS was found to be 0.8830 mm.Keywords: quantitative imageanalysis, magneticresonance, whole-mounthistology, imageregistration,prostate,cancer, B-splines, COFEMI, hierarchical, non-rigid
Accuracy of a radiographic stitching technique to measure tibial plateau angle in large and giant breed dogs (2014)

This novel digital stitching method provides an alternative technique for accurately measuring TPA utilizing a stifle-centred radiograph that may be useful when traditional TPLO radiographs are difficult to obtain. This may be particularly useful in large and giant breed dogs because collimation to include the entire tibial length can preclude proper centring of the radiographic beam over the stifle.
Toward Biocomposites Recycling: Localized Interphase Degradation in PCL-Cellulose Biocomposites and its Mitigation (2020)

Recyclable biocomposites based on degradable polymer systems and cellulosic plant fibers are attractive in a sustainable society, because of enhanced polymer properties and also from an end-of-life perspective. Improved understanding is required for how the degradable polymer matrix is affected during compounding in addition to effects from the cellulosic fiber structure and its chemical nature. This work reveals that a poly(ε-caprolactone) matrix undergoes localized, heterogeneous polymer degradation in the fiber-matrix interphase region during melt-compounding. The extent of localized degradation correlates with the initial moisture content in the wood cellulose fiber, where moisture content is controlled by different fiber modification methods by PCL-grafting. As an effect, high moisture content results in a destabilized and degraded fiber-matrix interphase. This was found through careful analysis of how the polymer population changed after compounding, using two different methods: molar mass distribution from SEC and end-group concentration from NMR. The results are important not only with regard to fiber/matrix interface compatibility but also to understand fiber modification for improved biocomposites recycling.
Estimating Acoustic Direction of Arrival Using a Single Structural Sensor on a Resonant Surface (2023)

The direction of arrival (DOA) of an acoustic source is a signal characteristic used by smart audio devices to enable signal enhancement algorithms. Though DOA estimations are traditionally made using a multi-microphone array, we propose that the resonant modes of a surface excited by acoustic waves contain sufficient spatial information that DOA may be estimated using a singular structural vibration sensor. In this work, sensors are affixed to an acrylic panel and used to record acoustic noise signals at various angles of incidence. From these recordings, feature vectors containing the sums of the energies in the panel’s isolated modal regions are extracted and used to train deep neural networks to estimate DOA. Experimental results show that when all 13 of the acrylic panel’s isolated modal bands are utilized, the DOA of incident acoustic waves for a broadband noise signal may be estimated by a single structural sensor to within ±5° with a reliability of 98.4%. The size of the feature set may be reduced by eliminating the resonant modes that do not have strong spatial coupling to the incident acoustic wave. Reducing the feature set to the 7 modal bands that provide the most spatial information produces a reliability of 89.7% for DOA estimates within ±5° using a single sensor.
Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins (2008)

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications (PTMs). Although PTMs are a critical aspect of cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit (DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium, Desulfovibrio desulfuricans G20, also showed similar +42 Da modifications in the same pathway. Here, we discuss our methods and implications of potential trimethylation in the D. vulgaris sulfate reduction pathway.
Cyanine Masking: A Strategy to Test Functional Group Effects on Antibody Conjugate Targeting (2022)

Conjugates of small molecule and antibodies are broadly employed diagnostic and therapeutic agents. Appending a small molecule to an antibody often significantly impacts the properties of the resulting conjugate. Here we detail a systematic study investigating the effect of various functional groups on the properties of antibody-fluorophore conjugates. This was done through the preparation and analysis of a series of masked heptamethine cyanines (CyMasks) bearing amides with varied functional groups. These were designed to exhibit a broad range of physical properties, and include hydrophobic (-NMe2), pegylated (NH-PEG-8 or NH-PEG-24), cationic (NH-(CH2)2NMe3+) anionic (NH-(CH2)2SO3-), and zwitterionic (N-(CH2)2NMe3+)-(CH2)3SO3-) variants. The CyMask series was appended to tumor targeting monoclonal antibodies (mAbs) and analyzed for effects on tumor targeting, clearance and non-specific organ uptake. Among the series, zwitterionic and cationic dye conjugates showed the highest tumor-to-background ratio (TBR), although the latter also exhibited an elevated liver-to-background ratio (LBR). Overall, these studies provide a strategy to test the functional group effects and suggest that zwitterionic substituents are an attractive strategy to mask hydrophobic payloads, with the potential to improve the properties of bioconjugates in vivo.
Clinical leadership: the challenge of making the most of doctors in management (2011)

The need to develop the leadership and management capability of clinicians is deemed fundamental to address the cost and quality issues associated with health-care provision. The challenge facing the NHS is how best to bring this about.
Chemical and Electrochemical Insertion of Lithium into Two Allotropic Varieties of NbPO5 (2002)

The chemical and electrochemical insertions of lithium into α-NbPO5 (P4/n) and β-NbPO5 (P21/c) are compared. Both materials were evaluated as positive electrodes in lithium-type rechargeable batteries through galvanostatic, GITT, and PITT cycling modes within various voltage windows. They present distinct behaviors with regard to lithium insertion. β-LixNbPO5 rapidly and reversibly uptakes lithium leading to a sustained capacity of 90−120 mA·h/g (i.e., operating to the Nb5+/Nb4+ couple) for more than 100 cycles at ∼2 V vs Li+/Li. This reversibility was confirmed by in situ X-ray diffraction in the range 0 ≤ x ≤ 0.7 that additionally revealed a series of single- and two-phase insertion mechanisms. On the other hand, α-LixNbPO5 displays an insertion plateau at ∼1.7 V vs Li+/Li indicative of a two-phase process that was found to be poorly reversible. Both materials, when discharged at voltages lower than 1 V, present irreversible reactions with complete amorphization.
Second harmonic generation in quantum wells enhanced via coupling to metamaterials (2014)

We experimentally demonstrate efficient second harmonic generation using a metamaterial-coupled III-V heterostructure at mid-infrared wavelengths. Our approach exploits the large second-order nonlinear susceptibilities of intersubband transitions and the near-field enhancement and polarization manipulation flexibility offered by metamaterial resonators.
Multifunctional Block Copolymers Based on Styrene Derivatives (2009)

Abstract Several functionalized block copolymers based on polystyrene with considerably different block polarities have been prepared using controlled radical polymerization techniques (NMRP, RAFT). The target polymers, having hydroxy, alkyne or amine functionalities in at least one block were characterized by techniques like NMR, GPC and DSC to verify structure, molar masses, molecular weight distributions and thermal properties. With the example of partly protected hydroxystyrene based block copolymers, regular structured film surfaces could be created and were shown to be converted into homogeneous polymer surfaces by applying heat as external trigger. With alkyne functionalized block copolymers, modifications with objects of varying sizes were carried out, employing the 1,3‐dipolar cycloaddition of alkynes with azides. Once again, the “click approach” proved its high efficiency as the reactions proceeded completely even with objects of high steric demand. Studying the influence on the macromolecular architecture, we found a strong alteration of glass transition temperatures for the compared polymer materials, indicating a bracing of the chains due to steric hindrance between the bulky side objects.
Cardiogenic Induction of Pluripotent Stem Cells Streamlined Through a Conserved SDF-1/VEGF/BMP2 Integrated Network (2010)

Transcriptome-wide dissection of a conserved progenitor profile thus revealed functional highways that coordinate cardiogenic maturation from a pluripotent ground state. Validating the bioinformatics algorithm established a strategy to rationally modulate cell fate, and optimize stem cell-derived cardiogenesis.