gebhart/patrepeval huggingface dataset:
Design of Form Birefringent Computer Generated Holograms (1997)

Form birefringence is a well known effect of subwavelength periodic microstructures. The electric fields parallel to the grating grooves (TE polarization) and perpendicular to the grating grooves (TM polarization) need to satisfy different boundary conditions, resulting in different effective refractive indices for TE and TM polarized waves. 1 . Many researchers have demonstrated this effect in the far infrared (IR) region. 2 , 3 Recently, with the help of the advances in nanofabrication, 200 nm period gratings were fabricated in GaAs substrate showing strong form birefringence in near IR. 4 Furthermore, these results were found to be in agreement with the numerical simulation results obtained using rigorous couple wave analysis (RCWA). 5 , 6 Chen et. al. have demonstrated a polarization insensitive diffractive optical element using two dimensional subwavelength periodic microstructures. 7 Due to its unique properties, form birefringent material is suitable in constructing novel birefringent computer generated holograms (BCGHs). Such BCGHs are general purpose diffractive optical elements (DOEs) that have independent impulse responses for the two orthogonal polarizations 8 , 9 . Aoyama et. al. have demonstrated a grating beam splitting polarizer using subwavelength grating fabricated in photo resist. 10 The polarization contrast ratios, defined as the ratio of intensities obtained under two orthogonal polarizations at the designed diffraction order, were about 6:1 and 3:1 for the zeroth and first diffraction orders, respectively. In contrast, our approach is based on creating artificially a birefringent layer using a high spatial frequency grating (HSFG) which is then modulated by a large period diffractive structure similar to conventional DOEs. We call this approach form birefringent CGH (FBCGH). In our preliminary work 11 we have designed, fabricated and experimentally evaluated a novel FBCGH that implements a diffractive polarization beam splitter. In this manuscript we describe a general design method of FBCGH and discuss specific design examples.
1720 Detection of CMP Defects with Electrostatic Force Microscopy (2012)

We investigated surface potential with electrostatic force microscopy (EFM) to analyze the relationship between surface potential and chemical mechanical planarization (CMP). We have succeeded to detect the non-visual defects (NVD) such as organic (surfactant) and complex residues (Cu-BTA) Scratches and polishing non-uniformity those were not detected in topographic image were also cleary seen in surface potential images EFM metrology is markedly useful for evaluating the relationship between surface potential and defect generation during CMP.
Digital Rock Technology for Quantitative Prediction of Acid Stimulation Efficiency in Carbonates (2015)

Abstract The complex pore structure and porosity in carbonate rocks have a strong influence on the stimulation efficiency of the acid. Recently, it was shown that nondestructive tracers can be used to predict pore volume of acid to breakthrough (PVBT) for both plain and emulsified acids [1, 2]. The present study explores the use of digital rock technology to simulate tracer injection in carbonate rocks. The accuracy of the digital rock method is compared to the laboratory measured values for five carbonate rocks of different porosity types and heterogeneity scales. The digital rock simulations are performed by an industry-unique direct hydrodynamic pore flow simulator that operates on pore geometries from digital rock models obtained from 3D scanning electron microscope images. The pressure-volume-temperature and rheological models used in the simulator represent real treatment and reservoir fluids. Fluid-solid interactions are introduced using distributed microscale wetting properties. The simulator uses the density functional approach applied to the hydrodynamics of complex systems. The simulations are used to calculate a measure of the accessible rock volume which is then used to predict the acid response. Conventional laboratory testing methods require large volumes of formation rocks for optimization of acid type and volume and it often prohibitively expensive. The digital rock methodology has the potential of significantly reducing the required volume of formation cores, which could be an enabler for more frequent carbonate porosity specific stimulation optimization. The present study explores the limits of its applicability.
Decoding the Cardiac Message (2011)

Our understanding of the molecular underpinnings of cardiac development and stress-response has progressed non-linearly over the past 40 years. Preliminary observations that cardiac RNA content inc...
Analysis of the thylakoid outer surface. Coupling factor is limited to unstacked membrane regions. (1976)

The structure of the spinach thylakoid outer surface has been examined by deepetching, a technique which exposes the true surfaces of biological membranes by sublimination of frozen dilute buffer. The membrane surface is covered with large (150 A average diameter) and small (90 A average diameter) particles. Approximately 30% of the large particles can be removed under conditions reported to selectively remove carboxydismutase from the membrane surface. The remaining large particles can be removed only under conditions which cause a loss of coupling factor activity. When purified coupling factor is readded to membranes from which all coupling factor activity has been removed, large particles reappear, indicating that they represent coupling factor molecules. Since the number of particles and the amount of ATPase activity in the reconstituted and control membranes were the same, coupling factor molecules may be attached to specific binding sites. Analysis of antibody labeling experiments, enzyme assays, and experiments involving the unstacking and restacking of thylakoid membranes indicate that coupling factor is excluded from regions of membrane stacking (grana) and is present only in unstacked membrane regions. The exclusion of coupling factor from grana, which are known to be centers of intense photosynthetic activity, strongly suggests that the mechanism coupling electron transport to photophosphorylation is indirect. In addition to the large and small particles, in some cases regularly spaced ridges are visible on the outer surface after unstacking. Coupling factor binding sites seem to be excluded from regions where these structures occur.
A predictive algorithm for runway overrun protection (2017)

Algorithms to make an aircraft aware of overrunning a runway on landing and alert it are proposed. These algorithms use a predictive model based on the minimization of the generalized work functional, a detailed description of the affecting factors, and the control scenario in the final phase of the approach to landing and on landing refined in real time.
Oligomerization of Uniquely Folded Mini-Protein Motifs:  Development of a Homotrimeric ββα Peptide (2001)

The discovery of a discretely folded homotrimeric betabetaalpha motif (BBAT1) was recently reported (J. Am. Chem. Soc. 2001, 123, 1002-1003). Herein the design, synthesis, and analysis of a small library of peptides which led to the isolation of BBAT1 is described. betabetaalpha peptides based on the monomeric sequence of BBA5 (Folding Des. 1998, 120, 95-103) were synthesized to include the anthranilic acid/nitrotyrosine fluorescence quenching pair to rapidly detect interpeptide association. In the first generation of peptides synthesized, truncations in the loop region connecting the beta-hairpin to the alpha-helix revealed that a two-residue deletion in the loop promoted an interpeptide association as detected by fluorescence quenching. An additional library of 22 loop-truncated betabetaalpha peptides was subsequently synthesized to include a variety of sequence mutations in an effort to enhance the observed peptide-peptide binding. From the fluorescence quenching screen, peptide B2 was found to possess the strongest fluorescence-quenching response, indicative of a strong peptide-peptide association. Due the poor solubility of peptide B2, the S-methylated cysteine at position 9 in the loop was substituted with a glycine to generate peptide BBAT1 which possessed greatly improved water solubility and formed discrete trimers. The successful design of this oligomeric betabetaalpha structure will likely aid the design of more complex alpha-beta superstructures and further our understanding of the factors controlling protein-protein interactions at alpha-beta protein interfaces.
SUMO1 Affects Synaptic Function, Spine Density and Memory (2015)

Abstract Small ubiquitin-like modifier-1 (SUMO1) plays a number of roles in cellular events and recent evidence has given momentum for its contributions to neuronal development and function. Here, we have generated a SUMO1 transgenic mouse model with exclusive overexpression in neurons in an effort to identify in vivo conjugation targets and the functional consequences of their SUMOylation. A high-expressing line was examined which displayed elevated levels of mono-SUMO1 and increased high molecular weight conjugates in all brain regions. Immunoprecipitation of SUMOylated proteins from total brain extract and proteomic analysis revealed ~95 candidate proteins from a variety of functional classes, including a number of synaptic and cytoskeletal proteins. SUMO1 modification of synaptotagmin-1 was found to be elevated as compared to non-transgenic mice. This observation was associated with an age-dependent reduction in basal synaptic transmission and impaired presynaptic function as shown by altered paired pulse facilitation, as well as a decrease in spine density. The changes in neuronal function and morphology were also associated with a specific impairment in learning and memory while other behavioral features remained unchanged. These findings point to a significant contribution of SUMO1 modification on neuronal function which may have implications for mechanisms involved in mental retardation and neurodegeneration.
ERA: Entity Relationship Aware Video Summarization with Wasserstein GAN (2021)

Video summarization aims to simplify large scale video browsing by generating concise, short summaries that diver from but well represent the original video. Due to the scarcity of video annotations, recent progress for video summarization concentrates on unsupervised methods, among which the GAN based methods are most prevalent. This type of methods includes a summarizer and a discriminator. The summarized video from the summarizer will be assumed as the final output, only if the video reconstructed from this summary cannot be discriminated from the original one by the discriminator. The primary problems of this GAN based methods are two folds. First, the summarized video in this way is a subset of original video with low redundancy and contains high priority events/entities. This summarization criterion is not enough. Second, the training of the GAN framework is not stable. This paper proposes a novel Entity relationship Aware video summarization method (ERA) to address the above problems. To be more specific, we introduce an Adversarial Spatio Temporal network to construct the relationship among entities, which we think should also be given high priority in the summarization. The GAN training problem is solved by introducing the Wasserstein GAN and two newly proposed video patch/score sum losses. In addition, the score sum loss can also relieve the model sensitivity to the varying video lengths, which is an inherent problem for most current video analysis tasks. Our method substantially lifts the performance on the target benchmark datasets and exceeds the current leaderboard Rank 1 state of the art CSNet (2.1% F1 score increase on TVSum and 3.1% F1 score increase on SumMe). We hope our straightforward yet effective approach will shed some light on the future research of unsupervised video summarization.
Kinetic Analysis of Drug-Nucleic Acid Binding Modes: Absolute Rates and Effects of Salt Concentration (1994)

Kinetic studies, particularly if carried out at several salt concentrations, provide information about nucleic acid complexes and how they form which is available from no other method. Kinetic experiments as a function of salt concentration, for example, can be used to determine variations in drug binding mode to different sequences of nucleic acids or between two different helical forms such as the A and B duplex states. The focus of this chapter will be on how to use kinetic results at different salt concentrations to obtain such information. Most of the kinetic results reported to date have been on duplex DNA-drug complexes; however, as a result of the interest in RNA as a potential receptor for antiviral drugs (Ratmeyer et al., 1992), and therapeutic strategies involving combined addition of a drug and a third strand to a DNA duplex (Mergny et al., 1992), an increasing number of studies on drug complexes with RNA and triple helical nucleic acids should appear.
Ce-doped single crystal and ceramic garnet for γ-ray detection (2007)

Ceramic and single crystal Lutetium Aluminum Garnet scintillators exhibit energy resolution with bialkali photomultiplier tube detection as good as 8.6% at 662 keV. Ceramic fabrication allows production of garnets that cannot easily be grown as single crystals, such as Gadolinium Aluminum Garnet and Terbium Aluminum Garnet. Measured scintillation light yields of Cerium-doped ceramic garnets indicate prospects for high energy resolution.
Pharmacokinetics and pharmacodynamics of ponesimod, a selective S1P1 receptor modulator, in the first‐in‐human study (2013)

Single doses of ponesimod up to and including 75 mg were well tolerated. The results of this ascending single-dose study indicate an immunomodulator potential for ponesimod and a pharmacokinetic/pharmacodynamic profile consistent with once-a-day dosing.
[Capability of clinical and laboratory findings to predict the grade of fibrosis and the diagnosis in diffuse interstitial lung diseases]. (1995)

Our objective was to assess the capacity of clinical and laboratory information to predict findings in the lung biopsy in interstitial lung diseases (ILD). We studied 121 patients with ILD as a cohort recruited in our institute from 1983 to 1987 with the diagnosis of hypersensitivity pneumonitis (HP) and usual interstitial pneumonia (UIP). Histologic diagnosis (HP vs UIP) and degree of fibrosis (< 50% of the biopsy surface vs > or = 50%) were used as the gold standard to compare a series of clinical and laboratory variables in the initial assessment. We used a stepwise logistic regression model to predict the biopsy results. The model was calculated in half of the patients selected by random sampling, and the calculated model was tested in the other half of the patients. Variables found to predict degree of fibrosis were (with relative risk RR and 95% confidence interval): a radiographic pattern of honeycombing (RR 5.0 from 0.9-29), digital clubbing (RR 8 from 1.4-48) and gender (RR 2.9 from 0.4-20). This model classified correctly 72% of the biopsies, with a sensitivity of 0.38, a specificity of 0.85 and a kappa of 0.25 +/- 0.19 (p = 0.17 NS). For histologic diagnosis (NIU vs NH), the model included gender (RR 6.6, 1.3-33), honeycombing (RR 1.6, from 0.4-6.0), digital clubbing (RR 4.6, from 1.2-18), and vital capacity expressed as percent of predicted (RR 0.96, from 0.92-1.00).(ABSTRACT TRUNCATED AT 250 WORDS)
A comparison of kinematics and performance measures of two rowing ergometers. (2006)

Rowing injuries have been attributed to poor technique, suggesting a need to understand the mechanics of rowing and the influence on technique of different training regimes and ergometers. The aims of this study were to investigate the repeatability of the kinematics of the lumbopelvic region during rowing and to compare these kinematics between rowing on two different ergometers. An electromagnetic motion measuring device in conjunction with a load cell was used to determine the ergometer rowing kinematics of 12 rowers. Subjects were tested on three occasions at two different stroke rates, with an interval of one week between testing. Two datasets were obtained for the Concept II, to establish the repeatability of the kinematics, and one for the WaterRower. Bland and Altman's mean difference technique was used to test for consistency of technique, and the difference between ergometers was assessed using Students' paired T-tests. The kinematic measures of the lumbo pelvic region during rowing demonstrated high repeatability. The two ergometers showed a similarity in force profiles but some significant differences in rowing kinematics. There was greater rotation of the thigh segment in the sagittal plane throughout the stroke on the WaterRower (p < 0.01). There were also trends indicating that rotation of the pelvis in the sagittal plane was different between the two ergometers, for example on the Concept the mean angle of the pelvis at the catch was 5.4° and on the WaterRower it was 2.4° (p < 0.05). Measurement of lumbopelvic kinematics during rowing on a Concept II ergometer is repeatable. However, rowing kinematics varies between ergometers. Because a full analysis comparing rowing kinematics on water with rowing ergometers has not been made in this study, no conclusions regarding which ergometer simulates rowing on water can be made. The implications of the effect of these differences in technique requires further investigation. Key PointsMeasurement of lumbopelvic kinematics during rowing on a Concept II ergometer is repeatable.Rowing kinematics varies between the WaterRower and Concept II.
In vivo study of an extended release bupivacaine formulation following site-directed nerve injection (2014)

Site-directed administration of local anesthetic agents incorporated into a slow controlled-release injectable implant prolongs the analgesic effect. However, there are potential neuro- and myotoxic consequences. We evaluated a local anesthetic agent (bupivacaine) loaded into a slow-release biodegradable polymer based on castor oil and poly(lactic acid). The formulation was applied directly to the sciatic nerve area in female imprinting control region mice along with appropriate controls. Local nerve and muscle and systemic toxicity were evaluated over a 3-month period following injection of 0.05, 0.1, and 0.125 mL of the 15% bupivacaine–polymer formulation. Histological samples were prepared and examined; no signs of severe inflammation were observed. Histological inflammation signs were more prominent in both nerves and muscles following application of the largest volumes of the polymer formulation (0.1 and 0.125 mL). Following application of 0.1 mL, 15% bupivacaine–polymer formulation, maximal changes were seen in nerve samples two days and two weeks after injection, with complete resolution one month following injection. Neither blank polymer nor plain bupivacaine 0.5% caused any histological changes. Local nerve and muscle toxicity were affected by duration the of exposure and dose of the local anesthetic agent. However, there were clear indications of time-related healing process 3 months after injection.
Experimental models and their use in studies of diabetic retinal microangiopathy. (1998)

Diabetes produces dramatic changes in retinal microvasculature, triggering endothelial cell proliferation and microaneurysms. Capillaries become weakened, releasing blood into vitreal and retinal spaces. Photoreceptors become occluded and separated from the choriocapillaris, resulting in visual acuity decline, detachment and cell death. Several models have been developed that have proved useful for the study of this disease, resulting in a better understanding of the processes involved. Streptozotocin treatment affects the pancreatic beta cells, rapidly reducing them until insulin is no longer synthesized in sufficient amounts. The galactosemic model shifts metabolism away from glucose, increasing aldose reductase and retinal polyol metabolism. Finally, two weeks of cycled oxygen from high to low tension every 24 hours, followed by return to room air, triggers microangiogenesis in developing retinas. Use of these models, separately or in combination, as well as electroretinographic analysis, has begun to reveal the events taking place as diabetic retinopathy progresses. Endothelial cells become separated from pericytes as basement membranes thicken, and vascular endothelial growth factor increases, triggering their proliferation. Finally, early changes occurring within photoreceptors can now be studied.
A genome-wide optical pooled screen reveals regulators of cellular antiviral responses (2023)

The infection of mammalian cells by viruses and innate immune responses to infection are spatiotemporally organized processes. Cytosolic RNA sensors trigger nuclear translocation of the transcription factor interferon regulatory factor 3 (IRF3) and consequent induction of host immune responses to RNA viruses. Previous genetic screens for factors involved in viral sensing did not resolve changes in the subcellular localization of host or viral proteins. Here, we increased the throughput of our optical pooled screening technology by over fourfold. This allowed us to carry out a genome-wide CRISPR knockout screen using high-resolution multiparameter imaging of cellular responses to Sendai virus infection coupled with in situ cDNA sequencing by synthesis (SBS) to identify 80,408 single guide RNAs (sgRNAs) in 10,366,390 cells-over an order of magnitude more genomic perturbations than demonstrated previously using an in situ SBS readout. By ranking perturbations using human-designed and deep learning image feature scores, we identified regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. Among the hits, we found that ATP13A1, an ER-localized P5A-type ATPase, is essential for viral sensing and is required for targeting of mitochondrial antiviral signaling protein (MAVS) to mitochondrial membranes where MAVS must be localized for effective signaling through retinoic acid-inducible gene I (RIG-I). The ability to carry out genome-wide pooled screens with complex high-resolution image-based phenotyping dramatically expands the scope of functional genomics approaches.
Software for interactive on-line conferences (1984)

A layered architecture for the implementation of real-time conferences is presented. In a real-time conference a group of users each at his or her own workstation, share identical views of on-line application information. The users cooperate in a problem solving task by interactively modifying or editing the shared view or the underlying information, and can use a voice communication channel for discussion and negotiation.
Supplementary Figure 5 from An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance (2023)

&lt;p&gt;PDF file - 50K, Mesenchymal lines are sensitive to Axl inhibition by SGI-7079&lt;/p&gt;