gebhart/patrepeval huggingface dataset:
Disentangling Second Harmonic Generation from Multiphoton Photoluminescence in Halide Perovskites using Multidimensional Harmonic Generation (2020)

Metal halide perovskites are an intriguing class of semiconductor materials being explored for their linear and non-linear optical, and potentially ferroelectric properties. In particular, layered two-dimensional Ruddlesden-Popper (RP) halide perovskites have shown non-linear optoelectronic properties. Optical second harmonic generation (SHG) is commonly used to screen for non-centrosymmetric and ferroelectric materials, however, SHG measurements of perovskites are complicated by their intense multiphoton photoluminescence (mPL) which can be mistaken for SHG signal. In this work, we introduce multidimensional harmonic generation as a method to eliminate the complications caused by mPL. By scanning and correlating both excitation and emission frequencies, we un-ambiguously assess whether a material supports SHG by examining if an emission feature scales as twice the excitation frequency. Careful multidimensional harmonic generation measurements of a series of n=2 and n=3 RP perovskites reveal that, contrary to previous belief, n-butylammonium (BA) RP perovskites display no SHG, thus they have inversion symmetry; but RP perovskites with phenylethylammonium (PEA) and 2-thiophenemethylammonium (TPMA) spacer cations display SHG. Multidimensional harmonic generation is also able to confirm the SHG and thus non-centrosymmetry of a recently reported ferroelectric RP perovskite even in the presence of an obscuring mPL background. This work establishes multidimensional harmonic generation as a definitive method to measure the SHG properties of materials and demonstrates that tuning organic cations can allow the design of new non-centrosymmetric or even ferroelectric RP perovskites.&lt;br&gt;
Resolving Ultrafast Wave-packet Dynamics of D_2 ^+ Using Multiple Harmonic Pulses of Ti:sapphire laser (2012)

We have resolved the vibrational wave-packet dynamics of D2+ with a period of ~20-fs generated with sub-10 fs XUV harmonic field. The real-time evolution is probed with the sub-10 fs VUV and DUV harmonic fields.
AutoCast (2022)

Autonomous vehicles use 3D sensors for perception. Cooperative perception enables vehicles to share sensor readings with each other to improve safety. Prior work in cooperative perception scales poorly even with infrastructure support. AUTOCAST1 enables scalable infrastructure-less cooperative perception using direct vehicle-to-vehicle communication. It carefully determines which objects to share based on positional relationships between traffic participants, and the time evolution of their trajectories. It coordinates vehicles and optimally schedules transmissions in a distributed fashion. Extensive evaluation results under different scenarios show that, unlike competing approaches, AUTOCAST can avoid crashes and near-misses which occur frequently without cooperative perception, its performance scales gracefully in dense traffic scenarios providing 2-4x visibility into safety critical objects compared to existing cooperative perception schemes, its transmission schedules can be completed on the real radio testbed, and its scheduling algorithm is near-optimal with negligible computation overhead.
Synthesis and odour perception of a series of highly substituted cyclohexane derivatives (2021)

Abstract A series of novel‐substituted cyclohexane derivatives has been prepared and their olfactory evaluation is presented. The different structures are derived from the cyclization of an unsaturated ketal under catalytic conditions. Its further functionalization allowed for the preparation of a series of 22 new compounds. Most of the new cyclic compounds present fruity and/or woody notes.
CNN-based pose estimation for assessing quality of ankle-joint X-ray images (2022)

A novel technology for estimating both the pose and the joint flexion from a single musculoskeletal X-ray image is presented for automatic quality assessment of patient positioning. The method is based on convolutional neural networks and does not require pose or flexion labels of the X-ray images for the training phase. The task is split into two steps: (i) detection of relevant bone contours in the X-ray by a feature-detection network and (ii) regression of the pose and flexion parameters by a pose-estimation network based upon the detected contours. This separation enables the pose-estimation network to be trained using synthetic contours, which are generated via projections of an articulated 3D model of the target anatomy. It is demonstrated that the use of data-augmentation techniques during training of the pose-estimation network significantly contributes to the robustness of the algorithm. Feasibility of the approach is illustrated using lateral ankle X-ray exams. Validation was performed using X-rays of an anthropomorphic phantom of the foot-ankle joint, imaged in various controlled positions. Reference pose parameters were established by an expert using an interactive tool to align the articulated 3D joint model with the phantom image. Errors in pose estimation are in the range of 2 degrees per pose angle and at the level of the expert performance. Using the rigid foot phantom the flexion parameter was constant, but the overall results indicate accurate estimation also of this parameter.
Multi-copper ferroxidase deficiency leads to iron accumulation and oxidative damage in astrocytes and oligodendrocytes (2019)

Accumulation of iron has been associated with the pathobiology of various disorders of the central nervous system. Our previous work has shown that hephaestin (Heph) and ceruloplasmin (Cp) double knockout (KO) mice induced iron accumulation in multiple brain regions and that this was paralleled by increased oxidative damage and deficits in cognition and memory. In this study, we enriched astrocytes and oligodendrocytes from the cerebral cortex of neonatal wild-type (WT), Heph KO and Cp KO mice. We demonstrated that Heph is highly expressed in oligodendrocytes, while Cp is mainly expressed in astrocytes. Iron efflux was impaired in Cp KO astrocytes and Heph KO oligodendrocytes and was associated with increased oxidative stress. The expression of Heph, Cp, and other iron-related genes was examined in astrocytes and oligodendrocytes both with and without iron treatment. Interestingly, we found that the expression of the mRNA encoding ferroportin 1, a transmembrane protein that cooperates with CP and HEPH to export iron from cells, was positively correlated with Cp expression in astrocytes, and with Heph expression in oligodendrocytes. Our findings collectively demonstrate that HEPH and CP are important for the prevention of glial iron accumulation and thus may be protective against oxidative damage.
A Generalized System for Photoresponsive Membrane Rupture in Polymersomes (2010)

Polymersomes are vesicles whose membranes are comprised of self-assembled block co-polymers. We recently showed that co-encapsulating conjugated multi-porphyrin dyes in a polymersome membrane with ferritin protein in the aqueous lumen confers photo-lability to the polymersome. In the present study, we illustrate that the photo-lability can be extended to vesicles containing dextran, an inert and inexpensive polysaccharide, as the luminal solute. Here we explore how structural features of the polymersome/porphyrin/dextran composite affect its photo-response. Increasing dextran molecular weight, decreasing block copolymer molecular weight, and altering fluorophore-membrane interactions results in increasing the photo-responsiveness of the polymersomes. Amphiphilic interactions of the luminal encapsulant with the membrane coupled with localized heat production in the hydrophobic bilayer likely cause differential thermal expansion in the membrane and the subsequent membrane rupture. This study suggests a general approach to impart photo-responsiveness to any biomimetic vesicle system without chemical modification, as well as a simple, bio-inert method for constructing photo-sensitive carriers for controlled release of encapsulants.
Theta burst stimulation: Technical aspects about TMS devices (2020)

Theta burst stimulation (TBS), delivers bursts of TMS pulses at gamma frequency (e.g. 50 Hz) which are repeated at theta frequency intervals (e.g. 5 Hz). In animals, TBS can induce long-lasting neural changes in neuronal behaviour [1–3]. Similar observations have been reported when applying TBS in humans [4,5] using TMS. Continuous TBS (cTBS) applies three pulses at 50 Hz frequency (the burst) every 200 ms (5 Hz) [4,5]. There is considerable inter- and intra-individual variability in response to TBS, despite comparable stimulation parameters and methodologies across studies [6–10].
Finite Precision Rational Arithmetic: Slash Number Systems (1983)

&lt;p&gt;Fraction number systems described by fixed-slash and floating slash formats are specified. The structure of arithmetic over such systems is prescribed by the rounding obtained from ''best rational approximation''.&lt;/p&gt;&lt;p&gt;Multi-tiered precision hierarchies of both fixed-slash and floating-slash type are proposed and analyzed with regards to their support of both exact rational and approximative real computation.&lt;/p&gt;
Interaction of acyl-CoA binding protein (ACBP) on processes for which acyl-CoA is a substrate, product or inhibitor (1993)

It is shown that acyl-CoA binding protein (ACBP), in contrast with fatty acid binding protein (FABP), stimulates the synthesis of long-chain acyl-CoA esters by mitochondria. ACBP effectively opposes the product feedback inhibition of the long-chain acyl-CoA synthetase by sequestration of the synthesized acyl-CoA esters. Feedback inhibition of microsomal long-chain acyl-CoA synthesis could not be observed, due to the formation of small acyl-CoA binding vesicles during preparation and/or incubation. Microsomal membrane preparations are therefore unsuitable for studying feedback inhibition of long-chain acyl-CoA synthesis. ACBP was found to have a strong attenuating effect on the long-chain acyl-CoA inhibition of both acetyl-CoA carboxylase and mitochondrial adenine nucleotide translocase. Both processes were unaffected by the presence of long-chain acyl-CoA esters when the ratio of long-chain acyl-CoA to ACBP was below 1, independent of the acyl-CoA concentration used. It is therefore not the acyl-CoA concentration as such which is important from a regulatory point of view, but the ratio of acyl-CoA to ACBP. The cytosolic ratio of long-chain acyl-CoA to ACBP was shown to be well below 1 in the liver of fed rats. ACBP could compete with the triacylglycerol-synthesizing pathway, but not with the phospholipid-synthesizing enzymes, for acyl-CoA esters. Furthermore, in contrast with FABP, ACBP was able to protect long-chain acyl-CoA esters against hydrolysis by microsomal acyl-CoA hydrolases. The results suggest that long-chain acyl-CoA esters synthesized for either triacylglycerol synthesis or beta-oxidation have to pass through the acyl-CoA/ACBP pool before utilization. This means that acyl-CoA synthesized by microsomal or mitochondrial synthetases is uniformly available in the cell. It is suggested that ACBP has a duel function in (1) creating a cytosolic pool of acyl-CoA protected against acyl-CoA hydrolases, and (2) protecting vital cellular processes from being affected by long-chain acyl-CoA esters.
Influences of Atmospheric Pressure and Temperature on Intraocular Pressure (2008)

An increase of the ATM to 2 Bar (equal to conditions experienced during underwater diving at 10 meters) modestly but significantly decreased the IOP independently of the temperature change. During the period of increased ATM (60 minutes), the IOP decrease remained stable and was independent of blood pressure change or corneal thickness.
Preparation of 1,5-Dihydropyrazolo[3′,4′:5,6]pyrano[3,4-<i>b</i>]pyridines via a Microwave-Assisted, Palladium-Catalyzed Regioselective C–H Heteroarylation of Electron-Rich Pyrazoles (2019)

Here we report the first synthesis of a family of novel heterocyclic compounds based on a 5-dihydropyrazolo[3',4':5,6]pyrano[3,4- b]pyridine core. In the course of our drug discovery programs, we had need to access the previously unknown 5-dihydropyrazolo[3',4':5,6]pyrano[3,4- b]pyridine core. Initial attempts required long reaction times, which led to degradation and side products. Reaction optimization identified a Pd-catalyzed, microwave-assisted C-H heteroarylation protocol for the rapid, general, and high yielding synthesis of this tricyclic core (as well as related analogs) suitable to drive optimization efforts.
Efficient and Accurate Abnormality Mining from Radiology Reports with Customized False Positive Reduction (2018)

Obtaining datasets labeled to facilitate model development is a challenge for most machine learning tasks. The difficulty is heightened for medical imaging, where data itself is limited in accessibility and labeling requires costly time and effort by trained medical specialists. Medical imaging studies, however, are often accompanied by a medical report produced by a radiologist, identifying important features on the corresponding scan for other physicians not specifically trained in radiology. We propose a methodology for approximating image-level labels for radiology studies from associated reports using a general purpose language processing tool for medical concept extraction and sentiment analysis, and simple manually crafted heuristics for false positive reduction. Using this approach, we label more than 175,000 Head CT studies for the presence of 33 features indicative of 11 clinically relevant conditions. For 27 of the 30 keywords that yielded positive results (3 had no occurrences), the lower bound of the confidence intervals created to estimate the percentage of accurately labeled reports was above 85%, with the average being above 95%. Though noisier then manual labeling, these results suggest this method to be a viable means of labeling medical images at scale.
Laser‐Induced Graphene Strain Sensors Produced by Ultraviolet Irradiation of Polyimide (2018)

Abstract Laser‐induced graphene (LIG) can be obtained by irradiation of a polymer by a laser source. The present work demonstrates that it is possible to obtain this kind of material using an ultraviolet laser instead of the typical infrared source. Using this approach, a fourfold decrease in the penetration depth (5 µm) is achieved, while the spatial resolution is doubled. Electromechanical strain LIG sensors are patterned in polyimide substrates with different thicknesses and their performance to strain, bending, and force inputs is measured. A low‐cost arterial pulse wave monitor is built, exploring the high force sensitivity of the sensors produced on the thinner substrates.
Evaluation of a vaccine passport to improve vaccine coverage in people living with HIV (2018)

An increased risk of vaccine-preventable infections (VPIs) is seen in people living with HIV (PLWH), and current vaccine coverage and immunity is variable. Vaccine passports have the potential to improve vaccine coverage. The objective was to assess how successful a vaccine passport was in improving vaccine coverage in PLWH. Baseline immunity to VPIs was established in PLWH attending a single HIV clinic and vaccinations required were determined based on the BHIVA Vaccination Guidelines (2015). The passport was completed and the PLWH informed about additional vaccines they should obtain from primary care. After 6-9 months the passport was reviewed including confirmation if vaccines were given. PLWH satisfaction with the system was evaluated by a survey. Seventy-three PLWH provided sufficient data for analysis. At baseline significant proportions of PLWH were not immune/unvaccinated to the main VPIs, especially human papillomavirus, pneumococcus and measles. After the passport was applied immunity improved significantly (56% overall, p < 0.01) for most VPIs; however, full coverage was not achieved. The system was popular with PLWH. The passport was successful in increasing vaccination coverage although full or near-full coverage was not achieved. A more successful service would probably be achieved by commissioning English HIV clinics to provide all vaccines.
Analysis of a Radioisotope Thermal Rocket Engine (2017)

The Triton Hopper is a concept for a vehicle to explore the surface of Neptunes moon Triton, which uses a radioisotope heated rocket engine and in-situ propellant acquisition. The initial Triton Hopper conceptual design stores pressurized Nitrogen in a spherical tank to be used as the propellant. The aim of the research was to investigate the benefits of storing propellant at ambient temperature and heating it through a thermal block during engine operation, as opposed to storing gas at a high temperature.
Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets (2016)

Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension-functionality supporting preservation of file system structure within Dataverse-which is essential for both in-place computation and supporting non-HTTP data transfers.
TRANSFORMING CONJUNCTIVE MATCH INTO RETE: A CALL-GRAPH CACHING APPROACH (1991)

Conjunctive match is often used in Artificial Intelligence as the kernel of a pattern-directed inference [37] engine. Conjunctive match entails generating and testing all possible combinations of objects against a pattern of constraints. While simple to program, it is an expensive, exponential cost computation. To reduce this average match cost in production system engines, the RETE match algorithm [8] was devised. RETE compiles each rule's pattern of constraints into a network, and then incrementally updates partial matches as objects are inserted and deleted. RETE, however, has its own cost: conceptual and implementational complexity. Call-graph caching (CGC) [20] is a mechanism for transforming recursive specifications into highly optimized networks. In this paper, we describe CGC, and use it to transform a family of recursive conjunctive match formulations into their corresponding RETE networks. Our approach illustrates the ideas behind RETE, and shows their application to other algorithms.
Conservation of G-Protein Epitopes in Respiratory Syncytial Virus (Group A) Despite Broad Genetic Diversity: Is Antibody Selection Involved in Virus Evolution? (2015)

An unusual characteristic of the G glycoprotein of human respiratory syncytial virus (hRSV) is the accumulation of nonsynonymous (N) changes at higher rates than synonymous (S) changes, reaching dN/dS values at certain sites predictive of positive selection. Since these sites cluster preferentially in the C-terminal third of the G protein, like certain epitopes recognized by murine antibodies, it was proposed that immune (antibody) selection might be driving the apparent positive selection, analogous to the antigenic drift observed in the influenza virus hemagglutinin (HA). However, careful antigenic and genetic comparison of the G glycoprotein does not provide evidence of antigenic drift in the G molecule, in agreement with recently published data which did not indicate antigenic drift in the G protein with human sera. Alternative explanations to the immune-driven selection hypothesis are offered to account for the high level of G-protein genetic diversity highlighted in this study.
G-Protein-Coupled Receptor Affinity Prediction Based on the Use of a Profiling Dataset:  QSAR Design, Synthesis, and Experimental Validation (2005)

A QSAR model accounting for "average" G-protein-coupled receptor (GPCR) binding was built from a large set of experimental standardized binding data (1939 compounds systematically tested over 40 different GPCRs) and applied to the design of a library of "GPCR-predicted" compounds. Three hundred and sixty of these compounds were randomly selected and tested in 21 GPCR binding assays. Positives were defined by their ability to inhibit by more than 70% the binding of reference compounds at 10 microM. A 5.5-fold enrichment in positives was observed when comparing the "GPCR-predicted" compounds with 600 randomly selected compounds predicted as "non-GPCR" from a general collection. The model was efficient in predicting strongest binders, since enrichment was greater for higher cutoffs. Significant enrichment was also observed for peptidic GPCRs and receptors not included to develop the QSAR model, suggesting the usefulness of the model to design ligands binding with newly identified GPCRs, including orphan ones.
The encapsulation of enterotoxigenic Escherichia coli colonization factor CS3 in biodegradable microspheres enhances the murine antibody response following intranasal administration (2006)

The aim of this study was to measure serum and mucosal antibody responses following intranasal administration of biodegradable poly(DL-lactide-co-glycolide) (PLGA) microspheres loaded with the CS3 colonization factor isolated from enterotoxigenic Escherichia coli (ETEC). The response was compared against that measured in mice similarly administered the native CS3 antigen and in mice co-administered, along with the CS3 antigen, a known mucosal adjuvant, the R192G mutant heat-labile enterotoxin (mLT). The integrity of the CS3 antigen released from the microspheres was maintained as determined by SDS-PAGE and immunoblotting. Native CS3 induced serum and mucosal (bronchoalveolar, small intestinal and faecal) IgG and IgA responses. The co-administration of the mLT mucosal adjuvant significantly enhanced (P<0.001) serum and mucosal antibody responses to the CS3 protein. Likewise, the CS3-loaded PLGA microspheres induced significantly greater (P<0.001) serum and mucosal antibody responses than native CS3, as well as inducing antibody responses superior to those of the CS3 plus mLT formulation. Following administration of CS3 plus mLT, the mice became distressed (loss of activity, increased huddling, ruffled fur), a situation not seen following administration of the CS3-loaded PLGA microspheres. The results in this trial show that the CS3-loaded PLGA microspheres when administered intranasally to mice caused no observable distress to the mice and significantly (P<0.001) enhanced the immunogenicity of the CS3 protein.
Evidence for a dual function of the herbicide‐binding D1 protein in photosystem II (1986)

The LF‐1 mutant of the green alga Scenedesmus obliquus is completely blocked on the oxidizing (water‐splitting) side of photosystem II (PS II) while the reaction center and reducing side remain functional. A 34‐kDa protein found in the PS II reaction center core complex of wild‐type cells is replaced by a 36‐kDa protein in the mutant cells. Both of these proteins are labeled by azido[ 14 C]atrazine and are recognized by polyclonal antibodies raised against the herbicide‐binding, D1 protein of Amaranthus hybridus . The data provide a new perspective on the role of the D1 protein by implying that it affects the oxidizing side of PS II in addition to performing its well established function on the reducing side.