gebhart/patrepeval huggingface dataset:
Ultrafast Study of 9-Diazofluorene:  Direct Observation of the First Two Singlet States of Fluorenylidene (2007)

Ultrafast photolysis of 9-diazofluorene (DAF) produces a broadly absorbing transient within the instrument time resolution (300 fs), which is assigned to an excited state of the diazo compound. The diazo excited state fragments to form fluorenylidene (Fl) in both its lowest energy singlet state (1Fl, 405-430 nm, depending on the solvent) and a higher energy singlet state (370 nm, 1Fl*). The excited singlet carbene has a lifetime of 20.9 ps in acetonitrile and decays to the lower energy singlet state (1Fl), which relaxes to the triplet ground state (3Fl) in acetonitrile, cyclohexane, benzene, and hexafluorobenzene. The equilibrium mixture of singlet and triplet fluorenylidene reacts with these solvents. Singlet fluorenylidene reacts with methanol and cyclohexene in competition with relaxation to 3Fl. One of the reaction products in methanol is the 9-fluorenyl cation. The rate of intersystem crossing (ISC) in hexafluorobenzene and other halogenated solvents is remarkably slow given that carbene ISC rates are generally fastest in nonpolar solvents. An explanation of this effect is advanced.
Synthèse et optimisation d'un reflectarray bipolarisé en bande Ku (2009)

National audience
Nonrandom chromosomal imbalances in primary mediastinal b-cell lymphoma detected by arbitrarily primed PCR fingerprinting (1999)

We used arbitrarily primed polymerase chain reaction (AP-PCR) fingerprinting to identify chromosomal imbalances in six primary mediastinal B-cell lymphomas (PMBLs). Seventy-four chromosomal imbalances were detected, consisting of 49 sequence gains and 25 losses. Amplifications on chromosome X were seen in five cases, four of which involved the same chromosomal locus. Nonrandom gains at the same locus were also identified on chromosomes 2 and 7 in four cases and on chromosomes 5, 9, and 12 in three cases. Five PMBLs were also analyzed by comparative genomic hybridization (CGH), which found chromosome arm 9p amplification as the only nonrandom imbalance. Our data demonstrate that chromosomal amplifications outnumber losses in PMBL. These mainly involve chromosomes 9 and X and may reflect more complex phenomena, such as translocations or other chromosomal rearrangements, as AP-PCR found coexistent gains and losses on these chromosomes. Comparison between AP-PCR and CGH suggests that anomalies affecting the same chromosomal regions may occur at much higher frequencies than expected by CGH, suggesting that genomic amplifications are usually confined to DNA segments smaller than the megabase long segments required for detection in CGH. Modest increases in genetic material may be as effective as higher-level amplifications when affecting sites where a proto-oncogene resides.
Correction for Feng et al., Constitutive BDNF/TrkB signaling is required for normal cardiac contraction and relaxation (2015)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Self‐Sustaining Fluorination of Active Methylene Compounds and High‐Yielding Fluorination of Highly Basic Aryl and Alkenyl Lithium Species with a Sterically Hindered N‐Fluorosulfonamide Reagent (2022)

Abstract Fluorination of carbanions is pivotal for the synthesis of fluorinated compounds, but the current N ‐F fluorinating agents have significant drawbacks due to many reactive locations that surround the reactive N−F site. By developing a sterically hindered N ‐fluorosulfonamide reagent, namely N ‐fluoro‐ N ‐( tert ‐butyl)‐ tert ‐butanesulfonamide (NFBB), we discovered a conceptually novel base‐catalyzed, self‐sustaining fluorination of active methylene compounds and achieved the high‐yielding fluorination of the hitherto difficult highly basic (hetero)aryl and alkenyl lithium species. In the former, the mild and high yield fluorination of active methylene compounds exhibited wide functional group tolerance and its novel catalytic fluorination‐deprotonation cycle mechanism was demonstrated by deuterium‐tracing experiments. In the latter, NFBB reacted with a variety of highly basic (hetero)aryl and alkenyl lithium species to provide the desired fluoro (hetero)arenes and alkenes in unprecedented high or quantitative yields.
Anomalous frequency-dependent ionic conductivity of lesion-laden human-brain tissue (2017)

We study the effect of lesions on our four-electrode measurements of the ionic conductivity of (∼1 cm3) samples of human brain excised from patients undergoing pediatric epilepsy surgery. For most (∼94%) samples, the low-frequency ionic conductivity rises upon increasing the applied frequency. We attributed this behavior to the long-range (∼0.4 mm) diffusion of solvated sodium cations before encountering intrinsic impenetrable blockages such as cell membranes, blood vessels, and cell walls. By contrast, the low-frequency ionic conductivity of some (∼6%) brain-tissue samples falls with increasing applied frequency. We attribute this unusual frequency-dependence to the electric-field induced liberation of sodium cations from traps introduced by the unusually severe pathology observed in samples from these patients. Thus, the anomalous frequency-dependence of the ionic conductivity indicates trap-producing brain lesions.
MAGNETIC FIELD ORIENTATION AND SPATIAL EFFECTS ON THE RETENTION OF PARAMAGNETIC NANOPARTICLES WITH MAGNETITE (2002)

The magnetic force exerted on a paramagnetic nanoparticle by a 3-D array of magnetite particles was investigated to extend previous work that only involved one magnetite particle. The separation between the magnetite particles in the array, the orientation of the magnetic field, and the distance between the nanoparticle and the surface of the magnetite array were studied. At magnetite particle separations of less than two magnetite diameters, a reduction in the net force on the nanoparticle compared to that associated with a single magnetite particle was realized due to the overlapping behavior of the magnetic fields of the magnetite array. The net force was still strong to overcome thermal (Brownian) motion and attract and retain the nanoparticle. The magnetite array also gives rise to retention zones at any orientation of the magnetite field; this was not true of a single magnetite particle, which exhibited repulsive zones depending on the orientation of the field. When the separation between the magnetite particles was greater than two magnetite diameters, the effect of the array was lost and the nanoparticle interacted essentially with only one of the magnetite particles. The close proximity of the magnetite particles and the associated smoothing effect translated into long-range interactions that leveled off with distance between the nanoparticle and the array. Although too weak to retain the nanoparticle, they were suspected to be strong enough to retain much larger particles approaching the size of the array. These effects could be explained only by the fact that when the magnetite particles were closer to each other they started behaving as a single large particle. Overall, these results suggest that both nanoparticles and particles of the size the array can be attracted to and retained by a magnetic matrix comprising clusters of small and similarly sized magnetite particles.
Defining equitable genomic testing uptake in gastrointestinal oncology: Ensuring capture of demographic data. (2023)

794 Background: Tumor genomic testing (GT) has increased diagnostic accuracy and treatment options for patients (pts) with cancer. Dana-Farber Cancer Institute (DFCI) has made GT accessible as an institute-supported research effort for &gt;10 yrs. We estimate 50% standard therapies and 15-35% clinical trials in Gastrointestinal Cancer Clinic (GCC) require GT to determine eligibility. Pts in GCC with certain cancers are eligible for GT as a clinical test – these include metastatic/locally advanced colorectal, gastric, pancreatic, or biliary cancers. Clinical testing requires CLIA lab certification and insurance reimbursement; research does not. Herein we ID gaps in our GT database. Methods: We reviewed data on GT uptake in GCC between 4/2015 - 6/2022. 20,096 pts were captured by the GT tracking system. Data included: testing ordered and completed (proportion, type, time to receiving tissue for testing [TR], time to testing completion [TC]). Demographic data is not captured in the tracking system; matching unique patient identifiers with electronic health record is pending. Results: Most pts received GT (57.6%); 12% were not eligible; 30.4% declined consent. Most testing was completed (67.6%), but 21.3% of tests failed (45.5% of these from insufficient tissue). Research testing (71%) comprised most tests, but clinical tests were completed faster (median 34 days research vs 20 days clinical). Ampullary (91%), anal (90%), colon (90%) had highest completion rates; pancreatic (59%), hepatocellular carcinoma (56%) had lowest (from insufficient viable tumor in submitted specimens). Conclusions: GCC has a robust recruitment program that has yielded high GT uptake. Given the frequency that GT is used for treatment and trials, building a demographically representative dataset is crucial, especially for pts with largest burden of morbidity and mortality from cancer. We ID'd data gaps in the GT tracking system, which lacks demographics and reason for not testing. Demographic data is available in the electronic health record but does not speak with the GT tracking system so this analysis is not routinely done. Ability to visualize this data is important to ensure equitable GT uptake. Future efforts will focus on improving rates of consent in genomics databases and cancer clinical trials. Genomic testing at Dana-Farber Cancer Institute Gastrointestinal Cancer Center, 4/2015 – 6/2022.[Table: see text]
Cofactor effects on the protein folding reaction: Acceleration of α‐lactalbumin refolding by metal ions (2006)

About 30% of proteins require cofactors for their proper folding. The effects of cofactors on the folding reaction have been investigated with alpha-lactalbumin as a model protein and metal ions as cofactors. Metal ions accelerate the refolding of alpha-lactalbumin by lessening the energy barrier between the molten globule state and the transition state, mainly by decreasing the difference of entropy between the two states. These effects are linked to metal ion binding to the protein in the native state. Hence, relationships between the metal affinities for the intermediate states and those for the native state are observed. Some residual specificity for the calcium ion is still observed in the molten globule state, this specificity getting closer in the transition state to that of the native state. The comparison between kinetic and steady-state data in association with the Phi value method indicates the binding of the metal ions on the unfolded state of alpha-lactalbumin. Altogether, these results provide insight into cofactor effects on protein folding. They also suggest new possibilities to investigate the presence of residual native structures in the unfolded state of protein and the effects of such structures on the protein folding reaction and on protein stability.
Continuous Ethanol Production from Concentrated Wood Hydrolysates in an Internal Membrane-Filtration Bioreactor (2000)

Continuous culture for the production of ethanol from wood hydrolysate was carried out in an internal membrane-filtration bioreactor. The hydrolysate medium was sterilized at a relatively low temperature of 60 degrees C with the intention of reducing the formation of inhibitory compounds during the sterilization. The maximum ethanol concentration and productivity obtained in this study were 76.9 g/L and 16.9 g/L-h, respectively, which were much higher than those (57.2-67 g/L and 0.3-1.0 g/L-h) obtained in batch cultures using hydrolysate media sterilized at 60 degrees C. The productivity was also found to be much higher than that (6.7 g/L-h) obtained in a continuous cell retention culture using a wood hydrolysate sterilized at 121 degrees C. These results show that the internal membrane-filtration bioreactor in combination with low-temperature sterilization could be very effective for ethanol production from wood hydrolysate.
Ferroelectric nematic liquids with conics (2023)

Spontaneous electric polarization of solid ferroelectrics follows aligning directions of crystallographic axes. Domains of differently oriented polarization are separated by domain walls (DWs), which are predominantly flat and run along directions dictated by the bulk translational order and the sample surfaces. Here we explore DWs in a ferroelectric nematic (N<sub>F</sub>) liquid crystal, which is a fluid with polar long-range orientational order but no crystallographic axes nor facets. We demonstrate that DWs in the absence of bulk and surface aligning axes are shaped as conic sections. The conics bisect the angle between two neighboring polarization fields to avoid electric charges. The remarkable bisecting properties of conic sections, known for millennia, play a central role as intrinsic features of liquid ferroelectrics. The findings could be helpful in designing patterns of electric polarization and space charge.
Demonstrating ATSC ROUTE-DASH delivery (2016)

DASH content delivery via ROUTE is being standardized within ATSC and is supported by the interoperability efforts within DASH-IF. The goals achieved by this work include effectively demonstrating the key technological features of the nascent standards on a variety of platforms. These features include demonstration of hybrid services delivery and customized advertisement insertion, etc. At the same time, this demonstration is accomplished using open-source tools, content, and components to help foster harnessing and utilizing the full potential of these technologies in the industry. All of this is supplemented by near-product grade stable and optimized performance demonstration.
Novel iterative reconstruction method with optimal dose usage for partially redundant CT-acquisition (2015)

In CT imaging, a variety of applications exist which are strongly SNR limited. However, in some cases redundant data of the same body region provide additional quanta. Examples in dual energy CT, the spatial resolution has to be compromised to provide good SNR for material decomposition. However, the respective spectral dataset of the same body region provides additional quanta which might be utilized to improve SNR of each spectral component. Perfusion CT is a high dose application, and dose reduction is highly desirable. However, a meaningful evaluation of perfusion parameters might be impaired by noisy time frames. On the other hand, the SNR of the average of all time frames is extremely high.In redundant CT acquisitions, multiple image datasets can be reconstructed and averaged to composite image data. These composite image data, however, might be compromised with respect to contrast resolution and/or spatial resolution and/or temporal resolution. These observations bring us to the idea of transferring high SNR of composite image data to low SNR 'source' image data, while maintaining their resolution.It has been shown that the noise characteristics of CT image data can be improved by iterative reconstruction (Popescu et al 2012 Book of Abstracts, 2nd CT Meeting (Salt Lake City, UT) p 148). In case of data dependent Gaussian noise it can be modelled with image-based iterative reconstruction at least in an approximate manner (Bruder et al 2011 Proc. SPIE 7961 79610J). We present a generalized update equation in image space, consisting of a linear combination of the previous update, a correction term which is constrained by the source image data, and a regularization prior, which is initialized by the composite image data. This iterative reconstruction approach we call bimodal reconstruction (BMR). Based on simulation data it is shown that BMR can improve low contrast detectability, substantially reduces the noise power and has the potential to recover spatial resolution of the source image data.For different CT applications: dual energy imaging, liver imaging, spiral imaging, cardiac imaging, we show that SNR can efficiently be transferred from the composite image to the source image data at constant patient dose, while maintaining resolution properties of the source data.
Polymer-Stabilized Liquid Metal Nanoparticles as a Scalable Current Collector Engineering Approach Enabling Lithium Metal Anodes (2022)

Dendrites and dead lithium formation over prolonged cycling have long been challenges that hinder the safe implementation of metallic Li anodes. Herein, we employ polymer-stabilized liquid metal nanoparticles (LM-P NPs) of eutectic gallium indium (EGaIn) to create uniform Li nucleation sites enabling homogeneous lithium electrodeposition. Block copolymers of poly(ethylene oxide) and poly(acrylic acid) (PEO-b-PAA) were grafted onto the EGaIn surface, forming stabilized, well-dispersed NPs. Using a scalable spray coating approach, LM-P NPs were fabricated on copper current collectors, providing lithiophilic PEO sites and interactive carboxyl groups to guide Li deposition. The Li-EGaIn alloying process greatly reduced the Li+ diffusion barrier, enabling fast Li transport through the coating layer, resulting in decreased nucleation overpotential. Therefore, about five times lower Li nucleation overpotential was obtained on the LM-P modified Cu with an optimal composition of the polymers than the bare Cu substrates. DFT computations was used to reveal the binding properties between the LM-P layer and Li. Due to the regulated Li plating/stripping process, as-obtained 30 μm Li anodes paired with LiNi0.8Co0.1Mn0.1O2 (NCM811) with a negative/positive electrode capacity (N/P) ratio ∼ 10 exhibited stable cycling performance at 0.5C for over 250 cycles, with an average Coulombic efficiency of 99.55%. Ultrathin Li (1 μm) anodes with an N/P ratio ∼ 0.6 were also demonstrated in Li|LiFePO4 cells, which examined the stabilization of Li by LM-P NPs and monitored practical loadings of Li anodes that are close to anode-free systems.
Metamaterial Blazed Gratings (2011)

We design, fabricate, and test a graded index diffractive structure based on non-resonant I-beam metamaterials. The measured diffraction spectrum is in good agreement with simulation, and suggests a path toward metamaterial based diffractive optics.
Gauss-core resonator: a novel stable resonator with a large-diameter diffraction-limited output beam (1995)

A novel cavity design based on a stable resonator configuration is presented. The output coupler of the new stable resonator has a circular partial-reflection region in the center that is surrounded by an antireflection region. This resonator operates in a large-volume TEM(00) mode that is mainly determined by the partial-reflection region of the output coupler and is characterized by the use of an additional laser beam that is spread from the optical path in the cavity because of diffraction and is amplified by a laser medium. By combining part of a beam transmitted from the partial-reflection region with the amplified diffraction beam, a laser beam having a large diameter is obtained. A diffraction-limited output beam with the M(2) factor of 1.3 is obtained, as predicted theoretically when the new stable resonator is applied to a high-power cw CO(2) laser.
Alternative splicing of BCR/ABL in chronic myelogenous leukemia (1999)

The hallmark of chronic myelogenous leukemia (CML) is the presence of the Philadelphia chromosome and its resultant fusion message, BCR-ABL, and fusion protein, p210.Patients with Philadelphia positive acute lymphoblastic leukemia (ALL) can have a srnaller K R -A B L fusion transcript possessing only the first exon of BCR fused to ABL.This smaller transcript encodes a 190 kD protein that is more strongly transforming than the p210 protein derived from the larger CML-associa ted transcrip t.We examined the peripheral blood or marrow of 67 patients with CML and found that 35 of thern expressed both transcripts while the remainder expressed the p210-encoding transcript exclusively.A cornparison of patients CO-expressing the p190-and p210-encoding transcripts with those patients who only expressed the p210-encoding transcript detected significantly higher white blood ce11 (WBC) counts and blast ce11 counts at time of testing as well as significantly higher white blood ceil counts at diagnosis.We believe that the expression of the pl9O-encoding transcript in the chronic phase of CML is due to alternative splicing.B C R and BCRIABL minigenes were constructed to study this phenornenon in more detail.These constnicts were transfected into various ce11 types and splicing was assessed by RT-PCR.While the basic BCR minigene expressed exon-inclusive hanscripts only, insertion of genomic DNA spanning ABL exon 2 induced exon-skipping but only when expressed in the CML ce11 lines K562 or EM3.In this study we localize the required sequence element to ABL exon 2 itself.These results mimic the splicing phenotype displayed by most CML patients.RNA-binding assays using nuclear extracts from both CML and non-CM' cells detected differential binding to ABL exon 2. We propose a mode1 where tram-factors present in some CML cells interact with ABL exon 2 pre-mRNA to promote skipping of upstream BCR exons.The road to the completion of my graduate studies has been a long and winding one.There were many people who helped me along the way and 1 appreciate everything they did for me.It is impossible to mention them all but I will endeavour to thank those whose aid was most sigxuficant.1 would first Iike to thank mv wife Kellv.She was a constant source of J d encouragement and support.This chapter in our lives together is now coming to a close and I will always remernber it as a period in which we struggled together to complete our education as we becarne ever doser.I am looking iorward to the next chapter as we travel the road of life together.1 would also like to thank my family.My parents have always supported me in whatever 1 have done.This support
Effect of Electroacupuncture on Visceral Hyperalgesia, Serotonin and Fos Expression in an Animal Model of Irritable Bowel Syndrome (2010)

Electro acupuncture attenuates visceral hyperlagesia through down-regulation of central serotonergic activities in the brain-gut axis.
Exhaled volatile organic compounds as markers for medication use in asthma (2019)

We have linked exhaled VOCs to urinary detection of salbutamol and OCSs. This merits further development of breathomics into a point-of-care tool for therapeutic drug monitoring.