gebhart/patrepeval huggingface dataset:
Letter of Intent for the LHCb Upgrade (2011)

The primary goal of LHCb is to measure the effects of new particles or forces beyond the Standard Model. Results obtained from data collected in 2010 show that the detector is robust and functioning well. While LHCb will be able to measure a host of interesting channels in heavy flavour decays in the upcoming few years, a limit of about 1 fb^−1 of data per year cannot be overcome without upgrading the detector. The LHC machine does not face such a limitation. With the upgraded detector, read out at 40MHz, a much more flexible software-based triggering strategy will allow a large increase not only in data rate, as the detector would collect 5 fb^−1 per year, but also the ability to increase trigger efficiencies especially in decays to hadronic final states. In addition, it will be possible to change triggers to explore different physics as LHC discoveries point us to the most interesting channels. Our physics scope extends beyond that of flavour. Possibilities for interesting discoveries exist over a whole variety of phenomena including searches for Majorana neutrinos, exotic Higgs decays and precision electroweak measurements. Here we describe the physics motivations and proposed detector changes for exploring new phenomena in proton-proton collisions near 14 TeV centre-of-mass energy.
Hydrogen bonding in a family of triamides: conformation-directing effects in solution versus the solid state (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrogen bonding in a family of triamides: conformation-directing effects in solution versus the solid stateGregory P. Dado, John M. Desper, and Samuel H. GellmanCite this: J. Am. Chem. Soc. 1990, 112, 23, 8630–8632Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/ja00179a084https://doi.org/10.1021/ja00179a084research-articleACS PublicationsRequest reuse permissionsArticle Views164Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Connectomic Atlas of the Human Cerebrum—Chapter 1: Introduction, Methods, and Significance (2018)

This multipart supplement aims to build on the work of the HCP. We present this information in the hope that the complexity of cerebral connectomics will be conveyed in a more manageable format that will allow neurosurgeons and neuroscientists to accurately communicate and formulate hypotheses regarding cerebral anatomy and connectivity. We believe access to this information may provide a foundation for improving surgical outcomes by preserving lesser-known networks.
Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors (2019)

Cancer is often seen as a disease of mutations and chromosomal abnormalities. However, some cancers, including pediatric rhabdoid tumors (RTs), lack recurrent alterations targetable by current drugs and need alternative, informed therapeutic options. To nominate potential targets, we performed a high-throughput small-molecule screen complemented by a genome-scale CRISPR-Cas9 gene-knockout screen in a large number of RT and control cell lines. These approaches converged to reveal several receptor tyrosine kinases (RTKs) as therapeutic targets, with RTK inhibition effective in suppressing RT cell growth in vitro and against a xenograft model in vivo. RT cell lines highly express and activate (phosphorylate) different RTKs, creating dependency without mutation or amplification. Downstream of RTK signaling, we identified PTPN11, encoding the pro-growth signaling protein SHP2, as a shared dependency across all RT cell lines. This study demonstrates that large-scale perturbational screening can uncover vulnerabilities in cancers with "quiet" genomes.
Super-Resolution Spectrum Analysis Regularization : Burg, Capon & Ago-Antagonistic Algorithms (1996)

Publication in the conference proceedings of EUSIPCO, Trieste, Italy, 1996
Data quality measurement project (2002)

General Electric Aircraft Engines used an old ASCII based system to track x-ray quality in internal engine parts. The system was neither user friendly nor scalable. A new system was developed using Visual Basic 6 and Microsoft Access 2000 in order to address the underlying problems of the legacy system. The new system encompasses all previous functionality, but also has an improved graphical user interface, employs a contemporary relational database management system, and minimizes human error.
Oxytocin Receptor Down-Regulation Is Not Necessary for Reducing Oxytocin-Induced Prostaglandin F2α Accumulation by Interferon-τ in a Bovine Endometrial Epithelial Cell Line (2008)

Interferon-tau (IFNtau) is the embryonic signal responsible for pregnancy recognition in ruminants. The primary action of IFNtau is believed to be mediated through inhibition of prostaglandin F(2alpha) (PGF(2alpha)) released from the endometrial epithelial cells in response to oxytocin (OT). Our working hypothesis was that the antiluteolytic effect of IFNtau also involved modulation of PG production downstream of OT receptor (OTR) and/or cyclooxygenase 2 (COX2). There is currently no OT-sensitive endometrial cell line to study the molecular mechanisms underlying our hypotheses. Therefore, we established an immortalized bovine endometrial epithelial cell line (bEEL) exhibiting OT response. These cells were cytokeratin positive, expressed steroid receptors, and exhibited preferential accumulation of PGF(2alpha) over PGE(2). The bEEL cells were highly sensitive to OT, showing time- and concentration-dependent increase in COX2 transcript and protein and PGF(2alpha) accumulation. Interestingly, IFNtau (20 ng/ml) significantly reduced OT-induced PGF(2alpha) accumulation, but surprisingly, the effect was not mediated through down-regulation of either OTR or COX2. Rather, IFNtau up-regulated COX2 in a time- and concentration-dependent manner while decreasing OT-induced PG accumulation. This suggests that COX2 is not a primary target for the antiluteolytic effect of IFNtau. Because IFNtau reduced OT-stimulated PGF(2alpha) accumulation within 3 h, the mechanism likely involves a direct interference at the level of the OT signaling or transcription in addition to the down-regulation of OTR observed in vivo. In summary, bEEL cells offer a unique in vitro model for investigating the cellular and molecular mechanisms underlying OT and IFNtau response in relation with luteolysis and recognition of pregnancy in the bovine.
Conformational studies of poly‐L‐alanine in water (1968)

Abstract The conformational properties of poly‐ L ‐alanine have been examined in aqueous solutions in order to investigate the influence of hydrophobic interactions on the helix–random coil transition. Since water is a poor solvent for poly‐ L ‐alanine, water‐soluble copolymers of the type ( D , L ‐lysine) m –( L alanine) n ‐( D , L ‐lysine) m , having 10, 160, 450, and 1000 alanyl residues, respectively, in the central block, were synthezised. The optical rotatory dispersion of the samples was investigated in the range 190–500 mμ, and the rotation at 231 mμ was related to the α‐helix content, θ H , of the alanine section. In salt‐free solutions, at neutral pH, the three large polymers show high θ H values, which are greatly reduced when the temperature is increased from 5 to 80°C. No helicity was observed for the small ( n = 10) polymer. By applying the Lifson‐Roig theory, the following parameters were obtained for the transition of a residue from a coil to a helical state: ν = 0.012; Δ H = −190 ± 40 cal./mole; Δ S = −0.55 ± 0.12 e.u. Since Δ H and Δ S differ from the values expected for a process involving only the formation of a hydrogen bond, and in a manner predicted by theories for the influence of hydrophobic bonding on helix stability, it is concluded that a hydrophobic interaction is also involved. In the presence of salt (0.2 M NaCl), or when the ε‐amino groups of the lysyl residues are not protonated (pH = 12), the helical form of the two large polymers ( n = 450 and n = 1000) is more stable than in water. Since the electrostatic repulsion between the lysine end blocks is greatly reduced under these conditions, the alanine helical sections fold back on themselves, and this conformation is stabilized by interchain hydrophobia bonds. This structure was predicted by the theory for the equilibrium between such interacting helices, non‐interacting helices, and the random coil.
THE REPROCESSING PLANT OF THE FUTURE : A SINGLE EXTRACTION CYCLE (2005)

In France, COGEMA has been reprocessing spent nuclear fuel on an industrial scale for over 40 years, and has consistently worked to optimize facility design and operations. In COGEMA-La Hague’s UP3 reprocessing plant, to achieve the necessary decontamination needed to produce purified uranium and plutonium, five extraction cycles were implemented and used at start-up: first cycle for separation of fission products, uranium and plutonium, two uranium purification cycles and two plutonium purification cycle. By modifying processes at the design stage and making adjustments during operations, we saw that further decontamination of uranium could be achieved with only one cycle. Radiological specification of plutonium was also obtained at the end of the first plutonium purification cycle. These good performance levels were taken into account for the design of the UP2-800 plant where uranium is purified using a single cycle, and for the recent R4 facility which features only one plutonium purification cycle. Relevant information on extraction cycles in first-generation French reprocessing plants (UP1 and UP2-400) as well as design characteristics for the extraction cycles of reprocessing facilities currently operating at the COGEMA-La Hague plant is given. Experience shows that we can obtain adequate performance levels using only three cycles. We will also present potential evolutions for extraction cycles, e.g., neptunium decontamination, and demonstrate that one cycle can be sufficient for reprocessing the spent nuclear currently available. The benefits associated with a single extraction cycle will be detailed in the presentation.
Computational Thermal Analysis of the Photothermal Effect of Thermoplasmonic Optical Fiber for Localized Neural Stimulation In Vivo (2021)

Optical neuromodulation is a versatile neural stimulation technology that enables highly localized excitatory or inhibitory stimulation of neuronal activities. Photothermal neural stimulation using thermoplasmonic metallic nanoparticles for light to heat conversion has been suggested as an optical neural stimulation technology without genetic modification. Optical fibers implementing the thermoplasmonic effect were recently developed for localized neural stimulation, and the successful demonstration of localized neural stimulation in vitro was reported. However, before photothermal neural stimulation is further applied in the brains of live animals and ultimately in human trials, a safety analysis must carefully be performed for the thermal effect of stimulation in vivo. With the complexity of the physical structure and different thermal properties of the brain and surrounding body, the resulting thermal effect could vary despite the same power of light delivered to the optical fiber. In addition, dynamic thermal properties of the brain such as the daily blood perfusion rate change or metabolic heat generation must also be carefully considered for the precise implementation of photothermal neural stimulation. In this work, an in-depth computational analysis was conducted of the photothermal effects using a thermoplasmonic optical fiber for in vivo neural stimulation. The effects of the experimental design and stimulation protocols on the thermal effect in the brain were analyzed. We believe that the results provide a good experimental guideline for safely conducting photothermal neural stimulation using the thermoplasmonic optical fiber technology.
Movie 4 from HER2 Isoforms Uniquely Program Intratumor Heterogeneity and Predetermine Breast Cancer Trajectories During the Occult Tumorigenic Phase (2023)

&lt;p&gt;p95HER2 microinvasive carcinoma. p95HER2 shown in magenta. Krt14 antibody staining shown in green.&lt;/p&gt;
Multi-Omic Biomarkers Improve Indeterminate Pulmonary Nodule Malignancy Risk Assessment (2023)

The clinical management of patients with indeterminate pulmonary nodules is associated with unintended harm to patients and better methods are required to more precisely quantify lung cancer risk in this group. Here, we combine multiple noninvasive approaches to more accurately identify lung cancer in indeterminate pulmonary nodules. We analyzed 94 quantitative radiomic imaging features and 41 qualitative semantic imaging variables with molecular biomarkers from blood derived from an antibody-based microarray platform that determines protein, cancer-specific glycan, and autoantibody-antigen complex content with high sensitivity. From these datasets, we created a PSR (plasma, semantic, radiomic) risk prediction model comprising nine blood-based and imaging biomarkers with an area under the receiver operating curve (AUROC) of 0.964 that when tested in a second, independent cohort yielded an AUROC of 0.846. Incorporating known clinical risk factors (age, gender, and smoking pack years) for lung cancer into the PSR model improved the AUROC to 0.897 in the second cohort and was more accurate than a well-characterized clinical risk prediction model (AUROC = 0.802). Our findings support the use of a multi-omics approach to guide the clinical management of indeterminate pulmonary nodules.
Effect of Environmental Temperature on Ultraviolet Irradiated PP and its Composite (2010)

Some oxygen-containing groups such as C—O and C=O were introduced onto the molecular chains of polypropylene (PP) through ultraviolet irradiation at different environmental temperatures in air. The concentration of the oxygen-containing groups was increased with the increasing environmental temperature after the same ultraviolet irradiation time. After irradiation at different environmental temperatures, there was no gel formed in PP. The crystal shape of irradiated PP kept unchanged, which was still monoclinic crystal. After the same ultraviolet irradiation time, the melt temperature of the irradiated PP decreased and its crystallinity was increased with the increasing environmental temperature. Compared with those of PP, the melt flow rate and hydrophilicity of the irradiated PP was improved, and their variation ranges was expanded with the increasing environmental temperature. The mechanical properties of PP/CaCO3 composite compatibilized by irradiated PP at different environmental temperatures were en...
Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum (2007)

Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication-divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immediate divergence alone may explain more than 60% of biological network data in both domains.
Ionic liquid promoted highly efficient aziridination of alkenes with Chloramine-T using N-bromosuccinimide as catalyst (2006)

Ionic liquids [bmim]BF4 and [bmim]PF6 were found to be recyclable reaction media as well as promoters for the aziridination of alkenes in excellent yields at a faster rate than previously reported methods using Chloramine-T as nitrene donor and NBS as catalyst under mild reaction conditions.
Bidirectional amplified WDM-PON using a single LOA (2005)

To increase the coverage distance in access network, a bidirectional amplified WDM-PON with a single LOA is demonstrated. We report the margin improvement of 12.8 dB for downstream and 11.4 dB for upstream channel with low transient response. (2 pages)
Three-dimensional in vitro cancer spheroid models for photodynamic therapy: strengths and opportunities (2015)

Three dimensional, in vitro spheroid cultures offer considerable utility for the development and testing of anticancer photodynamic therapy regimens. More complex than monolayer cultures, three-dimensional spheroid systems replicate many of the important cell-cell and cell-matrix interactions that modulate treatment response in vivo. Simple enough to be grown by the thousands and small enough to be optically interrogated, spheroid cultures lend themselves to high-content and high-throughput imaging approaches. These advantages have enabled studies investigating photosensitizer uptake, spatiotemporal patterns of therapeutic response, alterations in oxygen diffusion and consumption during therapy, and the exploration of mechanisms that underlie therapeutic synergy. The use of quantitative imaging methods, in particular, has accelerated the pace of three-dimensional in vitro photodynamic therapy studies, enabling the rapid compilation of multiple treatment response parameters in a single experiment. Improvements in model cultures, the creation of new molecular probes of cell state and function, and innovations in imaging toolkits will be important for the advancement of spheroid culture systems for future photodynamic therapy studies.
Surgical Treatment of Chronic Lower Extremity Neuropathic Pain (2001)

The current authors retrospectively reviewed 147 lower extremity peripheral nerve procedures in 114 patients (average age, 42 years) with chronic lower extremity neuropathic pain to determine whether surgical treatment based on an empirically derived algorithm could reduce pain and improve function. This algorithm assigns crush, stretch, and chronic transection injuries to treatment with transection and containment. Peripheral nerve stimulation was used in conjunction with transection and containment for patients with more chronic presentations for whom previous transections had been unsuccessful. Patients with adhesive neuralgia underwent revision neurolysis with vein wrapping. Patients with repetitive nerve trauma (overuse) underwent primary or revision neurolysis. Duration of symptoms averaged 37 months, and mechanisms of nerve injury included chronic transection, crush, adhesive neuralgia, stretch, repetitive trauma, and idiopathic etiology. Time to followup averaged 38 months. Pain and dysfunction were ranked from 0 points (no pain or dysfunction) to 10 points (pain prompting request for amputation or functional deficit warranting wheelchair use); preoperative and followup work status were documented. Average pain and dysfunction scores improved: 8.8 to 5.6 points and 7.6 to 5.0 points, respectively. Of the 114 patients, 52 (46%) patients improved their work status, including 35 of 87 (40%) involved in workers’ compensation. There were no statistically significant differences in outcome based on mechanism of nerve injury or type of procedure. The consistent average improvement suggests this algorithm assigns the appropriate procedure to a given mechanism of injury.
Toward image-based scene representation using view morphing (1996)

The question of which views map be inferred from a set of basis images is addressed. Under certain conditions, a discrete set of images implicitly describes scene appearance for a continuous range of viewpoints. In particular it is demonstrated that two basis views of a static scene determine the set of all views an the line between their optical centers. Additional basis views further extend the range of predictable views to a two- or three-dimensional region of viewspace. These results are shown to apply under perspective projection subject to a generic visibility constraint called monotonicity. In addition, a simple scanline algorithm is presented for actually generating these views from a set of basis images. The technique, called view morphing map be applied to both calibrated and uncalibrated images. At a minimum, two basis views and their fundamental matrix are needed. Experimental results are presented an real images. This work provides a theoretical foundation for image-based representations of 3D scenes by demonstrating that perspective view synthesis is a theoretically well-posed problem.
Supplementary Table S1 from Epigenetic Silencing of miR-490-3p Reactivates the Chromatin Remodeler SMARCD1 to Promote <i>Helicobacter pylori</i>–Induced Gastric Carcinogenesis (2023)

&lt;p&gt;Supplementary Table S1: Absolute expression levels of miR-490-3p, miR-375 and let-7b in non-cancerous gastric mucosa.&lt;/p&gt;