gebhart/patrepeval huggingface dataset:
Applicability of density functional theory in reproducing accurate vibrational spectra of surface bound species (2014)

The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energy for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of -2.62 and -1.1% for the N-N stretching and Rh-H stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the Rh-H and N-N stretching modes from the bulk phonons and by solving one- and two-dimensional Schrödinger equation associated with the Rh-H, Rh-N, and N-N potential energy we calculated the anharmonic correction for N-N and Rh-H stretching modes as -31 cm(-1) and -77 cm(-1) at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments.
High-Fidelity Ion State Detection Using Trap-Integrated Avalanche Photodiodes (2022)

Integrated technologies greatly enhance the prospects for practical quantum information processing and sensing devices based on trapped ions. High-speed and high-fidelity ion state readout is critical for any such application. Integrated detectors offer significant advantages for system portability and can also greatly facilitate parallel operations if a separate detector can be incorporated at each ion-trapping location. Here, we demonstrate ion quantum state detection at room temperature utilizing single-photon avalanche diodes (SPADs) integrated directly into the substrate of silicon ion trapping chips. We detect the state of a trapped Sr^{+} ion via fluorescence collection with the SPAD, achieving 99.92(1)% average fidelity in 450 μs, opening the door to the application of integrated state detection to quantum computing and sensing utilizing arrays of trapped ions.
Zeolite-catalysed conversion of C3 sugars to alkyl lactates (2010)

The direct conversion of C3 sugars (or trioses) to alkyl lactates was achieved using zeolite catalysts. This reaction represents a key step towards the efficient conversion of bio-glycerol or formaldehyde to added-value chemicals such as lactate derivatives. The highest yields and selectivities towards the desired lactate product were obtained with Ultrastable zeolite Y materials having a low Si/Al ratio and a high content of extra-framework aluminium. Correlating the types and amounts of acid sites present in the different zeolites reveals that two acid functions are required to achieve excellent catalysis. Brønsted acid sites catalyse the conversion of trioses to the reaction intermediate pyruvic aldehyde, while Lewis acid sites further assist in the intramolecular rearrangement of the aldehyde into the desired lactate ester product. The presence of strong zeolitic Brønsted acid sites should be avoided as much as possible, since they convert the intermediate pyruvic aldehyde into alkyl acetals instead of lactate esters. A tentative mechanism for the acid catalysis is proposed based on reference reactions and isotopically labelled experiments. Reusability of the USY catalyst is demonstrated for the title reaction.
Competition between [1,7] hydrogen migration and electrocyclic ring closure in 6-methylhepta-1,3,5-triene (1979)

(Z)-6-Methylhepta-1,3,5-triene and (Z,Z)-2-methylhepta-1,3,5-triene have previously been proposed as intermediates in the thermolysis of 5,5-dimethylcyclohexa-1,3-diene, the latter compound derived from the former by fast [1,7] antarafacial hydrogen migration in the gas phase. (Z)-6-Methylhepta-1,3,5-triene has now been synthesized and its thermal behaviour in the gas phase studied in the range 481–533 K. The thermal behaviour of both (Z)-6-methylhepta-1,3,5-triene and (Z)-2,7-dimethylocta-2,4,6-triene indicates that [1,7] hydrogen migration in acyclic trienes is not nearly as ready as has been previously postulated in the literature.
Analysis of ADAM12-Mediated Ephrin-A1 Cleavage and Its Biological Functions (2021)

Accumulating evidence indicates that an elevated ephrin-A1 expression is positively correlated with a worse prognosis in some cancers such as colon and liver cancer. The detailed mechanism of an elevated ephrin-A1 expression in a worse prognosis still remains to be fully elucidated. We previously reported that ADAM12-cleaved ephrin-A1 enhanced lung vascular permeability and thereby induced lung metastasis. However, it is still unclear whether or not cleaved forms of ephrin-A1 are derived from primary tumors and have biological activities. We identified the ADAM12-mediated cleavage site of ephrin-A1 by a Matrix-assisted laser desorption ionization mass spectrometry and checked levels of ephrin-A1 in the serum and the urine derived from the primary tumors by using a mouse model. We found elevated levels of tumor-derived ephrin-A1 in the serum and the urine in the tumor-bearing mice. Moreover, inhibition of ADAM-mediated cleavage of ephrin-A1 or antagonization of the EphA receptors resulted in a significant reduction of lung metastasis. The results suggest that tumor-derived ephrin-A1 is not only a potential biomarker to predict lung metastasis from the primary tumor highly expressing ephrin-A1 but also a therapeutic target of lung metastasis.
N-dimentional multiplexing link with 1.036-Pbit/s transmission capacity and 112.6-bit/s/Hz spectral efficiency using OFDM-8QAM signals over 368 WDM pol-muxed 26 OAM modes (2014)

By exploiting N-dimensional multiplexing, i.e. 54.139-Gbit/s OFDM-8QAM signals over 368 WDM pol-muxed 26 orbital angular momentum (OAM) modes, we experimentally demonstrate a free-space data link with an aggregate transmission capacity of 1.036 Pbit/s and a high spectral efficiency of 112.6 bit/s/Hz.
Decreased Infectivity despite Unaltered C3 Binding by a ΔhbhAMutant ofMycobacterium tuberculosis (2002)

HbhA of Mycobacterium tuberculosis is a multifunctional binding protein, binding to both sulfated sugars such as heparin and to human complement component C3. HbhA may therefore interact with host molecules and/or host cells during M. tuberculosis infection and play a role in the pathogenesis of this bacterium. The purpose of this study was to use allelic exchange to create an M. tuberculosis strain deficient in expression of HbhA to determine whether this protein's C3-binding activity plays a role in the pathogenesis of M. tuberculosis. An in-frame, 576-bp unmarked deletion in the hbhA gene was created using sacB as a counterselectable marker. Southern blotting and PCR analyses confirmed deletion of hbhA in the DeltahbhA mutant. The DeltahbhA mutant strain grew at a rate similar to that of the parent in broth culture and in J774.A1 murine macrophage-like cells but was deficient in growth compared to the parent strain in the lungs, liver, and spleen of infected mice. In addition, the DeltahbhA mutation did not reduce binding of M. tuberculosis to human C3 or to J774.A1 cells in the presence or absence of serum, suggesting that in the absence of HbhA, other molecules serve as C3-binding molecules on the M. tuberculosis surface. Taken together, these data indicate that HbhA is important in the infectivity of M. tuberculosis, but its ability to bind C3 is not required for mycobacterial adherence to macrophage-like cells. Using the DeltahbhA mutant strain, a second M. tuberculosis C3-binding protein similar in size to HbhA was identified as HupB, but the role of HupB as a C3-binding protein in intact organisms remains to be determined.
Réformer sous contrainte d'injonctions contradictoires : l'exemple du comité Balladur sur la réforme des collectivités locales (2010)

Le Comité pour la réforme des collectivités locales, créé en novembre 2008 et présidé parl’ancien Premier ministre Édouard Balladur, a rendu son rapport en mars 2009. Cet article analyseles raisons qui ont conduit à confier cette réflexion à un comité ad hoc , souligne le poids descontraintes qui s’exercent sur les réformateurs et questionne leur stratégie de changement. Il meten évidence les tensions qui traversent l’activité de réformateurs tentés par des changementsradicaux, en raison des enjeux budgétaires qui s’y attachent, mais soumis à de fortes contraintesconstitutionnelles et politiques. Il formule quelques hypothèses relatives à l’inégale faisabilitéparlementaire des solutions proposées par le Comité.
Microstructural characterization and high-temperature strength of hot-pressed silicon nitride ceramics with Lu2O3additives (2003)

The microstructures of two hot-pressed Si3N4 ceramics, with 3.33 and 12.51 wt% Lu2O3 additive, have been characterized using transmission electron microscopy. The microstructures of both samples consisted of elongated β-Si3N4 grains and a secondary phase, contained in pockets surrounded by the grains, with a crystalline or amorphous form. In the 3.33 wt% Lu2O3-containing Si3N4 ceramic, all the multiple-grain junctions were completely crystalline while, in the 12.51 wt% Lu2O3-containing Si3N4 ceramic, approximately half the junctions were devitrified. A thin intergranular amorphous film present between the two-grain boundary was common; however, a film-free grain boundary was observed in the 12.51 wt% Lu2O3 sample. The film-free grain boundary was determined to be approximately 35%. Both ceramics fractured in four-point flexure between 1200 and 1600°C. Their high-temperature strength is closely associated with the nature of the grain-boundary phase formed during the sintering process.
The Pulmonary Fibrosis Foundation Patient Registry. Rationale, Design, and Methods (2020)

Detailed understanding of longitudinal behavior, response to therapy, and applicable biomarkers for interstitial lung diseases (ILDs) is lacking. There is a need for a large multicenter registry that provides researchers and clinicians access to well-characterized data not limited to patients with idiopathic pulmonary fibrosis. The Pulmonary Fibrosis Foundation Patient Registry (PFF-PR) is a database that collects baseline and longitudinal demographic and clinical information about patients with ILDs in the United States. The objective of this study is to describe the patient population, data collection process, and opportunities for retrospective and prospective research with the PFF-PR. Individuals 18 years or older who had ILD diagnosed and who were seen at PFF-PR centers who provided informed consent were eligible to participate. Baseline and longitudinal demographic, spirometric, radiographic, morbidity, and mortality data are recorded into a secure electronic data capture system. Starting in 2016, the PFF-PR has collected data on 2,003 patients at 42 clinical sites in the United States. At the time of enrollment, the mean age of participants was 68 years old. Most (62%) of participants were male, and 58% had a positive smoking history. The mean forced vital capacity was 69% predicted, and the mean diffusing capacity of the lung for carbon monoxide was 43% predicted. Forty-one percent of patients were using supplemental oxygen, and 39% were on antifibrotic therapy. Reasons for attrition were mostly death or transplant, with low rates of loss to follow-up or withdrawal. The PFF-PR is a large multicenter United States-based registry that provides researchers and clinicians access to well-characterized ILD patient data.
In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon–Carbon Bond Formation (2021)

In vitro selection of randomized RNA libraries for ribozymes that catalyze different chemical transformations is a method that has been established in the mid-1990ies. Until now, the method has led to many RNAs that catalyze a wide variety of reactions, several of which are highly relevant for supporting the RNA world hypothesis. According to this hypothesis, there was a phase in the evolution of the earliest life forms on earth around 3.9 billion years ago in which protein enzymes had not been established the way they are now. Instead, prebiotic catalysis was likely carried out by ribozymes. In this chapter, I discuss examples of ribozymes with particular emphasis on the catalysis of C-C-bond formations and their hypothetical role for RNA-catalyzed metabolism in an RNA world.
The dual role of bismuth in Li 2 O–Bi 2 O 3 –B 2 O 3 glasses along the orthoborate join (2022)

Abstract The structures of glasses in the lithium–bismuth orthoborate composition range deviate significantly from the short‐range order structure of the two crystalline end‐members. Although binary Li 3 BO 3 and BiBO 3 are solely of comprised trigonal orthoborate anions, all glasses formed by their combination contain four‐coordinated borate tetrahedra. We analyze the structure of (75−1.5 x )Li 2 O– x Bi 2 O 3 –(25+0.5 x )B 2 O 3 glasses in increments of x = 5, with 11 B magic‐angle spinning nuclear magnetic resonance (NMR), infrared (IR), and Raman spectroscopy. For the full series, the oxygen‐to‐boron ratio remains constant at O/B = 3:1. NMR quantifies an increase in the fraction of tetrahedral boron with increasing bismuth oxide content. Evolution of the mid‐IR profile suggests multiple types of tetrahedral boron sites. Raman spectroscopy reveals that Bi 2 O 3 tends to cluster within the lithium borate matrix when initially introduced and that this behavior transforms into a bismuthate network with increasing bismuth oxide content. In all cases, mixed Bi–O–B linkages are observed. The dual role of bismuth as network modifier and network former is likewise observed in the far IR. The glass transition temperature continuously increases with bismuth oxide content; however, the glass stability displays a maximum in the multicomponent glass of x = 40.
A Zeolite Structure (ITQ‐13) with Three Sets of Medium‐Pore Crossing Channels Formed by9‐ and 10‐Rings (2003)

Die einzigartige Struktur des Zeoliths ITQ-13 wurde bestimmt: Sie besteht aus einem System sich durchkreuzender Kanäle mit mittelgroßem Querschnitt; Neuner- und Zehnerring-Öffnungen verlaufen parallel zu den kristallographischen Achsen (siehe Bild). Darüber hinaus konnten auch saure Zentren in die Struktur eingebaut werden, Anwendungen in der (heterogenen) Säurekatalyse stehen somit in Aussicht.
Cross-cultural measurement equivalence of the 5-level EQ-5D (EQ-5D-5L) in patients with type 2 diabetes mellitus in Singapore (2015)

This study provided evidence for the measurement equivalence of the different language versions of EQ-5D-5L in Singapore.
Uncertainty analysis of absolute concentration measurement with continuous-wave cavity ringdown spectroscopy (2001)

To evaluate the uncertainty of concentration measurement using cavity ringdown spectroscopy, we analytically derived expressions for uncertainty for parameters, such as temperature, laser frequency, and ringdown time deviation, from the model equation. The uncertainties that are due to systematic errors in a practical cavity ringdown system were assessed through an experimental study of the PQ(35) transition in an A band of molecular oxygen. We found that, except for the line strength that is regarded as a reference value independent of the measurement, the laser frequency jitter is the largest uncertainty source in the system. Some practical requirements for minimizing the uncertainty in concentration measurements are discussed. We also demonstrated determination of the line strength of the PQ(35) transition line of oxygen to be 8.63(3) x 10(-27) cm(-1) with a relative uncertainty of less than 0.4%.
Photopolymere in der Industrie (2014)

Abstract Die Ortsselektivität der Photopolymerisation macht sie den üblichen thermisch initiierten Vernetzungen von Polymeren überlegen. Industrielle Anwendungen reichen von der Informationsspeicherung über Lithografie und Lacke bis zu Dentalkompositen.
Synthesis of Highly Labile SG1-Based Alkoxyamines under Photochemical Conditions (2008)

Highly labile SG1-based alkoxyamines were synthesized using the photodecomposition of both azo compounds and dithiocarbamates. The former method was a straightforward procedure to obtain the alkoxyamines, but a high [azo]/[nitroxide] ratio is needed. The latter method required only a stoichiometric amount of dithiocarbamate and allowed the recovery of the disulfide after irradiation. This enabled combination of the two methods in a process where only 0.75 equiv of azo compound is needed and where sulfurous compounds acted only as intermediates.
Exhaustive search for small fully absorbing sets and the corresponding low error-floor decoder (2010)

This work provides an exhaustive search algorithm for finding small fully absorbing sets (FASs) of arbitrary low-density parity-check (LDPC) codes. In particular, given any LDPC code, the problem of finding all FASs of size less than t is formulated as an integer programming problem, for which a new branch-&-bound algorithm is devised. New node selection and the tree-trimming mechanisms are designed to further enhance the efficiency of the algorithm. The proposed algorithm is capable of finding all FASs of size ≤ 11 with no larger than 2 induced odd-degree check nodes for LDPC codes of length ≤ 1000. The resulting exhaustive list of small FASs is then used to devise a new post-processing decoder. Numerical results show that by taking advantage of the exhaustive list of small FASs, the proposed decoder significantly lowers the error floor for codes of practical lengths and outperforms the state-of-the-art low-error-floor decoders.
Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation (2023)

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Prior work focused on supervised learning methods using a large set of binding affinity data for small molecules, but it is hard to apply the same strategy to other drug classes like antibodies as labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network called Neural Euler's Rotation Equations (NERE) for SE(3) score matching. It predicts a rotation by modeling the force and torque between protein and ligand atoms, where the force is defined as the gradient of an energy function with respect to atom coordinates. We evaluate NERE on protein-ligand and antibody-antigen binding affinity prediction benchmarks. Our model outperforms all unsupervised baselines (physics-based and statistical potentials) and matches supervised learning methods in the antibody case.
A classification based framework for quantitative description of large-scale microarray data (2006)

Genome-wide surveys of transcription depend on gene classifications for the purpose of data interpretation. We propose a new information-theoretical-based method to: assess significance of co-expression within any gene group; quantitatively describe condition-specific gene-class activity; and systematically evaluate conditions in terms of gene-class activity. We applied this technique to describe microarray data tracking Escherichia coli transcriptional responses to more than 30 chemical and physiological perturbations. We correlated the nature and breadth of the responses with the nature of perturbation, identified gene group proxies for the perturbation classes and quantitatively compared closely related physiological conditions.
Solution-processable electron injection materials for organic light-emitting devices (2015)

Solution-processed organic light-emitting devices (OLEDs) have progressed as potential candidates for cost-effective solid-state lighting and flat panel displays.
The DLR MiroSurge - A robotic system for surgery (2009)

This video presents the in-house developed DLR MiroSurge robotic system for surgery. As shown, the system is suitable for both minimally invasive and open surgery. Essential part of the system is the MIRO robot: The soft robotics feature enables intuitive interaction with the robot.
Absolute stereochemistry assignment of N‐phosphorylimine‐derived aza‐Diels‐Alder adducts with TDDFT CD calculations (2005)

N-phosphorylimines undergo Lewis acid-catalyzed Diels-Alder reactions with Danishefsky's diene. Application of the chiral catalyst zinc(II)-(S)-BINOL results in good-to-low asymmetric induction but poor chemical conversion. However, the absolute stereochemistry of novel aza-Diels-Alder cycloadducts, such as diethyl 4-oxo-2-phenyl-3,4-dihydropyridin-1(2H)-ylphosphonate, can be determined using circular dichroism (CD). Comparison between experimental and TDDFT-calculated CD spectrum shows that use of the (S)-catalyst results in predominant formation of the (6R) cycloadducts.
Antisense oligonucleotide therapy for H3.3K27M diffuse midline glioma (2023)

Diffuse midline gliomas (DMGs) are pediatric high-grade brain tumors in the thalamus, midbrain, or pons; the latter subgroup are termed diffuse intrinsic pontine gliomas (DIPG). The brain stem location of these tumors limits the clinical management of DIPG, resulting in poor outcomes for patients. A heterozygous, somatic point mutation in one of two genes coding for the noncanonical histone H3.3 is present in most DIPG tumors. This dominant mutation in the <i>H3-3A</i> gene results in replacement of lysine 27 with methionine (K27M) and causes a global reduction of trimethylation on K27 of all wild-type histone H3 proteins, which is thought to be a driving event in gliomagenesis. In this study, we designed and systematically screened 2'-<i>O</i>-methoxyethyl phosphorothioate antisense oligonucleotides (ASOs) that direct RNase H-mediated knockdown of <i>H3-3A</i> mRNA. We identified a lead ASO that effectively reduced <i>H3-3A</i> mRNA and H3.3K27M protein and restored global H3K27 trimethylation in patient-derived neurospheres. We then tested the lead ASO in two mouse models of DIPG: an immunocompetent mouse model using transduced mutant human <i>H3-3A</i> cDNA and an orthotopic xenograft with patient-derived cells. In both models, ASO treatment restored K27 trimethylation of histone H3 proteins and reduced tumor growth, promoted neural stem cell differentiation into astrocytes, neurons, and oligodendrocytes, and increased survival. These results demonstrate the involvement of the H3.3K27M oncohistone in tumor maintenance, confirm the reversibility of the aberrant epigenetic changes it promotes, and provide preclinical proof of concept for DMG antisense therapy.