gebhart/patrepeval huggingface dataset:
Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) (2016)

Kinesin super family protein 2A (KIF2A) is an ATP-dependent microtubule destabilizer, that belongs to the kinesin-13 family. It is highly expressed in juvenile brains, but its postnatal function has not been determined due to mortality in KIF2A-deficient mice. In addition, KIF2A is a causal gene in human Malformation of Cortical Development (MCD) with epilepsy, but the contribution of KIF2A to its pathogenesis is not yet understood due to the small number of human patients. In this study, we first analyzed the prenatal function of KIF2A using kif2a-KO mice. These mice were pale, breathed irregularly, and exhibited frequent twitching in addition to malformations resembling those in kif2a-mutated human patients. To determine the post-migration function of KIF2A, we generated newly tamoxifen-inducible conditional knockout mice. Despite successful neuronal migration, all offspring displayed hyper-activity, weight loss, severe cortical/hippocampal-focus epilepsy, and died. Interestingly, KIF2A was highly expressed in excitatory axons, in cortical neurites in layers II/III/V and in dentate mossy fibers (MF). In the cortex, the loss of KIF2A generated aberrant axon sprouting in those layers. In the hippocampus, the loss of KIF2A resulted in the development of hippocampal sclerosis, MF sprouting, and recurrent excitatory circuits resembling but different from TLE. These phenotypes developed without excitation. cKO granule cells exhibited failed axon/dendrite determination, and developed multiple short axons throughout the entire molecular layer. These results suggest that KIF2A is crucial postnatally for establishing accurate neuronal circuits, in addition to its role in prenatal cell survival, migration, and axon elongation.
SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue (2022)

Abstract Profiling cellular heterogeneity in formalin-fixed paraffin-embedded (FFPE) tissues is key to characterizing clinical specimens for biomarkers, therapeutic targets, and drug responses. Here, we optimize methods for isolating intact nuclei and single nucleus RNA-Seq from FFPE tissues in the mouse brain, and demonstrate a pilot application to a human clinical specimen of lung adenocarcinoma. Our method opens the way to broad applications of snRNA-Seq to archival tissues, including clinical samples.
Napier88—a database programming language? (1989)

This is a description of the Napier88 type system based on “A Framework for Comparing Type Systems for Database Programming Languages” by Albano et al.
Adaptive Statistical and Grammar Models of Language for Application to Speech Recognition (1993)

The statistical and syntactic approaches to the modelling of language are consolidated in order to improve performance in speech recognition. The authors also aim to minimise the need for human intervention in the training of the language model from a corpus. Hybrid speech recognition systems using both bigram and grammar models can yield improved performance compared with the use of either model alone, but performance is still sub-optimal because the grammar is abandoned completely for sentences which fail to parse overall. Extending the concept of a bigram to the most informative (rather than the immediate) previous word leads to a reduction in perplexity: a purely statistical approach is presented. Incorporating syntax from a substring parser will require these principles to be extended to strings of nonterminal symbols, raising important training issues but opening the way towards a language model with greater capacity for adaptive enhancement of performance.
Speech recognition in cars with noise suppression and car radio compensation (1990)

S.509-516 : Abb.,Lit.
Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers (2007)

These findings suggest that epigenetic transcriptome changes, more than genotypic variation, account for age-associated differences in sporadic breast cancer incidence and prognosis.
Automatic Optical Coherence Tomography Imaging of Stationary and Moving Eyes with a Robotically-Aligned Scanner (2019)

Optical coherence tomography (OCT) has found great success in ophthalmology where it plays a key role in screening and diagnostics. Clinical ophthalmic OCT systems are typically deployed as tabletop instruments that require chinrest stabilization and trained ophthalmic photographers to operate. These requirements preclude OCT diagnostics in bedbound or unconscious patients who cannot use a chinrest, and restrict OCT screening to ophthalmology offices. We present a robotically-aligned OCT scanner capable of automatic eye imaging without chinrests. The scanner features eye tracking from fixed-base RGB-D cameras for coarse and stereo pupil cameras for fine alignment, as well as galvanometer aiming for fast lateral tracking, reference arm adjustment for fast axial tracking, and a commercial robot arm for slow lateral and axial tracking. We demonstrate the system's performance autonomously aligning with stationary eyes, pursuing moving eyes, and tracking eyes undergoing physiologic motion. The system demonstrates sub-millimeter eye tracking accuracy, 12 μm lateral pupil tracking accuracy, 83.2 ms stabilization time following step disturbance, and 9.7 Hz tracking bandwidth.
A coarse-grain three-site-per-nucleotide model for DNA with explicit ions (2011)

The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the local structure and organization of ions in bulk water and in the presence of DNA. The resulting model, 3SPN.1-I, is capable of reproducing the local structure observed in detailed atomistic simulations, as well as the experimental melting temperature of DNA for a range of DNA oligonucleotide lengths, CG-content, Na(+) concentration, and Mg(2+) concentration.
Reconstruction of the Interface of Oxidatively Functionalized Polyethylene (PE-CO2H) and Derivatives on Heating. Revision. (1987)

Oxidation of low-density polyethylene film with aqueous chromic acid results in a material (PE-CO2H) having hydrophilic carboxylic acid and ketone groups in a thin oxidatively-functionalized interface. This interface is indefinitely stable at room temperature. On heating in vacuum, it rapidly becomes hydrophobic and similar in it wettability to unfunctionalized polyethylene film. The progression of the contact angle with water from the initial value (55) to the final value (103) follows kinetics that suggest that the polar functional groups disappear from the interface by diffusion. The magnitude of the apparent diffusion constant derived from these studies can be described approximately by an Arrhenius equation over a significant portion of the temperature range explored, with an Arrehnius activation energy of diffusion of approx kcal/mol. Comparison of the properties of interfaces composed of carboxylic acid groups with those containing other species demonstrates that the structure of the interfacial groups also significantly influences the rate of reconstruction .
2Disk test rig for determining the tribological profile under slip-rolling (2017)

The slip-rolling 2Disk tribometer from Optimol Instruments represented the technological evolution in tribotesting of the well-known AMSLER-type tribometer marketed in 1922. Both use two discs with the same outer diameter rolling against each other on their circumference. In the AMSLER, the lower disc dips into an oil reservoir, whereas in the 2Disk the oil is injected into the contact. The oil supply of the 2Disk is controlled by pump and temperature by a heat exchanger.
Data-Driven and Ontological Analysis of FrameNet for Natural Language Reasoning. (2010)

This paper focuses on the improvement of the conceptual structure of FrameNet for the sake of applying this resource to knowledgeintensive NLP tasks requiring reasoning, such as question answering, information extraction etc. Ontological analysis supported by data-driven methods is used for axiomatizing, enriching and cleaning up frame relations. The impact of the achieved axiomatization is investigated on recognizing textual entailment. 1.
Optical Inclinometer Based on a Phase-Shifted Bragg Grating in a Taper Configuration (2014)

A simple optical inclinometer based on a phase-shifted Bragg grating in a taper configuration is proposed. Two phase-shifted fiber Bragg gratings were fabricated using a DUV femtosecond laser technique in the taper region, with taper waist diameters of 30 μm and 50 μm. Both sensing heads were compared based on their response to angle and strain. Whereas the higher diameter sensor yielded a higher sensitivity to curvature (23.8±0.3 pm/degree), the lower diameter one was more sensitive to strain (8.94±0.04 pm/με).
Expression of the Two Major Envelope Proteins of Equine Arteritis Virus as a Heterodimer Is Necessary for Induction of Neutralizing Antibodies in Mice Immunized with Recombinant Venezuelan Equine Encephalitis Virus Replicon Particles (2020)

RNA replicon particles derived from a vaccine strain of Venezuelan equine encephalitis virus (VEE) were used as a vector for expression of the major envelope proteins (GL and M) of equine arteritis virus (EAV), both individually and in heterodimer form (GL/M). Open reading frame 5 (ORF5) encodes the GL protein, which expresses the known neutralizing determinants of EAV (U. B. R. Balasuriya, J. F. Patton, P. V. Rossitto, P. J. Timoney, W. H. McCollum, and N. J. MacLachlan, Virology 232:114–128, 1997). ORF5 and ORF6 (which encodes the M protein) of EAV were cloned into two different VEE replicon vectors that contained either one or two 26S subgenomic mRNA promoters. These replicon RNAs were packaged into VEE replicon particles by VEE capsid protein and glycoproteins supplied in trans in cells that were coelectroporated with replicon and helper RNAs. The immunogenicity of individual replicon particle preparations (pVR21-GL, pVR21-M, and pVR100-GL/M) in BALB/c mice was determined. All mice developed antibodies against the recombinant proteins with which they were immunized, but only the mice inoculated with replicon particles expressing the GL/M heterodimer developed antibodies that neutralize EAV. The data further confirmed that authentic posttranslational modification and conformational maturation of the recombinant GL protein occur only in the presence of the M protein and that this interaction is necessary for induction of neutralizing antibodies.
Faculty Opinions recommendation of Crystal structure of methylornithine synthase (PylB): insights into the pyrrolysine biosynthesis. (2012)

No abstract available PMID: 22095926
Safety study of the Bio-10-SAD Bern strain of the rabies virus on the rhesus macaque monkey species (2013)

Based on a WHO recommendation, residual pathogenicity of the Bio-10-SAD Bern rabies virus strain (component of the Lysvulpen por. ad us. vet. vaccine) was tested on rhesus macaque monkeys. Each of the ten monkeys, females, two years old, was administered orally 2 ml × 10 9 TCID 50 of the Bio-10-SAD Bern rabies strain. The animals were monitored for 90 days. Subsequently, the animals were sacrificed and their brains were examined for presence of the vaccination rabies virus by the immunofluorescence and PCR methods. The occurrence of anti-rabies antibodies prior to and following administration of the vaccination rabies virus was also evaluated. No clinical signs of rabies were observed nor did any of the animals die of rabies following application of the virus. No rabies was detected in the study animals by post mortem examination. All of the 10 animals developed anti-rabies antibodies during the 90 days following administration of the rabies virus. It can be concluded, that Bio-10-SAD Bern virus administered at a dose equal to the tenfold maximum dose specified for field uses is safe to monkeys of the rhesus macaque species. This study is the first of its type performed in rhesus macaque monkey species.
Preparation and functionalization of reactive monodisperse macroporous poly(chloromethylstyrene-co-styrene-co-divinylbenzene) beads by a staged templated suspension polymerization (1997)

Reactive monodisperse porous poly(chloromethylstyrene-co-styrene-co-divinylbenzene) beads have been prepared by a staged templated suspension polymerization method with different concentrations of linear polystyrene porogen and chloromethylstyrene in the polymerization mixture. The presence of a small amount of linear polystyrene in the polymerization mixture leads to a dramatic increase in both the pore size and the pore volume of the resulting beads. In contrast, addition of chloromethylstyrene leads to lower surface areas and smoother surfaces due to the reduced compatibility between the polystyrene porogen and the newly formed crosslinked chains. The modification of chloromethylstyrene beads by Gabriel synthesis to obtain aminated beads has also been studied. The final number of primary amino groups is related to the starting concentration of functional benzyl chloride moieties rather than to the porous properties. Both π-basic and π-acidic type chiral selectors, (R)-1-(1-naphthyl)-ethylamine and (R)-N-(3,5-dinitrobenzoyl)phenylglycine, respectively, have been attached to the amino functionalized beads, and the resulting chiral beads have been used in the model HPLC separations of enantiomers. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 2631–2643 1997
In vivo autofluorescence and specific fluorescence unmixing by Non negative Matrix Factorization (2010)

International audience
Dynamics and squeeze film gas damping of a capacitive RF MEMS switch (2004)

We report on measurements of the time-dependent capacitance of an RF MEMS shunt switch. A high time-resolution detection set-up is used to determine switching time and motion of the device. From the equation of motion the damping force is extracted. The measured damping force is found to be approximately proportional to the speed over the gap to the third power (FD ∝ v/z3), in good agreement with squeeze film damping theory. Significant influence of slip–flow effects on the motion is observed. Measurements at low pressure show underdamped harmonic oscillations in the opening motion and contact bounce effects in the closing motion. Effects of dielectric charging on the C–V curves are discussed. Experimental results are compared with electromechanical and damping simulations.
Algebraic and information-theoretic conditions for operator quantum error correction (2007)

Operator quantum error correction is a technique for robustly storing quantum information in the presence of noise. It generalizes the standard theory of quantum error correction, and provides a unified framework for topics such as quantum error correction, decoherence-free subspaces, and noiseless subsystems. This paper develops (a) easily applied algebraic and information-theoretic conditions that characterize when operator quantum error correction is feasible; (b) a representation theorem for a class of noise processes that can be corrected using operator quantum error correction; and (c) generalizations of the coherent information and quantum data processing inequality to the setting of operator quantum error correction.
Streaming liver VI: streaming intra‐hepatic bile ducts (1990)

Thirty male adult rats, weighing 250-300 g, were injected with 0.5 muCi [3H]-thymidine. The rats were killed in groups of five, at the following times: 1 h, 14, 30, 60, 90 and 120 days. The livers were fixed in formalin, embedded in paraffin and cut into 5-microns-thick sections, which were then dipped into liquid emulsion for autoradiography. Bile ducts were evaluated in all portal tracts of a section. Obliquely cut bile ducts were excluded. The number of cells paving the duct lumen was defined as bile duct class. Class is roughly proportional to bile duct size. One hour after labelling, labelling index was 3.39 +/- 0.06% (the second number is one standard error of the mean). With time it declined, reaching 0.22 +/- 0.15 on day 60. Initially labelled cells were found in narrow bile ducts and the mean labelled cell was located at class 7.48 +/- 0.63. With time, labelled cells proceeded into wider bile ducts advancing daily 0.122 +/- 0.025 classes. Intra-hepatic bile duct epithelium renews its cells continuously in the same way as epidermis or gastro-intestinal mucosa do. It consists of two kinetic compartments, a progenitor (P) and a functional (Q) compartment. P feeds Q with cells.
Decoupling the Effects of the Amyloid Precursor Protein From Amyloid-β Plaques on Axonal Transport Dynamics in the Living Brain (2019)

Amyloid precursor protein (APP) is the precursor to Aβ plaques. The cytoplasmic domain of APP mediates attachment of vesicles to molecular motors for axonal transport. In APP-KO mice, transport of Mn<sup>2+</sup> is decreased. In old transgenic mice expressing mutated human (APP<sup>SwInd</sup>) linked to Familial Alzheimer's Disease, with both expression of APP<sup>SwInd</sup> and plaques, the rate and destination of Mn<sup>2+</sup> axonal transport is altered, as detected by time-lapse manganese-enhanced magnetic resonance imaging (MEMRI) of the brain in living mice. To determine the relative contribution of expression of APP<sup>SwInd</sup> versus plaque on transport dynamics, we developed a Tet-off system to decouple expression of APP<sup>SwInd</sup> from plaque, and then studied hippocampal to forebrain transport by MEMRI. Three groups of mice were compared to wild-type (WT): Mice with plaque and APP<sup>SwInd</sup> expression; mice with plaque but suppression of APP<sup>SwInd</sup> expression; and mice with APP<sup>SwInd</sup> suppressed from mating until 2 weeks before imaging with no plaque. MR images were captured before at successive time points after stereotactic injection of Mn<sup>2+</sup> (3-5 nL) into CA3 of the hippocampus. Mice were returned to their home cage between imaging sessions so that transport would occur in the awake freely moving animal. Images of multiple mice from the three groups (suppressed or expressed) together with C57/B6J WT were aligned and processed with our automated computational pipeline, and voxel-wise statistical parametric mapping (SPM) performed. At the conclusion of MR imaging, brains were harvested for biochemistry or histopathology. Paired <i>T</i>-tests within-group between time points (<i>p</i> = 0.01 <i>FDR corrected</i>) support the impression that both plaque alone and APP<sup>SwInd</sup> expression alone alter transport rates and destination of Mn<sup>2+</sup> accumulation. Expression of APP<sup>SwInd</sup> in the absence of plaque or detectable Aβ also resulted in transport defects as well as pathology of hippocampus and medial septum, suggesting two sources of pathology occur in familial Alzheimer's disease, from toxic mutant protein as well as plaque. Alternatively mice with plaque without APP<sup>SwInd</sup> expression resemble the human condition of sporadic Alzheimer's, and had better transport. Thus, these mice with APP<sup>SwInd</sup> expression suppressed after plaque formation will be most useful in preclinical trials.
Cost-based dynamic reconfiguration system for intelligent agent negotiation (2004)

Autonomous, highly distributed control architectures are composed of a significant number of agents that can reason and act on behalf of represented processes or artifacts in a coordinated manner. Depending on the social organization capabilities of the agents, the autonomous system could evolve into complex agent organizations called temporal holarchies. Cost-based negotiation supports the holarchy formation. Dynamic hierarchical teamworks architecture of middle-agents is described to increase robustness of the architecture.
Probing the Disorder inside the Cubic Unit Cell of Halide Perovskites\n from First-Principles (2021)

Strong deviations in the finite temperature atomic structure of halide\nperovskites from their average geometry can have profound impacts on\noptoelectronic and other device-relevant properties. Detailed mechanistic\nunderstandings of these structural fluctuations and their consequences remain,\nhowever, limited by the experimental and theoretical challenges involved in\ncharacterizing strongly anharmonic vibrational characteristics and their impact\non other properties. We overcome some of these challenges by a theoretical\ncharacterization of the vibrational interactions that occur among the atoms in\nthe prototypical cubic CsPbBr$_3$. Our investigation based on first-principles\nmolecular dynamics calculations finds that the motions of neighboring Cs-Br\natoms interlock, which appears as the most likely Cs-Br distance being\nsignificantly shorter than what is inferred from an ideal cubic structure. This\nform of dynamic Cs-Br coupling coincides with very shallow dynamic potential\nwells for Br motions that occur across a locally and dynamically disordered\nenergy landscape. We reveal an interesting dynamic coupling mechanism among the\natoms within the nominal unit cell of cubic CsPbBr$_3$ and quantify the\nimportant local structural fluctuations on an atomic scale.\n
Inside Cover: Evidence for the Existence of a Specific G Protein‐Coupled Receptor Activated by Guanosine (ChemMedChem 6/2011) (2011)

The inside cover picture shows the activation of a G protein-coupled receptor by guanosine. This effect has been detected at rat brain membranes through the innovative DELFIA Eu-GTP binding assay, which allows the measurement of a fluorescence signal following receptor activation. Several guanosine derivatives are able to stimulate this elusive receptor, and in particular, O6-cyclopentylguanosine proved to be more potent than the parent compound. For more information, see the Full Paper by Gloria Cristalli et al. on p. 1074 ff.